Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012103369.1 CKL_RS14730 FadD protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000016505.1:WP_012103369.1 Length = 489 Score = 186 bits (473), Expect = 1e-51 Identities = 130/531 (24%), Positives = 242/531 (45%), Gaps = 46/531 (8%) Query: 35 FADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEW 94 F D V + + ++V + +Y ++ + + L G + + V + S N+ + Sbjct: 3 FTDYVFEEFKDSDKIAVIDKNKISYREIYGGVNYVTYLLQENGCSKENSVLVISDNSVFF 62 Query: 95 VLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEW 154 + + G + V +NP ++ Y ++ + K++ +++ Sbjct: 63 IKTYFGIIKNGSICVPVNPTISENDMRYIMDILKIKIVFCQKKYRN-------------- 108 Query: 155 QGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQ 214 + K+ T+V+ ++ DE L F + Sbjct: 109 --------KVDKIVCRDTMVYSEESIWASKDETNLSGFIN-------------------E 141 Query: 215 ATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVL 274 D I FTSG+T PKG LTH N++ N I E +KLT DR+ + +P Y+C+G L Sbjct: 142 KEDTALIMFTSGSTSKPKGVMLTHYNLMYNTNSIIEYLKLTKNDRVEVVLPFYYCYGTSL 201 Query: 275 GNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTL 334 N F G ++V N P TV++ ++ CTG GVP+ + L L +L Sbjct: 202 LNTH-FRCGGSLVINNRFMFPETVIEDIKKYNCTGFAGVPSTYQILLRMTSIKTAKLPSL 260 Query: 335 RTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQ 394 R AG P + + E + ++ I YG TE + + ++ ++G Sbjct: 261 RYVTQAGGRLPEVFISELCEALEGTDVYIMYGQTEAT-ARLSYLPPEQIKNKLGSIGCGI 319 Query: 395 PHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATM 454 P E+ +++ + G +G+ GE +G ++M GY+ D+ +T++ + + G ++TGDLA Sbjct: 320 PRTELVVLNRE-GNPTSVGEVGEIAARGGNIMKGYFNDQEETKKVL-KNGLLYTGDLAFR 377 Query: 455 DAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWII 514 D +GY+ +V R K+++ G I P+EIE + +V + V+GV D GE + A+++ Sbjct: 378 DEDGYIFVVSREKNIIKCAGNRISPKEIENTICSIKEVVECAVIGVEDDILGEAIKAFVV 437 Query: 515 AKPGTQPTEDD-IRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 K +D I +C + YK+P+Y++F++ P +GK+ K++D Sbjct: 438 LKDKNSSIDDKYIIDYCSSVLPRYKLPKYVQFLSQLPKNSSGKVLFAKLKD 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: 545 Number of extensions: 20 Number of successful extensions: 5 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: 489 Length adjustment: 35 Effective length of query: 543 Effective length of database: 454 Effective search space: 246522 Effective search space used: 246522 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: 52 (24.6 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