Query 035227
Match_columns 70
No_of_seqs 102 out of 140
Neff 4.8
Searched_HMMs 29240
Date Mon Mar 25 16:50:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035227.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/035227hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3dgp_B RNA polymerase II trans 100.0 5.9E-38 2E-42 191.4 6.8 65 2-69 1-65 (71)
2 1ydl_A TFIIH, general transcri 100.0 7.7E-38 2.6E-42 194.2 7.3 68 3-70 11-78 (79)
3 3j21_5 50S ribosomal protein L 42.2 20 0.00067 21.3 2.5 20 29-48 18-38 (83)
4 1f46_A Cell division protein Z 41.8 15 0.00052 23.4 2.1 28 37-64 112-139 (140)
5 2q22_A Uncharacterized protein 37.4 12 0.00042 24.4 1.2 8 5-12 111-118 (139)
6 2hg7_A Phage-like element PBSX 32.4 56 0.0019 20.6 3.6 42 27-69 14-62 (110)
7 1dip_A Delta-sleep-inducing pe 30.6 18 0.00063 21.7 1.1 26 40-65 6-32 (78)
8 3pk1_B Apoptosis regulator BAX 28.2 21 0.00071 18.4 0.9 13 11-23 4-16 (34)
9 1v6f_A MGMF-beta, GLIA maturat 27.9 1E+02 0.0036 19.1 4.4 43 5-47 9-53 (151)
10 2lqo_A Putative glutaredoxin R 27.8 91 0.0031 17.9 4.8 48 10-61 36-83 (92)
11 1whv_A Poly(A)-specific ribonu 27.4 62 0.0021 20.1 3.1 35 32-66 41-75 (100)
12 3l51_A Structural maintenance 25.9 20 0.00067 22.7 0.7 27 9-40 104-130 (161)
13 2joy_A 50S ribosomal protein L 23.9 48 0.0017 19.8 2.1 20 29-48 18-38 (96)
14 3nwc_A SMC protein; structural 23.4 23 0.00079 23.4 0.7 27 9-40 113-139 (189)
15 1d3b_A Protein (small nuclear 22.2 28 0.00094 19.7 0.7 13 4-16 27-39 (75)
16 3m48_A General control protein 22.2 37 0.0013 17.3 1.1 14 52-65 4-17 (33)
17 1kd8_B GABH BLL, GCN4 acid bas 21.1 49 0.0017 17.1 1.5 16 50-65 3-18 (36)
18 3epr_A Hydrolase, haloacid deh 20.3 91 0.0031 19.9 3.1 32 31-63 5-36 (264)
No 1
>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} SCOP: d.295.1.0 PDB: 3dom_B
Probab=100.00 E-value=5.9e-38 Score=191.39 Aligned_cols=65 Identities=26% Similarity=0.560 Sum_probs=61.9
Q ss_pred ccceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCC
Q 035227 2 VNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKP 69 (70)
Q Consensus 2 v~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~ 69 (70)
+||+|||||+|||||||||++||++ +++|||+|||||||||+++++++||++|+++|++|+|+||
T Consensus 1 ~~A~kGvLi~CDpa~Kq~il~lde~---~~~FIIedLDdtHl~V~~~~v~~lk~~l~~~l~~n~~~~~ 65 (71)
T 3dgp_B 1 ARARKGALVQCDPSIKALILQIDAK---MSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPM 65 (71)
T ss_dssp CEEEEEEEEECCHHHHHHHHHHHHH---HCSSEEEEEETTEEEECGGGHHHHHHHHHHHHHSCSCC--
T ss_pred CCceeEEEEEcCHHHHHHHHHHcCC---CCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCCc
Confidence 6999999999999999999999997 8999999999999999999999999999999999999998
No 2
>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A
Probab=100.00 E-value=7.7e-38 Score=194.18 Aligned_cols=68 Identities=32% Similarity=0.640 Sum_probs=66.3
Q ss_pred cceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCCC
Q 035227 3 NAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA 70 (70)
Q Consensus 3 ~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~~ 70 (70)
||+|||||+|||||||||++|||++|++++|||+|||||||||+++++++||+||+++|++|+|++++
T Consensus 11 ~~~kGvLI~CDpa~Kq~Il~lde~~~~~~kFIIedLDdtHLfV~~~~v~~lk~~l~~~ld~ns~~~~~ 78 (79)
T 1ydl_A 11 GTRKGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQ 78 (79)
T ss_dssp CCCCCEEEECCHHHHHHHHHHHHTTTTSSCCEEEECSSSEEEECTTHHHHHHHHHHHTSCCCTTTTTT
T ss_pred ccccceEEEeCHHHHHHHHHHhccCCcCCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCccc
Confidence 79999999999999999999999999999999999999999999999999999999999999999863
No 3
>3j21_5 50S ribosomal protein L14E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=42.15 E-value=20 Score=21.27 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=15.5
Q ss_pred CCCCeEEEe-ccCceeEEccc
Q 035227 29 QSQKFIIHI-LDSTHLFVQPN 48 (70)
Q Consensus 29 ~~~~FIIed-LDdthlfV~~~ 48 (70)
.|+.++|-+ +|+.|++|.-.
