Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_066601288.1 V473_RS05365 sugar porter family MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_001046645.1:WP_066601288.1 Length = 470 Score = 426 bits (1095), Expect = e-124 Identities = 229/465 (49%), Positives = 313/465 (67%), Gaps = 5/465 (1%) Query: 8 SQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGS 67 S N+ FV I VA +GGF+FG+D+ VING L+ F L G++V L+GS Sbjct: 5 SAEKVNMAFVAAIVAVATIGGFMFGYDSGVINGTQKGLEAAFDLGKLGIGVNVGAILVGS 64 Query: 68 ALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVI 127 ++GAFGAG +AD GR M+L+A+LF S++ +G + FIF R++GG+GVGAASVI Sbjct: 65 SIGAFGAGRMADIIGRRGVMMLSAILFLGSALLAGAAGSSAIFIFARIIGGLGVGAASVI 124 Query: 128 APAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRW 187 +P YI+EV+PA++RGRL S+QQ+ I+SG+ A ++N+ +A AGGS WL AWRW Sbjct: 125 SPVYISEVTPANVRGRLSSVQQVMIISGLTGAFIANFVLARYAGGSTAPLWL-DYPAWRW 183 Query: 188 MFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGG-DVPSRIEEIQATVS 246 MFW + IPA +Y + IPESPRYLVA+G+ A A+L ++ G + ++ EI+A++S Sbjct: 184 MFWLQAIPAAIYFLALLAIPESPRYLVARGRDADALAVLTRLFGSLEAARKVGEIRASLS 243 Query: 247 LD-HKPRFSDLLSR-RGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSL 304 D H+P+ SDL+S+ G + PIVW G+GL+ QQ VGINV+FYY + LW +VGF+E+ +L Sbjct: 244 ADHHRPKLSDLISKTTGKIRPIVWTGIGLAVFQQLVGINVVFYYGATLWEAVGFSEDNAL 303 Query: 305 LITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGA-TVVNGQPT 363 I +++G ++I L I VDK GRKPLLL+GS GM +TL I++ F A T +G + Sbjct: 304 QINILSGVLSIGACLGTIMLVDKIGRKPLLLVGSAGMAVTLAIVAYAFSTAVTGADGAVS 363 Query: 364 LTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIIS 423 L G G++AL+ ANLYV F SWGPI+WVLLGEMF N+IR + L+VA QWIAN IS Sbjct: 364 LPGHNGLMALIAANLYVVFFNLSWGPIMWVLLGEMFPNQIRGSGLAVAGFAQWIANAAIS 423 Query: 424 TTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 +FP L + GL Y YA AAIS FF+ V ETKG+ LE M Sbjct: 424 VSFPALAVSPGLVMTYTGYALFAAISFFFVRKMVHETKGRELEDM 468 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: 602 Number of extensions: 32 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: 470 Length adjustment: 33 Effective length of query: 435 Effective length of database: 437 Effective search space: 190095 Effective search space used: 190095 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