Query         gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 340
No_of_seqs    150 out of 5691
Neff          7.1 
Searched_HMMs 33803
Date          Wed Jun  1 15:26:29 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780610.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1v9f_A Ribosomal large subuni 100.0       0       0  463.5  14.9  311    9-339     2-313 (325)
  2 >1v9k_A Ribosomal large subuni 100.0       0       0  378.6  14.1  226   90-340     2-227 (228)
  3 >2i82_A Ribosomal large subuni 100.0       0       0  344.3  12.1  208   87-327     9-216 (217)
  4 >2gml_A Ribosomal large subuni 100.0       0       0  330.5   9.1  212   87-339     4-223 (237)
  5 >3dh3_A Ribosomal large subuni 100.0       0       0  317.6   6.1  205   94-339     1-213 (227)
  6 >2oml_A Ribosomal large subuni 100.0       0       0  293.9   7.2  183   88-308     2-185 (189)
  7 >1ksk_A Ribosomal small subuni 100.0 1.6E-42       0  272.8   7.0  171   94-315     2-172 (176)
  8 >1vio_A Ribosomal small subuni 100.0 5.6E-42       0  269.6   7.7  184   93-316     1-184 (186)
  9 >2olw_A Ribosomal large subuni  99.9 5.7E-24 1.7E-28  162.2   4.1  100   39-171     2-101 (119)
 10 >1dm9_A Hypothetical 15.5 KD p  99.9 8.8E-24 2.6E-28  161.1   2.6  124   15-163     1-131 (133)
 11 >2olw_A Ribosomal large subuni  99.8 4.6E-21 1.4E-25  144.9   3.1   96  179-279     1-97  (98)
 12 >2k6p_A Uncharacterized protei  99.8 7.5E-21 2.2E-25  143.6  -0.1   90   23-114     1-91  (92)
 13 >3dh3_A Ribosomal large subuni  99.0 2.8E-10 8.3E-15   80.6   5.2   57   18-77      2-58  (63)
 14 >1p9k_A ORF, hypothetical prot  98.9   2E-10   6E-15   81.5   0.8   71    4-75      2-72  (79)
 15 >1ksk_A Ribosomal small subuni  98.9 5.5E-09 1.6E-13   72.9   6.4   53   21-75      2-54  (58)
 16 >1vio_A Ribosomal small subuni  98.8 8.5E-09 2.5E-13   71.8   6.4   52   22-75      2-53  (57)
 17 >2vqe_D 30S ribosomal protein   98.4 6.4E-07 1.9E-11   60.6   6.6   51   24-75      1-51  (94)
 18 >3hp7_A Hemolysin, putative; s  98.4 2.6E-07 7.8E-12   62.9   3.4   58   17-75      1-60  (65)
 19 >1h3f_A Tyrosyl-tRNA synthetas  98.2 8.6E-06 2.5E-10   53.9   7.4   66    9-75      3-71  (83)
 20 >3i1m_D 30S ribosomal protein   98.1 1.3E-06 3.9E-11   58.8   3.1   52   24-76      1-52  (94)
 21 >3bbn_D Ribosomal protein S4;   98.1 1.4E-06 4.2E-11   58.5   2.5   54   21-75      6-59  (120)
 22 >1s1h_D 40S ribosomal protein   98.0 7.4E-06 2.2E-10   54.3   4.4   55   20-75      6-60  (99)
 23 >2cqj_A BRMS2, U3 small nucleo  97.8 1.4E-05 4.2E-10   52.6   3.2   55   19-74      4-60  (71)
 24 >2aus_C Pseudouridine synthase  96.9 0.00048 1.4E-08   43.5   2.6   84   95-202    14-97  (215)
 25 >2apo_A Probable tRNA pseudour  96.9  0.0007 2.1E-08   42.5   2.9   85   94-202    13-97  (216)
 26 >2jan_A Tyrosyl-tRNA synthetas  96.8  0.0016 4.6E-08   40.4   4.1   51   19-70      8-58  (88)
 27 >3kbg_A 30S ribosomal protein   95.0   0.059 1.8E-06   31.0   5.7   70   22-103     7-76  (81)
 28 >1sgv_A TRNA pseudouridine syn  94.6   0.032 9.6E-07   32.6   3.5   55   94-164     3-57  (87)
 29 >1k8w_A TRNA pseudouridine syn  94.4   0.039 1.2E-06   32.1   3.5   55   94-164    22-76  (108)
 30 >1jil_A Tyrrs, tyrosyl-tRNA sy  94.3  0.0091 2.7E-07   35.9   0.0   52   19-71    103-154 (174)
 31 >1r3e_A TRNA pseudouridine syn  94.1   0.043 1.3E-06   31.8   3.2   52   97-164     3-54  (92)
 32 >2ts1_A Tyrosyl-tRNA synthetas  93.1    0.02 5.8E-07   33.9   0.0   51   20-71    104-154 (174)
 33 >1c05_A Ribosomal protein S4 d  92.9   0.095 2.8E-06   29.8   3.3   25   50-74      1-25  (83)
 34 >1fm0_D Molybdopterin converti  72.1     6.5 0.00019   18.9   4.7   51   22-76     25-77  (81)
 35 >2q5w_D Molybdopterin converti  63.1      10  0.0003   17.8   4.0   28   48-76     46-73  (77)
 36 >1vjk_A Molybdopterin converti  47.9      12 0.00036   17.3   2.2   26   50-76     69-94  (98)
 37 >2hj1_A Hypothetical protein;   46.2     2.7 8.1E-05   21.1  -1.3   69    4-79      6-88  (97)
 38 >1v8c_A MOAD related protein;   44.0      21 0.00061   15.9   3.0   60   11-76     15-83  (84)
 39 >2ff4_A Probable regulatory pr  41.8      23 0.00067   15.7   3.3   23   50-73     60-82  (99)
 40 >2rk0_A Glyoxalase/bleomycin r  39.2      25 0.00073   15.4   3.8   46  257-329    19-64  (69)
 41 >1rws_A Hypothetical protein P  38.5      12 0.00036   17.2   1.1   62    3-75      4-72  (77)
 42 >2qjl_A URM1, ubiquitin-relate  37.6      26 0.00077   15.3   3.1   48   27-76     39-95  (99)
 43 >1vc3_B L-aspartate-alpha-deca  36.1      14 0.00043   16.8   1.1   41   18-74     24-64  (96)
 44 >1c05_A Ribosomal protein S4 d  34.6      29 0.00087   15.0   2.6   27   22-49     29-55  (55)
 45 >3gqs_A Adenylate cyclase-like  32.8      31 0.00093   14.8   2.7   10  152-161    23-32  (106)
 46 >3dwg_C 9.5 kDa culture filtra  32.6      32 0.00094   14.8   3.1   26   51-76     61-89  (93)
 47 >2k9x_A Tburm1, uncharacterize  30.9      25 0.00075   15.4   1.7   27   51-77     70-99  (110)
 48 >1wgk_A Riken cDNA 2900073H19   30.7      34   0.001   14.6   2.6   27   50-76     75-104 (114)
 49 >2g1e_A Hypothetical protein T  30.1      29 0.00087   15.0   1.9   27   50-76     57-86  (90)
 50 >2c45_A Aspartate 1-decarboxyl  29.6      25 0.00075   15.4   1.5   22   48-73     66-87  (139)
 51 >2wyh_A Alpha-mannosidase; hyd  28.9      37  0.0011   14.4   2.6   29   22-53     35-65  (72)
 52 >1wv3_A Similar to DNA segrega  28.9      37  0.0011   14.4   3.3   26   48-73     54-79  (158)
 53 >1pqh_A Aspartate 1-decarboxyl  27.4      21 0.00063   15.8   0.8   15   93-107    55-69  (143)
 54 >3huh_A Virulence protein STM3  25.9      41  0.0012   14.1   3.7   49  258-330    21-71  (75)
 55 >1wxq_A GTP-binding protein; s  25.9      19 0.00056   16.1   0.3   25   50-75     54-78  (81)
 56 >2z0t_A Putative uncharacteriz  23.0      47  0.0014   13.7   2.4   35   41-75     10-44  (109)
 57 >3cuz_A MSA, malate synthase A  22.4      20  0.0006   15.9  -0.1   23   37-59     54-76  (134)
 58 >2pbt_A AP4A hydrolase; nudix   21.0      35   0.001   14.5   0.9   42   91-132     9-51  (134)
 59 >3cux_A Malate synthase; TIM b  20.5      29 0.00084   15.1   0.3   23   37-59     54-77  (134)

No 1  
>>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=463.50  Aligned_cols=311  Identities=38%  Similarity=0.580  Sum_probs=256.2

Q ss_pred             CCEEE-EEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHH
Q ss_conf             62499-99571136875789999871768898999999985990499899328675804898899970560111102332
Q gi|254780610|r    9 SSIKI-SLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQEN   87 (340)
Q Consensus         9 ~~~~~-~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~   87 (340)
                      +-|++ ++|+++++|+|||+||++.++ ++||+.++++|++|.|+|||+++..+++.+..++.+.............+..
T Consensus         2 ~~~~~~~~v~~~~~g~rl~~~L~~~~~-~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (325)
T 1v9f_A            2 QRVQLTATVSENQLGQRLDQALAEMFP-DYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQD   80 (325)
T ss_dssp             ---------------------------------------------------------------------------CCCCC
T ss_pred             CEEEEEEEECCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCC
T ss_conf             748999998976488669999998668-6799999999986998999999178320625898997325433222333344


Q ss_pred             HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             22221014402789962401110456787542100222222102443344443643244443323240572120357888
Q gi|254780610|r   88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQK  167 (340)
Q Consensus        88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~  167 (340)
                      .++.|||||++++|+|||+|++|||+++...+|+...+.......    .....+++|||||++|||+||+|||..+++.
T Consensus        81 ~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~  156 (325)
T 1v9f_A           81 IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI----ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTR  156 (325)
T ss_dssp             CCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG----GGSGGGGBCCCCCTTCEEEEEEESSHHHHHH
T ss_pred             CCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCC----CCCCCEEEEECCCCCCCCCEEEECCHHHHHH
T ss_conf             541125101105787078886548987778886323211344433----3334214653258898651466402588999


Q ss_pred             HHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCE
Q ss_conf             89999972113221334454320243323321100134344433221234445555530000122210112566775001
Q gi|254780610|r  168 LSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSL  247 (340)
Q Consensus       168 l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~sl  247 (340)
                      |.++|.    .+.+.|+|+|+|.|.+..+.+.+..+........     .......+++|.|+|.+...     ...+|+
T Consensus       157 l~~~~~----~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~a~~~~~~~~~-----~~~~sl  222 (325)
T 1v9f_A          157 LVESLQ----RREITREYEAVAIGHMTAGGTVDEPISRHPTKRT-----HMAVHPMGKPAVTHYRIMEH-----FRVHTR  222 (325)
T ss_dssp             HHHHHH----TTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT-----CEEECTTSBCCEEEEEEEEE-----CSSEEE
T ss_pred             HHHHHH----CCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC-----EEEECCCCCEEEEEEEEEEE-----CCCCEE
T ss_conf             998750----1210124234301354745662355335766653-----05876887157899898653-----388457


Q ss_pred             EEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCC
Q ss_conf             23443115899999999870978604154477554443345701355440798044321000424688976899984997
Q gi|254780610|r  248 LKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIP  327 (340)
Q Consensus       248 v~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP  327 (340)
                      ++|+|.|||+||||+|||++|||||||.+||........ .............+++|||+.|+|.||.+++.++|+||+|
T Consensus       223 ~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~-l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P  301 (325)
T 1v9f_A          223 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG-ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP  301 (325)
T ss_dssp             EEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT-CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC
T ss_pred             EEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH
T ss_conf             999977883179999999839976687778985545443-3166777651586434653705857789998899991797


