Query 025698
Match_columns 249
No_of_seqs 197 out of 361
Neff 4.0
Searched_HMMs 29240
Date Mon Mar 25 15:39:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025698.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/025698hhsearch_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 3E-115 1E-119 774.9 21.1 233 1-239 1-234 (236)
2 2xzm_Y RPS6E; ribosome, transl 100.0 3E-107 1E-111 738.7 22.8 225 1-230 1-229 (293)
3 3j20_G 30S ribosomal protein S 100.0 2.6E-59 8.8E-64 383.3 11.4 112 1-116 4-124 (125)
4 3iab_A Ribonucleases P/MRP pro 20.2 9.4 0.00032 32.3 -2.2 61 128-190 28-98 (158)
5 2pp6_A Gifsy-2 prophage ATP-bi 14.3 89 0.003 24.6 2.2 28 59-91 40-67 (102)
6 3bmb_A Regulator of nucleoside 13.1 1.2E+02 0.0041 23.8 2.7 19 24-42 95-113 (136)
7 2f23_A Anti-cleavage anti-GREA 10.6 1.2E+02 0.0043 24.2 2.1 19 24-42 126-144 (156)
8 3e1k_B Lactose regulatory prot 9.3 77 0.0026 18.5 0.2 15 145-159 3-17 (22)
9 3gmi_A UPF0348 protein MJ0951; 9.1 87 0.003 29.0 0.7 35 124-159 214-248 (357)
10 1rxl_A AFAE-DSC, afimbrial adh 8.7 1.8E+02 0.0061 24.4 2.3 35 28-62 105-143 (156)
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=3.3e-115 Score=774.90 Aligned_cols=233 Identities=61% Similarity=0.979 Sum_probs=222.5
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025698 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (249)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (249)
||||||||+|||||+||||||++|++|||++||+||+||+||+||+||+|+||||||+|||||+|||+|++||+||||+|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeeccccCCCCCCCCCCCcCCCCchhhhHhhhCCCCccchhhhhh
Q 025698 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVN 160 (249)
Q Consensus 81 ~~gyrp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~I~gLTd~~~p~~lgPKRaskIrKlFnLsk~ddv~kyV~ 160 (249)
|+|||| +++||||||||||||||+||||||++||++||+|||||||+|+|++|||||||+|||||||||+||||+||
T Consensus 81 ~~~yrp--rr~GERkRKsVRGciV~~~is~lNlvIVkkGek~IpgLtd~~~p~~lgPKRas~irklfnlsk~ddVr~yv- 157 (236)
T 3u5c_G 81 VSCYRP--RRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFV- 157 (236)
T ss_dssp BTTBCC--SSTTCCEEEEEECSBCCTTEEEEEEEEEECCSSCCHHHHTCCCCCSCCCCBHHHHHHHHTCTTTSCSSSSS-
T ss_pred CCccCC--CCCCceeeeeeeeeEecCCceeEEEEEEecCCccCccccCcccccccCCchhhhhHHHhCCCcccchhhee-
Confidence 999999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccccccCCC-CcccccCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhhhhh
Q 025698 161 TYRRTFTTKSG-KKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQRERRSESLAKKRSRL 239 (249)
Q Consensus 161 ~vrr~l~~k~g-k~~~KaPKIQrLvTp~~lqrk~~~~a~kk~~~~k~keea~eY~klla~r~ke~k~~~~~~~~r~~~s~ 239 (249)
||+||+ +| |+++|||||||||||++||||++++|+|++++++++|||+||++|||+||+|+++++++..+++++|+
T Consensus 158 -vrr~l~--~gkk~~~kapKIQrlvtp~~lqrk~~~~a~kk~r~~k~keea~eY~klla~r~ke~k~~~~~~~~~r~~~~ 234 (236)
