Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 201 bits (510), Expect = 3e-56 Identities = 117/292 (40%), Positives = 172/292 (58%), Gaps = 28/292 (9%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M T+ ++N+ K F GKT+V + VSI + G ++GPSG GK+T LR++AGLE + Sbjct: 1 MATLTLDNVKKSF--GKTDV--IHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVS 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG + D V++ + P R IAMVFQN+ALYP+M+VFDN+A+ LK+AKVPK +I Sbjct: 57 SGEVRIDGRVVNT-----LEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIA 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 ++V ++ L L L R PKELSGGQ QR A+ RA+V+ P V L DEP SNLDA++R Sbjct: 112 DRVAVAAKLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQ 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R ++ +QRE +T+L V+HD + +A++ V+ G QIG P E+Y P T +A Sbjct: 172 MRLEIKALQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVA 231 Query: 241 RLTGE--INLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLS 290 G N + A ++ G + +G+RP+ L ++ Sbjct: 232 GFIGSPPTNFLPADMVR-----------------AGPAGQQVGIRPEHLRVA 266 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: 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: 333 Length adjustment: 29 Effective length of query: 342 Effective length of database: 304 Effective search space: 103968 Effective search space used: 103968 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