Query 032554
Match_columns 138
No_of_seqs 169 out of 1414
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 02:57:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032554.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032554hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03346 chaperone_ClpB ATP-d 99.9 3.4E-20 7.3E-25 155.5 17.1 129 2-132 12-140 (852)
2 CHL00095 clpC Clp protease ATP 99.8 1.7E-19 3.6E-24 150.9 16.6 129 1-132 15-143 (821)
3 TIGR02639 ClpA ATP-dependent C 99.8 4E-19 8.6E-24 147.1 16.1 124 2-128 12-137 (731)
4 PRK10865 protein disaggregatio 99.8 2E-18 4.3E-23 144.8 16.8 131 2-134 17-147 (857)
5 COG0542 clpA ATP-binding subun 99.8 1.9E-18 4.2E-23 141.6 16.0 129 2-136 13-141 (786)
6 TIGR03345 VI_ClpV1 type VI sec 99.8 5E-18 1.1E-22 142.2 16.7 127 1-130 11-141 (852)
7 PRK11034 clpA ATP-dependent Cl 99.7 4.4E-16 9.6E-21 128.9 16.0 124 2-128 13-139 (758)
8 PF02861 Clp_N: Clp amino term 99.5 2.5E-14 5.3E-19 81.0 5.9 53 2-54 1-53 (53)
9 KOG1051 Chaperone HSP104 and r 99.5 1.7E-13 3.8E-18 114.0 12.4 134 1-135 22-156 (898)
10 PF02861 Clp_N: Clp amino term 99.3 1.9E-12 4.2E-17 73.1 5.0 53 79-132 1-53 (53)
11 TIGR03346 chaperone_ClpB ATP-d 98.5 5.1E-07 1.1E-11 76.7 8.6 63 68-131 1-63 (852)
12 CHL00095 clpC Clp protease ATP 98.5 5.4E-07 1.2E-11 76.3 8.0 64 67-131 4-67 (821)
13 TIGR03345 VI_ClpV1 type VI sec 98.4 1.1E-06 2.5E-11 74.5 9.0 62 68-130 1-62 (852)
14 TIGR02639 ClpA ATP-dependent C 98.3 3.6E-06 7.7E-11 70.6 8.1 60 68-130 1-60 (731)
15 PRK10865 protein disaggregatio 98.3 4.4E-06 9.5E-11 71.1 8.2 64 67-131 5-68 (857)
16 COG0542 clpA ATP-binding subun 98.1 2.1E-05 4.6E-10 65.8 8.3 63 67-132 1-63 (786)
17 PRK11034 clpA ATP-dependent Cl 98.0 3.5E-05 7.7E-10 64.8 8.0 60 68-130 2-61 (758)
18 KOG1051 Chaperone HSP104 and r 97.3 0.001 2.2E-08 56.8 7.8 63 65-128 9-72 (898)
19 PLN00154 histone H2A; Provisio 86.7 0.73 1.6E-05 30.9 2.6 40 72-114 74-113 (136)
20 PTZ00017 histone H2A; Provisio 86.3 0.83 1.8E-05 30.6 2.8 40 72-114 62-101 (134)
21 cd00074 H2A Histone 2A; H2A is 86.1 1 2.3E-05 29.3 3.1 39 73-114 56-94 (115)
22 PLN00157 histone H2A; Provisio 84.0 1.2 2.6E-05 29.8 2.6 40 72-114 61-100 (132)
23 PLN00153 histone H2A; Provisio 83.6 1.5 3.1E-05 29.2 2.9 39 73-114 60-98 (129)
24 PLN00156 histone H2AX; Provisi 83.1 1.6 3.5E-05 29.4 3.0 40 72-114 64-103 (139)
25 smart00414 H2A Histone 2A. 83.0 1.5 3.4E-05 28.1 2.8 39 73-114 45-83 (106)
26 KOG0871 Class 2 transcription 82.1 6.7 0.00015 26.7 5.7 27 2-28 55-81 (156)
27 KOG1756 Histone 2A [Chromatin 81.0 2.2 4.9E-05 28.2 3.0 40 73-115 63-102 (131)
28 PF13551 HTH_29: Winged helix- 78.8 13 0.00028 23.1 9.9 79 23-102 7-91 (112)
29 cd00074 H2A Histone 2A; H2A is 76.7 2.1 4.6E-05 27.9 2.0 33 2-36 62-94 (115)
30 PLN00154 histone H2A; Provisio 75.9 1.7 3.7E-05 29.2 1.4 32 2-35 81-112 (136)
31 PF00125 Histone: Core histone 74.7 5 0.00011 23.5 3.1 30 71-101 43-72 (75)
32 PTZ00017 histone H2A; Provisio 74.0 2.4 5.1E-05 28.4 1.7 33 2-36 69-101 (134)
33 PTZ00252 histone H2A; Provisio 73.5 4.1 8.9E-05 27.3 2.7 40 73-115 61-102 (134)
34 KOG1756 Histone 2A [Chromatin 73.4 3.3 7.1E-05 27.4 2.2 33 2-36 69-101 (131)
35 PF01978 TrmB: Sugar-specific 70.6 6.7 0.00014 22.5 3.0 39 18-56 12-50 (68)
36 PF13335 Mg_chelatase_2: Magne 70.5 14 0.0003 23.1 4.6 32 70-102 63-94 (96)
37 PLN00157 histone H2A; Provisio 70.2 2.7 5.8E-05 28.1 1.3 33 2-36 68-100 (132)
38 PF08369 PCP_red: Proto-chloro 69.6 4.8 0.0001 21.6 2.0 20 2-21 24-43 (45)
39 smart00414 H2A Histone 2A. 68.2 3.5 7.5E-05 26.5 1.5 33 2-36 51-83 (106)
40 PLN00153 histone H2A; Provisio 66.9 3.8 8.3E-05 27.2 1.5 33 2-36 66-98 (129)
41 PF00808 CBFD_NFYB_HMF: Histon 66.6 12 0.00027 21.2 3.5 25 76-101 41-65 (65)
42 smart00803 TAF TATA box bindin 66.3 15 0.00032 21.3 3.8 58 30-101 7-64 (65)
43 PLN00156 histone H2AX; Provisi 66.1 4.2 9.1E-05 27.4 1.6 33 2-36 71-103 (139)
44 cd07979 TAF9 TATA Binding Prot 65.7 16 0.00035 23.8 4.3 59 30-104 6-66 (117)
45 PF02954 HTH_8: Bacterial regu 62.9 19 0.0004 18.7 3.5 36 15-51 6-41 (42)
46 PF13412 HTH_24: Winged helix- 62.1 22 0.00047 18.7 4.5 38 18-55 7-44 (48)
47 PF02269 TFIID-18kDa: Transcri 59.3 5.9 0.00013 24.7 1.3 37 69-106 33-69 (93)
48 cd07981 TAF12 TATA Binding Pro 57.9 32 0.0007 20.2 4.3 30 73-103 37-66 (72)
49 PRK00056 mtgA monofunctional b 57.2 14 0.0003 27.3 3.1 39 16-57 69-107 (236)
50 PF12244 DUF3606: Protein of u 57.1 18 0.00039 20.4 2.9 23 108-130 22-44 (57)
51 COG5262 HTA1 Histone H2A [Chro 56.8 12 0.00026 24.5 2.4 32 73-105 62-93 (132)
52 TIGR00122 birA_repr_reg BirA b 56.3 23 0.00051 20.2 3.5 34 100-133 7-40 (69)
53 PF13404 HTH_AsnC-type: AsnC-t 56.1 28 0.00061 18.1 3.7 35 97-131 8-42 (42)
54 smart00550 Zalpha Z-DNA-bindin 55.9 31 0.00067 19.9 4.0 39 95-133 9-49 (68)
55 PF02291 TFIID-31kDa: Transcri 55.4 29 0.00063 23.1 4.1 33 70-103 44-76 (129)
56 PF12802 MarR_2: MarR family; 53.4 37 0.00079 18.6 4.1 40 17-56 8-49 (62)
57 PLN00035 histone H4; Provision 52.6 38 0.00082 21.7 4.1 35 69-104 60-94 (103)
58 PF02969 TAF: TATA box binding 52.5 45 0.00099 19.4 4.3 33 68-101 33-65 (66)
59 PF04221 RelB: RelB antitoxin; 51.7 51 0.0011 19.8 5.1 48 30-80 15-65 (83)
60 cd00076 H4 Histone H4, one of 51.2 44 0.00095 20.5 4.2 36 69-105 44-79 (85)
61 PF05402 PqqD: Coenzyme PQQ sy 50.8 44 0.00096 18.8 5.2 40 16-55 18-60 (68)
62 TIGR02384 RelB_DinJ addiction 49.6 58 0.0012 19.8 7.5 62 30-98 16-80 (83)
63 PTZ00015 histone H4; Provision 49.5 45 0.00097 21.3 4.1 36 68-104 60-95 (102)
64 TIGR02070 mono_pep_trsgly mono 48.9 17 0.00037 26.6 2.4 37 16-55 64-100 (224)
65 PF01022 HTH_5: Bacterial regu 48.5 29 0.00062 18.3 2.8 38 96-134 6-43 (47)
66 KOG1659 Class 2 transcription 47.8 66 0.0014 23.4 5.1 34 72-106 48-81 (224)
67 COG2036 HHT1 Histones H3 and H 47.3 48 0.001 20.7 3.9 33 70-103 51-83 (91)
68 PRK00411 cdc6 cell division co 46.1 74 0.0016 24.6 5.8 56 72-128 251-306 (394)
69 COG5247 BUR6 Class 2 transcrip 45.9 33 0.00071 21.9 3.0 32 73-105 59-90 (113)
70 PLN03060 inositol phosphatase- 44.3 1.2E+02 0.0026 21.9 8.2 99 28-132 72-183 (206)
71 PF11212 DUF2999: Protein of u 43.5 50 0.0011 19.7 3.4 35 17-52 19-53 (82)
72 PRK13481 glycosyltransferase; 43.5 33 0.00072 25.2 3.2 38 16-56 54-91 (232)
73 PF12554 MOZART1: Mitotic-spin 43.3 37 0.0008 18.5 2.6 17 115-131 32-48 (48)
74 PF09415 CENP-X: CENP-S associ 42.9 44 0.00096 19.8 3.2 25 74-99 38-63 (72)
75 PF04405 ScdA_N: Domain of Unk 42.7 58 0.0013 18.2 3.5 22 30-51 33-54 (56)
76 PRK11426 hypothetical protein; 42.4 83 0.0018 21.1 4.7 42 11-55 58-99 (132)
77 TIGR02337 HpaR homoprotocatech 41.1 92 0.002 19.7 6.8 73 13-85 25-105 (118)
78 KOG3334 Transcription initiati 40.6 67 0.0015 21.8 4.1 33 70-103 45-77 (148)
79 KOG1757 Histone 2A [Chromatin 40.5 5.7 0.00012 25.7 -0.9 62 41-105 32-98 (131)
80 PF08784 RPA_C: Replication pr 40.1 58 0.0013 20.2 3.7 27 30-56 67-93 (102)
81 smart00344 HTH_ASNC helix_turn 38.8 86 0.0019 19.3 4.4 38 19-56 8-45 (108)
82 TIGR02928 orc1/cdc6 family rep 37.7 1.2E+02 0.0026 23.1 5.7 58 70-128 241-298 (365)
83 cd07978 TAF13 The TATA Binding 37.6 1E+02 0.0022 19.1 6.5 36 69-106 34-69 (92)
84 COG5150 Class 2 transcription 37.0 1.3E+02 0.0028 20.1 5.0 26 2-27 54-79 (148)
85 PLN00047 photosystem II biogen 36.7 1.6E+02 0.0034 22.5 5.9 100 28-132 125-236 (283)
86 COG3355 Predicted transcriptio 36.3 1E+02 0.0022 20.5 4.4 38 19-56 32-70 (126)
87 PF09862 DUF2089: Protein of u 34.7 1.3E+02 0.0028 19.5 5.5 57 20-79 42-98 (113)
88 PRK05255 hypothetical protein; 34.4 1.5E+02 0.0031 20.8 5.2 39 17-55 110-149 (171)
89 PRK10265 chaperone-modulator p 34.0 1.2E+02 0.0026 19.0 5.8 70 31-104 10-79 (101)
90 PF01047 MarR: MarR family; I 32.6 87 0.0019 16.9 3.8 40 17-56 6-45 (59)
91 TIGR00764 lon_rel lon-related 32.3 93 0.002 26.2 4.6 37 66-103 353-390 (608)
92 PRK09862 putative ATP-dependen 32.2 1E+02 0.0022 25.5 4.7 34 69-103 458-491 (506)
93 COG3077 RelB DNA-damage-induci 31.6 1.3E+02 0.0028 18.6 5.8 51 30-81 18-68 (88)
94 smart00418 HTH_ARSR helix_turn 31.2 88 0.0019 16.5 4.4 30 26-55 8-37 (66)
95 PF00912 Transgly: Transglycos 30.3 22 0.00047 25.0 0.5 35 16-53 23-57 (178)
96 PF08230 Cpl-7: Cpl-7 lysozyme 30.3 93 0.002 16.5 3.2 22 32-53 20-41 (42)
97 PF10038 DUF2274: Protein of u 29.5 1.3E+02 0.0027 17.8 4.6 36 66-103 19-55 (69)
98 PF11994 DUF3489: Protein of u 28.9 1.3E+02 0.0029 17.9 3.7 38 18-55 13-51 (72)
99 COG1474 CDC6 Cdc6-related prot 28.6 2.8E+02 0.0062 21.7 6.5 60 70-130 232-291 (366)
100 COG5094 TAF9 Transcription ini 28.4 1.2E+02 0.0026 20.1 3.7 35 70-104 46-82 (145)
101 PF09012 FeoC: FeoC like trans 28.4 1.2E+02 0.0026 17.2 3.7 27 30-56 16-42 (69)
102 TIGR02702 SufR_cyano iron-sulf 27.9 1.7E+02 0.0037 20.6 4.8 39 17-55 4-42 (203)
103 PF03847 TFIID_20kDa: Transcri 27.5 1.3E+02 0.0028 17.5 3.4 28 74-102 36-63 (68)
104 PF01527 HTH_Tnp_1: Transposas 27.4 76 0.0017 18.1 2.5 25 29-53 24-48 (76)
105 cd00592 HTH_MerR-like Helix-Tu 27.2 1.5E+02 0.0033 18.0 8.0 70 31-105 3-72 (100)
106 PF08220 HTH_DeoR: DeoR-like h 27.0 1.2E+02 0.0026 16.7 4.7 38 19-56 5-42 (57)
107 PF01638 HxlR: HxlR-like helix 26.9 1.5E+02 0.0033 17.8 4.8 38 17-55 8-46 (90)
108 TIGR02787 codY_Gpos GTP-sensin 26.6 1.4E+02 0.0031 22.2 4.2 41 91-131 182-223 (251)
109 PF13654 AAA_32: AAA domain; P 26.5 1.3E+02 0.0029 24.8 4.5 33 70-103 473-505 (509)
110 PRK09416 lstR lineage-specific 26.1 2.1E+02 0.0046 19.2 5.8 62 64-130 18-87 (135)
111 PRK11179 DNA-binding transcrip 26.0 1.8E+02 0.0039 19.4 4.5 40 17-56 11-51 (153)
112 smart00345 HTH_GNTR helix_turn 25.9 1E+02 0.0022 16.2 2.8 25 109-133 23-47 (60)
113 PF13591 MerR_2: MerR HTH fami 25.8 1.6E+02 0.0034 17.7 5.6 68 31-103 3-70 (84)
114 PF02796 HTH_7: Helix-turn-hel 25.8 1.1E+02 0.0024 15.9 3.0 31 96-127 12-42 (45)
115 PRK11512 DNA-binding transcrip 25.3 2E+02 0.0044 18.8 7.9 74 9-82 33-114 (144)
116 PF02082 Rrf2: Transcriptional 25.2 1.3E+02 0.0029 17.7 3.4 23 109-131 28-50 (83)
117 TIGR03060 PS_II_psb29 photosys 25.0 2.8E+02 0.006 20.2 6.0 27 28-54 74-100 (214)
118 PRK03573 transcriptional regul 25.0 2E+02 0.0044 18.7 7.7 76 10-85 25-109 (144)
119 smart00576 BTP Bromodomain tra 24.7 1.6E+02 0.0034 17.3 7.7 31 72-103 40-70 (77)
120 cd01580 AcnA_IRP_Swivel Aconit 24.2 39 0.00085 23.6 0.9 35 90-124 4-38 (171)
121 PF12840 HTH_20: Helix-turn-he 24.0 1.3E+02 0.0029 16.5 3.0 36 97-132 15-50 (61)
122 PF15615 TerB-C: TerB-C domain 23.7 2.3E+02 0.005 18.9 5.2 36 18-53 80-118 (144)
123 PF04255 DUF433: Protein of un 23.6 1.4E+02 0.0031 16.4 4.6 37 90-128 17-54 (56)
124 PF13331 DUF4093: Domain of un 23.3 95 0.0021 19.1 2.4 18 111-128 70-87 (87)
125 KOG1556 26S proteasome regulat 23.2 1.3E+02 0.0028 22.6 3.5 18 12-29 169-186 (309)
126 PF04719 TAFII28: hTAFII28-lik 22.9 1.4E+02 0.003 18.5 3.1 80 19-100 3-86 (90)
127 smart00347 HTH_MARR helix_turn 22.5 1.8E+02 0.0038 17.1 4.4 68 17-84 13-86 (101)
128 PF09385 HisK_N: Histidine kin 22.3 81 0.0018 21.1 2.1 55 74-130 62-116 (133)
129 COG0703 AroK Shikimate kinase 22.3 2.8E+02 0.0061 19.4 6.3 75 2-79 19-95 (172)
130 COG1067 LonB Predicted ATP-dep 22.3 1.5E+02 0.0033 25.3 4.1 34 69-103 365-398 (647)
131 PF02662 FlpD: Methyl-viologen 22.2 1.7E+02 0.0037 19.0 3.7 16 108-123 81-96 (124)
132 TIGR02074 PBP_1a_fam penicilli 22.0 1.2E+02 0.0027 24.9 3.6 37 16-55 11-47 (530)
133 TIGR02702 SufR_cyano iron-sulf 22.0 1.8E+02 0.0039 20.4 4.0 37 95-131 4-40 (203)
134 PF04693 DDE_Tnp_2: Archaeal p 21.9 2.2E+02 0.0048 22.0 4.6 58 70-130 8-67 (327)
135 COG1378 Predicted transcriptio 21.8 2E+02 0.0043 21.2 4.3 38 19-56 21-58 (247)
136 smart00417 H4 Histone H4. 21.3 1.2E+02 0.0026 18.1 2.5 29 70-99 45-73 (74)
137 PRK03824 hypA hydrogenase nick 21.3 2.6E+02 0.0056 18.5 5.3 31 72-103 7-37 (135)
138 PRK11169 leucine-responsive tr 21.2 1.6E+02 0.0035 19.9 3.6 41 94-134 15-56 (164)
139 PF07026 DUF1317: Protein of u 21.1 32 0.00069 19.6 -0.0 20 2-21 38-59 (60)
140 PRK11235 bifunctional antitoxi 21.0 2.1E+02 0.0045 17.3 5.5 46 30-77 15-60 (80)
141 PF13518 HTH_28: Helix-turn-he 20.9 1.4E+02 0.0031 15.4 4.7 37 19-57 5-41 (52)
142 PRK01905 DNA-binding protein F 20.8 1.9E+02 0.0042 16.9 4.1 22 29-50 51-72 (77)
143 TIGR00100 hypA hydrogenase nic 20.8 59 0.0013 21.0 1.2 49 72-134 7-55 (115)
144 PF08828 DSX_dimer: Doublesex 20.6 1.9E+02 0.0041 16.7 3.3 37 17-53 10-49 (62)
145 COG1654 BirA Biotin operon rep 20.6 2.1E+02 0.0046 17.2 3.6 23 110-132 23-45 (79)
146 TIGR03362 VI_chp_7 type VI sec 20.6 3.5E+02 0.0075 20.7 5.5 50 30-79 138-192 (301)
147 TIGR00368 Mg chelatase-related 20.5 1.9E+02 0.0041 23.8 4.3 31 70-101 466-496 (499)
148 PF13384 HTH_23: Homeodomain-l 20.3 1.5E+02 0.0032 15.3 3.1 36 18-55 9-44 (50)
149 cd08050 TAF6 TATA Binding Prot 20.3 2.1E+02 0.0046 22.1 4.4 33 69-102 30-62 (343)
150 PF08221 HTH_9: RNA polymerase 20.1 1.8E+02 0.004 16.3 3.9 38 17-54 16-53 (62)
151 PF00406 ADK: Adenylate kinase 20.1 2.4E+02 0.0053 18.4 4.2 56 1-56 12-71 (151)
152 PF12096 DUF3572: Protein of u 20.0 1.5E+02 0.0034 18.3 2.9 25 25-49 18-42 (88)
153 PF14056 DUF4250: Domain of un 20.0 1.8E+02 0.0039 16.3 3.0 34 18-51 6-43 (55)
No 1
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=99.85 E-value=3.4e-20 Score=155.51 Aligned_cols=129 Identities=19% Similarity=0.178 Sum_probs=115.4
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVD 81 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~ 81 (138)
|+.+|.+++|.+|++||||++|+.++++.+.++|+++|+|++.++..+++.+++.|...+.++.+.+|+.++++|+.|+.
