Alignments for a candidate for frcA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Desulfovibrio vulgaris Hildenborough

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  262 bits (670), Expect = 2e-74
 Identities = 171/486 (35%), Positives = 260/486 (53%), Gaps = 21/486 (4%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P++ L  I K+F  VRA   + L    G + AL+GENGAGKSTLM ILSG    D G   
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTG-II 91

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
           H+DG+ V+   P+ A   G+ ++YQ   L  +++VAEN+ LG   Q    ++   M R  
Sbjct: 92  HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLG---QSGAWLSPVHMSRVV 148

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           A   AR G D  PAA V  LS+ +RQ VEI + ++ ++R+L++DEPT  L+  ET++LF 
Sbjct: 149 AELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFE 208

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGRD 250
            + ++   G AI++ISH+M E+  LAD + +LR G  V     + +  +A L   MVGR+
Sbjct: 209 ALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE 268

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310
           +     +   + +E    +   D   G  +KG SF++R GEV  +AG+ G G+ EL   V
Sbjct: 269 V---ILEVAAEPLEPGDRVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECV 325

Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370
            G      GEV +            P  G       G+AY+ EDR  QGL    S+    
Sbjct: 326 TGLRRPAEGEVELLGIPWRQFFTKAPRQG-------GLAYIPEDR--QGLATCLSLDLVD 376

Query: 371 NLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429
           N ++ AR     G  L+R +A     + +    ++   A+    +LSGGN QK+++ R  
Sbjct: 377 NFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREF 436

Query: 430 EIQPRVLILDEPTRGVDIGAKSEIY-RLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488
             +P +++ + PT+G+DI A  E++ RL+   + +GV  L++S +L EV+ L DRV VM 
Sbjct: 437 YRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAGV--LLVSGDLNEVLALADRVAVMY 494

Query: 489 EGTLAG 494
            G   G
Sbjct: 495 RGCFIG 500



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 58/223 (26%), Positives = 103/223 (46%), Gaps = 17/223 (7%)

Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343
           + D+  G +  L G  GAG++ L  ++ G  A+  G + +   A       +    P+ A
Sbjct: 54  TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEA-------VRFRSPKDA 106

Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403
           + AGI  + +   L       +V EN+ L+  +   L    ++R  A       +D    
Sbjct: 107 LKAGIGMVYQHFMLVD---SMTVAENV-LLGQSGAWLSPVHMSRVVAELAARYGLDI--- 159

Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463
                   V  LS G +Q+V + +LL    RVLILDEPT  +  G   +++  ++ +A++
Sbjct: 160 ---DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAEN 216

Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQ 506
           G AI+ IS ++ EV+ L D + ++R G +  E   +    E +
Sbjct: 217 GKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAE 259



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 64/236 (27%), Positives = 111/236 (47%), Gaps = 17/236 (7%)

Query: 29  LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88
           L+ +      GEV A+ G  G G+  L++ ++G       GE  + G   +    ++ R 
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGL-RRPAEGEVELLGIPWRQFFTKAPRQ 353

Query: 89  LGVAVIYQE---LSLAPNLSVAENIYLGRALQRRGLVARGDMV-RACAPTLAR-LGADFS 143
            G+A I ++   L+   +L + +N  L      RG   RG  + R  A   AR + A+++
Sbjct: 354 GGLAYIPEDRQGLATCLSLDLVDNFLL----TARGCFTRGPFLDRKSADAAARDILAEYN 409

Query: 144 -----PAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRG 198
                  A   SLS    Q + + R  + +  ++V + PT  L    T+ ++A + ++R 
Sbjct: 410 VQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRS 469

Query: 199 EGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQA-ALVKMMVGRDLSG 253
               +L +S  + E+  LADRV V+  GCF+G LDR+  ++  A+  MM G    G
Sbjct: 470 HA-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCEG 524


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: 655
Number of extensions: 36
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: 540
Length of database: 524
Length adjustment: 35
Effective length of query: 505
Effective length of database: 489
Effective search space:   246945
Effective search space used:   246945
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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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 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