T Consensus 18 ~Gk~~vIv~iiD~~~vlV~g~ 38 (83)
T 3j21_5 18 AGQKVVVVDIIDKNFVLVTGA 38 (83)
T ss_dssp SCCCEEEEEECSSSCEEEECC
T ss_pred CCCEEEEEEEcCCCEEEEECC
Confidence 467777777 69999999654
No 4
>1f46_A Cell division protein ZIPA; transmembrane, inner membrane, cell cycle; 1.50A {Escherichia coli} SCOP: d.129.4.1 PDB: 1f47_B 1s1j_A* 1s1s_A* 1y2g_A* 1f7w_A 1f7x_A 1y2f_A*
Probab=41.80 E-value=15 Score=23.42 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=25.9
Q ss_pred eccCceeEEccchHHHHHHHHHHHHHhc
Q 035227 37 ILDSTHLFVQPNMAEMIRSAIAEFRDQN 64 (70)
Q Consensus 37 dLDdthlfV~~~~v~~lk~~l~~~l~~n 64 (70)
-+||.+-...+..++.++++|.++.++|
T Consensus 112 llDd~r~~lt~~~~~~ir~~l~~~~~~~ 139 (140)
T 1f46_A 112 VLDDQRRMMTPQKLREYQDIIREVKDAN 139 (140)
T ss_dssp EECTTSCBCCHHHHHHHHHHHHHHHHHT
T ss_pred EECCCCCCCCHHHHHHHHHHHHHHHHhc
Confidence 4799999999999999999999998877
No 5
>2q22_A Uncharacterized protein; YP_323524.1, structural genomics, J center for structural genomics, JCSG, protein structure INI PSI-2; HET: PG4; 2.11A {Anabaena variabilis atcc 29413} SCOP: d.365.1.1
Probab=37.35 E-value=12 Score=24.43 Aligned_cols=8 Identities=38% Similarity=1.153 Sum_probs=7.2
Q ss_pred eeeeEEee
Q 035227 5 IKGLFISC 12 (70)
Q Consensus 5 ~kGvLi~C 12 (70)
.+||||+|
T Consensus 111 ~rGVLisc 118 (139)
T 2q22_A 111 HRGVLVSC 118 (139)
T ss_dssp CBEEEEEE
T ss_pred ccEEEEec
Confidence 58999999
No 6
>2hg7_A Phage-like element PBSX protein XKDW; dimer, GFT structural genomics, PSI, protein structure initiative; NMR {Bacillus subtilis} SCOP: d.186.2.1
Probab=32.36 E-value=56 Score=20.60 Aligned_cols=42 Identities=12% Similarity=0.206 Sum_probs=27.8
Q ss_pred CCCCCCeEEEeccCceeEE-------ccchHHHHHHHHHHHHHhcCCCCC
Q 035227 27 MPQSQKFIIHILDSTHLFV-------QPNMAEMIRSAIAEFRDQNSYEKP 69 (70)
Q Consensus 27 ~~~~~~FIIedLDdthlfV-------~~~~v~~lk~~l~~~l~~n~~~~~ 69 (70)
...+++|||++=.|. =+| .-.--+.|++--+++++.-.|+||
T Consensus 14 A~p~kDFilqnDGdG-sYI~eW~l~AP~PT~~eL~~wwee~q~np~yepP 62 (110)
T 2hg7_A 14 AVSRKDFELRNDGNG-SYIEKWNLRAPLPTQAELETWWEELQKNPPYEPP 62 (110)
T ss_dssp CCBTTTEEEEECSSC-EEEEEECSSSCCCCHHHHHHHHHHHHHSCCCC--
T ss_pred CCcccceeEeeCCCc-chHHhhccCCCCCCHHHHHHHHHHHHhCCCCCCc
Confidence 346889999996554 333 233456778877777777789988
No 7
>1dip_A Delta-sleep-inducing peptide immunoreactive peptide; structure, leucine zipper, PIG, acetylation; NMR {Sus scrofa} SCOP: h.1.12.1
