Alignments for a candidate for frcA in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Collimonas pratensis Ter91

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_061942326.1 CPter91_RS17210 ATP-binding cassette domain-containing protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001584185.1:WP_061942326.1
          Length = 513

 Score =  363 bits (931), Expect = e-104
 Identities = 216/510 (42%), Positives = 314/510 (61%), Gaps = 22/510 (4%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71
           +L +R I KTFPGV+AL  V L   +GE+HA++GENGAGKSTLMK+LSG Y      G+ 
Sbjct: 4   ILEMRGIGKTFPGVKALDNVNLVVRSGEIHAVVGENGAGKSTLMKVLSGVYPHGSYTGDI 63

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
           H  GQ  Q +G   + + G+ +I+QEL+L P LS+ ENI+LG      G++         
Sbjct: 64  HYQGQTRQFEGIADSEECGIIIIHQELALVPLLSITENIFLGNEQASHGVIDWEVSYAKT 123

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              LA++G   SP+A + +L + ++QL+EIA+A+  + ++L++DEPT  L+  ++D L  
Sbjct: 124 KELLAKVGLKESPSALITNLGVGKQQLIEIAKALSKQVKLLILDEPTASLNESDSDALLD 183

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVGR 249
           L+ +L+ +G++ + ISH++ EI ++AD +T+LRDG  V TLD  +  +S+  +++ MVGR
Sbjct: 184 LLLELKAQGISSILISHKLNEISKVADSITILRDGSTVDTLDCHKEVISEDRIIQNMVGR 243

Query: 250 DLSGFYTKTHGQAVEREVMLSVRDV-----ADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304
           +++  Y K   Q  E    +    V      + + +KG  F +R GE++G+AGL+GAGRT
Sbjct: 244 EMADRYPKRSPQIGETIFEVKQWRVHHPIHPERQVIKGVDFHVRKGEIVGIAGLMGAGRT 303

Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364
           ELA  +FG   R  G+ RI+      G   +     ++AID GIAY+TEDRK  GL LDQ
Sbjct: 304 ELAMSIFG---RAYGQ-RISGKVFLRGK-EIDVSTVQKAIDNGIAYVTEDRKGYGLILDQ 358

Query: 365 SVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420
            + +NI L     +A +  +  GR    AA  R       L IR ++    V  LSGGNQ
Sbjct: 359 DIKKNITLANLDGIADKTVIDEGREYSVAADYRRQ-----LKIRCSNVFQKVLNLSGGNQ 413

Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480
           QKV+LS+ L   P VLILDEPTRG+D+GAK EIY +I+ LA  G  I+MISSE+PE++G+
Sbjct: 414 QKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIISQLASEGKCIVMISSEMPELLGM 473

Query: 481 CDRVLVMREGTLAGEVRPAGSAAETQERII 510
           CDRV VM EG   GE+  A ++ E   R I
Sbjct: 474 CDRVYVMNEGNFVGEMTAAEASQEKIMRAI 503



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTL-MKILSGAYTADPGGECHIDGQRVQIDG 82
           P  + ++ V+     GE+  + G  GAG++ L M I   AY     G+  + G+ + +  
Sbjct: 274 PERQVIKGVDFHVRKGEIVGIAGLMGAGRTELAMSIFGRAYGQRISGKVFLRGKEIDVST 333

Query: 83  PQSARDLGVAVIYQE---LSLAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLAR 137
            Q A D G+A + ++     L  +  + +NI L     +  + ++  G      A    +
Sbjct: 334 VQKAIDNGIAYVTEDRKGYGLILDQDIKKNITLANLDGIADKTVIDEGREYSVAADYRRQ 393

Query: 138 LGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
           L    S     V +LS   +Q V +++ +     +L++DEPT  +       ++ +I QL
Sbjct: 394 LKIRCSNVFQKVLNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIISQL 453

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
             EG  I+ IS  M E+  + DRV V+ +G FVG +  A  SQ  +++ +V
Sbjct: 454 ASEGKCIVMISSEMPELLGMCDRVYVMNEGNFVGEMTAAEASQEKIMRAIV 504


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: 603
Number of extensions: 30
Number of successful extensions: 10
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: 513
Length adjustment: 35
Effective length of query: 505
Effective length of database: 478
Effective search space:   241390
Effective search space used:   241390
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 24 2021. 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