Query         gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 354
No_of_seqs    197 out of 4149
Neff          8.4 
Searched_HMMs 33803
Date          Wed Jun  1 12:51:31 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780406.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 7.8E-41 2.8E-45  276.6  -2.6  244    1-244     4-278 (325)
  2 >2gml_A Ribosomal large subuni 100.0 5.9E-33 1.7E-37  227.0  11.2  181   60-246     1-181 (237)
  3 >1ksk_A Ribosomal small subuni 100.0 2.1E-32 6.3E-37  223.5  12.4  174   70-245     2-176 (176)
  4 >3dh3_A Ribosomal large subuni 100.0 1.4E-31 4.1E-36  218.3  12.9  170   71-246     2-171 (227)
  5 >2oml_A Ribosomal large subuni 100.0   5E-31 1.5E-35  214.8  12.6  168   69-238     7-189 (189)
  6 >1vio_A Ribosomal small subuni 100.0 1.3E-30 3.9E-35  212.2  13.6  178   69-248     1-179 (186)
  7 >1v9k_A Ribosomal large subuni  99.9 8.4E-27 2.5E-31  188.2  -2.3  172   69-240     5-195 (228)
  8 >2i82_A Ribosomal large subuni  99.9 6.8E-25   2E-29  176.2  -1.3  169   57-225     2-186 (217)
  9 >2olw_A Ribosomal large subuni  99.8 1.2E-20 3.6E-25  149.4   1.8  102   28-139     2-103 (119)
 10 >1dm9_A Hypothetical 15.5 KD p  99.8 1.5E-19 4.4E-24  142.6   4.3  122    6-129     1-132 (133)
 11 >2olw_A Ribosomal large subuni  99.5   6E-14 1.8E-18  107.3  10.0   83  139-221     1-98  (98)
 12 >1vio_A Ribosomal small subuni  99.5 2.7E-14 8.1E-19  109.4   6.2   56   13-68      2-57  (57)
 13 >1ksk_A Ribosomal small subuni  99.5 4.5E-14 1.3E-18  108.1   6.3   57   12-68      2-58  (58)
 14 >3dh3_A Ribosomal large subuni  99.4 3.8E-13 1.1E-17  102.2   7.3   61   10-71      3-63  (63)
 15 >1p9k_A ORF, hypothetical prot  99.2 1.5E-12 4.4E-17   98.5   0.3   65    5-69     12-77  (79)
 16 >3hp7_A Hemolysin, putative; s  99.2 1.3E-11 3.8E-16   92.6   3.3   62    8-69      1-65  (65)
 17 >2k6p_A Uncharacterized protei  99.1 1.1E-11 3.1E-16   93.1  -1.3   76   14-90      1-91  (92)
 18 >2vqe_D 30S ribosomal protein   98.8 7.8E-09 2.3E-13   75.0   6.5   53   15-67      1-54  (94)
 19 >2cqj_A BRMS2, U3 small nucleo  98.5   7E-08 2.1E-12   69.1   3.5   56   11-66      5-63  (71)
 20 >1h3f_A Tyrosyl-tRNA synthetas  98.5 3.9E-07 1.1E-11   64.4   6.3   52   12-63     18-70  (83)
 21 >3i1m_D 30S ribosomal protein   98.4 1.8E-07 5.4E-12   66.4   3.2   51   15-65      1-52  (94)
 22 >2jan_A Tyrosyl-tRNA synthetas  98.3   2E-07 5.8E-12   66.2   2.6   70    9-78      7-77  (88)
 23 >3bbn_D Ribosomal protein S4;   98.3   3E-07   9E-12   65.0   2.6   53   14-66      8-61  (120)
 24 >2aus_C Pseudouridine synthase  98.2 9.8E-06 2.9E-10   55.5   9.2  157   73-246    16-195 (215)
 25 >1s1h_D 40S ribosomal protein   98.1 2.2E-06 6.6E-11   59.6   3.4   54   13-66      8-62  (99)
 26 >2apo_A Probable tRNA pseudour  97.9 0.00011 3.3E-09   48.9   9.7  156   73-245    16-193 (216)
 27 >1jil_A Tyrrs, tyrosyl-tRNA sy  97.4 2.9E-05 8.7E-10   52.5   0.0   69    9-77    102-171 (174)
 28 >2ts1_A Tyrosyl-tRNA synthetas  97.0 0.00013   4E-09   48.4   0.0   64   10-73    103-167 (174)
 29 >3kbg_A 30S ribosomal protein   96.0   0.012 3.6E-07   36.0   4.9   42   26-67     22-63  (81)
 30 >1c05_A Ribosomal protein S4 d  91.5    0.16 4.7E-06   29.0   3.1   26   40-65      2-27  (83)
 31 >1k8w_A TRNA pseudouridine syn  90.7     1.2 3.4E-05   23.6   8.0   66  159-226    72-145 (145)
 32 >2v9k_A Uncharacterized protei  87.8     1.9 5.5E-05   22.3   7.4   81  142-224     2-114 (120)
 33 >1sgv_A TRNA pseudouridine syn  81.3     0.3 8.8E-06   27.3  -0.3   47   72-126     5-53  (87)
 34 >1r3e_A TRNA pseudouridine syn  79.7    0.37 1.1E-05   26.7  -0.3   46   74-127     4-51  (92)
 35 >1k8w_A TRNA pseudouridine syn  78.9     0.4 1.2E-05   26.5  -0.3   48   71-126    23-72  (108)
 36 >2exu_A Transcription initiati  72.9       3 8.8E-05   21.0   2.8   47  115-161    43-90  (91)
 37 >1c05_A Ribosomal protein S4 d  64.7     7.2 0.00021   18.6   3.4   25   14-38     30-55  (55)
 38 >3gmg_A Uncharacterized protei  47.4      13 0.00039   16.9   2.4   31   39-69     68-102 (170)
 39 >1tke_A Threonyl-tRNA syntheta  46.2      14 0.00041   16.8   2.3   23   39-62     37-59  (63)
 40 >2r9q_A AGR_C_764P, 2'-deoxycy  44.6      20 0.00059   15.8   3.0   39   23-61     10-52  (174)
 41 >2kmm_A Guanosine-3',5'-BIS(di  44.3      18 0.00052   16.1   2.6   23   39-62     38-60  (73)
 42 >2z0t_A Putative uncharacteriz  38.1     7.7 0.00023   18.4  -0.0   39   30-68     10-48  (109)
 43 >2q5w_D Molybdopterin converti  36.9      26 0.00077   15.1   3.0   25   37-62     46-70  (77)
 44 >1qf6_A THRRS, threonyl-tRNA s  36.2      14 0.00041   16.8   1.1   23   39-62     37-59  (63)
 45 >1fm0_D Molybdopterin converti  34.8      28 0.00083   14.9   3.7   30   32-62     44-74  (81)
 46 >1rws_A Hypothetical protein P  34.4      13  0.0004   16.9   0.7   43   11-62     28-70  (77)
 47 >1wv3_A Similar to DNA segrega  32.3      31 0.00092   14.6   6.2   39   37-75     54-92  (158)
 48 >2qjl_A URM1, ubiquitin-relate  31.5      32 0.00094   14.5   2.7   24   39-62     66-92  (99)
 49 >3dwg_C 9.5 kDa culture filtra  31.5      32 0.00094   14.5   2.7   24   39-62     60-86  (93)
 50 >2g1e_A Hypothetical protein T  31.4      24 0.00071   15.3   1.6   26   37-62     55-83  (90)
 51 >3hvz_A Uncharacterized protei  30.6      33 0.00098   14.4   2.7   22   40-62     44-65  (78)
 52 >3h7h_A Transcription elongati  30.2      34 0.00099   14.4   2.5   39  114-152    56-95  (95)
 53 >1vjk_A Molybdopterin converti  30.1      27  0.0008   15.0   1.7   24   38-62     68-91  (98)
 54 >1nyr_A Threonyl-tRNA syntheta  28.6      21 0.00062   15.7   0.9   23   39-62     39-61  (65)
 55 >2ff4_A Probable regulatory pr  27.0      38  0.0011   14.0   4.0   30   38-68     59-88  (99)
 56 >1xne_A Hypothetical protein P  25.6      17  0.0005   16.3  -0.0   39   30-68     11-49  (113)
 57 >1wwt_A Threonyl-tRNA syntheta  25.1      31 0.00092   14.6   1.3   22   40-62     49-70  (88)
 58 >1h6l_A 3-phytase; hydrolase,   24.7      42  0.0012   13.8   3.1   33   96-129    53-86  (196)
 59 >1v8c_A MOAD related protein;   23.6      44  0.0013   13.6   2.9   24   39-62     54-80  (84)
 60 >1mio_A Nitrogenase molybdenum  23.2      45  0.0013   13.6   2.6   24  192-215    37-60  (107)
 61 >2k9x_A Tburm1, uncharacterize  22.0      31 0.00093   14.6   0.8   23   40-62     70-95  (110)
 62 >3f7f_A Nucleoporin NUP120; nu  22.0      40  0.0012   13.9   1.3   37   97-134    18-54  (56)
 63 >1wln_A Afadin; beta sandwich,  20.7      50  0.0015   13.3   2.6   10  107-116    36-45  (120)
 64 >1wgk_A Riken cDNA 2900073H19   20.3      28 0.00084   14.8   0.3   12  140-151    69-80  (114)

No 1  
>>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:)
Probab=100.00  E-value=7.8e-41  Score=276.59  Aligned_cols=244  Identities=17%  Similarity=0.103  Sum_probs=203.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE-------------
Q ss_conf             986534466677344788999886-877899999998698699999924068780799979999989-------------
Q gi|254780406|r    1 MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-------------   66 (354)
Q Consensus         1 ~~~~~~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~-------------   66 (354)
                      |+....+.++..++||++||+..+ .|||++++++|++|+|+|||+.+..+...+...+.+.+....             
T Consensus         4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (325)
T 1v9f_A            4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPL   83 (325)
T ss_dssp             ------------------------------------------------------------------------CCCCCCCC
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCCCCCCCCCCCCC
T ss_conf             89999989764886699999986686799999999986998999999178320625898997325433222333344541


Q ss_pred             CCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC------CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--C
Q ss_conf             2255643896027875156314433336442101102------3432002665543323202223676410001234--4
Q gi|254780406|r   67 LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--S  138 (354)
Q Consensus        67 i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~  138 (354)
                      ...+++..|+++|||.|+.|+..+.....++...+..      ....+++|||||++||||||||++++++++|..+  .
T Consensus        84 ~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~  163 (325)
T 1v9f_A           84 DIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQR  163 (325)
T ss_dssp             CEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHT
T ss_pred             CEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHC
T ss_conf             12510110578707888654898777888632321134443333342146532588986514664025889999987501


Q ss_pred             CCCEEEEEEEECCCCCHHHHHHHHHHHHCC---------CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC
Q ss_conf             574047752112455646788874000008---------76750343036402688079999995184289999999839
Q gi|254780406|r  139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN  209 (354)
Q Consensus       139 ~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~---------~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g  209 (354)
                      ..+.|+|++.|.|.+..+............         .+......+.+.......+++++.+.|||+||||+||+++|
T Consensus       164 ~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~sl~~~~~~TGR~HQIR~hla~~G  243 (325)
T 1v9f_A          164 REITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHIT  243 (325)
T ss_dssp             TCSEEEEEEEEESCCCCCEEEECCEEECSSCTTCEEECTTSBCCEEEEEEEEECSSEEEEEEEESCCCTTHHHHHHHHTT
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHC
T ss_conf             21012423430135474566235533576665305876887157899898653388457999977883179999999839


