Query 025767
Match_columns 248
No_of_seqs 61 out of 63
Neff 3.5
Searched_HMMs 29240
Date Mon Mar 25 17:10:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025767.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/025767hhsearch_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 3.4E-08 1.2E-12 66.6 3.4 42 20-63 10-52 (53)
2 2e31_A FBS1, F-box only protei 98.4 2.4E-07 8.2E-12 84.3 5.5 69 18-93 50-120 (297)
3 3l2o_B F-box only protein 4; s 98.2 7.4E-07 2.5E-11 82.3 4.6 47 21-69 7-54 (312)
4 1p22_A F-BOX/WD-repeat protein 98.0 3.4E-06 1.2E-10 73.4 4.8 48 20-69 12-64 (435)
5 2ovr_B FBW7, F-BOX/WD repeat p 98.0 4.3E-06 1.5E-10 72.5 4.9 47 20-68 20-67 (445)
6 3v7d_B Cell division control p 97.9 7.6E-06 2.6E-10 70.7 4.5 46 20-67 16-63 (464)
7 2ast_B S-phase kinase-associat 96.6 0.00093 3.2E-08 56.3 2.5 41 20-62 10-51 (336)
8 2p1m_B Transport inhibitor res 95.5 0.0095 3.2E-07 53.9 3.8 40 20-61 7-46 (594)
9 3ogk_B Coronatine-insensitive 94.2 0.027 9.4E-07 51.0 3.3 36 19-55 13-48 (592)
10 1twf_I B12.6, DNA-directed RNA 79.7 1.2 3.9E-05 35.3 2.9 81 136-229 23-109 (122)
11 4ayb_P DNA-directed RNA polyme 68.5 1.9 6.5E-05 30.2 1.3 23 182-204 20-42 (48)
12 3qt1_I DNA-directed RNA polyme 66.3 4.2 0.00014 33.0 3.2 94 120-226 25-125 (133)
13 3h0g_I DNA-directed RNA polyme 55.9 5.8 0.0002 30.8 2.2 76 137-226 24-105 (113)
14 4hfx_A Transcription elongatio 48.3 6.8 0.00023 30.5 1.5 57 22-91 13-71 (97)
15 1qyp_A RNA polymerase II; tran 46.9 18 0.00061 24.6 3.3 32 185-226 15-48 (57)
16 1vq8_Z 50S ribosomal protein L 38.8 18 0.00061 27.2 2.4 30 166-199 12-42 (83)
17 1tfi_A Transcriptional elongat 33.4 48 0.0016 22.5 3.7 33 184-226 8-42 (50)
18 1ffk_W Ribosomal protein L37AE 30.4 28 0.00097 25.8 2.3 24 166-193 12-35 (73)
19 3j21_i 50S ribosomal protein L 30.2 32 0.0011 26.2 2.6 25 166-194 20-44 (83)
20 3cc2_Z 50S ribosomal protein L 26.8 35 0.0012 27.5 2.4 24 166-193 45-68 (116)
21 3iz5_m 60S ribosomal protein L 24.1 45 0.0016 25.8 2.5 25 166-194 21-45 (92)
22 3jyw_9 60S ribosomal protein L 23.3 27 0.00091 25.9 1.0 25 166-194 11-35 (72)
23 3izc_m 60S ribosomal protein R 22.3 55 0.0019 25.4 2.7 24 166-193 21-44 (92)
24 3po3_S Transcription elongatio 21.9 93 0.0032 25.9 4.2 46 171-226 118-170 (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=98.57 E-value=3.4e-08 Score=66.64 Aligned_cols=42 Identities=21% Similarity=0.497 Sum_probs=37.3
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHH
Q 025767 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEF 63 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~ 63 (248)
..||+|+|..||.+|. |++++++++|||+|+.++.. .+||.+
T Consensus 10 ~~LP~eil~~I~~~L~--~~dl~~~~~Vck~w~~~~~~~~lW~~l 52 (53)
T 1fs1_A 10 DSLPDELLLGIFSCLC--LPELLKVSGVCKRWYRLASDESLWQTL 52 (53)
