Query         gi|254780874|ref|YP_003065287.1| peptide chain release factor 1 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 357
No_of_seqs    251 out of 3008
Neff          6.5 
Searched_HMMs 23785
Date          Tue May 31 22:35:15 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780874.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1zbt_A RF-1, peptide chain rel 100.0       0       0  969.5  31.3  355    3-357    13-371 (371)
  2 3d5a_X RF1, peptide chain rele 100.0       0       0  949.3  35.9  348    6-357     2-353 (354)
  3 1gqe_A Release factor 2, RF2;  100.0       0       0  938.6  32.9  331    8-346    26-363 (365)
  4 2b3t_B RF-1, peptide chain rel 100.0       0       0  958.1  16.2  353    1-357     1-358 (360)
  5 2ihr_1 Peptide chain release f 100.0       0       0  909.3  23.7  336    8-353    18-358 (365)
  6 1rq0_A RF-1, peptide chain rel 100.0       0       0  900.5  27.1  331   12-356     1-333 (342)
  7 2jva_A Peptidyl-tRNA hydrolase  99.7 1.7E-17   7E-22  145.4   8.0   68  214-281     7-99  (108)
  8 2jy9_A Putative tRNA hydrolase  99.7 1.9E-17 8.1E-22  144.9   7.4   68  214-281     7-99  (148)
  9 1j26_A Immature colon carcinom  99.7 1.7E-16   7E-21  138.1   7.2   70  210-279    10-105 (112)
 10 1gqe_A Release factor 2, RF2;   94.5    0.31 1.3E-05   28.0  10.6   60    6-66      8-84  (365)
 11 3ghg_A Fibrinogen alpha chain;  91.4    0.79 3.3E-05   25.1   7.3   15    8-22     65-79  (562)
 12 2ihr_1 Peptide chain release f  85.8   0.085 3.6E-06   32.1  -0.8   22  289-311   299-320 (365)
 13 1m1j_B Fibrinogen beta chain;   82.0     2.7 0.00012   21.2  10.8   22   79-100   173-194 (464)
 14 1deq_A Fibrinogen (alpha chain  77.7     3.7 0.00016   20.2  10.7   14   11-24     64-77  (390)
 15 1m1j_A Fibrinogen alpha subuni  68.4       6 0.00025   18.7  10.6   17    7-23     65-81  (491)
 16 3lss_A Seryl-tRNA synthetase;   56.1     9.8 0.00041   17.2  11.4   54    1-54      5-61  (484)
 17 3ghg_B Fibrinogen beta chain;   55.2      10 0.00042   17.1   8.6   21   79-99    168-188 (461)
 18 2pih_A Protein YMCA; regulate   50.6      12  0.0005   16.6   9.1   58    1-61      1-58  (151)
 19 1vq8_D 50S ribosomal protein L  48.6     6.6 0.00028   18.4   1.8   72  154-229    66-138 (177)
 20 2hdl_A Small inducible cytokin  48.3      12 0.00051   16.5   3.1   44  101-144    23-74  (78)
 21 3ofo_I 30S ribosomal protein S  48.1     9.4  0.0004   17.3   2.5   29  192-222     4-32  (127)
 22 3jyv_I 40S ribosomal protein S  46.8     9.2 0.00039   17.4   2.3   29  192-222     3-31  (138)
 23 2vqe_I 30S ribosomal protein S  46.1     7.9 0.00033   17.8   1.8   28  193-222     6-33  (128)
 24 1m1j_C Fibrinogen gamma chain;  43.1      15 0.00064   15.8   7.6   10  187-196   247-256 (409)
 25 2xoa_A Ryanodine receptor 1; m  37.6      18 0.00077   15.2   3.1   16  238-253   340-355 (559)
 26 1rpx_A Protein (ribulose-phosp  37.5      15 0.00064   15.8   2.2   58  112-174   145-212 (230)
 27 2pc6_A Probable acetolactate s  36.7      19 0.00079   15.1   3.1   61  132-193    18-83  (165)
 28 1tqj_A Ribulose-phosphate 3-ep  35.6      14 0.00059   16.0   1.8   38  112-149   139-176 (230)
 29 2f1f_A Acetolactate synthase i  35.4      20 0.00083   15.0   3.3   62  132-194    17-83  (164)
 30 3bbn_I Ribosomal protein S9; s  34.1      16 0.00066   15.7   1.8   16  193-208    74-89  (197)
 31 3inp_A D-ribulose-phosphate 3-  32.8      20 0.00082   15.0   2.1   33  114-146   163-195 (246)
 32 3lu0_D DNA-directed RNA polyme  32.2      22 0.00093   14.6   3.2   13  111-123   820-832 (1407)
 33 1m0d_A Endonuclease, endodeoxy  31.8      14 0.00059   16.1   1.2   13  136-148    98-110 (138)
 34 2zkq_i 40S ribosomal protein S  31.3      22 0.00094   14.6   2.2   29  192-222    11-39  (146)
 35 1dp7_P MHC class II transcript  30.7      23 0.00098   14.5   2.6   19  129-147    19-37  (76)
 36 1t9k_A Probable methylthioribo  29.4      24   0.001   14.3   5.6  125   56-186    97-239 (347)
 37 2dq0_A Seryl-tRNA synthetase;   29.4      24   0.001   14.3  13.5   35   80-114    82-126 (455)
 38 2jya_A AGR_C_3324P, uncharacte  28.2      13 0.00056   16.2   0.6   18  137-154    65-82  (106)
 39 2waq_A DNA-directed RNA polyme  27.4      26  0.0011   14.1   3.8   37  121-157   620-656 (880)
 40 3err_A Fusion protein of micro  26.5      27  0.0011   14.0   6.4   51   17-67    138-190 (536)
 41 3h0g_A DNA-directed RNA polyme  23.8      30  0.0013   13.7   1.8   27  180-208  1099-1125(1752)
 42 1n4k_A Inositol 1,4,5-trisphos  23.0      31  0.0013   13.5   2.5   39  103-154    29-68  (381)
 43 1t9h_A YLOQ, probable GTPase E  22.3      12 0.00049   16.7  -0.6  100   98-207   107-222 (307)
 44 1x9u_A Umecyanin; cupredoxin,   22.1      28  0.0012   13.9   1.4   34  135-191    20-53  (116)
 45 2fgc_A Acetolactate synthase,   21.8      33  0.0014   13.3   3.0   74  111-196    33-111 (193)
 46 2dq3_A Seryl-tRNA synthetase;   21.6      33  0.0014   13.3  11.8  111    3-116     1-127 (425)
 47 3nvt_A 3-deoxy-D-arabino-heptu  21.4      15 0.00063   15.8  -0.1  136    4-146    25-171 (385)
 48 1t9f_A Protein 1D10; structura  21.0      34  0.0014   13.2   4.9   20  239-258   127-146 (187)

No 1  
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural genomics, joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}
Probab=100.00  E-value=0  Score=969.53  Aligned_cols=355  Identities=44%  Similarity=0.712  Sum_probs=346.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             786898999999999999985385315799---99999998799999999999999998999999972037853566543
Q gi|254780874|r    3 FLSHKQICDLKNRFAEIELRMSESPSVDAY---IKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLA   79 (357)
Q Consensus         3 mi~~~kL~~l~~rl~ELE~~Lsdp~~w~d~---~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elA   79 (357)
                      |-+-+||+.+..|+.+|+.+|++|+||+|+   ++++|+++.|+++++.|+.|....+++.++.+|+.+.++|++|.+++
T Consensus        13 M~ifdkLe~i~~r~~eLe~~lsdp~~w~D~~ka~~l~kE~s~L~~~v~~~~~l~~~~~dl~el~eLl~e~~~D~el~ela   92 (371)
T 1zbt_A           13 MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIKDASGDPELEEMA   92 (371)
T ss_dssp             CCHHHHHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             12999999999999999998709841229999999999999899999999999999987999999985136885799999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCC
Q ss_conf             32223320005778889998640001135540378862268852178899999999999987649840013211354477
Q gi|254780874|r   80 QIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGG  159 (357)
Q Consensus        80 eeEl~~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aG  159 (357)
                      ++|+..+..+++.++++|+..|||+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|++||
T Consensus        93 ~eEl~~~~~~l~~l~~~le~~lL~~d~~D~~nailEIrAGaGG~EA~dwA~~L~RMY~r~Ae~~g~k~eiid~~~g~~gG  172 (371)
T 1zbt_A           93 KEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNMYQKYAENQGWKFEVMEASANGVGG  172 (371)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTSCCCTTTTSCEEEEEEECTTTHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEEECSSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCC
T ss_conf             99998755458999999999851589776668699996488853799999999999999999769834761435777677


Q ss_pred             CCEEEEEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf             21113777503111210002465026761254567851101688885303343322245434799985288875200063
Q gi|254780874|r  160 YKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNT  239 (357)
Q Consensus       160 ik~v~~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~  239 (357)
                      ||+|++.|+|++|||+||+|+|||||||||||+++||+|||||+|+|+|++++++++|+|+||+||||||||||||||||
T Consensus       173 iKsa~~~I~G~~ayg~Lk~E~GvHRv~Rip~~~s~~r~hts~~~v~v~p~~~~~~~~i~~~dl~idt~RssG~GGQ~VNk  252 (371)
T 1zbt_A          173 LKEVVAMVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNK  252 (371)
T ss_dssp             EEEEEEEEESTTHHHHHGGGCEEEEEEECCTTCSSCCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECC---------C
T ss_pred             CCEEEEEEEECEEHHCCEEECEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCCCCC
T ss_conf             12169999502121021340514799997887888870688789998056776544057775069983388887777776


Q ss_pred             CCCEEEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEE
Q ss_conf             2121588964984488-843654135899999999999999999999999987446522467423822104489981124
Q gi|254780874|r  240 TDSAVRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITD  318 (357)
Q Consensus       240 t~savri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~D  318 (357)
                      |+|||||||+||||+| ||+|||||+||++||++|++|||+++.+++.++..+.||+|||+|+||+|||||||||+||||
T Consensus       253 t~sAVRitH~pTGi~v~~q~eRSQ~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~rk~~~~~~~rs~~IRtY~~p~~~V~D  332 (371)
T 1zbt_A          253 VATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTD  332 (371)
T ss_dssp             CCCEEEEEETTTTEEEEECSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC----CCSCSCTTSEEEEEETTTTEEEE
T ss_pred             CCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             55158999934885899426514387999999999999999999999999999887304026643575081079775066


Q ss_pred             EECCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             321644178778728866999999999999999874059
Q gi|254780874|r  319 HRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE  357 (357)
Q Consensus       319 hR~~~~~~~~~~~l~G~l~~~i~~~~~~~~~~~l~~~~e  357 (357)
                      ||||++++|+++||||+||+||++|+.|+.+++|+++++
T Consensus       333 hR~~~~~~~~~~vldG~ld~~i~a~~~~~~~~~l~~~~~  371 (371)
T 1zbt_A          333 HRIGLTLQKLDSILSGKLDEVIDALILYDQTQKLEELNK  371 (371)
T ss_dssp             TTTTEEESCHHHHHTTCCHHHHHHHHHHHHHHHHHHCC-
T ss_pred             HCCCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             324886368357619866999999999999999996069


