Query 032773
Match_columns 134
No_of_seqs 134 out of 507
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:46:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032773.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032773hhsearch_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 5.5E-38 1.2E-42 243.4 9.0 109 1-111 35-150 (168)
2 KOG0871 Class 2 transcription 99.9 1.1E-23 2.3E-28 162.3 5.9 79 2-80 16-101 (156)
3 KOG0870 DNA polymerase epsilon 99.8 1.2E-21 2.7E-26 153.2 6.2 83 3-85 15-105 (172)
4 COG5150 Class 2 transcription 99.8 2.9E-19 6.3E-24 135.7 6.2 80 2-81 15-101 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.4 1.6E-13 3.4E-18 90.6 4.7 55 1-55 5-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.1 2E-10 4.4E-15 82.4 4.6 62 1-64 22-90 (91)
7 cd00076 H4 Histone H4, one of 97.6 0.00014 3E-09 51.7 4.7 49 14-62 28-82 (85)
8 PF00125 Histone: Core histone 97.4 0.0002 4.4E-09 47.6 4.0 53 4-56 11-73 (75)
9 cd07981 TAF12 TATA Binding Pro 97.3 0.00075 1.6E-08 45.8 5.5 54 4-57 7-66 (72)
10 PTZ00015 histone H4; Provision 97.3 0.0005 1.1E-08 50.4 4.7 48 15-62 46-99 (102)
11 PLN00035 histone H4; Provision 97.2 0.00066 1.4E-08 49.9 4.7 47 14-60 44-96 (103)
12 smart00803 TAF TATA box bindin 97.1 0.0013 2.8E-08 44.2 5.0 54 2-56 6-65 (65)
13 smart00427 H2B Histone H2B. 96.2 0.013 2.7E-07 42.2 5.1 55 4-58 7-67 (89)
14 smart00417 H4 Histone H4. 96.0 0.0053 1.1E-07 42.6 2.3 39 16-54 30-74 (74)
15 smart00576 BTP Bromodomain tra 95.5 0.025 5.4E-07 38.5 4.3 40 22-61 35-74 (77)
16 PLN00158 histone H2B; Provisio 95.2 0.048 1E-06 41.0 5.2 55 4-58 33-93 (116)
17 KOG3467 Histone H4 [Chromatin 95.1 0.034 7.5E-07 40.5 4.0 39 22-60 58-96 (103)
18 PTZ00463 histone H2B; Provisio 95.0 0.06 1.3E-06 40.6 5.2 55 4-58 34-94 (117)
19 PF07524 Bromo_TP: Bromodomain 95.0 0.056 1.2E-06 36.4 4.6 40 22-61 35-74 (77)
20 PF03847 TFIID_20kDa: Transcri 94.9 0.088 1.9E-06 35.7 5.3 55 3-57 4-64 (68)
21 PF15630 CENP-S: Kinetochore c 94.7 0.065 1.4E-06 37.2 4.4 52 4-55 11-70 (76)
22 KOG1657 CCAAT-binding factor, 94.3 0.033 7.2E-07 46.0 2.6 73 2-74 78-159 (236)
23 cd00074 H2A Histone 2A; H2A is 94.3 0.12 2.5E-06 38.6 5.3 56 2-57 24-85 (115)
24 cd08050 TAF6 TATA Binding Prot 93.9 0.1 2.2E-06 44.6 4.7 46 16-61 16-67 (343)
25 COG5208 HAP5 CCAAT-binding fac 92.5 0.13 2.8E-06 43.0 3.3 59 5-63 113-180 (286)
26 PF02269 TFIID-18kDa: Transcri 92.0 0.092 2E-06 37.3 1.6 37 21-57 30-66 (93)
27 cd07979 TAF9 TATA Binding Prot 91.3 0.98 2.1E-05 33.4 6.5 61 16-76 18-85 (117)
28 smart00428 H3 Histone H3. 89.3 1.1 2.5E-05 32.9 5.3 43 14-56 51-99 (105)
29 smart00414 H2A Histone 2A. 88.1 0.97 2.1E-05 33.1 4.3 54 4-57 12-74 (106)
30 KOG1744 Histone H2B [Chromatin 87.7 1.2 2.7E-05 34.0 4.8 55 4-58 43-103 (127)
31 cd08048 TAF11 TATA Binding Pro 87.3 1.5 3.2E-05 31.0 4.7 45 14-58 37-84 (85)
32 KOG1658 DNA polymerase epsilon 86.9 0.38 8.2E-06 38.0 1.6 53 4-56 62-123 (162)
33 cd07978 TAF13 The TATA Binding 86.5 1.3 2.7E-05 31.7 4.0 54 20-76 30-83 (92)
34 COG5262 HTA1 Histone H2A [Chro 84.3 2.4 5.2E-05 32.4 4.8 53 4-56 32-90 (132)
35 PLN00154 histone H2A; Provisio 82.2 2.1 4.5E-05 33.0 3.8 54 4-57 41-104 (136)
36 PHA03328 nuclear egress lamina 82.2 0.37 8.1E-06 41.6 -0.3 67 6-75 241-307 (316)
37 KOG1659 Class 2 transcription 81.0 4.3 9.2E-05 33.7 5.4 71 4-77 16-95 (224)
38 PF02861 Clp_N: Clp amino term 80.4 2.2 4.7E-05 25.7 2.8 26 34-59 1-26 (53)
39 PF15511 CENP-T: Centromere ki 80.1 1.8 3.9E-05 38.1 3.2 38 13-50 371-414 (414)
40 PLN00157 histone H2A; Provisio 78.6 3.4 7.5E-05 31.7 3.9 54 4-57 29-91 (132)
41 PF15510 CENP-W: Centromere ki 76.3 4 8.7E-05 30.0 3.5 36 22-57 60-95 (102)
42 KOG1756 Histone 2A [Chromatin 75.5 6.8 0.00015 30.1 4.8 53 5-57 31-92 (131)
43 PF02969 TAF: TATA box binding 75.1 6.4 0.00014 26.6 4.1 34 23-56 33-66 (66)
44 PLN00156 histone H2AX; Provisi 74.0 6.5 0.00014 30.4 4.4 54 4-57 32-94 (139)
45 PF04719 TAFII28: hTAFII28-lik 72.5 7.7 0.00017 27.7 4.2 56 3-58 28-90 (90)
46 PTZ00017 histone H2A; Provisio 71.0 9 0.0002 29.4 4.5 54 4-57 30-92 (134)
47 PLN00153 histone H2A; Provisio 65.6 12 0.00027 28.6 4.3 54 4-57 27-89 (129)
48 PF07647 SAM_2: SAM domain (St 63.6 9.2 0.0002 24.1 2.8 25 45-69 3-27 (66)
49 PF02718 Herpes_UL31: Herpesvi 63.5 2.4 5.3E-05 35.7 0.1 64 6-77 191-254 (258)
50 PTZ00252 histone H2A; Provisio 63.4 18 0.00039 27.9 4.8 54 4-57 28-92 (134)
51 PTZ00018 histone H3; Provision 62.6 16 0.00036 28.1 4.5 49 7-55 75-129 (136)
52 KOG1142 Transcription initiati 61.8 7.4 0.00016 32.9 2.7 48 10-57 166-219 (258)
53 PLN00161 histone H3; Provision 59.9 24 0.00053 27.2 5.0 45 11-55 73-123 (135)
54 PLN00121 histone H3; Provision 59.8 20 0.00043 27.6 4.5 46 10-55 78-129 (136)
55 cd04752 Commd4 COMM_Domain con 59.5 25 0.00055 27.2 5.2 50 22-78 43-93 (174)
56 PF12010 DUF3502: Domain of un 59.1 9.2 0.0002 28.4 2.5 31 48-78 103-133 (134)
57 COG1067 LonB Predicted ATP-dep 59.0 8.7 0.00019 36.1 2.9 35 22-57 364-398 (647)
58 KOG3219 Transcription initiati 58.7 22 0.00048 29.0 4.8 51 10-60 129-180 (195)
59 cd00166 SAM Sterile alpha moti 58.5 7.9 0.00017 23.6 1.8 24 47-70 3-26 (63)
60 PF07499 RuvA_C: RuvA, C-termi 58.0 7.6 0.00017 24.0 1.7 15 48-62 3-17 (47)
61 PF02291 TFIID-31kDa: Transcri 57.4 18 0.00039 27.4 3.9 54 22-75 37-95 (129)
62 PF09415 CENP-X: CENP-S associ 56.1 21 0.00045 24.4 3.7 44 12-55 15-65 (72)
63 KOG3423 Transcription initiati 55.9 17 0.00036 29.3 3.6 40 22-61 115-168 (176)
64 PF00536 SAM_1: SAM domain (St 55.4 14 0.00031 23.1 2.7 22 47-68 4-25 (64)
65 smart00454 SAM Sterile alpha m 52.3 11 0.00023 23.1 1.7 25 46-70 4-28 (68)
66 PLN00160 histone H3; Provision 51.0 41 0.00088 24.5 4.7 44 12-55 40-89 (97)
67 COG5247 BUR6 Class 2 transcrip 50.7 25 0.00055 26.3 3.6 38 22-59 53-90 (113)
68 PF00531 Death: Death domain; 50.5 11 0.00023 24.5 1.5 30 42-71 54-83 (83)
69 TIGR03015 pepcterm_ATPase puta 50.0 27 0.00058 27.3 3.9 37 25-61 233-269 (269)
70 PF13654 AAA_32: AAA domain; P 50.0 21 0.00045 32.5 3.7 33 26-58 474-506 (509)
71 PF00403 HMA: Heavy-metal-asso 43.4 18 0.0004 22.4 1.7 16 46-61 47-62 (62)
72 PF08823 PG_binding_2: Putativ 43.2 49 0.0011 22.6 3.9 32 48-79 18-55 (74)
73 PRK00411 cdc6 cell division co 42.1 30 0.00066 28.8 3.3 34 30-63 254-287 (394)
74 TIGR02454 CbiQ_TIGR cobalt ABC 42.0 36 0.00078 25.7 3.5 38 44-81 112-160 (198)
75 PF13335 Mg_chelatase_2: Magne 40.2 29 0.00062 24.5 2.5 27 30-56 68-94 (96)
76 PF13405 EF-hand_6: EF-hand do 39.5 40 0.00087 18.4 2.6 24 36-59 7-31 (31)
77 COG1724 Predicted RNA binding 39.4 22 0.00048 24.4 1.7 18 45-62 6-23 (66)
78 KOG0093 GTPase Rab3, small G p 38.3 12 0.00027 30.0 0.4 30 35-64 133-162 (193)
79 PF13963 Transpos_assoc: Trans 36.1 48 0.001 22.4 3.0 38 22-61 20-66 (77)
80 TIGR02928 orc1/cdc6 family rep 35.9 37 0.0008 27.9 2.9 39 30-68 246-284 (365)
81 PF03130 HEAT_PBS: PBS lyase H 33.9 37 0.0008 18.4 1.8 23 51-73 5-27 (27)
82 PF13499 EF-hand_7: EF-hand do 33.5 1.2E+02 0.0025 18.6 5.1 44 34-77 5-49 (66)
83 PF02361 CbiQ: Cobalt transpor 33.3 61 0.0013 24.5 3.5 38 44-81 123-172 (224)
84 smart00027 EH Eps15 homology d 32.6 89 0.0019 21.2 3.9 29 33-61 14-42 (96)
85 PRK03992 proteasome-activating 31.2 63 0.0014 27.8 3.6 33 27-59 341-373 (389)
86 cd01102 Link_Domain The link d 31.0 49 0.0011 23.7 2.5 29 32-61 17-45 (92)
87 smart00445 LINK Link (Hyaluron 30.0 56 0.0012 23.6 2.7 29 32-61 18-46 (94)
88 KOG1775 U6 snRNA-associated Sm 29.9 16 0.00034 26.0 -0.2 29 57-85 34-62 (84)
89 TIGR01242 26Sp45 26S proteasom 29.7 72 0.0016 26.9 3.7 32 26-57 331-362 (364)
90 TIGR00764 lon_rel lon-related 28.3 69 0.0015 29.6 3.6 30 30-59 363-392 (608)
91 PTZ00361 26 proteosome regulat 28.3 74 0.0016 28.4 3.6 32 27-58 393-424 (438)
92 KOG0883 Cyclophilin type, U bo 27.9 40 0.00086 30.8 1.9 76 41-120 389-487 (518)
93 COG1474 CDC6 Cdc6-related prot 27.3 61 0.0013 28.1 2.9 39 29-67 236-274 (366)
94 COG4519 Uncharacterized protei 26.1 30 0.00066 25.0 0.7 18 47-64 38-56 (95)
95 cd03518 Link_domain_HAPLN_modu 25.8 81 0.0018 22.9 2.9 29 32-61 17-45 (95)
96 PF07352 Phage_Mu_Gam: Bacteri 25.6 49 0.0011 24.8 1.8 19 47-65 92-110 (149)
