Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_108401501.1 B9Z44_RS01335 cyclohexanecarboxylate-CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_003063475.1:WP_108401501.1 Length = 547 Score = 215 bits (547), Expect = 4e-60 Identities = 168/548 (30%), Positives = 264/548 (48%), Gaps = 31/548 (5%) Query: 28 EQTIGAFFADMVARQPEREALVSVH----QGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83 ++TI VA P++ AL +V + R+TY +L A R+A L +G+ D Sbjct: 23 DRTINDDLDACVATCPDKLALTAVQAESGKVTRFTYRELSNMADRVALGLTKLGVGQNDI 82 Query: 84 VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143 V N ++ + LA +++G V+ + +R E+ + L K+L+ F+ DY Sbjct: 83 VACQLPNWWQFTITYLACSRIGAVMNPLMHIFRERELSFMLKHGEAKVLIIPQTFRGFDY 142 Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203 M+ E+ P LP LK VV ++ G GA+ L + + A Sbjct: 143 EKMVNEIKPS-------------LPDLKHVVVVN---GAGANSFEALLSGPAWEKESNAT 186 Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIP 263 L Q G D + +TSGTTG PKG T ++ N + L D + + Sbjct: 187 AVLTQHRPG--PDDVTQLIYTSGTTGEPKGVMHTANTVMANIIPYAARLHLDANDVVLMA 244 Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL-D 322 P+ H G + G + ++ V D ++PL + ++ E T T F+ +L Sbjct: 245 SPMAHQTGFMYGLMMPIMLKSSAVLL-DVWEPLRAIDLIRHEGAT-FTMASTPFLTDLAK 302 Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382 + + + TLRT + AG+P P ++++ + + I A+GMTE V+ D P Sbjct: 303 NVEESGKKVPTLRTFLCAGAPIPGPLVEQARSVLGTK-IVSAWGMTENGAVTLIELND-P 360 Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442 + +T G P +E+K+V+ D GAV+P G+ G+ + S GY + D Sbjct: 361 DERAFTTDGLPLPGVELKVVNDD-GAVLPAGEAGKLYVRSCSNFGGYL--KRAHLNGTDA 417 Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502 GW TGDLA +DA+GYV I GR KD++IRGGENI EIE LYRHP + +V PD Sbjct: 418 EGWFDTGDLARLDAQGYVRITGRSKDVIIRGGENIPVVEIESLLYRHPAIAMAAIVAYPD 477 Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQ-IAHYKVPRYIRFVTSFPMTVTGKIQKFK 561 ++ GE CA ++ KPG + + K Q IA +P + + P T +GKIQKFK Sbjct: 478 ERLGERACAVVVLKPGQSLDLPALVDYLKAQKIALQYIPEKLEIRDAMPATPSGKIQKFK 537 Query: 562 IRDEMKDQ 569 +R+ ++D+ Sbjct: 538 LREILRDE 545 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: 673 Number of extensions: 40 Number of successful extensions: 5 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: 547 Length adjustment: 36 Effective length of query: 542 Effective length of database: 511 Effective search space: 276962 Effective search space used: 276962 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