Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 356 bits (914), Expect = e-102 Identities = 207/497 (41%), Positives = 298/497 (59%), Gaps = 13/497 (2%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +L G+ K++ A L ++ L++R GE+ AL GENGAGKSTL K++SG+ P G + Sbjct: 16 VLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTY 74 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+ A G + G+ ++ QEL + P ++VA N+F+ + L +R G I H +R Sbjct: 75 RGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDN-LPSRFGWISHKRLRQLAT 133 Query: 126 AVLRQLGAGFGASDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 A + ++G D G L I QQ VEIAR L+ ++I+DEPTA L+ RE LF Sbjct: 134 AAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFT 193 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 + RLR G+AI+YISHR+ E+ +A R+ VLRDG V + S +V +MVGR L Sbjct: 194 QIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGREL 253 Query: 245 SEFYQHQRIAPADAAQL--PTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELA 302 E R QL P + + G K+R SF+VRAGE+ G +GL+GAGRTEL Sbjct: 254 GEHIDLGR------RQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELL 307 Query: 303 RLLFGADPRSGGDILLEGRP--VHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360 RL++GAD G I L P V ID P+AA+RAGIA + EDRKG+GL L +++AN + Sbjct: 308 RLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIAL 367 Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420 +R G++ S + +A IQ + ++ A + VG+LSGGNQQKV++ RWLE Sbjct: 368 GNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDC 427 Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480 +VL+ DEPTRG+D+ AK +IY L+ LA QG A+VV+SS+L E++ ICDR+ V+ G + Sbjct: 428 QVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLI 487 Query: 481 GELAGAAITQENIMRLA 497 A +Q+ ++ A Sbjct: 488 DTFARDHWSQDQLLAAA 504 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: 739 Number of extensions: 45 Number of successful extensions: 8 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: 521 Length of database: 524 Length adjustment: 35 Effective length of query: 486 Effective length of database: 489 Effective search space: 237654 Effective search space used: 237654 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