Query T0600 3NJA, Chromobacterium violaceum ATCC 12472, 125 residues Match_columns 125 No_of_seqs 125 out of 10427 Neff 10.3 Searched_HMMs 22458 Date Mon Jul 5 09:06:41 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0600.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/T0600.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3eeh_A Putative light and redo 99.9 5E-24 2.2E-28 147.0 8.5 118 3-121 7-125 (125) 2 3h9w_A Diguanylate cyclase wit 99.9 2.7E-21 1.2E-25 132.3 12.0 109 15-124 1-110 (115) 3 3icy_A Sensor protein; sensory 99.8 1.7E-20 7.6E-25 128.1 7.1 115 5-121 2-118 (118) 4 2gj3_A Nitrogen fixation regul 99.8 8.6E-20 3.8E-24 124.3 10.7 117 5-123 3-119 (120) 5 2z6d_A Phototropin-2; PAS-fold 99.8 7.9E-20 3.5E-24 124.5 9.7 119 5-125 4-125 (130) 6 3lyx_A Sensory BOX/ggdef domai 99.8 8.7E-20 3.9E-24 124.3 9.4 116 8-125 8-123 (124) 7 3luq_A Sensor protein; PAS, hi 99.8 1.9E-18 8.3E-23 117.2 11.1 114 5-121 1-114 (114) 8 2wkq_A NPH1-1, RAS-related C3 99.8 3.7E-19 1.7E-23 120.9 6.9 116 8-125 12-130 (332) 9 3f1p_B ARYL hydrocarbon recept 99.8 8.6E-19 3.8E-23 119.0 6.4 116 8-125 2-120 (121) 10 2v0u_A NPH1-1, LOV2; kinase, t 99.8 5.5E-19 2.5E-23 120.0 5.2 116 8-125 3-121 (146) 11 3f1p_A Endothelial PAS domain- 99.7 3.4E-18 1.5E-22 115.7 7.1 108 16-125 8-116 (117) 12 2r78_A Sensor protein; sensory 99.7 6.6E-17 3E-21 108.9 7.3 110 4-121 8-117 (117) 13 2vlg_A Sporulation kinase A; h 99.7 3.6E-17 1.6E-21 110.3 4.5 110 10-124 2-111 (111) 14 1v9y_A Heme PAS sensor protein 99.7 1E-16 4.5E-21 107.9 6.7 118 4-125 37-158 (167) 15 3ewk_A Sensor protein; PAS dom 99.7 4.1E-16 1.8E-20 104.6 9.5 114 4-119 108-227 (227) 16 2qkp_A Uncharacterized protein 99.7 2.4E-16 1.1E-20 105.8 8.1 119 3-125 15-135 (151) 17 3gdi_A Period circadian protei 99.7 3.9E-17 1.7E-21 110.1 3.8 118 5-124 153-273 (309) 18 1wa9_A Period circadian protei 99.6 2.5E-17 1.1E-21 111.1 2.4 120 4-125 145-269 (368) 19 1byw_A Protein (human ERG pota 99.6 1.9E-16 8.5E-21 106.4 6.5 99 25-123 12-110 (110) 20 3mjq_A Uncharacterized protein 99.6 3.7E-16 1.6E-20 104.9 7.6 112 9-125 1-112 (126) 21 2pr5_A Blue-light photorecepto 99.6 3.6E-16 1.6E-20 104.9 6.2 111 11-125 3-116 (132) 22 1n9l_A PHOT-LOV1, putative blu 99.6 1.3E-15 5.7E-20 102.0 9.0 104 17-122 3-109 (109) 23 3bwl_A Sensor protein; structu 99.6 7.6E-16 3.4E-20 103.2 7.7 114 3-121 13-126 (126) 24 1d06_A Nitrogen fixation regul 99.6 3E-15 1.4E-19 100.0 7.1 114 4-121 13-130 (130) 25 3cax_A Uncharacterized protein 99.6 9.1E-15 4.1E-19 97.4 9.3 116 2-125 234-349 (369) 26 3fc7_A HTR-like protein, senso 99.5 1.4E-14 6.3E-19 96.4 5.6 111 3-121 15-125 (125) 27 2vv6_A FIXL, sensor protein FI 99.4 5.2E-13 2.3E-17 88.0 8.6 106 16-125 2-111 (119) 28 3fg8_A Uncharacterized protein 99.4 5.2E-13 2.3E-17 88.0 6.5 104 10-123 15-118 (118) 29 3mfx_A Sensory BOX/ggdef famil 99.4 3.1E-13 1.4E-17 89.2 4.6 115 3-122 3-124 (129) 30 3d72_A Vivid PAS protein VVD; 99.4 2.6E-12 1.2E-16 84.3 8.7 98 17-116 35-146 (149) 31 3clo_A Transcriptional regulat 99.3 8.3E-12 3.7E-16 81.6 9.3 120 4-124 30-167 (258) 32 1oj5_A Steroid receptor coacti 99.3 2.2E-12 9.8E-17 84.7 5.8 105 18-124 8-116 (132) 33 3ewk_A Sensor protein; PAS dom 99.3 7.8E-12 3.5E-16 81.7 7.7 104 20-125 2-105 (227) 34 3b33_A Sensor protein; structu 99.1 7.3E-11 3.3E-15 76.5 6.6 114 1-120 1-114 (115) 35 1wa9_A Period circadian protei 99.0 3.3E-11 1.5E-15 78.4 -0.6 104 20-125 10-138 (368) 36 3gdi_A Period circadian protei 98.9 2.1E-10 9.2E-15 74.1 0.5 113 11-125 19-137 (309) 37 1ll8_A PAS kinase; PAS domain, 98.8 1.4E-09 6.2E-14 69.7 3.9 104 14-121 5-113 (114) 38 3a0r_A Sensor protein; four he 98.8 6E-10 2.7E-14 71.6 1.6 107 10-125 11-118 (349) 39 1nwz_A PYP, photoactive yellow 98.8 4E-09 1.8E-13 67.2 5.4 105 10-120 20-125 (125) 40 3a0s_A Sensor protein; PAS-fol 98.6 1.2E-07 5.5E-12 59.3 8.4 94 17-119 2-96 (96) 41 1mzu_A PPR; photoactive yellow 98.6 9.8E-09 4.3E-13 65.2 1.8 102 8-113 23-125 (129) 42 2w0n_A Sensor protein DCUS; si 98.5 1.3E-08 5.7E-13 64.5 1.3 106 5-121 13-118 (118) 43 2jhe_A Transcription regulator 98.4 2.6E-08 1.1E-12 62.9 0.2 108 4-123 77-188 (190) 44 2ool_A Sensor protein; bacteri 93.8 0.04 1.8E-06 29.8 3.4 74 20-96 45-119 (337) 45 2vea_A Phytochrome-like protei 90.1 0.16 7.1E-06 26.6 2.9 98 20-123 32-130 (520) 46 2o9c_A Bacteriophytochrome; ph 86.2 0.67 3E-05 23.2 4.1 73 19-98 55-130 (342) 47 1p0z_A Sensor kinase CITA; tra 35.5 20 0.00089 15.3 4.0 87 8-122 40-127 (131) 48 2ggv_B NS3, non-structural pro 34.5 21 0.00093 15.2 2.8 22 96-117 131-152 (185) 49 3e90_B NS3 protease; trypsin-l 29.2 21 0.00095 15.2 2.0 20 96-115 136-155 (198) 50 3fos_A Sensor protein; sensor 29.1 26 0.0012 14.7 7.2 92 7-122 55-148 (214) 51 2fp7_B Polyprotein; flavivirus 28.9 20 0.00089 15.3 1.8 22 96-117 117-138 (172) 52 3e4o_A C4-dicarboxylate transp 27.3 28 0.0012 14.5 8.3 93 7-122 102-195 (305) 53 2khu_A Immunoglobulin G-bindin 26.0 20 0.00089 15.3 1.3 66 3-72 24-90 (108) 54 3lkw_A Fusion protein of nonst 25.8 25 0.0011 14.9 1.8 20 98-117 184-203 (236) 55 2fom_B Polyprotein; flavivirus 22.9 25 0.0011 14.8 1.3 20 97-116 133-152 (185) 56 1pn5_A Nacht-, LRR- and PYD-co 22.5 35 0.0015 14.0 3.0 65 3-73 24-89 (159) 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=99.90 E-value=5e-24 Score=146.99 Aligned_cols=118 Identities=19% Similarity=0.301 Sum_probs=108.7 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCC-EEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 68899999999861981899864899-89981689874113512245876689998875103789999999987504563 Q T0600 3 AMAEKLLHTAESDAGIGSWVLHMESG-RLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFD 81 (125) Q Consensus 3 a~SE~~l~~~~~~a~~g~w~~d~~~~-~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 81 (125) ..||++|+.++++++.++|.+|++++ .+|+|+++++++|++++.+...+..|++++||+|+..+...+..+..+ +.+. T Consensus 7 ~~se~r~~~i~e~~~~~i~~~d~~~~~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~ihpdd~~~~~~~~~~~~~~-~~~~ 85 (125) T 3eeh_A 7 AKSERRVRELTEATNDILWEFTADLSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQSLMDG-ESAD 85 (125) T ss_dssp ---CHHHHHHHSCCCCEEEEEETTSSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHHHHTT-CCEE T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCEEEEECHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHCCCC-CEEE T ss_conf 999999999986498449999998995999783886512345321111101442058752032035442220343-2046 Q ss_pred EEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 2578604433332223550056889996899988887321 Q T0600 82 VEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 82 ~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) .|||+++++|+.+|+++++.|++|++|++++++|+++||| T Consensus 86 ~e~r~~~~~G~~~wv~~~~~~i~d~~g~~~~~~g~~~DIT 125 (125) T 3eeh_A 86 VECRVNATEEYQRWVWIQGEPITNDAGETVRVAGFARDIT 125 (125) T ss_dssp EEEEECGGGTTCEEEEEEEEEEECTTSCEEEEEEEEEECC T ss_pred EEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEEC T ss_conf 7788786998789999999999999989999999999809 No 2 >3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.90A {Marinobacter aquaeolei VT8} Probab=99.86 E-value=2.7e-21 Score=132.32 Aligned_cols=109 Identities=17% Similarity=0.330 Sum_probs=99.8 Q ss_pred HCCCEEEEEECCCCEE-EEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCC Q ss_conf 6198189986489989-981689874113512245876689998875103789999999987504563257860443333 Q T0600 15 DAGIGSWVLHMESGRL-EWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQV 93 (125) Q Consensus 15 ~a~~g~w~~d~~~~~~-~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~ 93 (125) .++.++|++|++++.+ |+|+++++++|++++++.+ ...+..++||++...+...+...+.++..+..++|+++++|+. T Consensus 1 ~t~~~~W~~D~~t~~~~yvn~~~~~i~G~~~e~~~~-~~~~~~~i~pdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~ 79 (115) T 3h9w_A 1 MTKAIPWKINWQTMAFEYIGPQIEALLGWPQGSWKS-VEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHY 79 (115) T ss_dssp --CCEEEEEETTTTEEEEECTHHHHHHCSCGGGCCB-HHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSCE T ss_pred CCCEEEEEEECCCCEEEEECHHHHHHHCCCHHHCCC-CCHHHHEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCC T ss_conf 984799999899998999999999984999788289-3033201225679999999999985597078999999605652 Q ss_pred CCCCCCCEEEECCCCCEEEEEEEEEECHHHC Q ss_conf 2223550056889996899988887321124 Q T0600 94 RELLERNHIQRQASGQVDHLWGTVIDMTEHK 124 (125) Q Consensus 94 ~w~~~~~~~~~d~~g~~~~~vG~~~DITerK 124 (125) +|++++++|++|++|++.+++|+++|||++. T Consensus 80 ~wv~~~~~~~~d~~g~~~~~~g~~~DITee~ 110 (115) T 3h9w_A 80 VWIRDVVHVVRDDSGEVEALIGFMFDISLEH 110 (115) T ss_dssp EEEEEEEEEEECTTSCEEEEEEEEEECGGGG T ss_pred HHHEEECEEEECCCCCEEEEEEEEEEECCCC T ss_conf 0110201049999989999999999899787 No 3 >3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum} Probab=99.82 E-value=1.7e-20 Score=128.08 Aligned_cols=115 Identities=16% Similarity=0.219 Sum_probs=101.2 Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEE--EHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 8999999998619818998648998998--16898741135122458766899988751037899999999875045632 Q T0600 5 AEKLLHTAESDAGIGSWVLHMESGRLEW--SQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDV 82 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~~~~~~--s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 82 (125) ||++|+.++++++.++|.+|.+++..++ |+....++|++.. ......+.+.+||++++.+...+..+++++..+.. T Consensus 2 ~~e~~r~l~d~~p~~i~~~d~~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~i~p~~~~~~~~~~~~~~~~~~~~~~ 79 (118) T 3icy_A 2 NAEELQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHA--GTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLTL 79 (118) T ss_dssp HHHHHHHHHTTCCCCCEEECTTSCEEECCCCCGGGGGGEEEET--TEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEEE T ss_pred CHHHHHHHHHCCCEEEEEEECCCCEEEEECCHHHHCCCCCCHH--HHCCCCHHHHCCHHHHHHHHHHHCCCCCCCCCCCC T ss_conf 8899999985494018999888988999657687463284958--86589889956988998988520023322344312 Q ss_pred EEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 578604433332223550056889996899988887321 Q T0600 83 EYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 83 e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) |+++++++|..+|++++++|++|++|++.+++|++.||| T Consensus 80 e~~~~~~~g~~~wv~~~~~~~~d~~g~~~~~~g~~~DIT 118 (118) T 3icy_A 80 VYRIVTPEGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT 118 (118) T ss_dssp EEEEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECC T ss_pred CEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECC T ss_conf 015782599799999999999999979999999999779 No 4 >2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii} Probab=99.82 E-value=8.6e-20 Score=124.31 Aligned_cols=117 Identities=14% Similarity=0.045 Sum_probs=105.0 Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 89999999986198189986489989981689874113512245876689998875103789999999987504563257 Q T0600 5 AEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) ..++|+.+++.++.|+|..|.+++.+++|+++++++|++++++.+... ..+.+++....+.+.+...+..++.+..