T Consensus 12 A~~~A~~~~h~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~~~~vLe~A~~ 91 (852)
T TIGR03346 12 AQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPKVSGPGGQVYLSPELNRLLNLAEK 91 (852)
T ss_pred HHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHhcccccCCCCCCCCCcCHHHHHHHHHHHH
Confidence 78899999999999999999999999889999999999999999999999998766532222457899999999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 82 HKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 82 ~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
+|..+++ .+|+++|||+||+.++++ +..+|..+|++.+.+.+.+..+++
T Consensus 92 ~A~~~g~-~~I~teHLLlALl~e~~~-a~~iL~~~gi~~~~l~~~l~~~~~ 140 (852)
T TIGR03346 92 LAQKRGD-EFISSEHLLLALLDDKGT-LGKLLKEAGATADALEAAINAVRG 140 (852)
T ss_pred HHHHcCC-CcccHHHHHHHHHcCCcc-HHHHHHHcCCCHHHHHHHHHhhcc
Confidence 9999999 999999999999998765 578999999999999999877654
No 2
>CHL00095 clpC Clp protease ATP binding subunit
Probab=99.84 E-value=1.7e-19 Score=150.93 Aligned_cols=129 Identities=33% Similarity=0.474 Sum_probs=116.3
Q ss_pred ChHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHH
Q 032554 1 MGELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAV 80 (138)
Q Consensus 1 ~A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~ 80 (138)
.|+.+|.+++|.+|++||||++|+.++++.+..+|+.+|+|++.++..+++.+++.+.. ....+.||+.++++|+.|+
T Consensus 15 ~A~~~A~~~~h~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~l~~~~~~--~~~~~~~S~~~~~vL~~A~ 92 (821)
T CHL00095 15 LSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKIIGRGTGF--VAVEIPFTPRAKRVLEMSL 92 (821)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHHhcCCCC--CccccccCHHHHHHHHHHH
Confidence 37899999999999999999999999989999999999999999999999988765432 1245789999999999999
Q ss_pred HHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 81 DHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 81 ~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
.+|..+++ .+|+++|||+||+.++++++..+|+.+|++.+.++..+....+
T Consensus 93 ~~A~~~~~-~~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~~l~ 143 (821)
T CHL00095 93 EEARDLGH-NYIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILNLIG 143 (821)
T ss_pred HHHHHhCC-CcccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 99999999 9999999999999988888899999999999999988876544
No 3
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=99.82 E-value=4e-19 Score=147.15 Aligned_cols=124 Identities=24% Similarity=0.279 Sum_probs=109.9
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHc-CCCCCCC-CCCCCCCCHHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVG-KGDFFFF-SPEHPPLTEDAQRVIDWA 79 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~-~~~~~~~-~~~~~~~S~~l~~~l~~A 79 (138)
|+++|.+++|.+|++||||++||++++ +.++|+.+|+|++.+++.+++.++ ..|...+ .++.+.+|+.++++|+.|
T Consensus 12 A~~~A~~~~h~~V~~EHLLlaLL~~~~--~~~iL~~~gid~~~l~~~l~~~l~~~~p~~~~~~~~~~~~S~~lk~vL~~A 89 (731)
T TIGR02639 12 ALEEAKKRRHEFVTLEHILLALLFDSD--AIEILEECGGDVEALRKDLEDYLENNLPSITEENEADPEQTVGVQRVLQRA 89 (731)
T ss_pred HHHHHHHhCCCcCcHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCHHHHHHHHHH
Confidence 789999999999999999999999875 668999999999999999999887 4444221 123578999999999999
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHH
Q 032554 80 VDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELES 128 (138)
Q Consensus 80 ~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~ 128 (138)
+.+|..+++ .+|+++|||+||+.++++++..+|..+|++.+.+.+.+.
T Consensus 90 ~~~A~~~g~-~~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~ 137 (731)
T TIGR02639 90 LLHVKSAGK-KEIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYIS 137 (731)
T ss_pred HHHHHHcCC-CccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHH
Confidence 999999999 999999999999998888888999999999999988875
No 4
>PRK10865 protein disaggregation chaperone; Provisional
Probab=99.81 E-value=2e-18 Score=144.79 Aligned_cols=131 Identities=11% Similarity=0.063 Sum_probs=114.9
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVD 81 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~ 81 (138)
|+.+|.+++|.+|+++|||++|+.++.+.+..+|+.+|+|+..++..++..+.+.|...+..+.+.+|+.+.++|+.|+.
T Consensus 17 a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~ 96 (857)
T PRK10865 17 AQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQVEGTGGDVQPSQDLVRVLNLCDK 96 (857)
T ss_pred HHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHHhhCCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 78899999999999999999999998888999999999999999999999998777532223457899999999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCCC
Q 032554 82 HKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSEPG 134 (138)
Q Consensus 82 ~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~ 134 (138)
+|..+++ .+|+++|+|+|++.+++ ....+|..+|++.+.+.+.+.+++++.
T Consensus 97 ~~~~~~~-~~i~~~~ll~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~ 147 (857)
T PRK10865 97 LAQKRGD-NFISSELFVLAALESRG-TLADILKAAGATTANITQAIEQMRGGE 147 (857)
T ss_pred HHHHcCC-CcccHHHHHHHHHcCcc-hHHHHHHHcCCCHHHHHHHHHHhhccc
Confidence 9999999 99999999999998764 445689999999999999887766543
No 5
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=1.9e-18 Score=141.57 Aligned_cols=129 Identities=25% Similarity=0.267 Sum_probs=119.6
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVD 81 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~ 81 (138)
|+++|..++|++|++||||++|++++++. .++..+|++++.++..++..+.+.|...+ . +.+|+.+.++++.|+.
T Consensus 13 a~~~a~~~~h~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~~~~~~~~~~~--~-~~~s~~~~~~~~~a~~ 87 (786)
T COG0542 13 AQELARMRRHEYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEEFIDKLPKVLG--S-PYLSPRLKRVLERAWL 87 (786)
T ss_pred HHHHHHHhCCCcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHHHHhccCCCCC--C-CCCCHHHHHHHHHHHH
Confidence 78999999999999999999999998876 89999999999999999999999998642 2 8899999999999999
Q ss_pred HHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCCCCC
Q 032554 82 HKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSEPGSV 136 (138)
Q Consensus 82 ~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~~~ 136 (138)
.|+..++ +||+++|+|+|++.++++++..++...+++...+.+.+.+++++..+
T Consensus 88 ~a~~~~~-~~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 141 (786)
T COG0542 88 LAQSLGD-EYVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEELIEELRGGNEV 141 (786)
T ss_pred HHHhccC-ccccHHHHHHHHhcccchHHHHHHHhccCCHHHHHHHHHHHhccccc
Confidence 9999999 99999999999999998999999999999999999999999986543
No 6
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=99.79 E-value=5e-18 Score=142.21 Aligned_cols=127 Identities=19% Similarity=0.171 Sum_probs=110.5
Q ss_pred ChHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHH
Q 032554 1 MGELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAV 80 (138)
Q Consensus 1 ~A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~ 80 (138)
.|+++|.+++|.+|+++|||++|+.++++.+..+|+.+|+|++.++..+++.+.+.|... +..+.+|+.++++|+.|+
T Consensus 11 ~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~l~~~p~~~--~~~~~~S~~l~~vL~~A~ 88 (852)
T TIGR03345 11 QAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDKLPRGN--TRTPVFSPHLVELLQEAW 88 (852)
T ss_pred HHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCCC--CCCCCcCHHHHHHHHHHH
Confidence 378999999999999999999999998888999999999999999999999998777532 245789999999999999
Q ss_pred HH-HHhcCCCCCCCHHHHHHHHhcCCCc--HHHHHHHHc-CCCHHHHHHHHHhh
Q 032554 81 DH-KLKSGNSGEVTASDLLLGIWSETDS--PGHKILAAL-GFSDEKAKELESLS 130 (138)
Q Consensus 81 ~~-A~~~~~~~~I~~~hlLlall~~~~~--~~~~~l~~~-gi~~~~l~~~i~~~ 130 (138)
.. +..+++ .+|+++|||+||+.++++ ++..++..+ |++.+.+.+.+.++
T Consensus 89 ~~~a~~~g~-~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (852)
T TIGR03345 89 LLASLELGD-GRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPAL 141 (852)
T ss_pred HHHHHHcCC-CcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 74 456899 999999999999998665 556678777 99999998888765
No 7
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=99.71 E-value=4.4e-16 Score=128.93 Aligned_cols=124 Identities=27% Similarity=0.285 Sum_probs=106.2
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC-CCCCCCC--CCCCCCCHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK-GDFFFFS--PEHPPLTEDAQRVIDW 78 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~-~~~~~~~--~~~~~~S~~l~~~l~~ 78 (138)
|+.+|.+++|.+|++||||++|+.+++ +..+|+.+|+|.+.+++.+++.+.. .|...+. ...+.+|..++++|+.
T Consensus 13 a~~~a~~~~~~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 90 (758)
T PRK11034 13 AFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQR 90 (758)
T ss_pred HHHHHHHcCCCcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHHHHhhcCCcCCCCCCcCCcCCCHHHHHHHHH
Confidence 788999999999999999999998764 8999999999999999999998873 3322111 1246789999999999
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHH
Q 032554 79 AVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELES 128 (138)
Q Consensus 79 A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~ 128 (138)
|+.+|+..++ ++|+++|||+|+++++++++..+|+.+|++...+...+.
T Consensus 91 a~~~~~~~~~-~~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 139 (758)
T PRK11034 91 AVFHVQSSGR-SEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS 139 (758)
T ss_pred HHHHHHHcCC-CcccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHH
Confidence 9999999999 999999999999998888888999999999887766543
No 8
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=99.53 E-value=2.5e-14 Score=80.98 Aligned_cols=53 Identities=25% Similarity=0.324 Sum_probs=49.5
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHc
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVG 54 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~ 54 (138)
|+++|.+++|++|+++|||++|++++++.+.++|+++|+|++.+++.+++.++
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg 53 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG 53 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999988764
No 9
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.52 E-value=1.7e-13 Score=114.04 Aligned_cols=134 Identities=12% Similarity=-0.003 Sum_probs=112.0
Q ss_pred ChHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCC-CCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHH
Q 032554 1 MGELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANG-VTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWA 79 (138)
Q Consensus 1 ~A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g-~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A 79 (138)
.|+.+|+++||.+++|+|++.+||.+++|.+++++.+.+ ++..++..-+.-.+.+.|+..+++....++..+.+++..+
T Consensus 22 ~a~~~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralelc~~v~l~rlpt~~~p~~sn~l~aalkr~qa~q 101 (898)
T KOG1051|consen 22 QAVTEARRRGHAQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALELCFNVSLNRLPTSYGPPVSNALMAALKRAQAHQ 101 (898)
T ss_pred HHHHHHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHHHHHHHHHhccCCCCCccchHhHHHHHHHHHHH
Confidence 378999999999999999999999999999999999999 9999999999999999998753233345666666666666
Q ss_pred HHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCCCC
Q 032554 80 VDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSEPGS 135 (138)
Q Consensus 80 ~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~~ 135 (138)
......+++ ++|.+||..+.++-..+..+.++++.+|++...++..+++.++..+
T Consensus 102 rr~~~~~~~-~~vkvE~~~li~silDdp~vsrv~reag~~s~~vK~~ve~~~g~~~ 156 (898)
T KOG1051|consen 102 RRGCEEQQQ-QAVKVELEQLILSILDDPSVSRVMREAGFSSSAVKSAVEQPVGQFR 156 (898)
T ss_pred Hhcchhhcc-chhhHhHHhhheeeecCchHHHHHHHhcCChHHHHHHHHhhccccC
Confidence 666666788 8999999955555445568899999999999999999999987443
No 10
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=99.35 E-value=1.9e-12 Score=73.12 Aligned_cols=53 Identities=25% Similarity=0.329 Sum_probs=49.2
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 79 AVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 79 A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
|..+|+.+++ .+|+++|||+|+++++++.+.++|+++|+|++.+++.+++++|
T Consensus 1 A~~~A~~~~~-~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg 53 (53)
T PF02861_consen 1 AQELARERGH-QYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG 53 (53)
T ss_dssp HHHHHHHTTB-SSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred CHHHHHHcCC-CcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 6788999999 9999999999999999999999999999999999999999875
No 11
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=98.51 E-value=5.1e-07 Score=76.70 Aligned_cols=63 Identities=14% Similarity=0.181 Sum_probs=58.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
||+.++++|..|..+|+.+++ .+|+++|||+||+.++++.+..+|..+|++++.+++.+...-
T Consensus 1 fT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~l 63 (852)
T TIGR03346 1 FTEKFQEALQAAQSLALGRDH-QQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKEL 63 (852)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 689999999999999999999 999999999999998888899999999999999998887754
No 12
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.48 E-value=5.4e-07 Score=76.30 Aligned_cols=64 Identities=22% Similarity=0.262 Sum_probs=59.8
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 67 PLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 67 ~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
.||+.++++|..|...|+.+++ .+|+++|||+||+.++++.+..+|+.+|++.+.++..++...
