# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: domain1.hmmer # target sequence database: /home/chengji/software/prosys_database/cm_lib/pdb_cm # sequence reporting threshold: E-value <= 10 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: domain1-i5 [M=172] 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-45 157.1 0.3 4.5e-45 156.7 0.3 1.2 1 3BOJA 3.5e-45 157.0 0.3 4.8e-45 156.6 0.3 1.2 1 3BOHA 1.7e-43 151.5 0.0 2.4e-43 151.1 0.0 1.2 1 3BOBA 2.8e-43 150.8 0.1 3.7e-43 150.5 0.1 1.2 1 3UK8B 3e-43 150.7 0.1 4e-43 150.3 0.1 1.2 1 3UK8A ------ inclusion threshold ------ 0.92 12.4 0.0 1.6 11.7 0.0 1.3 1 5KZ8A Domain annotation for each sequence (and alignments): >> 3BOJA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 156.7 0.3 1.5e-49 4.5e-45 2 171 .. 28 180 .. 27 181 .. 0.98 Alignments for each domain: == domain 1 score: 156.7 bits; conditional E-value: 1.5e-49 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF domain1-i5 2 llveveakgklsCvDGReedeeskavlgvpGGdlgelllaalaalrrgtdveeklsellaalreaggkfyvHtddhaeepedvGCGhldllltirleey 100 +v+v+++g l+CvDGR +d+++ +++++pGG +++ a++r++t++e+ l++++++++++g++++vH+d++++ ++GCG+++l+ t+r++++ 3BOJA 28 EMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAI------AHNRGVTTLEG-LKQITKEVASKGHVPSVHGDHSSD---MLGCGFFKLWVTGRFDDM 116 589*********************************......99*********.*********************988...8***************** PP xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF domain1-i5 101 glrstqadleeifaklegkgavlevLeGeHeEkavvvnavegttldpnrvakpasagdqaFvvdawaaekl 171 g++++q+d+++ ++++e++g+v+e+++G+H+Ek+v++n ve++tl+p++ +dq+F+vd waa k+ 3BOJA 117 GYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDE-------DDQRFIVDGWAAGKF 180 *************************************************.......9**********9886 PP >> 3BOHA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 156.6 0.3 1.6e-49 4.8e-45 2 171 .. 32 184 .. 31 185 .. 0.98 Alignments for each domain: == domain 1 score: 156.6 bits; conditional E-value: 1.6e-49 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF domain1-i5 2 llveveakgklsCvDGReedeeskavlgvpGGdlgelllaalaalrrgtdveeklsellaalreaggkfyvHtddhaeepedvGCGhldllltirleey 100 +v+v+++g l+CvDGR +d+++ +++++pGG +++ a++r++t++e+ l++++++++++g++++vH+d++++ ++GCG+++l+ t+r++++ 3BOHA 32 EMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAI------AHNRGVTTLEG-LKQITKEVASKGHVPSVHGDHSSD---MLGCGFFKLWVTGRFDDM 120 589*********************************......99*********.*********************988...8***************** PP xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF domain1-i5 101 glrstqadleeifaklegkgavlevLeGeHeEkavvvnavegttldpnrvakpasagdqaFvvdawaaekl 171 g++++q+d+++ ++++e++g+v+e+++G+H+Ek+v++n ve++tl+p++ +dq+F+vd waa k+ 3BOHA 121 GYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDE-------DDQRFIVDGWAAGKF 184 *************************************************.......9**********9886 PP >> 3BOBA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 151.1 0.0 7.8e-48 2.4e-43 3 171 .. 29 180 .. 27 181 .. 0.98 Alignments for each domain: == domain 1 score: 151.1 bits; conditional E-value: 7.8e-48 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF domain1-i5 3 lveveakgklsCvDGReedeeskavlgvpGGdlgelllaalaalrrgtdveeklsellaalreaggkfyvHtddhaeepedvGCGhldllltirleeyg 101 lv+v+++g l+CvDGR +d+++++++++pGG +++ a++r++t++e+ l++++++++++g+ ++vH+d++++ ++GCG+++l+ t+r++++g 3BOBA 29 LVDVRPEGILKCVDGRGSDNTRMGGPKMPGGIYAI------AHNRGVTSIEG-LKQITKEVASKGHLPSVHGDHSSD---MLGCGFFKLWVTGRFDDMG 117 799********************************......99*********.