Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_002151265.1:WP_086510989.1 Length = 497 Score = 378 bits (970), Expect = e-109 Identities = 214/497 (43%), Positives = 305/497 (61%), Gaps = 10/497 (2%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 P L+ GI F AL + G++HALMGENGAGKSTL+KVLSGV+ P +G + Sbjct: 4 PYLRFDGISMVFPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGALW 63 Query: 65 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124 +DG + + A GI +IYQEL ++PN++VA N+ +G +L TR G I +R R Sbjct: 64 IDGERHVFANAREALAQGIAIIYQELTLSPNMTVAENLLLG-QLPTRHGFIKRRQLRERA 122 Query: 125 DAVLRQLGAG-FGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183 A+L LG G S LSI +QQ +EI RAL+ +RI+ DEPT++LS +ET QL Sbjct: 123 LAILADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLK 182 Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR-DEIDSERIVQMMVGR 242 ++ RLR+EG ++Y++HRM EV+ + D VTV RDG + +D + +V MVGR Sbjct: 183 RIISRLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGR 242 Query: 243 SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTEL 301 + + Y ++ + ++++ A+ G ++ P SF+VR GEV G GLVGAGR+EL Sbjct: 243 DIEDVYGYRERERGEV-----ILEIDAIEGRGLKAPVSFEVRRGEVFGLFGLVGAGRSEL 297 Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361 RL+ GA+ S G++ +G+ P A+R GIA PEDRK QG+F +VA N ++ Sbjct: 298 MRLVCGAERASAGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNIS 357 Query: 362 VASRHTRLGLVR-SRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420 R G++R +R A A IQRL++K P T +G LSGGNQQKV+LARWL Sbjct: 358 CRRFFRRWGVLRDTRRERANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLAEKI 417 Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480 ++ ++DEPTRG+D+ A+ +IY L+ L QG +VVVISS+L EV ICDR+ VMR+G + Sbjct: 418 ELFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRDGALV 477 Query: 481 GELAGAAITQENIMRLA 497 + TQE ++ LA Sbjct: 478 EVVPRHEATQERLLGLA 494 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: 647 Number of extensions: 27 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: 521 Length of database: 497 Length adjustment: 34 Effective length of query: 487 Effective length of database: 463 Effective search space: 225481 Effective search space used: 225481 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