Query         gi|254780625|ref|YP_003065038.1| formamidopyrimidine-DNA glycosylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 289
No_of_seqs    122 out of 2796
Neff          7.7 
Searched_HMMs 23785
Date          Tue May 31 18:50:30 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780625.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1tdz_A Formamidopyrimidine-DNA 100.0       0       0  546.5  22.2  271    1-289     1-271 (272)
  2 1k82_A Formamidopyrimidine-DNA 100.0       0       0  525.5  24.7  268    2-289     1-268 (268)
  3 1ee8_A MUTM (FPG) protein; bet 100.0       0       0  515.1  20.0  261    2-289     1-263 (266)
  4 3gpu_A DNA glycosylase; DNA gl 100.0       0       0  495.9  21.0  254    2-289     1-256 (256)
  5 1k3x_A Endonuclease VIII; hydr 100.0       0       0  489.8  20.9  259    2-289     1-262 (262)
  6 3a46_A Formamidopyrimidine-DNA 100.0       0       0  469.7  14.1  265    1-289     1-287 (289)
  7 1tdh_A NEI endonuclease VIII-l 100.0       0       0  416.4  13.7  260    1-288     1-286 (364)
  8 3doa_A Fibrinogen binding prot  96.3   0.026 1.1E-06   33.6   8.7   52  143-198   168-219 (288)
  9 1mu5_A Type II DNA topoisomera  96.2   0.025 1.1E-06   33.6   8.0   75  140-224   228-304 (471)
 10 2zkq_m 40S ribosomal protein S  95.6   0.013 5.6E-07   35.4   4.5   50  164-222    23-72  (152)
 11 2vqe_M 30S ribosomal protein S  95.4  0.0083 3.5E-07   36.7   3.0   50  164-222    12-61  (126)
 12 3ofp_M 30S ribosomal protein S  93.2    0.01 4.3E-07   36.1  -0.5   50  164-222    11-60  (113)
 13 3fut_A Dimethyladenosine trans  80.6     1.5 6.4E-05   22.2   3.9   58  156-223   212-269 (271)
 14 1qyr_A KSGA, high level kasuga  77.5       2 8.5E-05   21.4   3.7   52  157-223   199-250 (252)
 15 3ftd_A Dimethyladenosine trans  76.8     2.4  0.0001   20.9   3.9   46  158-222   200-245 (249)
 16 2avu_E Flagellar transcription  74.5       1 4.3E-05   23.3   1.5   27  261-288   135-161 (192)
 17 1vk6_A NADH pyrophosphatase; 1  74.0     1.6 6.6E-05   22.1   2.4   28  259-289   106-133 (269)
 18 1vd4_A Transcription initiatio  66.8     1.9 7.8E-05   21.6   1.5   26  262-288    16-46  (62)
 19 3ga8_A HTH-type transcriptiona  65.5     4.1 0.00017   19.4   3.0   24  155-178    54-77  (78)
 20 3na7_A HP0958; flagellar bioge  65.4    0.56 2.3E-05   25.0  -1.4   30  259-289   197-230 (256)
 21 3bbn_M Ribosomal protein S13;   60.8    0.98 4.1E-05   23.4  -0.8   41  164-208    57-97  (145)
 22 2jne_A Hypothetical protein YF  58.4     4.8  0.0002   18.9   2.4   25  262-287    63-87  (101)
 23 2jrp_A Putative cytoplasmic pr  54.7       5 0.00021   18.8   1.9   26  261-287    32-57  (81)
 24 1l1o_C Replication protein A 7  53.3     2.4   1E-04   20.9   0.1   21   96-117    78-98  (181)
 25 1nnq_A Rubrerythrin; structura  51.5     3.2 0.00014   20.1   0.5   21  262-288   141-161 (171)
 26 3m7n_A Putative uncharacterize  51.5     7.4 0.00031   17.8   2.4   26  255-289   139-164 (179)
 27 2f4m_A Peptide N-glycanase; gl  49.6     4.5 0.00019   19.2   1.0   10   74-83    157-166 (295)
 28 1yuz_A Nigerythrin; rubrythrin  43.8     9.2 0.00039   17.1   1.9   21  262-288   173-193 (202)
 29 1lko_A Rubrerythrin all-iron(I  43.2      13 0.00056   16.1   2.6   22  262-288   157-178 (191)
 30 2i5h_A Hypothetical protein AF  37.8      18 0.00076   15.3   4.1   53  153-206   114-166 (205)
 31 2edu_A Kinesin-like protein KI  36.8      19 0.00079   15.1   4.4   46  175-220    43-89  (98)
 32 2elo_A Zinc finger protein 406  34.8     7.4 0.00031   17.8   0.2   11  279-289     7-17  (37)
 33 2k4x_A 30S ribosomal protein S  32.6      13 0.00053   16.3   1.1   28  258-288    16-43  (55)
 34 1l8d_A DNA double-strand break  29.4      14 0.00059   16.0   0.9   14  258-272    45-58  (112)
 35 1i7d_A DNA topoisomerase III;   28.7      25  0.0011   14.3   3.4   19  259-278   615-633 (659)
 36 1v6g_A Actin binding LIM prote  28.3      11 0.00046   16.7   0.2   26  261-287    16-41  (81)
 37 2h1r_A Dimethyladenosine trans  28.3      26  0.0011   14.3   2.5   58  159-223   215-291 (299)
 38 1x3h_A Leupaxin; paxillin fami  27.1      13 0.00056   16.1   0.5   25  260-287    15-41  (80)
 39 2kdx_A HYPA, hydrogenase/ureas  27.1      18 0.00078   15.2   1.2   23  262-288    75-97  (119)
 40 2nn6_I 3'-5' exoribonuclease C  25.2      29  0.0012   13.9   2.4   23  262-289   171-193 (209)
 41 2h56_A DNA-3-methyladenine gly  24.6      30  0.0013   13.8   3.3   29  176-204   142-171 (233)
 42 1gax_A Valrs, valyl-tRNA synth  23.7      25   0.001   14.4   1.3   26  164-191   348-373 (862)
 43 2riq_A Poly [ADP-ribose] polym  23.6      28  0.0012   14.1   1.6   28  253-286    72-99  (160)
 44 1wd2_A Ariadne-1 protein homol  23.6     9.7 0.00041   17.0  -0.8   22  260-284     6-27  (60)
 45 3cc2_Z 50S ribosomal protein L  23.3      32  0.0013   13.7   2.2   27  259-289    59-86  (116)
 46 1weu_A Inhibitor of growth fam  23.0      19 0.00078   15.2   0.6   10  280-289    75-84  (91)
 47 1x6a_A LIMK-2, LIM domain kina  22.6      17  0.0007   15.5   0.3   25  262-287    17-41  (81)
 48 2e1m_A L-glutamate oxidase; L-  22.6      33  0.0014   13.6   3.5   13  266-278   335-347 (376)
 49 1s1i_9 L37A, YL35, 60S ribosom  22.3      11 0.00046   16.7  -0.7   26  259-288    34-60  (91)
 50 1odh_A MGCM1; transcription fa  22.2      26  0.0011   14.2   1.2   22  260-282   110-131 (174)
 51 1mek_A Protein disulfide isome  21.9      20 0.00086   14.9   0.6   11   57-67     24-34  (120)
 52 2kpi_A Uncharacterized protein  20.8      36  0.0015   13.4   2.8   26  261-289    11-36  (56)
 53 3f6q_B LIM and senescent cell   20.4      33  0.0014   13.6   1.4   26  259-287    10-39  (72)
 54 1d0q_A DNA primase; zinc-bindi  20.4      27  0.0011   14.2   1.0   27  262-289    39-66  (103)

No 1  
>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A*
Probab=100.00  E-value=0  Score=546.54  Aligned_cols=271  Identities=38%  Similarity=0.669  Sum_probs=254.9

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      ||||||||++++.|++.++|++|++|++.++++++..++++.+.|.|++|++|.|+||||+|+|+++.+|++||||+|+|
T Consensus         1 MPElPEVe~~~~~L~~~l~g~~I~~v~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~l~~HlgMtG~~   80 (272)
T 1tdz_A            1 MPELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKY   80 (272)
T ss_dssp             --CHHHHHHHHHHHHHHHTTCBCCEEEESCGGGBTTCHHHHHHHHTTCBEEEEEEETTEEEEEETTTEEEEEECTTTCEE
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEEECCCCEE
T ss_conf             98479999999999997389999999989864347872889977599899999820489999854894699863114446


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF  160 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l  160 (289)
                      ++.+..    ...++|.++.+.++++      .++|.|+|+||.+.+....+...++.++++||||+++.++.+.|.+.+
T Consensus        81 ~~~~~~----~~~~~~~~~~~~~~~~------~~~~~D~r~fg~~~~~~~~~~~~~~~~~~lgpd~l~~~~~~~~~~~~~  150 (272)
T 1tdz_A           81 RLATLD----APREKHDHLTMKFADG------QLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKL  150 (272)
T ss_dssp             EEECTT----CCCCTTEEEEEECSSC------EEEEECTTSCCEEEEEEGGGHHHHHHHHTCCCCSSTTTCCHHHHHHHH
T ss_pred             EEECCC----CCCCCCCEEEEECCCC------EEEEEECCCCEEEEEECCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHH
T ss_conf             750366----8887652699960398------499996232306777514101232133148987554435199999866