*********************988...8****************** PP xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF domain1-i5 102 lrstqadleeifaklegkgavlevLeGeHeEkavvvnavegttldpnrvakpasagdqaFvvdawaaekl 171 ++++q+d+++ +++++++g+ +e+++G+H+Ek+v++n ++tl+pn+ +dq+F+vd waa+k+ 3BOBA 118 YPRPQFDADQGANAVKDAGGIIEMHHGSHTEKVVYINLLANKTLEPNE-------NDQRFIVDGWAADKF 180 ************************************************.......9***********997 PP >> 3UK8B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 150.5 0.1 1.2e-47 3.7e-43 4 171 .. 30 180 .. 27 181 .. 0.97 Alignments for each domain: == domain 1 score: 150.5 bits; conditional E-value: 1.2e-47 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF domain1-i5 4 veveakgklsCvDGReedeeskavlgvpGGdlgelllaalaalrrgtdveeklsellaalreaggkfyvHtddhaeepedvGCGhldllltirleeygl 102 +v+++g l+CvDGR +d+++ +++++pGG +++ a++r++t++e+ l++++++++++g++++vH+d++++ ++GCG+++l+lt+r++++g+ 3UK8B 30 KRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAI------AHNRGVTTLEG-LKDITREVASKGHVPSVHGDHSSD---MLGCGFFKLWLTGRFDDMGY 118 57999*****************************......99*********.*********************988...8******************* PP xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF domain1-i5 103 rstqadleeifaklegkgavlevLeGeHeEkavvvnavegttldpnrvakpasagdqaFvvdawaaekl 171 +++++d+++ + +++++g+v+e+++G+HeEk+v++n v+g+tl+pn+ +dq+F+vd waa+k+ 3UK8B 119 PRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNE-------HDQRFIVDGWAASKF 180 ***********************************************.......9***********986 PP >> 3UK8A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 150.3 0.1 1.3e-47 4e-43 4 171 .. 35 185 .. 32 186 .. 0.97 Alignments for each domain: == domain 1 score: 150.3 bits; conditional E-value: 1.3e-47 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF domain1-i5 4 veveakgklsCvDGReedeeskavlgvpGGdlgelllaalaalrrgtdveeklsellaalreaggkfyvHtddhaeepedvGCGhldllltirleeygl 102 +v+++g l+CvDGR +d+++ +++++pGG +++ a++r++t++e+ l++++++++++g++++vH+d++++ ++GCG+++l+lt+r++++g+ 3UK8A 35 KRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAI------AHNRGVTTLEG-LKDITREVASKGHVPSVHGDHSSD---MLGCGFFKLWLTGRFDDMGY 123 57999*****************************......99*********.*********************988...8******************* PP xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF domain1-i5 103 rstqadleeifaklegkgavlevLeGeHeEkavvvnavegttldpnrvakpasagdqaFvvdawaaekl 171 +++++d+++ + +++++g+v+e+++G+HeEk+v++n v+g+tl+pn+ +dq+F+vd waa+k+ 3UK8A 124 PRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNE-------HDQRFIVDGWAASKF 185 ***********************************************.......9***********986 PP >> 5KZ8A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 5.3e-05 1.6 42 87 .. 94 150 .. 79 169 .. 0.82 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 5.3e-05 ..xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx RF domain1-i5 42 alaalrrgtdvee.klsellaalreaggkfyvHtddhaee..........pedvGCG 87 ++a+ r +++ k++++++a++ + kf vH+d +ae+ +d+GCG 5KZ8A 94 LVAHGRMKEKEARaKFRQIVSAVQYCHQKFIVHRDLKAENllldadmnikIADFGCG 150 344444443333247*********************999999999999999*****9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (172 nodes) Target sequences: 180940 (47973432 residues searched) Passed MSV filter: 3976 (0.0219741); expected 3618.8 (0.02) Passed bias filter: 3522 (0.019465); expected 3618.8 (0.02) Passed Vit filter: 281 (0.001553); expected 180.9 (0.001) Passed Fwd filter: 6 (3.31602e-05); expected 1.8 (1e-05) Initial search space (Z): 180940 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 1.20u 0.15s 00:00:01.35 Elapsed: 00:00:03.04 # Mc/sec: 2714.29 // [ok]