Query psy17954
Match_columns 143
No_of_seqs 166 out of 333
Neff 4.2
Searched_HMMs 29240
Date Fri Aug 16 18:37:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17954.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/17954hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3u5c_G RP9, S10, YS4, 40S ribo 100.0 2.9E-72 9.9E-77 461.3 4.2 135 1-143 1-188 (236)
2 2xzm_Y RPS6E; ribosome, transl 100.0 1.2E-68 4E-73 449.5 4.1 136 1-143 1-192 (293)
3 3j20_G 30S ribosomal protein S 100.0 7.2E-36 2.5E-40 226.1 6.9 88 1-90 4-109 (125)
4 3bmb_A Regulator of nucleoside 22.5 38 0.0013 24.4 1.7 19 25-43 96-114 (136)
5 2f23_A Anti-cleavage anti-GREA 19.0 47 0.0016 24.4 1.6 25 15-40 118-142 (156)
6 2wgn_B Inhibitor of cysteine p 18.5 1.2E+02 0.0043 21.8 3.8 19 6-24 51-69 (132)
7 1xao_A YDJ1, mitochondrial pro 17.0 1.2E+02 0.0041 21.2 3.4 81 2-96 12-100 (121)
8 1a62_A RHO; transcription term 11.7 1.5E+02 0.005 21.4 2.6 46 49-104 54-101 (130)
9 1grj_A GREA protein; transcrip 11.6 85 0.0029 23.1 1.3 19 25-43 128-146 (158)
10 2p4v_A Transcription elongatio 11.6 57 0.0019 24.2 0.3 19 25-43 126-144 (158)
No 1
>3u5c_G RP9, S10, YS4, 40S ribosomal protein S6-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3j16_C 3u5g_G
Probab=100.00 E-value=2.9e-72 Score=461.26 Aligned_cols=135 Identities=67% Similarity=1.119 Sum_probs=132.4
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccC--------------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQG-------------- 66 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqG-------------- 66 (143)
||||||||+|||||+||||||++|++|||++||+||+|++||+||+||+|+||||||+|||||+||
T Consensus 1 mKlnIS~P~tG~qk~iEvdde~kl~~f~gKrig~EV~gd~lG~e~kGY~~kItGGnDkqGFPMkqgVl~~~rvrlLLskG 80 (236)
T 3u5c_G 1 MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQGFPMKQGVLLPTRIKLLLTKN 80 (236)
T ss_dssp CEEEEEETTTTEEEEEECCCHHHHGGGTTCBTTCEEESGGGCSSSSSCEEEEEEEEEGGGCBBCTTCCCSSEEEEEECSS
T ss_pred CeEEEEcCCCceEEEEEeCChHHhhhhhcccccceechhccCcccCCcEEEEecccCCCCccccCCcCCCceEEEEecCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---------------------------------------CCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeEEee
Q psy17954 67 ---------------------------------------EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKR 107 (143)
Q Consensus 67 ---------------------------------------dIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yvvrr 107 (143)
|||||||+++|++|||||||+|||||||||+||||+||||+
T Consensus 81 ~~~yrprr~GERkRKsVRGciV~~~is~lNlvIVkkGek~IpgLtd~~~p~~lgPKRas~irklfnlsk~ddVr~yvvrr 160 (236)
T 3u5c_G 81 VSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRR 160 (236)
T ss_dssp BTTBCCSSTTCCEEEEEECSBCCTTEEEEEEEEEECCSSCCHHHHTCCCCCSCCCCBHHHHHHHHTCTTTSCSSSSSCCE
T ss_pred CCccCCCCCCceeeeeeeeeEecCCceeEEEEEEecCCccCccccCcccccccCCchhhhhHHHhCCCcccchhheeeee
Confidence 89999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCccccccccCCCcccccCcccccccC
Q psy17954 108 TLPPKPAKEGKKKVRKLYKAPKIQRLITPVTLQVSG 143 (143)
Q Consensus 108 ~~~~~~~k~gkk~~~~~~kapKIqrlvtp~~lq~k~ 143 (143)
