Query         T0527 APC67421.1, Burkholderia thailandensis E264, 142 residues
Match_columns 142
No_of_seqs    125 out of 13326
Neff          9.6 
Searched_HMMs 22458
Date          Fri May 21 18:04:21 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/hhm/T0527.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/hhm/T0527.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3eeh_A Putative light and redo  99.9 2.1E-26 9.1E-31  170.1  10.2  121    2-123     4-125 (125)
  2 2wkq_A NPH1-1, RAS-related C3   99.9 1.5E-22 6.6E-27  148.0   6.1  131    8-140    10-143 (332)
  3 2z6d_A Phototropin-2; PAS-fold  99.8 1.9E-21 8.3E-26  141.7   7.8  124    6-131     3-129 (130)
  4 2pr5_A Blue-light photorecepto  99.8 9.9E-21 4.4E-25  137.6  10.7  126   13-142     3-131 (132)
  5 2gj3_A Nitrogen fixation regul  99.8 5.4E-21 2.4E-25  139.1   8.6  116    8-125     4-119 (120)
  6 3h9w_A Diguanylate cyclase wit  99.8 3.3E-21 1.5E-25  140.3   7.3  109   18-127     2-111 (115)
  7 2v0u_A NPH1-1, LOV2; kinase, t  99.8 1.3E-21 5.7E-26  142.7   4.9  124   10-135     3-129 (146)
  8 1v9y_A Heme PAS sensor protein  99.8 7.4E-21 3.3E-25  138.3   7.3  131    1-135    32-166 (167)
  9 3lyx_A Sensory BOX/ggdef domai  99.8 2.4E-20 1.1E-24  135.4   8.2  116   10-127     8-123 (124)
 10 2r78_A Sensor protein; sensory  99.8 5.2E-20 2.3E-24  133.5   9.8  115    1-123     3-117 (117)
 11 3icy_A Sensor protein; sensory  99.8 5.3E-21 2.4E-25  139.1   3.9  116    6-123     1-118 (118)
 12 3f1p_B ARYL hydrocarbon recept  99.8 4.6E-20   2E-24  133.8   6.1  116   10-127     2-120 (121)
 13 3bwl_A Sensor protein; structu  99.8 1.4E-18 6.2E-23  125.3  10.1  117    2-123    10-126 (126)
 14 2vlg_A Sporulation kinase A; h  99.8 5.5E-19 2.4E-23  127.6   7.3  110   12-126     2-111 (111)
 15 3luq_A Sensor protein; PAS, hi  99.8   1E-18 4.6E-23  126.1   7.4  114    7-123     1-114 (114)
 16 3ewk_A Sensor protein; PAS dom  99.8 6.4E-18 2.9E-22  121.5  11.1  118    2-121   104-227 (227)
 17 3mjq_A Uncharacterized protein  99.7   2E-18 9.1E-23  124.4   8.0  119   11-134     1-119 (126)
 18 3f1p_A Endothelial PAS domain-  99.7 9.5E-19 4.2E-23  126.3   5.8  109   17-127     7-116 (117)
 19 1d06_A Nitrogen fixation regul  99.7 3.3E-18 1.5E-22  123.2   8.3  118    2-123     9-130 (130)
 20 2qkp_A Uncharacterized protein  99.7 6.8E-19   3E-23  127.1   4.1  128    7-138    17-146 (151)
 21 1wa9_A Period circadian protei  99.7 7.6E-21 3.4E-25  138.3  -7.2  131    2-134   141-276 (368)
 22 1n9l_A PHOT-LOV1, putative blu  99.7 2.1E-17 9.4E-22  118.6   8.4  105   18-124     2-109 (109)
 23 3gdi_A Period circadian protei  99.7 2.3E-18   1E-22  124.1   1.5  116    7-124   153-271 (309)
 24 2vv6_A FIXL, sensor protein FI  99.7   7E-17 3.1E-21  115.6   8.0  115   17-135     1-119 (119)
 25 3fc7_A HTR-like protein, senso  99.7 5.4E-17 2.4E-21  116.2   6.9  114    2-123    12-125 (125)
 26 1byw_A Protein (human ERG pota  99.7 1.2E-16 5.5E-21  114.2   6.7  104   22-125     4-110 (110)
 27 3mfx_A Sensory BOX/ggdef famil  99.6 4.7E-15 2.1E-19  105.2   8.2  116    5-125     3-125 (129)
 28 3cax_A Uncharacterized protein  99.6 7.2E-16 3.2E-20  109.8   3.5  119    7-133   237-355 (369)
 29 3ewk_A Sensor protein; PAS dom  99.6 1.4E-14 6.1E-19  102.5   9.6  119   21-141     1-119 (227)
 30 3d72_A Vivid PAS protein VVD;   99.5 9.1E-14 4.1E-18   97.8   8.4   99   18-118    34-146 (149)
 31 3clo_A Transcriptional regulat  99.5 1.4E-13 6.3E-18   96.7   8.3  124    2-126    26-167 (258)
 32 1oj5_A Steroid receptor coacti  99.5 1.1E-13 4.7E-18   97.4   7.1  109   17-127     5-117 (132)
 33 3fg8_A Uncharacterized protein  99.4   1E-13 4.5E-18   97.5   5.9  106   10-125    13-118 (118)
 34 1wa9_A Period circadian protei  99.4 3.8E-16 1.7E-20  111.4  -7.0  118   23-142    11-153 (368)
 35 3gdi_A Period circadian protei  99.4 2.4E-13   1E-17   95.4   3.6  120   12-133    18-143 (309)
 36 3a0r_A Sensor protein; four he  99.3 1.3E-13 5.8E-18   96.9  -0.5  118   10-136     9-127 (349)
 37 3b33_A Sensor protein; structu  99.2 3.2E-11 1.4E-15   83.2   7.7  107    9-122     7-114 (115)
 38 1ll8_A PAS kinase; PAS domain,  99.2 2.6E-11 1.2E-15   83.7   5.7  106   14-123     3-113 (114)
 39 1nwz_A PYP, photoactive yellow  99.1 3.8E-11 1.7E-15   82.8   5.4  107   10-122    18-125 (125)
 40 1mzu_A PPR; photoactive yellow  99.1 4.8E-11 2.1E-15   82.2   4.5  105    1-108    13-120 (129)
 41 2jhe_A Transcription regulator  99.0 6.5E-11 2.9E-15   81.5   3.0  110    3-124    74-187 (190)
 42 3a0s_A Sensor protein; PAS-fol  98.9 3.4E-09 1.5E-13   71.6   8.9   95   18-121     1-96  (96)
 43 2w0n_A Sensor protein DCUS; si  98.8 7.1E-10 3.2E-14   75.5   2.1  111    2-123     8-118 (118)
 44 2ool_A Sensor protein; bacteri  97.7 0.00012 5.3E-09   45.6   7.3   75   21-98     44-119 (337)
 45 2vea_A Phytochrome-like protei  96.4 0.00032 1.4E-08   43.2  -0.5   53   21-75     31-84  (520)
 46 2o9c_A Bacteriophytochrome; ph  96.0   0.023   1E-06   32.5   7.5  109   20-140    54-163 (342)
 47 3fos_A Sensor protein; sensor   83.0     2.3  0.0001   21.2   7.9   97    8-128    54-152 (214)
 48 3e4o_A C4-dicarboxylate transp  50.6      12 0.00054   17.0   6.5   99    4-125    97-196 (305)
 49 3lif_A Putative diguanylate cy  39.3      18 0.00082   16.0   7.3   97    8-127    57-156 (254)
 50 1p0z_A Sensor kinase CITA; tra  37.3      20 0.00088   15.8   3.4   28   97-124   100-127 (131)
 51 3ddj_A CBS domain-containing p  33.1      19 0.00083   15.9   2.2   40   99-139   257-296 (296)
 52 3fgx_A Rbstp2171; structural g  28.4      17 0.00077   16.1   1.4   20   55-74     68-87  (114)
 53 1vq8_K 50S ribosomal protein L  28.1      14 0.00063   16.6   0.9   35   86-120    78-114 (132)
 54 3bbo_M Ribosomal protein L14;   23.8      19 0.00083   15.9   0.8   33   85-117    66-100 (121)
 55 2zkr_k 60S ribosomal protein L  21.1      23   0.001   15.4   0.9   36   84-119    84-121 (140)
 56 2o0y_A Transcriptional regulat  20.3      41  0.0018   14.0   6.7   45   97-141   204-253 (260)
 57 3g6o_A Bacteriophytochrome; al  20.0      41  0.0018   14.0   6.2   61   21-88     28-88  (505)

No 1  
>3eeh_A Putative light and redox sensing histidine kinase; structural genomics, PSI, MCSG, protein structure initiative; HET: PG5; 1.95A {Haloarcula marismortui}
Probab=99.93  E-value=2.1e-26  Score=170.10  Aligned_cols=121  Identities=24%  Similarity=0.473  Sum_probs=113.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECC-CCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             579899999999987068279998079-8989986589986379987964312467887653224789987532102465
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPK-TGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD   80 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~-~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~   80 (142)
                      ++|++||++|+.+++++++++|.+|++ +.++|+|+++++++||+++++.+.+..|.+++||||++.+.+.+..+.. +.
T Consensus         4 ~~l~~se~r~~~i~e~~~~~i~~~d~~~~~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~-~~   82 (125)
T 3eeh_A            4 QQAAKSERRVRELTEATNDILWEFTADLSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQSLMD-GE   82 (125)
T ss_dssp             ------CHHHHHHHSCCCCEEEEEETTSSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHHHHT-TC
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHCCC-CC
T ss_conf             99999999999998649844999999899599978388651234532111110144205875203203544222034-32


Q ss_pred             CCCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             3222111001000243200025412455350367777788178
Q T0527            81 TYDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        81 ~~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      +++.+||+++++|+++|++.++.|++|++|++.+++|+++|||
T Consensus        83 ~~~~e~r~~~~~G~~~wv~~~~~~i~d~~g~~~~~~g~~~DIT  125 (125)
T 3eeh_A           83 SADVECRVNATEEYQRWVWIQGEPITNDAGETVRVAGFARDIT  125 (125)
T ss_dssp             CEEEEEEECGGGTTCEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEEC
T ss_conf             0467788786998789999999999999989999999999809


No 2  
>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*
Probab=99.86  E-value=1.5e-22  Score=148.02  Aligned_cols=131  Identities=15%  Similarity=0.190  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHCCCEEEEEE---CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9999999870682799980---7989899865899863799879643124678876532247899875321024653222
Q T0527             8 EERFQLAVSGASAGLWDWN---PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDV   84 (142)
Q Consensus         8 e~r~~~~~~~~~~~i~~~d---~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~   84 (142)
                      +-+|..++++++++++..|   +++.++|+|+++++|+||+.+++.|..  +..+.+|+..+.....+..++..+..+..
T Consensus        10 ~~~l~~~~e~~~~~~vi~D~~~~dg~Ii~vN~a~~~l~Gy~~~EliG~~--~~~l~~~~~~~~~~~~i~~~l~~~~~~~~   87 (332)
T 2wkq_A           10 HGSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRN--ARFLQGPETDRATVRKIRDAIDNQTEVTV   87 (332)
T ss_dssp             ----CCCGGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTCCHHHHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHHHCCCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             4399999970897599984899989499883899998883999985998--77717988899999999999984983999


Q ss_pred             HHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH
Q ss_conf             11100100024320002541245535036777778817899999999999999984
Q T0527            85 EYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREELR  140 (142)
Q Consensus        85 e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l~  140 (142)
                      +++..++||+.+|+..++.|++|++|++.+++|+++|||++|++|++|+++....+
T Consensus        88 e~~~~~kdG~~~~v~~~~~pi~d~~G~i~~~v~~~~DITe~k~~e~el~~~~~~~~  143 (332)
T 2wkq_A           88 QLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKK  143 (332)
T ss_dssp             EEEEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             99999789999999999996188999999999999957147898877888888888


No 3  
>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A*
Probab=99.85  E-value=1.9e-21  Score=141.73  Aligned_cols=124  Identities=15%  Similarity=0.238  Sum_probs=108.5

Q ss_pred             HHHHHHHHHHHHCCCEEEEEE---CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999999999870682799980---79898998658998637998796431246788765322478998753210246532
Q T0527             6 ASEERFQLAVSGASAGLWDWN---PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTY   82 (142)
Q Consensus         6 ~se~r~~~~~~~~~~~i~~~d---~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~   82 (142)
                      .+.+.|+.++++++.++.+.|   +++.++|+|+++++|+||+++++.|..  +..++||+..+.....+..++.++.++
T Consensus         3 r~~~~l~~~~~~~~~~~~i~D~~~~d~~I~~vN~a~~~~~G~~~~elig~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~   80 (130)
T 2z6d_A            3 RVSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRN--CRFLQGPDTDKNEVAKIRDCVKNGKSY   80 (130)
T ss_dssp             ----CHHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTSCHHHHHHHHHHHHTTCCE
T ss_pred             CHHHHHHHHHHHCCCCEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHHHCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             568999999983899699998989979899998799998892989975986--676538778889999999998630452


Q ss_pred             CCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHH
Q ss_conf             2211100100024320002541245535036777778817899999999
Q T0527            83 DVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDA  131 (142)
Q Consensus        83 ~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~  131 (142)
                      ..++++++++|+.+|+.++..|++|++|++.+++|+++|||++|+++++
T Consensus        81 ~~e~~~~~~dG~~~w~~~~~~pi~d~~g~~~~~i~~~~DITe~ke~~~e  129 (130)
T 2z6d_A           81 CGRLLNYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGVND  129 (130)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCTTC-----
T ss_pred             EEEEEEEECCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHHHHHC
T ss_conf             0699999628866999999999999999999999999988388899856


No 4  
>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, signaling protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*
Probab=99.84  E-value=9.9e-21  Score=137.60  Aligned_cols=126  Identities=18%  Similarity=0.261  Sum_probs=108.9

Q ss_pred             HHHHHCCCEEEEEEC---CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEE
Q ss_conf             998706827999807---98989986589986379987964312467887653224789987532102465322211100
Q T0527            13 LAVSGASAGLWDWNP---KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVR   89 (142)
Q Consensus        13 ~~~~~~~~~i~~~d~---~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~   89 (142)
                      .+++++|+||+..|+   ++.++|+|+++++++||+++++.+..  +..+.+|+..+.....+..++..+..++.+++++
T Consensus         3 ~l~d~~~~~i~v~d~~~~dg~I~~~N~a~~~~~G~s~~el~g~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~   80 (132)
T 2pr5_A            3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKN--CRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNY   80 (132)
T ss_dssp             ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSC--GGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEE
T ss_pred             HHHHCCCCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             68857884199998988979899996899999891999980541--0004441014999999999985288403565547


