Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_053937789.1 WG78_RS10575 long-chain-fatty-acid--CoA ligase FadD
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_001294205.1:WP_053937789.1 Length = 554 Score = 221 bits (562), Expect = 8e-62 Identities = 168/536 (31%), Positives = 260/536 (48%), Gaps = 26/536 (4%) Query: 39 VARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLM 97 VAR +R+A +++ G+ TY +L + A+ L + L+ G RVGI N ++ + Sbjct: 33 VARYADRDAFINM--GKAITYQELDQLSTAFAAYLQQTLRLSRGARVGIMMPNLLQYPVA 90 Query: 98 QLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK-TSDYLGMLRELAPEWQG 156 + G+V+VNINP Y E+E+ L G + +V +A F T D + Sbjct: 91 LFGILKAGMVVVNINPLYTPRELEHQLKDSGAEAIVIVANFAHTLDKCIGKTAVKHVIVS 150 Query: 157 QQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQAT 216 Q L K + V+ + + PG + F +A G A LA V L Sbjct: 151 QIGDMLDFPKRQLVNAVIKYIKKMVPAYNLPGAVSFNHALADGRAQT--LAPV--NLTLD 206 Query: 217 DPINIQFTSGTTGFPKGATLTHRNILNN--------GFFIGECMKLTPADRLCIPVPLYH 268 D +Q+T GTTG KGA LTHRNI+ N G + + +L + +PLYH Sbjct: 207 DLAFLQYTGGTTGVAKGAMLTHRNIVANMQQAHAWIGGVVADGREL-----IVTALPLYH 261 Query: 269 CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328 F + + GAT + + D ++ + T + GV T+F A ++HP F + Sbjct: 262 IFSLTANGMIFTKIGATNLLITNPRDIPGFIKELGKYPVTAITGVNTLFNALVNHPDFLK 321 Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388 + S+ + + G V + + + + AYG+TETSP + + L + Sbjct: 322 LDFSSWKLTLGGGMAVQQPVADKWKKVTGVTLVE-AYGLTETSPAAMINPMT--LREYNG 378 Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448 +G P + +I D G+V P G GE KG VM GYW +T + I G++ T Sbjct: 379 MIGLPVPSTDAQIRGED-GSVQPPGSAGELFIKGPQVMKGYWQRADETAKVIGADGYLAT 437 Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508 GD+A M G+ I R KDMV+ G N+YP E+E+ + RHP V +V VGVPD K GE Sbjct: 438 GDVAIMSPTGFFRIADRKKDMVLVSGFNVYPNEVEDVVARHPGVLEVACVGVPDDKSGEA 497 Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 + +++ K T TE + A+C+ Q+ +YKVPR + F + P + GKI + ++RD Sbjct: 498 VKIFVVRKDPTL-TEAALIAYCREQLTNYKVPRKVEFRDALPKSNVGKILRRELRD 552 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: 739 Number of extensions: 48 Number of successful extensions: 7 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: 554 Length adjustment: 36 Effective length of query: 542 Effective length of database: 518 Effective search space: 280756 Effective search space used: 280756 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