Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate H281DRAFT_02631 H281DRAFT_02631 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Burk376:H281DRAFT_02631 Length = 300 Score = 116 bits (291), Expect = 6e-31 Identities = 77/245 (31%), Positives = 133/245 (54%), Gaps = 8/245 (3%) Query: 57 NFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLVLLVGFTTICLVLGLFLA 116 + A+SF +++G+ TP + + L Y + +D F A +NNL+ LV F + LGL A Sbjct: 49 SIALSFYNWDGM-TPR-TFIGLANYVELFHADTFYLALKNNLIWLV-FFLLAPPLGLLFA 105 Query: 117 ILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGILNLVVTTLGFNPVDWLGN 176 + L+ I+ ++++ P LS VV ++ W ++ G+L L+V + + LG+ Sbjct: 106 LYLNQQIKGMRVVKSLFFAPFVLSGVVVGLVFSWFYDPAFGLLKLIVG----HGIPVLGD 161 Query: 177 PSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAARVDGASITRTYLRIIVPQLKE 236 P ++ A +W + Y MV+YL GL SI + EAAR++GA +I+PQL+ Sbjct: 162 PRTVTFGIVFAALWPQTPYCMVLYLTGLTSINPEVVEAARMEGAKGWSLLWHVILPQLRP 221 Query: 237 ASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATLMVRRAFKFGEWAYSAAIATML 296 A+ A V+ ++ AL++F + + G P + + +LA M +A K+ YSA+IA +L Sbjct: 222 ATFMAVVLTVIGALRSFDLISVMSGG-GPFDSSTVLAYYMYDQAIKYYREGYSASIAVVL 280 Query: 297 LIMAL 301 + L Sbjct: 281 FAIML 285 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: 240 Number of extensions: 13 Number of successful extensions: 4 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: 300 Length adjustment: 27 Effective length of query: 290 Effective length of database: 273 Effective search space: 79170 Effective search space used: 79170 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