Query 003706
Match_columns 801
No_of_seqs 305 out of 1051
Neff 3.8
Searched_HMMs 29240
Date Tue Mar 26 18:17:50 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/003706.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1755-1759//hhsearch_pdb/003706hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1rq8_A Conserved hypothetical 1.0 1 1 187.3 13.2 88 249-336 1-88 (104)
2 1rq8_A Conserved hypothetical 1.0 1 1 186.1 13.6 97 660-761 1-97 (104)
3 1jo0_A Hypothetical protein HI 1.0 1 1 185.8 12.6 87 249-335 2-88 (98)
4 1jo0_A Hypothetical protein HI 1.0 1 1 182.2 13.6 96 660-761 2-97 (98)
5 3ka5_A Ribosome-associated pro 1.0 1 1 16.0 6.0 50 292-341 1-53 (65)
6 3k2t_A LMO2511 protein; lister 1.0 1 1 15.8 3.2 48 293-340 2-52 (57)
7 3lyv_A Ribosome-associated fac 1.0 1 1 15.6 3.3 50 292-341 2-54 (66)
8 2e6x_A TT1592, hypothetical pr 1.0 1 1 15.5 1.7 17 311-327 3-19 (69)
9 2zkr_v 60S ribosomal protein L 1.0 1 1 15.0 0.0 15 746-761 72-86 (123)
10 2j01_J 50S ribosomal protein L 1.0 1 1 15.0 3.0 30 446-475 30-59 (173)
No 1
>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1
Probab=1.00 E-value=1 Score=187.29 Aligned_cols=88 Identities=19% Similarity=0.316 Sum_probs=55.0
Q ss_pred CCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEECCE
Q ss_conf 99989999999832069870771799988999999999864189178995289848699999999988398699798568
Q 003706 249 MIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (801)
Q Consensus 249 tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~rELVKVKv~~~~~~dmk~v~e~LEekTGGeVV~rIG~v 328 (801)
|||++|+++||++||+++|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||++||+||++
T Consensus 1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~ 80 (104)
T 1rq8_A 1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM 80 (104)
T ss_dssp CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEECCE
T ss_conf 97989999999974689986997788799999999999999789479998079877899999999998699999999999
Q ss_pred EEEEECCC
Q ss_conf 99951479
Q 003706 329 VVLFRGMA 336 (801)
Q Consensus 329 iILYRG~N 336 (801)
+||||++.
T Consensus 81 ~VLYR~~~ 88 (104)
T 1rq8_A 81 IVIYRESK 88 (104)
T ss_dssp EEEEECCC
T ss_pred EEEEECCC
T ss_conf 99995788
No 2
>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1
Probab=1.00 E-value=1 Score=186.11 Aligned_cols=97 Identities=25% Similarity=0.418 Sum_probs=92.5
Q ss_pred CCCHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEEECC
Q ss_conf 99999999999701699961760778889889999999987166288997489989799999999988399899733169
Q 003706 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP 739 (801)
Q Consensus 660 ~LT~eERk~LRKlGlklKpvV~IGK~GVtdgVIeeIh~alk~hELVKIkv~~~~~~d~keiA~~Le~~TGgiLVqVik~~ 739 (801)
|||++||++||++||+++|+|+|||+|||++|+++|++||++||||||+|++++.++++++|..|++.|||++||+|
T Consensus 1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~I--- 77 (104)
T 1rq8_A 1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVI--- 77 (104)
T ss_dssp CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEE---
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEE---
T ss_conf 97989999999974689986997788799999999999999789479998079877899999999998699999999---
Q ss_pred CCCEEEEECCCCCCCCCCCCCC
Q ss_conf 7829999806899999757865
Q 003706 740 KGIAIIVYRGKNYVRPLKLRPQ 761 (801)
Q Consensus 740 iG~tIILYRGKNY~rP~~l~P~ 761 (801)
|+++||||++. ..|.+.+|-
T Consensus 78 -G~~~VLYR~~~-~~~~i~~~~ 97 (104)
T 1rq8_A 78 -GSMIVIYRESK-ENKEIELPL 97 (104)
T ss_dssp -TTEEEEEECCC-SCCSCCCC-
T ss_pred -CCEEEEEECCC-CCCCEECCC
T ss_conf -99999995788-788523451
No 3
>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A
Probab=1.00 E-value=1 Score=185.82 Aligned_cols=87 Identities=17% Similarity=0.272 Sum_probs=56.7
Q ss_pred CCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEECCE
Q ss_conf 99989999999832069870771799988999999999864189178995289848699999999988398699798568
Q 003706 249 MIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (801)
Q Consensus 249 tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~rELVKVKv~~~~~~dmk~v~e~LEekTGGeVV~rIG~v 328 (801)
+||++|+++||++||+++|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||++||+||++
T Consensus 2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG~~ 81 (98)
T 1jo0_A 2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI 81 (98)
T ss_dssp CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTE
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEECCE
T ss_conf 89989999999975479986997787799999999999999779279998179877899999999999699999999999
Q ss_pred EEEEECC
Q ss_conf 9995147
Q 003706 329 VVLFRGM 335 (801)
Q Consensus 329 iILYRG~ 335 (801)
+||||++
T Consensus 82 ~vLyR~~ 88 (98)
T 1jo0_A 82 LVLYRPS 88 (98)
T ss_dssp EEEECCC
T ss_pred EEEECCC
T ss_conf 9998069
No 4
>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A
Probab=1.00 E-value=1 Score=182.18 Aligned_cols=96 Identities=20% Similarity=0.371 Sum_probs=90.7
Q ss_pred CCCHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEEECC
Q ss_conf 99999999999701699961760778889889999999987166288997489989799999999988399899733169
Q 003706 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP 739 (801)
Q Consensus 660 ~LT~eERk~LRKlGlklKpvV~IGK~GVtdgVIeeIh~alk~hELVKIkv~~~~~~d~keiA~~Le~~TGgiLVqVik~~ 739 (801)
.||++||++||++||+++|+|+||++|+|++|+.+|+.||++||||||+|++++.+++++++..|++.|||++||+|
T Consensus 2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~I--- 78 (98)
T 1jo0_A 2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTI--- 78 (98)
T ss_dssp CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEE---
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEE---
T ss_conf 89989999999975479986997787799999999999999779279998179877899999999999699999999---
Q ss_pred CCCEEEEECCCCCCCCCCCCCC
Q ss_conf 7829999806899999757865
Q 003706 740 KGIAIIVYRGKNYVRPLKLRPQ 761 (801)
Q Consensus 740 iG~tIILYRGKNY~rP~~l~P~ 761 (801)
|+++||||++.. |.+.+|+
T Consensus 79 -G~~~vLyR~~~~--~~i~lp~ 97 (98)
T 1jo0_A 79 -GHILVLYRPSEE--AKIQLPR 97 (98)
T ss_dssp -TTEEEEECCCSS--CCBCCCC
T ss_pred -CCEEEEECCCCC--CCCCCCC
T ss_conf -999999806998--7767989
No 5
>3ka5_A Ribosome-associated protein Y (PSRP-1); structural genomics, PSI-2, protein structure initiative; 1.80A {Clostridium acetobutylicum}
Probab=1.00 E-value=1 Score=16.00 Aligned_cols=50 Identities=12% Similarity=0.100 Sum_probs=37.3
Q ss_pred CEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEE---CCEEEEEECCCCCCCC
Q ss_conf 9178995289848699999999988398699798---5689995147989987
Q 003706 292 EVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRS---GSSVVLFRGMAYKLPC 341 (801)
Q Consensus 292 ELVKVKv~~~~~~dmk~v~e~LEekTGGeVV~rI---G~viILYRG~NY~~P~ 341 (801)
++|+.|-....+...++++.+++.--.--+|-+- |.+-|+||.++.++..
T Consensus 1 ~iVr~K~~~~kpMsveEAv~qmel~gh~F~vF~n~etg~~nVVYRR~dG~yGl 53 (65)
T 3ka5_A 1 EIVKTKRFAIKPMSEEEAVLEMELLGHNFFVFQNGDSNEVNVVYKRKDGNYGL 53 (65)
T ss_dssp CEEEEECSCCSCBCHHHHHHHHHHHTCSEEEEEETTTTEEEEEEECTTSCEEE
T ss_pred CEEEEEEECCCCCCHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEECCCCEEE
T ss_conf 95999860579899999999987079939999817899798999968997998
No 6
>3k2t_A LMO2511 protein; listeria monocytogenes,binding, structural genomics, PSI-2, protein structure initiative; 2.40A {Listeria monocytogenes}
Probab=1.00 E-value=1 Score=15.77 Aligned_cols=48 Identities=6% Similarity=0.090 Sum_probs=27.6
Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHHCCEEEEE---ECCEEEEEECCCCCCC
Q ss_conf 17899528984869999999998839869979---8568999514798998
Q 003706 293 VVKLKFEEPHSLQMKRTHEILERRTGGLVIWR---SGSSVVLFRGMAYKLP 340 (801)
Q Consensus 293 LVKVKv~~~~~~dmk~v~e~LEekTGGeVV~r---IG~viILYRG~NY~~P 340 (801)
+|+.|-....+...++++.+++.--.--++-+ .|.+-++||.++.++-
T Consensus 2 ivr~K~~~~kpmsveEAv~qmel~gh~F~vF~n~~t~~~nVvYrR~dG~yG 52 (57)
T 3k2t_A 2 IVRTKQFSLKPMDSEEAVLQMNLLGHSFYVYTDAETNGTNIVYSRKDGKYG 52 (57)
T ss_dssp CCCCCC---CCBCHHHHHHHHHHHTCSEEEEEBSSSCCEEEEEECTTSCEE
T ss_pred EEEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCEE
T ss_conf 389986267989999999998727995999980788989899996799799
No 7
>3lyv_A Ribosome-associated factor Y; ribosomal protein S30AE family, structural genomics, PSI-2, structure initiative; 2.70A {Streptococcus pyogenes}
Probab=1.00 E-value=1 Score=15.55 Aligned_cols=50 Identities=18% Similarity=0.258 Sum_probs=34.8
Q ss_pred CEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEE---CCEEEEEECCCCCCCC
Q ss_conf 9178995289848699999999988398699798---5689995147989987
Q 003706 292 EVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRS---GSSVVLFRGMAYKLPC 341 (801)
Q Consensus 292 ELVKVKv~~~~~~dmk~v~e~LEekTGGeVV~rI---G~viILYRG~NY~~P~ 341 (801)
++|+.|-....+...++++.+++---.--+|-+- |.+-|+||.++.++-.
