# 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/Methyltr_RsmB-F.hmm.txt
# target sequence database: proteomes/Dictyostelium_discoideum.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Methyltr_RsmB-F [M=200]
Accession: PF01189.16
Description: 16S rRNA methyltransferase RsmB/F
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.6e-73 246.2 0.0 3.5e-73 245.0 0.0 1.6 1 tr|Q54TL4|Q54TL4_DICDI Uncharacterized protein OS=Dictyostel
5.9e-38 130.0 0.0 5.7e-36 123.6 0.0 2.3 1 tr|Q54FX0|Q54FX0_DICDI Uncharacterized protein OS=Dictyostel
1.2e-37 129.0 0.0 2.6e-28 98.5 0.0 3.2 2 tr|C7G023|C7G023_DICDI NOL1/NOP2/Sun family protein OS=Dicty
7.4e-33 113.4 0.0 7.1e-19 67.8 0.0 2.6 2 tr|Q55DF6|Q55DF6_DICDI Uncharacterized protein OS=Dictyostel
1e-21 77.0 3.2 9.5e-13 47.8 2.1 3.8 2 tr|Q55G09|Q55G09_DICDI Uncharacterized protein OS=Dictyostel
0.0046 16.1 0.0 0.051 12.7 0.0 2.7 2 sp|Q86AH1|MRM2_DICDI rRNA methyltransferase 2, mitochondri
------ inclusion threshold ------
0.035 13.3 0.0 0.11 11.7 0.0 1.7 2 sp|Q9GPS6|PIMT_DICDI Probable protein-L-isoaspartate O-met
0.05 12.8 0.0 0.093 11.9 0.0 1.3 1 tr|Q54UI9|Q54UI9_DICDI Uncharacterized protein OS=Dictyostel
Domain annotation for each sequence (and alignments):
>> tr|Q54TL4|Q54TL4_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0204605 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 245.0 0.0 2.2e-76 3.5e-73 2 200 .] 352 559 .. 351 559 .. 0.95
Alignments for each domain:
== domain 1 score: 245.0 bits; conditional E-value: 2.2e-76
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE- CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaP 88
l+Lapq++e++lD+ca+PGgKTt+ia++mkn+gt+vA+d+nk R+k++++n++rLgv+n +v++ D+r++++vl+g fDr+L+DaP
tr|Q54TL4|Q54TL4_DICDI 352 LALAPQPNERVLDMCASPGGKTTYIAAMMKNTGTLVANDVNKDRIKSLVANIHRLGVKNCMVSNLDGRQYPSVLSG--FDRVLVDAP 436
78*************************************************************************9..********* PP
-CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTST CS
Methyltr_RsmB-F 89 Csgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepk 171
C g+gvi++dp++k++++e+d++++++ qkell aid++ +gG++vYsTCs++veEne+v+++aL++r+ + +++t ++ +
tr|Q54TL4|Q54TL4_DICDI 437 CVGLGVISKDPQIKISKSEQDVITCTHTQKELLLKAIDSVdassPTGGIIVYSTCSLTVEENEAVVDYALRNRDVIVVDTTIEFGVD 523
****************************************999889***************************88888888677777 PP
TSSECEEC.......T-EEE-TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 172 glklgeea.......gtlrllPhtenkdgffiaklk 200
g + +e+ t+r++Pht+n+dgf++aklk
tr|Q54TL4|Q54TL4_DICDI 524 GFTSFRESrfhpslaLTKRYYPHTHNMDGFYVAKLK 559
7776666689999999******************96 PP
>> tr|Q54FX0|Q54FX0_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0188951 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 123.6 0.0 3.6e-39 5.7e-36 2 199 .. 265 496 .. 264 497 .. 0.79
Alignments for each domain:
== domain 1 score: 123.6 bits; conditional E-value: 3.6e-39
HHH---TT-EEEECS-TT-HHHHHHHHHTTT..................TSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CC CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmkn..................kgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDar 69
