Query         gi|254780828|ref|YP_003065241.1| ATP-dependent protease peptidase subunit [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 190
No_of_seqs    110 out of 1354
Neff          8.0 
Searched_HMMs 23785
Date          Tue May 31 15:09:27 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780828.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2z3b_A ATP-dependent protease  100.0 1.1E-39 4.5E-44  266.7  14.0  175   12-186     2-180 (180)
  2 1m4y_A ATP-dependent protease  100.0 9.2E-39 3.9E-43  260.8  17.0  170   16-185     1-171 (171)
  3 1g3k_A ATP-dependent protease  100.0 6.8E-38 2.9E-42  255.4  17.0  172   16-187     1-174 (174)
  4 1iru_M 20S proteasome; cell cy 100.0 1.2E-34 5.1E-39  235.1  21.0  181    7-188     1-201 (213)
  5 1ryp_M 20S proteasome; multica 100.0 7.3E-34 3.1E-38  230.2  20.3  181    7-188     1-210 (222)
  6 2jay_A Proteasome; hydrolase;  100.0 2.6E-34 1.1E-38  233.0  17.1  169   13-182    55-244 (291)
  7 1q5r_H Proteasome beta-type su 100.0 8.3E-34 3.5E-38  229.9  18.1  175   13-188    63-265 (294)
  8 1ryp_H 20S proteasome; multica 100.0 5.5E-33 2.3E-37  224.7  19.1  174   14-188     8-190 (205)
  9 1iru_I 20S proteasome; cell cy 100.0 5.9E-33 2.5E-37  224.5  18.3  172   16-188     1-181 (234)
 10 1iru_H 20S proteasome; cell cy 100.0 1.4E-32 6.1E-37  222.1  20.0  172   16-188     1-182 (205)
 11 1ryp_J 20S proteasome; multica 100.0 2.4E-32   1E-36  220.7  20.5  179    9-189     2-193 (204)
 12 1ryp_I 20S proteasome; multica 100.0 2.5E-32   1E-36  220.6  20.1  173   16-189     1-182 (222)
 13 1iru_L 20S proteasome; cell cy 100.0 2.3E-32 9.8E-37  220.8  19.9  172   16-188     1-182 (204)
 14 1g0u_M Proteasome component PR 100.0   2E-32 8.3E-37  221.3  18.8  181    6-188    33-236 (266)
 15 1iru_J 20S proteasome; cell cy 100.0   7E-32 2.9E-36  217.8  20.7  179    9-188     2-193 (205)
 16 1iru_N 20S proteasome; cell cy 100.0 4.9E-32 2.1E-36  218.8  18.3  178    9-188     3-195 (219)
 17 1ryp_L 20S proteasome; multica 100.0 9.2E-32 3.9E-36  217.1  19.5  172   16-188     1-183 (212)
 18 1yar_H Proteasome beta subunit 100.0 1.5E-31 6.4E-36  215.7  20.0  175   14-189     7-190 (217)
 19 1ryp_N 20S proteasome; multica 100.0 2.1E-31 8.6E-36  214.9  18.9  178    9-188     3-203 (233)
 20 1q5q_H Proteasome beta-type su 100.0 4.2E-31 1.8E-35  213.0  19.2  171   16-187     1-199 (235)
 21 1j2q_H Proteasome beta subunit 100.0 1.3E-30 5.5E-35  209.9  19.8  172   16-188     1-183 (202)
 22 3h4p_a Proteasome subunit beta 100.0 9.8E-30 4.1E-34  204.4  19.1  173   15-188     1-185 (219)
 23 1iru_K 20S proteasome; cell cy 100.0 4.9E-30 2.1E-34  206.3  17.6  173   15-188     1-186 (201)
 24 1iru_C 20S proteasome; cell cy 100.0 7.2E-30   3E-34  205.2  18.1  175   13-188    29-219 (261)
 25 1ryp_C 20S proteasome; multica 100.0 1.7E-29   7E-34  203.0  19.0  175   13-188    29-218 (244)
 26 1ryp_K 20S proteasome; multica 100.0 1.9E-29 7.9E-34  202.6  18.7  173   15-188     1-187 (198)
 27 3h4p_A Proteasome subunit alph 100.0 2.9E-28 1.2E-32  195.2  16.2  171   14-188    37-221 (264)
 28 1iru_B 20S proteasome; cell cy 100.0   1E-27 4.2E-32  191.8  18.7  171   14-187    30-214 (233)
 29 1yar_A Proteasome alpha subuni 100.0 2.1E-27   9E-32  189.8  19.9  174   13-189    32-219 (233)
 30 1ryp_B 20S proteasome; multica 100.0 1.3E-27 5.4E-32  191.2  17.7  172   14-188    30-217 (250)
 31 1ryp_E 20S proteasome; multica 100.0 2.7E-27 1.1E-31  189.2  18.3  173   14-189    25-218 (242)
 32 1j2p_A Alpha-ring, proteasome  100.0 5.9E-27 2.5E-31  187.0  19.0  173   14-189    33-218 (246)
 33 1iru_E 20S proteasome; cell cy 100.0 5.2E-27 2.2E-31  187.3  17.9  173   14-189    33-224 (241)
 34 1ryp_G 20S proteasome; multica 100.0 1.1E-26 4.5E-31  185.4  18.7  173   14-188    29-218 (244)
 35 1iru_G 20S proteasome; cell cy 100.0 4.4E-27 1.8E-31  187.8  16.4  174   14-189    32-220 (254)
 36 1ryp_D 20S proteasome; multica  99.9 1.6E-26 6.8E-31  184.3  17.2  172   14-189    27-217 (241)
 37 3bdm_F Proteasome component C1  99.9 3.7E-26 1.5E-30  182.1  17.8  174   14-189    32-222 (287)
 38 1iru_F 20S proteasome; cell cy  99.9 1.3E-26 5.3E-31  185.0  15.4  171   14-188    31-218 (263)
 39 1ryp_A 20S proteasome; multica  99.9 2.5E-26 1.1E-30  183.0  16.8  173   13-188    28-222 (243)
 40 3mi0_A Proteasome subunit alph  99.9 8.1E-26 3.4E-30  179.9  19.1  166   14-188    26-216 (248)
 41 1iru_D 20S proteasome; cell cy  99.9 5.2E-26 2.2E-30  181.1  17.3  173   14-188    28-214 (248)
 42 1iru_A 20S proteasome; cell cy  99.9   1E-25 4.3E-30  179.2  17.5  173   13-188    34-223 (246)
 43 1ryp_F 20S proteasome; multica  99.9 2.7E-25 1.2E-29  176.6  16.9  171   14-188    30-218 (233)
 44 1q5q_A Proteasome alpha-type s  99.9 2.1E-24 8.7E-29  171.1  17.4  166   14-188    26-214 (259)
 45 1cuk_A RUVA protein; DNA repai  34.2      20 0.00086   14.8   3.5   35  135-169   168-202 (203)
 46 2pk0_A Serine/threonine protei  24.9      29  0.0012   13.8   5.2   36  153-190   213-248 (250)
 47 3bb7_A Interpain A; cysteine p  20.5      29  0.0012   13.9   1.1   18   20-37     17-34  (321)
 48 1dki_A Pyrogenic exotoxin B zy  20.0      37  0.0015   13.2   1.7   20   18-37     53-72  (371)

No 1  
>2z3b_A ATP-dependent protease HSLV; N-terminal nucleophIle hydrolase; 2.50A {Bacillus subtilis} SCOP: d.153.1.4 PDB: 2z3a_A 1yyf_D*
Probab=100.00  E-value=1.1e-39  Score=266.67  Aligned_cols=175  Identities=51%  Similarity=0.843  Sum_probs=156.6

Q ss_pred             EECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEE-EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf             76371799999799799981365450536774451057981597599-97313058899999999999998536656306
Q gi|254780828|r   12 KMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNII-AGFAGSSADAFTLLERLEKKLEQYPNQLLRSS   90 (190)
Q Consensus        12 ~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~-~g~ag~a~d~~~~~~~~~~~~~~~~~~~~~~~   90 (190)
                      ++||||||||+|+||||||||||+|+|+++.+|+.+|++++.++.++ ++.++...+.+.+.+....+.++++.......
T Consensus         2 ~~~GTTivavk~~~GVvlAaDtR~s~G~~i~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (180)
T 2z3b_A            2 SFHATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYNGNLKRAA   81 (180)
T ss_dssp             CBCCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTTTCHHHHH
T ss_pred             CCCCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             97762899999999999998984427764897362379997169869953624678999999999999987515420149


Q ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCC---CHHHHHHHHHH
Q ss_conf             799999976112220131045137876469980586311413279960642345788985207899---98999999999
Q gi|254780828|r   91 VELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQN---SAEEIARKAMS  167 (190)
Q Consensus        91 ~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~---sa~ela~~Al~  167 (190)
                      ...++.+...+|.+++.+.+......+++++..++.+..++++|+|+|||+++|+|+||..|+|+|   +|+||+++||+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~g~L~~~y~~~~~~~eA~~la~~Al~  161 (180)
T 2z3b_A           82 VELAKEWRSDKVLRKLEAMLIVMNQDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAGESMSASEIARAALE  161 (180)
T ss_dssp             HHHHHHHHHCTTGGGCCCCEEEECSSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHGGGCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCCCEEECCCCCEEECCCCEEEECCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             99999998866654125516787326753743785102046648984435799999999873558986679999999999


Q ss_pred             HHHCCCEEECCCEEEEEEE
Q ss_conf             7540110225956999994
Q gi|254780828|r  168 IAADICVYTNHNIVLETLK  186 (190)
Q Consensus       168 ~A~erDvyTgd~i~i~~i~  186 (190)
                      +|+|||||||||++|++||
T Consensus       162 ~Aae~diyT~~~~~v~~~~  180 (180)
T 2z3b_A          162 TAGEICVYTNDQIILEELE  180 (180)
T ss_dssp             HHHHHCTTCCSCCEEEEEC
T ss_pred             HHHHHCEECCCCEEEEEEC
T ss_conf             9875228809958999839


No 2  
>1m4y_A ATP-dependent protease HSLV; N-terminal catalytic threonine residue, hydrolase; 2.10A {Thermotoga maritima} SCOP: d.153.1.4
Probab=100.00  E-value=9.2e-39  Score=260.84  Aligned_cols=170  Identities=57%  Similarity=0.960  Sum_probs=150.0

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             17999997997999813654505367744510579815975999731305889999999999999853665630679999
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQLLRSSVELAK   95 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (190)
                      ||||||+|+||||||||||+|+|++|.+|+++||+++++++++++.++.+++++.+......+.+++.......+...++
T Consensus         1 TTivai~~~dgVvlAaDtr~S~G~~i~~r~~~Ki~~i~~~~~~~~~g~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (171)
T 1m4y_A            1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAK   80 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEEECCCCEEEECCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             95999998999999988875148878917988888838994999974624458999999999887640455201599999


Q ss_pred             HHHHHHHHHHCCCEEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCE
Q ss_conf             9976112220131045137876469980586311413279960642345788985207-899989999999997540110
Q gi|254780828|r   96 DWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS-TQNSAEEIARKAMSIAADICV  174 (190)
Q Consensus        96 ~~~~~~y~~~~~~~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~-~~~sa~ela~~Al~~A~erDv  174 (190)
                      .+....+.+++...+...+..+++++..++.+..++++|+|+|||+.||+|+|+.+|+ ++++|+||+++||++|+||||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~a~GSG~~~a~g~l~~~~~~~~~~A~ela~~Ai~~Aae~dv  160 (171)
T 1m4y_A           81 DWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICI  160 (171)
T ss_dssp             HHHHCTTGGGCCCEEEEECSSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEEECCCCEEEECCCEEEEECCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCE
T ss_conf             99986666543223320146653388438965687378999964789999999960647899999999999999760154


Q ss_pred             EECCCEEEEEE
Q ss_conf             22595699999
Q gi|254780828|r  175 YTNHNIVLETL  185 (190)
Q Consensus       175 yTgd~i~i~~i  185 (190)
                      ||||+|+|+||
T Consensus       161 yTgd~v~i~~i  171 (171)
T 1m4y_A          161 YTNQNIVIEEV  171 (171)
T ss_dssp             TCCSCCEEEEC
T ss_pred             ECCCCEEEEEC
T ss_conf             62996899979


No 3  
>1g3k_A ATP-dependent protease HSLV; hydrolase; 1.90A {Haemophilus influenzae} SCOP: d.153.1.4 PDB: 1g3i_G 1jjw_A 1kyi_G* 1ofh_G* 1ofi_G* 1e94_A* 1g4a_B* 1g4b_M 1hqy_A* 1ht1_C* 1ht2_A* 1ned_A
Probab=100.00  E-value=6.8e-38  Score=255.43  Aligned_cols=172  Identities=58%  Similarity=0.863  Sum_probs=154.3

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             17999997997999813654505367744510579815975999731305889999999999999853665630679999
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQLLRSSVELAK   95 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (190)
                      ||||||+|+||||||||||+|+|++|.+|+++||++++++.++++.+|.+++++.+.+.+..++++++..........++
T Consensus         1 TTivgi~~~~GVVlAADtR~T~G~~i~~~~~~Ki~~i~~~~~~~~~~g~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (174)
T 1g3k_A            1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQGHLLKSAVELAK   80 (174)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCEEEEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             95999998999999989874058776827621789945982999736158889999999886655414863035999999


Q ss_pred             HHHHHHHHHHCCCEEEECC-CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCC
Q ss_conf             9976112220131045137-876469980586311413279960642345788985207-89998999999999754011
Q gi|254780828|r   96 DWRMDKYLRNLEAMILIAD-KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS-TQNSAEEIARKAMSIAADIC  173 (190)
Q Consensus        96 ~~~~~~y~~~~~~~~~~~~-~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~-~~~sa~ela~~Al~~A~erD  173 (190)
                      ......|..+....+...+ ...++.+..++.+..++.+|+|+|||+.||+|+|+..|+ ++++|+||+++||++|+|||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~g~~~~~~~~~~~eA~ela~~Ai~~A~~~d  160 (174)
T 1g3k_A           81 DWRTDRALRKLEAMLIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVENTELSAHEIVEKSLRIAGDIC  160 (174)
T ss_dssp             HHHHSTTGGGCCCEEEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCEEEEECCCCCCCCCCCCCCEEECCCCEEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHC
T ss_conf             99975202001023554025676301478761223588889966709999999998620699899999999999976016


Q ss_pred             EEECCCEEEEEEEC
Q ss_conf             02259569999941
Q gi|254780828|r  174 VYTNHNIVLETLKV  187 (190)
Q Consensus       174 vyTgd~i~i~~i~~  187 (190)
                      |||||||+|++|+.
T Consensus       161 v~T~~~~~i~~~~~  174 (174)
T 1g3k_A          161 VFTNTNFTIEELPN  174 (174)
T ss_dssp             TTCCSCCEEEEEC-
T ss_pred             EECCCCEEEEEECC
T ss_conf             77199689999069


No 4  
>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=1.2e-34  Score=235.08  Aligned_cols=181  Identities=18%  Similarity=0.178  Sum_probs=155.9

Q ss_pred             CCCCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--
Q ss_conf             778177637179999979979998136545053677445105798159759997313058899999999999998536--
Q gi|254780828|r    7 KHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--   84 (190)
Q Consensus         7 ~~~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--   84 (190)
                      ||+||.+||||+|||+++||||||||+|+|.|.++.+++.+||++|++|++++ .+|.++|++.+.+.++.++++++.  
T Consensus         1 ~f~py~~nG~Tivgi~~~dgVvlaaD~r~~~~~~~~~~~~~Ki~~I~~~i~~~-~sG~~~D~~~l~~~l~~~~~~~~~~~   79 (213)
T 1iru_M            1 RFSPYVFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIG-CSGFHGDCLTLTKIIEARLKMYKHSN   79 (213)
T ss_dssp             CCCSCCCCCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             98886578807999997999999987875558766638765299957987999-40657999999999999988889870


