Query         gi|254780454|ref|YP_003064867.1| DNA polymerase III subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 385
No_of_seqs    121 out of 2231
Neff          8.0 
Searched_HMMs 23785
Date          Mon May 30 11:42:48 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780454.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3d1g_A DNA polymerase III subu 100.0       0       0  607.5  39.6  365    1-385     1-366 (366)
  2 1vpk_A DNA polymerase III, bet 100.0       0       0  588.7  39.2  363    1-385    13-377 (378)
  3 2avt_A DNA polymerase III beta 100.0       0       0  578.2  41.2  367    1-385     2-377 (378)
  4 3k4x_A PCNA, proliferating cel  99.6 3.2E-10 1.4E-14   79.7  34.0  113  236-360   386-511 (798)
  5 3d1g_A DNA polymerase III subu  99.6   4E-12 1.7E-16   91.2  22.9  201  130-338     3-209 (366)
  6 1rwz_A DNA polymerase sliding   99.6 2.3E-12 9.8E-17   92.7  20.5  224  130-382     4-240 (245)
  7 3k4x_A PCNA, proliferating cel  99.5 1.3E-09 5.3E-14   76.1  34.3  188  174-382   578-792 (798)
  8 1vpk_A DNA polymerase III, bet  99.5 4.1E-12 1.7E-16   91.2  20.3  213  128-352    13-231 (378)
  9 2avt_A DNA polymerase III beta  99.4 8.3E-11 3.5E-15   83.3  20.8  213    2-225   134-352 (378)
 10 3ifv_A PCNA; processivity fact  99.0 1.9E-08 8.1E-13   68.9  15.7  225  131-382     5-242 (247)
 11 3fds_C DNA polymerase sliding   99.0 5.2E-07 2.2E-11   60.2  21.8  221  133-382     8-247 (249)
 12 1plq_A Proliferating cell nucl  99.0 3.1E-07 1.3E-11   61.6  20.6  218  133-382     8-252 (258)
 13 2ijx_A DNA polymerase sliding   99.0 4.3E-07 1.8E-11   60.7  20.8  219  133-382     7-242 (244)
 14 3fds_D DNA polymerase sliding   98.9 5.6E-07 2.4E-11   60.0  19.4  220  132-382     7-243 (245)
 15 1u7b_A PCNA, cyclin, prolifera  98.9 8.7E-07 3.7E-11   58.9  19.7  220  132-382     7-253 (261)
 16 1iz5_A Proliferating cell nucl  98.9 1.4E-06 6.1E-11   57.5  19.6  219  133-382     9-245 (249)
 17 1rwz_A DNA polymerase sliding   98.8 1.7E-06 7.3E-11   57.0  19.2  205    2-231     3-224 (245)
 18 2zvv_A PCNA 1, proliferating c  98.8 5.2E-06 2.2E-10   54.2  20.3  220  132-382    27-273 (276)
 19 3fds_C DNA polymerase sliding   98.6 1.7E-05 7.2E-10   51.0  19.0  208    1-227     2-227 (249)
 20 1ud9_A DNA polymerase sliding   98.6 3.4E-05 1.4E-09   49.2  21.0  217  133-382     7-242 (245)
 21 1plq_A Proliferating cell nucl  98.5 1.6E-05 6.6E-10   51.2  16.7  210    1-232     2-239 (258)
 22 3g65_A Cell cycle checkpoint c  98.5 2.9E-05 1.2E-09   49.6  16.8  130  237-383   122-265 (296)
 23 2ijx_A DNA polymerase sliding   98.4 6.9E-05 2.9E-09   47.3  18.2  204    1-227     1-222 (244)
 24 3a1j_A Cell cycle checkpoint c  98.4 1.6E-05 6.6E-10   51.2  14.9  209  156-383    23-265 (266)
 25 3ifv_A PCNA; processivity fact  98.4 3.2E-05 1.3E-09   49.4  15.9  203    1-227     2-221 (247)
 26 1iz5_A Proliferating cell nucl  98.3 0.00014 5.9E-09   45.5  18.7  204    1-227     1-225 (249)
 27 2zvv_A PCNA 1, proliferating c  98.3 6.7E-05 2.8E-09   47.4  15.6  206    1-227    22-253 (276)
 28 1u7b_A PCNA, cyclin, prolifera  98.3 0.00012 5.2E-09   45.8  16.0  201    5-227     7-233 (261)
 29 3fds_D DNA polymerase sliding   98.2 0.00025 1.1E-08   43.9  16.9  203    1-227     2-223 (245)
 30 1ud9_A DNA polymerase sliding   97.9  0.0009 3.8E-08   40.6  17.2  200    6-227     7-222 (245)
 31 3a1j_A Cell cycle checkpoint c  97.8 0.00074 3.1E-08   41.1  13.3  135    1-145     1-160 (266)
 32 3a1j_C Cell cycle checkpoint p  97.7  0.0025 1.1E-07   37.9  20.9   99  253-361   135-243 (263)
 33 3g65_A Cell cycle checkpoint c  97.5  0.0048   2E-07   36.1  17.7  134    1-144     1-159 (296)
 34 3a1j_C Cell cycle checkpoint p  96.0   0.071   3E-06   29.1  15.9  184   31-227    26-237 (263)
 35 1b77_A GP45, protein (sliding   60.8     6.9 0.00029   17.0  14.6  202    1-239     1-218 (228)
 36 2p0g_A Selenoprotein W-related  56.4       3 0.00013   19.2   1.0   56  197-252    15-72  (105)
 37 2ojl_A Hypothetical protein; B  56.3     2.8 0.00012   19.4   0.8   50  204-253    28-78  (108)
 38 2oka_A Hypothetical protein; P  46.0     6.3 0.00026   17.2   1.3   57  197-253    17-75  (104)
 39 2npb_A Selenoprotein W; struct  43.5      11 0.00046   15.8   2.2   49  205-253    23-73  (96)
 40 2fa8_A Hypothetical protein AT  40.8     6.8 0.00029   17.0   0.8   48  204-251    27-75  (105)
 41 3a8g_A NitrIle hydratase subun  22.3      30  0.0013   13.1   1.6   13  263-275   182-194 (207)
 42 3dex_A SAV_2001; alpha-beta pr  22.0      22 0.00092   13.9   0.8   57  196-253    23-81  (107)
 43 2zzd_C Thiocyanate hydrolase s  21.4      32  0.0013   13.0   1.6   27  252-278   189-215 (243)

No 1  
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A*
Probab=100.00  E-value=0  Score=607.53  Aligned_cols=365  Identities=35%  Similarity=0.624  Sum_probs=345.3

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEEEEEEEEE-EEECCCCEEEEEHHHHHHHHH
Q ss_conf             9589859999999998750203788861013389999899799999678289999997-775268079994998778874
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-ASVDVCGSITVSAHLLYDIVR   79 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~~i~~~i~-~~i~~~G~~~v~a~~l~~iik   79 (385)
                      |||+|+|++|.++|+++++++++|++.|||+|++|++++++|+++|||++++++++++ +++.++|+++|||+.|.+++|
T Consensus         1 Mk~~i~k~~L~~~l~~v~~~i~~k~~~piL~~ili~a~~~~l~l~atd~e~~i~~~i~~~~v~~~G~~~v~ak~l~~ivr   80 (366)
T 3d1g_A            1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICR   80 (366)
T ss_dssp             CEEEEEHHHHHHHHHHHSTTCSSCCCSGGGGEEEEEEETTEEEEEEECSSEEEEEEEECCSCCBCEEEEEEHHHHHHHHH
T ss_pred             CEEEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECCEEEEEEECCCEEEEEEEECCEECCCCEEEEECHHHHHHHH
T ss_conf             98999899999999999756188987388747899998999999998887399999904152357469992356777874


Q ss_pred             CCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCCCEEE
Q ss_conf             07777730477733675089998678202430366211432123324304505611355420220230024556521011
Q gi|254780454|r   80 KLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNG  159 (385)
Q Consensus        80 ~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~~L~G  159 (385)
                      +||++..+.+..+   ++++.|++|+++|+|+++++++||.+|..+....+.++++.|+++|++|.||+|+|++||+|+|
T Consensus        81 ~l~~~~~i~~~~~---~~~l~I~~~~~~f~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~v~~a~s~d~~r~~L~G  157 (366)
T 3d1g_A           81 GLPEGAEIAVQLE---GERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNG  157 (366)
T ss_dssp             HSCTTCEEEEEEE---TTEEEEEETTEEEEEECBCGGGSCCCCCCCCSEEEEECHHHHHHHHHHHGGGSCSSCSSGGGSE
T ss_pred             CCCCCCEEEEEEC---CCEEEEEECCEEEEEECCCHHHCCCCCCCCCCCEEEECHHHHHHHHHHEEEECCCCCCCEEEEE
T ss_conf             4799974999961---8889999898899960688110876111366614887699999866547731256567432555


Q ss_pred             EEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEECCEEEEEE
Q ss_conf             66776178734899985341576666435787533100000100012222102776464331334553010025069998
Q gi|254780454|r  160 IFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV  239 (385)
Q Consensus       160 v~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~~i~~~~~~~~~~s  239 (385)
                      |||+++++  ++++|||||||||.++.+++... ...+++||+|.+.++.+++.+.+++++++++++++.|.+++.+++|
T Consensus       158 v~~~~~~~--~l~~vaTDg~RLa~~~~~~~~~~-~~~~~iip~k~l~~~~~~~~~~~~~v~i~~~~~~i~f~~~~~~~~s  234 (366)
T 3d1g_A          158 MLFETEGE--ELRTVATDGHRLAVCSMPIGQSL-PSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS  234 (366)
T ss_dssp             EEEEEEEE--EEEEEEECSSEEEEEEEEEEEEE-EEEEEEEEHHHHHHHHHTCCSSSCCEEEEECSSEEEEEETTEEEEE
T ss_pred             EEEEECCC--EEEEEECCCCEEEEEEECCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCEEEEEECCEEEEE
T ss_conf             99996499--99999906843899983046777-6323101523699987664045514787427855999989999999


Q ss_pred             EECCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEEECCCC
Q ss_conf             51266553221013555661799848998888988741012355530256517659999807873268999998962884
Q gi|254780454|r  240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECP  319 (385)
Q Consensus       240 rLi~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~~  319 (385)
                      |||+|+||||+++||+.++.+++++|++|+++++|++++++++++.|.+.++++.+++++.++|.|+++|+++++|+|++
T Consensus       235 rlieg~yP~y~~vip~~~~~~~~v~~~~l~~al~r~~~~~~~~~~~v~l~~~~~~l~l~~~~~d~g~~~e~i~~~~~G~~  314 (366)
T 3d1g_A          235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAE  314 (366)
T ss_dssp             ECCSSCCCCHHHHSCSCCCEEEEEEHHHHHHHHHHHHHTSCTTTCEEEEEEETTEEEEEEECTTCCEEEEEEECBCCSCC
T ss_pred             EEECCCCCCCCEECCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCCEEEEECCCEEEEEECCCCCCEEEEEEEEEECCCC
T ss_conf             95056776410305787762257503565666654301014677723799629959999727876515699976852897


Q ss_pred             EEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             399963889988987357533466338999658987589943776544455566763799832129
Q gi|254780454|r  320 MDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI  385 (385)
Q Consensus       320 ~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMPvri  385 (385)
                      ++|+||++||+|+|+++++     ++|.|++.++.+|++|++.++         ++|+||||||||
T Consensus       315 ~~i~fN~~yL~d~L~~~~~-----~~V~i~~~~~~~p~~i~~~~~---------~~~~~liMPvrl  366 (366)
T 3d1g_A          315 MEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQIEDAAS---------QSAAYVVMPMRL  366 (366)
T ss_dssp             EEEEEEHHHHHHHHHHCCS-----SEEEEEECCTTSCEEEEETTE---------EEEEEEECCBCC
T ss_pred             EEEEECHHHHHHHHHCCCC-----CEEEEEECCCCCCEEEECCCC---------CCEEEEEEEEEC
T ss_conf             7999889999999854899-----879999838998589977999---------854899952109


No 2  
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1
Probab=100.00  E-value=0  Score=588.70  Aligned_cols=363  Identities=26%  Similarity=0.485  Sum_probs=340.1

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEEEEEEEEE-EEECCCCEEEEEHHHHHHHHH
Q ss_conf             9589859999999998750203788861013389999899799999678289999997-775268079994998778874
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-ASVDVCGSITVSAHLLYDIVR   79 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~~i~~~i~-~~i~~~G~~~v~a~~l~~iik   79 (385)
                      |||+|++++|.++|+++++++++|++.|||+|+||++++++|+++|||++++++++++ ++++++|+++|||+.|.+++|
T Consensus        13 Mk~~i~k~~L~~~l~~~~~~i~~~~~~piL~~ilie~~~~~l~l~atd~e~~i~~~i~~~~i~~~G~~~vpak~l~~ivk   92 (378)
T 1vpk_A           13 MKVTVTTLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAAEISGEARFVVPGDVIQKMVK   92 (378)
T ss_dssp             EEEEEEHHHHHHHHHHHGGGCCCSSSCGGGGEEEEEEETTEEEEEEECSSEEEEEECCCSEEEECEEEEEEC-CHHHHHT
T ss_pred             EEEEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECCEEEEEEECCCEEEEEEEECCEECCCEEEEEEHHHHHHHHH
T ss_conf             79999899999999998755277987488759899998999999998884599999963166155689986799999986


Q ss_pred             CCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCCCEEE
Q ss_conf             07777730477733675089998678202430366211432123324304505611355420220230024556521011
Q gi|254780454|r   80 KLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNG  159 (385)
Q Consensus        80 ~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~~L~G  159 (385)
                      +||++. +.+..+   ++++.|++|+++|+|+++++++||.+|..+...+++++++.|+++|++|.||+++|++||+|+|
T Consensus        93 ~l~~~~-i~l~~~---~~~l~I~~g~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~v~~a~s~d~~r~~L~G  168 (378)
T 1vpk_A           93 VLPDEI-TELSLE---GDALVISSGSTVFRITTMPADEFPEITPAESGITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNG  168 (378)
T ss_dssp             TCCSSE-EEEEEE---TTEEEEEETTEEEEEECBCCTTSCCCCCCCSSEEEEEEHHHHHHHHHHHGGGSCCCTTCTTTSE
T ss_pred             HCCCCE-EEEEEE---CCEEEEECCCEEEEEECCCHHHCCCCCCCCCCCEEECCHHHHHHHHHHHHHHHCCCCCHHHEEE
T ss_conf             278752-699940---8899995375089996148233343223467715860899999999767875174001224422


Q ss_pred             EEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCC-CCCCCCCCCCCCEEEECCEEEEE
Q ss_conf             66776178734899985341576666435787533100000100012222102776-46433133455301002506999
Q gi|254780454|r  160 IFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSK-DSSVKVSLSESRIHLNIESLSMS  238 (385)
Q Consensus       160 v~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~-~~~v~i~~~~~~i~~~~~~~~~~  238 (385)
                      |+|+++++  ++++|||||||||+++.+.+..  ...++++|+|.+.++.|++.+. ++.+.++.+++++.|.+++++++
T Consensus       169 v~~~~~~~--~l~~vATDg~RLa~~~~~~~~~--~~~~~iip~k~l~~l~k~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (378)
T 1vpk_A          169 VFWELHKN--LLRLVASDGFRLALAEEQIENE--EEASFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETV  244 (378)
T ss_dssp             EEEEEETT--EEEEEEECSSEEEEEEEECCCC--SCEEEEEEHHHHHHHHHHHHTCCCSEEEEEECSSEEEEECSSEEEE
T ss_pred             EEEEECCC--EEEEEECCCCCEEEEECCCCCC--CCCCEEEEHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCEEEE
T ss_conf             89997187--6999983797168875035776--6530475088999998621245673499963011027862555999


Q ss_pred             EEECCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEEECCC
Q ss_conf             85126655322101355566179984899888898874101235553025651765999980787326899999896288
Q gi|254780454|r  239 VRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNEC  318 (385)
Q Consensus       239 srLi~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~  318 (385)
                      ||||+|+||||+++||+++++++.++|.+|+++++|++++++++.+.+.|.++++.+++++.++|.|++.|+++|+|+|+
T Consensus       245 srli~g~yP~y~~vip~~~~~~~~i~r~~l~~al~r~~~~~~~~~~~v~l~~~~~~l~l~~~~~e~g~~~e~i~~~~~Ge  324 (378)
T 1vpk_A          245 MRVVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPDYGEVVDEVEVQKEGE  324 (378)
T ss_dssp             EECCSSCCCCGGGGSCSCCSEEEEEEHHHHHHHHHHHHHHHTTTTCCEEEEECSSEEEEEEEETTTEEEEEEEECEEEEC
T ss_pred             EEECCCCCCCHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHCCCCCCCEEEEECCCEEEEEECCCCCCEEEEEEEEEECCC
T ss_conf             98527776577571566663389983166787898764410357662589704881799975897621799998785288


Q ss_pred             CEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             4399963889988987357533466338999658987589943776544455566763799832129
Q gi|254780454|r  319 PMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI  385 (385)
Q Consensus       319 ~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMPvri  385 (385)
                      +++|+||++||+|+|+++++     ++|.|+++++.+|++|++.++         ++|+||||||||
T Consensus       325 ~~~i~fN~~yL~d~L~~~~~-----e~V~i~~~~~~~p~~i~~~~~---------~~~~~lvMPvRi  377 (378)
T 1vpk_A          325 DLVIAFNPKFIEDVLKHIET-----EEIEMNFVDSTSPCQINPLDI---------SGYLYIVMPIRL  377 (378)
T ss_dssp             CEEEEECHHHHHHHHHHCCS-----SEEEEEESCTTSCEEEEETTC---------CSEEEEECCBCC
T ss_pred             CEEEEECHHHHHHHHHCCCC-----CEEEEEECCCCCCEEEECCCC---------CCEEEEEEEEEC
T ss_conf             78999989999999860899-----879999858998689974888---------952899983771


No 3  
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*
Probab=100.00  E-value=0  Score=578.22  Aligned_cols=367  Identities=23%  Similarity=0.402  Sum_probs=338.5

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEEEEEEEEEEE-------ECCCCEEEEEHHH
Q ss_conf             958985999999999875020378886101338999989979999967828999999777-------5268079994998
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS-------VDVCGSITVSAHL   73 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~~i~~~i~~~-------i~~~G~~~v~a~~   73 (385)
                      |||+|+|++|.++|+++++++++|++.|||+|+||++.+++|+++|||++++++++++++       +.++|+++|||+.
T Consensus         2 Mkf~i~k~~l~~~l~~~~~~i~~k~~~piL~~ilie~~~~~l~l~atd~~~~i~~~i~~~~~~~~~~v~~~G~~~v~~k~   81 (378)
T 2avt_A            2 IQFSINRTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPVSNENAGLLITSPGAILLEASF   81 (378)
T ss_dssp             CEEEEEHHHHHHHHHHHGGGCCSSCSSGGGGEEEEEEETTEEEEEEECSSEEEEEEEEC-----CEEEEECEEEEEEHHH
T ss_pred             EEEEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECCEEEEEEECCCEEEEEEEEEEECCCCCEEEECEEEEHHHHH
T ss_conf             79999799999999999746178987278728899999999999998574699999981230568358404244024899


Q ss_pred             HHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCEEEECCCCCC
Q ss_conf             77887407777730477733675089998678202430366211432123324304505611355420220230024556
Q gi|254780454|r   74 LYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEI  153 (385)
Q Consensus        74 l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~  153 (385)
                      |.+++|+||++.. .+...+  ++.+.|++|+++|+|+++|+++||.+|..+...++.++++.|+++|++|.||+++|++
T Consensus        82 l~~iik~l~~~~i-~~~~~e--~~~l~I~~~~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~v~~a~s~d~~  158 (378)
T 2avt_A           82 FINIISSLPDISI-NVKEIE--QHQVVLTSGKSEITLKGKDVDQYPRLQEVSTENPLILKTKLLKSIIAETAFAASLQES  158 (378)
T ss_dssp             HHHHHHHCSSSEE-EEEEET--TTEEEEEETTEEEEEECBCGGGSCCCCCCCCSSCEEEEHHHHHHHHHHHGGGSCCCTT
T ss_pred             HHHHHHCCCCCEE-EEEECC--CCEEEEEECCCEEEECCCCHHCCCCCCCCCCCCEEEECHHHHHHHHHHHHEEECCCCH
T ss_conf             9999863898538-999647--9789998256358875655300886334566733898899999998542142047702


Q ss_pred             CCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             52101166776178734899985341576666435787533100000100012222102776464331334553010025
Q gi|254780454|r  154 RYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIE  233 (385)
Q Consensus       154 r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~~i~~~~~  233 (385)
                      ||+|+||+|++.++. .+.+||||||||+.++.+..... ..+.+++|++.+.++.+++.+.++++.++++++++.|.++
T Consensus       159 r~~l~Gv~~~~~~~~-~l~~vatD~~rl~~~~~~~~~~~-~~~~~iip~~~~~~~~~l~~~~~~~v~i~~~~~~~~~~~~  236 (378)
T 2avt_A          159 RPILTGVHIVLSNHK-DFKAVATDSHRMSQRLITLDNTS-ADFMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSE  236 (378)
T ss_dssp             SGGGGEEEEEEETTT-EEEEEEECSSEEEEEEEECSSCC-CCEEEEEEHHHHHHHHHHSCTTCCEEEEEECSSEEEEECS
T ss_pred             HHHHCCEEEEEECCC-CEEEEECCCCHHHEEEECCCCCC-CCCCCCCCHHHHHHHHHHHCCCCCCEEEEECCCEEEEEEC
T ss_conf             444404479992684-07999958873232550123544-3211244313699987650356553267605747999989