T ss_dssp CSSCHHHHHHHHTTSC--GGGHHHHHTTCHHHHHHHTCGGGC---
T ss_pred HHCCHHHHHHHHHcCC--HHHHHHHHHHHHHHHHHhCChHHHHhc
Confidence 6799999999999997 99999999999999999998 899863
No 2
>2e31_A FBS1, F-box only protein 2; ubiquitin, SCF, ubiquitin ligase, FBS1; 2.40A {Mus musculus} PDB: 2e32_A
Probab=98.40 E-value=2.4e-07 Score=84.26 Aligned_cols=69 Identities=16% Similarity=0.363 Sum_probs=53.9
Q ss_pred cCCcCcHHHHHHHHHhcCCChHHHH-HHhhcchhHHHHHHH-hhhHHHHHhhhhhhHHhhhhcCCCCCCCcHHHHHhh
Q 025767 18 TKGHLSEDVIFLVFQHMNWNPKTIA-ALSCTCKWFDDLAKR-VLWKEFCRTRAPKMMVDLQSSGSHSVDGNWRALGKL 93 (248)
Q Consensus 18 ~~g~L~EdvL~~VF~~lnwdPr~la-r~AcVcr~f~~lar~-vlWr~~C~~raP~mv~~L~~~~~~~~~G~W~aL~KL 93 (248)
.-..|+||+|.+||.+|. |+.|+ +.++|||+|++|+.+ .+||..|.... ...... ......+|+.+...
T Consensus 50 ~~~~LP~ell~~Il~~Lp--~~~L~~r~~~VCk~Wr~l~~~~~~w~~~~~~~g--~~~~~~---~~~~~~~Wk~~y~~ 120 (297)
T 2e31_A 50 YLAELPEPLLLRVLAELP--ATELVQACRLVCLRWKELVDGAPLWLLKCQQEG--LVPEGS---ADEERDHWQQFYFL 120 (297)
T ss_dssp CTTSSCHHHHHHHHHTSC--HHHHHHTGGGTCHHHHHHHTSHHHHHHHHHHTT--CCCC--------CCSCHHHHHHH
T ss_pred ChhhCCHHHHHHHHHcCC--HHHHHHHHHHHhHHHHHHhcChHHHHHHhhccC--cccccc---cCCCCCChhhhheh
Confidence 347899999999999997 99999 999999999999998 99999999871 111111 11246779999744
No 3
>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=98.23 E-value=7.4e-07 Score=82.25 Aligned_cols=47 Identities=21% Similarity=0.574 Sum_probs=44.5
Q ss_pred cCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhh
Q 025767 21 HLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAP 69 (248)
Q Consensus 21 ~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP 69 (248)
.||+||++.||+.|+ |++||++++|||.|+.+|.+ .|||.+|.+..|
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 589999999999998 99999999999999999999 999999997655
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=98.04 E-value=3.4e-06 Score=73.36 Aligned_cols=48 Identities=17% Similarity=0.347 Sum_probs=44.6
Q ss_pred CcCcHH----HHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhhh
Q 025767 20 GHLSED----VIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRAP 69 (248)
Q Consensus 20 g~L~Ed----vL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~raP 69 (248)
..||+| |+..||+.|. |++|+++++|||+|+.++.. .+||.+|.+.++
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 458899 9999999997 99999999999999999998 999999998864
No 5
>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=98.01 E-value=4.3e-06 Score=72.54 Aligned_cols=47 Identities=26% Similarity=0.669 Sum_probs=43.8
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHHHHHhhh
Q 025767 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKEFCRTRA 68 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~~C~~ra 68 (248)
..||+|++..||..|. |++|+++++|||+|+.++.+ .+||.+|.+..
