GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisP in Pseudomonas fluorescens FW300-N2E2

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate Pf6N2E2_5663 Arginine/ornithine ABC transporter, ATP-binding protein AotP

Query= SwissProt::P02915
         (258 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5663 Arginine/ornithine
           ABC transporter, ATP-binding protein AotP
          Length = 254

 Score =  356 bits (914), Expect = e-103
 Identities = 178/253 (70%), Positives = 211/253 (83%), Gaps = 1/253 (0%)

Query: 6   KLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIV 65
           KL V DLHKRYG HEVLKGVSL+A AGDVISIIGSSGSGKSTFLRCIN LE+P  G I++
Sbjct: 3   KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62

Query: 66  NGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLS 125
           N + + LV  KDG LK AD  QL+ +R+RL+MVFQHFNLWSHMT LEN+MEAP+ VLG++
Sbjct: 63  NNEELKLVAGKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVT 122

Query: 126 KHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALD 185
           K  ARE+A  YL KVG+  R +  YP H+SGG+QQRV+IARALAMEP+V+LFDEPTSALD
Sbjct: 123 KAQAREKAEHYLNKVGVAHR-KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALD 181

Query: 186 PELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQ 245
           PELVG+VL++MQ LA EG+TMVVVTHEMGFAR VS+ ++FLH+G +EE G+P +V  NPQ
Sbjct: 182 PELVGDVLKVMQGLALEGRTMVVVTHEMGFAREVSNQLVFLHKGIVEESGNPREVLVNPQ 241

Query: 246 SPRLQQFLKGSLK 258
           S RLQQFL GSLK
Sbjct: 242 SERLQQFLSGSLK 254


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: 243
Number of extensions: 7
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: 258
Length of database: 254
Length adjustment: 24
Effective length of query: 234
Effective length of database: 230
Effective search space:    53820
Effective search space used:    53820
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: 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 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