GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Amantichitinum ursilacus IGB-41

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate WP_053937455.1 WG78_RS08855 transporter substrate-binding domain-containing protein

Query= uniprot:A0A1N7UK26
         (258 letters)



>NCBI__GCF_001294205.1:WP_053937455.1
          Length = 260

 Score =  121 bits (304), Expect = 1e-32
 Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 19/254 (7%)

Query: 7   LFAALLLPLCATAHAQEWKE-------IRFGVFPEYPPFESVAADGSLQGFDIELGNAIC 59
           L AALL    A+A A +  +       +R  V   YPPF +   +G L GFD+E+  A+ 
Sbjct: 7   LIAALLGITAASAMAADLLDSVKQRGTLRVAVEGTYPPF-NYKDNGQLTGFDVEIAQALA 65

Query: 60  AKLEVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRK 119
            KL VK  +   E+ G++  L A K+D I++ + +T  R++  DFSD   LS   ++ RK
Sbjct: 66  QKLGVKAEFTTTEWSGILAGLSAGKYDVIVNQVGITAKRQESFDFSDPYVLSQAQLVVRK 125

Query: 120 --SADFGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLD 177
             S +F  T + L GK+VGV QG+    +A    A  G  +K Y  + +   DL   R+D
Sbjct: 126 DDSRNF-KTLDDLKGKKVGVGQGT---NFAEMLKAVNGIDVKTYPGEQEYLQDLALSRID 181

Query: 178 ATLTDKLEAQLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQ 237
           A L D L   + +L        K G    +P+L     +   KN+   +A +NK +A ++
Sbjct: 182 AALNDTL--MIPYLIHKTNLPLKAGAGVGEPSLN---GIPFVKNNPKFKAALNKALADIK 236

Query: 238 ADGTYAQIQKKYFG 251
           ADGTY +I  K+FG
Sbjct: 237 ADGTYNKISTKWFG 250


Lambda     K      H
   0.319    0.135    0.393 

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: 146
Number of extensions: 9
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: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 (21.8 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