Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 370 bits (949), Expect = e-107 Identities = 209/509 (41%), Positives = 325/509 (63%), Gaps = 24/509 (4%) Query: 12 MEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--G 69 M IL+ KGI K FPGV A+D+V+ V E EI +LIGENGAGKSTL+K+L+GV + G Sbjct: 3 MPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDG 62 Query: 70 EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129 EI G+ F D+ + GI +IHQEL L +++ EN+FL G ++ +D Sbjct: 63 EIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFL------GNEQASRGVID 116 Query: 130 ENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189 + R++ELL L+G P+ L+ ++ ++Q+VEI KAL KE +++ +DEPT+SL Sbjct: 117 WDAATLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNE 176 Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDV--DT 247 +++ L E++ K+RGI+ + +SH+L+E+ +++DR+ ++RDG + L E V D Sbjct: 177 SDSDALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDR 236 Query: 248 IIKMMVGREVEFFPHGIETRPGEIALEVRNLK-------WKDKVKNVSFEVRKGEVLGFA 300 II+ MVGR + T PG++ EV+ + V++V+ VR+GEV+G A Sbjct: 237 IIRGMVGRALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIA 296 Query: 301 GLVGAGRTETMLLVFGVNQKES--GDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLV 358 GL+GAGRTE + +FG + + G +++GR++++ A+ G+ EDRK GLV Sbjct: 297 GLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLV 356 Query: 359 LRMTVKDNIVLPSLKKIS-RWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQ 417 L ++ N+ L +L+ ++ RW V+D +E +++E++ +RL I+ ++Q T NLSGGNQ Sbjct: 357 LDNDIRHNVTLANLRGVAKRW--VIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQ 414 Query: 418 QKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNL 477 QKVVL+KWL + +LI DEPTRGIDVGAK EI+ +I +L A+G+ V++ISSE+PE+L + Sbjct: 415 QKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGV 474 Query: 478 SDRIVVMWEGEITAVLDNREKRVTQEEIM 506 +DRI VM GE+ A + E +QE+IM Sbjct: 475 ADRIYVMNAGEMVAEMPAAE--ASQEKIM 501 Lambda K H 0.319 0.138 0.381 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: 40 Number of successful extensions: 10 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: 520 Length of database: 518 Length adjustment: 35 Effective length of query: 485 Effective length of database: 483 Effective search space: 234255 Effective search space used: 234255 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 (21.7 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