Q ss_pred             HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r  161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV  240 (289)
Q Consensus       161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~  240 (289)
                      ..++++||++||||++||||||||+|||||+|||||++++++|+++|      +.+|+++++.+|..|++.||+++++| 
T Consensus       151 ~~~~~~Ik~~LlDQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~L~~~e------~~~L~~~~~~vl~~a~~~~~~~~~~~-  223 (272)
T 1tdz_A          151 RKSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESS------IHLLHDSIIEILQKAIKLGGSSIRTY-  223 (272)
T ss_dssp             HHCCSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHH------HHHHHHHHHHHHHHHHHTTCCCC----
T ss_pred             HHCCCCCCEEEECCCEECCCCHHHHHHHHHHHCCCCCCCHHHCCHHH------HHHHHHHHHHHHHHHHHCCCCCCCCC-
T ss_conf             42033200267507635444473798998872798676752407999------99999999999999998199823245-


Q ss_pred             CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             6778778741331665738771078778878999987812063877679
Q gi|254780625|r  241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ...++.|.++.+|+||+|+|+|| |+||++|++++++||+|||||.|||
T Consensus       224 ~~~~~~g~~~~~~~Vy~r~g~~C-p~Cg~~I~~~~~~gR~t~~Cp~CQk  271 (272)
T 1tdz_A          224 SALGSTGKMQNELQVYGKTGEKC-SRCGAEIQKIKVAGRGTHFCPVCQQ  271 (272)
T ss_dssp             --CCCCCCGGGGCSSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTSC
T ss_pred             CCCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCEEECCCCCC
T ss_conf             77898787764048838898979-9999989999999981099927789


No 2  
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=100.00  E-value=0  Score=525.48  Aligned_cols=268  Identities=39%  Similarity=0.665  Sum_probs=248.5

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             67643678898899986797788999648332657877899972898899996053089995035531001525532799
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFI   81 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~~   81 (289)
                      |||||||+++++|++.++|++|++|.+.+++++.+.++. .+.|.|++|++|.|+||+|+++|+++ +|++||||+|+|+
T Consensus         1 PElPEv~~~~~~l~~~l~Gk~I~~v~~~~~~~~~~~~~~-~~~l~g~~i~~v~r~GK~l~~~~~~~-~l~~HlgM~G~~~   78 (268)
T 1k82_A            1 PELPEVETSRRGIEPHLVGATILHAVVRNGRLRWPVSEE-IYRLSDQPVLSVQRRAKYLLLELPEG-WIIIHLGMSGSLR   78 (268)
T ss_dssp             CCHHHHHHHHHHHHHHHBTCEEEEEEESCCBSSSBCCHH-HHHCCSEEBCEEEEETTEEEEECSSC-EEEEECTTTCEEE
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHH-HHHHCCCEEEEEEEEEEEEEEECCCC-CEEEEECCCCEEE
T ss_conf             973899999999999848999989998998625878855-89817998778984069999980588-3788632551467


Q ss_pred             EECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             81478542245876633899970688760489998158766410014553010053235655533221110678887420
Q gi|254780625|r   82 IEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFH  161 (289)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~  161 (289)
                      +.....    +.+++.++.+.++++.     .++|.|+|+||.+.+.+..  +.++.++++|||||+++|+.++|.+.+.
T Consensus        79 ~~~~~~----~~~~~~~~~~~~~~~~-----~l~~~d~r~~g~~~~~~~~--~~~~~~~~lgpD~l~~~~~~~~~~~~~~  147 (268)
T 1k82_A           79 ILPEEL----PPEKHDHVDLVMSNGK-----VLRYTDPRRFGAWLWTKEL--EGHNVLTHLGPEPLSDDFNGEYLHQKCA  147 (268)
T ss_dssp             EESSSC----CCCTTCCEEEEETTSC-----EEEEECSSCCCEEEEESCS--SSSTTTTTCCCCTTSTTSCHHHHHHHHT
T ss_pred             EEECCC----CCCCCCEEEEEECCCC-----EEEEEECCCEEEEEECCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             740347----9987656999957997-----8999963610689944844--5413887359897971049999999860


Q ss_pred             CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             14542100111265435641368999999871787783122220010158999999998788767654218875531116
Q gi|254780625|r  162 KKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVH  241 (289)
Q Consensus       162 ~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~  241 (289)
                      +++.+||++||||++||||||||+|||||+|||||++++++|+++|      +.+|++++++||..|++.+|+++.||.+
T Consensus       148 ~~~~~ik~~LlDQ~~iaGIGN~y~~EiLf~a~IhP~~~~~~L~~~e------~~~L~~~~~~vl~~a~~~~g~~~~~~~~  221 (268)
T 1k82_A          148 KKKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAE------CELLARVIKAVLLRSIEQGGTTLKDFLQ  221 (268)
T ss_dssp             TCCSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHH------HHHHHHHHHHHHHHHHHTTCCCCC----
T ss_pred             CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             6665541488617604667588999999872798668632399999------9999999999999999948973654405


Q ss_pred             CCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             778778741331665738771078778878999987812063877679
Q gi|254780625|r  242 IDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       242 ~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ++|++|+|+.+|+||+|+|+|| ++||++|++++++||+|||||+|||
T Consensus       222 ~~g~~g~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~ty~Cp~CQk  268 (268)
T 1k82_A          222 SDGKPGYFAQELQVYGRKGEPC-RVCGTPIVATKHAQRATFYCRQCQK  268 (268)
T ss_dssp             ----CCSCGGGCSSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTCC
T ss_pred             CCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECHHHCC
T ss_conf             7898787630568948798979-9999988999988974298931139


No 3  
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=100.00  E-value=0  Score=515.11  Aligned_cols=261  Identities=39%  Similarity=0.688  Sum_probs=240.7

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             67643678898899986797788999648332657877899972898899996053089995035531001525532799
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFI   81 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~~   81 (289)
                      |||||||+++++|++.+.|++|++|.+.++....     ..+.|.|++|++|.|+||||+|+||++.+|++||||+|+|.
T Consensus         1 PElPEVe~~~~~L~~~l~Gk~I~~v~~~~~~~~~-----~~~~l~G~~i~~v~r~GK~l~~~~~~~~~l~~hlgm~G~~~   75 (266)
T 1ee8_A            1 PELPEVETTRRRLRPLVLGQTLRQVVHRDPARYR-----NTALAEGRRILEVDRRGKFLLFALEGGVELVAHLGMTGGFR   75 (266)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCEEEEEECSCTTTEE-----SGGGGTTEEEEEEEEETTEEEEEETTTEEEEEECTTTCEEE
T ss_pred             CCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCC-----CHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEECCCCEEEE
T ss_conf             9728999999999998389999999867975344-----14542898998998301499987158978998156642773


Q ss_pred             EECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             81478542245876633899970688760489998158766410014553010053235655533221110678887420
Q gi|254780625|r   82 IEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFH  161 (289)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~  161 (289)
                      +.         .++|.|+.|.+++.      .++|.|+|+||.+.+++..+....+.+..+||||++++|+.+.|.+.++
T Consensus        76 ~~---------~~~~~~~~~~~~~~------~l~~~d~r~fg~~~~~~~~~~~~~~~l~~~g~d~~~~~~~~~~~~~~~~  140 (266)
T 1ee8_A           76 LE---------PTPHTRAALVLEGR------TLYFHDPRRFGRLFGVRRGDYREIPLLLRLGPEPLSEAFAFPGFFRGLK  140 (266)
T ss_dssp             SS---------CCTTEEEEEEESSC------EEEEECTTCCCEEEEEETTCCTTCTHHHHCCCCTTSTTCCHHHHHHHHH
T ss_pred             CC---------CCCCCEEEEECCCC------EEEEEECCHHEEEEECCCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHHH
T ss_conf             03---------47986267602330------7999734200123201222211242554279973321124678888875


Q ss_pred             CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC--C
Q ss_conf             14542100111265435641368999999871787783122220010158999999998788767654218875531--1
Q gi|254780625|r  162 KKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRD--Y  239 (289)
Q Consensus       162 ~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~--~  239 (289)
                      +++++||++||||++||||||||+|||||+|||||++++++|+++|      +.+||++++++|..|++.||+++.|  |
T Consensus       141 ~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~L~~~e------~~~L~~~~~~vl~~a~~~gg~t~~~~~~  214 (266)
T 1ee8_A          141 ESARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEE------ARRLYRALREVLAEAVELGGSTLSDQSY  214 (266)
T ss_dssp             TCCSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHH------HHHHHHHHHHHHHHHHHTTCCCCSSCCC
T ss_pred             HCCCHHHHHHCCCCEECCCCHHHHHHHHHHHCCCHHHCCCCCCHHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             1364065762157612246699999999985798023267289999------9999999999999999838953676543


Q ss_pred             CCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             16778778741331665738771078778878999987812063877679
Q gi|254780625|r  240 VHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       240 ~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .++++.+|+++.+|+||+|+|++| ++||++|+++++|||+|||||+||+
T Consensus       215 ~~~~~~~g~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~g~R~t~~CP~CQ~  263 (266)
T 1ee8_A          215 RQPDGLPGGFQTRHAVYGREGLPC-PACGRPVERRVVAGRGTHFCPTCQG  263 (266)
T ss_dssp             CCTTSCCCSCGGGCSSTTCTTSBC-TTTCCBCEEEESSSCEEEECTTTTT
T ss_pred             CCCCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCEEECCCCCC
T ss_conf             367888677631238848898978-9999989999988982099989779


No 4  
>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 3go8_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* ...
Probab=100.00  E-value=0  Score=495.93  Aligned_cols=254  Identities=35%  Similarity=0.613  Sum_probs=232.1

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCC-C-CCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCE
Q ss_conf             676436788988999867977889996483326-5-78778999728988999960530899950355310015255327
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLR-F-DFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGS   79 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~-~-~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~   79 (289)
                      |||||||+++++|++.+.|++|++|.+.+++.. . ..++.|.+.|.|++|++|+|+||+|+|+|++ .+|++||||+|+
T Consensus         1 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~~~~~l~G~~i~~v~r~GK~l~~~~~~-~~l~~HlgMtG~   79 (256)
T 3gpu_A            1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDR-DALISHLRMEGR   79 (256)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCBEEEEEESCGGGEEESSSHHHHHHHHTTCBCCEEEEETTEEEEECSS-EEEEEECTTTCE
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCEECCCCHHHHHHHCCCCEEEEEEECCEEEHHHCCC-CCEEEEEEECCE
T ss_conf             9748999999999998389999899986887462689969999774998998998632888002067-724522343544


