GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Caldicellulosiruptor hydrothermalis 108

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_013402767.1 CALHY_RS04220 amino acid ABC transporter permease

Query= TCDB::A1VZQ3
         (250 letters)



>NCBI__GCF_000166355.1:WP_013402767.1
          Length = 220

 Score =  142 bits (357), Expect = 7e-39
 Identities = 70/199 (35%), Positives = 120/199 (60%), Gaps = 2/199 (1%)

Query: 49  IYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYALP 108
           + T+E++ +A+ I  +FG +  +   S+ K++      YV LF+  PL++QIFF++Y LP
Sbjct: 18  VVTIELTAIAVTIGLVFGLVAALFRISKIKVLNYIGSFYVWLFRGTPLLLQIFFIYYGLP 77

Query: 109 --VLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYII 166
             V  + L  F  G + +    GAY +E++R+ IL++ +GQ+EA+ + G TY+Q MRY+I
Sbjct: 78  KIVPALTLPAFLAGAIALIINSGAYTAEIIRAAILSIDKGQYEAAKALGMTYLQTMRYVI 137

Query: 167 VPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYF 226
           VPQT + ++PP+ N+ + L+K++S++  +G  ELM +A   A+  G  A  YI A V+Y 
Sbjct: 138 VPQTYKRLIPPIGNEFIALLKDSSLVSTIGMVELMRAAQLKASATGRDAEIYIAALVIYL 197

Query: 227 IICYPLAYFAKAYENKLKK 245
            +    +      E +L K
Sbjct: 198 ALTTVFSTIFNWLEKRLGK 216


Lambda     K      H
   0.328    0.143    0.422 

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: 151
Number of extensions: 9
Number of successful extensions: 2
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: 250
Length of database: 220
Length adjustment: 23
Effective length of query: 227
Effective length of database: 197
Effective search space:    44719
Effective search space used:    44719
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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