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCC-----EEEECCCC-CCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHH------
Q ss_conf             656306799999976112220131-----04513787-646998058631141327996064234578898520------
Q gi|254780828|r   85 QLLRSSVELAKDWRMDKYLRNLEA-----MILIADKT-ITLVITGMGDVLEPENGVMAIGSGGSYALSAARALM------  152 (190)
Q Consensus        85 ~~~~~~~~~~~~~~~~~y~~~~~~-----~~~~~~~~-~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y------  152 (190)
                      ....++..+++.++...|.++..|     .+.+.|.. +|.+|..|+.|+..+..|.|+|||+.+|+++||..|      
T Consensus        80 ~~~~~~~~la~~ls~~~~~~~~~p~~v~~lvaG~d~~g~p~ly~iD~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~  159 (213)
T 1iru_M           80 NKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQ  159 (213)
T ss_dssp             SSCCCHHHHHHHHHHHHHHTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCS
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCHHEEEEEEEECCCCCCEEEEECCCCEEEEEEEECCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             99676269999999999862787320011477770689965899858853888226557845999999999751523212


Q ss_pred             ---CCCCC---HHHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             ---78999---8999999999754011022595699999417
Q gi|254780828|r  153 ---STQNS---AEEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       153 ---~~~~s---a~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                         +++|+   |.+++++||..|.+||+.||++++|.+|+.+
T Consensus       160 ~~~~~~~~~eea~~l~~~al~~~~~rd~~sg~~~~v~vi~k~  201 (213)
T 1iru_M          160 NVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKE  201 (213)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCC
T ss_conf             334689999999999999999999757778990899999389


No 5  
>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 1g0u_L 2zcy_L* ...
Probab=100.00  E-value=7.3e-34  Score=230.22  Aligned_cols=181  Identities=15%  Similarity=0.105  Sum_probs=152.6

Q ss_pred             CCCCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--
Q ss_conf             778177637179999979979998136545053677445105798159759997313058899999999999998536--
Q gi|254780828|r    7 KHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--   84 (190)
Q Consensus         7 ~~~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--   84 (190)
                      +|+||.+||||+|||+++||||||||+|+|.|+++.+++.+|||+++++++++ ++|..+|++.+.+.++.++++++.  
T Consensus         1 ~f~py~~nGtTivgi~~~dgVviaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~-~sG~~aD~~~l~~~~~~~~~~~~~~~   79 (222)
T 1ryp_M            1 QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMS-ANGFAADGDALVKRFKNSVKWYHFDH   79 (222)
T ss_dssp             CCCCCCCCCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEEEETTEEEE-EEESHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCEEEEEEECCEEEEEECCCCCCCCEECCCCCCCEEEECCCEEEE-CCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             98874478817999997999999987865668763268755289926989999-25273478999999999986678751


Q ss_pred             -CCCCCHHHHHHHHHHHHHHHHCCC---E--EEECCCC-CCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC----
Q ss_conf             -656306799999976112220131---0--4513787-6469980586311413279960642345788985207----
Q gi|254780828|r   85 -QLLRSSVELAKDWRMDKYLRNLEA---M--ILIADKT-ITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS----  153 (190)
Q Consensus        85 -~~~~~~~~~~~~~~~~~y~~~~~~---~--~~~~~~~-~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~----  153 (190)
                       .....+...+.......+..+..|   .  +.+.|.. +|.++..|+.|+..+.++.|+|||+.+|+++||+.|+    
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~lvaG~d~~g~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~  159 (222)
T 1ryp_M           80 NDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQ  159 (222)
T ss_dssp             TTCCCCHHHHHHHHHHHHHTTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHCCCCC
T ss_conf             78888799999988887775148863024678898078987999987998589834687446558899999976312434


Q ss_pred             -------------CCCCH---HHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             -------------89998---999999999754011022595699999417
Q gi|254780828|r  154 -------------TQNSA---EEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       154 -------------~~~sa---~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                                   ++||.   .+++++||..|.+||++||+++.|.+|+.+
T Consensus       160 ~~~~~~~~~~~~~~~~t~eea~~l~~~al~~~~~rd~~sg~~v~v~vi~kd  210 (222)
T 1ryp_M          160 YEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKD  210 (222)
T ss_dssp             BCTTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETT
T ss_pred             CCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             575410111101224899999999999999999860768997799999489


No 6  
>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H
Probab=100.00  E-value=2.6e-34  Score=233.04  Aligned_cols=169  Identities=24%  Similarity=0.234  Sum_probs=136.6

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCC--H
Q ss_conf             63717999997997999813654505367744510579815975999731305889999999999999853665630--6
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQLLRS--S   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~~~~--~   90 (190)
                      -||||||||+|+||||||+|+|+|+|++|.+|+++||+++++++++ +++|.++|++.+.+.++.++++++......  +
T Consensus        55 ~hGTTivai~~~dGVVlAaD~R~T~g~~i~~~~~~KI~~id~~i~~-~~aG~~aD~~~l~~~l~~e~~~y~~~~~~~~s~  133 (291)
T 2jay_A           55 PHGTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTAT-GIAGTAAVAVEFARLYAVELEHYEKLEGVPLTF  133 (291)
T ss_dssp             ---CCEEEEEETTEEEEEECCC--------CCCCCCEEEEETTEEE-EEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             CCCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEECCCCEEE-EECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             9853699999899999998887677875543775638992897899-955768999999999998888888732888878


Q ss_pred             HHHHHHHHHHH------HHHHCCC--EEEECC------CCCCEEEEECCCCC--EECCCEEEEECCHHHHHHHHHHHHCC
Q ss_conf             79999997611------2220131--045137------87646998058631--14132799606423457889852078
Q gi|254780828|r   91 VELAKDWRMDK------YLRNLEA--MILIAD------KTITLVITGMGDVL--EPENGVMAIGSGGSYALSAARALMST  154 (190)
Q Consensus        91 ~~~~~~~~~~~------y~~~~~~--~~~~~~------~~~~~~~~~d~~g~--~~~~~~~a~GSGs~~A~g~Le~~y~~  154 (190)
                      ...++.+....      +.+++..  .+.+.|      ..++.+|+.|+.|.  .++.+|+|+|||+.+|+++||+.|++
T Consensus       134 ~~~a~~la~~~~~~~~~~~~p~~v~~liaG~D~~g~~~~~~~~Ly~~D~~G~~~~~~~~~~AiGsGs~~A~~~Lek~y~~  213 (291)
T 2jay_A          134 AGKINRLAIMVRGNLAAAMQGLLALPLLAGYDIHASDPQSAGRIVSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQ  213 (291)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHTCCCEEEEEEECTTCSCSTTCEEEEEECTTSCEEECSSSEEEESTTHHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCCEEEEEECCCCEEECCCCEEEECCCHHHHHHHHHHHCCC
T ss_conf             99999999999998874248850478875324667666888608999489973641599899816789999999975237


Q ss_pred             CCCHH---HHHHHHHHHHHCCCEEECCCEEE
Q ss_conf             99989---99999999754011022595699
Q gi|254780828|r  155 QNSAE---EIARKAMSIAADICVYTNHNIVL  182 (190)
Q Consensus       155 ~~sa~---ela~~Al~~A~erDvyTgd~i~i  182 (190)
                      +|+.+   +++++||..|++||.+||+...+
T Consensus       214 ~ms~eeA~~la~~aL~~A~~rD~~SGg~~~~  244 (291)
T 2jay_A          214 VTDGDSGLRVAVEALYDAADDDSATGGPDLV  244 (291)
T ss_dssp             CCSHHHHHHHHHHHHHHC-------------
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             9999999999999999998633557995100


No 7  
>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H
Probab=100.00  E-value=8.3e-34  Score=229.85  Aligned_cols=175  Identities=21%  Similarity=0.167  Sum_probs=140.9

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCC--CCH
Q ss_conf             637179999979979998136545053677445105798159759997313058899999999999998536656--306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQLL--RSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~~--~~~   90 (190)
                      .||||||||+|+||||||+|+|+|+|++|.+++++||++++++++++ ++|.++|++.+.+.++.++++++....  .++
T Consensus        63 ~hGTTiVai~~~dGVviAaD~r~t~g~~i~~~~~~KI~~i~d~i~i~-~aG~~aD~~~l~~~l~~e~~~y~~~~g~~~s~  141 (294)
T 1q5r_H           63 PHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEAVYVTDEYSAAG-IAGTAGIAIELVRLFAVELEHYEKIEGVPLTF  141 (294)
T ss_dssp             CBCCCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEE-EEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             CCCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             98554999998999999988865678765358765399968988999-85568999999999999888888760998668


Q ss_pred             HHHHHHHHHHHHH------HHCC--CEEEECC------CCCCEEEEECCCCCEE--CCCEEEEECCHHHHHHHHHHHHCC
Q ss_conf             7999999761122------2013--1045137------8764699805863114--132799606423457889852078
Q gi|254780828|r   91 VELAKDWRMDKYL------RNLE--AMILIAD------KTITLVITGMGDVLEP--ENGVMAIGSGGSYALSAARALMST  154 (190)
Q Consensus        91 ~~~~~~~~~~~y~------~~~~--~~~~~~~------~~~~~~~~~d~~g~~~--~~~~~a~GSGs~~A~g~Le~~y~~  154 (190)
                      ...++.+....+.      +++.  +.+.+.|      ..++.+|.+|+.|+..  ..+|+|+|||+.+|+++||+.|++
T Consensus       142 ~~~a~~la~~l~~~~~~~~~~~~v~~l~aG~d~~g~d~~~~g~L~~~D~~G~~~~~~~~~~AiGsGs~~A~~~Lek~~~~  221 (294)
T 1q5r_H          142 DGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSP  221 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTTCEEEEEEEECTTCSCTTSCEEEEEECSSSCEEECCSSEEEESTTHHHHHHHHHHHCCS
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEECEEEEEECCCCCCCCCCEEEEEECCCCEEEECCCEEEEECCHHHHHHHHHHHCCC
T ss_conf             89999999999752343567744011067884247767788659999547987886257689847899999999875326


Q ss_pred             CCCHHH---HHHHHHHHHHCCCEEECCC-------EEEEEEECC
Q ss_conf             999899---9999999754011022595-------699999417
Q gi|254780828|r  155 QNSAEE---IARKAMSIAADICVYTNHN-------IVLETLKVG  188 (190)
Q Consensus       155 ~~sa~e---la~~Al~~A~erDvyTgd~-------i~i~~i~~~  188 (190)
                      +|+.+|   ++++||..|+++|.+||+.       +.+.+|+-+
T Consensus       222 ~ms~eeA~~la~~AL~~a~~~D~~sGG~d~~~~~~~~v~~i~~~  265 (294)
T 1q5r_H          222 DSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQA  265 (294)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECC
T ss_conf             99999999999999999996244568854345550489999589


No 8  
>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* 3gpj_N* 3gpt_N* 3gpw_N* ...
Probab=100.00  E-value=5.5e-33  Score=224.71  Aligned_cols=174  Identities=18%  Similarity=0.136  Sum_probs=145.6

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCC-HHH
Q ss_conf             3717999997997999813654505367744510579815975999731305889999999999999853665630-679
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQLLRS-SVE   92 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~~~~-~~~   92 (190)
                      +|||+|||+++||||||+|+|+|.|.++.+++.+||++++|+++++ .+|..+|++.+.+.++.++++++...... +..
T Consensus         8 ~GtTivgi~~kdgVvlaaD~r~s~~~~i~~~~~~Ki~~i~d~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   86 (205)
T 1ryp_H            8 LGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCC-RSGSAADTQAIADIVQYHLELYTSQYGTPSTET   86 (205)
T ss_dssp             CCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEE-EEEBHHHHHHHHHHHHHHHHHHHHHHSSCCHHH
T ss_pred             CCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             7664999999999999988875568676536643599906978899-407689999999999999999888739962789


Q ss_pred             HHHHHHHHHHH--HHCCCE--EEECC-CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCH---HHHHHH
Q ss_conf             99999761122--201310--45137-87646998058631141327996064234578898520789998---999999
Q gi|254780828|r   93 LAKDWRMDKYL--RNLEAM--ILIAD-KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSA---EEIARK  164 (190)
Q Consensus        93 ~~~~~~~~~y~--~~~~~~--~~~~~-~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~ela~~  164 (190)
                      .++.+....|.  +++...  +.+.| ..+|.+|..|+.|+..+.+|.|+|||+.+|+++||+.|+|+|+.   .+++++
T Consensus        87 ~~~~~~~~~~~~~~p~~~~~lvaG~d~~~~p~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ls~~ea~~l~~~  166 (205)
T 1ryp_H           87 AASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKH  166 (205)
T ss_dssp             HHHHHHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCEEEEEEEEECCCCCCEEEEECCCCCEEECCEEEECCCCHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             99999999983535530577887660799968999979951996487998168279999999775527999999999999


Q ss_pred             HHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             999754011022595699999417
Q gi|254780828|r  165 AMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       165 Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ||..|.+||++||+++++.+|+.+
T Consensus       167 al~~~~~rD~~sg~~v~v~vi~~~  190 (205)
T 1ryp_H          167 SLSQAIKWDGSSGGVIRMVVLTAA  190 (205)
T ss_dssp             HHHHHHHHBTTCCSCEEEEEEETT
T ss_pred             HHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             999999751778998899999489


No 9  
>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=5.9e-33  Score=224.52  Aligned_cols=172  Identities=17%  Similarity=0.111  Sum_probs=147.6

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHH
Q ss_conf             1799999799799981365450536774451057981597599973130588999999999999985366--56306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQ--LLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~--~~~~~~~~   93 (190)
                      ||+|||+++||||||||+|+|+|.++.+++++||++|+++++++ .+|..+|++.+.+.++.++++++..  ...++...
T Consensus         1 TTivGi~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~I~~~i~~~-~aG~~aD~~~l~~~~~~~~~~~~~~~g~~~~v~~~   79 (234)
T 1iru_I            1 TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCC-GAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTA   79 (234)
T ss_dssp             CCEEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEE-EEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCCEEEECCCEEEE-EECCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             92999998999999996886668786258745479967979999-95072899999999999999867860998989999


Q ss_pred             HHHHHHHHHHHH--CCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH---HHHHHHH
Q ss_conf             999976112220--131--045137876469980586311413279960642345788985207899989---9999999
Q gi|254780828|r   94 AKDWRMDKYLRN--LEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE---EIARKAM  166 (190)
Q Consensus        94 ~~~~~~~~y~~~--~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~---ela~~Al  166 (190)
                      ++.+....|.++  +..  .+.+.|..+|++|..|+.|+..+.+|.|+|||+.+|+++||+.|+++|+.+   +|+++||
T Consensus        80 ~~~l~~~l~~~~~~~~~~liiaG~D~~gp~Ly~idp~Gs~~~~~~~a~Gsgs~~a~~~Le~~~~~~ms~eeA~~l~~~al  159 (234)
T 1iru_I           80 NRMLKQMLFRYRGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAI  159 (234)
T ss_dssp             HHHHHHHHHHTTTCSCEEEEEEEECSSCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHTHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCEEEEEEEEECCCCEEEEEECCCCEEEEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             99999999736788736999999808998189990894289960785367538899999974358979999999999999


Q ss_pred             HHHHCCCEEECCCEEEEEEECC
Q ss_conf             9754011022595699999417
Q gi|254780828|r  167 SIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       167 ~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ..+.+||.++|+++++.+|+.+
T Consensus       160 ~~~~~~d~~sg~~v~i~vitkd  181 (234)
T 1iru_I          160 AAGIFNDLGSGSNIDLCVISKN  181 (234)
T ss_dssp             HHHHHHCTTCCSCEEEEEEETT
T ss_pred             HHHHHHCCCCCCCEEEEEEECC
T ss_conf             9999646888995899999689


No 10 
>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=1.4e-32  Score=222.12  Aligned_cols=172  Identities=19%  Similarity=0.135  Sum_probs=147.8

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHH
Q ss_conf             17999997997999813654505367744510579815975999731305889999999999999853--6656306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~~~   93 (190)
                      ||+|||+++||||||+|+|+|+|+++.+++.+||++|+++++++ .+|..+|++.+.+.++.++++++  .....++...
T Consensus         1 TTivgi~~~dgVviaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~-~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~   79 (205)
T 1iru_H            1 TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCC-RSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTA   79 (205)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEECCCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             94999998999999988864638776448765399937974999-85245889999999999999999870898618999


