Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012171821.1 AZC_RS16990 malonyl-CoA synthase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000010525.1:WP_012171821.1 Length = 508 Score = 238 bits (607), Expect = 4e-67 Identities = 174/541 (32%), Positives = 262/541 (48%), Gaps = 51/541 (9%) Query: 34 FFADMVARQPEREALVSVH-QGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNA 92 FFA + A P+ ++ H G TY + RLA+ L+ G+ PGDRV + + Sbjct: 7 FFAAIRAAMPDLSKPLATHPDGAMETYGDALALSARLANVLVKRGVKPGDRVAVQVEKSW 66 Query: 93 EWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAP 152 ++ LA + G V + +N AY AE+EY L+ ++V + P Sbjct: 67 TAFVLYLAALRAGAVYLPLNTAYTLAELEYFLSDAEPTVVV----------------VRP 110 Query: 153 EWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD---PRLAQV 209 E G +P ++T+ G+D G L TE A + + PR A Sbjct: 111 EVAGDVKALAAKLGVPHVETL---------GSDGKGSL--TEAAAGESESFEDVPRAADD 159 Query: 210 AAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHC 269 AG I +TSGTTG KGA LTH N+L+N + + + T D L +P++H Sbjct: 160 LAG--------ILYTSGTTGRAKGAMLTHENLLSNAVTLRDYWRFTSDDVLIHALPIFHT 211 Query: 270 FGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEF 329 G+ + GA++++ FD VL+ + + T L GVPT + LDHP Sbjct: 212 HGLFVAGDIILMAGASMIFCPK-FDASEVLRLMP--KATTLMGVPTFYTRLLDHPGLTRE 268 Query: 330 NLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS--KRV 387 + +R + +P E R ++ + I YGMTET +T P + Sbjct: 269 ATAHMRLFVSGSAPLLAET-HRAFQEKTGKAILERYGMTETG-----MNTSNPYDGERIA 322 Query: 388 STVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMH 447 TVG P + V+I DP TGAV+ + G KG +V GYW KT +G ++ Sbjct: 323 GTVGFPLPGVSVRITDPATGAVLGADEIGSIEVKGPNVFKGYWKLPEKTASEFHDGFFI- 381 Query: 448 TGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGE 507 TGDL +DA GYV+IVGR KD+VI GG N+YP+E+E + P V + V+G+P + +GE Sbjct: 382 TGDLGKIDARGYVHIVGRGKDLVITGGFNVYPKEVEGEIDALPGVLESAVIGLPHKDFGE 441 Query: 508 ELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 + A I+ PG TE ++ +G++A +K+P+ + FV P GK+QK +RD K Sbjct: 442 GVTAVIVRTPGASLTEAEVHQALEGRLAKFKLPKKVFFVDELPRNTMGKVQKNILRDTYK 501 Query: 568 D 568 D Sbjct: 502 D 502 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: 650 Number of extensions: 35 Number of successful extensions: 6 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: 508 Length adjustment: 35 Effective length of query: 543 Effective length of database: 473 Effective search space: 256839 Effective search space used: 256839 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