Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Ac3H11_4478 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4478 Length = 536 Score = 228 bits (582), Expect = 4e-64 Identities = 168/528 (31%), Positives = 263/528 (49%), Gaps = 41/528 (7%) Query: 54 GRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINP 113 G+ T+AQL + A+ L +G+ G+ V ++ +N ++V+ ++G ++ P Sbjct: 31 GQPLTWAQLDAASDAFAARLQALGVAKGEPVALFMNNCPQYVMAHYGIQKIGAIVCPCGP 90 Query: 114 AYRTAEVEYALNKVGCKLLVSM---------ARFKTS-DYLGMLR--ELAPEWQGQQPGH 161 + E+EY L + +++V+ R KT+ ++ ++R EL P+ P Sbjct: 91 LNKEHELEYQLTDLQTRVIVAADVLLPVVDKVRAKTALQHVFVVRYAELLPDGT---PSI 147 Query: 162 LQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221 A+L ++T + G+ G F L A A P A VA + D I++ Sbjct: 148 DVPAELLNMRTAM--------GSVPAGCEDF--LAATRTGARP--APVALSM---DDISL 192 Query: 222 Q-FTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLG-NLAC 279 +TSGTTG PKGA L++ N +C +TP + L PLYH GMV+G NL Sbjct: 193 MTYTSGTTGLPKGAMLSYGNATFKTAASADCNGMTPHETLLAVAPLYHIAGMVMGVNLPV 252 Query: 280 FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIM 339 +T GAT V FDPL V Q ++ R T + + M A + P + + S LR + Sbjct: 253 YT-GATAVLLYR-FDPLGVAQALERHRVTWWYSIAPMNGALMQVPGARDMDWSALRRNPV 310 Query: 340 AGSPCP-TEVMKRVVEQM--NLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPH 396 TE + + +Q N AYG++ET V D + R T GQ P Sbjct: 311 TSFGITFTEALAQQWQQFAPNCIAHEAAYGLSETHTVDTAMPVD---AIRWGTQGQPVPG 367 Query: 397 LEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDA 456 ++IVDPDTGA +P G+ GE G GYW T + + +G W++TGD+ +DA Sbjct: 368 NTIRIVDPDTGAPLPTGEVGEITIHGPGNFKGYWNKPEATAKTLRDG-WVYTGDMGKIDA 426 Query: 457 EGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAK 516 +GY+ +GR K+M+ G +++P E+E L +HP V V+GVPD + GE A+I+ K Sbjct: 427 DGYLTFIGRFKEMIKVSGYSVFPEEVETLLIKHPAVAQAAVIGVPDAEKGEVARAFIVKK 486 Query: 517 PGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 PG + A+C+ +A YK PR +RF+ + P T GK+ + +RD Sbjct: 487 PGQDLDAAALVAWCRENMAPYKAPREVRFIDALPATGAGKVLRRLLRD 534 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: 717 Number of extensions: 36 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: 536 Length adjustment: 36 Effective length of query: 542 Effective length of database: 500 Effective search space: 271000 Effective search space used: 271000 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