Q ss_pred             HHHHHHHHHHHH--CCC--EEEECC-CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCC---HHHHHHHH
Q ss_conf             999976112220--131--045137-8764699805863114132799606423457889852078999---89999999
Q gi|254780828|r   94 AKDWRMDKYLRN--LEA--MILIAD-KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNS---AEEIARKA  165 (190)
Q Consensus        94 ~~~~~~~~y~~~--~~~--~~~~~~-~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~s---a~ela~~A  165 (190)
                      ++.++...|.++  +..  .+.+.| .+++.++..|+.|+..+.+|.|+|||+.+|+++|++.|+++|+   |.+++++|
T Consensus        80 a~~l~~~l~~~~~p~~~~~llaG~D~~~~~~l~~id~~G~~~~~~~~a~G~g~~~a~~~L~~~~~~~mt~~eA~~l~~~a  159 (205)
T 1iru_H           80 ASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANA  159 (205)
T ss_dssp             HHHHHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEECCCCCEEEEEEEEEECCHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             99999999851576348999976646898389998899977872189996875999999987600798999999999999


Q ss_pred             HHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99754011022595699999417
Q gi|254780828|r  166 MSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       166 l~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      |..|.+||++||++++|.+|+.+
T Consensus       160 l~~a~~~D~~sg~~v~v~~i~k~  182 (205)
T 1iru_H          160 LALAMERDGSSGGVIRLAAIAES  182 (205)
T ss_dssp             HHHHHHHBTTCCSCEEEEEEETT
T ss_pred             HHHHHHHCCCCCCCEEEEEEECC
T ss_conf             99999636777996899999389


No 11 
>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 1g0u_I 1fnt_J 1z7q_J 2zcy_I* ...
Probab=100.00  E-value=2.4e-32  Score=220.71  Aligned_cols=179  Identities=14%  Similarity=0.110  Sum_probs=152.9

Q ss_pred             CCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCC
Q ss_conf             817763717999997997999813654505367744510579815975999731305889999999999999853--665
Q gi|254780828|r    9 YAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQL   86 (190)
Q Consensus         9 ~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~   86 (190)
                      +|+++||||+|||+++||||||||+|+|+|.++.+++.+||+++ +++++ +++|.++|++.+.+.++.+++.++  ...
T Consensus         2 ~p~~~nG~T~vgi~~~dgVvlaaD~r~t~~~~~~~~~~~Ki~~~-~~i~~-~~aG~~aD~~~l~~~l~~~~~~~~~~~~~   79 (204)
T 1ryp_J            2 DPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFL-GITGLATDVTTLNEMFRYKTNLYKLKEER   79 (204)
T ss_dssp             CGGGSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEE-TTEEE-EEEECHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCEEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEE-CCEEE-EEEECHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             98776873899999899999998788666888561775479994-99999-99766898999999999998888987399


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCE-----EEECCC--CCCEEEEECCCCCEEC-CCEEEEECCHHHHHHHHHHHHCCCCCH
Q ss_conf             63067999999761122201310-----451378--7646998058631141-327996064234578898520789998
Q gi|254780828|r   87 LRSSVELAKDWRMDKYLRNLEAM-----ILIADK--TITLVITGMGDVLEPE-NGVMAIGSGGSYALSAARALMSTQNSA  158 (190)
Q Consensus        87 ~~~~~~~~~~~~~~~y~~~~~~~-----~~~~~~--~~~~~~~~d~~g~~~~-~~~~a~GSGs~~A~g~Le~~y~~~~sa  158 (190)
                      +.++..+++.++...|.++..|+     +.+.|.  +.|.+|..|+.|...+ ..+++.|+|+.+|+++|++.|+++|+.
T Consensus        80 ~~~~~~la~~l~~~~~~~~~~p~~~~~lvaG~d~~~g~~~l~~~D~~G~~~~~~~~~a~G~gs~~a~~~L~~~~~~~ls~  159 (204)
T 1ryp_J           80 AIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEP  159 (204)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCH
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCEEEECCEECCCCCCEEEEECCCCEEEEECCCEEEECCHHHHHHHHHHCCCCCCCH
T ss_conf             87568899999999886175420100201055547897079998699829970364896076699999997302247999


Q ss_pred             HH---HHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             99---99999997540110225956999994178
Q gi|254780828|r  159 EE---IARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       159 ~e---la~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      +|   ++++||..|.+||++||++++|.+|+.+.
T Consensus       160 ~ea~~l~~~al~~a~~~d~~sg~~~~v~ii~kdg  193 (204)
T 1ryp_J          160 EDLFETISQALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCC
T ss_conf             9999999999999987467669838999998995


No 12 
>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3bdm_H* 1fnt_I* ...
Probab=100.00  E-value=2.5e-32  Score=220.64  Aligned_cols=173  Identities=18%  Similarity=0.165  Sum_probs=147.3

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHH
Q ss_conf             1799999799799981365450536774451057981597599973130588999999999999985366--56306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQ--LLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~--~~~~~~~~   93 (190)
                      ||+|||+++||||||||+|+|.|+++.+++.+||++|+++++++ ++|..+|++.+.+.++.+.++++..  ....+...
T Consensus         1 TTiVgi~~~dgVviaaD~r~t~g~~i~~~~~~KI~~I~d~i~~a-~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~   79 (222)
T 1ryp_I            1 TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCA-GAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSA   79 (222)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCCEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             92999998999999986875568555347744489968979999-87867999999999999999987863898749999


Q ss_pred             HHHHHHHHHH--HHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCH---HHHHHHHH
Q ss_conf             9999761122--20131--04513787646998058631141327996064234578898520789998---99999999
Q gi|254780828|r   94 AKDWRMDKYL--RNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSA---EEIARKAM  166 (190)
Q Consensus        94 ~~~~~~~~y~--~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~ela~~Al  166 (190)
                      ++.+....|.  +++..  .+.+.|..+|++|..|+.|...+.+|+|+|||+++|+++||+.|+++|+.   .+++++||
T Consensus        80 a~~~~~~~~~~~~p~~~~~iiaG~d~~g~~Ly~id~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~ms~~ea~~l~~~al  159 (222)
T 1ryp_I           80 LQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAI  159 (222)
T ss_dssp             HHHHHHHHHHTTTCSCEEEEEEEEETTEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEECCCCEEECCEEEECCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             99999999874016754899999849998799980775664136799879956889999965238989999999999999


Q ss_pred             HHHHCCCEEECCCEEEEEEECCC
Q ss_conf             97540110225956999994178
Q gi|254780828|r  167 SIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       167 ~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      ..|.+||++||++++|.+|+-+.
T Consensus       160 ~~a~~~d~~sg~~iei~vi~~~~  182 (222)
T 1ryp_I          160 QAGIWNDLGSGSNVDVCVMEIGK  182 (222)
T ss_dssp             HHHHHHCTTCCSCEEEEEEETTS
T ss_pred             HHHHHHCCCCCCCEEEEEEECCC
T ss_conf             99986557789978999999599


No 13 
>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=2.3e-32  Score=220.80  Aligned_cols=172  Identities=21%  Similarity=0.158  Sum_probs=150.2

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHH
Q ss_conf             17999997997999813654505367744510579815975999731305889999999999999853--6656306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~~~   93 (190)
                      ||+|||+++||||||||+|+|+|+++.+++++||++++|+++++ ++|.++|.+.+.+.++.++++++  .....++..+
T Consensus         1 TT~iai~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~i~d~i~~~-~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~   79 (204)
T 1iru_L            1 TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGT-MAGGAADCSFWERLLARQCRIYELRNKERISVAAA   79 (204)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEE-CCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCCEEEECCCEEEE-EECCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             95999998999999988864648777558755289978975899-84471678999999999999877630789867899


Q ss_pred             HHHHHHHHHHHHCCC-----EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH---HHHHHH
Q ss_conf             999976112220131-----045137876469980586311413279960642345788985207899989---999999
Q gi|254780828|r   94 AKDWRMDKYLRNLEA-----MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE---EIARKA  165 (190)
Q Consensus        94 ~~~~~~~~y~~~~~~-----~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~---ela~~A  165 (190)
                      ++.+....|.++..|     .+.+.|..+|.++..|+.|...+.+++|+|||+++|+++|++.|+++|+.+   +++++|
T Consensus        80 ~~~l~~~~~~~~~~p~~~~~i~~G~d~~g~~l~~~d~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~ms~~ea~~l~~~a  159 (204)
T 1iru_L           80 SKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRA  159 (204)
T ss_dssp             HHHHHHHHHTTTTSCCCBEEEEEEECSSSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEECCCCEEEECCEEEECCCCHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99999999972799852789999995488679999278328984357726885899999985545998999999999999


Q ss_pred             HHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99754011022595699999417
Q gi|254780828|r  166 MSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       166 l~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      |+.|.+||..+|+++++.+|+.+
T Consensus       160 l~~~~~~d~~sg~~i~v~~i~~~  182 (204)
T 1iru_L          160 IYQATYRDAYSGGAVNLYHVRED  182 (204)
T ss_dssp             HHHHHHHBTTCCSEEEEEEECSS
T ss_pred             HHHHHHHCCCCCCCEEEEEEECC
T ss_conf             99999727778996699999489


No 14 
>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M*
Probab=100.00  E-value=2e-32  Score=221.26  Aligned_cols=181  Identities=15%  Similarity=0.145  Sum_probs=150.3

Q ss_pred             CCCCCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             77781776371799999799799981365450536774451057981597599973130588999999999999985366
Q gi|254780828|r    6 DKHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQ   85 (190)
Q Consensus         6 ~~~~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~   85 (190)
                      +..+|+. +|||+|||+++||||||||+|+|.|+++.+++++||++|+++++++ .+|.++|.+.+.+.++.++.++...
T Consensus        33 ~~~~p~~-tGtTvvgi~~~dGVvlaaD~r~t~g~l~~~~~~~KI~~I~d~i~~~-~sG~~aD~~~l~~~l~~~~~~~~~~  110 (266)
T 1g0u_M           33 NTQQPIV-TGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVG-ISGDISDMQHIERLLKDLVTENAYD  110 (266)
T ss_dssp             -CCCCCE-EECCEEEEEETTEEEEEEECCEEETTEEEECCCCCEEECTTSEEEE-EEEEHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCC-CCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             3338814-7533999998999999986876668665348765289957978999-8347077999999999999999975


Q ss_pred             -------CCCCHHHHHHHHHHHHHHH-----HCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHH
Q ss_conf             -------5630679999997611222-----0131--0451378-76469980586311413279960642345788985
Q gi|254780828|r   86 -------LLRSSVELAKDWRMDKYLR-----NLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARA  150 (190)
Q Consensus        86 -------~~~~~~~~~~~~~~~~y~~-----~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~  150 (190)
                             ....+..+++.+.+..|..     ++..  .+.+.|. +++.++..|+.|...+.+|+|+|||+.+|+++||+
T Consensus       111 ~~~~~~~~~~~~~~~a~~ls~~~y~~~~~~~P~~vs~liaG~d~~g~~~l~~iD~~G~~~~~~~~aiGsGs~~a~~~Le~  190 (266)
T 1g0u_M          111 NPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRK  190 (266)
T ss_dssp             CTTTTTTTSCCHHHHHHHHHHHHHHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHTHHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCEEEEEECCCCCEEECCEEEECCCHHHHHHHHHH
T ss_conf             47667774027999999999988875433376640789988817997399998798557873779988768999999999


Q ss_pred             HHC-----CCCC---HHHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             207-----8999---8999999999754011022595699999417
Q gi|254780828|r  151 LMS-----TQNS---AEEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       151 ~y~-----~~~s---a~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      .|+     ++|+   |.+++++||+++.+||..+|++|+|.+|+.+
T Consensus       191 ~~~~~~~~~~ms~eea~~l~~~al~~~~~rD~~sg~~i~i~vI~kd  236 (266)
T 1g0u_M          191 VVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKN  236 (266)
T ss_dssp             TCSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETT
T ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             8631278889899999999999999999645668996799999699


No 15 
>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=7e-32  Score=217.83  Aligned_cols=179  Identities=14%  Similarity=0.159  Sum_probs=151.8

Q ss_pred             CCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCC
Q ss_conf             817763717999997997999813654505367744510579815975999731305889999999999999853--665
Q gi|254780828|r    9 YAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQL   86 (190)
Q Consensus         9 ~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~   86 (190)
                      .++++||||+|||+++||||||+|+|+|.|.++.+++.+||++|+++++++ ++|..+|++.+.+.++.++++++  ...
T Consensus         2 ~~~~~nG~Tvigi~~~dgVvlaaD~r~t~~~~i~~~~~~Ki~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~   80 (205)
T 1iru_J            2 SIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIG-LAGLATDVQTVAQRLKFRLNLYELKEGR   80 (205)
T ss_dssp             CCTTSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEE-CCSCHHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             CCCCCCCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EECCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             743126743999998999999998875669766527654699957982899-7238178999999999988776665155


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCC-----EEEECCCC--CCEEEEECCCCC-EECCCEEEEECCHHHHHHHHHHHHCCCCCH
Q ss_conf             6306799999976112220131-----04513787--646998058631-141327996064234578898520789998
Q gi|254780828|r   87 LRSSVELAKDWRMDKYLRNLEA-----MILIADKT--ITLVITGMGDVL-EPENGVMAIGSGGSYALSAARALMSTQNSA  158 (190)
Q Consensus        87 ~~~~~~~~~~~~~~~y~~~~~~-----~~~~~~~~--~~~~~~~d~~g~-~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa  158 (190)
                      ..++..+++.+....|.++..+     .+.+.|.+  .++++..|+.+. .++..|.|.|+|+.+++++||+.|+++|+.
T Consensus        81 ~~~~~~la~~l~~~~~~~~~~p~~~~~liaG~d~~~~~~~l~~~d~~g~~~~~~~~~a~G~g~~~~~~~le~~~~~~mt~  160 (205)
T 1iru_J           81 QIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDP  160 (205)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCH
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEEEECCCCCEEEECCEEEECCCHHHHHHHHHHHCCCCCCH
T ss_conf             65417999999999886326883378999998579981799997399643562226674475599999999743334678


Q ss_pred             HH---HHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99---9999999754011022595699999417
Q gi|254780828|r  159 EE---IARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       159 ~e---la~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +|   ++++||..|.+||++||++++|.+|+.+
T Consensus       161 ~ea~~l~~~~l~~~~~rd~~sg~~v~v~ii~kd  193 (205)
T 1iru_J          161 DHLFETISQAMLNAVDRDAVSGMGVIVHIIEKD  193 (205)
T ss_dssp             HHHHHHHHHHHHHHGGGBTTSCSCEEEEEEESS
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             999999999999998644668991899999389


No 16 
>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=100.00  E-value=4.9e-32  Score=218.78  Aligned_cols=178  Identities=19%  Similarity=0.106  Sum_probs=152.2

Q ss_pred             CCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC---CC
Q ss_conf             817763717999997997999813654505367744510579815975999731305889999999999999853---66
Q gi|254780828|r    9 YAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP---NQ   85 (190)
Q Consensus         9 ~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~---~~   85 (190)
                      +|+. +|||+|||+++||||||+|+|+|.|.++.+++++||++|+++++++ ++|.++|++.+.+.++.++.+++   ..
T Consensus         3 ~~~~-~GtTivgi~~~dgVvlaaD~r~t~g~~~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~l~~~~~~~~~~~~~   80 (219)
T 1iru_N            3 NPMV-TGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLG-ASGDYADFQYLKQVLGQMVIDEELLGDG   80 (219)
T ss_dssp             SCCS-EECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEE-EEEEHHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             CCCC-CCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-ECCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9867-6217999998999999987876678665137765099917980599-4127779999999999999984664468


