Query 026896
Match_columns 231
No_of_seqs 180 out of 1633
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 14:14:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00095 clpC Clp protease ATP 99.8 4.1E-19 9E-24 178.0 18.4 141 81-224 1-141 (821)
2 TIGR03346 chaperone_ClpB ATP-d 99.8 2.3E-18 5E-23 173.2 18.3 138 85-224 1-138 (852)
3 TIGR02639 ClpA ATP-dependent C 99.8 6.6E-18 1.4E-22 167.5 17.7 135 85-222 1-137 (731)
4 PRK10865 protein disaggregatio 99.7 5.2E-17 1.1E-21 163.4 18.3 144 80-225 1-144 (857)
5 TIGR03345 VI_ClpV1 type VI sec 99.7 1.7E-16 3.8E-21 159.5 17.9 137 85-224 1-141 (852)
6 COG0542 clpA ATP-binding subun 99.7 2E-16 4.4E-21 155.7 17.2 137 84-226 1-137 (786)
7 PRK11034 clpA ATP-dependent Cl 99.6 1.3E-14 2.8E-19 144.2 17.4 135 85-222 2-139 (758)
8 KOG1051 Chaperone HSP104 and r 99.4 1.8E-12 3.8E-17 129.6 13.9 149 82-231 9-159 (898)
9 PF02861 Clp_N: Clp amino term 99.2 3.2E-11 6.9E-16 80.4 5.9 53 96-148 1-53 (53)
10 PF02861 Clp_N: Clp amino term 99.0 9.4E-10 2E-14 73.2 5.5 53 173-226 1-53 (53)
11 TIGR03346 chaperone_ClpB ATP-d 98.1 1.1E-05 2.4E-10 82.0 8.6 62 162-224 1-62 (852)
12 CHL00095 clpC Clp protease ATP 98.0 1.4E-05 3E-10 81.0 8.4 63 161-224 4-66 (821)
13 TIGR03345 VI_ClpV1 type VI sec 98.0 1.9E-05 4.1E-10 80.3 8.5 61 162-223 1-61 (852)
14 TIGR02639 ClpA ATP-dependent C 97.8 5.2E-05 1.1E-09 75.9 8.2 60 162-224 1-60 (731)
15 PRK10865 protein disaggregatio 97.8 8.6E-05 1.9E-09 75.6 8.4 63 161-224 5-67 (857)
16 PRK11034 clpA ATP-dependent Cl 97.4 0.00039 8.5E-09 69.9 8.0 59 162-223 2-60 (758)
17 COG0542 clpA ATP-binding subun 97.3 0.0008 1.7E-08 67.5 8.2 61 162-225 2-62 (786)
18 KOG1051 Chaperone HSP104 and r 96.4 0.01 2.2E-07 60.6 7.9 59 160-219 10-69 (898)
19 PLN00154 histone H2A; Provisio 80.5 2.4 5.3E-05 34.0 3.8 40 89-130 74-113 (136)
20 cd00074 H2A Histone 2A; H2A is 79.4 3.6 7.7E-05 32.1 4.3 40 89-130 55-94 (115)
21 PTZ00017 histone H2A; Provisio 78.8 3.4 7.3E-05 33.1 4.1 40 89-130 62-101 (134)
22 KOG1756 Histone 2A [Chromatin 77.9 4.1 9E-05 32.3 4.3 41 89-131 62-102 (131)
23 PLN00157 histone H2A; Provisio 76.4 3.7 8E-05 32.8 3.7 40 89-130 61-100 (132)
24 PLN00153 histone H2A; Provisio 75.3 4.6 9.9E-05 32.2 3.9 40 89-130 59-98 (129)
25 PLN00156 histone H2AX; Provisi 74.1 5.1 0.00011 32.3 4.0 40 89-130 64-103 (139)
26 smart00414 H2A Histone 2A. 73.7 5.4 0.00012 30.6 3.9 39 90-130 45-83 (106)
27 PF13551 HTH_29: Winged helix- 72.2 35 0.00077 24.9 9.4 82 115-197 5-92 (112)
28 cd00074 H2A Histone 2A; H2A is 70.0 5.9 0.00013 30.9 3.4 40 166-208 55-94 (115)
29 PLN00154 histone H2A; Provisio 69.7 4.6 0.0001 32.4 2.8 34 166-200 74-107 (136)
30 PTZ00017 histone H2A; Provisio 69.0 5.2 0.00011 32.1 2.9 34 166-200 62-95 (134)
31 PF12802 MarR_2: MarR family; 68.6 11 0.00023 24.9 4.1 41 189-229 8-50 (62)
32 PTZ00252 histone H2A; Provisio 66.3 8.9 0.00019 30.7 3.8 40 89-130 60-101 (134)
33 PF13412 HTH_24: Winged helix- 66.1 15 0.00032 23.2 4.2 40 190-229 7-46 (48)
34 PLN00157 histone H2A; Provisio 65.3 6.3 0.00014 31.5 2.8 40 166-208 61-100 (132)
35 smart00550 Zalpha Z-DNA-bindin 64.8 19 0.0004 25.0 4.8 41 190-230 10-52 (68)
36 smart00414 H2A Histone 2A. 63.7 7.9 0.00017 29.7 3.0 40 166-208 44-83 (106)
37 PLN00153 histone H2A; Provisio 62.7 8.6 0.00019 30.6 3.1 40 166-208 59-98 (129)
38 PLN00156 histone H2AX; Provisi 62.2 9.1 0.0002 30.8 3.2 40 166-208 64-103 (139)
39 KOG1756 Histone 2A [Chromatin 61.5 10 0.00022 30.1 3.2 40 166-208 62-101 (131)
40 PF01978 TrmB: Sugar-specific 57.6 13 0.00028 25.3 3.0 41 189-229 11-51 (68)
41 PF08369 PCP_red: Proto-chloro 54.8 20 0.00044 23.0 3.3 27 90-116 18-44 (45)
42 PF00125 Histone: Core histone 51.6 21 0.00047 24.7 3.4 30 165-195 43-72 (75)
43 PF00125 Histone: Core histone 51.3 22 0.00047 24.7 3.3 30 88-117 43-72 (75)
44 smart00418 HTH_ARSR helix_turn 49.8 40 0.00086 21.4 4.3 32 198-229 8-39 (66)
45 PTZ00252 histone H2A; Provisio 49.1 20 0.00043 28.7 3.1 40 166-208 60-101 (134)
46 PF13335 Mg_chelatase_2: Magne 48.9 1.1E+02 0.0024 22.7 10.1 90 86-196 5-94 (96)
47 PF01022 HTH_5: Bacterial regu 48.2 36 0.00077 21.5 3.7 38 191-229 7-44 (47)
48 PF01047 MarR: MarR family; I 48.0 31 0.00068 22.4 3.6 41 189-229 6-46 (59)
49 smart00344 HTH_ASNC helix_turn 44.6 44 0.00095 24.6 4.3 39 191-229 8-46 (108)
50 TIGR00122 birA_repr_reg BirA b 44.2 52 0.0011 22.4 4.3 38 192-229 5-42 (69)
51 PF02082 Rrf2: Transcriptional 44.1 46 0.00099 23.7 4.2 40 190-229 12-54 (83)
52 COG1654 BirA Biotin operon rep 44.1 47 0.001 24.1 4.2 28 203-230 22-49 (79)
53 PRK11512 DNA-binding transcrip 44.0 1.2E+02 0.0026 23.7 6.9 44 186-229 38-83 (144)
54 PF13463 HTH_27: Winged helix 43.7 58 0.0013 21.6 4.5 40 190-229 7-47 (68)
55 TIGR02337 HpaR homoprotocatech 43.6 1.2E+02 0.0027 22.6 6.8 41 189-229 31-71 (118)
56 PF00808 CBFD_NFYB_HMF: Histon 43.1 43 0.00094 22.6 3.8 28 167-195 38-65 (65)
57 smart00420 HTH_DEOR helix_turn 43.1 75 0.0016 19.5 4.7 39 191-229 5-43 (53)
58 COG2317 Zn-dependent carboxype 42.6 2.2E+02 0.0049 27.6 9.5 95 81-179 124-221 (497)
59 PRK10265 chaperone-modulator p 41.3 1.1E+02 0.0023 22.9 6.0 68 125-196 10-77 (101)
60 smart00803 TAF TATA box bindin 40.9 56 0.0012 22.6 4.0 32 163-195 33-64 (65)
61 PF13601 HTH_34: Winged helix 40.1 49 0.0011 23.7 3.8 39 191-229 5-43 (80)
62 PRK13777 transcriptional regul 40.1 1.1E+02 0.0025 25.5 6.5 64 164-229 24-88 (185)
63 PF00808 CBFD_NFYB_HMF: Histon 38.7 55 0.0012 22.1 3.7 26 92-117 40-65 (65)
64 smart00347 HTH_MARR helix_turn 37.6 69 0.0015 22.5 4.4 41 189-229 13-53 (101)
65 smart00803 TAF TATA box bindin 37.5 68 0.0015 22.2 4.0 33 85-117 32-64 (65)
66 smart00576 BTP Bromodomain tra 36.3 1.5E+02 0.0033 20.8 7.0 66 113-197 3-70 (77)
67 cd07979 TAF9 TATA Binding Prot 36.2 69 0.0015 24.8 4.3 60 124-199 6-67 (117)
68 COG5262 HTA1 Histone H2A [Chro 35.9 58 0.0013 25.6 3.7 40 89-130 61-100 (132)
69 PF01978 TrmB: Sugar-specific 34.0 50 0.0011 22.3 2.9 39 112-150 12-50 (68)
70 cd00090 HTH_ARSR Arsenical Res 32.0 1.1E+02 0.0023 19.8 4.4 39 190-229 11-49 (78)
71 PF09339 HTH_IclR: IclR helix- 31.7 77 0.0017 20.3 3.4 39 191-229 8-47 (52)
72 COG5247 BUR6 Class 2 transcrip 30.6 64 0.0014 24.7 3.1 34 166-200 58-91 (113)
73 TIGR01610 phage_O_Nterm phage 30.3 2.2E+02 0.0047 20.8 6.6 45 185-229 24-76 (95)
74 cd07981 TAF12 TATA Binding Pro 30.0 1.2E+02 0.0025 21.2 4.3 31 166-197 36-66 (72)
75 PLN00035 histone H4; Provision 29.1 1.1E+02 0.0023 23.5 4.2 33 164-197 61-93 (103)
76 COG1378 Predicted transcriptio 28.6 87 0.0019 27.5 4.2 43 187-229 17-59 (247)
77 PF13335 Mg_chelatase_2: Magne 28.3 1.3E+02 0.0029 22.2 4.6 31 87-117 63-93 (96)
78 COG1846 MarR Transcriptional r 27.7 1.1E+02 0.0023 22.2 4.1 43 186-229 22-65 (126)
79 PF13591 MerR_2: MerR HTH fami 27.4 2.4E+02 0.0051 20.2 5.9 55 125-182 3-57 (84)
80 COG5262 HTA1 Histone H2A [Chro 27.4 60 0.0013 25.5 2.6 34 166-200 61-94 (132)
81 cd07981 TAF12 TATA Binding Pro 27.3 1.4E+02 0.0031 20.8 4.3 33 86-118 33-65 (72)
82 PRK00411 cdc6 cell division co 27.1 4.7E+02 0.01 23.6 10.2 92 89-191 251-342 (394)
83 KOG1659 Class 2 transcription 27.1 1.1E+02 0.0024 26.5 4.3 40 160-200 38-81 (224)
84 PRK09416 lstR lineage-specific 27.0 3E+02 0.0065 22.1 6.6 67 158-229 18-92 (135)
85 PF09415 CENP-X: CENP-S associ 26.9 94 0.002 22.0 3.4 28 88-115 35-63 (72)
86 COG5247 BUR6 Class 2 transcrip 26.7 96 0.0021 23.8 3.5 34 89-122 58-91 (113)
87 PF04405 ScdA_N: Domain of Unk 26.4 1E+02 0.0023 20.7 3.3 23 123-145 32-54 (56)
88 PF08220 HTH_DeoR: DeoR-like h 26.3 1.8E+02 0.004 19.1 4.6 39 191-229 5-43 (57)
89 COG2036 HHT1 Histones H3 and H 26.1 1.2E+02 0.0027 22.5 4.0 33 164-197 51-83 (91)
90 PF09862 DUF2089: Protein of u 25.9 3.2E+02 0.0069 21.2 7.6 54 117-173 45-98 (113)
91 PF02269 TFIID-18kDa: Transcri 25.8 37 0.0008 25.2 1.1 36 86-121 33-68 (93)
92 PTZ00015 histone H4; Provision 25.0 1.4E+02 0.003 22.8 4.2 33 163-196 61-93 (102)
93 cd07979 TAF9 TATA Binding Prot 25.0 1.6E+02 0.0035 22.7 4.7 35 86-120 32-66 (117)
94 COG5150 Class 2 transcription 25.0 1.6E+02 0.0034 23.5 4.5 35 85-119 31-77 (148)
95 PLN03060 inositol phosphatase- 25.0 3.9E+02 0.0084 23.0 7.3 27 122-148 72-98 (206)
96 cd00076 H4 Histone H4, one of 24.9 1.5E+02 0.0033 21.7 4.2 34 163-197 44-77 (85)
97 KOG1659 Class 2 transcription 24.9 1.6E+02 0.0035 25.5 4.9 34 89-122 48-81 (224)
98 PF09012 FeoC: FeoC like trans 24.7 2E+02 0.0042 19.6 4.7 29 201-229 15-43 (69)
99 KOG0871 Class 2 transcription 24.3 86 0.0019 25.6 3.0 27 94-120 53-79 (156)
100 PF02662 FlpD: Methyl-viologen 23.7 90 0.002 24.3 3.0 17 107-123 39-55 (124)
101 TIGR02928 orc1/cdc6 family rep 23.7 2.5E+02 0.0054 25.1 6.4 58 164-222 241-298 (365)
102 PRK11179 DNA-binding transcrip 23.6 1.5E+02 0.0033 23.5 4.5 42 188-229 10-52 (153)
103 TIGR02928 orc1/cdc6 family rep 23.4 5.3E+02 0.012 22.9 10.6 61 87-147 241-301 (365)
104 PF12840 HTH_20: Helix-turn-he 23.2 1.8E+02 0.0039 19.2 4.1 39 191-229 15-53 (61)
105 smart00265 BH4 BH4 Bcl-2 homol 23.2 41 0.00088 19.5 0.7 11 221-231 14-24 (27)
106 PF13518 HTH_28: Helix-turn-he 23.1 1.6E+02 0.0034 18.2 3.7 37 191-229 5-41 (52)
107 PF13384 HTH_23: Homeodomain-l 23.0 1.2E+02 0.0025 18.9 3.0 30 201-230 18-47 (50)
108 PRK03573 transcriptional regul 22.9 3.6E+02 0.0077 20.8 6.9 45 185-229 28-75 (144)
109 TIGR02337 HpaR homoprotocatech 22.0 3.4E+02 0.0073 20.2 9.5 69 112-180 32-106 (118)
110 PF02269 TFIID-18kDa: Transcri 21.9 52 0.0011 24.4 1.3 37 163-200 33-69 (93)
111 PF08784 RPA_C: Replication pr 21.8 1.3E+02 0.0029 22.0 3.6 29 201-229 66-94 (102)
112 PF02969 TAF: TATA box binding 21.7 2.3E+02 0.0049 19.8 4.4 33 85-117 33-65 (66)
113 TIGR03433 padR_acidobact trans 21.6 1.2E+02 0.0026 22.4 3.2 42 188-229 5-54 (100)
114 KOG0869 CCAAT-binding factor, 21.6 3.3E+02 0.0072 22.5 5.9 75 39-130 23-109 (168)
115 PF04693 DDE_Tnp_2: Archaeal p 21.5 1.9E+02 0.0041 26.6 4.9 63 164-229 8-72 (327)
116 PF12983 DUF3867: Protein of u 21.3 99 0.0021 26.0 2.9 34 184-225 53-86 (186)
117 PF10845 DUF2576: Protein of u 21.2 97 0.0021 20.2 2.2 18 209-226 8-25 (48)
118 PF08279 HTH_11: HTH domain; 21.1 2.3E+02 0.005 17.9 4.9 39 190-228 4-43 (55)
119 PF02954 HTH_8: Bacterial regu 21.0 1.8E+02 0.0039 17.8 3.5 31 115-145 11-41 (42)
120 PF13730 HTH_36: Helix-turn-he 20.9 1.3E+02 0.0028 19.2 2.9 26 204-229 29-54 (55)