|+ T Consensus 3 ~~~~~~~~~e~s~~~i~i~d~~g~i~~~N~a~~~~~G~~~~el~g~~~--~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~ 80 (120) T 2gj3_A 3 LPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNE--SILSNGTTPRLVYQALWGRLAQKKPWSGVL 80 (120) T ss_dssp CHHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHCCCTTGGGGCBG--GGGCCTTSCHHHHHHHHHHHHTTCCEEEEE T ss_pred HHHHHHHHHHCCCHHEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCC--CCCEECCCCHHHHHHHHHHHCCCCCCEEEE T ss_conf 899999999712415299969999999968999987969566167540--001101353678999876330697306125 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHH Q ss_conf 860443333222355005688999689998888732112 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEH 123 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITer 123 (125) +..++||..+|+++++.|++|++|++.+++|+++||||. T Consensus 81 ~~~~kdG~~~~~~~~~~~i~d~~g~~~~~i~~~~DITel 119 (120) T 2gj3_A 81 VNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSEL 119 (120) T ss_dssp EEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCSC T ss_pred EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCC T ss_conf 558699989999999999999998999999999956677 No 5 >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=99.81 E-value=7.9e-20 Score=124.51 Aligned_cols=119 Identities=13% Similarity=0.033 Sum_probs=105.2 Q ss_pred HHHHHHHHHHHCCCEEEEEE---CCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 89999999986198189986---489989981689874113512245876689998875103789999999987504563 Q T0600 5 AEKLLHTAESDAGIGSWVLH---MESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFD 81 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d---~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 81 (125) +++.|+.+++..+.++...| ++++++|+|+++++|+|++++++.+.. +..+++++........+...+..+..+. T Consensus 4 ~~~~l~~~~~~~~~~~~i~D~~~~d~~I~~vN~a~~~~~G~~~~elig~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~~ 81 (130) T 2z6d_A 4 VSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRN--CRFLQGPDTDKNEVAKIRDCVKNGKSYC 81 (130) T ss_dssp ---CHHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTSCHHHHHHHHHHHHTTCCEE T ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHHHCCCCCCHHHHHHHHHHHHHHCCCE T ss_conf 68999999983899699998989979899998799998892989975986--6765387788899999999986304520 Q ss_pred EEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 25786044333322235500568899968999888873211249 Q T0600 82 VEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 82 ~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) .|+++++++|..+|+.++..|++|++|++.+++|++.|||++|+ T Consensus 82 ~e~~~~~~dG~~~w~~~~~~pi~d~~g~~~~~i~~~~DITe~ke 125 (130) T 2z6d_A 82 GRLLNYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTE 125 (130) T ss_dssp EEEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCTTC- T ss_pred EEEEEEECCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHH T ss_conf 69999962886699999999999999999999999998838889 No 6 >3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea} Probab=99.81 E-value=8.7e-20 Score=124.29 Aligned_cols=116 Identities=15% Similarity=0.104 Sum_probs=103.0 Q ss_pred HHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE Q ss_conf 99999986198189986489989981689874113512245876689998875103789999999987504563257860 Q T0600 8 LLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIV 87 (125) Q Consensus 8 ~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~ 87 (125) .+..+++.+++|++.+|.+++.+++|+++++++|++++++.+.. +..++++++.......+...+..+..+..++++. 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 CCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 44333322235500568899968999888873211249 Q T0600 88 RPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 88 ~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) +++|..+|+.++..|++|++|++.+++++++|||+||| 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 7 >3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens} Probab=99.77 E-value=1.9e-18 Score=117.15 Aligned_cols=114 Identities=17% Similarity=0.100 Sum_probs=100.7 Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 89999999986198189986489989981689874113512245876689998875103789999999987504563257 Q T0600 5 AEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) ||++|+.+++++++|+|.+|.+++.+++|+++++++|++++.+.+.... ..++.............+.++.....+. T Consensus 1 Se~~lr~i~~~~p~~i~~~D~~g~~~~~N~~~~~~~g~~~~~~~g~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (114) T 3luq_A 1 SDERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHY---DIFPEIGEEWKSVHRRGLAGEVIRVEED 77 (114) T ss_dssp CCHHHHHHHHTCSSEEEEEETTCBEEEECHHHHHHTTCCSSCCTTCBHH---HHCTTCCHHHHHHHHHHHTTCCEEEEEE T ss_pred CHHHHHHHHHHHCHHHEEECCCCCEEEECHHHHHHHCCCCHHCCCCCCC---CCCCCCCHHHHHHHHHHHCCCCCEEEEE T ss_conf 9799999997104672999799969999499898724570002687620---0123310233358999980898400342 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 8604433332223550056889996899988887321 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) +..+++|..+|+.+++.|++|++|++.+++|+++||| 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 8 >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=99.77 E-value=3.7e-19 Score=120.89 Aligned_cols=116 Identities=14% Similarity=0.055 Sum_probs=102.0 Q ss_pred HHHHHHHHCCCEEEEEE---CCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 99999986198189986---489989981689874113512245876689998875103789999999987504563257 Q T0600 8 LLHTAESDAGIGSWVLH---MESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 8 ~l~~~~~~a~~g~w~~d---~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) +|+.+++..+.|+...| ++++++|+|+++++|+||+.+++.+.... .+.+++..+.....+...+..+..+..|+ T Consensus 12 ~l~~~~e~~~~~~vi~D~~~~dg~Ii~vN~a~~~l~Gy~~~EliG~~~~--~l~~~~~~~~~~~~i~~~l~~~~~~~~e~ 89 (332) T 2wkq_A 12 SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNAR--FLQGPETDRATVRKIRDAIDNQTEVTVQL 89 (332) T ss_dssp --CCCGGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGG--GGCCTTCCHHHHHHHHHHHHTTCCEEEEE T ss_pred HHHHHHHCCCCEEEEECCCCCCCEEEEECHHHHHHHCCCHHHHCCCCHH--HHCCCCCCHHHHHHHHHHHHCCCEEEEEE T ss_conf 9999997089759998489998949988389999888399998599877--71798889999999999998498399999 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 86044333322235500568899968999888873211249 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) +..++||+.+|+++++.|++|++|++.+++|++.|||+||| T Consensus 90 ~~~~kdG~~~~v~~~~~pi~d~~G~i~~~v~~~~DITe~k~ 130 (332) T 2wkq_A 90 INYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR 130 (332) T ss_dssp EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCC T ss_pred EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHH T ss_conf 99978999999999999618899999999999995714789 No 9 >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=99.75 E-value=8.6e-19 Score=118.97 Aligned_cols=116 Identities=10% Similarity=0.050 Sum_probs=102.3 Q ss_pred HHHHHHHHCCCEE-EEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCEEEE Q ss_conf 9999998619818-9986489989981689874113512245876689998875103789999999987504-5632578 Q T0600 8 LLHTAESDAGIGS-WVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDR-PFDVEYR 85 (125) Q Consensus 8 ~l~~~~~~a~~g~-w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~e~r 85 (125) +||.+...++... ...|++++.+|+|+++++++|++++++.+. .+.+++|+++...+...+...+..+. ....+++ 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 EECCCCCCCCCCCCCEEEECC-CCCEEEEEEEEEECHHHCC Q ss_conf 604433332223550056889-9968999888873211249 Q T0600 86 IVRPDGQVRELLERNHIQRQA-SGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 86 ~~~~~g~~~w~~~~~~~~~d~-~g~~~~~vG~~~DITerK~ 125 (125) ++++||+.+|+++++.|++|+ +|+|.+++|+..|||+||| 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 10 >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=99.75 E-value=5.5e-19 Score=119.99 Aligned_cols=116 Identities=14% Similarity=0.058 Sum_probs=102.4 Q ss_pred HHHHHHHHCCCEEEEEEC---CCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 999999861981899864---89989981689874113512245876689998875103789999999987504563257 Q T0600 8 LLHTAESDAGIGSWVLHM---ESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 8 ~l~~~~~~a~~g~w~~d~---~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) +|+.+++.++.|+...|. ++.++|+|+++++|+||+++++.+.... .+.+|+........+...+..+..+..|+ T Consensus 3 ~l~~~~e~~~~~~vi~d~~~~dg~I~~vN~a~~~~~Gy~~~el~G~~~~--~l~~~~~~~~~~~~l~~~l~~~~~~~~e~ 80 (146) T 2v0u_A 3 FLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCR--FLQGPETDRATVRKIRDAIDNQTEVTVQL 80 (146) T ss_dssp SCCCTGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGG--GGCCTTSCHHHHHHHHHHHHTTCCEEEEE T ss_pred HHHHHHHHCCCCEEEEECCCCCCEEEEECHHHHHHHCCCHHHHHCCCHH--HHCCCCCCHHHHHHHHHHHHCCCCCEEEE T ss_conf 8999998189809999588998979999679999889699998177422--02033454999999999998199752799 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 86044333322235500568899968999888873211249 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) +.+++||+.+|++++..|++|++|++.++++++.|||++|+ T Consensus 81 ~~~~kdG~~~~v~~~~~p~~d~~g~~~~~v~v~~DITe~k~ 121 (146) T 2v0u_A 81 INYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR 121 (146) T ss_dssp EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCC T ss_pred EEEECCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHH T ss_conf 87843884699999999999799899999999998889999 No 11 >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=99.73 E-value=3.4e-18 Score=115.75 Aligned_cols=108 Identities=9% Similarity=0.055 Sum_probs=98.4 Q ss_pred CCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCC Q ss_conf 19818998648998998168987411351224587668999887510378999999998750456325786044333322 Q T0600 16 AGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVRE 95 (125) Q Consensus 16 a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w 95 (125) +...+...+++++.+|+|+++++++|++++++.+. .+..+++|++...+.+.+..++.++.....+++++++||+.+| T Consensus 8 s~~fi~~~~~dg~i~~~N~~~~~~~G~~~~el~g~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~iw 85 (117) T 3f1p_A 8 SKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR--SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW 85 (117) T ss_dssp GGEEEEEECTTCBEEEECTHHHHHHCCCHHHHTTS--BGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEEE T ss_pred CCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CEEEEECHHHCCHHHHHHHHCCCCCCCEECCEEEECCCCCEEE T ss_conf 58289999999989999989999859696791163--0016727135111233332111112210011001879997999 Q ss_pred CCCCCEEEECCC-CCEEEEEEEEEECHHHCC Q ss_conf 235500568899-968999888873211249 Q T0600 96 LLERNHIQRQAS-GQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 96 ~~~~~~~~~d~~-g~~~~~vG~~~DITerK~ 125 (125) ++.+++|++|++ |+|.+++++..|||++|| T Consensus 86 v~~~~~~i~d~~~~~~~~iv~~~~dITe~k~ 116 (117) T 3f1p_A 86 LETQGTVIYNPRNLQPQCIMCVNYVLSEIEK 116 (117) T ss_dssp EEEEEEEEEETTTTEEEEEEEEEEECSCCBC T ss_pred EEEEEEEEEECCCCCEEEEEEEEEECCHHHC T ss_conf 9999999997899939999999999952304 No 12 >2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca} Probab=99.67 E-value=6.6e-17 Score=108.86 Aligned_cols=110 Identities=17% Similarity=0.189 Sum_probs=97.8 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 88999999998619818998648998998168987411351224587668999887510378999999998750456325 Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVE 83 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e 83 (125) .