Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Pedo557:CA265_RS04220 Length = 550 Score = 290 bits (743), Expect = 7e-83 Identities = 165/451 (36%), Positives = 261/451 (57%), Gaps = 8/451 (1%) Query: 8 LSFIDIMVFAIYVAIIIGVGLWV-SRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANIS 66 +S DI++ Y+ I+ +GLW +R KK + ++ +YFLAGK+L W +G +L A NIS Sbjct: 2 ISTTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNIS 61 Query: 67 AEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKL 126 + ++ SG+ GL ++EWM+A TLI++ F+P +I GI T+P+F+E+R+N+ Sbjct: 62 CLHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRAC 121 Query: 127 KTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVV 186 + LA I I +++ GG+ LET+ GI + SI+ +AL +Y+I GGL AVV Sbjct: 122 RDWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRAVV 181 Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNL 246 T+ IQ L+ G + TY A + +GG D A + K + A MI + M+ Sbjct: 182 VTETIQSLVLITGAIIITYFAWNKVGGWDHMTAILQK--ENAMDKLSMIRPIGDKSGMS- 238 Query: 247 PGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGI 306 IAV + G V ++YW +Q I+QR L AK + A+ G +F F+K++ F+ VLPG+ Sbjct: 239 -WIAVFL-GYPVLGIWYWCADQTIVQRVLGAKDENHARVGSLFCGFIKILPVFIFVLPGL 296 Query: 307 AAYVITSDPQLMASLGDIAATNLPSAANADKAYP-WLTQFLPVGVKGVVFAALAAAIVSS 365 AY++ + S +N + N Y +TQ LP G+ G++ AAL + ++S Sbjct: 297 FAYILYKSGTMDLSSLQTVGSNGETVLNTKGIYTLMITQLLPKGLVGILVAALLSGLMSQ 356 Query: 366 LASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAFQ 425 +A LNS AT+ + D+YK + P++ D KLV+VGR +A +AL ++ + P+L F Sbjct: 357 IAGALNSIATLSSYDLYKRF-KPETSDKKLVSVGRWSAGIALTVSIGLLPLLNSYESLFN 415 Query: 426 YIQEYTGLVSPGILAVFLLGLFWKKTTSKGA 456 I + ++P I VFLLG+FWKK ++KGA Sbjct: 416 GINDVIAHIAPPITCVFLLGVFWKKASAKGA 446 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: 883 Number of extensions: 47 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: 543 Length of database: 550 Length adjustment: 36 Effective length of query: 507 Effective length of database: 514 Effective search space: 260598 Effective search space used: 260598 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 Apr 09 2024. 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