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             899999998851
Q gi|254780610|r  328 EDMLTVIRKLNE  339 (340)
Q Consensus       328 ~~~~~~l~~L~~  339 (340)
                      ++|..+|++|+.
T Consensus       302 ~~f~~~l~~l~~  313 (325)
T 1v9f_A          302 QDMVELIEVMRA  313 (325)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999730


No 2  
>>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=378.58  Aligned_cols=226  Identities=31%  Similarity=0.422  Sum_probs=188.4

Q ss_pred             HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r   90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS  169 (340)
Q Consensus        90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~  169 (340)
                      +.|||||++|+|+|||+||+|||++++...|+.+.+..+...        .++++|||||++|||+||+|||..+++.++
T Consensus         2 ~~Iiyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~--------~~~~~vhRLD~~TSGlll~ak~~~~a~~l~   73 (228)
T 1v9k_A            2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA--------RFLELVHRLDRDTSGVLLVAKKRSALRSLH   73 (228)
T ss_dssp             CCEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHSTTC--------SCCEESSCCCTTCEEEEEEESSHHHHHHHH
T ss_pred             CEEEEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCC--------CCCCEEEECCCCCCCEEEEECCHHHHHHHH
T ss_conf             989996899999999999863899899536999999867787--------653166404643221367523579999999


Q ss_pred             HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEE
Q ss_conf             99997211322133445432024332332110013434443322123444555553000012221011256677500123
Q gi|254780610|r  170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK  249 (340)
Q Consensus       170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~  249 (340)
                      ++|.    ++.+.|+|+|+|.|.++...+.+..++..........  ........+.|.++|.+...     ....++++
T Consensus        74 ~~~~----~~~v~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~  142 (228)
T 1v9k_A           74 EQLR----EKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGER--IVRVSQEGKPSETRFKVEER-----YAFATLVR  142 (228)
T ss_dssp             HHHH----TTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCE--EEEECTTSBCCCEEEEEEEE-----CSSEEEEE
T ss_pred             HHHH----HHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCEE--EEECCCCCCCCCEEECHHHH-----CCCCEEEE
T ss_conf             9987----4034543210346864223575223300001101015--55207888422155005553-----58737999


Q ss_pred             EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHH
Q ss_conf             44311589999999987097860415447755444334570135544079804432100042468897689998499789
Q gi|254780610|r  250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED  329 (340)
Q Consensus       250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~  329 (340)
                      ++|.|||+||||+||+++||||+||.+||.......      ........++++|||++|+|+||.|++.+.|+||+|++
T Consensus       143 ~~~~tGR~HQIR~h~a~~g~PIvgD~~Y~~~~~~~~------~~~~~~~~~~~~Lha~~l~f~~p~~~~~~~~~ap~P~~  216 (228)
T 1v9k_A          143 CSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQ------LTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEG  216 (228)
T ss_dssp             EEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHHHH------HHHTTCCCCSCCEEEEEEEEECTTTCCEEEEECCCCHH
T ss_pred             EEECCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHH------HHHHCCCCCHHHHHCCCCEEECCCCCCEEEEEECCHHH
T ss_conf             994757357888888854972135774130000023------33202686237887150392879999889999178699


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999988519
Q gi|254780610|r  330 MLTVIRKLNEK  340 (340)
Q Consensus       330 ~~~~l~~L~~~  340 (340)
                      |.++|++|+++
T Consensus       217 ~~~~l~~~~~~  227 (228)
T 1v9k_A          217 LKRCLQKXRNA  227 (228)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHHHC
T ss_conf             99999998737


No 3  
>>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=344.32  Aligned_cols=208  Identities=31%  Similarity=0.439  Sum_probs=172.1

Q ss_pred             HHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             22222101440278996240111045678754210022222210244334444364324444332324057212035788
Q gi|254780610|r   87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQ  166 (340)
Q Consensus        87 ~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~  166 (340)
                      ..+++|||||++|+|+|||+||+||++++....++...+......         ++++|||||++|||+||+||+.++++
T Consensus         9 ~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~~~~~~~---------~l~~vhRLD~~TSGllllak~~~~~~   79 (217)
T 2i82_A            9 EPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYP---------QAESVHRLDXATSGVIVVALTKAAER   79 (217)
T ss_dssp             SSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCT---------TCEESSCCCTTCEEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCC---------CCCCCCCCCCCCCEEEEEEECHHHHH
T ss_conf             999529997998999999999825799887760389997644103---------32223455542101589860317777


Q ss_pred             HHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC
Q ss_conf             88999997211322133445432024332332110013434443322123444555553000012221011256677500
Q gi|254780610|r  167 KLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS  246 (340)
Q Consensus       167 ~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s  246 (340)
                      .|+++|.    .+.+.|+|+|++.|.+...++.+..+............  ......++.+.+.|.++.     ....+|
T Consensus        80 ~l~~~~~----~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~-----~~~~~s  148 (217)
T 2i82_A           80 ELKRQFR----EREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQK--VCYETGKPAQTEYEVVEY-----AADNTA  148 (217)
T ss_dssp             HHHHHHH----TTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEE--ECTTTCBCCEEEEEEEEE-----ETTTEE
T ss_pred             HHHHHHH----HCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCE--ECCCCCCCCCCEECCCCC-----CCCCCE
T ss_conf             8898765----14010368988615446664067410123224332200--012247630010101111-----233104


Q ss_pred             EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCC
Q ss_conf             12344311589999999987097860415447755444334570135544079804432100042468897689998499
Q gi|254780610|r  247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI  326 (340)
Q Consensus       247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~apl  326 (340)
                      +++|+|.|||+||||+||+++||||+||.+||.....             ...+|++|||++|+|+||.|||.+.|+||+
T Consensus       149 ~~~~~~~TGr~HQIR~h~a~lg~PIlgD~~Yg~~~~~-------------~~~~~~~Lha~~l~f~~p~~ge~~~~~~p~  215 (217)
T 2i82_A          149 RVVLKPITGRSHQLRVHXLALGHPILGDRFYASPEAR-------------AXAPRLLLHAEXLTITHPAYGNSXTFKAPA  215 (217)
T ss_dssp             EEEEEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHH-------------HTCSSCCEEEEEEEEECTTTCCEEEEECCC
T ss_pred             EEEEEECCCCHHHHHHHHHHHCCEEECCCCCCCHHHC-------------CCCCCHHHHCCCCEEECCCCCCEEEEECCC
T ss_conf             7889850262378999999719768167676885563-------------688466676276788998999889997899


Q ss_pred             C
Q ss_conf             7
Q gi|254780610|r  327 P  327 (340)
Q Consensus       327 P  327 (340)
                      |
T Consensus       216 P  216 (217)
T 2i82_A          216 D  216 (217)
T ss_dssp             C
T ss_pred             C
T ss_conf             9


No 4  
>>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=330.54  Aligned_cols=212  Identities=15%  Similarity=0.044  Sum_probs=163.7

Q ss_pred             HHHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             22222101440278996240111045678754210022222210244334444364324444332324057212035788
Q gi|254780610|r   87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQ  166 (340)
Q Consensus        87 ~~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~  166 (340)
                      +.++.|||||++|+|||||+|++||+++.... ++.+.+.           ...++++|||||++||||||||++.+++.
T Consensus         4 ~~~~~ii~ed~~~ivvnKP~G~~~~~~~~~~~-~~~~~l~-----------~~~~~~~vhRLD~~TSGlll~a~~~~~~~   71 (237)
T 2gml_A            4 SHHHHHHGSDLVLIALNKPVGIVSTTEDGERD-NIVDFVN-----------HSKRVFPIGRLDKDSQGLIFLTNHGDLVN   71 (237)
T ss_dssp             ---------CCCEEEEEECTTCBCCSSSSCSS-BHHHHSC-----------CSSCCEEESCCCTTCEEEEEEESCHHHHH
T ss_pred             CCCCCCCCCCEEEEEEECCCCEEECCCCCCCC-CCHHHCC-----------CCCCEEECCCCCCCCCCCEEEECCHHHHH
T ss_conf             55555568523999997999389722899999-7442157-----------64561141246888888589841668888


Q ss_pred             HHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCC
Q ss_conf             88999997211322133445432024332332110013434443322123444555553000012221011256677500
Q gi|254780610|r  167 KLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVS  246 (340)
Q Consensus       167 ~l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s  246 (340)
                      .+..++.      .+.|+|+|+|.|.+..+.+.+..+....                  .+.+.+...     ....+.+
T Consensus        72 ~~~~~~~------~i~K~Y~a~v~G~~~~~~~~~~~~~~~~------------------~~~~~~~~~-----~~~~~~~  122 (237)
T 2gml_A           72 KILRAGN------DHEKEYLVTVDKPITEEFIRGXSAGVPI------------------LGTVTKKCK-----VKKEAPF  122 (237)
T ss_dssp             HHHHHHH------HSCEEEEEEESSCCCHHHHHHHSSCCEE------------------TTEECCCCE-----EEEEETT
T ss_pred             HHHHHCC------CCCEEEEEEECCCCCHHHHHHHHCCCEE------------------CCEEEECHH-----HCCCCCE
T ss_conf             8765313------5514887785267999999999759887------------------775742000-----0356654


Q ss_pred             EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCC--------HHHHHHCCCCCHHHHHCEEEEECCCCCC
Q ss_conf             12344311589999999987097860415447755444334570--------1355440798044321000424688976
Q gi|254780610|r  247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNN--------NAKSAILSLARQALHAHSLSFSHPRNNQ  318 (340)
Q Consensus       247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~--------~~~~~~~~~~r~~LHA~~l~f~hP~t~~  318 (340)
                      ++++.|.|||+||||+||+++||||+||.+||...........+        ..........+++|||++|.|.||.|++
T Consensus       123 ~v~~~~~tGR~HQIR~h~~~~G~pI~gD~~y~~~~~~~~~l~~g~~~~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~t~e  202 (237)
T 2gml_A          123 VFRITLVQGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAG  202 (237)
T ss_dssp             EEEEEECCCSTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHTTSTTCC---------------
T ss_pred             EEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEEECCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             99999816886199999998699766699999888880897997838999999999998763345666886667887666


Q ss_pred             EEEEECCCCHHHHHHHHHHHC
Q ss_conf             899984997899999998851
Q gi|254780610|r  319 DMDFQVPIPEDMLTVIRKLNE  339 (340)
Q Consensus       319 ~~~f~aplP~~~~~~l~~L~~  339 (340)
                      .+.|+||+|++|.++++.|..
T Consensus       203 ~~~~~~p~p~~~~~~~~~l~~  223 (237)
T 2gml_A          203 IKRPVVKXEKTAEKGGRPASN  223 (237)
T ss_dssp             ---------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCC
T ss_conf             678877777777888898889


No 5  
>>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:64-290)
Probab=100.00  E-value=0  Score=317.64  Aligned_cols=205  Identities=16%  Similarity=0.065  Sum_probs=160.2

Q ss_pred             CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf             14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r   94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV  173 (340)
Q Consensus        94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~  173 (340)
                      -||++|+|||||+||+||+++++.. |+.+.+..+           .++.+|||||++|||||||||+.+++..+..++ 
T Consensus         1 aEd~~~ivinKP~Gl~~~~~~~~~~-~l~~~l~~~-----------~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~-   67 (227)
T 3dh3_A            1 AEDLVLIALNKPVGIVSTTEDGERD-NIVDFVNHS-----------KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAG-   67 (227)
T ss_dssp             GGGCCEEEEEECTTCBCCCCSSCTT-BHHHHHTCS-----------SCCEESSCCCTTCEEEEEEESCTTHHHHHHCGG-
T ss_pred             CCCEEEEECCCCCCEEECCCCCCCC-CCHHHCCCC-----------CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHH-
T ss_conf             2311356436665212033347777-501101344-----------431224656767631489943987998887631-


