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 BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 377 bits (967), Expect = e-109 Identities = 215/504 (42%), Positives = 321/504 (63%), Gaps = 18/504 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + +SK + AL+ V + GEVHAL+GENGAGKSTL+KILS D+G + Sbjct: 9 LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68 Query: 63 AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRL-GLVDWSRLR 118 GQ +D PRDA ++ GIA I+QE N P+++VAEN++LG+EP G++D R+ Sbjct: 69 DGQAIDIRTPRDA----RKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMH 124 Query: 119 ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178 +A+ LN + ++P AP+ L++ QQMVEIA+A++ NA+++++DEPTAALS E + Sbjct: 125 REAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQ 184 Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238 L+ +IA ++ V ++Y+SHR+ EV + +R TV RDG ++ + ++ +V D+VR+MVG Sbjct: 185 LYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVG 244 Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298 R + + R PG V+L+V + +A + P VSF GE+V ++GLVG+GR Sbjct: 245 RQIVDLYQHEPRTPGDVLLEVRDLAGSA---TGP-----VSFEVSAGEVVSMSGLVGSGR 296 Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358 T++ARL+FGADP + G V + + + P AI GI +V EDRK QG FL HS+ N+ Sbjct: 297 TEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNI 356 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 + SL A G V + R V ++LR++ E + LSGGNQQK L R + Sbjct: 357 DISSLDNFVA-GGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLL 415 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478 ++LI+DEPTRG+DIGAK E+++++ LA G A++VISS+L E + +SDR++V R G Sbjct: 416 RDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGG 475 Query: 479 VIVADLDAQTATEEGLMAYMATGT 502 IV L + +ATEE +M + ATGT Sbjct: 476 RIVHQLPSCSATEEEVMLH-ATGT 498 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: 703 Number of extensions: 27 Number of successful extensions: 9 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: 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