Q ss_pred             EEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             99814785422458766338999706887604899981587664100145530100532356555332211106788874
Q gi|254780625|r   80 FIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQ  159 (289)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~  159 (289)
                      |.+.+.+.    +.++|.|+.+.|+++.     .+.|.|.|+||.+.+.........+.+..+||||+++.++.+.|.+.
T Consensus        80 ~~~~~~~~----~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~d~l~~~~~~~~~~~~  150 (256)
T 3gpu_A           80 YAVASALE----PLEPHTHVVFCFTDGS-----ELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAER  150 (256)
T ss_dssp             EEEEETTS----CCCTTEEEEEEETTSE-----EEEEECTTCCCEEEEEEHHHHTTSTTTTTCCCCTTSTTSCHHHHHHH
T ss_pred             EEEEECCC----CCCCCCEEEEEECCCC-----EEEEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             32320236----7888616999975997-----69998513344101104541013321034688821001689999888


Q ss_pred             HHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             20145421001112654356413689999998717877831222200101589999999987887676542188755311
Q gi|254780625|r  160 FHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDY  239 (289)
Q Consensus       160 l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~  239 (289)
                      +++++++||++||||++||||||||+|||||+|||||++++++||++|      +++|+++++.||.+|++.|+      
T Consensus       151 ~~~~~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~------~~~L~~~~~~vl~~ai~~g~------  218 (256)
T 3gpu_A          151 AVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKE------IERLHEEMVATIGEAVMKGQ------  218 (256)
T ss_dssp             HHTCCSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHH------HHHHHHHHHHHHHHHHC---------
T ss_pred             HHCCCCCHHHHHCCCCEECCCCHHHHHHHHHHHHCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHCCC------
T ss_conf             755776455631136513343488999999973148376313389999------99999999999999996688------


Q ss_pred             CCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             16778778741331665738771078778878999987812063877679
Q gi|254780625|r  240 VHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       240 ~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                                 ++++||+|+|+|| |+||++|++++++||+|||||.|||
T Consensus       219 -----------~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~t~~Cp~CQk  256 (256)
T 3gpu_A          219 -----------HHLYVYGRQGNPC-KRCGTPIEKTVVAGRGTHYCPRCQR  256 (256)
T ss_dssp             -------------CCSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTCC
T ss_pred             -----------CEEEECCCCCCCC-CCCCCEEEEEEECCCCEEECCCCCC
T ss_conf             -----------4088738997967-9999989999999982098713149


No 5  
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*
Probab=100.00  E-value=0  Score=489.81  Aligned_cols=259  Identities=22%  Similarity=0.426  Sum_probs=223.5

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             67643678898899986797788999648332657877899972898899996053089995035531001525532799
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFI   81 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~~   81 (289)
                      |||||||++++.|++.+.|++|++|.+..+..     +.+.+.|.|++|++|+|+||||+|+||++.+|++||||+|+|+
T Consensus         1 PElPEVe~~~~~L~~~~~g~~I~~v~~~~~~~-----~~~~~~L~G~~i~~v~RrGK~l~~~l~~~~~L~~HLgMtG~~~   75 (262)
T 1k3x_A            1 PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQL-----KTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWR   75 (262)
T ss_dssp             CCHHHHHHHHHHHHHHHBTCCCSEEEESSGGG-----TTHHHHHTTCCEEEEEEETTEEEEEETTSCEEEEECTTTCEEE
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEEEECCCCH-----HHHHHHCCCCEEEEEEECEEEEEECCCCCEEEEECCCCCEEEE
T ss_conf             97489999999999986898898999889855-----6589776998998999651388360478439997155433788


Q ss_pred             EECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             81478542245876633899970688760489998158766410014553010053235655533221110678887420
Q gi|254780625|r   82 IEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFH  161 (289)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~  161 (289)
                      +...+.    .+.++.++.+.+.++..   ..+.|.|.    .+.++.......++.+++||||||+++|+.+.|.+.+.
T Consensus        76 ~~~~~~----~~~~~~~~~~~~~~~~~---~~~~~~~~----~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~  144 (262)
T 1k3x_A           76 VVDTGE----EPQTTRVLRVKLQTADK---TILLYSAS----DIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLL  144 (262)
T ss_dssp             EEETTC----CCCCSSCEEEEEECSSE---EEEEESCC----EEEEECTTHHHHSHHHHHCCCBTTCTTCCHHHHHHHHH
T ss_pred             EECCCC----CCCCCEEEEEECCCCCE---EEEEECCC----EEEEECHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             731434----55432034443056866---99997352----05995242300024898669987984776999999987


Q ss_pred             C---CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             1---4542100111265435641368999999871787783122220010158999999998788767654218875531
Q gi|254780625|r  162 K---KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRD  238 (289)
Q Consensus       162 ~---~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~  238 (289)
                      .   ++++||++||||++||||||||+|||||+|||||++++++||++|      +.+|+++++.||..|++.+|++..+
T Consensus       145 ~~k~~~~~Ik~~LlDQ~~iaGIGNiya~EiLf~a~I~P~~~~~~Ls~~~------~~~L~~~i~~vl~~a~~~~g~~~~~  218 (262)
T 1k3x_A          145 SPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQ------LDALAHALLEIPRFSYATRGQVDEN  218 (262)
T ss_dssp             STTTTTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHH------HHHHHHHHHHHHHHHHHHCC-----
T ss_pred             HHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHH------HHHHHHHHHHHHHHHHHCCCEECCC
T ss_conf             4002006899998417744565699999999872068545013444778------9999999999888785528665777


Q ss_pred             CCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             116778778741331665738771078778878999987812063877679
Q gi|254780625|r  239 YVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       239 ~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                           +..|.+ ..++||+|+|+|| |+||++|++++++||+|||||.||-
T Consensus       219 -----~~~g~~-~~~~Vy~r~g~~C-~~Cg~~I~~~~~~~R~t~~Cp~CQh  262 (262)
T 1k3x_A          219 -----KHHGAL-FRFKVFHRDGEPC-ERCGSIIEKTTLSSRPFYWCPGCQH  262 (262)
T ss_dssp             ---------CC-CCCSSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTCC
T ss_pred             -----CCCCCE-EEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             -----888854-6788926596979-9999889999989981488745359


No 6  
>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A
Probab=100.00  E-value=0  Score=469.74  Aligned_cols=265  Identities=23%  Similarity=0.293  Sum_probs=223.0

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHH--HCCCEEEEEEECCEEEEEEECCCC------CCCC
Q ss_conf             96764367889889998679778899964833265787789997--289889999605308999503553------1001
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAA--TRGKKIIDVSRRAKYLLIELEGNL------SIIV   72 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~--L~G~~I~~v~r~GK~l~l~l~~~~------~L~~   72 (289)
                      |||||||+++++.|++.+.|++|++|++.++++.+..+..+.+.  +.|++|++|.|+||||+|+|+++.      .|..
T Consensus         1 MPElPEV~~~~~~l~~~~~g~~I~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~r~GK~l~~~l~~~~~~~~~~~~~~   80 (289)
T 3a46_A            1 MPEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWN   80 (289)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCEEEEEEECSSHHHHSCCBTHHHHHHTCCEEEEEEEEETTEEEEEEEETTEEEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCHHHHHHCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEE
T ss_conf             98769999999999997189999899988885235788679999733785898999876799999536765456647984


Q ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCH
Q ss_conf             52553279981478542245876633899970688760489998158766410014553010053235655533221110
Q gi|254780625|r   73 HLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFN  152 (289)
Q Consensus        73 HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~  152 (289)
                      ||+|+|.|.+         .+++|+|+.+.|+++.     .++|.|+|+||++.+.++... ..+.+.+||||||++   
T Consensus        81 ~l~m~g~~~~---------~~~~~~~~~~~~~~~~-----~l~f~D~R~fg~~~l~~~~~~-~~~~l~~lGpD~l~~---  142 (289)
T 3a46_A           81 TFGLTGMWSL---------FEAKYTRAVLSFDNEL-----MAYFSDMRNFGTFKFSNSEKE-LKRKLNELGPDFLKN---  142 (289)
T ss_dssp             ECTTTEEEES---------SCCTTEEEEEEEGGGC-----EEEEEESSCCCEEEEECCHHH-HHHHHTTSCCBTTTC---
T ss_pred             EEEECCCCEE---------CCCCCCEEEECCCCCE-----EEEEEECCCCCEEEEECCHHH-HHHHHHCCCCCHHHH---
T ss_conf             6664264011---------1476305664034306-----999981221453566120110-014441047623566---


Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCC-CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             6788874201454210011126543-564136899999987178778312222001015899999999878876765421
Q gi|254780625|r  153 AIYLTHQFHKKNSNLKNALLNQKIV-AGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDA  231 (289)
Q Consensus       153 ~~~~~~~l~~~~~~Ik~~LlDQ~~i-aGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~  231 (289)
                      .+.+.+.+++++++||.+||||+.| |||||||+|||||+|||||++++++||++|      +++|+++|+.+|..|++.
T Consensus       143 ~~~~~~~~~~~~~~ik~~LLdq~~i~aGIGNiya~EiLf~a~I~P~~~~~~Ls~~e------~~~L~~~i~~vl~~a~~~  216 (289)
T 3a46_A          143 DDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQE------IENLWYWIKYETKLAYDS  216 (289)
T ss_dssp             SCCCGGGGGGCCSBHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHH------HHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEECCCCHHHHHHHHHHHHCCHHHHHHHCCHHH------HHHHHHHHHHHHHHHHHC
T ss_conf             79999997542022457752466267064089999999985068546667499999------999999999999999982


