Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_025274631.1 HALAL_RS0114190 long-chain fatty acid--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000527155.1:WP_025274631.1 Length = 513 Score = 255 bits (652), Expect = 3e-72 Identities = 176/533 (33%), Positives = 268/533 (50%), Gaps = 35/533 (6%) Query: 37 DMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVL 96 D R P+R+A+V +R +YA + A+++A L G+ PGDRV + N + + Sbjct: 10 DTARRLPDRDAVVL--GDKRLSYAAVNAAANQVAQLLSSRGIGPGDRVALSCPNLPYFPI 67 Query: 97 MQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQG 156 + + G ++V +N +++ EV Y L G K E E Sbjct: 68 VYYGILKAGAIVVPLNVLFKSREVAYHLADSGAKAYFCF-------------EGTAEMPI 114 Query: 157 QQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAG--LQ 214 Q G+ A+ + + I + G+ F E A L G + Sbjct: 115 GQEGYEGFAESDECEHFFMITADPTASTPIEGVTTFAE-------ATKDLPTTFEGPVVD 167 Query: 215 ATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVL 274 A D + +TSGTTG PKGA LTH N+ N + D + +PL+H FG + Sbjct: 168 ANDTAVVLYTSGTTGRPKGAELTHANMTMNAVTCHKLFGTVDHDVHLVALPLFHSFGQTV 227 Query: 275 GNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD---HPRFAEFNL 331 A F GAT+V FD L ++ E+ + GVPTM+ L R Sbjct: 228 QLNAGFGSGATLVLL-PRFDADQALGLMESEQVSFFAGVPTMYWGLLSADKSKRDVSAIA 286 Query: 332 STLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK-RVSTV 390 LR I G+ P E++++V E+ + +I YG++ETSPV+ S + P K + T+ Sbjct: 287 QNLRRAISGGAALPVEILRQVEEEFGV-QIREGYGLSETSPVA---SFNHPGKKVKPGTI 342 Query: 391 GQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450 GQ +E+K+VD + V P G+ GE +G+++M GY G T E+I +G W TGD Sbjct: 343 GQPIWGVEMKLVDENWNDV-PEGETGEIAIRGHNIMKGYLGRPEATAESIRDG-WFRTGD 400 Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510 + D EGY +IV R KDM++RGG N+YPRE+EE + HP V V V+G+P Q++GEE+ Sbjct: 401 IGRRDEEGYYSIVDRAKDMIVRGGFNVYPRELEEVMMTHPAVSLVAVIGIPHQRHGEEIK 460 Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563 A ++ + T+ +E+D+ A+CK +A YK PR + F PMT TGK+ K ++R Sbjct: 461 AVVVREQETEISENDLVAWCKENMAGYKYPRMVEFRDQLPMTSTGKVLKRELR 513 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: 728 Number of extensions: 38 Number of successful extensions: 6 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: 513 Length adjustment: 35 Effective length of query: 543 Effective length of database: 478 Effective search space: 259554 Effective search space used: 259554 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