121 PF12244 DUF3606: Protein of u 20.8 1.2E+02 0.0027 20.3 2.8 26 201-226 21-46 (57)
122 PRK00056 mtgA monofunctional b 20.6 93 0.002 27.3 2.8 33 112-147 71-103 (236)
123 smart00346 HTH_ICLR helix_turn 20.5 2.3E+02 0.0051 19.7 4.6 39 191-229 10-49 (91)
124 PF02291 TFIID-31kDa: Transcri 20.4 1.8E+02 0.004 23.0 4.2 33 165-198 45-77 (129)
125 PRK00411 cdc6 cell division co 20.2 3E+02 0.0065 24.9 6.2 56 166-222 251-306 (394)
126 cd00592 HTH_MerR-like Helix-Tu 20.2 3.4E+02 0.0074 19.5 8.1 70 125-199 3-72 (100)
127 PF13551 HTH_29: Winged helix- 20.1 1.6E+02 0.0036 21.2 3.8 29 202-230 14-42 (112)
128 PLN00035 histone H4; Provision 20.0 2.2E+02 0.0048 21.7 4.4 37 85-121 59-95 (103)
No 1
>CHL00095 clpC Clp protease ATP binding subunit
Probab=99.82 E-value=4.1e-19 Score=178.00 Aligned_cols=141 Identities=30% Similarity=0.493 Sum_probs=129.1
Q ss_pred CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCC
Q 026896 81 KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERP 160 (231)
Q Consensus 81 ~~~kfT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~ 160 (231)
++++||++++++|..|+++|++++|.+|++||||+|||.++++.+.++|+++|+|.+.++.+++..+++.+.. .+..+
T Consensus 1 m~~rfT~~a~~vL~~A~~~A~~~~h~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~l~~~~~~--~~~~~ 78 (821)
T CHL00095 1 MFERFTEKAIKVIMLSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKIIGRGTGF--VAVEI 78 (821)
T ss_pred ChhhHhHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHHhcCCCC--Ccccc
Confidence 4679999999999999999999999999999999999999999999999999999999999999998764432 23468
Q ss_pred ccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 161 ~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
++|+.++++|+.|+.+|..+++ ++|+++|||+||+.++++.+..+|..+|++.+.+++.+...
T Consensus 79 ~~S~~~~~vL~~A~~~A~~~~~-~~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~~ 141 (821)
T CHL00095 79 PFTPRAKRVLEMSLEEARDLGH-NYIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILNL 141 (821)
T ss_pred ccCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHH
Confidence 8999999999999999999999 99999999999999988888899999999999998877653
No 2
>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=99.79 E-value=2.3e-18 Score=173.23 Aligned_cols=138 Identities=19% Similarity=0.201 Sum_probs=124.7
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCH
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~ 164 (231)
||++++++|..|+.+|++++|.+|++||||+||+.++++.+.++|+++|+|++.++++++..++..+...+.+..+++|+
T Consensus 1 fT~~a~~vL~~A~~~A~~~~h~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~l~~~~~~~~~~~~~~~S~ 80 (852)
T TIGR03346 1 FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPKVSGPGGQVYLSP 80 (852)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHhcccccCCCCCCCCCcCH
Confidence 79999999999999999999999999999999999998999999999999999999999999987654322224678999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 165 QAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 165 ~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
.++++|+.|+.+|..+|+ ++|+++|||+||+.++++ +.++|..+|++.+.+.+.+..+
T Consensus 81 ~~~~vLe~A~~~A~~~g~-~~I~teHLLlALl~e~~~-a~~iL~~~gi~~~~l~~~l~~~ 138 (852)
T TIGR03346 81 ELNRLLNLAEKLAQKRGD-EFISSEHLLLALLDDKGT-LGKLLKEAGATADALEAAINAV 138 (852)
T ss_pred HHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHcCCcc-HHHHHHHcCCCHHHHHHHHHhh
Confidence 999999999999999999 999999999999999776 5689999999999998887654
No 3
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=99.78 E-value=6.6e-18 Score=167.51 Aligned_cols=135 Identities=21% Similarity=0.226 Sum_probs=120.6
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhc-CCCCcCC-CCCCCcc
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG-KSDLFFF-SPERPPL 162 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~-~~~~~~~-~~~~~~~ 162 (231)
+|++++++|..|+++|++++|.+|++||||+|||.+++ +.++|+++|+|.+.++++++..++ ..+...+ .+..+++
T Consensus 1 ~~~~a~~~L~~A~~~A~~~~h~~V~~EHLLlaLL~~~~--~~~iL~~~gid~~~l~~~l~~~l~~~~p~~~~~~~~~~~~ 78 (731)
T TIGR02639 1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSD--AIEILEECGGDVEALRKDLEDYLENNLPSITEENEADPEQ 78 (731)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCCCCCCCCc
Confidence 58899999999999999999999999999999999865 679999999999999999999886 3343211 1245789
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026896 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (231)
Q Consensus 163 S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~ 222 (231)
|+.++++|+.|+.+|..+|+ ++|+++|||+||+.++++.+..+|..+|++.+.+.+.+.
T Consensus 79 S~~lk~vL~~A~~~A~~~g~-~~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~ 137 (731)
T TIGR02639 79 TVGVQRVLQRALLHVKSAGK-KEIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYIS 137 (731)
T ss_pred CHHHHHHHHHHHHHHHHcCC-CccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHH
Confidence 99999999999999999999 999999999999999888888899999999999988775
No 4
>PRK10865 protein disaggregation chaperone; Provisional
Probab=99.75 E-value=5.2e-17 Score=163.42 Aligned_cols=144 Identities=13% Similarity=0.114 Sum_probs=127.3
Q ss_pred CCchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCC
Q 026896 80 DKIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPER 159 (231)
Q Consensus 80 ~~~~kfT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~ 159 (231)
|++++||+.++++|..|+.+|+.++|.+|++||||++|+.++++.+.++|+++|+|.+.++++++..+...+...+.+..
T Consensus 1 ~~~~~~~~~~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 80 (857)
T PRK10865 1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQVEGTGGD 80 (857)
T ss_pred CChHHhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHHhhCCCCCCCCCC
Confidence 35789999999999999999999999999999999999999888999999999999999999999998876643222245
Q ss_pred CccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhh
Q 026896 160 PPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVS 225 (231)
Q Consensus 160 ~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~ 225 (231)
+++|+.++++|+.|+.+|..+|+ .+|+++|||+||+.++++. ..+|..+|++.+.+.+.+..+.
T Consensus 81 ~~~~~~~~~~l~~a~~~~~~~~~-~~i~~~~ll~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~ 144 (857)
T PRK10865 81 VQPSQDLVRVLNLCDKLAQKRGD-NFISSELFVLAALESRGTL-ADILKAAGATTANITQAIEQMR 144 (857)
T ss_pred CCcCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHcCcchH-HHHHHHcCCCHHHHHHHHHHhh
Confidence 78999999999999999999999 9999999999999986544 4589999999999988776543
No 5
>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=99.72 E-value=1.7e-16 Score=159.48 Aligned_cols=137 Identities=22% Similarity=0.271 Sum_probs=120.3
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCH
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTE 164 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~ 164 (231)
+|++++++|..|+.+|++++|.+|++||||+|||.++++.+.++|+.+|+|.+.++.+++..+...+.. .+..+++|+
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~l~~~p~~--~~~~~~~S~ 78 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDKLPRG--NTRTPVFSP 78 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCC--CCCCCCcCH
Confidence 588999999999999999999999999999999999888999999999999999999999999876643 223578999
Q ss_pred HHHHHHHHHHHH-HHHcCCCCCCCHHHHHHHHhhCCCc--hHHHHHHhC-CCCHHHHHHHHHHh
Q 026896 165 QAQRALDWAFNE-KLKSGESGEITTNHLLLGIWSEKES--AGHKILATL-GFNDEKAKEIAKSV 224 (231)
Q Consensus 165 ~l~~vLe~A~~~-A~~~g~~~~I~teHLLLALl~d~~~--~~~~iL~~l-Gvd~~~l~e~l~~i 224 (231)
.++++|+.|+.+ +..+|+ .+|+++|||+||+.++++ .+..++..+ |++.+.+.+.+..+
T Consensus 79 ~l~~vL~~A~~~~a~~~g~-~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (852)
T TIGR03345 79 HLVELLQEAWLLASLELGD-GRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPAL 141 (852)
T ss_pred HHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 999999999974 566999 999999999999998765 555677777 99999998877654
No 6
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=2e-16 Score=155.65 Aligned_cols=137 Identities=26% Similarity=0.367 Sum_probs=128.4
Q ss_pred hhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccC
Q 026896 84 KWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLT 163 (231)
Q Consensus 84 kfT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S 163 (231)
+||++++++|..|+++|..++|+++++||||++|+.++++. .+++.+|++++.++.+++..+.+.+...+ . +.+|
T Consensus 1 ~~~~~~~~~l~~a~~~a~~~~h~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~~~~~~~~~~~--~-~~~s 75 (786)
T COG0542 1 KLTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEEFIDKLPKVLG--S-PYLS 75 (786)
T ss_pred CcCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHHHHhccCCCCC--C-CCCC
Confidence 58999999999999999999999999999999999998876 99999999999999999999999887643 2 7889
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhc
Q 026896 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSS 226 (231)
Q Consensus 164 ~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~ 226 (231)
+.+.++++.|+.+|+..++ +||+++|||+|++.++++.+.++|...|++...+++.+..+++
T Consensus 76 ~~~~~~~~~a~~~a~~~~~-~~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 137 (786)
T COG0542 76 PRLKRVLERAWLLAQSLGD-EYVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEELIEELRG 137 (786)
T ss_pred HHHHHHHHHHHHHHHhccC-ccccHHHHHHHHhcccchHHHHHHHhccCCHHHHHHHHHHHhc
Confidence 9999999999999999999 9999999999999999999999999999999999888888775
No 7
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=99.62 E-value=1.3e-14 Score=144.21 Aligned_cols=135 Identities=21% Similarity=0.228 Sum_probs=117.4
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcC-CCCcCC--CCCCCc
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGK-SDLFFF--SPERPP 161 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~-~~~~~~--~~~~~~ 161 (231)
+|+.++++|..|.++|++++|.+|++||||++||.+++ +..+|+++|+|.+.++++++..+.. .+...+ .+..++
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQ 79 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHHHHhhcCCcCCCCCCcCCcC
Confidence 78999999999999999999999999999999998754 8999999999999999999998863 221111 112467
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~ 222 (231)
++..++++|+.|+.+|..+++ ++|+++|||+||++++++.+..+|..+|++...+.+.+.
