Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_092052197.1 BQ4888_RS00245 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_900111775.1:WP_092052197.1 Length = 551 Score = 578 bits (1491), Expect = e-169 Identities = 285/554 (51%), Positives = 382/554 (68%), Gaps = 7/554 (1%) Query: 26 LIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVG 85 L+ T+GA D R P+ +ALV +G R +Y + R+A L+ +G+ G+ + Sbjct: 4 LLHFTLGALLEDTARRFPDNDALVYPDRGLRLSYREFDALCDRVAKGLMAIGVKKGEHLA 63 Query: 86 IWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLG 145 IW+ N EWV++Q ATA++G VLV +N +Y++AE+EY LN+ L + FK ++Y+ Sbjct: 64 IWATNVPEWVVLQFATAKIGAVLVTVNTSYKSAELEYVLNQSDSTTLFLVQGFKDTNYVE 123 Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNA-ADP 204 + + PE G L AKLP LK V+++ G G+L + EL G D Sbjct: 124 TVNTVVPELTSAPFGQLACAKLPFLKNVIFLG-----GGAPAGMLAYAELEKLGEKITDA 178 Query: 205 RLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPV 264 LA V A L + IN+Q+TSGTTGFPKG LTH N++NNGF IGECMK T DRLCIPV Sbjct: 179 ELAAVKASLDEHEVINMQYTSGTTGFPKGVMLTHHNLVNNGFNIGECMKFTEQDRLCIPV 238 Query: 265 PLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHP 324 P +HCFG VLG LAC THG+T+V P + F+P VL+ ++ ERCT +HGVPTMFIAE++HP Sbjct: 239 PFFHCFGCVLGVLACVTHGSTMV-PVETFNPEAVLKAIEAERCTAVHGVPTMFIAEMEHP 297 Query: 325 RFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS 384 F +++LSTLR+GIMAGSPCP EVMKRV+ M+ EITI YG TE+SP + TD P+ Sbjct: 298 AFRKYDLSTLRSGIMAGSPCPIEVMKRVIRDMHCSEITITYGQTESSPGITMTRTDDPIE 357 Query: 385 KRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGG 444 RV++VG+ P +EVKI+D +TGA +P G++GE CT+GY VM GY+ +T +AID G Sbjct: 358 LRVASVGRALPDVEVKIIDIETGAALPPGKQGELCTRGYHVMKGYYKMPEETAKAIDGDG 417 Query: 445 WMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQK 504 W+HTGDLA MD GY I GRIK+M+IRGGEN+YPREIEEFLY HP+V DVQV GVPD K Sbjct: 418 WLHTGDLAVMDENGYCKITGRIKNMIIRGGENVYPREIEEFLYTHPKVADVQVYGVPDAK 477 Query: 505 YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 YGE++ A + K G +E++I+ FC+G+IA+YK+P Y++FV +PMT +GKIQKFK+R+ Sbjct: 478 YGEQVMAAVKIKDGVSCSEEEIKDFCRGRIANYKIPYYVKFVDEYPMTASGKIQKFKLRE 537 Query: 565 EMKDQLGLEEQKTA 578 +L LEE +TA Sbjct: 538 MAIRELRLEEAETA 551 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: 771 Number of extensions: 25 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: 551 Length adjustment: 36 Effective length of query: 542 Effective length of database: 515 Effective search space: 279130 Effective search space used: 279130 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