Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= TCDB::Q1XF07 (519 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 192 bits (488), Expect = 2e-53 Identities = 134/461 (29%), Positives = 228/461 (49%), Gaps = 32/461 (6%) Query: 37 AMLASMTSILLGYDIGVMSGAAIYIKRDLKVSDVKIEILLGIINLY-SLIGSGLAGRTSD 95 A + S+T L G+D V+SGA + +K + SD + + L+ ++IG+ L G Sbjct: 9 AFIVSLTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCH 68 Query: 96 WIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFGRFIAGIGIGYALMIAPVYTAEVSPAS 155 +GR+ T+ + G +F V AL + + + F RF+ G+ IG + + AP Y +E+S A Sbjct: 69 HLGRKNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAY 128 Query: 156 SRGFLTSFPEVFINGGILLGYISNFAFSKLSLKVGWRMMLGVGALPSVILGVGVLAMPES 215 RG ++ I GIL+ Y+SN+ + WR ML +P++I +L +PES Sbjct: 129 QRGRRVGLYQINIVSGILVAYVSNYLLQGVGDHNDWRWMLAAEIIPAIIYLAFILDIPES 188 Query: 216 PRWLVMRGRLGDAIKVLNKTSDSPEEAQLRLADIKRAAGIPESCTDDVVEVSKRSTGEGV 275 PRWL+++ + A + + K + + QL L+ + S RS Sbjct: 189 PRWLILKQKDESAAQKVLKKITTGKIDQLLLS---------------IKHDSLRS----- 228 Query: 276 WKELFLYPTPAIRHIVIAALGIHFFQQASGIDAVVLYSPTIFEKAGIKSDTDKLLATVAV 335 K++ L+ + +A + I F Q SGI+ ++ Y+P I EKAG + T LL V + Sbjct: 229 -KKMKLFSAKNRLPLFLAGI-IAIFNQLSGINFILYYAPEIMEKAGFVT-TTSLLGAVCI 285 Query: 336 GFVKTCFILVATFMLDRIGRRPLLLTSVGGMVLSLLTLGTSLTIIDRSDTKVTWAVGLSI 395 GF F L+ ++D+ GR+ L+L G ++SL + S D S + Sbjct: 286 GFTNLIFTLIGMSLIDKTGRKQLMLIGSMGYIISLGLV--SYGFYDSSSPL------FIL 337 Query: 396 ATVLSYVATFSIGAGPITWVYSSEIFPLRLRAQGCAMGVVVNRVTSGVISMTFLSLSKGI 455 ++L ++A IG G + WV+ SEIFP ++RA G + G V+ + +I++ L + Sbjct: 338 TSILIFIAAHGIGQGAVIWVFISEIFPNKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTL 397 Query: 456 TIGGAFFLFGGIAICGWIFFYTMLPETRGKTLEDMEGSFGQ 496 F +F + I ++F + +PET+G LE++ Q Sbjct: 398 MPFQIFMVFMALMILQFVFVWRYMPETKGLELENLHSKLAQ 438 Lambda K H 0.323 0.140 0.414 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: 580 Number of extensions: 40 Number of successful extensions: 6 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: 519 Length of database: 450 Length adjustment: 34 Effective length of query: 485 Effective length of database: 416 Effective search space: 201760 Effective search space used: 201760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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