Query 029063
Match_columns 199
No_of_seqs 174 out of 289
Neff 4.8
Searched_HMMs 29240
Date Mon Mar 25 10:59:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029063.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/029063hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2h9u_A DNA/RNA-binding protein 99.7 6.3E-17 2.2E-21 123.8 5.9 60 1-66 40-101 (102)
2 3toe_A MTH10B, DNA/RNA-binding 99.5 2.5E-14 8.5E-19 107.6 7.0 55 1-63 37-91 (91)
3 1nfj_A ALBA, conserved hypothe 99.5 2E-14 6.9E-19 107.3 6.0 52 1-62 36-89 (89)
4 1nh9_A MJA10B, DNA-binding pro 99.5 1.8E-14 6.1E-19 107.2 5.1 52 1-62 34-87 (87)
5 2bky_A DNA/RNA-binding protein 99.5 5.9E-14 2E-18 106.4 5.8 53 1-63 42-97 (97)
6 2bky_X DNA/RNA-binding protein 99.3 1.5E-12 5.3E-17 97.3 4.9 50 1-63 39-88 (89)
7 1vm0_A Unknown protein; struct 98.9 6.7E-10 2.3E-14 88.3 5.1 53 1-64 54-108 (130)
8 3iab_B Ribonucleases P/MRP pro 97.9 2.4E-05 8.1E-10 62.8 6.5 60 1-61 68-139 (140)
9 3iab_A Ribonucleases P/MRP pro 97.3 0.00037 1.3E-08 56.8 6.5 58 2-64 85-146 (158)
10 1b34_A Protein (small nuclear 91.9 0.03 1E-06 43.0 0.0 7 52-58 54-60 (119)
11 2k9u_B Filamin-binding LIM pro 59.0 6.2 0.00021 22.8 2.1 19 49-67 6-24 (26)
12 2ntx_A EMB|CAB41934.1, prone8; 42.9 4.3 0.00015 36.6 -0.5 29 5-34 292-320 (365)
13 2ee7_A Sperm flagellar protein 28.2 23 0.00079 27.2 1.6 38 4-41 39-80 (127)
No 1
>2h9u_A DNA/RNA-binding protein ALBA 2; archaea, DNA binding protein, structural G NPPSFA, national project on protein structural and function analyses; 2.00A {Aeropyrum pernix} PDB: 3u6y_A*
Probab=99.66 E-value=6.3e-17 Score=123.82 Aligned_cols=60 Identities=33% Similarity=0.464 Sum_probs=53.4
Q ss_pred CchhhHHHHHHHHHHHHhh-cCCc-cceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCCCC
Q 029063 1 MGRAINKTVMIAELIKRRI-AGLH-QNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKDLD 66 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi-~gLh-Q~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~elD 66 (199)
||+||+|||+||||||+|| ++|| |.++|++.++.|+|+ +|++ ++|+||+|+|+|+++|..
T Consensus 40 ~G~AIskAV~vaEilk~r~~~gl~~q~i~i~s~~i~d~~e---~g~~---~~r~vS~IeI~Lsk~~~~ 101 (102)
T 2h9u_A 40 RGRNINRAVDAVEIVRKRFAKNIEIKDIKIDSQEIEVQTP---EGQT---RTRRVSSIEICLEKAGES 101 (102)
T ss_dssp ETTHHHHHHHHHHHHHHHTTTTEEEEEEEEEEEEEEEECT---TSCE---EEEEEEEEEEEEEECSSC
T ss_pred echhhhHHHHHHHHHHHhccCCceEEEEEEeeEEEecccc---CCcc---ceeEeeeEEEEEEccCCC
Confidence 6999999999999999999 8999 999999999998864 4432 789999999999998753
No 2
>3toe_A MTH10B, DNA/RNA-binding protein ALBA; SAC10B family, alpha/beta mixed, homodimer, unknown function; 2.20A {Methanothermobacter thermautotrophicusorganism_taxid}
Probab=99.51 E-value=2.5e-14 Score=107.59 Aligned_cols=55 Identities=35% Similarity=0.437 Sum_probs=50.1
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKK 63 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~ 63 (199)
||+||||||+||||||+|| |. .++|++++|.++|.+.++| .+++||+|+|+|+++
T Consensus 37 ~G~aIskAVdvaei~k~R~--~~-~v~v~~I~I~se~~~~e~G-----~~r~VS~IeI~L~k~ 91 (91)
T 3toe_A 37 RGIAISRAVDVAEIVRNRF--IP-DIQIENIDICTEEIIGNEG-----TATNVSAIEIQLRKD 91 (91)
T ss_dssp ETTHHHHHHHHHHHHHHHT--CT-TCEEEEEEEEEEEEECTTS-----SEEEEEEEEEEEEC-
