Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_086511945.1 BZY95_RS21570 cyclohexanecarboxylate-CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_002151265.1:WP_086511945.1 Length = 548 Score = 227 bits (578), Expect = 1e-63 Identities = 172/545 (31%), Positives = 274/545 (50%), Gaps = 32/545 (5%) Query: 28 EQTIGAFFADMVARQPEREALVSVHQ--GRRY--TYAQLQTEAHRLASALLGMGLTPGDR 83 ++ I + + V E+ A+++ G R +Y +L + R+A L+ +G+ GD Sbjct: 23 DKIIADYLDEAVTSAGEKAAIITYRMADGSRVELSYRELNEKVTRIAVGLVELGVRKGDI 82 Query: 84 VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143 V N + + LA ++G VL + P +R E+E+ L K+LV F+ D+ Sbjct: 83 VSCQLPNWWQMTALHLACVRIGAVLNPLMPIFREHELEFMLGMAESKVLVVPQTFRKFDH 142 Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203 M EL LP+L ++ I E G+ + E LL AA Sbjct: 143 GAMAHELK-------------RSLPKLAHILVIGSE-GEDSFERVLLERAWETEIDTAAL 188 Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIP 263 R + + D + I +TSGTTG PKG T +L+N + E + L AD + +P Sbjct: 189 FRERRPSGD----DVVQILYTSGTTGKPKGVMHTSNTLLSNIRPMAERLSLGEADTIFMP 244 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 PL H G + G L +T V D + P + ++ ER + + G T F+A++ Sbjct: 245 SPLAHQLGFLYGLLLPIYLKSTAVL-QDTWLPEEAVAIIRAERASLMLGA-TPFLADIAE 302 Query: 324 PRFAEF-NLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382 +L +L + AG+P P+ ++++ + R I+ A+GMTE V+ D P Sbjct: 303 QAIEHGPDLQSLTLFLSAGAPIPSPLVEKAARNLPTRIIS-AWGMTENGAVTTTLPEDDP 361 Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442 + V T G P++E+K+ D + G +P GQ G +G S+ GY+ + +D+ Sbjct: 362 -KRAVHTDGAPLPYIELKVTDME-GNPLPPGQEGSLYMRGASLFVGYF--KQPELYGVDD 417 Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502 GW TGDLA +D +GYV I GR KD+VIRGGENI +IE LY+HP +Q V +VG PD Sbjct: 418 EGWFPTGDLARLDEQGYVRITGRSKDVVIRGGENIPIVDIENALYQHPAIQAVALVGKPD 477 Query: 503 QKYGEELCAWIIAKPGTQP-TEDDIRAFC-KGQIAHYKVPRYIRFVTSFPMTVTGKIQKF 560 ++ GE LCA++ K G Q T +++ AF + ++ P ++ + P T +GKIQKF Sbjct: 478 ERLGERLCAYVALKEGHQSLTLEEVCAFLNERKVTRQYQPEFLVVLDELPRTPSGKIQKF 537 Query: 561 KIRDE 565 K+R++ Sbjct: 538 KLREQ 542 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: 675 Number of extensions: 40 Number of successful extensions: 7 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: 548 Length adjustment: 36 Effective length of query: 542 Effective length of database: 512 Effective search space: 277504 Effective search space used: 277504 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 24 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