Q ss_pred             CCCCC-CCCC---CCCCCCCCC--------HHHEEEECCCCCCCC-CCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             88755-3111---677877874--------133166573877107-8778878999987812063877679
Q gi|254780625|r  232 GGSSL-RDYV---HIDGSIGYF--------QNAFSVYGKTGEPCL-SNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       232 gG~~~-~~~~---~~~g~~g~~--------~~~~~vy~r~g~~C~-~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      +|.+. .++.   ...|..+++        +.+|+||+|+|+||+ +.||++|.+..++||+|||||+|||
T Consensus       217 ~g~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~Vy~r~~~pc~~~~c~~~I~~~~~~gR~ty~CP~CQk  287 (289)
T 3a46_A          217 NHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQK  287 (289)
T ss_dssp             SCSSSCGGGHHHHTTSCCCCCSTTCCCSCSSCCCSSTTCSBCTTSCBCEEECCSCCTTCCCCEEECTTTCB
T ss_pred             CCCCCEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCEEEEEECCCEEEEECCCCCC
T ss_conf             89662011356666678736555655556642689989998988887578779997818832499767386


No 7  
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Probab=100.00  E-value=0  Score=416.39  Aligned_cols=260  Identities=23%  Similarity=0.306  Sum_probs=202.4

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEEC---------CCCCCC
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503---------553100
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELE---------GNLSII   71 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~---------~~~~L~   71 (289)
                      ||||||||++++.|++.+.|++|..+.......++....    ...+..+..+.++||+|++.|+         ++.+|+
T Consensus         1 MPELPEVe~v~r~L~~~l~g~~i~~~i~~~~~~~~~~~~----~~~~~~~i~~~~rGK~l~~~l~~~~~~~~~~~~~~L~   76 (364)
T 1tdh_A            1 MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVP----FESSAYRISASARGKELRLILSPLPGAQPQQEPLALV   76 (364)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCCEEEECEECSSCCSCCCC----CEEEEEEEEEEEETTEEEEEEEECTTCSSCCCCEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCC----CCCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCEEE
T ss_conf             971799999999999985797898999814446786554----3566638999963339999943665334457871699


Q ss_pred             CCCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCC--
Q ss_conf             152553279981478542245876633899970688760489998158766410014553010053235655533221--
Q gi|254780625|r   72 VHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADN--  149 (289)
Q Consensus        72 ~HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~--  149 (289)
                      +||||+|+|++....     ..++|.|+.|.|.++..  ...|+|+|+|+||++++.+.       ....+|||||+.  
T Consensus        77 ~HLGMsG~~~i~~~~-----~~~kh~h~~~~~~~~~~--~~~L~f~D~RrFG~~~l~~~-------~~~~lGPdpl~~~~  142 (364)
T 1tdh_A           77 FRFGMSGSFQLVPRE-----ELPRHAHLRFYTAPPGP--RLALCFVDIRRFGRWDLGGK-------WQPGRGPCVLQEYQ  142 (364)
T ss_dssp             EECTTTCEEEEEEGG-----GCCTTEEEEEEBCSSSS--CEEEEEECTTCCCEEEESSC-------CCTTCCCCTTTCHH
T ss_pred             EECCCCEEEEECCCC-----CCCCCCEEEEEEECCCC--EEEEEEECCCCCEEEEECCC-------HHHHCCCCCCCCCC
T ss_conf             977872699961688-----78977559999927998--48999955411203563140-------56652976566544


Q ss_pred             CCHHHHHHHHHH-CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHH--------------HHHH
Q ss_conf             110678887420-1454210011126543564136899999987178778312222001015--------------8999
Q gi|254780625|r  150 SFNAIYLTHQFH-KKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTP--------------KDIL  214 (289)
Q Consensus       150 ~~~~~~~~~~l~-~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~--------------~~~~  214 (289)
                      .|+...+...+. .++++||++||||++||||||||+|||||+|+|||.+++++|++++...              +..+
T Consensus       143 ~f~~~~~~~~~~k~~~~~IK~~LLDQ~iiaGIGNIYadEiLf~A~IhP~r~a~~ls~~~~~~~~~~~~~l~~~~r~k~~~  222 (364)
T 1tdh_A          143 QFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQN  222 (364)
T ss_dssp             HHHHHHHHTTTSGGGGSBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----CCSCHHHHHHHTTTS
T ss_pred             CCCHHHHHHHHHHCCCCCHHHHHHCCCEECCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             41099999987521576089987247702254288999999984899667412345766413442110033444557788


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             99999878876765421887553111677877874133166573877107877887899998781206387767
Q gi|254780625|r  215 YKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       215 ~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      ..|+++++.||.+||+.||++.+++....| .|+|+++|.||||+|++|. +|        -+||++|||+.|+
T Consensus       223 ~~l~~~~~~Vl~~ai~~GG~s~~~~~g~~g-~g~Fq~~l~vYgr~g~~Cl-~~--------~~Grt~~~~~~~~  286 (364)
T 1tdh_A          223 PDLLELCHSVPKEVVQLGGRGYGSESGEED-FAAFRAWLRCYGMPGMSSL-QD--------RHGRTIWFQGDPG  286 (364)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCTTSSCHHHH-HHHHHHHCSSTTCTTCEEE-EC--------TTSCEEEESSCCC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCHHHHCEEECCCCCCCCC-CC--------CCCCEEEECCCCC
T ss_conf             999999999999999818987658878776-1004433841378998244-16--------8997898688886


No 8  
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp}
Probab=96.30  E-value=0.026  Score=33.57  Aligned_cols=52  Identities=17%  Similarity=0.222  Sum_probs=41.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             55332211106788874201454210011126543564136899999987178778
Q gi|254780625|r  143 GPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIR  198 (289)
Q Consensus       143 GpD~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~  198 (289)
                      +.||+  +.+.+.|.+.+.....++...|+..  +.|+|..++.|++++|++.+..
T Consensus       168 ~~~p~--~~~~e~~~~~l~~~~~~l~k~L~~~--~~g~~~~l~~ei~~ra~~~~~~  219 (288)
T 3doa_A          168 KINPY--DITGAEVLKYIDFNAGNIAKQLLNQ--FEGFSPLITNEIVSRRQFMTSS  219 (288)
T ss_dssp             CBCGG--GCCHHHHGGGCCGGGCCHHHHHHHH--BTTCCHHHHHHHHTTSSSCSTT
T ss_pred             CCCCC--CCCHHHHHHHHHHCCCCHHHHHHHH--CCCCCHHHHHHHHHHCCCCCCC
T ss_conf             59965--4899999998750864199999986--3899989999999974999755


No 9  
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Probab=96.16  E-value=0.025  Score=33.61  Aligned_cols=75  Identities=19%  Similarity=0.320  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC--CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             56555332211106788874201--4542100111265435641368999999871787783122220010158999999
Q gi|254780625|r  140 RTLGPEPADNSFNAIYLTHQFHK--KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKL  217 (289)
Q Consensus       140 ~~lGpD~l~~~~~~~~~~~~l~~--~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L  217 (289)
                      ..+.|.|..  .+...+...++.  ....+..+|  ++-|+.||+-.+.||+-.++++|.....+|+++|      +.+|
T Consensus       228 ~eikPHP~g--v~l~~l~~ml~~~~~~~~l~~FL--~~~Fs~V~~~~a~~i~~~~g~~~~~~p~~l~~~e------~~~l  297 (471)
T 1mu5_A          228 QEVKPHPYG--VDREEIKILINNLKRDYTIKEFL--VNEFQSIGDTTADKILELAGLKPNKKVKNLTEEE------ITRL  297 (471)
T ss_dssp             CCCCCCGGG--CCHHHHHHHSTTCSSCCBHHHHH--TTSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTH------HHHH
T ss_pred             HHCCCCCCC--CCHHHHHHHHHHCCCCCCHHHHH--HHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHH
T ss_conf             312688002--00677999998554666267888--8754776989999999974999777714499999------9999


Q ss_pred             HHHHHHH
Q ss_conf             9987887
Q gi|254780625|r  218 IQEIQKV  224 (289)
Q Consensus       218 ~~~i~~v  224 (289)
                      .++.+++
T Consensus       298 ~~a~~~~  304 (471)
T 1mu5_A          298 VETFKKY  304 (471)
T ss_dssp             HHHHHHC
T ss_pred             HHHHHHH
T ss_conf             9999853


No 10 
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M 3jyv_M*
Probab=95.57  E-value=0.013  Score=35.41  Aligned_cols=50  Identities=18%  Similarity=0.390  Sum_probs=41.0

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      +.+|.-+|   +.|-|||...|..||-.++|+|..++.+||++|      +..|-+.+.
T Consensus        23 ~K~v~~aL---t~I~GIG~~~A~~Ic~~lgI~~~~kvg~Lt~~q------l~kl~~~I~   72 (152)
T 2zkq_m           23 RRKIAFAI---TAIKGVGRRYAHVVLRKADIDLTKRAGELTEDE------VERVITIMQ   72 (152)
T ss_dssp             SSBHHHHG---GGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHH------HHHHHHHHH
T ss_pred             CCEEEEEE---ECCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHH------HHHHHHHHH
T ss_conf             97887650---021065899999999993899543015199999------999999985


No 11 
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...
Probab=95.40  E-value=0.0083  Score=36.71  Aligned_cols=50  Identities=24%  Similarity=0.416  Sum_probs=40.2

