# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: H1.4.fa # target HMM database: /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm # output directed to file: H1.4.PFam-27-A # per-seq hits tabular output: H1.4.hmmscan.tblout # number of worker threads: 16 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: histone_H1.4_[Homo_sapiens]gi|4885379|ref|NP_005312.1 [L=219] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-22 78.5 2.3 2.9e-22 78.5 1.6 1.9 2 Linker_histone linker histone H1 and H5 family Domain annotation for each model (and alignments): >> Linker_histone linker histone H1 and H5 family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.5 1.6 2e-26 2.9e-22 3 77 .] 38 109 .. 36 109 .. 0.95 2 ? -2.7 0.9 0.44 6.5e+03 58 70 .. 132 145 .. 119 152 .. 0.62 Alignments for each domain: == domain 1 score: 78.5 bits; conditional E-value: 2e-26 --HHHHHHHHCCCCCCCTSEEHHHHHHHHHC.CTCCCCCSTTHHHHHHHHHHHHHH CS Linker_histone 3 ppyseMiveaikalkerkGsSvqaikKyiea.nykveinasnlasllklaLkkgvk 57 pp+se+i++a++a+ker+G S +a+kK ++a y+ve+n+ s++kl Lk++v+ histone_H1.4_[Homo_sapiens]gi|4885379|ref|NP_005312.1 38 PPVSELITKAVAASKERSGVSLAALKKALAAaGYDVEKNN----SRIKLGLKSLVS 89 9****************************99689988888....************ PP CTSEE-TT..TTTSEEEESS CS Linker_histone 58 sGeLvqvkgtGasGsfklak 77 +G+Lvq+kgtGasGsfkl+k histone_H1.4_[Homo_sapiens]gi|4885379|ref|NP_005312.1 90 KGTLVQTKGTGASGSFKLNK 109 ******************97 PP == domain 2 score: -2.7 bits; conditional E-value: 0.44 CTSEE-TT...TTT CS Linker_histone 58 sGeLvqvk.gtGas 70 +G+ +++k +tGa+ histone_H1.4_[Homo_sapiens]gi|4885379|ref|NP_005312.1 132 AGAAKKPKkATGAA 145 44555555567765 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (219 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 979 (0.0660104); expected 296.6 (0.02) Passed bias filter: 304 (0.0204976); expected 296.6 (0.02) Passed Vit filter: 70 (0.00471984); expected 14.8 (0.001) Passed Fwd filter: 23 (0.00155081); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.27u 0.48s 00:00:00.75 Elapsed: 00:00:01.93 # Mc/sec: 296.20 //