Query psy2693
Match_columns 122
No_of_seqs 104 out of 167
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 22:47:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2693.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2693hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06957 COPI_C: Coatomer (COP 100.0 2.1E-43 4.7E-48 302.7 5.2 98 2-101 325-422 (422)
2 KOG0292|consensus 100.0 3.3E-33 7.2E-38 256.7 5.7 95 1-97 1108-1202(1202)
3 COG4391 Uncharacterized protei 92.6 0.076 1.7E-06 36.0 1.7 20 48-68 40-59 (62)
4 cd00350 rubredoxin_like Rubred 92.6 0.1 2.2E-06 30.3 2.0 26 58-83 2-27 (33)
5 PRK12496 hypothetical protein; 92.2 0.091 2E-06 40.3 1.9 35 46-80 110-150 (164)
6 PF05191 ADK_lid: Adenylate ki 91.6 0.13 2.8E-06 30.9 1.7 23 59-81 3-29 (36)
7 PF10276 zf-CHCC: Zinc-finger 91.4 0.14 3E-06 31.6 1.7 21 48-68 20-40 (40)
8 PF13240 zinc_ribbon_2: zinc-r 90.3 0.13 2.9E-06 28.0 0.8 20 59-80 1-20 (23)
9 PF14446 Prok-RING_1: Prokaryo 90.0 0.17 3.7E-06 33.3 1.3 28 41-71 8-35 (54)
10 PF08271 TF_Zn_Ribbon: TFIIB z 88.8 0.21 4.6E-06 30.2 1.0 23 59-81 2-27 (43)
11 PRK00398 rpoP DNA-directed RNA 87.3 0.55 1.2E-05 28.6 2.2 12 57-68 21-32 (46)
12 cd00729 rubredoxin_SM Rubredox 87.2 0.5 1.1E-05 27.8 1.9 25 58-82 3-27 (34)
13 PRK05452 anaerobic nitric oxid 86.5 2 4.3E-05 37.7 6.0 73 6-83 375-468 (479)
14 PF13248 zf-ribbon_3: zinc-rib 86.2 0.37 7.9E-06 26.6 0.9 22 58-81 3-24 (26)
15 PF00301 Rubredoxin: Rubredoxi 86.1 0.57 1.2E-05 29.7 1.8 26 58-83 2-44 (47)
16 TIGR02300 FYDLN_acid conserved 85.1 0.52 1.1E-05 35.9 1.5 33 41-73 9-42 (129)
17 PF09538 FYDLN_acid: Protein o 84.8 0.51 1.1E-05 34.4 1.4 30 41-70 9-39 (108)
18 PRK00420 hypothetical protein; 80.6 0.96 2.1E-05 33.5 1.4 27 58-84 24-51 (112)
19 PF13901 DUF4206: Domain of un 78.8 1.5 3.3E-05 34.4 2.1 38 42-80 156-196 (202)
20 PF13913 zf-C2HC_2: zinc-finge 78.7 0.83 1.8E-05 25.1 0.5 15 56-70 1-15 (25)
21 smart00659 RPOLCX RNA polymera 78.3 1.6 3.4E-05 27.2 1.7 23 44-68 8-30 (44)
22 COG1996 RPC10 DNA-directed RNA 78.2 1.4 3E-05 28.5 1.4 26 44-70 12-37 (49)
23 COG1645 Uncharacterized Zn-fin 75.9 1.5 3.2E-05 33.5 1.3 55 58-113 29-88 (131)
24 TIGR00622 ssl1 transcription f 75.7 1.9 4E-05 32.1 1.7 24 58-85 2-27 (112)
25 PF14354 Lar_restr_allev: Rest 74.1 1.7 3.6E-05 27.4 1.0 11 58-68 4-14 (61)
26 smart00531 TFIIE Transcription 73.8 2.6 5.7E-05 31.3 2.1 27 54-80 96-130 (147)
27 cd00730 rubredoxin Rubredoxin; 73.6 2.6 5.7E-05 26.9 1.8 12 59-70 3-14 (50)
28 PF14369 zf-RING_3: zinc-finge 71.2 3.1 6.7E-05 24.7 1.6 27 44-70 8-34 (35)
29 PRK00566 DNA-directed RNA poly 70.5 4.5 9.6E-05 40.1 3.4 63 16-83 17-82 (1156)
30 smart00834 CxxC_CXXC_SSSS Puta 69.5 2.7 5.8E-05 24.2 1.1 10 56-65 25-34 (41)
31 PRK14892 putative transcriptio 69.2 4.1 8.8E-05 29.5 2.2 31 52-82 16-51 (99)
32 TIGR03847 conserved hypothetic 69.2 2.7 5.8E-05 33.6 1.3 18 59-78 158-175 (177)
33 PF13465 zf-H2C2_2: Zinc-finge 69.0 3.4 7.3E-05 22.5 1.3 16 53-68 10-25 (26)
34 PF12660 zf-TFIIIC: Putative z 68.3 3.6 7.8E-05 29.2 1.7 31 39-70 38-68 (99)
35 PF14255 Cys_rich_CPXG: Cystei 68.2 2.5 5.3E-05 27.4 0.8 11 58-68 1-11 (52)
36 PF10571 UPF0547: Uncharacteri 68.1 2.9 6.4E-05 23.4 1.0 21 59-81 2-22 (26)
37 TIGR00100 hypA hydrogenase nic 68.0 4 8.7E-05 29.5 1.9 29 55-83 68-96 (115)
38 PF12773 DZR: Double zinc ribb 67.1 4.4 9.5E-05 24.5 1.7 25 54-80 26-50 (50)
39 PF01155 HypA: Hydrogenase exp 66.8 2 4.3E-05 30.9 0.1 30 55-84 68-97 (113)
40 PRK12380 hydrogenase nickel in 66.6 4.8 0.0001 29.1 2.1 28 55-82 68-95 (113)
41 PF05605 zf-Di19: Drought indu 65.7 3 6.5E-05 26.0 0.8 10 57-66 2-11 (54)
42 TIGR00595 priA primosomal prot 64.3 5.9 0.00013 35.0 2.7 38 44-85 228-265 (505)
43 TIGR02605 CxxC_CxxC_SSSS putat 64.3 4 8.7E-05 24.9 1.2 9 57-65 26-34 (52)
44 PF08274 PhnA_Zn_Ribbon: PhnA 64.3 3.1 6.6E-05 24.3 0.6 22 59-80 4-26 (30)
45 PF06677 Auto_anti-p27: Sjogre 64.0 4.5 9.8E-05 25.0 1.4 23 58-80 18-41 (41)
46 PF02892 zf-BED: BED zinc fing 63.7 4.3 9.4E-05 23.9 1.2 23 48-70 7-29 (45)
47 PRK00432 30S ribosomal protein 62.8 5.1 0.00011 25.5 1.5 26 58-83 21-47 (50)
48 PF11290 DUF3090: Protein of u 62.6 4.2 9.1E-05 32.3 1.3 16 59-76 156-171 (171)
49 PF03604 DNA_RNApol_7kD: DNA d 62.2 5.2 0.00011 23.5 1.3 15 54-68 14-28 (32)
50 PF07282 OrfB_Zn_ribbon: Putat 61.5 7.3 0.00016 24.9 2.1 27 56-82 27-55 (69)
51 PRK12495 hypothetical protein; 60.9 4.7 0.0001 33.3 1.3 23 57-80 42-65 (226)
52 PF13894 zf-C2H2_4: C2H2-type 60.0 5.1 0.00011 19.7 0.9 11 59-69 2-12 (24)
53 PF14206 Cys_rich_CPCC: Cystei 60.0 6.3 0.00014 27.5 1.7 28 58-85 2-32 (78)
54 COG1579 Zn-ribbon protein, pos 57.9 3.1 6.8E-05 34.3 -0.2 25 43-67 199-231 (239)
55 PRK13130 H/ACA RNA-protein com 57.7 8.5 0.00019 25.3 1.9 26 56-85 4-29 (56)
56 COG1592 Rubrerythrin [Energy p 57.6 7.3 0.00016 30.6 1.9 13 54-66 146-158 (166)
57 PRK14714 DNA polymerase II lar 57.5 6.9 0.00015 39.4 2.0 44 25-81 657-700 (1337)
58 PRK10246 exonuclease subunit S 57.0 4.6 0.0001 38.7 0.8 15 57-71 503-517 (1047)
59 PRK03824 hypA hydrogenase nick 56.9 8.5 0.00018 28.6 2.0 16 55-70 68-83 (135)
60 TIGR02098 MJ0042_CXXC MJ0042 f 56.9 7.9 0.00017 22.3 1.5 12 56-67 24-35 (38)
61 COG3931 Predicted N-formylglut 56.8 6.5 0.00014 33.2 1.5 67 37-110 142-234 (263)
62 PF14446 Prok-RING_1: Prokaryo 56.8 6.1 0.00013 26.0 1.1 26 56-81 4-29 (54)
63 PF01783 Ribosomal_L32p: Ribos 55.2 12 0.00027 23.9 2.3 23 56-81 25-47 (56)
64 PRK06266 transcription initiat 55.1 8 0.00017 30.0 1.7 28 54-81 114-144 (178)
65 PF06943 zf-LSD1: LSD1 zinc fi 54.7 8.4 0.00018 21.7 1.3 13 53-65 12-24 (25)
66 PF02150 RNA_POL_M_15KD: RNA p 54.5 4.8 0.0001 23.8 0.3 24 59-82 3-29 (35)
67 TIGR00373 conserved hypothetic 54.2 5.8 0.00013 30.1 0.8 26 55-80 107-135 (158)
68 PRK00464 nrdR transcriptional 54.0 7.3 0.00016 30.0 1.3 34 59-94 2-47 (154)
69 COG1545 Predicted nucleic-acid 53.2 9.6 0.00021 28.5 1.8 24 57-82 29-52 (140)
70 PF14447 Prok-RING_4: Prokaryo 51.7 8.2 0.00018 25.5 1.1 19 52-70 34-52 (55)
71 smart00661 RPOL9 RNA polymeras 51.7 11 0.00024 22.7 1.6 24 59-82 2-29 (52)
72 PF04981 NMD3: NMD3 family ; 50.8 7.5 0.00016 30.9 0.9 25 60-85 1-25 (236)
73 COG4530 Uncharacterized protei 50.2 8.1 0.00017 29.4 1.0 28 41-68 9-37 (129)
74 PF13878 zf-C2H2_3: zinc-finge 49.6 13 0.00027 22.6 1.6 14 57-70 13-26 (41)
75 TIGR02159 PA_CoA_Oxy4 phenylac 49.6 7.7 0.00017 29.5 0.8 21 57-77 105-128 (146)
76 TIGR03655 anti_R_Lar restricti 49.4 7.6 0.00016 24.3 0.6 10 59-68 3-12 (53)
77 TIGR02387 rpoC1_cyan DNA-direc 49.3 18 0.00038 33.9 3.2 51 28-83 33-86 (619)
78 PRK14873 primosome assembly pr 49.1 13 0.00028 34.5 2.3 64 12-84 358-433 (665)
79 PRK00564 hypA hydrogenase nick 49.0 12 0.00026 27.2 1.7 29 55-83 69-98 (117)
80 PRK02625 rpoC1 DNA-directed RN 48.5 19 0.00041 33.7 3.2 49 28-81 40-91 (627)
81 PF08792 A2L_zn_ribbon: A2L zi 48.3 11 0.00024 22.1 1.2 15 53-67 17-31 (33)
82 PF00096 zf-C2H2: Zinc finger, 46.5 10 0.00022 19.2 0.7 11 59-69 2-12 (23)
83 PF03811 Zn_Tnp_IS1: InsA N-te 46.4 10 0.00022 22.7 0.8 11 57-67 5-15 (36)
84 PRK05580 primosome assembly pr 46.4 16 0.00034 33.6 2.4 50 32-84 372-432 (679)
85 PRK00133 metG methionyl-tRNA s 46.2 30 0.00066 31.6 4.2 63 10-81 97-160 (673)
86 PF14353 CpXC: CpXC protein 45.8 12 0.00027 26.6 1.3 15 57-71 38-52 (128)
87 PRK12286 rpmF 50S ribosomal pr 45.7 14 0.0003 24.1 1.5 22 56-80 26-47 (57)
88 COG1675 TFA1 Transcription ini 45.6 18 0.00038 28.7 2.3 52 10-67 88-142 (176)
89 TIGR01053 LSD1 zinc finger dom 44.1 21 0.00046 20.7 1.9 14 53-66 15-28 (31)
90 PF11672 DUF3268: Protein of u 44.0 11 0.00025 27.4 0.9 32 57-89 2-46 (102)
91 TIGR01031 rpmF_bact ribosomal 43.8 15 0.00033 23.7 1.4 24 55-81 24-47 (55)
92 COG3809 Uncharacterized protei 42.8 14 0.00029 26.6 1.1 18 74-93 2-19 (88)
93 PF01430 HSP33: Hsp33 protein; 42.4 11 0.00023 30.8 0.6 16 53-68 262-277 (280)
94 PRK03681 hypA hydrogenase nick 42.1 20 0.00044 25.8 2.0 28 55-82 68-96 (114)
95 TIGR01384 TFS_arch transcripti 41.6 15 0.00031 25.4 1.1 22 60-81 3-24 (104)
96 COG0675 Transposase and inacti 41.6 13 0.00028 28.7 1.0 24 55-81 307-330 (364)
97 PHA00159 endonuclease I 41.6 26 0.00057 27.4 2.6 34 16-58 75-108 (148)
98 PF03833 PolC_DP2: DNA polymer 41.6 8.7 0.00019 37.3 0.0 63 10-82 629-701 (900)
99 COG1592 Rubrerythrin [Energy p 41.3 14 0.00031 29.0 1.1 24 57-81 134-157 (166)
100 COG1281 Disulfide bond chapero 41.0 13 0.00029 31.5 1.0 17 53-69 262-278 (286)
101 PF13719 zinc_ribbon_5: zinc-r 40.8 16 0.00036 21.4 1.1 12 58-69 3-14 (37)
102 PRK00423 tfb transcription ini 40.5 17 0.00038 30.0 1.6 27 55-81 9-38 (310)
103 smart00614 ZnF_BED BED zinc fi 40.3 18 0.00038 22.2 1.3 17 53-69 14-30 (50)
104 PF02591 DUF164: Putative zinc 40.3 10 0.00022 23.8 0.2 17 50-66 39-55 (56)
105 PF04606 Ogr_Delta: Ogr/Delta- 39.9 13 0.00029 22.8 0.6 10 59-68 1-10 (47)
106 PF04423 Rad50_zn_hook: Rad50 39.7 8.5 0.00018 24.0 -0.3 13 59-71 22-34 (54)
107 PF12172 DUF35_N: Rubredoxin-l 39.1 18 0.00039 20.8 1.1 22 58-81 12-33 (37)
108 COG1110 Reverse gyrase [DNA re 39.1 11 0.00025 37.4 0.3 38 43-84 682-719 (1187)
109 COG1439 Predicted nucleic acid 38.8 18 0.00039 28.9 1.4 24 55-80 137-160 (177)
110 CHL00018 rpoC1 RNA polymerase 38.7 42 0.0009 31.7 3.9 51 28-84 38-95 (663)
111 PF09889 DUF2116: Uncharacteri 38.3 13 0.00028 24.7 0.4 23 56-80 2-25 (59)
112 cd00498 Hsp33 Heat shock prote 38.1 16 0.00036 29.8 1.1 15 54-68 259-273 (275)
113 COG1405 SUA7 Transcription ini 37.9 18 0.00038 30.4 1.3 25 58-82 2-29 (285)
114 COG4049 Uncharacterized protei 37.7 12 0.00025 25.5 0.1 16 53-68 13-28 (65)
115 PRK14906 DNA-directed RNA poly 37.7 42 0.00091 34.4 4.0 61 17-82 20-83 (1460)
116 TIGR02487 NrdD anaerobic ribon 37.6 45 0.00098 30.3 3.9 46 13-66 500-547 (579)
117 PF03119 DNA_ligase_ZBD: NAD-d 37.5 19 0.00041 20.3 1.0 18 59-76 1-20 (28)
118 PRK08665 ribonucleotide-diphos 37.2 19 0.0004 33.9 1.4 26 58-83 725-750 (752)
119 PF09723 Zn-ribbon_8: Zinc rib 37.0 20 0.00043 21.6 1.1 11 55-65 24-34 (42)
120 PRK00114 hslO Hsp33-like chape 36.9 17 0.00038 30.0 1.1 15 54-68 265-279 (293)
121 KOG4080|consensus 36.6 11 0.00024 30.1 -0.1 22 55-79 91-112 (176)
122 COG4888 Uncharacterized Zn rib 36.5 16 0.00035 27.0 0.8 28 55-82 20-55 (104)
123 KOG2807|consensus 36.1 46 0.001 29.5 3.5 53 28-85 247-302 (378)
124 PRK06393 rpoE DNA-directed RNA 36.1 25 0.00054 23.8 1.5 43 57-105 5-47 (64)
125 COG1198 PriA Primosomal protei 35.9 89 0.0019 29.7 5.6 67 9-82 406-484 (730)
126 PF13824 zf-Mss51: Zinc-finger 35.5 27 0.00058 23.0 1.6 12 55-66 12-23 (55)
127 PF09297 zf-NADH-PPase: NADH p 35.5 18 0.00039 20.4 0.7 23 59-81 5-29 (32)
128 TIGR00269 conserved hypothetic 35.5 20 0.00043 25.2 1.1 23 55-81 78-100 (104)
129 TIGR03829 YokU_near_AblA uncha 35.3 17 0.00037 26.0 0.7 20 51-70 29-48 (89)
130 PF13717 zinc_ribbon_4: zinc-r 34.9 24 0.00051 20.8 1.2 11 58-68 3-13 (36)
131 PRK08351 DNA-directed RNA poly 34.7 35 0.00075 22.9 2.0 42 59-106 5-46 (61)
132 PRK12268 methionyl-tRNA synthe 34.6 71 0.0015 28.0 4.5 60 10-80 99-161 (556)
133 PRK06260 threonine synthase; V 34.3 27 0.00058 29.6 1.8 23 58-80 4-26 (397)
134 COG3919 Predicted ATP-grasp en 34.1 41 0.00089 29.8 2.9 34 5-38 242-275 (415)
135 smart00238 BIR Baculoviral inh 33.7 34 0.00074 21.7 1.9 18 52-69 30-48 (71)
136 PF09986 DUF2225: Uncharacteri 32.9 23 0.00049 28.1 1.1 31 55-85 3-60 (214)
137 PF06676 DUF1178: Protein of u 32.9 21 0.00046 27.5 0.9 16 54-69 29-44 (148)
138 COG4357 Zinc finger domain con 32.7 20 0.00044 26.5 0.8 30 41-72 62-95 (105)
139 PLN02294 cytochrome c oxidase 32.7 22 0.00047 28.5 0.9 28 46-74 127-158 (174)
140 PF07754 DUF1610: Domain of un 32.6 29 0.00063 19.3 1.2 19 44-64 4-23 (24)
141 PRK06450 threonine synthase; V 32.4 28 0.00061 29.2 1.6 22 58-80 4-25 (338)
142 KOG3352|consensus 32.2 80 0.0017 24.8 4.0 56 17-73 71-149 (153)
143 PRK07591 threonine synthase; V 31.7 29 0.00063 29.9 1.7 23 57-80 18-40 (421)
144 PF03884 DUF329: Domain of unk 31.7 37 0.0008 22.4 1.8 29 57-85 2-34 (57)
145 COG3677 Transposase and inacti 31.1 30 0.00066 25.6 1.5 35 43-77 35-73 (129)
146 COG2093 DNA-directed RNA polym 30.5 37 0.00081 23.2 1.7 30 73-104 18-47 (64)
147 PF14311 DUF4379: Domain of un 30.5 25 0.00054 21.9 0.8 37 43-79 14-55 (55)
148 PRK09783 copper/silver efflux 30.4 28 0.00061 29.7 1.3 33 41-75 44-76 (409)
149 TIGR03826 YvyF flagellar opero 30.3 17 0.00037 27.6 -0.0 22 58-80 4-25 (137)
150 PF14169 YdjO: Cold-inducible 30.0 31 0.00067 23.0 1.2 19 53-71 35-53 (59)
151 COG1656 Uncharacterized conser 29.7 49 0.0011 26.2 2.5 10 60-69 133-142 (165)
152 PF05325 DUF730: Protein of un 28.8 38 0.00083 25.3 1.6 32 31-63 19-50 (122)
153 COG1571 Predicted DNA-binding 28.7 31 0.00066 30.9 1.3 24 58-81 351-375 (421)
154 PF13806 Rieske_2: Rieske-like 28.5 34 0.00074 24.0 1.3 21 53-74 60-80 (104)
155 PRK01343 zinc-binding protein; 28.5 47 0.001 22.0 1.8 31 54-85 6-37 (57)
156 TIGR01206 lysW lysine biosynth 28.4 33 0.00072 22.3 1.1 13 56-68 21-33 (54)
157 cd00924 Cyt_c_Oxidase_Vb Cytoc 28.3 30 0.00064 24.9 1.0 26 47-73 66-95 (97)
158 TIGR00244 transcriptional regu 28.2 25 0.00054 27.3 0.6 7 59-65 2-8 (147)
159 cd03532 Rieske_RO_Alpha_VanA_D 28.1 56 0.0012 22.8 2.4 35 42-78 44-81 (116)
160 PF04641 Rtf2: Rtf2 RING-finge 27.9 56 0.0012 26.4 2.6 60 26-85 84-162 (260)
161 PF15616 TerY-C: TerY-C metal 27.9 58 0.0013 24.7 2.5 26 41-66 89-114 (131)
162 PF13408 Zn_ribbon_recom: Reco 27.9 35 0.00076 20.5 1.1 17 55-71 3-19 (58)
163 PF13395 HNH_4: HNH endonuclea 27.8 26 0.00057 21.9 0.5 11 60-70 1-11 (54)
164 COG4311 SoxD Sarcosine oxidase 27.5 25 0.00055 25.7 0.5 15 57-71 3-17 (97)
165 COG1143 NuoI Formate hydrogenl 27.4 44 0.00095 26.1 1.8 36 26-65 67-102 (172)
166 PRK14559 putative protein seri 26.8 37 0.0008 31.6 1.5 22 59-82 29-50 (645)
167 TIGR00201 comF comF family pro 26.7 31 0.00068 26.1 0.9 19 60-80 1-19 (190)
168 smart00109 C1 Protein kinase C 26.3 64 0.0014 18.3 2.0 23 59-81 13-35 (49)
169 PF08782 c-SKI_SMAD_bind: c-SK 26.1 26 0.00057 25.4 0.4 30 41-70 9-41 (96)
170 PF12760 Zn_Tnp_IS1595: Transp 25.8 32 0.0007 20.8 0.7 9 58-66 19-27 (46)
171 TIGR02487 NrdD anaerobic ribon 25.8 44 0.00095 30.4 1.8 25 55-81 522-546 (579)
172 PRK01402 hslO Hsp33-like chape 25.7 36 0.00079 29.0 1.2 15 54-68 305-319 (328)
173 cd00022 BIR Baculoviral inhibi 25.6 58 0.0013 20.5 1.9 15 55-69 32-46 (69)
174 PRK09263 anaerobic ribonucleos 25.5 42 0.00092 31.4 1.7 8 58-65 660-667 (711)
