Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16105 (291 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 138 bits (348), Expect = 1e-37 Identities = 85/269 (31%), Positives = 143/269 (53%), Gaps = 19/269 (7%) Query: 32 GVIAWLVALLLFFPIFWMTITAFKTEQQAYASSLFFI------PTLDSFREVFARSNYFS 85 G++AW V FP W +T+ K S+LF + P+L ++ +F + Sbjct: 18 GIVAWAV-----FPFAWAIVTSLKA-----GSALFTVEAWPSQPSLANYAAIFKEQPFGR 67 Query: 86 FAWNSILISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLL 145 NS+L ++ V L L LAV AAYA+ R +L +L M P V VL ++ L Sbjct: 68 NILNSLLAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFEL 127 Query: 146 WKNSGLLDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLM 205 + GL + + LV+ Y + LP VW+ T+ E+P+++ EA +DGA + + + + Sbjct: 128 VRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFL 187 Query: 206 PMSLPGLASTALLLVILSWNEAFWSINLSSSNAA---PLTVFIASYSSPEGLFWAKLSAA 262 P+ P LA+T LL I +WNE +++ + ++ A P+ + + S +S L W ++ AA Sbjct: 188 PLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAA 247 Query: 263 SLLAVAPILIVGWLSQKQLVRGLTFGAVK 291 S++ P++ + L Q+++V GLT GAVK Sbjct: 248 SVVVTVPLIGLVLLFQRRIVSGLTAGAVK 276 Lambda K H 0.326 0.136 0.421 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: 252 Number of extensions: 14 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: 291 Length of database: 277 Length adjustment: 26 Effective length of query: 265 Effective length of database: 251 Effective search space: 66515 Effective search space used: 66515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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