T ss_pred ehhHHHHHHHHHHHHHHhc--cC-CcEEEEEEeeeEEeecCCC-----ceeEeeEEEEEEECC
Confidence 6999999999999999999 54 4889999999999999987 899999999999974
No 3
>1nfj_A ALBA, conserved hypothetical protein AF1956; SIR2, HDAC, gene regulation, transcription; 2.00A {Archaeoglobus fulgidus} SCOP: d.68.6.1 PDB: 1nfh_A 2z7c_A*
Probab=99.50 E-value=2e-14 Score=107.34 Aligned_cols=52 Identities=35% Similarity=0.645 Sum_probs=45.8
Q ss_pred CchhhHHHHHHHHHHHHhh-cCCc-cceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccC
Q 029063 1 MGRAINKTVMIAELIKRRI-AGLH-QNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSK 62 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi-~gLh-Q~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk 62 (199)
||+||+|||+||||||+|| ++|| |.++|++.++.+ ++| .+|+||+|+|+|++
T Consensus 36 ~G~AIskAV~vaeilk~r~~~gl~i~~i~i~s~~i~~-----e~g-----~~r~vs~IeI~L~k 89 (89)
T 1nfj_A 36 RGRAISRAVDVAEIVRNRFMPGVKVKEIKIDTEELES-----EQG-----RRSNVSTIEIVLAK 89 (89)
T ss_dssp ETTHHHHHHHHHHHHHHHTCTTCEEEEEEEEEEECCC-----BTT-----BCCEEEEEEEEEEC
T ss_pred ecHHHHHHHHHHHHHHHhccCCcEEEEEEEeEEEEEc-----CCC-----cEEEeeEEEEEEEC
Confidence 6999999999999999999 8999 888888887654 454 78999999999985
No 4
>1nh9_A MJA10B, DNA-binding protein ALBA; 2.00A {Methanocaldococcus jannaschii} SCOP: d.68.6.1
Probab=99.49 E-value=1.8e-14 Score=107.21 Aligned_cols=52 Identities=37% Similarity=0.632 Sum_probs=42.1
Q ss_pred CchhhHHHHHHHHHHHHhh-cCCc-cceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccC
Q 029063 1 MGRAINKTVMIAELIKRRI-AGLH-QNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSK 62 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi-~gLh-Q~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk 62 (199)
||+||+|||+||||||+|| ++|| |.++|++.++.+ ++| .+|+||+|+|+|++
T Consensus 34 ~G~AIskAV~vaeilk~r~~~~l~v~~i~i~s~~i~~-----e~g-----~~r~vS~IeI~L~k 87 (87)
T 1nh9_A 34 RGKAINKAVDVAEMIRNRFIKDIKIKKIEIGTDKVKN-----PDG-----REVNVSTIEIVLAK 87 (87)
T ss_dssp EGGGHHHHHHHHHHHHHHTCTTCEEEEEEEEEEC-----------------CCCEEEEEEEEEC
T ss_pred echHHHHHHHHHHHHHHhccCCeEEEEEEEeEEEEEc-----CCC-----cEEEeeEEEEEEEC
Confidence 6999999999999999999 7899 999999988776 344 78899999999985
No 5
>2bky_A DNA/RNA-binding protein ALBA 1; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 1h0x_A* 1h0y_A* 1y9x_A
Probab=99.46 E-value=5.9e-14 Score=106.42 Aligned_cols=53 Identities=34% Similarity=0.548 Sum_probs=46.7
Q ss_pred CchhhHHHHHHHHHHHHhhcC--C-ccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCC
Q 029063 1 MGRAINKTVMIAELIKRRIAG--L-HQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKK 63 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~g--L-hQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~ 63 (199)
+|+||+|||+||||||+||.+ | ||.++|++.++.+ ++| .+|+||+|+|+|+++
T Consensus 42 ~G~AIskAV~vaeilk~r~~~~~l~~~~i~i~s~~i~~-----e~G-----~~r~vS~IeI~L~k~ 97 (97)
T 2bky_A 42 RGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTS-----QDG-----RQSRVSTIEIAIRKK 97 (97)
T ss_dssp ETTHHHHHHHHHHHHHHHTSTTTEEEEEEEEEEEEEEE-----TTS-----CEEEEEEEEEEEEEC
T ss_pred echHHHHHHHHHHHHHHhccCCceEEEEEEeeeEEEec-----CCC-----cEEEeeEEEEEEEcC
Confidence 699999999999999999955 8 7999999998876 444 789999999999974
No 6
