Query         gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 247
No_of_seqs    126 out of 3058
Neff          7.3 
Searched_HMMs 39220
Date          Tue May 24 18:09:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780295.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00021 truA tRNA pseudouridi 100.0       0       0  576.9  20.8  244    1-246     1-244 (244)
  2 PRK12434 tRNA pseudouridine sy 100.0       0       0  577.2  19.7  244    1-246     1-245 (245)
  3 COG0101 TruA Pseudouridylate s 100.0       0       0  568.7  18.9  244    1-246     1-244 (266)
  4 cd02570 PseudoU_synth_EcTruA P 100.0       0       0  556.3  19.0  239    6-246     1-239 (239)
  5 cd00497 PseudoU_synth_TruA_lik 100.0       0       0  514.1  18.2  219    8-246     1-224 (224)
  6 TIGR00071 hisT_truA tRNA pseud 100.0       0       0  516.5  15.6  237    2-241     1-326 (326)
  7 cd02866 PseudoU_synth_TruA_Arc 100.0       0       0  511.9  17.6  217    6-246     1-221 (221)
  8 cd02569 PseudoU_synth_ScPus3 P 100.0       0       0  500.3  17.1  223    6-246     1-256 (256)
  9 cd02568 PseudoU_synth_PUS1_PUS 100.0       0       0  492.2  16.5  223    6-246     1-245 (245)
 10 KOG2553 consensus              100.0       0       0  377.2  13.0  241    2-247    37-329 (416)
 11 KOG4393 consensus              100.0       0       0  351.8  11.0  245    2-246     5-276 (295)
 12 KOG2554 consensus              100.0       0       0  342.8  13.0  226    3-246    67-320 (425)
 13 pfam01416 PseudoU_synth_1 tRNA 100.0 3.2E-30 8.1E-35  195.5   6.2  103  145-247     1-103 (103)
 14 pfam10105 DUF2344 Uncharacteri  97.0   0.012   3E-07   35.6   9.5  143   25-186    18-172 (186)
 15 COG1258 Predicted pseudouridyl  91.9    0.34 8.6E-06   27.1   4.7  153   23-194   189-355 (398)
 16 pfam01416 PseudoU_synth_1 tRNA  87.7 0.00089 2.3E-08   42.1 -11.2   53    8-63      3-76  (103)
 17 cd01291 PseudoU_synth PseudoU_  86.4       1 2.6E-05   24.4   3.8   40   22-63      4-43  (87)
 18 COG5011 Uncharacterized protei  82.0     2.6 6.7E-05   22.0   4.4   73   42-116    45-118 (228)
 19 PRK10187 trehalose-6-phosphate  76.7     3.2 8.3E-05   21.4   3.5   48    3-51     14-63  (266)
 20 TIGR01227 hutG formimidoylglut  63.6     6.6 0.00017   19.6   2.7   23  137-159   234-256 (328)
 21 TIGR01213 TIGR01213 conserved   43.7      26 0.00067   16.2   3.7  154   25-194   243-412 (450)
 22 pfam02358 Trehalose_PPase Treh  42.8      24 0.00062   16.4   2.8   43    8-51      2-46  (235)
 23 TIGR02735 purC_vibrio phosphor  39.1      18 0.00047   17.1   1.7   32   48-80     14-45  (365)
 24 pfam05125 Phage_cap_P2 Phage m  38.7      23 0.00058   16.5   2.1   33   24-56     29-80  (333)
 25 TIGR01892 AcOrn-deacetyl acety  35.6      13 0.00034   17.9   0.5   14   48-61    196-209 (386)
 26 PRK05647 purN phosphoribosylgl  33.8      38 0.00097   15.2   4.9   91    1-106     1-102 (200)
 27 TIGR00130 frhD coenzyme F420-r  31.0       5 0.00013   20.3  -2.2   62   40-107    36-100 (162)
 28 TIGR02407 ectoine_ectB diamino  30.7      27  0.0007   16.1   1.5   31  184-223   341-372 (413)
 29 TIGR02774 rexB_recomb ATP-depe  27.5      27 0.00068   16.1   1.0   96  138-239   263-367 (1116)
 30 TIGR02311 HpaI 2,4-dihydroxyhe  24.9      50  0.0013   14.5   2.0   23   17-39    179-201 (249)
 31 TIGR02635 RhaI_grampos L-rhamn  24.8      45  0.0011   14.8   1.7   31   11-41     23-55  (382)
 32 pfam03645 Tctex-1 Tctex-1 fami  24.7      53  0.0013   14.4   2.1   38   25-62     31-72  (101)
 33 COG1877 OtsB Trehalose-6-phosp  24.7      55  0.0014   14.3   4.1   58    2-60     17-76  (266)
 34 TIGR01900 dapE-gram_pos succin  24.7      55  0.0014   14.3   3.7   84   25-116    16-115 (373)
 35 TIGR02610 PHA_gran_rgn putativ  24.6      43  0.0011   14.9   1.6   52   31-83     21-90  (91)
 36 KOG2894 consensus               22.4      61  0.0016   14.0   4.3   17  194-210   272-288 (331)
 37 pfam09153 DUF1938 Domain of un  22.2      59  0.0015   14.1   1.9   26  182-207    25-50  (86)
 38 TIGR01484 HAD-SF-IIB HAD-super  21.4      64  0.0016   13.9   2.5   52    6-58      2-55  (261)
 39 TIGR01822 2am3keto_CoA 2-amino  21.0      55  0.0014   14.3   1.6   69   26-116    85-153 (395)
 40 cd01243 PH_MRCK MRCK (myotonic  20.7      46  0.0012   14.7   1.1   36   12-47      1-36  (122)
 41 pfam07782 DC_STAMP DC-STAMP-li  20.3      41   0.001   15.0   0.8   35  179-213    94-128 (191)

No 1  
>PRK00021 truA tRNA pseudouridine synthase A; Validated
Probab=100.00  E-value=0  Score=576.91  Aligned_cols=244  Identities=49%  Similarity=0.775  Sum_probs=240.0

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf             92299999971668720048753877889999999997099569997112138612223468864063211046899999
Q gi|254780295|r    1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN   80 (247)
Q Consensus         1 M~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN   80 (247)
                      |+||++.|+||||+|+|||+||+.+||||+||+||.++.++++.+.+|||||+||||++||+||+++.+++++.+..+||
T Consensus         1 M~r~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~l~~~lN   80 (244)
T PRK00021          1 MMRYALTIEYDGTNFHGWQRQPNVRTVQGELEKALSKIAGEPVRVIGAGRTDAGVHALGQVAHFDTPADRPPEKWRRALN   80 (244)
T ss_pred             CCEEEEEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             93799999997998128735889989999999999997498538998514667843246689997388899999999998


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECC
Q ss_conf             86188876543443226777550002100223556852443202333210244333335665565676520011001024
Q gi|254780295|r   81 AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS  160 (247)
Q Consensus        81 ~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~  160 (247)
                      +.|  |+||+|+++.+|+++||||++|++|+|+|+|++++.++++.++++|+.+.+||+++|++|++.|+|+|||++||+
T Consensus        81 ~~L--p~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~f~G~HDF~~F~~  158 (244)
T PRK00021         81 ALL--PDDIAVLWAEEVPDDFHARFSATARRYRYRIYNRPFRPPLLRGYVWHYPRPLDVEAMNEAAQYLLGTHDFTSFRA  158 (244)
T ss_pred             HHC--CHHHHHHEEEECCCCCCEEEECCEEEEEEEEECCCCCCHHHCCCCEEECCCCCHHHHHHHHHHHCCCCCHHHCCC
T ss_conf             668--740334310224887462750302699998505777983552661344376669999999998138843441047


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             56553332110331111233320011315888899999999999999976899888999998358821166636989847
Q gi|254780295|r  161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY  240 (247)
Q Consensus       161 ~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~  240 (247)
                      .+++.++++|+|++++|.+.++.+.|+|+|+||||||||+|||+++++|+|++++++|+++|++++|...+++|||+||+
T Consensus       159 ~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~sFL~~mVR~mVg~ll~v~~g~~~~~~i~~~l~~~~r~~~~~~APa~GL~  238 (244)
T PRK00021        159 SGCQSKSPVRTIYEADVTRDGDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEWIKELLEAKDRKLAGPTAPAEGLY  238 (244)
T ss_pred             CCCCCCCCCEEEEEEEEEEECCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf             99999997279999999992888999987778999999999999999987999999999998667855587745898758


Q ss_pred             EEEEEE
Q ss_conf             633043
Q gi|254780295|r  241 FDSVEY  246 (247)
Q Consensus       241 L~~V~Y  246 (247)
                      |++|.|
T Consensus       239 L~~V~Y  244 (244)
T PRK00021        239 LVRVDY  244 (244)
T ss_pred             EEEEEC
T ss_conf             931299


No 2  
>PRK12434 tRNA pseudouridine synthase A; Reviewed
Probab=100.00  E-value=0  Score=577.17  Aligned_cols=244  Identities=38%  Similarity=0.629  Sum_probs=238.8

Q ss_pred             CCEEEEEEEECCCCCEEEEECC-CCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHH
Q ss_conf             9229999997166872004875-387788999999999709956999711213861222346886406321104689999
Q gi|254780295|r    1 MIRYCMIIEYNGSGYFGWQRQK-NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKAL   79 (247)
Q Consensus         1 M~r~~~~i~YdGt~y~G~q~Q~-~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~l   79 (247)
                      |.||++.|+||||+|+|||+|| +.+||||+||+||.+++++++.+.+|||||+||||++||+||+++..++++.+.++|
T Consensus         1 M~~~~l~i~YdGt~f~G~Q~Q~~~~~TVq~~le~aL~~~~~~~v~~~~agRTD~GVHA~~Qv~~f~~~~~~~~~~l~~~l   80 (245)
T PRK12434          1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTGEEIELIGCGRTDAGVHALNQVANFHTDEKLSEDKIKKYL   80 (245)
T ss_pred             CCEEEEEEEEECCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             94799999990897016867799898889999999999749971899876787882815008999758879989999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEEC
Q ss_conf             98618887654344322677755000210022355685244320233321024433333566556567652001100102
Q gi|254780295|r   80 NAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFR  159 (247)
Q Consensus        80 N~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~  159 (247)
                      |+.|  |+||+|+++.+||++|||||+|++|+|+|+|.+++.++||.+++.|+++++||+++|++|++.|+|+|||++||
T Consensus        81 N~~L--P~dI~v~~~~~v~~~FhaR~~a~~r~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~m~~a~~~~~G~HDF~~F~  158 (245)
T PRK12434         81 NEYL--PNDIVVTNVEEVSERFHARYNVKSKTYLYKIWNEKFHDVFMRKYSYHVNEKLDVKAMKEAAKYLVGSHDFTSFT  158 (245)
T ss_pred             HHHC--CCCCCCCEEEECCCCCCCCCCCCCCEEEEEECCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHC
T ss_conf             8268--98751255685699968642176651897755788899778576533050226999999998711776589870


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             45655333211033111123332001131588889999999999999997689988899999835882116663698984
Q gi|254780295|r  160 SIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGL  239 (247)
Q Consensus       160 ~~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL  239 (247)
                      +.+++.++++|+|++++|.+.++.+.|+|+||||||||||+|||+|++||+|++++++|+++|++++|..+.|+|||+||
T Consensus       159 ~~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL  238 (245)
T PRK12434        159 NAKSKKKSTVRTIYSIDIMEEDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKDILEAKDRNQANCTAPASGL  238 (245)
T ss_pred             CCCCCCCCCEEEEEEEEEEECCEEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             77989999749999999996675999986665889999999999999998699999999999857883348886699877


Q ss_pred             EEEEEEE
Q ss_conf             7633043
Q gi|254780295|r  240 YFDSVEY  246 (247)
Q Consensus       240 ~L~~V~Y  246 (247)
                      ||++|+|
T Consensus       239 ~L~~V~Y  245 (245)
T PRK12434        239 YLENVEY  245 (245)
T ss_pred             EECCCCC
T ss_conf             8811599


