Query 005475
Match_columns 695
No_of_seqs 162 out of 309
Neff 3.2
Searched_HMMs 29240
Date Tue Mar 26 18:57:33 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/005475.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1980-1984//hhsearch_pdb/005475hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2v3m_A NAF1; ribosomal protein 1.0 1 1 223.0 9.4 119 276-396 2-127 (131)
2 2eqn_A Hypothetical protein LO 1.0 1 1 182.9 9.7 100 281-381 3-103 (103)
3 3u28_C H/ACA ribonucleoprotein 1.0 1 1 104.8 10.1 82 298-383 22-104 (114)
4 2hvy_B GAR1, small nucleolar R 1.0 1 1 99.6 9.3 77 300-383 5-82 (104)
5 2ey4_C Small nucleolar RNP sim 1.0 1 1 97.8 8.0 76 300-382 5-81 (82)
6 1lsh_B Lipovitellin (LV-2); vi 1.0 1 1 26.0 0.0 17 316-336 88-104 (319)
7 4aco_A Centromere DNA-binding 1.0 1 1 21.4 0.0 28 329-358 838-866 (956)
8 4fp9_B Mterf domain-containing 1.0 1 1 20.4 -0.3 33 235-267 299-331 (335)
9 3eoj_A Bacteriochlorophyll A p 1.0 1 1 16.5 -0.1 101 253-358 7-123 (366)
10 3r8s_E 50S ribosomal protein L 1.0 1 1 16.3 3.0 26 666-695 48-73 (201)
No 1
>2v3m_A NAF1; ribosomal protein, GAR1, snoRNP, phosphorylation, hypothetical protein; 2.74A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=223.02 Aligned_cols=119 Identities=29% Similarity=0.519 Sum_probs=106.8
Q ss_pred CCCCCCCCCCC--CCCCCCCCEECCCCCCEEECCEEEEEECCEEEEECCC--CCCCCCCCCEEEECCCCEEEEEEEEEEC
Q ss_conf 97545667676--8998887500199986463200433415369995268--9888899985998269812377652003
Q 005475 276 GPIRSKNELQV--LPLVPQVNVVLQPHHQMLPVGVVLSVRGVQVIVEGAE--KHNPLNEGSILWITESRVPLGLIDEIFG 351 (695)
Q Consensus 276 gPiRTKNEi~e--lPPVppldIsI~ed~~I~pIGtIsSIVdn~VIVkS~~--e~~VLDeGSVLcLtEDRtvIGkVfEVFG 351 (695)
+|+|||||+.+ +|++|+ +++|+++++|+++|+|+|+|++.+||++.. +.++|++||+||+ +||++||+|+||||
T Consensus 2 ~p~rtknE~~~~~~p~~p~-~~~i~~~~~v~~lG~i~~ive~~vVik~~~~g~~~vl~~~s~l~l-edr~~IGkV~EiFG 79 (131)
T 2v3m_A 2 GPILSKNEILEETVPELPE-DYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCL-EDRTLIGMLTEVFG 79 (131)
T ss_dssp -------------CCCCCT-TCCCCTTSCEEEEEEEEEEETTEEEEEEC-----CCCCTTCEEEE-TTCCEEEECCEEES
T ss_pred CCCCCCCCCCCCCCCCCCC-CEECCCCCEEEEEEEEEEEECCCEEEEECCCCCCCCCCCCCEEEE-CCCCEEEEEEEEEC
T ss_conf 8861356356343799997-515099997788066989808809999657777335679999894-48958788999867
Q ss_pred CCCCCEEEEECCCC--CCCC-CCCCCCCEEEECCCCCCEEECCCCCCC
Q ss_conf 87883899972888--8863-102357679964476522433311112
Q 005475 352 PVKNPYYVVRYNSE--NEIP-AEIRVGTSISFVQDFANHVLDDKNLYK 396 (695)
Q Consensus 352 PVsqPyYsVRFnS~--eEI~-~~IkvGtkVYYVpe~S~fVlt~qL~~~ 396 (695)
||++|||+|||++. +++. .++++|++|||+++|++||++.+|+..
