Query 032777
Match_columns 134
No_of_seqs 136 out of 506
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:49:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032777hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 2.4E-38 5.2E-43 245.0 8.6 109 1-111 35-150 (168)
2 KOG0871 Class 2 transcription 99.9 5.2E-24 1.1E-28 163.8 7.0 79 2-80 16-101 (156)
3 KOG0870 DNA polymerase epsilon 99.9 7E-22 1.5E-26 154.3 6.5 84 3-86 15-106 (172)
4 COG5150 Class 2 transcription 99.8 6.2E-19 1.3E-23 133.6 6.3 80 2-81 15-101 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.5 8.1E-14 1.8E-18 92.0 5.2 55 1-55 5-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.1 9.8E-11 2.1E-15 83.9 4.4 62 1-64 22-90 (91)
7 cd00076 H4 Histone H4, one of 97.8 6.9E-05 1.5E-09 53.1 5.8 61 2-63 17-83 (85)
8 PTZ00015 histone H4; Provision 97.6 0.00019 4.2E-09 52.5 6.0 61 2-63 34-100 (102)
9 PLN00035 histone H4; Provision 97.6 0.00019 4.1E-09 52.7 6.0 59 2-61 33-97 (103)
10 PF00125 Histone: Core histone 97.5 0.00018 3.8E-09 47.9 4.3 53 4-56 11-73 (75)
11 smart00803 TAF TATA box bindin 97.4 0.00033 7.1E-09 47.1 5.0 54 2-56 6-65 (65)
12 cd07981 TAF12 TATA Binding Pro 97.3 0.00086 1.9E-08 45.5 5.5 54 4-57 7-66 (72)
13 smart00417 H4 Histone H4. 96.3 0.0026 5.7E-08 44.1 2.2 52 2-54 17-74 (74)
14 smart00427 H2B Histone H2B. 96.1 0.016 3.5E-07 41.6 5.3 56 4-59 7-68 (89)
15 smart00576 BTP Bromodomain tra 95.8 0.017 3.6E-07 39.3 4.3 39 23-61 36-74 (77)
16 KOG3467 Histone H4 [Chromatin 95.6 0.019 4E-07 41.7 4.0 39 23-61 59-97 (103)
17 cd00074 H2A Histone 2A; H2A is 95.6 0.031 6.7E-07 41.6 5.2 56 2-57 24-85 (115)
18 PF07524 Bromo_TP: Bromodomain 95.2 0.047 1E-06 36.8 4.7 39 23-61 36-74 (77)
19 PF15630 CENP-S: Kinetochore c 95.1 0.048 1E-06 37.8 4.6 53 4-56 11-71 (76)
20 PLN00158 histone H2B; Provisio 95.0 0.061 1.3E-06 40.4 5.3 56 4-59 33-94 (116)
21 PTZ00463 histone H2B; Provisio 94.8 0.073 1.6E-06 40.0 5.2 56 4-59 34-95 (117)
22 KOG1657 CCAAT-binding factor, 94.4 0.035 7.7E-07 45.8 2.9 73 2-74 78-159 (236)
23 PF03847 TFIID_20kDa: Transcri 94.4 0.14 3E-06 34.7 5.3 55 3-57 4-64 (68)
24 cd08050 TAF6 TATA Binding Prot 93.9 0.085 1.9E-06 45.0 4.4 46 16-61 16-67 (343)
25 cd07979 TAF9 TATA Binding Prot 93.0 0.39 8.5E-06 35.4 6.1 62 16-77 18-86 (117)
26 PF02269 TFIID-18kDa: Transcri 92.6 0.075 1.6E-06 37.8 1.7 36 22-57 31-66 (93)
27 smart00414 H2A Histone 2A. 90.5 0.57 1.2E-05 34.3 4.5 54 4-57 12-74 (106)
28 smart00428 H3 Histone H3. 90.4 0.97 2.1E-05 33.2 5.7 43 14-56 51-99 (105)
29 COG5262 HTA1 Histone H2A [Chro 90.2 0.77 1.7E-05 35.0 5.1 54 3-56 31-90 (132)
30 COG5208 HAP5 CCAAT-binding fac 89.3 0.41 8.9E-06 40.1 3.3 59 5-63 113-180 (286)
31 PLN00154 histone H2A; Provisio 87.8 1.1 2.4E-05 34.5 4.5 45 13-57 54-104 (136)
32 PF02969 TAF: TATA box binding 87.8 1.9 4.2E-05 29.1 5.3 41 16-56 20-66 (66)
33 PHA03328 nuclear egress lamina 87.6 0.19 4.1E-06 43.3 0.4 70 4-76 239-308 (316)
34 KOG1744 Histone H2B [Chromatin 87.0 1.4 3E-05 33.6 4.7 54 4-58 43-103 (127)
35 PLN00157 histone H2A; Provisio 85.7 1.4 3E-05 33.7 4.1 54 4-57 29-91 (132)
36 PLN00156 histone H2AX; Provisi 85.1 1.8 4E-05 33.4 4.5 54 4-57 32-94 (139)
37 KOG1756 Histone 2A [Chromatin 84.6 2.4 5.2E-05 32.5 4.9 52 5-56 31-91 (131)
38 cd07978 TAF13 The TATA Binding 84.5 1.8 4E-05 30.8 4.1 53 22-77 32-84 (92)
39 PF15510 CENP-W: Centromere ki 82.9 1.8 4E-05 31.6 3.5 35 23-57 61-95 (102)
40 PF02861 Clp_N: Clp amino term 82.4 1.8 3.9E-05 26.1 2.9 26 34-59 1-26 (53)
41 KOG1658 DNA polymerase epsilon 82.2 0.74 1.6E-05 36.3 1.4 52 4-55 62-122 (162)
42 cd08048 TAF11 TATA Binding Pro 81.9 5.1 0.00011 28.2 5.4 55 3-58 21-84 (85)
43 PF15511 CENP-T: Centromere ki 80.1 1.7 3.8E-05 38.2 3.1 38 13-50 371-414 (414)
44 PLN00153 histone H2A; Provisio 79.8 3.8 8.2E-05 31.3 4.5 54 4-57 27-89 (129)
45 PTZ00017 histone H2A; Provisio 79.2 4.3 9.3E-05 31.1 4.6 43 15-57 44-92 (134)
46 PF04719 TAFII28: hTAFII28-lik 73.1 8.1 0.00018 27.6 4.4 57 2-58 27-90 (90)
47 KOG1659 Class 2 transcription 71.6 8.2 0.00018 32.0 4.7 61 4-64 16-85 (224)
48 PTZ00252 histone H2A; Provisio 70.3 11 0.00023 29.1 4.8 54 4-57 28-92 (134)
49 KOG1142 Transcription initiati 69.5 4.3 9.3E-05 34.3 2.7 48 10-57 166-219 (258)
50 PF02718 Herpes_UL31: Herpesvi 69.2 1.9 4.2E-05 36.2 0.6 66 4-77 189-254 (258)
51 PF09415 CENP-X: CENP-S associ 69.2 11 0.00023 25.8 4.2 54 4-57 5-67 (72)
52 cd04752 Commd4 COMM_Domain con 68.7 14 0.00029 28.7 5.2 50 22-78 43-93 (174)
53 PF07647 SAM_2: SAM domain (St 64.9 8.7 0.00019 24.2 2.9 25 45-69 3-27 (66)
54 PF02291 TFIID-31kDa: Transcri 64.7 11 0.00023 28.6 3.8 46 30-75 49-95 (129)
55 COG1067 LonB Predicted ATP-dep 64.1 7.6 0.00016 36.5 3.4 31 27-57 368-398 (647)
56 KOG3219 Transcription initiati 64.0 19 0.00041 29.3 5.2 60 2-61 116-181 (195)
57 PF12010 DUF3502: Domain of un 63.5 7.4 0.00016 28.9 2.7 31 48-78 103-133 (134)
58 PTZ00018 histone H3; Provision 61.5 20 0.00044 27.5 4.8 45 11-55 79-129 (136)
59 cd00166 SAM Sterile alpha moti 59.0 8.2 0.00018 23.5 1.9 24 47-70 3-26 (63)
60 PLN00121 histone H3; Provision 58.4 24 0.00052 27.1 4.7 44 12-55 80-129 (136)
61 PF07499 RuvA_C: RuvA, C-termi 58.3 7.6 0.00016 23.9 1.7 26 48-75 3-28 (47)
62 PF00536 SAM_1: SAM domain (St 56.0 14 0.00031 23.1 2.7 22 47-68 4-25 (64)
63 PF13654 AAA_32: AAA domain; P 55.7 15 0.00032 33.4 3.8 34 25-58 473-506 (509)
64 PLN00161 histone H3; Provision 55.1 35 0.00077 26.2 5.2 45 11-55 73-123 (135)
65 PF00531 Death: Death domain; 54.5 9.1 0.0002 24.8 1.7 29 43-71 55-83 (83)
66 smart00454 SAM Sterile alpha m 52.2 12 0.00025 22.9 1.8 25 46-70 4-28 (68)
67 PLN00160 histone H3; Provision 52.0 44 0.00095 24.3 5.0 44 12-55 40-89 (97)
68 TIGR03015 pepcterm_ATPase puta 49.3 28 0.0006 27.2 4.0 37 25-61 233-269 (269)
69 COG5247 BUR6 Class 2 transcrip 47.1 32 0.00069 25.7 3.7 42 23-64 54-95 (113)
70 PF00403 HMA: Heavy-metal-asso 44.0 18 0.0004 22.3 1.8 16 46-61 47-62 (62)
71 KOG3423 Transcription initiati 43.9 38 0.00082 27.2 3.9 39 23-61 116-168 (176)
72 PRK00411 cdc6 cell division co 42.8 30 0.00066 28.8 3.4 35 29-63 253-287 (394)
73 PF13405 EF-hand_6: EF-hand do 41.2 35 0.00075 18.6 2.5 24 36-59 7-31 (31)
74 KOG0093 GTPase Rab3, small G p 40.5 12 0.00025 30.1 0.5 29 35-63 133-161 (193)
75 PF08823 PG_binding_2: Putativ 38.7 63 0.0014 22.0 3.9 32 48-79 18-55 (74)
76 COG1724 Predicted RNA binding 37.9 25 0.00053 24.1 1.7 18 45-62 6-23 (66)
77 PF13335 Mg_chelatase_2: Magne 37.8 43 0.00092 23.6 3.1 27 30-56 68-94 (96)
78 PF13963 Transpos_assoc: Trans 37.7 45 0.00098 22.5 3.1 38 22-61 20-66 (77)
79 TIGR02928 orc1/cdc6 family rep 36.3 38 0.00083 27.8 3.0 39 30-68 246-284 (365)
80 smart00027 EH Eps15 homology d 34.5 82 0.0018 21.3 4.0 30 33-62 14-43 (96)
81 PRK03992 proteasome-activating 32.6 58 0.0013 28.0 3.7 35 26-60 340-374 (389)
82 TIGR02454 CbiQ_TIGR cobalt ABC 31.1 74 0.0016 24.0 3.7 38 44-81 112-160 (198)
83 TIGR01242 26Sp45 26S proteasom 30.5 68 0.0015 27.0 3.7 32 26-57 331-362 (364)
84 PF03484 B5: tRNA synthetase B 30.2 35 0.00075 22.4 1.5 17 45-61 18-34 (70)
85 TIGR00764 lon_rel lon-related 30.1 62 0.0013 29.9 3.6 30 30-59 363-392 (608)
86 PF03130 HEAT_PBS: PBS lyase H 29.9 52 0.0011 17.8 1.9 23 51-73 5-27 (27)
87 PF07928 Vps54: Vps54-like pro 29.8 18 0.00038 27.3 0.0 66 6-74 23-97 (135)
88 cd01102 Link_Domain The link d 29.6 55 0.0012 23.5 2.5 29 32-61 17-45 (92)
89 smart00445 LINK Link (Hyaluron 28.9 61 0.0013 23.3 2.7 29 32-61 18-46 (94)
90 PF13499 EF-hand_7: EF-hand do 28.3 1.5E+02 0.0032 18.1 5.0 44 34-77 5-49 (66)
91 KOG2389 Predicted bromodomain 28.2 79 0.0017 28.0 3.7 51 23-73 59-112 (353)
92 PF02361 CbiQ: Cobalt transpor 27.8 91 0.002 23.5 3.7 38 44-81 123-172 (224)
93 PTZ00361 26 proteosome regulat 27.4 78 0.0017 28.3 3.6 32 27-58 393-424 (438)
94 PTZ00184 calmodulin; Provision 27.2 2E+02 0.0043 19.7 5.1 49 23-71 66-126 (149)
95 KOG3334 Transcription initiati 27.0 1.3E+02 0.0028 23.6 4.4 46 30-75 50-96 (148)
96 TIGR00308 TRM1 tRNA(guanine-26 26.9 1.5E+02 0.0033 25.8 5.2 40 22-61 296-344 (374)
97 cd03518 Link_domain_HAPLN_modu 26.5 78 0.0017 22.9 2.9 29 32-61 17-45 (95)
98 PRK11034 clpA ATP-dependent Cl 25.7 1E+02 0.0022 29.5 4.3 27 30-56 9-35 (758)
99 PF07352 Phage_Mu_Gam: Bacteri 25.5 50 0.0011 24.7 1.8 19 47-65 92-110 (149)
100 PTZ00183 centrin; Provisional 25.3 2.4E+02 0.0053 19.7 5.8 39 23-61 72-122 (158)
101 smart00874 B5 tRNA synthetase 25.2 56 0.0012 20.9 1.8 17 45-61 18-34 (71)
102 KOG1775 U6 snRNA-associated Sm 25.2 22 0.00047 25.3 -0.2 22 57-78 34-55 (84)
103 cd03515 Link_domain_TSG_6_like 25.1 92 0.002 22.5 3.0 29 32-61 17-45 (93)
104 PTZ00454 26S protease regulato 24.7 91 0.002 27.3 3.5 32 27-58 355-386 (398)
105 COG1474 CDC6 Cdc6-related prot 24.7 75 0.0016 27.5 3.0 39 28-66 235-273 (366)
