# 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/UPF0020.hmm.txt
# target sequence database: proteomes/Branchiostoma_floridae.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: UPF0020 [M=197]
Accession: PF01170.17
Description: Putative RNA methylase family UPF0020
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
8.5e-18 65.4 0.2 3e-11 44.0 0.1 2.4 2 tr|C3Z2W5|C3Z2W5_BRAFL Uncharacterized protein OS=Branchiost
1.4e-10 41.9 0.0 4.3e-10 40.3 0.0 1.7 1 tr|C3Y8E7|C3Y8E7_BRAFL Uncharacterized protein (Fragment) OS
4.7e-06 27.1 0.1 9.8e-06 26.0 0.1 1.8 1 tr|C3Y4C4|C3Y4C4_BRAFL Uncharacterized protein OS=Branchiost
1.4e-05 25.5 0.0 5e-05 23.7 0.0 1.8 1 tr|C3Y1E8|C3Y1E8_BRAFL Uncharacterized protein OS=Branchiost
0.00014 22.3 0.0 0.00043 20.7 0.0 1.6 2 tr|C3YPG1|C3YPG1_BRAFL Uncharacterized protein (Fragment) OS
0.00031 21.1 0.1 0.0009 19.6 0.0 1.7 2 tr|C3XVM5|C3XVM5_BRAFL Uncharacterized protein OS=Branchiost
------ inclusion threshold ------
0.026 14.9 0.3 0.26 11.6 0.1 2.5 3 tr|C3XVW9|C3XVW9_BRAFL Uncharacterized protein OS=Branchiost
0.045 14.1 0.0 0.093 13.1 0.0 1.4 1 tr|C3ZRS9|C3ZRS9_BRAFL Uncharacterized protein OS=Branchiost
0.08 13.3 0.3 0.95 9.8 0.0 2.4 3 tr|C3ZB63|C3ZB63_BRAFL Uncharacterized protein OS=Branchiost
0.11 12.8 0.0 2.7 8.3 0.0 2.2 1 tr|C3ZHD7|C3ZHD7_BRAFL Uncharacterized protein OS=Branchiost
0.21 11.9 0.0 0.34 11.2 0.0 1.3 1 tr|C3ZB51|C3ZB51_BRAFL Uncharacterized protein OS=Branchiost
0.21 11.9 0.0 0.39 11.0 0.0 1.4 1 tr|C3YGA5|C3YGA5_BRAFL Uncharacterized protein OS=Branchiost
0.32 11.3 0.0 0.53 10.6 0.0 1.3 1 tr|C3ZXN5|C3ZXN5_BRAFL Uncharacterized protein OS=Branchiost
Domain annotation for each sequence (and alignments):
>> tr|C3Z2W5|C3Z2W5_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_66490 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 44.0 0.1 1.4e-14 3e-11 4 46 .. 328 369 .. 324 388 .. 0.89
2 ! 19.0 0.0 6.4e-07 0.0014 136 192 .. 402 461 .. 399 466 .. 0.84
Alignments for each domain:
== domain 1 score: 44.0 bits; conditional E-value: 1.4e-14
S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHH CS
UPF0020 4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEa 46
+gp++L++t+ +++r+a++++ge++ DPmCGsG+i IE
tr|C3Z2W5|C3Z2W5_BRAFL 328 Q-HFGPTTLRSTIVNSMLRIANVQAGEVICDPMCGSGAISIEC 369
3.456*************************************5 PP
== domain 2 score: 19.0 bits; conditional E-value: 6.4e-07
--HHHHHHHHHHHHHHHHHH-TT...-EEEEEESSHHHHHCC---..ESEEEEEEETTEE CS
UPF0020 136 gskkalekLYseflrelkrvlrgg.grlvlltsenkalekaleer..alrkvkeknvklg 192
gsk+ +++LY+ + r ++rv+r gr+vllt+++k+l+k+l e + k+ + ++k+g
tr|C3Z2W5|C3Z2W5_BRAFL 402 GSKQGNWELYRRTVRDMARVCRYAtGRAVLLTEDKKCLNKVLTEYdsLWSKKLVLFIKMG 461
78999*****************988*****************997555666666666555 PP
>> tr|C3Y8E7|C3Y8E7_BRAFL Uncharacterized protein (Fragment) OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_204971 PE=
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 40.3 0.0 2e-13 4.3e-10 3 138 .. 191 319 .. 190 326 .. 0.85
Alignments for each domain:
== domain 1 score: 40.3 bits; conditional E-value: 2e-13
SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHH CS
UPF0020 3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvv 89
+R+ g++++ + L+ ++ ++a +++++ +DP+ G+G++l+ a g+++ + +++ + + +++r++ k +g D +