Q ss_pred             CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHH
Q ss_conf             86868897587054518755474886799999875
Q gi|254780406|r  210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ  244 (354)
Q Consensus       210 ~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l  244 (354)
                      ++|+.+++.++|++.+++|+.|+|++++..+...|
T Consensus       244 ~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~L  278 (325)
T 1v9f_A          244 HPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQAL  278 (325)
T ss_dssp             CCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSE
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHH
T ss_conf             97668777898554544331667776515864346


No 2  
>>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:)
Probab=100.00  E-value=5.9e-33  Score=226.99  Aligned_cols=181  Identities=24%  Similarity=0.389  Sum_probs=160.9

Q ss_pred             EEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             99999892255643896027875156314433336442101102343200266554332320222367641000123445
Q gi|254780406|r   60 IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST  139 (354)
Q Consensus        60 v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~  139 (354)
                      |.||+++-..+++..|+++|||+|+.|+..+.. ..++++.+... .++++|||||++||||||||+|++.+++++.+..
T Consensus         1 v~~~~~~~ii~ed~~~ivvnKP~G~~~~~~~~~-~~~~~~~l~~~-~~~~~vhRLD~~TSGlll~a~~~~~~~~~~~~~~   78 (237)
T 2gml_A            1 MGSSHHHHHHGSDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNHS-KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGN   78 (237)
T ss_dssp             ------------CCCEEEEEECTTCBCCSSSSC-SSBHHHHSCCS-SCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC-CCCCHHHCCCC-CCEEECCCCCCCCCCCEEEECCHHHHHHHHHHCC
T ss_conf             985555555685239999979993897228999-99744215764-5611412468888885898416688888765313


Q ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             74047752112455646788874000008767503430364026880799999951842899999998398686889758
Q gi|254780406|r  140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS  219 (354)
Q Consensus       140 ~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~  219 (354)
                      .++|+|++.|.|.+..+.......+..........+...    ....+++++.+.+||+||||.||+++|++|+++++++
T Consensus        79 ~i~K~Y~a~v~G~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~v~~~~~tGR~HQIR~h~~~~G~pI~gD~~y~  154 (237)
T 2gml_A           79 DHEKEYLVTVDKPITEEFIRGXSAGVPILGTVTKKCKVK----KEAPFVFRITLVQGLNRQIRRXCEHFGYEVKKLERTR  154 (237)
T ss_dssp             HSCEEEEEEESSCCCHHHHHHHSSCCEETTEECCCCEEE----EEETTEEEEEECCCSTTHHHHHHHHTTCCEEEEEEEE
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHCCCEECCEEEECHHHC----CCCCEEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEE
T ss_conf             551488778526799999999975988777574200003----5665499999816886199999998699766699999


Q ss_pred             ECCEECCCCCCCCEEECCHHHHHHHHH
Q ss_conf             705451875547488679999987532
Q gi|254780406|r  220 YGPFQLGTLLAGSTREVSKKILREQLG  246 (354)
Q Consensus       220 ~G~~~l~~L~~G~~r~l~~~e~~~l~~  246 (354)
                      ++++.+++|++|+|++|+..|+..+..
T Consensus       155 ~~~~~~~~l~~g~~~~l~~~e~~~~~~  181 (237)
T 2gml_A          155 IXNVSLSGIPLGEWRDLTDDELIDLFK  181 (237)
T ss_dssp             ETTEECTTCCTTCEEECCHHHHHHHHT
T ss_pred             ECCEEECCCCCCCEEECCHHHHHHHHH
T ss_conf             888880897997838999999999998


No 3  
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234)
Probab=100.00  E-value=2.1e-32  Score=223.47  Aligned_cols=174  Identities=24%  Similarity=0.368  Sum_probs=158.9

Q ss_pred             CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             56438960278751563144333364421011023432002665543323202223676410001234457404775211
Q gi|254780406|r   70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF  149 (354)
Q Consensus        70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v  149 (354)
                      ||+..++++|||.|+.|+..+.....++.........++++|||||++|||||+||+|++.+.++.+....++|+|.+.|
T Consensus         2 Yed~~~ivvnKP~gl~~~~~~~~~~~~~~~l~~~~~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~~~~~~~k~y~~~v   81 (176)
T 1ksk_A            2 QHGPRYFXLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLXTDDGQWSHRITSPRHHCEKTYLVTL   81 (176)
T ss_dssp             CCCCCEEEEEECTTCBSSSSCSSSCBGGGGCCCTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEEE
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCHHHHHHHHHHHCCCCEEEEECC
T ss_conf             57857999989998505665554431000012444563656013885557558860586888877554238847998446


Q ss_pred             CCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CC
Q ss_conf             24556467888740000087675034303640268807999999518428999999983986868897587054518-75
Q gi|254780406|r  150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL  228 (354)
Q Consensus       150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L  228 (354)
                      .+.+..........++..+...........  .....+|+++.+.+||+||||+||+++|++|..+.+.++|++.+. .|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~s~~~~~~~tGr~HQIR~h~~~~g~pI~gD~~Y~~~~~~~~~~l  159 (176)
T 1ksk_A           82 ESPVADDTAEQFAKGVQLHNEKDLTKPAVL--EVITPTQVRLTISEGRYHQVKRXFAAVGNHVVELHRERIGGITLDADL  159 (176)
T ss_dssp             SSCCCTTHHHHHHHCCCCTTCSSCCCCCEE--EEEETTEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTTC
T ss_pred             CCCCCHHHHHHHHEEEEECCCEEEEEEEEE--ECCCCCEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCC
T ss_conf             788887897775302563895755534684--037996899996359839999999987997989999998865047989


Q ss_pred             CCCCEEECCHHHHHHHH
Q ss_conf             54748867999998753
Q gi|254780406|r  229 LAGSTREVSKKILREQL  245 (354)
Q Consensus       229 ~~G~~r~l~~~e~~~l~  245 (354)
                      +.|+||+|+++|++.||
T Consensus       160 ~l~~~r~l~~~e~~~ll  176 (176)
T 1ksk_A          160 APGEYRPLTEEEIASVV  176 (176)
T ss_dssp             CTTCEEECCHHHHTTCC
T ss_pred             CCCCEEECCHHHHHHHC
T ss_conf             99751599999999659


No 4  
>>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=99.97  E-value=1.4e-31  Score=218.34  Aligned_cols=170  Identities=25%  Similarity=0.425  Sum_probs=151.1

Q ss_pred             CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             64389602787515631443333644210110234320026655433232022236764100012344574047752112
Q gi|254780406|r   71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH  150 (354)
Q Consensus        71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~  150 (354)
                      |+..+|++|||.|+.|+..+.. ..++.+.+... .++++|||||++||||||||+|+++++.|+++...++|+|++.|.
T Consensus         2 Ed~~~ivinKP~Gl~~~~~~~~-~~~l~~~l~~~-~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~   79 (227)
T 3dh3_A            2 EDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNHS-KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVD   79 (227)
T ss_dssp             GGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTCS-SCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGCCCEEEEEEES
T ss_pred             CCEEEEECCCCCCEEECCCCCC-CCCCHHHCCCC-CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCEEEC
T ss_conf             3113564366652120333477-77501101344-431224656767631489943987998887631244322112760


Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC
Q ss_conf             45564678887400000876750343036402688079999995184289999999839868688975870545187554
Q gi|254780406|r  151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA  230 (354)
Q Consensus       151 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~  230 (354)
                      |.++.+....+..+..........+.    ......+|+++.+.+|++||||+||+++|++|+.+.++++|++.|.+|+.
T Consensus        80 G~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~tGr~hQIR~h~a~~g~pI~gd~~y~~~~~~l~~l~~  155 (227)
T 3dh3_A           80 KPITEEFIRGMSAGVPILGTVTKKCK----VKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPL  155 (227)
T ss_dssp             SCCCHHHHHHHHTCCBCSSSBCCCCE----EEECSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECTTCCT
T ss_pred             CCCCHHHHHHHHCCCEECCEEEEEEE----EEECCCCEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC
T ss_conf             57999999999759984565744257----75226725899925885259999999879967669999987877489799


Q ss_pred             CCEEECCHHHHHHHHH
Q ss_conf             7488679999987532
Q gi|254780406|r  231 GSTREVSKKILREQLG  246 (354)
Q Consensus       231 G~~r~l~~~e~~~l~~  246 (354)
                      |+||+|+..|+..+..
T Consensus       156 g~~r~l~~~e~~~~~~  171 (227)
T 3dh3_A          156 GEWRDLTDDELIDLFK  171 (227)
T ss_dssp             TCEEECCHHHHHHHHH
T ss_pred             CCEEECCHHHHHHHHH
T ss_conf             7738899999999998


No 5  
>>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:)
Probab=99.97  E-value=5e-31  Score=214.82  Aligned_cols=168  Identities=30%  Similarity=0.527  Sum_probs=149.3

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             55643896027875156314433336442101102343200266554332320222367641000123445740477521
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR  148 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~  148 (354)
                      .+++..|+++|||.|+.|+..+.....++...+..  .++++|||||++|+||||||+|+++++.|+.+...+.|+|.+.
T Consensus         7 l~ed~~~ivinKP~g~~~~~~~~~~~~~~~~~l~~--~~l~~vhRLD~~tsGlll~a~~~~~~~~l~~~~~~i~k~Y~a~   84 (189)
T 2oml_A            7 ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQ   84 (189)
T ss_dssp             -CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCCC--SSCEESSCCCTTCEEEEEEESCHHHHHHHHSTTSCCCEEEEEE
T ss_pred             CCCCCEEEEEECCCCEEEECCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCEEEEECCCHHHHHCCCCCEEEEEEEEEE
T ss_conf             88998899998999838607799888658896371--2534731026120007999325302221031230377899999


Q ss_pred             ECCCCCHHHHHHHHHHHHCCCEEEEC---------------CCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE
Q ss_conf             12455646788874000008767503---------------430364026880799999951842899999998398686
Q gi|254780406|r  149 FHGQVDQDKLNLLKKGIVIQGICYGD---------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN  213 (354)
Q Consensus       149 v~~~~~~~~~~~~~~g~~~~~~~~~~---------------~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~  213 (354)
                      |.+.+..+....+..+....+.....               ..+.........+++.+++.+||+||||+||+++|++|.
T Consensus        85 v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~tGr~hQIR~hl~~lg~pIv  164 (189)
T 2oml_A           85 VEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL  164 (189)
T ss_dssp             EESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CTTSCEEEEEEEESCCCTTHHHHHHHHTTCCEE
T ss_pred             EECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEEEECCCCEEEEEEECCCHHHHHHHHHHCCCEEE
T ss_conf             93279989999986494507851576579995356641024557888740565079999945977999999998699698


Q ss_pred             EEEEEEECCEECCCCCCCCEEECCH
Q ss_conf             8897587054518755474886799
Q gi|254780406|r  214 RLIRISYGPFQLGTLLAGSTREVSK  238 (354)
Q Consensus       214 ~L~Rv~~G~~~l~~L~~G~~r~l~~  238 (354)
                      .+.++++|++.+++|++|+||+||.
T Consensus       165 gD~~Y~~~~~~~~~l~l~~~R~lt~  189 (189)
T 2oml_A          165 RLIRYAMGDYSLDNLANGEWREVTD  189 (189)
T ss_dssp             EEEEEEETTEECTTCCTTCEEECCC
T ss_pred             EEEEEEECCEECCCCCCCCCEECCC
T ss_conf             9899999998507889988377979


