Align sugar transport protein 13 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091463 (526 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 188 bits (478), Expect = 3e-52 Identities = 151/494 (30%), Positives = 233/494 (47%), Gaps = 52/494 (10%) Query: 13 VEFEAKITPIVIISCIMAATGGLMFGYDVGVSGGVTSMPDFLEKFFPVVYRKVVAGADKD 72 VE E + T V++ AA GG +FG+D V G V GA + Sbjct: 7 VEGEGRATARVVLIAAAAALGGFLFGFDTAVINGAVD----------AVRGSFGLGAGR- 55 Query: 73 SNYCKYDNQGLQLFTSSLYLAGLTATFFASYTTRTLGRRLTMLIAGVFFII---GVALNA 129 + S L ++A GR TM +A V I G L A Sbjct: 56 ----------IGFAVSCALLGSALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVA 105 Query: 130 GAQDLAMLIAGRILLGCGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLV 189 G DL + R++ G GVG A+ P +++E++P R+RG L L QL + +GI A L Sbjct: 106 GVWDLVLW---RLVGGIGVGVASVIAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLS 162 Query: 190 NYGTAKIKGGWGWRLSLGL---------AGIPALLLTVGALLVTETPNSLVERGRLDEGK 240 + A GG +L LGL A +PAL+ L V E+P LV +GR+DE K Sbjct: 163 DAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPALIYGSLVLGVPESPRHLVAKGRMDEAK 222 Query: 241 AVLRRIRGTDNVEPEFADLLEASRLAKEVKHPFRNLLQRRNR------PQLVIAVALQIF 294 VLR++ +++ E A + +A+ ++ +R L+ P + + + L +F Sbjct: 223 QVLRQVL---DLQDEHALQHKLGDIAQSLRSEYRPGLRDLRGSMAGLLPVVWVGILLSVF 279 Query: 295 QQCTGINAIMFYAPVLFSTLGFGSDASLYSAVVTGAVNVLSTLVSIYSVDKVGRRVLLLE 354 QQ GIN I +Y+ L+ ++GF + +VVT VNVL TLV+I VD++GR+ LL Sbjct: 280 QQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAI 339 Query: 355 AGVQMFFSQVVIAIILGVKV-TDTSTNLSKGFAILVVVMICTYVAAFAWSWGPLGWLIPS 413 M + ++A + + +L + ++ +V YV F SWGP+ W++ Sbjct: 340 GSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVALVAANAYVVFFGLSWGPMVWVLLG 399 Query: 414 ETFPLETRSAGQSVTVCVNLLFTFIIAQAF--LSML-CHFKFGIFIFFSAWVLIMSVFVM 470 E FP R+ +V + FII +F LS L F +G++ FF+ L+ VFV+ Sbjct: 400 EMFPNRIRAIALAVAAAAQWVANFIITSSFPALSELGLSFAYGVYAFFA---LVSLVFVV 456 Query: 471 FLLPETKNIPIEEM 484 + ETK + +EEM Sbjct: 457 KAVRETKGMELEEM 470 Lambda K H 0.326 0.141 0.425 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: 594 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 526 Length of database: 472 Length adjustment: 34 Effective length of query: 492 Effective length of database: 438 Effective search space: 215496 Effective search space used: 215496 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