Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_1871 Echvi_1871 transporter, SSS family
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Cola:Echvi_1871 Length = 547 Score = 593 bits (1528), Expect = e-174 Identities = 294/547 (53%), Positives = 395/547 (72%), Gaps = 19/547 (3%) Query: 11 IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70 +D++VF Y +II +G+ VSR+KKG K ++DYFLA K+LPWWAVGASLIA+NISAEQF Sbjct: 6 LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65 Query: 71 IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTIL 130 IGMSGSG+++GLAI++YEWM+A TL++V +FLPI++++GIYT+P+F+ +R++ +++T++ Sbjct: 66 IGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTVM 125 Query: 131 AVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVWTDV 190 A+FW+ +Y+FVNLTSVLYLG L+LETI+G+PL Y I+GLALFA+VYSIYGGL AV WTDV Sbjct: 126 AIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTDV 185 Query: 191 IQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQ-----------S 239 +QV FLV GG TTY+A+S +G D W G+ + AAP HF MI+++ S Sbjct: 186 VQVVFLVAGGLATTYLALSLVGDGDVW-EGIGILRKAAPSHFSMIIEKGEMMIPDGSGGS 244 Query: 240 NPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPF 299 Y++LPG++VLIGG+W+ NL YWG NQYI QR LAAKS+ EAQ G+VFA FLKL++P Sbjct: 245 RDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMPL 304 Query: 300 LVVLPGIAAYVIT---SDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFA 356 +VV+PGIAAYVI +D + S+ D + A +D+AYP L LP G+KG+ FA Sbjct: 305 IVVIPGIAAYVIVQKGADASFIESMTD----PVTGLAKSDRAYPTLLHLLPPGLKGLAFA 360 Query: 357 ALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPM 416 AL AAIVSSLASM NST+TIFT+DIYKE+ + + + K V +GR AVVA IIA ++AP Sbjct: 361 ALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQ 420 Query: 417 LGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLS 476 L + QAFQYIQEYTG VSPG+ A+F+ G FWKKTTS A+ V +IP + K + + Sbjct: 421 LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPN 480 Query: 477 MPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLA 536 +PF+D+M L V+I SL D K I V + +F T F + A I +L Sbjct: 481 LPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTSTKFKVGAVLICGILV 540 Query: 537 VLYTLFW 543 LY++FW Sbjct: 541 ALYSVFW 547 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: 962 Number of extensions: 46 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: 547 Length adjustment: 35 Effective length of query: 508 Effective length of database: 512 Effective search space: 260096 Effective search space used: 260096 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