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      +.+|.-+|   +.|=|||.-.|..||..++|+|..++.+||++|      +..|-+.+.
T Consensus        12 ~K~v~~aL---t~I~GIG~~~A~~Ic~~lGId~~~kvg~Lt~~q------i~~l~~~i~   61 (126)
T 2vqe_M           12 NKRVDVAL---TYIYGIGKARAKEALEKTGINPATRVKDLTEAE------VVRLREYVE   61 (126)
T ss_dssp             SSBHHHHH---TTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHH------HHHHHHHHH
T ss_pred             CCEEEEEE---CCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHH
T ss_conf             97878762---043483899999999985979663016399999------999999983


No 12 
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ...
Probab=93.22  E-value=0.01  Score=36.11  Aligned_cols=50  Identities=20%  Similarity=0.139  Sum_probs=39.6

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      +.+|.-+|   +.|-|||...+..||-.++|||..++++|+++|.      ..|-+.+.
T Consensus        11 ~K~v~~AL---t~I~GIG~~~A~~Ic~~lgi~~~~rv~~Lt~~qi------~~l~~~i~   60 (113)
T 3ofp_M           11 HKHAVIAL---TSIYGVGKTRSKAILAAAGIAEDVKISELSEGQI------DTLRDEVA   60 (113)
T ss_dssp             CCCHHHHH---TSSSSCCSSHHHHGGGTTTCCSSCCSSSCCTTSS------TTTHHHHH
T ss_pred             CCEEEEEE---ECEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHH------HHHHHHHH
T ss_conf             97866550---1434748999999999849898740485999999------99999986


No 13 
>3fut_A Dimethyladenosine transferase; methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase; 1.52A {Thermus thermophilus HB8} PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A*
Probab=80.63  E-value=1.5  Score=22.17  Aligned_cols=58  Identities=28%  Similarity=0.312  Sum_probs=43.4

Q ss_pred             HHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             88742014542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r  156 LTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       156 ~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      +...+..+++.|++.|-.    .+..+--..++|-.++|+|...+.+||-+|      +.+|++++..
T Consensus       212 v~~~F~~RRK~l~n~L~~----~~~~~~~~~~~l~~~~i~~~~R~e~Ls~~~------~~~L~~~l~~  269 (271)
T 3fut_A          212 VEAAFGKRRKTLLNALAA----AGYPKARVEEALRALGLPPRVRAEELDLEA------FRRLREGLEG  269 (271)
T ss_dssp             HHHHTSSTTSCHHHHHHH----TTCCHHHHHHHHHHTTCCTTCCGGGCCHHH------HHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHH----HCCCHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHC
T ss_conf             999998665799999876----368888999999986979663915499999------9999999865


No 14 
>1qyr_A KSGA, high level kasugamycin resistance protein, S-; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} SCOP: c.66.1.24
Probab=77.48  E-value=2  Score=21.36  Aligned_cols=52  Identities=15%  Similarity=0.359  Sum_probs=39.0

Q ss_pred             HHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8742014542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r  157 THQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK  223 (289)
Q Consensus       157 ~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~  223 (289)
                      ...+..++++|++.|-         +++..|+|=.++|+|...+.+|+.+|      +.+|++.+.+
T Consensus       199 ~~~F~~rRK~l~n~L~---------~~~~~~~l~~~~i~~~~R~e~Ls~~~------~~~L~~~l~~  250 (252)
T 1qyr_A          199 TEAFNQRRKTIRNSLG---------NLFSVEVLTGMGIDPAMRAENISVAQ------YCQMANYLAE  250 (252)
T ss_dssp             HHHHHTTTSBHHHHTT---------TTCCHHHHHHTTCCTTSBGGGSCHHH------HHHHHHHHHH
T ss_pred             HHHHHCCHHHHHHHHH---------HHCCHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHH
T ss_conf             9998545288999874---------04419999977988233933399999------9999999984


No 15 
>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, antibiotic resistance, methyltransferase; 1.44A {Aquifex aeolicus VF5} PDB: 3ftc_A 3fte_A 3ftf_A*
Probab=76.81  E-value=2.4  Score=20.92  Aligned_cols=46  Identities=22%  Similarity=0.365  Sum_probs=34.9

Q ss_pred             HHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             74201454210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r  158 HQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ  222 (289)
Q Consensus       158 ~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~  222 (289)
                      ..+..++++++..|             .+++|=.++|+|...+.+|+.+|      +.+|++.+.
T Consensus       200 ~~F~~rRK~l~~~l-------------~~~~l~~~~i~~~~R~e~Ls~~~------~~~L~~~l~  245 (249)
T 3ftd_A          200 KIFQNRRKVLRKKI-------------PEELLKEAGINPDARVEQLSLED------FFKLYRLIE  245 (249)
T ss_dssp             HHHSSTTSCGGGTS-------------CHHHHHHTTCCTTCCGGGCCHHH------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH-------------HHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHH
T ss_conf             99875045565878-------------99999987959888947799999------999999999


No 16 
>2avu_E Flagellar transcriptional activator FLHC; C4-type zinc finger, transcription activator; 3.00A {Escherichia coli} SCOP: e.64.1.1
Probab=74.49  E-value=1  Score=23.31  Aligned_cols=27  Identities=26%  Similarity=0.663  Sum_probs=22.1

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             7107877887899998781206387767
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .+| ++||+.-......-.+.|.||-||
T Consensus       135 ~~C-~~Cgg~fv~~~~~~~~~f~C~lC~  161 (192)
T 2avu_E          135 SSC-NCCGGNFITHAHQPVGSFACSLCQ  161 (192)
T ss_dssp             EEC-TTTCCEEEEESSCCSSCCCCTTC-
T ss_pred             CCC-CCCCCCEECCCCCCCCCCCCCCCC
T ss_conf             657-878995155666667687389999


No 17 
>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; HET: MSE; 2.20A {Escherichia coli K12} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A
Probab=73.98  E-value=1.6  Score=22.07  Aligned_cols=28  Identities=18%  Similarity=0.558  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             8771078778878999987812063877679
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .-+-| ++||++....  .+.....||.|+.
T Consensus       106 ~~rfC-~~CG~~~~~~--~~~~~~~C~~C~~  133 (269)
T 1vk6_A          106 SHKYC-GYCGHEMYPS--KTEWAMLCSHCRE  133 (269)
T ss_dssp             TTSBC-TTTCCBEEEC--SSSSCEEESSSSC
T ss_pred             CCCCC-CCCCCCCCCC--CCCEEEECCCCCC
T ss_conf             29868-6679877436--7980488989988


No 18 
>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=66.80  E-value=1.9  Score=21.60  Aligned_cols=26  Identities=27%  Similarity=0.747  Sum_probs=11.2

Q ss_pred             CCCCCCCCEEEEEEE-----CCCCEEECCCCC
Q ss_conf             107877887899998-----781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQ-----AGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~-----~gR~ty~Cp~CQ  288 (289)
                      .| |.|+.+..-...     ....+|-|-.|+
T Consensus        16 ~C-p~C~k~ys~Lda~~Lld~~~~~F~C~~C~   46 (62)
T 1vd4_A           16 KC-PVCSSTFTDLEANQLFDPMTGTFRCTFCH   46 (62)
T ss_dssp             EC-SSSCCEEEHHHHHHHEETTTTEEBCSSSC
T ss_pred             EC-CCCCCEECHHHHHHHCCCCCCEEEECCCC
T ss_conf             88-89888823755988359678919736889


No 19 
>3ga8_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, Zn-binding protein, DNA-binding, transcription regulation; HET: PE4; 1.70A {Escherichia coli k-12} PDB: 3hi2_A
Probab=65.53  E-value=4.1  Score=19.39  Aligned_cols=24  Identities=4%  Similarity=0.115  Sum_probs=12.2

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCC
Q ss_conf             888742014542100111265435
Q gi|254780625|r  155 YLTHQFHKKNSNLKNALLNQKIVA  178 (289)
Q Consensus       155 ~~~~~l~~~~~~Ik~~LlDQ~~ia  178 (289)
                      ...+.+..-++.|.+.++|+.+|+
T Consensus        54 ~~~~a~~af~~~Vd~~~~~p~~i~   77 (78)
T 3ga8_A           54 AFMAQVKAFRASVNAETVAPEFIV   77 (78)
T ss_dssp             HHHHHHHHHHHHHHHC--------
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHC
T ss_conf             999999999998525246816642


No 20 
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}
Probab=65.36  E-value=0.56  Score=24.97  Aligned_cols=30  Identities=17%  Similarity=0.553  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCEEEEEEE----CCCCEEECCCCCC
Q ss_conf             877107877887899998----7812063877679
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQ----AGRSTFYCTYCQK  289 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~----~gR~ty~Cp~CQk  289 (289)
                      .+..| .-|+..|--..+    .+....+||.|+|
T Consensus       197 ~~~~C-~gC~~~l~~~~~~~~~~~~~i~~C~~CgR  230 (256)
T 3na7_A          197 KKQAC-GGCFIRLNDKIYTEVLTSGDMITCPYCGR  230 (256)
T ss_dssp             BTTBC-TTTCCBCCHHHHHHHHHSSSCEECTTTCC
T ss_pred             ECCCC-CCCCCCCCHHHHHHHHCCCCEEECCCCCC
T ss_conf             59916-88782438999999885999048989997


No 21 
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa}
Probab=60.76  E-value=0.98  Score=23.38  Aligned_cols=41  Identities=17%  Similarity=0.297  Sum_probs=34.2

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHH
Q ss_conf             542100111265435641368999999871787783122220010
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNG  208 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~  208 (289)
                      +..|.-.|   +.|-|||.-.|..||-.++|+| +++.+|+++|.
T Consensus        57 nK~V~~AL---T~IyGIG~~~A~~Ic~~lgId~-kkv~dLteeel   97 (145)
T 3bbn_M           57 HKRVEYSL---QYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEV   97 (145)
T ss_dssp             SSBTTTGG---GGSTTCCSSTTTGGGTTTTCCS-CBTTSCCSSTT
T ss_pred             CCEEEEHH---HHHHCCCHHHHHHHHHHCCCCH-HHHHHCCHHHH
T ss_conf             97721235---5674638899999999859974-66765478799