Probab=30.62 E-value=18 Score=21.71 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=19.3
Q ss_pred CceeE-EccchHHHHHHHHHHHHHhcC
Q 035227 40 STHLF-VQPNMAEMIRSAIAEFRDQNS 65 (70)
Q Consensus 40 dthlf-V~~~~v~~lk~~l~~~l~~n~ 65 (70)
.|||. .=.+-|+.||+++.++.++|+
T Consensus 6 KtHLm~AVREEVevLKe~I~EL~e~~~ 32 (78)
T 1dip_A 6 KNHLMYAVREEVEILKEQIRELVEKNS 32 (78)
T ss_dssp TTGGGGTCTTSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45543 345678999999999998874
No 8
>3pk1_B Apoptosis regulator BAX; BCL-2 family fold, regulation of apoptosis, mitochondri apoptosis-apoptosis regulator complex; 2.49A {Homo sapiens} PDB: 3pl7_C 2xa0_C
Probab=28.18 E-value=21 Score=18.39 Aligned_cols=13 Identities=8% Similarity=0.036 Sum_probs=6.9
Q ss_pred eeCHHHHHHHHHh
Q 035227 11 SCDIPMAQFIINM 23 (70)
Q Consensus 11 ~CDpaiKq~il~l 23 (70)
-|||.+|...-.|
T Consensus 4 ~~Dp~~K~l~~cL 16 (34)
T 3pk1_B 4 PQDASTKKLSECL 16 (34)
T ss_dssp ---CTHHHHHHHH
T ss_pred CCCccHHHHHHHH
Confidence 4788888766554
No 9
>1v6f_A MGMF-beta, GLIA maturation factor, beta; actin binding protein, cytoskeleton, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.109.1.2
Probab=27.89 E-value=1e+02 Score=19.09 Aligned_cols=43 Identities=7% Similarity=0.023 Sum_probs=32.4
Q ss_pred eeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccC--ceeEEcc
Q 035227 5 IKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDS--THLFVQP 47 (70)
Q Consensus 5 ~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDd--thlfV~~ 47 (70)
..|+.+..++.+++-+..+-.......+|||=-+|+ +.+.+..
T Consensus 9 ~~~~~~~v~~e~~~a~~~lr~~k~~~~~~iifki~~~~~~I~v~~ 53 (151)
T 1v6f_A 9 ESLVVCDVAEDLVEKLRKFRFRKETHNAAIIMKIDKDERLVVLDE 53 (151)
T ss_dssp CCCCCCEECHHHHHHHHHHHTCCCSSCEEEEEEECSSSCEEEEEE
T ss_pred CCceEEEECHHHHHHHHHHHhccCCCccEEEEEEcCCCcEEEEEe
Confidence 468999999999999988866422246899999986 4566654
No 10
>2lqo_A Putative glutaredoxin RV3198.1/MT3292; TRX fold, oxidoreductase; NMR {Mycobacterium tuberculosis}
Probab=27.78 E-value=91 Score=17.90 Aligned_cols=48 Identities=10% Similarity=0.252 Sum_probs=29.8
Q ss_pred EeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHH
Q 035227 10 ISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFR 61 (70)
Q Consensus 10 i~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l 61 (70)
|+-||..++.+..++.-.. +=.-|+ ++|.+.++.++. +.|+++|+++.
