Query psy15975
Match_columns 312
No_of_seqs 235 out of 1295
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 17:48:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15975.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15975hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815|consensus 100.0 2.2E-58 4.8E-63 453.8 16.0 305 4-311 118-428 (444)
2 KOG1812|consensus 100.0 7.7E-29 1.7E-33 239.2 7.7 172 7-202 198-374 (384)
3 KOG0006|consensus 99.9 9.4E-24 2E-28 192.7 6.1 140 9-152 282-437 (446)
4 KOG1814|consensus 99.9 1.4E-23 3E-28 197.6 7.5 141 7-151 237-405 (445)
5 smart00647 IBR In Between Ring 99.6 4.2E-15 9.1E-20 107.7 5.7 62 27-88 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.5 6.1E-15 1.3E-19 106.7 0.8 62 27-88 1-64 (64)
7 smart00647 IBR In Between Ring 98.4 3E-07 6.5E-12 66.2 4.4 39 111-151 17-59 (64)
8 PF01485 IBR: IBR domain; Int 98.4 1.3E-07 2.9E-12 68.0 2.2 39 111-151 17-59 (64)
9 KOG1814|consensus 96.5 0.00085 1.8E-08 64.7 1.0 48 110-163 271-320 (445)
10 PF10571 UPF0547: Uncharacteri 93.4 0.04 8.6E-07 32.7 1.0 24 113-142 1-24 (26)
11 PF14952 zf-tcix: Putative tre 93.1 0.062 1.3E-06 35.7 1.7 33 106-142 5-37 (44)
12 KOG1812|consensus 91.8 0.1 2.2E-06 51.0 2.2 50 33-87 297-346 (384)
13 KOG1815|consensus 91.7 0.13 2.7E-06 51.3 2.8 46 111-163 157-205 (444)
14 PHA00626 hypothetical protein 90.5 0.22 4.8E-06 34.9 2.3 28 114-143 2-34 (59)
15 TIGR00570 cdk7 CDK-activating 90.4 0.17 3.7E-06 47.8 2.2 53 46-126 5-57 (309)
16 smart00661 RPOL9 RNA polymeras 90.2 0.23 5E-06 33.9 2.2 28 113-142 1-30 (52)
17 PF09297 zf-NADH-PPase: NADH p 89.8 0.48 1E-05 29.3 3.2 29 111-141 2-30 (32)
18 PF13719 zinc_ribbon_5: zinc-r 89.4 0.33 7.1E-06 31.2 2.3 28 45-74 3-35 (37)
19 PF02150 RNA_POL_M_15KD: RNA p 89.3 0.3 6.5E-06 31.0 2.0 28 44-73 1-29 (35)
20 PRK00420 hypothetical protein; 87.7 7.5 0.00016 31.4 9.5 23 111-135 22-45 (112)
21 PF13717 zinc_ribbon_4: zinc-r 86.3 0.66 1.4E-05 29.6 2.3 28 45-74 3-35 (36)
22 PRK00432 30S ribosomal protein 86.3 0.45 9.8E-06 32.8 1.6 31 108-142 16-47 (50)
23 KOG2906|consensus 86.0 0.92 2E-05 35.6 3.3 28 45-74 2-31 (105)
24 PF03119 DNA_ligase_ZBD: NAD-d 85.6 0.87 1.9E-05 27.4 2.4 23 114-136 1-23 (28)
25 KOG0317|consensus 85.6 0.11 2.5E-06 48.2 -2.2 42 110-162 237-278 (293)
26 PRK14559 putative protein seri 85.5 0.54 1.2E-05 49.1 2.4 11 139-149 40-50 (645)
27 KOG0823|consensus 85.2 0.63 1.4E-05 42.0 2.3 36 66-124 61-96 (230)
28 PRK00398 rpoP DNA-directed RNA 84.8 0.97 2.1E-05 30.3 2.6 30 113-144 4-33 (46)
29 KOG0823|consensus 84.1 0.32 7E-06 43.9 0.0 24 138-161 65-88 (230)
30 TIGR02098 MJ0042_CXXC MJ0042 f 83.7 1.2 2.6E-05 28.3 2.6 28 113-142 3-35 (38)
31 PF15227 zf-C3HC4_4: zinc fing 82.8 0.39 8.4E-06 31.7 0.0 24 138-161 16-40 (42)
32 PF07975 C1_4: TFIIH C1-like d 82.7 0.41 8.9E-06 33.1 0.1 24 63-86 19-43 (51)
33 KOG0317|consensus 81.7 0.29 6.2E-06 45.6 -1.3 18 65-82 251-269 (293)
34 PLN03208 E3 ubiquitin-protein 81.5 0.31 6.8E-06 43.0 -1.1 32 112-151 18-49 (193)
35 PRK00398 rpoP DNA-directed RNA 81.2 1.6 3.4E-05 29.2 2.5 29 45-76 4-33 (46)
36 PF13920 zf-C3HC4_3: Zinc fing 81.1 0.19 4.2E-06 34.1 -2.0 34 65-124 15-49 (50)
37 PF00097 zf-C3HC4: Zinc finger 81.1 0.19 4.1E-06 32.5 -2.0 24 137-161 16-39 (41)
38 smart00661 RPOL9 RNA polymeras 80.9 1.3 2.9E-05 30.0 2.1 26 46-73 2-29 (52)
39 PRK14559 putative protein seri 80.5 1.2 2.6E-05 46.5 2.6 10 45-56 2-11 (645)
40 KOG2906|consensus 80.3 1.4 3E-05 34.6 2.2 28 114-143 3-32 (105)
41 PF13923 zf-C3HC4_2: Zinc fing 80.2 0.33 7.1E-06 31.2 -1.0 22 130-153 11-32 (39)
42 KOG0978|consensus 80.2 0.5 1.1E-05 49.3 -0.3 47 42-122 641-688 (698)
43 PRK04023 DNA polymerase II lar 79.2 1.4 3.1E-05 47.6 2.7 33 42-83 624-662 (1121)
44 PF08274 PhnA_Zn_Ribbon: PhnA 79.1 1.7 3.8E-05 26.6 2.0 27 113-142 3-29 (30)
45 PF13719 zinc_ribbon_5: zinc-r 78.8 2 4.4E-05 27.4 2.4 28 113-142 3-35 (37)
46 PF14369 zf-RING_3: zinc-finge 78.3 2.2 4.8E-05 27.1 2.4 28 45-74 3-31 (35)
47 COG4647 AcxC Acetone carboxyla 78.0 5 0.00011 33.1 4.9 113 7-125 13-133 (165)
48 cd00162 RING RING-finger (Real 77.1 0.62 1.3E-05 29.7 -0.5 32 115-153 2-33 (45)
49 KOG0320|consensus 76.8 1.1 2.3E-05 39.1 0.8 31 68-124 149-179 (187)
50 TIGR00622 ssl1 transcription f 76.6 2.2 4.8E-05 34.4 2.5 66 19-86 25-103 (112)
51 PF13240 zinc_ribbon_2: zinc-r 76.3 1 2.2E-05 25.8 0.4 10 115-124 2-11 (23)
52 PRK14714 DNA polymerase II lar 76.2 2.4 5.2E-05 47.0 3.4 9 45-55 668-676 (1337)
53 PF13248 zf-ribbon_3: zinc-rib 76.1 1.2 2.7E-05 26.1 0.7 12 112-123 2-13 (26)
54 PF07282 OrfB_Zn_ribbon: Putat 75.9 2.1 4.6E-05 30.9 2.1 29 111-141 27-55 (69)
55 PRK08665 ribonucleotide-diphos 75.5 1.7 3.7E-05 46.3 2.0 27 113-143 725-751 (752)
56 PF09538 FYDLN_acid: Protein o 74.7 1.8 3.9E-05 34.8 1.5 27 113-142 10-36 (108)
57 PF01396 zf-C4_Topoisom: Topoi 74.6 4.1 8.9E-05 26.4 3.0 27 113-140 2-32 (39)
58 COG1645 Uncharacterized Zn-fin 73.8 2.2 4.8E-05 35.3 1.9 25 112-140 28-52 (131)
59 PF06677 Auto_anti-p27: Sjogre 73.5 3.5 7.6E-05 27.2 2.4 24 112-139 17-41 (41)
60 PF14803 Nudix_N_2: Nudix N-te 73.4 3.1 6.7E-05 26.3 2.1 26 113-140 1-30 (34)
61 PF14835 zf-RING_6: zf-RING of 73.2 2 4.2E-05 31.2 1.2 23 113-135 8-33 (65)
62 PF14569 zf-UDP: Zinc-binding 72.8 2.4 5.1E-05 31.9 1.6 58 46-130 11-69 (80)
63 PF07191 zinc-ribbons_6: zinc- 72.7 3.2 6.8E-05 30.7 2.3 45 114-162 3-55 (70)
64 PHA02929 N1R/p28-like protein; 72.4 1.5 3.2E-05 40.1 0.6 45 111-161 173-220 (238)
65 PF12773 DZR: Double zinc ribb 72.2 1.9 4E-05 29.2 0.9 10 113-122 30-39 (50)
66 PLN03086 PRLI-interacting fact 71.7 5 0.00011 41.2 4.2 32 41-74 404-445 (567)
67 PF13639 zf-RING_2: Ring finge 71.0 0.7 1.5E-05 30.4 -1.4 40 114-161 2-41 (44)
68 PLN03208 E3 ubiquitin-protein 70.6 2.6 5.7E-05 37.2 1.7 59 46-124 20-80 (193)
69 COG1198 PriA Primosomal protei 69.0 5.7 0.00012 42.1 4.1 39 113-153 445-489 (730)
70 TIGR03655 anti_R_Lar restricti 68.4 4.2 9.1E-05 28.0 2.1 27 113-141 2-35 (53)
71 TIGR00373 conserved hypothetic 68.2 6.1 0.00013 33.8 3.5 32 40-73 105-137 (158)
72 KOG4367|consensus 67.9 8.4 0.00018 38.1 4.7 79 63-151 174-254 (699)
73 PF13453 zf-TFIIB: Transcripti 67.5 2.2 4.7E-05 27.8 0.4 31 114-152 1-31 (41)
74 smart00184 RING Ring finger. E 66.3 1.4 3E-05 26.9 -0.7 15 138-152 16-30 (39)
75 PF12861 zf-Apc11: Anaphase-pr 66.0 2.3 5E-05 32.6 0.4 44 113-162 33-76 (85)
76 PF14634 zf-RING_5: zinc-RING 65.1 3.3 7.2E-05 27.2 1.0 33 114-151 1-33 (44)
77 PRK06266 transcription initiat 64.3 8.1 0.00018 33.7 3.5 59 11-73 85-145 (178)
78 PHA02926 zinc finger-like prot 64.3 1.5 3.1E-05 39.7 -1.1 73 23-123 155-230 (242)
79 PHA02929 N1R/p28-like protein; 64.2 2.3 5E-05 38.9 0.1 51 45-123 175-227 (238)
80 PRK05654 acetyl-CoA carboxylas 64.2 1.7 3.7E-05 41.0 -0.8 29 112-142 27-56 (292)
81 PRK09710 lar restriction allev 63.7 6.6 0.00014 28.4 2.3 29 110-140 4-35 (64)
82 COG2051 RPS27A Ribosomal prote 63.5 6.8 0.00015 28.6 2.4 31 44-76 19-50 (67)
83 COG1998 RPS31 Ribosomal protei 63.4 4.8 0.0001 27.6 1.5 28 111-140 18-45 (51)
84 TIGR01384 TFS_arch transcripti 62.9 4.8 0.0001 31.6 1.7 25 113-141 1-25 (104)
85 COG1997 RPL43A Ribosomal prote 62.0 6.5 0.00014 30.2 2.2 29 112-142 35-63 (89)
86 PRK14892 putative transcriptio 61.8 6.7 0.00015 31.0 2.3 29 111-141 20-51 (99)
87 PF09723 Zn-ribbon_8: Zinc rib 61.2 9.3 0.0002 25.0 2.6 12 113-124 27-39 (42)
88 COG1594 RPB9 DNA-directed RNA 60.7 7.5 0.00016 31.4 2.5 29 112-142 2-32 (113)
89 smart00531 TFIIE Transcription 59.0 12 0.00027 31.4 3.6 33 40-74 95-133 (147)
90 TIGR01206 lysW lysine biosynth 59.0 11 0.00023 26.4 2.7 31 113-145 3-35 (54)
91 CHL00174 accD acetyl-CoA carbo 58.7 2.3 4.9E-05 40.2 -1.0 29 112-142 38-67 (296)
92 COG2888 Predicted Zn-ribbon RN 58.7 4.9 0.00011 28.7 0.9 15 114-128 29-44 (61)
93 PLN02638 cellulose synthase A 58.2 6 0.00013 43.4 1.9 55 51-130 22-77 (1079)
94 TIGR00515 accD acetyl-CoA carb 57.9 2.5 5.4E-05 39.7 -0.9 29 112-142 26-55 (285)
95 PF01428 zf-AN1: AN1-like Zinc 57.1 6 0.00013 26.1 1.1 38 47-92 1-39 (43)
96 PLN03086 PRLI-interacting fact 56.6 6.5 0.00014 40.4 1.8 30 111-142 432-463 (567)
97 KOG2932|consensus 56.4 2.7 5.8E-05 39.7 -0.9 55 41-130 87-141 (389)
98 PLN02189 cellulose synthase 56.2 7.5 0.00016 42.5 2.2 59 46-131 36-95 (1040)
99 PF08271 TF_Zn_Ribbon: TFIIB z 55.3 11 0.00025 24.6 2.3 26 46-73 2-28 (43)
100 PF09151 DUF1936: Domain of un 54.8 8.6 0.00019 23.7 1.4 28 114-141 3-35 (36)
101 TIGR00686 phnA alkylphosphonat 54.6 11 0.00023 30.3 2.3 30 113-153 3-32 (109)
102 KOG2807|consensus 53.8 8.8 0.00019 36.6 2.0 61 19-85 300-366 (378)
103 TIGR02300 FYDLN_acid conserved 53.5 8.3 0.00018 31.8 1.6 27 112-141 9-35 (129)
104 PF00098 zf-CCHC: Zinc knuckle 53.4 8.7 0.00019 20.6 1.2 16 74-89 2-17 (18)
105 PRK00415 rps27e 30S ribosomal 53.1 14 0.00029 26.4 2.4 30 45-76 12-42 (59)
106 TIGR00622 ssl1 transcription f 53.1 10 0.00022 30.7 2.0 39 112-152 55-101 (112)
107 PF01363 FYVE: FYVE zinc finge 53.0 11 0.00024 27.0 2.1 41 107-151 3-44 (69)
108 COG0777 AccD Acetyl-CoA carbox 52.5 5.2 0.00011 37.3 0.3 30 111-142 27-57 (294)
109 KOG2907|consensus 51.0 3.6 7.9E-05 33.1 -0.8 30 43-82 6-35 (116)
110 PF12861 zf-Apc11: Anaphase-pr 50.8 10 0.00023 29.0 1.7 14 112-125 71-84 (85)
111 PLN02915 cellulose synthase A 50.5 10 0.00022 41.6 2.1 29 51-79 20-49 (1044)
112 PLN02400 cellulose synthase 49.8 13 0.00028 40.9 2.8 29 51-79 41-70 (1085)
113 KOG2177|consensus 49.5 7.8 0.00017 34.8 1.0 17 129-147 96-112 (386)
114 PLN02436 cellulose synthase A 49.4 11 0.00025 41.3 2.3 59 46-131 38-97 (1094)
115 PF14354 Lar_restr_allev: Rest 49.4 13 0.00027 26.1 1.9 27 112-140 3-37 (61)
116 PHA02926 zinc finger-like prot 49.4 8.2 0.00018 35.0 1.1 52 110-162 168-224 (242)
117 PRK10220 hypothetical protein; 47.8 16 0.00035 29.3 2.4 31 112-153 3-33 (111)
118 PF06827 zf-FPG_IleRS: Zinc fi 47.7 14 0.0003 22.2 1.6 23 113-135 2-26 (30)
119 smart00659 RPOLCX RNA polymera 47.7 18 0.0004 24.1 2.3 23 115-140 5-27 (44)
120 PF08792 A2L_zn_ribbon: A2L zi 47.6 19 0.0004 22.5 2.2 29 112-142 3-31 (33)
121 PF01667 Ribosomal_S27e: Ribos 47.0 20 0.00044 25.2 2.5 30 45-76 8-38 (55)
122 PRK11827 hypothetical protein; 46.2 17 0.00037 26.0 2.1 26 112-139 8-33 (60)
123 KOG2164|consensus 45.6 9 0.0002 38.6 0.8 34 70-124 204-237 (513)
124 COG2816 NPY1 NTP pyrophosphohy 45.4 17 0.00037 34.0 2.6 34 106-142 106-139 (279)
125 COG1594 RPB9 DNA-directed RNA 45.2 18 0.00038 29.2 2.3 29 44-74 2-32 (113)
126 PF14353 CpXC: CpXC protein 45.2 21 0.00045 29.0 2.8 11 113-123 39-49 (128)
127 PF12760 Zn_Tnp_IS1595: Transp 45.1 43 0.00094 22.2 3.9 29 111-141 17-46 (46)
128 PF04606 Ogr_Delta: Ogr/Delta- 45.0 22 0.00047 23.9 2.4 9 114-122 1-9 (47)
129 TIGR00570 cdk7 CDK-activating 44.9 2.8E+02 0.0062 26.4 13.2 37 113-152 4-41 (309)
130 PF07754 DUF1610: Domain of un 43.8 18 0.00039 21.0 1.5 6 114-119 18-23 (24)
131 PRK09710 lar restriction allev 43.6 22 0.00048 25.7 2.3 49 42-97 4-53 (64)
132 PRK14714 DNA polymerase II lar 43.0 17 0.00037 40.6 2.5 33 112-152 667-704 (1337)
133 PF05129 Elf1: Transcription e 43.0 16 0.00034 27.7 1.6 30 111-142 21-56 (81)
134 PF01599 Ribosomal_S27: Riboso 42.7 14 0.00031 25.1 1.2 28 111-140 17-46 (47)
135 TIGR02443 conserved hypothetic 42.6 23 0.00051 25.2 2.3 27 113-141 10-40 (59)
136 COG0266 Nei Formamidopyrimidin 42.5 21 0.00046 33.3 2.7 25 111-135 244-270 (273)
137 PRK14811 formamidopyrimidine-D 42.3 21 0.00046 33.1 2.7 23 112-134 235-259 (269)
138 PF13445 zf-RING_UBOX: RING-ty 42.2 4.6 0.0001 26.8 -1.3 23 138-160 19-42 (43)
139 TIGR00577 fpg formamidopyrimid 42.0 22 0.00047 33.0 2.8 24 112-135 245-270 (272)
140 KOG0006|consensus 41.7 17 0.00037 34.6 1.9 53 27-85 383-438 (446)
141 PF09788 Tmemb_55A: Transmembr 41.7 22 0.00049 32.7 2.7 19 42-60 121-139 (256)
142 PRK01103 formamidopyrimidine/5 41.6 22 0.00048 33.0 2.7 25 111-135 244-270 (274)
143 PTZ00083 40S ribosomal protein 41.3 24 0.00053 27.0 2.4 35 44-80 35-70 (85)
144 PLN00209 ribosomal protein S27 41.1 24 0.00053 27.0 2.3 34 44-79 36-70 (86)
145 PRK10445 endonuclease VIII; Pr 41.0 23 0.0005 32.7 2.7 25 111-135 234-260 (263)
146 PRK13945 formamidopyrimidine-D 39.9 24 0.00051 33.0 2.6 25 111-135 253-279 (282)
147 PRK14810 formamidopyrimidine-D 39.8 24 0.00052 32.8 2.7 24 111-134 243-268 (272)
148 PRK04023 DNA polymerase II lar 39.8 22 0.00048 38.9 2.6 33 110-150 624-661 (1121)
149 KOG1493|consensus 39.5 32 0.0007 25.9 2.7 53 67-122 22-80 (84)
150 PF03604 DNA_RNApol_7kD: DNA d 39.4 18 0.00039 22.5 1.2 20 115-135 3-22 (32)
151 PF09889 DUF2116: Uncharacteri 39.1 13 0.00027 26.6 0.5 12 113-124 4-15 (59)
152 PF02748 PyrI_C: Aspartate car 39.0 27 0.00058 24.2 2.1 32 43-74 5-45 (52)
153 PF09526 DUF2387: Probable met 39.0 27 0.00059 25.8 2.3 27 113-141 9-39 (71)
154 PF01873 eIF-5_eIF-2B: Domain 38.8 29 0.00063 28.5 2.7 27 113-141 94-123 (125)
155 COG5574 PEX10 RING-finger-cont 38.1 8.2 0.00018 35.7 -0.7 33 114-154 217-250 (271)
156 PRK00420 hypothetical protein; 37.9 78 0.0017 25.5 5.0 44 23-80 5-48 (112)
157 COG2824 PhnA Uncharacterized Z 37.8 25 0.00054 28.1 2.0 30 112-152 3-32 (112)
158 TIGR00599 rad18 DNA repair pro 37.6 8.2 0.00018 38.0 -0.8 33 113-153 27-59 (397)
159 KOG4739|consensus 37.6 16 0.00036 33.2 1.1 17 69-85 22-38 (233)
160 PF03833 PolC_DP2: DNA polymer 37.2 11 0.00024 40.3 0.0 42 44-122 655-702 (900)
161 PRK14065 exodeoxyribonuclease 37.0 1.5E+02 0.0032 22.8 6.0 37 209-245 34-71 (86)
162 PF14149 YhfH: YhfH-like prote 36.9 2.3 4.9E-05 27.4 -3.2 25 111-135 12-36 (37)
163 PF06044 DRP: Dam-replacing fa 36.9 20 0.00044 32.8 1.6 37 103-142 23-63 (254)
164 PLN02195 cellulose synthase A 36.7 27 0.00058 38.2 2.7 29 51-79 11-40 (977)
165 smart00834 CxxC_CXXC_SSSS Puta 36.4 24 0.00052 22.3 1.5 12 113-124 27-38 (41)
166 PRK12286 rpmF 50S ribosomal pr 36.2 21 0.00046 25.2 1.3 24 110-140 25-48 (57)
167 PRK00241 nudC NADH pyrophospha 35.8 27 0.00059 32.2 2.3 30 110-141 97-126 (256)
168 KOG2041|consensus 35.7 56 0.0012 34.7 4.7 53 22-81 1090-1150(1189)
169 COG3024 Uncharacterized protei 35.4 18 0.00038 26.2 0.8 17 111-127 6-22 (65)
170 KOG0250|consensus 35.1 3.8E+02 0.0082 29.9 10.9 45 226-270 254-298 (1074)
171 TIGR00595 priA primosomal prot 34.6 33 0.00072 34.8 2.9 34 114-149 224-262 (505)
172 PF03966 Trm112p: Trm112p-like 34.0 38 0.00083 24.4 2.4 12 113-124 54-65 (68)
173 PRK09521 exosome complex RNA-b 34.0 31 0.00066 30.1 2.3 25 114-141 151-175 (189)
174 COG1579 Zn-ribbon protein, pos 33.3 22 0.00048 32.5 1.3 47 22-72 173-229 (239)
175 KOG3091|consensus 32.7 2.7E+02 0.0058 28.3 8.7 33 250-283 456-488 (508)
176 TIGR01053 LSD1 zinc finger dom 32.3 51 0.0011 20.3 2.4 25 114-140 3-27 (31)
177 KOG0320|consensus 31.8 11 0.00024 32.9 -0.9 35 112-152 131-165 (187)
178 PF15616 TerY-C: TerY-C metal 30.7 42 0.00091 27.9 2.4 12 111-122 76-87 (131)
179 PF11793 FANCL_C: FANCL C-term 29.8 25 0.00054 25.7 0.8 12 113-124 56-67 (70)
180 COG5175 MOT2 Transcriptional r 29.6 9.8 0.00021 36.5 -1.7 49 114-168 16-68 (480)
181 PF02318 FYVE_2: FYVE-type zin 29.3 44 0.00096 26.9 2.3 36 111-149 53-88 (118)
182 COG1198 PriA Primosomal protei 29.3 44 0.00094 35.7 2.8 13 22-34 406-418 (730)
183 PF10276 zf-CHCC: Zinc-finger 29.2 52 0.0011 21.5 2.2 11 64-74 28-39 (40)
184 COG1096 Predicted RNA-binding 29.2 40 0.00086 29.7 2.1 24 113-140 150-173 (188)
185 PRK08115 ribonucleotide-diphos 29.1 28 0.0006 37.7 1.3 25 113-141 828-853 (858)
186 KOG3800|consensus 28.9 2.3E+02 0.0051 26.7 7.1 39 113-154 1-39 (300)
187 KOG2879|consensus 28.8 29 0.00063 32.4 1.2 32 111-149 238-269 (298)
188 KOG3002|consensus 28.6 30 0.00065 32.8 1.3 33 42-81 46-78 (299)
189 PRK05580 primosome assembly pr 28.4 47 0.001 35.0 2.9 35 113-149 391-430 (679)
190 PF14570 zf-RING_4: RING/Ubox 28.0 19 0.00041 24.6 -0.1 34 115-152 1-34 (48)
191 PHA02325 hypothetical protein 28.0 30 0.00065 25.1 0.9 12 111-122 2-13 (72)
192 PRK08332 ribonucleotide-diphos 27.4 38 0.00083 39.5 2.1 27 114-144 1706-1738(1740)
193 PRK14873 primosome assembly pr 27.2 48 0.001 35.0 2.7 35 113-149 393-431 (665)
194 cd00065 FYVE FYVE domain; Zinc 26.9 40 0.00087 22.9 1.4 37 112-152 2-38 (57)
195 KOG3803|consensus 26.8 1.3E+02 0.0029 31.5 5.5 77 32-108 677-784 (968)
196 COG3809 Uncharacterized protei 26.5 43 0.00094 25.3 1.6 34 113-154 2-35 (88)
197 PF12677 DUF3797: Domain of un 25.9 57 0.0012 22.3 1.9 27 112-141 13-47 (49)
198 TIGR00311 aIF-2beta translatio 25.5 50 0.0011 27.5 2.0 27 113-141 98-127 (133)
199 PF07417 Crl: Transcriptional 25.5 1.5E+02 0.0032 24.4 4.6 40 243-282 65-110 (125)
200 PF06943 zf-LSD1: LSD1 zinc fi 25.3 88 0.0019 18.4 2.4 24 115-140 1-24 (25)
201 PF14169 YdjO: Cold-inducible 25.2 52 0.0011 23.5 1.7 29 44-72 18-47 (59)
202 PF03884 DUF329: Domain of unk 25.0 27 0.00058 24.8 0.2 34 112-154 2-40 (57)
203 COG5574 PEX10 RING-finger-cont 25.0 24 0.00052 32.7 -0.0 18 64-81 226-244 (271)
204 smart00532 LIGANc Ligase N fam 24.8 49 0.0011 33.1 2.1 24 112-135 399-422 (441)
205 smart00653 eIF2B_5 domain pres 24.7 53 0.0011 26.4 1.9 26 113-140 81-109 (110)
206 KOG4684|consensus 24.7 56 0.0012 29.5 2.2 18 42-59 136-153 (275)
207 PF14446 Prok-RING_1: Prokaryo 24.5 33 0.00072 24.0 0.6 18 51-71 10-28 (54)
208 KOG2807|consensus 24.4 51 0.0011 31.6 2.0 36 111-151 329-364 (378)
209 KOG0824|consensus 24.2 26 0.00057 33.1 0.1 14 136-149 23-36 (324)
210 PF06524 NOA36: NOA36 protein; 24.1 63 0.0014 30.1 2.5 15 111-125 208-222 (314)
211 PF08209 Sgf11: Sgf11 (transcr 24.1 42 0.0009 21.0 0.9 13 113-125 5-17 (33)
212 smart00440 ZnF_C2C2 C2C2 Zinc 23.5 78 0.0017 20.4 2.2 7 114-120 2-8 (40)
213 PF11682 DUF3279: Protein of u 23.5 44 0.00096 27.6 1.3 17 111-127 109-125 (128)
214 PRK03988 translation initiatio 23.4 57 0.0012 27.3 2.0 28 112-141 102-132 (138)
215 PRK09678 DNA-binding transcrip 23.4 48 0.001 24.6 1.4 9 114-122 3-11 (72)
216 PF02284 COX5A: Cytochrome c o 23.0 4E+02 0.0087 21.4 6.8 93 179-285 9-105 (108)
217 PF14392 zf-CCHC_4: Zinc knuck 22.9 31 0.00067 23.3 0.2 18 72-89 31-48 (49)
218 PF01783 Ribosomal_L32p: Ribos 22.8 61 0.0013 22.6 1.7 22 111-139 25-46 (56)
