# 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/TruD.hmm.txt # target sequence database: proteomes/Trichoplax_adhaerens.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TruD [M=416] Accession: PF01142.17 Description: tRNA pseudouridine synthase D (TruD) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-72 242.7 0.0 3.8e-65 219.7 0.0 3.3 3 tr|B3RVM0|B3RVM0_TRIAD Uncharacterized protein OS=Trichoplax 1.6e-66 224.3 0.0 2.4e-66 223.7 0.0 1.2 1 tr|B3RRZ1|B3RRZ1_TRIAD Uncharacterized protein OS=Trichoplax Domain annotation for each sequence (and alignments): >> tr|B3RVM0|B3RVM0_TRIAD Uncharacterized protein OS=Trichoplax adhaerens OX=10228 GN=TRIADDRAFT_23629 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.1 0.0 1.1e-07 0.00062 2 32 .. 61 91 .. 60 103 .. 0.87 2 ? -2.7 0.0 0.21 1.2e+03 211 247 .. 115 149 .. 102 161 .. 0.70 3 ! 219.7 0.0 6.6e-69 3.8e-65 39 416 .] 215 601 .. 202 601 .. 0.91 Alignments for each domain: == domain 1 score: 18.1 bits; conditional E-value: 1.1e-07 TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32 +gi y+++ ++i+G+++++ DFiV+Ei+ tr|B3RVM0|B3RVM0_TRIAD 61 VGITEYISQLDPIQGSIKQRFADFIVHEINL 91 89***************************54 PP == domain 2 score: -2.7 bits; conditional E-value: 0.21 TruD 211 reavaetgdleealeelpkslryEramlkrLaekpkd 247 +++ + dle+ l+el +s + ++++ L+e++ + tr|B3RVM0|B3RVM0_TRIAD 115 DNMI--STDLENRLQELSSSHSSKKSVIIDLKENESN 149 3333..7899999999999999999999999995433 PP == domain 3 score: 219.7 bits; conditional E-value: 6.6e-69 TruD 39 akegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeeleklei..kdvelevvgrarrklrlG 123 +++++y+ +r+ k+n+dt+++++ + + +g++ + +g+aGtKD+rA+TtQ i+ kv p++l++++ ++v+l ++ ++ +l+lG tr|B3RVM0|B3RVM0_TRIAD 215 NEHDKYCKFRLYKENIDTMNAINLICKFTGLKPSIFGYAGTKDRRAITTQEITAFKVLPSKLHHVNSvtHKVRLGNFTYSKDRLTLG 301 567899*******************************************************999954469***************** PP TruD 124 dLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtrea 210 dLaGN+F++++r+v+ + ++++e+ +++lke+g + Ny+G+QRFG+ t+ +Gka++ g++++ +e ++ kp+ ++s +t ea tr|B3RVM0|B3RVM0_TRIAD 302 DLAGNHFTLTLRNVKGS---EEQIEKSMASLKETG-FINYYGLQRFGTSHIPTYQIGKALLLGNWRKSIE-LILKPTRTDSFRTMEA 383 *************8433...469**********99.********************************97.6779999********* PP TruD 211 reavaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296 re+ ++++d ++al++l ++ +E +lk L+e +++ A+ ++p+n + l+v +yqS ++N v s+R+++ +pv GD+vi tr|B3RVM0|B3RVM0_TRIAD 384 REHWWQHRDPSAALRLLRSRRGIEYYLLKGLVEhGSTSPVTAIMKIPRNARLLYVYSYQSLIWNLVASRRIKEF-G-LKPVVGDLVI 468 *********************************3456689********************************98.4.48******** PP TruD 297 faeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaill 383 ++ r ++ + +++ +++pl+G++++ ++ e+++ ++ ++ +g++ ++ + + +e+s G +R++++ tr|B3RVM0|B3RVM0_TRIAD 469 SNSAR-----------QQDLPHYS------IHDIVLPLPGYNVMYPQHEANDWYHQQMKADGISIKNLENRH-KEFSLCGMYRKLVV 537 99655...........33333333......34689**********************************554.7************* PP