GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Pedobacter sp. GW460-11-11-14-LB5

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__Pedo557:CA265_RS16020
          Length = 250

 Score =  120 bits (302), Expect = 2e-32
 Identities = 82/229 (35%), Positives = 124/229 (54%), Gaps = 9/229 (3%)

Query: 6   LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65
           +I ++DI   Y+  +    L G+S +  EG    I+G +GSGK+TL + + GL  P+SG 
Sbjct: 1   MIEIKDI---YKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGS 57

Query: 66  IEVAG---IQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLEN-NGVPREEMIE 121
           +   G     +T E   EVRK+IGM+FQ     F   TV +++ F L       R+E +E
Sbjct: 58  VLYDGRDFTPMTYEQRIEVRKEIGMLFQG-SALFDSMTVEENIMFPLNMFTDQSRKEKLE 116

Query: 122 RVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEV 181
           RVD+ +++VN+       P  LSGG K+RV IA  I+  P  +  DE  S LDP     +
Sbjct: 117 RVDFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNSGLDPKTSIVI 176

Query: 182 LETVRHLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEI 229
            E ++ + E+   T I +THD+N      D I+ ++ GKK+ EG  +EI
Sbjct: 177 DELIQEITEEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEGSNKEI 225


Lambda     K      H
   0.316    0.135    0.383 

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: 198
Number of extensions: 14
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: 281
Length of database: 250
Length adjustment: 25
Effective length of query: 256
Effective length of database: 225
Effective search space:    57600
Effective search space used:    57600
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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