Query psy16895
Match_columns 93
No_of_seqs 109 out of 589
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 16:26:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00160 histone H3; Provision 100.0 5.4E-49 1.2E-53 259.6 8.3 92 1-92 3-95 (97)
2 PTZ00018 histone H3; Provision 100.0 4E-47 8.7E-52 263.3 8.4 93 1-93 44-136 (136)
3 PLN00121 histone H3; Provision 100.0 4.3E-47 9.2E-52 263.2 8.3 93 1-93 44-136 (136)
4 smart00428 H3 Histone H3. 100.0 6.3E-47 1.4E-51 252.9 8.6 92 1-92 11-104 (105)
5 PLN00161 histone H3; Provision 100.0 5.4E-47 1.2E-51 262.0 8.6 92 1-92 37-129 (135)
6 KOG1745|consensus 100.0 4.1E-45 8.8E-50 252.9 5.8 93 1-93 45-137 (137)
7 COG2036 HHT1 Histones H3 and H 100.0 4E-30 8.7E-35 168.1 7.6 87 1-92 1-87 (91)
8 PF00125 Histone: Core histone 99.9 2.9E-22 6.3E-27 124.3 6.7 75 15-89 1-75 (75)
9 cd00076 H4 Histone H4, one of 99.6 1.4E-14 3E-19 93.7 6.6 75 13-92 7-81 (85)
10 PLN00035 histone H4; Provision 99.5 4.1E-14 8.8E-19 94.5 6.7 73 14-91 24-96 (103)
11 cd07981 TAF12 TATA Binding Pro 99.5 4.8E-14 1E-18 88.1 6.4 64 20-87 2-65 (72)
12 PTZ00015 histone H4; Provision 99.5 6.8E-14 1.5E-18 93.2 6.4 76 11-91 22-97 (102)
13 smart00803 TAF TATA box bindin 99.4 2.7E-13 5.8E-18 83.6 5.2 64 19-87 2-65 (65)
14 smart00417 H4 Histone H4. 99.4 2.9E-13 6.3E-18 85.6 4.5 67 13-84 7-73 (74)
15 cd07979 TAF9 TATA Binding Prot 99.1 8.1E-10 1.8E-14 74.9 7.2 65 26-91 4-68 (117)
16 PF00808 CBFD_NFYB_HMF: Histon 99.0 9.9E-10 2.1E-14 66.6 5.3 63 20-86 3-65 (65)
17 smart00576 BTP Bromodomain tra 98.8 3.3E-08 7.1E-13 62.1 6.2 54 38-91 20-73 (77)
18 cd00074 H2A Histone 2A; H2A is 98.6 7.2E-08 1.6E-12 65.4 4.7 68 16-87 17-84 (115)
19 PF15630 CENP-S: Kinetochore c 98.6 2.1E-07 4.5E-12 59.1 5.5 65 23-87 5-71 (76)
20 cd08050 TAF6 TATA Binding Prot 98.4 5.6E-07 1.2E-11 70.1 6.6 62 29-91 5-66 (343)
21 PF15511 CENP-T: Centromere ki 98.3 7.1E-07 1.5E-11 71.2 5.3 62 20-81 352-414 (414)
22 KOG0870|consensus 98.3 7.5E-07 1.6E-11 64.0 4.8 70 16-87 7-76 (172)
23 PF02969 TAF: TATA box binding 98.2 5.9E-06 1.3E-10 51.2 5.6 58 29-87 9-66 (66)
24 PF03847 TFIID_20kDa: Transcri 98.1 1.5E-05 3.4E-10 49.5 6.1 59 25-87 5-63 (68)
25 PF02291 TFIID-31kDa: Transcri 98.0 2.5E-05 5.4E-10 54.0 7.0 65 26-91 15-79 (129)
26 KOG1142|consensus 97.8 2.9E-05 6.4E-10 59.0 4.8 73 11-87 146-218 (258)
27 KOG0869|consensus 97.7 0.00012 2.6E-09 52.4 5.8 72 16-90 29-100 (168)
28 KOG3467|consensus 97.6 0.00022 4.9E-09 46.8 5.5 67 20-91 30-96 (103)
29 PF07524 Bromo_TP: Bromodomain 97.1 0.003 6.5E-08 39.2 6.5 54 38-91 20-73 (77)
30 smart00427 H2B Histone H2B. 97.1 0.0041 8.9E-08 40.7 7.1 64 26-89 4-67 (89)
31 PLN00158 histone H2B; Provisio 97.0 0.0047 1E-07 42.1 7.1 69 21-89 25-93 (116)
32 PTZ00463 histone H2B; Provisio 97.0 0.0048 1E-07 42.1 6.9 68 22-89 27-94 (117)
33 KOG3334|consensus 96.9 0.0035 7.6E-08 44.3 5.9 66 26-92 16-81 (148)
34 KOG0871|consensus 96.7 0.0075 1.6E-07 42.9 6.1 72 16-90 9-80 (156)
35 smart00414 H2A Histone 2A. 96.0 0.01 2.2E-07 39.7 3.8 67 17-87 7-73 (106)
36 KOG2549|consensus 96.0 0.02 4.4E-07 47.9 6.0 53 38-90 25-77 (576)
37 PF02269 TFIID-18kDa: Transcri 95.7 0.017 3.7E-07 37.6 3.7 59 29-87 7-65 (93)
38 PLN00154 histone H2A; Provisio 95.6 0.03 6.4E-07 39.2 4.8 68 17-87 36-103 (136)
39 PTZ00017 histone H2A; Provisio 95.5 0.019 4E-07 40.1 3.4 67 17-87 25-91 (134)
40 PLN00157 histone H2A; Provisio 94.7 0.038 8.3E-07 38.5 3.1 67 17-87 24-90 (132)
41 PLN00156 histone H2AX; Provisi 94.5 0.052 1.1E-06 38.1 3.5 67 17-87 27-93 (139)
42 KOG1744|consensus 94.3 0.13 2.8E-06 35.6 5.0 65 25-89 39-103 (127)
43 PLN00153 histone H2A; Provisio 94.2 0.059 1.3E-06 37.4 3.3 67 17-87 22-88 (129)
44 COG5262 HTA1 Histone H2A [Chro 94.2 0.09 2E-06 36.3 4.1 66 17-86 24-89 (132)
45 COG5150 Class 2 transcription 93.5 0.32 6.9E-06 34.1 5.9 71 15-88 7-77 (148)
46 PTZ00252 histone H2A; Provisio 93.1 0.14 3E-06 35.8 3.6 68 16-87 22-91 (134)
47 KOG1756|consensus 93.0 0.16 3.4E-06 35.4 3.7 67 17-87 25-91 (131)
48 KOG4336|consensus 92.6 0.54 1.2E-05 37.0 6.6 55 38-92 19-73 (323)
49 cd07978 TAF13 The TATA Binding 92.3 1 2.3E-05 29.2 6.7 62 25-87 4-65 (92)
50 cd08045 TAF4 TATA Binding Prot 91.9 0.6 1.3E-05 34.0 5.9 57 17-74 42-98 (212)
51 COG5094 TAF9 Transcription ini 91.8 0.5 1.1E-05 33.0 4.9 62 27-89 18-82 (145)
52 COG5208 HAP5 CCAAT-binding fac 91.6 0.38 8.3E-06 36.6 4.6 80 7-87 85-173 (286)
53 PF05236 TAF4: Transcription i 91.0 0.34 7.3E-06 36.4 3.9 58 17-75 41-98 (264)
54 KOG1657|consensus 90.2 0.5 1.1E-05 35.6 4.1 72 14-86 66-137 (236)
55 COG5248 TAF19 Transcription in 89.1 2.5 5.4E-05 28.9 6.4 61 25-87 11-71 (126)
56 KOG3901|consensus 88.3 3.2 7E-05 28.0 6.5 63 22-87 8-70 (109)
57 KOG2389|consensus 87.0 1.6 3.5E-05 34.8 5.2 53 38-90 43-95 (353)
58 COG5095 TAF6 Transcription ini 84.5 2.6 5.6E-05 34.0 5.2 61 29-90 11-71 (450)
59 PF09415 CENP-X: CENP-S associ 82.0 2.4 5.2E-05 26.4 3.4 56 29-84 5-63 (72)
60 PF09123 DUF1931: Domain of un 81.8 2.9 6.2E-05 29.4 4.0 60 25-89 1-60 (138)
61 COG1224 TIP49 DNA helicase TIP 77.0 5.7 0.00012 32.5 4.9 71 18-88 354-431 (450)
62 KOG1757|consensus 73.1 6.8 0.00015 26.9 3.8 67 23-91 31-97 (131)
63 KOG1658|consensus 71.8 3.6 7.7E-05 29.6 2.3 51 36-86 71-122 (162)
64 TIGR02902 spore_lonB ATP-depen 70.0 17 0.00036 30.1 6.2 49 39-87 280-330 (531)
65 TIGR00764 lon_rel lon-related 62.9 41 0.0009 28.4 7.2 64 26-89 315-391 (608)
66 PF13654 AAA_32: AAA domain; P 61.0 50 0.0011 27.4 7.3 67 23-90 430-507 (509)
67 KOG2680|consensus 55.0 30 0.00065 28.1 4.9 51 38-88 374-428 (454)
68 PRK07452 DNA polymerase III su 53.8 38 0.00083 25.4 5.2 59 26-86 136-196 (326)
69 PF10788 DUF2603: Protein of u 51.5 12 0.00026 26.2 2.0 33 3-36 97-129 (137)
70 PF08369 PCP_red: Proto-chloro 51.0 24 0.00051 19.9 2.8 19 67-85 26-44 (45)
71 cd08048 TAF11 TATA Binding Pro 49.1 67 0.0015 20.4 6.5 63 20-87 17-82 (85)
72 TIGR03015 pepcterm_ATPase puta 46.0 80 0.0017 22.6 5.7 49 39-87 213-264 (269)
73 PF07962 Swi3: Replication For 44.7 19 0.0004 22.8 1.9 25 8-32 38-62 (83)
74 PRK05907 hypothetical protein; 44.3 72 0.0016 24.6 5.4 67 20-86 131-200 (311)
75 PF10911 DUF2717: Protein of u 42.0 83 0.0018 20.0 4.5 60 6-68 2-64 (77)
76 PF06709 DUF1196: Protein of u 39.1 24 0.00053 20.5 1.6 20 16-35 11-30 (51)
77 KOG1659|consensus 38.6 83 0.0018 23.8 4.8 65 20-85 11-75 (224)
78 COG2118 DNA-binding protein [G 38.0 68 0.0015 21.9 3.9 32 50-89 68-99 (116)
79 PRK08487 DNA polymerase III su 37.8 1.2E+02 0.0025 23.2 5.7 47 38-86 151-197 (328)
80 TIGR02030 BchI-ChlI magnesium 37.3 73 0.0016 25.0 4.5 51 38-88 251-308 (337)
81 PRK14562 haloacid dehalogenase 35.3 77 0.0017 23.1 4.2 26 38-63 71-96 (204)
82 PF13060 DUF3921: Protein of u 33.8 1.1E+02 0.0023 18.2 4.0 28 37-64 21-48 (58)
83 TIGR02530 flg_new flagellar op 33.5 1.2E+02 0.0027 20.0 4.5 59 24-84 1-64 (96)
84 PRK06585 holA DNA polymerase I 32.3 1.2E+02 0.0026 22.9 5.0 49 38-86 158-207 (343)
