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_013402972.1 CALHY_RS05380 energy-coupling factor transporter ATPase

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_000166355.1:WP_013402972.1
          Length = 288

 Score =  239 bits (611), Expect = 4e-68
 Identities = 123/262 (46%), Positives = 176/262 (67%), Gaps = 4/262 (1%)

Query: 2   KTPFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAG 61
           KTPFE+ AL +IN SI +G ++ +IG TGSGKSTL+Q +NGLL P  G + +        
Sbjct: 15  KTPFEKKALENINLSITKGEFIGIIGKTGSGKSTLVQLMNGLLVPQIGDVVVDGINT--- 71

Query: 62  KKNKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGL 121
           K  K  K++RK+VG+VFQ+PE+QLFEETV KDI+FGP N G  +++ +++ +E+ +L+ +
Sbjct: 72  KDKKRAKEIRKRVGLVFQYPEYQLFEETVYKDIAFGPQNLGFSEDEVKRRVKEVCELLEI 131

Query: 122 SEELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQR 181
            +ELL++SPFELSGGQ RR+AIAG+LAMDPE ++LDEPTAGLD RGRK I  +  +LH+ 
Sbjct: 132 PKELLEKSPFELSGGQKRRIAIAGILAMDPECIILDEPTAGLDMRGRKRIFSIIEKLHKE 191

Query: 182 GNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQ 241
              T IL++HS+ED A   + +I+++KG IQ  G     F   E +   GL LP  I + 
Sbjct: 192 AKKTIILISHSLEDVAMLCERVIILNKGKIQFDGPKHQAFENVELLEKSGL-LPPDILYL 250

Query: 242 RHLEAALGVRFNEPMLTIEDAA 263
           +H     G + +    ++E  A
Sbjct: 251 QHRLKLKGFKIDRFEYSVEKVA 272


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: 230
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: 276
Length of database: 288
Length adjustment: 26
Effective length of query: 250
Effective length of database: 262
Effective search space:    65500
Effective search space used:    65500
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