Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_041642232.1 AZO_RS02365 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000061505.1:WP_041642232.1 Length = 398 Score = 356 bits (914), Expect = e-103 Identities = 196/393 (49%), Positives = 260/393 (66%), Gaps = 5/393 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYE-GNIDDLIIGCATP 59 +++A IV+ RTPV K + G+ VRPDD+ A ++ + + + G I D+I GCA P Sbjct: 5 IQDAYIVAAVRTPVAK-RNGAFRHVRPDDMLAHVLRAVVAQVPALDAGEIGDVITGCAMP 63 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+N+AR LAGLP VP +T+NR+C+S LQ++A AA +I LG D IA G ES Sbjct: 64 EAEQGMNVARIGLLLAGLPERVPGVTLNRFCASSLQAVADAANRIRLGEADVMIAAGTES 123 Query: 120 MSQVP-MMGHVT--RPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNA 176 MS +P +MG+ P + ++ + MG TAE+VA+++ VSR DQDAFA++SHQ A Sbjct: 124 MSAMPQIMGNKVSLNPEIFARQENIDIAYGMGLTAEKVAEEWKVSRADQDAFALQSHQRA 183 Query: 177 AKALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236 + A+A+G F DEI P V GE + + DEG R T + L+ L+P F+ Sbjct: 184 SAAIADGSFGDEIAPYTVRSHLPGEGGTVRIAERIVDTDEGPRADATLEALARLKPVFAA 243 Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296 G+VTAGNSSQ SDGA AV+LM G+ PL +FRS+AV GVPP VMGIGPVEAIP Sbjct: 244 RGSVTAGNSSQMSDGAGAVLLMSETALQRYGVTPLARFRSYAVAGVPPRVMGIGPVEAIP 303 Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356 RAL+LAGL L + ELNEAFA+QA+ VIR LG+D +VN GGAIALGHPLG TG Sbjct: 304 RALRLAGLGLDALDRIELNEAFAAQALAVIRTLGLDPARVNPQGGAIALGHPLGATGAIR 363 Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 T +L+ M++ + G++TMC+G GMGAA +FE Sbjct: 364 TATLMRAMRQGGVRHGMITMCVGTGMGAAAIFE 396 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: 433 Number of extensions: 15 Number of successful extensions: 2 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: 398 Length adjustment: 31 Effective length of query: 360 Effective length of database: 367 Effective search space: 132120 Effective search space used: 132120 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_041642232.1 AZO_RS02365 (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.15342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-140 454.3 6.2 1.8e-140 454.2 6.2 1.0 1 lcl|NCBI__GCF_000061505.1:WP_041642232.1 AZO_RS02365 acetyl-CoA C-acyltra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_041642232.1 AZO_RS02365 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.2 6.2 1.8e-140 1.8e-140 1 385 [] 10 396 .. 10 396 .. 0.98 Alignments for each domain: == domain 1 score: 454.2 bits; conditional E-value: 1.8e-140 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 iv+avRtp++k +g++++++++d+la+v++++++++ ld+ +i +vi+G++++++eq +n+aR +l lcl|NCBI__GCF_000061505.1:WP_041642232.1 10 IVAAVRTPVAKRNGAFRHVRPDDMLAHVLRAVVAQVpALDAGEIGDVITGCAMPEAEQgMNVARIGLLL 78 8*********99********************************************************* PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglpe+vp++t+nr+CaS+lqAva+aa++i+ Geadv++a+G EsmS +p ++ ++ sl+++ + + lcl|NCBI__GCF_000061505.1:WP_041642232.1 79 AGLPERVPGVTLNRFCASSLQAVADAANRIRLGEADVMIAAGTESMSAMPQIMGNK---VSLNPEIFAR 144 ***************************************************99997...7899988888 PP TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.... 201 ++ + ++ mg tAe++a+++++sR +qD++al+Shq+a++Ai++g f dei p++v+ + lcl|NCBI__GCF_000061505.1:WP_041642232.1 145 QE-----NIDIAYGMGLTAEKVAEEWKVSRADQDAFALQSHQRASAAIADGSFGDEIAPYTVRSHlpge 208 88.....455789*************************************************999**** PP TIGR01930 202 .......kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263 +++v++Deg+r++ tle+La+Lkp+f+ gs vtAgNssq++DGA+a+llmse++++++g+ lcl|NCBI__GCF_000061505.1:WP_041642232.1 209 ggtvriaERIVDTDEGPRADATLEALARLKPVFAA-RGS-VTAGNSSQMSDGAGAVLLMSETALQRYGV 275 *******9*************************96.8*7.***************************** PP TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekv 332 tplar++s+avagv+p++mg+gpv+Ai++aL+ agl ++ +d +E+nEAFAaq+lav++ lg ld+++v lcl|NCBI__GCF_000061505.1:WP_041642232.1 276 TPLARFRSYAVAGVPPRVMGIGPVEAIPRALRLAGLGLDALDRIELNEAFAAQALAVIRTLG-LDPARV 343 **************************************************************.99**** PP TIGR01930 333 NvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 N +GGAiAlGHPlGa+Ga+ ++tl++++++ g++ G++t+Cvg+G+GaA+i+e lcl|NCBI__GCF_000061505.1:WP_041642232.1 344 NPQGGAIALGHPLGATGAIRTATLMRAMRQGGVRHGMITMCVGTGMGAAAIFE 396 ***************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (398 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: 00:00:00.01 # Mc/sec: 9.75 // [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