GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Pedobacter sp. GW460-11-11-14-LB5

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  119 bits (298), Expect = 7e-32
 Identities = 75/204 (36%), Positives = 114/204 (55%), Gaps = 4/204 (1%)

Query: 9   ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68
           AL  ++  I +G +VA++G +GSGKSTL+  L  L  P+ G   L  T +     +   +
Sbjct: 24  ALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAE 83

Query: 69  KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDR 128
              +++G VFQ   + L   T L +++   +  G  K+D + +A   L+ VGL   + D 
Sbjct: 84  VRNQEIGFVFQ-TFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRM-DH 141

Query: 129 SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTIL 188
            P ELSGGQ +RVA+A  L  +P +++ DEPT  LD +   EIM +  E+H +GN T IL
Sbjct: 142 KPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSKGN-TIIL 200

Query: 189 VTHSMEDAAAYADEMIVMHKGTIQ 212
           VTH  ED A +A  ++ M  G I+
Sbjct: 201 VTHE-EDIAQHAHRIVRMRDGLIE 223


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: 153
Number of extensions: 12
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: 252
Length adjustment: 25
Effective length of query: 251
Effective length of database: 227
Effective search space:    56977
Effective search space used:    56977
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 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