Query 038657
Match_columns 112
No_of_seqs 102 out of 186
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 13:17:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038657hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4068 Uncharacterized conser 100.0 3.9E-48 8.4E-53 286.5 12.6 110 1-111 65-174 (174)
2 PF05871 ESCRT-II: ESCRT-II co 100.0 6.9E-38 1.5E-42 227.7 6.9 80 1-80 60-139 (139)
3 KOG4068 Uncharacterized conser 91.4 0.59 1.3E-05 35.4 5.4 60 37-98 27-87 (174)
4 PF05158 RNA_pol_Rpc34: RNA po 90.9 0.57 1.2E-05 38.4 5.4 58 36-101 6-63 (327)
5 PF05871 ESCRT-II: ESCRT-II co 88.1 0.71 1.5E-05 33.7 3.5 55 37-98 22-82 (139)
6 PF05158 RNA_pol_Rpc34: RNA po 87.0 4.3 9.4E-05 33.2 7.9 88 2-100 39-135 (327)
7 PF10309 DUF2414: Protein of u 81.3 4.6 9.9E-05 25.7 4.6 41 2-44 16-59 (62)
8 PF00392 GntR: Bacterial regul 81.1 4.4 9.6E-05 24.7 4.4 51 41-99 6-58 (64)
9 KOG3233 RNA polymerase III, su 80.4 13 0.00029 30.4 8.0 80 2-93 39-128 (297)
10 cd01319 AMPD AMP deaminase (AM 78.5 7 0.00015 34.0 6.2 45 4-55 165-211 (496)
11 cd03527 RuBisCO_small Ribulose 76.1 5.5 0.00012 27.6 4.0 37 2-38 12-53 (99)
12 PF09012 FeoC: FeoC like trans 76.0 3 6.5E-05 26.1 2.6 25 1-25 25-49 (69)
13 CHL00130 rbcS ribulose-1,5-bis 75.2 6.1 0.00013 29.1 4.3 36 2-37 14-54 (138)
14 PF13182 DUF4007: Protein of u 74.8 19 0.0004 28.8 7.4 66 36-102 199-265 (286)
15 TIGR01429 AMP_deaminase AMP de 74.8 9.9 0.00022 34.0 6.2 57 4-67 276-341 (611)
16 COG4901 Ribosomal protein S25 73.0 5.2 0.00011 28.2 3.3 56 37-100 39-94 (107)
17 PLN02768 AMP deaminase 69.8 13 0.00029 34.4 6.0 59 4-69 488-555 (835)
18 PLN03055 AMP deaminase; Provis 69.3 15 0.00033 32.8 6.1 59 4-69 255-322 (602)
19 cd00103 IRF Interferon Regulat 68.4 14 0.00031 25.6 4.8 46 10-55 7-61 (107)
20 PRK11014 transcriptional repre 68.3 10 0.00022 26.7 4.1 30 73-102 33-62 (141)
21 PF04703 FaeA: FaeA-like prote 68.2 7.9 0.00017 24.5 3.1 33 2-35 27-59 (62)
22 smart00345 HTH_GNTR helix_turn 65.8 11 0.00024 21.6 3.3 27 72-98 27-53 (60)
23 PF02082 Rrf2: Transcriptional 65.4 19 0.00041 23.0 4.7 54 39-101 8-61 (83)
24 PF08784 RPA_C: Replication pr 65.1 9.3 0.0002 25.4 3.2 52 36-95 44-95 (102)
25 PTZ00310 AMP deaminase; Provis 63.8 18 0.00039 35.5 5.8 45 4-55 950-996 (1453)
26 PF09012 FeoC: FeoC like trans 63.0 7.8 0.00017 24.2 2.4 27 75-101 24-50 (69)
27 PTZ00310 AMP deaminase; Provis 62.9 21 0.00045 35.1 6.1 44 4-54 312-359 (1453)
28 cd00092 HTH_CRP helix_turn_hel 62.7 10 0.00022 22.5 2.8 51 40-98 5-58 (67)
29 PRK15431 ferrous iron transpor 60.7 14 0.0003 24.6 3.3 24 1-24 27-50 (78)
30 cd00090 HTH_ARSR Arsenical Res 60.6 31 0.00066 19.9 5.5 43 2-49 32-74 (78)
31 cd07153 Fur_like Ferric uptake 59.3 11 0.00024 25.2 2.7 54 43-102 5-58 (116)
32 PF03551 PadR: Transcriptional 58.3 7 0.00015 24.5 1.5 44 58-101 10-53 (75)
33 COG0735 Fur Fe2+/Zn2+ uptake r 57.4 21 0.00045 25.6 4.1 27 76-102 52-78 (145)
34 smart00550 Zalpha Z-DNA-bindin 57.1 25 0.00055 21.9 4.0 53 36-98 3-55 (68)
35 PF04157 EAP30: EAP30/Vps36 fa 57.0 21 0.00045 27.2 4.2 70 38-111 93-164 (223)
36 cd07377 WHTH_GntR Winged helix 56.6 12 0.00026 21.8 2.4 23 73-95 33-55 (66)
37 COG4152 ABC-type uncharacteriz 56.4 16 0.00034 30.0 3.6 64 37-100 104-187 (300)
38 PLN02289 ribulose-bisphosphate 55.6 24 0.00052 27.0 4.2 36 2-37 76-128 (176)
39 PF08679 DsrD: Dissimilatory s 54.4 32 0.00068 22.4 4.1 29 2-30 32-60 (67)
40 TIGR02328 conserved hypothetic 54.0 28 0.0006 25.1 4.1 41 53-93 77-117 (120)
41 PF01047 MarR: MarR family; I 53.7 19 0.0004 21.1 2.8 52 37-102 3-54 (59)
42 PF00101 RuBisCO_small: Ribulo 51.7 18 0.00039 24.9 2.9 36 2-37 11-51 (99)
43 smart00348 IRF interferon regu 51.1 49 0.0011 22.9 5.0 44 11-54 6-59 (107)
44 PF09106 SelB-wing_2: Elongati 51.0 12 0.00027 22.6 1.8 23 76-98 31-53 (59)
45 PF02082 Rrf2: Transcriptional 50.4 36 0.00079 21.7 4.0 38 1-39 36-73 (83)
46 PF01978 TrmB: Sugar-specific 49.8 36 0.00079 20.7 3.8 47 42-100 11-57 (68)
47 COG1959 Predicted transcriptio 48.9 28 0.00061 25.2 3.6 31 73-103 33-63 (150)
48 PF01475 FUR: Ferric uptake re 48.2 21 0.00045 24.1 2.7 54 43-102 12-65 (120)
49 PF05584 Sulfolobus_pRN: Sulfo 47.6 12 0.00025 24.7 1.3 32 57-96 18-49 (72)
50 smart00419 HTH_CRP helix_turn_ 47.4 22 0.00047 19.6 2.3 25 73-97 16-40 (48)
51 PF08970 Sda: Sporulation inhi 47.3 23 0.00049 21.4 2.4 18 1-18 20-37 (46)
52 KOG1736 Glia maturation factor 46.7 21 0.00045 26.2 2.6 37 29-69 88-131 (143)
53 PF08220 HTH_DeoR: DeoR-like h 45.7 54 0.0012 19.7 4.1 45 42-98 3-47 (57)
54 PF13730 HTH_36: Helix-turn-he 45.3 26 0.00056 20.3 2.5 20 74-93 34-53 (55)
55 PF00605 IRF: Interferon regul 43.9 54 0.0012 22.8 4.3 45 10-54 7-61 (109)
56 TIGR01610 phage_O_Nterm phage 43.1 35 0.00076 22.6 3.2 27 73-99 55-81 (95)
57 KOG1096 Adenosine monophosphat 42.8 52 0.0011 30.2 5.0 42 5-53 425-468 (768)
58 PRK15431 ferrous iron transpor 42.8 34 0.00074 22.8 3.0 25 75-99 26-50 (78)
59 PHA02825 LAP/PHD finger-like p 42.4 22 0.00047 26.8 2.2 20 44-63 142-161 (162)
60 PF08743 Nse4_C: Nse4 C-termin 42.2 28 0.00061 23.2 2.6 18 85-102 24-41 (93)
61 PF04567 RNA_pol_Rpb2_5: RNA p 41.7 27 0.00057 20.7 2.2 17 11-27 1-17 (48)
62 PF10264 Stork_head: Winged he 41.4 21 0.00046 23.9 1.8 54 40-96 12-68 (80)
63 KOG4828 Uncharacterized conser 40.5 50 0.0011 23.8 3.7 40 53-92 41-89 (125)
64 PF09098 Dehyd-heme_bind: Quin 40.4 13 0.00028 28.2 0.8 48 1-48 50-127 (167)
65 PRK11920 rirA iron-responsive 40.2 46 0.00099 24.0 3.6 30 73-102 32-61 (153)
66 TIGR01446 DnaD_dom DnaD and ph 38.8 38 0.00083 20.9 2.7 23 74-96 27-49 (73)
67 TIGR02010 IscR iron-sulfur clu 38.4 60 0.0013 22.6 3.9 38 57-102 25-62 (135)
68 PTZ00123 phosphoglycerate muta 38.3 78 0.0017 24.1 4.8 44 52-96 192-235 (236)
69 PF09339 HTH_IclR: IclR helix- 38.2 39 0.00085 19.6 2.5 30 58-95 19-48 (52)
70 PF07106 TBPIP: Tat binding pr 37.6 27 0.00059 25.3 2.1 45 42-96 4-49 (169)
71 PRK10906 DNA-binding transcrip 37.6 52 0.0011 25.6 3.8 46 41-98 7-52 (252)
72 PF08672 APC2: Anaphase promot 37.5 48 0.001 20.7 2.9 23 2-24 33-55 (60)
73 PF08679 DsrD: Dissimilatory s 37.0 38 0.00082 22.0 2.4 28 74-101 29-56 (67)
74 PF03823 Neurokinin_B: Neuroki 36.7 28 0.00061 22.0 1.8 21 67-87 36-56 (59)
75 PF13812 PPR_3: Pentatricopept 36.0 42 0.00091 16.8 2.2 16 3-18 16-31 (34)
76 TIGR02325 C_P_lyase_phnF phosp 35.7 53 0.0011 24.4 3.5 28 73-100 40-67 (238)
77 TIGR03792 uncharacterized cyan 35.4 1.1E+02 0.0024 20.7 4.6 32 18-49 37-71 (90)
78 PF12646 DUF3783: Domain of un 35.0 49 0.0011 20.2 2.7 21 74-94 6-26 (58)
79 PF07106 TBPIP: Tat binding pr 34.6 79 0.0017 22.9 4.1 32 2-35 30-61 (169)
80 COG4989 Predicted oxidoreducta 34.5 53 0.0012 26.9 3.4 26 77-102 133-158 (298)
81 COG1932 SerC Phosphoserine ami 34.0 81 0.0018 26.7 4.5 80 5-99 250-330 (365)
82 TIGR02018 his_ut_repres histid 33.3 59 0.0013 24.3 3.4 28 73-100 33-60 (230)
83 PRK11014 transcriptional repre 33.2 1E+02 0.0022 21.5 4.5 47 2-51 37-83 (141)
84 PRK10434 srlR DNA-bindng trans 32.6 91 0.002 24.2 4.5 50 38-99 4-53 (256)
85 PF02241 MCR_beta: Methyl-coen 32.6 12 0.00026 29.8 -0.5 19 42-60 62-80 (255)
86 TIGR02404 trehalos_R_Bsub treh 32.3 65 0.0014 24.1 3.5 29 73-101 32-60 (233)
87 TIGR01664 DNA-3'-Pase DNA 3'-p 32.1 1.9E+02 0.0042 20.8 6.2 88 5-100 45-135 (166)
88 smart00529 HTH_DTXR Helix-turn 32.0 50 0.0011 21.0 2.5 23 74-96 8-30 (96)
89 PRK14999 histidine utilization 32.0 63 0.0014 24.4 3.4 29 73-101 44-72 (241)
90 PRK04984 fatty acid metabolism 31.7 89 0.0019 23.3 4.2 28 74-101 40-67 (239)
91 PRK09464 pdhR transcriptional 31.4 88 0.0019 23.6 4.1 28 73-100 42-69 (254)
92 TIGR03433 padR_acidobact trans 31.2 24 0.00053 23.5 0.9 40 59-98 19-58 (100)
93 PF11334 DUF3136: Protein of u 31.0 45 0.00098 21.5 2.0 16 80-95 11-26 (64)
94 PF15581 Imm35: Immunity prote 30.8 54 0.0012 22.6 2.5 53 58-110 16-83 (93)
95 COG2188 PhnF Transcriptional r 30.8 76 0.0016 24.2 3.7 30 73-102 39-68 (236)
96 TIGR00683 nanA N-acetylneurami 30.5 2.4E+02 0.0052 22.2 6.6 51 1-53 17-69 (290)
97 COG4451 RbcS Ribulose bisphosp 30.4 1E+02 0.0022 22.3 4.0 36 2-37 19-59 (127)
98 PF02295 z-alpha: Adenosine de 29.9 1.3E+02 0.0028 18.9 4.1 51 38-98 3-53 (66)
99 PTZ00095 40S ribosomal protein 29.9 1.1E+02 0.0023 23.3 4.2 94 4-97 34-137 (169)
100 PF08221 HTH_9: RNA polymerase 29.6 1E+02 0.0023 18.9 3.6 46 41-98 15-60 (62)
101 PRK09764 DNA-binding transcrip 29.6 79 0.0017 23.9 3.6 29 73-101 37-65 (240)
102 KOG0481 DNA replication licens 29.4 32 0.0007 31.0 1.5 24 75-98 696-719 (729)
103 PRK10079 phosphonate metabolis 28.3 79 0.0017 23.8 3.4 28 73-100 43-70 (241)
104 PF01193 RNA_pol_L: RNA polyme 28.2 39 0.00086 20.8 1.4 15 78-92 50-64 (66)
105 PF12039 DUF3525: Protein of u 27.6 76 0.0017 26.6 3.3 41 5-46 315-357 (453)
106 PF14394 DUF4423: Domain of un 27.4 1.7E+02 0.0038 21.5 5.0 63 1-91 52-114 (171)
107 TIGR00288 conserved hypothetic 27.1 2.7E+02 0.0058 20.7 8.7 60 7-90 43-102 (160)
108 PRK10857 DNA-binding transcrip 27.0 90 0.0019 22.9 3.4 37 57-101 25-61 (164)
109 PF03428 RP-C: Replication pro 27.0 1.1E+02 0.0025 22.9 4.0 33 72-104 78-110 (177)
110 PRK03837 transcriptional regul 26.6 1E+02 0.0023 22.8 3.7 29 73-101 45-73 (241)
111 TIGR02944 suf_reg_Xantho FeS a 26.5 1E+02 0.0023 21.0 3.5 51 39-99 9-59 (130)
112 PF05378 Hydant_A_N: Hydantoin 26.2 1.1E+02 0.0023 22.6 3.7 36 58-93 112-147 (176)
113 CHL00128 psbW photosystem II p 25.9 2.1E+02 0.0046 20.4 4.9 26 29-54 81-109 (113)
114 PRK11460 putative hydrolase; P 25.7 2.9E+02 0.0062 20.7 6.2 47 36-92 162-208 (232)
115 PRK10225 DNA-binding transcrip 25.7 1.2E+02 0.0026 22.9 4.0 28 73-100 41-68 (257)
116 PF14177 YkyB: YkyB-like prote 25.6 64 0.0014 23.8 2.3 18 82-99 29-46 (140)
117 TIGR00498 lexA SOS regulatory 25.6 1.2E+02 0.0026 22.2 3.8 58 43-111 10-69 (199)
118 TIGR03047 PS_II_psb28 photosys 25.3 2.2E+02 0.0047 20.2 4.8 26 29-54 78-106 (109)
119 PRK03902 manganese transport t 25.3 1E+02 0.0022 21.5 3.3 49 36-96 5-53 (142)
120 PRK09333 30S ribosomal protein 25.3 57 0.0012 24.2 2.0 93 4-96 10-112 (150)
121 PF00488 MutS_V: MutS domain V 25.1 1.3E+02 0.0029 23.0 4.1 38 54-91 189-231 (235)
122 PF13463 HTH_27: Winged helix 25.0 1.5E+02 0.0033 17.3 4.1 30 73-102 26-55 (68)
123 TIGR03257 met_CoM_red_bet meth 24.8 32 0.00069 29.4 0.7 45 42-86 246-302 (433)
124 PF11735 CAP59_mtransfer: Cryp 24.7 2.7E+02 0.0059 21.9 5.9 53 37-99 16-69 (241)
125 PF12802 MarR_2: MarR family; 24.6 1.5E+02 0.0033 17.0 4.1 29 73-101 29-57 (62)
126 COG2186 FadR Transcriptional r 24.6 82 0.0018 24.2 2.9 56 36-101 11-70 (241)
127 smart00667 LisH Lissencephaly 24.2 90 0.0019 15.6 2.2 16 4-19 4-19 (34)
128 PF13558 SbcCD_C: Putative exo 24.1 82 0.0018 20.5 2.4 22 70-91 69-90 (90)
129 PRK13612 photosystem II reacti 24.0 2.4E+02 0.0052 20.1 4.9 26 29-54 81-109 (113)
130 PF14947 HTH_45: Winged helix- 23.6 86 0.0019 19.9 2.4 22 74-95 28-49 (77)
131 PF01638 HxlR: HxlR-like helix 23.4 89 0.0019 20.2 2.5 25 74-98 28-52 (90)
132 PLN00039 photosystem II reacti 23.4 2.5E+02 0.0054 19.9 4.9 26 29-54 79-107 (111)
133 PRK13611 photosystem II reacti 23.0 2.7E+02 0.0058 19.6 4.9 25 29-53 74-101 (104)
134 PF02230 Abhydrolase_2: Phosph 23.0 2.5E+02 0.0054 20.5 5.1 46 36-91 169-214 (216)
135 KOG1572 Predicted protein tyro 22.9 2E+02 0.0044 23.1 4.8 63 30-97 87-151 (249)
136 PF03445 DUF294: Putative nucl 22.8 1.4E+02 0.0031 20.9 3.7 47 6-52 90-136 (138)
137 smart00344 HTH_ASNC helix_turn 22.4 2.3E+02 0.0049 18.3 5.9 63 2-67 29-99 (108)
138 TIGR01232 lacD tagatose 1,6-di 22.3 3E+02 0.0065 23.0 5.9 73 29-101 124-206 (325)
139 PRK11402 DNA-binding transcrip 22.3 1.3E+02 0.0028 22.6 3.6 28 73-100 41-68 (241)
140 PRK11512 DNA-binding transcrip 22.3 90 0.002 21.6 2.5 29 73-101 62-90 (144)
141 PF08777 RRM_3: RNA binding mo 22.2 2.1E+02 0.0045 19.4 4.3 59 8-68 16-81 (105)
142 TIGR03338 phnR_burk phosphonat 22.2 1.3E+02 0.0027 22.0 3.4 28 73-100 42-69 (212)
143 PRK12399 tagatose 1,6-diphosph 22.2 3.2E+02 0.0068 22.8 6.0 72 29-100 123-204 (324)
144 COG1846 MarR Transcriptional r 22.0 97 0.0021 19.7 2.5 30 72-101 43-72 (126)
145 PF03492 Methyltransf_7: SAM d 22.0 91 0.002 25.4 2.8 42 5-46 201-242 (334)
146 PF00325 Crp: Bacterial regula 21.9 1.2E+02 0.0027 16.6 2.5 21 73-93 10-30 (32)
147 PF13545 HTH_Crp_2: Crp-like h 21.9 1.3E+02 0.0029 18.1 3.0 54 41-97 4-60 (76)
148 PRK09334 30S ribosomal protein 21.7 2.3E+02 0.005 19.1 4.3 31 2-33 53-83 (86)
149 PF08513 LisH: LisH; InterPro 21.6 61 0.0013 16.8 1.2 15 42-56 5-19 (27)
150 COG2996 Predicted RNA-bindinin 21.5 2.3E+02 0.0049 23.3 4.9 54 36-97 222-278 (287)
151 PF00646 F-box: F-box domain; 21.3 35 0.00076 19.0 0.2 17 74-90 3-19 (48)
152 COG5111 RPC34 DNA-directed RNA 21.2 1.3E+02 0.0029 24.4 3.5 48 36-93 82-129 (301)
153 PF03297 Ribosomal_S25: S25 ri 21.2 1.6E+02 0.0034 20.5 3.5 33 2-35 71-103 (105)
154 PF12793 SgrR_N: Sugar transpo 21.1 2.4E+02 0.0052 19.5 4.5 55 2-56 31-88 (115)
155 cd03284 ABC_MutS1 MutS1 homolo 21.0 1.2E+02 0.0026 22.8 3.2 37 53-89 175-216 (216)
156 PF13511 DUF4124: Domain of un 21.0 5.9 0.00013 23.8 -3.4 16 38-53 9-24 (60)
157 smart00347 HTH_MARR helix_turn 20.7 2.2E+02 0.0047 17.5 5.5 24 2-25 36-59 (101)
158 PF01535 PPR: PPR repeat; Int 20.4 1.1E+02 0.0023 14.7 2.0 15 4-18 16-30 (31)
159 PRK11534 DNA-binding transcrip 20.2 2.2E+02 0.0048 21.0 4.4 28 73-100 38-65 (224)
160 PF13412 HTH_24: Winged helix- 20.2 1.3E+02 0.0028 16.8 2.5 23 73-95 25-47 (48)
161 COG0174 GlnA Glutamine synthet 20.2 1.5E+02 0.0032 25.5 3.8 34 57-96 92-125 (443)
No 1
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.9e-48 Score=286.52 Aligned_cols=110 Identities=34% Similarity=0.621 Sum_probs=107.6
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHH
Q 038657 1 SLNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRT 80 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~ 80 (112)
+||++++++|+++|.++|+|+|+|+++++++||||+|+|||++||+|+.++|++|||||||||++||+|..+||||||+.
T Consensus 65 ~Ls~~~i~~Il~~l~k~g~~e~~Dk~rt~f~I~Wrs~dewgnmIyqW~~dsg~~nti~TlYElt~Gddt~~~efh~lde~ 144 (174)
T KOG4068|consen 65 RLSQEFIDEILEELEKKGLAEPTDKRRTRFFIYWRSLDEWGNMIYQWVSDSGQLNTICTLYELTEGDDTVNEEFHGLDEA 144 (174)
T ss_pred cCCHHHHHHHHHHHHHccCCcccccCceEEEEEEcCHHHHHHHHHHHHHHcCcCCCceEEEEeccCCcccchhhcCccHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCceeEEecCCCCCcceEEc
Q 038657 81 ILMRALKLLEHKGKVAIFKGTSADDEGVKFS 111 (112)
Q Consensus 81 vL~kaL~~L~k~gkAql~~~~~~~~~GVKf~ 111 (112)
+|.|||+.|+++|||++|++++ +..|||||
T Consensus 145 lL~~aL~~L~ek~raelm~~~~-~~~gvKf~ 174 (174)
T KOG4068|consen 145 LLLKALKLLEEKGRAELMKDSN-KVIGVKFF 174 (174)
T ss_pred HHHHHHHHHHhcCceeEeecCC-CceeEEeC
Confidence 9999999999999999999886 57899997
No 2
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=100.00 E-value=6.9e-38 Score=227.67 Aligned_cols=80 Identities=39% Similarity=0.769 Sum_probs=72.0
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHH
Q 038657 1 SLNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRT 80 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~ 80 (112)
|||++++++|+++|+++|+|+|+|+++++|+||||||+|||++||+||++||++|||||||||++||++.++||||||++
T Consensus 60 ~L~~e~~~~Il~~Lv~~g~aew~~~~~~~~~I~Wrt~~eWa~~I~~Wv~~~G~~gtV~TlyEL~~Gd~t~~~ef~gm~~~ 139 (139)
T PF05871_consen 60 RLSPEFIREILDELVQKGNAEWIDKSKTRCLIYWRTPEEWADLIYDWVESTGQLGTVCTLYELTEGDDTEGEEFHGMDEE 139 (139)
T ss_dssp E--HHHHHHHHHHHHCTTSEEECSTTSCEEEE-SS-HHHHHHHHHHHHHCCTTTTSEEEHHHHHCTTTTTTSTTTT--H-
T ss_pred CCCHHHHHHHHHHHHhcCCeEEeeCCCCEEEEEeCCHHHHHHHHHHHHHhCCCCCCeEEehhcccCCCCCCccccCCCCC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999975
No 3
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.43 E-value=0.59 Score=35.38 Aligned_cols=60 Identities=22% Similarity=0.385 Sum_probs=43.2
Q ss_pred hHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccc-cCCCHHHHHHHHHHHHhcCceeEE
Q 038657 37 IQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTEL-HGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef-~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
.+-|+++|.+|+..+.+ +-||+-|-++...=.++.. .-+|.+++...|.-|+|+|+|+-.
T Consensus 27 l~aW~~lil~ycr~~k~--~smsI~~~~~s~LfnN~~l~R~Ls~~~i~~Il~~l~k~g~~e~~ 87 (174)
T KOG4068|consen 27 LAAWIDLILQYCRHNKI--WSMSIDEAQESPLFNNEKLQRRLSQEFIDEILEELEKKGLAEPT 87 (174)
T ss_pred HHHHHHHHHHHHHhcCe--EEEEecchhcccccchHHHhccCCHHHHHHHHHHHHHccCCccc
Confidence 57899999999999876 3355544333322222222 248999999999999999999877
No 4
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=90.94 E-value=0.57 Score=38.35 Aligned_cols=58 Identities=17% Similarity=0.339 Sum_probs=45.4
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
++.+.++.||+.+.+. ..+...|.-+|.+. |-++|...+..||+.|.++|+.++++..
T Consensus 6 ~~~~~~~~l~~~~~~~-~~~~~~~~~~L~~~-------~~~~~~~~~~~~in~Ll~~~~~~~~~~~ 63 (327)
T PF05158_consen 6 KLSELEKKLLELCREN-PSPKGFSQEDLQQL-------IPGLDLQELVKAINELLSSGLLKLLKKG 63 (327)
T ss_dssp -HHHHHHHHHHHHHH----SS-EEHHHHHHH--------TTS-HHHHHHHHHHHHHHTSEEEEE-S
T ss_pred hHHHHHHHHHHHHHHh-cCCCCcCHHHHHhh-------cCCCCHHHHHHHHHHHHhCCCEEEEEcC
Confidence 5788999999999999 77788888888754 7789999999999999999999999843
No 5
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=88.10 E-value=0.71 Score=33.66 Aligned_cols=55 Identities=16% Similarity=0.362 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCcccc------CCCHHHHHHHHHHHHhcCceeEE
Q 038657 37 IQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELH------GMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~------gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
.+.|+++|.+|+..+..- .+.+-|..+ ..=|+ .|+++.++..|+.|+++|+|+-.
T Consensus 22 l~~W~~lIl~y~~~~k~~--~l~~~e~~~-----~~lF~N~~I~R~L~~e~~~~Il~~Lv~~g~aew~ 82 (139)
T PF05871_consen 22 LELWSDLILDYCRHHKIF--RLSLSEALE-----SPLFNNESINRRLSPEFIREILDELVQKGNAEWI 82 (139)
T ss_dssp HHHHHHHHHHHHHHTT-S--EEECHHHHC-----CCTTEETTTTEE--HHHHHHHHHHHHCTTSEEEC
T ss_pred HHHHHHHHHHHHHHhcee--eeecccccC-----CCCccCccccCCCCHHHHHHHHHHHHhcCCeEEe
Confidence 578999999999977652 333333332 23354 48999999999999999999998
No 6
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=87.05 E-value=4.3 Score=33.24 Aligned_cols=88 Identities=20% Similarity=0.230 Sum_probs=56.8
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChH---------HHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCc
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQ---------DWADIILGFVKDNGLEDSVMTVEEIRLGIESRGT 72 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~---------eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ 72 (112)
++.+.+..+++.|.++|+..-...+. ....-+++++ .=..+||+-+++.|..|- ..=+|..
T Consensus 39 ~~~~~~~~~in~Ll~~~~~~~~~~~~-~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GI--w~~~i~~------- 108 (327)
T PF05158_consen 39 LDLQELVKAINELLSSGLLKLLKKGG-GLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAGNKGI--WTKDIKK------- 108 (327)
T ss_dssp S-HHHHHHHHHHHHHHTSEEEEE-SS-SEEEEE--SSS-----SSSCCHHHHHHHHHHHTTT-E--EHHHHHH-------
T ss_pred CCHHHHHHHHHHHHhCCCEEEEEcCC-EEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCC--cHHHHHH-------
Confidence 46778899999999999988776443 3222244222 223499999999998872 1222222
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
=-|||..+|.|+|+.|+.++-..=++.
T Consensus 109 -~t~l~~~~~~k~lk~Le~k~lIK~vks 135 (327)
T PF05158_consen 109 -KTNLHQTQLTKILKSLESKKLIKSVKS 135 (327)
T ss_dssp -HCT--HHHHHHHHHHHHHTTSEEEE--
T ss_pred -HcCCCHHHHHHHHHHHHhCCCEEEecC
Confidence 246999999999999999997777665
No 7
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=81.29 E-value=4.6 Score=25.72 Aligned_cols=41 Identities=20% Similarity=0.464 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHh---cCCeeEecCCCcEEEEEecChHHHHHHH
Q 038657 2 LNNEARETFLSALVS---EGRAEWLDKGHRKCLILWHRIQDWADII 44 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~---~g~aew~d~~~~~~~I~Wr~~~eWa~~I 44 (112)
||.+.|...+.+-.. -.+.||+|.. +|-|.|.+++.=+..+
T Consensus 16 lsT~dI~~y~~~y~~~~~~~~IEWIdDt--ScNvvf~d~~~A~~AL 59 (62)
T PF10309_consen 16 LSTDDIKAYFSEYFDEEGPFRIEWIDDT--SCNVVFKDEETAARAL 59 (62)
T ss_pred CCHHHHHHHHHHhcccCCCceEEEecCC--cEEEEECCHHHHHHHH
Confidence 678888888877732 3579999987 7999999987644443
No 8
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=81.13 E-value=4.4 Score=24.72 Aligned_cols=51 Identities=24% Similarity=0.268 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcCC-CCceE-EeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEe
Q 038657 41 ADIILGFVKDNGL-EDSVM-TVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 41 a~~Iy~Wv~~tG~-~~tV~-TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~ 99 (112)
++.|.+++.+... -|+-+ |.-+|. +-+|+.....++||+.|+++|-.+...
T Consensus 6 ~~~l~~~I~~g~~~~g~~lps~~~la--------~~~~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 6 YDQLRQAILSGRLPPGDRLPSERELA--------ERYGVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp HHHHHHHHHTTSS-TTSBE--HHHHH--------HHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHcCCCCCCCEeCCHHHHH--------HHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence 4445555554433 33444 444444 459999999999999999999998873
No 9
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=80.42 E-value=13 Score=30.40 Aligned_cols=80 Identities=21% Similarity=0.349 Sum_probs=56.8
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEec-ChHH---------HHHHHHHHHHhcCCCCceEEeeeeccCCCcCC
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWH-RIQD---------WADIILGFVKDNGLEDSVMTVEEIRLGIESRG 71 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr-~~~e---------Wa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~ 71 (112)
+|...+...++.|.++|...-...+ .-.+|-+ .|.+ =-.++|+.++++|..| .+..||..+
T Consensus 39 ~~~~~~~salN~lLs~~~l~llr~~--~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe~sg~~G--IW~k~ik~k----- 109 (297)
T KOG3233|consen 39 ISATDRASALNILLSRGLLDLLRQN--TGLVYRAKDPKSASKGKGMENEEKLVYSLIEESGNEG--IWSKEIKRK----- 109 (297)
T ss_pred CcHHHHHHHHHHHHhcCcchhhccC--CcceEeccCchhhcccccCChHHHHHHHHHHHcCCCc--eeeehhhhc-----
Confidence 4666777788888888766554332 1223322 2333 1248999999999988 577888866
Q ss_pred ccccCCCHHHHHHHHHHHHhcC
Q 038657 72 TELHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 72 ~ef~gmd~~vL~kaL~~L~k~g 93 (112)
.|||..++.|+|+.|+++.
T Consensus 110 ---snLp~~~v~K~LkSLEsKk 128 (297)
T KOG3233|consen 110 ---SNLPQTVVNKILKSLESKK 128 (297)
T ss_pred ---cCCCHHHHHHHHHHHHHHH
Confidence 5799999999999999876
No 10
>cd01319 AMPD AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.
Probab=78.52 E-value=7 Score=34.01 Aligned_cols=45 Identities=24% Similarity=0.345 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHhcCC--eeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCC
Q 038657 4 NEARETFLSALVSEGR--AEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLED 55 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~--aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~ 55 (112)
.+.++++++.+.+++. ||| |.-||=|+++||. .+-+|+.++|...
T Consensus 165 Ael~k~v~~~le~~kyq~~E~------rlsiyG~~~~Ew~-~lA~W~~~~~l~s 211 (496)
T cd01319 165 AEITKEVFSDLEESKYQHAEY------RLSIYGRSKDEWD-KLASWVVDNDLFS 211 (496)
T ss_pred HHHHHHHHHHHHhccceeEEE------EEEEeCCCHHHHH-HHHHHHHHcCCCC
Confidence 4678899999998854 777 7899999999996 5789999999843
No 11
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=76.08 E-value=5.5 Score=27.58 Aligned_cols=37 Identities=19% Similarity=0.409 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhcCC---eeEecCCC--cEEEEEecChH
Q 038657 2 LNNEARETFLSALVSEGR---AEWLDKGH--RKCLILWHRIQ 38 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~---aew~d~~~--~~~~I~Wr~~~ 38 (112)
|+.+.+..=+++|+++|- +|+.|+.+ +++|-+|+-|.
T Consensus 12 lt~~~i~~QI~yll~qG~~~~lE~ad~~~~~~~yW~mwklP~ 53 (99)
T cd03527 12 LTDEQIAKQIDYIISNGWAPCLEFTEPEHYDNRYWTMWKLPM 53 (99)
T ss_pred CCHHHHHHHHHHHHhCCCEEEEEcccCCCCCCCEEeeccCCC
Confidence 788899999999999996 67777765 67888888775
No 12
>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=76.04 E-value=3 Score=26.09 Aligned_cols=25 Identities=28% Similarity=0.416 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEecC
Q 038657 1 SLNNEARETFLSALVSEGRAEWLDK 25 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d~ 25 (112)
.+|++.++.+|+.|+++|+++-.+.
T Consensus 25 ~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 25 GISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred CcCHHHHHHHHHHHHHCCcEEEecC
Confidence 3789999999999999999886654
No 13
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=75.18 E-value=6.1 Score=29.06 Aligned_cols=36 Identities=28% Similarity=0.489 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHhcCC---eeEecCCC--cEEEEEecCh
Q 038657 2 LNNEARETFLSALVSEGR---AEWLDKGH--RKCLILWHRI 37 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~---aew~d~~~--~~~~I~Wr~~ 37 (112)
|+.+.|..=+++++++|- .|+.++++ .++|-+|+-|
T Consensus 14 LTdeqI~kQI~Y~i~~GW~p~iEft~~~~~~~~YW~MWkLP 54 (138)
T CHL00130 14 LTDQQIEKQIQYAISKGWALNVEWTDDPHPRNSYWELWGLP 54 (138)
T ss_pred CCHHHHHHHHHHHHhcCCeEEEEecCCCCcCccEEeeeCCc
Confidence 788999999999999995 67766655 5799999876
No 14
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=74.80 E-value=19 Score=28.83 Aligned_cols=66 Identities=17% Similarity=0.211 Sum_probs=55.9
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhc-CceeEEecCC
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHK-GKVAIFKGTS 102 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~-gkAql~~~~~ 102 (112)
+|.--+..|+++++........++|-+|..++.+.+ -..+||++-|.+.|..|++. |..++-...+
T Consensus 199 ~~~i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPG-riF~L~~~~l~~~L~~l~~~~g~i~~~~TaG 265 (286)
T PF13182_consen 199 PPEIFLYALLDFAERESPGRNSISFDELLNEPGSPG-RIFKLDEESLAERLEQLEEIYGFISWSDTAG 265 (286)
T ss_pred CHHHHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcc-eEeccCHHHHHHHHHHHHhhcCcEEEEEcCC
Confidence 457778999999988888888999999999886655 56689999999999999999 8888774443
No 15
>TIGR01429 AMP_deaminase AMP deaminase. This model describes AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the region included in the model.
Probab=74.76 E-value=9.9 Score=33.98 Aligned_cols=57 Identities=14% Similarity=0.168 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHhcCC--eeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCC-------ceEEeeeeccCC
Q 038657 4 NEARETFLSALVSEGR--AEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLED-------SVMTVEEIRLGI 67 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~--aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~-------tV~TlyEL~~Gd 67 (112)
.+.++++++.+.+++. ||| |.-||=|+++||. .+-+|+.++|... +|--+|.+..+.
T Consensus 276 Aelik~v~~~le~skyQ~~E~------rlsiyG~~~~EW~-kLA~W~~~~~l~s~n~rW~IqiPRly~v~k~~ 341 (611)
T TIGR01429 276 AELVKEVFTDLEDSKYQYAEP------RLSIYGRSPKEWD-SLARWIIDHDVFSPNVRWLIQVPRLYDVYRSK 341 (611)
T ss_pred HHHHHHHHHHHHhcCceeEEE------EEEEeCCCHHHHH-HHHHHHHHcCCCCCCccEEEEcchhHHHHhcC
Confidence 4678899999998864 777 7899999999996 5789999998743 355566664443
No 16
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=73.03 E-value=5.2 Score=28.21 Aligned_cols=56 Identities=16% Similarity=0.208 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 37 IQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
...-...+++=+..-=..-+|.|.|.|.+- +|+.-.+-+++|+.|+++|=.+++..