T Consensus 4 rfT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~l 67 (821)
T CHL00095 4 RFTEKAIKVIMLSQEEARRLGH-NFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKII 67 (821)
T ss_pred hHhHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4899999999999999999999 999999999999998888999999999999999998887753
No 13
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=98.45 E-value=1.1e-06 Score=74.54 Aligned_cols=62 Identities=23% Similarity=0.255 Sum_probs=57.8
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
+|+.++++|..|..+|..+++ .+|+++|||+||+.++++.+..+|+.+|++.+.+++.++..
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h-~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~ 62 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGH-PEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARA 62 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHH
Confidence 588999999999999999999 99999999999999887888999999999999998888874
No 14
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=98.28 E-value=3.6e-06 Score=70.57 Aligned_cols=60 Identities=23% Similarity=0.276 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
+|+.++++|..|..+|..+++ .+|+++|||+||+++++ +..+|+.+|++.+.+++.+...
T Consensus 1 ~~~~a~~~L~~A~~~A~~~~h-~~V~~EHLLlaLL~~~~--~~~iL~~~gid~~~l~~~l~~~ 60 (731)
T TIGR02639 1 ISEELERILDAALEEAKKRRH-EFVTLEHILLALLFDSD--AIEILEECGGDVEALRKDLEDY 60 (731)
T ss_pred CCHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHHH
Confidence 588999999999999999999 99999999999998764 5689999999999999888774
No 15
>PRK10865 protein disaggregation chaperone; Provisional
Probab=98.26 E-value=4.4e-06 Score=71.11 Aligned_cols=64 Identities=14% Similarity=0.115 Sum_probs=59.2
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 67 PLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 67 ~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
.||+.++.+|+.|...|..++| .+|+++|||++|+.++++.+..+|+.+|++...+++.+....
T Consensus 5 ~~~~~~~~~l~~a~~~a~~~~~-~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~ 68 (857)
T PRK10865 5 RLTNKFQLALADAQSLALGHDN-QFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQAL 68 (857)
T ss_pred HhCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4899999999999999999999 999999999999998878889999999999999988887753
No 16
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=2.1e-05 Score=65.80 Aligned_cols=63 Identities=22% Similarity=0.256 Sum_probs=57.1
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 67 PLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 67 ~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
.||+.++++|..|..+|...++ .+++++|+|++|+.++.+. .++..+|++++.+++.++..-+
T Consensus 1 ~~~~~~~~~l~~a~~~a~~~~h-~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~~~~ 63 (786)
T COG0542 1 KLTERAQKALELAQELARMRRH-EYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEEFID 63 (786)
T ss_pred CcCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHHHHh
Confidence 4789999999999999999999 9999999999999987665 9999999999999998887543
No 17
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=97.97 E-value=3.5e-05 Score=64.80 Aligned_cols=60 Identities=15% Similarity=0.140 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
+|+.+.++|..|..+|..+++ .+|+++|+|++|+.+++ +..+++.+|++...+++.+...
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~-~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 61 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRH-EFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAF 61 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCC-CcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHHH
Confidence 789999999999999999999 99999999999998653 7899999999999998887764
No 18
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.001 Score=56.79 Aligned_cols=63 Identities=17% Similarity=0.129 Sum_probs=56.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcC-CCHHHHHHHHH
Q 032554 65 HPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALG-FSDEKAKELES 128 (138)
Q Consensus 65 ~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~g-i~~~~l~~~i~ 128 (138)
+..||+++.++|..|...|++.|| ..++|.|++.+|+..+++++.+++.+.+ ++...++..+.
T Consensus 9 ~q~lT~~Aa~~L~~a~~~Arrrgh-~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralelc~~ 72 (898)
T KOG1051|consen 9 QQTLTEEAATVLKQAVTEARRRGH-AQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALELCFN 72 (898)
T ss_pred HhhhCHHHHHHHHHHHHHHHHcCC-CCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHHHHH
Confidence 356999999999999999999999 9999999999999999999999999988 77777764433
No 19
>PLN00154 histone H2A; Provisional
Probab=86.69 E-value=0.73 Score=30.87 Aligned_cols=40 Identities=15% Similarity=0.178 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
+.++|+.|.+.|+..+. ..|++.|+.+|+-.|. ....+|+
T Consensus 74 tAEVLELAGNaA~d~kk-~RItPrHi~lAIrnDe--EL~~Ll~ 113 (136)
T PLN00154 74 TAEVLELAGNASKDLKV-KRITPRHLQLAIRGDE--ELDTLIK 113 (136)
T ss_pred HHHHHHHHHHHHHhhCC-ceecHHHhhhhccCcH--HHHHHhc
Confidence 34689999999999999 9999999999997754 3455554
No 20
>PTZ00017 histone H2A; Provisional
Probab=86.32 E-value=0.83 Score=30.57 Aligned_cols=40 Identities=20% Similarity=0.283 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
+.++|+.|...|+..+. ..|++.|+.+|+-.|. ....+|.
T Consensus 62 taEILELAgNaa~d~kk-~RItPrHi~lAI~nDe--EL~~Ll~ 101 (134)
T PTZ00017 62 TAEVLELAGNAAKDNKK-KRITPRHIQLAIRNDE--ELNKLLA 101 (134)
T ss_pred HHHHHHHHHHHHHhcCC-CeecHHHHHhhccCcH--HHHHHHc
Confidence 34578889999998888 9999999999998754 3455554
No 21
>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=86.08 E-value=1 Score=29.33 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
.++++.|...|+..+. ..|+++|+-+|+-.|. ....+++
T Consensus 56 aEIlelA~n~ak~~k~-krItp~hi~lAi~nD~--EL~~L~~ 94 (115)
T cd00074 56 AEVLELAGNAARDNKK-KRITPRHLQLAVRNDE--ELNKLLK 94 (115)
T ss_pred HHHHHHHHHHHHHcCC-CeEcHHHHHHHHhccH--HHHHHHc
Confidence 5688899999999898 9999999999998754 3455554
No 22
>PLN00157 histone H2A; Provisional
Probab=83.99 E-value=1.2 Score=29.78 Aligned_cols=40 Identities=15% Similarity=0.254 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
+.++|+.|...|+..+. ..|++.|+.+|+-.|. ....+|+
T Consensus 61 taEVLELAgnaa~d~kk-~RItPrHi~lAI~nDe--EL~~Ll~ 100 (132)
T PLN00157 61 AAEVLELAGNAARDNKK-SRIVPRHIQLAVRNDE--ELSKLLG 100 (132)
T ss_pred HHHHHHHHHHHHHhcCC-ccccHHHHhhcccCcH--HHHHHHc
Confidence 35688899999998888 9999999999997754 3456664
No 23
>PLN00153 histone H2A; Provisional
Probab=83.63 E-value=1.5 Score=29.23 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
.++|+.|...|+..+. ..|+|.|+.+|+-.|. -...+|+
T Consensus 60 aEVLELAgnaa~d~kk-~RItPrHi~lAI~nDe--EL~~Ll~ 98 (129)
T PLN00153 60 AEVLELAGNAARDNKK-NRIVPRHIQLAIRNDE--ELGKLLG 98 (129)
T ss_pred HHHHHHHHHHHHhcCC-CccChHHHHhhccCcH--HHHHHHC
Confidence 4688999999998888 8999999999997654 3456665
No 24
>PLN00156 histone H2AX; Provisional
Probab=83.09 E-value=1.6 Score=29.38 Aligned_cols=40 Identities=15% Similarity=0.254 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
+.++|+.|...|+..+. ..|+|.|+.+|+-.|. -...+|+
T Consensus 64 taEVLELAgNaa~d~kk-~RItPrHi~lAIrnDe--EL~~Ll~ 103 (139)
T PLN00156 64 AAEVLELAGNAARDNKK-NRIVPRHIQLAVRNDE--ELSKLLG 103 (139)
T ss_pred HHHHHHHHHHHHHHcCC-CcCcHHHHHhhccCcH--HHHHHHC
Confidence 34688889888888888 8999999999997754 3455664
No 25
>smart00414 H2A Histone 2A.
Probab=82.98 E-value=1.5 Score=28.11 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHH
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILA 114 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~ 114 (138)
.++|+.|...|+..+. ..|++.|+-+|+-.|. ....+++
T Consensus 45 aEILeLagn~a~~~k~-~rItp~hi~lAi~nD~--EL~~L~~ 83 (106)
T smart00414 45 AEVLELAGNAARDNKK-RRITPRHLQLAIRNDE--ELNKLLK 83 (106)
T ss_pred HHHHHHHHHHHHhcCC-CccchHHHhhhccCCH--HHHHHHc
Confidence 5688889888988888 8999999999997754 3455554
No 26
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=82.11 E-value=6.7 Score=26.68 Aligned_cols=27 Identities=15% Similarity=0.081 Sum_probs=22.0
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCC
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGT 28 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~ 28 (138)
|.+.|.+..-..|.+||++.||=..+.
T Consensus 55 Aneic~~e~KKTIa~EHV~KALe~LgF 81 (156)
T KOG0871|consen 55 ANEICNKEAKKTIAPEHVIKALENLGF 81 (156)
T ss_pred HHHHHhHHhcccCCHHHHHHHHHHcch
Confidence 566777888899999999999976653
No 27
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=80.96 E-value=2.2 Score=28.18 Aligned_cols=40 Identities=18% Similarity=0.266 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHH
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAA 115 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~ 115 (138)
.++++.|-..|+..+. ..|+|.|+.+|+-.|+ -...+|..
T Consensus 63 Aeile~agnaardnkk-~ri~PrH~~lAI~NDe--EL~~lL~~ 102 (131)
T KOG1756|consen 63 AEILELAGNAARDNKK-TRITPRHLQLAIRNDE--ELNKLLGK 102 (131)
T ss_pred HHHHHHhHHHhhhcCc-cccChHHHHHHHhCcH--HHHHHhcc
Confidence 4577778888888888 8999999999998754 34666653
No 28
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.83 E-value=13 Score=23.06 Aligned_cols=79 Identities=16% Similarity=0.038 Sum_probs=47.7
Q ss_pred HhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC----CCCCCCCCC-CC-CCHHHHHHHHHHHHHHHhcCCCCCCCHHH
Q 032554 23 ILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG----DFFFFSPEH-PP-LTEDAQRVIDWAVDHKLKSGNSGEVTASD 96 (138)
Q Consensus 23 ll~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~----~~~~~~~~~-~~-~S~~l~~~l~~A~~~A~~~~~~~~I~~~h 96 (138)
++.++.+...++.+.+|++...+...+..+-..+ ....+.++. .. ++++....+......--..+. ...+...
T Consensus 7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~-~~~t~~~ 85 (112)
T PF13551_consen 7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGR-SRWTLEE 85 (112)
T ss_pred HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCC-CcccHHH
Confidence 4454443489999999999999999998876554 110111222 22 787777766555442211233 4577777
Q ss_pred HHHHHh
Q 032554 97 LLLGIW 102 (138)
Q Consensus 97 lLlall 102 (138)
|-..++
T Consensus 86 l~~~l~ 91 (112)
T PF13551_consen 86 LAEWLI 91 (112)
T ss_pred HHHHHH
Confidence 766553
No 29
>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=76.68 E-value=2.1 Score=27.89 Aligned_cols=33 Identities=15% Similarity=0.118 Sum_probs=25.3
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|.+.|...+...|+|+|+-+|+-++++ +..+|+
T Consensus 62 A~n~ak~~k~krItp~hi~lAi~nD~E--L~~L~~ 94 (115)
T cd00074 62 AGNAARDNKKKRITPRHLQLAVRNDEE--LNKLLK 94 (115)
T ss_pred HHHHHHHcCCCeEcHHHHHHHHhccHH--HHHHHc
Confidence 567788899999999999999977542 444444
No 30
>PLN00154 histone H2A; Provisional
Probab=75.91 E-value=1.7 Score=29.15 Aligned_cols=32 Identities=9% Similarity=0.123 Sum_probs=24.9
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFL 35 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il 35 (138)
|-+.|...+...|+|.|+.+|+-++++ +..+|
T Consensus 81 AGNaA~d~kk~RItPrHi~lAIrnDeE--L~~Ll 112 (136)
T PLN00154 81 AGNASKDLKVKRITPRHLQLAIRGDEE--LDTLI 112 (136)
T ss_pred HHHHHHhhCCceecHHHhhhhccCcHH--HHHHh
Confidence 556788899999999999999977543 44454
No 31
>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=74.67 E-value=5 Score=23.51 Aligned_cols=30 Identities=13% Similarity=0.154 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 71 DAQRVIDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 71 ~l~~~l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
-+.++++.|...|...+. ..|++.|+.+|+
T Consensus 43 ~~~~il~~A~~~a~~~kR-~tI~~~DI~~A~ 72 (75)
T PF00125_consen 43 LLVEILEEAGNLARHAKR-KTITPRDIQLAV 72 (75)
T ss_dssp HHHHHHHHHHHHHHHTTB-SEEGHHHHHHHH
T ss_pred hhhhhhhHHHHHHhhcCC-cEecHHHHHHHH
Confidence 345677888999998888 899999999986
No 32
>PTZ00017 histone H2A; Provisional
Probab=73.96 E-value=2.4 Score=28.43 Aligned_cols=33 Identities=18% Similarity=0.118 Sum_probs=26.0
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-+.|...+...|+|+|+.+|+-++++ +..+|.
T Consensus 69 AgNaa~d~kk~RItPrHi~lAI~nDeE--L~~Ll~ 101 (134)
T PTZ00017 69 AGNAAKDNKKKRITPRHIQLAIRNDEE--LNKLLA 101 (134)
T ss_pred HHHHHHhcCCCeecHHHHHhhccCcHH--HHHHHc
Confidence 556788899999999999999987653 555554
No 33
>PTZ00252 histone H2A; Provisional
Probab=73.55 E-value=4.1 Score=27.25 Aligned_cols=40 Identities=10% Similarity=0.180 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHh--cCCCCCCCHHHHHHHHhcCCCcHHHHHHHH
Q 032554 73 QRVIDWAVDHKLK--SGNSGEVTASDLLLGIWSETDSPGHKILAA 115 (138)
Q Consensus 73 ~~~l~~A~~~A~~--~~~~~~I~~~hlLlall~~~~~~~~~~l~~ 115 (138)
.++|+.|...|+. .+. ..|+++|+.+|+-.|. -...+|+.
T Consensus 61 aEVLELAgnaa~d~~~kk-~RItPrHi~lAIrNDe--EL~~Ll~~ 102 (134)
T PTZ00252 61 AELLELSVKAAAQQAKKP-KRLTPRTVTLAVRHDD--DLGSLLKN 102 (134)
T ss_pred HHHHHHHHHHHHhccCCc-ccccHHHHHhhccChH--HHHHHHcC
Confidence 4678888888864 455 6899999999997654 34566653
No 34
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=73.35 E-value=3.3 Score=27.42 Aligned_cols=33 Identities=18% Similarity=0.129 Sum_probs=26.5
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-..|+..+-..|+|.|+.+|+-++++ ..++|.
