Query 022473
Match_columns 296
No_of_seqs 57 out of 59
Neff 3.0
Searched_HMMs 29240
Date Mon Mar 25 06:02:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022473.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/022473hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1fs1_A SKP2 F-BOX, cyclin A/CD 98.6 2.2E-08 7.5E-13 68.7 2.4 43 23-67 9-52 (53)
2 3l2o_B F-box only protein 4; s 98.4 3E-07 1E-11 86.4 5.5 47 25-73 7-54 (312)
3 2e31_A FBS1, F-box only protei 98.3 9.4E-07 3.2E-11 81.7 6.3 69 23-99 51-121 (297)
4 1p22_A F-BOX/WD-repeat protein 98.1 1.3E-06 4.6E-11 76.7 4.1 48 24-73 12-64 (435)
5 3v7d_B Cell division control p 98.0 3.9E-06 1.3E-10 73.2 4.3 46 24-71 16-63 (464)
6 2ovr_B FBW7, F-BOX/WD repeat p 97.9 4.8E-06 1.6E-10 72.9 3.9 48 23-72 19-67 (445)
7 2ast_B S-phase kinase-associat 96.5 0.00072 2.4E-08 57.6 1.3 44 23-68 9-53 (336)
8 2p1m_B Transport inhibitor res 95.2 0.012 4E-07 53.9 3.7 40 24-65 7-46 (594)
9 3ogk_B Coronatine-insensitive 94.2 0.021 7.2E-07 52.3 2.7 34 25-59 15-48 (592)
10 4ayb_P DNA-directed RNA polyme 79.5 0.62 2.1E-05 33.6 1.1 24 188-211 20-43 (48)
11 1qyp_A RNA polymerase II; tran 50.5 9.8 0.00033 26.5 2.5 32 191-232 15-48 (57)
12 1vq8_Z 50S ribosomal protein L 42.0 11 0.00036 29.2 1.7 28 173-204 13-41 (83)
13 2apo_B Ribosome biogenesis pro 38.5 3.7 0.00013 30.4 -1.3 37 173-211 2-38 (60)
14 4avr_A PA4485; unknown functio 31.1 17 0.00059 28.8 1.3 31 188-224 55-85 (95)
15 4hfx_A Transcription elongatio 30.2 14 0.00047 29.5 0.6 58 26-97 13-72 (97)
16 2aus_D NOP10, ribosome biogene 30.2 6.1 0.00021 29.3 -1.3 37 174-212 2-38 (60)
17 1twf_I B12.6, DNA-directed RNA 30.1 46 0.0016 26.6 3.7 92 126-235 5-109 (122)
18 1ffk_W Ribosomal protein L37AE 30.0 25 0.00084 26.8 2.0 23 173-199 13-35 (73)
19 1p91_A Ribosomal RNA large sub 28.7 22 0.00077 29.4 1.7 13 226-238 17-29 (269)
20 3cc2_Z 50S ribosomal protein L 24.6 30 0.001 28.6 1.7 23 173-199 46-68 (116)
21 3j21_i 50S ribosomal protein L 24.5 37 0.0013 26.5 2.1 23 174-200 22-44 (83)
22 2fiy_A Protein FDHE homolog; F 24.2 43 0.0015 31.0 2.9 12 223-234 249-260 (309)
23 3jyw_9 60S ribosomal protein L 23.4 32 0.0011 26.2 1.5 24 173-200 12-35 (72)
24 1oy3_D Transcription factor in 23.4 17 0.00058 29.1 0.0 19 241-259 259-277 (282)
25 3h0g_L DNA-directed RNA polyme 22.7 29 0.00099 25.8 1.1 12 190-201 37-48 (63)
26 2jvm_A Uncharacterized protein 21.7 25 0.00087 27.3 0.7 11 190-200 52-62 (80)
27 3po3_S Transcription elongatio 20.9 62 0.0021 27.6 3.0 45 177-232 118-170 (178)
No 1
>1fs1_A SKP2 F-BOX, cyclin A/CDK2-associated P19; F-BOX, LRR, leucine-rich repeat, SCF, ubiquitin, ubiquitin protein ligase; 1.80A {Homo sapiens} SCOP: a.158.1.1 PDB: 1ldk_E