85 KOG1942|consensus 32.1 1.1E+02 0.0024 24.9 4.8 51 38-88 383-437 (456)
86 PF05258 DUF721: Protein of un 31.3 88 0.0019 18.5 3.4 63 24-89 1-65 (89)
87 PF13581 HATPase_c_2: Histidin 30.7 1.1E+02 0.0025 19.1 4.0 45 25-69 7-51 (125)
88 PF04719 TAFII28: hTAFII28-lik 30.0 1.6E+02 0.0034 19.0 5.0 48 20-71 24-71 (90)
89 PF10083 DUF2321: Uncharacteri 29.1 62 0.0013 23.2 2.7 23 34-56 72-94 (158)
90 PRK05629 hypothetical protein; 28.5 1.7E+02 0.0036 22.1 5.2 59 27-86 130-189 (318)
91 PF07278 DUF1441: Protein of u 28.4 2.2E+02 0.0047 20.2 5.8 64 6-69 76-150 (152)
92 smart00350 MCM minichromosome 27.8 2E+02 0.0044 23.5 5.8 39 40-89 466-504 (509)
93 PRK00411 cdc6 cell division co 26.9 2.9E+02 0.0062 21.0 7.1 47 41-87 228-280 (394)
94 PF08681 DUF1778: Protein of u 25.7 1.7E+02 0.0036 18.0 4.1 50 39-88 3-60 (80)
95 cd00913 PCD_DCoH_subfamily_a P 25.2 36 0.00079 20.7 0.8 13 77-89 62-74 (76)
96 TIGR02442 Cob-chelat-sub cobal 25.0 1.3E+02 0.0029 25.4 4.4 51 38-88 246-303 (633)
97 PRK13877 conjugal transfer rel 25.0 1.1E+02 0.0024 20.5 3.2 52 39-91 14-67 (114)
98 PF04604 L_biotic_typeA: Type- 24.9 73 0.0016 18.7 2.0 20 45-64 7-26 (51)
99 TIGR01924 rsbW_low_gc serine-p 24.6 1.8E+02 0.004 19.8 4.4 45 22-66 15-59 (159)
100 CHL00081 chlI Mg-protoporyphyr 24.4 1.9E+02 0.004 23.0 4.9 51 38-88 264-321 (350)
101 cd00488 PCD_DCoH PCD_DCoH: The 24.2 39 0.00084 20.4 0.8 13 77-89 61-73 (75)
102 COG5624 TAF61 Transcription in 23.4 23 0.00051 29.3 -0.4 50 37-86 398-447 (505)
103 COG1598 Predicted nuclease of 23.4 1.3E+02 0.0029 18.1 3.1 25 44-68 34-58 (73)
104 PRK09862 putative ATP-dependen 23.3 2E+02 0.0043 24.0 5.0 51 40-90 437-493 (506)
105 PRK13407 bchI magnesium chelat 23.0 2.5E+02 0.0055 21.9 5.4 51 38-88 248-305 (334)
106 PRK07914 hypothetical protein; 23.0 2.1E+02 0.0045 21.6 4.8 60 26-86 131-191 (320)
107 PF06428 Sec2p: GDP/GTP exchan 22.2 1.7E+02 0.0036 19.2 3.6 32 45-76 15-46 (100)
108 PF01997 Translin: Translin fa 22.1 1.6E+02 0.0035 21.0 3.9 24 39-62 62-85 (200)
109 PF01031 Dynamin_M: Dynamin ce 22.1 1.1E+02 0.0023 22.9 3.0 34 16-55 186-219 (295)
110 PF12767 SAGA-Tad1: Transcript 21.2 1.6E+02 0.0035 21.7 3.8 31 38-68 219-250 (252)
111 PF01325 Fe_dep_repress: Iron 20.1 40 0.00087 19.8 0.3 27 51-83 3-29 (60)
112 COG1466 HolA DNA polymerase II 20.1 2.8E+02 0.0061 21.2 5.0 49 38-86 156-204 (334)
113 cd00914 PCD_DCoH_subfamily_b P 20.1 52 0.0011 20.0 0.8 13 77-89 62-74 (76)
No 1
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=5.4e-49 Score=259.56 Aligned_cols=92 Identities=71% Similarity=1.061 Sum_probs=89.5
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhcc-ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP 79 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~ 79 (93)
|||+||+|||+||+||++||||+||+||||||++++. +++||+++|+.+||||+|+|||++|||||+||+||||||||+
T Consensus 3 pGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~ 82 (97)
T PLN00160 3 PGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMP 82 (97)
T ss_pred CccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccch
Confidence 8999999999999999999999999999999999986 569999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHhccc
Q psy16895 80 KDIQLARRIRGER 92 (93)
Q Consensus 80 ~Di~La~~irg~~ 92 (93)
+||+|+.+|||+.
T Consensus 83 kD~~L~~rirg~~ 95 (97)
T PLN00160 83 KDMQLARRIRGQT 95 (97)
T ss_pred hhHHHHHHhhccc
Confidence 9999999999973
No 2
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=4e-47 Score=263.28 Aligned_cols=93 Identities=95% Similarity=1.326 Sum_probs=91.2
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~ 80 (93)
||+++|+|||+||+||++||||+||+||||||++++.+++||+++|+++|||++|+|||++|||+|+||+||||||||++
T Consensus 44 pGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~k 123 (136)
T PTZ00018 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
T ss_pred CchhHHHHHHHHcccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhcccC
Q psy16895 81 DIQLARRIRGERA 93 (93)
Q Consensus 81 Di~La~~irg~~~ 93 (93)
||+|+.+|||+.+
T Consensus 124 D~~L~~rirg~~~ 136 (136)
T PTZ00018 124 DIQLARRIRGERS 136 (136)
T ss_pred hHHHHHHhcccCC
Confidence 9999999999863
No 3
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=4.3e-47 Score=263.16 Aligned_cols=93 Identities=95% Similarity=1.323 Sum_probs=91.4
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~ 80 (93)
||+++|+|||+||+||++||||+||+||||||++++.+++||+++|+.+|||++|+|||++|||+|+||+||||||||++
T Consensus 44 pGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~k 123 (136)
T PLN00121 44 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
T ss_pred chhHHHHHHHHhccccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhcccC
Q psy16895 81 DIQLARRIRGERA 93 (93)
Q Consensus 81 Di~La~~irg~~~ 93 (93)
||+|+.+|||+.+
T Consensus 124 D~~L~~rirg~~~ 136 (136)
T PLN00121 124 DIQLARRIRGERA 136 (136)
T ss_pred hHHHHHHhccccC
Confidence 9999999999864
No 4
>smart00428 H3 Histone H3.
Probab=100.00 E-value=6.3e-47 Score=252.87 Aligned_cols=92 Identities=89% Similarity=1.231 Sum_probs=90.4
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhccc--cccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccC
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIM 78 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~~--~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~ 78 (93)
||++||+|||+||+||++||||+||+||||||++++.+ ++|||++|+.+||+++|+|++++||+|++||.||||||||
T Consensus 11 pg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~ 90 (105)
T smart00428 11 PGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIM 90 (105)
T ss_pred CcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCc
Confidence 89999999999999999999999999999999999986 9999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHhccc
Q psy16895 79 PKDIQLARRIRGER 92 (93)
Q Consensus 79 ~~Di~La~~irg~~ 92 (93)
++||+||.+|||++
T Consensus 91 ~kDi~La~rir~~~ 104 (105)
T smart00428 91 PKDIQLARRIRGER 104 (105)
T ss_pred HhhHHHHHHHhccC
Confidence 99999999999975
No 5
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=5.4e-47 Score=262.01 Aligned_cols=92 Identities=74% Similarity=1.090 Sum_probs=89.6
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhcc-ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP 79 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~ 79 (93)
|||+||+|||+||+||++|||++||+||||||++++. +++||+++|+.+||||+|+|||++|||||+||+||||||||+
T Consensus 37 pGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~ 116 (135)
T PLN00161 37 PGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMP 116 (135)
T ss_pred CcchHHHHHHHHccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccch
Confidence 8999999999999999999999999999999999996 589999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHhccc
Q psy16895 80 KDIQLARRIRGER 92 (93)
Q Consensus 80 ~Di~La~~irg~~ 92 (93)
+||+|+.+|||+.
