Query psy1895
Match_columns 140
No_of_seqs 195 out of 1109
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 18:59:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01363 FYVE: FYVE zinc finge 99.8 2.1E-22 4.6E-27 130.9 1.8 64 69-132 1-68 (69)
2 smart00064 FYVE Protein presen 99.8 4.2E-20 9.1E-25 119.7 3.4 64 69-132 2-67 (68)
3 KOG1729|consensus 99.7 1.5E-18 3.4E-23 140.5 0.6 71 63-133 154-226 (288)
4 KOG1818|consensus 99.6 2.7E-16 5.9E-21 137.5 3.1 67 66-135 157-225 (634)
5 cd00065 FYVE FYVE domain; Zinc 99.6 6.1E-16 1.3E-20 96.7 2.0 53 77-129 2-56 (57)
6 PTZ00303 phosphatidylinositol 99.6 1.3E-15 2.8E-20 135.3 3.3 66 67-132 449-530 (1374)
7 KOG1819|consensus 99.5 3.2E-15 7E-20 128.4 1.9 63 68-130 892-961 (990)
8 KOG1842|consensus 99.4 9.5E-14 2.1E-18 117.1 1.3 67 67-134 170-261 (505)
9 KOG1841|consensus 99.1 1.8E-11 4E-16 112.0 1.1 64 64-127 544-608 (1287)
10 KOG1843|consensus 98.6 1.4E-08 3E-13 85.5 0.9 109 23-131 100-218 (473)
11 KOG1409|consensus 98.4 3.7E-08 8.1E-13 81.6 0.2 62 69-133 277-351 (404)
12 KOG4424|consensus 98.3 2.1E-07 4.6E-12 81.2 1.4 65 68-134 408-474 (623)
13 PF02318 FYVE_2: FYVE-type zin 97.9 5.7E-05 1.2E-09 53.9 7.1 51 76-131 53-104 (118)
14 KOG1811|consensus 97.6 4.4E-06 9.4E-11 74.3 -3.5 63 68-130 313-382 (1141)
15 KOG0230|consensus 97.3 0.00014 3E-09 69.5 2.9 49 77-134 5-53 (1598)
16 KOG0230|consensus 96.8 0.00067 1.5E-08 65.0 2.6 34 72-107 92-125 (1598)
17 KOG0993|consensus 95.5 0.0017 3.6E-08 55.5 -1.9 65 69-133 460-526 (542)
18 KOG1841|consensus 94.4 0.022 4.8E-07 53.8 2.0 56 67-133 647-702 (1287)
19 KOG1729|consensus 93.0 0.018 3.8E-07 47.3 -1.1 62 69-130 12-81 (288)
20 PF07975 C1_4: TFIIH C1-like d 91.9 0.031 6.8E-07 34.4 -0.8 43 79-127 1-49 (51)
21 TIGR00622 ssl1 transcription f 91.6 0.15 3.1E-06 36.4 2.2 35 76-110 54-98 (112)
22 KOG4275|consensus 90.6 0.03 6.6E-07 46.1 -2.3 52 72-130 39-90 (350)
23 KOG3799|consensus 88.9 1.3 2.7E-05 32.9 5.3 50 77-129 65-115 (169)
24 PF09538 FYDLN_acid: Protein o 88.4 0.33 7.2E-06 34.3 1.9 32 69-103 4-36 (108)
25 PF14634 zf-RING_5: zinc-RING 87.6 0.12 2.6E-06 30.2 -0.7 42 79-127 1-42 (44)
26 PRK00464 nrdR transcriptional 87.4 0.3 6.5E-06 36.5 1.3 25 79-103 2-38 (154)
27 PF13717 zinc_ribbon_4: zinc-r 86.6 0.41 9E-06 27.1 1.3 25 79-103 4-35 (36)
28 smart00154 ZnF_AN1 AN1-like Zi 86.3 0.44 9.5E-06 27.5 1.3 26 80-107 1-26 (39)
29 PF07191 zinc-ribbons_6: zinc- 85.8 0.26 5.6E-06 32.3 0.1 55 79-133 3-62 (70)
30 PF13719 zinc_ribbon_5: zinc-r 85.7 0.4 8.8E-06 27.2 0.9 25 79-103 4-35 (37)
31 KOG2164|consensus 84.5 0.26 5.7E-06 43.2 -0.3 51 78-133 187-237 (513)
32 TIGR02300 FYDLN_acid conserved 83.5 0.79 1.7E-05 33.4 1.8 26 78-103 10-36 (129)
33 KOG0320|consensus 82.7 0.15 3.2E-06 39.2 -2.3 47 78-133 132-179 (187)
34 KOG3576|consensus 82.4 0.26 5.6E-06 39.0 -1.1 32 72-103 112-155 (267)
35 PF13639 zf-RING_2: Ring finge 80.7 0.46 1E-05 27.4 -0.2 33 79-112 2-34 (44)
36 PF12773 DZR: Double zinc ribb 80.2 1.3 2.7E-05 26.3 1.6 29 74-102 9-38 (50)
37 PF01485 IBR: IBR domain; Int 79.4 1.8 3.8E-05 26.3 2.2 33 78-110 19-57 (64)
38 KOG0978|consensus 78.9 0.73 1.6E-05 42.0 0.4 44 78-130 644-687 (698)
39 PRK00420 hypothetical protein; 78.0 1.5 3.4E-05 31.1 1.8 25 78-102 24-49 (112)
40 cd00162 RING RING-finger (Real 77.7 0.22 4.7E-06 27.7 -2.2 42 80-129 2-43 (45)
41 PRK00398 rpoP DNA-directed RNA 75.9 1.8 3.8E-05 25.5 1.4 24 79-102 5-30 (46)
