# 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/RrnaAD.hmm.txt
# target sequence database: proteomes/Thermococcus_kodakarensis.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: RrnaAD [M=265]
Accession: PF00398.19
Description: Ribosomal RNA adenine dimethylase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.4e-54 181.3 0.0 2.6e-54 181.1 0.0 1.1 1 sp|Q5JI54|RSMA_THEKO Probable ribosomal RNA small subunit
4.7e-07 26.2 0.0 6.8e-07 25.7 0.0 1.2 1 tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransf
1.3e-06 24.7 0.0 1.7e-06 24.4 0.0 1.1 1 tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransf
0.00018 17.7 0.0 0.00028 17.1 0.0 1.3 1 tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE
0.00025 17.3 0.0 0.00036 16.7 0.0 1.2 1 tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransfe
0.0027 13.9 0.0 0.0037 13.4 0.0 1.1 1 tr|Q5JDP7|Q5JDP7_THEKO Predicted DNA methylase OS=Thermococc
0.01 12.0 0.0 0.014 11.6 0.0 1.2 1 tr|Q5JDR0|Q5JDR0_THEKO SAM-dependent methyltransferase, UPF0
------ inclusion threshold ------
0.016 11.4 0.0 0.02 11.0 0.0 1.1 1 tr|Q5JEU8|Q5JEU8_THEKO Predicted SAM-dependent methyltransfe
0.022 10.9 0.0 0.031 10.4 0.0 1.2 1 tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransfe
0.025 10.7 0.0 0.034 10.3 0.0 1.2 1 tr|Q5JH62|Q5JH62_THEKO Uncharacterized protein OS=Thermococc
Domain annotation for each sequence (and alignments):
>> sp|Q5JI54|RSMA_THEKO Probable ribosomal RNA small subunit methyltransferase A OS=Thermococcus kodakarensis (strain A
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 181.1 0.0 1.1e-56 2.6e-54 5 231 .. 17 226 .. 13 268 .. 0.91
Alignments for each domain:
== domain 1 score: 181.1 bits; conditional E-value: 1.1e-56
XXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHH CS
RrnaAD 5 rksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpee 93
++++gqnfl+ + +i++ ++ +++ ek+tvleigpG G+lT +L kra +v ++E+d r++++l+ + + +++++++ D+lk e pe+
sp|Q5JI54|RSMA_THEKO 17 NRDLGQNFLIVPDIIERNIERAEVGEKDTVLEIGPGLGVLTDPLSKRAGKVYAIEKDCRIVEILRREYN-WPNVEIIEGDALKVEWPEF 104
899***************************************************************777.9*****************5 PP
HCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS-- CS
RrnaAD 94 vtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPpp 182
++v+nlPy+is++ ++ll+ f ++++l++q efa+r++a+pg+k++srls+++ a + ++lv+ ++k +f+P p
sp|Q5JI54|RSMA_THEKO 105 N----------KMVSNLPYQISSPVTFKLLS-REF--ERAVLIFQLEFAERMVAKPGDKNYSRLSLMVRAKARAELVERIGKGAFWPRP 180
5..........89*****************6.555..9*************************************************** PP
SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTC CS
RrnaAD 183 kvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpg 231
kvdsa+v le+k+++ + ++ e +v++l+ +r t+s++lk+ ++
sp|Q5JI54|RSMA_THEKO 181 KVDSAVVVLEPKPPE---ERIDLNENLVKALFQHRRSTVSAALKKSAHM 226
*************98...6899999******************987665 PP
>> tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 25.7 0.0 2.9e-09 6.8e-07 22 74 .. 85 140 .. 76 156 .. 0.89
Alignments for each domain:
== domain 1 score: 25.7 bits; conditional E-value: 2.9e-09
HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTTT CS
RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkklsk 74
I+ + +++ +tv+e g+G G+lT La+ + +v ++E +++++++ +k++++
tr|Q5JGS7|Q5JGS7_THEKO 85 IIAYAGISPGDTVIEAGAGSGALTIFLANAVgptGKVISYEVRKDFYEIAKKNVEL 140
7888999************************9999*****************9983 PP
>> tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 24.4 0.0 7.2e-09 1.7e-06 22 92 .. 69 142 .. 59 166 .. 0.85
Alignments for each domain:
== domain 1 score: 24.4 bits; conditional E-value: 7.2e-09
HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92
l+ ++l++ ++vleig+G G + + + + v +E ++L+++ + +l+ +++ v+ D+ k p+
tr|Q5JEE1|Q5JEE1_THEKO 69 MLELADLKPGMNVLEIGTGSGWNAALISELVkTDVYTIERIPELVEFARRNLEraGVKNVHVILGDGTKGFPPK 142
577899*************************778999****************98899********99876666 PP
>> tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE/COQ5 family OS=Thermococcus kodakarensis (strain ATCC B
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.1 0.0 1.2e-06 0.00028 20 94 .. 31 106 .. 26 135 .. 0.88
Alignments for each domain:
== domain 1 score: 17.1 bits; conditional E-value: 1.2e-06
HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHH CS
RrnaAD 20 neIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeev 94
+eI+++ +e + vl+++ G+Gi T eLa+r +v l l e+++ + + k + + ++k + ++l+ ++ ee
tr|Q5JGN8|Q5JGN8_THEKO 31 EEIFREDAKREVKRVLDLACGTGIPTLELAERGYEVLGLDLHEEMLRVARRKAEaRGLNVKFIRGNALDISFEEEF 106
6777777778999**************************************9999999**************9965 PP
>> tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransferase, DUF890 family OS=Thermococcus kodakarensis (strain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 16.7 0.0 1.6e-06 0.00036 28 82 .. 79 136 .. 69 140 .. 0.87
Alignments for each domain:
== domain 1 score: 16.7 bits; conditional E-value: 1.6e-06
GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE- CS
RrnaAD 28 leekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kdeklkvvh 82
l+ +vleig+G ++ + +a+r+ v++ Elde++++ + +++ ++ ++k ++
tr|Q5JJ79|Q5JJ79_THEKO 79 LRGGEKVLEIGTGHTAMMALMAERLfnCDVTATELDEEFFEYAKRNIEkNGANVKPIK 136
566789*******************9999***************99996677777666 PP
>> tr|Q5JDP7|Q5JDP7_THEKO Predicted DNA methylase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.4 0.0 1.6e-05 0.0037 30 105 .. 47 134 .. 32 141 .. 0.79
Alignments for each domain:
== domain 1 score: 13.4 bits; conditional E-value: 1.6e-05
TTSEEEEES-TTTCCHHHH.HCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHHCT.........TTCCCCE CS
RrnaAD 30 ekltvleigpGkGilTeeL.akrakqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeevte.........kdsihqe 103
e + + ++g+G+G+l + a++v ++E d++ +++ +++ + + k++ v++D+ +f++ + + + ++
tr|Q5JDP7|Q5JDP7_THEKO 47 EGKVIADLGAGTGVLGIGAvLLGAENVYAVERDKEALEIARENARslgVEDKIEFVNADVSEFSVNVDT-VimnppfgsqVKHADRP 132
677899*********976526667******************9889999**************998744.23556666655555555 PP
EE CS
RrnaAD 104 fl 105
fl
tr|Q5JDP7|Q5JDP7_THEKO 133 FL 134
65 PP
>> tr|Q5JDR0|Q5JDR0_THEKO SAM-dependent methyltransferase, UPF0020 family OS=Thermococcus kodakarensis (strain ATCC BAA
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 11.6 0.0 6.1e-05 0.014 24 87 .. 121 189 .. 111 227 .. 0.83
Alignments for each domain:
== domain 1 score: 11.6 bits; conditional E-value: 6.1e-05
HHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.....TCCCEEEE-S-CCG CS
RrnaAD 24 dklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.....kdeklkvvhqDflk 87
+++ ++e tvl+ G G + e kr v +E+d++ +++ + ++ ++k++v++ D+ +
tr|Q5JDR0|Q5JDR0_THEKO 121 NTVMPREGETVLDTCMGLGYTAIEASKRGAYVITIEKDPNVIEIARINPWsrelfTGGKIQVIQGDAFE 189
5666789**********************************998876544455559**********865 PP
>> tr|Q5JEU8|Q5JEU8_THEKO Predicted SAM-dependent methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.0 0.0 8.8e-05 0.02 32 88 .. 43 104 .. 34 167 .. 0.81
Alignments for each domain:
== domain 1 score: 11.0 bits; conditional E-value: 8.8e-05
SEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGH CS
RrnaAD 32 ltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls...kdeklkvvhqDflkf 88
vl+i +G+G+ + Lak k ++vl +++ ++l ++ l+ ++ l++v+ D+ +
tr|Q5JEU8|Q5JEU8_THEKO 43 GRVLDICAGTGVAGVALAKATgaKLLTVLDARKDDLELAKEWLKiadINPELNLVQGDAREV 104
57*****************9999*******99887777777777766899999999998765 PP
>> tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 10.4 0.0 0.00013 0.031 31 90 .. 58 120 .. 40 139 .. 0.77
Alignments for each domain:
== domain 1 score: 10.4 bits; conditional E-value: 0.00013
TSEEEEES-TTTCCHHHH.HCC-.SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHH CS
RrnaAD 31 kltvleigpGkGilTeeL.akra.kqvvvlElderLakllqkkls.kdeklkvvhqDflkfet 90
k +vl++g G+G+lT ++ +k + vv + e+ +++ + ++ k v+ +fl++ +
tr|Q5JFS6|Q5JFS6_THEKO 58 KGKVLDVGCGTGVLTFKMaLKNGvEMVVGVDRKEEVIEFCNRLGDrVTKNAKFVQGNFLEMGL 120
669************998644434899988888876666666333567899999999987765 PP
>> tr|Q5JH62|Q5JH62_THEKO Uncharacterized protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 10.3 0.0 0.00015 0.034 23 91 .. 40 113 .. 36 143 .. 0.75
Alignments for each domain:
== domain 1 score: 10.3 bits; conditional E-value: 0.00015
HHHH-GGTTSEEEEES-TT.TCCHHHHHCC-...SEEEEE-S.-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHH CS
RrnaAD 23 ldklnleekltvleigpGk.GilTeeLakra...kqvvvlEl.derLakllqkklskdeklkvvhqDflkfetp 91
l+ + l+e ++vleig G +i+T++La + vv++ + + +++++ + +++++ ++ D+ + +p
tr|Q5JH62|Q5JH62_THEKO 40 LRFAPLREGMNVLEIGCGAhAITTVPLAYLVdetGRVVAVDKaRWHFFEEITSVAGLKHRIIPMKLDARELPFP 113
5667799***********73678888877776666677776536788888888555777777777777666655 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (265 nodes)
Target sequences: 2301 (637680 residues searched)
Passed MSV filter: 77 (0.0334637); expected 46.0 (0.02)
Passed bias filter: 60 (0.0260756); expected 46.0 (0.02)
Passed Vit filter: 16 (0.0069535); expected 2.3 (0.001)
Passed Fwd filter: 10 (0.00434594); expected 0.0 (1e-05)
Initial search space (Z): 2301 [actual number of targets]
Domain search space (domZ): 10 [number of targets reported over threshold]
# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8449.26
//
[ok]