Q ss_pred             HHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEEC
Q ss_conf             72113221334454320243323321100134344433221234445555530000122210112566775001234431
Q gi|254780610|r  174 DHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLE  253 (340)
Q Consensus       174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~  253 (340)
                           ++++|+|+|+|.|.+.++.+.+..++....                  ..+.+.+..     ....++++++.+.
T Consensus        68 -----~~i~K~Y~a~v~G~~~~~~~~~~~~~~~~~------------------~~~~~~~~~-----~~~~~~~~~~~~~  119 (227)
T 3dh3_A           68 -----NDHEKEYLVTVDKPITEEFIRGMSAGVPIL------------------GTVTKKCKV-----KKEAPFVFRITLV  119 (227)
T ss_dssp             -----GCCCEEEEEEESSCCCHHHHHHHHTCCBCS------------------SSBCCCCEE-----EECSSSEEEEEES
T ss_pred             -----CCCCCCCCEEECCCCCHHHHHHHHCCCEEC------------------CEEEEEEEE-----EECCCCEEEEEEC
T ss_conf             -----244322112760579999999997599845------------------657442577-----5226725899925


Q ss_pred             HHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCC--------HHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECC
Q ss_conf             1589999999987097860415447755444334570--------13554407980443210004246889768999849
Q gi|254780610|r  254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNN--------NAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP  325 (340)
Q Consensus       254 TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~--------~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~ap  325 (340)
                      |||+||||+||+++||||+||.+||.+.........+        ..........+++|||+++.|+||.+++.++|+||
T Consensus       120 tGr~hQIR~h~a~~g~pI~gd~~y~~~~~~l~~l~~g~~r~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~~~e~~~~~ap  199 (227)
T 3dh3_A          120 QGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVK  199 (227)
T ss_dssp             CCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTCCCCSSCC-------------------
T ss_pred             CCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             88525999999987996766999998787748979977388999999999987632456678876678877666788777


Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             97899999998851
Q gi|254780610|r  326 IPEDMLTVIRKLNE  339 (340)
Q Consensus       326 lP~~~~~~l~~L~~  339 (340)
                      +|++|..++++|++
T Consensus       200 ~p~~~~~~~~~l~~  213 (227)
T 3dh3_A          200 MEKTAEKGGRPASN  213 (227)
T ss_dssp             --------------
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             77787888998889


No 6  
>>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=293.86  Aligned_cols=183  Identities=23%  Similarity=0.192  Sum_probs=149.6

Q ss_pred             HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             22221014402789962401110456787542100222222102443344443643244443323240572120357888
Q gi|254780610|r   88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQK  167 (340)
Q Consensus        88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~  167 (340)
                      .+++|||||++++|||||+|++|||++++...++..++.            ..++++|||||++|||+||||++.+++..
T Consensus         2 ~~~~vl~ed~~~ivinKP~g~~~~~~~~~~~~~~~~~l~------------~~~l~~vhRLD~~tsGlll~a~~~~~~~~   69 (189)
T 2oml_A            2 TRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP------------VQGVYAAGRLDRDSEGLLVLTNNGALQAR   69 (189)
T ss_dssp             ------CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC------------CSSCEESSCCCTTCEEEEEEESCHHHHHH
T ss_pred             CCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCHHHHCC------------CCCCEECCCCCCCCCCEEEEECCCHHHHH
T ss_conf             865778899889999899983860779988865889637------------12534731026120007999325302221


Q ss_pred             HHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCEECCCCCEEECCCCCCCCC
Q ss_conf             899999721132213344543202433233211001343444332212-3444555553000012221011256677500
Q gi|254780610|r  168 LSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRA-VKGIDDKTADSAITHYQTIEIYNKNSNFAVS  246 (340)
Q Consensus       168 l~~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~-~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~s  246 (340)
                      +..+|      +.+.|+|+|+|.|.+.++.+++..++.....+..+.. ........++.+.+.|.++.     .....+
T Consensus        70 l~~~~------~~i~k~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~  138 (189)
T 2oml_A           70 LTQPG------KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER-----KSIPTS  138 (189)
T ss_dssp             HHSTT------SCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-C-----TTSCEE
T ss_pred             CCCCC------EEEEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEE-----EECCCC
T ss_conf             03123------0377899999932799899999864945078515765799953566410245578887-----405650


Q ss_pred             EEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCE
Q ss_conf             12344311589999999987097860415447755444334570135544079804432100
Q gi|254780610|r  247 LLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHS  308 (340)
Q Consensus       247 lv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~  308 (340)
                      +++++|.|||+||||+||+++||||+||.+||.+..               .+.|+.||||+
T Consensus       139 ~~~~~l~tGr~hQIR~hl~~lg~pIvgD~~Y~~~~~---------------~~~~l~l~~~R  185 (189)
T 2oml_A          139 WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDY---------------SLDNLANGEWR  185 (189)
T ss_dssp             EEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTE---------------ECTTCCTTCEE
T ss_pred             EEEEEEECCCHHHHHHHHHHCCCEEEEEEEEEECCE---------------ECCCCCCCCCE
T ss_conf             799999459779999999986996989899999998---------------50788998837


No 7  
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234)
Probab=100.00  E-value=1.6e-42  Score=272.79  Aligned_cols=171  Identities=17%  Similarity=0.132  Sum_probs=129.0

Q ss_pred             CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf             14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r   94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV  173 (340)
Q Consensus        94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~  173 (340)
                      |||++++|||||+||+||++++.... +.+.+..+.         ..++++|||||++|||||+|||+..++..+..+  
T Consensus         2 Yed~~~ivvnKP~gl~~~~~~~~~~~-~~~~l~~~~---------~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~~--   69 (176)
T 1ksk_A            2 QHGPRYFXLNKPQGYVCSTDDPDHPT-VLYFLDEPV---------AWKLHAAGRLDIDTTGLVLXTDDGQWSHRITSP--   69 (176)
T ss_dssp             CCCCCEEEEEECTTCBSSSSCSSSCB-GGGGCCCTT---------GGGCEESSCCCTTCEEEEEEESCHHHHHHHHCT--
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCCC-CCCCCCCCC---------CCCEEEECCCCCCCCCEEEEECCHHHHHHHHHH--
T ss_conf             57857999989998505665554431-000012444---------563656013885557558860586888877554--


Q ss_pred             HHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEEC
Q ss_conf             72113221334454320243323321100134344433221234445555530000122210112566775001234431
Q gi|254780610|r  174 DHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLE  253 (340)
Q Consensus       174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~  253 (340)
                          .+.+.|+|+|+|.|.+......+.....               ...+..+.+.+...+      ....|++++.|.
T Consensus        70 ----~~~~~k~y~~~v~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~------~~~~s~~~~~~~  124 (176)
T 1ksk_A           70 ----RHHCEKTYLVTLESPVADDTAEQFAKGV---------------QLHNEKDLTKPAVLE------VITPTQVRLTIS  124 (176)
T ss_dssp             ----TSCCCEEEEEEESSCCCTTHHHHHHHCC---------------CCTTCSSCCCCCEEE------EEETTEEEEEES
T ss_pred             ----HCCCCEEEEECCCCCCCHHHHHHHHEEE---------------EECCCEEEEEEEEEE------CCCCCEEEEEEC
T ss_conf             ----2388479984467888878977753025---------------638957555346840------379968999963


Q ss_pred             HHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCC
Q ss_conf             15899999999870978604154477554443345701355440798044321000424688
Q gi|254780610|r  254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPR  315 (340)
Q Consensus       254 TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~  315 (340)
                      |||+||||+||+++||||+||.+||......              ..|++||||++-|.++.
T Consensus       125 tGr~HQIR~h~~~~g~pI~gD~~Y~~~~~~~--------------~~~l~l~~~r~l~~~e~  172 (176)
T 1ksk_A          125 EGRYHQVKRXFAAVGNHVVELHRERIGGITL--------------DADLAPGEYRPLTEEEI  172 (176)
T ss_dssp             CCCTTHHHHHHHHTTCCEEEEEEEEETTEEC--------------CTTCCTTCEEECCHHHH
T ss_pred             CCCHHHHHHHHHHCCCEEEEEEEEEECCCCC--------------CCCCCCCCEEECCHHHH
T ss_conf             5983999999998799798999999886504--------------79899975159999999


No 8  
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243)
Probab=100.00  E-value=5.6e-42  Score=269.56  Aligned_cols=184  Identities=16%  Similarity=0.184  Sum_probs=134.5

Q ss_pred             CCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             01440278996240111045678754210022222210244334444364324444332324057212035788889999
Q gi|254780610|r   93 LYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQF  172 (340)
Q Consensus        93 lyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f  172 (340)
                      .|||++++|||||+|++||++++... ++.+.+..+..         .++.+|||||++||||||||||..++..+..+|
T Consensus         1 ~yed~~~ivinKP~gl~~~~~~~~~~-~~~~~l~~~~~---------~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~   70 (186)
T 1vio_A            1 WIEEGQYFMLNKPQGCVCSNDDGDYP-TIYQFFDYPLA---------GKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPK   70 (186)
T ss_dssp             SSCCCCEEEEEECTTCBSSCCC--CC-BGGGGSCTTGG---------GGCEESSCCCTTCEEEEEEESCHHHHHHHHCTT
T ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCE-EEEEEECCCCC---------CEEEECCCCCCCCCCEEEEECCCCCCCCCCCCC
T ss_conf             22221035540258864333443201-45420024533---------136540212401221378741775320001112


Q ss_pred             HHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEE
Q ss_conf             97211322133445432024332332110013434443322123444555553000012221011256677500123443
Q gi|254780610|r  173 VDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHL  252 (340)
Q Consensus       173 ~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~  252 (340)
                            ..++|+|+|+|.|.+..+...+.......               .+. ........     ......++++++|
T Consensus        71 ------~~~~k~y~~~v~g~~~~~~~~~~~~~~~~---------------~~~-~~~~~~~~-----~~~~~~~~~~~~~  123 (186)
T 1vio_A           71 ------HHCEKTYLVTLADPVEENYSAACAEGILL---------------RGE-KEPTKPAK-----LEILDDYNVNLTI  123 (186)
T ss_dssp             ------SCCCEEEEEEESSCCCTTHHHHHHHCCCC---------------TTC-SSCCCCCE-----EEECSSSEEEEEE
T ss_pred             ------CCCCEEEEEEEEEECCHHHHHHHHCCEEC---------------CCC-CCCEEEEE-----ECCCCCCEEEEEE
T ss_conf             ------45520112599851204478898536561---------------683-01023322-----0135684489885


Q ss_pred             CHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCC
Q ss_conf             1158999999998709786041544775544433457013554407980443210004246889
Q gi|254780610|r  253 ETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRN  316 (340)
Q Consensus       253 ~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t  316 (340)
                      .|||+||||+||+++||||+||.+||.+.......+..   .....+.++.||+..+.|.||.+
T Consensus       124 ~tGr~hQIR~h~a~lg~pIvgD~~yg~~~~~~~~~l~~---g~~r~l~~~~l~~~~l~~~~~~~  184 (186)
T 1vio_A          124 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEE---GEYRPLTQSEIEKLVEGGSHHHH  184 (186)
T ss_dssp             SCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTCCT---TCEEECCHHHHHHTC--------
T ss_pred             CCCCCHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCC---CCEEECCHHHHHHHHHCCCCCCC
T ss_conf             05760799999998599793889999887247999999---76259999999999957986545


No 9  
>>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217)
Probab=99.89  E-value=5.7e-24  Score=162.24  Aligned_cols=100  Identities=19%  Similarity=0.173  Sum_probs=81.6

