Query 042232
Match_columns 144
No_of_seqs 11 out of 13
Neff 1.9
Searched_HMMs 29240
Date Mon Mar 25 06:47:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042232.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042232hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1exn_A 5'-exonuclease, 5'-nucl 97.3 9.9E-05 3.4E-09 60.2 2.6 45 86-144 18-63 (290)
2 3q8k_A Flap endonuclease 1; he 96.2 0.0017 5.9E-08 53.1 2.0 57 85-143 25-83 (341)
3 3h7i_A Ribonuclease H, RNAse H 95.5 0.0091 3.1E-07 49.9 3.5 51 86-144 12-67 (305)
4 1ul1_X Flap endonuclease-1; pr 95.2 0.0045 1.6E-07 50.8 0.9 56 86-143 26-83 (379)
5 1b43_A Protein (FEN-1); nuclea 94.5 0.031 1.1E-06 44.7 3.9 55 86-143 20-75 (340)
6 1rxw_A Flap structure-specific 94.2 0.049 1.7E-06 43.5 4.4 50 86-137 20-70 (336)
7 2izo_A FEN1, flap structure-sp 93.3 0.12 4.1E-06 41.6 5.2 50 86-137 17-67 (346)
8 1a76_A Flap endonuclease-1 pro 92.4 0.14 4.8E-06 40.7 4.4 48 86-135 20-68 (326)
9 1bgx_T TAQ DNA polymerase; DNA 91.5 0.029 9.9E-07 51.0 -0.5 53 85-143 10-62 (832)
10 3ory_A Flap endonuclease 1; hy 89.4 0.25 8.7E-06 40.8 3.4 54 85-141 33-90 (363)
11 2hjd_A Quorum-sensing antiacti 66.1 2.8 9.6E-05 30.9 1.9 40 81-142 59-99 (102)
12 1rfy_A TRAM protein;, transcri 66.0 2.8 9.7E-05 30.9 1.9 39 81-141 59-98 (102)
13 2q0o_C Probable transcriptiona 57.7 4.7 0.00016 29.9 1.8 31 97-141 69-100 (107)
14 2pln_A HP1043, response regula 42.4 40 0.0014 20.9 4.2 32 80-111 12-43 (137)
15 2b4a_A BH3024; flavodoxin-like 34.8 55 0.0019 20.2 3.9 36 76-111 5-40 (138)
16 1k68_A Phytochrome response re 31.2 69 0.0024 19.3 3.9 26 86-111 2-27 (140)
17 3eod_A Protein HNR; response r 30.6 84 0.0029 19.0 4.2 28 84-111 5-32 (130)
18 3qe9_Y Exonuclease 1; exonucle 29.4 30 0.001 28.2 2.5 20 86-105 23-42 (352)
19 4dad_A Putative pilus assembly 29.3 52 0.0018 20.5 3.2 30 81-110 15-44 (146)
20 2j48_A Two-component sensor ki 25.6 1E+02 0.0034 17.7 3.8 26 86-111 1-26 (119)
21 3cg0_A Response regulator rece 24.3 1E+02 0.0036 18.7 3.8 29 83-111 6-34 (140)
22 1k66_A Phytochrome response re 23.9 1.2E+02 0.004 18.5 4.0 28 84-111 4-31 (149)
23 3eul_A Possible nitrate/nitrit 21.5 99 0.0034 19.4 3.4 31 82-112 11-41 (152)
24 2qxy_A Response regulator; reg 20.3 1.4E+02 0.0048 18.3 3.9 27 85-111 3-29 (142)
25 3cg4_A Response regulator rece 20.0 1.5E+02 0.0051 18.1 3.9 28 84-111 5-32 (142)
No 1
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Probab=97.30 E-value=9.9e-05 Score=60.16 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=32.1
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV 144 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~ 144 (144)
++|++||||.+++||||| ..+|.- .++.-+..++.+++ +.|+|++
T Consensus 18 ~~~lllIDg~~llyRa~~----------~~~G~p----av~Gf~~~l~~ll~~~~p~~~v 63 (290)
T 1exn_A 18 RRNLMIVDGTNLGFRFKH----------NNSKKP----FASSYVSTIQSLAKSYSARTTI 63 (290)
T ss_dssp -CEEEEEEHHHHHHHHHH----------HCSSSC----CHHHHHHHHHHHHHHTTEEEEE
T ss_pred CCCEEEEECcHHHHHHHh----------CCCCch----HHHHHHHHHHHHHHHcCCCeEE
