Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_043745132.1 AMB_RS18210 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_000009985.1:WP_043745132.1 Length = 394 Score = 553 bits (1425), Expect = e-162 Identities = 280/392 (71%), Positives = 329/392 (83%) Query: 3 MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62 M+ DPIVIV A RTPMGGFQG+ SL+APQLGAAAIRAAVER+G+A D V+EV GCVL Sbjct: 1 MTTDPIVIVGAARTPMGGFQGDFASLAAPQLGAAAIRAAVERSGLAPDQVDEVFMGCVLP 60 Query: 63 AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122 AG+GQAPARQA+LGAGL +S CTT++K+CGSGM+AA+LAHD+L+AG+A V+VAGGMESM Sbjct: 61 AGVGQAPARQASLGAGLPRSAGCTTISKVCGSGMKAAMLAHDLLVAGTAKVMVAGGMESM 120 Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDE 182 SNAPYLLD+AR GYR+GHGKVLDHMFLDGLEDAYD+GRLMGTFAE+CA + FTREAQD Sbjct: 121 SNAPYLLDKARGGYRLGHGKVLDHMFLDGLEDAYDRGRLMGTFAEECAGSYKFTREAQDG 180 Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDG 242 FA+AS +RA++AI DG F AEI P+ V K + LIT DEQP KA DKI +LKPAF Sbjct: 181 FALASLSRAKKAIADGLFAAEITPVAVAGRKGETLITIDEQPGKALPDKIPTLKPAFAKD 240 Query: 243 GTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKK 302 GTVTAANSSSISDGAAAL++MRRSEAEKRGLKPLA + GH FA P LF APVGAIK Sbjct: 241 GTVTAANSSSISDGAAALVMMRRSEAEKRGLKPLATVLGHTNFAQEPALFTTAPVGAIKT 300 Query: 303 LLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARIL 362 LL K G +++L+E+NEAFAVV++ M L++ H +VNVHGGACALGHPIGASGARI+ Sbjct: 301 LLDKVGCKAGDIDLWEINEAFAVVTMAAMHDLKLEHERVNVHGGACALGHPIGASGARII 360 Query: 363 VTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 VTLLSAL+ G+KRGVA++CIGGGEATA+ VE Sbjct: 361 VTLLSALKTYGMKRGVASLCIGGGEATALMVE 392 Lambda K H 0.318 0.133 0.378 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: 548 Number of extensions: 6 Number of successful extensions: 1 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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_043745132.1 AMB_RS18210 (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.24363.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-126 407.1 5.0 4.2e-126 406.9 5.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043745132.1 AMB_RS18210 acetyl-CoA C-acyltra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043745132.1 AMB_RS18210 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.9 5.0 4.2e-126 4.2e-126 1 385 [] 8 392 .. 8 392 .. 0.97 Alignments for each domain: == domain 1 score: 406.9 bits; conditional E-value: 4.2e-126 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a+Rtp+g ++g +++l a +L+aa+i++++er+gl p+++dev +G+vl+ag ++++aR+a l ag lcl|NCBI__GCF_000009985.1:WP_043745132.1 8 IVGAARTPMGGFQGDFASLAAPQLGAAAIRAAVERSGLAPDQVDEVFMGCVLPAGVGQAPARQASLGAG 76 89********99********************************************************* PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 lp s +t+++vC+Sg++A +la + + aG+a+v+vaGG+EsmS++p+ll+++ r +++lg+ k+ d lcl|NCBI__GCF_000009985.1:WP_043745132.1 77 LPRSAGCTTISKVCGSGMKAAMLAHDLLVAGTAKVMVAGGMESMSNAPYLLDKA--RGGYRLGHGKVLD 143 ****************************************************98..89*********** PP TIGR01930 139 qllkdl....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201 ++ d+ + + mg+ Ae++a y+++Re qD +al+S ++a+kAi++g f++ei+pv v g+ lcl|NCBI__GCF_000009985.1:WP_043745132.1 144 HMFLDGledaYDRGRLMGTFAEECAGSYKFTREAQDGFALASLSRAKKAIADGLFAAEITPVAVAGRkg 212 999999999888999***************************************************995 PP TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270 ++ ++ De++ + +k+ +Lkpaf++ +g tvtA+Nss+++DGAaal++m ++ a++ gl+pla++ lcl|NCBI__GCF_000009985.1:WP_043745132.1 213 ETLITIDEQP-GKALPDKIPTLKPAFAK-DG-TVTAANSSSISDGAAALVMMRRSEAEKRGLKPLATVL 278 5555556655.57789**********95.9*.6************************************ PP TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339 ++++ + +p+ ++++pv Ai+ +L+k g ++ didl+EinEAFA++++a++++l+ l++e+vNv+GGA lcl|NCBI__GCF_000009985.1:WP_043745132.1 279 GHTNFAQEPALFTTAPVGAIKTLLDKVGCKAGDIDLWEINEAFAVVTMAAMHDLK-LEHERVNVHGGAC 346 *******************************************************.88*********** PP TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 AlGHP+GasGari++tll++Lk g+k+G+a+lC+ggG ++A+++e lcl|NCBI__GCF_000009985.1:WP_043745132.1 347 ALGHPIGASGARIIVTLLSALKTYGMKRGVASLCIGGGEATALMVE 392 ******************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (394 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.72 // [ok]
This GapMind analysis is from Sep 17 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