Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_078430082.1 BK574_RS21800 acetyl-CoA C-acetyltransferase
Query= BRENDA::P42765 (397 letters) >NCBI__GCF_002019605.1:WP_078430082.1 Length = 392 Score = 405 bits (1042), Expect = e-118 Identities = 199/389 (51%), Positives = 278/389 (71%), Gaps = 1/389 (0%) Query: 7 VFVVAAKRTPFGAYGGLLKDFTATDLSEFAAKAALSAGKVSPETVDSVIMGNVLQSSSDA 66 V+++ RT FG++GG K + DL A++ A+ ++ PE +D V GNV+ ++ + Sbjct: 4 VYIIEGARTAFGSFGGAFKGISDIDLGVAASQEAIKRSQMKPEQIDHVYFGNVIHTNKSS 63 Query: 67 IYLARHVGLRVGIPKETPALTINRLCGSGFQSIVNGCQEICVKEAEVVLCGGTESMSQAP 126 YLAR++GL+ G+P E PALT+NRLCGSG Q++V+G Q+I + + + L GG E+MSQ+P Sbjct: 64 SYLARYIGLKSGVPHEAPALTLNRLCGSGLQALVSGAQQIMLGDGKTALVGGAENMSQSP 123 Query: 127 YCVRNVRFGTKLGSDIKLEDSLWVSLTDQHVQLPMAMTAENLAVKHKISREECDKYALQS 186 + +R+ RFG+KLG+ +++D LW +LTD + M +TAENLA K+ ISREE D+++ +S Sbjct: 124 HVLRDTRFGSKLGAP-QIDDMLWETLTDHNAGCGMGVTAENLAEKYNISREEQDEFSTRS 182 Query: 187 QQRWKAANDAGYFNDEMAPIEVKTKKGKQTMQVDEHARPQTTLEQLQKLPPVFKKDGTVT 246 Q AA + G F E+ P+ +K +KG + DEH + TT ++L L P FKKDGTVT Sbjct: 183 HQLAAAARENGRFEKEIVPVVLKGRKGDIVIDKDEHIKADTTADKLSNLKPAFKKDGTVT 242 Query: 247 AGNASGVADGAGAVIIASEDAVKKHNFTPLARIVGYFVSGCDPSIMGIGPVPAISGALKK 306 AGNASG+ DGA AV +ASE VK++N PLA+IV + ++G DP+ MGIGPVPA AL+K Sbjct: 243 AGNASGINDGAAAVTLASESFVKENNIKPLAKIVSWGIAGVDPAYMGIGPVPASKIALQK 302 Query: 307 AGLSLKDMDLVEVNEAFAPQYLAVERSLDLDISKTNVNGGAIALGHPLGGSGSRITAHLV 366 AGLS++D+DL+E+NEAFA QYLAVE+ L LD K NVNGGAIALGHP+G SG+RI L Sbjct: 303 AGLSIEDIDLIELNEAFAAQYLAVEKELGLDRQKVNVNGGAIALGHPVGASGARIVYSLA 362 Query: 367 HELRRRGGKYAVGSACIGGGQGIAVIIQS 395 EL+ + KY + S CIGGGQGI+VII++ Sbjct: 363 QELKLQNKKYGLASLCIGGGQGISVIIEA 391 Lambda K H 0.317 0.133 0.383 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: 356 Number of extensions: 10 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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_078430082.1 BK574_RS21800 (acetyl-CoA C-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.933639.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-152 491.8 1.3 7.4e-152 491.7 1.3 1.0 1 NCBI__GCF_002019605.1:WP_078430082.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002019605.1:WP_078430082.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 491.7 1.3 7.4e-152 7.4e-152 1 385 [] 6 390 .. 6 390 .. 0.99 Alignments for each domain: == domain 1 score: 491.7 bits; conditional E-value: 7.4e-152 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 i++++Rt++g++gg++k +s dL++a+ +e+++r++++pe+id+v++Gnv+++++ + +aR + l++g+p+ NCBI__GCF_002019605.1:WP_078430082.1 6 IIEGARTAFGSFGGAFKGISDIDLGVAASQEAIKRSQMKPEQIDHVYFGNVIHTNKSsSYLARYIGLKSGVPH 78 89*******************************************************9*************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144 + palt+nr+C+SglqA+ ++aq+i+ G+ +++++GG+E+mS++p++l++ r + klg+ + +d+l ++l NCBI__GCF_002019605.1:WP_078430082.1 79 EAPALTLNRLCGSGLQALVSGAQQIMLGDGKTALVGGAENMSQSPHVLRDT--RFGSKLGAPQIDDMLWETLt 149 ************************************************997..89999********9999999 PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 +++ mg+tAenla+ky+isReeqDe++ rShq aa+A e+g+f++eivpv++kg+ + v++kDe+i+++ NCBI__GCF_002019605.1:WP_078430082.1 150 dHNAGCGMGVTAENLAEKYNISREEQDEFSTRSHQLAAAARENGRFEKEIVPVVLKGRkgDIVIDKDEHIKAD 222 9999*****************************************************99999*********** PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 tt++kL++Lkpafk+ +g tvtAgN+s++nDGAaa+ l+se+++ke +++pla+ivs+++agvdp++mg+gpv NCBI__GCF_002019605.1:WP_078430082.1 223 TTADKLSNLKPAFKK-DG-TVTAGNASGINDGAAAVTLASESFVKENNIKPLAKIVSWGIAGVDPAYMGIGPV 293 *************95.9*.6***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 pA++ aL+kaglsi+didl+E+nEAFAaq+lavekelg ld++kvNvnGGAiAlGHP+GasGariv +l++eL NCBI__GCF_002019605.1:WP_078430082.1 294 PASKIALQKAGLSIEDIDLIELNEAFAAQYLAVEKELG-LDRQKVNVNGGAIALGHPVGASGARIVYSLAQEL 365 **************************************.99******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 k ++kkyGla+lC+ggGqG++vi+e NCBI__GCF_002019605.1:WP_078430082.1 366 KLQNKKYGLASLCIGGGQGISVIIE 390 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 00:00:00.00 # Mc/sec: 26.27 // [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