Q ss_pred             HHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEEEECCCHHHCCCCCCCCC
Q ss_conf             89999999859904998993286758048988999705601111023322222101440278996240111045678754
Q gi|254780610|r   39 RSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWT  118 (340)
Q Consensus        39 R~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llvinKPaGl~vhp~~~~~~  118 (340)
                      |++++++|++|.|+|||+++++++. +      .+.              ...|+|||++++|+|||+|++|||+.+...
T Consensus         2 Rr~~~~~i~~G~V~Vng~~v~~~d~-i------~~~--------------~~~I~yed~~~ivvnKP~g~~~~~~~~~~~   60 (119)
T 2olw_A            2 RQFIISENTMQKTSFRNHQVKRFSS-Q------RST--------------RRKPENQPTRVILFNKPYDVLPQFTDEAGR   60 (119)
T ss_dssp             --------------------------------------------------------CCCCEEEEEECTTBCSCSSCCTTS
T ss_pred             CEEEECCCEEECCCCCCCCCCCCCC-C------CCC--------------CCCCCCCCCEEEEEECCCCEEEECCCCCCC
T ss_conf             5367068714212255422120554-0------035--------------568878998899998999959707799888


Q ss_pred             CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             21002222221024433444436432444433232405721203578888999
Q gi|254780610|r  119 GTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQ  171 (340)
Q Consensus       119 ~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~  171 (340)
                      +|+.+.+.            ..++++|||||++|||+|+|||+..+++.|.++
T Consensus        61 ~tl~~~~~------------~~~l~~vhRLDr~TSGLll~ak~~~~~~~L~~~  101 (119)
T 2olw_A           61 KTLKEFIP------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP  101 (119)
T ss_dssp             BCGGGTCC------------CCSCEESSCCCTTCEEEEEEESCHHHHHHHHCT
T ss_pred             CCHHHHCC------------CCCCEECCCCCCCEEEEEEEECCCHHHHHHHHC
T ss_conf             76889657------------126347531143120069984360565453110


No 10 
>>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} (A:)
Probab=99.88  E-value=8.8e-24  Score=161.12  Aligned_cols=124  Identities=19%  Similarity=0.218  Sum_probs=98.9

Q ss_pred             EECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHC-------CHHHHH
Q ss_conf             9571136875789999871768898999999985990499899328675804898899970560111-------102332
Q gi|254780610|r   15 LLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKL-------NIAQEN   87 (340)
Q Consensus        15 ~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~-------~~~~~~   87 (340)
                      +|+++++|+|||+||++.++ .+||+++++||+.|+|+|||++++ +++++..||.+.+........       ......
T Consensus         1 iv~~~~~g~RLDk~L~~~~~-~~sR~~a~~li~~G~V~VNG~~~~-~s~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~~~   78 (133)
T 1dm9_A            1 MKEKPAVEVRLDKWLWAARF-YKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQGNDERTVIVKAITEQRRPA   78 (133)
T ss_dssp             ----CTTCCBHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEEETTEEEEEEECEEESCCCCH
T ss_pred             CCCCCCCCEEHHHHHHHCCC-CCCHHHHHHHHHCCEEEECCEECC-CCCEECCCCEEEEEECCEEEEEEEEEEEECCCCC
T ss_conf             99887764629999987867-168999999998691888999734-5856159998999879986589999876225673


Q ss_pred             HHHHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH
Q ss_conf             2222101440278996240111045678754210022222210244334444364324444332324057212035
Q gi|254780610|r   88 IPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDL  163 (340)
Q Consensus        88 ~~~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~  163 (340)
                      .++.++|||++.+++|||+|+.+|+....                       .++++|||||+.|||.|+++++..
T Consensus        79 ~~~~~~~ed~~~~v~~kp~~~~~~~~~~~-----------------------~r~~~vgRLDk~~t~~ll~l~~dg  131 (133)
T 1dm9_A           79 SEAALLYEETAESVEKREKMALARKLNAL-----------------------TMPHPDRRPDKKERRDLLRFKHGD  131 (133)
T ss_dssp             HHHGGGEEECHHHHHHHHHHHHHHHHHHT-----------------------C-----------------------
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHCCC-----------------------CCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             03566632368871134577776652245-----------------------578899786859999999875589


No 11 
>>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200)
Probab=99.81  E-value=4.6e-21  Score=144.89  Aligned_cols=96  Identities=24%  Similarity=0.186  Sum_probs=72.6

Q ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHH
Q ss_conf             221334454320243323321100134344433-2212344455555300001222101125667750012344311589
Q gi|254780610|r  179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNR-LRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRT  257 (340)
Q Consensus       179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~-~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRt  257 (340)
                      ++|+|+|+|+|.|.++++.+.+........... ....+.......++.|.|.|+++..     ...+|++++.|.|||+
T Consensus         1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~-----~~~~s~~~i~l~tGr~   75 (98)
T 2olw_A            1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERK-----SIPTSWLKITLYEGRN   75 (98)
T ss_dssp             CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CC-----SSCEEEEEEEESCCCT
T ss_pred             CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEE-----CCCCEEEEEEEECCCH
T ss_conf             22215899999456888999998659365785357756999535544331010477742-----1550589999915975


Q ss_pred             HHHHHHHHHHCCEEECCCCCCC
Q ss_conf             9999999870978604154477
Q gi|254780610|r  258 HQIRVHMAHKGNPLIGDPLYGK  279 (340)
Q Consensus       258 HQIRvhla~lG~PIvGD~~YG~  279 (340)
                      ||||+||+++||||+||.+||.
T Consensus        76 HQIR~~la~~g~pI~gd~ry~~   97 (98)
T 2olw_A           76 RQVRRMTAHVGFPTLRLIRYAM   97 (98)
T ss_dssp             THHHHHHHHTTCCEEEEEEEEE
T ss_pred             HHHHHHHHHCCCEEEEEEEEEE
T ss_conf             9999999985997989899999


No 12 
>>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:)
Probab=99.79  E-value=7.5e-21  Score=143.63  Aligned_cols=90  Identities=20%  Similarity=0.211  Sum_probs=78.5

Q ss_pred             CCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCH-HCCHHHHHHHHHHCCCCCEEEE
Q ss_conf             757899998717688989999999859904998993286758048988999705601-1110233222221014402789
Q gi|254780610|r   23 GRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQ-KLNIAQENIPLDILYEDDDIIV  101 (340)
Q Consensus        23 ~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~-~~~~~~~~~~~~IlyED~~llv  101 (340)
                      +|||+||.+.++ ..||++++++|++|+|+|||+++. ++++|..||.|.+...... .....+...++.|+|||++++|
T Consensus         1 mRLD~~L~~~~~-~~sr~~~~k~i~~g~I~VNg~~~~-~~~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~i~yed~~~lv   78 (92)
T 2k6p_A            1 MRIDKFLQSVGL-VKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYI   78 (92)
T ss_dssp             CBHHHHSTTTTS-CCCCCSSCCHHHHTCCEETTEECC-TTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSE
T ss_pred             CCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEEE-ECCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCHHHHCCCE
T ss_conf             967899987277-159999999998997998989986-624718999999984896368999978865898645506159


Q ss_pred             EECCCHHHCCCCC
Q ss_conf             9624011104567
Q gi|254780610|r  102 INKPAGLVVHPAP  114 (340)
Q Consensus       102 inKPaGl~vhp~~  114 (340)
                      +|||+||+|||+.
T Consensus        79 inKpagl~~hp~~   91 (92)
T 2k6p_A           79 APKTKELEHHHHH   91 (92)
T ss_dssp             EECCCC-------
T ss_pred             EECHHCCCCCCCC
T ss_conf             8063216244457


No 13 
>>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:1-63)
Probab=99.03  E-value=2.8e-10  Score=80.64  Aligned_cols=57  Identities=21%  Similarity=0.260  Sum_probs=50.3

Q ss_pred             HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECC
Q ss_conf             113687578999987176889899999998599049989932867580489889997056
Q gi|254780610|r   18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPA   77 (340)
Q Consensus        18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~   77 (340)
                      .+++++|||+||+...  .+||+.++++|++|.|+|||++++ ++++|..||.|.+..+.
T Consensus         2 ~~~~~~RLDk~La~~~--~~SR~~~~~li~~G~V~Vng~~vk-~~~~v~~~d~I~v~~~~   58 (63)
T 3dh3_A            2 LPDSSVRLNKYISESG--ICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQL   58 (63)
T ss_dssp             --CCCEEHHHHHHTTT--SSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEE
T ss_pred             CCCCCCCHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEE
T ss_conf             7988704999998778--851999999998793898999947-88896999989999999


No 14 
>>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} (A:)
Probab=98.92  E-value=2e-10  Score=81.47  Aligned_cols=71  Identities=17%  Similarity=0.131  Sum_probs=62.1

Q ss_pred             CCHHCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             511016249999571136875789999871768898999999985990499899328675804898899970
Q gi|254780610|r    4 TLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus         4 ~~~~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      +|.+--......+.....++|||+||.+... ..||++++++|..|.|+|||++++++++.|.+||.|.+..
T Consensus         2 ~m~~~~~~~~~~~~~~~~~~RLd~~L~~~~~-~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~   72 (79)
T 1p9k_A            2 SMIHRMSNMATFSLGKHPHVELCDLLKLEGW-SESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG   72 (79)
T ss_dssp             CCCCSSCCCCEEECCSCSCCCHHHHHHHHTS-CSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETT
T ss_pred             CHHHCCCCCCEEECCCCCCEEHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC
T ss_conf             5100014771386499971979999987788-3689999999984997989999277887989999999999


No 15 
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58)
Probab=98.86  E-value=5.5e-09  Score=72.92  Aligned_cols=53  Identities=21%  Similarity=0.368  Sum_probs=48.8

Q ss_pred             CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             6875789999871768898999999985990499899328675804898899970
Q gi|254780610|r   21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      ..+|||+||++..  .+||++++++|+.|.|+|||++++++++.+.+||.|.+.-
T Consensus         2 ~~~RLDk~L~~~~--~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~g   54 (58)
T 1ksk_A            2 SHXRLDKFIAQQL--GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDG   54 (58)
T ss_dssp             CCEEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETT
T ss_pred             CCCHHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEEE
T ss_conf             8400999998778--9689999999988929999999466885807867699721


No 16 
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57)
Probab=98.82  E-value=8.5e-09  Score=71.83  Aligned_cols=52  Identities=21%  Similarity=0.340  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             875789999871768898999999985990499899328675804898899970
Q gi|254780610|r   22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      .+|||+||++..  .+||++++++|++|.|+|||++++++++.+.+||.|.+.-
T Consensus         2 ~~RLDk~L~~~~--~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~g   53 (57)
T 1vio_A            2 SLRLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFED   53 (57)
T ss_dssp             CEEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETT
T ss_pred             CHHHHHHHHHCC--CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEEE
T ss_conf             558999999877--8589999999987978999999154895868878787620


No 17 
>>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (D:100-193)
Probab=98.42  E-value=6.4e-07  Score=60.65  Aligned_cols=51  Identities=27%  Similarity=0.401  Sum_probs=45.3

Q ss_pred             CHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             5789999871768898999999985990499899328675804898899970
Q gi|254780610|r   24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      |||+||.+.-. .-||.+++++|..|+|.|||++++.|++.+.+||.|.+..
T Consensus         1 RLD~~l~r~~~-~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~   51 (94)
T 2vqe_D            1 RLDNVVYRLGF-AVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAE   51 (94)
T ss_dssp             BHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECG
T ss_pred             HHHHHHHHCCC-HHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHH
T ss_conf             99999985352-0028988899870684508879975367852886001211


No 18 
>>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65)
Probab=98.36  E-value=2.6e-07  Score=62.94  Aligned_cols=58  Identities=21%  Similarity=0.242  Sum_probs=50.1

