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_041723415.1 CALHY_RS08670 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_000166355.1:WP_041723415.1
          Length = 302

 Score =  102 bits (254), Expect = 9e-27
 Identities = 69/216 (31%), Positives = 112/216 (51%), Gaps = 12/216 (5%)

Query: 24  AVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYLGKSI-KGKGAWDLV 82
           AV  ++ E+ EGE+   +G NGAGKTTT++ +   +   DG +   GK I KG   W+  
Sbjct: 18  AVNKINIEIEEGEIYGFVGLNGAGKTTTIRMLLRMMKPTDGKVFLFGKDIAKGFEQWN-- 75

Query: 83  KEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD--IEKMFTIFPRLRERKDQLA 140
              +  + E    +  +T+ ENL++   +RK K   L D  IEK+     +L E ++ LA
Sbjct: 76  --DIGYIVESTYAYPNLTVRENLELFFMLRKLKEKTLIDNIIEKL-----KLNEYQNILA 128

Query: 141 GTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDVYALGVTIVLVEQ 200
             +S G  Q L + +AL+ +PK+L+LDEP  GL PI + ++ E++R++   G TI +   
Sbjct: 129 KNLSLGNLQRLGLAKALIHKPKLLILDEPLNGLDPIGIIEVREMLRELSQNGTTIFVSSH 188

Query: 201 NASRALAIADRGYVMESGLITMTGPGQQLLNDPKVR 236
             +    IA +  ++  G +       QL    K R
Sbjct: 189 ILAELAKIATKIGIIHRGKLVKELTSVQLEKQLKKR 224


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: 155
Number of extensions: 10
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: 302
Length adjustment: 25
Effective length of query: 217
Effective length of database: 277
Effective search space:    60109
Effective search space used:    60109
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