Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 206 bits (523), Expect = 1e-57 Identities = 110/271 (40%), Positives = 171/271 (63%), Gaps = 8/271 (2%) Query: 23 VDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSPE 82 VDN S+ + +LGPSG GKTT +R+IAGLE+PT G I+ + V+ P+ Sbjct: 19 VDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEIWIGDRMVNDDL-----PK 73 Query: 83 KRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLNRYPKE 142 R +AMVFQN+ LYP+MT+F+NIA+PL++ V K +I +V+ +E++ L+ L+R PK Sbjct: 74 DRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQVELTKFLHRKPKA 133 Query: 143 LSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVSHD 202 LSGGQ QR A+ARA+V+ PKV L+DEP SNLDA++R + RA ++ + RE ++TT+ V+HD Sbjct: 134 LSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLSRELQITTVYVTHD 193 Query: 203 PADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGE--INLIQAKIIENNAII 260 + +A++ V+ +G Q+GTP EIY PA +A G +NLI +E+ + Sbjct: 194 QIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMNLINGS-VEDGMFV 252 Query: 261 ANLKVPLNNMELKGQSNIVIGLRPDDLTLSD 291 L + ++ ++G+R DD+ + + Sbjct: 253 TTGGTRLVKVPSPDRARAILGVRADDMQVHE 283 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: 319 Number of extensions: 9 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: 352 Length adjustment: 29 Effective length of query: 342 Effective length of database: 323 Effective search space: 110466 Effective search space used: 110466 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