Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= TCDB::Q1XF07 (519 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 194 bits (492), Expect = 8e-54 Identities = 154/509 (30%), Positives = 247/509 (48%), Gaps = 78/509 (15%) Query: 32 YAFACAMLASMTSILLGYDIGVMSGAAIYIKRD-LKVSDVKI-EILLGIINLYSLIGSGL 89 Y ++ +A + +L GYD V+SGA ++ L SD + +++ GI + +LIG L Sbjct: 12 YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVL 71 Query: 90 AGRTS----DWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFG-------------RFI 132 G S +GRR ++ A +FF+ AL + P F +G R + Sbjct: 72 GGALSGVFASRLGRRNSLRLAAVLFFLSAL-GSYYPEVLFFEYGKPNMDLLIAFNLYRVL 130 Query: 133 AGIGIGYALMIAPVYTAEVSPASSRGFLTSFPEVFINGGILLGYISNF------------ 180 GIG+G A + P+Y AE++P++ RG L S + I G+L+ Y N+ Sbjct: 131 GGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIIL 190 Query: 181 --AFSKLSLKV---------GWRMMLGVGALPSVILGVGVLAMPESPRWLVMRGRLGDAI 229 A LS+ GWR M G A P+ G+ + +P++PR+LV+ + A Sbjct: 191 KDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAY 250 Query: 230 KVLNKTSDSPEEAQLRLADIKRAAGIPESCTDDVVEVSKRSTGEGVWKELFLYPTPAIRH 289 +L K + ++AQ L DIK +T + ++LF Y Sbjct: 251 TILEKINGK-KKAQEILNDIK-------------------ATAQEKTEKLFTYGVT---- 286 Query: 290 IVIAALGIHFFQQASGIDAVVLYSPTIFEKAGIKSDTDKLLATVAVGFVKTCFILVATFM 349 +++ + + FQQA GI+AV+ Y+P IFE AG ++ ++ TV +G V F LVA F Sbjct: 287 VIVIGILLSVFQQAIGINAVLYYAPRIFENAG--AEGGGMMQTVIMGIVNIIFTLVAIFT 344 Query: 350 LDRIGRRPLLLTSVGGMVLSLLTLGTSLTIIDRSDTKVTWAVGLSIATVLSYVATFSIGA 409 +DR GR+PLL+ GM + + D+ V L + +++ Y A F + Sbjct: 345 VDRFGRKPLLIIGSIGMAVGAFAVAMC-------DSMAIKGV-LPVLSIIVYAAFFMMSW 396 Query: 410 GPITWVYSSEIFPLRLRAQGCAMGVVVNRVTSGVISMTFLSLSKGITIGGAFFLFGGIAI 469 GPI WV SEIFP +R + A+ V + + ++S TF +L + A+ L+G I + Sbjct: 397 GPICWVLISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPAL-YDFSPMFAYSLYGIICV 455 Query: 470 CGWIFFYTMLPETRGKTLEDMEGSFGQSK 498 IF + +PET+GKTLEDM + ++K Sbjct: 456 AAAIFVWRWVPETKGKTLEDMSKLWKKNK 484 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: 601 Number of extensions: 40 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 519 Length of database: 484 Length adjustment: 34 Effective length of query: 485 Effective length of database: 450 Effective search space: 218250 Effective search space used: 218250 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