Query 030670
Match_columns 173
No_of_seqs 149 out of 582
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 02:49:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030670hhsearch_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 4.3E-42 9.3E-47 275.6 13.9 119 1-120 1-120 (168)
2 KOG0871 Class 2 transcription 100.0 2.4E-28 5.1E-33 194.7 9.4 112 26-141 6-117 (156)
3 KOG0870 DNA polymerase epsilon 99.9 2.8E-25 6E-30 179.8 8.5 95 25-119 3-98 (172)
4 COG5150 Class 2 transcription 99.9 4.8E-22 1E-26 155.8 9.5 99 27-125 6-104 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 5E-19 1.1E-23 121.8 7.6 64 32-96 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 6.3E-17 1.4E-21 120.3 6.3 79 25-105 12-90 (91)
7 cd00076 H4 Histone H4, one of 99.2 6.4E-11 1.4E-15 87.1 8.3 71 32-104 13-83 (85)
8 PLN00035 histone H4; Provision 99.2 1.2E-10 2.7E-15 88.5 8.3 75 28-104 25-99 (103)
9 PTZ00015 histone H4; Provision 99.1 4.1E-10 9E-15 85.4 8.4 76 27-104 25-100 (102)
10 smart00803 TAF TATA box bindin 99.0 2.2E-09 4.7E-14 75.1 7.5 64 32-97 2-65 (65)
11 smart00417 H4 Histone H4. 98.9 2.3E-09 5.1E-14 77.1 6.3 63 31-95 12-74 (74)
12 COG5208 HAP5 CCAAT-binding fac 98.9 1.9E-09 4.1E-14 91.9 4.1 77 29-107 106-183 (286)
13 cd07981 TAF12 TATA Binding Pro 98.8 2E-08 4.3E-13 71.1 8.3 65 33-98 2-66 (72)
14 PF00125 Histone: Core histone 98.8 1.7E-08 3.7E-13 70.4 6.3 68 30-97 3-73 (75)
15 KOG1657 CCAAT-binding factor, 98.6 2.9E-08 6.2E-13 84.9 4.2 88 30-118 72-162 (236)
16 smart00428 H3 Histone H3. 98.6 1.1E-07 2.3E-12 72.6 6.8 72 26-97 23-99 (105)
17 smart00576 BTP Bromodomain tra 98.4 2.1E-06 4.4E-11 61.2 8.0 66 35-102 9-74 (77)
18 cd00074 H2A Histone 2A; H2A is 98.3 1.8E-06 3.9E-11 66.8 6.9 70 28-98 16-85 (115)
19 cd07979 TAF9 TATA Binding Prot 98.1 1.7E-05 3.6E-10 61.2 8.3 79 36-116 5-84 (117)
20 PLN00160 histone H3; Provision 98.1 8.4E-06 1.8E-10 61.5 6.4 71 26-96 15-89 (97)
21 PLN00121 histone H3; Provision 98.1 5.5E-06 1.2E-10 65.9 5.6 70 27-96 57-129 (136)
22 PLN00161 histone H3; Provision 98.1 1.2E-05 2.5E-10 64.0 7.2 71 26-96 49-123 (135)
23 PTZ00018 histone H3; Provision 98.0 8.5E-06 1.8E-10 64.8 5.4 70 27-96 57-129 (136)
24 KOG1659 Class 2 transcription 98.0 1.9E-05 4.2E-10 67.0 6.4 85 31-116 12-96 (224)
25 cd08050 TAF6 TATA Binding Prot 97.8 6.9E-05 1.5E-09 66.7 8.2 66 34-101 1-66 (343)
26 KOG1142 Transcription initiati 97.8 0.00014 3.1E-09 63.1 8.5 92 5-97 125-218 (258)
27 PF03847 TFIID_20kDa: Transcri 97.7 0.00017 3.8E-09 50.9 7.0 63 35-98 2-64 (68)
28 PF15511 CENP-T: Centromere ki 97.7 7.2E-05 1.6E-09 68.3 6.2 66 26-91 345-414 (414)
29 smart00427 H2B Histone H2B. 97.7 0.00021 4.5E-09 53.3 7.4 62 37-99 6-67 (89)
30 PF15630 CENP-S: Kinetochore c 97.7 0.00018 3.9E-09 52.0 6.7 61 37-97 10-71 (76)
31 COG5247 BUR6 Class 2 transcrip 97.6 0.0003 6.4E-09 54.0 7.2 81 28-109 19-99 (113)
32 KOG3467 Histone H4 [Chromatin 97.6 0.0003 6.5E-09 52.7 7.0 68 33-102 30-97 (103)
33 PF07524 Bromo_TP: Bromodomain 97.5 0.00072 1.6E-08 47.7 8.2 65 36-102 10-74 (77)
34 PF09415 CENP-X: CENP-S associ 97.5 0.00015 3.2E-09 51.9 4.4 64 34-97 1-66 (72)
35 cd08048 TAF11 TATA Binding Pro 97.4 0.00098 2.1E-08 49.0 8.0 66 32-99 16-84 (85)
36 PLN00158 histone H2B; Provisio 97.4 0.00073 1.6E-08 52.6 7.5 65 34-99 29-93 (116)
37 PTZ00463 histone H2B; Provisio 97.4 0.00086 1.9E-08 52.3 7.4 61 37-98 33-93 (117)
38 COG5262 HTA1 Histone H2A [Chro 97.3 0.00055 1.2E-08 53.7 5.5 70 27-97 21-90 (132)
39 smart00414 H2A Histone 2A. 97.1 0.0015 3.3E-08 49.8 6.3 68 30-98 7-74 (106)
40 PF04719 TAFII28: hTAFII28-lik 97.1 0.0027 5.9E-08 47.3 7.1 67 32-99 23-90 (90)
41 PF02969 TAF: TATA box binding 97.0 0.0061 1.3E-07 43.0 7.6 64 32-97 3-66 (66)
42 KOG1658 DNA polymerase epsilon 96.9 0.0007 1.5E-08 55.2 2.5 67 30-98 57-124 (162)
43 PLN00154 histone H2A; Provisio 96.8 0.0037 8E-08 49.9 6.2 69 29-97 35-103 (136)
44 PTZ00017 histone H2A; Provisio 96.7 0.0046 9.9E-08 49.3 5.6 68 29-97 24-91 (134)
45 KOG1745 Histones H3 and H4 [Ch 96.5 0.0019 4E-08 51.6 2.7 72 27-98 58-132 (137)
46 PLN00153 histone H2A; Provisio 96.5 0.015 3.3E-07 46.0 7.7 69 28-97 20-88 (129)
47 PLN00157 histone H2A; Provisio 96.3 0.009 2E-07 47.5 5.4 68 29-97 23-90 (132)
48 PLN00156 histone H2AX; Provisi 96.3 0.012 2.6E-07 47.2 5.9 68 29-97 26-93 (139)
49 PF15510 CENP-W: Centromere ki 96.2 0.0091 2E-07 45.1 4.7 66 31-97 15-94 (102)
50 KOG1756 Histone 2A [Chromatin 96.2 0.014 3.1E-07 46.2 6.0 70 27-97 22-91 (131)
51 PF02269 TFIID-18kDa: Transcri 96.1 0.0073 1.6E-07 44.8 3.9 60 38-98 7-66 (93)
52 KOG1744 Histone H2B [Chromatin 96.1 0.024 5.2E-07 44.8 6.7 67 27-97 35-101 (127)
53 PTZ00252 histone H2A; Provisio 94.8 0.16 3.4E-06 40.6 7.4 68 29-97 22-91 (134)
54 cd07978 TAF13 The TATA Binding 94.8 0.26 5.7E-06 36.6 8.2 74 36-113 6-79 (92)
55 PF02291 TFIID-31kDa: Transcri 94.6 0.2 4.4E-06 39.5 7.6 86 29-116 7-95 (129)
56 KOG3219 Transcription initiati 94.4 0.058 1.3E-06 45.5 4.3 69 32-102 112-181 (195)
57 KOG3423 Transcription initiati 91.9 0.91 2E-05 37.7 7.5 69 32-102 86-168 (176)
58 KOG4336 TBP-associated transcr 91.5 1.3 2.7E-05 40.0 8.5 76 38-117 11-86 (323)
59 TIGR03015 pepcterm_ATPase puta 90.9 0.88 1.9E-05 37.5 6.6 70 32-101 191-268 (269)
60 PRK00411 cdc6 cell division co 88.0 2.7 5.9E-05 36.8 7.9 69 35-103 209-286 (394)
61 KOG2549 Transcription initiati 87.7 2.5 5.3E-05 40.9 7.8 65 34-100 13-77 (576)
62 TIGR02928 orc1/cdc6 family rep 84.9 4.9 0.00011 34.7 7.7 75 35-109 201-284 (365)
63 KOG2389 Predicted bromodomain 83.3 3.4 7.4E-05 37.7 6.2 69 31-101 28-96 (353)
64 TIGR02902 spore_lonB ATP-depen 77.7 6.4 0.00014 37.1 6.3 66 35-101 265-334 (531)
65 PF13654 AAA_32: AAA domain; P 76.9 11 0.00025 35.7 7.7 58 38-98 436-505 (509)
66 TIGR00764 lon_rel lon-related 73.9 13 0.00027 36.0 7.3 50 51-100 330-392 (608)
67 COG1067 LonB Predicted ATP-dep 71.6 3.7 8E-05 40.2 3.1 49 51-99 338-399 (647)
68 cd08045 TAF4 TATA Binding Prot 70.5 29 0.00063 28.8 7.9 80 28-107 40-127 (212)
69 COG5095 TAF6 Transcription ini 70.0 9.9 0.00022 35.0 5.3 53 49-101 20-72 (450)
70 PF13335 Mg_chelatase_2: Magne 67.6 21 0.00045 26.3 5.8 47 51-97 42-94 (96)
71 KOG3334 Transcription initiati 63.0 21 0.00045 29.1 5.4 65 52-116 31-96 (148)
72 KOG3901 Transcription initiati 62.3 21 0.00046 27.6 5.0 47 48-97 24-70 (109)
73 PF00531 Death: Death domain; 60.7 15 0.00033 24.9 3.7 60 52-112 24-83 (83)
74 KOG1757 Histone 2A [Chromatin 60.0 16 0.00035 28.8 4.1 65 29-97 27-95 (131)
75 COG5162 Transcription initiati 58.5 64 0.0014 27.1 7.5 50 52-101 106-188 (197)
76 COG5248 TAF19 Transcription in 58.4 28 0.0006 27.4 5.1 48 48-97 24-71 (126)
77 PF02861 Clp_N: Clp amino term 57.3 9 0.0002 23.9 2.0 25 75-99 1-25 (53)
78 TIGR00635 ruvB Holliday juncti 57.3 57 0.0012 27.5 7.4 70 33-102 159-232 (305)
79 PRK00080 ruvB Holliday junctio 56.0 51 0.0011 28.6 7.0 72 32-103 179-254 (328)
80 TIGR02442 Cob-chelat-sub cobal 53.3 49 0.0011 31.9 7.0 49 49-97 247-302 (633)
81 TIGR02030 BchI-ChlI magnesium 51.8 64 0.0014 28.9 7.1 54 43-97 247-307 (337)
82 KOG2680 DNA helicase TIP49, TB 50.4 47 0.001 30.8 6.1 50 48-97 374-427 (454)
83 PRK13765 ATP-dependent proteas 49.6 46 0.00099 32.6 6.2 48 51-98 339-399 (637)
84 PRK13406 bchD magnesium chelat 48.8 41 0.00089 32.5 5.7 59 37-97 183-248 (584)
85 PRK09862 putative ATP-dependen 48.3 65 0.0014 30.7 6.9 54 50-103 437-496 (506)
86 PF09114 MotA_activ: Transcrip 47.2 30 0.00065 26.2 3.6 33 36-68 51-87 (96)
87 COG5624 TAF61 Transcription in 45.8 11 0.00025 35.5 1.4 76 32-107 383-461 (505)
88 PF03540 TFIID_30kDa: Transcri 45.2 94 0.002 20.9 6.4 48 32-81 2-49 (51)
89 TIGR00368 Mg chelatase-related 44.7 54 0.0012 31.0 5.7 47 51-97 445-497 (499)
90 CHL00081 chlI Mg-protoporyphyr 43.4 68 0.0015 29.1 6.0 54 43-97 260-320 (350)
91 COG1474 CDC6 Cdc6-related prot 42.9 90 0.002 28.3 6.7 73 36-108 193-274 (366)
92 TIGR01052 top6b DNA topoisomer 42.5 32 0.0007 32.7 3.9 58 44-115 427-484 (488)
93 TIGR01128 holA DNA polymerase 42.5 1.2E+02 0.0027 25.1 7.1 66 32-97 110-176 (302)
94 cd04752 Commd4 COMM_Domain con 41.7 72 0.0015 25.8 5.4 49 63-118 43-92 (174)
95 PF00356 LacI: Bacterial regul 41.6 59 0.0013 21.0 4.0 32 32-67 10-41 (46)
96 PF08369 PCP_red: Proto-chloro 41.5 35 0.00076 22.0 2.9 42 53-95 2-44 (45)
97 PRK12402 replication factor C 40.1 75 0.0016 26.9 5.5 71 33-105 184-255 (337)
98 PRK13407 bchI magnesium chelat 39.4 95 0.0021 27.9 6.2 53 43-96 244-303 (334)
99 PRK09526 lacI lac repressor; R 38.2 23 0.00051 29.7 2.1 39 32-75 16-54 (342)
100 PLN00138 large subunit ribosom 38.1 89 0.0019 24.1 5.1 44 70-115 3-46 (113)