106 PLN03239 histone acetyltransfe 23.7 69 0.0015 28.3 2.5 36 42-77 292-333 (351)
107 smart00567 EZ_HEAT E-Z type HE 23.6 73 0.0016 17.1 1.8 22 51-72 7-28 (30)
108 PF00543 P-II: Nitrogen regula 23.5 56 0.0012 22.7 1.6 17 47-63 9-25 (102)
109 PF13833 EF-hand_8: EF-hand do 23.4 1.7E+02 0.0037 17.2 3.8 20 43-62 2-21 (54)
110 KOG4336 TBP-associated transcr 23.2 2.2E+02 0.0048 24.9 5.5 50 25-76 37-86 (323)
111 COG1400 SEC65 Signal recogniti 23.1 63 0.0014 23.3 1.9 17 46-62 32-48 (93)
112 TIGR03261 phnS2 putative 2-ami 22.8 1.8E+02 0.0038 23.7 4.7 59 22-80 262-331 (334)
113 PF01256 Carb_kinase: Carbohyd 22.0 1.2E+02 0.0026 24.7 3.5 31 22-55 210-240 (242)
114 PF09840 DUF2067: Uncharacteri 21.9 2E+02 0.0043 23.0 4.7 38 44-81 84-136 (190)
115 cd08779 Death_PIDD Death Domai 21.8 65 0.0014 22.2 1.7 32 39-70 54-85 (86)
116 COG4519 Uncharacterized protei 21.6 42 0.0009 24.2 0.7 18 47-64 38-56 (95)
117 cd08777 Death_RIP1 Death Domai 21.4 90 0.0019 21.6 2.3 31 38-68 54-84 (86)
118 cd00194 UBA Ubiquitin Associat 21.2 1.7E+02 0.0036 16.4 3.2 25 49-75 2-26 (38)
119 PF07927 YcfA: YcfA-like prote 21.1 64 0.0014 19.7 1.4 14 49-62 2-15 (56)
120 PF08369 PCP_red: Proto-chloro 21.1 1.2E+02 0.0026 18.7 2.7 26 29-54 19-44 (45)
121 cd00051 EFh EF-hand, calcium b 21.0 1.7E+02 0.0036 16.2 4.5 36 38-73 9-44 (63)
122 PF01922 SRP19: SRP19 protein; 21.0 48 0.001 23.5 0.9 20 46-65 29-48 (95)
123 PF04664 OGFr_N: Opioid growth 20.9 66 0.0014 26.2 1.8 26 47-72 130-155 (213)
124 PF10440 WIYLD: Ubiquitin-bind 20.7 1.1E+02 0.0024 20.7 2.5 24 51-74 14-39 (65)
125 cd03521 Link_domain_KIAA0527_l 20.7 1.2E+02 0.0027 22.1 3.0 30 32-61 17-46 (95)
126 TIGR01716 RGG_Cterm transcript 20.1 1.2E+02 0.0026 23.1 3.0 29 48-76 191-219 (220)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=2.4e-38 Score=244.99 Aligned_cols=109 Identities=46% Similarity=0.758 Sum_probs=92.3
Q ss_pred ChhHHHHH-HhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH
Q 032777 1 MARSLRML-RILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 73 (134)
Q Consensus 1 ~anv~Rik-~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~ 73 (134)
||||.||| +.||+|.|||||| |++|||+|||+||+|+|+++||||||+|||||||.+|||++|++||+.||.+
T Consensus 35 IANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~k 114 (168)
T KOG0869|consen 35 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQK 114 (168)
T ss_pred HHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHH
Confidence 69999996 5999999999999 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccCCCCCCCCCCCcccccCCCCCchhhhhhcC
Q 032777 74 YREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQG 111 (134)
Q Consensus 74 yre~~~~kk~s~k~~~~~~~~~~~~~~~~~~~~~~~~~ 111 (134)
||+.++++..+.+++... .+.....-++..++..||
T Consensus 115 YRe~e~e~~~~~~~~~~~--~~~~~~~~~~~~~~~~~g 150 (168)
T KOG0869|consen 115 YRELEGERGRSGKGGQMT--GGNGIDEHGPSGEVPEQG 150 (168)
T ss_pred HHHHhhhcccccccCccc--ccccccccCCCcCCCCCC
Confidence 999999988877766522 322222333344445555
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.90 E-value=5.2e-24 Score=163.81 Aligned_cols=79 Identities=27% Similarity=0.443 Sum_probs=74.3
Q ss_pred hhHHHH-HHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHH
Q 032777 2 ARSLRM-LRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 2 anv~Ri-k~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~y 74 (134)
|-|.+| ++.||.+++|+||+ ||.|||+.|||+||++|.++.||||+++||++||+.|||.+|++.+...|+.|
T Consensus 16 Atv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee~~~vl~~~ 95 (156)
T KOG0871|consen 16 ATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEEAEEVLENC 95 (156)
T ss_pred HHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHHHHHHHHHH
Confidence 446777 77999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcc
Q 032777 75 REMEGD 80 (134)
Q Consensus 75 re~~~~ 80 (134)
+...+.
T Consensus 96 K~~~~~ 101 (156)
T KOG0871|consen 96 KEEAKK 101 (156)
T ss_pred HHHHHH
Confidence 987654
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.85 E-value=7e-22 Score=154.27 Aligned_cols=84 Identities=29% Similarity=0.440 Sum_probs=78.5
Q ss_pred hHHHH-HHhcCCC-ceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHH
Q 032777 3 RSLRM-LRILYRN-VSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 3 nv~Ri-k~~LP~n-~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~y 74 (134)
=|.|| |+.||.. +.|+||| ++++||+|||+.|+++|+..+||||+++|||.||+++||..|++||+..|+.|
T Consensus 15 iI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~plk~~Le~y 94 (172)
T KOG0870|consen 15 IITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPLKSALEAY 94 (172)
T ss_pred HHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHHHHHHHHH
Confidence 36788 7899998 9999999 69999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccCCCCC
Q 032777 75 REMEGDTKGSAR 86 (134)
Q Consensus 75 re~~~~kk~s~k 86 (134)
|...++||.++.
T Consensus 95 k~~~k~Kk~~~~ 106 (172)
T KOG0870|consen 95 KKAVKQKKLAKA 106 (172)
T ss_pred HHHHHHHHHhcc
Confidence 999998887544
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.77 E-value=6.2e-19 Score=133.60 Aligned_cols=80 Identities=25% Similarity=0.438 Sum_probs=75.5
Q ss_pred hhHHHHH-HhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHH
Q 032777 2 ARSLRML-RILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 2 anv~Rik-~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~y 74 (134)
|-|.+|- +.||.+.-+.||| ||.+||++|||+||+.|..+.+|||.++||+.||+.|||.+|++.+.+.+..|
T Consensus 15 ATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~~~e~~~n~ 94 (148)
T COG5150 15 ATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEHENY 94 (148)
T ss_pred HHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence 4577884 5999999999999 89999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccc
Q 032777 75 REMEGDT 81 (134)
Q Consensus 75 re~~~~k 81 (134)
+..++.|
T Consensus 95 k~~qK~k 101 (148)
T COG5150 95 KSYQKQK 101 (148)
T ss_pred HHHHhhc
Confidence 9988765
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.47 E-value=8.1e-14 Score=91.97 Aligned_cols=55 Identities=27% Similarity=0.346 Sum_probs=49.5
Q ss_pred ChhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 1 MARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 1 ~anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
++.|.||++.-|+..+||+|| |+.+||.||+.+|++.|..++||||+++||..||
T Consensus 5 ~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 5 LARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred hHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 378999987669999999999 8999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.10 E-value=9.8e-11 Score=83.91 Aligned_cols=62 Identities=31% Similarity=0.325 Sum_probs=56.8
Q ss_pred ChhHHHHHH-hcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccch
Q 032777 1 MARSLRMLR-ILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYI 64 (134)
Q Consensus 1 ~anv~Rik~-~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv 64 (134)
++||.||.+ ..++ +||.|| ++.+|+..|+..|+++|...|||||.++||.-||+.+||..|.
T Consensus 22 ~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~~ 90 (91)
T COG2036 22 KAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYG 90 (91)
T ss_pred chHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccccc
Confidence 489999954 6776 999999 6889999999999999999999999999999999999998764
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=97.78 E-value=6.9e-05 Score=53.10 Aligned_cols=61 Identities=21% Similarity=0.197 Sum_probs=49.2
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccc
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dy 63 (134)
+.|.||.+.- .--+||.|+ ...+|+.-|...|..+|+..+||||+++||..||+..|-.-|
T Consensus 17 ~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 17 PAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred HHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 3566774422 246889888 467999999999999999999999999999999999885433
No 8
>PTZ00015 histone H4; Provisional
Probab=97.60 E-value=0.00019 Score=52.52 Aligned_cols=61 Identities=20% Similarity=0.196 Sum_probs=48.3
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccc
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dy 63 (134)
+.|.||.+.- .--+||.|+ ...+|+.-|..+|..+|+-.+||||+++||..||+..|=.-|
T Consensus 34 ~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 34 GAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 3456664422 235788888 466999999999999999999999999999999998875433
No 9
>PLN00035 histone H4; Provisional
Probab=97.60 E-value=0.00019 Score=52.67 Aligned_cols=59 Identities=19% Similarity=0.153 Sum_probs=47.5
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+.|.||.+.- .--+||.|+ ...+|+.-|..+|..+|+..+||||+++||..||+..|=.
