Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Dyella79:N515DRAFT_1417 Length = 562 Score = 238 bits (608), Expect = 4e-67 Identities = 178/551 (32%), Positives = 273/551 (49%), Gaps = 33/551 (5%) Query: 30 TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWS 88 ++ A + A+ +R A S G+ +Y Q+ + + A L G + L GDR+ I Sbjct: 26 SVAAVLEEAFAKFRDRPAFHSF--GKELSYGQIDELSRQFAGYLTGVLKLGKGDRIAIMM 83 Query: 89 HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148 N ++ + + GLV+VN NP Y E+++ L G K +V + F + L+ Sbjct: 84 PNVLQYPIALFGALRAGLVVVNTNPMYTARELKHQLEDAGAKAIVVLDNFAAT-----LQ 138 Query: 149 ELAPEWQGQQP-----GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203 ++ E + + G L K + V+ + P +RF + +A+G AA Sbjct: 139 QVVAETEVEHIVTTGIGDLLGLKGTLINFVLKHIKKMVPDYRLPHAVRFRDALAQG-AAH 197 Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN----GFFIGECMKLTPADR 259 P + +V G D +Q+T GTTG KGA L+H N++ N G +IG K P + Sbjct: 198 P-VPKVDLGHD--DLAFLQYTGGTTGVAKGAMLSHGNMVANMLQAGAWIGTNAK--PGEE 252 Query: 260 LCIP-VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFI 318 + I +PLYH F + L G + D ++ ++ R T L GV T+F Sbjct: 253 VIITALPLYHIFSLTANGLVFTRLGGLNWLITNPRDMPGFVKELKKSRFTALTGVNTLFN 312 Query: 319 AELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKR--VVEQMNLREITIAYGMTETSPVSCQ 376 L+ P FAE + S L + G V +R V + L E AYG+TETSP +C Sbjct: 313 GLLNTPGFAEVDFSRLHLSLGGGMAVQRAVAERWKKVTGVTLAE---AYGLTETSPAACI 369 Query: 377 SSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKT 436 + D L S++G P +V I D+ + PIG+ GE KG VM GYW +T Sbjct: 370 NPLD--LKDYNSSIGLPIPSTDVAIWSEDSQPL-PIGEVGELMVKGPQVMQGYWKRPDET 426 Query: 437 REAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQ 496 + + GW+HTGD+A MDA GYV IV R KDM++ G N+YP E+E+ + HP V +V Sbjct: 427 AKVLGADGWLHTGDIARMDANGYVYIVDRKKDMILVSGFNVYPNEVEDIVMTHPGVAEVA 486 Query: 497 VVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGK 556 VGVPD+ GE + +++ K T + ++ FC+ + YK P+ I F + P + GK Sbjct: 487 AVGVPDEHSGEVVKLFVVRK-DPNLTVEALKEFCRENLTGYKRPKLIEFRDALPKSNVGK 545 Query: 557 IQKFKIRDEMK 567 I + ++RDE K Sbjct: 546 ILRRELRDEKK 556 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: 769 Number of extensions: 46 Number of successful extensions: 6 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: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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 17 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