Alignments for a candidate for frcA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudarthrobacter sulfonivorans Ar51

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  348 bits (892), Expect = e-100
 Identities = 199/496 (40%), Positives = 298/496 (60%), Gaps = 11/496 (2%)

Query: 4   MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63
           M +     PLL +R + K F GV+AL+ V+L    GEVH +MG+NGAGKSTL+K LSG +
Sbjct: 1   MFEEDQPRPLLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVH 60

Query: 64  TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVA 123
             D GGE   +G+++ +  P +A DLG+A +YQEL +   LSVAENI+LG      G++ 
Sbjct: 61  QPD-GGEIRWEGKQITLPRPTAALDLGIATMYQELDVVDGLSVAENIFLGHERSTGGVLH 119

Query: 124 RGDMVRACAPTLARLG-ADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182
                      L RLG    SP+  V +LS A +Q+V +ARA+  + ++++MDEP+  L 
Sbjct: 120 VKKTNAIARTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILD 179

Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGT-LDRAHLSQAA 241
           + E   LF ++R+L  +G+A++YISHR+ EI ++ DR++V++DG      L      ++ 
Sbjct: 180 SGEVSNLFRVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSE 239

Query: 242 LVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGA 301
           L+++M GRD++  + +      +  V+L V ++      +  S  +RAGE+LG AGLVG+
Sbjct: 240 LIRLMTGRDVANVFPERKPVPADAPVVLDVDNLELYGHFEKVSLTVRAGEILGFAGLVGS 299

Query: 302 GRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 361
            R+E+   ++GA   + G V +   A   G VT        A++AGI    E+RK QGL 
Sbjct: 300 KRSEILETIYGARKASSGRVSVNGKALRPGSVT-------SAVNAGIGLSPEERKSQGLI 352

Query: 362 LDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQ 421
           LD+ + +N+ L    R A  +G LN  A R    E I  L +R A        LSGGNQQ
Sbjct: 353 LDEPLFKNVTLSTFERFAR-MGYLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQ 411

Query: 422 KVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLC 481
           K++L+R L     VL+LDEPTRGVD+GA+SEIY LI  LA++G AI+++SSE+ EV+GL 
Sbjct: 412 KILLARWLVHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLA 471

Query: 482 DRVLVMREGTLAGEVR 497
           D VLV+ +G +  + +
Sbjct: 472 DNVLVIDDGKVLTQTK 487


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: 602
Number of extensions: 37
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 506
Length adjustment: 35
Effective length of query: 505
Effective length of database: 471
Effective search space:   237855
Effective search space used:   237855
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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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