Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 373 bits (958), Expect = e-108 Identities = 197/500 (39%), Positives = 302/500 (60%), Gaps = 4/500 (0%) Query: 19 SVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGD 78 S PV+ LR + K F ALD +AAG VH L+GENGAGKSTL+K+L+G+++ D+G Sbjct: 2 STPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGS 61 Query: 79 ILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELN 138 +LLDG+P PRQ + LGIG IHQE L + + +F G E R G +D Sbjct: 62 LLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERR--FGPLLDRRSQQ 119 Query: 139 RQAAAIFAR-MRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIA 197 R+AA + L + + +GEL+ A QQMV+I +AL RVL+ DEP+ AL E+ Sbjct: 120 REAARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVE 179 Query: 198 ELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 L RI++ L+ G+ IVYISH + E+ + DRV+V+R+G+ +A V + TS++ I +MV Sbjct: 180 RLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMV 239 Query: 258 GRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317 R + GE ++L+VRGL R RA + + +R+GEI+G GL+G+G E+ R Sbjct: 240 NREV-GELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLR 298 Query: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377 ++FG P ++GE+ + G ++SP +AVA G+ + E+R+ G+A+ + VQ N L+++ Sbjct: 299 SLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAAL 358 Query: 378 GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDIL 437 RF R+G + R + +L IK + R LSGGNQQK+ +AKW R + Sbjct: 359 SRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLY 418 Query: 438 FFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497 DEP+ GIDVGAK EIY+L+ L ++G ++++SS+LPE++ + R+ VM G I Sbjct: 419 LLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARF 478 Query: 498 ARADATQEKIMQLATQRESA 517 A +A ++++ +AT + A Sbjct: 479 AAGEANSDRLLAVATGAQRA 498 Lambda K H 0.320 0.135 0.372 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: 632 Number of extensions: 31 Number of successful extensions: 7 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: 512 Length adjustment: 35 Effective length of query: 485 Effective length of database: 477 Effective search space: 231345 Effective search space used: 231345 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