T Consensus 80 ~~~~~~~~l~~a~~~~~~~~~-~~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 139 (758)
T PRK11034 80 PTLSFQRVLQRAVFHVQSSGR-SEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS 139 (758)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHH
Confidence 899999999999999999999 999999999999999888888899999999888766544
No 8
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.43 E-value=1.8e-12 Score=129.57 Aligned_cols=149 Identities=11% Similarity=0.004 Sum_probs=128.1
Q ss_pred chhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcC-CChHHHHHHHHHHhcCCCCcCCCCCCC
Q 026896 82 IPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANG-ITLFKVREETLNLLGKSDLFFFSPERP 160 (231)
Q Consensus 82 ~~kfT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~g-id~~~lr~~l~~~L~~~~~~~~~~~~~ 160 (231)
...||++|.++|..|+.+|+++||.+++|+|++.+||.+++|.+.+++.+.+ ++...++..+...+.+.|...+++...
T Consensus 9 ~q~lT~~Aa~~L~~a~~~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralelc~~v~l~rlpt~~~p~~sn 88 (898)
T KOG1051|consen 9 QQTLTEEAATVLKQAVTEARRRGHAQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALELCFNVSLNRLPTSYGPPVSN 88 (898)
T ss_pred HhhhCHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHHHHHHHHHhccCCCCCccch
Confidence 4569999999999999999999999999999999999999999999999999 999999999999999988875544456
Q ss_pred ccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhh-cCCCCC
Q 026896 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVS-SRSYDC 231 (231)
Q Consensus 161 ~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~-~~~~~~ 231 (231)
.++..+++++..+.+....+++ .+|.+||+.+.+.-.++..+.+++..+|++...++..++..+ ..+++|
T Consensus 89 ~l~aalkr~qa~qrr~~~~~~~-~~vkvE~~~li~silDdp~vsrv~reag~~s~~vK~~ve~~~g~~~~~~ 159 (898)
T KOG1051|consen 89 ALMAALKRAQAHQRRGCEEQQQ-QAVKVELEQLILSILDDPSVSRVMREAGFSSSAVKSAVEQPVGQFRSPS 159 (898)
T ss_pred HhHHHHHHHHHHHHhcchhhcc-chhhHhHHhhheeeecCchHHHHHHHhcCChHHHHHHHHhhccccCCCC
Confidence 6777778888887777777888 999999996666666677889999999999999998776654 345543
No 9
>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=99.21 E-value=3.2e-11 Score=80.45 Aligned_cols=53 Identities=25% Similarity=0.294 Sum_probs=49.7
Q ss_pred HHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhc
Q 026896 96 AELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLG 148 (231)
Q Consensus 96 A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~ 148 (231)
|+++|+.++|++|++||||++|+.++++.+.++|+++|+|++.+++++++.++
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 78999999999999999999999999999999999999999999999998764
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=98.99 E-value=9.4e-10 Score=73.24 Aligned_cols=53 Identities=26% Similarity=0.388 Sum_probs=48.4
Q ss_pred HHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhc
Q 026896 173 AFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSS 226 (231)
Q Consensus 173 A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~ 226 (231)
|..+|.++|+ .+|+++|||+||++++++.+.++|+++|+|++++++.++.+++
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 5678999999 9999999999999999999999999999999999999988753
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=98.08 E-value=1.1e-05 Score=82.02 Aligned_cols=62 Identities=23% Similarity=0.287 Sum_probs=57.9
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
||+.++++|+.|..+|.+++| ++|+++|||+||+.++++.+.++|..+|+|.+.+++.++..
T Consensus 1 fT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~ 62 (852)
T TIGR03346 1 FTEKFQEALQAAQSLALGRDH-QQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKE 62 (852)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHH
Confidence 689999999999999999999 99999999999999988888899999999999998877663
No 12
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.04 E-value=1.4e-05 Score=80.96 Aligned_cols=63 Identities=21% Similarity=0.327 Sum_probs=58.7
Q ss_pred ccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 161 ~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
.||+.++++|..|..+|.+++| ++|+++|||+||+.++++.+.++|..+|+|.+.+.+.++..
T Consensus 4 rfT~~a~~vL~~A~~~A~~~~h-~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~ 66 (821)
T CHL00095 4 RFTEKAIKVIMLSQEEARRLGH-NFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKI 66 (821)
T ss_pred hHhHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHH
Confidence 4799999999999999999999 99999999999999988888999999999999998877664
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=98.00 E-value=1.9e-05 Score=80.30 Aligned_cols=61 Identities=25% Similarity=0.294 Sum_probs=57.0
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~ 223 (231)
+|+.++++|+.|..+|.+++| .+|+++|||+||+.++++.+..+|..+|+|.+.+++.++.
T Consensus 1 Lt~~a~~~L~~A~~~A~~~~h-~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~ 61 (852)
T TIGR03345 1 LNPTSRRALEQAAALCVARGH-PEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLAR 61 (852)
T ss_pred CCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHH
Confidence 578999999999999999999 9999999999999998888889999999999999887775
No 14
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=97.83 E-value=5.2e-05 Score=75.90 Aligned_cols=60 Identities=25% Similarity=0.327 Sum_probs=54.3
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
+|+.++++|+.|..+|.+++| ++|+++|||+||+.+++ +.++|..+|+|.+.+++.++..
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 578999999999999999999 99999999999998865 4589999999999998877663
No 15
>PRK10865 protein disaggregation chaperone; Provisional
Probab=97.75 E-value=8.6e-05 Score=75.61 Aligned_cols=63 Identities=21% Similarity=0.194 Sum_probs=58.5
Q ss_pred ccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHh
Q 026896 161 PLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSV 224 (231)
Q Consensus 161 ~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i 224 (231)
.||+.++++|+.|..+|.+++| .+|+++|||+||+.++++.+..+|..+|+|.+.+++.++..
T Consensus 5 ~~~~~~~~~l~~a~~~a~~~~~-~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~ 67 (857)
T PRK10865 5 RLTNKFQLALADAQSLALGHDN-QFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQA 67 (857)
T ss_pred HhCHHHHHHHHHHHHHHHHcCC-CcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4899999999999999999999 99999999999999988888899999999999998877764
No 16
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=97.44 E-value=0.00039 Score=69.95 Aligned_cols=59 Identities=19% Similarity=0.267 Sum_probs=54.1
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHH
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKS 223 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~ 223 (231)
+++.++++|+.|..+|.+++| .+|+++|||+||+.+++ +..+|..+|++.+.+++.++.
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~~-~~~~~~h~l~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~ 60 (758)
T PRK11034 2 LNQELELSLNMAFARAREHRH-EFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEA 60 (758)
T ss_pred cCHHHHHHHHHHHHHHHHcCC-CcchHHHHHHHHHcChh--HHHHHHHcCCCHHHHHHHHHH
Confidence 689999999999999999999 99999999999998764 778999999999999887776
No 17
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=0.0008 Score=67.53 Aligned_cols=61 Identities=26% Similarity=0.346 Sum_probs=55.7
Q ss_pred cCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhh
Q 026896 162 LTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVS 225 (231)
Q Consensus 162 ~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~ 225 (231)
|++.++++|..|..+|...+| .+|+++|||++|+.++.+. .++..+|++.+.++..+...-
T Consensus 2 ~~~~~~~~l~~a~~~a~~~~h-~~~~~eHll~~ll~~~~~~--~~l~~~~~~~~~l~~~~~~~~ 62 (786)
T COG0542 2 LTERAQKALELAQELARMRRH-EYVTPEHLLLALLDQPKGD--ELLNLCGIDLDKLRQELEEFI 62 (786)
T ss_pred cCHHHHHHHHHHHHHHHHhCC-CcccHHHHHHHHHcCCchH--HHHHHcCCCHHHHHHHHHHHH
Confidence 789999999999999999999 9999999999999988776 799999999999988776643
No 18
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=96.43 E-value=0.01 Score=60.61 Aligned_cols=59 Identities=19% Similarity=0.171 Sum_probs=54.1
Q ss_pred CccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCC-CCHHHHHH
Q 026896 160 PPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLG-FNDEKAKE 219 (231)
Q Consensus 160 ~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lG-vd~~~l~e 219 (231)
-.||+++.++|..|..+|++.|| +.+++.|++.||+.++++...+++.+.+ ++...++.
T Consensus 10 q~lT~~Aa~~L~~a~~~Arrrgh-~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralel 69 (898)
T KOG1051|consen 10 QTLTEEAATVLKQAVTEARRRGH-AQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALEL 69 (898)
T ss_pred hhhCHHHHHHHHHHHHHHHHcCC-CCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHH
Confidence 35999999999999999999999 9999999999999999999999999988 77766664
No 19
>PLN00154 histone H2A; Provisional
Probab=80.46 E-value=2.4 Score=33.96 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+..+...|+|.|+.+++-.++ ...++|+
T Consensus 74 tAEVLELAGNaA~d~kk~RItPrHi~lAIrnDe--EL~~Ll~ 113 (136)
T PLN00154 74 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDE--ELDTLIK 113 (136)
T ss_pred HHHHHHHHHHHHHhhCCceecHHHhhhhccCcH--HHHHHhc
Confidence 356899999999999999999999999997654 3455553
No 20
>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=79.38 E-value=3.6 Score=32.10 Aligned_cols=40 Identities=15% Similarity=0.173 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++++.|.+.|+..+...|+|+|+-+++-.+. ....+++
T Consensus 55 ~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~--EL~~L~~ 94 (115)
T cd00074 55 TAEVLELAGNAARDNKKKRITPRHLQLAVRNDE--ELNKLLK 94 (115)
T ss_pred HHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccH--HHHHHHc
Confidence 467899999999999999999999999997653 3444544
No 21
>PTZ00017 histone H2A; Provisional
Probab=78.78 E-value=3.4 Score=33.12 Aligned_cols=40 Identities=15% Similarity=0.128 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+..+...|+|+|+.+++-.++ ...++|.
T Consensus 62 taEILELAgNaa~d~kk~RItPrHi~lAI~nDe--EL~~Ll~ 101 (134)
T PTZ00017 62 TAEVLELAGNAAKDNKKKRITPRHIQLAIRNDE--ELNKLLA 101 (134)
T ss_pred HHHHHHHHHHHHHhcCCCeecHHHHHhhccCcH--HHHHHHc
Confidence 356899999999999999999999999997754 4566664
No 22
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=77.92 E-value=4.1 Score=32.27 Aligned_cols=41 Identities=17% Similarity=0.142 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRA 131 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~ 131 (231)
+.++++.|-+.|+..+-..|+|.|+.+|+-+++ ...++|.+
T Consensus 62 ~Aeile~agnaardnkk~ri~PrH~~lAI~NDe--EL~~lL~~ 102 (131)
T KOG1756|consen 62 TAEILELAGNAARDNKKTRITPRHLQLAIRNDE--ELNKLLGK 102 (131)
T ss_pred HHHHHHHhHHHhhhcCccccChHHHHHHHhCcH--HHHHHhcc
Confidence 467889999999999999999999999998764 46777763
No 23
>PLN00157 histone H2A; Provisional
Probab=76.37 E-value=3.7 Score=32.80 Aligned_cols=40 Identities=18% Similarity=0.150 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+..+...|+|+|+.+++-.++ ...++|+
T Consensus 61 taEVLELAgnaa~d~kk~RItPrHi~lAI~nDe--EL~~Ll~ 100 (132)
T PLN00157 61 AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDE--ELSKLLG 100 (132)
T ss_pred HHHHHHHHHHHHHhcCCccccHHHHhhcccCcH--HHHHHHc
Confidence 456899999999999999999999999997654 4566665
No 24
>PLN00153 histone H2A; Provisional
Probab=75.30 E-value=4.6 Score=32.17 Aligned_cols=40 Identities=18% Similarity=0.127 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+..+...|+|+|+.+++-.++ ...++|+
T Consensus 59 taEVLELAgnaa~d~kk~RItPrHi~lAI~nDe--EL~~Ll~ 98 (129)
T PLN00153 59 TAEVLELAGNAARDNKKNRIVPRHIQLAIRNDE--ELGKLLG 98 (129)
T ss_pred HHHHHHHHHHHHHhcCCCccChHHHHhhccCcH--HHHHHHC
Confidence 346899999999999999999999999997654 4566665
No 25
>PLN00156 histone H2AX; Provisional
Probab=74.15 E-value=5.1 Score=32.26 Aligned_cols=40 Identities=18% Similarity=0.140 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+..+-..|+|+|+.+++-.+. ...++|+
T Consensus 64 taEVLELAgNaa~d~kk~RItPrHi~lAIrnDe--EL~~Ll~ 103 (139)
T PLN00156 64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDE--ELSKLLG 103 (139)
T ss_pred HHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcH--HHHHHHC
Confidence 456899999999999999999999999997654 4566665
No 26
>smart00414 H2A Histone 2A.
