Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012970623.1 ALVIN_RS06980 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000025485.1:WP_012970623.1 Length = 519 Score = 242 bits (617), Expect = 3e-68 Identities = 171/552 (30%), Positives = 265/552 (48%), Gaps = 48/552 (8%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWS 88 +T+ F R + A+++ R +TYA L + +A+ L G+ PGDRVG++ Sbjct: 5 RTLPELFRHTAKRFDDAPAILT--DERIWTYADLDDASDGIAAGLAERGIAPGDRVGLYC 62 Query: 89 HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148 N A +V L + G +V IN + + LN G K L A F Sbjct: 63 PNGAAFVCGYLGILKAGACVVPINLLLPPTAIAFVLNDAGAKALCFHAAFAEQ------- 115 Query: 149 ELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLL--RFTELIARGNAADPRL 206 AA L ++ V G G +P + R L N + PR+ Sbjct: 116 --------------AAAALTEVPGVTL---RLGIGPVDPETVDVRLDALTTAANPSAPRI 158 Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL---TPADRLCIP 263 +P I +TSGTTG PKGA LTH N+ N + E +++ DR+ + Sbjct: 159 DP------DQEPAVILYTSGTTGRPKGAVLTHANLAANATAVAEVLEIRSGADGDRVLVV 212 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMF--IAEL 321 +P++H F +G L GA +V P FD + + + R T GVP+++ + L Sbjct: 213 LPMFHAFAATVGLLMPLLAGAALV-PVARFDAALITEAIGTHRATLFLGVPSLYAVLLRL 271 Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381 D + A + ++R + G+ P VM+ + + I G TE PV+C + Sbjct: 272 DDAQVARWG--SVRLCVSGGAAMPEAVMQAFETRFAI-PILEGDGPTECGPVTCVNPPAG 328 Query: 382 PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAID 441 P ++ +VG P +E++I DPD G +P G+ GE C +G SVM GYW +TR + Sbjct: 329 P--RKPCSVGPALPGVEMRIADPD-GNWLPDGEHGEVCVRGPSVMRGYWNLPEETRASF- 384 Query: 442 EGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVP 501 G W TGDL D++G+ +V RIKD++I G N+YPR IEE L RHP V + VVG P Sbjct: 385 HGDWFRTGDLGWRDSDGWFYLVDRIKDLIITNGMNVYPRIIEEVLIRHPGVAEAAVVGEP 444 Query: 502 DQKYGEELCAWIIAKPGTQPTE-DDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKF 560 +GE A++ A PG + D++ +C+ ++ ++VPR I V + P +GKI K Sbjct: 445 HPLHGEIPIAYVTATPGQGELDTHDLKDWCRARLGRHEVPRRIECVATLPKNASGKILKR 504 Query: 561 KIRDEMKDQLGL 572 ++R + + G+ Sbjct: 505 ELRRTGEHERGV 516 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: 733 Number of extensions: 37 Number of successful extensions: 7 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: 519 Length adjustment: 36 Effective length of query: 542 Effective length of database: 483 Effective search space: 261786 Effective search space used: 261786 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