Align sodium/glucose cotransporter 1 (characterized)
to candidate Echvi_1880 Echvi_1880 transporter, SSS family
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__Cola:Echvi_1880 Length = 624 Score = 276 bits (705), Expect = 3e-78 Identities = 165/484 (34%), Positives = 271/484 (55%), Gaps = 27/484 (5%) Query: 28 DISIIVIYFVVVMAVGLWAMFSTNRG---TVGGFFLAGRSMVWWPIGASLFASNIGSGHF 84 D I ++Y + +++VGLW T +G T +FLA +S+ WW +GASL A+NI + HF Sbjct: 9 DYVIFIVYALAIVSVGLWVS-RTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEHF 67 Query: 85 VGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVY 144 +G +G+G A G+ I +EW A + ++++ F+PI++K GV TMP++L +RF + + Sbjct: 68 IGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERF-NKGVSTA 126 Query: 145 LSLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTD 204 ++ LL+Y+F +++ + GA+ ++ +G+ L I LL + +Y+I GGL AV +TD Sbjct: 127 FAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186 Query: 205 TLQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTF-----QEKCYTPR 259 +Q +I++ G LI T A VG D + + +D F Q + P Sbjct: 187 VVQVIILVAGGLITTFLALDAVGMGDGI----FAGMSNLYNDAKDHFVMIMPQGRVMVP- 241 Query: 260 ADSFHIFRDPLTGDLPWPGFIF-GMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCG 318 D RD DLP I GM + L YW +Q I+Q+ L+AK++ K G + G Sbjct: 242 -DGLGGSRDAFQ-DLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAG 299 Query: 319 YLKLMPMFIMVMPGMISRILYT----EKIACVVPSECEKYCGTKVGCTNIAYPTLVVELM 374 YLKL+ I+V+PG+ + +L E++A ++ E + GT + ++ AYP L+ + Sbjct: 300 YLKLLMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVE-HIGT-IQKSDEAYPWLLRNFI 357 Query: 375 PNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIY-AKVRKRASEKELMIAGRLFILVL 433 PNG+RGL + + A+++SSL S+ NS ST+FTMDIY + A+ +L+ GR I+ + Sbjct: 358 PNGIRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGR--IVAV 415 Query: 434 IGISIAWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGL 493 + ++IA + Q A Q+F YIQ T Y+ P + VF + + W++ A W I + Sbjct: 416 VALAIAMIVAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATI 475 Query: 494 LIGI 497 GI Sbjct: 476 PAGI 479 Lambda K H 0.327 0.141 0.436 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: 899 Number of extensions: 44 Number of successful extensions: 6 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: 664 Length of database: 624 Length adjustment: 38 Effective length of query: 626 Effective length of database: 586 Effective search space: 366836 Effective search space used: 366836 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: 54 (25.4 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