Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 152 bits (385), Expect = 1e-41 Identities = 91/243 (37%), Positives = 145/243 (59%), Gaps = 5/243 (2%) Query: 2 TTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTS 61 T I V+NL+K ++ + + NVS I G ++G SG GK+T L+ I GL + Sbjct: 4 TIISVKNLTKQYQA--EQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDE 61 Query: 62 GYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIEN 121 G I+F+++ V P ++ P + + MV Q+++L V+DNIA L + K K E Sbjct: 62 GEIFFEDKRVKGPDEQLI-PGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDL-KTKAE- 118 Query: 122 KVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESA 181 K ++ E L + + N+ ELSGG+ QR AIA+A+V D +VLLLDEPFS +DA ++ Sbjct: 119 KTLQIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQL 178 Query: 182 RALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIAR 241 RA ++++ E +T ++VSHDPAD +A++ ++ NG+ Q G P+EIY++P A+ Sbjct: 179 RADIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQ 238 Query: 242 LTG 244 + G Sbjct: 239 ILG 241 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: 237 Number of extensions: 15 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: 330 Length adjustment: 29 Effective length of query: 342 Effective length of database: 301 Effective search space: 102942 Effective search space used: 102942 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