Probab=98.56 E-value=2.2e-08 Score=68.67 Aligned_cols=43 Identities=21% Similarity=0.366 Sum_probs=37.7
Q ss_pred CCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHH
Q 022473 23 SGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKL 67 (296)
Q Consensus 23 ~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~ 67 (296)
-..|++|||..||.+|. |++++++++|||+|+.++. +.+||.+
T Consensus 9 ~~~LP~eil~~I~~~L~--~~dl~~~~~Vck~w~~~~~~~~lW~~l 52 (53)
T 1fs1_A 9 WDSLPDELLLGIFSCLC--LPELLKVSGVCKRWYRLASDESLWQTL 52 (53)
T ss_dssp CCSSCHHHHHHHHTTSC--GGGHHHHHTTCHHHHHHHTCGGGC---
T ss_pred HHHCCHHHHHHHHHcCC--HHHHHHHHHHHHHHHHHhCChHHHHhc
Confidence 36799999999999998 9999999999999999999 6899864
No 2
>3l2o_B F-box only protein 4; small G protein fold, UBL conjugation pathway, ubiquitin Pro ligase, protein binding-cell cycle complex; 2.80A {Homo sapiens}
Probab=98.36 E-value=3e-07 Score=86.39 Aligned_cols=47 Identities=19% Similarity=0.321 Sum_probs=44.4
Q ss_pred ccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhc
Q 022473 25 IFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAP 73 (296)
Q Consensus 25 ~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP 73 (296)
.||+||++.||+.|+ |++||++++|||.|+.+|+ +.|||.+|.+..|
T Consensus 7 ~LP~ei~l~IlsfL~--p~DL~~l~~vcr~Wr~la~D~~LWr~~l~rd~~ 54 (312)
T 3l2o_B 7 RLPIDVQLYILSFLS--PHDLCQLGSTNHYWNETVRDPILWRYFLLRDLP 54 (312)
T ss_dssp HSCHHHHHHHHHTSC--HHHHHHHHTTCHHHHHHHTCHHHHHHHHHSSGG
T ss_pred hCCHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHhccchHHHHHHhccCC
Confidence 589999999999999 9999999999999999999 7999999997655
No 3
>2e31_A FBS1, F-box only protein 2; ubiquitin, SCF, ubiquitin ligase, FBS1; 2.40A {Mus musculus} PDB: 2e32_A
Probab=98.27 E-value=9.4e-07 Score=81.72 Aligned_cols=69 Identities=14% Similarity=0.220 Sum_probs=53.2
Q ss_pred CCccchHHHHHHHHHcCCChHHHH-HHhhccHHHHHHHH-HHhHHHHHHhhhchhHHHhhcCCCCCCCCCchhHhHHHh
Q 022473 23 SGIFNERILLLVFESVGWDLHMLC-LTASLDRKLRAIAE-RLLWRKLCECRAPRMIETLANGAPNGRINGGWHALAKLM 99 (296)
Q Consensus 23 ~g~LsEdVLllVF~~LnwdPr~la-r~ACVCrkfr~lar-rvLWRe~C~~raP~mv~dL~~~~~~~~i~GgW~AL~KLl 99 (296)
-..|++|||.+||.+|. |+.|+ +.+||||+|++|+. +.+||..|..+.- ............|..+...-
T Consensus 51 ~~~LP~ell~~Il~~Lp--~~~L~~r~~~VCk~Wr~l~~~~~~w~~~~~~~g~------~~~~~~~~~~~~Wk~~y~~~ 121 (297)
T 2e31_A 51 LAELPEPLLLRVLAELP--ATELVQACRLVCLRWKELVDGAPLWLLKCQQEGL------VPEGSADEERDHWQQFYFLS 121 (297)
T ss_dssp TTSSCHHHHHHHHHTSC--HHHHHHTGGGTCHHHHHHHTSHHHHHHHHHHTTC------CCC-----CCSCHHHHHHHH
T ss_pred hhhCCHHHHHHHHHcCC--HHHHHHHHHHHhHHHHHHhcChHHHHHHhhccCc------ccccccCCCCCChhhhhehe