Q ss_pred             EEEEEEEECCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCC-CCCEEEEECCEEEEEECCCCCEEEEEEEE
Q ss_conf             06999851266553221013555661799848998888988741012355-53025651765999980787326899999
Q gi|254780454|r  234 SLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRI-QAVKLSLSSDKLCMTVDNPDMGKAIESMN  312 (385)
Q Consensus       234 ~~~~~srLi~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~~-~~i~l~~~~~~l~i~~~~~e~g~~~e~i~  312 (385)
                      +++++|||++|+||||+++||++++++++++|++|++||+|+++++++.. ..+.|+++++.+++++.++|.|++.|+++
T Consensus       237 ~~~~~srli~g~fP~y~~vip~~~~~~~~v~r~~l~~al~Rv~~~~~~~~~~~i~l~~~~~~l~l~~~~~d~g~~~e~i~  316 (378)
T 2avt_A          237 HISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQNHISAHVNSPEVGKVNEDLD  316 (378)
T ss_dssp             SEEEEEECCCSCCCCCGGGSCCCCSEEEEEEHHHHHHHHHHHHHHHTTSTTCCEEEEEETTEEEEEEEETTTEEEEEECC
T ss_pred             CEEEEEECCCCCCCCHHHCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCCEEEECCCEEEEEECCCCCCCCEEEEE
T ss_conf             88999740567999745504556872588647888999976434022224575134413746999966876565048973


Q ss_pred             -EEECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             -8962884399963889988987357533466338999658987589943776544455566763799832129
Q gi|254780454|r  313 -VYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI  385 (385)
Q Consensus       313 -~~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMPvri  385 (385)
                       +.|+|++++|+||++||+|+|+++++     ++|.|+|.++.+|++|++.+++        .+|+|||||||+
T Consensus       317 ~~~~~Ge~~~i~fN~~yL~d~L~~~~~-----~~v~i~~~~~~~p~~i~~~~~~--------~~~~~liMPvr~  377 (378)
T 2avt_A          317 IVSQSGSDLTISFNPTYLIESLKAIKS-----ETVKIHFLSPVRPFTLTPGDEE--------ESFIQLITPVRT  377 (378)
T ss_dssp             CSEEEECCEEEEECHHHHHHHHHTCCS-----SEEEEEECCTTSCEEEEETTCC--------SEEEEEECCCCC
T ss_pred             ECCCCCCCEEEEECHHHHHHHHHCCCC-----CEEEEEECCCCCCEEEEECCCC--------CCEEEEEEEEEC
T ss_conf             101358967999889999999855899-----8799997689997799807988--------746999910315


No 4  
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}
Probab=99.59  E-value=3.2e-10  Score=79.69  Aligned_cols=113  Identities=24%  Similarity=0.419  Sum_probs=49.2

Q ss_pred             EEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEE
Q ss_conf             99985126655322101355-56617998489988889887410123555302565176599998078732689999989
Q gi|254780454|r  236 SMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVY  314 (385)
Q Consensus       236 ~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~  314 (385)
                      .|.-+|++-.-....  +|+ +++..++++-.+|.+.++-+..+++    .|.+..+++.+.+++.+ +.|++.-.+...
T Consensus       386 ~f~l~lidi~~~~~~--iP~~e~~~~i~~~S~~f~~~~kdl~~~~d----~i~i~~~~~~~~~~~~g-d~~~~~~~~~~~  458 (798)
T 3k4x_A          386 EYSLKLMDIDADFLK--IEELQYDSTLSLPSSEFSKIVRDLSQLSD----SINIMITKETIKFVADG-DIGSGSVIIKPF  458 (798)
T ss_dssp             EEEEECBCCCCCCCC--CCCCCCSEEEEEEHHHHHHHHHHHHTTCS----EEEEEEETTEEEEEEEC-SSCEEEEEECCB
T ss_pred             EEEEEEECCCCCCCC--CCCCCCCEEEEEEHHHHHHHHHHHHHCCC----EEEEEEECCEEEEEEEC-CCCEEEEEEECC
T ss_conf             999963147866689--99988767999998999999999986498----79999979999999981-273799999347


Q ss_pred             ------------ECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEE
Q ss_conf             ------------6288439996388998898735753346633899965898758994
Q gi|254780454|r  315 ------------YNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIR  360 (385)
Q Consensus       315 ------------~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~  360 (385)
                                  -..++++..|..+||..+.++..-    .+.|++++... .|+.++
T Consensus       459 ~~~~~~~~~~~~~~~~~~~~~fsl~yL~~~~k~~~l----s~~V~i~~~~d-~Pl~l~  511 (798)
T 3k4x_A          459 VDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSL----SDRVGIRLSSE-APALFQ  511 (798)
T ss_dssp             CCSSSGGGCBEEEESSCEEEEEEHHHHHHHGGGGGT----CSEEEEEECSS-SCEEEE
T ss_pred             CCCCCCCCEEEEECCCCEEEEEEHHHHHHHHHHHCC----CCEEEEEECCC-CCEEEE
T ss_conf             776553310454128726899978999987505147----98799998599-778999


No 5  
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A*
Probab=99.57  E-value=4e-12  Score=91.25  Aligned_cols=201  Identities=15%  Similarity=0.213  Sum_probs=93.2

Q ss_pred             EECCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHH
Q ss_conf             50561135542022023002455652101166776178734899985341576666435787533100000100012222
Q gi|254780454|r  130 FELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEIL  209 (385)
Q Consensus       130 ~~i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~  209 (385)
                      |.++.+.|.++|..+..++++..+.|+|.||+++..++  ++++.|||+-.=...+++.. ...++..++||+|.+.++.
T Consensus         3 ~~i~k~~L~~~l~~v~~~i~~k~~~piL~~ili~a~~~--~l~l~atd~e~~i~~~i~~~-~v~~~G~~~v~ak~l~~iv   79 (366)
T 3d1g_A            3 FTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADG--TLSLTGTDLEMEMVARVALV-QPHEPGATTVPARKFFDIC   79 (366)
T ss_dssp             EEEEHHHHHHHHHHHSTTCSSCCCSGGGGEEEEEEETT--EEEEEEECSSEEEEEEEECC-SCCBCEEEEEEHHHHHHHH
T ss_pred             EEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECC--EEEEEEECCCEEEEEEEECC-EECCCCEEEEECHHHHHHH
T ss_conf             99989999999999975618898738874789999899--99999988873999999041-5235746999235677787


Q ss_pred             HHCCCCCCCCCCCCCCCCEEEECCEEEEEEEECC-CCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCC-CCC----
Q ss_conf             1027764643313345530100250699985126-6553221013555661799848998888988741012-355----
Q gi|254780454|r  210 RILSSKDSSVKVSLSESRIHLNIESLSMSVRLID-GEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSS-VRI----  283 (385)
Q Consensus       210 k~l~~~~~~v~i~~~~~~i~~~~~~~~~~srLi~-g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~-~~~----  283 (385)
                      |-++++ ..+.+...++++.++.++..|.-+.++ ..||.....   +....+.++..+|.++++++...++ +..    
T Consensus        80 r~l~~~-~~i~~~~~~~~l~I~~~~~~f~l~~~~~~~fP~~~~~---~~~~~~~i~~~~l~~~i~~v~~a~s~d~~r~~L  155 (366)
T 3d1g_A           80 RGLPEG-AEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDW---QSEVEFTLPQATMKRLIEATQFSMAHQDVRYYL  155 (366)
T ss_dssp             HHSCTT-CEEEEEEETTEEEEEETTEEEEEECBCGGGSCCCCCC---CCSEEEEECHHHHHHHHHHHGGGSCSSCSSGGG
T ss_pred             HCCCCC-CEEEEEECCCEEEEEECCEEEEEECCCHHHCCCCCCC---CCCCEEEECHHHHHHHHHHEEEECCCCCCCEEE
T ss_conf             447999-7499996188899998988999606881108761113---666148876999998665477312565674325


Q ss_pred             CCCEEEEECCEEEEEECCCCCEEEEEEEEEEECCCCEEEEECHHHHHHHHHHCCC
Q ss_conf             5302565176599998078732689999989628843999638899889873575
Q gi|254780454|r  284 QAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISS  338 (385)
Q Consensus       284 ~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~~~~i~fN~~yl~d~L~~~~~  338 (385)
                      ++|.|.++++.+++.+.+. +-=+.-.+++....++..+...++.+.+..+.+..
T Consensus       156 ~Gv~~~~~~~~l~~vaTDg-~RLa~~~~~~~~~~~~~~~iip~k~l~~~~~~~~~  209 (366)
T 3d1g_A          156 NGMLFETEGEELRTVATDG-HRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDG  209 (366)
T ss_dssp             SEEEEEEEEEEEEEEEECS-SEEEEEEEEEEEEEEEEEEEEEHHHHHHHHHTCCS
T ss_pred             EEEEEEECCCEEEEEECCC-CEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             5599996499999999068-43899983046777632310152369998766404


No 6  
>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A*
Probab=99.56  E-value=2.3e-12  Score=92.67  Aligned_cols=224  Identities=20%  Similarity=0.254  Sum_probs=165.8

Q ss_pred             EECCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCC------CCCCHHCCCCC
Q ss_conf             505611355420220230024556521011667761787348999853415766664357875------33100000100
Q gi|254780454|r  130 FELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------AKMPSIIVPRK  203 (385)
Q Consensus       130 ~~i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k  203 (385)
                      +.+++..|+.+++         ..+..+..++|++..++  +...|.|..|.+.....++...      +++..+-|+.+
T Consensus         4 ~~~~~~~~k~i~~---------~l~~l~~e~~~~~~~~G--i~i~~~D~s~v~li~~~l~~~~F~~y~~~~~~~igi~~~   72 (245)
T 1rwz_A            4 VIMTGELLKTVTR---------AIVALVSEARIHFLEKG--LHSRAVDPANVAMVIVDIPKDSFEVYNIDEEKTIGVDMD   72 (245)
T ss_dssp             EEEEHHHHHHHHH---------HHHTTCSEEEEEEETTE--EEEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHH
T ss_pred             EEECHHHHHHHHH---------HHHHHHCCEEEEEECCE--EEEEEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEHH
T ss_conf             6861899999999---------99997585899993895--799999877489999997878793752698879999989


Q ss_pred             HHHHHHHHCCCCCCCCCCCC-CCCCEEEECCEEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCC
Q ss_conf             01222210277646433133-45530100250699985126655322101355-56617998489988889887410123
Q gi|254780454|r  204 AVGEILRILSSKDSSVKVSL-SESRIHLNIESLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSV  281 (385)
Q Consensus       204 ~l~el~k~l~~~~~~v~i~~-~~~~i~~~~~~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~  281 (385)
                      .|..+.|.+.. ++.+.+.+ +++.+.+..++..+..+|++..+.+-.--+|+ +++..++++.++|.++++.+..+++ 
T Consensus        73 ~l~kilk~~~~-~d~l~l~~~~~~~l~i~~~~~~~~~~l~~~d~~~~~~~ip~~e~~~~i~m~s~~f~~~i~~l~~~~d-  150 (245)
T 1rwz_A           73 RIFDISKSIST-KDLVELIVEDESTLKVKFGSVEYKVALIDPSAIRKEPRIPELELPAKIVMDAGEFKKAIAAADKISD-  150 (245)
T ss_dssp             HHHHHHTTSCT-TSEEEEEESSSSEEEEEETTEEEEEECBCGGGSCCCCCCCCCCCSEEEEEEHHHHHHHHHHHHTTCS-
T ss_pred             HHHHHHHCCCC-CCEEEEEECCCCCEEEEEEEEEEEEEECCHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHCCC-
T ss_conf             98988732589-9659999806882499998612456402411022467999855317999629999999999860577-


Q ss_pred             CCCCCEEEEECCEEEEEECCCCCEEEEEEEE----EEECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCE
Q ss_conf             5553025651765999980787326899999----896288439996388998898735753346633899965898758
Q gi|254780454|r  282 RIQAVKLSLSSDKLCMTVDNPDMGKAIESMN----VYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSV  357 (385)
Q Consensus       282 ~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~----~~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~  357 (385)
                         .|.+..+++++.+++.+ +.|++.-.+.    .++++++.+..|+.+||.+++++....    ++|++++.+ ..|+
T Consensus       151 ---~i~i~~~~~~l~~~~~g-~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~ls----~~V~i~~~~-~~Pl  221 (245)
T 1rwz_A          151 ---QVIFRSDKEGFRIEAKG-DVDSIVFHMTETELIEFNGGEARSMFSVDYLKEFCKVAGSG----DLLTIHLGT-NYPV  221 (245)
T ss_dssp             ---EEEEEEETTEEEEEEEC-SSCEEEEEECGGGSSEECCCCEEEEEEHHHHHHHGGGCCTT----CEEEEEECS-SSCE
T ss_pred             ---EEEEEEECCEEEEEEEC-CCCEEEEEECCCCCCEECCCCCCCEEEHHHHHHHHHHCCCC----CEEEEEECC-CCCE
T ss_conf             ---57999826779999994-67439999368741000367545287489999987450589----869999759-9878


Q ss_pred             EEECC-CCCCCCCCCCCCCEEEEEEE
Q ss_conf             99437-76544455566763799832
Q gi|254780454|r  358 FIRGK-DKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       358 ~i~~~-~~~~~~~~~~~~~~~~liMP  382 (385)
                      .+.-. .++       .....|.|-|
T Consensus       222 ~l~y~~~~~-------~g~i~f~lAP  240 (245)
T 1rwz_A          222 RLVFELVGG-------RAKVEYILAP  240 (245)
T ss_dssp             EEEEEETTT-------TEEEEEEECC
T ss_pred             EEEEEECCC-------CEEEEEEECC
T ss_conf             999998698-------3899999887


No 7  
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}
Probab=99.54  E-value=1.3e-09  Score=76.08  Aligned_cols=188  Identities=21%  Similarity=0.303  Sum_probs=122.5

Q ss_pred             EEECCEEEEEEEEECCCCC------CCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCC--CEEEECC------EEEEEE
Q ss_conf             9853415766664357875------3310000010001222210277646433133455--3010025------069998
Q gi|254780454|r  174 VATDGHRLAVAEVDIVAQI------AKMPSIIVPRKAVGEILRILSSKDSSVKVSLSES--RIHLNIE------SLSMSV  239 (385)
Q Consensus       174 vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~--~i~~~~~------~~~~~s  239 (385)
                      -|.|..|.+...+.++...      +.+..+-|..+.|..+.|.+.. .+.+++.++++  .+.+.+.      ...|.-
T Consensus       578 q~mD~s~v~lv~l~l~~~~F~~Y~~d~~~~igi~~~~l~kilk~~~~-~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l  656 (798)
T 3k4x_A          578 QAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNN-TDTLTLIADNTPDSIILLFEDTKKDRIAEYSL  656 (798)
T ss_dssp             EEECTTSSEEEEEEEEGGGEEEEECSSCEEEEEEHHHHHHHHHHSCS-SSEEEEECCSSCSEEEEEEECSSCCCEEEEEE
T ss_pred             EEECCCCEEEEEEEECHHHCCEEECCCCEEEEEEHHHHHHHHCCCCC-CCEEEEEEECCCCEEEEEEEECCCCEEEEEEE
T ss_conf             99988858999999998869738849987999998998999703889-97899999589987999998078872899998


Q ss_pred             EECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEE-----
Q ss_conf             5126655322101355-5661799848998888988741012355530256517659999807873268999998-----
Q gi|254780454|r  240 RLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNV-----  313 (385)
Q Consensus       240 rLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~-----  313 (385)
                      +|++-..+..  -+|+ +++..++++-..|.++++-+..+++    .|.+..+++++.+++.+ |.|++.-.+..     
T Consensus       657 ~lidi~~~~~--~iP~~e~~~~i~m~s~~f~~iik~l~~~~d----~i~i~~~~~~~~f~~~g-d~~~~~~~~~~~~~~~  729 (798)
T 3k4x_A          657 KLMDIDADFL--KIEELQYDSTLSLPSSEFSKIVRDLSQLSD----SINIMITKETIKFVADG-DIGSGSVIIKPFVDME  729 (798)
T ss_dssp             ECCCCCCCCC--CCCCCCCSEEEEEEHHHHHHHHHHHHTTCS----EEEEEEETTEEEEEEEC-SSCEEEEEECCBCCSS
T ss_pred             EEECCCCCCC--CCCCCCCCEEEEEEHHHHHHHHHHHHHCCC----EEEEEEECCEEEEEEEC-CCCEEEEEEECCCCCC
T ss_conf             7462575468--999988877999998999999999985199----89999929999999982-1635899993266667


Q ss_pred             ------E-ECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             ------9-62884399963889988987357533466338999658987589943776544455566763799832
Q gi|254780454|r  314 ------Y-YNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       314 ------~-~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                            . ..+++++..|..+||..+.++..-    .++|++++. +..|+.+.-.-+.        ....|.|-|
T Consensus       730 ~~~~~~~~~~~~~~~~~fsl~yL~~~~k~~~l----s~~V~i~~~-~d~Pl~l~y~i~~--------g~i~f~LAP  792 (798)
T 3k4x_A          730 HPETSIKLEMDQPVDLTFGAKYLLDIIKGSSL----SDRVGIRLS-SEAPALFQFDLKS--------GFLQFFLAP  792 (798)
T ss_dssp             CGGGCBEEEESSCEEEEEEHHHHHHHGGGGGT----CSEEEEEEC-SSSCEEEEEEETT--------EEEEEEECC
T ss_pred             CCCCEEEEECCCCEEEEEEHHHHHHHHHHHCC----CCEEEEEEE-CCCCEEEEEEECC--------EEEEEEECC
T ss_conf             75412788528837999988999998745058----988999996-9946999999689--------899999965


No 8  
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1
Probab=99.54  E-value=4.1e-12  Score=91.15  Aligned_cols=213  Identities=17%  Similarity=0.294  Sum_probs=146.0

Q ss_pred             EEEECCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHH
Q ss_conf             04505611355420220230024556521011667761787348999853415766664357875331000001000122
Q gi|254780454|r  128 YSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGE  207 (385)
Q Consensus       128 ~~~~i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~e  207 (385)
                      =.|.++.+.|.++|..+..++++..+.|+|.||+++..++  .|++.|||+-.-....++. ....++..++||+|.+.+
T Consensus        13 Mk~~i~k~~L~~~l~~~~~~i~~~~~~piL~~ilie~~~~--~l~l~atd~e~~i~~~i~~-~~i~~~G~~~vpak~l~~   89 (378)
T 1vpk_A           13 MKVTVTTLELKDKITIASKALAKKSVKPILAGFLFEVKDG--NFYICATDLETGVKATVNA-AEISGEARFVVPGDVIQK   89 (378)
T ss_dssp             EEEEEEHHHHHHHHHHHGGGCCCSSSCGGGGEEEEEEETT--EEEEEEECSSEEEEEECCC-SEEEECEEEEEEC-CHHH
T ss_pred             EEEEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECC--EEEEEEECCCEEEEEEEEC-CEECCCEEEEEEHHHHHH
T ss_conf             7999989999999999875527798748875989999899--9999998884599999963-166155689986799999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCEEEECCEEEEEEEEC-CCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCC-CCCC-
Q ss_conf             22102776464331334553010025069998512-66553221013555661799848998888988741012-3555-
Q gi|254780454|r  208 ILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLI-DGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSS-VRIQ-  284 (385)
Q Consensus       208 l~k~l~~~~~~v~i~~~~~~i~~~~~~~~~~srLi-~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~-~~~~-  284 (385)
                      +.|-+++  +.+.+...++++.++.++..+....+ ...||.+...   +....+.++...|.++++++...++ +..+ 
T Consensus        90 ivk~l~~--~~i~l~~~~~~l~I~~g~~~~~l~~~~~~~fP~~~~~---~~~~~~~i~~~~l~~~i~~v~~a~s~d~~r~  164 (378)
T 1vpk_A           90 MVKVLPD--EITELSLEGDALVISSGSTVFRITTMPADEFPEITPA---ESGITFEVDTSLLEEMVEKVIFAAAKDEFMR  164 (378)
T ss_dssp             HHTTCCS--SEEEEEEETTEEEEEETTEEEEEECBCCTTSCCCCCC---CSSEEEEEEHHHHHHHHHHHGGGSCCCTTCT
T ss_pred             HHHHCCC--CEEEEEEECCEEEEECCCEEEEEECCCHHHCCCCCCC---CCCCEEECCHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             9862787--5269994088999953750899961482333432234---6771586089999999976787517400122


Q ss_pred             ---CCEEEEECCEEEEEECCCCCEEEEEEEEEEECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             ---30256517659999807873268999998962884399963889988987357533466338999658
Q gi|254780454|r  285 ---AVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDS  352 (385)
Q Consensus       285 ---~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~  352 (385)
                         +|.|.++++.+++.+.+. +-=+.-.++.. ...+..+....+.+.+..+.+....  .+.+.+...+
T Consensus       165 ~L~Gv~~~~~~~~l~~vATDg-~RLa~~~~~~~-~~~~~~~iip~k~l~~l~k~l~~~~--~~~~~~~~~~  231 (378)
T 1vpk_A          165 NLNGVFWELHKNLLRLVASDG-FRLALAEEQIE-NEEEASFLLSLKSMKEVQNVLDNTT--EPTITVRYDG  231 (378)
T ss_dssp             TTSEEEEEEETTEEEEEEECS-SEEEEEEEECC-CCSCEEEEEEHHHHHHHHHHHHTCC--CSEEEEEECS
T ss_pred             HEEEEEEEECCCEEEEEECCC-CCEEEEECCCC-CCCCCCEEEEHHHHHHHHHHHCCCC--CCEEEEEEEC
T ss_conf             442289997187699998379-71688750357-7665304750889999986212456--7349996301


