# 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/Pseudomonas_aeruginosa.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
    ------- ------ -----    ------- ------ -----   ---- --  --------             -----------
    1.7e-58  196.8   0.0    9.2e-39  131.7   0.0    2.1  2  sp|Q9HY04|TRUD_PSEAE  tRNA pseudouridine synthase D OS=Pseudo


Domain annotation for each sequence (and alignments):
>> sp|Q9HY04|TRUD_PSEAE  tRNA pseudouridine synthase D OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.0   1.7e-42   9.2e-39      17     171 ..      23     172 ..      16     178 .. 0.89
   2 !   63.2   0.0     1e-21   5.8e-18     255     416 .]     191     340 ..     175     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.7e-42
                  TruD  17 rlrespeDFiVeEieefsgeeeakegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisi..rkvepeelekl 103
                            l++ +eDF V+E+ e+  +    ege+l+l+vekr+ +t +++r+l ra+g+++k+v++aG+KD++A+T+Q++s+   +    +l ++
  sp|Q9HY04|TRUD_PSEAE  23 VLKAVAEDFQVDEVLEIPLS---GEGEHLWLWVEKRGLNTEEAARRLGRAAGVQQKNVSYAGLKDRQALTRQWFSLhlPGKADPDLGAA 108
                           7999**********999553...67**************************************************83334444568888 PP

                  TruD 104 eikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileelkekggvPNyfGvQRFGs 171
                           e  d++++   r++rkl+ G +a N F++r++++ a    +++ +++ le++++ g vPNyfG+QRFG 
  sp|Q9HY04|TRUD_PSEAE 109 EGADLRILRCTRHSRKLQRGAHAANGFTLRLTGLrA----ERAPLDARLERIAADG-VPNYFGLQRFGH 172
                           99*******************************833....24689********988.***********6 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 1e-21
                  TruD 255 lpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelae 343
                            ++nL++ F++A +SylFNr+l+eR+++g +++++  GD++ f+++r     ++ l+ e++ ++++  +   + ++t+pl G   + + 
  sp|Q9HY04|TRUD_PSEAE 191 ANRNLRSRFLSAGRSYLFNRLLAERVAEG-SWNRAAVGDLLAFTDSR-----SFFLAGEEECRDAR--LAALDLHPTGPLWGEGDPPSG 271
                           5799*************************.9*************888.....77777777777776..9999***********999877 PP

                  TruD 344 gevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsa.eedeltleFsLpkGsYATvvlrEi 416
                             v + e ++   +g e++  +  +  + +++ +rR ++l+++ l+ +  e d l+leF Lp G++ATvv+rEi
  sp|Q9HY04|TRUD_PSEAE 272 AGVLDRELAL---AGREPALCRWLA--KAGMAHERRILRLPIQGLAWHYpEPDVLQLEFVLPAGCFATVVVREI 340
                           6655555544...455677666444..789999**********777665145669******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (416 nodes)
Target sequences:                         5563  (1857172 residues searched)
Passed MSV filter:                       137  (0.024627); expected 111.3 (0.02)
Passed bias filter:                      108  (0.019414); expected 111.3 (0.02)
Passed Vit filter:                        11  (0.00197735); expected 5.6 (0.001)
Passed Fwd filter:                         1  (0.000179759); expected 0.1 (1e-05)
Initial search space (Z):               5563  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.03
# Mc/sec: 25752.79
//
[ok]