Query         029664
Match_columns 190
No_of_seqs    129 out of 615
Neff          8.4 
Searched_HMMs 46136
Date          Fri Mar 29 16:32:38 2013
Command       hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029664.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029664hhsearch_cdd -cpu 12 -v 0 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF07823 CPDase:  Cyclic phosph 100.0 2.4E-32 5.2E-37  212.7  14.3  169   16-187     2-196 (196)
  2 COG1514 LigT 2'-5' RNA ligase  100.0 1.7E-27 3.6E-32  182.8  16.2  166   16-189     2-180 (180)
  3 PRK15124 2'-5' RNA ligase; Pro  99.9   3E-26 6.6E-31  175.8  12.9  159   13-188     5-175 (176)
  4 PRK13679 hypothetical protein;  99.9 9.7E-25 2.1E-29  166.3  17.1  163   16-188     2-168 (168)
  5 TIGR02258 2_5_ligase 2'-5' RNA  99.9   9E-25 1.9E-29  167.8  16.6  164   15-187     3-179 (179)
  6 PF13563 2_5_RNA_ligase2:  2'-5  99.8 2.3E-20 4.9E-25  139.1   4.7  143   23-172     1-152 (153)
  7 PHA02574 57B hypothetical prot  99.8 4.7E-19   1E-23  131.5   9.0  113   10-133     6-119 (149)
  8 PF10469 AKAP7_NLS:  AKAP7 2'5'  99.4 2.2E-11 4.8E-16   95.8  15.3  170   17-187     3-209 (209)
  9 PF02834 LigT_PEase:  LigT like  99.0 5.7E-10 1.2E-14   75.6   6.2   75   22-96      2-87  (87)
 10 TIGR03223 Phn_opern_protn puta  98.8 1.7E-07 3.7E-12   74.1  11.9  134   47-189    56-228 (228)
 11 PLN00108 unknown protein; Prov  98.7 9.7E-07 2.1E-11   71.0  15.5  175   13-189    34-256 (257)
 12 PF02834 LigT_PEase:  LigT like  98.4 2.3E-07 4.9E-12   62.7   2.7   76  102-179     8-87  (87)
 13 PF09749 HVSL:  Uncharacterised  98.1  0.0004 8.6E-09   55.8  15.8  117   19-136    46-192 (239)
 14 PHA02977 hypothetical protein;  97.8 0.00048   1E-08   50.6  10.5   57   93-149   124-189 (201)
 15 PF06299 DUF1045:  Protein of u  97.6   0.001 2.2E-08   50.0  10.0  113   52-171     1-153 (160)
 16 PF05213 Corona_NS2A:  Coronavi  96.9   0.003 6.4E-08   49.4   5.8  102   27-134    20-132 (248)
 17 COG5255 Uncharacterized protei  95.4   0.068 1.5E-06   41.6   6.6  116   14-133    40-186 (239)
 18 PF08302 tRNA_lig_CPD:  Fungal   94.0     1.5 3.2E-05   35.7  11.5  113   13-134    71-211 (257)
 19 PRK13679 hypothetical protein;  93.6    0.18 3.9E-06   38.1   5.3   71   95-166     3-74  (168)
 20 PF06299 DUF1045:  Protein of u  91.3    0.27 5.8E-06   37.1   3.5   41   47-87    107-148 (160)
 21 PHA02574 57B hypothetical prot  90.5    0.69 1.5E-05   34.5   5.0   35   17-54     80-117 (149)
 22 COG1514 LigT 2'-5' RNA ligase   90.2     1.2 2.6E-05   34.2   6.3   74   95-169     3-81  (180)
 23 PF13563 2_5_RNA_ligase2:  2'-5  87.2    0.34 7.4E-06   35.2   1.5   49  121-169    21-69  (153)
 24 TIGR02258 2_5_ligase 2'-5' RNA  87.0     3.1 6.7E-05   31.3   6.8   72   95-168     3-80  (179)
 25 PF07823 CPDase:  Cyclic phosph  86.7    0.71 1.5E-05   35.9   3.1   39   94-133     4-46  (196)
 26 TIGR03223 Phn_opern_protn puta  86.3       1 2.2E-05   36.0   3.8   41   47-87    167-208 (228)
 27 KOG3102 Uncharacterized conser  79.1      23 0.00049   28.1   8.5   86   48-135   121-220 (269)
 28 PHA02977 hypothetical protein;  78.4     3.3 7.2E-05   30.7   3.6   40   44-84    160-199 (201)
 29 PF08975 2H-phosphodiest:  Doma  74.9      23 0.00049   25.4   7.0   74   14-87     12-111 (118)
 30 PRK15124 2'-5' RNA ligase; Pro  68.6      21 0.00046   26.9   6.2   41  125-167    41-82  (176)
 31 PF07476 MAAL_C:  Methylasparta  57.8      16 0.00035   29.2   3.7   58   49-114    72-134 (248)
 32 KOG2814 Transcription coactiva  35.4 2.2E+02  0.0049   24.1   7.3  112   74-187   212-345 (345)
 33 PF07485 DUF1529:  Domain of Un  34.7 1.1E+02  0.0025   21.9   4.9   59   55-117    61-121 (123)
 34 PF08302 tRNA_lig_CPD:  Fungal   33.2 2.6E+02  0.0057   22.6  11.0   97   28-135     3-125 (257)
 35 PF13466 STAS_2:  STAS domain    31.8      45 0.00097   21.2   2.2   37   51-87      1-38  (80)
 36 PF13822 ACC_epsilon:  Acyl-CoA  31.8      74  0.0016   19.8   3.1   26  125-150     1-26  (62)
 37 PRK11633 cell division protein  29.7   1E+02  0.0022   24.6   4.4   68   55-127   155-226 (226)
 38 PF05213 Corona_NS2A:  Coronavi  28.6      93   0.002   24.8   3.8   39  104-143    23-61  (248)
 39 PF04571 Lipin_N:  lipin, N-ter  26.8      86  0.0019   22.1   3.0   45   51-100    22-67  (110)
 40 TIGR02157 PA_CoA_Oxy2 phenylac  26.7      34 0.00074   23.2   1.0   15   14-28     42-56  (90)
 41 PRK13781 paaB phenylacetate-Co  21.6      49  0.0011   22.7   1.0   15   14-28     47-61  (95)
 42 PF05881 CNPase:  2',3'-cyclic   20.3 3.1E+02  0.0067   21.9   5.2   83   46-133    59-149 (235)
 43 cd07016 S14_ClpP_1 Caseinolyti  20.3 1.4E+02  0.0029   21.9   3.3   36   50-86      2-41  (160)

No 1  
>PF07823 CPDase:  Cyclic phosphodiesterase-like protein;  InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction  Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate.  ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=100.00  E-value=2.4e-32  Score=212.71  Aligned_cols=169  Identities=38%  Similarity=0.704  Sum_probs=117.1

Q ss_pred             eEEEEEeCCh--hHHHHHHHHHHHHHhhcCC--CCCCCeEEeecCCcC-ChhHHHHHHHHHhccCCce-----eEEEcee
Q 029664           16 FYSVWAIPPD--EVRARVKKLMEGLRSEFGG--PQFDPHVTVVGAMSL-TADDALEKFKSACNGLKAY-----NCTVNRV   85 (190)
Q Consensus        16 ~~slwl~P~~--~~~~~l~~~~~~l~~~~~~--~~~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf-----~l~~~~v   85 (190)
                      .||||++|++  +.+++|..+|+.|+..+.+  |.|.|||||.|.+.. ..+++.+.|+.++.+.+++     .++++++
T Consensus         2 ~~SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~~p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v~~~~v   81 (196)
T PF07823_consen    2 PYSLWLVPPPGSPLYERLKTLISSLASLFPGSPPPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTVRFDKV   81 (196)
T ss_dssp             -EEEEEEE-T--TTHHHHHHHHHHHHHHST---------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EEEEEEE
T ss_pred             eEEEEEcCCCCccHHHHHHHHHHHHHHHCCCCCCCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEEEeeeE
Confidence            4999999999  8999999999999999985  899999999988875 5778888898888889999     9999999


Q ss_pred             eeccceeeEEEEEeeCCccccchHHHHhhhh----------CCCCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccc--
Q 029664           86 ATGTFFYQCVFLLLHPTPEVAEPSSHCCGHF----------GYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDES--  153 (190)
Q Consensus        86 ~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~----------g~~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~--  153 (190)
                      ..++.|+|+||+.++++++|.+|++.+++.+          +.....+|+|||||+|+++...+++.+..........  
T Consensus        82 ~~g~~yfq~vyl~v~~t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLlY~d~~~~e~~~~~~~~~~i~~~l~  161 (196)
T PF07823_consen   82 ASGDKYFQCVYLEVEKTPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLLYGDLPPEEKAEAAEIAQRIDDALG  161 (196)
T ss_dssp             EEEEETTEEEEEEE---HHHHHHHCHHHHCT----------T----S----EEEEE-----HHHHHHHHHHHHHH-TT--
T ss_pred             eeCCeEEEEEEEEecCChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEEEcCCCcccHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999987          2335679999999999999877665544444443333  


Q ss_pred             ----cCCccEEeceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          154 ----IGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       154 ----~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                          ..+.+|.+++|.||++++   ++..|++|++++|
T Consensus       162 ~~~~~~~~~~~~~~l~lv~t~g---~v~~W~~l~~~~l  196 (196)
T PF07823_consen  162 VDSGISGLGWEGGELKLVRTDG---PVEEWEVLASVDL  196 (196)
T ss_dssp             ----GTT-EEEEEEEEEEE--T---T-TT-EEEEEEE-
T ss_pred             ccccCCCCCEeccEEEEEEcCC---CCCcEEEEEEEeC
Confidence                345699999999999988   4789999999986


No 2  
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.96  E-value=1.7e-27  Score=182.76  Aligned_cols=166  Identities=16%  Similarity=0.225  Sum_probs=133.4

Q ss_pred             eEEEEEeCChhHHHHHHHHHHHHHhhc---CCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeecc
Q 029664           16 FYSVWAIPPDEVRARVKKLMEGLRSEF---GGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGT   89 (190)
Q Consensus        16 ~~slwl~P~~~~~~~l~~~~~~l~~~~---~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~   89 (190)
                      .|.+.+.||+++++.+.++++.++...   +..+.++||||+  |+++. ..+++.+.|..+.... +|+++++|+|+|+
T Consensus         2 RlFiAl~~p~~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~F~   80 (180)
T COG1514           2 RLFIALDPPAEIAERLARIRARLKGARAIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGSFP   80 (180)
T ss_pred             eeEEEecCCHHHHHHHHHHHHhcCcccccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcccC
Confidence            466777799999999999999998876   355679999999  99986 5677888888888777 9999999999865