||++|+.+++.+++|+|.+|.+++.+++|+++++++|++++++.+. .+.++++|++...+...+..+.. +.....| T Consensus 8 ~~e~~fr~i~e~~~~~i~i~d~~g~i~~~N~~~~~~~g~~~~~l~g~--~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~e 84 (117) T 2r78_A 8 FQSNAYRALFEHAIDGIFIMDAEGHYLDVNPAICSAIGYTRDEFLAL--DWGVLSRGVDSGWAAASLARIVG-GEPLREE 84 (117) T ss_dssp HHHHHHHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTC--BTTTTTTCSTTSHHHHHHHHHHT-TCCEEEE T ss_pred HHHHHHHHHHHHCCHHEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHC-CCCCEEE T ss_conf 99999999998167450999699989999399999879597894126--73214540013657899999983-9983789 Q ss_pred EEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 78604433332223550056889996899988887321 Q T0600 84 YRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 84 ~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) +++++++|+.+|+++++.|+.| |+ ++|+++||| T Consensus 85 ~~~~~~dG~~~~~~~~~~~i~d--~~---~~~~~~DIT 117 (117) T 2r78_A 85 RTVWTRNGDQLTVELSAHLLPD--GK---ILGIARDVS 117 (117) T ss_dssp EEEECTTSCEEEEEEEEEECTT--SC---EEEEEEC-- T ss_pred EEEECCCCCEEEEEEEEEEEEC--CE---EEEEEEECC T ss_conf 9999799999999999999889--98---999999794 No 13 >2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis} Probab=99.66 E-value=3.6e-17 Score=110.30 Aligned_cols=110 Identities=10% Similarity=0.002 Sum_probs=97.7 Q ss_pred HHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC Q ss_conf 99998619818998648998998168987411351224587668999887510378999999998750456325786044 Q T0600 10 HTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRP 89 (125) Q Consensus 10 ~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~ 89 (125) +.+++.++++++..|.+++.+|+|+++++++||+++++.+. .+.+++||+|...+...+.. .......+||++++ 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 CCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHC Q ss_conf 33332223550056889996899988887321124 Q T0600 90 DGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHK 124 (125) Q Consensus 90 ~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK 124 (125) ||+.+|++.++++++++.|.+.+.+.+..|||++| 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 14 >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=99.66 E-value=1e-16 Score=107.90 Aligned_cols=118 Identities=12% Similarity=0.098 Sum_probs=96.7 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---- Q ss_conf 8899999999861981899864899899816898741135122458766899988751037899999999875045---- Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP---- 79 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~---- 79 (125) .||.+|+.+++.+++|++.+|.+++++++|++++++||++.+++.+.. +..++++++.......+......+.. T Consensus 37 ~~~~~~~~~le~s~dgi~i~d~~g~Ii~~N~a~~~l~G~~~~eliG~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (167) T 1v9y_A 37 AADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNN--IDMLIPRDLRPAHPEYIRHNREGGKARVEG 114 (167) T ss_dssp ---CCHHHHHHTCSSEEEEECTTSBEEEECHHHHHHHSCCGGGTTTSB--GGGGSCGGGTTTHHHHHHHHHC-------- T ss_pred HHHHHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--CCCCCCCCCCCCHHHHHHHHHHHHCCCCCC T ss_conf 889999999973876299995989899997799998657888824677--433322223320012467776641133454 Q ss_pred CCEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 6325786044333322235500568899968999888873211249 Q T0600 80 FDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 80 ~~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ...+...+++||..+|++++..|+... |. ..++++++|||++|+ T Consensus 115 ~~~e~~~~~kdG~~~~v~isi~~i~~~-~~-~~~v~i~~DITe~k~ 158 (167) T 1v9y_A 115 MSRELQLEKKDGSKIWTRFALSKVSAE-GK-VYYLALVRDASVEMA 158 (167) T ss_dssp --CEEEEECTTSCEEEEEEEEEEEEET-TE-EEEEEEEEC------ T ss_pred CCEEEEEEEEECCCCCEEEEEEEEEEC-CE-EEEEEEEEECHHHHH T ss_conf 316999998402353207999999969-98-999999999879999 No 15 >3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transferase, flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Probab=99.66 E-value=4.1e-16 Score=104.63 Aligned_cols=114 Identities=8% Similarity=-0.085 Sum_probs=100.0 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 88999999998619818998648998998168987411351224587668999887510378999999998750456325 Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVE 83 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e 83 (125) .+.++++.+++.++.++|.+|.+++.+++|+++++++|++++++.+. .+..++++++.......+...+..+..+..+ T Consensus 108 ~~~~~~~~~l~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 185 (227) T 3ewk_A 108 AQLARLKQAMDANSEMILLTDRAGRIIYANPALCRFSGMAEGELLGQ--SPSILDSPLADQETLAAMQEALQAGQPWSGR 185 (227) T ss_dssp HHHHHHHHHHHTCCSEEEEECTTSCEEEECHHHHHHHTCCTHHHHSS--CGGGGBCTTSCHHHHHHHHHHHHHTCCEECC T ss_pred HHHHHHHHHHHHHHCEEEEECCCCEEEEECHHHHHHCCCCHHHHHCC--CCCCCCCCCCCHHHHHHHHHHHHCCCCEEEE T ss_conf 99876799998641026998489759999868876449997996214--6542114542101345667765226746999 Q ss_pred EEEEC------CCCCCCCCCCCCEEEECCCCCEEEEEEEEEE Q ss_conf 78604------4333322235500568899968999888873 Q T0600 84 YRIVR------PDGQVRELLERNHIQRQASGQVDHLWGTVID 119 (125) Q Consensus 84 ~r~~~------~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~D 119 (125) ++..+ ++|+.+|+++++.|++|++|++.+++|++.| T Consensus 186 ~~~~~k~~~~~~dG~~~wv~~~~~pi~~~~g~~~~~~~i~~D 227 (227) T 3ewk_A 186 LLNRRRTGPAPHDAEDYWAEISTTPIHTDGNGLVGYVQIQHD 227 (227) T ss_dssp EEEEEECCSSSSCEEEEEEEEEEEEEECSSSCEEEEEEEEEC T ss_pred EEEEEECCCCCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEC T ss_conf 999984374567982999999999999899999999999989 No 16 >2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; 1.75A {Streptococcus mutans UA159} Probab=99.65 E-value=2.4e-16 Score=105.84 Aligned_cols=119 Identities=7% Similarity=-0.014 Sum_probs=89.7 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHH--HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 6889999999986198189986489989981689874--11351224587668999887510378999999998750456 Q T0600 3 AMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDI--FGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPF 80 (125) Q Consensus 3 a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~--~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 80 (125) .+|+++|+.+++.+|+|++.+|.+++.+++|+++..+ +|..+....+. ...++++++..+.+...+..+ ..+... T Consensus 15 ~ls~e~l~~il~~~P~~i~~~D~~~~i~~~N~~~~~~~~~~~~~~~~iG~--~~~~~~p~~~~~~~~~~~~~~-~~~~~~ 91 (151) T 2qkp_A 15 YLSVEQANLILNHLPLEITFVNKDDIFQYYNDSVPAAEMVFKRTPSQVGR--NVELCHPPKVLDKVKKVFELL-RNGQRD 91 (151) T ss_dssp EECHHHHHHHHHHSSSEEEEEETTSBEEEECCCSCGGGCSSCCCGGGTTS--BGGGSSCHHHHHHHHHHHHHH-HTTSBS T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCEEEEECCCHHHCEECCCHHHHHCC--CEEEECCCCCCCCCHHEEECC-CCCCCC T ss_conf 75699999999639830999969997999832313122024780786075--114881553344201102101-246511 Q ss_pred CEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 325786044333322235500568899968999888873211249 Q T0600 81 DVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 81 ~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ..++.+ ..++..+|+.++..|++|.+|++.+++++++|||++|+ T Consensus 92 ~~~~~~-~~~~~gr~i~~~~~pv~d~~G~~~g~i~~~~DITe~k~ 135 (151) T 2qkp_A 92 KVNMWF-QSERLGKFVYVTYAAVRDQAGDFQGVLEYVQDIKPFFE 135 (151) T ss_dssp EEEEEE-EETTTTEEEEEEEEEEECTTCCEEEEEEEEEECGGGGG T ss_pred EECCCC-CCCCCCCEEEEEEEEEECCCCCEEEEEEEEEECHHHHH T ss_conf 000000-01257715888633468799989999999998979999 No 17 >3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Probab=99.65 E-value=3.9e-17 Score=110.10 Aligned_cols=118 Identities=9% Similarity=-0.036 Sum_probs=96.4 Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCE Q ss_conf 899999999861981899864899899816898741135122458766899988751037899999999875045--632 Q T0600 5 AEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP--FDV 82 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~--~~~ 82 (125) |+.+++.+.+.++.++|.+|.++..+++|+.+++++|++++++.+. .+..++||+|...+...+..+...+.. ... 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 EEEEECCCCCCCCCCCCCEEEECCCC-CEEEEEEEEEECHHHC Q ss_conf 57860443333222355005688999-6899988887321124 Q T0600 83 EYRIVRPDGQVRELLERNHIQRQASG-QVDHLWGTVIDMTEHK 124 (125) Q Consensus 83 e~r~~~~~g~~~w~~~~~~~~~d~~g-~~~~~vG~~~DITerK 124 (125) ++|++++||+++|+...+.|++|+.| .+.+++|+..|||++| T Consensus 231 e~r~~~~dG~~~wv~~~~~~i~~~~~~~~~~i~~~~~~~~~~~ 273 (309) T 3gdi_A 231 PIRFRTRNGEYITLDTSWSSFINPWSRKISFIIGRHKVRVGPL 273 (309) T ss_dssp EEEEECTTSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCS T ss_pred EEEEECCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCCHH T ss_conf 5566769991999999999999179995689999999886432 No 18 >1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock protein, phosphorylation, polymorphism; 3.15A {Drosophila melanogaster} PDB: 3gec_A Probab=99.65 E-value=2.5e-17 Score=111.10 Aligned_cols=120 Identities=7% Similarity=-0.098 Sum_probs=104.4 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC----- Q ss_conf 889999999986198189986489989981689874113512245876689998875103789999999987504----- Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDR----- 78 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~----- 78 (125) .||++++.+.+.++.|+|.+|.+.+.+++|+.++.++|+++....+. .+...+|++|...+...+......+. T Consensus 145 ~~e~~~r~l~e~~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~ 222 (368) T 1wa9_A 145 SYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGR--SIMDFYHHEDLSVMKETYETVMKKGQTAGAS 222 (368) T ss_dssp SCCSTTCBCCTTSCEEEEEEETTCBEEEECGGGHHHHCCCHHHHTTS--BGGGGBCTTTHHHHHHHHHHHHHHTTSTTCC T ss_pred HHHHHHHHHHHCCCCEEEEEECCCCEEEEECHHHHCCCCCCHHHCCC--CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC T ss_conf 55778899985197069999169968852001121134440120223--2234554234999999998755531356665 Q ss_pred CCCEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 56325786044333322235500568899968999888873211249 Q T0600 79 PFDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 79 ~~~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) .+..++++++++|.++|++.++.|++|+.|....+++++.|||++|+ T Consensus 223 ~~~~e~r~~~k~G~~~wv~~~~~~~~d~~g~~~~~v~~~~dIt~~~~ 269 (368) T 1wa9_A 223 FCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPK 269 (368) T ss_dssp EECCCEEEECTTSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCS T ss_pred CCHHHHEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCCHH T ss_conf 42110100205898899999999999789980789999999141253 No 19 >1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6 Probab=99.64 E-value=1.9e-16 Score=106.40 Aligned_cols=99 Identities=15% Similarity=0.086 Sum_probs=83.7 Q ss_pred CCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCEEEE Q ss_conf 48998998168987411351224587668999887510378999999998750456325786044333322235500568 Q T0600 25 MESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVRELLERNHIQR 104 (125) Q Consensus 25 ~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w~~~~~~~~~ 104 (125) ++..++|+|+++++|+|++++++.+......-..+++........+..++.++..+..|++..++||+.+|+++++.