Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase
Query= reanno::SB2B:6935813 (387 letters) >FitnessBrowser__azobra:AZOBR_RS20220 Length = 382 Score = 342 bits (876), Expect = 1e-98 Identities = 201/384 (52%), Positives = 254/384 (66%), Gaps = 11/384 (2%) Query: 5 VIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQTLEQ 64 VI R+P + G VR + L A ++ AL+ R GV+P IEDV+ GC EQ Sbjct: 9 VIAGYARSPFAFANKGELAKVRPDDLLAHVVAALVERT-GVNPQDIEDVVVGCAFPEGEQ 67 Query: 65 GFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEHMGHV 124 G NIAR S LA +P TAGA T+NR CGSSM+A+HQA+ AI G G+ F+ GG+E M V Sbjct: 68 GMNIARTVSFLAKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRV 127 Query: 125 PM-NHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAASIEG 183 PM + HPGL + +A MG+TAE + + + ISR Q+ A SH +A AA G Sbjct: 128 PMMGYNPLPHPGLKDHYPEAYCSMGVTAENVARRYEISRADQEAMAAESHAKAAAAQQAG 187 Query: 184 RFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSALSD 243 R A EI AI+ A V+ D IRP T+ E+L+GL+P F A+G+VTAGTSS L+D Sbjct: 188 RLAEEIVAIQT-----AAGLVERDGCIRPGTSGETLSGLKPAF-LADGSVTAGTSSPLTD 241 Query: 244 GAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQDMD 303 GA+A+LV E A+A GL I AR+RS+AVAGC +MG GPVPA QKALARAGLSI+D+D Sbjct: 242 GASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQKALARAGLSIRDID 301 Query: 304 VIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLMEHK 363 VIELNEAFAAQ++ C++DL D+ KVNL+GGAIALGHPLG +GARI+ L++ + Sbjct: 302 VIELNEAFAAQAIACMRDL---DIDPAKVNLDGGAIALGHPLGATGARITGKAAALLKRE 358 Query: 364 DATLGLATMCIGLGQGIATVFERV 387 LAT CIG GQGIATV E V Sbjct: 359 GKQFALATQCIGGGQGIATVLEAV 382 Lambda K H 0.319 0.134 0.384 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: 433 Number of extensions: 19 Number of successful extensions: 5 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: 387 Length of database: 382 Length adjustment: 30 Effective length of query: 357 Effective length of database: 352 Effective search space: 125664 Effective search space used: 125664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate AZOBR_RS20220 AZOBR_RS20220 (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.10932.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-134 432.7 8.1 7.4e-134 432.4 8.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.4 8.1 7.4e-134 7.4e-134 1 385 [] 10 380 .. 10 380 .. 0.97 Alignments for each domain: == domain 1 score: 432.4 bits; conditional E-value: 7.4e-134 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaala 67 i +++R+p++ + +g l++++++dLla+v+ +l+er+g++p++i++v++G+++++geq +niaR++ + lcl|FitnessBrowser__azobra:AZOBR_RS20220 10 IAGYARSPFAfANKGELAKVRPDDLLAHVVAALVERTGVNPQDIEDVVVGCAFPEGEQgMNIARTVSFL 78 67899*****977******************************************************** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 a+lp + a+t+nr+C+S++qA+++aa +i++G+ +v++ GG+EsmSrvp++ + ++g ++ lcl|FitnessBrowser__azobra:AZOBR_RS20220 79 AKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRVPMMGYNP----LPHPGLKDH 143 ***************************************************98886....677766666 PP TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvv 205 + ++ smg+tAen+a++y+isR +q++ a++Sh kaa+A+++g++++eiv ++ + v lcl|FitnessBrowser__azobra:AZOBR_RS20220 144 YP-------EAYCSMGVTAENVARRYEISRADQEAMAAESHAKAAAAQQAGRLAEEIVAIQTA--AGLV 203 65.......8899*********************************************97776..5899 PP TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaav 274 ++D +irp+t+ e+L++Lkpaf +gs vtAg ss+l+DGA+a+l+++e+ ak+ gl +lari+s+av lcl|FitnessBrowser__azobra:AZOBR_RS20220 204 ERDGCIRPGTSGETLSGLKPAFLA-DGS-VTAGTSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAV 270 **********************95.9*7.**************************************** PP TIGR01930 275 agvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGH 343 ag+ pe+mglgpvpA +kaL++aglsi+did++E+nEAFAaq++a++++l+ +d++kvN GGAiAlGH lcl|FitnessBrowser__azobra:AZOBR_RS20220 271 AGCAPEVMGLGPVPAAQKALARAGLSIRDIDVIELNEAFAAQAIACMRDLD-IDPAKVNLDGGAIALGH 338 ***************************************************.88*************** PP TIGR01930 344 PlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 PlGa+Gari+ + + Lk++gk+++lat C+ggGqG+A++le lcl|FitnessBrowser__azobra:AZOBR_RS20220 339 PLGATGARITGKAAALLKREGKQFALATQCIGGGQGIATVLE 380 ****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (382 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: 10.82 // [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