No 6  
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243)
Probab=99.97  E-value=1.3e-30  Score=212.17  Aligned_cols=178  Identities=24%  Similarity=0.333  Sum_probs=161.3

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEE
Q ss_conf             55643896027875156314433336442101102343200266554332320222367641000123445740477521
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR  148 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~  148 (354)
                      .+|+..||++|||.|+.|+..+.....++.........++++|+|||++||||||||+|++.+.+++.+...++|+|.+.
T Consensus         1 ~yed~~~ivinKP~gl~~~~~~~~~~~~~~~l~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~k~y~~~   80 (186)
T 1vio_A            1 WIEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVT   80 (186)
T ss_dssp             SSCCCCEEEEEECTTCBSSCCC--CCBGGGGSCTTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSCCCEEEEEE
T ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCCEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             22221035540258864333443201454200245331365402124012213787417753200011124552011259


Q ss_pred             ECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-C
Q ss_conf             124556467888740000087675034303640268807999999518428999999983986868897587054518-7
Q gi|254780406|r  149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-T  227 (354)
Q Consensus       149 v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~  227 (354)
                      |.+.+..+.......++...+..........  .....+++++.+.+||+||||+||+++|++|.+.+++++|++.++ .
T Consensus        81 v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~tGr~hQIR~h~a~lg~pIvgD~~yg~~~~~~~~~  158 (186)
T 1vio_A           81 LADPVEENYSAACAEGILLRGEKEPTKPAKL--EILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDES  158 (186)
T ss_dssp             ESSCCCTTHHHHHHHCCCCTTCSSCCCCCEE--EECSSSEEEEEESCCCTTHHHHHHHHTTCCEEEEEEEEETTEECCTT
T ss_pred             EEEECCHHHHHHHHCCEECCCCCCCEEEEEE--CCCCCCEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEECCCCCCCC
T ss_conf             9851204478898536561683010233220--13568448988505760799999998599793889999887247999


Q ss_pred             CCCCCEEECCHHHHHHHHHHH
Q ss_conf             554748867999998753210
Q gi|254780406|r  228 LLAGSTREVSKKILREQLGPH  248 (354)
Q Consensus       228 L~~G~~r~l~~~e~~~l~~~~  248 (354)
                      |+.|+||+|++.|+..+....
T Consensus       159 l~~g~~r~l~~~~l~~~~l~~  179 (186)
T 1vio_A          159 LEEGEYRPLTQSEIEKLVEGG  179 (186)
T ss_dssp             CCTTCEEECCHHHHHHTC---
T ss_pred             CCCCCEEECCHHHHHHHHHCC
T ss_conf             999762599999999999579


No 7  
>>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:)
Probab=99.91  E-value=8.4e-27  Score=188.22  Aligned_cols=172  Identities=14%  Similarity=0.074  Sum_probs=140.2

Q ss_pred             CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEE
Q ss_conf             556438960278751563144333364421011023--432002665543323202223676410001234--4574047
Q gi|254780406|r   69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV  144 (354)
Q Consensus        69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~  144 (354)
                      .+++..|+++|||.|+.|+..+.....++++.+...  ..++++|||||++||||||+|+|+++++.|.++  ...+.|+
T Consensus         5 iyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~a~~l~~~~~~~~v~K~   84 (228)
T 1v9k_A            5 XYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKD   84 (228)
T ss_dssp             EEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEE
T ss_pred             EEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCC
T ss_conf             99689999999999986389989953699999986778765316640464322136752357999999999874034543


Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC------------CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEE
Q ss_conf             752112455646788874000008------------76750343036402688079999995184289999999839868
Q gi|254780406|r  145 YRVRFHGQVDQDKLNLLKKGIVIQ------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV  212 (354)
Q Consensus       145 Y~v~v~~~~~~~~~~~~~~g~~~~------------~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V  212 (354)
                      |++.|.+.++.........+....            +.......+.........+++++.+.+||+||||.||+++|++|
T Consensus        85 Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGR~HQIR~h~a~~g~PI  164 (228)
T 1v9k_A           85 YLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPI  164 (228)
T ss_dssp             EEEEEESCCCTTCCEECCCEEEEECTTSCEEEEECTTSBCCCEEEEEEEECSSEEEEEEEESSCCTTHHHHHHHHTTCCB
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHCCCCCCEEEEECCCCCCCCCEEECHHHHCCCCEEEEEEECCCCHHHHHHHHHHCCCCC
T ss_conf             21034686422357522330000110101555207888422155005553587379999947573578888888549721


Q ss_pred             EEEEEEEECCEECCCCCCCC---EEECCHHH
Q ss_conf             68897587054518755474---88679999
Q gi|254780406|r  213 NRLIRISYGPFQLGTLLAGS---TREVSKKI  240 (354)
Q Consensus       213 ~~L~Rv~~G~~~l~~L~~G~---~r~l~~~e  240 (354)
                      ++.++..++.+.+..++.|+   |+.|...+
T Consensus       165 vgD~~Y~~~~~~~~~~~~~~~~~~~~Lha~~  195 (228)
T 1v9k_A          165 AFDDRYGDREFDRQLTEAGTGLNRLFLHAAA  195 (228)
T ss_dssp             TTCTTTSCHHHHHHHHHTTCCCCSCCEEEEE
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCHHHHHCCC
T ss_conf             3577413000002333202686237887150


No 8  
>>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:)
Probab=99.88  E-value=6.8e-25  Score=176.20  Aligned_cols=169  Identities=13%  Similarity=0.068  Sum_probs=128.5

Q ss_pred             CCEEEECCEECC-CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCC
Q ss_conf             997999998922-55643896027875156314433336442101102-3432002665543323202223676410001
Q gi|254780406|r   57 TDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL  134 (354)
Q Consensus        57 ~d~v~vdg~~i~-~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l  134 (354)
                      +|.+.+++..+. .+++..|+++|||.|+.|+..+.....++...+.. ...++++|||||++||||||||+|+++++.|
T Consensus         2 ~~~~~~~~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~vhRLD~~TSGllllak~~~~~~~l   81 (217)
T 2i82_A            2 ENYNPPQEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAESVHRLDXATSGVIVVALTKAAEREL   81 (217)
T ss_dssp             CCCCCCCSSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHCTTCEESSCCCTTCEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCCCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECHHHHHHH
T ss_conf             88894989995299979989999999998257998877603899976441033222345554210158986031777788


Q ss_pred             CCC--CCCCEEEEEEEECCCCCHHHHHHHHHHH------------HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHH
Q ss_conf             234--4574047752112455646788874000------------00876750343036402688079999995184289
Q gi|254780406|r  135 ELP--STQWLRVYRVRFHGQVDQDKLNLLKKGI------------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE  200 (354)
Q Consensus       135 ~~p--~~~~~k~Y~v~v~~~~~~~~~~~~~~g~------------~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~q  200 (354)
                      .++  ...+.|.|.+.+.+.+............            ...+.......+.........+++++.+.+||+||
T Consensus        82 ~~~~~~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~TGr~HQ  161 (217)
T 2i82_A           82 KRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQ  161 (217)
T ss_dssp             HHHHHTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEEECTTTCBCCEEEEEEEEEETTTEEEEEEEESSCCTTH
T ss_pred             HHHHHHCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCEECCCCCCCCCCEECCCCCCCCCCEEEEEEECCCCHHH
T ss_conf             98765140103689886154466640674101232243322000122476300101011112331047889850262378


Q ss_pred             HHHHHHHCCCEEEEEEEEEECCEEC
Q ss_conf             9999998398686889758705451
Q gi|254780406|r  201 IKKVFEFFNWKVNRLIRISYGPFQL  225 (354)
Q Consensus       201 Irr~~~~~g~~V~~L~Rv~~G~~~l  225 (354)
                      ||+||+++|++|.+..+...+.+.+
T Consensus       162 IR~h~a~lg~PIlgD~~Yg~~~~~~  186 (217)
T 2i82_A          162 LRVHXLALGHPILGDRFYASPEARA  186 (217)
T ss_dssp             HHHHHHHTTCCBTTCTTTSCHHHHH
T ss_pred             HHHHHHHHCCEEECCCCCCCHHHCC
T ss_conf             9999997197681676768855636


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=99.79  E-value=1.2e-20  Score=149.39  Aligned_cols=102  Identities=27%  Similarity=0.419  Sum_probs=91.8

Q ss_pred             HHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCC
Q ss_conf             89999999869869999992406878079997999998922556438960278751563144333364421011023432
Q gi|254780406|r   28 RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR  107 (354)
Q Consensus        28 Rr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~  107 (354)
                      ||+++++|++|+|+|||++|+       ++|.|.++|..|.+ ++..|+++|||.|+.|+..+.....++.+.+..  .+
T Consensus         2 Rr~~~~~i~~G~V~Vng~~v~-------~~d~i~~~~~~I~y-ed~~~ivvnKP~g~~~~~~~~~~~~tl~~~~~~--~~   71 (119)
T 2olw_A            2 RQFIISENTMQKTSFRNHQVK-------RFSSQRSTRRKPEN-QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QG   71 (119)
T ss_dssp             -------------------------------------------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCCC--CS
T ss_pred             CEEEECCCEEECCCCCCCCCC-------CCCCCCCCCCCCCC-CCCEEEEEECCCCEEEECCCCCCCCCHHHHCCC--CC
T ss_conf             536706871421225542212-------05540035568878-998899998999959707799888768896571--26


Q ss_pred             EECCCCCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             00266554332320222367641000123445
Q gi|254780406|r  108 VISVGRLDINTEGLLLLTNDGGLARVLELPST  139 (354)
Q Consensus       108 ~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~  139 (354)
                      +++|||||++||||||||+|+++++.|++|+-
T Consensus        72 l~~vhRLDr~TSGLll~ak~~~~~~~L~~~~~  103 (119)
T 2olw_A           72 VYAAGRLDRDSEGLLVLTNNGALQARLTQPGD  103 (119)
T ss_dssp             CEESSCCCTTCEEEEEEESCHHHHHHHHCTTT
T ss_pred             CEECCCCCCCEEEEEEEECCCHHHHHHHHCCC
T ss_conf             34753114312006998436056545311038


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=99.77  E-value=1.5e-19  Score=142.56  Aligned_cols=122  Identities=13%  Similarity=0.060  Sum_probs=91.3

Q ss_pred             CCCCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE--CCEECCCCCCEEEEECCCCC
Q ss_conf             446667734478899988687-789999999869869999992406878079997999--99892255643896027875
Q gi|254780406|r    6 IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYHKPI   82 (354)
Q Consensus         6 ~~~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v--dg~~i~~~~~~~~~~~~KP~   82 (354)
                      ++++...++||||||+.+++| ||++|++||+.|+|+|||++++ ++++|.++|.|.|  ++...... ...+...+++.
T Consensus         1 iv~~~~~g~RLDk~L~~~~~~~sR~~a~~li~~G~V~VNG~~~~-~s~~v~~gD~i~i~~~~~~~~~~-~~~~~~~~~~~   78 (133)
T 1dm9_A            1 MKEKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQGNDERTVI-VKAITEQRRPA   78 (133)
T ss_dssp             ----CTTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEEETTEEEEEE-ECEEESCCCCH
T ss_pred             CCCCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEECC-CCCEECCCCEEEEEECCEEEEEE-EEEEEECCCCC
T ss_conf             99887764629999987867168999999998691888999734-58561599989998799865899-99876225673