|++ T Consensus 12 ~d~~I~~vN~a~~~~~G~~~~ei~G~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdg~~~w~~~~~~pv~ 91 (110) T 1byw_A 12 ENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVK 91 (110) T ss_dssp SSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEEEEEEEEEEE T ss_pred CCCEEEEECHHHHHHHCCCHHHHCCCCHHHHEEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEEEE T ss_conf 98949999889999889697896699804521001023167788888877523642026899957996999999999999 Q ss_pred CCCCCEEEEEEEEEECHHH Q ss_conf 8999689998888732112 Q T0600 105 QASGQVDHLWGTVIDMTEH 123 (125) Q Consensus 105 d~~g~~~~~vG~~~DITer 123 (125) |++|++++++|+++||||| T Consensus 92 d~~G~i~~~i~~~~DITeR 110 (110) T 1byw_A 92 NEDGAVIMFILNFEVVMEK 110 (110) T ss_dssp CTTCCEEEEEEEEEEEEEC T ss_pred CCCCCEEEEEEEEEECCCC T ss_conf 9998999999999976899 No 20 >3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense} Probab=99.64 E-value=3.7e-16 Score=104.87 Aligned_cols=112 Identities=10% Similarity=0.078 Sum_probs=94.0 Q ss_pred HHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEC Q ss_conf 99999861981899864899899816898741135122458766899988751037899999999875045632578604 Q T0600 9 LHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVR 88 (125) Q Consensus 9 l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~ 88 (125) |+.+++..++++|.+|.+++.+++|+++.+++|++++++.+. .+...+++++.......+... ..+.....+++.++ T Consensus 1 l~~ile~~~d~i~i~d~~g~i~~~N~a~~~~~g~~~~e~lg~--~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~e~~~~~ 77 (126) T 3mjq_A 1 MKNFLETIEDMILIINREGRLLYANTAVPKKLGYTHEELMSM--HILTITSAGKMAEGEKILAEL-FAGKKESLPLSLEK 77 (126) T ss_dssp -CTTGGGCSSEEEEEETTSBEEEECTHHHHHHSCCHHHHHHS--BHHHHHCTTCHHHHHHHHHHH-HHTCCSEEEEEEEC T ss_pred CHHHHHCCCCCEEEECCCCCEEEEEHHHHHCCCCCHHHHCCC--EEEEEECCCCCCCCHHHHHHH-HCCCCCEEEEEEEC T ss_conf 968985092245999299959999025330279986880131--023540243332201345554-22576148999995 Q ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 4333322235500568899968999888873211249 Q T0600 89 PDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 89 ~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ++|+.+|+++++.|+++.++ ..++|++.|||+||| T Consensus 78 ~~G~~~~v~~~~~~i~~~~~--~~~~~i~~DITerK~ 112 (126) T 3mjq_A 78 KEGTSIPAKARIWQGKWHNE--PCLFAIIKDLSKEER 112 (126) T ss_dssp TTSCEEEEEEEEEEEESSSS--EEEEEEEEECC---- T ss_pred CCCCEEEEEEEEEEEEECCE--EEEEEEEEECCHHHH T ss_conf 79989999999999998996--699999998889999 No 21 >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=99.62 E-value=3.6e-16 Score=104.92 Aligned_cols=111 Identities=10% Similarity=0.034 Sum_probs=93.9 Q ss_pred HHHHHCCCEEEEEEC---CCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE Q ss_conf 999861981899864---89989981689874113512245876689998875103789999999987504563257860 Q T0600 11 TAESDAGIGSWVLHM---ESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIV 87 (125) Q Consensus 11 ~~~~~a~~g~w~~d~---~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~ 87 (125) .+++++++|+...|. +++++++|+++++++|++++++.+... ..+.+++........+...+..+..+..|++++ 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 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNC--RFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNY 80 (132) T ss_dssp ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCG--GGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEE T ss_pred HHHHCCCCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCCH--HCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEE T ss_conf 688578841999989889798999968999998919999805410--004441014999999999985288403565547 Q ss_pred CCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 44333322235500568899968999888873211249 Q T0600 88 RPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 88 ~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) +++|..+|+.++..|+.+.+| ..++++++|||+||+ T Consensus 81 ~~dG~~~~~~~~~~~i~~~~~--~~~i~~~~DITe~k~ 116 (132) T 2pr5_A 81 KKDGTMFWNELNIDPMEIEDK--TYFVGIQNDITKQKE 116 (132) T ss_dssp CTTSCEEEEEEEEEEEEETTE--EEEEEEEEECHHHHH T ss_pred CCCCCEEEEEEEEEEEECCCC--CEEEEEEEECCHHHH T ss_conf 479979999988888990991--299889997659999 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=99.62 E-value=1.3e-15 Score=102.00 Aligned_cols=104 Identities=13% Similarity=0.026 Sum_probs=90.0 Q ss_pred CCEEEEEEC---CCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCC Q ss_conf 981899864---89989981689874113512245876689998875103789999999987504563257860443333 Q T0600 17 GIGSWVLHM---ESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQV 93 (125) Q Consensus 17 ~~g~w~~d~---~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~ 93 (125) ..++...|. ++.++|+|+++++++|++++++.+... ..+.+++........+...+..+..+..|++++++||+. T Consensus 3 ~~~~vi~Da~~pDg~Ii~vN~a~~~~~Gy~~~el~G~~~--~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~~ 80 (109) T 1n9l_A 3 RHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNC--RFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTP 80 (109) T ss_dssp SCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCG--GGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCE T ss_pred CCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCCH--HHHCCCCCCHHHHHHHHHHHCCCCEEEEEEEEECCCCCE T ss_conf 762999948899896999968999988939999808523--212465579999999988640596299999999179989 Q ss_pred CCCCCCCEEEECCCCCEEEEEEEEEECHH Q ss_conf 22235500568899968999888873211 Q T0600 94 RELLERNHIQRQASGQVDHLWGTVIDMTE 122 (125) Q Consensus 94 ~w~~~~~~~~~d~~g~~~~~vG~~~DITe 122 (125) +|++++..|++|++|++.++++++.|||. T Consensus 81 ~w~~~~~~pi~d~~G~~~~~v~~~~DITa 109 (109) T 1n9l_A 81 FWNLLTVTPIKTPDGRVSKFVGVQVDVTS 109 (109) T ss_dssp EEEEEEEEEEECTTSCEEEEEEEEEECCC T ss_pred EEEEEEEEEEECCCCCEEEEEEEEEECCC T ss_conf 99999986899999999999999997699 No 23 >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=99.62 E-value=7.6e-16 Score=103.18 Aligned_cols=114 Identities=16% Similarity=0.026 Sum_probs=96.6 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 68899999999861981899864899899816898741135122458766899988751037899999999875045632 Q T0600 3 AMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDV 82 (125) Q Consensus 3 a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 82 (125) ..||++|+.+++.++.|++.+|.+++.+++|+++++++|++++++.+. .+.+++++.+...+...+... ..+....+ T Consensus 13 ~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~a~~~~~g~~~eel~g~--~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 89 (126) T 3bwl_A 13 EETSSRLEALFENSPDMIDVLDADGTICEVNQRFCAELGYDESEVLGR--SIWEFDLMFDAEDVQTQLSGF-SVDERRKF 89 (126) T ss_dssp HHHHHHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHHTCCGGGTTTS--BGGGTBTTCCHHHHHHHHHTC-CTTCEEEE T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCEEEEEHHHHHHHCCCHHHHHCC--CHHHHCCCCCHHHHHHHHHHH-HHCCCEEE T ss_conf 999999999997197329999099989998457688869889998359--898916834899999999999-81996699 Q ss_pred EEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 578604433332223550056889996899988887321 Q T0600 83 EYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 83 e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) +.++++++|+.+|+++++.|+. .+|++ .+++++.||| T Consensus 90 e~~~~~kdG~~~~~~~~~~~~~-~~~~~-~~~~v~~DIT 126 (126) T 3bwl_A 90 EGLYERRDGSTMSVEVHLLRFN-LEGED-RFLAISRDIT 126 (126) T ss_dssp EEEEECTTSCEEEEEEEEEEEE-ETTEE-EEEEEEEEC- T ss_pred EEEEEECCCCEEEEEEEEEEEE-ECCEE-EEEEEEEECC T ss_conf 9999965995999999999998-59929-9999999879 No 24 >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=99.57 E-value=3e-15 Score=99.98 Aligned_cols=114 Identities=14% Similarity=0.056 Sum_probs=97.1 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---- Q ss_conf 8899999999861981899864899899816898741135122458766899988751037899999999875045---- Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP---- 79 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~---- 79 (125) .+|++|+.++++++.|++..|.+++..++|++++++||++++++.+.. +..++++++...+...+...+..+.. T Consensus 13 ~~e~~l~~i~~~~~~~ii~~D~~g~i~~~N~~~~~~~G~~~~el~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (130) T 1d06_A 13 ARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQN--LRILMPEPYRHEHDGYLQRYMATGEKRIIG 90 (130) T ss_dssp HHTSCHHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTHHHHHHHHHHHHHHHCCCSSTT T ss_pred HHHHHHHHHHHCCCCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCC--CCCCCCHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 999999999970762169998999699887999988796979974997--543368121799999999999719875565 Q ss_pred CCEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 632578604433332223550056889996899988887321 Q T0600 80 FDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 80 ~~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) ...++...+++|..+|++++..++.+.++ ..++++++||| T Consensus 91 ~~~e~~~~~~~G~~~~v~~~~s~~~~~~~--~~~~~i~~DIT 130 (130) T 1d06_A 91 IDRVVSGQRKDGSTFPMKLAVGEMRSGGE--RFFTGFIRDLT 130 (130) T ss_dssp SCEEEEEECTTSCEEEEEEEEEEEEETTE--EEEEEEEEECC T ss_pred EEEEEEEECCCCCEEEEEEEEEEEEECCE--EEEEEEEEECC T ss_conf 16899999489999999999999998994--89999999787 No 25 >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=9.1e-15 Score=97.42 Aligned_cols=116 Identities=10% Similarity=0.042 Sum_probs=86.7 Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 06889999999986198189986489989981689874113512245876689998875103789999999987504563 Q T0600 2 NAMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFD 81 (125) Q Consensus 2 ~a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 81 (125) +++|++.|+.++++.++|++.+|.+++..|+|++ +.+++.+. ...+. ...++++++....+...+.. +..++... T Consensus 234 ~~ls~~~l~~il~~~p~~i~~vD~~~~i~~~N~a-~~~~~~~~-~~iG~--~~~~~~p~~~~~~~~~~~~~-~~~g~~~~ 308 (369) T 3cax_A 234 GYLNIEELKAIFEALPVDVTFIDKDDRVRFFSPG-ERIFTRTP-SVLGR--PVQLCHPPKSVYVVNKILKA-FKEGRKKE 308 (369) T ss_dssp CEECHHHHHHHHHHSSSEEEEECTTSBEEEECCS-SCSSCCCG-GGTTC--BTTTSSCGGGHHHHHHHHHH-HHHTSCSC T ss_pred CCCCHHHHHHHHHCCCCCEEEECCCCEEEEECHH-HHHHCCCH-HHHCC--CHHHHCCHHHHHHHHHHHHH-HHCCCCEE T ss_conf 3165999999997297878999289939998677-78749888-98298--42672897679999999999-97799538 Q ss_pred EEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 25786044333322235500568899968999888873211249 Q T0600 82 VEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 82 ~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) .++.+ +.+| +|+.++..|++|++|++.+++++++|||++|+ T Consensus 309 ~e~~~-~~~g--~~~~~~~~Pv~d~~G~~~G~v~~~~DITe~k~ 349 (369) T 3cax_A 309 ATFWL-RLRE--KYVYIKYVPLFNEKGEYIGTLEMTMDIAPYKK 349 (369) T ss_dssp EEEEE-EETT--EEEEEEEEEEECTTSCEEEEEEEEEECHHHHT T ss_pred EEEEE-EECC--EEEEEEEEEEECCCCCEEEEEEEEEECHHHHH T ss_conf 99999-3199--89999999899989899999999999869999 No 26 >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=99.50 E-value=1.4e-14 Score=96.38 Aligned_cols=111 Identities=14% Similarity=0.043 Sum_probs=96.6 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE Q ss_conf 68899999999861981899864899899816898741135122458766899988751037899999999875045632 Q T0600 3 AMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDV 82 (125) Q Consensus 3 a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 82 (125) -.||++|+.+++++++|+|.+|.+++.+++|+++++++|++++++.+. .+.+++++++...+...+..