Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_052668598.1 NITAL_RS22845 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000969705.1:WP_052668598.1 Length = 547 Score = 628 bits (1620), Expect = 0.0 Identities = 316/558 (56%), Positives = 391/558 (70%), Gaps = 26/558 (4%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S A G T PLIE TIG +VAR +REA+V GRR+TYA+L + ++A LL Sbjct: 6 SEASGPTTAPLIEDTIGVLLERVVARHSDREAMVDRPSGRRWTYAELDRDVDKIALGLLD 65 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +G+ GDRVG+W+ N EW L+QLATA+VG +LVN+NPAYRT E+ YAL + GC+LLV+ Sbjct: 66 LGVNKGDRVGLWATNVPEWTLVQLATAKVGAILVNVNPAYRTHELAYALRQSGCRLLVAE 125 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 F+ S ++ + + LP L+ V+++ G+ E L TE Sbjct: 126 PEFRGSSSTEIVASVRDD-------------LPDLEQVIYL------GSPEWDALAGTE- 165 Query: 196 IARGNAADPRLAQVAAG-LQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 A D + G L A DPINIQ+TSGTTGFPKGATL+H NILNN +F G+ Sbjct: 166 -----ATDTTSLRERMGRLSAHDPINIQYTSGTTGFPKGATLSHHNILNNAYFTGQGCGY 220 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 T DR+CIPVP YHCFGMV+GNL THGAT+V P FDP L+ VQDE+CT L+GVP Sbjct: 221 TEQDRVCIPVPFYHCFGMVMGNLGAITHGATMVIPAASFDPSATLRAVQDEQCTSLYGVP 280 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIAEL F+ F+L++LRTGIMAGSPCP EVMK+V+ M E+TI YGMTETSPVS Sbjct: 281 TMFIAELALSDFSSFDLASLRTGIMAGSPCPIEVMKQVITDMGCAEVTICYGMTETSPVS 340 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 Q+ D + +R STVG V PH+EVKIVDP TG VP+G GEFCT+GYSVM GYW + Sbjct: 341 TQTRVDDDIVRRTSTVGVVHPHVEVKIVDPHTGDTVPLGTAGEFCTRGYSVMLGYWEEPE 400 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 K+ EAID GWMHTGDLATMDA+GYVNIVGRIKDMVIRGGEN+YPREIEEFL+ HP V D Sbjct: 401 KSAEAIDTEGWMHTGDLATMDADGYVNIVGRIKDMVIRGGENLYPREIEEFLFTHPSVSD 460 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 QVVGVPD+KYGEELCAW+ K G T++ I+ FC+G++AH+K+PRY+ SFPMTVT Sbjct: 461 AQVVGVPDEKYGEELCAWVRLKDGCTETQESIQEFCRGRLAHFKIPRYVLLADSFPMTVT 520 Query: 555 GKIQKFKIRDEMKDQLGL 572 GKI+K ++R ++LGL Sbjct: 521 GKIRKVEMRQLSVERLGL 538 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: 866 Number of extensions: 28 Number of successful extensions: 2 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: 547 Length adjustment: 36 Effective length of query: 542 Effective length of database: 511 Effective search space: 276962 Effective search space used: 276962 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