T Consensus 33 ~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 33 PAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 3566664422 146788888 3568999999999999999999999999999999988643
No 10
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=97.49 E-value=0.00018 Score=47.91 Aligned_cols=53 Identities=28% Similarity=0.259 Sum_probs=41.8
Q ss_pred HHHHHHhcCCC----ceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 4 SLRMLRILYRN----VSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 4 v~Rik~~LP~n----~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
+.|+.+.+.++ .+|+++| .+-.|+.-|...|...|...||+||++.||..|++
T Consensus 11 ~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 11 FSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp HHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred EeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 56775544444 8999999 23355566778899999999999999999999975
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=97.43 E-value=0.00033 Score=47.05 Aligned_cols=54 Identities=19% Similarity=0.105 Sum_probs=46.3
Q ss_pred hhHHHHHHhcCCCceeccchh------HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 2 ARSLRMLRILYRNVSLSSSAS------LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDAc------aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
+.|.||.+.+.-. +||.|+. +..|+.-|.-+|..+++..+|||++++||-.||+
T Consensus 6 ~~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 6 ETIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5688998877544 7999983 6688888999999999999999999999999884
No 12
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=97.26 E-value=0.00086 Score=45.48 Aligned_cols=54 Identities=11% Similarity=0.061 Sum_probs=46.4
Q ss_pred HHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
+.-+.+.+-++.+++.|+ .+.+|+.-++..|...|+..+|+||.++||.-+|+.
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 444545555578999999 588999999999999999999999999999999875
No 13
>smart00417 H4 Histone H4.
Probab=96.35 E-value=0.0026 Score=44.08 Aligned_cols=52 Identities=19% Similarity=0.165 Sum_probs=39.7
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHH
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWA 54 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~A 54 (134)
+.|.||.+-- .--+||.|+ ..-+|+.-|...|..+|+..+||||+++||..|
T Consensus 17 ~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 17 PAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred HHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3466664321 234788777 245899999999999999999999999999754
No 14
>smart00427 H2B Histone H2B.
Probab=96.09 E-value=0.016 Score=41.59 Aligned_cols=56 Identities=16% Similarity=0.214 Sum_probs=43.9
Q ss_pred HHHHHHhcCCCceeccch--hHHHHH----HHHHhHhhhHhhhcCCCccChhHHHHHhhhcC
Q 032777 4 SLRMLRILYRNVSLSSSA--SLPASF----SFLSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDA--caseFI----~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~Lg 59 (134)
|.|+.+.+-|++.||+.+ -..-|+ .=|++||...|...+|+||++.+|-.|.+-+=
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 567755555578999999 222344 44899999999999999999999999987653
No 15
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.84 E-value=0.017 Score=39.35 Aligned_cols=39 Identities=23% Similarity=0.246 Sum_probs=35.4
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
.-.||.-|...+..+|+..+|++.++.||..||+++|..
T Consensus 36 ~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 36 LQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 557778899999999999999999999999999999974
No 16
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=95.62 E-value=0.019 Score=41.72 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=36.5
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
..|||.-+-+.|..+++..|||||++-||+-+|+..|-.
T Consensus 59 ~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 59 LKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 779999999999999999999999999999999998754
No 17
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=95.60 E-value=0.031 Score=41.56 Aligned_cols=56 Identities=23% Similarity=0.295 Sum_probs=38.8
Q ss_pred hhHHHHHHhcCCCceeccch--hHHHHHHHHHhH----hhhHhhhcCCCccChhHHHHHhhh
Q 032777 2 ARSLRMLRILYRNVSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA--caseFI~ylTSe----And~c~~~kRKTI~~dDVL~AL~~ 57 (134)
+.|.|+++.---..+|+.+| ..+.-+-||++| |...|+..+||+|+++||-.|+..
T Consensus 24 ~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 24 GRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred HHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 34555543211248999999 344556666655 556788899999999999999865
No 18
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=95.20 E-value=0.047 Score=36.79 Aligned_cols=39 Identities=21% Similarity=0.194 Sum_probs=36.3
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+..||.-|...+..+|+..+|...++.||..||+++|+.
T Consensus 36 ~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 36 LQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 668888899999999999999999999999999999984
No 19
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.12 E-value=0.048 Score=37.81 Aligned_cols=53 Identities=23% Similarity=0.186 Sum_probs=33.7
Q ss_pred HHHHH-H-hcCCCceeccch--hHHHHH-HHHHhHhhh---HhhhcCCCccChhHHHHHhh
Q 032777 4 SLRML-R-ILYRNVSLSSSA--SLPASF-SFLSCRASD---KCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 4 v~Rik-~-~LP~n~kISKDA--caseFI-~ylTSeAnd---~c~~~kRKTI~~dDVL~AL~ 56 (134)
|.||- + ..+.++.++++. |.+|.+ .++..-|.| .|+..||+||++|||+-..+
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 56773 3 578899999999 444332 223334444 58999999999999986543
No 20
>PLN00158 histone H2B; Provisional
Probab=95.05 E-value=0.061 Score=40.38 Aligned_cols=56 Identities=14% Similarity=0.197 Sum_probs=43.4
Q ss_pred HHHHHHhcCCCceeccch--hHHHHH----HHHHhHhhhHhhhcCCCccChhHHHHHhhhcC
Q 032777 4 SLRMLRILYRNVSLSSSA--SLPASF----SFLSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDA--caseFI----~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~Lg 59 (134)
|.|+.+.+-|++.||..+ -..-|| .=|++||...|.-.+|+||++.+|-.|.+-+=
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence 567755555588899988 223344 44899999999999999999999999987653
No 21
>PTZ00463 histone H2B; Provisional
Probab=94.81 E-value=0.073 Score=40.03 Aligned_cols=56 Identities=14% Similarity=0.274 Sum_probs=43.1
Q ss_pred HHHHHHhcCCCceeccch--hHHHHH----HHHHhHhhhHhhhcCCCccChhHHHHHhhhcC
Q 032777 4 SLRMLRILYRNVSLSSSA--SLPASF----SFLSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDA--caseFI----~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~Lg 59 (134)
|.|+.+.+-|++-||+.+ -..-|| .=|++||...|.-.+|+||++.+|-.|.+-+=
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL 95 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL 95 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence 566655554588899998 223344 34899999999999999999999999977653
No 22
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=94.39 E-value=0.035 Score=45.80 Aligned_cols=73 Identities=21% Similarity=0.222 Sum_probs=56.5
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhc---CCccchhHHHHHHH
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATL---GFEDYIDPLKAYLM 72 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~L---gF~dyv~~Lk~~L~ 72 (134)
|.|.+||+.=++=-.|+.|| ||-.||..||..|...++..+|+|+...|+-.|+..- +|--.+-|-+..++
T Consensus 78 aRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~DivP~~~~~~ 157 (236)
T KOG1657|consen 78 ARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIVPRKILAE 157 (236)
T ss_pred hhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccccchhccc
Confidence 55666665444444899999 7899999999999999999999999999999999765 33333445566666
Q ss_pred HH
Q 032777 73 RY 74 (134)
Q Consensus 73 ~y 74 (134)
+|
T Consensus 158 ~~ 159 (236)
T KOG1657|consen 158 KY 159 (236)
T ss_pred cc
Confidence 66
No 23
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=94.35 E-value=0.14 Score=34.71 Aligned_cols=55 Identities=11% Similarity=0.085 Sum_probs=41.4
Q ss_pred hHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 3 RSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 3 nv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
++.-+.+.+-|+.++..|+ .+.+||.-+++.|...|+..+-.||...||.-.|+.
T Consensus 4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 3445566677799999998 699999999999999999999999999999988864
No 24
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=93.91 E-value=0.085 Score=45.01 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=41.9
Q ss_pred eeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 16 SLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 16 kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+++.|| .+..+|.-|..+|...++..+|||++++||=.||+.++.+
T Consensus 16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 788888 4788999999999999999999999999999999987654
No 25
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=92.99 E-value=0.39 Score=35.45 Aligned_cols=62 Identities=11% Similarity=0.096 Sum_probs=45.3
Q ss_pred eeccch--h----HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccch-hHHHHHHHHHHHH
Q 032777 16 SLSSSA--S----LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYI-DPLKAYLMRYREM 77 (134)
Q Consensus 16 kISKDA--c----aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv-~~Lk~~L~~yre~ 77 (134)
.++.++ + +-.++.=|..+|..+++..+|+||++|||--|++..+-..|. .+-+++|-..-..
T Consensus 18 ~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~a~~ 86 (117)
T cd07979 18 EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLELARE 86 (117)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHHHHH
Confidence 566666 3 333344477889999999999999999999999888765554 4477777655543
No 26
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=92.56 E-value=0.075 Score=37.76 Aligned_cols=36 Identities=22% Similarity=0.247 Sum_probs=13.8
Q ss_pred hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
-+.+||.-+..+|...|...++++|+.||++.+|+.
T Consensus 31 iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 31 IVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 478999999999999999999999999999999985
No 27
>smart00414 H2A Histone 2A.
Probab=90.48 E-value=0.57 Score=34.33 Aligned_cols=54 Identities=22% Similarity=0.369 Sum_probs=37.3
Q ss_pred HHHHHHhcCC---Cceeccch--hHHHHHHHHHhH----hhhHhhhcCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKDA--caseFI~ylTSe----And~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|.||.+.|-+ ..+|+..| ..+--+-||++| |-..|...+++.|++.|+-.|+..
T Consensus 12 VgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 12 VGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred hHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 3455444433 35888888 344456677777 555677789999999999999865
No 28
>smart00428 H3 Histone H3.
Probab=90.36 E-value=0.97 Score=33.22 Aligned_cols=43 Identities=26% Similarity=0.124 Sum_probs=37.1
Q ss_pred Cceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 14 NVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 14 n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
+.+++.|| ++-.|+.-+...|+..+...||+||.++|+--|..
T Consensus 51 ~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 51 DLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred CceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 78999999 45567777889999999999999999999976653
No 29
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=90.16 E-value=0.77 Score=34.95 Aligned_cols=54 Identities=22% Similarity=0.306 Sum_probs=39.1
Q ss_pred hHHHHHHhcCCCceeccch--hHHHHHHHHHhHhhh----HhhhcCCCccChhHHHHHhh
Q 032777 3 RSLRMLRILYRNVSLSSSA--SLPASFSFLSCRASD----KCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 3 nv~Rik~~LP~n~kISKDA--caseFI~ylTSeAnd----~c~~~kRKTI~~dDVL~AL~ 56 (134)
.|.|+++----.++|+++| ..+--+.||++|--| .+...++|.|.|.|+-.|+.
T Consensus 31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 3445544233469999999 455667788777555 46679999999999988875
No 30
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=89.27 E-value=0.41 Score=40.05 Aligned_cols=59 Identities=22% Similarity=0.291 Sum_probs=47.0
Q ss_pred HHHHHhc--CCCce-eccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccc
Q 032777 5 LRMLRIL--YRNVS-LSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 5 ~Rik~~L--P~n~k-ISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dy 63 (134)
.|||+.+ -++++ ||.+| .|-.||.=||-.|-=.+++.||+|+--.||-.|++.-+.-||
T Consensus 113 ARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDF 180 (286)
T COG5208 113 ARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDF 180 (286)
T ss_pred HHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhH
Confidence 4555532 33444 67777 477999999999999999999999999999999998876655
No 31
>PLN00154 histone H2A; Provisional
Probab=87.79 E-value=1.1 Score=34.54 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=33.7
Q ss_pred CCceeccchh--HHHHHHHHHhHhh----hHhhhcCCCccChhHHHHHhhh
Q 032777 13 RNVSLSSSAS--LPASFSFLSCRAS----DKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 13 ~n~kISKDAc--aseFI~ylTSeAn----d~c~~~kRKTI~~dDVL~AL~~ 57 (134)
-..+|+..|. .+--+-|||+|-- ..|+..+++-|++.||..|+..
