Align Rhizopine-binding protein (characterized, see rationale)
to candidate GFF3639 PGA1_262p00430 D-xylose-binding periplasmic protein XylF
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__Phaeo:GFF3639 Length = 341 Score = 94.0 bits (232), Expect = 5e-24 Identities = 86/289 (29%), Positives = 139/289 (48%), Gaps = 19/289 (6%) Query: 5 IRFASLALSLMLASGAALA---DLRIGVSMSQF-DDTWLTYLRESMDKQAKSMPDGVKLQ 60 ++F S +L A+ A++A D+ +GVS S F ++ W T + +A G Sbjct: 1 MKFLSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKT---DEAAIKAALEAKGATYV 57 Query: 61 FEDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDL 120 DA+S KQLS +ES I+Q VDA++V D A +AA GIP+V +R +D Sbjct: 58 SADAQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDG 117 Query: 121 KLPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVL--- 177 + + +++E G+MQ + + E + G+ V++ G + + G +E++ Sbjct: 118 R----AFYLTFDNVEVGRMQARAVLE-AQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAA 172 Query: 178 AKYPGIKI-DQEQTGTWSRDKGMTLVNDWLT-QGRKFDAIVSNNDEMAIGAAMALKQAGV 235 IKI + T W + LT K DA+V++ND A G AL G+ Sbjct: 173 IDSGDIKIVGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGM 232 Query: 236 EKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAK 284 E + ++G DG L V KG VSV++DA + + AV+MA+ Sbjct: 233 E--GIAVSGQDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAE 279 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: 254 Number of extensions: 12 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: 341 Length adjustment: 28 Effective length of query: 280 Effective length of database: 313 Effective search space: 87640 Effective search space used: 87640 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