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 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)
Query= SwissProt::Q28728 (674 letters) >FitnessBrowser__Btheta:349869 Length = 523 Score = 265 bits (677), Expect = 4e-75 Identities = 162/530 (30%), Positives = 285/530 (53%), Gaps = 46/530 (8%) Query: 24 LEPGDIAVLVLYFLFVLAVGLWSTVKTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGH 83 L+ D +L+ YFL ++A+G+W++ K K+ + FLA + W +G S++ +NVG Sbjct: 6 LDTLDWGILIAYFLILIAIGIWASSKRKKGS--SLFLAEHSLRWHHIGFSMWGTNVGPSM 63 Query: 84 FVGLAGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFGGSRIAI 143 + A +G TGI Y + + +LA++F P Y+ +V+T+PE++ +RFG S I Sbjct: 64 LIASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRFGQSTRNI 123 Query: 144 TLAVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLSVVGLLAVTALYTVAGGLAAVIYT 203 LA + + + +++ ++AG + I+Q + ++ S + LL ++A +T+ GGL AV YT Sbjct: 124 -LAWYTIVTILISWLALTLFAGGVLIRQVFDIPMWQSALILLIISAFFTMLGGLKAVAYT 182 Query: 204 DALQTLIMLVGALTLMGYSFAAVGGMEGLQEKYFLALPSNRSENSSCGLPREDAFHLFRD 263 + Q +++++ + L VGG+ L + A+P+ D ++LFR Sbjct: 183 NVYQMILLILVSAALAIVGIYKVGGISALTD----AVPA-------------DFWNLFRP 225 Query: 264 PLTSDLPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLPLFIM 323 + PW I+ G + +W+WCTDQ +VQ LAAK+L + G+ +LK+L + + Sbjct: 226 NDDTAFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGWLKILDVPLY 285 Query: 324 VFPGMVSRILFPDQVACADPETCQRVCNNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVA 383 + PG++ LFP NP D AY +V L P G+ GL++AV+ A Sbjct: 286 ILPGIICLALFPQ-------------LENP----DEAYMTMVTHLFPVGMVGLVLAVLTA 328 Query: 384 ALMSSLTSIFNSASTIFTMDLW-NHVRPRASEKELMIVGRVFVLLLVLVSVLWIPVVQAS 442 AL+S++ S N+ ST+FTMD++ +RP+A +KE++ VG+V + L+SV+ + + Sbjct: 329 ALVSTIGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISVIITIAIDSI 388 Query: 443 QGGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANEKGAFWGLVLGLLLGFIRLILDFIYV 502 G LF Q++ ++ PP+A VF+ G FWKR A L +G + I + + +++V Sbjct: 389 HGLNLFNVFQSVLGFIAPPMAAVFLFGVFWKRTTTLAANAALTVGTVFS-IGVGVLYLWV 447 Query: 503 EPACHQPDERPSVVKNVHYLYFSMILSSVTVLTVTVMSLLTEPPSKEMIS 552 PA Q P H++ S L + + + V+ LL + P +++ Sbjct: 448 FPA-DQYSAWP------HFMLLSFYLFVIIGIGMVVVGLLDKTPQTAILN 490 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: 754 Number of extensions: 37 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: 674 Length of database: 523 Length adjustment: 37 Effective length of query: 637 Effective length of database: 486 Effective search space: 309582 Effective search space used: 309582 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