Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 286 bits (731), Expect = 2e-81 Identities = 171/495 (34%), Positives = 278/495 (56%), Gaps = 8/495 (1%) Query: 11 SVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGE 70 S PV+E + K FG+T AL+ S+RV G H LVG NGAGKSTL+ +L G+ +PD G Sbjct: 2 STPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGS 61 Query: 71 VRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRD 130 + G + R R + ++Q + +V E LF + G ++D ++ +R+ Sbjct: 62 LLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQRE 121 Query: 131 ARALLD-HWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189 A LLD ++ + + +A G+LS +Q+V+I RAL R ++ DEP+ L E++RL Sbjct: 122 AARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERL 181 Query: 190 FRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGE 249 R + L+ +G+ ++ISH+LQE+ +C VTVLR+ R + A VS PR +E +T Sbjct: 182 LRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDV--AEVS--PRNTSLEQITRL 237 Query: 250 RGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATSSGRTSV 308 V + + A+PA A+ L+++ L A Y+G+ V+RGE+VGLTG SG + Sbjct: 238 MVNREVGELYPKVAVPAG-ALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKEL 296 Query: 309 AEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368 ++ GL G + +DG L ++A G+ +P++R +G+ L SV EN ++ Sbjct: 297 LRSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLA 356 Query: 369 IARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPN 428 + G+ +PA++ ++I+ L I A G V LSGGNQQKV +A+ A + Sbjct: 357 ALSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSS 416 Query: 429 VLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMFRGRVAA 487 + +L +P+ G+DV +K + ++ + +EG VL++S +L +L CDR+ VM RG +AA Sbjct: 417 LYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAA 476 Query: 488 EFPAGWQDHDLIASV 502 F AG + D + +V Sbjct: 477 RFAAGEANSDRLLAV 491 Lambda K H 0.318 0.134 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: 583 Number of extensions: 28 Number of successful extensions: 9 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: 510 Length of database: 512 Length adjustment: 35 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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