T Consensus 117 kDm~La~rirg~~ 129 (135)
T PLN00161 117 KDMQLARRIRGPI 129 (135)
T ss_pred hhHHHHHHhcccc
Confidence 9999999999974
No 6
>KOG1745|consensus
Probab=100.00 E-value=4.1e-45 Score=252.94 Aligned_cols=93 Identities=95% Similarity=1.341 Sum_probs=91.5
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~ 80 (93)
||+++++|||+||+||++||+|+||+||||||.+++..++|||++|+.+||||+|+|||+||||+|+||+||||||||++
T Consensus 45 pg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpk 124 (137)
T KOG1745|consen 45 PGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 124 (137)
T ss_pred CchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEeccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhcccC
Q psy16895 81 DIQLARRIRGERA 93 (93)
Q Consensus 81 Di~La~~irg~~~ 93 (93)
||+||++|||+++
T Consensus 125 diQlArrirg~~~ 137 (137)
T KOG1745|consen 125 DIQLARRIRGERA 137 (137)
T ss_pred ceehhhhcccCCC
Confidence 9999999999874
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.96 E-value=4e-30 Score=168.11 Aligned_cols=87 Identities=49% Similarity=0.684 Sum_probs=83.8
Q ss_pred CccchhhhhhhhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcc
Q psy16895 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80 (93)
Q Consensus 1 pg~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~ 80 (93)
||+..++|+|+||+++.++||++||+|++|+. +..|||.+|.++||+++|.|+..++++|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~-----~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKA-----GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHH-----hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 79999999999999999999999999999999 5569999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccc
Q psy16895 81 DIQLARRIRGER 92 (93)
Q Consensus 81 Di~La~~irg~~ 92 (93)
||+|+.+.+|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999999853
No 8
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.87 E-value=2.9e-22 Score=124.25 Aligned_cols=75 Identities=48% Similarity=0.641 Sum_probs=71.2
Q ss_pred chhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 15 st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
+|...||+.||.|++|++..+....+||+++|+..||.++|.+++++|++|+.+|.|+||+||+++||++|.+++
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 467899999999999999888777799999999999999999999999999999999999999999999999885
No 9
>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=99.55 E-value=1.4e-14 Score=93.75 Aligned_cols=75 Identities=23% Similarity=0.271 Sum_probs=69.1
Q ss_pred hcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhccc
Q psy16895 13 QKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 92 (93)
Q Consensus 13 Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~~ 92 (93)
++.+..-||++|..||+|.. |..|++.++.+++.++.|.|+.++..||+.+|.||+|+||+..||.++.+-.|..
T Consensus 7 ~~~~~~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~ 81 (85)
T cd00076 7 LRDNIKGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 81 (85)
T ss_pred HHHhhccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCC
Confidence 34444459999999999998 9999999999999999999999999999999999999999999999999998853
No 10
>PLN00035 histone H4; Provisional
Probab=99.52 E-value=4.1e-14 Score=94.45 Aligned_cols=73 Identities=21% Similarity=0.229 Sum_probs=67.8
Q ss_pred cchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 14 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 14 ~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
+..-.=||++|..||+|.. +..|++.+|.++|.++.|.|+.++..||+..|.||+|+||+.+|+.++.+-.|.
T Consensus 24 ~d~i~~ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 24 RDNIQGITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred HhhhccCCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 3333449999999999999 999999999999999999999999999999999999999999999999998875
No 11
>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=99.51 E-value=4.8e-14 Score=88.15 Aligned_cols=64 Identities=27% Similarity=0.325 Sum_probs=56.0
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
+++--.+.|++++ .+..|++++|.++||+.+|+|+.+++++|..+|.|+||+||+++||+|+.+
T Consensus 2 ~~k~~l~~lv~~i----d~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 2 LTKRKLQELLKEI----DPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred CcHHHHHHHHHhh----CCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3444455666666 456999999999999999999999999999999999999999999999975
No 12
>PTZ00015 histone H4; Provisional
Probab=99.49 E-value=6.8e-14 Score=93.23 Aligned_cols=76 Identities=20% Similarity=0.216 Sum_probs=69.3
Q ss_pred hhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 11 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 11 ~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
+.++....-||++|..||+|.. +..|++.++.+++.++.|.|+.++..+|+.+|.||+|+||+.+||.++.+-.|
T Consensus 22 k~~r~~i~gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 22 KVLRDNIRGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQG 96 (102)
T ss_pred HHHhhcccCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcC
Confidence 3334444459999999999999 99999999999999999999999999999999999999999999999999887
Q ss_pred c
Q psy16895 91 E 91 (93)
Q Consensus 91 ~ 91 (93)
.
T Consensus 97 ~ 97 (102)
T PTZ00015 97 R 97 (102)
T ss_pred C
Confidence 5
No 13
>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=99.43 E-value=2.7e-13 Score=83.60 Aligned_cols=64 Identities=20% Similarity=0.207 Sum_probs=61.3
Q ss_pred hcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 19 LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 19 lIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.+|+.|..|+.+.. |..|+++++..+|.+..|.++-++.++|..++.|+||+||+++||.+|.+
T Consensus 2 ~~p~~~i~ria~~~-----Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-----GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999998 99999999999999999999999999999999999999999999999863
No 14
>smart00417 H4 Histone H4.
Probab=99.41 E-value=2.9e-13 Score=85.63 Aligned_cols=67 Identities=19% Similarity=0.214 Sum_probs=61.5
Q ss_pred hcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHH
Q psy16895 13 QKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 84 (93)
Q Consensus 13 Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~L 84 (93)
++.+-.-||++|..||+|.- |..|++.++.+++.++.|.|+..+..+|+.+|.||+|+||+.+|+..
T Consensus 7 ~~d~i~gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 7 LRDNIQGITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred HHhhhcCCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 33444459999999999998 99999999999999999999999999999999999999999999864
No 15
>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=99.05 E-value=8.1e-10 Score=74.85 Aligned_cols=65 Identities=22% Similarity=0.361 Sum_probs=58.6
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
.++|..|..+. |..++++++...|-+.++.|..++..+|...|.||||.||+.+|++||.+.|+.
T Consensus 4 ~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 46666665544 678999999999999999999999999999999999999999999999999875
No 16
>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=99.00 E-value=9.9e-10 Score=66.62 Aligned_cols=63 Identities=24% Similarity=0.294 Sum_probs=54.1
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
+|.+...|++|.. .+..+++.+|..+++.++|.|+..|...|+..|.+.+|+||+.+|+.-|.
T Consensus 3 lP~a~vkri~k~~----~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 3 LPLARVKRIMKSD----PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHHT----STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhccC----CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 6888888888776 35678999999999999999999999999999999999999999998763
No 17
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.75 E-value=3.3e-08 Score=62.14 Aligned_cols=54 Identities=24% Similarity=0.155 Sum_probs=51.2
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
|-.+++++|++.|.+..|.|+..+.+.+...|.|++|.++++.|+.++..--|.
T Consensus 20 Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 20 GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 778999999999999999999999999999999999999999999999877664
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=98.60 E-value=7.2e-08 Score=65.44 Aligned_cols=68 Identities=22% Similarity=0.182 Sum_probs=62.6
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
..+.+|-.++.|++|+- ....|++.+|...|-.+.|.+..+++|.|...|.|.+|.+|+++|++++.+
T Consensus 17 agL~fPV~ri~R~Lk~~----~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 17 AGLQFPVGRIHRYLKKG----RYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred cCccCcHHHHHHHHHcC----ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 36889999999999872 157999999999999999999999999999999999999999999999975
No 19
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.55 E-value=2.1e-07 Score=59.07 Aligned_cols=65 Identities=28% Similarity=0.260 Sum_probs=52.8
Q ss_pred ccHHHHHHHHHHhc--cccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 23 LPFQRLVREIAQDF--KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 23 ~pF~Rlvrei~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
+.+..-|-+|+.+. ..+..++++.+.+|-|.+=.++..+..|--..|.||||.||+++|+.|..|
T Consensus 5 aal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 5 AALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 34445566666665 468899999999999999999999999999999999999999999999864
No 20
>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=98.44 E-value=5.6e-07 Score=70.08 Aligned_cols=62 Identities=21% Similarity=0.253 Sum_probs=55.0
Q ss_pred HHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 29 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
|+.|+... |..+++++|..+|.+-+|.++-++.++|..+|.|+||+||+++||++|.+.++.
T Consensus 5 i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 5 IKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 44444322 677999999999999999999999999999999999999999999999999864
No 21
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.35 E-value=7.1e-07 Score=71.21 Aligned_cols=62 Identities=26% Similarity=0.311 Sum_probs=43.9
Q ss_pred cccccHHHHHHHHHHh-ccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCccc
Q psy16895 20 IRKLPFQRLVREIAQD-FKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 81 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~-~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~D 81 (93)
+|..+..+++.-.+.. +....+++++|+.+|.+++|-|..+|-+|--..|.|||||||...|
T Consensus 352 lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 352 LPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4555555555555442 2357999999999999999999999999999999999999999877
No 22
>KOG0870|consensus
Probab=98.35 E-value=7.5e-07 Score=63.96 Aligned_cols=70 Identities=24% Similarity=0.264 Sum_probs=64.2
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.++.+|++-..||||+...+. +.-++.+|..++++++=-|+.-|.-.|+..|.-.+|+|++++|+-=++.
T Consensus 7 ~dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 7 EDLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HHhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 468899999999999997765 6899999999999999999999999999999999999999999876654
No 23
>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=98.18 E-value=5.9e-06 Score=51.17 Aligned_cols=58 Identities=28% Similarity=0.318 Sum_probs=45.1
Q ss_pred HHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 29 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
||.++... |-...++++...|.+-+|.-+-++.++|..++.|+||.++++.||..|.|
T Consensus 9 vk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 9 VKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 44554433 33468999999999999999999999999999999999999999998875
No 24
>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=98.09 E-value=1.5e-05 Score=49.46 Aligned_cols=59 Identities=24% Similarity=0.292 Sum_probs=46.6
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
++.||++| .+...+.+++-+.|.+.+++|+.+....|..+|.|.|--||.++|+++..+
T Consensus 5 l~~Lv~~i----Dp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 5 LQELVKQI----DPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHCC-----SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHc----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 34455555 678999999999999999999999999999999999999999999999875
No 25
>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=98.03 E-value=2.5e-05 Score=53.99 Aligned_cols=65 Identities=26% Similarity=0.362 Sum_probs=52.4
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
.|+|..|..+. |-..+++.++..|-|.+=.|..++++||...|.||+|.+|..+|++||...|.+
T Consensus 15 a~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 57888887766 344589999999999999999999999999999999999999999999988753
No 26
>KOG1142|consensus
Probab=97.83 E-value=2.9e-05 Score=59.04 Aligned_cols=73 Identities=19% Similarity=0.278 Sum_probs=66.1
Q ss_pred hhhcchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 11 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 11 ~~Q~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.++.+++.++-|--...||++| .++..+.+++-+.|.+.|++|+..+-.-|-.+|+|.|-.||-++||+|+.+
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 5667888888888888888888 568889999999999999999999999999999999999999999999864
No 27
>KOG0869|consensus
Probab=97.69 E-value=0.00012 Score=52.38 Aligned_cols=72 Identities=15% Similarity=0.208 Sum_probs=64.4
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
.+-++|.+-..|+.|.+ +..+-.++++|.+..||.+=.|+-=+-..|..-.---||+||+.+|+-.|+--.|
T Consensus 29 qDr~LPIANV~RIMK~~---lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 29 QDRFLPIANVSRIMKKA---LPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhhccHHHHHHHHHhc---CCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 34569999999999999 4488899999999999999999999999999999999999999999998876554
No 28
>KOG3467|consensus
Probab=97.58 E-value=0.00022 Score=46.83 Aligned_cols=67 Identities=24% Similarity=0.281 Sum_probs=59.8
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
|-|....||.|.- +--|+..-..+....++-.|+.....+|...+-||||+||+.-|+--+.+-.|.
