Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058857525.1 AS188_RS02550 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001482365.1:WP_058857525.1 Length = 509 Score = 247 bits (630), Expect = 9e-70 Identities = 188/551 (34%), Positives = 272/551 (49%), Gaps = 56/551 (10%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWS 88 Q IG++ +A+ +R A+V H GR TYAQL HRLA AL G+ DRV Sbjct: 4 QGIGSWLDRRLAKSADRTAVV--HGGRTLTYAQLHERFHRLAGALAEAGVGRRDRVASLG 61 Query: 89 HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148 N+ ++ A +G VLV IN + EV Y L G +LV A G+ Sbjct: 62 ENSPAFLEALFAAGLLGAVLVPINTRLASPEVCYQLEDAGVSVLVHDA--------GLTG 113 Query: 149 ELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQ 208 P A LP + V + +E QG P L + + G A P Sbjct: 114 LAVPA----------ARDLPGITRWV-VAEEPVQGT--PTL----DAVVAG--ARPWTED 154 Query: 209 VAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL-----TPADRLCIP 263 V GL+ D I +TSGTTG PKGA LTH N F C+ + AD + + Sbjct: 155 VPVGLE--DLAVILYTSGTTGRPKGACLTHGN------FTWNCVNVLVDYDVSADEVALM 206 Query: 264 V-PLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322 + P++H + +G L GAT+V + F+P VL+ ++ R T L GVPT + + Sbjct: 207 ISPMFHVASLGMGVLPILLKGATLVLESR-FEPGRVLELIERHRVTWLSGVPTTYQMLCE 265 Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382 HP +A +LS+LR GS P V+ E L T +YGMTETSP +T+ P Sbjct: 266 HPDWARTDLSSLRKLTCGGSAVPMRVLD-AYEDRGLA-FTASYGMTETSP----GATNLP 319 Query: 383 LSKRVSTVGQVQ-PHL--EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREA 439 ++ G PH +V++V PD P G+ GE G +V+ YW Sbjct: 320 AARSREKAGSSGLPHFFSDVRVVGPDGSPAAP-GETGEILLSGPNVITEYWNRPDAAGSF 378 Query: 440 IDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVG 499 E GW H+GDL +DA+G++ + R+KDM+I GGEN+YP E+E + P V V V+G Sbjct: 379 --EDGWFHSGDLGHLDADGFLFVSDRMKDMIISGGENVYPAEVEAAILELPAVAAVAVIG 436 Query: 500 VPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQK 559 VPD+K+GE A ++ + G T + ++ G++A YKVP+ + V P T +GKI+K Sbjct: 437 VPDEKWGEVPHAVVVPREGHDLTAEALQERLAGRLARYKVPKTLTLVDEMPRTASGKIRK 496 Query: 560 FKIRDEMKDQL 570 +R E++ ++ Sbjct: 497 NVLRSELRPEV 507 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: 657 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 509 Length adjustment: 35 Effective length of query: 543 Effective length of database: 474 Effective search space: 257382 Effective search space used: 257382 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