# 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/Petromyzon_marinus.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
6.2e-34 115.5 6.7 1.2e-17 63.3 0.7 3.0 2 tr|S4RC13|S4RC13_PETMA DNA topoisomerase OS=Petromyzon marin
1.7e-31 107.6 28.4 2.2e-18 65.7 1.5 4.6 5 tr|S4RD41|S4RD41_PETMA Nei-like DNA glycosylase 3 OS=Petromy
Domain annotation for each sequence (and alignments):
>> tr|S4RC13|S4RC13_PETMA DNA topoisomerase OS=Petromyzon marinus OX=7757 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.3 0.8 1.2e-18 7.8e-15 2 44 .. 810 849 .. 809 850 .. 0.95
2 ! 63.3 0.7 1.8e-21 1.2e-17 1 42 [. 877 918 .. 877 922 .. 0.95
Alignments for each domain:
== domain 1 score: 54.3 bits; conditional E-value: 1.2e-18
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
C+cg +a+lltv+k+g NkGR FYkC+ C+FF Wad+
tr|S4RC13|S4RC13_PETMA 810 VCNCGIEATLLTVKKEGINKGRMFYKCSSSV---CNFFLWADQ 849
7***************************998...********7 PP
== domain 2 score: 63.3 bits; conditional E-value: 1.8e-21
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWa 42
++C c ++av++t k+gpNkGR+FY+C+k++++qCgFF W
tr|S4RC13|S4RC13_PETMA 877 VMCSCNNPAVMRTIVKDGPNKGRQFYTCSKPRDEQCGFFLWM 918
69***************************************6 PP
>> tr|S4RD41|S4RD41_PETMA Nei-like DNA glycosylase 3 OS=Petromyzon marinus OX=7757 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.4 0.1 0.29 2e+03 25 32 .. 24 31 .. 21 41 .. 0.72
2 ! 5.9 2.6 0.0015 10 5 33 .. 46 73 .. 43 75 .. 0.73
3 ? -3.2 0.1 1.1 7.4e+03 12 22 .. 273 283 .. 270 283 .. 0.65
4 ! 52.7 1.4 3.7e-18 2.5e-14 3 43 .. 301 342 .. 299 344 .. 0.95
5 ! 65.7 1.5 3.2e-22 2.2e-18 1 43 [. 346 388 .. 346 390 .. 0.97
Alignments for each domain:
== domain 1 score: -1.4 bits; conditional E-value: 0.29
zf-GRF 25 FYkCpkgk 32
FY+C k
tr|S4RD41|S4RD41_PETMA 24 FYQCRKTG 31
9***8765 PP
== domain 2 score: 5.9 bits; conditional E-value: 0.0015
zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgke 33
cg+ ++ +v + g+ +GR Y Cp ++
tr|S4RD41|S4RD41_PETMA 46 CGQCRTRVVVCRLGE-NGRMTYFCPHCQH 73
777555555555665.5*********986 PP
== domain 3 score: -3.2 bits; conditional E-value: 1.1
zf-GRF 12 ltvrktgpNkG 22
+t ++ g+N G
tr|S4RD41|S4RD41_PETMA 273 RTPNNRGQNSG 283
56667777766 PP
== domain 4 score: 52.7 bits; conditional E-value: 3.7e-18
zf-GRF 3 Ck.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
C + r++ l +v+k gpN+GR+F++C++++++qC F+Wad
tr|S4RD41|S4RD41_PETMA 301 CRgHDRPCALHVVQKAGPNRGRHFHACALPQKQQCQHFEWAD 342
99788************************************9 PP
== domain 5 score: 65.7 bits; conditional E-value: 3.2e-22
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
p C +g ++v++tv k gpN+GR+FY+C++g+++qC FF+Wad
tr|S4RD41|S4RD41_PETMA 346 PECDHGLRCVMRTVLKLGPNNGRNFYACAQGRDRQCAFFQWAD 388
57****************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (45 nodes)
Target sequences: 13539 (5048892 residues searched)
Passed MSV filter: 561 (0.0414359); expected 270.8 (0.02)
Passed bias filter: 259 (0.0191299); expected 270.8 (0.02)
Passed Vit filter: 17 (0.00125563); expected 13.5 (0.001)
Passed Fwd filter: 2 (0.000147721); expected 0.1 (1e-05)
Initial search space (Z): 13539 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 7573.34
//
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