Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Koxy:BWI76_RS23380 Length = 296 Score = 127 bits (318), Expect = 4e-34 Identities = 81/245 (33%), Positives = 133/245 (54%), Gaps = 7/245 (2%) Query: 57 NFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLVGFTT-ICLVLGLFL 115 +F +SFT+Y+ + P ++ +E Y L+ D + V T + L L + Sbjct: 30 SFFLSFTEYDLMSPPVFN--GIENYRYMLTEDGLFWKSMGVTFAYVFLTIPLKLAFALGI 87 Query: 116 AILLDHGIRFSEKFQTVYLLPMSL-SFVVTAQLWLWMFNVESGILNLVVTTLGFNPVDWL 174 A +L+ +R F+T Y +P L S V A LW +F ++ G+LN + LGF+PV+WL Sbjct: 88 AFVLNFKLRGIGFFRTAYYIPSILGSSVAIAVLWRALFAID-GLLNSFIGVLGFDPVNWL 146 Query: 175 GNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGASITRTYLRIIVPQL 234 G PS+AL +V L +WQF G MV++LA LQ++P Q+EAA +DGAS + ++++ VP + Sbjct: 147 GEPSLALMSVTLLRVWQF-GSAMVIFLAALQNVPQSQYEAAMIDGASKWQMFMKVTVPLI 205 Query: 235 KEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAFKFGEWAYSAAIAT 294 ++ A + FT Y + G P T + + + AFK+ + Y AA+A Sbjct: 206 TPVIFFNFIMQTTQAFQEFTGPYVITGG-GPTYSTYLFSLYIYDTAFKYFDMGYGAALAW 264 Query: 295 MLLIM 299 +L ++ Sbjct: 265 VLFLV 269 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: 299 Number of extensions: 21 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: 317 Length of database: 296 Length adjustment: 27 Effective length of query: 290 Effective length of database: 269 Effective search space: 78010 Effective search space used: 78010 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