Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011734419.1 PPRO_RS02310 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000015045.1:WP_011734419.1 Length = 568 Score = 543 bits (1400), Expect = e-159 Identities = 267/553 (48%), Positives = 368/553 (66%), Gaps = 7/553 (1%) Query: 25 PLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRV 84 P + TIG +F +VA QP+ + ++ + R+++ Q LA LL +GL GD + Sbjct: 8 PFSDLTIGQYFDTVVAAQPDHDCIIYPDRNLRWSWGQFNARVDALAKGLLAIGLEKGDHL 67 Query: 85 GIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYL 144 G+W+ N +W+ ATA++G+V V +NP Y++ E+ Y L + K L + F+ DY+ Sbjct: 68 GMWARNVPDWLTFMFATAKIGVVFVTVNPVYKSHELAYVLTQSDMKALCIIDSFRDVDYV 127 Query: 145 GMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAAD 203 ++REL PE Q+ GHL +A+ P LK ++++ E +G EL+ G + +D Sbjct: 128 SIVRELVPEAATQERGHLDSAQFPFLKKLIYMGPEKHRG-----FYTVPELLLLGEHYSD 182 Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIP 263 A GL A D IN+Q+TSGTTGFPKG L+ RNILNNG++IGE K T DR+C+P Sbjct: 183 DDYAAAREGLVADDVINMQYTSGTTGFPKGVMLSSRNILNNGYYIGERQKFTKMDRICLP 242 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323 VPL+HCFG VLG +A THG+T+V + FDPL L VQ E+CT ++GVPTMFIAEL H Sbjct: 243 VPLFHCFGCVLGVMAMLTHGSTLVML-EIFDPLMALAAVQKEKCTAIYGVPTMFIAELTH 301 Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383 P F F+ S+LRTGIMAGSPCP E MK+V+ M+ EITIAYG+TE SPV Q+STD + Sbjct: 302 PMFPLFDTSSLRTGIMAGSPCPIETMKQVMSDMHASEITIAYGLTEGSPVFIQTSTDDTI 361 Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443 +R T+G P +EV++VDP+TG P G GE +GY+VM GY+ +T AID Sbjct: 362 ERRCETIGTAMPEIEVRVVDPETGQDCPPGVPGELICRGYNVMKGYYKMPEQTAAAIDAA 421 Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503 GW+H+GDL T+D GY + GRIKDM+IRGGENIYPREIEEFLY P V+DVQ+VGVPD+ Sbjct: 422 GWLHSGDLGTVDEHGYYRVTGRIKDMIIRGGENIYPREIEEFLYTMPGVKDVQIVGVPDE 481 Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 KYGE + A+++ G+ +E+D+R F + +IA YK PR++ FV FPMT + KIQK+K+R Sbjct: 482 KYGEVVGAFVMRSKGSDISEEDVREFAQTRIARYKCPRHVWFVEEFPMTASNKIQKYKLR 541 Query: 564 DEMKDQLGLEEQK 576 + + LG+ + K Sbjct: 542 EMAAELLGVSDVK 554 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: 824 Number of extensions: 36 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: 568 Length adjustment: 36 Effective length of query: 542 Effective length of database: 532 Effective search space: 288344 Effective search space used: 288344 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