Align sodium/glucose cotransporter 1 (characterized)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__Pedo557:CA265_RS04220 Length = 550 Score = 323 bits (827), Expect = 2e-92 Identities = 174/524 (33%), Positives = 295/524 (56%), Gaps = 32/524 (6%) Query: 25 NAADISIIVIYFVVVMAVGLWAMFSTNRG---TVGGFFLAGRSMVWWPIGASLFASNIGS 81 + DI I + Y + ++ +GLW + T G +FLAG+++ W IG +LFA+NI Sbjct: 3 STTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNISC 62 Query: 82 GHFVGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRI 141 H V LA +G SG+ G FEW A +++L LF+P YI++G+ T+P++L +R+ + Sbjct: 63 LHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRY-NRAC 121 Query: 142 QVYLSLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVI 201 + +L+ +S+L I I+ +G I + G+++Y++I ++ +T LYTI GGL AV+ Sbjct: 122 RDWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRAVV 181 Query: 202 YTDTLQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRAD 261 T+T+Q+++++ G++I+T FA+++VGG+D +M A I+ N + P D Sbjct: 182 VTETIQSLVLITGAIIITYFAWNKVGGWD-----HMTA---ILQKENAMDKLSMIRPIGD 233 Query: 262 SFHIFRDPLTGDLPWPGFIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLK 321 + W G +L +WYWC DQ IVQR L AK+ +H + G + CG++K Sbjct: 234 K---------SGMSWIAVFLGYPVLGIWYWCADQTIVQRVLGAKDENHARVGSLFCGFIK 284 Query: 322 LMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGL 381 ++P+FI V+PG+ + ILY + + G V T Y ++ +L+P GL G+ Sbjct: 285 ILPVFIFVLPGLFAYILYKSGTMDLSSLQTVGSNGETVLNTKGIYTLMITQLLPKGLVGI 344 Query: 382 MLSVMLASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIGISIAWV 441 +++ +L+ LMS + NS +TL + D+Y + + S+K+L+ GR + + +SI + Sbjct: 345 LVAALLSGLMSQIAGALNSIATLSSYDLYKRFKPETSDKKLVSVGRWSAGIALTVSIGLL 404 Query: 442 PIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGLLIGISRMI 501 P++ S +S LF+ I + +++ PPI VFLL +FWK+ + GA + L+LG +IG + Sbjct: 405 PLLNSYES--LFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAGVFV 462 Query: 502 TEFAYGTGSCMEPSNCPTIICGVHYLYFAIILFAISFITIVVIS 545 YGT TII + ++ A LF I + VV S Sbjct: 463 VNKVYGT---------ETIIGQIPFMMMAFYLFCICVLIQVVFS 497 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: 791 Number of extensions: 39 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: 550 Length adjustment: 37 Effective length of query: 627 Effective length of database: 513 Effective search space: 321651 Effective search space used: 321651 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 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