Align Major myo-inositol transporter IolT (characterized)
to candidate WP_084931685.1 HA51_RS02405 sugar porter family MFS transporter
Query= SwissProt::O34718 (473 letters) >NCBI__GCF_002095475.1:WP_084931685.1 Length = 469 Score = 402 bits (1034), Expect = e-116 Identities = 216/459 (47%), Positives = 301/459 (65%), Gaps = 16/459 (3%) Query: 11 LRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLFGAALGAVFG 70 +R I +VST GGL FGYDTGV++GAL +M LNL EG +TS LLFGAALG++FG Sbjct: 13 MRLITIVSTIGGLCFGYDTGVISGALIFMKY--DLNLTPTQEGFITSFLLFGAALGSLFG 70 Query: 71 GRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVPAYLAE 130 G +SD GRRKN+L++A IF +G FA +V MI++RF+LG+AVG ASVTVP Y++E Sbjct: 71 GYLSDKQGRRKNLLWVAAIFMFGALGTAFAWDVPSMIVARFILGLAVGCASVTVPIYISE 130 Query: 131 MSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIASLPALFLFFG 190 ++ + R R+VT NELMIV+GQ LA+ NA + + H WR ML I +LP L+FG Sbjct: 131 LARADQRERLVTVNELMIVTGQFLAYSVNAAIVNLYPEMQHNWRIMLAIPALPGALLWFG 190 Query: 191 MIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQLEKATFKDLSV 250 M+ MPESPR+ + +G E A++VLK +R + E++EI+ K D+++ F +L Sbjct: 191 MLMMPESPRFFIRRGETEKAVKVLKTLRLPEEVDREVKEIQ-QIVKADEVKFNLFAELKN 249 Query: 251 PWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIANGVISVLATFV 310 WV ++V IGL I + ++TGVN+IMYY +L+ +G AA+ G +ANG+ISVLAT + Sbjct: 250 RWVIQLVLIGLMIVLATRVTGVNTIMYYAPTVLKATGLGDAAAVTGAVANGIISVLATLL 309 Query: 311 GIWLLGRVGRRPMLMTGLIGTTTALLLIGI-FSL-----VLEGSPAL-------PYVVLS 357 G+ L+G+ RR M TG G T +L+LIG+ F L + G L PYV+L Sbjct: 310 GMALIGKHSRRKMFFTGQAGVTVSLVLIGLAFKLFFHTETINGVDTLHANFANAPYVILG 369 Query: 358 LTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIG 417 L + FL F QG I+PV WLML+EI+PLR+RG+GMG VF LW+ +F + FP LL G Sbjct: 370 LMLVFLVFMQGWIAPVFWLMLAEIYPLRMRGVGMGFAVFGLWIFDFMIQSIFPYLLGHYG 429 Query: 418 LSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEENFR 456 TF F + ++ + ++LPET+GL+LEQ+E+ FR Sbjct: 430 GGMTFGFFGATNVIMLILLVKYLPETRGLTLEQIEKKFR 468 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: 650 Number of extensions: 25 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: 473 Length of database: 469 Length adjustment: 33 Effective length of query: 440 Effective length of database: 436 Effective search space: 191840 Effective search space used: 191840 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 24 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