Confidence 789999999999999998 234443 55666666666665 4588863
No 2
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*
Probab=96.20 E-value=0.0017 Score=53.05 Aligned_cols=57 Identities=21% Similarity=0.274 Sum_probs=38.5
Q ss_pred CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh--ccCCCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHV 143 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~--~~PSH~ 143 (144)
-.|++++|||++.+||+||.+-.....|... +|--.-.++.-+..++.+|+ ..|.||
T Consensus 25 l~gk~l~IDgs~~lyr~~~a~~~~~~~l~~~--~G~~T~al~g~~~~~~~ll~~~i~P~~V 83 (341)
T 3q8k_A 25 YFGRKVAIDASMSIYQFLIAVRQGGDVLQNE--EGETTSHLMGMFYRTIRMMENGIKPVYV 83 (341)
T ss_dssp GTTCEEEEEHHHHHHHHHHHCEETTEECBCT--TSCBCHHHHHHHHHHHHHHTTTCEEEEE
T ss_pred hCCCEEEEecHHHHHHHHHccccccCCCCCC--CCCCchHHHHHHHHHHHHHHCCCCceEE
Confidence 3589999999999999999743111234433 44455566666667777776 677764
No 3
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A
Probab=95.47 E-value=0.0091 Score=49.93 Aligned_cols=51 Identities=14% Similarity=0.006 Sum_probs=31.9
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHH-HHHHHHHHhhc----cCCCCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFS-ALSLIIDVLEF----IPSHVV 144 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~-Als~iid~L~~----~PSH~~ 144 (144)
+-++|||||+|++||||+.- ++-.+| -=+=.|+. -+.++..+++- .|+|++
T Consensus 12 ~~~llLIDgssl~~ra~~~~------f~~~~g--~~tnav~ggf~~~L~~ll~~~k~~~P~~ia 67 (305)
T 3h7i_A 12 KEGICLIDFSQIALSTALVN------FPDKEK--INLSMVRHLILNSIKFNVKKAKTLGYTKIV 67 (305)
T ss_dssp SCCEEEEEHHHHHHHHHHHH------SCSSSC--CCHHHHHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred CCCEEEEeccHHHHHHHHHh------cCCCCC--cchHHHHHHHHHHHHHHHHhhhccCCCEEE
Confidence 44899999999999998532 333332 22333433 44555555544 899874
No 4
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Probab=95.23 E-value=0.0045 Score=50.76 Aligned_cols=56 Identities=21% Similarity=0.290 Sum_probs=33.0
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh--ccCCCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHV 143 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~--~~PSH~ 143 (144)
.|++++|||++.+||+||.+--....|... .|...-.++.-+..++.+|+ ..|.||
T Consensus 26 ~g~~l~IDg~~~lyr~~~a~~~~~~~l~~~--~G~~t~~l~g~~~~~~~ll~~~i~P~~V 83 (379)
T 1ul1_X 26 FGRKVAIDASMSIYQFLIAVRQGGDVLQNE--EGETTSHLMGMFYRTIRMMENGIKPVYV 83 (379)
T ss_dssp TTCCEEEEHHHHHHHHHSCC---------------CCHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred CCCEEEEEchHHHHHHHHhCCCcccccCcC--CCCCchHHHHHHHHHHHHHHCCCCeEEE
Confidence 578999999999999999652111123333 34444456666677777776 467664
No 5
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A
Probab=94.47 E-value=0.031 Score=44.74 Aligned_cols=55 Identities=20% Similarity=0.269 Sum_probs=34.3
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhhccCCCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV 143 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~~~PSH~ 143 (144)
+|++++|||.+.+||+||.+=...| .|...+|. -.-.++.-+..++.+++ .|.|.