Confidence 46799999999999998 99999 99999999999999 7999999998721 11100011355699887543
No 4
>1p22_A F-BOX/WD-repeat protein 1A; ubiquitination, degradation, signaling protein; HET: SEP; 2.95A {Homo sapiens} SCOP: a.158.1.1 b.69.4.1
Probab=98.13 E-value=1.3e-06 Score=76.67 Aligned_cols=48 Identities=19% Similarity=0.335 Sum_probs=44.3
Q ss_pred CccchH----HHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhhc
Q 022473 24 GIFNER----ILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRAP 73 (296)
Q Consensus 24 g~LsEd----VLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~raP 73 (296)
..||++ |++.||..|. |+.|+++++|||+|+.++. +.|||.+|.+.++
T Consensus 12 ~~lp~e~~~~~~~~i~~~l~--~~~l~~~~~v~~~w~~~~~~~~~w~~~~~~~~~ 64 (435)
T 1p22_A 12 TALPARGLDHIAENILSYLD--AKSLCAAELVCKEWYRVTSDGMLWKKLIERMVR 64 (435)
T ss_dssp HHTGGGTCHHHHHHHHTTCC--HHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHT
T ss_pred HHCCcchHHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHhcChHHHHHHHHhhcC
Confidence 358888 9999999998 9999999999999999999 5999999998864
No 5
>3v7d_B Cell division control protein 4; WD 40 domain, phospho-peptide complex, E3 ubiquitin ligase, cell cycle, phospho binding protein, phosphorylation; HET: SEP; 2.31A {Saccharomyces cerevisiae} PDB: 1nex_B* 3mks_B*
Probab=98.00 E-value=3.9e-06 Score=73.16 Aligned_cols=46 Identities=17% Similarity=0.268 Sum_probs=42.2
Q ss_pred CccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH--HHhHHHHHHhh
Q 022473 24 GIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE--RLLWRKLCECR 71 (296)
Q Consensus 24 g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar--rvLWRe~C~~r 71 (296)
..||++|++.||..|. |+.|++++.|||+|+.++. +.+||++|.+.
T Consensus 16 ~~lp~~~~~~i~~~l~--~~~l~~~~~v~~~w~~~~~~~~~~w~~~~~~~ 63 (464)
T 3v7d_B 16 TSLPFEISLKIFNYLQ--FEDIINSLGVSQNWNKIIRKSTSLWKKLLISE 63 (464)
T ss_dssp HHSCHHHHHHHHTTSC--HHHHHHHHTTCHHHHHHHTTCHHHHHHHHHHT
T ss_pred HHCCHHHHHHHHhcCC--HHHHHHHHHHHHHHHHHHcCCHHHHHHHHhcc
Confidence 4699999999999996 9999999999999999998 59999999644
No 6
>2ovr_B FBW7, F-BOX/WD repeat protein 7, F-box PROT; WD40 domains, double phosphorylation, transcription-C complex; HET: TPO; 2.50A {Homo sapiens} SCOP: a.158.1.1 b.69.4.1 PDB: 2ovp_B* 2ovq_B*
Probab=97.95 E-value=4.8e-06 Score=72.93 Aligned_cols=48 Identities=27% Similarity=0.417 Sum_probs=44.2
Q ss_pred CCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHHHhhh
Q 022473 23 SGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLCECRA 72 (296)
Q Consensus 23 ~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C~~ra 72 (296)
-..||++++..||..|. |++|+++++|||+|+.++. +.+||.+|.+..
