GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Pseudomonas simiae WCS417

Align FAA hydrolase family protein (characterized, see rationale)
to candidate GFF3551 PS417_18185 5-carboxymethyl-2-hydroxymuconate isomerase

Query= uniprot:A0A2E7P912
         (281 letters)



>FitnessBrowser__WCS417:GFF3551
          Length = 283

 Score =  155 bits (391), Expect = 1e-42
 Identities = 100/285 (35%), Positives = 151/285 (52%), Gaps = 9/285 (3%)

Query: 1   MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDA----SLDKIRKLDLESLPA 56
           MKL  +   G+   GV++   ++ DL + +K   GA L  A     L ++    L  LP 
Sbjct: 1   MKLASFIVHGRTTYGVVE-GDQLIDLES-VKSTFGADLKQAIAANRLGELTPAVLAPLPR 58

Query: 57  VE-GSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIP 115
           V          + N GK +CIG+NYA H  E+   +P  P++F ++  + V     +  P
Sbjct: 59  VPLADVTFLPVIANPGKVLCIGINYATHVRETGRDMPTYPMIFTRFADSQVAHLQPIIRP 118

Query: 116 RGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGC 175
           + S K D+E EL VVIGK   +++  DA+ +VAGY   ND S R++Q +    +  GK  
Sbjct: 119 KVSHKLDFEGELAVVIGKTARHVNAADALDYVAGYACYNDGSVRDWQ-KHTLQFVPGKNF 177

Query: 176 DTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQP 235
              G  GPW+VT DE+ DPQ+L +   ++G+  Q+  TS MIF V  ++ Y S F  L P
Sbjct: 178 PQTGGFGPWMVTHDEINDPQELELTTRLNGEVMQHTRTSDMIFDVRQLIEYCSTFTELAP 237

Query: 236 GDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQKTID 280
           GDVI +GT  GVG   +P  V+++ G T+ + I G+G  +    D
Sbjct: 238 GDVIVSGTTGGVGAFREP-PVWMKPGDTVEVEITGIGRLRNSIAD 281


Lambda     K      H
   0.316    0.138    0.419 

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: 236
Number of extensions: 11
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 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