Alignments for a candidate for frcA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudomonas simiae WCS417

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  360 bits (923), Expect = e-104
 Identities = 213/489 (43%), Positives = 293/489 (59%), Gaps = 17/489 (3%)

Query: 11  APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70
           A  L    I KTFPGV+AL  +  +A+ G+VHALMGENGAGKSTL+KIL GAY  +  G 
Sbjct: 3   AAALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPN-SGT 61

Query: 71  CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRA 130
            HI  Q +       +   GVAVI+QEL L P +SVAEN++LG    R G+V RG + + 
Sbjct: 62  LHIGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQ 121

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
               L  L  +  PA  +  LS+ QRQLVEIA+A+   A ++  DEPT+ LS  E DRL 
Sbjct: 122 ALACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 181

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGR 249
           A+I +LR EG  +LY+SHRM E+  + + VTV +DG +V T  D + L+   LV  MVGR
Sbjct: 182 AIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGR 241

Query: 250 DLSGFY---TKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306
           D+   Y    + HG     EV L V  +      +  SF++R GE+LGL GLVGAGRTEL
Sbjct: 242 DIQDIYDYRPREHG-----EVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTEL 296

Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366
            RL+ G +  + G++ +           L    PR AI AG+    EDRK +G+    SV
Sbjct: 297 FRLLSGLERASAGQLELCGE-------PLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSV 349

Query: 367 HENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426
            ENIN+      +     L     +    + I+ + ++  +A   +  LSGGNQQK +L 
Sbjct: 350 AENINISARGAHSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILG 409

Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486
           R L +  +VL+LDEPTRG+DIGAK+EIY++I+ LA  G+A++++SS+L EV+G+ DR+LV
Sbjct: 410 RWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILV 469

Query: 487 MREGTLAGE 495
           + EG L GE
Sbjct: 470 LCEGALRGE 478



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 61/236 (25%), Positives = 112/236 (47%), Gaps = 10/236 (4%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83
           PG+R    V      GE+  L G  GAG++ L ++LSG   A   G+  + G+ + +  P
Sbjct: 267 PGLR--EPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLERAS-AGQLELCGEPLHLQSP 323

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARL 138
           + A   GV +  ++     + P  SVAENI +    A    G + R    +  A      
Sbjct: 324 RDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLREGWEKGNADQQINA 383

Query: 139 GADFSP--AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
               +P  A  +  LS   +Q   + R +    ++L++DEPT  +       ++ +I  L
Sbjct: 384 MKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 443

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252
             +G+A++ +S  + E+  +ADR+ VL +G   G   R H +++ L+++ + R ++
Sbjct: 444 AAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHATESNLLQLALPRSVA 499


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: 617
Number of extensions: 26
Number of successful extensions: 9
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: 500
Length adjustment: 35
Effective length of query: 505
Effective length of database: 465
Effective search space:   234825
Effective search space used:   234825
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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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