No 22 
>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1
Probab=58.43  E-value=4.8  Score=18.94  Aligned_cols=25  Identities=20%  Similarity=0.646  Sum_probs=16.5

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             10787788789999878120638776
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      -| |.|+.++++.+-=|-..|||-+|
T Consensus        63 ~C-PdC~~~Lq~LkACGAvdYFC~~c   87 (101)
T 2jne_A           63 LC-PDCHQPLQVLKACGAVDYFCQHG   87 (101)
T ss_dssp             EC-TTTCSBCEEEEETTEEEEEETTT
T ss_pred             CC-CCCCCHHHHHHHCCCHHHHHCCC
T ss_conf             69-74020999998716137776338


No 23 
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}
Probab=54.74  E-value=5  Score=18.83  Aligned_cols=26  Identities=19%  Similarity=0.636  Sum_probs=23.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             710787788789999878120638776
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      .-| |.|+.++++.+-=|-..|||-+|
T Consensus        32 a~C-PdC~~~Lq~LkACGAvdYFC~~c   57 (81)
T 2jrp_A           32 ALC-PDCRQPLQVLKACGAVDYFCQNG   57 (81)
T ss_dssp             EEC-SSSCSCCCEEEETTEEEECCTTT
T ss_pred             EEC-CCCCCHHHHHHHCCCHHHHHCCC
T ss_conf             648-76436799987726215765479


No 24 
>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3
Probab=53.26  E-value=2.4  Score=20.94  Aligned_cols=21  Identities=0%  Similarity=0.251  Sum_probs=10.6

Q ss_pred             CCEEEEEEECCCCCEEEEEEEE
Q ss_conf             6338999706887604899981
Q gi|254780625|r   96 HNHVTISLTNNTNTKKYRVIYN  117 (289)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~l~~~  117 (289)
                      ...+.+.+.|++... ...+|.
T Consensus        78 ry~l~~~i~D~Tg~~-~~~~F~   98 (181)
T 1l1o_C           78 RMILSVNIADFQENQ-WVTCFQ   98 (181)
T ss_dssp             EEEEEEEEECSSCEE-EEEEEH
T ss_pred             EEEEEEEEECCCCCE-EEEEEH
T ss_conf             999999998289979-999807


No 25 
>1nnq_A Rubrerythrin; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 2.35A {Pyrococcus furiosus} SCOP: a.25.1.1 g.41.5.1 PDB: 2hr5_A
Probab=51.53  E-value=3.2  Score=20.08  Aligned_cols=21  Identities=29%  Similarity=0.725  Sum_probs=14.9

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| ++||....    | .--=.||.|.
T Consensus       141 vC-~~CG~i~~----g-~~P~~CPvC~  161 (171)
T 1nnq_A          141 IC-PICGYTAV----D-EAPEYCPVCG  161 (171)
T ss_dssp             EC-TTTCCEEE----S-CCCSBCTTTC
T ss_pred             EC-CCCCCCCC----C-CCCCCCCCCC
T ss_conf             89-98939389----9-9999797999


No 26 
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A
Probab=51.52  E-value=7.4  Score=17.75  Aligned_cols=26  Identities=27%  Similarity=0.634  Sum_probs=18.6

Q ss_pred             EECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             65738771078778878999987812063877679
Q gi|254780625|r  255 VYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       255 vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ||.    .| +.||..+.+    ......||.|..
T Consensus       139 v~a----~c-~~c~~~l~~----~~~~~~C~~cg~  164 (179)
T 3m7n_A          139 LRA----LC-SNCKTEMVR----EGDILKCPECGR  164 (179)
T ss_dssp             EEC----BC-TTTCCBCEE----CSSSEECSSSCC
T ss_pred             EEE----EC-CCCCCEEEE----ECCEEECCCCCC
T ss_conf             999----67-877860777----099999999998


No 27 
>2f4m_A Peptide N-glycanase; glycoproteins, ubiquitin-dependent protein degradation, nucleotide excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: d.3.1.4 PDB: 2f4o_A*
Probab=49.59  E-value=4.5  Score=19.16  Aligned_cols=10  Identities=20%  Similarity=0.727  Sum_probs=5.2

Q ss_pred             CCCCCEEEEE
Q ss_conf             2553279981
Q gi|254780625|r   74 LGMSGSFIIE   83 (289)
Q Consensus        74 lgM~G~~~~~   83 (289)
                      +|..-+|.+.
T Consensus       157 ~G~~aR~V~~  166 (295)
T 2f4m_A          157 LGFEARYVWD  166 (295)
T ss_dssp             TTCCEEEEEE
T ss_pred             CCCCEEEEEC
T ss_conf             5996499942


No 28 
>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIRON center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A
Probab=43.78  E-value=9.2  Score=17.14  Aligned_cols=21  Identities=29%  Similarity=0.719  Sum_probs=15.1

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| ++||....     |...-.||.|-
T Consensus       173 ~C-~~CG~i~~-----g~~p~~CP~C~  193 (202)
T 1yuz_A          173 LC-PICGYIHK-----GEDFEKCPICF  193 (202)
T ss_dssp             EC-SSSCCEEE-----SSCCSBCTTTC
T ss_pred             EC-CCCCCEEC-----CCCCCCCCCCC
T ss_conf             88-99998524-----99899899999


No 29 
>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubredoxin-like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A
Probab=43.19  E-value=13  Score=16.14  Aligned_cols=22  Identities=27%  Similarity=0.690  Sum_probs=14.8

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| ++||.+..-...-.    .||.|.
T Consensus       157 ~C-~~CG~i~~g~~~p~----~CP~C~  178 (191)
T 1lko_A          157 RC-RNCGYVHEGTGAPE----LCPACA  178 (191)
T ss_dssp             EE-TTTCCEEEEEECCS----BCTTTC
T ss_pred             EC-CCCCCCCCCCCCCC----CCCCCC
T ss_conf             89-99986012899988----597999


No 30 
>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1
Probab=37.83  E-value=18  Score=15.25  Aligned_cols=53  Identities=11%  Similarity=0.216  Sum_probs=38.6

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf             678887420145421001112654356413689999998717877831222200
Q gi|254780625|r  153 AIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQN  206 (289)
Q Consensus       153 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~  206 (289)
                      .+.|..- =++..||..-|--=..++||||-.+.+||=.=+-.|+..-.+|++.
T Consensus       114 E~~FV~F-fN~A~pItlrlH~leLLPGIGKK~~~~IleeR~k~~FeSFedi~~R  166 (205)
T 2i5h_A          114 EKKYVDF-FNKADSITTRMHQLELLPGVGKKMMWAIIEERKKRPFESFEDIAQR  166 (205)
T ss_dssp             HHHHHHH-HC--CCBCSSSBGGGGSTTCCHHHHHHHHHHHHHSCCCSHHHHHHH
T ss_pred             CHHCCEE-ECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             0201013-2468886187888875235058999999999655898899999988


No 31 
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7
Probab=36.76  E-value=19  Score=15.15  Aligned_cols=46  Identities=15%  Similarity=0.296  Sum_probs=38.2

Q ss_pred             CCCCCCCHHHHHHHH-HHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             543564136899999-9871787783122220010158999999998
Q gi|254780625|r  175 KIVAGIGNIYVCEAL-WRAKLSPIRKTRSLIQNNGTPKDILYKLIQE  220 (289)
Q Consensus       175 ~~iaGIGN~y~~EiL-f~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~  220 (289)
                      .-++|||-..|..|. |+..--|++...+|..-...+...++++.++
T Consensus        43 ~~lpgIg~~~A~~Iv~~R~~~G~f~sledL~~v~Gi~~k~~eki~k~   89 (98)
T 2edu_A           43 RSLQRIGPKKAQLIVGWRELHGPFSQVEDLERVEGITGKQMESFLKA   89 (98)
T ss_dssp             HHSTTCCHHHHHHHHHHHHHHCCCSSGGGGGGSTTCCHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHC
T ss_conf             64799899999999999998599288999844899899999999983


No 32 
>2elo_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=34.79  E-value=7.4  Score=17.78  Aligned_cols=11  Identities=27%  Similarity=0.920  Sum_probs=7.0

Q ss_pred             CCEEECCCCCC
Q ss_conf             12063877679
Q gi|254780625|r  279 RSTFYCTYCQK  289 (289)
Q Consensus       279 R~ty~Cp~CQk  289 (289)
                      ..+|-||.|.|
T Consensus         7 g~~yscp~cek   17 (37)
T 2elo_A            7 GRSYSCPVCEK   17 (37)
T ss_dssp             CCCCEETTTTE
T ss_pred             CCCCCCCCHHH
T ss_conf             86214861220


No 33 
>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8
Probab=32.64  E-value=13  Score=16.26  Aligned_cols=28  Identities=25%  Similarity=0.599  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             3877107877887899998781206387767
Q gi|254780625|r  258 KTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       258 r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      |....| |+||.-+-.....+|  +||-.|.
T Consensus        16 r~~k~C-P~CG~GvFmA~H~dR--~~CGKCg   43 (55)
T 2k4x_A           16 RKHRFC-PRCGPGVFLAEHADR--YSCGRCG   43 (55)
T ss_dssp             CSSCCC-TTTTTTCCCEECSSE--EECTTTC
T ss_pred             EECCCC-CCCCCCEEEEECCCC--CCCCCCC
T ss_conf             933759-899994772005897--5636755


No 34 
>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1
Probab=29.41  E-value=14  Score=15.99  Aligned_cols=14  Identities=29%  Similarity=0.743  Sum_probs=9.2

