Align Major myo-inositol transporter IolT (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= SwissProt::O34718 (473 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 278 bits (710), Expect = 4e-79 Identities = 165/465 (35%), Positives = 255/465 (54%), Gaps = 28/465 (6%) Query: 8 MSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLFGAALGA 67 M + I+ V+T GGLLFGYD+G +NG G L+ G SLL G +GA Sbjct: 9 MGLIMAIVAVATIGGLLFGYDSGAVNGTQD--GLKSAFALSEGGLGFTVGSLLIGCFIGA 66 Query: 68 VFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVPAY 127 GR++D GRR ++ AV+F I + F+ + + +R G+AVG ASV PAY Sbjct: 67 FLAGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAASVLSPAY 126 Query: 128 LAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHV-------WRFMLVIA 180 ++E++P RGRM T ++MI+SG AFV N L T G ++++ WR+M + Sbjct: 127 ISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYEAWRWMYWMQ 186 Query: 181 SLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQL 240 ++PA + +PESPR+LVSKGR +A RVL + A +L EI+ +F Sbjct: 187 AIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASFSD---- 242 Query: 241 EKATFKDLSVP---WVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGN 297 + T +D+ P VR IV+ GL +A+ QQ+ G+N I YYG + + +GF AL+ N Sbjct: 243 HRPTLRDILDPVKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTENDALLIN 302 Query: 298 IANGVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALL-LIGIFS---------LVLEG 347 I +G +S+ A FV + L+ R+GR+P+L+ G G AL ++ FS LVL Sbjct: 303 IVSGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDAQGKLVL-- 360 Query: 348 SPALPYVVLSLTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSF 407 S L + + ++ F + PV W+ML E+FP ++RG + V F W N+ ++ Sbjct: 361 SQQLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQ 420 Query: 408 TFPILLAAIGLSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLE 452 +FPI+ A +GL+ ++ + + S V +F+ ETKG+ LE ++ Sbjct: 421 SFPIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDMQ 465 Lambda K H 0.327 0.142 0.418 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: 563 Number of extensions: 33 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: 473 Length of database: 466 Length adjustment: 33 Effective length of query: 440 Effective length of database: 433 Effective search space: 190520 Effective search space used: 190520 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: 51 (24.3 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