T Consensus 30 itKpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred cchHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 3477788888877 788999999999999999999999999999999999999999999888877664
No 29
>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=97.12 E-value=0.003 Score=39.17 Aligned_cols=54 Identities=22% Similarity=0.137 Sum_probs=49.4
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
|=...++.|++.|-+.+..|+..+...+...|-|++|-...+.|+.++..--|.
T Consensus 20 GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 20 GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 334789999999999999999999999999999999999999999999876664
No 30
>smart00427 H2B Histone H2B.
Probab=97.09 E-value=0.0041 Score=40.66 Aligned_cols=64 Identities=16% Similarity=0.202 Sum_probs=54.8
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
..-+..+..+..++..++..|+..+--..-++...+..+|..++...||.||+.+||+.|.++.
T Consensus 4 ~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 4 AIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 3344444444567889999999999999999999999999999999999999999999998875
No 31
>PLN00158 histone H2B; Provisional
Probab=97.00 E-value=0.0047 Score=42.15 Aligned_cols=69 Identities=14% Similarity=0.215 Sum_probs=61.5
Q ss_pred ccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 21 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 21 pk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
++..|..-|..+..+..++..++..|+..+--...++...+..+|..++...+|.||+.+||+-+.++.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 356777777777777778999999999999999999999999999999999999999999999998875
No 32
>PTZ00463 histone H2B; Provisional
Probab=96.98 E-value=0.0048 Score=42.15 Aligned_cols=68 Identities=10% Similarity=0.128 Sum_probs=60.7
Q ss_pred cccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 22 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 22 k~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
+..|..-|..++.+..++..++..|+..+--..-++...+..+|..++...+|.||+.+||+-+.++.
T Consensus 27 ~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 27 YDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred cchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 45677777777777778999999999999999999999999999999999999999999999999875
No 33
>KOG3334|consensus
Probab=96.90 E-value=0.0035 Score=44.29 Aligned_cols=66 Identities=24% Similarity=0.416 Sum_probs=54.2
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhccc
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 92 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~~ 92 (93)
.+++..|..+++ -.-+.+..+.-|-|.+=.|.+.+++||...+.||++.||..+|++||...++.+
T Consensus 16 a~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 16 ARVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 355555655443 344567778888899999999999999999999999999999999999988764
No 34
>KOG0871|consensus
Probab=96.66 E-value=0.0075 Score=42.88 Aligned_cols=72 Identities=18% Similarity=0.259 Sum_probs=65.5
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
-++-+||+....+|+|++ ..+.||..+|-+.+++++=.|+--+--.||..+.--.++||.++-+.=|..-.|
T Consensus 9 de~sLPkAtv~KmIke~l---P~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEML---PKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhC---CcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 456799999999999994 479999999999999999999999999999999999999999999887776655
No 35
>smart00414 H2A Histone 2A.
Probab=96.03 E-value=0.01 Score=39.69 Aligned_cols=67 Identities=25% Similarity=0.198 Sum_probs=58.8
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
++.+|-.-|.|++|+- .-..|++..|..-|--+.|....+++|-|...+...|+..|+++|++++.+
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 5677888888888765 236799999999999999999999999999999999999999999999864
No 36
>KOG2549|consensus
Probab=95.97 E-value=0.02 Score=47.86 Aligned_cols=53 Identities=21% Similarity=0.218 Sum_probs=49.8
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
|-..++.+|..+|-+-.|.-+-++.++|.+++.|+||-+++.+|+.-|.+.+.
T Consensus 25 Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 25 GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 67789999999999999999999999999999999999999999999988763
No 37
>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=95.70 E-value=0.017 Score=37.55 Aligned_cols=59 Identities=14% Similarity=0.214 Sum_probs=30.7
Q ss_pred HHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 29 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
|++++-.++....-.++....+.+..=.|++.+...|..+|...+|.+|+.+|+.++.|
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 45555566666777889999999999999999999999999999999999999988764
No 38
>PLN00154 histone H2A; Provisional
Probab=95.59 E-value=0.03 Score=39.21 Aligned_cols=68 Identities=19% Similarity=0.125 Sum_probs=60.2
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.|.+|-..+.|+.|+-.. ...|+...|..-|--+.|....+++|-|...|...++..|++++++|+.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 677888888888887621 35799999999999999999999999999999999999999999999863
No 39
>PTZ00017 histone H2A; Provisional
Probab=95.46 E-value=0.019 Score=40.10 Aligned_cols=67 Identities=24% Similarity=0.186 Sum_probs=59.8
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.|.+|-.-+.|+.++- ....|+...|..-|--+.|....+++|-|...+...++..|++++++++.+
T Consensus 25 gL~FPVgRi~R~Lk~g----~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKG----RYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhcc----chhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 6778888888888764 236799999999999999999999999999999999999999999999864
No 40
>PLN00157 histone H2A; Provisional
Probab=94.65 E-value=0.038 Score=38.46 Aligned_cols=67 Identities=25% Similarity=0.199 Sum_probs=59.1
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.|.+|-.-+.|++|+- ....|++..|..-|--..|....+++|-|...|...++..|++++++++.+
T Consensus 24 gL~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 6778888888888763 246799999999999999999999999999999999999999999999863
No 41
>PLN00156 histone H2AX; Provisional
Probab=94.46 E-value=0.052 Score=38.11 Aligned_cols=67 Identities=25% Similarity=0.198 Sum_probs=58.3
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.|.+|-..+.|+.++- ....|+...|..-|--+.|....+++|-|...+...++..|+|+.++|+.+
T Consensus 27 gL~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 5667777777777664 246799999999999999999999999999999999999999999999864
No 42
>KOG1744|consensus
Probab=94.25 E-value=0.13 Score=35.64 Aligned_cols=65 Identities=23% Similarity=0.322 Sum_probs=53.6
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
|...|..++.+...+.-++..|+..+--..=+++..+...|+.+|-.-||-||..++|+.|.++.
T Consensus 39 ~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 39 YSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred eeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 33444445444455677999999999888888888999999999999999999999999999875
No 43
>PLN00153 histone H2A; Provisional
Probab=94.24 E-value=0.059 Score=37.39 Aligned_cols=67 Identities=25% Similarity=0.194 Sum_probs=59.0
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.+.+|-..+.|++|+- ....|+...|..-|--..|....+++|-|...|...++..|+|+.++++.+
T Consensus 22 gL~FpVgRi~R~Lr~g----~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKG----KYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcC----chhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 5778878888887763 246799999999999999999999999999999999999999999999864
No 44
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.21 E-value=0.09 Score=36.27 Aligned_cols=66 Identities=23% Similarity=0.235 Sum_probs=55.5
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
.+..|---..|+.| .-....|+.++|...|--..|....++.|-|-..|.--|-+.|+|+-++||.
T Consensus 24 gl~fpvgrvkr~lk----~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAI 89 (132)
T COG5262 24 GLIFPVGRVKRLLK----KGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAI 89 (132)
T ss_pred CccccHHHHHHHHH----cCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHh
Confidence 34455555555554 3346899999999999999999999999999999999999999999999985
No 45
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=93.53 E-value=0.32 Score=34.06 Aligned_cols=71 Identities=21% Similarity=0.182 Sum_probs=62.5
Q ss_pred chhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 15 st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
+.++-+||+..+..|.+|. ..++-|+.+|-+.++++.=.|+.-+--.||.++-.-..+||.++-+-=|..-
T Consensus 7 dDe~sLPKATVqKMvS~iL---p~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 7 DDENSLPKATVQKMVSSIL---PKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred cccccCcHHHHHHHHHHhc---cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 3456799999999999994 4899999999999999999999999999999999999999999877655543
No 46
>PTZ00252 histone H2A; Provisional
Probab=93.11 E-value=0.14 Score=35.80 Aligned_cols=68 Identities=19% Similarity=0.169 Sum_probs=56.8
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhh--cCccccCcccHHHHHH
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 87 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akR~Tl~~~Di~La~~ 87 (93)
.+|.+|-..+.|++|+- ....|+...|..-|--+.|....+++|-|...|.. .|+..|+++.++|+.+
T Consensus 22 AGL~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 35777777777877664 23679999999999999999999999999999865 5778999999999864
No 47
>KOG1756|consensus
Probab=92.97 E-value=0.16 Score=35.35 Aligned_cols=67 Identities=25% Similarity=0.225 Sum_probs=57.5
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
++..|---..|+.|+ -....|++.+|...|--..|.....+.|.|-..|.-.++..|+|+-++||.+
T Consensus 25 gl~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred ccccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 455666666666666 2368999999999999999999999999999999999999999999999964
No 48
>KOG4336|consensus
Probab=92.61 E-value=0.54 Score=36.99 Aligned_cols=55 Identities=16% Similarity=0.066 Sum_probs=49.7
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhccc
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 92 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~~ 92 (93)
+---++..|++.|-++.-.|+-.+|+.+-..+.|+||--.+..|+.|.....|..