Q ss_pred             ECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             10002432000254124553503677777881789999999999999998429
Q T0527            90 TRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREELRRL  142 (142)
Q Consensus        90 ~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l~~l  142 (142)
                      +++|..+|+..+..|+.+++|.  .++++++|||++|++|++|+++..+|+.|
T Consensus        81 ~~dG~~~~~~~~~~~i~~~~~~--~~i~~~~DITe~k~~e~~L~~~~~~l~~l  131 (132)
T 2pr5_A           81 KKDGTMFWNELNIDPMEIEDKT--YFVGIQNDITKQKEYEKLLEDSLTEITAL  131 (132)
T ss_dssp             CTTSCEEEEEEEEEEEEETTEE--EEEEEEEECHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCEEEEEEEEEEEECCCCC--EEEEEEEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             4799799999888889909912--99889997659999999999999999813


No 5  
>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}
Probab=99.84  E-value=5.4e-21  Score=139.09  Aligned_cols=116  Identities=19%  Similarity=0.213  Sum_probs=104.8

Q ss_pred             HHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             99999998706827999807989899865899863799879643124678876532247899875321024653222111
Q T0527             8 EERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYR   87 (142)
Q Consensus         8 e~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r   87 (142)
                      .++|+.+++++|++++..|++|.++|+|+++++++||+++++.+..  +..+.||++.+.+.+.+...+..+.+|+.+++
T Consensus         4 ~~~~~~~~e~s~~~i~i~d~~g~i~~~N~a~~~~~G~~~~el~g~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~   81 (120)
T 2gj3_A            4 PEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN--ESILSNGTTPRLVYQALWGRLAQKKPWSGVLV   81 (120)
T ss_dssp             HHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHCCCTTGGGGCB--GGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHCCCHHEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--CCCCEECCCCHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             9999999971241529996999999996899998796956616754--00011013536789998763306973061255


Q ss_pred             EEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHH
Q ss_conf             00100024320002541245535036777778817899
Q T0527            88 VRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDR  125 (142)
Q Consensus        88 i~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~  125 (142)
                      .+++||+.+|+..+++|++|++|++.+++|+++|||+.
T Consensus        82 ~~~kdG~~~~~~~~~~~i~d~~g~~~~~i~~~~DITel  119 (120)
T 2gj3_A           82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSEL  119 (120)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCSC
T ss_pred             EECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCC
T ss_conf             58699989999999999999998999999999956677


No 6  
>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.90A {Marinobacter aquaeolei VT8}
Probab=99.84  E-value=3.3e-21  Score=140.30  Aligned_cols=109  Identities=20%  Similarity=0.435  Sum_probs=99.4

Q ss_pred             CCCEEEEEECCC-CEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCC
Q ss_conf             682799980798-9899865899863799879643124678876532247899875321024653222111001000243
Q T0527            18 ASAGLWDWNPKT-GAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFR   96 (142)
Q Consensus        18 ~~~~i~~~d~~~-~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~   96 (142)
                      +++++|.+|+++ .+.|+|+++.+++||+++++.+. ..|.+++||||++.+...+...+.++.+++.++|+++++|.++
T Consensus         2 t~~~~W~~D~~t~~~~yvn~~~~~i~G~~~e~~~~~-~~~~~~i~pdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~   80 (115)
T 3h9w_A            2 TKAIPWKINWQTMAFEYIGPQIEALLGWPQGSWKSV-EDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHYV   80 (115)
T ss_dssp             -CCEEEEEETTTTEEEEECTHHHHHHCSCGGGCCBH-HHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSCEE
T ss_pred             CCEEEEEEECCCCEEEEECHHHHHHHCCCHHHCCCC-CHHHHEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCH
T ss_conf             847999998999989999999999849997882893-0332012256799999999999855970789999996056520


Q ss_pred             CEEEEEEECCCCCCEEEEEEEEEEEHHHHHH
Q ss_conf             2000254124553503677777881789999
Q T0527            97 WIQSRGQALWNSAGEPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        97 w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~  127 (142)
                      |++.++.|++|++|++.+++|+++|||++..
T Consensus        81 wv~~~~~~~~d~~g~~~~~~g~~~DITee~~  111 (115)
T 3h9w_A           81 WIRDVVHVVRDDSGEVEALIGFMFDISLEHH  111 (115)
T ss_dssp             EEEEEEEEEECTTSCEEEEEEEEEECGGGGC
T ss_pred             HHEEECEEEECCCCCEEEEEEEEEEECCCCC
T ss_conf             1102010499999899999999998997876


No 7  
>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal transduction, phototropin1; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*
Probab=99.83  E-value=1.3e-21  Score=142.69  Aligned_cols=124  Identities=15%  Similarity=0.210  Sum_probs=108.1

Q ss_pred             HHHHHHHHCCCEEEEEE---CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             99999870682799980---798989986589986379987964312467887653224789987532102465322211
Q T0527            10 RFQLAVSGASAGLWDWN---PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEY   86 (142)
Q Consensus        10 r~~~~~~~~~~~i~~~d---~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~   86 (142)
                      +|+.+++++++++.+.|   +++.++|+|+++++|+||+++++.|..  +..+.+|+..+.....+...+.++.+|..++
T Consensus         3 ~l~~~~e~~~~~~vi~d~~~~dg~I~~vN~a~~~~~Gy~~~el~G~~--~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~   80 (146)
T 2v0u_A            3 FLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRN--CRFLQGPETDRATVRKIRDAIDNQTEVTVQL   80 (146)
T ss_dssp             SCCCTGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTSCHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCEEEEECHHHHHHHCCCHHHHHCCC--HHHHCCCCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf             89999981898099995889989799996799998896999981774--2202033454999999999998199752799


Q ss_pred             HEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHH
Q ss_conf             1001000243200025412455350367777788178999999999999
Q T0527            87 RVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVS  135 (142)
Q Consensus        87 ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~  135 (142)
                      +.+++||+.+|+..+..|++|++|++.+++++++|||++|+.+++++.+
T Consensus        81 ~~~~kdG~~~~v~~~~~p~~d~~g~~~~~v~v~~DITe~k~~~~e~~~~  129 (146)
T 2v0u_A           81 INYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGV  129 (146)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHHHHHHH
T ss_pred             EEEECCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHHHHHHHHHH
T ss_conf             8784388469999999999979989999999999888999999999999


No 8  
>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli K12} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*
Probab=99.83  E-value=7.4e-21  Score=138.31  Aligned_cols=131  Identities=16%  Similarity=0.185  Sum_probs=108.8

Q ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             95798999999999870682799980798989986589986379987964312467887653224789987532102465
Q T0527             1 SNALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD   80 (142)
Q Consensus         1 ~~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~   80 (142)
                      .+|+++++.+|+.+++++++|++.+|.+|.++++|++++++|||+++++.+..  +..++++++.......+.....++.
T Consensus        32 ~~~~~~~~~~~~~~le~s~dgi~i~d~~g~Ii~~N~a~~~l~G~~~~eliG~~--~~~l~~~~~~~~~~~~~~~~~~~~~  109 (167)
T 1v9y_A           32 TDADNAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNN--IDMLIPRDLRPAHPEYIRHNREGGK  109 (167)
T ss_dssp             --------CCHHHHHHTCSSEEEEECTTSBEEEECHHHHHHHSCCGGGTTTSB--GGGGSCGGGTTTHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--CCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             99998889999999973876299995989899997799998657888824677--4333222233200124677766411


Q ss_pred             C----CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHH
Q ss_conf             3----222111001000243200025412455350367777788178999999999999
Q T0527            81 T----YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVS  135 (142)
Q Consensus        81 ~----~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~  135 (142)
                      .    ...+...+++||..+|+..+..|+..++ .+ .++++++|||++|++|++|++.
T Consensus       110 ~~~~~~~~e~~~~~kdG~~~~v~isi~~i~~~~-~~-~~v~i~~DITe~k~~ee~l~~L  166 (167)
T 1v9y_A          110 ARVEGMSRELQLEKKDGSKIWTRFALSKVSAEG-KV-YYLALVRDASVEMAQKEQTRQL  166 (167)
T ss_dssp             -------CEEEEECTTSCEEEEEEEEEEEEETT-EE-EEEEEEEC--------------
T ss_pred             CCCCCCCEEEEEEEEECCCCCEEEEEEEEEECC-EE-EEEEEEEECHHHHHHHHHHHHH
T ss_conf             334543169999984023532079999999699-89-9999999987999999999703


No 9  
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}
Probab=99.82  E-value=2.4e-20  Score=135.35  Aligned_cols=116  Identities=15%  Similarity=0.187  Sum_probs=104.1

Q ss_pred             HHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEE
Q ss_conf             99999870682799980798989986589986379987964312467887653224789987532102465322211100
Q T0527            10 RFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVR   89 (142)
Q Consensus        10 r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~   89 (142)
                      ++..+++++|++++.+|++|.+++||++++++|||+++++.+..  +..+++|.+...+...+...+..+..+..++++.
T Consensus         8 ~~~~~fd~~~d~i~~~d~~g~i~~~N~~~~~~~g~~~~e~lg~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   85 (124)
T 3lyx_A            8 QRAKAFDYVFDAIVVTDLQGFIIDWNKGSETLYGYSKEQAIGQP--VNMLHVPGDTEHITSEVISAVENQGKWTGEIRML   85 (124)
T ss_dssp             HHHHGGGTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTTHHHHHHHHHHHHHHTSCEEEEEEEE
T ss_pred             HHHHHHHCCCCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCC--HHEEECHHHHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             99999964711508997999799891999999882999992997--4225561454567788898875068520266552


Q ss_pred             ECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHH
Q ss_conf             10002432000254124553503677777881789999
Q T0527            90 TRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        90 ~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~  127 (142)
                      +++|+.+|+..+.+|++|++|++.+++++++|||++|+
T Consensus        86 ~~~g~~~~~~~~~~pi~d~~g~~~~~i~i~~DITerK~  123 (124)
T 3lyx_A           86 HKDGHIGWIESMCVPIYGENYQMVGALGINRDITKRKK  123 (124)
T ss_dssp             CTTSCEEEEEEEEEEEECSTTCEEEEEEEEEECSCC--
T ss_pred             CCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHC
T ss_conf             36996889999987899899999999999999937735


No 10 
>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}
Probab=99.82  E-value=5.2e-20  Score=133.50  Aligned_cols=115  Identities=18%  Similarity=0.222  Sum_probs=103.4

Q ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             95798999999999870682799980798989986589986379987964312467887653224789987532102465
Q T0527             1 SNALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD   80 (142)
Q Consensus         1 ~~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~   80 (142)
                      +|+|+.|+++|+.+++++++++|.+|+++.++++|+++++++||+++++.+.  .+.+++||+|.+.+...+..+.. +.
T Consensus         3 ~e~L~~~e~~fr~i~e~~~~~i~i~d~~g~i~~~N~~~~~~~g~~~~~l~g~--~~~~~~~~~~~~~~~~~~~~~~~-~~   79 (117)
T 2r78_A            3 TENLYFQSNAYRALFEHAIDGIFIMDAEGHYLDVNPAICSAIGYTRDEFLAL--DWGVLSRGVDSGWAAASLARIVG-GE   79 (117)
T ss_dssp             CCSHHHHHHHHHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTC--BTTTTTTCSTTSHHHHHHHHHHT-TC
T ss_pred             HHHHHHHHHHHHHHHHHCCHHEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHC-CC
T ss_conf             8999999999999998167450999699989999399999879597894126--73214540013657899999983-99


Q ss_pred             CCCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             3222111001000243200025412455350367777788178
Q T0527            81 TYDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        81 ~~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      ++..++++++++|+.+|+.+++.|+.|  |+   ++|+++|||
T Consensus        80 ~~~~e~~~~~~dG~~~~~~~~~~~i~d--~~---~~~~~~DIT  117 (117)
T 2r78_A           80 PLREERTVWTRNGDQLTVELSAHLLPD--GK---ILGIARDVS  117 (117)
T ss_dssp             CEEEEEEEECTTSCEEEEEEEEEECTT--SC---EEEEEEC--
T ss_pred             CCEEEEEEECCCCCEEEEEEEEEEEEC--CE---EEEEEEECC
T ss_conf             837899999799999999999999889--98---999999794


No 11 
>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}
Probab=99.81  E-value=5.3e-21  Score=139.15  Aligned_cols=116  Identities=22%  Similarity=0.318  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCEEE--ECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9999999998706827999807989899--86589986379987964312467887653224789987532102465322
Q T0527             6 ASEERFQLAVSGASAGLWDWNPKTGAMY--LSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYD   83 (142)
Q Consensus         6 ~se~r~~~~~~~~~~~i~~~d~~~~~~~--~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~   83 (142)
                      .|+++|+.+++++|++||.+|++++..+  +|+.+..++|++..+.  ....+.+++||+|++.+...+..+..++.++.
T Consensus         1 ~~~e~~r~l~d~~p~~i~~~d~~g~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~p~~~~~~~~~~~~~~~~~~~~~   78 (118)
T 3icy_A            1 SNAEELQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHAGT--TRLNTLSMIHHDDRHMLSNAYSKLREAKHSLT   78 (118)
T ss_dssp             CHHHHHHHHHTTCCCCCEEECTTSCEEECCCCCGGGGGGEEEETTE--EEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEE
T ss_pred             CCHHHHHHHHHCCCEEEEEEECCCCEEEEECCHHHHCCCCCCHHHH--CCCCHHHHCCHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             9889999998549401899988898899965768746328495886--58988995698899898852002332234431


Q ss_pred             CHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             2111001000243200025412455350367777788178
Q T0527            84 VEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        84 ~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      .++++++++|..+|+..++.|++|++|++.+++|+++|||
T Consensus        79 ~e~~~~~~~g~~~wv~~~~~~~~d~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           79 LVYRIVTPEGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT  118 (118)
T ss_dssp             EEEEEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             CCEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECC
T ss_conf             2015782599799999999999999979999999999779


No 12 
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A* 2k7s_A 2a24_B
Probab=99.80  E-value=4.6e-20  Score=133.80  Aligned_cols=116  Identities=15%  Similarity=0.264  Sum_probs=104.5