T Consensus 19 ~~~lp~e~~~~i~~~l~--~~~l~~~~~v~~~~~~~~~~~~~w~~~~~~~~ 67 (445)
T 2ovr_B 19 ISLLPKELALYVLSFLE--PKDLLQAAQTCRYWRILAEDNLLWREKCKEEG 67 (445)
T ss_dssp TTSSCHHHHHHHHTTSC--HHHHHHHTTSCHHHHHHHTCSHHHHHHHTTTT
T ss_pred hHHCCHHHHHHHHHhCC--HHHHHHHHHHhHHHHhhcCchhHhhhheeecc
Confidence 36799999999999997 9999999999999999999 689999998664
No 7
>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A
Probab=96.48 E-value=0.00072 Score=57.64 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=38.3
Q ss_pred CCccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH-HHhHHHHH
Q 022473 23 SGIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE-RLLWRKLC 68 (296)
Q Consensus 23 ~g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar-rvLWRe~C 68 (296)
-..||+|||..||++|. ++++.+++.|||+|+.++. +.+|+.+-
T Consensus 9 ~~~LP~eil~~If~~L~--~~d~~~~~~vc~~W~~~~~~~~~~~~l~ 53 (336)
T 2ast_B 9 WDSLPDELLLGIFSCLC--LPELLKVSGVCKRWYRLASDESLWQTLD 53 (336)
T ss_dssp SSSSCHHHHHHHHTTSC--HHHHHHTTSSCHHHHHHHTCSTTSSEEE
T ss_pred hhhCCHHHHHHHHHhCC--HHHHHHHHHHHHHHHHHhcCchhheeec
Confidence 36799999999999998 9999999999999999986 56777543
No 8
>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*
Probab=95.23 E-value=0.012 Score=53.85 Aligned_cols=40 Identities=23% Similarity=0.092 Sum_probs=32.2
Q ss_pred CccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHHHHhHH
Q 022473 24 GIFNERILLLVFESVGWDLHMLCLTASLDRKLRAIAERLLWR 65 (296)
Q Consensus 24 g~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~larrvLWR 65 (296)
..||+|||..||++|. +++++++++.|||+|+.+ ....|+
T Consensus 7 ~~LPdevL~~If~~L~-~~~d~~~~s~vck~W~~~-~~~~~~ 46 (594)
T 2p1m_B 7 LSFPEEVLEHVFSFIQ-LDKDRNSVSLVCKSWYEI-ERWCRR 46 (594)
T ss_dssp ---CHHHHHHHHHTCC-CHHHHHHHHTSCHHHHHH-HHHHCC
T ss_pred hhCCHHHHHHHHhhcC-CchhHHHHHHHHHHHHHh-hhhhce
Confidence 4699999999999997 589999999999999998 344454
No 9
>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*
Probab=94.24 E-value=0.021 Score=52.33 Aligned_cols=34 Identities=12% Similarity=0.014 Sum_probs=30.9
Q ss_pred ccchHHHHHHHHHcCCChHHHHHHhhccHHHHHHH
Q 022473 25 IFNERILLLVFESVGWDLHMLCLTASLDRKLRAIA 59 (296)
Q Consensus 25 ~LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~la 59 (296)
.||||||..||.+|. +++++++++.|||+|+.+.
T Consensus 15 ~LPdeil~~I~~~L~-~~~d~~~~s~vck~W~~~~ 48 (592)
T 3ogk_B 15 ATVDDVIEQVMTYIT-DPKDRDSASLVCRRWFKID 48 (592)
T ss_dssp CCGGGTHHHHHTTCC-CHHHHHHHTTSCHHHHHHH
T ss_pred CCCHHHHHHHHHhcC-CHHHHHHHHHHhHHHHHhh
Confidence 599999999999993 3999999999999999884
No 10
>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X
Probab=79.50 E-value=0.62 Score=33.56 Aligned_cols=24 Identities=29% Similarity=0.711 Sum_probs=19.7
Q ss_pred ccccccCCCCCcccchhhhccccc
Q 022473 188 LEERVKCPYCGARVWSMTAARLVP 211 (296)
Q Consensus 188 l~~~~~CpyC~ar~Wsm~~A~~lp 211 (296)
.-|.++|||||-|+.=++-+.++.
T Consensus 20 ~lP~IrCpyCGyrii~KvR~p~vK 43 (48)
T 4ayb_P 20 VLPGVRCPYCGYKIIFMVRKPTIK 43 (48)
T ss_dssp CCSSSCCTTTCCSCEECCCCCSCE
T ss_pred hCCCcccCccCcEEEEEecCCcce
Confidence 348899999999998888777665
No 11
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=50.52 E-value=9.8 Score=26.51 Aligned_cols=32 Identities=22% Similarity=0.747 Sum_probs=22.4
Q ss_pred cccCCCCCcc--cchhhhcccccccccccccccCCceeEEEeec
Q 022473 191 RVKCPYCGAR--VWSMTAARLVPKSAARRLGSHDGGLEYFVCIN 232 (296)
Q Consensus 191 ~~~CpyC~ar--~Wsm~~A~~lp~sa~rrlG~~edgveyyVC~N 232 (296)
.+.||-|+.+ +|..++-+ .+-|.---+|+|.+
T Consensus 15 ~~~Cp~Cg~~~~~~~q~Q~r----------sadep~T~fy~C~~ 48 (57)
T 1qyp_A 15 KITCPKCGNDTAYWWEMQTR----------AGDEPSTIFYKCTK 48 (57)
T ss_dssp ECCCTTTCCSEEEEEEECCS----------SSSCSSEEEEEESS
T ss_pred EeECCCCCCCEEEEEEeecc----------cCCCCCcEEEEcCC
Confidence 4789999995 78766643 22234478999986
No 12
>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...