No 2  
>3d5a_X RF1, peptide chain release factor 1; ribosome, coiled coil, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding; 3.21A {Thermus thermophilus HB27} PDB: 2b64_Y 3d5c_X 3mr8_V 3ms0_V
Probab=100.00  E-value=0  Score=949.28  Aligned_cols=348  Identities=45%  Similarity=0.718  Sum_probs=338.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             89899999999999998538531579---999999998799999999999999998999999972037853566543322
Q gi|254780874|r    6 HKQICDLKNRFAEIELRMSESPSVDA---YIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIE   82 (357)
Q Consensus         6 ~~kL~~l~~rl~ELE~~Lsdp~~w~d---~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elAeeE   82 (357)
                      -+||+.+..|+.+|+.+|++|+||+|   +++++|+++.|+++++.++.|.+...++.++.+|+    +|+++.+++++|
T Consensus         2 ~dKLe~i~~r~~eLe~~l~dp~~w~D~~ka~~l~ke~~~L~~~v~~~~~l~~~~~dl~el~el~----~D~e~~ela~ee   77 (354)
T 3d5a_X            2 LDKLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQAESLL----DDPELKEMAKAE   77 (354)
T ss_dssp             HHHHHHHTHHHHHHHHHTTSTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTST----TCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCHHHHHHHHHH
T ss_conf             1579999999999999861983223999999999999999999999999999999899999885----281107899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCE
Q ss_conf             23320005778889998640001135540378862268852178899999999999987649840013211354477211
Q gi|254780874|r   83 VLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKE  162 (357)
Q Consensus        83 l~~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~  162 (357)
                      +..+...++.++++|+..+||+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|+.||||+
T Consensus        78 ~~~l~~~l~~l~~ele~~lL~~~~~D~~nailEIrAGaGG~EA~dwA~~L~RMY~r~ae~~g~k~evi~~~~~~~~Gik~  157 (354)
T 3d5a_X           78 REALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSK  157 (354)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCCCCCCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEEECTTSSEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCE
T ss_conf             99998778889999999717798655547179985167872499999999999999997475047861246655677505


Q ss_pred             EEEEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCC
Q ss_conf             13777503111210002465026761254567851101688885303343322245434799985288875200063212
Q gi|254780874|r  163 IVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDS  242 (357)
Q Consensus       163 v~~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~s  242 (357)
                      |+|.|+|++|||+||+|+|||||||||||+++||+|||||+|+|+|+++++++.|+++||+|||||||||||||||||+|
T Consensus       158 ~~~~i~G~~ayg~Lk~E~GvHRv~Rip~~e~~~r~hTs~a~V~v~p~~~~~~~~i~~~dl~i~t~RssG~GGQ~VNkt~s  237 (354)
T 3d5a_X          158 VVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDS  237 (354)
T ss_dssp             EEEEEESTTHHHHHGGGCSEEEEEECCSSCSSCCCEEEEEEEEEEECCCCCCCCCCGGGEEEEEECCCSCCHHHHHHCCC
T ss_pred             EEEEEECCCCCEEEEEECCCEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCHHHEEEEEECCCCCCCCCCCCCC
T ss_conf             99999826630011440574268856988778855778889999455555545667103225643457887666565454


Q ss_pred             EEEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEEEEC
Q ss_conf             1588964984488-843654135899999999999999999999999987446522467423822104489981124321
Q gi|254780874|r  243 AVRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRI  321 (357)
Q Consensus       243 avri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~DhR~  321 (357)
                      ||||||+||||+| ||+|||||+||++||++|++|||+++.+++.++.++.|++|||+|+||+|||||||||+|||||||
T Consensus       238 AVRitH~ptGi~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~~~~~r~~~~~~~~r~~~iRtY~~p~~rV~DhR~  317 (354)
T 3d5a_X          238 AVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNFPQSRVTDHRI  317 (354)
T ss_dssp             EEEEEETTTTEEEEECCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCGGGGSCSSEEEETTTTEEEETTT
T ss_pred             EEEEEEECCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHCC
T ss_conf             47999706766887133022899999999999999999999999999998887337244667884670069875133044


Q ss_pred             CCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             644178778728866999999999999999874059
Q gi|254780874|r  322 NLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE  357 (357)
Q Consensus       322 ~~~~~~~~~~l~G~l~~~i~~~~~~~~~~~l~~~~e  357 (357)
                      |++++|+++||+|+||+||++|+.|+++++|+++.|
T Consensus       318 ~~~~~~~~~vl~G~ld~~i~~~~~~~~~~~l~~~~e  353 (354)
T 3d5a_X          318 GFTTHDLEGVLSGHLTPILEALKRADQERQLAALAE  353 (354)
T ss_dssp             TEEECCHHHHTTTCCHHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             886368057758873999999999999999997518


No 3  
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} SCOP: e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Probab=100.00  E-value=0  Score=938.62  Aligned_cols=331  Identities=34%  Similarity=0.548  Sum_probs=307.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             899999999999998538531579---99999999879999999999999999899999997203785356654332223
Q gi|254780874|r    8 QICDLKNRFAEIELRMSESPSVDA---YIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVL   84 (357)
Q Consensus         8 kL~~l~~rl~ELE~~Lsdp~~w~d---~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elAeeEl~   84 (357)
                      .++.++.|+.+|+.+|++|+||+|   +++++|+++.|+++++.|+.|.+...++.++.+|+.++ +|+++.+++..++.
T Consensus        26 d~d~~~~rl~eLe~~l~~p~~w~D~~~a~kl~ke~~~L~~~v~~~~~l~~~~~dl~el~el~~ee-~d~e~~~e~~~el~  104 (365)
T 1gqe_A           26 DYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEA-DDEETFNEAVAELD  104 (365)
T ss_dssp             THHHHHHHHHHHHHHHHSGGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf             98999999999999864972554999999999999999999999999999999899999887601-32788999999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEE
Q ss_conf             32000577888999864000113554037886226885217889999999999998764984001321135447721113
Q gi|254780874|r   85 AIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIV  164 (357)
Q Consensus        85 ~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~  164 (357)
                      .+...++.    |+..++|+||+|.+||||||||||||+||||||+||||||+|||+++||+++++++++|+.||||+|+
T Consensus       105 ~l~~~l~~----le~~ll~~d~~D~~nailEIrAGaGG~EA~dfA~~L~RMY~ryAE~kgwk~evid~~~~e~gGik~v~  180 (365)
T 1gqe_A          105 ALEEKLAQ----LEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVT  180 (365)
T ss_dssp             HHHHHHHH----HGGGGGCCSTTTTSCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEEECSSSSEEEEE
T ss_pred             HHHHHHHH----HHHHCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEE
T ss_conf             99999999----87513689966555745999847996899999999999999999985992589861677767327999


Q ss_pred             EEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECC-CCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf             7775031112100024650267612545678511016888853033-433222454347999852888752000632121
Q gi|254780874|r  165 ATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEA-AEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSA  243 (357)
Q Consensus       165 ~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~-~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~sa  243 (357)
                      |.|+|+||||+||+|+||||||||||||++||||||||||+|+|++ ++++++|+|+||||||||||||||||||||+||
T Consensus       181 ~~I~G~~aYg~Lk~EsGVHRvqRvp~tes~gR~HTS~asV~V~P~~~~~~~i~i~~~Dl~id~~rssG~GGQ~vNkt~sa  260 (365)
T 1gqe_A          181 IKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESA  260 (365)
T ss_dssp             EEEESTTHHHHHGGGCEEEEEEEECTTSSSCCEEEEEEEEEEEECCBTTBCCCCCGGGEEEEEECCCCSSCCSTTSSCCE
T ss_pred             EEEECCCHHHHHHHCCCCEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCEECCHHHEEEEEEECCCCCCCCCCCCCCE
T ss_conf             99974672566631487303675688688884798667899825788764043165782798655688876765653434


Q ss_pred             EEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCCCEEECCCCCCCEEEEE
Q ss_conf             588964984488-84365413589999999999999999999999998744--652246742382210448998112432
Q gi|254780874|r  244 VRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANR--KLQIGSGDRSERIRTYNFSQGRITDHR  320 (357)
Q Consensus       244 vri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r--~~~~g~~~rs~~iRtY~~~~~rv~DhR  320 (357)
                      |||||+||||+| ||+|||||+||++||++|++|||+++.+++.++....|  +.++|   ||+||||||||||||||||
T Consensus       261 Vri~H~ptgi~v~~q~ersq~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~---~g~~IRtYnf~~~rVtDhR  337 (365)
T 1gqe_A          261 VRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIG---WGSQIRSYVLDDSRIKDLR  337 (365)
T ss_dssp             EEEEETTTCCEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSTTCCCCC---SCSEEEEEEGGGTEEEETT
T ss_pred             EEEEEECCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---CCCCCCCCCCCCCCCEECC
T ss_conf             8999707864999606020477899999999999999999999999999884311355---7698567548998140306


Q ss_pred             CCCEECCHHHHHCCCHHHHHHHHHHH
Q ss_conf             16441787787288669999999999
Q gi|254780874|r  321 INLTLYKLEYVLQGYIDDIINPLLTA  346 (357)
Q Consensus       321 ~~~~~~~~~~~l~G~l~~~i~~~~~~  346 (357)
                      ||++++|+++||+|+||+||++|+.+
T Consensus       338 ~~~~~~~~~~vl~G~ld~~i~a~l~~  363 (365)
T 1gqe_A          338 TGVETRNTQAVLDGSLDQFIEASLKA  363 (365)
T ss_dssp             TCCEESCHHHHHTTCCHHHHHHHHHT
T ss_pred             CCCEECCHHHHHCCCHHHHHHHHHHC
T ss_conf             59745786787698759999999977


No 4  
>2b3t_B RF-1, peptide chain release factor 1; translation termination, methylation, conformational changes; HET: SAH; 3.10A {Escherichia coli} SCOP: e.38.1.1
Probab=100.00  E-value=0  Score=958.10  Aligned_cols=353  Identities=49%  Similarity=0.817  Sum_probs=339.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             9678689899999999999998538531579---9999999987999999999999999989999999720378535665
Q gi|254780874|r    1 MVFLSHKQICDLKNRFAEIELRMSESPSVDA---YIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRD   77 (357)
Q Consensus         1 m~mi~~~kL~~l~~rl~ELE~~Lsdp~~w~d---~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~e   77 (357)
                      |.-...+||+.+..|+++|+.+|++|++|+|   +++++|+++.|+++++.++.|.....++.++.+|+.    |+++.+
T Consensus         1 M~~sl~~kLe~i~~r~~eLe~~lsdp~~w~D~~~a~~l~kE~~~L~~~v~~~~~~~~~~~~l~el~el~~----d~e~~e   76 (360)
T 2b3t_B            1 MKPSIVAKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDIETAQMMLD----DPEMRE   76 (360)
T ss_dssp             ------CCSHHHHHHHHHHHHHHHHHTTSSCCSSHHHHHHHHHHHHHHHHHHHHHTTCC---------------------
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCHHH
T ss_conf             9778999999999999999998719862009999999999999999999999999999998999998744----840189


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCC
Q ss_conf             43322233200057788899986400011355403788622688521788999999999999876498400132113544
Q gi|254780874|r   78 LAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDD  157 (357)
Q Consensus        78 lAeeEl~~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~  157 (357)
                      ++++|+..+..+++.++++++.+|+|+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|+.
T Consensus        77 la~ee~~~~~~~l~~l~~~l~~~Ll~~~~~D~~nailEIraGaGG~EA~~fA~~L~rMY~r~ae~~gwk~eii~~~~~e~  156 (360)
T 2b3t_B           77 MAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEH  156 (360)
T ss_dssp             ------------------CCCCCCCSCCSGGGSCEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEEECTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             99999999999999999999997079995645584999925888467999999999999999976588527844215677


