Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BWI76_RS23695 BWI76_RS23695 putative acyl-CoA synthase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Koxy:BWI76_RS23695 Length = 518 Score = 171 bits (434), Expect = 5e-47 Identities = 149/543 (27%), Positives = 231/543 (42%), Gaps = 65/543 (11%) Query: 40 ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGM-GLTPGDRVGIWSHNNAEWVLMQ 98 AR P+ AL + RRY Y R + L + L GDR+ + N+ + + Sbjct: 20 ARSPD--ALALAFEDRRYLYRDFHLRVQRAMAQLDRIWSLRKGDRILLAWGNHPAFCEVL 77 Query: 99 LATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQ 158 A +G+ +V + + AE E + + + ++ A + +W Q Sbjct: 78 FAALGLGIEVVPFSTKLKQAESEELVGHIAPRAVLFDATVQ-------------DWLKQT 124 Query: 159 PGHL-------QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAA 211 P L QA LP DP L ++ Sbjct: 125 PDALCVSLSEWQALSLP----------------------------------DP-LTRLPT 149 Query: 212 GLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFG 271 + D + FTSGTTG PKGA +TH N+L + + LT AD + VP+YH G Sbjct: 150 PVNRDDTAVMMFTSGTTGEPKGAIITHHNLLCAIDAYAQKLNLTAADSTILAVPIYHITG 209 Query: 272 MVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFI----AELDHPRFA 327 + LA F ++ F+ V+ T++++ T LHG PT+FI A + Sbjct: 210 LS-ALLALFISLGASLWLQHRFNAPQVINTLREQNITFLHGSPTIFILLCQAAREQSASH 268 Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRV 387 + LRT ++ + I YG+TET+ + D S + Sbjct: 269 PGDFPALRTIACGAGHLSDGLIAELKTLFPHTAIQPIYGLTETTSPATIFPGDVWGSDKC 328 Query: 388 STVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMH 447 + GQ P L + I + D +P GQ G KG V+ YW ++ R + D GW Sbjct: 329 GSSGQAIPGLAIAIRN-DRQQPLPAGQIGHIWLKGDVVIREYW-QHSERRPSCDAQGWFC 386 Query: 448 TGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGE 507 TGDL +D EG++ I R KDM+ RGGE IY E+E L + V++V V+ P YGE Sbjct: 387 TGDLGYLDDEGWLYIKDRSKDMINRGGEKIYSLELENILSTYRGVREVAVIPTPSPVYGE 446 Query: 508 ELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 E A+I+ T ++I + K +IA +K+P I F P T GK+ K +++ + Sbjct: 447 EPVAFIVPDGQHHLTSEEILGWLKVKIARFKLPARIIFTRVLPRTHNGKVSKQQLKARLA 506 Query: 568 DQL 570 + + Sbjct: 507 ESI 509 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: 650 Number of extensions: 38 Number of successful extensions: 6 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: 518 Length adjustment: 36 Effective length of query: 542 Effective length of database: 482 Effective search space: 261244 Effective search space used: 261244 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 17 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