175 PRK10445 endonuclease VIII; Pr 25.5 1.5E+02 0.0032 24.1 4.7 63 10-80 196-262 (263)
176 PF14122 YokU: YokU-like prote 25.5 41 0.00089 24.2 1.2 18 53-70 31-48 (87)
177 PF13597 NRDD: Anaerobic ribon 25.4 77 0.0017 28.6 3.2 49 12-67 465-514 (546)
178 PRK09710 lar restriction allev 25.2 30 0.00066 23.5 0.5 9 58-66 7-15 (64)
179 PF11238 DUF3039: Protein of u 24.8 23 0.0005 23.7 -0.1 27 42-68 29-55 (58)
180 PF14569 zf-UDP: Zinc-binding 24.5 37 0.0008 24.1 0.9 22 68-92 4-25 (80)
181 PRK09678 DNA-binding transcrip 24.4 33 0.00072 23.5 0.6 9 59-67 3-11 (72)
182 PF14690 zf-ISL3: zinc-finger 24.0 37 0.00081 19.9 0.7 10 58-67 3-12 (47)
183 PRK14894 glycyl-tRNA synthetas 23.8 50 0.0011 30.5 1.8 40 41-80 62-111 (539)
184 PRK14526 adenylate kinase; Pro 23.4 51 0.0011 25.8 1.6 30 56-85 121-154 (211)
185 PHA02942 putative transposase; 23.2 76 0.0017 27.3 2.7 33 56-92 324-358 (383)
186 PF11475 VP_N-CPKC: Virion pro 23.2 10 0.00022 22.5 -1.8 18 41-65 7-24 (32)
187 PF06044 DRP: Dam-replacing fa 23.2 26 0.00057 29.5 -0.1 23 58-80 32-60 (254)
188 PRK00241 nudC NADH pyrophospha 23.2 45 0.00098 27.1 1.3 21 53-73 113-133 (256)
189 TIGR01374 soxD sarcosine oxida 23.0 31 0.00068 24.4 0.3 14 58-71 2-15 (84)
190 cd03531 Rieske_RO_Alpha_KSH Th 22.9 84 0.0018 22.1 2.5 56 43-103 42-100 (115)
191 PRK01103 formamidopyrimidine/5 22.8 1.4E+02 0.0029 24.3 3.9 65 10-80 200-272 (274)
192 PF09862 DUF2089: Protein of u 22.6 39 0.00084 25.1 0.7 24 60-85 1-24 (113)
193 PRK08579 anaerobic ribonucleos 22.6 52 0.0011 30.5 1.7 22 57-80 568-589 (625)
194 smart00647 IBR In Between Ring 22.5 78 0.0017 19.1 2.0 15 53-67 36-50 (64)
195 PRK09603 bifunctional DNA-dire 22.5 96 0.0021 34.1 3.6 62 17-83 1407-1472(2890)
196 cd03469 Rieske_RO_Alpha_N Ries 22.4 93 0.002 21.1 2.6 32 42-75 41-76 (118)
197 COG2260 Predicted Zn-ribbon RN 22.4 55 0.0012 22.0 1.3 18 59-80 7-24 (59)
198 TIGR02378 nirD_assim_sml nitri 22.3 55 0.0012 22.2 1.4 17 57-74 64-80 (105)
199 PRK08329 threonine synthase; V 22.3 49 0.0011 27.6 1.3 21 58-80 2-22 (347)
200 COG0333 RpmF Ribosomal protein 22.3 57 0.0012 21.6 1.4 22 57-81 27-48 (57)
201 PRK00420 hypothetical protein; 22.2 60 0.0013 24.0 1.6 28 44-71 26-54 (112)
202 PRK08271 anaerobic ribonucleos 22.1 56 0.0012 30.3 1.8 11 13-23 542-552 (623)
203 PF11023 DUF2614: Protein of u 22.0 41 0.00089 25.3 0.7 25 56-80 68-92 (114)
204 TIGR02386 rpoC_TIGR DNA-direct 21.8 91 0.002 31.3 3.2 61 18-83 11-74 (1140)
205 PF01215 COX5B: Cytochrome c o 21.7 25 0.00055 26.8 -0.4 27 46-73 98-128 (136)
206 PF11789 zf-Nse: Zinc-finger o 21.6 46 0.001 21.4 0.8 34 42-78 12-53 (57)
207 PF04267 SoxD: Sarcosine oxida 21.6 36 0.00077 24.1 0.3 14 58-71 2-15 (84)
208 PRK14810 formamidopyrimidine-D 21.5 1.7E+02 0.0037 23.8 4.3 66 10-80 199-271 (272)
209 PRK14844 bifunctional DNA-dire 21.5 92 0.002 34.2 3.3 62 17-83 1459-1523(2836)
210 cd03474 Rieske_T4moC Toluene-4 20.9 1E+02 0.0022 20.9 2.5 51 42-103 40-93 (108)
211 PF11793 FANCL_C: FANCL C-term 20.8 42 0.00091 22.2 0.5 13 58-70 56-68 (70)
212 PHA02551 19 tail tube protein; 20.8 59 0.0013 25.5 1.4 22 29-50 138-159 (163)
213 PRK05638 threonine synthase; V 20.7 58 0.0013 28.1 1.5 21 58-80 2-22 (442)
214 COG1327 Predicted transcriptio 20.5 43 0.00094 26.4 0.6 22 59-80 2-35 (156)
215 TIGR02827 RNR_anaer_Bdell anae 20.2 1.6E+02 0.0036 27.2 4.3 44 14-65 509-554 (586)
216 smart00249 PHD PHD zinc finger 20.2 77 0.0017 17.4 1.5 20 53-72 10-29 (47)
217 PF02489 Herpes_glycop_H: Herp 20.0 52 0.0011 29.9 1.1 27 42-68 546-572 (657)
No 1
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=100.00 E-value=2.1e-43 Score=302.70 Aligned_cols=98 Identities=54% Similarity=0.981 Sum_probs=72.3
Q ss_pred cccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693 2 EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 2 ~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+|||++|++++++||||||++|||+|||+|+||||+||||+||++||||||+|+++|+||||||+|+|+|||+||+||+|
T Consensus 325 RLLel~p~~~~a~qArKil~~~e~~~tDa~~i~yD~~npF~ICa~s~tPIY~G~~~v~CP~cgA~y~~~~kG~lC~vC~l 404 (422)
T PF06957_consen 325 RLLELNPSPEVAEQARKILQACERNPTDAHEIDYDERNPFDICAASYTPIYRGSPSVKCPYCGAKYHPEYKGQLCPVCEL 404 (422)
T ss_dssp HHHCT--SCHHHHHHHHHHHHHCCS--BSS--S--TTS-EEEBTTT--EEETTS-EEE-TTT--EEEGGGTTSB-TTTTT
T ss_pred HHHHcCCCHHHHHHHHHHHHHHhcCCCCceecCCCCCCCceeeecccccccCCCCCeeCCCCCCccChhhCCCCCCCCcc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCcccCcceecccch
Q psy2693 82 SVIDTHRNAYGLQICAGLMK 101 (122)
Q Consensus 82 s~IG~~~~a~GLr~~~~~~~ 101 (122)
++|| ++++|||++++|+|
T Consensus 405 ~~IG--~~a~GLris~~q~r 422 (422)
T PF06957_consen 405 SEIG--ADASGLRISPSQFR 422 (422)
T ss_dssp BBTT-----S----SGGG--
T ss_pred eeeC--CcceeeEecccccC
Confidence 9999 99999999999998
No 2
>KOG0292|consensus
Probab=99.97 E-value=3.3e-33 Score=256.73 Aligned_cols=95 Identities=47% Similarity=0.905 Sum_probs=93.0
Q ss_pred CcccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCccc
Q psy2693 1 MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 1 ~~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
|+||++.|++++|+|||||+++||+||+|+++|+||+||||+||++||+|||+|+|.++||||||+|+|.++|++|.||+
T Consensus 1108 ~rLlel~~~~~~A~q~rki~~a~eknp~Da~~l~yd~~n~f~iC~~t~~Piy~g~p~~~cp~cga~y~~~~~g~iCtvc~ 1187 (1202)
T KOG0292|consen 1108 RRLLELAPSPPVAEQARKIKQAAEKNPTDAYELNYDPHNPFVICGATYVPIYRGRPDVSCPYCGACFVPSSKGNICTVCD 1187 (1202)
T ss_pred HHHHhhCCCChHHHHHHHHHHHhhcCcccccccCcccCCCeeEecccceeeecCCCCcCCCcccceeccccCCceeeeee
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecCCCcccCcceec
Q psy2693 81 VSVIDTHRNAYGLQICA 97 (122)
Q Consensus 81 ls~IG~~~~a~GLr~~~ 97 (122)
|++|| ++++||||++
T Consensus 1188 V~~ig--~~~~Glris~ 1202 (1202)
T KOG0292|consen 1188 VGVIG--ADASGLRISA 1202 (1202)
T ss_pred eeeec--CcccceeecC
Confidence 99999 9999999964
No 3
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.65 E-value=0.076 Score=35.98 Aligned_cols=20 Identities=20% Similarity=0.629 Sum_probs=15.8
Q ss_pred ceeccCCCcceecCCCCceec
Q psy2693 48 YTPIYHGRESEACVYCGASYL 68 (122)
Q Consensus 48 ~tPIY~G~~~v~CP~CgA~Y~ 68 (122)
|-+| .-+.+|.|||||.+|.
T Consensus 40 ~L~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 40 FLDM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEc-CCCCcEecCccccEEE
Confidence 4444 4588999999999985
No 4
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.60 E-value=0.1 Score=30.27 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=21.9
Q ss_pred eecCCCCceecCCCCCcccCccccee
Q psy2693 58 EACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
-.|+.||-.|.++.....|++|+..+
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCcH
Confidence 36999999999988899999998653
No 5
>PRK12496 hypothetical protein; Provisional
Probab=92.20 E-value=0.091 Score=40.31 Aligned_cols=35 Identities=23% Similarity=0.660 Sum_probs=26.1
Q ss_pred ccceecc-CCCcc-----eecCCCCceecCCCCCcccCccc
Q psy2693 46 RSYTPIY-HGRES-----EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 46 ~S~tPIY-~G~~~-----v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
..+.+|. +|-.. ..|+-||..|.-.+.+..|++|+
T Consensus 110 i~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG 150 (164)
T PRK12496 110 IKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICG 150 (164)
T ss_pred CeEeccccccchhheeeeEECCCCCccccCCCCCCcCCCCC
Confidence 3445543 45444 35999999998888899999998
No 6
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=91.61 E-value=0.13 Score=30.91 Aligned_cols=23 Identities=26% Similarity=0.713 Sum_probs=19.4
Q ss_pred ecCCCCceecCCCC----CcccCcccc
Q psy2693 59 ACVYCGASYLPKYK----GELCAVCTV 81 (122)
Q Consensus 59 ~CP~CgA~Y~p~~k----G~lC~VC~l 81 (122)
.||-||+.|+-.|+ ..+|.+|+-
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCC
Confidence 69999999998776 488988874
No 7
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=91.35 E-value=0.14 Score=31.64 Aligned_cols=21 Identities=29% Similarity=0.757 Sum_probs=14.0
Q ss_pred ceeccCCCcceecCCCCceec
Q psy2693 48 YTPIYHGRESEACVYCGASYL 68 (122)
Q Consensus 48 ~tPIY~G~~~v~CP~CgA~Y~ 68 (122)
|=+|-+....+.|||||..|.
T Consensus 20 yl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 20 YLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp EEE-TTTTCEEEETTTTEEEE
T ss_pred EEecCCCCCeEECCCCCCEEC
Confidence 334433345799999999984
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.26 E-value=0.13 Score=28.05 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=16.6
Q ss_pred ecCCCCceecCCCCCcccCccc
Q psy2693 59 ACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.||.||+...+. .+.|+.|+
T Consensus 1 ~Cp~CG~~~~~~--~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDD--AKFCPNCG 20 (23)
T ss_pred CCcccCCCCCCc--CcchhhhC
Confidence 489999999876 78898886
No 9
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.00 E-value=0.17 Score=33.28 Aligned_cols=28 Identities=25% Similarity=0.711 Sum_probs=21.5
Q ss_pred eeeecccceeccCCCcceecCCCCceecCCC
Q psy2693 41 FQICARSYTPIYHGRESEACVYCGASYLPKY 71 (122)
Q Consensus 41 F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~ 71 (122)
=.+|...|+| |.+.|.||-|||.||-+-
T Consensus 8 C~~Cg~~~~~---~dDiVvCp~CgapyHR~C 35 (54)
T PF14446_consen 8 CPVCGKKFKD---GDDIVVCPECGAPYHRDC 35 (54)
T ss_pred ChhhCCcccC---CCCEEECCCCCCcccHHH
Confidence 3456665554 789999999999999763
No 10
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=88.81 E-value=0.21 Score=30.17 Aligned_cols=23 Identities=30% Similarity=0.866 Sum_probs=15.3
Q ss_pred ecCCCCceec--CCCCCc-ccCcccc
Q psy2693 59 ACVYCGASYL--PKYKGE-LCAVCTV 81 (122)
Q Consensus 59 ~CP~CgA~Y~--p~~kG~-lC~VC~l 81 (122)
+||.||+++. ....|+ +|+.|+.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 6999999762 233454 8999863
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.31 E-value=0.55 Score=28.63 Aligned_cols=12 Identities=42% Similarity=0.955 Sum_probs=7.3
Q ss_pred ceecCCCCceec
Q psy2693 57 SEACVYCGASYL 68 (122)
Q Consensus 57 ~v~CP~CgA~Y~ 68 (122)
..+||+||+...
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 566666666554
No 12
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=87.25 E-value=0.5 Score=27.77 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=16.6
Q ss_pred eecCCCCceecCCCCCcccCcccce
Q psy2693 58 EACVYCGASYLPKYKGELCAVCTVS 82 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ls 82 (122)
-.|+.||-.|.-+..-..|++|+..
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 4677777777655555677777653
No 13
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=86.50 E-value=2 Score=37.72 Aligned_cols=73 Identities=15% Similarity=0.138 Sum_probs=42.7
Q ss_pred cCCChHHHHH----HHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCC---------
Q psy2693 6 KFQIIPVATQ----ARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK--------- 72 (122)
Q Consensus 6 l~p~~~va~q----ArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~k--------- 72 (122)
..|..+..++ +|++.++-.+.|-++...+=+-..+-.. .+| -......+|+.||-.|.|+.-
T Consensus 375 ~~P~ee~~~~~~~~g~~la~~~~~~~~~~~~~~~~~~~~~~~----~~~-~~~~~~~~c~~c~~~yd~~~g~~~~~~~~g 449 (479)
T PRK05452 375 WRPDQDALELCREHGREIARQWALAPLPQSTVNTVVKEETSA----TTT-ADLGPRMQCSVCQWIYDPAKGEPMQDVAPG 449 (479)
T ss_pred ecCCHHHHHHHHHHHHHHHHHHhhCCcccccccccccccccc----ccc-cCCCCeEEECCCCeEECCCCCCcccCCCCC
Confidence 4455444433 5666655545555544333331111111 444 256788899999999999841
Q ss_pred --------CcccCccccee
Q psy2693 73 --------GELCAVCTVSV 83 (122)
Q Consensus 73 --------G~lC~VC~ls~ 83 (122)
.-.||+|+.++
T Consensus 450 t~~~~lp~~~~cp~c~~~k 468 (479)
T PRK05452 450 TPWSEVPDNFLCPECSLGK 468 (479)
T ss_pred CChhhCCCCCcCcCCCCcH
Confidence 13899998765
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=86.18 E-value=0.37 Score=26.63 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=17.3
Q ss_pred eecCCCCceecCCCCCcccCcccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+.||.||+...++ -+.|+.|+-
T Consensus 3 ~~Cp~Cg~~~~~~--~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcc--cccChhhCC
Confidence 5799999976666 678888874
No 15
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=86.12 E-value=0.57 Score=29.69 Aligned_cols=26 Identities=31% Similarity=0.667 Sum_probs=18.3
Q ss_pred eecCCCCceecCCCCC-----------------cccCccccee
Q psy2693 58 EACVYCGASYLPKYKG-----------------ELCAVCTVSV 83 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG-----------------~lC~VC~ls~ 83 (122)
.+|+.||-.|.|+.-. =.|++|+.++
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~K 44 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAPK 44 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSBG
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCcc
Confidence 4789999999988632 1788888765
No 16
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=85.08 E-value=0.52 Score=35.93 Aligned_cols=33 Identities=21% Similarity=0.449 Sum_probs=26.4
Q ss_pred eeeecccceeccC-CCcceecCCCCceecCCCCC
Q psy2693 41 FQICARSYTPIYH-GRESEACVYCGASYLPKYKG 73 (122)
Q Consensus 41 F~ICa~S~tPIY~-G~~~v~CP~CgA~Y~p~~kG 73 (122)
..+|..+=+.-|- ++..+.|||||+.|.+++..
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccCcchhh
Confidence 4577777777775 78899999999999998543
No 17
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=84.84 E-value=0.51 Score=34.42 Aligned_cols=30 Identities=20% Similarity=0.625 Sum_probs=22.1
Q ss_pred eeeecccceeccC-CCcceecCCCCceecCC
Q psy2693 41 FQICARSYTPIYH-GRESEACVYCGASYLPK 70 (122)
Q Consensus 41 F~ICa~S~tPIY~-G~~~v~CP~CgA~Y~p~ 70 (122)
-.+|..+=+.-|- ++..+.|||||+.|.++
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3456666666664 55668899999999998
No 18
>PRK00420 hypothetical protein; Validated
Probab=80.61 E-value=0.96 Score=33.46 Aligned_cols=27 Identities=26% Similarity=0.485 Sum_probs=16.5
Q ss_pred eecCCCCceecC-CCCCcccCcccceee
Q psy2693 58 EACVYCGASYLP-KYKGELCAVCTVSVI 84 (122)
Q Consensus 58 v~CP~CgA~Y~p-~~kG~lC~VC~ls~I 84 (122)
..||.||+...- +---..|++|+-..+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 467777776665 333346777776544
No 19
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=78.85 E-value=1.5 Score=34.43 Aligned_cols=38 Identities=18% Similarity=0.557 Sum_probs=29.5
Q ss_pred eeecccceeccC-C-CcceecCCCCceecCCC-CCcccCccc
Q psy2693 42 QICARSYTPIYH-G-RESEACVYCGASYLPKY-KGELCAVCT 80 (122)
Q Consensus 42 ~ICa~S~tPIY~-G-~~~v~CP~CgA~Y~p~~-kG~lC~VC~ 80 (122)
++|..+ .+||+ . +..++|+-|+|.||.+- ...-|+-|.
