Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012281735.1 HM1_RS02690 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000019165.1:WP_012281735.1 Length = 497 Score = 250 bits (639), Expect = 8e-71 Identities = 170/524 (32%), Positives = 261/524 (49%), Gaps = 54/524 (10%) Query: 43 PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATA 102 PE+ AL+ H RY+YA LQ R L G+ PG+RVG++ N+A+++ +A A Sbjct: 19 PEKTALIEKHS--RYSYAALQETVDRYRRCLYARGVRPGERVGLFCRNSADFIFAYMAIA 76 Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162 +G V++ +N +R E+ Y L+ G + +V+ L ELA L Sbjct: 77 SLGAVVIPLNIMFRPREIGYILSDAGSRHVVT----------DRLLELAS-------AEL 119 Query: 163 QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQ 222 + LP + + + A + P A D + DP I Sbjct: 120 NDSDLPAQHLLSELRETAPAYSHHP-------------APD-------VPITPEDPCVIL 159 Query: 223 FTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTH 282 +TSGTTG PKGA L+HRN+++N E + AD +PL+H F + Sbjct: 160 YTSGTTGRPKGAVLSHRNLISNARSYTETIGAAEADNYLCVLPLFHSFAWTCCVTTALLN 219 Query: 283 GATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMF--IAELDHPRFAEFNLSTLRTGIMA 340 GATI + F P L +Q + GVP M+ + P +L+ +R + Sbjct: 220 GATITIM-EAFQPKEALAMIQTHGVNVVTGVPAMYGIYTSVARPE----DLAGVRLFVSG 274 Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK-RVSTVGQVQPHLEV 399 G+ P E + E+ + I YG++E SPV T P+ + + ++G P + V Sbjct: 275 GASLPVETLNSFKEKTG-QPIVEGYGLSEASPVV----TFNPIGRTKPGSIGLQIPAVSV 329 Query: 400 KIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGY 459 KIVD + G +P G+ GE +G +VM GY G +T AI +G W+HTGDLA D EGY Sbjct: 330 KIVDAE-GRELPPGEVGELICQGPNVMSGYLGLPQETAAAIRDG-WLHTGDLAYKDDEGY 387 Query: 460 VNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGT 519 + IV R KD++I GG N+YPRE+EE LY HP V++ V+G PD+ GE + A+++ + G Sbjct: 388 LFIVDRKKDLIIVGGLNVYPREVEEVLYSHPSVKEAAVIGTPDKTRGEAVRAFVVVREGM 447 Query: 520 QPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 ++ A+ + +A YK+PR I + + P TGK+ K ++R Sbjct: 448 ALNRKELMAYLRTNLATYKLPREIVELEALPRNATGKVLKKELR 491 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: 668 Number of extensions: 33 Number of successful extensions: 4 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: 497 Length adjustment: 35 Effective length of query: 543 Effective length of database: 462 Effective search space: 250866 Effective search space used: 250866 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: 52 (24.6 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