Align inositol transporter 4 (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091598 (582 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 186 bits (472), Expect = 2e-51 Identities = 114/356 (32%), Positives = 185/356 (51%), Gaps = 24/356 (6%) Query: 27 IMRLALSAGIGGLLFGYDTGVISGALLFIKEDFDEVDKKTWLQSTIVSMAVAGAIVGAAV 86 IM + A IGGLLFGYD+G ++G +K F + L T+ S+ + G +GA + Sbjct: 12 IMAIVAVATIGGLLFGYDSGAVNGTQDGLKSAF--ALSEGGLGFTVGSLLI-GCFIGAFL 68 Query: 87 GGWINDKFGRRMSILIADVLFLIGAIVMAFAPAPWVIIVGRIFVGFGVGMASMTSPLYIS 146 G + D GRR +++ VLFLIGA++ F+ W+ + RI G VG AS+ SP YIS Sbjct: 69 AGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAASVLSPAYIS 128 Query: 147 EASPARIRGALVSTNGLLITGGQFFSYLINLAFVHTPG-----------TWRWMLGVAGV 195 E +PA IRG + + ++I G ++++N T G WRWM + + Sbjct: 129 EVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYEAWRWMYWMQAI 188 Query: 196 PAIVQFVLMLSLPESPRWLYRKDRIAESRAILERIYPADEVEAEMEALKLSVEAEKADEA 255 PA V + + +PESPR+L K R AE+ +L ++ A ++ ++ S + Sbjct: 189 PATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASFSDHRPTLR 248 Query: 256 IIGDSFSAKLKGAFGNPVVRRGLAAGITVQVAQQFVGINTVMYYSPSIVQFAGYASNKTA 315 I D +KG VR + AG+ + V QQ VGIN + YY ++ Q AG+ N A Sbjct: 249 DILD----PVKGG-----VRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTEN-DA 298 Query: 316 MALSLITSGLNALGSIVSMMFVDRYGRRKLMIISMFGIIACLIILATVFSQAAIHA 371 + +++++ ++ V++ VDR GR+ L++I G+ L + FS+ ++ A Sbjct: 299 LLINIVSGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDA 354 Score = 65.1 bits (157), Expect = 6e-15 Identities = 27/103 (26%), Positives = 57/103 (55%) Query: 455 KFGFLAIVFLGLYIVVYAPGMGTVPWIVNSEIYPLRYRGLGGGIAAVSNWVSNLIVSESF 514 + G +A++ LY+V + G V W++ E++P + RG + + W SN ++++SF Sbjct: 363 QLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQSF 422 Query: 515 LSLTHALGSSGTFLLFAGFSTIGLFFIWLLVPETKGLQFEEVE 557 + LG + ++ +A + I F + + ETKG++ E+++ Sbjct: 423 PIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDMQ 465 Lambda K H 0.324 0.139 0.422 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: 649 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 582 Length of database: 466 Length adjustment: 35 Effective length of query: 547 Effective length of database: 431 Effective search space: 235757 Effective search space used: 235757 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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