Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 6937763 Sama_1904 AMP-binding domain protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__SB2B:6937763 Length = 573 Score = 629 bits (1623), Expect = 0.0 Identities = 314/569 (55%), Positives = 397/569 (69%), Gaps = 7/569 (1%) Query: 3 SSAAATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQL 62 S A N PL SH G+ LI+ TIG + + R P+ EA+V HQ R++Y Q Sbjct: 5 SDHTAPNPLPLTQSHYLGSDAPELIQDTIGRYLECIANRYPDHEAIVMHHQNIRWSYRQY 64 Query: 63 QTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEY 122 TE RLA+ LL +G+ PGDRVGIWS NN EW L Q ATA++G ++V INPAYR E+EY Sbjct: 65 LTEIDRLATGLLALGIGPGDRVGIWSPNNIEWCLTQFATARIGAIMVCINPAYRPEELEY 124 Query: 123 ALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQ 182 AL VGCK L++ +FK+SDYL ML+ LAPE + G LQ+++LP LK V+ EA Sbjct: 125 ALVNVGCKALITHDKFKSSDYLAMLQSLAPELAHCEAGQLQSSRLPDLKLVIRTGSEA-- 182 Query: 183 GADEPGLLRFTELIARGNAAD-PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNI 241 PG+L F ++ + G+ A+ L ++ L DPINIQFTSGTTG PKGATL+H NI Sbjct: 183 ---TPGMLNFDKVCSLGSDAEYADLQGISEKLSPFDPINIQFTSGTTGNPKGATLSHHNI 239 Query: 242 LNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQT 301 LNNG + + M+ + DRLCIPVPLYHCFGMVLGNL C GAT V+P D FDP T L Sbjct: 240 LNNGMLVAKGMRFSHLDRLCIPVPLYHCFGMVLGNLVCVATGATAVFPGDAFDPATTLAV 299 Query: 302 VQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREI 361 V+ E CT LHGVPTMFIAEL+ F +++LS+LRTG+MAG+ CP EVMKRV M+++E+ Sbjct: 300 VEKEHCTALHGVPTMFIAELELANFNDYDLSSLRTGVMAGATCPEEVMKRVQTLMHMQEV 359 Query: 362 TIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTK 421 I YG TE SP++ + D+ L RV+TVG+ H EVKIVD G PIG+ G+ C++ Sbjct: 360 VIGYGQTECSPINNLTEIDSSLELRVTTVGRALAHTEVKIVDV-FGKTQPIGEPGDVCSR 418 Query: 422 GYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPRE 481 GY VM GYW D+AKTR+ ID GW+H+GDL MD GYV IVGRIKDM+IRGGENIYPRE Sbjct: 419 GYCVMLGYWNDDAKTRDTIDSEGWLHSGDLGVMDEHGYVRIVGRIKDMIIRGGENIYPRE 478 Query: 482 IEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPR 541 IEE L+ HPQVQD V GV KYGEE+CAWI +PG E +IR F ++A++KVPR Sbjct: 479 IEEKLFTHPQVQDAAVFGVQSDKYGEEVCAWIKLRPGANLDEQEIRHFLTEKVAYFKVPR 538 Query: 542 YIRFVTSFPMTVTGKIQKFKIRDEMKDQL 570 YI+FV S+PMTVTGK+QKF++R+ M ++L Sbjct: 539 YIKFVESYPMTVTGKLQKFRMRELMYEEL 567 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: 907 Number of extensions: 41 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: 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