Q ss_pred             CHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCE--EECCEEECCCCCEECCCCEEEEEE
Q ss_conf             71136875789999871768898999999985990--499899328675804898899970
Q gi|254780610|r   17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFI--SINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        17 ~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V--~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      ++....+|||++|.+.-. .-||++++++|..|.|  +|||+++.+|++.+.+||.|.+.-
T Consensus         1 s~~~~~~RLD~~L~~~g~-~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~~   60 (65)
T 3hp7_A            1 SNAXPKERVDVLAYKQGL-FETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLKG   60 (65)
T ss_dssp             --CCCEEEHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETT
T ss_pred             CCCCCHHHHHHHHHHCCC-CCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEEC
T ss_conf             996508899999998758-124999999998599423209989568867879999899807


No 19 
>>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432)
Probab=98.15  E-value=8.6e-06  Score=53.92  Aligned_cols=66  Identities=17%  Similarity=0.103  Sum_probs=54.9

Q ss_pred             CCEEEEEECHHHC---CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             6249999571136---875789999871768898999999985990499899328675804898899970
Q gi|254780610|r    9 SSIKISLLSDSTA---EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus         9 ~~~~~~~V~~~~~---g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      ..|..+.++.++.   +.|||.+|.+.= -.-|+++++++|+.|.|+|||++++.+++.+..||.+.+..
T Consensus         3 e~~p~~~i~~~~~~~~~~rl~~~l~~~g-l~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~~   71 (83)
T 1h3f_A            3 EEIPEVTIPASELKEGRIWVARLFTLAG-LTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQR   71 (83)
T ss_dssp             CCSCEEEECGGGCBTTEEEHHHHHHHTT-SSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEEE
T ss_pred             CCCCCEEECHHHHCCCCCCHHHHHHHCC-CCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
T ss_conf             5798157438783258634999999849-86778999999985998989998248770215898089984


No 20 
>>3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... (D:97-190)
Probab=98.14  E-value=1.3e-06  Score=58.77  Aligned_cols=52  Identities=23%  Similarity=0.218  Sum_probs=46.2

Q ss_pred             CHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf             57899998717688989999999859904998993286758048988999705
Q gi|254780610|r   24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP   76 (340)
Q Consensus        24 RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~   76 (340)
                      |||.||-+.- -.-|+.+++++|..|.|+|||+++..|++.|++||.|.+...
T Consensus         1 RLD~~l~r~g-fa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~   52 (94)
T 3i1m_D            1 RLDNVVYRMG-FGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREK   52 (94)
T ss_dssp             STTHHHHTTT-SCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSS
T ss_pred             HHHHHHHHCC-HHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCC
T ss_conf             8888866031-254099999999850376088799763177058977886232


No 21 
>>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201)
Probab=98.10  E-value=1.4e-06  Score=58.55  Aligned_cols=54  Identities=20%  Similarity=0.206  Sum_probs=47.1

Q ss_pred             CCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             6875789999871768898999999985990499899328675804898899970
Q gi|254780610|r   21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        21 ~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      -++|||.+|-+.- -.-|+.+++++|..|.|+|||++++.|++.+++||.|.+..
T Consensus         6 LE~RLD~~l~R~g-fa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~   59 (120)
T 3bbn_D            6 LEMRLDNILFRLG-MAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARD   59 (120)
T ss_dssp             HHSBTTTTTTTTT-SSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECS
T ss_pred             HHHHHHHEEEECC-CCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCC
T ss_conf             9875310355057-33576888899987513615489816572546166300100


No 22 
>>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} (D:81-179)
Probab=97.98  E-value=7.4e-06  Score=54.31  Aligned_cols=55  Identities=16%  Similarity=0.068  Sum_probs=48.2

Q ss_pred             HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             36875789999871768898999999985990499899328675804898899970
Q gi|254780610|r   20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      --.+|||..|-+.- -.-|+.+++++|..|.|.|||++++.|++.|++||.|.+..
T Consensus         6 ~LErRLD~il~R~g-fa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~   60 (99)
T 1s1h_D            6 FLERRLQTQVYKLG-LAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDF   60 (99)
T ss_dssp             SGGGBHHHHHHHHT-SSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCS
T ss_pred             HHHHHHHHHHHHHC-CCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEE
T ss_conf             88750788999815-65889999999873772589999876246840587560556


No 23 
>>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=97.80  E-value=1.4e-05  Score=52.59  Aligned_cols=55  Identities=13%  Similarity=0.079  Sum_probs=46.3

Q ss_pred             HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCC--CEEEEE
Q ss_conf             13687578999987176889899999998599049989932867580489--889997
Q gi|254780610|r   19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPG--DSFLIT   74 (340)
Q Consensus        19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~g--d~I~i~   74 (340)
                      +...+|||.+|.+.-. .-|+.+++++|..|.|+|||++++.|++.|..|  |.|.+.
T Consensus         4 ~~lerRLd~~l~~~g~-a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~   60 (71)
T 2cqj_A            4 GSSGRRLPTVLLKLRM-AQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWV   60 (71)
T ss_dssp             SCCEEEHHHHHHHTTC-SSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEES
T ss_pred             HHHHCCHHHHHHHHCC-CCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEE
T ss_conf             3444126899998055-27899999999849899899995569858358998869984


No 24 
>>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A (C:31-245)
Probab=96.94  E-value=0.00048  Score=43.51  Aligned_cols=84  Identities=20%  Similarity=0.240  Sum_probs=53.8

Q ss_pred             CCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf             44027899624011104567875421002222221024433444436432444433232405721203578888999997
Q gi|254780610|r   95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVD  174 (340)
Q Consensus        95 ED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~  174 (340)
                      .-+.+|++|||.|+.+|        .+++.+...+..        .+.+-..-||-..||+++++-+...  .+.+.|. 
T Consensus        14 ~~~G~l~~~KP~g~tS~--------~vv~~ik~~~~~--------~kvGh~GTLDp~atGvl~i~vg~aT--kl~~~~~-   74 (215)
T 2aus_C           14 IQYGVINLDKPPGPTSH--------EVVAWIKRILNL--------EKAGHGGTLDPKVSGVLPVALERAT--RVVQALL-   74 (215)
T ss_dssp             HHTEEEEEEECSSSCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG--GGGGGGT-
T ss_pred             HCCCEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCCCCEEEEECHHH--HHHHHHC-
T ss_conf             47838999579989999--------999999987183--------4257898789865034767873899--8999974-


Q ss_pred             HCCCCCEEEEEEEEEECCCCCCCCCCCC
Q ss_conf             2113221334454320243323321100
Q gi|254780610|r  175 HGKSTRLKRAYYAMVWGIPLPDSGIINA  202 (340)
Q Consensus       175 ~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~  202 (340)
                           .-.|+|.|.+..-...++..++.
T Consensus        75 -----~~~K~Y~~~~~~g~~t~t~d~~~   97 (215)
T 2aus_C           75 -----PAGKEYVALMHLHGDVPEDKIRA   97 (215)
T ss_dssp             -----TCCEEEEEEEEESSCCCHHHHHH
T ss_pred             -----CCCCEEEEEEEECCCCCCCHHHE
T ss_conf             -----58859999988723444440013


No 25 
>>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} (A:51-266)
Probab=96.87  E-value=0.0007  Score=42.52  Aligned_cols=85  Identities=19%  Similarity=0.171  Sum_probs=52.9

Q ss_pred             CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH
Q ss_conf             14402789962401110456787542100222222102443344443643244443323240572120357888899999
Q gi|254780610|r   94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFV  173 (340)
Q Consensus        94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~  173 (340)
                      |--+.|+++|||+|+.+|.        +++.+.+.+..        .+.+-...||-..||+|+++-+...  .+...| 
T Consensus        13 ~~~~G~l~i~KP~g~tS~~--------vv~~~k~~~~~--------~kvgh~GtLDp~a~GvLiv~ig~~T--kl~~~~-   73 (216)
T 2apo_A           13 LIKYGVVVVDKPRGPTSHE--------VSTWVKKILNL--------DKAGHGGTLDPKVTGVLPVALERAT--KTIPMW-   73 (216)
T ss_dssp             HHHTEEEEEEECSSSCHHH--------HHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG--GGGGGT-
T ss_pred             HHCCCEEEEECCCCCCHHH--------HHHHHHHHHCC--------CCCCCCCCCCCCCCCCHHHEECHHH--HHHHHH-
T ss_conf             8549989997999899899--------99999998487--------7357787789634365532118653--221775-


Q ss_pred             HHCCCCCEEEEEEEEEECCCCCCCCCCCC
Q ss_conf             72113221334454320243323321100
Q gi|254780610|r  174 DHGKSTRLKRAYYAMVWGIPLPDSGIINA  202 (340)
Q Consensus       174 ~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~  202 (340)
                           ..-.|+|.|.+.=-...++..++.
T Consensus        74 -----~~~~K~Y~~~~~lG~~Tdt~di~~   97 (216)
T 2apo_A           74 -----HIPPKEYVCLMHLHRDASEEDILR   97 (216)
T ss_dssp             -----TSSCEEEEEEEEESSCCCHHHHHH
T ss_pred             -----CCCCCEEEEEEEEEECCCCCHHHH
T ss_conf             -----058827999999831243214999


No 26 
>>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} (A:345-432)
Probab=96.76  E-value=0.0016  Score=40.44  Aligned_cols=51  Identities=20%  Similarity=0.113  Sum_probs=41.3

Q ss_pred             HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCE
Q ss_conf             1368757899998717688989999999859904998993286758048988
Q gi|254780610|r   19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDS   70 (340)
Q Consensus        19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~   70 (340)
                      -+.+.+|..+|...-. .-|++.++++|++|.|+|||+++++++..+.++|.
T Consensus         8 ~~~~~~i~~lL~~~gl-~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~   58 (88)
T 2jan_A            8 PGSPDGIVDLLVASGL-SASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF   58 (88)
T ss_dssp             SSSCCSHHHHHHHHTS-CSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS
T ss_pred             CCCCCCHHHHHHHCCC-CCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHH
T ss_conf             5787779999998288-67899999999939999899981694330278782


No 27 
>>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} (A:1-81)
Probab=95.03  E-value=0.059  Score=31.04  Aligned_cols=70  Identities=16%  Similarity=0.216  Sum_probs=52.9

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCHHCCHHHHHHHHHHCCCCCEEEE
Q ss_conf             87578999987176889899999998599049989932867580489889997056011110233222221014402789
Q gi|254780610|r   22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIV  101 (340)
Q Consensus        22 g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~~~~~~~~~~~~~IlyED~~llv  101 (340)
                      +.-|--||...|.-..+.+-+++.+.+|.|.|||++.++..+.+-.-|.|++.-+            .+.++|....-++
T Consensus         7 siPL~i~LRd~Lk~A~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~~e------------~yRvl~d~kgr~~   74 (81)
T 3kbg_A            7 SVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEINGE------------SYRVVYNDQGALV   74 (81)
T ss_dssp             CEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEETTE------------EEEEEECTTSCEE
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECCC------------EEEEEECCCCEEE
T ss_conf             5654378644645226589999998679389899996238998870679997997------------7999985897399


Q ss_pred             EE
Q ss_conf             96
Q gi|254780610|r  102 IN  103 (340)
Q Consensus       102 in  103 (340)
                      +.
T Consensus        75 l~   76 (81)
T 3kbg_A           75 LX   76 (81)
T ss_dssp             EE
T ss_pred             EE
T ss_conf             99


No 28 
>>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} (A:1-60,A:206-232)
Probab=94.64  E-value=0.032  Score=32.60  Aligned_cols=55  Identities=31%  Similarity=0.438  Sum_probs=37.8

