Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::Q8K0E3 (673 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 260 bits (664), Expect = 1e-73 Identities = 153/473 (32%), Positives = 250/473 (52%), Gaps = 41/473 (8%) Query: 28 DIAVLVLYFLFVLAVGLWSTVRTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGHFIGL 87 D V+ +Y V+A+G+W +T+ T + FLAG + W +G SLFASN+ + +GL Sbjct: 13 DYGVIAVYLAIVIAIGVWVARKTR--TGEDLFLAGRSLGWAAIGFSLFASNISTSTLVGL 70 Query: 88 AGSGAAVGISVAAYELNGLFSVLMLAWVFLPIYIAGQVTTMPEYLRRRFGGNRISITLAV 147 GS G++V++YE +L +A++F P+++ +++T PEYL R+ R+ + + Sbjct: 71 TGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYS-RRVRLYFSG 129 Query: 148 LYLFIYIFTKISVDMYAGAIFIQQSL-HLDLYLAIVGLLAITALYTVAGGLAAVIYTDAL 206 L + + + +YAGA+ ++ LD++++ V + +YT GGL AV+YTD L Sbjct: 130 LTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVYTDIL 189 Query: 207 QTVIMLIGAFILMGYSFAAVGGMEGLKDQYFLALASNRSENSSCGLPREDAFHIFRDPLT 266 Q V+++ G + + +V + S RS+ L P+ Sbjct: 190 QAVVLICGTGLTAFLMYQSVD----------FSWESVRSQVPEGHLS-------IVQPID 232 Query: 267 SD-LPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLPLFLMVF 325 D LPWPG+ G+ + WYW T+Q IVQR L AK+LS+A+ G+++ LK+LP F ++ Sbjct: 233 DDTLPWPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTFFIIL 292 Query: 326 PGMVSRVLFPDQVACAHPDICQRVCSNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVAAL 385 PG+++ V PD N SD +P ++ E+LP+GL GL+MA ++AA+ Sbjct: 293 PGVMALVTLPD-------------IQN----SDQVFPIIITEVLPSGLTGLVMAGLIAAI 335 Query: 386 MSSLTSIFNSASTIFTMDLWNHIRPRASERELMIVGRIFVFALVLVSILWIPIVQASQGG 445 MS++ S NS+ST+ D G + ++++I W P++Q G Sbjct: 336 MSTVDSTLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQ--YFG 393 Query: 446 QLFIYIQSISSYLQPPVAMVFIMGCFWKRTNEKGAFSGLILGLLLGLVRLILD 498 L+ YIQ S L PP+ + F +G W R E AF LI+G LGLV +L+ Sbjct: 394 GLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLN 446 Lambda K H 0.325 0.139 0.426 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: 861 Number of extensions: 43 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: 673 Length of database: 526 Length adjustment: 37 Effective length of query: 636 Effective length of database: 489 Effective search space: 311004 Effective search space used: 311004 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: 53 (25.0 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