BLAST tutorial (part 2)

Introduction to BLAST Output

These are the results of a BLAST search of the non-redundant database using the uncharacterized protein, MJ0577, from Methanococcus jannashii as the query sequence. Listed below are each of the elements of BLAST output in their usual order. Explanatory notes have been added in light grey boxes. Additional details about BLAST are available through the

buttons.

Scroll down the page and learn how to analyze BLAST output, step by step.

Step 1. Overview of the Query

Query: = gi|2501594|sp|Q57997|Y577_METJA PROTEIN MJ0577 (162 letters)
Database: Non-redundant GenBank CDS translations+PDB+SwissProt+SPupdate+PIR 437,713 sequences; 134,605,311 total letters

Step 2. Graphical overview of database matches exceeding the E value threshold set in the query.

From the graphical overview, it is apparent that there are several high-scoring sequences that are highly related to the MJ0577 query. The top two bars (red) are matches to MJ0577 itself. The next five (pink) hits are probable homologs. The full-length green, blue and black bars may represent more distantly related homologs. Partial length bars reflect similarity between a portion of the query and a database entry. These regions of similarity may be a shared domain or motif. The nature of these lower scoring hits can be further explored by examining the corresponding alignment. To facilitate viewing any alignment of interest, each bar in the graphic and each E value in a description line (which are found below the graphic) is linked (click on it) to the corresponding alignment. Note, however, if the formatting options were set such that the number of alignments to be displayed is less than the number of descriptions (e.g. 100 descriptions; 50 alignments are the default values, and the values used in this tutorial), not all the links will be functional. If alignments for descriptions 51-100 are of interest, the number of alignments can be changed from 50 to 100 on the intermediate BLAST queue page. To see the new alignments, use the "format results" button once again.

Distribution of 95 Blast Hits on the Query Sequence

Step 3. Descriptions of each significant alignment. The score and E value are listed at the end of each line.

The description (also called definition) lines are listed below under the heading "Sequences producing significant alignments". The term "significant" simply refers to all those hits whose E value was less than the threshold. It does not imply biological significance.

                                                         
Sequences producing significant alignments: Score(bits)   E Value

1.  sp|Q57997|Y577_METJA  PROTEIN MJ0577 >gi|2128018|pir||A64372...   314  2e-85
2.  pdb|1MJH|    Structure-Based Assignment Of The Biochemical F...   272  1e-72

The description lines reveal that the sequence in the database with greatest similarity to MJ0577 is MJ0577 itself. The second hit is to the database entry associated with the determination of the MJ0577 structure. The score for the structure entry is somewhat lower and E value somewhat higher because (see pairwise alignment - the missing residues will appear as dashes) a certain number of residues were omitted from this database entry because they were disordered in the structure. To further evaluate any hits of potential interest, examine the corresponding alignments. Click on the score to the right of the description line to jump down to the alignment for any hits of interest.

3.  dbj|BAA29916|  (AP000003) 170aa long hypothetical protein [P...   107  6e-23
4.  sp|Q57951|Y531_METJA  HYPOTHETICAL PROTEIN MJ0531 >gi|212801...    91  4e-18
5.  gi|2622094  (AE000872) conserved protein [Methanobacterium t...    85  4e-16
6.  gi|2621993  (AE000865) conserved protein [Methanobacterium t...    81  4e-15
7.  gi|2621194  (AE000803) conserved protein [Methanobacterium t...    80  7e-15

The set of entries corresponding to the pink bars in the overview are to orthologous sequences in two other Archaeal species, Pyrococcus horikoshii (#3) and Methanobacterium thermoautotrophicum (#5,6,7)). Interestingly, the top hits also include sets of paralogs in Methanococcus jannaschii (#1,4) and Methanobacterium thermoautotrophicum (#5,6,7). To examine the relationship among these sequences, they have been subject to multiple alignment using the multiple alignment algorithm, ClustalW. The alignment can be seen here. A multiple alignment can also be generated using the "flat query-anchored with identities" formatting option in BLAST. A multiple alignment generated by BLAST is simply a compilation of all pairwise alignments, whereas Clustal W uses a progressive approach, first aligning the most similar sequences, and then adding more distant sequences to the alignment. Therefore, the two types of alignments may not be identical. Consult the Details button for more on how to generate a multiple alignment from within BLAST.

8.  gi|2622163  (AE000877) conserved protein [Methanobacterium t...    79  2e-14
9.  sp|P42297|YXIE_BACSU  HYPOTHETICAL 15.9 KD PROTEIN IN BGLH-W...    76  1e-13
10. sp|Q50777|YB54_METTM  HYPOTHETICAL 16.1 KD PROTEIN IN MTR RE...    66  2e-10
11. gi|2648791  (AE000981) conserved hypothetical protein [Archa...    65  3e-10
12. gi|2648610  (AE000970) conserved hypothetical protein [Archa...    64  5e-10
13. gi|2983400  (AE000710) hypothetical protein [Aquifex aeolicus]     64  6e-10
14. sp|P73475|YC30_SYNY3  HYPOTHETICAL 31.2 KD PROTEIN SLR1230 >...    63  1e-09
15. gi|2983527  (AE000719) hypothetical protein [Aquifex aeolicus]     61  4e-09
16. sp|O27222|YB54_METTH  HYPOTHETICAL PROTEIN MTH1154 >gi|26222...    59  2e-08
17. dbj|BAA30650|  (AP000006) 208aa long hypothetical protein [P...    57  6e-08
18. dbj|BAA31039.1|  (AP000007) 149aa long hypothetical protein ...    56  1e-07
19. emb|CAB50594.1|  (AJ248288) hypothetical protein [Pyrococcus...    55  2e-07
20. sp|P39177|UP12_ECOLI  UNKNOWN PROTEIN FROM 2D-PAGE (SPOTS PR...    55  2e-07
21. sp|P74148|YD88_SYNY3  HYPOTHETICAL 17.3 KD PROTEIN SLL1388 >...    52  2e-06

The set of entries corresponding to the green bars in the overview are to more distantly related Archaeal sequences. The scores and E values are respectable and most of the alignments extend the length of the query.

Since all of the closest homologs of MJ0577 are unannotated, it is of interest to examine a few of the highest scoring annotated sequence in the BLAST hit list. The first sequences in the hit list (scroll down to find these) with positive identification are gi|2648945, whose annotation indicates that this sequence encodes a cationic amino acid transporter and gi|1787640, a putative filament protein. The scores and E values of these hits put the significance of the alignments in the "twilight zone" with respect to significance. Since the transporter entry is 780 aa long, it is apparent that MJ0577 is not itself a homolog of a transporter. It may however, share a domain with this family of proteins. The filament protein is harder to dismiss, however manual filtering of the coiled-coil region in the query (MJ0577) causes the filament protein hit to drop off the hit list (E > 10). This could be an indication that the sequence similarity between MJ0577 and the putative filament protein is non-specific.

The results of this BLAST search have revealed that MJ0577 is one member of a moderate size family of proteins that are found in Archaea and in Eubacteria. To gain insight into the function of the MJ0577 family of proteins, a more sensitive search with the profile based tool, PSI-BLAST, would be one way to proceed.

sp|P45680|YFMU_COXBU  HYPOTHETICAL 15.8 KD PROTEIN IN FMU-RP...    49  2e-05
gb|AAF11689.1|AE002048_9  (AE002048) hypothetical protein [D...    48  3e-05
dbj|BAA16707|  (D90900) hypothetical protein [Synechocystis ...    48  3e-05
dbj|BAA79051.1|  (AP000058) 243aa long hypothetical protein ...    48  4e-05
gi|2650517  (AE001097) conserved hypothetical protein [Archa...    47  7e-05
emb|CAA74460.1|  (Y14080) hypothetical protein [Bacillus sub...    47  9e-05
gb|AAD47991.1|  (AF157801) hypothetical protein B [Pseudomon...    46  1e-04
emb|CAA73748|  (Y13308) hypothetical protein [Yersinia enter...    46  1e-04
emb|CAB08889|  (Z95554) hypothetical protein Rv1636 [Mycobac...    46  2e-04
sp|P72817|YG54_SYNY3  HYPOTHETICAL 16.8 KD PROTEIN SLL1654 >...    46  2e-04
emb|CAA22850.1|  (AL035248) hypothetical protein [Schizosacc...    45  3e-04
gi|2160182  (AC000132) ESTs gb|ATTS1236,gb|T43334,gb|N97019,...    45  3e-04
sp|P87132|YDM1_SCHPO  HYPOTHETICAL PROTEIN C57A7.01 IN CHROM...    45  3e-04
gb|AAD46412.1|AF096262_1  (AF096262) ER6 protein [Lycopersic...    44  6e-04
sp|P74897|YQA3_THEAQ  HYPOTHETICAL 14.6 KD PROTEIN IN QAH/OA...    44  6e-04
dbj|BAA16954|  (D90902) hypothetical protein [Synechocystis ...    44  7e-04
gb|AAF11911.1|AE002067_3  (AE002067) conserved hypothetical ...    43  0.001
pir||JN0292  antigen 332 - Plasmodium falciparum (fragments)       43  0.001
gi|2650286  (AE001080) conserved hypothetical protein [Archa...    42  0.002
gi|1002877  (U34353) ORF278 [Paracoccus denitrificans]             41  0.004
sp|P44195|YDAA_HAEIN  HYPOTHETICAL PROTEIN HI1426                  41  0.005 