Probab=41.99 E-value=11 Score=29.15 Aligned_cols=28 Identities=18% Similarity=0.249 Sum_probs=17.6
Q ss_pred chhhHHHHHhhccccccccccCCCCCcc-cchh
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGAR-VWSM 204 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~ar-~Wsm 204 (296)
-|.+|+++.+.... .-.||||++. +++.
T Consensus 13 lRk~vk~ie~~q~~----~y~Cp~CG~~~v~r~ 41 (83)
T 1vq8_Z 13 SRRRVAEIESEMNE----DHACPNCGEDRVDRQ 41 (83)
T ss_dssp HHHHHHHHHHHHHS----CEECSSSCCEEEEEE
T ss_pred HHHHHHHHHHhccc----cCcCCCCCCcceecc
Confidence 34556666554433 4689999984 6554
No 13
>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A
Probab=38.46 E-value=3.7 Score=30.36 Aligned_cols=37 Identities=16% Similarity=0.356 Sum_probs=25.6
Q ss_pred chhhHHHHHhhccccccccccCCCCCcccchhhhccccc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGARVWSMTAARLVP 211 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp 211 (296)
|+|++++|=.-+.--| ...||.||..+=+-+-|+.=|
T Consensus 2 Mks~mr~C~~CgvYTL--k~~CP~CG~~T~~~hParfSp 38 (60)
T 2apo_B 2 VEMRMKKCPKCGLYTL--KEICPKCGEKTVIPKPPKFSL 38 (60)
T ss_dssp -CCCCEECTTTCCEES--SSBCSSSCSBCBCCCCCCCCT
T ss_pred chhhceeCCCCCCEec--cccCcCCCCcCCCCCCCCCCC
Confidence 3444444444444455 478999999999988888777
No 14
>4avr_A PA4485; unknown function, GRAM-negative bacteria, infectious disease structure-based inhibitor design; 1.08A {Pseudomonas aeruginosa PA01}
Probab=31.12 E-value=17 Score=28.83 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=25.3
Q ss_pred ccccccCCCCCcccchhhhcccccccccccccccCCc
Q 022473 188 LEERVKCPYCGARVWSMTAARLVPKSAARRLGSHDGG 224 (296)
Q Consensus 188 l~~~~~CpyC~ar~Wsm~~A~~lp~sa~rrlG~~edg 224 (296)
....-+||||+.|+.||- +.|+++||..+.|
T Consensus 55 VrVnDRGP~~~griIDLS------~aAa~~Lg~~~~G 85 (95)
T 4avr_A 55 VRINDRGPFRRGRIIDVS------RKAAEGLGMIRSG 85 (95)
T ss_dssp EEEEECCCCSTTEEEEEC------HHHHHHHTCTTTS
T ss_pred EEEccCCCCCCCCEEEeC------HHHHHHhCCcCCC
Confidence 333468999999999975 5688999999988
No 15
>4hfx_A Transcription elongation factor B polypeptide 3; structural genomics, PSI-biology, northeast structural genom consortium, NESG; 2.54A {Homo sapiens}
Probab=30.16 E-value=14 Score=29.51 Aligned_cols=58 Identities=17% Similarity=0.283 Sum_probs=31.1
Q ss_pred cchHHHHHHHHHcCCChHHHHHHhhccHHHHHHHH--HHhHHHHHHhhhchhHHHhhcCCCCCCCCCchhHhHH
Q 022473 26 FNERILLLVFESVGWDLHMLCLTASLDRKLRAIAE--RLLWRKLCECRAPRMIETLANGAPNGRINGGWHALAK 97 (296)
Q Consensus 26 LsEdVLllVF~~LnwdPr~lar~ACVCrkfr~lar--rvLWRe~C~~raP~mv~dL~~~~~~~~i~GgW~AL~K 97 (296)