TruD 384 rve..............................dlelsaeede.ltleFsLpkGsYATvvlrEi 416 r++ ++++ + ++ l+l+FsLp+ sYAT+ lrE+ tr|B3RVM0|B3RVM0_TRIAD 538 RPKnlswstaryddftiplystdldqirqnkiiNNSVADGKNLaLLLSFSLPPSSYATMALREV 601 ****************************99987444444443359******************6 PP >> tr|B3RRZ1|B3RRZ1_TRIAD Uncharacterized protein OS=Trichoplax adhaerens OX=10228 GN=TRIADDRAFT_22091 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 223.7 0.0 4.1e-70 2.4e-66 38 416 .] 203 629 .. 187 629 .. 0.86 Alignments for each domain: == domain 1 score: 223.7 bits; conditional E-value: 4.1e-70 TruD 38 eakegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.....eikdvelevvgrarrk 119 ++++ yl + ++krn++tld+++++a+alg + +++++aG+KD rA+T+Q +++++v+p+++ ++ + ++++ + + + + tr|B3RRZ1|B3RRZ1_TRIAD 203 NNDNPLYLKFILRKRNVETLDAIHKIAKALGCHLSDFSYAGIKDCRAITYQQVTVKNVKPQQMINAlqkikSQEHIQYGNYQFIHTP 289 34445569999***************************************************76666744444788889999999** PP TruD 120 lrlGdLaGNkFeirvrdv.aeee........eaakraeeileelkekggvPNyfGvQRFGsr..rpvthlvGkaivkgdleeAveay 195 +rlG+L+GN+F+i +rd+ +++ ++ +++ + +ee+k++g + NyfG QRFG++ +++ +G a++++d + Ave + tr|B3RRZ1|B3RRZ1_TRIAD 290 IRLGQLKGNRFRILLRDIrLQDHdsslidiaDLHSQIIQSMEEVKKQG-FINYFGNQRFGKTisTVNSYDIGLAMLRRDEKMAVELI 375 ******************754447999988888888999999999988.***********96336799******************* PP TruD 196 vgkpfeeese.dtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylFNrvlse 278 +++ e+ s+ t +a +++ +gdl + l+++p+ + +lk+L + + + y+kAl ++p+n++++++h+y S l+Nr+++ tr|B3RRZ1|B3RRZ1_TRIAD 376 LSTVDEDISDnATMQALKYYHTSGDLVSTLKKIPSYKSRVYLILKALHRygqNIEGYRKALLNIPHNMRKIYIHSYCSLLWNRLVNY 462 **99988765157899999*9**************999888899999985556677******************************* PP TruD 279 RlerglpldepveGDvvifaeer.lpdtdrlqlvteknveevkrl....ier.grafvtaplvGtetelaegevgeierevleeegl 359 R+e++ ++veGD+v+ + + +pd++++++++++++ ++ + +++ + v++pl+G++t ++ g + +++l+++g+ tr|B3RRZ1|B3RRZ1_TRIAD 463 RIEKY--GYNVVEGDLVLLGNVDnKPDSTDTDAINQDQLVKLVTKtdlaLNKyNIYDVVLPLLGSKTIYPSNTSGSVYKDMLANDGI 547 ***99..468*******998766689999999999988655433311113331445799**************************** PP TruD 360 eledFklpklpelsskGtrRaillrve..........................dlelsaeedeltleFsLpkGsYATvvlrEi 416 + ++F p + +++ kG++R+il ++ ++++ +++ +++le +L++GsYATv lrEi tr|B3RRZ1|B3RRZ1_TRIAD 548 NDSSFVNP-MLNIKIKGAYRKILSVPKdvnfslhilncqhlhddchdccsnilKNQTCNSRFHFKLEMTLNPGSYATVCLREI 629 *****977.79***********999999*****************9999876543434444458999999************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 11518 (5222075 residues searched) Passed MSV filter: 497 (0.0431499); expected 230.4 (0.02) Passed bias filter: 221 (0.0191874); expected 230.4 (0.02) Passed Vit filter: 12 (0.00104185); expected 11.5 (0.001) Passed Fwd filter: 2 (0.000173641); expected 0.1 (1e-05) Initial search space (Z): 11518 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.07 # Mc/sec: 31034.05 // [ok]