Alignments for a candidate for frcA in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Tistlia consotensis USBA 355

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_085120648.1 B9O00_RS01470 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_900177295.1:WP_085120648.1
          Length = 634

 Score =  333 bits (855), Expect = 9e-96
 Identities = 206/509 (40%), Positives = 304/509 (59%), Gaps = 24/509 (4%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           +L    I KTF   RAL   +L   AGEVH L+G NGAGKSTL K++SG    D G   +
Sbjct: 14  ILVASGIEKTFDRTRALAGADLELRAGEVHGLLGANGAGKSTLSKVISGHVQRDAGRLVY 73

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132
             G+ + +   + A + G+A++ QE SLAP+LSV ENI+L   L R GL++ G M R   
Sbjct: 74  -KGRPLALRSTREALEAGIAIVMQETSLAPDLSVLENIFLPE-LGRPGLLSYGSMRRRAV 131

Query: 133 PTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
             LA LG +     +  VA LS AQRQLVEIA+A+  +A +++ DEPT  LS  E +RLF
Sbjct: 132 GLLANLGHEHVLPLDREVARLSAAQRQLVEIAKALALDADLIIFDEPTASLSPSEVERLF 191

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD-RAHLSQAALVKMMVGR 249
            ++ +LR +G A++++SHR+ E+  + DRVT++R+G  V      A L+QA +++ MVGR
Sbjct: 192 DIMAKLRDDGRALIFVSHRLEEVFAITDRVTIMREGATVAASQPTASLTQAEVIRHMVGR 251

Query: 250 DLSGFYTKTHGQAVERE---VMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306
           D+   Y  T G   E E    + SV ++A    V+  SF +R GE+LGL GLVGAGR+E 
Sbjct: 252 DIGALYA-TPGLQEEDERAPAVFSVENLAAPPAVRNVSFFVRRGEILGLGGLVGAGRSET 310

Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366
           A  +FG   R+ G +R+           +    P  A+ AGI ++ EDR++Q +  D SV
Sbjct: 311 AEAIFGLRPRSAGTIRLEGRE-------IAPRKPADAVRAGIGFVAEDRRVQNIVPDLSV 363

Query: 367 HENINLI-VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHA-QVNVGALSGGNQQKVM 424
            EN+ L  + A    GLG   R   R++  E +  LG+        N+   SGG QQK++
Sbjct: 364 KENLLLAHLGAHRGFGLGYRRR---RQKVEELMAALGLPAERLLDANMLNFSGGMQQKII 420

Query: 425 LSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRV 484
           ++R L ++P+VLILDEPT+GVDIG +  IY ++  +A  GVA+++ISS+  E++G+C+RV
Sbjct: 421 IARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEGVAVVVISSDFEELLGVCERV 480

Query: 485 LVMREGTLAGEVRPAGSAAETQERIIALA 513
           +VM +G    ++    SA   +E++  LA
Sbjct: 481 VVMSDGNAIADL---PSALLDEEKLTLLA 506



 Score = 77.8 bits (190), Expect = 1e-18
 Identities = 61/229 (26%), Positives = 105/229 (45%), Gaps = 9/229 (3%)

Query: 28  ALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSAR 87
           A+R V      GE+  L G  GAG+S   + + G       G   ++G+ +    P  A 
Sbjct: 283 AVRNVSFFVRRGEILGLGGLVGAGRSETAEAIFGLRPRS-AGTIRLEGREIAPRKPADAV 341

Query: 88  DLGVAVIYQEL---SLAPNLSVAENIYLGRALQRRGLVA----RGDMVRACAPTLARLGA 140
             G+  + ++    ++ P+LSV EN+ L      RG       R   V      L  L A
Sbjct: 342 RAGIGFVAEDRRVQNIVPDLSVKENLLLAHLGAHRGFGLGYRRRRQKVEELMAALG-LPA 400

Query: 141 DFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEG 200
           +    AN+ + S   +Q + IAR +  E ++L++DEPT  +       ++ ++R++  EG
Sbjct: 401 ERLLDANMLNFSGGMQQKIIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEG 460

Query: 201 MAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
           +A++ IS    E+  + +RV V+ DG  +  L  A L +  L  +   R
Sbjct: 461 VAVVVISSDFEELLGVCERVVVMSDGNAIADLPSALLDEEKLTLLAAPR 509


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: 773
Number of extensions: 51
Number of successful extensions: 11
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: 634
Length adjustment: 37
Effective length of query: 503
Effective length of database: 597
Effective search space:   300291
Effective search space used:   300291
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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