Q ss_pred             --ceeeEEEEEeeCCccccchHHHHhhh---hCCC-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcc-cccCCccEEec
Q 029664           90 --FFYQCVFLLLHPTPEVAEPSSHCCGH---FGYK-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLD-ESIGSLSFPIT  162 (190)
Q Consensus        90 --~~~~vv~l~v~~~~~L~~L~~~l~~~---~g~~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~-~~~~~~~~~v~  162 (190)
                        .+++++|+++++++.|.+|++.+.+.   .|+. +.++|+|||||+|.+.. .   .+.+.+..+. ..+ + ++.|+
T Consensus        81 ~~~~~rvi~~~v~~~~~L~~L~~~l~~~~~~~g~~~~~r~F~PHvTl~r~k~~-~---~~~~~~~~~~~~~~-~-~~~vd  154 (180)
T COG1514          81 NPRRPRVIWVGVEETEELRALAEELERALARLGLRPEERPFVPHVTLARVKSK-D---KLVEALGEFKNVEF-G-EMEVD  154 (180)
T ss_pred             CCCCCcEEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCCCcCCCEEEEeeccc-c---hhhhhhhhhccccc-c-ceEee
Confidence              47899999999989999999999974   4664 78999999999998761 1   2222222211 111 2 67899


Q ss_pred             eEEEEEecCCCCCcCCceEeEEEcCCC
Q 029664          163 RLQLWKTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       163 ~l~L~~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      +|.||+|..++ .|+.|+.+.+|+|.+
T Consensus       155 ~~~L~~S~l~~-~gp~Y~~~~~~~L~~  180 (180)
T COG1514         155 RFSLYSSTLTP-GGPIYETLKEFPLSG  180 (180)
T ss_pred             EEEEEEEeeCC-CCCEEEEEEEEecCC
Confidence            99999998876 589999999999975


No 3  
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.94  E-value=3e-26  Score=175.83  Aligned_cols=159  Identities=16%  Similarity=0.232  Sum_probs=119.7

Q ss_pred             CCceEEEEEeCChhHHHHHHHHHHHHHhh---cCCCCCCCeEEee--cCCcCChhHHHHHHHHHhc--cCCceeEEEcee
Q 029664           13 KKGFYSVWAIPPDEVRARVKKLMEGLRSE---FGGPQFDPHVTVV--GAMSLTADDALEKFKSACN--GLKAYNCTVNRV   85 (190)
Q Consensus        13 ~~~~~slwl~P~~~~~~~l~~~~~~l~~~---~~~~~~~pHiTL~--g~~~~~~~~~~~~l~~~~~--~~~pf~l~~~~v   85 (190)
                      ++.+++|+  +|+++++.|.++++.+...   .+.++.+.||||+  |+++.   +.++.+.++++  ..+||+++++|+
T Consensus         5 ~RlFiAl~--~p~~~~~~l~~~~~~~~~~~~~rwv~~~nlHiTL~FlG~v~~---~~~~~l~~~l~~~~~~pF~l~l~~~   79 (176)
T PRK15124          5 KRLFFAID--LPDEIRQQIIHWRATHFPPEAGRPVAAANLHLTLAFLGEVSA---EKQQALSQLAGRIRQPGFTLTLDDA   79 (176)
T ss_pred             eEEEEEeC--CCHHHHHHHHHHHHHhccccCcccccccccEEEEEecCCCCH---HHHHHHHHHHHhcccCCeEEEECcc
Confidence            34455544  8889999999999887543   2345678999999  99863   34444444444  478999999999


Q ss_pred             eeccceeeEEEEEeeC-CccccchHHHHhhh---hCC-CCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEE
Q 029664           86 ATGTFFYQCVFLLLHP-TPEVAEPSSHCCGH---FGY-KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFP  160 (190)
Q Consensus        86 ~~~~~~~~vv~l~v~~-~~~L~~L~~~l~~~---~g~-~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (190)
                      |+|+ .|++||+++++ .+.|.+||+++++.   +|+ .+.++|+|||||||......   .    +..  . .....|.
T Consensus        80 g~Fp-~prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~~e~r~f~PHiTLaR~~~~~~---~----~~~--~-~~~~~~~  148 (176)
T PRK15124         80 GQWP-RSRVVWLGMRQPPRGLLQLANMLRSQAARSGCYQSPQPFHPHITLLRDASRPV---A----IPP--P-GFNWSFP  148 (176)
T ss_pred             cCcC-CCCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCCCCCCCCCCCEeeccCCCCcc---c----ccC--C-CCCCceE
Confidence            9976 58999999975 67999999999874   577 47899999999999643211   1    111  1 1133689


Q ss_pred             eceEEEEEecCCCCCcCCceEeEEEcCC
Q 029664          161 ITRLQLWKTDTEDTTLKSWEMVAECNLS  188 (190)
Q Consensus       161 v~~l~L~~s~~~~~~~~~w~~l~~~~L~  188 (190)
                      |++|.||+|...+ .|+.|+++++|+|.
T Consensus       149 v~~~~L~~S~l~~-~g~~Y~~l~~~~L~  175 (176)
T PRK15124        149 VTEFTLYASSFAR-GRTRYTPLQRWPLT  175 (176)
T ss_pred             cCEEEEEEEeccC-CCCEEEEEEEEeCC
Confidence            9999999998765 57899999999996


No 4  
>PRK13679 hypothetical protein; Provisional
Probab=99.93  E-value=9.7e-25  Score=166.30  Aligned_cols=163  Identities=16%  Similarity=0.203  Sum_probs=126.5

Q ss_pred             eEEEEEeCChhHHHHHHHHHHHHHhhcCCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeecccee
Q 029664           16 FYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGTFFY   92 (190)
Q Consensus        16 ~~slwl~P~~~~~~~l~~~~~~l~~~~~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~   92 (190)
                      .|+|.+.|+.++++.+.++++.+...  ...++|||||.  |+++. ..+++.+.+++++....||+++++++++++..+
T Consensus         2 ~~~iai~~p~~~~~~l~~~~~~~~~~--~~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~F~~~~   79 (168)
T PRK13679          2 KYGIVLFPSKKIQDFANSYRKRYDPH--YALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAPTN   79 (168)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhhCcc--cccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEeccccCCCCC
Confidence            67888889998888888888777543  23467899998  66754 456788888888888999999999999876556


Q ss_pred             eEEEEEeeCCccccchHHHHhhhh-CCCCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecC
Q 029664           93 QCVFLLLHPTPEVAEPSSHCCGHF-GYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDT  171 (190)
Q Consensus        93 ~vv~l~v~~~~~L~~L~~~l~~~~-g~~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~  171 (190)
                      ++||++++++++|.+||+++++.+ +..+.++|+|||||||... .++...+.+.++..   -....|.|++|.||....
T Consensus        80 ~vl~l~~~~~~~L~~L~~~l~~~~~~~~~~~~f~PHiTlar~~~-~~~~~~~~~~l~~~---~~~~~~~v~~i~L~~~~~  155 (168)
T PRK13679         80 NVIYFKVEKTEELEELHERLHSGDFYGEAEYAFVPHITIGQGLS-DDEHEDVLGQLKMA---DVDHEETIDRFHLLYQLE  155 (168)
T ss_pred             CEEEEEccCCHHHHHHHHHHHhcccccccCCCCCCeEEeeCCCC-cHHHHHHHHHHhcC---CcceeEEECeEEEEEECC
Confidence            999999999899999999998743 3346788999999998643 34445555555431   223378999999996544


Q ss_pred             CCCCcCCceEeEEEcCC
Q 029664          172 EDTTLKSWEMVAECNLS  188 (190)
Q Consensus       172 ~~~~~~~w~~l~~~~L~  188 (190)
                      +    ..|+.+.+|.|+
T Consensus       156 ~----~~w~~~~~~~~~  168 (168)
T PRK13679        156 N----GSWTVYETFRLG  168 (168)
T ss_pred             C----CeEEEEEEeeCC
Confidence            3    499999999986


No 5  
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.93  E-value=9e-25  Score=167.78  Aligned_cols=164  Identities=14%  Similarity=0.221  Sum_probs=122.6

Q ss_pred             ceEEEEEeCChhHHHHHHHHHHHHHhhc----CCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           15 GFYSVWAIPPDEVRARVKKLMEGLRSEF----GGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        15 ~~~slwl~P~~~~~~~l~~~~~~l~~~~----~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      .+++|+  |+.++++.|.++++.++...    +.++.++||||.  |+++. ..+++.+.|.+++  .++|+++++|+|+
T Consensus         3 ~FiAl~--~p~~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~~   78 (179)
T TIGR02258         3 LFIAID--LPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIGV   78 (179)
T ss_pred             EEEEec--CCHHHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeeee
Confidence            445555  88899999999999987432    234567899998  87763 3445666666654  3669999999998


Q ss_pred             ccc--eeeEEEEEeeCCccccchHHHHhhhh---CCC-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEe
Q 029664           88 GTF--FYQCVFLLLHPTPEVAEPSSHCCGHF---GYK-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPI  161 (190)
Q Consensus        88 ~~~--~~~vv~l~v~~~~~L~~L~~~l~~~~---g~~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v  161 (190)
                      ++.  .++++|++++.++.|.+|++.+.+.+   |+. +.++|+|||||||......   .+.+.+.... ...+..|.|
T Consensus        79 F~~~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~~g~~~~~~~f~PHiTlar~~~~~~---~~~~~~~~~~-~~~~~~~~v  154 (179)
T TIGR02258        79 FGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKP---GVPEFLQEFA-NEEFGSFHV  154 (179)
T ss_pred             CCCCCCCeEEEEeeCCCHHHHHHHHHHHHHHHHcCCCCCCCCcCCCEEEEEecCCcH---hHHHHHHHhC-CCCCCceEe
Confidence            643  47899999998889999999998753   553 6789999999999765432   2223333222 144679999


Q ss_pred             ceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          162 TRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       162 ~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                      ++|.||+|.... .|+.|+++++|+|
T Consensus       155 ~~i~L~~S~~~~-~g~~Y~~l~~~~l  179 (179)
T TIGR02258       155 DEFHLYSSTLTP-GGPIYEPLARFQL  179 (179)
T ss_pred             eEEEEEEeeccC-CCCcceEEEEEcC
Confidence            999999987765 4789999999997


