Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF2964 PS417_15170 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__WCS417:GFF2964 Length = 567 Score = 232 bits (591), Expect = 3e-65 Identities = 168/556 (30%), Positives = 264/556 (47%), Gaps = 28/556 (5%) Query: 20 GATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLT 79 G D P + + F + + + ER A VS+ G TYA Q + A+ L G G+ Sbjct: 28 GIEDYPSLREV----FLEHLEKFRERVAYVSI--GTEMTYADWQVQGVAFAAWLQGQGVR 81 Query: 80 PGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK 139 G+RV + N ++ + L T G V+VN+NP Y + E+++ L G + +V F Sbjct: 82 KGERVALMMPNCLQYPICLLGTILAGAVVVNVNPLYTSHELKHLLKDSGAETVVIFENFA 141 Query: 140 -TSDYL---GMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 T + + ++ + G G + A + + V + + PG +RF ++ Sbjct: 142 HTLEKVITGSSVKRVVIAAIGDLLGTFKGAAMNFILRRV---QKQVPAFNLPGSVRFNQV 198 Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGF----FIGEC 251 + +G A + ++ A +Q+T GTTG KG L+HRNI+ N ++G+ Sbjct: 199 LKQGRALNHFPVEMHLDALAF----LQYTGGTTGDAKGVMLSHRNIIANLLQAKAWVGDQ 254 Query: 252 MKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLH 311 + + +PLYH F + + L G + + D V ++ ER G+ Sbjct: 255 LDQDKQETNVTLLPLYHIFSLTVNCLMFMCLGGRNILIANPRDVKRVQMILRKERFNGIA 314 Query: 312 GVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETS 371 GV T+F L++ F + S LR I G T V KR E L I YG+TE S Sbjct: 315 GVNTLFNGLLENEAFCARDFSDLRMVIAGGMATHTAVAKRWKEVTGL-PIIEGYGLTECS 373 Query: 372 PVSCQSSTDTPLSKRVSTVGQVQ---PHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHG 428 PV S D + + G + P V+ V D G + IG++GE +G VM G Sbjct: 374 PVVSISPIDIARMREMEFTGSIGVPLPSTWVRFVRED-GELAEIGEQGELQVRGPQVMQG 432 Query: 429 YWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYR 488 YW T E +D GW+ TGD+ MDA GY+ +V R KDM++ G N+YP EIE+ + Sbjct: 433 YWQRPEATAEVLDAEGWLSTGDIGVMDARGYIRLVDRKKDMILVSGFNVYPNEIEDVVAL 492 Query: 489 HPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRF-VT 547 HP V +V +GV D GE++ I+ + T++ I A C+ + YK+P+Y+ F T Sbjct: 493 HPAVAEVAAIGVEDGVTGEKV-KIIVVRKDPNLTQEQILAHCREYLTGYKMPKYVEFRTT 551 Query: 548 SFPMTVTGKIQKFKIR 563 P T GK+ + +R Sbjct: 552 ELPKTTVGKVLRRALR 567 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: 716 Number of extensions: 30 Number of successful extensions: 6 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: 567 Length adjustment: 36 Effective length of query: 542 Effective length of database: 531 Effective search space: 287802 Effective search space used: 287802 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 17 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