T Consensus 54 ~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 54 AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3468998883 4445678888744 4577789999999999999853
No 32
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=87.77 E-value=1.9 Score=29.11 Aligned_cols=41 Identities=22% Similarity=0.220 Sum_probs=31.2
Q ss_pred eeccchh------HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 16 SLSSSAS------LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 16 kISKDAc------aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
.++.|++ +.--|..|..+|....+..+|++++++||=.||+
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4677773 5667788999999999999999999999999885
No 33
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=87.65 E-value=0.19 Score=43.34 Aligned_cols=70 Identities=14% Similarity=0.179 Sum_probs=55.1
Q ss_pred HHHHHHhcCCCceeccchhHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHHHH
Q 032777 4 SLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 76 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDAcaseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~yre 76 (134)
+.+|+.++| +.+|+-|..-+-||.-++-.+-.....+..=||+++||-.+|.+|.|++ |-+.+|..-|..
T Consensus 239 L~~Ll~n~~-gY~i~adv~~~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d--El~~Ey~kly~~ 308 (316)
T PHA03328 239 IDRLLTACP-GYRIIAHVWQTTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG--ELLLEYKRLYAT 308 (316)
T ss_pred HHHHHHhCC-CCeEEEEEecceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--HHHHHHHHHHHH
Confidence 455677887 9999999988888888875554455678899999999999999999997 555666665543
No 34
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=86.99 E-value=1.4 Score=33.61 Aligned_cols=54 Identities=22% Similarity=0.292 Sum_probs=42.1
Q ss_pred HHHHHH-hcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhc
Q 032777 4 SLRMLR-ILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 4 v~Rik~-~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~L 58 (134)
|.|+.+ .-|+ +-|+..+ -..+|+--|+++|+..+.-.+|.||+..+|-.|.+-|
T Consensus 43 v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 667754 4454 7788777 2456666689999999999999999999999987654
No 35
>PLN00157 histone H2A; Provisional
Probab=85.67 E-value=1.4 Score=33.74 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=37.2
Q ss_pred HHHHHHhcCC---Cceeccch--hHHHHHHHHHhH----hhhHhhhcCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKDA--caseFI~ylTSe----And~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|.||.+.|-+ ..+|+..| ..+--+-||++| |-..|...+++-|++.||..|+..
T Consensus 29 VgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 29 VGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred hHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 4455555543 36888888 344456677776 444577789999999999999853
No 36
>PLN00156 histone H2AX; Provisional
Probab=85.07 E-value=1.8 Score=33.40 Aligned_cols=54 Identities=19% Similarity=0.270 Sum_probs=37.2
Q ss_pred HHHHHHhcCC---Cceeccch--hHHHHHHHHHhHhhh----HhhhcCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASD----KCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKDA--caseFI~ylTSeAnd----~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|.||.+.|.+ ..+|+..| ..+--+-||++|--+ .|...+++-|+|.||..|+..
T Consensus 32 VgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 32 VGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred hHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 4555555543 35888888 344446677776554 467789999999999999853
No 37
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=84.57 E-value=2.4 Score=32.51 Aligned_cols=52 Identities=21% Similarity=0.327 Sum_probs=37.3
Q ss_pred HHHHHhcCC---Cceeccch--hHHHHHHHHHhHhhhH----hhhcCCCccChhHHHHHhh
Q 032777 5 LRMLRILYR---NVSLSSSA--SLPASFSFLSCRASDK----CQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 5 ~Rik~~LP~---n~kISKDA--caseFI~ylTSeAnd~----c~~~kRKTI~~dDVL~AL~ 56 (134)
.||.+.|=+ -.+|+.+| ..+--+-||++|.-+. ++.+++.-|+|.||..|+.
T Consensus 31 gri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 31 GRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred HHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 445444433 37788888 3445567888887776 4557888999999999986
No 38
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=84.52 E-value=1.8 Score=30.77 Aligned_cols=53 Identities=17% Similarity=0.242 Sum_probs=38.2
Q ss_pred hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHHHHH
Q 032777 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREM 77 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~yre~ 77 (134)
.+.+||.-++.+|.+.+. ..+.-|+.||++-+|+.= .-.+.-|+.+|.--.+.
T Consensus 32 iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~~k~~~ 84 (92)
T cd07978 32 IVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLSMKDEL 84 (92)
T ss_pred HHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHHHHHHH
Confidence 588999999999999999 444446999999999642 23344555666544443
No 39
>PF15510 CENP-W: Centromere kinetochore component W
Probab=82.86 E-value=1.8 Score=31.64 Aligned_cols=35 Identities=20% Similarity=0.072 Sum_probs=31.8
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|-.||+-|+-||..-+=.+|-.||..|||+.|-+.
T Consensus 61 cLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv 95 (102)
T PF15510_consen 61 CLLFVHRLAEEARTNACENKCGTIKKEHVLAAAKV 95 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 78999999999999999999999999999998543
No 40
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=82.35 E-value=1.8 Score=26.07 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=21.5
Q ss_pred hhhHhhhcCCCccChhHHHHHhhhcC
Q 032777 34 ASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 34 And~c~~~kRKTI~~dDVL~AL~~Lg 59 (134)
|.+.|+..+...|+++|+|.||=+-+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56789999999999999999976654
No 41
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=82.16 E-value=0.74 Score=36.35 Aligned_cols=52 Identities=23% Similarity=0.112 Sum_probs=43.3
Q ss_pred HHHHHH--hcCCCceeccch-------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 4 SLRMLR--ILYRNVSLSSSA-------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 4 v~Rik~--~LP~n~kISKDA-------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
+.||+. -||+++.++.|. ++--||.+|+-.+...+...+|||+.--|+=.|.
T Consensus 62 L~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai 122 (162)
T KOG1658|consen 62 LARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAI 122 (162)
T ss_pred HHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccc
Confidence 357877 478899999998 5779999999999999999999999876664443
No 42
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=81.88 E-value=5.1 Score=28.18 Aligned_cols=55 Identities=15% Similarity=0.038 Sum_probs=42.2
Q ss_pred hHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCC---CccChhHHHHHhhhc
Q 032777 3 RSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKR---KTINGDDLLWAMATL 58 (134)
Q Consensus 3 nv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kR---KTI~~dDVL~AL~~L 58 (134)
.+.||...+- +.+++.+. -+-+||.=|..+|.++..+.+. .-|.|+||-.|.+.|
T Consensus 21 ~iKr~~~~~~-~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 21 AIKRLIQSVT-GQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred HHHHHHHHHc-CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 4566655332 25555555 4779999999999999998766 889999999998876
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=80.13 E-value=1.7 Score=38.18 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=28.0
Q ss_pred CCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhH
Q 032777 13 RNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDD 50 (134)
Q Consensus 13 ~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dD 50 (134)
.+++|+||| |.-.|.--|..-=..++...+||||...|
T Consensus 371 sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 371 SKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 578999999 77788888888888889999999998876
No 44
>PLN00153 histone H2A; Provisional
Probab=79.81 E-value=3.8 Score=31.28 Aligned_cols=54 Identities=19% Similarity=0.293 Sum_probs=35.9
Q ss_pred HHHHHHhcCC---Cceeccch--hHHHHHHHHHhHhhh----HhhhcCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASD----KCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKDA--caseFI~ylTSeAnd----~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|.||.+.|-+ ..+|+..| ..+--+-||++|--+ .|...+++-|+|.||..|+..
T Consensus 27 VgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 27 VGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred hHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 3455444432 35888888 344445666666444 467789999999999999853
No 45
>PTZ00017 histone H2A; Provisional
Probab=79.18 E-value=4.3 Score=31.14 Aligned_cols=43 Identities=21% Similarity=0.365 Sum_probs=31.0
Q ss_pred ceeccch--hHHHHHHHHHhH----hhhHhhhcCCCccChhHHHHHhhh
Q 032777 15 VSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 15 ~kISKDA--caseFI~ylTSe----And~c~~~kRKTI~~dDVL~AL~~ 57 (134)
-+|+..| ..+--+-||++| |-..|...+++-|+|.||..|+..
T Consensus 44 ~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 44 KRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred ccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 5888888 233445566666 444577789999999999999853
No 46
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=73.08 E-value=8.1 Score=27.60 Aligned_cols=57 Identities=18% Similarity=0.092 Sum_probs=37.1
Q ss_pred hhHHHHHHhcCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCC-ccChhHHHHHhhhc
Q 032777 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRK-TINGDDLLWAMATL 58 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRK-TI~~dDVL~AL~~L 58 (134)
++|.||...+-.|..|+... .+.+||-=|-.+|-+++...+.. -|.|+|+-+|.+.|
T Consensus 27 ~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 27 AAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 35677765332345555554 58899999999999999875543 79999999998765
No 47
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=71.59 E-value=8.2 Score=31.99 Aligned_cols=61 Identities=16% Similarity=0.188 Sum_probs=42.3
Q ss_pred HHHHHHhcCCCceeccch---------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccch
Q 032777 4 SLRMLRILYRNVSLSSSA---------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYI 64 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDA---------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv 64 (134)
+.|||+++-.+=-|-|=+ +.--|+.-|-..+-++++..+-||||++|+..|...-.==||.
T Consensus 16 ~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFL 85 (224)
T KOG1659|consen 16 PARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFL 85 (224)
T ss_pred HHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHH
Confidence 356666554443333333 2446888888899999999999999999999998765433343
No 48
>PTZ00252 histone H2A; Provisional
Probab=70.32 E-value=11 Score=29.05 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=36.4
Q ss_pred HHHHHHhcCC---Cceeccch--hHHHHHHHHHhHhhhHhhh------cCCCccChhHHHHHhhh
Q 032777 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASDKCQK------EKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKDA--caseFI~ylTSeAnd~c~~------~kRKTI~~dDVL~AL~~ 57 (134)
|.||-+-|-+ .-+|+..| ..+--+-||++|--+.+-+ .+++-|+++||..|+..
T Consensus 28 VgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 28 VGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred hHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 3444444433 34777777 3455677888887776533 47788999999999853
No 49
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.50 E-value=4.3 Score=34.28 Aligned_cols=48 Identities=13% Similarity=0.130 Sum_probs=42.1
Q ss_pred hcCCCceeccchh------HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 10 ILYRNVSLSSSAS------LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 10 ~LP~n~kISKDAc------aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
.+-.+.+|-.|++ |-.||.-|+.-|...|+..|..||-+-||.-.|+.
T Consensus 166 qId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 166 QIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred hhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 3455777888884 88999999999999999999999999999988875
No 50
>PF02718 Herpes_UL31: Herpesvirus UL31-like protein; InterPro: IPR021152 This is a family of Herpesvirus proteins, belong to the UL31 family, which including UL31, UL53, and the product of ORF69 in some strains. The proteins in this family have no known function.
Probab=69.16 E-value=1.9 Score=36.22 Aligned_cols=66 Identities=17% Similarity=0.229 Sum_probs=48.1
Q ss_pred HHHHHHhcCCCceeccchhHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHHHHH
Q 032777 4 SLRMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREM 77 (134)
Q Consensus 4 v~Rik~~LP~n~kISKDAcaseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~yre~ 77 (134)
+.+|+.++ ++.+|+-|-.-.-||.-++-.+.+- ..=+|+++||-.++.+|+|++ +|....++|...
