# 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/Monodelphis_domestica.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.4e-37 125.4 17.1 6.6e-20 71.2 4.3 3.3 3 tr|F6QP60|F6QP60_MONDO DNA topoisomerase OS=Monodelphis dome
9.3e-19 67.5 4.3 9.3e-19 67.5 4.3 2.5 2 tr|F6UFS2|F6UFS2_MONDO ERI1 exoribonuclease family member 2
7.8e-15 54.9 3.6 7.8e-15 54.9 3.6 2.9 2 tr|F6YW89|F6YW89_MONDO Nei like DNA glycosylase 3 OS=Monodel
8.6e-15 54.8 2.8 8.6e-15 54.8 2.8 2.7 2 tr|F6R8E8|F6R8E8_MONDO Zinc finger CCHC-type containing 4 OS
1.3e-14 54.3 2.1 2.7e-14 53.2 2.1 1.6 1 tr|F6UJU8|F6UJU8_MONDO Uncharacterized protein OS=Monodelphi
2.8e-13 50.0 0.8 2.8e-13 50.0 0.8 1.9 2 tr|F7CHS1|F7CHS1_MONDO DNA-(apurinic or apyrimidinic site) l
7e-06 26.3 1.6 7e-06 26.3 1.6 2.8 2 tr|F7EQ64|F7EQ64_MONDO Transcription termination factor 2 OS
Domain annotation for each sequence (and alignments):
>> tr|F6QP60|F6QP60_MONDO DNA topoisomerase OS=Monodelphis domestica OX=13616 GN=TOP3A PE=3 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.8 0.1 2.7 8.3e+03 3 19 .. 575 588 .. 574 593 .. 0.50
2 ! 62.1 1.2 1.5e-20 4.5e-17 2 43 .. 729 767 .. 728 769 .. 0.96
3 ! 71.2 4.3 2.2e-23 6.6e-20 2 45 .] 801 844 .. 800 844 .. 0.97
Alignments for each domain:
== domain 1 score: -2.8 bits; conditional E-value: 2.7
zf-GRF 3 Ck.cgrlavlltvrktgp 19
C+ c+r vl+ ++
tr|F6QP60|F6QP60_MONDO 575 CPqCHRDMVLK----RRK 588
55555555444....333 PP
== domain 2 score: 62.1 bits; conditional E-value: 1.5e-20
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
C+cg++a lltvrk+gpN+GR FYkC +g+ C+FF Wad
tr|F6QP60|F6QP60_MONDO 729 VCNCGQEALLLTVRKEGPNQGRLFYKCHAGS---CNFFLWAD 767
7*****************************9...*******9 PP
== domain 3 score: 71.2 bits; conditional E-value: 2.2e-23
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45
+C c ++av++tv+k+gpNkGR+F++C+k++e+qCgFF+Wade+
tr|F6QP60|F6QP60_MONDO 801 TCLCSQPAVTRTVQKEGPNKGRQFHTCSKPREQQCGFFQWADEN 844
7*****************************************96 PP
>> tr|F6UFS2|F6UFS2_MONDO ERI1 exoribonuclease family member 2 OS=Monodelphis domestica OX=13616 GN=ERI2 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.0 0.2 0.18 5.3e+02 33 43 .. 144 155 .. 139 157 .. 0.79
2 ! 67.5 4.3 3.1e-22 9.3e-19 1 44 [. 601 648 .. 601 649 .. 0.96
Alignments for each domain:
== domain 1 score: 1.0 bits; conditional E-value: 0.18
zf-GRF 33 e.kqCgFFkWad 43
e k+C F W d
tr|F6UFS2|F6UFS2_MONDO 144 EvKSCAFVTWSD 155
3489******98 PP
== domain 2 score: 67.5 bits; conditional E-value: 3.1e-22
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke....kqCgFFkWade 44
plC+cgr++++l+v+k+gpN+G++FY Cp+gk+ k+Cg+FkW+++
tr|F6UFS2|F6UFS2_MONDO 601 PLCNCGRRSKRLIVSKNGPNHGKAFYSCPVGKYqknrKNCGYFKWEQT 648
79*******************************99999********96 PP
>> tr|F6YW89|F6YW89_MONDO Nei like DNA glycosylase 3 OS=Monodelphis domestica OX=13616 GN=NEIL3 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 3.2 3.4 0.038 1.2e+02 5 33 .. 256 283 .. 253 285 .. 0.85
2 ! 54.9 3.6 2.6e-18 7.8e-15 2 40 .. 521 560 .. 520 561 .. 0.95
Alignments for each domain:
== domain 1 score: 3.2 bits; conditional E-value: 0.038
zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgke 33
cg+ ++ tv + g+N+ R Y Cp +++
tr|F6YW89|F6YW89_MONDO 256 CGQCSSKITVCRLGENN-RMTYFCPRCQK 283
9*9999999999**998.888889*9986 PP
== domain 2 score: 54.9 bits; conditional E-value: 2.6e-18
zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFk 40
C+ + rl+vl++vrk+g+ kGR+FY+Cp++k++qCgFFk
