Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 394 bits (1012), Expect = e-114 Identities = 211/497 (42%), Positives = 320/497 (64%), Gaps = 10/497 (2%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 L ++ ++K+FPGV+AL V L + G+V AL+GENGAGKST++KIL+ + D G + Sbjct: 21 LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADAQ 122 GQ + P P G+ I+QE LF ELSVAEN++LG PR GL+DW + +A+ Sbjct: 81 GQPV-PFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENAR 139 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 ALL +G L+PD ++ L +A + +V IA+A+++ AR++IMDEPTAALS +E++ L+ + Sbjct: 140 ALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYEL 199 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + LKA+ +++++SH+ E+ + D YTV RDG+ + G +ADV AD+V++MVGR V Sbjct: 200 VESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVS 259 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 +R G VL V+G + P +SF R GEI+G GLVGAGR++ Sbjct: 260 QIFPQRAPNVGDTVLTVQG-------YAHPTEFDDISFTLREGEILGFYGLVGAGRSEFM 312 Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 + +FG +AG V + + SP DA+ GI+ VPEDR +QG LD I +N++LPS Sbjct: 313 QSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPS 372 Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 L +S G ++ E L Y ++L ++ A +T +G LSGGNQQKV++ + +A P+ Sbjct: 373 LGRISRKG-FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPR 431 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 V+I+DEPT+G+DIG+KA VH +++LA G+AV+++SSE+ EV+ +SDR++V REG IVA Sbjct: 432 VIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVA 491 Query: 483 DLDAQTATEEGLMAYMA 499 +L E L+ + A Sbjct: 492 ELAGDDLQPETLVRHAA 508 Score = 72.8 bits (177), Expect = 3e-17 Identities = 69/229 (30%), Positives = 105/229 (45%), Gaps = 15/229 (6%) Query: 20 DQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAG---QVLDPRDAPLRR 76 D + + GE+ G GAG+S ++ L AG+V G ++ P DA Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAV--- 342 Query: 77 QQLGIATIYQEFN---LFPELSVAENMYL---GREPRRLGLVDWSRLRADAQALLNDLGL 130 GI + ++ +L + +N+ L GR R+ G + + A A+ L L Sbjct: 343 -DHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRK-GFLRLAEEFALAREYTERLDL 400 Query: 131 -PLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKAR 189 + D V L+ QQ V IAK + R+II+DEPT + +H +A L A+ Sbjct: 401 RAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQ 460 Query: 190 SVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238 ++VI VS + EV M DR VMR+GR VA D++ +VR G Sbjct: 461 GLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509 Lambda K H 0.320 0.136 0.380 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: 641 Number of extensions: 33 Number of successful extensions: 10 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: 515 Length of database: 510 Length adjustment: 35 Effective length of query: 480 Effective length of database: 475 Effective search space: 228000 Effective search space used: 228000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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