# 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: pfam_list/zf-GRF.hmm.txt # target sequence database: proteomes/Anolis_carolinensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: zf-GRF [M=45] Accession: PF06839.12 Description: GRF zinc finger 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-36 121.8 28.3 2.5e-18 65.9 4.5 4.3 4 tr|G1KVD5|G1KVD5_ANOCA Nei like DNA glycosylase 3 OS=Anolis 5.2e-35 119.3 16.6 2.9e-18 65.7 5.0 3.0 2 tr|H9GF12|H9GF12_ANOCA DNA topoisomerase OS=Anolis carolinen 5.1e-16 58.5 2.6 5.1e-16 58.5 2.6 2.7 2 tr|H9GK10|H9GK10_ANOCA Zinc finger CCHC-type containing 4 OS 3.1e-14 52.8 0.1 8e-14 51.5 0.1 1.8 1 tr|G1KKD2|G1KKD2_ANOCA Uncharacterized protein OS=Anolis car 8e-12 45.1 1.2 2.5e-11 43.5 1.2 1.9 1 tr|G1KKZ7|G1KKZ7_ANOCA DNA-(apurinic or apyrimidinic site) l 3.1e-10 40.0 5.9 1.1e-07 31.9 1.6 3.0 2 tr|G1KY69|G1KY69_ANOCA Uncharacterized protein OS=Anolis car 4.8e-09 36.2 7.8 1.2e-08 34.9 2.0 2.8 2 tr|H9GFI6|H9GFI6_ANOCA ERI1 exoribonuclease family member 2 Domain annotation for each sequence (and alignments): >> tr|G1KVD5|G1KVD5_ANOCA Nei like DNA glycosylase 3 OS=Anolis carolinensis OX=28377 GN=NEIL3 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.4 0.0 0.5 1.3e+03 24 30 .. 40 46 .. 20 49 .. 0.81 2 ? 2.2 4.0 0.074 2e+02 4 33 .. 62 90 .. 60 93 .. 0.78 3 ! 65.4 1.9 1.3e-21 3.6e-18 2 43 .. 316 358 .. 315 360 .. 0.94 4 ! 65.9 4.5 9.6e-22 2.5e-18 1 44 [. 362 405 .. 362 406 .. 0.97 Alignments for each domain: == domain 1 score: -0.4 bits; conditional E-value: 0.5 zf-GRF 24 kFYkCpk 30 FYkC k tr|G1KVD5|G1KVD5_ANOCA 40 LFYKCRK 46 6****76 PP == domain 2 score: 2.2 bits; conditional E-value: 0.074 zf-GRF 4 kcgrlavlltvrktgpNkGRkFYkCpkgke 33 +cg+ tv + g+N+ R Y Cp++++ tr|G1KVD5|G1KVD5_ANOCA 62 NCGQCGAKITVCRLGENN-RMTYFCPQCQK 90 699776666666799998.88888**9986 PP == domain 3 score: 65.4 bits; conditional E-value: 1.3e-21 zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 C+ + r++vl++vrk+g+NkGR+FY+Cp++ke+ C +F+Wad tr|G1KVD5|G1KVD5_ANOCA 316 RCNkHSRFCVLRVVRKDGENKGRQFYACPLPKEARCDYFEWAD 358 699677************************************9 PP == domain 4 score: 65.9 bits; conditional E-value: 9.6e-22 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 p+C++g+++ ++tv k gpN+G++F++Cp+gk+kqC FF+Wa++ tr|G1KVD5|G1KVD5_ANOCA 362 PFCNHGKRCIMRTVLKIGPNNGKNFFVCPLGKDKQCDFFQWAEN 405 68***************************************986 PP >> tr|H9GF12|H9GF12_ANOCA DNA topoisomerase OS=Anolis carolinensis OX=28377 GN=TOP3A PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 58.3 3.7 2.3e-19 6.1e-16 2 44 .. 814 853 .. 813 854 .. 0.95 2 ! 65.7 5.0 1.1e-21 2.9e-18 2 45 .] 894 937 .. 893 937 .. 0.97 Alignments for each domain: == domain 1 score: 58.3 bits; conditional E-value: 2.3e-19 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 C+cg++a ltvrk+gpN+GR+FYkC g CgFF Wad+ tr|H9GF12|H9GF12_ANOCA 814 VCNCGEEALFLTVRKEGPNQGRQFYKCRSGG---CGFFLWADQ 853 7**************************9988...********7 PP == domain 2 score: 65.7 bits; conditional E-value: 1.1e-21 zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45 Ckcg++a ++tv+++g NkGR+F++C+k++e+qCgFF+W de+ tr|H9GF12|H9GF12_ANOCA 894 VCKCGQPAITRTVQREGANKGRQFHTCAKPREQQCGFFQWTDEN 937 6*****************************************96 PP >> tr|H9GK10|H9GK10_ANOCA Zinc finger CCHC-type containing 4 OS=Anolis carolinensis OX=28377 GN=ZCCHC4 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 58.5 2.6 1.9e-19 5.1e-16 1 45 [] 4 48 .. 4 48 .. 0.96 2 ? -9.3 7.9 7 1.9e+04 29 36 .. 