++..++...+ T Consensus 15 ~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (125) T 3fc7_A 15 ERTRKKFESLVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQ--QLSAVMDSEAANQRLEAGKSAVENGTATRS 92 (125) T ss_dssp -----------CCSCCEEEEEETTSBEEEECHHHHHHHTSCHHHHTTS--BGGGSSCHHHHHHHHHHHHHHHHHTSCEEE T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCCC T ss_conf 999999999997641123233543069998620000222322222221--222222211124567788876531444310 Q ss_pred EEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 578604433332223550056889996899988887321 Q T0600 83 EYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 83 e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) ++... .+|+.....|+ +.+|++.+++++++||| T Consensus 93 ~~~~~-----~r~~~~~~~pv-~~~~~~~~~~~v~~DIT 125 (125) T 3fc7_A 93 EDAVG-----GRHYHNQYIPV-DSHRKSDTFQLVSRDIT 125 (125) T ss_dssp EEEET-----TEEEEEEEEES-STTTTTTEEEEEEEECC T ss_pred EEEEC-----CCCCCEEEEEE-EECCCEEEEEEEEEECC T ss_conf 11100-----11453089999-90898999999999793 No 27 >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=99.42 E-value=5.2e-13 Score=88.02 Aligned_cols=106 Identities=19% Similarity=0.094 Sum_probs=87.4 Q ss_pred CCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCEEEEEECCCC Q ss_conf 1981899864899899816898741135122458766899988751037899999999875045----632578604433 Q T0600 16 AGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP----FDVEYRIVRPDG 91 (125) Q Consensus 16 a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~----~~~e~r~~~~~g 91 (125) .++|++.+|.++..+++|+++++|+|++.+++.+.. +..++++++.......+......+.. ...+...++++| T Consensus 2 ~pd~i~~~d~~g~I~~~N~~~~~l~G~~~~el~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G 79 (119) T 2vv6_A 2 IPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQN--VNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDG 79 (119) T ss_dssp CCCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTTS T ss_pred CCEEEEEECCCCCEEEEHHHHHHHHCCCHHHHHCCC--CCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCC T ss_conf 772999998999299871999998657899972566--444566310356789999999648664356406999861255 Q ss_pred CCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 3322235500568899968999888873211249 Q T0600 92 QVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 92 ~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ..+|+.++..|+.+.+ . ..++++++|||++|+ T Consensus 80 ~~~~~~~~~~~~~~~~-~-~~~~~~i~DITe~k~ 111 (119) T 2vv6_A 80 TTFPMHLSIGEMQSGG-E-PYFTGFVRDLTEHQQ 111 (119) T ss_dssp CEEEEEEEEEEEEETT-E-EEEEEEEEECC---- T ss_pred CEEEEEEEECCEECCC-C-EEEEEEEEECHHHHH T ss_conf 1322356753203399-6-499999998189999 No 28 >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=99.38 E-value=5.2e-13 Score=88.03 Aligned_cols=104 Identities=8% Similarity=-0.012 Sum_probs=89.2 Q ss_pred HHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC Q ss_conf 99998619818998648998998168987411351224587668999887510378999999998750456325786044 Q T0600 10 HTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRP 89 (125) Q Consensus 10 ~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~ 89 (125) +.+++.+++|++.+|.+++.+++|+++++++|++++++.+. .+.+++++.....+...+.+++..+.+...|+....+ T Consensus 15 e~~~~~~~~Gi~~vD~dgri~~~N~a~~~llG~~~eeliGk--~~~e~~p~~~~~~~~~~~~~~~~~g~~~~~e~~~~~~ 92 (118) T 3fg8_A 15 ENLYFQGGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGR--VVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYS 92 (118) T ss_dssp CCSSSCTTCEEEEECTTCBEEEECHHHHHHHTCCHHHHTTS--BHHHHCGGGTTSHHHHHHHHHHHHCCCEEEEEECSSS T ss_pred HHHHHCCCCEEEEECCCCEEEEEHHHHHHHHCCCHHHHCCC--CHHHHCCHHHCCCHHHHHHHHHHCCCEEEEEEEEECC T ss_conf 99997089899999799829989899898857899998599--6999484533110567899998539849999999888 Q ss_pred CCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHH Q ss_conf 3333222355005688999689998888732112 Q T0600 90 DGQVRELLERNHIQRQASGQVDHLWGTVIDMTEH 123 (125) Q Consensus 90 ~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITer 123 (125) +| +|+++++.|.. + +++++++|||++ T Consensus 93 ~~--~w~~v~~~p~~--d----Gi~v~~rDIT~q 118 (118) T 3fg8_A 93 PG--MTIEVTAAADS--G----ALVVHFRDVTAE 118 (118) T ss_dssp TT--CEEEEEEEEET--T----EEEEEEEECSCC T ss_pred CC--EEEEEEEEECC--C----EEEEEEEECCCC T ss_conf 99--89999999879--9----999999982799 No 29 >3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis} Probab=99.36 E-value=3.1e-13 Score=89.20 Aligned_cols=115 Identities=7% Similarity=0.011 Sum_probs=88.9 Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------- Q ss_conf 6889999999986198189986489989981689874113512245876689998875103789999999987------- Q T0600 3 AMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVL------- 75 (125) Q Consensus 3 a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~------- 75 (125) ..|+++|+.++++++.|++..|.+++..++|+++++|||++++++.+. .+..++++++.......+..... T Consensus 3 h~s~~~~~~il~~~~d~i~~~D~~G~I~~~N~aa~~l~G~~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (129) T 3mfx_A 3 HSSLETIELFIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQ--DWRNFLTEHHQARYDNLLSHDVQLGTNCGQ 80 (129) T ss_dssp HHHHHHHHHHHTTCSSEEEEEETTSBEEEECHHHHHHTTSCHHHHTTS--BGGGGBCTTCCGGGGCTTC----------C T ss_pred HHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 789999999997235215999599989999979995655997998599--099980716577789999999985032203 Q ss_pred HHCCCCEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHH Q ss_conf 50456325786044333322235500568899968999888873211 Q T0600 76 GDRPFDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTE 122 (125) Q Consensus 76 ~~~~~~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITe 122 (125) +......|..++++||+.+|++++..++.+.++ .++|++.||-. T Consensus 81 ~~~~~~~Ev~~~~~dG~~~~velsis~~~~~~~---~~v~v~rDI~~ 124 (129) T 3mfx_A 81 PVQHPAQETTLICASGKAKDVELSISYIPGHEP---MFVMVMHDLEH 124 (129) T ss_dssp CSCEEEEEEEEECTTSCEEEEEEEEEEECSSSC---EEEEEEEEC-- T ss_pred CCCCCEEEEEEECCCCCEEEEEEEEEEEECCCC---EEEEEEEECCC T ss_conf 546650479999789979999999999989996---99999998975 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=99.35 E-value=2.6e-12 Score=84.27 Aligned_cols=98 Identities=13% Similarity=0.084 Sum_probs=78.7 Q ss_pred CCEEEEEECC---CCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHCCCCE Q ss_conf 9818998648---99899816898741135122458766899988751-----------037899999999875045632 Q T0600 17 GIGSWVLHME---SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPD-----------DRARVRRELDRHVLGDRPFDV 82 (125) Q Consensus 17 ~~g~w~~d~~---~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~-----------~~~~~~~~~~~~~~~~~~~~~ 82 (125) .+++...|.. ..++|+|+++++|+||+++++.+....+ +.+++ ........+...+..+..+.. T Consensus 35 s~ai~i~D~~~~D~~Ii~vN~af~~~tGys~eEviGr~~~~--l~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~ 112 (149) T 3d72_A 35 SVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRF--LQSPDGMVKPKSTRKYVDSNTINTMRKAIDRNAEVQV 112 (149) T ss_dssp TSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGG--GGSTTSCCCTTCCCSSSCHHHHHHHHHHHHHTCCEEE T ss_pred CCEEEEEECCCCCCEEEEECHHHHHHHCCCHHHHCCCCCCE--ECCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEE T ss_conf 53199996999989799986899988892999985986213--0171021354322222799999999999976985999 Q ss_pred EEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEE Q ss_conf 5786044333322235500568899968999888 Q T0600 83 EYRIVRPDGQVRELLERNHIQRQASGQVDHLWGT 116 (125) Q Consensus 83 e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~ 116 (125) |++.++++|+.+|+..+..|++|++|++.+++|+ T Consensus 113 E~~~~~kdG~~~wv~~~~~pv~De~G~v~~~vGi 146 (149) T 3d72_A 113 EVVNFKKNGQRFVNFLTMIPVRDETGEYRYSMGF 146 (149) T ss_dssp EEEEECTTCCEEEEEEEEEEEECTTSSEEEEEEE T ss_pred EEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEE T ss_conf 9987859998999999999999999899999999 No 31 >3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Probab=99.31 E-value=8.3e-12 Score=81.59 Aligned_cols=120 Identities=12% Similarity=0.144 Sum_probs=89.4 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCE-EEEEHHHHHHHCCCCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHH- Q ss_conf 88999999998619818998648998-99816898741135122458------76689998875103789999999987- Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGR-LEWSQAVHDIFGTDSATFDA------TEDAYFQRVHPDDRARVRRELDRHVL- 75 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~-~~~s~~~~~~~g~~~~~~~~------~~~~~~~~i~~~~~~~~~~~~~~~~~- 75 (125) .+++.++.+.+.++..+|.+|+.++. +|+|+.+.+++|+++++... ....|..++||+|............+ T Consensus 30 ~~~~~~~~~a~~~~~~~~i~Dl~~~~~~y~s~~~~~~lGy~~~e~~~~~i~s~~~~~~~~~ihP~D~~~~~~~~~~~~~~ 109 (258) T 3clo_A 30 QHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYKFFQK 109 (258) T ss_dssp HHHHHHHHHHHHHSSEEEEEETTTTEEEEEECTTCGGGCCCHHHHHCCEESSSSCHHHHTTBCHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCEEEEECCCHHHHHCCCHHHCCCHHHHCCCCHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999999998578878999887888999865399983999666231454304404666258978999999999999998 Q ss_pred -------HHC--CCCEEEEEECCCCCCCCCCCCCEEE-ECCCCCEEEEEEEEEECHHHC Q ss_conf -------504--5632578604433332223550056-889996899988887321124 Q T0600 76 -------GDR--PFDVEYRIVRPDGQVRELLERNHIQ-RQASGQVDHLWGTVIDMTEHK 124 (125) Q Consensus 76 -------~~~--~~~~e~r~~~~~g~~~w~~~~~~~~-~d~~g~~~~~vG~~~DITerK 124 (125) ... ....+||+++++|.++|+..++.++ .+++|++.. .+.+.|++..+ T Consensus 110 l~~~~~~er~~y~~~~~~R~~~~~G~y~wv~~r~~vl~~~~~g~i~~-~l~~~d~~~~~ 167 (258) T 3clo_A 110 TFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWL-IFCLYSLSADQ 167 (258) T ss_dssp HTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECTTSCEEE-EEEEEEECSCC T ss_pred HHHCCHHHHHEEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCEEE-CCCCCCCCCCC T ss_conf 75178654111357899999869999999986677874389988011-13323444333 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=99.30 E-value=2.2e-12 Score=84.67 Aligned_cols=105 Identities=13% Similarity=0.066 Sum_probs=85.8 Q ss_pred CEEEEEECCCCEEEEEHHHH-HHHCCCCCCCCCCHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCEEEEEECCCCCCC Q ss_conf 81899864899899816898-7411351224587668999887510378--99999999875045632578604433332 Q T0600 18 IGSWVLHMESGRLEWSQAVH-DIFGTDSATFDATEDAYFQRVHPDDRAR--VRRELDRHVLGDRPFDVEYRIVRPDGQVR 94 (125) Q Consensus 18 ~g~w~~d~~~~~~~~s~~~~-~~~g~~~~~~~~~~~~~~~~i~~~~~~~--~~~~~~~~~~~~~~~~~e~r~~~~~g~~~ 94 (125) -.+-..|++++.+++|+++. .++||.++++.+. .+.+++||+|... ...........+...+.+||++++||.++ T Consensus 8 ~F~trh~ldg~i~~vd~~~~~~l~gy~~eelig~--s~~~~~Hp~D~~~~~~~~~~~~~~~~~~~~t~~yR~r~KdG~~v 85 (132) T 1oj5_A 8 SFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRK--CIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML 85 (132) T ss_dssp EEEEEECTTCCEEEEECHHHHTTCCSCHHHHHHH--HHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE T ss_pred EEEEEECCCCEEEEECCHHHHHHHCCCHHHHCCC--CHHHEECCCCCHHHHHHHHHHHHHCCCCCCCHHHEEEECCCEEE T ss_conf 6899997997199998178676608897999499--19893884531356677788877516851134550365498099 Q ss_pred CCCCCCEEEECCCC-CEEEEEEEEEECHHHC Q ss_conf 22355005688999-6899988887321124 Q T0600 95 ELLERNHIQRQASG-QVDHLWGTVIDMTEHK 124 (125) Q Consensus 95 w~~~~~~~~~d~~g-~~~~~vG~~~DITerK 124 (125) |++.++++++|+.