Alignments for a candidate for rbsA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Desulfovibrio vulgaris Hildenborough

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 207875 DVU2387 ABC transporter, ATP-binding protein

Query= uniprot:A0A166R419
         (517 letters)



>MicrobesOnline__882:207875
          Length = 592

 Score =  129 bits (323), Expect = 4e-34
 Identities = 142/500 (28%), Positives = 220/500 (44%), Gaps = 52/500 (10%)

Query: 23  VLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAP----TTGQMRFQGRDYRPGSRS 78
           VL G+ LT+ RGE+ AL G +G+GKS  ++ + GL+ P    T G +RF+G        S
Sbjct: 29  VLHGVGLTMRRGEIHALVGASGSGKSLTARAVLGLLPPGARLTHGNIRFEGAQLAHAPES 88

Query: 79  QAEEL---GIRMVMQE-LNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEAMAQVGL 134
               L    I MV Q+ L+ L  L   E    + L  H G I   + R  A+E +  VGL
Sbjct: 89  ALRALRGDRIGMVFQDPLSSLNPLHTIERQVAEPLAIHKG-IRGPRARARALELLDMVGL 147

Query: 135 DAIDPDTLVG----ELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITR 190
           D  +P+  +     +L  G +Q V +A  L  D  +LI DEPT  L       +   I  
Sbjct: 148 D--EPEARLASYPHQLSGGQRQRVALAMALANDPALLIADEPTTALDTTVQSQILRLIDT 205

Query: 191 LQAR-GVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNS---EQLVTLMVGRE- 245
           L+ R G+ ++ +SH L  +  +A  I V+  G +V   P     S     +   ++G E 
Sbjct: 206 LRHRLGMGVLIVSHDLGVVRSLADVIHVMDAGCIVESAPTTRIFSAPASPVTRALLGAEG 265

Query: 246 ------LGEHIDMGP-----RKIGAPALTVKGL-----TRSDKVRDVSFEVRAGEIFGIS 289
                 L E     P     R +G      +GL     T  D +   SF +R GE  G+ 
Sbjct: 266 PSGPAPLPETTATQPALLEARDMGVTFTRQRGLFGLRKTGHDALVSASFTLRRGECLGVV 325

Query: 290 GLIGAGRTEL----LRLIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKG 345
           G  G+G++ L    LRLI     A  G V L               +   +  + +D   
Sbjct: 326 GESGSGKSTLALAVLRLI-----ASRGRVTLDGQRLDTLDEEALRPLRRKVQAVFQD-PF 379

Query: 346 EGLLLTQSISANIALG---NMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSEL 402
             L    +++ +IA G   + P +     +    + +LA   ++ + +      +   EL
Sbjct: 380 SALNPRMTVAESIAEGLTTHFPDLRGRQGLKAMHDKTLA--ALDEVGLSDDFMQRYPGEL 437

Query: 403 SGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGAKFDIYALLGEL-TRQGKALVVVSSDL 461
           SGG  Q+VVI R L     V++ DEPT  +D   +F + ALL +L  R G A + ++ DL
Sbjct: 438 SGGQCQRVVIARALALRPEVLVLDEPTSSLDRALQFQVVALLRDLQLRHGMACLFITHDL 497

Query: 462 RELMLICDRIGVLSAGRLID 481
             +   C R+ VL  G +++
Sbjct: 498 SLVRSFCHRVMVLHRGHVVE 517



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 68/223 (30%), Positives = 105/223 (47%), Gaps = 10/223 (4%)

Query: 14  GIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGR--D 71
           G+ KT     L     TL RGE L + GE+G+GKSTL+  +  L+A + G++   G+  D
Sbjct: 300 GLRKT-GHDALVSASFTLRRGECLGVVGESGSGKSTLALAVLRLIA-SRGRVTLDGQRLD 357

Query: 72  YRPGSRSQAEELGIRMVMQE--LNLLPTLSVAENL---FLDNLPSHGGWISRKQLRKAAI 126
                  +     ++ V Q+    L P ++VAE++      + P   G    K +    +
Sbjct: 358 TLDEEALRPLRRKVQAVFQDPFSALNPRMTVAESIAEGLTTHFPDLRGRQGLKAMHDKTL 417

Query: 127 EAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186
            A+ +VGL         GEL  G  Q V IAR L     VL+LDEPT+ L       +  
Sbjct: 418 AALDEVGLSDDFMQRYPGELSGGQCQRVVIARALALRPEVLVLDEPTSSLDRALQFQVVA 477

Query: 187 QITRLQAR-GVSIIYISHRLEELARVAQRIAVLRDGNLVCVEP 228
            +  LQ R G++ ++I+H L  +     R+ VL  G++V   P
Sbjct: 478 LLRDLQLRHGMACLFITHDLSLVRSFCHRVMVLHRGHVVEAGP 520



 Score = 49.7 bits (117), Expect = 3e-10
 Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 1/83 (1%)

Query: 401 ELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGAKFDIYALLGELT-RQGKALVVVSS 459
           +LSGG +Q+V +   L  D  +++ DEPT  +D   +  I  L+  L  R G  +++VS 
Sbjct: 160 QLSGGQRQRVALAMALANDPALLIADEPTTALDTTVQSQILRLIDTLRHRLGMGVLIVSH 219

Query: 460 DLRELMLICDRIGVLSAGRLIDT 482
           DL  +  + D I V+ AG ++++
Sbjct: 220 DLGVVRSLADVIHVMDAGCIVES 242


Lambda     K      H
   0.319    0.137    0.384 

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: 688
Number of extensions: 37
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 4
Length of query: 517
Length of database: 592
Length adjustment: 36
Effective length of query: 481
Effective length of database: 556
Effective search space:   267436
Effective search space used:   267436
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: 53 (25.0 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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