T Consensus 156 e~C~~~-~~IfPF~~~~~~~C~~C~~v~H~~C~~~~~CpkC~ 196 (202)
T PF13901_consen 156 EICNSD-DIIFPFQIDTTVRCPKCKSVFHKSCFRKKSCPKCA 196 (202)
T ss_pred ccCCCC-CCCCCCCCCCeeeCCcCccccchhhcCCCCCCCcH
Confidence 578777 99997 3 48999999999999764 334677764
No 20
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=78.70 E-value=0.83 Score=25.10 Aligned_cols=15 Identities=33% Similarity=0.815 Sum_probs=12.5
Q ss_pred cceecCCCCceecCC
Q psy2693 56 ESEACVYCGASYLPK 70 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~ 70 (122)
+.+.||+||-+|.|+
T Consensus 1 ~l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 1 ELVPCPICGRKFNPD 15 (25)
T ss_pred CCCcCCCCCCEECHH
Confidence 357899999999875
No 21
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.34 E-value=1.6 Score=27.17 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=15.8
Q ss_pred ecccceeccCCCcceecCCCCceec
Q psy2693 44 CARSYTPIYHGRESEACVYCGASYL 68 (122)
Q Consensus 44 Ca~S~tPIY~G~~~v~CP~CgA~Y~ 68 (122)
|...++. .....++||+||.+.+
T Consensus 8 Cg~~~~~--~~~~~irC~~CG~rIl 30 (44)
T smart00659 8 CGRENEI--KSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCEeec--CCCCceECCCCCceEE
Confidence 4444443 2467899999999876
No 22
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=78.24 E-value=1.4 Score=28.50 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=16.6
Q ss_pred ecccceeccCCCcceecCCCCceecCC
Q psy2693 44 CARSYTPIYHGRESEACVYCGASYLPK 70 (122)
Q Consensus 44 Ca~S~tPIY~G~~~v~CP~CgA~Y~p~ 70 (122)
|...+.-+ ...+.++|||||.+.+-+
T Consensus 12 Cg~~~~~~-~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 12 CGREVELD-QETRGIRCPYCGSRILVK 37 (49)
T ss_pred cCCeeehh-hccCceeCCCCCcEEEEe
Confidence 44444322 356778999999887644
No 23
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.94 E-value=1.5 Score=33.46 Aligned_cols=55 Identities=18% Similarity=0.372 Sum_probs=34.8
Q ss_pred eecCCCCceecCCCCCc-ccCcccceeecCCCcccC----cceecccchhhhhhccchhhh
Q psy2693 58 EACVYCGASYLPKYKGE-LCAVCTVSVIDTHRNAYG----LQICAGLMKSDVINNIDSSLA 113 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~-lC~VC~ls~IG~~~~a~G----Lr~~~~~~~~~~~~~~~~~~~ 113 (122)
..||-||...+- +.|+ .|+||+..+.+.-.+.-+ ........++.+..+++....
T Consensus 29 ~hCp~Cg~PLF~-KdG~v~CPvC~~~~~~v~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (131)
T COG1645 29 KHCPKCGTPLFR-KDGEVFCPVCGYREVVVEEEEEEVEAEVQEQLRRSRPELPDDSDELKK 88 (131)
T ss_pred hhCcccCCccee-eCCeEECCCCCceEEEeecccccchhhhhcchhhcccccccchhhhhc
Confidence 479999999998 5565 699999666651112222 244445666666666665543
No 24
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.67 E-value=1.9 Score=32.08 Aligned_cols=24 Identities=33% Similarity=0.725 Sum_probs=21.0
Q ss_pred eecCCCCcee--cCCCCCcccCcccceeec
Q psy2693 58 EACVYCGASY--LPKYKGELCAVCTVSVID 85 (122)
Q Consensus 58 v~CP~CgA~Y--~p~~kG~lC~VC~ls~IG 85 (122)
..||-|+|+| +| ..|+||+|.-|-
T Consensus 2 Y~CPrC~skvC~LP----~~CpiCgLtLVs 27 (112)
T TIGR00622 2 YFCPQCRAKVCELP----VECPICGLTLIL 27 (112)
T ss_pred ccCCCCCCCccCCC----CcCCcCCCEEec
Confidence 3699999999 77 589999999886
No 25
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=74.12 E-value=1.7 Score=27.38 Aligned_cols=11 Identities=27% Similarity=1.078 Sum_probs=7.5
Q ss_pred eecCCCCceec
Q psy2693 58 EACVYCGASYL 68 (122)
Q Consensus 58 v~CP~CgA~Y~ 68 (122)
.-|||||+.-.
T Consensus 4 kPCPFCG~~~~ 14 (61)
T PF14354_consen 4 KPCPFCGSADV 14 (61)
T ss_pred cCCCCCCCcce
Confidence 34999996543
No 26
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=73.78 E-value=2.6 Score=31.31 Aligned_cols=27 Identities=22% Similarity=0.472 Sum_probs=16.2
Q ss_pred CCcceecCCCCceecCC-------CCC-cccCccc
Q psy2693 54 GRESEACVYCGASYLPK-------YKG-ELCAVCT 80 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~p~-------~kG-~lC~VC~ 80 (122)
+.....||-||.+|... ..| =.|+.|+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg 130 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCG 130 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCC
Confidence 45667777777777541 112 4577775
No 27
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=73.57 E-value=2.6 Score=26.91 Aligned_cols=12 Identities=42% Similarity=0.941 Sum_probs=9.3
Q ss_pred ecCCCCceecCC
Q psy2693 59 ACVYCGASYLPK 70 (122)
Q Consensus 59 ~CP~CgA~Y~p~ 70 (122)
+|..||-.|.|+
T Consensus 3 ~C~~CgyiYd~~ 14 (50)
T cd00730 3 ECRICGYIYDPA 14 (50)
T ss_pred CCCCCCeEECCC
Confidence 678888888876
No 28
>PF14369 zf-RING_3: zinc-finger
Probab=71.17 E-value=3.1 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.383 Sum_probs=17.5
Q ss_pred ecccceeccCCCcceecCCCCceecCC
Q psy2693 44 CARSYTPIYHGRESEACVYCGASYLPK 70 (122)
Q Consensus 44 Ca~S~tPIY~G~~~v~CP~CgA~Y~p~ 70 (122)
|.++..+--.+.+.+.||.|+.-++-+
T Consensus 8 C~~~V~~~~~~~~~~~CP~C~~gFvEe 34 (35)
T PF14369_consen 8 CNRFVRIAPSPDSDVACPRCHGGFVEE 34 (35)
T ss_pred CCCEeEeCcCCCCCcCCcCCCCcEeEe
Confidence 444555433456667899999877643
No 29
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=70.54 E-value=4.5 Score=40.06 Aligned_cols=63 Identities=29% Similarity=0.595 Sum_probs=46.1
Q ss_pred HHHHHHHHhcCCCCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCccccee
Q psy2693 16 ARKLLAICNANPTDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 16 ArKIl~~ce~~~tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
..+|.+.+--.=+..-.|||.-+.| =-.|..=|.|+ ....| .||.....+|+|.+|.-|++-.
T Consensus 17 pe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~----kd~eC-~Cgkyk~~~~~~~~C~~cgve~ 82 (1156)
T PRK00566 17 PEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPT----KDYEC-LCGKYKRVRYKGIICERCGVEV 82 (1156)
T ss_pred HHHHHHhhcceEccccccccCCCccCCCCcccchhcCcc----cCcEE-eCccccccCcCCcCCCCCCcee
Confidence 3456666655556777899976654 33788888885 45788 9997666889999999997643
No 30
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=69.47 E-value=2.7 Score=24.23 Aligned_cols=10 Identities=30% Similarity=0.787 Sum_probs=5.2
Q ss_pred cceecCCCCc
Q psy2693 56 ESEACVYCGA 65 (122)
Q Consensus 56 ~~v~CP~CgA 65 (122)
+.+.||.||+
T Consensus 25 ~~~~CP~Cg~ 34 (41)
T smart00834 25 PLATCPECGG 34 (41)
T ss_pred CCCCCCCCCC
Confidence 3445555555
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=69.24 E-value=4.1 Score=29.48 Aligned_cols=31 Identities=19% Similarity=0.295 Sum_probs=19.7
Q ss_pred cCCCcceecCCCCceecC----C-CCCcccCcccce
Q psy2693 52 YHGRESEACVYCGASYLP----K-YKGELCAVCTVS 82 (122)
Q Consensus 52 Y~G~~~v~CP~CgA~Y~p----~-~kG~lC~VC~ls 82 (122)
++-...+.||+||+.-++ + -.-..|++|+..
T Consensus 16 ~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 16 PKLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred cCCCcEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 344567899999975553 0 113568888765
No 32
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=69.16 E-value=2.7 Score=33.59 Aligned_cols=18 Identities=33% Similarity=0.942 Sum_probs=16.5
Q ss_pred ecCCCCceecCCCCCcccCc
Q psy2693 59 ACVYCGASYLPKYKGELCAV 78 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~V 78 (122)
.||+||....|+ |.+|+-
T Consensus 158 ~CPlCg~PldP~--GH~Cpr 175 (177)
T TIGR03847 158 PCPLCGRPIDPD--GHICPR 175 (177)
T ss_pred CCCCCCCCCCCC--CccCCC
Confidence 599999999999 999974
No 33
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=69.04 E-value=3.4 Score=22.48 Aligned_cols=16 Identities=38% Similarity=0.949 Sum_probs=13.4
Q ss_pred CCCcceecCCCCceec
Q psy2693 53 HGRESEACVYCGASYL 68 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~ 68 (122)
.|+....||+|+.+|.
T Consensus 10 ~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSSEEESSSSEEES
T ss_pred CCCCCCCCCCCcCeeC
Confidence 4778899999998874
No 34
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=68.32 E-value=3.6 Score=29.19 Aligned_cols=31 Identities=26% Similarity=0.543 Sum_probs=17.7
Q ss_pred CCeeeecccceeccCCCcceecCCCCceecCC
Q psy2693 39 NPFQICARSYTPIYHGRESEACVYCGASYLPK 70 (122)
Q Consensus 39 npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~ 70 (122)
.-|.-|+.||-||- .-..-.|+.||.+|+..
T Consensus 38 H~w~RC~lT~l~i~-~~~~r~C~~C~~~~l~~ 68 (99)
T PF12660_consen 38 HVWPRCALTFLPIQ-TPGVRVCPVCGRRALDP 68 (99)
T ss_dssp -EEEB-SSS-SBS--SS-EEE-TTT--EEE-G
T ss_pred CEEeeeeeeeeeec-cCCeeEcCCCCCEEecC
Confidence 45999999999995 33337899999988754
No 35
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=68.20 E-value=2.5 Score=27.38 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=8.9
Q ss_pred eecCCCCceec
Q psy2693 58 EACVYCGASYL 68 (122)
Q Consensus 58 v~CP~CgA~Y~ 68 (122)
+.|||||....
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 57999998764
No 36
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=68.11 E-value=2.9 Score=23.44 Aligned_cols=21 Identities=29% Similarity=0.751 Sum_probs=14.7
Q ss_pred ecCCCCceecCCCCCcccCcccc
Q psy2693 59 ACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+||-|++...-. -+.|+.|+.
T Consensus 2 ~CP~C~~~V~~~--~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPES--AKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhh--cCcCCCCCC
Confidence 578888877544 567777764
No 37
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=67.97 E-value=4 Score=29.51 Aligned_cols=29 Identities=17% Similarity=0.314 Sum_probs=23.8
Q ss_pred CcceecCCCCceecCCCCCcccCccccee
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
....+|+-||..|.+......||.|+-..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 45689999999999976678899999544
No 38
>PF12773 DZR: Double zinc ribbon
Probab=67.08 E-value=4.4 Score=24.50 Aligned_cols=25 Identities=28% Similarity=0.796 Sum_probs=16.1
Q ss_pred CCcceecCCCCceecCCCCCcccCccc
Q psy2693 54 GRESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
....+.||.||+...+. -+.|+.|+
T Consensus 26 ~~~~~~C~~Cg~~~~~~--~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPN--AKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCC--cCccCccc
Confidence 34556777777776555 56666664
No 39
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=66.84 E-value=2 Score=30.90 Aligned_cols=30 Identities=20% Similarity=0.454 Sum_probs=21.7
Q ss_pred CcceecCCCCceecCCCCCcccCcccceee
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTVSVI 84 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~I 84 (122)
...++|.-||..|.++.....||.|+=..+
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSPDV 97 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS-E
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCCCc
Confidence 356899999999999888888999986654
No 40
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=66.56 E-value=4.8 Score=29.07 Aligned_cols=28 Identities=14% Similarity=0.262 Sum_probs=22.5
Q ss_pred CcceecCCCCceecCCCCCcccCcccce
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTVS 82 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~ls 82 (122)
....+|+-||..+.++...-.||.|+-.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 4578999999999987556669999943
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=65.70 E-value=3 Score=26.04 Aligned_cols=10 Identities=50% Similarity=1.148 Sum_probs=8.3
Q ss_pred ceecCCCCce
Q psy2693 57 SEACVYCGAS 66 (122)
Q Consensus 57 ~v~CP~CgA~ 66 (122)
+..|||||..
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 5689999993
No 42
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.33 E-value=5.9 Score=35.03 Aligned_cols=38 Identities=24% Similarity=0.408 Sum_probs=26.7
Q ss_pred ecccceeccCCCcceecCCCCceecCCCCCcccCcccceeec
Q psy2693 44 CARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVID 85 (122)
Q Consensus 44 Ca~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG 85 (122)
|..++|- ++.+...+|.|||..+... ..|+.|+-..+-
T Consensus 228 C~~~l~~-h~~~~~l~Ch~Cg~~~~~~---~~Cp~C~s~~l~ 265 (505)
T TIGR00595 228 CDVSLTY-HKKEGKLRCHYCGYQEPIP---KTCPQCGSEDLV 265 (505)
T ss_pred CCCceEE-ecCCCeEEcCCCcCcCCCC---CCCCCCCCCeeE
Confidence 3445554 3567789999999777643 589999866554
No 43
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=64.32 E-value=4 Score=24.92 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=4.2
Q ss_pred ceecCCCCc
Q psy2693 57 SEACVYCGA 65 (122)
Q Consensus 57 ~v~CP~CgA 65 (122)
.+.||.||+
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 344555554
No 44
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=64.29 E-value=3.1 Score=24.26 Aligned_cols=22 Identities=27% Similarity=0.717 Sum_probs=8.5
Q ss_pred ecCCCCceec-CCCCCcccCccc
Q psy2693 59 ACVYCGASYL-PKYKGELCAVCT 80 (122)
Q Consensus 59 ~CP~CgA~Y~-p~~kG~lC~VC~ 80 (122)
+||.||+.|. .+-.--+|+-|.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECG 26 (30)
T ss_dssp --TTT-----EE-SSSEEETTTT
T ss_pred CCCCCCCcceeccCCEEeCCccc
Confidence 6889988775 443445666664
No 45
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=64.02 E-value=4.5 Score=24.96 Aligned_cols=23 Identities=30% Similarity=0.790 Sum_probs=14.5
Q ss_pred eecCCCCceecCCCCC-cccCccc
Q psy2693 58 EACVYCGASYLPKYKG-ELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG-~lC~VC~ 80 (122)
..||-||........| .+|++|+
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCCC
Confidence 4677888777763333 4576664
No 46
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=63.65 E-value=4.3 Score=23.91 Aligned_cols=23 Identities=26% Similarity=0.561 Sum_probs=13.6
Q ss_pred ceeccCCCcceecCCCCceecCC
Q psy2693 48 YTPIYHGRESEACVYCGASYLPK 70 (122)
Q Consensus 48 ~tPIY~G~~~v~CP~CgA~Y~p~ 70 (122)
|+++..+...++|-||+..+.-.
T Consensus 7 F~~~~~~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 7 FTKIPGDKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CEE--GCSS-EEETTTTEE----
T ss_pred EEEccCCcCeEEeCCCCeEEeeC
Confidence 45555789999999999988754
No 47
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.83 E-value=5.1 Score=25.47 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=20.1
Q ss_pred eecCCCCc-eecCCCCCcccCccccee
Q psy2693 58 EACVYCGA-SYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 58 v~CP~CgA-~Y~p~~kG~lC~VC~ls~ 83 (122)
..||-||+ -..+....-.|.-|+..+
T Consensus 21 ~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcchheccCCcEECCCcCCEE
Confidence 48999999 566666677899988764
No 48
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=62.64 E-value=4.2 Score=32.28 Aligned_cols=16 Identities=38% Similarity=1.136 Sum_probs=14.8
Q ss_pred ecCCCCceecCCCCCccc
Q psy2693 59 ACVYCGASYLPKYKGELC 76 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC 76 (122)
.||+||....|+ |.+|
T Consensus 156 ~CPlCg~PlDP~--GH~C 171 (171)
T PF11290_consen 156 PCPLCGEPLDPE--GHIC 171 (171)
T ss_pred CCCCCCCCCCCC--CCcC
Confidence 599999999999 9988
No 49
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=62.23 E-value=5.2 Score=23.50 Aligned_cols=15 Identities=27% Similarity=0.547 Sum_probs=10.7
Q ss_pred CCcceecCCCCceec
Q psy2693 54 GRESEACVYCGASYL 68 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~ 68 (122)
..+.++||+||.+.+
T Consensus 14 ~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 14 PGDPIRCPECGHRIL 28 (32)
T ss_dssp TSSTSSBSSSS-SEE
T ss_pred CCCcEECCcCCCeEE
Confidence 356789999998754
No 50
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=61.52 E-value=7.3 Score=24.91 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=19.2
Q ss_pred cceecCCCCceecC--CCCCcccCcccce
Q psy2693 56 ESEACVYCGASYLP--KYKGELCAVCTVS 82 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p--~~kG~lC~VC~ls 82 (122)
.+-.||.||..... ....-.|+.|+..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45668888887776 6666678887765
No 51
>PRK12495 hypothetical protein; Provisional
Probab=60.86 E-value=4.7 Score=33.34 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=16.9
Q ss_pred ceecCCCCceecCCCCCcc-cCccc
Q psy2693 57 SEACVYCGASYLPKYKGEL-CAVCT 80 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~l-C~VC~ 80 (122)
...|+.||.... .+.|.+ |++|+
T Consensus 42 a~hC~~CG~PIp-a~pG~~~Cp~CQ 65 (226)
T PRK12495 42 NAHCDECGDPIF-RHDGQEFCPTCQ 65 (226)
T ss_pred hhhcccccCccc-CCCCeeECCCCC
Confidence 456888888766 667765 88887
No 52
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=60.03 E-value=5.1 Score=19.69 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=6.8
Q ss_pred ecCCCCceecC
Q psy2693 59 ACVYCGASYLP 69 (122)
Q Consensus 59 ~CP~CgA~Y~p 69 (122)
.|++||..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 68999888753
No 53
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=60.01 E-value=6.3 Score=27.46 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=21.0
Q ss_pred eecCCCCceecCCCC---CcccCcccceeec
Q psy2693 58 EACVYCGASYLPKYK---GELCAVCTVSVID 85 (122)
Q Consensus 58 v~CP~CgA~Y~p~~k---G~lC~VC~ls~IG 85 (122)
+.||-||-.-+++-. -.+|+||.---=|
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~ 32 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWEDDG 32 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcccCC
Confidence 579999999887653 3599999765444
No 54
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=57.93 E-value=3.1 Score=34.29 Aligned_cols=25 Identities=24% Similarity=0.541 Sum_probs=18.6
Q ss_pred eecccceecc--------CCCcceecCCCCcee
Q psy2693 43 ICARSYTPIY--------HGRESEACVYCGASY 67 (122)
Q Consensus 43 ICa~S~tPIY--------~G~~~v~CP~CgA~Y 67 (122)
+|++=+--|+ ++.+.|+||+||+..
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 6766555544 578999999999853
No 55
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=57.68 E-value=8.5 Score=25.31 Aligned_cols=26 Identities=31% Similarity=0.682 Sum_probs=20.9
Q ss_pred cceecCCCCceecCCCCCcccCcccceeec
Q psy2693 56 ESEACVYCGASYLPKYKGELCAVCTVSVID 85 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG 85 (122)
...+|+-||...+ ...|++|+....-
T Consensus 4 ~mr~C~~CgvYTL----k~~CP~CG~~t~~ 29 (56)
T PRK13130 4 KIRKCPKCGVYTL----KEICPVCGGKTKN 29 (56)
T ss_pred cceECCCCCCEEc----cccCcCCCCCCCC
Confidence 4568999999999 6789999876555
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=57.63 E-value=7.3 Score=30.56 Aligned_cols=13 Identities=46% Similarity=1.050 Sum_probs=7.4
Q ss_pred CCcceecCCCCce
Q psy2693 54 GRESEACVYCGAS 66 (122)
Q Consensus 54 G~~~v~CP~CgA~ 66 (122)
|.+...||.|||.
T Consensus 146 ge~P~~CPiCga~ 158 (166)
T COG1592 146 GEAPEVCPICGAP 158 (166)
T ss_pred CCCCCcCCCCCCh
Confidence 3555666666653
No 57
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=57.47 E-value=6.9 Score=39.37 Aligned_cols=44 Identities=25% Similarity=0.522 Sum_probs=24.0
Q ss_pred cCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693 25 ANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 25 ~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+.+.-++++. +..|..==++++. ..||.||+...|.| .|+.|+.
