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_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 333 bits (853), Expect = 1e-95 Identities = 201/495 (40%), Positives = 293/495 (59%), Gaps = 15/495 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L + QVS+ F V+ L VD + GEVHAL+GENGAGKST +KIL+ A AG V Sbjct: 5 VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64 Query: 63 AGQVLDPRDAPLRRQQ--LGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120 G+ P P R+ G+ I+QEFNL L+V EN++LGRE +R +D ++A+ Sbjct: 65 DGR---PVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAE 121 Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180 ++ LL L ++P A V L+V +QMVEIAKA+ L AR++IMDEPTA L+ RE D L Sbjct: 122 SRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181 Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240 + L+A +++Y SH+L EV + DR TV+RDGR V + + M MVGR Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241 Query: 241 VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 + + P VL+V G+T PG++R SF R GE++G AGLVG+GRT+ Sbjct: 242 LSGLFPPKSSPAPEPVLEVAGLT-------VPGFVRDASFTLRRGEVLGFAGLVGSGRTE 294 Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 L I G P A G V ++ PL S A AG++ + EDRK++G L + NL+L Sbjct: 295 LMEGIVGLRP-ATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTL 353 Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 +L + +D+ AE + I++ D + G LSGGNQQK+LL + M Sbjct: 354 LALDRFGRV--LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411 Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 P+V+I+DEPTRGID+G K +++ ++ LA G +V+V+SSEL EV+ +++R+VV G I Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471 Query: 481 VADLDAQTATEEGLM 495 +++ + TEE ++ Sbjct: 472 AGEVEGEAITEENIV 486 Score = 84.7 bits (208), Expect = 7e-21 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 23/232 (9%) Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334 L V F R GE+ L G GAG++ +++ G +AG VL+D +P+ S R+A A Sbjct: 21 LFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLDGRPVHFPSSREAEAA 80 Query: 335 GIMLVPEDRK-------QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387 G++++ ++ ++ FL ++R G ++D RA + E+ R Sbjct: 81 GVVMIHQEFNLATPLTVEENIFLGRELKR-------------GPFLDHRAMQ--AESRRL 125 Query: 388 KLRIKMA-DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLS 446 R+ A D + LS N+Q V + +A+ L +VLI+DEPT + + + + Sbjct: 126 LERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVD 185 Query: 447 DLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498 L G A++ S +L EV ++DR+ V R+G V A+ +E+ + M Sbjct: 186 RLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETM 237 Score = 55.8 bits (133), Expect = 3e-12 Identities = 57/218 (26%), Positives = 93/218 (42%), Gaps = 13/218 (5%) Query: 29 GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQEF 88 GEV G G+G++ L++ + A G V G L P + + G+ + ++ Sbjct: 279 GEVLGFAGLVGSGRTELMEGIVGLRPA-TGEVRMEGSPL-PHASVSAARAAGLVYLTEDR 336 Query: 89 NLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA-------LLNDLGLPLNPDAPVRG- 140 E + LG L L + R+ D A ++D + + G Sbjct: 337 K---EKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGS 393 Query: 141 LTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRL 200 L+ QQ + +AK M R++I+DEPT + +++ IA L A SVI VS L Sbjct: 394 LSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSEL 453 Query: 201 GEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238 EV + +R VM GR + + ++VRL +G Sbjct: 454 PEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491 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: 709 Number of extensions: 33 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 499 Length adjustment: 34 Effective length of query: 481 Effective length of database: 465 Effective search space: 223665 Effective search space used: 223665 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