No 6  
>PF13563 2_5_RNA_ligase2:  2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.81  E-value=2.3e-20  Score=139.10  Aligned_cols=143  Identities=22%  Similarity=0.397  Sum_probs=79.5

Q ss_pred             CChhHHHHHHHHHHHHHhhcC--CCCCCCeEEeecCCcC--ChhHHHHHHHHHhccCCceeEEEceeeeccceeeEEEEE
Q 029664           23 PPDEVRARVKKLMEGLRSEFG--GPQFDPHVTVVGAMSL--TADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLL   98 (190)
Q Consensus        23 P~~~~~~~l~~~~~~l~~~~~--~~~~~pHiTL~g~~~~--~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~~vv~l~   98 (190)
                      ||+++.+++.++.   +..+.  ....+|||||.+....  ..+++.+.|..++.+.++|+++++++++++...++||+.
T Consensus         1 pp~~~~~~i~~lr---~~~~~~~~~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~~~~vi~l~   77 (153)
T PF13563_consen    1 PPDELAEEIEALR---RQKGDKRYPRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPGKGRVIFLN   77 (153)
T ss_dssp             ------------G---T-TTEEE--GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESSSSSSEEEE
T ss_pred             Ccccccccchhhh---cccCCCCCCCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCCCCCEEEEE
Confidence            5665666655554   12222  4556799999954443  337899999999999999999999999865445699999


Q ss_pred             eeCCccccchHHHHhhhhC---CC-CC-CCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecCC
Q 029664           99 LHPTPEVAEPSSHCCGHFG---YK-SS-TPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTE  172 (190)
Q Consensus        99 v~~~~~L~~L~~~l~~~~g---~~-~~-~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~  172 (190)
                      ++.++.|.+||+++.+.+.   .. +. ++|+|||||||....... ..+.+.+   .....+.+|.|++|.|++++..
T Consensus        78 ~~~~~~L~~L~~~l~~~~~~~~~~~~~~~~~~PHiTia~~~~~~~~-~~~~~~~---~~~~~~~~~~v~~l~L~~~~~~  152 (153)
T PF13563_consen   78 VEPSPELEALHRALREALRPFGFKQDSYRPFRPHITIARRLSPKQA-AEAIEKL---QSEFPPISFTVDELALVRSDGN  152 (153)
T ss_dssp             EEE-HHHHHHHHHHHHHHHHHHGGGGGGS----EEEEEEESS---------------------EEEEE-EEEEEEEE--
T ss_pred             cCCCHHHHHHHHHHHHHHHHcCCccccCCCcceEEEEeccCCcchh-HHHHHHH---hCcCCCcEEEEeEEEEEEECCc
Confidence            9999999999999998643   22 22 899999999997655332 3333333   2235567999999999997653


No 7  
>PHA02574 57B hypothetical protein; Provisional
Probab=99.79  E-value=4.7e-19  Score=131.50  Aligned_cols=113  Identities=12%  Similarity=0.074  Sum_probs=90.0

Q ss_pred             eCCCCceEEEEEeCChhHHHHHHHHHHHHHhhcCCCCCCCeEEeecCCcCChhHHHHHHHHHhccCCceeEEEceeeecc
Q 029664           10 DKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGT   89 (190)
Q Consensus        10 ~~~~~~~~slwl~P~~~~~~~l~~~~~~l~~~~~~~~~~pHiTL~g~~~~~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~   89 (190)
                      ....+.+++||  ++++++++|.++++++......++.++|+||+-+     ++.++.+..   +.++|.++++|+|.++
T Consensus         6 ~~~~RlF~Al~--~~~~~r~~L~~lq~~l~~~r~V~~enLHlTL~F~-----~~~v~~l~~---~~~~F~l~l~glG~F~   75 (149)
T PHA02574          6 EFSQGTYVAAK--FSEATLDALERLQRTLRIPNPVPRDKLHSTIVYS-----RVYVPFIPA---SGSTEVASSGHLEVWE   75 (149)
T ss_pred             cccceEEEEEc--CCHHHHHHHHHHHHhccCCcccCHHHCEEEEecC-----HHHhHHHhc---cCCCeEEEeccccccC
Confidence            33567888888  8889999999999997553345677899999861     233333433   6799999999999975


Q ss_pred             c-eeeEEEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeeeC
Q 029664           90 F-FYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYG  133 (190)
Q Consensus        90 ~-~~~vv~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar~  133 (190)
                      . .+|+||++++ +++|.+|++++++.+.-.+.++|+|||||+|.
T Consensus        76 ~~~~rvlWlg~~-~~~L~~L~~~l~~~l~~~~~r~F~PHITLaR~  119 (149)
T PHA02574         76 TQDKNALVLVLE-SEYLQCRHKYARALGATHDFDDYTPHITLSYD  119 (149)
T ss_pred             CCCCCEEEEEeC-CHHHHHHHHHHHHHhhcCCCCCcCCcEEEeec
Confidence            3 5899999998 99999999999997544556789999999994


No 8  
>PF10469 AKAP7_NLS:  AKAP7 2'5' RNA ligase-like domain;  InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus. 
Probab=99.39  E-value=2.2e-11  Score=95.75  Aligned_cols=170  Identities=15%  Similarity=0.161  Sum_probs=109.6

Q ss_pred             EEEEEeC-ChhHHHHHHHHHHHHHhhcC-------CCCCCCeEEee--cCCcC-ChhHHHHHHHHH---hcc----CCce
Q 029664           17 YSVWAIP-PDEVRARVKKLMEGLRSEFG-------GPQFDPHVTVV--GAMSL-TADDALEKFKSA---CNG----LKAY   78 (190)
Q Consensus        17 ~slwl~P-~~~~~~~l~~~~~~l~~~~~-------~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~---~~~----~~pf   78 (190)
                      |.|.+.- .+++.+.+.++++.+.....       .++..+||||.  +-.+. ..+...+.|+.+   +..    ..++
T Consensus         3 hFl~ipl~~~~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~~   82 (209)
T PF10469_consen    3 HFLCIPLNSPEIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPPL   82 (209)
T ss_pred             eEEEEECCCHHHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCCc
Confidence            5555544 36788999999998876543       23457899998  22221 233344444433   222    4999


Q ss_pred             eEEEceeeecc---ceeeEEEEEeeC---CccccchHHHHhhhh---CCC---CCC-CCcceeEeeeCCCC--HHHH--H
Q 029664           79 NCTVNRVATGT---FFYQCVFLLLHP---TPEVAEPSSHCCGHF---GYK---SST-PYMPHLSLLYGDLT--DDEK--K  141 (190)
Q Consensus        79 ~l~~~~v~~~~---~~~~vv~l~v~~---~~~L~~L~~~l~~~~---g~~---~~~-~f~PHlTLar~~~~--~~~~--~  141 (190)
                      .+++.|++++.   ...+|+|+++++   ...|.++.+.+.+.|   |+.   +.+ +|.||+||++....  ...+  .
T Consensus        83 ~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~~~~~~  162 (209)
T PF10469_consen   83 KITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKKRRQGN  162 (209)
T ss_pred             eEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEeccccccccccccC
Confidence            99999999832   245999999986   378999999998754   653   234 38999999996541  0010  1


Q ss_pred             --HHHHHHHhcccccCCccEEeceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          142 --IAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       142 --~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                        ...+.++.+.. ...+.+.|++|+|.+....+....-|..+++++|
T Consensus       163 ~~d~~~~~~~~~~-~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l  209 (209)
T PF10469_consen  163 KFDASELLEKYKD-FDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL  209 (209)
T ss_pred             ccccHHHHHHcCC-CccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence              11223333322 3335789999999885222223679999999987


No 9  
>PF02834 LigT_PEase:  LigT like Phosphoesterase;  InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=99.04  E-value=5.7e-10  Score=75.58  Aligned_cols=75  Identities=19%  Similarity=0.358  Sum_probs=59.6

Q ss_pred             eCChhHHHHHHHHHHHHHhhcC------CCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeeccc--
Q 029664           22 IPPDEVRARVKKLMEGLRSEFG------GPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGTF--   90 (190)
Q Consensus        22 ~P~~~~~~~l~~~~~~l~~~~~------~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~--   90 (190)
                      .|+++++++|.++++.++....      ..++++||||.  |+++. ..+++.+.+..++....+|++++++++.+++  
T Consensus         2 ~~p~~~~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~   81 (87)
T PF02834_consen    2 DLPEEIKEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRL   81 (87)
T ss_dssp             E-THHHHHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCC
Confidence            3788899999999999995542      35789999999  88863 4566788888888899999999999997543  


Q ss_pred             eeeEEE
Q 029664           91 FYQCVF   96 (190)
Q Consensus        91 ~~~vv~   96 (190)
                      .++++|
T Consensus        82 ~~rvi~   87 (87)
T PF02834_consen   82 RPRVIW   87 (87)
T ss_dssp             TCEEEE
T ss_pred             CCCCcC
Confidence            678888


No 10 
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=98.76  E-value=1.7e-07  Score=74.13  Aligned_cols=134  Identities=13%  Similarity=0.232  Sum_probs=94.0

Q ss_pred             CCCeEEeecCCcC----ChhHHHHHHHHHhccCCceeEE---EceeeeccceeeEEEEEeeCCccccchHHHHhhhhC-C
Q 029664           47 FDPHVTVVGAMSL----TADDALEKFKSACNGLKAYNCT---VNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFG-Y  118 (190)
Q Consensus        47 ~~pHiTL~g~~~~----~~~~~~~~l~~~~~~~~pf~l~---~~~v~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~g-~  118 (190)
                      .-.|+||+-+|..    +.+++.++++..+....||++.   +..+|.  +   .-+..+.++++|.+|+.++.+.|. +
T Consensus        56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~~~pf~i~~L~l~~Lg~--F---lAL~P~~~~~~L~~LAa~~V~~~d~f  130 (228)
T TIGR03223        56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAATRAPFALPPLRVALLGG--F---LALRPAAPCPALQALAAACVRELDPF  130 (228)
T ss_pred             cccceeecCCcccCCCCCHHHHHHHHHHHHhcCCCccCCcceeeeeCC--E---EEEeeCCCCHHHHHHHHHHHHhhhhc
Confidence            4579999988864    4678999999999999999865   333332  1   112234568999999999987542 1