T Consensus 39 av~vdee~~~ki~KEV~~~r~VTpy~la~r--------~gI~~SvAr~vLR~LeeeGvv~lvsk 94 (107)
T COG4901 39 AVTVDEELLDKIRKEVPRERVVTPYVLASR--------YGINGSVARIVLRHLEEEGVVQLVSK 94 (107)
T ss_pred hhhccHHHHHHHHHhcccceeecHHHHHHH--------hccchHHHHHHHHHHHhCCceeeecc
Confidence 344456778888888889999999999854 88999999999999999999999854
No 17
>PLN02768 AMP deaminase
Probab=69.84 E-value=13 Score=34.36 Aligned_cols=59 Identities=15% Similarity=0.257 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHhcCC--eeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCC-------ceEEeeeeccCCCc
Q 038657 4 NEARETFLSALVSEGR--AEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLED-------SVMTVEEIRLGIES 69 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~--aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~-------tV~TlyEL~~Gd~t 69 (112)
.+.++++++.+.+++. ||| |.-||=|+++||. .+-+|+.++|... +|.-+|.+-.+...
T Consensus 488 AELiK~V~~dlE~sKyQ~aE~------RlsIYGr~~~EW~-kLA~W~v~~~l~S~nvRWlIQIPRlY~i~k~~g~ 555 (835)
T PLN02768 488 AELTKQVFSDLEASKYQMAEY------RISIYGRKQSEWD-QLASWIVNNELYSENVVWLIQLPRLYNVYKEMGI 555 (835)
T ss_pred HHHHHHHHHHHHhccceeeEE------EEEecCCCHHHHH-HHHHHHHHcCCCCCCceEEEEcccchhhhhcCCc
Confidence 4668889999998754 777 7889999999996 5789999999743 46677777766644
No 18
>PLN03055 AMP deaminase; Provisional
Probab=69.26 E-value=15 Score=32.78 Aligned_cols=59 Identities=15% Similarity=0.256 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHhcC--CeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCC-------ceEEeeeeccCCCc
Q 038657 4 NEARETFLSALVSEG--RAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLED-------SVMTVEEIRLGIES 69 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g--~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~-------tV~TlyEL~~Gd~t 69 (112)
.+.++++++.+.+++ .||| |.-||=|+++||. .+-+|+.++|... +|.-+|.+..+...
T Consensus 255 Ael~k~v~~~le~skyQ~~E~------rlsiYG~~~~EW~-kLA~W~~~~~l~s~n~rW~IqiPRly~~~~~~g~ 322 (602)
T PLN03055 255 AELTKEVFSDLEASKYQMAEY------RISIYGRKQSEWD-QLASWIVNNRLYSENVVWLIQLPRLYNVYKEMGI 322 (602)
T ss_pred HHHHHHHHHHHHhccceeEEE------EEEEeCCCHHHHH-HHHHHHHHcCcCCCCceEEEecCcchhhhhcCCC
Confidence 456788999998885 4777 7899999999996 5789999999743 35556666665543
No 19
>cd00103 IRF Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Probab=68.43 E-value=14 Score=25.60 Aligned_cols=46 Identities=24% Similarity=0.440 Sum_probs=36.7
Q ss_pred HHHHHHhcCC---eeEecCCCcEEEEEecC------hHHHHHHHHHHHHhcCCCC
Q 038657 10 FLSALVSEGR---AEWLDKGHRKCLILWHR------IQDWADIILGFVKDNGLED 55 (112)
Q Consensus 10 Il~~lv~~g~---aew~d~~~~~~~I~Wr~------~~eWa~~Iy~Wv~~tG~~~ 55 (112)
=|-..+.+|+ ..|+|..++.+.|=|+. .++=+.+.-+|+..+|.-.
T Consensus 7 WL~~~i~sg~ypGL~W~d~ek~~FrIPWkh~~~~~~~e~d~~iFkawa~~~Gk~~ 61 (107)
T cd00103 7 WLVEQVDSGTYPGLIWLDEEKTIFRIPWKHAARHDVQEADAKIFKAWAVERGIYQ 61 (107)
T ss_pred HHHHHhccCCCCCCeEecCCCCEEECCCccCcccCcchhhhHHHHHHHHHhCCCC
Confidence 3445555654 89999999999999984 4577899999999999853
No 20
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=68.30 E-value=10 Score=26.72 Aligned_cols=30 Identities=23% Similarity=0.509 Sum_probs=26.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
+-.|+|++.++|+|+.|.+.|=.+...+.+
T Consensus 33 ~~~~is~~~vrk~l~~L~~~Glv~s~~G~~ 62 (141)
T PRK11014 33 EVYGVSRNHMVKIINQLSRAGYVTAVRGKN 62 (141)
T ss_pred HHHCcCHHHHHHHHHHHHhCCEEEEecCCC
Confidence 458999999999999999999888886654
No 21
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=68.23 E-value=7.9 Score=24.48 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEec
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWH 35 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr 35 (112)
+|.-.++-.|+.|.+.|.++-.+.++... .|||
T Consensus 27 ls~~~aR~yL~~Le~eG~V~~~~~~rG~~-~~W~ 59 (62)
T PF04703_consen 27 LSIYQARYYLEKLEKEGKVERSPVRRGKS-TYWR 59 (62)
T ss_dssp S-HHHHHHHHHHHHHCTSEEEES-SSSSS--EEE
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCCCcc-eeee
Confidence 57778899999999999999766544333 4786
No 22
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=65.80 E-value=11 Score=21.57 Aligned_cols=27 Identities=33% Similarity=0.338 Sum_probs=22.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 72 TELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 72 ~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
.+.+|+..+-+.++|+.|+++|-....
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 367899999999999999999975543
No 23
>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=65.37 E-value=19 Score=23.01 Aligned_cols=54 Identities=22% Similarity=0.286 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 39 DWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 39 eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+.|=.+.-++-..+..+ .+|.-||.+ -.++|+..+.+.++.|++.|=.+-.+|.
T Consensus 8 ~~Al~~l~~la~~~~~~-~~s~~eiA~--------~~~i~~~~l~kil~~L~~~Gli~s~~G~ 61 (83)
T PF02082_consen 8 DYALRILLYLARHPDGK-PVSSKEIAE--------RLGISPSYLRKILQKLKKAGLIESSRGR 61 (83)
T ss_dssp HHHHHHHHHHHCTTTSC--BEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEETST
T ss_pred HHHHHHHHHHHhCCCCC-CCCHHHHHH--------HHCcCHHHHHHHHHHHhhCCeeEecCCC
Confidence 34444444554333322 378888874 4788999999999999999987666554
No 24
>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=65.07 E-value=9.3 Score=25.37 Aligned_cols=52 Identities=27% Similarity=0.507 Sum_probs=37.5
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCce
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKV 95 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkA 95 (112)
......+.|++.+.+......=+.+-||. +.| +||+.-+++||+.|...|.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~-------~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIA-------QQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHH-------HHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHH-------HHh-CcCHHHHHHHHHHHHhCCeE
Confidence 78889999999999955444446666666 356 99999999999999999974
No 25
>PTZ00310 AMP deaminase; Provisional
Probab=63.75 E-value=18 Score=35.49 Aligned_cols=45 Identities=13% Similarity=0.254 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHhc--CCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCC
Q 038657 4 NEARETFLSALVSE--GRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLED 55 (112)
Q Consensus 4 ~e~~~~Il~~lv~~--g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~ 55 (112)
.|.+++|++.|.++ -+||| |.-||=|+++||. .+-+|+.++|...
T Consensus 950 Ael~K~v~~~le~skyq~aE~------RlSIYG~~~~EW~-kLA~W~~~~~l~S 996 (1453)
T PTZ00310 950 AELIKDVFEQYSRDRFTYAEN------RLSIYGINVKEWD-DLAHWFDTHGMAS 996 (1453)
T ss_pred HHHHHHHHHHHHhccceeeee------eEeeeCCCHHHHH-HHHHHHHHcCCCC
Confidence 36788999999876 35787 8999999999995 5789999999853
No 26
>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=63.01 E-value=7.8 Score=24.15 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=21.7
Q ss_pred cCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 75 HGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 75 ~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
-++|++.+.-.|..|+++|+.+-....
T Consensus 24 ~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 24 FGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp TT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 578999999999999999999877543
No 27
>PTZ00310 AMP deaminase; Provisional
Probab=62.90 E-value=21 Score=35.08 Aligned_cols=44 Identities=11% Similarity=0.160 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhcCC----eeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCC
Q 038657 4 NEARETFLSALVSEGR----AEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLE 54 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~----aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~ 54 (112)
.+.+++++..+.+++. +|| +.-||=|+++||. .+-+|+.++|..
T Consensus 312 a~liK~vi~~lE~sKyQ~q~~E~------rlSIYGr~~~EW~-kLA~Wvv~~~l~ 359 (1453)
T PTZ00310 312 GKLLRRELERREYQKQQPQATEY------SLPLYGHHPEELT-DLAEWVRRQGFG 359 (1453)
T ss_pred HHHHHHHHHHHHhccccceeeEE------EEEEeCCChhHHH-HHHHHHHHCCCC
Confidence 4577889999988754 788 8999999999997 689999999974
No 28
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=62.74 E-value=10 Score=22.50 Aligned_cols=51 Identities=27% Similarity=0.380 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhcCC---CCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 40 WADIILGFVKDNGL---EDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 40 Wa~~Iy~Wv~~tG~---~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
-|..|+......|. .+--+|.-|| .+..|++.+-+.++|+.|+++|-....
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~el--------a~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEI--------ADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHH--------HHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 35566777777664 1111222222 256889999999999999999987765
No 29
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=60.67 E-value=14 Score=24.64 Aligned_cols=24 Identities=21% Similarity=0.239 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEec
Q 038657 1 SLNNEARETFLSALVSEGRAEWLD 24 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d 24 (112)
+.|++.++..|+.++..|+++-++
T Consensus 27 ~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 27 NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred CcCHHHHHHHHHHHHHCCCeEeec
Confidence 368999999999999999999874
No 30
>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=60.61 E-value=31 Score=19.93 Aligned_cols=43 Identities=19% Similarity=0.217 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHH
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVK 49 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~ 49 (112)
+|...+...++.|.+.|-+.....+ +...|.-++ +..+++.+.
T Consensus 32 i~~~~i~~~l~~L~~~g~i~~~~~~--~~~~~~~~~---g~~~~~~~~ 74 (78)
T cd00090 32 LSQSTVSRHLKKLEEAGLVESRREG--RRVYYSLTD---AERLLALLE 74 (78)
T ss_pred cCHhHHHHHHHHHHHCCCeEEEEec--cEEEEEeCC---chHHHHHHH
Confidence 5677888999999999987765544 344555555 555555544
No 31
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=59.26 E-value=11 Score=25.16 Aligned_cols=54 Identities=26% Similarity=0.299 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 43 IILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 43 ~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
.|++.+.+. +.-+|.+||.+-- ..+..+++..-.-++|+.|++.|-+.-+..++
T Consensus 5 ~Il~~l~~~---~~~~sa~ei~~~l---~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~ 58 (116)
T cd07153 5 AILEVLLES---DGHLTAEEIYERL---RKKGPSISLATVYRTLELLEEAGLVREIELGD 58 (116)
T ss_pred HHHHHHHhC---CCCCCHHHHHHHH---HhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC
Confidence 456666554 3445666665432 22345789999999999999999999886554
No 32
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=58.33 E-value=7 Score=24.52 Aligned_cols=44 Identities=27% Similarity=0.238 Sum_probs=32.4
Q ss_pred EEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 58 MTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 58 ~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
++-|||.+-=......|..+++.-|-.+|+.|+++|=.+....+
T Consensus 10 ~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~ 53 (75)
T PF03551_consen 10 MHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEE 53 (75)
T ss_dssp EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred CcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeec
Confidence 45566655422233357889999999999999999998887654
No 33
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=57.41 E-value=21 Score=25.64 Aligned_cols=27 Identities=33% Similarity=0.447 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 76 GMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 76 gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
++...-.-++|+.|++.|=..-+...+
T Consensus 52 ~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 52 GISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 445555669999999999999997665
No 34
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=57.06 E-value=25 Score=21.94 Aligned_cols=53 Identities=28% Similarity=0.364 Sum_probs=40.7
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
++++=...|++.+.+.|-. -+|.-||. +--||+..-..+.|..|+++|.++--
T Consensus 3 ~~~~~~~~IL~~L~~~g~~--~~ta~eLa--------~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 3 TQDSLEEKILEFLENSGDE--TSTALQLA--------KNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred CchHHHHHHHHHHHHCCCC--CcCHHHHH--------HHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4556667888888888653 25666666 34689999999999999999998654
No 35
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=57.04 E-value=21 Score=27.24 Aligned_cols=70 Identities=20% Similarity=0.167 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHhcCCCCc-eEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCc-eeEEecCCCCCcceEEc
Q 038657 38 QDWADIILGFVKDNGLEDS-VMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGK-VAIFKGTSADDEGVKFS 111 (112)
Q Consensus 38 ~eWa~~Iy~Wv~~tG~~~t-V~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gk-Aql~~~~~~~~~GVKf~ 111 (112)
.|-|-.|.++...+-..|. ++|+-|+.+-=.-......-+.|+=+.+|++.|..-|- .++++..+ |++++
T Consensus 93 ~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~s----g~~vv 164 (223)
T PF04157_consen 93 YELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGS----GVKVV 164 (223)
T ss_dssp HHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETT----TEEEE
T ss_pred HHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCC----CcEEE
Confidence 5778899999998877544 99998887642221123347899999999999999995 78876664 67765
No 36
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=56.62 E-value=12 Score=21.83 Aligned_cols=23 Identities=43% Similarity=0.536 Sum_probs=20.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCce
Q 038657 73 ELHGMDRTILMRALKLLEHKGKV 95 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkA 95 (112)
+..+++.+-+.++|+.|+++|=.
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLV 55 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCE
Confidence 56799999999999999999953
No 37
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=56.40 E-value=16 Score=29.96 Aligned_cols=64 Identities=16% Similarity=0.250 Sum_probs=45.9
Q ss_pred hHHHHHHHHHHHHhcCCCCceE-EeeeeccCC---------------C-cCCccccCCCH---HHHHHHHHHHHhcCcee
Q 038657 37 IQDWADIILGFVKDNGLEDSVM-TVEEIRLGI---------------E-SRGTELHGMDR---TILMRALKLLEHKGKVA 96 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~-TlyEL~~Gd---------------~-t~~~ef~gmd~---~vL~kaL~~L~k~gkAq 96 (112)
-.|-...+-.|.+.-+..+--- -+-+|..|. . -..+-|.|+|| ++|++++.-|-++|++-
T Consensus 104 ~~e~~~~~~~wLer~~i~~~~~~kIk~LSKGnqQKIQfisaviHePeLlILDEPFSGLDPVN~elLk~~I~~lk~~GatI 183 (300)
T COG4152 104 KAEIQKKLQAWLERLEIVGKKTKKIKELSKGNQQKIQFISAVIHEPELLILDEPFSGLDPVNVELLKDAIFELKEEGATI 183 (300)
T ss_pred HHHHHHHHHHHHHhccccccccchHHHhhhhhhHHHHHHHHHhcCCCEEEecCCccCCChhhHHHHHHHHHHHHhcCCEE
Confidence 4567778888988766543221 233455554 2 25678999997 79999999999999999
Q ss_pred EEec
Q 038657 97 IFKG 100 (112)
Q Consensus 97 l~~~ 100 (112)
||..
T Consensus 184 ifSs 187 (300)
T COG4152 184 IFSS 187 (300)
T ss_pred EEec
Confidence 9964
No 38
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=55.63 E-value=24 Score=26.96 Aligned_cols=36 Identities=14% Similarity=0.192 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHHhcCC---eeEecCC--------C------cEEEEEecCh
Q 038657 2 LNNEARETFLSALVSEGR---AEWLDKG--------H------RKCLILWHRI 37 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~---aew~d~~--------~------~~~~I~Wr~~ 37 (112)
|+.+.|..=+++|+++|- .|+.+.. + .|+|-+|+-|
T Consensus 76 LtdeqI~kQVeYli~~GW~pclEf~~~~~~~~r~~~~s~~yyD~rYWtMWKLP 128 (176)
T PLN02289 76 LTDEELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLP 128 (176)
T ss_pred CCHHHHHHHHHHHHhCCCeeeeeeccCCceeEecCCCCCCcccCceeEEeccc
Confidence 788999999999999995 5666542 2 2689999876
No 39
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=54.44 E-value=32 Score=22.42 Aligned_cols=29 Identities=21% Similarity=0.405 Sum_probs=22.0
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEE
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKC 30 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~ 30 (112)
..+..+.-|++.||+.|.+++=..+.|..
T Consensus 32 ~k~R~vKKi~~~LV~Eg~l~yWSSGSTTm 60 (67)
T PF08679_consen 32 AKPREVKKIVNELVNEGKLEYWSSGSTTM 60 (67)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEEETTEEE
T ss_pred cCHHHHHHHHHHHHhhCeEEEEcCCCcEE
Confidence 35678899999999999988766655443
No 40
>TIGR02328 conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown.
