Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012755263.1 RLEG_RS23870 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000023185.1:WP_012755263.1 Length = 528 Score = 206 bits (525), Expect = 1e-57 Identities = 156/530 (29%), Positives = 241/530 (45%), Gaps = 53/530 (10%) Query: 43 PEREALVSVHQGRRYTYAQLQTEAHRLASALLGM--GLTPGDRVGIWSHNNAEWVLMQLA 100 P+R AL + R+ +YA+L T R A L + G RV + + N+ + +++ A Sbjct: 30 PDRPALFEIATNRQLSYAELDTRIARCAGLLSDVLGARRDGGRVALLARNSLDSIVLAFA 89 Query: 101 TAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPG 160 + G + V +N AE+ L LLV F + Sbjct: 90 CQRAGAIYVPLNWRLNAAELRPILADCAPVLLVHDEEFAAT-----------------VA 132 Query: 161 HLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN 220 L A P++ + D AG AR A+ P A V+A A Sbjct: 133 SLAGAD-PEMAVISTADGPAG-------------FAARIEASLPA-APVSA--DADGACV 175 Query: 221 IQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACF 280 + +TSGTTG PKG +T RN F ++ P +P +H G++ Sbjct: 176 LLYTSGTTGQPKGVVITRRNAFFAAFNFSVVGEIGPGSVALCDLPFFHTIGLIAVARTTL 235 Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLH--GVPTMFIAELDHPRFAEFNLSTLRTGI 338 G T+V +D F P L + D + H VP + +A + P ++ L+ L Sbjct: 236 MLGGTLVV-SDRFTPARTLAALADRQRAVTHYFAVPQIALALRNDPVYSAAALAGLHALF 294 Query: 339 MAGSPCPTEVMKRVVEQMNLREITIAYGMTETS-----PVSCQSSTDTPLSKRVSTVGQV 393 + G+P +++ ++ + YGM+E P+ ++ D P +VG Sbjct: 295 VGGAPLTQALIESYLDDGVA--LVNGYGMSEAGTVLHVPIDRRAVQDNP-----GSVGLP 347 Query: 394 QPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLAT 453 P L+++IV D G V G+ GE +G +V GYW +T A EG W TGDL Sbjct: 348 APLLDIRIVGED-GREVDDGETGELWLRGPAVTPGYWNKPQETAAAFTEG-WYRTGDLGR 405 Query: 454 MDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWI 513 +A G+ +IV R+KDM I GGEN+YP E+E L HP + D VVG+PD ++GE A++ Sbjct: 406 REANGFYHIVDRLKDMYISGGENVYPAEVEAALASHPAILDAAVVGIPDIRWGECGLAYV 465 Query: 514 IAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 + +PG T D+I C ++A +K P I FV + P T +GK+QK+ +R Sbjct: 466 VLRPGAVATGDEIAGHCAARLAAFKRPARILFVEAIPRTASGKVQKYVLR 515 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: 639 Number of extensions: 42 Number of successful extensions: 4 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: 528 Length adjustment: 36 Effective length of query: 542 Effective length of database: 492 Effective search space: 266664 Effective search space used: 266664 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