219 PF11023 DUF2614: Protein of u 22.6 48 0.0011 26.7 1.3 10 74-83 87-96 (114)
220 PF15605 Toxin_52: Putative to 22.5 4E+02 0.0087 21.2 6.9 53 220-278 43-96 (103)
221 PF04981 NMD3: NMD3 family ; 22.3 45 0.00098 30.2 1.2 7 129-135 34-40 (236)
222 PRK12495 hypothetical protein; 21.9 1.7E+02 0.0037 26.5 4.7 27 43-81 41-67 (226)
223 KOG3183|consensus 21.8 46 0.001 30.4 1.2 58 45-125 9-68 (250)
224 PRK03681 hypA hydrogenase nick 21.3 55 0.0012 26.3 1.4 14 43-58 69-82 (114)
225 PHA02862 5L protein; Provision 21.2 99 0.0021 26.2 2.9 46 73-122 3-52 (156)
226 PHA02109 hypothetical protein 21.0 1.2E+02 0.0027 26.4 3.5 22 286-307 206-227 (233)
227 TIGR00575 dnlj DNA ligase, NAD 20.9 78 0.0017 33.3 2.8 27 113-139 393-419 (652)
228 KOG1584|consensus 20.9 1.5E+02 0.0033 28.1 4.4 31 260-290 193-223 (297)
229 PLN02248 cellulose synthase-li 20.8 52 0.0011 36.6 1.5 38 45-82 125-162 (1135)
230 PF04216 FdhE: Protein involve 20.8 50 0.0011 30.8 1.2 35 113-149 173-220 (290)
231 smart00064 FYVE Protein presen 20.8 56 0.0012 23.2 1.2 43 106-152 3-46 (68)
232 PF13913 zf-C2HC_2: zinc-finge 20.7 45 0.00097 19.2 0.6 9 66-74 3-12 (25)
233 PF01096 TFIIS_C: Transcriptio 20.4 71 0.0015 20.5 1.5 7 114-120 2-8 (39)
234 PRK12336 translation initiatio 20.3 68 0.0015 28.5 1.9 28 112-141 98-128 (201)
235 PF08646 Rep_fac-A_C: Replicat 20.3 84 0.0018 25.9 2.4 26 113-141 19-46 (146)
236 COG4640 Predicted membrane pro 20.2 54 0.0012 32.2 1.3 23 113-141 2-24 (465)
237 TIGR00595 priA primosomal prot 20.2 84 0.0018 31.9 2.8 30 51-81 227-262 (505)
238 TIGR01031 rpmF_bact ribosomal 20.1 66 0.0014 22.4 1.4 24 110-140 24-47 (55)
239 KOG3799|consensus 20.0 37 0.00079 28.4 0.1 37 125-164 77-114 (169)
No 1
>KOG1815|consensus
Probab=100.00 E-value=2.2e-58 Score=453.83 Aligned_cols=305 Identities=53% Similarity=0.930 Sum_probs=275.8
Q ss_pred cccccCCCChHHHhhhCCCHHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCCceEcCCCcccccccCCccC
Q psy15975 4 IVLIRPGVDDGTVMRLVRDPKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWH 83 (312)
Q Consensus 4 ~~~~~~~i~~~~i~~~l~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H 83 (312)
..-+.++++++.|..++++++..++|.+++.++||+.+..++|||+|+|++++.........|.|.||+.|||+|+.+||
T Consensus 118 ~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H 197 (444)
T KOG1815|consen 118 AHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESH 197 (444)
T ss_pred CCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccCCCccceeCCCCchhHhhcccccc
Confidence 34577889999999999876788999999999999999999999999999999875556789999999999999999999
Q ss_pred CCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCC-CCCCCC
Q psy15975 84 DPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSS-WYSCNR 162 (312)
Q Consensus 84 ~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~-~~~C~~ 162 (312)
.|.+|..+..|+++..+++++.+||..|+++||+|..+|||++|||||+|..+.|+++|||+|+++|..|+.. +|.|++
T Consensus 198 ~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~ 277 (444)
T KOG1815|consen 198 SPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNR 277 (444)
T ss_pred CCCcccchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccccccceeeeee
Confidence 9999999999999999999999999999999999999999999999999998889999999999999999876 899999
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-HHHH-HhcCcCHHHHHHHHHHHHHHHHHH
Q psy15975 163 YDEEEAKVARGAQERSRAALQRYLFYCNRYMNHMQSLKFEHKLYASVKEK-MEEM-QQHNMSWIEVQFLKKAVDILCQCR 240 (312)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~l~ry~~y~~r~~~h~~s~~~e~~l~~~~~~~-~~~~-~~~~~~~~d~~fl~~a~~~l~~~R 240 (312)
|+...... +++.++..+.||.|||+||++|+.+++++..+...+.+. +..+ ....++|+|++|+.+|+..|++||
T Consensus 278 ~~~~~~~~---~~~~a~~~l~r~~~~~~~~~~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r 354 (444)
T KOG1815|consen 278 YVDGKSKS---ARSKARRSLKRYTHYYNRWMEHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECR 354 (444)
T ss_pred eechhhhh---HHHHHHHHHHHHHHHHhhHHhhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhh
Confidence 99865433 467888999999999999999999999998887776532 2222 222467999999999999999999
Q ss_pred HHhhccceeeeecccCccchhHHHHHHHHHHHHHHHHHHHhh---cCCcchHHHHHHHHHHHHHHHHHHhhhhc
Q psy15975 241 QTLMYTYVFAYYLRKNNQSVLFEDNQKDLESATEKLSEYLER---DITSENLANIKQQVQDKYRLVEIQLKYSY 311 (312)
Q Consensus 241 ~~L~~sY~~~yy~~~~~~~~~fe~~Q~~le~~~e~Ls~~le~---~~~~~~~~~~k~~~~~~~~~~~~~~~~~~ 311 (312)
++|+|||+|+||+..++++++||++|.+||..+|.||..++. +.+..++.++|++|.+++++++.|+..|+
T Consensus 355 ~~l~~s~~~~~~~~~~~~~~~fe~~q~~~~~~~e~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (444)
T KOG1815|consen 355 RTLKWTYAYAYYLSENNKRNLFEDNQTDLESAVEPLSSCLEESLKDISSETLAEFKQKLTDLTSYVRNRFENLL 428 (444)
T ss_pred hhhhhhhhhhhhhcccchhhhhHHHHHHHhhhhhhhHHHhccccccCCcccHHHHHhhccccchhhhhHHHHHH
Confidence 999999999999998888899999999999999999999999 55678899999999999999999988765
No 2
>KOG1812|consensus
Probab=99.95 E-value=7.7e-29 Score=239.22 Aligned_cols=172 Identities=27% Similarity=0.692 Sum_probs=149.9
Q ss_pred ccCCCChHHHhhhCCCHHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceecccC----CCCceEcC-CCcccccccCCc
Q psy15975 7 IRPGVDDGTVMRLVRDPKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHV----EARPVVCK-CGHRFCFACGEN 81 (312)
Q Consensus 7 ~~~~i~~~~i~~~l~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~----~~~~v~C~-C~~~fC~~C~~~ 81 (312)
+...++.+....++. +++.+.|++.+.+.++.....+ +||+|+|...+..... ......|+ |+..||.+|+.+
T Consensus 198 C~~~l~~~~c~~llt-~kl~e~~e~~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~ 275 (384)
T KOG1812|consen 198 CESRLTLESCRKLLT-PKLREMWEQRLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVP 275 (384)
T ss_pred CCccCCHHHHhhhcC-HHHHHHHHHHHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCc
Confidence 566778888888886 5899999999999999998888 9999999988765542 34456788 999999999999
Q ss_pred cCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCC
Q psy15975 82 WHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCN 161 (312)
Q Consensus 82 ~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~ 161 (312)
||++.+|+++++|......++.+.++++.+|+.||+|+..||+++|||||+|+ ||++|||.|+++|..|++.++.|.
T Consensus 276 wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~Cr---C~~~fcy~C~~~~~~~~~~~~~~~ 352 (384)
T KOG1812|consen 276 WHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCR---CGHQFCYMCGGDWKTHNGECYECC 352 (384)
T ss_pred CCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceeeeecCCcceEEee---ccccchhhcCcchhhCCccccCcc
Confidence 99999999999999877788899999999999999999999999999999999 999999999999999998888888
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q psy15975 162 RYDEEEAKVARGAQERSRAALQRYLFYCNRYMNHMQSLKFE 202 (312)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~l~ry~~y~~r~~~h~~s~~~e 202 (312)
+++.+ .+++.++.+|..+..++
T Consensus 353 r~~~~-------------------~~~~~~~~~~~~~~~~~ 374 (384)
T KOG1812|consen 353 RYKES-------------------THYFEDDENHDKSIQLE 374 (384)
T ss_pred ccccc-------------------ccccccccccccccccc
Confidence 87753 56677777776665543
No 3
>KOG0006|consensus
Probab=99.89 E-value=9.4e-24 Score=192.72 Aligned_cols=140 Identities=31% Similarity=0.688 Sum_probs=111.4
Q ss_pred CCCChHHHhhhCCCHHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCCceEcC--CCcccccccCCccCCCC
Q psy15975 9 PGVDDGTVMRLVRDPKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCK--CGHRFCFACGENWHDPV 86 (312)
Q Consensus 9 ~~i~~~~i~~~l~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~--C~~~fC~~C~~~~H~p~ 86 (312)
.+|.+-..++++. .+.|.+|+++..+.+|-.... +-||.|+|+..+.++ ++...|+|+ ||..||..|.+.+|.+.
T Consensus 282 s~i~e~HHF~ilg-~e~Y~rYQr~atEe~vlq~gG-VlCP~pgCG~gll~E-PD~rkvtC~~gCgf~FCR~C~e~yh~ge 358 (446)
T KOG0006|consen 282 SLIKELHHFRILG-EEQYNRYQRYATEECVLQMGG-VLCPRPGCGAGLLPE-PDQRKVTCEGGCGFAFCRECKEAYHEGE 358 (446)
T ss_pred HHHHhhhhheecc-hhHHHHHHHhhhhhheeecCC-EecCCCCCCcccccC-CCCCcccCCCCchhHhHHHHHhhhcccc
Confidence 3455556666765 788999999999999987775 589999999998776 467899999 99999999999999873
Q ss_pred CchhhHH--------H--hh----hcccchhhhHHhhhcCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 87 RCSLLRR--------W--IK----KCDDDSETSNWIAANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 87 ~C~~~~~--------w--~~----~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
|..... + .+ ...=|..+..-|...||+||+|.+|.|+||||+||.|+.++||.++||.|+-+|..
T Consensus 359 -C~~~~~as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 359 -CSAVFEASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred -ceeeeccccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 331110 0 00 00003444555778999999999999999999999999999999999999999975
No 4
>KOG1814|consensus
Probab=99.89 E-value=1.4e-23 Score=197.63 Aligned_cols=141 Identities=28% Similarity=0.685 Sum_probs=119.2
Q ss_pred ccCCCChHHHhhhCCCHHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCC
Q psy15975 7 IRPGVDDGTVMRLVRDPKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDP 85 (312)
Q Consensus 7 ~~~~i~~~~i~~~l~~~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p 85 (312)
+....++..+.+++ +.++++||++++.++.++...++++||.+.|..++ ..+++...+.|. |...||+.|+..||..
T Consensus 237 C~~~a~~g~vKelv-g~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~-~~d~~~~l~~CskCnFaFCtlCk~t~HG~ 314 (445)
T KOG1814|consen 237 CGSVAPPGQVKELV-GDELFARYEKLMLQKTLELMSDVVYCPRACCQLPV-KQDPGRALAICSKCNFAFCTLCKLTWHGV 314 (445)
T ss_pred CcccCCchHHHHHH-HHHHHHHHHHHHHHHHHHhhcccccCChhhccCcc-ccCchhhhhhhccCccHHHHHHHHhhcCC
Confidence 44556777788887 57999999999999999999999999999999999 445678899999 9999999999999999
Q ss_pred CCchhh--------HHHhhh-------------------cccchhhhHHhhhcCCCCCCCCceeEecCCCCceeecCCCC
Q psy15975 86 VRCSLL--------RRWIKK-------------------CDDDSETSNWIAANTKECPKCLVTIEKDGGCNHMVCKNQSC 138 (312)
Q Consensus 86 ~~C~~~--------~~w~~~-------------------~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C 138 (312)
.+|.-- ..|... ...+-.+..|+..|.|+||+|+++|||++|||||+|.. |
T Consensus 315 s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~--c 392 (445)
T KOG1814|consen 315 SPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTK--C 392 (445)
T ss_pred CcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeecc--c
Confidence 899843 223210 11133466899999999999999999999999999998 9
Q ss_pred CcceecccCCCCC
Q psy15975 139 KAEFCWVCLGPWE 151 (312)
Q Consensus 139 ~~~FCw~C~~~w~ 151 (312)
++.|||+|+....
T Consensus 393 ~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 393 GTYFCWICAELLY 405 (445)
T ss_pred cccceeehhhhcC
Confidence 9999999998765
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.56 E-value=4.2e-15 Score=107.65 Aligned_cols=62 Identities=48% Similarity=1.120 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHhhCCCceecCCcCCCCceecc-cCCCCceEcC-CCcccccccCCccCCCCCc
Q psy15975 27 LKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQ-HVEARPVVCK-CGHRFCFACGENWHDPVRC 88 (312)
Q Consensus 27 ~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~-~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C 88 (312)
++|++++++++|+.+++++|||+|+|+.++... +.+...|.|+ |+..||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 489999999999999999999999999999887 4567899997 9999999999999999988
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.48 E-value=6.1e-15 Score=106.73 Aligned_cols=62 Identities=42% Similarity=1.066 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCC-ceEcC-CCcccccccCCccCCCCCc
Q psy15975 27 LKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEAR-PVVCK-CGHRFCFACGENWHDPVRC 88 (312)
Q Consensus 27 ~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~-~v~C~-C~~~fC~~C~~~~H~p~~C 88 (312)
++|++++++.||+.+++++|||+|+|+.++..++.... .|+|+ |++.||+.|+.+||.|++|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 57999999999999999999999999999988866444 39999 9999999999999999987
No 7
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.42 E-value=3e-07 Score=66.15 Aligned_cols=39 Identities=38% Similarity=1.032 Sum_probs=35.7
Q ss_pred cCCCCC--CCCceeEecC--CCCceeecCCCCCcceecccCCCCC
Q psy15975 111 NTKECP--KCLVTIEKDG--GCNHMVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 111 ~~k~CP--~C~~~IeK~~--GCnhMtC~~~~C~~~FCw~C~~~w~ 151 (312)
+.+.|| +|+..|+..+ |..+|+|.. |++.|||.|+.+|.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~--C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPK--CGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCC--CCCeECCCCCCcCC
Confidence 578899 9999999975 999999976 99999999999994
No 8
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.41 E-value=1.3e-07 Score=67.97 Aligned_cols=39 Identities=49% Similarity=1.218 Sum_probs=30.2
Q ss_pred cCCCCCC--CCceeEecCCCCc--eeecCCCCCcceecccCCCCC
Q psy15975 111 NTKECPK--CLVTIEKDGGCNH--MVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 111 ~~k~CP~--C~~~IeK~~GCnh--MtC~~~~C~~~FCw~C~~~w~ 151 (312)
+.+.||+ |...|+..+|.++ |+|.. |++.|||.|+++|.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~--C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPS--CGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTS--CCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCC--CCCcCccccCcccC
Confidence 5689988 9999999999999 99998 99999999999994
No 9
>KOG1814|consensus
Probab=96.54 E-value=0.00085 Score=64.65 Aligned_cols=48 Identities=27% Similarity=0.785 Sum_probs=41.0
Q ss_pred hcCCCCCC--CCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCCCC
Q psy15975 110 ANTKECPK--CLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCNRY 163 (312)
Q Consensus 110 ~~~k~CP~--C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~~~ 163 (312)
+++.-||+ |..|+-...|+.-..|.+ |.+.||..|...|.+ .. .|..-
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~Csk--CnFaFCtlCk~t~HG--~s--~Ck~~ 320 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSK--CNFAFCTLCKLTWHG--VS--PCKVK 320 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhcc--CccHHHHHHHHhhcC--CC--cccCc
Confidence 46799998 999997789999999998 999999999999965 22 57643
No 10
>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=93.36 E-value=0.04 Score=32.74 Aligned_cols=24 Identities=29% Similarity=0.870 Sum_probs=16.6
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
|.||.|+..|-.+ -+.|.. |||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~--CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPH--CGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCC--CCCCC
Confidence 6799999888432 245665 88776
No 11
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=93.08 E-value=0.062 Score=35.71 Aligned_cols=33 Identities=33% Similarity=0.673 Sum_probs=27.0
Q ss_pred HHhhhcCCCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 106 NWIAANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 106 ~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
.|+....+.||+|++.- |+--+.|.++.|++.|
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchhh
Confidence 46677889999999976 8888999887787654
No 12
>KOG1812|consensus
Probab=91.77 E-value=0.1 Score=51.05 Aligned_cols=50 Identities=32% Similarity=0.924 Sum_probs=38.0
Q ss_pred HHHHHHhhCCCceecCCcCCCCceecccCCCCceEcCCCcccccccCCccCCCCC
Q psy15975 33 ITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVR 87 (312)
Q Consensus 33 ~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~ 87 (312)
....++. ...+-|| .|...|....+ ...++|.||+.||+.|+++|+....
T Consensus 297 ~~~~~la--~~wr~Cp--kC~~~ie~~~G-Cnhm~CrC~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 297 ITLKYLA--KRWRQCP--KCKFMIELSEG-CNHMTCRCGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred HHHHHHH--HhcCcCc--ccceeeeecCC-cceEEeeccccchhhcCcchhhCCc
Confidence 3334444 4567899 69999877654 8899999999999999999865443
No 13
>KOG1815|consensus
Probab=91.66 E-value=0.13 Score=51.33 Aligned_cols=46 Identities=26% Similarity=0.521 Sum_probs=37.4
Q ss_pred cCCCCC--CCCceeEe-cCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCCCC
Q psy15975 111 NTKECP--KCLVTIEK-DGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCNRY 163 (312)
Q Consensus 111 ~~k~CP--~C~~~IeK-~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~~~ 163 (312)
..|-|| .|+..+.. .+.+.-+.|. |++.|||.|+.+|..-. +|+..
T Consensus 157 ~lkwCP~~~C~~av~~~~~~~~~v~C~---~g~~FC~~C~~~~H~p~----~C~~~ 205 (444)
T KOG1815|consen 157 PLKWCPAPGCGLAVKFGSLESVEVDCG---CGHEFCFACGEESHSPV----SCPGA 205 (444)
T ss_pred ccccCCCCCCCceeeccCCCccceeCC---CCchhHhhccccccCCC----cccch
Confidence 356666 69999988 8889999999 99999999999996543 67654
No 14
>PHA00626 hypothetical protein
Probab=90.54 E-value=0.22 Score=34.94 Aligned_cols=28 Identities=32% Similarity=0.638 Sum_probs=22.4
Q ss_pred CCCCCCc-eeEecCCCCc----eeecCCCCCccee
Q psy15975 114 ECPKCLV-TIEKDGGCNH----MVCKNQSCKAEFC 143 (312)
Q Consensus 114 ~CP~C~~-~IeK~~GCnh----MtC~~~~C~~~FC 143 (312)
.||+|+. .|.|++-|+. -.|.. ||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkd--CGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCD--CGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCC--CCCeec
Confidence 5999999 5889888766 77887 887773
No 15
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.43 E-value=0.17 Score=47.79 Aligned_cols=53 Identities=25% Similarity=0.599 Sum_probs=33.1
Q ss_pred ecCCcCCCCceecccCCCCceEcCCCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEec
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEKD 125 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~ 125 (312)
-|| -|..-......-...+. +|||.||.+|-... | .....+||.|+.++.++
T Consensus 5 ~CP--~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l-----------~--------------~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 5 GCP--RCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL-----------F--------------VRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCC--cCCCCCccCcccccccC-CCCCcccHHHHHHH-----------h--------------cCCCCCCCCCCCccchh
Confidence 488 48775433322223455 89999999885321 1 12235899999988665
Q ss_pred C
Q psy15975 126 G 126 (312)
Q Consensus 126 ~ 126 (312)
.
