Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Pf1N1B4_4285 Inositol transport system sugar-binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4285 Length = 308 Score = 162 bits (411), Expect = 8e-45 Identities = 98/300 (32%), Positives = 167/300 (55%), Gaps = 21/300 (7%) Query: 9 ATAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVK-----DGTVQL 63 A+ ALSL+ S A AD K+G ++ QF W+ L+E K DG V+L Sbjct: 8 ASLALSLMFASGAALAD---MKIGVSM----SQFDDTWLTYLRESMDTKAKSYPDG-VKL 59 Query: 64 TVFDGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVAD 123 D D + Q +Q+E+ ++Q+ DAI+ P+DT A +AA+ + ++ N + D Sbjct: 60 QFEDARSDVVRQLSQVESFISQKVDAIVVNPVDTAATKKITEAAVKAGIPLVYVNRRPDD 119 Query: 124 ASVPY----VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGK 179 ++P V ++D+E G++Q Q + +K+ GKG++VI+ G + ++ +R KG EVL K Sbjct: 120 LNLPKGVVTVASNDLEAGQMQMQYLAEKMGGKGDIVILLGDLANNSTTNRTKGVKEVLTK 179 Query: 180 HPDIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSK 239 +P+IKI ++++ W R + + L DWL K + V++ ND+MA+GA AL+ G+ Sbjct: 180 YPNIKIEQEQSGIWSRDKGMTLVNDWLTQGRK-FDAVVSNNDEMAIGAAMALQQAGVAKG 238 Query: 240 DVPVTSIDGMPDAIQAAKKDE-VTTFLQDAQAQSQGALDVALRALAGKDYKPQSVIWERY 298 V + +DG PD + A KK + + QDA+ Q+ G++D A++ + +P +W Y Sbjct: 239 SVLIAGVDGTPDGLNAVKKGSLLVSVFQDAKGQADGSIDTAVKMAKNEPVEP--AVWVPY 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: 263 Number of extensions: 17 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