Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011765428.1 AZO_RS08590 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000061505.1:WP_011765428.1 Length = 550 Score = 221 bits (563), Expect = 6e-62 Identities = 170/543 (31%), Positives = 257/543 (47%), Gaps = 41/543 (7%) Query: 43 PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATA 102 P+R A++ H RRYT+ + T + RLASAL +G+ D V + +N E Sbjct: 37 PDRVAVI--HGKRRYTWLESYTRSRRLASALKQLGVGKNDTVAVILNNTPEMFECHFGVP 94 Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162 G VL +N V + LN K+L++ + S +G ELA +P + Sbjct: 95 ACGAVLNTVNTRLDAEGVAFILNHGEAKVLITDREY--SRMVGKAIELA-----NRPDMI 147 Query: 163 QAAKLPQLKTVVWIDDEAGQGADEP-GLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221 V+ +DD G E G L + L+ GN P G D I++ Sbjct: 148 ----------VIDVDDPEYTGPGERVGKLDYEALLETGN---PEFEYEQPG-DEWDAISL 193 Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFT 281 +TSGTTG PKG HR N + P +P++HC G Sbjct: 194 NYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHCNGWCFAWTMAAN 253 Query: 282 HGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAG 341 G + DP + +++ T G P + + P ++ +G++A Sbjct: 254 AGVNVCLRR--VDPRLIFDAMREHGVTHYCGAPIVHSMLANAPEEWRKGINHKVSGLVAA 311 Query: 342 SPCPTEVMKRVVEQMNLREITIAYGMTET-SPVSCQSS----TDTPLSKRVSTVGQ--VQ 394 +P P V++ + + + + +IT YG+TET P S + D PL+++V+ G+ V+ Sbjct: 312 APPPAAVIEGMAK-IGI-DITHVYGLTETYGPASVCAKHDEWRDLPLAEQVAKNGRQGVR 369 Query: 395 PHLE--VKIVDPDTGAVVPIGQR--GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450 H + + ++DP T VP GE +G VM GY +E T E+ GGW HTGD Sbjct: 370 YHAQEGITVLDPTTMEPVPWDNETMGEIMFRGNLVMKGYLKNEKATEESF-RGGWYHTGD 428 Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510 LA M +GYV I R KD++I GGENI E+E+ LY+HP V VV PD+K+GE C Sbjct: 429 LAVMQPDGYVKIKDRSKDVIISGGENISSIEVEDALYKHPAVMAAAVVAAPDEKWGEVPC 488 Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQL 570 A++ K G T ++I A C+ +A +K P+ + F + P T TGKIQKF +R++ K Sbjct: 489 AFVELKDGATVTAEEIIAHCREHLAGFKTPKKVIF-GALPKTSTGKIQKFVLREQAKSSS 547 Query: 571 GLE 573 +E Sbjct: 548 AIE 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: 742 Number of extensions: 41 Number of successful extensions: 7 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 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