T Consensus 657 ~~G~ieVEV~------~rkCPkCG~~t~~----~fCP~CGs~te~vy---~CPsCGa 700 (1337)
T PRK14714 657 EGGVIEVEVG------RRRCPSCGTETYE----NRCPDCGTHTEPVY---VCPDCGA 700 (1337)
T ss_pred cCCeEEEEEE------EEECCCCCCcccc----ccCcccCCcCCCce---eCccCCC
Confidence 4444445554 4556554444432 27777777765554 5666655
No 58
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=57.04 E-value=4.6 Score=38.68 Aligned_cols=15 Identities=27% Similarity=0.780 Sum_probs=12.2
Q ss_pred ceecCCCCceecCCC
Q psy2693 57 SEACVYCGASYLPKY 71 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~ 71 (122)
-.-||.|||..||.-
T Consensus 503 GePCPVCGS~~HP~~ 517 (1047)
T PRK10246 503 GQPCPLCGSTSHPAV 517 (1047)
T ss_pred CCCcCCCCcccCcCc
Confidence 445999999999954
No 59
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.89 E-value=8.5 Score=28.60 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=12.8
Q ss_pred CcceecCCCCceecCC
Q psy2693 55 RESEACVYCGASYLPK 70 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~ 70 (122)
.....|+-||..+..+
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3678899999888775
No 60
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=56.85 E-value=7.9 Score=22.28 Aligned_cols=12 Identities=25% Similarity=0.648 Sum_probs=7.7
Q ss_pred cceecCCCCcee
Q psy2693 56 ESEACVYCGASY 67 (122)
Q Consensus 56 ~~v~CP~CgA~Y 67 (122)
..++||.||..+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 367777777654
No 61
>COG3931 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=56.78 E-value=6.5 Score=33.16 Aligned_cols=67 Identities=24% Similarity=0.371 Sum_probs=40.1
Q ss_pred CCCCeeeecccceeccCCCccee-------------cCC-------------CCceecCCCCCcccCcccceeecCCCcc
Q psy2693 37 EHNPFQICARSYTPIYHGRESEA-------------CVY-------------CGASYLPKYKGELCAVCTVSVIDTHRNA 90 (122)
Q Consensus 37 ~~npF~ICa~S~tPIY~G~~~v~-------------CP~-------------CgA~Y~p~~kG~lC~VC~ls~IG~~~~a 90 (122)
.+.+|.+---||||+|+|.+.-- .|+ -.-.|.|.-.+. -.+=.|+.+
T Consensus 142 G~~~~vvsvHSFTPvy~G~~Rpw~iGiL~d~D~R~a~pll~~lr~~~~l~Vg~NEPY~~ad~~~-------~Tl~rH~~~ 214 (263)
T COG3931 142 GRAPFVVSVHSFTPVYKGRPRPWHIGILHDNDDRLADPLLAALRANAGLTVGDNEPYDPADRVD-------DTLYRHAIA 214 (263)
T ss_pred CCCcEEEEEeccCccccCCCCccEEEEeeccchhHHHHHHHHHHhcCCcEeccCCCCCcccccc-------chhhhhhcc
Confidence 35689999999999999976310 000 111223322210 112235677
Q ss_pred cCcceecccchhhhhhccch
Q psy2693 91 YGLQICAGLMKSDVINNIDS 110 (122)
Q Consensus 91 ~GLr~~~~~~~~~~~~~~~~ 110 (122)
-|+-....-.|.|.|++-..
T Consensus 215 rG~p~vliEIRnDlIad~~g 234 (263)
T COG3931 215 RGLPHVLIEIRNDLIADEGG 234 (263)
T ss_pred cCccchhhhhhhhhhcChhH
Confidence 88877778888888876543
No 62
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.77 E-value=6.1 Score=26.00 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=22.6
Q ss_pred cceecCCCCceecCCCCCcccCcccc
Q psy2693 56 ESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
...+|+.||-.+.++-..-+|+.|+-
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~Cga 29 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGA 29 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCC
Confidence 34689999999999999999999974
No 63
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=55.19 E-value=12 Score=23.93 Aligned_cols=23 Identities=30% Similarity=0.807 Sum_probs=18.6
Q ss_pred cceecCCCCceecCCCCCcccCcccc
Q psy2693 56 ESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
..+.||-||+.-+|- .+|+-|+.
T Consensus 25 ~l~~c~~cg~~~~~H---~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPH---RVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEESTT---SBCTTTBB
T ss_pred ceeeeccCCCEeccc---EeeCCCCe
Confidence 568999999877775 68999964
No 64
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.07 E-value=8 Score=30.04 Aligned_cols=28 Identities=18% Similarity=0.265 Sum_probs=18.8
Q ss_pred CCcceecCCCCceecCC---CCCcccCcccc
Q psy2693 54 GRESEACVYCGASYLPK---YKGELCAVCTV 81 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~p~---~kG~lC~VC~l 81 (122)
...+..||-||.+|.-. -.|=.|++|+=
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 45667788888887532 13778888863
No 65
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=54.65 E-value=8.4 Score=21.74 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=11.8
Q ss_pred CCCcceecCCCCc
Q psy2693 53 HGRESEACVYCGA 65 (122)
Q Consensus 53 ~G~~~v~CP~CgA 65 (122)
+|.++|+|+.|.+
T Consensus 12 ~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 12 RGAPSVRCACCHT 24 (25)
T ss_pred CCCCCeECCccCc
Confidence 6999999999975
No 66
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=54.48 E-value=4.8 Score=23.76 Aligned_cols=24 Identities=33% Similarity=0.692 Sum_probs=18.5
Q ss_pred ecCCCCceecCCCCCcc---cCcccce
Q psy2693 59 ACVYCGASYLPKYKGEL---CAVCTVS 82 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~l---C~VC~ls 82 (122)
.||.||.-..|+-.... |+.|+..
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCc
Confidence 58899988888877777 8888754
No 67
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=54.19 E-value=5.8 Score=30.12 Aligned_cols=26 Identities=12% Similarity=0.098 Sum_probs=13.0
Q ss_pred CcceecCCCCceecCCC---CCcccCccc
Q psy2693 55 RESEACVYCGASYLPKY---KGELCAVCT 80 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~---kG~lC~VC~ 80 (122)
..+..||-|+++|.-.- .|=.|++|+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg 135 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCG 135 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCC
Confidence 34445555665553211 255666665
No 68
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=53.99 E-value=7.3 Score=29.98 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=22.5
Q ss_pred ecCCCCc--------eecCC-CC---CcccCcccceeecCCCcccCcc
Q psy2693 59 ACVYCGA--------SYLPK-YK---GELCAVCTVSVIDTHRNAYGLQ 94 (122)
Q Consensus 59 ~CP~CgA--------~Y~p~-~k---G~lC~VC~ls~IG~~~~a~GLr 94 (122)
+|||||. .|.++ +. -.-|+-|+-.=.+ .+..++.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~--~e~~~~~ 47 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT--FERVELV 47 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE--eEeccCc
Confidence 6999995 33333 00 1569999988877 7777663
No 69
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=53.16 E-value=9.6 Score=28.47 Aligned_cols=24 Identities=29% Similarity=0.827 Sum_probs=20.8
Q ss_pred ceecCCCCceecCCCCCcccCcccce
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCTVS 82 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~ls 82 (122)
-.+|+-||..|+|- -..|+-|+-.
T Consensus 29 g~kC~~CG~v~~PP--r~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFPP--RAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcCC--cccCCCCCCC
Confidence 46899999999998 6889999876
No 70
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=51.74 E-value=8.2 Score=25.54 Aligned_cols=19 Identities=21% Similarity=0.768 Sum_probs=15.8
Q ss_pred cCCCcceecCCCCceecCC
Q psy2693 52 YHGRESEACVYCGASYLPK 70 (122)
Q Consensus 52 Y~G~~~v~CP~CgA~Y~p~ 70 (122)
+.|+.+--|||||.++.+.
T Consensus 34 f~~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 34 FPGERYNGCPFCGTPFEFD 52 (55)
T ss_pred cChhhccCCCCCCCcccCC
Confidence 4688999999999988754
No 71
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=51.70 E-value=11 Score=22.68 Aligned_cols=24 Identities=29% Similarity=0.654 Sum_probs=14.4
Q ss_pred ecCCCCceecCCCC----CcccCcccce
Q psy2693 59 ACVYCGASYLPKYK----GELCAVCTVS 82 (122)
Q Consensus 59 ~CP~CgA~Y~p~~k----G~lC~VC~ls 82 (122)
.||.||.-..++-. --+|+.|+..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 47777776665532 1357777754
No 72
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=50.78 E-value=7.5 Score=30.92 Aligned_cols=25 Identities=32% Similarity=0.729 Sum_probs=16.2
Q ss_pred cCCCCceecCCCCCcccCcccceeec
Q psy2693 60 CVYCGASYLPKYKGELCAVCTVSVID 85 (122)
Q Consensus 60 CP~CgA~Y~p~~kG~lC~VC~ls~IG 85 (122)
||.||..-.|.+. .+|.-|-+.+.+
T Consensus 1 C~~CG~~~~~~~~-~lC~~C~~~~~~ 25 (236)
T PF04981_consen 1 CPRCGREIEPLID-GLCPDCYLKRFD 25 (236)
T ss_pred CCCCCCCCCCccc-ccChHHhcccCC
Confidence 7777776665543 377777666655
No 73
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.24 E-value=8.1 Score=29.39 Aligned_cols=28 Identities=25% Similarity=0.370 Sum_probs=22.0
Q ss_pred eeeecccceeccC-CCcceecCCCCceec
Q psy2693 41 FQICARSYTPIYH-GRESEACVYCGASYL 68 (122)
Q Consensus 41 F~ICa~S~tPIY~-G~~~v~CP~CgA~Y~ 68 (122)
-.||..+=+..|- .+..+.|||||.+|-
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~P 37 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSYP 37 (129)
T ss_pred cccCccccchhhccCCCccccCcccccch
Confidence 4577777777775 677889999999993
No 74
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=49.64 E-value=13 Score=22.58 Aligned_cols=14 Identities=36% Similarity=0.878 Sum_probs=11.8
Q ss_pred ceecCCCCceecCC
Q psy2693 57 SEACVYCGASYLPK 70 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~ 70 (122)
.++||.||=.|.|.
T Consensus 13 ~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 13 ATTCPTCGMLYSPG 26 (41)
T ss_pred CcCCCCCCCEECCC
Confidence 47999999999875
No 75
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=49.60 E-value=7.7 Score=29.45 Aligned_cols=21 Identities=24% Similarity=0.551 Sum_probs=15.0
Q ss_pred ceecCCCCceec---CCCCCcccC
Q psy2693 57 SEACVYCGASYL---PKYKGELCA 77 (122)
Q Consensus 57 ~v~CP~CgA~Y~---p~~kG~lC~ 77 (122)
.|.||+|||.+- .+|-.+.|+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~ck 128 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACK 128 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhH
Confidence 599999999864 455555553
No 76
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=49.42 E-value=7.6 Score=24.33 Aligned_cols=10 Identities=30% Similarity=1.125 Sum_probs=8.0
Q ss_pred ecCCCCceec
Q psy2693 59 ACVYCGASYL 68 (122)
Q Consensus 59 ~CP~CgA~Y~ 68 (122)
-|||||..-.
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 5999998655
No 77
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=49.34 E-value=18 Score=33.87 Aligned_cols=51 Identities=29% Similarity=0.594 Sum_probs=36.1
Q ss_pred CCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCccccee
Q psy2693 28 TDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 28 tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
+...+|||-.+.| =-.|-.-|-|+. +-.| .||..-.-+|+|.+|.-|++--
T Consensus 33 ~kp~TinyrT~KPE~dGLFCerIFGP~k----~~eC-~CGkyk~~~~~~~~C~~CgvE~ 86 (619)
T TIGR02387 33 TKPETINYRTLKPEMDGLFCEKIFGPSK----DWEC-HCGKYKRVRHRGIVCERCGVEV 86 (619)
T ss_pred CCCcccccCCCCCCCCCEeechhcCCCc----CcEE-eCCCccccCcCCcCCCCCCCEE
Confidence 4556889865544 347888888864 4567 8995333578999999997543
No 78
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.05 E-value=13 Score=34.48 Aligned_cols=64 Identities=16% Similarity=0.235 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHhcCCCCceeecCCCCCCeeee------------cccceeccCCCcceecCCCCceecCCCCCcccCcc
Q psy2693 12 VATQARKLLAICNANPTDEHTIDYDEHNPFQIC------------ARSYTPIYHGRESEACVYCGASYLPKYKGELCAVC 79 (122)
Q Consensus 12 va~qArKIl~~ce~~~tDa~eIdYD~~npF~IC------------a~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC 79 (122)
..+..++.|+ ++ .==+.+|-.-+.||..| ..++|- .+++...+|.|||... ....|+.|
T Consensus 358 l~~~i~~~L~---~g-qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~-h~~~~~l~Ch~CG~~~----~p~~Cp~C 428 (665)
T PRK14873 358 AFRAARDALE---HG-PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGL-PSAGGTPRCRWCGRAA----PDWRCPRC 428 (665)
T ss_pred HHHHHHHHHh---cC-cEEEEecCCCCCCeeEhhhCcCeeECCCCCCceeE-ecCCCeeECCCCcCCC----cCccCCCC
Confidence 3344444443 33 33456677778888765 445553 3567789999999753 26799999
Q ss_pred cceee
Q psy2693 80 TVSVI 84 (122)
Q Consensus 80 ~ls~I 84 (122)
+=..+
T Consensus 429 gs~~l 433 (665)
T PRK14873 429 GSDRL 433 (665)
T ss_pred cCCcc
Confidence 86544
No 79
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.03 E-value=12 Score=27.16 Aligned_cols=29 Identities=17% Similarity=0.384 Sum_probs=21.3
Q ss_pred CcceecCCCCceecCCCCCcc-cCccccee
Q psy2693 55 RESEACVYCGASYLPKYKGEL-CAVCTVSV 83 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~l-C~VC~ls~ 83 (122)
....+|.-||..+.+...+.. ||-|+=..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 467899999988887643444 99998443
No 80
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=48.51 E-value=19 Score=33.72 Aligned_cols=49 Identities=29% Similarity=0.594 Sum_probs=35.4
Q ss_pred CCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693 28 TDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 28 tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+...+|||-.+.| =-.|-.-|-|+. +-.| .||..-.-+|+|.+|.-|++
T Consensus 40 ~kpeTinyrT~KPE~dGLFCerIFGP~k----~~eC-~CGkyk~~~~~~~~C~~Cgv 91 (627)
T PRK02625 40 TKPETINYRTLKPEMDGLFCEKIFGPSK----DWEC-HCGKYKRVRHRGIVCERCGV 91 (627)
T ss_pred CCCcccccCCCCCCCCCEeechhcCCcc----CcEE-eCCCccccCcCCcCCCCCCc
Confidence 4556889876544 347888888874 4567 78853335789999999987
No 81
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=48.25 E-value=11 Score=22.10 Aligned_cols=15 Identities=33% Similarity=1.114 Sum_probs=11.1
Q ss_pred CCCcceecCCCCcee
Q psy2693 53 HGRESEACVYCGASY 67 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y 67 (122)
+-+....|++||++|
T Consensus 17 ~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSF 31 (33)
T ss_pred ecCCeEEcccCCcEe
Confidence 666777788888776
No 82
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=46.51 E-value=10 Score=19.18 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=8.8
Q ss_pred ecCCCCceecC
Q psy2693 59 ACVYCGASYLP 69 (122)
Q Consensus 59 ~CP~CgA~Y~p 69 (122)
+||.||..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 68999988864
No 83
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=46.42 E-value=10 Score=22.72 Aligned_cols=11 Identities=18% Similarity=0.489 Sum_probs=9.2
Q ss_pred ceecCCCCcee
Q psy2693 57 SEACVYCGASY 67 (122)
Q Consensus 57 ~v~CP~CgA~Y 67 (122)
.|.||+|++.-
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 58999999875
No 84
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.41 E-value=16 Score=33.57 Aligned_cols=50 Identities=16% Similarity=0.276 Sum_probs=30.7
Q ss_pred eecCCCCCCeeeecccceec-----------cCCCcceecCCCCceecCCCCCcccCcccceee
Q psy2693 32 TIDYDEHNPFQICARSYTPI-----------YHGRESEACVYCGASYLPKYKGELCAVCTVSVI 84 (122)
Q Consensus 32 eIdYD~~npF~ICa~S~tPI-----------Y~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~I 84 (122)
-++=..+.+|..|..==..+ .+.+....|.|||..+... ..|+.|+=..+
T Consensus 372 ~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~---~~Cp~Cg~~~l 432 (679)
T PRK05580 372 FLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIP---KACPECGSTDL 432 (679)
T ss_pred EEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCC---CCCCCCcCCee
Confidence 44445556666654322221 2467778999999776543 47999966544
No 85
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=46.25 E-value=30 Score=31.56 Aligned_cols=63 Identities=17% Similarity=0.294 Sum_probs=33.6
Q ss_pred hHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeeccccee-ccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693 10 IPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTP-IYHGRESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tP-IY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
+.-.+.++.+++....++ ..++-+|+ ..|.+-+.+|-| -| =.-.||+||+. +..|..|..|+-
T Consensus 97 ~~h~~~v~~~~~~L~~~G-~iy~~~~~--~~y~~~~~~~l~~~~---v~g~cp~C~~~---d~~g~~ce~cg~ 160 (673)
T PRK00133 97 EENRELAQEIYLKLKENG-YIYEKTIE--QLYDPEKGMFLPDRF---VKGTCPKCGAE---DQYGDNCEVCGA 160 (673)
T ss_pred HHHHHHHHHHHHHHHHCC-CEEEeeeE--EEEeCCCCCCccchh---eecccCCCCCc---ccCCchhhhccc
Confidence 344556777777666654 23333332 124444444443 22 11259999986 345777877764
No 86
>PF14353 CpXC: CpXC protein
Probab=45.79 E-value=12 Score=26.65 Aligned_cols=15 Identities=33% Similarity=0.749 Sum_probs=12.9
Q ss_pred ceecCCCCceecCCC
Q psy2693 57 SEACVYCGASYLPKY 71 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~ 71 (122)
.++||.||+.+..+|
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 689999999987766
No 87
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=45.75 E-value=14 Score=24.12 Aligned_cols=22 Identities=32% Similarity=0.810 Sum_probs=15.0
Q ss_pred cceecCCCCceecCCCCCcccCccc
Q psy2693 56 ESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
..+.||-||+.-.| -.+|+.|+
T Consensus 26 ~l~~C~~CG~~~~~---H~vC~~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKLP---HRVCPSCG 47 (57)
T ss_pred cceECCCCCCccCC---eEECCCCC
Confidence 44677777776666 46777776
No 88
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.56 E-value=18 Score=28.67 Aligned_cols=52 Identities=15% Similarity=0.338 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCC---CcceecCCCCcee
Q psy2693 10 IPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHG---RESEACVYCGASY 67 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G---~~~v~CP~CgA~Y 67 (122)
.....+.++++.+..+. +.|+..|+|-+|.....+---. .---.||-||+..
T Consensus 88 ~~l~~~~~~~le~Lk~~------le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 88 EVLKGKKRKILEKLKRK------LEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred HHHHHHHHHHHHHHHHH------HHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchh
Confidence 34456788888888765 6777788899997776663111 1225677776643
No 89
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=44.15 E-value=21 Score=20.74 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=12.3
Q ss_pred CCCcceecCCCCce
Q psy2693 53 HGRESEACVYCGAS 66 (122)
Q Consensus 53 ~G~~~v~CP~CgA~ 66 (122)
+|.++++|+.|.+.
T Consensus 15 ~gA~~vrCs~C~~v 28 (31)
T TIGR01053 15 RGASSVRCALCQTV 28 (31)
T ss_pred CCCCeEECCCCCeE
Confidence 69999999999864
No 90
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=43.99 E-value=11 Score=27.37 Aligned_cols=32 Identities=28% Similarity=0.771 Sum_probs=20.7
Q ss_pred ceecCCCCceec---------CCC-CC---cccCcccceeecCCCc
Q psy2693 57 SEACVYCGASYL---------PKY-KG---ELCAVCTVSVIDTHRN 89 (122)
Q Consensus 57 ~v~CP~CgA~Y~---------p~~-kG---~lC~VC~ls~IG~~~~ 89 (122)
.+.|||||.... -.+ .+ -+|+-|+ +-||.|..
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~-AyVG~H~~ 46 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCD-AYVGCHPG 46 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCC-ceeeeeCC
Confidence 478999997532 122 11 4799988 56886663
No 91
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=43.76 E-value=15 Score=23.71 Aligned_cols=24 Identities=29% Similarity=0.710 Sum_probs=17.6
Q ss_pred CcceecCCCCceecCCCCCcccCcccc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
...+.||-||+..+|- .+|+.|+.