Q ss_pred             EEEECCCCCC-----CCCCCCEEE-CCCCCCEECCCCCCC-CCCCEEEECCCCC
Q ss_conf             1563144333-----364421011-023432002665543-3232022236764
Q gi|254780406|r   83 GLVTTHSDPD-----GRSTVFDNL-PSIFSRVISVGRLDI-NTEGLLLLTNDGG  129 (354)
Q Consensus        83 g~~~~~~~~~-----~~~~~~~~~-~~~~~~~~~vgRLD~-~t~GLlllTndg~  129 (354)
                      +..+......     ..+..+..+ .....++++|||||+ +|+|||+|||||.
T Consensus        79 ~~~~~~~ed~~~~v~~kp~~~~~~~~~~~~r~~~vgRLDk~~t~~ll~l~~dgs  132 (133)
T 1dm9_A           79 SEAALLYEETAESVEKREKMALARKLNALTMPHPDRRPDKKERRDLLRFKHGDS  132 (133)
T ss_dssp             HHHGGGEEECHHHHHHHHHHHHHHHHHHTC------------------------
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             035666323688711345777766522455788997868599999998755899


No 11 
>>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200)
Probab=99.53  E-value=6e-14  Score=107.28  Aligned_cols=83  Identities=24%  Similarity=0.445  Sum_probs=74.7

Q ss_pred             CCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEE---------------EECCCCEEEEEEEEEECCHHHHHH
Q ss_conf             57404775211245564678887400000876750343036---------------402688079999995184289999
Q gi|254780406|r  139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKK  203 (354)
Q Consensus       139 ~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~---------------~~~~~~~~~~~v~l~eGr~~qIrr  203 (354)
                      ..|+|+|++.|.|+++++.+..+..|+.+.+....++.+..               .......+|++++|.|||+||||+
T Consensus         1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~~~~~s~~~i~l~tGr~HQIR~   80 (98)
T 2olw_A            1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRR   80 (98)
T ss_dssp             CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CCSSCEEEEEEEESCCCTTHHHH
T ss_pred             CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEECCCCEEEEEEEECCCHHHHHH
T ss_conf             22215899999456888999998659365785357756999535544331010477742155058999991597599999


Q ss_pred             HHHHCCCEEEEEEEEEEC
Q ss_conf             999839868688975870
Q gi|254780406|r  204 VFEFFNWKVNRLIRISYG  221 (354)
Q Consensus       204 ~~~~~g~~V~~L~Rv~~G  221 (354)
                      ||+++|++|..++|++||
T Consensus        81 ~la~~g~pI~gd~ry~~G   98 (98)
T 2olw_A           81 MTAHVGFPTLRLIRYAMG   98 (98)
T ss_dssp             HHHHTTCCEEEEEEEEET
T ss_pred             HHHHCCCEEEEEEEEEEC
T ss_conf             999859979898999999


No 12 
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57)
Probab=99.50  E-value=2.7e-14  Score=109.41  Aligned_cols=56  Identities=27%  Similarity=0.367  Sum_probs=54.3

Q ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             34478899988687789999999869869999992406878079997999998922
Q gi|254780406|r   13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        13 ~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      ++|||||||++|+|||++|++||++|+|+|||+++++++++|+++|.|.|||++|.
T Consensus         2 ~~RLDk~L~~~~~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~g~~it   57 (57)
T 1vio_A            2 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLT   57 (57)
T ss_dssp             CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETTEECC
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEEECCCC
T ss_conf             55899999987785899999999879789999991548958688787876203222


No 13 
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58)
Probab=99.49  E-value=4.5e-14  Score=108.06  Aligned_cols=57  Identities=32%  Similarity=0.438  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             734478899988687789999999869869999992406878079997999998922
Q gi|254780406|r   12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      +.+|||||||+.++|||++|++||.+|+|+|||++|++++++|+++|.|+|||++|.
T Consensus         2 ~~~RLDk~L~~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~g~~it   58 (58)
T 1ksk_A            2 SHXRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLA   58 (58)
T ss_dssp             CCEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETTEEEC
T ss_pred             CCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEEEEEEE
T ss_conf             840099999877896899999999889299999994668858078676997210565


No 14 
>>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=99.43  E-value=3.8e-13  Score=102.23  Aligned_cols=61  Identities=33%  Similarity=0.423  Sum_probs=56.7

Q ss_pred             CCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCC
Q ss_conf             67734478899988687789999999869869999992406878079997999998922556
Q gi|254780406|r   10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE   71 (354)
Q Consensus        10 ~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~   71 (354)
                      ...++|||||||+.|+|||++|++||++|+|+|||++|+ ++++|.++|.|+|+++++.+.+
T Consensus         3 ~~~~~RLDk~La~~~~~SR~~~~~li~~G~V~Vng~~vk-~~~~v~~~d~I~v~~~~~~~~e   63 (63)
T 3dh3_A            3 PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPRE   63 (63)
T ss_dssp             -CCCEEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEECC-TTCEECTTCCEEETTEEECCCC
T ss_pred             CCCCCCHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEEEEEEE
T ss_conf             988704999998778851999999998793898999947-8889699998999999921120


No 15 
>>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=99.22  E-value=1.5e-12  Score=98.47  Aligned_cols=65  Identities=15%  Similarity=0.271  Sum_probs=59.9

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             3446667734478899988687-7899999998698699999924068780799979999989225
Q gi|254780406|r    5 NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus         5 ~~~~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      ........++||++||+.+++| ||++|++||.+|.|+|||++++.++++|.++|.|+|+++++.+
T Consensus        12 ~~~~~~~~~~RLd~~L~~~~~~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~~~~~~   77 (79)
T 1p9k_A           12 TFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV   77 (79)
T ss_dssp             EEECCSCSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETTEEEEE
T ss_pred             EEECCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCEEEEE
T ss_conf             386499971979999987788368999999998499798999927788798999999999999999


No 16 
>>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65)
Probab=99.17  E-value=1.3e-11  Score=92.55  Aligned_cols=62  Identities=18%  Similarity=0.324  Sum_probs=57.2

Q ss_pred             CCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCE--EECCEECCCCCEEECCCCEEEECCEECCC
Q ss_conf             6667734478899988687-78999999986986--99999924068780799979999989225
Q gi|254780406|r    8 QENFTPQRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus         8 ~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V--~Vng~~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      ++....+|||++|+.+|+| ||++|++||..|.|  +|||++|+.|++.|.++|.|.|+++++.+
T Consensus         1 s~~~~~~RLD~~L~~~g~~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~~~~~~y   65 (65)
T 3hp7_A            1 SNAXPKERVDVLAYKQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLKGEKLRY   65 (65)
T ss_dssp             --CCCEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETTCCCCS
T ss_pred             CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEECCCCCC
T ss_conf             99650889999999875812499999999859942320998956886787999989980777664


No 17 
>>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:)
Probab=99.06  E-value=1.1e-11  Score=93.12  Aligned_cols=76  Identities=22%  Similarity=0.238  Sum_probs=65.0

Q ss_pred             HHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC----EE---------C-CCCCCEEEEEC
Q ss_conf             44788999886-8778999999986986999999240687807999799999----89---------2-25564389602
Q gi|254780406|r   14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VP---------L-RKAERTRLWLY   78 (354)
Q Consensus        14 ~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg----~~---------i-~~~~~~~~~~~   78 (354)
                      +||++||+..+ .+||+.+.++|+.|.|+|||+++. +++.|..+|.|++..    .+         + ..+++..|+++
T Consensus         1 mRLD~~L~~~~~~~sr~~~~k~i~~g~I~VNg~~~~-~~~~v~~gD~i~i~~~~~~~~~~~~~~~~~~~i~yed~~~lvi   79 (92)
T 2k6p_A            1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYIA   79 (92)
T ss_dssp             CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECC-TTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSEE
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEE-ECCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCHHHHCCCEE
T ss_conf             967899987277159999999998997998989986-6247189999999848963689999788658986455061598


Q ss_pred             CCCCEEEECCCC
Q ss_conf             787515631443
Q gi|254780406|r   79 HKPIGLVTTHSD   90 (354)
Q Consensus        79 ~KP~g~~~~~~~   90 (354)
                      |||+|++++...
T Consensus        80 nKpagl~~hp~~   91 (92)
T 2k6p_A           80 PKTKELEHHHHH   91 (92)
T ss_dssp             ECCCC-------
T ss_pred             ECHHCCCCCCCC
T ss_conf             063216244457


No 18 
>>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=98.83  E-value=7.8e-09  Score=75.04  Aligned_cols=53  Identities=28%  Similarity=0.449  Sum_probs=49.8

Q ss_pred             HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC
Q ss_conf             478899988687-78999999986986999999240687807999799999892
Q gi|254780406|r   15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL   67 (354)
Q Consensus        15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i   67 (354)
                      |||++|.++|+| ||.+|.++|..|.|.|||++|+.|++.|.++|.|++.+...
T Consensus         1 RLD~~l~r~~~~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~~~~   54 (94)
T 2vqe_D            1 RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSR   54 (94)
T ss_dssp             BHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGGGT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHHHHH
T ss_conf             999999853520028988899870684508879975367852886001211010


No 19 
>>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=98.51  E-value=7e-08  Score=69.07  Aligned_cols=56  Identities=16%  Similarity=0.188  Sum_probs=49.8

Q ss_pred             CCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEECCEE
Q ss_conf             7734478899988687-789999999869869999992406878079--9979999989
Q gi|254780406|r   11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVP   66 (354)
Q Consensus        11 ~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vdg~~   66 (354)
                      .-..|||.+|.++|++ ||.+|.+||..|.|+|||++|+.|++.|.+  +|.|++.++.
T Consensus         5 ~lerRLd~~l~~~g~a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~~~~   63 (71)
T 2cqj_A            5 SSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSS   63 (71)
T ss_dssp             CCEEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESCCS
T ss_pred             HHHCCHHHHHHHHCCCCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEECCC
T ss_conf             44412689999805527899999999849899899995569858358998869984688


No 20 
>>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432)
Probab=98.46  E-value=3.9e-07  Score=64.36  Aligned_cols=52  Identities=19%  Similarity=0.320  Sum_probs=48.1

Q ss_pred             CCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEEC
Q ss_conf             734478899988687-7899999998698699999924068780799979999
Q gi|254780406|r   12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD   63 (354)
Q Consensus        12 ~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vd   63 (354)
                      ...||+++|..+|+| |+++|.++|.+|-|+|||+.|+++++.|.++|.|.|.
T Consensus        18 ~~~rl~~~l~~~gl~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~   70 (83)
T 1h3f_A           18 GRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQ   70 (83)
T ss_dssp             TEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEE
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
T ss_conf             86349999998498677899999998599898999824877021589808998


No 21 
>>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=98.39  E-value=1.8e-07  Score=66.41  Aligned_cols=51  Identities=24%  Similarity=0.472  Sum_probs=48.2

Q ss_pred             HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE
Q ss_conf             478899988687-789999999869869999992406878079997999998
Q gi|254780406|r   15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV   65 (354)
Q Consensus        15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~   65 (354)
                      |||.+|.++|++ ||.+|.+||..|.|.|||++|+.|++.|.++|.|+|..+
T Consensus         1 RLD~~l~r~gfa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~   52 (94)
T 3i1m_D            1 RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREK   52 (94)
T ss_dssp             STTHHHHTTTSCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSS
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCC
T ss_conf             8888866031254099999999850376088799763177058977886232


No 22 
>>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=98.35  E-value=2e-07  Score=66.24  Aligned_cols=70  Identities=20%  Similarity=0.281  Sum_probs=58.8