No 9  
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*
Probab=99.44  E-value=8.3e-11  Score=83.26  Aligned_cols=213  Identities=12%  Similarity=0.181  Sum_probs=100.5

Q ss_pred             EEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECC-EEEEEEECCEEEEEEEEEEEE-CCCCEEEEEHHHHHHHHH
Q ss_conf             589859999999998750203788861013389999899-799999678289999997775-268079994998778874
Q gi|254780454|r    2 KITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDG-LLEIKASGPEIEITGAIPASV-DVCGSITVSAHLLYDIVR   79 (385)
Q Consensus         2 k~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~-~l~l~atd~~~~i~~~i~~~i-~~~G~~~v~a~~l~~iik   79 (385)
                      .+.++...|.++|..+..+++...+.|+|.|++++..++ .+.+.|||+-.-....++... .....+++|++.+.++.+
T Consensus       134 ~~~i~~~~l~~~i~~v~~a~s~d~~r~~l~Gv~~~~~~~~~l~~vatD~~rl~~~~~~~~~~~~~~~~iip~~~~~~~~~  213 (378)
T 2avt_A          134 PLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAVATDSHRMSQRLITLDNTSADFMVVLPSKSLREFSA  213 (378)
T ss_dssp             CEEEEHHHHHHHHHHHGGGSCCCTTSGGGGEEEEEEETTTEEEEEEECSSEEEEEEEECSSCCCCEEEEEEHHHHHHHHH
T ss_pred             EEEECHHHHHHHHHHHHEEECCCCHHHHHCCEEEEEECCCCEEEEECCCCHHHEEEECCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             38988999999985421420477024444044799926840799995887323255012354432112443136999876


Q ss_pred             CCCCCC-CEEEEEECCCCEEEEEEECCCEEEEECCCCCCCCCCCC---CCCCEEEECCCHHHHHHHCCEEEECCCCCCCC
Q ss_conf             077777-30477733675089998678202430366211432123---32430450561135542022023002455652
Q gi|254780454|r   80 KLQDGA-QISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKE---EEYVYSFELASSVLKNLVERTHFAMATEEIRY  155 (385)
Q Consensus        80 ~L~~~~-~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~fP~~~~---~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~  155 (385)
                      -+.+.. .+.+..+   +.++.+.+++..+....++. .||.+..   .+....+.++...|.++++|+.-.++ +... 
T Consensus       214 l~~~~~~~v~i~~~---~~~~~~~~~~~~~~srli~g-~fP~y~~vip~~~~~~~~v~r~~l~~al~Rv~~~~~-~~~~-  287 (378)
T 2avt_A          214 VFTDDIETVEVFFS---PSQILFRSEHISFYTRLLEG-NYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISN-ATQN-  287 (378)
T ss_dssp             HSCTTCCEEEEEEC---SSEEEEECSSEEEEEECCCS-CCCCCGGGSCCCCSEEEEEEHHHHHHHHHHHHHHHT-TSTT-
T ss_pred             HHCCCCCCEEEEEC---CCEEEEEECCEEEEEECCCC-CCCCHHHCCCCCCCCEEEEEHHHHHHHHHHHHHCCC-CCCC-
T ss_conf             50356553267605---74799998988999740567-999745504556872588647888999976434022-2245-


Q ss_pred             CEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             1011667761787348999853415766664357875331000001000122221027764643313345
Q gi|254780454|r  156 YLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSE  225 (385)
Q Consensus       156 ~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~  225 (385)
                        .-+.+.+.++..++.....|.-+ +.-+.+.....+++..+-.-.+.|.+.++.+.+  ++|.+.+.+
T Consensus       288 --~~i~l~~~~~~l~l~~~~~d~g~-~~e~i~~~~~~Ge~~~i~fN~~yL~d~L~~~~~--~~v~i~~~~  352 (378)
T 2avt_A          288 --GTVKLEITQNHISAHVNSPEVGK-VNEDLDIVSQSGSDLTISFNPTYLIESLKAIKS--ETVKIHFLS  352 (378)
T ss_dssp             --CCEEEEEETTEEEEEEEETTTEE-EEEECCCSEEEECCEEEEECHHHHHHHHHTCCS--SEEEEEECC
T ss_pred             --CCCEEEECCCEEEEEECCCCCCC-CEEEEEECCCCCCCEEEEECHHHHHHHHHCCCC--CEEEEEECC
T ss_conf             --75134413746999966876565-048973101358967999889999999855899--879999768


No 10 
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A
Probab=99.04  E-value=1.9e-08  Score=68.89  Aligned_cols=225  Identities=18%  Similarity=0.269  Sum_probs=151.7

Q ss_pred             ECCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCC-----CCHHCCCCCHH
Q ss_conf             0561135542022023002455652101166776178734899985341576666435787533-----10000010001
Q gi|254780454|r  131 ELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAK-----MPSIIVPRKAV  205 (385)
Q Consensus       131 ~i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~-----~~~~iiP~k~l  205 (385)
                      .+++..|+++++...         ....-+.|.+..++  +.+.|.|..|.+.....++...-.     ...+-|+.+.|
T Consensus         5 ~~~a~~~k~i~~~l~---------~l~~e~~~~~~~~G--i~i~~mD~shv~Lv~l~l~~~~F~~Y~~d~~~igv~~~~l   73 (247)
T 3ifv_A            5 IVSAATLRDALDSVS---------VLVDECKIRLNEES--LSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRL   73 (247)
T ss_dssp             EECHHHHHHHHHHHH---------TTCSSEEEC---CE--EEEEEECTTSSEEEEEEEEGGGSSBC-----CEEECHHHH
T ss_pred             EECHHHHHHHHHHHH---------HHHCEEEEEECCCE--EEEEEECCCCEEEEEEEECHHHCCEEEECCCEEEEEHHHH
T ss_conf             972999999999999---------87542899991784--7999997873799999988786978981285899998999


Q ss_pred             HHHHHHCCCCCCCCCCCCCC--CCEEEECCEEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCCC
Q ss_conf             22221027764643313345--530100250699985126655322101355-566179984899888898874101235
Q gi|254780454|r  206 GEILRILSSKDSSVKVSLSE--SRIHLNIESLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSVR  282 (385)
Q Consensus       206 ~el~k~l~~~~~~v~i~~~~--~~i~~~~~~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~  282 (385)
                      ..+.|.... ++.+.+.+++  ..+.+..++..+.-+|++-..+...--+|+ ++...++++-+.|.+.++-+..+++. 
T Consensus        74 ~kilk~~~~-~d~l~l~~~~~~~~l~i~~~~~~~~~~l~~i~~~~~~~~iP~~~~~~~i~~~s~~f~~~~~~l~~~~d~-  151 (247)
T 3ifv_A           74 EEVAGMAGA-GDLIHLTLDEETRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMVSDH-  151 (247)
T ss_dssp             HHHHTTC-----CEEECC-------EEEETTEEEEC---CTTC----CCCCCCCCSEEEEEEHHHHHHHHHHHHHHCSE-
T ss_pred             HHHHHHCCC-CCEEEEEECCCCCEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHCCCCE-
T ss_conf             999973179-947999992799878999723068998453543222568888664389994089988776676436986-


Q ss_pred             CCCCEEEEECCEEEEEECC-CCCEEEEEEEEE----EECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCE
Q ss_conf             5530256517659999807-873268999998----96288439996388998898735753346633899965898758
Q gi|254780454|r  283 IQAVKLSLSSDKLCMTVDN-PDMGKAIESMNV----YYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSV  357 (385)
Q Consensus       283 ~~~i~l~~~~~~l~i~~~~-~e~g~~~e~i~~----~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~  357 (385)
                         +.+..+++++.+++.+ .+.|+..-.++.    .++.++....|+.+||..+.++...    .+.|++++.. ..|+
T Consensus       152 ---i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~Yl~~~~k~~~l----s~~V~i~~~~-~~Pl  223 (247)
T 3ifv_A          152 ---IRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPT----DAEVTVELGE-EFPV  223 (247)
T ss_dssp             ---EEEEEETTTTEEEEEEECSSCEEEEEECGGGCSEEEECCCEEEEEHHHHHHHHHHSCT----TCEEEEEECB-SSCE
T ss_pred             ---EEEEEEECEEEEEEEEECCEEEEEEEECCCCCEEEEECCCCCEEEHHHHHHHHHHCCC----CCEEEEEECC-CCCE
T ss_conf             ---9999980345999995156279999848986168850444528878999988744468----9869999769-9778


Q ss_pred             EEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             9943776544455566763799832
Q gi|254780454|r  358 FIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       358 ~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      .+.-.-.      ++...-.|.|.|
T Consensus       224 ~l~y~i~------~~~g~i~f~LAP  242 (247)
T 3ifv_A          224 KLHYQIA------EGMGTITYMLAP  242 (247)
T ss_dssp             EEEEEEG------GGTEEEEEEECC
T ss_pred             EEEEEEC------CCCEEEEEEECC
T ss_conf             9999987------985699999866


No 11 
>3fds_C DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C*
Probab=99.00  E-value=5.2e-07  Score=60.20  Aligned_cols=221  Identities=10%  Similarity=0.154  Sum_probs=139.6

Q ss_pred             CCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCC------CCCHHCCCCCHHH
Q ss_conf             6113554202202300245565210116677617873489998534157666643578753------3100000100012
Q gi|254780454|r  133 ASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIA------KMPSIIVPRKAVG  206 (385)
Q Consensus       133 ~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~------~~~~~iiP~k~l~  206 (385)
                      ++..|+++++..         +....-++|++..++  |.+.+.|..|.+.....+....-      .+..+-|+.+.+.
T Consensus         8 ~ak~f~~~i~~l---------~~i~~e~~~~~~~~g--l~~~~~D~s~~~l~~~~l~~~~F~~Y~~~~~~~~gi~~~~l~   76 (249)
T 3fds_C            8 NAKDFFSFINSI---------TNVTDSIILNFTEDG--IFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVK   76 (249)
T ss_dssp             CHHHHHHHHHHH---------TTTCSSEEEEECSSE--EEEEEECTTSSEEEEEEEEGGGSSEEECSSCEEEEECHHHHH
T ss_pred             CHHHHHHHHHHH---------HHHHCCEEEEECCCE--EEEEEECCCCEEEEEEEECHHHCEEEECCCCEEEEEEHHHHH
T ss_conf             879999999999---------986580999983574--899998788189999993867675760689869998899999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCE--EEEC--CEE--EEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCC
Q ss_conf             2221027764643313345530--1002--506--99985126655322101355-566179984899888898874101
Q gi|254780454|r  207 EILRILSSKDSSVKVSLSESRI--HLNI--ESL--SMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMS  279 (385)
Q Consensus       207 el~k~l~~~~~~v~i~~~~~~i--~~~~--~~~--~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~  279 (385)
                      .+.|.....+..+.....++..  .+..  ++.  .+..++++.  ....--+|+ +++..+.++.+.|.+.++.+..+.
T Consensus        77 kilk~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~l~~~--~~~~~~~p~~~~~~~i~i~s~~f~~~~~~l~~~~  154 (249)
T 3fds_C           77 KILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKG--QVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVG  154 (249)
T ss_dssp             HHHTTCCCSCEEEEEEECSSEEEEEEEETTTCCEEEEEEECEEC--CCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHC
T ss_pred             HHHHHCCCCCCEEEEECCCCCEEEEEEECCCCEEEEEEEECCCC--CHHCCCCCCCCCCEEEEECHHHHHHHHHHHHCCC
T ss_conf             99832466640378841798517999955897379999720245--3202578876652689964899999987540249


Q ss_pred             CCCCCCCEEEEECCEEEEEECCCCCEEEEEEEE-----EE-ECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             235553025651765999980787326899999-----89-628843999638899889873575334663389996589
Q gi|254780454|r  280 SVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMN-----VY-YNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSS  353 (385)
Q Consensus       280 ~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~-----~~-~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~  353 (385)
                      +.    |.+..+++++.+++.+. .+.......     .. ..+++....|+.+||.++++.+.+-   .+.|.++++ +
T Consensus       155 d~----v~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~f~l~yl~~~~k~~~~~---s~~v~i~~~-~  225 (249)
T 3fds_C          155 EE----MRISTEEDKIKIEAGEE-GKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGF---SAPTMVSFG-E  225 (249)
T ss_dssp             SE----EEEEEETTEEEEEEEET-TEEEEEEEEETBEESEEEESSCCEEEEEHHHHHHHHHTTTTC---CSCEEEEEC-T
T ss_pred             CE----EEEEEECCEEEEEEECC-CCEEEEEECCCCCEEEEECCCCEEEEEEHHHHHHHHHHHHCC---CCEEEEEEC-C
T ss_conf             78----99999899999999027-854799973898515785287311399789999999763214---883899972-9


Q ss_pred             CCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             87589943776544455566763799832
Q gi|254780454|r  354 NSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       354 ~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      ..|+.+.-.-.+       ...-.|.|-|
T Consensus       226 ~~Pl~~~~~~~~-------~g~~~f~lAP  247 (249)
T 3fds_C          226 NLPMKIDVEAVS-------GGHMIFWIAP  247 (249)
T ss_dssp             TCCEEEEEECTT-------SCEEEEEECC
T ss_pred             CCCEEEEEECCC-------CEEEEEEECC
T ss_conf             998999998289-------8189999925


No 12 
>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity factor; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3l0x_B
Probab=99.00  E-value=3.1e-07  Score=61.59  Aligned_cols=218  Identities=20%  Similarity=0.315  Sum_probs=148.8

Q ss_pred             CCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCC------CCCCHHCCCCCHHH
Q ss_conf             611355420220230024556521011667761787348999853415766664357875------33100000100012
Q gi|254780454|r  133 ASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------AKMPSIIVPRKAVG  206 (385)
Q Consensus       133 ~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k~l~  206 (385)
                      ++..|+++++..         +....=++|++..++.++  .|.|..|.+...+.++...      +++..+-|..+.+.
T Consensus         8 ~a~~fk~i~~~l---------~~l~~e~~~~~~~~Gi~i--~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~~gi~~~~l~   76 (258)
T 1plq_A            8 EASLFKRIIDGF---------KDCVQLVNFQCKEDGIIA--QAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLS   76 (258)
T ss_dssp             SHHHHHHHHHHH---------TTTCSEEEEEEETTEEEE--EEECTTSSEEEEEEEEGGGSSEECCSSCEEEEEEHHHHH
T ss_pred             CHHHHHHHHHHH---------HHHHCEEEEEEECCEEEE--EEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEHHHHH
T ss_conf             769999999999---------887653999993897899--999899789999998889892652686689999989989


Q ss_pred             HHHHHCCCCCCCCCCCCCCC--CEEEECCE------EEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHH
Q ss_conf             22210277646433133455--30100250------699985126655322101355-5661799848998888988741
Q gi|254780454|r  207 EILRILSSKDSSVKVSLSES--RIHLNIES------LSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSI  277 (385)
Q Consensus       207 el~k~l~~~~~~v~i~~~~~--~i~~~~~~------~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i  277 (385)
                      .+.|.+.. .+.+.+.+.++  .+.+...+      ..+..+|++-...+..  +|. +++..++++-..|.+.++-+..
T Consensus        77 kilk~~~~-~d~l~l~~~~~~~~l~~~~~~~~~~~~~~~~l~l~d~~~~~~~--ip~~~~~~~i~~~s~~f~~~~k~l~~  153 (258)
T 1plq_A           77 KILRCGNN-TDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLK--IEELQYDSTLSLPSSEFSKIVRDLSQ  153 (258)
T ss_dssp             HHTTCSTT-TSEEEEEECSSCSEEEEEEECSSSSCEEEEEEECBCCCCCCCC--CCCSCCSEEEEEEHHHHHHHHHHHHT
T ss_pred             HHHHHCCC-CCEEEEEEECCCCEEEEEEECCCCCCEEEEEEECCCCCCCCCC--CCCCCCCEEEEEEHHHHHHHHHHHHH
T ss_conf             99861478-8679999955887169999558876379999733678721246--88767646899759999999998771


Q ss_pred             CCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEE------------EECCCCEEEEECHHHHHHHHHHCCCCCCCCCE
Q ss_conf             012355530256517659999807873268999998------------96288439996388998898735753346633
Q gi|254780454|r  278 MSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNV------------YYNECPMDICFNYKYLLEIIDNISSDEVVDDE  345 (385)
Q Consensus       278 ~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~------------~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~  345 (385)
                      +++    .+.+..+++++.+++.+ |.|++.-.+..            .-.+++++..|..+||..+++....    .+.
T Consensus       154 ~~d----~i~i~~~~~~~~f~~~g-d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l----s~~  224 (258)
T 1plq_A          154 LSD----SINIMITKETIKFVADG-DIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSL----SDR  224 (258)
T ss_dssp             TCS----EEEEEEETTEEEEEEEC-SSCEEEEEECCBCCTTCGGGCBEEEESSCEEEEEEHHHHHHHGGGGGT----CSE
T ss_pred             HCC----EEEEEECCCCEEEEEEE-CCCEEEEEEECCCCCCCCCCEEEEECCCCEEEEEEHHHHHHHHHHCCC----CCE
T ss_conf             388----79999858830899980-364389998035666775420465227713489958999998725257----988


Q ss_pred             EEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             8999658987589943776544455566763799832
Q gi|254780454|r  346 VVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       346 i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      |+++++ +..|+.+.-.-+.        ..-.|.|.|
T Consensus       225 v~i~~~-~~~Pl~~~~~~~~--------g~i~f~lAP  252 (258)
T 1plq_A          225 VGIRLS-SEAPALFQFDLKS--------GFLQFFLAP  252 (258)
T ss_dssp             EEEEEC-SSSCEEEEEEETT--------EEEEEEECC
T ss_pred             EEEEEE-CCCCEEEEEEECC--------EEEEEEECC
T ss_conf             999982-8966899999588--------799999936


No 13 
>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotrimer, DNA binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C*
Probab=98.99  E-value=4.3e-07  Score=60.73  Aligned_cols=219  Identities=13%  Similarity=0.184  Sum_probs=146.5

Q ss_pred             CCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCC------CCCCHHCCCCCHHH
Q ss_conf             611355420220230024556521011667761787348999853415766664357875------33100000100012
Q gi|254780454|r  133 ASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------AKMPSIIVPRKAVG  206 (385)
Q Consensus       133 ~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k~l~  206 (385)
                      ++..|+++++...         ....-++|++..++  +.+.|.|..|.+.....++...      +++..+-|+.+.+.
T Consensus         7 ~~~~fk~i~~~l~---------~l~~e~~~~~~~~G--i~i~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~igi~~~~l~   75 (244)
T 2ijx_A            7 DVRVLKDIIQALA---------RLVDEAVLKFKQDS--VELVALDRAHISLISVNLPREMFKEYDVNDEFKFGFNTQYLM   75 (244)
T ss_dssp             CHHHHHHHHHHHH---------HHCSEEEEEECSSE--EEEEEECTTSSEEEEEEEEGGGCSEEECSSCEEEEEEHHHHH
T ss_pred             CHHHHHHHHHHHH---------HHHCEEEEEEECCE--EEEEEECCCCEEEEEEEECHHHCCEECCCCCEEEEEEHHHHH
T ss_conf             7899999999999---------87582999993897--899999899689999998877693332377779899999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCC--CEEEEC--CEEEEEEEECCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCC
Q ss_conf             22210277646433133455--301002--50699985126655322101355566179984899888898874101235
Q gi|254780454|r  207 EILRILSSKDSSVKVSLSES--RIHLNI--ESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVR  282 (385)
Q Consensus       207 el~k~l~~~~~~v~i~~~~~--~i~~~~--~~~~~~srLi~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~  282 (385)
                      .++|....+ +.+++.++++  .+....  .+..+..++++..-++..- .+.+++..+.++.+.|.+.++.+..+.+  
T Consensus        76 kilk~~~~~-d~l~l~~~~~~~~~i~~~~~~~~~~~l~l~d~~~~~~~~-p~~~~~~~i~~~s~~f~~~ik~l~~~~d--  151 (244)
T 2ijx_A           76 KILKVAKRK-EAIEIASESPDSVIINIIGSTNREFNVRNLEVSEQEIPE-INLQFDISATISSDGFKSAISEVSTVTD--  151 (244)
T ss_dssp             HHHTTCCSS-CEEEEEEEETTEEEEEEESSSEEEEEEECCCCCCCCCCC-CCCCCSEEEEEEHHHHHHHHHHHTTTCS--
T ss_pred             HHHHCCCCC-CEEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCC-CCCCCCEEEEECHHHHHHHHHHHHHCCC--
T ss_conf             998446889-749999935985499970674279996135665356899-8866637998249999999999872198--


Q ss_pred             CCCCEEEEECCEEEEEECCCCCEEEEEEEE------EEE-CCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             553025651765999980787326899999------896-2884399963889988987357533466338999658987
Q gi|254780454|r  283 IQAVKLSLSSDKLCMTVDNPDMGKAIESMN------VYY-NECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNS  355 (385)
Q Consensus       283 ~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~------~~~-~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~  355 (385)
                        .+.++.+++++.+++.+.  |++.-.++      ..+ ..++.+..|..+||....++..-    .+.|++++. +..
T Consensus       152 --~i~i~~~~~~i~f~~~gd--~~~~~~~~~~~~~~~~~~~~~~~~~~fs~~yl~~~~k~~~l----s~~v~i~~~-~~~  222 (244)
T 2ijx_A          152 --NVVVEGHEDRILIKAEGE--SEVEVEFSKDTGGLQDLEFSKESKNSYSAEYLDDVLSLTKL----SDYVKISFG-NQK  222 (244)
T ss_dssp             --EEEEEEETTEEEEEETTC--TTSEEEEETTTTCEEEEEESSCEEEEEEHHHHHHTGGGGGG----CSEEEEEEE-TTE
T ss_pred             --EEEEEEECCEEEEEEECC--CCEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCC----CCEEEEEEC-CCC
T ss_conf             --799999375699999737--61479980589860788750332453138999998714368----986999974-997