97 PF03484 B5: tRNA synthetase B 25.3 46 0.001 21.8 1.4 17 45-61 18-34 (70)
98 cd03521 Link_domain_KIAA0527_l 25.2 87 0.0019 22.9 2.9 30 32-61 17-46 (95)
99 KOG2389 Predicted bromodomain 25.0 95 0.0021 27.5 3.6 52 22-73 58-112 (353)
100 cd03515 Link_domain_TSG_6_like 24.4 94 0.002 22.4 3.0 29 32-61 17-45 (93)
101 smart00567 EZ_HEAT E-Z type HE 24.2 68 0.0015 17.2 1.8 22 51-72 7-28 (30)
102 PTZ00454 26S protease regulato 23.9 1E+02 0.0022 27.0 3.7 33 26-58 354-386 (398)
103 PF09077 Phage-MuB_C: Mu B tra 23.9 52 0.0011 23.0 1.5 26 32-58 53-78 (78)
104 PTZ00184 calmodulin; Provision 23.5 2.5E+02 0.0054 19.2 5.0 32 40-71 95-126 (149)
105 PF08369 PCP_red: Proto-chloro 23.5 1.5E+02 0.0032 18.3 3.4 26 29-54 19-44 (45)
106 PF01726 LexA_DNA_bind: LexA D 23.2 1.4E+02 0.003 19.6 3.4 28 34-61 28-56 (65)
107 cd08779 Death_PIDD Death Domai 22.2 61 0.0013 22.4 1.6 32 39-70 54-85 (86)
108 cd08777 Death_RIP1 Death Domai 22.2 82 0.0018 21.8 2.3 31 38-68 54-84 (86)
109 PF00543 P-II: Nitrogen regula 22.1 61 0.0013 22.5 1.6 17 47-63 9-25 (102)
110 PF09840 DUF2067: Uncharacteri 22.0 1.9E+02 0.0042 23.1 4.6 40 44-83 84-138 (190)
111 COG1400 SEC65 Signal recogniti 21.9 68 0.0015 23.2 1.8 18 46-63 32-49 (93)
112 PF09957 DUF2191: Uncharacteri 21.9 1.2E+02 0.0027 18.9 2.8 39 43-81 2-42 (47)
113 TIGR03261 phnS2 putative 2-ami 21.7 1.8E+02 0.0039 23.7 4.5 59 22-80 262-331 (334)
114 PF10440 WIYLD: Ubiquitin-bind 20.9 1E+02 0.0023 20.9 2.5 23 52-74 15-39 (65)
115 smart00874 B5 tRNA synthetase 20.7 76 0.0017 20.2 1.8 17 45-61 18-34 (71)
116 PF14384 DUF4415: Domain of un 20.6 1.1E+02 0.0024 19.8 2.6 25 49-74 37-61 (62)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=5.5e-38 Score=243.41 Aligned_cols=109 Identities=46% Similarity=0.743 Sum_probs=94.3
Q ss_pred ChhHHHH-HhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHH
Q 032773 1 MARSLRM-LRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 73 (134)
Q Consensus 1 ~anv~Ri-k~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 7999996 66999999999998 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccCCCCCCCCCCCCCCccCCCCCCcchhhccC
Q 032773 74 YREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQG 111 (134)
Q Consensus 74 yre~~~~Kk~~~k~~~~~~~~~~~~~~~~~~~~~~~~g 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 999999998887777533 333233444455555565
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.89 E-value=1.1e-23 Score=162.34 Aligned_cols=79 Identities=27% Similarity=0.443 Sum_probs=73.7
Q ss_pred hhHHHH-HhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHH
Q 032773 2 ARSLRM-LRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 2 anv~Ri-k~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 346675 88999999999998 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcc
Q 032773 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 986653
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.85 E-value=1.2e-21 Score=153.15 Aligned_cols=83 Identities=29% Similarity=0.447 Sum_probs=77.5
Q ss_pred hHHHH-HhccCCC-cccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHH
Q 032773 3 RSLRM-LRILYRN-VSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 3 nv~Ri-k~~LP~n-~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 36775 8899987 9999998 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccCCCC
Q 032773 75 REMEGDTKGSA 85 (134)
Q Consensus 75 re~~~~Kk~~~ 85 (134)
|...+.||.++
T Consensus 95 k~~~k~Kk~~~ 105 (172)
T KOG0870|consen 95 KKAVKQKKLAK 105 (172)
T ss_pred HHHHHHHHHhc
Confidence 99988887643
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.78 E-value=2.9e-19 Score=135.67 Aligned_cols=80 Identities=25% Similarity=0.422 Sum_probs=75.4
Q ss_pred hhHHHH-HhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHH
Q 032773 2 ARSLRM-LRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 2 anv~Ri-k~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 457777 66999999999998 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccc
Q 032773 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 9987765
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=99.43 E-value=1.6e-13 Score=90.63 Aligned_cols=55 Identities=27% Similarity=0.346 Sum_probs=49.3
Q ss_pred ChhHHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHH
Q 032773 1 MARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 1 ~anv~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 368999877669999999998 9999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.05 E-value=2e-10 Score=82.39 Aligned_cols=62 Identities=27% Similarity=0.281 Sum_probs=56.9
Q ss_pred ChhHHHH-HhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcch
Q 032773 1 MARSLRM-LRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYI 64 (134)
Q Consensus 1 ~anv~Ri-k~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 5899997 557777 999998 9999999999999999999999999999999999999998764
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=97.56 E-value=0.00014 Score=51.67 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=43.2
Q ss_pred Ccccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCc
Q 032773 14 NVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFED 62 (134)
Q Consensus 14 n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~d 62 (134)
--+||.|+ +..+|+.-|...|..+|+-.+||||+++||..||+..|-.-
T Consensus 28 vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~ 82 (85)
T cd00076 28 VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL 82 (85)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCc
Confidence 35688776 77899999999999999999999999999999999988543
No 8
>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=97.44 E-value=0.0002 Score=47.63 Aligned_cols=53 Identities=28% Similarity=0.259 Sum_probs=41.0
Q ss_pred HHHHHhccCCC----cccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 4 SLRMLRILYRN----VSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 4 v~Rik~~LP~n----~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 45665555444 8999998 33444446778899999999999999999999875
No 9
>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=97.29 E-value=0.00075 Score=45.81 Aligned_cols=54 Identities=11% Similarity=0.061 Sum_probs=47.0
Q ss_pred HHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 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 344555566778999997 999999999999999999999999999999999875
No 10
>PTZ00015 histone H4; Provisional
Probab=97.27 E-value=0.0005 Score=50.40 Aligned_cols=48 Identities=19% Similarity=0.216 Sum_probs=41.8
Q ss_pred cccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCc
Q 032773 15 VSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFED 62 (134)
Q Consensus 15 ~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~d 62 (134)
-+||.|+ +..+|+.-|..+|..+|+-.+||||+++||..||+..|=.-
T Consensus 46 kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~ 99 (102)
T PTZ00015 46 KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTL 99 (102)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCC
Confidence 3577776 77899999999999999999999999999999999887543
No 11
>PLN00035 histone H4; Provisional
Probab=97.19 E-value=0.00066 Score=49.91 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=41.0
Q ss_pred Ccccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCC
Q 032773 14 NVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGF 60 (134)
Q Consensus 14 n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF 60 (134)
--+||.|+ ...+|+.-|...|..+|+-.+||||+++||..||+..|=
T Consensus 44 vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 44 VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 34577776 668889999999999999999999999999999998764
No 12
>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=97.09 E-value=0.0013 Score=44.19 Aligned_cols=54 Identities=19% Similarity=0.102 Sum_probs=43.7
Q ss_pred hhHHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 4677886655333 688886 45677888999999999999999999999999874
No 13
>smart00427 H2B Histone H2B.
