GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Magnetovibrio blakemorei MV-1

Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_069956878.1 BEN30_RS03080 amino acid ABC transporter ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>NCBI__GCF_001746755.1:WP_069956878.1
          Length = 253

 Score =  234 bits (598), Expect = 1e-66
 Identities = 130/251 (51%), Positives = 171/251 (68%), Gaps = 12/251 (4%)

Query: 2   SENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61
           +E  + ++D++K YGE  VLK ++L    G+ I I G SGSGKST +RCIN LE+  +G 
Sbjct: 9   NELAVQLVDVNKWYGEFHVLKNINLNVTPGERIVICGPSGSGKSTMIRCINRLEEHQKGK 68

Query: 62  IVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 121
           I+VNG  I L  D    LK  D+     +R  + M FQHFNL+ H+TVLEN   API V 
Sbjct: 69  IIVNG--IELTED----LKRIDE-----VRREVGMCFQHFNLFPHLTVLENCTLAPIWVR 117

Query: 122 GLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTS 181
            + K EA + A+ YL +V I E+A  KYP  LSGGQQQRV+IAR+L M P+++LFDEPTS
Sbjct: 118 KMPKSEAVKIAMHYLERVKIPEQAD-KYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTS 176

Query: 182 ALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFG 241
           ALDPE++ EVL +M +LAEEG TM+ VTHEMGFA+ V+  VIF+  G++ EE  P + F 
Sbjct: 177 ALDPEMIKEVLDVMVELAEEGMTMLCVTHEMGFAKLVANRVIFMDAGQVVEENEPHEFFD 236

Query: 242 NPQSPRLQRFL 252
           NPQ+ R + FL
Sbjct: 237 NPQNDRTKLFL 247


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: 182
Number of extensions: 7
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: 257
Length of database: 253
Length adjustment: 24
Effective length of query: 233
Effective length of database: 229
Effective search space:    53357
Effective search space used:    53357
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 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