Align Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= TCDB::AGG19156.1 (491 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 186 bits (471), Expect = 2e-51 Identities = 151/496 (30%), Positives = 234/496 (47%), Gaps = 81/496 (16%) Query: 4 ILLGYDIGVMSGAAIYIEKD-LKVTDTQI-EILLGILNLYSLIGSAMAGRTS----DWVG 57 +L GYD V+SGA +E L +D Q +++ GI + +LIG + G S +G Sbjct: 25 LLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVLGGALSGVFASRLG 84 Query: 58 RRYTIVISGAIFFTGAILMGLSTNYTFLMCG-------------RFVAGLGVGYALTIAP 104 RR ++ ++ +FF A L F G R + G+GVG A + P Sbjct: 85 RRNSLRLAAVLFFLSA-LGSYYPEVLFFEYGKPNMDLLIAFNLYRVLGGIGVGLASAVCP 143 Query: 105 VYAAEVSPASSRGFLTSFPEVFVNVGILLGYISNYAF----------------------- 141 +Y AE++P++ RG L S + + G+L+ Y NY Sbjct: 144 MYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIILKDAAGVLSVSAES 203 Query: 142 SFCALDLGWRLMLGVGAIPSVILAIGVLAMPESPRWLVMQGRLGDARQVLDKTSDSKEES 201 + GWR M G A P+ + + +P++PR+LV+ + A +L+K + K+ Sbjct: 204 DMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAYTILEKINGKKKAQ 263 Query: 202 MLRLADIKEAAGIPEDCNDDIVQVTGHSHGEGVWKELFVHP-TPTVLHILIAALGFHFFQ 260 + L DIK A + ++LF + T V+ IL++ FQ Sbjct: 264 EI-LNDIKATA-------------------QEKTEKLFTYGVTVIVIGILLSV-----FQ 298 Query: 261 QASGIDALVLYSPRVFEKAGITSSDQLLLCTVGVGLSKTVFTLVATFFLDRVGRRPLLLT 320 QA GI+A++ Y+PR+FE AG ++ TV +G+ +FTLVA F +DR GR+PLL+ Sbjct: 299 QAIGINAVLYYAPRIFENAGAEGGG--MMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLII 356 Query: 321 SMAGMVVSLVCLGTSLTIVDQHEGARMTWAVVLCLFCVLAFVGFFSTGIGPIAWVYSSEI 380 GM V ++ + D M VL + ++ + FF GPI WV SEI Sbjct: 357 GSIGMAVGAF----AVAMCDS-----MAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEI 407 Query: 381 FPLRLRAQGCGMGVAVNRVMSGILSMTFISLYKAITMGGAFFLYAAIGAVGWIFFFTMLP 440 FP +R + + VA + + I+S TF +LY M A+ LY I IF + +P Sbjct: 408 FPNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDFSPM-FAYSLYGIICVAAAIFVWRWVP 466 Query: 441 ETQGRTLEDMEVLFGK 456 ET+G+TLEDM L+ K Sbjct: 467 ETKGKTLEDMSKLWKK 482 Lambda K H 0.326 0.141 0.428 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: 652 Number of extensions: 44 Number of successful extensions: 8 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: 484 Length adjustment: 34 Effective length of query: 457 Effective length of database: 450 Effective search space: 205650 Effective search space used: 205650 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