T Consensus 69 agnaardnkk~ri~PrH~~lAI~NDeE--L~~lL~ 101 (131)
T KOG1756|consen 69 AGNAARDNKKTRITPRHLQLAIRNDEE--LNKLLG 101 (131)
T ss_pred hHHHhhhcCccccChHHHHHHHhCcHH--HHHHhc
Confidence 456788889999999999999988653 666665
No 35
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=70.63 E-value=6.7 Score=22.48 Aligned_cols=39 Identities=18% Similarity=0.245 Sum_probs=32.9
Q ss_pred HHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 18 AILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 18 HlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
.++..|+..+...+.++-+.+|++...+...+++...++
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G 50 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKG 50 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 467778877777889999999999999999998887654
No 36
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=70.51 E-value=14 Score=23.13 Aligned_cols=32 Identities=13% Similarity=0.113 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHh
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIW 102 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall 102 (138)
....+++.-|+-+|---+. +.|+.+||.-|+-
T Consensus 63 R~~~rilrvARTIADL~~~-~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 63 RGYHRILRVARTIADLEGS-ERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHHHHHHhHcCC-CCCCHHHHHHHHh
Confidence 5678899999999987788 9999999999873
No 37
>PLN00157 histone H2A; Provisional
Probab=70.20 E-value=2.7 Score=28.09 Aligned_cols=33 Identities=18% Similarity=0.127 Sum_probs=26.0
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-+.|...+...|+|+|+.+|+-++++ +..+|+
T Consensus 68 Agnaa~d~kk~RItPrHi~lAI~nDeE--L~~Ll~ 100 (132)
T PLN00157 68 AGNAARDNKKSRIVPRHIQLAVRNDEE--LSKLLG 100 (132)
T ss_pred HHHHHHhcCCccccHHHHhhcccCcHH--HHHHHc
Confidence 556788889999999999999977553 556655
No 38
>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=69.63 E-value=4.8 Score=21.59 Aligned_cols=20 Identities=20% Similarity=0.031 Sum_probs=15.2
Q ss_pred hHHHHHhcCCCCcCHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILM 21 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLl 21 (138)
+...|+..|...|+++|+.-
T Consensus 24 ~E~~Ar~~G~~~IT~e~v~~ 43 (45)
T PF08369_consen 24 AEKYARERGYDEITVEVVDA 43 (45)
T ss_dssp HHHHHHHCT-SEE-HHHHHH
T ss_pred HHHHHHHcCCCeECHHHHHh
Confidence 45789999999999999864
No 39
>smart00414 H2A Histone 2A.
Probab=68.18 E-value=3.5 Score=26.49 Aligned_cols=33 Identities=18% Similarity=0.124 Sum_probs=24.4
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-+.|...+...|+|+|+-+++-++++ ...+|+
T Consensus 51 agn~a~~~k~~rItp~hi~lAi~nD~E--L~~L~~ 83 (106)
T smart00414 51 AGNAARDNKKRRITPRHLQLAIRNDEE--LNKLLK 83 (106)
T ss_pred HHHHHHhcCCCccchHHHhhhccCCHH--HHHHHc
Confidence 556788888999999999999877542 444444
No 40
>PLN00153 histone H2A; Provisional
Probab=66.93 E-value=3.8 Score=27.25 Aligned_cols=33 Identities=21% Similarity=0.117 Sum_probs=25.4
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-+.|...+-..|+|+|+.+++-++++ +..+|+
T Consensus 66 Agnaa~d~kk~RItPrHi~lAI~nDeE--L~~Ll~ 98 (129)
T PLN00153 66 AGNAARDNKKNRIVPRHIQLAIRNDEE--LGKLLG 98 (129)
T ss_pred HHHHHHhcCCCccChHHHHhhccCcHH--HHHHHC
Confidence 556788888899999999999977543 555554
No 41
>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=66.57 E-value=12 Score=21.25 Aligned_cols=25 Identities=12% Similarity=0.078 Sum_probs=18.5
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 76 IDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 76 l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
...|+..|...+. ..|+.+|+..|+
T Consensus 41 ~~~A~~~a~~~~r-kti~~~Dv~~Av 65 (65)
T PF00808_consen 41 AKEANEIAQRDKR-KTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHTTS-SEE-HHHHHHHH
T ss_pred HHHHHHHHHHcCC-CccCHHHHHHHC
Confidence 3456777877777 899999998775
No 42
>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=66.26 E-value=15 Score=21.30 Aligned_cols=58 Identities=16% Similarity=0.178 Sum_probs=39.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
.+.++.++.|+.. +...+...+. ..+...+.++++.|..++...+- ..++++++-.|+
T Consensus 7 ~i~ria~~~Gi~r--is~~a~~~l~-----------~~~e~rl~~i~~~A~k~~~hakR-ktlt~~DI~~Al 64 (65)
T smart00803 7 TIKDVAESLGIGN--LSDEAAKLLA-----------EDVEYRIKEIVQEALKFMRHSKR-TTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHCCCcc--ccHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHhCC-CeecHHHHHHHh
Confidence 4667777777752 2222222221 02345678899999999999888 999999997775
No 43
>PLN00156 histone H2AX; Provisional
Probab=66.08 E-value=4.2 Score=27.41 Aligned_cols=33 Identities=18% Similarity=0.114 Sum_probs=25.5
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLW 36 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~ 36 (138)
|-+.|...+-..|+|+|+.+++-++++ +..+|+
T Consensus 71 AgNaa~d~kk~RItPrHi~lAIrnDeE--L~~Ll~ 103 (139)
T PLN00156 71 AGNAARDNKKNRIVPRHIQLAVRNDEE--LSKLLG 103 (139)
T ss_pred HHHHHHHcCCCcCcHHHHHhhccCcHH--HHHHHC
Confidence 556678888899999999999977553 555655
No 44
>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=65.65 E-value=16 Score=23.75 Aligned_cols=59 Identities=24% Similarity=0.242 Sum_probs=41.9
Q ss_pred HHHHHHHHCCCCH--HHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcC
Q 032554 30 LAAKFLWANGVTL--FKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSE 104 (138)
Q Consensus 30 ~~~~il~~~g~~~--~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~ 104 (138)
.+..+|+++|+.. +.+...+.++. -.-+..++.+|..+|+..+. ..|+.+++-+|+-..
T Consensus 6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~---------------~ry~~~il~dA~~~a~hA~r-~tV~~eDV~lAi~~r 66 (117)
T cd07979 6 VIAAILKSMGITEYEPRVINQLLEFA---------------YRYTTDVLDDAKVYSEHAGK-ANIDADDVKLAIQSR 66 (117)
T ss_pred HHHHHHHHCCCCccCHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHHH
Confidence 4677888888742 22333332222 24567899999999999888 999999999998653
No 45
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=62.86 E-value=19 Score=18.67 Aligned_cols=36 Identities=11% Similarity=-0.016 Sum_probs=23.1
Q ss_pred CHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHH
Q 032554 15 GTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVK 51 (138)
Q Consensus 15 ~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~ 51 (138)
+.+++.-+| +.-.+...++-+.+|++...|...+++
T Consensus 6 E~~~i~~aL-~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 6 EKQLIRQAL-ERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHH-HHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHH-HHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 334444444 444566788889999999988887764
No 46
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=62.09 E-value=22 Score=18.68 Aligned_cols=38 Identities=16% Similarity=-0.002 Sum_probs=28.7
Q ss_pred HHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 18 AILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 18 HlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
.+|..|.+.+.-...++-+.+|++...+...+......
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 46667777776677889999999999999988877654
No 47
>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=59.35 E-value=5.9 Score=24.70 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=9.3
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCC
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETD 106 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~ 106 (138)
...+..++..|...|...|. ..|++++|+..+=.++.
T Consensus 33 ~~~i~~l~~~A~~~a~~rg~-~~i~~eDl~F~lR~D~~ 69 (93)
T PF02269_consen 33 REYIIELCQEAMEVAQRRGS-KKIKVEDLLFLLRKDPK 69 (93)
T ss_dssp HHHHHHHHHHHHC-------------------------
T ss_pred HHHHHHHHHHHHHHHhcccc-CcCcHHHHHHHHhcCHH
Confidence 45566777788888888888 89999999999988764
No 48
>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=57.92 E-value=32 Score=20.18 Aligned_cols=30 Identities=13% Similarity=0.116 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
.++++.|..+|+..+. ..|...++.+++=.
T Consensus 37 ~~v~~~a~~lAkHr~~-~tv~~~Di~l~l~r 66 (72)
T cd07981 37 DDVVEDACRLAKHRKS-DTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHcCC-CCCCHHHHHHHHHH
Confidence 4567778889998888 88999999998744
No 49
>PRK00056 mtgA monofunctional biosynthetic peptidoglycan transglycosylase; Provisional
Probab=57.18 E-value=14 Score=27.26 Aligned_cols=39 Identities=10% Similarity=0.083 Sum_probs=31.0
Q ss_pred HHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCC
Q 032554 16 TEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57 (138)
Q Consensus 16 ~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~ 57 (138)
|.|+..|++..+| .+++...|+|...+..++.+.+..+.
T Consensus 69 p~~l~~Avia~ED---~rF~~H~GvD~~~i~rA~~~~~~~g~ 107 (236)
T PRK00056 69 SPNLKRAVIAAED---QKFPEHWGFDWDAIQKALEHNERNGK 107 (236)
T ss_pred CHHHHHHhHhhhc---CcccCCCCcCHHHHHHHHHHHHhcCC
Confidence 4589999998887 66788999999999888876665333
No 50
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=57.10 E-value=18 Score=20.35 Aligned_cols=23 Identities=13% Similarity=0.122 Sum_probs=19.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhh
Q 032554 108 PGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 108 ~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
-...|.+++|++.++|++++...
T Consensus 22 ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHH
Confidence 45678889999999999998865
No 51
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=56.82 E-value=12 Score=24.47 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCC
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSET 105 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~ 105 (138)
.++++-|-+-|+..+. ..|.|.||-+||-.|.
T Consensus 62 aEilelAgNaA~d~kk-kri~PrHlqlAIrnD~ 93 (132)
T COG5262 62 AEILELAGNAARDNKK-KRIIPRHLQLAIRNDE 93 (132)
T ss_pred HHHHHHhhhhhhhcCc-ceechHHHHHHhcCcH
Confidence 4677888888888888 9999999999998754
No 52
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=56.34 E-value=23 Score=20.21 Aligned_cols=34 Identities=21% Similarity=0.209 Sum_probs=25.8
Q ss_pred HHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCC
Q 032554 100 GIWSETDSPGHKILAALGFSDEKAKELESLSSEP 133 (138)
Q Consensus 100 all~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~ 133 (138)
.++.+.......+.+.+|++...+.+.+..+++.
T Consensus 7 ~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 7 ALLADNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred HHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3454444457788899999999999999888653
No 53
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=56.14 E-value=28 Score=18.14 Aligned_cols=35 Identities=11% Similarity=0.115 Sum_probs=23.2
Q ss_pred HHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 97 LLLGIWSETDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 97 lLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
||-.+-.+..-....+=+..|++...+.+.+..++
T Consensus 8 Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 34444455555667888899999999999887653
No 54
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.92 E-value=31 Score=19.90 Aligned_cols=39 Identities=13% Similarity=0.147 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCC--cHHHHHHHHcCCCHHHHHHHHHhhcCC
Q 032554 95 SDLLLGIWSETD--SPGHKILAALGFSDEKAKELESLSSEP 133 (138)
Q Consensus 95 ~hlLlall~~~~--~~~~~~l~~~gi~~~~l~~~i~~~r~~ 133 (138)
+.+|..|...+. ..+..+-+.+|++...+.+.+..+...
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344555544444 456788889999999999998877553
No 55
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=55.36 E-value=29 Score=23.09 Aligned_cols=33 Identities=24% Similarity=0.208 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
.-+..+|+.|..+|...+. ..|+.+++-+|+-.
T Consensus 44 RYt~~vL~DA~~ya~hA~~-~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 44 RYTSDVLEDAQVYADHAGR-STIDADDVRLAIQS 76 (129)
T ss_dssp HHHHHHHHHHHHHHHHTT--SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccc-ccCChHHHHHHHHH
Confidence 4567899999999999888 99999999999963
No 56
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=53.39 E-value=37 Score=18.58 Aligned_cols=40 Identities=15% Similarity=0.106 Sum_probs=29.9
Q ss_pred HHHHHHHhhcCC--cHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 17 EAILMGILVEGT--SLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 17 eHlLlall~~~~--~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
-++|..|...++ -...++-+.+|++...+...++....++
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 356666666665 4789999999999999988888776553
No 57
>PLN00035 histone H4; Provisional
Probab=52.57 E-value=38 Score=21.67 Aligned_cols=35 Identities=23% Similarity=0.124 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcC
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSE 104 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~ 104 (138)
..-+.+++.+|..+|...+- ..|+.+++.+|+=..
T Consensus 60 e~~l~~I~~dav~ya~HA~R-KTV~~~DV~~Alkr~ 94 (103)
T PLN00035 60 KIFLENVIRDAVTYTEHARR-KTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHHc
Confidence 45566788889999988888 999999999998543
No 58
>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=52.50 E-value=45 Score=19.41 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
.+-.++++++.|...++..+. ..+++.++=.||
T Consensus 33 veyrlreiiq~a~kfm~hskR-~~Lt~~Di~~AL 65 (66)
T PF02969_consen 33 VEYRLREIIQEALKFMRHSKR-TKLTTDDINSAL 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHTT--SSB-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCC-CCCCHHHHHHHh
Confidence 356789999999999999888 899999986664
No 59
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=51.73 E-value=51 Score=19.80 Aligned_cols=48 Identities=23% Similarity=0.095 Sum_probs=24.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHc---CCCCCCCCCCCCCCCHHHHHHHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVG---KGDFFFFSPEHPPLTEDAQRVIDWAV 80 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~---~~~~~~~~~~~~~~S~~l~~~l~~A~ 80 (138)
.+..+|+++|+++......+-+.+. ..|.. ...+.........+..+.
T Consensus 15 ~a~~il~~~Glt~s~ai~~fl~qiv~~~~iPF~---~~~~~~~~~~~~a~~e~~ 65 (83)
T PF04221_consen 15 EAEAILEELGLTLSDAINMFLKQIVREGGIPFE---LSLPEPNEETIKAIAEAE 65 (83)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHHHHSS-S-------SS-SSHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHhCCCCcc---ccCCCCCHHHHHHHHHHH
Confidence 4688999999999876665544432 33432 233334455555555553
No 60
>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=51.18 E-value=44 Score=20.53 Aligned_cols=36 Identities=22% Similarity=0.147 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCC
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSET 105 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~ 105 (138)
..-+.+++.+|..++...+- .-|+.+++.+|+=...
T Consensus 44 ~~~l~~I~~dav~ya~Ha~R-KTVt~~DV~~alkr~g 79 (85)
T cd00076 44 KSYLEDVIRDAVTYTEHAKR-KTVTAMDVVYALKRQG 79 (85)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHHCC
Confidence 45567788899999998888 9999999999985543
No 61
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=50.81 E-value=44 Score=18.80 Aligned_cols=40 Identities=10% Similarity=0.101 Sum_probs=24.7
Q ss_pred HHHHHHHHhhcCC---cHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 16 TEAILMGILVEGT---SLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 16 ~eHlLlall~~~~---~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
+...+|.+++.+. ..+..+.++++++++.++..+..++..
T Consensus 18 ~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 18 TAAFIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp HHHHHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4556677776543 245667778889998888888877654
No 62
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=49.62 E-value=58 Score=19.75 Aligned_cols=62 Identities=18% Similarity=-0.019 Sum_probs=36.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHc---CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVG---KGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLL 98 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~---~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlL 98 (138)
.+..+|+++|+++......+-..+. ..|.. ... ......++++.+... ..... .+-+...++
T Consensus 16 ~a~~i~~~lGl~~s~ai~~fl~qvv~~~~lPF~---~~~--~n~et~~a~~e~~~~-~~~~~-~f~s~~el~ 80 (83)
T TIGR02384 16 EAYAVFEELGLTPSTAIRMFLKQVIREQGLPFD---LRL--PNDETLAAIEEIKEL-RKLSH-KFESVDDLL 80 (83)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---cCC--CCHHHHHHHHHHHHh-cccCC-CcCCHHHHH
Confidence 4678999999999876555444433 23322 121 256777777777653 22334 565665554
No 63
>PTZ00015 histone H4; Provisional
Probab=49.53 E-value=45 Score=21.29 Aligned_cols=36 Identities=17% Similarity=0.103 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcC
Q 032554 68 LTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSE 104 (138)
Q Consensus 68 ~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~ 104 (138)
+..-+.+++.+|..+|...+- ..|+.+++.+|+=..
T Consensus 60 le~~l~~I~rdav~~aeHA~R-KTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 60 LKAFLENVVRDSTAYTEYARR-KTVTAMDVVYALKRQ 95 (102)
T ss_pred HHHHHHHHHHHHHHHHHhcCC-CcccHHHHHHHHHhc
Confidence 345567788899999998888 999999999997443
No 64
>TIGR02070 mono_pep_trsgly monofunctional biosynthetic peptidoglycan transglycosylase. This family is one of the transglycosylases involved in the late stages of peptidoglycan biosynthesis. Members tend to be small, about 240 amino acids in length, and consist almost entirely of a domain described by pfam model pfam00912 for transglycosylases. Species with this protein will have several other transglycosylases as well. All species with this protein are Proteobacteria that produce murein (peptidoglycan).