+ ++..++|+...|+++. T Consensus 86 Wv~t~~~l~~~~~~~~~~~Ii~~h~i~~e~~ 116 (132) T 1oj5_A 86 SAHTRCKLCYPQSPDMQPFIMGIHIIDREHS 116 (132) T ss_dssp EEEEEEEEECC----CCCEEEEEEEEECC-- T ss_pred EEEEEEEEEECCCCCCCEEEEEEEEECCCCC T ss_conf 9999889998279998159999999525743 No 33 >3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transferase, flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Probab=99.28 E-value=7.8e-12 Score=81.74 Aligned_cols=104 Identities=11% Similarity=0.005 Sum_probs=89.6 Q ss_pred EEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCC Q ss_conf 89986489989981689874113512245876689998875103789999999987504563257860443333222355 Q T0600 20 SWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVRELLER 99 (125) Q Consensus 20 ~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w~~~~ 99 (125) ++..|.+++.+++|+++++++|++++++.+... ..+.++++..............+.....+..+++++|..+|+..+ T Consensus 2 i~i~D~~G~i~~~N~a~~~~~G~~~eel~G~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~ 79 (227) T 3ewk_A 2 VSITDLQGRILYANDNFCAVSRYGREELVGQDH--RIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDST 79 (227) T ss_dssp EEEEETTCBEEEECHHHHHHTTCCHHHHTTSBG--GGGCCSCSCHHHHHHHHHHHTTTCCEEEEEEEECSSSCEEEEEEE T ss_pred EEEECCCCCEEEECHHHHHHHCCCHHHHCCCCH--HHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCEEEEEEE T ss_conf 999959999898338899988929999949988--892894134677667777640277245899999415434876556 Q ss_pred CEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf 00568899968999888873211249 Q T0600 100 NHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 100 ~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ..|+++..|....++.+..|+|++++ T Consensus 80 ~~~~~~~~g~~~~~~~~~~d~~~~~~ 105 (227) T 3ewk_A 80 IVPLMDNAGKPRQYISIRRDITAQKE 105 (227) T ss_dssp EEEEECSSSCEEEEEEEEEECTTTTH T ss_pred EEEEECCCCCEEEEEEEEHHHHHHHH T ss_conf 65565368976332123202369999 No 34 >3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein, APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633} Probab=99.13 E-value=7.3e-11 Score=76.53 Aligned_cols=114 Identities=12% Similarity=-0.025 Sum_probs=87.7 Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 90688999999998619818998648998998168987411351224587668999887510378999999998750456 Q T0600 1 SNAMAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPF 80 (125) Q Consensus 1 ~~a~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 80 (125) |+|+.-.+++.++++.+.|++..|.+++.+++|++++++||++.+++.+... .++++..+. ....+..+++.+... T Consensus 1 s~~~~~~l~~~il~~~~~~i~~iD~~g~I~~~N~aa~~l~g~s~~el~G~~~--~~~~~~~~~--~~~~~~~~l~~~~~~ 76 (115) T 3b33_A 1 SNAMDTSLPSAILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQSL--SQLIQHASL--DLALLTQPLQSGQSI 76 (115) T ss_dssp -----CCHHHHHHHHCSSEEEEECTTCBEEEECHHHHHHTTSCHHHHTTCBH--HHHCSEEEC--CTHHHHHHHHHCCCE T ss_pred CCCHHHHHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHHHHHHHHCCCCH--HHHCCCCHH--HHHHHHHHHHCCCCE T ss_conf 9414178999998514765999979999999896999774654887749859--998598067--789999999829971 Q ss_pred CEEEEEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEC Q ss_conf 3257860443333222355005688999689998888732 Q T0600 81 DVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDM 120 (125) Q Consensus 81 ~~e~r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DI 120 (125) ..+....+.+|+.+|+.+++.|+.++.|.. ++-.++|| T Consensus 77 ~~~~~~~~~~G~~~~v~~s~~pi~~~~~~~--ilv~~rdi 114 (115) T 3b33_A 77 TDSDVTFVVDGRPLMLEVTVSPITWQRQLM--LLVEMRKI 114 (115) T ss_dssp EEEEEEEEETTEEEEEEEEEEEEEETTEEE--EEEEEEEC T ss_pred EEEEEEEEECCCEEEEEEEEEEEEECCCEE--EEEEEEEC T ss_conf 789999997991999999999999599779--99999968 No 35 >1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock protein, phosphorylation, polymorphism; 3.15A {Drosophila melanogaster} PDB: 3gec_A Probab=98.97 E-value=3.3e-11 Score=78.40 Aligned_cols=104 Identities=13% Similarity=0.093 Sum_probs=74.2 Q ss_pred EEEEE-CCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-----HHCCCCEEEEE------- Q ss_conf 89986-489989981689874113512245876689998875103789999999987-----50456325786------- Q T0600 20 SWVLH-MESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVL-----GDRPFDVEYRI------- 86 (125) Q Consensus 20 ~w~~d-~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-----~~~~~~~e~r~------- 86 (125) ...+. .++.++|+|++++++|||+++++.+. .+.+++||+|+..+.+.+..... .........++ T Consensus 10 ~~vi~~~dG~I~~vN~~~~~ilGys~eEliG~--~~~dlihPeD~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (368) T 1wa9_A 10 CCVISMHDGIVLYTTPSITDVLGYPRDMWLGR--SFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCVMLRRY 87 (368) T ss_dssp EEEEETTTCBEEEECTTHHHHHCCCTTSSTTS--BGGGGBCTTTHHHHHHHTTSCC------------CCCEEEEEEECS T ss_pred EEEEECCCCEEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHCCCCCCHHHCCCCCCCEEEEEEEECCC T ss_conf 99999999889999879999879399998699--7999649978999999862366653010245656607999962220 Q ss_pred ------------ECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHHHCC Q ss_conf ------------044333322235500568899968999888873211249 Q T0600 87 ------------VRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 87 ------------~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITerK~ 125 (125) ...++...|+....+++++..|.+..++++..|||++|+ T Consensus 88 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~d~~~~~~~~~~~~~Dit~~k~ 138 (368) T 1wa9_A 88 RGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVIC 138 (368) T ss_dssp CCCSSCCSSSCCCCCCEEEEEEECCBCCCCCCCC------CCSCCCEEEEE T ss_pred CCEEECCEEEECCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHH T ss_conf 230573346653446448999999998634456773322244423779999 No 36 >3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Probab=98.87 E-value=2.1e-10 Score=74.10 Aligned_cols=113 Identities=12% Similarity=0.074 Sum_probs=83.9 Q ss_pred HHHHHCCCEEEEEEC-CCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCEEEEEEC Q ss_conf 999861981899864-8998998168987411351224587668999887510378999999998750-45632578604 Q T0600 11 TAESDAGIGSWVLHM-ESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGD-RPFDVEYRIVR 88 (125) Q Consensus 11 ~~~~~a~~g~w~~d~-~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~e~r~~~ 88 (125) .+++++......++. +++.+|+|+++++++||+++++.+. .+.+++||+|+..+...+....... .....+.+... T Consensus 19 ~~l~~~~~f~iv~~~~dG~I~~vN~~~~~llGys~eEl~g~--~~~~lihp~d~~~~~~~l~~~~~~~~~~~~~~~~~~~ 96 (309) T 3gdi_A 19 YIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDA--KFVEFLAPHDVSVFHSYTTPYKLPPWSVCSGLDSFTQ 96 (309) T ss_dssp ----CTTEEEEEECTTTCBEEEECTTTTTTC-------CCS--BGGGGBCTTTHHHHHHHTCTTSSCBCC---------- T ss_pred HHHHHCCCEEEEEECCCCEEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEE T ss_conf 99970588799999799879999789999859799998599--7889389888899999976531477653320444553 Q ss_pred CCCCCCCCCCCCEEEEC----CCCCEEEEEEEEEECHHHCC Q ss_conf 43333222355005688----99968999888873211249 Q T0600 89 PDGQVRELLERNHIQRQ----ASGQVDHLWGTVIDMTEHKQ 125 (125) Q Consensus 89 ~~g~~~w~~~~~~~~~d----~~g~~~~~vG~~~DITerK~ 125 (125) ..+...|+.+...+..+ ..+.++.+.|+..|||++|+ T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dit~~~~ 137 (309) T 3gdi_A 97 ECMEEKSFFCRVSVGKHHENEIRYQPFRMTPYLVKVQEQQG 137 (309) T ss_dssp ----CCCEEEEECCCC----CCCCEEEEEEEEEEECC---- T ss_pred CCCCCEEEEEEEECCCCCCCCCEEEEEEEEEEEEECCCHHH T ss_conf 05652378875211444345761789999889987400223 No 37 >1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5 Probab=98.84 E-value=1.4e-09 Score=69.69 Aligned_cols=104 Identities=13% Similarity=0.072 Sum_probs=81.1 Q ss_pred HHCCCEEEEEECC-CCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCEEEEEEC Q ss_conf 8619818998648-9989981689874113512245876689998875103789999999987504----5632578604 Q T0600 14 SDAGIGSWVLHME-SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDR----PFDVEYRIVR 88 (125) Q Consensus 14 ~~a~~g~w~~d~~-~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~e~r~~~ 88 (125) +..+..++..|.+ ++++++|++++++|||+++++.+. .+.+++++++.......+....+.+. ....+..+++ T Consensus 5 ~~~n~ai~~~d~~~G~I~~vN~~a~~l~Gys~~el~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (114) T 1ll8_A 5 PEFNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQ--KLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDIIS 82 (114) T ss_dssp TTTTCEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTS--BGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEECC T ss_pred HHCCEEEEEEECCCCEEEEHHHHHHHHHCCCHHHHHCC--CCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEEEEEEEC T ss_conf 11271899999999999962389999878598999298--0001138005999999999999658970001025988881 Q ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 433332223550056889996899988887321 Q T0600 89 PDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 89 ~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) ++|+.+|++++.+++..+.+ + .++++++||+ T Consensus 83 kdG~~~pv~l~~~~i~~~~~-~-~~v~vi~dv~ 113 (114) T 1ll8_A 83 RSGEKIPVSVWMKRMRQERR-L-CCVVVLEPVE 113 (114) T ss_dssp TTCCCEEEECCEECCBSSSS-B-EEEEEEEECC T ss_pred CCCEEEEEEEEEEEEEECCE-E-EEEEEEEECC T ss_conf 59979999999999999994-7-9999999764 No 38 >3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transferase, two-component regulatory system; 3.80A {Thermotoga maritima} Probab=98.83 E-value=6e-10 Score=71.62 Aligned_cols=107 Identities=15% Similarity=0.090 Sum_probs=74.3 Q ss_pred HHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC Q ss_conf 99998619818998648998998168987411351224587668999887510378999999998750456325786044 Q T0600 10 HTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRP 89 (125) Q Consensus 10 ~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~ 89 (125) +.++++.+.|++.+|.+++.+++|+++.++||++++++.+.. +.++.++++.. .........+.... .-... T Consensus 11 e~il~~~~~gi~v~d~~g~i~~~N~aa~~llg~~~~e~~g~~--~~~l~~~~~~~---~~~~~~~~~~~~~~---~~~~~ 82 (349) T 3a0r_A 11 ESILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRR--LKDLPDFEEIG---SVAESVFENKEPVF---LNFYK 82 (349) T ss_dssp CSSGGGSSSEEEEEESSSBCSCBCHHHHHHHSCCSTTTTTCB--STTSTTTTHHH---HHHHHHHHHCCCCE---EECCC T ss_pred HHHHHHHHHHHEEECCCCCCHHHHHHHHHHHCCCHHHHCCCC--HHHCCCHHHHH---HHHHHHHHCCCEEE---EEEEC T ss_conf 999986426748998959002706999999782989985998--78948978899---99999982598399---99970 Q ss_pred CCCCCCCCCCCEEEECCCCC-EEEEEEEEEECHHHCC Q ss_conf 33332223550056889996-8999888873211249 Q T0600 90 DGQVRELLERNHIQRQASGQ-VDHLWGTVIDMTEHKQ 125 (125) Q Consensus 90 ~g~~~w~~~~~~~~~d~~g~-~~~~vG~~~DITerK~ 125 (125) +| .+|+.++..|+.+.++. +.+++.++.|||++|+ T Consensus 83 ~~-~~~~~~~~~~~~~~~~~~~~g~v~~~~DIT~~~~ 118 (349) T 3a0r_A 83 FG-ERYFNIRFSPFRNAKTQLLEGVIITIDDVTELYK 118 (349) T ss_dssp BT-TBCCEEEEEEECCTTTTSSCEEEEEEECCSTTTT T ss_pred CC-CEEEEEEEEEEECCCCCEEEEEEEEEEEHHHHHH T ss_conf 88-1899999999982898778899999984559999 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=98.81 E-value=4e-09 Score=67.25 Aligned_cols=105 Identities=15% Similarity=0.107 Sum_probs=79.2 Q ss_pred HHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCEEEEEEC Q ss_conf 9999861981899864899899816898741135122458766899988751-037899999999875045632578604 Q T0600 10 HTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPD-DRARVRRELDRHVLGDRPFDVEYRIVR 88 (125) Q Consensus 10 ~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~-~~~~~~~~~~~~~~~~~~~~~e~r~~~ 88 (125) ...