T Consensus 57 ~ 57 (309)
T TIGR00570 57 N 57 (309)
T ss_pred h
Confidence 3
No 16
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.17 E-value=0.23 Score=33.87 Aligned_cols=28 Identities=36% Similarity=0.687 Sum_probs=21.7
Q ss_pred CCCCCCCceeEecCC--CCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKDGG--CNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~~G--CnhMtC~~~~C~~~F 142 (312)
+-||.|+..+...++ -++..|+. ||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~--Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRK--CGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCc--CCCeE
Confidence 469999998877644 46899998 99753
No 17
>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=89.85 E-value=0.48 Score=29.28 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=19.7
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
+.+-||.|+.+.+...|=.-|.|.. |+++
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~--Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPS--CGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESS--SS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCC--CcCE
Confidence 4588999999999998877899987 9865
No 18
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.40 E-value=0.33 Score=31.17 Aligned_cols=28 Identities=39% Similarity=0.917 Sum_probs=22.1
Q ss_pred eecCCcCCCCceecccC----CCCceEcC-CCccc
Q psy15975 45 RWCPSPDCNNAIKVQHV----EARPVVCK-CGHRF 74 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~----~~~~v~C~-C~~~f 74 (312)
.-|| +|+....+++. ....|+|+ |++.|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 5688 69998877653 45689999 99887
No 19
>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=89.29 E-value=0.3 Score=31.04 Aligned_cols=28 Identities=32% Similarity=0.979 Sum_probs=18.6
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCcc
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGHR 73 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~ 73 (312)
+++|| .|++.+.+.......+.|. |++.
T Consensus 1 m~FCp--~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 1 MRFCP--ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp --BET--TTTSBEEEEEETTTTEEESSSS-E
T ss_pred CeeCC--CCCccceEcCCCccCcCCCCCCCc
Confidence 46899 7999998876555445787 7764
No 20
>PRK00420 hypothetical protein; Validated
Probab=87.68 E-value=7.5 Score=31.41 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=18.1
Q ss_pred cCCCCCCCCceeEe-cCCCCceeecC
Q psy15975 111 NTKECPKCLVTIEK-DGGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK-~~GCnhMtC~~ 135 (312)
-...||.|+.|..+ ++| ...|+.
T Consensus 22 l~~~CP~Cg~pLf~lk~g--~~~Cp~ 45 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG--EVVCPV 45 (112)
T ss_pred ccCCCCCCCCcceecCCC--ceECCC
Confidence 34899999999988 666 666765
No 21
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.31 E-value=0.66 Score=29.61 Aligned_cols=28 Identities=36% Similarity=0.926 Sum_probs=21.4
Q ss_pred eecCCcCCCCceecccC----CCCceEcC-CCccc
Q psy15975 45 RWCPSPDCNNAIKVQHV----EARPVVCK-CGHRF 74 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~----~~~~v~C~-C~~~f 74 (312)
.-|| +|+....+++. ....|+|+ |++.|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4688 59998877653 45689999 99876
No 22
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=86.31 E-value=0.45 Score=32.76 Aligned_cols=31 Identities=19% Similarity=0.466 Sum_probs=22.8
Q ss_pred hhhcCCCCCCCCc-eeEecCCCCceeecCCCCCcce
Q psy15975 108 IAANTKECPKCLV-TIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 108 i~~~~k~CP~C~~-~IeK~~GCnhMtC~~~~C~~~F 142 (312)
|..+.+.||+|+. .+.... +.++|.+ ||+.+
T Consensus 16 v~~~~~fCP~Cg~~~m~~~~--~r~~C~~--Cgyt~ 47 (50)
T PRK00432 16 VKRKNKFCPRCGSGFMAEHL--DRWHCGK--CGYTE 47 (50)
T ss_pred EEEccCcCcCCCcchheccC--CcEECCC--cCCEE
Confidence 3445679999998 443334 7999998 99875
No 23
>KOG2906|consensus
Probab=85.99 E-value=0.92 Score=35.56 Aligned_cols=28 Identities=32% Similarity=0.808 Sum_probs=18.1
Q ss_pred eecCCcCCCCceecccCCC-CceEcC-CCccc
Q psy15975 45 RWCPSPDCNNAIKVQHVEA-RPVVCK-CGHRF 74 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~-~~v~C~-C~~~f 74 (312)
.+|| .|++.+.+...+. ..+.|+ |+..|
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCcee
Confidence 4799 5999988876543 445555 54443
No 24
>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=85.64 E-value=0.87 Score=27.42 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=14.8
Q ss_pred CCCCCCceeEecCCCCceeecCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQ 136 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~ 136 (312)
.||.|+..+.+.+|=-...|.++
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--C
T ss_pred CcCCCCCEeEcCCCCEeEECCCC
Confidence 49999999999999888888864
No 25
>KOG0317|consensus
Probab=85.63 E-value=0.11 Score=48.15 Aligned_cols=42 Identities=26% Similarity=0.745 Sum_probs=29.7
Q ss_pred hcCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCCC
Q psy15975 110 ANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCNR 162 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~~ 162 (312)
.++.+|-=|-...+ |-+|.. |||-|||-|...|-.... .|+.
T Consensus 237 ~a~~kC~LCLe~~~------~pSaTp--CGHiFCWsCI~~w~~ek~---eCPl 278 (293)
T KOG0317|consen 237 EATRKCSLCLENRS------NPSATP--CGHIFCWSCILEWCSEKA---ECPL 278 (293)
T ss_pred CCCCceEEEecCCC------CCCcCc--CcchHHHHHHHHHHcccc---CCCc
Confidence 45666666655542 456776 999999999999976553 4663
No 26
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.52 E-value=0.54 Score=49.05 Aligned_cols=11 Identities=18% Similarity=0.359 Sum_probs=7.6
Q ss_pred CcceecccCCC
Q psy15975 139 KAEFCWVCLGP 149 (312)
Q Consensus 139 ~~~FCw~C~~~ 149 (312)
+..||-.||.+
T Consensus 40 ~~~fC~~CG~~ 50 (645)
T PRK14559 40 DEAHCPNCGAE 50 (645)
T ss_pred ccccccccCCc
Confidence 34588888776
No 27
>KOG0823|consensus
Probab=85.15 E-value=0.63 Score=42.04 Aligned_cols=36 Identities=42% Similarity=1.030 Sum_probs=23.0
Q ss_pred eEcCCCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 66 VVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 66 v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
|.=.|||.|||-|.-. |+. +..+.+.||-|+..|-.
T Consensus 61 VvTlCGHLFCWpClyq------------Wl~-----------~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 61 VVTLCGHLFCWPCLYQ------------WLQ-----------TRPNSKECPVCKAEVSI 96 (230)
T ss_pred EEeecccceehHHHHH------------HHh-----------hcCCCeeCCcccccccc
Confidence 3334999999988532 321 12367889999877643
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.77 E-value=0.97 Score=30.26 Aligned_cols=30 Identities=20% Similarity=0.457 Sum_probs=22.6
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceec
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCW 144 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw 144 (312)
-.||+|+..++.+.+=..++|+. ||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~--CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPY--CGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCC--CCCeEEE
Confidence 36999999888876655789987 8876543
No 29
>KOG0823|consensus
Probab=84.08 E-value=0.32 Score=43.88 Aligned_cols=24 Identities=33% Similarity=0.910 Sum_probs=17.9
Q ss_pred CCcceecccCCCCCCCCCCCCCCC
Q psy15975 138 CKAEFCWVCLGPWEPHGSSWYSCN 161 (312)
Q Consensus 138 C~~~FCw~C~~~w~~h~~~~~~C~ 161 (312)
|||-|||-|+-.|-.....--.|+
T Consensus 65 CGHLFCWpClyqWl~~~~~~~~cP 88 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQTRPNSKECP 88 (230)
T ss_pred cccceehHHHHHHHhhcCCCeeCC
Confidence 999999999999976543323344
No 30
>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=83.69 E-value=1.2 Score=28.34 Aligned_cols=28 Identities=18% Similarity=0.582 Sum_probs=19.2
Q ss_pred CCCCCCCceeEecC-----CCCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKDG-----GCNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~~-----GCnhMtC~~~~C~~~F 142 (312)
-.||+|+..+.-.. +=..+.|++ ||+.|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~--C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGK--CGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCC--CCCEE
Confidence 36999998766541 113789988 88765
No 31
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=82.79 E-value=0.39 Score=31.68 Aligned_cols=24 Identities=33% Similarity=0.684 Sum_probs=15.5
Q ss_pred CCcceecccCCCCCCCCCC-CCCCC
Q psy15975 138 CKAEFCWVCLGPWEPHGSS-WYSCN 161 (312)
Q Consensus 138 C~~~FCw~C~~~w~~h~~~-~~~C~ 161 (312)
|||.||..|+..|...... .+.|+
T Consensus 16 CGH~FC~~Cl~~~~~~~~~~~~~CP 40 (42)
T PF15227_consen 16 CGHSFCRSCLERLWKEPSGSGFSCP 40 (42)
T ss_dssp SSSEEEHHHHHHHHCCSSSST---S
T ss_pred CcCHHHHHHHHHHHHccCCcCCCCc
Confidence 9999999999986554332 25565
No 32
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=82.65 E-value=0.41 Score=33.15 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=14.0
Q ss_pred CCceEcC-CCcccccccCCccCCCC
Q psy15975 63 ARPVVCK-CGHRFCFACGENWHDPV 86 (312)
Q Consensus 63 ~~~v~C~-C~~~fC~~C~~~~H~p~ 86 (312)
.....|+ |+..||+.|..-.|+.+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 3578999 99999998877666553
No 33
>KOG0317|consensus
Probab=81.66 E-value=0.29 Score=45.58 Aligned_cols=18 Identities=39% Similarity=1.130 Sum_probs=13.7
Q ss_pred ceEcC-CCcccccccCCcc
Q psy15975 65 PVVCK-CGHRFCFACGENW 82 (312)
Q Consensus 65 ~v~C~-C~~~fC~~C~~~~ 82 (312)
.-+|. |||.|||.|-.+|
T Consensus 251 ~pSaTpCGHiFCWsCI~~w 269 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEW 269 (293)
T ss_pred CCCcCcCcchHHHHHHHHH
Confidence 34566 9999999996654
No 34
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=81.46 E-value=0.31 Score=43.01 Aligned_cols=32 Identities=31% Similarity=0.950 Sum_probs=23.9
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~ 151 (312)
.-.||-|.-.+. +.+. .. |||.|||.|...|-
T Consensus 18 ~~~CpICld~~~-----dPVv-T~--CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVR-----DPVV-TL--CGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCC-----CcEE-cC--CCchhHHHHHHHHH
Confidence 458999987663 1233 34 99999999999994
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.17 E-value=1.6 Score=29.22 Aligned_cols=29 Identities=28% Similarity=0.716 Sum_probs=21.2
Q ss_pred eecCCcCCCCceecccCCCCceEcC-CCccccc
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCF 76 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~ 76 (312)
..|| +|+..+..+.... .++|| ||..+=.
T Consensus 4 y~C~--~CG~~~~~~~~~~-~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCA--RCGREVELDEYGT-GVRCPYCGYRILF 33 (46)
T ss_pred EECC--CCCCEEEECCCCC-ceECCCCCCeEEE
Confidence 3588 6999888775433 79999 9986643
No 36
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=81.12 E-value=0.19 Score=34.12 Aligned_cols=34 Identities=41% Similarity=0.863 Sum_probs=23.4
Q ss_pred ceEcCCCcc-cccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 65 PVVCKCGHR-FCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 65 ~v~C~C~~~-fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
.+.=||||. ||..|...+. . +.+.||-|+.+|++
T Consensus 15 ~~~~pCgH~~~C~~C~~~~~-------------------------~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 15 VVLLPCGHLCFCEECAERLL-------------------------K-RKKKCPICRQPIES 49 (50)
T ss_dssp EEEETTCEEEEEHHHHHHHH-------------------------H-TTSBBTTTTBB-SE
T ss_pred eEEeCCCChHHHHHHhHHhc-------------------------c-cCCCCCcCChhhcC
Confidence 344469999 9998853321 1 45899999999975
No 37
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=81.08 E-value=0.19 Score=32.45 Aligned_cols=24 Identities=33% Similarity=0.821 Sum_probs=17.2
Q ss_pred CCCcceecccCCCCCCCCCCCCCCC
Q psy15975 137 SCKAEFCWVCLGPWEPHGSSWYSCN 161 (312)
Q Consensus 137 ~C~~~FCw~C~~~w~~h~~~~~~C~ 161 (312)
+|||.||..|+..|-.. .....|+
T Consensus 16 ~C~H~fC~~C~~~~~~~-~~~~~CP 39 (41)
T PF00097_consen 16 PCGHSFCRDCLRKWLEN-SGSVKCP 39 (41)
T ss_dssp TTSEEEEHHHHHHHHHH-TSSSBTT
T ss_pred cCCCcchHHHHHHHHHh-cCCccCC
Confidence 39999999999988653 2234565
No 38
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=80.88 E-value=1.3 Score=30.03 Aligned_cols=26 Identities=35% Similarity=0.957 Sum_probs=18.0
Q ss_pred ecCCcCCCCceecccCCC-CceEcC-CCcc
Q psy15975 46 WCPSPDCNNAIKVQHVEA-RPVVCK-CGHR 73 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~-~~v~C~-C~~~ 73 (312)
+|| .|+..+.+..... ....|+ ||+.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 788 6999887764433 367788 7753
No 39
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=80.45 E-value=1.2 Score=46.46 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=6.0
Q ss_pred eecCCcCCCCce
Q psy15975 45 RWCPSPDCNNAI 56 (312)
Q Consensus 45 ~~CP~~~C~~~i 56 (312)
+.|| .|+..+
T Consensus 2 ~~Cp--~Cg~~n 11 (645)
T PRK14559 2 LICP--QCQFEN 11 (645)
T ss_pred CcCC--CCCCcC
Confidence 3566 477664
No 40
>KOG2906|consensus
Probab=80.26 E-value=1.4 Score=34.59 Aligned_cols=28 Identities=29% Similarity=0.709 Sum_probs=21.2
Q ss_pred CCCCCCceeEe--cCCCCceeecCCCCCccee
Q psy15975 114 ECPKCLVTIEK--DGGCNHMVCKNQSCKAEFC 143 (312)
Q Consensus 114 ~CP~C~~~IeK--~~GCnhMtC~~~~C~~~FC 143 (312)
-||.|+..+.- .+.||...|.. |.|.|=
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~t--CpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRT--CPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCC--CCceee
Confidence 59999876444 44599999998 987663
No 41
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=80.23 E-value=0.33 Score=31.21 Aligned_cols=22 Identities=23% Similarity=0.611 Sum_probs=17.0
Q ss_pred ceeecCCCCCcceecccCCCCCCC
Q psy15975 130 HMVCKNQSCKAEFCWVCLGPWEPH 153 (312)
Q Consensus 130 hMtC~~~~C~~~FCw~C~~~w~~h 153 (312)
.+.-.. |||.||+.|...|...
T Consensus 11 ~~~~~~--CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 11 PVVVTP--CGHSFCKECIEKYLEK 32 (39)
T ss_dssp EEEECT--TSEEEEHHHHHHHHHC
T ss_pred cCEECC--CCCchhHHHHHHHHHC
Confidence 334555 9999999999988654
No 42
>KOG0978|consensus
Probab=80.21 E-value=0.5 Score=49.28 Aligned_cols=47 Identities=32% Similarity=0.775 Sum_probs=29.9
Q ss_pred CCceecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCc
Q psy15975 42 RLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLV 120 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~ 120 (312)
+.+..||. |. -.+. .+.=+ |||.||..|-.+ .+....+.||+|+.
T Consensus 641 K~~LkCs~--Cn--~R~K-----d~vI~kC~H~FC~~Cvq~-------------------------r~etRqRKCP~Cn~ 686 (698)
T KOG0978|consen 641 KELLKCSV--CN--TRWK-----DAVITKCGHVFCEECVQT-------------------------RYETRQRKCPKCNA 686 (698)
T ss_pred HhceeCCC--cc--Cchh-----hHHHHhcchHHHHHHHHH-------------------------HHHHhcCCCCCCCC
Confidence 45667884 65 2221 22223 999999988543 22244589999998
Q ss_pred ee
Q psy15975 121 TI 122 (312)
Q Consensus 121 ~I 122 (312)
+.
T Consensus 687 aF 688 (698)
T KOG0978|consen 687 AF 688 (698)
T ss_pred CC
Confidence 76
No 43
>PRK04023 DNA polymerase II large subunit; Validated
Probab=79.15 E-value=1.4 Score=47.58 Aligned_cols=33 Identities=30% Similarity=0.591 Sum_probs=22.1
Q ss_pred CCceecCCcCCCCceecccCCCCceEcC-CCc-----ccccccCCccC
Q psy15975 42 RLLRWCPSPDCNNAIKVQHVEARPVVCK-CGH-----RFCFACGENWH 83 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~-----~fC~~C~~~~H 83 (312)
...+.|| .|+... ....|| ||. .||..|+....
T Consensus 624 Vg~RfCp--sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 624 IGRRKCP--SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred ccCccCC--CCCCcC-------CcccCCCCCCCCCcceeCccccCcCC
Confidence 3556888 588763 346888 885 47888865533
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=79.05 E-value=1.7 Score=26.63 Aligned_cols=27 Identities=30% Similarity=0.741 Sum_probs=14.2
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
-+||.|+....-.+|. .|.|.. |++++
T Consensus 3 p~Cp~C~se~~y~D~~-~~vCp~--C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-LLVCPE--CGHEW 29 (30)
T ss_dssp ---TTT-----EE-SS-SEEETT--TTEEE
T ss_pred CCCCCCCCcceeccCC-EEeCCc--ccccC
Confidence 3799999998887775 467987 98875
No 45
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.80 E-value=2 Score=27.44 Aligned_cols=28 Identities=25% Similarity=0.695 Sum_probs=20.5
Q ss_pred CCCCCCCceeEec-----CCCCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKD-----GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~-----~GCnhMtC~~~~C~~~F 142 (312)
-.||+|++...-. .+=-.+.|++ |++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~--C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPK--CGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCC--CCcEe
Confidence 3799999887653 2234899998 99876
No 46
>PF14369 zf-RING_3: zinc-finger
Probab=78.25 E-value=2.2 Score=27.07 Aligned_cols=28 Identities=29% Similarity=0.845 Sum_probs=20.4
Q ss_pred eecCCcCCCCceecccCCCCceEcC-CCccc
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCK-CGHRF 74 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~f 74 (312)
-||- .|...|.........+.|| |+..|
T Consensus 3 ywCh--~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH--QCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCc--cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 5898 6999998764444456799 88765
No 47
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=78.00 E-value=5 Score=33.14 Aligned_cols=113 Identities=21% Similarity=0.406 Sum_probs=54.9
Q ss_pred ccCCCChHHHhhhCC---CHHHHHHHHHHHHHHHHh-hCCCceecCCcCCCCceecccCCCCceEcCCCcccccccCCcc
Q psy15975 7 IRPGVDDGTVMRLVR---DPKVKLKYQHLITNSFVE-CNRLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENW 82 (312)
Q Consensus 7 ~~~~i~~~~i~~~l~---~~e~~~~y~~~~~~~~v~-~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~ 82 (312)
+.--++=...+++++ |.+-+.+|...+... |+ +++-+ =|- =...+..+++....++|.||+.||-- ...|
T Consensus 13 v~gtl~w~qt~r~msa~kdhdrf~kylavlqdr-v~~~dpil--lpv--g~hlfi~qs~~~rv~rcecghsf~d~-r~nw 86 (165)
T COG4647 13 VEGTLPWPQTRRMMSAYKDHDRFFKYLAVLQDR-VDWDDPIL--LPV--GDHLFICQSAQKRVIRCECGHSFGDY-RENW 86 (165)
T ss_pred hcCCCCcHHHHHHHhccccHHHHHHHHHHHHhh-cccCCCee--eec--CCcEEEEecccccEEEEeccccccCh-hhCc
Confidence 333444444555554 444444554444332 22 22211 232 22344444455668999999999942 2223
Q ss_pred --CCCCCchhhHH-Hhhh-cccchhhhHHhhhcCCCCCCCCceeEec
Q psy15975 83 --HDPVRCSLLRR-WIKK-CDDDSETSNWIAANTKECPKCLVTIEKD 125 (312)
Q Consensus 83 --H~p~~C~~~~~-w~~~-~~~~~~~~~~i~~~~k~CP~C~~~IeK~ 125 (312)
|....=..-.+ ..+. -..+....+|+...--.||.|+...+-.
T Consensus 87 kl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~eve 133 (165)
T COG4647 87 KLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHEVE 133 (165)
T ss_pred eeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceeeec
Confidence 32221111000 0010 1123345678777777999999987654
No 48
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=77.11 E-value=0.62 Score=29.66 Aligned_cols=32 Identities=31% Similarity=0.808 Sum_probs=21.9
Q ss_pred CCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCC
Q psy15975 115 CPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPH 153 (312)
Q Consensus 115 CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h 153 (312)
||-|...+ -+-+.-.. |||.||+.|+..|...
T Consensus 2 C~iC~~~~-----~~~~~~~~--C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 2 CPICLEEF-----REPVVLLP--CGHVFCRSCIDKWLKS 33 (45)
T ss_pred CCcCchhh-----hCceEecC--CCChhcHHHHHHHHHh
Confidence 66676665 12233343 9999999999988654
No 49
>KOG0320|consensus
Probab=76.84 E-value=1.1 Score=39.10 Aligned_cols=31 Identities=42% Similarity=0.946 Sum_probs=21.7
Q ss_pred cCCCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 68 CKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 68 C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
=.|||.||..|-.. ...++.+||-|+..|-+
T Consensus 149 TkCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccchhHHHHHHHH--------------------------HHHhCCCCCCcccccch
Confidence 34899999988532 12466899999976643
No 50
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.60 E-value=2.2 Score=34.43 Aligned_cols=66 Identities=24% Similarity=0.567 Sum_probs=40.3
Q ss_pred hCCCHHHHHHHHHHHH-HHHHhh----CCCceecCCcCCCCceeccc-------CCCCceEcC-CCcccccccCCccCCC
Q psy15975 19 LVRDPKVKLKYQHLIT-NSFVEC----NRLLRWCPSPDCNNAIKVQH-------VEARPVVCK-CGHRFCFACGENWHDP 85 (312)
Q Consensus 19 ~l~~~e~~~~y~~~~~-~~~v~~----~~~~~~CP~~~C~~~i~~~~-------~~~~~v~C~-C~~~fC~~C~~~~H~p 85 (312)
|++++.+...|..++- ..|.+. ...-..|- +|...+.... .......|+ |+..||..|..-+|+.
T Consensus 25 LVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 25 LILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred EeccchHHHhhhccCCCcccccccccccCCCCccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 5566777777777543 334322 11223566 5877654321 123457899 9999999998877754
Q ss_pred C
Q psy15975 86 V 86 (312)
Q Consensus 86 ~ 86 (312)
+
T Consensus 103 L 103 (112)
T TIGR00622 103 L 103 (112)
T ss_pred c
Confidence 3
No 51
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.28 E-value=1 Score=25.85 Aligned_cols=10 Identities=50% Similarity=1.169 Sum_probs=6.9
Q ss_pred CCCCCceeEe
Q psy15975 115 CPKCLVTIEK 124 (312)
Q Consensus 115 CP~C~~~IeK 124 (312)
||+|+..|+.
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 7777777753
No 52
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.20 E-value=2.4 Score=47.00 Aligned_cols=9 Identities=44% Similarity=1.298 Sum_probs=5.3
Q ss_pred eecCCcCCCCc
Q psy15975 45 RWCPSPDCNNA 55 (312)
Q Consensus 45 ~~CP~~~C~~~ 55 (312)
..|| .|+..
T Consensus 668 rkCP--kCG~~ 676 (1337)
T PRK14714 668 RRCP--SCGTE 676 (1337)
T ss_pred EECC--CCCCc
Confidence 5666 46654
No 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.09 E-value=1.2 Score=26.12 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=8.0
Q ss_pred CCCCCCCCceeE
Q psy15975 112 TKECPKCLVTIE 123 (312)
Q Consensus 112 ~k~CP~C~~~Ie 123 (312)
.+.||+|+..|.