Q ss_pred             CCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEEC
Q ss_conf             667734478899988687-7899999998698699999924068780799979999989225564389602
Q gi|254780406|r    9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY   78 (354)
Q Consensus         9 ~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~   78 (354)
                      +=..+++|.++|..+|+| |+++|.++|.+|-|+|||+.++++...+.++|.+.-+.-.|..-+..++++.
T Consensus         7 ~~~~~~~i~~lL~~~gl~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~i~~~~~~lr~GKK~~~~i~   77 (88)
T 2jan_A            7 KPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVLRRGKRSIAGVE   77 (88)
T ss_dssp             CSSSCCSHHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGSBTTTEEEEESSSSCEEEEE
T ss_pred             CCCCCCCHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHHCCCCEEEEEECCCCEEEEE
T ss_conf             35787779999998288678999999999399998999816943302787822798899997670289999


No 23 
>>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201)
Probab=98.30  E-value=3e-07  Score=65.03  Aligned_cols=53  Identities=17%  Similarity=0.346  Sum_probs=49.7

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             4478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      .|||-+|.++|++ |+.+|.+||..|.|.|||++|+.|++.|.++|.|++..+.
T Consensus         8 ~RLD~~l~R~gfa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~~~   61 (120)
T 3bbn_D            8 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQ   61 (120)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSST
T ss_pred             HHHHHEEEECCCCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCCHH
T ss_conf             753103550573357688889998751361548981657254616630010013


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=98.24  E-value=9.8e-06  Score=55.53  Aligned_cols=157  Identities=17%  Similarity=0.135  Sum_probs=97.8

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||.|+.++..-...+..      ....++...|-||-..+|+|++.-.  -+.+|..--....|+|.+++..-
T Consensus        16 ~G~l~~~KP~g~tS~~vv~~ik~~------~~~~kvGh~GTLDp~atGvl~i~vg--~aTkl~~~~~~~~K~Y~~~~~~g   87 (215)
T 2aus_C           16 YGVINLDKPPGPTSHEVVAWIKRI------LNLEKAGHGGTLDPKVSGVLPVALE--RATRVVQALLPAGKEYVALMHLH   87 (215)
T ss_dssp             TEEEEEEECSSSCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEG--GGGGGGGGGTTCCEEEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCCEEEEEC--HHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             838999579989999999999987------1834257898789865034767873--89989999745885999998872


Q ss_pred             CCHHHHHHHHHHHHCCCE----------------EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------
Q ss_conf             564678887400000876----------------7503430364026880799999951842899999998398------
Q gi|254780406|r  153 VDQDKLNLLKKGIVIQGI----------------CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------  210 (354)
Q Consensus       153 ~~~~~~~~~~~g~~~~~~----------------~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------  210 (354)
                      ...+..+.-..-..+.+.                ...-.......-+.....++|....|-|  ||-++..+|.      
T Consensus        88 ~~t~t~d~~~~~~~~~g~~~Q~pP~~SA~k~~g~r~y~~ar~g~~~~~p~~~~~v~cs~GTY--IRsL~~Dig~~Lg~~a  165 (215)
T 2aus_C           88 GDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEILEIDGRDVLFRVGVEAGTY--IRSLIHHIGLALGVGA  165 (215)
T ss_dssp             SCCCHHHHHHHHHHTSEEEECC------------EEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHSSCE
T ss_pred             CCCCCCHHHEEECCCEEEEEECCCHHHHHHCCCCCEEEEEEEEEECCCCEEEEEEEECCCCE--EEHHHHHHHHHHCCCC
T ss_conf             34444400133023214488888845631014654067899986226733899999549937--5038999766650152


Q ss_pred             EEEEEEEEEECCEECCC-CCCCCEEECCHHHHHHHHH
Q ss_conf             68688975870545187-5547488679999987532
Q gi|254780406|r  211 KVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG  246 (354)
Q Consensus       211 ~V~~L~Rv~~G~~~l~~-L~~G~~r~l~~~e~~~l~~  246 (354)
                      .+..|.|+++|+|.+++ |       ++-+||.++..
T Consensus       166 ~l~~L~Rt~~G~F~l~~al-------~~l~~l~~~~~  195 (215)
T 2aus_C          166 HMAELRRTRSGPFKEDETL-------VTLHDLVDYYH  195 (215)
T ss_dssp             EEEEEEEEEETTEESSTTE-------ECHHHHHHHHH
T ss_pred             EEEEEEEEEECCCCHHHHH-------HHHHHHHHHHH
T ss_conf             1414796445686889975-------44999998999


No 25 
>>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=98.09  E-value=2.2e-06  Score=59.58  Aligned_cols=54  Identities=19%  Similarity=0.294  Sum_probs=49.6

Q ss_pred             CHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE
Q ss_conf             34478899988687-7899999998698699999924068780799979999989
Q gi|254780406|r   13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP   66 (354)
Q Consensus        13 ~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~   66 (354)
                      ..|||-+|.++|++ |+.+|.++|..|.|.|||++|+.|++.|.++|.|.|..+.
T Consensus         8 ErRLD~il~R~gfa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~~~   62 (99)
T 1s1h_D            8 ERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP   62 (99)
T ss_dssp             GGBHHHHHHHHTSSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCSSC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEEEC
T ss_conf             7507889998156588999999987377258999987624684058756055606


No 26 
>>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=97.93  E-value=0.00011  Score=48.88  Aligned_cols=156  Identities=16%  Similarity=0.085  Sum_probs=94.3

Q ss_pred             EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             38960278751563144333364421011023432002665543323202223676410001234457404775211245
Q gi|254780406|r   73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus        73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      .-++++|||.|+.++..=...+..      ....++...|.||-..+|+|++--.  -+.++..--....|+|.+++.--
T Consensus        16 ~G~l~i~KP~g~tS~~vv~~~k~~------~~~~kvgh~GtLDp~a~GvLiv~ig--~~Tkl~~~~~~~~K~Y~~~~~lG   87 (216)
T 2apo_A           16 YGVVVVDKPRGPTSHEVSTWVKKI------LNLDKAGHGGTLDPKVTGVLPVALE--RATKTIPMWHIPPKEYVCLMHLH   87 (216)
T ss_dssp             TEEEEEEECSSSCHHHHHHHHHHH------TTCSCEEESSCCCTTCEEEEEEEEG--GGGGGGGGTTSSCEEEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCCHHHEEC--HHHHHHHHHCCCCCEEEEEEEEE
T ss_conf             998999799989989999999998------4877357787789634365532118--65322177505882799999983


Q ss_pred             C--CHHHHHHHHHHHH--------------CCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------
Q ss_conf             5--6467888740000--------------08767503430364026880799999951842899999998398------
Q gi|254780406|r  153 V--DQDKLNLLKKGIV--------------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------  210 (354)
Q Consensus       153 ~--~~~~~~~~~~g~~--------------~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------  210 (354)
                      .  +.+.++.....+.              +.+....-....-..-+.....++|....|-|  ||.++..+|.      
T Consensus        88 ~~Tdt~di~~~l~~f~g~~~q~pp~~Savk~~g~~ayelar~g~~~~~p~~~~~v~cs~GtY--IRsL~~Dlg~~Lg~~a  165 (216)
T 2apo_A           88 RDASEEDILRVFKEFTGRIYQRPPLKAAVKRRLRIRKIHELELLDKDGKDVLFRVKCQSGTY--IRKLCEDIGEALGTSA  165 (216)
T ss_dssp             SCCCHHHHHHHHHHHSEEEECC-----------CEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHTTSCE
T ss_pred             ECCCCCHHHHHHHHCCCCEEECCCCHHHCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCC--HHHHHHHHHHHCCCCE
T ss_conf             12432149999985376043248614310134445279999986258884899999658816--7999999998605447


Q ss_pred             EEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHH
Q ss_conf             68688975870545187554748867999998753
Q gi|254780406|r  211 KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL  245 (354)
Q Consensus       211 ~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~  245 (354)
                      .+..|.|+++|+|.+++-       ++-++|.+..
T Consensus       166 ~~~~LrRt~~G~f~~~~a-------~~l~~l~~~~  193 (216)
T 2apo_A          166 HMQELRRTKSGCFEEKDA-------VYLQDLLDAY  193 (216)
T ss_dssp             EEEEEEEEEETTEEGGGC-------BCHHHHHHHH
T ss_pred             EEEECCCCCCCCCCCCCC-------CCHHHHHHHH
T ss_conf             883053655699062334-------7899999878


No 27 
>>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420)
Probab=97.38  E-value=2.9e-05  Score=52.53  Aligned_cols=69  Identities=14%  Similarity=0.274  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEE
Q ss_conf             667734478899988687-789999999869869999992406878079997999998922556438960
Q gi|254780406|r    9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL   77 (354)
Q Consensus         9 ~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~   77 (354)
                      .....++|..+|..+|+| |+++|.++|.+|-|+|||++|+++.+.+..+|.+.-..-.|...+..++++
T Consensus       102 ~~~~~~~l~~lL~~~~l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~~~~~~ilr~GKk~~~~i  171 (174)
T 1jil_A          102 LSNDTTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKIDGEFTIIRRGKKKYFMV  171 (174)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             ECCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCCCCCEEEEEECCCCEEEE
T ss_conf             1588878999999838846799999999849989999981384440077570489789999558747999


No 28 
>>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419)
Probab=96.97  E-value=0.00013  Score=48.38  Aligned_cols=64  Identities=17%  Similarity=0.234  Sum_probs=48.0

Q ss_pred             CCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCE
Q ss_conf             677344788999886-8778999999986986999999240687807999799999892255643
Q gi|254780406|r   10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT   73 (354)
Q Consensus        10 ~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~   73 (354)
                      .....+|..+|..+| ..|+++|.++|.+|-|+|||+.|+++...+...|.+.=..-.|...+..
T Consensus       103 ~~~~~~l~~lL~~~gl~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~~~~~~ilr~GKk~  167 (174)
T 2ts1_A          103 EGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRRGKKK  167 (174)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             CCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCCCCCEEEEEECCCC
T ss_conf             57997699999985986778999999986998989998238422017757148978999957954


No 29 
>>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=95.98  E-value=0.012  Score=36.04  Aligned_cols=42  Identities=31%  Similarity=0.424  Sum_probs=38.3

Q ss_pred             CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC
Q ss_conf             778999999986986999999240687807999799999892
Q gi|254780406|r   26 ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL   67 (354)
Q Consensus        26 ~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i   67 (354)
                      -+.|||...|.+|.|+|||++.++..+.|---|+|++.|+-.
T Consensus        22 ~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~~e~y   63 (81)
T 3kbg_A           22 DKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEINGESY   63 (81)
T ss_dssp             TCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEETTEEE
T ss_pred             CCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECCCEE
T ss_conf             658999999867938989999623899887067999799779


No 30 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159)
Probab=91.52  E-value=0.16  Score=29.00  Aligned_cols=26  Identities=19%  Similarity=0.215  Sum_probs=23.9

Q ss_pred             EEECCEECCCCCEEECCCCEEEECCE
Q ss_conf             69999992406878079997999998
Q gi|254780406|r   40 VKVNGILLERAAVNVMSTDHIEVDGV   65 (354)
Q Consensus        40 V~Vng~~v~~~~~~v~~~d~v~vdg~   65 (354)
                      |.|||+.|.-|++.+.++|.|+|..+
T Consensus         2 i~VNgkkVdIPSy~~k~gD~I~ik~k   27 (83)
T 1c05_A            2 ILVDGSRVNIPSYRVKPGQTIAVREK   27 (83)
T ss_dssp             EEETTEECCCSSCBCCTTCEEEECGG
T ss_pred             EECCCEEEEECCEEECCCCEEEECCC
T ss_conf             36043699843416217848750200