.+=++|.-|+.+.+ |..|.++==-+. .++. +.||+.+|.+-+|.- .+ ..+-.|..|.-
T Consensus 13 ~Py~lL~PVLek~t--p~QL~~IE~~nP---~L~~dTdeLWk~~c~rdF~~~-------~p--~e~esWRelY~ 72 (97)
T 4hfx_A 13 VPYSVLEPVLERCT--PDQLYRIEEYNH---VLIEETDQLWKVHCHRDFKEE-------RP--EEYESWREMYL 72 (97)
T ss_dssp -------CCGGGCC--HHHHHHHHTC---------CCHHHHHHHC----CCS-------CC--CSSSCHHHHHH
T ss_pred CcHHHHHHHHccCC--HHHHHHHHHhCc---ccchhhHHHHHHHHHhHCccc-------CC--CCCCCHHHHHH
Confidence 35577888888865 999999988876 5555 799999999999941 11 33458988753
No 16
>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B
Probab=30.15 E-value=6.1 Score=29.28 Aligned_cols=37 Identities=27% Similarity=0.578 Sum_probs=24.5
Q ss_pred hhhHHHHHhhccccccccccCCCCCcccchhhhcccccc
Q 022473 174 KSTTRACLIRRRVELEERVKCPYCGARVWSMTAARLVPK 212 (296)
Q Consensus 174 ~Srvr~~Li~~~~~l~~~~~CpyC~ar~Wsm~~A~~lp~ 212 (296)
+|++|+|=.-..--| ...||.||..+-+-+-|+.=|.
T Consensus 2 ks~mr~C~~Cg~YTL--k~~CP~CG~~t~~ahParfSP~ 38 (60)
T 2aus_D 2 RFRIRKCPKCGRYTL--KETCPVCGEKTKVAHPPRFSPE 38 (60)
T ss_dssp --CCEECTTTCCEES--SSBCTTTCSBCEESSCCCCCSC
T ss_pred CccceECCCCCCEEc--cccCcCCCCccCCCCCCCCCCC
Confidence 444444444333344 4789999999999999888773
No 17
>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...
Probab=30.05 E-value=46 Score=26.57 Aligned_cols=92 Identities=18% Similarity=0.424 Sum_probs=50.0
Q ss_pred ccccccCCccccccc--CCceeeecCCCCCCCCCCCCceeeeeeeccccchhhHH--HHHh-h----ccccccccccCCC
Q 022473 126 RFSKTSGRSFLTKKC--RGDLLYVSDPCEHPMGNKEDDLGIFRGVFRGFLKSTTR--ACLI-R----RRVELEERVKCPY 196 (296)
Q Consensus 126 rfSRtsG~sfL~~rc--R~D~LYVsDpCeH~~~ge~~d~glfRGVFk~F~~Srvr--~~Li-~----~~~~l~~~~~Cpy 196 (296)
+|-.+-|+-|.++.= .....|+|.-|.+... ...--+||=.+.. .++ .-++ + ...+ .....||-
T Consensus 5 ~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~--~~~~~v~~~~~~~----~~~e~~~v~~~~~~~~t~p-~t~~~Cp~ 77 (122)
T 1twf_I 5 RFCRDCNNMLYPREDKENNRLLFECRTCSYVEE--AGSPLVYRHELIT----NIGETAGVVQDIGSDPTLP-RSDRECPK 77 (122)
T ss_dssp CBCSSSCCBCEEEEETTTTEEEEECSSSSCEEE--CSCSEEEEEESSC----CTTSSTTCCTTGGGCTTSC-CCCCCCTT
T ss_pred CcccccCccCcccccCcCCCCEEECCcCCCeee--cCccEEEEEeecc----ccccccccccccccccccc-ccCCCCCC
Confidence 455566666665543 3468999999988743 2222344433221 111 1111 1 1111 12478999
Q ss_pred CCcc--cchhhhcccccccccccccccCCc-eeEEEeec-Cce
Q 022473 197 CGAR--VWSMTAARLVPKSAARRLGSHDGG-LEYFVCIN-GHL 235 (296)
Q Consensus 197 C~ar--~Wsm~~A~~lp~sa~rrlG~~edg-veyyVC~N-GHv 235 (296)
|+.+ +|-..| +.+-|++ .-+|+|.| ||.