T Consensus 19 gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~ 73 (323)
T KOG4336|consen 19 GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK 73 (323)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC
Confidence 4445888999999999999999999999999999999999999999999887753
No 49
>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=92.25 E-value=1 Score=29.20 Aligned_cols=62 Identities=16% Similarity=0.266 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
|..=++..+-.++..-.=.++....+.+..=.|++.+.-.|..+|. .+|-.++++|+..+.|
T Consensus 4 f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 4 FTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 4455566666666666677899999999999999999999999998 6666669999998864
No 50
>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=91.92 E-value=0.6 Score=34.02 Aligned_cols=57 Identities=18% Similarity=0.224 Sum_probs=50.7
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCc
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR 74 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR 74 (93)
..++..-|+.+.+..|+.+.+-. -++++.+..|..|+|.+|-.+.++...++.|...
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~ 98 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVD 98 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 46888899999999998876544 8899999999999999999999999999999743
No 51
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.75 E-value=0.5 Score=33.01 Aligned_cols=62 Identities=24% Similarity=0.303 Sum_probs=45.6
Q ss_pred HHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCc---ccHHHHHHHh
Q psy16895 27 RLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLARRIR 89 (93)
Q Consensus 27 Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~---~Di~La~~ir 89 (93)
||+.=|....+ -....+....-|-+.+--|..++.+||...|.|++|-.+.. +|++||.--+
T Consensus 18 rlihliL~Slg-i~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 18 RLIHLILRSLG-IEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred hHHHHHHHhcC-chhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 55555544332 23344555666778899999999999999999999976655 9999997544
No 52
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=91.63 E-value=0.38 Score=36.56 Aligned_cols=80 Identities=20% Similarity=0.215 Sum_probs=59.7
Q ss_pred hhhhhhhcchhhh---------cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCcccc
Q psy16895 7 REIRRYQKSTELL---------IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI 77 (93)
Q Consensus 7 rEIr~~Q~st~ll---------Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl 77 (93)
+=+|+||++.+.+ ...+||.|+=| ++..-.+--=++++|=...-.++|-|+..|--.|...|...||-|+
T Consensus 85 ~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkk-vMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtL 163 (286)
T COG5208 85 RISRYWQQTIKAAEEERQILLKDHNLPLARIKK-VMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTL 163 (286)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHH-HHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHH
Confidence 4478888765433 23478888743 3221112234677888889999999999999999999999999999
Q ss_pred CcccHHHHHH
Q psy16895 78 MPKDIQLARR 87 (93)
Q Consensus 78 ~~~Di~La~~ 87 (93)
...||.-|.+
T Consensus 164 QksDia~Av~ 173 (286)
T COG5208 164 QKSDIAAAVK 173 (286)
T ss_pred HHHHHHHHHH
Confidence 9999987764
No 53
>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=91.04 E-value=0.34 Score=36.38 Aligned_cols=58 Identities=21% Similarity=0.273 Sum_probs=38.6
Q ss_pred hhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCcc
Q psy16895 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRV 75 (93)
Q Consensus 17 ~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~ 75 (93)
.+++...|+.+-+++|+.+.+ ...+.++.+..|--|+|.+|-.|.+++...|.|....
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 467777889999999986554 6789999999999999999999999999999997554
No 54
>KOG1657|consensus
Probab=90.19 E-value=0.5 Score=35.64 Aligned_cols=72 Identities=19% Similarity=0.192 Sum_probs=59.9
Q ss_pred cchhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 14 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 14 ~st~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
...++.+..+|..|+ |.|...-..---|+.+|....-.++|.++..|-..|+.-|--++|.|+...|+.-+.
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 456778888999997 455443333448999999999999999999999999999999999999999887654
No 55
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=89.11 E-value=2.5 Score=28.93 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=51.9
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
|..=++..+-.|+....=..+.+++|.+..=+|++.+.-.|-.+|- .|-.++.+|.+.+.+
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 6666777777777777777899999999999999999999988887 777889999999875
No 56
>KOG3901|consensus
Probab=88.33 E-value=3.2 Score=28.00 Aligned_cols=63 Identities=19% Similarity=0.260 Sum_probs=52.1
Q ss_pred cccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 22 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 22 k~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
+--|++=+|..+-.|+.+..=-.+.+++|.+..=.|++.+...|..+. +|=.+.++|+..+.|
T Consensus 8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 345888888888888877777789999999999999999977666665 888899999998764
No 57
>KOG2389|consensus
Probab=87.01 E-value=1.6 Score=34.83 Aligned_cols=53 Identities=21% Similarity=0.104 Sum_probs=47.4
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
+---++..|++.|+..+=.|+-++.+.|-..+.|++|+-....||-++..--|
T Consensus 43 g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls 95 (353)
T KOG2389|consen 43 GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS 95 (353)
T ss_pred CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence 34456777999999999999999999999999999999999999999886554
No 58
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=84.48 E-value=2.6 Score=33.96 Aligned_cols=61 Identities=20% Similarity=0.252 Sum_probs=51.6
Q ss_pred HHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 29 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
+|..++. .|--.+..+++.+|.--.|.-+-++-+.|.+.+.|.||--++..||.-|.+-+.
T Consensus 11 ~KdvAes-lGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 11 LKDVAES-LGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHH-cCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 4444432 345678899999999999999999999999999999999999999999987653
No 59
>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=81.99 E-value=2.4 Score=26.38 Aligned_cols=56 Identities=5% Similarity=0.041 Sum_probs=40.9
Q ss_pred HHHHHHhc--cccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccc-cCcccHHH
Q psy16895 29 VREIAQDF--KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQL 84 (93)
Q Consensus 29 vrei~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~T-l~~~Di~L 84 (93)
|..|.... +...|++++|+....+..+-|...-..-|+.-+.--+-.+ |.++|++=
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 34444433 3689999999999999999999999888888777777777 88888763
No 60
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=81.85 E-value=2.9 Score=29.40 Aligned_cols=60 Identities=22% Similarity=0.305 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
|.|+.|+. ..+-+.++=+.-+-+..|.-+-.||.-|...|.--+|-+|.+.|+.+...+.
T Consensus 1 fe~lFR~a-----a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGlq 60 (138)
T PF09123_consen 1 FERLFRKA-----AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGLQ 60 (138)
T ss_dssp HHHHHHHH-----HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHH
T ss_pred ChHHHHHH-----hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHHH
Confidence 67788877 5677778888999999999999999999999999999999999998877654
No 61
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=77.03 E-value=5.7 Score=32.55 Aligned_cols=71 Identities=24% Similarity=0.407 Sum_probs=56.8
Q ss_pred hhcccccHHH-HHHHHHHhc--cccccchHHHHHHHHHHHHH----HHHHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 18 LLIRKLPFQR-LVREIAQDF--KTDLRFQSAAIGALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 18 llIpk~pF~R-lvrei~~~~--~~~~r~~~~Al~aLqea~E~----~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
++|+-.|+.| =+|+|..-- ..+.-.+++|++-|-...|. |.++|.+-|+..|.-.++.+|..+|++-|..+
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l 431 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL 431 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH
Confidence 4556666654 466664421 25788999999999988886 99999999999999999999999999987754
No 62
>KOG1757|consensus
Probab=73.06 E-value=6.8 Score=26.95 Aligned_cols=67 Identities=24% Similarity=0.280 Sum_probs=55.7
Q ss_pred ccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhcc
Q psy16895 23 LPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91 (93)
Q Consensus 23 ~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg~ 91 (93)
.|..|+=|-.-......-|+...|..-.-...|....+.+|-|-..+.--|=+.|+|+-.||+ |||+
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGD 97 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGD 97 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCc
Confidence 466777666655556788999999888888899999999999999999988899999999988 4665
No 63
>KOG1658|consensus
Probab=71.80 E-value=3.6 Score=29.59 Aligned_cols=51 Identities=24% Similarity=0.215 Sum_probs=43.9
Q ss_pred ccccccchH-HHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 36 FKTDLRFQS-AAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 36 ~~~~~r~~~-~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
...++++.. +|+..+-.++|-++-.|-..++-++.-.+|+|+..+|+..+.
T Consensus 71 l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai 122 (162)
T KOG1658|consen 71 LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAI 122 (162)
T ss_pred CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccc
Confidence 356788765 566778999999999999999999999999999999987654
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=70.00 E-value=17 Score=30.05 Aligned_cols=49 Identities=14% Similarity=0.202 Sum_probs=40.5
Q ss_pred cccchHHHHHHHHHHHHH--HHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 39 DLRFQSAAIGALQEASEA--YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 39 ~~r~~~~Al~aLqea~E~--~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
.+.++++|++.|...+.. .+..+.+.|...|...+|.+|+.+|++-+..
T Consensus 280 ~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 280 GINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred CCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 478899999987766653 6788888888888888999999999998864
No 65
>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=62.90 E-value=41 Score=28.38 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=46.3
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHH-H------------HHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEA-S------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea-~------------E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
.+.+.....+.+.-..|+.+|+..|-+. + ...+..+...|...|...+..+|+.+|++-|...+
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3444444333333348999999998642 2 46788899999888888899999999999876544
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=61.00 E-value=50 Score=27.41 Aligned_cols=67 Identities=22% Similarity=0.282 Sum_probs=49.0
Q ss_pred ccHHHHHHHHHHhccccccchHHHHHHHHHHHH-----------HHHHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 23 LPFQRLVREIAQDFKTDLRFQSAAIGALQEASE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 23 ~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E-----------~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
..|.++|..++.+. +-..|+.+|+..|=+.+= ..+..++..|+..|.-.+...|+.+||+-|..-|-
T Consensus 430 ~~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r~ 507 (509)
T PF13654_consen 430 RQYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEERR 507 (509)
T ss_dssp HHHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH--
T ss_pred HHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHccc
Confidence 35777787777655 345778888888766542 47899999999999999999999999999987664
No 67
>KOG2680|consensus
Probab=54.97 E-value=30 Score=28.13 Aligned_cols=51 Identities=24% Similarity=0.394 Sum_probs=46.7
Q ss_pred ccccchHHHHHHHHHHHHH----HHHHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~----~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
.+.-.+++|++.|-...|+ |...|...|+..+...|-.++..+|++-|.++
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~L 428 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL 428 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence 5788899999999988887 99999999999999999999999999988765
No 68
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=53.80 E-value=38 Score=25.37 Aligned_cols=59 Identities=19% Similarity=0.220 Sum_probs=46.5
Q ss_pred HHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhh--cCccccCcccHHHHH
Q psy16895 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAR 86 (93)
Q Consensus 26 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akR~Tl~~~Di~La~ 86 (93)
.+.|++.+. .....++++|+..|.+.++.-+..+-..-.+++.. ++..+|+.+|++-+.
