GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013402123.1 CALHY_RS00760 ATP-binding cassette domain-containing protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_000166355.1:WP_013402123.1
          Length = 317

 Score = 99.4 bits (246), Expect = 8e-26
 Identities = 71/239 (29%), Positives = 126/239 (52%), Gaps = 9/239 (3%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +++V+ L   YG   A+  + FEV++GE+V  +G NGAGK+TTM  ITG LS  +G    
Sbjct: 1   MIKVEHLTKKYGQHYAIHDISFEVQKGEIVGFLGPNGAGKSTTMNIITGYLSPTEGTAYV 60

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK-DKAGILADIEKMFT 127
            G  I  +   + VK+ +  +PE   ++  MT+ E L   + I+K DK      ++K+  
Sbjct: 61  DGFDILEEP--EEVKKRIGYLPENPPLYMDMTVQEYLDFVSDIKKVDKKEKKRSMDKIME 118

Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187
               +   +++L   +S G +Q + + +AL+  P VL+LDEP++GL P  + +I  V++ 
Sbjct: 119 TV-GIAHVRNRLIKNLSKGYKQRVGLAQALIGNPPVLILDEPTIGLDPKQIIEIRSVIKS 177

Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLI----TMTGPGQQLLNDPKVRAAYLGE 242
           + +   TI+L         A+ +R  ++  G I    T     ++L +  K++   LG+
Sbjct: 178 LRS-EHTIILSSHILPEVSAVCERVLIINKGKIVASDTPENLSKRLTHGSKLQLRVLGQ 235


Lambda     K      H
   0.317    0.136    0.373 

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: 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: 242
Length of database: 317
Length adjustment: 25
Effective length of query: 217
Effective length of database: 292
Effective search space:    63364
Effective search space used:    63364
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