Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N1B4

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  350 bits (897), Expect = e-100
 Identities = 209/484 (43%), Positives = 283/484 (58%), Gaps = 11/484 (2%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L    I KTFPGV+AL  +   A+ G+VHALMGENGAGKSTL+KIL GAYT    G+  I
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPS-SGDLQI 74

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
             Q+        +   GVAVI+QEL L P ++VAEN++LG      GL+ RG + +    
Sbjct: 75  GEQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALA 134

Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193
            L  L  +  P   V  LS+ QRQLVEIA+A+   A ++  DEPT+ LS  E DRL A+I
Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGRDLS 252
            +LR EG  +LY+SHRM E+  + + VTV +DG FV T  D + L+   LV  MVGRD+ 
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254

Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312
             Y   +       V L V  +      +  SF+   GE+LGL GLVGAGRTEL R++ G
Sbjct: 255 DIY--DYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSG 312

Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372
               T G + +           L    PR AI AGI    EDRK +G+    SV ENIN+
Sbjct: 313 LTRNTAGRLELRGR-------ELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINI 365

Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQ 432
                 +     L     +    + I  L ++  +A   +  LSGGNQQK +L R L + 
Sbjct: 366 SARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMP 425

Query: 433 PRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492
            +VL+LDEPTRG+DIGAK+EIY++I+ LA SG+A++++SS+L EV+G+ DR+LV+ EG +
Sbjct: 426 MKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAM 485

Query: 493 AGEV 496
            GE+
Sbjct: 486 RGEL 489



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 61/233 (26%), Positives = 114/233 (48%), Gaps = 10/233 (4%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83
           PG+R    V   A+ GE+  L G  GAG++ L ++LSG  T +  G   + G+ +++  P
Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGL-TRNTAGRLELRGRELKLHSP 333

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARL 138
           + A   G+ +  ++     + P  SVAENI +    A    G + RG   +  A    + 
Sbjct: 334 RDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKA 393

Query: 139 GADFSP--AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
               +P  A  +  LS   +Q   + R +    ++L++DEPT  +       ++ +I  L
Sbjct: 394 LKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
              G+A++ +S  + E+  ++DR+ VL +G   G L R   +++ L+++ + R
Sbjct: 454 AASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPR 506


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: 615
Number of extensions: 35
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: 514
Length adjustment: 35
Effective length of query: 505
Effective length of database: 479
Effective search space:   241895
Effective search space used:   241895
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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