Q ss_pred             CEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             589943776544455566763799832
Q gi|254780454|r  356 SVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       356 p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      |+.+.-.-++       .....|.|-|
T Consensus       223 Pl~~~~~~~~-------~g~i~f~lAP  242 (244)
T 2ijx_A          223 PLQLFFNMEG-------GGKVTYLLAP  242 (244)
T ss_dssp             EEEEEEECGG-------GCEEEEEECC
T ss_pred             CEEEEEECCC-------CEEEEEEECC
T ss_conf             7899999289-------8699999914


No 14 
>3fds_D DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B*
Probab=98.92  E-value=5.6e-07  Score=60.01  Aligned_cols=220  Identities=14%  Similarity=0.194  Sum_probs=149.6

Q ss_pred             CCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCH-------HCCCCCH
Q ss_conf             561135542022023002455652101166776178734899985341576666435787533100-------0001000
Q gi|254780454|r  132 LASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPS-------IIVPRKA  204 (385)
Q Consensus       132 i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~-------~iiP~k~  204 (385)
                      .++..|+.+++..         .....=++|++..++.++  -|.|..|.+.....++...-....       +=|..+.
T Consensus         7 ~~a~~fk~i~~~l---------~~l~~e~~~~~~~~Gi~i--~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~~igi~l~~   75 (245)
T 3fds_D            7 IDAVSFSYILRTV---------GDFLSEANFIVTKEGIRV--SGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLED   75 (245)
T ss_dssp             SCHHHHHHHHHHH---------HTTCSEEEEEEETTEEEE--EEECTTSSEEEEEEEEGGGEEEEEESSSCEEEEEEHHH
T ss_pred             CCHHHHHHHHHHH---------HHHHCEEEEEEECCEEEE--EEECCCCEEEEEEEECHHHCCEEEECCCCCEEEEEHHH
T ss_conf             5679999999999---------987563999990781799--99988867999999787769489847976278888899


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCEEEECC---EEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCC
Q ss_conf             12222102776464331334553010025---0699985126655322101355-5661799848998888988741012
Q gi|254780454|r  205 VGEILRILSSKDSSVKVSLSESRIHLNIE---SLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSS  280 (385)
Q Consensus       205 l~el~k~l~~~~~~v~i~~~~~~i~~~~~---~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~  280 (385)
                      |..+.|.+.. .+.+.+..+++.+.+..+   ...+..++++-...+..  +|. +++..+.++-..|.+.++-+..+++
T Consensus        76 l~kilk~~~~-~d~l~l~~~~~~l~i~~~~~~~~~~~l~l~d~~~~~~~--~p~~e~~~~i~~~s~~f~~~~k~l~~~~d  152 (245)
T 3fds_D           76 VNDILKRVLK-DDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPP--SVNLEFPFKAQLLTITFADIIDELSDLGE  152 (245)
T ss_dssp             HHHHHTTCCT-TCEEEEEECSSEEEEEEESSSEEEEEEECCCCCCCCC------CCCSEEEEEEHHHHHHHHHHHTTTCS
T ss_pred             HHHHHHCCCC-CCEEEEEECCCCEEEEEEECCEEEEEEECCCCCCCCCC--CCCCCCCEEEEEEHHHHHHHHHHHHHCCC
T ss_conf             8998732479-97799995389708999835058999621345422567--88888756998509999999998862487


Q ss_pred             CCCCCCEEEEECCEEEEEECCCCCEEEEEEEEE------EECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf             355530256517659999807873268999998------96288439996388998898735753346633899965898
Q gi|254780454|r  281 VRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNV------YYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSN  354 (385)
Q Consensus       281 ~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~------~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~  354 (385)
                          .|.+..+++.+.+++.+ |.|+++-.++.      ...+++.+..|+.+||..+.++..-    .++|++++.. .
T Consensus       153 ----~i~i~~~~~~l~~~~~g-d~~~~~~~~~~~~~~~~~~~~~~~~~~ysl~yl~~~~K~~~l----s~~v~i~~~~-~  222 (245)
T 3fds_D          153 ----VLNIHSKENKLYFEVIG-DLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRA----SDSMELYFGS-Q  222 (245)
T ss_dssp             ----EEEEEEETTEEEEEEEC-SSCEEEEEECTTSSSCSEEEECCCEEEEEHHHHHHGGGGGGT----CSEEEEEECT-T
T ss_pred             ----EEEEEEECCEEEEEEEC-CCCEEEEEECCCCCCCEEECCCCEEEEEEHHHHHHHHCCCCC----CCEEEEEECC-C
T ss_conf             ----58999716789999973-463489998689984124216751459868999987554468----9869999759-9


Q ss_pred             CCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             7589943776544455566763799832
Q gi|254780454|r  355 SSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       355 ~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      .|+.+.-.-.+       .....|++-|
T Consensus       223 ~Pl~~~~~i~~-------~g~i~f~LAP  243 (245)
T 3fds_D          223 IPLKLRFKLPQ-------EGYGDFYIAP  243 (245)
T ss_dssp             SCEEEEEECST-------TCEEEEEECC
T ss_pred             CCEEEEEEECC-------CEEEEEEECC
T ss_conf             67899999089-------8189999902


No 15 
>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A*
Probab=98.90  E-value=8.7e-07  Score=58.86  Aligned_cols=220  Identities=14%  Similarity=0.251  Sum_probs=148.2

Q ss_pred             CCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCC------CCCHHCCCCCHH
Q ss_conf             56113554202202300245565210116677617873489998534157666643578753------310000010001
Q gi|254780454|r  132 LASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIA------KMPSIIVPRKAV  205 (385)
Q Consensus       132 i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~------~~~~~iiP~k~l  205 (385)
                      ..+..|+.++....         ....=++|++..++.++  .|.|..|.+.....++...-      ++..+-|+.+.+
T Consensus         7 ~~a~~fk~i~~~l~---------~l~~e~~~~~~~~Gi~i--~~mD~s~v~li~~~l~~~~F~~y~~~~~~~igi~~~~l   75 (261)
T 1u7b_A            7 VQGSILKKVLEALK---------DLINEACWDISSSGVNL--QSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSM   75 (261)
T ss_dssp             SCTHHHHHHHHHHH---------TTCSEEEEEEETTEEEE--EEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHHHH
T ss_pred             CCHHHHHHHHHHHH---------HHHCEEEEEEECCEEEE--EEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEHHHH
T ss_conf             56799999999999---------87563999990896899--99988878999999897889050557768999999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCC--CEEEEC--C----EEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHH
Q ss_conf             222210277646433133455--301002--5----0699985126655322101355-566179984899888898874
Q gi|254780454|r  206 GEILRILSSKDSSVKVSLSES--RIHLNI--E----SLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVS  276 (385)
Q Consensus       206 ~el~k~l~~~~~~v~i~~~~~--~i~~~~--~----~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~  276 (385)
                      ..+.|.+.. ...+.+.+.++  ++.+..  +    ...|.-+|++-.-+++.  +|+ +++..++++-+.|.++++-+.
T Consensus        76 ~kilk~~~~-~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l~l~d~~~~~~~--ip~~~~~~~i~~~s~~f~~~~~~l~  152 (261)
T 1u7b_A           76 SKILKCAGN-EDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLG--IPEQEYSCVVKMPSGEFARICRDLS  152 (261)
T ss_dssp             HHHHTTSCT-TCEEEEEECTTCSEEEEEEECTTSSCEEEEEEECCCCCCCCCB--CCCCCCSEEEEEEHHHHHHHHHHHH
T ss_pred             HHHHHHCCC-CCEEEEEECCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCCC--CCCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             999963558-9549999836887169999806876226898740346600125--7877755899950899999999997


Q ss_pred             HCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEE------------ECCCCEEEEECHHHHHHHHHHCCCCCCCCC
Q ss_conf             10123555302565176599998078732689999989------------628843999638899889873575334663
Q gi|254780454|r  277 IMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVY------------YNECPMDICFNYKYLLEIIDNISSDEVVDD  344 (385)
Q Consensus       277 i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~------------~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e  344 (385)
                      .+.+.    +.+..+++.+.+++.+ |.|++.-.+.-.            -.+++.+..|..+||..+++.....    +
T Consensus       153 ~~~d~----v~i~~~~~~~~~~~~g-d~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~ls----~  223 (261)
T 1u7b_A          153 HIGDA----VVISCAKDGVKFSASG-ELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLS----S  223 (261)
T ss_dssp             TTCSE----EEEEEETTEEEEEEEE-TTEEEEEEECCCC----CCSCCEEEESSCEEEEEEHHHHHHHGGGGGGC----S
T ss_pred             HCCCE----EEEEECCCCEEEEEEE-CCCEEEEEEECCCCCCCCCCEEEEECCCCEEEEEEHHHHHHHHHHCCCC----C
T ss_conf             42880----8999818827999972-2654799992477877743126763387403899589999876333689----8


Q ss_pred             EEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             38999658987589943776544455566763799832
Q gi|254780454|r  345 EVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       345 ~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      .|++++.. ..|+.+.-.-.+       ...-.|.|-|
T Consensus       224 ~V~i~~~~-~~Pl~~~~~~~~-------~g~i~f~lAP  253 (261)
T 1u7b_A          224 TVTLSMSA-DVPLVVEYKIAD-------MGHLKYYLAP  253 (261)
T ss_dssp             EEEEEECT-TSCEEEEEEETT-------TEEEEEEECC
T ss_pred             EEEEEECC-CCCEEEEEEECC-------CCEEEEEECC
T ss_conf             79999819-988999999289-------8299999967


No 16 
>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A
Probab=98.86  E-value=1.4e-06  Score=57.53  Aligned_cols=219  Identities=16%  Similarity=0.275  Sum_probs=145.7

Q ss_pred             CCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCC------CCCCHHCCCCCHHH
Q ss_conf             611355420220230024556521011667761787348999853415766664357875------33100000100012
Q gi|254780454|r  133 ASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------AKMPSIIVPRKAVG  206 (385)
Q Consensus       133 ~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k~l~  206 (385)
                      ++..|+++++..         +....=+.|++..++.++  -+.|..|-+...+.+....      +++..+-|+.+.|.
T Consensus         9 ~~~~f~~ii~~l---------~~~~~e~~~~~~~~Gl~i--~~~d~s~v~l~~l~l~~~~F~~Y~~~~~~~~gi~~~~L~   77 (249)
T 1iz5_A            9 GAKEFAQLIDTA---------SKLIDEAAFKVTEDGISM--RAMDPSRVVLIDLNLPSSIFSKYEVVEPETIGVNLDHLK   77 (249)
T ss_dssp             CHHHHHHHHHHH---------TSSCSEEEEEECSSEEEE--EEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHHHHH
T ss_pred             CHHHHHHHHHHH---------HHHHCEEEEEEECCEEEE--EEECCCCEEEEEEEECHHHCCEECCCCCEEEEEEHHHHH
T ss_conf             689999999999---------987584999997896899--999898789999998988794654588889999969989


Q ss_pred             HHHHHCCCCCCCCCCCCCCC-CEEEECC---EEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCC
Q ss_conf             22210277646433133455-3010025---0699985126655322101355-56617998489988889887410123
Q gi|254780454|r  207 EILRILSSKDSSVKVSLSES-RIHLNIE---SLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSV  281 (385)
Q Consensus       207 el~k~l~~~~~~v~i~~~~~-~i~~~~~---~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~  281 (385)
                      .+.|.+... +.+.+..+++ .+.+...   ...+..++++....+.  -+|. +++..+.+.-+.|.+.++-+..+.+ 
T Consensus        78 kilk~~~~~-d~l~~~~~~~~~l~i~~~~~~~~~~~i~l~~~~~~~~--~ip~~~~~~~i~~~s~~f~~i~~~l~~~~d-  153 (249)
T 1iz5_A           78 KILKRGKAK-DTLILKKGEENFLEITIQGTATRTFRVPLIDVEEMEV--DLPELPFTAKVVVLGEVLKAAVKAASLVSD-  153 (249)
T ss_dssp             HHHTTCCTT-CEEEEEECSSSEEEEEEESSSEEEEEEECBCCCC-------CCCCCCEEEEEEHHHHHHHHHHHTTTCS-
T ss_pred             HHHHCCCCC-CEEEEEECCCCEEEEEEECCCEEEEEEEECCCCCCCC--CCCCCCCCEEEEECHHHHHHHHHHHHCCCC-
T ss_conf             998436899-6699995588627999953512799986033453346--788877654997249999999987501598-


Q ss_pred             CCCCCEEEEECCEEEEEECCCCCEEEEEEEEE------E-ECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf             55530256517659999807873268999998------9-6288439996388998898735753346633899965898
Q gi|254780454|r  282 RIQAVKLSLSSDKLCMTVDNPDMGKAIESMNV------Y-YNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSN  354 (385)
Q Consensus       282 ~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~------~-~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~  354 (385)
                         .|.+..+++++.+++.+ |.|.++-.+..      . -.+++.+..|+.+||..+.++..-    .+.|.+++. +.
T Consensus       154 ---~i~i~~~~~~i~~~s~g-d~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~yl~~~~k~~~l----s~~v~l~~~-~~  224 (249)
T 1iz5_A          154 ---SIKFIARENEFIMKAEG-ETQEVEIKLTLEDEGLLDIEVQEETKSAYGVSYLSDMVKGLGK----ADEVTIKFG-NE  224 (249)
T ss_dssp             ---EEEEEEETTEEEEEEEC-SSCEEEEEEETTTTSSSEEEESSCEEEEEEHHHHHHHHTTSCT----TCEEEEEEC-TT
T ss_pred             ---EEEEEECCCEEEEEEEC-CCCEEEEEEECCCCCCEEEECCCCCCEEEHHHHHHHHHHHCCC----CCEEEEEEC-CC
T ss_conf             ---89999938838999963-6655899982167640456507750036638899999875368----985999974-99


Q ss_pred             CCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             7589943776544455566763799832
Q gi|254780454|r  355 SSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       355 ~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      .|+.+.-.-++       .....+.|-|
T Consensus       225 ~Pl~~~~~i~~-------~g~i~f~lAP  245 (249)
T 1iz5_A          225 MPMQMEYYIRD-------EGRLTFLLAP  245 (249)
T ss_dssp             CCEEEEEEETT-------TEEEEEEECC
T ss_pred             CCEEEEEEECC-------CCEEEEEECC
T ss_conf             77999999689-------8199999836


No 17 
>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A*
Probab=98.83  E-value=1.7e-06  Score=57.03  Aligned_cols=205  Identities=12%  Similarity=0.233  Sum_probs=133.4

Q ss_pred             EEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEHHH
Q ss_conf             5898599999999987502037888610133899998997999996782--899999977------75268079994998
Q gi|254780454|r    2 KITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSAHL   73 (385)
Q Consensus         2 k~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a~~   73 (385)
                      +..++.+.|...++.+..+++         .+.+++.++++.++|.|..  .-+...+++      +++++-.+.|+.+.
T Consensus         3 ~~~~~~~~~k~i~~~l~~l~~---------e~~~~~~~~Gi~i~~~D~s~v~li~~~l~~~~F~~y~~~~~~~igi~~~~   73 (245)
T 1rwz_A            3 DVIMTGELLKTVTRAIVALVS---------EARIHFLEKGLHSRAVDPANVAMVIVDIPKDSFEVYNIDEEKTIGVDMDR   73 (245)
T ss_dssp             EEEEEHHHHHHHHHHHHTTCS---------EEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHHH
T ss_pred             EEEECHHHHHHHHHHHHHHHC---------CEEEEEECCEEEEEEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEHHH
T ss_conf             668618999999999999758---------58999938957999998774899999978787937526988799999899


Q ss_pred             HHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCC---CCCCCCCCCCCEEEECCCHHHHHHHCCEEEECCC
Q ss_conf             7788740777773047773367508999867820243036621---1432123324304505611355420220230024
Q gi|254780454|r   74 LYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPES---EFPSTKEEEYVYSFELASSVLKNLVERTHFAMAT  150 (385)
Q Consensus        74 l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~---~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~  150 (385)
                      |..++|.+..+..+.+..+++  ..+.+.-+..++++..++.+   +.+.+|+.+....+.+++..|+++++... ..+ 
T Consensus        74 l~kilk~~~~~d~l~l~~~~~--~~l~i~~~~~~~~~~l~~~d~~~~~~~ip~~e~~~~i~m~s~~f~~~i~~l~-~~~-  149 (245)
T 1rwz_A           74 IFDISKSISTKDLVELIVEDE--STLKVKFGSVEYKVALIDPSAIRKEPRIPELELPAKIVMDAGEFKKAIAAAD-KIS-  149 (245)
T ss_dssp             HHHHHTTSCTTSEEEEEESSS--SEEEEEETTEEEEEECBCGGGSCCCCCCCCCCCSEEEEEEHHHHHHHHHHHH-TTC-
T ss_pred             HHHHHHCCCCCCEEEEEECCC--CCEEEEEEEEEEEEEECCHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHH-HCC-
T ss_conf             898873258996599998068--8249999861245640241102246799985531799962999999999986-057-


Q ss_pred             CCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCC-----CCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             55652101166776178734899985341576666435787-----5331000001000122221027764643313345
Q gi|254780454|r  151 EEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQ-----IAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSE  225 (385)
Q Consensus       151 d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~-----~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~  225 (385)
                      |.       |.|...++...+.   ++|.. ......+...     ..++....-+.+.|..+.|...- .+.|++.++.
T Consensus       150 d~-------i~i~~~~~~l~~~---~~g~~-~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l-s~~V~i~~~~  217 (245)
T 1rwz_A          150 DQ-------VIFRSDKEGFRIE---AKGDV-DSIVFHMTETELIEFNGGEARSMFSVDYLKEFCKVAGS-GDLLTIHLGT  217 (245)
T ss_dssp             SE-------EEEEEETTEEEEE---EECSS-CEEEEEECGGGSSEECCCCEEEEEEHHHHHHHGGGCCT-TCEEEEEECS
T ss_pred             CE-------EEEEEECCEEEEE---EECCC-CEEEEEECCCCCCEECCCCCCCEEEHHHHHHHHHHCCC-CCEEEEEECC
T ss_conf             75-------7999826779999---99467-43999936874100036754528748999998745058-9869999759


Q ss_pred             CC-EEEE
Q ss_conf             53-0100
Q gi|254780454|r  226 SR-IHLN  231 (385)
Q Consensus       226 ~~-i~~~  231 (385)
                      +. +.+.
T Consensus       218 ~~Pl~l~  224 (245)
T 1rwz_A          218 NYPVRLV  224 (245)
T ss_dssp             SSCEEEE
T ss_pred             CCCEEEE
T ss_conf             9878999


No 18 
>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A
Probab=98.78  E-value=5.2e-06  Score=54.17  Aligned_cols=220  Identities=17%  Similarity=0.264  Sum_probs=145.2

Q ss_pred             CCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCC------CCCHHCCCCCHH
Q ss_conf             56113554202202300245565210116677617873489998534157666643578753------310000010001
Q gi|254780454|r  132 LASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIA------KMPSIIVPRKAV  205 (385)
Q Consensus       132 i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~------~~~~~iiP~k~l  205 (385)
                      ..+..|+++++.         ......=+.|++..++.  .+-|.|..|.+...+.++...-      ....+-|..+.+
T Consensus        27 ~~~~~~k~i~~~---------l~~l~~e~~~~~~~~Gi--~i~~mD~s~vali~i~l~~~~F~~Y~~~~~~~igi~~~~l   95 (276)
T 2zvv_A           27 VQGSLLKKVLES---------IKDLVNDANFDCSSTGF--SLQAMDSSHVALVSLLLRSEGFEHYRCDRNLSMGMNLGNM   95 (276)
T ss_dssp             SCTHHHHHHHHH---------HTTTCSEEEEEEETTEE--EEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHHHH
T ss_pred             CCHHHHHHHHHH---------HHHHHCEEEEEEECCEE--EEEEECCCCEEEEEEEECHHHCEEEEECCCEEEEEEHHHH
T ss_conf             676999999999---------99875829999927978--9999988878999999897879088517975899997998


Q ss_pred             HHHHHHCCCCCCCCCCCCCCC--CEEEECC------EEEEEEEECCCCCCCCCCCCC-CCCCCEEEEEHHHHHHHHHHHH
Q ss_conf             222210277646433133455--3010025------069998512665532210135-5566179984899888898874
Q gi|254780454|r  206 GEILRILSSKDSSVKVSLSES--RIHLNIE------SLSMSVRLIDGEFPNYQNVIP-CSNDKELRVNCTNLRQAVDRVS  276 (385)
Q Consensus       206 ~el~k~l~~~~~~v~i~~~~~--~i~~~~~------~~~~~srLi~g~yPdy~~vip-~~~~~~~~v~r~~l~~al~Rv~  276 (385)
                      ..+.|.+.. .+.+.+.+..+  .+.+...      ...+..++++..-.  .--+| .+++..++++-+.|.+.++-+.
T Consensus        96 ~kilk~~~~-~d~l~l~~~~~~~~~~~~~~~~~~~~~~~~~l~l~d~~~~--~~~ip~~~~~~~i~~~S~~f~~~ik~l~  172 (276)
T 2zvv_A           96 SKMLKCAGN-DDIITIKADDGGDTVTFMFESPTQDKIADFEMKLMDIDSE--HLGIPDAEYHSIVRMPSNEFSRICKDLS  172 (276)
T ss_dssp             HHHHHTSCT-TCEEEEEECTTCSEEEEEEECTTSSCEEEEEEECCCEECC--CCCCCCCCCSEEEEEEHHHHHHHHHHHH
T ss_pred             HHHHHHCCC-CCEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCC--CCCCCCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             999874469-9679999943876213677415665167888501345521--1333456776799973799999999874


