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_085120648.1 B9O00_RS01470 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_900177295.1:WP_085120648.1 Length = 634 Score = 326 bits (836), Expect = 1e-93 Identities = 218/515 (42%), Positives = 300/515 (58%), Gaps = 33/515 (6%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L S + K+F RAL DL + GEVH LLG NGAGKSTL K++S DAG + + Sbjct: 14 ILVASGIEKTFDRTRALAGADLELRAGEVHGLLGANGAGKSTLSKVISGHVQRDAGRLVY 73 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 G+ L R + GIA + QE +L P+LSV EN++L E R GL+ + +R A Sbjct: 74 KGRPLALRSTR-EALEAGIAIVMQETSLAPDLSVLENIFLP-ELGRPGLLSYGSMRRRAV 131 Query: 123 ALLNDLG----LPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178 LL +LG LPL D V L+ A++Q+VEIAKA+ L+A LII DEPTA+LS EV+R Sbjct: 132 GLLANLGHEHVLPL--DREVARLSAAQRQLVEIAKALALDADLIIFDEPTASLSPSEVER 189 Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGD-VADVEVADMVRLMV 237 L I+A L+ ++I+VSHRL EV A+ DR T+MR+G VA+ A + A+++R MV Sbjct: 190 LFDIMAKLRDDGRALIFVSHRLEEVFAITDRVTIMREGATVAASQPTASLTQAEVIRHMV 249 Query: 238 GRHVE-------FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGL 290 GR + + R P V VE L+AP +R VSF R GEI+GL Sbjct: 250 GRDIGALYATPGLQEEDERAP---AVFSVEN-------LAAPPAVRNVSFFVRRGEILGL 299 Query: 291 AGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFL 350 GLVGAGR++ A IFG P +AG + ++ + + R P DA++AGI V EDR+ Q Sbjct: 300 GGLVGAGRSETAEAIFGLRPRSAGTIRLEGREIAPRKPADAVRAGIGFVAEDRRVQNIVP 359 Query: 351 DHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRI---KMADAETAIGKLSGGN 407 D S++ NL L L A G + R R VE L + ++ DA SGG Sbjct: 360 DLSVKENLLLAHLGAHRGFG--LGYRRRRQKVEELMAALGLPAERLLDANML--NFSGGM 415 Query: 408 QQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMA 467 QQK+++ R + L PKVLI+DEPT+G+DIG + ++ +L +AD GVAVVVISS+ E++ Sbjct: 416 QQKIIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEGVAVVVISSDFEELLG 475 Query: 468 VSDRIVVFREGVIVADLDAQTATEEGLMAYMATGT 502 V +R+VV +G +ADL + EE L A T Sbjct: 476 VCERVVVMSDGNAIADLPSALLDEEKLTLLAAPRT 510 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: 802 Number of extensions: 49 Number of successful extensions: 10 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: 634 Length adjustment: 36 Effective length of query: 479 Effective length of database: 598 Effective search space: 286442 Effective search space used: 286442 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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