Probab=96.18 E-value=0.013 Score=42.20 Aligned_cols=55 Identities=16% Similarity=0.248 Sum_probs=44.7
Q ss_pred HHHHHhccCCCcccccch--hHHHHHH----HHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 4 SLRMLRILYRNVSLSSSA--SLPASFS----FLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda--caseFI~----ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
|+|+-+.+-|+..||+.+ -..-|+. =|+++|...|.-.+|+||++.+|-.|.+-+
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 577766666788999998 3334554 489999999999999999999999998765
No 14
>smart00417 H4 Histone H4.
Probab=95.99 E-value=0.0053 Score=42.64 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=33.3
Q ss_pred ccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHH
Q 032773 16 SLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWA 54 (134)
Q Consensus 16 kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~A 54 (134)
+||.|+ ...+|+.-|...|..+|+-.+||||+++||..|
T Consensus 30 RIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 30 RISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 477665 556899999999999999999999999999753
No 15
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.55 E-value=0.025 Score=38.55 Aligned_cols=40 Identities=23% Similarity=0.225 Sum_probs=35.1
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 61 (134)
-...|+.-|...+..+|+..+|++.+++||..||+++|..
T Consensus 35 i~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 35 ILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 4556667788999999999999999999999999999874
No 16
>PLN00158 histone H2B; Provisional
Probab=95.24 E-value=0.048 Score=41.01 Aligned_cols=55 Identities=15% Similarity=0.231 Sum_probs=44.5
Q ss_pred HHHHHhccCCCcccccch--hHHHHHH----HHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 4 SLRMLRILYRNVSLSSSA--SLPASFS----FLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda--caseFI~----ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
|+|+-+.+-|+..||+.+ ...-||. =|++||...|.-.+|+||++.+|-.|.+-+
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 567766666788899988 4444555 489999999999999999999999997755
No 17
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=95.12 E-value=0.034 Score=40.45 Aligned_cols=39 Identities=23% Similarity=0.266 Sum_probs=36.4
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCC
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGF 60 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF 60 (134)
...|||--+-+.|...++-.|||||++-||+-+|+..|-
T Consensus 58 ~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 58 VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 788999999999999999999999999999999998864
No 18
>PTZ00463 histone H2B; Provisional
Probab=95.00 E-value=0.06 Score=40.56 Aligned_cols=55 Identities=15% Similarity=0.298 Sum_probs=44.4
Q ss_pred HHHHHhccCCCcccccch--hHHHHHH----HHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 4 SLRMLRILYRNVSLSSSA--SLPASFS----FLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda--caseFI~----ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
|+|+-+.+-|++.||+.+ -..-||. =|++||...|.-.+|+||++.+|-.|.+-+
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 567655666788899998 4445555 489999999999999999999999997755
No 19
>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=94.99 E-value=0.056 Score=36.43 Aligned_cols=40 Identities=20% Similarity=0.175 Sum_probs=36.5
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 61 (134)
-+..||.-|.+.+..+|+..+|...++.||..||+++|+.
T Consensus 35 i~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 35 ILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 5667888899999999999999999999999999999984
No 20
>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=94.87 E-value=0.088 Score=35.75 Aligned_cols=55 Identities=11% Similarity=0.085 Sum_probs=42.0
Q ss_pred hHHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 3 RSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 3 nv~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 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 3445667788999999987 999999999999999999999999999999988864
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=94.70 E-value=0.065 Score=37.22 Aligned_cols=52 Identities=23% Similarity=0.151 Sum_probs=33.5
Q ss_pred HHHH-Hh-ccCCCcccccch--hHHHHHH-HHHhHhhH---HhHhcCCCccChhHHHHHH
Q 032773 4 SLRM-LR-ILYRNVSLSSSA--SLPASFS-FLSCRASD---KCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 4 v~Ri-k~-~LP~n~kISKda--caseFI~-ylTSeAnd---~c~~ekRKTI~~dDVL~AL 55 (134)
|.|| .+ ..+.++.+|++. |.+|.+- ++..-|.| .|+-.||+||++|||+-..
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~ 70 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLA 70 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHT
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHh
Confidence 5566 33 568899999997 5555443 34444444 5788999999999998654
No 22
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=94.34 E-value=0.033 Score=46.00 Aligned_cols=73 Identities=21% Similarity=0.222 Sum_probs=56.5
Q ss_pred hhHHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhc---CCCcchHHHHHHHH
Q 032773 2 ARSLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATL---GFEDYIDPLKAYLM 72 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL---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 45556655444444788898 9999999999999999999999999999999999876 44433445666666
Q ss_pred HH
Q 032773 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
>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=94.33 E-value=0.12 Score=38.56 Aligned_cols=56 Identities=23% Similarity=0.295 Sum_probs=37.5
Q ss_pred hhHHHHHhccCCCcccccch--hHHHHHHHHHhH----hhHHhHhcCCCccChhHHHHHHhh
Q 032773 2 ARSLRMLRILYRNVSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 2 anv~Rik~~LP~n~kISKda--caseFI~ylTSe----And~c~~ekRKTI~~dDVL~AL~e 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 34455433211237899988 444445566655 556778889999999999999865
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=93.86 E-value=0.1 Score=44.62 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=41.1
Q ss_pred ccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 16 SLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 16 kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 677776 7888999999999999999999999999999999987544
No 25
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=92.52 E-value=0.13 Score=43.03 Aligned_cols=59 Identities=22% Similarity=0.268 Sum_probs=48.6
Q ss_pred HHHHhc--cCCCcc-cccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcc
Q 032773 5 LRMLRI--LYRNVS-LSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 5 ~Rik~~--LP~n~k-ISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 466663 336666 67776 889999999999999999999999999999999998865554
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=91.99 E-value=0.092 Score=37.33 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=14.6
Q ss_pred hhHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 21 ASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 21 acaseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 57 (134)
.-+.+||.-+..+|...|...++++|+.||++.+|+.
T Consensus 30 ~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 30 DIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3788999999999999999999999999999999985
No 27
>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=91.26 E-value=0.98 Score=33.37 Aligned_cols=61 Identities=13% Similarity=0.114 Sum_probs=43.3
Q ss_pred ccccch--hHHHHHH----HHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcc-hHHHHHHHHHHHH
Q 032773 16 SLSSSA--SLPASFS----FLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY-IDPLKAYLMRYRE 76 (134)
Q Consensus 16 kISKda--caseFI~----ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dy-v~~Lk~~L~~yre 76 (134)
.++.++ +-.+|+. =|..+|..+++-.+|+||++|||--|++..+-..| .++-+++|...-.
T Consensus 18 ~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~a~ 85 (117)
T cd07979 18 EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLELAR 85 (117)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHHHH
Confidence 344444 4444443 36677888889999999999999999988866555 4447777766544
No 28
>smart00428 H3 Histone H3.
Probab=89.29 E-value=1.1 Score=32.91 Aligned_cols=43 Identities=26% Similarity=0.124 Sum_probs=37.2
Q ss_pred Ccccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 14 NVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 14 n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 78999998 77777778889999999999999999999976653
No 29
>smart00414 H2A Histone 2A.