Q ss_pred             ----C---------------------------CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEE
Q 029664          119 ----K---------------------------SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLW  167 (190)
Q Consensus       119 ----~---------------------------~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~  167 (190)
                          .                           --..|+-||||-- .+.......+.+.+...-..+.+..+.|+.|.|+
T Consensus       131 RAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg-~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laLf  209 (228)
T TIGR03223       131 RAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTG-RLDEEERAAVLARLEARFAPLLADPLAVDGLALF  209 (228)
T ss_pred             cCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecC-CCChHHHHHHHHHHHHHhhhccCCCeeeeeEEEE
Confidence                0                           1247999999984 4555555555555554322344568999999999


Q ss_pred             EecCCCCCcCCceEeEEEcCCC
Q 029664          168 KTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       168 ~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      .-..   .|.....+..++|++
T Consensus       210 ~e~~---~g~pF~~~~~~~l~~  228 (228)
T TIGR03223       210 VEPE---PGAPFRLIARVALAG  228 (228)
T ss_pred             eccC---CCCCcEEEEeecCCC
Confidence            6444   356799999999975


No 11 
>PLN00108 unknown protein; Provisional
Probab=98.73  E-value=9.7e-07  Score=70.96  Aligned_cols=175  Identities=11%  Similarity=0.058  Sum_probs=106.7

Q ss_pred             CCceEEEEEeC--ChhHHHHHHHHHHHHHhh--------------cC------CCCCCCeEEee-cCCcC--ChhHHHHH
Q 029664           13 KKGFYSVWAIP--PDEVRARVKKLMEGLRSE--------------FG------GPQFDPHVTVV-GAMSL--TADDALEK   67 (190)
Q Consensus        13 ~~~~~slwl~P--~~~~~~~l~~~~~~l~~~--------------~~------~~~~~pHiTL~-g~~~~--~~~~~~~~   67 (190)
                      .+..|.|.+..  .+++.+.+.++++.+-..              ++      ..+..+||||. -.+..  ..+...+.
T Consensus        34 ~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~  113 (257)
T PLN00108         34 EVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNI  113 (257)
T ss_pred             CCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHH
Confidence            34566777666  378999999988886542              11      12346899997 22221  12222222


Q ss_pred             HHHH---hc---cCCceeEEEceeeec---cceeeEEEEEeeCC---ccccchHHHHhhhh---CCC--C-CCCCcceeE
Q 029664           68 FKSA---CN---GLKAYNCTVNRVATG---TFFYQCVFLLLHPT---PEVAEPSSHCCGHF---GYK--S-STPYMPHLS  129 (190)
Q Consensus        68 l~~~---~~---~~~pf~l~~~~v~~~---~~~~~vv~l~v~~~---~~L~~L~~~l~~~~---g~~--~-~~~f~PHlT  129 (190)
                      |++.   +.   +.+|+.+++.|++..   +..-+|||+.|+..   +.|..+.+.+.+.|   |+.  + .+++.+|+|
T Consensus       114 L~s~~~~i~~~l~~~pl~I~lkGL~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d~~~~vKLH~T  193 (257)
T PLN00108        114 LKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSRLKLHAT  193 (257)
T ss_pred             HHHHHHHHHHhhCCCCeEEEEEeehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccccCcceeeEeE
Confidence            3222   21   359999999999983   22358999999863   56777777887754   763  3 368999999


Q ss_pred             eeeCCCCHH---HHH--HHHHHHHhcccccCCccEEeceEEEEEecCCCCCcCCceEeEEEcCCC
Q 029664          130 LLYGDLTDD---EKK--IAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       130 Lar~~~~~~---~~~--~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      |........   .+.  .+-+.++.+.. ...+.+.|++++|-+....+ .-.=|+..++++|.+
T Consensus       194 lmNt~~rk~k~~k~~sFDA~~Il~~f~d-~~FG~~~i~~vhls~r~s~~-~dGyY~~~~sl~~~~  256 (257)
T PLN00108        194 LMNASYRKDKSKKMDTFDAREIHKEFEN-KDWGTYLIREAHISQRYKYD-PNGYFHCCASLPFPH  256 (257)
T ss_pred             EechhhhhcccCccccccHHHHHHhccC-cccceEEecEEEEEeecccC-CCCCEEEEEEeecCC
Confidence            997521110   000  11123443322 33468899999995422122 234899999999864


No 12 
>PF02834 LigT_PEase:  LigT like Phosphoesterase;  InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=98.38  E-value=2.3e-07  Score=62.70  Aligned_cols=76  Identities=12%  Similarity=0.293  Sum_probs=53.5

Q ss_pred             CccccchHHHHhhh---hCCCCCCCCcceeEeeeC-CCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecCCCCCcC
Q 029664          102 TPEVAEPSSHCCGH---FGYKSSTPYMPHLSLLYG-DLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLK  177 (190)
Q Consensus       102 ~~~L~~L~~~l~~~---~g~~~~~~f~PHlTLar~-~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~  177 (190)
                      .+.|.+|++.+.+.   +|+...++|.|||||++. +...+....+.+.++.......+.+++++++.+|.+...  ++.
T Consensus         8 ~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~~--~rv   85 (87)
T PF02834_consen    8 KEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRLR--PRV   85 (87)
T ss_dssp             HHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEET--CEE
T ss_pred             HHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCCC--CCC
Confidence            36789999999854   355444899999999994 445555666666666543335566899999999998764  344


Q ss_pred             Cc
Q 029664          178 SW  179 (190)
Q Consensus       178 ~w  179 (190)
                      .|
T Consensus        86 i~   87 (87)
T PF02834_consen   86 IW   87 (87)
T ss_dssp             EE
T ss_pred             cC
Confidence            55


No 13 
>PF09749 HVSL:  Uncharacterised conserved protein;  InterPro: IPR019146  This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown. 
Probab=98.07  E-value=0.0004  Score=55.81  Aligned_cols=117  Identities=14%  Similarity=0.179  Sum_probs=80.9

Q ss_pred             EEEeCChhHHHHHHHHHHHHHhhcC--------------CCCCCCeEEeecCCcC---ChhHHHHHHHHHh--ccCCcee
Q 029664           19 VWAIPPDEVRARVKKLMEGLRSEFG--------------GPQFDPHVTVVGAMSL---TADDALEKFKSAC--NGLKAYN   79 (190)
Q Consensus        19 lwl~P~~~~~~~l~~~~~~l~~~~~--------------~~~~~pHiTL~g~~~~---~~~~~~~~l~~~~--~~~~pf~   79 (190)
                      |=..|+.+..+.|..+++.+.+...              +.+.++||+|.-.+..   ..+...+.|++.+  ....+|.
T Consensus        46 i~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~~lr~~~id~f~~~lr~~l~~~~~~~F~  125 (239)
T PF09749_consen   46 IEWPPSEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTFPLRTHQIDPFVDSLRQALRSSNIRPFY  125 (239)
T ss_pred             EEecCcHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCccccHHHHHHHHHHHHHHHhhcCCceEE
Confidence            3334556677788888888776543              1235799999977765   3566888999999  7999999


Q ss_pred             EEEceeee--ccceeeEEEEE--eeC-Ccc-ccchHHHHhhh---hCCCC-C-CCCcceeEeeeCCCC
Q 029664           80 CTVNRVAT--GTFFYQCVFLL--LHP-TPE-VAEPSSHCCGH---FGYKS-S-TPYMPHLSLLYGDLT  136 (190)
Q Consensus        80 l~~~~v~~--~~~~~~vv~l~--v~~-~~~-L~~L~~~l~~~---~g~~~-~-~~f~PHlTLar~~~~  136 (190)
                      +.++++..  +....| .|++  |.. ... |..|-+.+.+.   +|... . .+..||||||.....
T Consensus       126 v~f~~~~~~~N~e~TR-~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~lp~~Y~~~~~fHvSIAw~~~~  192 (239)
T PF09749_consen  126 VSFSGLDVYTNDEKTR-SFLALRVSEGSNNELKRLLDRINEVLKEFGLPPFYDEDPSFHVSIAWTLGD  192 (239)
T ss_pred             EEeCceEEEecCCCCe-EEEEEEecccccHHHHHHHHHHHHHHHHhCCCcccCCCCCCEEEEEEECCC
Confidence            99999886  322333 3333  333 233 88888888764   56643 3 578999999996444


No 14 
>PHA02977 hypothetical protein; Provisional
Probab=97.80  E-value=0.00048  Score=50.58  Aligned_cols=57  Identities=25%  Similarity=0.350  Sum_probs=42.9

Q ss_pred             eEEEEEeeCCccccchHHHHhhh-------hCC-CCCCCCcceeEeeeCCCCHH-HHHHHHHHHHh
Q 029664           93 QCVFLLLHPTPEVAEPSSHCCGH-------FGY-KSSTPYMPHLSLLYGDLTDD-EKKIAQEKAHK  149 (190)
Q Consensus        93 ~vv~l~v~~~~~L~~L~~~l~~~-------~g~-~~~~~f~PHlTLar~~~~~~-~~~~~~~~l~~  149 (190)
                      +.+.+.++.++.|.+|+..+-++       ||- ....+|.||||++|....++ .+.++.+.++.
T Consensus       124 ~avvmkle~sddlkalrnvl~n~vp~pkdifg~i~~d~~w~phitigyv~~dd~dnk~r~ie~~~~  189 (201)
T PHA02977        124 CAVVMKLEASDDLKALRNVLFNAVPCPKDIFGDILSDNPWCPHITIGYVKADDEDNKKRFIECAEA  189 (201)
T ss_pred             cEEEEEEEechHHHHHHHHhhcccCCcHHhhcccccCCCCCCceEEEeecccchhhHHHHHHHHHH
Confidence            56888888899999999999774       342 24679999999999755543 55677666654


No 15 
>PF06299 DUF1045:  Protein of unknown function (DUF1045);  InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=97.60  E-value=0.001  Score=50.02  Aligned_cols=113  Identities=17%  Similarity=0.278  Sum_probs=74.5