101 PF05236 TAF4: Transcription i 38.1 50 0.0011 28.2 4.1 75 27-101 38-120 (264)
102 TIGR02031 BchD-ChlD magnesium 37.2 1.1E+02 0.0025 29.3 6.8 55 42-97 195-256 (589)
103 PF08681 DUF1778: Protein of u 36.5 31 0.00068 24.5 2.2 51 49-99 3-61 (80)
104 smart00350 MCM minichromosome 36.4 1.8E+02 0.004 27.2 7.9 65 31-98 416-503 (509)
105 PF07647 SAM_2: SAM domain (St 35.3 41 0.00088 22.0 2.5 25 86-110 3-27 (66)
106 PRK03992 proteasome-activating 35.2 48 0.001 29.9 3.7 35 66-100 339-373 (389)
107 PRK07452 DNA polymerase III su 34.9 1.1E+02 0.0024 26.2 5.8 53 49-101 147-201 (326)
108 PTZ00373 60S Acidic ribosomal 34.8 1.1E+02 0.0024 23.7 5.1 43 70-114 5-47 (112)
109 COG1224 TIP49 DNA helicase TIP 34.5 82 0.0018 29.8 5.1 84 31-117 359-447 (450)
110 PTZ00361 26 proteosome regulat 34.4 48 0.001 30.9 3.7 32 68-99 393-424 (438)
111 cd00166 SAM Sterile alpha moti 34.1 32 0.0007 21.7 1.9 24 88-111 3-26 (63)
112 TIGR01242 26Sp45 26S proteasom 33.2 55 0.0012 28.9 3.7 32 67-98 331-362 (364)
113 PRK10423 transcriptional repre 32.9 37 0.0008 28.2 2.5 37 33-74 10-46 (327)
114 PF00536 SAM_1: SAM domain (St 32.1 48 0.001 21.6 2.4 21 88-108 4-24 (64)
115 COG1389 DNA topoisomerase VI, 31.3 37 0.0008 32.7 2.4 46 43-88 434-479 (538)
116 KOG1528 Salt-sensitive 3'-phos 29.8 1.5E+02 0.0032 27.3 5.8 75 25-100 43-124 (351)
117 PRK14987 gluconate operon tran 29.4 36 0.00077 28.6 1.8 39 32-75 16-54 (331)
118 PF12010 DUF3502: Domain of un 29.4 53 0.0012 25.3 2.7 62 54-119 72-133 (134)
119 PRK05574 holA DNA polymerase I 28.7 1.7E+02 0.0037 24.8 5.9 65 32-97 145-211 (340)
120 PF12627 PolyA_pol_RNAbd: Prob 28.6 13 0.00029 24.4 -0.8 58 50-111 2-63 (64)
121 smart00354 HTH_LACI helix_turn 28.2 1E+02 0.0023 20.8 3.7 33 31-67 10-42 (70)
122 PF07499 RuvA_C: RuvA, C-termi 27.9 39 0.00085 21.6 1.4 14 90-103 4-17 (47)
123 PTZ00183 centrin; Provisional 27.7 2E+02 0.0043 21.1 5.5 20 79-98 62-81 (158)
124 PRK14975 bifunctional 3'-5' ex 27.6 3.3E+02 0.0072 25.9 8.1 90 30-122 161-270 (553)
125 PRK14868 DNA topoisomerase VI 27.3 74 0.0016 32.2 3.8 56 29-87 614-669 (795)
126 PTZ00454 26S protease regulato 27.1 79 0.0017 28.9 3.7 31 68-98 355-385 (398)
127 cd00823 TopoIIB_Trans TopoIIB_ 26.9 1.2E+02 0.0025 24.9 4.2 34 43-76 111-144 (151)
128 smart00454 SAM Sterile alpha m 26.7 49 0.0011 21.0 1.7 25 87-111 4-28 (68)
129 cd05833 Ribosomal_P2 Ribosomal 26.4 1.9E+02 0.0041 22.1 5.1 42 70-113 3-44 (109)
130 PRK10727 DNA-binding transcrip 26.3 45 0.00097 28.2 1.9 51 32-87 12-62 (343)
131 TIGR01481 ccpA catabolite cont 25.8 68 0.0015 26.7 2.9 38 32-74 12-49 (329)
132 PF13405 EF-hand_6: EF-hand do 24.6 75 0.0016 18.0 2.1 26 75-100 5-31 (31)
133 COG1724 Predicted RNA binding 24.0 48 0.001 23.6 1.4 17 86-102 6-22 (66)
134 PHA03328 nuclear egress lamina 23.9 82 0.0018 28.6 3.2 80 27-116 228-307 (316)
135 PRK14867 DNA topoisomerase VI 23.0 1E+02 0.0022 30.6 3.8 36 51-86 592-627 (659)
136 PF02361 CbiQ: Cobalt transpor 21.6 1.3E+02 0.0028 23.8 3.6 66 51-122 95-172 (224)
137 PF15605 Toxin_52: Putative to 21.5 2.6E+02 0.0057 21.5 5.0 44 27-71 51-94 (103)
138 PRK04184 DNA topoisomerase VI 21.0 73 0.0016 30.7 2.3 56 43-98 431-488 (535)
139 PF13499 EF-hand_7: EF-hand do 21.0 2.4E+02 0.0051 18.0 4.6 45 75-119 5-50 (66)
140 COG1239 ChlI Mg-chelatase subu 20.7 1.8E+02 0.0038 27.5 4.7 52 45-97 262-320 (423)
141 PRK06585 holA DNA polymerase I 20.3 2.5E+02 0.0055 24.2 5.4 49 49-97 159-208 (343)
142 smart00027 EH Eps15 homology d 20.1 1.8E+02 0.0038 20.5 3.7 27 76-102 16-42 (96)
143 PF14434 Imm6: Immunity protei 20.0 3.8E+02 0.0082 20.8 5.8 36 70-105 25-61 (122)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=4.3e-42 Score=275.62 Aligned_cols=119 Identities=71% Similarity=1.140 Sum_probs=108.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030670 1 MAEAPTSPAGGSHESGGEQSP-HAGGVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKC 79 (173)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~ 79 (173)
|++++..+ ++.++.++.+.+ .+..++++|++||||||.||||+.||.+++|||||++.||+|++|||+|||+||+++|
T Consensus 1 m~~s~~~~-~~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC 79 (168)
T KOG0869|consen 1 MAESDHDS-GGGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKC 79 (168)
T ss_pred CCCCcCCC-CccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 66766665 456776665555 4468999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHhhhc
Q 030670 80 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREGDT 120 (173)
Q Consensus 80 ~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~ 120 (173)
.+++||||++|||||||..|||++|+++|+.||.+|||.+.
T Consensus 80 ~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~ 120 (168)
T KOG0869|consen 80 QREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEG 120 (168)
T ss_pred HHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999654
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=2.4e-28 Score=194.68 Aligned_cols=112 Identities=31% Similarity=0.565 Sum_probs=102.7
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030670 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 26 ~~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (173)
-..+++.||+|+|.+|||+.||.+++|.+||+++|..||.+||+.|+++|+++|.++.||||++|||++||+.|||.+|+
T Consensus 6 ~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYi 85 (156)
T KOG0871|consen 6 KEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYI 85 (156)
T ss_pred cccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhhccCCCCCCCCCCccCcCCCCCC
Q 030670 106 DPLKAYLMRYREGDTKGSARGGDGSAKRDTIGALPG 141 (173)
Q Consensus 106 ~~Lk~~L~~yre~~~~~~~k~~~~~~~~~~~~~~~~ 141 (173)
+.+...+++|+...+++ +.+++|....|++..
T Consensus 86 ee~~~vl~~~K~~~~~~----~~kssk~e~~Gi~eE 117 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKKR----RRKSSKFEKSGIPEE 117 (156)
T ss_pred HHHHHHHHHHHHHHHHh----hhhhhhHHhcCCCHH
Confidence 99999999999887654 445677777776643
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.92 E-value=2.8e-25 Score=179.81 Aligned_cols=95 Identities=34% Similarity=0.575 Sum_probs=91.1
Q ss_pred CCCcccccCchhHHHHHHHhhCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030670 25 GVREQDRYLPIANISRIMKKALPAN-GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 25 ~~~~~D~~LP~A~V~RImK~aLP~~-~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (173)
..+++|+.||+|+|.||+|+.||+. +.|+|||+.+|+++|++||+|||+.|+++|+.++||||+++||++||++|+|..
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~ 82 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSS 82 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHH
Confidence 3578999999999999999999986 899999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHhhh
Q 030670 104 YIDPLKAYLMRYREGD 119 (173)
Q Consensus 104 yv~~Lk~~L~~yre~~ 119 (173)
|+.||+..|+.|+...
T Consensus 83 f~~plk~~Le~yk~~~ 98 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAV 98 (172)
T ss_pred HhhHHHHHHHHHHHHH
Confidence 9999999999999544
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.87 E-value=4.8e-22 Score=155.80 Aligned_cols=99 Identities=25% Similarity=0.504 Sum_probs=93.8
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 106 (173)
..++..||+|+|.+.+-+.||.+..++|||++.+++||.+||+.|+++|+++|..+.+|||.++||++||+.|+|.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 56778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhccCCCC
Q 030670 107 PLKAYLMRYREGDTKGSAR 125 (173)
Q Consensus 107 ~Lk~~L~~yre~~~~~~~k 125 (173)
.+.+.+.+|++.++.+.+|
T Consensus 86 ~~~e~~~n~k~~qK~ke~k 104 (148)
T COG5150 86 SCMEEHENYKSYQKQKESK 104 (148)
T ss_pred HHHHHHHHHHHHHhhchhh
Confidence 9999999999988765433
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=99.78 E-value=5e-19 Score=121.82 Aligned_cols=64 Identities=36% Similarity=0.624 Sum_probs=59.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.68 E-value=6.3e-17 Score=120.31 Aligned_cols=79 Identities=30% Similarity=0.465 Sum_probs=74.9
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030670 25 GVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 25 ~~~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (173)
..+..+..||+++|.||||++.++ +||.+|++++++|+++|+..|+..|++.|.++|||||+++||..|++.+||..|
T Consensus 12 ~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 12 YQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred hhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 457789999999999999999985 999999999999999999999999999999999999999999999999999866
Q ss_pred h
Q 030670 105 I 105 (173)
Q Consensus 105 v 105 (173)
.