No 3  
>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=568.67  Aligned_cols=244  Identities=46%  Similarity=0.722  Sum_probs=239.5

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf             92299999971668720048753877889999999997099569997112138612223468864063211046899999
Q gi|254780295|r    1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN   80 (247)
Q Consensus         1 M~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN   80 (247)
                      |+||++.|+||||+|+|||+||+.+||||+||+||.++.++++.+.+|||||+||||.|||+||+++....+..+..+||
T Consensus         1 m~ri~l~iaYdGt~f~G~Q~Qp~~~TVQ~~le~aL~~i~~~~~~i~~AGRTD~GVHA~gqv~hfd~~~~~~~~~~~~~lN   80 (266)
T COG0101           1 MKRIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGGESVRVIGAGRTDAGVHALGQVVHFDTPADRPLEKLVRALN   80 (266)
T ss_pred             CCEEEEEEEECCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             93299999985872002502899998899999999996287641688667875766255579997677655899999998


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECC
Q ss_conf             86188876543443226777550002100223556852443202333210244333335665565676520011001024
Q gi|254780295|r   81 AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS  160 (247)
Q Consensus        81 ~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~  160 (247)
                      ++|  |+||+|+++.+||++|||||+|++|+|+|.|++...+++++.+++|+++++||+++|++|++.|+|+|||++||+
T Consensus        81 ~~L--p~dI~V~~~~~v~~~FhaRfsa~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~HDF~sF~~  158 (266)
T COG0101          81 ALL--PPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRK  158 (266)
T ss_pred             HCC--CCCCEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             319--988489998877999887504262689999757667886661322014676789999999987234445311025


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             56553332110331111233320011315888899999999999999976899888999998358821166636989847
Q gi|254780295|r  161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY  240 (247)
Q Consensus       161 ~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~  240 (247)
                      .+++.++++|||++++|.+.++++.|+|+||||||||||+|||+|++||+|+++++++.++|++++|..++|+|||+||+
T Consensus       159 ~~~~~~s~vRti~~~~v~~~~~~i~i~i~g~sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~~~~~~Apa~GL~  238 (266)
T COG0101         159 AGCQSKSPVRTIYRIDVSRDGDLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLY  238 (266)
T ss_pred             CCCCCCCCEEEEEEEEEEECCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf             78846897699999999963998999999575589999999999999858999999999987523844477888987308


Q ss_pred             EEEEEE
Q ss_conf             633043
Q gi|254780295|r  241 FDSVEY  246 (247)
Q Consensus       241 L~~V~Y  246 (247)
                      |++|.|
T Consensus       239 L~~v~Y  244 (266)
T COG0101         239 LVRVDY  244 (266)
T ss_pred             EEEECC
T ss_conf             974204


No 4  
>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E.  coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA.  psi38 and psi39 in tRNAs are highly phylogenetically conserved.  P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.
Probab=100.00  E-value=0  Score=556.31  Aligned_cols=239  Identities=47%  Similarity=0.769  Sum_probs=234.2

Q ss_pred             EEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCC
Q ss_conf             99997166872004875387788999999999709956999711213861222346886406321104689999986188
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI   85 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~   85 (247)
                      |+|+||||+|+|||+||+.+|||++||+||.++.++++.+.+|||||+||||++|+++|+++.+++++.+...||++|  
T Consensus         1 l~i~Y~Gt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~l~~~LN~~L--   78 (239)
T cd02570           1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAGEPVRVIGAGRTDAGVHALGQVAHFDTPSEIPLEKLIKALNSLL--   78 (239)
T ss_pred             CEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHC--
T ss_conf             989995898027707869989999999999998498648998415677854101199997478899999999998549--


Q ss_pred             CCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCCCCCC
Q ss_conf             87654344322677755000210022355685244320233321024433333566556567652001100102456553
Q gi|254780295|r   86 SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA  165 (247)
Q Consensus        86 p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~~~~~  165 (247)
                      |+||+|+++.+|+++||||++|++|+|+|+|.++..++|++++++|+++.++|+++|++|++.|+|+|||++||+.+++.
T Consensus        79 P~dI~i~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~~~~a~~~~~G~HdF~~F~~~~~~~  158 (239)
T cd02570          79 PPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQS  158 (239)
T ss_pred             CCCEEEEEEEECCCCCCEEEECCEEEEEEEECCCCCCCHHHCCCEEEECCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCC
T ss_conf             99869999698288756176033479999961688899667774566646465999999998705881356432799999


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             33211033111123332001131588889999999999999997689988899999835882116663698984763304
Q gi|254780295|r  166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE  245 (247)
Q Consensus       166 ~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~  245 (247)
                      ++++|+|++++|.+.++++.|+|+|+||||||||+|||++++||+|++++++|+++|++++|....++|||+||||++|.
T Consensus       159 ~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mvG~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~  238 (239)
T cd02570         159 KSTVRTIYRADVYREGDLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYLVKVE  238 (239)
T ss_pred             CCCEEEEEEEEEEECCCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEECCCC
T ss_conf             99708999999998599899998677789999999999999998799999999999867885558673489876890039


Q ss_pred             E
Q ss_conf             3
Q gi|254780295|r  246 Y  246 (247)
Q Consensus       246 Y  246 (247)
                      |
T Consensus       239 Y  239 (239)
T cd02570         239 Y  239 (239)
T ss_pred             C
T ss_conf             9


No 5  
>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67.  C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph
Probab=100.00  E-value=0  Score=514.10  Aligned_cols=219  Identities=34%  Similarity=0.499  Sum_probs=204.7

Q ss_pred             EEECCCCCEEEEECCCCCCHHHHHHHHHHHHH----CCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             99716687200487538778899999999970----99569997112138612223468864063211046899999861
Q gi|254780295|r    8 IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYL   83 (247)
Q Consensus         8 i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~----~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L   83 (247)
                      |+||||+|+|||+||+.+||||+||+||.++.    ++++.+.+|||||+||||++||+||+++.++  ..+..+||++|
T Consensus         1 i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~i~~agRTDaGVHA~~qv~~f~~~~~~--~~~~~~lN~~L   78 (224)
T cd00497           1 IAYDGWKYHGFQRQPDVPTVEGELFKALLKTGLIESPKPSNYSRAGRTDKGVSALGQVVSLETRSKL--KPYPDILNGLL   78 (224)
T ss_pred             CEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCEEEEECCCCC--HHHHHHHHHHC
T ss_conf             9476888207877888989999999999973342378705899733566782415558999877772--77999998359


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCCCC
Q ss_conf             88876543443226777550002100223556852443202333210244333335665565676520011001024565
Q gi|254780295|r   84 KISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHC  163 (247)
Q Consensus        84 ~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~~~  163 (247)
                        |+||+|+++.+|+++||||++|++|+|+|.++                ..++|+++|++|++.|+|+|||++||+.++
T Consensus        79 --p~dI~v~~~~~v~~~FhaR~~a~~r~Y~Y~~~----------------~~~ld~~~m~~a~~~~~G~HDF~~F~~~~~  140 (224)
T cd00497          79 --PKDIRVLAWAPVPEDFHARFSCVSRTYRYYFP----------------GGDLDIEAMREAAKLLLGTHDFRNFCKKDG  140 (224)
T ss_pred             --CCCCEEEEEEECCCCCCCCCCCCCEEEEEEEC----------------CCCCCHHHHHHHHHHHCCCCCHHHHHCCCC
T ss_conf             --89878989999288766443787269999675----------------898779999999998048534786217688


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCC-CCCCCCCCCCCEEE
Q ss_conf             53332110331111233320011315888899999999999999976899888999998358821-16663698984763
Q gi|254780295|r  164 QASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRK-ECGPLAPPEGLYFD  242 (247)
Q Consensus       164 ~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~-~~~~~APa~GL~L~  242 (247)
                      +.++++|||++++|.+.++++.|+|+||||||||||+|||+|++||+|++++++|.++|+.+++. ...++|||+||||+
T Consensus       141 ~~~~~vRtI~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvGtl~~vg~gk~~~~~i~~~l~~~~~~~~~~~~APa~GL~L~  220 (224)
T cd00497         141 RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGLEPPSIISRLLDEEKRPSKPQYPAPPEPLVLW  220 (224)
T ss_pred             CCCCCEEEEEEEEEEECCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEE
T ss_conf             89996599999999977989999980788999999999999999987999999999998478865569887899887893


Q ss_pred             EEEE
Q ss_conf             3043
Q gi|254780295|r  243 SVEY  246 (247)
Q Consensus       243 ~V~Y  246 (247)
                      +|.|
T Consensus       221 ~V~Y  224 (224)
T cd00497         221 DCKY  224 (224)
T ss_pred             EEEC
T ss_conf             2499


No 6  
>TIGR00071 hisT_truA tRNA pseudouridine synthase A; InterPro: IPR001406 Transfer RNA-pseudouridine synthetase contains one atom of zinc essential for its native conformation and tRNA recognition  and has a strictly conserved aspartic acid that is likely to be involved in catalysis. It is involved in the formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer-RNAs. Pseudouridine is the most abundant modified nucleoside found in all cellular RNAs.; GO: 0000049 tRNA binding, 0016439 tRNA-pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0008033 tRNA processing.
Probab=100.00  E-value=0  Score=516.48  Aligned_cols=237  Identities=40%  Similarity=0.612  Sum_probs=230.6

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHC-----------CCEEEEECCCCCCCCEEEEEEEEEEECCCC
Q ss_conf             229999997166872004875387788999999999709-----------956999711213861222346886406321
Q gi|254780295|r    2 IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-----------EIVVVHGAGRTDSGVHALRQVAHFDLVREW   70 (247)
Q Consensus         2 ~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~-----------~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~   70 (247)
                      .++++.|+|||++|+|||+||+.+||||+||+||..+..           ++++|.+||||||||||.+||+||+++.++
T Consensus         1 ~kia~~iaY~G~~y~G~Q~QP~~~Tvq~~le~aL~~~~~i~~~nS~~l~~~~~~~~~aGRTDkGVHA~~Qv~sf~~~~~~   80 (326)
T TIGR00071         1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEKIGKISKENSEDLKKKKIKVISAGRTDKGVHALGQVISFDTPKEI   80 (326)
T ss_pred             CEEEEEEEECCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCEEEEECCCCCCEECCCCEEEEEECCCC
T ss_conf             97899997447665024771888982438999999872024220000421697799943777010105647999861778


Q ss_pred             CCHHHHHH--HHHHHCCCCCCCCCC-CCCCCCCCCCEECCCCE-------------------------------------
Q ss_conf             10468999--998618887654344-32267775500021002-------------------------------------
Q gi|254780295|r   71 VPVILCKA--LNAYLKISDTISILN-LSIVDKQFHARFSAIRR-------------------------------------  110 (247)
Q Consensus        71 ~~~~~~~~--lN~~L~~p~~Irv~~-~~~v~~~FhaR~~a~~R-------------------------------------  110 (247)
                      ++..|...  ||+.|  |+||+|+. +..|+++|||||+|.+|                                     
T Consensus        81 ~~~~l~~~hvLN~~L--p~dI~v~~~~~~V~~~FhaRf~~~~R~YeYLi~~~~L~g~~~~S~L~R~~~~S~~E~~S~E~W  158 (326)
T TIGR00071        81 PDNKLNAKHVLNALL--PPDIRVKAVLEPVNDNFHARFSAQKRVYEYLIPTFSLIGPKRSSLLYRDVEESKRELESKEVW  158 (326)
T ss_pred             CHHHHHHHHHHHHCC--CCCCEEEEEEEECCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHH
T ss_conf             755557776664127--455578311120477888684333231212032110378897515665253210113314478


