Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013840621.1 DESRU_RS02840 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000215085.1:WP_013840621.1 Length = 553 Score = 282 bits (721), Expect = 3e-80 Identities = 181/554 (32%), Positives = 299/554 (53%), Gaps = 27/554 (4%) Query: 22 TDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPG 81 T V + Q++ F + P+ +A++ ++Q + TY +L+ R A+AL +G+ G Sbjct: 17 TQVHIPNQSLYHFLDQATQKYPDHQAVIFMNQ--QLTYCELKERVDRFATALHVLGVKKG 74 Query: 82 DRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARF--K 139 DRV I N + V+ A ++G ++V NP Y E+ Y LN G + ++ + +F K Sbjct: 75 DRVAIMLPNCPQTVIAYYAVIRLGAIVVMNNPLYVERELLYQLNNSGAETIIFLDQFQPK 134 Query: 140 TSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG 199 S+ G A LP +T ++ G +L F +L+ + Sbjct: 135 ISNIKSQTSLKVFISTGISDYLAMPAMLPAPETQPVLNPPPGTD-----ILCFEDLLQKN 189 Query: 200 NAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR 259 + P+ +V + + +Q+T GTTG KGA LTH+N++ N G + + R Sbjct: 190 S---PKPPEVELDFEKELAV-LQYTGGTTGVSKGAMLTHKNLVANVLQTGAWLTICKEAR 245 Query: 260 ---LCIPVPLYHCFGMVLG-NLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315 C+ +P YH F M NL+ + A I+ P + L L+ + D R T VP+ Sbjct: 246 ERFFCV-LPFYHVFAMTTCMNLSIYLSSAMILIPRLELNNL--LKLINDYRPTIFQAVPS 302 Query: 316 MFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSC 375 +++A + HP +++LS++ + G+P P EV ++ E + ++ YG+TE +PV+ Sbjct: 303 LYVAIISHPEVQQYDLSSISCCLSGGAPLPIEVQEKF-EAITGGKLVEGYGLTEAAPVTH 361 Query: 376 QSSTDTPLSKRVS-TVGQVQPHLEVKIVDPDTGAV-VPIGQRGEFCTKGYSVMHGYWGDE 433 + + K+V+ ++G P+ +VKIV+ + G VP+G+ GE C KG VM GYW Sbjct: 362 CNPIE---GKKVNGSIGLAFPNTDVKIVEVEKGLEEVPLGETGELCIKGPQVMKGYWHMP 418 Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493 +T A+ +G W++TGD+A MD +G+ IV R KDMVI G N+YPRE+EE LY+HP+V+ Sbjct: 419 EETAAALRDG-WLYTGDIARMDEQGFTYIVDRKKDMVITWGYNVYPREVEEVLYQHPKVK 477 Query: 494 DVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553 + V+G+PD GE + A+I+ K G Q T+++I FC+ +A+YKVPR I F + P + Sbjct: 478 EAAVIGIPDATRGEVIKAFIVLKEGQQATKEEIAGFCRKNLANYKVPRKIEFRSELPKSP 537 Query: 554 TGKIQKFKIRDEMK 567 GKI + + +E K Sbjct: 538 VGKILRRMLSEETK 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: 694 Number of extensions: 35 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: 553 Length adjustment: 36 Effective length of query: 542 Effective length of database: 517 Effective search space: 280214 Effective search space used: 280214 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