T Consensus 90 ~ 90 (91)
T COG2036 90 G 90 (91)
T ss_pred c
Confidence 4
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=99.22 E-value=6.4e-11 Score=87.12 Aligned_cols=71 Identities=20% Similarity=0.329 Sum_probs=66.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (173)
.||++.|.||++... ..+||.|+.+.+.++.++|+..|...|...|++++||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 599999999999984 57899999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.18 E-value=1.2e-10 Score=88.47 Aligned_cols=75 Identities=16% Similarity=0.263 Sum_probs=67.6
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030670 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 28 ~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (173)
.....||++.|.||++..- ..+||.|+.+.+.+..++|+..|...|...|++.+||||+++||..||+..|-.-|
T Consensus 25 d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 25 DNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred hhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 3344599999999999984 57899999999999999999999999999999999999999999999998875433
No 9
>PTZ00015 histone H4; Provisional
Probab=99.10 E-value=4.1e-10 Score=85.44 Aligned_cols=76 Identities=20% Similarity=0.354 Sum_probs=68.9
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (173)
+.-...||++.|.||++..- ..+||.|+.+.+.++.++|+..|...|...|++.+||||+++||..||+..|-.-|
T Consensus 25 r~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred hhcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 45556799999999999983 56899999999999999999999999999999999999999999999998886543
No 10
>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=98.99 E-value=2.2e-09 Score=75.10 Aligned_cols=64 Identities=25% Similarity=0.280 Sum_probs=60.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.||++.|.||.+... -.+||.|+...+.+-++.|+.-|..+|...+++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G--i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG--IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999873 3479999999999999999999999999999999999999999999984
No 11
>smart00417 H4 Histone H4.
Probab=98.94 E-value=2.3e-09 Score=77.11 Aligned_cols=63 Identities=17% Similarity=0.312 Sum_probs=58.4
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHH
Q 030670 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWA 95 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~A 95 (173)
..||++.|.||+|... .-+||.++.+.+.+..++|+..|...|...|++.+||||+++||..|
T Consensus 12 ~gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3699999999999983 46899999999999999999999999999999999999999999754
No 12
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.86 E-value=1.9e-09 Score=91.91 Aligned_cols=77 Identities=25% Similarity=0.335 Sum_probs=69.4
Q ss_pred ccccCchhHHHHHHHhhCCCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030670 29 QDRYLPIANISRIMKKALPANG-KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~-kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~ 107 (173)
.+..||+|+|+|+||.. +++ .||.||..++.+.|+.||..||..|+-.+++++|+|+-..||..|+++.++.+|+-.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 35679999999999965 445 599999999999999999999999999999999999999999999999988877543
No 13
>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=98.85 E-value=2e-08 Score=71.13 Aligned_cols=65 Identities=15% Similarity=0.324 Sum_probs=61.1
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 33 LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
|++..+..++|+.-| ..+++.||.++|++.++.|+.-++..|...|++.||+||..+||.-+|++
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 677889999999876 68999999999999999999999999999999999999999999999975
No 14
>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=98.79 E-value=1.7e-08 Score=70.38 Aligned_cols=68 Identities=25% Similarity=0.331 Sum_probs=61.6
Q ss_pred cccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 30 DRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 30 D~~LP~A~V~RImK~aLP~---~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
...+|...|.|+.|+..++ ..+||++|.+.|+.+++.|+.-|...|...|.+.||+||+++||..|+.
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 3567888999999888763 2699999999999999999999999999999999999999999999985
No 15
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.63 E-value=2.9e-08 Score=84.94 Aligned_cols=88 Identities=26% Similarity=0.324 Sum_probs=75.8
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH---hcCCcchhh
Q 030670 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA---TLGFEDYID 106 (173)
Q Consensus 30 D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~---~LgF~~yv~ 106 (173)
...||+++|++|||..-. .-+|+.||..++.+||+.||..|+..|+..+...+|+|+...|+..|+. ..+|.-.+-
T Consensus 72 ~~~lPlaRiKkimK~ded-v~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Div 150 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDED-VSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIV 150 (236)
T ss_pred hccCcHhhcccccccccc-ccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccc
Confidence 347999999999997632 3379999999999999999999999999999999999999999999998 456666677
Q ss_pred HHHHHHHHHHhh
Q 030670 107 PLKAYLMRYREG 118 (173)
Q Consensus 107 ~Lk~~L~~yre~ 118 (173)
|.+..+++|...
T Consensus 151 P~~~~~~~~~~~ 162 (236)
T KOG1657|consen 151 PRKILAEKYPSL 162 (236)
T ss_pred cchhcccccccc
Confidence 778888877433
No 16
>smart00428 H3 Histone H3.
Probab=98.62 E-value=1.1e-07 Score=72.61 Aligned_cols=72 Identities=17% Similarity=0.187 Sum_probs=65.3
Q ss_pred CCcccccCchhHHHHHHHhhCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 26 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 26 ~~~~D~~LP~A~V~RImK~aLP~-----~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.+..++.+|+....|++++...+ +.+++.+|.++||++++.|+.-+...|+..|.+.||+||.++|+.-|..
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 46678899999999999988653 6799999999999999999999999999999999999999999987763
No 17
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.39 E-value=2.1e-06 Score=61.24 Aligned_cols=66 Identities=18% Similarity=0.265 Sum_probs=59.6
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030670 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 35 ~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (173)
+-.|.+|+|.+. =-+++.+|.+.|.+....|+..|+..+...|.+.+|++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 345788888773 247999999999999999999999999999999999999999999999999973
No 18
>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=98.33 E-value=1.8e-06 Score=66.77 Aligned_cols=70 Identities=17% Similarity=0.231 Sum_probs=63.2
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 28 ~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
-..+.||.+.|.|+||+.-- ..+|+.+|...|..+.+-+...|...|...|++.+|++|+++||..|+..
T Consensus 16 ragL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 16 RAGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred ccCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 34688999999999998433 37999999999999999999999999999999999999999999999863
No 19
>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=98.12 E-value=1.7e-05 Score=61.20 Aligned_cols=79 Identities=14% Similarity=0.216 Sum_probs=66.3
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh-HHHHHHHH
Q 030670 36 ANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMR 114 (173)
Q Consensus 36 A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~-~Lk~~L~~ 114 (173)
..|.||+|+. +..+++.+++..|.+.+..++.-|..+|...|++.+|+||+.+||.-|++...-..|.. +-+++|.+
T Consensus 5 ~~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 3588899986 34589999999999999999999999999999999999999999999998665544444 46777765
Q ss_pred HH
Q 030670 115 YR 116 (173)
Q Consensus 115 yr 116 (173)
.-
T Consensus 83 ~a 84 (117)
T cd07979 83 LA 84 (117)
T ss_pred HH
Confidence 54
No 20
>PLN00160 histone H3; Provisional
Probab=98.11 E-value=8.4e-06 Score=61.53 Aligned_cols=71 Identities=15% Similarity=0.106 Sum_probs=63.8
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 26 ~~~~D~~LP~A~V~RImK~aLP----~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
.+..++.+|++...|++++... .+.++..+|..++|++++.|+.-+-..++--|.+.||.||.+.|+.-|.
T Consensus 15 Qkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 15 QKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred ccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 3556789999999999998853 3589999999999999999999999999999999999999999997775
No 21
>PLN00121 histone H3; Provisional
Probab=98.11 E-value=5.5e-06 Score=65.90 Aligned_cols=70 Identities=14% Similarity=0.170 Sum_probs=63.9
Q ss_pred CcccccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 27 REQDRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~---~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
...++.+|+....|++++...+ +.++..+|.++||++++.|+.-+...++-.|.+.||.||.+.|+.-++
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 4568899999999999998754 789999999999999999999999999999999999999999997775
No 22
>PLN00161 histone H3; Provisional
Probab=98.10 E-value=1.2e-05 Score=63.98 Aligned_cols=71 Identities=15% Similarity=0.182 Sum_probs=63.8
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 26 ~~~~D~~LP~A~V~RImK~aLP----~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
.+..++.+|++...|++++... .+.++..+|.++||++++.|+.-+...|+--|.+.||.||.+.|+.-|.
T Consensus 49 Qkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 49 QKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred ccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 3566788999999999998853 3689999999999999999999999999999999999999999997775
No 23
>PTZ00018 histone H3; Provisional
Probab=98.04 E-value=8.5e-06 Score=64.84 Aligned_cols=70 Identities=14% Similarity=0.174 Sum_probs=63.5
Q ss_pred CcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 27 REQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP---~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
+..|+.+|+....|++++... .+.++..+|.++||++++.|+..|...++--|.+.||.||.+.|+.-|.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 455889999999999999863 3689999999999999999999999999999999999999999997775
No 24
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.96 E-value=1.9e-05 Score=66.99 Aligned_cols=85 Identities=16% Similarity=0.217 Sum_probs=72.8
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHH
Q 030670 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKA 110 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~ 110 (173)
-.+|.++|.|||...-. -.+|+.-....+.++.+.|+.-|...+.++++..+-|||+++|+..++..-.-.+|+..+-.
T Consensus 12 trfp~aRiKKIMQ~dEd-IGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDED-IGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhhh-hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 36899999999986532 56899999999999999999999999999999999999999999999998887888776554
Q ss_pred HHHHHH
Q 030670 111 YLMRYR 116 (173)
Q Consensus 111 ~L~~yr 116 (173)
-+..+.
T Consensus 91 ~vpd~~ 96 (224)
T KOG1659|consen 91 KVPDRQ 96 (224)
T ss_pred hcCCCc
Confidence 444443
No 25
>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=97.84 E-value=6.9e-05 Score=66.67 Aligned_cols=66 Identities=18% Similarity=0.187 Sum_probs=57.8
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030670 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 34 P~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (173)
|..+|.-|.++.. -.++++||..++.+.++.++..|..+|...+++.||||++++||-.||+.++.
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 4556777777662 34899999999999999999999999999999999999999999999996554
No 26
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.75 E-value=0.00014 Score=63.14 Aligned_cols=92 Identities=17% Similarity=0.305 Sum_probs=71.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC--cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 030670 5 PTSPAGGSHESGGEQSPHAGGVR--EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE 82 (173)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~--~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~ 82 (173)
|.-+.||+-..|+..|+.+.... .....|=+-.|.-++++.- .+.+|-+|+.++|.+.|..||..|+..|...|++.
T Consensus 125 P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHR 203 (258)
T KOG1142|consen 125 PVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHR 203 (258)
T ss_pred CCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33333455554455555443322 3334566777888999874 47899999999999999999999999999999999
Q ss_pred CCCCcCchhhHHHHH
Q 030670 83 KRKTINGDDLLWAMA 97 (173)
Q Consensus 83 kRKTI~~eDVl~AL~ 97 (173)
|..||-..||.-.|+
T Consensus 204 KsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 204 KSDTVEVRDIQLHLE 218 (258)
T ss_pred ccCccchhheeeeee
Confidence 999999999999998
No 27
>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=97.72 E-value=0.00017 Score=50.94 Aligned_cols=63 Identities=19% Similarity=0.306 Sum_probs=51.2
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 35 ~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
+..+.-+|++.-| +.++.+|+.++|.+.|.+||.-++..|...|++.+-.||...||.-.|++
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 3467888998755 88999999999999999999999999999999999999999999998874
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.70 E-value=7.2e-05 Score=68.32 Aligned_cols=66 Identities=20% Similarity=0.257 Sum_probs=47.2
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchh
Q 030670 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (173)
Q Consensus 26 ~~~~D~~LP~A~V~RImK~aLP----~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eD 91 (173)
..+.--.||.+.|+|++..... .+++|+|||..+|.+|...|-..|+.--.-.|.++|||||..+|
T Consensus 345 hgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 345 HGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4555667999999988877644 47899999999999999999999999888999999999999876
No 29
>smart00427 H2B Histone H2B.