42 PF09297 zf-NADH-PPase: NADH p 73.7 2.2 4.7E-05 23.2 1.3 26 102-129 4-29 (32)
43 TIGR02098 MJ0042_CXXC MJ0042 f 73.1 2.2 4.9E-05 23.8 1.3 12 79-90 4-15 (38)
44 PF10571 UPF0547: Uncharacteri 72.8 2.1 4.6E-05 22.5 1.0 23 79-103 2-24 (26)
45 TIGR00570 cdk7 CDK-activating 72.1 0.91 2E-05 37.6 -0.7 49 78-133 4-55 (309)
46 PF13901 DUF4206: Domain of un 71.2 2 4.2E-05 33.3 0.9 41 95-135 2-49 (202)
47 PF13923 zf-C3HC4_2: Zinc fing 71.1 1.4 3E-05 24.8 0.1 29 80-111 1-29 (39)
48 PHA02768 hypothetical protein; 70.5 2.5 5.5E-05 26.3 1.2 25 79-103 7-41 (55)
49 PLN03208 E3 ubiquitin-protein 70.3 0.83 1.8E-05 35.5 -1.3 56 73-132 14-79 (193)
50 PF13445 zf-RING_UBOX: RING-ty 68.7 1.6 3.5E-05 25.6 0.0 30 80-110 1-30 (43)
51 KOG1814|consensus 68.5 9.3 0.0002 33.0 4.5 43 69-112 361-405 (445)
52 COG2126 RPL37A Ribosomal prote 67.5 2.9 6.2E-05 26.5 1.0 16 87-102 8-25 (61)
53 PF01927 Mut7-C: Mut7-C RNAse 65.4 7.6 0.00017 28.3 3.1 20 70-89 84-103 (147)
54 KOG0823|consensus 64.7 1.6 3.5E-05 34.7 -0.7 32 97-131 63-94 (230)
55 KOG0317|consensus 64.6 1.9 4E-05 35.5 -0.4 45 78-132 240-284 (293)
56 PF06221 zf-C2HC5: Putative zi 64.2 2.4 5.2E-05 26.6 0.1 15 91-105 16-30 (57)
57 TIGR02605 CxxC_CxxC_SSSS putat 63.8 3.5 7.5E-05 24.5 0.8 14 79-92 7-20 (52)
58 PRK14559 putative protein seri 63.7 4.6 9.9E-05 36.7 1.9 33 74-110 12-50 (645)
59 TIGR00100 hypA hydrogenase nic 63.1 3.8 8.2E-05 28.9 1.0 25 77-101 70-94 (115)
60 PF07282 OrfB_Zn_ribbon: Putat 62.8 6.7 0.00014 24.6 2.1 28 76-103 27-56 (69)
61 KOG4739|consensus 62.7 2.5 5.4E-05 33.8 0.0 43 79-131 5-47 (233)
62 PF05191 ADK_lid: Adenylate ki 62.4 3.1 6.8E-05 23.5 0.4 16 119-134 19-34 (36)
63 PF10367 Vps39_2: Vacuolar sor 62.1 43 0.00094 22.1 7.5 33 75-109 76-108 (109)
64 PF01155 HypA: Hydrogenase exp 61.8 2.7 5.8E-05 29.6 0.0 24 78-101 71-94 (113)
65 smart00659 RPOLCX RNA polymera 61.8 4.7 0.0001 23.8 1.1 23 79-101 4-27 (44)
66 smart00647 IBR In Between Ring 61.7 7.5 0.00016 23.5 2.1 32 79-110 20-57 (64)
67 COG5151 SSL1 RNA polymerase II 61.0 3.9 8.5E-05 34.3 0.9 41 70-110 355-405 (421)
68 PF15227 zf-C3HC4_4: zinc fing 60.8 1.4 3E-05 25.6 -1.3 15 98-112 15-29 (42)
69 TIGR01031 rpmF_bact ribosomal 60.1 6.1 0.00013 24.4 1.4 26 71-100 19-46 (55)
70 PRK00432 30S ribosomal protein 59.9 6.9 0.00015 23.7 1.6 27 77-103 20-47 (50)
71 KOG3173|consensus 58.4 5.2 0.00011 30.3 1.1 29 76-107 104-132 (167)
72 PF00097 zf-C3HC4: Zinc finger 58.2 3.5 7.7E-05 23.0 0.1 30 80-112 1-30 (41)
73 PF14353 CpXC: CpXC protein 57.8 5.2 0.00011 28.3 1.0 11 93-103 38-48 (128)
74 PF03107 C1_2: C1 domain; Int 57.6 9.9 0.00022 20.3 1.9 28 79-107 2-29 (30)
75 PF08271 TF_Zn_Ribbon: TFIIB z 57.0 7.2 0.00016 22.5 1.3 9 79-87 2-10 (43)
76 PHA02926 zinc finger-like prot 56.9 2 4.3E-05 34.3 -1.4 54 78-132 171-230 (242)
77 PF04438 zf-HIT: HIT zinc fing 56.8 6.5 0.00014 21.3 1.0 23 78-105 3-25 (30)
78 smart00834 CxxC_CXXC_SSSS Puta 56.7 5.6 0.00012 22.2 0.8 13 79-91 7-19 (41)
79 PRK12380 hydrogenase nickel in 55.3 6.1 0.00013 27.8 1.0 24 78-101 71-94 (113)
80 PF15616 TerY-C: TerY-C metal 54.5 8.6 0.00019 28.1 1.7 24 78-106 78-101 (131)
81 PF14803 Nudix_N_2: Nudix N-te 54.1 8.4 0.00018 21.5 1.2 27 103-129 2-30 (34)
82 PRK12495 hypothetical protein; 53.7 17 0.00036 28.9 3.3 12 77-88 42-53 (226)
83 PF03604 DNA_RNApol_7kD: DNA d 53.7 9.5 0.00021 21.0 1.4 23 79-101 2-25 (32)
84 PRK00564 hypA hydrogenase nick 52.8 7.2 0.00016 27.6 1.0 24 78-101 72-96 (117)