T Consensus 80 pV~~P~ysVk~~~~~~e~i~~~~~~~G~kvY~~~~~s~fv~t~~~~~~ 127 (131)
T 2v3m_A 80 PLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVTPDAHWIDTFELKHH 127 (131)
T ss_dssp CSSSCEEEEECCGGGHHHHHHHHTTTTSEEEEEC--------------
T ss_pred CCCCCEEEEEECCCCHHHHHHCCCCCCCEEEECCCCCCEEECHHHCCC
T ss_conf 889847999858764022021046789979987672436823330123
No 2
>2eqn_A Hypothetical protein LOC92345; NAF1 domain, hypothetical protein BC008207 [HOMO sapiens], structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=182.86 Aligned_cols=100 Identities=32% Similarity=0.604 Sum_probs=92.8
Q ss_pred CCCCCCCCCCCCCCEECCCCCCEEECCEEEEEECCEEEEECCCCCCCCCCCCEEEECCCCEEEEEEEEEECCCCCCEEEE
Q ss_conf 66767689988875001999864632004334153699952689888899985998269812377652003878838999
Q 005475 281 KNELQVLPLVPQVNVVLQPHHQMLPVGVVLSVRGVQVIVEGAEKHNPLNEGSILWITESRVPLGLIDEIFGPVKNPYYVV 360 (695)
Q Consensus 281 KNEi~elPPVppldIsI~ed~~I~pIGtIsSIVdn~VIVkS~~e~~VLDeGSVLcLtEDRtvIGkVfEVFGPVsqPyYsV 360 (695)
-..++++||+++++++++++++|+++|+|+|++++.+||++..+.++|++||+||+ +||+.||+|+||||||++|||+|
T Consensus 3 ~~~~~~lPp~~~~~i~~~~~~~v~~lG~v~~~~e~~vvik~~~~~~vl~~~s~l~~-edk~~IGkV~EiFGpV~~PyysV 81 (103)
T 2eqn_A 3 SGSSGELPSVEELTIILPEDIELKPLGMVSSIIEQLVIIESMTNLPPVNEETVIFK-SDRQAAGKIFEIFGPVAHPFYVL 81 (103)
T ss_dssp CCCSCCCSSCCCCCCBCCTTSCCEEEEEEEEECSSSEEEEECSSCCCCCTTCEEEC-TTSBEEEEEEEEESCSSSCEEEE
T ss_pred CCCCCCCCCCCCCCEECCCCCEEEEEEEEEEECCCEEEEEECCCCCCCCCCCEEEE-CCCCEEEEEEEEECCCCCCEEEE
T ss_conf 66425279888752385998746984899998298099996798757768999993-69958789989778878878999
Q ss_pred ECCCCCCCC-CCCCCCCEEEEC
Q ss_conf 728888863-102357679964
Q 005475 361 RYNSENEIP-AEIRVGTSISFV 381 (695)
Q Consensus 361 RFnS~eEI~-~~IkvGtkVYYV 381 (695)
||++.++++ .++++|++|||+
T Consensus 82 k~~~~~~i~a~~~~~G~kvY~~ 103 (103)
T 2eqn_A 82 RFNSSDHIESKGIKIKETMYFA 103 (103)
T ss_dssp CCSSHHHHHHHTCCTTCEEEEC
T ss_pred EECCCCCCCCCCCCCCCEEEEC
T ss_conf 7186103630255689979859
No 3
>3u28_C H/ACA ribonucleoprotein complex subunit 1; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_C
Probab=1.00 E-value=1 Score=104.75 Aligned_cols=82 Identities=16% Similarity=0.414 Sum_probs=71.8
Q ss_pred CCCCCEEECCEEEEEECCEEEEECCCCCCCCCCCCEEEECCCCEEEEEEEEEECCCCCCEEEEECCCCCCCC-CCCCCCC
Q ss_conf 999864632004334153699952689888899985998269812377652003878838999728888863-1023576
Q 005475 298 QPHHQMLPVGVVLSVRGVQVIVEGAEKHNPLNEGSILWITESRVPLGLIDEIFGPVKNPYYVVRYNSENEIP-AEIRVGT 376 (695)
Q Consensus 298 ~ed~~I~pIGtIsSIVdn~VIVkS~~e~~VLDeGSVLcLtEDRtvIGkVfEVFGPVsqPyYsVRFnS~eEI~-~~IkvGt 376 (695)
.|-+.++++|+++|++++.+|+++... .++.+++.+++ ++++.||+|+||||||++||++|+... .+. ..+++|+
T Consensus 22 gpp~~v~elG~f~H~ceg~lV~k~~~~-~VP~fNapVy~-enK~~IGKVdEIFGPin~~YfsVK~~~--gv~a~Sfk~gd 97 (114)
T 3u28_C 22 GPPDTVLEMGAFLHPCEGDIVCRSINT-KIPYFNAPIYL-ENKTQVGKVDEILGPLNEVFFTIKCGD--GVQATSFKEGD 97 (114)
T ss_dssp -CCSCEEEEEEEEEEETTEEEEEECSS-SEECTTCEEEC-TTCCEEEEEEEEESBTTSCEEEEEECT--TCCGGGCCTTC
T ss_pred CCCHHHHEEEEEEEEECCEEEEEECCC-CCCCCCCEEEC-CCCCCCEEEEEEECCCCCCEEEEEECC--CCCCCCCCCCC
T ss_conf 988787151668987088599986778-77877997383-477545368588678885079999668--97653121488
Q ss_pred EEEECCC
Q ss_conf 7996447
Q 005475 377 SISFVQD 383 (695)
Q Consensus 377 kVYYVpe 383 (695)
++|+.+.