gi|1787640  (AE000234) putative filament protein [Escherichi...    41  0.005
sp|P37903|UP03_ECOLI  UNKNOWN PROTEIN 2D_000B3L FROM 2D-PAGE...    41  0.005
pir||G64029  hypothetical protein HI1426 - Haemophilus influ...    41  0.005
emb|CAB57770.1|  (Y18930) hypothetical protein [Sulfolobus s...    40  0.011
sp|Q10851|YK05_MYCTU  HYPOTHETICAL 30.9 KD PROTEIN RV2005C >...    40  0.011
emb|CAB53139.1|  (AL109962) hypothetical protein SCJ1.21 [St...    39  0.019
gi|2649775  (AE001047) conserved hypothetical protein [Archa...    39  0.025
gi|2649038  (AE000997) conserved hypothetical protein [Archa...    39  0.025
sp|P72745|YB01_SYNY3  HYPOTHETICAL 12.2 KD PROTEIN SLR1101 >...    39  0.025
gb|AAF01537.1|AC009325_7  (AC009325) unknown protein [Arabid...    38  0.033
gi|2088796  (AF003150) weak similarity to the bZIP superfami...    38  0.033
gi|2648945  (AE000991) cationic amino acid transporter (cat-...    38  0.043
gi|152197  (L07487) DNA-region 1 to 268 is overlapping with ...    38  0.043
sp|P03807|YDAA_ECOLI  35.6 KD PROTEIN IN TPX-FNR INTERGENIC ...    38  0.056
emb|CAA89821.2|  (Z49746) ORF277 [Rhodobacter sphaeroides]         37  0.073
gi|2649611  (AE001036) conserved hypothetical protein [Archa...    37  0.073
gi|3493653  (AF083219) unknown [Azospirillum brasilense]           37  0.096
emb|CAB53147.1|  (AL109962) hypothetical protein SCJ1.29c [S...    36  0.17
emb|CAB53134.1|  (AL109962) conserved hypothetical protein S...    36  0.17
gi|3845107  (AE001375) hypothetical protein [Plasmodium falc...    36  0.17
gi|2338738  (AF016223) unknown [Rhodobacter capsulatus]            36  0.17
pir||E64477  replication factor C homolog - Methanococcus ja...    36  0.17
emb|CAB53148.1|  (AL109962) hypothetical protein SCJ1.30c [S...    36  0.22
emb|CAA15002|  (AJ235272) N UTILIZATION SUBSTANCE PROTEIN A ...    36  0.22
emb|CAA21268|  (AL031853) hypothetical protein [Schizosaccha...    36  0.22
sp|Q10862|YJ96_MYCTU  HYPOTHETICAL 33.9 KD PROTEIN RV1996 >g...    35  0.28
gi|3482924  (AC003970) Highly similar to cinnamyl alcohol de...    35  0.37
sp|Q58250|Y840_METJA  HYPOTHETICAL PROTEIN MJ0840 >gi|212854...    35  0.37
pir||S70533  bbK2.10 protein precursor - Lyme disease spiroc...    35  0.37
emb|CAA17240|  (AL021899) hypothetical protein Rv2026c [Myco...    34  0.49
gi|2826443  (U67604) chromosome segretation protein (smc1) [...    34  0.49
pir||E64456  hypothetical protein MJ1254 - Methanococcus jan...    34  0.49
pir||A64505  P115 homolog - Methanococcus jannaschii               34  0.49
dbj|BAA13206|  (D86970) similar to myosin heavy chain: Conta...    34  0.64
emb|CAB53422.1|  (AL109989) hypothetical protein SCJ12.10c [...    34  0.83
gb|AAD21759.1|  (AC006569) putative myosin heavy chain [Arab...    34  0.83
emb|CAB39003.1|  (AL034558) predicted using hexExon; MAL3P2....    34  0.83
dbj|BAA29642|  (AP000002) 399aa long hypothetical protein [P...    34  0.83
gb|AAD07556.1|  (AE000563) H. pylori predicted coding region...    34  0.83

The description list is truncated at E = 1.0, as requested on the query page. It is interesting to note that even had the E value been left at the default of 10, the list would have truncated at E = 1.9. In this case the list would have been limited by our selection of 100 as the number of description lines to report. When hits with higher E values are of interest, they can be viewed by returning to the query page and resetting both the E value and the description options.

Step 4. Pairwise alignments

Below are the alignments of each "significant" hit to the query. These are shown below in pairwise format, because that option was selected while setting up the query. The query-anchored format is another useful way to inspect the relationship of hits to a query. There will be as many alignments here as were specified on the query page. One efficient way to inspect alignments of interest is to use the links from specific entries from within the graphic or from within the list of descriptions. It may also be useful to scroll through the alignments to inspect the overall match quality. For example, if the aligned residues are all hydrophobic, it may indicate that a transmembrane or coiled-coil domain in the query is causing non-specific hits. Scroll through the alignments now, or skip over the alignments and go to Step 5.

 sp|Q57997|Y577_METJA  MJ0577 - Methanococcus jannaschii >gi|5107801|pdb|1MJH|A
           Chain A, Structure-Based Assignment Of The Biochemical
           Function Of Hypothetical Protein Mj0577: A Test Case Of
           Structural Genomics >gi|5107802|pdb|1MJH|B Chain B,
           Structure-Based Assignment Of The Biochemical Function
           Of Hypothetical Protein Mj0577: A Test Case Of
           Structural Genomics >gi|1591284 (U67506) conserved
           hypothetical protein [Methanococcus jannaschii]
           Length = 162
           
 Score =  314 bits (796), Expect = 2e-85

 Identities = 162/162 (100%), Positives = 162/162 (100%)


Query: 1   MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60
           MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA
Sbjct: 1   MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60

Query: 61  GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEG 120
           GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEG
Sbjct: 61  GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEG 120

Query: 121 VDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 162
           VDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS
Sbjct: 121 VDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 162

 pdb|1MJH|   Structure-Based Assignment Of The Biochemical Function Of
           Hypothetical Protein Mj0577: A Test Case Of Structural
           Genomics
           Length = 287
           
 Score =  272 bits (687), Expect = 1e-72
 Identities = 145/161 (90%), Positives = 145/161 (90%), Gaps = 16/161 (9%)

Query: 2   SVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           SVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK             
Sbjct: 143 SVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK------------- 189

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
              SVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV
Sbjct: 190 ---SVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 246

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 162
           DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS
Sbjct: 247 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 287

 Score =  268 bits (678), Expect = 2e-71
 Identities = 143/160 (89%), Positives = 143/160 (89%), Gaps = 17/160 (10%)

Query: 3   VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGL 62
           VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK              
Sbjct: 1   VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIK-------------- 46

Query: 63  NKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVD 122
              VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVD
Sbjct: 47  ---VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVD 103

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 162
           IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS
Sbjct: 104 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 143

 dbj|BAA29916| (AP000003) 170aa long hypothetical protein [Pyrococcus horikoshii]
           Length = 170
           
 Score =  107 bits (264), Expect = 6e-23
 Identities = 63/160 (39%), Positives = 97/160 (60%), Gaps = 7/160 (4%)

Query: 1   MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60
           M  M++K+L+PTDFSE A  A++  +    ++  EVILLHVIDE  +++     L+ G +
Sbjct: 1   MIFMFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEE-----LMDGYS 55

Query: 61  GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDV--GFKVKDIIVVGIPHEEIVKIAED 118
               + E    ++K KL EEA  K++   +E++       V+ II  GIP +EIVK+AE+
Sbjct: 56  FFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEE 115

Query: 119 EGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           E V +II+ S GK +L    LGS    V++K+ KPVL++K
Sbjct: 116 ENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIK 155

 sp|Q57951|Y531_METJA HYPOTHETICAL PROTEIN MJ0531 >gi|2128015|pir||C64366 hypothetical
           protein homolog MJ0531 - Methanococcus jannaschii
           >gi|1591234 (U67502) conserved hypothetical protein
           [Methanococcus jannaschii]
           Length = 170
           
