Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028988594.1 G579_RS0100325 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000423825.1:WP_028988594.1 Length = 584 Score = 183 bits (465), Expect = 1e-50 Identities = 151/486 (31%), Positives = 217/486 (44%), Gaps = 87/486 (17%) Query: 61 QLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEV 120 ++ +E R A LL +G+ PGDRV I + N+ EW ++ A VG V V I P Y E Sbjct: 43 EMASEVRRWARGLLALGVRPGDRVAIMAGNSPEWAMLDFAVLSVGAVTVPIYPTYGLTET 102 Query: 121 EYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEA 180 + L G L++ R + L LR+ AP G L +L ++ D A Sbjct: 103 LFVLEDSGASLMLVDGRMQ----LEALRDTAP-------GCLPEGRL-------YVRDPA 144 Query: 181 GQGADEPGLLRFTELIARGNAADPRLAQVA-AGLQATDPINIQFTSGTTGFPKGATLTHR 239 A GL + L G +P L A + D + +TSGT+G+PKG L+H Sbjct: 145 D--AQRAGLPSWEALKDLGERINPELVDARLAAVGREDLATLVYTSGTSGWPKGVMLSHG 202 Query: 240 NILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVL 299 NIL N + L P+DR+ +PL H F G+ + G + Y P T++ Sbjct: 203 NILANIEGFLRVVPLLPSDRVLSFLPLSHVFERGTGHFGAYLAGLEVAYAER---PDTII 259 Query: 300 QTVQDERCTGLHGVPTMF----------IAELDHP------------------------- 324 + + R T L VP +F +A P Sbjct: 260 RDLTRARPTILISVPRLFQVLYARLLRDVAGKKGPLGFVLRRGLGLDIGGLVTGQGKGAS 319 Query: 325 RFAEFNL----------STLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 R+ +L LR + G+P P E+ + +E + L I YGMTE SPV Sbjct: 320 RWLALHLLRLALHRRLGGRLRFFVSGGAPLPVEIGRFFLE-LGL-PIVEGYGMTEASPVI 377 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 S + P R TVG V P+LE++ G+ GE +G SVM GYW +E Sbjct: 378 ---SANPPGKVRPGTVGPVLPNLELRF-----------GEDGEILVRGPSVMRGYWKNEP 423 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIR-GGENIYPREIEEFLYRHPQVQ 493 TREA+ GGW+HTGD+ +D GY+ I R K++++ GGEN+ P++IE L HP + Sbjct: 424 ATREAL-AGGWLHTGDVGRLDEAGYLVITDRKKELIVNSGGENVAPQKIEMRLATHPLIN 482 Query: 494 DVQVVG 499 V G Sbjct: 483 QAVVFG 488 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: 778 Number of extensions: 46 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: 584 Length adjustment: 36 Effective length of query: 542 Effective length of database: 548 Effective search space: 297016 Effective search space used: 297016 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 Apr 09 2024. 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