Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013418020.1 RVAN_RS01630 malonyl-CoA synthase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000166055.1:WP_013418020.1 Length = 505 Score = 219 bits (559), Expect = 2e-61 Identities = 163/522 (31%), Positives = 243/522 (46%), Gaps = 45/522 (8%) Query: 49 VSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVL 108 + + GR++ Y + R A+AL+ G+ PGDRV + + E + + LA + G Sbjct: 23 LETNDGRQFRYRDILALTARFANALVAAGVKPGDRVAVQVEKSPEALFLYLACVRAGAAY 82 Query: 109 VNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLP 168 + +N AY AE+EY L + V+ +P H A P Sbjct: 83 LPLNTAYTDAELEYFLGDAEPTVFVA-----------------------RPTHASA---P 116 Query: 169 QLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTT 228 L T + GAD G L EL A +A+ L A I +TSGTT Sbjct: 117 ALCTKTGVAGCYTLGADGDGTL--IELAADKAETFENIARGPDDLAA-----ILYTSGTT 169 Query: 229 GFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVY 288 G KGA TH N+ +N + E + T D L +P++H G+ + + F GA++++ Sbjct: 170 GRSKGAMTTHENLASNARALAEYWRFTDRDVLLHALPIFHTHGLFVASNVIFRSGASMLF 229 Query: 289 PNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEV 348 FDP V + + R T + GVPT + +D R + +R I +P + Sbjct: 230 LPK-FDPNEVFRLLP--RATTMMGVPTFYTRLIDDARLSRETTKEMRLFISGSAPLLADT 286 Query: 349 MKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS-KRV-STVGQVQPHLEVKIVDPDT 406 R E+ I YGMTET+ + T P +RV VG P + V+I +P+T Sbjct: 287 -HRAFEEKTGHRILERYGMTETNMI-----TSNPYDGERVPGAVGFPLPGVSVRIANPET 340 Query: 407 GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRI 466 G ++ + G G +V GYW KT +G W TGDL +DA GYV+IVGR Sbjct: 341 GELLGADEIGMIEVTGPNVFIGYWRMPEKTASEFRDG-WFITGDLGKIDATGYVHIVGRG 399 Query: 467 KDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDI 526 KD+VI GG N+YP+E+E + P V + V+GVP +GE + A ++ E I Sbjct: 400 KDLVITGGYNVYPKEVESEIDALPGVFESAVIGVPHPDFGEGVVAVVVKTKDAAIDEKAI 459 Query: 527 RAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 K ++A+YK+P+ + FV P K+QK +RD KD Sbjct: 460 HDALKVRLANYKLPKRVFFVDDLPRNTMAKVQKNVLRDAHKD 501 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: 639 Number of extensions: 32 Number of successful extensions: 5 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: 505 Length adjustment: 35 Effective length of query: 543 Effective length of database: 470 Effective search space: 255210 Effective search space used: 255210 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: 52 (24.6 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