Probab=97.69 E-value=0.00021 Score=53.30 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=56.8
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 37 ~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
-|+|++|+.-| +.-||..|...|.-.+.-+..-|+.||...|.-.+|+||+..+|..|+.-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 48999999998 568999999999998888889999999999999999999999999998643
No 30
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.68 E-value=0.00018 Score=51.98 Aligned_cols=61 Identities=15% Similarity=0.198 Sum_probs=51.2
Q ss_pred HHHHHHHhhC-CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 37 NISRIMKKAL-PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 37 ~V~RImK~aL-P~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.|.||+.+.. +.++.+|+++..+|.+.+-.++..++..---.|+++||+||+.|||+-...
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 5788998875 557889999999999999999999998888899999999999999987654
No 31
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.59 E-value=0.0003 Score=53.95 Aligned_cols=81 Identities=17% Similarity=0.275 Sum_probs=68.8
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030670 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 28 ~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~ 107 (173)
---..+|+|.|.|||.-.-+ -.+|+.-....+.++.+.|+..|-.++.+.++..+-|.|+.+++..|.+.-+=.+|+..
T Consensus 19 ~~ktrFP~ar~KkIMQ~deD-iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~ 97 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDED-IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKN 97 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhh-hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHH
Confidence 34457999999999985532 56899999999999999999999999999999999999999999999987666666555
Q ss_pred HH
Q 030670 108 LK 109 (173)
Q Consensus 108 Lk 109 (173)
+.
T Consensus 98 ~~ 99 (113)
T COG5247 98 ME 99 (113)
T ss_pred HH
Confidence 44
No 32
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.59 E-value=0.0003 Score=52.75 Aligned_cols=68 Identities=18% Similarity=0.291 Sum_probs=60.6
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030670 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 33 LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (173)
+-+-+|.||.+..- .-+|+--.-+.+..++.+||..+-+-|...+.+.|||||++-||+-+|+++|.-
T Consensus 30 itKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 55678999999873 457888888899999999999999999999999999999999999999998864
No 33
>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=97.55 E-value=0.00072 Score=47.73 Aligned_cols=65 Identities=18% Similarity=0.267 Sum_probs=57.0
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030670 36 ANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 36 A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (173)
-.|.+|++.+. =-.++..|.+.|...+..||..|+..+...|...+|...+..||..||+++|+.
T Consensus 10 ~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34666666652 136999999999999999999999999999999999999999999999999984
No 34
>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=97.52 E-value=0.00015 Score=51.88 Aligned_cols=64 Identities=20% Similarity=0.302 Sum_probs=53.2
Q ss_pred chhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-cCchhhHHHHH
Q 030670 34 PIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT-INGDDLLWAMA 97 (173)
Q Consensus 34 P~A~V~RImK~aLP-~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKT-I~~eDVl~AL~ 97 (173)
|...|.||++.... ++.+|++||..++.+....||..-...|.+.++.++..+ |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 78899999997663 578999999999999999999999999999999999888 99999877653
No 35
>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=97.44 E-value=0.00098 Score=49.02 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=60.7
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCcCchhhHHHHHhc
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR---KTINGDDLLWAMATL 99 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kR---KTI~~eDVl~AL~~L 99 (173)
.||++.|.|||...++ ..++.+...+|.-.+.+||--|.-+|.++..+.+. .-|.++||-.|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 4999999999999987 68999999999999999999999999999987665 889999999998775
No 36
>PLN00158 histone H2B; Provisional
Probab=97.42 E-value=0.00073 Score=52.59 Aligned_cols=65 Identities=17% Similarity=0.290 Sum_probs=58.3
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 34 P~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
-..-|+|++|+.-| +.-||..+...|.-.+.-+..-|+.||...|.-.+|+||+..+|-.|+.-+
T Consensus 29 y~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 34569999999998 568999999999999998889999999999999999999999999998533
No 37
>PTZ00463 histone H2B; Provisional
Probab=97.38 E-value=0.00086 Score=52.26 Aligned_cols=61 Identities=20% Similarity=0.382 Sum_probs=56.0
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 37 ~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
-|+|++|+.-| +.-||..|...|.-.+.-...-|+.||...|.-.+|+||+..+|-.|+.-
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 49999999998 56899999999998888888899999999999999999999999999853
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.29 E-value=0.00055 Score=53.70 Aligned_cols=70 Identities=19% Similarity=0.235 Sum_probs=61.6
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.-..+.+|...|.||||..- -.+||+++|...+.-|.+-.+..|+.-|-..|+..++|.|.+.|+-.|+.
T Consensus 21 a~agl~fpvgrvkr~lk~~~-~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 21 AKAGLIFPVGRVKRLLKKGN-YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hhcCccccHHHHHHHHHcCc-cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 44567899999999999543 37899999999999999888888888888999999999999999999985
No 39
>smart00414 H2A Histone 2A.
Probab=97.12 E-value=0.0015 Score=49.81 Aligned_cols=68 Identities=15% Similarity=0.257 Sum_probs=59.4
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 30 D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
.+.||.+.|.|+||+.-- ..+|+..|...|.-+.+=+...|-..|...|+..+++.|+++||..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 578999999999998643 45999999999999888888888777888899999999999999999864
No 40
>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=97.08 E-value=0.0027 Score=47.28 Aligned_cols=67 Identities=21% Similarity=0.226 Sum_probs=51.7
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCcCchhhHHHHHhc
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEK-RKTINGDDLLWAMATL 99 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~k-RKTI~~eDVl~AL~~L 99 (173)
.||++.|.|||...+. +..|+.-...+|.-.+.+||-.|-.+|.+++...+ -.-|.+.|+-.|..+|
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5999999999999986 57899999999999999999999999999998655 3489999999998764
No 41
>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=96.96 E-value=0.0061 Score=42.98 Aligned_cols=64 Identities=19% Similarity=0.204 Sum_probs=48.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.+|..+|.-+.... . -..++.|+...|.+=++--|..|..+|....++.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~-G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-G-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-T----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 36777776666554 3 3469999999999999999999999999999999999999999999984
No 42
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.87 E-value=0.0007 Score=55.16 Aligned_cols=67 Identities=25% Similarity=0.302 Sum_probs=58.1
Q ss_pred cccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 30 DRYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 30 D~~LP~A~V~RImK~aLP~~~k-ISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
-..||++.|..+|| ++++.. ..+|++.++.+++..||.+|...+...+...+|||+.-.|+=.|++.
T Consensus 57 l~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 57 LSRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 35799999999998 556665 66788999999999999999999999999999999998888777653
No 43
>PLN00154 histone H2A; Provisional
Probab=96.82 E-value=0.0037 Score=49.90 Aligned_cols=69 Identities=19% Similarity=0.250 Sum_probs=57.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
-.+.||.+.|.|++|+-..-..+|+..|...|.-+.+=+...|...|-..|++.+++-|++.||..|+.
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 368899999999999975434699999999888877666666666677788899999999999999985
No 44
>PTZ00017 histone H2A; Provisional
Probab=96.65 E-value=0.0046 Score=49.25 Aligned_cols=68 Identities=15% Similarity=0.226 Sum_probs=59.8
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
-.+.||...|.|+||+.-- ..+|+..|...|.-+.+-+...|-..|...|+..+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4688999999999998643 3599999999999988888888888888889999999999999999985
No 45
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.53 E-value=0.0019 Score=51.64 Aligned_cols=72 Identities=15% Similarity=0.201 Sum_probs=60.2
Q ss_pred CcccccCchhHHHHHHHhh---CCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 27 REQDRYLPIANISRIMKKA---LPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~a---LP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
+..|+.+++....|++++. .-.+.++...|..+||++++.|+.-|--.+|--|.+.||-||.+.||--|..-
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArri 132 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 132 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhc
Confidence 3567777777777777743 33478999999999999999999999999998889999999999999877653
No 46
>PLN00153 histone H2A; Provisional
Probab=96.52 E-value=0.015 Score=46.04 Aligned_cols=69 Identities=16% Similarity=0.221 Sum_probs=59.3
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 28 ~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
--.+.||...|.|++|+.-- ..+|+..|...|.-+.+-.+..|-..|...|...+++-|+++||..|+.
T Consensus 20 ragL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 20 KAGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred ccCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 34788999999999998644 4699999999998888877777777788888999999999999999985
No 47
>PLN00157 histone H2A; Provisional
Probab=96.31 E-value=0.009 Score=47.48 Aligned_cols=68 Identities=13% Similarity=0.186 Sum_probs=58.5
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..+|+..|...|.-+.+-.+..|-..|...|...+++-|+++||..|+.
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 3688999999999998643 4699999999998887777777777788888999999999999999985
No 48
>PLN00156 histone H2AX; Provisional
Probab=96.27 E-value=0.012 Score=47.18 Aligned_cols=68 Identities=13% Similarity=0.201 Sum_probs=57.1
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..+|+..|...|.-+.+=....|...|...|...+++-|+++||..|+.
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 3678999999999998643 4599999999998887766666666677788889999999999999985
No 49
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.22 E-value=0.0091 Score=45.11 Aligned_cols=66 Identities=21% Similarity=0.259 Sum_probs=54.9
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 31 RYLPIANISRIMKKALPANGKIAKDAKDT--------------VQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP~~~kISkDA~~a--------------l~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
+.-|++.+.|++|..-| ..++....-.+ +.--|-.||+-|+-||...|=.+|-.||+.+||+.|-
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 45799999999998877 56665554444 5566889999999999988888999999999999986
Q ss_pred H
Q 030670 97 A 97 (173)
Q Consensus 97 ~ 97 (173)
+
T Consensus 94 K 94 (102)
T PF15510_consen 94 K 94 (102)
T ss_pred H
Confidence 5
No 50
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.21 E-value=0.014 Score=46.18 Aligned_cols=70 Identities=16% Similarity=0.246 Sum_probs=54.8
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.-..+.+|...|.|++|+. ---.+|+.+|...|.-|.+-....|+.-|-..++.+++.-|++.||..|+.
T Consensus 22 ~~agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 22 SRAGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hhcccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 4456789999999999993 224689999999999665544555555555666778899999999999986
No 51
>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=96.15 E-value=0.0073 Score=44.75 Aligned_cols=60 Identities=25% Similarity=0.326 Sum_probs=29.8
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 38 V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
|..+|-.- .+...-..|...+|-+.+.+||..|..+|.+.|...++++|+.+|++-+|..
T Consensus 7 I~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 44556544 3355788999999999999999999999999999999999999999999984
No 52
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.07 E-value=0.024 Score=44.82 Aligned_cols=67 Identities=22% Similarity=0.291 Sum_probs=58.4
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
+.+.+..+ |+|++|+.-|+ .-|+.++...|.-....++-.|+.+|+..+.-.+|.||+..+|-.|..
T Consensus 35 ~~e~~s~y---v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 35 RKESYSEY---VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred ccCceeee---hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 34444444 67799999886 679999999999999999999999999999999999999999999874
No 53
>PTZ00252 histone H2A; Provisional
Probab=94.85 E-value=0.16 Score=40.60 Aligned_cols=68 Identities=7% Similarity=0.165 Sum_probs=49.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~--~kRKTI~~eDVl~AL~ 97 (173)
-.+.||...|.|.+|+.-- ..+|+.-|...|.-+.+=....|-..|...|++ .+++-|+++||..|+.