T Consensus 24 p~l~~C~~cG~~~~~H---~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKLPH---RVCPSCGY 47 (55)
T ss_pred CcceECCCCCCcccCe---eECCccCe
Confidence 3557899999876664 68888873
No 92
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.79 E-value=14 Score=26.62 Aligned_cols=18 Identities=28% Similarity=0.658 Sum_probs=11.8
Q ss_pred cccCcccceeecCCCcccCc
Q psy2693 74 ELCAVCTVSVIDTHRNAYGL 93 (122)
Q Consensus 74 ~lC~VC~ls~IG~~~~a~GL 93 (122)
.+|++|+++-+- ...+|.
T Consensus 2 llCP~C~v~l~~--~~rs~v 19 (88)
T COG3809 2 LLCPICGVELVM--SVRSGV 19 (88)
T ss_pred cccCcCCceeee--eeecCc
Confidence 467777777666 555555
No 93
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=42.36 E-value=11 Score=30.83 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=10.9
Q ss_pred CCCcceecCCCCceec
Q psy2693 53 HGRESEACVYCGASYL 68 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~ 68 (122)
.|.-.+.|.|||.+|+
T Consensus 262 ~~~iev~C~fC~~~Y~ 277 (280)
T PF01430_consen 262 NGKIEVTCEFCGKKYR 277 (280)
T ss_dssp CSEEEEE-TTT--EEE
T ss_pred CCCEEEEeeCCCCEEE
Confidence 3778899999999996
No 94
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=42.10 E-value=20 Score=25.85 Aligned_cols=28 Identities=14% Similarity=0.226 Sum_probs=20.3
Q ss_pred CcceecCCCCceecCCCCC-cccCcccce
Q psy2693 55 RESEACVYCGASYLPKYKG-ELCAVCTVS 82 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG-~lC~VC~ls 82 (122)
....+|+-||..|...... ..||.|+=.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 4578999999888764333 569999843
No 95
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=41.65 E-value=15 Score=25.41 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=11.2
Q ss_pred cCCCCceecCCCCCcccCcccc
Q psy2693 60 CVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 60 CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
||.||+-..|+-.--.|+.|+-
T Consensus 3 C~~Cg~~l~~~~~~~~C~~C~~ 24 (104)
T TIGR01384 3 CPKCGSLMTPKNGVYVCPSCGY 24 (104)
T ss_pred CcccCcccccCCCeEECcCCCC
Confidence 5555555555433344555553
No 96
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.63 E-value=13 Score=28.70 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=16.2
Q ss_pred CcceecCCCCceecCCCCCcccCcccc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
-.+..||.||. .+-.--.|+.|+.
T Consensus 307 ~tS~~C~~cg~---~~~r~~~C~~cg~ 330 (364)
T COG0675 307 YTSKTCPCCGH---LSGRLFKCPRCGF 330 (364)
T ss_pred CCcccccccCC---ccceeEECCCCCC
Confidence 45688999999 2222236999986
No 97
>PHA00159 endonuclease I
Probab=41.58 E-value=26 Score=27.38 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=26.7
Q ss_pred HHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcce
Q psy2693 16 ARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESE 58 (122)
Q Consensus 16 ArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v 58 (122)
=+|++.+.||.|.=.+.+-| ..|.++||+|++..
T Consensus 75 R~K~lli~eQ~P~ldiR~VF---------s~s~~klyKgSkTt 108 (148)
T PHA00159 75 RKKHLLIREQYPELDIRFVF---------SSSRTKLYKGSPTS 108 (148)
T ss_pred HHHHHHHHHHCCCccEEEEE---------ecCCchhhcCCCCc
Confidence 47999999999876555544 56889999998864
No 98
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=41.57 E-value=8.7 Score=37.25 Aligned_cols=63 Identities=22% Similarity=0.384 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHhcCC-CCceeecCC------CCCCeeee--cccce-eccCCCcceecCCCCceecCCCCCcccCcc
Q psy2693 10 IPVATQARKLLAICNANP-TDEHTIDYD------EHNPFQIC--ARSYT-PIYHGRESEACVYCGASYLPKYKGELCAVC 79 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~-tDa~eIdYD------~~npF~IC--a~S~t-PIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC 79 (122)
++.--..|-|..+++... +..++|-.- ....+..| |.+.| |+| .||-||..+.++ .|+-|
T Consensus 629 G~~GG~~R~i~~A~~~~~g~i~vei~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~------~Cp~C~~~~~~~----~C~~C 698 (900)
T PF03833_consen 629 GEAGGSRRDIQKAAKKGKGTIEVEIGRRRCPKCGKETFYNRCPECGSHTEPVY------VCPDCGIEVEED----ECPKC 698 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCcccccHHHHHhcCCCeeEEeeecccCcccCCcchhhcCcccCCccccce------eccccccccCcc----ccccc
Confidence 443445677777777554 566666431 11234444 34443 232 566666555544 56666
Q ss_pred cce
Q psy2693 80 TVS 82 (122)
Q Consensus 80 ~ls 82 (122)
+.-
T Consensus 699 ~~~ 701 (900)
T PF03833_consen 699 GRE 701 (900)
T ss_dssp ---
T ss_pred ccc
Confidence 544
No 99
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=41.26 E-value=14 Score=28.98 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=20.9
Q ss_pred ceecCCCCceecCCCCCcccCcccc
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
...||.||-...- -.-..||||+-
T Consensus 134 ~~vC~vCGy~~~g-e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG-EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC-CCCCcCCCCCC
Confidence 6799999999887 67889999984
No 100
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=40.99 E-value=13 Score=31.48 Aligned_cols=17 Identities=35% Similarity=0.856 Sum_probs=14.9
Q ss_pred CCCcceecCCCCceecC
Q psy2693 53 HGRESEACVYCGASYLP 69 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p 69 (122)
.|.-.+.|.|||.+|+=
T Consensus 262 dg~iev~C~FC~~~Y~f 278 (286)
T COG1281 262 DGGIEVTCEFCGTKYLF 278 (286)
T ss_pred CCCeEEEeeccCCEEec
Confidence 47889999999999973
No 101
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=40.77 E-value=16 Score=21.44 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=10.2
Q ss_pred eecCCCCceecC
Q psy2693 58 EACVYCGASYLP 69 (122)
Q Consensus 58 v~CP~CgA~Y~p 69 (122)
++||-|++.|.-
T Consensus 3 i~CP~C~~~f~v 14 (37)
T PF13719_consen 3 ITCPNCQTRFRV 14 (37)
T ss_pred EECCCCCceEEc
Confidence 689999999973
No 102
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=40.51 E-value=17 Score=30.05 Aligned_cols=27 Identities=30% Similarity=0.600 Sum_probs=17.6
Q ss_pred CcceecCCCCce---ecCCCCCcccCcccc
Q psy2693 55 RESEACVYCGAS---YLPKYKGELCAVCTV 81 (122)
Q Consensus 55 ~~~v~CP~CgA~---Y~p~~kG~lC~VC~l 81 (122)
.....||.||+. +..+---.+|.-|++
T Consensus 9 ~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 9 EEKLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred ccCCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 444679999872 233334568888887
No 103
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=40.34 E-value=18 Score=22.19 Aligned_cols=17 Identities=29% Similarity=0.862 Sum_probs=14.3
Q ss_pred CCCcceecCCCCceecC
Q psy2693 53 HGRESEACVYCGASYLP 69 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p 69 (122)
.|.+.+.|-+|+..|.-
T Consensus 14 ~g~~~a~C~~C~~~l~~ 30 (50)
T smart00614 14 NGKQRAKCKYCGKKLSR 30 (50)
T ss_pred CCCeEEEecCCCCEeee
Confidence 46689999999999963
No 104
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.33 E-value=10 Score=23.81 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=13.4
Q ss_pred eccCCCcceecCCCCce
Q psy2693 50 PIYHGRESEACVYCGAS 66 (122)
Q Consensus 50 PIY~G~~~v~CP~CgA~ 66 (122)
-|.++.+.+.||.||.-
T Consensus 39 ~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 39 EIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHcCCCeEECcCCCcc
Confidence 34467899999999963
No 105
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=39.91 E-value=13 Score=22.80 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=7.6
Q ss_pred ecCCCCceec
Q psy2693 59 ACVYCGASYL 68 (122)
Q Consensus 59 ~CP~CgA~Y~ 68 (122)
+||.||++..
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 4899998754
No 106
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=39.71 E-value=8.5 Score=24.00 Aligned_cols=13 Identities=23% Similarity=0.580 Sum_probs=7.0
Q ss_pred ecCCCCceecCCC
Q psy2693 59 ACVYCGASYLPKY 71 (122)
Q Consensus 59 ~CP~CgA~Y~p~~ 71 (122)
.||+||..+.++.
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999887653
No 107
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=39.14 E-value=18 Score=20.83 Aligned_cols=22 Identities=27% Similarity=0.774 Sum_probs=12.7
Q ss_pred eecCCCCceecCCCCCcccCcccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
-+|+-||..+.|- -..|+-|+-
T Consensus 12 ~rC~~Cg~~~~pP--r~~Cp~C~s 33 (37)
T PF12172_consen 12 QRCRDCGRVQFPP--RPVCPHCGS 33 (37)
T ss_dssp EE-TTT--EEES----SEETTTT-
T ss_pred EEcCCCCCEecCC--CcCCCCcCc
Confidence 4788899888877 478888863
No 108
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=39.06 E-value=11 Score=37.43 Aligned_cols=38 Identities=21% Similarity=0.656 Sum_probs=30.4
Q ss_pred eecccceeccCCCcceecCCCCceecCCCCCcccCcccceee
Q psy2693 43 ICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVI 84 (122)
Q Consensus 43 ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~I 84 (122)
.-...|.|+| ..--+|--||..|.-. ...||.|+=-.|
T Consensus 682 ~~~~~~vPvY--~tIKrC~dcg~q~~~~--~~~cP~Cgs~~v 719 (1187)
T COG1110 682 VKDGKYVPVY--DTIKRCRDCGEQFVDS--EDKCPRCGSRNV 719 (1187)
T ss_pred ccCCceEehH--HHHHHHhhcCceeccc--cccCCCCCCccc
Confidence 3445699999 7777899999999988 449999986554
No 109
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=38.79 E-value=18 Score=28.85 Aligned_cols=24 Identities=17% Similarity=0.511 Sum_probs=19.1
Q ss_pred CcceecCCCCceecCCCCCcccCccc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.-..+|-=|+..|. +.+..|++|+
T Consensus 137 ~w~~rC~GC~~~f~--~~~~~Cp~CG 160 (177)
T COG1439 137 KWRLRCHGCKRIFP--EPKDFCPICG 160 (177)
T ss_pred eeeEEEecCceecC--CCCCcCCCCC
Confidence 44567889998888 6688999996
No 110
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=38.73 E-value=42 Score=31.69 Aligned_cols=51 Identities=33% Similarity=0.651 Sum_probs=35.7
Q ss_pred CCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceec-CC---CCCcccCcccceee
Q psy2693 28 TDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYL-PK---YKGELCAVCTVSVI 84 (122)
Q Consensus 28 tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~-p~---~kG~lC~VC~ls~I 84 (122)
+...+|||-.+.| =-.|-.=|-|+. +-.| .||. |. -+ |+|.+|.-|++--.
T Consensus 38 ~kp~TinyrT~KPE~dGLFCErIFGP~k----~~~C-~CGk-yk~~~~~~~~~~~C~~CgVE~t 95 (663)
T CHL00018 38 TKPYTIHYKTNKPEKDGLFCERIFGPIK----SGIC-ACGN-YRVIGDEKEDPKFCEQCGVEFT 95 (663)
T ss_pred CCCccccccCCCCCCCCEeechhcCCCc----CCEE-eCCC-ccccCccccCCCccCCcCCEec
Confidence 5666899975544 347888888864 3467 7884 44 33 89999999977544
No 111
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=38.32 E-value=13 Score=24.66 Aligned_cols=23 Identities=26% Similarity=0.798 Sum_probs=16.9
Q ss_pred cceecCCCCceecCCCCCcccC-ccc
Q psy2693 56 ESEACVYCGASYLPKYKGELCA-VCT 80 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~-VC~ 80 (122)
|.-.||+||....|+ -..|+ .|+
T Consensus 2 ~HkHC~~CG~~Ip~~--~~fCS~~C~ 25 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPD--ESFCSPKCR 25 (59)
T ss_pred CCCcCCcCCCcCCcc--hhhhCHHHH
Confidence 455799999988887 66774 553
No 112
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=38.12 E-value=16 Score=29.81 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=13.2
Q ss_pred CCcceecCCCCceec
Q psy2693 54 GRESEACVYCGASYL 68 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~ 68 (122)
|.-.+.|.|||.+|.
T Consensus 259 g~iev~C~FC~~~Y~ 273 (275)
T cd00498 259 GGIEVTCEFCGEKYH 273 (275)
T ss_pred CCEEEEEeCCCCEEe
Confidence 567899999999996
No 113
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=37.86 E-value=18 Score=30.36 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=20.2
Q ss_pred eecCCCCce---ecCCCCCcccCcccce
Q psy2693 58 EACVYCGAS---YLPKYKGELCAVCTVS 82 (122)
Q Consensus 58 v~CP~CgA~---Y~p~~kG~lC~VC~ls 82 (122)
..||.||+. +..++--.+|.-|++-
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~V 29 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLV 29 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEE
Confidence 479999998 6666777899999864
No 114
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=37.71 E-value=12 Score=25.54 Aligned_cols=16 Identities=31% Similarity=0.667 Sum_probs=13.7
Q ss_pred CCCcceecCCCCceec
Q psy2693 53 HGRESEACVYCGASYL 68 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~ 68 (122)
.|+.+.+||-||+.|-
T Consensus 13 DGE~~lrCPRC~~~FR 28 (65)
T COG4049 13 DGEEFLRCPRCGMVFR 28 (65)
T ss_pred CCceeeeCCchhHHHH
Confidence 4899999999999763
No 115
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=37.70 E-value=42 Score=34.42 Aligned_cols=61 Identities=23% Similarity=0.519 Sum_probs=42.5
Q ss_pred HHHHHHHhcCCCCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCcccce
Q psy2693 17 RKLLAICNANPTDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVS 82 (122)
Q Consensus 17 rKIl~~ce~~~tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls 82 (122)
.+|...+--.=+....|||--..| =-.|..-|-|+. ...| .||..-..+|+|.+|.-|++-
T Consensus 20 e~Ir~WS~GEV~kpeTINyrT~KPE~dGLFCerIFGP~k----d~eC-~CGKyk~~~~~g~~C~~CGVE 83 (1460)
T PRK14906 20 EDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTK----DWEC-ACGKYKRIRFKGIVCERCGVE 83 (1460)
T ss_pred HHHHhhhceeEcCccccccccCCCCCCCeeeceeccCcc----CcEE-eCccccccCcCCeEcCCCCcE
Confidence 455555544445666899976654 347888888863 5678 799533368999999999654
No 116
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=37.60 E-value=45 Score=30.28 Aligned_cols=46 Identities=20% Similarity=0.462 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHhcCCCCceeecCCCCCCeeeecc-cceeccCCCcc-eecCCCCce
Q psy2693 13 ATQARKLLAICNANPTDEHTIDYDEHNPFQICAR-SYTPIYHGRES-EACVYCGAS 66 (122)
Q Consensus 13 a~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~-S~tPIY~G~~~-v~CP~CgA~ 66 (122)
.+..++|+..+-+++..-..++. +|++|-. . |.|+-. .+||.||+.
T Consensus 500 ~eal~~lv~~a~~~~i~Y~~~n~----~~~~C~~CG----~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 500 PEALKDITKKAMKNGIGYFGINP----PVDVCEDCG----YTGEGLNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHHhcCCceEEecc----CCccCCCCC----CCCCCCCCcCcCCCCc
Confidence 35566777766555333333333 3777763 2 234443 567777764
No 117
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=37.48 E-value=19 Score=20.31 Aligned_cols=18 Identities=22% Similarity=0.575 Sum_probs=8.8
Q ss_pred ecCCCCceec--CCCCCccc
Q psy2693 59 ACVYCGASYL--PKYKGELC 76 (122)
Q Consensus 59 ~CP~CgA~Y~--p~~kG~lC 76 (122)
.||.||+... ++.....|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 4888988887 44333333
No 118
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=37.19 E-value=19 Score=33.91 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=21.8
Q ss_pred eecCCCCceecCCCCCcccCccccee
Q psy2693 58 EACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
..||-||.....+---.+|..|+.|+
T Consensus 725 ~~Cp~Cg~~l~~~~GC~~C~~CG~sk 750 (752)
T PRK08665 725 GACPECGSILEHEEGCVVCHSCGYSK 750 (752)
T ss_pred CCCCCCCcccEECCCCCcCCCCCCCC
Confidence 47999999888777778899998876
No 119
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=37.00 E-value=20 Score=21.57 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=8.1
Q ss_pred CcceecCCCCc
Q psy2693 55 RESEACVYCGA 65 (122)
Q Consensus 55 ~~~v~CP~CgA 65 (122)
.+.+.||-||+
T Consensus 24 ~~~~~CP~Cg~ 34 (42)
T PF09723_consen 24 DDPVPCPECGS 34 (42)
T ss_pred CCCCcCCCCCC
Confidence 56777888877
No 120
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=36.91 E-value=17 Score=29.97 Aligned_cols=15 Identities=40% Similarity=1.081 Sum_probs=13.4
Q ss_pred CCcceecCCCCceec
Q psy2693 54 GRESEACVYCGASYL 68 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~ 68 (122)
|.-.+.|.||+.+|.
T Consensus 265 ~~iev~C~FC~~~Y~ 279 (293)
T PRK00114 265 GGAEMVCQFCGNKYL 279 (293)
T ss_pred CCEEEEEeCCCCEEE
Confidence 567899999999996
No 121
>KOG4080|consensus
Probab=36.56 E-value=11 Score=30.15 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=17.3
Q ss_pred CcceecCCCCceecCCCCCcccCcc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVC 79 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC 79 (122)
....+||-||. |++. ++||.-|
T Consensus 91 ~nl~~CP~CGh-~k~a--~~LC~~C 112 (176)
T KOG4080|consen 91 DNLNTCPACGH-IKPA--HTLCDYC 112 (176)
T ss_pred hccccCcccCc-cccc--cccHHHH
Confidence 45789999995 4454 8999988
No 122
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=36.46 E-value=16 Score=27.01 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=17.7
Q ss_pred CcceecCCCCceecCC-------CCC-cccCcccce
Q psy2693 55 RESEACVYCGASYLPK-------YKG-ELCAVCTVS 82 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~-------~kG-~lC~VC~ls 82 (122)
.....||+||+--... ..| -.|.+|+++
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcce
Confidence 3457899999876551 112 257777765
No 123
>KOG2807|consensus
Probab=36.09 E-value=46 Score=29.45 Aligned_cols=53 Identities=15% Similarity=0.311 Sum_probs=37.3
Q ss_pred CCceeecCCCCC---CeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccceeec
Q psy2693 28 TDEHTIDYDEHN---PFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVID 85 (122)
Q Consensus 28 tDa~eIdYD~~n---pF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG 85 (122)
-+.+.+.|-.+. .-.+|+--..+++.| ..||-|+|++-.= -.-|++|++.-|-
T Consensus 247 ~sLvkmGFP~~~~e~~ps~C~CH~~~~~~G---y~CP~CkakvCsL--P~eCpiC~ltLVs 302 (378)
T KOG2807|consen 247 CSLVKMGFPSRSPEDTPSFCACHSELSGGG---YFCPQCKAKVCSL--PIECPICSLTLVS 302 (378)
T ss_pred CceEEecCCCcccccCcchheeccccccCc---eeCCcccCeeecC--CccCCccceeEec
Confidence 345677774332 135676665566655 6899999999754 5679999999887
No 124
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=36.06 E-value=25 Score=23.85 Aligned_cols=43 Identities=19% Similarity=0.245 Sum_probs=24.4
Q ss_pred ceecCCCCceecCCCCCcccCcccceeecCCCcccCcceecccchhhhh
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVI 105 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG~~~~a~GLr~~~~~~~~~~~ 105 (122)
...|--|+..- .++.|++|+-+..- .+-.|+-+...-.+|.|-
T Consensus 5 ~~AC~~C~~i~----~~~~Cp~Cgs~~~S--~~w~G~v~i~dPe~S~vA 47 (64)
T PRK06393 5 YRACKKCKRLT----PEKTCPVHGDEKTT--TEWFGFLIITEPEGSAIA 47 (64)
T ss_pred hhhHhhCCccc----CCCcCCCCCCCcCC--cCcceEEEEECCchhHHH
Confidence 34455555544 24467777766555 666677555544455543
No 125
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.93 E-value=89 Score=29.71 Aligned_cols=67 Identities=18% Similarity=0.266 Sum_probs=46.7
Q ss_pred ChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeee------------cccceeccCCCcceecCCCCceecCCCCCccc
Q psy2693 9 IIPVATQARKLLAICNANPTDEHTIDYDEHNPFQIC------------ARSYTPIYHGRESEACVYCGASYLPKYKGELC 76 (122)
Q Consensus 9 ~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~IC------------a~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC 76 (122)
+++..+..++-|++-||. -+-+|---+.||..| ..+||- ++.+..-+|.|||....+ -.-|
T Consensus 406 S~~Ll~~i~~~l~~geQ~---llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~-H~~~~~L~CH~Cg~~~~~---p~~C 478 (730)
T COG1198 406 SPALLEAIRKTLERGEQV---LLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTL-HKATGQLRCHYCGYQEPI---PQSC 478 (730)
T ss_pred CHHHHHHHHHHHhcCCeE---EEEEccCCccceeecccCCCcccCCCCCcceEE-ecCCCeeEeCCCCCCCCC---CCCC
Confidence 477777788877776654 345566666777765 345554 567889999999988443 3579
Q ss_pred Ccccce
Q psy2693 77 AVCTVS 82 (122)
Q Consensus 77 ~VC~ls 82 (122)
+-|+=-
T Consensus 479 p~Cgs~ 484 (730)
T COG1198 479 PECGSE 484 (730)
T ss_pred CCCCCC
Confidence 999854
No 126
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.54 E-value=27 Score=23.03 Aligned_cols=12 Identities=25% Similarity=0.564 Sum_probs=5.5
Q ss_pred CcceecCCCCce
Q psy2693 55 RESEACVYCGAS 66 (122)
Q Consensus 55 ~~~v~CP~CgA~ 66 (122)
.....||.||=.
