GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Dinoroseobacter shibae DFL-12

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 3610306 Dshi_3686 ABC transporter related (RefSeq)

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__Dino:3610306
          Length = 221

 Score =  142 bits (358), Expect = 6e-39
 Identities = 76/208 (36%), Positives = 123/208 (59%), Gaps = 9/208 (4%)

Query: 22  RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81
           R  L  +++ + E   + I+G NGSGKST AR  NGL  P SG I + G       + ++
Sbjct: 14  RPILSDINIDLNEKR-IGIIGRNGSGKSTFARLFNGLEKPSSGSITLEG----SAELKDL 68

Query: 82  RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPH 141
           R+K+G VFQNPDNQ V   V +D+AFGL+N  +P   + ER+   + +  ++   D+  H
Sbjct: 69  RRKVGFVFQNPDNQIVYPIVDEDLAFGLKNLKLPSATIKERITEVMARFQIEHLKDRLTH 128

Query: 142 HLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITH 201
            LSGG++Q VA+AGV+  +P +I+ DE T++LD   ++ ++  +  LKE     V+ ++H
Sbjct: 129 QLSGGERQMVALAGVLVMQPQMIVFDEPTTLLDLWNKKRLMRAIADLKEH----VVLVSH 184

Query: 202 DLNEAAKADRIIVMNGGKKYAEGPPEEI 229
           DL+   + DR+I +  G+   +G P  +
Sbjct: 185 DLDLLREFDRVIHIEAGRIVGDGEPNAV 212


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: 174
Number of extensions: 8
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: 221
Length adjustment: 24
Effective length of query: 257
Effective length of database: 197
Effective search space:    50629
Effective search space used:    50629
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: 46 (22.3 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