Q ss_pred             CCCCHHHHHHHHHHHHHHHH-----CC--CEEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC--CCC
Q ss_conf             56306799999976112220-----13--1045137876469980586311413279960642345788985207--899
Q gi|254780828|r   86 LLRSSVELAKDWRMDKYLRN-----LE--AMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS--TQN  156 (190)
Q Consensus        86 ~~~~~~~~~~~~~~~~y~~~-----~~--~~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~--~~~  156 (190)
                      ...++..+++.++...|.++     +.  ..+.+.|.++|+++..|+.|...+.+++|+|||+++|+++||+.|+  ++|
T Consensus        81 ~~~~~~~~a~~l~~~~y~~~~~~~p~~~~~l~aG~d~~~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~l  160 (219)
T 1iru_N           81 HSYSPRAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADGESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVL  160 (219)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHTTCCCCEEEEEEEEETTEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECCCEEEEECCEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf             87878899999999999754324861179999997588866999889704666149998078899999999975224799


Q ss_pred             C---HHHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             9---8999999999754011022595699999417
Q gi|254780828|r  157 S---AEEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       157 s---a~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +   |.+++++||+.|.+||+++|+++++.+|+.+
T Consensus       161 s~~ea~~l~~~al~~~~~~d~~sg~~i~v~~i~~~  195 (219)
T 1iru_N          161 SQTEARDLVERCMRVLYYRDARSYNRFQTATVTEK  195 (219)
T ss_dssp             CHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETT
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             99999999999999999851768994899999589


No 17 
>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g0u_K 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* 3hye_K* ...
Probab=100.00  E-value=9.2e-32  Score=217.07  Aligned_cols=172  Identities=19%  Similarity=0.143  Sum_probs=147.7

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHH
Q ss_conf             17999997997999813654505367744510579815975999731305889999999999999853--6656306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~~~   93 (190)
                      ||+|||+++||||||+|+|+|.|+++.+++.+||++++++++++ ++|.++|.+.+.+.++.++.+++  .....++..+
T Consensus         1 TT~iai~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~v~~l   79 (212)
T 1ryp_L            1 TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGT-MAGGAADCQFWETWLGSQCRLHELREKERISVAAA   79 (212)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEE-CCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-EEECCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             93999998999999985875658676358754189967957999-74271768999999999988888750898878999


Q ss_pred             HHHHHHHHHHHHCCC-----EEEEC-CCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH---HHHHH
Q ss_conf             999976112220131-----04513-7876469980586311413279960642345788985207899989---99999
Q gi|254780828|r   94 AKDWRMDKYLRNLEA-----MILIA-DKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE---EIARK  164 (190)
Q Consensus        94 ~~~~~~~~y~~~~~~-----~~~~~-~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~---ela~~  164 (190)
                      ++.+....|.++..+     .+++. +..+|++|..|+.|+..+.+++|+|+|+.+|+++||+.|+++|+.+   +++++
T Consensus        80 a~~l~~~~~~~~~~p~~~~~li~G~~~~~gp~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~eea~~l~~~  159 (212)
T 1ryp_L           80 SKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKR  159 (212)
T ss_dssp             HHHHHHHHHHTTTSCCCBEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEEEEECCCCCEEEEECCCEEEEECCCEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             99999999985379861688998996189528999859868997671798885288999999874369998999999999


Q ss_pred             HHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             999754011022595699999417
Q gi|254780828|r  165 AMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       165 Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ||..|.+||.++|++++|.+|+-+
T Consensus       160 al~~~~~rd~~sg~~v~v~vvtkd  183 (212)
T 1ryp_L          160 SILAAAHRDAYSGGSVNLYHVTED  183 (212)
T ss_dssp             HHHHHHHHBTTCCSEEEEEEEETT
T ss_pred             HHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             999999746878996599999389


No 18 
>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase/hydrolase activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H
Probab=100.00  E-value=1.5e-31  Score=215.73  Aligned_cols=175  Identities=17%  Similarity=0.143  Sum_probs=149.1

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|+|.|+++.+++.+|||+|+++++++ ++|.++|++.+.+.++.+++.++.  ....++.
T Consensus         7 ~GtTivgi~~kdgVvlaaD~r~~~~~~~~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   85 (217)
T 1yar_H            7 TGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMT-IAGLVGDAQVLVRYMKAELELYRLQRRVNMPIE   85 (217)
T ss_dssp             --CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEECCCCCCCCEECCCCCCEEEEECCCCEEE-CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             7463999998999999987876668763278755199977982267-555617899999999999777787428888999


Q ss_pred             HHHHHHHHHHHHHHCCCE----EEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCH---HHHHHH
Q ss_conf             999999761122201310----4513787646998058631141327996064234578898520789998---999999
Q gi|254780828|r   92 ELAKDWRMDKYLRNLEAM----ILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSA---EEIARK  164 (190)
Q Consensus        92 ~~~~~~~~~~y~~~~~~~----~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~ela~~  164 (190)
                      ..+..++...+..++.|+    ++++.+.+|.++..|+.|+..+..++|+|+|+.+|+++||+.|+++|+.   .+++++
T Consensus        86 ~~~~~l~~~~~~~~~~p~~~~~liaG~d~~~~l~~iD~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~s~~ea~~l~~~  165 (217)
T 1yar_H           86 AVATLLSNMLNQVKYMPYMVQLLVGGIDTAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIR  165 (217)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEEEEEEESSSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCEEEECCCCEEEEEEEEECCCCHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99999999987226677427889974248875786179824887547853765599999999744379899999999999


Q ss_pred             HHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             9997540110225956999994178
Q gi|254780828|r  165 AMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       165 Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      ||..+.+||+.+|+++++.+|+.++
T Consensus       166 al~~~~~~d~~s~~~iev~~i~~~~  190 (217)
T 1yar_H          166 AISAAKQRDSASGGMIDVAVITRKD  190 (217)
T ss_dssp             HHHHHHHHCTTCCSCCEEEEEETTT
T ss_pred             HHHHHHHHCCCCCCEEEEEEEECCC
T ss_conf             9999997478889869999997899


No 19 
>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R
Probab=100.00  E-value=2.1e-31  Score=214.89  Aligned_cols=178  Identities=15%  Similarity=0.131  Sum_probs=147.0

Q ss_pred             CCEEECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCC--
Q ss_conf             817763717999997997999813654505367744510579815975999731305889999999999999853665--
Q gi|254780828|r    9 YAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQL--   86 (190)
Q Consensus         9 ~~~~~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~--   86 (190)
                      +|+.. |||+|||+++||||||||+|+|.|.++.+++.+||++|++|++++ ++|.++|.+.+.+.++.+..+++...  
T Consensus         3 ~~i~t-GtTvvgi~~~dgVvlaaD~r~s~g~l~~~~~~~KI~~I~~~i~~~-~aG~~aD~~~l~~~l~~~~~~~~~~~~~   80 (233)
T 1ryp_N            3 QPIVT-GTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVG-ISGDISDMQHIERLLKDLVTENAYDNPL   80 (233)
T ss_dssp             CCCEE-ECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEE-EEEEHHHHHHHHHHHHHHHHHHHTTCTT
T ss_pred             CCCCC-CCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-ECCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             87166-635999998999999984786668664047755389966967999-6267078999999999999999874277


Q ss_pred             -----CCCHHHHHHHHHHHHHH-----HHCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC
Q ss_conf             -----63067999999761122-----20131--0451378-76469980586311413279960642345788985207
Q gi|254780828|r   87 -----LRSSVELAKDWRMDKYL-----RNLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS  153 (190)
Q Consensus        87 -----~~~~~~~~~~~~~~~y~-----~~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~  153 (190)
                           ...+..+++.+....|.     +++..  .+.+.|. +.+.++..|+.|...+.++.|+|||+++|+++||+.|+
T Consensus        81 ~~~~~~l~~~~~a~~l~~~~y~~~~~~~P~~v~~li~G~d~~g~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~  160 (233)
T 1ryp_N           81 ADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVD  160 (233)
T ss_dssp             TTTTTSCCHHHHHHHHHHHHHHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCEEEEEECCCEEEEECCEEEECCCHHHHHHHHHHHHH
T ss_conf             78763027999999999888765433477624899999807998599997797778884789989867999999999853


Q ss_pred             -----CCCC---HHHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             -----8999---8999999999754011022595699999417
Q gi|254780828|r  154 -----TQNS---AEEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       154 -----~~~s---a~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                           ++|+   |.+++++||+.|.+||+++|+++++.+|+-+
T Consensus       161 ~~~~~~~ms~eea~~l~~~al~~~~~rD~~sg~~i~v~vitkd  203 (233)
T 1ryp_N          161 RESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKN  203 (233)
T ss_dssp             SGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             1278889899999999999999999645668996899999899


No 20 
>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4
Probab=100.00  E-value=4.2e-31  Score=212.97  Aligned_cols=171  Identities=22%  Similarity=0.177  Sum_probs=138.7

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHHHH
Q ss_conf             179999979979998136545053677445105798159759997313058899999999999998536--656306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~~~   93 (190)
                      ||+|||+++||||||||+|+|+|+++.+++.+||++|+++++++ ++|..+|++.+.+.++.++++++.  ....++..+
T Consensus         1 TTivgIk~kdgVvlaaD~r~t~g~~i~~~~~~KI~~i~d~i~~~-~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~   79 (235)
T 1q5q_H            1 TTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAG-IAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGK   79 (235)
T ss_dssp             CCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-ECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             91999998999999988875569776358765299978978999-80547889999999876423444200567648999


Q ss_pred             HHHHHHHHHHH------HC--CCEEEECC------CCCCEEEEECCCCCEE--CCCEEEEECCHHHHHHHHHHHHCCCCC
Q ss_conf             99997611222------01--31045137------8764699805863114--132799606423457889852078999
Q gi|254780828|r   94 AKDWRMDKYLR------NL--EAMILIAD------KTITLVITGMGDVLEP--ENGVMAIGSGGSYALSAARALMSTQNS  157 (190)
Q Consensus        94 ~~~~~~~~y~~------~~--~~~~~~~~------~~~~~~~~~d~~g~~~--~~~~~a~GSGs~~A~g~Le~~y~~~~s  157 (190)
                      ++.+....+.+      ++  .+.+.+.+      ..+|.+|..|+.|...  +.+|+|+|||+.+|+++||+.|+++||
T Consensus        80 a~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~g~d~~~~~~ly~~d~~G~~~~~~~~~~a~GsG~~~a~~~Le~~~~~~ms  159 (235)
T 1q5q_H           80 ANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSD  159 (235)
T ss_dssp             HHHHHHHHHTTHHHHTTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEECCCEEEECCCEEEEECCHHHHHHHHHHHCCCCCC
T ss_conf             99999999870453334653145798853246667898559999846967874367689967889999999975568999


Q ss_pred             HH---HHHHHHHHHHHCCCEEECC-------CEEEEEEEC
Q ss_conf             89---9999999975401102259-------569999941
Q gi|254780828|r  158 AE---EIARKAMSIAADICVYTNH-------NIVLETLKV  187 (190)
Q Consensus       158 a~---ela~~Al~~A~erDvyTgd-------~i~i~~i~~  187 (190)
                      .+   +++++||+.|++||.+||+       ++.+.+|+.
T Consensus       160 ~eea~~la~~al~~a~~rD~~sGg~~~~~~~~~~~~~~~~  199 (235)
T 1q5q_H          160 EETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQ  199 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEET
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEC
T ss_conf             9999999999999998624556884323443259999948


No 21 
>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4
Probab=99.98  E-value=1.3e-30  Score=209.88  Aligned_cols=172  Identities=17%  Similarity=0.079  Sum_probs=148.1

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHHHH
Q ss_conf             179999979979998136545053677445105798159759997313058899999999999998536--656306799
Q gi|254780828|r   16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSVEL   93 (190)
Q Consensus        16 TTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~~~   93 (190)
                      ||+|||+++||||||||+|+|.|.++.+++.+||++|+++++++ ++|..+|.+.+.+.++.+++.++.  ....++..+
T Consensus         1 TT~vgi~~~dgVvlaaD~r~s~~~~~~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~   79 (202)
T 1j2q_H            1 TTTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMT-TAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAI   79 (202)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-ECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             91999998999999986876658765068756299967982898-32560789999999999987777504898769999


Q ss_pred             HHHHHHHHHHHHCCC-----EEEECCCCCCEEEEECCCCCEE-CCCEEEEECCHHHHHHHHHHHHCCCCCH---HHHHHH
Q ss_conf             999976112220131-----0451378764699805863114-1327996064234578898520789998---999999
Q gi|254780828|r   94 AKDWRMDKYLRNLEA-----MILIADKTITLVITGMGDVLEP-ENGVMAIGSGGSYALSAARALMSTQNSA---EEIARK  164 (190)
Q Consensus        94 ~~~~~~~~y~~~~~~-----~~~~~~~~~~~~~~~d~~g~~~-~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~ela~~  164 (190)
                      ++.++...+.+++.|     .+.+.|..+|.++..|+.|... ..+|+|+|||+.+|+++|++.|+++|+.   .+++++
T Consensus        80 a~~l~~~~~~~~~~p~~~~~liaG~d~~~~~l~~~d~~G~~~~~~~~~a~G~g~~~~~~~L~~~~~~~ms~~ea~~l~~~  159 (202)
T 1j2q_H           80 ATLTSNLLNSYRYFPYLVQLLIGGIDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVR  159 (202)
T ss_dssp             HHHHHHHHHHTTTSCCCEEEEEEEEETTEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEEECCCCEEEECCEEECCCCHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99987888750668701278999994899789999679987871446883687189999999656799699999999999


Q ss_pred             HHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             999754011022595699999417
Q gi|254780828|r  165 AMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       165 Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ||..|.++|.+||+++++.+|+.+
T Consensus       160 ~l~~~~~~d~~~g~~i~v~~i~~~  183 (202)
T 1j2q_H          160 AIYSAMKRDSASGDGIDVVKITED  183 (202)
T ss_dssp             HHHHHHTTCTTSCSCEEEEEECSS
T ss_pred             HHHHHHHHCCCCCCEEEEEEEECC
T ss_conf             999999746888983899999889


No 22 
>3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}
Probab=99.97  E-value=9.8e-30  Score=204.39  Aligned_cols=173  Identities=21%  Similarity=0.139  Sum_probs=144.9

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHHH
Q ss_conf             717999997997999813654505367744510579815975999731305889999999999999853--665630679
Q gi|254780828|r   15 ATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSVE   92 (190)
Q Consensus        15 GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~~   92 (190)
                      -||+|||+++||||||+|+|+|.|.++.+++.+||++|+++++++ ++|..+|.+.+.+.++.++++++  ......+..
T Consensus         1 MTT~vgi~~~dgVvlaaD~r~t~~~~~~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~   79 (219)
T 3h4p_a            1 MTTTVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMT-IAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLA   79 (219)
T ss_dssp             -CCEEEEEETTEEEEECCCCEEETTEEEETTCCCEEEEETTEEEE-CCSCHHHHHHHHHHHHHHHHHHHHHTSSCCCHHH
T ss_pred             CCEEEEEEECCEEEEEECCCCCCCCEECCCCCCEEEEECCCEEEE-ECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             932999998999999983886668663068755699978968999-6446388999999999998876540255665478


Q ss_pred             HHHHHHHHHHHHHCCC---E--EEECC-CCCCEEEEECCCCCE-ECCCEEEEECCHHHHHHHHHHHHCCCCCHH---HHH
Q ss_conf             9999976112220131---0--45137-876469980586311-413279960642345788985207899989---999
Q gi|254780828|r   93 LAKDWRMDKYLRNLEA---M--ILIAD-KTITLVITGMGDVLE-PENGVMAIGSGGSYALSAARALMSTQNSAE---EIA  162 (190)
Q Consensus        93 ~~~~~~~~~y~~~~~~---~--~~~~~-~~~~~~~~~d~~g~~-~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~---ela  162 (190)
                      +++.+....|.++..|   .  +.+.+ .++|+++..|+.|.. +..+|.|+|+|+.+|+++||+.|+++|+.+   +++
T Consensus        80 ~a~~l~~~~~~~~~~P~~~~~llaG~d~~~~~~L~~~d~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~ea~~l~  159 (219)
T 3h4p_a           80 CATLLSNILHSSRMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEGIKLA  159 (219)
T ss_dssp             HHHHHHHHHHHTTTTTCCCCCEEEEEETTTEEEEEEECSSCCEEECSSEEEESTTHHHHHHHHHTSCCTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCEEEEECCCCCEEECCEEEEEECCCHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             99999999985167773489999998258993576652898802334047743671876546761567799999999999