T Consensus 189 i~~ll~n~-~~Y~i~~dv~~~~fvL~v~~~~~~~----~~~~I~~~~I~~ki~dld~~d---El~~ey~k~~~~ 254 (258)
T PF02718_consen 189 IRQLLDNC-PGYKISADVWQGTFVLVVRPDREEQ----TSPKIDADDIYCKICDLDFPD---ELKEEYEKYYAL 254 (258)
T ss_pred HHHHHHhC-CCCeEEEEEecCEEEEEEEeCCCcC----CCcccCHHHHHHHHHcCCCCh---HHHHHHHHHHHH
Confidence 45567778 5899998886666666665553322 377889999999999999996 666666666543
No 51
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=69.15 E-value=11 Score=25.77 Aligned_cols=54 Identities=15% Similarity=0.140 Sum_probs=32.1
Q ss_pred HHHHHH-hc-CCCceeccch--hHHH----HHHHHHhHhhhHhhhcCCCc-cChhHHHHHhhh
Q 032777 4 SLRMLR-IL-YRNVSLSSSA--SLPA----SFSFLSCRASDKCQKEKRKT-INGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~-~L-P~n~kISKDA--case----FI~ylTSeAnd~c~~~kRKT-I~~dDVL~AL~~ 57 (134)
|.||.. .- -++++|++|| -+++ ||.=-...|.+.++.++... |..+|+=+.+-.
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 456644 22 4789999999 3444 44444555566666788888 999998765443
No 52
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=68.67 E-value=14 Score=28.70 Aligned_cols=50 Identities=18% Similarity=0.236 Sum_probs=38.6
Q ss_pred hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc-cchhHHHHHHHHHHHHh
Q 032777 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYREME 78 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~-dyv~~Lk~~L~~yre~~ 78 (134)
.+.+.++||-.+|. |.-++++++..-|+.|||+ +.++.+..++..+|+.-
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 57788888887776 4559999999999999998 66666666666666543
No 53
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=64.88 E-value=8.7 Score=24.23 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=20.8
Q ss_pred ccChhHHHHHhhhcCCccchhHHHH
Q 032777 45 TINGDDLLWAMATLGFEDYIDPLKA 69 (134)
Q Consensus 45 TI~~dDVL~AL~~LgF~dyv~~Lk~ 69 (134)
+=++++|..-|+.+||++|++.+..
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3478999999999999999877654
No 54
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=64.70 E-value=11 Score=28.58 Aligned_cols=46 Identities=22% Similarity=0.267 Sum_probs=23.4
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhh-hcCCccchhHHHHHHHHHH
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMA-TLGFEDYIDPLKAYLMRYR 75 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~-~LgF~dyv~~Lk~~L~~yr 75 (134)
|-..|..++...+|++|+.+||--|.+ .+++.-..++-+++|-..-
T Consensus 49 vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~llelA 95 (129)
T PF02291_consen 49 VLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLLELA 95 (129)
T ss_dssp HHHHHHHHHHHTT-SSB-HHHHHHHHHHT------------------
T ss_pred HHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHHHHH
Confidence 567889999999999999999999998 5677766777777776544
No 55
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=64.12 E-value=7.6 Score=36.45 Aligned_cols=31 Identities=29% Similarity=0.285 Sum_probs=27.1
Q ss_pred HHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 27 FSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 27 I~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
|--|-.+|+++|..++++-|+++||.||++.
T Consensus 368 l~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 368 LGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 3334459999999999999999999999987
No 56
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=63.97 E-value=19 Score=29.34 Aligned_cols=60 Identities=12% Similarity=0.072 Sum_probs=48.1
Q ss_pred hhHHHHHH-----hcCCCceeccchhHHHHHHHHHhHhhhHhhhcCC-CccChhHHHHHhhhcCCc
Q 032777 2 ARSLRMLR-----ILYRNVSLSSSASLPASFSFLSCRASDKCQKEKR-KTINGDDLLWAMATLGFE 61 (134)
Q Consensus 2 anv~Rik~-----~LP~n~kISKDAcaseFI~ylTSeAnd~c~~~kR-KTI~~dDVL~AL~~LgF~ 61 (134)
|+|.|++. .+.+|+.|+...-+-+||-=|--+|-++|..-+. --|-|.||=.|...|.-.
T Consensus 116 a~iKkL~~~itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 116 AQIKKLMSSITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred HHHHHHHHHHhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 35666643 4688999999999999999999999999988554 458899998887777543
No 57
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=63.46 E-value=7.4 Score=28.88 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=27.2
Q ss_pred hhHHHHHhhhcCCccchhHHHHHHHHHHHHh
Q 032777 48 GDDLLWAMATLGFEDYIDPLKAYLMRYREME 78 (134)
Q Consensus 48 ~dDVL~AL~~LgF~dyv~~Lk~~L~~yre~~ 78 (134)
-.+++..|+..|++..+++++.-|+.|++..
T Consensus 103 ~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 103 LPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred HHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 4567888999999999999999999998753
No 58
>PTZ00018 histone H3; Provisional
Probab=61.53 E-value=20 Score=27.52 Aligned_cols=45 Identities=24% Similarity=0.115 Sum_probs=37.7
Q ss_pred cCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 11 LYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 11 LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
.-.++++..+| ++-.|+.-+-..++-.+...||-||.+.|+.-|.
T Consensus 79 ~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 79 FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 34578999998 4557888888899999999999999999997664
No 59
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=58.97 E-value=8.2 Score=23.50 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.8
Q ss_pred ChhHHHHHhhhcCCccchhHHHHH
Q 032777 47 NGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~dyv~~Lk~~ 70 (134)
++++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999998888776553
No 60
>PLN00121 histone H3; Provisional
Probab=58.39 E-value=24 Score=27.11 Aligned_cols=44 Identities=25% Similarity=0.103 Sum_probs=36.8
Q ss_pred CCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 12 YRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 12 P~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
-.++++..+| ++-.|+.-+-..++-.+...||-||.+.|+.-++
T Consensus 80 ~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 80 KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred CccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 3478999998 4556777788899999999999999999997665
No 61
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=58.28 E-value=7.6 Score=23.94 Aligned_cols=26 Identities=19% Similarity=0.279 Sum_probs=17.3
Q ss_pred hhHHHHHhhhcCCccchhHHHHHHHHHH
Q 032777 48 GDDLLWAMATLGFEDYIDPLKAYLMRYR 75 (134)
Q Consensus 48 ~dDVL~AL~~LgF~dyv~~Lk~~L~~yr 75 (134)
-+|++.||..|||.. ......+.+..
T Consensus 3 ~~d~~~AL~~LGy~~--~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSK--AEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-H--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCH--HHHHHHHHHhh
Confidence 379999999999985 44444444433
No 62
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=56.02 E-value=14 Score=23.12 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.3
Q ss_pred ChhHHHHHhhhcCCccchhHHH
Q 032777 47 NGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~dyv~~Lk 68 (134)
++++|..-|+.+|++.|++...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999987763
No 63
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=55.70 E-value=15 Score=33.35 Aligned_cols=34 Identities=21% Similarity=0.108 Sum_probs=26.9
Q ss_pred HHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhc
Q 032777 25 ASFSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 25 eFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~L 58 (134)
.-|.=|-.+|+.+|+.+++++|+++||..|+++-
T Consensus 473 ~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 473 SWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 3455567999999999999999999999999863
No 64
>PLN00161 histone H3; Provisional
Probab=55.07 E-value=35 Score=26.25 Aligned_cols=45 Identities=20% Similarity=0.078 Sum_probs=37.3
Q ss_pred cCCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 11 LYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 11 LP~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
.+.++++..+| ++-.|+--+-..|+-.+...||-||.+.|+--|.
T Consensus 73 ~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 73 LREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred CCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 35679999998 4556777778889999999999999999997664
No 65
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=54.47 E-value=9.1 Score=24.84 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=24.7
Q ss_pred CCccChhHHHHHhhhcCCccchhHHHHHH
Q 032777 43 RKTINGDDLLWAMATLGFEDYIDPLKAYL 71 (134)
Q Consensus 43 RKTI~~dDVL~AL~~LgF~dyv~~Lk~~L 71 (134)
...-+.++++.||+++|..+-++.|+.+|
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 45678899999999999999999888765
No 66
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=52.20 E-value=12 Score=22.94 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=20.0
Q ss_pred cChhHHHHHhhhcCCccchhHHHHH
Q 032777 46 INGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 46 I~~dDVL~AL~~LgF~dyv~~Lk~~ 70 (134)
-+.++|..-|+.+||++|++.+...
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678999999999999877766544
No 67
>PLN00160 histone H3; Provisional
Probab=52.03 E-value=44 Score=24.26 Aligned_cols=44 Identities=23% Similarity=0.046 Sum_probs=35.4
Q ss_pred CCCceeccch------hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 12 YRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 12 P~n~kISKDA------caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
+.+.++..+| ++--|+--+-..|+-.+...||-||.+.|+--|.
T Consensus 40 ~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 40 REAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 4568999988 3445666677888888999999999999996664
No 68
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=49.31 E-value=28 Score=27.21 Aligned_cols=37 Identities=22% Similarity=0.313 Sum_probs=30.5
Q ss_pred HHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 25 ASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 25 eFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
-.|..+...|-..+-..+.++|+.++|-.++.++.|+
T Consensus 233 ~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 233 RLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred cHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 3577777778777777888999999999999998764
No 69
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=47.08 E-value=32 Score=25.68 Aligned_cols=42 Identities=14% Similarity=0.105 Sum_probs=33.5
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccch
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYI 64 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv 64 (134)
.--||.-|-..+-..++..+-|-|+++++..|.+.-+==||.
T Consensus 54 lE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL 95 (113)
T COG5247 54 LEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFL 95 (113)
T ss_pred HHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHH
Confidence 446888888999999999999999999999997764433333
No 70
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=44.04 E-value=18 Score=22.33 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=14.6
Q ss_pred cChhHHHHHhhhcCCc
Q 032777 46 INGDDLLWAMATLGFE 61 (134)
Q Consensus 46 I~~dDVL~AL~~LgF~ 61 (134)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 7889999999999995
No 71
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=43.95 E-value=38 Score=27.20 Aligned_cols=39 Identities=23% Similarity=0.219 Sum_probs=33.2
Q ss_pred HHHHHHHHHhHhhhHhhh--------------cCCCccChhHHHHHhhhcCCc
Q 032777 23 LPASFSFLSCRASDKCQK--------------EKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~--------------~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+-.||+=|+.-|-++|+- ++|-|++-+|+-.||++.|..
T Consensus 116 AQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 116 AQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred HHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcc
Confidence 668999999999999875 446689999999999999874
No 72
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=42.78 E-value=30 Score=28.82 Aligned_cols=35 Identities=17% Similarity=0.115 Sum_probs=27.1
Q ss_pred HHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccc
Q 032777 29 FLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 29 ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dy 63 (134)
.+...|-+.+..+++.+|+.+||-+|++.+....+
T Consensus 253 ~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 253 DLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 34456667777788999999999999999854433
No 73
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=41.21 E-value=35 Score=18.60 Aligned_cols=24 Identities=21% Similarity=0.259 Sum_probs=18.6
Q ss_pred hHhhhcCCCccChhHHHHHhh-hcC
Q 032777 36 DKCQKEKRKTINGDDLLWAMA-TLG 59 (134)
Q Consensus 36 d~c~~~kRKTI~~dDVL~AL~-~Lg 59 (134)
...-.++..+|+.+++..+|+ .||
T Consensus 7 ~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 7 KMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 344567788999999999999 676
No 74
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.45 E-value=12 Score=30.15 Aligned_cols=29 Identities=24% Similarity=0.448 Sum_probs=25.4
Q ss_pred hhHhhhcCCCccChhHHHHHhhhcCCccc
Q 032777 35 SDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 35 nd~c~~~kRKTI~~dDVL~AL~~LgF~dy 63 (134)
-.+|-.+..++|+.|.++.-.++|||+-|
T Consensus 133 gnKCDmd~eRvis~e~g~~l~~~LGfefF 161 (193)
T KOG0093|consen 133 GNKCDMDSERVISHERGRQLADQLGFEFF 161 (193)
T ss_pred ecccCCccceeeeHHHHHHHHHHhChHHh
Confidence 34688899999999999999999999644
No 75
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=38.71 E-value=63 Score=22.01 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=26.6
Q ss_pred hhHHHHHhhhcCC------ccchhHHHHHHHHHHHHhc
Q 032777 48 GDDLLWAMATLGF------EDYIDPLKAYLMRYREMEG 79 (134)
Q Consensus 48 ~dDVL~AL~~LgF------~dyv~~Lk~~L~~yre~~~ 79 (134)
++.|-.+|..||| +.|-+.++..|..|...+.
