Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter
Query= SwissProt::A0A0H2VG78 (446 letters) >NCBI__GCF_000226135.1:WP_010537714.1 Length = 309 Score = 199 bits (505), Expect = 1e-55 Identities = 114/301 (37%), Positives = 174/301 (57%), Gaps = 22/301 (7%) Query: 6 YLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSG 63 YLIF ++ ALGG L+GYD VISG + + + L++ +G V LIG+IVG +G Sbjct: 9 YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68 Query: 64 PLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEM 123 L+DKLGR+ +++ A++F AL A S + L+I R+I G+ +G P+Y+SE+ Sbjct: 69 ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128 Query: 124 APTEYRGSLGSLNQLMITIGILAAYLVNYAFAD------------------IEGWRWMLG 165 + +YRG L SL QL +T+G L AYLVNY E WR MLG Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188 Query: 166 LAVVPSVILLVGIYFMPESPRWLLENRNEEAARQVMKITYDD-SEIDKELKEMKEI-NAI 223 + ++P+V+ + I+F+PESPRWL+ EE A +++ Y+ SE +L E K + + Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVLTSE 248 Query: 224 SESTWTVIKSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVGI 283 ++S W ++ P + + +I+G AI QF+G+NAV++Y SIF AGL S+ V + Sbjct: 249 TKSEWALLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQVLV 308 Query: 284 G 284 G Sbjct: 309 G 309 Score = 28.9 bits (63), Expect = 2e-04 Identities = 28/100 (28%), Positives = 47/100 (47%), Gaps = 20/100 (20%) Query: 241 IVGCIFA-IFQQFIGINAVIFYSSSIFAKAGLGEAAS----------ILGSVGIGTINVL 289 IVG +FA I +G + S+ +F+ + LG A S I+G VGIG + Sbjct: 61 IVGVLFAGILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIG----V 116 Query: 290 VTIVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIG 329 V+IV+ + ++ V G + SL +A+ + +G Sbjct: 117 VSIVSPLYISEVS-----VAQYRGRLVSLYQLAVTVGFLG 151 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: 406 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 446 Length of database: 309 Length adjustment: 30 Effective length of query: 416 Effective length of database: 279 Effective search space: 116064 Effective search space used: 116064 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: 49 (23.5 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