Q ss_pred             HHHHHHHHCCCEEE-EEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCHHH
Q ss_conf             99999870682799-98079898998658998637998796431246788765322478998753210246-53222111
Q T0527            10 RFQLAVSGASAGLW-DWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHR-DTYDVEYR   87 (142)
Q Consensus        10 r~~~~~~~~~~~i~-~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~-~~~~~e~r   87 (142)
                      +|+.+.+.+|..++ ..|++|+++|+|+++++++||+++++.+.  .+.+++||+|++.+...+...+.++ ..+..+++
T Consensus         2 ~f~~l~~~~p~~fi~r~d~dG~i~~vn~~~~~i~Gy~~~el~g~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~   79 (121)
T 3f1p_B            2 EFKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGK--NIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFR   79 (121)
T ss_dssp             ------CCCCCEEEEEECTTSBEEEECTTHHHHHSCCGGGTTTS--BGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEE
T ss_pred             CCCCCCCCCCCEEEEEECCCCCEEEECHHHHHHHCCCHHHHHHH--HHHHHHCCCHHHEEEEEECCCCCCCCCEEEEEEE
T ss_conf             43112205995099999899999999989998879699998653--4566400000102222100010123430458997


Q ss_pred             EEECCCCCCCEEEEEEECCCC-CCEEEEEEEEEEEHHHHHH
Q ss_conf             001000243200025412455-3503677777881789999
Q T0527            88 VRTRSGDFRWIQSRGQALWNS-AGEPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        88 i~~~~G~~~w~~~~~~~~~d~-~g~~~~~~g~~~DITe~k~  127 (142)
                      ++++||+++|++.++.|++|+ +|++..++|+.+|||++|+
T Consensus        80 ~~~kdG~~~w~~~~~~~i~d~~~g~~~~ii~v~~DIt~rkq  120 (121)
T 3f1p_B           80 FRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQ  120 (121)
T ss_dssp             EECTTSCEEEEEEEEEEECCTTCCCCCEEEEEEEECCCC--
T ss_pred             EECCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCC
T ss_conf             47699959999999999993899969999999999953026


No 13 
>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protein, PSI-2, protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}
Probab=99.77  E-value=1.4e-18  Score=125.30  Aligned_cols=117  Identities=15%  Similarity=0.123  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             57989999999998706827999807989899865899863799879643124678876532247899875321024653
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~   81 (142)
                      ++|++++++|+.+++++|++++.+|++|.++++|+++++++||+++++.+.  .+.++++|++.+.+...+..+. .+..
T Consensus        10 ~~L~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~a~~~~~g~~~eel~g~--~~~~~~~~~~~~~~~~~~~~~~-~~~~   86 (126)
T 3bwl_A           10 KRLEETSSRLEALFENSPDMIDVLDADGTICEVNQRFCAELGYDESEVLGR--SIWEFDLMFDAEDVQTQLSGFS-VDER   86 (126)
T ss_dssp             HHHHHHHHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHTCCGGGTTTS--BGGGTBTTCCHHHHHHHHHTCC-TTCE
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEHHHHHHHCCCHHHHHCC--CHHHHCCCCCHHHHHHHHHHHH-HCCC
T ss_conf             999999999999997197329999099989998457688869889998359--8989168348999999999998-1996


Q ss_pred             CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             222111001000243200025412455350367777788178
Q T0527            82 YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        82 ~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      ...+++++++||+++|+..+.+|+. .+|++ .++++++|||
T Consensus        87 ~~~e~~~~~kdG~~~~~~~~~~~~~-~~~~~-~~~~v~~DIT  126 (126)
T 3bwl_A           87 RKFEGLYERRDGSTMSVEVHLLRFN-LEGED-RFLAISRDIT  126 (126)
T ss_dssp             EEEEEEEECTTSCEEEEEEEEEEEE-ETTEE-EEEEEEEEC-
T ss_pred             EEEEEEEEECCCCEEEEEEEEEEEE-ECCEE-EEEEEEEECC
T ss_conf             6999999965995999999999998-59929-9999999879


No 14 
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}
Probab=99.77  E-value=5.5e-19  Score=127.64  Aligned_cols=110  Identities=14%  Similarity=0.177  Sum_probs=99.0

Q ss_pred             HHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEEC
Q ss_conf             99987068279998079898998658998637998796431246788765322478998753210246532221110010
Q T0527            12 QLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTR   91 (142)
Q Consensus        12 ~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~   91 (142)
                      +.++++++++++..|.+|.++|+|+++++++||+++++.+.  .+.+++||+|+..+...+..   .+.....+||++++
T Consensus         2 ~~~l~~~~D~i~~~d~~G~i~~vN~~~~~i~Gy~~~el~g~--~~~~~~hped~~~~~~~~~~---~~~~~~~~~r~~~k   76 (111)
T 2vlg_A            2 EFPLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGS--FLKTFLHEEDQFLVESYFYN---EHHLMPCTFRFIKK   76 (111)
T ss_dssp             -------CCEEEEECTTSBEEEECTTHHHHHSCCHHHHTTS--BGGGGBCGGGHHHHHHHHHC---SCCSSCEEEEEECT
T ss_pred             EEEEEECCCEEEEECCCCEEEEECHHHHHHHCCCHHHHHHH--HHHCCCCHHHHHHHHHHHHH---HCCCEEEEEEEECC
T ss_conf             17668367379999899849999989999878998896554--43115988899999999985---04860644568958


Q ss_pred             CCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHH
Q ss_conf             00243200025412455350367777788178999
Q T0527            92 SGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRK  126 (142)
Q Consensus        92 ~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k  126 (142)
                      ||+++|++.++.++.++.|.+.+.+.+..|||++|
T Consensus        77 dG~~~Wve~~~~~i~~~~g~~~r~i~~~~di~e~k  111 (111)
T 2vlg_A           77 DHTIVWVEAAVEIVTTRAERTEREIILKMKVLEEE  111 (111)
T ss_dssp             TSCEEEEEEEEEEC-------CCCEEEEEEEC---
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEEEEEECCCC
T ss_conf             99999999999999879979407999998803279


No 15 
>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}
Probab=99.76  E-value=1e-18  Score=126.06  Aligned_cols=114  Identities=18%  Similarity=0.199  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             99999999870682799980798989986589986379987964312467887653224789987532102465322211
Q T0527             7 SEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEY   86 (142)
Q Consensus         7 se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~   86 (142)
                      ||++|+.+++++|+++|.+|.+++++++|+++++++|++++++.+...   ..++|.+.+.....+...+.++.....+.
T Consensus         1 Se~~lr~i~~~~p~~i~~~D~~g~~~~~N~~~~~~~g~~~~~~~g~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (114)
T 3luq_A            1 SDERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSH---YDIFPEIGEEWKSVHRRGLAGEVIRVEED   77 (114)
T ss_dssp             CCHHHHHHHHTCSSEEEEEETTCBEEEECHHHHHHTTCCSSCCTTCBH---HHHCTTCCHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CHHHHHHHHHHHCHHHEEECCCCCEEEECHHHHHHHCCCCHHCCCCCC---CCCCCCCCHHHHHHHHHHHCCCCCEEEEE
T ss_conf             979999999710467299979996999949989872457000268762---00123310233358999980898400342


Q ss_pred             HEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             1001000243200025412455350367777788178
Q T0527            87 RVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        87 ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      +..+++|..+|+..++.|++|++|++.+++++++|||
T Consensus        78 ~~~~~~g~~~~~~~~~~pi~d~~G~v~g~~~~~~DIT  114 (114)
T 3luq_A           78 CFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             EEEC--CCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECC
T ss_conf             2101378329999999999999999999999999859


No 16 
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transferase, flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}
Probab=99.75  E-value=6.4e-18  Score=121.52  Aligned_cols=118  Identities=15%  Similarity=0.168  Sum_probs=105.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             57989999999998706827999807989899865899863799879643124678876532247899875321024653
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~   81 (142)
                      .+++++.++++.+++++++++|.+|+++.++++|+++++++||+++++.+.  .+..++||++.......+..++..+..
T Consensus       104 ~~~~~~~~~~~~~l~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (227)
T 3ewk_A          104 KEAEAQLARLKQAMDANSEMILLTDRAGRIIYANPALCRFSGMAEGELLGQ--SPSILDSPLADQETLAAMQEALQAGQP  181 (227)
T ss_dssp             THHHHHHHHHHHHHHTCCSEEEEECTTSCEEEECHHHHHHHTCCTHHHHSS--CGGGGBCTTSCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHCEEEEECCCCEEEEECHHHHHHCCCCHHHHHCC--CCCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             999999876799998641026998489759999868876449997996214--654211454210134566776522674


Q ss_pred             CCCHHHEEE------CCCCCCCEEEEEEECCCCCCEEEEEEEEEEE
Q ss_conf             222111001------0002432000254124553503677777881
Q T0527            82 YDVEYRVRT------RSGDFRWIQSRGQALWNSAGEPYRMVGWIMD  121 (142)
Q Consensus        82 ~~~e~ri~~------~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~D  121 (142)
                      +..+++.++      ++|+.+|+..++.|++|++|++.+++|+++|
T Consensus       182 ~~~e~~~~~k~~~~~~dG~~~wv~~~~~pi~~~~g~~~~~~~i~~D  227 (227)
T 3ewk_A          182 WSGRLLNRRRTGPAPHDAEDYWAEISTTPIHTDGNGLVGYVQIQHD  227 (227)
T ss_dssp             EECCEEEEEECCSSSSCEEEEEEEEEEEEEECSSSCEEEEEEEEEC
T ss_pred             EEEEEEEEEECCCCCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEC
T ss_conf             6999999984374567982999999999999899999999999989


No 17 
>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}
Probab=99.75  E-value=2e-18  Score=124.35  Aligned_cols=119  Identities=12%  Similarity=0.029  Sum_probs=101.2

Q ss_pred             HHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEE
Q ss_conf             99998706827999807989899865899863799879643124678876532247899875321024653222111001
Q T0527            11 FQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRT   90 (142)
Q Consensus        11 ~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~   90 (142)
                      |+.+++++++++|.+|.+|+++++|+++.+++|++++++.+.  .+.++++|++...+...+..+. .+..+..++++++
T Consensus         1 l~~ile~~~d~i~i~d~~g~i~~~N~a~~~~~g~~~~e~lg~--~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~e~~~~~   77 (126)
T 3mjq_A            1 MKNFLETIEDMILIINREGRLLYANTAVPKKLGYTHEELMSM--HILTITSAGKMAEGEKILAELF-AGKKESLPLSLEK   77 (126)
T ss_dssp             -CTTGGGCSSEEEEEETTSBEEEECTHHHHHHSCCHHHHHHS--BHHHHHCTTCHHHHHHHHHHHH-HTCCSEEEEEEEC
T ss_pred             CHHHHHCCCCCEEEECCCCCEEEEEHHHHHCCCCCHHHHCCC--EEEEEECCCCCCCCHHHHHHHH-CCCCCEEEEEEEC
T ss_conf             968985092245999299959999025330279986880131--0235402433322013455542-2576148999995


Q ss_pred             CCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHH
Q ss_conf             00024320002541245535036777778817899999999999
Q T0527            91 RSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRV  134 (142)
Q Consensus        91 ~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~  134 (142)
                      ++|.++|+.++..|+.++++  ..++++++|||++|++|..+..
T Consensus        78 ~~G~~~~v~~~~~~i~~~~~--~~~~~i~~DITerK~Ae~~~~~  119 (126)
T 3mjq_A           78 KEGTSIPAKARIWQGKWHNE--PCLFAIIKDLSKEERASSPPFL  119 (126)
T ss_dssp             TTSCEEEEEEEEEEEESSSS--EEEEEEEEECC-----------
T ss_pred             CCCCEEEEEEEEEEEEECCE--EEEEEEEEECCHHHHHHHHHHH
T ss_conf             79989999999999998996--6999999988899998668976


No 18 
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A
Probab=99.75  E-value=9.5e-19  Score=126.27  Aligned_cols=109  Identities=15%  Similarity=0.291  Sum_probs=99.9

Q ss_pred             HCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCC
Q ss_conf             06827999807989899865899863799879643124678876532247899875321024653222111001000243
Q T0527            17 GASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFR   96 (142)
Q Consensus        17 ~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~   96 (142)
                      .++..++..+++|.++|+|+++++++||+++++.+.  .+..++||+|...+.+.+...+.++..+..+++++++||.++
T Consensus         7 ds~~fi~~~~~dg~i~~~N~~~~~~~G~~~~el~g~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~i   84 (117)
T 3f1p_A            7 DSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR--SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYV   84 (117)
T ss_dssp             GGGEEEEEECTTCBEEEECTHHHHHHCCCHHHHTTS--BGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEE
T ss_pred             CCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CEEEEECHHHCCHHHHHHHHCCCCCCCEECCEEEECCCCCEE
T ss_conf             758289999999989999989999859696791163--001672713511123333211111221001100187999799


Q ss_pred             CEEEEEEECCCC-CCEEEEEEEEEEEHHHHHH
Q ss_conf             200025412455-3503677777881789999
Q T0527            97 WIQSRGQALWNS-AGEPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        97 w~~~~~~~~~d~-~g~~~~~~g~~~DITe~k~  127 (142)
                      |+..+++|++|+ +|+|..++++.+|||++|+
T Consensus        85 wv~~~~~~i~d~~~~~~~~iv~~~~dITe~k~  116 (117)
T 3f1p_A           85 WLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK  116 (117)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEEEECSCCBC
T ss_pred             EEEEEEEEEEECCCCCEEEEEEEEEECCHHHC
T ss_conf             99999999997899939999999999952304


No 19 
>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two- component system; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*
Probab=99.74  E-value=3.3e-18  Score=123.17  Aligned_cols=118  Identities=11%  Similarity=0.092  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             57989999999998706827999807989899865899863799879643124678876532247899875321024653
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~   81 (142)
                      ++|++++++|+.+++++++|++.+|.+|.++++|++++++|||+++++.+.+  +..+++|+++......+...+.++..
T Consensus         9 ~~l~~~e~~l~~i~~~~~~~ii~~D~~g~i~~~N~~~~~~~G~~~~el~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (130)
T 1d06_A            9 DVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQN--LRILMPEPYRHEHDGYLQRYMATGEK   86 (130)
T ss_dssp             HHHHHHTSCHHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCC--CCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999970762169998999699887999988796979974997--54336812179999999999971987


Q ss_pred             ----CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             ----222111001000243200025412455350367777788178
Q T0527            82 ----YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        82 ----~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                          +..++...+++|..+|+..+.+++.+.++  ..++++++|||
T Consensus        87 ~~~~~~~e~~~~~~~G~~~~v~~~~s~~~~~~~--~~~~~i~~DIT  130 (130)
T 1d06_A           87 RIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGE--RFFTGFIRDLT  130 (130)
T ss_dssp             SSTTSCEEEEEECTTSCEEEEEEEEEEEEETTE--EEEEEEEEECC
T ss_pred             CCCCEEEEEEEECCCCCEEEEEEEEEEEEECCE--EEEEEEEEECC
T ss_conf             556516899999489999999999999998994--89999999787


