Alignments for a candidate for frcA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Desulfovibrio vulgaris Miyazaki F

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  238 bits (608), Expect = 3e-67
 Identities = 165/483 (34%), Positives = 256/483 (53%), Gaps = 22/483 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P++ L  ICK+F  VRA   + L    G + AL+GENGAGKSTLM IL+G    D  G  
Sbjct: 28  PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQD-AGTI 86

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            +DG       P+ A   G+ ++YQ   L  +++VAEN+ LG   Q   ++ R   +R  
Sbjct: 87  VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLG---QSPDMLLRPARMRDE 143

Query: 132 APTLA-RLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
              LA R G    PAA V  LS+ +RQ VEI + ++ ++R+L++DEPT  L+  ETD+LF
Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGR 249
             + ++  +G A+++ISH++ E+  +AD + +LR G  V     A + +Q  L   MVGR
Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263

Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309
           D+         +    + +LSV  ++ G  +   S  +R GE++ +AG+ G G+ EL   
Sbjct: 264 DV--VLQVDAKRLTPVDTVLSVEHLS-GAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320

Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369
           + G      GEVRI             AG P +    G+AY+ EDR  QGL   + +   
Sbjct: 321 ICGLARPEAGEVRILGRPWR----EFFAGPPGR---RGLAYIPEDR--QGLATCRHLDLV 371

Query: 370 INLIVAARDALGLG-RLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 428
            N ++  R+    G  L+RT A       +    ++         ALSGGN QK+++ R 
Sbjct: 372 DNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGRE 431

Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIY-RLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
              +P V++ + PT+G+DI A  E++ RL+ A + SGV  L+++ +L E + L DR+ VM
Sbjct: 432 FFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTSGV--LLVTGDLNEALELADRIAVM 489

Query: 488 REG 490
             G
Sbjct: 490 YRG 492



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 64/222 (28%), Positives = 105/222 (47%), Gaps = 16/222 (7%)

Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343
           + D+R G +  L G  GAG++ L  ++ G   +  G + +       G+ T+ A  PR A
Sbjct: 49  TLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV------DGVPTVFAS-PRDA 101

Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403
           + AGI  + +   L       +V EN+ L+  + D L    L     R       +  G+
Sbjct: 102 LRAGIGMVYQHFMLVD---SMTVAENV-LLGQSPDML----LRPARMRDEVAALAERYGL 153

Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463
            V  A   VG LS G +Q+V + +LL    RVLILDEPT  +      +++  +  +A  
Sbjct: 154 AVDPA-ARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMWRMADQ 212

Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAET 505
           G A++ IS +L EV+ + D + ++R G +  E   A    +T
Sbjct: 213 GKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQT 254



 Score = 48.9 bits (115), Expect = 5e-10
 Identities = 55/229 (24%), Positives = 98/229 (42%), Gaps = 16/229 (6%)

Query: 29  LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQ--RVQIDGPQSA 86
           L  V L    GE+ A+ G  G G+  L++ + G    +  GE  I G+  R    GP   
Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPE-AGEVRILGRPWREFFAGPPGR 349

Query: 87  RDLG-VAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLA--RLGADFS 143
           R L  +    Q L+   +L + +N  L      R   A+G  +     T A  R+  +++
Sbjct: 350 RGLAYIPEDRQGLATCRHLDLVDNFLL----TTRNQFAKGVFLDRTEATNAVKRVVWEYN 405

Query: 144 P-----AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRG 198
                  A   +LS    Q + I R    +  ++V + PT  L    T+ ++  + + R 
Sbjct: 406 VQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARS 465

Query: 199 EGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
               +L ++  + E  ELADR+ V+  G F+   D+   ++   + +M+
Sbjct: 466 TS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513


Lambda     K      H
   0.320    0.136    0.382 

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: 647
Number of extensions: 36
Number of successful extensions: 6
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: 540
Length of database: 537
Length adjustment: 35
Effective length of query: 505
Effective length of database: 502
Effective search space:   253510
Effective search space used:   253510
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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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