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 444445555443
No 127
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=35.48 E-value=18 Score=20.42 Aligned_cols=23 Identities=30% Similarity=0.608 Sum_probs=10.8
Q ss_pred ecCCCCceecCCCC--CcccCcccc
Q psy2693 59 ACVYCGASYLPKYK--GELCAVCTV 81 (122)
Q Consensus 59 ~CP~CgA~Y~p~~k--G~lC~VC~l 81 (122)
-||-||+.-.+.-. ..+|+.|+.
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 47778877765544 346666654
No 128
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=35.46 E-value=20 Score=25.20 Aligned_cols=23 Identities=26% Similarity=0.808 Sum_probs=17.2
Q ss_pred CcceecCCCCceecCCCCCcccCcccc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
.+.-.|..||..-. |.+|++|.+
T Consensus 78 ~~~~~C~~CG~pss----~~iC~~C~l 100 (104)
T TIGR00269 78 EDLRRCERCGEPTS----GRICKACKF 100 (104)
T ss_pred ccCCcCCcCcCcCC----ccccHhhhh
Confidence 34567999995432 789999987
No 129
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=35.27 E-value=17 Score=26.00 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=16.9
Q ss_pred ccCCCcceecCCCCceecCC
Q psy2693 51 IYHGRESEACVYCGASYLPK 70 (122)
Q Consensus 51 IY~G~~~v~CP~CgA~Y~p~ 70 (122)
+-+..|...|+-||..|+.+
T Consensus 29 vIknVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 29 EIKETPSISCSHCGMEYQDD 48 (89)
T ss_pred EEecCCcccccCCCcEeecH
Confidence 34678999999999999865
No 130
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.92 E-value=24 Score=20.78 Aligned_cols=11 Identities=36% Similarity=0.733 Sum_probs=9.9
Q ss_pred eecCCCCceec
Q psy2693 58 EACVYCGASYL 68 (122)
Q Consensus 58 v~CP~CgA~Y~ 68 (122)
+.||-|+++|.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 68999999996
No 131
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=34.66 E-value=35 Score=22.86 Aligned_cols=42 Identities=21% Similarity=0.395 Sum_probs=28.5
Q ss_pred ecCCCCceecCCCCCcccCcccceeecCCCcccCcceecccchhhhhh
Q psy2693 59 ACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVIN 106 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~ls~IG~~~~a~GLr~~~~~~~~~~~~ 106 (122)
.|--|+..-. ++.|++|+-+..= .+-.|+-+...--+|.+-.
T Consensus 5 AC~~C~~i~~----~~~CP~Cgs~~~T--~~W~G~viI~dPe~S~IAk 46 (61)
T PRK08351 5 ACRHCHYITT----EDRCPVCGSRDLS--DEWFDLVIIIDVENSRIAK 46 (61)
T ss_pred hhhhCCcccC----CCcCCCCcCCccc--cccccEEEEeCCcHhHHHH
Confidence 4666665552 4468888888877 7888887766566676653
No 132
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=34.55 E-value=71 Score=28.05 Aligned_cols=60 Identities=18% Similarity=0.314 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHHhcCC---CCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCccc
Q psy2693 10 IPVATQARKLLAICNANP---TDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~---tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
++-.+.+++++...-+++ +......|++. |-..++.-| -.-.||.|++ .+..|..|-.|+
T Consensus 99 ~~~~~~~~~~~~~L~~~G~~y~~~~~~~~~~~-----~~~~l~~~~---v~g~cp~c~~---~~~~G~~ce~cg 161 (556)
T PRK12268 99 PNHHEVVQEFFLKLYENGYIYKKTIEQAYCPS-----DGRFLPDRY---VEGTCPYCGY---EGARGDQCDNCG 161 (556)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEeeeEEEecCC-----CCcCcCccc---eeccCCCCCC---cccCCchhhhcc
Confidence 445566777777665555 24455555544 222222222 1125888885 244677777774
No 133
>PRK06260 threonine synthase; Validated
Probab=34.29 E-value=27 Score=29.62 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=17.1
Q ss_pred eecCCCCceecCCCCCcccCccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.+|+-||..|.++..-..|+-|+
T Consensus 4 ~~C~~cg~~~~~~~~~~~Cp~cg 26 (397)
T PRK06260 4 LKCIECGKEYDPDEIIYTCPECG 26 (397)
T ss_pred EEECCCCCCCCCCCccccCCCCC
Confidence 57888888888776556687774
No 134
>COG3919 Predicted ATP-grasp enzyme [General function prediction only]
Probab=34.05 E-value=41 Score=29.83 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=29.8
Q ss_pred ccCCChHHHHHHHHHHHHHhcCCCCceeecCCCC
Q psy2693 5 AKFQIIPVATQARKLLAICNANPTDEHTIDYDEH 38 (122)
Q Consensus 5 el~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~ 38 (122)
++.....+.++||++|...+-.+--+++.-||++
T Consensus 242 evvDn~Q~i~aar~~L~si~htGlvevefK~D~R 275 (415)
T COG3919 242 EVVDNQQVIQAARDFLESIEHTGLVEVEFKYDPR 275 (415)
T ss_pred EecCcHHHHHHHHHHHHhhcccceEEEEEEecCC
Confidence 3444578899999999999999999999999998
No 135
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=33.70 E-value=34 Score=21.72 Aligned_cols=18 Identities=28% Similarity=0.820 Sum_probs=13.4
Q ss_pred cCC-CcceecCCCCceecC
Q psy2693 52 YHG-RESEACVYCGASYLP 69 (122)
Q Consensus 52 Y~G-~~~v~CP~CgA~Y~p 69 (122)
|.| ...++|.+||-.+..
T Consensus 30 y~~~~d~v~C~~C~~~l~~ 48 (71)
T smart00238 30 YTGVGDEVKCFFCGGELDN 48 (71)
T ss_pred ECCCCCEEEeCCCCCCcCC
Confidence 455 557999999987654
No 136
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=32.94 E-value=23 Score=28.05 Aligned_cols=31 Identities=29% Similarity=0.836 Sum_probs=23.6
Q ss_pred CcceecCCCCceec-------------------CCCCC--------cccCcccceeec
Q psy2693 55 RESEACVYCGASYL-------------------PKYKG--------ELCAVCTVSVID 85 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~-------------------p~~kG--------~lC~VC~ls~IG 85 (122)
...++||+|+..+. |.|+| .+|+.|+.+..-
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 56789999998764 33443 589999999886
No 137
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=32.90 E-value=21 Score=27.53 Aligned_cols=16 Identities=25% Similarity=0.632 Sum_probs=11.3
Q ss_pred CCcceecCCCCceecC
Q psy2693 54 GRESEACVYCGASYLP 69 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~p 69 (122)
....+.||+||+.-..
T Consensus 29 ~~glv~CP~Cgs~~V~ 44 (148)
T PF06676_consen 29 ARGLVSCPVCGSTEVS 44 (148)
T ss_pred HcCCccCCCCCCCeEe
Confidence 4567889999886543
No 138
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=32.74 E-value=20 Score=26.51 Aligned_cols=30 Identities=30% Similarity=0.630 Sum_probs=20.1
Q ss_pred eeeeccc---ceec-cCCCcceecCCCCceecCCCC
Q psy2693 41 FQICARS---YTPI-YHGRESEACVYCGASYLPKYK 72 (122)
Q Consensus 41 F~ICa~S---~tPI-Y~G~~~v~CP~CgA~Y~p~~k 72 (122)
-.||+.- +|-- | ...++||||.+.+.|.-+
T Consensus 62 ~iiCGvC~~~LT~~EY--~~~~~Cp~C~spFNp~Ck 95 (105)
T COG4357 62 AIICGVCRKLLTRAEY--GMCGSCPYCQSPFNPGCK 95 (105)
T ss_pred cEEhhhhhhhhhHHHH--hhcCCCCCcCCCCCcccc
Confidence 4566653 3331 4 345679999999999854
No 139
>PLN02294 cytochrome c oxidase subunit Vb
Probab=32.67 E-value=22 Score=28.47 Aligned_cols=28 Identities=14% Similarity=0.380 Sum_probs=20.6
Q ss_pred ccceecc----CCCcceecCCCCceecCCCCCc
Q psy2693 46 RSYTPIY----HGRESEACVYCGASYLPKYKGE 74 (122)
Q Consensus 46 ~S~tPIY----~G~~~v~CP~CgA~Y~p~~kG~ 74 (122)
.+..+++ +|++. +||-||..|.-+|-|.
T Consensus 127 Dsh~v~Wf~L~kGkp~-RCpeCG~~fkL~~vG~ 158 (174)
T PLN02294 127 DEHDVVWFWLEKGKSF-ECPVCTQYFELEVVGP 158 (174)
T ss_pred CCceeEEEEecCCCce-eCCCCCCEEEEEEeCC
Confidence 3666663 68654 5999999999887663
No 140
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.58 E-value=29 Score=19.34 Aligned_cols=19 Identities=32% Similarity=0.791 Sum_probs=10.1
Q ss_pred ecccceeccCC-CcceecCCCC
Q psy2693 44 CARSYTPIYHG-RESEACVYCG 64 (122)
Q Consensus 44 Ca~S~tPIY~G-~~~v~CP~Cg 64 (122)
|...+.| ++ .-...||-||
T Consensus 4 C~~~i~~--r~~~v~f~CPnCG 23 (24)
T PF07754_consen 4 CGRPIAP--REQAVPFPCPNCG 23 (24)
T ss_pred CCCcccC--cccCceEeCCCCC
Confidence 4444555 22 4445677776
No 141
>PRK06450 threonine synthase; Validated
Probab=32.35 E-value=28 Score=29.18 Aligned_cols=22 Identities=32% Similarity=0.760 Sum_probs=16.2
Q ss_pred eecCCCCceecCCCCCcccCccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.+|+-||..|.+.+. ..|+-|+
T Consensus 4 ~~C~~Cg~~~~~~~~-~~C~~cg 25 (338)
T PRK06450 4 EVCMKCGKERESIYE-IRCKKCG 25 (338)
T ss_pred eEECCcCCcCCCccc-ccCCcCC
Confidence 478888888877443 6788885
No 142
>KOG3352|consensus
Probab=32.23 E-value=80 Score=24.81 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCCCceeecCCCC------CCee------------eecccce-----eccCCCcceecCCCCceecCCCCC
Q psy2693 17 RKLLAICNANPTDEHTIDYDEH------NPFQ------------ICARSYT-----PIYHGRESEACVYCGASYLPKYKG 73 (122)
Q Consensus 17 rKIl~~ce~~~tDa~eIdYD~~------npF~------------ICa~S~t-----PIY~G~~~v~CP~CgA~Y~p~~kG 73 (122)
.|---.++..+.|.++++|+.. +|-. +|...=. =|++|+..- ||-||..|.=+..|
T Consensus 71 Ek~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge~~r-c~eCG~~fkL~~v~ 149 (153)
T KOG3352|consen 71 EKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGETQR-CPECGHYFKLVPVG 149 (153)
T ss_pred HHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCCccc-CCcccceEEeeecC
Confidence 3444467788889888888754 2222 2333222 246777665 99999998765544
No 143
>PRK07591 threonine synthase; Validated
Probab=31.74 E-value=29 Score=29.86 Aligned_cols=23 Identities=30% Similarity=0.629 Sum_probs=18.0
Q ss_pred ceecCCCCceecCCCCCcccCccc
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
..+|+-||..|.+++. -.|+-|+
T Consensus 18 ~l~C~~Cg~~~~~~~~-~~C~~cg 40 (421)
T PRK07591 18 ALKCRECGAEYPLGPI-HVCEECF 40 (421)
T ss_pred EEEeCCCCCcCCCCCC-ccCCCCC
Confidence 3688888888888776 7788784
No 144
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=31.66 E-value=37 Score=22.37 Aligned_cols=29 Identities=14% Similarity=0.291 Sum_probs=13.7
Q ss_pred ceecCCCCceecCCCCCcccC----cccceeec
Q psy2693 57 SEACVYCGASYLPKYKGELCA----VCTVSVID 85 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~----VC~ls~IG 85 (122)
.+.||-||...........=+ -|.+--+|
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg 34 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCKLIDLG 34 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHHHHHHS
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhcccCHH
Confidence 478999999998833333222 34555555
No 145
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.14 E-value=30 Score=25.65 Aligned_cols=35 Identities=23% Similarity=0.452 Sum_probs=26.6
Q ss_pred eecccc----eeccCCCcceecCCCCceecCCCCCcccC
Q psy2693 43 ICARSY----TPIYHGRESEACVYCGASYLPKYKGELCA 77 (122)
Q Consensus 43 ICa~S~----tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~ 77 (122)
.|..++ .++.+|.+..+|+-|+..+.-++...++.
T Consensus 35 ~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~~ 73 (129)
T COG3677 35 RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGSPLSK 73 (129)
T ss_pred CCCccceeeECCccccccccccCCcCcceeeeccCcccc
Confidence 355555 44566788889999999998888888877
No 146
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=30.52 E-value=37 Score=23.18 Aligned_cols=30 Identities=30% Similarity=0.581 Sum_probs=21.3
Q ss_pred CcccCcccceeecCCCcccCcceecccchhhh
Q psy2693 73 GELCAVCTVSVIDTHRNAYGLQICAGLMKSDV 104 (122)
Q Consensus 73 G~lC~VC~ls~IG~~~~a~GLr~~~~~~~~~~ 104 (122)
-++|++|+-.+.- .+-.||-+...--+|+.
T Consensus 18 ~e~CP~Cgs~~~t--e~W~G~~iIidpe~SeI 47 (64)
T COG2093 18 TEICPVCGSTDLT--EEWFGLLIIIDPEKSEI 47 (64)
T ss_pred CccCCCCCCcccc--hhhccEEEEEcCcHHHH
Confidence 5678888888777 78888866655555543
No 147
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.49 E-value=25 Score=21.87 Aligned_cols=37 Identities=22% Similarity=0.452 Sum_probs=21.5
Q ss_pred eecccceeccCCCcceecCCCCceecCCC-----CCcccCcc
Q psy2693 43 ICARSYTPIYHGRESEACVYCGASYLPKY-----KGELCAVC 79 (122)
Q Consensus 43 ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~-----kG~lC~VC 79 (122)
+-...++|=....-.=+|+.||-.|...- .+.-|+.|
T Consensus 14 ~~p~~v~~~s~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 14 LDPSEVTPGSNKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CCHHHhCcCCCCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 44444444333344468999988887542 35556655
No 148
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=30.37 E-value=28 Score=29.71 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=24.1
Q ss_pred eeeecccceeccCCCcceecCCCCceecCCCCCcc
Q psy2693 41 FQICARSYTPIYHGRESEACVYCGASYLPKYKGEL 75 (122)
Q Consensus 41 F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~l 75 (122)
|-.|.. -|=++-...-+||+||--+.|.|.|+-
T Consensus 44 ~~~~pm--~p~~~~~~pg~~p~~~m~lvp~y~~~~ 76 (409)
T PRK09783 44 FWYDPM--YPNTRFDKPGKSPFMDMDLVPKYADEE 76 (409)
T ss_pred EEeCCC--CCCcCCCCCCCCCCCCCeeeEEecCCC
Confidence 344543 476666667799999999999987653
No 149
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=30.33 E-value=17 Score=27.61 Aligned_cols=22 Identities=23% Similarity=0.786 Sum_probs=18.4
Q ss_pred eecCCCCceecCCCCCcccCccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
..||-||.-|... ...+|+.|.
T Consensus 4 ~nC~~CgklF~~~-~~~iCp~C~ 25 (137)
T TIGR03826 4 ANCPKCGRLFVKT-GRDVCPSCY 25 (137)
T ss_pred ccccccchhhhhc-CCccCHHHh
Confidence 4699999999885 567999996
No 150
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=30.02 E-value=31 Score=23.05 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=13.9
Q ss_pred CCCcceecCCCCceecCCC
Q psy2693 53 HGRESEACVYCGASYLPKY 71 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p~~ 71 (122)
..+..-.||+|++.-..+.
T Consensus 35 s~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred ccCCCccCCCcCCccccce
Confidence 4566678999998776553
No 151
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.73 E-value=49 Score=26.20 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=5.6
Q ss_pred cCCCCceecC
Q psy2693 60 CVYCGASYLP 69 (122)
Q Consensus 60 CP~CgA~Y~p 69 (122)
||.||..|=+
T Consensus 133 C~~CgkiYW~ 142 (165)
T COG1656 133 CPKCGKIYWK 142 (165)
T ss_pred CCCCcccccC
Confidence 6666655543
No 152
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=28.80 E-value=38 Score=25.35 Aligned_cols=32 Identities=28% Similarity=0.393 Sum_probs=26.6
Q ss_pred eeecCCCCCCeeeecccceeccCCCcceecCCC
Q psy2693 31 HTIDYDEHNPFQICARSYTPIYHGRESEACVYC 63 (122)
Q Consensus 31 ~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~C 63 (122)
+.|++| -|.-++-+.|..||-.|.-..+|||=
T Consensus 19 v~ie~d-cnakvvvats~dpvts~klyfscpye 50 (122)
T PF05325_consen 19 VPIECD-CNAKVVVATSRDPVTSGKLYFSCPYE 50 (122)
T ss_pred cceecc-CCceEEEEeccCCcccceeeecCccc
Confidence 566775 46678889999999999999999983
No 153
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.73 E-value=31 Score=30.89 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=18.3
Q ss_pred eecCCCCceecCCCC-CcccCcccc
Q psy2693 58 EACVYCGASYLPKYK-GELCAVCTV 81 (122)
Q Consensus 58 v~CP~CgA~Y~p~~k-G~lC~VC~l 81 (122)
-.||+||.+....=+ |--|+-|+-
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~ 375 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGT 375 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccc
Confidence 379999999887755 667888863
No 154
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=28.49 E-value=34 Score=24.05 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=17.1
Q ss_pred CCCcceecCCCCceecCCCCCc
Q psy2693 53 HGRESEACVYCGASYLPKYKGE 74 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p~~kG~ 74 (122)
.|.+.|.||+.++.|.-+ .|+
T Consensus 60 ~g~~~V~CPlH~~~f~L~-tG~ 80 (104)
T PF13806_consen 60 NGEPCVACPLHKWRFDLR-TGE 80 (104)
T ss_dssp TTEEEEEETTTTEEEETT-TTE
T ss_pred CCCEEEECCCCCCeEECC-CcC
Confidence 467799999999999986 353
No 155
>PRK01343 zinc-binding protein; Provisional
Probab=28.45 E-value=47 Score=22.04 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=21.5
Q ss_pred CCcceecCCCCceecCCCCCccc-Ccccceeec
Q psy2693 54 GRESEACVYCGASYLPKYKGELC-AVCTVSVID 85 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~p~~kG~lC-~VC~ls~IG 85 (122)
..+.+.||-||.....+|. -.| .-|..--+|
T Consensus 6 ~~p~~~CP~C~k~~~~~~r-PFCS~RC~~iDLg 37 (57)
T PRK01343 6 LRPTRPCPECGKPSTREAY-PFCSERCRDIDLN 37 (57)
T ss_pred CCCCCcCCCCCCcCcCCCC-cccCHHHhhhhHH
Confidence 3578999999998877665 344 346655555
No 156
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=28.42 E-value=33 Score=22.25 Aligned_cols=13 Identities=38% Similarity=0.580 Sum_probs=10.8
Q ss_pred cceecCCCCceec
Q psy2693 56 ESEACVYCGASYL 68 (122)
Q Consensus 56 ~~v~CP~CgA~Y~ 68 (122)
..|.||-||+.|-
T Consensus 21 eiV~Cp~CGaele 33 (54)
T TIGR01206 21 ELVICDECGAELE 33 (54)
T ss_pred CEEeCCCCCCEEE
Confidence 4789999999874
No 157
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=28.32 E-value=30 Score=24.88 Aligned_cols=26 Identities=27% Similarity=0.428 Sum_probs=19.3
Q ss_pred cceec----cCCCcceecCCCCceecCCCCC
Q psy2693 47 SYTPI----YHGRESEACVYCGASYLPKYKG 73 (122)
Q Consensus 47 S~tPI----Y~G~~~v~CP~CgA~Y~p~~kG 73 (122)
++.++ .+| +..+||-||..|.=.+.|
T Consensus 66 ~h~v~W~~l~~g-~~~rC~eCG~~fkL~~v~ 95 (97)
T cd00924 66 SHDVIWMWLEKG-KPKRCPECGHVFKLVDVG 95 (97)
T ss_pred CceEEEEEEeCC-CceeCCCCCcEEEEEECC
Confidence 45555 478 689999999999766544
No 158
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=28.23 E-value=25 Score=27.30 Aligned_cols=7 Identities=29% Similarity=1.127 Sum_probs=6.1
Q ss_pred ecCCCCc
Q psy2693 59 ACVYCGA 65 (122)
Q Consensus 59 ~CP~CgA 65 (122)
+|||||.
