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_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_000469325.1:WP_022528026.1 Length = 515 Score = 317 bits (813), Expect = 5e-91 Identities = 185/507 (36%), Positives = 300/507 (59%), Gaps = 26/507 (5%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L + +SKSF R LD +D+ V G V L+GENGAGKST++K L D G Sbjct: 22 MLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFYL 81 Query: 63 AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLR 118 G+ + P+DA + GIA ++QE N + SV +N++LGR P LG+VD ++R Sbjct: 82 DGKEVSFQGPKDA----LENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQMR 137 Query: 119 ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178 +A L LG+ +N P+R ++V+++QMVEIAKA++ ++++I++DEPT++L +EVD+ Sbjct: 138 REATELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDK 197 Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238 L ++ LK + +S+I++SH++ EV +CD +V+RDG V + AD + ++V+ MVG Sbjct: 198 LFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAMVG 257 Query: 239 RHVEFERRKRRRPP-----GAVVLKVEGV-TPAAPRLSAPGYLRQVSFAARGGEIVGLAG 292 R ++ R PP G +L+V + T +P YL+ ++F+ GEI GL G Sbjct: 258 RPLD-----NRFPPVDNVVGKTILQVSHLSTKFSP------YLQDITFSVGQGEIFGLYG 306 Query: 293 LVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH 352 LVGAGRT+L IFG AAGRV + K S ++A+ G ++ E+RK G FL Sbjct: 307 LVGAGRTELLETIFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKG 366 Query: 353 SIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVL 412 S+ N ++ +L A G + E+ Q + K + I LSGGNQQKV+ Sbjct: 367 SLTFNTTITNLDAYKR-GVALSEQKMTKATLKEIQVMNTKTMGPDELIASLSGGNQQKVI 425 Query: 413 LGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472 +G+ + P++ ++DEPTRGID+GAK E+++++ +A G ++V+SSE+ E++ +++RI Sbjct: 426 IGKWLERLPQLFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRI 485 Query: 473 VVFREGVIVADLDAQTATEEGLMAYMA 499 V G + ++ + +E L+ A Sbjct: 486 GVMSNGRLAGIVNTKQTNQEELLRLSA 512 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: 544 Number of extensions: 23 Number of successful extensions: 9 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: 515 Length adjustment: 35 Effective length of query: 480 Effective length of database: 480 Effective search space: 230400 Effective search space used: 230400 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