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 4679999999999998754 468999998888766543333333334444433 5778999999999985
No 54
>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=94.84 E-value=0.26 Score=36.59 Aligned_cols=74 Identities=18% Similarity=0.258 Sum_probs=54.5
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHH
Q 030670 36 ANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLM 113 (173)
Q Consensus 36 A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~ 113 (173)
.-|..+|-.... ...-..|...+|-+.+.+||..|+.+|.+.|. .+|.-++.||++-+|..= ...+.-++.+|.
T Consensus 6 ~ei~~mmy~~GD-~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~ 79 (92)
T cd07978 6 KEIRQMMYGFGD-VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLS 79 (92)
T ss_pred HHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHH
Confidence 346677776543 45678999999999999999999999999998 444445999999999631 123344444443
No 55
>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=94.64 E-value=0.2 Score=39.49 Aligned_cols=86 Identities=21% Similarity=0.264 Sum_probs=47.0
Q ss_pred ccccCchh--HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH-hcCCcchh
Q 030670 29 QDRYLPIA--NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA-TLGFEDYI 105 (173)
Q Consensus 29 ~D~~LP~A--~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~-~LgF~~yv 105 (173)
+...+|+. .|.-|+|+. +-......+...|.+.+-.|+.-|-..|...+.+.+|++|+.+||.-|++ .+++.-.-
T Consensus 7 ~~~~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 34456763 344555554 12346778888999999999999999999999999999999999999999 67777666
Q ss_pred hHHHHHHHHHH
Q 030670 106 DPLKAYLMRYR 116 (173)
Q Consensus 106 ~~Lk~~L~~yr 116 (173)
++-+++|.+.-
T Consensus 85 pppre~llelA 95 (129)
T PF02291_consen 85 PPPREFLLELA 95 (129)
T ss_dssp -----------
T ss_pred CCChHHHHHHH
Confidence 77777775554
No 56
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.41 E-value=0.058 Score=45.45 Aligned_cols=69 Identities=14% Similarity=0.188 Sum_probs=60.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCcCchhhHHHHHhcCCc
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEK-RKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~k-RKTI~~eDVl~AL~~LgF~ 102 (173)
.||+++|.|||...+.. .|+.-+..+|.-.+.+||-.|--+|.++|..-+ ---|-+.||-.|...|...
T Consensus 112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 59999999999999863 399999999999999999999999999998665 4468899999988877654
No 57
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.93 E-value=0.91 Score=37.69 Aligned_cols=69 Identities=26% Similarity=0.260 Sum_probs=56.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCCcCchhhHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE--------------KRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~--------------kRKTI~~eDVl~AL~ 97 (173)
.||=+.+.-+++.+. -.....-.+.+|.-++..||+-|+.-|.+.|+-. +|-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~aG--f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG--FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcC--CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 689999999998873 2234556678999999999999999999999743 345899999999999
Q ss_pred hcCCc
Q 030670 98 TLGFE 102 (173)
Q Consensus 98 ~LgF~ 102 (173)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98873
No 58
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=91.50 E-value=1.3 Score=39.95 Aligned_cols=76 Identities=18% Similarity=0.297 Sum_probs=64.0
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHh
Q 030670 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 117 (173)
Q Consensus 38 V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre 117 (173)
|.-|.++..= -.|++-|.+.|.+....+|.-|...+.-.|...+|-..+.-||.-.|-.+|+. +..|..+++.+..
T Consensus 11 V~~Ll~~~gf--d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 11 VSNLLKTKGF--DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHhCc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 4444444432 24999999999999999999999999999999999999999999999999997 5677777776654
No 59
>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=90.94 E-value=0.88 Score=37.48 Aligned_cols=70 Identities=14% Similarity=0.225 Sum_probs=54.8
Q ss_pred cCchhHHHHHHHhhCC-----CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030670 32 YLPIANISRIMKKALP-----ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP-----~~~kISkDA~~al~k~a~e---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (173)
.|....+..++...+. ....+++++.+.|.+.+.= .|+.+...|...+-..+.++|+.++|..++.++.|
T Consensus 191 ~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 191 PLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 3444555555554331 2346999999999998875 79999999998888889999999999999998875
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.01 E-value=2.7 Score=36.77 Aligned_cols=69 Identities=13% Similarity=0.174 Sum_probs=50.4
Q ss_pred hhHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030670 35 IANISRIMKKALPA---NGKIAKDAKDTVQECV------SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 35 ~A~V~RImK~aLP~---~~kISkDA~~al~k~a------~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (173)
...+..|++..+.. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||..|++.+....
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~ 286 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVH 286 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHH
Confidence 45566666654421 2358999988888877 334556667888889989999999999999999874433
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.72 E-value=2.5 Score=40.85 Aligned_cols=65 Identities=22% Similarity=0.257 Sum_probs=54.3
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030670 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 34 P~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (173)
|.-.+.-+++ .+. -..|++|+..+|.+=++.=|..|+.+|.+.-.+.||.+++.+||-.||..+.
T Consensus 13 ~~Es~k~vAE-slG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 13 PKESVKVVAE-SLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cHHHHHHHHH-HhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 3455544444 444 3469999999999999999999999999999999999999999999999553
No 62
>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=84.94 E-value=4.9 Score=34.73 Aligned_cols=75 Identities=8% Similarity=0.125 Sum_probs=50.9
Q ss_pred hhHHHHHHHhhCC---CCCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030670 35 IANISRIMKKALP---ANGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 35 ~A~V~RImK~aLP---~~~kISkDA~~al~k~a~------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (173)
...+..|++..+. ....+++|+.+.+.+.+. ..+..+...|.+.|..+++.+|+.+||..|++.+....+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3446666655442 133588888877766543 2444466677888888899999999999999988655554
Q ss_pred hHHH
Q 030670 106 DPLK 109 (173)
Q Consensus 106 ~~Lk 109 (173)
..++
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4443
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=83.32 E-value=3.4 Score=37.75 Aligned_cols=69 Identities=14% Similarity=0.160 Sum_probs=58.5
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030670 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (173)
..|-+..|..|+....=. ..-.-|.+.|+-.+..||.-|+..|...+...+|--.+..||+.||++|+.
T Consensus 28 ~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~ 96 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSA 96 (353)
T ss_pred HHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhh
Confidence 457777888999764322 233449999999999999999999999999999999999999999998876
No 64
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=77.67 E-value=6.4 Score=37.12 Aligned_cols=66 Identities=23% Similarity=0.298 Sum_probs=45.4
Q ss_pred hhHHHHHHHhhCC-CCCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030670 35 IANISRIMKKALP-ANGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 35 ~A~V~RImK~aLP-~~~kISkDA~~al~k~a~---eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (173)
...+.+|++..+. .+..|++++.+.|.+.+. +.++.+ ..|...|..++|++|+.+||.|++..-.|
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 4446666666653 246799999998877765 233333 34556777789999999999999764433
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=76.91 E-value=11 Score=35.66 Aligned_cols=58 Identities=24% Similarity=0.322 Sum_probs=43.6
Q ss_pred HHHHHHhh-CCCCCcccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 38 ISRIMKKA-LPANGKIAKDAKDTVQECVSE-----------FISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 38 V~RImK~a-LP~~~kISkDA~~al~k~a~e-----------FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
|.+++++. |+ .++++|...|-+.+.. -|.-|-.+|+..|+.+++++|+++||..|++.
T Consensus 436 i~~~~~~~~L~---~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 436 IASICQKEGLP---PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp HHHHHHHHSS-----BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred HHHHHHhCCCC---CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 45555544 32 4899998888877653 57778899999999999999999999999975
No 66
>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=73.95 E-value=13 Score=35.97 Aligned_cols=50 Identities=12% Similarity=0.145 Sum_probs=40.2
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030670 51 KIAKDAKDTVQECVS-------------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 51 kISkDA~~al~k~a~-------------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (173)
.++++|.+.|.+.++ .=+.-|-.+|..+|+.+++.+|+.+||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 699999998876544 33556677888899889999999999999997543
No 67
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=71.57 E-value=3.7 Score=40.20 Aligned_cols=49 Identities=24% Similarity=0.273 Sum_probs=36.9
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 51 KIAKDAKDTVQECVSEF-------------ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 51 kISkDA~~al~k~a~eF-------------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
.++++|..-|-+-+..- +--|-.+|.++|..++++-|+++||.+|++.-
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 47777766665554432 23344489999999999999999999999873
No 68
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) 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 4 (TAF4) 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 eukaryote. 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 hypotheses are
Probab=70.48 E-value=29 Score=28.78 Aligned_cols=80 Identities=10% Similarity=0.156 Sum_probs=57.3
Q ss_pred cccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCCcCchhhHHHHHhc
Q 030670 28 EQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQECVSEFISFITSEASDKCQKE------KRKTINGDDLLWAMATL 99 (173)
Q Consensus 28 ~~D~~LP~A~V~RImK~aLP~~~--kISkDA~~al~k~a~eFI~~LtseA~~~~~~~------kRKTI~~eDVl~AL~~L 99 (173)
....+|....|.+.|...+.... .|+.|...+|..||.+++..|-......|++- .-.+.-..||-.-|..|
T Consensus 40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 34456777766666665554322 69999999999999999999999998888754 34566677887777666
Q ss_pred CCcchhhH
Q 030670 100 GFEDYIDP 107 (173)
Q Consensus 100 gF~~yv~~ 107 (173)
+--+..+.
T Consensus 120 ~~~ek~e~ 127 (212)
T cd08045 120 EQLEREEE 127 (212)
T ss_pred HHHHHHHH
Confidence 55444333
No 69
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=70.00 E-value=9.9 Score=35.03 Aligned_cols=53 Identities=25% Similarity=0.246 Sum_probs=48.3
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030670 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 49 ~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (173)
-..|.+|+..++..-.+-=|+.+..+|...-.+.||..++-+||-.||..+..
T Consensus 20 i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNV 72 (450)
T COG5095 20 ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNV 72 (450)
T ss_pred CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCC
Confidence 34699999999999999999999999999999999999999999999997654
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=67.58 E-value=21 Score=26.31 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=39.2
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 51 kISkDA~~al~k~a~eF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.+++++..+|.+++..| ++-|..-|..+|--++...|..+||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 57888888888888766 455667788999999999999999999984
No 71
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=63.04 E-value=21 Score=29.05 Aligned_cols=65 Identities=14% Similarity=0.242 Sum_probs=50.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh-HHHHHHHHHH
Q 030670 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRYR 116 (173)
Q Consensus 52 ISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~-~Lk~~L~~yr 116 (173)
...-....|-+.+--++.-|-..|.-.+.+.++.||..|||..|++...=..|.. +=+++|-++-
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA 96 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA 96 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH
Confidence 4455566677778888888888999999999999999999999999666666665 5555555443
No 72
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=62.34 E-value=21 Score=27.64 Aligned_cols=47 Identities=19% Similarity=0.284 Sum_probs=39.1
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 48 ~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
++..=-.|..+++-..+.+||..++..|.++. +|--+..||++-+|.
