Align Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 (characterized)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter
Query= SwissProt::Q9JKZ2 (718 letters) >FitnessBrowser__Pedo557:CA265_RS19720 Length = 558 Score = 243 bits (621), Expect = 1e-68 Identities = 159/501 (31%), Positives = 266/501 (53%), Gaps = 55/501 (10%) Query: 4 VLEAADIAVVALYFILVMCIGFFAMWKSNRSTVSG---YFLAGRSMTWVAIGASLFVSNI 60 +L+ D V A+YF++V G + ++ +S +G YFLA S+TW AIGASL SNI Sbjct: 5 LLDTKDYIVFAIYFVIVAAYGLY-IYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNI 63 Query: 61 GSEHFIGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGH 120 +E FIG++GSG G A+ +E+ A L L ++ FIP+Y+++ + TMP++L +R+ G Sbjct: 64 SAEQFIGMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNG- 122 Query: 121 RIQVYFAALSLLLYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVA 180 + + A LLLY+ L+ LY GAL + G++L + + ++T+ GG+ Sbjct: 123 TVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKV 181 Query: 181 VIYTDTLQALLMIIGALTLMVISMVKIGGFEEVKRRYMLASPDVASILLKYNLSNTNACM 240 + YTD +Q +I+G L +++ V Y + I Y+L + A Sbjct: 182 IGYTDVIQVFFLILGGLATTYLAL------NLVSTHY-----GTSGIFEGYSLMTSKA-- 228 Query: 241 VHPKANALKMLRDPTDED-VPWPG---FILGQTPASVWYWCADQVIVQRVLAAKNIAHAK 296 + M+ P +E+ + PG + G ++ YW +Q I QR L A ++ A+ Sbjct: 229 ----SEHFHMILKPDNENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTAR 283 Query: 297 GSTLMAGFLKLLPMFIIVVPGMISRIVFAD--------EIACINPEHCMQVCGSRAGCSN 348 G L A FLKLL I+V+PG+ + +++ D + +NP+ Sbjct: 284 GGILFAAFLKLLMPIIVVLPGIAAYVLYKDGAFQSEMLQDGSVNPDR------------- 330 Query: 349 IAYPRLVMTLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKS-ASSREL 407 AYP +++ L+P GL+GL A + AA+++ L NS +TIFTLD+YK + K+ AS + L Sbjct: 331 -AYP-VLLNLLPAGLKGLSFAALTAAVVASLAGKANSIATIFTLDIYKKVLKTDASEKNL 388 Query: 408 MIVGRIFVAFMVVISIAWVPII-VEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCN 466 + G+I V +V+ + P + ++ +GG + YIQE +++P + A+F+L FWKR Sbjct: 389 VFTGKIAVVVAMVLGVVIAPYLGIDKKGG--FQYIQEYTGFVSPGIFAMFILGFFWKRAT 446 Query: 467 EQGAFYGGMAGFVLGAVRLIL 487 A + + GF L + +L Sbjct: 447 SNAALFATVGGFGLSLLLKVL 467 Lambda K H 0.326 0.139 0.420 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: 1019 Number of extensions: 50 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: 718 Length of database: 558 Length adjustment: 38 Effective length of query: 680 Effective length of database: 520 Effective search space: 353600 Effective search space used: 353600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 54 (25.4 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