Probab=73.66 E-value=5.4 Score=30.63 Aligned_cols=39 Identities=18% Similarity=0.177 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 90 IRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 90 ~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
.++++.|-+.|+..+...|+|+|+-+++-.++ ...++++
T Consensus 45 aEILeLagn~a~~~k~~rItp~hi~lAi~nD~--EL~~L~~ 83 (106)
T smart00414 45 AEVLELAGNAARDNKKRRITPRHLQLAIRNDE--ELNKLLK 83 (106)
T ss_pred HHHHHHHHHHHHhcCCCccchHHHhhhccCCH--HHHHHHc
Confidence 56889999999999999999999999997653 3455554
No 27
>PF13551 HTH_29: Winged helix-turn helix
Probab=72.24 E-value=35 Score=24.89 Aligned_cols=82 Identities=23% Similarity=0.124 Sum_probs=50.5
Q ss_pred HHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCC----CcCCCCCCCc--cCHHHHHHHHHHHHHHHHcCCCCCCCH
Q 026896 115 MGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSD----LFFFSPERPP--LTEQAQRALDWAFNEKLKSGESGEITT 188 (231)
Q Consensus 115 laLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~----~~~~~~~~~~--~S~~l~~vLe~A~~~A~~~g~~~~I~t 188 (231)
+.++.++.+...++.+.+|++...|...+..+..... .....++.+. ++++....|......--..|. ...+.
T Consensus 5 l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~-~~~t~ 83 (112)
T PF13551_consen 5 LLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGR-SRWTL 83 (112)
T ss_pred HHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCC-CcccH
Confidence 3345555545899999999999999999988765431 1011122222 788877766665553322344 46777
Q ss_pred HHHHHHHhh
Q 026896 189 NHLLLGIWS 197 (231)
Q Consensus 189 eHLLLALl~ 197 (231)
..|-..|++
T Consensus 84 ~~l~~~l~~ 92 (112)
T PF13551_consen 84 EELAEWLIE 92 (112)
T ss_pred HHHHHHHHH
Confidence 766665544
No 28
>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=69.95 E-value=5.9 Score=30.89 Aligned_cols=40 Identities=28% Similarity=0.372 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+||+.|...|...+. ..|+.+||-+|+-.|++. ..+|+
T Consensus 55 ~aEIlelA~n~ak~~k~-krItp~hi~lAi~nD~EL--~~L~~ 94 (115)
T cd00074 55 TAEVLELAGNAARDNKK-KRITPRHLQLAVRNDEEL--NKLLK 94 (115)
T ss_pred HHHHHHHHHHHHHHcCC-CeEcHHHHHHHHhccHHH--HHHHc
Confidence 47799999999999999 999999999999988643 33554
No 29
>PLN00154 histone H2A; Provisional
Probab=69.72 E-value=4.6 Score=32.40 Aligned_cols=34 Identities=29% Similarity=0.303 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
+.+|||.|...|+..+. ..|++.||.+|+-.|++
T Consensus 74 tAEVLELAGNaA~d~kk-~RItPrHi~lAIrnDeE 107 (136)
T PLN00154 74 TAEVLELAGNASKDLKV-KRITPRHLQLAIRGDEE 107 (136)
T ss_pred HHHHHHHHHHHHHhhCC-ceecHHHhhhhccCcHH
Confidence 46799999999999999 99999999999988764
No 30
>PTZ00017 histone H2A; Provisional
Probab=69.04 E-value=5.2 Score=32.08 Aligned_cols=34 Identities=26% Similarity=0.350 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
+.+|||.|...|...+. ..|++.||.+|+-.|++
T Consensus 62 taEILELAgNaa~d~kk-~RItPrHi~lAI~nDeE 95 (134)
T PTZ00017 62 TAEVLELAGNAAKDNKK-KRITPRHIQLAIRNDEE 95 (134)
T ss_pred HHHHHHHHHHHHHhcCC-CeecHHHHHhhccCcHH
Confidence 46799999999999998 99999999999998864
No 31
>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=68.59 E-value=11 Score=24.88 Aligned_cols=41 Identities=12% Similarity=0.251 Sum_probs=33.3
Q ss_pred HHHHHHHhhCCC--chHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 189 NHLLLGIWSEKE--SAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 189 eHLLLALl~d~~--~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
-++|..|...++ ....++-..+|+++..+...++.+.+.||
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Gl 50 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGL 50 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 356777777665 57788989999999999999999999887
No 32
>PTZ00252 histone H2A; Provisional
Probab=66.35 E-value=8.9 Score=30.71 Aligned_cols=40 Identities=8% Similarity=0.098 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHH--cCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARK--LKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~--~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++|+.|-+.|+. .+-..|+|+|+.+++-.++ ...++|+
T Consensus 60 taEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDe--EL~~Ll~ 101 (134)
T PTZ00252 60 TAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDD--DLGSLLK 101 (134)
T ss_pred HHHHHHHHHHHHHhccCCcccccHHHHHhhccChH--HHHHHHc
Confidence 35689999999976 4557999999999997654 4566665
No 33
>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=66.14 E-value=15 Score=23.22 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=32.1
Q ss_pred HHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 190 HLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 190 HLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.||..|.+++.....++-..+|++...+...++.+.+.||
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 5677777777777778888899999999999999988876
No 34
>PLN00157 histone H2A; Provisional
Probab=65.34 E-value=6.3 Score=31.50 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+|||.|...|...+. ..|++.||.+|+-.|++. .++|+
T Consensus 61 taEVLELAgnaa~d~kk-~RItPrHi~lAI~nDeEL--~~Ll~ 100 (132)
T PLN00157 61 AAEVLELAGNAARDNKK-SRIVPRHIQLAVRNDEEL--SKLLG 100 (132)
T ss_pred HHHHHHHHHHHHHhcCC-ccccHHHHhhcccCcHHH--HHHHc
Confidence 46799999999999998 999999999999987643 33554
No 35
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=64.79 E-value=19 Score=25.00 Aligned_cols=41 Identities=12% Similarity=0.191 Sum_probs=30.9
Q ss_pred HHHHHHhhCCC--chHHHHHHhCCCCHHHHHHHHHHhhcCCCC
Q 026896 190 HLLLGIWSEKE--SAGHKILATLGFNDEKAKEIAKSVSSRSYD 230 (231)
Q Consensus 190 HLLLALl~d~~--~~~~~iL~~lGvd~~~l~e~l~~i~~~~~~ 230 (231)
.||..|-.... ..+..+-+.+|++...+.+.+..+.++||=
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V 52 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKV 52 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 34444444434 566788889999999999999999988873
No 36
>smart00414 H2A Histone 2A.
Probab=63.70 E-value=7.9 Score=29.72 Aligned_cols=40 Identities=30% Similarity=0.380 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+||+.|...|...+. ..|+++|+-+|+-.|++. ..+++
T Consensus 44 taEILeLagn~a~~~k~-~rItp~hi~lAi~nD~EL--~~L~~ 83 (106)
T smart00414 44 TAEVLELAGNAARDNKK-RRITPRHLQLAIRNDEEL--NKLLK 83 (106)
T ss_pred HHHHHHHHHHHHHhcCC-CccchHHHhhhccCCHHH--HHHHc
Confidence 36799999999998888 899999999999987643 33554
No 37
>PLN00153 histone H2A; Provisional
Probab=62.70 E-value=8.6 Score=30.61 Aligned_cols=40 Identities=25% Similarity=0.347 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+|||.|...|...+. ..|.+.||.+|+-.|++. .++|.
T Consensus 59 taEVLELAgnaa~d~kk-~RItPrHi~lAI~nDeEL--~~Ll~ 98 (129)
T PLN00153 59 TAEVLELAGNAARDNKK-NRIVPRHIQLAIRNDEEL--GKLLG 98 (129)
T ss_pred HHHHHHHHHHHHHhcCC-CccChHHHHhhccCcHHH--HHHHC
Confidence 46799999999998888 999999999999887643 33554
No 38
>PLN00156 histone H2AX; Provisional
Probab=62.20 E-value=9.1 Score=30.85 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+|||.|...|...+. ..|.++||.+|+-.|++. ..+|.
T Consensus 64 taEVLELAgNaa~d~kk-~RItPrHi~lAIrnDeEL--~~Ll~ 103 (139)
T PLN00156 64 AAEVLELAGNAARDNKK-NRIVPRHIQLAVRNDEEL--SKLLG 103 (139)
T ss_pred HHHHHHHHHHHHHHcCC-CcCcHHHHHhhccCcHHH--HHHHC
Confidence 46799999999998888 999999999999987643 33554
No 39
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=61.48 E-value=10 Score=30.12 Aligned_cols=40 Identities=30% Similarity=0.361 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
..+|||.|-..|+..+. ..|.+.||.+|+-.|+. ..++|.
T Consensus 62 ~Aeile~agnaardnkk-~ri~PrH~~lAI~NDeE--L~~lL~ 101 (131)
T KOG1756|consen 62 TAEILELAGNAARDNKK-TRITPRHLQLAIRNDEE--LNKLLG 101 (131)
T ss_pred HHHHHHHhHHHhhhcCc-cccChHHHHHHHhCcHH--HHHHhc
Confidence 46789999999999898 99999999999998764 345654
No 40
>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=57.63 E-value=13 Score=25.34 Aligned_cols=41 Identities=15% Similarity=0.280 Sum_probs=34.5
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 189 eHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
..++.+|+......+..+-..+|++...+.+.++.+.+.|+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~Gl 51 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGL 51 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 35677787777777888999999999999999999988875
No 41
>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=54.81 E-value=20 Score=23.04 Aligned_cols=27 Identities=22% Similarity=0.081 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHcCCCCcCHHHHHHH
Q 026896 90 IRSFAMAELEARKLKYPNTGTEAFLMG 116 (231)
Q Consensus 90 ~~vl~~A~~~A~~~~~~~I~~eHLLla 116 (231)
..+=..++..|+..|..+|+.+|+--+
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 455578899999999999999998643
No 42
>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=51.58 E-value=21 Score=24.70 Aligned_cols=30 Identities=20% Similarity=0.105 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026896 165 QAQRALDWAFNEKLKSGESGEITTNHLLLGI 195 (231)
Q Consensus 165 ~l~~vLe~A~~~A~~~g~~~~I~teHLLLAL 195 (231)
-+.++++.|...|...+. ..|+..|+.+|+
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 357888999999999999 999999999986
No 43
>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=51.32 E-value=22 Score=24.68 Aligned_cols=30 Identities=13% Similarity=0.071 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026896 88 RAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (231)
Q Consensus 88 ~a~~vl~~A~~~A~~~~~~~I~~eHLLlaL 117 (231)
-+.+++..|.+.|...+...|++.|+.+++
T Consensus 43 ~~~~il~~A~~~a~~~kR~tI~~~DI~~A~ 72 (75)
T PF00125_consen 43 LLVEILEEAGNLARHAKRKTITPRDIQLAV 72 (75)
T ss_dssp HHHHHHHHHHHHHHHTTBSEEGHHHHHHHH
T ss_pred hhhhhhhHHHHHHhhcCCcEecHHHHHHHH
Confidence 456677889999999999999999999886
No 44
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=49.82 E-value=40 Score=21.41 Aligned_cols=32 Identities=16% Similarity=0.199 Sum_probs=25.6
Q ss_pred CCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 198 EKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 198 d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.+......+...+|++...+.+.++.+.+.++
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~ 39 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGL 39 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 44456667888899999999999998887765
No 45
>PTZ00252 histone H2A; Provisional
Probab=49.14 E-value=20 Score=28.71 Aligned_cols=40 Identities=10% Similarity=0.218 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHH--cCCCCCCCHHHHHHHHhhCCCchHHHHHH
Q 026896 166 AQRALDWAFNEKLK--SGESGEITTNHLLLGIWSEKESAGHKILA 208 (231)
Q Consensus 166 l~~vLe~A~~~A~~--~g~~~~I~teHLLLALl~d~~~~~~~iL~ 208 (231)
+.+|||.|...|.. ... ..|.++||.+|+-.|++. .++|.
T Consensus 60 taEVLELAgnaa~d~~~kk-~RItPrHi~lAIrNDeEL--~~Ll~ 101 (134)
T PTZ00252 60 TAELLELSVKAAAQQAKKP-KRLTPRTVTLAVRHDDDL--GSLLK 101 (134)
T ss_pred HHHHHHHHHHHHHhccCCc-ccccHHHHHhhccChHHH--HHHHc
Confidence 36789999998865 444 689999999999987643 34555
No 46
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=48.92 E-value=1.1e+02 Score=22.72 Aligned_cols=90 Identities=14% Similarity=0.007 Sum_probs=56.0
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHH
Q 026896 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQ 165 (231)
Q Consensus 86 T~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~ 165 (231)
|...++-+..|.+....+..... .+..-....+-+-|.++... ...++..+.+..-. ...