T Consensus 98 k~YId~~ 104 (114)
T 3u28_C 98 KFYIAAD 104 (114)
T ss_dssp EEEEEGG
T ss_pred EEEECCC
T ss_conf 8997852
No 4
>2hvy_B GAR1, small nucleolar RNP similar to GAR1; H/ACA RNA, RNP, pseudouridine synthase, guide RNA, isomerase biosynthetic protein-RNA complex; HET: ATP; 2.30A {Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3hay_B*
Probab=1.00 E-value=1 Score=99.58 Aligned_cols=77 Identities=21% Similarity=0.272 Sum_probs=65.9
Q ss_pred CCCEEECCEEEEEE-CCEEEEECCCCCCCCCCCCEEEECCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCEE
Q ss_conf 98646320043341-53699952689888899985998269812377652003878838999728888863102357679
Q 005475 300 HHQMLPVGVVLSVR-GVQVIVEGAEKHNPLNEGSILWITESRVPLGLIDEIFGPVKNPYYVVRYNSENEIPAEIRVGTSI 378 (695)
Q Consensus 300 d~~I~pIGtIsSIV-dn~VIVkS~~e~~VLDeGSVLcLtEDRtvIGkVfEVFGPVsqPyYsVRFnS~eEI~~~IkvGtkV 378 (695)
...|++||+|+|++ +..+||++. .++.+|+.|| +++++.||+|+||||||++||++|++.+. .+ .. .+|++|
T Consensus 5 ~~~mk~lG~~~H~~~~g~lVvk~~---~vP~~na~Vy-~enk~~IGKV~DIfGPV~~pY~sVKp~~~-s~-~~-~~G~kl 77 (104)
T 2hvy_B 5 GEKMKRLGKVLHYAKQGFLIVRTN---WVPSLNDRVV-DKRLQFVGIVKDVFGPVKMPYVAIKPKVS-NP-EI-YVGEVL 77 (104)
T ss_dssp ---CEEEEEEEEEETTTEEEEECS---SCCCTTCEEE-CTTCCEEEEEEEEEEESSSCEEEEEECSS-CG-GG-GTTCEE
T ss_pred CCEEEEEEEEEEECCCCCEEEEEC---CCCCCCCEEE-CCCCCEEEEEEEEECCCCCCEEEEEECCC-CC-CC-CCCCEE
T ss_conf 514268378999828988999847---7788999859-68887817998987888875799996678-83-31-579879
Q ss_pred EECCC
Q ss_conf 96447
Q 005475 379 SFVQD 383 (695)
Q Consensus 379 YYVpe 383 (695)
|+.+.
