Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_3497 Echvi_3497 transporter, SSS family
Query= SwissProt::P96169 (543 letters) >FitnessBrowser__Cola:Echvi_3497 Length = 527 Score = 258 bits (660), Expect = 3e-73 Identities = 167/535 (31%), Positives = 280/535 (52%), Gaps = 49/535 (9%) Query: 11 IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70 I I+ F + +++ V W+ + +K S + YFL G+SL + S+I NIS E Sbjct: 3 ITILTFIAFT-LLVAVYAWL-KTRKENLDSEDGYFLGGRSLTGVVIAGSMIMTNISTEHL 60 Query: 71 IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTIL 130 +GM+GS Y G I ++E SA+ LI+ YF+P +++ G+ T+P+++E RF+ ++++ Sbjct: 61 VGMNGSSYKNGFVIVAWEVTSALALIVAAVYFVPRYLKMGLTTVPQYLENRFDAGTRSLV 120 Query: 131 AVFWISLYIFVNLTSVLYLGGLALETILGIP----------LMYSILGLALFALVYSIYG 180 A F + + L VLY G + LE++ I L Y++L + +Y+I+G Sbjct: 121 AFFLLISFAVTLLPIVLYTGAINLESLFNISDTLNISQEQGLWYTVLAVGGIGSIYAIFG 180 Query: 181 GLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSN 240 GL AV +D I + L+L G M +A+ IG + G+ ++ + +P F ++ + + Sbjct: 181 GLKAVAVSDTINGYGLLLAGLMVPVIALFMIGDNNP-LLGLERVFENSPEKFNVVGGKDS 239 Query: 241 PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFL 300 LP + L GL + LY+W NQ IIQR L AK++ EAQKG+++ LKL+VPF+ Sbjct: 240 V----LP-FSTLFTGLIINQLYFWCMNQTIIQRALGAKNLKEAQKGLLYTGALKLLVPFI 294 Query: 301 VVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLT-QFLPVGVKGVVFAALA 359 +VLPG+ + D N D YP L + LPVG+ GV A + Sbjct: 295 IVLPGVIGFYFFGDRLY---------------ENQDMVYPELVKKVLPVGLTGVFAAVIM 339 Query: 360 AAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGG 419 A++S+ S+LNS +TIF++DIYK I P + +LV G+ +A + I + + APM+ Sbjct: 340 GAVLSTFNSVLNSASTIFSIDIYKRLIRPGASAGQLVKAGKLSATILAITSMVAAPMVAN 399 Query: 420 IGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFM-PLSM 477 + FQ +Q+ G+ I ++ L G F K + A + +V + F + F+ + + Sbjct: 400 APEGLFQLLQQLNGIFFIPIASIMLAGFFTKWVSPLAAKVALVTGLTFYVLTTFVFDIGI 459 Query: 478 PF-----MDQMLYTLLFTMVVIAF--------TSLSTSINDDDPKGISVTSSMFV 519 F ++ +L L+ +V +A+ T +S IN D K S+ S + V Sbjct: 460 HFVHIWGIEFVLNVLIMYVVSVAWPMAKPTEKTLISAKINTDKWKYASLVSIILV 514 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: 816 Number of extensions: 48 Number of successful extensions: 4 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: 527 Length adjustment: 35 Effective length of query: 508 Effective length of database: 492 Effective search space: 249936 Effective search space used: 249936 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