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.
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