+ L+p+ +++i+D+caaPGgKTt+ia l+++ k +++A+d+nk ++k++++ krL++ +++l D +
tr|Q54FX0|Q54FX0_DICDI 265 YQLEPKLGDKIIDMCAAPGGKTTLIASLIQQfeinnnqnnqkyqnnneiKTEIFALDKNKGKVKKIIDLCKRLSLDkYVTCLAKDSS 351
679***********************99753222222223223222222357***********************85689999**** PP
CCHHHHCC..........--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCT CS
Methyltr_RsmB-F 70 kidkvlgg..........elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEn 146
k k + + fD++LlD PCsg+g r + + + d+++ ++ qk+l++ a+ llk+gG+lvYsTCs+++eEn
tr|Q54FX0|Q54FX0_DICDI 352 KLTKENQQdpldkirfqsNSFDKVLLDGPCSGLGSRPR---LIESSSLVDLTNSSEFQKKLIDQAVSLLKPGGILVYSTCSINPEEN 435
9988887789999**99999*************96444...44568899************************************** PP
HHHHHHHHHH-TTEEEESS..BSTTSTTSSECEEC....T-EEE-TTTTS...-SEEEEEE CS
Methyltr_RsmB-F 147 eevieeaLkkredvelvet..elsepkglklgeea....gtlrllPhten..kdgffiakl 199
e + ++L++ ++++l++ ++s+p ++g ++ r+ P +n + gffiak+
tr|Q54FX0|Q54FX0_DICDI 436 ELNVSYLLNNYPEMKLIPQipHISQPGLPNCGLTEqqckLVSRFDPSDSNigTIGFFIAKF 496
****************986212333333333333344656778888877622458999998 PP
>> tr|C7G023|C7G023_DICDI NOL1/NOP2/Sun family protein OS=Dictyostelium discoideum OX=44689 GN=DDB_G0295715 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 25.1 0.0 5.3e-09 8.5e-06 3 34 .. 206 237 .. 204 251 .. 0.81
2 ! 98.5 0.0 1.7e-31 2.6e-28 32 199 .. 268 487 .. 263 488 .. 0.91
Alignments for each domain:
== domain 1 score: 25.1 bits; conditional E-value: 5.3e-09
HH---TT-EEEECS-TT-HHHHHHHHHTTTTS CS
Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkg 34
+L+ q + ilD+caaPG+KTt i+e ++ k
tr|C7G023|C7G023_DICDI 206 FLDVQSHYNILDMCAAPGSKTTQILEDLHMKH 237
799999******************98655554 PP
== domain 2 score: 98.5 bits; conditional E-value: 1.7e-31
TTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC........--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHH CS
Methyltr_RsmB-F 32 nkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg........elfDriLlDaPCsgtgvirrdpdvklrrkekdi 110
+kg+++A+d++++R +++ ++rLg +iv++ +a++++ ++ + +DriL D+PCsg g+ r++p+v + + +
tr|C7G023|C7G023_DICDI 268 PKGCIIANDVDTNRCYMLVTQTTRLGSPAIIVTNHEAQNFPLLYSKnsdgsespIYMDRILCDVPCSGDGTTRKNPEVWKKWTHAGS 354
689**************************************999999999999999**********************777799999 PP
CCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-T.TEEEESSBSTTSTTS.SECEEC................ CS
Methyltr_RsmB-F 111 aqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkre.dvelvetelsepkgl.klgeea................ 179
+ l++lq ++ + +llk gG +vYsTCs+++ Ene+vi+++++k ++lv+++ + p+ + + g ++
tr|C7G023|C7G023_DICDI 355 IGLHQLQIKIATRGCQLLKVGGRMVYSTCSMNPVENEAVIAQIIQKSGgSIKLVDVSSQYPSLIrRPGLHSwtvidkagnfptfesq 441
9*******************************************998527889888766655431455555999999999999999* PP
..........................T-EEE-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 180 ..........................gtlrllPhtenkdgffiakl 199
+r++Ph +++ gffia l
tr|C7G023|C7G023_DICDI 442 pedkkyklsktlwpptpqeaidmhleYCMRVYPHLQDTGGFFIAVL 487
*************999999999999889999999999999999987 PP
>> tr|Q55DF6|Q55DF6_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0190459 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 42.9 0.0 1.9e-14 3e-11 2 73 .. 158 229 .. 157 239 .. 0.95
