Align sodium/glucose cotransporter 1 (characterized)
to candidate Ga0059261_1623 Ga0059261_1623 transporter, SSS family
Query= CharProtDB::CH_091086 (664 letters) >FitnessBrowser__Korea:Ga0059261_1623 Length = 549 Score = 242 bits (618), Expect = 3e-68 Identities = 160/549 (29%), Positives = 280/549 (51%), Gaps = 69/549 (12%) Query: 28 DISIIVIYFVVVMAVGLWAMFST--NRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFV 85 D+ ++++Y + + A+ W + +FLA +S+ WW IGASL A+NI + V Sbjct: 8 DLIVVIVYAIGIFALAQWVSREKAGHAKDTSDYFLASKSLPWWAIGASLIAANISAEQIV 67 Query: 86 GLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYL 145 G++G+G A G+AI +EW A + ++++G F+PI++K + TMP++L +RF G I+ + Sbjct: 68 GMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPIFLKNEIYTMPQFLEQRF-GPTIRTVM 126 Query: 146 SLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTDT 205 ++ L LYIF +++ ++ G+I + G++ +A+F L A +Y + GGL AV TD Sbjct: 127 AVFWLALYIFVNLTSILWLGSIAVTQVAGVDQDIALFGLGAFALVYQLRGGLKAVALTDI 186 Query: 206 LQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRADSFHI 265 +Q ++++G L+++ ++GG M + + + + D Sbjct: 187 VQVTLLVLGGLVISYLTLSKIGGDAGVMGGFTRLTTELPG-------------KFDMILA 233 Query: 266 FRDPLTGDLPWPG-FIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLKLMP 324 +P DLP I GM I L YW +Q I+QR L+AK++S + G + +LKL+ Sbjct: 234 PDNPFYKDLPGLSVLIGGMWIANLSYWGFNQYIIQRALAAKSLSEAQKGVVFAAFLKLLM 293 Query: 325 MFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGLMLS 384 I+V+PG+ + IL + + + AYPT+ + L+P GL GL+ + Sbjct: 294 PVIIVLPGIAAVILAPD-----------------LAKPDQAYPTM-MRLLPVGLLGLVFA 335 Query: 385 VMLASLMSSLTSIFNSASTLFTMDIYAKVR--------------------KRASEKELMI 424 ++A++++S S NS +T+FT+D+YAK + A EK+L+ Sbjct: 336 ALVAAIIASTASKINSIATIFTLDLYAKAKGVQSRAQDAATASASGDSGLTAAHEKQLVR 395 Query: 425 AGRLFILVLIGISIAWV-PIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEP 483 GR +V ++I P++ S Q F YIQ + ++ P I +FLL +FW R E Sbjct: 396 VGRTTAVVATLLAIFTARPLLGSLD--QAFQYIQEFSGFVTPGITVIFLLGLFWPRATEA 453 Query: 484 GAFWGLILGLLIGISRMITEFAYGTGSCMEPSNCPTIICGVHYLYFAIILFAISFITIVV 543 GA G + +L+ + F G + V ++ +I+F +S VV Sbjct: 454 GALTGAVASVLLS---FLFWFPADWGGI-------ATLNAVPFMNRMMIVFFVSLALAVV 503 Query: 544 ISLLTKPIP 552 +SL+ +P P Sbjct: 504 VSLV-RPAP 511 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: 726 Number of extensions: 38 Number of successful extensions: 5 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: 549 Length adjustment: 37 Effective length of query: 627 Effective length of database: 512 Effective search space: 321024 Effective search space used: 321024 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