T Consensus 2 ~~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 2 EMFCPNCGAEID 13 (26)
T ss_pred cCCCcccCCcCC
Confidence 356777777663
No 54
>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=75.88 E-value=2.1 Score=30.88 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=22.9
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
.++.||.|+....++..=..++|.. ||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~--Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPN--CGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCC--CCCE
Confidence 5789999999999955555788887 7743
No 55
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=75.53 E-value=1.7 Score=46.28 Aligned_cols=27 Identities=37% Similarity=1.018 Sum_probs=24.1
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCccee
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFC 143 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FC 143 (312)
..||.|+..+...+||. +|.. ||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~--CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHS--CGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCC--CCCCCC
Confidence 36999999999999998 9998 998766
No 56
>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=74.67 E-value=1.8 Score=34.76 Aligned_cols=27 Identities=30% Similarity=0.784 Sum_probs=18.7
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
+.||+|++..-=-.- +.++|+. ||..|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~--CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPK--CGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCC--CCCcc
Confidence 689999876543222 8899997 77443
No 57
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=74.59 E-value=4.1 Score=26.39 Aligned_cols=27 Identities=33% Similarity=0.759 Sum_probs=18.1
Q ss_pred CCCCCCCceeEe---cCCCCceeecC-CCCCc
Q psy15975 113 KECPKCLVTIEK---DGGCNHMVCKN-QSCKA 140 (312)
Q Consensus 113 k~CP~C~~~IeK---~~GCnhMtC~~-~~C~~ 140 (312)
+.||.|+.++.. ..| ..+.|++ |.|++
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs~yP~C~~ 32 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCSNYPECKY 32 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECCCCCCcCC
Confidence 589999876655 345 6777876 45554
No 58
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.78 E-value=2.2 Score=35.31 Aligned_cols=25 Identities=32% Similarity=0.820 Sum_probs=18.6
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
.+.||.|++|..+-.| -+.|+. |++
T Consensus 28 ~~hCp~Cg~PLF~KdG--~v~CPv--C~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDG--EVFCPV--CGY 52 (131)
T ss_pred HhhCcccCCcceeeCC--eEECCC--CCc
Confidence 4799999999988665 566665 553
No 59
>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=73.52 E-value=3.5 Score=27.18 Aligned_cols=24 Identities=25% Similarity=0.863 Sum_probs=19.0
Q ss_pred CCCCCCCCceeEe-cCCCCceeecCCCCC
Q psy15975 112 TKECPKCLVTIEK-DGGCNHMVCKNQSCK 139 (312)
Q Consensus 112 ~k~CP~C~~~IeK-~~GCnhMtC~~~~C~ 139 (312)
...||.|+.|.-+ .+| .+.|.. |+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~--C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVS--CG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCC--CC
Confidence 4699999999998 555 678876 64
No 60
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=73.37 E-value=3.1 Score=26.27 Aligned_cols=26 Identities=31% Similarity=0.731 Sum_probs=14.6
Q ss_pred CCCCCCCceeEec----CCCCceeecCCCCCc
Q psy15975 113 KECPKCLVTIEKD----GGCNHMVCKNQSCKA 140 (312)
Q Consensus 113 k~CP~C~~~IeK~----~GCnhMtC~~~~C~~ 140 (312)
|-||.|+.+++.. ++=..+.|.. ||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~--Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPA--CGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETT--TTE
T ss_pred CccccccChhhhhcCCCCCccceECCC--CCC
Confidence 4699999999884 4455588987 884
No 61
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=73.16 E-value=2 Score=31.23 Aligned_cols=23 Identities=30% Similarity=1.003 Sum_probs=8.9
Q ss_pred CCCCCCCceeEec---CCCCceeecC
Q psy15975 113 KECPKCLVTIEKD---GGCNHMVCKN 135 (312)
Q Consensus 113 k~CP~C~~~IeK~---~GCnhMtC~~ 135 (312)
-.|++|....... +||.|+.|+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHH
Confidence 5899998776442 5555555544
No 62
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=72.81 E-value=2.4 Score=31.90 Aligned_cols=58 Identities=21% Similarity=0.580 Sum_probs=21.6
Q ss_pred ecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
-|- -|+.-|.....+...|-|. |+.-.|..| -++.+ ....+-||.|+++..+
T Consensus 11 iCq--iCGD~VGl~~~Ge~FVAC~eC~fPvCr~C----------yEYEr---------------keg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 11 ICQ--ICGDDVGLTENGEVFVACHECAFPVCRPC----------YEYER---------------KEGNQVCPQCKTRYKR 63 (80)
T ss_dssp B-S--SS--B--B-SSSSB--S-SSS-----HHH----------HHHHH---------------HTS-SB-TTT--B---
T ss_pred ccc--cccCccccCCCCCEEEEEcccCCccchhH----------HHHHh---------------hcCcccccccCCCccc
Confidence 354 4888777766667888899 988888744 33321 2456899999999988
Q ss_pred cCCCCc
Q psy15975 125 DGGCNH 130 (312)
Q Consensus 125 ~~GCnh 130 (312)
..|+..
T Consensus 64 ~kgsp~ 69 (80)
T PF14569_consen 64 HKGSPR 69 (80)
T ss_dssp -TT---
T ss_pred ccCCCC
Confidence 877654
No 63
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=72.68 E-value=3.2 Score=30.67 Aligned_cols=45 Identities=40% Similarity=0.863 Sum_probs=28.3
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCc-----ceecccCCCCCC---CCCCCCCCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKA-----EFCWVCLGPWEP---HGSSWYSCNR 162 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~-----~FCw~C~~~w~~---h~~~~~~C~~ 162 (312)
.||.|+.+++.++ .+..|.. |+. -+|-.|+.+... .|.--|.|+.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~--C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~ 55 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEA--CQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNH 55 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETT--T--EEEEEEE-TTT-SB-EEEEETTEEEEE-TT
T ss_pred cCCCCCCccEEeC--CEEECcc--ccccceecccCCCcccHHHHHHHhcccceeecc
Confidence 6999999999999 6899998 985 469999998653 4443466664
No 64
>PHA02929 N1R/p28-like protein; Provisional
Probab=72.43 E-value=1.5 Score=40.14 Aligned_cols=45 Identities=24% Similarity=0.698 Sum_probs=31.6
Q ss_pred cCCCCCCCCceeEecCCCCc---eeecCCCCCcceecccCCCCCCCCCCCCCCC
Q psy15975 111 NTKECPKCLVTIEKDGGCNH---MVCKNQSCKAEFCWVCLGPWEPHGSSWYSCN 161 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnh---MtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~ 161 (312)
....||=|...+...+.-+. +.- +|+|.||..|...|..... .|+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~---~C~H~FC~~CI~~Wl~~~~---tCP 220 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILS---NCNHVFCIECIDIWKKEKN---TCP 220 (238)
T ss_pred CCCCCccCCcccccCccccccceecC---CCCCcccHHHHHHHHhcCC---CCC
Confidence 35789999998765543221 222 3999999999999976432 576
No 65
>PF12773 DZR: Double zinc ribbon
Probab=72.18 E-value=1.9 Score=29.15 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=4.5
Q ss_pred CCCCCCCcee
Q psy15975 113 KECPKCLVTI 122 (312)
Q Consensus 113 k~CP~C~~~I 122 (312)
+.||+|+..+
T Consensus 30 ~~C~~Cg~~~ 39 (50)
T PF12773_consen 30 KICPNCGAEN 39 (50)
T ss_pred CCCcCCcCCC
Confidence 3444444443
No 66
>PLN03086 PRLI-interacting factor K; Provisional
Probab=71.69 E-value=5 Score=41.22 Aligned_cols=32 Identities=25% Similarity=0.533 Sum_probs=20.3
Q ss_pred CCCceecCCcCCCCceecccC-------CCCceEcC---CCccc
Q psy15975 41 NRLLRWCPSPDCNNAIKVQHV-------EARPVVCK---CGHRF 74 (312)
Q Consensus 41 ~~~~~~CP~~~C~~~i~~~~~-------~~~~v~C~---C~~~f 74 (312)
..+.+.||+ |...|..... ....|.|+ ||..|
T Consensus 404 ~~~~V~C~N--C~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~ 445 (567)
T PLN03086 404 DVDTVECRN--CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVL 445 (567)
T ss_pred CCCeEECCC--CCCccchhHHHHHHhhCCCcceeCCccccccee
Confidence 456778886 8888765543 23456776 66555
No 67
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=70.97 E-value=0.7 Score=30.38 Aligned_cols=40 Identities=33% Similarity=0.718 Sum_probs=25.4
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCN 161 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~ 161 (312)
.||-|...++. +=.-+... |||.||+.|+..|-... ..|+
T Consensus 2 ~C~IC~~~~~~--~~~~~~l~---C~H~fh~~Ci~~~~~~~---~~CP 41 (44)
T PF13639_consen 2 ECPICLEEFED--GEKVVKLP---CGHVFHRSCIKEWLKRN---NSCP 41 (44)
T ss_dssp CETTTTCBHHT--TSCEEEET---TSEEEEHHHHHHHHHHS---SB-T
T ss_pred CCcCCChhhcC--CCeEEEcc---CCCeeCHHHHHHHHHhC---CcCC
Confidence 36666666644 22233344 99999999999997653 2565
No 68
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=70.63 E-value=2.6 Score=37.24 Aligned_cols=59 Identities=25% Similarity=0.743 Sum_probs=31.8
Q ss_pred ecCCcCCCCceecccCCCCceEcCCCcccccccCCccCCCCCchhhHHHhhhcccchh-hhHHh-hhcCCCCCCCCceeE
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSE-TSNWI-AANTKECPKCLVTIE 123 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~-~~~~i-~~~~k~CP~C~~~Ie 123 (312)
-|| =|...+. . .|.-+|||.||+.|-..|.. ....... ...+- ..+...||-|+.+|.
T Consensus 20 ~Cp--ICld~~~-----d-PVvT~CGH~FC~~CI~~wl~------------~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 20 DCN--ICLDQVR-----D-PVVTLCGHLFCWPCIHKWTY------------ASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred CCc--cCCCcCC-----C-cEEcCCCchhHHHHHHHHHH------------hccccccccccccccCCCCcCCCCCCcCC
Confidence 577 3665431 1 24446999999999765521 1000000 00000 134568999999985
Q ss_pred e
Q psy15975 124 K 124 (312)
Q Consensus 124 K 124 (312)
.
T Consensus 80 ~ 80 (193)
T PLN03208 80 E 80 (193)
T ss_pred h
Confidence 4
No 69
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=69.02 E-value=5.7 Score=42.14 Aligned_cols=39 Identities=21% Similarity=0.509 Sum_probs=31.9
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcc-----eecccCCC-CCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAE-----FCWVCLGP-WEPH 153 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~-----FCw~C~~~-w~~h 153 (312)
-.||+|..+..-..+=|.|.|-- ||++ .|-.|+.. +..-
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~--Cg~~~~~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHY--CGYQEPIPQSCPECGSEHLRAV 489 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCC--CCCCCCCCCCCCCCCCCeeEEe
Confidence 48999999888877779999998 9977 89999887 4433
No 70
>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=68.42 E-value=4.2 Score=28.04 Aligned_cols=27 Identities=30% Similarity=0.508 Sum_probs=16.7
Q ss_pred CCCCCCCceeE------ecCCCCce-eecCCCCCcc
Q psy15975 113 KECPKCLVTIE------KDGGCNHM-VCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~Ie------K~~GCnhM-tC~~~~C~~~ 141 (312)
|+||.|+..-+ .+.+..++ .|.. ||..
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~--Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECST--CGAS 35 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCC--CCCC
Confidence 79999977655 12344444 3665 6654
No 71
>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=68.19 E-value=6.1 Score=33.76 Aligned_cols=32 Identities=19% Similarity=0.450 Sum_probs=22.9
Q ss_pred hCCCceecCCcCCCCceecccCCCCceEcC-CCcc
Q psy15975 40 CNRLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHR 73 (312)
Q Consensus 40 ~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~ 73 (312)
.++.+-.|| .|+.-+.+.+.-...++|| ||..
T Consensus 105 ~~~~~Y~Cp--~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICP--NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECC--CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 456777898 5887777665545678888 8765
No 72
>KOG4367|consensus
Probab=67.95 E-value=8.4 Score=38.11 Aligned_cols=79 Identities=24% Similarity=0.543 Sum_probs=44.8
Q ss_pred CCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEecCCCCc-eeecCCCCCc
Q psy15975 63 ARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEKDGGCNH-MVCKNQSCKA 140 (312)
Q Consensus 63 ~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCnh-MtC~~~~C~~ 140 (312)
...|-|. |...+|--|+..-|+|- =+.++.-+.- ..+...... ...+.--.|. --+|=|| |.|.. |+-
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~r-gplakh~l~~-~~~grvs~~--~s~r~~~~ct----~h~~e~~smyc~~--ck~ 243 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPR-GPLAKHRLVP-PAQGRVSRR--LSPRKVSTCT----DHELENHSMYCVQ--CKM 243 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCC-CchhhcccCC-cccCceeec--cchhhhhhcc----CCCCCCceEEEEe--cCC
Confidence 3468899 99999999998888763 1111211100 001110000 0111111221 2345566 99998 999
Q ss_pred ceecccCCCCC
Q psy15975 141 EFCWVCLGPWE 151 (312)
Q Consensus 141 ~FCw~C~~~w~ 151 (312)
--|+.|+++-+
T Consensus 244 pvc~~clee~k 254 (699)
T KOG4367|consen 244 PVCYQCLEEGK 254 (699)
T ss_pred hHHHHHHHhhc
Confidence 99999999854
No 73
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=67.50 E-value=2.2 Score=27.83 Aligned_cols=31 Identities=26% Similarity=0.621 Sum_probs=18.7
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
.||+|+...+.... .. =...-|-.|+|.|-+
T Consensus 1 ~CP~C~~~l~~~~~-~~-------~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GD-------VEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE-CC-------EEEEECCCCCeEEcc
Confidence 59999998776544 11 223334456677743
No 74
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=66.29 E-value=1.4 Score=26.87 Aligned_cols=15 Identities=33% Similarity=1.086 Sum_probs=13.7
Q ss_pred CCcceecccCCCCCC
Q psy15975 138 CKAEFCWVCLGPWEP 152 (312)
Q Consensus 138 C~~~FCw~C~~~w~~ 152 (312)
|+|.||+.|+..|-.
T Consensus 16 C~H~~c~~C~~~~~~ 30 (39)
T smart00184 16 CGHTFCRSCIRKWLK 30 (39)
T ss_pred CCChHHHHHHHHHHH
Confidence 999999999999865
No 75
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=66.01 E-value=2.3 Score=32.59 Aligned_cols=44 Identities=27% Similarity=0.565 Sum_probs=33.0
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCNR 162 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~~ 162 (312)
..||.|+.| .+.|.-+.+. |++.|=..|...|-...++...|+.
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~---C~H~FH~hCI~kWl~~~~~~~~CPm 76 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK---CSHNFHMHCILKWLSTQSSKGQCPM 76 (85)
T ss_pred cCCCCccCC---CCCCceeecc---CccHHHHHHHHHHHccccCCCCCCC
Confidence 467888877 4668777777 9999999999999775433346774
No 76
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=65.11 E-value=3.3 Score=27.22 Aligned_cols=33 Identities=24% Similarity=0.612 Sum_probs=22.6
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcceecccCCCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~ 151 (312)
.||.|...+..+.. ..+ . +|||-||..|+..+.
T Consensus 1 ~C~~C~~~~~~~~~-~~l--~--~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYSEERR-PRL--T--SCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCccccCCCC-eEE--c--ccCCHHHHHHHHhhc
Confidence 47888888832222 111 2 399999999999887
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=64.30 E-value=8.1 Score=33.71 Aligned_cols=59 Identities=15% Similarity=0.397 Sum_probs=31.8
Q ss_pred CChHHHhhhCCCHHHHHHHHHHHHHHHH-hhCCCceecCCcCCCCceecccCCCCceEcC-CCcc
Q psy15975 11 VDDGTVMRLVRDPKVKLKYQHLITNSFV-ECNRLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHR 73 (312)
Q Consensus 11 i~~~~i~~~l~~~e~~~~y~~~~~~~~v-~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~ 73 (312)
++.+.+...+. .++ .+-.+.+.+..- +.++.+-.||. |+.-+.+.+.-...+.|| ||..
T Consensus 85 l~~~~i~d~ik-~~~-~~~~~klk~~l~~e~~~~~Y~Cp~--C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 85 PELEKLPEIIK-KKK-MEELKKLKEQLEEEENNMFFFCPN--CHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred eCHHHHHHHHH-HHH-HHHHHHHHHHhhhccCCCEEECCC--CCcEEeHHHHhhcCCcCCCCCCC
Confidence 34455555553 222 222233333322 34556778984 998777765544567777 6654
No 78
>PHA02926 zinc finger-like protein; Provisional
Probab=64.28 E-value=1.5 Score=39.68 Aligned_cols=73 Identities=22% Similarity=0.514 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceeccc---CCCCceEcCCCcccccccCCccCCCCCchhhHHHhhhcc
Q psy15975 23 PKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQH---VEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCD 99 (312)
Q Consensus 23 ~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~---~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~ 99 (312)
|....+|+.....+ .. .-|+ =|-..+.... .....+.=+|+|.||+.|-..|.... .
T Consensus 155 ~~il~~ye~~~~~S-----kE-~eCg--ICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r------------~ 214 (242)
T PHA02926 155 IKILDKYEDVYRVS-----KE-KECG--ICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTR------------R 214 (242)
T ss_pred hHHHHHHHHHHhcc-----CC-CCCc--cCccccccccccccccccccCCCCchHHHHHHHHHHHhc------------c
Confidence 45566666555433 12 3466 3665543211 11122333499999999976554311 0
Q ss_pred cchhhhHHhhhcCCCCCCCCceeE
Q psy15975 100 DDSETSNWIAANTKECPKCLVTIE 123 (312)
Q Consensus 100 ~~~~~~~~i~~~~k~CP~C~~~Ie 123 (312)
+ ....+.||-|+....
T Consensus 215 -~-------~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 215 -E-------TGASDNCPICRTRFR 230 (242)
T ss_pred -c-------cCcCCcCCCCcceee
Confidence 0 023478999998765
No 79
>PHA02929 N1R/p28-like protein; Provisional
Probab=64.24 E-value=2.3 Score=38.89 Aligned_cols=51 Identities=24% Similarity=0.685 Sum_probs=30.4
Q ss_pred eecCCcCCCCceecccCC--CCceEcCCCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCcee
Q psy15975 45 RWCPSPDCNNAIKVQHVE--ARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTI 122 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~--~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~I 122 (312)
.-||- |...+..+... ...+.-+|+|.||..|-.. |.. . ...||-|+.++
T Consensus 175 ~eC~I--Cle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~------------Wl~-------------~-~~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAI--CMEKVYDKEIKNMYFGILSNCNHVFCIECIDI------------WKK-------------E-KNTCPVCRTPF 226 (238)
T ss_pred CCCcc--CCcccccCccccccceecCCCCCcccHHHHHH------------HHh-------------c-CCCCCCCCCEe
Confidence 46773 76655322111 1234556999999988544 321 1 24799999887
Q ss_pred E
Q psy15975 123 E 123 (312)
Q Consensus 123 e 123 (312)
.
T Consensus 227 ~ 227 (238)
T PHA02929 227 I 227 (238)
T ss_pred e
Confidence 5
No 80
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=64.18 E-value=1.7 Score=40.98 Aligned_cols=29 Identities=24% Similarity=0.548 Sum_probs=23.7
Q ss_pred CCCCCCCCceeEec-CCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKD-GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~-~GCnhMtC~~~~C~~~F 142 (312)
|..||+|+..|-+. -.=|.+.|+. |+|+|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~--c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPK--CGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCC--CCCCe
Confidence 58999999988763 4456789998 99988
No 81
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=63.72 E-value=6.6 Score=28.43 Aligned_cols=29 Identities=28% Similarity=0.594 Sum_probs=18.6
Q ss_pred hcCCCCCCCCceeEe---cCCCCceeecCCCCCc
Q psy15975 110 ANTKECPKCLVTIEK---DGGCNHMVCKNQSCKA 140 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK---~~GCnhMtC~~~~C~~ 140 (312)
.++|+||.|+..+.. .+|=-...|.. |+.
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~--CgA 35 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNG--CES 35 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCC--CCc
Confidence 357999999987666 34433355554 553
No 82
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=63.52 E-value=6.8 Score=28.56 Aligned_cols=31 Identities=32% Similarity=0.591 Sum_probs=22.0
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCccccc
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCF 76 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~ 76 (312)
.+.|| ||++.-..-+..+..|+|. ||...+-
T Consensus 19 ~VkCp--dC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEeccCceEEEecccccEEEe
Confidence 45788 8998643333346789999 9988774
No 83
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=63.37 E-value=4.8 Score=27.61 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=18.9
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
--+.||+|+-.+.-..-=+...|.+ ||+
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGk--Cgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGK--CGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEecc--ccc
Confidence 3479999996544433334678887 885
No 84
>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=62.90 E-value=4.8 Score=31.58 Aligned_cols=25 Identities=40% Similarity=0.806 Sum_probs=19.2
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
+.||.|+.++...+| .+.|.. |++.
T Consensus 1 ~fC~~Cg~~l~~~~~--~~~C~~--C~~~ 25 (104)
T TIGR01384 1 KFCPKCGSLMTPKNG--VYVCPS--CGYE 25 (104)
T ss_pred CCCcccCcccccCCC--eEECcC--CCCc
Confidence 369999999876553 788887 8765
No 85
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.00 E-value=6.5 Score=30.22 Aligned_cols=29 Identities=31% Similarity=0.571 Sum_probs=22.8
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
--.||.|+.+..+..+=---.|.+ ||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~k--Cg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRK--CGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCC--CCCee
Confidence 358999999999988877777776 77544
No 86
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.75 E-value=6.7 Score=30.96 Aligned_cols=29 Identities=24% Similarity=0.511 Sum_probs=20.0
Q ss_pred cCCCCCCCCcee---EecCCCCceeecCCCCCcc
Q psy15975 111 NTKECPKCLVTI---EKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 111 ~~k~CP~C~~~I---eK~~GCnhMtC~~~~C~~~ 141 (312)
+.-.||.|+... ....|=-|..|.+ ||+.
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~--CG~y 51 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGN--CGLY 51 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCC--CCCc
Confidence 445899999432 2344677999998 8844
No 87
>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=61.20 E-value=9.3 Score=25.04 Aligned_cols=12 Identities=25% Similarity=0.841 Sum_probs=7.6
Q ss_pred CCCCCCCc-eeEe
Q psy15975 113 KECPKCLV-TIEK 124 (312)
Q Consensus 113 k~CP~C~~-~IeK 124 (312)
..||.|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 46777776 5544
No 88
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=60.73 E-value=7.5 Score=31.39 Aligned_cols=29 Identities=28% Similarity=0.606 Sum_probs=20.7
Q ss_pred CCCCCCCCceeEec--CCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKD--GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~--~GCnhMtC~~~~C~~~F 142 (312)
.+-||+|+..+.-. ++=+-+.|++ ||+++
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~k--Cgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRK--CGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCC--CCcch
Confidence 36899999887762 1233899998 88653
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=59.04 E-value=12 Score=31.36 Aligned_cols=33 Identities=21% Similarity=0.618 Sum_probs=20.7
Q ss_pred hCCCceecCCcCCCCceecccCC-----CCceEcC-CCccc
Q psy15975 40 CNRLLRWCPSPDCNNAIKVQHVE-----ARPVVCK-CGHRF 74 (312)
Q Consensus 40 ~~~~~~~CP~~~C~~~i~~~~~~-----~~~v~C~-C~~~f 74 (312)
.+.....|| .|+.-+...+.. ...+.|| ||...
