# 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/Xenopus_tropicalis.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.8e-34 117.9 20.5 7.7e-19 67.9 4.8 3.2 3 tr|F7A1S4|F7A1S4_XENTR DNA topoisomerase OS=Xenopus tropical
4.1e-31 107.2 35.4 5.5e-18 65.2 5.3 4.5 5 tr|F6TL99|F6TL99_XENTR Nei like DNA glycosylase 3 OS=Xenopus
1.2e-15 57.7 4.6 1.2e-15 57.7 4.6 2.9 3 tr|F6R566|F6R566_XENTR ERI1 exoribonuclease family member 2
6.1e-15 55.4 1.0 1.3e-14 54.4 1.0 1.6 1 tr|F7EQY8|F7EQY8_XENTR Zinc finger, GRF-type-containing 1 OS
1.6e-14 54.1 3.0 1.6e-14 54.1 3.0 2.9 2 sp|Q66IH9|ZCHC4_XENTR Zinc finger CCHC domain-containing pr
5.9e-13 49.1 5.1 5.9e-13 49.1 5.1 2.4 3 tr|F6QX16|F6QX16_XENTR Apurinic/apyrimidinic endodeoxyribonu
Domain annotation for each sequence (and alignments):
>> tr|F7A1S4|F7A1S4_XENTR DNA topoisomerase OS=Xenopus tropicalis OX=8364 GN=top3a PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.4 0.2 1.7 7e+03 3 15 .. 662 675 .. 661 678 .. 0.75
2 ! 59.1 2.9 1.1e-19 4.6e-16 2 44 .. 826 865 .. 825 866 .. 0.96
3 ! 67.9 4.8 1.9e-22 7.7e-19 2 45 .] 911 954 .. 910 954 .. 0.97
Alignments for each domain:
== domain 1 score: -2.4 bits; conditional E-value: 1.7
zf-GRF 3 Ck.cgrlavlltvr 15
C+ c + vl+t r
tr|F7A1S4|F7A1S4_XENTR 662 CPqCNKDMVLKTKR 675
88788888888887 PP
== domain 2 score: 59.1 bits; conditional E-value: 1.1e-19
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
C+cg av+ltvrk+gpN+GR FYkC+ g C+FF Wad+
tr|F7A1S4|F7A1S4_XENTR 826 VCNCGVAAVQLTVRKEGPNQGRPFYKCNGGA---CNFFLWADQ 865
7****************************99...*******97 PP
== domain 3 score: 67.9 bits; conditional E-value: 1.9e-22
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45
C c ++av++tv+k+g NkGR+F++C+k++e+qCgFF+Wade+
tr|F7A1S4|F7A1S4_XENTR 911 VCMCNQPAVTRTVQKDGANKGRQFHTCSKPREQQCGFFQWADEN 954
6*****************************************96 PP
>> tr|F6TL99|F6TL99_XENTR Nei like DNA glycosylase 3 OS=Xenopus tropicalis OX=8364 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.4 0.0 0.91 3.7e+03 24 30 .. 237 243 .. 229 246 .. 0.83
2 ? 1.9 4.7 0.08 3.2e+02 4 33 .. 259 287 .. 257 291 .. 0.86
3 ? -3.4 0.1 3.7 1.5e+04 10 22 .. 471 482 .. 469 482 .. 0.80
4 ! 56.2 3.4 8.8e-19 3.6e-15 2 43 .. 512 554 .. 511 556 .. 0.93
5 ! 65.2 5.3 1.4e-21 5.5e-18 1 43 [. 558 600 .. 558 602 .. 0.96
Alignments for each domain:
== domain 1 score: -1.4 bits; conditional E-value: 0.91
zf-GRF 24 kFYkCpk 30
FYkC k
tr|F6TL99|F6TL99_XENTR 237 LFYKCRK 243
5****76 PP
== domain 2 score: 1.9 bits; conditional E-value: 0.08
zf-GRF 4 kcgrlavlltvrktgpNkGRkFYkCpkgke 33
+cg+ + tv + g+N+ R Y Cpk+++
tr|F6TL99|F6TL99_XENTR 259 NCGQCDKKITVCRLGENN-RMTYFCPKCQN 287
699999999999999998.88889***997 PP
== domain 3 score: -3.4 bits; conditional E-value: 3.7
zf-GRF 10 vlltvrktgpNkG 22
+l+tv+ + pNk+
tr|F6TL99|F6TL99_XENTR 471 KLKTVH-QTPNKT 482
689998.999985 PP
== domain 4 score: 56.2 bits; conditional E-value: 8.8e-19
zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
C + ++ l++vrk+g+NkGR FY+C++++e++C FF+Wad
tr|F6TL99|F6TL99_XENTR 512 NCStHNVPCALQVVRKEGENKGRSFYTCSLPRERCCQFFEWAD 554
6986779***********************************9 PP
== domain 5 score: 65.2 bits; conditional E-value: 1.4e-21
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
p+C++g+++ ++tv k gpN+G++FY+Cp gk+kqC+FF+Wa
tr|F6TL99|F6TL99_XENTR 558 PFCNHGKRCIVRTVLKLGPNNGKNFYVCPMGKDKQCNFFEWAK 600
68***************************************95 PP
>> tr|F6R566|F6R566_XENTR ERI1 exoribonuclease family member 2 OS=Xenopus tropicalis OX=8364 GN=eri2 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.3 0.0 0.13 5.2e+02 30 43 .. 141 154 .. 127 156 .. 0.87