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 3567889999999 6788899999999987654
No 76
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=37.92 E-value=25 Score=24.11 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.6
Q ss_pred ccChhHHHHHhhhcCCcc
Q 032777 45 TINGDDLLWAMATLGFED 62 (134)
Q Consensus 45 TI~~dDVL~AL~~LgF~d 62 (134)
.+++.+|+.+|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 367899999999999973
No 77
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=37.77 E-value=43 Score=23.59 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=23.5
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
|---|-.+|--++...|..+||..||.
T Consensus 68 ilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 68 ILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 556788889999999999999999974
No 78
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=37.74 E-value=45 Score=22.46 Aligned_cols=38 Identities=21% Similarity=0.354 Sum_probs=31.3
Q ss_pred hHHHHHHHHHhHhhhH---------hhhcCCCccChhHHHHHhhhcCCc
Q 032777 22 SLPASFSFLSCRASDK---------CQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeAnd~---------c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
-+.+||.|..+.+... |.+ ++-.+.++|..=|-.-||.
T Consensus 20 Gv~~Fi~~A~~~~~~~~~i~CPC~~C~N--~~~~~~~~V~~HL~~~Gf~ 66 (77)
T PF13963_consen 20 GVEEFIDFAFSNPSNDNMIRCPCRKCKN--EKRQSRDDVHEHLVCRGFM 66 (77)
T ss_pred HHHHHHHHHHhcccCCCceECCchhhcc--CccCCHHHHHHHHHHhCCC
Confidence 3889999999888776 444 4449999999999999997
No 79
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=36.28 E-value=38 Score=27.83 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=28.7
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHH
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk 68 (134)
+-..|-+.|..+++.+|+.+||-.|+..+..+.+.+.++
T Consensus 246 ~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~~~i~ 284 (365)
T TIGR02928 246 LLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIR 284 (365)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 334566677788889999999999999986555444443
No 80
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=34.54 E-value=82 Score=21.30 Aligned_cols=30 Identities=13% Similarity=0.159 Sum_probs=23.5
Q ss_pred HhhhHhhhcCCCccChhHHHHHhhhcCCcc
Q 032777 33 RASDKCQKEKRKTINGDDLLWAMATLGFED 62 (134)
Q Consensus 33 eAnd~c~~~kRKTI~~dDVL~AL~~LgF~d 62 (134)
++-..+-.++...|+.++|..+|..+|+..
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~~ 43 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLPQ 43 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCCH
Confidence 334455667888999999999999998753
No 81
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=32.58 E-value=58 Score=28.02 Aligned_cols=35 Identities=14% Similarity=0.163 Sum_probs=28.2
Q ss_pred HHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCC
Q 032777 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGF 60 (134)
Q Consensus 26 FI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF 60 (134)
=|.-|..+|...|.+++++.|+.+|+..|++..-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 34456778888888899999999999999887643
No 82
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=31.08 E-value=74 Score=24.00 Aligned_cols=38 Identities=26% Similarity=0.180 Sum_probs=30.0
Q ss_pred CccChhHHHHHhhhcCCc-----------cchhHHHHHHHHHHHHhccc
Q 032777 44 KTINGDDLLWAMATLGFE-----------DYIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 44 KTI~~dDVL~AL~~LgF~-----------dyv~~Lk~~L~~yre~~~~k 81 (134)
-|.+++|++.+|+.+|+. .|++.+.+..+.-++.++.+
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999987 57777777777777766554
No 83
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=30.53 E-value=68 Score=27.01 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=27.0
Q ss_pred HHHHHHhHhhhHhhhcCCCccChhHHHHHhhh
Q 032777 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 26 FI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~ 57 (134)
-|..+..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34456778888888999999999999999875
No 84
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=30.15 E-value=35 Score=22.38 Aligned_cols=17 Identities=24% Similarity=0.608 Sum_probs=12.5
Q ss_pred ccChhHHHHHhhhcCCc
Q 032777 45 TINGDDLLWAMATLGFE 61 (134)
Q Consensus 45 TI~~dDVL~AL~~LgF~ 61 (134)
.|+.+++...|+.|||.
T Consensus 18 ~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 18 DISPEEIIKILKRLGFK 34 (70)
T ss_dssp ---HHHHHHHHHHTT-E
T ss_pred CCCHHHHHHHHHHCCCE
Confidence 78999999999999997
No 85
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=30.05 E-value=62 Score=29.93 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=24.8
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhhhcC
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~~Lg 59 (134)
|-.+|++++..+++.+|+.+||.+|++.-.
T Consensus 363 llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 363 LVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred HHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 445677788888999999999999988654
No 86
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=29.87 E-value=52 Score=17.77 Aligned_cols=23 Identities=22% Similarity=0.127 Sum_probs=18.6
Q ss_pred HHHHhhhcCCccchhHHHHHHHH
Q 032777 51 LLWAMATLGFEDYIDPLKAYLMR 73 (134)
Q Consensus 51 VL~AL~~LgF~dyv~~Lk~~L~~ 73 (134)
..++|-.+|-+..+++|.+.|+.
T Consensus 5 Aa~aLg~igd~~ai~~L~~~L~d 27 (27)
T PF03130_consen 5 AARALGQIGDPRAIPALIEALED 27 (27)
T ss_dssp HHHHHGGG-SHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHhcC
Confidence 46889999999999999988863
No 87
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=29.79 E-value=18 Score=27.30 Aligned_cols=66 Identities=18% Similarity=0.257 Sum_probs=0.0
Q ss_pred HHHHhcCCCceeccch--hHHHHHHHHHhHhhhH------hhhcCCCccChhHHHHHhhhcCCc-cchhHHHHHHHHH
Q 032777 6 RMLRILYRNVSLSSSA--SLPASFSFLSCRASDK------CQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRY 74 (134)
Q Consensus 6 Rik~~LP~n~kISKDA--caseFI~ylTSeAnd~------c~~~kRKTI~~dDVL~AL~~LgF~-dyv~~Lk~~L~~y 74 (134)
++.+.+|. ++.|. ...||+...-|.+.+. .+..+-|+||+.|+--|-+.|+|- .+++.++.++++.
T Consensus 23 ~~~~~~P~---~a~di~~~l~elLk~fNSr~~qlVLGAGA~~~agLK~IT~KhLALasq~L~~~~~lip~i~~~~~~~ 97 (135)
T PF07928_consen 23 QLASNFPS---LAPDILSRLLELLKLFNSRCCQLVLGAGAMRSAGLKTITAKHLALASQSLSFIISLIPYIREFFERH 97 (135)
T ss_dssp ------------------------------------------------------------------------------
T ss_pred HHHHHCch---hHHHHHHHHHHHHHHHHHHHHHHHhccchhhccCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445553 34444 4566666665655554 244679999999999999999996 7788888888776
No 88
>cd01102 Link_Domain The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of
Probab=29.60 E-value=55 Score=23.47 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=26.7
Q ss_pred hHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
.+|.+.|+..+=.--+.++|..|-++ ||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~~-G~~ 45 (92)
T cd01102 17 AEAALACKARGAHLATPGQLEAAWQD-GFD 45 (92)
T ss_pred HHHHHHHHHcCCEeCCHHHHHHHHHc-chh
Confidence 78999999999999999999999886 987
No 89
>smart00445 LINK Link (Hyaluronan-binding).
Probab=28.91 E-value=61 Score=23.32 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=27.0
Q ss_pred hHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+||.+.|+..+=.--+.++|..|.++ ||+
T Consensus 18 ~eA~~aC~~~ga~lAs~~QL~~Aw~~-Gld 46 (94)
T smart00445 18 AEAREACRAQGATLATVGQLYAAWQD-GFD 46 (94)
T ss_pred HHHHHHHHHcCCEeCCHHHHHHHHHh-chh
Confidence 79999999999999999999999886 987
No 90
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=28.35 E-value=1.5e+02 Score=18.13 Aligned_cols=44 Identities=23% Similarity=0.281 Sum_probs=32.9
Q ss_pred hhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH-HHHH
Q 032777 34 ASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR-YREM 77 (134)
Q Consensus 34 And~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~-yre~ 77 (134)
+-+.+-.++.-.|+.+++..++..++..-.-+.+...++. ++..
T Consensus 5 ~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (66)
T PF13499_consen 5 AFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQIFREF 49 (66)
T ss_dssp HHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHH
T ss_pred HHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHh
Confidence 3345566788899999999999999988766667766655 4443
No 91
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=28.18 E-value=79 Score=27.97 Aligned_cols=51 Identities=18% Similarity=0.059 Sum_probs=41.5
Q ss_pred HHHHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCc---cchhHHHHHHHH
Q 032777 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE---DYIDPLKAYLMR 73 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~---dyv~~Lk~~L~~ 73 (134)
...||.-|.-.|+.+..--+|---|..||+.||++|+-. .++-....+|.+
T Consensus 59 ~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~~~~~~s~~L~d 112 (353)
T KOG2389|consen 59 LQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGASGSSGESHCLLD 112 (353)
T ss_pred HHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccccccchhHHHhh
Confidence 678999999999999999999999999999999999754 233334455554
No 92
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=27.83 E-value=91 Score=23.48 Aligned_cols=38 Identities=26% Similarity=0.249 Sum_probs=31.5
Q ss_pred CccChhHHHHHhhhcCCcc------------chhHHHHHHHHHHHHhccc
Q 032777 44 KTINGDDLLWAMATLGFED------------YIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 44 KTI~~dDVL~AL~~LgF~d------------yv~~Lk~~L~~yre~~~~k 81 (134)
.|.+++|++.+|+.+++.. |++.+.+.+.+-++..+-+
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~R 172 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLR 172 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4788999999999999987 8888888888877776554
No 93
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=27.35 E-value=78 Score=28.25 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=27.6
Q ss_pred HHHHHhHhhhHhhhcCCCccChhHHHHHhhhc
Q 032777 27 FSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 27 I~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~L 58 (134)
|..|-.+|...|.+++|..|+.+|+..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55677889999999999999999999998764
No 94
>PTZ00184 calmodulin; Provisional
Probab=27.17 E-value=2e+02 Score=19.72 Aligned_cols=49 Identities=12% Similarity=0.226 Sum_probs=31.4
Q ss_pred HHHHHHHHHhHh------------hhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHH
Q 032777 23 LPASFSFLSCRA------------SDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 71 (134)
Q Consensus 23 aseFI~ylTSeA------------nd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L 71 (134)
-.+|+.++.... -..+-.++.-.|+.+++..+|..+|+.--.+.++..+
T Consensus 66 ~~ef~~~l~~~~~~~~~~~~~~~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~ 126 (149)
T PTZ00184 66 FPEFLTLMARKMKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMI 126 (149)
T ss_pred HHHHHHHHHHhccCCcHHHHHHHHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 457887766431 1122335777899999999999998764444444443
No 95
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=26.95 E-value=1.3e+02 Score=23.57 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=35.0
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchh-HHHHHHHHHH
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRYR 75 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~-~Lk~~L~~yr 75 (134)
|-..|.-++.-.+|.||.+|||-.|.+...=-.|.. +=+++|-.+-
T Consensus 50 vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA 96 (148)
T KOG3334|consen 50 VLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA 96 (148)
T ss_pred HHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH
Confidence 445677778888999999999999999887777766 5555555443
No 96
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=26.91 E-value=1.5e+02 Score=25.82 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=31.2
Q ss_pred hHHHHHHHHHhHh---------hhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 22 SLPASFSFLSCRA---------SDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeA---------nd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
.....+..+..|. .++|..-+-.+..-++|+.+|+++||.
