Align polyol transporter 5 (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= CharProtDB::CH_091483 (539 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 230 bits (586), Expect = 1e-64 Identities = 139/479 (29%), Positives = 252/479 (52%), Gaps = 28/479 (5%) Query: 21 PESVLPAKPPKRNNYAFACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAG 80 P S P P + A++A++ +L GYD GV+SGA++++ +L + G++ Sbjct: 15 PNSETPTTP-----FVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTS 69 Query: 81 SLNIYSLIGSCAAGRTSDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGV 140 SL + G+ +G ++ GR+ I+ +F GAI ++P+ +++F R I G+ V Sbjct: 70 SLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAV 129 Query: 141 GYALMIAPVYTAEVSPASSRGFLNSFPEVFINAGIMLGYVSNLAFSNL-PLKVGWRLMLG 199 G A PVY AE++PA+ RG L + E+ I +G +L Y+SN F + + WR ML Sbjct: 130 GGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLA 189 Query: 200 IGAVPSVILAIGVLAMPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIP 259 + +P+V+L G++ MP+SPRW M+GRL +A+RVL++T +H + Sbjct: 190 VATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERT--------------RHKDDVE 235 Query: 260 ADCHDDVVQVSRRNSHGEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPR 319 + + + + + G+ + E++ TP + ++ + IGI QQ +G++ ++ ++P Sbjct: 236 WELLEITETLDEQRNLGKPRFSEIM---TPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPT 292 Query: 320 IFKTAGLKTDHQQLLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGT 379 + + G+ TD+ L AT+A GVV V ++L +IGRRP+ + G L +G Sbjct: 293 VLTSVGM-TDNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGA 351 Query: 380 SLTIIDQS---EKKVMWAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSM 436 ++ ++ + + A +V +A ++ +++ P+TW+ SEIFP RLR Sbjct: 352 VSYLLPETVNGQPDALRAYMV-LAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGG 410 Query: 437 GVVVNRVTSGVISISFLPMSKAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMD 495 V + + +IS+ F + + G F++F GI +F +PET+ R LE ++ Sbjct: 411 AVFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIE 469 Lambda K H 0.322 0.137 0.410 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: 782 Number of extensions: 48 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: 539 Length of database: 499 Length adjustment: 35 Effective length of query: 504 Effective length of database: 464 Effective search space: 233856 Effective search space used: 233856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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