Q ss_pred             ----------------------------------EEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEE
Q ss_conf             ----------------------------------2355685244320233321024433333566556567652001100
Q gi|254780295|r  111 ----------------------------------SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT  156 (247)
Q Consensus       111 ----------------------------------~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~  156 (247)
                                                        .|+|.+.+...++++.. ++||+..++|+++|++|++.|+|+|||+
T Consensus       159 ~~F~~~~~~~FS~~E~~~~~~~~~~~~~~~~~~~~YrY~~~~~~~~~~~~~-~~~hy~~~ld~~~~~~a~~~~~G~hdF~  237 (326)
T TIGR00071       159 DEFKKDAREKFSTDELEALLDYVQKLRDEDDLVEHYRYILYNEKLPPLLAG-YATHYYSPLDLEKMRAAAKEFLGKHDFS  237 (326)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHCEEEECCCCCCHHHHH-HHCCCCCHHHHHHHHHHHHHCCCCCCCH
T ss_conf             899987324678789999998400000245424322021205655112342-2202253121899999876313642510


Q ss_pred             EECCCC---CCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCC
Q ss_conf             102456---55333211033111123-33200113158888999999999999999768998889999983588211666
Q gi|254780295|r  157 TFRSIH---CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP  232 (247)
Q Consensus       157 ~F~~~~---~~~~~~~R~I~~~~v~~-~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~  232 (247)
                      |||+.+   ++.++++|+|.+++|.+ .+++|.|+|.|+||||||||+|||+|++||++++++++|+.+|+.++|..+.+
T Consensus       238 nF~~~~~~~~~~~~~~R~i~~~~~~~~~~~~~~~~I~G~~FL~~mVR~iV~~l~~~g~~~~~~e~~~~ll~~~~r~~~~~  317 (326)
T TIGR00071       238 NFSKAKGAKSKSRSPVRTISKIKVSEESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVQKLLDAKKRELAPT  317 (326)
T ss_pred             HHCCCCCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             01000025677777258898889962588889999885430388899999999997516888899999854677575676


Q ss_pred             CCCCCCCEE
Q ss_conf             369898476
Q gi|254780295|r  233 LAPPEGLYF  241 (247)
Q Consensus       233 ~APa~GL~L  241 (247)
                      +||++||+|
T Consensus       318 ~ap~~gL~L  326 (326)
T TIGR00071       318 TAPANGLYL  326 (326)
T ss_pred             CCCCCCCCC
T ss_conf             887567889


No 7  
>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,. This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. This group of proteins make Psedouridine in tRNAs.
Probab=100.00  E-value=0  Score=511.94  Aligned_cols=217  Identities=36%  Similarity=0.591  Sum_probs=204.3

Q ss_pred             EEEEECCCCCEEEEECCCCCCHHHHHHHHHHHH----HCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             999971668720048753877889999999997----0995699971121386122234688640632110468999998
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLV----TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNA   81 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~----~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~   81 (247)
                      |.|+||||+|+|||+||+.+||||+||+||.++    .++++++.+|||||+||||++||+||+++.+..    .+.||.
T Consensus         1 l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~~agRTDaGVHA~~qv~~f~~~~~~~----~~~lN~   76 (221)
T cd02866           1 LKVAYDGTPYHGFQRQPDVRTVEGELIKALRRLGIIESPKRPRLYSAGRTDAGVSALGNVVAFETEKELT----PPAINN   76 (221)
T ss_pred             CEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCEEEEEEEEECCCCCC----HHHHHH
T ss_conf             9899928982368888989899999999999723310598258998515778852000389995674013----899983


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCC
Q ss_conf             61888765434432267775500021002235568524432023332102443333356655656765200110010245
Q gi|254780295|r   82 YLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSI  161 (247)
Q Consensus        82 ~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~  161 (247)
                      .|  |+||+|+++.+|+++|||||+|++|+|+|.+.                ..++|+++|++|++.|+|+|||++||+.
T Consensus        77 ~L--p~dI~v~~~~~v~~~FhaR~~a~~r~Y~Y~~~----------------~~~ld~~~m~~a~~~~~G~HDF~~F~~~  138 (221)
T cd02866          77 AL--PKDIRVWAWAKVPEDFHPRRDARRRYYRYYLG----------------AEDYDVEAMAEAAKKLIGTHDFSNFSKR  138 (221)
T ss_pred             HC--CCCEEEEEEEEECCCCCCEEECCEEEEEEEEC----------------CCCCCHHHHHHHHHHHCCCCCHHHHHCC
T ss_conf             59--99889999999497978425234699999852----------------5767899999999983271576664111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             65533321103311112333200113158888999999999999999768998889999983588211666369898476
Q gi|254780295|r  162 HCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYF  241 (247)
Q Consensus       162 ~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L  241 (247)
                        +.++++|||+++++.+.++.+.|+|+||||||||||+|||+|++||+|++++++|+++|++++|...+++|||+||||
T Consensus       139 --~~~~~vRtI~~~~v~~~~~~~~~~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L  216 (221)
T cd02866         139 --DGRDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSLVGKGKRENEWVDKLLDGEFRKKDGVPAPPEGLIL  216 (221)
T ss_pred             --CCCCCEEEEEEEEEEECCCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEE
T ss_conf             --589972599999999429899999608999999999999999999879999999999974788555888659987789


Q ss_pred             EEEEE
Q ss_conf             33043
Q gi|254780295|r  242 DSVEY  246 (247)
Q Consensus       242 ~~V~Y  246 (247)
                      ++|.|
T Consensus       217 ~~V~Y  221 (221)
T cd02866         217 VDVKY  221 (221)
T ss_pred             CCCCC
T ss_conf             21599


No 8  
>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like. This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.
Probab=100.00  E-value=0  Score=500.32  Aligned_cols=223  Identities=28%  Similarity=0.416  Sum_probs=196.2

Q ss_pred             EEEEECCCCCEEEEECCCC-CCHHHHHHHHHHHHH----CCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCH-------
Q ss_conf             9999716687200487538-778899999999970----9956999711213861222346886406321104-------
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVT----GEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPV-------   73 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~-~TVq~~le~aL~~~~----~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~-------   73 (247)
                      |.|+||||+|+|||+||+. +||||+||+||.++.    .+++.+.+|||||+||||++||+||+++...+++       
T Consensus         1 L~i~YdGt~f~G~Q~Q~~~~~TVqg~Le~aL~k~~~i~~~~~~~~~~agRTDaGVHA~~qv~~f~~~~~~~~~~~~~~~~   80 (256)
T cd02569           1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPST   80 (256)
T ss_pred             CEEEEECCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             98999589800785789999788999999999722645786068983366652432135579999504677521123322


Q ss_pred             -----------HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHH
Q ss_conf             -----------689999986188876543443226777550002100223556852443202333210244333335665
Q gi|254780295|r   74 -----------ILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENM  142 (247)
Q Consensus        74 -----------~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l  142 (247)
                                 .+.+.||++|  |+||+|+++.+||++|||||+|++|+|+|+++.                .+||+++|
T Consensus        81 ~~~~~~~~~~~~~~~~LN~~L--P~dIrv~~~~~v~~~FhaR~~a~~R~Y~Y~~~~----------------~~ld~~~m  142 (256)
T cd02569          81 DVKSTADEEELPYCKILNRVL--PPDIRILAWAPVPPDFSARFSCVSRTYRYFFPK----------------GDLDIELM  142 (256)
T ss_pred             CCCCCCCCHHHHHHHHHHHCC--CCCEEEEEEEECCCCCCCCCCCCCEEEEEEECC----------------CCCCHHHH
T ss_conf             222122202567999998149--997599999988998885523431699997059----------------98799999


Q ss_pred             HHHHHHHHCCHHEEEECCCCC--CCCCCCCCCCCCCCCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             565676520011001024565--53332110331111233------3200113158888999999999999999768998
Q gi|254780295|r  143 RIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWT  214 (247)
Q Consensus       143 ~~a~~~l~G~HdF~~F~~~~~--~~~~~~R~I~~~~v~~~------~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~  214 (247)
                      ++|+++|+|+|||++||+...  +.++++|+|+++++++.      ++++.|+|+||||||||||+|||+|++||+|+++
T Consensus       143 ~~a~~~f~GtHDF~~F~~~~~~~~~~~~~R~i~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~mVR~mVGtL~~vg~G~~~  222 (256)
T cd02569         143 RKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEP  222 (256)
T ss_pred             HHHHHHCCCCCCHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999714861667627778899888874699999999855656887389999993056899899999999999779999


Q ss_pred             HHHHHHHHHCCCCCC--CCCCCCCCCCEEEEEEE
Q ss_conf             889999983588211--66636989847633043
Q gi|254780295|r  215 STDLEKALQAQDRKE--CGPLAPPEGLYFDSVEY  246 (247)
Q Consensus       215 ~~~i~~~L~~~~r~~--~~~~APa~GL~L~~V~Y  246 (247)
                      +++|+++|+.+++..  ...+|||+||+||+|.|
T Consensus       223 ~~~i~~~L~~~~~~~~~~~~~AP~~GL~L~~V~Y  256 (256)
T cd02569         223 PSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF  256 (256)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             8999999865567667886789998738998589


No 9  
>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p,  S.  cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67.  C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,  psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal.  Psi44 in U
Probab=100.00  E-value=0  Score=492.22  Aligned_cols=223  Identities=26%  Similarity=0.397  Sum_probs=197.4

Q ss_pred             EEEEECCCCCEEEEECCCC-CCHHHHHHHHHHHH---------HCCCEEEEECCCCCCCCEEEEEEEEEEECC-----CC
Q ss_conf             9999716687200487538-77889999999997---------099569997112138612223468864063-----21
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHALRQVAHFDLVR-----EW   70 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~-~TVq~~le~aL~~~---------~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~-----~~   70 (247)
                      |+|+||||+|+|||+||+. +|||++||+||.++         .++++.+.+|||||+||||.+||+||+++.     ..
T Consensus         1 l~i~YdGt~f~G~Q~Q~~~~~TVq~~le~aL~k~~~i~~~~~~~~~~i~~~~agRTDaGVHA~~qv~~f~~~~~~~~~~~   80 (245)
T cd02568           1 LLFGYCGTGYHGMQYNPGNYKTIEGELERALVKAGAISESNAGDPKKIGFSRAARTDKGVHAARNVVSLKVIIDDPEGLG   80 (245)
T ss_pred             CEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCC
T ss_conf             98999789820880889999898999999999802544322357735788761467687120400899964567731227


Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             10468999998618887654344322677755000210022355685244320233321024433333566556567652
Q gi|254780295|r   71 VPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLV  150 (247)
Q Consensus        71 ~~~~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~  150 (247)
                      +++.+.++||++|  |+||+|+++.+|+++|||||+|++|+|+|.++....               -|+++|++|++.|+
T Consensus        81 ~~~~~~~~lN~~L--P~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~ip~~~~---------------~~~~~m~~a~~~~~  143 (245)
T cd02568          81 IGEDLVEKLNSHL--PEDIRVFGITRVTKSFNARKACDSRTYEYLLPTFAL---------------ETLDRFNEILKLYV  143 (245)
T ss_pred             CHHHHHHHHHHHC--CCCEEEEEEEECCCCCCCCHHHHHCCEEEECCCCCC---------------CHHHHHHHHHHHHH
T ss_conf             9999999998229--998599999988999875631343016897753342---------------66999999999853


Q ss_pred             CCHHEEEECCC-CCCCCCCCCCCCCCCCCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             00110010245-6553332110331111233------3200113158888999999999999999768998889999983
Q gi|254780295|r  151 GRHDFTTFRSI-HCQASSPIRTIDHFDVNSF------GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ  223 (247)
Q Consensus       151 G~HdF~~F~~~-~~~~~~~~R~I~~~~v~~~------~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~  223 (247)
                      |+|||++||+. ..+.++++|+|.++++.+.      .+++.|+|+||||||||||+|||+|++||+|+++++.++.+|+
T Consensus       144 G~HDF~~F~~~~~~~~~~~~r~i~~i~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~mVGtL~~vg~g~~~~~~i~~ll~  223 (245)
T cd02568         144 GTHNFHNFTVRKKFEDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIDLSFN  223 (245)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCEEEEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHC
T ss_conf             86476244656777899984589999998635523896499999994365898899999999999879999899999966