T 3u5c_G 158 -IRREVT--KGEKTYTKAPKIQRLVTPQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSL 234 (236)
T ss_dssp -CCEEEE--CSSCEEEECCCCBSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------
T ss_pred -eeeecc--cCCCCCCCCCCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999998 66 99999999999999999999999999999999999999999999999999999999988544444444
No 2
>2xzm_Y RPS6E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Y
Probab=100.00 E-value=3.4e-107 Score=738.68 Aligned_cols=225 Identities=57% Similarity=0.919 Sum_probs=221.8
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025698 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (249)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (249)
||||||||+||+||+|||||+++++.|||++||+||+||+||+||+||+|+||||||+|||||+|||+|++||+|||++|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeeccccCCCCCCCCCCCcCCCCchhhhHhhhCCCCccc---hhh
Q 025698 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDD---VRK 157 (249)
Q Consensus 81 ~~gyrp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~I~gLTd~~~p~~lgPKRaskIrKlFnLsk~dd---v~k 157 (249)
|+|||| +|+||||||||||||||+|||||||+||++||++||||||+++|++|||||||+||||||||++|| ||+
T Consensus 81 ~sgYRP--rr~GERKRKSVRGciVs~disqLNlvIVkkGek~IpgLTD~~~PrrlGPKRAskIRKlFnLsKeDD~~~Vrk 158 (293)
T 2xzm_Y 81 HSCFTS--RRSGFRKRKSVRGCIVGPDMRVLALQIVKKGVAEIDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKK 158 (293)
T ss_dssp CSSCCC--SSSCCCEEEEEECSSCCTTEEEEEEEEEECCSSCCHHHHTCCCCCCCCCCSHHHHHHHHCCCTTCCHHHHHH
T ss_pred CCCCCC--CCCCceeeeeeeeeeecCCceeEEEEEEecCCccCccccCCcCCCCCCCchhhhhHHHhCCCcccchhhhhh
Confidence 999999 999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred hhhhhccccccCCC-CcccccCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 025698 158 YVNTYRRTFTTKSG-KKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQRERRSE 230 (249)
Q Consensus 158 yV~~vrr~l~~k~g-k~~~KaPKIQrLvTp~~lqrk~~~~a~kk~~~~k~keea~eY~klla~r~ke~k~~~~~ 230 (249)
|| ||++++ ++| |+++|+|||||||||.+||||++++++|+++++++++|++||++||++|++|+++++++
T Consensus 159 yV--irr~~~-kegkk~~~KaPKIQRLVTp~~lqrKr~~~a~Kk~r~~k~keea~eY~klla~r~~e~k~~~~~ 229 (293)
T 2xzm_Y 159 SV--IRRTFK-TAKGKDRTKCPKIQRLITPERILRKKVYKAEKTQRYVKTNAAKEEYEKFLSEWKKQRAAKAHA 229 (293)
T ss_dssp TS--CCEEEE-CTTSCEEEECCCCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred hh--eecccc-ccCCcccccCCCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99 999998 888 88999999999999999999999999999999999999999999999999999998754
No 3
>3j20_G 30S ribosomal protein S6E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=100.00 E-value=2.6e-59 Score=383.34 Aligned_cols=112 Identities=39% Similarity=0.752 Sum_probs=110.2
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCC--------cc-cCcEEEEccccCCCCCcccCCCCCCc
