Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO356_05100 AO356_05100 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05100 Length = 563 Score = 237 bits (605), Expect = 8e-67 Identities = 161/540 (29%), Positives = 266/540 (49%), Gaps = 42/540 (7%) Query: 54 GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 G+ TY +L + A+ L L PGDR+ + N ++ + + GL++VN N Sbjct: 47 GKTITYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNVLQYPVAVFGAIRAGLIVVNTN 106 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKL-PQLK 171 P Y E+E+ N G K LV +A + + P+ + + A L P LK Sbjct: 107 PLYTAREMEHQFNDSGAKALVCLANMAH-----LAETVVPKTGVKHVIVTEVADLLPPLK 161 Query: 172 -----TVVWIDDEAGQGADEPGLLRFTELIARG-----NAADPRLAQVAAGLQATDPINI 221 +V+ + P ++F +++++G N A+P VA + Sbjct: 162 RLLINSVIKYVKKMVPAYHLPKAVKFNDVLSKGHGQPVNEANPTSDDVAV---------L 212 Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR------LCIPVPLYHCFGMVLG 275 Q+T GTTG KGA L+HRN++ N +C L ++ L P+PLYH + Sbjct: 213 QYTGGTTGVAKGAMLSHRNLVANML---QCKALMGSNLNEGCEVLITPLPLYHIYAFTFH 269 Query: 276 NLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLR 335 +A G + ++ D +++ + + +G G+ T+F+A ++ F + + S L+ Sbjct: 270 CMAMMLIGNHNILISNPRDLSAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSALK 329 Query: 336 TGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK-RVSTVGQVQ 394 + G +R + + I YGMTETSPV+ T P+ ++ T+G Sbjct: 330 VTLSGGMALQLAAAERW-KAVTGCPICEGYGMTETSPVA----TVNPIQNIQIGTIGIPV 384 Query: 395 PHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATM 454 P K+++ D G P+G+ GE C KG VM GYW + T E +D GW+ TGD+A + Sbjct: 385 PSTLCKVIN-DAGVEQPLGEIGELCVKGPQVMKGYWQRQEATDEILDSEGWLKTGDIALI 443 Query: 455 DAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWII 514 +GY+ IV R KDM++ G N+YP E+E+ L P V +GVPD+K GE + +I+ Sbjct: 444 QPDGYMRIVDRKKDMILISGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIV 503 Query: 515 AKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLEE 574 A+PG T++ + + + YKVP+ + F + P T GKI + ++RDE +LGL++ Sbjct: 504 ARPGVTLTKEQVMEHMRANVTGYKVPKAVEFRDALPTTNVGKILRRELRDEELRKLGLKK 563 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: 742 Number of extensions: 36 Number of successful extensions: 5 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: 578 Length of database: 563 Length adjustment: 36 Effective length of query: 542 Effective length of database: 527 Effective search space: 285634 Effective search space used: 285634 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