T Consensus 20 ~~lp~e~~~~i~~~l~--~~~l~~~~~v~~~~~~~~~~~~~w~~~~~~~~ 67 (445)
T 2ovr_B 20 SLLPKELALYVLSFLE--PKDLLQAAQTCRYWRILAEDNLLWREKCKEEG 67 (445)
T ss_dssp TSSCHHHHHHHHTTSC--HHHHHHHTTSCHHHHHHHTCSHHHHHHHTTTT
T ss_pred HHCCHHHHHHHHHhCC--HHHHHHHHHHhHHHHhhcCchhHhhhheeecc
Confidence 6899999999999996 99999999999999999998 79999997654
No 6
>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=97.91 E-value=7.6e-06 Score=70.69 Aligned_cols=46 Identities=13% Similarity=0.310 Sum_probs=42.1
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH--hhhHHHHHhh
Q 025767 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR--VLWKEFCRTR 67 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~--vlWr~~C~~r 67 (248)
..||+|+++.||+.|. |++|++++.|||+|+.++.. .+||++|.+.
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 4699999999999995 99999999999999999985 9999999643
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=96.57 E-value=0.00093 Score=56.32 Aligned_cols=41 Identities=22% Similarity=0.493 Sum_probs=36.9
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH-hhhHH
Q 025767 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR-VLWKE 62 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~-vlWr~ 62 (248)
..||+||+..||+.|+ ++++.+++.|||+|+.++.. .+|+.
T Consensus 10 ~~LP~eil~~If~~L~--~~d~~~~~~vc~~W~~~~~~~~~~~~ 51 (336)
T 2ast_B 10 DSLPDELLLGIFSCLC--LPELLKVSGVCKRWYRLASDESLWQT 51 (336)
T ss_dssp SSSCHHHHHHHHTTSC--HHHHHHTTSSCHHHHHHHTCSTTSSE
T ss_pred hhCCHHHHHHHHHhCC--HHHHHHHHHHHHHHHHHhcCchhhee
Confidence 6799999999999997 99999999999999999864 56764
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=95.45 E-value=0.0095 Score=53.87 Aligned_cols=40 Identities=23% Similarity=0.328 Sum_probs=32.0
Q ss_pred CcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHHhhhH
Q 025767 20 GHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKRVLWK 61 (248)
Q Consensus 20 g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~vlWr 61 (248)
..||||||..||+.|. +++++++++.|||+|+.+ ....|+
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 5799999999999996 589999999999999998 334444
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=94.16 E-value=0.027 Score=50.97 Aligned_cols=36 Identities=22% Similarity=0.293 Sum_probs=32.3
Q ss_pred CCcCcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHH
Q 025767 19 KGHLSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLA 55 (248)
Q Consensus 19 ~g~L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~la 55 (248)
...||||+|..||+.|. +++++++++.|||+|+.+.
T Consensus 13 ~~~LPdeil~~I~~~L~-~~~d~~~~s~vck~W~~~~ 48 (592)
T 3ogk_B 13 CVATVDDVIEQVMTYIT-DPKDRDSASLVCRRWFKID 48 (592)