No 20 
>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; 1.75A {Streptococcus mutans UA159}
Probab=99.74  E-value=6.8e-19  Score=127.10  Aligned_cols=128  Identities=9%  Similarity=-0.005  Sum_probs=101.5

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             99999999870682799980798989986589986--3799879643124678876532247899875321024653222
Q T0527             7 SEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKI--MGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDV   84 (142)
Q Consensus         7 se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l--~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~   84 (142)
                      |+++|+.+++++|++|+.+|.++.++|+|+++..+  +|+++.+..|..  +.++++|++.+.+...+..+..+ .....
T Consensus        17 s~e~l~~il~~~P~~i~~~D~~~~i~~~N~~~~~~~~~~~~~~~~iG~~--~~~~~p~~~~~~~~~~~~~~~~~-~~~~~   93 (151)
T 2qkp_A           17 SVEQANLILNHLPLEITFVNKDDIFQYYNDSVPAAEMVFKRTPSQVGRN--VELCHPPKVLDKVKKVFELLRNG-QRDKV   93 (151)
T ss_dssp             CHHHHHHHHHHSSSEEEEEETTSBEEEECCCSCGGGCSSCCCGGGTTSB--GGGSSCHHHHHHHHHHHHHHHTT-SBSEE
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCEEEEECCCHHHCEECCCHHHHHCCC--EEEECCCCCCCCCHHEEECCCCC-CCCEE
T ss_conf             6999999996398309999699979998323131220247807860751--14881553344201102101246-51100


Q ss_pred             HHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHH
Q ss_conf             111001000243200025412455350367777788178999999999999999
Q T0527            85 EYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREE  138 (142)
Q Consensus        85 e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~  138 (142)
                      ++.+ ..+|..+|+..+..|++|++|++.+++++++|||++|++|++|++++..
T Consensus        94 ~~~~-~~~~~gr~i~~~~~pv~d~~G~~~g~i~~~~DITe~k~~e~el~r~e~~  146 (151)
T 2qkp_A           94 NMWF-QSERLGKFVYVTYAAVRDQAGDFQGVLEYVQDIKPFFELDSEFNRDEGH  146 (151)
T ss_dssp             EEEE-EETTTTEEEEEEEEEEECTTCCEEEEEEEEEECGGGGGGGGC-------
T ss_pred             CCCC-CCCCCCCEEEEEEEEEECCCCCEEEEEEEEEECHHHHHHHHHHHHHHCC
T ss_conf             0000-0125771588863346879998999999999897999999999996566


No 21 
>1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock protein, phosphorylation, polymorphism; 3.15A {Drosophila melanogaster} PDB: 3gec_A
Probab=99.73  E-value=7.6e-21  Score=138.27  Aligned_cols=131  Identities=9%  Similarity=0.046  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----
Q ss_conf             5798999999999870682799980798989986589986379987964312467887653224789987532102----
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLE----   77 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~----   77 (142)
                      ++|++++.+|+.+++++++++|.+|.++.++++|++++.++||++.++.+.  .+..++||+|++.+...+.....    
T Consensus       141 ~~l~~~e~~~r~l~e~~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~d~~~~~~~~~~~~~~~~~  218 (368)
T 1wa9_A          141 PIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGR--SIMDFYHHEDLSVMKETYETVMKKGQT  218 (368)
T ss_dssp             ECCCSCCSTTCBCCTTSCEEEEEEETTCBEEEECGGGHHHHCCCHHHHTTS--BGGGGBCTTTHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECHHHHCCCCCCHHHCCC--CCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             887755778899985197069999169968852001121134440120223--223455423499999999875553135


Q ss_pred             -CCCCCCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHH
Q ss_conf             -465322211100100024320002541245535036777778817899999999999
Q T0527            78 -HRDTYDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRV  134 (142)
Q Consensus        78 -~~~~~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~  134 (142)
                       .+..+..++|+++++|.++|+..++.|++|++|....++++++|||+++++++++++
T Consensus       219 ~~~~~~~~e~r~~~k~G~~~wv~~~~~~~~d~~g~~~~~v~~~~dIt~~~~~e~~~~~  276 (368)
T 1wa9_A          219 AGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQCNVFEA  276 (368)
T ss_dssp             TTCCEECCCEEEECTTSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCSSSCTTSC
T ss_pred             CCCCCCHHHHEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCCHHHHHHHHH
T ss_conf             6665421101002058988999999999997899807899999991412532999997


No 22 
>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*
Probab=99.71  E-value=2.1e-17  Score=118.55  Aligned_cols=105  Identities=15%  Similarity=0.179  Sum_probs=92.6

Q ss_pred             CCCEEEEEEC---CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCC
Q ss_conf             6827999807---9898998658998637998796431246788765322478998753210246532221110010002
Q T0527            18 ASAGLWDWNP---KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGD   94 (142)
Q Consensus        18 ~~~~i~~~d~---~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~   94 (142)
                      +..++...|+   ++.++|+|+++++++||+++++.|+.  +..+.||++.+.....+...+..+.+++.|++++++||+
T Consensus         2 ~~~~~vi~Da~~pDg~Ii~vN~a~~~~~Gy~~~el~G~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~   79 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHN--CRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGT   79 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSC
T ss_pred             CCCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHHHCCCCCCHHHHHHHHHHHCCCCEEEEEEEEECCCCC
T ss_conf             776299994889989699996899998893999980852--321246557999999998864059629999999917998


Q ss_pred             CCCEEEEEEECCCCCCEEEEEEEEEEEHHH
Q ss_conf             432000254124553503677777881789
Q T0527            95 FRWIQSRGQALWNSAGEPYRMVGWIMDVTD  124 (142)
Q Consensus        95 ~~w~~~~~~~~~d~~g~~~~~~g~~~DITe  124 (142)
                      .+|+..+..|++|++|++.+++++++|||.
T Consensus        80 ~~w~~~~~~pi~d~~G~~~~~v~~~~DITa  109 (109)
T 1n9l_A           80 PFWNLLTVTPIKTPDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEEEEEEEEECTTSCEEEEEEEEEECCC
T ss_pred             EEEEEEEEEEEECCCCCEEEEEEEEEECCC
T ss_conf             999999986899999999999999997699


No 23 
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}
Probab=99.69  E-value=2.3e-18  Score=124.07  Aligned_cols=116  Identities=17%  Similarity=0.123  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCC
Q ss_conf             99999999870682799980798989986589986379987964312467887653224789987532102465--3222
Q T0527             7 SEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD--TYDV   84 (142)
Q Consensus         7 se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~--~~~~   84 (142)
                      ++.++..+.+++++++|.+|.++.++++|+++++++||+++++.+.  .+.+++||+|++.+.+.+..+...+.  .+..
T Consensus       153 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~n~~~~~~lG~~~~e~~~~--~~~~~~hpeD~~~~~~~~~~~~~~~~~~~~~~  230 (309)
T 3gdi_A          153 SGYEAPRIPPEKRIFTTTHTPNCLFQAVDERAVPLLGYLPQDLIET--PVLVQLHPSDRPLMLAIHKKILQAGGQPFDYS  230 (309)
T ss_dssp             CTTSSSCCCGGGCEEEEEECTTCBEEEECTTHHHHHSCCHHHHTTS--BHHHHBCTTSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CHHHHHHHHCCCCCEEEEECCCCEEEEECHHHHHHCCCCCCCCCCC--CCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             1445443320476238997178519997627742024575322233--32345540119999999999987547873123


Q ss_pred             HHHEEECCCCCCCEEEEEEECCCCCC-EEEEEEEEEEEHHH
Q ss_conf             11100100024320002541245535-03677777881789
Q T0527            85 EYRVRTRSGDFRWIQSRGQALWNSAG-EPYRMVGWIMDVTD  124 (142)
Q Consensus        85 e~ri~~~~G~~~w~~~~~~~~~d~~g-~~~~~~g~~~DITe  124 (142)
                      ++|++++||+++|+...++|++|+.| .+..++|+..|||+
T Consensus       231 e~r~~~~dG~~~wv~~~~~~i~~~~~~~~~~i~~~~~~~~~  271 (309)
T 3gdi_A          231 PIRFRTRNGEYITLDTSWSSFINPWSRKISFIIGRHKVRVG  271 (309)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEEC
T ss_pred             EEEEECCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCC
T ss_conf             55667699919999999999991799956899999998864


No 24 
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen fixation, PER-ARNT-SIM, metal-binding, PAS, iron; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A*
Probab=99.68  E-value=7e-17  Score=115.58  Aligned_cols=115  Identities=12%  Similarity=0.119  Sum_probs=94.6

Q ss_pred             HCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC----CCCHHHEEECC
Q ss_conf             06827999807989899865899863799879643124678876532247899875321024653----22211100100
Q T0527            17 GASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT----YDVEYRVRTRS   92 (142)
Q Consensus        17 ~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~----~~~e~ri~~~~   92 (142)
                      ++|+||+.+|.+|.++++|++++++|||+.+++.|..  +..+++|+++......+.....++..    +..+...+++|
T Consensus         1 t~pd~i~~~d~~g~I~~~N~~~~~l~G~~~~el~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (119)
T 2vv6_A            1 TIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQN--VNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRD   78 (119)
T ss_dssp             -CCCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTT
T ss_pred             CCCEEEEEECCCCCEEEEHHHHHHHHCCCHHHHHCCC--CCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECC
T ss_conf             9772999998999299871999998657899972566--44456631035678999999964866435640699986125


Q ss_pred             CCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHH
Q ss_conf             0243200025412455350367777788178999999999999
Q T0527            93 GDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVS  135 (142)
Q Consensus        93 G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~  135 (142)
                      |..+|+..+.+|+.+.++ + .++++++|||++|++|++|++.
T Consensus        79 G~~~~~~~~~~~~~~~~~-~-~~~~~i~DITe~k~~e~~L~~L  119 (119)
T 2vv6_A           79 GTTFPMHLSIGEMQSGGE-P-YFTGFVRDLTEHQQTQARLQEL  119 (119)
T ss_dssp             SCEEEEEEEEEEEEETTE-E-EEEEEEEECC------------
T ss_pred             CCEEEEEEEECCEECCCC-E-EEEEEEEECHHHHHHHHHHHCC
T ss_conf             513223567532033996-4-9999999818999999998477


No 25 
>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 43049, structural genomics, PSI-2; 2.65A {Haloarcula marismortui}
Probab=99.68  E-value=5.4e-17  Score=116.22  Aligned_cols=114  Identities=15%  Similarity=0.137  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             57989999999998706827999807989899865899863799879643124678876532247899875321024653
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~   81 (142)
                      .++++++++|+.+++++|+++|.+|++|.++++|+++++++||+++++.+.  .+.+++||++.+.+...+..++.++.+
T Consensus        12 ~~~~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (125)
T 3fc7_A           12 VSQERTRKKFESLVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQ--QLSAVMDSEAANQRLEAGKSAVENGTA   89 (125)
T ss_dssp             --------------CCSCCEEEEEETTSBEEEECHHHHHHHTSCHHHHTTS--BGGGSSCHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             999999999999997641123233543069998620000222322222221--222222211124567788876531444


Q ss_pred             CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             222111001000243200025412455350367777788178
Q T0527            82 YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        82 ~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      ...++.+     ..+|+..+..|+. .+|++.+++++++|||
T Consensus        90 ~~~~~~~-----~~r~~~~~~~pv~-~~~~~~~~~~v~~DIT  125 (125)
T 3fc7_A           90 TRSEDAV-----GGRHYHNQYIPVD-SHRKSDTFQLVSRDIT  125 (125)
T ss_dssp             EEEEEEE-----TTEEEEEEEEESS-TTTTTTEEEEEEEECC
T ss_pred             CCCEEEE-----CCCCCCEEEEEEE-ECCCEEEEEEEEEECC
T ss_conf             3101110-----0114530899999-0898999999999793


No 26 
>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6
Probab=99.65  E-value=1.2e-16  Score=114.18  Aligned_cols=104  Identities=15%  Similarity=0.110  Sum_probs=85.7

Q ss_pred             EEEEE---CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCCCE
Q ss_conf             99980---798989986589986379987964312467887653224789987532102465322211100100024320
Q T0527            22 LWDWN---PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFRWI   98 (142)
Q Consensus        22 i~~~d---~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~w~   98 (142)
                      ..++|   ++..++|+|+++++|+||+++++.|+.....-+.+|++.+.....+..++.++.++..++++.++||+.+|+
T Consensus         4 ~~i~~a~~~d~~I~~vN~a~~~~~G~~~~ei~G~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdg~~~w~   83 (110)
T 1byw_A            4 FIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLC   83 (110)
T ss_dssp             EEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEEE
T ss_pred             EEEECCCCCCCEEEEECHHHHHHHCCCHHHHCCCCHHHHEEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEE
T ss_conf             99975889989499998899998896978966998045210010231677888888775236420268999579969999


Q ss_pred             EEEEEECCCCCCEEEEEEEEEEEHHHH
Q ss_conf             002541245535036777778817899
Q T0527            99 QSRGQALWNSAGEPYRMVGWIMDVTDR  125 (142)
Q Consensus        99 ~~~~~~~~d~~g~~~~~~g~~~DITe~  125 (142)
                      ..+..|++|++|++.+++++++|||||
T Consensus        84 ~~~~~pv~d~~G~i~~~i~~~~DITeR  110 (110)
T 1byw_A           84 LVDVVPVKNEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EEEEEEEECTTCCEEEEEEEEEEEEEC
T ss_pred             EEEEEEEECCCCCEEEEEEEEEECCCC
T ss_conf             999999999998999999999976899


No 27 
>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}
Probab=99.58  E-value=4.7e-15  Score=105.16  Aligned_cols=116  Identities=12%  Similarity=0.036  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-----
Q ss_conf             899999999987068279998079898998658998637998796431246788765322478998753210246-----
Q T0527             5 SASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHR-----   79 (142)
Q Consensus         5 ~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~-----   79 (142)
                      .+|.++|+.+++++++|++.+|.+|.+.++|++++++|||+++++.|..  +..+++++++......+......+     
T Consensus         3 h~s~~~~~~il~~~~d~i~~~D~~G~I~~~N~aa~~l~G~~~~eliG~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   80 (129)
T 3mfx_A            3 HSSLETIELFIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQD--WRNFLTEHHQARYDNLLSHDVQLGTNCGQ   80 (129)
T ss_dssp             HHHHHHHHHHHTTCSSEEEEEETTSBEEEECHHHHHHTTSCHHHHTTSB--GGGGBCTTCCGGGGCTTC----------C
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHHCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             7899999999972352159995999899999799956559979985990--99980716577789999999985032203