Q ss_pred             CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH
Q ss_conf             14402789962401110456787542100222222102443344443643244443323240572120357
Q gi|254780610|r   94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA  164 (340)
Q Consensus        94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a  164 (340)
                      |.-+.++++|||.|+.+|        .+++.+...+..        .+.+-..-||-..||+|+++-+...
T Consensus         3 ~~~~Gil~idKP~G~TS~--------~vv~~iKk~l~~--------kKVGH~GTLDP~AtGvLiv~iG~aT   57 (87)
T 1sgv_A            3 ATGPGIVVIDKPAGMTSH--------DVVGRCRRIFAT--------RRVGHAGTLDPMATGVLVIGIERAT   57 (87)
T ss_dssp             CCCSEEEEEEECTTCCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CCCCEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH
T ss_conf             889889999769989989--------999999998488--------8556387889736423999989676


No 29 
>>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:1-79,A:225-253)
Probab=94.41  E-value=0.039  Score=32.09  Aligned_cols=55  Identities=16%  Similarity=0.356  Sum_probs=37.9

Q ss_pred             CCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH
Q ss_conf             14402789962401110456787542100222222102443344443643244443323240572120357
Q gi|254780610|r   94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA  164 (340)
Q Consensus        94 yED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a  164 (340)
                      ++-+.|+++|||.|+.++        .+++.+...+..        .+.|-..-||-..||||+++-...+
T Consensus        22 ~~~~Gil~idKP~G~TS~--------~vV~~vkk~l~~--------kKVGH~GTLDP~AtGvLiv~iG~aT   76 (108)
T 1k8w_A           22 MDINGVLLLDKPQGMSSN--------DALQKVKRIYNA--------NRAGHTGALDPLATGMLPICLGEAT   76 (108)
T ss_dssp             CCCCEEEEEEECTTCCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CCCCEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH
T ss_conf             885369998479989989--------999999998589--------9687686579746135999988888


No 30 
>>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420)
Probab=94.27  E-value=0.0091  Score=35.89  Aligned_cols=52  Identities=25%  Similarity=0.209  Sum_probs=39.8

Q ss_pred             HHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEE
Q ss_conf             13687578999987176889899999998599049989932867580489889
Q gi|254780610|r   19 STAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF   71 (340)
Q Consensus        19 ~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I   71 (340)
                      ...+.+|...|.+.- -.-|++.++++|.+|.|+|||++++++++.+..+|.+
T Consensus       103 ~~~~~~l~~lL~~~~-l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~  154 (174)
T 1jil_A          103 SNDTTNIVEVLIETG-ISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI  154 (174)
T ss_dssp             -----------------------------------------------------
T ss_pred             CCCCCCHHHHHHHCC-CCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCC
T ss_conf             588878999999838-8467999999998499899999813844400775704


No 31 
>>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} (A:1-57,A:190-224)
Probab=94.13  E-value=0.043  Score=31.85  Aligned_cols=52  Identities=25%  Similarity=0.378  Sum_probs=36.1

Q ss_pred             CEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH
Q ss_conf             02789962401110456787542100222222102443344443643244443323240572120357
Q gi|254780610|r   97 DDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLA  164 (340)
Q Consensus        97 ~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a  164 (340)
                      +.++.+|||.|+.+|        .++..+.+.+..        .+.+-..-||-..||+|+++-+...
T Consensus         3 nGil~idKP~G~TS~--------~vV~~iKk~l~~--------kKVGH~GTLDP~AtGvLii~iG~aT   54 (92)
T 1r3e_A            3 HGILVAYKPKGPTSH--------DVVDEVRKKLKT--------RKVGHGGTLDPFACGVLIIGVNQGT   54 (92)
T ss_dssp             CEEEEEEECSSSCHH--------HHHHHHHHHTTC--------SCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CEEEEEECCCCCCHH--------HHHHHHHHHHCC--------CCCCCCCCCCCCCEEEEEEEECHHH
T ss_conf             559999669989989--------999999998688--------8787785679746446999988675


No 32 
>>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419)
Probab=93.09  E-value=0.02  Score=33.91  Aligned_cols=51  Identities=16%  Similarity=0.109  Sum_probs=36.9

Q ss_pred             HCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEE
Q ss_conf             3687578999987176889899999998599049989932867580489889
Q gi|254780610|r   20 TAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF   71 (340)
Q Consensus        20 ~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I   71 (340)
                      ..+.++-..|...-. .-|++.++++|.+|.|+|||++++++++.+...+.+
T Consensus       104 ~~~~~l~~lL~~~gl-~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~  154 (174)
T 2ts1_A          104 GGDVPLVELLVSAGI-SPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL  154 (174)
T ss_dssp             ----------------------------------------------------
T ss_pred             CCCCCHHHHHHHCCC-CCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCC
T ss_conf             799769999998598-677899999998699898999823842201775714


No 33 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159)
Probab=92.86  E-value=0.095  Score=29.80  Aligned_cols=25  Identities=24%  Similarity=0.503  Sum_probs=23.2

Q ss_pred             CEEECCEEECCCCCEECCCCEEEEE
Q ss_conf             9049989932867580489889997
Q gi|254780610|r   50 FISINGMVSKNPNRKVVPGDSFLIT   74 (340)
Q Consensus        50 ~V~vnG~~~~~~~~~l~~gd~I~i~   74 (340)
                      +|.|||+++.-|++.+++||.|.+.
T Consensus         1 Hi~VNgkkVdIPSy~~k~gD~I~ik   25 (83)
T 1c05_A            1 HILVDGSRVNIPSYRVKPGQTIAVR   25 (83)
T ss_dssp             CEEETTEECCCSSCBCCTTCEEEEC
T ss_pred             CEECCCEEEEECCEEECCCCEEEEC
T ss_conf             6360436998434162178487502


No 34 
>>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:)
Probab=72.13  E-value=6.5  Score=18.86  Aligned_cols=51  Identities=12%  Similarity=0.194  Sum_probs=33.6

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHCC--CEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf             8757899998717688989999999859--904998993286758048988999705
Q gi|254780610|r   22 EGRIDRWLATSLKEQFSRSYVKILILNG--FISINGMVSKNPNRKVVPGDSFLITVP   76 (340)
Q Consensus        22 g~RLD~~L~~~l~~~~sR~~i~kli~~G--~V~vnG~~~~~~~~~l~~gd~I~i~~~   76 (340)
                      +..+... .+.|...++  .++..+...  .|.|||+.+. .++.+..||+|.+..|
T Consensus        25 ~~tv~~l-~~~L~~~~p--~~~~~l~~~~~~v~vn~~~v~-~~~~l~~gdeVai~PP   77 (81)
T 1fm0_D           25 FPTVEAL-RQHMAAQSD--RWALALEDGKLLAAVNQTLVS-FDHPLTDGDEVAFFPP   77 (81)
T ss_dssp             CSBHHHH-HHHHHTTCH--HHHHHHCCTTCEEEETTEECC-TTCBCCTTCEEEEECC
T ss_pred             CCCHHHH-HHHHHHHCC--HHHHHHCCCCEEEECCCEECC-CCCCCCCCCEEEEECC
T ss_conf             9999999-999987682--488862789589972845979-9978599999999699


No 35 
>>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B* (D:)
Probab=63.12  E-value=10  Score=17.75  Aligned_cols=28  Identities=14%  Similarity=0.255  Sum_probs=23.1

Q ss_pred             CCCEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf             59904998993286758048988999705
Q gi|254780610|r   48 NGFISINGMVSKNPNRKVVPGDSFLITVP   76 (340)
Q Consensus        48 ~G~V~vnG~~~~~~~~~l~~gd~I~i~~~   76 (340)
                      .-.|.|||+.+. .++.|+.||+|.+..|
T Consensus        46 ~~~v~vN~~~v~-~~~~l~dgDeVai~PP   73 (77)
T 2q5w_D           46 KFQVAVNEEFVQ-KSDFIQPNDTVALIPP   73 (77)
T ss_dssp             CCEEEETTEEEC-TTSEECTTCEEEEECS
T ss_pred             HHHHHCCCEECC-CCCCCCCCCEEEEECC
T ss_conf             313410880768-8867099899999799


No 36 
>>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:)
Probab=47.88  E-value=12  Score=17.27  Aligned_cols=26  Identities=23%  Similarity=0.293  Sum_probs=21.2

Q ss_pred             CEEECCEEECCCCCEECCCCEEEEEEC
Q ss_conf             904998993286758048988999705
Q gi|254780610|r   50 FISINGMVSKNPNRKVVPGDSFLITVP   76 (340)
Q Consensus        50 ~V~vnG~~~~~~~~~l~~gd~I~i~~~   76 (340)
                      .|.|||+.+. .++.|..||+|.+..|
T Consensus        69 ~v~vN~~~v~-~~~~l~dgdeV~i~PP   94 (98)
T 1vjk_A           69 NIAVNGRYVS-WDEELKDGDVVGVFPP   94 (98)
T ss_dssp             EEEETTBCCC-TTCBCCTTCEEEEESC
T ss_pred             EEEECCEECC-CCCCCCCCCEEEEECC
T ss_conf             9986788869-8978199999999798


No 37 
>>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative; 2.10A {Haemophilus influenzae 86-028np} (A:)
Probab=46.22  E-value=2.7  Score=21.11  Aligned_cols=69  Identities=14%  Similarity=0.106  Sum_probs=41.5

Q ss_pred             CCHHCCCEEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHH--------------HHCCCEEECCEEECCCCCEECCCC
Q ss_conf             511016249999571136875789999871768898999999--------------985990499899328675804898
Q gi|254780610|r    4 TLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKIL--------------ILNGFISINGMVSKNPNRKVVPGD   69 (340)
Q Consensus         4 ~~~~~~~~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kl--------------i~~G~V~vnG~~~~~~~~~l~~gd   69 (340)
                      .|++.+.|++.++.+.-..+.+-   .-.++.+.+   +.++              +....+-|=|+.+ ..++.|+.||
T Consensus         6 ~m~~~~~i~VeV~YA~p~~q~~~---~l~v~~GtT---v~~Ai~~SGil~~fPeidl~~~~vGIfgk~v-~~d~~L~~GD   78 (97)
T 2hj1_A            6 HHHSLNQINIEIAYAFPERYYLK---SFQVDEGIT---VQTAITQSGILSQFPEIDLSTNKIGIFSRPI-KLTDVLKEGD   78 (97)
T ss_dssp             -----CEEEEEEEEEETTEEEEE---EEEEETTCB---HHHHHHHHTHHHHCTTCCTTTSEEEEEECSC-CTTCBCCTTC
T ss_pred             CCCCCCEEEEEEEEECCCEEEEE---EEECCCCCC---HHHHHHHCCCHHHCCCCCCCCCCEEEECCCC-CCCCCCCCCC
T ss_conf             53411536999999879957999---998799893---9999987593545966470106155689385-8877178999


Q ss_pred             EEEEEECCCH
Q ss_conf             8999705601
Q gi|254780610|r   70 SFLITVPAAQ   79 (340)
Q Consensus        70 ~I~i~~~~~~   79 (340)
                      +|.++.|-.-
T Consensus        79 RVEIYRPL~~   88 (97)
T 2hj1_A           79 RIEIYRPLLA   88 (97)
T ss_dssp             EEEECCCCC-
T ss_pred             EEEEECCCCC
T ss_conf             9999456555


No 38 
>>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84)
Probab=44.05  E-value=21  Score=15.87  Aligned_cols=60  Identities=13%  Similarity=0.148  Sum_probs=35.0