T ss_dssp CCCCGGGTHHHHHTTCC-CHHHHHHHTTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHHhcC-CHHHHHHHHHHhHHHHHhh
Confidence 35699999999999994 4999999999999999884
No 10
>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=79.68 E-value=1.2 Score=35.30 Aligned_cols=81 Identities=14% Similarity=0.405 Sum_probs=42.7
Q ss_pred CCeeEeeCCCcccCCCCCceeeeecccccchhHHHHHHHHHHh---ccCCCCCCCCCCccce--eccccccccccccccc
Q 025767 136 TDVLYVSDPCEHLDQGEEGDVGFFRGVFKSFQMSKVRKMLIKR---GAQLHPTEACPYCKAK--LWSMLQAKMIPQSASC 210 (248)
Q Consensus 136 ~D~LYVsD~CeH~~~~e~r~~g~FRGvFK~F~~S~vrr~L~~r---~a~~~~~~~CpfCg~~--~Wsm~~a~~~p~sa~r 210 (248)
....|+|+.|-+..... .--+|+=.+.. ..+.+...+.+- .....+...||-||.. +|-..|-+
T Consensus 23 ~~~~~~C~~C~y~~~~~--~~~v~~~~~~~-~~~e~~~v~~~~~~~~t~p~t~~~Cp~C~~~~a~~~q~q~r-------- 91 (122)
T 1twf_I 23 NRLLFECRTCSYVEEAG--SPLVYRHELIT-NIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQR-------- 91 (122)
T ss_dssp TEEEEECSSSSCEEECS--CSEEEEEESSC-CTTSSTTCCTTGGGCTTSCCCCCCCTTTCCCCEEEEECSSC--------
T ss_pred CCCEEECCcCCCeeecC--ccEEEEEeecc-cccccccccccccccccccccCCCCCCCCCCEEEEEEecCc--------
Confidence 35899999998876422 22233322211 111111111110 1112345789999983 44333321
Q ss_pred ccCCccCceEEEEeeC-Cee
Q 025767 211 RLGAYEDCIEYYVCLN-GHM 229 (248)
Q Consensus 211 Rl~~ye~~veyyVC~N-GHv 229 (248)
-+-||..-+|+|.| ||-
T Consensus 92 --sade~~t~fy~C~~C~~~ 109 (122)
T 1twf_I 92 --RKDTSMVLFFVCLSCSHI 109 (122)
T ss_dssp --CTTCCCCEEEEETTTCCE
T ss_pred --cCCCCceEEEEeCCCCCE
Confidence 13689999999998 663
No 11
>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=68.54 E-value=1.9 Score=30.20 Aligned_cols=23 Identities=35% Similarity=0.730 Sum_probs=19.1
Q ss_pred CCCCCCCCCccceeccccccccc
Q 025767 182 LHPTEACPYCKAKLWSMLQAKMI 204 (248)
Q Consensus 182 ~~~~~~CpfCg~~~Wsm~~a~~~ 204 (248)
.-|.+.|||||-++.-++.+..+
T Consensus 20 ~lP~IrCpyCGyrii~KvR~p~v 42 (48)
T 4ayb_P 20 VLPGVRCPYCGYKIIFMVRKPTI 42 (48)
T ss_dssp CCSSSCCTTTCCSCEECCCCCSC
T ss_pred hCCCcccCccCcEEEEEecCCcc
Confidence 44789999999999888877666
No 12
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=66.28 E-value=4.2 Score=32.95 Aligned_cols=94 Identities=19% Similarity=0.388 Sum_probs=24.9
Q ss_pred eeecccCCcccccccc--CCeeEeeCCCcccCCCCCceeeeecccccchhHH--HHHH-HHHHhccCCCCCCCCCCccce
Q 025767 120 RFSRTSGKSFLLPQCR--TDVLYVSDPCEHLDQGEEGDVGFFRGVFKSFQMS--KVRK-MLIKRGAQLHPTEACPYCKAK 194 (248)
Q Consensus 120 rfSrtsG~s~L~~rcR--~D~LYVsD~CeH~~~~e~r~~g~FRGvFK~F~~S--~vrr-~L~~r~a~~~~~~~CpfCg~~ 194 (248)
+|--+-||=|.++.=+ +.++|+|..|-+... -..--.+|-.++.=... .+.. .+.+... ...++.||-||.+
T Consensus 25 ~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~~--~~~~~v~r~~~~~~~~e~~~vv~dv~~dptl-p~t~~~CpkCg~~ 101 (133)
T 3qt1_I 25 RFCRDCNNMLYPREDKENNRLLFECRTCSYVEE--AGSPLVYRHELITNIGETAGVVQDIGSDPTL-PRSDRECPKCHSR 101 (133)