T Consensus 95 ~~~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 455677898 599877654321 2238888 77643
No 90
>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=58.96 E-value=11 Score=26.43 Aligned_cols=31 Identities=35% Similarity=0.686 Sum_probs=22.3
Q ss_pred CCCCCCCceeEecCCC--CceeecCCCCCcceecc
Q psy15975 113 KECPKCLVTIEKDGGC--NHMVCKNQSCKAEFCWV 145 (312)
Q Consensus 113 k~CP~C~~~IeK~~GC--nhMtC~~~~C~~~FCw~ 145 (312)
-.||.|+..|+-.+.= -.+.|.. ||.++=-+
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~--CGaeleVv 35 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDE--CGAELEVV 35 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCC--CCCEEEEE
Confidence 4799999999886542 3578887 88766333
No 91
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=58.75 E-value=2.3 Score=40.17 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=22.3
Q ss_pred CCCCCCCCceeEec-CCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKD-GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~-~GCnhMtC~~~~C~~~F 142 (312)
|..||+|+..|-+. -.=|.+.|+. |+|+|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~--c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQ--CGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCC--CCCCc
Confidence 47899998888764 3466788987 99876
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=58.70 E-value=4.9 Score=28.67 Aligned_cols=15 Identities=40% Similarity=0.921 Sum_probs=8.0
Q ss_pred CCCCCC-ceeEecCCC
Q psy15975 114 ECPKCL-VTIEKDGGC 128 (312)
Q Consensus 114 ~CP~C~-~~IeK~~GC 128 (312)
+||+|+ ..|-+-.-|
T Consensus 29 ~CPnCGe~~I~Rc~~C 44 (61)
T COG2888 29 PCPNCGEVEIYRCAKC 44 (61)
T ss_pred eCCCCCceeeehhhhH
Confidence 566666 555444443
No 93
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=58.25 E-value=6 Score=43.43 Aligned_cols=55 Identities=20% Similarity=0.512 Sum_probs=37.8
Q ss_pred CCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEecCCCC
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEKDGGCN 129 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK~~GCn 129 (312)
-|+.-|.....+...|-|. |+.-.|..|- ++.+ ....+-||.|++...+--||.
T Consensus 22 ICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY----------EYEr---------------~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 22 ICGDNVGKTVDGEPFVACDVCAFPVCRPCY----------EYER---------------KDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred ecccccCcCCCCCEEEEeccCCCccccchh----------hhhh---------------hcCCccCCccCCchhhhcCCC
Confidence 4888887776677889999 9999998664 3221 123467888888776555544
Q ss_pred c
Q psy15975 130 H 130 (312)
Q Consensus 130 h 130 (312)
.
T Consensus 77 r 77 (1079)
T PLN02638 77 A 77 (1079)
T ss_pred C
Confidence 4
No 94
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=57.86 E-value=2.5 Score=39.73 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=23.3
Q ss_pred CCCCCCCCceeEec-CCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKD-GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~-~GCnhMtC~~~~C~~~F 142 (312)
|..||+|+..|-+. -.=|.+.|++ |+|+|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~--c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPK--CDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCC--CCCcC
Confidence 57999999998774 3456789998 99886
No 95
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=57.07 E-value=6 Score=26.06 Aligned_cols=38 Identities=34% Similarity=0.736 Sum_probs=19.7
Q ss_pred cCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhH
Q psy15975 47 CPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLR 92 (312)
Q Consensus 47 CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~ 92 (312)
|..++|..... ..+.|+ |+..||..-+.+. ...|....
T Consensus 1 C~~~~C~~~~~------~~~~C~~C~~~FC~~Hr~~e--~H~C~~~~ 39 (43)
T PF01428_consen 1 CSFPGCKKKDF------LPFKCKHCGKSFCLKHRLPE--DHNCSKLQ 39 (43)
T ss_dssp -SSTTT--BCT------SHEE-TTTS-EE-TTTHSTT--TCT-SSTT
T ss_pred CccCcCcCccC------CCeECCCCCcccCccccCcc--ccCCcchh
Confidence 45567776543 358999 9999999877532 12565433
No 96
>PLN03086 PRLI-interacting factor K; Provisional
Probab=56.60 E-value=6.5 Score=40.43 Aligned_cols=30 Identities=27% Similarity=0.769 Sum_probs=26.0
Q ss_pred cCCCCCC--CCceeEecCCCCceeecCCCCCcce
Q psy15975 111 NTKECPK--CLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 111 ~~k~CP~--C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
+...||+ |+..+.+...=+|.+|.. |+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~--Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEK--CGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCC--CCCcc
Confidence 5578995 999999999999999998 88665
No 97
>KOG2932|consensus
Probab=56.44 E-value=2.7 Score=39.73 Aligned_cols=55 Identities=22% Similarity=0.577 Sum_probs=36.4
Q ss_pred CCCceecCCcCCCCceecccCCCCceEcCCCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCc
Q psy15975 41 NRLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLV 120 (312)
Q Consensus 41 ~~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~ 120 (312)
++.+-+|- .|+..|.+-+- .+ +|.++||..|-.. | ..|.||.|.-
T Consensus 87 ~p~VHfCd--~Cd~PI~IYGR---mI--PCkHvFCl~CAr~-~---------------------------~dK~Cp~C~d 131 (389)
T KOG2932|consen 87 GPRVHFCD--RCDFPIAIYGR---MI--PCKHVFCLECARS-D---------------------------SDKICPLCDD 131 (389)
T ss_pred CcceEeec--ccCCcceeeec---cc--ccchhhhhhhhhc-C---------------------------ccccCcCccc
Confidence 34455555 57776654321 12 3789999988542 1 1389999999
Q ss_pred eeEecCCCCc
Q psy15975 121 TIEKDGGCNH 130 (312)
Q Consensus 121 ~IeK~~GCnh 130 (312)
.|+|.+-|..
T Consensus 132 ~VqrIeq~~~ 141 (389)
T KOG2932|consen 132 RVQRIEQIMM 141 (389)
T ss_pred HHHHHHHhcc
Confidence 9999988743
No 98
>PLN02189 cellulose synthase
Probab=56.17 E-value=7.5 Score=42.55 Aligned_cols=59 Identities=27% Similarity=0.621 Sum_probs=41.0
Q ss_pred ecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
-|. -|+.-|.....+...|.|. |+.-.|..|-+ +.+ ....+.||.|++...+
T Consensus 36 ~C~--iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye----------yer---------------~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 36 VCE--ICGDEIGLTVDGDLFVACNECGFPVCRPCYE----------YER---------------REGTQNCPQCKTRYKR 88 (1040)
T ss_pred ccc--ccccccCcCCCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCchhh
Confidence 566 4888887766667889999 99999986642 211 1234688888888876
Q ss_pred cCCCCce
Q psy15975 125 DGGCNHM 131 (312)
Q Consensus 125 ~~GCnhM 131 (312)
--|++.+
T Consensus 89 ~kgs~~v 95 (1040)
T PLN02189 89 LKGSPRV 95 (1040)
T ss_pred ccCCCCc
Confidence 5565543
No 99
>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=55.25 E-value=11 Score=24.59 Aligned_cols=26 Identities=35% Similarity=0.726 Sum_probs=14.2
Q ss_pred ecCCcCCCCceecccCCCCceEcC-CCcc
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCK-CGHR 73 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~-C~~~ 73 (312)
.|| .|+..-...+.....+.|+ ||.+
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCCE
Confidence 477 5887543333445556666 6543
No 100
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=54.80 E-value=8.6 Score=23.73 Aligned_cols=28 Identities=36% Similarity=0.760 Sum_probs=14.1
Q ss_pred CCCCCCceeEe----cCC-CCceeecCCCCCcc
Q psy15975 114 ECPKCLVTIEK----DGG-CNHMVCKNQSCKAE 141 (312)
Q Consensus 114 ~CP~C~~~IeK----~~G-CnhMtC~~~~C~~~ 141 (312)
.||+|+..+-- ..| =.-..|++|-|.++
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsnpacdye 35 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSNPACDYE 35 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES-TT---E
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCCCccccC
Confidence 69999875432 233 34477887777654
No 101
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=54.57 E-value=11 Score=30.27 Aligned_cols=30 Identities=27% Similarity=0.793 Sum_probs=21.4
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPH 153 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h 153 (312)
-+||+|..-.-=..|=+ +.|+. |+ .+|...
T Consensus 3 p~CP~C~seytY~dg~~-~iCpe--C~--------~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPS--CL--------YEWNEN 32 (109)
T ss_pred CcCCcCCCcceEecCCe-eECcc--cc--------cccccc
Confidence 57999998887777754 67775 55 567654
No 102
>KOG2807|consensus
Probab=53.82 E-value=8.8 Score=36.58 Aligned_cols=61 Identities=30% Similarity=0.696 Sum_probs=39.3
Q ss_pred hCCCHHHHHHHHHHHH-HHHHhh----CCCceecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCC
Q psy15975 19 LVRDPKVKLKYQHLIT-NSFVEC----NRLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDP 85 (312)
Q Consensus 19 ~l~~~e~~~~y~~~~~-~~~v~~----~~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p 85 (312)
+++++.+...|..++- +.|++. +.+...|- .|+.-. .+....+|. |...||..|..-.|..
T Consensus 300 LVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~~~----~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 300 LVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQGEL----LSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred EecchHHHHHHHhhcCCcchhhccccccCCCccee--eecccc----CCCCcEEchhccceeeccchHHHHhh
Confidence 5567888888887753 444442 23444565 463222 245579999 9999999887766644
No 103
>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=53.51 E-value=8.3 Score=31.79 Aligned_cols=27 Identities=11% Similarity=0.107 Sum_probs=18.7
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
-+.||+|++..---.- +.++|+. ||..
T Consensus 9 Kr~Cp~cg~kFYDLnk-~p~vcP~--cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR-RPAVSPY--TGEQ 35 (129)
T ss_pred cccCCCcCccccccCC-CCccCCC--cCCc
Confidence 3689999876543222 7899987 7744
No 104
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=53.35 E-value=8.7 Score=20.57 Aligned_cols=16 Identities=44% Similarity=0.912 Sum_probs=13.8
Q ss_pred cccccCCccCCCCCch
Q psy15975 74 FCFACGENWHDPVRCS 89 (312)
Q Consensus 74 fC~~C~~~~H~p~~C~ 89 (312)
.|++|++.-|.-..|+
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5999999999887775
No 105
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=53.14 E-value=14 Score=26.43 Aligned_cols=30 Identities=33% Similarity=0.623 Sum_probs=20.9
Q ss_pred eecCCcCCCCceecccCCCCceEcC-CCccccc
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCF 76 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~ 76 (312)
+.|| +|++.-.+-+-....|.|. ||...+-
T Consensus 12 VkCp--~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECC--CCCCeEEEEecCCcEEECcccCCCccc
Confidence 5688 7998654333346679999 8887763
No 106
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.09 E-value=10 Score=30.68 Aligned_cols=39 Identities=26% Similarity=0.452 Sum_probs=28.1
Q ss_pred CCCCCCCCceeEec--------CCCCceeecCCCCCcceecccCCCCCC
Q psy15975 112 TKECPKCLVTIEKD--------GGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 112 ~k~CP~C~~~IeK~--------~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
.+.|-.|..++... ..=..-.|.+ |+..||..|---+..
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~--C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAV--CKNVFCVDCDVFVHE 101 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCC--CCCccccccchhhhh
Confidence 35799999977532 1123566988 999999999776654
No 107
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=52.98 E-value=11 Score=26.97 Aligned_cols=41 Identities=20% Similarity=0.473 Sum_probs=22.7
Q ss_pred Hhhh-cCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCC
Q psy15975 107 WIAA-NTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 107 ~i~~-~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~ 151 (312)
|+.. ....|+.|+... +-.-..-.|.. ||.-||-.|.....
T Consensus 3 W~~d~~~~~C~~C~~~F--~~~~rrhhCr~--CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 3 WVPDSEASNCMICGKKF--SLFRRRHHCRN--CGRVVCSSCSSQRI 44 (69)
T ss_dssp SSSGGG-SB-TTT--B---BSSS-EEE-TT--T--EEECCCS-EEE
T ss_pred cCCCCCCCcCcCcCCcC--CCceeeEccCC--CCCEECCchhCCEE
Confidence 4433 568999999998 44455678998 99999999987543
No 108
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=52.53 E-value=5.2 Score=37.29 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=24.4
Q ss_pred cCCCCCCCCceeEec-CCCCceeecCCCCCcce
Q psy15975 111 NTKECPKCLVTIEKD-GGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~-~GCnhMtC~~~~C~~~F 142 (312)
-|-.||+|+..+-+. -+=|.+.|.+ |+|+|
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~--c~~h~ 57 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPK--CGHHM 57 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccc--cCccc
Confidence 357999999988774 5678899998 99876
No 109
>KOG2907|consensus
Probab=51.01 E-value=3.6 Score=33.08 Aligned_cols=30 Identities=23% Similarity=0.698 Sum_probs=19.2
Q ss_pred CceecCCcCCCCceecccCCCCceEcCCCcccccccCCcc
Q psy15975 43 LLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENW 82 (312)
Q Consensus 43 ~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~ 82 (312)
.+.+|| +||.++..... ...+. |.+|+.+|
T Consensus 6 ~~~FC~--~CG~ll~~~~~-~~~~~-------C~~Ck~~~ 35 (116)
T KOG2907|consen 6 DLDFCS--DCGSLLEEPSA-QSTVL-------CIRCKIEY 35 (116)
T ss_pred Ccchhh--hhhhhcccccc-cCceE-------eccccccC
Confidence 456888 79999876643 22333 66666655
No 110
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=50.78 E-value=10 Score=29.04 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=10.9
Q ss_pred CCCCCCCCceeEec
Q psy15975 112 TKECPKCLVTIEKD 125 (312)
Q Consensus 112 ~k~CP~C~~~IeK~ 125 (312)
...||-|+.+.+-.
T Consensus 71 ~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 71 KGQCPMCRQPWKFK 84 (85)
T ss_pred CCCCCCcCCeeeeC
Confidence 36999999987643
No 111
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=50.47 E-value=10 Score=41.58 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=23.1
Q ss_pred CCCCceecccCCCCceEcC-CCcccccccC
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CGHRFCFACG 79 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~ 79 (312)
-|+.-|.....+...|-|. |+.-.|..|-
T Consensus 20 iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy 49 (1044)
T PLN02915 20 VCGDEVGVKEDGQPFVACHVCGFPVCKPCY 49 (1044)
T ss_pred ccccccCcCCCCCEEEEeccCCCccccchh
Confidence 4777776666667889999 9999998775
No 112
>PLN02400 cellulose synthase
Probab=49.78 E-value=13 Score=40.91 Aligned_cols=29 Identities=24% Similarity=0.597 Sum_probs=23.2
Q ss_pred CCCCceecccCCCCceEcC-CCcccccccC
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CGHRFCFACG 79 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~ 79 (312)
-|+.-|.....+...|-|. |+.-.|..|-
T Consensus 41 ICGD~VG~t~dGe~FVAC~eCaFPVCRpCY 70 (1085)
T PLN02400 41 ICGDDVGVTETGDVFVACNECAFPVCRPCY 70 (1085)
T ss_pred ecccccCcCCCCCEEEEEccCCCccccchh
Confidence 4887777766667889999 9999998775
No 113
>KOG2177|consensus
Probab=49.52 E-value=7.8 Score=34.77 Aligned_cols=17 Identities=18% Similarity=0.606 Sum_probs=15.5
Q ss_pred CceeecCCCCCcceecccC
Q psy15975 129 NHMVCKNQSCKAEFCWVCL 147 (312)
Q Consensus 129 nhMtC~~~~C~~~FCw~C~ 147 (312)
.++.|.. |+...|+.|.
T Consensus 96 ~~~~c~~--~~~~~c~~c~ 112 (386)
T KOG2177|consen 96 LKLFCEE--DEKLLCVLCR 112 (386)
T ss_pred ceEEecc--cccccCCCCC
Confidence 6789998 9999999998
No 114
>PLN02436 cellulose synthase A
Probab=49.42 E-value=11 Score=41.32 Aligned_cols=59 Identities=24% Similarity=0.590 Sum_probs=39.9
Q ss_pred ecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 46 WCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 46 ~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
-|. -|+.-|.....+...|-|. |+.-.|..|-. +.+ ....+.||.|++...+
T Consensus 38 iCq--ICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye----------yer---------------~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 38 TCQ--ICGDEIELTVDGEPFVACNECAFPVCRPCYE----------YER---------------REGNQACPQCKTRYKR 90 (1094)
T ss_pred ccc--ccccccCcCCCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCchhh
Confidence 454 4887776665567889999 99999986642 211 1234688888888876
Q ss_pred cCCCCce
Q psy15975 125 DGGCNHM 131 (312)
Q Consensus 125 ~~GCnhM 131 (312)
--|++.+
T Consensus 91 ~kgs~~~ 97 (1094)
T PLN02436 91 IKGSPRV 97 (1094)
T ss_pred ccCCCCc
Confidence 5555543
No 115
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=49.39 E-value=13 Score=26.06 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=17.0
Q ss_pred CCCCCCCCceeEec---CCC-----CceeecCCCCCc
Q psy15975 112 TKECPKCLVTIEKD---GGC-----NHMVCKNQSCKA 140 (312)
Q Consensus 112 ~k~CP~C~~~IeK~---~GC-----nhMtC~~~~C~~ 140 (312)
.|+||.|+.+.... .|= ..+.|.. ||.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~--Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTD--CGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCC--CCC
Confidence 58999998654432 221 4577776 664
No 116
>PHA02926 zinc finger-like protein; Provisional
Probab=49.35 E-value=8.2 Score=34.95 Aligned_cols=52 Identities=23% Similarity=0.496 Sum_probs=31.4
Q ss_pred hcCCCCCCCCcee-Eec-CCCCceeecCCCCCcceecccCCCCCCCC---CCCCCCCC
Q psy15975 110 ANTKECPKCLVTI-EKD-GGCNHMVCKNQSCKAEFCWVCLGPWEPHG---SSWYSCNR 162 (312)
Q Consensus 110 ~~~k~CP~C~~~I-eK~-~GCnhMtC~~~~C~~~FCw~C~~~w~~h~---~~~~~C~~ 162 (312)
+.-+.|+=|-..+ +|. .++.. .-.-++|+|-||+.|...|.... +....|+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRr-FGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi 224 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRY-FGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224 (242)
T ss_pred cCCCCCccCcccccccccccccc-ccccCCCCchHHHHHHHHHHHhccccCcCCcCCC
Confidence 3458999998665 332 11110 01123599999999999998632 11245773
No 117
>PRK10220 hypothetical protein; Provisional
Probab=47.78 E-value=16 Score=29.25 Aligned_cols=31 Identities=23% Similarity=0.674 Sum_probs=21.4
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPH 153 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h 153 (312)
.-+||+|..-.-=.+|= .+.|+. |+ .+|.+.
T Consensus 3 lP~CP~C~seytY~d~~-~~vCpe--C~--------hEW~~~ 33 (111)
T PRK10220 3 LPHCPKCNSEYTYEDNG-MYICPE--CA--------HEWNDA 33 (111)
T ss_pred CCcCCCCCCcceEcCCC-eEECCc--cc--------CcCCcc
Confidence 35899998887776664 366775 55 667654
No 118
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=47.70 E-value=14 Score=22.18 Aligned_cols=23 Identities=30% Similarity=0.774 Sum_probs=12.2
Q ss_pred CCCCCCCceeEec--CCCCceeecC
Q psy15975 113 KECPKCLVTIEKD--GGCNHMVCKN 135 (312)
Q Consensus 113 k~CP~C~~~IeK~--~GCnhMtC~~ 135 (312)
++||.|+.+|+.. +|=+...|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~r 26 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPR 26 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TT
T ss_pred CcCccCCCcceEeEecCCCCeECcC
Confidence 6899999999774 4444455554
No 119
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.66 E-value=18 Score=24.06 Aligned_cols=23 Identities=22% Similarity=0.547 Sum_probs=11.5
Q ss_pred CCCCCceeEecCCCCceeecCCCCCc
Q psy15975 115 CPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 115 CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
|..|+..++...+ .-+.|+. ||+
T Consensus 5 C~~Cg~~~~~~~~-~~irC~~--CG~ 27 (44)
T smart00659 5 CGECGRENEIKSK-DVVRCRE--CGY 27 (44)
T ss_pred CCCCCCEeecCCC-CceECCC--CCc
Confidence 5555555555433 4455554 553
No 120
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=47.64 E-value=19 Score=22.52 Aligned_cols=29 Identities=28% Similarity=0.427 Sum_probs=19.3
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
.+.|+.|+....-+.-=..+.|.. |+..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~--Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIF--CGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEccc--CCcEe
Confidence 467888887766544445677776 77543
No 121
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=47.03 E-value=20 Score=25.16 Aligned_cols=30 Identities=30% Similarity=0.541 Sum_probs=17.6
Q ss_pred eecCCcCCCCceecccCCCCceEcC-CCccccc
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCF 76 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~ 76 (312)
+.|| +|.+.-.+=+-....|.|. ||...|-
T Consensus 8 VkCp--~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEecCCeEEEcccCCCEecC
Confidence 5688 7998643333346789999 9998885
No 122
>PRK11827 hypothetical protein; Provisional
Probab=46.21 E-value=17 Score=25.99 Aligned_cols=26 Identities=19% Similarity=0.390 Sum_probs=21.0
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCK 139 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~ 139 (312)
+-.||.|+.+.+-..+=+...|.. |+
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~--~~ 33 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKL--DN 33 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCc--cC
Confidence 458999999998877667788886 66
No 123
>KOG2164|consensus
Probab=45.63 E-value=9 Score=38.56 Aligned_cols=34 Identities=35% Similarity=0.726 Sum_probs=22.0
Q ss_pred CCcccccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCceeEe
Q psy15975 70 CGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTIEK 124 (312)
Q Consensus 70 C~~~fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~IeK 124 (312)
|||.||+.|-- +-|..- .....+.||-|...|-.
T Consensus 204 CGHiFC~~CiL-----------qy~~~s----------~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 204 CGHIFCGPCIL-----------QYWNYS----------AIKGPCSCPICRSTITL 237 (513)
T ss_pred cCceeeHHHHH-----------HHHhhh----------cccCCccCCchhhhccc
Confidence 99999998842 333211 11345789999888743
No 124
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=45.41 E-value=17 Score=33.99 Aligned_cols=34 Identities=24% Similarity=0.537 Sum_probs=27.9
Q ss_pred HHhhhcCCCCCCCCceeEecCCCCceeecCCCCCcce
Q psy15975 106 NWIAANTKECPKCLVTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 106 ~~i~~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
.|. ...+-||+|+.+.+-..|=-.|.|++ ||+.+
T Consensus 106 ~w~-~~~RFCg~CG~~~~~~~~g~~~~C~~--cg~~~ 139 (279)
T COG2816 106 EWY-RSHRFCGRCGTKTYPREGGWARVCPK--CGHEH 139 (279)
T ss_pred HHH-hhCcCCCCCCCcCccccCceeeeCCC--CCCcc
Confidence 343 35589999999999999989999998 98654
No 125
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.24 E-value=18 Score=29.23 Aligned_cols=29 Identities=31% Similarity=0.858 Sum_probs=19.1
Q ss_pred ceecCCcCCCCceecccC-CCCceEcC-CCccc
Q psy15975 44 LRWCPSPDCNNAIKVQHV-EARPVVCK-CGHRF 74 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~-~~~~v~C~-C~~~f 74 (312)
+++|| .|++.+.+... ......|+ ||+..
T Consensus 2 m~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 57899 79999877432 23366666 66544
No 126
>PF14353 CpXC: CpXC protein
Probab=45.20 E-value=21 Score=29.00 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=5.7
Q ss_pred CCCCCCCceeE
Q psy15975 113 KECPKCLVTIE 123 (312)
Q Consensus 113 k~CP~C~~~Ie 123 (312)
-.||+|+..+.
T Consensus 39 ~~CP~Cg~~~~ 49 (128)
T PF14353_consen 39 FTCPSCGHKFR 49 (128)
T ss_pred EECCCCCCcee
Confidence 45555555553
No 127
>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=45.05 E-value=43 Score=22.16 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=18.7
Q ss_pred cCCCCCCCCce-eEecCCCCceeecCCCCCcc
Q psy15975 111 NTKECPKCLVT-IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 111 ~~k~CP~C~~~-IeK~~GCnhMtC~~~~C~~~ 141 (312)
+.-.||+|+.. +-...+=....|.. |+++
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~--C~~q 46 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKA--CRKQ 46 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCC--CCCc
Confidence 45679999974 33344445677776 7753
No 128
>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=45.01 E-value=22 Score=23.87 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=6.5
Q ss_pred CCCCCCcee
Q psy15975 114 ECPKCLVTI 122 (312)
Q Consensus 114 ~CP~C~~~I 122 (312)
.||.|+.+.