T Consensus 2 ~CP~C~~ 8 (147)
T TIGR00244 2 HCPFCQH 8 (147)
T ss_pred CCCCCCC
Confidence 6999997
No 159
>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad
Probab=28.12 E-value=56 Score=22.81 Aligned_cols=35 Identities=20% Similarity=0.473 Sum_probs=25.0
Q ss_pred eeecccceeccCC---CcceecCCCCceecCCCCCcccCc
Q psy2693 42 QICARSYTPIYHG---RESEACVYCGASYLPKYKGELCAV 78 (122)
Q Consensus 42 ~ICa~S~tPIY~G---~~~v~CP~CgA~Y~p~~kG~lC~V 78 (122)
++|.---.|+..| ...+.|||-|+.|.. .|++-.+
T Consensus 44 n~CpH~g~~L~~G~~~~~~i~Cp~Hg~~fd~--~G~~~~~ 81 (116)
T cd03532 44 DRCPHRSAPLSKGSVEGGGLVCGYHGLEFDS--DGRCVHM 81 (116)
T ss_pred CcCCCCCCCccCCcccCCEEEeCCCCcEEcC--CCCEEeC
Confidence 3666666666544 457999999999994 5876543
No 160
>PF04641 Rtf2: Rtf2 RING-finger
Probab=27.92 E-value=56 Score=26.39 Aligned_cols=60 Identities=15% Similarity=0.277 Sum_probs=39.8
Q ss_pred CCCCceeecCCCC--------------CCeeeecccceeccCCCcceecCCCCceec----CCCC-CcccCcccceeec
Q psy2693 26 NPTDEHTIDYDEH--------------NPFQICARSYTPIYHGRESEACVYCGASYL----PKYK-GELCAVCTVSVID 85 (122)
Q Consensus 26 ~~tDa~eIdYD~~--------------npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~----p~~k-G~lC~VC~ls~IG 85 (122)
...|-++|+|-+. ..-.+|..|+..+-....+|-=-=||-.|. .+.+ +..|++|+-.--.
T Consensus 84 ~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 84 SLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTE 162 (260)
T ss_pred CccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcccc
Confidence 4567778877533 334599999999854566666566777664 3445 6788888755433
No 161
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.92 E-value=58 Score=24.70 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=14.6
Q ss_pred eeeecccceeccCCCcceecCCCCce
Q psy2693 41 FQICARSYTPIYHGRESEACVYCGAS 66 (122)
Q Consensus 41 F~ICa~S~tPIY~G~~~v~CP~CgA~ 66 (122)
|.+|.=--..=|.|+..+.||-||..
T Consensus 89 fa~C~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 89 FAVCGCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred EEEecCCCEEEeCCCCCEECCCCCCe
Confidence 55554443344566666666666654
No 162
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=27.91 E-value=35 Score=20.48 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=13.3
Q ss_pred CcceecCCCCceecCCC
Q psy2693 55 RESEACVYCGASYLPKY 71 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~ 71 (122)
+..+.|+.||+.+....
T Consensus 3 ~g~l~C~~CG~~m~~~~ 19 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRK 19 (58)
T ss_pred CCcEEcccCCcEeEEEE
Confidence 34689999999988643
No 163
>PF13395 HNH_4: HNH endonuclease
Probab=27.76 E-value=26 Score=21.86 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=9.1
Q ss_pred cCCCCceecCC
Q psy2693 60 CVYCGASYLPK 70 (122)
Q Consensus 60 CP~CgA~Y~p~ 70 (122)
|+|||.....+
T Consensus 1 C~Y~g~~i~~~ 11 (54)
T PF13395_consen 1 CPYCGKPISIE 11 (54)
T ss_pred CCCCCCCCChh
Confidence 89999888765
No 164
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=27.52 E-value=25 Score=25.73 Aligned_cols=15 Identities=27% Similarity=0.685 Sum_probs=11.0
Q ss_pred ceecCCCCceecCCC
Q psy2693 57 SEACVYCGASYLPKY 71 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~ 71 (122)
.+.|||||-+-.-+|
T Consensus 3 LI~CP~Cg~R~e~EF 17 (97)
T COG4311 3 LIPCPYCGERPEEEF 17 (97)
T ss_pred eecCCCCCCCchhhe
Confidence 368999999655554
No 165
>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]
Probab=27.44 E-value=44 Score=26.14 Aligned_cols=36 Identities=19% Similarity=0.426 Sum_probs=23.9
Q ss_pred CCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCc
Q psy2693 26 NPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGA 65 (122)
Q Consensus 26 ~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA 65 (122)
=|+|++++.-++..+ -.+-.+-+..=...+|-|||=
T Consensus 67 CP~~aI~m~~~~~~~----~g~~~~~~~~In~grCIfCg~ 102 (172)
T COG1143 67 CPANAITMETAERKV----DGRKKPKRPDINLGRCIFCGL 102 (172)
T ss_pred CCcCceEEEEcccCC----CCccccccceeccccccccCc
Confidence 378899888887765 333333344556778888873
No 166
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.81 E-value=37 Score=31.61 Aligned_cols=22 Identities=23% Similarity=0.608 Sum_probs=17.1
Q ss_pred ecCCCCceecCCCCCcccCcccce
Q psy2693 59 ACVYCGASYLPKYKGELCAVCTVS 82 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~ls 82 (122)
.||-||+...++ .+.|+-|+-.
T Consensus 29 ~Cp~CG~~~~~~--~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVPVD--EAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCCcc--cccccccCCc
Confidence 688888887777 5689988853
No 167
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=26.74 E-value=31 Score=26.14 Aligned_cols=19 Identities=37% Similarity=0.976 Sum_probs=12.0
Q ss_pred cCCCCceecCCCCCcccCccc
Q psy2693 60 CVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 60 CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
|+.||+...+. ..+|..|.
T Consensus 1 C~~C~~~~~~~--~~~C~~C~ 19 (190)
T TIGR00201 1 CSLCGRPYQSV--HALCRQCG 19 (190)
T ss_pred CCccccccccc--cCCchhhC
Confidence 67777765543 45777774
No 168
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=26.31 E-value=64 Score=18.33 Aligned_cols=23 Identities=30% Similarity=0.762 Sum_probs=11.4
Q ss_pred ecCCCCceecCCCCCcccCcccc
Q psy2693 59 ACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
.|-.|+....-...|--|..|++
T Consensus 13 ~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 13 KCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CccccccccCcCCCCcCCCCCCc
Confidence 45555555443223555555544
No 169
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=26.06 E-value=26 Score=25.41 Aligned_cols=30 Identities=27% Similarity=0.742 Sum_probs=17.1
Q ss_pred eeeeccccee-ccC--CCcceecCCCCceecCC
Q psy2693 41 FQICARSYTP-IYH--GRESEACVYCGASYLPK 70 (122)
Q Consensus 41 F~ICa~S~tP-IY~--G~~~v~CP~CgA~Y~p~ 70 (122)
|--|-++|.| .|. ..+-++|-+|+..|.|+
T Consensus 9 ~g~c~G~f~P~lY~~~~a~CI~C~~C~~~FsP~ 41 (96)
T PF08782_consen 9 FGGCRGSFIPELYSSPNAKCIECLECRGMFSPQ 41 (96)
T ss_dssp TT-EEEEE-GGG--STT---EEETTT--EE-HH
T ss_pred cCccceEechhhcCCCCCCceEcccCCCEeCCc
Confidence 6678999999 564 46899999999999885
No 170
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.78 E-value=32 Score=20.79 Aligned_cols=9 Identities=33% Similarity=0.903 Sum_probs=7.6
Q ss_pred eecCCCCce
Q psy2693 58 EACVYCGAS 66 (122)
Q Consensus 58 v~CP~CgA~ 66 (122)
+.||.||+.
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 569999986
No 171
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=25.76 E-value=44 Score=30.36 Aligned_cols=25 Identities=24% Similarity=0.611 Sum_probs=18.8
Q ss_pred CcceecCCCCceecCCCCCcccCcccc
Q psy2693 55 RESEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
.+.-.|+-|| |.-++.+..||.|+=
T Consensus 522 ~~~~~C~~CG--~~g~~~~~~CP~Cgs 546 (579)
T TIGR02487 522 PPVDVCEDCG--YTGEGLNDKCPKCGS 546 (579)
T ss_pred cCCccCCCCC--CCCCCCCCcCcCCCC
Confidence 4667899998 456655578999983
No 172
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=25.71 E-value=36 Score=28.98 Aligned_cols=15 Identities=33% Similarity=0.846 Sum_probs=13.5
Q ss_pred CCcceecCCCCceec
Q psy2693 54 GRESEACVYCGASYL 68 (122)
Q Consensus 54 G~~~v~CP~CgA~Y~ 68 (122)
|.-.+.|-|||.+|+
T Consensus 305 g~iev~CeFC~~~Y~ 319 (328)
T PRK01402 305 GKISVTCEFCSRVYR 319 (328)
T ss_pred CCEEEEeeCCCCEEE
Confidence 677899999999997
No 173
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=25.63 E-value=58 Score=20.52 Aligned_cols=15 Identities=20% Similarity=0.676 Sum_probs=12.1
Q ss_pred CcceecCCCCceecC
Q psy2693 55 RESEACVYCGASYLP 69 (122)
Q Consensus 55 ~~~v~CP~CgA~Y~p 69 (122)
...++|.||+-.+..
T Consensus 32 ~d~v~C~~C~~~~~~ 46 (69)
T cd00022 32 GDEVKCFFCGLELKN 46 (69)
T ss_pred CCEEEeCCCCCCccC
Confidence 578999999987754
No 174
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.55 E-value=42 Score=31.44 Aligned_cols=8 Identities=38% Similarity=0.920 Sum_probs=4.0
Q ss_pred eecCCCCc
Q psy2693 58 EACVYCGA 65 (122)
Q Consensus 58 v~CP~CgA 65 (122)
..||.||+
T Consensus 660 ~~CP~CG~ 667 (711)
T PRK09263 660 FTCPKCGN 667 (711)
T ss_pred CcCcCCCC
Confidence 34555554
No 175
>PRK10445 endonuclease VIII; Provisional
Probab=25.50 E-value=1.5e+02 Score=24.09 Aligned_cols=63 Identities=17% Similarity=0.278 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCC----CcccCccc
Q psy2693 10 IPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK----GELCAVCT 80 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~k----G~lC~VC~ 80 (122)
..+.+.+++||+.+=....... ..+....| .. .-+| |..-..||-||+.....-- --.|+.|+
T Consensus 196 ~~L~~~i~~vl~~ai~~gg~~~--~~~~~g~~----~~-~~Vy-~r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 196 DALAHALLDIPRLSYATRGQVD--ENKHHGAL----FR-FKVF-HRDGEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred HHHHHHHHHHHHHHHHcCCCCC--CCCCCCCc----ce-EEEe-CCCCCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 4456778888887654432221 00111222 11 2345 3444568888887653221 22566665
No 176
>PF14122 YokU: YokU-like protein
Probab=25.48 E-value=41 Score=24.20 Aligned_cols=18 Identities=22% Similarity=0.523 Sum_probs=16.0
Q ss_pred CCCcceecCCCCceecCC
Q psy2693 53 HGRESEACVYCGASYLPK 70 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p~ 70 (122)
...|++.|.-||..|..+
T Consensus 31 ~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 31 TDTPAIICSNCGMVYQDD 48 (87)
T ss_pred cCCceeeecCCCcEEehh
Confidence 567999999999999876
No 177
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=25.44 E-value=77 Score=28.61 Aligned_cols=49 Identities=24% Similarity=0.395 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHhc-CCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCcee
Q psy2693 12 VATQARKLLAICNA-NPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASY 67 (122)
Q Consensus 12 va~qArKIl~~ce~-~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y 67 (122)
-.++.++++..+=+ ....=+.|++ ||++|..=-. .+.....||.||+.-
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in~----~~~~C~~CG~---~~~~~~~CP~CGs~~ 514 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTINP----PIDICPDCGY---IGGEGDKCPKCGSEN 514 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE------EEEETTT------S--EEE-CCC----
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEec----CcccccCCCc---CCCCCCCCCCCCCcc
Confidence 44556666665544 2222233333 3777755432 223366777777763
No 178
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=25.21 E-value=30 Score=23.52 Aligned_cols=9 Identities=33% Similarity=1.305 Sum_probs=6.9
Q ss_pred eecCCCCce
Q psy2693 58 EACVYCGAS 66 (122)
Q Consensus 58 v~CP~CgA~ 66 (122)
.-|||||-.
T Consensus 7 KPCPFCG~~ 15 (64)
T PRK09710 7 KPCPFCGCP 15 (64)
T ss_pred cCCCCCCCc
Confidence 459999964
No 179
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.80 E-value=23 Score=23.72 Aligned_cols=27 Identities=19% Similarity=0.544 Sum_probs=20.9
Q ss_pred eeecccceeccCCCcceecCCCCceec
Q psy2693 42 QICARSYTPIYHGRESEACVYCGASYL 68 (122)
Q Consensus 42 ~ICa~S~tPIY~G~~~v~CP~CgA~Y~ 68 (122)
.+|+..|.|.-.-+++-.||-|...|.
T Consensus 29 ALCGk~wvp~rdp~~~PVCP~Ck~iye 55 (58)
T PF11238_consen 29 ALCGKVWVPTRDPKPFPVCPECKEIYE 55 (58)
T ss_pred eeeCceeCCCCCCCCCCCCcCHHHHHH
Confidence 589999999766677888888877663
No 180
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=24.46 E-value=37 Score=24.10 Aligned_cols=22 Identities=23% Similarity=0.685 Sum_probs=8.6
Q ss_pred cCCCCCcccCcccceeecCCCcccC
Q psy2693 68 LPKYKGELCAVCTVSVIDTHRNAYG 92 (122)
Q Consensus 68 ~p~~kG~lC~VC~ls~IG~~~~a~G 92 (122)
+.+..|++|.||+ -.|| ..+.|
T Consensus 4 ~k~~~~qiCqiCG-D~VG--l~~~G 25 (80)
T PF14569_consen 4 LKNLNGQICQICG-DDVG--LTENG 25 (80)
T ss_dssp -S--SS-B-SSS---B----B-SSS
T ss_pred hhhcCCccccccc-Cccc--cCCCC
Confidence 4567899999997 3455 44444
No 181
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=24.45 E-value=33 Score=23.49 Aligned_cols=9 Identities=22% Similarity=0.648 Sum_probs=7.7
Q ss_pred ecCCCCcee
Q psy2693 59 ACVYCGASY 67 (122)
Q Consensus 59 ~CP~CgA~Y 67 (122)
.||+||+..
T Consensus 3 ~CP~Cg~~a 11 (72)
T PRK09678 3 HCPLCQHAA 11 (72)
T ss_pred cCCCCCCcc
Confidence 699999876
No 182
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.98 E-value=37 Score=19.92 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=6.9
Q ss_pred eecCCCCcee
Q psy2693 58 EACVYCGASY 67 (122)
Q Consensus 58 v~CP~CgA~Y 67 (122)
..||.||+.-
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 4688888554
No 183
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=23.82 E-value=50 Score=30.52 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=31.1
Q ss_pred eeeecccceec----cCC------CcceecCCCCceecCCCCCcccCccc
Q psy2693 41 FQICARSYTPI----YHG------RESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 41 F~ICa~S~tPI----Y~G------~~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
+.|.+..++|- +.| .+.|.|.-|+.+|-.+.-...|+.|+
T Consensus 62 ~~id~~il~~~~v~~aSGH~~~F~DpmV~CkkCk~ryRaD~LiikCP~CG 111 (539)
T PRK14894 62 EGLDAAILMNRLVWKYSGHEETFNDPLVDCRDCKMRWRADHIQGVCPNCG 111 (539)
T ss_pred EEeeccccCCHhHeeeccCCCCCCCceeECCCCCccccCccceeeCCCCC
Confidence 56777777662 223 67899999999998887777899997
No 184
>PRK14526 adenylate kinase; Provisional
Probab=23.40 E-value=51 Score=25.79 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=19.7
Q ss_pred cceecCCCCceecCCCC----CcccCcccceeec
Q psy2693 56 ESEACVYCGASYLPKYK----GELCAVCTVSVID 85 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~k----G~lC~VC~ls~IG 85 (122)
..-.||-||..|+-.|. ...|.+|+=--++
T Consensus 121 ~R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~~ 154 (211)
T PRK14526 121 GRRICKSCNNIFNIYTLPTKEKGICDVCKGDLYQ 154 (211)
T ss_pred CCCcccccCCccccccCCCCccCcCCCCCCeeec
Confidence 34569999999985543 4467777533333
No 185
>PHA02942 putative transposase; Provisional
Probab=23.22 E-value=76 Score=27.33 Aligned_cols=33 Identities=24% Similarity=0.507 Sum_probs=21.2
Q ss_pred cceecCCCCceecCCCCC--cccCcccceeecCCCcccC
Q psy2693 56 ESEACVYCGASYLPKYKG--ELCAVCTVSVIDTHRNAYG 92 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG--~lC~VC~ls~IG~~~~a~G 92 (122)
.+-.||.||.... +..+ -.|+-|+.. .. ++..|
T Consensus 324 TSq~Cs~CG~~~~-~l~~r~f~C~~CG~~-~d--rD~nA 358 (383)
T PHA02942 324 SSVSCPKCGHKMV-EIAHRYFHCPSCGYE-ND--RDVIA 358 (383)
T ss_pred CCccCCCCCCccC-cCCCCEEECCCCCCE-eC--cHHHH
Confidence 5678999998764 3333 378888874 33 55443
No 186
>PF11475 VP_N-CPKC: Virion protein N terminal domain ; InterPro: IPR021573 This is the N-terminal domain of a family of virion proteins which contains a zinc finger domain. Currently no function is known. ; PDB: 2BAI_A.
Probab=23.20 E-value=10 Score=22.52 Aligned_cols=18 Identities=50% Similarity=0.833 Sum_probs=9.5
Q ss_pred eeeecccceeccCCCcceecCCCCc
Q psy2693 41 FQICARSYTPIYHGRESEACVYCGA 65 (122)
Q Consensus 41 F~ICa~S~tPIY~G~~~v~CP~CgA 65 (122)
-+||+.|++ ++.||-|.|
T Consensus 7 qeicahslt-------f~ecpkcsa 24 (32)
T PF11475_consen 7 QEICAHSLT-------FEECPKCSA 24 (32)
T ss_dssp S---SSSS--------GGGHHHHH-
T ss_pred HHHHhcccc-------cccCcchhH
Confidence 368888876 467888876
No 187
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=23.20 E-value=26 Score=29.49 Aligned_cols=23 Identities=30% Similarity=0.827 Sum_probs=8.4
Q ss_pred eecCCCCceecCCCCCc------ccCccc
Q psy2693 58 EACVYCGASYLPKYKGE------LCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~------lC~VC~ 80 (122)
.-||-||+.++.+|... .|+.|+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~ 60 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCN 60 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT-
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCc
Confidence 46888888877777554 577774
No 188
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.18 E-value=45 Score=27.07 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=13.8
Q ss_pred CCCcceecCCCCceecCCCCC
Q psy2693 53 HGRESEACVYCGASYLPKYKG 73 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y~p~~kG 73 (122)
.+.-.-.||-||..+.|....
T Consensus 113 ~~~~~~~C~~c~~~~yp~~~p 133 (256)
T PRK00241 113 KTEWAMLCPHCRERYYPRIAP 133 (256)
T ss_pred CCceeEECCCCCCEECCCCCC
Confidence 344556688888777777543
No 189
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=22.98 E-value=31 Score=24.44 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=10.9
Q ss_pred eecCCCCceecCCC
Q psy2693 58 EACVYCGASYLPKY 71 (122)
Q Consensus 58 v~CP~CgA~Y~p~~ 71 (122)
+.||+||.+=..+|
T Consensus 2 I~CP~CG~R~~~EF 15 (84)
T TIGR01374 2 IPCPYCGPRPEEEF 15 (84)
T ss_pred ccCCCCCCccHhhE
Confidence 57999997766665
No 190
>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.
