Align sodium/glucose cotransporter 1 (characterized)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 249 bits (636), Expect = 2e-70 Identities = 149/471 (31%), Positives = 250/471 (53%), Gaps = 56/471 (11%) Query: 28 DISIIVIYFVVVMAVGLWAMFSTNRGT--VGGFFLAGRSMVWWPIGASLFASNIGSGHFV 85 DI I+++Y + ++ + LW R +FLAG+++ WW IGASL ASNI + + Sbjct: 6 DIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISAEQII 65 Query: 86 GLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYL 145 G++G+G A G+AI +EW A + ++++G +PI+IK + TMP+YL +RF +R++ L Sbjct: 66 GMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRF-DKRVKTTL 124 Query: 146 SLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTDT 205 +L L +YI ++A ++ G + I G++ + L + Y++ GGL AV YTD Sbjct: 125 ALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAYTDI 184 Query: 206 LQTVIMLVGSLILTGFAFHEV-------GGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTP 258 +Q V+++ G L+L+ A V G+D + I+S N + Sbjct: 185 IQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQSNPHY------- 237 Query: 259 RADSFHIFRDPLTGDLPWPG---FIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCI 315 + PG + G+ I+ + YW +Q I+QR L+AK+++ + G Sbjct: 238 ---------------MSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIA 282 Query: 316 LCGYLKLMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMP 375 YLKL+ I+V+PG+ + +LY + + AYP+++ LMP Sbjct: 283 FAAYLKLLMPLIVVLPGIAAVLLY-----------------PGLESPDQAYPSMMA-LMP 324 Query: 376 NGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIG 435 G++GL+ + ++A+++SSL S+ NS ST+FTMDIYA +R SE ++ GRL L+ + Sbjct: 325 AGVKGLVFAALVAAIVSSLASMTNSISTIFTMDIYAMLRPAKSEGHYVLVGRLSSLISLL 384 Query: 436 ISIAWV-PIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGA 485 I++ P++ + Q F YIQ T P I +FL +FW+R GA Sbjct: 385 IALVMAQPLL--GEFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGA 433 Lambda K H 0.327 0.141 0.436 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: 731 Number of extensions: 33 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: 664 Length of database: 519 Length adjustment: 37 Effective length of query: 627 Effective length of database: 482 Effective search space: 302214 Effective search space used: 302214 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: 53 (25.0 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