GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artP in Klebsiella michiganensis M5al

Align histidine transport ATP-binding protein hisP (characterized)
to candidate BWI76_RS20320 BWI76_RS20320 histidine/lysine/arginine/ornithine ABC transporter ATP-binding protein HisP

Query= CharProtDB::CH_003210
         (257 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20320 BWI76_RS20320
           histidine/lysine/arginine/ornithine ABC transporter
           ATP-binding protein HisP
          Length = 257

 Score =  469 bits (1207), Expect = e-137
 Identities = 238/257 (92%), Positives = 249/257 (96%)

Query: 1   MSENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60
           MS+NKLNVIDLHKRYGEHEVLKGVSL+A AGDVISIIGSSGSGKSTFLRCINFLEKPSEG
Sbjct: 1   MSDNKLNVIDLHKRYGEHEVLKGVSLRAKAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60

Query: 61  SIVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV 120
           +IVVNGQ I LVRDKDGQLKV+DKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
Sbjct: 61  TIVVNGQNIGLVRDKDGQLKVSDKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV 120

Query: 121 LGLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180
           LGLSKQEAR+RAVKYLAKVGIDER Q KYPVHLSGGQQQRVSIARALAMEP+VLLFDEPT
Sbjct: 121 LGLSKQEARDRAVKYLAKVGIDERQQIKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT 180

Query: 181 SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLF 240
           SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVS+HVIFLHQGKIEEEG P+ +F
Sbjct: 181 SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGHPDDVF 240

Query: 241 GNPQSPRLQRFLKGSLK 257
           GNP+S RLQ+FLKGSLK
Sbjct: 241 GNPKSQRLQQFLKGSLK 257


Lambda     K      H
   0.318    0.134    0.375 

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: 327
Number of extensions: 3
Number of successful extensions: 1
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: 257
Length of database: 257
Length adjustment: 24
Effective length of query: 233
Effective length of database: 233
Effective search space:    54289
Effective search space used:    54289
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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