Align Major myo-inositol transporter IolT (characterized)
to candidate WP_084932255.1 HA51_RS04135 sugar porter family MFS transporter
Query= SwissProt::O34718 (473 letters) >NCBI__GCF_002095475.1:WP_084932255.1 Length = 474 Score = 571 bits (1471), Expect = e-167 Identities = 272/456 (59%), Positives = 353/456 (77%), Gaps = 2/456 (0%) Query: 1 MNKQGNQMSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLL 60 M Q ++R II+++TFGGLLFGYD GV+NGALPYM + L LN+ + GL+TS+LL Sbjct: 1 MFDQAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAK--SLGLNSLSTGLITSALL 58 Query: 61 FGAALGAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGA 120 GA GA+ GG++SD GRRKNILFLA++FF+ST+GC+ AP++ M++ RFVLG AVGGA Sbjct: 59 MGAVFGAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGA 118 Query: 121 SVTVPAYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIA 180 SVTVP YLAEM+P +SRGRMVT NELMIV G L+AF+ NA+LG T+G+N HVWR+ML +A Sbjct: 119 SVTVPTYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHVWRYMLALA 178 Query: 181 SLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQL 240 +PA+ LFFGM+ +PESPRWLV +GR+ +A VL++IRDE A EL I+ A E QL Sbjct: 179 MIPAVCLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGIELYNIKHAISHEQQL 238 Query: 241 EKATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIAN 300 K F++L++PW+RRI+ IG+ +A+ Q TGVNSIMY+GTEILR++G +T AALIGN A Sbjct: 239 GKVKFRELNIPWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAGLETSAALIGNTAF 298 Query: 301 GVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGIFSLVLEGSPALPYVVLSLTV 360 G+ISVL+TF GIWLL R GRRPM++ GL GTT LL+I I + +L G+PA+PYVVL+LTV Sbjct: 299 GLISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIATSMLAGNPAMPYVVLTLTV 358 Query: 361 TFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIGLST 420 FLAF QGAI PV W+ LSEIFPLR+RG GMG++V LW+ NF + TFP++L GLS Sbjct: 359 IFLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWITNFFIGLTFPMMLEGFGLSG 418 Query: 421 TFFIFVGLGICSVLFVKRFLPETKGLSLEQLEENFR 456 TFF F +G+ + +K F PETKG SLE++EE+F+ Sbjct: 419 TFFAFAAIGVVGFIIMKMFFPETKGKSLEEIEESFK 454 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: 712 Number of extensions: 20 Number of successful extensions: 3 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: 474 Length adjustment: 33 Effective length of query: 440 Effective length of database: 441 Effective search space: 194040 Effective search space used: 194040 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