Alignments for a candidate for araVsh in Maridesulfovibrio bastinii DSM 16055

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Maridesulfovibrio bastinii DSM 16055

Align ABC transporter related (characterized, see rationale)
to candidate WP_027178119.1 G496_RS0103835 ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000429985.1:WP_027178119.1
          Length = 513

 Score =  202 bits (513), Expect = 3e-56
 Identities = 144/476 (30%), Positives = 251/476 (52%), Gaps = 17/476 (3%)

Query: 2   SLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61
           S I+ LK I+K +  V A   + L L+ G + ALLGENGAGKSTL+ ++ G    D G I
Sbjct: 22  SPIVSLKGITKRFGKVVANNKIVLDLYPGRIKALLGENGAGKSTLMSMLAGRFQPDEGHI 81

Query: 62  LFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADA 121
              G+   F++  DA  AGI  VYQ   LV ++TV +N+ LG E      ++ K+M    
Sbjct: 82  EVDGKRVDFSSSKDAINAGIGMVYQHFMLVDSMTVTENVLLGQEGG--FFVNPKEMSRRV 139

Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181
           + +   ++L+ID  A ++  S+  +Q + I + +   ++VL+ DEPTA L  +E   LF 
Sbjct: 140 KKLAEDYELEIDPDARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLTPRETFRLFE 199

Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241
            L  +  +G +IVFI+H L++V  I+D + +LR G      + +E+P+ K+        L
Sbjct: 200 ALWAMTRQGKSIVFISHKLEEVMAIADEVAILRRG-----CVDSEVPREKITSK---ADL 251

Query: 242 QEQLVDKQ---EKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRS 298
             ++V K+   E +R        +L ++ ++  G ++++N+ V +G+ VG+ G+ G+G+ 
Sbjct: 252 ACRMVGKEVLLEIDRNEVEIGDKVLEVKSLNGLG-LKNINIEVHRGEVVGIVGVAGNGQQ 310

Query: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358
            +   V GL +    S+ + G+           +  ++  PEDR        L + +N++
Sbjct: 311 ALVEGVCGLRMPPKDSVFIMGKAWREFFAKMTWNHSLSYIPEDRLDLATARELDLVDNLL 370

Query: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418
           L  +        L   +  E+A+  ++   +          QLSGGN QK++LAR L  E
Sbjct: 371 LTTRQGFCSGPVLHRDKAAEVAKKLVEDHDVRPGRIQALAWQLSGGNLQKLVLARELYRE 430

Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS-LLVASSELDELVAFSNKVVVL 473
           P L+V ++PT+G+DI A  E+    R L    M+ +L+ + +L+E +  S+++ V+
Sbjct: 431 PHLIVAEQPTQGLDISATEEVWN--RLLEARKMAGVLLVTGDLNEALQLSDRIAVM 484



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 58/233 (24%), Positives = 123/233 (52%), Gaps = 12/233 (5%)

Query: 262 LLSLEDVSVK-GSIQSMN---LTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHL 317
           ++SL+ ++ + G + + N   L +  G+   L G  G+G+S + + + G    D G I +
Sbjct: 24  IVSLKGITKRFGKVVANNKIVLDLYPGRIKALLGENGAGKSTLMSMLAGRFQPDEGHIEV 83

Query: 318 AGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQ 377
            G++++ S   DAI+AGI +  +   +   +  +++ EN++L  +          + R +
Sbjct: 84  DGKRVDFSSSKDAINAGIGMVYQHFML---VDSMTVTENVLLGQEGGFFVNPKEMSRRVK 140

Query: 378 EIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHA 437
           ++A+ +  +L+I   D D  I QLS G +Q+V + + L  E  +L+ DEPT  +      
Sbjct: 141 KLAEDY--ELEI---DPDARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLTPRETF 195

Query: 438 EIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQ 490
            + + +  +  +G S++  S +L+E++A +++V +LR      E+   ++TS+
Sbjct: 196 RLFEALWAMTRQGKSIVFISHKLEEVMAIADEVAILRRGCVDSEVPREKITSK 248



 Score = 48.9 bits (115), Expect = 4e-10
 Identities = 47/235 (20%), Positives = 106/235 (45%), Gaps = 32/235 (13%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE+K ++        L+++++ +  GEV  ++G  G G+  LV+ + G +      +  
Sbjct: 275 VLEVKSLNG-----LGLKNINIEVHRGEVVGIVGVAGNGQQALVEGVCGLRMPPKDSVFI 329

Query: 64  LGEP----------QHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIH 113
           +G+            H  + +   +  ++T  +E++LV NL +           R G   
Sbjct: 330 MGKAWREFFAKMTWNHSLSYIPEDRLDLATA-RELDLVDNLLLTT---------RQGFCS 379

Query: 114 FKKMYADARAVLTQFKLDIDVSAPLSDYSIAVQ------QLIAIARGVAMSAKVLVLDEP 167
              ++ D  A + +  ++     P    ++A Q      Q + +AR +     ++V ++P
Sbjct: 380 GPVLHRDKAAEVAKKLVEDHDVRPGRIQALAWQLSGGNLQKLVLARELYREPHLIVAEQP 439

Query: 168 TASLDAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEY 222
           T  LD    + ++  L + + K   ++ +T  L++  Q+SDRI V+  G+ + ++
Sbjct: 440 TQGLDISATEEVWNRLLEAR-KMAGVLLVTGDLNEALQLSDRIAVMYRGEIMDQF 493


Lambda     K      H
   0.319    0.136    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 537
Number of extensions: 27
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 513
Length adjustment: 34
Effective length of query: 465
Effective length of database: 479
Effective search space:   222735
Effective search space used:   222735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources