Query 004180
Match_columns 770
No_of_seqs 167 out of 210
Neff 4.8
Searched_HMMs 29240
Date Mon Mar 25 16:50:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004180.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/004180hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4bbr_M Transcription initiatio 98.1 1.6E-05 5.4E-10 86.0 12.9 146 170-407 132-289 (345)
2 3k7a_M Transcription initiatio 97.8 7.2E-05 2.5E-09 80.7 10.6 107 258-407 171-289 (345)
3 1ais_B TFB TFIIB, protein (tra 96.0 0.1 3.4E-06 51.3 13.8 107 258-407 54-162 (200)
4 1c9b_A General transcription f 95.6 0.24 8.2E-06 48.9 15.2 144 172-407 13-156 (207)
5 1zp2_A RNA polymerase II holoe 94.4 1.9 6.5E-05 43.3 18.0 154 171-407 35-188 (235)
6 1nui_A DNA primase/helicase; z 92.3 0.054 1.8E-06 55.4 2.5 33 5-37 9-42 (255)
7 1pft_A TFIIB, PFTFIIBN; N-term 92.1 0.094 3.2E-06 41.1 3.1 32 9-40 4-36 (50)
8 3rgf_B Cyclin-C; protein kinas 90.9 8.5 0.00029 39.9 17.4 167 172-416 51-218 (285)
9 1vq8_Z 50S ribosomal protein L 89.0 0.17 5.7E-06 44.4 2.1 31 10-40 27-57 (83)
10 2i53_A Cyclin K; cell cycle, t 88.9 16 0.00054 36.8 17.2 121 258-407 86-209 (258)
11 1dl6_A Transcription factor II 88.5 0.27 9.1E-06 40.2 2.9 31 10-40 11-42 (58)
12 2b9r_A Human cyclin B1; cell c 88.3 6.8 0.00023 40.2 14.1 121 258-423 83-204 (269)
13 2ivx_A Cyclin-T2; transcriptio 87.0 19 0.00065 36.3 16.4 123 258-407 76-201 (257)
14 3j20_Y 30S ribosomal protein S 84.7 0.54 1.9E-05 37.4 2.7 29 10-38 19-47 (50)
15 3k1f_M Transcription initiatio 83.7 0.61 2.1E-05 46.3 3.2 35 6-40 17-54 (197)
16 1qyp_A RNA polymerase II; tran 82.1 0.84 2.9E-05 36.7 2.9 31 9-39 14-54 (57)
17 2k4x_A 30S ribosomal protein S 80.6 1.2 4.2E-05 36.0 3.3 28 10-37 18-45 (55)
18 1jkw_A Cyclin H; cell cycle, c 80.2 32 0.0011 36.4 15.2 150 173-407 66-224 (323)
19 2pk2_A Cyclin-T1, protein TAT; 79.4 11 0.00038 40.6 11.5 122 258-407 83-208 (358)
20 2akl_A PHNA-like protein PA012 78.7 1 3.4E-05 42.6 2.6 29 10-39 27-55 (138)
21 2cch_B Cyclin A2, cyclin-A; co 74.3 12 0.00042 38.0 9.6 121 258-422 84-206 (260)
22 3j21_g 50S ribosomal protein L 73.5 1.1 3.8E-05 35.9 1.2 25 10-38 14-38 (51)
23 2jr6_A UPF0434 protein NMA0874 68.1 3.2 0.00011 35.0 3.0 31 9-39 7-37 (68)
24 2js4_A UPF0434 protein BB2007; 67.9 3.1 0.0001 35.3 2.8 31 9-39 7-37 (70)
25 2pk7_A Uncharacterized protein 67.9 3 0.0001 35.3 2.7 31 9-39 7-37 (69)
26 1tfi_A Transcriptional elongat 67.7 2.9 0.0001 33.1 2.5 33 5-37 4-46 (50)
27 2hf1_A Tetraacyldisaccharide-1 67.6 3.2 0.00011 34.9 2.9 30 10-39 8-37 (68)
28 2jny_A Uncharacterized BCR; st 67.1 4.6 0.00016 34.0 3.7 32 8-39 8-39 (67)
29 3j21_i 50S ribosomal protein L 66.4 3.2 0.00011 36.5 2.6 31 10-40 35-65 (83)
30 3iz5_m 60S ribosomal protein L 64.6 3.6 0.00012 36.8 2.7 30 11-40 37-66 (92)
31 3jyw_9 60S ribosomal protein L 64.1 3.4 0.00012 35.4 2.3 31 10-40 26-56 (72)
32 3izc_m 60S ribosomal protein R 62.8 4 0.00014 36.5 2.6 31 10-40 36-66 (92)
33 3h0g_I DNA-directed RNA polyme 62.6 4.3 0.00015 37.0 3.0 28 12-39 6-37 (113)
34 4a17_Y RPL37A, 60S ribosomal p 61.1 3.7 0.00013 37.3 2.2 30 11-40 37-66 (103)
35 3cc2_Z 50S ribosomal protein L 60.6 3.8 0.00013 38.0 2.1 30 10-40 60-90 (116)
36 2w96_A G1/S-specific cyclin-D1 58.1 63 0.0022 32.9 11.1 109 258-407 102-215 (271)
37 1gnf_A Transcription factor GA 53.6 3.7 0.00013 32.2 0.7 27 10-36 4-33 (46)
38 1ffk_W Ribosomal protein L37AE 53.2 6.1 0.00021 33.9 2.1 31 10-40 27-57 (73)
39 3u50_C Telomerase-associated p 52.9 6.5 0.00022 38.6 2.5 28 9-37 41-68 (172)
40 2vut_I AREA, nitrogen regulato 50.2 4.9 0.00017 31.0 0.9 27 11-37 2-31 (43)
41 1twf_I B12.6, DNA-directed RNA 48.9 7.1 0.00024 36.1 2.0 29 11-39 5-37 (122)
42 4gat_A Nitrogen regulatory pro 48.0 7.3 0.00025 32.7 1.7 31 8-38 7-40 (66)
43 3qt1_I DNA-directed RNA polyme 45.8 8.4 0.00029 36.3 2.0 29 11-39 25-57 (133)
44 3dfx_A Trans-acting T-cell-spe 45.2 5.4 0.00019 33.2 0.5 32 7-38 4-38 (63)
45 4hc9_A Trans-acting T-cell-spe 44.3 6.5 0.00022 36.2 1.0 29 8-36 3-34 (115)
46 1g3n_C V-cyclin; cyclin-depend 41.5 48 0.0017 33.5 7.0 110 258-407 96-209 (257)
47 1c9b_A General transcription f 39.4 1.6E+02 0.0055 28.4 10.2 51 258-308 144-194 (207)
48 1twf_L ABC10-alpha, DNA-direct 37.8 11 0.00037 32.0 1.2 25 11-36 29-53 (70)
49 2f2c_A Cyclin homolog, V-cycli 37.6 75 0.0026 32.0 7.7 110 258-407 97-210 (254)
50 1twf_I B12.6, DNA-directed RNA 36.7 21 0.00073 32.9 3.1 30 10-39 72-111 (122)
51 3irb_A Uncharacterized protein 35.9 13 0.00043 35.3 1.5 30 5-38 42-71 (145)
52 1l1o_C Replication protein A 7 34.4 22 0.00076 34.6 3.0 29 10-39 43-73 (181)
53 3cng_A Nudix hydrolase; struct 32.8 23 0.00079 33.7 2.8 27 11-37 4-34 (189)
54 1gh9_A 8.3 kDa protein (gene M 30.4 25 0.00087 29.8 2.3 27 11-39 5-31 (71)
55 1vtn_C HNF-3/FORK head DNA-rec 30.4 33 0.0011 31.0 3.2 45 255-303 4-49 (102)
56 1ptq_A Protein kinase C delta 29.4 26 0.0009 26.6 2.1 30 6-36 7-36 (50)
57 2gnr_A Conserved hypothetical 29.2 17 0.0006 34.5 1.2 29 5-37 42-70 (145)
58 2kae_A GATA-type transcription 29.1 15 0.00051 31.3 0.6 29 9-38 7-40 (71)
59 4hc9_A Trans-acting T-cell-spe 26.5 20 0.00067 33.0 1.0 31 8-38 57-90 (115)
60 3bpy_A FORK head domain, forkh 26.5 42 0.0014 29.2 3.1 40 253-293 4-44 (85)
61 4esj_A Type-2 restriction enzy 24.7 34 0.0011 35.5 2.4 30 10-39 34-67 (257)
62 3l2c_A Forkhead box protein O4 24.4 48 0.0016 30.3 3.2 42 252-294 22-64 (110)
63 2kpi_A Uncharacterized protein 24.3 63 0.0021 26.0 3.5 30 7-38 7-38 (56)
64 4gop_C Putative uncharacterize 22.4 38 0.0013 37.2 2.6 29 10-39 308-338 (444)
65 1vk6_A NADH pyrophosphatase; 1 22.3 41 0.0014 34.7 2.6 31 10-40 107-137 (269)
66 3h0g_L DNA-directed RNA polyme 22.1 39 0.0013 28.1 1.9 28 10-38 21-48 (63)
67 3h0g_I DNA-directed RNA polyme 21.2 64 0.0022 29.2 3.4 29 11-39 73-111 (113)
68 3o9x_A Uncharacterized HTH-typ 20.5 41 0.0014 30.2 2.0 29 12-40 4-48 (133)
69 2fiy_A Protein FDHE homolog; F 20.4 43 0.0015 35.7 2.3 25 9-37 207-231 (309)
70 1x0t_A Ribonuclease P protein 20.2 59 0.002 29.9 2.9 34 5-39 60-105 (120)
71 1dxg_A Desulforedoxin; non-hem 20.1 35 0.0012 24.9 1.1 15 26-40 4-18 (36)
72 3g33_B CCND3 protein; Ser/Thr 20.0 93 0.0032 32.5 4.8 78 324-407 148-229 (306)
No 1
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M
Probab=98.11 E-value=1.6e-05 Score=86.02 Aligned_cols=146 Identities=11% Similarity=0.070 Sum_probs=50.8
Q ss_pred HHHHHHHhcCCChhHHHHHHHHHHHHHhhcCCCCCCchhhhhcccccccccccCcCcccCCCCCCccccchhhHHHHHHH
Q 004180 170 QCEALVDKFNVCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELESKDFQPRAKYRDEPHTLHGQRAVMIWYKL 249 (770)
Q Consensus 170 Q~~aLI~~~G~ppELe~VVrdLWlRyL~~~~v~~~~~ad~~~~dsesqE~e~~sSq~~~~~~~e~~~~~~~Rk~~~wprl 249 (770)
.+..+...+|+|..+......|+.+.....- ..|++...
T Consensus 132 ~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~------------------------------------~rGrs~e~----- 170 (345)
T 4bbr_M 132 KITMLCDAAELPKIVKDCAKEAYKLCHDEKT------------------------------------LKGKSMES----- 170 (345)
T ss_dssp HHHHHHHHTTCCHHHHHHHHHHHHHHTTCTT------------------------------------TTTCCHHH-----
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHhcCC------------------------------------ccCCCHHH-----
Confidence 4466778899999999888888866543210 01111111
Q ss_pred HhhcCCcchhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHH
Q 004180 250 LRQKIPLSSSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLES 329 (770)
Q Consensus 250 lr~~Lp~~~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~ 329 (770)
..-|-+|+||..-+.|.++-||.....-..- .|-+
T Consensus 171 --------vaAAclYiACR~~~~prtl~eI~~~~~v~~k-------------------------------------eigr 205 (345)
T 4bbr_M 171 --------IMAASILIGCRRAEVARTFKEIQSLIHVKTK-------------------------------------EFGK 205 (345)
T ss_dssp --------HHHHHHHHHHHHTCCBCCHHHHHHHHTCCTT-------------------------------------HHHH
T ss_pred --------HHHHHHHHHHHhcCCCccHHHHHHHhCCCHH-------------------------------------HHHH
Confidence 3458899999999999999999886642211 1222
Q ss_pred HHHHHHHHhCC------------CCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHH
Q 004180 330 FAASIAESIGL------------HLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVM 397 (770)
Q Consensus 330 la~~ia~~~gL------------~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~Lm 397 (770)
.-..+.+.+++ .+|++....++.||+..|+||.+ +...+.+|++..... +. ...+-|. ..+.