+++++.|++..|.+++.++||+++++|+|++++++.+.. +...++|+ ..+.+...+.+.+..+.....+....+ T Consensus 20 ~~~ld~~~~Gii~lD~~G~i~~~N~a~~~l~G~~~~e~iG~~--~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~~~ 97 (125) T 1nwz_A 20 DGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKN--FFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFD 97 (125) T ss_dssp HHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSB--CCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEEEC T ss_pred HHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCC--HHHCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC T ss_conf 999856882699997999997688999988586668767970--444048700179999999999974997158999971 Q ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEEEEEEC Q ss_conf 43333222355005688999689998888732 Q T0600 89 PDGQVRELLERNHIQRQASGQVDHLWGTVIDM 120 (125) Q Consensus 89 ~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DI 120 (125) ++|..+|++++..+ .++|...+ -.++|| T Consensus 98 ~~g~~~~V~v~~~~--~~~g~~~~--v~V~~i 125 (125) T 1nwz_A 98 YQMTPTKVKVHMKK--ALSGDSYW--VFVKRV 125 (125) T ss_dssp TTSCCEEEEEEEEE--CSSSSEEE--EEEEEC T ss_pred CCCCEEEEEEEEEE--ECCCCEEE--EEEEEC T ss_conf 49968999999999--13899699--999989 No 40 >3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A* Probab=98.63 E-value=1.2e-07 Score=59.27 Aligned_cols=94 Identities=14% Similarity=0.035 Sum_probs=70.1 Q ss_pred CCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC Q ss_conf 98189986489989981689874113512245876689998875103789999999987504563257860443333222 Q T0600 17 GIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVREL 96 (125) Q Consensus 17 ~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w~ 96 (125) +.|+...|.+++.++||+++++|+|++.+++.+.... ++.+. ......+.+.+..+..... ..+++..+|+ T Consensus 2 ~~gvi~~D~~g~I~~~N~~a~~l~g~~~~e~iG~~~~--~~~~~---~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~ 72 (96) T 3a0s_A 2 ETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLK--DLPDF---EEIGSVAESVFENKEPVFL----NFYKFGERYF 72 (96) T ss_dssp CCEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGG--GSTTC---HHHHHHHHHHHHHTCCEEE----EEEEETTEEE T ss_pred CEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHH--HHHHH---HHHHHHHHHHHHCCCEEEE----EEECCCCEEE T ss_conf 8799999898989999879898759998997698399--95010---0132589999847958999----9987991999 Q ss_pred CCCCEEEECCCCCEE-EEEEEEEE Q ss_conf 355005688999689-99888873 Q T0600 97 LERNHIQRQASGQVD-HLWGTVID 119 (125) Q Consensus 97 ~~~~~~~~d~~g~~~-~~vG~~~D 119 (125) .++..|+++++|+.+ +++.++.| T Consensus 73 ~v~~~Pi~~~~~~~i~g~v~~~~D 96 (96) T 3a0s_A 73 NIRFSPFRNAKTQLLEGVIITIDD 96 (96) T ss_dssp EEEEEEEECTTTCCEEEEEEEEEC T ss_pred EEEEEEEECCCCCEEEEEEEEEEC T ss_conf 999999891899999999999989 No 41 >1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1 Probab=98.59 E-value=9.8e-09 Score=65.16 Aligned_cols=102 Identities=4% Similarity=-0.102 Sum_probs=74.9 Q ss_pred HHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCEEEEE Q ss_conf 999999861981899864899899816898741135122458766899988751037899999999875045-6325786 Q T0600 8 LLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP-FDVEYRI 86 (125) Q Consensus 8 ~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~e~r~ 86 (125) .++.++++++.|++.+|.++++++||+++++|+|++++++.+.... ..+.++++...+...+.+.+..+.. ...++.+ T Consensus 23 ~~~a~lda~p~GIi~~D~~GrI~~~N~aa~~l~G~~~eeliGr~~~-~~~~P~~~~~~~~~~~~~~l~~G~~~~~~~~~~ 101 (129) T 1mzu_A 23 MGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFF-TEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVF 101 (129) T ss_dssp --CTTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCC-CCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEEE T ss_pred HHHHHHHCCCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHH-HEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEE T ss_conf 9999986599059999899959999789998868398997799377-807876667899999999997599861589999 Q ss_pred ECCCCCCCCCCCCCEEEECCCCCEEEE Q ss_conf 044333322235500568899968999 Q T0600 87 VRPDGQVRELLERNHIQRQASGQVDHL 113 (125) Q Consensus 87 ~~~~g~~~w~~~~~~~~~d~~g~~~~~ 113 (125) +++|..+|++++.... +.|.-+++ T Consensus 102 -~~~g~~~~V~v~l~~~--p~~~~~~v 125 (129) T 1mzu_A 102 -DFQMAPVRVQIRMQNA--GVPDRYWI 125 (129) T ss_dssp -ECSSCEEEEEEEEEEC--SSTTEEEE T ss_pred -ECCCCEEEEEEEEEEC--CCCCEEEE T ss_conf -4399669999999982--68997999 No 42 >2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli} Probab=98.54 E-value=1.3e-08 Score=64.54 Aligned_cols=106 Identities=12% Similarity=0.001 Sum_probs=74.2 Q ss_pred HHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 89999999986198189986489989981689874113512245876689998875103789999999987504563257 Q T0600 5 AEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 5 SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) ..+.++.+++..+.|++.+|.+++.+++|++++++||++.+.......... .++.. ...+.+.+.++.....+. T Consensus 13 ~~~~~~~il~~i~dgvi~iD~~g~I~~~N~aa~~i~~~~~~~~~~~~~~~~--~~~~~----~~~~~~~l~~~~~~~~~~ 86 (118) T 2w0n_A 13 LFEQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLS--HSWSQ----VVDVSEVLRDGTPRRDEE 86 (118) T ss_dssp THHHHHHHHHCCCCCCEEEBTTTBCCCBCHHHHHHHCSCTTTTTSSCCCTT--CCCSC----THHHHHHHHTTCCCCCCC T ss_pred HHHHHHHHHHHCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCHHHHC--CCCHH----HCHHHHHHHCCCEEEEEE T ss_conf 999999999714781899989990999998999886689889679367754--78023----253899985598346699 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECH Q ss_conf 8604433332223550056889996899988887321 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMT 121 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DIT 121 (125) ...+| +++.++..|+++ +|++.+++.+++||| T Consensus 87 --~~~~~--~~~~v~~~Pi~~-~~~~~G~V~~~~DIT 118 (118) T 2w0n_A 87 --ITIKD--RLLLINTVPVRS-NGVIIGAISTFRDKT 118 (118) T ss_dssp --EESSS--CEECCCEECCCC-SSCCCCEEECCCCCC T ss_pred --EEECC--EEEEEEEEEEEE-CCEEEEEEEEEEECC T ss_conf --99899--999999999999-998999999999669 No 43 >2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protein, nucleotide-binding, transcription regulation, activator, repressor; HET: PG4; 2.30A {Escherichia coli} Probab=98.41 E-value=2.6e-08 Score=62.91 Aligned_cols=108 Identities=12% Similarity=-0.050 Sum_probs=74.1 Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 88999999998619818998648998998168987411351224587668999887510378999999998750456325 Q T0600 4 MAEKLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVE 83 (125) Q Consensus 4 ~SE~~l~~~~~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e 83 (125) .++++|+.+++.++.|++..|.+++.++||++++++||++++++.+.... .+++..+. ......... ... T Consensus 77 ~~~~~~~~il~~~~d~i~~~D~~g~i~~~N~aa~~l~g~~~~~~~g~~~~--~l~~~~~~-------~~~~~~~~~-~~~ 146 (190) T 2jhe_A 77 REHLALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLDRLRNHTAA--QLINGFNF-------LRWLESEPQ-DSH 146 (190) T ss_dssp HHHHHHHHHHHHCSSCEEEECTTCBEEEECHHHHHHHTSCHHHHTTSBGG--GTSTTCCH-------HHHHHTCCC-SCE T ss_pred HHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHHHCCHH--HHCCCHHH-------HHHHHHCCC-CCC T ss_conf 99999999997064243999899999998999999879199999638799--95896769-------999970776-442 Q ss_pred EEEECCCCCCCCCCCCCEEEE----CCCCCEEEEEEEEEECHHH Q ss_conf 786044333322235500568----8999689998888732112 Q T0600 84 YRIVRPDGQVRELLERNHIQR----QASGQVDHLWGTVIDMTEH 123 (125) Q Consensus 84 ~r~~~~~g~~~w~~~~~~~~~----d~~g~~~~~vG~~~DITer 123 (125) ......+|+.+.+. ..|+. |.+|.+++.|-++.|+|.- T Consensus 147 ~~~v~~~G~~~~~~--~~pi~~~~~~~~~~~~G~Vi~~r~~tr~ 188 (190) T 2jhe_A 147 NEHVVINGQNFLME--ITPVYLQDENDQHVLTGAVVMLRSTIRM 188 (190) T ss_dssp EEEEEETTEEEEEE--EEEETTTTEEEEEEEE-HHHHHHHHTTT T ss_pred EEEEEECCEEEEEE--EEEEEEECCCCCCEEEEEEEEEECHHHC T ss_conf 19999999799999--9999986468983899999999878884 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=93.80 E-value=0.04 Score=29.79 Aligned_cols=74 Identities=16% Similarity=0.146 Sum_probs=49.6 Q ss_pred EEEEEC-CCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC Q ss_conf 899864-89989981689874113512245876689998875103789999999987504563257860443333222 Q T0600 20 SWVLHM-ESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVREL 96 (125) Q Consensus 20 ~w~~d~-~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w~ 96 (125) +...|. +..+.++|+++.+++|++++++.+. .+.+++++++...+.+.+....... ....++.+..+.+...|. T Consensus 45 Ll~ld~~d~~I~~vS~N~~~llG~~peellG~--~l~~ll~~~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 119 (337) T 2ool_A 45 LFVVSETDLRIASVSANVEDLLRQPPASLLNV--PIAHYLTAASAARLTHALHGGDPAA-INPIRLDVVTPDGERAFN 119 (337) T ss_dssp EEEECTTTCBEEEEETTHHHHHSSCGGGGTTC--BGGGGBCHHHHHHHHHHHCC----C-CCSEEEEEEETTEEEEEE T ss_pred EEEEECCCCEEEEECCHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHCCCCCC-CCCEEEEEECCCCCCEEE T ss_conf 99998899979998661998839698998399--8889769888999999863147455-886899984168982268 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=90.11 E-value=0.16 Score=26.57 Aligned_cols=98 Identities=8% Similarity=-0.037 Sum_probs=53.6 Q ss_pred EEEEECC-CCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCC Q ss_conf 8998648-998998168987411351224587668999887510378999999998750456325786044333322235 Q T0600 20 SWVLHME-SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQVRELLE 98 (125) Q Consensus 20 ~w~~d~~-~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~~g~~~w~~~ 98 (125) +...|.. ..++++|+++.+++|++++++.+. .+.+++++++...+...+......... ...+..+...+...++. T Consensus 32 Ll~~d~~~~~I~~vS~n~~~lLG~~~eeLLGr--~l~dLl~~~~~~~i~~~l~~~~~~~~~-~~~~~~~~~~~~~~~~~- 107 (520) T 2vea_A 32 VVVLQEPDLTISQISANCTGILGRSPEDLLGR--TLGEVFDSFQIDPIQSRLTAGQISSLN-PSKLWARVMGDDFVIFD- 107 (520) T ss_dssp EEEEETTTTEEEEEETTHHHHTSCCTTTSSTT--TTTTTSBCC--------CCCTTHHHHS-SEEEEEECC--CEEEEE- T ss_pred EEEEECCCCEEEEECCHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHHHHCCCCCCC-CEEEEEEECCCCCEEEE- T ss_conf 99999899989999554998869398998299--778978978899999997513124578-75899998489956899- Q ss_pred CCEEEECCCCCEEEEEEEEEECHHH Q ss_conf 5005688999689998888732112 Q T0600 99 RNHIQRQASGQVDHLWGTVIDMTEH 123 (125) Q Consensus 99 ~~~~~~d~~g~~~~~vG~~~DITer 123 (125) +...++.+|.++ ......+.++. T Consensus 108 -~~ihr~~~~~~i-~~~~~~~~~~~ 130 (520) T 2vea_A 108 -GVFHRNSDGLLV-CELEPAYTSDN 130 (520) T ss_dssp -EEEEECSSCCEE-EEEEECCTTSC T ss_pred -EEEEECCCCEEE-EEECCCCCCCC T ss_conf -999981791699-99415666432 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=86.20 E-value=0.67 Score=23.22 Aligned_cols=73 Identities=10% Similarity=0.115 Sum_probs=43.5 Q ss_pred EEEEEECC-CCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCEEEEEECCCCCCCC Q ss_conf 18998648-99899816898741135122458766899988751037899999999875045--6325786044333322 Q T0600 19 GSWVLHME-SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRP--FDVEYRIVRPDGQVRE 95 (125) Q Consensus 19 g~w~~d~~-~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~--~~~e~r~~~~~g~~~w 95 (125) .++..|.. ..++++|.++.+++|++++++.+.. +.+ +.+++...... .+..+.. ......+..+++...