Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 263 bits (673), Expect = 9e-75 Identities = 173/556 (31%), Positives = 289/556 (51%), Gaps = 50/556 (8%) Query: 4 IEHGLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAA 63 I+ L+ +D V A+Y+AI+I +G+WV+R + + ED FLAG+SL W A+G SL A+ Sbjct: 5 IDANLTMLDYGVIAVYLAIVIAIGVWVARKTR----TGEDLFLAGRSLGWAAIGFSLFAS 60 Query: 64 NISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFN 123 NIS +G++GS Y+ GL ++SYEWM+ I L+ + F P+F++ I T PE++E R++ Sbjct: 61 NISTSTLVGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYS 120 Query: 124 KKLKTILAVFWISLYIFVNLTSVLYLGGLALETIL-GIPLMYSILGLALFALVYSIYGGL 182 ++++ + I + V+ LY G + L+ + + S + + LFA +Y+ GGL Sbjct: 121 RRVRLYFSGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGL 180 Query: 183 SAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQ 242 AVV+TD++Q L+ G +T ++ + F+ S GH I+ + Sbjct: 181 RAVVYTDILQAVVLICGTGLTAFLMYQSVD-----FSWESVRSQVPEGHLS-IVQPIDDD 234 Query: 243 YMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVV 302 + PG L G+W+ +YW NQYI+QR L AK +S AQ G + LK++ F ++ Sbjct: 235 TLPWPG---LFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTFFII 291 Query: 303 LPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYP-WLTQFLPVGVKGVVFAALAAA 361 LPG+ A V LP N+D+ +P +T+ LP G+ G+V A L AA Sbjct: 292 LPGVMALV-----------------TLPDIQNSDQVFPIIITEVLPSGLTGLVMAGLIAA 334 Query: 362 IVSSLASMLNSTATIFTMD-IYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGI 420 I+S++ S LNS++T+ D + + PD K G A + ++IA AP++ Sbjct: 335 IMSTVDSTLNSSSTLLINDFLTRPEKEPDPETAK--KWGMMATLGFMVIAIAWAPLIQYF 392 Query: 421 GQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFM 480 G + YIQ+ ++ P ++ F LG W + T A ++ I L L L+ + Sbjct: 393 GGLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLI--IGHTLGLVVFMLNQFGI 450 Query: 481 DQMLYTLLFTMV--VIAFTSLSTSINDDDP----KGISVTSSMFVTDRSF-----NIAAY 529 + YT+ T++ V A ++ S+ DD P + + F T + N+ + Sbjct: 451 WPLHYTISVTIMTAVSAAIFVALSLRDDTPDVREDALWQRADAFDTPATTAPVLKNVKTH 510 Query: 530 GIMIVLAVLYT--LFW 543 I+++L ++ T LFW Sbjct: 511 AILLILLMIGTLVLFW 526 Lambda K H 0.326 0.141 0.421 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: 890 Number of extensions: 39 Number of successful extensions: 7 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: 543 Length of database: 526 Length adjustment: 35 Effective length of query: 508 Effective length of database: 491 Effective search space: 249428 Effective search space used: 249428 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: 52 (24.6 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