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 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 363 bits (931), Expect = e-104 Identities = 213/507 (42%), Positives = 315/507 (62%), Gaps = 20/507 (3%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 + ++ + KSF V AL V+L V GE+HALLGENGAGKSTL+K+LS H GT+T Sbjct: 6 ISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITIN 65 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR----LGLVDWSRLRA 119 + D L Q LGI IYQE ++ EL+V EN+Y+GR + + ++DW +R Sbjct: 66 NISYNKLDHKLAAQ-LGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRV 124 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 A +L +GL ++ D V L+++ +QM+EIAK + L+A++IIMDEPT++L+ +EVD L Sbjct: 125 RAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYL 184 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 I+ L+ +++Y+SH+L E++ +CDRYTVM+DG V SG V+DV D+VRLMVGR Sbjct: 185 FLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMVGR 244 Query: 240 HVE--FERRKRRRPPGA--VVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVG 295 ++ F K A V +V VT + +R +SF+ GEI+G AGLVG Sbjct: 245 ELQNRFNAMKENVSNLAHETVFEVRNVTSRDRK-----KVRDISFSVCRGEILGFAGLVG 299 Query: 296 AGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355 +GRT+L +FG D A G + ++ K + RSP DA++ G+ + E R+ G F + SI Sbjct: 300 SGRTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIA 359 Query: 356 RNLSLP-SLK---ALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKV 411 +N+++ SLK A+G + E E+ E R+ L +K I +LSGGNQQKV Sbjct: 360 QNMAISRSLKDGGYKGAMGLF-HEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKV 418 Query: 412 LLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDR 471 L+ + + P+V+I DEPTRGID+GAKAE+++V+ LAD G ++++SSEL E++ V DR Sbjct: 419 LISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDR 478 Query: 472 IVVFREGVIVADL-DAQTATEEGLMAY 497 I VF EG + L + +EE +MA+ Sbjct: 479 IAVFCEGRLTQILTNRDDMSEEEIMAW 505 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: 587 Number of extensions: 29 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: 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