Q ss_pred             HHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99999754011022595699999417
Q gi|254780828|r  163 RKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       163 ~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ++||..|.+||+++|++++|.+|+.+
T Consensus       160 ~~al~~~~~~d~~s~~~v~v~vi~~~  185 (219)
T 3h4p_a          160 LNALKSAMERDTFSGNGISLAVITKD  185 (219)
T ss_dssp             HHHHHHHHTSCSSCCSCCCEEEEETT
T ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECC
T ss_conf             99999998636788996799999789


No 23 
>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.97  E-value=4.9e-30  Score=206.26  Aligned_cols=173  Identities=14%  Similarity=0.095  Sum_probs=144.4

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHHH
Q ss_conf             7179999979979998136545053677445105798159759997313058899999999999998536--65630679
Q gi|254780828|r   15 ATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSVE   92 (190)
Q Consensus        15 GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~~   92 (190)
                      -||+|||+++||||||||+|+|+|+++.+++.+|||+++++++++ .+|..+|++.+.+.++.++++++.  .....+..
T Consensus         1 Mt~vvgi~~~dgVviaaDtr~~~g~~~~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   79 (201)
T 1iru_K            1 MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLL-CVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTA   79 (201)
T ss_dssp             CCCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEE-EEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHH
T ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCCCCCCCCEEEEECCCEEEE-ECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             909999998999999987875679731168755199946968999-7146488999999998776666663088676899


Q ss_pred             HHHHHHHHHHHH-----HCCC--EEEECC-CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCH---HHH
Q ss_conf             999997611222-----0131--045137-87646998058631141327996064234578898520789998---999
Q gi|254780828|r   93 LAKDWRMDKYLR-----NLEA--MILIAD-KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSA---EEI  161 (190)
Q Consensus        93 ~~~~~~~~~y~~-----~~~~--~~~~~~-~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~el  161 (190)
                      .++.+....|..     ++..  .+.+.+ ..+|.++..|+.|...+.+|+|+|||+.+|+++|++.|+++|+.   .++
T Consensus        80 ~~~~~~~~~~~~~~~~~p~~~~~liaG~d~~~~~~l~~~d~~G~~~~~~~~a~Gsg~~~~~~~L~~~~~~~~~~~ea~~l  159 (201)
T 1iru_K           80 AANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVEL  159 (201)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCEEEEEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEEECCCEEEEECCEEEEECCCHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             99999999999986468850454461162589827999749853886683466055488999998651489599999999


Q ss_pred             HHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             999999754011022595699999417
Q gi|254780828|r  162 ARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       162 a~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +++||..|.+||++||++++|.+|+.+
T Consensus       160 ~~~~l~~~~~rd~~~g~~~~v~vv~~~  186 (201)
T 1iru_K          160 LRKCLEELQKRFILNLPTFSVRIIDKN  186 (201)
T ss_dssp             HHHHHHHHHHTBCBCCCCEEEEEEETT
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             999999999864877991599999389


No 24 
>1iru_C 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.97  E-value=7.2e-30  Score=205.24  Aligned_cols=175  Identities=17%  Similarity=0.079  Sum_probs=146.3

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCH
Q ss_conf             63717999997997999813654505367744510579815975999731305889999999999999853--6656306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~   90 (190)
                      -+|||+|||+++||||||||+|++.|.++.+++.+||++|++|++++ .+|..+|.+.+.+.++.++.+++  .....++
T Consensus        29 ~~G~T~vgik~kdgVvlaad~r~~~~~~~~~~~~~KI~~I~d~i~~~-~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~  107 (261)
T 1iru_C           29 GHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACS-VAGITSDANVLTNELRLIAQRYLLQYQEPIPC  107 (261)
T ss_dssp             TTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             HCCCCEEEEEECCEEEEEEECCCCCCCCCCCCCCCEEEECCCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             75887899997999999997776667832566455089847977999-67807999999999999999879971999983


Q ss_pred             HHHHHHHHHHHHH-------HHCCCE--EEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHC-CCCCHH
Q ss_conf             7999999761122-------201310--451378-76469980586311413279960642345788985207-899989
Q gi|254780828|r   91 VELAKDWRMDKYL-------RNLEAM--ILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMS-TQNSAE  159 (190)
Q Consensus        91 ~~~~~~~~~~~y~-------~~~~~~--~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~-~~~sa~  159 (190)
                      ..+++.+....+.       +++...  +.+.|. .+|.+|..|+.|+..+.++.|+|||+.+|+++|++.|+ ++|+.+
T Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~v~~ii~G~D~~~gp~Ly~~d~~Gs~~~~~~~a~G~gs~~~~~~Le~~~~~~~mt~e  187 (261)
T 1iru_C          108 EQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLK  187 (261)
T ss_dssp             HHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEECSEEEESTTTTHHHHHHHHHCCTTCCCHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEECCEEEECCCCHHHHHHHHHHCCCCCCCHH
T ss_conf             89999999998887502455765505699987179985688658996378107289889709999999951677898999


Q ss_pred             ---HHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             ---99999999754011022595699999417
Q gi|254780828|r  160 ---EIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       160 ---ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                         +++++||+.|.+||..++++++|.+|+.+
T Consensus       188 ea~~la~~al~~a~~~d~~s~~~iev~vi~k~  219 (261)
T 1iru_C          188 SALALAIKVLNKTMDVSKLSAEKVEIATLTRE  219 (261)
T ss_dssp             HHHHHHHHHHHHSSSCTTCCSTTCEEEEEECC
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEEEEECC
T ss_conf             99999999999986054788981899999816


No 25 
>1ryp_C 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_B* 1g65_B 2f16_B* 2fak_B* 2fny_B* 2gpl_B* 3d29_B* 3dy3_B* 3dy4_B* 3e47_B* 3gpj_B* 3gpt_B* 3gpw_B* 3hye_B* 3bdm_B* 1z7q_C* 2zcy_B* 1g0u_B 1fnt_C 1vsy_C ...
Probab=99.97  E-value=1.7e-29  Score=202.95  Aligned_cols=175  Identities=18%  Similarity=0.142  Sum_probs=146.3

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCH
Q ss_conf             637179999979979998136545053677445105798159759997313058899999999999998536--656306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~   90 (190)
                      .+|||+|||+++||||||+|+|+++|..+.+++.+||++++++++++ ++|.++|.+.+.+.++.++++++.  ....++
T Consensus        29 ~~G~t~vgi~~~dgVvlaad~~~~~~~~~~~~~~~Ki~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (244)
T 1ryp_C           29 SHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVA-VAGLTADAEILINTARIHAQNYLKTYNEDIPV  107 (244)
T ss_dssp             TTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             HCCCCEEEEEECCEEEEEEECCCCCCCCCCCCCCCEEEEECCCCEEE-EECCHHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             66887899996999999996776777760367542599907982699-94670659999999999999999984999999


Q ss_pred             HHHHHHHHHHHH-------HHHCCCE--EEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHHH
Q ss_conf             799999976112-------2201310--451378-764699805863114132799606423457889852078999899
Q gi|254780828|r   91 VELAKDWRMDKY-------LRNLEAM--ILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAEE  160 (190)
Q Consensus        91 ~~~~~~~~~~~y-------~~~~~~~--~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~e  160 (190)
                      ..+++.+....+       .+++...  +.+.|. .+|.+|..|+.|+..+.++.|+|+|+.+|+++|++.|+++|+.+|
T Consensus       108 ~~l~~~l~~~~~~~~~~~~~rP~~v~~lvaG~d~~~gp~Ly~id~~Gs~~~~~~~a~G~gs~~~~~~Le~~y~~~ms~ee  187 (244)
T 1ryp_C          108 EILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDD  187 (244)
T ss_dssp             HHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCEEEEECCCEEEEEECEEEECCCHHHHHHHHHHHCCCCCCHHH
T ss_conf             99999999999876412566775278999998089997799966988898538799994889999999755766999999


Q ss_pred             ---HHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             ---9999999754011022595699999417
Q gi|254780828|r  161 ---IARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       161 ---la~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                         ++++||..|.+||..+|++++|.+|+.+
T Consensus       188 ai~l~~~al~~~~~~d~~~~~~iev~iv~k~  218 (244)
T 1ryp_C          188 AIELALKTLSKTTDSSALTYDRLEFATIRKG  218 (244)
T ss_dssp             HHHHHHHHHHHHCSSSSCCGGGEEEEEEECC
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEEEECC
T ss_conf             9999999999997235888884699999868


No 26 
>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ...
Probab=99.97  E-value=1.9e-29  Score=202.62  Aligned_cols=173  Identities=17%  Similarity=0.186  Sum_probs=144.2

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHHH
Q ss_conf             717999997997999813654505367744510579815975999731305889999999999999853--665630679
Q gi|254780828|r   15 ATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSVE   92 (190)
Q Consensus        15 GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~~   92 (190)
                      -||+|||+++|||+||||+|+|.|.++.+++.+|||+|+++++++ ++|.++|.+.+.+.++.++.+++  .....++..
T Consensus         1 M~Tivgi~~~dgVviaaD~r~~~g~~~~~~~~~Ki~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   79 (198)
T 1ryp_K            1 MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMS-FAGEAGDTVQFAEYIQANIQLYSIREDYELSPQA   79 (198)
T ss_dssp             CCCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEE-EEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHH
T ss_pred             CEEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEE-ECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             919999998999999997886669776447734499916978999-7677626899999999998888987299998889


Q ss_pred             HHHHHHHHHHH-----HHCCCEE--EECC--CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH---H
Q ss_conf             99999761122-----2013104--5137--876469980586311413279960642345788985207899989---9
Q gi|254780828|r   93 LAKDWRMDKYL-----RNLEAMI--LIAD--KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE---E  160 (190)
Q Consensus        93 ~~~~~~~~~y~-----~~~~~~~--~~~~--~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~---e  160 (190)
                      +++..+...|.     +++...+  .+.|  .++|++|..|+.|...+.+|.|+|+|+.+|+++|++.|+++|+.+   +
T Consensus        80 ~~~~~~~~~~~~~~~~rP~~~~~ivaG~D~~~~~p~L~~id~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~m~~~ea~~  159 (198)
T 1ryp_K           80 VSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLD  159 (198)
T ss_dssp             HHHHHHHHHHHHTTSSSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCEEEEECCCCCEEECCEEEEEECCCCHHHHHHHHCCCCCCHHHHHH
T ss_conf             99999999988765578731688898871678975798755986478647589973661026899965669979999999


Q ss_pred             HHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             9999999754011022595699999417
Q gi|254780828|r  161 IARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       161 la~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ++++||.++.+||.+++++++|.+|+.+
T Consensus       160 l~~~al~~~~~~d~~s~~~~~v~ii~k~  187 (198)
T 1ryp_K          160 LLKLCVQELEKRMPMDFKGVIVKIVDKD  187 (198)
T ss_dssp             HHHHHHHHHHHHCSBCCCCEEEEEEETT
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             9999999998646767995799999289


No 27 
>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}
Probab=99.96  E-value=2.9e-28  Score=195.24  Aligned_cols=171  Identities=22%  Similarity=0.142  Sum_probs=141.4

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCC--CCCCHH
Q ss_conf             371799999799799981365450536774451057981597599973130588999999999999985366--563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQ--LLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~--~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|.+ ++++.+++.+||++|+++++++ ++|.++|++.+.+.++.++++++..  ...++.
T Consensus        37 ~G~TvIgik~~dgVvlaad~r~t-~~~~~~~~~~KI~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  114 (264)
T 3h4p_A           37 RGTTAIGIACKDGVVLAVDRRIT-SKLVKIRSIEKIFQIDDHVAAA-TSGLVADARVLIDRARLEAQIYRLTYGEEISIE  114 (264)
T ss_dssp             HSCCEEEECCSSEEEEEEECCCC-STTBCTTTCCCEEEEETTEEEE-EEECSHHHHHHHTTHHHHHHHHHHTTCSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCC-CCCCCCCCCCEEEEECCCCEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             59878999969999999956777-7763467666389960783389-514538899999999999999899878987489


Q ss_pred             HHHHHHHHHHH-------HHHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCH---H
Q ss_conf             99999976112-------220131--04513787646998058631141327996064234578898520789998---9
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSA---E  159 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa---~  159 (190)
                      .+++.++...+       .+++..  .+.+.+..+|.+|..|+.|+..+.++.|+|+|+.+|+++|++.|+++|+.   .
T Consensus       115 ~la~~~~~~~~~~~~~~~~rP~~v~~liaG~d~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~y~~~ms~eeai  194 (264)
T 3h4p_A          115 MLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDKNEARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDDITLDEGL  194 (264)
T ss_dssp             HHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEETTEEEEEEECTTCCCEEESEEEESTTHHHHTTTHHHHCCTTCCSHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCEEEEECCCCCEECCCCEEECCCHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             99999999999875356767665367999961799828995677362235624444768999999997644899999999


Q ss_pred             HHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99999999754011022595699999417
Q gi|254780828|r  160 EIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       160 ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +++++||..|.+++  ++++++|.+|..+
T Consensus       195 ~lal~aL~~a~~~~--~~~~~ei~ii~~~  221 (264)
T 3h4p_A          195 ELAITALTKANEDI--KPENVDVCIITVK  221 (264)
T ss_dssp             HHHHHHHHHHSSSC--CTTSEEEEEEETT
T ss_pred             HHHHHHHHHHHHCC--CCCCEEEEEEEEC
T ss_conf             99999999985446--8786799999954


No 28 
>1iru_B 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.96  E-value=1e-27  Score=191.84  Aligned_cols=171  Identities=14%  Similarity=0.035  Sum_probs=141.3

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|.+++.. ..++.+|||+|+++++++ .+|..+|.+.+.+.++.+.++++.  ....++.
T Consensus        30 ~Gttvigik~~dgVvlaaD~r~~~~~~-~~~~~~ki~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  107 (233)
T 1iru_B           30 GGAPSVGIKAANGVVLATEKKQKSILY-DERSVHKVEPITKHIGLV-YSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTA  107 (233)
T ss_dssp             TSCCEEEEECSSCEEEEEECCCCCSSB-CSTTCCSSEESSSSEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCC-CCCCCCEEEEEECCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             698789999599999999677666773-557653399960762268-886438899999999999999999849989899


Q ss_pred             HHHHHHHHHHHH-------HHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHHH--
Q ss_conf             999999761122-------20131--0451378764699805863114132799606423457889852078999899--
Q gi|254780828|r   92 ELAKDWRMDKYL-------RNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAEE--  160 (190)
Q Consensus        92 ~~~~~~~~~~y~-------~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~e--  160 (190)
                      .+++.++...+.       +++..  .+.+.+.++|+++..|+.|+..+.++.++|+|+.+|+++||+.|+++|+.+|  
T Consensus       108 ~l~~~~~~~~~~~~~~~~~~p~~~~~ii~g~d~~~p~l~~id~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~s~eea~  187 (233)
T 1iru_B          108 QLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELEDAI  187 (233)
T ss_dssp             HHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECSSSEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCEEEEECCCCEEEEECEEEECCCHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             99999999998851301468617998751135788758999278059984538754754889999986477998999999


Q ss_pred             -HHHHHHHHHHCCCEEECCCEEEEEEEC
Q ss_conf             -999999975401102259569999941
Q gi|254780828|r  161 -IARKAMSIAADICVYTNHNIVLETLKV  187 (190)
Q Consensus       161 -la~~Al~~A~erDvyTgd~i~i~~i~~  187 (190)
                       ++++||+.+.+||. +++++++.+|+.
T Consensus       188 ~l~~~~l~~~~~~d~-~~~~iev~ii~~  214 (233)
T 1iru_B          188 HTAILTLKESFEGQM-TEDNIEVGICNE  214 (233)
T ss_dssp             HHHHHHHHTTCCSCC-CSSSEEEEEEET
T ss_pred             HHHHHHHHHHHHCCC-CCCCEEEEEEEC
T ss_conf             999999999985668-889789999958