Q ss_pred             CCCCCCCCCCCCEEE
Q ss_conf             387710787788789
Q gi|254780625|r  258 KTGEPCLSNCGQMIR  272 (289)
Q Consensus       258 r~g~~C~~~CG~~I~  272 (289)
                      ..+..| |+||.++-
T Consensus        45 ~a~GkC-PvCgreLt   58 (112)
T 1l8d_A           45 KAKGKC-PVCGRELT   58 (112)
T ss_dssp             TCSEEC-TTTCCEEC
T ss_pred             HHCCCC-CCCCCCCC
T ss_conf             747879-98899376


No 35 
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Probab=28.72  E-value=25  Score=14.31  Aligned_cols=19  Identities=16%  Similarity=0.106  Sum_probs=12.9

Q ss_pred             CCCCCCCCCCCEEEEEEECC
Q ss_conf             87710787788789999878
Q gi|254780625|r  259 TGEPCLSNCGQMIRRIVQAG  278 (289)
Q Consensus       259 ~g~~C~~~CG~~I~~~~~~g  278 (289)
                      .+.+| |.||..+.+.+-..
T Consensus       615 ~~~~c-p~cg~~~~~~~~~~  633 (659)
T 1i7d_A          615 RGIVA-PGSGGSADKKKAAP  633 (659)
T ss_dssp             TTCCC-C-------------
T ss_pred             CCCCC-CCCCCCCCCCCCCC
T ss_conf             58889-65689765457888


No 36 
>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Probab=28.31  E-value=11  Score=16.67  Aligned_cols=26  Identities=27%  Similarity=0.515  Sum_probs=11.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             710787788789999878120638776
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      ..| ..|+.+|.-..+......|.|.|
T Consensus        16 ~~C-~~C~~~I~~~~v~a~~~~~H~~C   41 (81)
T 1v6g_A           16 TRC-FSCDQFIEGEVVSALGKTYHPDC   41 (81)
T ss_dssp             CBC-TTTCCBCCSCCEEETTEEECTTT
T ss_pred             CCC-HHCCCCCCCEEEEECCEEECCCC
T ss_conf             525-30499812418998991885558


No 37 
>2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum}
Probab=28.30  E-value=26  Score=14.26  Aligned_cols=58  Identities=19%  Similarity=0.346  Sum_probs=36.3

Q ss_pred             HHHCCCCCCCEEEECCCCCCCCCHHH-------------------HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             42014542100111265435641368-------------------99999987178778312222001015899999999
Q gi|254780625|r  159 QFHKKNSNLKNALLNQKIVAGIGNIY-------------------VCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQ  219 (289)
Q Consensus       159 ~l~~~~~~Ik~~LlDQ~~iaGIGN~y-------------------~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~  219 (289)
                      .+..++++|++.|=-..+..-+++.|                   ..++|=.++|.+ +.+.+||.+|      +.+|++
T Consensus       215 ~F~~RRK~l~n~Lkk~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~i~~-~R~e~Ls~ed------f~~L~~  287 (299)
T 2h1r_A          215 CFSRKRKTLHAIFKRNAVLNMLEHNYKNWCTLNKQVPVNFPFKKYCLDVLEHLDMCE-KRSINLDEND------FLKLLL  287 (299)
T ss_dssp             HHTTTTSBHHHHHTSHHHHHHHHHHHHHHHHHTTCCCCSSCHHHHHHHHHHHTTCTT-CBGGGCCHHH------HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCC-CCCHHCCHHH------HHHHHH
T ss_conf             974414488988634003566677677775312014555335789999998569754-7803399999------999999


Q ss_pred             HHHH
Q ss_conf             8788
Q gi|254780625|r  220 EIQK  223 (289)
Q Consensus       220 ~i~~  223 (289)
                      +..+
T Consensus       288 ~~~~  291 (299)
T 2h1r_A          288 EFNK  291 (299)
T ss_dssp             HHHH
T ss_pred             HHHH
T ss_conf             9997


No 38 
>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Probab=27.15  E-value=13  Score=16.12  Aligned_cols=25  Identities=12%  Similarity=0.458  Sum_probs=12.9

Q ss_pred             CCCCCCCCCCEEE--EEEECCCCEEECCCC
Q ss_conf             7710787788789--999878120638776
Q gi|254780625|r  260 GEPCLSNCGQMIR--RIVQAGRSTFYCTYC  287 (289)
Q Consensus       260 g~~C~~~CG~~I~--~~~~~gR~ty~Cp~C  287 (289)
                      +..| ..|+.+|.  .+...|+  .|.|.|
T Consensus        15 ~~~C-~~C~~~I~~~~v~~~~~--~~H~~C   41 (80)
T 1x3h_A           15 SPKC-GGCNRPVLENYLSAMDT--VWHPEC   41 (80)
T ss_dssp             SCBC-TTTCCBCCSSCEEETTE--EECTTT
T ss_pred             CCCH-HHCCCEECCEEEEECCC--EECCCC
T ss_conf             9100-42599502809999992--367589


No 39 
>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}
Probab=27.08  E-value=18  Score=15.21  Aligned_cols=23  Identities=17%  Similarity=0.635  Sum_probs=10.4

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf             107877887899998781206387767
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .| +.||....   +.....+.||.|+
T Consensus        75 ~C-~~Cg~~~~---~~~~~~~~CP~Cg   97 (119)
T 2kdx_A           75 EC-KDCSHVFK---PNALDYGVCEKCH   97 (119)
T ss_dssp             EC-SSSSCEEC---SCCSTTCCCSSSS
T ss_pred             EC-CCCCCEEC---CCCCCCCCCCCCC
T ss_conf             98-78998833---4775477290978


No 40 
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2
Probab=25.16  E-value=29  Score=13.90  Aligned_cols=23  Identities=13%  Similarity=0.149  Sum_probs=16.4

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             1078778878999987812063877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .| +.|+..+..   . ....+||.|-+
T Consensus       171 ~c-~~c~~~l~~---~-~~~m~C~~cg~  193 (209)
T 2nn6_I          171 HS-ESGIQMVPI---S-WCEMQCPKTHT  193 (209)
T ss_dssp             BC-SSSCBCEEE---E-TTEEECTTTTC
T ss_pred             EC-CCCCCCEEE---C-CCEEECCCCCC
T ss_conf             88-899851776---6-99889999999


No 41 
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans}
Probab=24.59  E-value=30  Score=13.83  Aligned_cols=29  Identities=10%  Similarity=-0.104  Sum_probs=23.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCC-CCCCCC
Q ss_conf             43564136899999987178778-312222
Q gi|254780625|r  176 IVAGIGNIYVCEALWRAKLSPIR-KTRSLI  204 (289)
Q Consensus       176 ~iaGIGN~y~~EiLf~a~I~P~~-~~~~Ls  204 (289)
                      -|.|||.|-++-+|-.+-=+|.. ++++|.
T Consensus       142 ~ikGIGpWTA~~illf~lgr~DvfP~~Dl~  171 (233)
T 2h56_A          142 AIKGIGQWTAEMFMMFSLGRLDVLSVGDVG  171 (233)
T ss_dssp             TSTTCCHHHHHHHHHHTTCCSCCCCTTCHH
T ss_pred             HCCCCCHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             068848789999999968999789863799


No 42 
>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold, coiled coil, riken structural genomics/proteomics initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus} SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A* 1iyw_A
Probab=23.75  E-value=25  Score=14.39  Aligned_cols=26  Identities=15%  Similarity=0.123  Sum_probs=11.3

Q ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             5421001112654356413689999998
Q gi|254780625|r  164 NSNLKNALLNQKIVAGIGNIYVCEALWR  191 (289)
Q Consensus       164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~  191 (289)
                      +.++-..+.+|-++. ++. ++++.+-.
T Consensus       348 ~~~~~~~~~~qwf~~-~~~-~~~~~~~~  373 (862)
T 1gax_A          348 GTPIEYAIFPQWWLR-MRP-LAEEVLKG  373 (862)
T ss_dssp             CSBCCEEECCEEEEC-HHH-HHHHHHHH
T ss_pred             CCCEEEEECHHHHHH-HHH-HHHHHHHH
T ss_conf             981255303356765-335-66643345


No 43 
>2riq_A Poly [ADP-ribose] polymerase 1; Zn-binding domain, Zn ribbon, Zn finger, ADP-ribosylation, DNA damage, DNA repair, DNA-binding, glycosyltransferase; 1.70A {Homo sapiens} PDB: 2jvn_A
Probab=23.59  E-value=28  Score=14.09  Aligned_cols=28  Identities=29%  Similarity=0.670  Sum_probs=17.8

Q ss_pred             EEEECCCCCCCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf             1665738771078778878999987812063877
Q gi|254780625|r  253 FSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTY  286 (289)
Q Consensus       253 ~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~  286 (289)
                      ..+||.- .+| |.|++.+.   +.+ ..|+|..
T Consensus        72 gm~FGaL-~~C-P~C~g~l~---~~~-~~Y~C~G   99 (160)
T 2riq_A           72 GMVFGAL-LPC-EECSGQLV---FKS-DAYYCTG   99 (160)
T ss_dssp             HHHHCEE-CCC-TTTCCCEE---EET-TEEEECC
T ss_pred             HHHHCCC-CCC-CCCCCEEE---EEC-CCEEECC
T ss_conf             9971788-899-98899788---708-8258678


No 44 
>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1
Probab=23.59  E-value=9.7  Score=17.01  Aligned_cols=22  Identities=23%  Similarity=0.623  Sum_probs=15.5

