Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_035241337.1 Q366_RS17165 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000745975.1:WP_035241337.1 Length = 562 Score = 220 bits (560), Expect = 1e-61 Identities = 168/562 (29%), Positives = 264/562 (46%), Gaps = 22/562 (3%) Query: 16 SHARGAT-DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL 74 S+A+G V + I + V P+ AL+ QG T+ QL R A+AL Sbjct: 15 SYAQGVPLHVDFEDVLIPQYLERSVKAVPDNPALI--FQGYTLTFTQLNDMVCRFAAALK 72 Query: 75 GMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVS 134 G + GD+V I N V+ AT ++G ++V NP Y E+E+ G L++ Sbjct: 73 GFDIKKGDKVAILLPNVIPCVVAYYATLKIGGIVVFNNPLYADRELEHQFTDSGATFLIT 132 Query: 135 MARFKTSDYLGMLRE---LAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLR 191 + +D + LRE + +L K V A A P L + Sbjct: 133 LDLL--ADRMVKLREKTDITTIVYTSIGDYLPFVKRLLFPLVAKKKGLAKDVAPAPNLYK 190 Query: 192 FTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGEC 251 F ++IA+ P Q + D Q+T GTTG KG LTH+NI + Sbjct: 191 FKDIIAQ---YAPDTCQENVSMD--DVAMYQYTGGTTGISKGVMLTHKNISYQVQQLEAW 245 Query: 252 MKLTPADRLCI--PVPLYHCFGMVLG-NLACFTHGATIVYPNDGFDPLTVLQTVQDERCT 308 D+ I +P +H FGM N A ++ P PL L+ + + + Sbjct: 246 FPALEKDKETILGALPFFHVFGMSTSMNFAIKMGWGNVLVPKPQPGPL--LEAISKFKAS 303 Query: 309 GLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMT 368 VPTM+I L+HP + +LS+++ +P P +V+ ++ I +G+T Sbjct: 304 FAPLVPTMYIGMLNHPNMEKTDLSSIKGCFSGSAPLPVDVINTFQKKTG-GVIVEGFGLT 362 Query: 369 ETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVD-PDTGAVVPIGQRGEFCTKGYSVMH 427 E++PV+ + D + V ++G KIVD D +PIG+ GE KG +M Sbjct: 363 ESTPVTHINPFDG--KRVVGSIGLPISDTVCKIVDLEDNTKEMPIGEPGELLIKGPQIMK 420 Query: 428 GYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLY 487 GY T + I E G++ TGD+A MD GY IV RIKDM++ GG N+YPR+I+E L+ Sbjct: 421 GYLNRPDATAQTITEDGFLCTGDVARMDENGYFYIVDRIKDMILSGGYNVYPRDIDEVLF 480 Query: 488 RHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVT 547 HP++ + VG+P GE + A++I K G TE ++ +C ++A YK+P + F Sbjct: 481 EHPKILEACAVGIPHPTRGEAVKAFVILKQGETMTEKEVIDYCGTKLAKYKLPVVVEFRD 540 Query: 548 SFPMTVTGKIQKFKIRDEMKDQ 569 P + GK+ + +R E +++ Sbjct: 541 QLPKSNVGKVLRKDLRAEEQNK 562 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: 721 Number of extensions: 33 Number of successful extensions: 4 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: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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 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