Probab=53.97 E-value=28 Score=25.07 Aligned_cols=41 Identities=15% Similarity=0.054 Sum_probs=29.5
Q ss_pred CCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcC
Q 038657 53 LEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 53 ~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~g 93 (112)
..|..|.-|+-.+-......-+-.=|..-|..||.-|..+|
T Consensus 77 yRG~~~~~y~~l~~~~~~~PiY~eHd~~Yl~eCl~NL~~Kg 117 (120)
T TIGR02328 77 YRGQNCPNYDLLEEIKLTTPIYPEHNDDYLNECLANLRAKG 117 (120)
T ss_pred ccCCcCCcccccchhhcCCCCChhhhHHHHHHHHHHHHHcC
Confidence 46777887876655544444455568899999999998877
No 41
>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=53.71 E-value=19 Score=21.11 Aligned_cols=52 Identities=29% Similarity=0.432 Sum_probs=35.8
Q ss_pred hHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 37 IQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
+.+|. +..++.+.|. +|..||. ++-+++.+-+.++++.|+++|=.+--...+
T Consensus 3 ~~q~~--iL~~l~~~~~----~~~~~la--------~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 3 PSQFR--ILRILYENGG----ITQSELA--------EKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp HHHHH--HHHHHHHHSS----EEHHHHH--------HHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHH--HHHHHHHcCC----CCHHHHH--------HHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 44443 3334445544 5666665 678899999999999999999887775543
No 42
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=51.75 E-value=18 Score=24.91 Aligned_cols=36 Identities=22% Similarity=0.313 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHhcCC---eeEecCCC--cEEEEEecCh
Q 038657 2 LNNEARETFLSALVSEGR---AEWLDKGH--RKCLILWHRI 37 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~---aew~d~~~--~~~~I~Wr~~ 37 (112)
|+.+.+..=+++|.++|. +|+.|+.+ +++|-+|.-|
T Consensus 11 l~~~~i~~Qv~~ll~qG~~i~iE~ad~r~~r~~~W~mW~~p 51 (99)
T PF00101_consen 11 LTDEEIAKQVRYLLSQGWIIGIEHADPRRFRTSYWQMWKLP 51 (99)
T ss_dssp --HHHHHHHHHHHHHTT-EEEEEEESCGGSTSSS-EEESSE
T ss_pred CCHHHHHHHHHhhhhcCceeeEEecCCCCCCCCEeecCCCC
Confidence 566788888999999996 67777755 5778888654
No 43
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=51.06 E-value=49 Score=22.93 Aligned_cols=44 Identities=23% Similarity=0.432 Sum_probs=33.0
Q ss_pred HHHHHhcCC---eeEecCCCcEEEEEecCh-------HHHHHHHHHHHHhcCCC
Q 038657 11 LSALVSEGR---AEWLDKGHRKCLILWHRI-------QDWADIILGFVKDNGLE 54 (112)
Q Consensus 11 l~~lv~~g~---aew~d~~~~~~~I~Wr~~-------~eWa~~Iy~Wv~~tG~~ 54 (112)
|-.++.+|+ ..|.|..++.+.|=|+.. ++=+.+.-+|+..+|..
T Consensus 6 L~~~i~sg~ypGL~W~d~ekt~FrIPWkh~~~~~~~~e~D~~iFkaWa~~~Gk~ 59 (107)
T smart00348 6 LVEQVESGQYPGLCWEDEEKTRFRIPWKHAGRSGFDEERDAEIFKAYCVARGIY 59 (107)
T ss_pred HHHHhccCCCCCceEecCCCCEEEeccccCCcCCCCchhccHHHHHHHHHhCCC
Confidence 334455543 899999999999999433 33456888999999985
No 44
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=50.97 E-value=12 Score=22.63 Aligned_cols=23 Identities=13% Similarity=0.255 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHhcCceeEE
Q 038657 76 GMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 76 gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
++|+.++...|+.|+++|+...-
T Consensus 31 ~l~~k~~~~ll~~l~~~g~l~~~ 53 (59)
T PF09106_consen 31 RLPPKLFNALLEALVAEGRLKVE 53 (59)
T ss_dssp TS-HCCHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHHHHHHCCCeeeE
Confidence 78999999999999999998765
No 45
>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=50.43 E-value=36 Score=21.67 Aligned_cols=38 Identities=16% Similarity=0.097 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHH
Q 038657 1 SLNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQD 39 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~e 39 (112)
.+|+..++.|+..|++.|-.+-.. ++..-+.+=|+|++
T Consensus 36 ~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~~~~ 73 (83)
T PF02082_consen 36 GISPSYLRKILQKLKKAGLIESSR-GRGGGYRLARPPEE 73 (83)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-CCG
T ss_pred CcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecCCHHH
Confidence 378999999999999999877543 33456667777765
No 46
>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=49.80 E-value=36 Score=20.68 Aligned_cols=47 Identities=38% Similarity=0.405 Sum_probs=35.3
Q ss_pred HHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 42 DIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
..+|..+-++|- +|..||.+ --|+|.+-..++|+.|+++|=++...+
T Consensus 11 ~~vy~~Ll~~~~----~t~~eIa~--------~l~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 11 AKVYLALLKNGP----ATAEEIAE--------ELGISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHCH----EEHHHHHH--------HHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCC----CCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 345555554443 67777764 468999999999999999999988853
No 47
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=48.86 E-value=28 Score=25.15 Aligned_cols=31 Identities=26% Similarity=0.417 Sum_probs=27.5
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecCCC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGTSA 103 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~~~ 103 (112)
+.+|+|+..|.|.+..|.|.|=.+-..|.+|
T Consensus 33 ~~~~is~~~L~kil~~L~kaGlV~S~rG~~G 63 (150)
T COG1959 33 ERQGISPSYLEKILSKLRKAGLVKSVRGKGG 63 (150)
T ss_pred HHhCcCHHHHHHHHHHHHHcCCEEeecCCCC
Confidence 6799999999999999999999888877543
No 48
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=48.22 E-value=21 Score=24.14 Aligned_cols=54 Identities=24% Similarity=0.261 Sum_probs=35.7
Q ss_pred HHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 43 IILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 43 ~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
.|++.+.++.. -.|.+||..-= ......++..-.-++|+.|++.|-+.-+..++
T Consensus 12 ~Il~~l~~~~~---~~ta~ei~~~l---~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~ 65 (120)
T PF01475_consen 12 AILELLKESPE---HLTAEEIYDKL---RKKGPRISLATVYRTLDLLEEAGLIRKIEFGD 65 (120)
T ss_dssp HHHHHHHHHSS---SEEHHHHHHHH---HHTTTT--HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHHHHcCCC---CCCHHHHHHHh---hhccCCcCHHHHHHHHHHHHHCCeEEEEEcCC
Confidence 45666666554 45555555431 23446778888899999999999999886654
No 49
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=47.60 E-value=12 Score=24.70 Aligned_cols=32 Identities=28% Similarity=0.486 Sum_probs=26.6
Q ss_pred eEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCcee
Q 038657 57 VMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 57 V~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAq 96 (112)
-||+-||. +..|++.+.|...|..|.++|...
T Consensus 18 c~TLeeL~--------ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 18 CCTLEELE--------EKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred cCCHHHHH--------HHHCCCHHHHHHHHHHHHHCCCee
Confidence 45666665 678999999999999999999654
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=47.37 E-value=22 Score=19.58 Aligned_cols=25 Identities=40% Similarity=0.607 Sum_probs=22.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeE
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAI 97 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql 97 (112)
+..|++.+-+.++|+.|+++|-.+.
T Consensus 16 ~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 16 ELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 6678999999999999999998764
No 51
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=47.33 E-value=23 Score=21.40 Aligned_cols=18 Identities=6% Similarity=0.087 Sum_probs=14.6
Q ss_pred CCCHHHHHHHHHHHHhcC
Q 038657 1 SLNNEARETFLSALVSEG 18 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g 18 (112)
.|+++||+.+.+++.++|
T Consensus 20 ~L~~dFI~Ll~~Ei~rR~ 37 (46)
T PF08970_consen 20 NLDPDFIRLLEEEIQRRS 37 (46)
T ss_dssp T--HHHHHHHHHHHHHCT
T ss_pred CCCHHHHHHHHHHHHHcC
Confidence 488999999999999986
No 52
>KOG1736 consensus Glia maturation factor beta [Extracellular structures]
Probab=46.65 E-value=21 Score=26.21 Aligned_cols=37 Identities=19% Similarity=0.379 Sum_probs=26.5
Q ss_pred EEEEEecC---hHHHHHHHH----HHHHhcCCCCceEEeeeeccCCCc
Q 038657 29 KCLILWHR---IQDWADIIL----GFVKDNGLEDSVMTVEEIRLGIES 69 (112)
Q Consensus 29 ~~~I~Wr~---~~eWa~~Iy----~Wv~~tG~~~tV~TlyEL~~Gd~t 69 (112)
-|+|||++ +.||. ++| +|+.++. .+.-++|+...|+.
T Consensus 88 L~~Iyw~P~~~~~e~~-MmYAgak~~~~~~~---~~~KvfEir~tdD~ 131 (143)
T KOG1736|consen 88 LCFIYWSPVGCKPEQQ-MMYAGAKNMLVQTA---ELTKVFEIRSTDDL 131 (143)
T ss_pred EEEEEecCccCCHHHH-HHHHHHHHHHHHHh---hheEEEEecccccc
Confidence 69999997 56774 555 4666554 45678999987765
No 53
>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=45.70 E-value=54 Score=19.67 Aligned_cols=45 Identities=29% Similarity=0.476 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 42 DIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
+.|.+++.+.| .+|+-||+ +..|..+.-+++=|+.|+++|+..-.
T Consensus 3 ~~Il~~l~~~~----~~s~~ela--------~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 3 QQILELLKEKG----KVSVKELA--------EEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHcC----CEEHHHHH--------HHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 35777777654 45677776 34589999999999999999997655
No 54
>PF13730 HTH_36: Helix-turn-helix domain
Probab=45.35 E-value=26 Score=20.32 Aligned_cols=20 Identities=45% Similarity=0.594 Sum_probs=17.6
Q ss_pred ccCCCHHHHHHHHHHHHhcC
Q 038657 74 LHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~g 93 (112)
.-|+...-..++|+.|++.|
T Consensus 34 ~~g~s~~Tv~~~i~~L~~~G 53 (55)
T PF13730_consen 34 DLGVSRRTVQRAIKELEEKG 53 (55)
T ss_pred HHCcCHHHHHHHHHHHHHCc
Confidence 34888999999999999987
No 55
>PF00605 IRF: Interferon regulatory factor transcription factor; InterPro: IPR001346 Viral infections induce the expression of type I interferons (IFN-alpha and IFN-beta) genes. The induction is due to the transcriptional activation of the IFN genes. Interferon regulatory factor I (IRF-1) is one of the transcription factors responsible for that activation. IRF-1 binds to an upstream regulatory cis element, known as the interferon consensus sequence (ICS), which is found in the promoters of type I IFN and IFN-inducible MHC class I genes. Interferon regulatory factor 2 (IRF-2) is a protein that also interacts with the ICS, but that does not function as an activator; rather, it suppresses the function of IRF-1 under certain circumstances []. These proteins share a highly conserved N-terminal domain of about 100 amino acid residues which is involved in DNA-binding and which contain five conserved tryptophans. This domain is known as a 'tryptophan pentad repeat' or a 'tryptophan cluster' and is also present in: Interferon consensus sequence binding protein (ICSBP) [], a transcription factor expressed predominantly in lymphoid tissues and induced by IFN-gamma that also binds to the ICS. Transcriptional regulator ISGF3 gamma subunit []. ISGF3 is responsible for the initial stimulation of interferon-alpha-responsive genes. It recognises and binds to the interferon-stimulated response element (ISRE) within the regulatory sequences of target genes. Interferon regulatory factor 3 (IRF-3). Interferon regulatory factor 4 (IRF-4) which binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Interferon regulatory factor 5 (IRF-5). Interferon regulatory factor 6 (IRF-6). Interferon regulatory factor 7 (IRF-7). Gamma Herpesviruses vIRF-1, -2 and -3, proteins with homology to the cellular transcription factors of the IRF family []. Neither vIRF-1 nor vIRF-2 bind to DNA with the same specificity as cellular IRFs, indicating that if vIRFs are DNA-binding proteins, their binding has a pattern distinct from that of the cellular IRFs. Whether vIRF-3 can bind DNA with the same specificity as cellular IRFs is not known. The IRF tryptophan pentad repeat DNA-binding domain has an alpha/beta architecture comprising a cluster of three alpha-helices (alpha1-alpha3) flanked on one side by a mixed four-stranded beta-sheet (beta1-beta4). It forms a helix-turn-helix motif that binds to ISRE consensus sequences found in target promoters. Three of the tryptophan residues contact DNA by recognising a GAAA sequence []. This entry represents the IRF tryptophan pentad repeat DNA-binding domain.; GO: 0000975 regulatory region DNA binding; PDB: 2IRF_H 1IRF_A 1IRG_A 2DLL_A 3QU3_C 2PI0_D 2O6G_G 1T2K_A 2O61_A 3QU6_C ....
Probab=43.89 E-value=54 Score=22.84 Aligned_cols=45 Identities=27% Similarity=0.494 Sum_probs=35.6
Q ss_pred HHHHHHhcCC---eeEecCCCcEEEEEecCh-------HHHHHHHHHHHHhcCCC
Q 038657 10 FLSALVSEGR---AEWLDKGHRKCLILWHRI-------QDWADIILGFVKDNGLE 54 (112)
Q Consensus 10 Il~~lv~~g~---aew~d~~~~~~~I~Wr~~-------~eWa~~Iy~Wv~~tG~~ 54 (112)
-|-.++.+|. ..|+|..++.+.|=|+.. ++=+.+.-+|+.-+|.-
T Consensus 7 WL~~~i~sg~ypGL~W~d~~kt~FrIPWkH~~r~~~~~~~D~~iFkaWA~~~Gk~ 61 (109)
T PF00605_consen 7 WLIEQIDSGRYPGLEWLDEEKTIFRIPWKHAGRQDWDQEEDAKIFKAWAVHRGKY 61 (109)
T ss_dssp HHHHHHHHTCSTTSEESSTTSSEEEEETTSTTSTTSSHCGGGHHHHHHHHHTTSS
T ss_pred HHHHHHhcCCCCCcEEEcCCCCEEEeeCccCCCCCccccchHHHHHHHHHHhccc
Confidence 3445556665 689999999999999853 46678999999999984
No 56
>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=43.12 E-value=35 Score=22.61 Aligned_cols=27 Identities=30% Similarity=0.341 Sum_probs=23.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEe
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~ 99 (112)
++-|++.+-..|+|+.|+++|=...-.
T Consensus 55 ~~~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 55 ELTGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence 578999999999999999999887543
No 57
>KOG1096 consensus Adenosine monophosphate deaminase [Nucleotide transport and metabolism]
Probab=42.84 E-value=52 Score=30.22 Aligned_cols=42 Identities=24% Similarity=0.282 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhcC--CeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCC
Q 038657 5 EARETFLSALVSEG--RAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGL 53 (112)
Q Consensus 5 e~~~~Il~~lv~~g--~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~ 53 (112)
+.+++++.+|..+. +||. |.-||-|+++||- .+-+|+..+..
T Consensus 425 ei~Kev~~dleeSKYQ~ae~------rlsiygrs~~EW~-klA~W~v~~~v 468 (768)
T KOG1096|consen 425 EILKEVLSDLEESKYQLAEP------RLSIYGRSRDEWD-KLASWLVDNKV 468 (768)
T ss_pred HHHHHHHhhHHHhhhhhcce------eEEEeeeCHHHHH-HHHHHHHHccc
Confidence 45667777777653 4665 8999999999996 46788877653
No 58
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=42.82 E-value=34 Score=22.79 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.6
Q ss_pred cCCCHHHHHHHHHHHHhcCceeEEe
Q 038657 75 HGMDRTILMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 75 ~gmd~~vL~kaL~~L~k~gkAql~~ 99 (112)
.++|++++.-=|..|+..||++=+.
T Consensus 26 ~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 26 LNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4689999999999999999999885
No 59
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=42.40 E-value=22 Score=26.85 Aligned_cols=20 Identities=15% Similarity=0.291 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCceEEeeee
Q 038657 44 ILGFVKDNGLEDSVMTVEEI 63 (112)
Q Consensus 44 Iy~Wv~~tG~~~tV~TlyEL 63 (112)
+|++.-.+...||+.|+||+
T Consensus 142 ~~~y~~~~~~~n~~~~~~e~ 161 (162)
T PHA02825 142 LYTYFLATRKRNTIHTVYEL 161 (162)
T ss_pred HHHHHHHHhccCceeeeeec
Confidence 59999999999999999997
No 60
>PF08743 Nse4_C: Nse4 C-terminal; InterPro: IPR014854 Nse4 is a component of the Smc5/6 DNA repair complex. It forms interactions with Smc5 and Nse1 [].
Probab=42.21 E-value=28 Score=23.17 Aligned_cols=18 Identities=33% Similarity=0.431 Sum_probs=14.9
Q ss_pred HHHHHHhcCceeEEecCC
Q 038657 85 ALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 85 aL~~L~k~gkAql~~~~~ 102 (112)
.+..|+|.|||.|..+++
T Consensus 24 ~lSFLVkdG~v~i~~d~~ 41 (93)
T PF08743_consen 24 YLSFLVKDGRVKIEKDED 41 (93)
T ss_pred HHHHHHhcCeEEEEECCC
Confidence 356899999999998754
No 61
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=41.70 E-value=27 Score=20.69 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=14.8
Q ss_pred HHHHHhcCCeeEecCCC
Q 038657 11 LSALVSEGRAEWLDKGH 27 (112)
Q Consensus 11 l~~lv~~g~aew~d~~~ 27 (112)
++.|+++|.+||+|..-
T Consensus 1 w~~ll~~G~vE~id~eE 17 (48)
T PF04567_consen 1 WDDLLKEGVVEYIDAEE 17 (48)
T ss_dssp HHHHHHTTSEEEEETTT
T ss_pred ChhHhhCCCEEEecchh
Confidence 57899999999999854
No 62
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=41.39 E-value=21 Score=23.87 Aligned_cols=54 Identities=17% Similarity=0.220 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCC---CHHHHHHHHHHHHhcCcee
Q 038657 40 WADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGM---DRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 40 Wa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gm---d~~vL~kaL~~L~k~gkAq 96 (112)
-++.|..=+.+-...+..+|+--|.+- ....|-+| ..+++..||..|.++||.=
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~---L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY 68 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREH---LRKHYPGIAIPSQEVLYNTLGTLIKERKIY 68 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHH---HHHhCCCCCCCCHHHHHHHHHHHHHcCcee
Confidence 356777777777777888887777653 44567777 4689999999999999853
No 63
>KOG4828 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.47 E-value=50 Score=23.81 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=26.4
Q ss_pred CCCceEEeeeeccC---CCcCCcccc-----C-CCHHHHHHHHHHHHhc
Q 038657 53 LEDSVMTVEEIRLG---IESRGTELH-----G-MDRTILMRALKLLEHK 92 (112)
Q Consensus 53 ~~~tV~TlyEL~~G---d~t~~~ef~-----g-md~~vL~kaL~~L~k~ 92 (112)
|.|-+-|+|-+.-. ++....+|| | .|+++++-+.+.|+.+
T Consensus 41 Q~Gkmgti~~~~~~~~~s~v~~P~f~vsV~~g~~Dep~~~~~a~~LV~~ 89 (125)
T KOG4828|consen 41 QLGKMGTIYNVHFDVKKSEVDNPEFHVSVPIGMLDEPETRSAAQFLVNR 89 (125)
T ss_pred eccccceeEEeeeccccccccCCeEEEEEeecccCCHHHHHHHHHHHHH
Confidence 34444455554432 445566775 5 8999999999998865
No 64
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=40.45 E-value=13 Score=28.16 Aligned_cols=48 Identities=13% Similarity=0.247 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHhc-CCeeEecC-----------------C------------CcEEEEEecChHHHHHHHHHHH
Q 038657 1 SLNNEARETFLSALVSE-GRAEWLDK-----------------G------------HRKCLILWHRIQDWADIILGFV 48 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~-g~aew~d~-----------------~------------~~~~~I~Wr~~~eWa~~Iy~Wv 48 (112)
++|++..++|++||.++ |-|.-.-+ . -.|..+-=||++||..+|.=.+
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~~~ry~~er~~~~~e~~~~e~~~~~C~rCHs~aR~~lQrRt~~eW~~lv~fH~ 127 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETAPVRYALERRPNTVEQFPNEEITQMCARCHSGARVALQRRTAEEWEKLVHFHL 127 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCTT-CCCCCT-TT-----SCHHHHHHHSSSS-THHHHTEEE-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhcchhhhhhcCcchhhcccchHHHHHHHHhhhhhHHHHhhCCHHHHHHHHHHHH
Confidence 47899999999999997 54432211 0 0144556789999999987544
No 65
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=40.25 E-value=46 Score=24.02 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=24.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
+-+++|+..|.|.+..|.+.|=.+-..|.+
T Consensus 32 ~~~~is~~~L~kIl~~L~~aGlv~S~rG~~ 61 (153)
T PRK11920 32 RAYGVSELFLFKILQPLVEAGLVETVRGRN 61 (153)
T ss_pred HHHCcCHHHHHHHHHHHHHCCCEEeecCCC
Confidence 457999999999999999999666665543
No 66
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=38.81 E-value=38 Score=20.86 Aligned_cols=23 Identities=22% Similarity=0.195 Sum_probs=18.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCcee
Q 038657 74 LHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAq 96 (112)
-+|+|++++..|++.-.++|+..