Q ss_pred             CCCCEEEEEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCC-CCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             7721113777503111210002465026761254567851101688885303343-322245434799985288875200
Q gi|254780874|r  158 GGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAE-IDVDIPLEDIRIDTMRASGSGGQH  236 (357)
Q Consensus       158 aGik~v~~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~-~~~~i~~~dl~i~~~rssG~GGQ~  236 (357)
                      ||||+|++.|+|++|||+||+|+|||||||||||+++||+|||||+|+|+|++++ ++++|||+||+|||||||||||||
T Consensus       157 ~G~k~~~~~I~G~~ayg~Lk~EsGVHRvqRvp~~~~~~r~hTs~~~v~v~p~~~~~~~~~i~~~dl~i~t~RssG~GGQ~  236 (360)
T 2b3t_B          157 GGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQH  236 (360)
T ss_dssp             SSEEEEEEEECSSSCHHHHGGGCEEEEEEECCTTCSSCCCEEEEEEEECCBCCCTTTCCCCCSSSEEEEECCSSCCCTTT
T ss_pred             CCEEEEEEEEECCCHHHHHHHCCCCEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCCCCC
T ss_conf             86258999997576124554347862699747888888267777799995577753001427111569987779999877


Q ss_pred             CCCCCCEEEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCC
Q ss_conf             0632121588964984488-843654135899999999999999999999999987446522467423822104489981
Q gi|254780874|r  237 VNTTDSAVRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGR  315 (357)
Q Consensus       237 vN~t~savri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~r  315 (357)
                      ||||+|||||||+||||+| ||+|||||+||++||++||+|||+.+.+++.++..+.||+|||||+||+|||||||||+|
T Consensus       237 VNkt~sAVRitH~PTGi~v~~q~eRSQ~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~rk~~vg~~~rse~IRtYn~p~~~  316 (360)
T 2b3t_B          237 VNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGR  316 (360)
T ss_dssp             CCCSSEEEEEEETTTCCEEEEEESSCHHHHHHHHHHHHHHHHTTTTTTSCC------CCC-------CCEEEEEETTTTE
T ss_pred             CCCHHHCEEEEECCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf             66131212789658876999727024799999999999999999999999999999876004001233752745179776


Q ss_pred             EEEEECCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             124321644178778728866999999999999999874059
Q gi|254780874|r  316 ITDHRINLTLYKLEYVLQGYIDDIINPLLTAHQAKMIGSASE  357 (357)
Q Consensus       316 v~DhR~~~~~~~~~~~l~G~l~~~i~~~~~~~~~~~l~~~~e  357 (357)
                      |||||||++++|+++||+|+||+||++|+.|+++++|++++|
T Consensus       317 V~DhR~~~~~~~~~~vl~G~ld~~i~a~~~~~~~~~l~~~~~  358 (360)
T 2b3t_B          317 VTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLAALSE  358 (360)
T ss_dssp             EEEGGGTEEESCHHHHHHTCTHHHHHHHHHHHHHHHCC----
T ss_pred             CHHHCCCCEECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             443145887778357649872999999999999999987555


No 5  
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Probab=100.00  E-value=0  Score=909.30  Aligned_cols=336  Identities=34%  Similarity=0.499  Sum_probs=306.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             89999999999999853853157999---999999879999999999999999899999997203785356654332223
Q gi|254780874|r    8 QICDLKNRFAEIELRMSESPSVDAYI---KLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVL   84 (357)
Q Consensus         8 kL~~l~~rl~ELE~~Lsdp~~w~d~~---klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elAeeEl~   84 (357)
                      .++.++.|+.+|+.+|++|+||+|+.   +++|+++.|+++++.|+.+.   +++.++.+|+.+  .|+++.++++.|+.
T Consensus        18 Dle~~~~rl~ELE~~lsdP~fW~D~~kA~kl~KE~s~L~~iV~~~~~l~---~~ledl~EL~ee--~d~E~~e~~~~El~   92 (365)
T 2ihr_1           18 DIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFRSLE---SDLQGLLELMEE--LPAEEREALKPELE   92 (365)
T ss_dssp             SHHHHHHHHTTTTTSTTCGGGTTTGGGSSSTTHHHHHTHHHHHHHHHHH---HHTTTHHHHTTC--SCCTTGGGTGGGTH
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH--HHHHHHHHHHHHHH
T ss_conf             9999999999999987198044499999999999999999999999999---999999999863--01536889987443


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEE
Q ss_conf             32000577888999864000113554037886226885217889999999999998764984001321135447721113
Q gi|254780874|r   85 AIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIV  164 (357)
Q Consensus        85 ~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~  164 (357)
                      .+.+.++.++    ..++|+||+|.+||||||||||||+||||||+||||||+|||+++||++++++.++|++||||+|+
T Consensus        93 ~l~~~l~~le----~~~ll~~~~D~~nailEIrAGaGG~EA~dwA~~L~RMY~r~Ae~~g~k~eii~~~~~e~~Gik~~~  168 (365)
T 2ihr_1           93 EAAKKLDELY----HQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQ  168 (365)
T ss_dssp             HHHHHHHHHH----HHHHTCSSSTTSEEEEEEEECSSTHHHHHHHHHHHHHHHHHHHTTTCEEEEEEEEECSSSSEEEEE
T ss_pred             HHHHHHHHHH----HHHHCCCCCCCCCHHEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCEEEE
T ss_conf             4555799999----987146833125413288626860689999999999999999767984899874045688860699


Q ss_pred             EEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECC-CCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCE
Q ss_conf             7775031112100024650267612545678511016888853033-433222454347999852888752000632121
Q gi|254780874|r  165 ATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEA-AEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSA  243 (357)
Q Consensus       165 ~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~-~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~sa  243 (357)
                      +.|+|++|||+||+|+|||||||||||+++||||||||+|+|+|++ +++++.|+|+||+|||||||||||||||||+||
T Consensus       169 ~~I~G~~ayg~lk~E~GvHRv~Rv~~~~~~~r~hts~~~v~v~P~~~~~~~~~i~~~dl~i~t~rssG~GGQ~vNkt~sA  248 (365)
T 2ihr_1          169 ILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSA  248 (365)
T ss_dssp             EEEESTTHHHHHGGGCEEEEEEEECTTSSSCCEEEEEEEEEEEEECCSSSSCCCCGGGEEEEEECCCCSSCCSGGGSCSE
T ss_pred             EEEECCCHHHCCCCCCCEEEEEEECCCCCCCCEEEEEEEEEEECCCCCHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCE
T ss_conf             99965653320332163288986389789997244467899976776113200330111589886688987886651324


Q ss_pred             EEEEECCCCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEEEECC
Q ss_conf             588964984488-8436541358999999999999999999999999874465224674238221044899811243216
Q gi|254780874|r  244 VRITHIPTGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRIN  322 (357)
Q Consensus       244 vri~H~ptgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~DhR~~  322 (357)
                      |||||+||||+| ||+|||||+||++||++|++|||+++.++++++..+.| +|+|+++||+|||||||||+||||||||
T Consensus       249 Vri~H~ptgi~v~~q~ersq~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~~-~~~~~~~r~~~iRtY~fp~~rVtDhR~~  327 (365)
T 2ihr_1          249 VRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALR-GEVRPIEWGSQIRSYVLDKNYVKDHRTG  327 (365)
T ss_dssp             EEEEETTTTEEEEECSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT-CCSCCSCCCSCSEEEEGGGTEEEETTTC
T ss_pred             EEEEECCCCCEEEHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCCCCEECCCCCCCCCCCC
T ss_conf             799973872255430121477659999999999999999999999999988-4747777658811525898834201649


Q ss_pred             CEECCHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             4417877872886699999999999999987
Q gi|254780874|r  323 LTLYKLEYVLQGYIDDIINPLLTAHQAKMIG  353 (357)
Q Consensus       323 ~~~~~~~~~l~G~l~~~i~~~~~~~~~~~l~  353 (357)
                      ++++|+++||+|+||+||++++.|..+++..
T Consensus       328 ~~~~~~~~vl~G~ld~~i~a~l~~~~~~~~~  358 (365)
T 2ihr_1          328 LMRHDPENVLDGDLMDLIWAGLEWKAGRRQG  358 (365)
T ss_dssp             CEESCHHHHTTTCCHHHHHHHHHHHHTTC--
T ss_pred             CEECCHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8557868876887099999999999999873


No 6  
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide release factor 1, ribosome, structural genomics, BSGC structure funded by NIH; 2.65A {Thermotoga maritima} SCOP: e.38.1.1 PDB: 2fvo_A
Probab=100.00  E-value=0  Score=900.54  Aligned_cols=331  Identities=46%  Similarity=0.737  Sum_probs=303.7

Q ss_pred             HHHHHHHHHHHHCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998538531579-99999999879999999999999999899999997203785356654332223320005
Q gi|254780874|r   12 LKNRFAEIELRMSESPSVDA-YIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEI   90 (357)
Q Consensus        12 l~~rl~ELE~~Lsdp~~w~d-~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e~D~El~elAeeEl~~l~~~l   90 (357)
                      |+.|+.+|+.+|++|++|+| ++++++++++|+++++.++.+.    ++.++.+++.+. .|.+      .|+..+..++
T Consensus         1 L~er~~ELe~~ls~P~~~~d~~~~l~ke~~~L~~i~~l~~~l~----d~~el~el~~ee-~d~e------~el~~l~~~l   69 (342)
T 1rq0_A            1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIK----ETQEFIELLREE-GENE------LEIEKYEKEL   69 (342)
T ss_dssp             CTTTTTHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHTTTTTT-TTCC------SCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHCC-CCCH------HHHHHHHHHH
T ss_conf             9689999999971899899999999999999999999999999----899999997458-9858------9999999999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECC
Q ss_conf             77888999864000113554037886226885217889999999999998764984001321135447721113777503
Q gi|254780874|r   91 RELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGR  170 (357)
Q Consensus        91 ~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~  170 (357)
                      +.++.+|.++   .+|+|++||||||||||||+||||||+||||||+|||+++||+++++++++|+.||||+|++.|+|+
T Consensus        70 ~~l~~el~~l---l~p~D~~nailEIrAGaGG~EA~~fA~~L~RMY~r~Ae~kgwk~eil~~~~~~~gGik~~~~~I~G~  146 (342)
T 1rq0_A           70 DQLYQELLFL---LSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGK  146 (342)
T ss_dssp             HHHHHHHHHH---HSCSSCSEEEEEEEECSSTHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEEECTTSCEEEEEEEEEST
T ss_pred             HHHHHHHHHH---CCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEECC
T ss_conf             9999998740---7877778869999679985379999999999999997651335422333544456764136998341


Q ss_pred             CHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             11121000246502676125456785110168888530334332224543479998528887520006321215889649
Q gi|254780874|r  171 GVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIP  250 (357)
Q Consensus       171 ~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~savri~H~p  250 (357)
                      +|||+||+|+|||||||||||+++||||||||+|+|+|+.++++|+|+|+||+|||||||||||||||||+|||||||+|
T Consensus       147 ~ayg~Lk~E~GvHRvqRvp~~es~gr~hTS~a~V~v~p~~~~~~i~i~~~dl~i~t~RssG~GGQ~VNkt~saVRitH~P  226 (342)
T 1rq0_A          147 NAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLP  226 (342)
T ss_dssp             THHHHHGGGCEEEEEEECCTTSCSCCCEEEEEEEEEEECCCGGGSCCCGGGEEEEEECCCC----CCSSSSEEEEEEETT
T ss_pred             HHHHHCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCEEECHHHEEEEEECCCCCCCCCCCCCCEEEEEEECC
T ss_conf             26653101065589997179888887576777999946677665365522402541037874324466666069999748


