Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013256973.1 DEBA_RS00680 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000143965.1:WP_013256973.1 Length = 581 Score = 246 bits (628), Expect = 2e-69 Identities = 182/578 (31%), Positives = 279/578 (48%), Gaps = 57/578 (9%) Query: 23 DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82 D+ + + A D P A ++ QG T+AQ++ A RLA+ L G+ D Sbjct: 19 DIDGYNKPVFAMLDDAARNYPN--ATYTIFQGGMRTFAQVKDTADRLANFLASRGIKHED 76 Query: 83 RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMAR---FK 139 RV I+ N ++ + +++ G V NP Y E+ Y L G K + M +K Sbjct: 77 RVAIFLPNIPQYPEVFFGSSKAGAACVTCNPLYTIEELNYQLKDSGAKAVFCMDHPQFYK 136 Query: 140 TSD-----------YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPG 188 T+ + ++ P+ +G G L KLP+ ++ +P Sbjct: 137 TTCEAIKGTDVQTVVICNIKSYLPKIKGFLGGLL--GKLPKAES------------HDPS 182 Query: 189 LLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFI 248 + ++IA P++ A D I +T GTTG PKGA L H N +N + Sbjct: 183 HFMYDDIIASSRPEPPKVNFDAE----KDLAVILYTGGTTGVPKGAELKHTNFYSNVVAL 238 Query: 249 GECMKLT--PADR-----------LCIPVPLYHCFGMVLGNL-ACFTHGATIVYPND--G 292 + +++ P +R +P YH FG+ + L +C++ + P+ G Sbjct: 239 NKWIRVPNRPGERPGPMESGGAHTFLGVLPWYHSFGLTVCMLGSCYSANRLVCIPDPKAG 298 Query: 293 FDPLT-VLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKR 351 P T VL+ +QD + T VPT++ A ++H +F+LS++ +P P EV+KR Sbjct: 299 NPPFTEVLKAIQDYKVTMTVAVPTIYTAFVNHALIKKFDLSSMAACSSGAAPLPPEVLKR 358 Query: 352 VVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAV-V 410 E++ I YG+TET+PV + T +++ +VG P ++KIVD DTG V + Sbjct: 359 F-EEITGGVIFEGYGLTETTPVLTTNPTFAD-KRKIGSVGMPLPGTDIKIVDLDTGLVEL 416 Query: 411 PIGQRGEFCTKGYSVMHGYW---GDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIK 467 P G+ GE G +M GYW A+ I+ + TGD+ +D +G+V I R K Sbjct: 417 PHGEDGEIAAAGPQIMRGYWQRPDANAEVFREIEGKRFFLTGDIGHIDEDGFVVITDRKK 476 Query: 468 DMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIR 527 D+++ GG N YP+EIEE LY HP+V VVGVPD GE + A+I KPG TE +I Sbjct: 477 DLILVGGFNAYPKEIEEVLYTHPKVAQAAVVGVPDPSSGEAVKAFIQLKPGVTATEKEIL 536 Query: 528 AFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565 FCK +A YK PR I F P +V GKI + +R E Sbjct: 537 DFCKDHLAGYKRPREIEFRDELPTSVVGKILRRVLRSE 574 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: 797 Number of extensions: 47 Number of successful extensions: 7 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: 581 Length adjustment: 36 Effective length of query: 542 Effective length of database: 545 Effective search space: 295390 Effective search space used: 295390 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