Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3610022 Dshi_3403 AMP-dependent synthetase and ligase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Dino:3610022 Length = 579 Score = 666 bits (1718), Expect = 0.0 Identities = 324/564 (57%), Positives = 404/564 (71%), Gaps = 7/564 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 SH GA + PL+E TI AR P A + QG R+TY L E LA LL Sbjct: 22 SHVLGAQEPPLLELTIPELLVQTAARFPNHVAAIFEAQGIRWTYRDLIREVDALAGGLLQ 81 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +GL PGDRVG+W+ N AEW+L Q ATA++G++LVN+NPAYR E+ YAL K GC L+ Sbjct: 82 LGLKPGDRVGVWAPNCAEWLLAQFATARLGIILVNVNPAYRPFELSYALKKTGCTALILA 141 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 A+FK SDY+ ML E+ PE PG L AA+LP L+ V+ + EA G ++ F +L Sbjct: 142 AQFKNSDYVAMLSEVVPEIAASDPGALHAAELPDLRAVIVTEAEAPDG-----MIAFPDL 196 Query: 196 IARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 IA+G A + L + L DPINIQFTSGTTG PKGATLTHRNI+NN + +KL Sbjct: 197 IAKGRAVVAKDLDAITRKLDCHDPINIQFTSGTTGLPKGATLTHRNIVNNAASVTSAIKL 256 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 D LCIPVP YHCFGMV+G L C T GA IV P GFDP+T L TV RCT L+GVP Sbjct: 257 IEQDMLCIPVPFYHCFGMVMGTLGCVTKGAAIVVPGPGFDPITTLDTVSKHRCTALYGVP 316 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMF+ L+HPRFAE++LS+LRTGIMAG+PCP E+M++V +M++ E+TIAYGMTETSPVS Sbjct: 317 TMFVGMLEHPRFAEYDLSSLRTGIMAGAPCPIEIMRQVQSRMHMSEVTIAYGMTETSPVS 376 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 QS+TD P+ KRVS+VG++QPH+EVKIVD D+ VVP+G +GE T+GYSVM GYW + Sbjct: 377 FQSATDDPVQKRVSSVGRIQPHVEVKIVDEDS-VVVPVGAQGELLTRGYSVMQGYWDEPD 435 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 KT EAID GWMHTGDLAT+D +G+ I GR+KDM++RGGEN+YPREIEEFLY HP + Sbjct: 436 KTAEAIDADGWMHTGDLATLDVDGFCKITGRVKDMIVRGGENVYPREIEEFLYTHPAISQ 495 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 VQV G+PDQK+GE + AW++AKPG PTE +I FC+ IAH+KVP +RF S PMTVT Sbjct: 496 VQVFGIPDQKFGEIVVAWLVAKPGADPTEAEILDFCRDSIAHFKVPAMVRFKNSLPMTVT 555 Query: 555 GKIQKFKIRDEMKDQLGLEEQKTA 578 GK QKF +R +M ++LGLEE +TA Sbjct: 556 GKPQKFIMRAQMVEELGLEEIETA 579 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: 897 Number of extensions: 27 Number of successful extensions: 3 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: 579 Length adjustment: 36 Effective length of query: 542 Effective length of database: 543 Effective search space: 294306 Effective search space used: 294306 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 17 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