T Consensus 136 ~~~i~~~~~--~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 136 KQLVERTAQ--ELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHH--HcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 344444433 24678999999999999999888888888888888 568889999998764
No 69
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=51.48 E-value=12 Score=26.20 Aligned_cols=33 Identities=24% Similarity=0.519 Sum_probs=27.2
Q ss_pred cchhhhhhhhhcchhhhcccccHHHHHHHHHHhc
Q psy16895 3 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 36 (93)
Q Consensus 3 ~~~lrEIr~~Q~st~llIpk~pF~Rlvrei~~~~ 36 (93)
.||+.||+++..+.+.+ |...+.+||++|=.+.
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~H 129 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKEH 129 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHhC
Confidence 47999999997776666 9999999999995543
No 70
>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=51.00 E-value=24 Score=19.87 Aligned_cols=19 Identities=16% Similarity=-0.060 Sum_probs=11.0
Q ss_pred HHhhhcCccccCcccHHHH
Q psy16895 67 LCAIHAKRVTIMPKDIQLA 85 (93)
Q Consensus 67 ~~a~HakR~Tl~~~Di~La 85 (93)
.+|...|...|+++++.-|
T Consensus 26 ~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 26 KYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHcCCCeECHHHHHhh
Confidence 3456777777777776544
No 71
>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=49.12 E-value=67 Score=20.40 Aligned_cols=63 Identities=14% Similarity=0.236 Sum_probs=52.3
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCc---cccCcccHHHHHH
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLARR 87 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR---~Tl~~~Di~La~~ 87 (93)
+|+....|++..+ .+..++.+...++.-.+-.|+..+-|.|..+...-+- --|.|+.+.-|.+
T Consensus 17 f~k~~iKr~~~~~-----~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r 82 (85)
T cd08048 17 FPKAAIKRLIQSV-----TGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR 82 (85)
T ss_pred ccHHHHHHHHHHH-----cCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence 8888888888777 4578899999999999999999999999998877554 5677777776654
No 72
>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=46.02 E-value=80 Score=22.57 Aligned_cols=49 Identities=16% Similarity=0.144 Sum_probs=41.1
Q ss_pred cccchHHHHHHHHHHHHH---HHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 39 DLRFQSAAIGALQEASEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 39 ~~r~~~~Al~aLqea~E~---~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
...|++++++.|.+.+.- ++..+...+...|.-.+-.+|+.+|++-+.+
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 356999999999999997 7788888888887777888999999988764
No 73
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=44.75 E-value=19 Score=22.76 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=22.2
Q ss_pred hhhhhhcchhhhcccccHHHHHHHH
Q psy16895 8 EIRRYQKSTELLIRKLPFQRLVREI 32 (93)
Q Consensus 8 EIr~~Q~st~llIpk~pF~Rlvrei 32 (93)
=+..||.=..-+.|+++|...+..|
T Consensus 38 ll~~Yq~W~h~LfPk~~F~d~i~~v 62 (83)
T PF07962_consen 38 LLQFYQLWAHRLFPKASFEDFIERV 62 (83)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 3678998899999999999999877
No 74
>PRK05907 hypothetical protein; Provisional
Probab=44.32 E-value=72 Score=24.62 Aligned_cols=67 Identities=12% Similarity=0.040 Sum_probs=51.6
Q ss_pred cccccHHHHHHHHHHhcc-ccccchHHHHHHHHHHH-HHHHHHHHHHhHHHhhh-cCccccCcccHHHHH
Q psy16895 20 IRKLPFQRLVREIAQDFK-TDLRFQSAAIGALQEAS-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 86 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~-~~~r~~~~Al~aLqea~-E~~lv~lfe~a~~~a~H-akR~Tl~~~Di~La~ 86 (93)
.++..-..+.+=|.+.++ ....++.+|+..|-+.+ +.-|..+...-.+++.. +++.+|+.+|++.+.
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 444444666666666663 57899999999999988 68788888888888888 669999999998763
No 75
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=42.00 E-value=83 Score=20.04 Aligned_cols=60 Identities=27% Similarity=0.451 Sum_probs=43.7
Q ss_pred hhhhhhhhcchhhhcccccHHHHHHHHHH-hccccccchHHHHHHHHH--HHHHHHHHHHHHhHHH
Q psy16895 6 LREIRRYQKSTELLIRKLPFQRLVREIAQ-DFKTDLRFQSAAIGALQE--ASEAYLVGLFEDTNLC 68 (93)
Q Consensus 6 lrEIr~~Q~st~llIpk~pF~Rlvrei~~-~~~~~~r~~~~Al~aLqe--a~E~~lv~lfe~a~~~ 68 (93)
|++|.+|+...+- ||-.| |.+.|-.+ .|+.++-.....+..|++ .+|+|+..+.+-.+.+
T Consensus 2 L~~I~h~l~np~D-iP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPDD-IPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCcc-cCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 6889999887653 45443 66666654 346677777788888875 5899999998877766
No 76
>PF06709 DUF1196: Protein of unknown function (DUF1196); InterPro: IPR009585 This family consists of several hypothetical bacterial proteins of around 51 residues in length which seem to be specific to Vibrio cholerae. The function of this family is unknown.
Probab=39.10 E-value=24 Score=20.50 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=16.7
Q ss_pred hhhhcccccHHHHHHHHHHh
Q psy16895 16 TELLIRKLPFQRLVREIAQD 35 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~ 35 (93)
-.+++|-.||.++.+.|..+
T Consensus 11 ~V~~~~t~~FK~v~KGI~~K 30 (51)
T PF06709_consen 11 CVFLCPTLPFKGVAKGIYAK 30 (51)
T ss_pred HHHHHccchHHHHHHHHHHh
Confidence 35789999999999999654
No 77
>KOG1659|consensus
Probab=38.61 E-value=83 Score=23.78 Aligned_cols=65 Identities=18% Similarity=0.170 Sum_probs=45.6
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHH
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La 85 (93)
+-+.|-.|+ |+|++.-..-=++....=...-.+.|-|+..|...+...|.-.+=+||++.-|+=+
T Consensus 11 ~trfp~aRi-KKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~ 75 (224)
T KOG1659|consen 11 KTRFPPARI-KKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQA 75 (224)
T ss_pred hccCCHHHH-HHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHH
Confidence 344566664 77877322112333333445778999999999999999999999999988776644
No 78
>COG2118 DNA-binding protein [General function prediction only]
Probab=38.01 E-value=68 Score=21.92 Aligned_cols=32 Identities=28% Similarity=0.319 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 50 LQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 50 Lqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
+-+++|.+|..|.. .||+|.+.+|=+|..-+.
T Consensus 68 ~AeavE~qLi~Laq--------tGri~~~I~e~~lk~IL~ 99 (116)
T COG2118 68 LAEAVENQLIQLAQ--------TGRITHKIDEEELKEILE 99 (116)
T ss_pred HHHHHHHHHHHHHH--------cCCCCCCCCHHHHHHHHH
Confidence 67899999999865 799999999988876554
No 79
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=37.79 E-value=1.2e+02 Score=23.16 Aligned_cols=47 Identities=23% Similarity=0.113 Sum_probs=40.4
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
....++++|+..|-+.++.-+..+-..--+++..++ +|+.+|++.+.
T Consensus 151 ~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 151 LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 467899999999999999988888888888888876 69999998764
No 80
>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=37.35 E-value=73 Score=24.95 Aligned_cols=51 Identities=14% Similarity=0.113 Sum_probs=39.7
Q ss_pred ccccchHHHHHHHHHHHHHHHH-------HHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
....++++.+..+.+.+.+.-+ .+...|-..|.-.+|-.|+++|++.+...
T Consensus 251 ~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~ 308 (337)
T TIGR02030 251 PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVL 308 (337)
T ss_pred ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4566777777777776666443 37788899999999999999999976543
No 81
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=35.32 E-value=77 Score=23.05 Aligned_cols=26 Identities=35% Similarity=0.240 Sum_probs=20.5
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFE 63 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe 63 (93)
+.++|+...-.++||.+|+....-+-
T Consensus 71 ~~~~y~~~~~~~lQEyvEA~~f~~~l 96 (204)
T PRK14562 71 PELYYAGYVGTALQEYVEALLVYSLL 96 (204)
T ss_pred chhhhhhhcchHHHHHHHHHHHHHHH
Confidence 56788888889999999987665544
No 82
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=33.77 E-value=1.1e+02 Score=18.18 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=22.3
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHH
Q psy16895 37 KTDLRFQSAAIGALQEASEAYLVGLFED 64 (93)
Q Consensus 37 ~~~~r~~~~Al~aLqea~E~~lv~lfe~ 64 (93)
+...-.+.-+.+.+|.+-|.||..+--+
T Consensus 21 gkei~~~g~~~d~i~kaqeeylsals~e 48 (58)
T PF13060_consen 21 GKEIDLQGVIADEIQKAQEEYLSALSHE 48 (58)
T ss_pred hHHhhhcchHHHHHHHHHHHHHHHhhHH
Confidence 4456677889999999999999877543
No 83
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=33.51 E-value=1.2e+02 Score=19.96 Aligned_cols=59 Identities=17% Similarity=0.277 Sum_probs=43.0
Q ss_pred cHHHHHHHHHHhccccccchHHHHHHHHH----HHHHHHHHHHHHhHHHhhhcCccccC-cccHHH
Q psy16895 24 PFQRLVREIAQDFKTDLRFQSAAIGALQE----ASEAYLVGLFEDTNLCAIHAKRVTIM-PKDIQL 84 (93)
Q Consensus 24 pF~Rlvrei~~~~~~~~r~~~~Al~aLqe----a~E~~lv~lfe~a~~~a~HakR~Tl~-~~Di~L 84 (93)
+|..+..+-.. ...++|+..|.+-|++ .++.-+..+-+......-.+.|-++. .+|+.|
T Consensus 1 ~F~~~L~~~~~--~~~lkfSkHA~~RL~~R~I~l~~~~~~~i~~av~~A~~KG~kesLvl~~d~Al 64 (96)
T TIGR02530 1 SFKDVLQEEIQ--LAELKLSKHALERMRERNISINPDDWKKLLEAVEEAESKGVKDSLILMNDAAL 64 (96)
T ss_pred CHHHHHHHhhc--ccCeeEcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhcCCCceEEEeCCEEE
Confidence 37777766531 2469999999999999 88888888888888887777776643 344433
No 84
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=32.34 E-value=1.2e+02 Score=22.87 Aligned_cols=49 Identities=16% Similarity=0.098 Sum_probs=39.4
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcC-ccccCcccHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLAR 86 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak-R~Tl~~~Di~La~ 86 (93)
....++++|+..|-+.++.-+..+..+-.+++..++ ..+|+.+|++-+.