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 34456678999999999999999988887776 566788899999997
No 73
>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=60.65 E-value=15 Score=24.89 Aligned_cols=60 Identities=15% Similarity=0.272 Sum_probs=38.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHH
Q 030670 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (173)
Q Consensus 52 ISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L 112 (173)
++..-.+.|..+... ...=+.+............-+.++++.||.++|..+-++.++.+|
T Consensus 24 ~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 24 LSESEIENIEEENPD-LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp S-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 555555555554422 222333334444444566778899999999999999999888764
No 74
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=60.01 E-value=16 Score=28.79 Aligned_cols=65 Identities=20% Similarity=0.327 Sum_probs=49.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCCcCchhhHHHHH
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE----KRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~----kRKTI~~eDVl~AL~ 97 (173)
..+.+|..+|.|.+|.-.-...+|..-+..-+ ...+.|||.|-.+.|.+. |-|.|++.|+--|+.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 45689999999999999887888866443332 345679999988888655 457899998877764
No 75
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=58.53 E-value=64 Score=27.09 Aligned_cols=50 Identities=20% Similarity=0.241 Sum_probs=38.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHH-h------------------c--------------CCCCcCchhhHHHHHh
Q 030670 52 IAKDAKDTVQECVSEFISFITSEASDKCQ-K------------------E--------------KRKTINGDDLLWAMAT 98 (173)
Q Consensus 52 ISkDA~~al~k~a~eFI~~LtseA~~~~~-~------------------~--------------kRKTI~~eDVl~AL~~ 98 (173)
...-.+.++.-.+..||+-|+..|.+..+ + . ++-+++..|+-.||++
T Consensus 106 ~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~E 185 (197)
T COG5162 106 SDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEE 185 (197)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHH
Confidence 44456788899999999999988775432 1 1 4567899999999998
Q ss_pred cCC
Q 030670 99 LGF 101 (173)
Q Consensus 99 LgF 101 (173)
.|+
T Consensus 186 yGi 188 (197)
T COG5162 186 YGI 188 (197)
T ss_pred hcc
Confidence 887
No 76
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=58.36 E-value=28 Score=27.36 Aligned_cols=48 Identities=19% Similarity=0.328 Sum_probs=41.8
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 48 ~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
+.+.=..|..+++.+.+.-+++.+...|..+|+ .|-.+..||+.-||.
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 455667899999999999999999999999988 566678899999997
No 77
>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=57.32 E-value=9 Score=23.93 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=20.3
Q ss_pred HHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 75 ASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
|.+.|+..+...|+.+|++.||=.-
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~ 25 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLED 25 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhh
Confidence 5678899999999999999997543
No 78
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=57.29 E-value=57 Score=27.47 Aligned_cols=70 Identities=19% Similarity=0.194 Sum_probs=47.3
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030670 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 33 LP~A~V~RImK~aLP-~~~kISkDA~~al~k~a~e---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (173)
++...+..|++.... .+..++.|+.+.|.+.+.= ++..+...+.+.+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 444556666665442 2467999998888776532 334444456667666666789999999999987654
No 79
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=55.98 E-value=51 Score=28.59 Aligned_cols=72 Identities=13% Similarity=0.189 Sum_probs=49.7
Q ss_pred cCchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030670 32 YLPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP-~~~kISkDA~~al~k~a~e---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (173)
.++...+..|++.... .++.++.|+...|.+.|.- .+..+-..+.+.+...+.+.|+.++|..+++.++...
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 3555666666665432 2578999998888877632 3444444556666666677999999999999877654
No 80
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=53.31 E-value=49 Score=31.95 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=41.3
Q ss_pred CCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 49 NGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 49 ~~kISkDA~~al~k~a~eFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.+.|+.+..+.+...+..+- .++...|..+|.-++|.+|+.+||..|+.
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 67899999999999887762 45666777888899999999999999986
No 81
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=51.81 E-value=64 Score=28.91 Aligned_cols=54 Identities=22% Similarity=0.198 Sum_probs=40.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
++.++ .+.|+++....+.+.|..+= .++...|...|.-++|..|+++||..+..
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44455 67899999888888776653 23556677788888999999999998764
No 82
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=50.38 E-value=47 Score=30.84 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=41.7
Q ss_pred CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 48 ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 48 ~~~kISkDA~~al~k~a~e----FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
+++.++.||++.+.+.... |-.+|-+.|+-.|.+.|-+++..+||-.+-.
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 4788999999999876543 5566667788999999999999999999863
No 83
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=49.65 E-value=46 Score=32.59 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=38.8
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 51 KIAKDAKDTVQECVSEF-------------ISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 51 kISkDA~~al~k~a~eF-------------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
.++++|...|-+-++.- |.-|-.+|..+|+.++++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 58999988887766532 3337788999999999999999999999843
No 84
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=48.85 E-value=41 Score=32.51 Aligned_cols=59 Identities=15% Similarity=0.141 Sum_probs=47.3
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 37 ~V~RImK~aLP~~~kISkDA~~al~k~a~eFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.|.+.-+ .++ ++.|+.+....+.++|..|- .++...|..+|--++|.+|+.+||..|+.
T Consensus 183 ~I~~AR~-rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAARA-RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHHH-HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4444433 455 78999999998888887774 46778888999999999999999999986
No 85
>PRK09862 putative ATP-dependent protease; Provisional
Probab=48.34 E-value=65 Score=30.70 Aligned_cols=54 Identities=11% Similarity=0.109 Sum_probs=42.2
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030670 50 GKIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 50 ~kISkDA~~al~k~a~eF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (173)
..+++++...+.+++..+ .+.|..-|..+|--++|..|+.+||..|+.=-+++.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~ 496 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDR 496 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccH
Confidence 467888888777765544 567777888999999999999999999997544443
No 86
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=47.15 E-value=30 Score=26.22 Aligned_cols=33 Identities=21% Similarity=0.318 Sum_probs=26.7
Q ss_pred hHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHHH
Q 030670 36 ANISRIMKKAL----PANGKIAKDAKDTVQECVSEFI 68 (173)
Q Consensus 36 A~V~RImK~aL----P~~~kISkDA~~al~k~a~eFI 68 (173)
++|.+++|+-| .+...++.++.+.++++++.|-
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a 87 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWA 87 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHH
Confidence 56788999877 3467899999999999999983
No 87
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=45.75 E-value=11 Score=35.47 Aligned_cols=76 Identities=11% Similarity=0.183 Sum_probs=61.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh---cCCcchhhH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT---LGFEDYIDP 107 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~---LgF~~yv~~ 107 (173)
.+-+-.+.-+.+..+....+|-.|.-+++-..+-.|+.-+|..+...+++.+-+||-+.||---|++ +-++.|+..
T Consensus 383 l~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d 461 (505)
T COG5624 383 LDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDD 461 (505)
T ss_pred hhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHH
Confidence 4445556666777777778999999999999999999999999999999999999999999777763 334566655
No 88
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=45.17 E-value=94 Score=20.92 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=35.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK 81 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~ 81 (173)
.+|=+.+.-+++.+.=+ .-..-.+-++.=++..||..|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~--~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQ--TSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCC--CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46778888888877321 1233345688889999999999999998863
No 89
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=44.72 E-value=54 Score=31.04 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 51 kISkDA~~al~k~a~eF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.++++++..|.+++..| .+-|..-|..+|--+++..|..+||..|+.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46889999999988876 566777888999999999999999999984
No 90
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=43.38 E-value=68 Score=29.11 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=43.2
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
++.++ .+.|+++....+.+.|..+= .++...|.-.|--++|..++++||..+..
T Consensus 260 r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 260 QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44455 68899999999988888763 35666777788889999999999998864
No 91
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=42.85 E-value=90 Score=28.27 Aligned_cols=73 Identities=15% Similarity=0.191 Sum_probs=48.8
Q ss_pred hHHHHHHHhhCCC---CCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh
Q 030670 36 ANISRIMKKALPA---NGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (173)
Q Consensus 36 A~V~RImK~aLP~---~~kISkDA~~al~k~a~------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 106 (173)
.-|.-|+++-... ...++.++.+.+..-+. .+...+...|.++|+.+++.+++.+||..|-+..+..-+.+
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 3455555544321 34677777666653322 34456777899999999999999999999977666654444
Q ss_pred HH
Q 030670 107 PL 108 (173)
Q Consensus 107 ~L 108 (173)
.+
T Consensus 273 ~~ 274 (366)
T COG1474 273 VL 274 (366)
T ss_pred HH
Confidence 43
No 92
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=42.51 E-value=32 Score=32.69 Aligned_cols=58 Identities=16% Similarity=0.295 Sum_probs=40.4
Q ss_pred hhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHH
Q 030670 44 KALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (173)
Q Consensus 44 ~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (173)
+++.+.--|-+|.+.||++||...=.||...-...-+.+++++ |..|++.+...|...
T Consensus 427 e~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 427 QSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 3333344588889999999999999999987665555555544 445666666666544
No 93
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=42.50 E-value=1.2e+02 Score=25.13 Aligned_cols=66 Identities=18% Similarity=0.113 Sum_probs=44.8
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~-~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.+....+.+++++.+.. +..|+.++...|...+.-=+..+-.+-...|.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 34555666666655442 5679999999998887755556666666655544444799999977765
No 94
>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=41.66 E-value=72 Score=25.78 Aligned_cols=49 Identities=20% Similarity=0.298 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc-chhhHHHHHHHHHHhh
Q 030670 63 CVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYREG 118 (173)
Q Consensus 63 ~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~-~yv~~Lk~~L~~yre~ 118 (173)
.+.+.++||-.+|. |.-++.+++..-|+.|||+ +.++.+......+++.
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~ 92 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSK 92 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 45566777776663 4459999999999999997 5777777776666643
No 95
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=41.65 E-value=59 Score=20.96 Aligned_cols=32 Identities=13% Similarity=0.419 Sum_probs=26.5
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eF 67 (173)
.+-.++|.|++... ..||.+.++-+.+++.+.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 46789999999865 479999999999988763
No 96
>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=41.55 E-value=35 Score=22.02 Aligned_cols=42 Identities=12% Similarity=0.088 Sum_probs=25.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHH-HHHHHHhcCCCCcCchhhHHH
Q 030670 53 AKDAKDTVQECVSEFISFITSE-ASDKCQKEKRKTINGDDLLWA 95 (173)
Q Consensus 53 SkDA~~al~k~a~eFI~~Ltse-A~~~~~~~kRKTI~~eDVl~A 95 (173)
+.||...|.+. =.||.--... +-..|+..|...|+.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 35666666664 4455544443 346778889999999998765
No 97
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=40.10 E-value=75 Score=26.85 Aligned_cols=71 Identities=7% Similarity=0.033 Sum_probs=42.9
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030670 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 33 LP~A~V~RImK~aLP-~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (173)
++...+..++++.+. .+..++.++.+.|.+.+.-=+..+-......|. +.++|+.+||..++.....++.+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i 255 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVI 255 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHH
Confidence 445566666665443 256799999999988773323333332323332 23479999999988765544333
No 98
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=39.39 E-value=95 Score=27.85 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.3
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (173)
++.++ .+.|+++....+.+.|..+= .+|...|.-.|--++|..|+.+||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 34455 67899999999988887764 2366777788889999999999996654
No 99
>PRK09526 lacI lac repressor; Reviewed
Probab=38.20 E-value=23 Score=29.72 Aligned_cols=39 Identities=13% Similarity=0.472 Sum_probs=31.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA 75 (173)
..-+++|.|++... ..||.+.++-+.+++.+ +.|.-..+
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~~ 54 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPNRV 54 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcCHH
Confidence 46689999999753 46999999999999999 56765433
No 100
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=38.12 E-value=89 Score=24.09 Aligned_cols=44 Identities=14% Similarity=0.081 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHH
Q 030670 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (173)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (173)
||+ |+-.|.-.+...++.+||...|+..|.+---..++.++...
T Consensus 3 yva--Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L 46 (113)
T PLN00138 3 VVA--AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEV 46 (113)
T ss_pred HHH--HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHH
Confidence 554 56788888999999999999999998864334444555444
No 101
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=38.09 E-value=50 Score=28.23 Aligned_cols=75 Identities=9% Similarity=0.102 Sum_probs=34.5
Q ss_pred CcccccCchhHHHHHHHhhCCC--CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CCcCchhhHHHHHh
Q 030670 27 REQDRYLPIANISRIMKKALPA--NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR------KTINGDDLLWAMAT 98 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~--~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kR------KTI~~eDVl~AL~~ 98 (173)
..++.+|....+.+-|.+.... ...|..|...+|.-||.+.+..|-..+..+|++-.. .+.-..||-..|..
