GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Shewanella oneidensis MR-1

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  193 bits (490), Expect = 7e-54
 Identities = 100/249 (40%), Positives = 155/249 (62%), Gaps = 9/249 (3%)

Query: 22  AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSP 81
           AVD+V++ I +G    +LGPSG GKTT LR+IAGLE+  SG + F+ E +++        
Sbjct: 17  AVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKFNGEDITTQH-----V 71

Query: 82  EKRGIAMVFQNWALYPNMTVFDNIAFPLKL----AKVPKDKIENKVKEVSEELGLSGVLN 137
            +RG+  VFQ++AL+ +MTVF+N+A+ L +     +  K +I  KV  + + + L    +
Sbjct: 72  SERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSLLKLVQLDWTAD 131

Query: 138 RYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTL 197
           RYP +LSGGQ QR A+ARAL  +PKVLLLDEPF  LDA++R   R  +R++  E  +TT+
Sbjct: 132 RYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLRRLHDEINVTTV 191

Query: 198 IVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQAKIIENN 257
            V+HD  +   +A+K  V+  G+  Q GTP E+Y+ P+   +    G +NL  A++   +
Sbjct: 192 FVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGNVNLFHARVKHGH 251

Query: 258 AIIANLKVP 266
           + I N+ +P
Sbjct: 252 STIGNIHIP 260


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: 300
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: 371
Length of database: 354
Length adjustment: 29
Effective length of query: 342
Effective length of database: 325
Effective search space:   111150
Effective search space used:   111150
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