>2bky_X DNA/RNA-binding protein ALBA 2; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 2a2y_A 1udv_A
Probab=99.30 E-value=1.5e-12 Score=97.31 Aligned_cols=50 Identities=24% Similarity=0.313 Sum_probs=39.8
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKK 63 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~ 63 (199)
||+||+|||+||||||+||.+++| |.+++|..+ + ..+|+||+|+|+|+++
T Consensus 39 ~G~aIskAVdvaeilk~R~~~~~~---i~~i~i~se-----~-----~~~r~VS~IeI~L~k~ 88 (89)
T 2bky_X 39 TGREISKAVDVYNSLKDRLGDGVQ---LVNVQTGSE-----V-----RDRRRISYILLRLKRV 88 (89)
T ss_dssp ETTHHHHHHHHHHHHHHHHGGGEE---EEEEEEEEE-----E-----ETTEEEEEEEEEEEEC
T ss_pred echHHHHHHHHHHHHHHhccCceE---EEEEEeccc-----c-----CcceEeeeEEEEEEec
Confidence 699999999999999999977655 555555432 1 3689999999999974
No 7
>1vm0_A Unknown protein; structural genomics, protein structure initiative, CESG, AT2 unknown function, nitrate; 1.80A {Arabidopsis thaliana} SCOP: d.68.6.2 PDB: 2q3v_A
Probab=98.94 E-value=6.7e-10 Score=88.26 Aligned_cols=53 Identities=28% Similarity=0.363 Sum_probs=36.8
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceee--EEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCC
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSI--GSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKD 64 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i--~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~e 64 (199)
||+||+|||+||||||+|+ |+++++| ++.++.+. .+ ....+||.|+|+|++.+
T Consensus 54 ~G~AIskAV~VAEiLkrr~--l~~ikkI~t~t~~i~~~-----~~----~r~v~~skIEI~L~k~~ 108 (130)
T 1vm0_A 54 LGMAIATVVTVTEILKNNG--FAVEKKIMTSIVDIKDD-----AR----GRPVQKAKIEITLVKSE 108 (130)
T ss_dssp EGGGHHHHHHHHHHHHHTT--SEEEEEEEEEEEEEC---------------CEEEEEEEEEEEECT
T ss_pred chHHHHHHHHHHHHHHhcC--cceEEEEEeeeEEeccC-----CC----CcccccceEEEEEEecC
Confidence 6999999999999999998 6665544 33333321 11 14456799999999865
No 8
>3iab_B Ribonucleases P/MRP protein subunit POP7; RNAse P, ribonuclease P, ribonuclease MRP, POP6, POP6P, POP7, POP7P, NME1, yeast, tRNA; 2.70A {Saccharomyces cerevisiae}
Probab=97.88 E-value=2.4e-05 Score=62.80 Aligned_cols=60 Identities=15% Similarity=0.147 Sum_probs=44.7
Q ss_pred CchhhHHHHHHHHHHHHhhcCCccceeeEEEeccceeeeCCCC------------CCCCceeeeeeEEEEEcc
Q 029063 1 MGRAINKTVMIAELIKRRIAGLHQNTSIGSTDITDMWEPLEEG------------LLPLETTRHVSMITITLS 61 (199)
Q Consensus 1 mG~AIsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~d~wEP~eEG------------L~~le~tR~Vs~I~ItLS 61 (199)
||+||.||++||-.|..+. +|.-....+++.+.|..+|.++- .++...+|+||+|+|-+.
T Consensus 68 mGkAIeKal~lAl~fq~~~-~~~V~V~T~TV~vvDd~~~~~~~~~~~d~~~~d~d~e~~~rkR~vS~VeirIy 139 (140)
T 3iab_B 68 MGKAVEKTLALGCHFQDQK-NKKIEVYTKTIEVLDEVITEGQADIDMESDVEDDDKETQLKKRAVSGVELRIY 139 (140)
T ss_dssp EGGGHHHHHHHHHHHHHTT-CCCEEEEEEEEEEEEECC--------------------CEEEEEEEEEEEEEE
T ss_pred chHHHHHHHHHHHHHhhcC-CEEEEEEeceEEEEEeeeecCCcccccccccccccccchheeeeeeeEEEEEe
Confidence 7999999999999999874 57666778888888888776653 456778999999999864
No 9
>3iab_A Ribonucleases P/MRP protein subunit POP6; RNAse P, ribonuclease P, ribonuclease MRP, POP6, POP6P, POP7, POP7P, NME1, yeast, tRNA; 2.70A {Saccharomyces cerevisiae}
