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 Echvi_1880 Echvi_1880 transporter, SSS family
Query= SwissProt::Q28728 (674 letters) >FitnessBrowser__Cola:Echvi_1880 Length = 624 Score = 284 bits (726), Expect = 1e-80 Identities = 165/487 (33%), Positives = 268/487 (55%), Gaps = 36/487 (7%) Query: 28 DIAVLVLYFLFVLAVGLW--STVKTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGHFV 85 D + ++Y L +++VGLW T K T + YFLA + WW VGASL A+N+ + HF+ Sbjct: 9 DYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEHFI 68 Query: 86 GLAGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFGGSRIAITL 145 G +GSG A G+ ++AYE+ +++++A FLPI++ V TMP++L RF ++ Sbjct: 69 GTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERF-NKGVSTAF 127 Query: 146 AVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLSVVGLLAVTALYTVAGGLAAVIYTDA 205 AV +L +Y+F ++ Y GA+ + + + + L ++GLL + +Y++ GGL AV +TD Sbjct: 128 AVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWTDV 187 Query: 206 LQTLIMLVGALTLMGYSFAAVGGMEGL-----------QEKYFLALPSNRSENSSCGLPR 254 +Q +I++ G L + AVG +G+ ++ + + +P R Sbjct: 188 VQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGLGGS 247 Query: 255 EDAFHLFRDPLTSDLPWPG-ILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAA 313 DAF DLP IL GM + +L YW +Q I+Q+ LAAK++ AK G L A Sbjct: 248 RDAF--------QDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAG 299 Query: 314 YLKVLPLFIMVFPGMVSRILFPDQVACADPETCQRVCNNP------SGCSDIAYPKLVLE 367 YLK+L I+V PG+ + +L D PE + N P SD AYP L+ Sbjct: 300 YLKLLMPIIVVIPGIAAYVLINDY----SPEQLAAILNMPVEHIGTIQKSDEAYPWLLRN 355 Query: 368 LLPTGLRGLMMAVMVAALMSSLTSIFNSASTIFTMDLWN-HVRPRASEKELMIVGRVFVL 426 +P G+RGL A + AA++SSL S+ NS STIFTMD++ + +P A+ +L+ GR+ + Sbjct: 356 FIPNGIRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAV 415 Query: 427 LLVLVSVLWIPVVQASQGGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANEKGAFWGLVL 486 + + ++++ P Q + Q+F YIQ + Y+ P V +VF +G W++A A W + Sbjct: 416 VALAIAMIVAP--QLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIA 473 Query: 487 GLLLGFI 493 + G + Sbjct: 474 TIPAGIV 480 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: 886 Number of extensions: 51 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 674 Length of database: 624 Length adjustment: 38 Effective length of query: 636 Effective length of database: 586 Effective search space: 372696 Effective search space used: 372696 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: 54 (25.4 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