Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012675670.1 PERMA_RS09560 fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000021565.1:WP_012675670.1 Length = 518 Score = 223 bits (569), Expect = 1e-62 Identities = 161/517 (31%), Positives = 261/517 (50%), Gaps = 36/517 (6%) Query: 53 QGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 + R+ T+ +L+ LA L +G+ GD V + N+ E+++ LA +++G V + IN Sbjct: 29 EDRKITHKELKHYVDSLARYLELIGIRKGDHVALLLTNSKEFIISLLAISKLGAVTIPIN 88 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKT 172 + E+EY L K+L++ +F +E++ +Q ++ Sbjct: 89 TFLKKQEIEYILQNSDSKVLITQTKFS--------KEVSDVFQTSD-----------IEK 129 Query: 173 VVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPK 232 ++W+DD DE L F E ++ D + A L D I +TSGTTG PK Sbjct: 130 IIWVDDYPN--LDEKNL-SFEEGLS---IEDYEHLKPQADLD--DTFVIIYTSGTTGKPK 181 Query: 233 GATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDG 292 G L++RNI +N I + +T DR +P++H F + + L + IV Sbjct: 182 GVMLSYRNIFSNILNIKKLGNITEKDRFIAYLPMFHTFTLTVSVLLPLYTASPIVIIKSI 241 Query: 293 FDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNL--STLRTGIMAGSPCPTEVMK 350 +++ +R T GVP +F A L +F + + +R I G+P ++ Sbjct: 242 MPFSNIIKQTLLKRVTIFIGVPEVFSA-LSKAKFPWYFMWFHRIRYFISGGAPLSKTTLE 300 Query: 351 RVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVV 410 R+ ++ + YG++E SPV + + P ++ +VG P +VKIVD D + Sbjct: 301 RMRQKFRRTPLLEGYGLSECSPVV---AVNRPEKQKDLSVGPPLPDYQVKIVDSDLMELP 357 Query: 411 PIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMV 470 P G+ GE KG VM GY+ + T E I GW+ TGDL +D EGY+ IV R+KD++ Sbjct: 358 P-GEIGEVIVKGDCVMKGYYKNPYATEEVI-VNGWLLTGDLGYLDEEGYLYIVDRLKDLI 415 Query: 471 IRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWI-IAKPGTQPTEDDIRAF 529 I G NIYPREIEE L HP +++ VVG D+ +GE A++ + + + E IRA+ Sbjct: 416 ISKGINIYPREIEEILNAHPDIEESAVVGKKDEHHGEIPVAFVKLVENVEKFDEKKIRAY 475 Query: 530 CKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566 K +A+YK+P++I + FP TGKI K +R+ + Sbjct: 476 LKENLANYKIPKHIYVLEDFPRNATGKILKRVLRERL 512 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: 586 Number of extensions: 30 Number of successful extensions: 7 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: 518 Length adjustment: 36 Effective length of query: 542 Effective length of database: 482 Effective search space: 261244 Effective search space used: 261244 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