Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate BPHYT_RS16105 BPHYT_RS16105 mannitol ABC transporter permease
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS16105 Length = 291 Score = 172 bits (435), Expect = 1e-47 Identities = 90/257 (35%), Positives = 145/257 (56%), Gaps = 2/257 (0%) Query: 16 LIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIA 75 L+ + FP +WM T+ KT+ A + +I PTL ++RE NS++I+ Sbjct: 37 LVALLLFFPIFWMTITAFKTEQQAYASSLFFI--PTLDSFREVFARSNYFSFAWNSILIS 94 Query: 76 ISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDK 135 T L L+L VPAA+A+A F R + + W ++ +M+ + + +P +L+ +N GLLD Sbjct: 95 AGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGLLDS 154 Query: 136 HITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAV 195 L+++Y NLPI +W+ F IP D+ EA R++GA+ + + + +P+++PG+A Sbjct: 155 VSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPGLAS 214 Query: 196 SAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLIFA 255 +A+ I SWNE + + L+ S A S+ L + K+ A S L V P+LI Sbjct: 215 TALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPILIVG 274 Query: 256 LIASKQLVRGLTMGAVK 272 ++ KQLVRGLT GAVK Sbjct: 275 WLSQKQLVRGLTFGAVK 291 Lambda K H 0.331 0.143 0.431 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: 11 Number of successful extensions: 2 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: 272 Length of database: 291 Length adjustment: 26 Effective length of query: 246 Effective length of database: 265 Effective search space: 65190 Effective search space used: 65190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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