Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_010960838.1 MCA_RS07725 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000008325.1:WP_010960838.1 Length = 510 Score = 244 bits (624), Expect = 5e-69 Identities = 170/524 (32%), Positives = 259/524 (49%), Gaps = 46/524 (8%) Query: 55 RRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPA 114 RR +A+ + +A+ L G+ G+R+G++ N+ E+ L + G V+V IN Sbjct: 27 RRVDFAEFDRASDAIAAGLAVRGVAKGERIGLYCINSVEFTLAYAGIVKAGAVVVPINLL 86 Query: 115 YRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAA--KLPQLKT 172 EV Y L G L+ + GQ + A +L LK Sbjct: 87 LSAEEVHYNLADAGVSGLI--------------------YHGQVSANAAAVADRLSGLKV 126 Query: 173 VVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPK 232 AG G D+ + L+ +A+P + A D I +TSGTTG PK Sbjct: 127 ------RAGIGLDDQDGDVWRALLEE--SAEPPSIEFDA---VEDLAAILYTSGTTGHPK 175 Query: 233 GATLTHRNILNNGFFIGECMKLTPA-DRLCIPVPLYHCFGMVLGNLACFTHGATIVYPND 291 GA LTH N+L N + E + P DR+ + +P++H F +G L HG ++ P Sbjct: 176 GAMLTHGNLLANTTSVREALDWRPGEDRVLVVLPMFHAFAATVGMLTPLLHGCALI-PLA 234 Query: 292 GFDPLTVLQTVQDERCTGLHGVPTMF--IAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349 F+P V T+ R T GVP+M+ + L R A F T+R + G+ P VM Sbjct: 235 KFEPDRVADTIGRHRATLFLGVPSMYALLCRLGEERIARFG--TVRLCVSGGAALPPSVM 292 Query: 350 KRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAV 409 ++ + L I G TE SPV+C + P+ + TVG P +E+KI+ D G Sbjct: 293 EQFQARFGL-PIHEGDGPTECSPVTCVNPVAGPVKR--GTVGLPVPGVEMKILGED-GVE 348 Query: 410 VPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDM 469 +P G+ GE +G +V GYW TRE +G W TGDL +D +GY +IV R KD+ Sbjct: 349 LPRGELGEIAVRGANVFKGYWNQPEATRECFRDG-WFLTGDLGQVDDDGYFSIVDRKKDL 407 Query: 470 VIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAF 529 +I G N+YPR IEE L RHP V++V VVG PD +GE + A+++ +E +IRA+ Sbjct: 408 IIVNGMNVYPRVIEEVLCRHPAVREVAVVGDPDPLHGERVVAYVVL--DAPASEAEIRAW 465 Query: 530 CKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLE 573 CK + +++PR ++ + P GKI K ++R + + + G++ Sbjct: 466 CKPYLGRHEIPRQVKALQQLPRNAAGKIVKRQLRRQGEVERGVD 509 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: 715 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 510 Length adjustment: 35 Effective length of query: 543 Effective length of database: 475 Effective search space: 257925 Effective search space used: 257925 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