Q ss_pred             EEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCC------CEEECCEEEC---CCCCEECCCCEEEEEEC
Q ss_conf             499995711368757899998717688989999999859------9049989932---86758048988999705
Q gi|254780610|r   11 IKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNG------FISINGMVSK---NPNRKVVPGDSFLITVP   76 (340)
Q Consensus        11 ~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G------~V~vnG~~~~---~~~~~l~~gd~I~i~~~   76 (340)
                      .....|+....+.=|+ .|.++++ .+    .+.++..|      .|.|||+.++   ..++.|..||+|.+..|
T Consensus        15 ~~~~~v~~~Tv~~ll~-~L~~~~p-~~----~~~l~~~g~~~~~v~i~vNg~~i~~~~~~~t~l~dgDeVai~PP   83 (84)
T 1v8c_A           15 KSQLELPGATVGEVLE-NLVRAYP-AL----KEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPP   83 (84)
T ss_dssp             CSEEECCCSBHHHHHH-HHHHHCG-GG----HHHHEETTEECTTCEEEETTEEGGGTTGGGCBCCTTCEEEEECS
T ss_pred             CEEEEECCCCHHHHHH-HHHHHCC-CC----HHHCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCEEEEECC
T ss_conf             9079957899999999-9985786-30----22003443510138999878774145788868699999999699


No 39 
>>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, transcription; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis H37RV} (A:290-388)
Probab=41.78  E-value=23  Score=15.66  Aligned_cols=23  Identities=13%  Similarity=0.118  Sum_probs=10.4

Q ss_pred             CEEECCEEECCCCCEECCCCEEEE
Q ss_conf             904998993286758048988999
Q gi|254780610|r   50 FISINGMVSKNPNRKVVPGDSFLI   73 (340)
Q Consensus        50 ~V~vnG~~~~~~~~~l~~gd~I~i   73 (340)
                      .++|||+++. ..+.|..||.|.+
T Consensus        60 g~~vng~~v~-~~~~L~~Gd~i~i   82 (99)
T 2ff4_A           60 GVHVQHERIR-SAVTLNDGDHIRI   82 (99)
T ss_dssp             CCEETTEECS-SEEEECTTCEEEE
T ss_pred             CEEECCEECC-CCEECCCCCEEEE
T ss_conf             8579999987-8567899999999


No 40 
>>2rk0_A Glyoxalase/bleomycin resistance protein/dioxygenase domain; 11002Z, glyoxylase, PSI-II, newyork structural genomix research consortium (nysgrc); 2.04A {Frankia SP} (A:68-136)
Probab=39.17  E-value=25  Score=15.42  Aligned_cols=46  Identities=11%  Similarity=0.131  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHH
Q ss_conf             9999999987097860415447755444334570135544079804432100042468897689998499789
Q gi|254780610|r  257 THQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED  329 (340)
Q Consensus       257 tHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~  329 (340)
                      --+++.+|...|.+|.+-.-.|.                          .++|-|..| +|-.+++.++-|..
T Consensus        19 l~~~~~~L~~~gv~~~~~~~~g~--------------------------~~siyf~DP-dG~~iEl~~~~p~~   64 (69)
T 2rk0_A           19 LDVLEERLAKAGAAFTPTQELPF--------------------------GWILAFRDA-DNIALEAXLGREGH   64 (69)
T ss_dssp             HHHHHHHHHHHTCCBCCCEEETT--------------------------EEEEEEECT-TCCEEEEEEECTTS
T ss_pred             HHHHHHHHHHCCCEECCCCCCCC--------------------------EEEEEEECC-CCCEEEEEECCCCC
T ss_conf             99999999978986478661798--------------------------499999999-99989999999855


No 41 
>>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:)
Probab=38.54  E-value=12  Score=17.23  Aligned_cols=62  Identities=16%  Similarity=0.271  Sum_probs=36.6

Q ss_pred             CCCHHCCCEEEEEEC-------HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             651101624999957-------1136875789999871768898999999985990499899328675804898899970
Q gi|254780610|r    3 QTLDNCSSIKISLLS-------DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus         3 ~~~~~~~~~~~~~V~-------~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      +.+.....|++.+.-       +-..+..+..+| ..|  +++..       .=.|.+||+.+. .++.|+.||.|.+..
T Consensus         4 ~~~~~~~mm~i~v~~~~~~~~~~~~~~~Tv~~ll-~~L--~l~~~-------~v~v~vNg~~v~-~~~~L~dgD~v~i~~   72 (77)
T 1rws_A            4 HHHHGSKMIKVKVIGRNIEKEIEWREGMKVRDIL-RAV--GFNTE-------SAIAKVNGKVVL-EDDEVKDGDFVEVIP   72 (77)
T ss_dssp             ------CCCCCBSTTCCCCCCCCCCSSCCHHHHH-HTT--TCSSC-------SSCEEETTEEEC-SSSCCCSSCCCBCSC
T ss_pred             CCCCCCEEEEEEEECCCCEEEEECCCCCCHHHHH-HHH--CCCCH-------HHHEEECCEECC-CCCCCCCCCEEEEEE
T ss_conf             5667875999999625606899879969999999-980--99830-------101559999969-972869999999990


No 42 
>>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:)
Probab=37.62  E-value=26  Score=15.27  Aligned_cols=48  Identities=17%  Similarity=0.160  Sum_probs=29.1

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHCC------CEEECCEEEC---CCCCEECCCCEEEEEEC
Q ss_conf             99998717688989999999859------9049989932---86758048988999705
Q gi|254780610|r   27 RWLATSLKEQFSRSYVKILILNG------FISINGMVSK---NPNRKVVPGDSFLITVP   76 (340)
Q Consensus        27 ~~L~~~l~~~~sR~~i~kli~~G------~V~vnG~~~~---~~~~~l~~gd~I~i~~~   76 (340)
                      ..|..+++ .. +..+.-.-..|      .|.|||+-++   ..++.|+.||+|.+..+
T Consensus        39 ~~l~~~~p-~~-~~~~~~~~~~~~~~~~~~v~vNg~~i~~~~~~~t~L~~gDeV~i~pp   95 (99)
T 2qjl_A           39 DHIVSTMI-NN-PNDVSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTST   95 (99)
T ss_dssp             HHHHHHTC-SS-GGGHHHHEETTEECTTEEEEETTEEGGGGTGGGCBCCTTCEEEEEEC
T ss_pred             HHHHHHCC-CC-HHHHHHHCCCCCEEEEEEEEECCCEEECCCCCCCCCCCCCEEEEECC
T ss_conf             99998745-53-03433112345423228999879587817887758599799999678


No 43 
>>1vc3_B L-aspartate-alpha-decarboxylase heavy chain; tetramer, pyruvoyl group, riken structural genomics/proteomics initiative, RSGI; 1.50A {Thermus thermophilus} PDB: 2eeo_B (B:)
Probab=36.09  E-value=14  Score=16.81  Aligned_cols=41  Identities=32%  Similarity=0.513  Sum_probs=22.7

Q ss_pred             HHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
Q ss_conf             113687578999987176889899999998599049989932867580489889997
Q gi|254780610|r   18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLIT   74 (340)
Q Consensus        18 ~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~   74 (340)
                      .-+.|.|+.+|...-     .+       -+|.|.+||.-    .+.+++||.|.+.
T Consensus        24 Nv~NG~Rf~TY~I~G-----~~-------GSg~I~lNGAA----Arl~~~GD~vII~   64 (96)
T 1vc3_B           24 DITNGARLTTYALPG-----ER-------GSGVIGINGAA----AHLVKPGDLVILV   64 (96)
T ss_dssp             ETTTCCEEEEECEEE-----CT-------TTTCEEEEGGG----GGTCCTTCEEEEE
T ss_pred             ECCCCCEEEEEEEEC-----CC-------CCCEEEECCHH----HEECCCCCEEEEE
T ss_conf             998994898799963-----67-------66879855856----4235999999999


No 44 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:22-76)
Probab=34.55  E-value=29  Score=14.97  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf             8757899998717688989999999859
Q gi|254780610|r   22 EGRIDRWLATSLKEQFSRSYVKILILNG   49 (340)
Q Consensus        22 g~RLD~~L~~~l~~~~sR~~i~kli~~G   49 (340)
                      ++|||..+-+. .-.-|+.+++++|..|
T Consensus        29 E~RLD~vvyR~-gfa~S~~~ARQlV~HG   55 (55)
T 1c05_A           29 ESRLDNLVYRL-GLARTRRQARQLVTHG   55 (55)
T ss_dssp             HHBHHHHHHHT-TSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHHCCC-CCCCCHHHHHHHHHHC
T ss_conf             98754541157-7437888899888735


No 45 
>>3gqs_A Adenylate cyclase-like protein; FHA domain, structural genomics, PSI-2, protein structure initiative; 2.20A {Chlamydia trachomatis D} (A:)
Probab=32.78  E-value=31  Score=14.80  Aligned_cols=10  Identities=10%  Similarity=0.282  Sum_probs=3.6

Q ss_pred             CCCEEEEECC
Q ss_conf             3240572120
Q gi|254780610|r  152 TTGVMVVAKN  161 (340)
Q Consensus       152 TSGlll~Ak~  161 (340)
                      +++...+++.
T Consensus        23 ~~~~~~IGR~   32 (106)
T 3gqs_A           23 SGKTYIVGSD   32 (106)
T ss_dssp             TTCEEEEESC
T ss_pred             CCCEEEEEEC
T ss_conf             9983998188


No 46 
>>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis H37RV} PDB: 3dwm_A (C:)
Probab=32.58  E-value=32  Score=14.78  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=20.6

Q ss_pred             EEECCEEECC---CCCEECCCCEEEEEEC
Q ss_conf             0499899328---6758048988999705
Q gi|254780610|r   51 ISINGMVSKN---PNRKVVPGDSFLITVP   76 (340)
Q Consensus        51 V~vnG~~~~~---~~~~l~~gd~I~i~~~   76 (340)
                      |.|||+.+..   .++.|..||+|.+..|
T Consensus        61 v~vNg~~v~~~~~~~t~l~~gDeV~ilPp   89 (93)
T 3dwg_C           61 IYVNDEDVRFSGGLATAIADGDSVTILPA   89 (93)
T ss_dssp             EEETTEEGGGTTGGGCBCCTTCEEEEEEC
T ss_pred             EEECCEEECCCCCCCCCCCCCCEEEEECC
T ss_conf             99857451001476663799899999688


No 47 
>>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:)
Probab=30.92  E-value=25  Score=15.37  Aligned_cols=27  Identities=11%  Similarity=0.135  Sum_probs=20.3

Q ss_pred             EEECCEEEC---CCCCEECCCCEEEEEECC
Q ss_conf             049989932---867580489889997056
Q gi|254780610|r   51 ISINGMVSK---NPNRKVVPGDSFLITVPA   77 (340)
Q Consensus        51 V~vnG~~~~---~~~~~l~~gd~I~i~~~~   77 (340)
                      |.|||+.+.   ..++.|+.||.|.+..|-
T Consensus        70 v~VN~~~v~~~~~~~t~L~~gDeV~ilppv   99 (110)
T 2k9x_A           70 VLVNSCDAEVVGGMDYVLNDGDTVEFISTL   99 (110)
T ss_dssp             EEESSSBHHHHTSSCCCCCSSCEEEEEECC
T ss_pred             EEECCCEEECCCCCCCCCCCCCEEEEECCC
T ss_conf             998895624388856485997999997888


No 48 
>>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:)
Probab=30.72  E-value=34  Score=14.59  Aligned_cols=27  Identities=19%  Similarity=0.196  Sum_probs=19.5

Q ss_pred             CEEECCEEEC---CCCCEECCCCEEEEEEC
Q ss_conf             9049989932---86758048988999705
Q gi|254780610|r   50 FISINGMVSK---NPNRKVVPGDSFLITVP   76 (340)
Q Consensus        50 ~V~vnG~~~~---~~~~~l~~gd~I~i~~~   76 (340)
                      .|.|||+.+.   ..++.|+.||.|.+..+
T Consensus        75 ~v~vN~~~v~~~~~~~t~l~~gDeV~i~Pp  104 (114)
T 1wgk_A           75 LVLINDADWELLGELDYQLQDQDSILFIST  104 (114)
T ss_dssp             EEEESSSBHHHHCTTTCBCCSSEEEEEEEC
T ss_pred             EEEECCCEEEECCCCCCCCCCCCEEEEECC
T ss_conf             999758424605686637699799999788


