GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Pseudomonas fluorescens GW456-L13

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039
          Length = 367

 Score =  194 bits (494), Expect = 2e-54
 Identities = 114/300 (38%), Positives = 176/300 (58%), Gaps = 19/300 (6%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  ++++NL K F+ G + +K +D   + ++       +GPSG GK+T LRLIAGLEE +
Sbjct: 1   MANLKIKNLQKGFE-GFSIIKGID---LEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVS 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I  D   ++      +SP KR +AMVFQ +ALYP+M+V  N++F L LA V K ++E
Sbjct: 57  GGTIELDGRDITE-----VSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVE 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            KV E +  L L  +L R PK+LSGGQ QR AI RA+V++PK+ L DEP SNLDA +R  
Sbjct: 112 KKVSEAARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQ 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  + ++ +E + T + V+HD  +   +A+K  V+  GK  Q+G+P ++Y  PA   +A
Sbjct: 172 MRLELLRLHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVA 231

Query: 241 RLTG--EINLIQAKI--IENNAIIANL------KVPLNNMELKGQSNIVIGLRPDDLTLS 290
              G  ++  ++ KI  +++      L       +PL    L   S + +G+RP+ L L+
Sbjct: 232 GFLGTPKMGFLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELA 291


Lambda     K      H
   0.317    0.136    0.374 

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: 285
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: 371
Length of database: 367
Length adjustment: 30
Effective length of query: 341
Effective length of database: 337
Effective search space:   114917
Effective search space used:   114917
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: 49 (23.5 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