Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter
Query= SwissProt::O52733 (457 letters) >NCBI__GCF_001482365.1:WP_058858199.1 Length = 482 Score = 275 bits (704), Expect = 2e-78 Identities = 161/444 (36%), Positives = 260/444 (58%), Gaps = 14/444 (3%) Query: 7 GFVYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPS 66 G + GGLLFGYDTGVI+GA+ + +++ L + +G V S+++ A +GA G Sbjct: 27 GLISIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRI 86 Query: 67 SDRFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAP 126 SD +GRR+ +LL A++FFVG + F+P + L+ R+ LG+AVG ASA++P +LAELAP Sbjct: 87 SDAWGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAP 146 Query: 127 SDKRGTVSSLFQLMVMTGILLAYITNYSFSGFY----TGWRWMLGFAAIPAALLFLGGLI 182 + RG+++ ++ ++ G L A++ N + + WR+M +A+PA LF+G L Sbjct: 147 YEIRGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLR 206 Query: 183 LPESPRFLVKSGHLDEARHVLDTMNKHDQ-VAVNKEINDI--QESAKIVSGGWSELFGKM 239 +PESPR+LV+ G +EA VL ++ ++ VA E+ + +ESA+ G + L K Sbjct: 207 MPESPRWLVEKGRHEEALEVLRSVRSEERAVAELGEVEHVAEEESAENRIGLGAVLRNKW 266 Query: 240 VRPSLIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAV 299 + +++GIGL I QQ+ G N+++YY + + GF SAAL+A+I G+ V+ IA+ Sbjct: 267 LIRIMLVGIGLGIAQQLTGINSIMYYGQIVLIESGFSASAALIANIAPGVIAVVGGFIAL 326 Query: 300 AIMDKIDRKKIVNIG-AVGMGISLFVMSIGMKFSGGSQTAAIISVIALTVYIAFFSATWG 358 A+MD++DR+K IG ++ L + + G+ + + + ++ Sbjct: 327 AMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEEGNPLRPFVILALVVAFVGSMQTFLN 386 Query: 359 PVMWVMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLD---FFGTGSLFIGYGIL 415 +WV + EVFPL++RG G + W AN ++SL FPSL+D GT LF G G+L Sbjct: 387 VAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVDAVGITGTFFLFAGVGVL 446 Query: 416 CFASIWFVQKKVFETRNRSLEDIE 439 ++ FV +V ETR R+LE +E Sbjct: 447 ---ALVFVATQVPETRGRTLEALE 467 Lambda K H 0.327 0.141 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: 572 Number of extensions: 41 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: 457 Length of database: 482 Length adjustment: 33 Effective length of query: 424 Effective length of database: 449 Effective search space: 190376 Effective search space used: 190376 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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