Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 276 bits (707), Expect = 8e-79 Identities = 159/455 (34%), Positives = 258/455 (56%), Gaps = 20/455 (4%) Query: 23 VILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGF 82 V+LI+ AA LGG L+G+DTAVI+GA+ ++ + L G +S ++G +G +G Sbjct: 17 VVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGP 76 Query: 83 LSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAA 142 L+DR+GR + + AA+L AISA+ S L V L++ R++GG+G+G+ S ++ TYI E + Sbjct: 77 LADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVS 136 Query: 143 PPAIRGSLSSLYQLFTILGISATYFIN--LAVQRSGTYE--WGVHTGWRWMLAYGMVPSV 198 P +RG L SL QL +LGI A + LA G + W WRWM +VP++ Sbjct: 137 PARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPAL 196 Query: 199 IFFLVLLVVPESPRWLAKAGKTNEALKILTRI---NGETVAKEELKNIENSLKIEQMGSL 255 I+ ++L VPESPR L G+ +EA ++L ++ E + +L +I SL+ E L Sbjct: 197 IYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPGL 256 Query: 256 SQL--FKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVV 313 L GL + +GILL++F Q +G+N I YY ++ +GF ++ F + + VV Sbjct: 257 RDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSVV 316 Query: 314 EVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILI----------GTSFYFELTSGIMMI 363 V+ T++A+ L+D++GRK L++IGSA M + + L+ G + G++ + Sbjct: 317 NVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVAL 376 Query: 364 VLILGFVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSF 423 V +V F +S GP+ W+++ E+FPN +RA A +A W AN+ I P + Sbjct: 377 VAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFP-ALSEL 435 Query: 424 GLAYTFWIFAVINILCFLFVVTICPETKNKSLEEI 458 GL++ + ++A ++ +FVV ETK LEE+ Sbjct: 436 GLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.327 0.142 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: 523 Number of extensions: 27 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: 464 Length of database: 472 Length adjustment: 33 Effective length of query: 431 Effective length of database: 439 Effective search space: 189209 Effective search space used: 189209 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: 51 (24.3 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