Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_008625717.1 C943_RS06720 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_000330725.2:WP_008625717.1 Length = 469 Score = 297 bits (761), Expect = 4e-85 Identities = 175/463 (37%), Positives = 267/463 (57%), Gaps = 20/463 (4%) Query: 15 KFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQ-TDSLLTGLSVSLALLGSALGAFG 73 K++ +IS AALGGFLFG+D V+ GA + F T G S AL+G +GA Sbjct: 10 KYIWMISLTAALGGFLFGYDWVVVGGAKPFYEPFFNLTSPSEQGWGTSSALVGCMVGAIA 69 Query: 74 AGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIA 133 ++D+ GR K +I+A +LF++S+IG+ L T W F F+R++GGI +G A ++P YIA Sbjct: 70 CIFLSDQFGRKKLLIIAGLLFSISAIGTALAPTFWWFNFYRIVGGIAMGIALNLSPLYIA 129 Query: 134 EVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALM-------AGGSAQNPWLFGAAAWR 186 E+SPAH RG L ++ QL I+ G+ +A L NW I+L+ AG G WR Sbjct: 130 EISPAHKRGTLVTINQLLIMIGVLLAQLINWRISLLDIELPEDAGFQMIAASWSGTFGWR 189 Query: 187 WMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGD-VPSRIEEIQATV 245 WMF E IPA ++ + F +PESPR+LV + ++A IL K+ G S + EIQ + Sbjct: 190 WMFGVEAIPAFVFFLSMFWVPESPRWLVKADRMDEAKKILGKIGGPQYTESALAEIQQNL 249 Query: 246 SLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLL 305 +L+ + + +L +V IG+ LS LQQ+ G+NVI YY++ ++++ GF ++ +L Sbjct: 250 TLEDPNNSGIGVWLKAPILKVVAIGIFLSFLQQWSGVNVIIYYAADIFQAAGFNLKQMML 309 Query: 306 ITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLT 365 V+ G + +L+ + I VD+FGRK LLL+G+ M I ++ F Sbjct: 310 NIVVIGGVMVLSVFITIYTVDRFGRKVLLLIGTSSMAILYLLIGYSFFAE---------Q 360 Query: 366 GAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTT 425 A ++ LV N+ V+S F+ P++WV+L E+F KIR AA+S+AA W+ NF ++ Sbjct: 361 DGASLVVLVLVNVGVYS--FTLAPLLWVVLSEIFPIKIRGAAMSIAALAHWVGNFTLTYF 418 Query: 426 FPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 FP + + +G + LY A F I F + ETKGK+LEQ+ Sbjct: 419 FPVIKENLGWANNFWLYGAICAFGFFVILFVLPETKGKSLEQI 461 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: 618 Number of extensions: 28 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: 468 Length of database: 469 Length adjustment: 33 Effective length of query: 435 Effective length of database: 436 Effective search space: 189660 Effective search space used: 189660 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 Sep 24 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