Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_004300932.1 C665_RS04230 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000310185.1:WP_004300932.1 Length = 399 Score = 364 bits (935), Expect = e-105 Identities = 206/394 (52%), Positives = 266/394 (67%), Gaps = 6/394 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 +++A IV+ RTPV K + G+ VRPDDL A ++E + + + I D++ GCA P Sbjct: 5 IQDAYIVAAVRTPVAK-RNGAFRAVRPDDLLARVLREVVAKVPNLDAREIGDVVTGCAMP 63 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+N+AR LAGLP +VP IT+NR+C+SGLQ++A AA +I LG D IA G ES Sbjct: 64 EAEQGMNVARIGLLLAGLPDSVPGITINRFCASGLQAVADAASRIRLGEADVMIAAGTES 123 Query: 120 MSQVP-MMGHVTRPNLALAEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQNA 176 MS +P +MG+ N + +A ++ MG TAE+VA+++ VSREDQDAFAV SH+ A Sbjct: 124 MSAMPQIMGNKVSLNPEIFARAENLSIAYGMGLTAEKVAQQWKVSREDQDAFAVESHRRA 183 Query: 177 AKALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236 A+A G+F DEI+P V G D + + DEG RP AD L L+P F+ Sbjct: 184 CAAIAAGQFADEILPYAVKSYAPGVDGTVRITERLVEHDEGPRPDAAADRLGKLKPVFAA 243 Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296 G+VTAGNSSQ SDGAAAV+LM + P+ +F SFAV GVPPEVMGIGPVEAIP Sbjct: 244 RGSVTAGNSSQMSDGAAAVLLMSETALKRYDVTPIARFSSFAVAGVPPEVMGIGPVEAIP 303 Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356 RAL AG+ L DIG ELNEAFA+QA+ V+R+LG+D KVN GGAIALGHPLG TG Sbjct: 304 RALARAGVALADIGWTELNEAFAAQALAVMRQLGMDPAKVNPLGGAIALGHPLGATGAIR 363 Query: 357 TLSLIHEMKR-RNEQFGVVTMCIGGGMGAAGVFE 389 T +L+ M+R ++G+++MCIG GMGAAGVFE Sbjct: 364 TATLMAAMQRDPGLRYGMISMCIGTGMGAAGVFE 397 Lambda K H 0.316 0.133 0.377 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: 425 Number of extensions: 18 Number of successful extensions: 4 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: 391 Length of database: 399 Length adjustment: 31 Effective length of query: 360 Effective length of database: 368 Effective search space: 132480 Effective search space used: 132480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_004300932.1 C665_RS04230 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01930.hmm # target sequence database: /tmp/gapView.4724.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-141 457.3 5.6 2.3e-141 457.1 5.6 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004300932.1 C665_RS04230 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004300932.1 C665_RS04230 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.1 5.6 2.3e-141 2.3e-141 1 385 [] 10 397 .. 10 397 .. 0.98 Alignments for each domain: == domain 1 score: 457.1 bits; conditional E-value: 2.3e-141 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 iv+avRtp++k +g+++ ++++dLla v++e+++++ +ld+++i +v++G++++++eq +n+aR +l lcl|NCBI__GCF_000310185.1:WP_004300932.1 10 IVAAVRTPVAKRNGAFRAVRPDDLLARVLREVVAKVpNLDAREIGDVVTGCAMPEAEQgMNVARIGLLL 78 8*********99********************************************************* PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp+svp++t+nr+CaSglqAva+aa +i+ Geadv++a+G EsmS +p ++ ++ sl+++ + + lcl|NCBI__GCF_000310185.1:WP_004300932.1 79 AGLPDSVPGITINRFCASGLQAVADAASRIRLGEADVMIAAGTESMSAMPQIMGNK---VSLNPEIFAR 144 ***************************************************99997...7999988888 PP TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.... 201 ++ + ++ mg tAe++a+++++sRe+qD++a++Sh++a +Ai++g+f+dei+p+ vk lcl|NCBI__GCF_000310185.1:WP_004300932.1 145 AE-----NLSIAYGMGLTAEKVAQQWKVSREDQDAFAVESHRRACAAIAAGQFADEILPYAVKSYapgv 208 88.....456789*************************************************98899** PP TIGR01930 202 .......kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263 ++ v++Deg+rp+ +++L+kLkp+f+ gs vtAgNssq++DGAaa+llmse+++k++++ lcl|NCBI__GCF_000310185.1:WP_004300932.1 209 dgtvritERLVEHDEGPRPDAAADRLGKLKPVFAA-RGS-VTAGNSSQMSDGAAAVLLMSETALKRYDV 275 ******9999***********************96.8*7.***************************** PP TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekv 332 tp+ar+ s+avagv+pe+mg+gpv+Ai++aL++ag+ + di + E+nEAFAaq+lav+++lg +d++kv lcl|NCBI__GCF_000310185.1:WP_004300932.1 276 TPIARFSSFAVAGVPPEVMGIGPVEAIPRALARAGVALADIGWTELNEAFAAQALAVMRQLG-MDPAKV 343 **************************************************************.88**** PP TIGR01930 333 NvnGGAiAlGHPlGasGarivltllkeLker.gkkyGlatlCvggGqGaAvile 385 N GGAiAlGHPlGa+Ga+ ++tl+ +++++ g +yG++++C+g+G+GaA ++e lcl|NCBI__GCF_000310185.1:WP_004300932.1 344 NPLGGAIALGHPLGATGAIRTATLMAAMQRDpGLRYGMISMCIGTGMGAAGVFE 397 ******************************999*****************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (399 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.05 # Mc/sec: 2.81 // [ok]
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