Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_041098264.1 SUTH_RS07380 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000828635.1:WP_041098264.1 Length = 398 Score = 350 bits (899), Expect = e-101 Identities = 187/393 (47%), Positives = 260/393 (66%), Gaps = 5/393 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 +++A IV+ RTP+GKA +G RPDDL ++ + + G + I+D IIGC+ P Sbjct: 5 LQDAYIVAATRTPIGKAPRGMFRNTRPDDLLVYAIQSAMAQVPGLDPKLIEDAIIGCSFP 64 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 E E GLNMARN LAGLP TV +TVNR+C+SG+ ++A AA++I +G D IAGGAES Sbjct: 65 EGESGLNMARNAVLLAGLPNTVGGVTVNRFCASGITAVAMAADRIRVGQADVMIAGGAES 124 Query: 120 MSQVPMMGHVTRPNLAL-AEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAK 178 MS VPM G+ N+ + ++ MG TAE+VA ++ ++RE QD FA++SHQ A Sbjct: 125 MSMVPMGGNHPSINMGVFKDENVGMAYGMGLTAEKVANQWKITREMQDEFALQSHQRAIA 184 Query: 179 ALAEGKFKDEIVPVEVT--VTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236 G+F +E VE+ V + ++K+ V ++DEG R + L+ L+P F+ Sbjct: 185 GQQAGEFDNETTAVEIVDRVPNLATGEVDLKKRSV-NRDEGARADSNLAALAKLKPVFAA 243 Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296 G+VTAGNSSQTSDGA A++L+ + L PL +F SFAV GVPPE+MGIGP EAIP Sbjct: 244 KGSVTAGNSSQTSDGAGALILVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIP 303 Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356 A + AG+ + ELNEAFA+Q++ VI++L +D KVN GGAIALGHPLG TG Sbjct: 304 VACRAAGITQDQLDWIELNEAFAAQSLAVIKDLDLDPAKVNPIGGAIALGHPLGATGAIR 363 Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 + ++IH ++RRN ++G+VTMC+G GMGAAG+FE Sbjct: 364 SATVIHALRRRNLKYGMVTMCVGTGMGAAGIFE 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: 430 Number of extensions: 19 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: 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_041098264.1 SUTH_RS07380 (acetyl-CoA acetyltransferase)
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.9931.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-141 457.0 4.5 2.9e-141 456.8 4.5 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041098264.1 SUTH_RS07380 acetyl-CoA acetyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041098264.1 SUTH_RS07380 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.8 4.5 2.9e-141 2.9e-141 1 385 [] 10 396 .. 10 396 .. 0.98 Alignments for each domain: == domain 1 score: 456.8 bits; conditional E-value: 2.9e-141 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv+a+Rtpig + +g +++++++dLl+ +i+++++++ gldp+ i+++i+G+++++ge n+aR+a+l lcl|NCBI__GCF_000828635.1:WP_041098264.1 10 IVAATRTPIGkAPRGMFRNTRPDDLLVYAIQSAMAQVpGLDPKLIEDAIIGCSFPEGESgLNMARNAVL 78 8*********988******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 aglp++v ++tvnr+CaSg++Ava+aa++i++G+adv++aGG+EsmS vp++ ++ s+++g +k lcl|NCBI__GCF_000828635.1:WP_041098264.1 79 LAGLPNTVGGVTVNRFCASGITAVAMAADRIRVGQADVMIAGGAESMSMVPMGGNHP----SINMGVFK 143 ***************************************************988875....99****** PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +e+ v ++ mg tAe++a++++i+Re+qDe+al+Shq+a + +++g+f++e + ve+ ++ lcl|NCBI__GCF_000828635.1:WP_041098264.1 144 DEN------VGMAYGMGLTAEKVANQWKITREMQDEFALQSHQRAIAGQQAGEFDNETTAVEIVDRvpn 206 **9......6789***************************************************99*** PP TIGR01930 202 .........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakel 261 k++v++Deg r++++l++LakLkp+f+ kgs vtAgNssq++DGA+al+l+se+++k++ lcl|NCBI__GCF_000828635.1:WP_041098264.1 207 latgevdlkKRSVNRDEGARADSNLAALAKLKPVFAA-KGS-VTAGNSSQTSDGAGALILVSEKILKQF 273 *********99************************96.8*7.*************************** PP TIGR01930 262 gltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldle 330 +ltplar+vs+av gv+pe+mg+gp +Ai+ a + ag++ +++d++E+nEAFAaq lav+k+l+ ld++ lcl|NCBI__GCF_000828635.1:WP_041098264.1 274 NLTPLARFVSFAVRGVPPEIMGIGPKEAIPVACRAAGITQDQLDWIELNEAFAAQSLAVIKDLD-LDPA 341 ****************************************************************.99** PP TIGR01930 331 kvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 kvN GGAiAlGHPlGa+Ga+ +t++++L++r+ kyG++t+Cvg+G+GaA i+e lcl|NCBI__GCF_000828635.1:WP_041098264.1 342 KVNPIGGAIALGHPLGATGAIRSATVIHALRRRNLKYGMVTMCVGTGMGAAGIFE 396 ****************************************************997 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.29 // [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