Q ss_pred             CCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             58821166636989847633043
Q gi|254780295|r  224 AQDRKECGPLAPPEGLYFDSVEY  246 (247)
Q Consensus       224 ~~~r~~~~~~APa~GL~L~~V~Y  246 (247)
                       +++...+|+|||+||||++|+|
T Consensus       224 -~~~~~~~~~APa~GL~L~~v~Y  245 (245)
T cd02568         224 -KAKRIIIPLAPGLGLLLEYPHF  245 (245)
T ss_pred             -CCCCCCCCCCCCCCCEECCCCC
T ss_conf             -8754576887998777845699


No 10 
>KOG2553 consensus
Probab=100.00  E-value=0  Score=377.22  Aligned_cols=241  Identities=26%  Similarity=0.361  Sum_probs=203.2

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHC---------CCEEEEECCCCCCCCEEEEEEEEEEECCCCCC
Q ss_conf             229999997166872004875387788999999999709---------95699971121386122234688640632110
Q gi|254780295|r    2 IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG---------EIVVVHGAGRTDSGVHALRQVAHFDLVREWVP   72 (247)
Q Consensus         2 ~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~---------~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~   72 (247)
                      .++++.++|+|++|+|+|+||+.+||||+|+.||.+...         +++.+..|+||||||||.+|+++.+++.+.  
T Consensus        37 rKVail~gY~G~gY~GmQ~N~~~kTIEgeL~~al~~aGaI~e~n~~dpkk~~~~raARTDKGVhA~~nviSlK~~~~~--  114 (416)
T KOG2553          37 RKVAILLGYCGTGYHGMQYNPPLKTIEGELFEALFKAGAISESNAGDPKKIGFARAARTDKGVHAAGNVISLKLELDD--  114 (416)
T ss_pred             EEEEEEEEECCCCCCCEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHEEEEEEEECC--
T ss_conf             179999986367753212189987347899999997297033444686776667763134114334305689986176--


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHH-----HH------------------
Q ss_conf             4689999986188876543443226777550002100223556852443202333-----21------------------
Q gi|254780295|r   73 VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEK-----GR------------------  129 (247)
Q Consensus        73 ~~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~-----~~------------------  129 (247)
                      ..+...+|..|  |++||||++.+|++.|+||..|.+|+|+|.++.-...++-..     ..                  
T Consensus       115 ~~lv~~lN~~L--p~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~~~~~e~~~~f~~~~~~~~  192 (416)
T KOG2553         115 PELVEKLNEIL--PEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDIQYDKEFEKEFWNTYPLSA  192 (416)
T ss_pred             HHHHHHHHHHC--CCCEEEEEEEECCCCCCCCCCCCCEEEEEECCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             88999886438--8531798777447887841002200578866325614789753777665544443133213464666


Q ss_pred             ---------CCCCCCCC---CHHHHHHHHHHHHCCHHEEEECCCC-CCCCCCCCCCCCCCCC-------CCCCHHHHHHH
Q ss_conf             ---------02443333---3566556567652001100102456-5533321103311112-------33320011315
Q gi|254780295|r  130 ---------AWLIPKSL---DCENMRIAAQHLVGRHDFTTFRSIH-CQASSPIRTIDHFDVN-------SFGNLIEIRVV  189 (247)
Q Consensus       130 ---------~~~~~~~l---D~~~l~~a~~~l~G~HdF~~F~~~~-~~~~~~~R~I~~~~v~-------~~~~~i~i~i~  189 (247)
                               .......+   .++.++++++.++|+||||||+... ...++..|.|.++.+.       ..-+++.++|+
T Consensus       193 ~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnFHNfT~~~~~~dpss~R~I~s~~~~~pfv~~~~~~e~V~i~i~  272 (416)
T KOG2553         193 KERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNFHNFTTGKDFTDPSSNRFIKSFTVSEPFVINDEGVEFVKIKIH  272 (416)
T ss_pred             HHHHCCCCCCCCCCEEECHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCEEEEEEECCCCEECCCCCEEEEEEEE
T ss_conf             52102222002345231889999999999885254320100046787894401234578805761362678239999997


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEC
Q ss_conf             8888999999999999999768998889999983588211666369898476330439
Q gi|254780295|r  190 ARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVEYS  247 (247)
Q Consensus       190 g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  247 (247)
                      |+|||.||||+|||++|++.++..+.+.|+..++ +..+..+|.||+.||+|.++.|.
T Consensus       273 GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~-~~~ri~IP~AP~~gLlL~~~~F~  329 (416)
T KOG2553         273 GQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFN-KEHKINIPKAPGEGLLLEEPHFE  329 (416)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCCCCCCCCCCCCEEEEECCCCC
T ss_conf             6105999999999999999853898889888627-77101456787525884045434


No 11 
>KOG4393 consensus
Probab=100.00  E-value=0  Score=351.85  Aligned_cols=245  Identities=30%  Similarity=0.471  Sum_probs=221.1

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCC--CHHHHHHHHHHHHHC-CCEEEEECCCCCCCCEEEEEEEEEEECCC--CCCHHHH
Q ss_conf             229999997166872004875387--788999999999709-95699971121386122234688640632--1104689
Q gi|254780295|r    2 IRYCMIIEYNGSGYFGWQRQKNGS--SIQGSIEKAIFLVTG-EIVVVHGAGRTDSGVHALRQVAHFDLVRE--WVPVILC   76 (247)
Q Consensus         2 ~r~~~~i~YdGt~y~G~q~Q~~~~--TVq~~le~aL~~~~~-~~~~~~~a~RTD~GVhA~~qv~~f~~~~~--~~~~~~~   76 (247)
                      +||.+.|+||||.|.|||++....  |||+-||++....++ ++.++.++||||+||||.+|.+|++++..  ..+....
T Consensus         5 ~ryll~i~ydgT~f~e~a~~~s~~~~tIq~~leea~eeqt~l~~l~l~~ssrtDa~Vha~~naa~~~vpr~sg~~~~~~~   84 (295)
T KOG4393           5 MRYLLKIPYDGTAFEESAERLSKVARTIQGFLEEASEEQTGLDRLDLESSSRTDAGVHAYLNAAHYIVPRFSGSQQQAKD   84 (295)
T ss_pred             HEEEEEECCCCCCCHHHHHCCCCCCEEHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHEEEEEEEEEEECCCCCCHHHHH
T ss_conf             22678851466555777742377540023443666875058853252225877630421011579984122477377888


Q ss_pred             HHHHHHHC-CCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCC-CHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHH
Q ss_conf             99998618-88765434432267775500021002235568524432-02333210244333335665565676520011
Q gi|254780295|r   77 KALNAYLK-ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAP-LALEKGRAWLIPKSLDCENMRIAAQHLVGRHD  154 (247)
Q Consensus        77 ~~lN~~L~-~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~-~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~Hd  154 (247)
                      .++|..|. -|.||+|+++..||.+||||++|.+|+|.|+|..+..+ ++|+++++|+.+..||..+|++|+++|+|+||
T Consensus        85 ~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla~g~d~l~~fERd~cW~lp~~lna~kmqeaa~lf~G~hd  164 (295)
T KOG4393          85 RAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLASGSDPLSIFERDRCWHLPEELNARKMQEAAPLFEGSHD  164 (295)
T ss_pred             HHHHCCCCCCCCCEEEEEEEECCCCHHHEECCCCEEEEEEEECCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHCCCHH
T ss_conf             87751434798865899964148532110001220689984038986673440421028721288999865332035213


Q ss_pred             EEEECCCCCCCCCCCCCCCCCCCCC----------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             0010245655333211033111123----------------332001131588889999999999999997689988899
Q gi|254780295|r  155 FTTFRSIHCQASSPIRTIDHFDVNS----------------FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDL  218 (247)
Q Consensus       155 F~~F~~~~~~~~~~~R~I~~~~v~~----------------~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i  218 (247)
                      |.+|.+..+....+++|+....+..                ..+++.+++.+.|||+.|||+|+..||.+|.+.+....+
T Consensus       165 fsaf~~ats~~y~P~~t~rr~sv~~~g~~~a~~~~~~~e~~~~~~~nve~e~~gflyrQvRrm~a~LV~~g~~al~~~qv  244 (295)
T KOG4393         165 FSAFTEATSTVYFPSITERRLSVLNNGDPLACSNQPETEGVTTNVGNVEGETEGFLYRQVRRMRAYLVTAGSRALLYHQV  244 (295)
T ss_pred             HHHHHCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEEECCHHHHHHHHHHEEEEEECCCCCCHHHH
T ss_conf             45664078888887420101221036775335567722221024678999863169999976624556413566646552


Q ss_pred             HHHHHCCCCC----CCCCCCCCCCCEEEEEEE
Q ss_conf             9998358821----166636989847633043
Q gi|254780295|r  219 EKALQAQDRK----ECGPLAPPEGLYFDSVEY  246 (247)
Q Consensus       219 ~~~L~~~~r~----~~~~~APa~GL~L~~V~Y  246 (247)
                      ..+|+.++..    ..++.|||+||+|..|.|
T Consensus       245 ~~iLe~~~~~~l~k~~~~vapphglfL~sv~Y  276 (295)
T KOG4393         245 LYILEVRDIVGLLKCVGTVAPPHGLFLSSVEY  276 (295)
T ss_pred             HHHHHCCCHHHHHHCCCCCCCCCCCEEEEEEE
T ss_conf             56640632135664067788885422554784


No 12 
>KOG2554 consensus
Probab=100.00  E-value=0  Score=342.82  Aligned_cols=226  Identities=28%  Similarity=0.377  Sum_probs=193.9

Q ss_pred             EEEEEEEECCCCCEEEEECCC--CCCHHHHHHHHHHHH-HC---CCEEEEECCCCCCCCEEEEEEEEEEECCCCCC----
Q ss_conf             299999971668720048753--877889999999997-09---95699971121386122234688640632110----
Q gi|254780295|r    3 RYCMIIEYNGSGYFGWQRQKN--GSSIQGSIEKAIFLV-TG---EIVVVHGAGRTDSGVHALRQVAHFDLVREWVP----   72 (247)
Q Consensus         3 r~~~~i~YdGt~y~G~q~Q~~--~~TVq~~le~aL~~~-~~---~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~----   72 (247)
                      .++|.|+|+|.+|.|++.|++  .+||+|.|+.||.+. +.   +......||||||||+|.|||++.++...+++    
T Consensus        67 ~IAlkiaY~GW~Y~Gla~Qe~T~~~TIEg~l~eAL~kt~Lies~~~~~ysRCGRTDKGVSAfgQviSl~lRS~~p~~~s~  146 (425)
T KOG2554          67 HIALKIAYLGWNYQGLAPQEHTNNPTIEGKLFEALKKTRLIESRQTCNYSRCGRTDKGVSAFGQVISLVLRSRIPMPDSQ  146 (425)
T ss_pred             EEEEEEEEECCCCCCEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHEEEEEEECCCCCCHHH
T ss_conf             89999987345557621478899854678999999860124673214502037765203454323345420368995142


Q ss_pred             -----------HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHH
Q ss_conf             -----------468999998618887654344322677755000210022355685244320233321024433333566
Q gi|254780295|r   73 -----------VILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCEN  141 (247)
Q Consensus        73 -----------~~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~  141 (247)
                                 ...+..||..|  |+||||..+.+||+.|+|||+|..|+|+|.++                ...||+++
T Consensus       147 ~~~~~~a~~~Ei~Y~~mLN~vL--P~dIRi~awapvp~~FsARFsC~~RtYrY~F~----------------k~dLdI~~  208 (425)
T KOG2554         147 RDAVATADSEEIPYVHMLNRVL--PPDIRIVAWAPVPPTFSARFSCVQRTYRYYFP----------------KKDLDIDR  208 (425)
T ss_pred             HCCCCCCCCCCCCHHHHHHCCC--CCCCEEEEEECCCCCCCCEEEHHHCEEEEECC----------------CCCCCHHH
T ss_conf             0133324456464888874138--98605999725998755134510122467526----------------88968899