Probab=88.08 E-value=0.97 Score=33.14 Aligned_cols=54 Identities=22% Similarity=0.369 Sum_probs=35.7
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhH----hhHHhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCR----ASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSe----And~c~~ekRKTI~~dDVL~AL~e 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 33777776 333334577777 445567778999999999999875
No 30
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=87.75 E-value=1.2 Score=33.95 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=41.5
Q ss_pred HHHHHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 4 SLRMLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
|+|+.+..-|+.-|+.++ -..+++--|.++|+..+.-.+|.||+..+|-.|.+-|
T Consensus 43 v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 567645444557788887 3344444588999999999999999999999886544
No 31
>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=87.33 E-value=1.5 Score=30.97 Aligned_cols=45 Identities=16% Similarity=0.038 Sum_probs=36.6
Q ss_pred CcccccchhHHHHHHHHHhHhhHHhHhcCC---CccChhHHHHHHhhc
Q 032773 14 NVSLSSSASLPASFSFLSCRASDKCQKEKR---KTINGDDLLWAMATL 58 (134)
Q Consensus 14 n~kISKdacaseFI~ylTSeAnd~c~~ekR---KTI~~dDVL~AL~eL 58 (134)
|+.|.--.-+.+||.=|+.+|.++..+.+. ..|-|+||-+|...|
T Consensus 37 ~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 37 NVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 333333338899999999999999988766 889999999998876
No 32
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=86.85 E-value=0.38 Score=38.04 Aligned_cols=53 Identities=23% Similarity=0.110 Sum_probs=44.7
Q ss_pred HHHHHh--ccCCCcccccch-------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 4 SLRMLR--ILYRNVSLSSSA-------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 4 v~Rik~--~LP~n~kISKda-------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~ 56 (134)
..||+. -+||++.++.|+ ++--||.+|.-.+...++..+|||+.--|+=.|.+
T Consensus 62 L~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~ 123 (162)
T KOG1658|consen 62 LARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIE 123 (162)
T ss_pred HHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccccc
Confidence 357877 566999999997 89999999999999999999999998777655543
No 33
>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=86.51 E-value=1.3 Score=31.66 Aligned_cols=54 Identities=17% Similarity=0.220 Sum_probs=39.0
Q ss_pred chhHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHHHH
Q 032773 20 SASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 76 (134)
Q Consensus 20 dacaseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L~~yre 76 (134)
|..+.+||.-++.+|.+.+. .++.-|+.||++-+|..= .-.+.-++.+|.--.+
T Consensus 30 E~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~~k~~ 83 (92)
T cd07978 30 EDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLSMKDE 83 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHHHHHH
Confidence 44899999999999999999 444456999999999642 2334455555554333
No 34
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=84.30 E-value=2.4 Score=32.42 Aligned_cols=53 Identities=21% Similarity=0.272 Sum_probs=37.4
Q ss_pred HHHHHhccCCCcccccch--hHHHHHHHHHhHhhHH----hHhcCCCccChhHHHHHHh
Q 032773 4 SLRMLRILYRNVSLSSSA--SLPASFSFLSCRASDK----CQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda--caseFI~ylTSeAnd~----c~~ekRKTI~~dDVL~AL~ 56 (134)
|.|+.+----.++|++++ ..+--+.||++|--|. +...++|.|.|.|+-.|..
T Consensus 32 vkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 32 VKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 444433223568899998 5555667887776555 5668999999999988875
No 35
>PLN00154 histone H2A; Provisional
Probab=82.16 E-value=2.1 Score=33.05 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=35.0
Q ss_pred HHHHHhccCC----Ccccccch--hHHHHHHHHHhHhh----HHhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR----NVSLSSSA--SLPASFSFLSCRAS----DKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~----n~kISKda--caseFI~ylTSeAn----d~c~~ekRKTI~~dDVL~AL~e 57 (134)
|.||.+.|-. ..+|+..+ -..--+-|||+|-- ..|.+.+++-|++.||..|+..
T Consensus 41 VgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 41 VGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred hHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3454444443 35787776 11222458888754 4557778999999999999854
No 36
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=82.16 E-value=0.37 Score=41.65 Aligned_cols=67 Identities=15% Similarity=0.216 Sum_probs=51.6
Q ss_pred HHHhccCCCcccccchhHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHHH
Q 032773 6 RMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYR 75 (134)
Q Consensus 6 Rik~~LP~n~kISKdacaseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L~~yr 75 (134)
+|+..+| +.+|+-|-.-+-||.-++-.+-.....+..=||+++||-.+|.+|+|++ |-+.+|..-|.
T Consensus 241 ~Ll~n~~-gY~i~adv~~~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d--El~~Ey~kly~ 307 (316)
T PHA03328 241 RLLTACP-GYRIIAHVWQTTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG--ELLLEYKRLYA 307 (316)
T ss_pred HHHHhCC-CCeEEEEEecceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--HHHHHHHHHHH
Confidence 4677775 8999999888888888876555556778899999999999999999986 34445554444
No 37
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=81.02 E-value=4.3 Score=33.69 Aligned_cols=71 Identities=17% Similarity=0.142 Sum_probs=47.4
Q ss_pred HHHHHhccCCCcccccch---------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHH
Q 032773 4 SLRMLRILYRNVSLSSSA---------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 4 v~Rik~~LP~n~kISKda---------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L~~y 74 (134)
+.|||+++-.+=-|-|=+ +.--|+.-|-..+-++++..+-|||+++|+..|.+.-.== +-|++.++.+
T Consensus 16 ~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~F---dFLk~~v~~v 92 (224)
T KOG1659|consen 16 PARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKF---DFLKEVVEKV 92 (224)
T ss_pred HHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchh---HHHHHHHHhc
Confidence 356776655443333322 5567888788889999999999999999999997754322 3344445444
Q ss_pred HHH
Q 032773 75 REM 77 (134)
Q Consensus 75 re~ 77 (134)
...
T Consensus 93 pd~ 95 (224)
T KOG1659|consen 93 PDR 95 (224)
T ss_pred CCC
Confidence 433
No 38
>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=80.37 E-value=2.2 Score=25.72 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=21.6
Q ss_pred hhHHhHhcCCCccChhHHHHHHhhcC
Q 032773 34 ASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 34 And~c~~ekRKTI~~dDVL~AL~eLg 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 39
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=80.09 E-value=1.8 Score=38.13 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=28.4
Q ss_pred CCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhH
Q 032773 13 RNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDD 50 (134)
Q Consensus 13 ~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 568899997 99999999888888889999999998876
No 40
>PLN00157 histone H2A; Provisional
Probab=78.65 E-value=3.4 Score=31.67 Aligned_cols=54 Identities=19% Similarity=0.278 Sum_probs=35.3
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhHh----hHHhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRA----SDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSeA----nd~c~~ekRKTI~~dDVL~AL~e 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 4555555543 34677776 2233345777764 44557779999999999999854
No 41
>PF15510 CENP-W: Centromere kinetochore component W
Probab=76.34 E-value=4 Score=29.97 Aligned_cols=36 Identities=19% Similarity=0.078 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 57 (134)
-|-.||+-|+-||..-+=.+|-.||..|||+.|-+.
T Consensus 60 ncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv 95 (102)
T PF15510_consen 60 NCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAKV 95 (102)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 567899999999999999999999999999988553
No 42
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=75.52 E-value=6.8 Score=30.11 Aligned_cols=53 Identities=21% Similarity=0.324 Sum_probs=35.6
Q ss_pred HHHHhccCC---Ccccccch--hHHHHHHHHHhHhhHHh----HhcCCCccChhHHHHHHhh
Q 032773 5 LRMLRILYR---NVSLSSSA--SLPASFSFLSCRASDKC----QKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 5 ~Rik~~LP~---n~kISKda--caseFI~ylTSeAnd~c----~~ekRKTI~~dDVL~AL~e 57 (134)
.||.+.|-+ -.+|+.++ -.+--+.||+++.-|.+ ...++.-|+|.||..|+..
T Consensus 31 gri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 31 GRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred HHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 344444433 35677776 23333558888887776 4568888999999999863
No 43
>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=75.11 E-value=6.4 Score=26.60 Aligned_cols=34 Identities=18% Similarity=0.154 Sum_probs=26.9
Q ss_pred HHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 23 LPASFSFLSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 23 aseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~ 56 (134)
+.--|..|..+|....+..+|++++++||=.||+
T Consensus 33 veyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 33 VEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 3455667889999999999999999999998885
No 44
>PLN00156 histone H2AX; Provisional
Probab=74.04 E-value=6.5 Score=30.43 Aligned_cols=54 Identities=19% Similarity=0.270 Sum_probs=35.5
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhHhhH----HhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASD----KCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSeAnd----~c~~ekRKTI~~dDVL~AL~e 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 34677776 333334577777554 456678999999999999853
No 45
>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=72.46 E-value=7.7 Score=27.75 Aligned_cols=56 Identities=14% Similarity=0.082 Sum_probs=36.8
Q ss_pred hHHHHHhc------cCCCcccccchhHHHHHHHHHhHhhHHhHhcCC-CccChhHHHHHHhhc
Q 032773 3 RSLRMLRI------LYRNVSLSSSASLPASFSFLSCRASDKCQKEKR-KTINGDDLLWAMATL 58 (134)
Q Consensus 3 nv~Rik~~------LP~n~kISKdacaseFI~ylTSeAnd~c~~ekR-KTI~~dDVL~AL~eL 58 (134)
+|.|+... +|+++.|.--..+.+||-=|-.+|.+++...+. ..|.|+|+-+|...|
T Consensus 28 ~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 28 AIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 45565443 233333333448999999999999999986543 379999999997764
No 46
>PTZ00017 histone H2A; Provisional
Probab=70.98 E-value=9 Score=29.43 Aligned_cols=54 Identities=20% Similarity=0.322 Sum_probs=33.5
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhHh----hHHhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRA----SDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSeA----nd~c~~ekRKTI~~dDVL~AL~e 57 (134)
|.||.+-|-. ..+|+..+ ..+--+-||++|- -..|.+.+++-|+|.||..|+..