T Consensus 78 YI~~~ 82 (104)
T 2hvy_B 78 YVDER 82 (104)
T ss_dssp EECC-
T ss_pred EECCC
T ss_conf 98475
No 5
>2ey4_C Small nucleolar RNP similar to GAR1; trimeric complex, structural genomics, PSI, protein structur initiative; 2.11A {Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3mqk_C 2rfk_C
Probab=1.00 E-value=1 Score=97.80 Aligned_cols=76 Identities=21% Similarity=0.281 Sum_probs=66.0
Q ss_pred CCCEEECCEEEEEE-CCEEEEECCCCCCCCCCCCEEEECCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCEE
Q ss_conf 98646320043341-53699952689888899985998269812377652003878838999728888863102357679
Q 005475 300 HHQMLPVGVVLSVR-GVQVIVEGAEKHNPLNEGSILWITESRVPLGLIDEIFGPVKNPYYVVRYNSENEIPAEIRVGTSI 378 (695)
Q Consensus 300 d~~I~pIGtIsSIV-dn~VIVkS~~e~~VLDeGSVLcLtEDRtvIGkVfEVFGPVsqPyYsVRFnS~eEI~~~IkvGtkV 378 (695)
...|+++|+|+|++ +..+||++. .++.+++.+| +++++.||+|+||||||++||++|++.+. .+ ..+ +|+++
T Consensus 5 ~~~mk~lG~~~h~~~~g~lV~k~~---~~P~~na~Vy-~e~~~~IGkV~dIfGPv~~pY~sVk~~~~-~~-~s~-~g~kl 77 (82)
T 2ey4_C 5 GEKMKRLGKVLHYAKQGFLIVRTN---WVPSLNDRVV-DKRLQFVGIVKDVFGPVKMPYVAIKPKVS-NP-EIY-VGEVL 77 (82)
T ss_dssp ---CBCCCCEEEEETTTEEEEECS---SCCCTTCEEE-CTTCCCCEEEEEEEEESSSCEEEEEECSS-SC-STT-BTCCC
T ss_pred CCEEEEEEEEEEECCCCCEEEEEC---CCCCCCCEEE-CCCCCEEEEEEEEECCCCCCEEEEEECCC-CH-HHC-CCCEE
T ss_conf 515379488999838988999857---7788999969-68887807999998888875899996778-80-022-79869
Q ss_pred EECC
Q ss_conf 9644
Q 005475 379 SFVQ 382 (695)
Q Consensus 379 YYVp 382 (695)
|+.+
T Consensus 78 Yi~~ 81 (82)
T 2ey4_C 78 YVDE 81 (82)
T ss_dssp EEC-
T ss_pred EECC
T ss_conf 8568
No 6
>1lsh_B Lipovitellin (LV-2); vitellogenin, lipoprotein, plasma apolipoprote apolipoprotein B, APOB; HET: PLD UPL; 1.90A {Ichthyomyzon unicuspis} SCOP: f.7.1.1
Probab=1.00 E-value=1 Score=25.98 Aligned_cols=17 Identities=6% Similarity=-0.089 Sum_probs=7.8
Q ss_pred EEEEECCCCCCCCCCCCEEEE
Q ss_conf 699952689888899985998
Q 005475 316 QVIVEGAEKHNPLNEGSILWI 336 (695)
Q Consensus 316 ~VIVkS~~e~~VLDeGSVLcL 336 (695)
++|+....+ +..--+|+
T Consensus 88 q~~~s~~~~----~~nwk~Ca 104 (319)
T 1lsh_B 88 KIVAVELSD----LSVWKLCA 104 (319)
T ss_dssp EEEEEESCT----TCCCEEEE
T ss_pred EEEEEECCC----CCCCEEEE
T ss_conf 999951676----77706898
No 7
>4aco_A Centromere DNA-binding protein complex CBF3 subun; 1.89A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=21.36 Aligned_cols=28 Identities=29% Similarity=0.417 Sum_probs=15.6
Q ss_pred CCCCEEEECCC-CEEEEEEEEEECCCCCCEE
Q ss_conf 99985998269-8123776520038788389
Q 005475 329 NEGSILWITES-RVPLGLIDEIFGPVKNPYY 358 (695)
Q Consensus 329 DeGSVLcLtED-RtvIGkVfEVFGPVsqPyY 358 (695)
..+++..+..+ -++=|.|.|=|-| +|-|
T Consensus 838 ~~~~~F~l~p~i~sIe~IIlEWFTP--Np~~ 866 (956)
T 4aco_A 838 TDEQEFMLDKSIDSIEGIILEWFTP--NAKY 866 (956)
T ss_dssp -------------------------------
T ss_pred CCCCEEEECCCCCHHHHHHHHHCCC--CCCC
T ss_conf 7886067478614399999987389--9343
No 8
>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}
Probab=1.00 E-value=1 Score=20.40 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCC
