GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA1 in Pseudomonas fluorescens FW300-N1B4

Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate Pf1N1B4_2210 Glutamate transport ATP-binding protein

Query= uniprot:P40735
         (281 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2210
          Length = 245

 Score =  132 bits (331), Expect = 1e-35
 Identities = 84/214 (39%), Positives = 124/214 (57%), Gaps = 6/214 (2%)

Query: 21  ERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAG--IQLTEESV 78
           +   L G+ L V EG+ +AI+G +GSGKSTL R LNGL     G IEV G  +      +
Sbjct: 15  DHHVLKGIDLSVDEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVIEVDGEYLDAARADL 74

Query: 79  WEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLEN-NGVPREEMIERVDWAVKQVNMQDFLD 137
             +R+K+GMVFQ   N F   TV ++V    +    VP+ +  E     +++V + +  D
Sbjct: 75  RSLRQKVGMVFQQ-FNLFPHLTVGENVMLAPQVVQKVPKAKAAELARQMLERVGLGEKFD 133

Query: 138 QEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVI 197
             P  LSGGQ+QRVAIA  +A  P +++ DE TS LDP    EVL  VR L ++GM T+I
Sbjct: 134 AFPDRLSGGQQQRVAIARALAMSPKVLLCDEITSALDPELVNEVLSVVRQLAKEGM-TLI 192

Query: 198 SITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230
            +TH++  A +  D+++ M+ GK +  G P+ +F
Sbjct: 193 MVTHEMRFAREVGDKLVFMHHGKVHEVGDPKVLF 226


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: 155
Number of extensions: 5
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: 245
Length adjustment: 25
Effective length of query: 256
Effective length of database: 220
Effective search space:    56320
Effective search space used:    56320
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