Q 025698 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDALGE--------EF-KGYVFKIMGGCDKQGFPMKQGVLTPG 71 (249)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~--------e~-kGY~~~ItGGnDkqGFPMkqgVl~~~ 71 (249)
||||||||+|||||+||||||. +++||||+||+||+|++||+ || +||+|+||||||+|||||+|||+||+
T Consensus 4 ~Kl~Is~P~tG~qk~iEidde~-~~~f~gkrig~ev~g~~lG~~~~~~~~~e~~kGy~~~ItGG~DkqGFPMkqgV~~~~ 82 (125)
T 3j20_G 4 FKLVISDPKSGIAKQVEITGAE-TEKLIGKRIGDQIPAKELNINLNELFGKEFPEDVKLEIRGGTDKDGFPMRPDIHGPR 82 (125)
T ss_dssp EEEEEEETTTTEEEEEEECSTT-GGGTTTCCTTCEECSTTTCSSSCSSSSSCSCSCCCEEEEEEEETTCCBBCTTCCSSS
T ss_pred eEEEEEcCCCCEEEEEEcCchh-hhhhccccceeEEeeeecCcccccccccccCCCcEEEEccCcCCCCccccCCcCCCc
Confidence 8999999999999999999995 89999999999999999999 99 99999999999999999999999999
Q ss_pred eEEEeeeCCCCcccCCCCCCCcceeeeeeceeecCCcceEEEEEE
Q 025698 72 RVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIV 116 (249)
Q Consensus 72 RvrlLLskG~~gyrp~~rr~GERkRKSVRGciV~~~is~LNlvIV 116 (249)
||+||||+| +|||| +|+||||||||||||||+||||||++||
T Consensus 83 rvrlLLskG-~gyrp--rr~GeRkRKsVRG~~V~~~i~~lNlviv 124 (125)
T 3j20_G 83 RVRVLLSKG-PGFRP--KEKGERRKKTVRGNTISPEIVQVNVKLV 124 (125)
T ss_dssp EEEEECCSS-CSSCC--CCSSCCCEEEEECSSCCTTEEEEEEEEC
T ss_pred eEEEEecCC-CccCC--CCCCcEeeEEeeceEEcCCeEEEEEEEe
Confidence 999999999 99999 9999999999999999999999999997
No 4
>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=20.21 E-value=9.4 Score=32.27 Aligned_cols=61 Identities=25% Similarity=0.451 Sum_probs=39.0
Q ss_pred CCCCCCcCCC--CchhhhHhhhCCCCccchhhhhhhhcccccc-C--CCCc-----ccccCCcccCcchHHHH
Q 025698 128 DTEKPRMRGP--KRASKIRKLFNLSKEDDVRKYVNTYRRTFTT-K--SGKK-----VSKAPKIQRLVTPLTLQ 190 (249)
Q Consensus 128 d~~~p~~lgP--KRaskIrKlFnLsk~ddv~kyV~~vrr~l~~-k--~gk~-----~~KaPKIQrLvTp~~lq 190 (249)
|..+|..|++ -+ ..|. .+.+||-|.|.+.|..+..-+.. . .|.. ....|=||+|+|=.-+-
T Consensus 28 ~~iip~~l~~~~~~-~~I~-~~kIsKNDnIK~~V~kL~~~l~~~~~s~~~~~~V~l~syg~hIQKmLSIvEI~ 98 (158)
T 3iab_A 28 ETVIPSLANNGNNS-TSIQ-YHGISKNDNIKKSVNKLDKQINMADRSLGLQQVVCIFSYGPHIQKMLSILEIF 98 (158)
T ss_dssp HTTTTTTCCCSSSS-EEEE-EEECCTTCCHHHHHHHHHHHHTCSCTTTTCEEEEEEEEEGGGHHHHHHHHHHH
T ss_pred HHhhHHHhcCcCCc-cceE-EEEeccCchHHHHHHHHHHHHhhhccccccCceEEEEecChHHHHHHHHHHHH
Confidence 4566777776 23 2676 78899999999998666555421 0 1111 23678899988765443
No 5
>2pp6_A Gifsy-2 prophage ATP-binding sugar transporter-LI protein; beta barrel, 4 helix bundle, structural genomics, PSI-2; 2.70A {Salmonella typhimurium LT2} SCOP: b.106.1.2
Probab=14.32 E-value=89 Score=24.59 Aligned_cols=28 Identities=14% Similarity=0.033 Sum_probs=14.3
Q ss_pred CCCcccCCCCCCceEEEeeeCCCCcccCCCCCC
Q 025698 59 QGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRD 91 (249)
Q Consensus 59 qGFPMkqgVl~~~RvrlLLskG~~gyrp~~rr~ 91 (249)
..-|.-.+|-+.+|--+|.| +|||| +|.
