Align ABC transporter related (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 288 bits (737), Expect = 3e-82 Identities = 170/495 (34%), Positives = 283/495 (57%), Gaps = 8/495 (1%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 MS+ +E + ++K + V+ L V L G V+ LLGENGAGKSTL+K++ G +S G+ Sbjct: 1 MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60 Query: 61 ILFLGEPQHFNTPMDAQKA-GISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYA 119 ++ G + A +A GI ++QE NL +LT+AQN+FLG+E +R + K M Sbjct: 61 VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMRE 120 Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 R L + L +D + +A +QL+ IAR +A +A++L++DEPTA+L E + L Sbjct: 121 KTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERL 180 Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 F ++ LKA GV I++I+H LD+V + +D + V+R+G + TA + + ++ M+GR Sbjct: 181 FALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGR 240 Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299 +L D + + A +++ ++V G + ++ V +G+ +G AGL+G+GR+E Sbjct: 241 ----ELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTE 296 Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-I 358 + + GL +G++ +AGQ + L P DA G+ EDRK G+ +R N+ + Sbjct: 297 LFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTL 356 Query: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418 +AL+ W L +Q + + + I T + LSGGNQQK+ LA+ L Sbjct: 357 MALERYAKPW--LDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPG 414 Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 P ++VLDEPTRG+D+GA EI L++ L ++G++++V SSEL EL+ ++V V+R Sbjct: 415 PSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRL 474 Query: 479 VRELSGAELTSQHVM 493 L LT + ++ Sbjct: 475 QTTLQEPHLTEEELI 489 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: 553 Number of extensions: 25 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: 499 Length of database: 496 Length adjustment: 34 Effective length of query: 465 Effective length of database: 462 Effective search space: 214830 Effective search space used: 214830 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