T Consensus 20 ~g~~l~ID~~~~l~r~~~a~~~~~~~~l~~~~G~--~t~~l~g~~~~l~~ll~-~~i~p 75 (340)
T 1b43_A 20 YGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGR--ITSHLSGLFYRTINLME-AGIKP 75 (340)
T ss_dssp TTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSC--BCHHHHHHHHHHHHHHH-TTCEE
T ss_pred CCCEEEEEhHHHHHHHHHHhccccCCccccccCC--chHHHHHHHHHHHHHHh-CCCEE
Confidence 4789999999999999996511122 23333333 33455555556667776 56553
No 6
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Probab=94.18 E-value=0.049 Score=43.51 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=32.7
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhh
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLE 137 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~ 137 (144)
+|++++|||.+.+||+||.+=...| .+.. ..|...-.++.-+..++.+++
T Consensus 20 ~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~--~~G~~t~a~~g~~~~l~~ll~ 70 (336)
T 1rxw_A 20 SGKKIAVDAFNTLYQFISIIRQPDGTPLKD--SQGRITSHLSGILYRVSNMVE 70 (336)
T ss_dssp TTCEEEEEHHHHHHHHHHHSBCTTSCBCBC--TTSCBCHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEhHHHHHHHHHhhccccCCcccc--cCCCccHHHHHHHHHHHHHHH
Confidence 4689999999999999996411112 2333 344455566666666666665
No 7
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}
Probab=93.26 E-value=0.12 Score=41.65 Aligned_cols=50 Identities=26% Similarity=0.377 Sum_probs=31.8
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhh
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLE 137 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~ 137 (144)
+|++++|||.+.+||+||-+=...| .|. +..|...-.++.-+..++.+++
T Consensus 17 ~~~~l~IDg~~~l~r~~~a~~~~~g~~l~--~~~G~~t~al~g~~~~~~~ll~ 67 (346)
T 2izo_A 17 KGKRVSIDGYNALYQFLAAIRQPDGTPLM--DSQGRVTSHLSGLFYRTINILE 67 (346)
T ss_dssp TTEEEEEEHHHHHHHHHHSCCCC---CCB--CSSSCBCHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEhHHHHHHHHHhcccccccccc--ccCCCccHHHHHHHHHHHHHHH
Confidence 4789999999999999984310011 132 3345555566666666666765
No 8
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A
Probab=92.42 E-value=0.14 Score=40.73 Aligned_cols=48 Identities=23% Similarity=0.384 Sum_probs=28.5
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHH
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDV 135 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~ 135 (144)
+|++++|||.+.+||+||.+-...| .+...+| .-.-.++.-+..++.+
T Consensus 20 ~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~~~G--~~t~~l~g~~~~l~~l 68 (326)
T 1a76_A 20 KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKG--EITSAYNGVFYKTIHL 68 (326)
T ss_dssp TTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTS--CBCHHHHHHHHHHHHH
T ss_pred CCCEEEEEhHHHHHHHHHhhccccccccccccC--CccHHHHHHHHHHHHH
Confidence 5789999999999999996511112 2333333 3333444444444444
No 9
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*
Probab=91.47 E-value=0.029 Score=51.03 Aligned_cols=53 Identities=25% Similarity=0.473 Sum_probs=34.9
Q ss_pred CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCCCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV 143 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PSH~ 143 (144)
-+|+++||||++++|||||-+- .|... +|..+=.|+.-+..++.+|+-...|+
T Consensus 10 ~~~~~llIDg~~~l~ra~~a~~----~l~~~--~G~~t~av~gf~~~l~~ll~~~~~~~ 62 (832)
T 1bgx_T 10 PKGRVLLVDGHHLAYRTFHALK----GLTTS--RGEPVQAVYGFAKSLLKALKEDGDAV 62 (832)
T ss_dssp CCTTSCCCCCSTHHHHTTSSCT----TCBCS--SSCBCSSSTTHHHHHHHGGGTCCSCC
T ss_pred hCCCEEEEEChHHHHHHHhcCC----ccccC--CCcEehHHHHHHHHHHHHHHHcCCeE
Confidence 3568999999999999998651 23333 34444345555667777776644554
No 10
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}
Probab=89.42 E-value=0.25 Score=40.75 Aligned_cols=54 Identities=20% Similarity=0.421 Sum_probs=32.0
Q ss_pred CCCeEEEEeCchHHHHHHHHHHHh-cC-CccCCCCCCCeehhHHHHHHHHHHHhh--ccCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILLH-HG-HLSHADGNGDWVLTIFSALSLIIDVLE--FIPS 141 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlllh-hg-~l~hadgn~DWVLTiF~Als~iid~L~--~~PS 141 (144)
-+|++++|||.+.+||+|+ .+-+ .| .|...+|. =.-.++.-+..++.+|+ ..|.
