Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate WP_066328313.1 BLR17_RS01540 sodium/solute symporter
Query= SwissProt::P96169 (543 letters) >NCBI__GCF_900100165.1:WP_066328313.1 Length = 561 Score = 423 bits (1087), Expect = e-122 Identities = 233/575 (40%), Positives = 350/575 (60%), Gaps = 57/575 (9%) Query: 8 LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67 L F D VF +Y + G + R ++ + + YFLA +L WWA+GASLIA+NISA Sbjct: 5 LEFADYAVFIVYFLAVSIYGYIIYRKREKNEHDAKAYFLAEGTLTWWAIGASLIASNISA 64 Query: 68 EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127 EQFIGMSG G+ +G+A+A+YEW++AI LIIVG +F+P++++ IYT+P+F++ R+N Sbjct: 65 EQFIGMSGEGFFLGIAVAAYEWVAAIALIIVGIWFIPVYLKNKIYTMPQFLKTRYNDTTA 124 Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSI-LGLALFALVYSIYGGLSAVV 186 I+AVFW+ LY+FVNLTS+LYLG +A+ + G ++ I LGLA+FAL+ S+ GG+ V Sbjct: 125 LIMAVFWLFLYVFVNLTSILYLGAVAINGLAGGDYLHVIMLGLAIFALIISL-GGMKVVA 183 Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIG-----GTDGWFAGVSKMVDAAPGHFEMILDQSN- 240 +TDVIQV L++GG +T+Y+A++ +G G D AG +++ AP HF+MI+ + Sbjct: 184 YTDVIQVAVLIIGGLVTSYIALTTVGQYFGVGQDA-IAGFKVLMERAPEHFKMIIPRPTA 242 Query: 241 -------PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFL 293 +Y+ PG+ + G+W+ NL YWG NQYI QR L A ++ A+ G++FA L Sbjct: 243 SSTQLEIDKYLTFPGVLSYLAGIWIINLNYWGCNQYITQRALGA-DLTTARTGLLFAGML 301 Query: 294 KLIVPFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGV 353 KL++P +V+LPGIAAYV+ L +G D AY + FLP G+KG+ Sbjct: 302 KLLMPVIVMLPGIAAYVLYEGGHLPQLVG-----------GKDGAYSAMLTFLPTGLKGL 350 Query: 354 VFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLI 413 AAL AAIV+SLA +NS +TI+T+D++K+YI ++ D VN+GR A A+++A L Sbjct: 351 SVAALTAAIVASLAGKVNSISTIYTLDVHKKYIQKEASDRAQVNIGRYAVFAAMVLAVLF 410 Query: 414 A----PMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFA-L 468 +GG+G F YIQ+YTG +SPG+ A+F LG+FWK+TT AI+GV+A + L Sbjct: 411 TWNDLLGIGGVG-GFTYIQKYTGFISPGVFAMFFLGMFWKRTTGTAAIVGVLAGFLLSVL 469 Query: 469 FLKFMP-------------------LSMPFMDQMLYTLLFTMV-VIAFTSLSTSINDDDP 508 F ++ P +PF M + LFTM+ ++A + +N P Sbjct: 470 FNEYAPAMFGNETFLYTAYANGKGAFEIPFHVCMGLSFLFTMILMVAVSYAGPKVN---P 526 Query: 509 KGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543 K + + MF + ++++A LY FW Sbjct: 527 KAFELDTEMFKVKPQTTVLIIITLLIIAALYVKFW 561 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: 1054 Number of extensions: 66 Number of successful extensions: 9 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: 561 Length adjustment: 36 Effective length of query: 507 Effective length of database: 525 Effective search space: 266175 Effective search space used: 266175 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 24 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