T Consensus 296 ~~~~lL~~~~~E~~~~p~~y~~~~i~~~~k~~~p~~~~~~~~L~~~Gy~ 344 (374)
T TIGR00308 296 RVLKMLSLIKNELSDPPGYYSPHHIASVLKLSVPPLKDVVAGLKSLGFE 344 (374)
T ss_pred HHHHHHHHHHhccCCCCeEEeHHHHHHhcCCCCCCHHHHHHHHHHCCCe
Confidence 4555666666665 457887777889999999999999996
No 97
>cd03518 Link_domain_HAPLN_module_1 Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.
Probab=26.51 E-value=78 Score=22.89 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=26.6
Q ss_pred hHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
++|.+.|+..+=.-=+.++|..|.+ .||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~-~Gld 45 (95)
T cd03518 17 HEAQQACEEQDATLASFEQLYQAWT-EGLD 45 (95)
T ss_pred HHHHHHHHHcCCeeCCHHHHHHHHH-cCcc
Confidence 7899999999999999999999977 8987
No 98
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=25.69 E-value=1e+02 Score=29.49 Aligned_cols=27 Identities=15% Similarity=0.179 Sum_probs=23.5
Q ss_pred HHhHhhhHhhhcCCCccChhHHHHHhh
Q 032777 30 LSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 30 lTSeAnd~c~~~kRKTI~~dDVL~AL~ 56 (134)
+-..|.+.|..-++..|+++|+|+||-
T Consensus 9 ~l~~a~~~a~~~~~~~~~~~h~l~~l~ 35 (758)
T PRK11034 9 SLNMAFARAREHRHEFMTVEHLLLALL 35 (758)
T ss_pred HHHHHHHHHHHcCCCcchHHHHHHHHH
Confidence 345888999999999999999999883
No 99
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=25.53 E-value=50 Score=24.75 Aligned_cols=19 Identities=16% Similarity=0.407 Sum_probs=14.6
Q ss_pred ChhHHHHHhhhcCCccchh
Q 032777 47 NGDDLLWAMATLGFEDYID 65 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~dyv~ 65 (134)
+-+.||.+|+++||.+|+.
T Consensus 92 ~~~~vl~~Lk~~gl~~~Ir 110 (149)
T PF07352_consen 92 DEEKVLEWLKENGLKEFIR 110 (149)
T ss_dssp -HHHHHHHHHHCT-GCC--
T ss_pred CHHHHHHHHHHcCchhhEE
Confidence 7899999999999999975
No 100
>PTZ00183 centrin; Provisional
Probab=25.26 E-value=2.4e+02 Score=19.66 Aligned_cols=39 Identities=15% Similarity=0.155 Sum_probs=26.1
Q ss_pred HHHHHHHHHhH------------hhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 23 LPASFSFLSCR------------ASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 23 aseFI~ylTSe------------And~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
-.+|+.++... +-..+-.++.-.|+.+++..+|..+|..
T Consensus 72 ~~eF~~~~~~~~~~~~~~~~l~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~ 122 (158)
T PTZ00183 72 FEEFLDIMTKKLGERDPREEILKAFRLFDDDKTGKISLKNLKRVAKELGET 122 (158)
T ss_pred HHHHHHHHHHHhcCCCcHHHHHHHHHHhCCCCCCcCcHHHHHHHHHHhCCC
Confidence 45787765432 2233445667789999999999888754
No 101
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=25.18 E-value=56 Score=20.87 Aligned_cols=17 Identities=24% Similarity=0.548 Sum_probs=15.6
Q ss_pred ccChhHHHHHhhhcCCc
Q 032777 45 TINGDDLLWAMATLGFE 61 (134)
Q Consensus 45 TI~~dDVL~AL~~LgF~ 61 (134)
.|+.+++...|+.|||+
T Consensus 18 ~i~~~ei~~~L~~lg~~ 34 (71)
T smart00874 18 DLSAEEIEEILKRLGFE 34 (71)
T ss_pred CCCHHHHHHHHHHCCCe
Confidence 58899999999999996
No 102
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=25.18 E-value=22 Score=25.27 Aligned_cols=22 Identities=18% Similarity=0.492 Sum_probs=16.3
Q ss_pred hcCCccchhHHHHHHHHHHHHh
Q 032777 57 TLGFEDYIDPLKAYLMRYREME 78 (134)
Q Consensus 57 ~LgF~dyv~~Lk~~L~~yre~~ 78 (134)
-+||+||+.-+-+-.-.|....
T Consensus 34 L~GFDd~VNmvLeDvtEye~~~ 55 (84)
T KOG1775|consen 34 LVGFDDFVNMVLEDVTEYEITP 55 (84)
T ss_pred EechHHHHHHHHHhhhheeeCC
Confidence 4699999988877776666443
No 103
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=25.10 E-value=92 Score=22.45 Aligned_cols=29 Identities=28% Similarity=0.350 Sum_probs=26.7
Q ss_pred hHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
+||.+.|+..+=.-=+.++|..|.+ .||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~-~G~d 45 (93)
T cd03515 17 TEAKAACEAEGAHLATYSQLSAAQQ-LGFH 45 (93)
T ss_pred HHHHHHHHHcCCccCCHHHHHHHHH-cCcc
Confidence 7899999999999999999999988 6998
No 104
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=24.73 E-value=91 Score=27.29 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=27.1
Q ss_pred HHHHHhHhhhHhhhcCCCccChhHHHHHhhhc
Q 032777 27 FSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 27 I~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~L 58 (134)
|..|..+|.-.|.++.|+.|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 55677888888999999999999999997763
No 105
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=24.68 E-value=75 Score=27.51 Aligned_cols=39 Identities=13% Similarity=0.105 Sum_probs=30.8
Q ss_pred HHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhH
Q 032777 28 SFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 66 (134)
Q Consensus 28 ~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~ 66 (134)
.-+...|.++|+.+++.+|+.+||-.|-++.+..-+.+.
T Consensus 235 idilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~ 273 (366)
T COG1474 235 IDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEV 273 (366)
T ss_pred HHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHH
Confidence 335578889999999999999999999777666644443
No 106
>PLN03239 histone acetyltransferase; Provisional
Probab=23.66 E-value=69 Score=28.26 Aligned_cols=36 Identities=28% Similarity=0.520 Sum_probs=24.8
Q ss_pred CCCccChhHHHHHhhhcCCccchh------HHHHHHHHHHHH
Q 032777 42 KRKTINGDDLLWAMATLGFEDYID------PLKAYLMRYREM 77 (134)
Q Consensus 42 kRKTI~~dDVL~AL~~LgF~dyv~------~Lk~~L~~yre~ 77 (134)
+..-|..+||+.+|+.||.-.|.. .-...|+++.+.
T Consensus 292 ~~Tgi~~~DIi~tL~~l~~l~~~~g~~~i~~~~~~l~~~~~~ 333 (351)
T PLN03239 292 KKTSIMAEDIVFALNQLGILKFINGIYFIAAEKGLLEELAEK 333 (351)
T ss_pred HHhCCCHHHHHHHHHHCCcEEEECCeEEEEeCHHHHHHHHHH
Confidence 355699999999999999654432 245556666553
No 107
>smart00567 EZ_HEAT E-Z type HEAT repeats. Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role.
Probab=23.64 E-value=73 Score=17.06 Aligned_cols=22 Identities=27% Similarity=0.321 Sum_probs=18.1
Q ss_pred HHHHhhhcCCccchhHHHHHHH
Q 032777 51 LLWAMATLGFEDYIDPLKAYLM 72 (134)
Q Consensus 51 VL~AL~~LgF~dyv~~Lk~~L~ 72 (134)
..++|..+|-++-++.|..+|.
T Consensus 7 aa~aLg~~~~~~a~~~L~~~l~ 28 (30)
T smart00567 7 AAFALGQLGDEEAVPALIKALE 28 (30)
T ss_pred HHHHHHHcCCHhHHHHHHHHhc
Confidence 4678888999988888888774
No 108
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=23.49 E-value=56 Score=22.70 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=14.5
Q ss_pred ChhHHHHHhhhcCCccc
Q 032777 47 NGDDLLWAMATLGFEDY 63 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~dy 63 (134)
..++|..||.++||..+
T Consensus 9 ~~~~v~~aL~~~G~~g~ 25 (102)
T PF00543_consen 9 KLEEVIEALREAGVPGM 25 (102)
T ss_dssp GHHHHHHHHHHTTGSCE
T ss_pred HHHHHHHHHHHCCCCeE
Confidence 36899999999999865
No 109
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=23.39 E-value=1.7e+02 Score=17.25 Aligned_cols=20 Identities=25% Similarity=0.496 Sum_probs=15.5
Q ss_pred CCccChhHHHHHhhhcCCcc
Q 032777 43 RKTINGDDLLWAMATLGFED 62 (134)
Q Consensus 43 RKTI~~dDVL~AL~~LgF~d 62 (134)
+-.|+.+++..+|..+|..+
T Consensus 2 ~G~i~~~~~~~~l~~~g~~~ 21 (54)
T PF13833_consen 2 DGKITREEFRRALSKLGIKD 21 (54)
T ss_dssp SSEEEHHHHHHHHHHTTSSS
T ss_pred cCEECHHHHHHHHHHhCCCC
Confidence 44688888888888888774
No 110
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=23.23 E-value=2.2e+02 Score=24.91 Aligned_cols=50 Identities=12% Similarity=0.233 Sum_probs=40.9
Q ss_pred HHHHHHHhHhhhHhhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHHHHH
Q 032777 25 ASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 76 (134)
Q Consensus 25 eFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~yre 76 (134)
..|.=|.-++.-+|+-.+|..-+.-||--+|-++|+. +..|..+++++-.
T Consensus 37 ~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 37 SYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 3444466778889999999999999999999999998 5777777776554
No 111
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=23.11 E-value=63 Score=23.34 Aligned_cols=17 Identities=18% Similarity=0.280 Sum_probs=15.5
Q ss_pred cChhHHHHHhhhcCCcc
Q 032777 46 INGDDLLWAMATLGFED 62 (134)
Q Consensus 46 I~~dDVL~AL~~LgF~d 62 (134)
.+.++|..|+++|||+-
T Consensus 32 P~~~ei~~a~~~LGl~~ 48 (93)
T COG1400 32 PSLEEIAEALRELGLKP 48 (93)
T ss_pred CCHHHHHHHHHHcCCCe
Confidence 67899999999999984
No 112
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=22.83 E-value=1.8e+02 Score=23.73 Aligned_cols=59 Identities=7% Similarity=-0.067 Sum_probs=37.2
Q ss_pred hHHHHHHHHHhHhhhHhh-hcCCCccC----------hhHHHHHhhhcCCccchhHHHHHHHHHHHHhcc
Q 032777 22 SLPASFSFLSCRASDKCQ-KEKRKTIN----------GDDLLWAMATLGFEDYIDPLKAYLMRYREMEGD 80 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~-~~kRKTI~----------~dDVL~AL~~LgF~dyv~~Lk~~L~~yre~~~~ 80 (134)
.|..||.|+.|...+..- +.....++ ++++...+-.++++...+.....+++|....+.
