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 PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 350 bits (898), Expect = e-101 Identities = 204/486 (41%), Positives = 298/486 (61%), Gaps = 12/486 (2%) Query: 19 LDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQ 78 L +V L + GEV AL GENGAGKSTL K++S G +T+ GQ P ++ Sbjct: 31 LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRG-EAER 89 Query: 79 LGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDLGLP-LNPDAP 137 LG+ + QE NL P L+VAEN++L P R G + RLR A A + +GL ++PD P Sbjct: 90 LGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAAMARVGLDAIDPDTP 149 Query: 138 VRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVS 197 V L + QQMVEIA+ + + ++I+DEPTA L+ REV L I L+AR V+++Y+S Sbjct: 150 VGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYIS 209 Query: 198 HRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEFERRKRRRPPGAVVL 257 HRL E++ + R V+RDG+ V + A++V LMVGR + RR GA +L Sbjct: 210 HRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLGAPLL 269 Query: 258 KVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVL 317 KV+ +L +R+VSF R GEI G++GL+GAGRT+L RLI+GAD +G + Sbjct: 270 KVD-------KLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIA 322 Query: 318 VDDKP--LRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDE 375 + P + + SP+ A++AGI L+ EDRK +G L SI N++L +L A+S G +D Sbjct: 323 LGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGV-LDS 381 Query: 376 RAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDI 435 AE+ L E Q +RI+ A A+ +G+LSGGNQQKV++GR + +VL+ DEPTRGID+ Sbjct: 382 EAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDV 441 Query: 436 GAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLM 495 GAK +++ +L++LA G A+VV+SS+L E+M + DRI V G ++ +++ L+ Sbjct: 442 GAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLL 501 Query: 496 AYMATG 501 A G Sbjct: 502 AAAFAG 507 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: 680 Number of extensions: 36 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: 524 Length adjustment: 35 Effective length of query: 480 Effective length of database: 489 Effective search space: 234720 Effective search space used: 234720 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