T Consensus 1 ~CP~Cg~~a 9 (47)
T PF04606_consen 1 RCPHCGSKA 9 (47)
T ss_pred CcCCCCCee
Confidence 488887754
No 129
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.95 E-value=2.8e+02 Score=26.42 Aligned_cols=37 Identities=24% Similarity=0.582 Sum_probs=24.7
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCC-CCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGP-WEP 152 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~-w~~ 152 (312)
..||.|++..-.+..=.-|.=. |||.||-.|... |..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~---CGH~~C~sCv~~l~~~ 41 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNV---CGHTLCESCVDLLFVR 41 (309)
T ss_pred CCCCcCCCCCccCcccccccCC---CCCcccHHHHHHHhcC
Confidence 4799999966555443223223 899999999887 543
No 130
>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=43.81 E-value=18 Score=21.04 Aligned_cols=6 Identities=50% Similarity=1.470 Sum_probs=3.0
Q ss_pred CCCCCC
Q psy15975 114 ECPKCL 119 (312)
Q Consensus 114 ~CP~C~ 119 (312)
.||+|+
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 455554
No 131
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=43.56 E-value=22 Score=25.75 Aligned_cols=49 Identities=20% Similarity=0.328 Sum_probs=26.6
Q ss_pred CCceecCCcCCCCceecccCCCCceEcC-CCcccccccCCccCCCCCchhhHHHhhh
Q psy15975 42 RLLRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGENWHDPVRCSLLRRWIKK 97 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~~~H~p~~C~~~~~w~~~ 97 (312)
..++-||+-+|..+.......-..|.|. |+..-+ +.+..=..+..|.++
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~-------~~~te~~Aie~WN~R 53 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESRTG-------YGGSEKEALERWNKR 53 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcCcc-------cccCHHHHHHHHHhh
Confidence 4678899855554443333334457777 777533 223222455566654
No 132
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.97 E-value=17 Score=40.63 Aligned_cols=33 Identities=24% Similarity=0.677 Sum_probs=24.7
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcc-----eecccCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAE-----FCWVCLGPWEP 152 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~-----FCw~C~~~w~~ 152 (312)
...||+|+..+... .|.. ||.. +|-.|+..-..
T Consensus 667 ~rkCPkCG~~t~~~------fCP~--CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 667 RRRCPSCGTETYEN------RCPD--CGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EEECCCCCCccccc------cCcc--cCCcCCCceeCccCCCccCC
Confidence 37999999987432 8887 8866 48888887544
No 133
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=42.97 E-value=16 Score=27.74 Aligned_cols=30 Identities=33% Similarity=0.808 Sum_probs=16.3
Q ss_pred cCCCCCCCC------ceeEecCCCCceeecCCCCCcce
Q psy15975 111 NTKECPKCL------VTIEKDGGCNHMVCKNQSCKAEF 142 (312)
Q Consensus 111 ~~k~CP~C~------~~IeK~~GCnhMtC~~~~C~~~F 142 (312)
.+=.||.|+ .-|.+..|=-+++|.. ||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~--Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRV--CGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESS--S--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecC--CCCeE
Confidence 345899998 2355567777899987 86444
No 134
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=42.71 E-value=14 Score=25.10 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=19.9
Q ss_pred cCCCCC--CCCceeEecCCCCceeecCCCCCc
Q psy15975 111 NTKECP--KCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 111 ~~k~CP--~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
.-+.|| .|+.-+.-..=-+...|.+ |++
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGK--Cg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGK--CGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETT--TSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCC--ccc
Confidence 347999 9998765555567899998 885
No 135
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=42.61 E-value=23 Score=25.21 Aligned_cols=27 Identities=22% Similarity=0.606 Sum_probs=20.3
Q ss_pred CCCCCCCce----eEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVT----IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~----IeK~~GCnhMtC~~~~C~~~ 141 (312)
-.||+|+.. .-+..|=.++.|.. |||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~--Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVE--CGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecc--CCCc
Confidence 379999764 34466778999998 9864
No 136
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.45 E-value=21 Score=33.34 Aligned_cols=25 Identities=32% Similarity=0.635 Sum_probs=19.5
Q ss_pred cCCCCCCCCceeEec--CCCCceeecC
Q psy15975 111 NTKECPKCLVTIEKD--GGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~--~GCnhMtC~~ 135 (312)
..++|+.|+.+|+|. +|=+-.-|+.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~ 270 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPV 270 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCC
Confidence 457999999999994 7766666665
No 137
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.29 E-value=21 Score=33.11 Aligned_cols=23 Identities=39% Similarity=0.821 Sum_probs=16.0
Q ss_pred CCCCCCCCceeEec--CCCCceeec
Q psy15975 112 TKECPKCLVTIEKD--GGCNHMVCK 134 (312)
Q Consensus 112 ~k~CP~C~~~IeK~--~GCnhMtC~ 134 (312)
.++||.|+.+|++. +|=.--.|+
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp 259 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCP 259 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECC
Confidence 57999999999983 553333343
No 138
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=42.16 E-value=4.6 Score=26.79 Aligned_cols=23 Identities=26% Similarity=0.726 Sum_probs=14.1
Q ss_pred CCcceecccCCCCCCCCC-CCCCC
Q psy15975 138 CKAEFCWVCLGPWEPHGS-SWYSC 160 (312)
Q Consensus 138 C~~~FCw~C~~~w~~h~~-~~~~C 160 (312)
|||-||..|+..+...+. ....|
T Consensus 19 CGH~~c~~cl~~l~~~~~~~~~kC 42 (43)
T PF13445_consen 19 CGHVFCKDCLQKLSKKSDRNRFKC 42 (43)
T ss_dssp SS-EEEHHHHHHHHHH-S-S-B--
T ss_pred CccHHHHHHHHHHHhcCCCCeeeC
Confidence 999999999998876442 33455
No 139
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.01 E-value=22 Score=33.04 Aligned_cols=24 Identities=33% Similarity=0.675 Sum_probs=16.6
Q ss_pred CCCCCCCCceeEec--CCCCceeecC
Q psy15975 112 TKECPKCLVTIEKD--GGCNHMVCKN 135 (312)
Q Consensus 112 ~k~CP~C~~~IeK~--~GCnhMtC~~ 135 (312)
.++||.|+.+|++. +|=.-..|+.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCC
Confidence 46999999999984 5533344443
No 140
>KOG0006|consensus
Probab=41.69 E-value=17 Score=34.59 Aligned_cols=53 Identities=19% Similarity=0.671 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCCceEcC---CCcccccccCCccCCC
Q psy15975 27 LKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCK---CGHRFCFACGENWHDP 85 (312)
Q Consensus 27 ~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~---C~~~fC~~C~~~~H~p 85 (312)
++|+...... .....+.|| .|--+...++ +.-.+.|+ ||...||.|+-+|...
T Consensus 383 arwd~as~~T---Ik~tTkpCP--kChvptErnG-GCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 383 ARWDAASKET---IKKTTKPCP--KCHVPTERNG-GCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred hhhhhhhhhh---hhhccCCCC--CccCccccCC-ceEEeecCCCCCCceeEeccCChhhhh
Confidence 4555544322 223446787 6988877664 45678898 9999999999998754
No 141
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=41.67 E-value=22 Score=32.70 Aligned_cols=19 Identities=26% Similarity=0.614 Sum_probs=14.3
Q ss_pred CCceecCCcCCCCceeccc
Q psy15975 42 RLLRWCPSPDCNNAIKVQH 60 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~~ 60 (312)
....-||.|+|.++|....
T Consensus 121 S~rIaCPRp~CkRiI~L~~ 139 (256)
T PF09788_consen 121 SQRIACPRPNCKRIINLGP 139 (256)
T ss_pred cccccCCCCCCcceEEeCC
Confidence 3446899999999986543
No 142
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=41.65 E-value=22 Score=32.99 Aligned_cols=25 Identities=32% Similarity=0.700 Sum_probs=16.9
Q ss_pred cCCCCCCCCceeEec--CCCCceeecC
Q psy15975 111 NTKECPKCLVTIEKD--GGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~--~GCnhMtC~~ 135 (312)
..++||.|+.+|++. +|=.-..|+.
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQGGRSTFFCPR 270 (274)
T ss_pred CCCCCCCCCCeeEEEEECCCCcEECcC
Confidence 357999999999983 5533344443
No 143
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=41.35 E-value=24 Score=26.98 Aligned_cols=35 Identities=26% Similarity=0.602 Sum_probs=24.0
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCcccccccCC
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGE 80 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~ 80 (312)
-+-|| +|.+.-.+-+-....|.|. ||...|--=++
T Consensus 35 ~VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGG 70 (85)
T PTZ00083 35 DVKCP--GCSQITTVFSHAQTVVLCGGCSSQLCQPTGG 70 (85)
T ss_pred EEECC--CCCCeeEEEecCceEEEccccCCEeeccCCC
Confidence 35788 7998644333356789999 99998854333
No 144
>PLN00209 ribosomal protein S27; Provisional
Probab=41.12 E-value=24 Score=27.04 Aligned_cols=34 Identities=29% Similarity=0.512 Sum_probs=23.4
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCcccccccC
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACG 79 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~ 79 (312)
-+-|| +|.+.-.+-+-....|.|. ||...|--=+
T Consensus 36 ~VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~~PTG 70 (86)
T PLN00209 36 DVKCQ--GCFNITTVFSHSQTVVVCGSCQTVLCQPTG 70 (86)
T ss_pred EEECC--CCCCeeEEEecCceEEEccccCCEeeccCC
Confidence 35788 7998644333346789999 9999885333
No 145
>PRK10445 endonuclease VIII; Provisional
Probab=41.05 E-value=23 Score=32.75 Aligned_cols=25 Identities=24% Similarity=0.429 Sum_probs=17.7
Q ss_pred cCCCCCCCCceeEe--cCCCCceeecC
Q psy15975 111 NTKECPKCLVTIEK--DGGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK--~~GCnhMtC~~ 135 (312)
..++||.|+.+|++ .+|=.-..|++
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~gR~t~~CP~ 260 (263)
T PRK10445 234 DGEACERCGGIIEKTTLSSRPFYWCPG 260 (263)
T ss_pred CCCCCCCCCCEeEEEEECCCCcEECCC
Confidence 36899999999998 36644444444
No 146
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.88 E-value=24 Score=33.00 Aligned_cols=25 Identities=36% Similarity=0.610 Sum_probs=17.9
Q ss_pred cCCCCCCCCceeEe--cCCCCceeecC
Q psy15975 111 NTKECPKCLVTIEK--DGGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK--~~GCnhMtC~~ 135 (312)
..++||.|+.+|++ .+|=.-..|+.
T Consensus 253 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~ 279 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLAGRSTHWCPN 279 (282)
T ss_pred CcCCCCcCCCeeEEEEECCCccEECCC
Confidence 35799999999998 36644444544
No 147
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.80 E-value=24 Score=32.77 Aligned_cols=24 Identities=21% Similarity=0.527 Sum_probs=16.4
Q ss_pred cCCCCCCCCceeEec--CCCCceeec
Q psy15975 111 NTKECPKCLVTIEKD--GGCNHMVCK 134 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~--~GCnhMtC~ 134 (312)
..++||.|+.+|++. +|=.--.|+
T Consensus 243 ~g~pCprCG~~I~~~~~~gR~t~~CP 268 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAGRSSHYCP 268 (272)
T ss_pred CCCcCCCCCCeeEEEEECCCccEECc
Confidence 357999999999983 553333343
No 148
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.76 E-value=22 Score=38.91 Aligned_cols=33 Identities=21% Similarity=0.356 Sum_probs=26.4
Q ss_pred hcCCCCCCCCceeEecCCCCceeecCCCCCc-----ceecccCCCC
Q psy15975 110 ANTKECPKCLVTIEKDGGCNHMVCKNQSCKA-----EFCWVCLGPW 150 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~-----~FCw~C~~~w 150 (312)
...+.||+|+... ....|.. ||. .||-.|+..-
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~--CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPF--CGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCC--CCCCCCcceeCccccCcC
Confidence 4678999999985 5678988 995 4999996654
No 149
>KOG1493|consensus
Probab=39.50 E-value=32 Score=25.87 Aligned_cols=53 Identities=23% Similarity=0.552 Sum_probs=30.7
Q ss_pred EcC-CCccc---ccccCCccCCCCCchhhHHHhhhcccchhhhHHhhh--cCCCCCCCCcee
Q psy15975 67 VCK-CGHRF---CFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAA--NTKECPKCLVTI 122 (312)
Q Consensus 67 ~C~-C~~~f---C~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~--~~k~CP~C~~~I 122 (312)
+|. |...| |..|+.+ +-+|+.+--.-...-..--..+|+.+ +-..||-|+...
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~P---gDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLP---GDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCC---CCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 777 77666 8888875 55677643211111112234567654 456899997654
No 150
>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=39.37 E-value=18 Score=22.47 Aligned_cols=20 Identities=25% Similarity=0.695 Sum_probs=8.5
Q ss_pred CCCCCceeEecCCCCceeecC
Q psy15975 115 CPKCLVTIEKDGGCNHMVCKN 135 (312)
Q Consensus 115 CP~C~~~IeK~~GCnhMtC~~ 135 (312)
|..|+..++-..+ ..+.|..
T Consensus 3 C~~Cg~~~~~~~~-~~irC~~ 22 (32)
T PF03604_consen 3 CGECGAEVELKPG-DPIRCPE 22 (32)
T ss_dssp ESSSSSSE-BSTS-STSSBSS
T ss_pred CCcCCCeeEcCCC-CcEECCc
Confidence 4455555543322 3345554
No 151
>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=39.06 E-value=13 Score=26.57 Aligned_cols=12 Identities=42% Similarity=0.816 Sum_probs=9.0
Q ss_pred CCCCCCCceeEe
Q psy15975 113 KECPKCLVTIEK 124 (312)
Q Consensus 113 k~CP~C~~~IeK 124 (312)
|.||.||.+|.-
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 678888888854
No 152
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=39.04 E-value=27 Score=24.18 Aligned_cols=32 Identities=25% Similarity=0.566 Sum_probs=17.9
Q ss_pred CceecCCcCCCCc----e----ecccCCCCceEcC-CCccc
Q psy15975 43 LLRWCPSPDCNNA----I----KVQHVEARPVVCK-CGHRF 74 (312)
Q Consensus 43 ~~~~CP~~~C~~~----i----~~~~~~~~~v~C~-C~~~f 74 (312)
++..||+|+|-.- | ...+.+....+|. |+..+
T Consensus 5 gvl~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 5 GVLKCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCERII 45 (52)
T ss_dssp SSSE-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--EE
T ss_pred eEEEcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCCEe
Confidence 4568999999755 1 1112245678888 87654
No 153
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=39.01 E-value=27 Score=25.81 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=20.4
Q ss_pred CCCCCCCce----eEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVT----IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~----IeK~~GCnhMtC~~~~C~~~ 141 (312)
-.||+|+.. +-+..|=.++.|.. |||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~--CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVE--CGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecC--CCCe
Confidence 379999764 33467788999998 9864
No 154
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=38.75 E-value=29 Score=28.50 Aligned_cols=27 Identities=33% Similarity=0.712 Sum_probs=23.0
Q ss_pred CCCCCCCce---eEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVT---IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~---IeK~~GCnhMtC~~~~C~~~ 141 (312)
-.||.|+.| +.+.++-..|.|.. ||..
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~a--CGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKA--CGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETT--TSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecc--cCCc
Confidence 489999876 77889999999998 9864
No 155
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.13 E-value=8.2 Score=35.71 Aligned_cols=33 Identities=33% Similarity=0.727 Sum_probs=23.6
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcceecccCCC-CCCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGP-WEPHG 154 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~-w~~h~ 154 (312)
.|+-|...++. -.|.. |||-|||.|+-. |....
T Consensus 217 kC~lC~e~~~~------ps~t~--CgHlFC~~Cl~~~~t~~k 250 (271)
T COG5574 217 KCFLCLEEPEV------PSCTP--CGHLFCLSCLLISWTKKK 250 (271)
T ss_pred ceeeeecccCC------ccccc--ccchhhHHHHHHHHHhhc
Confidence 37766665532 34665 999999999888 97654
No 156
>PRK00420 hypothetical protein; Validated
Probab=37.91 E-value=78 Score=25.55 Aligned_cols=44 Identities=18% Similarity=0.312 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecCCcCCCCceecccCCCCceEcCCCcccccccCC
Q psy15975 23 PKVKLKYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGE 80 (312)
Q Consensus 23 ~e~~~~y~~~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~ 80 (312)
++...+.-+++++-+.--+ ..|| .|+..+..... |..||..|+.
T Consensus 5 ~~~~k~~a~~Ll~Ga~ml~---~~CP--~Cg~pLf~lk~---------g~~~Cp~Cg~ 48 (112)
T PRK00420 5 EDIVKKAAELLLKGAKMLS---KHCP--VCGLPLFELKD---------GEVVCPVHGK 48 (112)
T ss_pred HHHHHHHHHHHHhHHHHcc---CCCC--CCCCcceecCC---------CceECCCCCC
Confidence 3444555556665444433 4798 59988765211 4556666654
No 157
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=37.84 E-value=25 Score=28.11 Aligned_cols=30 Identities=27% Similarity=0.827 Sum_probs=19.8
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
.-+||+|..-.-=.+|= .|.|+. |. .+|.+
T Consensus 3 lp~cp~c~sEytYed~~-~~~cpe--c~--------~ew~~ 32 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG-QLICPE--CA--------HEWNE 32 (112)
T ss_pred CCCCCccCCceEEecCc-eEeCch--hc--------ccccc
Confidence 35899996655444333 888886 55 67764
No 158
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.61 E-value=8.2 Score=37.98 Aligned_cols=33 Identities=18% Similarity=0.542 Sum_probs=24.0
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPH 153 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h 153 (312)
-.||-|.-.+. +.+. .. |||.||..|...|-..
T Consensus 27 l~C~IC~d~~~-----~Pvi-tp--CgH~FCs~CI~~~l~~ 59 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-TS--CSHTFCSLCIRRCLSN 59 (397)
T ss_pred cCCCcCchhhh-----CccC-CC--CCCchhHHHHHHHHhC
Confidence 58999987662 3332 33 9999999999887643
No 159
>KOG4739|consensus
Probab=37.58 E-value=16 Score=33.22 Aligned_cols=17 Identities=29% Similarity=0.630 Sum_probs=14.1
Q ss_pred CCCcccccccCCccCCC
Q psy15975 69 KCGHRFCFACGENWHDP 85 (312)
Q Consensus 69 ~C~~~fC~~C~~~~H~p 85 (312)
.|+|+||..|....|.+
T Consensus 22 aC~HvfC~~C~k~~~~~ 38 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSPD 38 (233)
T ss_pred echhhhhhhhcccCCcc
Confidence 49999999998877755
No 160
>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=37.25 E-value=11 Score=40.31 Aligned_cols=42 Identities=36% Similarity=0.858 Sum_probs=0.0
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCcc-----cccccCCccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCC
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGHR-----FCFACGENWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPK 117 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~-----fC~~C~~~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~ 117 (312)
.+.|| +|+.. ....+|+ ||.. +|..|+.. .+...||+
T Consensus 655 ~r~Cp--~Cg~~-------t~~~~Cp~CG~~T~~~~~Cp~C~~~----------------------------~~~~~C~~ 697 (900)
T PF03833_consen 655 RRRCP--KCGKE-------TFYNRCPECGSHTEPVYVCPDCGIE----------------------------VEEDECPK 697 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCc--ccCCc-------chhhcCcccCCccccceeccccccc----------------------------cCcccccc
Q ss_pred CCcee
Q psy15975 118 CLVTI 122 (312)
Q Consensus 118 C~~~I 122 (312)
|+...
T Consensus 698 C~~~~ 702 (900)
T PF03833_consen 698 CGRET 702 (900)
T ss_dssp -----
T ss_pred ccccC
No 161
>PRK14065 exodeoxyribonuclease VII small subunit; Provisional
Probab=36.96 E-value=1.5e+02 Score=22.76 Aligned_cols=37 Identities=16% Similarity=0.329 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCcCHHH-HHHHHHHHHHHHHHHHHhhc
Q psy15975 209 VKEKMEEMQQHNMSWIE-VQFLKKAVDILCQCRQTLMY 245 (312)
Q Consensus 209 ~~~~~~~~~~~~~~~~d-~~fl~~a~~~l~~~R~~L~~ 245 (312)
+++-++.|...++|..+ +....+|+..|..|+..|--
T Consensus 34 akeiLe~LndpeisL~eSvkLYkeG~~lL~eAqk~LE~ 71 (86)
T PRK14065 34 LEQAIDRLNDPNLSLKDGMDLYKTAMQELFLAQKLLEN 71 (86)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444556555555554 68889999999999988753
No 162
>PF14149 YhfH: YhfH-like protein
Probab=36.91 E-value=2.3 Score=27.42 Aligned_cols=25 Identities=28% Similarity=0.640 Sum_probs=21.1
Q ss_pred cCCCCCCCCceeEecCCCCceeecC
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKN 135 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~ 135 (312)
-.|.||.||..|+--.-|..++|..
T Consensus 12 p~K~C~~CG~~i~EQ~E~Y~n~C~~ 36 (37)
T PF14149_consen 12 PPKKCTECGKEIEEQAECYGNECDR 36 (37)
T ss_pred CCcccHHHHHHHHHHHHHHhCcCCC
Confidence 4689999999998888888888865
No 163
>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=36.86 E-value=20 Score=32.83 Aligned_cols=37 Identities=32% Similarity=0.775 Sum_probs=15.5
Q ss_pred hhhHHhhhcCCCCCCCCce-eEecCC---CCceeecCCCCCcce
Q psy15975 103 ETSNWIAANTKECPKCLVT-IEKDGG---CNHMVCKNQSCKAEF 142 (312)
Q Consensus 103 ~~~~~i~~~~k~CP~C~~~-IeK~~G---CnhMtC~~~~C~~~F 142 (312)
.+..|+..|. .||.|+.. +.+-+. =--..|.. |+.+|
T Consensus 23 ltE~Wv~~n~-yCP~Cg~~~L~~f~NN~PVaDF~C~~--C~eey 63 (254)
T PF06044_consen 23 LTEDWVAENM-YCPNCGSKPLSKFENNRPVADFYCPN--CNEEY 63 (254)
T ss_dssp HHHHHHHHH----TTT--SS-EE--------EEE-TT--T--EE
T ss_pred HHHHHHHHCC-cCCCCCChhHhhccCCCccceeECCC--CchHH
Confidence 4677988774 89999988 555322 11255665 55444
No 164
>PLN02195 cellulose synthase A
Probab=36.68 E-value=27 Score=38.22 Aligned_cols=29 Identities=28% Similarity=0.639 Sum_probs=24.4
Q ss_pred CCCCceecccCCCCceEcC-CCcccccccC
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CGHRFCFACG 79 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~ 79 (312)
-|+..|..+..+...|-|. |+.-.|..|-
T Consensus 11 ~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy 40 (977)
T PLN02195 11 TCGEEVGVDSNGEAFVACHECSYPLCKACL 40 (977)
T ss_pred ecccccCcCCCCCeEEEeccCCCccccchh
Confidence 5888887776677889999 9999998775
No 165
>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=36.42 E-value=24 Score=22.30 Aligned_cols=12 Identities=25% Similarity=0.827 Sum_probs=6.5
Q ss_pred CCCCCCCceeEe
Q psy15975 113 KECPKCLVTIEK 124 (312)
Q Consensus 113 k~CP~C~~~IeK 124 (312)
..||.|+..++|
T Consensus 27 ~~CP~Cg~~~~r 38 (41)
T smart00834 27 ATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCccee
Confidence 356666655544
No 166
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=36.20 E-value=21 Score=25.19 Aligned_cols=24 Identities=33% Similarity=0.677 Sum_probs=17.9
Q ss_pred hcCCCCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 110 ANTKECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
.+.-.||.|+.+... |-.|.. ||+
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~--CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPS--CGY 48 (57)
T ss_pred CcceECCCCCCccCC-----eEECCC--CCc
Confidence 466789999999854 777766 774
No 167
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.85 E-value=27 Score=32.19 Aligned_cols=30 Identities=17% Similarity=0.421 Sum_probs=24.0
Q ss_pred hcCCCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 110 ANTKECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
.+.+-||.|+.+.....|=..+.|.. |+..