| T Consensus 55 ~Ll~ld~~d~~I~~vS~N~~~iLG~~peelLG~~--l~~-llpe~~~~~~~----~l~~~~~~~~~~~~~~~~~~~~~~~ 127 (342) T 2o9c_A 55 ALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQT--LAA-LLPEQWPALQA----ALPPGCPDALQYRATLDWPAAGHLS 127 (342) T ss_dssp EEEEEETTTCBEEEEETTHHHHHSSCHHHHTTCB--HHH-HCTTTHHHHHH----HSCTTCCTTCCEEEEECCSSSSEEE T ss_pred EEEEEECCCCEEEEECCCHHHHHCCCHHHHCCCC--HHH-HCCHHHHHHHH----HHHCCCCCCEEEEEEEECCCCCEEE T ss_conf 7999988999499992889988592969985998--899-88846899998----7640798641467888158873799 Q ss_pred CCC Q ss_conf 235 Q T0600 96 LLE 98 (125) Q Consensus 96 ~~~ 98 (125) +.+ T Consensus 128 ~~i 130 (342) T 2o9c_A 128 LTV 130 (342) T ss_dssp EEE T ss_pred EEE T ss_conf 999 No 47 >1p0z_A Sensor kinase CITA; transferase; HET: FLC MO7; 1.60A {Klebsiella pneumoniae} SCOP: d.110.6.1 PDB: 2v9a_A 2j80_A* Probab=35.50 E-value=20 Score=15.33 Aligned_cols=87 Identities=14% Similarity=0.074 Sum_probs=45.9 Q ss_pred HHHHHHHHCCC-EEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 99999986198-18998648998998168987411351224587668999887510378999999998750456325786 Q T0600 8 LLHTAESDAGI-GSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRI 86 (125) Q Consensus 8 ~l~~~~~~a~~-g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r~ 86 (125) .+..+.+.+++ -++..|.++..+.-+. ...+|.. +.. ++. +..++ .+..+... . T Consensus 40 ~~~~~~~~~~~~~i~v~D~~G~vla~~~--~~~~G~~---~~~----------~~~-------~~a~~-~g~~~~~~--~ 94 (131) T 1p0z_A 40 LIDPMRSFSDATYITVGDASGQRLYHVN--PDEIGKS---MEG----------GDS-------DEALI-NAKSYVSV--R 94 (131) T ss_dssp HHHHHHHHSCCSEEEEEETTSBEEECSS--GGGTTSB---CCS----------SCC-------HHHHH-HCCCEEEE--E T ss_pred HHHHHHHHCCCEEEEEECCCCCEEEECC--HHHCCCC---CCC----------CCH-------HHHHH-CCCCEEEE--E T ss_conf 9999999739719999879987998079--6666986---778----------842-------88996-49848999--9 Q ss_pred ECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHH Q ss_conf 044333322235500568899968999888873211 Q T0600 87 VRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTE 122 (125) Q Consensus 87 ~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITe 122 (125) . ..+. .......|+++++|++++++.+-.++++ T Consensus 95 ~-g~~g--~~~~~~~PV~~~~G~viGvv~Vg~~l~~ 127 (131) T 1p0z_A 95 K-GSLG--SSLRGKSPIQDATGKVIGIVSVGYTIEQ 127 (131) T ss_dssp E-ETTE--EEEEEEEEEECTTCCEEEEEEEEEEGGG T ss_pred E-CCCC--EEEEEEEEEECCCCCEEEEEEEEEEHHH T ss_conf 6-4784--1899999679799979999999988577 No 48 >2ggv_B NS3, non-structural protein 3; beta barrel, serine protease, viral protease, flavivirus, hydrolase; 1.80A {West nile virus} PDB: 2ijo_B Probab=34.48 E-value=21 Score=15.24 Aligned_cols=22 Identities=18% Similarity=0.104 Sum_probs=18.1 Q ss_pred CCCCCEEEECCCCCEEEEEEEE Q ss_conf 2355005688999689998888 Q T0600 96 LLERNHIQRQASGQVDHLWGTV 117 (125) Q Consensus 96 ~~~~~~~~~d~~g~~~~~vG~~ 117 (125) .-.+++|+.|.+|+++++.|-- T Consensus 131 ~GtSGSPIi~~~G~vVGLYGnG 152 (185) T 2ggv_B 131 TGTSGSPIVDKNGDVIGLYGNG 152 (185) T ss_dssp GGGTTCEEECTTSCEEEEEEEE T ss_pred CCCCCCCEECCCCCEEEEECCE T ss_conf 9999997475598399985575 No 49 >3e90_B NS3 protease; trypsin-like serine protease, protease inhibitor, catalytic histidine, induced FIT, ATP-binding, capsid protein, helicase; HET: NKK; 2.45A {West nile virus} Probab=29.19 E-value=21 Score=15.17 Aligned_cols=20 Identities=20% Similarity=0.160 Sum_probs=17.0 Q ss_pred CCCCCEEEECCCCCEEEEEE Q ss_conf 23550056889996899988 Q T0600 96 LLERNHIQRQASGQVDHLWG 115 (125) Q Consensus 96 ~~~~~~~~~d~~g~~~~~vG 115 (125) .-.+++||.|.+|+++++.| T Consensus 136 ~GtSGSPIi~~~G~vVGLYG 155 (198) T 3e90_B 136 TGTSGSPIVDKNGDVIGLYG 155 (198) T ss_dssp TTCTTCEEECTTCCEEEECC T ss_pred CCCCCCCEECCCCCEEEEEC T ss_conf 99999964745896999853 No 50 >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=29.09 E-value=26 Score=14.73 Aligned_cols=92 Identities=10% Similarity=0.061 Sum_probs=50.0 Q ss_pred HHHHHHHHHCCC--EEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 999999986198--189986489989981689874113512245876689998875103789999999987504563257 Q T0600 7 KLLHTAESDAGI--GSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEY 84 (125) Q Consensus 7 ~~l~~~~~~a~~--g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~ 84 (125) +.|+...+..+. ++...|.+++.+..+..... |+ .+.++.. +..++.++...-.+. T Consensus 55 ~~L~~~~~~~~~~~~i~i~d~~G~~i~~s~~~~~--~~----------------~~~~r~~----~~~~~~~~~~~is~~ 112 (214) T 3fos_A 55 SILEKTFDSEPRFSGLYFLNAKGDVTASTTELKT--KV----------------NLADRSF----FIKAKETKKTVISDS 112 (214) T ss_dssp HHHHHHHTTCTTEEEEEEEETTCBEEEESSCCSS--CC----------------BCTTSHH----HHHHHHHCSCEECCC T ss_pred HHHHHHHHHCCCCCEEEEECCCCCEEECCCCCCC--CC----------------CHHHCHH----HHHHHHCCCCCCCCE T ss_conf 9999998618770089999599978980576678--88----------------9344636----777763377421330 Q ss_pred EEECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHH Q ss_conf 86044333322235500568899968999888873211 Q T0600 85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTE 122 (125) Q Consensus 85 r~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITe 122 (125) .+-...| .|+-.-+.|+++.+|+..++++...|+.. T Consensus 113 ~~~~~~g--~~~i~~s~pi~~~~G~~~Gvl~~~i~l~~ 148 (214) T 3fos_A 113 YSSRITG--QPIFTICVPVLDSKRNVTDYLVAAIQIDY 148 (214) T ss_dssp EECTTTC--SEEEEEEEEEECSSCCEEEEEEEEEEHHH T ss_pred EEECCCC--CEEEEEEEEEECCCCCEEEEEEEEEEHHH T ss_conf 3304678--45899998679689978999999964999 No 51 >2fp7_B Polyprotein; flavivirus, NS3 protease, NS2B cofactor, substrate-based inhibitor, viral protein/protease complex; HET: NDL; 1.68A {West nile virus} SCOP: b.47.1.3 Probab=28.86 E-value=20 Score=15.33 Aligned_cols=22 Identities=18% Similarity=0.104 Sum_probs=17.5 Q ss_pred CCCCCEEEECCCCCEEEEEEEE Q ss_conf 2355005688999689998888 Q T0600 96 LLERNHIQRQASGQVDHLWGTV 117 (125) Q Consensus 96 ~~~~~~~~~d~~g~~~~~vG~~ 117 (125) .-.++.|+.|.+|+++++.|-- T Consensus 117 ~GtSGSPIi~~~G~vVGLYGnG 138 (172) T 2fp7_B 117 TGTSGSPIVDKNGDVIGLYGNG 138 (172) T ss_dssp GGGTTCEEECTTSCEEEESCCE T ss_pred CCCCCCCEECCCCCEEEEECCE T ss_conf 9999996474589699985355 No 52 >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=27.25 E-value=28 Score=14.55 Aligned_cols=93 Identities=9% Similarity=-0.005 Sum_probs=52.2 Q ss_pred HHHHHHHHHC-CCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 9999999861-981899864899899816898741135122458766899988751037899999999875045632578 Q T0600 7 KLLHTAESDA-GIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYR 85 (125) Q Consensus 7 ~~l~~~~~~a-~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~e~r 85 (125) ++|+.+...+ -..+|..|.+++.+-.|+. -.+....+. ...+++.+ ..+++++.. ..+. T Consensus 102 ~~L~~~~~~~~a~~i~llD~~G~viasSn~------~~~~s~vg~--------n~s~RpYf----~~Al~g~~~--~~~~ 161 (305) T 3e4o_A 102 RKLEALATSAEAAVIYLIDRSGVAVAASNW------QEPTSFVGN--------DYAFRDYF----RLAVRDGMA--EHFA 161 (305) T ss_dssp HHHHHHHHHSSCSEEEEEETTSBEEEETTT------TSTTCCTTC--------BCTTSHHH----HHHHHHSEE--EEEE T ss_pred HHHHHHHHHCCEEEEEEECCCCCEEEECCC------CCCCCCCCC--------CCCCCHHH----HHHHCCCCC--EEEE T ss_conf 999999623072189999899999996687------787432366--------63331889----998717860--4676 Q ss_pred EECCCCCCCCCCCCCEEEECCCCCEEEEEEEEEECHH Q ss_conf 6044333322235500568899968999888873211 Q T0600 86 IVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTE 122 (125) Q Consensus 86 ~~~~~g~~~w~~~~~~~~~d~~g~~~~~vG~~~DITe 122 (125) +-...+.. ...-+.|+++ +|++++++++-.|+.. T Consensus 162 ~~~~~~~~--~~~~a~PV~~-~g~viGVvv~~v~l~~ 195 (305) T 3e4o_A 162 MGTVSKRP--GLYISRRVDG-PGGPLGVIVAKLEFDG 195 (305) T ss_dssp ECTTTCCE--EEEEEEEEEE-TTEEEEEEEEEECCHH T ss_pred ECCCCCCC--EEEEEEECCC-CCCEEEEEEEEECHHH T ss_conf 30466762--3899752156-7714799999971799 No 53 >2khu_A Immunoglobulin G-binding protein G, DNA polymerase IOTA; UBM, ubiquitin-binding domain, translesion synthesis, TLS, ubiquitin-binding protein; NMR {Streptococcus SP} PDB: 2khw_A Probab=25.98 E-value=20 Score=15.34 Aligned_cols=66 Identities=15% Similarity=0.231 Sum_probs=36.7 Q ss_pred HHHHHHHHHHH-HHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68899999999-86198189986489989981689874113512245876689998875103789999999 Q T0600 3 AMAEKLLHTAE-SDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDR 72 (125) Q Consensus 3 a~SE~~l~~~~-~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 72 (125) |.+|+-|+... ++.-.|.|.||..++.+.+..+..+-.-+++. +. +.-+ .-++++-.......+.+ T Consensus 24 atAEk~fkqyan~ngV~G~WtYddaTKTFTVTesadEkit~p~~-id--p~vf-~elpeevqkellaewkr 90 (108) T 2khu_A 24 ATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSDEKITFPSD-ID--PQVF-YELPEAVQKELLAEWKR 90 (108) T ss_dssp -------------------------------------CCCCCTT-CC--HHHH-TTSCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCCEEEECCCCEEEEEECCCCCCCCCCCC-CC--HHHH-HHCCHHHHHHHHHHHHH T ss_conf 98999999985146876168723761368872354346899988-98--7999-86889999999999987 No 54 >3lkw_A Fusion protein of nonstructural protein 2B and nonstructural protein 3; viral protease, serine protease, NS3 protease, NS2B cofactor; 2.00A {Dengue virus 1} PDB: 3l6p_A Probab=25.77 E-value=25 Score=14.85 Aligned_cols=20 Identities=15% Similarity=0.204 Sum_probs=15.9 Q ss_pred CCCEEEECCCCCEEEEEEEE Q ss_conf 55005688999689998888 Q T0600 98 ERNHIQRQASGQVDHLWGTV 117 (125) Q Consensus 98 ~~~~~~~d~~g~~~~~vG~~ 117 (125) .++.||.|.+|+++++.|-- T Consensus 184 TSGSPIin~~G~VVGLYGNG 203 (236) T 3lkw_A 184 TAGSPIVNREGKIVGLYGNG 203 (236) T ss_dssp CTTCEEECTTSCEEEESCCE T ss_pred CCCCCEECCCCCEEEEECCE T ss_conf 99996587899799985353 No 55 >2fom_B Polyprotein; flavivirus, NS3 protease, NS2B cofactor, viral protein/protease complex; 1.50A {Dengue virus 2} SCOP: b.47.1.3 PDB: 1df9_A 2qid_A 1bef_A Probab=22.85 E-value=25 Score=14.84 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=16.3 Q ss_pred CCCCEEEECCCCCEEEEEEE Q ss_conf 35500568899968999888 Q T0600 97 LERNHIQRQASGQVDHLWGT 116 (125) Q Consensus 97 ~~~~~~~~d~~g~~~~~vG~ 116 (125) -.++.|+.|.+|+++++.|- T Consensus 133 GtSGSPIin~~G~vVGLYGN 152 (185) T 2fom_B 133 GTSGSPIVDKKGKVVGLYGN 152 (185) T ss_dssp GGTTCEEECTTSCEEEETTC T ss_pred CCCCCCEECCCCCEEEEECC T ss_conf 99998658789869998656 No 56 >1pn5_A Nacht-, LRR- and PYD-containing protein 2; alpha-helix bundle, apoptosis; NMR {Homo sapiens} SCOP: a.77.1.5 Probab=22.55 E-value=35 Score=14.05 Aligned_cols=65 Identities=14% Similarity=0.216 Sum_probs=37.5 Q ss_pred HHHHHHHHHHH-HHCCCEEEEEECCCCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68899999999-861981899864899899816898741135122458766899988751037899999999 Q T0600 3 AMAEKLLHTAE-SDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRH 73 (125) Q Consensus 3 a~SE~~l~~~~-~~a~~g~w~~d~~~~~~~~s~~~~~~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~ 73 (125) |.+|.-|+... +..-.|.|.||..+..+.+..+ .|-|- .-......++-+.+++...|...+... T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~----~~~rLlwYLEeL~~eELKkFK~~L~~~ 89 (159) T 1pn5_A 24 ATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG--SMAGG----AWGRLACYLEFLKKEELKEFQLLLANK 89 (159) T ss_dssp -------------------------------------CCCS----SCTTHHHHHHHCCHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEEC--CCCCC----HHHHHHHHHHHCCHHHHHHHHHHHCCC T ss_conf 9999999998514798854661366215787406--75665----177999999965799999999997427 Done!