Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_03315 AO353_03315 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03315 Length = 562 Score = 251 bits (642), Expect = 4e-71 Identities = 172/541 (31%), Positives = 265/541 (48%), Gaps = 53/541 (9%) Query: 52 HQGRRYTYAQLQTEAHRLASALLGM-GLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 + G TYA+L+ + A L L PGDR+ + N + + + GL++VN Sbjct: 45 NMGVTLTYAELERYSAAFAGYLQTQTDLLPGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104 Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170 NP Y E+ + G + LV + F ++E+ P+ + Q +L AK+ L Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNMFGQK-----VQEVLPDTEIQ---YLIEAKMGDL 156 Query: 171 ---------KTVVWIDDEAGQGADEPGLLRFTELI--ARGNAADPRLAQVAAGLQATDPI 219 TVV + D P + F + RG + P+ + D Sbjct: 157 MPTAKGWLINTVVDKVKKMVPTYDLPQAISFKSALRLGRGQSIKPQ------NVSLDDVA 210 Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHC 269 +Q+T GTTG KGA LTH N++ N C+ +D + P+PLYH Sbjct: 211 VLQYTGGTTGLAKGAMLTHGNLVANMQQARACLGQFGSDGKPLLREGQEVMIAPLPLYHI 270 Query: 270 FGMVLGNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 + N C H I P D GF ++ +++ R + L G+ T+F+A +DH Sbjct: 271 YAFT-ANCMCMMVTGNHNVLITNPRDIAGF-----IKELKNWRFSALLGLNTLFVALMDH 324 Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383 P F + S+L+ G+ +R EQ+ IT YG+TETSPV+C + Sbjct: 325 PNFKTLDFSSLKLTNSGGTALVKATAERW-EQITGCRITEGYGLTETSPVACTNPYGD-- 381 Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443 R+ TVG P +K+++ D G P+G+RGE C KG +M GYW T E +D Sbjct: 382 KSRIGTVGLPVPGTTLKVINDD-GVEQPLGERGELCIKGPQIMKGYWQKPEATAEVLDAD 440 Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503 GW +GD+A +D +G+V IV R KDM+I G N+YP EIE+ + HP+V + V+GVPD+ Sbjct: 441 GWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGVPDE 500 Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 + GE + +++A+ E +++A+CK YKVP++I S PMT GKI + ++R Sbjct: 501 RSGEAVKLFVVAREAGISLE-ELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILRRELR 559 Query: 564 D 564 D Sbjct: 560 D 560 Lambda K H 0.320 0.136 0.412 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: 790 Number of extensions: 38 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: 578 Length of database: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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: 53 (25.0 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