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~--c~~~ 126 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPH--CRER 126 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCC--CCCE
Confidence 45799999999988765557789998 9843
No 168
>KOG2041|consensus
Probab=35.74 E-value=56 Score=34.74 Aligned_cols=53 Identities=26% Similarity=0.543 Sum_probs=32.8
Q ss_pred CHHHHHHHHHHHHHHHHhhCCC-----ceecCCcCCCCceecccCCCCceEcC-CCccc--ccccCCc
Q psy15975 22 DPKVKLKYQHLITNSFVECNRL-----LRWCPSPDCNNAIKVQHVEARPVVCK-CGHRF--CFACGEN 81 (312)
Q Consensus 22 ~~e~~~~y~~~~~~~~v~~~~~-----~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~f--C~~C~~~ 81 (312)
|++..++|+.+.++-|-+..+. .+-|. -|+..|. +....|+ |...| |..=+.+
T Consensus 1090 ~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~--~cg~~i~-----~~~~~c~ec~~kfP~CiasG~p 1150 (1189)
T KOG2041|consen 1090 DDAEKQEYENLAFRIFSKNPPVDPNSAKVDCS--VCGAKID-----PYDLQCSECQTKFPVCIASGRP 1150 (1189)
T ss_pred CHHHHHHHHHHHHHHhccCCCCCCCccceeee--ecCCcCC-----ccCCCChhhcCcCceeeccCCc
Confidence 5667899999999888876542 22232 2444443 2345788 87776 6655544
No 169
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.43 E-value=18 Score=26.23 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=13.7
Q ss_pred cCCCCCCCCceeEecCC
Q psy15975 111 NTKECPKCLVTIEKDGG 127 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~G 127 (312)
.+.+||.|+++++...-
T Consensus 6 ~~v~CP~Cgkpv~w~~~ 22 (65)
T COG3024 6 ITVPCPTCGKPVVWGEE 22 (65)
T ss_pred ccccCCCCCCccccccc
Confidence 46799999999988544
No 170
>KOG0250|consensus
Probab=35.11 E-value=3.8e+02 Score=29.93 Aligned_cols=45 Identities=18% Similarity=0.233 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHhhccceeeeecccCccchhHHHHHHHHH
Q psy15975 226 VQFLKKAVDILCQCRQTLMYTYVFAYYLRKNNQSVLFEDNQKDLE 270 (312)
Q Consensus 226 ~~fl~~a~~~l~~~R~~L~~sY~~~yy~~~~~~~~~fe~~Q~~le 270 (312)
..-+++-...|.....-+.|+.||-+=.+=++..+.|...|..+-
T Consensus 254 ~~~~e~~~~~l~~Lk~k~~W~~V~~~~~ql~~~~~~i~~~qek~~ 298 (1074)
T KOG0250|consen 254 LEQLEDLKENLEQLKAKMAWAWVNEVERQLNNQEEEIKKKQEKVD 298 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566677777789999998876554444444444444333
No 171
>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=34.64 E-value=33 Score=34.81 Aligned_cols=34 Identities=24% Similarity=0.562 Sum_probs=25.3
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcc-----eecccCCC
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAE-----FCWVCLGP 149 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~-----FCw~C~~~ 149 (312)
.||+|..+..--..=|.+.|.. ||+. .|-.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~--Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHY--CGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCC--CcCcCCCCCCCCCCCCC
Confidence 5889988876544556889988 9866 58888764
No 172
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=34.00 E-value=38 Score=24.39 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=5.6
Q ss_pred CCCCCCCceeEe
Q psy15975 113 KECPKCLVTIEK 124 (312)
Q Consensus 113 k~CP~C~~~IeK 124 (312)
-.||+|+....-
T Consensus 54 L~Cp~c~r~YPI 65 (68)
T PF03966_consen 54 LICPECGREYPI 65 (68)
T ss_dssp EEETTTTEEEEE
T ss_pred EEcCCCCCEEeC
Confidence 345555544433
No 173
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=33.98 E-value=31 Score=30.14 Aligned_cols=25 Identities=32% Similarity=0.768 Sum_probs=20.8
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
.||.|+.+..+. +.|.|.|.. |++.
T Consensus 151 ~~~~~g~~~~~~-~~~~~~c~~--~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVKK-GENELKCPN--CGNI 175 (189)
T ss_pred EccccCCceEEC-CCCEEECCC--CCCE
Confidence 699999999884 459999998 8853
No 174
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=33.29 E-value=22 Score=32.54 Aligned_cols=47 Identities=28% Similarity=0.584 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHHH-HH---hhCCCceecCCcCCCCceecccC-----CCCceEcC-CCc
Q psy15975 22 DPKVKLKYQHLITNS-FV---ECNRLLRWCPSPDCNNAIKVQHV-----EARPVVCK-CGH 72 (312)
Q Consensus 22 ~~e~~~~y~~~~~~~-~v---~~~~~~~~CP~~~C~~~i~~~~~-----~~~~v~C~-C~~ 72 (312)
||+++..|+++.... -+ .-.+ .-|. +|...+..... +...|+|| ||.
T Consensus 173 ~~ell~~yeri~~~~kg~gvvpl~g--~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 173 DPELLSEYERIRKNKKGVGVVPLEG--RVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred CHHHHHHHHHHHhcCCCceEEeecC--Cccc--CCeeeecHHHHHHHhcCCCCccCCccch
Confidence 799999999988755 11 1122 2355 57766654321 45678888 875
No 175
>KOG3091|consensus
Probab=32.72 E-value=2.7e+02 Score=28.31 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=23.9
Q ss_pred eeecccCccchhHHHHHHHHHHHHHHHHHHHhhc
Q psy15975 250 AYYLRKNNQSVLFEDNQKDLESATEKLSEYLERD 283 (312)
Q Consensus 250 ~yy~~~~~~~~~fe~~Q~~le~~~e~Ls~~le~~ 283 (312)
.||++.....++-|+++.+. .+++.|+..|..+
T Consensus 456 ~~~iD~~~~~e~~e~lt~~~-e~l~~Lv~Ilk~d 488 (508)
T KOG3091|consen 456 SYWIDFDKLIEMKEHLTQEQ-EALTKLVNILKGD 488 (508)
T ss_pred ceeechhhhHHHHHHHHHHH-HHHHHHHHHHHhH
Confidence 56777777788888888877 5666777666544
No 176
>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=32.31 E-value=51 Score=20.26 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=22.1
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
.|+.|++.+.-..|=..+.|+. |+.
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~--C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCAL--CQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCC--CCe
Confidence 6999999999999999999987 763
No 177
>KOG0320|consensus
Probab=31.83 E-value=11 Score=32.94 Aligned_cols=35 Identities=26% Similarity=0.562 Sum_probs=24.4
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
+-.||-|...+.+..- ...+|||-||-.|.+.--.
T Consensus 131 ~~~CPiCl~~~sek~~------vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVP------VSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred ccCCCceecchhhccc------cccccchhHHHHHHHHHHH
Confidence 4589999888877543 1124888888888877544
No 178
>PF15616 TerY-C: TerY-C metal binding domain
Probab=30.65 E-value=42 Score=27.87 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=9.3
Q ss_pred cCCCCCCCCcee
Q psy15975 111 NTKECPKCLVTI 122 (312)
Q Consensus 111 ~~k~CP~C~~~I 122 (312)
..--||.|+...
T Consensus 76 g~PgCP~CGn~~ 87 (131)
T PF15616_consen 76 GAPGCPHCGNQY 87 (131)
T ss_pred CCCCCCCCcChh
Confidence 347899999874
No 179
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=29.84 E-value=25 Score=25.69 Aligned_cols=12 Identities=42% Similarity=0.797 Sum_probs=7.8
Q ss_pred CCCCCCCceeEe
Q psy15975 113 KECPKCLVTIEK 124 (312)
Q Consensus 113 k~CP~C~~~IeK 124 (312)
-.||.|+.+|.-
T Consensus 56 G~CP~C~~~i~~ 67 (70)
T PF11793_consen 56 GECPYCSSPISW 67 (70)
T ss_dssp EE-TTT-SEEEG
T ss_pred cCCcCCCCeeeE
Confidence 469999999853
No 180
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=29.61 E-value=9.8 Score=36.48 Aligned_cols=49 Identities=24% Similarity=0.704 Sum_probs=33.2
Q ss_pred CCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCCCCCCCCC----CCchhHH
Q psy15975 114 ECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCN----RYDEEEA 168 (312)
Q Consensus 114 ~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~~~~~C~----~~~~~~~ 168 (312)
-||-|-.+|.-.+. |..-|. ||++.|--|.......-.+ .|+ .|++++.
T Consensus 16 ~cplcie~mditdk-nf~pc~---cgy~ic~fc~~~irq~lng--rcpacrr~y~denv 68 (480)
T COG5175 16 YCPLCIEPMDITDK-NFFPCP---CGYQICQFCYNNIRQNLNG--RCPACRRKYDDENV 68 (480)
T ss_pred cCcccccccccccC-CcccCC---cccHHHHHHHHHHHhhccC--CChHhhhhccccce
Confidence 49999988866543 778898 9998888887666543222 455 3665543
No 181
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=29.34 E-value=44 Score=26.87 Aligned_cols=36 Identities=22% Similarity=0.416 Sum_probs=27.0
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCC
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGP 149 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~ 149 (312)
+.+.|..|+.+.-.-++.. ..|.. |++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~--C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVD--CKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETT--TTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCc--CCccccCccCCc
Confidence 5679999998865555554 78887 999999999887
No 182
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.32 E-value=44 Score=35.65 Aligned_cols=13 Identities=8% Similarity=0.181 Sum_probs=7.5
Q ss_pred CHHHHHHHHHHHH
Q psy15975 22 DPKVKLKYQHLIT 34 (312)
Q Consensus 22 ~~e~~~~y~~~~~ 34 (312)
++.+++.-++.+.
T Consensus 406 S~~Ll~~i~~~l~ 418 (730)
T COG1198 406 SPALLEAIRKTLE 418 (730)
T ss_pred CHHHHHHHHHHHh
Confidence 4666666655544
No 183
>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=29.16 E-value=52 Score=21.51 Aligned_cols=11 Identities=64% Similarity=1.570 Sum_probs=9.0
Q ss_pred CceEcC-CCccc
Q psy15975 64 RPVVCK-CGHRF 74 (312)
Q Consensus 64 ~~v~C~-C~~~f 74 (312)
..+.|+ ||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 469999 99876
No 184
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.16 E-value=40 Score=29.72 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=20.4
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
-.|++|+.+.++ .=+.|+|++ ||+
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~--Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPN--CGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCC--CCC
Confidence 389999999999 447899998 885
No 185
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=29.09 E-value=28 Score=37.74 Aligned_cols=25 Identities=52% Similarity=1.205 Sum_probs=20.2
Q ss_pred CCCCCCCc-eeEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLV-TIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~-~IeK~~GCnhMtC~~~~C~~~ 141 (312)
-.||-|+. .||..|||| ||++ |+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~--c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTN--CGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccc--hhhh
Confidence 48999976 578899999 6887 8754
No 186
>KOG3800|consensus
Probab=28.89 E-value=2.3e+02 Score=26.72 Aligned_cols=39 Identities=23% Similarity=0.522 Sum_probs=29.2
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHG 154 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~ 154 (312)
+.||+|++-+-.|..=--|.=. |+|..|=.|....-..|
T Consensus 1 ~~Cp~CKt~~Y~np~lk~~in~---C~H~lCEsCvd~iF~~g 39 (300)
T KOG3800|consen 1 QACPKCKTDRYLNPDLKLMINE---CGHRLCESCVDRIFSLG 39 (300)
T ss_pred CCCcccccceecCccceeeecc---ccchHHHHHHHHHHhcC
Confidence 4699999999888765555443 99999999977655444
No 187
>KOG2879|consensus
Probab=28.77 E-value=29 Score=32.42 Aligned_cols=32 Identities=25% Similarity=0.650 Sum_probs=20.9
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCC
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGP 149 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~ 149 (312)
.++.||-|+.+= -+.|+=.. |+|-|||.|...
T Consensus 238 ~~~~C~~Cg~~P-----tiP~~~~~--C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 238 SDTECPVCGEPP-----TIPHVIGK--CGHIYCYYCIAT 269 (298)
T ss_pred CCceeeccCCCC-----CCCeeecc--ccceeehhhhhh
Confidence 457899998652 12222222 888999999775
No 188
>KOG3002|consensus
Probab=28.57 E-value=30 Score=32.77 Aligned_cols=33 Identities=30% Similarity=0.552 Sum_probs=25.1
Q ss_pred CCceecCCcCCCCceecccCCCCceEcCCCcccccccCCc
Q psy15975 42 RLLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGEN 81 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~ 81 (312)
..+.-|| -|...+.+ +.+.|+-||..|.+|...
T Consensus 46 ~~lleCP--vC~~~l~~-----Pi~QC~nGHlaCssC~~~ 78 (299)
T KOG3002|consen 46 LDLLDCP--VCFNPLSP-----PIFQCDNGHLACSSCRTK 78 (299)
T ss_pred hhhccCc--hhhccCcc-----cceecCCCcEehhhhhhh
Confidence 3566788 48877754 468899999999999853
No 189
>PRK05580 primosome assembly protein PriA; Validated
Probab=28.41 E-value=47 Score=35.04 Aligned_cols=35 Identities=23% Similarity=0.564 Sum_probs=25.9
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcc-----eecccCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAE-----FCWVCLGP 149 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~-----FCw~C~~~ 149 (312)
-.||+|..+..-...=+.+.|.. ||+. .|-.|++.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~--Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHH--CGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCC--CcCCCCCCCCCCCCcCC
Confidence 36999988876544457799988 9875 58888665
No 190
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=28.01 E-value=19 Score=24.59 Aligned_cols=34 Identities=21% Similarity=0.614 Sum_probs=17.0
Q ss_pred CCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 115 CPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 115 CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
||.|-..+ -..|=+..-|. ||++.|.-|......
T Consensus 1 cp~C~e~~-d~~d~~~~PC~---Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCE---CGFQICRFCYHDILE 34 (48)
T ss_dssp -TTTS-B---CCCTT--SST---TS----HHHHHHHTT
T ss_pred CCCccccc-ccCCCccccCc---CCCcHHHHHHHHHHh
Confidence 67777777 33444777887 999999999666554
No 191
>PHA02325 hypothetical protein
Probab=27.99 E-value=30 Score=25.07 Aligned_cols=12 Identities=50% Similarity=0.908 Sum_probs=9.5
Q ss_pred cCCCCCCCCcee
Q psy15975 111 NTKECPKCLVTI 122 (312)
Q Consensus 111 ~~k~CP~C~~~I 122 (312)
++|.||+|+..-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 578999998764
No 192
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.39 E-value=38 Score=39.49 Aligned_cols=27 Identities=30% Similarity=0.844 Sum_probs=23.4
Q ss_pred CCCCCCce------eEecCCCCceeecCCCCCcceec
Q psy15975 114 ECPKCLVT------IEKDGGCNHMVCKNQSCKAEFCW 144 (312)
Q Consensus 114 ~CP~C~~~------IeK~~GCnhMtC~~~~C~~~FCw 144 (312)
.||.|+.. ++..+||. +|.. ||+.=|-
T Consensus 1706 ~cp~c~~~~~~~~~~~~~~gc~--~c~~--cg~s~c~ 1738 (1740)
T PRK08332 1706 YCPVCYEKEGKLVELRMESGCA--TCPV--CGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCcceeeEecCCce--eCCC--CCCcccc
Confidence 49999999 88899997 9998 9977663
No 193
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.19 E-value=48 Score=34.96 Aligned_cols=35 Identities=17% Similarity=0.387 Sum_probs=23.4
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcc----eecccCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAE----FCWVCLGP 149 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~----FCw~C~~~ 149 (312)
-.||+|..+..-..+=+.|.|.. ||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~--CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRW--CGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCC--CcCCCcCccCCCCcCC
Confidence 47888887777655556788887 8863 35555443
No 194
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.87 E-value=40 Score=22.91 Aligned_cols=37 Identities=24% Similarity=0.526 Sum_probs=26.0
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEP 152 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~ 152 (312)
.+.|+.|+...-. .=..-.|.. ||.-||..|......
T Consensus 2 ~~~C~~C~~~F~~--~~rk~~Cr~--Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 2 ASSCMGCGKPFTL--TRRRHHCRN--CGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcCcccCccccC--CccccccCc--CcCCcChHHcCCeee
Confidence 3578888766544 233466777 999999999886543
No 195
>KOG3803|consensus
Probab=26.77 E-value=1.3e+02 Score=31.48 Aligned_cols=77 Identities=17% Similarity=0.324 Sum_probs=45.7
Q ss_pred HHHHHHHhhCCCceecCCcCCCCceecccC---------------------------CCCceEcC---CCcccccccCCc
Q psy15975 32 LITNSFVECNRLLRWCPSPDCNNAIKVQHV---------------------------EARPVVCK---CGHRFCFACGEN 81 (312)
Q Consensus 32 ~~~~~~v~~~~~~~~CP~~~C~~~i~~~~~---------------------------~~~~v~C~---C~~~fC~~C~~~ 81 (312)
..+++.+..+..-.-||.|+|..--...+. ..+.++|+ |...==.+=+..
T Consensus 677 ks~Rslma~~sqeLkCPTPGCDGSGHiTGnYasHRSLSGCPRa~k~gvkv~qtke~keD~elrCpv~GC~GqGHIsGkyt 756 (968)
T KOG3803|consen 677 KSLRSLMAAGSQELKCPTPGCDGSGHITGNYASHRSLSGCPRAKKSGVKVAQTKEDKEDPELRCPVPGCDGQGHISGKYT 756 (968)
T ss_pred HHHHHHHhcccccccCCCCCCCCCCcccccccccccccCCCCCCCCCceeccchhhccCceeecCCCCcCCcccccCccc
Confidence 345566655554557999999875433220 23568888 654444444556
Q ss_pred cCCCCC-chhhHHHhhhcccchhhhHHh
Q psy15975 82 WHDPVR-CSLLRRWIKKCDDDSETSNWI 108 (312)
Q Consensus 82 ~H~p~~-C~~~~~w~~~~~~~~~~~~~i 108 (312)
.|+.++ |+.+.+-.+...-...+..|.
T Consensus 757 SHRSaSGCPlAakrqke~~lngss~swk 784 (968)
T KOG3803|consen 757 SHRSASGCPLAAKRQKEGKLNGSSFSWK 784 (968)
T ss_pred ccccccCCcchHHHHhcccccCCCcccc
Confidence 687765 888766544333345556664
No 196
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.48 E-value=43 Score=25.32 Aligned_cols=34 Identities=26% Similarity=0.623 Sum_probs=23.3
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHG 154 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~ 154 (312)
..||.|++...-..- .+=-..+|-.|+|-|-..|
T Consensus 2 llCP~C~v~l~~~~r--------s~vEiD~CPrCrGVWLDrG 35 (88)
T COG3809 2 LLCPICGVELVMSVR--------SGVEIDYCPRCRGVWLDRG 35 (88)
T ss_pred cccCcCCceeeeeee--------cCceeeeCCccccEeecch
Confidence 469999887754321 1245677888999997765
No 197
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=25.93 E-value=57 Score=22.33 Aligned_cols=27 Identities=30% Similarity=0.564 Sum_probs=19.1
Q ss_pred CCCCCCCCceeEecCC--------CCceeecCCCCCcc
Q psy15975 112 TKECPKCLVTIEKDGG--------CNHMVCKNQSCKAE 141 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~G--------CnhMtC~~~~C~~~ 141 (312)
.-.||+|+.-..-|++ =-+=+|. ||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCk---CGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCK---CGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeec---cccc
Confidence 4589999988777654 3345787 8754
No 198
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=25.52 E-value=50 Score=27.47 Aligned_cols=27 Identities=30% Similarity=0.658 Sum_probs=21.4
Q ss_pred CCCCCCCce---eEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVT---IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~---IeK~~GCnhMtC~~~~C~~~ 141 (312)
-.||.|+.| +.|.+.=..+.|.. ||..
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~A--CGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEA--CGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEeccc--CCCC
Confidence 589999876 77776666789998 9864
No 199
>PF07417 Crl: Transcriptional regulator Crl; InterPro: IPR009986 This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [].These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. They also stimulate RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.; GO: 0016987 sigma factor activity, 0045893 positive regulation of transcription, DNA-dependent, 0005737 cytoplasm; PDB: 3RPJ_A.
Probab=25.49 E-value=1.5e+02 Score=24.42 Aligned_cols=40 Identities=30% Similarity=0.518 Sum_probs=21.9
Q ss_pred hhccceeeeecccCc--cchhHHHHHHHHHHHHH----HHHHHHhh
Q psy15975 243 LMYTYVFAYYLRKNN--QSVLFEDNQKDLESATE----KLSEYLER 282 (312)
Q Consensus 243 L~~sY~~~yy~~~~~--~~~~fe~~Q~~le~~~e----~Ls~~le~ 282 (312)
..|+|-+|.|-..|+ ...|=...|++++...+ +|+.+|+.
T Consensus 65 F~y~Y~~Glydk~G~W~~~~i~~~~~~~v~~Tl~~Fh~kL~~~L~~ 110 (125)
T PF07417_consen 65 FEYRYQFGLYDKEGNWQAEKIKKEVQEEVERTLRDFHQKLVELLEE 110 (125)
T ss_dssp EEEEEEEEEE-TTS-EES----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEeeccccCCCCeeecCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999988775 12233555555555554 55555555
No 200
>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=25.26 E-value=88 Score=18.35 Aligned_cols=24 Identities=21% Similarity=0.576 Sum_probs=20.2
Q ss_pred CCCCCceeEecCCCCceeecCCCCCc
Q psy15975 115 CPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 115 CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
|-+|++.+.-..|=.++.|.. |++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~--C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCAC--CHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCc--cCc
Confidence 668899999999999999987 764
No 201
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=25.22 E-value=52 Score=23.48 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=19.5
Q ss_pred ceecCCcCCCCceecccCCCCceEcC-CCc
Q psy15975 44 LRWCPSPDCNNAIKVQHVEARPVVCK-CGH 72 (312)
Q Consensus 44 ~~~CP~~~C~~~i~~~~~~~~~v~C~-C~~ 72 (312)
+=-|.+.+|..+++-+-.....-.|| |+.
T Consensus 18 VW~Ct~e~C~gWmR~nFs~~~~p~CPlC~s 47 (59)
T PF14169_consen 18 VWECTSEDCNGWMRDNFSFEEEPVCPLCKS 47 (59)
T ss_pred eEEeCCCCCCcccccccccCCCccCCCcCC
Confidence 34599999999997654433445666 654
No 202
>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=25.01 E-value=27 Score=24.75 Aligned_cols=34 Identities=29% Similarity=0.585 Sum_probs=16.9
Q ss_pred CCCCCCCCceeEecCCCCceeecCCCCCcceec-----ccCCCCCCCC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCW-----VCLGPWEPHG 154 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw-----~C~~~w~~h~ 154 (312)
+.+||.|+.+++-..+=.+ .-||- +=|+.|...+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~---------rPFCS~RCk~iDLg~W~~e~ 40 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPF---------RPFCSERCKLIDLGRWANEE 40 (57)
T ss_dssp EEE-TTT--EEE-SSSSS-----------SSSSHHHHHHHHS-SSSSS
T ss_pred cccCCCCCCeecccCCCCc---------CCcccHhhcccCHHHHhcCC
Confidence 4689999999988555322 23444 4577787543
No 203
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.97 E-value=24 Score=32.71 Aligned_cols=18 Identities=39% Similarity=0.969 Sum_probs=13.7
Q ss_pred CceEcC-CCcccccccCCc
Q psy15975 64 RPVVCK-CGHRFCFACGEN 81 (312)
Q Consensus 64 ~~v~C~-C~~~fC~~C~~~ 81 (312)
....|. |||.||+.|-..
T Consensus 226 ~~ps~t~CgHlFC~~Cl~~ 244 (271)
T COG5574 226 EVPSCTPCGHLFCLSCLLI 244 (271)
T ss_pred CCcccccccchhhHHHHHH
Confidence 345677 999999988643
No 204
>smart00532 LIGANc Ligase N family.