T ss_dssp CBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBCC--CSCSEEEECCC----------------------------------
T ss_pred eeCCCCCCEeeECccCCCceeEEECCCCCCcEE--cCCceEEEEEeeccccccceeEeeccccccC-CcccCCCCCCCCc
Confidence 5555556655555432 346899999998774 22223455444321111 1111 1111111 1235799999983
Q ss_pred --ecccccccccccccccccCCccCceEEEEeeC
Q 025767 195 --LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 195 --~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
+|-..|.+ -+-||...+|+|.|
T Consensus 102 ~a~f~q~Q~R----------saDE~mT~fy~C~~ 125 (133)
T 3qt1_I 102 ENVFFQLQIR----------SADEPMTTFYKCVN 125 (133)
T ss_dssp ----------------------------------
T ss_pred eEEEEEEeee----------cCCCCCcEEEEcCC
Confidence 33333321 13689999999986
No 13
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=55.92 E-value=5.8 Score=30.84 Aligned_cols=76 Identities=13% Similarity=0.257 Sum_probs=38.8
Q ss_pred CeeEeeCCCcccCCCCCceeeeecc-cccchhHHHHHHHHHHhcc---CCCCCCCCCCccce--eccccccccccccccc
Q 025767 137 DVLYVSDPCEHLDQGEEGDVGFFRG-VFKSFQMSKVRKMLIKRGA---QLHPTEACPYCKAK--LWSMLQAKMIPQSASC 210 (248)
Q Consensus 137 D~LYVsD~CeH~~~~e~r~~g~FRG-vFK~F~~S~vrr~L~~r~a---~~~~~~~CpfCg~~--~Wsm~~a~~~p~sa~r 210 (248)
...|+|..|-+....+. -.+|+= ++..- ..+-..+.+..+ -...+..||-||.. +|-..|-
T Consensus 24 ~~~~~C~~C~y~~~~~~--~~v~~~~~~~~~--~e~~~v~~~~~~~~tlp~~~~~Cp~C~~~~a~~~q~q~--------- 90 (113)
T 3h0g_I 24 VLRLACRNCDYSEIAAT--SKVYRHELQSSN--VENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHS--------- 90 (113)
T ss_dssp CCCEECSSSCCEECCSC--SEEEECCCCSCS--CTTCTTCTTSTTCSSSCBCCSCCSSSCCSCEEEECCCC---------
T ss_pred eeEEECCCCCCeEEcCC--CeEEEEEEeccc--ccccceeccccccccCCCcccCCCCCCCceEEEEEEec---------
Confidence 35799999988764222 233432 22111 111111211111 11234789999983 3322221
Q ss_pred ccCCccCceEEEEeeC
Q 025767 211 RLGAYEDCIEYYVCLN 226 (248)
Q Consensus 211 Rl~~ye~~veyyVC~N 226 (248)
| -+-||...+|+|.|
T Consensus 91 r-sade~mt~fy~C~~ 105 (113)
T 3h0g_I 91 R-RGDTMMTLIYVCVH 105 (113)
T ss_dssp S-SCCCCCCCEEEESS
T ss_pred c-cCCCCCeeEEEcCC
Confidence 1 23689999999986
No 14
>4hfx_A Transcription elongation factor B polypeptide 3; structural genomics, PSI-biology, northeast structural genom consortium, NESG; 2.54A {Homo sapiens}
Probab=48.33 E-value=6.8 Score=30.55 Aligned_cols=57 Identities=18% Similarity=0.306 Sum_probs=32.4
Q ss_pred CcHHHHHHHHHhcCCChHHHHHHhhcchhHHHHHHH--hhhHHHHHhhhhhhHHhhhhcCCCCCCCcHHHHH
Q 025767 22 LSEDVIFLVFQHMNWNPKTIAALSCTCKWFDDLAKR--VLWKEFCRTRAPKMMVDLQSSGSHSVDGNWRALG 91 (248)
Q Consensus 22 L~EdvL~~VF~~lnwdPr~lar~AcVcr~f~~lar~--vlWr~~C~~raP~mv~~L~~~~~~~~~G~W~aL~ 91 (248)
.+=++|.-|+.+.+ |..|.++-=-|. .++.. -||+.+|.+-+|.- ...-+-+|+.|.
