Align Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::Q6R4Q5 (597 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 281 bits (720), Expect = 4e-80 Identities = 173/528 (32%), Positives = 275/528 (52%), Gaps = 61/528 (11%) Query: 17 LTVVDIAIIAVYFALNVAVGIWSSCRASRNTVRGYFLAGRDMTWWPIGASLFASSEGSGL 76 LT++D +IAVY A+ +A+G+W + + T FLAGR + W IG SLFAS+ + Sbjct: 9 LTMLDYGVIAVYLAIVIAIGVWVARKT--RTGEDLFLAGRSLGWAAIGFSLFASNISTST 66 Query: 77 FIGLAGSGAAGGLAVAGFEWNATYVLLALAWVFVPIYLSSEIVTMPEYMQKRYGGQRIRM 136 +GL GS GGL V+ +EW A LL +A++F P++L S I T PEY++ RY +R+R+ Sbjct: 67 LVGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRY-SRRVRL 125 Query: 137 YLSVLSLLLSVFTKISIDLYAGALFVHICL-GWNFYLSTVIMLAITALYTIAGGLTAVIY 195 Y S L+++ +V + LYAGA+ + + + ++S V + +YT GGL AV+Y Sbjct: 126 YFSGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVY 185 Query: 196 TDALQTLVMVAGAVILTIKAFEQIGGYEQLAEAYAQAVPSRTISNTTCHVPRADAMHMFR 255 TD LQ +V++ G + ++ + + E+ VP +S Sbjct: 186 TDILQAVVLICGTGLTAFLMYQSV---DFSWESVRSQVPEGHLS--------------IV 228 Query: 256 DPYTAD-LPWTGMTFGLTIMAAWYWCTDQVIVQRSLSARDLNHAKGGSILASYLKMLPMG 314 P D LPW G+ G+ ++ WYW T+Q IVQR L A+DL++A+ G+IL LK+LP Sbjct: 229 QPIDDDTLPWPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTF 288 Query: 315 LMVMPGMISRVLFPDDVGCVVPAECLRACGAEIGCSNIAYPKLVMELMPTGLRGLMVAVM 374 +++PG+++ V PD I S+ +P ++ E++P+GL GL++A + Sbjct: 289 FIILPGVMALVTLPD-----------------IQNSDQVFPIIITEVLPSGLTGLVMAGL 331 Query: 375 MAALMSSLTSIFNSSSTLFTMDIWRRLRPRAGERELLLVGRLVIVVLVGVSVAWIPVLQG 434 +AA+MS++ S NSSSTL D R G + + + +++AW P++Q Sbjct: 332 IAAIMSTVDSTLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQY 391 Query: 435 SNGGQLFIYMQSVTSSLAPPVTAVFVLGIFWRRANEQGAFWGLMAGLAVGATRLVLEFLH 494 G L+ Y+Q S L PP+ F LG W R E AFW L+ G +G +L Sbjct: 392 FGG--LWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLN--- 446 Query: 495 PAPPCGHPDTRPPILHGVHYLHFAVALFLL---SGAVVVAGSLLTPHP 539 G+ LH+ +++ ++ S A+ VA SL P Sbjct: 447 --------------QFGIWPLHYTISVTIMTAVSAAIFVALSLRDDTP 480 Lambda K H 0.327 0.139 0.437 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: 768 Number of extensions: 32 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: 597 Length of database: 526 Length adjustment: 36 Effective length of query: 561 Effective length of database: 490 Effective search space: 274890 Effective search space used: 274890 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