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_012759083.1 RLEG_RS18595 L-arabinose ABC transporter ATP-binding protein AraG
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_000023185.1:WP_012759083.1 Length = 501 Score = 375 bits (963), Expect = e-108 Identities = 219/510 (42%), Positives = 319/510 (62%), Gaps = 18/510 (3%) Query: 1 MTLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTV 60 M L+ S +SK +PGV+AL V V G VH L+GENGAGKSTLI++LS AADAG + Sbjct: 1 MAFLEFSNISKGYPGVQALANVSFTVEKGAVHGLMGENGAGKSTLIRVLSGDQAADAGNI 60 Query: 61 TFAGQVLDPRDAPLRRQ-QLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119 G+ + R +R G+ I+QE L PEL+VAEN++LGR P + G++ L Sbjct: 61 LIDGE--EQRYGSVRDAFHAGVIVIHQELQLVPELTVAENLWLGRFPAKGGVIHTKVLIE 118 Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179 ++ L ++G+ ++P A V L++ +QMVEIAKA+ L+AR+I +DEPT++LS RE + L Sbjct: 119 TVRSKLEEIGIDVDPSAKVASLSIGARQMVEIAKAVMLDARVIALDEPTSSLSSRESEIL 178 Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVA-SGDVADVEVADMVRLMVG 238 ++I LKA+ ++YVSHRL E+ +CD TV+RDG+ A +A+ ++ MVG Sbjct: 179 FSLIDRLKAQGTVILYVSHRLDEIFRLCDSLTVLRDGKLAAHHPQIAETTREQIISEMVG 238 Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298 R + R RP G + L+V G+ + PRL P +SF+ R GEI+G GL+GAGR Sbjct: 239 REISNVWGWRERPFGGIRLEVNGL--SGPRLRHP-----ISFSVREGEILGFFGLIGAGR 291 Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358 +++ARL++GAD G+V +D + +P+ AI AG++L PEDRK G SI N+ Sbjct: 292 SEMARLLYGADARHQGQVTIDGVAVSPNNPKAAINAGMVLCPEDRKFDGIVQGRSIEENI 351 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 ++ S + S G + R E L + + KLR++ + I LSGGNQQKV+LGR ++ Sbjct: 352 AISSRRHFSPFG-ILSPRQEAALADRFIAKLRVRTPSRKQDIINLSGGNQQKVILGRWLS 410 Query: 419 LTP-KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477 KVL++DEPTRGID+GAK+E++++L +LA G+A+VVISSEL EVM +SDRI+V + Sbjct: 411 EQGIKVLVIDEPTRGIDVGAKSEIYEILYELAAGGMAIVVISSELPEVMGISDRIMVMCQ 470 Query: 478 GVIVA-----DLDAQTATEEGLMAYMATGT 502 G + A D D ++ L A GT Sbjct: 471 GRVAANVARPDFDERSILTAALPDKNAAGT 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: 638 Number of extensions: 35 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: 501 Length adjustment: 34 Effective length of query: 481 Effective length of database: 467 Effective search space: 224627 Effective search space used: 224627 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