tr|C3Y8E7|C3Y8E7_BRAFL 191 KRQHIGETSMDAGLSFVMANMAATRRNTVVFDPFVGTGSLLVSSAHFGSYVL---GTDIDSHIIHGWGRSTRHNKKWRGEDENI--- 271
5888899*********************************************...455677788999999999999*****875... PP
HHHHHHHHHTT-GGGE.EEEE--G.GG--STTS---EEEE----------H CS
UPF0020 90 qgareNaekagvgdli.efsqada.akLrlkegevdvivtnpPYGerlgsk 138
r N++++g+++l ++ + da +++ ++ + +d+ivt+pPYG+r s+
tr|C3Y8E7|C3Y8E7_BRAFL 272 ---RANLRQYGLEHLYlDVLVSDAaRSVWRPCQLFDAIVTDPPYGIREASQ 319
...57********985244444540455589999************97766 PP
>> tr|C3Y4C4|C3Y4C4_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_89653 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 26.0 0.1 4.4e-09 9.8e-06 79 134 .. 74 132 .. 24 178 .. 0.89
Alignments for each domain:
== domain 1 score: 26.0 bits; conditional E-value: 4.4e-09
EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--....STTS---EEEE------- CS
UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakLr....lkegevdvivtnpPYGer 134
+g+D+d+ ++ +++N ++ d+i+++qad+++L+ + ++ +d+++ npP+G +
tr|C3Y4C4|C3Y4C4_BRAFL 74 CVGFDIDEDALSMCQSNCTDLEL-DSIHLVQADVTHLHtcpgRWHKAFDTVIMNPPFGTK 132
68*******************98.68999*********999877789***********75 PP
>> tr|C3Y1E8|C3Y1E8_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_123579 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 23.7 0.0 2.3e-08 5e-05 49 132 .. 958 1014 .. 926 1016 .. 0.81
Alignments for each domain:
== domain 1 score: 23.7 bits; conditional E-value: 2.3e-08
HHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----- CS
UPF0020 49 lganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYG 132
++ ++++D+d+ +++ar Na +gv+d+ief q d +L + + dv+ pP+G
tr|C3Y1E8|C3Y1E8_BRAFL 958 TCER--------------------------VIAIDIDPVKLECARHNAAIYGVADRIEFLQGDYLHLA-EGLKADVVFLSPPWG 1014
3333..........................569**********************************9.5669**********9 PP
>> tr|C3YPG1|C3YPG1_BRAFL Uncharacterized protein (Fragment) OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_215391 PE=
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.2 0.0 2 4.5e+03 37 43 .. 126 132 .. 112 134 .. 0.74
2 ! 20.7 0.0 1.9e-07 0.00043 76 131 .. 141 202 .. 134 208 .. 0.85
Alignments for each domain:
== domain 1 score: -2.2 bits; conditional E-value: 2
-TTSHHH CS
UPF0020 37 CGsGtil 43
CGsG+i
tr|C3YPG1|C3YPG1_BRAFL 126 CGSGAIS 132
****996 PP
== domain 2 score: 20.7 bits; conditional E-value: 1.9e-07
H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--......STTS---EEEE---- CS
UPF0020 76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLr......lkegevdvivtnpPY 131
+++ ++D +++v+ ++ Nae+ g+ d+ ++ + + +L+ e ++dviv+npPY
tr|C3YPG1|C3YPG1_BRAFL 141 QAHCTAVDVTKEAVELTQHNAERLGLCDRLNIIKFIVLSLNdivfpaDFETKFDVIVSNPPY 202
566899********************99888888777777777788545559********** PP
>> tr|C3XVM5|C3XVM5_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_243389 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 19.6 0.0 4.1e-07 0.0009 68 124 .. 45 101 .. 15 106 .. 0.81
2 ? -1.6 0.0 1.3 2.8e+03 166 191 .. 180 205 .. 176 209 .. 0.83
Alignments for each domain:
== domain 1 score: 19.6 bits; conditional E-value: 4.1e-07
HHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---E CS
UPF0020 68 eaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdv 124
