Align polyol transporter 5 (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter
Query= CharProtDB::CH_091483 (539 letters) >NCBI__GCF_001482365.1:WP_058858199.1 Length = 482 Score = 224 bits (571), Expect = 6e-63 Identities = 142/459 (30%), Positives = 233/459 (50%), Gaps = 22/459 (4%) Query: 40 AILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDW 99 +I+A +L GYD GV++GA+ + +L + G++ SL + +G+ + GR SD Sbjct: 30 SIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDA 89 Query: 100 IGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASS 159 GRR TI+L +FF G +++ +PNY L+ GR G+ VG A + PV+ AE++P Sbjct: 90 WGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEI 149 Query: 160 RGFLNSFPEVFINAGIMLGYVSNLAFSNLPL--KVGWRLMLGIGAVPSVILAIGVLAMPE 217 RG + EV I G + +V N N+ + WR M I A+P+V L +G+L MPE Sbjct: 150 RGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPE 209 Query: 218 SPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHGE 277 SPRWLV +GR +A VL ++ S A L +++H A + S N G Sbjct: 210 SPRWLVEKGRHEEALEVL-RSVRSEERAVAELGEVEHVA----------EEESAENRIGL 258 Query: 278 GVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLATV 337 G + + R+M+ IG+ QQ +GI++++ + + +G L+A + Sbjct: 259 GA-----VLRNKWLIRIMLVGIGLGIAQQLTGINSIMYYGQIVLIESGFSAS-AALIANI 312 Query: 338 AVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVVV 397 A GV+ +A ++DR+ RR + +G + ++++ V Sbjct: 313 APGVIAVVGGFIALAMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEEGNP---LRPFV 369 Query: 398 AIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMSK 457 +A V+ +V + WVY SE+FPL +R G + + V +GV+S+ F + Sbjct: 370 ILALVVAFVGSMQTFLNVAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVD 429 Query: 458 AMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDE 496 A+ G F+LF G+ +A VF T +PET+GR LE ++E Sbjct: 430 AVGITGTFFLFAGVGVLALVFVATQVPETRGRTLEALEE 468 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: 706 Number of extensions: 38 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: 482 Length adjustment: 34 Effective length of query: 505 Effective length of database: 448 Effective search space: 226240 Effective search space used: 226240 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