Q ss_pred             --CCCCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHH
Q ss_conf             --5322211100100024320002541245535036777778817899
Q T0527            80 --DTYDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDR  125 (142)
Q Consensus        80 --~~~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~  125 (142)
                        .....|..++++||+.+|+.++.+++.+.++   .++|+++||-..
T Consensus        81 ~~~~~~~Ev~~~~~dG~~~~velsis~~~~~~~---~~v~v~rDI~~~  125 (129)
T 3mfx_A           81 PVQHPAQETTLICASGKAKDVELSISYIPGHEP---MFVMVMHDLEHH  125 (129)
T ss_dssp             CSCEEEEEEEEECTTSCEEEEEEEEEEECSSSC---EEEEEEEEC---
T ss_pred             CCCCCEEEEEEECCCCCEEEEEEEEEEEECCCC---EEEEEEEECCCC
T ss_conf             546650479999789979999999999989996---999999989753


No 28 
>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein structure initiative; 2.43A {Pyrococcus furiosus dsm 3638}
Probab=99.57  E-value=7.2e-16  Score=109.79  Aligned_cols=119  Identities=15%  Similarity=0.149  Sum_probs=90.6

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             99999999870682799980798989986589986379987964312467887653224789987532102465322211
Q T0527             7 SEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEY   86 (142)
Q Consensus         7 se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~   86 (142)
                      |.++|+.+++++|++|+.+|.+++++|+|++ ..+++.+. +++|..  +.++++|+..+.+...+..+. +|.....++
T Consensus       237 s~~~l~~il~~~p~~i~~vD~~~~i~~~N~a-~~~~~~~~-~~iG~~--~~~~~p~~~~~~~~~~~~~~~-~g~~~~~e~  311 (369)
T 3cax_A          237 NIEELKAIFEALPVDVTFIDKDDRVRFFSPG-ERIFTRTP-SVLGRP--VQLCHPPKSVYVVNKILKAFK-EGRKKEATF  311 (369)
T ss_dssp             CHHHHHHHHHHSSSEEEEECTTSBEEEECCS-SCSSCCCG-GGTTCB--TTTSSCGGGHHHHHHHHHHHH-HTSCSCEEE
T ss_pred             CHHHHHHHHHCCCCCEEEECCCCEEEEECHH-HHHHCCCH-HHHCCC--HHHHCCHHHHHHHHHHHHHHH-CCCCEEEEE
T ss_conf             5999999997297878999289939998677-78749888-982984--267289767999999999997-799538999


Q ss_pred             HEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHH
Q ss_conf             10010002432000254124553503677777881789999999999
Q T0527            87 RVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALR  133 (142)
Q Consensus        87 ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~  133 (142)
                      . ..++|  +|+.++..|++|++|++.+++++++|||++|++|++++
T Consensus       312 ~-~~~~g--~~~~~~~~Pv~d~~G~~~G~v~~~~DITe~k~~E~e~r  355 (369)
T 3cax_A          312 W-LRLRE--KYVYIKYVPLFNEKGEYIGTLEMTMDIAPYKKIEGEKR  355 (369)
T ss_dssp             E-EEETT--EEEEEEEEEEECTTSCEEEEEEEEEECHHHHTCCSCCC
T ss_pred             E-EEECC--EEEEEEEEEEECCCCCEEEEEEEEEECHHHHHHHHHHH
T ss_conf             9-93199--89999999899989899999999999869999999898


No 29 
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transferase, flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}
Probab=99.56  E-value=1.4e-14  Score=102.46  Aligned_cols=119  Identities=18%  Similarity=0.246  Sum_probs=102.6

Q ss_pred             EEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCCCEEE
Q ss_conf             79998079898998658998637998796431246788765322478998753210246532221110010002432000
Q T0527            21 GLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFRWIQS  100 (142)
Q Consensus        21 ~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~w~~~  100 (142)
                      .|++.|.+|+++++|+++++++||+++++.|..  +..+.+|++...+...+......+.++..+..+++++|..+|+..
T Consensus         1 li~i~D~~G~i~~~N~a~~~~~G~~~eel~G~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~   78 (227)
T 3ewk_A            1 LVSITDLQGRILYANDNFCAVSRYGREELVGQD--HRIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDS   78 (227)
T ss_dssp             CEEEEETTCBEEEECHHHHHHTTCCHHHHTTSB--GGGGCCSCSCHHHHHHHHHHHTTTCCEEEEEEEECSSSCEEEEEE
T ss_pred             CEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCEEEEEE
T ss_conf             799995999989833889998892999994998--889289413467766777764027724589999941543487655


Q ss_pred             EEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHC
Q ss_conf             25412455350367777788178999999999999999842
Q T0527           101 RGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREELRR  141 (142)
Q Consensus       101 ~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l~~  141 (142)
                      +.+|+.+.+|.+..++.+..|+|++++.++.+++.+.-+++
T Consensus        79 ~~~~~~~~~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~l~~  119 (227)
T 3ewk_A           79 TIVPLMDNAGKPRQYISIRRDITAQKEAEAQLARLKQAMDA  119 (227)
T ss_dssp             EEEEEECSSSCEEEEEEEEEECTTTTHHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66556536897633212320236999999998767999986


No 30 
>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A*
Probab=99.48  E-value=9.1e-14  Score=97.76  Aligned_cols=99  Identities=17%  Similarity=0.183  Sum_probs=78.2

Q ss_pred             CCCEEEEEEC---CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHCCCCCCCC
Q ss_conf             6827999807---9898998658998637998796431246788765322-----------4789987532102465322
Q T0527            18 ASAGLWDWNP---KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDD-----------RARVLAALKAHLEHRDTYD   83 (142)
Q Consensus        18 ~~~~i~~~d~---~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd-----------~~~~~~~~~~~~~~~~~~~   83 (142)
                      ...+++.+|+   ++.++|+|+++++|+||+++++.|+...  .+.++++           -+...+.+...+..+.+++
T Consensus        34 ~s~ai~i~D~~~~D~~Ii~vN~af~~~tGys~eEviGr~~~--~l~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~  111 (149)
T 3d72_A           34 TSVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCR--FLQSPDGMVKPKSTRKYVDSNTINTMRKAIDRNAEVQ  111 (149)
T ss_dssp             TTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGG--GGGSTTSCCCTTCCCSSSCHHHHHHHHHHHHHTCCEE
T ss_pred             CCCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCCCC--EECCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCEEE
T ss_conf             15319999699998979998689998889299998598621--3017102135432222279999999999997698599


Q ss_pred             CHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEE
Q ss_conf             21110010002432000254124553503677777
Q T0527            84 VEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGW  118 (142)
Q Consensus        84 ~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~  118 (142)
                      .|++.+++||..+|+..+.+|++|++|++.+++|+
T Consensus       112 ~E~~~~~kdG~~~wv~~~~~pv~De~G~v~~~vGi  146 (149)
T 3d72_A          112 VEVVNFKKNGQRFVNFLTMIPVRDETGEYRYSMGF  146 (149)
T ss_dssp             EEEEEECTTCCEEEEEEEEEEEECTTSSEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEE
T ss_conf             99987859998999999999999999899999999


No 31 
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}
Probab=99.46  E-value=1.4e-13  Score=96.67  Aligned_cols=124  Identities=10%  Similarity=0.078  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHCCCHHHHHHH------HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             579899999999987068279998079898-998658998637998796431------2467887653224789987532
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGA-MYLSPHFKKIMGYEDHELPDE------ITGHRESIHPDDRARVLAALKA   74 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~-~~~n~~~~~l~G~~~~~~~~~------~~~~~~~ihpdd~~~~~~~~~~   74 (142)
                      +.|+++++.++.+.+.+|..+|.+|+..+. +|+|+.+.+++||++++....      ...|.++|||||+.........
T Consensus        26 ~~le~~~~~~~~~a~~~~~~~~i~Dl~~~~~~y~s~~~~~~lGy~~~e~~~~~i~s~~~~~~~~~ihP~D~~~~~~~~~~  105 (258)
T 3clo_A           26 GIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYK  105 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHSSEEEEEETTTTEEEEEECTTCGGGCCCHHHHHCCEESSSSCHHHHTTBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCCEEEEECCCHHHHHCCCHHHCCCHHHHCCCCHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999999999999857887899988788899986539998399966623145430440466625897899999999999


Q ss_pred             HC------CCC--C--CCCCHHHEEECCCCCCCEEEEEEECC-CCCCEEEEEEEEEEEHHHHH
Q ss_conf             10------246--5--32221110010002432000254124-55350367777788178999
Q T0527            75 HL------EHR--D--TYDVEYRVRTRSGDFRWIQSRGQALW-NSAGEPYRMVGWIMDVTDRK  126 (142)
Q Consensus        75 ~~------~~~--~--~~~~e~ri~~~~G~~~w~~~~~~~~~-d~~g~~~~~~g~~~DITe~k  126 (142)
                      .+      ..+  .  .+..+||+++++|.|+|+..++.++. +++|++..+. .+.|++..+
T Consensus       106 ~~~~l~~~~~~er~~y~~~~~~R~~~~~G~y~wv~~r~~vl~~~~~g~i~~~l-~~~d~~~~~  167 (258)
T 3clo_A          106 FFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWLIF-CLYSLSADQ  167 (258)
T ss_dssp             HHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECTTSCEEEEE-EEEEECSCC
T ss_pred             HHHHHHHCCHHHHHEEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCEEECC-CCCCCCCCC
T ss_conf             99987517865411135789999986999999998667787438998801113-323444333


No 32 
>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8
Probab=99.46  E-value=1.1e-13  Score=97.40  Aligned_cols=109  Identities=8%  Similarity=0.046  Sum_probs=87.2

Q ss_pred             HCCCEEEEEECCCCEEEECHHH-HHHHCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCCCCCCCHHHEEECCC
Q ss_conf             0682799980798989986589-98637998796431246788765322478--99875321024653222111001000
Q T0527            17 GASAGLWDWNPKTGAMYLSPHF-KKIMGYEDHELPDEITGHRESIHPDDRAR--VLAALKAHLEHRDTYDVEYRVRTRSG   93 (142)
Q Consensus        17 ~~~~~i~~~d~~~~~~~~n~~~-~~l~G~~~~~~~~~~~~~~~~ihpdd~~~--~~~~~~~~~~~~~~~~~e~ri~~~~G   93 (142)
                      .+...+...|++|.++++|+.+ ..++||.++++.+.  .+.+++||+|++.  ...........+..+..+||++++||
T Consensus         5 ~~e~F~trh~ldg~i~~vd~~~~~~l~gy~~eelig~--s~~~~~Hp~D~~~~~~~~~~~~~~~~~~~~t~~yR~r~KdG   82 (132)
T 1oj5_A            5 GVESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRK--CIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDG   82 (132)
T ss_dssp             -CCEEEEEECTTCCEEEEECHHHHTTCCSCHHHHHHH--HHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTS
T ss_pred             CCEEEEEEECCCCEEEEECCHHHHHHHCCCHHHHCCC--CHHHEECCCCCHHHHHHHHHHHHHCCCCCCCHHHEEEECCC
T ss_conf             6486899997997199998178676608897999499--19893884531356677788877516851134550365498


Q ss_pred             CCCCEEEEEEECCCCCC-EEEEEEEEEEEHHHHHH
Q ss_conf             24320002541245535-03677777881789999
Q T0527            94 DFRWIQSRGQALWNSAG-EPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        94 ~~~w~~~~~~~~~d~~g-~~~~~~g~~~DITe~k~  127 (142)
                      .|+|++.++++++|+.+ .+..++|+-..|+++..
T Consensus        83 ~~vWv~t~~~l~~~~~~~~~~~Ii~~h~i~~e~~~  117 (132)
T 1oj5_A           83 TMLSAHTRCKLCYPQSPDMQPFIMGIHIIDREHSG  117 (132)
T ss_dssp             CEEEEEEEEEEECC----CCCEEEEEEEEECC---
T ss_pred             EEEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCC
T ss_conf             09999998899982799981599999995257434


No 33 
>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: 3PB; 1.80A {Rhodococcus SP}
Probab=99.44  E-value=1e-13  Score=97.50  Aligned_cols=106  Identities=13%  Similarity=0.040  Sum_probs=90.0

Q ss_pred             HHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEE
Q ss_conf             99999870682799980798989986589986379987964312467887653224789987532102465322211100
Q T0527            10 RFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVR   89 (142)
Q Consensus        10 r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~   89 (142)
                      .++.+++++++|++.+|.+++++++|+++++++|++++++.|+  .+.+++++++...+...+.+++.++.+...+++..
T Consensus        13 ~~e~~~~~~~~Gi~~vD~dgri~~~N~a~~~llG~~~eeliGk--~~~e~~p~~~~~~~~~~~~~~~~~g~~~~~e~~~~   90 (118)
T 3fg8_A           13 GRENLYFQGGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGR--VVTEVLPETQGSYFDALCRKVLATGREQQTRVDSL   90 (118)
T ss_dssp             CCCCSSSCTTCEEEEECTTCBEEEECHHHHHHHTCCHHHHTTS--BHHHHCGGGTTSHHHHHHHHHHHHCCCEEEEEECS
T ss_pred             HHHHHHHCCCCEEEEECCCCEEEEEHHHHHHHHCCCHHHHCCC--CHHHHCCHHHCCCHHHHHHHHHHCCCEEEEEEEEE
T ss_conf             5999997089899999799829989899898857899998599--69994845331105678999985398499999998


Q ss_pred             ECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHH
Q ss_conf             100024320002541245535036777778817899
Q T0527            90 TRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDR  125 (142)
Q Consensus        90 ~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~  125 (142)
                      .++|  +|+++++.|..  +|    ++++++|||++
T Consensus        91 ~~~~--~w~~v~~~p~~--dG----i~v~~rDIT~q  118 (118)
T 3fg8_A           91 YSPG--MTIEVTAAADS--GA----LVVHFRDVTAE  118 (118)
T ss_dssp             SSTT--CEEEEEEEEET--TE----EEEEEEECSCC
T ss_pred             CCCC--EEEEEEEEECC--CE----EEEEEEECCCC
T ss_conf             8899--89999999879--99----99999982799


No 34 
>1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock protein, phosphorylation, polymorphism; 3.15A {Drosophila melanogaster} PDB: 3gec_A
Probab=99.43  E-value=3.8e-16  Score=111.35  Aligned_cols=118  Identities=12%  Similarity=-0.008  Sum_probs=89.9