T Consensus 206 ~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~-v~~~A~~i~~~~~~~--~i--~~GR~P~-~IAA 279 (345)
T 4bbr_M 206 TLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQ-VTTSAEYTAKKCKEI--KE--IAGKSPI-TIAV 279 (345)
T ss_dssp HHHHHHHCC-----------------------------------------------------------------------
T ss_pred HHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHH-HHHHHHHHHHHHHhc--cc--ccCCChH-HHHH
Confidence 22223333332 36788888999999999999998 777777777632221 11 1124576 7777
Q ss_pred HHHHHHHHHh
Q 004180 398 SILIVSIRIL 407 (770)
Q Consensus 398 A~IIVAlKLL 407 (770)
|+|.+|.++.
T Consensus 280 AaIylAa~l~ 289 (345)
T 4bbr_M 280 VSIYLNILLF 289 (345)
T ss_dssp ----------
T ss_pred HHHHHHHHHh
Confidence 8888888763
No 2
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Probab=97.78 E-value=7.2e-05 Score=80.66 Aligned_cols=107 Identities=10% Similarity=0.094 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAES 337 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~~ 337 (770)
...|-+|+||..-+.|.++-||..-.. ++- ..|.+.-..+.+.
T Consensus 171 vaaAclyiAcR~e~~prtl~ei~~~~~---v~~----------------------------------keIgr~~~~l~~~ 213 (345)
T 3k7a_M 171 IMAASILIGCRRAEVARTFKEIQSLIH---VKT----------------------------------KEFGKTLNIMKNI 213 (345)
T ss_dssp HHTTTTTTTSBTTBSSCCHHHHHHSSS---CCS----------------------------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCccHHHHHHHHC---CCH----------------------------------HHHHHHHHHHHHH
Confidence 345679999999999999999977543 110 1222222233333
Q ss_pred hC------------CCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHH
Q 004180 338 IG------------LHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIR 405 (770)
Q Consensus 338 ~g------------L~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlK 405 (770)
++ +.+|++....++.||+..|+|+.+ +...+.+|++......+. ...-|. ..+.|+|.+|.+
T Consensus 214 L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~-v~~~A~~i~~~~~~~~l~----~Gr~P~-~IAaAaIylAa~ 287 (345)
T 3k7a_M 214 LRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQ-VTTSAEYTAKKCKEIKEI----AGKSPI-TIAVVSIYLNIL 287 (345)
T ss_dssp HTCC----------------------------------------------------------------------------
T ss_pred HhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhchh----cCCCHH-HHHHHHHHHHHH
Confidence 33 667778888999999999999988 777777777633222111 124466 677778888877
Q ss_pred Hh
Q 004180 406 IL 407 (770)
Q Consensus 406 LL 407 (770)
++
T Consensus 288 ~~ 289 (345)
T 3k7a_M 288 LF 289 (345)
T ss_dssp --
T ss_pred HH
Confidence 63
No 3
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*
Probab=95.96 E-value=0.1 Score=51.25 Aligned_cols=107 Identities=16% Similarity=0.183 Sum_probs=79.2
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAES 337 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~~ 337 (770)
...|-+|+||...+.|.++-||..-.. + +-..|.+.-..+.+.
T Consensus 54 vaaAclylAcr~~~~p~~l~di~~~~~---v----------------------------------~~~~i~~~~~~l~~~ 96 (200)
T 1ais_B 54 VMAACVYAACRLLKVPRTLDEIADIAR---V----------------------------------DKKEIGRSYRFIARN 96 (200)
T ss_dssp HHHHHHHHHHHHHTCCCCHHHHHHHTT---S----------------------------------CHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHC---C----------------------------------CHHHHHHHHHHHHHH
Confidence 466889999999999999999986421 0 114455666667777
Q ss_pred hCCCCCC--CCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 338 IGLHLPP--VNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 338 ~gL~fPp--iN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
+++.+|+ ++...++.||+..|+||.+ +...+.+|++......+. ...-|. ..+.|+|-+|.+++
T Consensus 97 L~~~~~~~~~~p~~~i~r~~~~L~l~~~-v~~~A~~i~~~~~~~~~~----~gr~P~-~iAaAaly~A~~~~ 162 (200)
T 1ais_B 97 LNLTPKKLFVKPTDYVNKFADELGLSEK-VRRRAIEILDEAYKRGLT----SGKSPA-GLVAAALYIASLLE 162 (200)
T ss_dssp TTCCTTTTCCCGGGGHHHHHHHHTCCHH-HHHHHHHHHHHHHHTTCC----TTSCHH-HHHHHHHHHHHHHT
T ss_pred hcccCCcCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHcCcc----cCCCHH-HHHHHHHHHHHHHh
Confidence 8999998 8899999999999999999 878888887632221111 124566 78888888888873
No 4
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*
Probab=95.64 E-value=0.24 Score=48.86 Aligned_cols=144 Identities=17% Similarity=0.204 Sum_probs=101.1
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhhcCCCCCCchhhhhcccccccccccCcCcccCCCCCCccccchhhHHHHHHHHh
Q 004180 172 EALVDKFNVCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELESKDFQPRAKYRDEPHTLHGQRAVMIWYKLLR 251 (770)
Q Consensus 172 ~aLI~~~G~ppELe~VVrdLWlRyL~~~~v~~~~~ad~~~~dsesqE~e~~sSq~~~~~~~e~~~~~~~Rk~~~wprllr 251 (770)
..+-..+|+|+........+-.|++....+.+ + . +. .
T Consensus 13 ~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~------------------------------------~-~----~~-~- 49 (207)
T 1c9b_A 13 TTMADRINLPRNIVDRTNNLFKQVYEQKSLKG------------------------------------R-A----ND-A- 49 (207)
T ss_dssp HHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTT------------------------------------S-C----HH-H-
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCC------------------------------------C-C----HH-H-
Confidence 35556789999999888888877765422110 0 0 01 1
Q ss_pred hcCCcchhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHH
Q 004180 252 QKIPLSSSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFA 331 (770)
Q Consensus 252 ~~Lp~~~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la 331 (770)
...|-+||||..-..|.++.||..-.. + +...|.+.-
T Consensus 50 ------v~aaclylAcK~ee~p~~l~di~~~~~---~----------------------------------~~~~i~~~~ 86 (207)
T 1c9b_A 50 ------IASACLYIACRQEGVPRTFKEICAVSR---I----------------------------------SKKEIGRCF 86 (207)
T ss_dssp ------HHHHHHHHHHHHTTCCCCHHHHHHTSS---S----------------------------------CHHHHHHHH
T ss_pred ------HHHHHHHHHHHhcCCCCCHHHHHHHHC---C----------------------------------CHHHHHHHH
Confidence 567889999999999999999975332 0 013344455
Q ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 332 ASIAESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 332 ~~ia~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
..+.+.+++.+|..+...++.||+..|+||.+ +...+..+++......+. ...-|. ..++|+|-+|.+++
T Consensus 87 ~~ll~~L~~~l~~~~p~~~l~r~~~~l~l~~~-~~~~A~~i~~~~~~~~l~----~g~~P~-~IAaAaiylA~~~~ 156 (207)
T 1c9b_A 87 KLILKALETSVDLITTGDFMSRFCSNLCLPKQ-VQMAATHIARKAVELDLV----PGRSPI-SVAAAAIYMASQAS 156 (207)
T ss_dssp HHHHHHTTCCCCCCCTHHHHHHHHHHTTCCHH-HHHHHHHHHHHHHHTTCS----TTCCHH-HHHHHHHHHHHHTS
T ss_pred HHHHHHHCCCcCcCCHHHHHHHHHHHCCCCHH-HHHHHHHHHHHHHHcCcc----CCCChH-HHHHHHHHHHHHHH
Confidence 56677788888889999999999999999998 888888888744332221 123465 88888888888875
No 5
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}
Probab=94.43 E-value=1.9 Score=43.35 Aligned_cols=154 Identities=12% Similarity=0.075 Sum_probs=106.5
Q ss_pred HHHHHHhcCCChhHHHHHHHHHHHHHhhcCCCCCCchhhhhcccccccccccCcCcccCCCCCCccccchhhHHHHHHHH
Q 004180 171 CEALVDKFNVCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELESKDFQPRAKYRDEPHTLHGQRAVMIWYKLL 250 (770)
Q Consensus 171 ~~aLI~~~G~ppELe~VVrdLWlRyL~~~~v~~~~~ad~~~~dsesqE~e~~sSq~~~~~~~e~~~~~~~Rk~~~wprll 250 (770)
+..+...+++|++.-...-.+-.|++....+.. + +. +. +
T Consensus 35 i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~-----------------------------------~-~~----~~-l 73 (235)
T 1zp2_A 35 VQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEK-----------------------------------G-FS----LE-A 73 (235)
T ss_dssp HHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCC-----------------------------------C-CC----HH-H
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHhccccc-----------------------------------c-cC----HH-H
Confidence 334456789999999888888888876532111 0 00 01 1
Q ss_pred hhcCCcchhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHH
Q 004180 251 RQKIPLSSSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESF 330 (770)
Q Consensus 251 r~~Lp~~~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~l 330 (770)
...|-+||||-.-..|..+.||+.-... -.| + . + ..+...|.++
T Consensus 74 -------v~~acL~lA~K~Ee~~~~l~d~~~~~~~-~~~-------------~--------~---~----~~~~~~I~~~ 117 (235)
T 1zp2_A 74 -------LVATCIYLSCKVEECPVHIRTICNEAND-LWS-------------L--------K---V----KLSRSNISEI 117 (235)
T ss_dssp -------HHHHHHHHHHHHTTCCCCHHHHHHHHHT-TCC-------------C--------S---S----CCCHHHHHHH
T ss_pred -------HHHHHHHHHhccccCcccHHHHHHHHHH-Hcc-------------c--------h---h----hccHHHHHHH
Confidence 5678899999999999999999864322 111 0 0 0 0123678888
Q ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 331 AASIAESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 331 a~~ia~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
=..+.+.++..+..++....+.||++.++++.+ +...+..+++-.+-.... ..+|+.+.++|+|.+|.+++
T Consensus 118 E~~iL~~L~f~l~~~~P~~~l~~~~~~~~~~~~-~~~~A~~~l~~s~~~~~~-----l~~~Ps~IAaAai~lA~~~~ 188 (235)
T 1zp2_A 118 EFEIISVLDAFLIVHHPYTSLEQAFHDGIINQK-QLEFAWSIVNDSYASSLC-----LMAHPHQLAYAALLISCCND 188 (235)
T ss_dssp HHHHHHHTTTCCCCCCTHHHHHHHHHTTSSCHH-HHHHHHHHHHHHTTTTGG-----GTSCHHHHHHHHHHHHHTSC
T ss_pred HHHHHHHCCCcEEecChHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHcCCch-----hccCHHHHHHHHHHHHHHhc
Confidence 788888888888888888999999999999998 778888888744332222 23344488888998998863
No 6
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2
Probab=92.35 E-value=0.054 Score=55.42 Aligned_cols=33 Identities=21% Similarity=0.505 Sum_probs=26.8
Q ss_pred cccccccccCCCCC-CceeecCCcceecccCCee
Q 004180 5 EGDIRRLKCKKCDN-VGFECAYDGFYYCTHCNAL 37 (770)
Q Consensus 5 ~~~~r~~~C~~C~S-~~w~~~~dG~~yC~~CGhv 37 (770)
..+.++.+|+.||+ ..+++-+||-++|-+||+-
T Consensus 9 ~~~~~~~~CP~Cg~~d~~~~~~dg~~~C~~Cg~~ 42 (255)
T 1nui_A 9 SVFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKW 42 (255)
T ss_dssp -CEEEEECCSSSCCSSCEEEETTSCEEETTTCCE
T ss_pred cceecCCcCCCCCCCCCceEeCCCCeecccCCCc
Confidence 56788999999999 4565547899999999985
No 7
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=92.08 E-value=0.094 Score=41.12 Aligned_cols=32 Identities=19% Similarity=0.415 Sum_probs=26.0
Q ss_pred cccccCCCCC-CceeecCCcceecccCCeeecc
Q 004180 9 RRLKCKKCDN-VGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 9 r~~~C~~C~S-~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
...+|++|++ ..-++...|...|..||.+.+.
T Consensus 4 ~~~~CP~C~~~~l~~d~~~gelvC~~CG~v~~e 36 (50)
T 1pft_A 4 KQKVCPACESAELIYDPERGEIVCAKCGYVIEE 36 (50)
T ss_dssp SCCSCTTTSCCCEEEETTTTEEEESSSCCBCCC
T ss_pred ccEeCcCCCCcceEEcCCCCeEECcccCCcccc
Confidence 3568999999 4445557899999999999874
No 8
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}
Probab=90.87 E-value=8.5 Score=39.93 Aligned_cols=167 Identities=19% Similarity=0.189 Sum_probs=106.6
Q ss_pred HHHHHhcCCChhHHHHHHHHHHHHHhhcCCCCCCchhhhhcccccccccccCcCcccCCCCCCccccchhhHHHHHHHHh
Q 004180 172 EALVDKFNVCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELESKDFQPRAKYRDEPHTLHGQRAVMIWYKLLR 251 (770)
Q Consensus 172 ~aLI~~~G~ppELe~VVrdLWlRyL~~~~v~~~~~ad~~~~dsesqE~e~~sSq~~~~~~~e~~~~~~~Rk~~~wprllr 251 (770)
..+...+++|++.-...-.+..||+....+...+ +. +
T Consensus 51 ~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~~~~-----------------------------------------~~-l- 87 (285)
T 3rgf_B 51 QALGEHLKLRQQVIATATVYFKRFYARYSLKSID-----------------------------------------PV-L- 87 (285)
T ss_dssp HHHHHHTTCCHHHHHHHHHHHHHHHHHSCTTTSC-----------------------------------------HH-H-
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhCCchhcC-----------------------------------------HH-H-
Confidence 3344578999999988888888887753321100 01 1
Q ss_pred hcCCcchhHHHHHHHHHHhhccc-ChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHH
Q 004180 252 QKIPLSSSLAISFLACHVVREAI-LPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESF 330 (770)
Q Consensus 252 ~~Lp~~~TLAI~YLAcl~LR~PV-~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~l 330 (770)
..+|-+||||-.--.|. .+.||+.-... +.+ .+.. . +.+.. + ....+.|..+
T Consensus 88 ------va~acLfLA~K~EE~~~~~~~di~~~~~~-----------~~k---~~~~-~-~~~~~-~----~~~~~~Il~~ 140 (285)
T 3rgf_B 88 ------MAPTCVFLASKVEEFGVVSNTRLIAAATS-----------VLK---TRFS-Y-AFPKE-F----PYRMNHILEC 140 (285)
T ss_dssp ------HHHHHHHHHHHHTTSCCCCHHHHHHHHHH-----------HHH---HHCT-T-TCCSC-C----CCCHHHHHHH
T ss_pred ------HHHHHHHHHHhhhccccccHHHHHHHHHH-----------HHc---cccc-c-cCchh-h----HHHHHHHHHH
Confidence 56788999999988877 67888764321 000 0000 0 00110 0 1233678888
Q ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHhhcc
Q 004180 331 AASIAESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRILYNI 410 (770)
Q Consensus 331 a~~ia~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLLfgL 410 (770)
=..+.+.++..+...+..-.+.+|++.|+++.+ +...+..+++-++-... ...+|+.+.++|+|.+|.+++ +.
T Consensus 141 E~~iL~~L~f~l~v~~P~~fL~~~~~~l~~~~~-~~~~A~~~l~~sl~t~~-----~l~~~Ps~IAaAaiylA~~~~-~~ 213 (285)
T 3rgf_B 141 EFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDM-LLPLAWRIVNDTYRTDL-----CLLYPPFMIALACLHVACVVQ-QK 213 (285)
T ss_dssp HHHHHHHTTTCCCCCCSHHHHHHHHHHHTCHHH-HHHHHHHHHHHHTTSSH-----HHHSCHHHHHHHHHHHHHHHT-TC
T ss_pred HHHHHHHcCCCeEeCChHHHHHHHHHHhCCCHH-HHHHHHHHHHHHHccCh-----hhccCHHHHHHHHHHHHHHHc-CC
Confidence 788888888877666778899999999999888 77778877774432222 223444488888888888864 44
Q ss_pred CCcchh
Q 004180 411 NGFGAW 416 (770)
Q Consensus 411 Dg~~eW 416 (770)
+. ..|
T Consensus 214 ~~-~~W 218 (285)
T 3rgf_B 214 DA-RQW 218 (285)
T ss_dssp CC-HHH
T ss_pred Ch-hhH
Confidence 33 345
No 9
>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=88.98 E-value=0.17 Score=44.43 Aligned_cols=31 Identities=16% Similarity=0.420 Sum_probs=26.0
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|++||...-.....|.|.|.+||+++.|
T Consensus 27 ~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~ag 57 (83)
T 1vq8_Z 27 DHACPNCGEDRVDRQGTGIWQCSYCDYKFTG 57 (83)
T ss_dssp CEECSSSCCEEEEEEETTEEEETTTCCEEEC
T ss_pred cCcCCCCCCcceeccCCCeEECCCCCCEecC
Confidence 4579999997654448999999999999887
No 10
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1
Probab=88.87 E-value=16 Score=36.81 Aligned_cols=121 Identities=17% Similarity=0.144 Sum_probs=81.0
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAES 337 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~~ 337 (770)
..+|-+||||-.-..|..+.||+.-... .+....-... . -.+.+.|..+=..+.+.
T Consensus 86 v~~acL~lA~K~eE~~~~l~d~~~~~~~----------~~~~~~~~~~----------~----~~~~~~i~~~E~~iL~~ 141 (258)
T 2i53_A 86 TGACCLFLAGKVEETPKKCKDIIKTARS----------LLNDVQFGQF----------G----DDPKEEVMVLERILLQT 141 (258)
T ss_dssp HHHHHHHHHHHHTTCCCCHHHHHHHHHH----------HSCHHHHGGG----------C----SCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccccccccHHHHHHHHHH----------Hhchhhhhhh----------h----hhHHHHHHHHHHHHHHH
Confidence 5678899999998899999999874321 0000000000 0 01225677777778888
Q ss_pred hCCCCCCCCHHHHHHHHHHHcCCChh---hhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 338 IGLHLPPVNFYALASRYLKQLCLPLG---KILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 338 ~gL~fPpiN~~lLL~Ryl~eL~LP~E---~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
++..+...+...++.+|++.|+++.+ .+...+..+++.++-.... ..+|+.+.++|+|.+|.+++
T Consensus 142 L~f~l~~~~P~~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~-----l~~~Ps~IAaAai~lA~~~~ 209 (258)
T 2i53_A 142 IKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLS-----LQWEPEIIAVAVMYLAGRLC 209 (258)
T ss_dssp TTTCCCCCCHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGG-----GTSCHHHHHHHHHHHHHHHH
T ss_pred CCCceeccChHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCch-----hccChHHHHHHHHHHHHHHh
Confidence 88888777888999999999999873 1666777777644332222 23444488889999998875
No 11
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A
Probab=88.54 E-value=0.27 Score=40.17 Aligned_cols=31 Identities=19% Similarity=0.407 Sum_probs=25.3
Q ss_pred ccccCCCCCCce-eecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGF-ECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w-~~~~dG~~yC~~CGhv~Eg 40 (770)
..+|+.|++... .+...|..+|..||.|++.
T Consensus 11 ~~~Cp~C~~~~lv~D~~~ge~vC~~CGlVl~e 42 (58)
T 1dl6_A 11 RVTCPNHPDAILVEDYRAGDMICPECGLVVGD 42 (58)
T ss_dssp CCSBTTBSSSCCEECSSSCCEECTTTCCEECC
T ss_pred cccCcCCCCCceeEeCCCCeEEeCCCCCEEec
Confidence 357999999654 4457899999999999975
No 12
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*
Probab=88.25 E-value=6.8 Score=40.24 Aligned_cols=121 Identities=13% Similarity=0.110 Sum_probs=85.8
Q ss_pred hhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAE 336 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~ 336 (770)
-.+|-+||||-.--. |..+.||+... ++ ..+.+.|.++=..+.+
T Consensus 83 v~~acL~iA~K~eE~~~p~~~d~~~~~-~~----------------------------------~~~~~eI~~mE~~IL~ 127 (269)
T 2b9r_A 83 VGVTAMFIASKYEEMYPPEIGDFAFVT-DN----------------------------------TYTKHQIRQMEMKILR 127 (269)
T ss_dssp HHHHHHHHHHHHHCSSCCCHHHHHHHT-CS----------------------------------SSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccccCccHHHHHHHh-cC----------------------------------CCCHHHHHHHHHHHHH
Confidence 567789999988665 77888887431 11 1123678888888888
Q ss_pred HhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHhhccCCcchh
Q 004180 337 SIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRILYNINGFGAW 416 (770)
Q Consensus 337 ~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLLfgLDg~~eW 416 (770)
.++..+..++..-++.||++.++++.+ +...+..+++.++-..... ..-|. +.++|+|.+|.+++ + ...|
T Consensus 128 ~L~f~l~~~tp~~fl~~~~~~~~~~~~-~~~~a~~l~e~sl~~~~~~----~~~Ps-~iAaAai~lA~~~l-~---~~~w 197 (269)
T 2b9r_A 128 ALNFGLGRPLPLHFLRRASKIGEVDVE-QHTLAKYLMELTMLDYDMV----HFPPS-QIAAGAFSLALKIL-D---NGEW 197 (269)
T ss_dssp HTTSCCCCCCHHHHHHHHHHSSCCCHH-HHHHHHHHHHHGGGCGGGS----SSCTT-HHHHHHHHHHHHHH-T---CCCS
T ss_pred HcCCccCCCCHHHHHHHHHHhcCCCHH-HHHHHHHHHHHHHhhhhhh----cCCHH-HHHHHHHHHHHHHh-C---CCCC
Confidence 888888778888999999999999988 8888888887544322221 13455 88888888888875 2 2368
Q ss_pred hhhcccc
Q 004180 417 EKSLSSR 423 (770)
Q Consensus 417 e~sLs~~ 423 (770)
...|...
T Consensus 198 ~~~l~~~ 204 (269)
T 2b9r_A 198 TPTLQHY 204 (269)
T ss_dssp CTTHHHH
T ss_pred CHHHHHH
Confidence 7766544
No 13
>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B*
Probab=87.01 E-value=19 Score=36.33 Aligned_cols=123 Identities=10% Similarity=0.063 Sum_probs=81.4
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCc--hHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVP--SQKLESFAASIA 335 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s--~~~I~~la~~ia 335 (770)
..+|-+||||-.-..|..+.||+.-+..-.-| ..|+. . ....... .+.|..+=..+.
T Consensus 76 v~~acL~lA~K~EE~p~~l~d~~~~~~~~~~~--------------~~~~~--~-----~~~~~y~~~~~~I~~~E~~iL 134 (257)
T 2ivx_A 76 ISSTALFLAAKVEEQARKLEHVIKVAHACLHP--------------LEPLL--D-----TKCDAYLQQTRELVILETIML 134 (257)
T ss_dssp HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHCT--------------TSCCC--C-----TTSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccccCCcCHHHHHHHHHHHhcc--------------CCCCC--C-----cchHHHHHHHHHHHHHHHHHH
Confidence 56788999999998899999998654320000 00000 0 0000111 256777777888
Q ss_pred HHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccC-CccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 336 ESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSM-PPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 336 ~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~-p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
+.++..+...+....+.+|++.++++.+ +...+..+++.++ .... ...+|+.+.++|+|.+|.+++
T Consensus 135 ~~L~f~l~~~~P~~fl~~~~~~l~~~~~-~~~~A~~~~~~sl~~~~~-----~l~~~Ps~IAaAai~lA~~~~ 201 (257)
T 2ivx_A 135 QTLGFEITIEHPHTDVVKCTQLVRASKD-LAQTSYFMATNSLHLTTF-----CLQYKPTVIACVCIHLACKWS 201 (257)
T ss_dssp HHTTTCCCCCCHHHHHHHHHHHTTCCHH-HHHHHHHHHHHHHHHCCG-----GGTSCHHHHHHHHHHHHHHHH
T ss_pred HHcccceEeeCcHHHHHHHHHHhCCCcH-HHHHHHHHHHhhhhcccH-----HHcCCHHHHHHHHHHHHHHHh
Confidence 8888888778888999999999999988 7777777765332 1111 123444488888888888875
No 14
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=84.67 E-value=0.54 Score=37.38 Aligned_cols=29 Identities=17% Similarity=0.422 Sum_probs=24.3
Q ss_pred ccccCCCCCCceeecCCcceecccCCeee
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~ 38 (770)
..-|++||+..+-....++++|..||...
T Consensus 19 ~k~CP~CG~~~fm~~~~~R~~C~kCG~t~ 47 (50)
T 3j20_Y 19 NKFCPRCGPGVFMADHGDRWACGKCGYTE 47 (50)
T ss_dssp SEECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred cccCCCCCCceEEecCCCeEECCCCCCEE
Confidence 46699999988766688999999999754
No 15
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}
Probab=83.69 E-value=0.61 Score=46.29 Aligned_cols=35 Identities=20% Similarity=0.333 Sum_probs=26.9
Q ss_pred ccccccccCCCCCC--c-eeecCCcceecccCCeeecc
Q 004180 6 GDIRRLKCKKCDNV--G-FECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 6 ~~~r~~~C~~C~S~--~-w~~~~dG~~yC~~CGhv~Eg 40 (770)
.......|+.|++. . -.+...|-++|..||-|++.
T Consensus 17 ~ln~~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEE 54 (197)
T 3k1f_M 17 NLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSD 54 (197)
T ss_dssp CCCCCCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCC
T ss_pred ccccCeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCC
Confidence 33455689999983 2 34458999999999999975
No 16
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=82.13 E-value=0.84 Score=36.68 Aligned_cols=31 Identities=29% Similarity=0.646 Sum_probs=24.0
Q ss_pred cccccCCCCCCc-------eeecCCc---ceecccCCeeec
Q 004180 9 RRLKCKKCDNVG-------FECAYDG---FYYCTHCNALDD 39 (770)
Q Consensus 9 r~~~C~~C~S~~-------w~~~~dG---~~yC~~CGhv~E 39 (770)
....|+.|+... |+..++| ||.|..|||.-.
T Consensus 14 ~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~ 54 (57)
T 1qyp_A 14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR 54 (57)
T ss_dssp EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred eEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEec
Confidence 457899999975 3445667 799999999853
No 17
>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8
Probab=80.57 E-value=1.2 Score=36.04 Aligned_cols=28 Identities=21% Similarity=0.444 Sum_probs=22.7
Q ss_pred ccccCCCCCCceeecCCcceecccCCee
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv 37 (770)
...|+.||+..+-....++++|..||..
T Consensus 18 ~~fCPkCG~~~~ma~~~dr~~C~kCgyt 45 (55)
T 2k4x_A 18 HRFCPRCGPGVFLAEHADRYSCGRCGYT 45 (55)
T ss_dssp SCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred cccCcCCCCceeEeccCCEEECCCCCCE
Confidence 5789999997763346789999999965
No 18
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A
Probab=80.17 E-value=32 Score=36.37 Aligned_cols=150 Identities=17% Similarity=0.197 Sum_probs=95.5
Q ss_pred HHHHhcC--CChhHHHHHHHHHHHHHhhcCCCCCCchhhhhcccccccccccCcCcccCCCCCCccccchhhHHHHHHHH
Q 004180 173 ALVDKFN--VCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELESKDFQPRAKYRDEPHTLHGQRAVMIWYKLL 250 (770)
Q Consensus 173 aLI~~~G--~ppELe~VVrdLWlRyL~~~~v~~~~~ad~~~~dsesqE~e~~sSq~~~~~~~e~~~~~~~Rk~~~wprll 250 (770)
.+...++ +|++.-...-.+..||+....+... . +. +
T Consensus 66 ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~----------------------------------~-------~~-l 103 (323)
T 1jkw_A 66 EFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEY----------------------------------H-------PR-I 103 (323)
T ss_dssp HHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTS----------------------------------C-------HH-H
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhc----------------------------------C-------HH-H
Confidence 3445678 9999888888888888765322110 0 11 1
Q ss_pred hhcCCcchhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHH
Q 004180 251 RQKIPLSSSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESF 330 (770)
Q Consensus 251 r~~Lp~~~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~l 330 (770)
..+|-+||||-.=..|+.+.||+.-+... | ... -.....|..+
T Consensus 104 -------va~acLfLA~K~EE~~~~l~d~v~~~~~~--p---------~~~-------------------~~~~~~Il~~ 146 (323)
T 1jkw_A 104 -------IMLTCAFLACKVDEFNVSSPQFVGNLRES--P---------LGQ-------------------EKALEQILEY 146 (323)
T ss_dssp -------HHHHHHHHHHHHTTCCCCHHHHGGGSSSC--H---------HHH-------------------HHHHHHHHHH
T ss_pred -------HHHHHHHHHHhhhcCCCCHHHHHHHhccC--h---------hhh-------------------HHHHHHHHHH
Confidence 56788999999999999999997532110 1 000 0112567777
Q ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHc-----CC--ChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHH
Q 004180 331 AASIAESIGLHLPPVNFYALASRYLKQL-----CL--PLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVS 403 (770)
Q Consensus 331 a~~ia~~~gL~fPpiN~~lLL~Ryl~eL-----~L--P~E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVA 403 (770)
=..+.+.++..+...+....+.+|+..+ ++ |.+ +...+..+++-++-... .+.+|+.+.++|+|.+|
T Consensus 147 E~~iL~~L~f~l~v~~P~~~L~~~l~~l~~~~~~~~~~~~-l~~~A~~~l~~sl~t~~-----~l~~~Ps~IAaAai~lA 220 (323)
T 1jkw_A 147 ELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEI-LRKTADDFLNRIALTDA-----YLLYTPSQIALTAILSS 220 (323)
T ss_dssp HHHHHHHTTTCCCCCCSHHHHHHHHHHHHHHCTTCCCHHH-HHHHHHHHHHHHTTSTH-----HHHSCHHHHHHHHHHHH
T ss_pred HHHHHHHCCCcEEcCChHHHHHHHHHHHHHHhccCCCHHH-HHHHHHHHHHHHHhccH-----HHcCCHHHHHHHHHHHH
Confidence 7777778888776667777788888776 23 444 66667677663332222 12344448888888888
Q ss_pred HHHh
Q 004180 404 IRIL 407 (770)
Q Consensus 404 lKLL 407 (770)
.+++
T Consensus 221 ~~~~ 224 (323)
T 1jkw_A 221 ASRA 224 (323)
T ss_dssp HHHH
T ss_pred HHHc
Confidence 8865
No 19
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C
Probab=79.39 E-value=11 Score=40.64 Aligned_cols=122 Identities=11% Similarity=0.078 Sum_probs=76.3
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhc---CCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIE---GKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASI 334 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~e---g~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~i 334 (770)
..+|-+||||-.--.|..+.||+.-+.. ..-| +... . ...+. ...+.|..+=..+
T Consensus 83 va~acLfLA~K~EE~p~~l~d~v~v~~~~~~~~~~----------------~~~~-~-~~~y~----~~~~~Il~~E~~I 140 (358)
T 2pk2_A 83 VAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQES----------------LPDT-R-SEAYL----QQVQDLVILESII 140 (358)
T ss_dssp HHHHHHHHHHHHTTCCCCHHHHHTTHHHHHCSSSC----------------CCCT-T-SHHHH----GGGTGGGTHHHHH
T ss_pred HHHHHHHHHHhhccCCCCHHHHHHHHHHHhccccc----------------cccc-c-chhhh----HHHHHHHHHHHHH
Confidence 5778899999999899999999864321 1100 0000 0 00000 0013355555566
Q ss_pred HHHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccC-CccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 335 AESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSM-PPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 335 a~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~~v~RL~~fs~-p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
.+.++..+...+....+.+|++.+.++.+ +...+..+++.++ ..... +.+|+.+.++|+|.+|.+++
T Consensus 141 L~~L~f~L~v~~P~~fL~~~~~~l~~~~~-l~~~A~~ll~~sl~~t~l~-----l~y~Ps~IAaAAI~lA~~~l 208 (358)
T 2pk2_A 141 LQTLGFELTIDHPHTHVVKCTQLVRASKD-LAQTSYFMATNSLHLTTFS-----LQYTPPVVACVCIHLACKWS 208 (358)
T ss_dssp HHHTTTCCCCCCTTHHHHHHHHHTTCCHH-HHHHHHHHHHHHTTTSCGG-----GTSCHHHHTTTTTTTHHHHT
T ss_pred HHHcCCceeCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHhcCcch-----hccCHHHHHHHHHHHHHHHh
Confidence 66677666555666788999999999988 7777777776443 12211 23444488888888888875
No 20
>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5
Probab=78.69 E-value=1 Score=42.64 Aligned_cols=29 Identities=14% Similarity=0.251 Sum_probs=25.9
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeec
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
-|.|++|.|.--|. +...|.|..|||.-.
T Consensus 27 lP~CP~C~seytYe-Dg~l~vCPeC~hEW~ 55 (138)
T 2akl_A 27 LPPCPQCNSEYTYE-DGALLVCPECAHEWS 55 (138)
T ss_dssp SCCCTTTCCCCCEE-CSSSEEETTTTEEEC
T ss_pred CCCCCCCCCcceEe-cCCeEECCccccccC
Confidence 48999999998787 888999999999874
No 21
>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ...
Probab=74.34 E-value=12 Score=37.97 Aligned_cols=121 Identities=11% Similarity=0.109 Sum_probs=84.1
Q ss_pred hhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAE 336 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~ 336 (770)
..+|-+||||-.-.. |..+.||+.. .++ ..+.+.|.++=..+.+
T Consensus 84 v~~acl~iA~K~ee~~~~~~~d~~~i-~~~----------------------------------~~~~~~i~~mE~~iL~ 128 (260)
T 2cch_B 84 VGTAAMLLASKFEEIYPPEVAEFVYI-TDD----------------------------------TYTKKQVLRMEHLVLK 128 (260)
T ss_dssp HHHHHHHHHHHHHCSSCCCHHHHHHH-TTS----------------------------------SSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHH-HcC----------------------------------CcCHHHHHHHHHHHHH
Confidence 567889999988776 8888888752 111 1123678888888888
Q ss_pred HhCCCCCCCCHHHHHHHHHHHcCCCh-hhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHhhccCCcch
Q 004180 337 SIGLHLPPVNFYALASRYLKQLCLPL-GKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRILYNINGFGA 415 (770)
Q Consensus 337 ~~gL~fPpiN~~lLL~Ryl~eL~LP~-E~iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLLfgLDg~~e 415 (770)
.++..+.+++..-++.+|++.++++. . +...+..+++.++-... ....+|+.+.++|+|.+|.+++=+ ..
T Consensus 129 ~L~~~l~~~tp~~fl~~~~~~l~~~~~~-~~~~a~~l~e~sl~~~~----~~~~~~Ps~iAaAai~lA~~~~~~----~~ 199 (260)
T 2cch_B 129 VLTFDLAAPTVNQFLTQYFLHQQPANCK-VESLAMFLGELSLIDAD----PYLKYLPSVIAGAAFHLALYTVTG----QS 199 (260)
T ss_dssp HTTTCCCCCCHHHHHHHHHTTCSSCCHH-HHHHHHHHHHHHHHCHH----HHTTSCHHHHHHHHHHHHHHHHHS----CC
T ss_pred HcCCccCCCCHHHHHHHHHHHcCCChHH-HHHHHHHHHHHHHHhHH----HHhCCCHHHHHHHHHHHHHHHhCC----Cc
Confidence 88888878889999999999999987 6 77777777764321111 012333338888888888887632 45
Q ss_pred hhhhccc
Q 004180 416 WEKSLSS 422 (770)
Q Consensus 416 We~sLs~ 422 (770)
|...|..