|| + +|+| +++|||||||||||++||||+
T Consensus 161 ~l----~-~gkk---~~~kapKIQrlvtp~~lqrk~ 188 (236)
T 3u5c_G 161 EV----T-KGEK---TYTKAPKIQRLVTPQRLQRKR 188 (236)
T ss_dssp EE----E-CSSC---EEEECCCCBSCCCHHHHHHHH
T ss_pred ec----c-cCCC---CCCCCCCccccCCHHHHHHHH
Confidence 99 3 8999 999999999999999999974
No 2
>2xzm_Y RPS6E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Y
Probab=100.00 E-value=1.2e-68 Score=449.47 Aligned_cols=136 Identities=59% Similarity=0.978 Sum_probs=133.3
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccC--------------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQG-------------- 66 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqG-------------- 66 (143)
||||||||+||||++|||||+++++.|||++||+||+|++||+||+||+|+||||||+|||||+||
T Consensus 1 mKLnISdP~tG~qk~iEIdde~klr~f~gKrIG~EVdgd~LGeE~kGYvlkITGGnDkqGFPMkqgVl~~~RvrLLLskG 80 (293)
T 2xzm_Y 1 MKFNISYPLTGAQKCIEIDDDKKCNIFMDKKMGQEVEGDTLGDEFKGYVFKIAGGNDKDGFPMKQGVMVRGRVRLLLSEG 80 (293)
T ss_dssp CEEEEEETTTTEEEEEECCSHHHHTTTTTCCTTCEEETTSCTTTCSSCEEEEEEEEETTSCBBCTTCCCSSEEEEEECTT
T ss_pred CeEEEecCCCceEEEEEeccHHHHHHHhhccccceEcccccccccCCcEEEEecccCCCCccccCCccCCceEEEEecCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---------------------------------------CCCCCcccCCCCcCCCcchhhhhcccCCCcCCC---ceeeE
Q psy17954 67 ---------------------------------------EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDD---VRQYV 104 (143)
Q Consensus 67 ---------------------------------------dIpGltd~~vPr~lgpKRaskIRKLf~lsk~dd---v~~yv 104 (143)
+||||||+++|++|||||||+||||||||++|| ||+||
T Consensus 81 ~sgYRPrr~GERKRKSVRGciVs~disqLNlvIVkkGek~IpgLTD~~~PrrlGPKRAskIRKlFnLsKeDD~~~VrkyV 160 (293)
T 2xzm_Y 81 HSCFTSRRSGFRKRKSVRGCIVGPDMRVLALQIVKKGVAEIDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKKSV 160 (293)
T ss_dssp CSSCCCSSSCCCEEEEEECSSCCTTEEEEEEEEEECCSSCCHHHHTCCCCCCCCCCSHHHHHHHHCCCTTCCHHHHHHTS
T ss_pred CCCCCCCCCCceeeeeeeeeeecCCceeEEEEEEecCCccCccccCCcCCCCCCCchhhhhHHHhCCCcccchhhhhhhh
Confidence 899999999999999999999999999999999 99999
Q ss_pred EeecCCCCCCCCCCccccccccCCCcccccCcccccccC
Q psy17954 105 IKRTLPPKPAKEGKKKVRKLYKAPKIQRLITPVTLQVSG 143 (143)
Q Consensus 105 vrr~~~~~~~k~gkk~~~~~~kapKIqrlvtp~~lq~k~ 143 (143)
||+++ ++||+| +++|||||||||||.+||||+
T Consensus 161 irr~~----~kegkk---~~~KaPKIQRLVTp~~lqrKr 192 (293)
T 2xzm_Y 161 IRRTF----KTAKGK---DRTKCPKIQRLITPERILRKK 192 (293)
T ss_dssp CCEEE----ECTTSC---EEEECCCCTTCCCHHHHHHHH
T ss_pred eeccc----cccCCc---ccccCCCccccCCHHHHHHHH
Confidence 99999 489999 999999999999999999984
No 3
>3j20_G 30S ribosomal protein S6E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=100.00 E-value=7.2e-36 Score=226.09 Aligned_cols=88 Identities=35% Similarity=0.605 Sum_probs=76.9
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCC--------cc-cccEEEEcCccCCCCcccccCCCCCC
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGD--------EW-KGYIVRISGGNDKQGFPMKQGEIPGL 71 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~--------e~-kGY~~~ItGGnDkqGFPMkqGdIpGl 71 (143)
||||||||+|||||+||||||. +++||||+||+||+|++||+ || +||+|+||||||+|||||+| +++|.