Probab=22.87 E-value=84 Score=22.05 Aligned_cols=56 Identities=13% Similarity=0.144 Sum_probs=32.7
Q ss_pred eecccceeccCC---CcceecCCCCceecCCCCCcccCcccceeecCCCcccCcceecccchhh
Q psy2693 43 ICARSYTPIYHG---RESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSD 103 (122)
Q Consensus 43 ICa~S~tPIY~G---~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG~~~~a~GLr~~~~~~~~~ 103 (122)
+|.---.|+-.| ...++|||-|..|.. .|+.-.+-....+. ...+|+.....-+.+
T Consensus 42 ~CpH~ga~L~~G~~~~~~i~CP~Hg~~fd~--~G~~~~~p~~~~~p---~~~~l~~ypv~~~~g 100 (115)
T cd03531 42 YCRHMGGDLSQGTVKGDEIACPFHDWRWGG--DGRCKAIPYARRVP---PLARTRAWPTLERNG 100 (115)
T ss_pred cCCCCCCCCccCcccCCEEECCCCCCEECC--CCCEEECCcccCCC---cccccceEeEEEECC
Confidence 566666666544 357999999999998 58655442222222 234455554444443
No 191
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.78 E-value=1.4e+02 Score=24.31 Aligned_cols=65 Identities=26% Similarity=0.452 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCceeecCCC----CCCeeeecccceeccCCCcceecCCCCceecCCCCC----cccCccc
Q psy2693 10 IPVATQARKLLAICNANPTDEHTIDYDE----HNPFQICARSYTPIYHGRESEACVYCGASYLPKYKG----ELCAVCT 80 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~tDa~eIdYD~----~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG----~lC~VC~ 80 (122)
..+.+.+++|++.+-+.+...+. +|-. ...|. ..--+| |..-..||-||+.....--| -.|+.|+
T Consensus 200 ~~L~~~~~~vl~~ai~~gg~t~~-~~~~~~g~~g~~~----~~l~Vy-~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 200 ERLVDAIKAVLAEAIEQGGTTLR-DYVNADGKPGYFQ----QSLQVY-GREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred HHHHHHHHHHHHHHHHcCCCccc-cccccCCCCCCcc----ceeEEc-CCCCCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 45567799999988776544332 3321 11121 111245 23334588888776643333 3577776
No 192
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.64 E-value=39 Score=25.06 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=16.5
Q ss_pred cCCCCceecCCCCCcccCcccceeec
Q psy2693 60 CVYCGASYLPKYKGELCAVCTVSVID 85 (122)
Q Consensus 60 CP~CgA~Y~p~~kG~lC~VC~ls~IG 85 (122)
||.||....-. .--|+.|+..--|
T Consensus 1 CPvCg~~l~vt--~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGELVVT--RLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCceEEE--EEEcCCCCCEEEe
Confidence 77777766544 4457777777777
No 193
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.61 E-value=52 Score=30.48 Aligned_cols=22 Identities=27% Similarity=0.487 Sum_probs=10.1
Q ss_pred ceecCCCCceecCCCCCcccCccc
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
...|+-||..+.-. +..||+|+
T Consensus 568 ~~~C~~CG~~~~g~--~~~CP~CG 589 (625)
T PRK08579 568 ITVCNKCGRSTTGL--YTRCPRCG 589 (625)
T ss_pred CccCCCCCCccCCC--CCcCcCCC
Confidence 34455555543211 44555554
No 194
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=22.52 E-value=78 Score=19.09 Aligned_cols=15 Identities=33% Similarity=0.775 Sum_probs=12.2
Q ss_pred CCCcceecCCCCcee
Q psy2693 53 HGRESEACVYCGASY 67 (122)
Q Consensus 53 ~G~~~v~CP~CgA~Y 67 (122)
.+.+.|+||.||..+
T Consensus 36 ~~~~~v~C~~C~~~f 50 (64)
T smart00647 36 EGCNRVTCPKCGFSF 50 (64)
T ss_pred CCCCeeECCCCCCeE
Confidence 378899999998766
No 195
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=22.48 E-value=96 Score=34.13 Aligned_cols=62 Identities=24% Similarity=0.557 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCCCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCc-ccCccccee
Q psy2693 17 RKLLAICNANPTDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGE-LCAVCTVSV 83 (122)
Q Consensus 17 rKIl~~ce~~~tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~-lC~VC~ls~ 83 (122)
.+|+..+--.=+..-.|||-.+.| =-.|..=|-|+. ...| .||..-..+|+|. +|.-|++-.
T Consensus 1407 e~I~~ws~GeV~kpeTinyrt~kPe~dGLFcerIFGp~k----d~eC-~Cgkyk~~~~~g~~~C~~Cgvev 1472 (2890)
T PRK09603 1407 EKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTK----DYEC-LCGKYKKPRFKDIGTCEKCGVAI 1472 (2890)
T ss_pred HHHHHhhceeEccccccccccCccCCCCEeeceeccCcc----CcEE-eCCCcccccCCCCEEcCCCCcEe
Confidence 456666655556666899976654 347888888863 4678 8995334789999 999997643
No 196
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=22.39 E-value=93 Score=21.13 Aligned_cols=32 Identities=22% Similarity=0.470 Sum_probs=23.8
Q ss_pred eeecccceeccC----CCcceecCCCCceecCCCCCcc
Q psy2693 42 QICARSYTPIYH----GRESEACVYCGASYLPKYKGEL 75 (122)
Q Consensus 42 ~ICa~S~tPIY~----G~~~v~CP~CgA~Y~p~~kG~l 75 (122)
++|.---.|+.. ....+.|||-|+.|..+ |+.
T Consensus 41 n~CpH~g~~L~~g~~~~~~~i~Cp~Hg~~Fd~~--G~~ 76 (118)
T cd03469 41 NVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLD--GKL 76 (118)
T ss_pred EeCCCCCCEeeeccCCCCCEEECCCCCCEECCC--CcE
Confidence 466666666644 34589999999999998 864
No 197
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=22.35 E-value=55 Score=22.03 Aligned_cols=18 Identities=44% Similarity=0.951 Sum_probs=9.1
Q ss_pred ecCCCCceecCCCCCcccCccc
Q psy2693 59 ACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 59 ~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
+||-||..-+. ..|++|+
T Consensus 7 kC~~cg~YTLk----e~Cp~CG 24 (59)
T COG2260 7 KCPKCGRYTLK----EKCPVCG 24 (59)
T ss_pred cCcCCCceeec----ccCCCCC
Confidence 45555554443 3566654
No 198
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=22.35 E-value=55 Score=22.21 Aligned_cols=17 Identities=18% Similarity=0.278 Sum_probs=14.3
Q ss_pred ceecCCCCceecCCCCCc
Q psy2693 57 SEACVYCGASYLPKYKGE 74 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~ 74 (122)
.+.||+.|+.|..+ .|.
T Consensus 64 ~i~Cp~Hg~~Fdl~-tG~ 80 (105)
T TIGR02378 64 WVACPLHKRNFRLE-DGR 80 (105)
T ss_pred EEECCcCCCEEEcC-Ccc
Confidence 49999999999987 454
No 199
>PRK08329 threonine synthase; Validated
Probab=22.31 E-value=49 Score=27.56 Aligned_cols=21 Identities=38% Similarity=0.872 Sum_probs=16.1
Q ss_pred eecCCCCceecCCCCCcccCccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.+|+-||..|.+++. ..| -|+
T Consensus 2 l~C~~Cg~~~~~~~~-~~C-~c~ 22 (347)
T PRK08329 2 LRCTKCGRTYEEKFK-LRC-DCG 22 (347)
T ss_pred cCcCCCCCCcCCCCc-eec-CCC
Confidence 479999999987765 678 574
No 200
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=22.26 E-value=57 Score=21.59 Aligned_cols=22 Identities=32% Similarity=0.771 Sum_probs=17.4
Q ss_pred ceecCCCCceecCCCCCcccCcccc
Q psy2693 57 SEACVYCGASYLPKYKGELCAVCTV 81 (122)
Q Consensus 57 ~v~CP~CgA~Y~p~~kG~lC~VC~l 81 (122)
.+.||-||..-+| ..+|..|+.
T Consensus 27 ~~~c~~cG~~~l~---Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLP---HRVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccC---ceEcCCCCC
Confidence 5789999988777 478888873
No 201
>PRK00420 hypothetical protein; Validated
Probab=22.18 E-value=60 Score=23.97 Aligned_cols=28 Identities=21% Similarity=0.469 Sum_probs=19.1
Q ss_pred ecccceeccC-CCcceecCCCCceecCCC
Q psy2693 44 CARSYTPIYH-GRESEACVYCGASYLPKY 71 (122)
Q Consensus 44 Ca~S~tPIY~-G~~~v~CP~CgA~Y~p~~ 71 (122)
|..=-+|.++ -...+.||-||..+.-+-
T Consensus 26 CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 26 CPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCcceecCCCceECCCCCCeeeecc
Confidence 3333366665 466899999999887543
No 202
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.12 E-value=56 Score=30.35 Aligned_cols=11 Identities=45% Similarity=0.510 Sum_probs=5.4
Q ss_pred HHHHHHHHHHH
Q psy2693 13 ATQARKLLAIC 23 (122)
Q Consensus 13 a~qArKIl~~c 23 (122)
.+..++++..+
T Consensus 542 ~eal~~lv~~~ 552 (623)
T PRK08271 542 EEGYRKLLNIA 552 (623)
T ss_pred HHHHHHHHHHH
Confidence 34455555544
No 203
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.04 E-value=41 Score=25.25 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=13.3
Q ss_pred cceecCCCCceecCCCCCcccCccc
Q psy2693 56 ESEACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 56 ~~v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
..|+||-|+...+--=+-..|.-|+
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~ 92 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCK 92 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCC
Confidence 4566777776654332234555553
No 204
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=21.85 E-value=91 Score=31.26 Aligned_cols=61 Identities=28% Similarity=0.586 Sum_probs=39.3
Q ss_pred HHHHHHhcCCCCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCccccee
Q psy2693 18 KLLAICNANPTDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 18 KIl~~ce~~~tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
+|++.+--.=+..-.|||-...| =-.|..=|-|+. ...| .||..-..+|+|.+|..|++--
T Consensus 11 ~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k----~~ec-~Cgkyk~~~~~~~~C~~Cgve~ 74 (1140)
T TIGR02386 11 TIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTK----DWEC-YCGKYKKIRYKGVVCERCGVEV 74 (1140)
T ss_pred HHHhhhceEEeccceecCCCCccCCCCcccchhcCCcc----Ccee-ccccccccCcCCcCCCCCCCCc
Confidence 34444433334556888864443 336888788863 4678 7995333578999999997643
No 205
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=21.68 E-value=25 Score=26.80 Aligned_cols=27 Identities=33% Similarity=0.626 Sum_probs=17.5
Q ss_pred ccceec----cCCCcceecCCCCceecCCCCC
Q psy2693 46 RSYTPI----YHGRESEACVYCGASYLPKYKG 73 (122)
Q Consensus 46 ~S~tPI----Y~G~~~v~CP~CgA~Y~p~~kG 73 (122)
.|+.++ .+|++ .+||-||..|.-++-|
T Consensus 98 ~sH~v~W~~l~~g~~-~RCpeCG~~fkL~~vg 128 (136)
T PF01215_consen 98 DSHDVIWFWLHKGKP-QRCPECGQVFKLKYVG 128 (136)
T ss_dssp -SSS-EEEEEETTSE-EEETTTEEEEEEEE--
T ss_pred CcceeEEEEEeCCCc-cCCCCCCeEEEEEEcC
Confidence 454554 47875 7999999999876644
No 206
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=21.58 E-value=46 Score=21.38 Aligned_cols=34 Identities=18% Similarity=0.477 Sum_probs=17.1
Q ss_pred eeecccceeccCCCcceecCCCCceecC--------CCCCcccCc
Q psy2693 42 QICARSYTPIYHGRESEACVYCGASYLP--------KYKGELCAV 78 (122)
Q Consensus 42 ~ICa~S~tPIY~G~~~v~CP~CgA~Y~p--------~~kG~lC~V 78 (122)
.+|..|..|+ +..|+..-||-.|.. ..+..-|++
T Consensus 12 ~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 12 LKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred cCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 3677777776 566666677766543 244555655
No 207
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=21.57 E-value=36 Score=24.08 Aligned_cols=14 Identities=21% Similarity=0.581 Sum_probs=11.3
Q ss_pred eecCCCCceecCCC
Q psy2693 58 EACVYCGASYLPKY 71 (122)
Q Consensus 58 v~CP~CgA~Y~p~~ 71 (122)
+.||+||.+=..+|
T Consensus 2 I~CP~CG~R~~~EF 15 (84)
T PF04267_consen 2 IPCPHCGPRDESEF 15 (84)
T ss_dssp EEETTTEEEEGGGS
T ss_pred ccCCCCCccchhhe
Confidence 47999999877776
No 208
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.54 E-value=1.7e+02 Score=23.82 Aligned_cols=66 Identities=18% Similarity=0.243 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHHHhcCCCCceeecCCC---CCCeeeecccceeccCCCcceecCCCCceecCCCC----CcccCccc
Q psy2693 10 IPVATQARKLLAICNANPTDEHTIDYDE---HNPFQICARSYTPIYHGRESEACVYCGASYLPKYK----GELCAVCT 80 (122)
Q Consensus 10 ~~va~qArKIl~~ce~~~tDa~eIdYD~---~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~k----G~lC~VC~ 80 (122)
..+.+..+.|++.+-+.+...+.--.+. ...|. ..| -+| |..-..||-||+.....-- --.|+.|+
T Consensus 199 ~~l~~a~~~vl~~ai~~gg~~~~~~~~~~g~~g~~~---~~~-~Vy-~R~g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 199 RKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGFFQ---LSH-RVY-QRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred HHHHHHHHHHHHHHHHcCCCccccccCCCCCCCcch---hhE-eec-CCCCCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 3445667888887776655443211111 11221 111 245 3444458888876642211 23566665
No 209
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=21.50 E-value=92 Score=34.18 Aligned_cols=62 Identities=21% Similarity=0.533 Sum_probs=42.1
Q ss_pred HHHHHHHhcCCCCceeecCCCCCC---eeeecccceeccCCCcceecCCCCceecCCCCCcccCccccee
Q psy2693 17 RKLLAICNANPTDEHTIDYDEHNP---FQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSV 83 (122)
Q Consensus 17 rKIl~~ce~~~tDa~eIdYD~~np---F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~ 83 (122)
.+|+..+--.=+..-.|||-.+.| =-.|..=|-|+. ...| .||..-..+|+|.+|.-|++-.
T Consensus 1459 e~I~~Ws~GeV~kpeTinyrt~kPE~dGLFcerIFGp~k----d~eC-~Cgkyk~~~~~g~~C~~Cgvev 1523 (2836)
T PRK14844 1459 ESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVN----DDEC-LCGKYKKRRHRGRICEKCGVEV 1523 (2836)
T ss_pred HHHHhhhceeECCcccccccCCCCCCCCeehhhhcCCCc----CcEE-ecccccccccCCcCcCCCCcEe
Confidence 455555544445666888865544 336888888863 4678 8995333589999999997643
No 210
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=20.88 E-value=1e+02 Score=20.89 Aligned_cols=51 Identities=12% Similarity=0.117 Sum_probs=34.1
Q ss_pred eeecccceeccCC---CcceecCCCCceecCCCCCcccCcccceeecCCCcccCcceecccchhh
Q psy2693 42 QICARSYTPIYHG---RESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSD 103 (122)
Q Consensus 42 ~ICa~S~tPIY~G---~~~v~CP~CgA~Y~p~~kG~lC~VC~ls~IG~~~~a~GLr~~~~~~~~~ 103 (122)
++|.---.|+-.| ...+.||+=|+.|..+ |..| ++ ....+|+......+.+
T Consensus 40 n~CpH~g~~L~~g~~~g~~i~CP~Hg~~Fdl~--~G~~-------~~--~~~~~L~~~~v~v~~g 93 (108)
T cd03474 40 GICPHQEIPLAEGGFDGGVLTCRAHLWQFDAD--TGEG-------LN--PRDCRLARYPVKVEGG 93 (108)
T ss_pred CcCCCCCCCcccCcccCCEEEeCCcCCEEECC--Cccc-------cC--CCCCccceEeEEEECC
Confidence 3677666676544 2479999999999987 4333 24 4556777766666554
No 211
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=20.82 E-value=42 Score=22.15 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=7.7
Q ss_pred eecCCCCceecCC
Q psy2693 58 EACVYCGASYLPK 70 (122)
Q Consensus 58 v~CP~CgA~Y~p~ 70 (122)
-+||||.+...-+
T Consensus 56 G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 56 GECPYCSSPISWS 68 (70)
T ss_dssp EE-TTT-SEEEGG
T ss_pred cCCcCCCCeeeEe
Confidence 5799998876543
No 212
>PHA02551 19 tail tube protein; Provisional
Probab=20.79 E-value=59 Score=25.45 Aligned_cols=22 Identities=18% Similarity=0.406 Sum_probs=18.5
Q ss_pred CceeecCCCCCCeeeeccccee
Q psy2693 29 DEHTIDYDEHNPFQICARSYTP 50 (122)
Q Consensus 29 Da~eIdYD~~npF~ICa~S~tP 50 (122)
-++|++||+.|+...|..+|.-
T Consensus 138 geveLdy~~nn~i~tF~Vtf~y 159 (163)
T PHA02551 138 GEIDLDWDSNNEIETFEVTFAL 159 (163)
T ss_pred cceeecccCCCcEEEEEEEEEe
Confidence 4789999999999988888753
No 213
>PRK05638 threonine synthase; Validated
Probab=20.72 E-value=58 Score=28.07 Aligned_cols=21 Identities=29% Similarity=0.812 Sum_probs=15.5
Q ss_pred eecCCCCceecCCCCCcccCccc
Q psy2693 58 EACVYCGASYLPKYKGELCAVCT 80 (122)
Q Consensus 58 v~CP~CgA~Y~p~~kG~lC~VC~ 80 (122)
.+|+-||..|.+++. ..| -|+
T Consensus 2 l~C~~Cg~~~~~~~~-~~C-~c~ 22 (442)
T PRK05638 2 MKCPKCGREYNSYIP-PFC-ICG 22 (442)
T ss_pred eEeCCCCCCCCCCCc-eec-CCC
Confidence 478888888877665 668 674
No 214
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=20.51 E-value=43 Score=26.37 Aligned_cols=22 Identities=32% Similarity=0.856 Sum_probs=14.2
Q ss_pred ecCCCCceec------CCCCC------cccCccc
Q psy2693 59 ACVYCGASYL------PKYKG------ELCAVCT 80 (122)
Q Consensus 59 ~CP~CgA~Y~------p~~kG------~lC~VC~ 80 (122)
+||||++... |.-.| .-|..|+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~ 35 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECG 35 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccc
Confidence 6999997653 22334 3588886
No 215
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=20.19 E-value=1.6e+02 Score=27.20 Aligned_cols=44 Identities=30% Similarity=0.500 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhcCCCCceeecCCCCC-Ceeeecc-cceeccCCCcceecCCCCc
Q psy2693 14 TQARKLLAICNANPTDEHTIDYDEHN-PFQICAR-SYTPIYHGRESEACVYCGA 65 (122)
Q Consensus 14 ~qArKIl~~ce~~~tDa~eIdYD~~n-pF~ICa~-S~tPIY~G~~~v~CP~CgA 65 (122)
+..++++..+-++ .|.|=..| +|+||.. .| | .|.-...||.||+
T Consensus 509 ea~~~lv~~~~~~-----~i~Y~tin~~~siC~~CGy--~-~g~~~~~CP~CGs 554 (586)
T TIGR02827 509 DGYRKLLRVAADT-----GCNYFCFNIKITICNDCHH--I-DKRTLHRCPVCGS 554 (586)
T ss_pred HHHHHHHHHHHhc-----CCceEEeCCCCeecCCCCC--c-CCCcCCcCcCCCC
Confidence 4556666654332 34443333 3777753 22 1 3444467777775
No 216
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF02489 Herpes_glycop_H: Herpesvirus glycoprotein H; InterPro: IPR003493 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH []. This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein []. Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells []. Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present [, ].; PDB: 3PHF_S 3M1C_A 2LQY_A 2XQY_A.
Probab=20.02 E-value=52 Score=29.94 Aligned_cols=27 Identities=30% Similarity=0.666 Sum_probs=13.1
Q ss_pred eeecccceeccCCCcceecCCCCceec
Q psy2693 42 QICARSYTPIYHGRESEACVYCGASYL 68 (122)
Q Consensus 42 ~ICa~S~tPIY~G~~~v~CP~CgA~Y~ 68 (122)
.+-.....-+|.-++...|+|||+...
T Consensus 546 ~~~~~~i~~~~Nit~~~~C~~Cgsv~l 572 (657)
T PF02489_consen 546 IIETRRIPVVYNITPSKDCPFCGSVFL 572 (657)
T ss_dssp -SEEEE--EE--SSS-SS-STTT-EEE
T ss_pred CCCccccCCCcCCCCCCCCCCCCcEEE
Confidence 334445555665557889999999865
Done!