T Consensus 27 ~~~~~~evI~~ai~~a~~~~~~~ 49 (73)
T TIGR01446 27 EFGNSPELIKEALKEAVSNNKAN 49 (73)
T ss_pred HhCCCHHHHHHHHHHHHHcCCCC
Confidence 36789999999999766677653
No 67
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=38.43 E-value=60 Score=22.59 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=28.9
Q ss_pred eEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 57 VMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 57 V~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
.+|.-||.+ =.++|+..+.|.|..|.+.|=..-..+.+
T Consensus 25 ~~s~~~ia~--------~~~ip~~~l~kil~~L~~~glv~s~~G~~ 62 (135)
T TIGR02010 25 PVTLADISE--------RQGISLSYLEQLFAKLRKAGLVKSVRGPG 62 (135)
T ss_pred cCcHHHHHH--------HHCcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence 456666653 37899999999999999999776655543
No 68
>PTZ00123 phosphoglycerate mutase like-protein; Provisional
Probab=38.28 E-value=78 Score=24.11 Aligned_cols=44 Identities=16% Similarity=0.133 Sum_probs=35.7
Q ss_pred CCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCcee
Q 038657 52 GLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 52 G~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAq 96 (112)
...|+-.+++|+..+ -+.-.-+|++|++-|.--+.....||||.
T Consensus 192 ~~~n~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (236)
T PTZ00123 192 NIPTGVPLVYELDEN-LKPIKKYYLLDEEELKAKMEAVANQGKAK 235 (236)
T ss_pred cCCCCceEEEEECCC-CCEeeeeecCCHHHHHHHHHHHHhccccC
Confidence 466777889999655 45566799999999998899999999984
No 69
>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=38.25 E-value=39 Score=19.64 Aligned_cols=30 Identities=30% Similarity=0.486 Sum_probs=22.7
Q ss_pred EEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCce
Q 038657 58 MTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKV 95 (112)
Q Consensus 58 ~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkA 95 (112)
+|+=||. +--|||..-..+.|+.|++.|=.
T Consensus 19 ~t~~eia--------~~~gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 19 LTLSEIA--------RALGLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp EEHHHHH--------HHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHH--------HHHCcCHHHHHHHHHHHHHCcCe
Confidence 4555655 33679999999999999999854
No 70
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=37.65 E-value=27 Score=25.31 Aligned_cols=45 Identities=29% Similarity=0.482 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCCCceEEeeeeccCCCcCCccccC-CCHHHHHHHHHHHHhcCcee
Q 038657 42 DIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHG-MDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~g-md~~vL~kaL~~L~k~gkAq 96 (112)
+.|++|+...+.-=|+-.++. -||+ ++...+.|||+.|+.+|+..
T Consensus 4 ~~Il~y~~~qNRPys~~di~~----------nL~~~~~K~~v~k~Ld~L~~~g~i~ 49 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFD----------NLHNKVGKTAVQKALDSLVEEGKIV 49 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHH----------HHHhhccHHHHHHHHHHHHhCCCee
Confidence 467777777666555544443 2443 88999999999999998654
No 71
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=37.63 E-value=52 Score=25.59 Aligned_cols=46 Identities=24% Similarity=0.352 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 41 ADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 41 a~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
-..|.+.+.+.|. +|+.||.+ -.++.+.-.+|=|+.|+++|+..-.
T Consensus 7 ~~~Il~~l~~~~~----~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGY----VSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCC----EeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4567888877764 78888886 3489999999999999999997654
No 72
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=37.55 E-value=48 Score=20.66 Aligned_cols=23 Identities=35% Similarity=0.501 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHHhcCCeeEec
Q 038657 2 LNNEARETFLSALVSEGRAEWLD 24 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d 24 (112)
.+++.++.+++.||+.|+.+..+
T Consensus 33 ~s~~eL~~fL~~lv~e~~L~~~~ 55 (60)
T PF08672_consen 33 ISLEELQEFLDRLVEEGKLECSG 55 (60)
T ss_dssp --HHHHHHHHHHHHHTTSEE--T
T ss_pred CCHHHHHHHHHHHHHCCcEEecC
Confidence 46889999999999999999873
No 73
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=37.00 E-value=38 Score=22.04 Aligned_cols=28 Identities=11% Similarity=0.210 Sum_probs=23.2
Q ss_pred ccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 74 LHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
|-.+.+-.+.|+++.|+..|+...+.+.
T Consensus 29 ~pd~k~R~vKKi~~~LV~Eg~l~yWSSG 56 (67)
T PF08679_consen 29 FPDAKPREVKKIVNELVNEGKLEYWSSG 56 (67)
T ss_dssp -TTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CCCcCHHHHHHHHHHHHhhCeEEEEcCC
Confidence 6678899999999999999999999553
No 74
>PF03823 Neurokinin_B: Neurokinin B; InterPro: IPR003635 Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes neurokinins, as well as many other peptides. Like other tachykinins, neurokinins are synthesized as larger protein precursors that are enzymatically converted to their mature forms.; GO: 0007217 tachykinin receptor signaling pathway
Probab=36.66 E-value=28 Score=22.03 Aligned_cols=21 Identities=14% Similarity=0.283 Sum_probs=16.2
Q ss_pred CCcCCccccCCCHHHHHHHHH
Q 038657 67 IESRGTELHGMDRTILMRALK 87 (112)
Q Consensus 67 d~t~~~ef~gmd~~vL~kaL~ 87 (112)
......++|.+|+.+|+|-.+
T Consensus 36 ~skKdsdLyqLPpslLRRLyd 56 (59)
T PF03823_consen 36 HSKKDSDLYQLPPSLLRRLYD 56 (59)
T ss_pred ccccCcchhhCCHHHHHHHHh
Confidence 334778899999999988543
No 75
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=36.02 E-value=42 Score=16.79 Aligned_cols=16 Identities=13% Similarity=0.358 Sum_probs=11.3
Q ss_pred CHHHHHHHHHHHHhcC
Q 038657 3 NNEARETFLSALVSEG 18 (112)
Q Consensus 3 s~e~~~~Il~~lv~~g 18 (112)
+++....++++|.+.|
T Consensus 16 ~~~~a~~~~~~M~~~g 31 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQG 31 (34)
T ss_pred CHHHHHHHHHHHHHhC
Confidence 3566777888887765
No 76
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=35.68 E-value=53 Score=24.42 Aligned_cols=28 Identities=29% Similarity=0.456 Sum_probs=24.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-||....-+++||+.|+++|-..-..+
T Consensus 40 ~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 40 ERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5699999999999999999997776644
No 77
>TIGR03792 uncharacterized cyanobacterial protein, TIGR03792 family. Members of this family are found, no more than one to a genome, exclusively in (but not universal to) the Cyanobacteria. These proteins are small, 100-150 amino acids. The function is unknown.
Probab=35.35 E-value=1.1e+02 Score=20.72 Aligned_cols=32 Identities=25% Similarity=0.563 Sum_probs=22.6
Q ss_pred CCeeEecCCC-c--EEEEEecChHHHHHHHHHHHH
Q 038657 18 GRAEWLDKGH-R--KCLILWHRIQDWADIILGFVK 49 (112)
Q Consensus 18 g~aew~d~~~-~--~~~I~Wr~~~eWa~~Iy~Wv~ 49 (112)
|+-.|.++.+ . ...|.|.|.+.|-+.=-+.++
T Consensus 37 g~ev~~~~e~pee~~llI~WeS~E~WK~i~~~~~~ 71 (90)
T TIGR03792 37 GKEVWWDPEKPEEGVLLIRWESREQWKAIPQEELE 71 (90)
T ss_pred ceEEEecCCCCCEEEEEEEEcCHHHHhcCCHHHHH
Confidence 6677777766 3 456889999999765554444
No 78
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.96 E-value=49 Score=20.20 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=19.5
Q ss_pred ccCCCHHHHHHHHHHHHhcCc
Q 038657 74 LHGMDRTILMRALKLLEHKGK 94 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gk 94 (112)
|+|++.+-|.+.|+.+.+.|-
T Consensus 6 ~~g~~~~el~~~l~~~r~~~~ 26 (58)
T PF12646_consen 6 FSGFSGEELDKFLDALRKAGI 26 (58)
T ss_pred ECCCCHHHHHHHHHHHHHcCC
Confidence 799999999999999999875
No 79
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=34.56 E-value=79 Score=22.87 Aligned_cols=32 Identities=28% Similarity=0.409 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEec
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWH 35 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr 35 (112)
++-..+.-+|+.|+.+|...-..-+|+. |||-
T Consensus 30 ~~K~~v~k~Ld~L~~~g~i~~K~~GKqk--iY~~ 61 (169)
T PF07106_consen 30 VGKTAVQKALDSLVEEGKIVEKEYGKQK--IYFA 61 (169)
T ss_pred ccHHHHHHHHHHHHhCCCeeeeeecceE--EEee
Confidence 4556788899999999999988878765 4443
No 80
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=34.47 E-value=53 Score=26.95 Aligned_cols=26 Identities=31% Similarity=0.388 Sum_probs=23.3
Q ss_pred CCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 77 MDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 77 md~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
||++-.-+|++.|+|+||+.=|.-++
T Consensus 133 md~eeVAeAf~~L~~sGKVr~fGVSN 158 (298)
T COG4989 133 MDAEEVAEAFTHLHKSGKVRHFGVSN 158 (298)
T ss_pred CCHHHHHHHHHHHHhcCCeeeeecCC
Confidence 89999999999999999999996544
No 81
>COG1932 SerC Phosphoserine aminotransferase [Coenzyme metabolism / Amino acid transport and metabolism]
Probab=33.98 E-value=81 Score=26.68 Aligned_cols=80 Identities=15% Similarity=0.119 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCC-CceEEeeeeccCCCcCCccccCCCHHHHH
Q 038657 5 EARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLE-DSVMTVEEIRLGIESRGTELHGMDRTILM 83 (112)
Q Consensus 5 e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~-~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~ 83 (112)
.....++++|..+|-.+++.+.. ++=|++||+|++.++.. |-|.. +.++-..+ -|.=-++++=.
T Consensus 250 y~~~lv~~Wlk~~GGl~~~~~rn----------~~ka~~LY~~id~s~fy~~~v~~--~~RS~mnV---~f~~~~~~ld~ 314 (365)
T COG1932 250 YLLGLVFKWLKSQGGLEALEARN----------QAKAQLLYDWIDKSDFYRNLVAK--ANRSRMNV---TFTLVDAELDK 314 (365)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHH----------HHHHHHHHHHHHhCCccccccch--hhccceeE---EEEcCcHHHHH
Confidence 35567899999999888876532 44589999999999984 44443 55443322 34444677767
Q ss_pred HHHHHHHhcCceeEEe
Q 038657 84 RALKLLEHKGKVAIFK 99 (112)
Q Consensus 84 kaL~~L~k~gkAql~~ 99 (112)
+-++.++++|=+.+..
T Consensus 315 ~fv~eae~~gl~~lkG 330 (365)
T COG1932 315 GFVAEAEAAGLIYLKG 330 (365)
T ss_pred HHHHHHHHcCCceecc
Confidence 7778889999887774
No 82
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=33.27 E-value=59 Score=24.29 Aligned_cols=28 Identities=29% Similarity=0.349 Sum_probs=24.4
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-||.....+++||+.|+++|-..-..+
T Consensus 33 ~~~~VSR~TVR~Al~~L~~eGli~r~~G 60 (230)
T TIGR02018 33 AQYGCSRMTVNRALRELTDAGLLERRQG 60 (230)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5699999999999999999998776654
No 83
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=33.21 E-value=1e+02 Score=21.50 Aligned_cols=47 Identities=11% Similarity=0.027 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhc
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDN 51 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~t 51 (112)
+|+..++.++..|.+.|-.+-....+..+ .+-++|++- -|++=+...
T Consensus 37 is~~~vrk~l~~L~~~Glv~s~~G~~GG~-~l~~~~~~i--tl~dI~~ai 83 (141)
T PRK11014 37 VSRNHMVKIINQLSRAGYVTAVRGKNGGI-RLGKPASTI--RIGDVVREL 83 (141)
T ss_pred cCHHHHHHHHHHHHhCCEEEEecCCCCCe-eecCCHHHC--CHHHHHHHH
Confidence 68999999999999999888665543333 445889883 355544444
No 84
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=32.57 E-value=91 Score=24.17 Aligned_cols=50 Identities=26% Similarity=0.407 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEe
Q 038657 38 QDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 38 ~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~ 99 (112)
+|=-..|.+.+.++|. +|+-||. +..++.++-.+|=|+.|+++|..+-..
T Consensus 4 ~eR~~~Il~~L~~~~~----v~v~eLa--------~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 4 RQRQAAILEYLQKQGK----TSVEELA--------QYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHHHcCC----EEHHHHH--------HHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3445678888888875 6777777 456889999999999999999876553
No 85
>PF02241 MCR_beta: Methyl-coenzyme M reductase beta subunit, C-terminal domain; InterPro: IPR022679 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the C-terminal domain from the beta subunit of methyl-conenzyme M reductase (MCR). The C-terminal domain of MCR beta has an all-alpha fold with buried central helix. This entry is found in assocation with PF02783 from PFAM.; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity; PDB: 1MRO_E 1HBM_B 3M30_B 3M32_B 1HBU_B 3M2U_E 3M2V_E 3M1V_B 1HBO_B 3POT_B ....
Probab=32.55 E-value=12 Score=29.75 Aligned_cols=19 Identities=37% Similarity=0.616 Sum_probs=15.4
Q ss_pred HHHHHHHHhcCCCCceEEe
Q 038657 42 DIILGFVKDNGLEDSVMTV 60 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~tV~Tl 60 (112)
+++|+-+++||+.|||-|+
T Consensus 62 NlvydlvK~NGk~GTvGtV 80 (255)
T PF02241_consen 62 NLVYDLVKENGKTGTVGTV 80 (255)
T ss_dssp THHHHHHHHHTTT--HHHH
T ss_pred hhHHHHHHhcCCCCchhHH
Confidence 5899999999999999876
No 86
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=32.30 E-value=65 Score=24.06 Aligned_cols=29 Identities=28% Similarity=0.480 Sum_probs=24.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+=+|+....+++||+.|+.+|-..-..+.
T Consensus 32 ~~~gVSR~TVR~Al~~L~~eGli~r~~G~ 60 (233)
T TIGR02404 32 DQYGASRETVRKALNLLTEAGYIQKIQGK 60 (233)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEeCCc
Confidence 45899999999999999999977766543
No 87
>TIGR01664 DNA-3'-Pase DNA 3'-phosphatase. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.
Probab=32.13 E-value=1.9e+02 Score=20.75 Aligned_cols=88 Identities=7% Similarity=-0.104 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHH
Q 038657 5 EARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMR 84 (112)
Q Consensus 5 e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~k 84 (112)
+.+.+.|+.|.++|.-.-+=.+++...-...+.+.....+...++..|..- +.+..+++. ..+.=++.++.+
T Consensus 45 pgv~e~L~~Lk~~G~~l~I~TN~~~~~~~~~~~~~~~~~i~~~l~~~gl~~-----~~ii~~~~~---~~~KP~p~~~~~ 116 (166)
T TIGR01664 45 PEIPAKLQELDDEGYKIVIFTNQSGIGRGKLSAESFKNKIEAFLEKLKVPI-----QVLAATHAG---LYRKPMTGMWEY 116 (166)
T ss_pred CCHHHHHHHHHHCCCEEEEEeCCcccccCcccHHHHHHHHHHHHHHcCCCE-----EEEEecCCC---CCCCCccHHHHH
Confidence 567889999998886444333322222222356667677888889988732 233333321 123334678889
Q ss_pred HHHHHH---hcCceeEEec
Q 038657 85 ALKLLE---HKGKVAIFKG 100 (112)
Q Consensus 85 aL~~L~---k~gkAql~~~ 100 (112)
|++.+- +...+-++.+
T Consensus 117 ~~~~~~~~~~~~~~v~VGD 135 (166)
T TIGR01664 117 LQSQYNSPIKMTRSFYVGD 135 (166)
T ss_pred HHHHcCCCCCchhcEEEEC
Confidence 998873 4555666643
No 88
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=32.05 E-value=50 Score=21.04 Aligned_cols=23 Identities=26% Similarity=0.302 Sum_probs=19.3
Q ss_pred ccCCCHHHHHHHHHHHHhcCcee
Q 038657 74 LHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAq 96 (112)
--+++++-+.++|+.|+++|=..
T Consensus 8 ~l~is~stvs~~l~~L~~~glI~ 30 (96)
T smart00529 8 RLNVSPPTVTQMLKKLEKDGLVE 30 (96)
T ss_pred HhCCChHHHHHHHHHHHHCCCEE
Confidence 35799999999999999998333
No 89
>PRK14999 histidine utilization repressor; Provisional
Probab=32.03 E-value=63 Score=24.36 Aligned_cols=29 Identities=28% Similarity=0.440 Sum_probs=24.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+-||.-..-+++||+.|+.+|-..-..+.
T Consensus 44 ~~~gVSR~TVR~Al~~L~~eGli~r~~Gk 72 (241)
T PRK14999 44 AQYGFSRMTINRALRELTDEGWLVRLQGV 72 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecCc
Confidence 45999999999999999999987766543
No 90
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=31.68 E-value=89 Score=23.29 Aligned_cols=28 Identities=36% Similarity=0.501 Sum_probs=24.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 74 LHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
=+|+...-+++||+.|+..|-.....+.