85 COG5574 PEX10 RING-finger-cont 52.6 3.2 6.8E-05 33.8 -0.9 44 79-130 217-260 (271)
86 PRK01253 preprotein translocas 52.3 3.6 7.8E-05 25.5 -0.5 24 1-24 11-34 (54)
87 PF09889 DUF2116: Uncharacteri 51.7 6.3 0.00014 24.9 0.5 27 93-133 3-30 (59)
88 PF09723 Zn-ribbon_8: Zinc rib 50.9 7.4 0.00016 22.5 0.7 9 80-88 8-16 (42)
89 PF12172 DUF35_N: Rubredoxin-l 50.8 5.9 0.00013 22.0 0.3 8 95-102 13-20 (37)
90 PF01907 Ribosomal_L37e: Ribos 50.5 9.8 0.00021 23.7 1.2 7 96-102 18-24 (55)
91 KOG1829|consensus 49.1 9.3 0.0002 34.4 1.3 56 76-131 339-403 (580)
92 COG1996 RPC10 DNA-directed RNA 49.1 8.4 0.00018 23.4 0.8 23 79-101 8-32 (49)
93 PF06750 DiS_P_DiS: Bacterial 48.9 7 0.00015 26.6 0.4 25 78-102 34-67 (92)
94 PF10497 zf-4CXXC_R1: Zinc-fin 48.6 5.4 0.00012 27.8 -0.2 52 76-129 6-69 (105)
95 PF15135 UPF0515: Uncharacteri 47.8 12 0.00026 30.4 1.7 35 70-104 125-166 (278)
96 PF02150 RNA_POL_M_15KD: RNA p 47.5 9.7 0.00021 21.2 0.8 26 102-128 2-27 (35)
97 PRK03824 hypA hydrogenase nick 46.6 10 0.00022 27.5 1.0 13 78-90 71-83 (135)
98 COG0675 Transposase and inacti 46.1 14 0.00031 29.1 1.9 26 75-103 307-332 (364)
99 PF13248 zf-ribbon_3: zinc-rib 45.8 12 0.00027 19.2 1.0 7 79-85 4-10 (26)
100 TIGR00373 conserved hypothetic 45.7 10 0.00022 28.1 1.0 28 76-103 108-138 (158)
101 PF10170 C6_DPF: Cysteine-rich 45.2 12 0.00027 25.9 1.2 34 93-134 49-84 (97)
102 PRK03681 hypA hydrogenase nick 45.2 11 0.00023 26.6 1.0 24 78-101 71-95 (114)
103 PF13920 zf-C3HC4_3: Zinc fing 44.6 2.7 5.9E-05 24.8 -1.9 44 78-131 3-47 (50)
104 PRK12496 hypothetical protein; 44.4 14 0.0003 27.7 1.5 11 93-103 127-137 (164)
105 KOG1314|consensus 44.0 10 0.00022 32.4 0.7 33 67-101 76-113 (414)
106 TIGR01384 TFS_arch transcripti 43.8 14 0.00031 25.1 1.3 26 79-104 2-27 (104)
107 COG1545 Predicted nucleic-acid 43.6 13 0.00027 27.2 1.1 8 96-103 32-39 (140)
108 PF11238 DUF3039: Protein of u 43.6 21 0.00046 22.4 2.0 15 118-132 41-55 (58)
109 PF01428 zf-AN1: AN1-like Zinc 42.6 15 0.00032 21.2 1.1 15 93-107 13-27 (43)
110 KOG3896|consensus 42.2 13 0.00029 31.6 1.2 31 82-113 14-44 (449)
111 PF07503 zf-HYPF: HypF finger; 41.2 6.6 0.00014 22.1 -0.5 16 80-95 2-18 (35)
112 COG1773 Rubredoxin [Energy pro 41.2 13 0.00028 23.1 0.8 37 92-128 2-43 (55)
113 COG1439 Predicted nucleic acid 41.0 13 0.00028 28.5 0.9 15 89-103 135-149 (177)
114 PRK04023 DNA polymerase II lar 40.7 24 0.00051 34.0 2.6 46 75-132 624-674 (1121)
115 KOG3362|consensus 40.7 11 0.00024 28.1 0.5 26 76-106 117-142 (156)
116 PF06741 LsmAD: LsmAD domain; 40.6 24 0.00052 23.1 2.0 36 5-42 2-37 (72)
117 PRK06266 transcription initiat 40.5 12 0.00025 28.5 0.6 28 76-103 116-146 (178)
118 PF01529 zf-DHHC: DHHC palmito 40.2 16 0.00035 26.5 1.3 28 73-102 44-71 (174)
119 smart00661 RPOL9 RNA polymeras 40.0 21 0.00045 20.9 1.5 8 121-128 20-27 (52)
120 PRK04136 rpl40e 50S ribosomal 39.3 18 0.00038 22.0 1.1 22 78-101 15-36 (48)
121 PF14835 zf-RING_6: zf-RING of 39.2 18 0.0004 23.3 1.2 41 79-131 9-50 (65)
122 PHA02929 N1R/p28-like protein; 39.1 6.2 0.00014 31.5 -1.2 51 76-132 173-227 (238)
123 PF14446 Prok-RING_1: Prokaryo 39.0 22 0.00048 22.0 1.5 25 78-102 6-30 (54)
124 PF13913 zf-C2HC_2: zinc-finge 38.9 5.9 0.00013 20.4 -0.9 13 79-91 4-16 (25)
125 PRK11595 DNA utilization prote 38.8 7.7 0.00017 30.2 -0.7 29 79-109 22-56 (227)
126 PF14471 DUF4428: Domain of un 38.6 18 0.0004 21.9 1.1 11 122-132 21-31 (51)
127 COG1327 Predicted transcriptio 38.4 16 0.00034 27.5 1.0 15 89-103 24-38 (156)