T Consensus 33 l~gk~l~IDg~~~l~r~~~-~~~~~~g~~l~~~~G~--~T~al~gf~~r~~~ll~~~i~Pv 90 (363)
T 3ory_A 33 LHGKIIVIDGYNALYQFLA-AIRQPDGTPLMDNNGR--ITSHLSGLFYRTINIVEAGIKPV 90 (363)
T ss_dssp GTTCEEEEEHHHHHHHHHH-HCBCTTSCBCBCTTSC--BCHHHHHHHHHHHHHHHTTCEEE
T ss_pred hCCCEEEEehHHHHHHHHH-hhhccCCCccCCCCCC--CccHHHHHHHHHHHHHHcCCCcE
Confidence 3589999999999999554 3321 22 45444443 33345555555555554 4554
No 11
>2hjd_A Quorum-sensing antiactivator; helix coiled coil, signaling protein; 2.10A {Agrobacterium tumefaciens}
Probab=66.13 E-value=2.8 Score=30.89 Aligned_cols=40 Identities=25% Similarity=0.415 Sum_probs=29.4
Q ss_pred ccCCCCCeEEEEeCchHHHHHHHHHH-HhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCCC
Q 042232 81 KKAPSNGRVMLIDGTSIIYRAYYKIL-LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSH 142 (144)
Q Consensus 81 ~~~~s~grimLiDGtsiiyRaYyKll-lhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PSH 142 (144)
+++++.| .-.+..|-.-+ -.|.+ -+|||+|||.|.|+|.=
T Consensus 59 ~~dps~~--------~~lh~eYi~~~ie~~AQ--------------q~~lstli~~LGyvP~v 99 (102)
T 2hjd_A 59 KIGTAAG--------GEQHLEYIEAMIEMHAQ--------------MSAVNTLVGLLGFIPKV 99 (102)
T ss_dssp HHTSCCC--------SHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHTSCCCC
T ss_pred ccCcccC--------cHHHHHHHHHHHHHHHH--------------HHHHHHHHHHhcCCCCC
Confidence 4466666 45688888777 44443 47999999999999963
No 12
>1rfy_A TRAM protein;, transcriptional repressor TRAM; inter- and intra-molcular two-helix coiled coil, homodimer; 1.60A {Agrobacterium tumefaciens} SCOP: a.2.13.1 PDB: 1us6_A 1upg_A
Probab=65.95 E-value=2.8 Score=30.86 Aligned_cols=39 Identities=31% Similarity=0.439 Sum_probs=29.2
Q ss_pred ccCCCCCeEEEEeCchHHHHHHHHHH-HhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCC
Q 042232 81 KKAPSNGRVMLIDGTSIIYRAYYKIL-LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPS 141 (144)
Q Consensus 81 ~~~~s~grimLiDGtsiiyRaYyKll-lhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PS 141 (144)
+++++.| .-.+..|-.-+ -.|.+ -+|||+|||.|.|+|.
T Consensus 59 ~~dps~~--------~~lh~eYi~~~ie~~AQ--------------q~~lstli~~LGyvP~ 98 (102)
T 1rfy_A 59 KTGQACG--------GPQHIRYIEASIEMHAQ--------------MSALNTLISILGFIPK 98 (102)
T ss_dssp HTTSSCC--------SHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHTSCCC
T ss_pred ccCcccC--------cHHHHHHHHHHHHHHHH--------------HHHHHHHHHHhcCCCC
Confidence 4566666 45788888777 44443 4799999999999995
No 13
>2q0o_C Probable transcriptional repressor TRAM; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}
Probab=57.71 E-value=4.7 Score=29.91 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=23.1
Q ss_pred HHHHHHHHHH-HhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCC
Q 042232 97 IIYRAYYKIL-LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPS 141 (144)
Q Consensus 97 iiyRaYyKll-lhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PS 141 (144)
-.++.|-.-+ -+|.+ -++|++|||.|.|+|-
T Consensus 69 ~~q~eYi~a~~e~~AQ--------------q~~lstLid~LGyvPk 100 (107)
T 2q0o_C 69 TLQDEYVARQKRSEAQ--------------QEELSDILDALGFVPD 100 (107)
T ss_dssp HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHCSCCC
T ss_pred HHHHHHHHHHHHHHHH--------------HHHHHHHHHHhcCCCC
Confidence 3567777666 44433 4799999999999995
No 14
>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A
Probab=42.42 E-value=40 Score=20.86 Aligned_cols=32 Identities=25% Similarity=0.200 Sum_probs=21.9
Q ss_pred cccCCCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 80 CKKAPSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 80 ~~~~~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
+.....+.||++||.....-...-++|...|.