No 29 
>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase/hydrolase activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A 1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A 3jse_A 3jtl_A
Probab=99.96  E-value=2.1e-27  Score=189.76  Aligned_cols=174  Identities=16%  Similarity=0.084  Sum_probs=141.3

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCH
Q ss_conf             637179999979979998136545053677445105798159759997313058899999999999998536--656306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~   90 (190)
                      -+|||+|||+++||||||+|+|.+.+ ++..++.+||++|+++++++ .+|.++|.+.+.+.++.++.+++.  ....++
T Consensus        32 ~~G~t~Igi~~~dgVvlaad~r~~~~-~~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  109 (233)
T 1yar_A           32 KKGSTALGMKFANGVLLISDKKVRSR-LIEQNSIEKIQLIDDYVAAV-TSGLVADARVLVDFARISAQQEKVTYGSLVNI  109 (233)
T ss_dssp             TTSCCEEEEEETTEEEEEECCCCCCT-TBCSTTCCSEEEEETTEEEE-EEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             HCCCCEEEEEECCEEEEEEECCCCCC-CCCCCCCCEEEEEECCEEEE-ECCCHHHHHHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             75876899996999999996676666-61567665079960652578-52150458999999999999999870996408


Q ss_pred             HHHHHHHHHHH----H---HHHCC--CEEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH--
Q ss_conf             79999997611----2---22013--1045137876469980586311413279960642345788985207899989--
Q gi|254780828|r   91 VELAKDWRMDK----Y---LRNLE--AMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE--  159 (190)
Q Consensus        91 ~~~~~~~~~~~----y---~~~~~--~~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~--  159 (190)
                      ...++.+....    +   .+++.  ..+.+.|.++|++|..|+.|+..+.++.|+|+|+++|.++|++.|+++|+.+  
T Consensus       110 ~~~~~~l~~~~~~~~~~~~~rP~~~~~iiaG~d~~gp~Ly~id~~Gs~~~~~~~a~G~gs~~~~~~L~~~~~~~ms~~ea  189 (233)
T 1yar_A          110 ENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEA  189 (233)
T ss_dssp             HHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSSCEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHCCCCHHHH
T ss_conf             99999999999998601466786368999997389980799647325774028998886699999998761237888999


Q ss_pred             -HHHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             -999999997540110225956999994178
Q gi|254780828|r  160 -EIARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       160 -ela~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                       +++++||..+.++|. +.++++|.+|+.++
T Consensus       190 ~~l~~~~L~~~~~~~~-~~~~iei~~i~~~~  219 (233)
T 1yar_A          190 VTLGIKALKSSLEEGE-ELKAPEIASITVGN  219 (233)
T ss_dssp             HHHHHHHHHHTSCSSC-CCCCCEEEEEETTS
T ss_pred             HHHHHHHHHHHHHCCC-CCCCEEEEEEECCC
T ss_conf             9999999999985467-88971999999299


No 30 
>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B 1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A* 2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A* 3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 1vsy_B ...
Probab=99.96  E-value=1.3e-27  Score=191.18  Aligned_cols=172  Identities=17%  Similarity=0.078  Sum_probs=136.7

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHH-H--CCCCCCCH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998-5--36656306
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQ-Y--PNQLLRSS   90 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~-~--~~~~~~~~   90 (190)
                      +|||+|||+++||||||+|+|++.+. +.+++.+||++|+++++++ .+|.++|.+.+.+.++..... +  ......++
T Consensus        30 ~G~Tvvgik~~dgVvlaad~r~~~~~-~~~~~~~Ki~~i~~~i~~~-~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~  107 (250)
T 1ryp_B           30 QGVTSLGIKATNGVVIATEKKSSSPL-AMSETLSKVSLLTPDIGAV-YSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPT  107 (250)
T ss_dssp             TSCCEEEEEETTEEEEEEECCCSCSS-BCGGGCCSSEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHTTHHHHSSCCCH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCC-CCCCCCCCEEEECCCCEEE-EEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             49868999959999999936766655-1556556379971662379-997343189999999999999999985989999


Q ss_pred             HHHHHHHH----HHHH---HHHCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHH-
Q ss_conf             79999997----6112---220131--0451378-76469980586311413279960642345788985207899989-
Q gi|254780828|r   91 VELAKDWR----MDKY---LRNLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAE-  159 (190)
Q Consensus        91 ~~~~~~~~----~~~y---~~~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~-  159 (190)
                      ..+++...    .+.+   .+++..  .+.+.|. .+|.+|..|+.|+..+.++.|+|||+.+|+++||+.|+++|+.+ 
T Consensus       108 ~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~~~gp~Ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~y~~~ms~ee  187 (250)
T 1ryp_B          108 KLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELED  187 (250)
T ss_dssp             HHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCEEEEECCCEEEEECCEEEECCCHHHHHHHHHHHCCCCCCHHH
T ss_conf             99999999999997641466772689999987289996799985867999756899678509999999976458999899


Q ss_pred             --HHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             --99999999754011022595699999417
Q gi|254780828|r  160 --EIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       160 --ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                        +++.+||..+.++|. +++++++.+|+.+
T Consensus       188 a~~la~~al~~~~~~d~-~~~~iev~vi~~~  217 (250)
T 1ryp_B          188 AIHIALLTLKESVEGEF-NGDTIELAIIGDE  217 (250)
T ss_dssp             HHHHHHHHHHHHCCSCC-STTTEEEEEECSC
T ss_pred             HHHHHHHHHHHHHHCCC-CCCCEEEEEEECC
T ss_conf             99999999999861668-8896899999679


No 31 
>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D* 1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D* 3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 2z5c_C 3bdm_D* 1z7q_E 1fnt_E* 2zcy_D* 1vsy_E ...
Probab=99.96  E-value=2.7e-27  Score=189.15  Aligned_cols=173  Identities=14%  Similarity=0.042  Sum_probs=142.6

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|.+.+ ++..++.+||++|+++++++ ++|..+|++.+.+.++.++++++.  ....++.
T Consensus        25 ~G~t~vgi~~~dgVvla~d~r~~~~-l~~~~~~~Ki~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  102 (242)
T 1ryp_E           25 LGSTAIGIATKEGVVLGVEKRATSP-LLESDSIEKIVEIDRHIGCA-MSGLTADARSMIEHARTAAVTHNLYYDEDINVE  102 (242)
T ss_dssp             TSCCEEEEECSSCEEEEEECCCSST-TBCGGGCCCEEEEETTEEEE-EEESGGGHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCC-CCCCCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             5987899995999999996776677-61567644299943979999-998479999999999999999899859999706


Q ss_pred             HHHHHHHHHHH-------------HHHCCCE--EEECC-CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCC
Q ss_conf             99999976112-------------2201310--45137-87646998058631141327996064234578898520789
Q gi|254780828|r   92 ELAKDWRMDKY-------------LRNLEAM--ILIAD-KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQ  155 (190)
Q Consensus        92 ~~~~~~~~~~y-------------~~~~~~~--~~~~~-~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~  155 (190)
                      .+++.+....+             .+++...  +.+.| .++|.+|..|+.|+..+.++.|+|+|+.+++++|++.|+++
T Consensus       103 ~l~~~la~~~~~~~~~~~~~~~~~~rP~~~~~li~G~D~~~~p~Ly~idp~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~  182 (242)
T 1ryp_E          103 SLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSS  182 (242)
T ss_dssp             HHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHCCCCCEEEEEEEEECCCCCCEEEEECCCEEEEEECEEECCCCHHHHHHHHHHHCCCC
T ss_conf             68999999999986412302554367717999998870799967998869878997243870676599999999754699


Q ss_pred             CCHH---HHHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             9989---999999997540110225956999994178
Q gi|254780828|r  156 NSAE---EIARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       156 ~sa~---ela~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      |+.+   +++.+||..+.++|. +++++++.+|..++
T Consensus       183 ms~~ea~~l~~~~l~~~~~~~~-~~~~~~v~~i~~~~  218 (242)
T 1ryp_E          183 LTLKEAELLVLKILKQVMEEKL-DENNAQLSCITKQD  218 (242)
T ss_dssp             CCHHHHHHHHHHHHHHHCSSCC-CTTSEEEEEEETTT
T ss_pred             CCHHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEECCC
T ss_conf             9999999999999999985458-99976999998799


No 32 
>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A {Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A*
Probab=99.95  E-value=5.9e-27  Score=187.03  Aligned_cols=173  Identities=18%  Similarity=0.144  Sum_probs=139.8

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHH
Q ss_conf             3717999997997999813654505367744510579815975999731305889999999999999853--66563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~   91 (190)
                      ||||+|||+++||||||||+|.+++.. .+++.+||++|+++++++ .+|.++|++.+.+.++.++.+++  .....++.
T Consensus        33 ~G~T~Igik~kdgVvlaad~~~~~~~~-~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  110 (246)
T 1j2p_A           33 RGATAIGIKCKEGVILIADKRVGSKLL-EKDTIEKIYKIDEHICAA-TSGLVADARVLIDRARIEAQINRLTYDIPITVK  110 (246)
T ss_dssp             TSCCEEEEEETTEEEEEEECCCSCTTB-CGGGCCSEEECSSSEEEE-EEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCC-CCCCCCCEEECCCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             598789999799999999667667672-556358789846979999-715678899999999999997189719988699


Q ss_pred             HHHHHHHHHHH-------HHHCCCE-EEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHHH---
Q ss_conf             99999976112-------2201310-451378764699805863114132799606423457889852078999899---
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEAM-ILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAEE---  160 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~~-~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~e---  160 (190)
                      .++..+....+       .+++... +++..+++|.+|..|+.|+..+.++.|+|+|+.+|+++||+.|+++|+.+|   
T Consensus       111 ~la~~l~~~~~~~~~~~~~rP~~v~~li~G~D~~p~Ly~id~~Gs~~~~~~~a~G~gs~~~~~~Le~~~~~~mt~eeai~  190 (246)
T 1j2p_A          111 ELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNEVPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDDLSFDDAMV  190 (246)
T ss_dssp             HHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESSSEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             99999999999998742778617999999977997289986887667554899888669999999965447999999999


Q ss_pred             HHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             99999997540110225956999994178
Q gi|254780828|r  161 IARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       161 la~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      ++.+||..+.++|..+ ++++|.+++.++
T Consensus       191 la~~al~~~~~~d~~~-~~iei~vv~~~~  218 (246)
T 1j2p_A          191 LGLVAMGLSIESELVP-ENIEVGYVKVDD  218 (246)
T ss_dssp             HHHHHHHHHHTSCCCG-GGEEEEEEETTT
T ss_pred             HHHHHHHHHHHCCCCC-CCEEEEEEEECC
T ss_conf             9999999997454777-966999999189


No 33 
>1iru_E 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.95  E-value=5.2e-27  Score=187.35  Aligned_cols=173  Identities=15%  Similarity=0.075  Sum_probs=142.8

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCCC--CCCHH
Q ss_conf             3717999997997999813654505367744510579815975999731305889999999999999853665--63067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQL--LRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~~--~~~~~   91 (190)
                      +|||+|||+++||||||+|+|.+.+. +..++.+||++|+++++++ ++|..+|++.+.+.++.++.+++...  ..++.
T Consensus        33 ~G~t~vgik~~dgVvla~d~r~~~~~-~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  110 (241)
T 1iru_E           33 LGSTAIGIQTSEGVCLAVEKRITSPL-MEPSSIEKIVEIDAHIGCA-MSGLIADAKTLIDKARVETQNHWFTYNETMTVE  110 (241)
T ss_dssp             TSCCEEEEEETTEEEEEEECCCCCTT-BCTTSCCSEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCC-CCCCCCCCEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             59878999959999999955677777-1556547589963989999-998789999999999999998888609999868


Q ss_pred             HHHHHHHHHHH------------HHHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCC
Q ss_conf             99999976112------------220131--0451378764699805863114132799606423457889852078999
Q gi|254780828|r   92 ELAKDWRMDKY------------LRNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNS  157 (190)
Q Consensus        92 ~~~~~~~~~~y------------~~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~s  157 (190)
                      .+++.++...+            .+++..  .+.+.|..+|++|..|+.|+..+.++.|+|||+.+++++||+.|+++|+
T Consensus       111 ~la~~ls~~~~~~~~~~~~~~~~~rP~~v~~ilaG~d~~gp~Ly~idp~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~s  190 (241)
T 1iru_E          111 SVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELYHKSMT  190 (241)
T ss_dssp             HHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEETTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCCEEEECEEEECCCHHHHHHHHHHHCCCCCC
T ss_conf             89999999999984224454434456325899999948999899992898675306697668619999999976458989


Q ss_pred             HHH---HHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             899---99999997540110225956999994178
Q gi|254780828|r  158 AEE---IARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       158 a~e---la~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      .+|   ++.+||..+.++|. ++++|++.+|+.++
T Consensus       191 ~eeav~~a~~~L~~~~~~~~-~~~~iev~vi~~~~  224 (241)
T 1iru_E          191 LKEAIKSSLIILKQVMEEKL-NATNIELATVQPGQ  224 (241)
T ss_dssp             HHHHHHHHHHHHHHHCSSCC-CTTSEEEEEECSSS
T ss_pred             HHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEECCC
T ss_conf             99999999999999874468-88968999998899


No 34 
>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F* 1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F* 3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F* 3l5q_L 1g0u_F
Probab=99.95  E-value=1.1e-26  Score=185.37  Aligned_cols=173  Identities=14%  Similarity=0.031  Sum_probs=143.1

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHH
Q ss_conf             3717999997997999813654505367744510579815975999731305889999999999999853--66563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|+++|..+ .++.+||++|+++++++ .+|..+|.+.+.+.++.++++++  .....++.
T Consensus        29 ~G~t~Vgik~~dgVvlaad~~~~~~~~~-~~~~~Ki~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (244)
T 1ryp_G           29 NGTTSIGIKCNDGVVFAVEKLITSKLLV-PQKNVKIQVVDRHIGCV-YSGLIPDGRHLVNRGREEAASFKKLYKTPIPIP  106 (244)
T ss_dssp             TSCCEEEEEETTEEEEEEEEECCCTTBC-TTTSCCCEEETTTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCCC-CCCCCEEEEECCCEEEE-EECCHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             5987899994999999995665667701-13345189976981589-843528799999999999999999719999889


Q ss_pred             HHHHHHHHHHHHH-------HCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHH---HHCCCCCHH
Q ss_conf             9999997611222-------0131--045137876469980586311413279960642345788985---207899989
Q gi|254780828|r   92 ELAKDWRMDKYLR-------NLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARA---LMSTQNSAE  159 (190)
Q Consensus        92 ~~~~~~~~~~y~~-------~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~---~y~~~~sa~  159 (190)
                      .+++.++...+.+       ++..  .+.+.|.++|.+|..|+.|+..+.++.|+|+|+.+|+++||+   .|+++|+.+
T Consensus       107 ~la~~~~~~~~~~t~~~~~rP~~v~~iiaG~D~~gp~Ly~~Dp~G~~~~~~~~a~G~g~~~a~~~Lek~~~~~~~~ms~e  186 (244)
T 1ryp_G          107 AFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAR  186 (244)
T ss_dssp             HHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHCTTCCCHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCEEEEECCCCCEECCCEEEECCCHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             99999999999850125667705899999972998889998498237713879988877999999986675279998999


Q ss_pred             H---HHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             9---9999999754011022595699999417
Q gi|254780828|r  160 E---IARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       160 e---la~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      |   ++.+||..+.+++.-++++++|.+++..
T Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~~ev~iv~~~  218 (244)
T 1ryp_G          187 EAVKQAAKIIYLAHEDNKEKDFELEISWCSLS  218 (244)
T ss_dssp             HHHHHHHHHHHHHGGGGTTSCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEE
T ss_conf             99999999999997323688872899999997


No 35 
>1iru_G 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.95  E-value=4.4e-27  Score=187.84  Aligned_cols=174  Identities=15%  Similarity=0.044  Sum_probs=143.0