T Consensus 200 w~~~l~~ 206 (260)
T 2cch_B 200 WPESLIR 206 (260)
T ss_dssp SCHHHHH
T ss_pred chHHHHH
Confidence 7665543
No 22
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=73.54 E-value=1.1 Score=35.93 Aligned_cols=25 Identities=20% Similarity=0.449 Sum_probs=21.5
Q ss_pred ccccCCCCCCceeecCCcceecccCCeee
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~ 38 (770)
.-+|+.|+++ . .-|-+.|+.|||..
T Consensus 14 k~iCpkC~a~---~-~~gaw~CrKCG~~~ 38 (51)
T 3j21_g 14 KYVCLRCGAT---N-PWGAKKCRKCGYKR 38 (51)
T ss_dssp EEECTTTCCE---E-CTTCSSCSSSSSCC
T ss_pred CccCCCCCCc---C-CCCceecCCCCCcc
Confidence 3579999998 4 78999999999983
No 23
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=68.10 E-value=3.2 Score=34.95 Aligned_cols=31 Identities=6% Similarity=-0.125 Sum_probs=25.5
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeec
Q 004180 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 9 r~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
--.+|+.|.+..-.....|..+|..||..-.
T Consensus 7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YP 37 (68)
T 2jr6_A 7 DILVCPVTKGRLEYHQDKQELWSRQAKLAYP 37 (68)
T ss_dssp CCCBCSSSCCBCEEETTTTEEEETTTTEEEE
T ss_pred hheECCCCCCcCeEeCCCCEEEcCCCCcEec
Confidence 3478999999987666789999999997653
No 24
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=67.88 E-value=3.1 Score=35.29 Aligned_cols=31 Identities=13% Similarity=-0.009 Sum_probs=25.4
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeec
Q 004180 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 9 r~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
--.+|+.|.+..-.....|..+|..||..-.
T Consensus 7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YP 37 (70)
T 2js4_A 7 DILVCPVCKGRLEFQRAQAELVCNADRLAFP 37 (70)
T ss_dssp CCCBCTTTCCBEEEETTTTEEEETTTTEEEE
T ss_pred hheECCCCCCcCEEeCCCCEEEcCCCCceec
Confidence 3578999999987665789999999997543
No 25
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1
Probab=67.88 E-value=3 Score=35.26 Aligned_cols=31 Identities=13% Similarity=-0.018 Sum_probs=25.5
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeec
Q 004180 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 9 r~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
--.+|+.|.+..-.....|..+|..||..-.
T Consensus 7 eiL~CP~ck~~L~~~~~~~~LiC~~cg~~YP 37 (69)
T 2pk7_A 7 DILACPICKGPLKLSADKTELISKGAGLAYP 37 (69)
T ss_dssp GTCCCTTTCCCCEECTTSSEEEETTTTEEEE
T ss_pred hheeCCCCCCcCeEeCCCCEEEcCCCCcEec
Confidence 3578999999987665789999999997653
No 26
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=67.73 E-value=2.9 Score=33.12 Aligned_cols=33 Identities=21% Similarity=0.566 Sum_probs=24.5
Q ss_pred cccccccccCCCCCCc--e-----eecCCc---ceecccCCee
Q 004180 5 EGDIRRLKCKKCDNVG--F-----ECAYDG---FYYCTHCNAL 37 (770)
Q Consensus 5 ~~~~r~~~C~~C~S~~--w-----~~~~dG---~~yC~~CGhv 37 (770)
.+......|+.|+... | +.+|+| ||.|..|||.
T Consensus 4 ~~~t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~ 46 (50)
T 1tfi_A 4 GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR 46 (50)
T ss_dssp CEECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCE
T ss_pred CceeCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCe
Confidence 3445667899999987 2 224566 7999999996
No 27
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1
Probab=67.65 E-value=3.2 Score=34.95 Aligned_cols=30 Identities=13% Similarity=0.017 Sum_probs=25.0
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeec
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
-.+|+.|.+..-.....|..+|..||..-.
T Consensus 8 iL~CP~ck~~L~~~~~~~~LiC~~cg~~YP 37 (68)
T 2hf1_A 8 ILVCPLCKGPLVFDKSKDELICKGDRLAFP 37 (68)
T ss_dssp ECBCTTTCCBCEEETTTTEEEETTTTEEEE
T ss_pred heECCCCCCcCeEeCCCCEEEcCCCCcEec
Confidence 468999999987665789999999997653
No 28
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1
Probab=67.09 E-value=4.6 Score=33.98 Aligned_cols=32 Identities=13% Similarity=-0.006 Sum_probs=26.4
Q ss_pred ccccccCCCCCCceeecCCcceecccCCeeec
Q 004180 8 IRRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 8 ~r~~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
.--.+|+.|.+..-...+.|..+|..||..-.
T Consensus 8 LeiL~CP~ck~~L~~~~~~g~LvC~~c~~~YP 39 (67)
T 2jny_A 8 LEVLACPKDKGPLRYLESEQLLVNERLNLAYR 39 (67)
T ss_dssp TCCCBCTTTCCBCEEETTTTEEEETTTTEEEE
T ss_pred HHHhCCCCCCCcCeEeCCCCEEEcCCCCcccc
Confidence 44579999999987776899999999997653
No 29
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=66.41 E-value=3.2 Score=36.47 Aligned_cols=31 Identities=19% Similarity=0.503 Sum_probs=26.3
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|+.|+...-.-...|-|.|..||..+-|
T Consensus 35 ky~CpfCGk~~vkR~a~GIW~C~kCg~~~AG 65 (83)
T 3j21_i 35 KHTCPVCGRKAVKRISTGIWQCQKCGATFAG 65 (83)
T ss_dssp CBCCSSSCSSCEEEEETTEEEETTTCCEEEC
T ss_pred ccCCCCCCCceeEecCcCeEEcCCCCCEEeC
Confidence 3579999999874448999999999998876
No 30
>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=64.59 E-value=3.6 Score=36.77 Aligned_cols=30 Identities=17% Similarity=0.502 Sum_probs=26.0
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004180 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
-.|+.|+...-.-..-|-|.|..||..+-|
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~Cg~~~AG 66 (92)
T 3iz5_m 37 YFCEFCGKFAVKRKAVGIWGCKDCGKVKAG 66 (92)
T ss_dssp BCCTTTCSSCBEEEETTEEECSSSCCEEEC
T ss_pred ccCcccCCCeeEecCcceEEcCCCCCEEeC
Confidence 479999999874447999999999999887
No 31
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}
Probab=64.08 E-value=3.4 Score=35.37 Aligned_cols=31 Identities=19% Similarity=0.520 Sum_probs=26.1
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|+.|+...-.....|-|.|..||..+-|
T Consensus 26 ky~C~fCgk~~vkR~a~GIW~C~~C~~~~AG 56 (72)
T 3jyw_9 26 RYDCSFCGKKTVKRGAAGIWTCSCCKKTVAG 56 (72)
T ss_dssp CBCCSSCCSSCBSBCSSSCBCCSSSCCCCCC
T ss_pred CccCCCCCCceeEecCCCeEECCCCCCEEeC
Confidence 3579999999874448999999999988876
No 32
>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=62.82 E-value=4 Score=36.47 Aligned_cols=31 Identities=19% Similarity=0.520 Sum_probs=26.2
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|+.|+.....-..-|-|.|..||..+-|
T Consensus 36 ky~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (92)
T 3izc_m 36 RYDCSFCGKKTVKRGAAGIWTCSCCKKTVAG 66 (92)
T ss_dssp CCCCSSSCSSCCEEEETTEEECTTTCCEEEC
T ss_pred CCcCCCCCCceeeecccceEEcCCCCCEEeC
Confidence 3579999999874447999999999999887
No 33
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=62.62 E-value=4.3 Score=37.03 Aligned_cols=28 Identities=18% Similarity=0.422 Sum_probs=22.4
Q ss_pred ccCCCCCCceeecCCc----ceecccCCeeec
Q 004180 12 KCKKCDNVGFECAYDG----FYYCTHCNALDD 39 (770)
Q Consensus 12 ~C~~C~S~~w~~~~dG----~~yC~~CGhv~E 39 (770)
-|+.|++-..-..+.| +|+|+.||.+..
T Consensus 6 FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~ 37 (113)
T 3h0g_I 6 YCIECNNMLYPREDKVDRVLRLACRNCDYSEI 37 (113)
T ss_dssp CCSSSCCCCEECCCTTTCCCCEECSSSCCEEC
T ss_pred eCcCCCCEeeEcccCCCCeeEEECCCCCCeEE
Confidence 4999999998543433 799999999775
No 34
>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y
Probab=61.08 E-value=3.7 Score=37.32 Aligned_cols=30 Identities=23% Similarity=0.546 Sum_probs=25.9
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004180 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
-.|+.|+.....-..-|-|.|..||..+-|
T Consensus 37 y~CpfCgk~~vKR~a~GIW~C~kCg~~~AG 66 (103)
T 4a17_Y 37 YGCPFCGKVAVKRAAVGIWKCKPCKKIIAG 66 (103)
T ss_dssp EECTTTCCEEEEEEETTEEEETTTTEEEEC
T ss_pred CCCCCCCCceeeecCcceEEcCCCCCEEeC
Confidence 469999999874447999999999999987
No 35
>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=60.63 E-value=3.8 Score=38.04 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=25.2
Q ss_pred ccccCCCCCCce-eecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGF-ECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w-~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|+.|+.... +. ..|-|.|..||.++-|
T Consensus 60 kytCPfCGk~~vKR~-avGIW~C~~Cgk~fAG 90 (116)
T 3cc2_Z 60 DHACPNCGEDRVDRQ-GTGIWQCSYCDYKFTG 90 (116)
T ss_dssp CEECSSSCCEEEEEE-ETTEEEETTTCCEEEC
T ss_pred CCcCCCCCCceeEec-CceeEECCCCCCEEEC
Confidence 347999999765 55 7899999999999876
No 36
>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A
Probab=58.05 E-value=63 Score=32.87 Aligned_cols=109 Identities=8% Similarity=0.156 Sum_probs=73.1
Q ss_pred hhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAE 336 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~ 336 (770)
-.+|-+||||-.-.. |..+.||.... ++ ..+.+.|.++=..+.+
T Consensus 102 v~~acL~iAsK~EE~~p~~~~~~~~~~-~~----------------------------------~~~~~eI~~mE~~IL~ 146 (271)
T 2w96_A 102 LGATCMFVASKMKETIPLTAEKLCIYT-DN----------------------------------SIRPEELLQMELLLVN 146 (271)
T ss_dssp HHHHHHHHHHHHHCSSCCCHHHHHHHT-TT----------------------------------SSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHh-cC----------------------------------CCCHHHHHHHHHHHHH
Confidence 567888999988776 88888886421 00 1133778888888888
Q ss_pred HhCCCCCCCCHHHHHHHHHHHcCCChhhhHH----HHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 337 SIGLHLPPVNFYALASRYLKQLCLPLGKILP----RALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 337 ~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy~----~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
.++..+.+++..-++.+|++.++++.+ ... .+..+++..+-..... ..-|. +.++|+|.+|.+.+
T Consensus 147 ~L~~~l~~~tp~~fl~~~~~~l~~~~~-~~~~~~~~a~~~l~~~~~d~~~~----~~~PS-~iAaAai~lA~~~l 215 (271)
T 2w96_A 147 KLKWNLAAMTPHDFIEHFLSKMPEAEE-NKQIIRKHAQTFVALCATDVKFI----SNPPS-MVAAGSVVAAVQGL 215 (271)
T ss_dssp HTTTCCCCCCHHHHHHHHHHTSCCCHH-HHHHHHHHHHHHHHHHHTSTHHH----HSCHH-HHHHHHHHHHHHHH
T ss_pred HCCCccCCCCHHHHHHHHHHHcCCCch-HHHHHHHHHHHHHHHHHhhhhhh----ccCHH-HHHHHHHHHHHHHh
Confidence 899888888999999999999999987 322 3334443221111111 12355 77888887777765
No 37
>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A
Probab=53.58 E-value=3.7 Score=32.16 Aligned_cols=27 Identities=22% Similarity=0.700 Sum_probs=23.5
Q ss_pred ccccCCCCCCc---eeecCCcceecccCCe
Q 004180 10 RLKCKKCDNVG---FECAYDGFYYCTHCNA 36 (770)
Q Consensus 10 ~~~C~~C~S~~---w~~~~dG~~yC~~CGh 36 (770)
...|.+|+... |+-+.+|...|-.||-
T Consensus 4 ~~~C~~C~tt~Tp~WR~gp~G~~LCNaCGl 33 (46)
T 1gnf_A 4 ARECVNCGATATPLWRRDRTGHYLCNACGL 33 (46)
T ss_dssp SCCCTTTCCCCCSSCBCCTTCCCBCSHHHH
T ss_pred CCCCCCcCCCCCCcCccCCCCCccchHHHH
Confidence 46799999885 9888999999999985
No 38
>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=53.24 E-value=6.1 Score=33.86 Aligned_cols=31 Identities=23% Similarity=0.492 Sum_probs=25.0
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
.-.|+.|+...-.-..-|-|.|..||.++-|
T Consensus 27 ky~C~fCgk~~vkR~a~GIW~C~~C~~~~AG 57 (73)
T 1ffk_W 27 KYKCPVCGFPKLKRASTSIWVCGHCGYKIAG 57 (73)
T ss_pred CccCCCCCCceeEEEEeEEEECCCCCcEEEC
Confidence 4579999987653337899999999999776
No 39
>3u50_C Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 2.50A {Tetrahymena thermophila}
Probab=52.86 E-value=6.5 Score=38.65 Aligned_cols=28 Identities=11% Similarity=0.422 Sum_probs=23.2
Q ss_pred cccccCCCCCCceeecCCcceecccCCee
Q 004180 9 RRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (770)
Q Consensus 9 r~~~C~~C~S~~w~~~~dG~~yC~~CGhv 37 (770)
.=+.|++|..+--.. .+|.|.|..||..