T Consensus 40 ~~gVSRt~VReAL~~L~~eGlv~~~~g~ 67 (239)
T PRK04984 40 LIGVTRTTLREVLQRLARDGWLTIQHGK 67 (239)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4899999999999999999988877543
No 91
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=31.37 E-value=88 Score=23.60 Aligned_cols=28 Identities=29% Similarity=0.353 Sum_probs=24.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-+|+..+.++.||..|+..|=.++..+
T Consensus 42 ~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 42 KQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred HHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4489999999999999999998888754
No 92
>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=31.25 E-value=24 Score=23.46 Aligned_cols=40 Identities=23% Similarity=0.197 Sum_probs=30.5
Q ss_pred EeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 59 TVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 59 TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
+=|||.+-=+.....+..+++..+-.+|+.|+++|=.+..
T Consensus 19 ~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 19 HGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred CHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEE
Confidence 4466666533334467889999999999999999987774
No 93
>PF11334 DUF3136: Protein of unknown function (DUF3136); InterPro: IPR021483 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=30.97 E-value=45 Score=21.50 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhcCce
Q 038657 80 TILMRALKLLEHKGKV 95 (112)
Q Consensus 80 ~vL~kaL~~L~k~gkA 95 (112)
++--|||+.|+++||-
T Consensus 11 ~~YckALr~Lv~~G~~ 26 (64)
T PF11334_consen 11 PLYCKALRRLVADGRS 26 (64)
T ss_pred hHHHHHHHHHHHcCCC
Confidence 5678999999999984
No 94
>PF15581 Imm35: Immunity protein 35
Probab=30.84 E-value=54 Score=22.57 Aligned_cols=53 Identities=23% Similarity=0.340 Sum_probs=34.0
Q ss_pred EEeeeeccCCCcC-----------CccccCCCHHHHHHHHHHHHhcCc--eeEEecCCCC--CcceEE
Q 038657 58 MTVEEIRLGIESR-----------GTELHGMDRTILMRALKLLEHKGK--VAIFKGTSAD--DEGVKF 110 (112)
Q Consensus 58 ~TlyEL~~Gd~t~-----------~~ef~gmd~~vL~kaL~~L~k~gk--Aql~~~~~~~--~~GVKf 110 (112)
.|+--+.+|.+|. ..|+.|||++...+.|+.-..+|+ -.++|-+++- -++|.|
T Consensus 16 IslsY~~q~~esa~~~i~~l~~lIe~eWRGl~~~qV~~kl~ava~~~~~~~~vvKkE~~~Iwfd~VrF 83 (93)
T PF15581_consen 16 ISLSYLRQGEESARRTIRNLESLIEHEWRGLPEEQVLYKLEAVAAKGPEAKIVVKKEGNIIWFDEVRF 83 (93)
T ss_pred eeHHHHhcchhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcceEEEecCCeEEEcceeE
Confidence 4565667776653 258999999999999987665543 2344445431 236666
No 95
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=30.81 E-value=76 Score=24.19 Aligned_cols=30 Identities=27% Similarity=0.395 Sum_probs=25.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
+-+|.-..-++|||+.|++.|-.+-..|.+
T Consensus 39 ~~f~VSR~TvRkAL~~L~~eGli~r~~G~G 68 (236)
T COG2188 39 EQFGVSRMTVRKALDELVEEGLIVRRQGKG 68 (236)
T ss_pred HHHCCcHHHHHHHHHHHHHCCcEEEEecCe
Confidence 458999999999999999999887776543
No 96
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=30.50 E-value=2.4e+02 Score=22.21 Aligned_cols=51 Identities=6% Similarity=0.093 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHhcC--CeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCC
Q 038657 1 SLNNEARETFLSALVSEG--RAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGL 53 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g--~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~ 53 (112)
+++.+.++..+++++..| ++.....+...+.-+ |++|+-.++..+++..+-
T Consensus 17 ~iD~~~~~~~i~~~i~~G~v~gi~~~GstGE~~~L--t~eEr~~~~~~~~~~~~~ 69 (290)
T TIGR00683 17 TINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFML--STEEKKEIFRIAKDEAKD 69 (290)
T ss_pred CcCHHHHHHHHHHHHhCCCcCEEEECCcccccccC--CHHHHHHHHHHHHHHhCC
Confidence 467889999999999999 566665554444444 999999999999998753
No 97
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=30.37 E-value=1e+02 Score=22.34 Aligned_cols=36 Identities=22% Similarity=0.405 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHhcCC---eeEecCCC--cEEEEEecCh
Q 038657 2 LNNEARETFLSALVSEGR---AEWLDKGH--RKCLILWHRI 37 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~---aew~d~~~--~~~~I~Wr~~ 37 (112)
|+.+.+.+=+.++..+|. .|+.|..+ +.+|-+|.+|
T Consensus 19 Ltd~qi~~QVrylL~QGykigvE~~d~rrprtgsWt~wg~p 59 (127)
T COG4451 19 LTDEQIAEQVRYLLSQGYKIGVEYVDDRRPRTGSWTMWGTP 59 (127)
T ss_pred CcHHHHHHHHHHHHhCCcccceeecccCCcccceeeecCCc
Confidence 567778888899999997 67777665 5789999985
No 98
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=29.90 E-value=1.3e+02 Score=18.90 Aligned_cols=51 Identities=35% Similarity=0.451 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 38 QDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 38 ~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
++-.+.|++.+.+.| ++-.|-..+.-|= ++|..-+.++|-.|+++|++.--
T Consensus 3 ~~~ee~Il~~L~~~g--~~~a~~ia~~~~L--------~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 3 QDLEEKILDFLKELG--GSTATAIAKALGL--------SVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHHHT--SSEEEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hhHHHHHHHHHHhcC--CccHHHHHHHhCc--------chhHHHHHHHHHHHHHCCCEeeC
Confidence 355678999999998 6666666666552 25789999999999999999754
No 99
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=29.89 E-value=1.1e+02 Score=23.26 Aligned_cols=94 Identities=12% Similarity=0.005 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHHhcCCe---eEecCCCcEE--EEEecChHHH----HHHHHHH-HHhcCCCCceEEeeeeccCCCcCCcc
Q 038657 4 NEARETFLSALVSEGRA---EWLDKGHRKC--LILWHRIQDW----ADIILGF-VKDNGLEDSVMTVEEIRLGIESRGTE 73 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~a---ew~d~~~~~~--~I~Wr~~~eW----a~~Iy~W-v~~tG~~~tV~TlyEL~~Gd~t~~~e 73 (112)
.++|..+-++|.++|+. +|.|--||.. -.=...|+=| |+++..- +...==.+...+.|-=..-..+.+..
T Consensus 34 ~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h 113 (169)
T PTZ00095 34 WRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNH 113 (169)
T ss_pred HHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCc
Confidence 57888889999988874 5665433211 1122233322 3333222 22222256677777766666678889
Q ss_pred ccCCCHHHHHHHHHHHHhcCceeE
Q 038657 74 LHGMDRTILMRALKLLEHKGKVAI 97 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAql 97 (112)
|..=.-.++++||+.||+-|=.+-
T Consensus 114 ~~~aSg~iiR~~LQqLE~~glVek 137 (169)
T PTZ00095 114 TVRASGKILRWICQQLEKLGLVEQ 137 (169)
T ss_pred ccCCchHHHHHHHHHHHHCCCEEe
Confidence 999999999999999999987664
No 100
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=29.64 E-value=1e+02 Score=18.91 Aligned_cols=46 Identities=22% Similarity=0.276 Sum_probs=30.4
Q ss_pred HHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 41 ADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 41 a~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
++.|.+-.-+.|. +|+-+|.+. -+||+...++||-+|.+.|=++-+
T Consensus 15 ~~~V~~~Ll~~G~----ltl~~i~~~--------t~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 15 VAKVGEVLLSRGR----LTLREIVRR--------TGLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHHHHC-S----EEHHHHHHH--------HT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcCC----cCHHHHHHH--------hCCCHHHHHHHHHHHHHcCCeeee
Confidence 4445555555553 466666643 449999999999999999987765
No 101
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=29.60 E-value=79 Score=23.86 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=24.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+-||+...-+++||+.|+++|-..-..+.
T Consensus 37 ~~~~VSR~TvR~Al~~L~~eGli~r~~G~ 65 (240)
T PRK09764 37 TEFGVSRVTVRQALRQLVEQQILESIQGS 65 (240)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecCc
Confidence 45899999999999999999987766543
No 102
>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]
Probab=29.36 E-value=32 Score=31.04 Aligned_cols=24 Identities=17% Similarity=0.415 Sum_probs=21.3
Q ss_pred cCCCHHHHHHHHHHHHhcCceeEE
Q 038657 75 HGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 75 ~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
||+++.+++|||..+.++|..|.-
T Consensus 696 ~~y~e~~v~kal~~m~~rg~iq~r 719 (729)
T KOG0481|consen 696 QGYSEHAVKKALQIMLRRGEIQHR 719 (729)
T ss_pred ccccHHHHHHHHHHHHhhhHHHHH
Confidence 499999999999999999987653
No 103
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.32 E-value=79 Score=23.82 Aligned_cols=28 Identities=32% Similarity=0.335 Sum_probs=24.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-||.-..-+++||+.|+++|-..-..+
T Consensus 43 ~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 43 ARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5699999999999999999997776644
No 104
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=28.23 E-value=39 Score=20.78 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHHHhc
Q 038657 78 DRTILMRALKLLEHK 92 (112)
Q Consensus 78 d~~vL~kaL~~L~k~ 92 (112)
|.++|.+|++.|.++
T Consensus 50 p~~~l~~A~~~l~~~ 64 (66)
T PF01193_consen 50 PKEALLKAIKILKEK 64 (66)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHh
Confidence 889999999998763
No 105
>PF12039 DUF3525: Protein of unknown function (DUF3525); InterPro: IPR021912 This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length.
Probab=27.57 E-value=76 Score=26.62 Aligned_cols=41 Identities=17% Similarity=0.385 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhcCCeeEecCCCcEEEEE--ecChHHHHHHHHH
Q 038657 5 EARETFLSALVSEGRAEWLDKGHRKCLIL--WHRIQDWADIILG 46 (112)
Q Consensus 5 e~~~~Il~~lv~~g~aew~d~~~~~~~I~--Wr~~~eWa~~Iy~ 46 (112)
+.+......+++..+-.=-.++.++++.+ || |+.||.+|-+
T Consensus 315 dvVELaytq~~~DEk~rIPEPkGTkILdMP~Wk-P~nwaklide 357 (453)
T PF12039_consen 315 DVVELAYTQFIQDEKERIPEPKGTKILDMPNWK-PDNWAKLIDE 357 (453)
T ss_pred hHHHHHHHHHHhhhcccCCCCCCCeeeecCCCC-CccHHHHHHH
Confidence 44555566667664433234555788877 75 7999998853
No 106
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=27.42 E-value=1.7e+02 Score=21.53 Aligned_cols=63 Identities=17% Similarity=0.149 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHH
Q 038657 1 SLNNEARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRT 80 (112)
Q Consensus 1 ~Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~ 80 (112)
.+|.+.++..|+.|++-|-++..+.++ -+.|-=-|+.|.+..+.-.++|...
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~g~----------------------------y~~t~~~l~~~~~~~~~avr~~h~q 103 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGDGK----------------------------YVQTDKSLTTSSEIPSEAVRSYHKQ 103 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCCCc----------------------------EEEecceeeCCCCCcHHHHHHHHHH
Confidence 367888889999999988888765532 2233333445555556666777777
Q ss_pred HHHHHHHHHHh
Q 038657 81 ILMRALKLLEH 91 (112)
Q Consensus 81 vL~kaL~~L~k 91 (112)
++..|.+.|.+
T Consensus 104 ~~~lA~~al~~ 114 (171)
T PF14394_consen 104 MLELAQEALDR 114 (171)
T ss_pred HHHHHHHHHHh
Confidence 77777777764
No 107
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=27.13 E-value=2.7e+02 Score=20.74 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHH
Q 038657 7 RETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRAL 86 (112)
Q Consensus 7 ~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL 86 (112)
++.|++.+.+.|++.- .|++.-|...+.| .+|+.+.|.. ++ ++.| ..|-.+-..|+
T Consensus 43 ~~~i~~~ls~~G~i~~-----~R~Y~~a~a~~~l----~~~l~~~Gf~--pv----~~kG---------~~Dv~laIDam 98 (160)
T TIGR00288 43 LDEIREILSEYGDIKI-----GKVLLNQYASDKL----IEAVVNQGFE--PI----IVAG---------DVDVRMAVEAM 98 (160)
T ss_pred HHHHHHHHHhcCCeEE-----EEEEechhccHHH----HHHHHHCCce--EE----EecC---------cccHHHHHHHH
Confidence 6789999999997663 3677777666554 6889999987 22 2344 58999999999
Q ss_pred HHHH
Q 038657 87 KLLE 90 (112)
Q Consensus 87 ~~L~ 90 (112)
+.|-
T Consensus 99 e~~~ 102 (160)
T TIGR00288 99 ELIY 102 (160)
T ss_pred HHhc
Confidence 9884
No 108
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=26.99 E-value=90 Score=22.91 Aligned_cols=37 Identities=22% Similarity=0.395 Sum_probs=28.0
Q ss_pred eEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 57 VMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 57 V~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
.+|.-||. +-.++|+..|.|.|+.|.+.|=..-..+.
T Consensus 25 ~vs~~eIA--------~~~~ip~~~l~kIl~~L~~aGLv~s~rG~ 61 (164)
T PRK10857 25 PVPLADIS--------ERQGISLSYLEQLFSRLRKNGLVSSVRGP 61 (164)
T ss_pred cCcHHHHH--------HHHCcCHHHHHHHHHHHHHCCCEEeCCCC
Confidence 45555555 45789999999999999999966654444
No 109
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=26.97 E-value=1.1e+02 Score=22.92 Aligned_cols=33 Identities=24% Similarity=0.317 Sum_probs=26.6
Q ss_pred ccccCCCHHHHHHHHHHHHhcCceeEEecCCCC
Q 038657 72 TELHGMDRTILMRALKLLEHKGKVAIFKGTSAD 104 (112)
Q Consensus 72 ~ef~gmd~~vL~kaL~~L~k~gkAql~~~~~~~ 104 (112)
+..|||++.-|++.|..|++-|=...=.+.+|+
T Consensus 78 ~r~~G~s~~tlrR~l~~LveaGLI~rrDS~Ngk 110 (177)
T PF03428_consen 78 ERLNGMSERTLRRHLARLVEAGLIVRRDSPNGK 110 (177)
T ss_pred HHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCC
Confidence 456899999999999999999977765444443
No 110
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.61 E-value=1e+02 Score=22.85 Aligned_cols=29 Identities=34% Similarity=0.534 Sum_probs=25.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+-+|+....++.||..|+..|=.++..+.
T Consensus 45 e~~gVSRt~VREAL~~L~~eGlv~~~~~~ 73 (241)
T PRK03837 45 AFFGVGRPAVREALQALKRKGLVQISHGE 73 (241)
T ss_pred HHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 56899999999999999999999987543
No 111
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=26.48 E-value=1e+02 Score=20.97 Aligned_cols=51 Identities=25% Similarity=0.389 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeEEe
Q 038657 39 DWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 39 eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql~~ 99 (112)
++|=.+...+...+ +.-+|+=||. +-.++|++.+.+.|+.|++.|=.+-..
T Consensus 9 ~yal~~l~~la~~~--~~~~s~~eia--------~~l~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 9 DYATLVLTTLAQND--SQPYSAAEIA--------EQTGLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred hHHHHHHHHHHhCC--CCCccHHHHH--------HHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence 44555555554322 2234555554 457899999999999999999665543
No 112
>PF05378 Hydant_A_N: Hydantoinase/oxoprolinase N-terminal region; InterPro: IPR008040 This domain is found at the N terminus of the hydantoinase/oxoprolinase IPR002821 from INTERPRO family.
Probab=26.24 E-value=1.1e+02 Score=22.61 Aligned_cols=36 Identities=28% Similarity=0.366 Sum_probs=31.8
Q ss_pred EEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcC
Q 038657 58 MTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 58 ~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~g 93 (112)
--.|++.++-+..|.+-.-+|++-++++++.|.++|
T Consensus 112 ~~~~~v~gr~~~~G~~i~~ld~~~v~~~~~~l~~~g 147 (176)
T PF05378_consen 112 ERVFEVDGRIDADGEVIEPLDEDEVREALRELKDKG 147 (176)
T ss_pred cCEEEECCccccCcEEecCCCHHHHHHHHHHHHhCC
Confidence 356788888888899999999999999999998886
No 113
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=25.90 E-value=2.1e+02 Score=20.36 Aligned_cols=26 Identities=19% Similarity=0.565 Sum_probs=21.2
Q ss_pred EEEEEecChHHHHHHH---HHHHHhcCCC
Q 038657 29 KCLILWHRIQDWADII---LGFVKDNGLE 54 (112)
Q Consensus 29 ~~~I~Wr~~~eWa~~I---y~Wv~~tG~~ 54 (112)
.|...|+++++|---+ ..|+++||+.
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~ 109 (113)
T CHL00128 81 EAIYIMKNPEAWDRFMRFMERYAEDNGLT 109 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCc
Confidence 6888899999998654 5788888863
No 114
>PRK11460 putative hydrolase; Provisional
Probab=25.75 E-value=2.9e+02 Score=20.65 Aligned_cols=47 Identities=17% Similarity=0.031 Sum_probs=33.6
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhc
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHK 92 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~ 92 (112)
-|.+++..+++++.+.|.. +++...-.+. |+++++.+..+.+-|.+.
T Consensus 162 vp~~~~~~~~~~L~~~g~~---~~~~~~~~~g-------H~i~~~~~~~~~~~l~~~ 208 (232)
T PRK11460 162 IDVAHAVAAQEALISLGGD---VTLDIVEDLG-------HAIDPRLMQFALDRLRYT 208 (232)
T ss_pred cCHHHHHHHHHHHHHCCCC---eEEEEECCCC-------CCCCHHHHHHHHHHHHHH
Confidence 3678999999999988733 3333333222 778999999999877654
No 115
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=25.68 E-value=1.2e+02 Score=22.94 Aligned_cols=28 Identities=39% Similarity=0.593 Sum_probs=24.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-+|+...-++.||+.|+..|=.++..+
T Consensus 41 ~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 41 EMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3489999999999999999998888754
No 116
>PF14177 YkyB: YkyB-like protein
Probab=25.65 E-value=64 Score=23.79 Aligned_cols=18 Identities=28% Similarity=0.281 Sum_probs=15.7
Q ss_pred HHHHHHHHHhcCceeEEe
Q 038657 82 LMRALKLLEHKGKVAIFK 99 (112)
Q Consensus 82 L~kaL~~L~k~gkAql~~ 99 (112)
=.+||..|.+.|||+.+.