T Consensus 4 ~Kl~Is~P~tG~qk~iEidde~-~~~f~gkrig~ev~g~~lG~~~~~~~~~e~~kGy~~~ItGG~DkqGFPMkq-gV~~~ 81 (125)
T 3j20_G 4 FKLVISDPKSGIAKQVEITGAE-TEKLIGKRIGDQIPAKELNINLNELFGKEFPEDVKLEIRGGTDKDGFPMRP-DIHGP 81 (125)
T ss_dssp EEEEEEETTTTEEEEEEECSTT-GGGTTTCCTTCEECSTTTCSSSCSSSSSCSCSCCCEEEEEEEETTCCBBCT-TCCSS
T ss_pred eEEEEEcCCCCEEEEEEcCchh-hhhhccccceeEEeeeecCcccccccccccCCCcEEEEccCcCCCCccccC-CcCCC
Confidence 8999999999999999999996 59999999999999999999 99 99999999999999999999 88774
Q ss_pred cc---------cCCCCcCCCcchhhhhc
Q psy17954 72 TD---------TTIPRRLGPKRASKIRK 90 (143)
Q Consensus 72 td---------~~vPr~lgpKRaskIRK 90 (143)
.. -..|++.|.+|...+|-
T Consensus 82 ~rvrlLLskG~gyrprr~GeRkRKsVRG 109 (125)
T 3j20_G 82 RRVRVLLSKGPGFRPKEKGERRKKTVRG 109 (125)
T ss_dssp SEEEEECCSSCSSCCCCSSCCCEEEEEC
T ss_pred ceEEEEecCCCccCCCCCCcEeeEEeec
Confidence 32 13477777777655554
No 4
>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli}
Probab=22.51 E-value=38 Score=24.36 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=13.9
Q ss_pred cccccccccceecCCccCC
Q psy17954 25 RVFYDKRMGMEVPADSIGD 43 (143)
Q Consensus 25 ~~f~gKrig~ev~g~~lG~ 43 (143)
+.++|++.||+|.-..=+-
T Consensus 96 ~ALlGk~~GD~v~v~~p~G 114 (136)
T 3bmb_A 96 AALLGLRVGDSIHWELPGG 114 (136)
T ss_dssp HHHTTCBTTCEEEEEETTT
T ss_pred HHHcCCCCCCEEEEEcCCC
Confidence 4688899999988764443
No 5
>2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus} SCOP: a.2.1.1 d.26.1.2 PDB: 2eul_A 3aoh_X* 3aoi_X* 2etn_A
Probab=18.97 E-value=47 Score=24.42 Aligned_cols=25 Identities=16% Similarity=0.243 Sum_probs=15.8
Q ss_pred EEEecCcccccccccccccceecCCc
Q psy17954 15 LVEIADEHKLRVFYDKRMGMEVPADS 40 (143)
Q Consensus 15 ~ievdde~~l~~f~gKrig~ev~g~~ 40 (143)
.|-+..+-. +.++|++.||+|.-..
T Consensus 118 ~IS~~SPlG-~ALlGk~~GD~v~~~~ 142 (156)
T 2f23_A 118 KISDASPMG-KALLGHRVGDVLSLDT 142 (156)
T ss_dssp EEETTSHHH-HHHTTCCTTCEEEEEE
T ss_pred EECCCCHHH-HHHcCCCCCCEEEEEc
Confidence 344444443 4688888888887654
No 6
>2wgn_B Inhibitor of cysteine peptidase compnd 3; hydrolase inhibitor, dynamics, peptidase inhibitor, cathepsi hydrolase inhibitor; NMR {Pseudomonas aeruginosa}
Probab=18.54 E-value=1.2e+02 Score=21.84 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=13.8
Q ss_pred ecCCCCeeEEEEecCcccc
Q psy17954 6 SYPATGCQKLVEIADEHKL 24 (143)
Q Consensus 6 S~P~tG~qk~ievdde~~l 24 (143)
++|.||.+..+...+...|
T Consensus 51 ~NPTTGY~W~~~~~~~~vl 69 (132)
T 2wgn_B 51 SNPTTGFRWELRNPAASVL 69 (132)
T ss_dssp CCTTTSCEEEEEECCTTTE
T ss_pred CCCCCCeEEEEecCCCceE
Confidence 6788899888877655433
No 7
>1xao_A YDJ1, mitochondrial protein import protein MAS5; beta sheets, chaperone; 2.07A {Saccharomyces cerevisiae}
Probab=16.99 E-value=1.2e+02 Score=21.16 Aligned_cols=81 Identities=14% Similarity=0.220 Sum_probs=44.4
Q ss_pred eEEeecC--CCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCccccc----CCCCCCcccC
Q psy17954 2 KLNISYP--ATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQ----GEIPGLTDTT 75 (143)
Q Consensus 2 KlnIS~P--~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkq----GdIpGltd~~ 75 (143)
.+.||.. ..|++..|. ++-|+.+--.|.+.-+-.. |++++|.| .|+|... ||+==-.+..