T Consensus 5 S~~ir~rV~~Ar~~Q~~R~~~~~----------~Na~l~~~~l~~~~~l~~~~-~~~l~~~~~~~~lS---------~R~ 64 (96)
T PF13335_consen 5 SAEIRERVEAARERQRERYGGIK----------CNAQLPGEELRKYCPLSSEA-KKLLEQAAEKLNLS---------ARG 64 (96)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCC----------ccccCCHHHHHhHcCCCHHH-HHHHHHHHHHcCcC---------HHH
Confidence 56677777777777766554211 12221223333335555432 33444444332211 267
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHh
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIW 196 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl 196 (231)
..++|.-|+-+|.--|. +.|+.+||.-||-
T Consensus 65 ~~rilrvARTIADL~~~-~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 65 YHRILRVARTIADLEGS-ERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHHHHhHcCC-CCCCHHHHHHHHh
Confidence 89999999999999999 9999999999873
No 47
>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=48.21 E-value=36 Score=21.53 Aligned_cols=38 Identities=11% Similarity=0.115 Sum_probs=30.2
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
||..|.+ ......++-+.+|++...+...++.+.+.|+
T Consensus 7 Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 7 ILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp HHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcC
Confidence 5666666 4566778999999999999999999988775
No 48
>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=47.96 E-value=31 Score=22.42 Aligned_cols=41 Identities=12% Similarity=0.235 Sum_probs=32.4
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 189 eHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
-++|..|.+.+......+-..++++...+-..++.+-+.||
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~ 46 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGL 46 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCC
Confidence 35666777767667778888899999999999999988876
No 49
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.59 E-value=44 Score=24.60 Aligned_cols=39 Identities=8% Similarity=0.154 Sum_probs=30.6
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
||.+|.+++......+-+.+|++...+.+.++.+.+.|+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 455555555566678888899999999999999988775
No 50
>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=44.16 E-value=52 Score=22.39 Aligned_cols=38 Identities=16% Similarity=0.318 Sum_probs=29.4
Q ss_pred HHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 192 LLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 192 LLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
++.++.+....+.++-..+|++...+.+.++.+.+.|+
T Consensus 5 il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 34445555555778888899999999999999988765
No 51
>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=44.14 E-value=46 Score=23.65 Aligned_cols=40 Identities=15% Similarity=0.273 Sum_probs=28.3
Q ss_pred HHHHHHhhCCC---chHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 190 HLLLGIWSEKE---SAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 190 HLLLALl~d~~---~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
|+|+.|....+ .....+-+.+|+++..+.+.+..+.+.||
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gl 54 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGL 54 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCe
Confidence 44444444433 35557778899999999999999988876
No 52
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=44.08 E-value=47 Score=24.10 Aligned_cols=28 Identities=18% Similarity=0.312 Sum_probs=24.2
Q ss_pred HHHHHHhCCCCHHHHHHHHHHhhcCCCC
Q 026896 203 GHKILATLGFNDEKAKEIAKSVSSRSYD 230 (231)
Q Consensus 203 ~~~iL~~lGvd~~~l~e~l~~i~~~~~~ 230 (231)
+.++=..+|+....+-+.|+.++..|||
T Consensus 22 Ge~La~~LgiSRtaVwK~Iq~Lr~~G~~ 49 (79)
T COG1654 22 GEKLAEELGISRTAVWKHIQQLREEGVD 49 (79)
T ss_pred HHHHHHHHCccHHHHHHHHHHHHHhCCc
Confidence 3456678999999999999999999986
No 53
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=43.97 E-value=1.2e+02 Score=23.68 Aligned_cols=44 Identities=11% Similarity=0.146 Sum_probs=33.8
Q ss_pred CCHHH--HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 186 ITTNH--LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 186 I~teH--LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
++..+ +|..|...+.....++-..+|++...+-..++.+-+.||
T Consensus 38 lt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~Gl 83 (144)
T PRK11512 38 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGW 83 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 44444 366665555556678888999999999999999999887
No 54
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=43.71 E-value=58 Score=21.59 Aligned_cols=40 Identities=15% Similarity=0.280 Sum_probs=27.9
Q ss_pred HHHHHHh-hCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 190 HLLLGIW-SEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 190 HLLLALl-~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.+|..|. .++......+-..+|++...+.+.++.+-+.||
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~gl 47 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGL 47 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 3455555 355566678888999999999999999988776
No 55
>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=43.61 E-value=1.2e+02 Score=22.65 Aligned_cols=41 Identities=5% Similarity=-0.082 Sum_probs=32.6
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 189 eHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
-++|..|...+......+-+.+|++...+-..++.+.+.||
T Consensus 31 ~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~Gl 71 (118)
T TIGR02337 31 WRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGL 71 (118)
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCC
Confidence 35676676666556678888899999999999999988876
No 56
>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=43.09 E-value=43 Score=22.65 Aligned_cols=28 Identities=14% Similarity=-0.003 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026896 167 QRALDWAFNEKLKSGESGEITTNHLLLGI 195 (231)
Q Consensus 167 ~~vLe~A~~~A~~~g~~~~I~teHLLLAL 195 (231)
..+...|+..|...+. ..|+.+||..||
T Consensus 38 ~~l~~~A~~~a~~~~r-kti~~~Dv~~Av 65 (65)
T PF00808_consen 38 QYLAKEANEIAQRDKR-KTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHHHTTS-SEE-HHHHHHHH
T ss_pred HHHHHHHHHHHHHcCC-CccCHHHHHHHC
Confidence 5566778888888888 899999998875
No 57
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=43.09 E-value=75 Score=19.49 Aligned_cols=39 Identities=8% Similarity=0.124 Sum_probs=27.8
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
++-.|.+........+...+|++...+...++.+.+.++
T Consensus 5 il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~ 43 (53)
T smart00420 5 ILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGL 43 (53)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 344444444445557777889999999999999887765
No 58
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=42.61 E-value=2.2e+02 Score=27.61 Aligned_cols=95 Identities=13% Similarity=0.016 Sum_probs=62.2
Q ss_pred CchhhcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCC--cHHHHHHHHcCCChHHHHHHHHHHhcCCCCcC-CCC
Q 026896 81 KIPKWSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGT--STTAKFLRANGITLFKVREETLNLLGKSDLFF-FSP 157 (231)
Q Consensus 81 ~~~kfT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~--s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~-~~~ 157 (231)
+|..|.+.+.++++.+.++|..++... .|--.||-+.+.+- ..+.+++..+ ...|..-+++.+.+..... ...
T Consensus 124 Df~~F~p~Lekiv~l~re~A~~~~~~~-~pYdaLld~yEpG~t~~~i~~vF~~L---k~~L~~ll~kv~~~~~~~~~~~~ 199 (497)
T COG2317 124 DFSIFKPYLEKIVELKREFAEYRGYEE-HPYDALLDLYEPGLTVRDVDRVFAEL---KKELVPLLDKVLEKGKSPRSDLL 199 (497)
T ss_pred cHhhhhHHHHHHHHHHHHHHHhccccc-CcHHHHHHhhcCCCcHHHHHHHHHHH---HHHHHHHHHHHHhccCCCccccc
Confidence 499999999999999999999999998 77778887777643 1223333222 2333344444444441111 112
Q ss_pred CCCccCHHHHHHHHHHHHHHHH
Q 026896 158 ERPPLTEQAQRALDWAFNEKLK 179 (231)
Q Consensus 158 ~~~~~S~~l~~vLe~A~~~A~~ 179 (231)
...+|..+-++.+...+....-
T Consensus 200 ~~~~~~~e~q~~~~~~vl~~lG 221 (497)
T COG2317 200 EKEKYDKEKQEALGLRVLELLG 221 (497)
T ss_pred ccCCCCHHHHHHHHHHHHHHhC
Confidence 3457889999988888875543
No 59
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=41.31 E-value=1.1e+02 Score=22.95 Aligned_cols=68 Identities=9% Similarity=-0.040 Sum_probs=47.6
Q ss_pred HHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHh
Q 026896 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIW 196 (231)
Q Consensus 125 a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl 196 (231)
...+++.+|++.+.|.+-++.-+-..... .++...|+...-..++.+.+....++- +..+. .+.+-|+
T Consensus 10 ~~Elc~~~gi~~~~l~eLve~GlIep~~~--~~~~~~F~~~~l~r~~~a~rL~~dl~i-n~~gi-alvl~LL 77 (101)
T PRK10265 10 ITEFCLHTGVSEEELNEIVGLGVIEPREI--QETTWVFDDHAAIVVQRAVRLRHELAL-DWPGI-AVALTLL 77 (101)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCeecCCC--CcccceECHHHHHHHHHHHHHHHHcCC-CHHHH-HHHHHHH
Confidence 47889999999999988887655332221 245677899888999999998888877 44333 3344444
No 60
>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=40.89 E-value=56 Score=22.61 Aligned_cols=32 Identities=13% Similarity=0.056 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Q 026896 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGI 195 (231)
Q Consensus 163 S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLAL 195 (231)
...+.++++.|..++...+. ..++++|+-+||
T Consensus 33 e~rl~~i~~~A~k~~~hakR-ktlt~~DI~~Al 64 (65)
T smart00803 33 EYRIKEIVQEALKFMRHSKR-TTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHhCC-CeecHHHHHHHh
Confidence 35678899999999999999 999999998875
No 61
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=40.10 E-value=49 Score=23.69 Aligned_cols=39 Identities=18% Similarity=0.348 Sum_probs=29.6
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
|+..|...+......+-+.+|++...+...++.+...||
T Consensus 5 Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~Gy 43 (80)
T PF13601_consen 5 ILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGY 43 (80)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTS
T ss_pred HHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCC
Confidence 444455546677788888999999999999999998887
No 62
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=40.09 E-value=1.1e+02 Score=25.53 Aligned_cols=64 Identities=14% Similarity=0.135 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHH-HHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 164 EQAQRALDWAFNEK-LKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 164 ~~l~~vLe~A~~~A-~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
..+.+.++..+... ..+|- ..+--++|..+...+......+-+.++++...+-..++.+-++||
T Consensus 24 ~~l~~~i~~~~~~~l~~~gL--t~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGl 88 (185)
T PRK13777 24 KALWKSVEKDWQQWIKPYDL--NINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGY 88 (185)
T ss_pred HHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCC
Confidence 34444444444333 23443 344446777666666566667777788999999999999998887
No 63
>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=38.72 E-value=55 Score=22.11 Aligned_cols=26 Identities=15% Similarity=-0.052 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026896 92 SFAMAELEARKLKYPNTGTEAFLMGI 117 (231)
Q Consensus 92 vl~~A~~~A~~~~~~~I~~eHLLlaL 117 (231)
+...|.+.|...+-..|+++|+..++
T Consensus 40 l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 40 LAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 34567778889999999999998775
No 64
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=37.61 E-value=69 Score=22.48 Aligned_cols=41 Identities=10% Similarity=0.165 Sum_probs=30.2
Q ss_pred HHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 189 NHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 189 eHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
-++|..|...+......+-..++++...+...++.+.+.+|
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~ 53 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGL 53 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCC
Confidence 34555555555455567778889999999999999888776
No 65
>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=37.52 E-value=68 Score=22.17 Aligned_cols=33 Identities=15% Similarity=-0.091 Sum_probs=29.5
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaL 117 (231)
...++.++++.|...++..+-..++++++-++|
T Consensus 32 ~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Al 64 (65)
T smart00803 32 VEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHh
Confidence 467889999999999999999999999997775
No 66
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=36.34 E-value=1.5e+02 Score=20.82 Aligned_cols=66 Identities=17% Similarity=0.135 Sum_probs=41.2
Q ss_pred HHHHHhccCCcHHHHHHHHcCCCh--HHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHHHHHHHHcCCCCCCCHHH
Q 026896 113 FLMGILVEGTSTTAKFLRANGITL--FKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNH 190 (231)
Q Consensus 113 LLlaLL~~~~s~a~kiL~~~gid~--~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A~~~A~~~g~~~~I~teH 190 (231)
+...+|+. .+.++|++.|.+. ....+.+...+. .=+.++.+.+..++...|. ..++.++
T Consensus 3 ~~~~ll~~---~Vaqil~~~Gf~~~~~sale~ltdi~~---------------~yl~~l~~~~~~~a~~agR-~~~~~~D 63 (77)
T smart00576 3 LAFALLRI---AVAQILESAGFDSFQESALETLTDILQ---------------SYIQELGRTAHSYAELAGR-TEPNLGD 63 (77)
T ss_pred HHHHHHHH---HHHHHHHHcCccccCHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHcCC-CCCCHHH
Confidence 34445543 4678888888653 112222222211 2256777788888888888 8899999
Q ss_pred HHHHHhh
Q 026896 191 LLLGIWS 197 (231)
Q Consensus 191 LLLALl~ 197 (231)
+.+|+-+
T Consensus 64 v~~Al~~ 70 (77)
T smart00576 64 VVLALEN 70 (77)
T ss_pred HHHHHHH
Confidence 9988764
No 67
>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=36.23 E-value=69 Score=24.81 Aligned_cols=60 Identities=25% Similarity=0.223 Sum_probs=42.5
Q ss_pred HHHHHHHHcCCCh--HHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCC
Q 026896 124 TTAKFLRANGITL--FKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEK 199 (231)
Q Consensus 124 ~a~kiL~~~gid~--~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~ 199 (231)
....+|+.+|+.. +.+...+.+... .-+..++..|..+|...|. ..|+.+++-+|+-.--
T Consensus 6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~~---------------ry~~~il~dA~~~a~hA~r-~tV~~eDV~lAi~~r~ 67 (117)
T cd07979 6 VIAAILKSMGITEYEPRVINQLLEFAY---------------RYTTDVLDDAKVYSEHAGK-ANIDADDVKLAIQSRV 67 (117)
T ss_pred HHHHHHHHCCCCccCHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHHHh
Confidence 4567788888752 223333322221 3466899999999999999 9999999999987643
No 68
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=35.94 E-value=58 Score=25.57 Aligned_cols=40 Identities=20% Similarity=0.130 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
+.++++.|-+.|+..+-..|.|-||=+|+-.++ ....++.
