Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Dino:3610525 Length = 533 Score = 280 bits (716), Expect = 1e-79 Identities = 165/500 (33%), Positives = 272/500 (54%), Gaps = 40/500 (8%) Query: 1 MSNIEHGLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASL 60 M + + L +ID + IY +I G++VSR ++ + YFLAG+SLPW+ +G SL Sbjct: 1 MGDAKFDLHWIDYAIVVIYFIGVIAHGVYVSRKN---EEGADGYFLAGRSLPWYLIGFSL 57 Query: 61 IAANISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEK 120 A+N+S F+G+ G Y+ G+ I +YEW +A+ LI+ + LP F++ I T+PEF+E+ Sbjct: 58 FASNMSGSSFVGLMGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQ 117 Query: 121 RFNKKLKTILAVFWISLYIFVNLTSVLYLGGLALETILG-IPLMYSILGLALFALVYSIY 179 R++ + + ++F I +F++ LY GGL + + G + L ++ LAL A +Y+I Sbjct: 118 RYDVRSRRAFSIFTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTIL 177 Query: 180 GGLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQS 239 GGLSAVV TD +Q L++G + ++ + IGG + F VD GH ++IL + Sbjct: 178 GGLSAVVVTDTVQAILLIIGAAILFWLGLDEIGGWEQLF------VDIPEGHDQLIL-PA 230 Query: 240 NPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPF 299 + ++ G + G+ + YYW NQ+++QRTL AK++ E Q G +FA FLKL F Sbjct: 231 DDDFLPWTG----LWGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIF 286 Query: 300 LVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLT-QFLPVGVKGVVFAAL 358 L+++PG+ IA P D A+P L + +P+GV+G++ AAL Sbjct: 287 LMIIPGV-----------------IALKLYPELETPDLAFPTLAFELMPIGVRGLIMAAL 329 Query: 359 AAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLG 418 AAI+SSL S +NS +T+ D + D G K V +GR ++ + AP + Sbjct: 330 IAAIMSSLDSAMNSASTLVVKDFVEPIWEVDEG--KQVWIGRLVTGAVMVFGAIYAPSIA 387 Query: 419 GIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGA----IIGVVASIPFALFLKFMP 474 G F Y Q + P I+ V+++GLF GA I+G+V IP + + Sbjct: 388 GFESLFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGIPLFIMKEVTG 447 Query: 475 LSMPF-MDQMLYTLLFTMVV 493 + + ++ YT++ T+++ Sbjct: 448 VWAGMGLPEIHYTIMSTLMM 467 Lambda K H 0.326 0.141 0.421 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: 1021 Number of extensions: 75 Number of successful extensions: 6 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: 543 Length of database: 533 Length adjustment: 35 Effective length of query: 508 Effective length of database: 498 Effective search space: 252984 Effective search space used: 252984 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: 52 (24.6 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