+ ++ r++ k++ D+++++++ ++e a+k g++d + +++ +a +L+ ++++vd+
tr|C3XVM5|C3XVM5_BRAFL 45 TTGTDDRKDSKVIICDINQSMLEVGKERAKKLGLEDDVVWVTGNAEELPFPDNSVDA 101
344455578889999**********************************99999995 PP
== domain 2 score: -1.6 bits; conditional E-value: 1.3
EESSHHHHHCC---ESEEEEEEETTE CS
UPF0020 166 tsenkalekaleeralrkvkeknvkl 191
++++++++++++e+ +r+v +n
tr|C3XVM5|C3XVM5_BRAFL 180 FPNQEEFAEMIREAGFRMVSYENLTS 205
678899999*****999999888765 PP
>> tr|C3XVW9|C3XVW9_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_106799 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -0.5 0.0 0.61 1.3e+03 69 100 .. 27 58 .. 9 75 .. 0.74
2 ? -2.8 0.0 3 6.6e+03 128 158 .. 236 266 .. 234 285 .. 0.63
3 ? 11.6 0.1 0.00012 0.26 23 89 .. 485 544 .. 471 552 .. 0.84
Alignments for each domain:
== domain 1 score: -0.5 bits; conditional E-value: 0.61
HHHHHHHH--EEEEES-HHHHHHHHHHHHHTT CS
UPF0020 69 aeeearaelklygsDldrrvvqgareNaekag 100
eee++++ ++++D d++ v +a++ e+
tr|C3XVW9|C3XVW9_BRAFL 27 QEEEENTDKANICADPDSSSVLKAETCKERED 58
34444455669**********99988766655 PP
== domain 2 score: -2.8 bits; conditional E-value: 3
----------HHHHHHHHHHHHHHHHHH-TT CS
UPF0020 128 npPYGerlgskkalekLYseflrelkrvlrg 158
n PY e l++k + +k l+++ ++++
tr|C3XVW9|C3XVW9_BRAFL 236 NVPYEEQLKQKTESQKVVLGKLSRAIENVNP 266
8899999999998876554444444444444 PP
== domain 3 score: 11.6 bits; conditional E-value: 0.00012
HTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHH CS
UPF0020 23 lagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvv 89
++ +++++ lD CG+Gti + a +++++ +el ++a e+a++++++ g+D+ + +
tr|C3XVW9|C3XVW9_BRAFL 485 WCDFTKDSTVLDVCCGTGTIGLTLAKHVKKVI-------GVELCQQAVEDAKVNANINGIDNAEFLC 544
58899***************999999999999.......5778999999999999999999987655 PP
>> tr|C3ZRS9|C3ZRS9_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_238289 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.1 0.0 4.2e-05 0.093 79 131 .. 74 126 .. 67 133 .. 0.90
Alignments for each domain:
== domain 1 score: 13.1 bits; conditional E-value: 4.2e-05
EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
+ Dl++r+ ++a + + +++ + ++ a L++ e++vdv++ npPY
tr|C3ZRS9|C3ZRS9_BRAFL 74 YLCTDLNPRAAECAARTGTQNNISVHPVLTDLVSALLPRLENKVDVMIFNPPY 126
5799*********99999999999999999999999999999*********** PP
>> tr|C3ZB63|C3ZB63_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_118790 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.8 0.0 0.00043 0.95 79 151 .. 84 151 .. 68 156 .. 0.76
2 ? 0.3 0.0 0.33 7.3e+02 78 114 .. 320 355 .. 313 368 .. 0.70
3 ? -3.3 0.0 4.3 9.5e+03 45 102 .. 434 493 .. 429 495 .. 0.47
Alignments for each domain:
== domain 1 score: 9.8 bits; conditional E-value: 0.00043
EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHH CS
UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflre 151
+ ++D+ ++ + r+N e g + + f qad++kL+ + +++d++ +n + s ++++L +++l++
tr|C3ZB63|C3ZB63_BRAFL 84 VTAVDFMESFI---RKNEEVNGHHKNVRFMQADVTKLEMPPKSFDIVFSN--WLMMYLSDAEVQALAEKVLTW 151
77777777777...5799999*****************9999*******9..555555555555555555555 PP
== domain 2 score: 0.3 bits; conditional E-value: 0.33
-EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG CS
UPF0020 78 klygsDldrrvvqgareNaekagvgdliefsqadaak 114
+ ++Dl ++++ a e a++ ++++ + f+ d +k