 Score = 91.3 bits (223), Expect = 4e-18
 Identities = 59/156 (37%), Positives = 88/156 (55%), Gaps = 14/156 (8%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           +YKKI+ PTD S+ +  A KH          EV  ++V+D          S  +G+    
Sbjct: 25  LYKKIVIPTDGSDVSLEAAKHAINIAKEFDAEVYAIYVVD---------VSPFVGLPA-- 73

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
           +   E  +EL   L EE +  ++ +KK  E+ G K+   ++ G+P  EIV+ AE +  D+
Sbjct: 74  EGSWELISEL---LKEEGQEALKKVKKMAEEWGVKIHTEMLEGVPANEIVEFAEKKKADL 130

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKR 159
           I+MG+ GKT L+ ILLGSV E VIK ++ PVLVVK+
Sbjct: 131 IVMGTTGKTGLERILLGSVAERVIKNAHCPVLVVKK 166

 gi|2622094 (AE000872) conserved protein [Methanobacterium thermoautotrophicum]
           Length = 143
           
 Score = 84.7 bits (206), Expect = 4e-16
 Identities = 56/156 (35%), Positives = 81/156 (51%), Gaps = 16/156 (10%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           MY KIL PTD S+ A  A +H          E+I L V++          S L+G+    
Sbjct: 1   MYSKILLPTDGSKQANKAAEHAIWIARESGAEIIALTVMET---------SSLVGLPA-- 49

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVV--GIPHEEIVKIAEDEGV 121
              ++    L+  L EEA   +E +KK +E+ G  +K  +    G P E I++  E EGV
Sbjct: 50  ---DDLIIRLREMLEEEASRSLEAVKKLVEESGADIKLTVRTDEGSPAEAILRTVEKEGV 106

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           D+++MG+ GK  L   LLGSV E V++ +  PVLVV
Sbjct: 107 DLVVMGTSGKHGLDRFLLGSVAEKVVRSAGCPVLVV 142

 gi|2621993 (AE000865) conserved protein [Methanobacterium thermoautotrophicum]
           Length = 149
           
 Score = 81.1 bits (197), Expect = 4e-15
 Identities = 56/157 (35%), Positives = 85/157 (53%), Gaps = 12/157 (7%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           MY+KIL  TD SE +  A  +          E++ L V +   +         L V  L 
Sbjct: 1   MYRKILLATDGSECSMQAAGYAIETAAQNRAELLALTVTETYPLDN-------LPVEELT 53

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
           + V     EL  K +EEA  K+E++   L D   KV+ ++V G P E I+K+A++E VD+
Sbjct: 54  RKV----TELFRKESEEALQKVEDLAVSL-DTPVKVRKMMVDGSPAETILKVADEENVDL 108

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 160
           I++G+ GK  L+  LLGSV+E +++ +  PVLVV  K
Sbjct: 109 IVVGASGKHALERFLLGSVSEKIVRHARVPVLVVHSK 145

 gi|2621194 (AE000803) conserved protein [Methanobacterium thermoautotrophicum]
           Length = 131
           
 Score = 80.4 bits (195), Expect = 7e-15
 Identities = 47/155 (30%), Positives = 80/155 (51%), Gaps = 24/155 (15%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           M++KI+ PTD SE A  A              VI +HVIDE+ I   D+           
Sbjct: 1   MFEKIMVPTDGSEYAARAEDMAIELAGRLGSVVIAVHVIDEKLIYPFDV----------- 49

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
                        L +E K  + +++++  + G +V +++V G P  ++ KI E  G D+
Sbjct: 50  -------------LEDEGKEILASVQRKGREAGVQVDEVLVFGSPAHDMKKITEKTGADL 96

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +++ SHG++ L+++L+GSV E  +K  + PVL+VK
Sbjct: 97  VVIASHGRSGLEKLLMGSVAETTLKTVDVPVLLVK 131

 gi|2622163 (AE000877) conserved protein [Methanobacterium thermoautotrophicum]
           Length = 147
           
 Score = 78.8 bits (191), Expect = 2e-14
 Identities = 48/161 (29%), Positives = 84/161 (51%), Gaps = 22/161 (13%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           MY++IL PTD S  A  A +H      +   +++ + V+D    K  D            
Sbjct: 1   MYRRILIPTDGSGDARKATRHAFHIAGMSGADILAISVVDTSYRKIWD------------ 48

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKEL---EDVGF----KVKDIIVVGIPHEEIVKIA 116
              E+    L+  L ++A+  +  +K+E    +++G     ++  +I+ G P E I+++ 
Sbjct: 49  ---EDISRRLEEILKKQAEKAISILKEEFSSQQELGHMTETRLDTVILEGNPAEVILEVM 105

Query: 117 EDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           EDE VD+++MGS GK  L  I+ GS+T  V+K + KP++VV
Sbjct: 106 EDEDVDLVVMGSSGKHGLDRIISGSITRKVLKSATKPMMVV 146

 sp|P42297|YXIE_BACSU HYPOTHETICAL 15.9 KD PROTEIN IN BGLH-WAPA INTERGENIC REGION
           PRECURSOR >gi|603780|dbj|BAA06654| (D31856) hypothetical
           protein [Bacillus subtilis] >gi|849027|dbj|BAA06258|
           (D29985) hypothetical 15.9-kDa protein [Bacillus
           subtilis] >gi|2636471|emb|CAB15961| (Z99124) similar to
           hypothetical proteins [Bacillus subtilis]
           Length = 148
           
 Score = 76.1 bits (184), Expect = 1e-13
 Identities = 47/155 (30%), Positives = 83/155 (53%), Gaps = 7/155 (4%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           M+ K+L   D S+ +  AL         +  E+ +LHV  E  +    +        G+ 
Sbjct: 1   MFNKMLVAIDGSDMSAKALDAAVHLAKEQQAELSILHVGREAVVTTSSL-------TGIV 53

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
              E F +E++N++ +E    +EN K++  + G + + I   G P  EI+  A+++GV +
Sbjct: 54  YVPEHFIDEIRNEVKKEGLKILENAKEKAAEKGVQAETIYANGEPAHEILNHAKEKGVSL 113

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           I++GS G + LKE++LGSV+  V + S  PVL+V+
Sbjct: 114 IVVGSRGISGLKEMMLGSVSHKVSQLSTCPVLIVR 148

 sp|Q50777|YB54_METTM HYPOTHETICAL 16.1 KD PROTEIN IN MTR REGION (ORF143)
           >gi|1296939|emb|CAA66198| (X97589) ORF143
           [Methanobacterium thermoautotrophicum]
           Length = 143
           
 Score = 66.0 bits (158), Expect = 2e-10
 Identities = 52/148 (35%), Positives = 81/148 (54%), Gaps = 22/148 (14%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           MY+KIL PT   E  +  ++H       +  EVI L+V+D               V  L 
Sbjct: 1   MYRKILVPT-MGEYMDELIEHTLDLLHGREAEVICLYVVDT-------------SVPFLT 46

Query: 64  -KSVEEFENELKNKLTEEAKNKMENIKKEL---EDVGFKVKDIIVVGIPHEEIVKIAEDE 119
            K V+E    +  +LTE  K  + +++K L   E+   K + +++ G P +EIVK+AE+E
Sbjct: 47  PKKVKEM---MVKELTERGKEILRDMEKGLTGPENPNVKFRGVMLEGNPADEIVKLAEEE 103

Query: 120 GVDIIIMGSHGKTNLKEILLGSVTENVI 147
            VD+IIMG+ GK+ + + LLGSV+E V+
Sbjct: 104 DVDVIIMGT-GKSLVDKHLLGSVSEKVV 130

 gi|2648791 (AE000981) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 270
           
 Score = 65.2 bits (156), Expect = 3e-10
 Identities = 47/153 (30%), Positives = 81/153 (52%), Gaps = 18/153 (11%)

Query: 8   ILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVE 67
           +L PTD SE +   L+++  FK +  EE+ +L VI+  ++      S + G   ++  ++
Sbjct: 1   MLLPTDLSENSFKVLEYLGDFKKVGVEEIGVLFVINLTKL------STVSGGIDIDHYID 54

Query: 68  EFENELKNKLTEEAKNKMENIKKELEDVGFKVKDI--IVVGIPHEEIVKIAEDEGVDIII 125
           E        ++E+A+  +  + +++E  G K + I     G P  EI+K +E+     I 
Sbjct: 55  E--------MSEKAEEVLPEVAQKIEAAGIKAEVIKPFPAGDPVVEIIKASEN--YSFIA 104

Query: 126 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           MGS G +  K+ILLGSV+E V+  S  PV + K
Sbjct: 105 MGSRGASKFKKILLGSVSEGVLHDSKVPVYIFK 137

