Align Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized)
to candidate Echvi_1680 Echvi_1680 transporter, SSS family
Query= TCDB::Q2A687 (662 letters) >FitnessBrowser__Cola:Echvi_1680 Length = 528 Score = 278 bits (710), Expect = 6e-79 Identities = 163/536 (30%), Positives = 281/536 (52%), Gaps = 51/536 (9%) Query: 27 PADISVIVIYFLLVLAVGIWAMVQSNRGTVGGFFLAGRSMSWWPIGASLFASNIGSGHFV 86 P D +V+ +Y + ++ +G W + R FLAG S+ W IG +++ +N+G + Sbjct: 9 PLDFAVLGLYLVTLIGIGYWVSFKKKRDADENLFLAGNSLGWPSIGFTMWGTNVGPSMLI 68 Query: 87 GLAGNGAAGGLATGGFEWNALVIVIVLGWLFVPIYIRAGVVTMPEYLKKRFGGNRIRIYL 146 A G G+ G F W A + + +L +F P Y+ A V T+PE++ KRFG + I L Sbjct: 69 ASASIGYTTGVVAGNFAWYAFIFIFLLAVVFAPRYLGARVQTLPEFMGKRFGSSTQNI-L 127 Query: 147 SVLSLFLYIFTKISADMFSGAIFIREALGLNIYVAVVILLSITALYTVTGGLAAVIYTDT 206 + ++ + + +S +F+G I IR+ L L ++++VVIL+ I A +T+ GGL A+ YT+ Sbjct: 128 AWYTIVTVLISWLSLTLFAGGILIRQILDLPLWLSVVILILIAAFFTIAGGLKAIAYTNV 187 Query: 207 LQTIIMVVGSFILMGYAFNAVGGYEAMREKYMNAITTQTFDPVLNISANCYTPRSDSFHL 266 Q ++++V S L VGG V + AN TP + ++L Sbjct: 188 FQMVLLIVVSLALTLTGLYKVGG-------------------VGELIAN--TP-GEYWNL 225 Query: 267 FRNPLTADLPWPGLIFGLSILAIWYWCTDQVIVQRCLSAKNMSHVKAGCVLCGYLKLLPM 326 + PW + G ++ +W+WCTDQ +VQ L AKN+ + G G+LK+L + Sbjct: 226 LLPADDPNYPWVAIALGYPVMGVWFWCTDQSMVQSVLGAKNLKEGQLGANFTGWLKILDV 285 Query: 327 YLMVFPGMISRILYTDTIACVVPSLCKQYCDTEVGCSNIAYPTLVVRLMPAGLRGLMLSV 386 L + PG+I +L+ D + + AY T+V +L P G+ GL+++V Sbjct: 286 ALFIIPGIICYVLFPD-----------------LDNPDEAYMTMVTKLFPVGMTGLVMAV 328 Query: 387 MLASLMSSLTSIFNSASTLFTMDIWT-KIRPKATEKELMLAGRVFTLVLIAISIAWIPIV 445 ++A+L+S++ S N+ ST+FTMDI+ K +P+AT+K+++ GRV T++ I+I + Sbjct: 329 LIAALVSTIDSALNALSTVFTMDIYVKKYKPEATQKQIVTIGRVVTVLGAVIAIFLTLAI 388 Query: 446 QTAQSGKLFDYIQSVTSYLGPPIASVFLLGIFVKRTNEKGAFWGLIFGLAMGLS-RMIPE 504 + + LFD QS+ ++ PP++ VFL G+ K+T K A L+FG + L ++ Sbjct: 389 DSIKGLNLFDVFQSILGFIAPPMSVVFLFGVLWKKTTTKAANTVLLFGTILSLGIGVLYL 448 Query: 505 FVFGTGSCVRPSNCPLIICGIHYLYFAIILFVATCLLVLIISLLTKPIEDKHLHRL 560 +VF H+L + +FV L+++IS + + +D H+ L Sbjct: 449 WVFPNAE---------YAFWPHFLLLSFYIFVFLAALIVVISYVERNRKDLHVSTL 495 Lambda K H 0.326 0.141 0.442 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: 926 Number of extensions: 41 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: 662 Length of database: 528 Length adjustment: 37 Effective length of query: 625 Effective length of database: 491 Effective search space: 306875 Effective search space used: 306875 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