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 RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 381 bits (979), Expect = e-110 Identities = 228/519 (43%), Positives = 321/519 (61%), Gaps = 23/519 (4%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + + K+FPGVRAL +V+L GEVHAL+GENGAGKSTL+KILS A+ AD G Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 D P + LG+A IYQE +L P LSVAEN+YLGR +R GLV + Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 129 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 L LG +P A V L++A++Q+VEIA+A+ AR+++MDEPT LS E DRL A+ Sbjct: 130 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 189 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 I L+ ++++Y+SHR+ E+ + DR TV+RDG FV + D A + A +V++MVGR + Sbjct: 190 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 249 Query: 243 --FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 + + + V+L V V ++ SF R GE++GLAGLVGAGRT+ Sbjct: 250 GFYTKTHGQAVEREVMLSVRDVADGR-------RVKGCSFDLRAGEVLGLAGLVGAGRTE 302 Query: 301 LARLIFGADPIAAGRVLVDDK-------PLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHS 353 LARL+FGAD G V + + L PR AI AGI + EDRK QG FLD S Sbjct: 303 LARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQS 362 Query: 354 IRRNLSLPSLKALSALGQW-VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVL 412 + N++L + A ALG ++ A R L I++A A+ +G LSGGNQQKV+ Sbjct: 363 VHENINL-IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVM 421 Query: 413 LGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472 L R + + P+VLI+DEPTRG+DIGAK+E++++++ LA GVA+++ISSEL EV+ + DR+ Sbjct: 422 LSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRV 481 Query: 473 VVFREGVIVADL---DAQTATEEGLMAYMATGTDRVAAP 508 +V REG + ++ + T+E ++A +ATG AAP Sbjct: 482 LVMREGTLAGEVRPAGSAAETQERIIA-LATGA-AAAAP 518 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: 749 Number of extensions: 41 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: 537 Length adjustment: 35 Effective length of query: 480 Effective length of database: 502 Effective search space: 240960 Effective search space used: 240960 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