Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::Q28728 (674 letters) >FitnessBrowser__Dino:3610525 Length = 533 Score = 273 bits (697), Expect = 2e-77 Identities = 174/534 (32%), Positives = 289/534 (54%), Gaps = 56/534 (10%) Query: 28 DIAVLVLYFLFVLAVGLWSTVKTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGHFVGL 87 D A++V+YF+ V+A G++ + K + + GYFLAG + W+ +G SLFASN+ FVGL Sbjct: 12 DYAIVVIYFIGVIAHGVYVSRKNE-EGADGYFLAGRSLPWYLIGFSLFASNMSGSSFVGL 70 Query: 88 AGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFG-GSRIAITLA 146 G A GI + YE+ +++ A LP ++ +++T+PE+L +R+ SR A ++ Sbjct: 71 MGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAFSIF 130 Query: 147 VLYLFIYIFTKISVDMYAGAIFIQQ-SLHLDLYLSVVGLLAVTALYTVAGGLAAVIYTDA 205 + ++I T + +YAG + I + +L+L+ +V L V +YT+ GGL+AV+ TD Sbjct: 131 TILAILFIDT--AGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGLSAVVVTDT 188 Query: 206 LQTLIMLVGALTLMGYSFAAVGGMEGLQEKYFLALPSNRSENSSCGLPREDAFHLFRDPL 265 +Q +++++GA L +GG E L F+ +P + LP +D F Sbjct: 189 VQAILLIIGAAILFWLGLDEIGGWEQL----FVDIPEGHDQ---LILPADDDF------- 234 Query: 266 TSDLPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLPLFIMVF 325 LPW G L+G+ + +YW +Q +VQR+L AKNL + G+L A +LK+ +F+M+ Sbjct: 235 ---LPWTG-LWGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIFLMII 290 Query: 326 PGMVSRILFPDQVACADPETCQRVCNNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVAAL 385 PG+++ L+P+ ET D+A+P L EL+P G+RGL+MA ++AA+ Sbjct: 291 PGVIALKLYPEL------ET-----------PDLAFPTLAFELMPIGVRGLIMAALIAAI 333 Query: 386 MSSLTSIFNSASTIFTMDLWNHVRP--RASEKELMIVGRVFVLLLVLVSVLWIPVVQASQ 443 MSSL S NSAST+ D V P E + + +GR+ +++ ++ P + + Sbjct: 334 MSSLDSAMNSASTLVVKDF---VEPIWEVDEGKQVWIGRLVTGAVMVFGAIYAPSIAGFE 390 Query: 444 GGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANEKGAFWGLVLGLLLGFIRLIL-DFIYV 502 LF Y Q+ SY+ P + +V+++G F N GAFW ++LGL++G I+ + V Sbjct: 391 --SLFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGIPLFIMKEVTGV 448 Query: 503 EPACHQPDERPSVVKNVHYLYFSMILSSVTVLTVTVMSLLTEPPSKEMISHLTW 556 P+ +HY S ++ + + T +S LT KE I L W Sbjct: 449 WAGMGLPE--------IHYTIMSTLMMCLGLATHFGISALTRKADKENIEDLVW 494 Lambda K H 0.325 0.138 0.426 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: 810 Number of extensions: 35 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: 674 Length of database: 533 Length adjustment: 37 Effective length of query: 637 Effective length of database: 496 Effective search space: 315952 Effective search space used: 315952 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: 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