Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 315 bits (807), Expect = 2e-90 Identities = 186/496 (37%), Positives = 289/496 (58%), Gaps = 17/496 (3%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 +E V K F V L GV + Q G++Y LLGENG GKSTL+KI++G + P G++V++ Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 76 GVPHARLSALEALAA-GIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLA 134 G A A A GI ++Q+ +L ++++A+N+ L HE + D + + Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLG-----HEIKRGLFLDDKAMR 119 Query: 135 ATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKE 194 AL VGLP + + T + +L +A +QLV IARA+A A+ +IMDEPT +LT E Sbjct: 120 EKTREALAKVGLPLDPD---TRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGE 176 Query: 195 VDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISEL 254 + L A++A L+A GVT++++SHKLDE EV+V+RDG +A+ A T+ Q++ L Sbjct: 177 TERLFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANL 236 Query: 255 MTGRHLSNERYRESAHAQD--IVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNE 312 M GR L++ + QD + VRG T G V F++ GEILG GL+ +GR E Sbjct: 237 MVGRELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTE 296 Query: 313 LARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVIT 372 L L G+ P +G V + GQ + L++P DA RH + Y+ EDR +GL + +R N+ Sbjct: 297 LFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTL 356 Query: 373 AMISSLRDRFGQ--IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLA 430 + +R+ + +D QA + V+E I T ++ SLSGGNQQ++ + + L Sbjct: 357 MAL----ERYAKPWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLH 412 Query: 431 IDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG 490 P V++L PT GVDVG+K IY ++QRL+++G+ +I+IS +L EL+ C R+ +M+ G Sbjct: 413 PGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAG 472 Query: 491 HVSAEYRADELSEADL 506 + + L+E +L Sbjct: 473 RLQTTLQEPHLTEEEL 488 Score = 52.0 bits (123), Expect = 5e-11 Identities = 55/236 (23%), Positives = 101/236 (42%), Gaps = 25/236 (10%) Query: 33 GVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGI 92 GV +RG+I G G G++ L + + G +P G + I G P S +A G+ Sbjct: 273 GVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGL 332 Query: 93 ETVYQD---------LSLLPNMSVAENVALTSELATHEGRLARTF-DRRVLAATAARALE 142 + +D L PN+++ +AL R A+ + D A A++ Sbjct: 333 TYLSEDRKGKGLHVHFGLRPNLTL---MALE--------RYAKPWLDPAAEQAALREAVQ 381 Query: 143 AVGL-PGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAV 201 G+ G+ E +++ L +Q +A+A+ + V++DEPT + + + Sbjct: 382 EFGIRTGSLEVRAS---SLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHL 438 Query: 202 LANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257 + L QG+ V+ +S +L E + V V+R G+ T+ ++ TG Sbjct: 439 VQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATG 494 Lambda K H 0.319 0.135 0.376 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: 568 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 515 Length of database: 496 Length adjustment: 34 Effective length of query: 481 Effective length of database: 462 Effective search space: 222222 Effective search space used: 222222 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