Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 403 bits (1035), Expect = e-117 Identities = 207/463 (44%), Positives = 297/463 (64%), Gaps = 5/463 (1%) Query: 9 QSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSA 68 +S AN+ ++ I VA +GG LFG+D+ +NG L+ F G +V L+G Sbjct: 4 ESRANMGLIMAIVAVATIGGLLFGYDSGAVNGTQDGLKSAFALSEGGLGFTVGSLLIGCF 63 Query: 69 LGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIA 128 +GAF AG +AD GR MIL AVLF + ++ G W F+ R+ GG+ VGAASV++ Sbjct: 64 IGAFLAGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAASVLS 123 Query: 129 PAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWM 188 PAYI+EV+PA++RGR+ ++QQ+ I+SG+ A + N+++A AG S W G AWRWM Sbjct: 124 PAYISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFW-GGYEAWRWM 182 Query: 189 FWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG-GDVPSRIEEIQATVSL 247 +W + IPA ++ + F IPESPRYLV++G+ +A +L + G G +++ EIQA+ S Sbjct: 183 YWMQAIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASFS- 241 Query: 248 DHKPRFSDLLSR-RGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLI 306 DH+P D+L +GG+ PIVW G+ L+ QQ VGINVIFYY + LW+ GFTE +LLI Sbjct: 242 DHRPTLRDILDPVKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTENDALLI 301 Query: 307 TVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFG-GATVVNGQPTLT 365 +++GF++I V +A VD+ GRKPLLL+GS GM + L + F G+ G+ L+ Sbjct: 302 NIVSGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDAQGKLVLS 361 Query: 366 GAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTT 425 GIIA++ ANLYV F SWGP++WV+LGEMF N+IR +AL+V QW +N++I+ + Sbjct: 362 QQLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQS 421 Query: 426 FPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 FP + +GL +Y YA A IS F + F+ ETKG LE M Sbjct: 422 FPIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDM 464 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: 641 Number of extensions: 35 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: 466 Length adjustment: 33 Effective length of query: 435 Effective length of database: 433 Effective search space: 188355 Effective search space used: 188355 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 17 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