Align polyol transporter 5 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091483 (539 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 174 bits (440), Expect = 9e-48 Identities = 143/468 (30%), Positives = 223/468 (47%), Gaps = 31/468 (6%) Query: 40 AILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDW 99 A A++ L G+D V++GA+ ++ + +IG + S +G+ AG +D Sbjct: 21 AAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGPLADR 80 Query: 100 IGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASS 159 GR T+ +A + A+ GL L+ R + GIGVG A +IAP Y AEVSPA Sbjct: 81 WGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVSPARV 140 Query: 160 RGFLNSFPEVFINAGIMLGYVSNL--------AFSNLPLKV-GWRLMLGIGAVPSVILAI 210 RG L S ++ I GI +S+ A L L + WR M + VP++I Sbjct: 141 RGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPALIYGS 200 Query: 211 GVLAMPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVS 270 VL +PESPR LV +GR+ +AK+VL + D E L +H G D+ Q S Sbjct: 201 LVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHAL-----QHKLG-------DIAQ-S 247 Query: 271 RRNSHGEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDH 330 R+ + G+ R+L + V+ I + FQQ GI+ + +S ++ + G ++ Sbjct: 248 LRSEYRPGL-RDLR-GSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGF-SES 304 Query: 331 QQLLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKK 390 +V VV LVA L+DRIGR+PLL GM ++L + + S Sbjct: 305 DAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAA 364 Query: 391 VM----WAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSG 446 + W +VA+ YV F + GP+ WV E+FP R+R+ ++ V + Sbjct: 365 LSLPAPWG-MVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANF 423 Query: 447 VISISFLPMSKAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDM 494 +I+ SF P + A+ ++ A V+ VF + ET+G LE+M Sbjct: 424 IITSSF-PALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 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: 703 Number of extensions: 39 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: 472 Length adjustment: 34 Effective length of query: 505 Effective length of database: 438 Effective search space: 221190 Effective search space used: 221190 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