Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate CCNA_03483 CCNA_03483 ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Caulo:CCNA_03483 Length = 314 Score = 110 bits (275), Expect = 7e-29 Identities = 78/227 (34%), Positives = 120/227 (52%), Gaps = 11/227 (4%) Query: 4 TPLLQMRGIRKSFGAT-LALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 62 T ++ ++G+ K++ + AL + L IR GEI AL+G NGAGK+TL+ ++ G+ P QG Sbjct: 8 TSIISVQGLTKTYASGHQALKRIDLDIRQGEIFALLGPNGAGKTTLISIICGIVNPSQGV 67 Query: 63 ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122 IL DG V +RD A+R I L+ QEL +V A V GL + Sbjct: 68 ILADGHDV-VRDYRAARTK-IGLVPQELHTDAFETVWATVSFSR------GLFGKPRNDA 119 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 + +LR L LS +++V IA+AL H I+ +DEPTA + + Sbjct: 120 LIEQILRDLSLWDKKDSKIMALSGGMKRRVMIAKALSHEPTILFLDEPTAGVDVELRRDM 179 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE 229 + +VR+LR+ G+ II +H + E +ADR+ V+ G + LV D+ Sbjct: 180 WEMVRKLRESGVTIILTTHYIEEAEEMADRIGVINKGEII--LVEDK 224 Score = 78.6 bits (192), Expect = 3e-19 Identities = 59/210 (28%), Positives = 105/210 (50%), Gaps = 23/210 (10%) Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334 ++ D+R GE+ G GAG+T L ++ G S G IL +G V D A + Sbjct: 27 LKRIDLDIRQGEIFALLGPNGAGKTTLISIICGIVNPSQGVILADGHDVVRDYRAARTKI 86 Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVAR--AAIQRLNVKV 392 G+ VP++ L AT++ SR L G R A I+++ + Sbjct: 87 GL--VPQE-----LHTDAFETVWATVSF-----------SRGLFGKPRNDALIEQILRDL 128 Query: 393 A---HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLAS 449 + ++ + LSGG +++V++A+ L P +L LDEPT GVD+ + +++++V +L Sbjct: 129 SLWDKKDSKIMALSGGMKRRVMIAKALSHEPTILFLDEPTAGVDVELRRDMWEMVRKLRE 188 Query: 450 QGVAVVVISSELPEVIGICDRVLVMREGMI 479 GV +++ + + E + DR+ V+ +G I Sbjct: 189 SGVTIILTTHYIEEAEEMADRIGVINKGEI 218 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: 345 Number of extensions: 20 Number of successful extensions: 4 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: 314 Length adjustment: 31 Effective length of query: 490 Effective length of database: 283 Effective search space: 138670 Effective search space used: 138670 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: 50 (23.9 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