Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate AO353_21380 AO353_21380 rhizopine-binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21380 Length = 308 Score = 161 bits (407), Expect = 2e-44 Identities = 97/300 (32%), Positives = 165/300 (55%), Gaps = 21/300 (7%) Query: 9 ATAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEH-----PAVKDGTVQL 63 A+ ALSL+ S A AD ++G ++ QF W+ L+E ++ DG V+L Sbjct: 8 ASLALSLMLASGAALAD---LRIGVSM----SQFDDTWLTYLRESMDKQAKSMPDG-VKL 59 Query: 64 TVFDGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVAD 123 D D + Q +Q+E+ ++Q+ DAI+ P+DT A +AA+ + ++ N + D Sbjct: 60 QFEDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDD 119 Query: 124 ASVPY----VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGK 179 +P V ++D+E G++Q Q + +K+ GKG++VI+ G + ++ +R KG EVL K Sbjct: 120 LKLPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLAK 179 Query: 180 HPDIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSK 239 +P IKI +++T W R + + L DWL K + +++ ND+MA+GA ALK G+ Sbjct: 180 YPGIKIDQEQTGTWSRDKGMTLVNDWLTQGRK-FDAIVSNNDEMAIGAAMALKQAGVEKG 238 Query: 240 DVPVTSIDGMPDAIQAAKK-DEVTTFLQDAQAQSQGALDVALRALAGKDYKPQSVIWERY 298 V + +DG PD ++A KK D + QDA Q+ ++D A++ K+ + +W Y Sbjct: 239 SVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVK--MAKNEPVEQAVWVPY 296 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: 261 Number of extensions: 18 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