Align Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 (characterized)
to candidate Echvi_1871 Echvi_1871 transporter, SSS family
Query= SwissProt::Q9JKZ2 (718 letters) >FitnessBrowser__Cola:Echvi_1871 Length = 547 Score = 239 bits (611), Expect = 2e-67 Identities = 160/482 (33%), Positives = 255/482 (52%), Gaps = 24/482 (4%) Query: 9 DIAVVALYFILVMCIGFFAMW--KSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFI 66 D+ V Y +L++ +G K + YFLA +++ W A+GASL SNI +E FI Sbjct: 7 DLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQFI 66 Query: 67 GLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYF 126 G++GSG A G A+ +E+ A L ++ F+PIY++ G+YTMP++L++R+ G R++ Sbjct: 67 GMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDG-RVRTVM 125 Query: 127 AALSLLLYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDT 186 A LL+Y+F L+ LY GAL ++ +G L +I L + ++ GGL AV +TD Sbjct: 126 AIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGLALFAMVYSIYGGLKAVAWTDV 185 Query: 187 LQALLMIIGAL--TLMVISMVKIGGFEEVKRRYMLASPDVASILLKYNLSNTNACMVHPK 244 +Q + ++ G L T + +S+V G E A+P S++++ M+ P Sbjct: 186 VQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIE------KGEMMIPD 239 Query: 245 ANALKMLRDPTDEDVPWPG---FILGQTPASVWYWCADQVIVQRVLAAKNIAHAKGSTLM 301 + D + PG I G ++ YW +Q I QR LAAK++ A+ + Sbjct: 240 GSG-----GSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVF 294 Query: 302 AGFLKLLPMFIIVVPGMISRIVFADEIACINPEHCMQVCGSRAGCSNIAYPRLVMTLVPV 361 AGFLKLL I+V+PG I+ V + A + M + S+ AYP L + L+P Sbjct: 295 AGFLKLLMPLIVVIPG-IAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTL-LHLLPP 352 Query: 362 GLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYK-LIRKSASSRELMIVGRIFVAFMVV 420 GL+GL A + AA++S L S+ NS STIFT+D+YK K+ S + + +GRI + Sbjct: 353 GLKGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFI 412 Query: 421 ISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVL 480 I+ P + ++ Q + YIQE +++P V A+F+ FWK+ A + L Sbjct: 413 IAAIVAPQLRQLD--QAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPL 470 Query: 481 GA 482 A Sbjct: 471 SA 472 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: 914 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: 718 Length of database: 547 Length adjustment: 38 Effective length of query: 680 Effective length of database: 509 Effective search space: 346120 Effective search space used: 346120 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 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