Q ss_pred             EeecCCcC----ChhHHHHHHHHHhccCCceeEE---EceeeeccceeeEEEEEe-eCCccccchHHHHhhhhC-C----
Q 029664           52 TVVGAMSL----TADDALEKFKSACNGLKAYNCT---VNRVATGTFFYQCVFLLL-HPTPEVAEPSSHCCGHFG-Y----  118 (190)
Q Consensus        52 TL~g~~~~----~~~~~~~~l~~~~~~~~pf~l~---~~~v~~~~~~~~vv~l~v-~~~~~L~~L~~~l~~~~g-~----  118 (190)
                      ||+-++..    +.+++..++...+....||.+.   +..+|.  +    +-+.. .++++|.+|+..+.+.|. +    
T Consensus         1 TLKaPF~La~g~~~~~L~~a~~~~a~~~~pf~l~~L~v~~lg~--F----lALvp~~~~~~L~~LAa~cV~~~d~fRAPl   74 (160)
T PF06299_consen    1 TLKAPFRLAEGASEADLLAALAAFAARFAPFELPGLEVARLGG--F----LALVPAGPCPALQALAAACVRAFDPFRAPL   74 (160)
T ss_pred             CCCCCcccCCCCCHHHHHHHHHHHhccCCCccCCceeEeeECC--E----EEEeeCCCCHHHHHHHHHHHHhhhhccCCC
Confidence            56655543    4578999999999999998744   455442  1    22222 347899999999876431 1    


Q ss_pred             --------------------------C-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecC
Q 029664          119 --------------------------K-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDT  171 (190)
Q Consensus       119 --------------------------~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~  171 (190)
                                                . --..|+.||||-.. +...+...+.+.+...-..+....+.|+++.|+.-..
T Consensus        75 s~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~-l~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e~~  153 (160)
T PF06299_consen   75 SEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGR-LDPAERARVEAALEAHFAPLLPEPLRIDSLALFGEPE  153 (160)
T ss_pred             ChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCC-CCHHHHHHHHHHHHHHHHhhcCCCeeecceEEEeccC
Confidence                                      0 12589999999854 5555566666666553233445688999999996443


No 16 
>PF05213 Corona_NS2A:  Coronavirus NS2A protein;  InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=96.87  E-value=0.003  Score=49.35  Aligned_cols=102  Identities=17%  Similarity=0.176  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHHhh-cCCC-CCCCeEEee-cCCc-CChhHHHHHHHHHhccC--CceeEEEceeeeccceeeEEEEEee
Q 029664           27 VRARVKKLMEGLRSE-FGGP-QFDPHVTVV-GAMS-LTADDALEKFKSACNGL--KAYNCTVNRVATGTFFYQCVFLLLH  100 (190)
Q Consensus        27 ~~~~l~~~~~~l~~~-~~~~-~~~pHiTL~-g~~~-~~~~~~~~~l~~~~~~~--~pf~l~~~~v~~~~~~~~vv~l~v~  100 (190)
                      .-....+++.++-+. ++.. --.|||||. =.+. ....+|...|+++.+..  .-..+++++---   --+++-+.| 
T Consensus        20 f~~~~~~LQ~~~~~eG~d~k~QkaPHlSl~mL~Isd~~i~~V~~~iq~ViddM~~~~~~it~tnp~M---Lg~~yV~nV-   95 (248)
T PF05213_consen   20 FMLNFKDLQFQLLEEGVDCKLQKAPHLSLGMLDISDEDIPDVETAIQKVIDDMVWFEGDITFTNPHM---LGRCYVANV-   95 (248)
T ss_pred             HHHHHHHHHHHHHHcCCCccccccCeeEEEEEEcChhhhhhHHHHHHHHHHHhhcccceEEecCcee---eccEEEEec-
Confidence            334556666665433 3332 246999997 2232 23556776777777654  333555554321   114444444 


Q ss_pred             CCccccchHHHHhhhh---CC--CCCCCCcceeEeeeCC
Q 029664          101 PTPEVAEPSSHCCGHF---GY--KSSTPYMPHLSLLYGD  134 (190)
Q Consensus       101 ~~~~L~~L~~~l~~~~---g~--~~~~~f~PHlTLar~~  134 (190)
                        ..+.+||..+.+.+   |.  ...|.|.||+||+...
T Consensus        96 --~Gv~slh~ki~n~~~~kgit~gQSRmwIPHiTia~~~  132 (248)
T PF05213_consen   96 --KGVLSLHDKIVNVFRKKGITFGQSRMWIPHITIAQLN  132 (248)
T ss_pred             --ccHHHHHHHHHHHHHHhCcCcCcccccccceehhhhh
Confidence              67889999998743   33  4589999999999964


No 17 
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.39  E-value=0.068  Score=41.61  Aligned_cols=116  Identities=16%  Similarity=0.149  Sum_probs=70.7

Q ss_pred             CceEEEEEeCCh-hHHHHHHHHHHHHHhhc-----C-CCCCCCeEEee-cCCcC---------------ChhHHHHHHHH
Q 029664           14 KGFYSVWAIPPD-EVRARVKKLMEGLRSEF-----G-GPQFDPHVTVV-GAMSL---------------TADDALEKFKS   70 (190)
Q Consensus        14 ~~~~slwl~P~~-~~~~~l~~~~~~l~~~~-----~-~~~~~pHiTL~-g~~~~---------------~~~~~~~~l~~   70 (190)
                      +.+.=++=++.. +..+.+-.+.+++...-     . .|....|+|+. |-++.               ..+++.+...+
T Consensus        40 pGNTVVchl~~gs~t~~vvl~i~~r~~~mpfadklt~tP~sSlHMTvfqg~~e~~R~~~~WpqdlPLDtpi~~~~~~~~e  119 (239)
T COG5255          40 PGNTVVCHLVTGSDTEEVVLIIRSRYLEMPFADKLTFTPVSSLHMTVFQGLIEERRELPYWPQDLPLDTPIDAITDYYAE  119 (239)
T ss_pred             CCCeEEEeccCCCchHHHHHHHHHHhhccchhhhhccCCcchhhHHHHHHHhhhcccCCCCCccCCCCCcHHHHHHHHHH
Confidence            344555555553 45666777777766431     1 34556899998 43321               12344444455


Q ss_pred             HhccC----CceeEEEceeeeccceeeEEEEEeeC--CccccchHHHHhhhhCC--CCCCCCcceeEeeeC
Q 029664           71 ACNGL----KAYNCTVNRVATGTFFYQCVFLLLHP--TPEVAEPSSHCCGHFGY--KSSTPYMPHLSLLYG  133 (190)
Q Consensus        71 ~~~~~----~pf~l~~~~v~~~~~~~~vv~l~v~~--~~~L~~L~~~l~~~~g~--~~~~~f~PHlTLar~  133 (190)
                      .++.+    .+|.+++.+++    .-.++..++.+  ...|.++++.+...||+  .+...|.=||||+|.
T Consensus       120 rLk~F~l~~~~~~mrvte~r----p~~i~v~paddad~~~l~~~Rd~ls~~~g~r~P~HDaY~FHITlgYl  186 (239)
T COG5255         120 RLKIFPLLDEEFNMRVTEMR----PQGILVEPADDADAKILEEWRDYLSEKFGYRHPDHDAYQFHITLGYL  186 (239)
T ss_pred             HHhcccCCchhhcchhhccc----ccceEeccCCHHHHHHHHHHHHHHhhhhcccCCCCcceEEEEEeeeE
Confidence            44433    25666666654    12334444433  35688999999888887  467789999999995


No 18 
>PF08302 tRNA_lig_CPD:  Fungal tRNA ligase phosphodiesterase domain;  InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=93.98  E-value=1.5  Score=35.70  Aligned_cols=113  Identities=14%  Similarity=0.272  Sum_probs=57.7

Q ss_pred             CCceEEEEEeCChhHHHHHHHHHHH--------HHhhcCCCC--CCCeEEee--cCCcCCh-hHHHHHHHHHhc----c-
Q 029664           13 KKGFYSVWAIPPDEVRARVKKLMEG--------LRSEFGGPQ--FDPHVTVV--GAMSLTA-DDALEKFKSACN----G-   74 (190)
Q Consensus        13 ~~~~~slwl~P~~~~~~~l~~~~~~--------l~~~~~~~~--~~pHiTL~--g~~~~~~-~~~~~~l~~~~~----~-   74 (190)
                      .+..||+-+ |..++...|..+...        +.......+  -.+||||.  ......+ .++.+.......    . 
T Consensus        71 ~p~Yf~i~i-~~~~i~~~l~~~f~~~~~~~~~~~~~L~~~~RvQ~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~  149 (257)
T PF08302_consen   71 KPEYFGISI-PTQDIKSLLEKLFEDSPPETARFYNQLKNSRRVQPEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKN  149 (257)
T ss_pred             CCeEEEEEC-CHHHHHHHHHHHhccCCHHHHHHHHHHHhCCCCCCCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccc
Confidence            346677765 666777777666643        222222222  25899999  2222222 244444433322    1 


Q ss_pred             ----------CCceeEEEceeeeccceeeEEEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeeeCC
Q 029664           75 ----------LKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGD  134 (190)
Q Consensus        75 ----------~~pf~l~~~~v~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar~~  134 (190)
                                ...+++++.++.+   ..|++-+.|+-.+.-..-..    .-++. -..=.||||++-.+
T Consensus       150 ~~~~~~~~~~~~~~~v~L~rlvw---d~rimai~V~~~~~~~~~~~----~~~~~-c~N~~~HITVGT~~  211 (257)
T PF08302_consen  150 PKQEPTQTPTLGSCDVRLERLVW---DDRIMAIVVRIVPPEDEEDE----VPEWE-CTNKIPHITVGTRD  211 (257)
T ss_pred             cccccccccccceEEEEEEEEEE---CCcEEEEEEEccCccccccc----cCCcc-cCCCCCEEEEEcCC
Confidence                      2458899988884   33566666553211000000    11222 23458999999853


No 19 
>PRK13679 hypothetical protein; Provisional
Probab=93.61  E-value=0.18  Score=38.10  Aligned_cols=71  Identities=11%  Similarity=0.230  Sum_probs=40.6

Q ss_pred             EEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEE
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQL  166 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L  166 (190)
                      ..+++...+.+.+.-+++++.++.. .+...|||||.. ++...+..+.+.+.+........+.+..++.+.-
T Consensus         3 ~~iai~~p~~~~~~l~~~~~~~~~~-~~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~   74 (168)
T PRK13679          3 YGIVLFPSKKIQDFANSYRKRYDPH-YALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSS   74 (168)
T ss_pred             eEEEEcCCHHHHHHHHHHHHhhCcc-cccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecccc
Confidence            3566766666666666666655432 345678999997 4555555555666555432223334445544433