128 COG1198 PriA Primosomal protei 38.3 20 0.00044 33.2 1.8 32 79-110 446-484 (730)
129 KOG0119|consensus 37.1 54 0.0012 29.2 4.1 40 8-47 190-229 (554)
130 cd02341 ZZ_ZZZ3 Zinc finger, Z 37.0 14 0.0003 22.2 0.4 30 79-109 2-34 (48)
131 smart00109 C1 Protein kinase C 36.6 19 0.00042 20.2 1.0 32 77-108 11-42 (49)
132 KOG2462|consensus 36.2 13 0.00027 30.5 0.2 54 77-131 187-253 (279)
133 PF07754 DUF1610: Domain of un 36.1 25 0.00054 18.2 1.2 8 93-100 16-23 (24)
134 smart00531 TFIIE Transcription 36.1 50 0.0011 24.0 3.3 30 74-103 96-133 (147)
135 PF00643 zf-B_box: B-box zinc 35.7 14 0.0003 20.7 0.2 29 78-110 4-32 (42)
136 PF11023 DUF2614: Protein of u 34.7 16 0.00034 26.1 0.4 24 79-102 71-94 (114)
137 PF00130 C1_1: Phorbol esters/ 34.7 29 0.00062 20.3 1.6 35 76-110 10-45 (53)
138 smart00184 RING Ring finger. E 34.5 8.8 0.00019 19.9 -0.7 15 97-111 14-28 (39)
139 PF01286 XPA_N: XPA protein N- 34.3 21 0.00046 20.0 0.8 11 78-88 4-14 (34)
140 PF14445 Prok-RING_2: Prokaryo 34.3 6.7 0.00014 24.2 -1.3 43 79-131 9-51 (57)
141 PF00301 Rubredoxin: Rubredoxi 33.9 20 0.00044 21.4 0.8 13 93-105 1-13 (47)
142 cd02340 ZZ_NBR1_like Zinc fing 33.7 19 0.00041 20.9 0.6 30 79-110 2-32 (43)
143 PF10013 DUF2256: Uncharacteri 33.5 25 0.00055 20.7 1.1 15 77-91 8-22 (42)
144 PTZ00073 60S ribosomal protein 33.4 22 0.00048 24.4 0.9 7 96-102 19-25 (91)
145 PF10263 SprT-like: SprT-like 33.2 24 0.00052 25.3 1.2 10 79-88 125-134 (157)
146 PRK14892 putative transcriptio 33.1 33 0.00072 23.8 1.8 43 77-122 21-64 (99)
147 smart00291 ZnF_ZZ Zinc-binding 33.0 19 0.0004 20.9 0.5 21 78-100 5-25 (44)
148 PF00096 zf-C2H2: Zinc finger, 32.9 15 0.00033 17.6 0.1 10 79-88 2-11 (23)
149 KOG4080|consensus 32.5 21 0.00046 27.2 0.8 14 119-132 104-117 (176)
150 TIGR00599 rad18 DNA repair pro 32.5 20 0.00043 30.8 0.8 48 75-132 24-71 (397)
151 PF13005 zf-IS66: zinc-finger 32.2 29 0.00063 19.9 1.3 11 78-88 3-13 (47)
152 cd00202 ZnF_GATA Zinc finger D 31.8 17 0.00036 22.3 0.1 29 80-110 2-30 (54)
153 KOG1812|consensus 31.6 21 0.00045 30.4 0.7 32 78-110 307-340 (384)
154 PF07130 YebG: YebG protein; 31.4 86 0.0019 20.7 3.5 43 11-53 26-68 (75)
155 PF09332 Mcm10: Mcm10 replicat 31.4 20 0.00043 30.2 0.6 9 77-85 252-260 (344)
156 PF02591 DUF164: Putative zinc 31.3 28 0.00061 21.0 1.1 25 78-102 23-55 (56)
157 KOG1311|consensus 31.1 22 0.00049 28.6 0.8 23 77-101 113-135 (299)
158 KOG2807|consensus 31.0 32 0.0007 29.1 1.7 51 71-128 324-374 (378)
159 TIGR00311 aIF-2beta translatio 30.9 23 0.0005 25.8 0.8 25 78-102 98-127 (133)
160 TIGR00244 transcriptional regu 30.6 30 0.00065 25.8 1.4 15 89-103 24-38 (147)
161 PF09947 DUF2180: Uncharacteri 29.9 16 0.00035 23.7 -0.1 39 94-132 17-67 (68)
162 cd02249 ZZ Zinc finger, ZZ typ 29.6 21 0.00045 20.8 0.3 30 79-110 2-32 (46)
163 PF09862 DUF2089: Protein of u 29.5 31 0.00067 24.5 1.2 26 80-107 1-26 (113)
164 PF05443 ROS_MUCR: ROS/MUCR tr 29.0 15 0.00033 26.7 -0.4 20 74-94 69-88 (132)
165 PF11781 RRN7: RNA polymerase 28.8 28 0.00061 19.5 0.7 24 79-102 10-34 (36)
166 PRK03564 formate dehydrogenase 28.4 45 0.00097 27.7 2.2 55 77-132 187-263 (309)
167 KOG3795|consensus 28.1 29 0.00062 26.9 0.9 23 87-109 9-34 (230)
168 PHA00733 hypothetical protein 28.0 1.2E+02 0.0027 21.6 4.2 26 78-103 74-109 (128)
169 PHA00732 hypothetical protein 28.0 47 0.001 21.9 1.8 9 80-88 4-12 (79)
170 TIGR00595 priA primosomal prot 27.7 40 0.00086 29.6 1.8 33 79-111 224-263 (505)
