# 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/Branchiostoma_floridae.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.4e-32 112.1 27.4 1e-18 67.8 5.9 3.7 4 tr|C3Z742|C3Z742_BRAFL DNA topoisomerase (Fragment) OS=Branc
3.6e-12 46.8 7.1 3.6e-12 46.8 7.1 3.4 3 tr|C3YZ80|C3YZ80_BRAFL Uncharacterized protein (Fragment) OS
6.2e-12 46.1 2.7 2.9e-11 43.9 2.7 2.3 1 tr|C3ZA89|C3ZA89_BRAFL DNA-(apurinic or apyrimidinic site) l
2.5e-05 24.9 0.1 0.00014 22.5 0.1 2.5 1 tr|C3Y3Q3|C3Y3Q3_BRAFL Uncharacterized protein OS=Branchiost
------ inclusion threshold ------
0.45 11.3 1.4 0.6 10.9 0.1 1.9 2 tr|C3Y416|C3Y416_BRAFL Uncharacterized protein OS=Branchiost
Domain annotation for each sequence (and alignments):
>> tr|C3Z742|C3Z742_BRAFL DNA topoisomerase (Fragment) OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_64736 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.1 0.1 0.12 7e+02 2 18 .. 298 314 .. 297 315 .. 0.83
2 ? -4.0 0.3 4.7 2.7e+04 16 27 .. 472 483 .. 470 486 .. 0.80
3 ! 56.2 3.7 7.5e-19 4.3e-15 2 45 .] 515 557 .. 514 557 .. 0.95
4 ! 67.8 5.9 1.8e-22 1e-18 1 44 [. 623 666 .. 623 667 .. 0.97
Alignments for each domain:
== domain 1 score: 1.1 bits; conditional E-value: 0.12
zf-GRF 2 lCk.cgrlavlltvrktg 18
C+ cg+ v++t + +g
tr|C3Z742|C3Z742_BRAFL 298 PCPqCGESMVIKTRK-DG 314
5999********985.55 PP
== domain 2 score: -4.0 bits; conditional E-value: 4.7
zf-GRF 16 ktgpNkGRkFYk 27
+ g ++R F++
tr|C3Z742|C3Z742_BRAFL 472 NRGAGNTRDFHT 483
6788899*9996 PP
== domain 3 score: 56.2 bits; conditional E-value: 7.5e-19
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45
C cg+ a+lltvrk+g N GR+FYkC+ ++ C FF Wad++
tr|C3Z742|C3Z742_BRAFL 515 VCICGQNARLLTVRKEGNNCGRQFYKCSRMDN-PCDFFLWADDN 557
7******************************8.8********85 PP
== domain 4 score: 67.8 bits; conditional E-value: 1.8e-22
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
p+C+cg+++v++tv+k+g NkGR+F++C k++++qCgFF+Wad+
tr|C3Z742|C3Z742_BRAFL 623 PQCNCGQPSVTRTVQKEGNNKGRQFHTCVKPRGEQCGFFQWADA 666
79****************************************97 PP
>> tr|C3YZ80|C3YZ80_BRAFL Uncharacterized protein (Fragment) OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_82922 PE=4
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.7 0.2 0.9 5.1e+03 25 31 .. 209 215 .. 203 227 .. 0.79
2 ? -0.7 2.6 0.43 2.4e+03 5 32 .. 231 257 .. 228 260 .. 0.78
3 ! 46.8 7.1 6.3e-16 3.6e-12 1 42 [. 492 533 .. 492 535 .. 0.96
Alignments for each domain:
== domain 1 score: -1.7 bits; conditional E-value: 0.9
zf-GRF 25 FYkCpkg 31
FYkC k
tr|C3YZ80|C3YZ80_BRAFL 209 FYKCRKE 215
9***764 PP
== domain 2 score: -0.7 bits; conditional E-value: 0.43
zf-GRF 5 cgrlavlltvrktgpNkGRkFYkCpkgk 32
cg+ + tv + g+N GR Y C ++
tr|C3YZ80|C3YZ80_BRAFL 231 CGQCQGRITVCRMGEN-GRMTYFCEGCQ 257
8877777788778877.99999998877 PP
== domain 3 score: 46.8 bits; conditional E-value: 6.3e-16
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWa 42
plC++g+++v +tv k+g N+G++FY+C + ++kqC FF+ +
tr|C3YZ80|C3YZ80_BRAFL 492 PLCNHGKRCVKRTVLKQGVNNGKNFYTCRLERGKQCPFFQHC 533
79*************************************966 PP
>> tr|C3ZA89|C3ZA89_BRAFL DNA-(apurinic or apyrimidinic site) lyase OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_124
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 43.9 2.7 5.1e-15 2.9e-11 1 42 [. 507 555 .. 507 558 .. 0.93
Alignments for each domain:
== domain 1 score: 43.9 bits; conditional E-value: 5.1e-15
zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42
p Ck + +++vl+tv+k+gpN G++FY+C+ +++ + C F+W+
tr|C3ZA89|C3ZA89_BRAFL 507 PPCKgHREPCVLRTVKKQGPNFGKQFYVCARPQGhssnpaARCDHFQWV 555
57**777*************************9999999999******7 PP
>> tr|C3Y3Q3|C3Y3Q3_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_85516 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 22.5 0.1 2.5e-08 0.00014 12 38 .. 3 28 .. 1 32 [. 0.87
Alignments for each domain:
== domain 1 score: 22.5 bits; conditional E-value: 2.5e-08
zf-GRF 12 ltvrktgpNkGRkFYkCpkgkekqCgF 38
+t +gpNkG+ FY C++ + +CgF
tr|C3Y3Q3|C3Y3Q3_BRAFL 3 KTGLSEGPNKGKSFYICSQMPQ-SCGF 28
677789**************96.8**9 PP
>> tr|C3Y416|C3Y416_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_84848 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.2 0.1 1.3 7.4e+03 2 7 .. 6 12 .. 5 15 .. 0.74
2 ? 10.9 0.1 0.0001 0.6 17 31 .. 59 73 .. 54 79 .. 0.83
Alignments for each domain:
== domain 1 score: -2.2 bits; conditional E-value: 1.3
zf-GRF 2 lCk.cgr 7
C+ cg+
tr|C3Y416|C3Y416_BRAFL 6 VCPiCGE 12
7888885 PP
== domain 2 score: 10.9 bits; conditional E-value: 0.0001
zf-GRF 17 tgpNkGRkFYkCpkg 31
+ pN+GR +Y C +
tr|C3Y416|C3Y416_BRAFL 59 DHPNPGRRYYGCHRR 73
78**********866 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (45 nodes)
Target sequences: 28542 (13248087 residues searched)
Passed MSV filter: 1830 (0.064116); expected 570.8 (0.02)
Passed bias filter: 611 (0.021407); expected 570.8 (0.02)
Passed Vit filter: 46 (0.00161166); expected 28.5 (0.001)
Passed Fwd filter: 17 (0.000595613); expected 0.3 (1e-05)
Initial search space (Z): 28542 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.10
# Mc/sec: 5961.64
//
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