Q ss_pred             EEE-ECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-----C---------------
Q ss_conf             998-0798989986589986379987964312467887653224789987532102465-----3---------------
Q T0527            23 WDW-NPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD-----T---------------   81 (142)
Q Consensus        23 ~~~-d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~-----~---------------   81 (142)
                      ..+ +.+|.++|+|+++++++||+++++.|.  .+.+++||||++.+.+.+........     .               
T Consensus        11 ~vi~~~dG~I~~vN~~~~~ilGys~eEliG~--~~~dlihPeD~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (368)
T 1wa9_A           11 CVISMHDGIVLYTTPSITDVLGYPRDMWLGR--SFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCVMLRRYR   88 (368)
T ss_dssp             EEEETTTCBEEEECTTHHHHHCCCTTSSTTS--BGGGGBCTTTHHHHHHHTTSCC------------CCCEEEEEEECSC
T ss_pred             EEEECCCCEEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHCCCCCCHHHCCCCCCCEEEEEEEECCCC
T ss_conf             9999999889999879999879399998699--79996499789999998623666530102456566079999622202


Q ss_pred             ----CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             ----2221110010002432000254124553503677777881789999999999999998429
Q T0527            82 ----YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREELRRL  142 (142)
Q Consensus        82 ----~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l~~l  142 (142)
                          .........++|.+.|+....+++.+.+|.+..+.++.+|||++|+++++|++++.+++.+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~d~~~~~~~~~~~~~Dit~~k~~e~~l~~~e~~~r~l  153 (368)
T 1wa9_A           89 GLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEIL  153 (368)
T ss_dssp             CCSSCCSSSCCCCCCEEEEEEECCBCCCCCCCC------CCSCCCEEEEEEEECCCSCCSTTCBC
T ss_pred             CEEECCEEEECCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             30573346653446448999999998634456773322244423779999888877557788999


No 35 
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}
Probab=99.36  E-value=2.4e-13  Score=95.41  Aligned_cols=120  Identities=13%  Similarity=0.102  Sum_probs=96.0

Q ss_pred             HHHHHHCCCEEEEEE-CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCHHHEE
Q ss_conf             999870682799980-798989986589986379987964312467887653224789987532102-465322211100
Q T0527            12 QLAVSGASAGLWDWN-PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLE-HRDTYDVEYRVR   89 (142)
Q Consensus        12 ~~~~~~~~~~i~~~d-~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~-~~~~~~~e~ri~   89 (142)
                      +.++++++..++.++ .+|+++|+|+++++++||+++++.|.  .+.+++||+|++.+.+.+..... .+.....+.+..
T Consensus        18 e~~l~~~~~f~iv~~~~dG~I~~vN~~~~~llGys~eEl~g~--~~~~lihp~d~~~~~~~l~~~~~~~~~~~~~~~~~~   95 (309)
T 3gdi_A           18 EYIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDA--KFVEFLAPHDVSVFHSYTTPYKLPPWSVCSGLDSFT   95 (309)
T ss_dssp             C----CTTEEEEEECTTTCBEEEECTTTTTTC-------CCS--BGGGGBCTTTHHHHHHHTCTTSSCBCC---------
T ss_pred             HHHHHHCCCEEEEEECCCCEEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEE
T ss_conf             999970588799999799879999789999859799998599--788938988889999997653147765332044455


Q ss_pred             ECCCCCCCEEEEEEECCCCC----CEEEEEEEEEEEHHHHHHHHHHHH
Q ss_conf             10002432000254124553----503677777881789999999999
Q T0527            90 TRSGDFRWIQSRGQALWNSA----GEPYRMVGWIMDVTDRKRDEDALR  133 (142)
Q Consensus        90 ~~~G~~~w~~~~~~~~~d~~----g~~~~~~g~~~DITe~k~~e~~L~  133 (142)
                      ..+|..+|+.+...+..+..    +.++.+.|+.+|||+++.++++++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dit~~~~~e~~l~  143 (309)
T 3gdi_A           96 QECMEEKSFFCRVSVGKHHENEIRYQPFRMTPYLVKVQEQQGAESQLC  143 (309)
T ss_dssp             -----CCCEEEEECCCC----CCCCEEEEEEEEEEECC--------EE
T ss_pred             ECCCCCEEEEEEEECCCCCCCCCEEEEEEEEEEEEECCCHHHHHHHHH
T ss_conf             305652378875211444345761789999889987400223445667


No 36 
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transferase, two-component regulatory system; 3.80A {Thermotoga maritima}
Probab=99.30  E-value=1.3e-13  Score=96.86  Aligned_cols=118  Identities=10%  Similarity=0.103  Sum_probs=86.2

Q ss_pred             HHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEE
Q ss_conf             99999870682799980798989986589986379987964312467887653224789987532102465322211100
Q T0527            10 RFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVR   89 (142)
Q Consensus        10 r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~   89 (142)
                      .++.+++++|+|++.+|.++.++++|+++++++||+++++.+..  +.++.++++...+..   ....++......   .
T Consensus         9 ~~e~il~~~~~gi~v~d~~g~i~~~N~aa~~llg~~~~e~~g~~--~~~l~~~~~~~~~~~---~~~~~~~~~~~~---~   80 (349)
T 3a0r_A            9 FSESILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRR--LKDLPDFEEIGSVAE---SVFENKEPVFLN---F   80 (349)
T ss_dssp             CCCSSGGGSSSEEEEEESSSBCSCBCHHHHHHHSCCSTTTTTCB--STTSTTTTHHHHHHH---HHHHHCCCCEEE---C
T ss_pred             HHHHHHHHHHHHHEEECCCCCCHHHHHHHHHHHCCCHHHHCCCC--HHHCCCHHHHHHHHH---HHHHCCCEEEEE---E
T ss_conf             99999986426748998959002706999999782989985998--789489788999999---998259839999---9


Q ss_pred             ECCCCCCCEEEEEEECCCCCCE-EEEEEEEEEEHHHHHHHHHHHHHHH
Q ss_conf             1000243200025412455350-3677777881789999999999999
Q T0527            90 TRSGDFRWIQSRGQALWNSAGE-PYRMVGWIMDVTDRKRDEDALRVSR  136 (142)
Q Consensus        90 ~~~G~~~w~~~~~~~~~d~~g~-~~~~~g~~~DITe~k~~e~~L~~~~  136 (142)
                      .++|. +|+.++..|+.+.+|. +.+++.+++|||++|++|+++++.+
T Consensus        81 ~~~~~-~~~~~~~~~~~~~~~~~~~g~v~~~~DIT~~~~~e~~l~~~e  127 (349)
T 3a0r_A           81 YKFGE-RYFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEEERKRRE  127 (349)
T ss_dssp             CCBTT-BCCEEEEEEECCTTTTSSCEEEEEEECCSTTTTTTTTTTHHH
T ss_pred             ECCCC-EEEEEEEEEEECCCCCEEEEEEEEEEEHHHHHHHHHHHHHHH
T ss_conf             70881-899999999982898778899999984559999999999999


No 37 
>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein, APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}
Probab=99.21  E-value=3.2e-11  Score=83.23  Aligned_cols=107  Identities=8%  Similarity=0.022  Sum_probs=81.2

Q ss_pred             HHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCHHH
Q ss_conf             99999987068279998079898998658998637998796431246788765322478998753210246532-22111
Q T0527             9 ERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTY-DVEYR   87 (142)
Q Consensus         9 ~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~-~~e~r   87 (142)
                      ..++.++++++++++.+|.+|.++|+|+++++++|++++++.|..  +.++++..+.  ....+.+++.++.++ ..+..
T Consensus         7 ~l~~~il~~~~~~i~~iD~~g~I~~~N~aa~~l~g~s~~el~G~~--~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~   82 (115)
T 3b33_A            7 SLPSAILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQS--LSQLIQHASL--DLALLTQPLQSGQSITDSDVT   82 (115)
T ss_dssp             CHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHTTSCHHHHTTCB--HHHHCSEEEC--CTHHHHHHHHHCCCEEEEEEE
T ss_pred             HHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHHHHHHHHCCCC--HHHHCCCCHH--HHHHHHHHHHCCCCEEEEEEE
T ss_conf             899999851476599997999999989699977465488774985--9998598067--789999999829971789999


Q ss_pred             EEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEH
Q ss_conf             00100024320002541245535036777778817
Q T0527            88 VRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDV  122 (142)
Q Consensus        88 i~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DI  122 (142)
                      + +++|..+|+.++..|+.+++|..+  +..++||
T Consensus        83 ~-~~~G~~~~v~~s~~pi~~~~~~~i--lv~~rdi  114 (115)
T 3b33_A           83 F-VVDGRPLMLEVTVSPITWQRQLML--LVEMRKI  114 (115)
T ss_dssp             E-EETTEEEEEEEEEEEEEETTEEEE--EEEEEEC
T ss_pred             E-EECCCEEEEEEEEEEEEECCCEEE--EEEEEEC
T ss_conf             9-979919999999999995997799--9999968


No 38 
>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5
Probab=99.17  E-value=2.6e-11  Score=83.72  Aligned_cols=106  Identities=13%  Similarity=0.120  Sum_probs=85.7

Q ss_pred             HHHHCCCEEEEEEC-CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----CCCCHHHE
Q ss_conf             98706827999807-98989986589986379987964312467887653224789987532102465----32221110
Q T0527            14 AVSGASAGLWDWNP-KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRD----TYDVEYRV   88 (142)
Q Consensus        14 ~~~~~~~~i~~~d~-~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~----~~~~e~ri   88 (142)
                      +.+..+.+|+.+|. +|.++++|++++++|||+++++.+.  .+.++++|++.......+.....++.    ....+..+
T Consensus         3 ~~~~~n~ai~~~d~~~G~I~~vN~~a~~l~Gys~~el~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   80 (114)
T 1ll8_A            3 MDPEFNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQ--KLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDI   80 (114)
T ss_dssp             SSTTTTCEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTS--BGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEE
T ss_pred             CHHHCCEEEEEEECCCCEEEEHHHHHHHHHCCCHHHHHCC--CCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEEEEEE
T ss_conf             4011271899999999999962389999878598999298--00011380059999999999996589700010259888


Q ss_pred             EECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             01000243200025412455350367777788178
Q T0527            89 RTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        89 ~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      ++++|..+|+..+.+++..+++ . .++++++||+
T Consensus        81 ~~kdG~~~pv~l~~~~i~~~~~-~-~~v~vi~dv~  113 (114)
T 1ll8_A           81 ISRSGEKIPVSVWMKRMRQERR-L-CCVVVLEPVE  113 (114)
T ss_dssp             CCTTCCCEEEECCEECCBSSSS-B-EEEEEEEECC
T ss_pred             ECCCCEEEEEEEEEEEEEECCE-E-EEEEEEEECC
T ss_conf             8159979999999999999994-7-9999999764


No 39 
>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold, signaling protein; HET: HC4; 0.82A {Halorhodospira halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A* 1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X* 1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A* 2qws_A* 2zoh_A* 2zoi_A* ...
Probab=99.14  E-value=3.8e-11  Score=82.79  Aligned_cols=107  Identities=7%  Similarity=0.026  Sum_probs=80.1

Q ss_pred             HHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCCCCCCCHHHE
Q ss_conf             9999987068279998079898998658998637998796431246788765322-478998753210246532221110
Q T0527            10 RFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDD-RARVLAALKAHLEHRDTYDVEYRV   88 (142)
Q Consensus        10 r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd-~~~~~~~~~~~~~~~~~~~~e~ri   88 (142)
                      ..+.+++++|+|++..|.+|.+++||+++++++||+++++.|+.  +..+++|++ .+.+...+..+..++.....+...
T Consensus        18 ~~~~~ld~~~~Gii~lD~~G~i~~~N~a~~~l~G~~~~e~iG~~--~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   95 (125)
T 1nwz_A           18 MDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKN--FFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYT   95 (125)
T ss_dssp             CCHHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSB--CCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEE
T ss_pred             HHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             99999856882699997999997688999988586668767970--4440487001799999999999749971589999


Q ss_pred             EECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEH
Q ss_conf             0100024320002541245535036777778817
Q T0527            89 RTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDV  122 (142)
Q Consensus        89 ~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DI  122 (142)
                      .+++|..+|++++..+..+.+  .. + .+++||
T Consensus        96 ~~~~g~~~~V~v~~~~~~~g~--~~-~-v~V~~i  125 (125)
T 1nwz_A           96 FDYQMTPTKVKVHMKKALSGD--SY-W-VFVKRV  125 (125)
T ss_dssp             ECTTSCCEEEEEEEEECSSSS--EE-E-EEEEEC
T ss_pred             ECCCCCEEEEEEEEEEECCCC--EE-E-EEEEEC
T ss_conf             714996899999999913899--69-9-999989


No 40 
>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1
Probab=99.10  E-value=4.8e-11  Score=82.21  Aligned_cols=105  Identities=6%  Similarity=-0.040  Sum_probs=80.5

Q ss_pred             CHHHHHH-HHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHCCC
Q ss_conf             9579899-9999999870682799980798989986589986379987964312467887653-2247899875321024
Q T0527             1 SNALSAS-EERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHP-DDRARVLAALKAHLEH   78 (142)
Q Consensus         1 ~~aL~~s-e~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihp-dd~~~~~~~~~~~~~~   78 (142)
                      ||.+++. +..++.+++++|+||+.+|.+|.+++||+++++|+||+++++.|..  +...+.| ++.+.+...+..++.+
T Consensus        13 ~~~~~~~~~~~~~a~lda~p~GIi~~D~~GrI~~~N~aa~~l~G~~~eeliGr~--~~~~~~P~~~~~~~~~~~~~~l~~   90 (129)
T 1mzu_A           13 TEQIRGTIDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRN--FFTEVAPCTNIPAFSGRFMDGVTS   90 (129)
T ss_dssp             -------CC---CTTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSB--CCCCCCGGGCSTTTHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHEECCCCCCHHHHHHHHHHHHC
T ss_conf             899999998899999865990599998999599997899988683989977993--778078766678999999999975


Q ss_pred             CCC-CCCHHHEEECCCCCCCEEEEEEECCCC
Q ss_conf             653-222111001000243200025412455
Q T0527            79 RDT-YDVEYRVRTRSGDFRWIQSRGQALWNS  108 (142)
Q Consensus        79 ~~~-~~~e~ri~~~~G~~~w~~~~~~~~~d~  108 (142)
                      |.. ...++.+ +++|..+|+.++.....+.
T Consensus        91 G~~~~~~~~~~-~~~g~~~~V~v~l~~~p~~  120 (129)
T 1mzu_A           91 GTLDARFDFVF-DFQMAPVRVQIRMQNAGVP  120 (129)
T ss_dssp             SCCEEEEEEEE-ECSSCEEEEEEEEEECSST
T ss_pred             CCCCCEEEEEE-ECCCCEEEEEEEEEECCCC
T ss_conf             99861589999-4399669999999982689