No 49 
>>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:)
Probab=30.07  E-value=29  Score=14.97  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=20.9

Q ss_pred             CEEECCEEECC---CCCEECCCCEEEEEEC
Q ss_conf             90499899328---6758048988999705
Q gi|254780610|r   50 FISINGMVSKN---PNRKVVPGDSFLITVP   76 (340)
Q Consensus        50 ~V~vnG~~~~~---~~~~l~~gd~I~i~~~   76 (340)
                      .|.|||+.++.   .++.|+.||+|.+..+
T Consensus        57 ~v~vNg~~v~~~~~~~t~l~~gD~V~ilPp   86 (90)
T 2g1e_A           57 IILVNGNNITSMKGLDTEIKDDDKIDLFPP   86 (90)
T ss_dssp             EEEESSSBGGGTCSSSCBCCTTCEEEEECC
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCEEEEECC
T ss_conf             457703000234465653799999999688


No 50 
>>2c45_A Aspartate 1-decarboxylase precursor; double-PSI beta barrel, lyase, zymogen, pantothenate biosynthesis, pyruvate; 2.99A {Mycobacterium tuberculosis} (A:)
Probab=29.63  E-value=25  Score=15.37  Aligned_cols=22  Identities=41%  Similarity=0.726  Sum_probs=9.6

Q ss_pred             CCCEEECCEEECCCCCEECCCCEEEE
Q ss_conf             59904998993286758048988999
Q gi|254780610|r   48 NGFISINGMVSKNPNRKVVPGDSFLI   73 (340)
Q Consensus        48 ~G~V~vnG~~~~~~~~~l~~gd~I~i   73 (340)
                      +|.|.+||.-    .+.+++||.|.+
T Consensus        66 Sg~I~lNGAA----Ar~~~~GD~vII   87 (139)
T 2c45_A           66 SGVIGINGAA----AHLVHPGDLVIL   87 (139)
T ss_dssp             TTCEEEESST----TTTSCTTCEEEE
T ss_pred             CCEEEECCHH----HEECCCCCEEEE
T ss_conf             7448754834----403488999999


No 51 
>>2wyh_A Alpha-mannosidase; hydrolase, glycosidase, glycoside hydrolase; 1.90A {Streptococcus pyogenes} PDB: 2wyi_A* (A:41-112)
Probab=28.94  E-value=37  Score=14.41  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=21.0

Q ss_pred             CCC--HHHHHHHHCCCCCCHHHHHHHHHCCCEEE
Q ss_conf             875--78999987176889899999998599049
Q gi|254780610|r   22 EGR--IDRWLATSLKEQFSRSYVKILILNGFISI   53 (340)
Q Consensus        22 g~R--LD~~L~~~l~~~~sR~~i~kli~~G~V~v   53 (340)
                      ||.  ||.||.-+ |.  -+.+++++|++|++.|
T Consensus        35 GQt~ileDYL~~~-Pe--~~eri~klv~~grL~i   65 (72)
T 2wyh_A           35 GQTIILDDYLKVR-PE--REPEIRQAIASGKLRI   65 (72)
T ss_dssp             TBTHHHHHHHHHC-GG--GHHHHHHHHHTTSEEC
T ss_pred             CHHHHHHHHHHCC-HH--HHHHHHHHHHCCCEEE
T ss_conf             1899999998659-99--9999999998698848


No 52 
>>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238)
Probab=28.92  E-value=37  Score=14.41  Aligned_cols=26  Identities=23%  Similarity=0.238  Sum_probs=15.8

Q ss_pred             CCCEEECCEEECCCCCEECCCCEEEE
Q ss_conf             59904998993286758048988999
Q gi|254780610|r   48 NGFISINGMVSKNPNRKVVPGDSFLI   73 (340)
Q Consensus        48 ~G~V~vnG~~~~~~~~~l~~gd~I~i   73 (340)
                      +|-+.+||+++....+.|+.||+|.+
T Consensus        54 ngt~~~n~~~~~~~~~~L~~Gd~i~i   79 (158)
T 1wv3_A           54 NTDVYINYELQEQLTNKAYIGDHIYV   79 (158)
T ss_dssp             TCCEEETTEECCSSEEEEETTCEEEE
T ss_pred             CCCEEECCEEEECCEEECCCCCEEEE
T ss_conf             98699878997255043048999999


No 53 
>>1pqh_A Aspartate 1-decarboxylase; pyruvoyl dependent decarboxylase, protein SELF-processing, lyase; 1.29A {Escherichia coli} (A:)
Probab=27.40  E-value=21  Score=15.82  Aligned_cols=15  Identities=27%  Similarity=0.468  Sum_probs=10.8

Q ss_pred             CCCCCEEEEEECCCH
Q ss_conf             014402789962401
Q gi|254780610|r   93 LYEDDDIIVINKPAG  107 (340)
Q Consensus        93 lyED~~llvinKPaG  107 (340)
                      |.+-+.+.|+|.-.|
T Consensus        55 i~~~E~V~V~Nv~NG   69 (143)
T 1pqh_A           55 ILENEAIDIWNVTNG   69 (143)
T ss_dssp             CCTTCEEEEEETTTC
T ss_pred             CCCCCEEEEEECCCC
T ss_conf             988988999999999


No 54 
>>3huh_A Virulence protein STM3117; structural genomics, nysgrc, target 13955A1BCT15P1, dioxygenase, PSI-2, protein structure initiative; 1.50A {Salmonella enterica subsp} PDB: 3hnq_A (A:78-152)
Probab=25.95  E-value=41  Score=14.08  Aligned_cols=49  Identities=10%  Similarity=0.209  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHCCEEECCC--CCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCHHH
Q ss_conf             999999987097860415--4477554443345701355440798044321000424688976899984997899
Q gi|254780610|r  258 HQIRVHMAHKGNPLIGDP--LYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDM  330 (340)
Q Consensus       258 HQIRvhla~lG~PIvGD~--~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~~~  330 (340)
                      .+...||++.|.+|++..  .+|....                       ..++-|..| .|-.++|.++.|..-
T Consensus        21 d~~~~~L~~~Gv~i~~~p~~~~~~~~~-----------------------~~siYf~DP-dG~~iEl~~~~~~~~   71 (75)
T 3huh_A           21 NDVVSEILQAGISIVEGPVERTGATGE-----------------------IMSIYIRDP-DGNLIEISQYVEGHH   71 (75)
T ss_dssp             HHHHHHHHHTTCCCSEEEEEEEETTEE-----------------------EEEEEEECT-TCCEEEEEEC-----
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCC-----------------------EEEEEEECC-CCCEEEEEEECCCCC
T ss_conf             899999987186522387332268886-----------------------899999999-999899988889876


No 55 
>>1wxq_A GTP-binding protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.60A {Pyrococcus horikoshii OT3} (A:317-397)
Probab=25.87  E-value=19  Score=16.13  Aligned_cols=25  Identities=8%  Similarity=-0.078  Sum_probs=15.4

Q ss_pred             CEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             90499899328675804898899970
Q gi|254780610|r   50 FISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        50 ~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      .+++||+++ ..++.|..||.|.+..
T Consensus        54 ~~~~~g~~v-~~d~~L~dgDvV~Iit   78 (81)
T 1wxq_A           54 INARTKRRV-GEDYELQFNDIVKIVS   78 (81)
T ss_dssp             EETTTCSBC-CTTCCCCTTEEEEEEE
T ss_pred             EECCCCEEE-CCCCEECCCCEEEEEE
T ss_conf             866776285-6984856898899995


No 56 
>>2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A (A:)
Probab=23.02  E-value=47  Score=13.75  Aligned_cols=35  Identities=26%  Similarity=0.337  Sum_probs=27.3

Q ss_pred             HHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEE
Q ss_conf             99999985990499899328675804898899970
Q gi|254780610|r   41 YVKILILNGFISINGMVSKNPNRKVVPGDSFLITV   75 (340)
Q Consensus        41 ~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~   75 (340)
                      ..-.+|++|.=+|-++.....-..++.||.|.+.-
T Consensus        10 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~n   44 (109)
T 2z0t_A           10 EYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEG   44 (109)
T ss_dssp             HHHHHHHTTSCCEEEEECCTTGGGCCTTCEEEEGG
T ss_pred             HHHHHHHCCCCEEEEECCHHHHHHCCCCCEEEEEC
T ss_conf             05799876998899982776786289999999947


No 57 
>>3cuz_A MSA, malate synthase A; TIM barrel, cytoplasm, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.04A {Escherichia coli} PDB: 3cv1_A 3cv2_A* (A:399-532)
Probab=22.41  E-value=20  Score=15.94  Aligned_cols=23  Identities=22%  Similarity=0.079  Sum_probs=15.9

Q ss_pred             CCHHHHHHHHHCCCEEECCEEEC
Q ss_conf             89899999998599049989932
Q gi|254780610|r   37 FSRSYVKILILNGFISINGMVSK   59 (340)
Q Consensus        37 ~sR~~i~kli~~G~V~vnG~~~~   59 (340)
                      +||+|+-+|++.|...-||++++
T Consensus        54 ISR~QlWQWi~hg~~l~dG~~vt   76 (134)
T 3cuz_A           54 ISRTSIWQWIHHQKTLSNGKPVT   76 (134)
T ss_dssp             HHHHHHHHHHHTTCBCTTSCBCC
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             99999999997677778884726


No 58 
>>2pbt_A AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A* (A:)
Probab=20.95  E-value=35  Score=14.49  Aligned_cols=42  Identities=12%  Similarity=0.292  Sum_probs=32.9

Q ss_pred             HHCCCCCEEEEEECCCHHHCCCCCCCCC-CCCHHHHHHHHCCC
Q ss_conf             2101440278996240111045678754-21002222221024
Q gi|254780610|r   91 DILYEDDDIIVINKPAGLVVHPAPGNWT-GTLVNALLYHCHNN  132 (340)
Q Consensus        91 ~IlyED~~llvinKPaGl~vhp~~~~~~-~tl~~~l~~~~~~~  132 (340)
                      -|++.|+.+|++....|.-..|++.... .|..+++.+.+.++
T Consensus         9 ~vv~~~~~vLl~~r~~g~w~~PgG~ie~gE~~~~aa~REl~EE   51 (134)
T 2pbt_A            9 GVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEE   51 (134)
T ss_dssp             EEEEETTEEEEEECTTSCEECCEEECCTTCCHHHHHHHHHHHH
T ss_pred             EEEEECCEEEEEEECCCCEECCEEEECCCCCHHHHHHHHHHHE
T ss_conf             9999899999999579988998715479989999975532120


No 59 
>>3cux_A Malate synthase; TIM barrel, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.70A {Bacillus anthracis} (A:395-528)
Probab=20.54  E-value=29  Score=15.05  Aligned_cols=23  Identities=22%  Similarity=0.049  Sum_probs=13.5

Q ss_pred             CCHHHHHHHHHCCCEEE-CCEEEC
Q ss_conf             89899999998599049-989932
Q gi|254780610|r   37 FSRSYVKILILNGFISI-NGMVSK   59 (340)
Q Consensus        37 ~sR~~i~kli~~G~V~v-nG~~~~   59 (340)
                      +||+|+-+||+.|.++. ||++++
T Consensus        54 ISR~QiWQWi~hg~~~~ddG~~vt   77 (134)
T 3cux_A           54 ISRAQVWQWIRHEGGKLNDGRNIT   77 (134)
T ss_dssp             HHHHHHHHHHHCTTCBCTTSCBCC
T ss_pred             HHHHHHHHHHHCCCEECCCCCCCC
T ss_conf             999999999972681446764427


Done!