 Score = 48.4 bits (113), Expect = 3e-05
 Identities = 40/156 (25%), Positives = 70/156 (44%), Gaps = 34/156 (21%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           ++ ++L   DFS+ A+ AL++ K        E+ ++HV ++ + K  D+           
Sbjct: 145 LFDRVLVAYDFSKWADRALEYAKFVVKKTGGELHIIHVSEDGD-KTADL----------- 192

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
                       ++ EE           +   G +V   I  G PH+ I+   E+     
Sbjct: 193 ------------RVMEEV----------IGAEGIEVHVHIESGTPHKAILAKREEINATT 230

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKR 159
           I MGS G  ++  ++LGS +E+VI++S  PV V KR
Sbjct: 231 IFMGSRGAGSVMTMILGSTSESVIRRSPVPVFVCKR 266

 gi|2648610 (AE000970) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 283
           
 Score = 64.4 bits (154), Expect = 5e-10
 Identities = 49/157 (31%), Positives = 78/157 (49%), Gaps = 22/157 (14%)

Query: 4   MYKKILYPTDFSETAEIALKHV--KAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           M KK+L+P DFS  +E A  +   K F T                +     F+ L+    
Sbjct: 1   MIKKVLFPVDFSVVSEYAFGNCIPKFFST--------------GALTSSFSFTRLMLTCN 46

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
           L +S++     L+  L +      EN ++   D G K + ++ +G P  EI KIAE+E V
Sbjct: 47  LLRSLK-----LQKSLKKVHGYDRENCRRVQRD-GDKRERVVRLGTPALEIAKIAEEENV 100

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           D+I M   G+  ++E+L+GS   NV + + KPVL+V+
Sbjct: 101 DLIYMPMKGENIIREMLIGSTAANVARVAKKPVLLVR 137

 Score = 56.2 bits (133), Expect = 1e-07
 Identities = 45/154 (29%), Positives = 72/154 (46%), Gaps = 29/154 (18%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           ++ + L+  DFS+  E  ++  + FK L  +E ILLHV+D                 G  
Sbjct: 156 VFDRPLFALDFSKCTEKIIQTTELFKEL-VKEAILLHVVDY----------------GKE 198

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDI 123
             VEE   +   KL E A           E + F  + ++  G   +EI+  A   G  +
Sbjct: 199 SEVEENIQKATQKLKEIA-----------EKLDFPSEVVVHSGDASKEILMTAPSVGATL 247

Query: 124 IIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           I++G  G+ N+ ++L+GS  E VI+ S  PVL+V
Sbjct: 248 IVIGKRGR-NILQLLMGSTAEIVIRNSVLPVLIV 280

 gi|2983400 (AE000710) hypothetical protein [Aquifex aeolicus]
           Length = 297
           
 Score = 64.0 bits (153), Expect = 6e-10
 Identities = 43/159 (27%), Positives = 81/159 (50%), Gaps = 26/159 (16%)

Query: 6   KKILYPTDFSETA----EIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           KK++   DFS+TA    E ALK +K FK      V ++HV +  E+              
Sbjct: 156 KKVVIAYDFSKTAQKTAEFALKFLKNFKV----SVEIVHVHESIEMPL------------ 199

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVK--IAEDE 119
               +E+ +++++ + +EE K  +  +K   E+ G K +   + G    +++   + E  
Sbjct: 200 ----IEKLKHKIEKEFSEEKKKILNELKGRFEEEGIKTEVKFLEGEDAVDVISSYVNETP 255

Query: 120 GVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
            V+++I+GS G + LK+++LG     ++ K NKP+L+ K
Sbjct: 256 EVELLIIGSKGLSGLKKLILGRTATKLLGKVNKPILIYK 294

 Score = 62.5 bits (149), Expect = 2e-09
 Identities = 49/153 (32%), Positives = 79/153 (51%), Gaps = 10/153 (6%)

Query: 7   KILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN-KS 65
           K L P DFSE     L+ VK        EV LLHVI          +   +GV+ ++ + 
Sbjct: 5   KFLVPVDFSEITNPLLRTVKRVGEKVDCEVHLLHVIPPVLYLP---YPETMGVSVIDIEL 61

Query: 66  VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIII 125
           +E+ E+E K     EAK K++ +++ L+ V  K +  + VG P + I+   E    D++ 
Sbjct: 62  LEKLEDEKK----AEAKEKLKALEEFLKPV--KARSHVDVGDPADVILDYEEKLNPDMVF 115

Query: 126 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +G H K  ++++L+GS TE V+K   K   V+K
Sbjct: 116 LGGHKKGLIEKLLIGSTTEKVVKHGKKSDFVIK 148

 sp|P73475|YC30_SYNY3 HYPOTHETICAL 31.2 KD PROTEIN SLR1230 >gi|1652594|dbj|BAA17515|
           (D90906) hypothetical protein [Synechocystis sp.]
           Length = 287
           
 Score = 62.8 bits (150), Expect = 1e-09
 Identities = 28/85 (32%), Positives = 52/85 (60%)

Query: 74  KNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTN 133
           K     +A   +   +K LE  GFK++  ++VG   E IV+  ED  +D+++MG+HG + 
Sbjct: 203 KTNQDPQAIANLGTAEKVLEKAGFKLEVELLVGHAEEAIVRYQEDNAIDLLLMGAHGHSR 262

Query: 134 LKEILLGSVTENVIKKSNKPVLVVK 158
           ++ +++GS T  V++K++ PVL  +
Sbjct: 263 IRHLVIGSTTAQVLRKTSIPVLTFR 287

 gi|2983527 (AE000719) hypothetical protein [Aquifex aeolicus]
           Length = 281
           
 Score = 61.3 bits (146), Expect = 4e-09
 Identities = 53/159 (33%), Positives = 84/159 (52%), Gaps = 18/159 (11%)

Query: 5   YKKILYPTDFSETAEIALKHVKAFKTLKAEE--VILLHVIDEREIKKRDIFSL--LLGVA 60
           + +I+   D S  + IA +H  AFK  K  +  VI ++VIDER + +  +  L  +LG  
Sbjct: 3   FNRIIVGIDGSPASLIATRH--AFKIGKHFDIPVIGMYVIDERLMDESFLLDLSSILGFT 60

Query: 61  ---GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAE 117
              G++  V+EF       L E+    ++   +E    G KV  + V GIP +EIVK A+
Sbjct: 61  FYPGISARVKEF-------LEEQGDLILKTFAEEGRKEGVKVSIVQVQGIPWQEIVKEAD 113

Query: 118 DEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLV 156
            E  D+I++G  GK  +K +L+ S  ENV + +  PV +
Sbjct: 114 KE--DLILIGKKGKKLIKGVLVSSNAENVARNAPCPVFM 150

 Score = 53.5 bits (126), Expect = 9e-07
 Identities = 30/83 (36%), Positives = 49/83 (58%), Gaps = 3/83 (3%)

Query: 79  EEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEIL 138
           EEAK + E +K+ L   G +     + GIP E IV    ++ +D + MG++GK  ++E  
Sbjct: 199 EEAKKREEEVKEVL---GEEHHFYGIKGIPEEVIVSFCREKEMDALFMGAYGKGPVREFF 255

Query: 139 LGSVTENVIKKSNKPVLVVKRKN 161
           LGSVT  V+   + P+L+V++ N
Sbjct: 256 LGSVTTYVMHNLDLPLLLVRQPN 278

 sp|O27222|YB54_METTH HYPOTHETICAL PROTEIN MTH1154 >gi|2622260 (AE000885) conserved
           protein [Methanobacterium thermoautotrophicum]
           Length = 146
           
 Score = 59.3 bits (141), Expect = 2e-08
 Identities = 49/151 (32%), Positives = 79/151 (51%), Gaps = 22/151 (14%)

Query: 1   MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60
           M  MY+KIL PT   E  +  ++H       +  EVI L+V+D               V 
Sbjct: 1   MIEMYRKILVPT-MGEYMDELIEHTLDLLHGREAEVICLYVVDT-------------AVP 46

Query: 61  GLN-KSVEEFENELKNKLTEEAKNKMENIKKEL---EDVGFKVKDIIVVGIPHEEIVKIA 116
            L  K V+E    +  +LT+     + +++K L   E+     + ++  G P +EIVK+A
Sbjct: 47  FLTPKKVKEM---MVKELTQRGNEILRDMEKGLTGPENPNVSFRAVMREGDPADEIVKVA 103

Query: 117 EDEGVDIIIMGSHGKTNLKEILLGSVTENVI 147
           E+E VD+I+MG+ GK+ + + LLGSV+E V+
Sbjct: 104 EEEDVDVIVMGT-GKSLVDKHLLGSVSEKVV 133

 dbj|BAA30650| (AP000006) 208aa long hypothetical protein [Pyrococcus horikoshii]
           Length = 208
           
 Score = 57.4 bits (136), Expect = 6e-08
 Identities = 43/160 (26%), Positives = 72/160 (44%), Gaps = 37/160 (23%)