Q ss_pred             CCEEE-EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEEEECCCEECCHH
Q ss_conf             84488-84365413589999999999999999999999998744652246742382210448998112432164417877
Q gi|254780874|r  251 TGIMV-TSSEKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLE  329 (357)
Q Consensus       251 tgi~v-~~~eRsQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~g~~~rs~~iRtY~~~~~rv~DhR~~~~~~~~~  329 (357)
                      |||+| ||+|||||+||++||++|++|||+.+.+++.++....|++|||+|+||+|||||||||+||||||||++++|++
T Consensus       227 TGi~v~~q~eRSQ~~Nk~~A~~~L~~kl~~~~~~~~~~~~~~~r~~~ig~~~rs~~iRtY~fp~~rV~DhR~~~~~~~l~  306 (342)
T 1rq0_A          227 TGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQ  306 (342)
T ss_dssp             TCCEEEEEESSCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCC----------CCCEEEEEETTTTEEEETTTTEEESCHH
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCEECCHH
T ss_conf             86388734602389999999999999999999999999999987636002356788626318988743312598107867


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             872886699999999999999987405
Q gi|254780874|r  330 YVLQGYIDDIINPLLTAHQAKMIGSAS  356 (357)
Q Consensus       330 ~~l~G~l~~~i~~~~~~~~~~~l~~~~  356 (357)
                      +||+|+||+||++|+.++..++|.++.
T Consensus       307 ~vl~G~ld~~i~~~~~~~~~~~l~~~~  333 (342)
T 1rq0_A          307 EILDGDLDEIISKLIEHDIENNLEEVL  333 (342)
T ss_dssp             HHHTTCCHHHHHHHHHHHHTTTHHHHC
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             875987399999999999999999986


No 7  
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural genomics, PSI-2, protein structure initiative; NMR {Pseudomonas syringae PV}
Probab=99.71  E-value=1.7e-17  Score=145.38  Aligned_cols=68  Identities=29%  Similarity=0.486  Sum_probs=61.4

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEECCCC------------------------EEEEE-CCCCCHHHHHH
Q ss_conf             222454347999852888752000632121588964984------------------------48884-36541358999
Q gi|254780874|r  214 DVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTG------------------------IMVTS-SEKSQHQNRLR  268 (357)
Q Consensus       214 ~~~i~~~dl~i~~~rssG~GGQ~vN~t~savri~H~ptg------------------------i~v~~-~eRsQ~~Nk~~  268 (357)
                      .+.|+++||++.+.|||||||||||||+|+|.|++-|++                        |+|.| ..|||++||+.
T Consensus         7 ~i~Ip~~el~~~f~RSSGPGGQ~VNK~~TkV~L~~~~~~~~~~~~~~~~l~~~~~~~i~~~g~l~I~s~~~RSQ~~Nr~~   86 (108)
T 2jva_A            7 NVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLKAQQYRTQEQNRAD   86 (108)
T ss_dssp             SCEECGGGEEEEECCCTTCSSSSSCCCCCCEEEEEETTTSCCCHHHHHHHHTCSCTTBCTTCEEEEEECCSSSHHHHHHH
T ss_pred             CCEECHHHEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             75098799389999878998765123252257897676555556899999997417305797099998874799999999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780874|r  269 AMKVLRARLYDVE  281 (357)
Q Consensus       269 A~~~L~~~l~~~~  281 (357)
                      |++.|...|.+..
T Consensus        87 a~~kL~~li~~a~   99 (108)
T 2jva_A           87 ALLRLSELIVNAA   99 (108)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999999


No 8  
>2jy9_A Putative tRNA hydrolase domain; GFT protein structure, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}
Probab=99.70  E-value=1.9e-17  Score=144.92  Aligned_cols=68  Identities=35%  Similarity=0.559  Sum_probs=59.0

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEE------ECCC---------------C---EEEEEC-CCCCHHHHHH
Q ss_conf             2224543479998528887520006321215889------6498---------------4---488843-6541358999
Q gi|254780874|r  214 DVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRIT------HIPT---------------G---IMVTSS-EKSQHQNRLR  268 (357)
Q Consensus       214 ~~~i~~~dl~i~~~rssG~GGQ~vN~t~savri~------H~pt---------------g---i~v~~~-eRsQ~~Nk~~  268 (357)
                      .|.|+++||+|.|.|||||||||||||+|+|.|.      ++|.               +   |+|.|+ .|||++|++.
T Consensus         7 ~i~Ip~~ei~~~f~RSsGPGGQnVNK~~TkV~Lr~~l~~~~l~~~~~~rl~~~~~~ri~~~g~lvI~sq~~RSQ~~Nr~~   86 (148)
T 2jy9_A            7 TVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQELNREA   86 (148)
T ss_dssp             SCCBCSTTCEEEEECCSCCCSSCSCSCSCEEEEEECSTTSCCCHHHHHHHHHSCCTTBCSSSCEEEEECSSSCHHHHHHH
T ss_pred             CCCCCHHHEEEEEEECCCCCCCCHHHHHHHHEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             77178799078888768998763115533312473145567998999999997366656895089997785899999999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780874|r  269 AMKVLRARLYDVE  281 (357)
Q Consensus       269 A~~~L~~~l~~~~  281 (357)
                      |+..|.+.|.+..
T Consensus        87 Al~kL~~~I~~a~   99 (148)
T 2jy9_A           87 AIARLVAVIKELT   99 (148)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999864


No 9  
>1j26_A Immature colon carcinoma transcript 1; peptide chain release factors, RF-1, the GGQ motif, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.4.1
Probab=99.65  E-value=1.7e-16  Score=138.14  Aligned_cols=70  Identities=29%  Similarity=0.452  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEECCC-------------------------CEEEEE-CCCCCH
Q ss_conf             343322245434799985288875200063212158896498-------------------------448884-365413
Q gi|254780874|r  210 AAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPT-------------------------GIMVTS-SEKSQH  263 (357)
Q Consensus       210 ~~~~~~~i~~~dl~i~~~rssG~GGQ~vN~t~savri~H~pt-------------------------gi~v~~-~eRsQ~  263 (357)
                      .......|+.++|++.+.|||||||||||||+|+|.|++.+.                         +|+|.| ..|||+
T Consensus        10 ~~~~~~~Ip~~~i~~~f~RSsGPGGQ~VNK~~TkV~L~~~l~~~~~l~~~~~~~l~~~~~~~i~~~g~l~I~s~~~RsQ~   89 (112)
T 1j26_A           10 AKQASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVLTSESSRYQF   89 (112)
T ss_dssp             CCSSCCCCCTTTSEEEEECCCCSSSSCCSSCCCEEEEEEEGGGCTTSCHHHHHHHHHHTTTTBCSSSEEEEEECCCSSHH
T ss_pred             HHHHCCCCCHHHEEEEEEECCCCCCCCCCCCCCCEEEEECHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHH
T ss_conf             33404704878937998876799998444303030589762323579999999999986373666983999988767999


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             5899999999999999
Q gi|254780874|r  264 QNRLRAMKVLRARLYD  279 (357)
Q Consensus       264 ~Nk~~A~~~L~~~l~~  279 (357)
                      +||+.|+..|...|.+
T Consensus        90 ~Nr~~a~~kL~~li~~  105 (112)
T 1j26_A           90 RNLAECLQKIRDMIAE  105 (112)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 10 
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular mimicry, translation; 1.81A {Escherichia coli} SCOP: e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Probab=94.48  E-value=0.31  Score=27.99  Aligned_cols=60  Identities=17%  Similarity=0.168  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCH-HHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             898999999999999985385315-7999999----------------999879999999999999999899999997
Q gi|254780874|r    6 HKQICDLKNRFAEIELRMSESPSV-DAYIKLT----------------EEYAAISPIISKISIYDQKKQEEQDLHTVI   66 (357)
Q Consensus         6 ~~kL~~l~~rl~ELE~~Lsdp~~w-~d~~kls----------------Ke~s~L~~iv~~~~~~~~~~~ei~el~eLl   66 (357)
                      ..+|+++..++..|...+. .+.. ..+..+.                +..++++.+...++.|..+...+.++.++.
T Consensus         8 ~~~i~~l~~~~~~l~~~ld-~d~~~~rl~eLe~~l~~p~~w~D~~~a~kl~ke~~~L~~~v~~~~~l~~~~~dl~el~   84 (365)
T 1gqe_A            8 NNRIQDLTERSDVLRGYLD-YDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLL   84 (365)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHSGGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999987679-8999999999999864972554999999999999999999999999999999899999


No 11 
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, alternative splicing, amyloid, amyloidosis, blood coagulation, coiled coil; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*
Probab=91.44  E-value=0.79  Score=25.07  Aligned_cols=15  Identities=33%  Similarity=0.390  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             899999999999998
Q gi|254780874|r    8 QICDLKNRFAEIELR   22 (357)
Q Consensus         8 kL~~l~~rl~ELE~~   22 (357)
                      +|++|+.++.++.+.
T Consensus        65 ~i~~l~~~~~~~~~~   79 (562)
T 3ghg_A           65 RINKLKNSLFEYQKN   79 (562)
T ss_dssp             HHHHHHHHHTHHHHH
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999988


No 12 
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation; 2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X 2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Probab=85.81  E-value=0.085  Score=32.05  Aligned_cols=22  Identities=32%  Similarity=0.388  Sum_probs=8.6

Q ss_pred             HHHHHHHHCCCCCCCCCEEECCC
Q ss_conf             98744652246742382210448
Q gi|254780874|r  289 RSANRKLQIGSGDRSERIRTYNF  311 (357)
Q Consensus       289 ~~~~r~~~~g~~~rs~~iRtY~~  311 (357)
                      +.+.....+|+--|+.-. .|+.
T Consensus       299 ~~~~~~~~r~~~iRtY~f-p~~r  320 (365)
T 2ihr_1          299 RGEVRPIEWGSQIRSYVL-DKNY  320 (365)
T ss_dssp             TCCSCCSCCCSCSEEEEG-GGTE
T ss_pred             HHCCCCCCCCCCCCCEEC-CCCC
T ss_conf             847477776588115258-9883


No 13 
>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*
Probab=82.02  E-value=2.7  Score=21.17  Aligned_cols=22  Identities=27%  Similarity=0.360  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3322233200057788899986
Q gi|254780874|r   79 AQIEVLAIEKEIRELENEINYL  100 (357)
Q Consensus        79 AeeEl~~l~~~l~~le~eL~~~  100 (357)
                      .+..+..+..++..++.++..+
T Consensus       173 Lq~~l~elq~kIq~LE~qI~q~  194 (464)
T 1m1j_B          173 LRAVIDSLHKKIQKLENAIATQ  194 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999878


No 14 
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos taurus} SCOP: i.9.1.1
Probab=77.72  E-value=3.7  Score=20.23  Aligned_cols=14  Identities=14%  Similarity=0.318  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             99999999999853
Q gi|254780874|r   11 DLKNRFAEIELRMS   24 (357)
Q Consensus        11 ~l~~rl~ELE~~Ls   24 (357)
                      ++..++++|..++.
T Consensus        64 ~~~~~i~~l~~~l~   77 (390)
T 1deq_A           64 DFTSRINKLRDSLF   77 (390)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999999


