Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS26915 RR42_RS26915 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Cup4G11:RR42_RS26915 Length = 573 Score = 718 bits (1854), Expect = 0.0 Identities = 352/563 (62%), Positives = 431/563 (76%), Gaps = 8/563 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 SH RG+TD+PL E T+ A A+ VAR P+REA+V QG R+++ + +A L Sbjct: 18 SHVRGSTDIPLSELTVPALLAETVARFPDREAVVFREQGIRWSWREFAQVVDAMAGGLRL 77 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +GL GDR+GIWS N EW++ Q ATA++GLVLVNINPAYR AE+EYALNKVGCK +V+ Sbjct: 78 LGLERGDRIGIWSPNRVEWLVTQFATARLGLVLVNINPAYRLAELEYALNKVGCKAIVAA 137 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 FKTS YL ML+ LAPE + +PG LQAA+LP L+ V+ + E PG+L + L Sbjct: 138 ESFKTSRYLEMLQTLAPELKSCEPGTLQAARLPALRWVIRMGAER-----TPGMLNYDAL 192 Query: 196 IARG-NAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 +A G +A L + A L DPINIQFTSGTTG PKGATLTHRNI+NN FI M+ Sbjct: 193 LAHGTHALTSELDALTAQLDRYDPINIQFTSGTTGAPKGATLTHRNIVNNARFIAMAMRF 252 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 + D+LCIPVP YHCFGMVL LAC + GA +V+P + F+P + V +ERCT LHGVP Sbjct: 253 SEQDKLCIPVPFYHCFGMVLAVLACVSTGACMVFPGEAFEPAATMAAVSEERCTALHGVP 312 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIA+LDHP FA+++ STLRTGIMAGSPCP E MKRV+ QM++ ++TIAYGMTETSPVS Sbjct: 313 TMFIAQLDHPDFAKYDFSTLRTGIMAGSPCPIETMKRVISQMHMAQVTIAYGMTETSPVS 372 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 QSST PL KRV+TVGQ+QPHLEVK+VD TG +VP+G++GE CT+GYSVM GYW DE Sbjct: 373 FQSSTTDPLDKRVTTVGQIQPHLEVKLVD-GTGEIVPVGEKGELCTRGYSVMQGYWDDEP 431 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 +TREAI + GWMHTGDLAT+DAEGY NIVGR+KDM+IRGGEN+YPREIEEFL+RHP+VQ Sbjct: 432 RTREAIRD-GWMHTGDLATIDAEGYCNIVGRVKDMLIRGGENVYPREIEEFLFRHPKVQA 490 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 VQV GVPD KYGEE+CAWI+ KPG TEDDIRAFC+ QIAHYK+PRYIRFV PMT+T Sbjct: 491 VQVFGVPDPKYGEEVCAWIVLKPGDTATEDDIRAFCRDQIAHYKIPRYIRFVDEMPMTIT 550 Query: 555 GKIQKFKIRDEMKDQLGLEEQKT 577 GK+QKF +R+ M +LGL ++ T Sbjct: 551 GKVQKFVMRERMTLELGLGDKTT 573 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: 915 Number of extensions: 34 Number of successful extensions: 4 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: 573 Length adjustment: 36 Effective length of query: 542 Effective length of database: 537 Effective search space: 291054 Effective search space used: 291054 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