No 41 
>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protein, nucleotide-binding, transcription regulation, activator, repressor; HET: PG4; 2.30A {Escherichia coli}
Probab=99.04  E-value=6.5e-11  Score=81.45  Aligned_cols=110  Identities=10%  Similarity=0.040  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             79899999999987068279998079898998658998637998796431246788765322478998753210246532
Q T0527             3 ALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTY   82 (142)
Q Consensus         3 aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~   82 (142)
                      ++++++++|+.+++++++|++.+|.+|.+++||++++++||++++++.+..  +..++++.+.....   .    .... 
T Consensus        74 ~~e~~~~~~~~il~~~~d~i~~~D~~g~i~~~N~aa~~l~g~~~~~~~g~~--~~~l~~~~~~~~~~---~----~~~~-  143 (190)
T 2jhe_A           74 PSEREHLALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLDRLRNHT--AAQLINGFNFLRWL---E----SEPQ-  143 (190)
T ss_dssp             TTTHHHHHHHHHHHHCSSCEEEECTTCBEEEECHHHHHHHTSCHHHHTTSB--GGGTSTTCCHHHHH---H----TCCC-
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHHHCC--HHHHCCCHHHHHHH---H----HCCC-
T ss_conf             779999999999970642439998999999989999998791999996387--99958967699999---7----0776-


Q ss_pred             CCHHHEEECCCCCCCEEEEEEECC----CCCCEEEEEEEEEEEHHH
Q ss_conf             221110010002432000254124----553503677777881789
Q T0527            83 DVEYRVRTRSGDFRWIQSRGQALW----NSAGEPYRMVGWIMDVTD  124 (142)
Q Consensus        83 ~~e~ri~~~~G~~~w~~~~~~~~~----d~~g~~~~~~g~~~DITe  124 (142)
                      .........+|+.+.+..  .|+.    +++|.+.+.+.+++|+|+
T Consensus       144 ~~~~~~v~~~G~~~~~~~--~pi~~~~~~~~~~~~G~Vi~~r~~tr  187 (190)
T 2jhe_A          144 DSHNEHVVINGQNFLMEI--TPVYLQDENDQHVLTGAVVMLRSTIR  187 (190)
T ss_dssp             SCEEEEEEETTEEEEEEE--EEETTTTEEEEEEEE-HHHHHHHHTT
T ss_pred             CCCEEEEEECCEEEEEEE--EEEEEECCCCCCEEEEEEEEEECHHH
T ss_conf             442199999997999999--99998646898389999999987888


No 42 
>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*
Probab=98.95  E-value=3.4e-09  Score=71.60  Aligned_cols=95  Identities=7%  Similarity=0.061  Sum_probs=71.4

Q ss_pred             CCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCCC
Q ss_conf             68279998079898998658998637998796431246788765322478998753210246532221110010002432
Q T0527            18 ASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFRW   97 (142)
Q Consensus        18 ~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~w   97 (142)
                      ++.|++..|.++.+++||+++++++||+.+++.|..  +.+++++++   +...+.....++.....    ..+++..+|
T Consensus         1 m~~gvi~~D~~g~I~~~N~~a~~l~g~~~~e~iG~~--~~~~~~~~~---~~~~~~~~~~~~~~~~~----~~~~~~~~~   71 (96)
T 3a0s_A            1 METAIITLSKDGRITEWNKKAEQLFGLKKENVLGRR--LKDLPDFEE---IGSVAESVFENKEPVFL----NFYKFGERY   71 (96)
T ss_dssp             CCCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSB--GGGSTTCHH---HHHHHHHHHHHTCCEEE----EEEEETTEE
T ss_pred             CCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHHHHHHH---HHHHHHHHHHCCCEEEE----EEECCCCEE
T ss_conf             987999998989899998798987599989976983--999501001---32589999847958999----998799199


Q ss_pred             EEEEEEECCCCCCEEE-EEEEEEEE
Q ss_conf             0002541245535036-77777881
Q T0527            98 IQSRGQALWNSAGEPY-RMVGWIMD  121 (142)
Q Consensus        98 ~~~~~~~~~d~~g~~~-~~~g~~~D  121 (142)
                      +..+.+|+++++|+.+ +++.++.|
T Consensus        72 ~~v~~~Pi~~~~~~~i~g~v~~~~D   96 (96)
T 3a0s_A           72 FNIRFSPFRNAKTQLLEGVIITIDD   96 (96)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEEEEC
T ss_pred             EEEEEEEEECCCCCEEEEEEEEEEC
T ss_conf             9999999891899999999999989


No 43 
>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}
Probab=98.83  E-value=7.1e-10  Score=75.50  Aligned_cols=111  Identities=12%  Similarity=0.069  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             57989999999998706827999807989899865899863799879643124678876532247899875321024653
Q T0527             2 NALSASEERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
Q Consensus         2 ~aL~~se~r~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~   81 (142)
                      +.|.+..+.++.+++++++|++.+|.+++++++|++++++||++.+.+.......  ..++.+...+.+.+    .++..
T Consensus         8 eei~~~~~~~~~il~~i~dgvi~iD~~g~I~~~N~aa~~i~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l----~~~~~   81 (118)
T 2w0n_A            8 YEISTLFEQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTL--SHSWSQVVDVSEVL----RDGTP   81 (118)
T ss_dssp             HHHCTTHHHHHHHHHCCCCCCEEEBTTTBCCCBCHHHHHHHCSCTTTTTSSCCCT--TCCCSCTHHHHHHH----HTTCC
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCHHHH--CCCCHHHCHHHHHH----HCCCE
T ss_conf             9999999999999971478189998999099999899988668988967936775--47802325389998----55983


Q ss_pred             CCCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHH
Q ss_conf             222111001000243200025412455350367777788178
Q T0527            82 YDVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVT  123 (142)
Q Consensus        82 ~~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DIT  123 (142)
                      ...+  ....+|.  ++.++..|+.+ +|++.+++.+++|||
T Consensus        82 ~~~~--~~~~~~~--~~~v~~~Pi~~-~~~~~G~V~~~~DIT  118 (118)
T 2w0n_A           82 RRDE--EITIKDR--LLLINTVPVRS-NGVIIGAISTFRDKT  118 (118)
T ss_dssp             CCCC--CEESSSC--EECCCEECCCC-SSCCCCEEECCCCCC
T ss_pred             EEEE--EEEECCE--EEEEEEEEEEE-CCEEEEEEEEEEECC
T ss_conf             4669--9998999--99999999999-998999999999669


No 44 
>2ool_A Sensor protein; bacteriophytochrome, photoconversion, photoreceptor, biliverdin, signaling protein; HET: LBV; 2.20A {Rhodopseudomonas palustris CGA009} SCOP: d.110.2.1 d.110.3.9
Probab=97.67  E-value=0.00012  Score=45.62  Aligned_cols=75  Identities=13%  Similarity=0.069  Sum_probs=52.3

Q ss_pred             EEEEEE-CCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCCCE
Q ss_conf             799980-798989986589986379987964312467887653224789987532102465322211100100024320
Q T0527            21 GLWDWN-PKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFRWI   98 (142)
Q Consensus        21 ~i~~~d-~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~w~   98 (142)
                      +...+| .++.++++|+++.+++||+++++.|.  .+.++++|++...+.+.+......+. ....+.+..++|...|.
T Consensus        44 ~Ll~ld~~d~~I~~vS~N~~~llG~~peellG~--~l~~ll~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  119 (337)
T 2ool_A           44 YLFVVSETDLRIASVSANVEDLLRQPPASLLNV--PIAHYLTAASAARLTHALHGGDPAAI-NPIRLDVVTPDGERAFN  119 (337)
T ss_dssp             EEEEECTTTCBEEEEETTHHHHHSSCGGGGTTC--BGGGGBCHHHHHHHHHHHCC----CC-CSEEEEEEETTEEEEEE
T ss_pred             EEEEEECCCCEEEEECCHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHCCCCCCC-CCEEEEEECCCCCCEEE
T ss_conf             799998899979998661998839698998399--88897698889999998631474558-86899984168982268


No 45 
>2vea_A Phytochrome-like protein CPH1; arginine finger, phosphorylation, tandem GAF domain, knot, kinase, receptor, PAS domain, chromophore; HET: CYC; 2.21A {Synechocystis SP} SCOP: d.110.2.1 d.110.2.4 d.110.3.9
Probab=96.40  E-value=0.00032  Score=43.20  Aligned_cols=53  Identities=13%  Similarity=0.050  Sum_probs=41.0

Q ss_pred             EEEEEEC-CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7999807-989899865899863799879643124678876532247899875321
Q T0527            21 GLWDWNP-KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAH   75 (142)
Q Consensus        21 ~i~~~d~-~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~   75 (142)
                      ++...|. ++.++++|+++.+++||+++++.|..  +.++++|++...+.+.+...
T Consensus        31 ~Ll~~d~~~~~I~~vS~n~~~lLG~~~eeLLGr~--l~dLl~~~~~~~i~~~l~~~   84 (520)
T 2vea_A           31 LVVVLQEPDLTISQISANCTGILGRSPEDLLGRT--LGEVFDSFQIDPIQSRLTAG   84 (520)
T ss_dssp             EEEEEETTTTEEEEEETTHHHHTSCCTTTSSTTT--TTTTSBCC--------CCCT
T ss_pred             EEEEEECCCCEEEEECCHHHHHHCCCHHHHCCCC--HHHHCCHHHHHHHHHHHHHC
T ss_conf             7999998999899995549988693989982997--78978978899999997513


No 46 
>2o9c_A Bacteriophytochrome; phytochrome chromophore, figure-OF-eight knot, phytochromobilin, biliverdin, PAS, GAF, transferase; HET: LBV; 1.45A {Deinococcus radiodurans} SCOP: d.110.2.1 d.110.3.9 PDB: 2o9b_A* 1ztu_A*
Probab=96.03  E-value=0.023  Score=32.52  Aligned_cols=109  Identities=12%  Similarity=0.057  Sum_probs=60.1

Q ss_pred             CEEEEEEC-CCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEECCCCCCCE
Q ss_conf             27999807-98989986589986379987964312467887653224789987532102465322211100100024320
Q T0527            20 AGLWDWNP-KTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGDFRWI   98 (142)
Q Consensus        20 ~~i~~~d~-~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri~~~~G~~~w~   98 (142)
                      .+++..|. ++.++++|+++.+++|++++++.+..  +.+ +.|++...+...+......  .......+..++|...|+
T Consensus        54 G~Ll~ld~~d~~I~~vS~N~~~iLG~~peelLG~~--l~~-llpe~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~  128 (342)
T 2o9c_A           54 GALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQT--LAA-LLPEQWPALQAALPPGCPD--ALQYRATLDWPAAGHLSL  128 (342)
T ss_dssp             SEEEEEETTTCBEEEEETTHHHHHSSCHHHHTTCB--HHH-HCTTTHHHHHHHSCTTCCT--TCCEEEEECCSSSSEEEE
T ss_pred             CEEEEEECCCCEEEEECCCHHHHHCCCHHHHCCCC--HHH-HCCHHHHHHHHHHHCCCCC--CEEEEEEEECCCCCEEEE
T ss_conf             47999988999499992889988592969985998--899-8884689999876407986--414678881588737999


Q ss_pred             EEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH
Q ss_conf             002541245535036777778817899999999999999984
Q T0527            99 QSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREELR  140 (142)
Q Consensus        99 ~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l~  140 (142)
                      ...    .. ++.  .++-+-.+.+.....+..|+..-.+++
T Consensus       129 ~ih----r~-~~~--li~E~E~~~~~~~~~~~~l~~~~~~Ir  163 (342)
T 2o9c_A          129 TVH----RV-GEL--LILEFEPTEAWDSTGPHALRNAMFALE  163 (342)
T ss_dssp             EEE----EE-TTE--EEEEEEEECGGGCCCHHHHHHHHHHHH
T ss_pred             EEE----EC-CCE--EEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             999----82-882--589988556333227999999999998


No 47 
>3fos_A Sensor protein; sensor histidine kinase domain, bacillus subtilis subsp. subtilis STR. 168, PSI-2, protein structure initiative; 2.48A {Bacillus subtilis subsp}
Probab=82.98  E-value=2.3  Score=21.16  Aligned_cols=97  Identities=14%  Similarity=0.080  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHCCC--EEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             9999999870682--79998079898998658998637998796431246788765322478998753210246532221
Q T0527             8 EERFQLAVSGASA--GLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVE   85 (142)
Q Consensus         8 e~r~~~~~~~~~~--~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e   85 (142)
                      ...|+.+.+..+.  +++.+|.+|.++..++...  .|+                .+.|++.+...    ..++...--+
T Consensus        54 ~~~L~~~~~~~~~~~~i~i~d~~G~~i~~s~~~~--~~~----------------~~~~r~~~~~~----~~~~~~~is~  111 (214)
T 3fos_A           54 QSILEKTFDSEPRFSGLYFLNAKGDVTASTTELK--TKV----------------NLADRSFFIKA----KETKKTVISD  111 (214)
T ss_dssp             HHHHHHHHTTCTTEEEEEEEETTCBEEEESSCCS--SCC----------------BCTTSHHHHHH----HHHCSCEECC
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCC--CCC----------------CHHHCHHHHHH----HHCCCCCCCC
T ss_conf             9999999861877008999959997898057667--888----------------93446367777----6337742133


Q ss_pred             HHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHHH
Q ss_conf             1100100024320002541245535036777778817899999
Q T0527            86 YRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRD  128 (142)
Q Consensus        86 ~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~~  128 (142)
                      ..+-...|  .|+..-+.|+++.+|++.++++...|+......
T Consensus       112 ~~~~~~~g--~~~i~~s~pi~~~~G~~~Gvl~~~i~l~~l~~~  152 (214)
T 3fos_A          112 SYSSRITG--QPIFTICVPVLDSKRNVTDYLVAAIQIDYLKNL  152 (214)
T ss_dssp             CEECTTTC--SEEEEEEEEEECSSCCEEEEEEEEEEHHHHHHH
T ss_pred             EEEECCCC--CEEEEEEEEEECCCCCEEEEEEEEEEHHHHHHH
T ss_conf             03304678--458999986796899789999999649999999