T Consensus 38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHH
Confidence 4566788888877777766533 346999999999999999999999999888865421 12335677666655
Q ss_pred cCC
Q 030670 99 LGF 101 (173)
Q Consensus 99 LgF 101 (173)
|.-
T Consensus 118 l~~ 120 (264)
T PF05236_consen 118 LEQ 120 (264)
T ss_dssp ---
T ss_pred HHH
Confidence 544
No 102
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=37.22 E-value=1.1e+02 Score=29.30 Aligned_cols=55 Identities=16% Similarity=0.232 Sum_probs=39.6
Q ss_pred HHhhCCCCCcccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 42 MKKALPANGKIAKDAKDTVQECVSEF-------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 42 mK~aLP~~~kISkDA~~al~k~a~eF-------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
+++.++ .+.|+.+..+.+.+.|..+ -.++...|.-.|.-++|.+|+.+||..|..
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 344455 5789999987777666443 124445666777888999999999999985
No 103
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=36.50 E-value=31 Score=24.47 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=28.4
Q ss_pred CCcccHHHHHHHHHHHH-------HHHHHHHHHHHHHH-HhcCCCCcCchhhHHHHHhc
Q 030670 49 NGKIAKDAKDTVQECVS-------EFISFITSEASDKC-QKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 49 ~~kISkDA~~al~k~a~-------eFI~~LtseA~~~~-~~~kRKTI~~eDVl~AL~~L 99 (173)
+++++.+.++.|.+++. .||.-.+.++.+.. .....-+++.+|.-.-++.|
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 36899999999999975 45554444433222 23334566666644444433
No 104
>smart00350 MCM minichromosome maintenance proteins.
Probab=36.37 E-value=1.8e+02 Score=27.18 Aligned_cols=65 Identities=11% Similarity=0.170 Sum_probs=45.7
Q ss_pred ccCchhHHHHHHHhh----CCCCCcccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCCc
Q 030670 31 RYLPIANISRIMKKA----LPANGKIAKDAKDTVQECVSEF-------------------ISFITSEASDKCQKEKRKTI 87 (173)
Q Consensus 31 ~~LP~A~V~RImK~a----LP~~~kISkDA~~al~k~a~eF-------------------I~~LtseA~~~~~~~kRKTI 87 (173)
..++...+.+.+.-+ .| +||+++.+.|.+...+. +..|-.-|--.|+-..|.+|
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P---~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKP---KLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCC---CCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 357777777766433 34 58999999887654442 23444556667888899999
Q ss_pred CchhhHHHHHh
Q 030670 88 NGDDLLWAMAT 98 (173)
Q Consensus 88 ~~eDVl~AL~~ 98 (173)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999753
No 105
>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=35.30 E-value=41 Score=22.02 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=20.2
Q ss_pred CcCchhhHHHHHhcCCcchhhHHHH
Q 030670 86 TINGDDLLWAMATLGFEDYIDPLKA 110 (173)
Q Consensus 86 TI~~eDVl~AL~~LgF~~yv~~Lk~ 110 (173)
+=+.+||..-|..+||.+|.+..+.
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 3467899999999999988877653
No 106
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=35.16 E-value=48 Score=29.87 Aligned_cols=35 Identities=20% Similarity=0.228 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030670 66 EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 66 eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (173)
-=|..|..+|...|.+++++.|+.+|+..|++..-
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 34566778888888888999999999999997653
No 107
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=34.87 E-value=1.1e+02 Score=26.17 Aligned_cols=53 Identities=13% Similarity=0.112 Sum_probs=39.9
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCcCchhhHHHHHhcCC
Q 030670 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 49 ~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~--~kRKTI~~eDVl~AL~~LgF 101 (173)
+..|+.+|...|.+++.-=...+..|-...|.- .++++|+.+||...+....+
T Consensus 147 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 147 GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 678999999999998886555566665566554 45778999999987765544
No 108
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=34.77 E-value=1.1e+02 Score=23.68 Aligned_cols=43 Identities=9% Similarity=0.145 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHH
Q 030670 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 114 (173)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~ 114 (173)
||+ |.-.|.-.++.+++.+||.+.|+..|.+---..++.++..
T Consensus 5 yva--AYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~ 47 (112)
T PTZ00373 5 YVA--AYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKS 47 (112)
T ss_pred HHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 554 5677888899999999999999998885333334444443
No 109
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=34.54 E-value=82 Score=29.75 Aligned_cols=84 Identities=18% Similarity=0.210 Sum_probs=57.4
Q ss_pred ccCchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030670 31 RYLPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP-~~~kISkDA~~al~k~a~e----FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (173)
+..+..-|.-|++--.. .++.+++||.+.+....++ |..-|-.-|+.+|+..++++|..+||-.|-+ =|.|-.
T Consensus 359 ~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~--lF~D~k 436 (450)
T COG1224 359 RPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE--LFLDVK 436 (450)
T ss_pred CCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH--HHhhHH
Confidence 34556667777664332 4788999999999876654 4445556788999999999999999999843 233322
Q ss_pred hHHHHHHHHHHh
Q 030670 106 DPLKAYLMRYRE 117 (173)
Q Consensus 106 ~~Lk~~L~~yre 117 (173)
. --+|++.|++
T Consensus 437 r-Sv~~v~~~~~ 447 (450)
T COG1224 437 R-SVEYVEKYEG 447 (450)
T ss_pred H-HHHHHHHHHh
Confidence 2 2345556653
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=34.43 E-value=48 Score=30.89 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
|..|..+|...|.+++|..|+.+||..|++..
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 56778889999999999999999999999763
No 111
>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=34.14 E-value=32 Score=21.70 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.5
Q ss_pred CchhhHHHHHhcCCcchhhHHHHH
Q 030670 88 NGDDLLWAMATLGFEDYIDPLKAY 111 (173)
Q Consensus 88 ~~eDVl~AL~~LgF~~yv~~Lk~~ 111 (173)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578999999999998888776543
No 112
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=33.23 E-value=55 Score=28.85 Aligned_cols=32 Identities=25% Similarity=0.267 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 67 FISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 67 FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
-|..|..+|...|...+|..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 35577778888888899999999999999975
No 113
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=32.86 E-value=37 Score=28.23 Aligned_cols=37 Identities=14% Similarity=0.363 Sum_probs=29.2
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030670 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (173)
Q Consensus 33 LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~Ltse 74 (173)
.-+++|.|.+... ..||.+.++-+.+++.+. .|.-..
T Consensus 10 VS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn~ 46 (327)
T PRK10423 10 VSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPSA 46 (327)
T ss_pred CcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCccH
Confidence 4578999999653 369999999999999985 565543
No 114
>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=32.10 E-value=48 Score=21.61 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=18.5
Q ss_pred CchhhHHHHHhcCCcchhhHH
Q 030670 88 NGDDLLWAMATLGFEDYIDPL 108 (173)
Q Consensus 88 ~~eDVl~AL~~LgF~~yv~~L 108 (173)
++++|..-|+.+|+++|++..
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F 24 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENF 24 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHH
Confidence 578999999999999998765
No 115
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=31.31 E-value=37 Score=32.69 Aligned_cols=46 Identities=17% Similarity=0.344 Sum_probs=36.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcC
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN 88 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~ 88 (173)
|+++.+.--|=+|.+.|+++||.+.=.||+....+.-+.+++++|.
T Consensus 434 KqsIa~vpeIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 434 KQSIADVPEIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred chhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444334458899999999999999999999998887777777763
No 116
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=29.82 E-value=1.5e+02 Score=27.27 Aligned_cols=75 Identities=19% Similarity=0.244 Sum_probs=49.1
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CCcCchhhHHHHH
Q 030670 25 GVREQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQEC-VSEFISFITSEASD-KCQKE--KR-KTINGDDLLWAMA 97 (173)
Q Consensus 25 ~~~~~D~~LP~A~V~RImK~aLP~~~--kISkDA~~al~k~-a~eFI~~LtseA~~-~~~~~--kR-KTI~~eDVl~AL~ 97 (173)
+|+..|+- --|.|.-.+++.+|+.- .|..|-...+.+. ++.|+.-|+.--++ .+..+ +- +.++.+||++|++
T Consensus 43 PVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID 121 (351)
T KOG1528|consen 43 PVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAID 121 (351)
T ss_pred Ccchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHh
Confidence 45555543 35788889999999654 4666666666655 56677777774443 22222 23 7899999999998
Q ss_pred hcC
Q 030670 98 TLG 100 (173)
Q Consensus 98 ~Lg 100 (173)
.-+
T Consensus 122 ~G~ 124 (351)
T KOG1528|consen 122 RGN 124 (351)
T ss_pred ccc
Confidence 443
No 117
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=29.39 E-value=36 Score=28.60 Aligned_cols=39 Identities=13% Similarity=0.370 Sum_probs=30.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA 75 (173)
..-+++|.|++... .+||.+.++.+.+++.+ +.|.-..+
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~~ 54 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPNRA 54 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCccHH
Confidence 45678999998643 37999999999999999 46765433
No 118
>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=29.38 E-value=53 Score=25.35 Aligned_cols=62 Identities=10% Similarity=0.178 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHhhh
Q 030670 54 KDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREGD 119 (173)
Q Consensus 54 kDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~ 119 (173)
...+.-|..|..+.-.|...-..=.. ----.-..+...|+..|++..+.++..-|++|+...
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 34455566666665555443221110 001124567888999999999999999999998643
No 119
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=28.73 E-value=1.7e+02 Score=24.79 Aligned_cols=65 Identities=17% Similarity=0.079 Sum_probs=44.6
Q ss_pred cCchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCcCchhhHHHHH
Q 030670 32 YLPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE-KRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP-~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~-kRKTI~~eDVl~AL~ 97 (173)
.+....+.+.|+..+- .+..|+.+|...|.+.+..=...+..|-...|.-. +++ |+.+||-..+.
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~ 211 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVP 211 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHh
Confidence 3455555665555543 35689999999999988776667777776666533 334 99998876655
No 120
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=28.59 E-value=13 Score=24.41 Aligned_cols=58 Identities=26% Similarity=0.398 Sum_probs=32.2
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc---CchhhHHHHHhcCCcchh-hHHHHH
Q 030670 50 GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI---NGDDLLWAMATLGFEDYI-DPLKAY 111 (173)
Q Consensus 50 ~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI---~~eDVl~AL~~LgF~~yv-~~Lk~~ 111 (173)
.+|.++...+|.+++. .+..|+.+ +-..+=.|.+ .+...+..|.++|+.+++ +.++.+
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 4678888888888777 44555443 2222223333 345566677788877664 555443
No 121
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=28.22 E-value=1e+02 Score=20.80 Aligned_cols=33 Identities=18% Similarity=0.475 Sum_probs=24.8
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030670 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (173)
Q Consensus 31 ~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eF 67 (173)
..+.+++|.|++... ..|+.+.++.+.+++.++
T Consensus 10 ~gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 356788888888643 457888888888888776
No 122
>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=27.90 E-value=39 Score=21.57 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.7
Q ss_pred hhhHHHHHhcCCcc
Q 030670 90 DDLLWAMATLGFED 103 (173)
Q Consensus 90 eDVl~AL~~LgF~~ 103 (173)
+|++.||..|||..
T Consensus 4 ~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 4 EDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHTTS-H
T ss_pred HHHHHHHHHcCCCH
Confidence 68999999999973
No 123
>PTZ00183 centrin; Provisional
Probab=27.74 E-value=2e+02 Score=21.14 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=12.1
Q ss_pred HHhcCCCCcCchhhHHHHHh
Q 030670 79 CQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 79 ~~~~kRKTI~~eDVl~AL~~ 98 (173)
+-.++...|+.++++.++..
