Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011764128.1 AZO_RS01980 acetyl-CoA C-acyltransferase
Query= reanno::acidovorax_3H11:Ac3H11_2994 (397 letters) >NCBI__GCF_000061505.1:WP_011764128.1 Length = 403 Score = 545 bits (1405), Expect = e-160 Identities = 274/395 (69%), Positives = 318/395 (80%), Gaps = 3/395 (0%) Query: 5 IQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMA 64 + DP+VIV ARTPMG QGD S L LG AIK+A+ERA ++P+ V EV+ G L A Sbjct: 1 MSDPVVIVSVARTPMGGFQGDLSGLTGPQLGAIAIKSAVERARLAPEQVQEVIMGCVLPA 60 Query: 65 GQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMT 124 G GQAPARQAA GLP AG T++K+CGSGMKA M+AHD+LLAG+++VMVAGGMESM+ Sbjct: 61 GVGQAPARQAALGAGLPLAAGCTTINKVCGSGMKATMLAHDLLLAGTNEVMVAGGMESMS 120 Query: 125 NAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEA---GRSMGTFGEDCAAKYSFTREQQ 181 NAPYLL K RGGYRLGH ++ DHM LDGLED+Y GR MGTF EDCA + F+R Q Sbjct: 121 NAPYLLPKARGGYRLGHGQLLDHMFLDGLEDSYSKENKGRLMGTFAEDCAGHFDFSRSAQ 180 Query: 182 DAFATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFK 241 DAFA AS +RA+AA GAF+ E+VPVTV R G+ VV DE P K +L+KI TLKPAFK Sbjct: 181 DAFAVASTERAQAAITEGAFSWEVVPVTVAGRKGDVVVDKDEQPLKAQLDKIGTLKPAFK 240 Query: 242 KDGTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGAT 301 KDGT+TAA+SSSI+DGAAALV+MR+STA KLG PLA IV HATHAQEP+WF TAP+GA Sbjct: 241 KDGTVTAANSSSISDGAAALVLMRKSTADKLGLAPLATIVGHATHAQEPQWFTTAPVGAM 300 Query: 302 QKALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGAR 361 QK LAKAGW VGDV LWEINEAFAVV MA MKEL+LPHDKVNVNGGACALGHPIGASGAR Sbjct: 301 QKVLAKAGWGVGDVDLWEINEAFAVVTMAAMKELNLPHDKVNVNGGACALGHPIGASGAR 360 Query: 362 IMVTLIHALKARGLTKGLATLCIGGGEATAVALEL 396 I+VTLI AL+ RGL +G+A+LCIGGGEATA+A+EL Sbjct: 361 ILVTLIGALRRRGLKRGVASLCIGGGEATAMAIEL 395 Lambda K H 0.317 0.131 0.376 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: 563 Number of extensions: 16 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: 397 Length of database: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_011764128.1 AZO_RS01980 (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.3934.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-132 425.5 4.5 1e-131 425.4 4.5 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764128.1 AZO_RS01980 acetyl-CoA C-acyltra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764128.1 AZO_RS01980 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.4 4.5 1e-131 1e-131 1 385 [] 7 394 .. 7 394 .. 0.98 Alignments for each domain: == domain 1 score: 425.4 bits; conditional E-value: 1e-131 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+ +Rtp+g ++g l+ l+ +L+a +ik+++era l pe++ evi+G+vl+ag ++++aR+aal ag lcl|NCBI__GCF_000061505.1:WP_011764128.1 7 IVSVARTPMGGFQGDLSGLTGPQLGAIAIKSAVERARLAPEQVQEVIMGCVLPAGVGQAPARQAALGAG 75 89********99********************************************************* PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 lp +t+n+vC+Sg++A +la + + aG+++v+vaGG+EsmS++p+ll+++ r +++lg+ +l d lcl|NCBI__GCF_000061505.1:WP_011764128.1 76 LPLAAGCTTINKVCGSGMKATMLAHDLLLAGTNEVMVAGGMESMSNAPYLLPKA--RGGYRLGHGQLLD 142 ****************************************************98..89*********** PP TIGR01930 139 qllkdl.......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkg 200 ++ d+ ++++ mg+ Ae +a ++++sR+ qD++a++S ++a++Ai eg f+ e+vpv+v g lcl|NCBI__GCF_000061505.1:WP_011764128.1 143 HMFLDGledsyskENKGRLMGTFAEDCAGHFDFSRSAQDAFAVASTERAQAAITEGAFSWEVVPVTVAG 211 9999999*****999999*************************************************** PP TIGR01930 201 k..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpla 267 + ++vv+kDe++ + +l+k+++Lkpafk+ +g tvtA+Nss+++DGAaal+lm +++a++lgl pla lcl|NCBI__GCF_000061505.1:WP_011764128.1 212 RkgDVVVDKDEQPL-KAQLDKIGTLKPAFKK-DG-TVTAANSSSISDGAAALVLMRKSTADKLGLAPLA 277 99888899999887.89************95.9*.6********************************* PP TIGR01930 268 rivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnG 336 +iv++a+ + +p+ ++++pv A++k+L+kag+ + d+dl+EinEAFA++++a++kel+ l ++kvNvnG lcl|NCBI__GCF_000061505.1:WP_011764128.1 278 TIVGHATHAQEPQWFTTAPVGAMQKVLAKAGWGVGDVDLWEINEAFAVVTMAAMKELN-LPHDKVNVNG 345 **********************************************************.88******** PP TIGR01930 337 GAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 GA AlGHP+GasGari++tl+ +L++rg k+G+a+lC+ggG ++A+ +e lcl|NCBI__GCF_000061505.1:WP_011764128.1 346 GACALGHPIGASGARILVTLIGALRRRGLKRGVASLCIGGGEATAMAIE 394 **********************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (403 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: 7.83 // [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