GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Caldicellulosiruptor hydrothermalis 108

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_013402971.1 CALHY_RS05375 energy-coupling factor transporter ATPase

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000166355.1:WP_013402971.1
          Length = 278

 Score =  166 bits (420), Expect = 5e-46
 Identities = 102/263 (38%), Positives = 157/263 (59%), Gaps = 17/263 (6%)

Query: 2   KTPFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAG 61
           KTP    AL DIN  I+ G +VA++G  GSGKSTL + +NGLL P KG + + S      
Sbjct: 21  KTP----ALIDINLKIERGEFVAILGLNGSGKSTLAKLINGLLIPEKGDVIVDSM----- 71

Query: 62  KKNKDLKKL---RKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQL 118
              KD++K+   R+K G +FQ P++QL    V +D++FGP N G+ +E   +     L  
Sbjct: 72  -NTKDVEKIWDIRRKCGYIFQNPDNQLVASIVEEDVAFGPENLGMPREKIRKAVDSALLT 130

Query: 119 VGLSEELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYEL 178
           V + E   + + ++LSGGQ +RVAIAGVLAM PE ++LDEPT+ LDP+GRKE++     L
Sbjct: 131 VEMME-YKNHATYKLSGGQKQRVAIAGVLAMKPECIILDEPTSMLDPKGRKEVIATVERL 189

Query: 179 HQRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETI 238
           ++    T +LVTH++ D    +   IV+ KG I+  G   +L LK +     G D+P+ +
Sbjct: 190 NKEEKKTIVLVTHNI-DEMLLSQRSIVLDKGHIKFDGPSFEL-LKLDWFYEMGFDMPQIL 247

Query: 239 KFQRHLEAALGVRFNEPMLTIED 261
           K    L+   GV+ ++ + ++++
Sbjct: 248 KLSIELKKR-GVKIDKEIWSVDE 269


Lambda     K      H
   0.318    0.136    0.380 

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: 206
Number of extensions: 17
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: 276
Length of database: 278
Length adjustment: 25
Effective length of query: 251
Effective length of database: 253
Effective search space:    63503
Effective search space used:    63503
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