Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_005458077.1 SACCYDRAFT_RS17075 fatty-acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000244975.1:WP_005458077.1 Length = 507 Score = 253 bits (646), Expect = 1e-71 Identities = 168/530 (31%), Positives = 249/530 (46%), Gaps = 35/530 (6%) Query: 40 ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQL 99 A Q + + ++H R + RLA L +G+ GDRV +++ N+ ++ + Sbjct: 10 ALQQFPDRIATIHGDRARDFTTHVQRVARLAGGLRSLGVESGDRVAMYALNSDRYLEHLM 69 Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQP 159 A VL +N + EV Y LN ++L+ F + P Sbjct: 70 AVPWADAVLAPVNTRWAEPEVVYGLNDCDARVLLVDDTFAPA----------------VP 113 Query: 160 GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPI 219 L A+ P +K VV+ AG+G G + + +L+A A DP V + D + Sbjct: 114 ALL--AECPGVKHVVY----AGEGPTPEGWVSYEDLVA---ACDP----VPDARRGGDAL 160 Query: 220 NIQF-TSGTTGFPKGATLTHRNILNNGF-FIGECMKLTPADRLCIPVPLYHCFGMVLGNL 277 F T GTTG PKG L+H +L + + TP R P++H + + Sbjct: 161 AALFYTGGTTGAPKGVALSHAGMLTSALGCVATGFMTTPGGRFLHAAPMFHLGDLAHWVM 220 Query: 278 ACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTG 337 T + P FDP +L + + T L VPTM LDHP F + LR Sbjct: 221 QSLTGNTQVTIP--AFDPAALLAALPEHGVTDLFLVPTMLRIVLDHPDFDPAAFAGLRRL 278 Query: 338 IMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHL 397 + A +P P E++ R E E+ AYGMTE SP + G+ PH Sbjct: 279 VYAAAPMPAELLDRASELFPHVELVQAYGMTELSPAITLLGPSDHAGPHRYSAGRAAPHS 338 Query: 398 EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457 EV++V PD G VP G GE T+G +M GYWG T E + +G WMHTGD +D Sbjct: 339 EVRVVAPD-GGEVPRGTVGEIVTRGGHLMLGYWGKPELTAEVVRDG-WMHTGDAGYLDEA 396 Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517 GY+ +V RIKDM+I GGEN+Y E+E L+ HP V V+G+PD +YGE + A ++ Sbjct: 397 GYLYVVDRIKDMIITGGENVYSAEVENVLHEHPLVATCAVIGLPDDRYGERVHAVVVPAG 456 Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567 P ++ A + ++A+YKVPR FV P++ GK+ K ++R + Sbjct: 457 DRHPDPAELDAHVRARLANYKVPRGYDFVDELPLSGAGKVLKHELRSRFR 506 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: 744 Number of extensions: 43 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: 507 Length adjustment: 35 Effective length of query: 543 Effective length of database: 472 Effective search space: 256296 Effective search space used: 256296 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: 52 (24.6 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