Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= TCDB::Q1XF07 (519 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 233 bits (594), Expect = 1e-65 Identities = 144/472 (30%), Positives = 251/472 (53%), Gaps = 20/472 (4%) Query: 23 PQKKPKRNKYAFACAMLASMTSILLGYDIGVMSGAAIYIKRDLKVSDVKIEILLGIINLY 82 P + + A++A++ +L GYD GV+SGA +++ +L ++ ++ + Sbjct: 15 PNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTSSLLFG 74 Query: 83 SLIGSGLAGRTSDWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFGRFIAGIGIGYALM 142 + G+ L+G ++ GR+ I++ +F +GA+ +P+ +++F R I G+ +G A Sbjct: 75 AAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAVGGAAA 134 Query: 143 IAPVYTAEVSPASSRGFLTSFPEVFINGGILLGYISNFAFSKL-SLKVGWRMMLGVGALP 201 PVY AE++PA+ RG L + E+ I G LL YISN F ++ + WR ML V LP Sbjct: 135 TVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLAVATLP 194 Query: 202 SVILGVGVLAMPESPRWLVMRGRLGDAIKVLNKTSDSPEEAQLRLADIKRAAGIPESCTD 261 +V+L G++ MP+SPRW M+GRL +A +VL +T ++ + L +I T+ Sbjct: 195 AVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHK-DDVEWELLEI----------TE 243 Query: 262 DVVEVSKRSTGEGVWKELFLYPTPAIRHIVIAALGIHFFQQASGIDAVVLYSPTIFEKAG 321 + E +R+ G+ + E+ TP + + + +GI QQ +G++ ++ Y+PT+ G Sbjct: 244 TLDE--QRNLGKPRFSEIM---TPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVG 298 Query: 322 IKSDTDKLLATVAVGFVKTCFILVATFMLDRIGRRPLLLTSVGGMVLSLLTLGTSLTIID 381 + +D L AT+A G V V +ML +IGRRP+ + G L+ +G ++ Sbjct: 299 M-TDNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLP 357 Query: 382 RSDTKVTWAVG--LSIATVLSYVATFSIGAGPITWVYSSEIFPLRLRAQGCAMGVVVNRV 439 + A+ + +A +L +++ P+TW+ SEIFP RLR V + Sbjct: 358 ETVNGQPDALRAYMVLAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWI 417 Query: 440 TSGVISMTFLSLSKGITIGGAFFLFGGIAICGWIFFYTMLPETRGKTLEDME 491 + +IS+ F L + + G FF+F GI + G IF +PETR ++LE +E Sbjct: 418 ANFLISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIE 469 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: 663 Number of extensions: 49 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: 499 Length adjustment: 34 Effective length of query: 485 Effective length of database: 465 Effective search space: 225525 Effective search space used: 225525 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