T Consensus 12 ~~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~ 43 (137)
T 2pln_A 12 SLVPRGSMRVLLIEKNSVLGGEIEKGLNVKGF 43 (137)
T ss_dssp ---CTTCSEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred cccCCCCCeEEEEeCCHHHHHHHHHHHHHcCc
Confidence 34566788999999998877766666655553
No 15
>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1
Probab=34.83 E-value=55 Score=20.22 Aligned_cols=36 Identities=17% Similarity=0.022 Sum_probs=20.6
Q ss_pred ceeecccCCCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 76 SIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 76 si~~~~~~~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
+...+......-||++||.....-...-++|...|.
T Consensus 5 ~~~~~~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~ 40 (138)
T 2b4a_A 5 KIHHHHHHMQPFRVTLVEDEPSHATLIQYHLNQLGA 40 (138)
T ss_dssp ---------CCCEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred hhhhccCCCCCCeEEEECCCHHHHHHHHHHHHHcCC
Confidence 344555677788999999998877666666655553
No 16
>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1
Probab=31.18 E-value=69 Score=19.28 Aligned_cols=26 Identities=12% Similarity=0.193 Sum_probs=21.4
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
+.||++||.....-...-++|...|.
T Consensus 2 ~~~ilivdd~~~~~~~l~~~L~~~~~ 27 (140)
T 1k68_A 2 HKKIFLVEDNKADIRLIQEALANSTV 27 (140)
T ss_dssp CCEEEEECCCHHHHHHHHHHHHTCSS
T ss_pred CCeEEEEeCCHHHHHHHHHHHHhcCC
Confidence 56899999999888888888776665
No 17
>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}
Probab=30.64 E-value=84 Score=19.04 Aligned_cols=28 Identities=4% Similarity=0.147 Sum_probs=21.7
Q ss_pred CCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 84 PSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 84 ~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
..+.|+++||.....-+..-+++.+.|.
T Consensus 5 ~~~~~ilivdd~~~~~~~l~~~L~~~g~ 32 (130)
T 3eod_A 5 LVGKQILIVEDEQVFRSLLDSWFSSLGA 32 (130)
T ss_dssp TTTCEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred CCCCeEEEEeCCHHHHHHHHHHHHhCCc
Confidence 4567999999999887777777766664
No 18
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Probab=29.40 E-value=30 Score=28.23 Aligned_cols=20 Identities=15% Similarity=0.255 Sum_probs=17.6
Q ss_pred CCeEEEEeCchHHHHHHHHH
Q 042232 86 NGRVMLIDGTSIIYRAYYKI 105 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKl 105 (144)
+|+.+.|||...+||++|..
T Consensus 23 ~Gk~vaIDas~wL~~~~~~~ 42 (352)
T 3qe9_Y 23 KGQVVAVDTYCWLHKGAIAC 42 (352)
T ss_dssp TTSEEEEETHHHHHHHHHHT
T ss_pred CCcEEEEecHHHHHHhhhcc
Confidence 58899999999999998763
No 19
>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A
Probab=29.28 E-value=52 Score=20.53 Aligned_cols=30 Identities=3% Similarity=-0.038 Sum_probs=22.8
Q ss_pred ccCCCCCeEEEEeCchHHHHHHHHHHHhcC
Q 042232 81 KKAPSNGRVMLIDGTSIIYRAYYKILLHHG 110 (144)
Q Consensus 81 ~~~~s~grimLiDGtsiiyRaYyKlllhhg 110 (144)
.....+.||++||.....-...-++|...|
T Consensus 15 ~~~~~~~~ilivdd~~~~~~~l~~~L~~~g 44 (146)
T 4dad_A 15 LYFQGMINILVASEDASRLAHLARLVGDAG 44 (146)
T ss_dssp CCCGGGCEEEEECSCHHHHHHHHHHHHHHC
T ss_pred CCcCCCCeEEEEeCCHHHHHHHHHHHhhCC
Confidence 345567899999999987777666776666
No 20
>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}
Probab=25.62 E-value=1e+02 Score=17.68 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=19.6
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
+.|+++||.....-...-+.+...|.
