Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_057687528.1 ABB28_RS16880 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001431535.1:WP_057687528.1 Length = 558 Score = 229 bits (584), Expect = 2e-64 Identities = 167/560 (29%), Positives = 265/560 (47%), Gaps = 18/560 (3%) Query: 12 PLVDSHARGA-TDVPLIE-QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRL 69 P + S+ +G ++ + E ++ + F VA+ +R A S G+ TY + + Sbjct: 6 PWLQSYPQGVPAEIDINEFHSVSSVFDASVAKYRDRPAYSSF--GKVLTYGETDALVEQF 63 Query: 70 ASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVG 128 A+ LLG + L GDRV + N ++ + + GL +VN+NP Y E+++ L G Sbjct: 64 AAYLLGELQLKKGDRVALMMPNCLQYPIATFGVLRAGLTVVNVNPLYTARELKHQLVDAG 123 Query: 129 CKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPG 188 LV + F + + G L AK + V+ + G Sbjct: 124 VTALVVVDNFGDTVQAVIADTQVKHVITTGLGDLLGAKGVVVNFVLKYIKKMVPNYTLKG 183 Query: 189 LLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN---- 244 +RFT+ + G D ++ D +Q+T GTTG KGA LT+RN++ N Sbjct: 184 AVRFTQALKLGRRHDLPKVEI----DHDDIAFLQYTGGTTGVAKGAMLTNRNLVANMQQA 239 Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQD 304 +IG + + +PLYH F + L G + D ++ ++ Sbjct: 240 SAWIGASGIEPGKEWIITALPLYHIFALTANGLVFMKFGGCNHLITNPRDMKGFVKELKG 299 Query: 305 ERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIA 364 R T + GV T+F L+ P F E + STL+ + G V +R + + + A Sbjct: 300 VRFTAITGVNTLFNGLLNTPGFDEVDFSTLKVTLGGGMAVQRSVAERWKKTTGVTLVE-A 358 Query: 365 YGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYS 424 YG+TETSP +C + L++ ++G P + I D D+G V+ + + GE C KG Sbjct: 359 YGLTETSPAACINPLT--LAEYNGSIGLPIPSTDACIKD-DSGKVLGLDEVGELCIKGPQ 415 Query: 425 VMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEE 484 VM GYW T AID GW+HTGD+A MDA+G+ IV R KDM++ G N+YP E+E+ Sbjct: 416 VMKGYWQRPEDTAAAIDADGWLHTGDMAKMDAQGFCYIVDRKKDMILVSGFNVYPNEVED 475 Query: 485 FLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIR 544 + P V +V VGVPD+K G E+ +I K T + ++ + + YK P+ + Sbjct: 476 VIAMMPGVLEVAAVGVPDEKSG-EIVKVVIVKKDPNLTAEQVKEHARANLTGYKHPKIVE 534 Query: 545 FVTSFPMTVTGKIQKFKIRD 564 F P T GKI + ++RD Sbjct: 535 FRKELPKTNVGKILRRELRD 554 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: 766 Number of extensions: 40 Number of successful extensions: 6 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: 558 Length adjustment: 36 Effective length of query: 542 Effective length of database: 522 Effective search space: 282924 Effective search space used: 282924 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