T Consensus 30 VgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 30 VGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred hHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 3455444432 24676666 2222244677664 44567778999999999999853
No 47
>PLN00153 histone H2A; Provisional
Probab=65.64 E-value=12 Score=28.56 Aligned_cols=54 Identities=19% Similarity=0.293 Sum_probs=34.1
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhHhhH----HhHhcCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASD----KCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSeAnd----~c~~ekRKTI~~dDVL~AL~e 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 34677666 223334577776544 456678999999999999843
No 48
>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=63.57 E-value=9.2 Score=24.14 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=21.0
Q ss_pred ccChhHHHHHHhhcCCCcchHHHHH
Q 032773 45 TINGDDLLWAMATLGFEDYIDPLKA 69 (134)
Q Consensus 45 TI~~dDVL~AL~eLgF~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 3478999999999999999987664
No 49
>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=63.53 E-value=2.4 Score=35.67 Aligned_cols=64 Identities=17% Similarity=0.257 Sum_probs=45.7
Q ss_pred HHHhccCCCcccccchhHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 032773 6 RMLRILYRNVSLSSSASLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREM 77 (134)
Q Consensus 6 Rik~~LP~n~kISKdacaseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L~~yre~ 77 (134)
+|..++ ++.+|+-|-.-.-||.-++..+.+. ..=+|+++||-.++.+|+|++ +|+...++|...
T Consensus 191 ~ll~n~-~~Y~i~~dv~~~~fvL~v~~~~~~~----~~~~I~~~~I~~ki~dld~~d---El~~ey~k~~~~ 254 (258)
T PF02718_consen 191 QLLDNC-PGYKISADVWQGTFVLVVRPDREEQ----TSPKIDADDIYCKICDLDFPD---ELKEEYEKYYAL 254 (258)
T ss_pred HHHHhC-CCCeEEEEEecCEEEEEEEeCCCcC----CCcccCHHHHHHHHHcCCCCh---HHHHHHHHHHHH
Confidence 456677 8888888876666666665553322 377889999999999999985 555555555543
No 50
>PTZ00252 histone H2A; Provisional
Probab=63.44 E-value=18 Score=27.92 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=35.1
Q ss_pred HHHHHhccCC---Ccccccch--hHHHHHHHHHhHhhHHhHh------cCCCccChhHHHHHHhh
Q 032773 4 SLRMLRILYR---NVSLSSSA--SLPASFSFLSCRASDKCQK------EKRKTINGDDLLWAMAT 57 (134)
Q Consensus 4 v~Rik~~LP~---n~kISKda--caseFI~ylTSeAnd~c~~------ekRKTI~~dDVL~AL~e 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 3455444433 23566655 3333466899988777744 46788999999999853
No 51
>PTZ00018 histone H3; Provisional
Probab=62.64 E-value=16 Score=28.06 Aligned_cols=49 Identities=22% Similarity=0.099 Sum_probs=39.4
Q ss_pred HHhccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHH
Q 032773 7 MLRILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 7 ik~~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL 55 (134)
|-...-.+.+++.++ ++-.|+--+-..++-.+.-.||-||.+.|+.-|.
T Consensus 75 I~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 75 IAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred HHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 333344678888887 7778888888899999999999999999996664
No 52
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=61.77 E-value=7.4 Score=32.94 Aligned_cols=48 Identities=13% Similarity=0.116 Sum_probs=41.1
Q ss_pred ccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 10 ILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 10 ~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 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 344566666665 889999999999999999999999999999998875
No 53
>PLN00161 histone H3; Provisional
Probab=59.87 E-value=24 Score=27.18 Aligned_cols=45 Identities=20% Similarity=0.078 Sum_probs=37.5
Q ss_pred cCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHH
Q 032773 11 LYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 11 LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 35678898887 7777888788899989999999999999996664
No 54
>PLN00121 histone H3; Provisional
Probab=59.77 E-value=20 Score=27.63 Aligned_cols=46 Identities=24% Similarity=0.086 Sum_probs=38.0
Q ss_pred ccCCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHH
Q 032773 10 ILYRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 10 ~LP~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL 55 (134)
..-.+.+++.++ ++-.|+--+-..++-.+.-.||-||.+.|+.-++
T Consensus 78 ~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 78 DFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred HhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 334578888887 7777888888899999999999999999996664
No 55
>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=59.50 E-value=25 Score=27.20 Aligned_cols=50 Identities=18% Similarity=0.236 Sum_probs=38.9
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC-cchHHHHHHHHHHHHHh
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYREME 78 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~-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 77777777766664 4459999999999999998 77888877777777643
No 56
>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=59.13 E-value=9.2 Score=28.38 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=26.9
Q ss_pred hhHHHHHHhhcCCCcchHHHHHHHHHHHHHh
Q 032773 48 GDDLLWAMATLGFEDYIDPLKAYLMRYREME 78 (134)
Q Consensus 48 ~dDVL~AL~eLgF~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 4567888999999999999999999998643
No 57
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=58.95 E-value=8.7 Score=36.09 Aligned_cols=35 Identities=26% Similarity=0.230 Sum_probs=28.7
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 57 (134)
|-..-...| .+|+++|..++++-|+++||.||++.
T Consensus 364 ~~rdl~~lv-~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 364 RLRDLGNLV-REAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CHHHHHHHH-HHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 434444444 59999999999999999999999987
No 58
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=58.65 E-value=22 Score=28.97 Aligned_cols=51 Identities=12% Similarity=0.021 Sum_probs=43.2
Q ss_pred ccCCCcccccchhHHHHHHHHHhHhhHHhHhcCC-CccChhHHHHHHhhcCC
Q 032773 10 ILYRNVSLSSSASLPASFSFLSCRASDKCQKEKR-KTINGDDLLWAMATLGF 60 (134)
Q Consensus 10 ~LP~n~kISKdacaseFI~ylTSeAnd~c~~ekR-KTI~~dDVL~AL~eLgF 60 (134)
.+.+|+.|....-+.+||-=|--+|-++|..-+. -.|-|.||=+|...|.-
T Consensus 129 ~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~ 180 (195)
T KOG3219|consen 129 SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKL 180 (195)
T ss_pred ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHh
Confidence 5688999999999999999999999999987554 45899999888777654
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=58.51 E-value=7.9 Score=23.59 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.6
Q ss_pred ChhHHHHHHhhcCCCcchHHHHHH
Q 032773 47 NGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 47 ~~dDVL~AL~eLgF~dyv~~Lk~~ 70 (134)
++++|..-|+.+|+++|++.+++.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999998887776543
No 60
>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=58.00 E-value=7.6 Score=23.96 Aligned_cols=15 Identities=33% Similarity=0.530 Sum_probs=12.3
Q ss_pred hhHHHHHHhhcCCCc
Q 032773 48 GDDLLWAMATLGFED 62 (134)
Q Consensus 48 ~dDVL~AL~eLgF~d 62 (134)
-+|++.||..|||..
T Consensus 3 ~~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 3 LEDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHHTTS-H
T ss_pred HHHHHHHHHHcCCCH
Confidence 379999999999983
No 61
>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=57.40 E-value=18 Score=27.38 Aligned_cols=54 Identities=20% Similarity=0.228 Sum_probs=26.8
Q ss_pred hHHHHHH-H---HHhHhhHHhHhcCCCccChhHHHHHHh-hcCCCcchHHHHHHHHHHH
Q 032773 22 SLPASFS-F---LSCRASDKCQKEKRKTINGDDLLWAMA-TLGFEDYIDPLKAYLMRYR 75 (134)
Q Consensus 22 caseFI~-y---lTSeAnd~c~~ekRKTI~~dDVL~AL~-eLgF~dyv~~Lk~~L~~yr 75 (134)
+--||.. | |-..|..++.-.+|++|+.+||--|.+ .+++.-..++-+++|...=
T Consensus 37 qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~llelA 95 (129)
T PF02291_consen 37 QLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLLELA 95 (129)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHHHHH
Confidence 5555655 3 346788899999999999999999998 5678777778778877544
No 62
>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=56.14 E-value=21 Score=24.41 Aligned_cols=44 Identities=11% Similarity=0.131 Sum_probs=27.7
Q ss_pred CCCcccccch--hHHHHHHHHHhHh----hHHhHhcCCCc-cChhHHHHHH
Q 032773 12 YRNVSLSSSA--SLPASFSFLSCRA----SDKCQKEKRKT-INGDDLLWAM 55 (134)
Q Consensus 12 P~n~kISKda--caseFI~ylTSeA----nd~c~~ekRKT-I~~dDVL~AL 55 (134)
.++++|++|+ -+.+++.....|| .+.++.++... |..+|+=+-+
T Consensus 15 ~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 15 DDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp STT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 4889999998 5666666555554 55556677777 9999986654
No 63
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=55.87 E-value=17 Score=29.28 Aligned_cols=40 Identities=23% Similarity=0.223 Sum_probs=34.0
Q ss_pred hHHHHHHHHHhHhhHHhHh--------------cCCCccChhHHHHHHhhcCCC
Q 032773 22 SLPASFSFLSCRASDKCQK--------------EKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~--------------ekRKTI~~dDVL~AL~eLgF~ 61 (134)
++-.||+=|...|-+.|+- ++|-|++-+|+-.||+|.|..