171 PF02148 zf-UBP: Zn-finger in 27.7 40 0.00086 20.8 1.4 16 91-106 9-24 (63)
172 TIGR01562 FdhE formate dehydro 27.5 49 0.0011 27.4 2.2 56 77-132 184-263 (305)
173 KOG2593|consensus 27.4 93 0.002 27.2 3.9 34 77-110 128-170 (436)
174 PF12760 Zn_Tnp_IS1595: Transp 27.4 44 0.00096 19.4 1.5 30 69-101 13-45 (46)
175 PF00569 ZZ: Zinc finger, ZZ t 27.2 20 0.00043 21.0 -0.1 22 78-100 5-26 (46)
176 KOG0153|consensus 26.8 29 0.00063 29.5 0.8 23 72-94 36-58 (377)
177 PRK05452 anaerobic nitric oxid 26.2 61 0.0013 28.2 2.7 40 90-129 422-466 (479)
178 PRK13729 conjugal transfer pil 26.1 2E+02 0.0044 25.5 5.8 44 4-47 55-100 (475)
179 COG1645 Uncharacterized Zn-fin 25.9 38 0.00082 24.8 1.2 24 78-109 29-52 (131)
180 COG1997 RPL43A Ribosomal prote 25.7 50 0.0011 22.6 1.6 26 78-105 36-65 (89)
181 COG4338 Uncharacterized protei 25.7 22 0.00047 21.7 -0.1 15 78-92 13-27 (54)
182 PF03833 PolC_DP2: DNA polymer 25.6 23 0.0005 33.4 0.0 32 92-130 654-689 (900)
183 PF11331 DUF3133: Protein of u 25.4 38 0.00081 20.3 0.9 16 118-133 3-18 (46)
184 KOG1356|consensus 25.3 32 0.00069 32.4 0.8 34 77-112 229-262 (889)
185 PF13465 zf-H2C2_2: Zinc-finge 25.3 38 0.00083 17.2 0.8 9 94-102 15-23 (26)
186 PRK14873 primosome assembly pr 25.1 40 0.00087 30.8 1.4 32 79-110 394-431 (665)
187 PRK03988 translation initiatio 25.1 34 0.00073 25.1 0.8 24 78-101 103-131 (138)
188 KOG1813|consensus 25.1 38 0.00082 28.2 1.1 28 79-110 243-270 (313)
189 KOG3183|consensus 24.9 26 0.00057 28.2 0.2 51 78-131 9-65 (250)
190 cd04476 RPA1_DBD_C RPA1_DBD_C: 24.9 37 0.0008 24.8 1.0 26 78-103 35-61 (166)
191 COG1998 RPS31 Ribosomal protei 24.8 44 0.00096 20.4 1.1 24 78-101 20-45 (51)
192 PF09845 DUF2072: Zn-ribbon co 24.7 34 0.00074 25.0 0.8 24 78-101 2-27 (131)
193 smart00653 eIF2B_5 domain pres 24.7 34 0.00074 24.1 0.7 24 78-101 81-109 (110)
194 cd00350 rubredoxin_like Rubred 24.5 42 0.00091 18.2 0.9 10 94-103 2-11 (33)
195 cd02345 ZZ_dah Zinc finger, ZZ 24.4 32 0.00069 20.5 0.5 27 79-107 2-30 (49)
196 PRK06260 threonine synthase; V 24.4 48 0.001 27.9 1.7 24 79-102 5-28 (397)
197 PRK05978 hypothetical protein; 24.4 42 0.00091 24.9 1.2 26 78-103 34-62 (148)
198 PRK14559 putative protein seri 24.3 60 0.0013 29.7 2.4 45 79-131 3-51 (645)
199 PRK14714 DNA polymerase II lar 24.2 44 0.00096 33.0 1.6 28 93-127 667-698 (1337)
200 COG2888 Predicted Zn-ribbon RN 24.2 63 0.0014 20.5 1.8 32 77-108 9-42 (61)
201 PF01190 Pollen_Ole_e_I: Polle 24.1 48 0.001 22.1 1.3 10 100-109 3-12 (97)
202 COG4530 Uncharacterized protei 24.0 41 0.00088 24.1 1.0 26 78-103 10-36 (129)
203 PF04423 Rad50_zn_hook: Rad50 24.0 27 0.00058 21.0 0.1 11 79-89 22-32 (54)
204 smart00504 Ubox Modified RING 24.0 36 0.00077 20.4 0.6 30 79-112 3-32 (63)
205 KOG1315|consensus 23.9 39 0.00084 28.1 1.0 10 120-129 125-134 (307)
206 PF13240 zinc_ribbon_2: zinc-r 23.9 39 0.00085 17.0 0.7 9 80-88 2-10 (23)
207 PRK03954 ribonuclease P protei 23.5 2.3E+02 0.0051 20.3 4.9 10 78-87 65-74 (121)
208 COG3364 Zn-ribbon containing p 23.4 31 0.00067 24.3 0.3 11 93-103 2-12 (112)
209 PRK07591 threonine synthase; V 23.3 50 0.0011 28.2 1.6 25 78-103 19-43 (421)
210 PRK12286 rpmF 50S ribosomal pr 23.3 55 0.0012 20.3 1.4 8 120-127 39-46 (57)
211 PRK14890 putative Zn-ribbon RN 23.1 84 0.0018 19.8 2.2 27 77-103 7-35 (59)
212 PF01147 Crust_neurohorm: Crus 23.0 22 0.00049 23.3 -0.4 16 118-133 17-32 (73)
213 PF13894 zf-C2H2_4: C2H2-type 23.0 32 0.0007 16.0 0.3 11 79-89 2-12 (24)