Q ss_pred             HCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEE------------EECCCCEEEEECHHHHHHHHHHCCCCCCCCC
Q ss_conf             1012355530256517659999807873268999998------------9628843999638899889873575334663
Q gi|254780454|r  277 IMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNV------------YYNECPMDICFNYKYLLEIIDNISSDEVVDD  344 (385)
Q Consensus       277 i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~------------~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e  344 (385)
                      .+.+    .+.+...++.+.+++.+ |.|++.-.+..            ...+++++..|..+||..++++..-    .+
T Consensus       173 ~~~d----~v~i~~~~~~~~~~~~g-d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l----s~  243 (276)
T 2zvv_A          173 SIGD----TVVISVTKEGVKFSTAG-DIGTANIVLRQNTTVDKPEDAIVIEMKEPVSLSFALRYMNSFTKATPL----SD  243 (276)
T ss_dssp             TTCS----EEEEEEETTEEEEEEEE-TTEEEEEEECCCSSCCSGGGCCEEEESSCEEEEEEHHHHHHHGGGGGG----CS
T ss_pred             CCCC----EEEEEECCCEEEEEEEC-CCCEEEEEECCCCCCCCCCCCEECCCCCCEEEEEEHHHHHHHHHHHCC----CC
T ss_conf             3487----69999859803999957-871799998334444564322010358725799978999998725158----98


Q ss_pred             EEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             38999658987589943776544455566763799832
Q gi|254780454|r  345 EVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       345 ~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      .|++++. ...|+.+.-.-++       .....|+|-|
T Consensus       244 ~V~l~~~-~~~Pl~l~~~i~~-------~g~i~f~LAP  273 (276)
T 2zvv_A          244 TVTISLS-SELPVVVEYKVAE-------MGYIRYYLAP  273 (276)
T ss_dssp             EEEEEEC-TTSCEEEEEEETT-------TEEEEEEECC
T ss_pred             EEEEEEE-CCCCEEEEEEECC-------CCEEEEEECC
T ss_conf             7999995-9957899999389-------8099999843


No 19 
>3fds_C DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C*
Probab=98.62  E-value=1.7e-05  Score=51.02  Aligned_cols=208  Identities=16%  Similarity=0.198  Sum_probs=130.0

Q ss_pred             CEEEE-EHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEH
Q ss_conf             95898-599999999987502037888610133899998997999996782--899999977------752680799949
Q gi|254780454|r    1 MKITV-ERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSA   71 (385)
Q Consensus         1 Mk~~i-~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a   71 (385)
                      ||+++ +-+.|.++++..++++         ..+.++...++|.+.+.|..  .-+...++.      +++++-.+.++.
T Consensus         2 ~~~~~~~ak~f~~~i~~l~~i~---------~e~~~~~~~~gl~~~~~D~s~~~l~~~~l~~~~F~~Y~~~~~~~~gi~~   72 (249)
T 3fds_C            2 VKIVYPNAKDFFSFINSITNVT---------DSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDV   72 (249)
T ss_dssp             CEEEESCHHHHHHHHHHHTTTC---------SSEEEEECSSEEEEEEECTTSSEEEEEEEEGGGSSEEECSSCEEEEECH
T ss_pred             EEEEECCHHHHHHHHHHHHHHH---------CCEEEEECCCEEEEEEECCCCEEEEEEEECHHHCEEEECCCCEEEEEEH
T ss_conf             8999578799999999999865---------8099998357489999878818999999386767576068986999889


Q ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC----EEEEECCCCCCC-CCCCCCCCCEEEECCCHHHHHHHCCEEE
Q ss_conf             98778874077777304777336750899986782----024303662114-3212332430450561135542022023
Q gi|254780454|r   72 HLLYDIVRKLQDGAQISFFKENELGTEVNISHGDS----NFYLQSFPESEF-PSTKEEEYVYSFELASSVLKNLVERTHF  146 (385)
Q Consensus        72 ~~l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~~~----~~~l~~~~~~~f-P~~~~~~~~~~~~i~~~~l~~~i~~t~~  146 (385)
                      +.+..++|.+.....+.....++.+..+.+...+.    .|.++.++.+.. |.+|..+....+.+++..|+++++....
T Consensus        73 ~~l~kilk~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~l~~~~~~~~~~p~~~~~~~i~i~s~~f~~~~~~l~~  152 (249)
T 3fds_C           73 SSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTL  152 (249)
T ss_dssp             HHHHHHHTTCCCSCEEEEEEECSSEEEEEEEETTTCCEEEEEEECEECCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCCEEEEECCCCCEEEEEEECCCCEEEEEEEECCCCCHHCCCCCCCCCCEEEEECHHHHHHHHHHHHC
T ss_conf             99999983246664037884179851799995589737999972024532025788766526899648999999875402


Q ss_pred             ECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECC----CCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             0024556521011667761787348999853415766664357----875331000001000122221027764643313
Q gi|254780454|r  147 AMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIV----AQIAKMPSIIVPRKAVGEILRILSSKDSSVKVS  222 (385)
Q Consensus       147 a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~----~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~  222 (385)
                        ..|+       |.+..+++...+.. ..||..-......-.    ...+.+.....+.+.+..+.|.+....+.|.++
T Consensus       153 --~~d~-------v~i~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~l~yl~~~~k~~~~~s~~v~i~  222 (249)
T 3fds_C          153 --VGEE-------MRISTEEDKIKIEA-GEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVS  222 (249)
T ss_dssp             --HCSE-------EEEEEETTEEEEEE-EETTEEEEEEEEETBEESEEEESSCCEEEEEHHHHHHHHHTTTTCCSCEEEE
T ss_pred             --CCCE-------EEEEEECCEEEEEE-ECCCCEEEEEECCCCCEEEEECCCCEEEEEEHHHHHHHHHHHHCCCCEEEEE
T ss_conf             --4978-------99999899999999-0278547999738985157852873113997899999997632148838999


Q ss_pred             CCCCC
Q ss_conf             34553
Q gi|254780454|r  223 LSESR  227 (385)
Q Consensus       223 ~~~~~  227 (385)
                      ++.++
T Consensus       223 ~~~~~  227 (249)
T 3fds_C          223 FGENL  227 (249)
T ss_dssp             ECTTC
T ss_pred             ECCCC
T ss_conf             72999


No 20 
>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2
Probab=98.58  E-value=3.4e-05  Score=49.19  Aligned_cols=217  Identities=13%  Similarity=0.210  Sum_probs=138.4

Q ss_pred             CCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCC------CCCHHCCCCCHHH
Q ss_conf             6113554202202300245565210116677617873489998534157666643578753------3100000100012
Q gi|254780454|r  133 ASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIA------KMPSIIVPRKAVG  206 (385)
Q Consensus       133 ~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~------~~~~~iiP~k~l~  206 (385)
                      ++..|+.+++...         ....=+.|++.+++.  .+-|.|.-|.+.....++...-      ++..+-|+.+.|.
T Consensus         7 ~a~~fk~i~~~l~---------~l~~e~~~~~~~~Gi--~i~~mD~s~v~lv~l~l~~~~F~~Y~~~~~~~igi~~~~l~   75 (245)
T 1ud9_A            7 DVRDLKAIIQALL---------KLVDEALFDIKPEGI--QLVAIDKAHISLIKIELPKEMFKEYDVPEEFKFGFNTQYMS   75 (245)
T ss_dssp             CHHHHHHHHHHHH---------HHCSEEEEEEETTEE--EEEEECTTSSEEEEEEEEGGGSSEEECSSCEEEEEEHHHHH
T ss_pred             CHHHHHHHHHHHH---------HHHCEEEEEEECCEE--EEEEECCCCEEEEEEEECHHHCCCCCCCCCEEEEEEHHHHH
T ss_conf             8899999999999---------875459999808967--99999787589999998878793104577789899989988


Q ss_pred             HHHHHCCCCCCCCCCCCCCCC-EEEEC--C-EEEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCC
Q ss_conf             222102776464331334553-01002--5-0699985126655322101355-56617998489988889887410123
Q gi|254780454|r  207 EILRILSSKDSSVKVSLSESR-IHLNI--E-SLSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSV  281 (385)
Q Consensus       207 el~k~l~~~~~~v~i~~~~~~-i~~~~--~-~~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~  281 (385)
                      .+.|.... ++.+++..++.. +.+..  + +..+...+++..-++..  +|+ +++..++++-..|.+.++.++.+++ 
T Consensus        76 kilk~~~~-~d~l~l~~~~~~~l~~~~~~~~~~~~~l~~id~~~~~~~--~p~~e~~~~i~~~s~~f~~~~~~l~~~~d-  151 (245)
T 1ud9_A           76 KLLKAAKR-KEEIIIDADSPEVVKLTLSGALNRVFNVNNIEVLPPEVP--EVNLEFDIKATINASGLKNAIGEIAEVAD-  151 (245)
T ss_dssp             HHHTTCCS-CCCEEEEEEETTEEEEEECSSSCEEEEEECCCCCCCCCC-----CCCSEEEEEEHHHHHHHHHHHHHHCS-
T ss_pred             HHHHHCCC-CCEEEEEECCCCCEEEEEEECCCEEEEECCCCCCCCCCC--CCCCCCCEEEEEEHHHHHHHHHHHHCCCC-
T ss_conf             88851689-967999965897059999823335897033234544577--77767667999789999999988743486-


Q ss_pred             CCCCCEEEEECCEEEEEECCCCCEEEEEEE--------EEEECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             555302565176599998078732689999--------989628843999638899889873575334663389996589
Q gi|254780454|r  282 RIQAVKLSLSSDKLCMTVDNPDMGKAIESM--------NVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSS  353 (385)
Q Consensus       282 ~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i--------~~~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~  353 (385)
                         .+.+..+++++.+++.+.  |.....+        .++ .+++.+..|..+||..+.++..-    .+.|++++. +
T Consensus       152 ---~i~i~~~~~~i~~~~~gd--~~~~~~~~~~~~~~~~~~-~~~~~~~~fsl~yl~~~~k~~~l----s~~V~i~~~-~  220 (245)
T 1ud9_A          152 ---TLLISGNEEKVVVKGEGE--NKVEVEFSKDTGSLADIE-FNKESSSAYDVEYLNDIISLTKL----SDYVKVAFA-D  220 (245)
T ss_dssp             ---EEEEEECSSEEEEEESSS--SCCCEEEEGGGTCEEEEE-ESSCEEEEEEHHHHHHTGGGGGG----CSEEEEEEC-T
T ss_pred             ---EEEEEEECCEEEEEEECC--CCEEEEECCCCCCEEEEE-EECCCCEEEHHHHHHHHHHHCCC----CCEEEEEEC-C
T ss_conf             ---799999578799997147--522689806898416888-70322246468789999843468----986999974-9


Q ss_pred             CCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             87589943776544455566763799832
Q gi|254780454|r  354 NSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       354 ~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      ..|+.+.-.-++       ...-.|.|-|
T Consensus       221 ~~Pl~l~y~~~~-------~g~i~f~LAP  242 (245)
T 1ud9_A          221 QKPMQLEFNMEG-------GGKVTYLLAP  242 (245)
T ss_dssp             TSCEEEEEECGG-------GCEEEEEECC
T ss_pred             CCCEEEEEEECC-------CEEEEEEEEC
T ss_conf             977899999489-------7699999903


No 21 
>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity factor; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3l0x_B
Probab=98.52  E-value=1.6e-05  Score=51.24  Aligned_cols=210  Identities=15%  Similarity=0.163  Sum_probs=129.9

Q ss_pred             CEEEE-EHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEH
Q ss_conf             95898-599999999987502037888610133899998997999996782--899999977------752680799949
Q gi|254780454|r    1 MKITV-ERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSA   71 (385)
Q Consensus         1 Mk~~i-~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a   71 (385)
                      |+++. +-+.|...++.+++++         ..+.+++..+++.+.|.|..  .-+...+++      +++++-.+.|+-
T Consensus         2 fe~~~~~a~~fk~i~~~l~~l~---------~e~~~~~~~~Gi~i~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~~gi~~   72 (258)
T 1plq_A            2 LEAKFEEASLFKRIIDGFKDCV---------QLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDL   72 (258)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTC---------SEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEECCSSCEEEEEEH
T ss_pred             CEEEECCHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEH
T ss_conf             0899667699999999998876---------5399999389789999989978999999888989265268668999998


Q ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCEEEEE--EECC----CEEEEECCCCC-CCCCCCCCCCCEEEECCCHHHHHHHCCE
Q ss_conf             987788740777773047773367508999--8678----20243036621-1432123324304505611355420220
Q gi|254780454|r   72 HLLYDIVRKLQDGAQISFFKENELGTEVNI--SHGD----SNFYLQSFPES-EFPSTKEEEYVYSFELASSVLKNLVERT  144 (385)
Q Consensus        72 ~~l~~iik~L~~~~~i~~~~~~~~~~~i~i--~~~~----~~~~l~~~~~~-~fP~~~~~~~~~~~~i~~~~l~~~i~~t  144 (385)
                      +.|..++|.+..+..+.+..+++. ..+.+  .+.+    .+|.++.++.+ +-+.+|..+....+.+++..|+++++..
T Consensus        73 ~~l~kilk~~~~~d~l~l~~~~~~-~~l~~~~~~~~~~~~~~~~l~l~d~~~~~~~ip~~~~~~~i~~~s~~f~~~~k~l  151 (258)
T 1plq_A           73 TSLSKILRCGNNTDTLTLIADNTP-DSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDL  151 (258)
T ss_dssp             HHHHHHTTCSTTTSEEEEEECSSC-SEEEEEEECSSSSCEEEEEEECBCCCCCCCCCCCSCCSEEEEEEHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCEEEEEEECCC-CEEEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHH
T ss_conf             998999861478867999995588-7169999558876379999733678721246887676468997599999999987


Q ss_pred             EEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCC-----------CCCCCCHHCCCCCHHHHHHHHCC
Q ss_conf             2300245565210116677617873489998534157666643578-----------75331000001000122221027
Q gi|254780454|r  145 HFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA-----------QIAKMPSIIVPRKAVGEILRILS  213 (385)
Q Consensus       145 ~~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~-----------~~~~~~~~iiP~k~l~el~k~l~  213 (385)
                      .- .+ |       -|.+...++...+.+-+ |.-+. ...+....           ..........+.+.|..+.|...
T Consensus       152 ~~-~~-d-------~i~i~~~~~~~~f~~~g-d~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~  220 (258)
T 1plq_A          152 SQ-LS-D-------SINIMITKETIKFVADG-DIGSG-SVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSS  220 (258)
T ss_dssp             HT-TC-S-------EEEEEEETTEEEEEEEC-SSCEE-EEEECCBCCTTCGGGCBEEEESSCEEEEEEHHHHHHHGGGGG
T ss_pred             HH-HC-C-------EEEEEECCCCEEEEEEE-CCCEE-EEEEECCCCCCCCCCEEEEECCCCEEEEEEHHHHHHHHHHCC
T ss_conf             71-38-8-------79999858830899980-36438-999803566677542046522771348995899999872525


Q ss_pred             CCCCCCCCCCCCCC-EEEEC
Q ss_conf             76464331334553-01002
Q gi|254780454|r  214 SKDSSVKVSLSESR-IHLNI  232 (385)
Q Consensus       214 ~~~~~v~i~~~~~~-i~~~~  232 (385)
                      - .+.|+++++.+. +.|.+
T Consensus       221 l-s~~v~i~~~~~~Pl~~~~  239 (258)
T 1plq_A          221 L-SDRVGIRLSSEAPALFQF  239 (258)
T ss_dssp             T-CSEEEEEECSSSCEEEEE
T ss_pred             C-CCEEEEEEECCCCEEEEE
T ss_conf             7-988999982896689999


No 22 
>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}
Probab=98.47  E-value=2.9e-05  Score=49.63  Aligned_cols=130  Identities=18%  Similarity=0.206  Sum_probs=71.4

Q ss_pred             EEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEEC-CEEEEEECCCC----CEE-EEE
Q ss_conf             9985126655322101355-5661799848998888988741012355530256517-65999980787----326-899
Q gi|254780454|r  237 MSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSS-DKLCMTVDNPD----MGK-AIE  309 (385)
Q Consensus       237 ~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~-~~l~i~~~~~e----~g~-~~e  309 (385)
                      +.-++++...  -+..+|+ ++++.+.++-+.|.+.++-+....++    |.+..++ +.+.+++....    .++ ..-
T Consensus       122 ~~l~l~d~e~--~~~~~~~~~~~~~i~i~s~~~~~~l~~~~~~~ee----iti~~~~~~~~~~~s~~~~~~~~~~~~~~t  195 (296)
T 3g65_A          122 HNLSFQDCES--LQAVFDPASCPHMLRAPARVLGEAVLPFSPALAE----VTLGIGRGRRVILRSYHEEEADSTAKAMVT  195 (296)
T ss_dssp             EEECCCCCCC--CCCCCCGGGCSCEEEEEHHHHHHHSTTSCTTCCE----EEEEEETTTEEEEEECCC-----CCCCCEE
T ss_pred             EEEEEECCCC--CCCCCCHHHCCEEEEECHHHHHHHHHHCCCCCCE----EEEEECCCCEEEEEECCCCCCCCCCCEEEE
T ss_conf             9966543563--3466784468689997579999999854145567----999977998599995356766655412588


Q ss_pred             EEEE------EE-CCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             9998------96-2884399963889988987357533466338999658987589943776544455566763799832
Q gi|254780454|r  310 SMNV------YY-NECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMP  382 (385)
Q Consensus       310 ~i~~------~~-~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMP  382 (385)
                      ++.+      .| -+++..+.|+-+||..+++..++-   ...|.++|..|.+|+++..+...        ....+++||
T Consensus       196 ~v~i~~~e~~~~~v~e~~~itfslk~~k~il~~a~~~---~~~v~i~f~~pg~Pi~~~~~~~~--------~~~~fvlaT  264 (296)
T 3g65_A          196 EMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAESA---NLNLSIHFDAPGRPAIFTIKDSL--------LDGHFVLAT  264 (296)
T ss_dssp             EEEECGGGCSEEECCTTCEEEEEHHHHHHHHHHHHHT---TCEEEEECCSTTSCEEEEEECSS--------CEEEEEECC
T ss_pred             EEEECCCCEEEEECCCCCEEEEEHHHHHHHHHHHHHC---CCCEEEEECCCCCCEEEEEECCC--------EEEEEEEEC
T ss_conf             8753566403798389928999999999999998756---98289998789977899995795--------899999944


Q ss_pred             E
Q ss_conf             1
Q gi|254780454|r  383 M  383 (385)
Q Consensus       383 v  383 (385)
                      +
T Consensus       265 ~  265 (296)
T 3g65_A          265 L  265 (296)
T ss_dssp             C
T ss_pred             C
T ss_conf             6


No 23 
>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotrimer, DNA binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C*
Probab=98.44  E-value=6.9e-05  Score=47.33  Aligned_cols=204  Identities=14%  Similarity=0.191  Sum_probs=125.2

Q ss_pred             CEEEE-EHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEH
Q ss_conf             95898-599999999987502037888610133899998997999996782--899999977------752680799949
Q gi|254780454|r    1 MKITV-ERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSA   71 (385)
Q Consensus         1 Mk~~i-~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a   71 (385)
                      ||+.. +-+.|...++.+++++         ..+.+++..+++.+.+.|..  .-+...++.      +++++-.+.|+-
T Consensus         1 m~~~~~~~~~fk~i~~~l~~l~---------~e~~~~~~~~Gi~i~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~igi~~   71 (244)
T 2ijx_A            1 MKVVYDDVRVLKDIIQALARLV---------DEAVLKFKQDSVELVALDRAHISLISVNLPREMFKEYDVNDEFKFGFNT   71 (244)
T ss_dssp             CEEEESCHHHHHHHHHHHHHHC---------SEEEEEECSSEEEEEEECTTSSEEEEEEEEGGGCSEEECSSCEEEEEEH
T ss_pred             CEEEECCHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCCEECCCCCEEEEEEH
T ss_conf             9799857899999999999875---------8299999389789999989968999999887769333237777989999


Q ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEC--CCEEEEECCCCCCCC-CCCCCCCCEEEECCCHHHHHHHCCEEEEC
Q ss_conf             987788740777773047773367508999867--820243036621143-21233243045056113554202202300
Q gi|254780454|r   72 HLLYDIVRKLQDGAQISFFKENELGTEVNISHG--DSNFYLQSFPESEFP-STKEEEYVYSFELASSVLKNLVERTHFAM  148 (385)
Q Consensus        72 ~~l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~--~~~~~l~~~~~~~fP-~~~~~~~~~~~~i~~~~l~~~i~~t~~a~  148 (385)
                      +.|..++|.+.++..+.+..+++. ..+....+  ...|.++.++.+..+ ..|..+....+.+++..|+++++...- .
T Consensus        72 ~~l~kilk~~~~~d~l~l~~~~~~-~~~i~~~~~~~~~~~l~l~d~~~~~~~~p~~~~~~~i~~~s~~f~~~ik~l~~-~  149 (244)
T 2ijx_A           72 QYLMKILKVAKRKEAIEIASESPD-SVIINIIGSTNREFNVRNLEVSEQEIPEINLQFDISATISSDGFKSAISEVST-V  149 (244)
T ss_dssp             HHHHHHHTTCCSSCEEEEEEEETT-EEEEEEESSSEEEEEEECCCCCCCCCCCCCCCCSEEEEEEHHHHHHHHHHHTT-T
T ss_pred             HHHHHHHHCCCCCCEEEEEEECCC-CEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHH-C
T ss_conf             999999844688974999993598-54999706742799961356653568998866637998249999999999872-1


