Alignments for a candidate for araVsh in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Desulfovibrio vulgaris Hildenborough

Align ABC transporter related (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  233 bits (595), Expect = 9e-66
 Identities = 149/473 (31%), Positives = 251/473 (53%), Gaps = 16/473 (3%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           ++ L+ I K +  V+A  D++L +  G + ALLGENGAGKSTL+ +++G  ++D G I  
Sbjct: 34  VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            GE   F +P DA KAGI  VYQ   LV ++TVA+N+ LG     L  +H  ++ A+  A
Sbjct: 94  DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAA 153

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
              ++ LDID +A + D S+  +Q + I + +   ++VL+LDEPTA L   E + LF  L
Sbjct: 154 ---RYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP-QPKLIEAMLGRS-L 241
           +++   G AIVFI+H + +V  ++D I +LR G+ + E+  +E+P + +L   M+GR  +
Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270

Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301
            E   +  E    V   + +            ++ ++  V KG+   +AG+ G+G+ E+ 
Sbjct: 271 LEVAAEPLEPGDRVLHVDGL--------AGDGLKGLSFEVRKGEVFAIAGVAGNGQRELV 322

Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361
             V GL     G + L G              G+A  PEDR+       L + +N +L  
Sbjct: 323 ECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTA 382

Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421
           +       +L        A+  + +  +    A+ P   LSGGN QK+++ R    +P L
Sbjct: 383 RGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL 442

Query: 422 LVLDEPTRGIDIGAHAEI-VKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
           +V + PT+G+DI A  E+  +L+      G  +L+ S +L+E++A +++V V+
Sbjct: 443 IVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLALADRVAVM 493



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 56/239 (23%), Positives = 115/239 (48%), Gaps = 18/239 (7%)

Query: 255 VTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGS 314
           V R E +  S   V     I    L +  G+   L G  G+G+S + + + G    D+G 
Sbjct: 34  VVRLEGIGKSFGPVRANHDI---TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGI 90

Query: 315 IHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWR---YL 371
           IH+ G+ +    P DA+ AGI +  +   +   +  +++ EN++L    + G W    ++
Sbjct: 91  IHVDGEAVRFRSPKDALKAGIGMVYQHFML---VDSMTVAENVLLG---QSGAWLSPVHM 144

Query: 372 SNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGI 431
           S    +  A++ +D       D    +  LS G +Q+V + + L  +  +L+LDEPT  +
Sbjct: 145 SRVVAELAARYGLDI------DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVL 198

Query: 432 DIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQ 490
             G   ++ + +  + + G +++  S ++ E++A ++++ +LR    V E   +E+  +
Sbjct: 199 TPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257



 Score = 56.2 bits (134), Expect = 3e-12
 Identities = 54/213 (25%), Positives = 98/213 (46%), Gaps = 19/213 (8%)

Query: 20  LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEP-QHFNTPMDAQ- 77
           L+ +S  +  GEV A+ G  G G+  LV+ +TG +    G++  LG P + F T    Q 
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354

Query: 78  --------KAGISTVYQEVNLVPN-LTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQF 128
                   + G++T    ++LV N L  A+  F      R   +  K   A AR +L ++
Sbjct: 355 GLAYIPEDRQGLATCLS-LDLVDNFLLTARGCFT-----RGPFLDRKSADAAARDILAEY 408

Query: 129 KLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187
            +      AP    S    Q + + R       ++V + PT  LD    + ++  L +++
Sbjct: 409 NVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVR 468

Query: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIG 220
           +    ++ ++  L++V  ++DR+ V+  G FIG
Sbjct: 469 SHA-GVLLVSGDLNEVLALADRVAVMYRGCFIG 500


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: 590
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 524
Length adjustment: 35
Effective length of query: 464
Effective length of database: 489
Effective search space:   226896
Effective search space used:   226896
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 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