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 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= SwissProt::Q28728 (674 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 265 bits (676), Expect = 5e-75 Identities = 157/461 (34%), Positives = 262/461 (56%), Gaps = 33/461 (7%) Query: 24 LEPGDIAVLVLYFLFVLAVGLWSTVKTKRDT--VKGYFLAGGDMVWWPVGASLFASNVGS 81 LE DI +L++Y L +L + LW + + KR K YFLAG + WW +GASL ASN+ + Sbjct: 2 LETLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISA 61 Query: 82 GHFVGLAGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFGGSRI 141 +G++GSG A G+++A+YE+ +++++ LPI+I ++ TMP+YL +RF R+ Sbjct: 62 EQIIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRF-DKRV 120 Query: 142 AITLAVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLSVVGLLAVTALYTVAGGLAAVI 201 TLA+ +L +YI ++ ++ G + I+ +D +V L + Y++ GGL AV Sbjct: 121 KTTLALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVA 180 Query: 202 YTDALQTLIMLVGALTLMGYSFAAVGGMEGLQEKYFLALPSNRSENSSCGLPREDAFHLF 261 YTD +Q ++++ G L L + V +G+ + + S LP L Sbjct: 181 YTDIIQVVLLIFGGLLLSYLALDRVADGQGVLAGF---------DRLSSALPEHFEMILS 231 Query: 262 R-DPLTSDLPWPGILF-GMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLP 319 + +P LP +L G+ I ++ YW +Q I+QR+LAAK+++ A+ G AAYLK+L Sbjct: 232 QSNPHYMSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLM 291 Query: 320 LFIMVFPGMVSRILFPDQVACADPETCQRVCNNPSGCSDIAYPKLVLELLPTGLRGLMMA 379 I+V PG+ + +L+P + D AYP + + L+P G++GL+ A Sbjct: 292 PLIVVLPGIAAVLLYPGLES-----------------PDQAYPSM-MALMPAGVKGLVFA 333 Query: 380 VMVAALMSSLTSIFNSASTIFTMDLWNHVRPRASEKELMIVGRVFVLLLVLVSVLWIPVV 439 +VAA++SSL S+ NS STIFTMD++ +RP SE ++VGR+ L+ +L++++ + Sbjct: 334 ALVAAIVSSLASMTNSISTIFTMDIYAMLRPAKSEGHYVLVGRLSSLISLLIALVMAQPL 393 Query: 440 QASQGGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANEKGA 480 + Q F YIQ + P + ++F+ G FW+RA +GA Sbjct: 394 -LGEFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGA 433 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: 775 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: 519 Length adjustment: 37 Effective length of query: 637 Effective length of database: 482 Effective search space: 307034 Effective search space used: 307034 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