GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Pseudomonas fluorescens FW300-N1B4

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate Pf1N1B4_3435 Arginine/ornithine ABC transporter, ATP-binding protein AotP

Query= SwissProt::P02915
         (258 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3435
          Length = 254

 Score =  361 bits (927), Expect = e-105
 Identities = 178/253 (70%), Positives = 214/253 (84%), 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 +EN+MEAP+ VLG+S
Sbjct: 63  NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122

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

Query: 186 PELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQ 245
           PELVG+VL++MQ LA+EG+TMVVVTHEMGFAR VS+ ++FLH+G +EE G+P +V  NPQ
Sbjct: 182 PELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQ 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: 249
Number of extensions: 6
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:

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