Aligments for a candidate for exuT in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for exuT in Pseudomonas fluorescens FW300-N2C3

Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate AO356_14055 AO356_14055 hexuronate transporter

Query= uniprot:D8IX31
         (418 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14055 AO356_14055
           hexuronate transporter
          Length = 432

 Score =  628 bits (1620), Expect = 0.0
 Identities = 301/426 (70%), Positives = 354/426 (83%), Gaps = 12/426 (2%)

Query: 4   VRGIRWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAVMQP 63
           ++GIRW+MV LVT  L+VNYLARNTLSVAAPT+M E+++ST+QYS+IVVAWQ+CYA+MQP
Sbjct: 3   IKGIRWWMVGLVTAGLMVNYLARNTLSVAAPTLMSEMNISTEQYSHIVVAWQVCYALMQP 62

Query: 64  VAGYILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGVKAS 123
           VAGYI+DA+GTK+GF IFA AWS+ CAAAA A+GWQ LAFFR LLG+TEAAG+P  VK S
Sbjct: 63  VAGYIIDAIGTKMGFAIFAFAWSIACAAAAMASGWQGLAFFRGLLGLTEAAGLPAAVKTS 122

Query: 124 TEWFPAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVLWML 183
           TEWFPAKERSVAIGWFNIGSSIGA+ APPLVVW IL+ GW+++F++VG LGV W  LW++
Sbjct: 123 TEWFPAKERSVAIGWFNIGSSIGAVLAPPLVVWAILNSGWELAFLIVGGLGVAWTFLWLI 182

Query: 184 FYKSPRDQKLLSPEERAYILEGQEK--SPEKVQRESWTKIVRSRNFWSIAIPRFLSEPAW 241
           FYK PRDQKLL   ER YIL GQE        ++ SW +I+ SRNF++IA  R LSEPAW
Sbjct: 183 FYKHPRDQKLLGDTERDYILSGQEAHFQDPTPKKGSWKRIIASRNFYAIASARILSEPAW 242

Query: 242 QTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSRK 301
           QTFNAWIPLY+ TERHMNIKEIAMFAWLPFLAAD+GCVLGGYLSP FHK+ KVSLFTSRK
Sbjct: 243 QTFNAWIPLYLMTERHMNIKEIAMFAWLPFLAADLGCVLGGYLSPFFHKYCKVSLFTSRK 302

Query: 302 LVMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATAT 361
           +V+L G+  MIGPAC+G V SPY AIALL IGGFAHQTLSGALY+ITSD F KN+VATAT
Sbjct: 303 MVLLFGASCMIGPACIGLVASPYTAIALLCIGGFAHQTLSGALYAITSDSFGKNEVATAT 362

Query: 362 GLTGMSGYLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAIAR---------- 411
           G+ GM GYLGA  FTLLFG++VTQIGY PLFVLLA FD++A  +V+ +AR          
Sbjct: 363 GMGGMFGYLGAAAFTLLFGVMVTQIGYSPLFVLLAIFDVIAAFIVWTVARELKQQPTTST 422

Query: 412 PRPEAI 417
           P P+A+
Sbjct: 423 PEPQAL 428


Lambda     K      H
   0.327    0.138    0.440 

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: 773
Number of extensions: 26
Number of successful extensions: 2
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: 418
Length of database: 432
Length adjustment: 32
Effective length of query: 386
Effective length of database: 400
Effective search space:   154400
Effective search space used:   154400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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, 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