GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Shewanella amazonensis SB2B

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  172 bits (436), Expect = 1e-47
 Identities = 96/263 (36%), Positives = 158/263 (60%), Gaps = 8/263 (3%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M+T+ ++ L   ++  +     +  +++T+  G    +LGPSG GKTT LR IAGL++ +
Sbjct: 1   MSTLSIQGLHSDYRGEQV----LRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDIS 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           +G I  + + VS+     ++PEKR I M+FQ++AL+P++TV DNI F ++  ++ K    
Sbjct: 57  AGSIAINGKTVSADG-CFVAPEKRSIGMIFQDYALFPHLTVADNILFGVR--QLDKQSRS 113

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +++E+   + L G+  RYP ELSGGQ QR +IARAL  +P +LLLDEPFSN+DAQ+R +
Sbjct: 114 VRLEEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRA 173

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
               +R I + R ++ + V+H   + FA A+   +   G+  Q G P  +Y+ P T  +A
Sbjct: 174 LMLEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVA 233

Query: 241 RLTGEINLIQAKIIENNAIIANL 263
              G  N +  + +E   +I+ L
Sbjct: 234 DFLGASNYLDVR-LEAGQLISTL 255


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: 212
Number of extensions: 10
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: 341
Length adjustment: 29
Effective length of query: 342
Effective length of database: 312
Effective search space:   106704
Effective search space used:   106704
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