No 15 
>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A
Probab=68.44  E-value=6  Score=18.71  Aligned_cols=17  Identities=12%  Similarity=0.397  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             98999999999999985
Q gi|254780874|r    7 KQICDLKNRFAEIELRM   23 (357)
Q Consensus         7 ~kL~~l~~rl~ELE~~L   23 (357)
                      .+|++|..++.+++...
T Consensus        65 ~ri~~Lq~~L~e~q~~~   81 (491)
T 1m1j_A           65 QRIDNIRQQLADSQNKY   81 (491)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999


No 16 
>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, serrs, translation, ATP-binding, nucleotide-binding, structural genomics; HET: ATP; 1.95A {Trypanosoma brucei} PDB: 3lsq_A*
Probab=56.06  E-value=9.8  Score=17.19  Aligned_cols=54  Identities=17%  Similarity=0.162  Sum_probs=28.6

Q ss_pred             CCCCCHHHHHHHH--HHH-HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9678689899999--999-99999853853157999999999879999999999999
Q gi|254780874|r    1 MVFLSHKQICDLK--NRF-AEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQ   54 (357)
Q Consensus         1 m~mi~~~kL~~l~--~rl-~ELE~~Lsdp~~w~d~~klsKe~s~L~~iv~~~~~~~~   54 (357)
                      |+|+..+.|-+-.  ..+ +.+...-.+++..+...++-++.+++..-++.+..-.+
T Consensus         5 ~~MLDikliRe~~n~d~vre~lkkR~~d~dlVD~il~lD~~rR~l~~e~e~Lr~erN   61 (484)
T 3lss_A            5 MMVLDIQLFRDETGANIIRESQRRRFADPDIVDAIIEADKKWRRTQFLTEASKKLIN   61 (484)
T ss_dssp             CCCCCGGGGGSHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEECCHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             000118998658986999999987499878999999999999999999999999986


No 17 
>3ghg_B Fibrinogen beta chain; triple-stranded coiled coil, beta sheets, alpha helices, alternative splicing, amyloid, amyloidosis, blood coagulation, coiled coil; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_B* 1deq_B 2a45_H*
Probab=55.20  E-value=10  Score=17.09  Aligned_cols=21  Identities=14%  Similarity=0.298  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             332223320005778889998
Q gi|254780874|r   79 AQIEVLAIEKEIRELENEINY   99 (357)
Q Consensus        79 AeeEl~~l~~~l~~le~eL~~   99 (357)
                      .+..+..+..++..|+.++..
T Consensus       168 LQ~~i~~l~~kIq~Leq~Isq  188 (461)
T 3ghg_B          168 LRSILENLRSKIQKLESDVSA  188 (461)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999988


No 18 
>2pih_A Protein YMCA; regulate community development, structural genomics, PSI-2, protein structure initiative; 2.10A {Bacillus subtilis} SCOP: a.281.1.1
Probab=50.59  E-value=12  Score=16.59  Aligned_cols=58  Identities=14%  Similarity=0.234  Sum_probs=35.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9678689899999999999998538531579999999998799999999999999998999
Q gi|254780874|r    1 MVFLSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQD   61 (357)
Q Consensus         1 m~mi~~~kL~~l~~rl~ELE~~Lsdp~~w~d~~klsKe~s~L~~iv~~~~~~~~~~~ei~e   61 (357)
                      |.|.+.+   +|...-.+|...+.+.+-..+++++.+.+..-..+.+.+..|.....++..
T Consensus         1 ~~~~t~e---dI~d~A~eL~~~I~~seey~~y~~A~~~i~~d~eaq~li~eF~~~q~e~~~   58 (151)
T 2pih_A            1 MTLYSKK---DIVQQARNLAKMISETEEVDFFKRAEAQINENDKVSTIVNQIKALQKQAVN   58 (151)
T ss_dssp             -CCBCHH---HHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHH---HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9855399---999999999999872999999999999998199999999999999999999


No 19 
>1vq8_D 50S ribosomal protein L5P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: d.77.1.1 PDB: 1vq4_D* 1vq5_D* 1vq6_D* 1vq7_D* 1s72_D* 1vq9_D* 1vqk_D* 1vql_D* 1vqm_D* 1vqn_D* 1vqo_D* 1vqp_D* 1yhq_D* 1yi2_D* 1yij_D* 1yit_D* 1yj9_D* 1yjn_D* 1yjw_D* 2otj_D* ...
Probab=48.64  E-value=6.6  Score=18.40  Aligned_cols=72  Identities=13%  Similarity=0.140  Sum_probs=44.4

Q ss_pred             CCCCCCCCEEEEEEECCCHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEEEEEECCC-CCCCCCCCCEEEEEEECC
Q ss_conf             3544772111377750311121000246502676125456785110168888530334-332224543479998528
Q gi|254780874|r  154 DNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAA-EIDVDIPLEDIRIDTMRA  229 (357)
Q Consensus       154 ~ge~aGik~v~~~I~G~~aYg~Lk~E~GvHRvqRip~~es~gR~hTS~a~V~V~P~~~-~~~~~i~~~dl~i~~~rs  229 (357)
                      +|+--|+|   +.+.|+.+|.+|.-=-.+- .-++..||.+|-..-.--...++|+++ |..+.|.-=|+-|.|-|.
T Consensus        66 kG~pIG~k---VTLRg~~m~~FL~kll~~v-~~~~k~FD~~GN~sfGi~e~~~FPei~~d~~~~i~GmdIti~t~~~  138 (177)
T 1vq8_D           66 EGDPIGAK---VTLRDEMAEEFLQTALPLA-ELATSQFDDTGNFSFGVEEHTEFPSQEYDPSIGIYGLDVTVNLVRP  138 (177)
T ss_dssp             SSSEEEEE---EEECTHHHHHHHHHHGGGS-CCCGGGBCSSSCEEEC--------------------CEEEEEEECG
T ss_pred             CCCEEEEE---EEEEHHHHHHHHHHHHHHC-CCCCCCCCCCCEEEECCHHHHCCCCCCCCCCCCCCCEEEEEEECCC
T ss_conf             79825899---9973888999999985224-8885454898648878278833664420466772011799995889


No 20 
>2hdl_A Small inducible cytokine B14; CXCL14, BRAK, chemokine; NMR {Homo sapiens}
Probab=48.34  E-value=12  Score=16.51  Aligned_cols=44  Identities=18%  Similarity=0.365  Sum_probs=33.8

Q ss_pred             HCCCCCC-CCCCEEEEEECCCC--CCHH-----HHHHHHHHHHHHHHHHHCC
Q ss_conf             4000113-55403788622688--5217-----8899999999999987649
Q gi|254780874|r  101 LLPKDTD-DDKSCILEIRAGTG--GSEA-----ALFVGDLFRMYERYAALRK  144 (357)
Q Consensus       101 LLpsde~-D~~nailEI~aGaG--G~EA-----~dwA~~L~rMY~r~ae~~g  144 (357)
                      .+|++++ +....|++..-|++  |.+-     +-|+.-|+.+|..|-+++.
T Consensus        23 v~p~gp~C~~~EII~TLKn~~~~~G~~vCLdP~a~~vkklik~~~~~~~k~r   74 (78)
T 2hdl_A           23 MKPKYPHCEEKMVIITTKSVSRYRGQEHCLHPKLQSTKRFIKWYNAWNEKRR   74 (78)
T ss_dssp             ECCSSTTSSSCCEEEEECSSSTTTTSEEEECTTSHHHHHHHHHHHHHHHHHT
T ss_pred             EECCCCCCCCCEEEEEECCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHCC
T ss_conf             9889998998589999603766778778768897799999999999876145


No 21 
>3ofo_I 30S ribosomal protein S9; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_I* 3iy8_I 2wwl_I 3ofp_I 2qal_I* 1p6g_I 1p87_I 2aw7_I 2avy_I 2i2u_I 2i2p_I* 2qan_I* 2qb9_I* 2qbb_I* 2qbd_I 2qbf_I 2qbh_I* 2qbj_I* 2qou_I* 2qow_I* ...
Probab=48.06  E-value=9.4  Score=17.29  Aligned_cols=29  Identities=28%  Similarity=0.375  Sum_probs=19.1

Q ss_pred             CCCCCCCEEEEEEEEEECCCCCCCCCCCCEE
Q ss_conf             5678511016888853033433222454347
Q gi|254780874|r  192 EASGRVHTSAATVAVLPEAAEIDVDIPLEDI  222 (357)
Q Consensus       192 es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl  222 (357)
                      =+-|||.||+|.|.+.|-.-  .|.||..++
T Consensus         4 y~~GrRKtaiArv~l~~G~G--~i~IN~~~~   32 (127)
T 3ofo_I            4 YGTGRRKSSAARVFIKPGNG--KIVINQRSL   32 (127)
T ss_dssp             CCCCBCSSCEEEEEEESCCS--CBCTTSSCT
T ss_pred             CCCCCCCCEEEEEEEEECCE--EEEECCEEH
T ss_conf             02060634899999993733--899998408


No 22 
>3jyv_I 40S ribosomal protein S16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_I
Probab=46.84  E-value=9.2  Score=17.37  Aligned_cols=29  Identities=14%  Similarity=0.129  Sum_probs=21.0

Q ss_pred             CCCCCCCEEEEEEEEEECCCCCCCCCCCCEE
Q ss_conf             5678511016888853033433222454347
Q gi|254780874|r  192 EASGRVHTSAATVAVLPEAAEIDVDIPLEDI  222 (357)
Q Consensus       192 es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl  222 (357)
                      .+.|||.||+|-|.+.|-  .-.|.||..++
T Consensus         3 ~~~GrRKta~A~v~l~~G--~G~i~INg~~~   31 (138)
T 3jyv_I            3 QTFGKKKSATAVAHVKAG--KGLIKVNGSPI   31 (138)
T ss_dssp             CCCCCSSSCEEEEEEEES--CCCEEETTEEH
T ss_pred             EEECCCCCEEEEEEEECC--CCEEEECCCCH
T ss_conf             417648318999999828--55699999115


No 23 
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.14.1.1 PDB: 1gix_L* 1hnw_I* 1hnx_I* 1hnz_I* 1hr0_I 1i94_I* 1i95_I* 1i96_I* 1i97_I* 1ibk_I* 1ibl_I* 1ibm_I 1j5e_I 1jgo_L* 1jgp_L* 1jgq_L* 1ml5_L* 1n32_I* 1n33_I* 1n34_I ...
Probab=46.14  E-value=7.9  Score=17.84  Aligned_cols=28  Identities=25%  Similarity=0.323  Sum_probs=18.2

Q ss_pred             CCCCCCEEEEEEEEEECCCCCCCCCCCCEE
Q ss_conf             678511016888853033433222454347
Q gi|254780874|r  193 ASGRVHTSAATVAVLPEAAEIDVDIPLEDI  222 (357)
Q Consensus       193 s~gR~hTS~a~V~V~P~~~~~~~~i~~~dl  222 (357)
                      +-|||.||+|.|.+.|=.  -.|.||..++
T Consensus         6 ~~GrRKta~Arv~l~~G~--G~I~INg~~~   33 (128)
T 2vqe_I            6 GTGRRKEAVARVFLRPGN--GKVTVNGQDF   33 (128)
T ss_dssp             ECCEETTEEEEEEEEESS--CCEEESSSBH
T ss_pred             EECCCCCEEEEEEEECCE--EEEEECCEEH
T ss_conf             857460389999998581--5799999869