T Consensus 262 ~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~~ 331 (334)
T TIGR03261 262 AAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYGA 331 (334)
T ss_pred HHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhhc
Confidence 689999999876444332 21111111 134444555667777788899999999887654
No 113
>PF01256 Carb_kinase: Carbohydrate kinase; InterPro: IPR000631 This family is related to Hydroxyethylthiazole kinase IPR000417 from INTERPRO and PfkB carbohydrate kinase IPR011611 from INTERPRO implying that it also a carbohydrate kinase. Several uncharacterised proteins have been shown to share regions of similarities, including yeast chromosome XI hypothetical protein YKL151c; Caenorhabditis elegans hypothetical protein R107.2; Escherichia coli hypothetical protein yjeF; Bacillus subtilis hypothetical protein yxkO; Helicobacter pylori hypothetical protein HP1363; Mycobacterium tuberculosis hypothetical protein MtCY77.05c; Mycobacterium leprae hypothetical protein B229_C2_201; Synechocystis sp. (strain PCC 6803) hypothetical protein sll1433; and Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1586. These are proteins of about 30 to 40 kDa whose central region is well conserved.; PDB: 3RSG_A 3RT9_A 3RRF_A 3RTB_A 3RRE_A 3RS9_A 3RSS_A 3RRB_A 3RTA_A 3RTD_A ....
Probab=21.99 E-value=1.2e+02 Score=24.67 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=23.0
Q ss_pred hHHHHHHHHHhHhhhHhhhcCCCccChhHHHHHh
Q 032777 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~~kRKTI~~dDVL~AL 55 (134)
|+..|+| ..|.+.+.++....+++.||++.|
T Consensus 210 ~~av~lH---g~Ag~~~~~~~~~~~~a~dli~~i 240 (242)
T PF01256_consen 210 CLAVYLH---GRAGDLAAEKYGRGMLASDLIDNI 240 (242)
T ss_dssp HHHHHHH---HHHHHHHCTTCSSC--HHHHHHHH
T ss_pred HHHHHHH---HHHHHHHHHhCCCcCcHHHHHHhc
Confidence 4556665 888899888877799999999875
No 114
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=21.90 E-value=2e+02 Score=22.96 Aligned_cols=38 Identities=18% Similarity=0.277 Sum_probs=27.5
Q ss_pred CccChhHHHHHhhhcCCc---------------cchhHHHHHHHHHHHHhccc
Q 032777 44 KTINGDDLLWAMATLGFE---------------DYIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 44 KTI~~dDVL~AL~~LgF~---------------dyv~~Lk~~L~~yre~~~~k 81 (134)
++|++|=++.+|+.+||. +.++-++.--+.|.+.....
T Consensus 84 ~~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~~~Lse~~~e~~~~~ 136 (190)
T PF09840_consen 84 YPVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELAERLSEIYKELRFQP 136 (190)
T ss_pred CCCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHHHHHHHHHHHHhcCc
Confidence 999999999999999985 34444555555666665443
No 115
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=21.80 E-value=65 Score=22.20 Aligned_cols=32 Identities=22% Similarity=0.250 Sum_probs=24.1
Q ss_pred hhcCCCccChhHHHHHhhhcCCccchhHHHHH
Q 032777 39 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 39 ~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~ 70 (134)
+.++...=+.+.+..||...|..+.++.|+..
T Consensus 54 ~~~~~~~atv~~L~~AL~~~gr~dlae~l~~~ 85 (86)
T cd08779 54 QRQAGDPDAVGKLVTALEESGRQDLADEVRAV 85 (86)
T ss_pred HhcCCCchHHHHHHHHHHHcCHHHHHHHHHhh
Confidence 33333334578999999999999999888764
No 116
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.57 E-value=42 Score=24.24 Aligned_cols=18 Identities=22% Similarity=0.606 Sum_probs=14.8
Q ss_pred ChhHHHHHhhhcCCc-cch
Q 032777 47 NGDDLLWAMATLGFE-DYI 64 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~-dyv 64 (134)
+.+|||+||..||.. +|+
T Consensus 38 T~QDvikAlpglgi~l~Fv 56 (95)
T COG4519 38 TAQDVIKALPGLGIVLEFV 56 (95)
T ss_pred HHHHHHHhCcCCCeEEEee
Confidence 569999999999986 444
No 117
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.41 E-value=90 Score=21.61 Aligned_cols=31 Identities=23% Similarity=0.025 Sum_probs=24.3
Q ss_pred hhhcCCCccChhHHHHHhhhcCCccchhHHH
Q 032777 38 CQKEKRKTINGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 38 c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk 68 (134)
..+++++-=+.+.++.||...|..|++..|-
T Consensus 54 ~~r~g~~~ATv~~L~~aL~~~~r~di~~~l~ 84 (86)
T cd08777 54 KMKEGSKGATVGKLAQALEGCIKPDLLVSLI 84 (86)
T ss_pred HHccCCCCcHHHHHHHHHHHcchhhHHHHHH
Confidence 3445555557899999999999999988763
No 118
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=21.23 E-value=1.7e+02 Score=16.35 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=16.8
Q ss_pred hHHHHHhhhcCCccchhHHHHHHHHHH
Q 032777 49 DDLLWAMATLGFEDYIDPLKAYLMRYR 75 (134)
Q Consensus 49 dDVL~AL~~LgF~dyv~~Lk~~L~~yr 75 (134)
+..+.-|.++||+ .+.+...|..+.
T Consensus 2 ~~~v~~L~~mGf~--~~~~~~AL~~~~ 26 (38)
T cd00194 2 EEKLEQLLEMGFS--REEARKALRATN 26 (38)
T ss_pred HHHHHHHHHcCCC--HHHHHHHHHHhC
Confidence 3567788888998 466666665443
No 119
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=21.08 E-value=64 Score=19.71 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=11.0
Q ss_pred hHHHHHhhhcCCcc
Q 032777 49 DDLLWAMATLGFED 62 (134)
Q Consensus 49 dDVL~AL~~LgF~d 62 (134)
+||+.+|+.+||..
T Consensus 2 ~el~k~L~~~G~~~ 15 (56)
T PF07927_consen 2 RELIKLLEKAGFEE 15 (56)
T ss_dssp HHHHHHHHHTT-EE
T ss_pred hHHHHHHHHCCCEE
Confidence 68899999999973
No 120
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=21.05 E-value=1.2e+02 Score=18.65 Aligned_cols=26 Identities=15% Similarity=-0.043 Sum_probs=18.9
Q ss_pred HHHhHhhhHhhhcCCCccChhHHHHH
Q 032777 29 FLSCRASDKCQKEKRKTINGDDLLWA 54 (134)
Q Consensus 29 ylTSeAnd~c~~~kRKTI~~dDVL~A 54 (134)
.+-..+-.+++..+...||.++|..|
T Consensus 19 ~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 19 KLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 34556667788999999999998765
No 121
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=21.00 E-value=1.7e+02 Score=16.22 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=25.0
Q ss_pred hhhcCCCccChhHHHHHhhhcCCccchhHHHHHHHH
Q 032777 38 CQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 73 (134)
Q Consensus 38 c~~~kRKTI~~dDVL~AL~~LgF~dyv~~Lk~~L~~ 73 (134)
+..++.-.|+.+++..+|+.++...-.+.+...+..
T Consensus 9 ~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~ 44 (63)
T cd00051 9 FDKDGDGTISADELKAALKSLGEGLSEEEIDEMIRE 44 (63)
T ss_pred hCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 344556689999999999999866545555554443
No 122
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=21.00 E-value=48 Score=23.51 Aligned_cols=20 Identities=15% Similarity=0.170 Sum_probs=16.0
Q ss_pred cChhHHHHHhhhcCCccchh
Q 032777 46 INGDDLLWAMATLGFEDYID 65 (134)
Q Consensus 46 I~~dDVL~AL~~LgF~dyv~ 65 (134)
-+.++|..|++.|||..-++
T Consensus 29 P~~~EI~~a~~~Lgl~~~~E 48 (95)
T PF01922_consen 29 PTLEEIADACKKLGLPCVVE 48 (95)
T ss_dssp --HHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHHHcCCCEEEc
Confidence 68899999999999997654
No 123
>PF04664 OGFr_N: Opioid growth factor receptor (OGFr) conserved region; InterPro: IPR006757 Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The opioid growth factor receptor is an integral membrane protein associated with the nucleus. This conserved domain is situated at the N terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminal [].; GO: 0004872 receptor activity, 0016020 membrane
Probab=20.94 E-value=66 Score=26.19 Aligned_cols=26 Identities=27% Similarity=0.588 Sum_probs=22.7
Q ss_pred ChhHHHHHhhhcCCccchhHHHHHHH
Q 032777 47 NGDDLLWAMATLGFEDYIDPLKAYLM 72 (134)
Q Consensus 47 ~~dDVL~AL~~LgF~dyv~~Lk~~L~ 72 (134)
--.-||..|..||++.|..+|-.++-
T Consensus 130 RITRILksL~~LG~e~~a~~L~~f~~ 155 (213)
T PF04664_consen 130 RITRILKSLGELGLEHYAAPLVKFFL 155 (213)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 34468999999999999999999887
No 124
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=20.67 E-value=1.1e+02 Score=20.74 Aligned_cols=24 Identities=42% Similarity=0.419 Sum_probs=17.4
Q ss_pred HHHHhhhcCCccc--hhHHHHHHHHH
Q 032777 51 LLWAMATLGFEDY--IDPLKAYLMRY 74 (134)
Q Consensus 51 VL~AL~~LgF~dy--v~~Lk~~L~~y 74 (134)
-+.||+.|||.+- .+.|+.-|+-|
T Consensus 14 A~dam~~lG~~~~~v~~vl~~LL~lY 39 (65)
T PF10440_consen 14 ALDAMRQLGFSKKQVRPVLKNLLKLY 39 (65)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 3889999999853 45666666665
No 125
>cd03521 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.
Probab=20.66 E-value=1.2e+02 Score=22.07 Aligned_cols=30 Identities=17% Similarity=0.184 Sum_probs=28.4
Q ss_pred hHhhhHhhhcCCCccChhHHHHHhhhcCCc
Q 032777 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~~kRKTI~~dDVL~AL~~LgF~ 61 (134)
.+|...|+..+-.--+.+++..|-++.||+
T Consensus 17 ~eA~~AC~~~gA~lAs~~QL~~AW~~~Gld 46 (95)
T cd03521 17 RAARQSCASLGARLASAAELRRAVVECFFS 46 (95)
T ss_pred HHHHHHHHHcCCEeccHHHHHHHHHHhCcc
Confidence 689999999999999999999999999998
No 126
>TIGR01716 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis.
Probab=20.08 E-value=1.2e+02 Score=23.07 Aligned_cols=29 Identities=10% Similarity=0.208 Sum_probs=25.4
Q ss_pred hhHHHHHhhhcCCccchhHHHHHHHHHHH
Q 032777 48 GDDLLWAMATLGFEDYIDPLKAYLMRYRE 76 (134)
Q Consensus 48 ~dDVL~AL~~LgF~dyv~~Lk~~L~~yre 76 (134)
.+.++..|+.||.+++++.++..++++.+
T Consensus 191 i~~~i~~l~~lg~~~~~~~~~~~~~~~~~ 219 (220)
T TIGR01716 191 IEQAIEIFDELGYPTLAAYYQKLLEKFVK 219 (220)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHhh
Confidence 78899999999999999999988887753
Done!