T Consensus 36 i~~d~~~~~~~~~~~~G~~-tVP~I~--i~Dg~~l~~~~~-~el~~~L~el~ 83 (92)
T 2lqo_A 36 IEHNRAAAEFVGSVNGGNR-TVPTVK--FADGSTLTNPSA-DEVKAKLVKIA 83 (92)
T ss_dssp TTTCHHHHHHHHHHSSSSS-CSCEEE--ETTSCEEESCCH-HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHcCCCC-EeCEEE--EeCCEEEeCCCH-HHHHHHHHHhc
Confidence 4458999999988854110 112222 366777888764 45778887764
No 11
>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*
Probab=27.37 E-value=62 Score=20.09 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=24.3
Q ss_pred CeEEEeccCceeEEccchHHHHHHHHHHHHHhcCC
Q 035227 32 KFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSY 66 (70)
Q Consensus 32 ~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~ 66 (70)
.|.|.=+||||.||--.--+..+.-+.-+....+|
T Consensus 41 gv~I~WidDTsAlvvf~~~~~a~~al~~i~k~~~y 75 (100)
T 1whv_A 41 NIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESY 75 (100)
T ss_dssp SCCCEEEETTEEEEECSCHHHHHHHHHHHHHCCSS
T ss_pred CEEEEEEcCCeEEEEecCHHHHHHHHHhcccCCce
Confidence 78999999999999766666665555544433333
No 12
>3l51_A Structural maintenance of chromosomes protein 2; structural maintenance of chromosomes (SMC), hinge domain, C cycle, cell division, cytoplasm; 1.51A {Mus musculus}
Probab=25.90 E-value=20 Score=22.67 Aligned_cols=27 Identities=7% Similarity=0.167 Sum_probs=19.9
Q ss_pred EEeeCHHHHHHHHHhhcCCCCCCCeEEEeccC
Q 035227 9 FISCDIPMAQFIINMNASMPQSQKFIIHILDS 40 (70)
Q Consensus 9 Li~CDpaiKq~il~lde~~~~~~~FIIedLDd 40 (70)
||+||+..+..+.++ .++-+|.+|||.
T Consensus 104 lv~~d~~~~~a~~~l-----lg~tlv~~dl~~ 130 (161)
T 3l51_A 104 LVDYKPELQKGMEFV-----FGTTFVCNNMDN 130 (161)
T ss_dssp GEECCGGGHHHHHHH-----HTTCEEESSHHH
T ss_pred HhcCCHHHHHHHHHH-----cCCEEEECCHHH
Confidence 688999888777666 355578887775
No 13
>2joy_A 50S ribosomal protein L14E; protein solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: b.34.5.7 PDB: 2kds_A
Probab=23.87 E-value=48 Score=19.82 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=13.6
Q ss_pred CCCCeEEEe-ccCceeEEccc
Q 035227 29 QSQKFIIHI-LDSTHLFVQPN 48 (70)
Q Consensus 29 ~~~~FIIed-LDdthlfV~~~ 48 (70)
.|+.++|-+ +|+.|++|.--
T Consensus 18 ~Gk~~VIv~~iD~~~vLV~gp 38 (96)
T 2joy_A 18 AGSKCVIVDIIDDNFVLVTGP 38 (96)
T ss_dssp TCCEEEEEEECSSSCEEEECC
T ss_pred CCCEEEEEEEeCCCEEEEECC
Confidence 356665555 59999998543
No 14
>3nwc_A SMC protein; structural maintenance of chromosomes (SMC), SMC hinge domai dimerization, DNA binding, cell cycle; 1.70A {Pyrococcus furiosus}
Probab=23.44 E-value=23 Score=23.35 Aligned_cols=27 Identities=11% Similarity=0.202 Sum_probs=20.9
Q ss_pred EEeeCHHHHHHHHHhhcCCCCCCCeEEEeccC