No 24 
>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C
Probab=43.10  E-value=15  Score=15.80  Aligned_cols=10  Identities=30%  Similarity=0.554  Sum_probs=4.0

Q ss_pred             EECCCCCCCC
Q ss_conf             6125456785
Q gi|254780874|r  187 RVPATEASGR  196 (357)
Q Consensus       187 Rip~~es~gR  196 (357)
                      ||--.+-.|.
T Consensus       247 ~i~l~d~~g~  256 (409)
T 1m1j_C          247 RIELEDWSGK  256 (409)
T ss_dssp             EEEEECTTSC
T ss_pred             EEEEECCCCC
T ss_conf             9999836898


No 25 
>2xoa_A Ryanodine receptor 1; metal transport, calcium channel, ION channel, membrane PROT malignant hyperthermia, cardiac arrhythmia; 2.50A {Oryctolagus cuniculus}
Probab=37.57  E-value=18  Score=15.22  Aligned_cols=16  Identities=19%  Similarity=0.453  Sum_probs=7.2

Q ss_pred             CCCCCEEEEEECCCCE
Q ss_conf             6321215889649844
Q gi|254780874|r  238 NTTDSAVRITHIPTGI  253 (357)
Q Consensus       238 N~t~savri~H~ptgi  253 (357)
                      ..-+|=|||.|..||.
T Consensus       340 ~~~dSy~~iqH~~t~~  355 (559)
T 2xoa_A          340 KYGESLCFVQHVASGL  355 (559)
T ss_dssp             BTTTCCBEEEETTTCC
T ss_pred             ECCCCEEEEEEEECCC
T ss_conf             1167579999960383


No 26 
>1rpx_A Protein (ribulose-phosphate 3-epimerase); chloroplast, calvin cycle, oxidative pentose phosphate pathway; 2.30A {Solanum tuberosum} SCOP: c.1.2.2
Probab=37.52  E-value=15  Score=15.79  Aligned_cols=58  Identities=22%  Similarity=0.247  Sum_probs=36.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCE----------EEEEEECCCHHH
Q ss_conf             378862268852178899999999999987649840013211354477211----------137775031112
Q gi|254780874|r  112 CILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKE----------IVATISGRGVFS  174 (357)
Q Consensus       112 ailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~----------v~~~I~G~~aYg  174 (357)
                      .+|.|.||.||..=..-+-.-.+-..+|...+++.+.|.     =.||++.          |-.-|.|.+.|+
T Consensus       145 lvMtV~PGf~GQ~f~~~~l~kI~~~~~~~~~~~~~~~I~-----VDGGIn~~~i~~l~~~Gad~~V~GS~if~  212 (230)
T 1rpx_A          145 LIMSVNPGFGGQSFIESQVKKISDLRKICAERGLNPWIE-----VDGGVGPKNAYKVIEAGANALVAGSAVFG  212 (230)
T ss_dssp             EEESSCTTCSSCCCCTTHHHHHHHHHHHHHHHTCCCEEE-----EESSCCTTTHHHHHHHTCCEEEESHHHHT
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEE-----EECCCCHHHHHHHHHCCCCEEEECHHHHC
T ss_conf             998876898754446889999999999998659935899-----98887889999999869999997868868


No 27 
>2pc6_A Probable acetolactate synthase isozyme III (small subunit); regulatory subunit, structural genomics, PSI; HET: MSE; 2.50A {Nitrosomonas europaea atcc 19718} SCOP: d.58.18.6 d.58.18.6
Probab=36.72  E-value=19  Score=15.13  Aligned_cols=61  Identities=15%  Similarity=0.200  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECCC-----HHHHHHCCCCCEEEEEECCCCC
Q ss_conf             9999999987649840013211354477211137775031-----1121000246502676125456
Q gi|254780874|r  132 LFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRG-----VFSRMKFESGVHRVQRVPATEA  193 (357)
Q Consensus       132 L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~~-----aYg~Lk~E~GvHRvqRip~~es  193 (357)
                      |.|.=- -..++||.++-+...|++..|+...|+.+.|+.     +-..|.-=--||.|+.+.+.+.
T Consensus        18 L~rv~g-lFsrRg~NIeSL~v~~te~~~iSR~Tiv~~g~~~~i~qi~kQL~KLidV~~V~dlt~~~~   83 (165)
T 2pc6_A           18 LSRVAG-LFSARGYNIESLSVAPTEDPTLSRMTLVTNGPDEIVEQITKQLNKLIEVVKLIDLSSEGY   83 (165)
T ss_dssp             HHHHHH-HHHHHTCCCCEEEEEECSSTTEEEEEEEEEECHHHHHHHHHHHHHSTTEEEEEEGGGSCE
T ss_pred             HHHHHH-HHHHCCCCEEEEEEECCCCCCEEEEEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCCCC
T ss_conf             999999-986267435788873247998079999997788999999999967846799994588540


No 28 
>1tqj_A Ribulose-phosphate 3-epimerase; beta-alpha barrel epimerase, isomerase; 1.60A {Synechocystis SP} SCOP: c.1.2.2
Probab=35.61  E-value=14  Score=16.05  Aligned_cols=38  Identities=18%  Similarity=0.165  Sum_probs=25.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCH
Q ss_conf             37886226885217889999999999998764984001
Q gi|254780874|r  112 CILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEV  149 (357)
Q Consensus       112 ailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~ei  149 (357)
                      -+|.|.||.||..-..-+-.-.+--.++...+++++.|
T Consensus       139 liM~V~PGf~GQ~f~~~~~~kI~~~~~~~~~~~~~~~I  176 (230)
T 1tqj_A          139 LIMSVNPGFGGQSFIPEVLPKIRALRQMCDERGLDPWI  176 (230)
T ss_dssp             EEESSCC----CCCCGGGHHHHHHHHHHHHHHTCCCEE
T ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             99985478787655602689999999997235997069


No 29 
>2f1f_A Acetolactate synthase isozyme III small subunit; ferredoxin fold, ACT domain, transferase; HET: P33 1PE; 1.75A {Escherichia coli} SCOP: d.58.18.6 d.58.18.6
Probab=35.43  E-value=20  Score=14.99  Aligned_cols=62  Identities=18%  Similarity=0.206  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECCC-----HHHHHHCCCCCEEEEEECCCCCC
Q ss_conf             9999999987649840013211354477211137775031-----11210002465026761254567
Q gi|254780874|r  132 LFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRG-----VFSRMKFESGVHRVQRVPATEAS  194 (357)
Q Consensus       132 L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~~-----aYg~Lk~E~GvHRvqRip~~es~  194 (357)
                      |.|.=-- ..++||.++-+...|++..|+...|+-+.|+.     +-..|.-=--||.|+.+.+.+.-
T Consensus        17 L~Rv~gl-FsrRg~NI~SL~v~~te~~~~SR~Tiv~~g~~~~i~qi~kQL~KlidVi~V~~~~~~~~v   83 (164)
T 2f1f_A           17 LSRVIGL-FSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQIEKQLHKLVDVLRVSELGQGAHV   83 (164)
T ss_dssp             HHHHHHH-HHTTTCCCSEEEEEECSCSSEEEEEEEEESCHHHHHHHHHHHHHSTTEEEEEEGGGSCEE
T ss_pred             HHHHHHH-HHCCCCCEEEEEEECCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCEEEEECCCCCCEE
T ss_conf             9999999-851675456788723379991799999989999999999998377358998518998668


No 30 
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=34.12  E-value=16  Score=15.71  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=12.9

Q ss_pred             CCCCCCEEEEEEEEEE
Q ss_conf             6785110168888530
Q gi|254780874|r  193 ASGRVHTSAATVAVLP  208 (357)
Q Consensus       193 s~gR~hTS~a~V~V~P  208 (357)
                      .-|||.||.|-|.+.|
T Consensus        74 gtGRRKtAiArV~l~~   89 (197)
T 3bbn_I           74 GTGRRKCAIARVVLQE   89 (197)
T ss_dssp             CCCEETTEEEEEEEEE
T ss_pred             EECCCCCEEEEEEEEE
T ss_conf             6468815799999980


No 31 
>3inp_A D-ribulose-phosphate 3-epimerase; IDP02542, isomerase, structural genomics, center for structural genomics of infectious diseases; 2.05A {Francisella tularensis subsp}
Probab=32.81  E-value=20  Score=15.01  Aligned_cols=33  Identities=12%  Similarity=0.203  Sum_probs=12.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             886226885217889999999999998764984
Q gi|254780874|r  114 LEIRAGTGGSEAALFVGDLFRMYERYAALRKWK  146 (357)
Q Consensus       114 lEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk  146 (357)
                      |.|.||.||..-..-+-.-.+-..++...++++
T Consensus       163 M~V~PGf~GQ~f~~~~l~kI~~l~~~~~~~~~~  195 (246)
T 3inp_A          163 MSVNPGFGGQKFIPAMLDKAKEISKWISSTDRD  195 (246)
T ss_dssp             ECSCTTC--CCCCTTHHHHHHHHHHHHHHHTSC
T ss_pred             EECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             421698876114577999999999887524777


No 32 
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=32.20  E-value=22  Score=14.63  Aligned_cols=13  Identities=8%  Similarity=0.031  Sum_probs=5.8

Q ss_pred             CEEEEEECCCCCC
Q ss_conf             0378862268852
Q gi|254780874|r  111 SCILEIRAGTGGS  123 (357)
Q Consensus       111 nailEI~aGaGG~  123 (357)
                      .-|+++.-|.-|.
T Consensus       820 g~IvQF~yG~Dgl  832 (1407)
T 3lu0_D          820 IMMTPVIEGGDVK  832 (1407)
T ss_dssp             CEEEESSCCCSSS
T ss_pred             CEEEEEECCCCCC
T ss_conf             0899951287320


No 33 
>1m0d_A Endonuclease, endodeoxyribonuclease I; holliday junction resolvase, homodimer, domain swapped, composite active site, hydrolase; 1.90A {Enterobacteria phage T7} SCOP: c.52.1.17 PDB: 1m0i_A 2pfj_A 1fzr_A 3cae_A
Probab=31.76  E-value=14  Score=16.07  Aligned_cols=13  Identities=15%  Similarity=0.307  Sum_probs=11.0

Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             9999876498400
Q gi|254780874|r  136 YERYAALRKWKVE  148 (357)
Q Consensus       136 Y~r~ae~~gwk~e  148 (357)
                      |-.||+++||++-
T Consensus        98 Ya~Wc~k~gf~w~  110 (138)
T 1m0d_A           98 YGEFCEKHGIKFA  110 (138)
T ss_dssp             HHHHHHHHTCCEE
T ss_pred             HHHHHHHCCCCCC
T ss_conf             9999987498633


No 34 
>2zkq_i 40S ribosomal protein S16E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=31.28  E-value=22  Score=14.59  Aligned_cols=29  Identities=14%  Similarity=0.133  Sum_probs=20.2

Q ss_pred             CCCCCCCEEEEEEEEEECCCCCCCCCCCCEE
Q ss_conf             5678511016888853033433222454347
Q gi|254780874|r  192 EASGRVHTSAATVAVLPEAAEIDVDIPLEDI  222 (357)
Q Consensus       192 es~gR~hTS~a~V~V~P~~~~~~~~i~~~dl  222 (357)
                      .+-|||.||+|.|.+.|-.-  .|.||..++
T Consensus        11 ~~~GrRKtaiArv~l~~G~G--~i~INgk~~   39 (146)
T 2zkq_i           11 QVFGRKKTATAVAHCKRGNG--LIKVNGRPL   39 (146)
T ss_dssp             EECCBCSSCEEEEEEEESSS--CEEETTEEH
T ss_pred             EEECCCEEEEEEEEEEECCC--CEEECCCCH
T ss_conf             99674603899999992766--589879458