T Consensus 40 e~~~emg~lsG~~rsLvvFS---sgYrP--~r~ 67 (102)
T 2pp6_A 40 DFLAELGPVEGNGKNVVVFS---GNVIP--RRG 67 (102)
T ss_dssp GGTC--------CEEEEECC---SSCCC--CTT
T ss_pred hhHHHhCCccCCceEEEEec---CCccc--CCC
Confidence 33455556888898888885 69999 653
No 6
>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli}
Probab=13.10 E-value=1.2e+02 Score=23.78 Aligned_cols=19 Identities=16% Similarity=0.261 Sum_probs=13.8
Q ss_pred hcccccccccceecCcccC
Q 025698 24 LRAFFDKRISQEVNGDALG 42 (249)
Q Consensus 24 l~~f~gKrig~eV~gd~lG 42 (249)
.+.++|++.||+|.-..=+
T Consensus 95 G~ALlGk~~GD~v~v~~p~ 113 (136)
T 3bmb_A 95 GAALLGLRVGDSIHWELPG 113 (136)
T ss_dssp HHHHTTCBTTCEEEEEETT
T ss_pred HHHHcCCCCCCEEEEEcCC
Confidence 4568888888888776544
No 7
>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=10.61 E-value=1.2e+02 Score=24.22 Aligned_cols=19 Identities=16% Similarity=0.226 Sum_probs=13.0
Q ss_pred hcccccccccceecCcccC
Q 025698 24 LRAFFDKRISQEVNGDALG 42 (249)
Q Consensus 24 l~~f~gKrig~eV~gd~lG 42 (249)
.+.++|++.||+|.-..=+
T Consensus 126 G~ALlGk~~GD~v~~~~p~ 144 (156)
T 2f23_A 126 GKALLGHRVGDVLSLDTPK 144 (156)
T ss_dssp HHHHTTCCTTCEEEEEETT
T ss_pred HHHHcCCCCCCEEEEEcCC
Confidence 4567888888887765443
No 8
>3e1k_B Lactose regulatory protein LAC9; transctiption, repressor, trans-activation, carbohydrate metabolism, DNA-binding, galactose metabolism; 3.00A {Kluyveromyces lactis}
Probab=9.26 E-value=77 Score=18.54 Aligned_cols=15 Identities=47% Similarity=0.829 Sum_probs=13.3
Q ss_pred hhhCCCCccchhhhh
Q 025698 145 KLFNLSKEDDVRKYV 159 (249)
Q Consensus 145 KlFnLsk~ddv~kyV 159 (249)
-|||-+--|||-.|+
T Consensus 3 ~mfntttmddvynyl 17 (22)
T 3e1k_B 3 QLFNTTTMDDVYNYI 17 (26)
T ss_pred cccccccHHHHHHHh
Confidence 489999999999997
No 9
>3gmi_A UPF0348 protein MJ0951; protein with unknown function, structural genomics, PSI, MCS protein structure initiative; 1.91A {Methanocaldococcus jannaschii}
Probab=9.08 E-value=87 Score=28.95 Aligned_cols=35 Identities=17% Similarity=0.064 Sum_probs=25.8
Q ss_pred CCCCCCCCCCcCCCCchhhhHhhhCCCCccchhhhh
Q 025698 124 PGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYV 159 (249)
Q Consensus 124 ~gLTd~~~p~~lgPKRaskIrKlFnLsk~ddv~kyV 159 (249)
+.+...++|| ++|=-||.||+++--..-|++.+||
T Consensus 214 ~~i~~~~i~R-~~~~SAS~IR~~i~~g~~~~~~~lV 248 (357)
T 3gmi_A 214 FNPKFVFVKR-LEGISGTKIREAIFSGKFEDIKNML 248 (357)
T ss_dssp CCCEEEEEEC-SCCCCHHHHHHHHHTTCGGGTGGGS
T ss_pred CCCeEEEecC-CCcccHHHHHHHHHcCChhHHHhcC
Confidence 4455566777 4589999999999654446788887
No 10
>1rxl_A AFAE-DSC, afimbrial adhesin AFA-III, AFA-III, AFAE-3; DAF, afimbrial sheath, DAEC, UPEC, IG-like domain, donor strand complemented; NMR {Escherichia coli} SCOP: b.2.3.6 PDB: 2ixq_B 2ver_A*
Probab=8.70 E-value=1.8e+02 Score=24.38 Aligned_cols=35 Identities=29% Similarity=0.506 Sum_probs=27.1
Q ss_pred ccccccceecCcccCCcccCcEEEEccc----cCCCCCc
Q 025698 28 FDKRISQEVNGDALGEEFKGYVFKIMGG----CDKQGFP 62 (249)
Q Consensus 28 ~gKrig~eV~gd~lG~e~kGY~~~ItGG----nDkqGFP 62 (249)
+|=.|+-.|+||-.-..---|.|..+|| ..+|||.
T Consensus 105 WgGti~i~V~GdQt~~ptG~YTLnL~GGyW~s~~~~~~~ 143 (156)
T 1rxl_A 105 WGGTIGIYVDGQQTNTPPGNYTLTLTGGYWAKDNKQGFT 143 (156)
T ss_dssp CCEEEEEEETTCCCCCSCCEEEEEEEEEEECSSSSCCEE
T ss_pred cccEEEEEEeCCcccCCCccEEEEecccEeeecCccccC
Confidence 3456888888888876655699999999 5688885
Done!