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 WP_106712778.1 CU102_RS19520 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_003010955.1:WP_106712778.1 Length = 505 Score = 366 bits (939), Expect = e-105 Identities = 209/500 (41%), Positives = 306/500 (61%), Gaps = 12/500 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + KSF G RALD VDL + GE+HALLGENGAGKSTLIK+L+ H D G + Sbjct: 7 LLAARGICKSFIGFRALDAVDLTIRRGEIHALLGENGAGKSTLIKVLTGVHQPDLGVMEL 66 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 GQ + RD L+ QQLGI T+YQE NL P +SVA+N+++GR+P R G +D R+ A+ Sbjct: 67 DGQPIHVRDT-LQAQQLGIGTVYQEVNLLPNMSVADNLFVGRQPMRFGFIDRRRMEKRAR 125 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 LL+ L ++ + + +VA QQ+V IA+A+ ++ R++I+DEPTA+L E + L A Sbjct: 126 ELLSQYDLHIDVSSDLSRYSVAVQQLVAIARAVDMSGRILILDEPTASLDRHETEILFAT 185 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR--- 239 + LK R + +++++H L +V +CDR TV+R+G+ S + + +V LM+GR Sbjct: 186 LRRLKERGLGIVFITHFLDQVYEICDRVTVLRNGKVAGSELTSQLPKMQLVSLMLGRALA 245 Query: 240 HVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299 V R+ R+ P +G+ R AP GE++G+AGL+G+GRT Sbjct: 246 AVTHNVRRDRQEPETKQFSFKGM--GRSRSVAP-----FDLDIGEGEVIGMAGLLGSGRT 298 Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 + ARL+FG D G+ VD P+R+RSP+DA+ G L PEDRK G D S+R N+ Sbjct: 299 ETARLLFGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLCPEDRKTDGIIGDLSVRENIV 358 Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 L +L+A + + R + L + + + L I+ D E I LSGGNQQKV+L R +A Sbjct: 359 L-ALQAQRGWFKRLPRRQQVALADKFVKALDIRTTDIEKPIKFLSGGNQQKVILARWLAT 417 Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 P+ LI+DEPTRGID+GA AE+ +++ L D G+A++VISSE+ E++A S R+VV R+ V Sbjct: 418 NPRFLILDEPTRGIDVGAHAEIIALINQLCDDGMALLVISSEIEEIVAYSTRVVVLRDRV 477 Query: 480 IVADLDAQTATEEGLMAYMA 499 +L T +M +A Sbjct: 478 QRGELAGDDITTTKIMQKIA 497 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: 648 Number of extensions: 41 Number of successful extensions: 8 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: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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 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