No 20 
>PF06299 DUF1045:  Protein of unknown function (DUF1045);  InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=91.27  E-value=0.27  Score=37.07  Aligned_cols=41  Identities=15%  Similarity=0.190  Sum_probs=29.3

Q ss_pred             CCCeEEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           47 FDPHVTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        47 ~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      |..|+||.|.++. ..+.+...++.......+=.+.++++.-
T Consensus       107 FRFHmTLTg~l~~~~~~~~~~~l~~~f~~~l~~p~~id~laL  148 (160)
T PF06299_consen  107 FRFHMTLTGRLDPAERARVEAALEAHFAPLLPEPLRIDSLAL  148 (160)
T ss_pred             CEeeEEeCCCCCHHHHHHHHHHHHHHHHhhcCCCeeecceEE
Confidence            6789999999964 2444667777766666556677788773


No 21 
>PHA02574 57B hypothetical protein; Provisional
Probab=90.46  E-value=0.69  Score=34.49  Aligned_cols=35  Identities=11%  Similarity=0.117  Sum_probs=22.0

Q ss_pred             EEEEEeCChhHHHHHHHHHHHHHhh---cCCCCCCCeEEee
Q 029664           17 YSVWAIPPDEVRARVKKLMEGLRSE---FGGPQFDPHVTVV   54 (190)
Q Consensus        17 ~slwl~P~~~~~~~l~~~~~~l~~~---~~~~~~~pHiTL~   54 (190)
                      -.+|+-+.   .+.|..+.+.++..   .+..+|.|||||.
T Consensus        80 rvlWlg~~---~~~L~~L~~~l~~~l~~~~~r~F~PHITLa  117 (149)
T PHA02574         80 NALVLVLE---SEYLQCRHKYARALGATHDFDDYTPHITLS  117 (149)
T ss_pred             CEEEEEeC---CHHHHHHHHHHHHHhhcCCCCCcCCcEEEe
Confidence            45887775   23344444444433   4456799999999


No 22 
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=90.19  E-value=1.2  Score=34.23  Aligned_cols=74  Identities=18%  Similarity=0.324  Sum_probs=45.9

Q ss_pred             EEEEeeCCccccchHHHHhhhhC----CCCCCCCcceeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEe
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFG----YKSSTPYMPHLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKT  169 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g----~~~~~~f~PHlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s  169 (190)
                      +++++..++++.+.-.++.+.+.    ..-..+-.+||||.. ++......+.+.+.+......+ +...+++.+..|..
T Consensus         3 lFiAl~~p~~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~F~~   81 (180)
T COG1514           3 LFIALDPPAEIAERLARIRARLKGARAIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGSFPN   81 (180)
T ss_pred             eEEEecCCHHHHHHHHHHHHhcCcccccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcccCC
Confidence            56777776655555444444322    123567889999998 5666555566666666544333 56777777777753


No 23 
>PF13563 2_5_RNA_ligase2:  2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=87.20  E-value=0.34  Score=35.25  Aligned_cols=49  Identities=14%  Similarity=0.209  Sum_probs=23.6

Q ss_pred             CCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEe
Q 029664          121 STPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKT  169 (190)
Q Consensus       121 ~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s  169 (190)
                      .....|||||.+........+.+.+.+...-....+....++.+..+..
T Consensus        21 ~~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~   69 (153)
T PF13563_consen   21 YPRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPG   69 (153)
T ss_dssp             --GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESS
T ss_pred             CCCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCC
Confidence            3455699999985333221123333333322234556778888888754


No 24 
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=87.04  E-value=3.1  Score=31.34  Aligned_cols=72  Identities=14%  Similarity=0.379  Sum_probs=36.3

Q ss_pred             EEEEeeCCccccchHHHHhhhhC-CCCCCCCcc----eeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEE
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFG-YKSSTPYMP----HLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWK  168 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g-~~~~~~f~P----HlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~  168 (190)
                      +|+++...+++.+.-.++.+.+. ......+.|    ||||+. ++......+.+.+.+....  ..+.++.++.+..|.
T Consensus         3 ~FiAl~~p~~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~~F~   80 (179)
T TIGR02258         3 LFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIGVFG   80 (179)
T ss_pred             EEEEecCCHHHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeeeeCC
Confidence            56777654433333333333222 111223333    999986 4555555555655555432  223466677776664


No 25 
>PF07823 CPDase:  Cyclic phosphodiesterase-like protein;  InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction  Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate.  ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=86.66  E-value=0.71  Score=35.91  Aligned_cols=39  Identities=23%  Similarity=0.466  Sum_probs=17.2

Q ss_pred             EEEEEeeC-CccccchHHHH---hhhhCCCCCCCCcceeEeeeC
Q 029664           94 CVFLLLHP-TPEVAEPSSHC---CGHFGYKSSTPYMPHLSLLYG  133 (190)
Q Consensus        94 vv~l~v~~-~~~L~~L~~~l---~~~~g~~~~~~f~PHlTLar~  133 (190)
                      +||+...+ ++.-..|+..+   ...++-. ...|-|||||.-+
T Consensus         4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~-~p~F~PHiTL~s~   46 (196)
T PF07823_consen    4 SLWLVPPPGSPLYERLKTLISSLASLFPGS-PPPFEPHITLTSG   46 (196)
T ss_dssp             EEEEEE-T--TTHHHHHHHHHHHHHHST----------EEEEEE
T ss_pred             EEEEcCCCCccHHHHHHHHHHHHHHHCCCC-CCCcCCeEEEeCC
Confidence            68999876 33344444444   3334411 3689999999974


No 26 
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=86.32  E-value=1  Score=35.97  Aligned_cols=41  Identities=22%  Similarity=0.286  Sum_probs=28.5

Q ss_pred             CCCeEEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           47 FDPHVTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        47 ~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      |..|+||.|.++. ..+.+...|+......-+-.+.++++.-
T Consensus       167 FrFHmTLTg~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laL  208 (228)
T TIGR03223       167 FRFHMTLTGRLDEEERAAVLARLEARFAPLLADPLAVDGLAL  208 (228)
T ss_pred             eEEEEEecCCCChHHHHHHHHHHHHHhhhccCCCeeeeeEEE
Confidence            5789999999974 2345667777766555545677788773


No 27 
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.10  E-value=23  Score=28.10  Aligned_cols=86  Identities=16%  Similarity=0.184  Sum_probs=54.7

Q ss_pred             CCeEEeecCCcC---ChhHHHHHHHHHhccCCceeEEEceeee--ccceeeEEEEEeeC-CccccchHHHH---hhh---
Q 029664           48 DPHVTVVGAMSL---TADDALEKFKSACNGLKAYNCTVNRVAT--GTFFYQCVFLLLHP-TPEVAEPSSHC---CGH---  115 (190)
Q Consensus        48 ~pHiTL~g~~~~---~~~~~~~~l~~~~~~~~pf~l~~~~v~~--~~~~~~vv~l~v~~-~~~L~~L~~~l---~~~---  115 (190)
                      ..||.|.-.+..   .+...+..|++.+.....|-+++.++..  +....|+ |++.+- +..+..+-+++   .+.   
T Consensus       121 ~fHlSLsr~VvLr~HqI~~fi~~L~~~l~s~~rf~~t~n~~~iytN~e~TRt-Fi~leitt~~~~~~~~~i~~vd~Vm~~  199 (269)
T KOG3102|consen  121 EFHLSLSRNVVLRVHQINSFISMLRQKLQSQKRFLITFNKWEIYTNDEHTRT-FISLEITTSGLSEISKQIDAVDEVMKL  199 (269)
T ss_pred             eEEEeeccceEEEeehhhHHHHHHHHHHhhhhhheEeecceEEEecccccee-EEEEEechhhHHHHHHHHHHHHHHHHH
Confidence            479988855543   5677889999999899999999999985  3333343 444442 34444444333   332   


Q ss_pred             hCCCC--CCCCcceeEeeeCCC
Q 029664          116 FGYKS--STPYMPHLSLLYGDL  135 (190)
Q Consensus       116 ~g~~~--~~~f~PHlTLar~~~  135 (190)
                      +.+.+  ..| .+|+||+-+-.
T Consensus       200 ~nL~~FY~DP-sfHiSL~WcvG  220 (269)
T KOG3102|consen  200 HNLPEFYKDP-SFHISLVWCVG  220 (269)
T ss_pred             cCchhhhcCC-CCCceEEEEec
Confidence            23322  233 89999998633


No 28 
>PHA02977 hypothetical protein; Provisional
Probab=78.43  E-value=3.3  Score=30.65  Aligned_cols=40  Identities=18%  Similarity=0.380  Sum_probs=25.9

Q ss_pred             CCCCCCeEEeecCCcCChhHHHHHHHHHhccCCceeEEEce
Q 029664           44 GPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNR   84 (190)
Q Consensus        44 ~~~~~pHiTL~g~~~~~~~~~~~~l~~~~~~~~pf~l~~~~   84 (190)
                      .++|.||||+ |-+..+.++-..++.+.++.+..-.+++.|
T Consensus       160 d~~w~phiti-gyv~~dd~dnk~r~ie~~~~frg~~ikv~g  199 (201)
T PHA02977        160 DNPWCPHITI-GYVKADDEDNKKRFIECAEAFRGQEIKVLG  199 (201)
T ss_pred             CCCCCCceEE-EeecccchhhHHHHHHHHHHhCCCeeEEee
Confidence            4679999999 555544455566777776666555555443


No 29 
>PF08975 2H-phosphodiest:  Domain of unknown function (DUF1868);  InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=74.89  E-value=23  Score=25.36  Aligned_cols=74  Identities=19%  Similarity=0.227  Sum_probs=38.0

Q ss_pred             CceEEEEEeCCh-hHHHHHHHHHHHHHhhcC------CCCCCCeEEeecCC-cC---------------ChhHHHHHHHH
Q 029664           14 KGFYSVWAIPPD-EVRARVKKLMEGLRSEFG------GPQFDPHVTVVGAM-SL---------------TADDALEKFKS   70 (190)
Q Consensus        14 ~~~~slwl~P~~-~~~~~l~~~~~~l~~~~~------~~~~~pHiTL~g~~-~~---------------~~~~~~~~l~~   70 (190)
                      +.+.-|+=+|.. +..+.+..+++.+++.-.      .|+...|+|+.+.+ +.               ..++.-+.+.+
T Consensus        12 pGNTvIchl~~~s~~~~al~~i~~~l~~~~~~~k~a~lP~sS~HMTVf~Gv~e~~R~~~~WP~~l~~d~~l~~~t~~~~~   91 (118)
T PF08975_consen   12 PGNTVICHLPQDSPFYAALLAIQQRLRESPFADKLAFLPPSSYHMTVFEGVIESRREPGFWPADLPLDAPLQECTRYFAE   91 (118)
T ss_dssp             -EEEEEEEB-TTSHHHHHHHHHHHHHHTSGGGGGEEE--GGG-EEEEEEEEETT--STTSS-TTS-TT--HHHHHHHHHH
T ss_pred             CCCeEEeecCCCChHHHHHHHHHHHHHhCccccceEecCcchhhhhhhccccccccCCCCCCCCCCCCCCHHHHHHHHHH
Confidence            455666666664 577789999998886421      35566899999322 21               13344455555