Q ss_conf 432258999998750337631012245767888
Q 005475 235 REEMTGGIDDDEDDEEDEVEMISVVDVDIDGGD 267 (695)
Q Consensus 235 Ge~~~~eiDdd~~eeed~~~m~~~~d~d~Deee 267 (695)
.++++...|.+.++.+++++-.+.-|.+.|+|+
T Consensus 299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 331 (335)
T 4fp9_B 299 DDDEEDNDEDDNDEDDDDEDDDEAEDNDEDEDD 331 (335)
T ss_dssp ---------------------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 432344667555677766443431213334455
No 9
>3eoj_A Bacteriochlorophyll A protein; excitation energy transfer, beta sheet, gamma-turns, chromophore, electron transport, magnesium; HET: BCL; 1.30A {Prosthecochloris aestuarii 2K} SCOP: b.75.1.1 PDB: 4bcl_A* 3oeg_A* 3vdi_A* 1m50_A* 3eni_A* 1ksa_A* 3bsd_A*
Probab=1.00 E-value=1 Score=16.51 Aligned_cols=101 Identities=18% Similarity=0.203 Sum_probs=0.0
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEECC----------EEEEEEC---CEEEE
Q ss_conf 6310122457678886778888897545667676899888750019998646320----------0433415---36999
Q 005475 253 VEMISVVDVDIDGGDEIDGCAREGPIRSKNELQVLPLVPQVNVVLQPHHQMLPVG----------VVLSVRG---VQVIV 319 (695)
Q Consensus 253 ~~m~~~~d~d~Deeed~~~~a~ggPiRTKNEi~elPPVppldIsI~ed~~I~pIG----------tIsSIVd---n~VIV 319 (695)
+...+.+|.||..|-... +-+.+|-.--+...|.+|-+...-.-....+||. .|.|||+ +.+.|
T Consensus 7 d~t~a~~dYeiiLeggsS---swg~vk~rAkvNvP~A~pLlpadcniKi~aKpld~~kgvVR~T~~ieSiVDstknkl~v 83 (366)
T 3eoj_A 7 DTTTAHSDYEIILEGGSS---SWGQVKGRAKVNVPAAIPLLPTDCNIRIDAKPLDAQKGVVRFTTKIESVVDSVKNTLNV 83 (366)
T ss_dssp -CCEEEEEEEEEECCTTC---CCEEEEEEEEECSCCSCSSSSEEEEEEEEEEECTTSTTCEEEEEEEEEEETTEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCC---CCCEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCCEEEEEEEEHHHHHHCCCEEEE
T ss_conf 776678871699716877---66303467760488777777766623762000576678699997613466521351589
Q ss_pred ECCCCCCCCCCCCEEEECCCCEEEEEEEEEE---CCCCCCEE
Q ss_conf 5268988889998599826981237765200---38788389
Q 005475 320 EGAEKHNPLNEGSILWITESRVPLGLIDEIF---GPVKNPYY 358 (695)
Q Consensus 320 kS~~e~~VLDeGSVLcLtEDRtvIGkVfEVF---GPVsqPyY 358 (695)
+++-.....+ ..+++-|...-+|.-.-.| |+|.+-||
T Consensus 84 E~DIANEtkd--rRiavGeG~vsVGdFSH~FsfEGsVvnm~Y 123 (366)
T 3eoj_A 84 EVDIANETKD--RRIAVGEGSLSVGDFSHSFSFEGSVVNMYY 123 (366)
T ss_dssp EEEEEESSSS--EEEEEEEEEEEETTEEEEEEEEEEEEEEES
T ss_pred EEEECCCCCC--CEEEECCCEEEECCCEEEEEEEEEEEEEEE
T ss_conf 9862357876--406733543876022145785204889999
No 10
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Probab=1.00 E-value=1 Score=16.32 Aligned_cols=26 Identities=31% Similarity=0.583 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 899989899986436897457985468899
Q 005475 666 NMGASSSRGRKPYHRGGGRFSGGRVRHQSR 695 (695)
Q Consensus 666 ~~~~~~~~gr~~~~~~ggrf~~grg~~~~~ 695 (695)
+.+..++.||||+++.| .||-|+-+.
T Consensus 48 traEv~G~grKp~rQKG----TGrAR~Gs~ 73 (201)
T 3r8s_E 48 TRAEVTGSGKKPWRQKG----TGRARSGSI 73 (201)
T ss_dssp BTTTSSCCCCCSSCSSS----SSSCCCCCT
T ss_pred CEEEECCCCCCCCCCCC----CCCCCCCCC
T ss_conf 40101488888775689----985365757
Done!