Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF1053 Psest_1086 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__psRCH2:GFF1053 Length = 560 Score = 654 bits (1686), Expect = 0.0 Identities = 324/561 (57%), Positives = 406/561 (72%), Gaps = 7/561 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ G PL+ TIGA F V R P+REALV HQ RYT+A+L R A LL Sbjct: 5 SYTCGPQSKPLLPMTIGAAFDRTVERFPQREALVVRHQQLRYTWAELAEAVDRCARGLLA 64 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +GL G+RVGIWS NNA+W + Q ATA++G+VLVNINPAYR +E+EYAL + GC+ L+ Sbjct: 65 LGLQAGERVGIWSPNNAQWCITQFATAKIGVVLVNINPAYRLSELEYALKQSGCRWLICA 124 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 FKTSDY ML EL PE + G LQ+ LP+L+ V+ + D+ G +L++ L Sbjct: 125 DAFKTSDYHAMLHELLPELESAAVGALQSHMLPELRGVISLCDKPVDG-----MLQWQAL 179 Query: 196 IARGNAADP-RLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 + P +L Q LQ DPINIQ+TSGTTGFPKGATL+H NILNNG+ +GE ++L Sbjct: 180 MEMAEQVGPEQLRQCGERLQFDDPINIQYTSGTTGFPKGATLSHYNILNNGYMVGESLRL 239 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 T DRL IPVPLYHCFGMV+GNL C THG T++YP+ F+PL LQ +E+ TG++GVP Sbjct: 240 TEHDRLVIPVPLYHCFGMVMGNLGCVTHGTTMIYPSAAFEPLAALQAAAEEKATGMYGVP 299 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIA LDHP +LS+LRTGIMAGS CP EVMKRV++ M+L E+ IAYGMTETSPVS Sbjct: 300 TMFIAMLDHPERQSLDLSSLRTGIMAGSTCPIEVMKRVIDDMHLAEMQIAYGMTETSPVS 359 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 Q+S D L +RV++VG+ QPHLE KIVD + GAVVP GQ GE CT+GYSVM GYW + Sbjct: 360 TQTSADDDLERRVTSVGRTQPHLESKIVD-EHGAVVPRGQIGELCTRGYSVMLGYWNNPD 418 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 TR+AID WMHTGDLA MD EGY+ IVGR KDM+IRGGEN+YPREIEEFL+ HP V D Sbjct: 419 ATRDAIDGARWMHTGDLAVMDDEGYIKIVGRNKDMIIRGGENVYPREIEEFLFTHPAVAD 478 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 VQV+GVPD K+GEE+ AW+ PG + + +R FCKG+IAH+K PR+I+FV FPMT++ Sbjct: 479 VQVIGVPDSKFGEEIVAWVKLHPGHEVEGEALREFCKGRIAHFKTPRHIKFVDDFPMTIS 538 Query: 555 GKIQKFKIRDEMKDQLGLEEQ 575 GK+QKF++R+ +LG+ EQ Sbjct: 539 GKVQKFRMREISVVELGISEQ 559 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: 855 Number of extensions: 31 Number of successful extensions: 3 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: 560 Length adjustment: 36 Effective length of query: 542 Effective length of database: 524 Effective search space: 284008 Effective search space used: 284008 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