T Consensus 12 ~~~Isl~eAllG~~i~v~--------tldG~~~~v~ip~g~v~~~--G~~~rl~G----~Gmp~~~~~~~GDL~V~~~V~ 77 (121)
T 1xao_A 12 EAEIDLLTAIAGGEFALE--------HVSGDWLKVGIVPGEVIAP--GMRKVIEG----KGMPIPKYGGYGNLIIKFTIK 77 (121)
T ss_dssp EEEEEHHHHHHCEEEEEE--------CTTSCEEEEEECTTSCCCT--TCEEEETT----CSCC------CCCEEEEEEEE
T ss_pred EEEcCHHHHhCCCEEEEe--------cCCCCEEEEEeCCCCeeCC--CcEEEECC----CCCCCCCCCCCCCEEEEEEEE
Confidence 3445444 467766554 3444434344543211123 88999886 6888532 2222123345
Q ss_pred CCCc--CCCcchhhhhcccCCCc
Q psy17954 76 IPRR--LGPKRASKIRKLFNLSK 96 (143)
Q Consensus 76 vPr~--lgpKRaskIRKLf~lsk 96 (143)
+|.. |-+.-...+++++....
T Consensus 78 ~P~~~~ls~~q~~~l~~l~~~~~ 100 (121)
T 1xao_A 78 FPENHFTSEENLKKLEEILPPRI 100 (121)
T ss_dssp CCCTTCSCHHHHHHHHHHSCCCC
T ss_pred CCCCCCCCHHHHHHHHHHccccc
Confidence 5777 77777788888887544
No 8
>1a62_A RHO; transcription termination, termination, RNA binding domain, transcription regulation, OB fold, F1-ATPase; 1.55A {Escherichia coli BL21} SCOP: a.140.3.1 b.40.4.5 PDB: 1a63_A 2a8v_A 1a8v_A
Probab=11.66 E-value=1.5e+02 Score=21.39 Aligned_cols=46 Identities=28% Similarity=0.478 Sum_probs=30.0
Q ss_pred EEEEcCccCCCCcccccC--CCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeE
Q psy17954 49 IVRISGGNDKQGFPMKQG--EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYV 104 (143)
Q Consensus 49 ~~~ItGGnDkqGFPMkqG--dIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yv 104 (143)
+|.|. .|--||--..+ =+||..|..|| .+.||+ |+|-..|-|.-.|
T Consensus 54 vlei~--~dG~GFlr~~~~~y~~~~~DiyVs-------~~~irr-f~lr~GD~V~g~v 101 (130)
T 1a62_A 54 VLEIL--QDGFGFLRSADSSYLAGPDDIYVS-------PSQIRR-FNLRTGDTISGKI 101 (130)
T ss_dssp EEEEC--TTSCEEEECGGGTTCCCTTCEEEC-------HHHHHH-TTCCTTCEEEEEE
T ss_pred EEEEc--CCCeEEEecCCcCCCCCCCCEEEC-------HHHHhH-hCCCCCCEEEEEE
Confidence 45554 33446654431 35778999987 466776 8998888766555
No 9
>1grj_A GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} SCOP: a.2.1.1 d.26.1.2
Probab=11.59 E-value=85 Score=23.10 Aligned_cols=19 Identities=21% Similarity=0.116 Sum_probs=11.5
Q ss_pred cccccccccceecCCccCC
Q psy17954 25 RVFYDKRMGMEVPADSIGD 43 (143)
Q Consensus 25 ~~f~gKrig~ev~g~~lG~ 43 (143)
+.++|++.||+|.-..=+-
T Consensus 128 ~ALlGk~~GD~v~v~~p~G 146 (158)
T 1grj_A 128 RGLIGKEEDDVVVIKTPGG 146 (158)
T ss_dssp HHHTTCBTTCEECC-----
T ss_pred HHHcCCCCCCEEEEEcCCC
Confidence 4688899999988764443
No 10
>2p4v_A Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli}
Probab=11.59 E-value=57 Score=24.19 Aligned_cols=19 Identities=16% Similarity=0.237 Sum_probs=13.0
Q ss_pred cccccccccceecCCccCC
Q psy17954 25 RVFYDKRMGMEVPADSIGD 43 (143)
Q Consensus 25 ~~f~gKrig~ev~g~~lG~ 43 (143)
+.++|++.||+|.-..=+-
T Consensus 126 ~ALlGk~vGD~v~v~~P~G 144 (158)
T 2p4v_A 126 RALLKKEVGDLAVVNTPAG 144 (158)
T ss_dssp HHSTTCCTTCEEEEECSSC
T ss_pred HHhcCCCCCCEEEEEcCCC
Confidence 4678888888887654433
Done!