Query: 2   SVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           S ++++ L   D SE +E  +K+++    +K  E IL HV+D  ++              
Sbjct: 79  SNIFERPLVALDLSECSEKIIKNIRNLPEVK--EAILFHVVDYGKV-------------- 122

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVG----FKVKDIIVVGIPHEEIVKIAE 117
                            EE +  + N KK L + G    +K+K  I  GI    I+  A 
Sbjct: 123 -----------------EELEANINNAKKALSEYGKLLPWKIKVEIQAGIASRGIIGAAI 165

Query: 118 DEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           +    ++++G  GK+ LKE+LLGS  E VI+    P L++
Sbjct: 166 NNVATLVVIGKKGKSILKELLLGSTAERVIRDCRLPTLLI 205

 Score = 55.8 bits (132), Expect = 2e-07
 Identities = 23/64 (35%), Positives = 46/64 (70%)

Query: 95  VGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPV 154
           +G  V+ ++ +GIP  EI ++A++E V++I++ S G+  L+++LLGS   N+ + + KPV
Sbjct: 1   MGINVETVVRIGIPSLEISEVAKEENVNLIVIPSKGQNILRQMLLGSTASNLARITRKPV 60

Query: 155 LVVK 158
           L+++
Sbjct: 61  LILR 64

 dbj|BAA31039.1| (AP000007) 149aa long hypothetical protein [Pyrococcus horikoshii]
           Length = 149
           
 Score = 56.2 bits (133), Expect = 1e-07
 Identities = 49/156 (31%), Positives = 77/156 (48%), Gaps = 12/156 (7%)

Query: 7   KILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSV 66
           K+L   D S+ ++ A  H  +    K  +VIL  V+D RE K    F L +    L K +
Sbjct: 2   KLLVLIDGSKWSQKAALHAFSIAKRKNAKVILFSVLDRREAKAL-AFHLSMRSDSLGK-I 59

Query: 67  EEFEN----ELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVD 122
           +EFE     E K  + E     +E  ++E  +  FK    IV G   EEI+K A      
Sbjct: 60  KEFEETIWRETKKSVKEVITTLLELGRREGINCSFK----IVEGSAKEEIIKEANSGKYS 115

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           ++IMG++G++    I  GS+ E V+ +   PV++V+
Sbjct: 116 MVIMGAYGRSGKTRI--GSLLEEVVGQIRIPVMIVR 149

 emb|CAB50594.1| (AJ248288) hypothetical protein [Pyrococcus abyssi]
           Length = 149
           
 Score = 55.4 bits (131), Expect = 2e-07
 Identities = 46/156 (29%), Positives = 77/156 (48%), Gaps = 12/156 (7%)

Query: 7   KILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSV 66
           K+L   D S+ ++ A  H  +       +VIL  V+D RE +    F L +    L K +
Sbjct: 2   KLLVLIDGSKWSQKAALHAFSIAKRSNAKVILFSVLDRREARAL-AFHLSMRSESLEK-I 59

Query: 67  EEFEN----ELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVD 122
            EFE     ++K  + E     +E  K+E  +  FK+ +    G   EEI+K A     D
Sbjct: 60  REFEETIWKDMKKSVKEVITTLLELGKREGVNCSFKIAE----GSAKEEILKEANSGKYD 115

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           ++IMG++G++    I  GS+ E V+ +   PV++V+
Sbjct: 116 MVIMGAYGRSGKTRI--GSLLEEVVGQIRIPVMIVR 149

 sp|P39177|UP12_ECOLI UNKNOWN PROTEIN FROM 2D-PAGE (SPOTS PR25/LM16/2D_000LR3)
           >gi|1778525 (U82598) hypothetical protein [Escherichia
           coli] >gi|1786824 (AE000166) orf, hypothetical protein
           [Escherichia coli] >gi|4062223|dbj|BAA35237| (D90701)
           Unknown protein from 2D-page (spots pr25/lm16/2d_000lr3)
           . [Escherichia coli] >gi|4062229|dbj|BAA35246| (D90702)
           Unknown protein from 2D-page (spots pr25/lm16/2d_000lr3)
           . [Escherichia coli]
           Length = 142
           
 Score = 55.4 bits (131), Expect = 2e-07
 Identities = 44/157 (28%), Positives = 79/157 (50%), Gaps = 17/157 (10%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVI--LLHVIDEREIKKRDIFSLLLGVAG 61
           MYK I+ P D  E  E++ K V+  + L  ++ +  LLHV+           S  L +  
Sbjct: 1   MYKTIIMPVDVFEM-ELSDKAVRHAEFLAQDDGVIHLLHVLPG---------SASLSLHR 50

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
               V  FE  L++    EA+ +++ +         ++K  +  G   +E+ ++AE+ G 
Sbjct: 51  FAADVRRFEEHLQH----EAQERLQTMVSHFTIDPSRIKQHVRFGSVRDEVNELAEELGA 106

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           D++++GS    ++   LLGS   +VI+ +N PVLVV+
Sbjct: 107 DVVVIGSR-NPSISTHLLGSNASSVIRHANLPVLVVR 142

 sp|P74148|YD88_SYNY3 HYPOTHETICAL 17.3 KD PROTEIN SLL1388 >gi|1653320|dbj|BAA18235|
           (D90912) hypothetical protein [Synechocystis sp.]
           Length = 154
           
 Score = 52.3 bits (123), Expect = 2e-06
 Identities = 42/159 (26%), Positives = 79/159 (49%), Gaps = 13/159 (8%)

Query: 5   YKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVI--DEREIKKRDIFSLLLGVAGL 62
           Y KIL   D SE A+  L+   A    ++ ++++ + I  D +++    I+    G A +
Sbjct: 3   YGKILVALDRSELAKEVLQQAIALGQKESSQLMVFYCIPVDSQDLS---IYPSFYGEAAI 59

Query: 63  NKSVEEFENELKNKLTE---EAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDE 119
                 F   +K  L E   EA+  +++I +++++ G   +  + VG P   I  +A++ 
Sbjct: 60  G-----FSQIIKEHLEEQQTEAREWLQSIVQQVQEDGVACEWDVKVGEPGRWIRDMAKNW 114

Query: 120 GVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
             D++++G  G   L E+ LGSV+  VI      VL+V+
Sbjct: 115 DADLVVLGRRGLKGLAEVFLGSVSSYVIHHVQCSVLIVQ 153

 sp|P45680|YFMU_COXBU HYPOTHETICAL 15.8 KD PROTEIN IN FMU-RPMH INTERGENIC REGION
           >gi|2126364|pir||I40650 hypothetical protein 146 -
           Coxiella burnetii >gi|511455 (U10529) unknown [Coxiella
           burnetii]
           Length = 146
           
 Score = 49.2 bits (115), Expect = 2e-05
 Identities = 47/158 (29%), Positives = 76/158 (47%), Gaps = 15/158 (9%)

Query: 5   YKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNK 64
           YKKIL        ++  L  V+  K L A     L++I    ++    +    GVA    
Sbjct: 4   YKKILVALALDPNSDRPL--VEKAKELSANRDAQLYLI--HAVEHLSSYGAAYGVAA--- 56

Query: 65  SVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDII 124
                  ++++ L EEAK +M  I  +L         I+ VG     I++ A++ GVD+I
Sbjct: 57  -----GVDVEDMLLEEAKKRMNEIASQLNISSDH--QIVKVGPAKFLILEQAKNWGVDLI 109

Query: 125 IMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS 162
           I+GSHG+  + ++LLGS +  V+  +   VL V+ K S
Sbjct: 110 IVGSHGRHGI-QLLLGSTSNAVLHGAKCDVLAVRIKGS 146

 gb|AAF11689.1|AE002048_9 (AE002048) hypothetical protein [Deinococcus radiodurans]
           Length = 150
           
 Score = 48.4 bits (113), Expect = 3e-05
 Identities = 43/154 (27%), Positives = 71/154 (45%), Gaps = 16/154 (10%)

Query: 6   KKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKS 65
           KKIL  TD S+    A +H +A       E++ L V  +        F     VA  N  
Sbjct: 2   KKILVTTDQSDLGWQATEHARALAEALGAELVALSVQADPSPAVTGEFGY---VAPANP- 57

Query: 66  VEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIP-HEEIVKIAEDEGVDII 124
            E+F  +    L    + K++  +  +E            G P    I+ +A++EGV +I
Sbjct: 58  -EDFILQQDQALAL-LRQKVQGARSRVERAA---------GRPVSRTIIDVAKEEGVSMI 106

Query: 125 IMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +M +HG+  L   LLGSV E V+  ++ PV++++
Sbjct: 107 VMTTHGRAGLGRALLGSVAEAVLHHAHVPVVLIR 140

 dbj|BAA16707| (D90900) hypothetical protein [Synechocystis sp.]
           Length = 284
           
