Align polyol transporter 5 (characterized)
to candidate WP_019614605.1 G327_RS0109855 sugar porter family MFS transporter
Query= CharProtDB::CH_091483 (539 letters) >NCBI__GCF_000381745.1:WP_019614605.1 Length = 466 Score = 224 bits (571), Expect = 5e-63 Identities = 146/481 (30%), Positives = 244/481 (50%), Gaps = 44/481 (9%) Query: 31 KRNNYAFACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGS 90 K N I+ ++ +L GYD V+SGA + ++ ++G A S + IG+ Sbjct: 2 KDNINVLHVTIVVALGGLLFGYDTAVISGATGSLTHFFGLSATELGFAASSALVGCFIGA 61 Query: 91 CAAGRTSDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVY 150 AG+ SD +GRR + +A +F AI + NY +F R + GIGVG A M++P+Y Sbjct: 62 LVAGKISDSMGRRGALKIAATLFLISAIGTAVPDNYWVFVFFRIVGGIGVGIASMVSPMY 121 Query: 151 TAEVSPASSRGFLNSFPEVFINAGIMLGYVSN----LAFSNLPLK-VGWRLMLGIGAVPS 205 AEV+P + RG L S + I G+++ Y N LA + + L VGWR M +P+ Sbjct: 122 IAEVAPPNKRGALVSCNQFAIIFGMLVVYFVNYGIALAGTEVWLNTVGWRYMFASECIPA 181 Query: 206 VILAIGVLAMPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHA-AGIPADCHD 264 ++ + + +PE+PRWL ++GR +A+ +L A + EDI+ GI + D Sbjct: 182 LLFLVLLFTVPETPRWLALKGRNQEARNLL--------RALNKNEDIEEQWQGIQSSLGD 233 Query: 265 DVVQVSRRNSHGEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTA 324 +VS + V++ I + QQ +GI+ + ++P IFK+ Sbjct: 234 TKGKVS---------------IAALGMMGVLVIGIMLSVLQQVTGINVFLYYAPEIFKSF 278 Query: 325 GLKTDHQQLLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTII 384 + LL T+ +G V +F +A F +D+ GRRPL++ G M +S+ A+GT+ Sbjct: 279 SDSSTDTALLQTILIGAVNLTFTAIAIFTVDKFGRRPLMIIGAGAMAVSMIAIGTA---- 334 Query: 385 DQSEKKVMWAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVT 444 + + ++ V+ Y+A F++ GP+TWV SEIFP +RS+ S+ V Sbjct: 335 --AYSNAIGGYLLFF--VLLYIAAFALSLGPVTWVLLSEIFPNSIRSKALSIAVFAQWFA 390 Query: 445 SGVISISFLPMS-------KAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDEL 497 + V+S SF M+ + G F+L+G F + F+PET+G+ LED++++ Sbjct: 391 NFVVSQSFPMMNDSNGYLFQTYNGGFPFWLYGFFGVFTVYFIWKFVPETKGKSLEDLEKI 450 Query: 498 F 498 + Sbjct: 451 W 451 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: 696 Number of extensions: 41 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: 466 Length adjustment: 34 Effective length of query: 505 Effective length of database: 432 Effective search space: 218160 Effective search space used: 218160 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 24 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