Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate AZOBR_RS00070 AZOBR_RS00070 glycerol-3-phosphate transporter permease
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__azobra:AZOBR_RS00070 Length = 294 Score = 100 bits (248), Expect = 6e-26 Identities = 67/227 (29%), Positives = 113/227 (49%), Gaps = 3/227 (1%) Query: 78 LEMYAQALSSDAFIAAAQNNLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPM 137 LE + LS ++ + +V T + L L LA++ D IR + ++T+ + P Sbjct: 55 LENFQAVLSDPNYLETVKTTIVFSASVTVLSLASALGLAVMADSKIRAASAYKTLLIWPY 114 Query: 138 SLSFVVTAQLWLWMFNVESGILNLVVTTLGFNPVDWLGNPSIALGAVILALIWQFSGYTM 197 +L+ V A LW+++FN + GIL + LG+ D+ N AL VILA W+ Y Sbjct: 115 ALAPAVAAVLWMFIFNPDIGILGRALNNLGY-AWDYRLNDGQALTMVILAASWKQVSYNF 173 Query: 198 VVYLAGLQSIPDDQFEAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFA-LKAFTFL 256 + +LAGLQ+IP EAA +DGA R + I P L + VV +V+A + F + Sbjct: 174 IFFLAGLQAIPRSVLEAASIDGAGAVRRFWTITFPLLSPTTFFLLVVNIVYAFFETFGTI 233 Query: 257 YALVGRYRPPNGTDILATLMVRRAFKFGEWAYSAAIATMLLIMALGV 303 +AL P T+ L + + + S+A + +L+++ + + Sbjct: 234 HALT-HGGPGKATETLIFRVYQDGVVNHDLGGSSAQSVILMVIVIAL 279 Lambda K H 0.326 0.140 0.424 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: 238 Number of extensions: 16 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: 317 Length of database: 294 Length adjustment: 27 Effective length of query: 290 Effective length of database: 267 Effective search space: 77430 Effective search space used: 77430 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 (21.6 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