Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate YP_004139345.1 Mesci_0122 AMP-dependent synthetase and ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000185905.1:YP_004139345.1 Length = 661 Score = 209 bits (531), Expect = 4e-58 Identities = 160/517 (30%), Positives = 245/517 (47%), Gaps = 29/517 (5%) Query: 64 TEAHRLASA----LLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAE 119 T+ RL++A L GL G RV + N ++ + +A + G V+VNINP Y E Sbjct: 158 TDVERLSAAFGAYLQSKGLQKGARVALMMPNVLQYPVAMMAILRAGYVVVNINPLYTPRE 217 Query: 120 VEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGH-LQAAKLPQLKTVVWIDD 178 +E+ L G + +V + F + + R G L K + VV Sbjct: 218 LEHQLKDSGAQAIVILENFANTLQAVIARTAVKHVVVAAMGDMLGGLKGTIVNFVVRRVK 277 Query: 179 EAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTH 238 + PG ++F + G R A+V +A D +Q+T GTTG KGATL H Sbjct: 278 KMVPAWSLPGHVKFNAAMKAGAGLGFRPAKV----EADDVAFLQYTGGTTGVSKGATLLH 333 Query: 239 RNILNNGFFIGECM------KLTPAD-RLCIPVPLYHCFGMVLGNLACFTHGA-TIVYPN 290 N+L N + M K PA +PLYH F + + L GA ++ PN Sbjct: 334 SNVLANVAQNAQWMEDAYTIKPKPAHPNFICALPLYHIFALTVNALMGMQQGARNVLIPN 393 Query: 291 DGFDPLTVLQTVQDERCTGLH---GVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTE 347 P + V++ + +H G+ T+F A L++ F + + L + G Sbjct: 394 ----PRDIPGFVKELQKYPVHIFPGLNTLFNALLNNEDFRKLDFKPLVLTLGGGMAVQKG 449 Query: 348 VMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTG 407 V +R + + +T YG++ETSPV+ ++ T+G P E+ I D D G Sbjct: 450 VAERW-KALTGCSVTEGYGLSETSPVA--TANKFTAGDFTGTIGLPLPSTEIAIRDED-G 505 Query: 408 AVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIK 467 +P+G+ GE C +G VM GYW +T + + + G+ +GD+ MD GY IV R K Sbjct: 506 NNLPLGEVGEVCIRGPQVMAGYWNRPDETAKVMTKDGYFKSGDMGFMDERGYTKIVDRKK 565 Query: 468 DMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIR 527 DM++ G N+YP E+EE + HP V +V +GVPD+ GE +++ K T + + Sbjct: 566 DMILVSGFNVYPNELEEVVAMHPGVLEVAAIGVPDEHSGEVPKLFVVRKDPAL-TAEALT 624 Query: 528 AFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 AFC+ + YK PRYI F T P T GKI + +R+ Sbjct: 625 AFCRENLTGYKRPRYIEFRTELPKTPVGKILRRALRE 661 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: 801 Number of extensions: 39 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: 661 Length adjustment: 37 Effective length of query: 541 Effective length of database: 624 Effective search space: 337584 Effective search space used: 337584 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