tr|F6YW89|F6YW89_MONDO 521 RCNkHNRLCVLRVVRKDGESKGRQFYACPLPKGSQCGFFK 560
699788*********************************8 PP
>> tr|F6R8E8|F6R8E8_MONDO Zinc finger CCHC-type containing 4 OS=Monodelphis domestica OX=13616 GN=ZCCHC4 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.8 2.8 2.8e-18 8.6e-15 1 45 [] 46 90 .. 46 90 .. 0.96
2 ? -4.6 1.5 7 2.1e+04 22 36 .. 413 425 .. 404 430 .. 0.66
Alignments for each domain:
== domain 1 score: 54.8 bits; conditional E-value: 2.8e-18
zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45
p+C++g +l++++++ +g+++ R FY+C+++++ k+C+FF+W+dek
tr|F6R8E8|F6R8E8_MONDO 46 PQCPHGpTLLFVKVS--QGKEEARRFYACSACRDrKDCNFFQWEDEK 90
79*************..6***************************95 PP
== domain 2 score: -4.6 bits; conditional E-value: 7
zf-GRF 22 GRkFYkCpkgkekqC 36
GR + C ++k+ C
tr|F6R8E8|F6R8E8_MONDO 413 GRRWKHCLLCKK--C 425
666666666664..4 PP
>> tr|F6UJU8|F6UJU8_MONDO Uncharacterized protein OS=Monodelphis domestica OX=13616 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 53.2 2.1 9e-18 2.7e-14 1 44 [. 170 213 .. 170 214 .. 0.96
Alignments for each domain:
== domain 1 score: 53.2 bits; conditional E-value: 9e-18
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
p+C ++++a+l v+k+gpNkGR FY+C + k +qC FFkW +e
tr|F6UJU8|F6UJU8_MONDO 170 PTCHHQQPAKLVMVKKEGPNKGRLFYTCDASKANQCKFFKWFEE 213
68***************************************887 PP
>> tr|F7CHS1|F7CHS1_MONDO DNA-(apurinic or apyrimidinic site) lyase OS=Monodelphis domestica OX=13616 GN=APEX2 PE=3 SV=
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.6 0.0 4.9 1.5e+04 19 25 .. 204 210 .. 203 210 .. 0.84
2 ! 50.0 0.8 9.2e-17 2.8e-13 1 42 [. 426 474 .. 426 477 .] 0.94
Alignments for each domain:
== domain 1 score: -3.6 bits; conditional E-value: 4.9
zf-GRF 19 pNkGRkF 25
+N+GR++
tr|F7CHS1|F7CHS1_MONDO 204 ENPGRQW 210
8****95 PP
== domain 2 score: 50.0 bits; conditional E-value: 9.2e-17
zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42
plCk +g+++vl+tvrk gpN GR+FY+C+ + + + C FF W+
tr|F7CHS1|F7CHS1_MONDO 426 PLCKgHGEPCVLRTVRKAGPNFGRQFYVCSRPVGhisnpaARCDFFLWV 474
79**9*************************999888999999******7 PP
>> tr|F7EQ64|F7EQ64_MONDO Transcription termination factor 2 OS=Monodelphis domestica OX=13616 GN=TTF2 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 26.3 1.6 2.3e-09 7e-06 2 38 .. 24 58 .. 23 63 .. 0.90
2 ? 1.7 0.4 0.11 3.4e+02 21 33 .. 90 102 .. 83 114 .. 0.72
Alignments for each domain:
== domain 1 score: 26.3 bits; conditional E-value: 2.3e-09
zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38
C +g+l++l+t ++gpNkG+ F++C + CgF
tr|F7EQ64|F7EQ64_MONDO 24 RCLeHGTLCFLKTGVREGPNKGKSFFVCRAEA---CGF 58
5887*********999************8877...999 PP
== domain 2 score: 1.7 bits; conditional E-value: 0.11
zf-GRF 21 kGRkFYkCpkgke 33
+ R FY+C+ k
tr|F7EQ64|F7EQ64_MONDO 90 EYRLFYRCNRSKA 102
5699****98876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (45 nodes)
Target sequences: 21272 (11266248 residues searched)
Passed MSV filter: 1068 (0.0502068); expected 425.4 (0.02)
Passed bias filter: 429 (0.0201674); expected 425.4 (0.02)
Passed Vit filter: 32 (0.00150432); expected 21.3 (0.001)
Passed Fwd filter: 8 (0.000376081); expected 0.2 (1e-05)
Initial search space (Z): 21272 [actual number of targets]
Domain search space (domZ): 7 [number of targets reported over threshold]
# CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.07
# Mc/sec: 7242.59
//
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