Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_034998568.1 DL88_RS16315 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000745425.1:WP_034998568.1 Length = 378 Score = 332 bits (850), Expect = 1e-95 Identities = 180/391 (46%), Positives = 241/391 (61%), Gaps = 13/391 (3%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60 M + VI R+P AKKG LATVRPDDL A +K + + G +I+DL++GCA PE Sbjct: 1 MSKVVIAGYLRSPFTLAKKGELATVRPDDLAAQVIKGLVAKTGIPAEDIEDLLLGCAFPE 60 Query: 61 AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120 EQG N+AR + +AGLP ++ A TVNR+C S + +I AA I + A + +A G ESM Sbjct: 61 GEQGFNIARLVSFIAGLPLSIAAATVNRFCGSSMTTIHMAAGAIQMNAGNAFVAAGVESM 120 Query: 121 SQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKAL 180 S+VPMMG PN LA P YM MG TAE VA K+ +SR++Q+ FA+RSHQ A A Sbjct: 121 SRVPMMGFNPLPNPELAASMPGAYMGMGDTAENVAAKWTISRKEQEEFALRSHQRATAAQ 180 Query: 181 AEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTV 240 EG+ DEIV + ++ D +RP+TT + L+ L+PAFS +G V Sbjct: 181 KEGRLTDEIVAI-------------AGRKGTIMLDGCIRPETTLEGLAELKPAFSANGVV 227 Query: 241 TAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALK 300 TAG SS +DGAAAV++ + A L L ++ AV G PE+MGIGPV A +AL Sbjct: 228 TAGTSSPLTDGAAAVLVCSEDYAKQHKLDVLASIKAIAVSGCSPEIMGIGPVAASRKALA 287 Query: 301 LAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSL 360 AGL++ I + ELNEAFASQ+I +REL + ++VN++GGAIALGHPLG TG ++ Sbjct: 288 RAGLEVSQIDIVELNEAFASQSIACMRELNLSVDRVNIDGGAIALGHPLGATGARIVGKA 347 Query: 361 IHEMKRRNEQFGVVTMCIGGGMGAAGVFELC 391 +KR ++ + T CIGGG G A V E C Sbjct: 348 ASLLKREKGKYALATQCIGGGQGIATVLEAC 378 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: 370 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 361 Effective length of database: 348 Effective search space: 125628 Effective search space used: 125628 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_034998568.1 DL88_RS16315 (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.16533.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-134 433.4 7.2 4.6e-134 433.1 7.2 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034998568.1 DL88_RS16315 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034998568.1 DL88_RS16315 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.1 7.2 4.6e-134 4.6e-134 1 385 [] 6 376 .. 6 376 .. 0.96 Alignments for each domain: == domain 1 score: 433.1 bits; conditional E-value: 4.6e-134 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaala 67 i +++R+p++ + +g l++++++dL+a+vik+l++++g+ +e+i+++ lG+++++geq +niaR + + lcl|NCBI__GCF_000745425.1:WP_034998568.1 6 IAGYLRSPFTlAKKGELATVRPDDLAAQVIKGLVAKTGIPAEDIEDLLLGCAFPEGEQgFNIARLVSFI 74 67889*****966******************************************************** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp s++a tvnr+C+S+++++++aa +i++ + +++va+GvEsmSrvp++ + +++ a + lcl|NCBI__GCF_000745425.1:WP_034998568.1 75 AGLPLSIAAATVNRFCGSSMTTIHMAAGAIQMNAGNAFVAAGVESMSRVPMMGFNP----LPNPELAAS 139 **************************************************977775....566655555 PP TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvv 205 + + + mg tAen+a+k+ isR+eq+e+alrShq+a++A++eg++ deiv + ++ ++ lcl|NCBI__GCF_000745425.1:WP_034998568.1 140 MP-------GAYMGMGDTAENVAAKWTISRKEQEEFALRSHQRATAAQKEGRLTDEIVAIAGRK--GTI 199 55.......7889*********************************************987765..799 PP TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274 D +irp+ttle La+Lkpaf +g +vtAg ss+l+DGAaa+l+ se+ ak+++l++la i ++av lcl|NCBI__GCF_000745425.1:WP_034998568.1 200 MLDGCIRPETTLEGLAELKPAFSA-NG-VVTAGTSSPLTDGAAAVLVCSEDYAKQHKLDVLASIKAIAV 266 9*********************95.9*.7**************************************** PP TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGH 343 +g++pe+mg+gpv A++kaL++agl++s+id+vE+nEAFA+q +a+++el+ l+ ++vN+ GGAiAlGH lcl|NCBI__GCF_000745425.1:WP_034998568.1 267 SGCSPEIMGIGPVAASRKALARAGLEVSQIDIVELNEAFASQSIACMRELN-LSVDRVNIDGGAIALGH 334 ***************************************************.889************** PP TIGR01930 344 PlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 PlGa+Gariv + ++ Lk++++ky+lat C+ggGqG+A++le lcl|NCBI__GCF_000745425.1:WP_034998568.1 335 PLGATGARIVGKAASLLKREKGKYALATQCIGGGQGIATVLE 376 ****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (378 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.20 // [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