T Consensus 78 C~~~~a~~~q~q-----------~rsade~~t~fy~C~~C~~~ 109 (122)
T 1twf_I 78 CHSRENVFFQSQ-----------QRRKDTSMVLFFVCLSCSHI 109 (122)
T ss_dssp TCCCCEEEEECS-----------SCCTTCCCCEEEEETTTCCE
T ss_pred CCCCEEEEEEec-----------CccCCCCceEEEEeCCCCCE
Confidence 9996 554433 2233444 88999998 663
No 18
>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*
Probab=30.04 E-value=25 Score=26.79 Aligned_cols=23 Identities=30% Similarity=0.743 Sum_probs=15.4
Q ss_pred chhhHHHHHhhccccccccccCCCCCc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGA 199 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~a 199 (296)
-|.+|+++.+.++++ -.||||+.
T Consensus 13 lRK~vkkie~~q~~k----y~C~fCgk 35 (73)
T 1ffk_W 13 IRVRVRDVEIKHKKK----YKCPVCGF 35 (73)
T ss_pred HHHHHHHHHHhcccC----ccCCCCCC
Confidence 455666666654444 67999997
No 19
>1p91_A Ribosomal RNA large subunit methyltransferase A; RLMA, RRMA, 23S rRNA, NESG, structural genomics, PSI, protein structure initiative; HET: SAM; 2.80A {Escherichia coli} SCOP: c.66.1.33
Probab=28.69 E-value=22 Score=29.39 Aligned_cols=13 Identities=15% Similarity=0.483 Sum_probs=10.3
Q ss_pred eEEEeecCceeee
Q 022473 226 EYFVCINGHLHGS 238 (296)
Q Consensus 226 eyyVC~NGHv~G~ 238 (296)
++|.|.|+|..+.
T Consensus 17 ~~~~C~~~~~~~~ 29 (269)
T 1p91_A 17 NSYICPQRHQFDM 29 (269)
T ss_dssp TEEECTTCCEEEB
T ss_pred CEEECCCCCcCCc
Confidence 3899999998653
No 20
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z
Probab=24.56 E-value=30 Score=28.58 Aligned_cols=23 Identities=17% Similarity=0.394 Sum_probs=15.0
Q ss_pred chhhHHHHHhhccccccccccCCCCCc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGA 199 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~a 199 (296)
-|.+|+++.+...++ -.||||+.
T Consensus 46 lRK~vkkiE~~q~ak----ytCPfCGk 68 (116)
T 3cc2_Z 46 SRRRVAEIESEMNED----HACPNCGE 68 (116)
T ss_dssp HHHHHHHHHHHHHSC----EECSSSCC
T ss_pred HHHHHHHHHHHhccC----CcCCCCCC
Confidence 345566665554444 78999997
No 21
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=24.49 E-value=37 Score=26.49 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=14.7
Q ss_pred hhhHHHHHhhccccccccccCCCCCcc
Q 022473 174 KSTTRACLIRRRVELEERVKCPYCGAR 200 (296)
Q Consensus 174 ~Srvr~~Li~~~~~l~~~~~CpyC~ar 200 (296)
|.+|+++-+..+++ -.||||+..
T Consensus 22 RK~vkkie~~q~~k----y~CpfCGk~ 44 (83)
T 3j21_i 22 RRRVAAVEAKMRQK----HTCPVCGRK 44 (83)
T ss_dssp HHHHHHHHHHHHSC----BCCSSSCSS
T ss_pred HHHHHHHHHHhhcc----cCCCCCCCc
Confidence 44555555554444 679999974
No 22
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1
Probab=24.24 E-value=43 Score=30.98 Aligned_cols=12 Identities=17% Similarity=0.127 Sum_probs=9.9
Q ss_pred CceeEEEeecCc
Q 022473 223 GGLEYFVCINGH 234 (296)
Q Consensus 223 dgveyyVC~NGH 234 (296)
++++++||.+=|
T Consensus 249 ~~~r~e~C~~C~ 260 (309)
T 2fiy_A 249 AVLRAETCPSCQ 260 (309)
T ss_dssp CSEEEEEETTTT
T ss_pred cceEEEEccccc
Confidence 569999998755
No 23
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}
Probab=23.41 E-value=32 Score=26.22 Aligned_cols=24 Identities=21% Similarity=0.686 Sum_probs=16.3
Q ss_pred chhhHHHHHhhccccccccccCCCCCcc
Q 022473 173 LKSTTRACLIRRRVELEERVKCPYCGAR 200 (296)
Q Consensus 173 ~~Srvr~~Li~~~~~l~~~~~CpyC~ar 200 (296)
-|.+|+++-+..+++ -.||||+..