T Consensus 41 ~Y~ACp~CnKKV~~~-~~g~~~CekC~~~ 68 (172)
T 3u50_C 41 YYYRCTCQGKSVLKY-HGDSFFCESCQQF 68 (172)
T ss_dssp EEEECTTSCCCEEEE-TTTEEEETTTTEE
T ss_pred EehhchhhCCEeeeC-CCCeEECCCCCCC
Confidence 346799998877655 8999999999987
No 40
>2vut_I AREA, nitrogen regulatory protein AREA; transcription regulation, protein-protein interactions, metal-binding, nitrate assimilation; HET: NAD; 2.3A {Emericella nidulans} SCOP: g.39.1.1 PDB: 2vus_I* 2vuu_I*
Probab=50.17 E-value=4.9 Score=31.01 Aligned_cols=27 Identities=19% Similarity=0.519 Sum_probs=22.8
Q ss_pred cccCCCCCCc---eeecCCcceecccCCee
Q 004180 11 LKCKKCDNVG---FECAYDGFYYCTHCNAL 37 (770)
Q Consensus 11 ~~C~~C~S~~---w~~~~dG~~yC~~CGhv 37 (770)
..|.+|+... |+-+.+|...|-.||-.
T Consensus 2 ~~C~~C~tt~Tp~WR~gp~G~~LCNaCGl~ 31 (43)
T 2vut_I 2 TTCTNCFTQTTPLWRRNPEGQPLCNACGLF 31 (43)
T ss_dssp CCCSSSCCCCCSCCEECTTSCEECHHHHHH
T ss_pred CcCCccCCCCCCccccCCCCCcccHHHHHH
Confidence 3699999885 99988999999999843
No 41
>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=48.90 E-value=7.1 Score=36.09 Aligned_cols=29 Identities=17% Similarity=0.606 Sum_probs=23.1
Q ss_pred cccCCCCCCceee----cCCcceecccCCeeec
Q 004180 11 LKCKKCDNVGFEC----AYDGFYYCTHCNALDD 39 (770)
Q Consensus 11 ~~C~~C~S~~w~~----~~dG~~yC~~CGhv~E 39 (770)
.-|+.|++-..-. ...+.|+|+.||++..
T Consensus 5 ~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~ 37 (122)
T 1twf_I 5 RFCRDCNNMLYPREDKENNRLLFECRTCSYVEE 37 (122)
T ss_dssp CBCSSSCCBCEEEEETTTTEEEEECSSSSCEEE
T ss_pred CcccccCccCcccccCcCCCCEEECCcCCCeee
Confidence 3599999999844 2357899999999775
No 42
>4gat_A Nitrogen regulatory protein AREA; DNA binding protein, transcription factor, zinc binding domain, complex (transcription regulation/DNA); HET: DNA; NMR {Emericella nidulans} SCOP: g.39.1.1 PDB: 5gat_A* 6gat_A* 7gat_A*
Probab=47.99 E-value=7.3 Score=32.71 Aligned_cols=31 Identities=16% Similarity=0.359 Sum_probs=25.7
Q ss_pred ccccccCCCCCCc---eeecCCcceecccCCeee
Q 004180 8 IRRLKCKKCDNVG---FECAYDGFYYCTHCNALD 38 (770)
Q Consensus 8 ~r~~~C~~C~S~~---w~~~~dG~~yC~~CGhv~ 38 (770)
.....|.+|+... |+-+.+|...|-.||-..
T Consensus 7 ~~~~~C~~C~t~~Tp~WR~gp~G~~LCNaCGl~~ 40 (66)
T 4gat_A 7 NGPTTCTNCFTQTTPLWRRNPEGQPLCNACGLFL 40 (66)
T ss_dssp SSSCCCTTTCCCCCSSCEEETTTEEECHHHHHHH
T ss_pred CCCCCCCCCCCCCCCcCCcCCCCCCccHHHHHHH
Confidence 3467899999885 988899999999999543
No 43
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}
Probab=45.85 E-value=8.4 Score=36.35 Aligned_cols=29 Identities=17% Similarity=0.593 Sum_probs=22.0
Q ss_pred cccCCCCCCceeecC----CcceecccCCeeec
Q 004180 11 LKCKKCDNVGFECAY----DGFYYCTHCNALDD 39 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~----dG~~yC~~CGhv~E 39 (770)
.-|+.|++-.+-..+ ..+|+|+.||.+.+
T Consensus 25 ~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~~ 57 (133)
T 3qt1_I 25 RFCRDCNNMLYPREDKENNRLLFECRTCSYVEE 57 (133)
T ss_dssp CBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBCC
T ss_pred eeCCCCCCEeeECccCCCceeEEECCCCCCcEE
Confidence 459999999985422 12799999999764
No 44
>3dfx_A Trans-acting T-cell-specific transcription factor GATA-3; activator, DNA-binding, metal-binding, nucleus; HET: DNA; 2.70A {Mus musculus} PDB: 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A*
Probab=45.24 E-value=5.4 Score=33.24 Aligned_cols=32 Identities=16% Similarity=0.383 Sum_probs=26.3
Q ss_pred cccccccCCCCCCc---eeecCCcceecccCCeee
Q 004180 7 DIRRLKCKKCDNVG---FECAYDGFYYCTHCNALD 38 (770)
Q Consensus 7 ~~r~~~C~~C~S~~---w~~~~dG~~yC~~CGhv~ 38 (770)
...+..|.+|+... |+-+.+|...|-.||-..
T Consensus 4 ~~~~~~C~~C~tt~Tp~WR~gp~G~~LCNACGl~~ 38 (63)
T 3dfx_A 4 RRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYY 38 (63)
T ss_dssp CCTTCCCTTTCCSCCSSCCCCTTSCCCCHHHHHHH
T ss_pred CCCCCcCCCcCCCCCCccCCCCCCCchhhHHHHHH
Confidence 34567899999885 998899999999999544
No 45
>4hc9_A Trans-acting T-cell-specific transcription factor; zinc finger, GATA transcription factor, DNA bridging, transc DNA complex; HET: DNA; 1.60A {Homo sapiens} PDB: 4hc7_A* 4hca_A* 3dfx_A* 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A* 1gnf_A 1y0j_A 2l6y_A 2l6z_A
Probab=44.30 E-value=6.5 Score=36.21 Aligned_cols=29 Identities=21% Similarity=0.521 Sum_probs=23.0
Q ss_pred ccccccCCCCCC---ceeecCCcceecccCCe
Q 004180 8 IRRLKCKKCDNV---GFECAYDGFYYCTHCNA 36 (770)
Q Consensus 8 ~r~~~C~~C~S~---~w~~~~dG~~yC~~CGh 36 (770)
..+..|.+|++. .|+-+.+|.+.|..||-
T Consensus 3 ~~~~~C~~Cg~~~Tp~WRr~~~g~~lCnaCgl 34 (115)
T 4hc9_A 3 HMGRECVNCGATSTPLWRRDGTGHYLCNACGL 34 (115)
T ss_dssp ---CCCTTTCCSCCSSCEECTTSCEECHHHHH
T ss_pred CCCCCCCCCCCccCCcceECCCCCCcCcchhh
Confidence 346789999955 59888999999999994
No 46
>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1
Probab=41.54 E-value=48 Score=33.48 Aligned_cols=110 Identities=12% Similarity=0.030 Sum_probs=72.8
Q ss_pred hhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAE 336 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~ 336 (770)
-.+|-+||||-.--. |..+.||.... ++ ..+.+.|.++=..+.+
T Consensus 96 v~~acl~iA~K~eE~~~p~~~d~~~~~-~~----------------------------------~~~~~~i~~mE~~iL~ 140 (257)
T 1g3n_C 96 TGSACLLVASKLRSLTPISTSSLCYAA-AD----------------------------------SFSRQELIDQEKELLE 140 (257)
T ss_dssp HHHHHHHHHHHHHCSSCCCHHHHHHHT-TT----------------------------------CSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHccccCCCHHHHHHHH-CC----------------------------------CCCHHHHHHHHHHHHH
Confidence 566778999977543 77788876421 11 1123678888888888
Q ss_pred HhCCCCCCCCHHHHHHHHHHHcCCChhh---hHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 337 SIGLHLPPVNFYALASRYLKQLCLPLGK---ILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 337 ~~gL~fPpiN~~lLL~Ryl~eL~LP~E~---iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
.++..+..++..-.+.+|++.++++.+. +...+..+++.++-... ...+|+.+.++|+|.+|.+.+
T Consensus 141 ~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~-----~~~~~PS~iAaAai~lA~~~l 209 (257)
T 1g3n_C 141 KLAWRTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPL-----TGSLPASIISAAGCALLVPAN 209 (257)
T ss_dssp HTTTCCCCCCHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTT-----GGGSCHHHHHHHHHHHHCCGG
T ss_pred HCCCcCCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcc-----hhCcCHHHHHHHHHHHHHHHh
Confidence 8888887888899999999999998762 23345555553322111 123344377888887777765
No 47
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*
Probab=39.44 E-value=1.6e+02 Score=28.41 Aligned_cols=51 Identities=12% Similarity=0.005 Sum_probs=40.8
Q ss_pred hhHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCC
Q 004180 258 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVAC 308 (770)
Q Consensus 258 ~TLAI~YLAcl~LR~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~ 308 (770)
-..|.+||||.+++.|.+..++..-+.-..--..+.++.|=+......|.|
T Consensus 144 IAaAaiylA~~~~~~~~~~~~i~~~~~v~~~tI~~~~~~l~~~l~~~~p~~ 194 (207)
T 1c9b_A 144 VAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTD 194 (207)
T ss_dssp HHHHHHHHHHHTSSSCCCHHHHHHHHTCCHHHHHHHHHHHGGGHHHHSCSS
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHhChHH
Confidence 678999999999999999999988777666666677777666666666666
No 48
>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...
