Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 380 bits (977), Expect = e-110 Identities = 213/498 (42%), Positives = 302/498 (60%), Gaps = 11/498 (2%) Query: 7 LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66 ++ R + K FG L + ++PG ++ L+GENGAGKSTLMK+L+G +P GE+++D Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 67 GRPVALRDPG----ASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122 G A+R PG A+ A GI LI+QE +A ++++A N+F+G E++ L +D AMR Sbjct: 65 G---AVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGL-FLDDKAMRE 120 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 +T L ++G +L +AE+Q VEIARAL +R++IMDEPTA L+ ETE+L Sbjct: 121 KTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERL 180 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 F ++ L+ G+ IIYISH++ EV D V V+RDG V + ++ +MVGR Sbjct: 181 FALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGR 240 Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELA 302 L++ + + AP D A TV + G F+VR GE+LGFAGLVGAGRTEL Sbjct: 241 ELADLFPPKLPAPQDGAPAITVRGLTV--PGWAEGVDFEVRRGEILGFAGLVGAGRTELF 298 Query: 303 RLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNV 362 L G PR+ G + + G+PV + PR A R G+ Y+ EDRKG+GL + + N T+ Sbjct: 299 EGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMA 358 Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422 R+ + L + + R A+Q ++ E LSGGNQQK+ LA+ L P V Sbjct: 359 LERYAKPWLDPAAEQAAL-REAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSV 417 Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482 ++LDEPTRGVD+ AK EIY LV RLA QG+AV+VISSEL E+IG+C RV VMR G + Sbjct: 418 VVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTT 477 Query: 483 LAGAAITQENIMRLATDT 500 L +T+E ++ AT T Sbjct: 478 LQEPHLTEEELIAHATGT 495 Score = 80.1 bits (196), Expect = 2e-19 Identities = 69/258 (26%), Positives = 124/258 (48%), Gaps = 20/258 (7%) Query: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 326 VR L G F ++ G V G G GAG++ L ++L G + + G+++++G + Sbjct: 17 VRVLHG-----VGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGA---VR 68 Query: 327 QP----RAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGL-VRSRSLGGVA 381 P RAA GI + ++ L + +A N + + GL + +++ Sbjct: 69 APGGGSRAAEAQGIVLIHQEFN---LADDLTIAQNIFLG---HEIKRGLFLDDKAMREKT 122 Query: 382 RAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIY 441 R A+ ++ + + P+T V KL +Q V +AR L ++LI+DEPT + ++ Sbjct: 123 REALAKVGLPL-DPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLF 181 Query: 442 QLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTN 501 L+ L + GV ++ IS +L EV D V+VMR+G++ A A++T+ + L Sbjct: 182 ALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRE 241 Query: 502 VPRTAPASHSSPTPLAPS 519 + P +P AP+ Sbjct: 242 LADLFPPKLPAPQDGAPA 259 Lambda K H 0.320 0.135 0.378 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: 717 Number of extensions: 45 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 496 Length adjustment: 34 Effective length of query: 487 Effective length of database: 462 Effective search space: 224994 Effective search space used: 224994 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