Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_013644894.1 METBO_RS06515 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_000191585.1:WP_013644894.1 Length = 453 Score = 307 bits (786), Expect = 5e-88 Identities = 167/455 (36%), Positives = 277/455 (60%), Gaps = 24/455 (5%) Query: 16 FVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAG 75 FV+L++ + ++GG LFG+DT VI+GA+ +++ F + ++VS L+G+ +GA +G Sbjct: 13 FVILVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISG 72 Query: 76 PIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEV 135 +ADR+GR ++LA+++F + +I S + + I RV+ GI +G AS I P YIAEV Sbjct: 73 ILADRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEV 132 Query: 136 SPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIP 195 +P ++RG L SL QLAI GI I+ + + + A GS WRWM +IP Sbjct: 133 APINIRGALVSLNQLAITLGIVISYMVDLYFA--PNGS-----------WRWMLGLAVIP 179 Query: 196 ALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGD-VPSRIEEIQATVSLDHKPRFS 254 +L+ + F +P SPR+L+++G KA A+L K+ G D V + EI+ T+ L+++ ++S Sbjct: 180 SLILALGMFFMPPSPRWLISKGFESKAVAVLKKIRGIDNVDKEVNEIEQTLLLENEGKWS 239 Query: 255 DLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGF-TEEKSLLITVITGFI 313 DLL + + + IG+GL+A QQ GIN + YY+ + G T ++ TV G + Sbjct: 240 DLLEPK--IRSALIIGIGLAAFQQLTGINTVIYYAPTILEFAGLQTATVTIFATVGIGVV 297 Query: 314 NILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIAL 373 N+L T+V+I +D+ GR+PLLL G GM ++LGI+ + F ++ P LT + G +A+ Sbjct: 298 NVLLTVVSILLIDRLGRRPLLLAGITGMIVSLGIMGLAF----II---PGLTSSLGWLAV 350 Query: 374 VTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDTV 433 + LYV SF S GPI W+++ E++ +IR A+S+ + W N +++ TF +++ + Sbjct: 351 ICLMLYVGSFAISLGPIFWLMIAEIYPLRIRGRAMSIVTMINWATNLVVAITFLTIIELL 410 Query: 434 GLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 G + LY A +S+ F+++ V ETKGK+LE++ Sbjct: 411 GASGTFWLYGVIAVLSLLFVYYRVPETKGKSLEEI 445 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: 544 Number of extensions: 36 Number of successful extensions: 7 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: 453 Length adjustment: 33 Effective length of query: 435 Effective length of database: 420 Effective search space: 182700 Effective search space used: 182700 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