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 AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 324 bits (830), Expect = 5e-93 Identities = 201/502 (40%), Positives = 292/502 (58%), Gaps = 13/502 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L VS + K++ L +DL + GEV AL GENGAGKSTL KI+ G + F Sbjct: 9 VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 G+ P + + ++LGI + QE NL P LSVAEN++L P G + +LR A Sbjct: 68 QGRDYRP-GSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAI 126 Query: 123 ALLNDLGLP-LNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 A + +GL ++PD V L + QQMVEIA+ + + ++I+DEPTA L+ REV+ L Sbjct: 127 AAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 I L+AR V++IY+SHRL E+ + R V+RDG V +A+ +V LMVGR + Sbjct: 187 QITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGREL 246 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 R GA L V+G LS +R VSF R GEI G++GL+GAGRT+L Sbjct: 247 GEHIDLGPRHIGAPALTVKG-------LSRSDKVRDVSFEVRSGEIFGISGLIGAGRTEL 299 Query: 302 ARLIFGADPIAAGRVLVDD--KPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 RLIFGAD +G V + + + +RSP DA+ GI L+ EDRK +G L SI N++ Sbjct: 300 LRLIFGADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIA 359 Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419 L ++ +S+ G V+ E L + +RI+ + + +LSGGNQQKV++GR + Sbjct: 360 LGNMPVISS-GGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLER 418 Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479 VL+ DEPTRGID+GAK +++ +L +L G A+VV+SS+L E+M + DRI V G Sbjct: 419 ECSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGR 478 Query: 480 IVADLDAQTATEEGLMAYMATG 501 ++ + + T++ L+A G Sbjct: 479 LIDTFERDSWTQDDLLAAAFAG 500 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: 635 Number of extensions: 31 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: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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 Apr 09 2024. 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