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|++.+ ++.+++.+||++|++|++++ .+|.++|.+.+.+.++.++++++.  ....++.
T Consensus        32 ~G~T~Vgik~kdgVvlaad~~~~~~-~~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~r~~~~~~~~~~g~~~~v~  109 (254)
T 1iru_G           32 NSSTAIGIRCKDGVVFGVEKLVLSK-LYEEGSNKRLFNVDRHVGMA-VAGLLADARSLADIAREEASNFRSNFGYNIPLK  109 (254)
T ss_dssp             TSCCEEEEECSSBEEEEEEEECSCT-TBCTTTTCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCC-CCCCCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             6886899994999999996666677-71667455389812878999-878578899999999999999999858999999


Q ss_pred             HHHHHHHHHHH-------HHHCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHHH-
Q ss_conf             99999976112-------220131--0451378-764699805863114132799606423457889852078999899-
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAEE-  160 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~e-  160 (190)
                      .+++.+....+       .+++..  .+.+.|. .+|.+|..|+.|+..+.++.|+|+|+.+|++.||+.|+++|+.+| 
T Consensus       110 ~la~~l~~~~~~~t~~~~~rP~~v~~llaG~D~~~gp~Ly~idp~G~~~~~~~~a~G~gs~~a~~~Lek~y~~~ms~eea  189 (254)
T 1iru_G          110 HLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDI  189 (254)
T ss_dssp             HHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHTTSCGGGCCHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCCEEEEECCCCCEEEECEEEECCCCHHHHHHHHHHCCCCCCHHHH
T ss_conf             99999999999973533766765899999886999838999869976784078998686789999999744689999999


Q ss_pred             --HHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             --99999997540110225956999994178
Q gi|254780828|r  161 --IARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       161 --la~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                        ++.+||..+.+.+.-++.++++.+|+.+.
T Consensus       190 i~l~~~~l~~~~~~~~~~~~~iei~~v~~~~  220 (254)
T 1iru_G          190 VKEVAKIIYIVHDEVKDKAFELELSWVGELT  220 (254)
T ss_dssp             HHHHHHHHHHHSCSSSSCCEEEEEEECBTTT
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEEEEECC
T ss_conf             9999999999975235887358999999448


No 36 
>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C* 1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C* 3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3bdm_C* 1z7q_D 1fnt_D* 2zcy_C* 1g0u_C 1vsy_D ...
Probab=99.95  E-value=1.6e-26  Score=184.29  Aligned_cols=172  Identities=14%  Similarity=0.132  Sum_probs=136.6

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|++++.++.+++.+||++|++|++++ ++|.++|.+.+.+.++.++..++.  ....++.
T Consensus        27 ~G~tvIgik~~dgVvlaad~~~~~~~~~~~~~~~Ki~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  105 (241)
T 1ryp_D           27 RGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLS-FSGLNADSRILIEKARVEAQSHRLTLEDPVTVE  105 (241)
T ss_dssp             TSCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCEEECCCCCCEEEECCCEEEE-EEECCCCHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             4986899995998999996465656641013511379827977999-532234099999999999999999739999999


Q ss_pred             HHHHHHHHHHH-------HHHCCC--EEEECC--CCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCC---CCC
Q ss_conf             99999976112-------220131--045137--8764699805863114132799606423457889852078---999
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEA--MILIAD--KTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMST---QNS  157 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~--~~~~~~--~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~---~~s  157 (190)
                      .+++.+....+       .+++..  .+.+.|  .++|++|..|+.|+..+.++.|+|+|+.+|+++||+.|++   +|+
T Consensus       106 ~la~~l~~~~~~~~~~~~~rP~~v~~li~G~D~~~~gp~Ly~idp~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~~t  185 (241)
T 1ryp_D          106 YLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPAT  185 (241)
T ss_dssp             HHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEEEBSEEEESTTHHHHHHHHHTTCCTTSCCCS
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCEEEEEECCEEEEEECEEEECCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999999999863134557765059999984778997799995772897425799897889999999854164667888


Q ss_pred             HHHHHH---HHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             899999---99997540110225956999994178
Q gi|254780828|r  158 AEEIAR---KAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       158 a~ela~---~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      ++|+++   +||..+.++   ++.+|+|.+|+.+.
T Consensus       186 ~~e~v~la~~al~~~~~~---~~~~iei~vi~~~~  217 (241)
T 1ryp_D          186 VEECVKLTVRSLLEVVQT---GAKNIEITVVKPDS  217 (241)
T ss_dssp             HHHHHHHHHHHHHHHHCS---CSTTEEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHCC---CCCCEEEEEEECCC
T ss_conf             999999999999997558---98817999998899


No 37 
>3bdm_F Proteasome component C1; ubiquitin, proteolysis, pathogen, virulence factor, cytoplasm, hydrolase, nucleus, protease; HET: GDT; 2.70A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_G* 2zcy_F* 1z7q_G
Probab=99.95  E-value=3.7e-26  Score=182.06  Aligned_cols=174  Identities=14%  Similarity=0.050  Sum_probs=142.6

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHC--CCCCCCHH
Q ss_conf             3717999997997999813654505367744510579815975999731305889999999999999853--66563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYP--NQLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~--~~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|++++.++ .++.+||++|++|++++ .+|..+|++.+.+.++.++..++  .....++.
T Consensus        32 ~G~t~Vgik~kdGVVlaadkr~~s~l~~-~~~~~KI~~I~~~i~~a-~sG~~aD~~~l~~~~r~e~~~~~~~~~~~i~~~  109 (287)
T 3bdm_F           32 NGTTSIGIKCNDGVVFAVEKLITSKLLV-PQKNVKIQVVDRHIGCV-YSGLIPDGRHLVNRGREEAASFKKLYKTPIPIP  109 (287)
T ss_dssp             TSCCEEEEEETTEEEEEEEEEECCTTBC-TTTSCCCEEETTTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCCC-CCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             5987899994999999993665666610-03333289977980799-987568899999999999999899709989889


Q ss_pred             HHHHHHHHHHH-------HHHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHH---HHCCCCCHH
Q ss_conf             99999976112-------220131--045137876469980586311413279960642345788985---207899989
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARA---LMSTQNSAE  159 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~---~y~~~~sa~  159 (190)
                      .+++.+....+       .+++..  .+.+.|.++|.+|..||.|+..+..+.|+|+|+++|+++||+   .|+++|+.+
T Consensus       110 ~la~~l~~~~~~~t~~~~~RPfgvs~liaG~D~~gp~Ly~iDpsG~~~~~~~~AiG~gs~~a~~~LEk~~~~~~~~ms~e  189 (287)
T 3bdm_F          110 AFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAR  189 (287)
T ss_dssp             HHHHHHHHHHHHTTSCTTBCCCSEEEEEEEEETTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHTCTTCCCHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCEEEEECCCEEEEEECEEEECCCHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             99999999998853203457658999999972998889998587558722869989888999999986665278998999


Q ss_pred             H---HHHHHHHHHHCCCEEECCCEEEEEEECCC
Q ss_conf             9---99999997540110225956999994178
Q gi|254780828|r  160 E---IARKAMSIAADICVYTNHNIVLETLKVGD  189 (190)
Q Consensus       160 e---la~~Al~~A~erDvyTgd~i~i~~i~~~~  189 (190)
                      |   ++.++|..+.+.+.-+..++++.+|..++
T Consensus       190 Eai~la~kaL~~~~d~~~~~~~~iev~~i~~~~  222 (287)
T 3bdm_F          190 EAVKQAAKIIYLAHEDNKEKDFELEISWCSLSE  222 (287)
T ss_dssp             HHHHHHHHHHHHHGGGSTTSEEEEEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEC
T ss_conf             999999999999861336877627999999606


No 38 
>1iru_F 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.95  E-value=1.3e-26  Score=184.96  Aligned_cols=171  Identities=13%  Similarity=0.035  Sum_probs=138.7

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|++++..   .+.+||++|++|++++ .+|.++|++.+.+.++.++.+++.  ....++.
T Consensus        31 ~G~t~Vgik~kdgVVlaad~r~~s~l~---~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~  106 (263)
T 1iru_F           31 QGSATVGLKSKTHAVLVALKRAQSELA---AHQKKILHVDNHIGIS-IAGLTADARLLCNFMRQECLDSRFVFDRPLPVS  106 (263)
T ss_dssp             HSCCEEEEECSSEEEEEEECCCSSTTB---CCCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCC---CCCCCEEEECCCEEEE-EEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             588789999699499999446666665---6511189946977999-777007589999999999999998628862188


Q ss_pred             HHHHHHHHH--HH-----HHHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCC--C---
Q ss_conf             999999761--12-----220131--045137876469980586311413279960642345788985207899--9---
Q gi|254780828|r   92 ELAKDWRMD--KY-----LRNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQN--S---  157 (190)
Q Consensus        92 ~~~~~~~~~--~y-----~~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~--s---  157 (190)
                      .+++.+...  .|     .+++..  .+.+.|..+|.+|..|+.|+..+..+.|+|+|+.+|+++||+.|+++|  +   
T Consensus       107 ~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~~gp~Ly~~Dp~Gs~~~~~~~aiG~g~~~a~~~Lek~~~~~~~~s~~e  186 (263)
T 1iru_F          107 RLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNE  186 (263)
T ss_dssp             HHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECSSSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHHCCCCCCCHHH
T ss_conf             99998889999887750677740699999984898879998599988986559987874878999998742267899999


Q ss_pred             HHHHHHHHHHHHHCCCE-EECCCEEEEEEECC
Q ss_conf             89999999997540110-22595699999417
Q gi|254780828|r  158 AEEIARKAMSIAADICV-YTNHNIVLETLKVG  188 (190)
Q Consensus       158 a~ela~~Al~~A~erDv-yTgd~i~i~~i~~~  188 (190)
                      +.+++.+||..|...|. .++++|+|.+|+.+
T Consensus       187 av~la~~aL~~~~~~~~~~~~~~iev~ii~k~  218 (263)
T 1iru_F          187 LVKHGLRALRETLPAEQDLTTKNVSIGIVGKD  218 (263)
T ss_dssp             HHHHHHHHHHTTSCTTCCCCTTTEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEEEEECC
T ss_conf             99999999999864203568785699999569


No 39 
>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G* 1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G* 3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G* 3l5q_A 1g0u_G 1fnt_A 1z7q_A 2zcy_G* ...
Probab=99.95  E-value=2.5e-26  Score=183.05  Aligned_cols=173  Identities=13%  Similarity=0.050  Sum_probs=139.9

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCH
Q ss_conf             637179999979979998136545053677445105798159759997313058899999999999998536--656306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~   90 (190)
                      -.|||+|||+++||||||+|+|++. .++.+++.+||++++++++++ ++|.++|.+.+.+.++.++.+++.  ....++
T Consensus        28 ~~g~t~igi~~~dgVvlaad~r~~~-~~~~~~~~~Ki~~i~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  105 (243)
T 1ryp_A           28 QTNINSLAVRGKDCTVVISQKKVPD-KLLDPTTVSYIFCISRTIGMV-VNGPIPDARNAALRAKAEAAEFRYKYGYDMPC  105 (243)
T ss_dssp             TTCCCEEEEECSSEEEEEEECCCCC-TTBCGGGCCSEEECSSSCEEE-EESCHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             CCCCCEEEEEECCEEEEEEECCCCC-CCCCCCCCCEEEEECCCEEEE-ECCCHHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             0696289999099999999766666-560467666389964887899-50667889999999999999999971999978


Q ss_pred             HHHHHHHHHHH-------HHHHCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCC----
Q ss_conf             79999997611-------2220131--0451378-76469980586311413279960642345788985207899----
Q gi|254780828|r   91 VELAKDWRMDK-------YLRNLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQN----  156 (190)
Q Consensus        91 ~~~~~~~~~~~-------y~~~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~----  156 (190)
                      ..+++.+....       +.+++..  .+.+.|. .+|.+|..|+.|+..+.++.|+|||+.+++++||+.|+++|    
T Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~~~~~ii~G~D~~~g~~ly~~D~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~~~  185 (243)
T 1ryp_A          106 DVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHI  185 (243)
T ss_dssp             HHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHHCSSSC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCEEEEECCCEEEEEECCEECCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999998643167887515799887179994699865875799735031575368999999997311443231


Q ss_pred             ---C---HHHHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             ---9---8999999999754011022595699999417
Q gi|254780828|r  157 ---S---AEEIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       157 ---s---a~ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                         +   +.+++.+||..|.++|. ++++++|.+|+.+
T Consensus       186 ~~~t~~eai~la~~al~~~~~~d~-~~~~iev~ii~k~  222 (243)
T 1ryp_A          186 NEESWEKVVEFAITHMIDALGTEF-SKNDLEVGVATKD  222 (243)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHTCCC-CTTSEEEEEEETT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEECC
T ss_conf             020299999999999999861457-8896899999789


No 40 
>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} PDB: 3h6f_A 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D
Probab=99.95  E-value=8.1e-26  Score=179.90  Aligned_cols=166  Identities=13%  Similarity=0.048  Sum_probs=130.9

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCCC---CCCCH
Q ss_conf             371799999799799981365450536774451057981597599973130588999999999999985366---56306
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPNQ---LLRSS   90 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~~---~~~~~   90 (190)
                      +|||+|||+++||||||+|+|.+        +.+||++|++|++++ .+|.++|++.+.+.++.++..++..   ...++
T Consensus        26 ~Gtt~vgik~kdGVVlaadkr~~--------s~~KI~~I~~~i~~~-~aG~~aD~~~l~~~~r~~a~~~~~~~~~~~i~~   96 (248)
T 3mi0_A           26 RAKSVVALAYAGGVLFVAENPSR--------SLQKISELYDRVGFA-AAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTG   96 (248)
T ss_dssp             TSCCEEEEEETTEEEEEEECCCS--------SSCSEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCH
T ss_pred             CCCCEEEEEECCEEEEEECCCCC--------CCCCEEEECCCEEEE-EECCHHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             58878999979989999776777--------723559965876899-704668899999999999999788609988779


Q ss_pred             HHHHHHHHH------HHHHHHCCCEEE--EC----CCCCCEEEEECCCCCEE-CCCEEEEECCHHHHHHHHHHHHCCCCC
Q ss_conf             799999976------112220131045--13----78764699805863114-132799606423457889852078999
Q gi|254780828|r   91 VELAKDWRM------DKYLRNLEAMIL--IA----DKTITLVITGMGDVLEP-ENGVMAIGSGGSYALSAARALMSTQNS  157 (190)
Q Consensus        91 ~~~~~~~~~------~~y~~~~~~~~~--~~----~~~~~~~~~~d~~g~~~-~~~~~a~GSGs~~A~g~Le~~y~~~~s  157 (190)
                      ..+++.+..      .++.+++...++  +.    +.++|.+|..||+|+.. +..|.|+|+|++.|+++||+.|+++|+
T Consensus        97 ~~la~~~a~~l~~~~t~~~RPfgvslLiaG~d~~~~~~gp~Ly~~dpsGs~~~~~~~~a~G~gs~~a~~~Le~~y~~~mt  176 (248)
T 3mi0_A           97 RQLANVYAQTLGTIFTEQAKPYEVELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENAS  176 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCEEEEEEECCCTTCCCCCEEEEECTTSCEEEESSEEEESSCHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCEEEEECCCCCEEECCCEEECCCCHHHHHHHHHHCCCCCCC
T ss_conf             99999999999988762477725899999986778889977999888987230364466387569999999852679989


Q ss_pred             HHH---HHHHHHHHHHCCCEEEC------CCEEEEEEECC
Q ss_conf             899---99999997540110225------95699999417
Q gi|254780828|r  158 AEE---IARKAMSIAADICVYTN------HNIVLETLKVG  188 (190)
Q Consensus       158 a~e---la~~Al~~A~erDvyTg------d~i~i~~i~~~  188 (190)
                      .+|   ++.+||+.+.++|..++      ++++|.+++.+
T Consensus       177 ~eeai~la~~aL~~~~~~d~~~~~~~l~~~~vEvavv~~~  216 (248)
T 3mi0_A          177 LTDALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDAN  216 (248)
T ss_dssp             HHHHHHHHHHHHHHC------------CCTTEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECC
T ss_conf             9999999999999984034677755467556389999778


