Align D-xylose-proton symporter (characterized)
to candidate BWI76_RS10225 BWI76_RS10225 MFS transporter
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Koxy:BWI76_RS10225 Length = 483 Score = 310 bits (795), Expect = 5e-89 Identities = 167/490 (34%), Positives = 283/490 (57%), Gaps = 41/490 (8%) Query: 6 NSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASAL 65 N Y+ I +A++ G++ GYD +VISG ++ L ++LS + A S G+ V++ + Sbjct: 7 NVPYLIFICAIASVSGIILGYDASVISGVIDPLT------EHLSLTPAQS--GWAVSNVI 58 Query: 66 IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125 +GCI+G G ++RFGR+ +L I A+LF IS +GSA LA Sbjct: 59 LGCIVGAWGVGRFTDRFGRKATLIITAILFAISAIGSA------------------LAND 100 Query: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFI 185 + FV+YR+IGG+ VG+AS ++P+YIAE++P +RG+++ Q ++ GQL+VY VNY I Sbjct: 101 LTWFVVYRMIGGLAVGMASAVTPLYIAEVSPKDLRGRMLGMQQMLMVGGQLVVYIVNYLI 160 Query: 186 ARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG 245 AR W+ + GWR+M AS IP +LFL++++ +PESPRW R ++E++ +L + Sbjct: 161 ARGMAHEWVVSIGWRWMLASALIPCVLFLVMVFFMPESPRWYAMRNQKEKSLKVLTSLSN 220 Query: 246 NTLATQAVQEIKHSLDHGRKTGGRLLMFGVG-----------VIVIGVMLSIFQQFVGIN 294 A + EI+ S+ T LL ++ IG +++ QQ GIN Sbjct: 221 PGHAERLYAEIRTSI----ATDSALLSIPTPRGILRDKKSSYILWIGCAIAVLQQVSGIN 276 Query: 295 VVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAI 354 +++Y+AP + + + +T ++ Q+I +G+ L +A++ D+ GR PL G+LG A Sbjct: 277 ILMYFAPSLLQNVTGNTQDSMFQSIFLGLALLAGVSIALVAFDRIGRLPLLRWGSLGCAA 336 Query: 355 GMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAA 414 + AF + G + ++ ++ ++ F MSW W+L+SEIFPN +R A+ A + Sbjct: 337 FLLFTSWAFMNEVKGYLPIVGLVGFIFVFGMSWSLGAWLLISEIFPNRMRAVAMGYAFCS 396 Query: 415 QWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEEL 474 W++N+ V+ +FPMM++N L+ HFH F + ++A F+ +F+PETKG +LE + Sbjct: 397 MWVSNFIVTQSFPMMNRNPVLMEHFHGAFPLLLCSGFSIIAFWFVGRFLPETKGVSLENI 456 Query: 475 EALWEPETKK 484 E L ++++ Sbjct: 457 EPLMLSKSRR 466 Lambda K H 0.326 0.140 0.433 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: 636 Number of extensions: 35 Number of successful extensions: 5 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: 491 Length of database: 483 Length adjustment: 34 Effective length of query: 457 Effective length of database: 449 Effective search space: 205193 Effective search space used: 205193 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 (21.7 bits) S2: 52 (24.6 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