GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Shewanella loihica PV-4

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 5211189 Shew_3605 cell division ATP-binding protein FtsE (RefSeq)

Query= SwissProt::P02915
         (258 letters)



>FitnessBrowser__PV4:5211189
          Length = 233

 Score =  139 bits (349), Expect = 7e-38
 Identities = 75/215 (34%), Positives = 125/215 (58%), Gaps = 12/215 (5%)

Query: 17  GGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDK 76
           GG + L  VS   + G++  + G SG+GKST L+ I  +E+ + G + +NG +I  +R K
Sbjct: 13  GGQKALTDVSFHLKRGEMAFLTGHSGAGKSTLLKLITVIERANAGRVAINGHDIANIRPK 72

Query: 77  DGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKY 136
           D          +  LR  + M+FQ+ +L    +V +N+   P+ + G + H+ ++R L  
Sbjct: 73  D----------VPFLRRDIGMIFQNHHLLMDRSVFDNIA-LPLVIEGFALHEIKKRVLAA 121

Query: 137 LAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIM 196
           L  VG+  + +  YP+ LSGG+QQRV IARA+  +P +LL DEPT  LDP+L  ++LR+ 
Sbjct: 122 LDMVGLYGKER-HYPIMLSGGEQQRVGIARAIVNKPPLLLADEPTGNLDPKLSMDILRLF 180

Query: 197 QQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKI 231
           +   + G T+++ TH++G    +    + L QG+I
Sbjct: 181 ETFNDAGTTVLIATHDLGLIARMRYRTLTLKQGRI 215


Lambda     K      H
   0.319    0.136    0.383 

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: 146
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: 258
Length of database: 233
Length adjustment: 24
Effective length of query: 234
Effective length of database: 209
Effective search space:    48906
Effective search space used:    48906
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 (21.7 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