214 smart00731 SprT SprT homologue 22.7 57 0.0012 23.5 1.6 10 79-88 114-123 (146)
215 PRK04351 hypothetical protein; 22.7 51 0.0011 24.3 1.4 13 119-131 130-142 (149)
216 cd02342 ZZ_UBA_plant Zinc fing 22.5 36 0.00079 20.1 0.4 28 79-107 2-30 (43)
217 PRK00762 hypA hydrogenase nick 22.5 44 0.00095 23.8 1.0 11 78-89 71-81 (124)
218 PF03966 Trm112p: Trm112p-like 22.5 55 0.0012 20.5 1.3 14 90-103 50-63 (68)
219 PF06397 Desulfoferrod_N: Desu 22.4 41 0.00088 19.1 0.6 11 93-103 6-16 (36)
220 PRK04179 rpl37e 50S ribosomal 22.3 42 0.00091 21.4 0.7 7 96-102 20-26 (62)
221 PF06677 Auto_anti-p27: Sjogre 22.0 55 0.0012 19.0 1.1 22 79-107 19-40 (41)
222 PRK09678 DNA-binding transcrip 21.8 61 0.0013 21.2 1.4 14 90-103 24-39 (72)
223 KOG4323|consensus 21.8 46 0.001 29.3 1.1 53 78-130 169-224 (464)
224 PF01667 Ribosomal_S27e: Ribos 21.7 62 0.0013 20.1 1.4 27 79-105 9-38 (55)
225 PF13912 zf-C2H2_6: C2H2-type 21.7 32 0.00069 17.1 0.1 11 79-89 3-13 (27)
226 cd07153 Fur_like Ferric uptake 21.6 47 0.001 22.5 0.9 13 96-108 76-88 (116)
227 PF04216 FdhE: Protein involve 21.4 47 0.001 26.8 1.0 55 77-131 172-248 (290)
228 PF07776 zf-AD: Zinc-finger as 21.0 30 0.00066 20.9 -0.1 16 118-133 42-57 (75)
229 KOG2932|consensus 21.0 45 0.00097 28.1 0.8 46 76-132 89-134 (389)
230 PF02945 Endonuclease_7: Recom 20.9 40 0.00088 22.4 0.5 30 78-107 23-58 (81)
231 cd02336 ZZ_RSC8 Zinc finger, Z 20.8 41 0.00089 19.9 0.4 10 121-130 23-32 (45)
232 PRK10061 DNA damage-inducible 20.7 95 0.002 21.5 2.2 43 11-53 26-68 (96)
233 PRK02935 hypothetical protein; 20.3 48 0.001 23.4 0.7 25 79-103 72-96 (110)
234 cd00730 rubredoxin Rubredoxin; 20.2 54 0.0012 19.8 0.9 12 93-104 1-12 (50)
235 PRK08197 threonine synthase; V 20.2 61 0.0013 27.3 1.5 24 78-102 8-31 (394)
236 PHA02942 putative transposase; 20.2 82 0.0018 26.7 2.3 28 76-103 324-352 (383)
237 PRK12336 translation initiatio 20.1 47 0.001 25.6 0.8 26 78-103 99-129 (201)
238 PRK05580 primosome assembly pr 20.1 67 0.0014 29.3 1.8 32 79-110 392-430 (679)
239 KOG2177|consensus 20.0 22 0.00047 26.9 -1.1 31 78-112 14-44 (386)
No 1
>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=99.85 E-value=2.1e-22 Score=130.89 Aligned_cols=64 Identities=50% Similarity=1.155 Sum_probs=47.8
Q ss_pred CccccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCC----CCCCCcccCcccHHHhh
Q psy1895 69 AQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALP----SAAKPVRVCDECNVKLV 132 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp----~~~~~~RVC~~C~~~l~ 132 (140)
|.|+||.++..|+.|+++|++++||||||.||.+||+.|+.+.+++| ....++|||+.||..|+
T Consensus 1 ~~W~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 1 PHWVPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp --SSSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CCcCCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 68999999999999999999999999999999999999999999888 23899999999999875
No 2
>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 KOG1729|consensus
Probab=99.71 E-value=1.5e-18 Score=140.53 Aligned_cols=71 Identities=48% Similarity=1.007 Sum_probs=65.7
Q ss_pred HhhccCCccccCcCCcccccccc-ccccccccccccccCceEeCCCCCCeeeCCCC-CCCcccCcccHHHhhc
Q psy1895 63 AKRATEAQWAKDKEAITCRACDK-EFTVTRRRHHCRNCGEIFCNMCSDNKMALPSA-AKPVRVCDECNVKLVE 133 (140)
Q Consensus 63 ~l~~~~~~W~~~~~~~~C~~C~~-~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~-~~~~RVC~~C~~~l~~ 133 (140)