Q ss_pred             CCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCC------CCCCCHHCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf             2455652101166776178734899985341576666435787------5331000001000122221027764643313
Q gi|254780454|r  149 ATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQ------IAKMPSIIVPRKAVGEILRILSSKDSSVKVS  222 (385)
Q Consensus       149 s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~------~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~  222 (385)
                      + |.       +.+..+++...+.   ++|.-=+......+..      ...+.....+.+.+..+.|...- .+.|++.
T Consensus       150 ~-d~-------i~i~~~~~~i~f~---~~gd~~~~~~~~~~~~~~~~~~~~~~~~~~fs~~yl~~~~k~~~l-s~~v~i~  217 (244)
T 2ijx_A          150 T-DN-------VVVEGHEDRILIK---AEGESEVEVEFSKDTGGLQDLEFSKESKNSYSAEYLDDVLSLTKL-SDYVKIS  217 (244)
T ss_dssp             C-SE-------EEEEEETTEEEEE---ETTCTTSEEEEETTTTCEEEEEESSCEEEEEEHHHHHHTGGGGGG-CSEEEEE
T ss_pred             C-CE-------EEEEEECCEEEEE---EECCCCEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCC-CCEEEEE
T ss_conf             9-87-------9999937569999---973761479980589860788750332453138999998714368-9869999


Q ss_pred             CCCCC
Q ss_conf             34553
Q gi|254780454|r  223 LSESR  227 (385)
Q Consensus       223 ~~~~~  227 (385)
                      ++.++
T Consensus       218 ~~~~~  222 (244)
T 2ijx_A          218 FGNQK  222 (244)
T ss_dssp             EETTE
T ss_pred             ECCCC
T ss_conf             74997


No 24 
>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A
Probab=98.44  E-value=1.6e-05  Score=51.24  Aligned_cols=209  Identities=17%  Similarity=0.163  Sum_probs=125.8

Q ss_pred             CEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCC----------HHCCCCCHHHHHHHHCCCCC---CCCCCC
Q ss_conf             10116677617873489998534157666643578753310----------00001000122221027764---643313
Q gi|254780454|r  156 YLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMP----------SIIVPRKAVGEILRILSSKD---SSVKVS  222 (385)
Q Consensus       156 ~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~----------~~iiP~k~l~el~k~l~~~~---~~v~i~  222 (385)
                      +...++|++..++  |.+.|.|..|.|...+.++...-+..          .+-++.|.+..+.|-+...+   ..+.+.
T Consensus        23 i~~ev~~~~~~~g--l~l~a~d~s~~al~~~~l~~~~F~~Y~~~~~~~~~~~~~v~~k~l~~ilk~~~~~~~~~~~~~l~  100 (266)
T 3a1j_A           23 IGDELYLEPLEDG--LSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCIS  100 (266)
T ss_dssp             TCSEEEEEEETTE--EEEEEECTTSCEEEEEEECGGGSSEEECCCSSSCCCCEEEEHHHHHHHHCCHHHHHHHEEEEEEE
T ss_pred             HCCEEEEEEECCE--EEEEEECCCCEEEEEEEECHHHCCEEECCCCCCCCEEEEEEHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             4182999994785--89999998887999999876747278756888755798764899999862012467642399999


Q ss_pred             CCC--CCEEEEC--CE---EEEEEEECCCCCCCCCCCCCC-CCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEEC-C
Q ss_conf             345--5301002--50---699985126655322101355-5661799848998888988741012355530256517-6
Q gi|254780454|r  223 LSE--SRIHLNI--ES---LSMSVRLIDGEFPNYQNVIPC-SNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSS-D  293 (385)
Q Consensus       223 ~~~--~~i~~~~--~~---~~~~srLi~g~yPdy~~vip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~-~  293 (385)
                      .++  +.+.+.+  .+   ..+.-+|++..-.  +-.+|+ +++..+.++-..|.+.++.+..++++    |.+..++ +
T Consensus       101 ~~~~~~~l~i~~~~~~~~~k~~~l~l~d~~~~--~~~~p~~~~~~~i~~~s~~f~~~~~~~~~~~d~----i~i~~~~~~  174 (266)
T 3a1j_A          101 LNGRSSRLVVQLHCKFGVRKTHNLSFQDCESL--QAVFDPASCPHMLRAPARVLGEAVLPFSPALAE----VTLGIGRGR  174 (266)
T ss_dssp             CCTTCSEEEEEEEEGGGCEEEEEEECEECCCC--CCCCCGGGCSEEEEEEHHHHHHHHTTSCTTCCE----EEEEECGGG
T ss_pred             ECCCCCEEEEEEECCCCCEEEEEEEECCCCCC--CCCCCCCCCCEEEEECHHHHHHHHHHHHHCCCE----EEEEECCCC
T ss_conf             64898559999905788179999653046644--577880008679997689999999975503877----999987998


Q ss_pred             EEEEEECCCCCE-----EEEEEEEE------EE-CCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEEC
Q ss_conf             599998078732-----68999998------96-2884399963889988987357533466338999658987589943
Q gi|254780454|r  294 KLCMTVDNPDMG-----KAIESMNV------YY-NECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRG  361 (385)
Q Consensus       294 ~l~i~~~~~e~g-----~~~e~i~~------~~-~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~  361 (385)
                      .+.+++.....+     ..+.++..      .| .+++..+.|+-+||..+++..++-   ...|.+++..+.+|+++.-
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~fslkyl~~~~~~a~~~---~~~v~i~~~~~g~Pl~~~~  251 (266)
T 3a1j_A          175 RVILRSYHEEEADSTAKAMVTEMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAESA---NLNLSIHFDAPGRPAIFTI  251 (266)
T ss_dssp             CEEEEEECCC-CCCSCCCCEEEEEECGGGCSEEECCTTCEEEEEHHHHHHHHHHHHHT---TCEEEEEECSTTSCEEEEE
T ss_pred             EEEEEEECCCCCCCCCCEEEEEECCCCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHC---CCEEEEEECCCCCCEEEEE
T ss_conf             4999985146665554114565405843127995389739999999999999998735---9859999889998789999


Q ss_pred             CCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             7765444555667637998321
Q gi|254780454|r  362 KDKDSKNNKDNKVNAFYVLMPM  383 (385)
Q Consensus       362 ~~~~~~~~~~~~~~~~~liMPv  383 (385)
                      ..+..        ...|++++|
T Consensus       252 ~~~~~--------~~~f~lAtl  265 (266)
T 3a1j_A          252 KDSLL--------DGHFVLATL  265 (266)
T ss_dssp             ECSSE--------EEEEEECCC
T ss_pred             ECCCE--------EEEEEEEEC
T ss_conf             65977--------999999977


No 25 
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A
Probab=98.41  E-value=3.2e-05  Score=49.35  Aligned_cols=203  Identities=14%  Similarity=0.207  Sum_probs=128.7

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEHH
Q ss_conf             95898599999999987502037888610133899998997999996782--899999977------7526807999499
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSAH   72 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a~   72 (385)
                      +|.+++-+.|...++.++++++.         +.+++.++++.++|.|..  .-+...++.      +++++ .+.|+-.
T Consensus         2 ~~~~~~a~~~k~i~~~l~~l~~e---------~~~~~~~~Gi~i~~mD~shv~Lv~l~l~~~~F~~Y~~d~~-~igv~~~   71 (247)
T 3ifv_A            2 FKAIVSAATLRDALDSVSVLVDE---------CKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGG-VIGVNLS   71 (247)
T ss_dssp             CCEEECHHHHHHHHHHHHTTCSS---------EEEC---CEEEEEEECTTSSEEEEEEEEGGGSSBC------CEEECHH
T ss_pred             EEEEECHHHHHHHHHHHHHHHCE---------EEEEECCCEEEEEEECCCCEEEEEEEECHHHCCEEEECCC-EEEEEHH
T ss_conf             69997299999999999987542---------8999917847999997873799999988786978981285-8999989


Q ss_pred             HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCC---CCCCCCCCCCCEEEECCCHHHHHHHCCEEEECC
Q ss_conf             87788740777773047773367508999867820243036621---143212332430450561135542022023002
Q gi|254780454|r   73 LLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPES---EFPSTKEEEYVYSFELASSVLKNLVERTHFAMA  149 (385)
Q Consensus        73 ~l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~---~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s  149 (385)
                      .|..++|.+..+..+.+..+++ ...+.++.++.++.+...+.+   +-|.+|+.+....+.+++..|+++++...-- +
T Consensus        72 ~l~kilk~~~~~d~l~l~~~~~-~~~l~i~~~~~~~~~~l~~i~~~~~~~~iP~~~~~~~i~~~s~~f~~~~~~l~~~-~  149 (247)
T 3ifv_A           72 RLEEVAGMAGAGDLIHLTLDEE-TRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMV-S  149 (247)
T ss_dssp             HHHHHHTTC----CEEECC--------EEEETTEEEEC---CTTC----CCCCCCCCSEEEEEEHHHHHHHHHHHHHH-C
T ss_pred             HHHHHHHHCCCCCEEEEEECCC-CCEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHCC-C
T ss_conf             9999997317994799999279-9878999723068998453543222568888664389994089988776676436-9


Q ss_pred             CCCCCCCEEEEEEEECCCCCEEEEEEECC-EEEEEEEEECCCCC-----CCCCHHCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             45565210116677617873489998534-15766664357875-----3310000010001222210277646433133
Q gi|254780454|r  150 TEEIRYYLNGIFFHINEEDLKLCAVATDG-HRLAVAEVDIVAQI-----AKMPSIIVPRKAVGEILRILSSKDSSVKVSL  223 (385)
Q Consensus       150 ~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg-~RLa~~~~~~~~~~-----~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~  223 (385)
                       |       -+.+..+.+...+.+.+..+ .+.   ....+...     ..+....-+.+.|..+.|...- .+.|++++
T Consensus       150 -d-------~i~i~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~fsl~Yl~~~~k~~~l-s~~V~i~~  217 (247)
T 3ifv_A          150 -D-------HIRLRVDGAEETFHIEAEGDTDDV---DLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPT-DAEVTVEL  217 (247)
T ss_dssp             -S-------EEEEEEETTTTEEEEEEECSSCEE---EEEECGGGCSEEEECCCEEEEEHHHHHHHHHHSCT-TCEEEEEE
T ss_pred             -C-------EEEEEEEECEEEEEEEEECCEEEE---EEEECCCCCEEEEECCCCCEEEHHHHHHHHHHCCC-CCEEEEEE
T ss_conf             -8-------699999803459999951562799---99848986168850444528878999988744468-98699997


Q ss_pred             CCCC
Q ss_conf             4553
Q gi|254780454|r  224 SESR  227 (385)
Q Consensus       224 ~~~~  227 (385)
                      +.++
T Consensus       218 ~~~~  221 (247)
T 3ifv_A          218 GEEF  221 (247)
T ss_dssp             CBSS
T ss_pred             CCCC
T ss_conf             6997


No 26 
>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A
Probab=98.34  E-value=0.00014  Score=45.47  Aligned_cols=204  Identities=14%  Similarity=0.211  Sum_probs=123.7

Q ss_pred             CEEEE---EHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEE
Q ss_conf             95898---599999999987502037888610133899998997999996782--899999977------7526807999
Q gi|254780454|r    1 MKITV---ERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITV   69 (385)
Q Consensus         1 Mk~~i---~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v   69 (385)
                      |+|.+   +-+.|..+++.++++         ...+.+++..++|.+++.|..  .-+...++.      +++++-.+.|
T Consensus         1 M~f~~~~~~~~~f~~ii~~l~~~---------~~e~~~~~~~~Gl~i~~~d~s~v~l~~l~l~~~~F~~Y~~~~~~~~gi   71 (249)
T 1iz5_A            1 MPFEIVFEGAKEFAQLIDTASKL---------IDEAAFKVTEDGISMRAMDPSRVVLIDLNLPSSIFSKYEVVEPETIGV   71 (249)
T ss_dssp             -CEEEEEECHHHHHHHHHHHTSS---------CSEEEEEECSSEEEEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEE
T ss_pred             CEEEEEECCHHHHHHHHHHHHHH---------HCEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCCEECCCCCEEEEE
T ss_conf             92899935689999999999987---------584999997896899999898789999998988794654588889999


Q ss_pred             EHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEE--CCC-EEEEECCCCCC-CCCCCCCCCCEEEECCCHHHHHHHCCEE
Q ss_conf             4998778874077777304777336750899986--782-02430366211-4321233243045056113554202202
Q gi|254780454|r   70 SAHLLYDIVRKLQDGAQISFFKENELGTEVNISH--GDS-NFYLQSFPESE-FPSTKEEEYVYSFELASSVLKNLVERTH  145 (385)
Q Consensus        70 ~a~~l~~iik~L~~~~~i~~~~~~~~~~~i~i~~--~~~-~~~l~~~~~~~-fP~~~~~~~~~~~~i~~~~l~~~i~~t~  145 (385)
                      +.+.|..++|.+.....+.+..+++  +.+.+..  +.. .|.++.++.+. -+.+|..+....+.+++..|+++++...
T Consensus        72 ~~~~L~kilk~~~~~d~l~~~~~~~--~~l~i~~~~~~~~~~~i~l~~~~~~~~~ip~~~~~~~i~~~s~~f~~i~~~l~  149 (249)
T 1iz5_A           72 NLDHLKKILKRGKAKDTLILKKGEE--NFLEITIQGTATRTFRVPLIDVEEMEVDLPELPFTAKVVVLGEVLKAAVKAAS  149 (249)
T ss_dssp             EHHHHHHHHTTCCTTCEEEEEECSS--SEEEEEEESSSEEEEEEECBCCCC-----CCCCCCEEEEEEHHHHHHHHHHHT
T ss_pred             EHHHHHHHHHCCCCCCEEEEEECCC--CEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             9699899984368996699995588--62799995351279998603345334678887765499724999999998750


Q ss_pred             EECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCC------CCCCCHHCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             3002455652101166776178734899985341576666435787------5331000001000122221027764643
Q gi|254780454|r  146 FAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQ------IAKMPSIIVPRKAVGEILRILSSKDSSV  219 (385)
Q Consensus       146 ~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~------~~~~~~~iiP~k~l~el~k~l~~~~~~v  219 (385)
                      - .+ |.       |.+...++...+...+ |+-+. ...+.....      ...........+.|..+.|...- .+.|
T Consensus       150 ~-~~-d~-------i~i~~~~~~i~~~s~g-d~~~~-~~~~~~~~~~~~~~~~~~~~~~~f~~~yl~~~~k~~~l-s~~v  217 (249)
T 1iz5_A          150 L-VS-DS-------IKFIARENEFIMKAEG-ETQEV-EIKLTLEDEGLLDIEVQEETKSAYGVSYLSDMVKGLGK-ADEV  217 (249)
T ss_dssp             T-TC-SE-------EEEEEETTEEEEEEEC-SSCEE-EEEEETTTTSSSEEEESSCEEEEEEHHHHHHHHTTSCT-TCEE
T ss_pred             C-CC-CE-------EEEEECCCEEEEEEEC-CCCEE-EEEEECCCCCCEEEECCCCCCEEEHHHHHHHHHHHCCC-CCEE
T ss_conf             1-59-88-------9999938838999963-66558-99982167640456507750036638899999875368-9859


Q ss_pred             CCCCCCCC
Q ss_conf             31334553
Q gi|254780454|r  220 KVSLSESR  227 (385)
Q Consensus       220 ~i~~~~~~  227 (385)
                      +++++++.
T Consensus       218 ~l~~~~~~  225 (249)
T 1iz5_A          218 TIKFGNEM  225 (249)
T ss_dssp             EEEECTTC
T ss_pred             EEEECCCC
T ss_conf             99974997


No 27 
>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A
Probab=98.31  E-value=6.7e-05  Score=47.42  Aligned_cols=206  Identities=10%  Similarity=0.125  Sum_probs=122.2

Q ss_pred             CEEEEE-HHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEH
Q ss_conf             958985-99999999987502037888610133899998997999996782--899999977------752680799949
Q gi|254780454|r    1 MKITVE-RSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSA   71 (385)
Q Consensus         1 Mk~~i~-~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a   71 (385)
                      |+++.. -+.|.+.++.+++++         ..+.+++..+++.+++.|..  .-+...++.      +++++-.+.|+-
T Consensus        22 ~~~~~~~~~~~k~i~~~l~~l~---------~e~~~~~~~~Gi~i~~mD~s~vali~i~l~~~~F~~Y~~~~~~~igi~~   92 (276)
T 2zvv_A           22 LELRLVQGSLLKKVLESIKDLV---------NDANFDCSSTGFSLQAMDSSHVALVSLLLRSEGFEHYRCDRNLSMGMNL   92 (276)
T ss_dssp             EEEEESCTHHHHHHHHHHTTTC---------SEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEH
T ss_pred             EEEEECCHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCEEEEECCCEEEEEEH
T ss_conf             9999767699999999999875---------8299999279789999988878999999897879088517975899997


Q ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCEEEEE-EECC----CEEEEECCCCC-CCCCCCCCCCCEEEECCCHHHHHHHCCEE
Q ss_conf             987788740777773047773367508999-8678----20243036621-14321233243045056113554202202
Q gi|254780454|r   72 HLLYDIVRKLQDGAQISFFKENELGTEVNI-SHGD----SNFYLQSFPES-EFPSTKEEEYVYSFELASSVLKNLVERTH  145 (385)
Q Consensus        72 ~~l~~iik~L~~~~~i~~~~~~~~~~~i~i-~~~~----~~~~l~~~~~~-~fP~~~~~~~~~~~~i~~~~l~~~i~~t~  145 (385)
                      +.|..++|.+..+..+.+...++....+.+ ...+    ..|.++.++.+ +-+.+|..+....+.+++..|+++++...
T Consensus        93 ~~l~kilk~~~~~d~l~l~~~~~~~~~~~~~~~~~~~~~~~~~l~l~d~~~~~~~ip~~~~~~~i~~~S~~f~~~ik~l~  172 (276)
T 2zvv_A           93 GNMSKMLKCAGNDDIITIKADDGGDTVTFMFESPTQDKIADFEMKLMDIDSEHLGIPDAEYHSIVRMPSNEFSRICKDLS  172 (276)
T ss_dssp             HHHHHHHHTSCTTCEEEEEECTTCSEEEEEEECTTSSCEEEEEEECCCEECCCCCCCCCCCSEEEEEEHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             99899987446996799999438762136774156651678885013455211333456776799973799999999874


Q ss_pred             EECCCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCC-----------CCCCCHHCCCCCHHHHHHHHCCC
Q ss_conf             3002455652101166776178734899985341576666435787-----------53310000010001222210277
Q gi|254780454|r  146 FAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQ-----------IAKMPSIIVPRKAVGEILRILSS  214 (385)
Q Consensus       146 ~a~s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~-----------~~~~~~~iiP~k~l~el~k~l~~  214 (385)
                       ..+ |.       |.+...++...+..- .|.-+. ...+.....           .........+.+.|..+.|...-
T Consensus       173 -~~~-d~-------v~i~~~~~~~~~~~~-gd~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l  241 (276)
T 2zvv_A          173 -SIG-DT-------VVISVTKEGVKFSTA-GDIGTA-NIVLRQNTTVDKPEDAIVIEMKEPVSLSFALRYMNSFTKATPL  241 (276)
T ss_dssp             -TTC-SE-------EEEEEETTEEEEEEE-ETTEEE-EEEECCCSSCCSGGGCCEEEESSCEEEEEEHHHHHHHGGGGGG
T ss_pred             -CCC-CE-------EEEEECCCEEEEEEE-CCCCEE-EEEECCCCCCCCCCCCEECCCCCCEEEEEEHHHHHHHHHHHCC
T ss_conf             -348-76-------999985980399995-787179-9998334444564322010358725799978999998725158


Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             6464331334553
Q gi|254780454|r  215 KDSSVKVSLSESR  227 (385)
Q Consensus       215 ~~~~v~i~~~~~~  227 (385)
                       .+.|+++++.+.
T Consensus       242 -s~~V~l~~~~~~  253 (276)
T 2zvv_A          242 -SDTVTISLSSEL  253 (276)
T ss_dssp             -CSEEEEEECTTS
T ss_pred             -CCEEEEEEECCC
T ss_conf             -987999995995


No 28 
>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A*
Probab=98.26  E-value=0.00012  Score=45.80  Aligned_cols=201  Identities=10%  Similarity=0.123  Sum_probs=123.9

Q ss_pred             EEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEHHHHHH
Q ss_conf             8599999999987502037888610133899998997999996782--899999977------75268079994998778
Q gi|254780454|r    5 VERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSAHLLYD   76 (385)
Q Consensus         5 i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a~~l~~   76 (385)
                      .+-+.|...++.+++++         ..+.+++..+++.+.+.|..  .-+...++.      +++++-.+.|+.+.|..
T Consensus         7 ~~a~~fk~i~~~l~~l~---------~e~~~~~~~~Gi~i~~mD~s~v~li~~~l~~~~F~~y~~~~~~~igi~~~~l~k   77 (261)
T 1u7b_A            7 VQGSILKKVLEALKDLI---------NEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSK   77 (261)
T ss_dssp             SCTHHHHHHHHHHHTTC---------SEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEEEESSCEEEEEEHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCEEECCCCCEEEEEEHHHHHH
T ss_conf             56799999999999875---------639999908968999998887899999989788905055776899999999999


