Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate BPHYT_RS05030 BPHYT_RS05030 sugar ABC transporter permease
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__BFirm:BPHYT_RS05030 Length = 312 Score = 143 bits (361), Expect = 5e-39 Identities = 87/276 (31%), Positives = 141/276 (51%), Gaps = 18/276 (6%) Query: 44 VLMSIAVYGGTGYNFAISFTDYEGLGT----PDYSTLDLEMYAQALSSDAFIAAAQNNLV 99 V+ I VYG I+ T Y L P Y + L+ Y + +D F +A N Sbjct: 39 VISLIFVYG------FIAITGYLSLSNSRLMPRYEFVGLDRYRELFDNDVFWTSAANLGW 92 Query: 100 LLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGIL 159 + F +C+ LGLFLAILLD IR + V+L PM+LSF+VT W W+ G+ Sbjct: 93 FGIPFIGVCIGLGLFLAILLDQQIRNEGALRAVFLYPMALSFIVTGTAWQWIMTPSIGLE 152 Query: 160 NLVV----TTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAA 215 + T+ F+ WLG+P A+ V++A +WQ +G+ M ++LAGL+ + + F+AA Sbjct: 153 KVFHDWGWTSFSFS---WLGDPDKAIFCVVIAAVWQSTGFVMALFLAGLRGVDGEIFKAA 209 Query: 216 RVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATL 275 ++DGA + Y +I++P ++ S ++L +K F + AL P + + A Sbjct: 210 QMDGAGLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLVVALTAG-GPGTSSSLPAIF 268 Query: 276 MVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQ 311 M +F G+ AA + M+L + V+ P +Y + Sbjct: 269 MYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLE 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: 247 Number of extensions: 14 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