Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AZOBR_RS31155 AZOBR_RS31155 AMP-dependent synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__azobra:AZOBR_RS31155 Length = 567 Score = 232 bits (592), Expect = 3e-65 Identities = 167/556 (30%), Positives = 278/556 (50%), Gaps = 34/556 (6%) Query: 23 DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82 + P+ + + A D AR ER L + G+R TYA++ R A +G++ G Sbjct: 25 NAPIPVKPLTALLEDAAARFAERPFLDFM--GKRSTYAEVARMVDRAARGFQAIGVSKGV 82 Query: 83 RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSD 142 RVG++ N +V+ A + G +VN NP Y E+ + + G +L+V++ Sbjct: 83 RVGLFLPNTPYFVICYFAILKAGGTVVNFNPLYAERELHHQITDSGVELMVTLDLKVL-- 140 Query: 143 YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPG---LLRFTELIARG 199 Y M R LA + A LP K ++ + + A P L F L+A Sbjct: 141 YGKMARMLAESGLKRLVICPMADILPFPKNWLFPIVKRAEVARIPADDRHLSFRRLVAND 200 Query: 200 NAADPRLAQVAAGLQATDPINI-QFTSGTTGFPKGATLTHRNILNNG-----FFIGECMK 253 A P + T+ + + Q+T GTTG PKGA LTH N+ N +F+G Sbjct: 201 GAPKP------VAIDPTEDVAVLQYTGGTTGVPKGAMLTHANLFANTEQCSLWFVG---A 251 Query: 254 LTPADRLCIPVPLYHCFGM-VLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHG 312 +R+ +P +H F M V+ N + ++ P F+ V++T+ + T Sbjct: 252 RQGEERMLGVLPFFHVFAMTVVMNFSIRIGAEIVMLPR--FELDQVMETIHARKPTLFPA 309 Query: 313 VPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSP 372 VPT++ A H +++LS++R + G+P P EV K E+ + YG++E+SP Sbjct: 310 VPTIYTAINHHRHLEKYDLSSIRYCLSGGAPLPVEV-KEAFERNTGCVLVEGYGLSESSP 368 Query: 373 VSCQSSTDTPLS--KRVSTVGQVQPHLEVKIVD-PDTGAVVPIGQRGEFCTKGYSVMHGY 429 V +T P++ + ++G P ++IV + V+P+G++GE C +G VM GY Sbjct: 369 V----ATANPITGLNKAGSIGLPLPGTLIEIVSLEEPRRVLPVGEKGEVCIRGPQVMKGY 424 Query: 430 WGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 489 W ++T + +G +HTGD+ MD +GY +IV RIKDM++ G N+YPR +EE +Y H Sbjct: 425 WNKPSETALTLVDGR-LHTGDVGYMDEDGYTHIVDRIKDMILCSGFNVYPRNVEEAIYLH 483 Query: 490 PQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSF 549 P V + V G+PD+ G+ + A+I G T +++ F K +++ ++P+ I F Sbjct: 484 PAVAECVVAGLPDEYRGQTVKAYIRVDDGKTLTREELIGFLKDKLSPIEMPKAIEFRGEL 543 Query: 550 PMTVTGKIQKFKIRDE 565 P T+ GK+ + + DE Sbjct: 544 PKTMIGKLSRKALLDE 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: 724 Number of extensions: 40 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 578 Length of database: 567 Length adjustment: 36 Effective length of query: 542 Effective length of database: 531 Effective search space: 287802 Effective search space used: 287802 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