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_1897 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1897
          Length = 386

 Score =  192 bits (487), Expect = 2e-53
 Identities = 110/302 (36%), Positives = 175/302 (57%), Gaps = 18/302 (5%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M T+ + N++K +  G  +   + N+ + ID G    ++GPSG GK+T +  IAGLE  +
Sbjct: 1   MATLELRNVNKTYGPGLPDT--LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETIS 58

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I  D+  +S      MSP+ R IAMVFQ++ALYP M+V DNIAF LK+ K+P  +I+
Sbjct: 59  GGAILVDDADISG-----MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEID 113

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V  VS+ L +  +L+R P +LSGGQ QR A+ RAL + PK+ L DEP SNLDA++R  
Sbjct: 114 EEVARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVE 173

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  ++ + +  K TT+ V+HD  +   + +K  V+ +G   Q GTP +IY  PA   +A
Sbjct: 174 MRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVA 233

Query: 241 RLTGE--INLIQAKIIENNAII--------ANLKVPLNNMELKGQS-NIVIGLRPDDLTL 289
              G   +N I  ++   +  +        A  ++PL   +   +   +++G+RP+ + L
Sbjct: 234 SFIGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIIL 293

Query: 290 SD 291
           ++
Sbjct: 294 AN 295


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: 337
Number of extensions: 11
Number of successful extensions: 2
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: 386
Length adjustment: 30
Effective length of query: 341
Effective length of database: 356
Effective search space:   121396
Effective search space used:   121396
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: 50 (23.9 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