 Score = 48.4 bits (113), Expect = 3e-05
 Identities = 42/158 (26%), Positives = 68/158 (42%), Gaps = 29/158 (18%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           M  KILY    +   +  LK +  F  ++   + +LHV+  +                  
Sbjct: 1   MLSKILYADSGTSQTQEMLKAMMDFPAVQKASITILHVVPPQI----------------- 43

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGF---KVKDIIVVGIPHEEIVKIAEDEG 120
            + E F        TE+     + +   LEDV     KV  ++  G P   +  +A +  
Sbjct: 44  -TTEAF--------TEKWAEGGKILADLLEDVAIEPSKVSTVLRQGDPKGVVCDVANEID 94

Query: 121 VDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
            D+IIMGS G   L+ IL  SV++ V + +N P+L+VK
Sbjct: 95  ADLIIMGSRGLKRLEAILENSVSQYVFQLTNHPMLLVK 132

 dbj|BAA79051.1| (AP000058) 243aa long hypothetical protein [Aeropyrum pernix]
           Length = 243
           
 Score = 48.0 bits (112), Expect = 4e-05
 Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 2/90 (2%)

Query: 71  NELKNKLTEEAKNKMENIKKELEDVGFKVK--DIIVVGIPHEEIVKIAEDEGVDIIIMGS 128
           + L   + + A+ K++ IKK + + G  V   + I VG P   I ++AE+ G   I+MGS
Sbjct: 12  SSLIRSIEKNAREKLDKIKKLMMEKGANVVVYEDIPVGNPGTVISEVAEEVGATEIVMGS 71

Query: 129 HGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
            G    + + LGS     +K S KPV+ +K
Sbjct: 72  KGLGIFRILPLGSTVRETVKISRKPVIRLK 101

 gi|2650517 (AE001097) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 167
           
 Score = 47.3 bits (110), Expect = 7e-05
 Identities = 27/96 (28%), Positives = 53/96 (55%), Gaps = 3/96 (3%)

Query: 66  VEEFENELK--NKLTEEAKNKMENIKKELEDVGFKVKDI-IVVGIPHEEIVKIAEDEGVD 122
           +  +E E+K    L  +A   +E  ++ LE+ G +VK + I++G   EE++++ +    D
Sbjct: 51  IASYEKEMKIYTSLRVKASKFVEFYRERLEEAGLEVKQVKIILGNVSEEVLRLEKLLNPD 110

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +I+ G   +  LK +L G   + +I ++  PV+V K
Sbjct: 111 LIVFGMEKRGFLKRLLRGDPYKEIIYETKAPVMVCK 146

 emb|CAA74460.1| (Y14080) hypothetical protein [Bacillus subtilis]
           >gi|2633304|emb|CAB12808| (Z99109) similar to
           hypothetical proteins [Bacillus subtilis]
           Length = 184
           
 Score = 46.9 bits (109), Expect = 9e-05
 Identities = 23/56 (41%), Positives = 36/56 (64%)

Query: 103 IVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           I+ G P E I++ A     D+I+ GS  +  LK+++ GSV+E +  KS+ PVL+VK
Sbjct: 129 ILEGDPAESIIEHANRISADMIVTGSRDQNRLKKLIFGSVSEKLSAKSDIPVLIVK 184

 gb|AAD47991.1| (AF157801) hypothetical protein B [Pseudomonas sp. R9]
           Length = 283
           
 Score = 46.5 bits (108), Expect = 1e-04
 Identities = 19/82 (23%), Positives = 49/82 (59%)

Query: 77  LTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKE 136
           + +EA  +++  +K L + GF V+     G     +    ++ G+D+++MG +G + +++
Sbjct: 202 VNDEASAQLDWAQKVLINAGFTVRAETRSGEIERTLHAYQKEHGIDLLVMGDYGHSRIRQ 261

Query: 137 ILLGSVTENVIKKSNKPVLVVK 158
            L+GS T ++++ +  P+L+++
Sbjct: 262 FLVGSTTTSMLRTTTSPLLLLR 283

 emb|CAA73748| (Y13308) hypothetical protein [Yersinia enterocolitica]
           Length = 288
           
 Score = 46.5 bits (108), Expect = 1e-04
 Identities = 15/49 (30%), Positives = 37/49 (74%)

Query: 110 EEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           + +++ AE+  VD+I+MG++G + L++  +GS T  +++K+ +P+L+++
Sbjct: 227 DALIRYAEENAVDLIVMGAYGHSRLRQFFIGSHTSEMLQKTQQPLLILR 275

 Score = 36.4 bits (82), Expect = 0.13
 Identities = 37/145 (25%), Positives = 72/145 (49%), Gaps = 22/145 (15%)

Query: 27  AFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKS------VEEFENELKNKLTEE 80
           A +TL+++ + LLHVI++       + S L G  GL+        + E E +    L  +
Sbjct: 25  AARTLQSQ-LALLHVIEK---DSTPVVSDLTGTLGLDSQQLLTDELVEIEGQRNRLLMAQ 80

Query: 81  AKNKMENIKKELEDVGFKVKDIIVV---GIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEI 137
            K  +E+  + L+  G    D++++   G P E + ++++   + ++++G  G  +    
Sbjct: 81  GKAILESCSELLQKQGSP--DVLLMQKHGTPDEVLAELSD---LRLMVLGRRGSQHP--- 132

Query: 138 LLGSVTENVIKKSNKPVLVVKRKNS 162
            +GS  E+VI+   KP+LVV    S
Sbjct: 133 -VGSHLESVIRLQKKPLLVVPENYS 156

 emb|CAB08889| (Z95554) hypothetical protein Rv1636 [Mycobacterium tuberculosis]
           Length = 146
           
 Score = 45.7 bits (106), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 85  MENIKKELEDVGFK-VKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVT 143
           + + K+   + G K V++  +VG P + +V +A++E  D++++G+ G + +   LLGSV 
Sbjct: 70  LHDAKERAHNAGAKNVEERPIVGAPVDALVNLADEEKADLLVVGNVGLSTIAGRLLGSVP 129

Query: 144 ENVIKKSNKPVLVV 157
            NV +++   VL+V
Sbjct: 130 ANVSRRAKVDVLIV 143

 sp|P72817|YG54_SYNY3 HYPOTHETICAL 16.8 KD PROTEIN SLL1654 >gi|1651906|dbj|BAA16832|
           (D90901) hypothetical protein [Synechocystis sp.]
           Length = 157

           
 Score = 45.7 bits (106), Expect = 2e-04
 Identities = 43/156 (27%), Positives = 65/156 (41%), Gaps = 21/156 (13%)

Query: 3   VMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGL 62
           +M+K IL+P D S  A  A + V     +   ++ILL V++                   
Sbjct: 21  IMFKTILFPLDRSREARDAAQMVADLVKIHQSQLILLSVVE------------------- 61

Query: 63  NKSVEEFENELKNKLTEEAKNKM-ENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
            K+    ++E     + EA  K+ E  +      G   K I   G+    I  +A++   
Sbjct: 62  -KNPPGQDHEAHGMDSPEAVAKLLEAAQAVFSQQGIATKTIEREGMASFTICDVADEVNA 120

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           D+I+MG  G     E +  SVT  VI  S  PVLVV
Sbjct: 121 DLIVMGCRGLGLTTEGVAESVTARVINLSPCPVLVV 156

 emb|CAA22850.1| (AL035248) hypothetical protein [Schizosaccharomyces pombe]
           Length = 601
           
 Score = 45.3 bits (105), Expect = 3e-04
 Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 7/95 (7%)

Query: 73  LKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIP--HEEIVKIAEDEGVD-----III 125
           +K+++  E    +E I K +  +  K    + V I   H E  K    E +D     +++
Sbjct: 477 VKDRMESEQLETLEKITKYILKLLSKTVLEVEVNIEVIHHEKAKHLIIEMIDYIEPSLVV 536

Query: 126 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 160
           MGS G+++LK +LLGS +  ++ KS+ PV+V ++K
Sbjct: 537 MGSRGRSHLKGVLLGSFSNYLVNKSSVPVMVARKK 571

 gi|2160182 (AC000132) ESTs gb|ATTS1236,gb|T43334,gb|N97019,gb|AA395203 come
           from this gene. [Arabidopsis thaliana]
           Length = 174
           
 Score = 45.3 bits (105), Expect = 3e-04
 Identities = 27/104 (25%), Positives = 50/104 (47%), Gaps = 4/104 (3%)

Query: 57  LGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIA 116
           L V     ++E+ +  + + + E A      I  E       VK  +V+G P  +I +  
Sbjct: 70  LEVPAFTAAIEQHQKRITDTILEHASQ----ICAEKSVSRVNVKTQVVIGDPKYKICEAV 125