Q ss_pred             HHHHHHHHHCCHHEEEECCCCC--CCCCCCCCCCCCCCCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             5565676520011001024565--53332110331111233320---011315888899999999999999976899888
Q gi|254780295|r  142 MRIAAQHLVGRHDFTTFRSIHC--QASSPIRTIDHFDVNSFGNL---IEIRVVARSFLHTQIRSFVGSLKLVGDGKWTST  216 (247)
Q Consensus       142 l~~a~~~l~G~HdF~~F~~~~~--~~~~~~R~I~~~~v~~~~~~---i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~  216 (247)
                      |.+||++++|+|||+|||+-..  ...++.|+|.++.|+..++.   +.++|.|++|||||||.||+.|..+|+|.-.++
T Consensus       209 M~kAA~l~vGe~DFrNFCK~D~~n~vtny~Rti~s~kV~~~~~~~~my~ldi~g~AFLwHqVRcimaiL~liGq~~E~p~  288 (425)
T KOG2554         209 MSKAASLLVGEHDFRNFCKIDVSNGVTNYERTILSAKVEDVGQTPGMYYLDIQGSAFLWHQVRCIMAILFLIGQGLEQPS  288 (425)
T ss_pred             HHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHEEEEEECCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHCCCCCCCH
T ss_conf             99999987240234456650304445788765241467873788845999961122399999999999999625667706


Q ss_pred             HHHHHHHCCCC--CCCCCCCCCCCCEEEEEEE
Q ss_conf             99999835882--1166636989847633043
Q gi|254780295|r  217 DLEKALQAQDR--KECGPLAPPEGLYFDSVEY  246 (247)
Q Consensus       217 ~i~~~L~~~~r--~~~~~~APa~GL~L~~V~Y  246 (247)
                      -|.++|+-+..  .+...+|--..|.|.++.|
T Consensus       289 lI~dLldIek~P~kPqY~mA~~~PL~LydC~f  320 (425)
T KOG2554         289 LISDLLDIEKNPQKPQYTMASDYPLELYDCDF  320 (425)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCCCEEEEECCC
T ss_conf             88998741248998614204578547775477


No 13 
>pfam01416 PseudoU_synth_1 tRNA pseudouridine synthase. Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.
Probab=99.96  E-value=3.2e-30  Score=195.48  Aligned_cols=103  Identities=32%  Similarity=0.487  Sum_probs=98.4

Q ss_pred             HHHHHHCCHHEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHC
Q ss_conf             56765200110010245655333211033111123332001131588889999999999999997689988899999835
Q gi|254780295|r  145 AAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQA  224 (247)
Q Consensus       145 a~~~l~G~HdF~~F~~~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~  224 (247)
                      |++.|+|+|||++||+..+..++++|+|++++|.+.++.+.|+|+||||||+|||.|||+++++|+|+.+++++.++|+.
T Consensus         1 aa~~~~G~hdF~~F~~~~~~~~~~~r~i~~~~~~~~~~~~~~~i~g~~Fl~~mvR~~vg~l~~vg~g~~~~~~v~~~L~~   80 (103)
T pfam01416         1 AAKLYDGTHDFSGFQKQRTVQKSLIRTIEKIGIERDGELYVFEIKGNGFLYHQVRIMVGALLRTGKGVHALEQVVSLLNS   80 (103)
T ss_pred             CHHHCEECCCHHHHHCCCCCCCCCEEEEEEEEEEECCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHC
T ss_conf             95583080166887289998999819999999998299999999900369999999999999998799999999999867


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEEC
Q ss_conf             88211666369898476330439
Q gi|254780295|r  225 QDRKECGPLAPPEGLYFDSVEYS  247 (247)
Q Consensus       225 ~~r~~~~~~APa~GL~L~~V~Y~  247 (247)
                      +.+....++|||+||+|++|.|+
T Consensus        81 ~~~~~~~~~ap~~gL~L~~v~Y~  103 (103)
T pfam01416        81 KLRPPAPPTAPAVGLYLFHVRYD  103 (103)
T ss_pred             CCCCCCCCCCCCCCCEEEEEECC
T ss_conf             88556867049987788210749


No 14 
>pfam10105 DUF2344 Uncharacterized protein conserved in bacteria (DUF2344). This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=96.96  E-value=0.012  Score=35.61  Aligned_cols=143  Identities=16%  Similarity=0.157  Sum_probs=95.4

Q ss_pred             CCHHHHHHHHHHHH---------HCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             77889999999997---------099569997112138612223468864063211046899999861888765434432
Q gi|254780295|r   25 SSIQGSIEKAIFLV---------TGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLS   95 (247)
Q Consensus        25 ~TVq~~le~aL~~~---------~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~p~~Irv~~~~   95 (247)
                      .-++-.+|.|+.+.         ++...++.-+.=.=-||-+.+-.+.+++..+++++.+...||..|  |++|+|.++.
T Consensus        18 LDl~r~~eRa~RRa~lP~a~S~GF~Phpkisf~~aLpvG~~S~~Ey~di~l~~~~~~~~~~~rLn~~L--P~Gi~i~~~~   95 (186)
T pfam10105        18 LDLMRLFERALRRAGLPIAFSEGFHPHPRISFALALPVGVESEGEYMDLELTEEIDPEEVRERLNAQL--PEGLEILEVE   95 (186)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHCC--CCCCEEEEEE
T ss_conf             88999999999981897687379899972744467556524032599999816589999999985239--9995789999


Q ss_pred             CCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECC-CCCC--CCCCCCCC
Q ss_conf             26777550002100223556852443202333210244333335665565676520011001024-5655--33321103
Q gi|254780295|r   96 IVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS-IHCQ--ASSPIRTI  172 (247)
Q Consensus        96 ~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~-~~~~--~~~~~R~I  172 (247)
                      +++...-+- .+.-..+.|.+...                ..+.+.+.++...|.....+---.+ ++.+  ..+-.-.|
T Consensus        96 ~i~~~~~sl-~~~v~~a~Y~v~~~----------------~~~~~~~~~~i~~~l~~~~i~v~r~tKKGk~~~~diRp~i  158 (186)
T pfam10105        96 EIPVKAPSL-MALIEAAEYRITLP----------------EESPEDLEEAVEAFLAAEELVVERTTKKGKKREVDIRPLL  158 (186)
T ss_pred             ECCCCCCCH-HHHHEEEEEEEEEC----------------CCCHHHHHHHHHHHHCCCEEEEEEECCCCCEEEEEHHHHH
T ss_conf             936888655-54410599999906----------------8998999999999986990899996699987788815500


Q ss_pred             CCCCCCCCCCHHHH
Q ss_conf             31111233320011
Q gi|254780295|r  173 DHFDVNSFGNLIEI  186 (247)
Q Consensus       173 ~~~~v~~~~~~i~i  186 (247)
                      .++++...++.+.+
T Consensus       159 ~~l~~~~~~~~~~l  172 (186)
T pfam10105       159 KELELEGDGNALVL  172 (186)
T ss_pred             HEEEEEECCCEEEE
T ss_conf             05999917997999


No 15 
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=91.90  E-value=0.34  Score=27.15  Aligned_cols=153  Identities=20%  Similarity=0.182  Sum_probs=98.5

Q ss_pred             CCCCHHHHHHHHHHH-HHCCCEEEEECCCCCCCCEEEEE----EEEEEEC--CCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             387788999999999-70995699971121386122234----6886406--3211046899999861888765434432
Q gi|254780295|r   23 NGSSIQGSIEKAIFL-VTGEIVVVHGAGRTDSGVHALRQ----VAHFDLV--REWVPVILCKALNAYLKISDTISILNLS   95 (247)
Q Consensus        23 ~~~TVq~~le~aL~~-~~~~~~~~~~a~RTD~GVhA~~q----v~~f~~~--~~~~~~~~~~~lN~~L~~p~~Irv~~~~   95 (247)
                      ...||+..|-..+.. ..+.+..+.+|||-|--|--+|.    |+-++-|  +..+.+.+...+|.-.    .+.|..+.
T Consensus       189 ~~~sve~~i~~~~~~~f~g~~~~fhgAGREDvDvRMLG~GRPfVlEvk~Pr~R~~dl~~l~~~in~~~----~vev~~l~  264 (398)
T COG1258         189 YPESVEELIKQPIKEAFGGLDAKFHGAGREDVDVRMLGTGRPFVLEVKEPRRRNVDLDELEEEINRGG----KVEVFDLE  264 (398)
T ss_pred             CCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCEEEECCCCCEEEEECCCCCCCCCHHHHHHHHCCCC----CEEEEEEE
T ss_conf             64419999878999860685069971687766346605898369992374225688678899763588----58999877


Q ss_pred             CCCCCCCCEE---CCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHC-CHHEEEECCCC--CCCCCCC
Q ss_conf             2677755000---2100223556852443202333210244333335665565676520-01100102456--5533321
Q gi|254780295|r   96 IVDKQFHARF---SAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVG-RHDFTTFRSIH--CQASSPI  169 (247)
Q Consensus        96 ~v~~~FhaR~---~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G-~HdF~~F~~~~--~~~~~~~  169 (247)
                      -+...=-.+.   .-..|+|+=.+.               +..+++.+.+.+++.-+.| +-.=..+....  ....-.+
T Consensus       265 f~~~e~v~~ik~~~~~rK~YrAlV~---------------~~~~v~~e~l~~~~~~L~g~~I~QrTP~RV~hrRadlvR~  329 (398)
T COG1258         265 FVGREEVEEIKETERHRKVYRALVY---------------SDRPVSDEKLEEVLGSLEGKTIRQRTPRRVLHRRADLVRI  329 (398)
T ss_pred             ECCHHHHHHHHHCCCCCEEEEEEEE---------------ECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHCCCCEE
T ss_conf             4479999998740342006899999---------------7798689999999742357678613927876641120147


Q ss_pred             CCCCCCCCCCC-CCHHHHHHHHHHHH
Q ss_conf             10331111233-32001131588889
Q gi|254780295|r  170 RTIDHFDVNSF-GNLIEIRVVARSFL  194 (247)
Q Consensus       170 R~I~~~~v~~~-~~~i~i~i~g~~FL  194 (247)
                      |.|+.+.+... +....+.|.+++=|
T Consensus       330 R~V~~l~~~~~~~~~~~~~i~~egGl  355 (398)
T COG1258         330 RRVYELSLDLIDDRHAELEIEAEGGL  355 (398)
T ss_pred             EEEEEEEEEECCCCEEEEEEEECCCC
T ss_conf             88998533660684699999941540


No 16 
>pfam01416 PseudoU_synth_1 tRNA pseudouridine synthase. Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.
Probab=87.72  E-value=0.00089  Score=42.10  Aligned_cols=53  Identities=38%  Similarity=0.544  Sum_probs=31.2

Q ss_pred             EEECCC-CCEEEEECCCCCCHHHHHHHHHHHH----HCCC--EE--------------EEECCCCCCCCEEEEEEEE
Q ss_conf             997166-8720048753877889999999997----0995--69--------------9971121386122234688
Q gi|254780295|r    8 IEYNGS-GYFGWQRQKNGSSIQGSIEKAIFLV----TGEI--VV--------------VHGAGRTDSGVHALRQVAH   63 (247)
Q Consensus         8 i~YdGt-~y~G~q~Q~~~~TVq~~le~aL~~~----~~~~--~~--------------~~~a~RTD~GVhA~~qv~~   63 (247)
                      ..|+|+ +|+|||+|+..   ++..+.++.++    .++.  +.              +-.+.|||+|||+..++..
T Consensus         3 ~~~~G~hdF~~F~~~~~~---~~~~~r~i~~~~~~~~~~~~~~~i~g~~Fl~~mvR~~vg~l~~vg~g~~~~~~v~~   76 (103)
T pfam01416         3 KLYDGTHDFSGFQKQRTV---QKSLIRTIEKIGIERDGELYVFEIKGNGFLYHQVRIMVGALLRTGKGVHALEQVVS   76 (103)
T ss_pred             HHCEECCCHHHHHCCCCC---CCCCEEEEEEEEEEECCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             583080166887289998---99981999999999829999999990036999999999999999879999999999


No 17 
>cd01291 PseudoU_synth PseudoU_synth:  Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families.  This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39  in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs).  Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=86.39  E-value=1  Score=24.35  Aligned_cols=40  Identities=23%  Similarity=0.189  Sum_probs=25.1

