Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 344 bits (882), Expect = 5e-99 Identities = 188/506 (37%), Positives = 302/506 (59%), Gaps = 13/506 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ +GIVK F A+D V + L+GENGAGKSTLIK+L G+ +PDAG +L+ Sbjct: 5 VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G+ SP + GI IHQE L TV E +F +E R +D Sbjct: 65 DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHE------RRFGPLLDRRSQ 118 Query: 134 YTRSKELLD-LIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 + LLD G + +AL+ L++A++QMV+I +AL+ +PR++ DEP+ +L E Sbjct: 119 QREAARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREV 178 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 ERL I++ L+ G+++V++SH L E+ + DR+ V+R+G+ + E+ ++ I ++M Sbjct: 179 ERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLM 238 Query: 253 VGREV-EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311 V REV E +P + G + L+VR L + + +VR+GE++G GLVG+G E + Sbjct: 239 VNREVGELYPK-VAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELL 297 Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 +FG+ +SG++ ++G+ + +++P +A+ G+ L+PE+R+ QG+ L ++V++N L + Sbjct: 298 RSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAA 357 Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 L + R GL L +E + + ++RL IK + LSGGNQQKV LAKW A + Sbjct: 358 LSRFVRLGL-LSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSS 416 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 + + DEP+ GIDVGAK EI+R+I EL +G V+++SS+LPE++ L DRI VM G I A Sbjct: 417 LYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAA 476 Query: 492 VLDNREKRVTQEEIMYYASG-QKKQN 516 E + ++ A+G Q+ QN Sbjct: 477 RFAAGE--ANSDRLLAVATGAQRAQN 500 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: 615 Number of extensions: 31 Number of successful extensions: 6 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 (21.7 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