Align sodium/glucose cotransporter 1 (characterized)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__Pedo557:CA265_RS19720 Length = 558 Score = 244 bits (622), Expect = 1e-68 Identities = 161/530 (30%), Positives = 279/530 (52%), Gaps = 36/530 (6%) Query: 28 DISIIVIYFVVVMAVGLWAMFSTNRGTVGG--FFLAGRSMVWWPIGASLFASNIGSGHFV 85 D + IYFV+V A GL+ + G +FLA S+ WW IGASL ASNI + F+ Sbjct: 10 DYIVFAIYFVIVAAYGLYIYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNISAEQFI 69 Query: 86 GLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYL 145 G++G+G G+AI +EW A + +V++ F+P+Y+K + TMP++L +R+ G + + + Sbjct: 70 GMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNG-TVAMIM 128 Query: 146 SLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTDT 205 ++ LLLY+ +++ ++ GA+ ++ G +L ++ + A + T+ GG+ + YTD Sbjct: 129 AVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKVIGYTDV 187 Query: 206 LQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRADSFHI 265 +Q +++G L T A + V + + + +G + K ++ FH+ Sbjct: 188 IQVFFLILGGLATTYLALNLVSTHYG---------TSGIFEGYSLMTSKA----SEHFHM 234 Query: 266 FRDPLTGD-LPWPG---FIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLK 321 P + + PG + GM I+ L YW +Q I QR L A ++ +GG + +LK Sbjct: 235 ILKPDNENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTARGGILFAAFLK 293 Query: 322 LMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGL 381 L+ I+V+PG+ + +LY + + E V + AYP L + L+P GL+GL Sbjct: 294 LLMPIIVVLPGIAAYVLYKDG-----AFQSEMLQDGSVN-PDRAYPVL-LNLLPAGLKGL 346 Query: 382 MLSVMLASLMSSLTSIFNSASTLFTMDIYAKVRKR-ASEKELMIAGRLFILVLIGISIAW 440 + + A++++SL NS +T+FT+DIY KV K ASEK L+ G++ ++V + + + Sbjct: 347 SFAALTAAVVASLAGKANSIATIFTLDIYKKVLKTDASEKNLVFTGKIAVVVAMVLGVVI 406 Query: 441 VPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFW----GLILGLLIG 496 P + + G F YIQ T ++ P I A+F+L FWKR A + G L LL+ Sbjct: 407 APYLGIDKKGG-FQYIQEYTGFVSPGIFAMFILGFFWKRATSNAALFATVGGFGLSLLLK 465 Query: 497 ISRMITEFAYGTGSCMEPSNCPTIICGVHYLYFAIILFAISFITIVVISL 546 + T+ ++ +G N + + +L +F I +V+ISL Sbjct: 466 VLPTWTDLSWLSGMGFSVKN-GVGVYEIPFLDRMGFVFVFCVIGMVIISL 514 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: 747 Number of extensions: 33 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: 558 Length adjustment: 37 Effective length of query: 627 Effective length of database: 521 Effective search space: 326667 Effective search space used: 326667 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