No 41 
>1iru_D 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.94  E-value=5.2e-26  Score=181.10  Aligned_cols=173  Identities=16%  Similarity=0.103  Sum_probs=140.7

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|++ +.++.+++.+||++|+++++++ .+|.++|.+.+.+.++.++.+++.  ...+++.
T Consensus        28 ~Gttvvgik~~dgVvlaad~r~~-~~l~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  105 (248)
T 1iru_D           28 KGSTAVGVRGRDIVVLGVEKKSV-AKLQDERTVRKICALDDNVCMA-FAGLTADARIVINRARVECQSHRLTVEDPVTVE  105 (248)
T ss_dssp             TSCCEEEECCSSEEEEEECCCCC-CSSSCGGGGCSEEESSSSCEEE-EEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCC-CCCCCCCCCCCEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             68878999979999999966666-7554677555189915987999-998578899999999999999998649984189


Q ss_pred             HHHHHHHHHHH-------HHHCCC--EEEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCC--HH
Q ss_conf             99999976112-------220131--0451378-764699805863114132799606423457889852078999--89
Q gi|254780828|r   92 ELAKDWRMDKY-------LRNLEA--MILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNS--AE  159 (190)
Q Consensus        92 ~~~~~~~~~~y-------~~~~~~--~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~s--a~  159 (190)
                      .+++.+....+       .+++..  .+.+.|. ++|.+|..|+.|+..+..+.|+|+|+.+|+++|++.|+++|+  .+
T Consensus       106 ~la~~i~~~~~~~t~~~~~rP~~v~~li~G~D~~~~p~Ly~idp~Gs~~~~~~~AiG~gs~~a~~~Le~~~~~~~~~~~~  185 (248)
T 1iru_D          106 YITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDD  185 (248)
T ss_dssp             HHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEEBSEEEESTTHHHHHHHHTTTCCSSTTCSHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCEEEEECCCEEEEECCEEEECCCHHHHHHHHHHHCCCCCCCCHH
T ss_conf             99999999999986303878600799999983689846997579847996170877787589999999862467663599


Q ss_pred             HHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99999999754011022595699999417
Q gi|254780828|r  160 EIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       160 ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      ++++.|+.+-.+++.-++++|+|.+|..+
T Consensus       186 ~~i~~ai~al~~~~~~~~~~iei~ii~k~  214 (248)
T 1iru_D          186 LTIKLVIKALLEVVQSGGKNIELAVMRRD  214 (248)
T ss_dssp             HHHHHHHHHHHTTSCTTSTTCCEEEEESS
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEEECC
T ss_conf             99999999999985279993899999779


No 42 
>1iru_A 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
Probab=99.94  E-value=1e-25  Score=179.25  Aligned_cols=173  Identities=15%  Similarity=0.044  Sum_probs=136.4

Q ss_pred             ECCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCH
Q ss_conf             637179999979979998136545053677445105798159759997313058899999999999998536--656306
Q gi|254780828|r   13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSS   90 (190)
Q Consensus        13 ~~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~   90 (190)
                      ..|||+|||+++||||||+|+|++.+. +..++.+||++|++|++++ .+|.++|.+.+.+.++.++++++.  ....++
T Consensus        34 ~gg~Tvigik~~dgVVlaad~r~~~~~-~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~v  111 (246)
T 1iru_A           34 QGGLTSVAVRGKDCAVIVTQKKVPDKL-LDSSTVTHLFKITENIGCV-MTGMTADSRSQVQRARYEAANWKYKYGYEIPV  111 (246)
T ss_dssp             TTCCEEEEEECSSEEEEEEECCCCCSS-BCGGGCCSEEESSSSCEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             CCCCEEEEEEECCEEEEEEECCCCCCC-CCCCCCCEEEEECCCEEEE-EEECHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             389308999809999999966677767-1367556399935987999-76657899999999999999999971999877


Q ss_pred             HHHHHHHHHH-------HHHHHCCCE--EEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCC--CCCH
Q ss_conf             7999999761-------122201310--451378-764699805863114132799606423457889852078--9998
Q gi|254780828|r   91 VELAKDWRMD-------KYLRNLEAM--ILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMST--QNSA  158 (190)
Q Consensus        91 ~~~~~~~~~~-------~y~~~~~~~--~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~--~~sa  158 (190)
                      ..+++.+...       ...+++...  +.+.|. .+|.+|..|+.|+..+.++.|+|+|+.+|+++||+.|++  +|+.
T Consensus       112 ~~la~~l~~~~~~~~~~~~~rP~~v~~il~G~D~~~gp~Ly~~dp~G~~~~~~~~A~G~gs~~~~~~Le~~~~~~~d~s~  191 (246)
T 1iru_A          112 DMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTF  191 (246)
T ss_dssp             HHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEEBSEEEEETTHHHHHHHHHHHTTSCCCCCH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHCCCCCCCCH
T ss_conf             99999999999998631577773789999987289895799870880689985999567769999999975364658999


Q ss_pred             H---HHHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             9---99999999754011022595699999417
Q gi|254780828|r  159 E---EIARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       159 ~---ela~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +   +++.+||..+.++|.- .++++|.+|+.+
T Consensus       192 eeai~la~~al~~~~~~d~~-~~~iei~vi~~~  223 (246)
T 1iru_A          192 EQTVETAITCLSTVLSIDFK-PSEIEVGVVTVE  223 (246)
T ss_dssp             HHHHHHHHHHHHHHTTCCCC-TTSEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHCCCC-CCCEEEEEEEEC
T ss_conf             99999999999999836788-686799999917


No 43 
>1ryp_F 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_E* 1g65_E 2f16_E* 2fak_E* 2fny_E* 2gpl_E* 3d29_E* 3dy3_E* 3dy4_E* 3e47_E* 3gpj_E* 3gpt_E* 3gpw_E* 3hye_E* 3bdm_E* 1fnt_F 1z7q_F 1vsy_F* 2zcy_E* 3l5q_K ...
Probab=99.94  E-value=2.7e-25  Score=176.60  Aligned_cols=171  Identities=13%  Similarity=0.026  Sum_probs=140.5

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
                      +|||+|||+++||||||+|+|.+...   ..+.+||++|+++++++ ++|..+|.+.+.+.++.++++++.  ....++.
T Consensus        30 ~G~t~igi~~~dgvvla~d~~~~~~l---~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~  105 (233)
T 1ryp_F           30 QGSVTVGLRSNTHAVLVALKRNADEL---SSYQKKIIKCDEHMGLS-LAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVE  105 (233)
T ss_dssp             TSCCEEEEECSSEEEEEEECCCSSTT---BCCCCCEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCC---CCCCCEEEEECCCEEEE-EEECCHHHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             58868999969959999953666667---76502489946982799-753537799999999999987566539978699


Q ss_pred             HHHHHHHHHH-------HHHHCCC--EEEECCCCCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHH----CCCCCH
Q ss_conf             9999997611-------2220131--04513787646998058631141327996064234578898520----789998
Q gi|254780828|r   92 ELAKDWRMDK-------YLRNLEA--MILIADKTITLVITGMGDVLEPENGVMAIGSGGSYALSAARALM----STQNSA  158 (190)
Q Consensus        92 ~~~~~~~~~~-------y~~~~~~--~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y----~~~~sa  158 (190)
                      .+++.++...       ..+++..  .+.+.|.++|.+|..|+.|+..+.++.|+|+|+..|.++||+.|    +++|+.
T Consensus       106 ~la~~l~~~~~~~t~~~~~RP~gvs~liaG~D~~gp~Ly~~Dp~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~d~~~  185 (233)
T 1ryp_F          106 RAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP  185 (233)
T ss_dssp             HHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECTTSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCSCH
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCEEEEECCCEEEEECCEEEECCCHHHHHHHHHHHHHHCCCCCCCH
T ss_conf             99999999999986241577863059999982899879996488779942789988771889999999875057778999


Q ss_pred             HH---HHHHHHHHHHCCCEEECCCEEEEEEECC
Q ss_conf             99---9999999754011022595699999417
Q gi|254780828|r  159 EE---IARKAMSIAADICVYTNHNIVLETLKVG  188 (190)
Q Consensus       159 ~e---la~~Al~~A~erDvyTgd~i~i~~i~~~  188 (190)
                      +|   ++.+||..+.++|..+++++++.+|+.+
T Consensus       186 eeai~la~~~l~~~~~~d~~~~~~iei~ii~k~  218 (233)
T 1ryp_F          186 DELIKAGVEAISQSLRDESLTVDNLSIAIVGKD  218 (233)
T ss_dssp             HHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECC
T ss_conf             999999999999986315788983999999899


No 44 
>1q5q_A Proteasome alpha-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_A 1q5r_A
Probab=99.93  E-value=2.1e-24  Score=171.10  Aligned_cols=166  Identities=13%  Similarity=0.009  Sum_probs=126.1

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--C-CCCCH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6-56306
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--Q-LLRSS   90 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~-~~~~~   90 (190)
                      +|||+|||+++||||||+|+|.++        .+||++|+||++++ ++|.++|++.+.+.++.++..++.  . ...+.
T Consensus        26 ~GtT~Vgi~~~dGVvlaad~r~~s--------~~KI~~I~d~i~~~-~aG~~aD~~~l~~~~r~ea~~~~~~~~~~~~~~   96 (259)
T 1q5q_A           26 RGRSVVVLTFRDGVLFVAENPSTA--------LHKVSELYDRLGFA-AVGKYNEFENLRRAGIVHADMRGYSYDRRDVTG   96 (259)
T ss_dssp             TSCCEEEEECSSEEEEEECCSCSS--------SCSEEEEETTEEEE-EEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCH
T ss_pred             CCCCEEEEEECCEEEEEEECCCCC--------CCCEEEECCCEEEE-EECCHHHHHHHHHHHHHHHHHHHHHCCCCCCCH
T ss_conf             688789999799799998037776--------46369974866899-704489999999999999999898638899869


Q ss_pred             HHHHHHHHH------HHHHHHCCCEE--EECC----CCCCEEEEECCCCCEE-CCCEEEEECCHHHHHHHHHHHHCCCCC
Q ss_conf             799999976------11222013104--5137----8764699805863114-132799606423457889852078999
Q gi|254780828|r   91 VELAKDWRM------DKYLRNLEAMI--LIAD----KTITLVITGMGDVLEP-ENGVMAIGSGGSYALSAARALMSTQNS  157 (190)
Q Consensus        91 ~~~~~~~~~------~~y~~~~~~~~--~~~~----~~~~~~~~~d~~g~~~-~~~~~a~GSGs~~A~g~Le~~y~~~~s  157 (190)
                      ..+++....      ....+++...+  .++|    ..+|.+|..|++|+.. +..|.++|||+++|.++||+.|+++|+
T Consensus        97 ~~la~~~a~~~~~~~~~~~rP~gv~~LvaG~D~~g~~~gp~Ly~vdpsG~~~~~~~~~a~G~~s~~a~~~Le~~y~~~ms  176 (259)
T 1q5q_A           97 RSLANAYAQTLGTIFTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLD  176 (259)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             99999999999999853688855999999975778878875899889998512122103787609999999986346999


Q ss_pred             HHH---HHHHHHHHHHCCCE----EECCCEEEEEEECC
Q ss_conf             899---99999997540110----22595699999417
Q gi|254780828|r  158 AEE---IARKAMSIAADICV----YTNHNIVLETLKVG  188 (190)
Q Consensus       158 a~e---la~~Al~~A~erDv----yTgd~i~i~~i~~~  188 (190)
                      .+|   ++.+||+.+.+.|.    .+.++++|.+++.+
T Consensus       177 ~eea~~lai~aL~~~~~~~~~~~~l~~~~ieVavv~~~  214 (259)
T 1q5q_A          177 LEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQS  214 (259)
T ss_dssp             HHHHHHHHHHHHTTCC--------CCSSCSEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECC
T ss_conf             99999999999999732567757567342899999668


No 45 
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Probab=34.19  E-value=20  Score=14.81  Aligned_cols=35  Identities=23%  Similarity=0.279  Sum_probs=28.7

Q ss_pred             EEEECCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             99606423457889852078999899999999975
Q gi|254780828|r  135 MAIGSGGSYALSAARALMSTQNSAEEIARKAMSIA  169 (190)
Q Consensus       135 ~a~GSGs~~A~g~Le~~y~~~~sa~ela~~Al~~A  169 (190)
                      .+-|.-..-|..++.+..+++++.+++.++||+.+
T Consensus       168 ~~LGy~~~ea~~ai~~~~~~~~~~e~lik~aLk~~  202 (203)
T 1cuk_A          168 VALGYKPQEASRMVSKIARPDASSETLIREALRAA  202 (203)
T ss_dssp             HHHTCCHHHHHHHHHHSCCSSCCHHHHHHHHHHTT
T ss_pred             HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             98799999999999986168999999999999971


No 46 
>2pk0_A Serine/threonine protein phosphatase STP1; signaling motif, signaling protein; 2.65A {Streptococcus agalactiae A909}
Probab=24.87  E-value=29  Score=13.80  Aligned_cols=36  Identities=14%  Similarity=0.224  Sum_probs=25.7

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEECCCEEEEEEECCCC
Q ss_conf             78999899999999975401102259569999941789
Q gi|254780828|r  153 STQNSAEEIARKAMSIAADICVYTNHNIVLETLKVGDE  190 (190)
Q Consensus       153 ~~~~sa~ela~~Al~~A~erDvyTgd~i~i~~i~~~~~  190 (190)
                      +...++++++++-+..|-++-  +-||+++..|+.++|
T Consensus       213 ~~~~~~~~~a~~L~~~A~~~g--~~DNiT~ivi~v~~~  248 (250)
T 2pk0_A          213 TQEKTLDDKNQDLITLANHRG--GLDNITVALVYVESE  248 (250)
T ss_dssp             TSSSCHHHHHHHHHHHHHHTT--CCSCEEEEEEEECC-
T ss_pred             HCCCCHHHHHHHHHHHHHHCC--CCCCEEEEEEEEECC
T ss_conf             559999999999999999739--999879999998157


No 47 
>3bb7_A Interpain A; cysteine protease, zymogen activation, bacterial odontopathogen, hydrolase; 1.50A {Prevotella intermedia} PDB: 3bba_A
Probab=20.48  E-value=29  Score=13.86  Aligned_cols=18  Identities=22%  Similarity=0.278  Sum_probs=13.6

Q ss_pred             EEEECCEEEEEECCCCCC
Q ss_conf             999799799981365450
Q gi|254780828|r   20 TVRKDGVVVIAGDGQVSL   37 (190)
Q Consensus        20 gi~~~dgVviAaDtR~S~   37 (190)
                      -..-+|+||++||.|+..
T Consensus        17 n~~~~GfvIVsaD~r~~p   34 (321)
T 3bb7_A           17 GYTDGGFAVISADDLAPE   34 (321)
T ss_dssp             EETTSCEEEECCCTTSCS
T ss_pred             ECCCCEEEEEECCCCCCC
T ss_conf             658987999976888777


No 48 
>1dki_A Pyrogenic exotoxin B zymogen; cysteine protease, papain-like; 1.60A {Streptococcus pyogenes} SCOP: d.3.1.1 PDB: 1pvj_A*
Probab=20.00  E-value=37  Score=13.19  Aligned_cols=20  Identities=20%  Similarity=0.541  Sum_probs=14.3

Q ss_pred             EEEEEECCEEEEEECCCCCC
Q ss_conf             99999799799981365450
Q gi|254780828|r   18 ILTVRKDGVVVIAGDGQVSL   37 (190)
Q Consensus        18 ivgi~~~dgVviAaDtR~S~   37 (190)
                      |+-+.-+++||++||.|+..
T Consensus        53 I~N~~~~GfvIVsaD~r~~p   72 (371)
T 1dki_A           53 VYNISTGGFVIVSGDKRSPE   72 (371)
T ss_dssp             EEC----CEEEEESCTTSCS
T ss_pred             EEEECCCCEEEEECCCCCCC
T ss_conf             99938982899978888677


Done!