T Consensus 1 ~~~iliv~~~~~~~~~l~~~l~~~g~ 26 (119)
T 2j48_A 1 AGHILLLEEEDEAATVVCEMLTAAGF 26 (119)
T ss_dssp CCEEEEECCCHHHHHHHHHHHHHTTC
T ss_pred CCEEEEEeCCHHHHHHHHHHHHhCCc
Confidence 35899999998887777777765554
No 21
>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}
Probab=24.28 E-value=1e+02 Score=18.69 Aligned_cols=29 Identities=10% Similarity=0.076 Sum_probs=20.9
Q ss_pred CCCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 83 APSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 83 ~~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
...+-||++||.....-...-+.|...|.
T Consensus 6 ~~~~~~iLivdd~~~~~~~l~~~L~~~g~ 34 (140)
T 3cg0_A 6 SDDLPGVLIVEDGRLAAATLRIQLESLGY 34 (140)
T ss_dssp --CCCEEEEECCBHHHHHHHHHHHHHHTC
T ss_pred CCCCceEEEEECCHHHHHHHHHHHHHCCC
Confidence 34567999999999887777777755554
No 22
>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1
Probab=23.93 E-value=1.2e+02 Score=18.52 Aligned_cols=28 Identities=7% Similarity=0.347 Sum_probs=22.4
Q ss_pred CCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 84 PSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 84 ~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
.++.||++||.....-+..-++|...|.
T Consensus 4 ~~~~~iLivdd~~~~~~~l~~~L~~~g~ 31 (149)
T 1k66_A 4 NATQPLLVVEDSDEDFSTFQRLLQREGV 31 (149)
T ss_dssp CTTSCEEEECCCHHHHHHHHHHHHHTTB
T ss_pred CCCccEEEEECCHHHHHHHHHHHHHcCC
Confidence 4567899999999888777777777665
No 23
>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}
Probab=21.54 E-value=99 Score=19.44 Aligned_cols=31 Identities=19% Similarity=0.292 Sum_probs=22.3
Q ss_pred cCCCCCeEEEEeCchHHHHHHHHHHHhcCCc
Q 042232 82 KAPSNGRVMLIDGTSIIYRAYYKILLHHGHL 112 (144)
Q Consensus 82 ~~~s~grimLiDGtsiiyRaYyKlllhhg~l 112 (144)
....+.||++||.....-...-++|...|..
T Consensus 11 ~~~~~~~iLivdd~~~~~~~l~~~L~~~~~~ 41 (152)
T 3eul_A 11 PQPEKVRVVVGDDHPLFREGVVRALSLSGSV 41 (152)
T ss_dssp ---CCEEEEEECSSHHHHHHHHHHHHHHSSE
T ss_pred CCCceEEEEEEcCCHHHHHHHHHHHhhCCCe
Confidence 3567789999999998877777777776643
No 24
>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}
Probab=20.26 E-value=1.4e+02 Score=18.30 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=20.3
Q ss_pred CCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
.+-||++||.....-+..-+.+...|.
T Consensus 3 ~~~~iLivdd~~~~~~~l~~~L~~~g~ 29 (142)
T 2qxy_A 3 LTPTVMVVDESRITFLAVKNALEKDGF 29 (142)
T ss_dssp CCCEEEEECSCHHHHHHHHHHHGGGTC
T ss_pred CCCeEEEEeCCHHHHHHHHHHHHhCCC
Confidence 356899999998887777777755553
No 25
>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}
Probab=20.03 E-value=1.5e+02 Score=18.09 Aligned_cols=28 Identities=29% Similarity=0.405 Sum_probs=20.8
Q ss_pred CCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 042232 84 PSNGRVMLIDGTSIIYRAYYKILLHHGH 111 (144)
Q Consensus 84 ~s~grimLiDGtsiiyRaYyKlllhhg~ 111 (144)
..+.||++||.....-...-++|...|.
T Consensus 5 ~~~~~iLivdd~~~~~~~l~~~L~~~g~ 32 (142)
T 3cg4_A 5 EHKGDVMIVDDDAHVRIAVKTILSDAGF 32 (142)
T ss_dssp -CCCEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred CCCCeEEEEcCCHHHHHHHHHHHHHCCe
Confidence 4577999999998877777777755553
Done!