T Consensus 62 ~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 62 VDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred hCCCCCCcEeHHHHHHHHHH
Confidence 33455666777777666653
No 124
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=27.57 E-value=3.3e+02 Score=25.87 Aligned_cols=90 Identities=14% Similarity=0.096 Sum_probs=54.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030670 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVS----------EFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 30 D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~----------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (173)
+.++|.+.|-.-|... .+.|..+....+..-.. .-+.-|..+..+......=.-=++.+|..+|+.+
T Consensus 161 ~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~~ 237 (553)
T PRK14975 161 AAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRA 237 (553)
T ss_pred HHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHC
Confidence 4466777776666654 57788877666555444 4556666666555422111334678999999988
Q ss_pred CCc----------chhhHHHHHHHHHHhhhccC
Q 030670 100 GFE----------DYIDPLKAYLMRYREGDTKG 122 (173)
Q Consensus 100 gF~----------~yv~~Lk~~L~~yre~~~~~ 122 (173)
|+. .-..|+-..+-+||+..+..
T Consensus 238 g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~ 270 (553)
T PRK14975 238 GIELPSTRKWELREIDHPAVEPLLEYRKLSKLL 270 (553)
T ss_pred CCCCCCCcHHHhccCCCchHHHHHHHHHHHHHH
Confidence 884 11224445666888766543
No 125
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=27.30 E-value=74 Score=32.25 Aligned_cols=56 Identities=20% Similarity=0.340 Sum_probs=39.3
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Q 030670 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI 87 (173)
Q Consensus 29 ~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI 87 (173)
-...+|-.... |+++.+.--|-+|.+.+|++||.+.=.||...-...-++++++++
T Consensus 614 aST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~ 669 (795)
T PRK14868 614 ASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVL 669 (795)
T ss_pred eecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444544333 444544446899999999999999999999877766666666654
No 126
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.11 E-value=79 Score=28.93 Aligned_cols=31 Identities=26% Similarity=0.221 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030670 68 ISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (173)
|..|..+|.-.|.+++|+.|+.+|+..|++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 6678888999999999999999999999875
No 127
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=26.93 E-value=1.2e+02 Score=24.88 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=26.3
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEAS 76 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~ 76 (173)
|+++.+.--|-+|.+.+|++||...=.||...-.
T Consensus 111 KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 111 KEAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444468889999999999999999987543
No 128
>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=26.68 E-value=49 Score=20.99 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=19.4
Q ss_pred cCchhhHHHHHhcCCcchhhHHHHH
Q 030670 87 INGDDLLWAMATLGFEDYIDPLKAY 111 (173)
Q Consensus 87 I~~eDVl~AL~~LgF~~yv~~Lk~~ 111 (173)
-+.++|..-|..+||.+|++.++..
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678899999999998877765543
No 129
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=26.39 E-value=1.9e+02 Score=22.09 Aligned_cols=42 Identities=12% Similarity=0.101 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHH
Q 030670 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLM 113 (173)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~ 113 (173)
||+ |.-.|.-.++..|+.+||...|+..|.+---..+..++.
T Consensus 3 yva--AylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~ 44 (109)
T cd05833 3 YVA--AYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVIS 44 (109)
T ss_pred HHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHH
Confidence 454 566788888889999999999999887533333334443
No 130
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.33 E-value=45 Score=28.23 Aligned_cols=51 Identities=14% Similarity=0.330 Sum_probs=34.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI 87 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI 87 (173)
.+-+++|.|++... .+||.+.++-+.+++.+ +.|.-..+...-+..+.++|
T Consensus 12 GVS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~e-lgY~pn~~ar~l~~~~~~~I 62 (343)
T PRK10727 12 GVSVATVSRVINNS----PKASEASRLAVHSAMES-LSYHPNANARALAQQSTETV 62 (343)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCCCHHHHhhhhCCCCeE
Confidence 35578999999653 46999999999999998 46655444333233333443
No 131
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=25.76 E-value=68 Score=26.75 Aligned_cols=38 Identities=13% Similarity=0.333 Sum_probs=29.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030670 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (173)
Q Consensus 32 ~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~Ltse 74 (173)
.+-.++|.|++... .+||++.++.+.+++++. .|.-..
T Consensus 12 gvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn~ 49 (329)
T TIGR01481 12 GVSMATVSRVVNGN----PNVKPATRKKVLEVIKRL-DYRPNA 49 (329)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCCCH
Confidence 35678999999753 479999999999999885 555443
No 132
>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=24.56 E-value=75 Score=17.96 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=19.3
Q ss_pred HHHHHHhcCCCCcCchhhHHHHH-hcC
Q 030670 75 ASDKCQKEKRKTINGDDLLWAMA-TLG 100 (173)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~-~Lg 100 (173)
+....-.++.-+|+.+++..+|+ .||
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 34555667788999999999998 576
No 133
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=24.00 E-value=48 Score=23.59 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=15.2
Q ss_pred CcCchhhHHHHHhcCCc
Q 030670 86 TINGDDLLWAMATLGFE 102 (173)
Q Consensus 86 TI~~eDVl~AL~~LgF~ 102 (173)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999995
No 134
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=23.95 E-value=82 Score=28.59 Aligned_cols=80 Identities=18% Similarity=0.317 Sum_probs=51.3
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 106 (173)
...++.||=.-|.+|+-. .| +.+|+-|... +.||..+....--....+..-||+++||..+|.+|+|++ |
T Consensus 228 ~~~slHL~~~~L~~Ll~n-~~-gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d--E 297 (316)
T PHA03328 228 PGKSLHLHYRLIDRLLTA-CP-GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG--E 297 (316)
T ss_pred CCCcccchHHHHHHHHHh-CC-CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--H
Confidence 445667787777777665 45 6666654432 245555554332244566789999999999999999975 2
Q ss_pred HHHHHHHHHH
Q 030670 107 PLKAYLMRYR 116 (173)
Q Consensus 107 ~Lk~~L~~yr 116 (173)
-+.+|..-|.
T Consensus 298 l~~Ey~kly~ 307 (316)
T PHA03328 298 LLLEYKRLYA 307 (316)
T ss_pred HHHHHHHHHH
Confidence 2334444443
No 135
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=23.01 E-value=1e+02 Score=30.56 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=28.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 030670 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT 86 (173)
Q Consensus 51 kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKT 86 (173)
-|-+|.+.+|++||.+.=.||...-...-+++++++
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~ 627 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKY 627 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466788889999999999999986666655666555
No 136
>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=21.58 E-value=1.3e+02 Score=23.80 Aligned_cols=66 Identities=17% Similarity=0.123 Sum_probs=43.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc------------hhhHHHHHHHHHHhh
Q 030670 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED------------YIDPLKAYLMRYREG 118 (173)
Q Consensus 51 kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~------------yv~~Lk~~L~~yre~ 118 (173)
.+..+. +..++..++..+..-..-.. =-.|.+.+|++.+++.+.+.. |++.+.+.+++-++.
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455543 44445555444443333222 134788999999999999988 888888888888877
Q ss_pred hccC
Q 030670 119 DTKG 122 (173)
Q Consensus 119 ~~~~ 122 (173)
++.+
T Consensus 169 ~~~R 172 (224)
T PF02361_consen 169 QRLR 172 (224)
T ss_pred HHHc
Confidence 7644
No 137
>PF15605 Toxin_52: Putative toxin 52
Probab=21.54 E-value=2.6e+02 Score=21.49 Aligned_cols=44 Identities=20% Similarity=0.359 Sum_probs=36.4
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHH
Q 030670 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFI 71 (173)
Q Consensus 27 ~~~D~~LP~A~V~RImK~aLP~~~kISkDA~~al~k~a~eFI~~L 71 (173)
+..|-..-+-++.|.++..|+ |-..+.+.+++++..-.+-..+|
T Consensus 51 Em~da~~GL~n~~~~le~~L~-np~l~~~~r~~lq~~l~ea~~~l 94 (103)
T PF15605_consen 51 EMQDAYRGLVNRKRTLEGSLK-NPNLSGRTRELLQSKLNEANNYL 94 (103)
T ss_pred HHHHHHHHHHHHHHHHHHhcC-CCCCchHHHHHHHHHHHHHHHHH
Confidence 455667788899999999998 67899999999999887766655
No 138
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=20.97 E-value=73 Score=30.73 Aligned_cols=56 Identities=20% Similarity=0.311 Sum_probs=39.9
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcC--chhhHHHHHh
Q 030670 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMAT 98 (173)
Q Consensus 43 K~aLP~~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~~kRKTI~--~eDVl~AL~~ 98 (173)
|+++.+.--|-+|.+.++++||...=.||...-...-+.++++++. ..+|..+|..
T Consensus 431 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~~~y~p~~a~~~~~ 488 (535)
T PRK04184 431 KEAIADVPEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARKLAE 488 (535)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444468899999999999999999999777666666666543 3455555553
No 139
>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=20.96 E-value=2.4e+02 Score=17.95 Aligned_cols=45 Identities=24% Similarity=0.259 Sum_probs=32.5
Q ss_pred HHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHH-HHhhh
Q 030670 75 ASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR-YREGD 119 (173)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~-yre~~ 119 (173)
+...+-.++.-.|+.+++..++..++..-.-..+...++. ++...
T Consensus 5 ~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~D 50 (66)
T PF13499_consen 5 AFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQIFREFD 50 (66)
T ss_dssp HHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHHT
T ss_pred HHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHhC
Confidence 4456666777889999999999999987666666666554 44444
No 140
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=20.69 E-value=1.8e+02 Score=27.52 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=42.6
Q ss_pred hCCCCCcccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030670 45 ALPANGKIAKDAKDTVQECVSEFIS-------FITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 45 aLP~~~kISkDA~~al~k~a~eFI~-------~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (173)
.|| .+.++.++...+.+.|..+-. .++..|..++.=.+|.+++.+||-.|++
T Consensus 262 ~l~-~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 262 LLS-EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred ccc-cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 344 578999999999998887743 4666777888889999999999999986
No 141
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=20.32 E-value=2.5e+02 Score=24.18 Aligned_cols=49 Identities=14% Similarity=0.039 Sum_probs=34.7
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCcCchhhHHHHH
Q 030670 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQK-EKRKTINGDDLLWAMA 97 (173)
Q Consensus 49 ~~kISkDA~~al~k~a~eFI~~LtseA~~~~~~-~kRKTI~~eDVl~AL~ 97 (173)
+.+|+.||...|.+++.-=...+..|-...+.- ...++|+.+||...+.
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 678999999999998876444555554455443 3456899999877654
No 142
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.08 E-value=1.8e+02 Score=20.54 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=20.1
Q ss_pred HHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030670 76 SDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 76 ~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (173)
...+-.++.-.|+.++|..+|..+|+.
T Consensus 16 F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 16 FRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 355556677788888888888888764
No 143
>PF14434 Imm6: Immunity protein Imm6
Probab=20.02 E-value=3.8e+02 Score=20.76 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhc-CCCCcCchhhHHHHHhcCCcchh
Q 030670 70 FITSEASDKCQKE-KRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 70 ~LtseA~~~~~~~-kRKTI~~eDVl~AL~~LgF~~yv 105 (173)
++..+|.+.|.+- ..+.+++|++..-|+..++.+..
T Consensus 25 ~~~~~aL~~cw~wle~~~~~~D~LY~lldn~D~~gi~ 61 (122)
T PF14434_consen 25 EFVREALDACWKWLEGKEVTGDELYSLLDNEDENGIF 61 (122)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHhCcccccHH
Confidence 3338888999743 23899999999999987776543
Done!