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_523 Inositol transport system ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  400 bits (1027), Expect = e-116
 Identities = 236/505 (46%), Positives = 324/505 (64%), Gaps = 17/505 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL + N+ K FPGV AL  V+L    G V ALMGENGAGKSTLMKI++G Y  D  GE  
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD-AGELR 84

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL--VARGDMVRA 130
           + G+ V  D P +A   G+A+I+QEL+L P++S+AENI++GR  Q  GL  V  G+M R 
Sbjct: 85  LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE-QLNGLHMVDHGEMHRC 143

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
            A  L RL     P   V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++  E   LF
Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
           ++I  L+ +G  I+YI+H+M E+  +AD V V RDG ++G      +   +L+ MMVGR+
Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 263

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310
           LS  +     Q +  +++LSVRD++     KG SFDL AGE+LG+AGL+G+GRT +A  +
Sbjct: 264 LSQLFP-VREQPIG-DLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAI 321

Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370
           FG    T GE+ +      G  V +    P  AI+ G A LTEDRKL GLF   SV EN+
Sbjct: 322 FGVTPSTGGEILL-----DGQPVRI--SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 374

Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430
            + V     +G G + + A R    +    L ++    +  +  LSGGNQQK +L+R L 
Sbjct: 375 EMAVLPH-YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433

Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490
             PR+LILDEPTRG+D+GAK+EIYRLI+ LA  G+A++MISSELPEV+G+ DRV+VM EG
Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 493

Query: 491 TLAGEVRPAGSAAETQERIIALATG 515
            L G +   G A  TQER++ LA+G
Sbjct: 494 DLMGTLN-RGEA--TQERVMQLASG 515


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: 630
Number of extensions: 27
Number of successful extensions: 10
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: 517
Length adjustment: 35
Effective length of query: 505
Effective length of database: 482
Effective search space:   243410
Effective search space used:   243410
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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