Align sodium/glucose cotransporter 1 (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 274 bits (701), Expect = 7e-78 Identities = 164/530 (30%), Positives = 277/530 (52%), Gaps = 63/530 (11%) Query: 28 DISIIVIYFVVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGL 87 D +I +Y +V+A+G+W T G FLAGRS+ W IG SLFASNI + VGL Sbjct: 13 DYGVIAVYLAIVIAIGVWVARKTRTGE--DLFLAGRSLGWAAIGFSLFASNISTSTLVGL 70 Query: 88 AGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYLSL 147 G+ G+ + +EW A + ++ + ++F P+++K+ + T PEYL R+ +R+++Y S Sbjct: 71 TGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRY-SRRVRLYFSG 129 Query: 148 LSLLLYIFTKISADIFSGAIFINLAL-GLNLYLAIFLLLAITALYTITGGLAAVIYTDTL 206 L+++ + + +++GA+ + + L+++++ + +YT TGGL AV+YTD L Sbjct: 130 LTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVYTDIL 189 Query: 207 QTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRADSFHIF 266 Q V+++ G+ LT F ++ D E +P +G+ + + Sbjct: 190 QAVVLICGT-GLTAFLMYQ--SVDFSWESVRSQVP----EGHLSIVQ------------- 229 Query: 267 RDPLTGD-LPWPGFIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLKLMPM 325 P+ D LPWPG G+ +L WYW T+Q IVQR L AK++S+ + G IL G LK++P Sbjct: 230 --PIDDDTLPWPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPT 287 Query: 326 FIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGLMLSV 385 F +++PG+++ + + + ++ +P ++ E++P+GL GL+++ Sbjct: 288 FFIILPGVMALVTLPD-----------------IQNSDQVFPIIITEVLPSGLTGLVMAG 330 Query: 386 MLASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIGISIAWVPIVQ 445 ++A++MS++ S NS+STL D + K + G + L + I+IAW P++Q Sbjct: 331 LIAAIMSTVDSTLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQ 390 Query: 446 SAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGLLIG-ISRMITEF 504 G L+ YIQ S L PP+ F L W R E AFW LI+G +G + M+ +F Sbjct: 391 --YFGGLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLNQF 448 Query: 505 AYGTGSCMEPSNCPTIICGVHYLYFAIILFAISFITIVVISLLTKPIPDV 554 I +HY I+ A+S V +S L PDV Sbjct: 449 G---------------IWPLHYTISVTIMTAVSAAIFVALS-LRDDTPDV 482 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: 773 Number of extensions: 29 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: 526 Length adjustment: 37 Effective length of query: 627 Effective length of database: 489 Effective search space: 306603 Effective search space used: 306603 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 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