T Consensus 29 Kk~aL~Kll~E~kA~kiG 46 (140)
T PF14177_consen 29 KKKALQKLLEEGKAKKIG 46 (140)
T ss_pred HHHHHHHHHHcCcceEEE
Confidence 367899999999999995
No 117
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=25.56 E-value=1.2e+02 Score=22.21 Aligned_cols=58 Identities=17% Similarity=0.258 Sum_probs=36.5
Q ss_pred HHHHHHHhcCC-CCceEEeeeeccCCCcCCccccCCC-HHHHHHHHHHHHhcCceeEEecCCCCCcceEEc
Q 038657 43 IILGFVKDNGL-EDSVMTVEEIRLGIESRGTELHGMD-RTILMRALKLLEHKGKVAIFKGTSADDEGVKFS 111 (112)
Q Consensus 43 ~Iy~Wv~~tG~-~~tV~TlyEL~~Gd~t~~~ef~gmd-~~vL~kaL~~L~k~gkAql~~~~~~~~~GVKf~ 111 (112)
.|++++.+... .+.-.|+-||. +.-|++ ..-..+.|+.|++.|-.+ .++|...|++|+
T Consensus 10 ~iL~~l~~~~~~~~~~~~~~ela--------~~~~~~s~~tv~~~l~~L~~~g~i~---~~~~~~~~~~~~ 69 (199)
T TIGR00498 10 EVLDLIRAHIESTGYPPSIREIA--------RAVGLRSPSAAEEHLKALERKGYIE---RDPGKPRAIRIL 69 (199)
T ss_pred HHHHHHHHHHHhcCCCCcHHHHH--------HHhCCCChHHHHHHHHHHHHCCCEe---cCCCCCCeEEeC
Confidence 34555554422 33335666766 457788 899999999999999644 233334466653
No 118
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=25.31 E-value=2.2e+02 Score=20.19 Aligned_cols=26 Identities=15% Similarity=0.500 Sum_probs=21.0
Q ss_pred EEEEEecChHHHHHHH---HHHHHhcCCC
Q 038657 29 KCLILWHRIQDWADII---LGFVKDNGLE 54 (112)
Q Consensus 29 ~~~I~Wr~~~eWa~~I---y~Wv~~tG~~ 54 (112)
.|...|+++++|---+ ..|+++||+-
T Consensus 78 Ea~y~m~s~~~WdRFMRFmeRYA~~ngl~ 106 (109)
T TIGR03047 78 EAVYIMKSEDEWDRFMRFMERYAEANGLG 106 (109)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCc
Confidence 6888899999998654 5788888863
No 119
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=25.30 E-value=1e+02 Score=21.50 Aligned_cols=49 Identities=14% Similarity=0.352 Sum_probs=35.8
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCcee
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAq 96 (112)
+.++.-..||......|.. |+=+| .+.-+++++-+.++|+.|+++|=..
T Consensus 5 ~~edyL~~I~~l~~~~~~~----~~~el--------a~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 5 SMEDYIEQIYLLIEEKGYA----RVSDI--------AEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred hHHHHHHHHHHHHhcCCCc----CHHHH--------HHHhCCChhHHHHHHHHHHHCCCEE
Confidence 4567778888888776655 22222 2567889999999999999999654
No 120
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=25.28 E-value=57 Score=24.21 Aligned_cols=93 Identities=20% Similarity=0.121 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHhcCCe---eEecCCCcEE--EEEecChHHH---HHHHHHHHHhcCC--CCceEEeeeeccCCCcCCcc
Q 038657 4 NEARETFLSALVSEGRA---EWLDKGHRKC--LILWHRIQDW---ADIILGFVKDNGL--EDSVMTVEEIRLGIESRGTE 73 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~a---ew~d~~~~~~--~I~Wr~~~eW---a~~Iy~Wv~~tG~--~~tV~TlyEL~~Gd~t~~~e 73 (112)
.++|..+-++|.++|+. +|.|--||.. -.=.-.|+=| +..|..-+--.|- .+...+.|-...-..+.+..
T Consensus 10 ~~~I~~~A~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h 89 (150)
T PRK09333 10 DLLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEH 89 (150)
T ss_pred HHHHHHHHHHHHhcCCcCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCc
Confidence 56888888999988874 5665333211 0112222211 3344444444554 45566777776666678889
Q ss_pred ccCCCHHHHHHHHHHHHhcCcee
Q 038657 74 LHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAq 96 (112)
|..=.-.++++||+.||+-|=.+
T Consensus 90 ~~~~sg~iiR~~LqqLE~~glVe 112 (150)
T PRK09333 90 FVKGSGSIIRKILQQLEKAGLVE 112 (150)
T ss_pred cccCccHHHHHHHHHHHHCCCee
Confidence 99999999999999999988665
No 121
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=25.09 E-value=1.3e+02 Score=23.04 Aligned_cols=38 Identities=29% Similarity=0.437 Sum_probs=26.6
Q ss_pred CCceEEeeeeccCCCcCCc-----cccCCCHHHHHHHHHHHHh
Q 038657 54 EDSVMTVEEIRLGIESRGT-----ELHGMDRTILMRALKLLEH 91 (112)
Q Consensus 54 ~~tV~TlyEL~~Gd~t~~~-----ef~gmd~~vL~kaL~~L~k 91 (112)
.+++.-.|-|..|-...+- +..|+|++++.+|.+++.+
T Consensus 189 ~~~~~f~Ykl~~G~~~~S~ai~iA~~~g~p~~II~rA~~i~~~ 231 (235)
T PF00488_consen 189 NDSLTFTYKLKEGICSSSYAIEIAKLAGLPEEIIERAKEILKQ 231 (235)
T ss_dssp TTEEEEEEEEEES--SSTCHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred ccccceeEEEeECCCCCcHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4778889999999654332 4589999999999988754
No 122
>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=25.00 E-value=1.5e+02 Score=17.30 Aligned_cols=30 Identities=30% Similarity=0.409 Sum_probs=24.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecCC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGTS 102 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~~ 102 (112)
+.-+++.+-+.++|+.|++.|=.+-..++.
T Consensus 26 ~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 26 ERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp HHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 578999999999999999999998886654
No 123
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=24.80 E-value=32 Score=29.36 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCCCceEEeee-ec---------cCCCcC--CccccCCCHHHHHHHH
Q 038657 42 DIILGFVKDNGLEDSVMTVEE-IR---------LGIESR--GTELHGMDRTILMRAL 86 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~tV~TlyE-L~---------~Gd~t~--~~ef~gmd~~vL~kaL 86 (112)
+++|+-+++||+.|||-|+-+ +. .-+.+. +--||.-+...|=.|.
T Consensus 246 NlvydlVK~Ngk~GTvGtVV~s~VerAieDgVI~~~k~~pSGy~~Y~~~D~~lWNAY 302 (433)
T TIGR03257 246 NLLYDLVKANGKDGTVGSVVESVVERAIEDGVISVDKTAPSGYNFYKANDVPKWNAY 302 (433)
T ss_pred hhHHHHHHhcCCCCchhHHHHHHHHHHHhcCceeccccCCCCceeecCCCHHHHHHH
Confidence 689999999999999988743 22 112222 3346777777666554
No 124
>PF11735 CAP59_mtransfer: Cryptococcal mannosyltransferase 1 ; InterPro: IPR021047 The capsule of pathogenic fungi is a complex polysaccharide whose formation is determined by a number of enzymes including, most importantly, alpha-1,3-mannosyltransferase 1 [, ]. It is responsible for addition of mannose residues in an alpha-1,3 linkage to a polymannosly precursor.
Probab=24.73 E-value=2.7e+02 Score=21.86 Aligned_cols=53 Identities=21% Similarity=0.219 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHH-HHHhcCceeEEe
Q 038657 37 IQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALK-LLEHKGKVAIFK 99 (112)
Q Consensus 37 ~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~-~L~k~gkAql~~ 99 (112)
|.-|++.|.+-+.--|-.|..+.+||=-++|.| ..+|. .|+ .|.+.|=.--+.
T Consensus 16 ~~~~~~~ll~li~~LGp~nv~vSIyE~~S~D~T---------~~~L~-~L~~~L~~lgv~~~i~ 69 (241)
T PF11735_consen 16 PSLWGDALLELIRFLGPENVFVSIYESGSWDGT---------KEALR-ALDAELDALGVPHSIV 69 (241)
T ss_pred HHHHHHHHHHHHHHhCcCeEEEEEEeCCCCccH---------HHHHH-HHHHHHHhCCCCeEEE
Confidence 578999999999999999999999998888877 34454 454 677777554443
No 125
>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=24.57 E-value=1.5e+02 Score=17.04 Aligned_cols=29 Identities=31% Similarity=0.411 Sum_probs=23.6
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+.-+++++-+.+.++.|+++|=++--.+.
T Consensus 29 ~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 29 ERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 56789999999999999999988877554
No 126
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=24.56 E-value=82 Score=24.22 Aligned_cols=56 Identities=32% Similarity=0.380 Sum_probs=40.4
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCC----ccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRG----TELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~----~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
..++-++.|.+-+.+..+. -||--.+ .+..|.-.++++.||+.|+..|=.++=.+.
T Consensus 11 l~~~v~~~i~~~I~~g~~~----------~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~ 70 (241)
T COG2186 11 LADEVAEQIGALIVSGELP----------PGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGS 70 (241)
T ss_pred hHHHHHHHHHHHHHcCCCC----------CCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCC
Confidence 4566677777777776542 3332211 378999999999999999999988877544
No 127
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=24.21 E-value=90 Score=15.59 Aligned_cols=16 Identities=25% Similarity=0.355 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHhcCC
Q 038657 4 NEARETFLSALVSEGR 19 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g~ 19 (112)
.+..+.|+++|.++|.
T Consensus 4 ~~l~~lI~~yL~~~g~ 19 (34)
T smart00667 4 SELNRLILEYLLRNGY 19 (34)
T ss_pred HHHHHHHHHHHHHcCH
Confidence 3456678888887774
No 128
>PF13558 SbcCD_C: Putative exonuclease SbcCD, C subunit; PDB: 3QG5_B 3QF7_A 3THO_A 3EUK_H 3EUJ_A 3AV0_B 3AUY_B 3AUX_A.
Probab=24.05 E-value=82 Score=20.50 Aligned_cols=22 Identities=18% Similarity=0.315 Sum_probs=19.1
Q ss_pred CCccccCCCHHHHHHHHHHHHh
Q 038657 70 RGTELHGMDRTILMRALKLLEH 91 (112)
Q Consensus 70 ~~~ef~gmd~~vL~kaL~~L~k 91 (112)
..+-|.+||++-..++++.|.+
T Consensus 69 lDEaF~~lD~~~~~~~~~~l~~ 90 (90)
T PF13558_consen 69 LDEAFSKLDEENIERLMDLLRQ 90 (90)
T ss_dssp EESTTTTCGHHHHHHHHHHHHH
T ss_pred EeCCCCcCCHHHHHHHHHHHhC
Confidence 4567999999999999999875
No 129
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=23.97 E-value=2.4e+02 Score=20.05 Aligned_cols=26 Identities=27% Similarity=0.741 Sum_probs=21.2
Q ss_pred EEEEEecChHHHHHHH---HHHHHhcCCC
Q 038657 29 KCLILWHRIQDWADII---LGFVKDNGLE 54 (112)
Q Consensus 29 ~~~I~Wr~~~eWa~~I---y~Wv~~tG~~ 54 (112)
.|...|+++++|---+ ..|+++||+.
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~ 109 (113)
T PRK13612 81 EATYIWKSEQEWDRFMRFMERYAKENGLG 109 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCc
Confidence 6888899999998654 5788888863
No 130
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=23.61 E-value=86 Score=19.86 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=17.9
Q ss_pred ccCCCHHHHHHHHHHHHhcCce
Q 038657 74 LHGMDRTILMRALKLLEHKGKV 95 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkA 95 (112)
.-||+...+.+.|+.|++.|=.
T Consensus 28 ~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 28 KANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp TST--HHHHHHHHHHHHHTTSE
T ss_pred HhCcCHHHHHHHHHHHHHCcCe
Confidence 4689999999999999999976
No 131
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=23.39 E-value=89 Score=20.17 Aligned_cols=25 Identities=36% Similarity=0.436 Sum_probs=20.4
Q ss_pred ccCCCHHHHHHHHHHHHhcCceeEE
Q 038657 74 LHGMDRTILMRALKLLEHKGKVAIF 98 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~k~gkAql~ 98 (112)
..|+.+.+|.+.|+.|++.|=.+--
T Consensus 28 l~~is~~~L~~~L~~L~~~GLv~r~ 52 (90)
T PF01638_consen 28 LPGISPKVLSQRLKELEEAGLVERR 52 (90)
T ss_dssp STTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred cchhHHHHHHHHHHHHHHcchhhcc
Confidence 4588999999999999999976544
No 132
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=23.38 E-value=2.5e+02 Score=19.92 Aligned_cols=26 Identities=15% Similarity=0.484 Sum_probs=21.2
Q ss_pred EEEEEecChHHHHHH---HHHHHHhcCCC
Q 038657 29 KCLILWHRIQDWADI---ILGFVKDNGLE 54 (112)
Q Consensus 29 ~~~I~Wr~~~eWa~~---Iy~Wv~~tG~~ 54 (112)
.|...|+++++|--- ...|+++||+.
T Consensus 79 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~ 107 (111)
T PLN00039 79 EAKYVMRSPREWDRFMRFMERYAEENGLG 107 (111)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCc
Confidence 688889999999865 45788888863
No 133
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=23.01 E-value=2.7e+02 Score=19.57 Aligned_cols=25 Identities=12% Similarity=0.306 Sum_probs=20.3
Q ss_pred EEEEEecChHHHHHHH---HHHHHhcCC
Q 038657 29 KCLILWHRIQDWADII---LGFVKDNGL 53 (112)
Q Consensus 29 ~~~I~Wr~~~eWa~~I---y~Wv~~tG~ 53 (112)
.|...|+++++|---+ ..|+++||+
T Consensus 74 Ea~y~m~s~~~wdRFMRFmeRYA~~Ngl 101 (104)
T PRK13611 74 EVIYDMETEAEWDRFLRFMERFSAANQM 101 (104)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCC
Confidence 6888899999998654 578888876
No 134
>PF02230 Abhydrolase_2: Phospholipase/Carboxylesterase; InterPro: IPR003140 This entry represents the alpha/beta hydrolase domain found in phospholipases [], carboxylesterases [] and thioesterases.; GO: 0016787 hydrolase activity; PDB: 3U0V_A 1AUR_A 1AUO_B 1FJ2_B 3CN9_A 3CN7_A.
Probab=22.96 E-value=2.5e+02 Score=20.46 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=31.3
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHh
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEH 91 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k 91 (112)
=|.+|+...++++.+.|.. .-.+.|+ .+. |.++++.+..+.+-|.+
T Consensus 169 vp~~~~~~~~~~L~~~~~~-v~~~~~~--g~g-------H~i~~~~~~~~~~~l~~ 214 (216)
T PF02230_consen 169 VPFEWAEKTAEFLKAAGAN-VEFHEYP--GGG-------HEISPEELRDLREFLEK 214 (216)
T ss_dssp STHHHHHHHHHHHHCTT-G-EEEEEET--T-S-------SS--HHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHhcCCC-EEEEEcC--CCC-------CCCCHHHHHHHHHHHhh
Confidence 4789999999999999993 3333332 222 78899999998888765
No 135
>KOG1572 consensus Predicted protein tyrosine phosphatase [Defense mechanisms]
Probab=22.89 E-value=2e+02 Score=23.12 Aligned_cols=63 Identities=21% Similarity=0.281 Sum_probs=46.3
Q ss_pred EEEEecChHHHHHHHHHHHHhcCCCCceEEeeee-ccCCCc-CCccccCCCHHHHHHHHHHHHhcCceeE
Q 038657 30 CLILWHRIQDWADIILGFVKDNGLEDSVMTVEEI-RLGIES-RGTELHGMDRTILMRALKLLEHKGKVAI 97 (112)
Q Consensus 30 ~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL-~~Gd~t-~~~ef~gmd~~vL~kaL~~L~k~gkAql 97 (112)
..|.|=.||+....-++++.+||-. +|-+ ++|+-. ...-|-+++.+.+++||++|..++.==+
T Consensus 87 ksIisL~pE~yp~~nl~f~~~~~Ik-----~~~i~ie~~k~~~k~P~~~~~~~~i~~~l~~lld~~N~P~ 151 (249)
T KOG1572|consen 87 KSIISLCPEPYPEENLNFLESNGIK-----LYQIGIEGEKDNKKEPFVNIPDHSIRKALKVLLDKRNYPI 151 (249)
T ss_pred heEEEecCCCCChHHHHHHHhcCce-----EEEEecccccccccCCCCCChHHHHHHHHHHHhcccCCce
Confidence 4588888998999999999998853 3333 344432 3467999999999999998776654333
No 136
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=22.83 E-value=1.4e+02 Score=20.93 Aligned_cols=47 Identities=11% Similarity=0.124 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHHHHHhcC
Q 038657 6 ARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILGFVKDNG 52 (112)
Q Consensus 6 ~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~Wv~~tG 52 (112)
+.+.+.+.|..-|-.-....--.+---+=+|.++|-..+-+|+.+-.