No 48 
>3e4o_A C4-dicarboxylate transport sensor protein DCTB; PAS domain, N-TERM helical dimerization domain, transferase; 2.30A {Sinorhizobium meliloti} PDB: 3e4p_A 3e4q_A 2zbb_A
Probab=50.58  E-value=12  Score=16.98  Aligned_cols=99  Identities=12%  Similarity=0.019  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHHHHC-CCEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             989999999998706-8279998079898998658998637998796431246788765322478998753210246532
Q T0527             4 LSASEERFQLAVSGA-SAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTY   82 (142)
Q Consensus         4 L~~se~r~~~~~~~~-~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~   82 (142)
                      +.+-++.|+.+...+ -..+|.+|.+|.++-.|..-      ++..+.+.  +      -.+++.|.+++    +++...
T Consensus        97 ~~~~~~~L~~~~~~~~a~~i~llD~~G~viasSn~~------~~~s~vg~--n------~s~RpYf~~Al----~g~~~~  158 (305)
T 3e4o_A           97 LDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQ------EPTSFVGN--D------YAFRDYFRLAV----RDGMAE  158 (305)
T ss_dssp             HHHHHHHHHHHHHHSSCSEEEEEETTSBEEEETTTT------STTCCTTC--B------CTTSHHHHHHH----HHSEEE
T ss_pred             HHHHHHHHHHHHHHCCEEEEEEECCCCCEEEECCCC------CCCCCCCC--C------CCCCHHHHHHH----CCCCCE
T ss_conf             999999999996230721899998999999966877------87432366--6------33318899987----178604


Q ss_pred             CCHHHEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHH
Q ss_conf             2211100100024320002541245535036777778817899
Q T0527            83 DVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDR  125 (142)
Q Consensus        83 ~~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~  125 (142)
                        .+-+-...|+  ..-.-+.|+++ +|++++++++-.|+...
T Consensus       159 --~~~~~~~~~~--~~~~~a~PV~~-~g~viGVvv~~v~l~~l  196 (305)
T 3e4o_A          159 --HFAMGTVSKR--PGLYISRRVDG-PGGPLGVIVAKLEFDGV  196 (305)
T ss_dssp             --EEEECTTTCC--EEEEEEEEEEE-TTEEEEEEEEEECCHHH
T ss_pred             --EEEECCCCCC--CEEEEEEECCC-CCCEEEEEEEEECHHHH
T ss_conf             --6763046676--23899752156-77147999999717999


No 49 
>3lif_A Putative diguanylate cyclase (ggdef) with PAS/PAC; PDC fold, signaling protein; HET: CIT; 2.70A {Rhodopseudomonas palustris}
Probab=39.30  E-value=18  Score=15.95  Aligned_cols=97  Identities=13%  Similarity=0.132  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHCC--CEEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             999999987068--279998079898998658998637998796431246788765322478998753210246532221
Q T0527             8 EERFQLAVSGAS--AGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVE   85 (142)
Q Consensus         8 e~r~~~~~~~~~--~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e   85 (142)
                      ++.++.+....+  ..++.+|++|.++..+..-.  -|+                ...+++.+.....  ..++..+ +.
T Consensus        57 ~~~l~~~~~~~~~~~~i~l~d~~G~~~~~~~~~~--~~~----------------~~~~r~~~~~~~~--~~~~~~~-~s  115 (254)
T 3lif_A           57 NERLRALADNLPQLSDVAILDADGQLTYASVKPV--PAL----------------DNSDRSYFRYHRA--NDDHTLL-IT  115 (254)
T ss_dssp             HHHHHHHHHHCTTEEEEEEECTTSBEEEESSSSE--ECC----------------BCTTSHHHHHHHH--CCCCCCE-EE
T ss_pred             HHHHHHHHHHCCCEEEEEEECCCCCEEECCCCCC--CCC----------------CCCHHHHHHHHHH--CCCCCEE-EE
T ss_conf             9999999852977159999959999883268887--778----------------8324278999984--7998459-80


Q ss_pred             HHEEEC-CCCCCCEEEEEEECCCCCCEEEEEEEEEEEHHHHHH
Q ss_conf             110010-002432000254124553503677777881789999
Q T0527            86 YRVRTR-SGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKR  127 (142)
Q Consensus        86 ~ri~~~-~G~~~w~~~~~~~~~d~~g~~~~~~g~~~DITe~k~  127 (142)
                      -.+..+ +|.  |+.....|+.+.+|.+.+++++..|+.....
T Consensus       116 ~~~~~~~~g~--~~~~i~~pi~~~~g~~~Gvl~~~l~l~~l~~  156 (254)
T 3lif_A          116 GPIQSRTSGV--WVFVVSRRLETTDGKFFGVVVATIESEYFST  156 (254)
T ss_dssp             EEEECTTTCC--EEEEEEEEEECTTCCEEEEEEEEECHHHHHH
T ss_pred             EEEECCCCCC--CCEEEEEEECCCCCCEEEEEEEECCHHHHHH
T ss_conf             0376267895--3046898731688866799998468899998


No 50 
>1p0z_A Sensor kinase CITA; transferase; HET: FLC MO7; 1.60A {Klebsiella pneumoniae} SCOP: d.110.6.1 PDB: 2v9a_A 2j80_A*
Probab=37.32  E-value=20  Score=15.77  Aligned_cols=28  Identities=7%  Similarity=0.035  Sum_probs=22.3

Q ss_pred             CEEEEEEECCCCCCEEEEEEEEEEEHHH
Q ss_conf             2000254124553503677777881789
Q T0527            97 WIQSRGQALWNSAGEPYRMVGWIMDVTD  124 (142)
Q Consensus        97 w~~~~~~~~~d~~g~~~~~~g~~~DITe  124 (142)
                      .......|+++++|++++++.+..++++
T Consensus       100 ~~~~~~~PV~~~~G~viGvv~Vg~~l~~  127 (131)
T 1p0z_A          100 SSLRGKSPIQDATGKVIGIVSVGYTIEQ  127 (131)
T ss_dssp             EEEEEEEEEECTTCCEEEEEEEEEEGGG
T ss_pred             EEEEEEEEEECCCCCEEEEEEEEEEHHH
T ss_conf             1899999679799979999999988577


No 51 
>3ddj_A CBS domain-containing protein; NP_344512.1, structural genomics, joint center for structural genomics, JCSG; HET: AMP; 1.80A {Sulfolobus solfataricus} SCOP: d.37.1.1 d.37.1.1
Probab=33.14  E-value=19  Score=15.91  Aligned_cols=40  Identities=10%  Similarity=-0.015  Sum_probs=23.7

Q ss_pred             EEEEEECCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHHHHH
Q ss_conf             00254124553503677777881789999999999999998
Q T0527            99 QSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRVSREEL  139 (142)
Q Consensus        99 ~~~~~~~~d~~g~~~~~~g~~~DITe~k~~e~~L~~~~~~l  139 (142)
                      ...+.|+.|++|++.+++ +.+||-+.-.-..-+.+.+++|
T Consensus       257 ~~~~l~Vvd~~g~l~Giv-T~~Dil~al~~~~~~~~~~e~~  296 (296)
T 3ddj_A          257 RIGSLLILNKDNTIRGII-TERDLLIALHHILVMEKFKEKL  296 (296)
T ss_dssp             TCSEEEEECTTSCEEEEE-EHHHHHHHHHHHHHHHHHHTC-
T ss_pred             CCCEEEEECCCCEEEEEE-EHHHHHHHHHHHHHCCHHHCCC
T ss_conf             998899990799899998-8999999998876130530639


No 52 
>3fgx_A Rbstp2171; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.90A {Bacillus stearothermophilus}
Probab=28.40  E-value=17  Score=16.09  Aligned_cols=20  Identities=15%  Similarity=0.139  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             67887653224789987532
Q T0527            55 GHRESIHPDDRARVLAALKA   74 (142)
Q Consensus        55 ~~~~~ihpdd~~~~~~~~~~   74 (142)
                      -.++.|||||++.+.+.+.+
T Consensus        68 lvLD~i~pd~~~~L~~d~EE   87 (114)
T 3fgx_A           68 LTFSCIVPEQEEELRQAAEE   87 (114)
T ss_dssp             HHHTTBCGGGHHHHHHHHHH
T ss_pred             HHHHCCCCCCHHHHHHHHHH
T ss_conf             75640578838999999987


No 53 
>1vq8_K 50S ribosomal protein L14P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.39.1.1 PDB: 1vq4_K* 1vq5_K* 1vq6_K* 1vq7_K* 1s72_K* 1vq9_K* 1vqk_K* 1vql_K* 1vqm_K* 1vqn_K* 1vqo_K* 1vqp_K* 1yhq_K* 1yi2_K* 1yij_K* 1yit_K* 1yj9_K* 1yjn_K* 1yjw_K* 2otj_K* ...
Probab=28.11  E-value=14  Score=16.62  Aligned_cols=35  Identities=14%  Similarity=0.202  Sum_probs=27.5

Q ss_pred             HHEEECCCCCCCEEEEEEECCCCCCEEEE--EEEEEE
Q ss_conf             11001000243200025412455350367--777788
Q T0527            86 YRVRTRSGDFRWIQSRGQALWNSAGEPYR--MVGWIM  120 (142)
Q Consensus        86 ~ri~~~~G~~~w~~~~~~~~~d~~g~~~~--~~g~~~  120 (142)
                      ..++++||.++-+..++.++.|++|+|.+  +.|.+-
T Consensus        78 k~~~R~dG~~i~FddNa~VLi~~~~~p~GTrI~GpV~  114 (132)
T 1vq8_K           78 KPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIA  114 (132)
T ss_dssp             SCEECTTSCEEEESSCEEEEECTTSCBSSSCBCSEEC
T ss_pred             CCEECCCCCEEECCCCEEEEECCCCCEEEEEEECCHH
T ss_conf             7239899998981797799998999993607956477


No 54 
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=23.78  E-value=19  Score=15.92  Aligned_cols=33  Identities=12%  Similarity=0.272  Sum_probs=25.7

Q ss_pred             HHHEEECCCCCCCEEEEEEECCCCCCEEEE--EEE
Q ss_conf             111001000243200025412455350367--777
Q T0527            85 EYRVRTRSGDFRWIQSRGQALWNSAGEPYR--MVG  117 (142)
Q Consensus        85 e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~--~~g  117 (142)
                      ...++++||.++-+..++.++.+++|+|.+  +.|
T Consensus        66 kk~~~R~dG~~i~F~~Na~VLi~~~~~P~GTrI~G  100 (121)
T 3bbo_M           66 CKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFG  100 (121)
T ss_dssp             SSCEECTTSCEECCSSCEEEECCTTSSCSSSCCCS
T ss_pred             ECCEECCCCCEEECCCCEEEEECCCCCEEEEEEEC
T ss_conf             04217389998870895599998999991746961


No 55 
>2zkr_k 60S ribosomal protein L23; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1i_R 3jyw_R
Probab=21.13  E-value=23  Score=15.36  Aligned_cols=36  Identities=19%  Similarity=0.328  Sum_probs=27.4

Q ss_pred             CHHHEEECCCCCCCEEEEEEECCCCCCEEEE--EEEEE
Q ss_conf             2111001000243200025412455350367--77778
Q T0527            84 VEYRVRTRSGDFRWIQSRGQALWNSAGEPYR--MVGWI  119 (142)
Q Consensus        84 ~e~ri~~~~G~~~w~~~~~~~~~d~~g~~~~--~~g~~  119 (142)
                      .-+.++++||.++-+..++.++.+++|+|.+  +.|.+
T Consensus        84 tk~~~~R~dG~~i~FddNavVLin~~~~P~GTRI~GPV  121 (140)
T 2zkr_k           84 QRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPV  121 (140)
T ss_dssp             CSSCEECTTSCEECCSSCEEEEBCTTSCBSSSCBCSCC
T ss_pred             ECCCEECCCCCEEECCCCEEEEECCCCCEEEEEEECCC
T ss_conf             68862989998897799459999899988040697550


No 56 
>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}
Probab=20.33  E-value=41  Score=13.99  Aligned_cols=45  Identities=16%  Similarity=0.023  Sum_probs=29.5

Q ss_pred             CEEEEEEECCCCCCEEEEEEEEEE---EHH--HHHHHHHHHHHHHHHHHC
Q ss_conf             200025412455350367777788---178--999999999999999842
Q T0527            97 WIQSRGQALWNSAGEPYRMVGWIM---DVT--DRKRDEDALRVSREELRR  141 (142)
Q Consensus        97 w~~~~~~~~~d~~g~~~~~~g~~~---DIT--e~k~~e~~L~~~~~~l~~  141 (142)
                      -+...+.|++|.+|.++..+++.-   .++  .....-+.|++.-+++..
T Consensus       204 g~~~iA~PV~~~~g~~~aal~v~~p~~r~~~~~~~~~~~~L~~~A~~Isa  253 (260)
T 2o0y_A          204 GSSGLSFPLVDSHGTVVAALTLGGPTGRFTEDRTPHYIECTRAAAEEISA  253 (260)
T ss_dssp             TEEEEEEEEECTTCCEEEEEEEEEEGGGSCTTTHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEECCCCCEEEEEEEEEEHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             94799998999999999999997585868998999999999999999997


No 57 
>3g6o_A Bacteriophytochrome; alpha/beta structure, PAS domain, chromophore, kinase, phosphoprotein, photoreceptor protein, receptor; HET: BLA; 2.85A {Pseudomonas aeruginosa} PDB: 3ibr_A* 3c2w_A*
Probab=20.03  E-value=41  Score=13.95  Aligned_cols=61  Identities=10%  Similarity=0.105  Sum_probs=36.4

Q ss_pred             EEEEEECCCCEEEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHE
Q ss_conf             79998079898998658998637998796431246788765322478998753210246532221110
Q T0527            21 GLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRV   88 (142)
Q Consensus        21 ~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~ri   88 (142)
                      ++..+|+++.++.+|.++.+++|++++...+..   .+.+.|+....+.    ..+.+..++...+++
T Consensus        28 ~Ll~ld~~~~I~~vS~N~~~~lg~~~~~l~~~~---~~~~~~~~~~~l~----~~~~~~~~~~~~~~~   88 (505)
T 3g6o_A           28 ALVTLRADGMVLAASENIQALLGFVASPGSYLT---QEQVGPEVLRMLE----EGLTGNGPWSNSVET   88 (505)
T ss_dssp             EEEEECTTCBEEEEETTHHHHSSCCCCTTCBCC---HHHHCHHHHHHHH----HHHHSCSCCEEEEEE
T ss_pred             EEEEEECCCCEEEEECCHHHHHCCCCCCCCCCC---HHHCCHHHHHHHH----HHHCCCCCCCEEEEE
T ss_conf             899990799589992779987389852035648---6761968999998----752238875037886


Done!