2 ! 67.8 0.0 4.4e-22 7.1e-19 32 199 .. 343 514 .. 338 515 .. 0.78
Alignments for each domain:
== domain 1 score: 42.9 bits; conditional E-value: 1.9e-14
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHH CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73
l+L+p++++ +lD+c+aPG K i++l++ +gt++ vd++++Rl ++ lk+ + n+ ++ D++k+++
tr|Q55DF6|Q55DF6_DICDI 158 LALNPKPGDNVLDICCAPGTKLCMISDLLEGNGTITGVDISESRLGTCKTILKKYKIPNARLFICDGTKFNS 229
68*****************************************************************99976 PP
== domain 2 score: 67.8 bits; conditional E-value: 4.4e-22
TTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE--CCGGGTT...T-TTHHHH.-CCHHCCHHH CS
Methyltr_RsmB-F 32 nkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCsgtgvir...rdpdvklrrkekdiaqlak 115
n++ +v ++k+R ++ a+ k + ++++ +++ ++ +gg l+D++++Da Cs ir + ++ + + + +ql +
tr|Q55DF6|Q55DF6_DICDI 343 NNNSIVSDLVEKKRKSKRASKKKTFDLEDLYFCNTFFMRY--SVGGGLYDKVIVDAECSLDASIRhllKYSKISRNLDLEKSKQLIN 427
5666777778888888888888999999888888877777..57777************999888222344444444556778999* PP
HHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEEC....T-EEE-TTTTS.-SEEEEE CS
Methyltr_RsmB-F 116 lqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeea....gtlrllPhtenkdgffiak 198
lqk l++ ++llk+gG lvYsTCs + ne v++++L+k +d+ +++ ++ + + +t r++P++ + g+fi+k
tr|Q55DF6|Q55DF6_DICDI 428 LQKGLIENGFKLLKPGGHLVYSTCSFSKDQNESVVQYLLNKYPDTSKLIPSFTTQNDIIIPFSPgfieNTFRFYPKN-GTSGMFISK 513
******************************************9976554445554444443333345599*****98.99*****99 PP
E CS
Methyltr_RsmB-F 199 l 199
+
tr|Q55DF6|Q55DF6_DICDI 514 I 514
7 PP
>> tr|Q55G09|Q55G09_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0189607 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 47.8 2.1 6e-16 9.5e-13 3 99 .. 251 348 .. 249 433 .. 0.89
2 ! 22.1 0.0 4.3e-08 6.9e-05 106 199 .. 443 542 .. 428 543 .. 0.72
Alignments for each domain:
== domain 1 score: 47.8 bits; conditional E-value: 6e-16
HH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE- CS
Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDaP 88
+L p ++ +D c+aPG KT+++++ mkn+g+++A++++++R +++ +kr ++n+ ++ + +++ + + ++ iL D
tr|Q55G09|Q55G09_DICDI 251 ILSPPPGSVCIDSCSAPGNKTSLLSAQMKNTGKIFAIEKDTKRCGTLIKLTKRSLCKNIETINDSFLNLKHDDPKfKDVEYILCDPS 337
799999*****************************************************99999888877766665789******** PP
-CCGGGTTT-T CS
Methyltr_RsmB-F 89 Csgtgvirrdp 99
Csg g+++r
tr|Q55G09|Q55G09_DICDI 338 CSGSGIVNRLD 348
*******9965 PP
== domain 2 score: 22.1 bits; conditional E-value: 4.3e-08
-CCHHCCHHHHHHHHHHH..HHHHEEEEEEEEEEES---CTCTHHHHHHHH....HH-TTEEEESS..BSTTSTTSSECEEC.T-EE CS
Methyltr_RsmB-F 106 kekdiaqlaklqkellsa..aidllkkgGvlvYsTCsvlveEneevieeaL....kkredvelvet..elsepkglklgeea.gtlr 183
+ek ++ la q +++ a++ +k ++YsTCs + Ene v+++a+ k+ e++++v++ ++++++gl + +++ +r
tr|Q55G09|Q55G09_DICDI 443 EEKRVKLLADFQLSIIQHsfAFPNVK---KVIYSTCSTHQVENEDVVKRAIdelnKDGEKWKVVKIlpHWTNSRGLPIYKNSdYSIR 526
56667777777777776511344555...49***************9998722223345677766533578888888766654789* PP
E-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 184 llPhtenkdgffiakl 199
