Alignments for a candidate for frcA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Trichormus variabilis ATCC 29413

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_011319366.1 AVA_RS13165 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_000204075.1:WP_011319366.1
          Length = 491

 Score =  263 bits (673), Expect = 9e-75
 Identities = 179/483 (37%), Positives = 262/483 (54%), Gaps = 27/483 (5%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L L NI K F    A   + L+  AG++H ++GENGAGK+TLM I+ G Y  D  GE ++
Sbjct: 3   LRLENISKRFNSFIANDNISLSVDAGKIHGILGENGAGKTTLMNIIGGLYQPD-AGEIYL 61

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
             Q V+I  P  A  LG+ +IYQ   L P L+V ENI LGR    R L  R       A 
Sbjct: 62  QDQPVKITSPNQAIKLGIGMIYQHFMLVPQLTVTENIILGRENSWR-LNLRQKQQEIAAL 120

Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193
           + A  G +  P A V  L +  +Q VEI + ++ +A++L++DEPT  L+  E + L  ++
Sbjct: 121 SQA-YGLEIDPTAKVEDLPVGTQQRVEILKVLYRQAKLLILDEPTAVLTPTEVESLINIL 179

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253
           RQL   G  I++ISH++ E+  L D VTVLR G  V T     ++   L ++MVGR++  
Sbjct: 180 RQLAAAGNTIIFISHKLEEVINLCDTVTVLRRGKVVATTTTKDMTPQKLAELMVGREVVL 239

Query: 254 FYTKTHGQAVEREVMLSVRD--VADGR---RVKGCSFDLRAGEVLGLAGLVGAGRTELAR 308
              K+    V  +V+LSV +  VAD R    V   SF L AGE+LG+AG+ G G+ ELA 
Sbjct: 240 QVNKS--AFVPGKVILSVENLQVADDRGILAVHNVSFQLLAGEILGIAGVDGNGQRELA- 296

Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368
               A A  RG +         G + L +  P+Q     I Y+ EDR+  GL L  ++ +
Sbjct: 297 ---DAIANLRGIL--------NGTIQLNSSSPQQK----IGYIPEDRQKMGLVLQFTIAQ 341

Query: 369 NINLIVAARDALGLGRLNRTAA-RRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427
           N+ L V  +       L +++  +     A+    IR     + V  LSGGNQQKV+L+R
Sbjct: 342 NLILNVFKKIPFCRHFLLKSSVIKHHAQVAMQEFDIRATGEDIQVSQLSGGNQQKVVLAR 401

Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
            L  +P +++  +PTRG+D+GA S ++  +      G AIL IS+EL EV+ + DR+ V+
Sbjct: 402 ELAGKPDLIVAMQPTRGLDVGATSAVHSRLLTERDRGAAILYISTELEEVMAMSDRIAVI 461

Query: 488 REG 490
             G
Sbjct: 462 YRG 464



 Score = 55.8 bits (133), Expect = 4e-12
 Identities = 53/230 (23%), Positives = 98/230 (42%), Gaps = 26/230 (11%)

Query: 25  GVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQ 84
           G+ A+  V     AGE+  + G +G G+  L   ++       G         +Q++   
Sbjct: 265 GILAVHNVSFQLLAGEILGIAGVDGNGQRELADAIANLRGILNG--------TIQLNSSS 316

Query: 85  SARDLG-VAVIYQELSLAPNLSVAENIYLG---------RALQRRGLVARGDMVRACAPT 134
             + +G +    Q++ L    ++A+N+ L            L +  ++     V      
Sbjct: 317 PQQKIGYIPEDRQKMGLVLQFTIAQNLILNVFKKIPFCRHFLLKSSVIKHHAQVAMQEFD 376

Query: 135 LARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIR 194
           +   G D      V+ LS   +Q V +AR +  +  ++V  +PT  L    T  + + + 
Sbjct: 377 IRATGEDIQ----VSQLSGGNQQKVVLARELAGKPDLIVAMQPTRGLDVGATSAVHSRLL 432

Query: 195 QLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVK 244
             R  G AILYIS  + E+  ++DR+ V+  G FV  LD    +Q A+++
Sbjct: 433 TERDRGAAILYISTELEEVMAMSDRIAVIYRGKFVAILD----AQTAIIE 478


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: 556
Number of extensions: 28
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 540
Length of database: 491
Length adjustment: 35
Effective length of query: 505
Effective length of database: 456
Effective search space:   230280
Effective search space used:   230280
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 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 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