Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_041099611.1 SUTH_RS12320 AMP-dependent synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000828635.1:WP_041099611.1 Length = 511 Score = 201 bits (511), Expect = 6e-56 Identities = 161/529 (30%), Positives = 243/529 (45%), Gaps = 47/529 (8%) Query: 42 QPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLAT 101 +P A+V Q R Y R+A LLG+G+ RV N E + A Sbjct: 14 RPHATAVVFGQQ--RLDYRDFNARVDRVAHLLLGLGVKKTGRVATLLPNTLELLETYWAC 71 Query: 102 AQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGH 161 A++G V V ++P + +N G LV+ L P Sbjct: 72 ARIGAVAVPLSPLLTGVGLSSLINDAGAVCLVTQ------------NSLLP--------- 110 Query: 162 LQAAKLPQLKT-----VVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQAT 216 + A LP+L T ++ ID D+P + L A +P AAG+ Sbjct: 111 VVEAVLPRLSTLAPPRILLID------GDQPPWGSYAALAAAAPEDEPP----AAGVTGD 160 Query: 217 DPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGN 276 D INI +TSGTTG PKG +HR +G ++TP + + + G + Sbjct: 161 DLINIMYTSGTTGLPKGIMHSHRVRAMYALLLGAAWRMTP-ESVVLHSGAIVFNGAFVTL 219 Query: 277 LACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRT 336 + F GAT + FD +L T+ E+ T + VP IA LD P F L++L+ Sbjct: 220 MPAFHLGATYILLRQ-FDAAEMLATIAREKVTHIMVVPAQIIALLDSPDFDPAKLASLQM 278 Query: 337 GIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPH 396 + G+P P + K + Q+ YG+TE ++ TD K+ +VG P Sbjct: 279 ILSLGAPLP-QPRKDQLNQLLPGRFHELYGLTEGF-LTILDRTDAV--KKAGSVGCPPPF 334 Query: 397 LEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDA 456 EV+IVD + G +P GQ GE +G VM GYWG T EA+ +G W+ +GD+ +D Sbjct: 335 SEVRIVD-EQGRDLPPGQAGEIVGRGPFVMQGYWGKPQLTAEALRDG-WIFSGDIGYLDD 392 Query: 457 EGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAK 516 EGY+ +V R KDM+ GG +YPR+IEE RHP + +V V G+P + +GE A ++ + Sbjct: 393 EGYLYLVDRKKDMIDSGGVKVYPRDIEEIAARHPAIAEVAVFGIPHETWGETPVAAVVLR 452 Query: 517 PGTQPTEDDIRAFCKGQI-AHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 G T D++R + ++ A Y+ + + FP GK K +R+ Sbjct: 453 VGAGATADELRDWINERVAARYQRVQTVIIKPEFPRNAAGKTLKRDMRE 501 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: 693 Number of extensions: 42 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: 511 Length adjustment: 35 Effective length of query: 543 Effective length of database: 476 Effective search space: 258468 Effective search space used: 258468 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