Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 486 bits (1250), Expect = e-142 Identities = 254/456 (55%), Positives = 332/456 (72%), Gaps = 6/456 (1%) Query: 17 VLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAGP 76 V+LI+ AALGGFLFGFDTAVINGAV A++ F + G +VS ALLGSALGA+ AGP Sbjct: 17 VVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGP 76 Query: 77 IADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEVS 136 +ADR GR++TM +AAVL +S++GSGL +WD + WR++GGIGVG ASVIAP YIAEVS Sbjct: 77 LADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVS 136 Query: 137 PAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPA 196 PA +RGRLGSLQQLAIV GIF ALLS+ ++A AGG++Q WL G AWRWMF ++PA Sbjct: 137 PARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWL-GLEAWRWMFLVAVVPA 195 Query: 197 LLYGVCAFLIPESPRYLVAQGQGEKAAAILWKV----EGGDVPSRIEEIQATVSLDHKPR 252 L+YG +PESPR+LVA+G+ ++A +L +V + + ++ +I ++ +++P Sbjct: 196 LIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPG 255 Query: 253 FSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGF 312 DL GLLP+VW+G+ LS QQFVGINVIFYYSS LW SVGF+E + I+V+T Sbjct: 256 LRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSV 315 Query: 313 INILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIA 372 +N+L TLVAIA VD+ GRKPLL +GS GMT+TLG+++ F A +L G++A Sbjct: 316 VNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVA 375 Query: 373 LVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDT 432 LV AN YV FG SWGP+VWVLLGEMF N+IRA AL+VAA QW+ANFII+++FP L + Sbjct: 376 LVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFPALSE- 434 Query: 433 VGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 +GL AYG+YA A +S+ F+ V+ETKG LE+M Sbjct: 435 LGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.325 0.140 0.430 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: 679 Number of extensions: 31 Number of successful extensions: 4 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: 468 Length of database: 472 Length adjustment: 33 Effective length of query: 435 Effective length of database: 439 Effective search space: 190965 Effective search space used: 190965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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