Align Major myo-inositol transporter IolT (characterized)
to candidate WP_057508163.1 ABB28_RS08195 MFS transporter
Query= SwissProt::O34718 (473 letters) >NCBI__GCF_001431535.1:WP_057508163.1 Length = 474 Score = 290 bits (742), Expect = 7e-83 Identities = 167/464 (35%), Positives = 262/464 (56%), Gaps = 17/464 (3%) Query: 4 QGNQMSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLFGA 63 QG +F+ I V+T GG LFG+D+GV+NG + G N + G +S+L G Sbjct: 12 QGENTAFIVLISCVATIGGFLFGFDSGVINGTVD--GLRTAFNSSEAALGFEVASMLLGC 69 Query: 64 ALGAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVT 123 A+GA GR+ D GRR ++ AV+F +S +G A + + +R + G AVG ASV Sbjct: 70 AIGAFLAGRLGDLLGRRSVLIISAVLFLLSALGAGAAHASWLFVAARVIGGFAVGAASVM 129 Query: 124 VPAYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHV-------WRFM 176 PAY+AE++ RG++ T ++ I+SG AF+ N +L G ++ V WR+M Sbjct: 130 APAYIAEVASARYRGKLATVQQIAIISGLFAAFLSNYLLARAAGASTEVLWLGQEAWRWM 189 Query: 177 LVIASLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKK 236 + ++P+L ++ +PESPR+LV KGR+ +A VL ++ A A+L EIE + + Sbjct: 190 FWMQAIPSLLFLALLLVIPESPRFLVVKGRRAEASAVLTRLYGAVEAQAKLGEIEHSLAQ 249 Query: 237 EDQLEK-ATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALI 295 A KD + +R IV++G+G+A++QQ+ G+N + YYG + + GF AL+ Sbjct: 250 HQHRPSFADLKDKASGKLRGIVWVGIGLAVLQQLVGINVVFYYGAVLWQAVGFSENDALL 309 Query: 296 GNIANGVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGIF----SLV---LEGS 348 N+ +G +S+ A V + L+ R+GR+P+L G +G AL L+ + SLV L+ S Sbjct: 310 INVLSGALSIGACLVTVVLIDRIGRKPLLWVGSVGMAIALALMVVAFSSGSLVDGRLQLS 369 Query: 349 PALPYVVLSLTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFT 408 + + L ++ F + PV W+ML E+FP ++RG + V W NFA++ T Sbjct: 370 DGMGRLALVAANVYVVFFNMSWGPVMWVMLGEMFPNQIRGSALAVAGAAQWTSNFAITVT 429 Query: 409 FPILLAAIGLSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLE 452 FPILLA IGL+ + I+ S+ FV R++ ETKG LEQ+E Sbjct: 430 FPILLAGIGLAGAYSIYAVAAFLSIFFVIRYVRETKGKELEQME 473 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: 578 Number of extensions: 35 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: 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