T Consensus 61 ~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~--EL~~l~~ 100 (132)
T COG5262 61 AAEILELAGNAARDNKKKRIIPRHLQLAIRNDE--ELNKLLG 100 (132)
T ss_pred HHHHHHHhhhhhhhcCcceechHHHHHHhcCcH--HHHHHhh
Confidence 467889999999999999999999999997654 3445444
No 69
>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=34.01 E-value=50 Score=22.33 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=33.0
Q ss_pred HHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCC
Q 026896 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKS 150 (231)
Q Consensus 112 HLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~ 150 (231)
.++..|+.++...+..+-+..|++...+...+.....+.
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 366778888888999999999999999999998877653
No 70
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=31.95 E-value=1.1e+02 Score=19.82 Aligned_cols=39 Identities=10% Similarity=0.143 Sum_probs=28.2
Q ss_pred HHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 190 HLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 190 HLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.++..+...+ ....++-..+|++...+.+.++.+.+.++
T Consensus 11 ~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~ 49 (78)
T cd00090 11 RILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGL 49 (78)
T ss_pred HHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCC
Confidence 4555555544 55567777889999999999988877665
No 71
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=31.69 E-value=77 Score=20.33 Aligned_cols=39 Identities=13% Similarity=0.262 Sum_probs=29.2
Q ss_pred HHHHHhhCCCc-hHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKES-AGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~-~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
||-++.+.+.. ....+-+.+|++...+.+.+..+...||
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~ 47 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGY 47 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 44444444443 5678889999999999999999999887
No 72
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=30.59 E-value=64 Score=24.69 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
+..++.....+|+..+. ..|+.+||--|...++.
T Consensus 58 l~~iv~~s~k~aR~~~s-kR~t~e~lk~a~~sdek 91 (113)
T COG5247 58 LTEIVGLSLKEARKKSS-KRMTSEFLKRATESDEK 91 (113)
T ss_pred HHHHHHHHHHHHHhccc-hhhHHHHHHHHHhhhHH
Confidence 46778888889999998 99999999999998874
No 73
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=30.34 E-value=2.2e+02 Score=20.81 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHhh--------CCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 185 EITTNHLLLGIWS--------EKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 185 ~I~teHLLLALl~--------d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.....++|+.|.. .....-.++-+.+|++.+.+.+.++.+.++||
T Consensus 24 ~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~Gl 76 (95)
T TIGR01610 24 SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRI 76 (95)
T ss_pred CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 4445555555552 22233446767789999999999999988876
No 74
>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=30.01 E-value=1.2e+02 Score=21.25 Aligned_cols=31 Identities=6% Similarity=0.016 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (231)
+..+++.|...|+..|. +.|..+++.+++=.
T Consensus 36 v~~v~~~a~~lAkHr~~-~tv~~~Di~l~l~r 66 (72)
T cd07981 36 VDDVVEDACRLAKHRKS-DTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHH
Confidence 46788899999999999 89999999998643
No 75
>PLN00035 histone H4; Provisional
Probab=29.15 E-value=1.1e+02 Score=23.47 Aligned_cols=33 Identities=6% Similarity=-0.017 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026896 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (231)
Q Consensus 164 ~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (231)
.-+.+|+..|..++...+- ..|.++++.+||=.
T Consensus 61 ~~l~~I~~dav~ya~HA~R-KTV~~~DV~~Alkr 93 (103)
T PLN00035 61 IFLENVIRDAVTYTEHARR-KTVTAMDVVYALKR 93 (103)
T ss_pred HHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHH
Confidence 4467788888888888888 99999999998754
No 76
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=28.61 E-value=87 Score=27.45 Aligned_cols=43 Identities=14% Similarity=0.248 Sum_probs=37.6
Q ss_pred CHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 187 TTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 187 ~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
...-+-+||+......+..+....||...++.+.++.+.++||
T Consensus 17 yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~ 59 (247)
T COG1378 17 YEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGL 59 (247)
T ss_pred HHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCC
Confidence 3455678888888888999999999999999999999999987
No 77
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=28.35 E-value=1.3e+02 Score=22.22 Aligned_cols=31 Identities=13% Similarity=-0.054 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026896 87 ARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (231)
Q Consensus 87 ~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaL 117 (231)
....+++..|.-+|.-.+...|+.+||.-|+
T Consensus 63 R~~~rilrvARTIADL~~~~~I~~~hi~EAl 93 (96)
T PF13335_consen 63 RGYHRILRVARTIADLEGSERITREHIAEAL 93 (96)
T ss_pred HHHHHHHHHHHHHHhHcCCCCCCHHHHHHHH
Confidence 3456788889999999999999999999886
No 78
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=27.73 E-value=1.1e+02 Score=22.19 Aligned_cols=43 Identities=12% Similarity=0.319 Sum_probs=32.6
Q ss_pred CCHHHHHHHHhhCCCchH-HHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 186 ITTNHLLLGIWSEKESAG-HKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 186 I~teHLLLALl~d~~~~~-~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
..--|+|..+...+ +.. ..+-..++++...+...++.+-+.||
T Consensus 22 ~~q~~~L~~l~~~~-~~~~~~la~~l~i~~~~vt~~l~~Le~~gl 65 (126)
T COG1846 22 PPQYQVLLALYEAG-GITVKELAERLGLDRSTVTRLLKRLEDKGL 65 (126)
T ss_pred HHHHHHHHHHHHhC-CCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 34445566666554 333 77888999999999999999998887
No 79
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=27.40 E-value=2.4e+02 Score=20.23 Aligned_cols=55 Identities=20% Similarity=0.035 Sum_probs=42.0
Q ss_pred HHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHHHHHHHHcCC
Q 026896 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGE 182 (231)
Q Consensus 125 a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A~~~A~~~g~ 182 (231)
...+++.+|++...|..-++.-+-.... ..+...|+...-.-++++.+....+|-
T Consensus 3 ~~e~~~~~~i~~~~l~~lve~Gli~p~~---~~~~~~f~~~~l~rl~~~~rL~~Dl~i 57 (84)
T PF13591_consen 3 LEEFCEACGIEPEFLRELVEEGLIEPEG---EEEEWYFSEEDLARLRRIRRLHRDLGI 57 (84)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCeeecC---CCCeeeECHHHHHHHHHHHHHHHHcCC
Confidence 4678899999999998888765543222 124567999999999999988888877
No 80
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=27.37 E-value=60 Score=25.50 Aligned_cols=34 Identities=29% Similarity=0.340 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
+.+|||.|-.-|+..+. ..|.+-||-+||-.|+.
T Consensus 61 ~aEilelAgNaA~d~kk-kri~PrHlqlAIrnD~E 94 (132)
T COG5262 61 AAEILELAGNAARDNKK-KRIIPRHLQLAIRNDEE 94 (132)
T ss_pred HHHHHHHhhhhhhhcCc-ceechHHHHHHhcCcHH
Confidence 46889999999999999 99999999999998764
No 81
>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=27.28 E-value=1.4e+02 Score=20.84 Aligned_cols=33 Identities=9% Similarity=-0.130 Sum_probs=28.0
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHh
Q 026896 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGIL 118 (231)
Q Consensus 86 T~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL 118 (231)
..-+.+++..|...|+.+|...|..+-+.+++=
T Consensus 33 e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 33 DDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 455667888999999999999999999988873
No 82
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=27.13 E-value=4.7e+02 Score=23.62 Aligned_cols=92 Identities=14% Similarity=-0.017 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHHHHH
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQR 168 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~ 168 (231)
+.+++..|...|...+...|+.+|+-.++-.-..+...+.++.+......+..++...... . ... -...+
T Consensus 251 a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~~~~~~--~----~~~----~~~~~ 320 (394)
T PRK00411 251 AIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIVRLLKK--G----GDE----VTTGE 320 (394)
T ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhc--C----CCc----ccHHH
Confidence 3455666777788788888999999877755444555667776665555565555443322 1 011 13455
Q ss_pred HHHHHHHHHHHcCCCCCCCHHHH
Q 026896 169 ALDWAFNEKLKSGESGEITTNHL 191 (231)
Q Consensus 169 vLe~A~~~A~~~g~~~~I~teHL 191 (231)
+.+.-...+.++|- ..++...+
T Consensus 321 i~~~y~~l~~~~~~-~~~~~~~~ 342 (394)
T PRK00411 321 VYEEYKELCEELGY-EPRTHTRF 342 (394)
T ss_pred HHHHHHHHHHHcCC-CcCcHHHH
Confidence 55555555555655 54444443
No 83
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=27.07 E-value=1.1e+02 Score=26.48 Aligned_cols=40 Identities=13% Similarity=0.191 Sum_probs=33.8
Q ss_pred CccCHH----HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 160 PPLTEQ----AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 160 ~~~S~~----l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
+..|.. +..++.++.++++..|. ..|+++||--++..++.
T Consensus 38 ViisralElFl~~l~~~t~~~t~~~~a-Kt~s~~hlkq~v~~~~~ 81 (224)
T KOG1659|consen 38 VIISRALELFLESLLQKTLEITRSRGA-KTVSSSHLKQAVESDPK 81 (224)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCc-cccCHHHHHHHHhccch
Confidence 344555 47888999999999999 99999999999999875
No 84
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=27.04 E-value=3e+02 Score=22.06 Aligned_cols=67 Identities=18% Similarity=0.258 Sum_probs=46.1
Q ss_pred CCCccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhC---C-----CCHHHHHHHHHHhhcCCC
Q 026896 158 ERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATL---G-----FNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 158 ~~~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~l---G-----vd~~~l~e~l~~i~~~~~ 229 (231)
.++.||+.-++++..-.... .. ..=.+.+++|++|.++ .++..+.+.+ + ++...+...++.+.+.||
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~Gl 92 (135)
T PRK09416 18 KHLSFSEQHQKAVREKIKQS---SE-KEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRF 92 (135)
T ss_pred hcCCcchhhHHHHHHHHHHH---hc-ccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCC
Confidence 35788888777665554433 23 5667999999999888 7777666542 2 356777788887776665
No 85
>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=26.91 E-value=94 Score=22.04 Aligned_cols=28 Identities=14% Similarity=-0.090 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHcCCCC-cCHHHHHH
Q 026896 88 RAIRSFAMAELEARKLKYPN-TGTEAFLM 115 (231)
Q Consensus 88 ~a~~vl~~A~~~A~~~~~~~-I~~eHLLl 115 (231)
-.++++..|...|+.-|... ++.+||=-
T Consensus 35 FV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 35 FVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 45677788888888888888 99999854
No 86
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=26.70 E-value=96 Score=23.77 Aligned_cols=34 Identities=15% Similarity=0.037 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCC
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGT 122 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~ 122 (231)
+..++..+..+|+..+...++.|||-.+.+.++.
T Consensus 58 l~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdek 91 (113)
T COG5247 58 LTEIVGLSLKEARKKSSKRMTSEFLKRATESDEK 91 (113)
T ss_pred HHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHH
Confidence 4567788899999999999999999999988764
No 87
>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=26.37 E-value=1e+02 Score=20.66 Aligned_cols=23 Identities=17% Similarity=0.101 Sum_probs=15.7
Q ss_pred cHHHHHHHHcCCChHHHHHHHHH
Q 026896 123 STTAKFLRANGITLFKVREETLN 145 (231)
Q Consensus 123 s~a~kiL~~~gid~~~lr~~l~~ 145 (231)
-....++++.|+|++.|.++|++
T Consensus 32 ~~L~eA~~~~~ld~~~vl~~L~~ 54 (56)
T PF04405_consen 32 RSLEEACEEKGLDPEEVLEELNA 54 (56)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH
Confidence 34567777777777777777654
No 88
>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=26.29 E-value=1.8e+02 Score=19.10 Aligned_cols=39 Identities=5% Similarity=0.114 Sum_probs=28.8
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
|+--|-+.+......+-+.+|++...++..+..+.+.++
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~ 43 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGL 43 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 444444445556667888899999999999998877664
No 89
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=26.10 E-value=1.2e+02 Score=22.53 Aligned_cols=33 Identities=9% Similarity=0.052 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026896 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (231)
Q Consensus 164 ~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (231)
.=+..+.+.|...|..-|. ..|..+++.+|+=.
