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.
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:
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