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEEEC
Q ss_conf             7710787788789999878120638
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTFYC  284 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty~C  284 (289)
                      -++| |.|+.+|++.  +|-.-..|
T Consensus         6 tK~C-P~C~~~IeK~--~GCnhm~C   27 (60)
T 1wd2_A            6 TKEC-PKCHVTIEKD--GGCNHMVC   27 (60)
T ss_dssp             CCCC-TTTCCCCSSC--CSCCSSSC
T ss_pred             CCCC-CCCCCEEEEC--CCCCCEEE
T ss_conf             8599-6999988868--89886597


No 45 
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y*
Probab=23.27  E-value=32  Score=13.67  Aligned_cols=27  Identities=30%  Similarity=0.844  Sum_probs=18.2

Q ss_pred             CCCCCCCCCCCE-EEEEEECCCCEEECCCCCC
Q ss_conf             877107877887-8999987812063877679
Q gi|254780625|r  259 TGEPCLSNCGQM-IRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       259 ~g~~C~~~CG~~-I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .--.| |.||.. +.+..+|   +|-|..|=+
T Consensus        59 aky~C-pfCgk~~vkR~a~G---IW~C~kCg~   86 (116)
T 3cc2_Z           59 EDHAC-PNCGEDRVDRQGTG---IWQCSYCDY   86 (116)
T ss_dssp             SCEEC-SSSCCEEEEEEETT---EEEETTTCC
T ss_pred             CCCCC-CCCCCCCEEEEEEE---EEECCCCCC
T ss_conf             79609-88899803889989---987489898


No 46 
>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2
Probab=22.97  E-value=19  Score=15.18  Aligned_cols=10  Identities=20%  Similarity=1.072  Sum_probs=8.2

Q ss_pred             CEEECCCCCC
Q ss_conf             2063877679
Q gi|254780625|r  280 STFYCTYCQK  289 (289)
Q Consensus       280 ~ty~Cp~CQk  289 (289)
                      ..||||.|++
T Consensus        75 ~~w~C~~C~~   84 (91)
T 1weu_A           75 GKWFCPRCSQ   84 (91)
T ss_dssp             SSCCCTTTCC
T ss_pred             CCEECCCCCC
T ss_conf             8689957918


No 47 
>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Probab=22.62  E-value=17  Score=15.49  Aligned_cols=25  Identities=16%  Similarity=0.381  Sum_probs=9.3

Q ss_pred             CCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf             10787788789999878120638776
Q gi|254780625|r  262 PCLSNCGQMIRRIVQAGRSTFYCTYC  287 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~~gR~ty~Cp~C  287 (289)
                      .| ..|+.+|.-..+-...-.|.|.|
T Consensus        17 ~C-~~C~~~I~~~~i~~~~~~~H~~C   41 (81)
T 1x6a_A           17 FC-HGCSLLMTGPFMVAGEFKYHPEC   41 (81)
T ss_dssp             BC-TTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             CC-CCCCCCCCCEEEEECCCEECCCC
T ss_conf             25-20699922407998982867899


No 48 
>2e1m_A L-glutamate oxidase; L-amino acid oxidase, FAD, L-GOX, flavoprotein, 3D-structure, oxidoreductase; HET: FAD; 2.80A {Streptomyces SP}
Probab=22.58  E-value=33  Score=13.58  Aligned_cols=13  Identities=23%  Similarity=0.176  Sum_probs=9.0

Q ss_pred             CCCCEEEEEEECC
Q ss_conf             7788789999878
Q gi|254780625|r  266 NCGQMIRRIVQAG  278 (289)
Q Consensus       266 ~CG~~I~~~~~~g  278 (289)
                      +++++|.++...+
T Consensus       335 ~~n~~V~~I~~~~  347 (376)
T 2e1m_A          335 VMGQRMVRLEYYD  347 (376)
T ss_dssp             ECSEEEEEEEECC
T ss_pred             EECCEEEEEEEEC
T ss_conf             9389835999989


No 49 
>1s1i_9 L37A, YL35, 60S ribosomal protein L43; 80S ribosome, 60S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1
Probab=22.34  E-value=11  Score=16.66  Aligned_cols=26  Identities=27%  Similarity=0.737  Sum_probs=14.6

Q ss_pred             CCCCCCCCCCCE-EEEEEECCCCEEECCCCC
Q ss_conf             877107877887-899998781206387767
Q gi|254780625|r  259 TGEPCLSNCGQM-IRRIVQAGRSTFYCTYCQ  288 (289)
Q Consensus       259 ~g~~C~~~CG~~-I~~~~~~gR~ty~Cp~CQ  288 (289)
                      .--.| |.||.. +.+..   -.+|-|-.|-
T Consensus        34 aky~C-p~Cgk~~vkR~a---~GIW~C~kC~   60 (91)
T 1s1i_9           34 ARYDC-SFCGKKTVKRGA---AGIWTCSCCK   60 (91)
T ss_dssp             SCCCC-TTTCSSCCCEET---TTEECCSSSC
T ss_pred             CCCCC-CCCCCCEEEEEE---EEEEECCCCC
T ss_conf             88239-899997348998---8886879999


No 50 
>1odh_A MGCM1; transcription factor/DNA, transcription factor, DNA-binding domain, protein/DNA complex; 2.85A {Mus musculus} SCOP: d.239.1.1
Probab=22.23  E-value=26  Score=14.20  Aligned_cols=22  Identities=27%  Similarity=0.619  Sum_probs=9.7

Q ss_pred             CCCCCCCCCCEEEEEEECCCCEE
Q ss_conf             77107877887899998781206
Q gi|254780625|r  260 GEPCLSNCGQMIRRIVQAGRSTF  282 (289)
Q Consensus       260 g~~C~~~CG~~I~~~~~~gR~ty  282 (289)
                      |++| |.|++.++-..-.|.+-|
T Consensus       110 ~k~C-pnC~g~L~~~~Crgh~gy  131 (174)
T 1odh_A          110 RKSC-PNCNGPLKLIPCRGHGGF  131 (174)
T ss_dssp             HSBC-SSSCCBEEEECCCTBTTB
T ss_pred             CCCC-CCCCCCEEEEECCCCCCC
T ss_conf             5889-899981577762576787


No 51 
>1mek_A Protein disulfide isomerase; electron transport, redox-active center, endoplasmic reticulum; NMR {Homo sapiens} SCOP: c.47.1.2
Probab=21.89  E-value=20  Score=14.93  Aligned_cols=11  Identities=45%  Similarity=0.721  Sum_probs=5.5

Q ss_pred             CEEEEEEECCC
Q ss_conf             30899950355
Q gi|254780625|r   57 AKYLLIELEGN   67 (289)
Q Consensus        57 GK~l~l~l~~~   67 (289)
                      +|.+++.|-.+
T Consensus        24 ~k~vlV~F~a~   34 (120)
T 1mek_A           24 HKYLLVEFYAP   34 (120)
T ss_dssp             CSEEEEEEECS
T ss_pred             CCCEEEEEECC
T ss_conf             99799999899


No 52 
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=20.82  E-value=36  Score=13.36  Aligned_cols=26  Identities=12%  Similarity=0.215  Sum_probs=16.7

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             71078778878999987812063877679
Q gi|254780625|r  261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ..| |.|++++...  .+....+|+.|+.
T Consensus        11 L~C-P~ck~~L~~~--~~~~~L~c~~~~l   36 (56)
T 2kpi_A           11 LAC-PACHAPLEER--DAELICTGQDCGL   36 (56)
T ss_dssp             CCC-SSSCSCEEEE--TTEEEECSSSCCC
T ss_pred             HCC-CCCCCCCEEC--CCCCEEECCCCCE
T ss_conf             338-8999945182--8768897388883


No 53 
>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B
Probab=20.44  E-value=33  Score=13.59  Aligned_cols=26  Identities=19%  Similarity=0.611  Sum_probs=13.4

Q ss_pred             CCCCCCCCCCCEEE---E-EEECCCCEEECCCC
Q ss_conf             87710787788789---9-99878120638776
Q gi|254780625|r  259 TGEPCLSNCGQMIR---R-IVQAGRSTFYCTYC  287 (289)
Q Consensus       259 ~g~~C~~~CG~~I~---~-~~~~gR~ty~Cp~C  287 (289)
                      .+..| ..|+.+|.   + +...|  .+|.|.|
T Consensus        10 ~~~~C-~~C~~~I~~~~~~v~~~~--~~~H~~C   39 (72)
T 3f6q_B           10 ASATC-ERCKGGFAPAEKIVNSNG--ELYHEQC   39 (72)
T ss_dssp             TTCBC-TTTCCBCCTTCEEEEETT--EEEETTT
T ss_pred             CCCCC-CCCCCEECCCCEEEEECC--CEECCCC
T ss_conf             89738-224999258928999798--5688699


No 54 
>1d0q_A DNA primase; zinc-binding motif, protein, transferase; HET: DNA; 1.71A {Geobacillus stearothermophilus} SCOP: g.41.3.2
Probab=20.37  E-value=27  Score=14.15  Aligned_cols=27  Identities=19%  Similarity=0.383  Sum_probs=16.1

Q ss_pred             CCCCCCCCEEEEEEE-CCCCEEECCCCCC
Q ss_conf             107877887899998-7812063877679
Q gi|254780625|r  262 PCLSNCGQMIRRIVQ-AGRSTFYCTYCQK  289 (289)
Q Consensus       262 ~C~~~CG~~I~~~~~-~gR~ty~Cp~CQk  289 (289)
                      +| |-|+..--...+ ....+|+|-.|++
T Consensus        39 ~C-Pfh~d~~~S~~v~~~~~~~~Cf~Cg~   66 (103)
T 1d0q_A           39 LC-PFHGEKTPSFSVSPEKQIFHCFGCGA   66 (103)
T ss_dssp             CC-SSSCCSSCCEEEETTTTEEEETTTCC
T ss_pred             EC-CCCCCCCCCEEEECCCCEEEECCCCC
T ss_conf             89-88899999879973887799888799


Done!