GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Nocardioides daejeonensis MJ31

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_110208468.1 DNK54_RS18405 ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_003194585.1:WP_110208468.1
          Length = 273

 Score =  140 bits (354), Expect = 2e-38
 Identities = 90/251 (35%), Positives = 146/251 (58%), Gaps = 13/251 (5%)

Query: 7   LHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVN 66
           + V ++HKR+G  E+LKG+++  R   + +++G SG+GKS  L+ I  L +P +G + V 
Sbjct: 27  VEVRNVHKRFGSSEILKGLTVDFRDNAITTVLGPSGTGKSVLLKHIVGLLEPDQGEVRVF 86

Query: 67  GQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 126
           GQNI        Q+   ++ +   LR R  ++FQ   L+  M + +NV     +    ++
Sbjct: 87  GQNI-------WQVPEIERYE---LRKRFGVLFQDGALFGSMNIYDNVAFPLRKHTQKTE 136

Query: 127 HDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDP 186
            + RE  +  L  VG+ E+A  K P  +SGG ++R   ARAL M+PDV+LFDEP S LDP
Sbjct: 137 REIREIVMDNLCVVGL-EQAIHKAPNEISGGMRKRAGFARALVMKPDVVLFDEPDSGLDP 195

Query: 187 ELVGEVLRIMQQLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQ 245
                + +++ ++ EE G T +V+TH++  AR VS +V  L +G+I    D +  FG+ Q
Sbjct: 196 VRTKLLSQLIAKIHEEYGGTYIVITHDIPTARTVSDYVAVLWKGEIVHYSDADGAFGS-Q 254

Query: 246 SPRLQQFLKGS 256
            P ++QFL G+
Sbjct: 255 DPFVRQFLAGA 265


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: 197
Number of extensions: 15
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: 258
Length of database: 273
Length adjustment: 25
Effective length of query: 233
Effective length of database: 248
Effective search space:    57784
Effective search space used:    57784
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