Probab=37.79 E-value=11 Score=32.01 Aligned_cols=25 Identities=16% Similarity=0.370 Sum_probs=14.4
Q ss_pred cccCCCCCCceeecCCcceecccCCe
Q 004180 11 LKCKKCDNVGFECAYDGFYYCTHCNA 36 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~dG~~yC~~CGh 36 (770)
-+|..||..-=.. +..-..|.+|||
T Consensus 29 Y~C~~CG~~~e~~-~~d~irCp~CG~ 53 (70)
T 1twf_L 29 YICAECSSKLSLS-RTDAVRCKDCGH 53 (70)
T ss_dssp EECSSSCCEECCC-TTSTTCCSSSCC
T ss_pred EECCCCCCcceeC-CCCCccCCCCCc
Confidence 3677777764322 223346777777
No 49
>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A
Probab=37.56 E-value=75 Score=31.99 Aligned_cols=110 Identities=9% Similarity=0.010 Sum_probs=71.9
Q ss_pred hhHHHHHHHHHHhh-cccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHH
Q 004180 258 SSLAISFLACHVVR-EAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAE 336 (770)
Q Consensus 258 ~TLAI~YLAcl~LR-~PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~ia~ 336 (770)
-.+|-+||||-.-- .|..+.||+.. .. . ..+.+.|.++=..+.+
T Consensus 97 v~~acl~iA~K~eE~~~p~~~d~~~~-~~---------------------------~-------~~~~~~i~~mE~~IL~ 141 (254)
T 2f2c_A 97 IGAACVLIGSKIRTVKPMTVSKLTYL-SC---------------------------D-------CFTNLELINQEKDILE 141 (254)
T ss_dssp HHHHHHHHHHHHHCSSCCCHHHHSTT-C-------------------------------------CCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHH-hC---------------------------C-------CCCHHHHHHHHHHHHH
Confidence 56677889987744 46667666421 00 0 1234778888888888
Q ss_pred HhCCCCCCCCHHHHHHHHHHHcCCChhh---hHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004180 337 SIGLHLPPVNFYALASRYLKQLCLPLGK---ILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 407 (770)
Q Consensus 337 ~~gL~fPpiN~~lLL~Ryl~eL~LP~E~---iy~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~IIVAlKLL 407 (770)
.++..+.+++..-++.+|++.++++.+. +...+..+++.++-... ...+|+.+.++|+|.+|.+.+
T Consensus 142 ~L~~~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~-----~~~~~PS~iAaAai~la~~~~ 210 (254)
T 2f2c_A 142 ALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPN-----IALLSPGLICAGGLLTTIETD 210 (254)
T ss_dssp HTTTCCCCCCGGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGG-----GTTSCHHHHHHHHHHHHHHTT
T ss_pred HCCCcCCCCCHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcc-----hhccCHHHHHHHHHHHHHHhc
Confidence 8888877778888999999999998872 23345555554432211 123344388888888998874
No 50
>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=36.70 E-value=21 Score=32.86 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=22.6
Q ss_pred ccccCCCCCCc--e-----eecCCc---ceecccCCeeec
Q 004180 10 RLKCKKCDNVG--F-----ECAYDG---FYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~C~S~~--w-----~~~~dG---~~yC~~CGhv~E 39 (770)
...|+.|+... | +.+++| ||.|..|||.-.
T Consensus 72 ~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~ 111 (122)
T 1twf_I 72 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFT 111 (122)
T ss_dssp CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEE
T ss_pred CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEec
Confidence 56799999986 2 224555 799999999853
No 51
>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}
Probab=35.92 E-value=13 Score=35.32 Aligned_cols=30 Identities=30% Similarity=0.575 Sum_probs=25.3
Q ss_pred cccccccccCCCCCCceeecCCcceecccCCeee
Q 004180 5 EGDIRRLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (770)
Q Consensus 5 ~~~~r~~~C~~C~S~~w~~~~dG~~yC~~CGhv~ 38 (770)
+++..+.+|..||...|.- +.+|..||...
T Consensus 42 ~grL~~~rC~~CG~~~~PP----r~~Cp~C~s~~ 71 (145)
T 3irb_A 42 QNKIIGSKCSKCGRIFVPA----RSYCEHCFVKI 71 (145)
T ss_dssp TTCCEEEECTTTCCEEESC----CSEETTTTEEC
T ss_pred cCeEEEEEeCCCCcEEcCc----hhhCcCCCCCc
Confidence 5788899999999999965 56899999754
No 52
>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3
Probab=34.37 E-value=22 Score=34.61 Aligned_cols=29 Identities=21% Similarity=0.591 Sum_probs=22.9
Q ss_pred ccccCC--CCCCceeecCCcceecccCCeeec
Q 004180 10 RLKCKK--CDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~--C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
-+.|++ |..+--.. ++|.|.|..|+....
T Consensus 43 Y~aC~~~~CnKKv~~~-~~g~~~CekC~~~~~ 73 (181)
T 1l1o_C 43 YQACPTQDCNKKVIDQ-QNGLYRCEKCDTEFP 73 (181)
T ss_dssp EEBCCSTTCCCBCEEE-TTTEEEETTTTEEES
T ss_pred ECCCCchhcCCccccC-CCCeEECCCCCCcCC
Confidence 467988 98876554 789999999986653
No 53
>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718}
Probab=32.79 E-value=23 Score=33.74 Aligned_cols=27 Identities=22% Similarity=0.594 Sum_probs=20.0
Q ss_pred cccCCCCCCceeecCCc----ceecccCCee
Q 004180 11 LKCKKCDNVGFECAYDG----FYYCTHCNAL 37 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~dG----~~yC~~CGhv 37 (770)
.-|++||+..-....+| +++|..||..
T Consensus 4 ~~C~~CG~~~~~~~~~G~~~~~~~~~~~~~~ 34 (189)
T 3cng_A 4 KFCSQCGGEVILRIPEGDTLPRYICPKCHTI 34 (189)
T ss_dssp CBCTTTCCBCEEECCTTCSSCEEEETTTTEE
T ss_pred ccCchhCCccccccccCCCCcceECCCCCCc
Confidence 45999999995432455 7899999943
No 54
>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1
Probab=30.41 E-value=25 Score=29.81 Aligned_cols=27 Identities=15% Similarity=0.454 Sum_probs=19.3
Q ss_pred cccCCCCCCceeecCCcceecccCCeeec
Q 004180 11 LKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 11 ~~C~~C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
.+|+ |+...+-...-=-.-|. ||+.++
T Consensus 5 v~C~-C~~~~~~~~~~kT~~C~-CG~~~~ 31 (71)
T 1gh9_A 5 FRCD-CGRALYSREGAKTRKCV-CGRTVN 31 (71)
T ss_dssp EEET-TSCCEEEETTCSEEEET-TTEEEE
T ss_pred EECC-CCCEEEEcCCCcEEECC-CCCeee
Confidence 4799 99885544344456798 998776
No 55
>1vtn_C HNF-3/FORK head DNA-recognition motif; protein-DNA complex, double helix, transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 1d5v_A
Probab=30.40 E-value=33 Score=30.97 Aligned_cols=45 Identities=18% Similarity=0.447 Sum_probs=33.4
Q ss_pred CcchhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccchhhhHHHhcc
Q 004180 255 PLSSSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAFVEIEKRFGQ 303 (770)
Q Consensus 255 p~~~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~~~LPkeMk~ 303 (770)
|+.+=.++|.+|+.-.-. -+++++|..||++ +.||++.. +..|+.
T Consensus 4 Pp~SY~~LI~~AI~~sp~~~LtL~eIY~~I~~-~fpyyr~~---~~gWqN 49 (102)
T 1vtn_C 4 PPYSYISLITMAIQQAPGKMLTLSEIYQWIMD-LFPYYREN---QQRWQN 49 (102)
T ss_dssp CSSCHHHHHHHHHHTSTTSCBCHHHHHHHHHH-HCGGGGSC---HHHHHH
T ss_pred cCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHH-cCCccccC---CCchhh
Confidence 455667888888876543 4899999999998 66999853 455544
No 56
>1ptq_A Protein kinase C delta type; phosphotransferase; 1.95A {Mus musculus} SCOP: g.49.1.1 PDB: 1ptr_A*
Probab=29.39 E-value=26 Score=26.60 Aligned_cols=30 Identities=17% Similarity=0.496 Sum_probs=23.2
Q ss_pred ccccccccCCCCCCceeecCCcceecccCCe
Q 004180 6 GDIRRLKCKKCDNVGFECAYDGFYYCTHCNA 36 (770)
Q Consensus 6 ~~~r~~~C~~C~S~~w~~~~dG~~yC~~CGh 36 (770)
++.+...|+.|++..|++.-.| +-|+.|+-
T Consensus 7 ~~~~pt~C~~C~~~l~g~~~qg-~~C~~C~~ 36 (50)
T 1ptq_A 7 NYMSPTFCDHCGSLLWGLVKQG-LKCEDCGM 36 (50)
T ss_dssp CCSSCCBCTTTCCBCCSSSSCE-EEETTTCC
T ss_pred cCCCCCCcCCCCceeeccCCcc-CEeCCCCC
Confidence 4456678999999999885566 56999983
No 57
>2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} PDB: 3irb_A
Probab=29.18 E-value=17 Score=34.48 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=24.6
Q ss_pred cccccccccCCCCCCceeecCCcceecccCCee
Q 004180 5 EGDIRRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (770)
Q Consensus 5 ~~~~r~~~C~~C~S~~w~~~~dG~~yC~~CGhv 37 (770)
++...+.+|..||...|-- +.+|..||..
T Consensus 42 ~g~L~~~rC~~CG~~~fPP----r~~Cp~C~s~ 70 (145)
T 2gnr_A 42 QNKIIGSKCSKCGRIFVPA----RSYCEHCFVK 70 (145)
T ss_dssp TTCCEEEECTTTCCEEESC----CSEETTTTEE
T ss_pred CCEEEEEEECCCCcEEeCC----CCCCCCCCCC
Confidence 6788899999999999854 4589999976
No 58
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=29.10 E-value=15 Score=31.30 Aligned_cols=29 Identities=17% Similarity=0.635 Sum_probs=22.7
Q ss_pred cccccCCCCCCc---eee--cCCcceecccCCeee
Q 004180 9 RRLKCKKCDNVG---FEC--AYDGFYYCTHCNALD 38 (770)
Q Consensus 9 r~~~C~~C~S~~---w~~--~~dG~~yC~~CGhv~ 38 (770)
...+|.+|+... |+- +.+| ..|-.||-..
T Consensus 7 ~~~~C~nC~tt~Tp~WRrg~~~~g-~LCNACGl~~ 40 (71)
T 2kae_A 7 KSFQCSNCSVTETIRWRNIRSKEG-IQCNACFIYQ 40 (71)
T ss_dssp -CCCCSSSCCSCCSSCCCCSSSSC-CCSSHHHHHH
T ss_pred CCCcCCccCCCCCCccccCCCCCC-ccchHHHHHH
Confidence 457899999885 987 6778 8899999543
No 59
>4hc9_A Trans-acting T-cell-specific transcription factor; zinc finger, GATA transcription factor, DNA bridging, transc DNA complex; HET: DNA; 1.60A {Homo sapiens} PDB: 4hc7_A* 4hca_A* 3dfx_A* 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A* 1gnf_A 1y0j_A 2l6y_A 2l6z_A
Probab=26.52 E-value=20 Score=33.03 Aligned_cols=31 Identities=16% Similarity=0.399 Sum_probs=25.8
Q ss_pred ccccccCCCCCCc---eeecCCcceecccCCeee
Q 004180 8 IRRLKCKKCDNVG---FECAYDGFYYCTHCNALD 38 (770)
Q Consensus 8 ~r~~~C~~C~S~~---w~~~~dG~~yC~~CGhv~ 38 (770)
..+..|.+|+... |+-+.+|...|-.||-..
T Consensus 57 ~~~~~C~~C~t~~tp~WRr~~~g~~lCNaCgl~~ 90 (115)
T 4hc9_A 57 RAGTSCANCQTTTTTLWRRNANGDPVCNACGLYY 90 (115)
T ss_dssp CTTCCCTTTCCSCCSSCEECTTSCEECHHHHHHH
T ss_pred cccccCCCcCCCCcceeEECCCCCCcchHHHHHH
Confidence 3467899999886 988899999999999443
No 60
>3bpy_A FORK head domain, forkhead transcription factor FOXO4, DNA binding domain; forkhead BOX, winged helix; 1.87A {Homo sapiens}
Probab=26.51 E-value=42 Score=29.24 Aligned_cols=40 Identities=20% Similarity=0.318 Sum_probs=31.3
Q ss_pred cCCcchhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccc
Q 004180 253 KIPLSSSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAA 293 (770)
Q Consensus 253 ~Lp~~~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A 293 (770)
.-|+.+=.+++.+|+.-.-. -+++.+|..||++ +.||++.