T Consensus 13 ~Py~lL~PVLek~t--p~QL~~IE~~nP---~L~~dTdeLWk~~c~rdF~~~--------~p~e~esWRelY 71 (97)
T 4hfx_A 13 VPYSVLEPVLERCT--PDQLYRIEEYNH---VLIEETDQLWKVHCHRDFKEE--------RPEEYESWREMY 71 (97)
T ss_dssp -------CCGGGCC--HHHHHHHHTC---------CCHHHHHHHC----CCS--------CCCSSSCHHHHH
T ss_pred CcHHHHHHHHccCC--HHHHHHHHHhCc---ccchhhHHHHHHHHHhHCccc--------CCCCCCCHHHHH
Confidence 46678888999864 999999988887 44444 89999999999932 235567999987
No 15
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=46.87 E-value=18 Score=24.57 Aligned_cols=32 Identities=25% Similarity=0.661 Sum_probs=23.9
Q ss_pred CCCCCCccce--ecccccccccccccccccCCccCceEEEEeeC
Q 025767 185 TEACPYCKAK--LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 185 ~~~CpfCg~~--~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
.+.||-||.+ +|...|-+ .+-||.--+|+|.|
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 4789999983 66655533 33589999999986
No 16
>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=38.78 E-value=18 Score=27.20 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=20.3
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc-eecccc
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA-KLWSML 199 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~-~~Wsm~ 199 (248)
.-|++|+++.+....+ -.|||||. .+++..
T Consensus 12 ~lRk~vk~ie~~q~~~----y~Cp~CG~~~v~r~a 42 (83)
T 1vq8_Z 12 VSRRRVAEIESEMNED----HACPNCGEDRVDRQG 42 (83)
T ss_dssp HHHHHHHHHHHHHHSC----EECSSSCCEEEEEEE
T ss_pred HHHHHHHHHHHhcccc----CcCCCCCCcceeccC
Confidence 4566777776664443 69999999 565543
No 17
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=33.39 E-value=48 Score=22.46 Aligned_cols=33 Identities=27% Similarity=0.498 Sum_probs=22.7
Q ss_pred CCCCCCCccce--ecccccccccccccccccCCccCceEEEEeeC
Q 025767 184 PTEACPYCKAK--LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 184 ~~~~CpfCg~~--~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
..+.||-||.+ +|-..|-+ -+-||.--+|+|.|
T Consensus 8 ~~~~Cp~Cg~~~a~f~q~Q~R----------saDE~mT~Fy~C~~ 42 (50)
T 1tfi_A 8 DLFTCGKCKKKNCTYTQVQTR----------SADEPMTTFVVCNE 42 (50)
T ss_dssp CCSCCSSSCSSCEEEEEECSS----------SSSSCCEEEEEESS
T ss_pred CccCCCCCCCCEEEEEEecCc----------CCCCCceEEEEcCC
Confidence 34789999983 44333321 13699999999987
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=30.43 E-value=28 Score=25.77 Aligned_cols=24 Identities=29% Similarity=0.459 Sum_probs=16.5
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA 193 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~ 193 (248)
.-|++|+++.+...++ -.|||||.
T Consensus 12 slRK~vkkie~~q~~k----y~C~fCgk 35 (73)
T 1ffk_W 12 KIRVRVRDVEIKHKKK----YKCPVCGF 35 (73)
T ss_pred hHHHHHHHHHHhcccC----ccCCCCCC
Confidence 4456666666664443 79999997
No 19
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=30.18 E-value=32 Score=26.17 Aligned_cols=25 Identities=24% Similarity=0.398 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccce
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKAK 194 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~~ 194 (248)
.-|++|.++.+...++ -.|||||..
T Consensus 20 slRK~vkkie~~q~~k----y~CpfCGk~ 44 (83)
T 3j21_i 20 KIRRRVAAVEAKMRQK----HTCPVCGRK 44 (83)
T ss_dssp HHHHHHHHHHHHHHSC----BCCSSSCSS
T ss_pred hHHHHHHHHHHHhhcc----cCCCCCCCc
Confidence 5567777777775555 689999984
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=26.79 E-value=35 Score=27.46 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA 193 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~ 193 (248)
.-|++|++..+...++ -.|||||.
