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 GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 393 bits (1009), Expect = e-114 Identities = 222/512 (43%), Positives = 329/512 (64%), Gaps = 16/512 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD-AGTVT 61 LL++ +SK+F G+R L V L V GE+HAL+GENGAGKSTL+KILS A+ AD G + Sbjct: 6 LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIR 65 Query: 62 FAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADA 121 AGQ++ P P + LGIA IYQE +L P LSVAEN+YLGRE RR +D + A Sbjct: 66 IAGQLI-PTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 +L LG P V L++AE+Q+VEIA+A+ +A++++MDEPT LS RE DRL A Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 +I L+++ +++IY+SHR+ E+ A+ DR +V+RDG ++ + +V++MVGR + Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDL 244 Query: 242 E--FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299 +++ PG VV++V + +R SF GE++G+AGLVGAGRT Sbjct: 245 SGFYKKEHAAYNPGNVVMRVRDMADGK-------RVRHCSFDLHAGEVLGIAGLVGAGRT 297 Query: 300 DLARLIFGADPIAAGRVLVDDKPLR-LRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358 +LARLIF ADP +G + V K + LR+P DAI+AG++ + EDRK QG FLD S+ N+ Sbjct: 298 ELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNI 357 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 ++ + + G +D + L I++A + G LSGGNQQKVLL R + Sbjct: 358 NVCACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLE 417 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478 + P VLI+DEPTRG+DIG+K+E++++++ LA G+ +VVISSEL E++ DR+++ REG Sbjct: 418 VKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREG 477 Query: 479 VIVADL---DAQTATEEGLMAYMATGTDRVAA 507 +VA++ Q ++E ++ +ATG D+V A Sbjct: 478 QLVAEVGGASGQAISQERIID-LATGGDQVVA 508 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: 723 Number of extensions: 36 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: 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