Q 035227 9 FISCDIPMAQFIINMNASMPQSQKFIIHILDS 40 (70)
Q Consensus 9 Li~CDpaiKq~il~lde~~~~~~~FIIedLDd 40 (70)
||+||+.....+.++ .++-+|++|||+
T Consensus 113 lv~~d~~~~~a~~~l-----lg~tlvv~dl~~ 139 (189)
T 3nwc_A 113 VIEYDQKIENAVKFA-----LGDTVIVNSMEE 139 (189)
T ss_dssp GEECCGGGHHHHHHH-----HTTEEEESCSGG
T ss_pred eeccCHHHHHHHHHH-----hCCEEEECCHHH
Confidence 789999887777666 356688888886
No 15
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1
Probab=22.21 E-value=28 Score=19.68 Aligned_cols=13 Identities=23% Similarity=0.401 Sum_probs=10.7
Q ss_pred ceeeeEEeeCHHH
Q 035227 4 AIKGLFISCDIPM 16 (70)
Q Consensus 4 a~kGvLi~CDpai 16 (70)
..+|.|..||+-|
T Consensus 27 ~~~G~L~~~D~~M 39 (75)
T 1d3b_A 27 VYRGKLIEAEDNM 39 (75)
T ss_dssp EEEEEEEEECTTC
T ss_pred EEEEEEEEEccce
Confidence 5789999999765
No 16
>3m48_A General control protein GCN4; leucine zipper, synthetic peptide, alpha helix, activa amino-acid biosynthesis, DNA-binding, nucleus; 1.45A {Synthetic} PDB: 3i1g_A 2ahp_A* 2o7h_A
Probab=22.20 E-value=37 Score=17.33 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHhcC
Q 035227 52 MIRSAIAEFRDQNS 65 (70)
Q Consensus 52 ~lk~~l~~~l~~n~ 65 (70)
.|..++++++.+|+
T Consensus 4 QLE~kVEeLl~~n~ 17 (33)
T 3m48_A 4 QLEAKVEELLSKNW 17 (33)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhH
Confidence 46778888887764
No 17
>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B
Probab=21.06 E-value=49 Score=17.14 Aligned_cols=16 Identities=6% Similarity=0.285 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHhcC
Q 035227 50 AEMIRSAIAEFRDQNS 65 (70)
Q Consensus 50 v~~lk~~l~~~l~~n~ 65 (70)
...|+++|++++.+|+
T Consensus 3 MnQLE~KVEeLl~~~~ 18 (36)
T 1kd8_B 3 VKQLKAKVEELKSKLW 18 (36)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHhH
Confidence 3456777777776653
No 18
>3epr_A Hydrolase, haloacid dehalogenase-like family; structural genomics, unknown function, HAD superfamily hydro PSI-2; 1.55A {Streptococcus agalactiae serogroup V} SCOP: c.108.1.14 PDB: 1ys9_A 1wvi_A 1ydf_A
Probab=20.30 E-value=91 Score=19.93 Aligned_cols=32 Identities=16% Similarity=0.120 Sum_probs=21.1
Q ss_pred CCeEEEeccCceeEEccchHHHHHHHHHHHHHh
Q 035227 31 QKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQ 63 (70)
Q Consensus 31 ~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~ 63 (70)
-|.|+-|||.| |+-....+..-++.|.++.++
T Consensus 5 ~kli~~DlDGT-Ll~~~~~i~~~~eal~~l~~~ 36 (264)
T 3epr_A 5 YKGYLIDLDGT-IYKGKSRIPAGERFIERLQEK 36 (264)
T ss_dssp CCEEEECCBTT-TEETTEECHHHHHHHHHHHHH
T ss_pred CCEEEEeCCCc-eEeCCEECcCHHHHHHHHHHC
Confidence 56899999988 655555555555666665554
Done!