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!