T Consensus 90 ~a~~~~~~L~~~G~~~C~g~vmasnp~W~~s~~~W~~~~~~w~~~p~ 136 (138)
T PF03445_consen 90 FAERLVDALDECGFPPCPGGVMASNPRWRGSLSEWREQLRRWIDNPD 136 (138)
T ss_pred HHHHHHHHHHHcCCCCCCCCcCccChhhCcCHHHHHHHHHHHHhCCC
Confidence 45666777777665443221000001233688999999999998643
No 137
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=22.40 E-value=2.3e+02 Score=18.32 Aligned_cols=63 Identities=14% Similarity=0.131 Sum_probs=44.2
Q ss_pred CCHHHHHHHHHHHHhcCCee-E---ecCCC----cEEEEEecChHHHHHHHHHHHHhcCCCCceEEeeeeccCC
Q 038657 2 LNNEARETFLSALVSEGRAE-W---LDKGH----RKCLILWHRIQDWADIILGFVKDNGLEDSVMTVEEIRLGI 67 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~ae-w---~d~~~----~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd 67 (112)
+|+..+...+..|.++|-.. . .|+.+ ..++|.++.+. ...+-+-++.-.....|.-.| .+.|+
T Consensus 29 ~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~--~~~~~~v~~~l~~~p~v~~~~-~~~G~ 99 (108)
T smart00344 29 LSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLES--PDKLEEFLEKLEKLPEVVEVY-LVTGD 99 (108)
T ss_pred cCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECC--hhHHHHHHHHHhCCcceEEee-EecCC
Confidence 68899999999999998655 2 12221 36788888773 334566666777778888888 44564
No 138
>TIGR01232 lacD tagatose 1,6-diphosphate aldolase. This family consists of Gram-positive proteins. Tagatose 1,6-diphosphate aldolase is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
Probab=22.34 E-value=3e+02 Score=22.96 Aligned_cols=73 Identities=14% Similarity=0.170 Sum_probs=55.8
Q ss_pred EEEEEecC--hHHHHHHHHHHHHhcCC---CCceEEeeeeccCC----CcCCccccCCCHHHHHHHHHHHHhcC-ceeEE
Q 038657 29 KCLILWHR--IQDWADIILGFVKDNGL---EDSVMTVEEIRLGI----ESRGTELHGMDRTILMRALKLLEHKG-KVAIF 98 (112)
Q Consensus 29 ~~~I~Wr~--~~eWa~~Iy~Wv~~tG~---~~tV~TlyEL~~Gd----~t~~~ef~gmd~~vL~kaL~~L~k~g-kAql~ 98 (112)
++++|||+ +++-.+.=+.|++.-|- -.-+--|.|+..=| +..+.+|..+=|.....|++.+.+-+ .+-++
T Consensus 124 K~Llyy~pD~~~ein~~k~a~vervg~ec~a~dipf~lE~ltYd~~~~~~~~~~yak~kP~~V~~a~kefs~~~~gvDVl 203 (325)
T TIGR01232 124 KFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAMKLFSEPRFNVDVL 203 (325)
T ss_pred EEEEEeCCCCChHHHHHHHHHHHHHHHHHHHCCCCeEEEEeccCCCCCCCCcHHHHHhChHHHHHHHHHhccCCCCCcEE
Confidence 78999995 56788888888888776 35567788877643 44667898888999999999988754 67777
Q ss_pred ecC
Q 038657 99 KGT 101 (112)
Q Consensus 99 ~~~ 101 (112)
|-+
T Consensus 204 KvE 206 (325)
T TIGR01232 204 KVE 206 (325)
T ss_pred EEe
Confidence 655
No 139
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=22.28 E-value=1.3e+02 Score=22.60 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=23.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-+|.-..-+++||+.|+++|-..=..+
T Consensus 41 ~~~~VSR~TvR~Al~~L~~eGli~r~~G 68 (241)
T PRK11402 41 TQYNVSRITIRKAISDLVADGVLIRWQG 68 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5689999999999999999997665544
No 140
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.27 E-value=90 Score=21.64 Aligned_cols=29 Identities=28% Similarity=0.271 Sum_probs=24.8
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
+.-+|+++-+.++++.|+++|=.+-..+.
T Consensus 62 ~~l~i~~~tvsr~l~~Le~~GlI~R~~~~ 90 (144)
T PRK11512 62 KVLSVDLGALTRMLDRLVCKGWVERLPNP 90 (144)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence 56789999999999999999987776543
No 141
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=22.21 E-value=2.1e+02 Score=19.39 Aligned_cols=59 Identities=19% Similarity=0.219 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCeeEecCC--CcEEEEEecChHHHHHHHHHHHHhc---CC--CCceEEeeeeccCCC
Q 038657 8 ETFLSALVSEGRAEWLDKG--HRKCLILWHRIQDWADIILGFVKDN---GL--EDSVMTVEEIRLGIE 68 (112)
Q Consensus 8 ~~Il~~lv~~g~aew~d~~--~~~~~I~Wr~~~eWa~~Iy~Wv~~t---G~--~~tV~TlyEL~~Gd~ 68 (112)
..|-+.+.+-|.+.|+|=. .+.++|-..+|+. |....+=+.+. +. .+.-. -.++.+||+
T Consensus 16 e~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~-A~~a~~~~~~~~~~~~~i~~~~~-~~~vLeGee 81 (105)
T PF08777_consen 16 EDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEA-AQKALEKLKEANDGKLKIKGKEV-TLEVLEGEE 81 (105)
T ss_dssp HHHHHHT-SS--EEEEE--TT-SEEEEEESS----HHHHHHHHHHTTTS-B-TTSSSE-EEE---HHH
T ss_pred HHHHHHHHhcCCcceEEecCCCCEEEEEECCcch-HHHHHHHHHhccCCceEEcCceE-EEEECCCHH
Confidence 3344444456899999854 3789999999998 77777777766 11 22222 346666653
No 142
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=22.20 E-value=1.3e+02 Score=21.97 Aligned_cols=28 Identities=29% Similarity=0.285 Sum_probs=24.7
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-+|+...-++.||..|+..|=.+...+
T Consensus 42 ~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 42 ARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred HHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 4579999999999999999999888744
No 143
>PRK12399 tagatose 1,6-diphosphate aldolase; Reviewed
Probab=22.15 E-value=3.2e+02 Score=22.81 Aligned_cols=72 Identities=14% Similarity=0.179 Sum_probs=51.9
Q ss_pred EEEEEecC--hHHHHHHHHHHHHhcCC---CCceEEeeeecc----CCCcCCccccCCCHHHHHHHHHHHHhcC-ceeEE
Q 038657 29 KCLILWHR--IQDWADIILGFVKDNGL---EDSVMTVEEIRL----GIESRGTELHGMDRTILMRALKLLEHKG-KVAIF 98 (112)
Q Consensus 29 ~~~I~Wr~--~~eWa~~Iy~Wv~~tG~---~~tV~TlyEL~~----Gd~t~~~ef~gmd~~vL~kaL~~L~k~g-kAql~ 98 (112)
++++|||+ |++--+.=..|++.-|- -.-+--|.|+.. +++..+.+|-.+-|.....|++.+-+-+ .+-++
T Consensus 123 K~Llyy~pD~~~~in~~k~a~vervg~eC~a~dipf~lE~ltY~~~~~d~~~~~yak~kP~~V~~a~kefs~~~~gvDVl 202 (324)
T PRK12399 123 KFLLYYDVDEPDEINEQKKAYIERIGSECVAEDIPFFLEILTYDEKIADNGSVEYAKVKPHKVNEAMKVFSKPRFGVDVL 202 (324)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEeeccCcccccccHHHHhhChHHHHHHHHHhccCCCCCcEE
Confidence 78999996 55666777778877654 345666777765 3344566888888888899999997644 66666
Q ss_pred ec
Q 038657 99 KG 100 (112)
Q Consensus 99 ~~ 100 (112)
|-
T Consensus 203 Kv 204 (324)
T PRK12399 203 KV 204 (324)
T ss_pred EE
Confidence 65
No 144
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=22.00 E-value=97 Score=19.68 Aligned_cols=30 Identities=37% Similarity=0.565 Sum_probs=24.9
Q ss_pred ccccCCCHHHHHHHHHHHHhcCceeEEecC
Q 038657 72 TELHGMDRTILMRALKLLEHKGKVAIFKGT 101 (112)
Q Consensus 72 ~ef~gmd~~vL~kaL~~L~k~gkAql~~~~ 101 (112)
.+.-+++.+-+.+.++.|+++|=..--.+.
T Consensus 43 a~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 43 AERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 367899999999999999999966665443
No 145
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=21.98 E-value=91 Score=25.38 Aligned_cols=42 Identities=17% Similarity=0.082 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhcCCeeEecCCCcEEEEEecChHHHHHHHHH
Q 038657 5 EARETFLSALVSEGRAEWLDKGHRKCLILWHRIQDWADIILG 46 (112)
Q Consensus 5 e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr~~~eWa~~Iy~ 46 (112)
+.+..+|..|++.|...-..-..-.+=+|.++++|--..|.+
T Consensus 201 ~~l~~~l~dMv~eGlI~~ek~dsfniP~Y~ps~eEv~~~I~~ 242 (334)
T PF03492_consen 201 DLLADALRDMVAEGLISEEKVDSFNIPIYFPSPEEVRAIIEE 242 (334)
T ss_dssp HHHHHHHHHHHHTTSS-HCCCCTG--SBB---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcCHHHhhceeCCccCCCHHHHHHHHhc
Confidence 578899999999998764322223456899999998887766
No 146
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=21.94 E-value=1.2e+02 Score=16.63 Aligned_cols=21 Identities=38% Similarity=0.634 Sum_probs=17.1
Q ss_pred cccCCCHHHHHHHHHHHHhcC
Q 038657 73 ELHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~g 93 (112)
++-|+-.+..-|+|+.|+++|
T Consensus 10 ~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 10 DYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp HHHTS-HHHHHHHHHHHHHTT
T ss_pred HHhCCcHHHHHHHHHHHHHcC
Confidence 356788899999999999987
No 147
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=21.89 E-value=1.3e+02 Score=18.08 Aligned_cols=54 Identities=20% Similarity=0.332 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcCCC---CceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCceeE
Q 038657 41 ADIILGFVKDNGLE---DSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVAI 97 (112)
Q Consensus 41 a~~Iy~Wv~~tG~~---~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAql 97 (112)
|..|+..++..|.. +...-..-++.-+-. ++-|+..+-+.+.|+.|+++|-.++
T Consensus 4 a~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA---~~~g~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 4 ARFLLELAERFGRRQDGDGIRIPLPLTQEEIA---DMLGVSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp HHHHHHHHHHHEEEEETTEEEEEEESSHHHHH---HHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHCCCCCCCCceEEecCCHHHHH---HHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 56677777777653 222222223333222 6789999999999999999997764
No 148
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=21.67 E-value=2.3e+02 Score=19.08 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEE
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLIL 33 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~ 33 (112)
++-...+.+|.+|.++|-..-..+.+ +..||
T Consensus 53 I~~SlAr~~Lr~L~~kG~Ik~V~~~~-~q~IY 83 (86)
T PRK09334 53 IKISVAKKVLRELEKRGVLVLYSKNR-RTPIY 83 (86)
T ss_pred chHHHHHHHHHHHHHCCCEEEEecCC-CeEEe
Confidence 45677899999999999987775543 55555
No 149
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=21.59 E-value=61 Score=16.84 Aligned_cols=15 Identities=20% Similarity=0.700 Sum_probs=7.8
Q ss_pred HHHHHHHHhcCCCCc
Q 038657 42 DIILGFVKDNGLEDS 56 (112)
Q Consensus 42 ~~Iy~Wv~~tG~~~t 56 (112)
.+||++...+|...|
T Consensus 5 ~lI~~YL~~~Gy~~t 19 (27)
T PF08513_consen 5 QLIYDYLVENGYKET 19 (27)
T ss_dssp HHHHHHHHHCT-HHH
T ss_pred HHHHHHHHHCCcHHH
Confidence 456666666665443
No 150
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=21.53 E-value=2.3e+02 Score=23.31 Aligned_cols=54 Identities=22% Similarity=0.329 Sum_probs=43.1
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCcc---ccCCCHHHHHHHHHHHHhcCceeE
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTE---LHGMDRTILMRALKLLEHKGKVAI 97 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~e---f~gmd~~vL~kaL~~L~k~gkAql 97 (112)
..++=|.+|+.+..++|= ++.=+|.+.+++ -.||...-++|||--|.|+||...
T Consensus 222 ~l~~daq~Il~yL~~~gG--------~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q 278 (287)
T COG2996 222 MLDEDAQMILTYLESNGG--------FMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ 278 (287)
T ss_pred hhhhhHHHHHHHHHHcCC--------ccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE
Confidence 357889999999999874 233455555554 579999999999999999999876
No 151
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=21.30 E-value=35 Score=18.96 Aligned_cols=17 Identities=29% Similarity=0.452 Sum_probs=12.5
Q ss_pred ccCCCHHHHHHHHHHHH
Q 038657 74 LHGMDRTILMRALKLLE 90 (112)
Q Consensus 74 f~gmd~~vL~kaL~~L~ 90 (112)
|.+||++++...++.|.
T Consensus 3 ~~~LP~~il~~Il~~l~ 19 (48)
T PF00646_consen 3 LSDLPDEILQEILSYLD 19 (48)
T ss_dssp HHHS-HHHHHHHHHTS-
T ss_pred HHHCCHHHHHHHHHHCc
Confidence 67899999999887653
No 152
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=21.18 E-value=1.3e+02 Score=24.37 Aligned_cols=48 Identities=17% Similarity=0.343 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHHHHhcCCCCceEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcC
Q 038657 36 RIQDWADIILGFVKDNGLEDSVMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKG 93 (112)
Q Consensus 36 ~~~eWa~~Iy~Wv~~tG~~~tV~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~g 93 (112)
|.+.--..+|.+++.+|..|-=.- +- ..=-+|+..+.-|||+.|+.++
T Consensus 82 tm~~~E~~vYs~i~~SG~EGiW~K----ti------k~rTNlh~~vV~kcLkSlESkr 129 (301)
T COG5111 82 TMDDYELTVYSLISQSGGEGIWLK----TI------KDRTNLHHNVVGKCLKSLESKR 129 (301)
T ss_pred ccchHHHHHHHHHHhcCCCceehh----hh------hhhccCcHHHHHHHHHHHHHHH
Confidence 466778899999999998763221 11 1235799999999999999876
No 153
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=21.17 E-value=1.6e+02 Score=20.51 Aligned_cols=33 Identities=24% Similarity=0.224 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCCCcEEEEEec
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKGHRKCLILWH 35 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~~~~~~I~Wr 35 (112)
++....+.+|.+|.++|...-..+.+ +..||=|
T Consensus 71 I~~SlAr~~Lr~L~~kG~Ik~V~k~~-~~~IYtr 103 (105)
T PF03297_consen 71 INGSLARKALRELESKGLIKPVSKHH-RQRIYTR 103 (105)
T ss_dssp CSCHHHHHHHHHHHHCCSSEEEECCT-TCEEEEE
T ss_pred hHHHHHHHHHHHHHHCCCEEEEeccC-CeEEEec
Confidence 45667899999999999988886654 5667655
No 154
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.07 E-value=2.4e+02 Score=19.52 Aligned_cols=55 Identities=15% Similarity=0.221 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecCC---CcEEEEEecChHHHHHHHHHHHHhcCCCCc
Q 038657 2 LNNEARETFLSALVSEGRAEWLDKG---HRKCLILWHRIQDWADIILGFVKDNGLEDS 56 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~~---~~~~~I~Wr~~~eWa~~Iy~Wv~~tG~~~t 56 (112)
.|+--.+.+|..|.+.|=..|.+.. +.+-+.+=++|++=-....+=.-+.|+...
T Consensus 31 cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~l~~g~~~~ 88 (115)
T PF12793_consen 31 CSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEELLEQGKYEQ 88 (115)
T ss_pred CCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHHHHcCCHHH
Confidence 4667789999999999999999753 335566667776644433333334444333
No 155
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=21.00 E-value=1.2e+02 Score=22.76 Aligned_cols=37 Identities=22% Similarity=0.361 Sum_probs=27.8
Q ss_pred CCCceEEeeeeccCCCcCCc-----cccCCCHHHHHHHHHHH
Q 038657 53 LEDSVMTVEEIRLGIESRGT-----ELHGMDRTILMRALKLL 89 (112)
Q Consensus 53 ~~~tV~TlyEL~~Gd~t~~~-----ef~gmd~~vL~kaL~~L 89 (112)
-.+++...|-|..|....+- +-.|+|++++.+|-++|
T Consensus 175 ~~~~l~~~ykl~~G~~~~s~a~~~a~~~g~~~~ii~rA~~~~ 216 (216)
T cd03284 175 KGGGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIERAREIL 216 (216)
T ss_pred eCCeEEEEEEECcCCCCCcHHHHHHHHhCcCHHHHHHHHHhC
Confidence 34667778999999764332 34799999999998764
No 156
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=21.00 E-value=5.9 Score=23.84 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHhcCC
Q 038657 38 QDWADIILGFVKDNGL 53 (112)
Q Consensus 38 ~eWa~~Iy~Wv~~tG~ 53 (112)
--.+..||.|++++|.
T Consensus 9 ~a~aa~vYk~~D~~G~ 24 (60)
T PF13511_consen 9 SAAAAEVYKWVDENGV 24 (60)
T ss_pred HHhhccEEEEECCCCC
Confidence 3456789999999997
No 157
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=20.72 E-value=2.2e+02 Score=17.45 Aligned_cols=24 Identities=17% Similarity=0.190 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHHhcCCeeEecC
Q 038657 2 LNNEARETFLSALVSEGRAEWLDK 25 (112)
Q Consensus 2 Ls~e~~~~Il~~lv~~g~aew~d~ 25 (112)
+|+..+...++.|++.|-++....
T Consensus 36 ~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 36 VSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred CCchhHHHHHHHHHHCCCeEecCC
Confidence 678889999999999999887644
No 158
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.42 E-value=1.1e+02 Score=14.71 Aligned_cols=15 Identities=13% Similarity=0.171 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHhcC
Q 038657 4 NEARETFLSALVSEG 18 (112)
Q Consensus 4 ~e~~~~Il~~lv~~g 18 (112)
.+....+++.|.++|
T Consensus 16 ~~~a~~~~~~M~~~g 30 (31)
T PF01535_consen 16 FEEALEVFDEMRERG 30 (31)
T ss_pred HHHHHHHHHHHhHCc
Confidence 456778888888776
No 159
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=20.22 E-value=2.2e+02 Score=20.96 Aligned_cols=28 Identities=18% Similarity=0.092 Sum_probs=24.2
Q ss_pred cccCCCHHHHHHHHHHHHhcCceeEEec
Q 038657 73 ELHGMDRTILMRALKLLEHKGKVAIFKG 100 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkAql~~~ 100 (112)
+-+|+...-++.||..|+..|=.++..+
T Consensus 38 e~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 38 SRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred HHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 3468999999999999999999888743
No 160
>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=20.18 E-value=1.3e+02 Score=16.80 Aligned_cols=23 Identities=43% Similarity=0.592 Sum_probs=18.3
Q ss_pred cccCCCHHHHHHHHHHHHhcCce
Q 038657 73 ELHGMDRTILMRALKLLEHKGKV 95 (112)
Q Consensus 73 ef~gmd~~vL~kaL~~L~k~gkA 95 (112)
+--|++.+-..+.|+.|++.|-.
T Consensus 25 ~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 25 EKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHhCCCHHHHHHHHHHHHHCcCc
Confidence 45689999999999999998853
No 161
>COG0174 GlnA Glutamine synthetase [Amino acid transport and metabolism]
Probab=20.16 E-value=1.5e+02 Score=25.52 Aligned_cols=34 Identities=29% Similarity=0.357 Sum_probs=25.9
Q ss_pred eEEeeeeccCCCcCCccccCCCHHHHHHHHHHHHhcCcee
Q 038657 57 VMTVEEIRLGIESRGTELHGMDRTILMRALKLLEHKGKVA 96 (112)
Q Consensus 57 V~TlyEL~~Gd~t~~~ef~gmd~~vL~kaL~~L~k~gkAq 96 (112)
+|.+|+- .++.|-+=|..+|+|+++.|.++|=.-
T Consensus 92 ~cdv~~~------~g~p~~~dPR~vlkr~~~~l~~~G~~~ 125 (443)
T COG0174 92 LCDVYDP------DGTPYPRDPRSVLKRALARLKDEGLAP 125 (443)
T ss_pred EEEEECC------CCCcCCCChHHHHHHHHHHHHhcCCcc
Confidence 4555554 244666689999999999999999653
Done!