Probab=48.93 E-value=17 Score=26.57 Aligned_cols=37 Identities=16% Similarity=0.188 Sum_probs=29.9
Q ss_pred HHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 16 TEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 16 ~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
|.|+..|++..+| .+++...|+|...+..++...+..
T Consensus 64 p~~l~~Avia~ED---~rF~~H~GvD~~~i~rA~~~~~~~ 100 (224)
T TIGR02070 64 SPNLKRAVIASED---AKFVEHHGFDWEAIQDALEKNEKS 100 (224)
T ss_pred CHHHHhceeeccc---CcccccCCcCHHHHHHHHHHHHhc
Confidence 5688888888877 667889999999998888766643
No 65
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=48.53 E-value=29 Score=18.29 Aligned_cols=38 Identities=16% Similarity=0.119 Sum_probs=28.5
Q ss_pred HHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCCC
Q 032554 96 DLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSEPG 134 (138)
Q Consensus 96 hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~ 134 (138)
.++..+.+ +...+..+.+.+|+++..+..-+..+++.+
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~g 43 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAG 43 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCc
Confidence 35566665 456788999999999999999988877643
No 66
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=47.85 E-value=66 Score=23.38 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCC
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETD 106 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~ 106 (138)
++.+++.+...++..+. ..|++.||-.++..++.
T Consensus 48 l~~l~~~t~~~t~~~~a-Kt~s~~hlkq~v~~~~~ 81 (224)
T KOG1659|consen 48 LESLLQKTLEITRSRGA-KTVSSSHLKQAVESDPK 81 (224)
T ss_pred HHHHHHHHHHHHHhcCc-cccCHHHHHHHHhccch
Confidence 35677788889999999 99999999999988653
No 67
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=47.26 E-value=48 Score=20.68 Aligned_cols=33 Identities=21% Similarity=0.201 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
.-+..+.+.|..+|..-+- ..|.++++.+++-.
T Consensus 51 ~~~~~i~~~A~~~A~ha~R-KTV~~~DI~la~~~ 83 (91)
T COG2036 51 EYLEEIAEDAVELAEHAKR-KTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHHHHHHHHHHcCC-CeecHHHHHHHHHH
Confidence 4456677889999998888 99999999999843
No 68
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=46.06 E-value=74 Score=24.59 Aligned_cols=56 Identities=14% Similarity=0.022 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHH
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELES 128 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~ 128 (138)
+..++..|...|...+. ..|+.+|+-.|+-.-..+.....+..+......+..++.
T Consensus 251 a~~ll~~a~~~a~~~~~-~~I~~~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~ 306 (394)
T PRK00411 251 AIDLLRRAGLIAEREGS-RKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIV 306 (394)
T ss_pred HHHHHHHHHHHHHHcCC-CCcCHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 34567777778877777 889999998887554334445556655544445555544
No 69
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=45.95 E-value=33 Score=21.89 Aligned_cols=32 Identities=13% Similarity=0.128 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCC
Q 032554 73 QRVIDWAVDHKLKSGNSGEVTASDLLLGIWSET 105 (138)
Q Consensus 73 ~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~ 105 (138)
+.++..+...|+..+. ..|+.+||-.|+..++
T Consensus 59 ~~iv~~s~k~aR~~~s-kR~t~e~lk~a~~sde 90 (113)
T COG5247 59 TEIVGLSLKEARKKSS-KRMTSEFLKRATESDE 90 (113)
T ss_pred HHHHHHHHHHHHhccc-hhhHHHHHHHHHhhhH
Confidence 4556677888888888 9999999999998765
No 70
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=44.28 E-value=1.2e+02 Score=21.92 Aligned_cols=99 Identities=11% Similarity=0.037 Sum_probs=51.5
Q ss_pred CcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCC------CCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 28 TSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFS------PEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 28 ~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~------~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
+.++..+++.+|.|++.+++..++...-....+.. .....-...+..+++.+ + .+. .+--+--+-++|
T Consensus 72 ~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~~~~~---~--~~~-~f~YSRl~AIGL 145 (206)
T PLN03060 72 DAIFKAYIEALGEDPDQYRKDAKKLEEWASSQSASGIADFNSGDGEVEAVLKDIAERA---A--GKT-KFHYSRFFAIGL 145 (206)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcccccchHHHHHHHHh---h--cCC-CcchHHHHHHHH
Confidence 45778889999999999999877655421111000 00001111222222211 1 222 333333333333
Q ss_pred h---cCCC----cHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 102 W---SETD----SPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 102 l---~~~~----~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
+ +..+ .....+.+.+|++.+.+.+-+.-.|+
T Consensus 146 ~~LLe~a~~~d~~~l~~l~~~L~ls~~kv~kDL~lYrs 183 (206)
T PLN03060 146 FRLLECAKASDPAVLEKLSKALNVSKRSVDRDLDVYRN 183 (206)
T ss_pred HHHHHHcCCCCHHHHHHHHHHcCCCHHHHHhhHHHHHh
Confidence 2 2111 24568888899999988887766554
No 71
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=43.51 E-value=50 Score=19.69 Aligned_cols=35 Identities=9% Similarity=0.092 Sum_probs=22.9
Q ss_pred HHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHH
Q 032554 17 EAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKI 52 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~ 52 (138)
.-+|.++-+++ -.+..++.++|+.++++..-+...
T Consensus 19 ~elFq~lT~NP-l~AMa~i~qLGip~eKLQ~lm~~V 53 (82)
T PF11212_consen 19 NELFQALTQNP-LAAMATIQQLGIPQEKLQQLMAQV 53 (82)
T ss_pred HHHHHHHhhCH-HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34566666654 245667788888888887655433
No 72
>PRK13481 glycosyltransferase; Provisional
Probab=43.45 E-value=33 Score=25.21 Aligned_cols=38 Identities=11% Similarity=0.111 Sum_probs=30.0
Q ss_pred HHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 16 TEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 16 ~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
|+|+..|++..+| .+++...|+|+..+..++...+..+
T Consensus 54 p~~l~~AviA~ED---~rFy~H~GvD~~~i~rA~~~~~~~g 91 (232)
T PRK13481 54 PEYVKGAFISMED---ERFYKHHGFDLKGTTRALFSTISDR 91 (232)
T ss_pred CHHHHHHHHHHhc---CccccCCCCCHHHHHHHHHHHhhCC
Confidence 6789999998877 6678899999998888776555433
No 73
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=43.34 E-value=37 Score=18.53 Aligned_cols=17 Identities=12% Similarity=-0.005 Sum_probs=14.3
Q ss_pred HcCCCHHHHHHHHHhhc
Q 032554 115 ALGFSDEKAKELESLSS 131 (138)
Q Consensus 115 ~~gi~~~~l~~~i~~~r 131 (138)
..|++++++-..+.++|
T Consensus 32 e~GVnPeaLA~vI~elr 48 (48)
T PF12554_consen 32 ENGVNPEALAAVIKELR 48 (48)
T ss_pred HCCCCHHHHHHHHHHhC
Confidence 45899999999888876
No 74
>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=42.90 E-value=44 Score=19.78 Aligned_cols=25 Identities=12% Similarity=0.181 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhcCCCCC-CCHHHHHH
Q 032554 74 RVIDWAVDHKLKSGNSGE-VTASDLLL 99 (138)
Q Consensus 74 ~~l~~A~~~A~~~~~~~~-I~~~hlLl 99 (138)
+++..|...|...+. .. |+.+||=-
T Consensus 38 EAv~Ra~~~a~~e~~-~~~le~e~LEk 63 (72)
T PF09415_consen 38 EAVARAAEQAEAEGD-EGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHHHHHHHTT--SSEE-HHHHHH
T ss_pred HHHHHHHHHHHHcCC-CCCCCHHHHHH
Confidence 344556666766777 66 99999843
No 75
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=42.74 E-value=58 Score=18.21 Aligned_cols=22 Identities=14% Similarity=-0.046 Sum_probs=13.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVK 51 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~ 51 (138)
.+.+++++.|+|++.+.++|+.
T Consensus 33 ~L~eA~~~~~ld~~~vl~~L~~ 54 (56)
T PF04405_consen 33 SLEEACEEKGLDPEEVLEELNA 54 (56)
T ss_pred hHHHHHHHcCCCHHHHHHHHHH
Confidence 3456666667777766666643
No 76
>PRK11426 hypothetical protein; Provisional
Probab=42.37 E-value=83 Score=21.06 Aligned_cols=42 Identities=10% Similarity=0.002 Sum_probs=34.0
Q ss_pred CCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 11 HPTTGTEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 11 ~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
+..|+++++--++=. ..+..+-.+.|++++.+...+-+++..
T Consensus 58 N~pIs~~ql~~~lG~---d~i~~lA~q~Gl~~~~~~~~LA~~LP~ 99 (132)
T PRK11426 58 NQSVSGEQLESALGT---NAVSDLGQKLGVDTSTASSLLAEQLPK 99 (132)
T ss_pred CCCCCHHHHHHHhCh---HHHHHHHHHHCcCHHHHHHHHHHHhHH
Confidence 678999999876632 368999999999999998888777643
No 77
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=41.12 E-value=92 Score=19.65 Aligned_cols=73 Identities=10% Similarity=-0.063 Sum_probs=47.9
Q ss_pred CcCHHH--HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC-----CCCC-CCCCCCCCCHHHHHHHHHHHHHHH
Q 032554 13 TTGTEA--ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG-----DFFF-FSPEHPPLTEDAQRVIDWAVDHKL 84 (138)
Q Consensus 13 ~i~~eH--lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~-----~~~~-~~~~~~~~S~~l~~~l~~A~~~A~ 84 (138)
.+++.+ +|..|-..+.-...++-+.+|++...+...+++...++ +... .....+.+|+.-..+++..+....
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~ 104 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQIE 104 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHH
Confidence 344444 55555554544578899999999998888887766543 1110 011236789999999998877665
Q ss_pred h
Q 032554 85 K 85 (138)
Q Consensus 85 ~ 85 (138)
.
T Consensus 105 ~ 105 (118)
T TIGR02337 105 E 105 (118)
T ss_pred H
Confidence 4
No 78
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=40.61 E-value=67 Score=21.84 Aligned_cols=33 Identities=21% Similarity=0.139 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
+-++.+|+.|..++...+. ..|+.+++-+|+--
T Consensus 45 rYtt~vL~DA~vys~HA~k-a~i~~eDVrlA~~~ 77 (148)
T KOG3334|consen 45 RYTTTVLDDAKVYSSHAKK-ATIDAEDVRLAIQM 77 (148)
T ss_pred HHHHHHHHHHHHHHHhccC-CCCcHHHHHHHHHH
Confidence 3457899999999998888 89999999999843
No 79
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=40.47 E-value=5.7 Score=25.68 Aligned_cols=62 Identities=10% Similarity=0.039 Sum_probs=38.4
Q ss_pred CHHHHHHHHHHHHcCCCCCCCCCCCCCCCHH-----HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCC
Q 032554 41 TLFKVRDESVKIVGKGDFFFFSPEHPPLTED-----AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSET 105 (138)
Q Consensus 41 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~-----l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~ 105 (138)
....+...+++....-..+ |. ....++.. ..++|+.|.+-++..+- ..|+|.||-+|+-.|+
T Consensus 32 pVgRihr~LK~r~t~h~rV-Ga-taavy~aaileYLTaEVLeLAgNasKdLKv-KRitprHlqLAiRGDe 98 (131)
T KOG1757|consen 32 PVGRIHRHLKTRTTSHGRV-GA-TAAVYSAAILEYLTAEVLELAGNASKDLKV-KRITPRHLQLAIRGDE 98 (131)
T ss_pred chHHHHHHHHHhccccccc-ch-HHHHHHHHHHHHHHHHHHHHccccccccee-eeccchhheeeecCcH
Confidence 5566666666554332222 11 11122222 35677888887888888 8999999999997654
No 80
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=40.07 E-value=58 Score=20.16 Aligned_cols=27 Identities=15% Similarity=0.105 Sum_probs=22.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
-+..|.++++++..+++..++..+..+
T Consensus 67 ~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 67 HVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp EHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred cHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 468899999999999999999887654
No 81
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=38.82 E-value=86 Score=19.33 Aligned_cols=38 Identities=16% Similarity=0.180 Sum_probs=28.8
Q ss_pred HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 19 ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 19 lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
+|..|-.++.-...++-+.+|++...++..+......+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 44455555545678899999999999999998877653
No 82
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=37.71 E-value=1.2e+02 Score=23.13 Aligned_cols=58 Identities=10% Similarity=-0.021 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHH
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELES 128 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~ 128 (138)
..+..++..|...|...+. ..|+.+|+--|+-....+.....+..+......+..++.
T Consensus 241 R~al~~l~~a~~~a~~~~~-~~it~~~v~~a~~~~~~~~~~~~i~~l~~~~~~~l~ai~ 298 (365)
T TIGR02928 241 RKAIDLLRVAGEIAEREGA-ERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIA 298 (365)
T ss_pred HHHHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3455677788888877777 789999998776443223334455544444444444444
No 83
>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=37.58 E-value=1e+02 Score=19.14 Aligned_cols=36 Identities=17% Similarity=0.203 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCC
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETD 106 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~ 106 (138)
...+..+...|...|. ++. ..+++++|+..|=.++.
T Consensus 34 ~~~i~~l~~~a~~~A~-~r~-~k~~~eD~~FliR~D~~ 69 (92)
T cd07978 34 VEYIIELCHKAAEVAQ-RRR-GKVKVEDLIFLLRKDPK 69 (92)
T ss_pred HHHHHHHHHHHHHHHH-cCC-CCCCHHHHHHHHhcCHH
Confidence 4556667777888887 555 67799999999977663
No 84
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=36.97 E-value=1.3e+02 Score=20.08 Aligned_cols=26 Identities=8% Similarity=0.003 Sum_probs=18.8
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcC
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEG 27 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~ 27 (138)
|.+.|..-....|.+||+..||=+.+
T Consensus 54 Ane~ce~EaKKTIa~EHviKALenLe 79 (148)
T COG5150 54 ANEACEEEAKKTIAYEHVIKALENLE 79 (148)
T ss_pred HHHHHHHHHhccccHHHHHHHHHhcc
Confidence 33445555667899999999986654
No 85
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=36.66 E-value=1.6e+02 Score=22.45 Aligned_cols=100 Identities=10% Similarity=0.043 Sum_probs=52.9
Q ss_pred CcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCC---CCCCHHHHHHHHHHHHHHHh--cCCCCCCCHHHHHHHHh
Q 032554 28 TSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEH---PPLTEDAQRVIDWAVDHKLK--SGNSGEVTASDLLLGIW 102 (138)
Q Consensus 28 ~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~---~~~S~~l~~~l~~A~~~A~~--~~~~~~I~~~hlLlall 102 (138)
+.++..+++.+|.|++.+++..++...-....++ ..- ......+...|.. +|.+ .++ .+--+--+-++|+
T Consensus 125 ~~IF~Alc~a~g~Dp~qyr~dA~~l~~~A~~~s~-~~l~~~l~~~~~l~~~l~~---IA~~a~~~~-~f~YSRlfAIGLf 199 (283)
T PLN00047 125 DAIFKAYIKALGEDPEQYRKDAAKLEEWARSQTG-SSLVDFSSKEGEIEGILKD---IAERAGSKG-KFSYSRFFAIGLF 199 (283)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCH-HHHHHHHhcchHHHHHHHH---HHHhhccCC-CcchHHHHHHHHH
Confidence 4577888999999999999987665542221110 000 1111233333322 2211 223 3333333333332
Q ss_pred ---cCCC----cHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 103 ---SETD----SPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 103 ---~~~~----~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
+..+ .....+.+.+|++.+.+.+-+.-+|+
T Consensus 200 ~LLe~a~~~d~~~l~~l~e~Lgls~~kv~KDLdlYrs 236 (283)
T PLN00047 200 RLLELANATEPTALEKLCAALNINKRSVDRDLDVYRG 236 (283)
T ss_pred HHHHhcCCCCHHHHHHHHHHcCCCHHHHHhhHHHHHh
Confidence 2211 35567888899999888877665544
No 86
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=36.32 E-value=1e+02 Score=20.46 Aligned_cols=38 Identities=11% Similarity=0.079 Sum_probs=30.2
Q ss_pred HHHHHh-hcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 19 ILMGIL-VEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 19 lLlall-~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
++.+|| .++...+..+-+.+|.+...+...+++.+..+
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G 70 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAG 70 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC
Confidence 456777 45555778888899999999999999988754
No 87
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.72 E-value=1.3e+02 Score=19.55 Aligned_cols=57 Identities=14% Similarity=0.115 Sum_probs=37.5
Q ss_pred HHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHH
Q 032554 20 LMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWA 79 (138)
Q Consensus 20 Llall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A 79 (138)
+...+... |-+.++=+.+|+++..+|..+++.+.+..... .....-...-.++|+.-
T Consensus 42 i~~Fi~~r-GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~--~~~~~~~~~~~~IL~~L 98 (113)
T PF09862_consen 42 IKLFIKNR-GNLKEMEKELGISYPTVRNRLDKIIEKLGYEE--DEEEEEEDERKEILDKL 98 (113)
T ss_pred HHHHHHhc-CCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC--CcccccchhHHHHHHHH
Confidence 34444543 55789999999999999999999987655421 11223345555666554
No 88
>PRK05255 hypothetical protein; Provisional
Probab=34.42 E-value=1.5e+02 Score=20.81 Aligned_cols=39 Identities=18% Similarity=0.117 Sum_probs=28.0
Q ss_pred HHHHHHHhhcCCcHHHHHHHHC-CCCHHHHHHHHHHHHcC
Q 032554 17 EAILMGILVEGTSLAAKFLWAN-GVTLFKVRDESVKIVGK 55 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~-g~~~~~l~~~l~~~l~~ 55 (138)
|.|-=.|+.++++.+..++..+ ..|...|++-+.+.-..
