Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate H281DRAFT_00167 H281DRAFT_00167 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Burk376:H281DRAFT_00167 Length = 312 Score = 144 bits (363), Expect = 3e-39 Identities = 89/279 (31%), Positives = 145/279 (51%), Gaps = 19/279 (6%) Query: 42 PFVLMSIA-VYGGTGYNFAISFTDYEGLGT----PDYSTLDLEMYAQALSSDAFIAAAQN 96 P V++S+ VYG I+ T Y L P Y + L+ Y + +D F +A N Sbjct: 36 PSVVISLVFVYG------FIAITGYLSLSNSRLMPRYEFVGLDRYRELFDNDVFWTSAAN 89 Query: 97 NLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVES 156 + F IC+ LGLFLAILLD IR + V+L PM+LSF+VT W W+ Sbjct: 90 LGWFGIPFIGICIGLGLFLAILLDQQIRNEGALRAVFLYPMALSFIVTGTAWQWIMTPSI 149 Query: 157 GILNLVV----TTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQF 212 G+ + T+ F+ WLG+P A+ V++A +WQ +G+ M ++LAGL+ + + F Sbjct: 150 GLEKVFHDWGWTSFSFS---WLGDPDKAIFCVVIAAVWQSTGFVMALFLAGLRGVDGEIF 206 Query: 213 EAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDIL 272 +AA++DGA++ Y +I++P ++ S ++L +K F + AL P + + Sbjct: 207 KAAQMDGANLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLVVALTAG-GPGTSSSLP 265 Query: 273 ATLMVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQ 311 A M +F G+ AA + M+L + V+ P +Y + Sbjct: 266 AIFMYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLE 304 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: 245 Number of extensions: 13 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: 312 Length adjustment: 27 Effective length of query: 290 Effective length of database: 285 Effective search space: 82650 Effective search space used: 82650 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