Align Rhizopine-binding protein (characterized, see rationale)
to candidate 3608607 Dshi_2000 D-xylose ABC transporter, periplasmic substrate-binding protein (RefSeq)
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__Dino:3608607 Length = 340 Score = 93.2 bits (230), Expect = 8e-24 Identities = 87/287 (30%), Positives = 138/287 (48%), Gaps = 18/287 (6%) Query: 5 IRFASLALSLMLA--SGAALADLRIGVSMSQF-DDTWLTYLRESMDKQAKSMPDGVKLQF 61 +R A LA +++ A + +A AD+ +GVS S F ++ W T + +A G Sbjct: 1 MRKAILAAAIVAAGVTTSAYADVTVGVSWSNFQEERWKT---DEAAIKAALEAAGATYVS 57 Query: 62 EDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK 121 DA+S KQLS VES I+Q VDA+++ D+ A +AA GIP+V +R +D Sbjct: 58 ADAQSSSAKQLSDVESLIAQGVDALIILAQDSQAIGPAVQAAADEGIPVVGYDRLIED-- 115 Query: 122 LPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLAKYP 181 P+ N +E G+MQ + + E+ +G+ V++ G + + G +E+L Sbjct: 116 -PRAFYLTFDN-VEVGRMQARAVLEQAP-EGNYVMIKGSPTDPNADFLRGGQQEILQDAI 172 Query: 182 GIK----IDQEQTGTWSRDKGMTLVNDWLT-QGRKFDAIVSNNDEMAIGAAMALKQAGVE 236 + + T W + LT Q + DA+V++ND A G AL G+E Sbjct: 173 DAGKITIVGEAYTDGWLPANAQRNMEQILTAQDNQVDAVVASNDGTAGGVVAALTAQGME 232 Query: 237 KGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMA 283 + ++G DG L V KG VSV++DA + + AV MA Sbjct: 233 --GIPVSGQDGDHAALNRVAKGTQTVSVWKDARDLGRAAGEIAVAMA 277 Lambda K H 0.315 0.130 0.360 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: 250 Number of extensions: 13 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: 308 Length of database: 340 Length adjustment: 28 Effective length of query: 280 Effective length of database: 312 Effective search space: 87360 Effective search space used: 87360 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 (21.5 bits) S2: 48 (23.1 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