No 31 
>>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:80-224)
Probab=90.68  E-value=1.2  Score=23.61  Aligned_cols=66  Identities=12%  Similarity=0.208  Sum_probs=42.5

Q ss_pred             HHHHHHHHCCCEEEE--CCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECC
Q ss_conf             887400000876750--3430364026880799999951842899999998398------6868897587054518
Q gi|254780406|r  159 NLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLG  226 (354)
Q Consensus       159 ~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~  226 (354)
                      +-.++|..++-..-.  --.+.+..-.....++++.-..|-+  ||.++..+|.      .+..|.|+++|+|.|+
T Consensus        72 elAr~G~~~~~~~r~v~I~~~~l~~~~~p~~~~~v~cs~GTY--IRsL~~dig~~Lg~~a~~~~L~Rt~~G~f~l~  145 (145)
T 1k8w_A           72 EYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTY--IRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVE  145 (145)
T ss_dssp             HHHHTTCCCCCCCEEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHTSCEEEEEEEEEEETTCCGG
T ss_pred             HHHHHCCCCCCCCEEEEEEEEEEEECCCCEEEEEEEECCCHH--HHHHHHHHHHHCCCCEEEEEEEEEEECCCCCH
T ss_conf             999756655578366465127984133548999999678458--99999998765089589837898888783803


No 32 
>>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domain, lyase; HET: EPE; 2.0A {Homo sapiens} (A:411-530)
Probab=87.82  E-value=1.9  Score=22.30  Aligned_cols=81  Identities=9%  Similarity=0.012  Sum_probs=50.1

Q ss_pred             EEEEEEEEC--CCCCHHHHHHHHHHHHCCCEEEECCC----------------EEEEECCCCEEEEEEEEEECCHHHHHH
Q ss_conf             047752112--45564678887400000876750343----------------036402688079999995184289999
Q gi|254780406|r  142 LRVYRVRFH--GQVDQDKLNLLKKGIVIQGICYGDMQ----------------VTLDTQKGSNAWVTVGLREGKNREIKK  203 (354)
Q Consensus       142 ~k~Y~v~v~--~~~~~~~~~~~~~g~~~~~~~~~~~~----------------~~~~~~~~~~~~~~v~l~eGr~~qIrr  203 (354)
                      .|+|.+++.  ..++.+.++....-....=.+..|+.                +.+..-......++|....|-+  ||.
T Consensus         2 ~K~Y~a~v~~g~~~~~edi~~~l~~f~g~i~Q~pP~~SA~K~~gk~R~~~I~~~~~~~~~~~~~~l~i~~s~GtY--IR~   79 (120)
T 2v9k_A            2 TKTYSALIWTNKAIQKKDIEFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYVDEHHFRLHLKTQAGTY--IKE   79 (120)
T ss_dssp             CEEEEEEEEESSCCCHHHHGGGGGCCSEEEEEECCGGGTTTSCCCEEEEEEEEEEEEEEETTEEEEEEEECTTCC--HHH
T ss_pred             CEEEEEEEEECCCCCHHHHHHHHHCCCCEEEECCCCHHHHCCCCCCEEEEEEEEEEEEECCCEEEEEEEECCCCE--EEE
T ss_conf             548999998479888899999872689668813740632105788504699999979943958999999507975--454


Q ss_pred             HHH--------HCC------CEEEEEEEEEECCEE
Q ss_conf             999--------839------868688975870545
Q gi|254780406|r  204 VFE--------FFN------WKVNRLIRISYGPFQ  224 (354)
Q Consensus       204 ~~~--------~~g------~~V~~L~Rv~~G~~~  224 (354)
                      ++.        .+|      ..+..|.|+++|++.
T Consensus        80 l~~~d~grt~pdlg~~lg~~~~~~~L~R~~vg~~~  114 (120)
T 2v9k_A           80 FVHGDFGRTKPNIGSLMNVTADILELDVESVDVDW  114 (120)
T ss_dssp             HHHCTTTTEESCHHHHHTSCEEEEEEEEEEECCCC
T ss_pred             EEECCCCCCCCCHHHHHCCCCEEEEEEEEEEEECC
T ss_conf             26179998677879984897569993751487158


No 33 
>>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=81.27  E-value=0.3  Score=27.30  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=32.7

Q ss_pred             CEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECC
Q ss_conf             43896027875156314433336442101102--34320026655433232022236
Q gi|254780406|r   72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN  126 (354)
Q Consensus        72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTn  126 (354)
                      ..-++++|||.|+.++..        ...+..  ...++...|-||-..+|+|++.-
T Consensus         5 ~~Gil~idKP~G~TS~~v--------v~~iKk~l~~kKVGH~GTLDP~AtGvLiv~i   53 (87)
T 1sgv_A            5 GPGIVVIDKPAGMTSHDV--------VGRCRRIFATRRVGHAGTLDPMATGVLVIGI   53 (87)
T ss_dssp             CSEEEEEEECTTCCHHHH--------HHHHHHHTTCSCEEESSCCCTTCEEEEEEEE
T ss_pred             CCEEEEEECCCCCCHHHH--------HHHHHHHHCCCCCCCCCCCCCCCEEEEEEEE
T ss_conf             988999976998998999--------9999998488855638788973642399998


No 34 
>>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=79.75  E-value=0.37  Score=26.73  Aligned_cols=46  Identities=22%  Similarity=0.243  Sum_probs=31.9

Q ss_pred             EEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECCC
Q ss_conf             896027875156314433336442101102--343200266554332320222367
Q gi|254780406|r   74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTND  127 (354)
Q Consensus        74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTnd  127 (354)
                      -++++|||.|+.++..-        ..+..  ...+....|-||-..+|+|++.-.
T Consensus         4 Gil~idKP~G~TS~~vV--------~~iKk~l~~kKVGH~GTLDP~AtGvLii~iG   51 (92)
T 1r3e_A            4 GILVAYKPKGPTSHDVV--------DEVRKKLKTRKVGHGGTLDPFACGVLIIGVN   51 (92)
T ss_dssp             EEEEEEECSSSCHHHHH--------HHHHHHTTCSCEEESSCCCTTCEEEEEEEEG
T ss_pred             EEEEEECCCCCCHHHHH--------HHHHHHHCCCCCCCCCCCCCCCEEEEEEEEC
T ss_conf             59999669989989999--------9999986888787785679746446999988


No 35 
>>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=78.88  E-value=0.4  Score=26.51  Aligned_cols=48  Identities=21%  Similarity=0.326  Sum_probs=33.1

Q ss_pred             CCEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECC
Q ss_conf             643896027875156314433336442101102--34320026655433232022236
Q gi|254780406|r   71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN  126 (354)
Q Consensus        71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTn  126 (354)
                      ...-++++|||.|+.++..        ...+..  ...++...|-||-..+|||++.-
T Consensus        23 ~~~Gil~idKP~G~TS~~v--------V~~vkk~l~~kKVGH~GTLDP~AtGvLiv~i   72 (108)
T 1k8w_A           23 DINGVLLLDKPQGMSSNDA--------LQKVKRIYNANRAGHTGALDPLATGMLPICL   72 (108)
T ss_dssp             CCCEEEEEEECTTCCHHHH--------HHHHHHHTTCSCEEESSCCCTTCEEEEEEEE
T ss_pred             CCCEEEEEECCCCCCHHHH--------HHHHHHHHCCCCCCCCCCCCCCCEEEEEEEE
T ss_conf             8536999847998998999--------9999998589968768657974613599998


No 36 
>>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae} (A:1-91)
Probab=72.90  E-value=3  Score=21.01  Aligned_cols=47  Identities=15%  Similarity=0.232  Sum_probs=38.9

Q ss_pred             CCCCCCEEEECC-CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHH
Q ss_conf             433232022236-76410001234457404775211245564678887
Q gi|254780406|r  115 DINTEGLLLLTN-DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL  161 (354)
Q Consensus       115 D~~t~GLlllTn-dg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~  161 (354)
                      -.+.+|++.+.+ +-.|+-+.+.-...+.-.|.+.|.+.+.++.+..|
T Consensus        43 T~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAi~V~g~lp~~i~~~l   90 (91)
T 2exu_A           43 SPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIKVDGRLPAEVVELL   90 (91)
T ss_dssp             ESCEEEEEEESCTTTCHHHHHTTCTTSCSEEEEEEECSCCCHHHHTTC
T ss_pred             CCCCCCEEEEECCHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             726164899967627399998578877886589995375877799999


No 37 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:22-76)
Probab=64.67  E-value=7.2  Score=18.59  Aligned_cols=25  Identities=24%  Similarity=0.631  Sum_probs=22.4

Q ss_pred             HHHHHHHHHCCCC-CHHHHHHHHHCC
Q ss_conf             4478899988687-789999999869
Q gi|254780406|r   14 QRVSKVIARAGIA-SRREVERMIAQQ   38 (354)
Q Consensus        14 ~RL~K~la~~g~~-SRr~a~~lI~~G   38 (354)
                      .|||-++-++|++ |+.+|.++|..|
T Consensus        30 ~RLD~vvyR~gfa~S~~~ARQlV~HG   55 (55)
T 1c05_A           30 SRLDNLVYRLGLARTRRQARQLVTHG   55 (55)
T ss_dssp             HBHHHHHHHTTSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHC
T ss_conf             87545411577437888899888735


No 38 
>>3gmg_A Uncharacterized protein RV1825/MT1873; structural genomics, unknown function, cell membrane, membrane, transmembrane, PSI-2; 1.50A {Mycobacterium tuberculosis} (A:)
Probab=47.37  E-value=13  Score=16.90  Aligned_cols=31  Identities=16%  Similarity=0.118  Sum_probs=22.7

Q ss_pred             CEEECCE----ECCCCCEEECCCCEEEECCEECCC
Q ss_conf             8699999----924068780799979999989225
Q gi|254780406|r   39 RVKVNGI----LLERAAVNVMSTDHIEVDGVPLRK   69 (354)
Q Consensus        39 ~V~Vng~----~v~~~~~~v~~~d~v~vdg~~i~~   69 (354)
                      -|.|||+    .+.....-...+..|.|||.++.+
T Consensus        68 AIsINgq~~~vRi~~~S~Ir~~G~~i~V~g~~i~~  102 (170)
T 3gmg_A           68 AIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSP  102 (170)
T ss_dssp             EEEEECSSCEEECCTTCCEEEETTEEEETTEEECS
T ss_pred             EEEECCCCCCEEEEEEEEEEECCCEEEECCEEECC
T ss_conf             79986875436994205999249989999999369


No 39 
>>1tke_A Threonyl-tRNA synthetase; ligase; 1.46A {Escherichia coli} (A:1-63)
Probab=46.24  E-value=14  Score=16.78  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=19.1

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE
Q ss_conf             869999992406878079997999
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      -++|||+++ ++.+.+..++.|++
T Consensus        37 ~a~vng~l~-dL~~~l~~d~~ve~   59 (63)
T 1tke_A           37 AGRVNGELV-DACDLIENDAQLSI   59 (63)
T ss_dssp             EEEETTEEE-ETTCCBCSCEEEEE
T ss_pred             EEEECCEEE-CCCCCCCCCCEEEE
T ss_conf             999999996-38844178758999


No 40 
>>2r9q_A AGR_C_764P, 2'-deoxycytidine 5'-triphosphate deaminase; structural genomics, MCSG, PSI-2, protein structure initiative; 2.20A {Agrobacterium tumefaciens str} (A:1-174)
Probab=44.58  E-value=20  Score=15.81  Aligned_cols=39  Identities=13%  Similarity=0.225  Sum_probs=26.3

