Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_046009720.1 OLEAN_RS13935 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000967895.1:WP_046009720.1 Length = 573 Score = 251 bits (641), Expect = 6e-71 Identities = 172/547 (31%), Positives = 266/547 (48%), Gaps = 37/547 (6%) Query: 41 RQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQL 99 R +R A S+ G TY Q+ + AS L L PGD + I N ++ + Sbjct: 36 RYADRPAFTSI--GYTLTYRQIDEYSAAFASYLQNHTTLKPGDSIAIQMPNILQYPIAMY 93 Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTS-----DYLGMLRELAPEW 154 + GL +VN NP Y E+ + N G K L+ M F S D G+ + Sbjct: 94 GALRAGLRVVNTNPLYTEREMLHQFNDSGAKALLCMDVFAKSVQGVKDQTGIKHIIVTSL 153 Query: 155 QGQQPGHLQA---AKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAA 211 PG + A +K +V P + F + G + Q Sbjct: 154 ADMLPGFKRVLINAAAKHIKKMV-------PAYSLPEAVSFRSCLKLGKG---KAFQENH 203 Query: 212 GLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFI----------GECMKLTPADRLC 261 D I +Q+T GTTG KGA LT+RN++ N G+ MK + Sbjct: 204 MKNPQDTIVLQYTGGTTGVAKGAELTNRNLVANMLQAASALGQVDEDGKPMKGDGQAVIV 263 Query: 262 IPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL 321 P+PLYH + + +A F G V + D T ++ ++ + TG+ G+ T+F++ + Sbjct: 264 APLPLYHIYSFTVHLMALFELGDHSVLIANPRDTETFIRFMKPWKLTGVVGLNTLFVSLM 323 Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381 PRF E + S ++ + G+ + KR E ++ AYG+TE SP + + Sbjct: 324 ASPRFKELDFSEMKLTLSGGTALVEDTAKRWKEFTGTG-VSEAYGLTECSPAVTMNPANG 382 Query: 382 PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAID 441 +R+ TVGQ P +K +D D G V +G+RGE C KG VM GYW T+++ Sbjct: 383 --LERMGTVGQAMPGTALKCID-DNGDEVAVGERGELCVKGPQVMKGYWNRPEATKDSFT 439 Query: 442 -EGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGV 500 +G W+ TGD+A +D +G+V IV RIKD+++ G N+YP E+E+ + HP V++ V+GV Sbjct: 440 PDGEWLRTGDVAVIDEDGFVKIVDRIKDLILVSGFNVYPNEVEDVVAGHPGVENCAVIGV 499 Query: 501 PDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKF 560 PD+K GE + +++A T +DI+ FCK ++ YK+PR I F PMT GKI + Sbjct: 500 PDEKTGEAVKLYVVASDANL-TAEDIKTFCKDKLTGYKLPRQIEFRDELPMTPVGKILRR 558 Query: 561 KIRDEMK 567 +++DE K Sbjct: 559 ELKDEEK 565 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: 764 Number of extensions: 33 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: 573 Length adjustment: 36 Effective length of query: 542 Effective length of database: 537 Effective search space: 291054 Effective search space used: 291054 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