GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Geotalea uraniireducens Rf4

Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  160 bits (405), Expect = 3e-44
 Identities = 94/253 (37%), Positives = 151/253 (59%), Gaps = 12/253 (4%)

Query: 1   MSENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60
           M+  +L+V DLH   G++ +LKGVSL  N G++++++G SGSGK+T LR I  LE PS G
Sbjct: 1   MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60

Query: 61  SIVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV 120
           SI +  Q +          + A K ++ + +  L  VFQ + LW H TV ENV    +++
Sbjct: 61  SIRIGEQMV---------FESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYG-LKL 110

Query: 121 LGLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180
             +   E R+R  + LA +G+ + ++ ++P  LSGGQQQRV++AR+L   P+V+L DEP 
Sbjct: 111 RKVPDGEIRQRVQEVLANLGLGDLSE-RHPHQLSGGQQQRVALARSLVYNPQVILLDEPL 169

Query: 181 SALDPELVGEV-LRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQL 239
           S LD +L  E  + + Q + +   + V VTH+   A  ++  V+ L  G IE+ G P+++
Sbjct: 170 SNLDAKLREEARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEM 229

Query: 240 FGNPQSPRLQRFL 252
           +G P+S  +  F+
Sbjct: 230 YGAPKSLFVAEFM 242


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: 193
Number of extensions: 7
Number of successful extensions: 4
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: 353
Length adjustment: 27
Effective length of query: 230
Effective length of database: 326
Effective search space:    74980
Effective search space used:    74980
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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