Q ss_pred             CCCCCHHHHHHHHHCCCEEECC----EECCCCCEEECCCCEEE
Q ss_conf             8687789999999869869999----99240687807999799
Q gi|254780406|r   23 AGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDHIE   61 (354)
Q Consensus        23 ~g~~SRr~a~~lI~~G~V~Vng----~~v~~~~~~v~~~d~v~   61 (354)
                      .++.|-++.+++|++|.+.++=    +.+...++.+..++.+.
T Consensus        10 ~~iLsd~~I~~~~~~~~l~~~~~~~~~~v~~~s~Dl~l~~~~~   52 (174)
T 2r9q_A           10 TGILADGAIRALFAGDKLKSEADLDVDQVQPASLDLRLGSKAY   52 (174)
T ss_dssp             SEECCHHHHHHHHHHTSEEESSCCCTTCBCSSCEEEEBCSEEE
T ss_pred             CEECCHHHHHHHHHCCCEEECCCCCHHHCCCCEEEEECCCEEE
T ss_conf             8678799999998779806079999677788469943586899


No 41 
>>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis} (A:)
Probab=44.29  E-value=18  Score=16.12  Aligned_cols=23  Identities=35%  Similarity=0.352  Sum_probs=19.1

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE
Q ss_conf             869999992406878079997999
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      -.+|||+.+ ++.+.+..++.|++
T Consensus        38 ~A~vng~l~-dL~~~l~~~~~ve~   60 (73)
T 2kmm_A           38 GAKVNHKLV-PLSYVLNSGDQVEV   60 (73)
T ss_dssp             EEEETTEEC-CTTCBCCSSSBEEE
T ss_pred             EEEECCEEC-CCCCCCCCCCEEEE
T ss_conf             998898599-88879589999999


No 42 
>>2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A (A:)
Probab=38.09  E-value=7.7  Score=18.40  Aligned_cols=39  Identities=23%  Similarity=0.340  Sum_probs=32.8

Q ss_pred             HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             999999869869999992406878079997999998922
Q gi|254780406|r   30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      +--.+|++|.=+|-+.+...--.++.++|.|.+.++.+.
T Consensus        10 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~n~~l~   48 (109)
T 2z0t_A           10 EYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEGGKLK   48 (109)
T ss_dssp             HHHHHHHTTSCCEEEEECCTTGGGCCTTCEEEEGGGTEE
T ss_pred             HHHHHHHCCCCEEEEECCHHHHHHCCCCCEEEEECCEEE
T ss_conf             057998769988999827767862899999999478389


No 43 
>>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=36.89  E-value=26  Score=15.06  Aligned_cols=25  Identities=16%  Similarity=0.263  Sum_probs=20.9

Q ss_pred             CCCEEECCEECCCCCEEECCCCEEEE
Q ss_conf             69869999992406878079997999
Q gi|254780406|r   37 QQRVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        37 ~G~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      .-.|.|||+.+. ..+.+..+|.|.+
T Consensus        46 ~~~v~vN~~~v~-~~~~l~dgDeVai   70 (77)
T 2q5w_D           46 KFQVAVNEEFVQ-KSDFIQPNDTVAL   70 (77)
T ss_dssp             CCEEEETTEEEC-TTSEECTTCEEEE
T ss_pred             HHHHHCCCEECC-CCCCCCCCCEEEE
T ss_conf             313410880768-8867099899999


No 44 
>>1qf6_A THRRS, threonyl-tRNA synthetase; tRNA(Thr), AMP, zinc, mRNA, aminoacylation, translational regulation, protein/RNA, ligase/RNA complex; HET: H2U AET G7M 5MU PSU AMP; 2.90A {Escherichia coli} (A:1-63)
Probab=36.20  E-value=14  Score=16.78  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=18.0

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE
Q ss_conf             869999992406878079997999
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      -++|||+++ ++.+.+..++.|++
T Consensus        37 ~a~vng~l~-dL~~~l~~d~~ve~   59 (63)
T 1qf6_A           37 AGRVNGELV-DACDLIENDAQLSI   59 (63)
T ss_dssp             EEEETTEEE-ETTSCBCSCEECCE
T ss_pred             EEEECCEEE-ECCCCCCCCCEEEE
T ss_conf             999999998-57851799988998


No 45 
>>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:)
Probab=34.79  E-value=28  Score=14.86  Aligned_cols=30  Identities=13%  Similarity=0.072  Sum_probs=22.8

Q ss_pred             HHHHHC-CCEEECCEECCCCCEEECCCCEEEE
Q ss_conf             999986-9869999992406878079997999
Q gi|254780406|r   32 ERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        32 ~~lI~~-G~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      +.++.. -+|.|||+.+. ..+.+.++|.|.+
T Consensus        44 ~~l~~~~~~v~vn~~~v~-~~~~l~~gdeVai   74 (81)
T 1fm0_D           44 LALEDGKLLAAVNQTLVS-FDHPLTDGDEVAF   74 (81)
T ss_dssp             HHHCCTTCEEEETTEECC-TTCBCCTTCEEEE
T ss_pred             HHHCCCCEEEECCCEECC-CCCCCCCCCEEEE
T ss_conf             862789589972845979-9978599999999


No 46 
>>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:)
Probab=34.43  E-value=13  Score=16.88  Aligned_cols=43  Identities=23%  Similarity=0.322  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE
Q ss_conf             7734478899988687789999999869869999992406878079997999
Q gi|254780406|r   11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      ..+.-+..+|...++-.        ..=-|.|||+++. +.+.+.++|.|.+
T Consensus        28 ~~~~Tv~~ll~~L~l~~--------~~v~v~vNg~~v~-~~~~L~dgD~v~i   70 (77)
T 1rws_A           28 REGMKVRDILRAVGFNT--------ESAIAKVNGKVVL-EDDEVKDGDFVEV   70 (77)
T ss_dssp             CSSCCHHHHHHTTTCSS--------CSSCEEETTEEEC-SSSCCCSSCCCBC
T ss_pred             CCCCCHHHHHHHHCCCC--------HHHHEEECCEECC-CCCCCCCCCEEEE
T ss_conf             99699999999809983--------0101559999969-9728699999999


No 47 
>>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238)
Probab=32.30  E-value=31  Score=14.60  Aligned_cols=39  Identities=26%  Similarity=0.199  Sum_probs=29.3

Q ss_pred             CCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEE
Q ss_conf             698699999924068780799979999989225564389
Q gi|254780406|r   37 QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL   75 (354)
Q Consensus        37 ~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~   75 (354)
                      +|-+.+||+++....+.+..+|.|.|.+..+.+.....-
T Consensus        54 ngt~~~n~~~~~~~~~~L~~Gd~i~iG~~~~~~~~~~~~   92 (158)
T 1wv3_A           54 NTDVYINYELQEQLTNKAYIGDHIYVEGIWLEVQADGLN   92 (158)
T ss_dssp             TCCEEETTEECCSSEEEEETTCEEEETTEEEEECSSEEE
T ss_pred             CCCEEECCEEEECCEEECCCCCEEEECCEEEEEECCCEE
T ss_conf             986998789972550430489999999899999742179


No 48 
>>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:)
Probab=31.53  E-value=32  Score=14.52  Aligned_cols=24  Identities=17%  Similarity=0.003  Sum_probs=18.1

Q ss_pred             CEEECCEECCC---CCEEECCCCEEEE
Q ss_conf             86999999240---6878079997999
Q gi|254780406|r   39 RVKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      .|.|||+.+..   +.+.+.++|.|.+
T Consensus        66 ~v~vNg~~i~~~~~~~t~L~~gDeV~i   92 (99)
T 2qjl_A           66 ITLINDTDWELEGEKDYILEDGDIISF   92 (99)
T ss_dssp             EEEETTEEGGGGTGGGCBCCTTCEEEE
T ss_pred             EEEECCCEEECCCCCCCCCCCCCEEEE
T ss_conf             999879587817887758599799999


No 49 
>>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=31.52  E-value=32  Score=14.52  Aligned_cols=24  Identities=17%  Similarity=0.231  Sum_probs=18.9

Q ss_pred             CEEECCEECCCC---CEEECCCCEEEE
Q ss_conf             869999992406---878079997999
Q gi|254780406|r   39 RVKVNGILLERA---AVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~---~~~v~~~d~v~v   62 (354)
                      .|.|||+.+...   .+.+.++|.|.+
T Consensus        60 ~v~vNg~~v~~~~~~~t~l~~gDeV~i   86 (93)
T 3dwg_C           60 NIYVNDEDVRFSGGLATAIADGDSVTI   86 (93)
T ss_dssp             EEEETTEEGGGTTGGGCBCCTTCEEEE
T ss_pred             EEEECCEEECCCCCCCCCCCCCCEEEE
T ss_conf             999857451001476663799899999


No 50 
>>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:)
Probab=31.38  E-value=24  Score=15.31  Aligned_cols=26  Identities=19%  Similarity=0.305  Sum_probs=20.0

Q ss_pred             CCCEEECCEECCC---CCEEECCCCEEEE
Q ss_conf             6986999999240---6878079997999
Q gi|254780406|r   37 QQRVKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        37 ~G~V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      .=.|.|||+.+..   +.+.+.++|.|.+
T Consensus        55 ~v~v~vNg~~v~~~~~~~t~l~~gD~V~i   83 (90)
T 2g1e_A           55 NVIILVNGNNITSMKGLDTEIKDDDKIDL   83 (90)
T ss_dssp             TCEEEESSSBGGGTCSSSCBCCTTCEEEE
T ss_pred             HEEEEEECCCCCCCCCCCCCCCCCCEEEE
T ss_conf             50457703000234465653799999999


No 51 
>>3hvz_A Uncharacterized protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.20A {Clostridium leptum dsm 753} (A:)
Probab=30.55  E-value=33  Score=14.42  Aligned_cols=22  Identities=27%  Similarity=0.431  Sum_probs=17.9

Q ss_pred             EEECCEECCCCCEEECCCCEEEE
Q ss_conf             69999992406878079997999
Q gi|254780406|r   40 VKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        40 V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      ..|||+.+ ++.+.+..++.|++
T Consensus        44 a~vng~l~-dL~~~l~~~~~vei   65 (78)
T 3hvz_A           44 AKVDGRIV-PIDYKVKTGEIIDV   65 (78)
T ss_dssp             EEETTEEE-CTTCBCCTTCBEEE
T ss_pred             EEECCEEC-CCCCCCCCCCEEEE
T ss_conf             79999999-99888589999999


No 52 
>>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, metal-binding, nucleus, repressor, transcription regulation, zinc; 1.55A {Homo sapiens} (A:1-95)
Probab=30.16  E-value=34  Score=14.38  Aligned_cols=39  Identities=15%  Similarity=0.221  Sum_probs=31.3

Q ss_pred             CCCCCCCEEEECC-CCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             5433232022236-76410001234457404775211245
Q gi|254780406|r  114 LDINTEGLLLLTN-DGGLARVLELPSTQWLRVYRVRFHGQ  152 (354)
Q Consensus       114 LD~~t~GLlllTn-dg~l~~~l~~p~~~~~k~Y~v~v~~~  152 (354)
                      +-.+.+|++.+.+ +..|+-+.+.-...+.-.|.+.|.++
T Consensus        56 tT~~f~G~i~i~dP~~SwvAk~l~i~~~vpG~YAi~V~g~   95 (95)
T 3h7h_A           56 TSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGR   95 (95)
T ss_dssp             EESCEEEEEEESCGGGCHHHHHTTCTTSCSEEEEEEECCC
T ss_pred             CCCCCCEEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCC
T ss_conf             4666333799956842389998645677897489884585


