Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 208580 DVU3065 AMP-binding enzyme family protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >MicrobesOnline__882:208580 Length = 550 Score = 506 bits (1304), Expect = e-148 Identities = 256/538 (47%), Positives = 352/538 (65%), Gaps = 7/538 (1%) Query: 28 EQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIW 87 E T+G + A+ P+ +A+V V + R TY + + LA L+ +G+ GD+V +W Sbjct: 8 EMTLGRILDETAAKFPDNDAVVYVDRDYRQTYREFVSVVDDLARGLMALGVKRGDKVALW 67 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147 + N WV +Q ATA++G VL+ +N YR +E+ Y L + C+ L M F+ D++ + Sbjct: 68 ATNVPYWVALQFATAKIGAVLLTVNTNYRESELRYLLEQSECENLFIMDGFRDHDFVQTI 127 Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAADPRL 206 ++ PE + Q G L+ LP LK V+++ E +G + E+++ G +D Sbjct: 128 YQVIPELRMQPRGQLRCEGLPHLKRVMFLGAEKHRG-----MYSVPEIVSLGVMVSDEEF 182 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 Q L D +N+Q+TSGTTGFPKG LTH I NNG++IG T DR+C+PVPL Sbjct: 183 RQRQDELDPYDVVNMQYTSGTTGFPKGVMLTHVGIGNNGYWIGRNQGFTEKDRVCLPVPL 242 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 +HCFG VLG +A HGA +V + F+P+ V+ +V E+CT L+GVPTMF+A L+H F Sbjct: 243 FHCFGCVLGVMAAINHGAALVIL-ENFNPMHVMASVDQEKCTALYGVPTMFLAVLEHKLF 301 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 F+ S+LRTGIMAGS CP +M+RV+E+MN+REITI YG+TE SPV Q+ D L +R Sbjct: 302 DRFDFSSLRTGIMAGSVCPEPLMRRVIEKMNMREITICYGLTEGSPVMTQTLVDDSLERR 361 Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 V TVG+ P +EV+IVDP+T VP G GE +GY+VM GY+ T +A+D GW+ Sbjct: 362 VQTVGRAMPGIEVRIVDPETNEEVPHGTPGEVVCRGYNVMKGYYNMPEATAKAVDGDGWL 421 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 H+GDL MD GYV I GRIKDM+IRGGENIYPREIEEFLY VQDVQVVGVP +KYG Sbjct: 422 HSGDLGIMDEHGYVRITGRIKDMIIRGGENIYPREIEEFLYGMEGVQDVQVVGVPSRKYG 481 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 EE+ A+II K G +D+R C+G+I+ YKVPR+I FV+ FPMT + KIQK+K+R+ Sbjct: 482 EEVGAFIIPKEGYDLAPEDVRDHCRGRISWYKVPRHIAFVSEFPMTASAKIQKYKLRE 539 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: 820 Number of extensions: 43 Number of successful extensions: 3 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: 550 Length adjustment: 36 Effective length of query: 542 Effective length of database: 514 Effective search space: 278588 Effective search space used: 278588 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