Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate CCNA_01382 CCNA_01382 long-chain-fatty-acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Caulo:CCNA_01382 Length = 583 Score = 229 bits (585), Expect = 2e-64 Identities = 171/538 (31%), Positives = 255/538 (47%), Gaps = 54/538 (10%) Query: 51 VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110 VH+ R + +A+ L G+ GDRV I N EW + +G ++ Sbjct: 69 VHEDERVNFEAFYRAVTHMAAELESFGVQKGDRVAIVMRNLPEWPVAFYGALSLGAIVTP 128 Query: 111 INPAYRTAEVEYALNKVGCKL-LVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQ 169 +N + E+EY L G K+ +V + R+ E G+ HL P Sbjct: 129 LNAWWTGPELEYGLVDSGAKVAIVDVERY--------------ERMGE---HLH--NCPD 169 Query: 170 LKTVVWIDDEAGQGADEPGLLRFTELIARGN----AADPRLAQVAAGLQATDPINIQFTS 225 LK V A + P ++ I N + L VA + A D I +TS Sbjct: 170 LKRVYV--SRAKEEITHPYVIPLESKIGGANDWAKLDEKPLPTVA--ITADDDATIFYTS 225 Query: 226 GTTGFPKGATLTHRNILNNGFFI-----------GECMKL----TPADRLCIPVPLYH-- 268 GTTG PKGA THRNI +N F GE P + VP +H Sbjct: 226 GTTGKPKGAIATHRNINSNIFAAAAAGARAFLRRGEAPPQPDPSAPQKGALLSVPFFHAT 285 Query: 269 -CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFA 327 CF ++ +L GA + +DP +Q +QDE+ T + GVPT+ ++HP A Sbjct: 286 GCFAVLNPSLFA---GAKLAMMRK-WDPERAMQVIQDEKLTQMGGVPTIAWQIIEHPNRA 341 Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRV 387 ++LS++ G+P E+++++ E +GMTETS + +S + R Sbjct: 342 NYDLSSIEAVAYGGAPSAPELVRKIKEIWPKSSPGNGWGMTETSATATSNSAED-YENRP 400 Query: 388 STVGQVQPHLEVKIVDPDTG-AVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 + G P ++KI+ + +PIG+ GE KG V+ GYW T + +G W+ Sbjct: 401 DSCGPAVPVTDLKIMTVEAPYRELPIGEVGELWCKGPQVVRGYWNKPEATAQTFVDG-WV 459 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 TGDLA +DAEG+ I+ R KDM+IRGGENIY E+E LY HP V D +VGVP + G Sbjct: 460 RTGDLARLDAEGFCFIIDRAKDMLIRGGENIYCIEVENCLYDHPAVMDAALVGVPHKTLG 519 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVP-RYIRFVTSFPMTVTGKIQKFKIR 563 EE A + KPG + TE ++RAF ++A +KVP + + + + P GKI K +++ Sbjct: 520 EEPAAVVTLKPGAEATEAELRAFVADRLAAFKVPVKVVFWPETLPRNANGKIMKNELK 577 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: 758 Number of extensions: 39 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: 583 Length adjustment: 36 Effective length of query: 542 Effective length of database: 547 Effective search space: 296474 Effective search space used: 296474 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