Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013841988.1 DESRU_RS10010 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000215085.1:WP_013841988.1 Length = 545 Score = 134 bits (336), Expect = 1e-35 Identities = 143/549 (26%), Positives = 235/549 (42%), Gaps = 65/549 (11%) Query: 37 DMVARQPEREALVSV----HQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNA 92 D A +P++ A++ V H+ RR T+ + +LA+ L G+ GD V + Sbjct: 31 DKWAEEPDKLAMLWVDEDDHEIRR-TFKDFSQRSKQLANILTHKGIKAGDVVILIMPRYI 89 Query: 93 EWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAP 152 EW LA +VG ++ ++ Y + +++ R T++ + ++E Sbjct: 90 EWWETFLACLRVGAIVSPGTVQLTVKDLAYRIETAAAAAIITDQR--TAEKIDEIKE--- 144 Query: 153 EWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRF-TELIARGNAADPRLAQVAA 211 +L +K + +++ G L + TEL + D + + Sbjct: 145 -------------ELSTVKVKMVVENP------REGWLHYQTEL--QQYPEDFKSIKT-- 181 Query: 212 GLQATDPINIQFTSGTTGFPKGATLTHRNI-----LNNGFF---IGECMKLTPADRLCIP 263 ++ +P + FTSGTTG PK TH + + ++ I E + +D Sbjct: 182 --RSDEPAILFFTSGTTGNPKMTLHTHSSYPYAHKVTGKYWLDLIPEDLHWNLSDTGWGK 239 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 FG A F H T F L+ +Q T L G PT + L Sbjct: 240 AAWSSLFGPWHMGAALFVHHET------RFKTKRCLEILQKYPITTLCGAPTNY-RMLVL 292 Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383 ++ +LR+ AG P EV+ E + I YG TET V + Sbjct: 293 EDLTQYKFPSLRSCTGAGEPLNPEVINTWQEATGIT-IRDGYGQTETVLVIGNFPC---V 348 Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTK-----GYSVMHGYWGDEAKTRE 438 R ++G+ P EV+++D D G ++P G+ G+ K + YW + +T+ Sbjct: 349 PVRPGSMGKPAPGFEVEVID-DAGNILPPGKEGDIAIKIRPERPAGLFKEYWQEPERTQN 407 Query: 439 AIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVV 498 G W TGD A D +GY VGR D+++ G I P E+E L HP V + VV Sbjct: 408 CF-RGNWYITGDRAVKDEDGYFWFVGRSDDVILAAGYRIGPFEVESTLIEHPAVAESAVV 466 Query: 499 GVPDQKYGEELCAWIIAKPGTQPTED---DIRAFCKGQIAHYKVPRYIRFVTSFPMTVTG 555 PD+ GE + A+++ G QP+ +++ + K A YK PR I FV S P TV+G Sbjct: 467 SSPDELRGEIVKAFVVLTEGYQPSPQLVKELQDYVKSVTAPYKYPREIEFVDSLPKTVSG 526 Query: 556 KIQKFKIRD 564 KI++ ++R+ Sbjct: 527 KIRRVQLRE 535 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: 738 Number of extensions: 41 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 578 Length of database: 545 Length adjustment: 36 Effective length of query: 542 Effective length of database: 509 Effective search space: 275878 Effective search space used: 275878 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