Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_046009210.1 OLEAN_RS10585 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000967895.1:WP_046009210.1 Length = 560 Score = 231 bits (588), Expect = 8e-65 Identities = 161/548 (29%), Positives = 260/548 (47%), Gaps = 29/548 (5%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIW 87 Q++ F VA+ ++ A + G+ TYA+L+TE+ A+ L L GDR+ + Sbjct: 24 QSVVEVFNGFVAKYADKPAFTCL--GQTITYAELETESAAFAAYLQNETALEVGDRIAVQ 81 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147 N ++ ++ + G+ +VN NP Y E+E+ N G K L+ +A + Sbjct: 82 LPNVLQYPIVVFGAMRAGMTVVNTNPLYTEREMEHQFNDSGAKALIVLANMAAKAERVLA 141 Query: 148 RELAPEWQGQQPGHL-QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206 + G + + K + +V+ + + + + + ++ G Sbjct: 142 NTSIETVIVTEVGDMHKMVKRVLINSVLKYVKKEVESYNIANAVSLRKALSLGKGK---- 197 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN-----GFFIGECMKLTPADRLC 261 A ++ D +Q+T GTTG KGA LTH N++ N G F M L Sbjct: 198 AFTTPAIKQDDVAVLQYTGGTTGVAKGAMLTHGNLIANMLQCHGLFT---MALDEGKETA 254 Query: 262 I-PVPLYHCFGMVLGNLACF---THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMF 317 I P+PLYH + + + H I P D + VLQ+ + GL+ T+F Sbjct: 255 IAPLPLYHIYAFTVHCMVLLETGNHSVLIPNPRDIPGFIKVLQSTKFSCFVGLN---TLF 311 Query: 318 IAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQS 377 +A + P F + S L+ I G + N EI +GMTETSPV Sbjct: 312 VALCNQPVFKGLDFSGLKLTISGGMALTKNAADQWKTITNC-EIAEGFGMTETSPVV--- 367 Query: 378 STDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTR 437 S + P ++ T+G K++D D G +PIG+ GE C KG VM GYW T Sbjct: 368 SFNPPGHVKLGTIGIPVASTNCKVID-DNGNELPIGEAGELCVKGPQVMKGYWQRPEATA 426 Query: 438 EAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQV 497 EAI GW+ TGD+A + +GY+ IV R KDM+I G N+YP E+E+ + HP + +V Sbjct: 427 EAISSDGWLKTGDVAVISEDGYMKIVDRKKDMIIVSGFNVYPNEVEDEIVTHPDIIEVAA 486 Query: 498 VGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKI 557 +G+PD+K E + ++++ T D++A+ + ++ YK+PR++ F P T GKI Sbjct: 487 IGIPDEKTSEAVKVFVVSS-NENLTAADVKAWARKRLTAYKIPRHVEFRDELPKTNVGKI 545 Query: 558 QKFKIRDE 565 + ++RDE Sbjct: 546 LRRELRDE 553 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: 713 Number of extensions: 42 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: 560 Length adjustment: 36 Effective length of query: 542 Effective length of database: 524 Effective search space: 284008 Effective search space used: 284008 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