No 35 
>1dp7_P MHC class II transcription factor HRFX1; winged helix, protein- DNA conovel mode of DNA recognition, transcription/DNA complex; HET: DNA BRU; 1.50A {Synthetic} SCOP: a.4.5.20
Probab=30.65  E-value=23  Score=14.46  Aligned_cols=19  Identities=16%  Similarity=0.153  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999987649840
Q gi|254780874|r  129 VGDLFRMYERYAALRKWKV  147 (357)
Q Consensus       129 A~~L~rMY~r~ae~~gwk~  147 (357)
                      ..+||..|..||+++|++.
T Consensus        19 r~~lY~~Y~~~C~~~~~~~   37 (76)
T 1dp7_P           19 RSTLYNHYLLHSQEQKLEP   37 (76)
T ss_dssp             HHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHCCCCC
T ss_conf             7999999999999859966


No 36 
>1t9k_A Probable methylthioribose-1-phosphate isomerase; structural genomics, translation initiation factor, AIF-2B subunit, PSI; 2.60A {Thermotoga maritima} SCOP: c.124.1.5
Probab=29.39  E-value=24  Score=14.31  Aligned_cols=125  Identities=14%  Similarity=0.103  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             99899999997203785356654332223320005778889998640001135540378862268852178899999999
Q gi|254780874|r   56 KQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRM  135 (357)
Q Consensus        56 ~~ei~el~eLl~e~e~D~El~elAeeEl~~l~~~l~~le~eL~~~LLpsde~D~~nailEI~aGaGG~EA~dwA~~L~rM  135 (357)
                      .+.+..+...+.+..+++++.+.+.++...+..+..+....+-..-  .+--.+.+.||+ |..+|..-...|-.-|-=+
T Consensus        97 ~nAv~rv~~~l~~~~~~~~~~~~~~~~a~~~~~ed~~~~~~i~~~g--~~~i~~g~~iLT-h~~s~~lat~~~gTal~~i  173 (347)
T 1t9k_A           97 FWALNRMEKVFFENADRENLFEILENEALKMAYEDIEVNKAIGKNG--AQLIKDGSTILT-HCNAGALATVDYGTALGVI  173 (347)
T ss_dssp             HHHHHHHHHHHHTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH--HTTSCTTEEEEE-CSCCSGGGSSSSCSHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCEEEE-ECCCCHHHEECCCCHHHHE
T ss_conf             9999999986441588688999999999999999999999999855--775348988998-5587513101343201023


Q ss_pred             HHHHHHHCCCCCCHHHHCCCCCC-----------CCCEEEEEEECCCHHHHHHCC-------CCCEEEE
Q ss_conf             99998764984001321135447-----------721113777503111210002-------4650267
Q gi|254780874|r  136 YERYAALRKWKVEVLSSSDNDDG-----------GYKEIVATISGRGVFSRMKFE-------SGVHRVQ  186 (357)
Q Consensus       136 Y~r~ae~~gwk~eii~~~~ge~a-----------Gik~v~~~I~G~~aYg~Lk~E-------~GvHRvq  186 (357)
                      +.-+...+.|+|=+.+.-|.-.|           ||. +++..  +.+=+++-..       -|.|||.
T Consensus       174 ~~a~~~gk~~~V~v~EtrP~~qG~~lta~~L~~~GI~-~tlI~--D~a~~~~m~~~~Vd~VivGAd~v~  239 (347)
T 1t9k_A          174 RAAVESGKRIRVFADETRPYLQGARLTAWELMKDGIE-VYVIT--DNMAGWLMKRGLIDAVVVGADRIA  239 (347)
T ss_dssp             HHHHHTTCCEEEEEECCTTTTHHHHTHHHHHHTTTCE-EEEEC--GGGHHHHHHTTCCSEEEECCSEEE
T ss_pred             EEEEECCCEEEEEECCCCCCCCHHHHHHHHHHHCCCE-EEEEE--CCHHHHHHHHCCCCEEEECCCCCC
T ss_conf             6775069547999626887663168899998654822-89996--548888865344007885010024


No 37 
>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A
Probab=29.39  E-value=24  Score=14.31  Aligned_cols=35  Identities=26%  Similarity=0.536  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--HCCC--------CCCCCCCEEE
Q ss_conf             322233200057788899986--4000--------1135540378
Q gi|254780874|r   80 QIEVLAIEKEIRELENEINYL--LLPK--------DTDDDKSCIL  114 (357)
Q Consensus        80 eeEl~~l~~~l~~le~eL~~~--LLps--------de~D~~nail  114 (357)
                      .+++..+++++..+++++..+  .+|+        |+.++.|.++
T Consensus        82 k~~ik~le~~l~~l~~~l~~lll~iPNl~~~~VP~G~de~dN~~i  126 (455)
T 2dq0_A           82 VKRIGELENEVEELKKKIDYYLWRLPNITHPSVPVGKDENDNVPI  126 (455)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCCCCCTTSCCCSSGGGCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEE
T ss_conf             999999999999999999999972767778666878886666467


No 38 
>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown function ATU1810, ontario centre for structural proteomics; NMR {Agrobacterium tumefaciens str}
Probab=28.23  E-value=13  Score=16.20  Aligned_cols=18  Identities=22%  Similarity=0.342  Sum_probs=12.9

Q ss_pred             HHHHHHCCCCCCHHHHCC
Q ss_conf             999876498400132113
Q gi|254780874|r  137 ERYAALRKWKVEVLSSSD  154 (357)
Q Consensus       137 ~r~ae~~gwk~eii~~~~  154 (357)
                      .+||+++||.++|++-..
T Consensus        65 i~yA~k~g~~y~V~ep~~   82 (106)
T 2jya_A           65 EAYAQRKGIEYRVILPKE   82 (106)
T ss_dssp             HHHHHHHTCEEEECCCTT
T ss_pred             HHHHHHCCCEEEEECCCC
T ss_conf             999998698399975676


No 39 
>2waq_A DNA-directed RNA polymerase RPO1N subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_A 2pmz_A 3hkz_A
Probab=27.40  E-value=26  Score=14.07  Aligned_cols=37  Identities=22%  Similarity=0.447  Sum_probs=29.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCC
Q ss_conf             8521788999999999999876498400132113544
Q gi|254780874|r  121 GGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDD  157 (357)
Q Consensus       121 GG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~  157 (357)
                      |...|..|...+.++-.+|+..+||++-+-|....+.
T Consensus       620 G~~~~~~fld~lq~l~~~~l~~~GfSvgi~D~~~~~~  656 (880)
T 2waq_A          620 SDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVSLGDD  656 (880)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHCCCCCGGGTCCCSS
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH
T ss_conf             2288999999999999999874576302352046577


No 40 
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP; 2.27A {Mus musculus}
Probab=26.48  E-value=27  Score=13.96  Aligned_cols=51  Identities=8%  Similarity=0.016  Sum_probs=31.5

Q ss_pred             HHHHH-HHCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999-85385315-79999999998799999999999999998999999972
Q gi|254780874|r   17 AEIEL-RMSESPSV-DAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIG   67 (357)
Q Consensus        17 ~ELE~-~Lsdp~~w-~d~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~   67 (357)
                      ..+.. .+++|+|- +...++|+-...|...+.....|....+.+..++.-+.
T Consensus       138 ~ki~k~yi~~~~F~~e~i~k~S~Aa~~L~~WV~A~~~y~~v~k~v~plk~eL~  190 (536)
T 3err_A          138 EKMKKNYMSNPSYNYEIVNRASLAAGPMVKWAIAQLNYADMLKRVEPLRNELQ  190 (536)
T ss_dssp             HHHHHHTTTSTTCSHHHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999755687889999999889999999999887449999999876688899


No 41 
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=23.78  E-value=30  Score=13.68  Aligned_cols=27  Identities=22%  Similarity=0.500  Sum_probs=10.0

Q ss_pred             CCCEEEEEECCCCCCCCCCEEEEEEEEEE
Q ss_conf             46502676125456785110168888530
Q gi|254780874|r  180 SGVHRVQRVPATEASGRVHTSAATVAVLP  208 (357)
Q Consensus       180 ~GvHRvqRip~~es~gR~hTS~a~V~V~P  208 (357)
                      -||=|+.-|  ++....+-|-..+|...|
T Consensus      1099 lGvPRLkEI--in~skniKTPs~tv~l~~ 1125 (1752)
T 3h0g_A         1099 LGVPRLKEI--LNVAKNIKTPSLTIYLMP 1125 (1752)
T ss_dssp             CSGGGHHHH--HTTCSCCSCCCCEECCCS
T ss_pred             CCCCHHHHH--HHHHCCCCCCEEEEEECC
T ss_conf             166035435--555036777616897422


No 42 
>1n4k_A Inositol 1,4,5-trisphosphate receptor type 1; IP3 receptor, IP3-binding core, calcium channel,protein- ligand complex, B-trefoil fold; HET: I3P; 2.20A {Mus musculus} SCOP: a.118.22.1 b.42.6.1
Probab=23.03  E-value=31  Score=13.52  Aligned_cols=39  Identities=18%  Similarity=0.302  Sum_probs=24.5

Q ss_pred             CCCCCCC-CCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCC
Q ss_conf             0011355-403788622688521788999999999999876498400132113
Q gi|254780874|r  103 PKDTDDD-KSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSD  154 (357)
Q Consensus       103 psde~D~-~nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~  154 (357)
                      .+++... .....++.++.||..+.+             .+--|.+|+++..+
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~W~iE~~~~~~   68 (381)
T 1n4k_A           29 TCDEHRKKQHVFLRTTGRQSATSATS-------------SKALWEVEVVQHDP   68 (381)
T ss_dssp             EEEECSSSEEEEEECCCSSSGGGCCC-------------GGGCEEEEECC---
T ss_pred             CCCCCCCCCCCEEEEEECCCCCCCCC-------------CCCCEEEEECCCCC
T ss_conf             34785677653366741477777788-------------76708998356776


No 43 
>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8
Probab=22.26  E-value=12  Score=16.65  Aligned_cols=100  Identities=18%  Similarity=0.254  Sum_probs=43.6

Q ss_pred             HHHHCCCCCCCCCCEEEEEECC--CCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECCCHHHH
Q ss_conf             9864000113554037886226--88521788999999999999876498400132113544772111377750311121
Q gi|254780874|r   98 NYLLLPKDTDDDKSCILEIRAG--TGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSR  175 (357)
Q Consensus        98 ~~~LLpsde~D~~nailEI~aG--aGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~~aYg~  175 (357)
                      ...|+......-..+| =++--  ....|..++...+..+|..+    |+.+-.++...++  |+....-.++|.-..  
T Consensus       107 dR~Lv~a~~~~i~~vi-vlnK~DL~~~~~~~~~~~~~~~~y~~~----gy~v~~vSa~~~~--gl~~L~~~l~~k~sv--  177 (307)
T 1t9h_A          107 DRFLVLVEANDIQPII-CITKMDLIEDQDTEDTIQAYAEDYRNI----GYDVYLTSSKDQD--SLADIIPHFQDKTTV--  177 (307)
T ss_dssp             HHHHHHHHTTTCEEEE-EEECGGGCCCHHHHHHHHHHHHHHHHH----TCCEEECCHHHHT--TCTTTGGGGTTSEEE--
T ss_pred             HHHHHHHHHCCCCEEE-EEECHHCCCCHHHHHHHHHHHHHHHHC----CCCEEEEECCCCH--HHHHHHHHHHCCEEE--
T ss_conf             9999999987994899-996320168488999999999998527----8743885068851--088999885187999--


