GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Synechococcus elongatus PCC 7942

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  197 bits (501), Expect = 3e-55
 Identities = 107/246 (43%), Positives = 160/246 (65%), Gaps = 9/246 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           I+V  +SK F       +AV +V +T+++G    +LGPSG GK+T LRLIAGLE+P SG 
Sbjct: 3   IQVSQVSKQFGS----FQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGR 58

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           I+      ++      S   R I  VFQ++AL+ ++TV  NIAF L+L K  K+K+  +V
Sbjct: 59  IFLTGRDATNE-----SVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARV 113

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
           +E+ E + L+G+ +RYP +LSGGQ QR A+ARAL   P+VLLLDEPF  LDA++R+  R+
Sbjct: 114 EELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRS 173

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            +RK+  E  +TT+ V+HD  +   +A++  V+ +GK  QIG+P EIY+ PAT  +    
Sbjct: 174 WLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFI 233

Query: 244 GEINLI 249
           G +N++
Sbjct: 234 GPVNVL 239


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: 274
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: 338
Length adjustment: 29
Effective length of query: 342
Effective length of database: 309
Effective search space:   105678
Effective search space used:   105678
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