Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E2

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  339 bits (870), Expect = 1e-97
 Identities = 200/483 (41%), Positives = 296/483 (61%), Gaps = 32/483 (6%)

Query: 44  LMGENGAGKSTLMKILSGAYTADPG-GECHIDGQRV-QIDGPQSARDLGVAVIYQELSLA 101
           L+GENGAGKST++KIL+GA  AD G G    +G  + + D P   +++G+  IYQE +L 
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 102 PNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEI 161
            ++SVAEN+YLGR   R G V    M       L  LG   +P   V  LS+A++Q+VEI
Sbjct: 61  ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120

Query: 162 ARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVT 221
           A+A+   A++++MDEPT  LS  E D+L  +I  L+ +G++I+Y+SH++ E+    DR T
Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180

Query: 222 VLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDV----ADG 277
           + RDG ++ + D   +S   +V++MVGRD+   + +        EVML V+ V    A G
Sbjct: 181 IFRDGAYITSGDVCDVSVDDIVRLMVGRDVE--FVRKPLTGAPGEVMLKVQSVSRTAAGG 238

Query: 278 RR------VKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGG 331
            R      +   S D+RAGE++G AGLVGAGRTELAR++FGAD    G + +       G
Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYV------NG 292

Query: 332 LVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAAR 391
               P   PR+ I AG+A + EDRK Q  FL  S+  N++L        GL R       
Sbjct: 293 RQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLG----GLQRWGMFIDD 348

Query: 392 RRTTEAID----TLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDI 447
           R  T+ I      L I++++  V +G LSGGNQQKV+L+R + ++P+VLI+DEPTRG+D+
Sbjct: 349 RAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDV 408

Query: 448 GAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQE 507
           GAK+E+++L+  +A++GVA+++ISSELPEV+ + DR++  REG + G V    SA E  E
Sbjct: 409 GAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIV----SADEATE 464

Query: 508 RII 510
            ++
Sbjct: 465 ELL 467



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 61/262 (23%), Positives = 121/262 (46%), Gaps = 27/262 (10%)

Query: 13  LLALRNICKTFPG------VRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTAD 66
           +L ++++ +T  G         L  + +   AGE+    G  GAG++ L +++ GA   D
Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284

Query: 67  PGGECHIDGQRVQ-IDGPQSARDLGVAVIYQEL---------SLAPNLSVAENIYLGRAL 116
            G   +++G++V     P+     GVA++ ++          S+  N+S+     LG  L
Sbjct: 285 EG-MIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPS---LG-GL 339

Query: 117 QRRGLV----ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARIL 172
           QR G+     A   +++     L    ++ S A  + +LS   +Q V +AR +  + ++L
Sbjct: 340 QRWGMFIDDRAETQLIQDYQKRLRIKMSNDSVA--IGTLSGGNQQKVILARCMALKPKVL 397

Query: 173 VMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL 232
           ++DEPT  +       +  L+  +   G+A++ IS  + E+  ++DR+   R+G   G +
Sbjct: 398 IVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIV 457

Query: 233 DRAHLSQAALVKMMVGRDLSGF 254
                ++  L+  M     S F
Sbjct: 458 SADEATEELLMARMAQGVSSSF 479


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: 629
Number of extensions: 35
Number of successful extensions: 8
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: 485
Length adjustment: 35
Effective length of query: 505
Effective length of database: 450
Effective search space:   227250
Effective search space used:   227250
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)
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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