+ P ++ + gff+a +
tr|Q55G09|Q55G09_DICDI 527 MTPSKDFTIGFFVALF 542
*************987 PP
>> sp|Q86AH1|MRM2_DICDI rRNA methyltransferase 2, mitochondrial OS=Dictyostelium discoideum OX=44689 GN=fsjB PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 12.7 0.0 3.2e-05 0.051 8 43 .. 428 463 .. 423 469 .. 0.91
2 ? -1.0 0.0 0.53 8.4e+02 108 135 .. 565 592 .. 561 608 .. 0.85
Alignments for each domain:
== domain 1 score: 12.7 bits; conditional E-value: 3.2e-05
TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSC CS
Methyltr_RsmB-F 8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdank 43
+++ ++Dl aaPGg +i e + n+g v+ vd+++
sp|Q86AH1|MRM2_DICDI 428 PGQIVVDLGAAPGGWSKYIQERVTNRGLVISVDTSS 463
67899****************************986 PP
== domain 2 score: -1.0 bits; conditional E-value: 0.53
CHHCCHHHHHHHHHHHHHHHEEEEEEEE CS
Methyltr_RsmB-F 108 kdiaqlaklqkellsaaidllkkgGvlv 135
d ++l lq+ l a+++lkkgG+ v
sp|Q86AH1|MRM2_DICDI 565 VDHSRLIDLQRLALFFAFKTLKKGGTFV 592
577889999999999**********988 PP
>> sp|Q9GPS6|PIMT_DICDI Probable protein-L-isoaspartate O-methyltransferase OS=Dictyostelium discoideum OX=44689 GN=pcm
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.7 0.0 6.7e-05 0.11 7 70 .. 124 190 .. 121 214 .. 0.81
2 ? -1.5 0.0 0.71 1.1e+03 117 135 .. 208 226 .. 188 229 .. 0.66
Alignments for each domain:
== domain 1 score: 11.7 bits; conditional E-value: 6.7e-05
-TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--...SEEEEES-CCC CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt...ntivleaDark 70
+ lD+ ++ G T+ + +lm ++g+v+ v++ e ++r +e +krL t ++ l +D+ k
sp|Q9GPS6|PIMT_DICDI 124 MSNGVALDIGSGSGYVTACLGHLMGCTGRVIGVEHIPELIERSIESIKRLDSTlldRIQFLVGDGIK 190
567789********************************************98754456666666554 PP
== domain 2 score: -1.5 bits; conditional E-value: 0.71
HHHHHHHHHHHEEEEEEEE CS
Methyltr_RsmB-F 117 qkellsaaidllkkgGvlv 135
++ +id+lk+gG +v
sp|Q9GPS6|PIMT_DICDI 208 SLQVARELIDQLKNGGRIV 226
345567789999****998 PP
>> tr|Q54UI9|Q54UI9_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB_G0281053 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.9 0.0 5.8e-05 0.093 7 81 .. 47 119 .. 43 122 .. 0.88
Alignments for each domain:
== domain 1 score: 11.9 bits; conditional E-value: 5.8e-05
-TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EE CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81
+e+ +ilD+ a+ G + + ++++++A+d++k +++++ +++ ++n++ +D++ +++ ++ fD
tr|Q54UI9|Q54UI9_DICDI 47 NENIKILDVGAGFGVLSIYA-STNYPNSEIIATDISKCMIDSLNYSIQGNQIKNVTAKVMDGQSMPELQSE-SFD 119
566679*****999877765.5568999*************************************999985.888 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (200 nodes)
Target sequences: 12739 (6856946 residues searched)
Passed MSV filter: 874 (0.0686082); expected 254.8 (0.02)
Passed bias filter: 270 (0.0211948); expected 254.8 (0.02)
Passed Vit filter: 32 (0.00251197); expected 12.7 (0.001)
Passed Fwd filter: 8 (0.000627993); expected 0.1 (1e-05)
Initial search space (Z): 12739 [actual number of targets]
Domain search space (domZ): 8 [number of targets reported over threshold]
# CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.06
# Mc/sec: 22856.49
//
[ok]