Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF2170 PS417_11070 rhizopine-binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >FitnessBrowser__WCS417:GFF2170 Length = 308 Score = 166 bits (420), Expect = 7e-46 Identities = 98/290 (33%), Positives = 166/290 (57%), Gaps = 14/290 (4%) Query: 11 AALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVFDGNY 70 A L LL + AA Y++G ++ + FM +VR E A + VQ+ D Sbjct: 9 ATLLLLFSQWSFAA----YRIGVSIARVDDNFM-TYVRTGLE-AAARQQDVQIQFEDAQG 62 Query: 71 DALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADASVPY-- 128 D + Q NQ+E + Q+ DA++ +P+DT A +AA++ ++ N + ++P Sbjct: 63 DVVRQLNQVEGFLNQKVDAVIVLPVDTAATANMTRAAVAAKTPLVYVNRHPDERTLPKGV 122 Query: 129 --VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKHPDIKII 186 V ++D+E G+LQ + + +KL GKGNV II G + Q+A DR +G +VL P IK++ Sbjct: 123 VTVASNDIEAGQLQMRYLAEKLAGKGNVAIIMGDLAQNATHDRTEGAKQVLKDFPGIKVV 182 Query: 187 EKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSKDVPVTSI 246 E+++A+W R++ + LT +WL A + + ++A ND+MA+GA AL+ G DV + I Sbjct: 183 EQQSADWQRSKGMDLTSNWLLAGTQ-FDAIVANNDEMAIGAAMALQQAGKAKGDVAIVGI 241 Query: 247 DGMPDAIQAAKKDEVT-TFLQDAQAQSQGALDVALRALAGKDYKPQSVIW 295 DG+PD + A K+ +T + QD +AQ+ A+ A+R + G+ +P+ +W Sbjct: 242 DGLPDGLAAIKRGLLTASVFQDPKAQATQAVQAAVRMIKGEAIEPE--VW 289 Lambda K H 0.314 0.130 0.373 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: 257 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: 335 Length of database: 308 Length adjustment: 28 Effective length of query: 307 Effective length of database: 280 Effective search space: 85960 Effective search space used: 85960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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