Q ss_pred             HHCCCCC--------------EEEEEECCCCCCCCCCEEEEEEEEE
Q ss_conf             0002465--------------0267612545678511016888853
Q gi|254780874|r  176 MKFESGV--------------HRVQRVPATEASGRVHTSAATVAVL  207 (357)
Q Consensus       176 Lk~E~Gv--------------HRvqRip~~es~gR~hTS~a~V~V~  207 (357)
                      |-+.|||              -+..=||.....|| ||++.+-.+.
T Consensus       178 ~~G~SGVGKSSLiN~L~~~~~~~T~~vs~~~~rGr-HTTt~~~l~~  222 (307)
T 1t9h_A          178 FAGQSGVGKSSLLNAISPELGLRTNEISEHLGRGK-HTTRHVELIH  222 (307)
T ss_dssp             EEESHHHHHHHHHHHHCC--------------------CCCCCEEE
T ss_pred             EECCCCCCHHHHHHCCCCHHCEEECCEECCCCCCE-EEEEHHHHHC
T ss_conf             99989855888975138600001005132169970-1522513315


No 44 
>1x9u_A Umecyanin; cupredoxin, phytocyanin, copper binding site, beta barrel, electron transport; 1.80A {Armoracia rusticana} PDB: 1x9r_A
Probab=22.15  E-value=28  Score=13.86  Aligned_cols=34  Identities=26%  Similarity=0.600  Sum_probs=21.8

Q ss_pred             HHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECCCHHHHHHCCCCCEEEEEECCC
Q ss_conf             999998764984001321135447721113777503111210002465026761254
Q gi|254780874|r  135 MYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVHRVQRVPAT  191 (357)
Q Consensus       135 MY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~~aYg~Lk~E~GvHRvqRip~~  191 (357)
                      -|..|+..+.|.+       ||.     +           .+++.+|.|-|+.++..
T Consensus        20 ~Y~~Wa~~~~f~v-------GD~-----l-----------~F~y~~~~h~V~~vs~~   53 (116)
T 1x9u_A           20 FYITWATGKTFRV-------GDE-----L-----------EFDFAAGMHDVAVVTKD   53 (116)
T ss_dssp             HHHHHHTTCCEET-------TCE-----E-----------EECCCTTTCCEEEECHH
T ss_pred             HHHHCCCCCCEEC-------CCE-----E-----------EEEECCCCCEEEEECHH
T ss_conf             3243224784848-------999-----9-----------99737998508997978


No 45 
>2fgc_A Acetolactate synthase, small subunit; regulatory subunit, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima MSB8} SCOP: d.58.18.6 d.58.18.6
Probab=21.79  E-value=33  Score=13.35  Aligned_cols=74  Identities=12%  Similarity=0.224  Sum_probs=54.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCEEEEEEECCC-----HHHHHHCCCCCEEE
Q ss_conf             0378862268852178899999999999987649840013211354477211137775031-----11210002465026
Q gi|254780874|r  111 SCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRG-----VFSRMKFESGVHRV  185 (357)
Q Consensus       111 nailEI~aGaGG~EA~dwA~~L~rMY~r~ae~~gwk~eii~~~~ge~aGik~v~~~I~G~~-----aYg~Lk~E~GvHRv  185 (357)
                      .++++=+||+           |.|+=. -..++||.++-+...+++..|+...|+-+.|+.     +-..|.-=--|++|
T Consensus        33 svlVeN~pGv-----------L~RV~g-lFsrRg~NIeSLsv~~te~~~iSRmTIv~~~~~~~i~qi~kQl~KLIdVi~V  100 (193)
T 2fgc_A           33 SMLVHNKPGV-----------MRKVAN-LFARRGFNISSITVGESETPGLSRLVIMVKGDDKTIEQIEKQAYKLVEVVKV  100 (193)
T ss_dssp             EEEEECCTTH-----------HHHHHH-HHHTTTCEEEEEEEEECSSTTEEEEEEEEEECTTHHHHHHHHHTTSTTEEEE
T ss_pred             EEEEECCCCH-----------HHHHHH-HHHCCCCCEEEEEEECCCCCCEEEEEEEEECCHHHHHHHHHHHHCCCCEEEE
T ss_conf             9999787888-----------999999-9864896854678502588884899999648989999999998637776899


Q ss_pred             EEECCCCCCCC
Q ss_conf             76125456785
Q gi|254780874|r  186 QRVPATEASGR  196 (357)
Q Consensus       186 qRip~~es~gR  196 (357)
                      +-+.+.+..-+
T Consensus       101 ~dl~~~~~~~~  111 (193)
T 2fgc_A          101 TPIDPLPENRV  111 (193)
T ss_dssp             EECCSSGGGEE
T ss_pred             EEECCCCHHHH
T ss_conf             87323413678


No 46 
>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 3.00A {Aquifex aeolicus VF5}
Probab=21.64  E-value=33  Score=13.33  Aligned_cols=111  Identities=14%  Similarity=0.227  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCCHHHH---
Q ss_conf             78689899999999999998538531--57999999999879999999999999999899999-9972037853566---
Q gi|254780874|r    3 FLSHKQICDLKNRFAEIELRMSESPS--VDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLH-TVIGDHNSDSEIR---   76 (357)
Q Consensus         3 mi~~~kL~~l~~rl~ELE~~Lsdp~~--w~d~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~-eLl~e~e~D~El~---   76 (357)
                      |+..+   -|+...+.+...+..-++  .....++-+-..+.+.+...++.+....+.+..-. .+....++..++.   
T Consensus         1 MlDik---~iRen~e~v~~~l~~R~~~~~~~id~il~Ld~~~r~l~~e~e~Lr~erN~iSKeIg~~kk~~~~~~~l~~~~   77 (425)
T 2dq3_A            1 MIDIN---LIREKPDYVKERLATRDKELVSLVDKVLELDKRRREIIKRLEALRSERNKLSKEIGKLKREGKDTTEIQNRV   77 (425)
T ss_dssp             CCCHH---HHHHCHHHHHHHHTTTCGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSSCSCTTTSTTHH
T ss_pred             CCCHH---HHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             98978---887699999999987099825559999999999999999999999999999999999986798899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH--HCCC--------CCCCCCCEEEEE
Q ss_conf             543322233200057788899986--4000--------113554037886
Q gi|254780874|r   77 DLAQIEVLAIEKEIRELENEINYL--LLPK--------DTDDDKSCILEI  116 (357)
Q Consensus        77 elAeeEl~~l~~~l~~le~eL~~~--LLps--------de~D~~nailEI  116 (357)
                      ....+++..++.++..++.++...  .+|+        |+.++.|.++..
T Consensus        78 ~~lk~~i~~le~~~~~i~~~l~~~ll~IPNi~~~~VP~G~de~dN~~i~~  127 (425)
T 2dq3_A           78 KELKEEIDRLEEELRKVEEELKNTLLWIPNLPHPSVPVGEDEKDNVEVRR  127 (425)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCCCTTSCCCSSGGGCEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEC
T ss_conf             99999999999999999999999997278987888899987225678833


No 47 
>3nvt_A 3-deoxy-D-arabino-heptulosonate 7-phosphate synth; bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismat listeria monocytogenes EGD-E; 1.95A {Listeria monocytogenes}
Probab=21.44  E-value=15  Score=15.83  Aligned_cols=136  Identities=13%  Similarity=0.203  Sum_probs=59.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHH
Q ss_conf             8689899999999999998538531579999999998799999999999999998999999972037--85356654332
Q gi|254780874|r    4 LSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDHN--SDSEIRDLAQI   81 (357)
Q Consensus         4 i~~~kL~~l~~rl~ELE~~Lsdp~~w~d~~klsKe~s~L~~iv~~~~~~~~~~~ei~el~eLl~e~e--~D~El~elAee   81 (357)
                      ++.+.|++++.++++|..++-+  ....-.++..+..+++..... .-|+ -..+-+-+..+.+...  -+++..+-.-.
T Consensus        25 m~~~~L~~lR~~ID~ID~~il~--Ll~~R~~l~~~Ig~~K~~~~~-~i~d-p~RE~~vl~ri~~~~~g~l~~~~i~~I~r  100 (385)
T 3nvt_A           25 MVNTNLEELRTQVDQLNIDLLE--LISKRANLVQEIGKIKGTQGS-LRFD-PLREREMLNTILAANEGPFEDSTVQKLFK  100 (385)
T ss_dssp             -------CCTTTTTHHHHHHHH--HHHHHHHHHHHHHHHCC------CCC-HHHHHHHHHHHHHHCCSSSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCC-CCCC-HHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             6703399999999999999999--999999999999997753699-7408-29999999999985789989999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHHHCCCCCCCCCCEEEEEECC-CCCCH-------HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             2233200057788899-9864000113554037886226-88521-------7889999999999998764984
Q gi|254780874|r   82 EVLAIEKEIRELENEI-NYLLLPKDTDDDKSCILEIRAG-TGGSE-------AALFVGDLFRMYERYAALRKWK  146 (357)
Q Consensus        82 El~~l~~~l~~le~eL-~~~LLpsde~D~~nailEI~aG-aGG~E-------A~dwA~~L~rMY~r~ae~~gwk  146 (357)
                      ++......+   +.++ ...|+|+.++...+-+++|..= -||.+       +..|..+++..+-+-+...|.+
T Consensus       101 ~Ii~~s~~l---q~~~~~~~l~~~r~~~~~~t~i~i~~~~~G~~~~~~IaGPCsiEs~e~~~~~A~~lk~~~~~  171 (385)
T 3nvt_A          101 EIFKAGLEL---QEEDHSKALLVSRKNKKEDTIVTVKGLPIGNGEPVFVFGPCSVESYEQVAAVAESIKAKGLK  171 (385)
T ss_dssp             HHHHHHHTT---STTCCTTSCTTBTTTCCSCCCEEETTEEETSSSCEEEEECSBCCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHH---HHHCCCCCCCCCCCCCCCCCEEEECCEEECCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             999999999---75335453466776678998899899998799878998788238999999999999866971


No 48 
>1t9f_A Protein 1D10; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 2.00A {Caenorhabditis elegans} SCOP: b.42.6.1
Probab=20.99  E-value=34  Score=13.24  Aligned_cols=20  Identities=20%  Similarity=0.308  Sum_probs=15.6

Q ss_pred             CCCCEEEEEECCCCEEEEEC
Q ss_conf             32121588964984488843
Q gi|254780874|r  239 TTDSAVRITHIPTGIMVTSS  258 (357)
Q Consensus       239 ~t~savri~H~ptgi~v~~~  258 (357)
                      ...+.+||.|++||--.++.
T Consensus       127 ~~~~~fRLkH~~t~~yL~ss  146 (187)
T 1t9f_A          127 LESEQFKLRHAVTGSYLSLS  146 (187)
T ss_dssp             BTTSEEEEEETTTCCEEEEE
T ss_pred             CCCCEEEEEECCCCEEEEEC
T ss_conf             15754999998889799617


Done!