GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14055
          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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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:

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:

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:

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:

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