Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 8501639 DvMF_2357 AMP-binding domain protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Miya:8501639 Length = 550 Score = 521 bits (1343), Expect = e-152 Identities = 265/550 (48%), Positives = 361/550 (65%), Gaps = 8/550 (1%) Query: 28 EQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIW 87 E+T+G + VA+ P+ +A++ V + R TY Q LA L+ +G+ G++V +W Sbjct: 8 ERTLGQILDETVAKYPDNDAVIYVDRDYRQTYRQFSQVVDDLAKGLMALGVRHGEKVAVW 67 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147 + N WV +Q ATA++G +L+ +N YR E+ Y L + C+ L + F+ DY+ + Sbjct: 68 ATNVPYWVALQFATAKMGAILLTVNTNYREHEIRYLLTQSECENLFIIDGFRDHDYVQTI 127 Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGA-DEPGLLRFTELIARGNAADPRL 206 + PE + Q G L+ + LP LK V+++ E +G P ++ + +++ D Sbjct: 128 YNMIPELKTQPRGQLRCSSLPHLKRVMFLGAEKHRGMYSVPEIISMSAMVS-----DEEY 182 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266 A+ L D +N+Q+TSGTTGFPKG LTH NI NNG++IG+ T DR+C+PVPL Sbjct: 183 AERQRALDPHDVVNMQYTSGTTGFPKGVMLTHVNIGNNGYWIGKNQHFTEKDRVCLPVPL 242 Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326 +HCFG VLG LA HGA +V + F P+ V+ +V E+CT L+GVPTMF+A L+H F Sbjct: 243 FHCFGCVLGVLAAINHGAALVIL-ESFSPMHVMASVDQEKCTALYGVPTMFLAVLEHKLF 301 Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386 F+ S+LRTGIMAGS CP +M+RVVE+M +REITI YG+TE SPV QS P +R Sbjct: 302 ERFDFSSLRTGIMAGSVCPEPLMRRVVEKMYMREITICYGLTEGSPVMTQSLVTDPFERR 361 Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446 V TVG+ P +EV+IVDPDT VP G +GE +GY+VM GY+ T AID GW+ Sbjct: 362 VQTVGRAMPCIEVRIVDPDTNEEVPRGTQGEVVCRGYNVMKGYYNMPEATTAAIDADGWL 421 Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506 H+GDL MD EGYV I GRIKDM+IRGGENIYPREIEEFLY VQDVQVVGV +KYG Sbjct: 422 HSGDLGVMDEEGYVVITGRIKDMIIRGGENIYPREIEEFLYGMDGVQDVQVVGVNSRKYG 481 Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566 EE+ A+II KPG + +D+R +C+G+IA +KVPRYI F+ ++PMT +GKIQKFK+R EM Sbjct: 482 EEVGAFIIPKPGVEMAPEDVRDYCRGRIAWHKVPRYISFIDAYPMTASGKIQKFKLR-EM 540 Query: 567 KDQLGLEEQK 576 +L E K Sbjct: 541 AAELFPEAMK 550 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: 793 Number of extensions: 39 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