T Consensus 45 slRK~vkkiE~~q~ak----ytCPfCGk 68 (116)
T 3cc2_Z 45 VSRRRVAEIESEMNED----HACPNCGE 68 (116)
T ss_dssp HHHHHHHHHHHHHHSC----EECSSSCC
T ss_pred HHHHHHHHHHHHhccC----CcCCCCCC
Confidence 5667777777765555 79999998
No 21
>3iz5_m 60S ribosomal protein L43 (L37AE); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 3izr_m 1ysh_D 2zkr_z
Probab=24.10 E-value=45 Score=25.79 Aligned_cols=25 Identities=16% Similarity=0.397 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccce
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKAK 194 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~~ 194 (248)
.-+.+|.++.+...++ -.|||||..
T Consensus 21 slRK~vkkie~~q~~k----y~CpfCgk~ 45 (92)
T 3iz5_m 21 SLRKQIKKMEVSQHSK----YFCEFCGKF 45 (92)
T ss_dssp HHHHHHHHHHHHHHSC----BCCTTTCSS
T ss_pred HHHHHHHHHHHHHhcc----ccCcccCCC
Confidence 4566777777775555 699999973
No 22
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}
Probab=23.31 E-value=27 Score=25.95 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccce
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKAK 194 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~~ 194 (248)
.-|++|.++.+...++ -.|||||..
T Consensus 11 slRK~vkkie~~q~~k----y~C~fCgk~ 35 (72)
T 3jyw_9 11 SLRRQVKKLEIQQHAR----YDCSFCGKK 35 (72)
T ss_dssp HHHTTTHHHHHHHHSC----BCCSSCCSS
T ss_pred hHHHHHHHHHHHhccC----ccCCCCCCc
Confidence 4456777777775555 689999974
No 23
>3izc_m 60S ribosomal protein RPL43 (L37AE); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_m 3o58_g 3o5h_g 3u5e_p 3u5i_p 4b6a_p 1s1i_9
Probab=22.28 E-value=55 Score=25.36 Aligned_cols=24 Identities=25% Similarity=0.528 Sum_probs=17.6
Q ss_pred hhHHHHHHHHHHhccCCCCCCCCCCccc
Q 025767 166 FQMSKVRKMLIKRGAQLHPTEACPYCKA 193 (248)
Q Consensus 166 F~~S~vrr~L~~r~a~~~~~~~CpfCg~ 193 (248)
.-+.+|.++.+...++ -.|||||.
T Consensus 21 slRK~vkkie~~q~~k----y~CpfCgk 44 (92)
T 3izc_m 21 SLRRQVKKLEIQQHAR----YDCSFCGK 44 (92)
T ss_dssp HHHHHHHHHHHHHHSC----CCCSSSCS
T ss_pred hHHHHHHHHHHHHhcC----CcCCCCCC
Confidence 4566777777765555 68999996
No 24
>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=21.88 E-value=93 Score=25.88 Aligned_cols=46 Identities=22% Similarity=0.327 Sum_probs=28.9
Q ss_pred HHHHHHHhccCCCC-----CCCCCCccc-e-ecccccccccccccccccCCccCceEEEEeeC
Q 025767 171 VRKMLIKRGAQLHP-----TEACPYCKA-K-LWSMLQAKMIPQSASCRLGAYEDCIEYYVCLN 226 (248)
Q Consensus 171 vrr~L~~r~a~~~~-----~~~CpfCg~-~-~Wsm~~a~~~p~sa~rRl~~ye~~veyyVC~N 226 (248)
..+.|.+.+.+-.+ ...||-||. + +|-..|- | .+-||..-+|+|.|
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 44566665554333 368999998 3 4433322 2 23689999999986
Done!