Q ss_pred             HHHCCCCCCCEEEEEECCCCEEEE--EEECC----CEEEEECCCCCC-CCCCCCCCCCEEEECCCHHHHHHHCCEEEECC
Q ss_conf             874077777304777336750899--98678----202430366211-43212332430450561135542022023002
Q gi|254780454|r   77 IVRKLQDGAQISFFKENELGTEVN--ISHGD----SNFYLQSFPESE-FPSTKEEEYVYSFELASSVLKNLVERTHFAMA  149 (385)
Q Consensus        77 iik~L~~~~~i~~~~~~~~~~~i~--i~~~~----~~~~l~~~~~~~-fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s  149 (385)
                      ++|.+..+..+.+..+++. ..+.  +.++.    .+|+++.++.+. -+.+|..+....+.+++..|+++++...-- +
T Consensus        78 ilk~~~~~d~l~l~~~~~~-~~l~i~~~~~~~~~~~~f~l~l~d~~~~~~~ip~~~~~~~i~~~s~~f~~~~~~l~~~-~  155 (261)
T 1u7b_A           78 ILKCAGNEDIITLRAEDNA-DTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHI-G  155 (261)
T ss_dssp             HHTTSCTTCEEEEEECTTC-SEEEEEEECTTSSCEEEEEEECCCCCCCCCBCCCCCCSEEEEEEHHHHHHHHHHHHTT-C
T ss_pred             HHHHCCCCCEEEEEECCCC-CCEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHC-C
T ss_conf             9963558954999983688-7169999806876226898740346600125787775589995089999999999742-8


Q ss_pred             CCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCC-----------CCCCCCHHCCCCCHHHHHHHHCCCCCCC
Q ss_conf             45565210116677617873489998534157666643578-----------7533100000100012222102776464
Q gi|254780454|r  150 TEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA-----------QIAKMPSIIVPRKAVGEILRILSSKDSS  218 (385)
Q Consensus       150 ~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~-----------~~~~~~~~iiP~k~l~el~k~l~~~~~~  218 (385)
                       |.       +.+...++...+.+-+ |+-+. ...+.-..           ...+......+.+.|..+.|...- .+.
T Consensus       156 -d~-------v~i~~~~~~~~~~~~g-d~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l-s~~  224 (261)
T 1u7b_A          156 -DA-------VVISCAKDGVKFSASG-ELGNG-NIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPL-SST  224 (261)
T ss_dssp             -SE-------EEEEEETTEEEEEEEE-TTEEE-EEEECCCC----CCSCCEEEESSCEEEEEEHHHHHHHGGGGGG-CSE
T ss_pred             -CE-------EEEEECCCCEEEEEEE-CCCEE-EEEEECCCCCCCCCCEEEEECCCCEEEEEEHHHHHHHHHHCCC-CCE
T ss_conf             -80-------8999818827999972-26547-9999247787774312676338740389958999987633368-987


Q ss_pred             CCCCCCCCC
Q ss_conf             331334553
Q gi|254780454|r  219 VKVSLSESR  227 (385)
Q Consensus       219 v~i~~~~~~  227 (385)
                      |+++++.++
T Consensus       225 V~i~~~~~~  233 (261)
T 1u7b_A          225 VTLSMSADV  233 (261)
T ss_dssp             EEEEECTTS
T ss_pred             EEEEECCCC
T ss_conf             999981998


No 29 
>3fds_D DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B*
Probab=98.22  E-value=0.00025  Score=43.94  Aligned_cols=203  Identities=12%  Similarity=0.153  Sum_probs=124.7

Q ss_pred             CEEE-EEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCC-EEEEE
Q ss_conf             9589-8599999999987502037888610133899998997999996782--899999977------752680-79994
Q gi|254780454|r    1 MKIT-VERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCG-SITVS   70 (385)
Q Consensus         1 Mk~~-i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G-~~~v~   70 (385)
                      |+.+ ++-+.|...++.+++++         ..+.+++..+++.+.+.|..  .-+...++.      +++++. .+.|+
T Consensus         2 ~~~~~~~a~~fk~i~~~l~~l~---------~e~~~~~~~~Gi~i~~~D~s~v~lv~~~l~~~~F~~Y~~~~~~~~igi~   72 (245)
T 3fds_D            2 MKAKVIDAVSFSYILRTVGDFL---------SEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFK   72 (245)
T ss_dssp             EEEEESCHHHHHHHHHHHHTTC---------SEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGEEEEEESSSCEEEEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCCEEEECCCCCEEEEE
T ss_conf             7999856799999999999875---------6399999078179999988867999999787769489847976278888


Q ss_pred             HHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECC-CEEEEECCCCCCC-CCCCCCCCCEEEECCCHHHHHHHCCEEEEC
Q ss_conf             99877887407777730477733675089998678-2024303662114-321233243045056113554202202300
Q gi|254780454|r   71 AHLLYDIVRKLQDGAQISFFKENELGTEVNISHGD-SNFYLQSFPESEF-PSTKEEEYVYSFELASSVLKNLVERTHFAM  148 (385)
Q Consensus        71 a~~l~~iik~L~~~~~i~~~~~~~~~~~i~i~~~~-~~~~l~~~~~~~f-P~~~~~~~~~~~~i~~~~l~~~i~~t~~a~  148 (385)
                      -+.|.+++|.+..+..+.+..+++ ...+.+..+. .+|+++.++.+.- +.+|+.+....+.+++..|+++++...-. 
T Consensus        73 l~~l~kilk~~~~~d~l~l~~~~~-~l~i~~~~~~~~~~~l~l~d~~~~~~~~p~~e~~~~i~~~s~~f~~~~k~l~~~-  150 (245)
T 3fds_D           73 LEDVNDILKRVLKDDTLILSSNES-KLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDL-  150 (245)
T ss_dssp             HHHHHHHHTTCCTTCEEEEEECSS-EEEEEEESSSEEEEEEECCCCCCCCC----CCCSEEEEEEHHHHHHHHHHHTTT-
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCC-CEEEEEEECCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHC-
T ss_conf             899899873247997799995389-708999835058999621345422567888887569985099999999988624-


Q ss_pred             CCCCCCCCEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCCC-------CCCHHCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             245565210116677617873489998534157666643578753-------3100000100012222102776464331
Q gi|254780454|r  149 ATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIA-------KMPSIIVPRKAVGEILRILSSKDSSVKV  221 (385)
Q Consensus       149 s~d~~r~~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~-------~~~~~iiP~k~l~el~k~l~~~~~~v~i  221 (385)
                      + |.       |.+..+++.  +.+. +.|.. ...+..+.....       .+....-+.+.+..+.|...- .++|++
T Consensus       151 ~-d~-------i~i~~~~~~--l~~~-~~gd~-~~~~~~~~~~~~~~~~~~~~~~~~~ysl~yl~~~~K~~~l-s~~v~i  217 (245)
T 3fds_D          151 G-EV-------LNIHSKENK--LYFE-VIGDL-STAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRA-SDSMEL  217 (245)
T ss_dssp             C-SE-------EEEEEETTE--EEEE-EECSS-CEEEEEECTTSSSCSEEEECCCEEEEEHHHHHHGGGGGGT-CSEEEE
T ss_pred             C-CE-------EEEEEECCE--EEEE-EECCC-CEEEEEECCCCCCCEEECCCCEEEEEEHHHHHHHHCCCCC-CCEEEE
T ss_conf             8-75-------899971678--9999-97346-3489998689984124216751459868999987554468-986999


Q ss_pred             CCCCCC
Q ss_conf             334553
Q gi|254780454|r  222 SLSESR  227 (385)
Q Consensus       222 ~~~~~~  227 (385)
                      +++.++
T Consensus       218 ~~~~~~  223 (245)
T 3fds_D          218 YFGSQI  223 (245)
T ss_dssp             EECTTS
T ss_pred             EECCCC
T ss_conf             975996


No 30 
>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2
Probab=97.95  E-value=0.0009  Score=40.56  Aligned_cols=200  Identities=13%  Similarity=0.152  Sum_probs=117.1

Q ss_pred             EHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCCEEEEEHHHHHHH
Q ss_conf             599999999987502037888610133899998997999996782--899999977------752680799949987788
Q gi|254780454|r    6 ERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCGSITVSAHLLYDI   77 (385)
Q Consensus         6 ~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G~~~v~a~~l~~i   77 (385)
                      +-+.|...++.+.+++         ..+.+++.++++.++|.|..  .-+...++.      +++++-.+.|+-..|..+
T Consensus         7 ~a~~fk~i~~~l~~l~---------~e~~~~~~~~Gi~i~~mD~s~v~lv~l~l~~~~F~~Y~~~~~~~igi~~~~l~ki   77 (245)
T 1ud9_A            7 DVRDLKAIIQALLKLV---------DEALFDIKPEGIQLVAIDKAHISLIKIELPKEMFKEYDVPEEFKFGFNTQYMSKL   77 (245)
T ss_dssp             CHHHHHHHHHHHHHHC---------SEEEEEEETTEEEEEEECTTSSEEEEEEEEGGGSSEEECSSCEEEEEEHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHH---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCCCCCCCCCEEEEEEHHHHHHH
T ss_conf             8899999999999875---------4599998089679999978758999999887879310457778989998998888


Q ss_pred             HHCCCCCCCEEEEEECCCCEEEEEEEC-CCEEEEECCCCCCC-CCCCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCC
Q ss_conf             740777773047773367508999867-82024303662114-3212332430450561135542022023002455652
Q gi|254780454|r   78 VRKLQDGAQISFFKENELGTEVNISHG-DSNFYLQSFPESEF-PSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRY  155 (385)
Q Consensus        78 ik~L~~~~~i~~~~~~~~~~~i~i~~~-~~~~~l~~~~~~~f-P~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~  155 (385)
                      +|.+..+..+.+..+++....+.+..+ +..|+++.++.+.- ..+|..+....+.+++..|+++++...-. + |    
T Consensus        78 lk~~~~~d~l~l~~~~~~~l~~~~~~~~~~~~~l~~id~~~~~~~~p~~e~~~~i~~~s~~f~~~~~~l~~~-~-d----  151 (245)
T 1ud9_A           78 LKAAKRKEEIIIDADSPEVVKLTLSGALNRVFNVNNIEVLPPEVPEVNLEFDIKATINASGLKNAIGEIAEV-A-D----  151 (245)
T ss_dssp             HTTCCSCCCEEEEEEETTEEEEEECSSSCEEEEEECCCCCCCCCC---CCCSEEEEEEHHHHHHHHHHHHHH-C-S----
T ss_pred             HHHCCCCCEEEEEECCCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHCC-C-C----
T ss_conf             851689967999965897059999823335897033234544577777676679997899999999887434-8-6----


Q ss_pred             CEEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCC------CCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             101166776178734899985341576666435787------533100000100012222102776464331334553
Q gi|254780454|r  156 YLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQ------IAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESR  227 (385)
Q Consensus       156 ~L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~------~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~~  227 (385)
                         -+.+..+++  ++.+.+...... ......+..      .+......-..+.+..+.|...- .+.|+++++.+.
T Consensus       152 ---~i~i~~~~~--~i~~~~~gd~~~-~~~~~~~~~~~~~~~~~~~~~~~fsl~yl~~~~k~~~l-s~~V~i~~~~~~  222 (245)
T 1ud9_A          152 ---TLLISGNEE--KVVVKGEGENKV-EVEFSKDTGSLADIEFNKESSSAYDVEYLNDIISLTKL-SDYVKVAFADQK  222 (245)
T ss_dssp             ---EEEEEECSS--EEEEEESSSSCC-CEEEEGGGTCEEEEEESSCEEEEEEHHHHHHTGGGGGG-CSEEEEEECTTS
T ss_pred             ---EEEEEEECC--EEEEEEECCCCE-EEEECCCCCCEEEEEEECCCCEEEHHHHHHHHHHHCCC-CCEEEEEECCCC
T ss_conf             ---799999578--799997147522-68980689841688870322246468789999843468-986999974997


No 31 
>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A
Probab=97.84  E-value=0.00074  Score=41.08  Aligned_cols=135  Identities=10%  Similarity=0.005  Sum_probs=89.8

Q ss_pred             CEEEEEH---HHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCE--EEEEEEEEE------EECCCC----
Q ss_conf             9589859---9999999987502037888610133899998997999996782--899999977------752680----
Q gi|254780454|r    1 MKITVER---SDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPE--IEITGAIPA------SVDVCG----   65 (385)
Q Consensus         1 Mk~~i~~---~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~--~~i~~~i~~------~i~~~G----   65 (385)
                      ||++++.   +.|.++++..+++.         ..+.|++.+++|.+.|-|..  ..+...++.      +++.++    
T Consensus         1 m~~~~~~~~~k~f~~~i~~l~~i~---------~ev~~~~~~~gl~l~a~d~s~~al~~~~l~~~~F~~Y~~~~~~~~~~   71 (266)
T 3a1j_A            1 MKCLVTGGNVKVLGKAVHSLSRIG---------DELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLL   71 (266)
T ss_dssp             CEEEEETHHHHHHHHHHHHHHTTC---------SEEEEEEETTEEEEEEECTTSCEEEEEEECGGGSSEEECCCSSSCCC
T ss_pred             CEEEECHHHHHHHHHHHHHHHHHC---------CEEEEEEECCEEEEEEECCCCEEEEEEEECHHHCCEEECCCCCCCCE
T ss_conf             989992378899999999999741---------82999994785899999988879999998767472787568887557


Q ss_pred             EEEEEHHHHHHHHHCCCCCC----CEEEEEECCCCEEEEE--EECCC---EEEEECCCCCC-CCCCCCCCCCEEEECCCH
Q ss_conf             79994998778874077777----3047773367508999--86782---02430366211-432123324304505611
Q gi|254780454|r   66 SITVSAHLLYDIVRKLQDGA----QISFFKENELGTEVNI--SHGDS---NFYLQSFPESE-FPSTKEEEYVYSFELASS  135 (385)
Q Consensus        66 ~~~v~a~~l~~iik~L~~~~----~i~~~~~~~~~~~i~i--~~~~~---~~~l~~~~~~~-fP~~~~~~~~~~~~i~~~  135 (385)
                      .+.++.+.+..++|.+.+..    .+....+++ ...+.+  .+..+   +|.|+.++.+. -|.+|..+....+.+++.
T Consensus        72 ~~~v~~k~l~~ilk~~~~~~~~~~~~~l~~~~~-~~~l~i~~~~~~~~~k~~~l~l~d~~~~~~~~p~~~~~~~i~~~s~  150 (266)
T 3a1j_A           72 RCKILMKSFLSVFRSLAMLEKTVEKCCISLNGR-SSRLVVQLHCKFGVRKTHNLSFQDCESLQAVFDPASCPHMLRAPAR  150 (266)
T ss_dssp             CEEEEHHHHHHHHCCHHHHHHHEEEEEEECCTT-CSEEEEEEEEGGGCEEEEEEECEECCCCCCCCCGGGCSEEEEEEHH
T ss_pred             EEEEEHHHHHHHHHHCCCCCCCCEEEEEEECCC-CCEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEECHH
T ss_conf             987648999998620124676423999996489-8559999905788179999653046644577880008679997689


Q ss_pred             HHHHHHCCEE
Q ss_conf             3554202202
Q gi|254780454|r  136 VLKNLVERTH  145 (385)
Q Consensus       136 ~l~~~i~~t~  145 (385)
                      .|+++++.-.
T Consensus       151 ~f~~~~~~~~  160 (266)
T 3a1j_A          151 VLGEAVLPFS  160 (266)
T ss_dssp             HHHHHHTTSC
T ss_pred             HHHHHHHHHH
T ss_conf             9999999755


No 32 
>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C
Probab=97.68  E-value=0.0025  Score=37.88  Aligned_cols=99  Identities=12%  Similarity=0.128  Sum_probs=71.2

Q ss_pred             CCC-CCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCE--EEEEECCCCCEEEEEEEEE------E-ECCCCEEE
Q ss_conf             355-566179984899888898874101235553025651765--9999807873268999998------9-62884399
Q gi|254780454|r  253 IPC-SNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDK--LCMTVDNPDMGKAIESMNV------Y-YNECPMDI  322 (385)
Q Consensus       253 ip~-~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~--l~i~~~~~e~g~~~e~i~~------~-~~G~~~~i  322 (385)
                      +|. ++..++.++-..|.++++-+..+++    .+.+..++++  +.+++.+ +.|++.-.++-      . -..++.+-
T Consensus       135 ~~~~~~~~~i~~~S~~l~~~i~dl~~~~d----~v~i~~~~~~~~~~~~~~g-~~g~~~v~~~~~~~~~~~~~~~~~~~~  209 (263)
T 3a1j_C          135 FCSTNVINKIILQSEGLREAFSELDMTSE----VLQITMSPDKPYFRLSTFG-NAGSSHLDYPKDSDLMEAFHCNQTQVN  209 (263)
T ss_dssp             CCTTTEEEEEEEEGGGGHHHHHTSCTTSS----EEEEEECSSSSSEEEEEEE-TTEEEEEEECTTCSSEEEEEECSCEEE
T ss_pred             CCCCCEEEEEEEEHHHHHHHHHHHHHCCC----EEEEEEECCCCEEEEEEEC-CCCEEEEEECCCCCCEEEEECCCCEEE
T ss_conf             88645418999989999999998872698----4999998387669999977-885799995289871478602783899


Q ss_pred             EECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEEC
Q ss_conf             963889988987357533466338999658987589943
Q gi|254780454|r  323 CFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRG  361 (385)
Q Consensus       323 ~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~  361 (385)
                      .|.-+||..+.|+..-.    ++|+++++. ..|..++-
T Consensus       210 ~Y~l~yl~~~~ka~~ls----~~V~i~~~~-~~pL~l~~  243 (263)
T 3a1j_C          210 RYKISLLKPSTKALVLS----CKVSIRTDN-RGFLSLQY  243 (263)
T ss_dssp             EEEHHHHTTHHHHHHHC----SEEEEEEET-TCCEEEEE
T ss_pred             EEEHHHHHHHHHHHCCC----CEEEEEECC-CCCEEEEE
T ss_conf             99889999987540548----879999759-97399999


No 33 
>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}
Probab=97.47  E-value=0.0048  Score=36.13  Aligned_cols=134  Identities=10%  Similarity=0.001  Sum_probs=88.1

Q ss_pred             CEEEEEH---HHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEE--EEEEEEEE------EECCCC----
Q ss_conf             9589859---99999999875020378886101338999989979999967828--99999977------752680----
Q gi|254780454|r    1 MKITVER---SDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEI--EITGAIPA------SVDVCG----   65 (385)
Q Consensus         1 Mk~~i~~---~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~--~i~~~i~~------~i~~~G----   65 (385)
                      ||++++.   +.|.++++-++++.         ..++|++..++|.+.|-|..-  .+...++.      +++.+.    
T Consensus         1 M~~~i~~~~~k~f~r~i~~Lski~---------~ev~i~~~~~gl~l~amn~s~sa~~~~~~~~~fF~~Y~~~~~~~~~~   71 (296)
T 3g65_A            1 MKCLVTGGNVKVLGKAVHSLSRIG---------DELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLL   71 (296)
T ss_dssp             CEEEEETHHHHHHHHHHHHHHTTC---------SEEEEEEETTEEEEEEECTTSCEEEEEEETTSSCCCCCC-------C
T ss_pred             CEEEECHHHHHHHHHHHHHHHHHC---------CCEEEEEECCEEEEEEECCCCEEEEEEEECHHHCHHEECCCCCCCEE
T ss_conf             989990177899999999999647---------81999992781899998877769999997658441035779987239


Q ss_pred             EEEEEHHHHHHHHHCCCCC----CCEEEEEECCCCEEE--EEEECC---CEEEEECCCCCC-CCCCCCCCCCEEEECCCH
Q ss_conf             7999499877887407777----730477733675089--998678---202430366211-432123324304505611
Q gi|254780454|r   66 SITVSAHLLYDIVRKLQDG----AQISFFKENELGTEV--NISHGD---SNFYLQSFPESE-FPSTKEEEYVYSFELASS  135 (385)
Q Consensus        66 ~~~v~a~~l~~iik~L~~~----~~i~~~~~~~~~~~i--~i~~~~---~~~~l~~~~~~~-fP~~~~~~~~~~~~i~~~  135 (385)
                      .+.++.|.+..++|.+...    ..+.+..+.+. ..+  .+.+..   -.|.|+.+|.+. -+.+|..+....+.+++.
T Consensus        72 ~~~i~~K~l~~i~k~~~~~~~~~e~l~i~~~~~~-~~l~i~~~~~~gi~k~~~l~l~d~e~~~~~~~~~~~~~~i~i~s~  150 (296)
T 3g65_A           72 RCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRS-SRLVVQLHCKFGVRKTHNLSFQDCESLQAVFDPASCPHMLRAPAR  150 (296)
T ss_dssp             CEEEEHHHHHTTTSSTTC----CCEEEEEECCC----EEEEEECGGGCEEEEEECCCCCCCCCCCCCGGGCSCEEEEEHH
T ss_pred             EEEEEHHHHHHHHCCCCCCCCCEEEEEEEECCCC-CEEEEEEEECCCCEEEEEEEEECCCCCCCCCCHHHCCEEEEECHH
T ss_conf             9999826888886551124652128999984898-669999993698289999665435633466784468689997579


Q ss_pred             HHHHHHCCE
Q ss_conf             355420220
Q gi|254780454|r  136 VLKNLVERT  144 (385)
Q Consensus       136 ~l~~~i~~t  144 (385)
                      .|+++++..
T Consensus       151 ~~~~~l~~~  159 (296)
T 3g65_A          151 VLGEAVLPF  159 (296)
T ss_dssp             HHHHHSTTS
T ss_pred             HHHHHHHHC
T ss_conf             999999854