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv 207 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVV 207 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHh
Confidence 568899999999999999977777777777777643 4679999997654
No 85
>KOG1942|consensus
Probab=32.09 E-value=1.1e+02 Score=24.90 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=43.9
Q ss_pred ccccchHHHHHHHHHH----HHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEA----SEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea----~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
..+.+.++|+..|-+. +=.|.++|+.-|..||.-.+|..|..+|++-+..+
T Consensus 383 E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~L 437 (456)
T KOG1942|consen 383 EGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTEL 437 (456)
T ss_pred hcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHH
Confidence 4688899999988773 44599999999999999999999999999877654
No 86
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=31.25 E-value=88 Score=18.47 Aligned_cols=63 Identities=17% Similarity=0.219 Sum_probs=41.6
Q ss_pred cHHHHHHHHHHhccccccc-hHHHHHHHHHHHHHHH-HHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 24 PFQRLVREIAQDFKTDLRF-QSAAIGALQEASEAYL-VGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 24 pF~Rlvrei~~~~~~~~r~-~~~Al~aLqea~E~~l-v~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
|++.++.+.... ..-. .......|+..-+..+ ..+.+.+....+..+..+|.++|--.+..++
T Consensus 1 pl~~~L~~~~~~---~~~~~~~~~~~~l~~~w~~ivg~~l~~~~~~~~i~~g~L~i~v~~~~~~~~L~ 65 (89)
T PF05258_consen 1 PLGDLLEELLKK---SGLKKRALQLARLQQNWKQIVGPELAQHTRPVSIKDGTLVIEVDSSAWAQELR 65 (89)
T ss_pred CHHHHHHHHHhh---hhHHHhhHHHHHHHHHHHHHhCHHHHccEEEEEEECCEEEEEECCHHHHHHHH
Confidence 455555555332 1112 3444555666666655 6788888888888999999999988777775
No 87
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=30.73 E-value=1.1e+02 Score=19.15 Aligned_cols=45 Identities=18% Similarity=0.102 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHh
Q psy16895 25 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 69 (93)
Q Consensus 25 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 69 (93)
.-+.++..+..+-....++.+....+.-++++.++...+.++...
T Consensus 7 ~i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~ 51 (125)
T PF13581_consen 7 DIREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGD 51 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 344455555555556788899999999999999888888777643
No 88
>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=30.00 E-value=1.6e+02 Score=19.03 Aligned_cols=48 Identities=8% Similarity=0.205 Sum_probs=35.2
Q ss_pred cccccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhh
Q psy16895 20 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH 71 (93)
Q Consensus 20 Ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H 71 (93)
+||....||+..++ ++..++.....++.-.+=.|+-++-|.|..+..-
T Consensus 24 ~~k~~ikkli~~~~----~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~ 71 (90)
T PF04719_consen 24 FNKAAIKKLINQVL----GNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEE 71 (90)
T ss_dssp --HHHHHHHHHHHH----S-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHc----CCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777777777763 4578999999999999999999999999887763
No 89
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.07 E-value=62 Score=23.23 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=19.7
Q ss_pred HhccccccchHHHHHHHHHHHHH
Q psy16895 34 QDFKTDLRFQSAAIGALQEASEA 56 (93)
Q Consensus 34 ~~~~~~~r~~~~Al~aLqea~E~ 56 (93)
.+++..|-|+..+|++..+.+|+
T Consensus 72 ~~CGkpyPWt~~~L~aa~el~ee 94 (158)
T PF10083_consen 72 HNCGKPYPWTENALEAANELIEE 94 (158)
T ss_pred HhCCCCCchHHHHHHHHHHHHHH
Confidence 45567899999999999999983
No 90
>PRK05629 hypothetical protein; Validated
Probab=28.46 E-value=1.7e+02 Score=22.09 Aligned_cols=59 Identities=14% Similarity=0.097 Sum_probs=40.3
Q ss_pred HHHHHHHHhc-cccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 27 RLVREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 27 Rlvrei~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
.+.+=|...+ +....++++|++.|-+.++.=+..+-..--+++.+.+ .+|+.+|++-+.
T Consensus 130 ~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 130 ERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 3333333333 2568899999999999998766666665566666654 469999988653
No 91
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=28.36 E-value=2.2e+02 Score=20.18 Aligned_cols=64 Identities=16% Similarity=0.193 Sum_probs=48.4
Q ss_pred hhhhhhhhcchhhhcccccHH----HHHHHHHHhc-------cccccchHHHHHHHHHHHHHHHHHHHHHhHHHh
Q psy16895 6 LREIRRYQKSTELLIRKLPFQ----RLVREIAQDF-------KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 69 (93)
Q Consensus 6 lrEIr~~Q~st~llIpk~pF~----Rlvrei~~~~-------~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 69 (93)
-+|=-+|++.+.-|||-.-+. .+++-+.+.+ .-+.-++++++..+|.+.-+...++.+..+.++
T Consensus 76 E~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 76 ENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345668999999999987554 4555555544 246889999999999999999988887766543
No 92
>smart00350 MCM minichromosome maintenance proteins.
Probab=27.76 E-value=2e+02 Score=23.52 Aligned_cols=39 Identities=18% Similarity=0.144 Sum_probs=28.1
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHHHHh
Q psy16895 40 LRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89 (93)
Q Consensus 40 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ir 89 (93)
..++.-++++|-.+||+ .|.=..|-+|+++|++-|.++-
T Consensus 466 ~~~t~R~l~sliRla~A-----------~A~l~~r~~V~~~Dv~~ai~l~ 504 (509)
T smart00350 466 IPITVRQLESIIRLSEA-----------HAKMRLSDVVEEADVEEAIRLL 504 (509)
T ss_pred cCcCHHHHHHHHHHHHH-----------HHHHcCCCccCHHHHHHHHHHH
Confidence 34555555655555555 4677789999999999998764
No 93
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=26.88 E-value=2.9e+02 Score=21.05 Aligned_cols=47 Identities=11% Similarity=0.184 Sum_probs=36.9
Q ss_pred cchHHHHHHHHHHHHH------HHHHHHHHhHHHhhhcCccccCcccHHHHHH
Q psy16895 41 RFQSAAIGALQEASEA------YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 87 (93)
Q Consensus 41 r~~~~Al~aLqea~E~------~lv~lfe~a~~~a~HakR~Tl~~~Di~La~~ 87 (93)
-|.+++++.+.+.+.. ++..+...|...|...++.+|+.+|++-|..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~ 280 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYE 280 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence 4788998888887754 4556777777788888889999999987664
No 94
>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=25.68 E-value=1.7e+02 Score=17.96 Aligned_cols=50 Identities=12% Similarity=0.153 Sum_probs=27.5
Q ss_pred cccchHHHHHHHHHHHHHHHHH--------HHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 39 DLRFQSAAIGALQEASEAYLVG--------LFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 39 ~~r~~~~Al~aLqea~E~~lv~--------lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
+.|++++..+.|+.|++....+ ..+.|-..-.-..+.++..+|.+.....
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~a 60 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAA 60 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHH
Confidence 4688888888888888764333 3333333223334556666766655443
No 95
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=25.21 E-value=36 Score=20.70 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=10.7
Q ss_pred cCcccHHHHHHHh
Q psy16895 77 IMPKDIQLARRIR 89 (93)
Q Consensus 77 l~~~Di~La~~ir 89 (93)
|+.+|+.||.+|-
T Consensus 62 lT~~D~~lA~~id 74 (76)
T cd00913 62 LSENDFIMAAKID 74 (76)
T ss_pred CCHHHHHHHHHHh
Confidence 6778999999873
No 96
>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=24.98 E-value=1.3e+02 Score=25.38 Aligned_cols=51 Identities=14% Similarity=0.184 Sum_probs=41.6
Q ss_pred ccccchHHHHHHHHHHHHHHH-------HHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYL-------VGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~l-------v~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
....++++++..|..++..+- ..+...|--.|.-.+|-+|+.+|++.|..+
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 457888899998888887754 346778888899999999999999887654
No 97
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=24.97 E-value=1.1e+02 Score=20.49 Aligned_cols=52 Identities=10% Similarity=0.061 Sum_probs=41.5
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCcc--ccCcccHHHHHHHhcc
Q psy16895 39 DLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRV--TIMPKDIQLARRIRGE 91 (93)
Q Consensus 39 ~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~--Tl~~~Di~La~~irg~ 91 (93)
.+|++++=...+.+-++....++-+..-.++. +.++ .+..+++.=..+|.|+
T Consensus 14 ~vrvt~eE~~~I~~kA~~AGlS~SeYLR~~aL-g~~I~s~~D~e~v~eL~~in~d 67 (114)
T PRK13877 14 RVPVLPDEKAEIEANAAAAGLSVARYLRDVGQ-GYQIKGVIDYEYVRELARINGD 67 (114)
T ss_pred EEEeCHHHHHHHHHHHHHhCCCHHHHHHHHHc-CCCccccCCHHHHHHHHHhccc
Confidence 57889999999999999988899999999999 6666 4555666666655554
No 98
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=24.89 E-value=73 Score=18.74 Aligned_cols=20 Identities=30% Similarity=0.393 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy16895 45 AAIGALQEASEAYLVGLFED 64 (93)
Q Consensus 45 ~Al~aLqea~E~~lv~lfe~ 64 (93)
+|+.+|||++++-|.++...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999988764
No 99
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=24.55 E-value=1.8e+02 Score=19.76 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=35.3
Q ss_pred cccHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHHHHHhH
Q psy16895 22 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTN 66 (93)
Q Consensus 22 k~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~ 66 (93)
..-+-+.+|..+..+-....++.+.+..++-+++..++...+.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 455677788887777677778888898899888888888877665
No 100
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=24.43 E-value=1.9e+02 Score=22.96 Aligned_cols=51 Identities=12% Similarity=0.082 Sum_probs=39.8
Q ss_pred ccccchHHHHHHHHHHHHHHH-------HHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYL-------VGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~l-------v~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
....++++.+..+.+.+.+.- ..+...|...|.-.+|-.|.++|++.+...