377 382 .. 358 398 .. 0.59 Alignments for each domain: == domain 1 score: 58.5 bits; conditional E-value: 1.9e-19 zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45 p C++g +l++ ++v +g+++GR FY+C++++e k+C+FF+W+dek tr|H9GK10|H9GK10_ANOCA 4 PHCPHGpTLLFAKIV--QGKEEGRRFYACSACRErKDCNFFQWEDEK 48 57*************..6***************************95 PP == domain 2 score: -9.3 bits; conditional E-value: 7 zf-GRF 29 pkgkekqC 36 ++k+ C tr|H9GK10|H9GK10_ANOCA 377 FLCKK--C 382 44443..3 PP >> tr|G1KKD2|G1KKD2_ANOCA Uncharacterized protein OS=Anolis carolinensis OX=28377 GN=zgrf1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 51.5 0.1 3e-17 8e-14 1 44 [. 162 205 .. 162 206 .. 0.97 Alignments for each domain: == domain 1 score: 51.5 bits; conditional E-value: 3e-17 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44 plCk+ a+l tv+k+g NkGR FY+C ++k C FFkW d+ tr|G1KKD2|G1KKD2_ANOCA 162 PLCKHKIVAKLVTVKKEGRNKGRLFYACDAPKADRCDFFKWLDD 205 79***************************************997 PP >> tr|G1KKZ7|G1KKZ7_ANOCA DNA-(apurinic or apyrimidinic site) lyase OS=Anolis carolinensis OX=28377 GN=APEX2 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 43.5 1.2 9.3e-15 2.5e-11 1 43 [. 450 499 .. 450 501 .] 0.90 Alignments for each domain: == domain 1 score: 43.5 bits; conditional E-value: 9.3e-15 zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWad 43 plCk +g+++vl+tv+k g N GR FY+C+ + + + C FF Wa tr|G1KKZ7|G1KKZ7_ANOCA 450 PLCKaHGEPCVLRTVKKPGANCGRRFYVCARPLGkssdprARCDFFLWAS 499 79**999**********************8776656889999******95 PP >> tr|G1KY69|G1KY69_ANOCA Uncharacterized protein OS=Anolis carolinensis OX=28377 GN=ttf2 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 31.9 1.6 4.2e-11 1.1e-07 2 38 .. 5 42 .. 4 44 .. 0.96 2 ! 9.0 0.2 0.00057 1.5 16 43 .. 69 99 .. 53 101 .. 0.78 Alignments for each domain: == domain 1 score: 31.9 bits; conditional E-value: 4.2e-11 zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38 C +g ++vl+t ++gpNk + FY C + ++++CgF tr|G1KY69|G1KY69_ANOCA 5 VCSaHGHPCVLKTGIRDGPNKNKSFYMCGVQNQQSCGF 42 799899*******************************9 PP == domain 2 score: 9.0 bits; conditional E-value: 0.00057 zf-GRF 16 ktgpNkGRkFYkCpkgke...kqCgFFkWad 43 + ++ R FY+C+k+k + Cg W + tr|G1KY69|G1KY69_ANOCA 69 EQEKETYRLFYRCSKAKAegkQWCGSVPWQE 99 4667778********9988877799877776 PP >> tr|H9GFI6|H9GFI6_ANOCA ERI1 exoribonuclease family member 2 OS=Anolis carolinensis OX=28377 GN=ERI2 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 3.7 0.4 0.026 68 28 43 .. 203 218 .. 200 220 .. 0.92 2 ! 34.9 2.0 4.7e-12 1.2e-08 1 30 [. 666 695 .. 666 696 .] 0.96 Alignments for each domain: == domain 1 score: 3.7 bits; conditional E-value: 0.026 zf-GRF 28 CpkgkekqCgFFkWad 43 C++ ++k C F W d tr|H9GFI6|H9GFI6_ANOCA 203 CAASEGKLCAFVTWSD 218 999***********98 PP == domain 2 score: 34.9 bits; conditional E-value: 4.7e-12 zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpk 30 p+Ckcgr+a++l v++ gpN+G+ FY Cp+ tr|H9GFI6|H9GFI6_ANOCA 666 PMCKCGRRARRLNVSNGGPNHGKVFYSCPV 695 79***************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (45 nodes) Target sequences: 18528 (9796552 residues searched) Passed MSV filter: 947 (0.0511118); expected 370.6 (0.02) Passed bias filter: 389 (0.0209953); expected 370.6 (0.02) Passed Vit filter: 25 (0.00134931); expected 18.5 (0.001) Passed Fwd filter: 7 (0.000377807); expected 0.2 (1e-05) Initial search space (Z): 18528 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.06 # Mc/sec: 7347.41 // [ok]