Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate WP_013644894.1 METBO_RS06515 sugar porter family MFS transporter
Query= SwissProt::A0A0H2VG78 (446 letters) >NCBI__GCF_000191585.1:WP_013644894.1 Length = 453 Score = 367 bits (941), Expect = e-106 Identities = 187/431 (43%), Positives = 289/431 (67%), Gaps = 3/431 (0%) Query: 7 LIFILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSGPLA 66 L+ + ++GGLL+GYD GVISGA+LFI +D L++T + + VS++LIGA++GA SG LA Sbjct: 16 LVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISGILA 75 Query: 67 DKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEMAPT 126 D+ GR+ +++L +I+F IGA+ + S N+ LII R+++G+A+G + VP+Y++E+AP Sbjct: 76 DRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEVAPI 135 Query: 127 EYRGSLGSLNQLMITIGILAAYLVNYAFADIEGWRWMLGLAVVPSVILLVGIYFMPESPR 186 RG+L SLNQL IT+GI+ +Y+V+ FA WRWMLGLAV+PS+IL +G++FMP SPR Sbjct: 136 NIRGALVSLNQLAITLGIVISYMVDLYFAPNGSWRWMLGLAVIPSLILALGMFFMPPSPR 195 Query: 187 WLLENRNEEAARQVMKITYDDSEIDKELKEMKEINAI-SESTWTVIKSPWLGRILIVGCI 245 WL+ E A V+K +DKE+ E+++ + +E W+ + P + LI+G Sbjct: 196 WLISKGFESKAVAVLKKIRGIDNVDKEVNEIEQTLLLENEGKWSDLLEPKIRSALIIGIG 255 Query: 246 FAIFQQFIGINAVIFYSSSIFAKAGLGEA-ASILGSVGIGTINVLVTIVAIFVVDKIDRK 304 A FQQ GIN VI+Y+ +I AGL A +I +VGIG +NVL+T+V+I ++D++ R+ Sbjct: 256 LAAFQQLTGINTVIYYAPTILEFAGLQTATVTIFATVGIGVVNVLLTVVSILLIDRLGRR 315 Query: 305 KLLVGGNIGMIASLLIMAILIWTIGIASS-AWIIIVCLSLFIVFFGISWGPVLWVMLPEL 363 LL+ G GMI SL IM + G+ SS W+ ++CL L++ F IS GP+ W+M+ E+ Sbjct: 316 PLLLAGITGMIVSLGIMGLAFIIPGLTSSLGWLAVICLMLYVGSFAISLGPIFWLMIAEI 375 Query: 364 FPMRARGAATGISALVLNIGTLIVSLFFPILSDALSTEWVFLIFAFIGVLAMIFVIKFLP 423 +P+R RG A I ++ L+V++ F + + L F ++ I VL+++FV +P Sbjct: 376 YPLRIRGRAMSIVTMINWATNLVVAITFLTIIELLGASGTFWLYGVIAVLSLLFVYYRVP 435 Query: 424 ETRGRSLEEIE 434 ET+G+SLEEIE Sbjct: 436 ETKGKSLEEIE 446 Lambda K H 0.327 0.144 0.422 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: 632 Number of extensions: 36 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: 446 Length of database: 453 Length adjustment: 33 Effective length of query: 413 Effective length of database: 420 Effective search space: 173460 Effective search space used: 173460 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 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