Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_035238694.1 Q366_RS10425 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000745975.1:WP_035238694.1 Length = 550 Score = 518 bits (1334), Expect = e-151 Identities = 253/544 (46%), Positives = 360/544 (66%), Gaps = 5/544 (0%) Query: 24 VPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83 +PL T+G V + P+ A+V V + R +Y+Q T A L+ +G+ G++ Sbjct: 5 LPLQSLTLGQILDRTVEKYPDNPAIVYVDRDFRLSYSQFATYVDETAKGLMALGVKKGEK 64 Query: 84 VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143 VGIW+ N WV +Q ATA++G VL+ +N Y+TAE+EY L + C+ L + ++ +DY Sbjct: 65 VGIWATNIPFWVTLQFATAKIGAVLLTVNTNYKTAELEYLLTQSDCENLFLIDGYQDTDY 124 Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203 + + EL PE + Q G+L++ K P LK V ++ E +G +R ++ Sbjct: 125 ISTIYELVPELKTCQRGYLKSPKFPHLKRVAFLGPEKHRGMYTIPEIRALSVMISEEEYQ 184 Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIP 263 R L D +N+Q+TSGTTGFPKG LTH NI NNG++IG L P DR+C+P Sbjct: 185 AR----QDSLDLHDVVNMQYTSGTTGFPKGVMLTHYNIGNNGYWIGANQNLGPDDRVCLP 240 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 VPL+HCFG VLG LA HG+ +V + FDPL ++ +V+ E+CTGL+GVPTMFIA LDH Sbjct: 241 VPLFHCFGCVLGVLAFINHGSCMVIL-EKFDPLLIMASVEQEKCTGLYGVPTMFIAVLDH 299 Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383 P F +F+ S+LRTGIMAGS CP VM++V+++MN+ EITI YG+TE SPV Q+ + Sbjct: 300 PLFKKFDFSSLRTGIMAGSNCPIHVMEQVIDKMNMTEITICYGLTEASPVLTQTRIHDDI 359 Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443 RV TVG+ PHLEVK++D DTG + G++GE C +GYS+M GY+ + T + ID+ Sbjct: 360 RVRVETVGRALPHLEVKVIDLDTGKELLPGKQGEVCVRGYSIMKGYYNNPEATAQVIDKD 419 Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503 GW+H+GDL MD G ++I GR KDM+IRGGENIYPRE+EEFLYR +++DVQV VP + Sbjct: 420 GWLHSGDLGVMDKAGNLSITGRHKDMIIRGGENIYPREVEEFLYRMDEIRDVQVAAVPSE 479 Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 KYGEE+ A++I K G+ DI+ FC+G+I+ YK+P+Y+ F+ +PMT +GKIQK+K+ Sbjct: 480 KYGEEVGAFVILKDGSNIEPSDIQDFCRGKISRYKIPKYVHFIDEYPMTASGKIQKYKLT 539 Query: 564 DEMK 567 + K Sbjct: 540 EMSK 543 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: 762 Number of extensions: 34 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: 550 Length adjustment: 36 Effective length of query: 542 Effective length of database: 514 Effective search space: 278588 Effective search space used: 278588 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 24 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