T Consensus 12 lRK~vkkie~~q~~k----y~C~fCgk~ 35 (72)
T 3jyw_9 12 LRRQVKKLEIQQHAR----YDCSFCGKK 35 (72)
T ss_dssp HHTTTHHHHHHHHSC----BCCSSCCSS
T ss_pred HHHHHHHHHHHhccC----ccCCCCCCc
Confidence 345666766665555 679999974
No 24
>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D
Probab=23.39 E-value=17 Score=29.14 Aligned_cols=19 Identities=37% Similarity=0.644 Sum_probs=0.0
Q ss_pred eeecCCCcccCCCCCCCCC
Q 022473 241 LVPLSSEEDACDEDDDEDG 259 (296)
Q Consensus 241 l~PLs~se~~~~~~~~~~~ 259 (296)
.-||..+....++|+++++
T Consensus 259 ~tpl~~a~~~~~~~~~~~~ 277 (282)
T 1oy3_D 259 LSPCSSSGSDSDSDNRDEG 277 (282)
T ss_dssp -------------------
T ss_pred cccccccCCcccccccccc
Confidence 3466555554444433333
No 25
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=22.71 E-value=29 Score=25.76 Aligned_cols=12 Identities=50% Similarity=1.129 Sum_probs=10.1
Q ss_pred ccccCCCCCccc
Q 022473 190 ERVKCPYCGARV 201 (296)
Q Consensus 190 ~~~~CpyC~ar~ 201 (296)
..++||+|+.|+
T Consensus 37 ~~iRC~~CG~RI 48 (63)
T 3h0g_L 37 EVIRCRECGHRV 48 (63)
T ss_dssp SCCCCSSSCCCC
T ss_pred CceECCCCCcEE
Confidence 459999999984
No 26
>2jvm_A Uncharacterized protein; alpha+beta, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodobacter sphaeroides 2}
Probab=21.72 E-value=25 Score=27.34 Aligned_cols=11 Identities=45% Similarity=1.029 Sum_probs=9.1
Q ss_pred ccccCCCCCcc
Q 022473 190 ERVKCPYCGAR 200 (296)
Q Consensus 190 ~~~~CpyC~ar 200 (296)
....||||+.+
T Consensus 52 g~~~CpYCg~~ 62 (80)
T 2jvm_A 52 GFVECGYCDRR 62 (80)
T ss_dssp CEEECSSSSCE
T ss_pred CeEECCCCCCE
Confidence 34789999987
No 27
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A
Probab=20.92 E-value=62 Score=27.57 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=27.1
Q ss_pred HHHHHhhcccccccc-----ccCCCCCcc--cchhhhcccccccccccccccCCc-eeEEEeec
Q 022473 177 TRACLIRRRVELEER-----VKCPYCGAR--VWSMTAARLVPKSAARRLGSHDGG-LEYFVCIN 232 (296)
Q Consensus 177 vr~~Li~~~~~l~~~-----~~CpyC~ar--~Wsm~~A~~lp~sa~rrlG~~edg-veyyVC~N 232 (296)
.++.|.+.+.+..++ ..||-|+.+ +|-..|- | +-|++ --+|+|.|
T Consensus 118 ~~e~l~~~~~~~~~~~~t~~~~Cp~C~~~~a~~~q~Q~----r-------saDE~mt~f~~C~~ 170 (178)
T 3po3_S 118 AKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQT----R-------SAAAPLTTFCTCEA 170 (178)
T ss_dssp HHHHHHHTBCCCCCCCCBSSSCCSSSCCSCEECCCCCC----S-------CTTSCCCCCEEETT
T ss_pred HHHHHHHhhhccccCCCcCCcCCCCCCCCceEEEEeec----c-------cCCCCCcEEEEcCC
Confidence 344565555554333 589999985 5544332 1 22444 78999986
Done!