Probab=97.35 E-value=0.00037 Score=56.77 Aligned_cols=58 Identities=22% Similarity=0.236 Sum_probs=43.6
Q ss_pred chhhHHHHHHHHHHHHhhc----CCccceeeEEEeccceeeeCCCCCCCCceeeeeeEEEEEccCCC
Q 029063 2 GRAINKTVMIAELIKRRIA----GLHQNTSIGSTDITDMWEPLEEGLLPLETTRHVSMITITLSKKD 64 (199)
Q Consensus 2 G~AIsKAV~vAEIlKrRi~----gLhQ~t~i~~~~i~d~wEP~eEGL~~le~tR~Vs~I~ItLSk~e 64 (199)
|..|.|+++|.||+|+.+. .|||++++.+.....+ ..+ +.++.+.+||.+-+.+++++
T Consensus 85 g~hIQKmLSIvEI~Kk~~~~~~~~l~Q~NkL~~f~~v~~---grN--ELle~r~~vPILi~~i~~~~ 146 (158)
T 3iab_A 85 GPHIQKMLSILEIFKKGYIKNNKKIYQWNKLTSFDIKRE---GRN--ELQEERLKVPILVTMVSDSE 146 (158)
T ss_dssp GGGHHHHHHHHHHHHHHHHTTTCCCEEEEEEEEEEEC------------CCCCEEEEEEEEEEESSS
T ss_pred ChHHHHHHHHHHHHHHHhhcCCccHHHHhhhhhhccCCc---ccc--HHHHhhcCCCEEEEEEeccc
Confidence 7889999999999999872 4999999998754332 111 45667788999998888876
No 10
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A
Probab=91.90 E-value=0.03 Score=42.98 Aligned_cols=7 Identities=14% Similarity=0.520 Sum_probs=2.7
Q ss_pred eeeEEEE
Q 029063 52 HVSMITI 58 (199)
Q Consensus 52 ~Vs~I~I 58 (199)
++..|.|
T Consensus 54 ~lg~v~I 60 (119)
T 1b34_A 54 QLETLSI 60 (119)
T ss_dssp EEEEEEE
T ss_pred EcceEEE
Confidence 3344433
No 11
>2k9u_B Filamin-binding LIM protein 1; cytoskeletal complex, alternative splicing, cell adhesion, cell junction, cell shape, cytoplasm, cytoskeleton; NMR {Homo sapiens}
Probab=58.96 E-value=6.2 Score=22.84 Aligned_cols=19 Identities=32% Similarity=0.301 Sum_probs=14.6
Q ss_pred eeeeeeEEEEEccCCCCCC
Q 029063 49 TTRHVSMITITLSKKDLDT 67 (199)
Q Consensus 49 ~tR~Vs~I~ItLSk~elD~ 67 (199)
.+|-+|+|+|||...-.|+
T Consensus 6 eKR~aSSvFITLapp~r~~ 24 (26)
T 2k9u_B 6 EKRVASSVFITLAPPRRDV 24 (26)
T ss_dssp SSSCEEEEEEEECCSSCCC
T ss_pred hhheeeeEEEEecCccccc
Confidence 5678999999998755443
No 12
>2ntx_A EMB|CAB41934.1, prone8; dimer, guanine nucleotide exchange factor, signaling protein; HET: MSE; 2.20A {Arabidopsis thaliana} PDB: 2nty_A* 2wbl_A
Probab=42.90 E-value=4.3 Score=36.60 Aligned_cols=29 Identities=28% Similarity=0.442 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHHhhcCCccceeeEEEecc
Q 029063 5 INKTVMIAELIKRRIAGLHQNTSIGSTDIT 34 (199)
Q Consensus 5 IsKAV~vAEIlKrRi~gLhQ~t~i~~~~i~ 34 (199)
+.+|=++--+||+|||+|.| |.|...+|+
T Consensus 292 ~eRAEtlL~~LKqRfPglpQ-TsLD~sKIQ 320 (365)
T 2ntx_A 292 EERAETILVLLKQKFPGLPQ-SSLDISKIQ 320 (365)
T ss_dssp HHHHHHHHHHHHHHCTTCCC-CHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCc-hHHHHHHHH
Confidence 34566777789999999999 556555553
No 13
>2ee7_A Sperm flagellar protein 1; all alpha protein, CH domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=28.22 E-value=23 Score=27.24 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=26.8
Q ss_pred hhHHHHHHHHHHHHhhcC---CccceeeEEEec-cceeeeCC
Q 029063 4 AINKTVMIAELIKRRIAG---LHQNTSIGSTDI-TDMWEPLE 41 (199)
Q Consensus 4 AIsKAV~vAEIlKrRi~g---LhQ~t~i~~~~i-~d~wEP~e 41 (199)
-.|..+.|||||++=++- ||..+.-.++.. .+.|+-.+
T Consensus 39 DFSdG~lvAEIl~~y~Pk~Vdlh~y~~~~S~~~K~~NW~~ln 80 (127)
T 2ee7_A 39 DFSDGVLVAEVIKFYFPKMVEMHNYVPANSLQQKLSNWGHLN 80 (127)
T ss_dssp HHTTSHHHHHHHHHHCTTTCCCSSCCCCSSHHHHHHHHHHHH
T ss_pred hccchhHHHHHHHHHCcCcccccccCCCCcHHHHHHhHHHHH
Confidence 357789999999998764 777666555433 55686654
Done!