T Consensus 115 aAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 115 AAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred HHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcc
Confidence 7788999999999888853 456789999999999999864
No 64
>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=55.38 E-value=14 Score=23.14 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.3
Q ss_pred ChhHHHHHHhhcCCCcchHHHH
Q 032773 47 NGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 47 ~~dDVL~AL~eLgF~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 6789999999999999998763
No 65
>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=52.26 E-value=11 Score=23.08 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=20.1
Q ss_pred cChhHHHHHHhhcCCCcchHHHHHH
Q 032773 46 INGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 46 I~~dDVL~AL~eLgF~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 4678999999999999887766554
No 66
>PLN00160 histone H3; Provisional
Probab=51.00 E-value=41 Score=24.48 Aligned_cols=44 Identities=23% Similarity=0.046 Sum_probs=35.5
Q ss_pred CCCcccccch------hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHH
Q 032773 12 YRNVSLSSSA------SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAM 55 (134)
Q Consensus 12 P~n~kISKda------caseFI~ylTSeAnd~c~~ekRKTI~~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 4568888887 6666777777888888899999999999996654
No 67
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=50.69 E-value=25 Score=26.27 Aligned_cols=38 Identities=13% Similarity=0.079 Sum_probs=32.3
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcC
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLg 59 (134)
+.--||.-|-..+...++..+-|-|+++++..|.+.-+
T Consensus 53 alE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sde 90 (113)
T COG5247 53 ALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDE 90 (113)
T ss_pred HHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhH
Confidence 56678888888899999999999999999999976543
No 68
>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=50.45 E-value=11 Score=24.53 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=25.1
Q ss_pred CCCccChhHHHHHHhhcCCCcchHHHHHHH
Q 032773 42 KRKTINGDDLLWAMATLGFEDYIDPLKAYL 71 (134)
Q Consensus 42 kRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L 71 (134)
....-+.++++.||+++|..+-++.++.+|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 345678899999999999999999988765
No 69
>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=50.04 E-value=27 Score=27.32 Aligned_cols=37 Identities=22% Similarity=0.313 Sum_probs=30.4
Q ss_pred HHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 25 ASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 25 eFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 61 (134)
-.|..+...|-..+-..+.++|+.++|-.++.++.|+
T Consensus 233 ~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 233 RLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred cHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 3577777777777777888999999999999998764
No 70
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=49.95 E-value=21 Score=32.48 Aligned_cols=33 Identities=21% Similarity=0.100 Sum_probs=26.2
Q ss_pred HHHHHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 26 FI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
.|.=|-.+|+.+|+.+++++|+++||..|+++-
T Consensus 474 ~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 474 WLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 445566999999999999999999999999864
No 71
>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=43.37 E-value=18 Score=22.36 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=14.5
Q ss_pred cChhHHHHHHhhcCCC
Q 032773 46 INGDDLLWAMATLGFE 61 (134)
Q Consensus 46 I~~dDVL~AL~eLgF~ 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 7789999999999995
No 72
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=43.16 E-value=49 Score=22.58 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=26.8
Q ss_pred hhHHHHHHhhcCC------CcchHHHHHHHHHHHHHhc
Q 032773 48 GDDLLWAMATLGF------EDYIDPLKAYLMRYREMEG 79 (134)
Q Consensus 48 ~dDVL~AL~eLgF------~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 7888999999999987653
No 73
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=42.07 E-value=30 Score=28.82 Aligned_cols=34 Identities=18% Similarity=0.162 Sum_probs=26.6
Q ss_pred HHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcc
Q 032773 30 LSCRASDKCQKEKRKTINGDDLLWAMATLGFEDY 63 (134)
Q Consensus 30 lTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dy 63 (134)
+-..|.+.|..+++.+|+.+||-+|++++....+
T Consensus 254 ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 254 LLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 3456667777788999999999999999854433
No 74
>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=42.01 E-value=36 Score=25.75 Aligned_cols=38 Identities=26% Similarity=0.180 Sum_probs=31.6
Q ss_pred CccChhHHHHHHhhcCCC-----------cchHHHHHHHHHHHHHhccc
Q 032773 44 KTINGDDLLWAMATLGFE-----------DYIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 44 KTI~~dDVL~AL~eLgF~-----------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 68888888888888777666
No 75
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=40.23 E-value=29 Score=24.50 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=23.1
Q ss_pred HHhHhhHHhHhcCCCccChhHHHHHHh
Q 032773 30 LSCRASDKCQKEKRKTINGDDLLWAMA 56 (134)
Q Consensus 30 lTSeAnd~c~~ekRKTI~~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 335678899999999999999999974
No 76
>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=39.50 E-value=40 Score=18.37 Aligned_cols=24 Identities=21% Similarity=0.259 Sum_probs=18.8
Q ss_pred HHhHhcCCCccChhHHHHHHh-hcC
Q 032773 36 DKCQKEKRKTINGDDLLWAMA-TLG 59 (134)
Q Consensus 36 d~c~~ekRKTI~~dDVL~AL~-eLg 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 445567888999999999999 576
No 77
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=39.39 E-value=22 Score=24.37 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.5
Q ss_pred ccChhHHHHHHhhcCCCc
Q 032773 45 TINGDDLLWAMATLGFED 62 (134)
Q Consensus 45 TI~~dDVL~AL~eLgF~d 62 (134)
.+++.+|+.+|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 368899999999999963
No 78
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.27 E-value=12 Score=30.04 Aligned_cols=30 Identities=23% Similarity=0.403 Sum_probs=26.2
Q ss_pred hHHhHhcCCCccChhHHHHHHhhcCCCcch
Q 032773 35 SDKCQKEKRKTINGDDLLWAMATLGFEDYI 64 (134)
Q Consensus 35 nd~c~~ekRKTI~~dDVL~AL~eLgF~dyv 64 (134)
..+|..+..++|+.|.++.-.++|||+-|.
T Consensus 133 gnKCDmd~eRvis~e~g~~l~~~LGfefFE 162 (193)
T KOG0093|consen 133 GNKCDMDSERVISHERGRQLADQLGFEFFE 162 (193)
T ss_pred ecccCCccceeeeHHHHHHHHHHhChHHhh
Confidence 467889999999999999999999996443
No 79
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=36.06 E-value=48 Score=22.39 Aligned_cols=38 Identities=24% Similarity=0.382 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhHhhHH---------hHhcCCCccChhHHHHHHhhcCCC
Q 032773 22 SLPASFSFLSCRASDK---------CQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 22 caseFI~ylTSeAnd~---------c~~ekRKTI~~dDVL~AL~eLgF~ 61 (134)
-+.+||.|..+.+... |.+.+ ..+.++|..=|-.-||.
T Consensus 20 Gv~~Fi~~A~~~~~~~~~i~CPC~~C~N~~--~~~~~~V~~HL~~~Gf~ 66 (77)
T PF13963_consen 20 GVEEFIDFAFSNPSNDNMIRCPCRKCKNEK--RQSRDDVHEHLVCRGFM 66 (77)
T ss_pred HHHHHHHHHHhcccCCCceECCchhhccCc--cCCHHHHHHHHHHhCCC
Confidence 7899999999888765 44444 48999999999999996
No 80
>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=35.88 E-value=37 Score=27.93 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=28.7
Q ss_pred HHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHH
Q 032773 30 LSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 30 lTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~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 334566777788889999999999999986555444443
No 81
>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=33.92 E-value=37 Score=18.41 Aligned_cols=23 Identities=22% Similarity=0.127 Sum_probs=18.7
Q ss_pred HHHHHhhcCCCcchHHHHHHHHH
Q 032773 51 LLWAMATLGFEDYIDPLKAYLMR 73 (134)
Q Consensus 51 VL~AL~eLgF~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 46889999999999999998863
No 82
>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=33.45 E-value=1.2e+02 Score=18.60 Aligned_cols=44 Identities=23% Similarity=0.281 Sum_probs=33.2
Q ss_pred hhHHhHhcCCCccChhHHHHHHhhcCCCcchHHHHHHHHH-HHHH
Q 032773 34 ASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR-YREM 77 (134)
Q Consensus 34 And~c~~ekRKTI~~dDVL~AL~eLgF~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 3455566788899999999999999988776777776665 4443
No 83
>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=33.32 E-value=61 Score=24.45 Aligned_cols=38 Identities=26% Similarity=0.249 Sum_probs=31.6
Q ss_pred CccChhHHHHHHhhcCCCc------------chHHHHHHHHHHHHHhccc
Q 032773 44 KTINGDDLLWAMATLGFED------------YIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 44 KTI~~dDVL~AL~eLgF~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 4788999999999999887 8888888888877766555
No 84
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.55 E-value=89 Score=21.16 Aligned_cols=29 Identities=14% Similarity=0.154 Sum_probs=22.5
Q ss_pred HhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 33 RASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 33 eAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 61 (134)
++-..+..++...|+.++|..+|..+|+.
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 33445556788899999999999998875
No 85
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=31.22 E-value=63 Score=27.84 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=26.9
Q ss_pred HHHHHhHhhHHhHhcCCCccChhHHHHHHhhcC
Q 032773 27 FSFLSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 27 I~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLg 59 (134)
|.-|..+|...|.+++++.|+.+|+..|++..-
T Consensus 341 l~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 341 LKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 445677888888889999999999999987653
No 86
>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=31.01 E-value=49 Score=23.74 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=26.6
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 68999999999999999999999887 887
No 87
>smart00445 LINK Link (Hyaluronan-binding).