T Consensus 264 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~ 321 (350)
T CHL00081 264 PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITL 321 (350)
T ss_pred CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 456677777777777777643 356788889999999999999999987653
No 101
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=24.22 E-value=39 Score=20.44 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=11.0
Q ss_pred cCcccHHHHHHHh
Q psy16895 77 IMPKDIQLARRIR 89 (93)
Q Consensus 77 l~~~Di~La~~ir 89 (93)
|+.+|+.||.+|-
T Consensus 61 lt~~D~~lA~~id 73 (75)
T cd00488 61 LTENDFILAAKID 73 (75)
T ss_pred CCHHHHHHHHHHh
Confidence 7889999999873
No 102
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.39 E-value=23 Score=29.33 Aligned_cols=50 Identities=18% Similarity=0.137 Sum_probs=43.4
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 37 KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 37 ~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
.+...+..+.-+.|-+.+-.+....-+-|-.+|.|.|-.||.+.|++|-.
T Consensus 398 d~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 398 DEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred CcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 46778888888888888988888888878889999999999999999864
No 103
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=23.39 E-value=1.3e+02 Score=18.11 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHH
Q psy16895 44 SAAIGALQEASEAYLVGLFEDTNLC 68 (93)
Q Consensus 44 ~~Al~aLqea~E~~lv~lfe~a~~~ 68 (93)
.+|+..+++|.|-|+..+.++....
T Consensus 34 eea~~n~~eai~l~~e~~~~~~~~i 58 (73)
T COG1598 34 EEALQNAKEAIELHLEALLEEGEPI 58 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcC
Confidence 5788999999999999988876543
No 104
>PRK09862 putative ATP-dependent protease; Provisional
Probab=23.32 E-value=2e+02 Score=23.99 Aligned_cols=51 Identities=18% Similarity=0.074 Sum_probs=42.0
Q ss_pred ccchHHHHHHHHHHHHHH------HHHHHHHhHHHhhhcCccccCcccHHHHHHHhc
Q psy16895 40 LRFQSAAIGALQEASEAY------LVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90 (93)
Q Consensus 40 ~r~~~~Al~aLqea~E~~------lv~lfe~a~~~a~HakR~Tl~~~Di~La~~irg 90 (93)
...+.++...|+.+.+.+ ...+.+-|.-.|.=.+|..|+++|++.|...|+
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~ 493 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRA 493 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhc
Confidence 356777777777777654 456788888999999999999999999999985
No 105
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=23.04 E-value=2.5e+02 Score=21.93 Aligned_cols=51 Identities=8% Similarity=0.049 Sum_probs=38.5
Q ss_pred ccccchHHHHHHHHHHHHHHH-------HHHHHHhHHHhhhcCccccCcccHHHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYL-------VGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~l-------v~lfe~a~~~a~HakR~Tl~~~Di~La~~i 88 (93)
....++++.+..+.+.+.+.- ..+...|...|...+|-.|+++|++-+...
T Consensus 248 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~~ 305 (334)
T PRK13407 248 PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVATM 305 (334)
T ss_pred CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHHH
Confidence 456677777777777766643 227788999999999999999999766543
No 106
>PRK07914 hypothetical protein; Reviewed
Probab=22.96 E-value=2.1e+02 Score=21.63 Aligned_cols=60 Identities=10% Similarity=0.102 Sum_probs=41.0
Q ss_pred HHHHHHHHHhc-cccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 26 QRLVREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 26 ~Rlvrei~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
..+.+=|.... +....++++|+..|.+.++.-+..+-..-..++.+.+ .+|+.+|++-+.
T Consensus 131 ~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 191 (320)
T PRK07914 131 AERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYH 191 (320)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHc
Confidence 44444444444 3467899999999999998766666666656665544 468888887654
No 107
>PF06428 Sec2p: GDP/GTP exchange factor Sec2p; InterPro: IPR009449 In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion []. It catalyzes the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. Binds the Rab GTPase YPT32, but does not have exhange activity on YPT32 [, , ].; PDB: 2EQB_C 2E7S_K 2OCY_A.
Probab=22.23 E-value=1.7e+02 Score=19.20 Aligned_cols=32 Identities=22% Similarity=0.295 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHhhhcCccc
Q psy16895 45 AAIGALQEASEAYLVGLFEDTNLCAIHAKRVT 76 (93)
Q Consensus 45 ~Al~aLqea~E~~lv~lfe~a~~~a~HakR~T 76 (93)
.....+..-.|+.-.+||+.||.+-.-++|-+
T Consensus 15 ~~~~~ie~ElEeLTasLFeEAN~MVa~ar~e~ 46 (100)
T PF06428_consen 15 QEKEQIESELEELTASLFEEANKMVADARRER 46 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556778889999999999999987777533
No 108
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=22.15 E-value=1.6e+02 Score=20.98 Aligned_cols=24 Identities=29% Similarity=0.193 Sum_probs=16.0
Q ss_pred cccchHHHHHHHHHHHHHHHHHHH
Q psy16895 39 DLRFQSAAIGALQEASEAYLVGLF 62 (93)
Q Consensus 39 ~~r~~~~Al~aLqea~E~~lv~lf 62 (93)
.+++....-.++||.+|+..-.-|
T Consensus 62 ~~~y~~~~s~~lQE~vEa~~f~~~ 85 (200)
T PF01997_consen 62 FYRYHGAYSPGLQEYVEAISFYHY 85 (200)
T ss_dssp HHHHGGGTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356777777778888887644433
No 109
>PF01031 Dynamin_M: Dynamin central region; InterPro: IPR000375 Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see IPR001401 from INTERPRO), and at the C terminus is a PH domain (see IPR001849 from INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.; GO: 0005525 GTP binding; PDB: 3ZVR_A 2AKA_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D 1JWY_B 1JX2_B 3SZR_A ....
Probab=22.09 E-value=1.1e+02 Score=22.91 Aligned_cols=34 Identities=18% Similarity=0.394 Sum_probs=23.0
Q ss_pred hhhhcccccHHHHHHHHHHhccccccchHHHHHHHHHHHH
Q psy16895 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASE 55 (93)
Q Consensus 16 t~llIpk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E 55 (93)
..+++|...|..||++.+. +|...|+.++..+.+
T Consensus 186 lp~f~p~~afe~Li~~~i~------~l~~Pa~~cv~~V~~ 219 (295)
T PF01031_consen 186 LPGFVPESAFESLIRKQIE------KLEEPALQCVEEVHE 219 (295)
T ss_dssp SS-SCCHHHHHHHHHHHHH------TTHHHHHHHHHHHHH
T ss_pred cccchhHHHHHHHHHHHHH------HHHhHHHHHHHHHHH
Confidence 4578999999999999965 444555555544443
No 110
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=21.15 E-value=1.6e+02 Score=21.72 Aligned_cols=31 Identities=19% Similarity=0.070 Sum_probs=26.9
Q ss_pred ccc-cchHHHHHHHHHHHHHHHHHHHHHhHHH
Q psy16895 38 TDL-RFQSAAIGALQEASEAYLVGLFEDTNLC 68 (93)
Q Consensus 38 ~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~ 68 (93)
..+ -++.+|...|.-+.|.||-++.+.+...
T Consensus 219 ~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 219 HGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345 8999999999999999999999987654
No 111
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=20.14 E-value=40 Score=19.76 Aligned_cols=27 Identities=30% Similarity=0.470 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHhHHHhhhcCccccCcccHH
Q psy16895 51 QEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 83 (93)
Q Consensus 51 qea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~ 83 (93)
.+..|+||..+|+.. .++..+...||-
T Consensus 3 t~~~e~YL~~Iy~l~------~~~~~v~~~~iA 29 (60)
T PF01325_consen 3 TESEEDYLKAIYELS------EEGGPVRTKDIA 29 (60)
T ss_dssp SCHHHHHHHHHHHHH------HCTSSBBHHHHH
T ss_pred CcHHHHHHHHHHHHH------cCCCCccHHHHH
Confidence 457899999999955 355666666654
No 112
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=20.10 E-value=2.8e+02 Score=21.16 Aligned_cols=49 Identities=22% Similarity=0.230 Sum_probs=38.6
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhHHHhhhcCccccCcccHHHHH
Q psy16895 38 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86 (93)
Q Consensus 38 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR~Tl~~~Di~La~ 86 (93)
...+++.+|++.|-+..|.=+-.+...-..++..++=.+|+.+|++.+.
T Consensus 156 ~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v 204 (334)
T COG1466 156 LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVV 204 (334)
T ss_pred cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHH
Confidence 5799999999999999998666666666666555544499999998764
No 113
>cd00914 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon
Probab=20.07 E-value=52 Score=20.02 Aligned_cols=13 Identities=38% Similarity=0.639 Sum_probs=10.6
Q ss_pred cCcccHHHHHHHh
Q psy16895 77 IMPKDIQLARRIR 89 (93)
Q Consensus 77 l~~~Di~La~~ir 89 (93)
|+.+|+.||.+|-
T Consensus 62 lT~~D~~lA~~id 74 (76)
T cd00914 62 LTERDIKLAKFIE 74 (76)
T ss_pred cCHHHHHHHHHHh
Confidence 6778999998873
Done!