Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_073038819.1 BUB04_RS09765 acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_900129305.1:WP_073038819.1 Length = 550 Score = 239 bits (610), Expect = 2e-67 Identities = 174/532 (32%), Positives = 266/532 (50%), Gaps = 36/532 (6%) Query: 41 RQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLA 100 R P + AL+ + TYAQL+ +R+A LL +GL DRV I +HN VL L Sbjct: 48 RYPHKPALI--FGDKVLTYAQLEEATNRVAQGLLSLGLRRFDRVAILAHNTLHHVLTWLG 105 Query: 101 TAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPG 160 TA+ G + + IN R ++ Y +N S ARF + L EL G Sbjct: 106 TAKAGGIYLAINYLLRGKDIAYCINH-------SEARFFIVE--DALAELVD-------G 149 Query: 161 HLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN 220 L +P + +W + AG+ A E G L F + +P A L DP+ Sbjct: 150 VLD--DMPTVSHRIWSNQGAGKTAPE-GWLDFDAWTEAQSPEEP-----AVDLYIEDPVQ 201 Query: 221 IQFTSGTTGFPKGATLTHRNILNNGFFIGECM--KLTPADRLCIPVPLYHCFGMVLGNLA 278 + +TSGT PKG LT+++++ ++G + + + D +P++HC + Sbjct: 202 MTYTSGTESLPKGVVLTNQSLMAQ--YMGAIVDGEYSSEDVNLNALPIFHCAQRDVFLTP 259 Query: 279 CFTHGAT-IVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTG 337 GAT ++ P D T+L+ ++ R T PT++I L HP F + +LS+++ G Sbjct: 260 FLWLGATNVLLPTA--DVPTILEQIERHRATVFFAPPTVWIGLLRHPDFEKRDLSSVQKG 317 Query: 338 IMAGSPCPTEVMKRVVEQM-NLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPH 396 S P E++K + ++ + R + YG TE SP L+K S G + Sbjct: 318 YYGASIMPVEILKEIQRRLPSCRRLYNYYGQTELSPYHTILKPADQLTKPGSA-GMGGLN 376 Query: 397 LEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDA 456 +E ++D V G GE C +G VM Y+ D KT EA+ GGW H+GD+ +D Sbjct: 377 METTLLDDLCQPVEVPGVPGEICGRGPHVMLMYFKDPEKTEEAM-AGGWFHSGDVGVLDG 435 Query: 457 EGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAK 516 + Y+ +V R KDMV GGEN+ RE+EE +Y P+V +V V+GVP K+ E + A ++ K Sbjct: 436 DRYITVVDRKKDMVKTGGENVSTREVEEVIYTDPRVSEVAVIGVPHPKWVEAVTAIVVPK 495 Query: 517 PGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 G TE++I A CK ++A +KVP+ + V + P T TGKI K +R D Sbjct: 496 AGETVTEEEIIALCKRELAGFKVPKAVVVVDALPKTPTGKILKRDLRKHYND 547 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: 736 Number of extensions: 38 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: 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