Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_1880 Echvi_1880 transporter, SSS family
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Cola:Echvi_1880 Length = 624 Score = 564 bits (1453), Expect = e-165 Identities = 275/517 (53%), Positives = 377/517 (72%), Gaps = 17/517 (3%) Query: 7 GLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANIS 66 G S +D ++F +Y I+ VGLWVSR KKG +K+ ++YFLA KSL WWAVGASL+AANIS Sbjct: 4 GFSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANIS 63 Query: 67 AEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKL 126 AE FIG SGSG++IGL I++YEW++AI LIIV KYFLPIF++ G+YT+P+F+ +RFNK + Sbjct: 64 AEHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGV 123 Query: 127 KTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVV 186 T AVFW+ +Y+FVNLTSV YLG LAL+ I+GIPL Y I+GL +F+ +YSIYGGL AV Sbjct: 124 STAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVA 183 Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQ-------- 238 WTDV+QV LV GG +TT++A+ +G DG FAG+S + + A HF MI+ Q Sbjct: 184 WTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDG 243 Query: 239 ---SNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKL 295 S + +LPG+AV++GG+W+ NL YWGFNQYIIQ+ LAAKS+ EA+KG++FA +LKL Sbjct: 244 LGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKL 303 Query: 296 IVPFLVVLPGIAAYVITSD--PQLMASLGDIAATNLPSAANADKAYPWLTQ-FLPVGVKG 352 ++P +VV+PGIAAYV+ +D P+ +A++ ++ ++ + +D+AYPWL + F+P G++G Sbjct: 304 LMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRG 363 Query: 353 VVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACL 412 + FAALAAAIVSSLASM+NST+TIFTMDIYK Y P++ +H+LV GR AVVAL IA + Sbjct: 364 LAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMI 423 Query: 413 IAPMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKF 472 +AP L + Q FQYIQEYTG + PG++ VF +GL W++ T+ A+ +A+IP + K Sbjct: 424 VAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKI 483 Query: 473 MPLSMPFMDQMLYT---LLFTMVVIAFTSLSTSINDD 506 MPF+ +M Y L F +I+F N D Sbjct: 484 FYPEMPFLLRMGYVFIILCFIASLISFAEKKKFANPD 520 Score = 44.3 bits (103), Expect = 1e-08 Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 8/90 (8%) Query: 457 IIGVVASI-PFALFLKFMPLSMP--FMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISV 513 I+G++ ++ FALF + + + FM L+ +L T I +T++ + DPK + Sbjct: 539 ILGIICAVLGFALFNSYEHVGIESIFMIAALFLMLGT---ILYTNVK--METADPKSFNT 593 Query: 514 TSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543 +F T SFN+ A GI++++ +LY FW Sbjct: 594 DPVLFNTTSSFNLGAAGIILIVGLLYYFFW 623 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: 1171 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 543 Length of database: 624 Length adjustment: 36 Effective length of query: 507 Effective length of database: 588 Effective search space: 298116 Effective search space used: 298116 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: 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