Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_073039840.1 BUB04_RS12080 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_900129305.1:WP_073039840.1 Length = 563 Score = 271 bits (693), Expect = 5e-77 Identities = 191/562 (33%), Positives = 295/562 (52%), Gaps = 59/562 (10%) Query: 26 LIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVG 85 L+EQT VA+ P A + G + TY L + R+ASAL +G+ GDRV Sbjct: 27 LLEQT--------VAKYPGNVA--TYFMGAKLTYKALWDQILRMASALSELGVKKGDRVA 76 Query: 86 IWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM---------- 135 I N + V+ AT VG V V NP Y E+E+ N G ++++++ Sbjct: 77 IMLPNCPQTVVAYYATLHVGAVAVMTNPMYVEREMEHQWNDAGAEVVITLDHLYPKVDKA 136 Query: 136 --ARFKTSDYLGMLRELAP---EWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLL 190 A + LRE P +W + A+ +L T V DD + Sbjct: 137 AAATRVRKIVVTSLRECLPFPLKWL-----YPLKARKDKLFTAVPYDDRR--------VY 183 Query: 191 RFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGE 250 FT ++ A+ P + A L+ D +Q+T GTTG KG LTH NIL N I Sbjct: 184 NFTRIL---RASAPSTSPCPATLE--DLALLQYTGGTTGVSKGVMLTHANILANVIQI-- 236 Query: 251 CMKLTPA----DRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDER 306 C L +R+ +P +H FGM + GAT++ F+ ++L+T+ + Sbjct: 237 CGWLPDLQWGKERVLGILPFFHVFGMTVAMNQPLYSGATLILL-PRFEIESLLKTLHKTK 295 Query: 307 CTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYG 366 T GVPT+++A ++HP+ E++LS++R + +P P E++K+ E++ I YG Sbjct: 296 PTLFPGVPTIYVAIVNHPKIKEYDLSSIRYCVTGSAPMPVEILKKF-EEITGGVIIEGYG 354 Query: 367 MTETSPVSCQSSTDTPLS--KRVSTVGQVQPHLEVKIVDPDTG-AVVPIGQRGEFCTKGY 423 ++E SPV+ + P+ ++ ++G + +I+ + G + VP+G+ GE KG Sbjct: 355 LSEASPVTHVN----PIGGLRKTGSIGVPVSDTDCRIISLEDGVSEVPMGEVGELTVKGP 410 Query: 424 SVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIE 483 VM GYW +T + + +G W++TGD+A MD +G+V IV R KDM+I GG NIYPREI+ Sbjct: 411 QVMPGYWNMPEETAQTLRDG-WLYTGDIAKMDEDGFVFIVDRKKDMIIAGGYNIYPREID 469 Query: 484 EFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYI 543 E LY HP+V D VGVPD GE + A+++ KPG T ++I AFCK ++A YKVP+ + Sbjct: 470 EVLYAHPKVLDAVTVGVPDPYRGETVKAFVVPKPGETVTPEEIIAFCKSKLAAYKVPKAV 529 Query: 544 RFVTSFPMTVTGKIQKFKIRDE 565 S P T+ GKI + ++R+E Sbjct: 530 EIRESLPKTMVGKILRKELREE 551 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: 768 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: 563 Length adjustment: 36 Effective length of query: 542 Effective length of database: 527 Effective search space: 285634 Effective search space used: 285634 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