Q ss_pred             Hhcc---CCceeEEEceeee
Q 029664           71 ACNG---LKAYNCTVNRVAT   87 (190)
Q Consensus        71 ~~~~---~~pf~l~~~~v~~   87 (190)
                      .+++   ..+|.+++.+.+.
T Consensus        92 rL~~f~~~~~f~m~v~~~~~  111 (118)
T PF08975_consen   92 RLKGFPLPGPFRMRVTRTGM  111 (118)
T ss_dssp             HGGG--------EEE--EEE
T ss_pred             HHhcCCCCCCeEEEEEeccc
Confidence            5543   5788888855554


No 30 
>PRK15124 2'-5' RNA ligase; Provisional
Probab=68.63  E-value=21  Score=26.90  Aligned_cols=41  Identities=15%  Similarity=0.437  Sum_probs=24.6

Q ss_pred             cceeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEEE
Q 029664          125 MPHLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLW  167 (190)
Q Consensus       125 ~PHlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~  167 (190)
                      .-||||.. |+.+.+..+.+.+.+...  ...+.+..++.+..|
T Consensus        41 nlHiTL~FlG~v~~~~~~~l~~~l~~~--~~~pF~l~l~~~g~F   82 (176)
T PRK15124         41 NLHLTLAFLGEVSAEKQQALSQLAGRI--RQPGFTLTLDDAGQW   82 (176)
T ss_pred             ccEEEEEecCCCCHHHHHHHHHHHHhc--ccCCeEEEECcccCc
Confidence            44999997 566655555665555542  234445666666555


No 31 
>PF07476 MAAL_C:  Methylaspartate ammonia-lyase C-terminus;  InterPro: IPR022662  Methylaspartate ammonia-lyase 4.3.1.2 from EC catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the C-terminal region of methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the PF01188 from PFAM. This domain represents the catalytic domain and contains a metal binding site []. ; PDB: 1KKO_B 1KKR_A 3ZVI_A 1KD0_B 1KCZ_B 3ZVH_A.
Probab=57.85  E-value=16  Score=29.23  Aligned_cols=58  Identities=12%  Similarity=0.116  Sum_probs=36.4

Q ss_pred             CeEEeecCC----cCChhHHHHHHHHHhccCCceeEEEceeee-ccceeeEEEEEeeCCccccchHHHHhh
Q 029664           49 PHVTVVGAM----SLTADDALEKFKSACNGLKAYNCTVNRVAT-GTFFYQCVFLLLHPTPEVAEPSSHCCG  114 (190)
Q Consensus        49 pHiTL~g~~----~~~~~~~~~~l~~~~~~~~pf~l~~~~v~~-~~~~~~vv~l~v~~~~~L~~L~~~l~~  114 (190)
                      .||-+.|-+    ..+.+.+.+-+.++.+...||.|++++.-- +...-        .-+.|.+|++.+.+
T Consensus        72 lHiDVYGtiG~~f~~d~~~~adYl~~l~~aA~P~~L~iEgP~d~g~r~~--------QI~~l~~Lr~~L~~  134 (248)
T PF07476_consen   72 LHIDVYGTIGLAFDNDPDRMADYLAELEEAAAPFKLRIEGPMDAGSREA--------QIEALAELREELDR  134 (248)
T ss_dssp             EEEE-TTHHHHHTTT-HHHHHHHHHHHHHHHTTS-EEEE-SB--SSHHH--------HHHHHHHHHHHHHH
T ss_pred             EEEEccchHHHHhCCCHHHHHHHHHHHHHhcCCCeeeeeCCcCCCChHH--------HHHHHHHHHHHHHh
Confidence            699999544    235677888888888899999999998653 21110        13566777777665


No 32 
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=35.43  E-value=2.2e+02  Score=24.14  Aligned_cols=112  Identities=13%  Similarity=0.154  Sum_probs=62.7

Q ss_pred             cCCceeEEEceeee-cc--ceeeEEEEEeeCCccccchHHHH----hhhh---CC--CCCCCCcceeEeeeCCC---CH-
Q 029664           74 GLKAYNCTVNRVAT-GT--FFYQCVFLLLHPTPEVAEPSSHC----CGHF---GY--KSSTPYMPHLSLLYGDL---TD-  137 (190)
Q Consensus        74 ~~~pf~l~~~~v~~-~~--~~~~vv~l~v~~~~~L~~L~~~l----~~~~---g~--~~~~~f~PHlTLar~~~---~~-  137 (190)
                      +-.|+.+.+.|+.. +.  .--+|+|+.|++...=..|...+    -.+|   |.  .+..+-.=|+|+.....   .. 
T Consensus       212 ~~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~k~~~~~kLH~TvmNsryrk~~~~  291 (345)
T KOG2814|consen  212 GEKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIKKESSSLKLHCTVMNSRYRKNGGE  291 (345)
T ss_pred             CCCceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchhccccccEEEEEEehhhhhhcCCC
Confidence            46899999999986 22  23489999998743333333333    2222   33  35667889999985311   11 


Q ss_pred             ----HHHH--HHHHHHHhcccccCCccEEeceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          138 ----DEKK--IAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       138 ----~~~~--~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                          .+.+  ..-+.++.+.. +...++...++++-.....+ ...-|...+++||
T Consensus       292 ~g~~K~~~~Fdar~ilk~fg~-f~fg~~~~~eih~~~~~~~d-~ng~y~~~gsi~f  345 (345)
T KOG2814|consen  292 PGLVKESESFDAREILKAFGQ-FLFGELKLQEIHLSVRFAAD-QNGNYNECGSIPF  345 (345)
T ss_pred             cchhhHhhhccHHHHHHHHhh-HhHhhcccceeeeeeeeccc-cccchhhhcCCCC
Confidence                0000  01112222211 22237777888886655544 3457777777664


No 33 
>PF07485 DUF1529:  Domain of Unknown Function (DUF1259);  InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis. 
Probab=34.68  E-value=1.1e+02  Score=21.87  Aligned_cols=59  Identities=8%  Similarity=0.037  Sum_probs=35.9

Q ss_pred             cCCcCChhHHHHHHHHHhccCCceeEEEceeee--ccceeeEEEEEeeCCccccchHHHHhhhhC
Q 029664           55 GAMSLTADDALEKFKSACNGLKAYNCTVNRVAT--GTFFYQCVFLLLHPTPEVAEPSSHCCGHFG  117 (190)
Q Consensus        55 g~~~~~~~~~~~~l~~~~~~~~pf~l~~~~v~~--~~~~~~vv~l~v~~~~~L~~L~~~l~~~~g  117 (190)
                      |++-...+|+...+..+.+    --+.+..+--  ....||+.|+-+...+.-..|++.+++++.
T Consensus        61 Gd~vll~~EV~pvi~aL~~----~GI~vtAlHNH~l~e~Prl~ymH~~~~gdp~~lA~~vr~Ald  121 (123)
T PF07485_consen   61 GDFVLLEDEVNPVISALRK----NGIEVTALHNHWLFEQPRLFYMHIWGVGDPAKLARKVRAALD  121 (123)
T ss_pred             ecEEecHHHHHHHHHHHHH----CCceEEEEecccccCCCCEEEEEEEecCCHHHHHHHHHHHHh
Confidence            5554434444443333322    2244444442  223699999999988888889998887653


No 34 
>PF08302 tRNA_lig_CPD:  Fungal tRNA ligase phosphodiesterase domain;  InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=33.23  E-value=2.6e+02  Score=22.64  Aligned_cols=97  Identities=12%  Similarity=0.148  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCeEEeecCCcCChhHHHHHHHHHhccCCc-eeEEEceeee-----------ccceeeEE
Q 029664           28 RARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKA-YNCTVNRVAT-----------GTFFYQCV   95 (190)
Q Consensus        28 ~~~l~~~~~~l~~~~~~~~~~pHiTL~g~~~~~~~~~~~~l~~~~~~~~p-f~l~~~~v~~-----------~~~~~~vv   95 (190)
                      ++-|..++++|...|..        |..+++ +.+++.++++.++.+..| |.-.+.+-+.           .....+..
T Consensus         3 ~eNle~Ii~~L~~~yP~--------Lv~~~P-s~e~id~A~~~Al~~Ykp~~~k~~~~~~~~~~~~~~~~~~~~kk~~p~   73 (257)
T PF08302_consen    3 RENLETIINELHKKYPN--------LVPEVP-SDEEIDEAFQKALNEYKPDFTKIIGKGSKNNKKKNNKSSPKKKKKKPE   73 (257)
T ss_pred             HHhHHHHHHHHHHhCch--------hcCCCC-CHHHHHHHHHHHHhhCCCceEEECCcCCccccccccccCcccccCCCe
Confidence            45677788888777641        122333 357888999999985544 6666664321           12244678


Q ss_pred             EEEeeCCccccchHHHHhhhhCC--------------CCCCCCcceeEeeeCCC
Q 029664           96 FLLLHPTPEVAEPSSHCCGHFGY--------------KSSTPYMPHLSLLYGDL  135 (190)
Q Consensus        96 ~l~v~~~~~L~~L~~~l~~~~g~--------------~~~~~f~PHlTLar~~~  135 (190)
                      |.++.=  ....+.+.+...|.-              ..+-.=.|||||+-...
T Consensus        74 Yf~i~i--~~~~i~~~l~~~f~~~~~~~~~~~~~L~~~~RvQ~~FHVTL~H~as  125 (257)
T PF08302_consen   74 YFGISI--PTQDIKSLLEKLFEDSPPETARFYNQLKNSRRVQPEFHVTLIHRAS  125 (257)
T ss_pred             EEEEEC--CHHHHHHHHHHHhccCCHHHHHHHHHHHhCCCCCCCCeEEEEeccc
Confidence            888853  222333333333321              12334567999998533