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEE
Q ss_conf             538778899999999970995699971121386122234688
Q gi|254780295|r   22 KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH   63 (247)
Q Consensus        22 ~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~   63 (247)
                      |+..|.+-..+.+- ...-..-++..|||+|+.++.. |.++
T Consensus         4 ~~~~t~~~~~~~~~-~~~~~~~~v~~aG~kDk~a~t~-Q~~s   43 (87)
T cd01291           4 PGGDTMEAARQLAK-LLGIPPKRVGYAGRKDKRAVTT-QLVS   43 (87)
T ss_pred             CCCCHHHHHHHHHH-HHCCCHHHEEECCCCCCCEEEE-EEEE
T ss_conf             68789999999999-8299877751744666655478-8764


No 18 
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.04  E-value=2.6  Score=21.98  Aligned_cols=73  Identities=15%  Similarity=0.187  Sum_probs=55.2

Q ss_pred             CEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECC-CCEEEEEEE
Q ss_conf             569997112138612223468864063211046899999861888765434432267775500021-002235568
Q gi|254780295|r   42 IVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA-IRRSYLYRI  116 (247)
Q Consensus        42 ~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~~a-~~R~Y~Y~i  116 (247)
                      .-++..|.----|+..-|-.+-|++....++++++..+|+.|  |+|+.+.++..++..--+-... -.-+|...+
T Consensus        45 ~prmsia~alpvG~~ssge~fd~eL~e~v~~dk~~etl~~~l--p~Dl~~~~v~~iD~ksps~nqvl~~arY~i~v  118 (228)
T COG5011          45 HPRMSIAQALPVGIYSSGEIFDFELTEEVSEDKFKETLNKAL--PNDLPAYDVEKIDKKSPSSNQVLEAARYFIKV  118 (228)
T ss_pred             CCCEEECCCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHC--CCCCCHHHEEEECCCCCCHHHHHHHHCEEEEE
T ss_conf             974221024433201476189998643117188999999757--88755131013067785689999742189999


No 19 
>PRK10187 trehalose-6-phosphate phosphatase; Provisional
Probab=76.70  E-value=3.2  Score=21.44  Aligned_cols=48  Identities=13%  Similarity=0.261  Sum_probs=39.4

Q ss_pred             EEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC--EEEEECCCC
Q ss_conf             2999999716687200487538778899999999970995--699971121
Q gi|254780295|r    3 RYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRT   51 (247)
Q Consensus         3 r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~--~~~~~a~RT   51 (247)
                      +++|.+=|||| -..++..|+.-.+-..+.++|..+....  .-.+.|||.
T Consensus        14 ~~AlfLDyDGT-Lapi~~~P~~a~~~~~~~~~L~~La~~~~~~vaIVSGR~   63 (266)
T PRK10187         14 NYAWFFDLDGT-LAEIKPHPDQVVVPDNILQGLQLLATANDGALALISGRS   63 (266)
T ss_pred             CEEEEEECCCC-CCCCCCCHHHCCCCHHHHHHHHHHHCCCCCCEEEEECCC
T ss_conf             87999805776-777879987776988899999999708599589993999


No 20 
>TIGR01227 hutG formimidoylglutamase; InterPro: IPR005923    Formiminoglutamase (3.5.3.8 from EC), the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase.  N-formimidoyl-L-glutamate + H2O = L-glutamate + formamide.   ; GO: 0016813 hydrolase activity acting on carbon-nitrogen (but not peptide) bonds in linear amidines, 0006548 histidine catabolic process.
Probab=63.62  E-value=6.6  Score=19.63  Aligned_cols=23  Identities=9%  Similarity=0.092  Sum_probs=16.6

Q ss_pred             CCHHHHHHHHHHHHCCHHEEEEC
Q ss_conf             33566556567652001100102
Q gi|254780295|r  137 LDCENMRIAAQHLVGRHDFTTFR  159 (247)
Q Consensus       137 lD~~~l~~a~~~l~G~HdF~~F~  159 (247)
                      .+++..+++++.|+-++||--||
T Consensus       234 ~~~~~~~~~l~~~~d~~D~~y~t  256 (328)
T TIGR01227       234 LLLPTIKDILEEFLDEVDHIYLT  256 (328)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             38645899999984158869998


No 21 
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912    The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.  .
Probab=43.72  E-value=26  Score=16.17  Aligned_cols=154  Identities=19%  Similarity=0.185  Sum_probs=98.2

Q ss_pred             CCHHHHHHHHHHH-HHCCCEEEEECCCCCCCCEEEEE----EEEEEEC--CCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             7788999999999-70995699971121386122234----6886406--321104689999986188876543443226
Q gi|254780295|r   25 SSIQGSIEKAIFL-VTGEIVVVHGAGRTDSGVHALRQ----VAHFDLV--REWVPVILCKALNAYLKISDTISILNLSIV   97 (247)
Q Consensus        25 ~TVq~~le~aL~~-~~~~~~~~~~a~RTD~GVhA~~q----v~~f~~~--~~~~~~~~~~~lN~~L~~p~~Irv~~~~~v   97 (247)
                      .||+..+-.-+.+ .-|.+..+.||||=|-=|=-+|+    |+=++-|  +.++++.+...+|+.- ...++.|..+.-.
T Consensus       243 ~sve~~i~~p~~~~~~G~~~~fHGaGREDvDvRMLG~GRPFVlEv~~Pr~R~~dl~~l~~eiN~~a-~GkGVEv~~~~f~  321 (450)
T TIGR01213       243 ESVEELIAKPFLKATGGTDAVFHGAGREDVDVRMLGTGRPFVLEVKEPRKRKIDLDELEEEINKGA-SGKGVEVLGLKFA  321 (450)
T ss_pred             CEEEEEEEHHHHHHCCCEEEEEEECCCCCEEEECCCCCCCEEEEECCCCCCCCCHHHHHHHHCCCC-CCCEEEEEEEEEC
T ss_conf             406888201466422880699962566400010178888359972588658888789999954678-8534899733315


Q ss_pred             CCCCCCEE--CCC--CEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCCCCCCC---CCCC
Q ss_conf             77755000--210--0223556852443202333210244333335665565676520011001024565533---3211
Q gi|254780295|r   98 DKQFHARF--SAI--RRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQAS---SPIR  170 (247)
Q Consensus        98 ~~~FhaR~--~a~--~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~~~~~~---~~~R  170 (247)
                      ...=-+++  .-.  .|+|+=...               +..+++-+.|..+.+-|.|.-=.+-=-+.-.+..   =-.|
T Consensus       322 ~~~~~~~~K~~~~r~~KvYrALV~---------------~~~~v~d~dl~~l~~~L~G~~I~QrTP~RV~hRRaDlvR~R  386 (450)
T TIGR01213       322 TREEVEEVKEEKHRVRKVYRALVE---------------VDDPVSDEDLEELVKELEGATIKQRTPKRVLHRRADLVRER  386 (450)
T ss_pred             CHHHHHHHHCCCCCEEEEEEEEEE---------------ECCCCCHHHHHHHHHHHCCCEEEECCCCCHHHCCCCEEEEE
T ss_conf             567888763057853315888688---------------75997889999999850798787027884210578613434


Q ss_pred             CCCCCCCCCCCC--HHHHHHHHHHHH
Q ss_conf             033111123332--001131588889
Q gi|254780295|r  171 TIDHFDVNSFGN--LIEIRVVARSFL  194 (247)
Q Consensus       171 ~I~~~~v~~~~~--~i~i~i~g~~FL  194 (247)
                      .|+++++...++  ...+.|.|+|=|
T Consensus       387 rvy~v~~~~~d~~P~~e~~i~~eGGL  412 (450)
T TIGR01213       387 RVYEVDLSKVDDNPHAELIIEAEGGL  412 (450)
T ss_pred             EEEEEEEEEECCCCEEEEEEEECCCC
T ss_conf             57664202115883368999726872


No 22 
>pfam02358 Trehalose_PPase Trehalose-phosphatase. This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. The aligned region is present in trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - pfam00982. It would appear that the two equivalent genes in the E. coli otsBA operon otsA the trehalose-6-phosphate synthase and otsB trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance.
Probab=42.81  E-value=24  Score=16.35  Aligned_cols=43  Identities=12%  Similarity=0.210  Sum_probs=33.5

Q ss_pred             EEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC--EEEEECCCC
Q ss_conf             99716687200487538778899999999970995--699971121
Q gi|254780295|r    8 IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRT   51 (247)
Q Consensus         8 i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~--~~~~~a~RT   51 (247)
                      +=|||| -..++..|+.-.+...+..+|.++...+  .-.+-|||-
T Consensus         2 LD~DGT-Lapi~~~p~~a~~~~~~~~~L~~L~~~~~~~vaIvSGR~   46 (235)
T pfam02358         2 LDYDGT-LSPIVEDPDAAVPSDRLLSLLNRLASDPPNTVAIISGRS   46 (235)
T ss_pred             CCCCCC-CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             775767-886877922366998999999999738897499997998


No 23 
>TIGR02735 purC_vibrio phosphoribosylaminoimidazole-succinocarboxamide synthase; InterPro: IPR014106   Members of this protein family appear to represent a novel form of phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICAR synthetase), significantly different in sequence from (IPR001636 from INTERPRO), which is found in a broad range of bacteria and eukaryotes. Members of this family are found within the gammaproteobacteria in the genera Vibrio, Shewanella, and Colwellia, and also (reported as a fragment) in the primitive eukaryote Guillardia theta (Cryptomonas phi)..
Probab=39.14  E-value=18  Score=17.06  Aligned_cols=32  Identities=25%  Similarity=0.137  Sum_probs=18.6

Q ss_pred             CCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf             112138612223468864063211046899999
Q gi|254780295|r   48 AGRTDSGVHALRQVAHFDLVREWVPVILCKALN   80 (247)
Q Consensus        48 a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN   80 (247)
                      --|||+-||+ |-|=|+-.-.+-+..++...-|
T Consensus        14 ~i~Td~~VHS-GKVRSVYWL~~~DSRRLI~~k~   45 (365)
T TIGR02735        14 PIRTDEPVHS-GKVRSVYWLTEEDSRRLIEEKG   45 (365)
T ss_pred             CCCCCCCCCC-CCEEEEEECCCHHHHHHHHHCC
T ss_conf             8888885235-6301465158023578886368


No 24 
>pfam05125 Phage_cap_P2 Phage major capsid protein, P2 family.
Probab=38.74  E-value=23  Score=16.51  Aligned_cols=33  Identities=30%  Similarity=0.353  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHHHHH---H------------HCCCEEEE----ECCCCCCCCE
Q ss_conf             87788999999999---7------------09956999----7112138612
Q gi|254780295|r   24 GSSIQGSIEKAIFL---V------------TGEIVVVH----GAGRTDSGVH   56 (247)
Q Consensus        24 ~~TVq~~le~aL~~---~------------~~~~~~~~----~a~RTD~GVh   56 (247)
                      .|+||..||+++..   +            .|+.+.+-    -+||||.+-.
T Consensus        29 ~P~v~q~L~~~i~ess~FL~~INv~~V~e~~Ge~v~lg~~g~iagrtdt~~~   80 (333)
T pfam05125        29 EPSVQQTLENTIQESSDFLKQINIVPVAEMKGEKIGIGVSGTIASTTDTGGD   80 (333)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf             8679999999999999998458525345345567961577760031027898


No 25 
>TIGR01892 AcOrn-deacetyl acetylornithine deacetylase (ArgE); InterPro: IPR010169   This entry represents a clade of acetylornithine deacetylases (argE) from proteobacteria, which catalyse the final step in arginine biosynthesis. The enzyme is closely related to and may share a common origin with dapE (succinyl-diaminopimelate desuccinylase), cpg2 (carboxypeptidase G2) and ACY1 (aminoacylase I), all of which are members of the metal-dependent aminoacylase family, ArgE/dapE/ACY1/CPG2/yscS .; GO: 0008270 zinc ion binding, 0008777 acetylornithine deacetylase activity, 0050897 cobalt ion binding, 0006526 arginine biosynthetic process, 0005737 cytoplasm.
Probab=35.58  E-value=13  Score=17.87  Aligned_cols=14  Identities=29%  Similarity=0.470  Sum_probs=12.2

