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_004127105.1 RHSP_RS28505 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_000359745.1:WP_004127105.1 Length = 513 Score = 385 bits (989), Expect = e-111 Identities = 212/498 (42%), Positives = 311/498 (62%), Gaps = 9/498 (1%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + K FPGV ALD V + G VHAL+GENGAGKSTL+KIL+ + D G V Sbjct: 23 LLSAEGIRKEFPGVLALDDVSFHLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGDVRL 82 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121 G + + +PL + GIA I+QE NL P ++VAEN+++ REP+ R G VD + +R Sbjct: 83 KGVEIRLK-SPLDALENGIAMIHQELNLMPYMTVAENIWIRREPKNRFGFVDHTEMRRKT 141 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 + L + L + ++P+ VR L+VA +QMVEIAKA++ N+ ++IMDEPT+AL+ REV L Sbjct: 142 EELFHRLNISIDPEIQVRELSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVAHLFQ 201 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 II L+ + + ++Y++H++ E+ + D ++V RDG+++ + DV D++R+MVGR + Sbjct: 202 IIRDLRTQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHASTDVTRDDIIRMMVGREI 261 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 K P G VL V+ LS G VSF R GEI+G+AGLVG+GR+++ Sbjct: 262 TQMFPKEEVPIGETVLSVKD-------LSLDGVFSNVSFDVRAGEILGVAGLVGSGRSNV 314 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 A IFG P ++G + + K + SP DAI+ + + EDRK GC L S+ N+ + Sbjct: 315 AETIFGVTPASSGTIQLFGKAATISSPADAIRHRMAFLTEDRKDTGCLLILSVLENMQVA 374 Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 L G +V E E +KLR+K + + I LSGGNQQK L+GR M P Sbjct: 375 VLHDKFVRGGFVQEGPIEQACEEMAKKLRVKTPNLDERIENLSGGNQQKALIGRWMLTNP 434 Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 ++LI+DEPTRGID+GAKAE+H++++++A GVAV++ISSE+ EV+ +SDRI+V EG + Sbjct: 435 RILILDEPTRGIDVGAKAEIHRLVTEMARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVT 494 Query: 482 ADLDAQTATEEGLMAYMA 499 LD AT+ +M A Sbjct: 495 GFLDRADATQVKVMELAA 512 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: 631 Number of extensions: 34 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: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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