Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate GFF3853 PGA1_78p00170 putative sn-glycerol-3-phosphate transport system permease protein UgpA
Query= uniprot:D4GP36 (317 letters) >FitnessBrowser__Phaeo:GFF3853 Length = 310 Score = 155 bits (393), Expect = 9e-43 Identities = 88/277 (31%), Positives = 156/277 (56%), Gaps = 11/277 (3%) Query: 41 IPFVLMSIAVY-GGTGYNFAISFTDYEGLGTPDYSTLDLEMYAQALSSDAFIAAAQNNLV 99 +P +L ++ V+ GGT + A SFT L P + + + Y + SS+ ++ + +N L+ Sbjct: 34 VPMILTALVVFMGGTAWTVAHSFTKSRLL--PKWKFVGFDQYERLWSSNRWLISVENLLI 91 Query: 100 LLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVESGIL 159 + + + +G LA LLD IRF F+T++L P +LSFVVT W W+ N + GI Sbjct: 92 YGLCSLVLTMAIGFTLAALLDRKIRFEGAFRTIFLYPFALSFVVTGLAWQWILNPDFGIQ 151 Query: 160 NLVVT----TLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQFEAA 215 N+V + + F+P L NP + V++A +WQ SG+ MV+ LAGL+ I +D ++AA Sbjct: 152 NVVRSWGWESFAFDP---LNNPETVIFGVLIAGLWQGSGFVMVIMLAGLRGIDEDIWKAA 208 Query: 216 RVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDILATL 275 RVDG +T+TY+R+I+P ++ V+A V++ +K + + A P +++ A Sbjct: 209 RVDGIGVTKTYVRVIIPMMRPVFVTALVIIASGIIKLYDLVVAQTNG-GPGISSEVPAKY 267 Query: 276 MVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQY 312 ++ F+ A +TM+L+ + ++ P+ Y ++ Sbjct: 268 VINYMFEAQNLGQGFAASTMMLLSVIIILVPWAYLEF 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: 265 Number of extensions: 17 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: 310 Length adjustment: 27 Effective length of query: 290 Effective length of database: 283 Effective search space: 82070 Effective search space used: 82070 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