Alignments for a candidate for xylG in Desulfovibrio vulgaris Hildenborough JW710

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Desulfovibrio vulgaris Hildenborough JW710

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__DvH:206505
          Length = 524

 Score =  297 bits (760), Expect = 7e-85
 Identities = 161/482 (33%), Positives = 280/482 (58%), Gaps = 6/482 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P++ ++ I K F  V A   ++++  PG + A++GENGAGKSTLM I++G    D G I 
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            +G  VR+  P +A+ AGI  V+Q   ++D+++VAEN+ +G     G ++    M R   
Sbjct: 93  VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS---GAWLSPVHMSRVVA 149

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           + +   +G++IDP  ++   S+  +Q VEI + +Y+ ++VLILDEPT+ LT  ETE+LFE
Sbjct: 150 E-LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFE 208

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKE-KIVEMMVGRK 241
            +  + E G AI+FISH+++E+  + D++++LR GE +       +  E ++   MVGR+
Sbjct: 209 ALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE 268

Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
           +      E  EPG+ VL V  L+G+  + +SF +R+GE+   AG+ G G+ EL+E + G 
Sbjct: 269 VILEVAAEPLEPGDRVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGL 328

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
           R    GE+ + G            + G+  +PEDR+ L   L + ++ N  L +     +
Sbjct: 329 RRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTR 388

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
           GPF+  K     A   +  ++++P   +     LSGGN QK+V+ +    KP +++ + P
Sbjct: 389 GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENP 448

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           T+G+D+ A  E++  + ++ +   GV+++S +L EVL ++DR+AVM  G   G++D  + 
Sbjct: 449 TQGLDIAATEEVWARLLEV-RSHAGVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDT 507

Query: 482 SQ 483
           ++
Sbjct: 508 NK 509



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 62/217 (28%), Positives = 112/217 (51%), Gaps = 13/217 (5%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           +++  +  G I    G  GAG++ LM  + G   +  G I+++G+ V    P DA++ GI
Sbjct: 52  DITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGI 111

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFIS-FKREKELADWAIKT-FDIRPAY 387
           G+V +      L+  M++  NV L      + G ++S     + +A+ A +   DI PA 
Sbjct: 112 GMVYQH---FMLVDSMTVAENVLLG-----QSGAWLSPVHMSRVVAELAARYGLDIDPA- 162

Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447
              +V  LS G +Q+V + K L    ++LILDEPT  +  G   +++  + ++A+ G  +
Sbjct: 163 --ARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAI 220

Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQE 484
           + IS ++ EVL ++D IA++  G++       E   E
Sbjct: 221 VFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 58/226 (25%), Positives = 101/226 (44%), Gaps = 10/226 (4%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNH-----PS 74
           LKG+S E   GEV AI G  G G+  L++ + G+ +P EGE+  E  G+ W       P 
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEV--ELLGIPWRQFFTKAPR 352

Query: 75  EAINAGIVTVFQELSVMDNLSVAENIFMGDEE--KRGIFIDYKKMYREAEKFMKEEFGIE 132
           +   A I    Q L+   +L + +N  +       RG F+D K     A   + E     
Sbjct: 353 QGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQP 412

Query: 133 IDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGV 192
              E      S    Q + + R  Y+K  +++ + PT  L    TE+++  +  ++    
Sbjct: 413 GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA- 471

Query: 193 AIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
            ++ +S  L E+  + D+V+V+  G +IG     +  K   + +M+
Sbjct: 472 GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMM 517


Lambda     K      H
   0.318    0.138    0.385 

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: 614
Number of extensions: 30
Number of successful extensions: 10
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: 494
Length of database: 524
Length adjustment: 34
Effective length of query: 460
Effective length of database: 490
Effective search space:   225400
Effective search space used:   225400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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