T Consensus 110 E~wRdrLi~~~d~al~e~~~~~P~~DrQ~LRqLiR~A~kE 149 (171)
T PRK05255 110 ERWRDRLLAEGDDALTEFLEEYPDADRQQLRQLIRNAKKE 149 (171)
T ss_pred HHHHHHHHhCCHHHHHHHHHHCchhhHHHHHHHHHHHHHH
Confidence 4455567776777788888888 57888888877666543
No 89
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=33.95 E-value=1.2e+02 Score=18.96 Aligned_cols=70 Identities=14% Similarity=0.043 Sum_probs=47.2
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcC
Q 032554 31 AAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSE 104 (138)
Q Consensus 31 ~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~ 104 (138)
..+++..+|++++-+.+.++--+-. |... .++...|+..-...++.|......++- ......+.+.+++.
T Consensus 10 ~~Elc~~~gi~~~~l~eLve~GlIe-p~~~-~~~~~~F~~~~l~r~~~a~rL~~dl~i--n~~gialvl~LLd~ 79 (101)
T PRK10265 10 ITEFCLHTGVSEEELNEIVGLGVIE-PREI-QETTWVFDDHAAIVVQRAVRLRHELAL--DWPGIAVALTLLDE 79 (101)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCee-cCCC-CcccceECHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHH
Confidence 5788999999999888776544422 2211 234567899888889999988887665 34444555566653
No 90
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=32.64 E-value=87 Score=16.88 Aligned_cols=40 Identities=18% Similarity=0.102 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 17 EAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
-|+|..|-+.+.-...++-+.++++...+...++....++
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 3556666666666778888999999999988888776653
No 91
>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=32.28 E-value=93 Score=26.21 Aligned_cols=37 Identities=24% Similarity=0.099 Sum_probs=29.9
Q ss_pred CCCC-HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 66 PPLT-EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 66 ~~~S-~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
++++ ..+.++++.|..+|...+. ..|+.+|+.-|+-.
T Consensus 353 lsl~~R~L~~llR~A~~iA~~~~~-~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 353 LTLRLRELGGLVRAAGDIAKSSGK-VYVTAEHVLKAKKL 390 (608)
T ss_pred cCCCHHHHHHHHHHHHHHHHhcCC-ceecHHHHHHHHHH
Confidence 4444 7888999999888887788 89999999988643
No 92
>PRK09862 putative ATP-dependent protease; Provisional
Probab=32.15 E-value=1e+02 Score=25.45 Aligned_cols=34 Identities=15% Similarity=-0.008 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
.....++++-|+.+|--.+. ++|+++|+..|+--
T Consensus 458 ~Ra~~rlLrvARTiADL~g~-~~V~~~hv~eAl~y 491 (506)
T PRK09862 458 IRAWQRLLKVARTIADIDQS-DIITRQHLQEAVSY 491 (506)
T ss_pred HHHHHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHh
Confidence 45567788889999988888 99999999999853
No 93
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=31.62 E-value=1.3e+02 Score=18.64 Aligned_cols=51 Identities=16% Similarity=0.101 Sum_probs=28.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVD 81 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~ 81 (138)
.+..+|+++|+++......+-+.+-+....+.....|. ...+.++++....
T Consensus 18 eA~~Vl~~mGlt~S~airm~L~~va~~~~lPfdl~~p~-N~~tl~ai~e~~~ 68 (88)
T COG3077 18 EATAVLEEMGLTISDAIRMFLTKVAREGALPFDLRLPS-NAETLQAIKELDK 68 (88)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCccccCcc-cHHHHHHHHHHHh
Confidence 46889999999998766655444432221111122222 4555555555543
No 94
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=31.24 E-value=88 Score=16.52 Aligned_cols=30 Identities=17% Similarity=0.109 Sum_probs=24.0
Q ss_pred cCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 26 EGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 26 ~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
.+.....++.+.+|++...+...++.....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344567889999999999999999877654
No 95
>PF00912 Transgly: Transglycosylase; InterPro: IPR001264 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 51 GT51 from CAZY comprises enzymes with only one known activity; murein polymerases (2.4 from EC). These enzymes utilise MurNAc-GlcNAc-P-P-lipid II as the sugar donor. The family includes the bifunctional penicillin-binding proteins that have a transglycosylase (N terminus) and transpeptidase (C terminus) domain [] and the monofunctional biosynthetic peptidoglycan transglycosylases [].; GO: 0003824 catalytic activity, 0009252 peptidoglycan biosynthetic process, 0009274 peptidoglycan-based cell wall; PDB: 3VMT_A 3VMS_B 3VMQ_A 3VMR_A 3D3H_A 3NB7_A 3NB6_A 2OQO_A 2V2F_A 3HZS_A ....
Probab=30.29 E-value=22 Score=24.97 Aligned_cols=35 Identities=9% Similarity=0.188 Sum_probs=27.7
Q ss_pred HHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHH
Q 032554 16 TEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIV 53 (138)
Q Consensus 16 ~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l 53 (138)
|+++..+++.-+| .+++...|+|+..+..++-..+
T Consensus 23 p~~~~~a~ia~ED---~~F~~H~GiD~~~i~rA~~~~~ 57 (178)
T PF00912_consen 23 PPNLIDALIASED---RRFYSHPGIDPKAIARAIVQNL 57 (178)
T ss_dssp -HHHHHHHHHHHS---TTTTTSSSSGHHHHHHHHTTHH
T ss_pred CHHHHHHHHHHHH---HHhhcCcCchHHHHHHHHHHHh
Confidence 5588888888777 5567899999999988876666
No 96
>PF08230 Cpl-7: Cpl-7 lysozyme C-terminal domain; InterPro: IPR013168 This domain was originally found in the C-terminal moiety of the Cp-7 lysin (lysozyme, P19385 from SWISSPROT) encoded by Bacteriophage Cp-7. It is assumed that this domain represents a cell wall binding motif although no direct evidence has been obtained so far to support this.
Probab=30.27 E-value=93 Score=16.48 Aligned_cols=22 Identities=23% Similarity=0.160 Sum_probs=18.1
Q ss_pred HHHHHHCCCCHHHHHHHHHHHH
Q 032554 32 AKFLWANGVTLFKVRDESVKIV 53 (138)
Q Consensus 32 ~~il~~~g~~~~~l~~~l~~~l 53 (138)
..-|...|-|++.+...+.+.+
T Consensus 20 k~~L~~aGydY~~VQ~~VN~~l 41 (42)
T PF08230_consen 20 KKRLTAAGYDYDAVQARVNELL 41 (42)
T ss_pred HHHHHHcCCCHHHHHHHHHHHc
Confidence 5567888999999999887765
No 97
>PF10038 DUF2274: Protein of unknown function (DUF2274); InterPro: IPR018733 Members of this family of hypothetical bacterial proteins have no known function.
Probab=29.52 E-value=1.3e+02 Score=17.78 Aligned_cols=36 Identities=14% Similarity=0.183 Sum_probs=27.3
Q ss_pred CCCCHHHHHHH-HHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 66 PPLTEDAQRVI-DWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 66 ~~~S~~l~~~l-~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
+.+...+.+-| ..|..+++..|. . +++..|+-.|++
T Consensus 19 i~lpa~l~rdL~~Ya~~~~~~~g~-~-~~~~~Li~~MLe 55 (69)
T PF10038_consen 19 IELPASLHRDLVAYAEALAREYGQ-A-ADPAKLIPPMLE 55 (69)
T ss_pred EeCCHHHHHHHHHHHHHHHHHhCC-C-CCHHHHHHHHHH
Confidence 45667766655 668888888887 5 999999888875
No 98
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=28.88 E-value=1.3e+02 Score=17.86 Aligned_cols=38 Identities=24% Similarity=0.205 Sum_probs=30.5
Q ss_pred HHHHHHhhcCCc-HHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 18 AILMGILVEGTS-LAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 18 HlLlall~~~~~-~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
-.+++||..+++ .+.++.+..|+.+..++..+...+.+
T Consensus 13 a~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kK 51 (72)
T PF11994_consen 13 AQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKK 51 (72)
T ss_pred HHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 456788887765 67899999999999999988777544
No 99
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=28.63 E-value=2.8e+02 Score=21.73 Aligned_cols=60 Identities=10% Similarity=-0.003 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
.....++..|...|...+. ..++.+|+-.|--..+.......++.+-.....+..++...
T Consensus 232 R~aidilr~A~eiAe~~~~-~~v~~~~v~~a~~~~~~~~~~~~~~~L~~~~ki~L~~i~~~ 291 (366)
T COG1474 232 RKAIDILRRAGEIAEREGS-RKVSEDHVREAQEEIERDVLEEVLKTLPLHQKIVLLAIVEL 291 (366)
T ss_pred HHHHHHHHHHHHHHHhhCC-CCcCHHHHHHHHHHhhHHHHHHHHHcCCHhHHHHHHHHHHh
Confidence 4456678889999998889 99999999999444333455566666655544444444433
No 100
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=28.44 E-value=1.2e+02 Score=20.08 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHhcCC--CCCCCHHHHHHHHhcC
Q 032554 70 EDAQRVIDWAVDHKLKSGN--SGEVTASDLLLGIWSE 104 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~--~~~I~~~hlLlall~~ 104 (138)
.-.+.+|+.|..+|...|. +.-++++++=+|+...
T Consensus 46 RYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 46 RYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred HHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 3457899999999987554 2335559999988653
No 101
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=28.41 E-value=1.2e+02 Score=17.25 Aligned_cols=27 Identities=19% Similarity=0.184 Sum_probs=21.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
...++-..+|++++.++..|+..+.++
T Consensus 16 S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 16 SLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp EHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 568899999999999999998887664
No 102
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=27.93 E-value=1.7e+02 Score=20.56 Aligned_cols=39 Identities=26% Similarity=0.216 Sum_probs=31.1
Q ss_pred HHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 17 EAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
..+|..|...+.-...++-+.+|++...++..++.....
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 467777777666678899999999999999998876543
No 103
>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=27.50 E-value=1.3e+02 Score=17.54 Aligned_cols=28 Identities=14% Similarity=0.197 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHh
Q 032554 74 RVIDWAVDHKLKSGNSGEVTASDLLLGIW 102 (138)
Q Consensus 74 ~~l~~A~~~A~~~~~~~~I~~~hlLlall 102 (138)
.++..|-..|+..+. +.+++.++.+.+=
T Consensus 36 ~v~~~ac~lAKhR~s-~tle~~Dv~~~Le 63 (68)
T PF03847_consen 36 DVVSFACRLAKHRKS-STLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHHHHHHHTT--SEE-HHHHHHHHH
T ss_pred HHHHHHHHHHhccCC-CCCCHHHHHHHHH
Confidence 566778888998888 8899999988763
No 104
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=27.37 E-value=76 Score=18.11 Aligned_cols=25 Identities=4% Similarity=-0.032 Sum_probs=21.8
Q ss_pred cHHHHHHHHCCCCHHHHHHHHHHHH
Q 032554 29 SLAAKFLWANGVTLFKVRDESVKIV 53 (138)
Q Consensus 29 ~~~~~il~~~g~~~~~l~~~l~~~l 53 (138)
..+..+.+.+||++..|..++..+.
T Consensus 24 ~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 24 ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CceEeeecccccccccccHHHHHHh
Confidence 4679999999999999999999887
No 105
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.21 E-value=1.5e+02 Score=17.99 Aligned_cols=70 Identities=13% Similarity=-0.050 Sum_probs=43.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCC
Q 032554 31 AAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSET 105 (138)
Q Consensus 31 ~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~ 105 (138)
..++.+.+|+++..++.....-+-. |... .++.-.|+..-...+......-. .|- .+..-.-++..+..+
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gll~-~~~~-~~g~r~y~~~dv~~l~~i~~l~~-~g~--~~~~i~~~l~~~~~~ 72 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGLLP-PERS-ENGYRLYSEEDLERLRLIRRLRE-LGL--SLKEIRELLDARDEE 72 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcC-CCcC-CCCCcccCHHHHHHHHHHHHHHH-cCC--CHHHHHHHHhccccc
Confidence 4567889999999999887644322 2221 23456789888887777766544 454 333333444444444
No 106
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=27.00 E-value=1.2e+02 Score=16.67 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=27.8
Q ss_pred HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 19 ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 19 lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
++--|-+.+.-.+.++.+.+|++...++..+...-..+
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34334444445678899999999999999998766544
No 107
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=26.88 E-value=1.5e+02 Score=17.82 Aligned_cols=38 Identities=11% Similarity=0.075 Sum_probs=30.0
Q ss_pred HHHHHHHhhcCCcHHHHHHHHC-CCCHHHHHHHHHHHHcC
Q 032554 17 EAILMGILVEGTSLAAKFLWAN-GVTLFKVRDESVKIVGK 55 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~-g~~~~~l~~~l~~~l~~ 55 (138)
-.+|..|.. +...+.++.+.+ |++...|.+.+......
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~ 46 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEA 46 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHc
Confidence 457777877 456889999999 89999999999877654
No 108
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=26.64 E-value=1.4e+02 Score=22.24 Aligned_cols=41 Identities=7% Similarity=-0.059 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHhcC-CCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 91 EVTASDLLLGIWSE-TDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 91 ~I~~~hlLlall~~-~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
.=..+|+|-.+-.+ ..-....+-+.+|+++..+++++..+.
T Consensus 182 leAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE 223 (251)
T TIGR02787 182 LEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLE 223 (251)
T ss_pred HHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34566777766552 334456888899999999999998863
No 109
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=26.51 E-value=1.3e+02 Score=24.76 Aligned_cols=33 Identities=18% Similarity=0.007 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
..+..+|..|-.+|+..+. ..|+.+|+-.|+-.
T Consensus 473 ~~l~~ll~EA~~~A~~~~~-~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 473 SWLADLLREANYWARKEGA-KVITAEHVEQAIEE 505 (509)
T ss_dssp HHHHHHHHHHHHHHHHCT--SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCC-CccCHHHHHHHHHc
Confidence 4778899999999998888 99999999988754
No 110
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=26.07 E-value=2.1e+02 Score=19.22 Aligned_cols=62 Identities=16% Similarity=0.178 Sum_probs=41.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHc---C-----CCHHHHHHHHHhh
Q 032554 64 EHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAAL---G-----FSDEKAKELESLS 130 (138)
Q Consensus 64 ~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~---g-----i~~~~l~~~i~~~ 130 (138)
.++.||..-+.+...-...+.. ..=.+..++++++... .+...+.+.+ + ++...|...+..+
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~----~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RL 87 (135)
T PRK09416 18 KHLSFSEQHQKAVREKIKQSSE----KEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRL 87 (135)
T ss_pred hcCCcchhhHHHHHHHHHHHhc----ccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHH
Confidence 4578898888877766555433 4457889999999877 7776666542 2 3455666665554
No 111
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=26.02 E-value=1.8e+02 Score=19.42 Aligned_cols=40 Identities=18% Similarity=0.146 Sum_probs=29.8
Q ss_pred HHHHHHHhhc-CCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 17 EAILMGILVE-GTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 17 eHlLlall~~-~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
.+-++.+|+. +.-...++-+.+|++...++..+++...++
T Consensus 11 D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 11 DRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3445555544 344678889999999999999999887664
No 112
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.92 E-value=1e+02 Score=16.25 Aligned_cols=25 Identities=24% Similarity=0.234 Sum_probs=19.9
Q ss_pred HHHHHHHcCCCHHHHHHHHHhhcCC
Q 032554 109 GHKILAALGFSDEKAKELESLSSEP 133 (138)
Q Consensus 109 ~~~~l~~~gi~~~~l~~~i~~~r~~ 133 (138)
...+.+.+|++...+.+.+..+.+.