T Consensus 4 ~kp~~SY~~LI~~Ai~~sp~~~ltL~eIY~~i~~-~fpyy~~ 44 (85)
T 3bpy_A 4 AWGNQSYAELISQAIESAPEKRLTLAQIYEWMVR-TVPYFKD 44 (85)
T ss_dssp TTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHH-HCGGGTT
T ss_pred CcCCCCHHHHHHHHHHhCCcCCccHHHHHHHHHH-hCcchhc
Confidence 33556777888899887654 3899999999987 5699885
No 61
>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}
Probab=24.66 E-value=34 Score=35.51 Aligned_cols=30 Identities=23% Similarity=0.559 Sum_probs=21.1
Q ss_pred ccccCCCCCCce-ee---cCCcceecccCCeeec
Q 004180 10 RLKCKKCDNVGF-EC---AYDGFYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~C~S~~w-~~---~~dG~~yC~~CGhv~E 39 (770)
.--|++||+..- .- .--.-|||..|+.+.|
T Consensus 34 n~yCPnCG~~~l~~f~nN~PVaDF~C~~C~EeyE 67 (257)
T 4esj_A 34 QSYCPNCGNNPLNHFENNRPVADFYCNHCSEEFE 67 (257)
T ss_dssp HCCCTTTCCSSCEEC----CCCEEECTTTCCEEE
T ss_pred CCcCCCCCChhhhhccCCCcccccccCCcchhhe
Confidence 456999999753 22 1234599999998877
No 62
>3l2c_A Forkhead box protein O4; winged helix, transcription-DNA COMP; 1.87A {Homo sapiens} SCOP: a.4.5.14 PDB: 3co6_C*
Probab=24.37 E-value=48 Score=30.27 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=33.3
Q ss_pred hcCCcchhHHHHHHHHHHhhc-ccChhHHHHHHhcCCcccccch
Q 004180 252 QKIPLSSSLAISFLACHVVRE-AILPTDIVKWSIEGKIPYFAAF 294 (770)
Q Consensus 252 ~~Lp~~~TLAI~YLAcl~LR~-PV~lsDLlRWI~eg~IPY~~A~ 294 (770)
+.-|+.+=.+||.+|+.-.-. -+++.+|..||++ +.||++..
T Consensus 22 ~~kPpySY~~LI~~AI~~sp~~~LtL~eIY~~I~~-~fPyyr~~ 64 (110)
T 3l2c_A 22 NAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVR-TVPYFKDK 64 (110)
T ss_dssp BTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHH-HCGGGTTC
T ss_pred CCCCCCCHHHHHHHHHHhCCccCcCHHHHHHHHHH-hCchhhcC
Confidence 344667888999999887665 3899999999997 56999853
No 63
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=24.25 E-value=63 Score=26.01 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=23.1
Q ss_pred cccccccCCCCCCceeecCCcceecc--cCCeee
Q 004180 7 DIRRLKCKKCDNVGFECAYDGFYYCT--HCNALD 38 (770)
Q Consensus 7 ~~r~~~C~~C~S~~w~~~~dG~~yC~--~CGhv~ 38 (770)
-..-.+|+.|.+..-.. +|..+|. .||+.-
T Consensus 7 lL~iL~CP~c~~~L~~~--~~~L~C~~~~c~~~Y 38 (56)
T 2kpi_A 7 LLEILACPACHAPLEER--DAELICTGQDCGLAY 38 (56)
T ss_dssp CTTSCCCSSSCSCEEEE--TTEEEECSSSCCCEE
T ss_pred HHhheeCCCCCCcceec--CCEEEcCCcCCCcEE
Confidence 34457999999986554 3999999 999754
No 64
>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}
Probab=22.43 E-value=38 Score=37.18 Aligned_cols=29 Identities=14% Similarity=0.324 Sum_probs=22.6
Q ss_pred ccccCC--CCCCceeecCCcceecccCCeeec
Q 004180 10 RLKCKK--CDNVGFECAYDGFYYCTHCNALDD 39 (770)
Q Consensus 10 ~~~C~~--C~S~~w~~~~dG~~yC~~CGhv~E 39 (770)
-+.|+. |..+--.. .+|.|.|..||...+
T Consensus 308 Y~aC~~~~C~kkv~~~-~~g~~~C~~C~~~~~ 338 (444)
T 4gop_C 308 YTACASEGCNKKVNLD-HENNWRCEKCDRSYA 338 (444)
T ss_dssp EEECCSTTCCCBEEEC-TTSCEEETTTTEEES
T ss_pred EccCCcccCCCccccC-CCccEECCCCCCcCc
Confidence 467987 98876554 789999999997653
No 65
>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A
Probab=22.26 E-value=41 Score=34.74 Aligned_cols=31 Identities=16% Similarity=0.358 Sum_probs=23.4
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~Eg 40 (770)
..-|..||+..-.....-.++|..||+..--
T Consensus 107 ~~fC~~CG~~~~~~~~~~~~~C~~C~~~~yp 137 (269)
T 1vk6_A 107 HKYCGYCGHEMYPSKTEWAMLCSHCRERYYP 137 (269)
T ss_dssp TSBCTTTCCBEEECSSSSCEEESSSSCEECC
T ss_pred CCccccCCCcCccCCCceeeeCCCCCCEecC
Confidence 4569999999866534446799999987653
No 66
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=22.06 E-value=39 Score=28.14 Aligned_cols=28 Identities=14% Similarity=0.312 Sum_probs=18.2
Q ss_pred ccccCCCCCCceeecCCcceecccCCeee
Q 004180 10 RLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (770)
Q Consensus 10 ~~~C~~C~S~~w~~~~dG~~yC~~CGhv~ 38 (770)
.-+|..|+...- +....-.-|.+|||.+
T Consensus 21 ~Y~C~~Cg~~~~-l~~~~~iRC~~CG~RI 48 (63)
T 3h0g_L 21 IYLCADCGARNT-IQAKEVIRCRECGHRV 48 (63)
T ss_dssp CCBCSSSCCBCC-CCSSSCCCCSSSCCCC
T ss_pred EEECCCCCCeee-cCCCCceECCCCCcEE
Confidence 346888876543 3244557788888765
No 67
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=21.20 E-value=64 Score=29.23 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=21.1
Q ss_pred cccCCCCCCc--e-----eecC---CcceecccCCeeec
Q 004180 11 LKCKKCDNVG--F-----ECAY---DGFYYCTHCNALDD 39 (770)
Q Consensus 11 ~~C~~C~S~~--w-----~~~~---dG~~yC~~CGhv~E 39 (770)
..|+.|++.. | +.++ .-||.|..|||+-.
T Consensus 73 ~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~ 111 (113)
T 3h0g_I 73 KECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFE 111 (113)
T ss_dssp SCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCC
T ss_pred cCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEe
Confidence 6799999985 2 1233 44799999999753
No 68
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A
Probab=20.50 E-value=41 Score=30.16 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=20.7
Q ss_pred ccCCCCCCc-----------e---eecCCc--ceecccCCeeecc
Q 004180 12 KCKKCDNVG-----------F---ECAYDG--FYYCTHCNALDDE 40 (770)
Q Consensus 12 ~C~~C~S~~-----------w---~~~~dG--~~yC~~CGhv~Eg 40 (770)
.|+.|+... + .+..++ .++|..||..+-.
T Consensus 4 ~Cp~Cg~~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~d 48 (133)
T 3o9x_A 4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMN 48 (133)
T ss_dssp BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEECC
T ss_pred CCCcCCCCceeeceEEEEEEECCEEEEECCCceeECCCCCCEeec
Confidence 699998751 1 223455 8999999988764
No 69
>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=20.42 E-value=43 Score=35.67 Aligned_cols=25 Identities=28% Similarity=0.648 Sum_probs=11.1
Q ss_pred cccccCCCCCCceeecCCcceecccCCee
Q 004180 9 RRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (770)
Q Consensus 9 r~~~C~~C~S~~w~~~~dG~~yC~~CGhv 37 (770)
|-..|.-|++ .|.. .+.-|.+||+.
T Consensus 207 R~l~Cs~C~t-~W~~---~R~~C~~Cg~~ 231 (309)
T 2fiy_A 207 RYLSCSLCAC-EWHY---VRIKCSHCEES 231 (309)
T ss_dssp EEEEETTTCC-EEEC---CTTSCSSSCCC
T ss_pred EEEEeCCCCC-EEee---cCcCCcCCCCC
Confidence 3444544443 2432 24455555543
No 70
>1x0t_A Ribonuclease P protein component 4; pyrococcus horikoshii OT3, hydrolase; 1.60A {Pyrococcus horikoshii} PDB: 2zae_B
Probab=20.20 E-value=59 Score=29.89 Aligned_cols=34 Identities=18% Similarity=0.385 Sum_probs=25.2
Q ss_pred cccccccccCCCCCCc-------eeecCCc-----ceecccCCeeec
Q 004180 5 EGDIRRLKCKKCDNVG-------FECAYDG-----FYYCTHCNALDD 39 (770)
Q Consensus 5 ~~~~r~~~C~~C~S~~-------w~~~~dG-----~~yC~~CGhv~E 39 (770)
+..+++..|..|++.. -++ ..| .+.|-.|||+.-
T Consensus 60 p~~~KR~~Ck~C~s~LiPG~t~~vri-~~~~~~~vv~tCl~Cg~~kR 105 (120)
T 1x0t_A 60 PRKWKRRYCKRCHTFLIPGVNARVRL-RTKRMPHVVITCLECGYIMR 105 (120)
T ss_dssp CTTTTTSBCTTTCCBCCBTTTEEEEE-ECSSSCEEEEEETTTCCEEE
T ss_pred CHHHHHHhccCCCCEeECCCceEEEE-ecCCccEEEEECCCCCCEEE
Confidence 4457788999998864 244 345 678999999874
No 71
>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A
Probab=20.15 E-value=35 Score=24.95 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=12.8
Q ss_pred CcceecccCCeeecc
Q 004180 26 DGFYYCTHCNALDDE 40 (770)
Q Consensus 26 dG~~yC~~CGhv~Eg 40 (770)
-.||.|..||++++=
T Consensus 4 ~~fY~C~~CGnivev 18 (36)
T 1dxg_A 4 GDVYKCELCGQVVKV 18 (36)
T ss_dssp TCEEECTTTCCEEEE
T ss_pred ccEEEcCCCCcEEEE
Confidence 358999999999984
No 72
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}
Probab=20.02 E-value=93 Score=32.53 Aligned_cols=78 Identities=13% Similarity=0.140 Sum_probs=50.9
Q ss_pred hHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhhhH----HHHHHhhhccCCccCccCCCCCCCChHHHHHHH
Q 004180 324 SQKLESFAASIAESIGLHLPPVNFYALASRYLKQLCLPLGKIL----PRALKIQEWSMPPDLWLSTNECRFPTRVCVMSI 399 (770)
Q Consensus 324 ~~~I~~la~~ia~~~gL~fPpiN~~lLL~Ryl~eL~LP~E~iy----~~v~RL~~fs~p~~l~~~~~~~~~Pe~V~LmA~ 399 (770)
...|.++=..+.+.++..+-.++..-++.+|++.++++.+ -. ..+..+++.++-.. ....+|+.+.++|+
T Consensus 148 ~~~i~~mE~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~-~~~~~~~~a~~~l~lsl~d~-----~~l~~~PS~IAaAa 221 (306)
T 3g33_B 148 PRQLRDWEVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRD-RQALVKKHAQTFLALCATDY-----TFAMYPPSMIATGS 221 (306)
T ss_dssp HHHHHHHHHHHHHHTTTCCCCCCGGGGHHHHHHTSSCCTT-THHHHHHHHHHHHHHHHHCG-----GGTTSCHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCccCCCCHHHHHHHHHHHcCCChh-HHHHHHHHHHHHHHHHHhhh-----hhccCCHHHHHHHH
Confidence 3678888888888888877666777889999999999865 33 23333443222111 12234443888888
Q ss_pred HHHHHHHh
Q 004180 400 LIVSIRIL 407 (770)
Q Consensus 400 IIVAlKLL 407 (770)
|.+|.+.+
T Consensus 222 i~lA~~~l 229 (306)
T 3g33_B 222 IGAAVQGL 229 (306)
T ss_dssp HHHHHHTC
T ss_pred HHHHHHHh
Confidence 88888765
Done!