.....++.|+||.++..|+.|++ .|+++.||||||+||.|||..|+.++..+|.. .+|+|||+.||..|..
T Consensus 154 ~~~~~~~~W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 154 PSNNSAAVWLPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEELEK 226 (288)
T ss_pred CCCCcCCcccCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHHhc
Confidence 34456799999999999999999 99999999999999999999999999889987 8999999999999864
No 4
>KOG1818|consensus
Probab=99.60 E-value=2.7e-16 Score=137.52 Aligned_cols=67 Identities=43% Similarity=1.019 Sum_probs=60.5
Q ss_pred ccCCccccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCC--CCCcccCcccHHHhhccc
Q psy1895 66 ATEAQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSA--AKPVRVCDECNVKLVEKL 135 (140)
Q Consensus 66 ~~~~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~--~~~~RVC~~C~~~l~~~~ 135 (140)
...+.|++.. .|..|..+|++++|+||||+||+|||..|++...+||.. .+|||||+.||+.+....
T Consensus 157 ~~~pdW~D~~---~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~~s 225 (634)
T KOG1818|consen 157 ETAPDWIDSE---ECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTRAS 225 (634)
T ss_pred cCCccccccc---ccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhhcc
Confidence 3568998754 899999999999999999999999999999999999987 699999999999987643
No 5
>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=99.58 E-value=6.1e-16 Score=96.69 Aligned_cols=53 Identities=64% Similarity=1.333 Sum_probs=49.6
Q ss_pred CccccccccccccccccccccccCceEeCCCCCCeeeCCC--CCCCcccCcccHH
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPS--AAKPVRVCDECNV 129 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~--~~~~~RVC~~C~~ 129 (140)
+..|..|+++|+++.|+|||+.||.+||..|+.+...+|. ...|+|||+.||.
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~~ 56 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHhC
Confidence 4579999999999999999999999999999999999987 4899999999985
No 6
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=99.56 E-value=1.3e-15 Score=135.32 Aligned_cols=66 Identities=32% Similarity=0.781 Sum_probs=53.9
Q ss_pred cCCccccCcCC-ccccccccccccc-----cccccccccCceEeCCCCCCeeeCC-------CC---CCCcccCcccHHH
Q psy1895 67 TEAQWAKDKEA-ITCRACDKEFTVT-----RRRHHCRNCGEIFCNMCSDNKMALP-------SA---AKPVRVCDECNVK 130 (140)
Q Consensus 67 ~~~~W~~~~~~-~~C~~C~~~F~~~-----~rkhhCr~CG~i~C~~Cs~~~~~lp-------~~---~~~~RVC~~C~~~ 130 (140)
..|.|++|+++ ..|+.|+++|+.+ .||||||+||.+||+.||+++...| .. ..+.|||+.||+.
T Consensus 449 hAPvWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD~CYdq 528 (1374)
T PTZ00303 449 HNPSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTCYKE 528 (1374)
T ss_pred cCCCCCCCcccCCcccCcCCcccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhHHHHHH
Confidence 45999999984 8899999999854 6999999999999999999876432 22 3467899999966
Q ss_pred hh
Q psy1895 131 LV 132 (140)
Q Consensus 131 l~ 132 (140)
+.
T Consensus 529 ~E 530 (1374)
T PTZ00303 529 YE 530 (1374)
T ss_pred HH
Confidence 53
No 7
>KOG1819|consensus
Probab=99.52 E-value=3.2e-15 Score=128.36 Aligned_cols=63 Identities=44% Similarity=0.994 Sum_probs=59.0
Q ss_pred CCccccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCC--CCCcccCc-----ccHHH
Q psy1895 68 EAQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSA--AKPVRVCD-----ECNVK 130 (140)
Q Consensus 68 ~~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~--~~~~RVC~-----~C~~~ 130 (140)
.|-|+||.++..|+.|+.+|+.|+|+||||+||.|||..|+...+|+|.. .+.+|||. .||..