Q ss_pred             CCCCCCCCEEEEEE
Q ss_conf             11213861222346
Q gi|254780295|r   48 AGRTDSGVHALRQV   61 (247)
Q Consensus        48 a~RTD~GVhA~~qv   61 (247)
                      ||+||.||+|...+
T Consensus       196 SS~p~~G~~Ai~~~  209 (386)
T TIGR01892       196 SSDPDRGVSAIELA  209 (386)
T ss_pred             CCCCCCCHHHHHHH
T ss_conf             68752441189999


No 26 
>PRK05647 purN phosphoribosylglycinamide formyltransferase; Reviewed
Probab=33.81  E-value=38  Score=15.24  Aligned_cols=91  Identities=22%  Similarity=0.188  Sum_probs=51.8

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEE-----EEECCCCCC---
Q ss_conf             922999999716687200487538778899999999970995699971121386122234688-----640632110---
Q gi|254780295|r    1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAH-----FDLVREWVP---   72 (247)
Q Consensus         1 M~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~-----f~~~~~~~~---   72 (247)
                      |+|+++.+|--||++.            .-++..-..-++-.+.+.-|.|.|+|+..+++-..     ++....-+.   
T Consensus         1 Mkkiavl~SG~GSNl~------------aii~a~~~~~l~~~i~~Visn~~~a~~l~~A~~~~Ip~~~i~~~~~~~r~~~   68 (200)
T PRK05647          1 MKRIVVLASGNGSNLQ------------AIIDACAAGQLPAEVVAVISDRPDAYGLERAEQAGIPTFVLDHKDFPSREAF   68 (200)
T ss_pred             CCEEEEEECCCCHHHH------------HHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHCCCCEEEECCCCCCCHHHH
T ss_conf             9789999915804499------------9999987599994899999789753665999975997699677667998999


Q ss_pred             -HHHHHHHHHHHCCCCCCCCCC--CCCCCCCCCCEEC
Q ss_conf             -468999998618887654344--3226777550002
Q gi|254780295|r   73 -VILCKALNAYLKISDTISILN--LSIVDKQFHARFS  106 (247)
Q Consensus        73 -~~~~~~lN~~L~~p~~Irv~~--~~~v~~~FhaR~~  106 (247)
                       +.+...|..+   ..|+-|+.  ..-.++.|-.+|.
T Consensus        69 d~~i~~~L~~~---~vDlIvLAGyMril~~~~l~~~~  102 (200)
T PRK05647         69 DAALVEALDAY---EPDLVVLAGFMRILGPTFVSAYE  102 (200)
T ss_pred             HHHHHHHHHHC---CCCEEEECCHHHHCCHHHHHHCC
T ss_conf             99999999864---99999998813338989995377


No 27 
>TIGR00130 frhD coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit).; InterPro: IPR004411   This group of sequence are classed as unassigned endopeptidases belonging to the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE). The sequences in this family represent the delta subunit, frhD, of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase otherwise known as coenzyme F420-reducing hydrogenase. The delta subunit is not part of the active FRH heterotrimer, which contains three known subunits, alpha, beta, and gamma. The alpha subunit contains the metallo centre, which binds nickel. When nickel binds to the metallo centre the alpha subunit is processed to the active enzyme by cleavage at a conserved site near the C-terminus. This entry contains the archaeal hydrogenase maturation endopeptidases of family A31 that are thought to be responsible for these cleavages . At present there is no direct evidence to support there classification as peptidases. ; GO: 0008233 peptidase activity, 0006464 protein modification process.
Probab=30.97  E-value=5  Score=20.32  Aligned_cols=62  Identities=19%  Similarity=0.182  Sum_probs=44.6

Q ss_pred             CCCEEEEECCCCCCCCEEEEEEEEEEECCC-CCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCEECC
Q ss_conf             995699971121386122234688640632-110468999998618887654344322677--75500021
Q gi|254780295|r   40 GEIVVVHGAGRTDSGVHALRQVAHFDLVRE-WVPVILCKALNAYLKISDTISILNLSIVDK--QFHARFSA  107 (247)
Q Consensus        40 ~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~-~~~~~~~~~lN~~L~~p~~Irv~~~~~v~~--~FhaR~~a  107 (247)
                      .+++.+     -|||+.|..++..+.-+.. +.---+.++++.-++ |..|+.+.+.++|+  .+..+.++
T Consensus        36 ~~~v~~-----~DAGtgg~~l~~~l~~e~~~~kKiiiVD~i~fg~~-PG~~~k~~v~~lpnna~k~~~~~~  100 (162)
T TIGR00130        36 KENVEV-----IDAGTGGFDLVNTLVDEEEKLKKIIIVDAIDFGLE-PGTVKKIEVEELPNNALKKYLIDA  100 (162)
T ss_pred             CCCCEE-----EECCCCHHHHHEECCCCCCCCCEEEEEEEEECCCC-CCEEEEECCCCCCCCCCCCCEECC
T ss_conf             378479-----97675545653210034687576899988707679-863776154206666678631011


No 28 
>TIGR02407 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase; InterPro: IPR012773    Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (2.6.1.76 from EC) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (Q9Z3R2 from SWISSPROT) or 1,3-diaminopropane (P44951 from SWISSPROT) biosynthesis. Ectoine is a compatible solute particularly effective in conferring salt tolerance.; GO: 0030170 pyridoxal phosphate binding, 0047307 diaminobutyrate-pyruvate transaminase activity, 0019491 ectoine biosynthetic process.
Probab=30.69  E-value=27  Score=16.06  Aligned_cols=31  Identities=19%  Similarity=0.276  Sum_probs=15.2

Q ss_pred             HH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             01-13158888999999999999999768998889999983
Q gi|254780295|r  184 IE-IRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ  223 (247)
Q Consensus       184 i~-i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~  223 (247)
                      .. .+..|.||++-         |++..+.+..+-.+.+++
T Consensus       341 ~~~~~~RGRGlm~G---------l~~~~~~~A~~i~~~aF~  372 (413)
T TIGR02407       341 LIEKSVRGRGLMQG---------LECGDGDLAGKIAKAAFE  372 (413)
T ss_pred             HCCCCCCCCCEEEE---------CCCCCHHHHHHHHHHHHH
T ss_conf             21311045201420---------004772468999999864


No 29 
>TIGR02774 rexB_recomb ATP-dependent nuclease subunit B; InterPro: IPR014141   DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RecAB) in other. The AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important. This entry represents RexB proteins as found in Streptococcus and Lactococcus..
Probab=27.52  E-value=27  Score=16.13  Aligned_cols=96  Identities=10%  Similarity=0.052  Sum_probs=48.3

Q ss_pred             CHHHHHHHHHHHHCCHHEEEECCCCC-CCCCCCCCCCCCCCCCCCCHHH-------HHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             35665565676520011001024565-5333211033111123332001-------1315-8888999999999999999
Q gi|254780295|r  138 DCENMRIAAQHLVGRHDFTTFRSIHC-QASSPIRTIDHFDVNSFGNLIE-------IRVV-ARSFLHTQIRSFVGSLKLV  208 (247)
Q Consensus       138 D~~~l~~a~~~l~G~HdF~~F~~~~~-~~~~~~R~I~~~~v~~~~~~i~-------i~i~-g~~FL~~mVR~mVG~li~v  208 (247)
                      .-+.+..+.+.|+|+|||+.-.-.-. +.+. .=+|++|  ...+|.|+       =... |...-|+=||.+-|=+=..
T Consensus       263 ~~~~f~~~S~~lEa~hDFS~~~~~l~~~d~~-~l~iW~c--~~QKeEvE~VAr~IRqkL~~gsd~rYKdilvLLGD~~SY  339 (1116)
T TIGR02774       263 SKDSFDKLSKLLEAKHDFSELALDLDDKDKD-ALTIWEC--LTQKEEVEHVARSIRQKLYEGSDYRYKDILVLLGDVDSY  339 (1116)
T ss_pred             CCHHHHHHHHHHCCCCCCCCCCHHHHHHHHH-CCCCCCC--CCCHHHHHHHHHHHHHHHHCCCCCCHHHEEEECCCHHHH
T ss_conf             4324899987514533632010340256641-3451001--251378899999998876248963011001212877787


Q ss_pred             HCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             7689988899999835882116663698984
Q gi|254780295|r  209 GDGKWTSTDLEKALQAQDRKECGPLAPPEGL  239 (247)
Q Consensus       209 ~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL  239 (247)
                         ++.+..|-+-.+-|-.-...-++-+|+|
T Consensus       340 ---qLql~~IF~~Y~IPfYlGkaE~MA~HPL  367 (1116)
T TIGR02774       340 ---QLQLGKIFDKYDIPFYLGKAEPMAAHPL  367 (1116)
T ss_pred             ---HCCCCCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf             ---5010002221368854566560011624


No 30 
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689    This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=24.95  E-value=50  Score=14.54  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             00487538778899999999970
Q gi|254780295|r   17 GWQRQKNGSSIQGSIEKAIFLVT   39 (247)
Q Consensus        17 G~q~Q~~~~TVq~~le~aL~~~~   39 (247)
                      |+--||+.|-||+.|++|+.++.
T Consensus       179 GH~GnPsHPEV~~AI~~Ai~~i~  201 (249)
T TIGR02311       179 GHLGNPSHPEVQDAIDDAIERIK  201 (249)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             56888696158999999999998


No 31 
>TIGR02635 RhaI_grampos L-rhamnose isomerase; InterPro: IPR013457    The proteins in this entry are closely related to the L-rhamnose isomerases (IPR013451 from INTERPRO) found in Pseudomonas stutzeri  and in a number of the Rhizobiales. They are encoded in similar genomic contexts, close to genes apparently involved in rhamnose catabolism such as rhamnulose-1-phosphate aldolase (IPR013454 from INTERPRO), sugar kinases, and sugar transporters..
Probab=24.83  E-value=45  Score=14.82  Aligned_cols=31  Identities=16%  Similarity=0.312  Sum_probs=23.3

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHH--HHHHCC
Q ss_conf             1668720048753877889999999--997099
Q gi|254780295|r   11 NGSGYFGWQRQKNGSSIQGSIEKAI--FLVTGE   41 (247)
Q Consensus        11 dGt~y~G~q~Q~~~~TVq~~le~aL--~~~~~~   41 (247)
                      .||+|.=|+...-.+||+..|++|-  .+++|-
T Consensus        23 SGTRF~VF~~~G~aR~v~EK~~DAA~VH~LTG~   55 (382)
T TIGR02635        23 SGTRFKVFKQEGAARNVFEKLEDAALVHKLTGI   55 (382)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             776300027768998765558889999886277


No 32 
>pfam03645 Tctex-1 Tctex-1 family. Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Probab=24.73  E-value=53  Score=14.41  Aligned_cols=38  Identities=18%  Similarity=0.220  Sum_probs=24.5

Q ss_pred             CCHHHHHHHHHHHHHCCCEE----EEECCCCCCCCEEEEEEE
Q ss_conf             77889999999997099569----997112138612223468
Q gi|254780295|r   25 SSIQGSIEKAIFLVTGEIVV----VHGAGRTDSGVHALRQVA   62 (247)
Q Consensus        25 ~TVq~~le~aL~~~~~~~~~----~~~a~RTD~GVhA~~qv~   62 (247)
                      ..+-+++.+.|.++...+-+    +.-..+++.|+|+..+..
T Consensus        31 ~~i~~~I~~~lk~l~~~ryK~vv~v~I~q~~~qgi~~~s~~~   72 (101)
T pfam03645        31 KEISETILKRLKELGGKRYKYVVQVTIGQKKGQGIHVASRCL   72 (101)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCEEEEEEE
T ss_conf             999999999998427987179999999860798716678877


No 33 
>COG1877 OtsB Trehalose-6-phosphatase [Carbohydrate transport and metabolism]
Probab=24.69  E-value=55  Score=14.30  Aligned_cols=58  Identities=12%  Similarity=0.159  Sum_probs=43.1