No 35 
>PF13466 STAS_2:  STAS domain
Probab=31.79  E-value=45  Score=21.15  Aligned_cols=37  Identities=11%  Similarity=0.169  Sum_probs=25.7

Q ss_pred             EEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           51 VTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        51 iTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      |+|.|+++. ..+++.+.+.+.+....++.+.+.++..
T Consensus         1 l~l~G~l~~~~~~~l~~~l~~~~~~~~~v~lDls~v~~   38 (80)
T PF13466_consen    1 LRLSGELDIATAPELRQALQALLASGRPVVLDLSGVEF   38 (80)
T ss_pred             CEEEEEEeHHHHHHHHHHHHHHHcCCCeEEEECCCCCe
Confidence            466677764 4566777777777655677788777774


No 36 
>PF13822 ACC_epsilon:  Acyl-CoA carboxylase epsilon subunit
Probab=31.79  E-value=74  Score=19.80  Aligned_cols=26  Identities=19%  Similarity=0.227  Sum_probs=21.1

Q ss_pred             cceeEeeeCCCCHHHHHHHHHHHHhc
Q 029664          125 MPHLSLLYGDLTDDEKKIAQEKAHKL  150 (190)
Q Consensus       125 ~PHlTLar~~~~~~~~~~~~~~l~~~  150 (190)
                      .|||.+.+++-+.+|...+...+..+
T Consensus         1 ~p~~rVvrGnPt~eElAAL~aVlaa~   26 (62)
T PF13822_consen    1 RPLIRVVRGNPTDEELAALTAVLAAR   26 (62)
T ss_pred             CCceEEeCCCCCHHHHHHHHHHHHHH
Confidence            59999999998888888777766553


No 37 
>PRK11633 cell division protein DedD; Provisional
Probab=29.70  E-value=1e+02  Score=24.58  Aligned_cols=68  Identities=13%  Similarity=0.245  Sum_probs=43.5

Q ss_pred             cCCcC--ChhHHHHHHHHHhccCCceeEEEceeeeccceeeEEEEEeeCC-ccccchHHHHhhhhCCCC-CCCCcce
Q 029664           55 GAMSL--TADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPT-PEVAEPSSHCCGHFGYKS-STPYMPH  127 (190)
Q Consensus        55 g~~~~--~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~~vv~l~v~~~-~~L~~L~~~l~~~~g~~~-~~~f~PH  127 (190)
                      |.|..  ..+.+.+.|+.  .++..|.......+.   ....||+|...+ +.+.+...+|.+..|+.. -..|.||
T Consensus       155 gaf~n~~~A~~l~~kL~~--~G~~Ay~~~~~~~~G---~~tRV~VGP~~sk~~ae~~~~~Lk~~~Gl~g~Vv~~~p~  226 (226)
T PRK11633        155 GALKNADKVNEIVAKLRL--SGYRVYTVPSTPVQG---KITRIYVGPDASKDKLKGSLGELKQLSGLSGVVMGYTPN  226 (226)
T ss_pred             cccCCHHHHHHHHHHHHH--CCCeeEEEeeecCCC---cEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEecCCC
Confidence            77764  23445555544  378888776554332   223589998765 789999999988777742 3456654


No 38 
>PF05213 Corona_NS2A:  Coronavirus NS2A protein;  InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=28.55  E-value=93  Score=24.80  Aligned_cols=39  Identities=21%  Similarity=0.184  Sum_probs=25.5

Q ss_pred             cccchHHHHhhhhCCCCCCCCcceeEeeeCCCCHHHHHHH
Q 029664          104 EVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIA  143 (190)
Q Consensus       104 ~L~~L~~~l~~~~g~~~~~~f~PHlTLar~~~~~~~~~~~  143 (190)
                      +...|+-++.+ -|+.-+..-.|||||+--++.++....+
T Consensus        23 ~~~~LQ~~~~~-eG~d~k~QkaPHlSl~mL~Isd~~i~~V   61 (248)
T PF05213_consen   23 NFKDLQFQLLE-EGVDCKLQKAPHLSLGMLDISDEDIPDV   61 (248)
T ss_pred             HHHHHHHHHHH-cCCCccccccCeeEEEEEEcChhhhhhH
Confidence            34455555544 2666667789999999877776544433


No 39 
>PF04571 Lipin_N:  lipin, N-terminal conserved region;  InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=26.81  E-value=86  Score=22.12  Aligned_cols=45  Identities=9%  Similarity=0.124  Sum_probs=29.4

Q ss_pred             EEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeeeccceeeEEEEEee
Q 029664           51 VTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLH  100 (190)
Q Consensus        51 iTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~~vv~l~v~  100 (190)
                      -||.|.++. -.++....+     .+.||.++|++++..+..-++|=+.|.
T Consensus        22 atlSGAiDVIVV~q~DGs~-----~sSPFhVRFGk~~vl~~~ek~V~I~VN   67 (110)
T PF04571_consen   22 ATLSGAIDVIVVEQPDGSL-----KSSPFHVRFGKLGVLRPREKVVDIEVN   67 (110)
T ss_pred             ccccCceeEEEEecCCCCE-----ecCccEEEEcceeeecccCcEEEEEEC
Confidence            577788864 111111111     489999999999975555678877774


No 40 
>TIGR02157 PA_CoA_Oxy2 phenylacetate-CoA oxygenase, PaaH subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.65  E-value=34  Score=23.21  Aligned_cols=15  Identities=13%  Similarity=0.412  Sum_probs=11.7

Q ss_pred             CceEEEEEeCChhHH
Q 029664           14 KGFYSVWAIPPDEVR   28 (190)
Q Consensus        14 ~~~~slwl~P~~~~~   28 (190)
                      ..+.|||++|...+.
T Consensus        42 ~e~vsiWVVp~~~I~   56 (90)
T TIGR02157        42 EEGVSIWVVKASHIV   56 (90)
T ss_pred             cCCcEEEEeeHHHhh
Confidence            358899999997554


No 41 
>PRK13781 paaB phenylacetate-CoA oxygenase subunit PaaB; Provisional
Probab=21.59  E-value=49  Score=22.67  Aligned_cols=15  Identities=20%  Similarity=0.618  Sum_probs=11.6

Q ss_pred             CceEEEEEeCChhHH
Q 029664           14 KGFYSVWAIPPDEVR   28 (190)
Q Consensus        14 ~~~~slwl~P~~~~~   28 (190)
                      ..+.|||++|..++.
T Consensus        47 ~e~vsiWVVp~~~I~   61 (95)
T PRK13781         47 NEGVSIWVVPSSAIT   61 (95)
T ss_pred             cCCcEEEEeeHHHcc
Confidence            358899999997653


No 42 
>PF05881 CNPase:  2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase);  InterPro: IPR008431 This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity [].; GO: 0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity, 0009214 cyclic nucleotide catabolic process, 0016020 membrane; PDB: 2YDB_A 2Y3X_B 2Y1P_A 2XMI_A 2YDD_A 2YDC_A 2ILX_A 1WOJ_A 2I3E_A.
Probab=20.35  E-value=3.1e+02  Score=21.88  Aligned_cols=83  Identities=13%  Similarity=-0.011  Sum_probs=43.9

Q ss_pred             CCCCeEEee----cCCcCChhH-HHHHHHHHhccCCceeEEEceeeeccceeeEEEEEeeCC-ccccchHHHHhhhhCCC
Q 029664           46 QFDPHVTVV----GAMSLTADD-ALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPT-PEVAEPSSHCCGHFGYK  119 (190)
Q Consensus        46 ~~~pHiTL~----g~~~~~~~~-~~~~l~~~~~~~~pf~l~~~~v~~~~~~~~vv~l~v~~~-~~L~~L~~~l~~~~g~~  119 (190)
                      +-.+|.|=+    |..+...+- ..+.+++.  -.+.|+|++.++=.   .||++=+.|+-+ ++|.-.-....+.+...
T Consensus        59 p~vLHCTtkfcdYGka~GAeeYAq~~~Vk~s--ygkaftL~isaLfv---TprT~GArv~L~e~ql~LWp~D~~ke~~~~  133 (235)
T PF05881_consen   59 PGVLHCTTKFCDYGKAAGAEEYAQQEVVKKS--YGKAFTLSISALFV---TPRTVGARVELTEEQLLLWPADVDKELSPS  133 (235)
T ss_dssp             TSSSEEEEEE-GGGTSTTHHHHHT-HHHHHH--TT-EEEEEEEEEEE----SSEEEEEEE--HHHHHTS-TCSSCSCSTT
T ss_pred             CCCceEeeeeccccCcccHHHHHhhHHHHHh--ccceEEEEEEEEEe---ccccccceeeechhhhccCCcchhcccCCC
Confidence            456899998    544321111 22344443  36889999999875   578888888743 34422222211211111


Q ss_pred             --CCCCCcceeEeeeC
Q 029664          120 --SSTPYMPHLSLLYG  133 (190)
Q Consensus       120 --~~~~f~PHlTLar~  133 (190)
                        -++.=+.||||+-.
T Consensus       134 ~~lp~GSRAHiTLGcA  149 (235)
T PF05881_consen  134 DSLPRGSRAHITLGCA  149 (235)
T ss_dssp             TTS-TTTTCEEEEEE-
T ss_pred             CCCCCCcceeEeeecc
Confidence              24567889999974


No 43 
>cd07016 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which a
Probab=20.25  E-value=1.4e+02  Score=21.89  Aligned_cols=36  Identities=11%  Similarity=0.226  Sum_probs=23.8

Q ss_pred             eEEeecCCcC----ChhHHHHHHHHHhccCCceeEEEceee
Q 029664           50 HVTVVGAMSL----TADDALEKFKSACNGLKAYNCTVNRVA   86 (190)
Q Consensus        50 HiTL~g~~~~----~~~~~~~~l~~~~~~~~pf~l~~~~v~   86 (190)
                      ||+|.|.++.    ..+++.+.|..+-.. .++.|.++..|
T Consensus         2 ~i~~~g~I~~~~~~~~~~~~~~l~~~~~~-~~i~l~inspG   41 (160)
T cd07016           2 EIYIYGDIGSDWGVTAKEFKDALDALGDD-SDITVRINSPG   41 (160)
T ss_pred             EEEEEeEeCCCcccCHHHHHHHHHhccCC-CCEEEEEECCC
Confidence            7778877765    355666666655434 67777777666


Done!