Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058930593.1 AU252_RS10060 o-succinylbenzoate--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001484605.1:WP_058930593.1 Length = 520 Score = 222 bits (565), Expect = 3e-62 Identities = 166/540 (30%), Positives = 247/540 (45%), Gaps = 32/540 (5%) Query: 31 IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90 IG++ + + AL+S + R +Y + RLA+AL G+ GDRV N Sbjct: 6 IGSWLQRRRPKSGNKTALISGN--RELSYEAFADRSVRLANALRDRGVAKGDRVAYLGEN 63 Query: 91 NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARF-----KTSDYLG 145 + ++ A +G + V +N E+++ L G +LV + SD Sbjct: 64 HPAFLETLFAAGLLGAIFVPLNTRLAPPEIQFQLQDCGAHILVHSQSLDVLGTRGSDATP 123 Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPR 205 + R + A P+ + VV ++D F ++A G Sbjct: 124 VARRIVVNDAADTAAATTAT--PRDQAVVSVED-------------FEAVLASGTE---E 165 Query: 206 LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVP 265 GL D I +TSGTTG PKGA LTH N++ N + D + P Sbjct: 166 FRDETVGLD--DGAMILYTSGTTGRPKGALLTHGNVVWNCMNVIVDFDFASTDVALMISP 223 Query: 266 LYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPR 325 ++H + +G L G T+V F+P L+ VQ R T L GVPT F +HP Sbjct: 224 MFHVASLDMGVLPTLLKGGTVVLEAK-FEPQRTLELVQKHRATTLSGVPTTFQMLCEHPD 282 Query: 326 FAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK 385 + +LS+L GS P V+ EQ L + YGMTET+P + D K Sbjct: 283 WEGTDLSSLTKLTCGGSAVPLRVLD-AYEQRGLH-FSNGYGMTETAPGATTLPADRSREK 340 Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445 S+ G +V+I D D G P GE KG +V+ YW ++ GW Sbjct: 341 AGSS-GLPHFFTDVRITDFD-GNQAPPETVGEIHIKGPNVIGQYWNRPEAIDQSTTADGW 398 Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505 +GD+ D +G+V I R+KDM+I GGENIYP E+E+ + V V V+GVPD+K+ Sbjct: 399 FKSGDMGYKDTDGFVFISDRLKDMIISGGENIYPAEVEQAITELVAVASVAVIGVPDEKW 458 Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565 GE A I+ + G TED ++ G++A YK+P+ + FV P T +GKI+K +R + Sbjct: 459 GEVPRAVILLREGAHLTEDQLKEHLNGRLARYKIPKSVVFVAEMPRTASGKIKKTGLRQQ 518 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: 652 Number of extensions: 25 Number of successful extensions: 5 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: 520 Length adjustment: 36 Effective length of query: 542 Effective length of database: 484 Effective search space: 262328 Effective search space used: 262328 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 Apr 09 2024. 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