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 3356778889999999999 99999999999754
No 90
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.92 E-value=3.2e+02 Score=21.22 Aligned_cols=54 Identities=15% Similarity=0.160 Sum_probs=35.9
Q ss_pred HhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHH
Q 026896 117 ILVEGTSTTAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWA 173 (231)
Q Consensus 117 LL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A 173 (231)
++.. .|...++=+.+||++..||..+++.+.+..-. ......-...-.+||+.-
T Consensus 45 Fi~~-rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~--~~~~~~~~~~~~~IL~~L 98 (113)
T PF09862_consen 45 FIKN-RGNLKEMEKELGISYPTVRNRLDKIIEKLGYE--EDEEEEEEDERKEILDKL 98 (113)
T ss_pred HHHh-cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCC--CCcccccchhHHHHHHHH
Confidence 3444 45679999999999999999999988764431 112223445566666543
No 91
>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=25.78 E-value=37 Score=25.21 Aligned_cols=36 Identities=14% Similarity=-0.010 Sum_probs=11.5
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccC
Q 026896 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEG 121 (231)
Q Consensus 86 T~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~ 121 (231)
......++..|...|...|...|.+|+++..|=.++
T Consensus 33 ~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 33 REYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp HHHHHHHHHHHHC-----------------------
T ss_pred HHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCH
Confidence 678888999999999999999999999999886654
No 92
>PTZ00015 histone H4; Provisional
Probab=25.00 E-value=1.4e+02 Score=22.77 Aligned_cols=33 Identities=3% Similarity=-0.069 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHh
Q 026896 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIW 196 (231)
Q Consensus 163 S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl 196 (231)
..-+.+|+..|..++...+- ..|+++++.+||=
T Consensus 61 e~~l~~I~rdav~~aeHA~R-KTVt~~DV~~AlK 93 (102)
T PTZ00015 61 KAFLENVVRDSTAYTEYARR-KTVTAMDVVYALK 93 (102)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcccHHHHHHHHH
Confidence 34567788889999988888 9999999999863
No 93
>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=24.99 E-value=1.6e+02 Score=22.72 Aligned_cols=35 Identities=9% Similarity=0.033 Sum_probs=30.2
Q ss_pred cHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhcc
Q 026896 86 SARAIRSFAMAELEARKLKYPNTGTEAFLMGILVE 120 (231)
Q Consensus 86 T~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~ 120 (231)
-..+.+++..|...|+..|...|+.+.+-+|+-..
T Consensus 32 ~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r 66 (117)
T cd07979 32 YRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSR 66 (117)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 35567889999999999999999999999998654
No 94
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=24.99 E-value=1.6e+02 Score=23.51 Aligned_cols=35 Identities=11% Similarity=0.055 Sum_probs=25.5
Q ss_pred hcHHHHHHHHH------------HHHHHHHcCCCCcCHHHHHHHHhc
Q 026896 85 WSARAIRSFAM------------AELEARKLKYPNTGTEAFLMGILV 119 (231)
Q Consensus 85 fT~~a~~vl~~------------A~~~A~~~~~~~I~~eHLLlaLL~ 119 (231)
||.+++.++.. |-+.|.+-.-..|.+||+..||=.
T Consensus 31 ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 31 FTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 78888877654 345556666778999999988854
No 95
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=24.98 E-value=3.9e+02 Score=22.98 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=22.5
Q ss_pred CcHHHHHHHHcCCChHHHHHHHHHHhc
Q 026896 122 TSTTAKFLRANGITLFKVREETLNLLG 148 (231)
Q Consensus 122 ~s~a~kiL~~~gid~~~lr~~l~~~L~ 148 (231)
++++..+++.+|.|++.+|+..++...
T Consensus 72 ~~IF~Alc~a~~~dp~~~r~dA~~l~~ 98 (206)
T PLN03060 72 DAIFKAYIEALGEDPDQYRKDAKKLEE 98 (206)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 457788999999999999998876654
No 96
>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=24.86 E-value=1.5e+02 Score=21.74 Aligned_cols=34 Identities=6% Similarity=0.014 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhh
Q 026896 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWS 197 (231)
Q Consensus 163 S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~ 197 (231)
..-+.+++..|..++...|- ..|+.+++.+||=.
T Consensus 44 ~~~l~~I~~dav~ya~Ha~R-KTVt~~DV~~alkr 77 (85)
T cd00076 44 KSYLEDVIRDAVTYTEHAKR-KTVTAMDVVYALKR 77 (85)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CcCcHHHHHHHHHH
Confidence 34567788888888888888 89999999988744
No 97
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=24.85 E-value=1.6e+02 Score=25.51 Aligned_cols=34 Identities=3% Similarity=-0.120 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCC
Q 026896 89 AIRSFAMAELEARKLKYPNTGTEAFLMGILVEGT 122 (231)
Q Consensus 89 a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~ 122 (231)
+..++..+.++++.++...++++||--+++.++.
T Consensus 48 l~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~ 81 (224)
T KOG1659|consen 48 LESLLQKTLEITRSRGAKTVSSSHLKQAVESDPK 81 (224)
T ss_pred HHHHHHHHHHHHHhcCccccCHHHHHHHHhccch
Confidence 5678889999999999999999999999998765
No 98
>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=24.74 E-value=2e+02 Score=19.61 Aligned_cols=29 Identities=10% Similarity=0.285 Sum_probs=23.2
Q ss_pred chHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 201 SAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 201 ~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
....++-..+|++++.++..++.+-+.||
T Consensus 15 ~S~~eLa~~~~~s~~~ve~mL~~l~~kG~ 43 (69)
T PF09012_consen 15 VSLAELAREFGISPEAVEAMLEQLIRKGY 43 (69)
T ss_dssp EEHHHHHHHTT--HHHHHHHHHHHHCCTS
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCc
Confidence 34557888999999999999999999887
No 99
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=24.30 E-value=86 Score=25.60 Aligned_cols=27 Identities=11% Similarity=-0.055 Sum_probs=22.2
Q ss_pred HHHHHHHHHcCCCCcCHHHHHHHHhcc
Q 026896 94 AMAELEARKLKYPNTGTEAFLMGILVE 120 (231)
Q Consensus 94 ~~A~~~A~~~~~~~I~~eHLLlaLL~~ 120 (231)
..|...|.+-.-.+|.+||++.||=.-
T Consensus 53 sEAneic~~e~KKTIa~EHV~KALe~L 79 (156)
T KOG0871|consen 53 SEANEICNKEAKKTIAPEHVIKALENL 79 (156)
T ss_pred HHHHHHHhHHhcccCCHHHHHHHHHHc
Confidence 457788888899999999999988543
No 100
>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=23.72 E-value=90 Score=24.29 Aligned_cols=17 Identities=12% Similarity=0.046 Sum_probs=12.4
Q ss_pred CcCHHHHHHHHhccCCc
Q 026896 107 NTGTEAFLMGILVEGTS 123 (231)
Q Consensus 107 ~I~~eHLLlaLL~~~~s 123 (231)
.|++.|++-++.+.-++
T Consensus 39 rv~~~~il~Af~~GADG 55 (124)
T PF02662_consen 39 RVDPEFILRAFEKGADG 55 (124)
T ss_pred ccCHHHHHHHHHcCCCE
Confidence 47888888888775444
No 101
>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=23.68 E-value=2.5e+02 Score=25.13 Aligned_cols=58 Identities=12% Similarity=0.008 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026896 164 EQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (231)
Q Consensus 164 ~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~ 222 (231)
..+..+++.|...|...+. ..|+.+|+--|+=.-......+.+..+......+...+.
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 3456677888888888777 889999998775544333333455555444443444443
No 102
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.62 E-value=1.5e+02 Score=23.50 Aligned_cols=42 Identities=7% Similarity=0.076 Sum_probs=31.6
Q ss_pred HHHHHHHHhhC-CCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 188 TNHLLLGIWSE-KESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 188 teHLLLALl~d-~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.++-++.+|+. .......+=+.+|++...+.+.++.+..+|+
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 45556666654 3445557778899999999999999988874
No 103
>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=23.41 E-value=5.3e+02 Score=22.94 Aligned_cols=61 Identities=13% Similarity=-0.047 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHh
Q 026896 87 ARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (231)
Q Consensus 87 ~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L 147 (231)
..+.+++..|...|...+...|+.+|+-.++=.-..+...+.++.+......+..++....
T Consensus 241 R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~~~i~~l~~~~~~~l~ai~~~~ 301 (365)
T TIGR02928 241 RKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIANLA 301 (365)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4555566677777777777888888887665433333445555554444444455544433
No 104
>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=23.25 E-value=1.8e+02 Score=19.15 Aligned_cols=39 Identities=13% Similarity=0.108 Sum_probs=28.7
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
||..|...+...+.++-..+|++...+..-++.+.+-|+
T Consensus 15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGl 53 (61)
T PF12840_consen 15 ILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGL 53 (61)
T ss_dssp HHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 444443555677788888999999999999998877653
No 105
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=23.15 E-value=41 Score=19.48 Aligned_cols=11 Identities=18% Similarity=0.395 Sum_probs=8.5
Q ss_pred HHHhhcCCCCC
Q 026896 221 AKSVSSRSYDC 231 (231)
Q Consensus 221 l~~i~~~~~~~ 231 (231)
--++++++|+|
T Consensus 14 ~yKLsQrgy~w 24 (27)
T smart00265 14 TYKLSQNGYEW 24 (27)
T ss_pred HHHHhhcCCCC
Confidence 34688999987
No 106
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.14 E-value=1.6e+02 Score=18.24 Aligned_cols=37 Identities=11% Similarity=0.068 Sum_probs=26.9
Q ss_pred HHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
++..+++ .. ....+...+||+...+...++.....|.
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 3444443 33 4567888999999999999998877664
No 107
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.99 E-value=1.2e+02 Score=18.94 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=16.7
Q ss_pred chHHHHHHhCCCCHHHHHHHHHHhhcCCCC
Q 026896 201 SAGHKILATLGFNDEKAKEIAKSVSSRSYD 230 (231)
Q Consensus 201 ~~~~~iL~~lGvd~~~l~e~l~~i~~~~~~ 230 (231)
-...++-+.+|++...+...++..++.|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~ 47 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYREEGLE 47 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT--------
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHccccccc
Confidence 344578888999999999999998887764
No 108
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=22.95 E-value=3.6e+02 Score=20.75 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=34.0
Q ss_pred CCCHHH--HHHHHhhCC-CchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 185 EITTNH--LLLGIWSEK-ESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 185 ~I~teH--LLLALl~d~-~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.++..+ +|..|...+ ......+-..+|++...+-..++.+.+.||
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~Gl 75 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGL 75 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCC
Confidence 456555 455555443 345678888999999999999999999987
No 109
>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=22.05 E-value=3.4e+02 Score=20.16 Aligned_cols=69 Identities=10% Similarity=-0.130 Sum_probs=46.6
Q ss_pred HHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHhcCCC-----CcCC-CCCCCccCHHHHHHHHHHHHHHHHc
Q 026896 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLLGKSD-----LFFF-SPERPPLTEQAQRALDWAFNEKLKS 180 (231)
Q Consensus 112 HLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L~~~~-----~~~~-~~~~~~~S~~l~~vLe~A~~~A~~~ 180 (231)
++|..|-.++.-....+-+..|++...+-..+++...+.- ...+ ....+.+|+.-.++++..+......
T Consensus 32 ~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~~~ 106 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQIEEI 106 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHHHH
Confidence 4555555555555789999999999988888777654421 1111 1124778999999999988776543
No 110
>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=21.93 E-value=52 Score=24.40 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=9.7
Q ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCC
Q 026896 163 TEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKE 200 (231)
Q Consensus 163 S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~ 200 (231)
.+-+..++..|...|.+.|. ..|.+++|+.+|=.|+.