T Consensus 23 ~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 23 ERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4567788899999999998887653
No 113
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=25.79 E-value=1.6e+02 Score=17.68 Aligned_cols=68 Identities=13% Similarity=0.016 Sum_probs=45.3
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 31 AAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 31 ~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
+.+++..+|++++-+...++.-+-. |.. ..+.+.|+..-..-++.+..+...++- ......+.+-+++
T Consensus 3 ~~e~~~~~~i~~~~l~~lve~Gli~-p~~--~~~~~~f~~~~l~rl~~~~rL~~Dl~i--n~~gi~lil~LLd 70 (84)
T PF13591_consen 3 LEEFCEACGIEPEFLRELVEEGLIE-PEG--EEEEWYFSEEDLARLRRIRRLHRDLGI--NLEGIALILDLLD 70 (84)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCee-ecC--CCCeeeECHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHH
Confidence 4678899999999888877644322 221 134578999999999999888777655 2333344444443
No 114
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.78 E-value=1.1e+02 Score=15.86 Aligned_cols=31 Identities=13% Similarity=0.152 Sum_probs=20.8
Q ss_pred HHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHH
Q 032554 96 DLLLGIWSETDSPGHKILAALGFSDEKAKELE 127 (138)
Q Consensus 96 hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i 127 (138)
.-+..|+.++ .....+.+.+||+...+...+
T Consensus 12 ~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKELYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 3445567766 556889999999999887654
No 115
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=25.30 E-value=2e+02 Score=18.78 Aligned_cols=74 Identities=14% Similarity=-0.002 Sum_probs=48.4
Q ss_pred cCCCCcCHHHH--HHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCC--C-CC---CCCCCCCCHHHHHHHHHHH
Q 032554 9 LKHPTTGTEAI--LMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDF--F-FF---SPEHPPLTEDAQRVIDWAV 80 (138)
Q Consensus 9 ~~~~~i~~eHl--Llall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~--~-~~---~~~~~~~S~~l~~~l~~A~ 80 (138)
.....+++.++ |..|-..+.-...++-+.+|++...+-..+++...++-- . .+ ....+.+|+.-..+++.+.
T Consensus 33 l~~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~ 112 (144)
T PRK11512 33 LSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCH 112 (144)
T ss_pred hcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHH
Confidence 34556777766 444444443356889999999999998888877655311 0 11 1123678999999888865
Q ss_pred HH
Q 032554 81 DH 82 (138)
Q Consensus 81 ~~ 82 (138)
..
T Consensus 113 ~~ 114 (144)
T PRK11512 113 QL 114 (144)
T ss_pred HH
Confidence 43
No 116
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=25.19 E-value=1.3e+02 Score=17.73 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=13.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHhhc
Q 032554 109 GHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 109 ~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
...+-+..++++..+.+.+.+++
T Consensus 28 ~~eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 28 SKEIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHHh
Confidence 34555566677766666666653
No 117
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=25.04 E-value=2.8e+02 Score=20.23 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=21.7
Q ss_pred CcHHHHHHHHCCCCHHHHHHHHHHHHc
Q 032554 28 TSLAAKFLWANGVTLFKVRDESVKIVG 54 (138)
Q Consensus 28 ~~~~~~il~~~g~~~~~l~~~l~~~l~ 54 (138)
+.++..+++.+|.|++.+++..++...
T Consensus 74 ~~IF~Alc~a~~~dp~~~r~dA~~l~~ 100 (214)
T TIGR03060 74 DALFDALCNSNGFDPEQLREDAKQLLE 100 (214)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 457788899999999999988766543
No 118
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=25.01 E-value=2e+02 Score=18.69 Aligned_cols=76 Identities=17% Similarity=-0.001 Sum_probs=50.0
Q ss_pred CCCCcCHHHH--HHHHhhcCC-cHHHHHHHHCCCCHHHHHHHHHHHHcCCCCC---CC---CCCCCCCCHHHHHHHHHHH
Q 032554 10 KHPTTGTEAI--LMGILVEGT-SLAAKFLWANGVTLFKVRDESVKIVGKGDFF---FF---SPEHPPLTEDAQRVIDWAV 80 (138)
Q Consensus 10 ~~~~i~~eHl--Llall~~~~-~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~---~~---~~~~~~~S~~l~~~l~~A~ 80 (138)
....+++.|+ |..+...++ ....++-+.+|++...+...+++...++--. .+ ....+.+|+.-..+++.+.
T Consensus 25 ~~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~ 104 (144)
T PRK03573 25 KPLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE 104 (144)
T ss_pred HhcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH
Confidence 3445777774 444444333 3468999999999999988888776553110 01 1123678999999998887
Q ss_pred HHHHh
Q 032554 81 DHKLK 85 (138)
Q Consensus 81 ~~A~~ 85 (138)
.....
T Consensus 105 ~~~~~ 109 (144)
T PRK03573 105 AVINK 109 (144)
T ss_pred HHHHH
Confidence 66543
No 119
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=24.71 E-value=1.6e+02 Score=17.32 Aligned_cols=31 Identities=19% Similarity=0.108 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
+.++.+.+..+|...|. ..+++.++.+|+.+
T Consensus 40 l~~l~~~~~~~a~~agR-~~~~~~Dv~~Al~~ 70 (77)
T smart00576 40 IQELGRTAHSYAELAGR-TEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHH
Confidence 56666777888877777 88889999888754
No 120
>cd01580 AcnA_IRP_Swivel Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=24.18 E-value=39 Score=23.61 Aligned_cols=35 Identities=26% Similarity=0.220 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHH
Q 032554 90 GEVTASDLLLGIWSETDSPGHKILAALGFSDEKAK 124 (138)
Q Consensus 90 ~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~ 124 (138)
+.|+++|+==|=-=.+++.+.+.|...|+.+..+.
T Consensus 4 D~iTTDHISPaG~I~~~s~ag~yL~~~gv~~~dfn 38 (171)
T cd01580 4 DSVTTDHISPAGSIAKDSPAGKYLAERGVKPRDFN 38 (171)
T ss_pred CCccccccCCCCCCCCCChHHHHHHHcCCChhhcc
Confidence 47888888655433456899999999999876653
No 121
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=23.98 E-value=1.3e+02 Score=16.49 Aligned_cols=36 Identities=17% Similarity=0.060 Sum_probs=25.3
Q ss_pred HHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcC
Q 032554 97 LLLGIWSETDSPGHKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 97 lLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
++..+...+...+..+-+.+|++...+...+..++.
T Consensus 15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 15 ILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 444442444466788888999999999988887755
No 122
>PF15615 TerB-C: TerB-C domain
Probab=23.70 E-value=2.3e+02 Score=18.88 Aligned_cols=36 Identities=11% Similarity=0.029 Sum_probs=26.5
Q ss_pred HHHHHHhhcCCc---HHHHHHHHCCCCHHHHHHHHHHHH
Q 032554 18 AILMGILVEGTS---LAAKFLWANGVTLFKVRDESVKIV 53 (138)
Q Consensus 18 HlLlall~~~~~---~~~~il~~~g~~~~~l~~~l~~~l 53 (138)
++|-.|+..+.. .+..+.+.+|+-++.+...|++..
T Consensus 80 ~lL~~Ll~~~~w~r~e~~~~a~~~glm~~~~ie~INE~a 118 (144)
T PF15615_consen 80 ALLRALLSRESWSREELEDIARDHGLMPDGAIESINEKA 118 (144)
T ss_pred HHHHHHHhCCCccHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 456666666441 347889999999999999888765
No 123
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=23.64 E-value=1.4e+02 Score=16.37 Aligned_cols=37 Identities=11% Similarity=0.114 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHhcCCCcHHHHHHHHcC-CCHHHHHHHHH
Q 032554 90 GEVTASDLLLGIWSETDSPGHKILAALG-FSDEKAKELES 128 (138)
Q Consensus 90 ~~I~~~hlLlall~~~~~~~~~~l~~~g-i~~~~l~~~i~ 128 (138)
..|.+.+++-.+ ..+ .....+++.+. ++.+.++.++.
T Consensus 17 TRI~v~~i~~~~-~~G-~s~eeI~~~yp~Lt~~~i~aAl~ 54 (56)
T PF04255_consen 17 TRIPVRDILDLL-AAG-ESPEEIAEDYPSLTLEDIRAALA 54 (56)
T ss_dssp SS-BHHHHHHHH-HTT---HHHHHHHSTT--HHHHHHHHH
T ss_pred ceecHHHHHHHH-HcC-CCHHHHHHHCCCCCHHHHHHHHH
Confidence 578888888777 444 34578899997 89999988875
No 124
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=23.25 E-value=95 Score=19.05 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=14.0
Q ss_pred HHHHHcCCCHHHHHHHHH
Q 032554 111 KILAALGFSDEKAKELES 128 (138)
Q Consensus 111 ~~l~~~gi~~~~l~~~i~ 128 (138)
+.|+.+||+++.+.++++
T Consensus 70 krLN~f~it~~e~~~alk 87 (87)
T PF13331_consen 70 KRLNMFGITREEFEEALK 87 (87)
T ss_pred HHHHHcCCCHHHHHHHhC
Confidence 455678999999988763
No 125
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=23.24 E-value=1.3e+02 Score=22.56 Aligned_cols=18 Identities=22% Similarity=0.228 Sum_probs=13.3
Q ss_pred CCcCHHHHHHHHhhcCCc
Q 032554 12 PTTGTEAILMGILVEGTS 29 (138)
Q Consensus 12 ~~i~~eHlLlall~~~~~ 29 (138)
.+|+.||||--+=++.-|
T Consensus 169 EEvGVEHLlRDikd~t~g 186 (309)
T KOG1556|consen 169 EEVGVEHLLRDIKDTTVG 186 (309)
T ss_pred HHhhHHHHHHHHHhhhhh
Confidence 469999999877665433
No 126
>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=22.87 E-value=1.4e+02 Score=18.55 Aligned_cols=80 Identities=10% Similarity=0.095 Sum_probs=38.9
Q ss_pred HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCC---CCHH-HHHHHHHHHHHHHhcCCCCCCCH
Q 032554 19 ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPP---LTED-AQRVIDWAVDHKLKSGNSGEVTA 94 (138)
Q Consensus 19 lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~---~S~~-l~~~l~~A~~~A~~~~~~~~I~~ 94 (138)
+|+.-+.++.-.-.+.+++.+.+...++.-+...++.... + .+-.+. ++.- +-++++.|......+++...|.|
T Consensus 3 ~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv-~-~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P 80 (90)
T PF04719_consen 3 LLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSV-S-QNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQP 80 (90)
T ss_dssp -------HHHHHHHHHHHH----HHHHHHHHHHHHS-S-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--H
T ss_pred HHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCC-C-hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 3444455444445788999999999999988887752221 1 000000 1111 23567888888888877467999
Q ss_pred HHHHHH
Q 032554 95 SDLLLG 100 (138)
Q Consensus 95 ~hlLla 100 (138)
.|+=-|
T Consensus 81 ~hlreA 86 (90)
T PF04719_consen 81 DHLREA 86 (90)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 998655
No 127
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=22.48 E-value=1.8e+02 Score=17.08 Aligned_cols=68 Identities=18% Similarity=0.088 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCCCC----CC--CCCCCCCCHHHHHHHHHHHHHHH
Q 032554 17 EAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGDFF----FF--SPEHPPLTEDAQRVIDWAVDHKL 84 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~~~----~~--~~~~~~~S~~l~~~l~~A~~~A~ 84 (138)
.++|..|...+......+.+.++++...+...+......+--. .+ ......+|+.-..++..+.....
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~~ 86 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEARH 86 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHHH
Confidence 3455555555544677888999999999988888776543210 00 11224567887777776655443
No 128
>PF09385 HisK_N: Histidine kinase N terminal; InterPro: IPR018984 This domain is found at the N-terminal of sensor histidine kinase proteins. ; PDB: 3PMC_B 3PMD_A.
Probab=22.34 E-value=81 Score=21.14 Aligned_cols=55 Identities=11% Similarity=0.084 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 74 RVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 74 ~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
.+=..|...|+..-. -.+....++.-.--. .+..-..+.+.|++.+.+...+++|
T Consensus 62 ~i~~la~KiAkER~~-A~iNIgeFVYN~NlG-R~~~~~~l~~~~~~~~el~~~i~~I 116 (133)
T PF09385_consen 62 EIQQLAYKIAKERAE-ANINIGEFVYNVNLG-RSELLKYLFKLGIDWNELQPIIEKI 116 (133)
T ss_dssp GGHHHHHHHHHHHHH-HT--THHHHHHHHHH-HHHHHHHHHCC---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhh-cCCcHHHHHHHhhHh-HHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 444567777776656 678999999987653 3677788889999999999988875
No 129
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=22.29 E-value=2.8e+02 Score=19.37 Aligned_cols=75 Identities=15% Similarity=0.163 Sum_probs=49.9
Q ss_pred hHHHHHhcCCCCcCHHHHHHHHhhcCCcHHHHHHHHCCCCHHH-HHHH-HHHHHcCCCCCCCCCCCCCCCHHHHHHHHHH
Q 032554 2 GELEARKLKHPTTGTEAILMGILVEGTSLAAKFLWANGVTLFK-VRDE-SVKIVGKGDFFFFSPEHPPLTEDAQRVIDWA 79 (138)
Q Consensus 2 A~~~A~~~~~~~i~~eHlLlall~~~~~~~~~il~~~g~~~~~-l~~~-l~~~l~~~~~~~~~~~~~~~S~~l~~~l~~A 79 (138)
...+|+.++-+++++.|++-.=... .+.+|++..|-+.-. +... +.+.+...+.+..-++...++++..+.|..-
T Consensus 19 Gr~LAk~L~~~F~D~D~~Ie~~~g~---sI~eIF~~~GE~~FR~~E~~vl~~l~~~~~~ViaTGGG~v~~~enr~~l~~~ 95 (172)
T COG0703 19 GRALAKALNLPFIDTDQEIEKRTGM---SIAEIFEEEGEEGFRRLETEVLKELLEEDNAVIATGGGAVLSEENRNLLKKR 95 (172)
T ss_pred HHHHHHHcCCCcccchHHHHHHHCc---CHHHHHHHHhHHHHHHHHHHHHHHHhhcCCeEEECCCccccCHHHHHHHHhC
Confidence 4678999999999999999877763 378999999975433 3333 3444444333221124466788888887653
No 130
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.27 E-value=1.5e+02 Score=25.30 Aligned_cols=34 Identities=21% Similarity=0.182 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
..++.++++.|-.+|..-+. .+|+.+|+..|+-.
T Consensus 365 ~rdl~~lv~~A~~ia~~~~~-~~I~ae~Ve~a~~~ 398 (647)
T COG1067 365 LRDLGNLVREAGDIAVSEGR-KLITAEDVEEALQK 398 (647)
T ss_pred HHHHHHHHHHhhHHHhcCCc-ccCcHHHHHHHHHh
Confidence 46788899999999998888 99999999999865
No 131
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=22.20 E-value=1.7e+02 Score=19.03 Aligned_cols=16 Identities=31% Similarity=0.476 Sum_probs=10.9
Q ss_pred HHHHHHHHcCCCHHHH
Q 032554 108 PGHKILAALGFSDEKA 123 (138)
Q Consensus 108 ~~~~~l~~~gi~~~~l 123 (138)
.+.++|+..|++++.+
T Consensus 81 ~~k~~L~~~Gi~~eRv 96 (124)
T PF02662_consen 81 RLKKLLEELGIEPERV 96 (124)
T ss_pred HHHHHHHHcCCChhHe
Confidence 3456788888887654
No 132
>TIGR02074 PBP_1a_fam penicillin-binding protein, 1A family. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (TIGR02071). This family also includes related proteins, often designated PBP 1A, from other bacterial lineages.
Probab=21.99 E-value=1.2e+02 Score=24.92 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=29.7
Q ss_pred HHHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 16 TEAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 16 ~eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
|+|+..|++.-+| .+++..-|+|+..+..++...+..