T Consensus 2 ~iVr~K~~~~kpMsveEAv~qMel~gh~F~vF~n~etg~~nVVYRR~dG~yGl 54 (66)
T 3lyv_A 2 QVVRTKNVTLKPMDVEEARLQMELLGHDFFIYTDSEDGATNILYRREDGNLGL 54 (66)
T ss_dssp CCCCCCCCCCCEECHHHHHHHHHTTTCSEEEEEETTTCSEEEEEECTTSSEEE
T ss_pred EEEEEEECCCCCCCHHHHHHHHHCCCCCEEEEEECCCCCEEEEEEECCCCEEE
T ss_conf 17999870579899999999987079939999817899898999978997999
No 8
>2e6x_A TT1592, hypothetical protein TTHA1281; unknown function protein, NPPSFA, national project on protei structural and functional analyses; 2.00A {Thermus thermophilus}
Probab=1.00 E-value=1 Score=15.45 Aligned_cols=17 Identities=29% Similarity=0.632 Sum_probs=14.0
Q ss_pred HHHHHHHCCEEEEEECC
Q ss_conf 99998839869979856
Q 003706 311 EILERRTGGLVIWRSGS 327 (801)
Q Consensus 311 e~LEekTGGeVV~rIG~ 327 (801)
..+-++.|+.+|||||.
T Consensus 3 ~d~L~~LG~~LvWRiGk 19 (69)
T 2e6x_A 3 KDLLDKLGQHLVWRMGR 19 (69)
T ss_dssp HHHHHHTTCCEEEEEEE
T ss_pred HHHHHHHHCEEEEEECC
T ss_conf 78999974102786435
No 9
>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=1.00 E-value=1 Score=15.05 Aligned_cols=15 Identities=60% Similarity=1.269 Sum_probs=5.9
Q ss_pred EECCCCCCCCCCCCCC
Q ss_conf 9806899999757865
Q 003706 746 VYRGKNYVRPLKLRPQ 761 (801)
Q Consensus 746 LYRGKNY~rP~~l~P~ 761 (801)
+|.|+.|. |..++|+
T Consensus 72 ~yk~kk~~-p~dlr~k 86 (123)
T 2zkr_v 72 FYKGKKYK-PLDLRPK 86 (123)
T ss_dssp ----------------
T ss_pred HHCCCCCC-CCCCCHH
T ss_conf 98389878-7543437
No 10
>2j01_J 50S ribosomal protein L10; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} PDB: 2j03_J 3d5b_J 3d5d_J 3i8i_Y 3kir_J 3kit_J 3kiw_J 3kiy_J 3mrz_I 3ms1_I 3pyt_I 3pyr_I 3pyo_I 3pyv_I
Probab=1.00 E-value=1 Score=15.05 Aligned_cols=30 Identities=20% Similarity=0.338 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHHHHHCCCCEEEECCCCHH
Q ss_conf 999948899999952029990772256324
Q 003706 446 PGLRDCETTEFRRLARKTPPHFALGRNREL 475 (801)
Q Consensus 446 ~~Ls~~E~t~LRk~ar~lpph~aLGRn~~~ 475 (801)
.+|+..+++.||+..|.--..|.++||...
T Consensus 30 ~gltv~~~~~LR~~lr~~g~~~~V~KNtL~ 59 (173)
T 2j01_J 30 QGLPAKETHALRQALKQNGARLFVAKNTLI 59 (173)
T ss_pred CCCCHHHHHHHHHHHHHCCCEEEEEHHHHH
T ss_conf 899889999999999977968999616899
Done!