GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Williamsia sterculiae CPCC 203464

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_900156495.1:WP_076482473.1
          Length = 250

 Score =  247 bits (631), Expect = 1e-70
 Identities = 128/240 (53%), Positives = 168/240 (70%), Gaps = 2/240 (0%)

Query: 14  KRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLV 73
           K +G  +VLKG+SL+   G+V  +IG SGSGKSTFLRC+N LE  + G + V+   I   
Sbjct: 9   KSFGALQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLYVDDDLIGY- 67

Query: 74  RDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERA 133
           R+K G+L           R  + MVFQHFNL+ H T L+N++EAPIQV G+ +  A ER 
Sbjct: 68  REKGGKLYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVVRARAVERG 127

Query: 134 LKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVL 193
              L +VG+ ++A   YP  LSGGQQQRV+IARALAM+P ++LFDEPTSALDPELVG+VL
Sbjct: 128 KDLLDQVGLADKASA-YPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDPELVGDVL 186

Query: 194 RIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFL 253
            +M+ LA++G TMVVVTHEMGFAR V+  ++F+  GK+ E+GDP +V  +PQ  R Q FL
Sbjct: 187 AVMRNLAKDGMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQHERTQSFL 246


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: 206
Number of extensions: 12
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: 250
Length adjustment: 24
Effective length of query: 234
Effective length of database: 226
Effective search space:    52884
Effective search space used:    52884
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 24 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