tr|C3ZB63|C3ZB63_BRAFL 320 VVTAMDLSTNMIEIATERASQENITK-VRFEISDCTK 355
5789***************9988864.4555555554 PP
== domain 3 score: -3.3 bits; conditional E-value: 4.3
HHHHHHTT--TTTT----SS.HHHHHHHHHH..HH--EEEEES-HHHHHHHHHHHHHTT-G CS
UPF0020 45 Eaallganiapgllrefvle.lkaeaeeear..aelklygsDldrrvvqgareNaekagvg 102
Ea+ + ++ +++f+ ++ a++ea+ + +k + + r +v+g + +++++++g
tr|C3ZB63|C3ZB63_BRAFL 434 EAGFINVQAED-RTQQFTDIlNREVARTEANkeEFIKEFSEEDFRYIVEGWKAKLHRCELG 493
55555555542.2222222222222333333324444666666667777777777777666 PP
>> tr|C3ZHD7|C3ZHD7_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_99360 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 8.3 0.0 0.0012 2.7 11 42 .. 53 85 .. 47 147 .. 0.84
Alignments for each domain:
== domain 1 score: 8.3 bits; conditional E-value: 0.0012
SS-HHHHHH.HHHHTT--TTS-EEETT-TTSHH CS
UPF0020 11 pLketLAaa.lvrlagwkpgepllDPmCGsGti 42
p+++++A +++ +w++g++ lD CG+G i
tr|C3ZHD7|C3ZHD7_BRAFL 53 PIQQEIAVMlMHQNFEWQEGDTVLDVGCGTGEI 85
7888888652678889**************977 PP
>> tr|C3ZB51|C3ZB51_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_68483 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.2 0.0 0.00015 0.34 79 128 .. 119 165 .. 107 189 .. 0.84
Alignments for each domain:
== domain 1 score: 11.2 bits; conditional E-value: 0.00015
EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
+ ++D+ ++ ++ +N e+ + + i+f qad++ L l++++vdv+ +n
tr|C3ZB51|C3ZB51_BRAFL 119 VTAVDFMESFIK---KNEEANRHLGNINFLQADVTRLDLPQESVDVVFSN 165
667777777764...6888888899**********************999 PP
>> tr|C3YGA5|C3YGA5_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_126775 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.0 0.0 0.00018 0.39 77 127 .. 217 267 .. 208 269 .. 0.85
Alignments for each domain:
== domain 1 score: 11.0 bits; conditional E-value: 0.00018
--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE CS
UPF0020 77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivt 127
yg+Dl +++v a++ a + g+++ i ++ da+kL+ ++++d ++t
tr|C3YGA5|C3YGA5_BRAFL 217 STYYGIDLSAEAVSMAKKEAAAKGITNVI-CNVGDATKLPeDWSEKFDYVIT 267
458**********************9988.5667******655569999998 PP
>> tr|C3ZXN5|C3ZXN5_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_105493 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 10.6 0.0 0.00024 0.53 75 126 .. 152 203 .. 132 227 .. 0.83
Alignments for each domain:
== domain 1 score: 10.6 bits; conditional E-value: 0.00024
HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEE CS
UPF0020 75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdviv 126
++ ++g Dldr +vq a + ++ g+ ++ ++q d+akL+ ++++d ++
tr|C3ZXN5|C3ZXN5_BRAFL 152 PNSTFVGTDLDRDAVQWAATESNRLGLVNTTFQVQ-DVAKLPaDWSDSFDYVL 203
45569*********************998866555.******65566888876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (197 nodes)
Target sequences: 28542 (13248087 residues searched)
Passed MSV filter: 806 (0.0282391); expected 570.8 (0.02)
Passed bias filter: 622 (0.0217924); expected 570.8 (0.02)
Passed Vit filter: 56 (0.00196202); expected 28.5 (0.001)
Passed Fwd filter: 13 (0.000455469); expected 0.3 (1e-05)
Initial search space (Z): 28542 [actual number of targets]
Domain search space (domZ): 13 [number of targets reported over threshold]
# CPU time: 0.23u 0.01s 00:00:00.24 Elapsed: 00:00:00.09
# Mc/sec: 28998.59
//
[ok]