Probab=29.97 E-value=56 Score=23.55 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=26.8
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 68999999999999999999999987 887
No 88
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=29.88 E-value=16 Score=26.01 Aligned_cols=29 Identities=14% Similarity=0.367 Sum_probs=21.5
Q ss_pred hcCCCcchHHHHHHHHHHHHHhcccCCCC
Q 032773 57 TLGFEDYIDPLKAYLMRYREMEGDTKGSA 85 (134)
Q Consensus 57 eLgF~dyv~~Lk~~L~~yre~~~~Kk~~~ 85 (134)
-+||+|||.-+-+-..+|......|+-.|
T Consensus 34 L~GFDd~VNmvLeDvtEye~~~egr~~tk 62 (84)
T KOG1775|consen 34 LVGFDDFVNMVLEDVTEYEITPEGRRMTK 62 (84)
T ss_pred EechHHHHHHHHHhhhheeeCCCcceeee
Confidence 36999999998888888876655555443
No 89
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=29.71 E-value=72 Score=26.87 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=27.2
Q ss_pred HHHHHHhHhhHHhHhcCCCccChhHHHHHHhh
Q 032773 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMAT 57 (134)
Q Consensus 26 FI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~e 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 34566778888888999999999999999875
No 90
>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=28.34 E-value=69 Score=29.64 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=24.2
Q ss_pred HHhHhhHHhHhcCCCccChhHHHHHHhhcC
Q 032773 30 LSCRASDKCQKEKRKTINGDDLLWAMATLG 59 (134)
Q Consensus 30 lTSeAnd~c~~ekRKTI~~dDVL~AL~eLg 59 (134)
|-.+|.++|..+++.+|+.+||.+|++.-.
T Consensus 363 llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 363 LVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred HHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 335567788888999999999999988654
No 91
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=28.26 E-value=74 Score=28.43 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=27.4
Q ss_pred HHHHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 27 FSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 27 I~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 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 55677889999999999999999999998763
No 92
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=27.95 E-value=40 Score=30.80 Aligned_cols=76 Identities=18% Similarity=0.253 Sum_probs=39.6
Q ss_pred cCCCc-----cChhHHHHHHhhcCCC---------------cchHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCccCCC
Q 032773 41 EKRKT-----INGDDLLWAMATLGFE---------------DYIDPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGAL 100 (134)
Q Consensus 41 ekRKT-----I~~dDVL~AL~eLgF~---------------dyv~~Lk~~L~~yre~~~~Kk~~~k~~~~~~~~~~~~~~ 100 (134)
+++.| +-+-|+|.||+.++-+ -||+|-++.-+ |.+++|++..+..+-...+.++ ++
T Consensus 389 d~KHTIFGrvVGGldtL~amEnve~d~~DrP~e~I~i~~~~VFVdPfeEa~~---e~~kEr~e~~k~~~e~~~k~~s-~~ 464 (518)
T KOG0883|consen 389 DNKHTIFGRVVGGLDTLTAMENVETDEKDRPKEEIKIEDAIVFVDPFEEADK---EREKERAERLKEEEEDNLKRTS-SQ 464 (518)
T ss_pred cccceeeeeeeccHHHHHHHhcCCCCCCCCcccceEEeeeEEeeCcHHHHHH---HHHHHHHHHhhccchhhhhhhc-cC
Confidence 45656 4678999999999876 36666655433 2223333222222212222222 23
Q ss_pred CCC---cchhhccCCcccCChhh
Q 032773 101 PGQ---NAQYALQGPLNYANPHV 120 (134)
Q Consensus 101 ~~~---~~~~~~~g~~~~~~~~~ 120 (134)
|.+ .++...+|..-|+.++.
T Consensus 465 ~~~~s~~~~~~~~gVGKYlk~~~ 487 (518)
T KOG0883|consen 465 PKSGSTTPHALGAGVGKYLKKAA 487 (518)
T ss_pred ccccCCCcccccccHHHHHHHHh
Confidence 333 23344566677776654
No 93
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=27.26 E-value=61 Score=28.08 Aligned_cols=39 Identities=15% Similarity=0.154 Sum_probs=31.6
Q ss_pred HHHhHhhHHhHhcCCCccChhHHHHHHhhcCCCcchHHH
Q 032773 29 FLSCRASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPL 67 (134)
Q Consensus 29 ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~dyv~~L 67 (134)
-+-..|.++|+.+++.+|+.+||-.|-++.+.+-+.+.+
T Consensus 236 dilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~ 274 (366)
T COG1474 236 DILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVL 274 (366)
T ss_pred HHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHH
Confidence 345788999999999999999999997777766555443
No 94
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.08 E-value=30 Score=25.01 Aligned_cols=18 Identities=22% Similarity=0.606 Sum_probs=14.8
Q ss_pred ChhHHHHHHhhcCCC-cch
Q 032773 47 NGDDLLWAMATLGFE-DYI 64 (134)
Q Consensus 47 ~~dDVL~AL~eLgF~-dyv 64 (134)
+++|||.||..||.. +|+
T Consensus 38 T~QDvikAlpglgi~l~Fv 56 (95)
T COG4519 38 TAQDVIKALPGLGIVLEFV 56 (95)
T ss_pred HHHHHHHhCcCCCeEEEee
Confidence 569999999999876 554
No 95
>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=25.81 E-value=81 Score=22.86 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=26.5
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 7899999999999999999999988 8887
No 96
>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=25.55 E-value=49 Score=24.79 Aligned_cols=19 Identities=16% Similarity=0.407 Sum_probs=14.6
Q ss_pred ChhHHHHHHhhcCCCcchH
Q 032773 47 NGDDLLWAMATLGFEDYID 65 (134)
Q Consensus 47 ~~dDVL~AL~eLgF~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 7899999999999999985
No 97
>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=25.32 E-value=46 Score=21.80 Aligned_cols=17 Identities=24% Similarity=0.608 Sum_probs=12.4
Q ss_pred ccChhHHHHHHhhcCCC
Q 032773 45 TINGDDLLWAMATLGFE 61 (134)
Q Consensus 45 TI~~dDVL~AL~eLgF~ 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 68999999999999997
No 98
>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=25.19 E-value=87 Score=22.90 Aligned_cols=30 Identities=17% Similarity=0.184 Sum_probs=28.2
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 689999999999999999999999999997
No 99
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=24.99 E-value=95 Score=27.52 Aligned_cols=52 Identities=17% Similarity=0.051 Sum_probs=41.6
Q ss_pred hHHHHHHHHHhHhhHHhHhcCCCccChhHHHHHHhhcCCC---cchHHHHHHHHH
Q 032773 22 SLPASFSFLSCRASDKCQKEKRKTINGDDLLWAMATLGFE---DYIDPLKAYLMR 73 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eLgF~---dyv~~Lk~~L~~ 73 (134)
-...||.-|.-.|+.++.--+|---|..||+.||++|+-. .++-....+|.+
T Consensus 58 ~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~~~~~~s~~L~d 112 (353)
T KOG2389|consen 58 VLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGASGSSGESHCLLD 112 (353)
T ss_pred HHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccccccchhHHHhh
Confidence 6678999999999999999999999999999999999654 233334455554
No 100
>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=24.40 E-value=94 Score=22.44 Aligned_cols=29 Identities=28% Similarity=0.350 Sum_probs=26.5
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhcCCC
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATLGFE 61 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eLgF~ 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 6899999999999999999999988 5887
No 101
>smart00567 EZ_HEAT E-Z type HEAT repeats. Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role.
Probab=24.22 E-value=68 Score=17.21 Aligned_cols=22 Identities=27% Similarity=0.321 Sum_probs=18.3
Q ss_pred HHHHHhhcCCCcchHHHHHHHH
Q 032773 51 LLWAMATLGFEDYIDPLKAYLM 72 (134)
Q Consensus 51 VL~AL~eLgF~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 4678888999999999888774
No 102
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=23.89 E-value=1e+02 Score=26.97 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=27.7
Q ss_pred HHHHHHhHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 26 SFSFLSCRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 26 FI~ylTSeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
=|..|..+|.-.|.+++|..|+.+|+..|++..
T Consensus 354 DI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 354 DIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 366678888888999999999999999997763
No 103
>PF09077 Phage-MuB_C: Mu B transposition protein, C terminal ; InterPro: IPR009084 Bacteriophage Mu can integrate into the host bacterial genome and replicate via transposition. Mu requires the activity of four proteins for DNA transposition. Two of these proteins are the phage-encoded A and B transposition proteins, while the other two are host-specified accessory factors HU and IHF. These four proteins can form nucleoprotein complexes (transposomes), which enable strand transfer. The stable protein-DNA intermediate is subsequently disassembled prior to DNA replication by host proteins. The Mu B transposition protein is an ATP-dependent, DNA-binding protein required for target capture and immunity, as well as for activating transpososome function []. The C-terminal domain of the B transposition protein is believed to be involved in both DNA-binding and protein-protein contacts with the Mu A transposition protein. The structure of the C-terminal domain consists of four helices in an irregular array [].; GO: 0003677 DNA binding, 0006313 transposition, DNA-mediated; PDB: 1F6V_A.
