GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Pseudomonas simiae WCS417

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3454 PS417_17680 ABC transporter

Query= uniprot:D8IUY7
         (241 letters)



>FitnessBrowser__WCS417:GFF3454
          Length = 231

 Score =  191 bits (486), Expect = 8e-54
 Identities = 100/234 (42%), Positives = 150/234 (64%), Gaps = 7/234 (2%)

Query: 5   ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64
           +L V+ +   Y     ++G+ L VN GELVTL+G NGAGKTTTL++I G +   +  G I
Sbjct: 1   MLIVENIHSYYDKSHVLEGVSLTVNPGELVTLLGRNGAGKTTTLRSILGIICPRK--GQI 58

Query: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124
            + GQ L G+K FE+ +  LA+VPE RG+F  ++++ENL +    +         ++  +
Sbjct: 59  HFNGQALVGQKIFEIARQGLALVPENRGIFRLLTVEENLRIATRKTS-----RWQLEDVY 113

Query: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184
            +FPRLKER       LSGGEQQMLA+ARAL++ PKLL+LDEP+ GL+P++V+++ +++R
Sbjct: 114 GMFPRLKERRKNAGHALSGGEQQMLAIARALLNDPKLLILDEPTEGLAPVIVDELVKILR 173

Query: 185 NVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYL 238
            V   G+ +LLVEQN  +  + A R YV+E G +  +G A+    DP +K  YL
Sbjct: 174 KVKDDGLPVLLVEQNLMVCDKLADRHYVLEQGRVVYEGSAEAFRADPTIKNRYL 227


Lambda     K      H
   0.317    0.134    0.365 

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: 170
Number of extensions: 7
Number of successful extensions: 3
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: 241
Length of database: 231
Length adjustment: 23
Effective length of query: 218
Effective length of database: 208
Effective search space:    45344
Effective search space used:    45344
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: 41 (21.6 bits)
S2: 46 (22.3 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