Query: 117 EDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 160
           E+   D+++MGS     +K + LGSV+      ++ PV+++K K
Sbjct: 126 ENLHADLLVMGSRAYGRIKRMFLGSVSNYCTNHAHCPVVIIKPK 169

 sp|P87132|YDM1_SCHPO HYPOTHETICAL PROTEIN C57A7.01 IN CHROMOSOME I
           >gi|2104436|emb|CAB08759.1| (Z95396) hypothetical
           protein [Schizosaccharomyces pombe]
           Length = 131
           
 Score = 45.3 bits (105), Expect = 3e-04
 Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 7/95 (7%)

Query: 73  LKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIP--HEEIVKIAEDEGVD-----III 125
           +K+++  E    +E I K +  +  K    + V I   H E  K    E +D     +++
Sbjct: 7   VKDRMESEQLETLEKITKYILKLLSKTVLEVEVNIEVIHHEKAKHLIIEMIDYIEPSLVV 66

Query: 126 MGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRK 160
           MGS G+++LK +LLGS +  ++ KS+ PV+V ++K
Sbjct: 67  MGSRGRSHLKGVLLGSFSNYLVNKSSVPVMVARKK 101

 gb|AAD46412.1|AF096262_1 (AF096262) ER6 protein [Lycopersicon esculentum]
           Length = 168
           
 Score = 44.1 bits (102), Expect = 6e-04
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 99  VKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           VK  +V+G P E+I    E+   D+++MGS     +K + LGSV+      +  PV++VK
Sbjct: 106 VKTQVVIGDPKEKICDAVEEMNADLLVMGSRAFGPIKRMFLGSVSNYCTNHAQCPVIIVK 165

 sp|P74897|YQA3_THEAQ HYPOTHETICAL 14.6 KD PROTEIN IN QAH/OAS SULFHYDRYLASE 3'REGION
           >gi|1526550|dbj|BAA13428| (D87664) hypothetical protein
           [Thermus aquaticus]
           Length = 137
           
 Score = 44.1 bits (102), Expect = 6e-04
 Identities = 40/156 (25%), Positives = 70/156 (44%), Gaps = 20/156 (12%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           M+K IL   D S+ A+ A    KA        ++++H  +       + F          
Sbjct: 1   MFKTILLAYDGSDHAKRAAAVAKAEAQAHGARLLVVHAYEPVPDYLGEPF---------- 50

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVV-GIPHEEIVKIAEDEGVD 122
                FE  LK +L    K + E +       G   +D +++ G P E I++ A  E  D
Sbjct: 51  -----FEEALKRRLERAEKVRAEAMAL----TGVPREDALLLQGRPAEAILQAAIGEKAD 101

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +I+MG+ G   +  + LGS ++ V+ ++  PVL+V+
Sbjct: 102 LIVMGTRGLGAVGSLFLGSQSQKVVAEAPCPVLLVR 137

 dbj|BAA16954| (D90902) hypothetical protein [Synechocystis sp.]
           Length = 291
           
 Score = 43.8 bits (101), Expect = 7e-04
 Identities = 37/156 (23%), Positives = 73/156 (46%), Gaps = 23/156 (14%)

Query: 4   MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLN 63
           M+K  L  TDFS+  +     V+        ++I LH +   E                 
Sbjct: 1   MFKHCLICTDFSDGLQRLAGFVEELSLSGITKLIFLHTVSVWE----------------- 43

Query: 64  KSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIV-KIAEDEGVD 122
              +E   ++     +EAK  +E++  ++   G +VK + V  + + ++V ++ E E +D
Sbjct: 44  ---DEHIADVDESKLKEAKTYLESLVGQVPP-GIEVK-VEVSSVRYVDLVNQLVEQEAID 98

Query: 123 IIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +II G   ++NL+  L GS T ++ K +  PV++++
Sbjct: 99  LIINGMPVRSNLESKLFGSHTLSLAKSTKVPVMILR 134

 gb|AAF11911.1|AE002067_3 (AE002067) conserved hypothetical protein
 [Deinococcus radiodurans]
           Length = 160
           
 Score = 43.4 bits (100), Expect = 0.001
 Identities = 36/153 (23%), Positives = 71/153 (45%), Gaps = 16/153 (10%)

Query: 5   YKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNK 64
           ++++L   DFS ++  AL+  +         + L HV D R +   D+      V G+  
Sbjct: 18  FQRLLVGIDFSPSSLHALEVART--RFPGARLRLAHVTDARAVAAPDV------VGGVTP 69

Query: 65  SVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDII 124
            + +    L   L +   N++  + ++ E+        ++VG P   ++  A   G D+I
Sbjct: 70  IMPD--PGLLQTLEDADSNRLSGLIRDGEE------SELLVGDPITGLLDAARAWGADLI 121

Query: 125 IMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
           ++G+H +  L+   +GS  E ++ +S  PVL V
Sbjct: 122 VVGTHPQGALEHFFIGSSAEKLVGRSAVPVLCV 154

 pir||JN0292 antigen 332 - Plasmodium falciparum (fragments)
           Length = 837
           
 Score = 43.4 bits (100), Expect = 0.001
 Identities = 37/132 (28%), Positives = 67/132 (50%), Gaps = 25/132 (18%)

Query: 29  KTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENI 88
           K   AEE++    + + E+         +G AG   S  E   E +  +T+E + K E++
Sbjct: 543 KESDAEEILETEFLSDEEV---------VGQAG---STSEEIVEEEGSVTKEVEEK-ESV 589

Query: 89  KKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIK 148
            +EL D G   ++++  G  HEE+V+    +GV +         N+ EI+ GSVTE +IK
Sbjct: 590 TEELVDEGSVTEELVDEGSVHEEVVR----QGVHV--------QNVPEIVEGSVTEEMIK 637

Query: 149 KSNKPVLVVKRK 160
           +  +  ++++ K
Sbjct: 638 EGLENEVILEWK 649

 gi|2650286 (AE001080) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 84
           
 Score = 42.2 bits (97), Expect = 0.002
 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 100 KDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEI--LLGSVTENVIKKSNKPVLVV 157
           K I+  G   + I+  AE+EGVD+I+M   G   + EI   LGS  E V + +  PVL+V
Sbjct: 24  KRIVKAGKCWKVIIDTAEEEGVDMIVMTERGSGAVAEIGDALGSCAEKVARHARNPVLIV 83

Query: 158 K 158
           +
Sbjct: 84  R 84

 gi|1002877 (U34353) ORF278 [Paracoccus denitrificans]
           Length = 278
           
 Score = 41.4 bits (95), Expect = 0.004
 Identities = 15/43 (34%), Positives = 30/43 (68%)

Query: 116 AEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           A + G D+++MG++G +  +E +LG  T N+++K+  PVL+ +
Sbjct: 236 ATEIGADMLVMGAYGHSRFREAILGGATRNMLEKAQVPVLMAR 278

 sp|P44195|YDAA_HAEIN HYPOTHETICAL PROTEIN HI1426
           Length = 309
           
 Score = 41.0 bits (94), Expect = 0.005
 Identities = 19/53 (35%), Positives = 34/53 (63%)

Query: 106 GIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           G P E I ++A++   +++I+G+ G+T L   LLG+  E+VI K +  +L +K
Sbjct: 251 GFPEEVIPEVAKEIEAELVILGTVGRTGLSAALLGNTAEHVISKLSCNLLGIK 303

 gi|1787640 (AE000234) putative filament protein [Escherichia coli]
           Length = 168
           
 Score = 41.0 bits (94), Expect = 0.005
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 15/157 (9%)

Query: 4   MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           M + IL P D S  E  +  + HV+    +   EV  L VI          +   LG+A 
Sbjct: 25  MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLP------YYASLGLA- 77

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
                   E    + L  EAK+++E I K+ +    +V   +  G P + I+++A+    
Sbjct: 78  -----YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPA 132

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
            +II+ SH + ++   LLGS    V++ +   VLVV+
Sbjct: 133 HMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 168

 sp|P37903|UP03_ECOLI UNKNOWN PROTEIN 2D_000B3L FROM 2D-PAGE >gi|1742248|dbj|BAA14980|
           (D90775) Unknown protein from 2D-PAGE (SPOT 2D_000B3L)
           (fragment). [Escherichia coli]
           Length = 144
           
 Score = 41.0 bits (94), Expect = 0.005
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 15/157 (9%)

Query: 4   MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
           M + IL P D S  E  +  + HV+    +   EV  L VI          +   LG+A 
Sbjct: 1   MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLP------YYASLGLA- 53

Query: 62  LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
                   E    + L  EAK+++E I K+ +    +V   +  G P + I+++A+    
Sbjct: 54  -----YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPA 108

Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
            +II+ SH + ++   LLGS    V++ +   VLVV+
Sbjct: 109 HMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 144

 pir||G64029 hypothetical protein HI1426 - Haemophilus influenzae (strain Rd
           KW20) >gi|1574260 (U32821) conserved hypothetical
           protein [Haemophilus influenzae Rd]
           Length = 340
           
 Score = 41.0 bits (94), Expect = 0.005
 Identities = 19/53 (35%), Positives = 34/53 (63%)

Query: 106 GIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           G P E I ++A++   +++I+G+ G+T L   LLG+  E+VI K +  +L +K
Sbjct: 282 GFPEEVIPEVAKEIEAELVILGTVGRTGLSAALLGNTAEHVISKLSCNLLGIK 334

 emb|CAB57770.1| (Y18930) hypothetical protein [Sulfolobus solfataricus]
           Length = 136
           
 Score = 39.9 bits (91), Expect = 0.011
 Identities = 41/157 (26%), Positives = 63/157 (40%), Gaps = 31/157 (19%)

Query: 1   MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60
           +S   +KIL P D SE +  AL     F      ++ ++HV  +      DI SL+    
Sbjct: 8   VSFWLRKILVPVDGSENSLRALDLAVDFGMRYGSKITIIHVCSDCN-NMNDIQSLI---- 62

Query: 61  GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEG 120
                    E  + NK+  + K    NIK+                    EI+K+  +E 
Sbjct: 63  ---------EKRINNKIEYDLKIVKINIKESSVS---------------NEILKVINEEP 98

Query: 121 VDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVV 157
            D IIMG+ G +   +I +GS    +    N PV V+
Sbjct: 99  YDAIIMGARGTSLNSDINIGSTALAI--SINAPVSVI 133

 sp|Q10851|YK05_MYCTU HYPOTHETICAL 30.9 KD PROTEIN RV2005C >gi|1403448|emb|CAA98383|
           (Z74025) hypothetical protein Rv2005c [Mycobacterium
           tuberculosis]
           Length = 295
           
 Score = 39.9 bits (91), Expect = 0.011
 Identities = 35/152 (23%), Positives = 70/152 (46%), Gaps = 19/152 (12%)

Query: 8   ILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVE 67
           +L   D S  +E+A        + +  E+I +H   + E+ +         + GL+ S  
Sbjct: 162 VLVGIDGSPVSELATAVAFDEASRRGVELIAVHAWSDVEVVE---------LPGLDFSAV 212

Query: 68  EFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMG 127
           + E EL          ++   ++   DV   V  ++V   P  ++V+  +     ++++G
Sbjct: 213 QQEAELS------LAERLAGWQERYPDV--PVSRVVVCDRPARKLVQ--KSASAQLVVVG 262

Query: 128 SHGKTNLKEILLGSVTENVIKKSNKPVLVVKR 159
           SHG+  L  +LLGSV+  V+  +  PV+V ++
Sbjct: 263 SHGRGGLTGMLLGSVSNAVLHAARVPVIVARQ 294

 Score = 36.7 bits (83), Expect = 0.096
 Identities = 19/64 (29%), Positives = 38/64 (58%), Gaps = 2/64 (3%)

Query: 94  DVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKP 153
           D    VK  +V   P   +V+I+ +   +++++GS G+  L   LLGSV+ ++++++  P
Sbjct: 86  DRKLSVKSELVFSTPVPTMVEISNE--AEMVVLGSSGRGALARGLLGSVSSSLVRRAGCP 143

Query: 154 VLVV 157
           V V+
Sbjct: 144 VAVI 147

 emb|CAB53139.1| (AL109962) hypothetical protein SCJ1.21 [Streptomyces coelicolor
           A3(2)]
           Length = 152
           
 Score = 39.1 bits (89), Expect = 0.019
 Identities = 17/62 (27%), Positives = 40/62 (64%), Gaps = 2/62 (3%)

Query: 99  VKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           +K+I+V G P E +++ ++  G +++++G  G+      +LGSV++   + +  PV+VV+
Sbjct: 86  LKEILVEGDPSETLIRASQ--GAELLVVGRRGRGAFARAMLGSVSQRCAQHAACPVVVVR 143

Query: 159 RK 160
           ++
Sbjct: 144 QE 145


 gi|2648945 (AE000991) cationic amino acid transporter (cat-1) 
[Archaeoglobus fulgidus] Length = 736
           
 Score = 37.9 bits (86), Expect = 0.043
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 78  TEEAKNKMENIKKELEDV--GFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLK 135
           +E+ + K E + +E  ++  G  V+    +     ++V   E E  D++I+G+  +T LK
Sbjct: 647 SEKEREKAEKVFEEAMEILNGLNVEREFAISSSPSDVVA-REAESFDLVIVGASERTFLK 705

Query: 136 EILLGSVTENVIKKSNKPVLVVKR 159
             L G   E V+ K++K V + ++
Sbjct: 706 NFLTGLFPEKVVMKTSKTVAMTRK 729



 Score = 36.7 bits (83), Expect = 0.096
 Identities = 37/151 (24%), Positives = 72/151 (47%), Gaps = 26/151 (17%)

Query: 32  KAEEVILLHVIDEREIKKRDIFSLLLGVAG--LNKSVEEFENELKNK-------LTEEAK 82
           K EE  ++ V  E+ ++K + +++L+ VA   + K +  F   +  K       L     
Sbjct: 450 KREEEEVMTVFTEKPVEKME-YTILVPVANPVIAKKLVRFAELIARKKKGAVVILNTVRL 508

Query: 83  NKMENIKKELEDVGFKVKDII------------VVGIPH---EEIVKIAEDEGVDIIIMG 127
            +   I    +DV  K K+++            VV + H   E I+  AE+   ++I+MG
Sbjct: 509 PQQTPISAPAKDVK-KAKELVEGLMNLSVPSGGVVKVSHSVSEAILSTAEEWKANMIVMG 567

Query: 128 SHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
             G+T  ++++LGS  + V+ K+   V+V++
Sbjct: 568 WRGRTFRRDVVLGSTIDPVLLKAKCDVVVIR 598

 gi|2649775 (AE001047) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 134
           
 Score = 38.7 bits (88), Expect = 0.025
 Identities = 17/51 (33%), Positives = 32/51 (62%)

Query: 108 PHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
           P ++IV  A++     I++G   ++   +++ GSV  +VI K+NKPV+ +K
Sbjct: 84  PPDDIVDFADEVDAIAIVIGIRKRSPTGKLIFGSVARDVILKANKPVICIK 134

 gi|2649038 (AE000997) conserved hypothetical protein [Archaeoglobus fulgidus]
           Length = 145
           
 Score = 38.7 bits (88), Expect = 0.025
 Identities = 27/97 (27%), Positives = 50/97 (50%), Gaps = 6/97 (6%)

Query: 67  EEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDI-IVVGIPHEEIVKIAEDEGVDIII 125
           EE E    ++L  ++  K+E  K +LE  G KV D+ +V G   + ++ + +    D+I+
Sbjct: 49  EEKELAAYHRLMTQSMKKLEGFKNQLEKAGLKVSDVSVVFGKYADRLLLVEKQIKPDLIV 108

Query: 126 MGSHGKTNLKEILLG----SVTENVIKKSNKPVLVVK 158
           +G  G   LK ++ G       E ++KKS   +L+ +
Sbjct: 109 VGFKGGL-LKRVIGGFFGKDPCEVLLKKSKASLLICR 144

Step 5. Beyond BLAST

The absence of annotated hits among the list of sequences bearing similarity to MJ0577 is unsatisfying. To continue the search for clues to the function of MJ0577 weak, yet significant alignments may be sought using profile-based searching available using PSI-BLAST. Find out more about MJ0577 function in the PSI-BLAST tutorial.

Step 6. Statistical details of the search

1.  Database: Non-redundant GenBank CDS
    translations+PDB+SwissProt+SPupdate+PIR
2. Posted date:  Feb 26, 2000 10:08 PM
3.  Number of letters in database: 142,135,17
    Number of sequences in database:  461,162
4. Lambda     K      H
   0.313    0.135    0.349 
Gapped Lambda     K      H
   0.270   0.0470    0.230 
5.  Matrix: BLOSUM62
6.  Gap Penalties: Existence: 11, Extension: 1
7. Number of Hits to DB: 39862250
Number of Sequences: 461162
Number of extensions: 1595704
Number of successful extensions: 8417
Number of sequences better than 1.0: 86
Number of HSP's better than 1.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 8293
Number of HSP's gapped (non-prelim): 121
8.  length of query: 162
length of database: 142,135,178
effective HSP length: 60
effective length of query: 102
effective length of database: 114,465,458
effective search space: 11675476716
effective search space used: 11675476716
9.  T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (21.9 bits)
S2: 75 (33.6 bits)

Revised June 6, 2000