# 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/Dictyostelium_discoideum.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-75 254.2 0.2 3.4e-71 239.8 0.0 3.6 2 tr|Q86JH5|Q86JH5_DICDI Uncharacterized protein OS=Dictyostel Domain annotation for each sequence (and alignments): >> tr|Q86JH5|Q86JH5_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0216877 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 8.5 0.0 4.3e-05 0.55 2 33 .. 81 112 .. 80 143 .. 0.82 2 ! 239.8 0.0 2.6e-75 3.4e-71 42 416 .] 230 662 .. 215 662 .. 0.90 Alignments for each domain: == domain 1 score: 8.5 bits; conditional E-value: 4.3e-05 TruD 2 lgielyvtdtegigGrlrespeDFiVeEieef 33 lgi+l++ ++ G l+++ DFiV+Ei e tr|Q86JH5|Q86JH5_DICDI 81 LGIKLFLGKSGSWSGLLKQRFSDFIVNEIDEQ 112 799999999999*****************655 PP == domain 2 score: 239.8 bits; conditional E-value: 2.6e-75 TruD 42 geylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.....ei.kdvelevvgrarrklrl 122 +y+ +++ k+n+dt+d ++ ++r l+ s+k+++faGtKDkr++TtQ +++ kv+pe+l +l ++ + v++ + +++lrl tr|Q86JH5|Q86JH5_DICDI 230 PKYVEFKLCKENRDTMDTLSMMSRILRNSEKNFSFAGTKDKRGITTQRVTVWKVTPEKLVELnnrisTLsPPVRIGEYRFVENHLRL 316 5789999***************************************************99998866533589*************** PP TruD 123 GdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtre 209 GdL GN+F i++r+++ ++ + ++e +e+ k++g + NyfG+QRFG+ t+++G a+++g++e+A++ ++ +p + e++d ++ tr|Q86JH5|Q86JH5_DICDI 317 GDLSGNRFSIVIREIQGAD--DQLITESIETFKKTG-FINYFGMQRFGTGAIPTYEIGIAMIQGNWEKAAK-LILDPRDGERDDATK 399 **************94344..478999999999998.********************************86.6789*********** PP TruD 210 areavaetgdleealeelpkslryEramlkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296 ar +++etgd+++ l lp+ l+ Er++l L++ + +y+ A+ ++p++L++l+ h+yqS ++N + +R+e +++p+ GD+vi tr|Q86JH5|Q86JH5_DICDI 400 ARLYYKETGDIKKTLTMLPRGLNAERKLLLGLKNGQSSYQDAFYSIPRTLRMLYTHSYQSLIWNLMATKRIELF-GFNKPIVGDLVI 485 ************************************************************************77.9*********** PP TruD 297 faeer.............................lpdtdrlqlvteknveevkrliergr.afvtaplvGtetelaegevgeierev 353 +ee+ +++++ +v+ + ++vk+ +r + +v++pl+G +t l++ ge+ e tr|Q86JH5|Q86JH5_DICDI 486 ISEESidnkkneeeskdnnnnsndgeeeiggdetEIEEKKVIKVDYVTEDDVKN--DRYTiQQVVLPLIGGSTILPKNIIGELYVEE 570 **99999*****************999998886645555555555555555553..3333146899********************* PP TruD 354 leeegleledFklpklpelsskGtrRaillrve...............................dlelsaeedeltleFsLpkGsYA 409 l+++++++++F ++ ++ +G +R++l + + d+ + +++ + + F Lp+ +YA tr|Q86JH5|Q86JH5_DICDI 571 LAKSNIQPSQFISKN-RAIDLRGGYRKLLETAKdttykifnyddftiplalsdieilkgsqepvDVP-NGKHKAVRVCFNLPSSTYA 655 ***********9766.89**********9999999**********************9998854322.344556************* PP TruD 410 TvvlrEi 416 T+ rEi tr|Q86JH5|Q86JH5_DICDI 656 TMAYREI 662 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 12739 (6856946 residues searched) Passed MSV filter: 599 (0.047021); expected 254.8 (0.02) Passed bias filter: 164 (0.0128739); expected 254.8 (0.02) Passed Vit filter: 11 (0.00086349); expected 12.7 (0.001) Passed Fwd filter: 1 (7.84991e-05); expected 0.1 (1e-05) Initial search space (Z): 12739 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.07 # Mc/sec: 40749.85 // [ok]