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 34567788888999999898 99999999999998864
No 111
>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=21.79 E-value=1.3e+02 Score=22.00 Aligned_cols=29 Identities=14% Similarity=0.234 Sum_probs=23.3
Q ss_pred chHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 201 SAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 201 ~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
.....|.++++++.+++++.++.+...|+
T Consensus 66 v~v~~I~~~l~~~~~~v~~al~~L~~eG~ 94 (102)
T PF08784_consen 66 VHVDEIAQQLGMSENEVRKALDFLSNEGH 94 (102)
T ss_dssp EEHHHHHHHSTS-HHHHHHHHHHHHHTTS
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHhCCe
Confidence 44557888899999999999999987775
No 112
>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=21.70 E-value=2.3e+02 Score=19.78 Aligned_cols=33 Identities=15% Similarity=-0.051 Sum_probs=26.7
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHH
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGI 117 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaL 117 (231)
-+-+++++++.|...++..+...+++.++=.||
T Consensus 33 veyrlreiiq~a~kfm~hskR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 33 VEYRLREIIQEALKFMRHSKRTKLTTDDINSAL 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 456889999999999999999999999886654
No 113
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=21.62 E-value=1.2e+02 Score=22.41 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=30.3
Q ss_pred HHHHHHHHhhCCCchHHHHHHhC--------CCCHHHHHHHHHHhhcCCC
Q 026896 188 TNHLLLGIWSEKESAGHKILATL--------GFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 188 teHLLLALl~d~~~~~~~iL~~l--------Gvd~~~l~e~l~~i~~~~~ 229 (231)
.+.++|+++..+..++..+.+.+ .++...+...++.+.+.|+
T Consensus 5 l~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~Gl 54 (100)
T TIGR03433 5 LDLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGW 54 (100)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCC
Confidence 56788899887777776666553 4667777788888777765
No 114
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=21.59 E-value=3.3e+02 Score=22.52 Aligned_cols=75 Identities=23% Similarity=0.243 Sum_probs=45.5
Q ss_pred cccccccccCCccccccCCcchhHHHhhhCCCCCCCCCCCCCCchhhcHHHHHHHHH------------HHHHHHHcCCC
Q 026896 39 KLLIRPQLNSSRFVTKYHRSSATATVSFSLPTTVKPETASPDKIPKWSARAIRSFAM------------AELEARKLKYP 106 (231)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~kfT~~a~~vl~~------------A~~~A~~~~~~ 106 (231)
++.++.|- ||+|... +++..=..||. ++ |.+.+|.++++. |-+.|.+-.-.
T Consensus 23 ~~~~reqD---r~LPIAN---V~RIMK~~lP~-----na------KIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRK 85 (168)
T KOG0869|consen 23 SLSLREQD---RFLPIAN---VSRIMKKALPA-----NA------KISKDAKETVQECVSEFISFVTGEASEKCQREKRK 85 (168)
T ss_pred ccccchhh---hhccHHH---HHHHHHhcCCc-----cc------ccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcC
Confidence 34455554 9998544 22222233444 24 567777776655 44557777888
Q ss_pred CcCHHHHHHHHhccCCcHHHHHHH
Q 026896 107 NTGTEAFLMGILVEGTSTTAKFLR 130 (231)
Q Consensus 107 ~I~~eHLLlaLL~~~~s~a~kiL~ 130 (231)
.|+-+.||+||-.-+=...+..|+
T Consensus 86 TIngdDllwAm~tLGFe~Y~eplk 109 (168)
T KOG0869|consen 86 TINGDDLLWAMSTLGFENYAEPLK 109 (168)
T ss_pred cccHHHHHHHHHHcCcHhHHHHHH
Confidence 999999999997654333334443
No 115
>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=21.48 E-value=1.9e+02 Score=26.57 Aligned_cols=63 Identities=16% Similarity=0.203 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHH--HHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 164 EQAQRALDWAFNEK--LKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 164 ~~l~~vLe~A~~~A--~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
++..++|+.|.... ...|-...+...-+|.+++. +.+.++-..+|+|++-+.+.+.++...+|
T Consensus 8 eey~kAln~~~~~v~~~~~~~~r~~~~~L~L~~lvG---g~at~~a~~~g~dY~~~Lk~Ld~la~~~~ 72 (327)
T PF04693_consen 8 EEYYKALNEALGVVFARMNGRRRDVALRLVLGGLVG---GRATNAAQTFGMDYENLLKNLDKLANADL 72 (327)
T ss_pred HHHHHHHHHHHHHHHHhhcCchHHHHHHHHhhheec---cchhHHHHHhCccHHHHHHHhhhhhccCc
Confidence 56778888888776 55555245666667777664 33558888999999999999998877654
No 116
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=21.33 E-value=99 Score=25.97 Aligned_cols=34 Identities=21% Similarity=0.391 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHHHhh
Q 026896 184 GEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAKSVS 225 (231)
Q Consensus 184 ~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~~i~ 225 (231)
+-|+.+-++- .-.++|.++|+|++.+++.++.++
T Consensus 53 NNISqeKf~n--------iQkk~mERYGfd~~~iE~q~K~~G 86 (186)
T PF12983_consen 53 NNISQEKFLN--------IQKKFMERYGFDPSEIEKQMKSMG 86 (186)
T ss_pred cCCcHHHHHH--------HHHHHHHHhCCCHHHHHHHHHHcC
Confidence 6777777652 225799999999999999988764
No 117
>PF10845 DUF2576: Protein of unknown function (DUF2576); InterPro: IPR022556 The function of this viral family of proteins is unknown. The entry contains Orf5 from Autographa californica nuclear polyhedrosis virus (AcMNPV).
Probab=21.17 E-value=97 Score=20.17 Aligned_cols=18 Identities=11% Similarity=0.237 Sum_probs=12.7
Q ss_pred hCCCCHHHHHHHHHHhhc
Q 026896 209 TLGFNDEKAKEIAKSVSS 226 (231)
Q Consensus 209 ~lGvd~~~l~e~l~~i~~ 226 (231)
....|.+++++.+..+|+
T Consensus 8 ~~dydreqlrrelnsLR~ 25 (48)
T PF10845_consen 8 QHDYDREQLRRELNSLRR 25 (48)
T ss_pred ccccCHHHHHHHHHHHHH
Confidence 345678888887777664
No 118
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.10 E-value=2.3e+02 Score=17.91 Aligned_cols=39 Identities=15% Similarity=0.232 Sum_probs=27.5
Q ss_pred HHHHHHhhCCC-chHHHHHHhCCCCHHHHHHHHHHhhcCC
Q 026896 190 HLLLGIWSEKE-SAGHKILATLGFNDEKAKEIAKSVSSRS 228 (231)
Q Consensus 190 HLLLALl~d~~-~~~~~iL~~lGvd~~~l~e~l~~i~~~~ 228 (231)
.||.-|++.++ ..+..+-..+||+...+...++.++..+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 34555545544 5566787889999999999999887654
No 119
>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=21.01 E-value=1.8e+02 Score=17.85 Aligned_cols=31 Identities=16% Similarity=0.044 Sum_probs=20.7
Q ss_pred HHHhccCCcHHHHHHHHcCCChHHHHHHHHH
Q 026896 115 MGILVEGTSTTAKFLRANGITLFKVREETLN 145 (231)
Q Consensus 115 laLL~~~~s~a~kiL~~~gid~~~lr~~l~~ 145 (231)
...|..-.+...++-+.+||+...|...+.+
T Consensus 11 ~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 11 RQALERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3344444567788888899999988877654
No 120
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.94 E-value=1.3e+02 Score=19.20 Aligned_cols=26 Identities=12% Similarity=0.291 Sum_probs=22.6
Q ss_pred HHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 204 HKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 204 ~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
..+-+.+|+....+.+.++.+.+.||
T Consensus 29 ~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 29 ETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 45667789999999999999999887
No 121
>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=20.76 E-value=1.2e+02 Score=20.32 Aligned_cols=26 Identities=15% Similarity=0.253 Sum_probs=20.4
Q ss_pred chHHHHHHhCCCCHHHHHHHHHHhhc
Q 026896 201 SAGHKILATLGFNDEKAKEIAKSVSS 226 (231)
Q Consensus 201 ~~~~~iL~~lGvd~~~l~e~l~~i~~ 226 (231)
.....+-+++|++.++++++|+..+-
T Consensus 21 ~ev~ywa~~~gvt~~~L~~AV~~vG~ 46 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREAVRAVGN 46 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHCc
Confidence 34456778899999999999988654
No 122
>PRK00056 mtgA monofunctional biosynthetic peptidoglycan transglycosylase; Provisional
Probab=20.61 E-value=93 Score=27.26 Aligned_cols=33 Identities=9% Similarity=0.067 Sum_probs=18.3
Q ss_pred HHHHHHhccCCcHHHHHHHHcCCChHHHHHHHHHHh
Q 026896 112 AFLMGILVEGTSTTAKFLRANGITLFKVREETLNLL 147 (231)
Q Consensus 112 HLLlaLL~~~~s~a~kiL~~~gid~~~lr~~l~~~L 147 (231)
|+..|++.-+| .++.++.|+|+..+..++...+
T Consensus 71 ~l~~Avia~ED---~rF~~H~GvD~~~i~rA~~~~~ 103 (236)
T PRK00056 71 NLKRAVIAAED---QKFPEHWGFDWDAIQKALEHNE 103 (236)
T ss_pred HHHHHhHhhhc---CcccCCCCcCHHHHHHHHHHHH
Confidence 44545554434 4566666666666666655444
No 123
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=20.53 E-value=2.3e+02 Score=19.69 Aligned_cols=39 Identities=15% Similarity=0.266 Sum_probs=26.6
Q ss_pred HHHHHhhC-CCchHHHHHHhCCCCHHHHHHHHHHhhcCCC
Q 026896 191 LLLGIWSE-KESAGHKILATLGFNDEKAKEIAKSVSSRSY 229 (231)
Q Consensus 191 LLLALl~d-~~~~~~~iL~~lGvd~~~l~e~l~~i~~~~~ 229 (231)
+|-.+.+. +.....++-+.+|++...+.+.++.+.+.||
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~ 49 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGY 49 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCC
Confidence 33334333 2355567888889999999988888776654
No 124
>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=20.43 E-value=1.8e+02 Score=22.98 Aligned_cols=33 Identities=21% Similarity=0.155 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhC
Q 026896 165 QAQRALDWAFNEKLKSGESGEITTNHLLLGIWSE 198 (231)
Q Consensus 165 ~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d 198 (231)
=+..||+.|..+|...|. ..|+.+++-+|+-.-
T Consensus 45 Yt~~vL~DA~~ya~hA~~-~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 45 YTSDVLEDAQVYADHAGR-STIDADDVRLAIQSR 77 (129)
T ss_dssp HHHHHHHHHHHHHHHTT--SSB-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHhccc-ccCChHHHHHHHHHH
Confidence 367899999999999999 999999999998744
No 125
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=20.22 E-value=3e+02 Score=24.94 Aligned_cols=56 Identities=14% Similarity=0.020 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCCCchHHHHHHhCCCCHHHHHHHHH
Q 026896 166 AQRALDWAFNEKLKSGESGEITTNHLLLGIWSEKESAGHKILATLGFNDEKAKEIAK 222 (231)
Q Consensus 166 l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~~~~~~~iL~~lGvd~~~l~e~l~ 222 (231)
+..++..|...|...|. ..|+.+|+-.|+-.-........+..+......+...+.
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 34667777778887787 889999998777654444445556655544444444433
No 126
>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=20.19 E-value=3.4e+02 Score=19.50 Aligned_cols=70 Identities=13% Similarity=-0.020 Sum_probs=43.9
Q ss_pred HHHHHHHcCCChHHHHHHHHHHhcCCCCcCCCCCCCccCHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhhCC
Q 026896 125 TAKFLRANGITLFKVREETLNLLGKSDLFFFSPERPPLTEQAQRALDWAFNEKLKSGESGEITTNHLLLGIWSEK 199 (231)
Q Consensus 125 a~kiL~~~gid~~~lr~~l~~~L~~~~~~~~~~~~~~~S~~l~~vLe~A~~~A~~~g~~~~I~teHLLLALl~d~ 199 (231)
..++-+.+||+...|+.....-+-. +.. ...+.-.|+.+--..+........ .|- +.-...+++ ..+..+
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gll~-~~~-~~~g~r~y~~~dv~~l~~i~~l~~-~g~-~~~~i~~~l-~~~~~~ 72 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGLLP-PER-SENGYRLYSEEDLERLRLIRRLRE-LGL-SLKEIRELL-DARDEE 72 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcC-CCc-CCCCCcccCHHHHHHHHHHHHHHH-cCC-CHHHHHHHH-hccccc
Confidence 3567778899999999887655433 222 123556788888777777776555 666 444444444 444443
No 127
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.10 E-value=1.6e+02 Score=21.17 Aligned_cols=29 Identities=14% Similarity=0.116 Sum_probs=22.2
Q ss_pred hHHHHHHhCCCCHHHHHHHHHHhhcCCCC
Q 026896 202 AGHKILATLGFNDEKAKEIAKSVSSRSYD 230 (231)
Q Consensus 202 ~~~~iL~~lGvd~~~l~e~l~~i~~~~~~ 230 (231)
...++...+|++...+...++.....|++
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~ 42 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIE 42 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHH
Confidence 35678888888888888888887776643
No 128
>PLN00035 histone H4; Provisional
Probab=20.03 E-value=2.2e+02 Score=21.72 Aligned_cols=37 Identities=5% Similarity=-0.067 Sum_probs=30.7
Q ss_pred hcHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHhccC
Q 026896 85 WSARAIRSFAMAELEARKLKYPNTGTEAFLMGILVEG 121 (231)
Q Consensus 85 fT~~a~~vl~~A~~~A~~~~~~~I~~eHLLlaLL~~~ 121 (231)
+...+.+++..|..+|...+-.+|+.+.+.++|=..+
T Consensus 59 le~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 59 LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 4566778889999999999999999999998875443
Done!