T Consensus 11 p~~~~~a~ia~ED---~~F~~h~Gvd~~~~~ra~~~~~~~ 47 (530)
T TIGR02074 11 PENLINAFLAIED---RRFYDHFGIDLKGIGRAAVNNITS 47 (530)
T ss_pred CHHHHhhHHhhhc---cccccCCCcCHHHHHHHHHHHhhc
Confidence 6788889998887 677889999999988877665543
No 133
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=21.98 E-value=1.8e+02 Score=20.44 Aligned_cols=37 Identities=14% Similarity=0.136 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhc
Q 032554 95 SDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSS 131 (138)
Q Consensus 95 ~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r 131 (138)
..+|..+...+......+-+.+|++...+.+.+..+.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566677665555567888899999999999988863
No 134
>PF04693 DDE_Tnp_2: Archaeal putative transposase ISC1217; InterPro: IPR006783 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the putative transposase ISC1217 from archaebacteria. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.93 E-value=2.2e+02 Score=22.03 Aligned_cols=58 Identities=14% Similarity=0.111 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHH--HhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhh
Q 032554 70 EDAQRVIDWAVDHK--LKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLS 130 (138)
Q Consensus 70 ~~l~~~l~~A~~~A--~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~ 130 (138)
++..+++++|.... ...+-+..+...-+|.+++. +.+..+-+.+|+|+..+.+.+.++
T Consensus 8 eey~kAln~~~~~v~~~~~~~~r~~~~~L~L~~lvG---g~at~~a~~~g~dY~~~Lk~Ld~l 67 (327)
T PF04693_consen 8 EEYYKALNEALGVVFARMNGRRRDVALRLVLGGLVG---GRATNAAQTFGMDYENLLKNLDKL 67 (327)
T ss_pred HHHHHHHHHHHHHHHHhhcCchHHHHHHHHhhheec---cchhHHHHHhCccHHHHHHHhhhh
Confidence 45566777776655 33333234556666666664 235688889999999999888775
No 135
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=21.78 E-value=2e+02 Score=21.23 Aligned_cols=38 Identities=29% Similarity=0.309 Sum_probs=32.9
Q ss_pred HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCC
Q 032554 19 ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKG 56 (138)
Q Consensus 19 lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~ 56 (138)
+.++||..+...+.++.+..|+...++.+-+....+++
T Consensus 21 vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG 58 (247)
T COG1378 21 VYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKG 58 (247)
T ss_pred HHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCC
Confidence 56788888888999999999999999999888777664
No 136
>smart00417 H4 Histone H4.
Probab=21.31 E-value=1.2e+02 Score=18.06 Aligned_cols=29 Identities=24% Similarity=0.156 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHH
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLL 99 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLl 99 (138)
.-+.+++.+|..++...+- .-|+.+++..
T Consensus 45 ~~l~~I~rdav~~a~ha~R-KTV~~~DV~~ 73 (74)
T smart00417 45 SFLENVVRDAVTYTEHARR-KTVTAMDVVY 73 (74)
T ss_pred HHHHHHHHHHHHHHHhcCC-CcccHHHhee
Confidence 4456677888888887777 8888887754
No 137
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.26 E-value=2.6e+02 Score=18.53 Aligned_cols=31 Identities=26% Similarity=0.391 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhc
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWS 103 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~ 103 (138)
++.+++.....|++.+. ..|+.-.+.++-+.
T Consensus 7 ~~~i~~~v~~~A~~~g~-~~V~~V~l~IG~ls 37 (135)
T PRK03824 7 AEAIVRTVIDYAQKEGA-SKVKALKVVLGELQ 37 (135)
T ss_pred HHHHHHHHHHHHHHcCC-chhHhHHhhHhhhh
Confidence 45677778888888888 88888888777765
No 138
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=21.25 E-value=1.6e+02 Score=19.92 Aligned_cols=41 Identities=12% Similarity=0.093 Sum_probs=28.8
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHcCCCHHHHHHHHHhhcCCC
Q 032554 94 ASDLLLGIWS-ETDSPGHKILAALGFSDEKAKELESLSSEPG 134 (138)
Q Consensus 94 ~~hlLlall~-~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~ 134 (138)
.+.-++.+|+ +..-....+-+..|++...+.+.+.++.+.+
T Consensus 15 ~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 15 IDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3445555554 4444456788889999999999999886643
No 139
>PF07026 DUF1317: Protein of unknown function (DUF1317); InterPro: IPR009750 This entry is represented by Bacteriophage lambda, Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.08 E-value=32 Score=19.61 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=13.2
Q ss_pred hHHHHHhcCC--CCcCHHHHHH
Q 032554 2 GELEARKLKH--PTTGTEAILM 21 (138)
Q Consensus 2 A~~~A~~~~~--~~i~~eHlLl 21 (138)
|+.+|.+++. ..+..||+|+
T Consensus 38 AqR~AE~~n~~~~~l~~~~~~~ 59 (60)
T PF07026_consen 38 AQRLAEELNSKQVNLCDEHLLL 59 (60)
T ss_pred HHHHHHHHHhhHhhhhhhhccc
Confidence 6777777544 4566788775
No 140
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.98 E-value=2.1e+02 Score=17.33 Aligned_cols=46 Identities=15% Similarity=0.065 Sum_probs=26.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHHHH
Q 032554 30 LAAKFLWANGVTLFKVRDESVKIVGKGDFFFFSPEHPPLTEDAQRVID 77 (138)
Q Consensus 30 ~~~~il~~~g~~~~~l~~~l~~~l~~~~~~~~~~~~~~~S~~l~~~l~ 77 (138)
.+..+|+++|+++......+-..+......+ -....+|+.-...++
T Consensus 15 ~A~~vl~~lGls~S~Ai~~fl~qi~~~~~iP--F~~~~~s~ed~~~l~ 60 (80)
T PRK11235 15 RAYAVLEKLGVTPSEALRLLLQYVAENGRLP--FKTVLLSDEDAALLE 60 (80)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC--CCCCCCCHHHHHHHH
Confidence 4788999999999876665544443322221 122345665444443
No 141
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.88 E-value=1.4e+02 Score=15.38 Aligned_cols=37 Identities=16% Similarity=0.018 Sum_probs=27.5
Q ss_pred HHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcCCC
Q 032554 19 ILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGKGD 57 (138)
Q Consensus 19 lLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~~~ 57 (138)
++..+++ +. ....+.+.+|++...+...+..+-..++
T Consensus 5 iv~~~~~-g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYLE-GE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHc-CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 3344444 33 5788999999999999999988876543
No 142
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.83 E-value=1.9e+02 Score=16.94 Aligned_cols=22 Identities=9% Similarity=-0.106 Sum_probs=11.5
Q ss_pred cHHHHHHHHCCCCHHHHHHHHH
Q 032554 29 SLAAKFLWANGVTLFKVRDESV 50 (138)
Q Consensus 29 ~~~~~il~~~g~~~~~l~~~l~ 50 (138)
+...+.-+.+|++...++..+.
T Consensus 51 gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 51 GNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 3345555555665555555443
No 143
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.81 E-value=59 Score=20.98 Aligned_cols=49 Identities=16% Similarity=0.112 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHcCCCHHHHHHHHHhhcCCC
Q 032554 72 AQRVIDWAVDHKLKSGNSGEVTASDLLLGIWSETDSPGHKILAALGFSDEKAKELESLSSEPG 134 (138)
Q Consensus 72 l~~~l~~A~~~A~~~~~~~~I~~~hlLlall~~~~~~~~~~l~~~gi~~~~l~~~i~~~r~~~ 134 (138)
++.+++.+...|++.+- ..|+.-+|-++-+. |++++.|+..+..++.+.
T Consensus 7 a~~iv~~v~~~a~~~~~-~~V~~V~l~iG~ls-------------~V~p~~L~faf~~~~~~t 55 (115)
T TIGR00100 7 AEAMLEIVEEQAEKHQA-KKVTRVTLEIGELS-------------CVNPSQLQFAFEVVREGT 55 (115)
T ss_pred HHHHHHHHHHHHHHhCC-CeEEEEEEEEcccc-------------ccCHHHHHHHHHHHhCCC
Confidence 35566777777777777 77777666666553 566777777766665544
No 144
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=20.62 E-value=1.9e+02 Score=16.65 Aligned_cols=37 Identities=8% Similarity=-0.125 Sum_probs=22.2
Q ss_pred HHHHHHHhhcC---CcHHHHHHHHCCCCHHHHHHHHHHHH
Q 032554 17 EAILMGILVEG---TSLAAKFLWANGVTLFKVRDESVKIV 53 (138)
Q Consensus 17 eHlLlall~~~---~~~~~~il~~~g~~~~~l~~~l~~~l 53 (138)
.|.|+--+.-+ -.+..-||+..|.|+++..+.|++..
T Consensus 10 cqkLlEkf~YpWEmmpLmyVILK~A~~D~eeA~rrI~E~~ 49 (62)
T PF08828_consen 10 CQKLLEKFRYPWEMMPLMYVILKYADADVEEASRRIDEAK 49 (62)
T ss_dssp HHHHHHHTT--GGGHHHHHHHHHHTTT-HHHHHHHHHH--
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 34444444332 13567899999999999888876543
No 145
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=20.57 E-value=2.1e+02 Score=17.23 Aligned_cols=23 Identities=22% Similarity=0.166 Sum_probs=19.1
Q ss_pred HHHHHHcCCCHHHHHHHHHhhcC
Q 032554 110 HKILAALGFSDEKAKELESLSSE 132 (138)
Q Consensus 110 ~~~l~~~gi~~~~l~~~i~~~r~ 132 (138)
..+=..+|+++.++-+.|+.+|.
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLRE 45 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHH
Confidence 45667889999999999999876
No 146
>TIGR03362 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=20.55 E-value=3.5e+02 Score=20.69 Aligned_cols=50 Identities=20% Similarity=0.203 Sum_probs=36.2
Q ss_pred HHHHHHHHCCCCH--HHHHHHHHHHHcCCCCCC---CCCCCCCCCHHHHHHHHHH
Q 032554 30 LAAKFLWANGVTL--FKVRDESVKIVGKGDFFF---FSPEHPPLTEDAQRVIDWA 79 (138)
Q Consensus 30 ~~~~il~~~g~~~--~~l~~~l~~~l~~~~~~~---~~~~~~~~S~~l~~~l~~A 79 (138)
++.+++.++|-+. +.|+.++..++.+.|... ..++.|..++.+...|...
T Consensus 138 ~~~qal~~lG~~~~a~aI~~el~~fL~RlP~L~~L~F~DGtPFad~~T~~WL~~~ 192 (301)
T TIGR03362 138 LSAQALERLGYAAVAQAIRDELAAFLERLPGLLELKFSDGTPFADDETRAWLAQH 192 (301)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhCcChhhcccCCCCCCCCHHHHHHHHhc
Confidence 4577788888522 457777888888888742 2456788899999999764
No 147
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=20.49 E-value=1.9e+02 Score=23.81 Aligned_cols=31 Identities=13% Similarity=0.123 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 032554 70 EDAQRVIDWAVDHKLKSGNSGEVTASDLLLGI 101 (138)
Q Consensus 70 ~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlal 101 (138)
....+++.-|+.+|--.+. +.|+.+|+.-|+
T Consensus 466 R~~~rilrvArTiAdL~g~-~~i~~~hv~eA~ 496 (499)
T TIGR00368 466 RATHRILKVARTIADLKEE-KNISREHLAEAI 496 (499)
T ss_pred hHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHH
Confidence 3456677788888887788 899999998886
No 148
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.34 E-value=1.5e+02 Score=15.34 Aligned_cols=36 Identities=14% Similarity=-0.058 Sum_probs=20.6
Q ss_pred HHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHcC
Q 032554 18 AILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVGK 55 (138)
Q Consensus 18 HlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~~ 55 (138)
+++..+.+ + -...++-+.+|++...+...++.+-..
T Consensus 9 ~ii~l~~~-G-~s~~~ia~~lgvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 9 QIIRLLRE-G-WSIREIAKRLGVSRSTVYRWIKRYREE 44 (50)
T ss_dssp -HHHHHHH-T---HHHHHHHHTS-HHHHHHHHT-----
T ss_pred HHHHHHHC-C-CCHHHHHHHHCcCHHHHHHHHHHcccc
Confidence 34444444 3 357889999999999999988776543
No 149
>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=20.34 E-value=2.1e+02 Score=22.15 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=29.5
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHh
Q 032554 69 TEDAQRVIDWAVDHKLKSGNSGEVTASDLLLGIW 102 (138)
Q Consensus 69 S~~l~~~l~~A~~~A~~~~~~~~I~~~hlLlall 102 (138)
...+.++++.|...++..+. ..++++|+-.|+-
T Consensus 30 e~~~~~i~~~A~k~~~hskR-~~l~~~Di~~Al~ 62 (343)
T cd08050 30 EYRLREIIQEAAKFMRHSKR-RKLTTSDVNHALR 62 (343)
T ss_pred HHHHHHHHHHHHHHHHHhCC-CcCCHHHHHHHHH
Confidence 46788999999999999999 9999999999974
No 150
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=20.14 E-value=1.8e+02 Score=16.34 Aligned_cols=38 Identities=13% Similarity=0.174 Sum_probs=26.4
Q ss_pred HHHHHHHhhcCCcHHHHHHHHCCCCHHHHHHHHHHHHc
Q 032554 17 EAILMGILVEGTSLAAKFLWANGVTLFKVRDESVKIVG 54 (138)
Q Consensus 17 eHlLlall~~~~~~~~~il~~~g~~~~~l~~~l~~~l~ 54 (138)
+-+.-.|++.+.....++.+..+++++.++..+--.+.
T Consensus 16 ~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ 53 (62)
T PF08221_consen 16 AKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQ 53 (62)
T ss_dssp HHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34555677777767899999999999999988766554
No 151
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=20.05 E-value=2.4e+02 Score=18.38 Aligned_cols=56 Identities=9% Similarity=-0.002 Sum_probs=38.1
Q ss_pred ChHHHHHhcCCCCcCHHHHHHHHhhcCCcHH---HHHHHHCCC-CHHHHHHHHHHHHcCC
Q 032554 1 MGELEARKLKHPTTGTEAILMGILVEGTSLA---AKFLWANGV-TLFKVRDESVKIVGKG 56 (138)
Q Consensus 1 ~A~~~A~~~~~~~i~~eHlLlall~~~~~~~---~~il~~~g~-~~~~l~~~l~~~l~~~ 56 (138)
+|..+|.+++-.+|++..+|-.-+..+.... ...+.+-+. +.+-+.+-+...+.+.
T Consensus 12 ~~~~la~~~~~~~is~~~llr~~~~~~s~~g~~i~~~l~~g~~vp~~~v~~ll~~~l~~~ 71 (151)
T PF00406_consen 12 QAKRLAKRYGLVHISVGDLLREEIKSDSELGKQIQEYLDNGELVPDELVIELLKERLEQP 71 (151)
T ss_dssp HHHHHHHHHTSEEEEHHHHHHHHHHTTSHHHHHHHHHHHTTSS--HHHHHHHHHHHHHSG
T ss_pred HHHHHHHhcCcceechHHHHHHHHhhhhHHHHHHHHHHHhhccchHHHHHHHHHHHHhhh
Confidence 3678899999999999999999998765333 333443333 4455555666666654
No 152
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=20.03 E-value=1.5e+02 Score=18.31 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=20.1
Q ss_pred hcCCcHHHHHHHHCCCCHHHHHHHH
Q 032554 25 VEGTSLAAKFLWANGVTLFKVRDES 49 (138)
Q Consensus 25 ~~~~~~~~~il~~~g~~~~~l~~~l 49 (138)
-.++....++|...|++++.||..+
T Consensus 18 a~d~e~l~rFLa~TG~~p~~LR~~a 42 (88)
T PF12096_consen 18 AGDPERLPRFLALTGLSPDDLRAAA 42 (88)
T ss_pred hCCHHHHHHHHHHhCCCHHHHHHHc
Confidence 3344588999999999999998865
No 153
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=20.02 E-value=1.8e+02 Score=16.28 Aligned_cols=34 Identities=9% Similarity=0.135 Sum_probs=25.4
Q ss_pred HHHHHHhhc----CCcHHHHHHHHCCCCHHHHHHHHHH
Q 032554 18 AILMGILVE----GTSLAAKFLWANGVTLFKVRDESVK 51 (138)
Q Consensus 18 HlLlall~~----~~~~~~~il~~~g~~~~~l~~~l~~ 51 (138)
.+|+++++. .-+....++..++++.+.|.+.+..
T Consensus 6 ~mLlS~VN~kLRD~~~sLd~Lc~~~~id~~~l~~kL~~ 43 (55)
T PF14056_consen 6 NMLLSIVNMKLRDEYSSLDELCYDYDIDKEELEEKLAS 43 (55)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 467777653 3445789999999999998887753
Done!