Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Ga0059261_1623 Ga0059261_1623 transporter, SSS family
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Korea:Ga0059261_1623 Length = 549 Score = 540 bits (1390), Expect = e-158 Identities = 283/565 (50%), Positives = 381/565 (67%), Gaps = 48/565 (8%) Query: 8 LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67 LS ID++V +Y I + WVSR+K G K T DYFLA KSLPWWA+GASLIAANISA Sbjct: 4 LSHIDLIVVIVYAIGIFALAQWVSREKAGHAKDTSDYFLASKSLPWWAIGASLIAANISA 63 Query: 68 EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127 EQ +GMSGSGY+IGLAIASYEWM+A+TL+IVGK+FLPIF++ IYT+P+F+E+RF ++ Sbjct: 64 EQIVGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPIFLKNEIYTMPQFLEQRFGPTIR 123 Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVW 187 T++AVFW++LYIFVNLTS+L+LG +A+ + G+ ++ GL FALVY + GGL AV Sbjct: 124 TVMAVFWLALYIFVNLTSILWLGSIAVTQVAGVDQDIALFGLGAFALVYQLRGGLKAVAL 183 Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLP 247 TD++QV LVLGG + +Y+ +S IGG G G +++ PG F+MIL NP Y +LP Sbjct: 184 TDIVQVTLLVLGGLVISYLTLSKIGGDAGVMGGFTRLTTELPGKFDMILAPDNPFYKDLP 243 Query: 248 GIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIA 307 G++VLIGG+W+ANL YWGFNQYIIQR LAAKS+SEAQKG+VFAAFLKL++P ++VLPGIA Sbjct: 244 GLSVLIGGMWIANLSYWGFNQYIIQRALAAKSLSEAQKGVVFAAFLKLLMPVIIVLPGIA 303 Query: 308 AYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLA 367 A ++ P A D+AYP + + LPVG+ G+VFAAL AAI++S A Sbjct: 304 AVILA-----------------PDLAKPDQAYPTMMRLLPVGLLGLVFAALVAAIIASTA 346 Query: 368 SMLNSTATIFTMDIYKE--------------YISPDSG-----DHKLVNVGRTAAVVALI 408 S +NS ATIFT+D+Y + S DSG + +LV VGRT AVVA + Sbjct: 347 SKINSIATIFTLDLYAKAKGVQSRAQDAATASASGDSGLTAAHEKQLVRVGRTTAVVATL 406 Query: 409 IACLIA-PMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFA 467 +A A P+LG + QAFQYIQE++G V+PGI +FLLGLFW + T GA+ G VAS+ + Sbjct: 407 LAIFTARPLLGSLDQAFQYIQEFSGFVTPGITVIFLLGLFWPRATEAGALTGAVASVLLS 466 Query: 468 LFLKFMPL---------SMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMF 518 FL + P ++PFM++M+ ++ + SL D + I++ F Sbjct: 467 -FLFWFPADWGGIATLNAVPFMNRMMIVFFVSLALAVVVSLVRPAPADSNR-ITMQGVSF 524 Query: 519 VTDRSFNIAAYGIMIVLAVLYTLFW 543 T SFN+A I+++L LY +W Sbjct: 525 GTTTSFNVAGVIIIMILIALYATWW 549 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: 959 Number of extensions: 57 Number of successful extensions: 4 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: 549 Length adjustment: 35 Effective length of query: 508 Effective length of database: 514 Effective search space: 261112 Effective search space used: 261112 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