# 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/Monodelphis_domestica.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
    ------- ------ -----    ------- ------ -----   ---- --  --------               -----------
      4e-67  227.1   0.0    5.3e-62  210.2   0.0    2.3  2  tr|F6VZX3|F6VZX3_MONDO  Uncharacterized protein OS=Monodelphi


Domain annotation for each sequence (and alignments):
>> tr|F6VZX3|F6VZX3_MONDO  Uncharacterized protein OS=Monodelphis domestica OX=13616 GN=PUS7 PE=4 SV=2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.2e-07     0.015       2      32 ..     115     145 ..     114     180 .. 0.89
   2 !  210.2   0.0   2.5e-66   5.3e-62      39     390 ..     259     593 ..     246     602 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-07
                    TruD   2 lgielyvtdtegigGrlrespeDFiVeEiee 32 
                             +gi  +v++++g+ G l+e++ DF+V+Ei +
  tr|F6VZX3|F6VZX3_MONDO 115 VGITKFVSSHQGFSGILKERYSDFVVHEIGK 145
                             89***************************54 PP

  == domain 2  score: 210.2 bits;  conditional E-value: 2.5e-66
                    TruD  39 akegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl..eikdvelevvgrarrklrlG 123
                              ++g+y+ + + k+n dt+d+++ l++ l+++ + ++++GtKDkrA+T+Q i++ k+++++l++l   + + +l ++  ++++l+lG
  tr|F6VZX3|F6VZX3_MONDO 259 RSRGSYCHFVLYKENKDTMDAINVLSKFLRVKPNIFSYMGTKDKRAITVQEIAVLKITAQRLAHLnkCLMNFKLGNFSYQKNPLKLG 345
                             567***********************************************************9996668****************** PP

                    TruD 124 dLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtrea 210
                             +L+GN+F++++r+++    + +++++ +++lke g + Ny+G+QRFG++   t+ vG+ai+++ ++e v+ ++     +e+    + 
  tr|F6VZX3|F6VZX3_MONDO 346 ELQGNHFTVVLRNITG---TDHQVQQAMNSLKEIG-FINYYGMQRFGTTAVPTYQVGRAILQNCWDEVVDLILKPRPGAEKGYLVKC 428
                             *************943...3469**********99.***********************************99999999******** PP

                    TruD 211 reavaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvi 296
                             re  a+t+d ++al++lp +  +E ++l+ L +   k++ +A+  +p+n + +++h+yqSy++N+++s+R+e++    +pv+GD+v+
  tr|F6VZX3|F6VZX3_MONDO 429 REEWAKTKDPDAALKKLPVKRCVEGQLLRGLSKyGLKNIVSAFGIIPRNNRLMYIHSYQSYVWNNMVSKRIEEY-G-LKPVQGDLVL 513
                             *********************************66799**********************************99.4.48*******9 PP

                    TruD 297 faeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaill 383
                             +   +         ++e+ v++++         v++pl+G+++  ++ + +e  +e+l  + l+ ++ + +k+ + s +G++R+i++
  tr|F6VZX3|F6VZX3_MONDO 514 KGATA-------THIEEADVNSYS------IHDVVMPLPGFDVIYPKHKISEAYKEMLTADCLNIDNMR-HKIRDYSLSGAYRKIII 586
                             99444.......455555555554......45799********************************99.5689************* PP

                    TruD 384 rvedlel 390
                             r+++++ 
  tr|F6VZX3|F6VZX3_MONDO 587 RPQNVSW 593
                             **98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (416 nodes)
Target sequences:                        21272  (11266248 residues searched)
Passed MSV filter:                       857  (0.0402877); expected 425.4 (0.02)
Passed bias filter:                      378  (0.0177698); expected 425.4 (0.02)
Passed Vit filter:                        24  (0.00112824); expected 21.3 (0.001)
Passed Fwd filter:                         1  (4.70102e-05); expected 0.2 (1e-05)
Initial search space (Z):              21272  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.29u 0.01s 00:00:00.30 Elapsed: 00:00:00.10
# Mc/sec: 46867.59
//
[ok]