Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 201132 SO1971 AMP-binding family protein (NCBI ptt file)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__MR1:201132 Length = 578 Score = 620 bits (1600), Expect = 0.0 Identities = 311/571 (54%), Positives = 391/571 (68%), Gaps = 7/571 (1%) Query: 1 VTSSAAATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYA 60 VT+ A +PL S RG L+E+TIG + D+ PE+ A+V HQ R+ Y Sbjct: 8 VTNQATNQTISPLKYSEFRGPNAPELVEKTIGQYLDDIANTYPEQLAVVVNHQDIRWNYR 67 Query: 61 QLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEV 120 Q LA+ LL +G+ PGDR+GIWS NN EW L Q ATA++G ++V INPAYR E+ Sbjct: 68 QYLARIDALAAGLLKLGIGPGDRIGIWSPNNIEWCLTQFATAKIGAIMVCINPAYRPEEL 127 Query: 121 EYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEA 180 +YAL VGC+ ++ +FK+S+YL ML LAPE + G LQA LP+L+ V+ + E Sbjct: 128 QYALTNVGCRAVICADKFKSSNYLQMLYTLAPELKECAAGQLQAKALPELQFVIRMGAEK 187 Query: 181 GQGADEPGLLRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHR 239 PG+L F +L+ +A D L ++A GL D INIQFTSGTTG PKGATL+H Sbjct: 188 S-----PGMLNFDDLLVEVSADDKAMLERIANGLSPYDAINIQFTSGTTGSPKGATLSHH 242 Query: 240 NILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVL 299 NILNNG+ + E MK T D+LCIPVPLYHCFGMVLGNL C GA V+P D FDPLT L Sbjct: 243 NILNNGYLVAEAMKFTCDDKLCIPVPLYHCFGMVLGNLVCLAKGAAAVFPGDSFDPLTTL 302 Query: 300 QTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLR 359 + V+ ERCT LHGVPTMFIAEL+HP F F+LS+LRTG+MAG+ CP EVM+RV + M ++ Sbjct: 303 EVVERERCTALHGVPTMFIAELEHPEFTRFDLSSLRTGVMAGATCPEEVMRRVQQLMYMQ 362 Query: 360 EITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFC 419 E+ I YG TE SP++ + D+P+ KRV TVG+ PH EVKIVD + G V+PI Q GE C Sbjct: 363 EVLIGYGQTECSPLNHITEIDSPVEKRVLTVGRALPHTEVKIVD-EFGEVLPINQPGEVC 421 Query: 420 TKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYP 479 ++GY +M YW D KT ID GW+H+GD+ MD +GYV IVGRIKDM+IRGGENIYP Sbjct: 422 SRGYCIMQCYWNDPEKTAATIDREGWLHSGDIGQMDEQGYVQIVGRIKDMIIRGGENIYP 481 Query: 480 REIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKV 539 REIEE LY H VQD V GV KYGEE+CAWI + G E+DIR F + A++KV Sbjct: 482 REIEEKLYTHKDVQDAAVFGVHSDKYGEEVCAWIKVRSGATIKEEDIRHFLTEKFAYFKV 541 Query: 540 PRYIRFVTSFPMTVTGKIQKFKIRDEMKDQL 570 PRYI+FV +PMTVTGKIQKFK+R+ M +L Sbjct: 542 PRYIKFVDQYPMTVTGKIQKFKMRELMYQEL 572 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: 857 Number of extensions: 32 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: 578 Length adjustment: 36 Effective length of query: 542 Effective length of database: 542 Effective search space: 293764 Effective search space used: 293764 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