2 ? -3.0 0.1 2.8 1.1e+04 10 21 .. 277 288 .. 274 291 .. 0.80
3 ! 57.7 4.6 3e-19 1.2e-15 1 43 [. 578 625 .. 578 627 .. 0.94
Alignments for each domain:
== domain 1 score: 1.3 bits; conditional E-value: 0.13
zf-GRF 30 kgkekqCgFFkWad 43
+++ k C F W d
tr|F6R566|F6R566_XENTR 141 AAEHKMCAFVTWSD 154
456699******98 PP
== domain 2 score: -3.0 bits; conditional E-value: 2.8
zf-GRF 10 vlltvrktgpNk 21
++t++k+ +N+
tr|F6R566|F6R566_XENTR 277 NIQTSKKDSENN 288
57899*****98 PP
== domain 3 score: 57.7 bits; conditional E-value: 3e-19
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke.....kqCgFFkWad 43
p+C+cgr+a++ltv++tgpN+G++FY+C++ k k C +FkW+
tr|F6R566|F6R566_XENTR 578 PMCNCGRRAKRLTVSNTGPNQGKAFYTCSVKKRneenkKGCDYFKWEH 625
79***************************9988789999*******96 PP
>> tr|F7EQY8|F7EQY8_XENTR Zinc finger, GRF-type-containing 1 OS=Xenopus tropicalis OX=8364 GN=zgrf1 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.4 1.0 3.3e-18 1.3e-14 1 44 [. 84 127 .. 84 128 .. 0.97
Alignments for each domain:
== domain 1 score: 54.4 bits; conditional E-value: 3.3e-18
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
plC ++++a+l v+k+gpNkGR FY+C ++k qC FFkW +e
tr|F7EQY8|F7EQY8_XENTR 84 PLCLHQQPAKLVMVKKEGPNKGRFFYTCDAPKSDQCKFFKWLNE 127
79***************************************986 PP
>> sp|Q66IH9|ZCHC4_XENTR Zinc finger CCHC domain-containing protein 4 OS=Xenopus tropicalis OX=8364 GN=zcchc4 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.1 3.0 4.1e-18 1.6e-14 1 44 [. 26 69 .. 26 70 .. 0.96
2 ? -14.5 14.2 6 2.4e+04 17 17 .. 386 386 .. 366 417 .. 0.62
Alignments for each domain:
== domain 1 score: 54.1 bits; conditional E-value: 4.1e-18
zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWade 44
p+C++g +l++++++ +g+++GR FY+C+++++ k+C FF+W+d+
sp|Q66IH9|ZCHC4_XENTR 26 PQCPHGpTLLFVKVS--QGKEQGRRFYACSACRDrKDCHFFQWEDD 69
79*************..6***************************7 PP
== domain 2 score: -14.5 bits; conditional E-value: 6
zf-GRF 17 t 17
sp|Q66IH9|ZCHC4_XENTR 386 C 386
1 PP
>> tr|F6QX16|F6QX16_XENTR Apurinic/apyrimidinic endodeoxyribonuclease 2 OS=Xenopus tropicalis OX=8364 GN=apex2 PE=4 SV=
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.7 0.0 4.6 1.9e+04 19 25 .. 204 210 .. 203 210 .. 0.84
2 ? -3.0 0.0 2.8 1.1e+04 9 20 .. 366 377 .. 365 378 .. 0.81
3 ! 49.1 5.1 1.5e-16 5.9e-13 1 42 [. 461 509 .. 461 512 .. 0.93
Alignments for each domain:
== domain 1 score: -3.7 bits; conditional E-value: 4.6
zf-GRF 19 pNkGRkF 25
+N+GR++
tr|F6QX16|F6QX16_XENTR 204 ENPGRQW 210
8****95 PP
== domain 2 score: -3.0 bits; conditional E-value: 2.8
zf-GRF 9 avlltvrktgpN 20
a++ tvrk g +
tr|F6QX16|F6QX16_XENTR 366 AEISTVRKRGSD 377
5789****9976 PP
== domain 3 score: 49.1 bits; conditional E-value: 1.5e-16
zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42
p Ck +g+++vl+tv+k gpN GR+FY+C+ +++ + C+FF W
tr|F6QX16|F6QX16_XENTR 461 PNCKgHGEPCVLRTVKKAGPNCGRQFYVCARPEGhstnpqARCNFFLWL 509
57**9****************************999999999******6 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (45 nodes)
Target sequences: 24182 (11782085 residues searched)
Passed MSV filter: 1155 (0.0477628); expected 483.6 (0.02)
Passed bias filter: 495 (0.0204698); expected 483.6 (0.02)
Passed Vit filter: 29 (0.00119924); expected 24.2 (0.001)
Passed Fwd filter: 6 (0.000248118); expected 0.2 (1e-05)
Initial search space (Z): 24182 [actual number of targets]
Domain search space (domZ): 6 [number of targets reported over threshold]
# CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.07
# Mc/sec: 7574.20
//
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