Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 352 bits (902), Expect = e-101 Identities = 211/505 (41%), Positives = 306/505 (60%), Gaps = 22/505 (4%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ--GE 62 P+L+M+GI K+F AL D++L++R GEIHAL+GENGAGKSTLMKVLSGV+ GE Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63 Query: 63 ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122 I G+P A R S GI +I+QELA+ P +S+ N+F+G+E +R G+ID A Sbjct: 64 IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASR-GVIDWDAATL 122 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 R +LR +G L + + +QQ VEIA+AL +++I+DEPTA+L+E +++ L Sbjct: 123 RARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDAL 182 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE--IDSERIVQMMV 240 ++ + + G+A I ISH++ E+ +ADRVT+LRDG+ V L E + +RI++ MV Sbjct: 183 LELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMV 242 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK--------IRPASFDVRAGEVLGFAG 292 GR+LS+ Y + P D + +V+ + +R + VR GEV+G AG Sbjct: 243 GRALSDRYPRRTTVPGDV-----LFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAG 297 Query: 293 LVGAGRTELARLLFGADPRSG--GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFL 350 L+GAGRTE A LFG G L+GR + + AM G+AY EDRK GL L Sbjct: 298 LMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVL 357 Query: 351 QMAVAANATM-NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQK 409 + N T+ N+ R + R + VA +RL ++ A LSGGNQQK Sbjct: 358 DNDIRHNVTLANLRGVAKRWVIDHEREVQ-VAEEFRRRLRIRCADVFQETVNLSGGNQQK 416 Query: 410 VLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICD 469 V+L++WL P+VLILDEPTRG+D+ AK EIY ++++L ++G VV+ISSE+PE++G+ D Sbjct: 417 VVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVAD 476 Query: 470 RVLVMREGMITGELAGAAITQENIM 494 R+ VM G + E+ A +QE IM Sbjct: 477 RIYVMNAGEMVAEMPAAEASQEKIM 501 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: 688 Number of extensions: 48 Number of successful extensions: 11 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: 518 Length adjustment: 35 Effective length of query: 486 Effective length of database: 483 Effective search space: 234738 Effective search space used: 234738 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