Probab=24.81 E-value=49 Score=33.10 Aligned_cols=24 Identities=25% Similarity=0.671 Sum_probs=18.2
Q ss_pred CCCCCCCCceeEecCCCCceeecC
Q psy15975 112 TKECPKCLVTIEKDGGCNHMVCKN 135 (312)
Q Consensus 112 ~k~CP~C~~~IeK~~GCnhMtC~~ 135 (312)
-..||.|+..+.+.+|=-++.|.+
T Consensus 399 P~~CP~C~s~l~~~~~~~~~~C~n 422 (441)
T smart00532 399 PTHCPSCGSELVREEGEVDIRCPN 422 (441)
T ss_pred CCCCCCCCCEeEecCCceEEEeCC
Confidence 368999999998866546677764
No 205
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=24.72 E-value=53 Score=26.36 Aligned_cols=26 Identities=27% Similarity=0.629 Sum_probs=21.2
Q ss_pred CCCCCCCce---eEecCCCCceeecCCCCCc
Q psy15975 113 KECPKCLVT---IEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 113 k~CP~C~~~---IeK~~GCnhMtC~~~~C~~ 140 (312)
-.||.|+.| ++|.++=.-|.|.. ||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~a--CGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEA--CGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccc--cCC
Confidence 489999876 77777777789998 985
No 206
>KOG4684|consensus
Probab=24.67 E-value=56 Score=29.47 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=13.3
Q ss_pred CCceecCCcCCCCceecc
Q psy15975 42 RLLRWCPSPDCNNAIKVQ 59 (312)
Q Consensus 42 ~~~~~CP~~~C~~~i~~~ 59 (312)
....-||.|+|.++|..+
T Consensus 136 SqRIACPRpnCkRiInL~ 153 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLD 153 (275)
T ss_pred cceeccCCCCcceeeecC
Confidence 345579999999988654
No 207
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.49 E-value=33 Score=24.02 Aligned_cols=18 Identities=39% Similarity=0.796 Sum_probs=9.4
Q ss_pred CCCCceecccCCCCceEcC-CC
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CG 71 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~ 71 (312)
-|+..+...+ ..|.|+ ||
T Consensus 10 ~Cg~~~~~~d---DiVvCp~Cg 28 (54)
T PF14446_consen 10 VCGKKFKDGD---DIVVCPECG 28 (54)
T ss_pred hhCCcccCCC---CEEECCCCC
Confidence 4776665432 245555 44
No 208
>KOG2807|consensus
Probab=24.37 E-value=51 Score=31.59 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=24.4
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCCcceecccCCCCC
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPWE 151 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~~FCw~C~~~w~ 151 (312)
+...|..|+ ..+.+=.-.+|.. |+..||-.|-.-..
T Consensus 329 ~~~~Cf~C~---~~~~~~~~y~C~~--Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 329 GSRFCFACQ---GELLSSGRYRCES--CKNVFCLDCDVFIH 364 (378)
T ss_pred CCcceeeec---cccCCCCcEEchh--ccceeeccchHHHH
Confidence 345699992 2223334578988 99999999966553
No 209
>KOG0824|consensus
Probab=24.20 E-value=26 Score=33.09 Aligned_cols=14 Identities=29% Similarity=1.008 Sum_probs=11.8
Q ss_pred CCCCcceecccCCC
Q psy15975 136 QSCKAEFCWVCLGP 149 (312)
Q Consensus 136 ~~C~~~FCw~C~~~ 149 (312)
+.|+|.|||+|.+-
T Consensus 23 l~C~HkFCyiCiKG 36 (324)
T KOG0824|consen 23 LYCFHKFCYICIKG 36 (324)
T ss_pred ccccchhhhhhhcc
Confidence 46999999999764
No 210
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=24.12 E-value=63 Score=30.06 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=11.0
Q ss_pred cCCCCCCCCceeEec
Q psy15975 111 NTKECPKCLVTIEKD 125 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~ 125 (312)
..-|||+|+....-.
T Consensus 208 k~~PCPKCg~et~eT 222 (314)
T PF06524_consen 208 KPIPCPKCGYETQET 222 (314)
T ss_pred CCCCCCCCCCccccc
Confidence 346999999887543
No 211
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=24.07 E-value=42 Score=21.03 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=9.1
Q ss_pred CCCCCCCceeEec
Q psy15975 113 KECPKCLVTIEKD 125 (312)
Q Consensus 113 k~CP~C~~~IeK~ 125 (312)
-.||+|+.+|.-+
T Consensus 5 ~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 5 VECPNCGRPVAAS 17 (33)
T ss_dssp EE-TTTSSEEEGG
T ss_pred EECCCCcCCcchh
Confidence 3699999988654
No 212
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.54 E-value=78 Score=20.44 Aligned_cols=7 Identities=57% Similarity=1.269 Sum_probs=4.8
Q ss_pred CCCCCCc
Q psy15975 114 ECPKCLV 120 (312)
Q Consensus 114 ~CP~C~~ 120 (312)
+||+|+.
T Consensus 2 ~Cp~C~~ 8 (40)
T smart00440 2 PCPKCGN 8 (40)
T ss_pred cCCCCCC
Confidence 5777764
No 213
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=23.45 E-value=44 Score=27.62 Aligned_cols=17 Identities=35% Similarity=0.444 Sum_probs=12.1
Q ss_pred cCCCCCCCCceeEecCC
Q psy15975 111 NTKECPKCLVTIEKDGG 127 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~G 127 (312)
..|.||+|++.|--.++
T Consensus 109 GeK~C~~C~tGiYS~e~ 125 (128)
T PF11682_consen 109 GEKYCPKCGTGIYSIEV 125 (128)
T ss_pred cCEecCCCCCcccceec
Confidence 35899999988754443
No 214
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=23.43 E-value=57 Score=27.27 Aligned_cols=28 Identities=32% Similarity=0.655 Sum_probs=22.2
Q ss_pred CCCCCCCCce---eEecCCCCceeecCCCCCcc
Q psy15975 112 TKECPKCLVT---IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 112 ~k~CP~C~~~---IeK~~GCnhMtC~~~~C~~~ 141 (312)
.-.||.|+.| ++|.+.=..+.|.. ||..
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~A--CGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEA--CGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEccc--CCCC
Confidence 3589999876 77777767799998 9864
No 215
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=23.41 E-value=48 Score=24.57 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=5.7
Q ss_pred CCCCCCcee
Q psy15975 114 ECPKCLVTI 122 (312)
Q Consensus 114 ~CP~C~~~I 122 (312)
.||.|+...
T Consensus 3 ~CP~Cg~~a 11 (72)
T PRK09678 3 HCPLCQHAA 11 (72)
T ss_pred cCCCCCCcc
Confidence 577776554
No 216
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 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 is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=23.03 E-value=4e+02 Score=21.36 Aligned_cols=93 Identities=14% Similarity=0.220 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCcCHHHHHHHHHHHHHHHHHHHHhhccceeeeec----c
Q psy15975 179 RAALQRYLFYCNRYMNHMQSLKFEHKLYASVKEKMEEMQQHNMSWIEVQFLKKAVDILCQCRQTLMYTYVFAYYL----R 254 (312)
Q Consensus 179 ~~~l~ry~~y~~r~~~h~~s~~~e~~l~~~~~~~~~~~~~~~~~~~d~~fl~~a~~~l~~~R~~L~~sY~~~yy~----~ 254 (312)
.+.-.||..||+|=. .... .++.-|..+...++ ..+-..+..|+ ..||||==++=+..++. +
T Consensus 9 eeF~ary~~~F~~~~--iD~w--------e~rrglN~l~~~Dl-VP~P~ii~aAL---rAcRRvND~a~AVR~lE~iK~K 74 (108)
T PF02284_consen 9 EEFDARYEKYFNRPD--IDGW--------ELRRGLNNLFGYDL-VPEPKIIEAAL---RACRRVNDFALAVRILEGIKDK 74 (108)
T ss_dssp HHHHHHHHHHHH-TT----HH--------HHHHHHHHHTTSSB----HHHHHHHH---HHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCcc--ccHH--------HHHHHHHHHhcccc-CCChHHHHHHH---HHHHHhhhHHHHHHHHHHHHHH
Confidence 345578888888511 1111 12233444544331 22334555554 78999988888888874 2
Q ss_pred cCccchhHHHHHHHHHHHHHHHHHHHhhcCC
Q psy15975 255 KNNQSVLFEDNQKDLESATEKLSEYLERDIT 285 (312)
Q Consensus 255 ~~~~~~~fe~~Q~~le~~~e~Ls~~le~~~~ 285 (312)
-+++.+++.+..++|.-..+.|.-.+-+++-
T Consensus 75 ~~~~~~~Y~~~lqElkPtl~ELGI~t~EeLg 105 (108)
T PF02284_consen 75 CGNKKEIYPYILQELKPTLEELGIPTPEELG 105 (108)
T ss_dssp TTT-TTHHHHHHHHHHHHHHHHT---TTTTT
T ss_pred ccChHHHHHHHHHHHhhHHHHhCCCCHHHhC
Confidence 3445569999999999999999876655543
No 217
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=22.91 E-value=31 Score=23.27 Aligned_cols=18 Identities=44% Similarity=1.043 Sum_probs=15.1
Q ss_pred cccccccCCccCCCCCch
Q psy15975 72 HRFCFACGENWHDPVRCS 89 (312)
Q Consensus 72 ~~fC~~C~~~~H~p~~C~ 89 (312)
..||+.|+...|.-..|+
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 469999999999887775
No 218
>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=22.76 E-value=61 Score=22.58 Aligned_cols=22 Identities=36% Similarity=0.777 Sum_probs=15.7
Q ss_pred cCCCCCCCCceeEecCCCCceeecCCCCC
Q psy15975 111 NTKECPKCLVTIEKDGGCNHMVCKNQSCK 139 (312)
Q Consensus 111 ~~k~CP~C~~~IeK~~GCnhMtC~~~~C~ 139 (312)
+.-.||.|+.+.. .|..|.. ||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~~--cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCPS--CG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCTT--TB
T ss_pred ceeeeccCCCEec-----ccEeeCC--CC
Confidence 5678999998773 4666665 65
No 219
>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=22.58 E-value=48 Score=26.74 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=6.3
Q ss_pred cccccCCccC
Q psy15975 74 FCFACGENWH 83 (312)
Q Consensus 74 fC~~C~~~~H 83 (312)
-|..|+.+-+
T Consensus 87 ~CM~C~~pLT 96 (114)
T PF11023_consen 87 ACMHCKEPLT 96 (114)
T ss_pred ccCcCCCcCc
Confidence 3777776544
No 220
>PF15605 Toxin_52: Putative toxin 52
Probab=22.47 E-value=4e+02 Score=21.17 Aligned_cols=53 Identities=25% Similarity=0.211 Sum_probs=43.8
Q ss_pred CcCHHHHHHHHHHHHHHHHHHHHhhccceeeeecccCc-cchhHHHHHHHHHHHHHHHHH
Q psy15975 220 NMSWIEVQFLKKAVDILCQCRQTLMYTYVFAYYLRKNN-QSVLFEDNQKDLESATEKLSE 278 (312)
Q Consensus 220 ~~~~~d~~fl~~a~~~l~~~R~~L~~sY~~~yy~~~~~-~~~~fe~~Q~~le~~~e~Ls~ 278 (312)
|..|.-++=+.+|..-|...+++|.-+ +.+.+ ....-+++|..|..++-.|-.
T Consensus 43 GgywdHlqEm~da~~GL~n~~~~le~~------L~np~l~~~~r~~lq~~l~ea~~~l~k 96 (103)
T PF15605_consen 43 GGYWDHLQEMQDAYRGLVNRKRTLEGS------LKNPNLSGRTRELLQSKLNEANNYLDK 96 (103)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHh------cCCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 678998999999999999999999998 66555 457788899988888766643
No 221
>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=22.31 E-value=45 Score=30.20 Aligned_cols=7 Identities=14% Similarity=0.624 Sum_probs=3.1
Q ss_pred CceeecC
Q psy15975 129 NHMVCKN 135 (312)
Q Consensus 129 nhMtC~~ 135 (312)
+-..|+.
T Consensus 34 ~v~~C~~ 40 (236)
T PF04981_consen 34 EVTICPK 40 (236)
T ss_pred CceECCC
Confidence 3344444
No 222
>PRK12495 hypothetical protein; Provisional
Probab=21.93 E-value=1.7e+02 Score=26.54 Aligned_cols=27 Identities=26% Similarity=0.699 Sum_probs=18.1
Q ss_pred CceecCCcCCCCceecccCCCCceEcCCCcccccccCCc
Q psy15975 43 LLRWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGEN 81 (312)
Q Consensus 43 ~~~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~ 81 (312)
...+|| +|+..|... . |..||..|...
T Consensus 41 sa~hC~--~CG~PIpa~---p-------G~~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCD--ECGDPIFRH---D-------GQEFCPTCQQP 67 (226)
T ss_pred chhhcc--cccCcccCC---C-------CeeECCCCCCc
Confidence 556898 699998732 1 55666666654
No 223
>KOG3183|consensus
Probab=21.84 E-value=46 Score=30.42 Aligned_cols=58 Identities=26% Similarity=0.652 Sum_probs=36.4
Q ss_pred eecCCcCCCCceecccCCCCceEcC-CCcccccccCC-ccCCCCCchhhHHHhhhcccchhhhHHhhhcCCCCCCCCcee
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCK-CGHRFCFACGE-NWHDPVRCSLLRRWIKKCDDDSETSNWIAANTKECPKCLVTI 122 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~-C~~~fC~~C~~-~~H~p~~C~~~~~w~~~~~~~~~~~~~i~~~~k~CP~C~~~I 122 (312)
+.|-.+.|... +-..++|. |+..||..-.. +.| .|+.... +....+.||.|..||
T Consensus 9 kHCs~~~Ckql------DFLPf~Cd~C~~~FC~eHrsye~H---~Cp~~~~--------------~~~~v~icp~cs~pv 65 (250)
T KOG3183|consen 9 KHCSVPYCKQL------DFLPFKCDGCSGIFCLEHRSYESH---HCPKGLR--------------IDVQVPICPLCSKPV 65 (250)
T ss_pred cccCcchhhhc------cccceeeCCccchhhhccchHhhc---CCCcccc--------------cceeecccCCCCCCC
Confidence 35666667643 23458999 99999986543 333 5654321 223457888888887
Q ss_pred Eec
Q psy15975 123 EKD 125 (312)
Q Consensus 123 eK~ 125 (312)
.-.
T Consensus 66 ~~~ 68 (250)
T KOG3183|consen 66 PTK 68 (250)
T ss_pred CCC
Confidence 654
No 224
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.30 E-value=55 Score=26.30 Aligned_cols=14 Identities=21% Similarity=0.826 Sum_probs=7.7
Q ss_pred CceecCCcCCCCceec
Q psy15975 43 LLRWCPSPDCNNAIKV 58 (312)
Q Consensus 43 ~~~~CP~~~C~~~i~~ 58 (312)
...||+ +|+..+..
T Consensus 69 ~~~~C~--~Cg~~~~~ 82 (114)
T PRK03681 69 AECWCE--TCQQYVTL 82 (114)
T ss_pred cEEEcc--cCCCeeec
Confidence 344666 57765544
No 225
>PHA02862 5L protein; Provisional
Probab=21.20 E-value=99 Score=26.22 Aligned_cols=46 Identities=20% Similarity=0.462 Sum_probs=30.2
Q ss_pred ccccccCCccC---CCCCchhhHHHhhhcccchhhhHHhhh-cCCCCCCCCcee
Q psy15975 73 RFCFACGENWH---DPVRCSLLRRWIKKCDDDSETSNWIAA-NTKECPKCLVTI 122 (312)
Q Consensus 73 ~fC~~C~~~~H---~p~~C~~~~~w~~~~~~~~~~~~~i~~-~~k~CP~C~~~I 122 (312)
..|+-|..+.. .|..|..--+|.- .+=...||.. ..+.||-|+.+.
T Consensus 3 diCWIC~~~~~e~~~PC~C~GS~K~VH----q~CL~~WIn~S~k~~CeLCkteY 52 (156)
T PHA02862 3 DICWICNDVCDERNNFCGCNEEYKVVH----IKCMQLWINYSKKKECNLCKTKY 52 (156)
T ss_pred CEEEEecCcCCCCcccccccCcchhHH----HHHHHHHHhcCCCcCccCCCCeE
Confidence 35777776533 4777887666643 3445678864 567888888777
No 226
>PHA02109 hypothetical protein
Probab=20.97 E-value=1.2e+02 Score=26.40 Aligned_cols=22 Identities=18% Similarity=0.288 Sum_probs=18.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHh
Q psy15975 286 SENLANIKQQVQDKYRLVEIQL 307 (312)
Q Consensus 286 ~~~~~~~k~~~~~~~~~~~~~~ 307 (312)
++....++.|++++..||..|.
T Consensus 206 S~E~~Q~~~Ki~N~R~~Vk~~L 227 (233)
T PHA02109 206 SDEACQVKHKILNLRAEVKRRL 227 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999998774
No 227
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=20.90 E-value=78 Score=33.33 Aligned_cols=27 Identities=26% Similarity=0.552 Sum_probs=21.0
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCC
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCK 139 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~ 139 (312)
..||.|+.++.+.+|=.++.|.++.|.
T Consensus 393 ~~CP~C~s~l~~~~~~~~~~C~n~~C~ 419 (652)
T TIGR00575 393 THCPSCGSPLVKIEEEAVIRCPNLNCP 419 (652)
T ss_pred CCCCCCCCEeEecCCcEEEEECCCCCH
Confidence 589999999998766567778765564
No 228
>KOG1584|consensus
Probab=20.87 E-value=1.5e+02 Score=28.08 Aligned_cols=31 Identities=29% Similarity=0.419 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCcchHH
Q psy15975 260 VLFEDNQKDLESATEKLSEYLERDITSENLA 290 (312)
Q Consensus 260 ~~fe~~Q~~le~~~e~Ls~~le~~~~~~~~~ 290 (312)
-.+|.+.+|++..+.+|.++|+.+.+.+...
T Consensus 193 l~YEdmk~dp~~~ikrlaeFLg~~~~~Ee~~ 223 (297)
T KOG1584|consen 193 LKYEDMKADPKGEIKKLAEFLGCPFTKEEED 223 (297)
T ss_pred EEHHHhhhCHHHHHHHHHHHhCCCCCHHHHh
Confidence 3489999999999999999999988765543
No 229
>PLN02248 cellulose synthase-like protein
Probab=20.81 E-value=52 Score=36.56 Aligned_cols=38 Identities=21% Similarity=0.612 Sum_probs=31.0
Q ss_pred eecCCcCCCCceecccCCCCceEcCCCcccccccCCcc
Q psy15975 45 RWCPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENW 82 (312)
Q Consensus 45 ~~CP~~~C~~~i~~~~~~~~~v~C~C~~~fC~~C~~~~ 82 (312)
..|..++|..-+..+..+.....|.|+...|..|-.++
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (1135)
T PLN02248 125 SSCAMPGCDGKVMRDERGEDLLPCECGFKICRDCYIDA 162 (1135)
T ss_pred CcccccCcccccccccccccCCcccccchhHHhHhhhh
Confidence 47888999988877666667889999999999986543
No 230
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.80 E-value=50 Score=30.83 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=16.7
Q ss_pred CCCCCCCce-----eEecC--CCCceeecCCCCCcce------ecccCCC
Q psy15975 113 KECPKCLVT-----IEKDG--GCNHMVCKNQSCKAEF------CWVCLGP 149 (312)
Q Consensus 113 k~CP~C~~~-----IeK~~--GCnhMtC~~~~C~~~F------Cw~C~~~ 149 (312)
..||-||.+ |...+ |=-++.|+- |++++ |-.|+..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~--C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSL--CGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETT--T--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCC--CCCeeeecCCCCcCCCCC
Confidence 699999976 33344 778899988 88775 7777775
No 231
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.75 E-value=45 Score=19.24 Aligned_cols=9 Identities=56% Similarity=1.512 Sum_probs=5.6
Q ss_pred eEcC-CCccc
Q psy15975 66 VVCK-CGHRF 74 (312)
Q Consensus 66 v~C~-C~~~f 74 (312)
+.|+ ||..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5566 66665
No 233
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.38 E-value=71 Score=20.47 Aligned_cols=7 Identities=57% Similarity=1.360 Sum_probs=2.9
Q ss_pred CCCCCCc
Q psy15975 114 ECPKCLV 120 (312)
Q Consensus 114 ~CP~C~~ 120 (312)
+||+|+.
T Consensus 2 ~Cp~Cg~ 8 (39)
T PF01096_consen 2 KCPKCGH 8 (39)
T ss_dssp --SSS-S
T ss_pred CCcCCCC
Confidence 5788864
No 234
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.32 E-value=68 Score=28.47 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=22.2
Q ss_pred CCCCCCCCce---eEecCCCCceeecCCCCCcc
Q psy15975 112 TKECPKCLVT---IEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 112 ~k~CP~C~~~---IeK~~GCnhMtC~~~~C~~~ 141 (312)
.-.||.|+.| ++|.++=..+.|.. ||..
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~a--CGa~ 128 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDA--CGAH 128 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEccc--CCCC
Confidence 3589999876 77887777889998 8854
No 235
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.27 E-value=84 Score=25.94 Aligned_cols=26 Identities=27% Similarity=0.791 Sum_probs=17.4
Q ss_pred CCCC--CCCceeEecCCCCceeecCCCCCcc
Q psy15975 113 KECP--KCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP--~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
..|| .|+..+..+ |=+...|.+ |+..
T Consensus 19 ~aC~~~~C~kKv~~~-~~~~y~C~~--C~~~ 46 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-GDGSYRCEK--CNKT 46 (146)
T ss_dssp EE-TSTTTS-B-EEE-TTTEEEETT--TTEE
T ss_pred CCCCCccCCCEeecC-CCcEEECCC--CCCc
Confidence 6899 999998888 335688877 8744
No 236
>COG4640 Predicted membrane protein [Function unknown]
Probab=20.20 E-value=54 Score=32.24 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=13.5
Q ss_pred CCCCCCCceeEecCCCCceeecCCCCCcc
Q psy15975 113 KECPKCLVTIEKDGGCNHMVCKNQSCKAE 141 (312)
Q Consensus 113 k~CP~C~~~IeK~~GCnhMtC~~~~C~~~ 141 (312)
+-||+||. ++++| .|.|++ ||+.
T Consensus 2 ~fC~kcG~--qk~Ed--~~qC~q--CG~~ 24 (465)
T COG4640 2 KFCPKCGS--QKAED--DVQCTQ--CGHK 24 (465)
T ss_pred Cccccccc--ccccc--cccccc--cCCc
Confidence 56888884 23444 344776 6643
No 237
>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=20.15 E-value=84 Score=31.90 Aligned_cols=30 Identities=23% Similarity=0.798 Sum_probs=18.0
Q ss_pred CCCCceecccCCCCceEcC-CCcc-----cccccCCc
Q psy15975 51 DCNNAIKVQHVEARPVVCK-CGHR-----FCFACGEN 81 (312)
Q Consensus 51 ~C~~~i~~~~~~~~~v~C~-C~~~-----fC~~C~~~ 81 (312)
.|+..+.+.. ......|+ ||+. .|..|+..
T Consensus 227 ~C~~~l~~h~-~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 227 NCDVSLTYHK-KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCceEEec-CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4555554442 24467788 8765 47777664
No 238
>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=20.10 E-value=66 Score=22.45 Aligned_cols=24 Identities=29% Similarity=0.566 Sum_probs=16.4
Q ss_pred hcCCCCCCCCceeEecCCCCceeecCCCCCc
Q psy15975 110 ANTKECPKCLVTIEKDGGCNHMVCKNQSCKA 140 (312)
Q Consensus 110 ~~~k~CP~C~~~IeK~~GCnhMtC~~~~C~~ 140 (312)
.+.-.||.|+.+.. .|-.|.. ||+
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~--cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPS--CGY 47 (55)
T ss_pred CcceECCCCCCccc-----CeeECCc--cCe
Confidence 35667999998873 4666665 663
No 239
>KOG3799|consensus
Probab=20.04 E-value=37 Score=28.37 Aligned_cols=37 Identities=30% Similarity=0.744 Sum_probs=25.9
Q ss_pred cCCCCceeecCCCCCcceecccCCCCCCCCC-CCCCCCCCc
Q psy15975 125 DGGCNHMVCKNQSCKAEFCWVCLGPWEPHGS-SWYSCNRYD 164 (312)
Q Consensus 125 ~~GCnhMtC~~~~C~~~FCw~C~~~w~~h~~-~~~~C~~~~ 164 (312)
.+||.|. |.- |...||-.|||.-....+ --..||.-.
T Consensus 77 ADG~GH~-C~Y--Cq~r~CARCGGrv~lrsNKv~wvcnlc~ 114 (169)
T KOG3799|consen 77 ADGCGHN-CSY--CQTRFCARCGGRVSLRSNKVMWVCNLCR 114 (169)
T ss_pred ccccCcc-cch--hhhhHHHhcCCeeeeccCceEEeccCCc
Confidence 5899995 554 999999999998654322 234576543
Done!