No 53 
>>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:)
Probab=30.09  E-value=27  Score=14.97  Aligned_cols=24  Identities=21%  Similarity=0.254  Sum_probs=16.8

Q ss_pred             CCEEECCEECCCCCEEECCCCEEEE
Q ss_conf             9869999992406878079997999
Q gi|254780406|r   38 QRVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        38 G~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      =.|.|||+.+. ..+.+..+|.|.+
T Consensus        68 ~~v~vN~~~v~-~~~~l~dgdeV~i   91 (98)
T 1vjk_A           68 VNIAVNGRYVS-WDEELKDGDVVGV   91 (98)
T ss_dssp             BEEEETTBCCC-TTCBCCTTCEEEE
T ss_pred             EEEEECCEECC-CCCCCCCCCEEEE
T ss_conf             79986788869-8978199999999


No 54 
>>1nyr_A Threonyl-tRNA synthetase 1; ATP, threonine, ligase; HET: ATP; 2.80A {Staphylococcus aureus} (A:1-65)
Probab=28.61  E-value=21  Score=15.67  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=17.6

Q ss_pred             CEEECCEECCCCCEEECCCCEEEE
Q ss_conf             869999992406878079997999
Q gi|254780406|r   39 RVKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      -++|||+++ ++.+.+..++.|++
T Consensus        39 aA~vng~lv-dL~~~l~~d~~ve~   61 (65)
T 1nyr_A           39 AGKFNGQLV-DLTKPLETDGSIEI   61 (65)
T ss_dssp             EEEETTEEE-CTTSCCCSCBCCCE
T ss_pred             EEEECCEEE-CCCCCCCCCCEEEE
T ss_conf             999999996-27851799988999


No 55 
>>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=27.03  E-value=38  Score=14.03  Aligned_cols=30  Identities=23%  Similarity=0.270  Sum_probs=16.5

Q ss_pred             CCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             9869999992406878079997999998922
Q gi|254780406|r   38 QRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        38 G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      .-|.|||+.+.. .+.+.++|.|.|.+..+.
T Consensus        59 ~g~~vng~~v~~-~~~L~~Gd~i~iG~~~~~   88 (99)
T 2ff4_A           59 NGVHVQHERIRS-AVTLNDGDHIRICDHEFT   88 (99)
T ss_dssp             SCCEETTEECSS-EEEECTTCEEEETTEEEE
T ss_pred             CCEEECCEECCC-CEECCCCCEEEECCEEEE
T ss_conf             785799999878-567899999999789999


No 56 
>>1xne_A Hypothetical protein PF0469; GFT structural genomics, protein structure initiative, PSI, NESG, PFR14, alpha and beta protein; NMR {Pyrococcus furiosus dsm 3638} (A:)
Probab=25.61  E-value=17  Score=16.25  Aligned_cols=39  Identities=10%  Similarity=0.089  Sum_probs=32.2

Q ss_pred             HHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC
Q ss_conf             999999869869999992406878079997999998922
Q gi|254780406|r   30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR   68 (354)
Q Consensus        30 ~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~   68 (354)
                      +--.+|++|.=+|-+.+...--.++.++|.|.+++....
T Consensus        11 ~~f~~I~~G~KtIEiRl~d~kr~~ik~GD~I~F~~~l~v   49 (113)
T 1xne_A           11 EYLEMVKSGKKRIEVRVAYPQLKDIKRGDKIIFNDLIPA   49 (113)
T ss_dssp             HHHHHHHHTCCCEEECCCTTTTTTCCTTCEEEETTTEEE
T ss_pred             CHHHHHHCCCCEEEEEECCHHHHHCCCCCEEEEECCEEE
T ss_conf             248998769977999825267861899999999301899


No 57 
>>1wwt_A Threonyl-tRNA synthetase, cytoplasmic; TGS domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ligase; NMR {Homo sapiens} (A:)
Probab=25.13  E-value=31  Score=14.58  Aligned_cols=22  Identities=18%  Similarity=0.231  Sum_probs=11.5

Q ss_pred             EEECCEECCCCCEEECCCCEEEE
Q ss_conf             69999992406878079997999
Q gi|254780406|r   40 VKVNGILLERAAVNVMSTDHIEV   62 (354)
Q Consensus        40 V~Vng~~v~~~~~~v~~~d~v~v   62 (354)
                      ..|||+.+ ++.+.+..++.|++
T Consensus        49 a~vng~l~-dL~~~l~~d~~ve~   70 (88)
T 1wwt_A           49 AKVNNVVW-DLDRPLEEDCTLEL   70 (88)
T ss_dssp             EEESSSEE-CSSSCCCSSEEEEE
T ss_pred             ECCCCEEE-EEEEECCCCCEEEE
T ss_conf             13298787-50178189999999


No 58 
>>1h6l_A 3-phytase; hydrolase, phosphatase, propeller, phosphate; 1.8A {Bacillus amyloliquefaciens} (A:1-69,A:227-353)
Probab=24.71  E-value=42  Score=13.77  Aligned_cols=33  Identities=27%  Similarity=0.462  Sum_probs=22.9

Q ss_pred             CCCEEECCCCCCEECCCCCCCCCCCEEEECC-CCC
Q ss_conf             4210110234320026655433232022236-764
Q gi|254780406|r   96 TVFDNLPSIFSRVISVGRLDINTEGLLLLTN-DGG  129 (354)
Q Consensus        96 ~~~~~~~~~~~~~~~vgRLD~~t~GLlllTn-dg~  129 (354)
                      .+++ |....-..+++|||-.|.|||-|+.. +++
T Consensus        53 ~vyd-l~G~~~q~~~~G~l~aDvEGltly~~~~~~   86 (196)
T 1h6l_A           53 AVYS-LEGKMLHSYHTGKLTPDIEGLTIYYAADGK   86 (196)
T ss_dssp             EEEE-TTCCEEEECCSSCCCSCEEEEEEEECGGGC
T ss_pred             EEEC-CCCCEEEECCCCCCCCCCCCCEEEECCCCC
T ss_conf             9987-898788863678733582113578756897


No 59 
>>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84)
Probab=23.57  E-value=44  Score=13.63  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=18.4

Q ss_pred             CEEECCEECCC---CCEEECCCCEEEE
Q ss_conf             86999999240---6878079997999
Q gi|254780406|r   39 RVKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        39 ~V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      .|.|||+-+..   +.+.+.++|.|.+
T Consensus        54 ~i~vNg~~i~~~~~~~t~l~dgDeVai   80 (84)
T 1v8c_A           54 SVFLEGRDVRYLQGLSTPLSPGATLDL   80 (84)
T ss_dssp             EEEETTEEGGGTTGGGCBCCTTCEEEE
T ss_pred             EEEECCEEECCCCCCCCCCCCCCEEEE
T ss_conf             999878774145788868699999999


No 60 
>>1mio_A Nitrogenase molybdenum iron protein (alpha chain); HET: HCA CFM CLP; 3.00A {Clostridium pasteurianum} (A:47-68,A:201-285)
Probab=23.24  E-value=45  Score=13.59  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=19.7

Q ss_pred             EEEECCHHHHHHHHHHCCCEEEEE
Q ss_conf             995184289999999839868688
Q gi|254780406|r  192 GLREGKNREIKKVFEFFNWKVNRL  215 (354)
Q Consensus       192 ~l~eGr~~qIrr~~~~~g~~V~~L  215 (354)
                      ....|-..+|++||+.+|++|..+
T Consensus        37 ~~~~~D~~EIkrlL~~~Gi~vn~~   60 (107)
T 1mio_A           37 YNIGGDAWEMDRVLEKIGYHVNAT   60 (107)
T ss_dssp             CCBTSHHHHHHHHHHHHTCEEEEE
T ss_pred             CCCCCCHHHHHHHHHHCCCCEEEE
T ss_conf             877214999999999859945897


No 61 
>>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:)
Probab=22.02  E-value=31  Score=14.57  Aligned_cols=23  Identities=26%  Similarity=0.148  Sum_probs=14.4

Q ss_pred             EEECCEECCC---CCEEECCCCEEEE
Q ss_conf             6999999240---6878079997999
Q gi|254780406|r   40 VKVNGILLER---AAVNVMSTDHIEV   62 (354)
Q Consensus        40 V~Vng~~v~~---~~~~v~~~d~v~v   62 (354)
                      |.|||+.+..   +.+.+.++|.|.+
T Consensus        70 v~VN~~~v~~~~~~~t~L~~gDeV~i   95 (110)
T 2k9x_A           70 VLVNSCDAEVVGGMDYVLNDGDTVEF   95 (110)
T ss_dssp             EEESSSBHHHHTSSCCCCCSSCEEEE
T ss_pred             EEECCCEEECCCCCCCCCCCCCEEEE
T ss_conf             99889562438885648599799999


No 62 
>>3f7f_A Nucleoporin NUP120; nuclear pore complex, macromolecular assembly, membrane coat, nucleocytoplasmic transport, beta-propeller; 2.60A {Saccharomyces cerevisiae} PDB: 3h7n_A 3hxr_A (A:270-325)
Probab=21.95  E-value=40  Score=13.88  Aligned_cols=37  Identities=22%  Similarity=0.375  Sum_probs=27.9

Q ss_pred             CCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCC
Q ss_conf             21011023432002665543323202223676410001
Q gi|254780406|r   97 VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL  134 (354)
Q Consensus        97 ~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l  134 (354)
                      +.-++|.. .-+|-+|-|+.|++|-|-+|--+-+...|
T Consensus        18 L~v~LPf~-NG~F~~gtL~v~~sg~l~~t~k~~i~tNL   54 (56)
T 3f7f_A           18 LVTLLPLE-NGLFQMGTLLVDSSGILTYTFQNNIPTNL   54 (56)
T ss_dssp             EEEEETTT-TCEEEEEEEEC-----CEEECCCEEECCC
T ss_pred             EEEECCCC-CCCEEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             99975567-87489999634776631245678789877


No 63 
>>1wln_A Afadin; beta sandwich, FHA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:)
Probab=20.74  E-value=50  Score=13.27  Aligned_cols=10  Identities=30%  Similarity=0.378  Sum_probs=4.1

Q ss_pred             CEECCCCCCC
Q ss_conf             2002665543
Q gi|254780406|r  107 RVISVGRLDI  116 (354)
Q Consensus       107 ~~~~vgRLD~  116 (354)
                      ..+.|||-..
T Consensus        36 ~~~~IGR~~~   45 (120)
T 1wln_A           36 SVTEVGTEKF   45 (120)
T ss_dssp             EEEECSSSCC
T ss_pred             CCEEECCCCC
T ss_conf             8389858878


No 64 
>>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:)
Probab=20.29  E-value=28  Score=14.84  Aligned_cols=12  Identities=8%  Similarity=-0.225  Sum_probs=4.0

Q ss_pred             CCEEEEEEEECC
Q ss_conf             740477521124
Q gi|254780406|r  140 QWLRVYRVRFHG  151 (354)
Q Consensus       140 ~~~k~Y~v~v~~  151 (354)
                      .+..-+.|-|++
T Consensus        69 ~~~~~i~v~vN~   80 (114)
T 1wgk_A           69 SVRPGILVLIND   80 (114)
T ss_dssp             SCCSSEEEEESS
T ss_pred             CCCEEEEEEECC
T ss_conf             850558999758


Done!