Align sugar transport protein 6 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 187 bits (474), Expect = 9e-52 Identities = 147/491 (29%), Positives = 232/491 (47%), Gaps = 56/491 (11%) Query: 14 EAKMTVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCK 73 E + T V + AA+GG +FG+D + G A+D F Sbjct: 10 EGRATARVVLIAAAAALGGFLFGFDTAVING--AVDAVRGSFGLGAGR------------ 55 Query: 74 YDNQFLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLI---GVGLTAGAVNL 130 + S L + + ++ A + GR TMQ A++ I G GL AG +L Sbjct: 56 -----IGFAVSCALLGSALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDL 110 Query: 131 VMLIIGRLFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTA 190 V+ RL G GVG + P +++E++PA++RG L + QL + +GI A + + + A Sbjct: 111 VLW---RLVGGIGVGVASVIAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLA 167 Query: 191 TVHP----------YGWRIALGGAGIPAVILLFGSLL--IIETPTSLIERNKNEEGKEAL 238 WR A +PA L++GSL+ + E+P L+ + + +E K+ L Sbjct: 168 GTAGGASQKLWLGLEAWRWMFLVAVVPA--LIYGSLVLGVPESPRHLVAKGRMDEAKQVL 225 Query: 239 RKIRGVDDINDEYESIVHACDIASQVKDPYRKLLKPASR------PPFIIGMLLQLFQQF 292 R++ D+ DE+ DIA ++ YR L+ P +G+LL +FQQF Sbjct: 226 RQVL---DLQDEHALQHKLGDIAQSLRSEYRPGLRDLRGSMAGLLPVVWVGILLSVFQQF 282 Query: 293 TGINAIMFYAPVLFQTVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSV 352 GIN I +Y+ L+ +VGF A +V+T +NVL T V I LVDR GR+ LL S Sbjct: 283 VGINVIFYYSSTLWHSVGFSESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSA 342 Query: 353 HMLICQLIIG--IILAKDLGVTGTLGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETF 410 M + ++ A G +L P +V ++ YV+ F SWGP+ W++ E F Sbjct: 343 GMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVALVAANAYVVFFGLSWGPMVWVLLGEMF 402 Query: 411 PLETRSAGFAVAVSCNMFFTFVIAQAF--LSML-CGMRSGIFFFFSGWIIVMGLFAFFFI 467 P R+ AVA + F+I +F LS L G++ FF+ +V +F + Sbjct: 403 PNRIRAIALAVAAAAQWVANFIITSSFPALSELGLSFAYGVYAFFA---LVSLVFVVKAV 459 Query: 468 PETKGIAIDDM 478 ETKG+ +++M Sbjct: 460 RETKGMELEEM 470 Lambda K H 0.329 0.144 0.446 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: 585 Number of extensions: 39 Number of successful extensions: 8 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: 507 Length of database: 472 Length adjustment: 34 Effective length of query: 473 Effective length of database: 438 Effective search space: 207174 Effective search space used: 207174 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 (21.8 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