No 34 
>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C
Probab=95.96  E-value=0.071  Score=29.05  Aligned_cols=184  Identities=10%  Similarity=0.093  Sum_probs=96.0

Q ss_pred             CEEEEEEECCEEEEEEECC-EEEEEEEEEEE------E-CCCCEEEEEHHHHHHHHHCCCCCCC------EEEEEECCCC
Q ss_conf             3389999899799999678-28999999777------5-2680799949987788740777773------0477733675
Q gi|254780454|r   31 CHVLLQANDGLLEIKASGP-EIEITGAIPAS------V-DVCGSITVSAHLLYDIVRKLQDGAQ------ISFFKENELG   96 (385)
Q Consensus        31 ~~ilie~~~~~l~l~atd~-~~~i~~~i~~~------i-~~~G~~~v~a~~l~~iik~L~~~~~------i~~~~~~~~~   96 (385)
                      ..+.+++.++++.++.-+. -..+...++.+      + +++-++.|+-..|..+++....+..      +.+...++ +
T Consensus        26 d~~~~~~~~~Gi~i~~d~s~v~l~~~~L~~~~F~~Y~~~~~~~~~ginl~~l~kiL~~~~~~d~~~~~~~~~i~~~~~-~  104 (263)
T 3a1j_C           26 EHATCFATKNGIKVTVENAKCVQANAFIQAGIFQEFKVQEESVTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGY-G  104 (263)
T ss_dssp             SEEEEEEETTEEEEEEEETTTEEEEEEEEGGGSSEEEESSSCEEEEEEHHHHHHHHTTTCSCCCTTCCCEEEEEECST-T
T ss_pred             CEEEEEECCCEEEEEEECCCEEEEEEEECHHHCCEEEECCCCEEEEEEHHHHHHHHHHCCCCCCCCCEEEEEEEECCC-C
T ss_conf             369999968928999978968999999998999418977975499986899999997436787655305899997599-9


Q ss_pred             EE--EEEEECC--CEEEEECCCCCCCCC--CCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCCCEEEEEEEECCCCCE
Q ss_conf             08--9998678--202430366211432--12332430450561135542022023002455652101166776178734
Q gi|254780454|r   97 TE--VNISHGD--SNFYLQSFPESEFPS--TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLK  170 (385)
Q Consensus        97 ~~--i~i~~~~--~~~~l~~~~~~~fP~--~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~~L~Gv~~~~~~~~~~  170 (385)
                      ..  +.++.++  .+|.++.+++++-+.  +|..+....+.++++.|+++++... ..+ |.       +.+....+...
T Consensus       105 ~~l~i~~e~~~~~~~~~l~l~~~~~~~~~~~~~~~~~~~i~~~S~~l~~~i~dl~-~~~-d~-------v~i~~~~~~~~  175 (263)
T 3a1j_C          105 YPLMLFLEEGGVVTVCKINTQEPEETLDFDFCSTNVINKIILQSEGLREAFSELD-MTS-EV-------LQITMSPDKPY  175 (263)
T ss_dssp             CCEEEEEEETTEEEEEEECCBCCCCCCCCCCCTTTEEEEEEEEGGGGHHHHHTSC-TTS-SE-------EEEEECSSSSS
T ss_pred             CEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEHHHHHHHHHHHH-HCC-CE-------EEEEEECCCCE
T ss_conf             8799999449908999998556675334588864541899998999999999887-269-84-------99999838766


Q ss_pred             EEEEEECCEEEEEEEEECCCCCC--------CCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             89998534157666643578753--------3100000100012222102776464331334553
Q gi|254780454|r  171 LCAVATDGHRLAVAEVDIVAQIA--------KMPSIIVPRKAVGEILRILSSKDSSVKVSLSESR  227 (385)
Q Consensus       171 l~~vaTDg~RLa~~~~~~~~~~~--------~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~~  227 (385)
                      +.+ .++|.. ...+..++...+        +.....-+.+.|..+.|...-. ..|+|.++.+.
T Consensus       176 ~~~-~~~g~~-g~~~v~~~~~~~~~~~~~~~~~~~~~Y~l~yl~~~~ka~~ls-~~V~i~~~~~~  237 (263)
T 3a1j_C          176 FRL-STFGNA-GSSHLDYPKDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLS-CKVSIRTDNRG  237 (263)
T ss_dssp             EEE-EEEETT-EEEEEEECTTCSSEEEEEECSCEEEEEEHHHHTTHHHHHHHC-SEEEEEEETTC
T ss_pred             EEE-EEECCC-CEEEEEECCCCCCEEEEECCCCEEEEEEHHHHHHHHHHHCCC-CEEEEEECCCC
T ss_conf             999-997788-579999528987147860278389999889999987540548-87999975997


No 35 
>1b77_A GP45, protein (sliding clamp); replisome; 2.10A {Enterobacteria phage RB69} SCOP: d.131.1.2 d.131.1.2 PDB: 1b8h_A* 1czd_A*
Probab=60.84  E-value=6.9  Score=16.99  Aligned_cols=202  Identities=13%  Similarity=0.166  Sum_probs=101.5

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEEEEEEEEEEEECCCCEEEEEHHHHHHHHHC
Q ss_conf             95898599999999987502037888610133899998997999996782899999977752680799949987788740
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRK   80 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~~i~~~i~~~i~~~G~~~v~a~~l~~iik~   80 (385)
                      ||++   +.-++.|+..+.         |-++|+++ .|+.|.=.+..-.+-.++.++-+...+- ..-.=..|+..+.-
T Consensus         1 Mkls---~~Ti~iLkNFs~---------IN~sI~~k-~Gn~i~Tis~~knilA~A~i~E~Fp~ef-aIYDLneFL~~lsL   66 (228)
T 1b77_A            1 MKLS---KDTIAILKNFAS---------INSGILLS-QGKFIMTRAVNGTTYAEANISDEIDFDV-ALYDLNSFLSILSL   66 (228)
T ss_dssp             CCCC---HHHHHHHHHHHT---------TCSCEEEC-SEEEEEEECTTSSEEEEEEEEEEECSCE-EESCHHHHHHHHTT
T ss_pred             CCCC---HHHHHHHHHHHH---------CCCCEEEC-CCCEEEEEECCCCEEEEEEECCCCCCCE-EEEEHHHHHHHHHC
T ss_conf             9677---889999876875---------28874985-8986786506420799997055577642-58769998768752


Q ss_pred             CCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCCC--CC--CCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCCC
Q ss_conf             77777304777336750899986782024303662114--32--123324304505611355420220230024556521
Q gi|254780454|r   81 LQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEF--PS--TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYY  156 (385)
Q Consensus        81 L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~f--P~--~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~~  156 (385)
                      +.+. ...+ .++.  ..+.+..++++++....|+.--  |+  +.-.+....|+++.++|.++.+    |++.=    .
T Consensus        67 ~~~~-~~~~-~~~~--~~i~~~~~~~~~~y~~ad~~ii~~P~K~i~~P~~dv~F~L~~edl~~i~k----Aa~vl----~  134 (228)
T 1b77_A           67 VSDD-AEIS-MHTD--GNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLR----VSRGL----Q  134 (228)
T ss_dssp             SCTT-CEEE-ECTT--SSEEEECSSEEEEECCBCGGGSCCCSSCCCCCCCSEEEEECHHHHHHHHH----HHHHT----T
T ss_pred             CCCC-CCCC-CCCC--EEEEECCCCEEEEEECCCCCEEECCCCCCCCCCHHHEEECCHHHHHHHHH----HHHHC----C
T ss_conf             1578-3101-4663--28997599548999838942240588746899746078849999999999----99751----9


Q ss_pred             EEEEEEEECCCCCEEEEEEECCE----------EEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             01166776178734899985341----------57666643578753310000010001222210277646433133455
Q gi|254780454|r  157 LNGIFFHINEEDLKLCAVATDGH----------RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSES  226 (385)
Q Consensus       157 L~Gv~~~~~~~~~~l~~vaTDg~----------RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~  226 (385)
                      +.=+.+.-  +++++.++++|..          ++-+.+    ......+.+.+-...|    |++.+ +=.|+|+...+
T Consensus       135 lpdl~~~~--~~g~i~l~v~D~~nds~~TSN~fsi~vg~----~~~~~~F~f~fkveNL----Kli~g-dY~V~Is~~s~  203 (228)
T 1b77_A          135 IDTIAITN--KDGKIVINGYNKVEDSGLTRPKYSLTLTD----YDGSNNFNFVINMANM----KIQPG-NYKVMLWGAGD  203 (228)
T ss_dssp             CCEEEEEE--ETTEEEEEEECTTTCTTCCSCSEEEEEEE----CCCSCCEEEEEEGGGC----CCCSS-CEEEEEEEETT
T ss_pred             CCCEEEEC--CCCCEEEEEEECCCCCCCCCCCEEEECCC----CCCCCEEEEEEEEEEE----EECCC-CEEEEEEECCC
T ss_conf             98279972--89818999850112577775407887265----3467017999982258----87789-88999965774


Q ss_pred             CE--EEECCEEEEEE
Q ss_conf             30--10025069998
Q gi|254780454|r  227 RI--HLNIESLSMSV  239 (385)
Q Consensus       227 ~i--~~~~~~~~~~s  239 (385)
                      +.  .|...+..+.-
T Consensus       204 k~is~f~~~~l~Y~I  218 (228)
T 1b77_A          204 KVAAKFESSQVSYVI  218 (228)
T ss_dssp             EEEEEEECSSCEEEE
T ss_pred             EEEEEEECCCEEEEE
T ss_conf             025886089779999


No 36 
>2p0g_A Selenoprotein W-related protein; VCR75, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.30A {Vibrio cholerae}
Probab=56.42  E-value=3  Score=19.21  Aligned_cols=56  Identities=16%  Similarity=0.229  Sum_probs=35.2

Q ss_pred             HHCCCC-CHHHHHHHHCCCCCCCCCCCCCC-CCEEEECCEEEEEEEECCCCCCCCCCC
Q ss_conf             000010-00122221027764643313345-530100250699985126655322101
Q gi|254780454|r  197 SIIVPR-KAVGEILRILSSKDSSVKVSLSE-SRIHLNIESLSMSVRLIDGEFPNYQNV  252 (385)
Q Consensus       197 ~~iiP~-k~l~el~k~l~~~~~~v~i~~~~-~~i~~~~~~~~~~srLi~g~yPdy~~v  252 (385)
                      .+...+ -...||+..+.+.-.+|.+.-+. ..+.+..++..+.+|.-+|.||+-+.+
T Consensus        15 ~wllRa~wlaqELL~tF~~~i~eVsL~P~~gGvFeV~vng~lI~sRk~~ggFPe~keL   72 (105)
T 2p0g_A           15 NWMLRSAWLSQELLHTFSEEIEYVALHPDTGGRFEIFCNGVQIWERKQEGGFPEAKVL   72 (105)
T ss_dssp             TCHHHHHHHHHHHHHHTTTTEEEEEEEEESTTCEEEEETTEEEEEHHHHTSCCCHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEEECCCEEEEEEECCEEEEEECCCCCCCCHHHH
T ss_conf             9808999999999986464356399697899179999899999985456899888999


No 37 
>2ojl_A Hypothetical protein; BPR68, NESG, Q7WAF1, structural genomics, PSI-2, protein structure initiative; 2.10A {Bordetella parapertussis 12822}
Probab=56.30  E-value=2.8  Score=19.39  Aligned_cols=50  Identities=16%  Similarity=0.254  Sum_probs=33.4

Q ss_pred             HHHHHHHHCCCCCCCCCCCCC-CCCEEEECCEEEEEEEECCCCCCCCCCCC
Q ss_conf             012222102776464331334-55301002506999851266553221013
Q gi|254780454|r  204 AVGEILRILSSKDSSVKVSLS-ESRIHLNIESLSMSVRLIDGEFPNYQNVI  253 (385)
Q Consensus       204 ~l~el~k~l~~~~~~v~i~~~-~~~i~~~~~~~~~~srLi~g~yPdy~~vi  253 (385)
                      ...||+..+.+.-.+|.+.-+ +..+.+..++..+++|+.+|.|||.+.+.
T Consensus        28 laqeLL~tF~~~i~evsL~Pg~~G~FeV~vng~lV~skk~~ggFPD~keLk   78 (108)
T 2ojl_A           28 MAQELLSTFGADLGEVALVPGTGGVFRIHYNGAPLWDREVDGGFPEAKVLK   78 (108)
T ss_dssp             HHHHHHHHHGGGSSEEEEEEECTTCEEEEETTEEEEEHHHHCSCCCHHHHH
T ss_pred             HHHHHHHHCCCCCCEEEEEECCCEEEEEEECCEEEEECCCCCCCCCHHHHH
T ss_conf             999999865764545987708996899998998978706579898989999


No 38 
>2oka_A Hypothetical protein; PAR82, NESG, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 2.50A {Pseudomonas aeruginosa} PDB: 2obk_A
Probab=45.95  E-value=6.3  Score=17.25  Aligned_cols=57  Identities=14%  Similarity=0.214  Sum_probs=35.2

Q ss_pred             HHCCCC-CHHHHHHHHCCCCCCCCCCCCC-CCCEEEECCEEEEEEEECCCCCCCCCCCC
Q ss_conf             000010-0012222102776464331334-55301002506999851266553221013
Q gi|254780454|r  197 SIIVPR-KAVGEILRILSSKDSSVKVSLS-ESRIHLNIESLSMSVRLIDGEFPNYQNVI  253 (385)
Q Consensus       197 ~~iiP~-k~l~el~k~l~~~~~~v~i~~~-~~~i~~~~~~~~~~srLi~g~yPdy~~vi  253 (385)
                      .+...+ -...||+..+.+.-.+|.+.-+ +..+.+..++..+.+|..+|.||+-+.+.
T Consensus        17 ~w~~Ra~w~aqELL~tF~~~i~eVsL~Pg~gGvFeV~v~gelIwsRk~~ggFPe~keLK   75 (104)
T 2oka_A           17 QWLLRAAWLAQELLSTFADDLGKVCLEPGTGGVFRITCDGVQVWERKADGGFPEAKALK   75 (104)
T ss_dssp             TCHHHHHHHHHHHHHHSTTTCSEEEEEEECTTCEEEEETTEEEEEHHHHTSCCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEECCEEEEEECCCCCCCCHHHHH
T ss_conf             98089999999999855664565997877994199998999989862578899889999


No 39 
>2npb_A Selenoprotein W; structure, thioredoxin-like fold, oxidoreductase; NMR {Mus musculus}
Probab=43.53  E-value=11  Score=15.77  Aligned_cols=49  Identities=0%  Similarity=-0.058  Sum_probs=30.2

Q ss_pred             HHHHHHHCCCCCCCC-CCCC-CCCCEEEECCEEEEEEEECCCCCCCCCCCC
Q ss_conf             122221027764643-3133-455301002506999851266553221013
Q gi|254780454|r  205 VGEILRILSSKDSSV-KVSL-SESRIHLNIESLSMSVRLIDGEFPNYQNVI  253 (385)
Q Consensus       205 l~el~k~l~~~~~~v-~i~~-~~~~i~~~~~~~~~~srLi~g~yPdy~~vi  253 (385)
                      ..+|..-+++..+.+ ++.- .+..+.+..++..+.||.-+|.|||.+.++
T Consensus        23 aqeLl~tF~~~i~~~~~l~p~~~G~FeV~vdg~lI~sKk~~ggFPd~ke~~   73 (96)
T 2npb_A           23 KEKLEHEFPGCLDICGEGTPQVTGFFEVTVAGKLVHSKKRGDGYVDTESKF   73 (96)
T ss_dssp             HHHHHHHSBTTEEEEECCCSSCCSCCEEEETTEEEEETTTTCCSSCSHHHH
T ss_pred             HHHHHHHCCCCCCCEEECCCCCCEEEEEEECCEEEEEEECCCCCCCHHHHH
T ss_conf             999998778633422640358974899998999989851468999869999


No 40 
>2fa8_A Hypothetical protein ATU0228; ALPH-beta structure, 4 helix bundle, structural genomics, PSI, protein structure initiative; 1.90A {Agrobacterium tumefaciens str} SCOP: c.47.1.23
Probab=40.83  E-value=6.8  Score=17.03  Aligned_cols=48  Identities=23%  Similarity=0.310  Sum_probs=31.9

Q ss_pred             HHHHHHHHCCCCCCCCCCCCC-CCCEEEECCEEEEEEEECCCCCCCCCC
Q ss_conf             012222102776464331334-553010025069998512665532210
Q gi|254780454|r  204 AVGEILRILSSKDSSVKVSLS-ESRIHLNIESLSMSVRLIDGEFPNYQN  251 (385)
Q Consensus       204 ~l~el~k~l~~~~~~v~i~~~-~~~i~~~~~~~~~~srLi~g~yPdy~~  251 (385)
                      ...||+..+.+.-.+|++.-+ +..+.+..+...+++|.-+|.|||-+.
T Consensus        27 laqELl~tF~~~i~evsL~P~~~G~FeV~vdg~lI~srk~~ggFPd~ke   75 (105)
T 2fa8_A           27 MAQEILQTFASDIGEVSLIPSTGGLFEITVDGTIIWERKRDGGFPGPKE   75 (105)
T ss_dssp             HHHHHHHHHGGGCSEEEEEEECTTCEEEEETTEEEEEHHHHTSCCCHHH
T ss_pred             HHHHHHHHCCCCCCEEEEEECCCEEEEEEECCEEEEEECCCCCCCCHHH
T ss_conf             9999998656535449868789917999989999999647899988899


No 41 
>3a8g_A NitrIle hydratase subunit alpha; Fe, iron, lyase, metal-binding, oxidation; 1.11A {Rhodococcus erythropolis} PDB: 3a8h_A 3a8l_A 3a8o_A 2zpb_A 2ahj_A 2cyz_A 2cz6_A 2cz7_A 2d0q_A 2cz1_A 2zpe_A 2zpf_A 2zpg_A 2zph_A 2zpi_A 2qdy_A 3a8m_A 2zcf_A 1ahj_A 2cz0_A*
Probab=22.26  E-value=30  Score=13.10  Aligned_cols=13  Identities=15%  Similarity=0.159  Sum_probs=5.9

Q ss_pred             EEHHHHHHHHHHH
Q ss_conf             8489988889887
Q gi|254780454|r  263 VNCTNLRQAVDRV  275 (385)
Q Consensus       263 v~r~~l~~al~Rv  275 (385)
                      .+-.+|...+.|-
T Consensus       182 lsee~La~lvtrd  194 (207)
T 3a8g_A          182 WSQEQLQEIVTKD  194 (207)
T ss_dssp             CCHHHHHHHCCHH
T ss_pred             CCHHHHHHHHHHH
T ss_conf             8999999774132


No 42 
>3dex_A SAV_2001; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Streptomyces avermitilis}
Probab=22.01  E-value=22  Score=13.94  Aligned_cols=57  Identities=11%  Similarity=0.099  Sum_probs=31.2

Q ss_pred             CHHCCCC-CHHHHHHHHCCCCCCCCCCCCCC-CCEEEECCEEEEEEEECCCCCCCCCCCC
Q ss_conf             0000010-00122221027764643313345-5301002506999851266553221013
Q gi|254780454|r  196 PSIIVPR-KAVGEILRILSSKDSSVKVSLSE-SRIHLNIESLSMSVRLIDGEFPNYQNVI  253 (385)
Q Consensus       196 ~~~iiP~-k~l~el~k~l~~~~~~v~i~~~~-~~i~~~~~~~~~~srLi~g~yPdy~~vi  253 (385)
                      .++...+ -...||+..+.++-.+|++.-+. ..+.+..++..+.+|. +|.||+-+.+.
T Consensus        23 C~wl~RA~wlaqELL~tF~~~i~eVsLvPg~gGvFeV~vdgelI~sRk-e~GFPe~keLk   81 (107)
T 3dex_A           23 CRWLPRAAWLAQELLTTFETELTELALKPGTGGVFVVRVDDEVVWDRR-EQGFPEPTAVK   81 (107)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTTEEEEEEEEESSSCEEEEETTEEEEEHH-HHCSCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCEEEEEEECCEEEEECC-CCCCCCHHHHH
T ss_conf             898189999999999867754563997877991699998999999717-79999889999


No 43 
>2zzd_C Thiocyanate hydrolase subunit gamma; scnase, cobalt, metalloprotein, sulfenic acid, sulfinic acid, nitrIle hydratase, carbonyl sulfide; HET: FRU TLA BGC; 1.78A {Thiobacillus thioparus} PDB: 2dxc_C* 2dxb_C 2dd5_C* 2dd4_C*
Probab=21.37  E-value=32  Score=12.99  Aligned_cols=27  Identities=19%  Similarity=0.241  Sum_probs=14.1

Q ss_pred             CCCCCCCCEEEEEHHHHHHHHHHHHHC
Q ss_conf             135556617998489988889887410
Q gi|254780454|r  252 VIPCSNDKELRVNCTNLRQAVDRVSIM  278 (385)
Q Consensus       252 vip~~~~~~~~v~r~~l~~al~Rv~i~  278 (385)
                      |||....-+--.+-.+|...+.|=+.+
T Consensus       189 VLP~rP~GTe~lse~~La~lVTRdsMI  215 (243)
T 2zzd_C          189 VMPVRPEGTDGWTEDQLAEIVTRDCLI  215 (243)
T ss_dssp             EECCCCSSCTTCCHHHHHHTCCHHHHH
T ss_pred             EECCCCCCCCCCCHHHHHHHHCCCCCE
T ss_conf             957899876788999998661601203


Done!