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC--EEEEECCCCCCCCEEEEE
Q ss_conf             22999999716687200487538778899999999970995--699971121386122234
Q gi|254780295|r    2 IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEI--VVVHGAGRTDSGVHALRQ   60 (247)
Q Consensus         2 ~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~--~~~~~a~RTD~GVhA~~q   60 (247)
                      .+.++.+-|||| -...-..|..-.+-+.+.+.|.++.-+.  +-.+-|||.=+.+...-.
T Consensus        17 ~~~~~~lDyDGT-l~~i~~~p~~a~~~~~l~~lL~~Las~~~~~v~iiSGR~~~~l~~~~~   76 (266)
T COG1877          17 RKRLLFLDYDGT-LTEIVPHPEAAVPDDRLLSLLQDLASDPRNVVAIISGRSLAELERLFG   76 (266)
T ss_pred             CCEEEEEECCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHCC
T ss_conf             661899953664-224456853347877899999999846797599994799899998548


No 34 
>TIGR01900 dapE-gram_pos succinyl-diaminopimelate desuccinylase; InterPro: IPR010174   This entry represents a clade of succinyl-diaminopimelate desuccinylases from actinobacteria (high-GC Gram-positives) and is based on the characterisation of the enzyme from Corynebacterium glutamicum . This enzyme is involved in the biosynthesis of lysine, and is related to the enzyme acetylornithine deacetylase and other amidases and peptidases. They are classified as non-peptidases homologs belonging to MEROPS peptidase family M20A.
Probab=24.67  E-value=55  Score=14.30  Aligned_cols=84  Identities=24%  Similarity=0.248  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHHHHHCCCEEEEE-----CCCCCCCCEEEEEEE-EEEEC---CCCC-----C-HHHHH-HHHHHHCCCCC
Q ss_conf             77889999999997099569997-----112138612223468-86406---3211-----0-46899-99986188876
Q gi|254780295|r   25 SSIQGSIEKAIFLVTGEIVVVHG-----AGRTDSGVHALRQVA-HFDLV---REWV-----P-VILCK-ALNAYLKISDT   88 (247)
Q Consensus        25 ~TVq~~le~aL~~~~~~~~~~~~-----a~RTD~GVhA~~qv~-~f~~~---~~~~-----~-~~~~~-~lN~~L~~p~~   88 (247)
                      .-+.+++|++|..+-.+-+.+..     -.|||.|--++=..+ |+|+-   ..++     | +.+.+ .+- +-+ |+|
T Consensus        16 ~~~~DE~E~~L~nl~~~~~~V~R~~~~V~A~T~~G~~SRV~LAGH~DTVP~~DNlPPkWlePGdslireeia-h~~-~ED   93 (373)
T TIGR01900        16 KQLADEVEDALRNLELEGLEVFRFNDTVLARTDFGKASRVILAGHLDTVPVIDNLPPKWLEPGDSLIREEIA-HAR-VED   93 (373)
T ss_pred             CCHHHHHHHHHHHCCCCCCEEEEECCEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHH-HCC-CCC
T ss_conf             630378999998517887179970783797507888421455244452042137784324765035565454-246-546


Q ss_pred             CCCCCCCCCCCCCCCEECCCCEEEEEEE
Q ss_conf             5434432267775500021002235568
Q gi|254780295|r   89 ISILNLSIVDKQFHARFSAIRRSYLYRI  116 (247)
Q Consensus        89 Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i  116 (247)
                      =..+.+-.|+.      -+.--.|.|.+
T Consensus        94 ~~lyG~G~~DM------K~~~AV~L~~~  115 (373)
T TIGR01900        94 RVLYGRGAVDM------KASLAVYLYLA  115 (373)
T ss_pred             CEEECCCCCCC------CHHHHHHHHHH
T ss_conf             35743775210------11468999998


No 35 
>TIGR02610 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein; InterPro: IPR013433    Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria..
Probab=24.57  E-value=43  Score=14.94  Aligned_cols=52  Identities=19%  Similarity=0.238  Sum_probs=30.4

Q ss_pred             HHHHHHHHH----------CCCEEEEECCCCCCCCEEEEEEEEEEECCCCC--------CHHHHHHHHHHH
Q ss_conf             999999970----------99569997112138612223468864063211--------046899999861
Q gi|254780295|r   31 IEKAIFLVT----------GEIVVVHGAGRTDSGVHALRQVAHFDLVREWV--------PVILCKALNAYL   83 (247)
Q Consensus        31 le~aL~~~~----------~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~--------~~~~~~~lN~~L   83 (247)
                      +|++..|++          |..+++..|| -|=-||-..|-+.++++..+-        ..+|.++|...|
T Consensus        21 ~e~la~KL~d~Ygl~~~W~GDtl~~aRsG-v~Gav~~g~~~irv~~eLG~llSaM~g~iksEI~raLdk~L   90 (91)
T TIGR02610        21 AEDLARKLTDRYGLASHWEGDTLRIARSG-VDGAVHLGEESIRVEVELGMLLSAMSGTIKSEIERALDKAL   90 (91)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEEECC-CCCEEEECCCEEEEEEEECHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             99999863654388545789766777516-77336427841688631011653028753688999988633


No 36 
>KOG2894 consensus
Probab=22.43  E-value=61  Score=14.04  Aligned_cols=17  Identities=12%  Similarity=0.216  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999976
Q gi|254780295|r  194 LHTQIRSFVGSLKLVGD  210 (247)
Q Consensus       194 L~~mVR~mVG~li~v~~  210 (247)
                      .+.-||.+--+.++-+.
T Consensus       272 vh~DVR~~sDAt~ekdE  288 (331)
T KOG2894         272 VHDDVRLISDATVEKDE  288 (331)
T ss_pred             CHHHHHHHHHHCCCCCC
T ss_conf             30033322210003465


No 37 
>pfam09153 DUF1938 Domain of unknown function (DUF1938). Members of this family, which are predominantly found in the archaeal protein O6-alkylguanine-DNA alkyltransferase, adopt a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. Their exact function has not, as yet, been defined, though it has been postulated that they confer thermostability to the archaeal protein.
Probab=22.21  E-value=59  Score=14.13  Aligned_cols=26  Identities=19%  Similarity=0.317  Sum_probs=22.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20011315888899999999999999
Q gi|254780295|r  182 NLIEIRVVARSFLHTQIRSFVGSLKL  207 (247)
Q Consensus       182 ~~i~i~i~g~~FL~~mVR~mVG~li~  207 (247)
                      .-+.|.+.|..||+++|+.|+..|-.
T Consensus        25 qGI~fSlDg~e~l~~ri~~L~~~L~k   50 (86)
T pfam09153        25 QGIAFSLDGPEFLKHRISRLISHLEK   50 (86)
T ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf             15999716388999999999999971


No 38 
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB; InterPro: IPR006379   This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterised by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (IPR006357 from INTERPRO) by homology and the predicted secondary structure of this domain by PSI-PRED. The IIB subfamilys Class II domain has the following predicted structure: Helix-Sheet-Sheet-(Helix or Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB subfamily consists of trehalose-6-phosphatase, plant and cyanobacterial sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase, a large subfamily of Cof-like hydrolases, containing many closely related bacterial sequences, a hypothetical equivalog containing the Escherichia coli YedP protein, as well as two other small clusters whose relationship to the other groups is unclear.; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=21.45  E-value=64  Score=13.92  Aligned_cols=52  Identities=13%  Similarity=0.208  Sum_probs=36.3

Q ss_pred             EEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCC-CEEE-EECCCCCCCCEEE
Q ss_conf             999971668720048753877889999999997099-5699-9711213861222
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGE-IVVV-HGAGRTDSGVHAL   58 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~-~~~~-~~a~RTD~GVhA~   58 (247)
                      +.+=|||| .-.+...|+...+..+++.+|.++... .+++ +.+||+=+-+-.+
T Consensus         2 ~~~D~DGT-L~~~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~~vTGR~~~~~~~l   55 (261)
T TIGR01484         2 LFFDLDGT-LLDPGPNPEAHELSEELIEALERLREKLGVKVVLVTGRSLAEIKEL   55 (261)
T ss_pred             EEEECCCC-CCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHH
T ss_conf             57402401-2789888422106867899999999716941899738658999999


No 39 
>TIGR01822 2am3keto_CoA 2-amino-3-ketobutyrate coenzyme A ligase; InterPro: IPR011282   This entry represents a narrowly defined clade of animal and bacterial (almost exclusively proteobacterial) 2-amino-3-ketobutyrate--CoA ligase. This enzyme can act in threonine catabolism. The closest homologue from Bacillus subtilis, and sequences like it, may be functionally equivalent but were not included in the model because of difficulty in finding reports of function.; GO: 0008890 glycine C-acetyltransferase activity.
Probab=21.04  E-value=55  Score=14.28  Aligned_cols=69  Identities=20%  Similarity=0.206  Sum_probs=45.5

Q ss_pred             CHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             78899999999970995699971121386122234688640632110468999998618887654344322677755000
Q gi|254780295|r   26 SIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARF  105 (247)
Q Consensus        26 TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~p~~Irv~~~~~v~~~FhaR~  105 (247)
                      .+-.+||+.|...++.+-.|..+|==|+    .|=+  |++-...+...+-++||... .=++||.              
T Consensus        85 d~HK~LE~~iA~F~~~EDtILY~scFDA----NgGl--FE~LLg~eDAiiSDaLNHAS-IIDGvRL--------------  143 (395)
T TIGR01822        85 DLHKELEAKIAAFLGTEDTILYASCFDA----NGGL--FETLLGEEDAIISDALNHAS-IIDGVRL--------------  143 (395)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHC----CCCC--CHHHCCCCCCCHHHHHCCCH-HHHHHHH--------------
T ss_conf             3568999999997165304454566630----5542--20104754422102224310-2300354--------------


Q ss_pred             CCCCEEEEEEE
Q ss_conf             21002235568
Q gi|254780295|r  106 SAIRRSYLYRI  116 (247)
Q Consensus       106 ~a~~R~Y~Y~i  116 (247)
                       ||.|+|+|.=
T Consensus       144 -CKAkrYRY~~  153 (395)
T TIGR01822       144 -CKAKRYRYAN  153 (395)
T ss_pred             -HHHHHHHHHC
T ss_conf             -2233432305


No 40 
>cd01243 PH_MRCK MRCK (myotonic dystrophy-related Cdc42-binding kinase)  pleckstrin homology (PH) domain. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH domain and a p21 binding motif. It has been shown to promote cytoskeletal reorganization, which affects many biological processes.  The MRCK PH domain is responsible for its targeting to cell to cell junctions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=20.69  E-value=46  Score=14.74  Aligned_cols=36  Identities=14%  Similarity=0.272  Sum_probs=22.3

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             668720048753877889999999997099569997
Q gi|254780295|r   12 GSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHG   47 (247)
Q Consensus        12 Gt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~   47 (247)
                      ||.|.||-+.|+.-.|..-=+++..-+.+.++-+.-
T Consensus         1 gtayEG~vkvPk~~~vkkGW~r~yvVv~~~Kl~lYd   36 (122)
T cd01243           1 GTAYEGHVKIPKPGGVKKGWQRALVVVCDFKLFLYD   36 (122)
T ss_pred             CCCEEEEEECCCCCCCCCCCEEEEEEEECCEEEEEE
T ss_conf             953057785258887655735889999678899986


No 41 
>pfam07782 DC_STAMP DC-STAMP-like protein. This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family.
Probab=20.30  E-value=41  Score=15.04  Aligned_cols=35  Identities=14%  Similarity=0.210  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             33320011315888899999999999999976899
Q gi|254780295|r  179 SFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKW  213 (247)
Q Consensus       179 ~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~  213 (247)
                      +....+.++|.|+|++-.+.|.++++.-...+...
T Consensus        94 ~~~~~v~i~i~G~g~~a~llr~~~~~f~~~~~~~~  128 (191)
T pfam07782        94 QGPHGVEVTVTGTGAMADLLRETVGAFNPSEKSSF  128 (191)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             57884589997562099999999984586554530


Done!