Probab=23.85 E-value=52 Score=22.99 Aligned_cols=26 Identities=23% Similarity=0.107 Sum_probs=17.7
Q ss_pred hHhhHHhHhcCCCccChhHHHHHHhhc
Q 032773 32 CRASDKCQKEKRKTINGDDLLWAMATL 58 (134)
Q Consensus 32 SeAnd~c~~ekRKTI~~dDVL~AL~eL 58 (134)
--|.-.|..++.. |+.+||..|.++|
T Consensus 53 rlA~m~A~g~g~~-i~~~~i~~A~~~l 78 (78)
T PF09077_consen 53 RLAAMFAKGEGEA-ITADHIRAAWKEL 78 (78)
T ss_dssp GGGT-TT-TTS---SSHHHHHHHHTSS
T ss_pred HHHHHHhccCCCc-CCHHHHHHHHHhC
Confidence 3466677777766 9999999999876
No 104
>PTZ00184 calmodulin; Provisional
Probab=23.52 E-value=2.5e+02 Score=19.20 Aligned_cols=32 Identities=16% Similarity=0.220 Sum_probs=23.4
Q ss_pred hcCCCccChhHHHHHHhhcCCCcchHHHHHHH
Q 032773 40 KEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 71 (134)
Q Consensus 40 ~ekRKTI~~dDVL~AL~eLgF~dyv~~Lk~~L 71 (134)
.+++-.|+.+|+..+|..+|+.--.+.++..+
T Consensus 95 ~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~ 126 (149)
T PTZ00184 95 RDGNGFISAAELRHVMTNLGEKLTDEEVDEMI 126 (149)
T ss_pred CCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 35777899999999999998764444455444
No 105
>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=23.51 E-value=1.5e+02 Score=18.35 Aligned_cols=26 Identities=15% Similarity=-0.043 Sum_probs=19.7
Q ss_pred HHHhHhhHHhHhcCCCccChhHHHHH
Q 032773 29 FLSCRASDKCQKEKRKTINGDDLLWA 54 (134)
Q Consensus 29 ylTSeAnd~c~~ekRKTI~~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 56667778889999999999998765
No 106
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=23.19 E-value=1.4e+02 Score=19.63 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=22.3
Q ss_pred hhHHhHhcCCC-ccChhHHHHHHhhcCCC
Q 032773 34 ASDKCQKEKRK-TINGDDLLWAMATLGFE 61 (134)
Q Consensus 34 And~c~~ekRK-TI~~dDVL~AL~eLgF~ 61 (134)
-.|+|..-+=+ |=++.+-|.+|++.||=
T Consensus 28 ~rEIa~~~g~~S~~tv~~~L~~Le~kG~I 56 (65)
T PF01726_consen 28 VREIAEALGLKSTSTVQRHLKALERKGYI 56 (65)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHhCCCChHHHHHHHHHHHHCcCc
Confidence 46788776654 88899999999999873
No 107
>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=22.22 E-value=61 Score=22.35 Aligned_cols=32 Identities=22% Similarity=0.250 Sum_probs=24.2
Q ss_pred HhcCCCccChhHHHHHHhhcCCCcchHHHHHH
Q 032773 39 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAY 70 (134)
Q Consensus 39 ~~ekRKTI~~dDVL~AL~eLgF~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 33333334578899999999999999988764
No 108
>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=22.19 E-value=82 Score=21.83 Aligned_cols=31 Identities=23% Similarity=0.025 Sum_probs=24.4
Q ss_pred hHhcCCCccChhHHHHHHhhcCCCcchHHHH
Q 032773 38 CQKEKRKTINGDDLLWAMATLGFEDYIDPLK 68 (134)
Q Consensus 38 c~~ekRKTI~~dDVL~AL~eLgF~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 3455555567899999999999999988763
No 109
>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=22.06 E-value=61 Score=22.53 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=14.5
Q ss_pred ChhHHHHHHhhcCCCcc
Q 032773 47 NGDDLLWAMATLGFEDY 63 (134)
Q Consensus 47 ~~dDVL~AL~eLgF~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 46899999999999865
No 110
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=22.01 E-value=1.9e+02 Score=23.08 Aligned_cols=40 Identities=20% Similarity=0.301 Sum_probs=29.5
Q ss_pred CccChhHHHHHHhhcCCC---------------cchHHHHHHHHHHHHHhcccCC
Q 032773 44 KTINGDDLLWAMATLGFE---------------DYIDPLKAYLMRYREMEGDTKG 83 (134)
Q Consensus 44 KTI~~dDVL~AL~eLgF~---------------dyv~~Lk~~L~~yre~~~~Kk~ 83 (134)
++|++|=+..+|+-+||. +.++.++.--+.|.+....-++
T Consensus 84 ~~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~~~Lse~~~e~~~~~~~ 138 (190)
T PF09840_consen 84 YPVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELAERLSEIYKELRFQPLG 138 (190)
T ss_pred CCCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHHHHHHHHHHHHhcCccC
Confidence 999999999999999985 4455555555667766655443
No 111
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=21.94 E-value=68 Score=23.21 Aligned_cols=18 Identities=17% Similarity=0.226 Sum_probs=15.8
Q ss_pred cChhHHHHHHhhcCCCcc
Q 032773 46 INGDDLLWAMATLGFEDY 63 (134)
Q Consensus 46 I~~dDVL~AL~eLgF~dy 63 (134)
.+.++|..|+++|||+--
T Consensus 32 P~~~ei~~a~~~LGl~~~ 49 (93)
T COG1400 32 PSLEEIAEALRELGLKPK 49 (93)
T ss_pred CCHHHHHHHHHHcCCCee
Confidence 678999999999999853
No 112
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.94 E-value=1.2e+02 Score=18.86 Aligned_cols=39 Identities=26% Similarity=0.185 Sum_probs=28.5
Q ss_pred CCccChhHHH--HHHhhcCCCcchHHHHHHHHHHHHHhccc
Q 032773 43 RKTINGDDLL--WAMATLGFEDYIDPLKAYLMRYREMEGDT 81 (134)
Q Consensus 43 RKTI~~dDVL--~AL~eLgF~dyv~~Lk~~L~~yre~~~~K 81 (134)
|-||+-||-| +|++-.|+..--+.+...|..|-...+.+
T Consensus 2 rTti~iDd~Ll~eA~~l~g~~tk~~~V~~ALr~~i~r~~~~ 42 (47)
T PF09957_consen 2 RTTIDIDDELLAEAMRLTGTKTKKEAVNEALRELIRRRKRR 42 (47)
T ss_pred cceEeeCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence 5566666633 67778899998899998888887655443
No 113
>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=21.67 E-value=1.8e+02 Score=23.69 Aligned_cols=59 Identities=7% Similarity=-0.067 Sum_probs=37.7
Q ss_pred hHHHHHHHHHhHhhHHhH-hcCCCccC----------hhHHHHHHhhcCCCcchHHHHHHHHHHHHHhcc
Q 032773 22 SLPASFSFLSCRASDKCQ-KEKRKTIN----------GDDLLWAMATLGFEDYIDPLKAYLMRYREMEGD 80 (134)
Q Consensus 22 caseFI~ylTSeAnd~c~-~ekRKTI~----------~dDVL~AL~eLgF~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 899999998776443332 22211111 134444555677777888899999999887654
No 114
>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=20.92 E-value=1e+02 Score=20.88 Aligned_cols=23 Identities=43% Similarity=0.469 Sum_probs=17.7
Q ss_pred HHHHhhcCCCc--chHHHHHHHHHH
Q 032773 52 LWAMATLGFED--YIDPLKAYLMRY 74 (134)
Q Consensus 52 L~AL~eLgF~d--yv~~Lk~~L~~y 74 (134)
+.||..|||.+ -.+.|+.-|.-|
T Consensus 15 ~dam~~lG~~~~~v~~vl~~LL~lY 39 (65)
T PF10440_consen 15 LDAMRQLGFSKKQVRPVLKNLLKLY 39 (65)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 88999999984 356677777666
No 115
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=20.67 E-value=76 Score=20.25 Aligned_cols=17 Identities=24% Similarity=0.548 Sum_probs=15.3
Q ss_pred ccChhHHHHHHhhcCCC
Q 032773 45 TINGDDLLWAMATLGFE 61 (134)
Q Consensus 45 TI~~dDVL~AL~eLgF~ 61 (134)
.|+.+++...|+.|||+
T Consensus 18 ~i~~~ei~~~L~~lg~~ 34 (71)
T smart00874 18 DLSAEEIEEILKRLGFE 34 (71)
T ss_pred CCCHHHHHHHHHHCCCe
Confidence 58899999999999995
No 116
>PF14384 DUF4415: Domain of unknown function (DUF4415)
Probab=20.61 E-value=1.1e+02 Score=19.84 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.5
Q ss_pred hHHHHHHhhcCCCcchHHHHHHHHHH
Q 032773 49 DDLLWAMATLGFEDYIDPLKAYLMRY 74 (134)
Q Consensus 49 dDVL~AL~eLgF~dyv~~Lk~~L~~y 74 (134)
.|||.+++..|=+ |..-+...|.+|
T Consensus 37 ~dVl~~fka~G~g-yQtriN~~Lr~~ 61 (62)
T PF14384_consen 37 PDVLEWFKAQGKG-YQTRINEALRKY 61 (62)
T ss_pred HHHHHHHHHHChh-HHHHHHHHHHHh
Confidence 5899999998766 999999999876
Done!