Align ABC transporter related (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 313 bits (801), Expect = 1e-89 Identities = 183/497 (36%), Positives = 283/497 (56%), Gaps = 8/497 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +LEL+ I K + +AL+ SLR+ AG VH L+GENGAGKSTL+KV+ G D G +L Sbjct: 5 VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 G+P +P ++ GI ++QE L TV + LF G+E R L+ + +A Sbjct: 65 DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124 Query: 124 VLTQ-FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 +L F L + +A + + S A QQ++ I R + + +VLV DEP+ +L +EV+ L I Sbjct: 125 LLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRI 184 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + +L+ G+AIV+I+H+L ++ + DR+TVLRNG+ + E ++ M+ R + Sbjct: 185 VQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREVG 244 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 E + A A+LL + + + Q ++L V +G+ VGL GL+GSG E+ Sbjct: 245 ELY------PKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLR 298 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 ++FGL DSG + L GQ L+L P +A++ G+AL PE+R+ G+ LS++EN LA Sbjct: 299 SLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAAL 358 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 +R LS R++ I++L+I A + QLSGGNQQKV LA+W A L Sbjct: 359 SRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLY 418 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 +LDEP+ GID+GA EI +LI L EG +L+ SS+L EL+ +++ V+ Sbjct: 419 LLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARF 478 Query: 483 SGAELTSQHVMQAIAEG 499 + E S ++ A+A G Sbjct: 479 AAGEANSDRLL-AVATG 494 Lambda K H 0.319 0.136 0.377 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: 616 Number of extensions: 29 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: 499 Length of database: 512 Length adjustment: 34 Effective length of query: 465 Effective length of database: 478 Effective search space: 222270 Effective search space used: 222270 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