T Consensus 892 ppawipd~~a~~cmacq~pf~afrrrhhcrncggifcg~cs~asapip~~gl~ka~rvcrpqsnldc~~r 961 (990)
T KOG1819|consen 892 PPAWIPDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSCASAPIPEHGLDKAPRVCRPQSNLDCLTR 961 (990)
T ss_pred CcccCCCCcchhhhhccCcHHHHHHhhhhcccCceeecccccCCCCCcccccccCceecCCcccccceee
Confidence 47899999999999999999999999999999999999999999999976 78999999 78754
No 8
>KOG1842|consensus
Probab=99.38 E-value=9.5e-14 Score=117.10 Aligned_cols=67 Identities=36% Similarity=0.879 Sum_probs=56.6
Q ss_pred cCCccccCcCCccccccccccccccccccccccCceEeCCCCCCeee-------------------------CCCCCCCc
Q psy1895 67 TEAQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMA-------------------------LPSAAKPV 121 (140)
Q Consensus 67 ~~~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~-------------------------lp~~~~~~ 121 (140)
....|++|.++..|+.|..+|++++|+||||.||.|+|.+|+.+ ++ |+....+.
T Consensus 170 svVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~-iSle~a~~ltsss~~dt~~e~~qq~~~lH~~~~~i 248 (505)
T KOG1842|consen 170 SVVPWLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKF-ISLEIAIGLTSSSASDTHFEPNQQKDDLHQHPQPI 248 (505)
T ss_pred ccccccCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHh-cChHHHHHHhhccCCCCCcCcccCcccccCChhHh
Confidence 44889999999999999999999999999999999999999876 22 11124569
Q ss_pred ccCcccHHHhhcc
Q psy1895 122 RVCDECNVKLVEK 134 (140)
Q Consensus 122 RVC~~C~~~l~~~ 134 (140)
|+|..|...|..+
T Consensus 249 RlC~hCl~~L~~R 261 (505)
T KOG1842|consen 249 RLCMHCLDNLFRR 261 (505)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999888643
No 9
>KOG1841|consensus
Probab=99.10 E-value=1.8e-11 Score=112.02 Aligned_cols=64 Identities=36% Similarity=0.765 Sum_probs=54.6
Q ss_pred hhccCCccccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCC-CCCcccCccc
Q psy1895 64 KRATEAQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSA-AKPVRVCDEC 127 (140)
Q Consensus 64 l~~~~~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~-~~~~RVC~~C 127 (140)
++...|.|+||..+..||.|..+|++++||||||+||+|+|+.|+..+..+-.. ..-.|||..|
T Consensus 544 lgkkqP~wvpdse~pncm~clqkft~ikrrhhcRacgkVlcgvccnek~~leyl~e~~~rv~nV~ 608 (1287)
T KOG1841|consen 544 LGKKQPSWVPDSEAPNCMDCLQKFTPIKRRHHCRACGKVLCGVCCNEKSALEYLSESEGRVSNVD 608 (1287)
T ss_pred cCCCCCccCccccCchHHHHHhhcccccccccchhccceeehhhcchhhhhhhcCcccccccccc
Confidence 455679999999999999999999999999999999999999999998777654 3445666555
No 10
>KOG1843|consensus
Probab=98.58 E-value=1.4e-08 Score=85.53 Aligned_cols=109 Identities=21% Similarity=0.163 Sum_probs=76.0
Q ss_pred hcchhhhhHHHHHHHHHHHHHhhhhhhHHHHH--HHHHH----HHHHhhccCCccccCcCCccccccccccc-ccccccc
Q psy1895 23 VKDNVSDDKYKESELALEELGAQLSKSKLQVS--DLMEE----HQIAKRATEAQWAKDKEAITCRACDKEFT-VTRRRHH 95 (140)
Q Consensus 23 ~~~~~~r~~~~~~~~~l~~~~~~l~~s~~~~~--~l~~~----~~~~l~~~~~~W~~~~~~~~C~~C~~~F~-~~~rkhh 95 (140)
+.+.+.-...+++.+.+.+++...-.+...+. .|-+. ....++.-+|.|.+++....|+.|..+|+ ++-||||
T Consensus 100 ltd~V~ilNs~~av~~f~~~G~itLGgn~svsAgPLgr~aea~a~asl~~~ap~f~yskskglfagvSvegsaI~erR~a 179 (473)
T KOG1843|consen 100 LTDFVIILNSALAVQSFARFGTITLGGNLSVSAGPLGRNAEAAASASLGGEAPVFLYSKSKGLFAGVSVEGSAIIERREA 179 (473)
T ss_pred HHHHHHhhcchHhhhhhhhcCeeeecCcceeccCcccccchhhhhhhhcCcCccccccccccceeeeecccceeeecchh
Confidence 44444444555666777776654321211111 11111 11134445699999999999999999999 7899999
Q ss_pred ccccCceEeCCCCCCeeeCC--CC-CCCcccCcccHHHh
Q psy1895 96 CRNCGEIFCNMCSDNKMALP--SA-AKPVRVCDECNVKL 131 (140)
Q Consensus 96 Cr~CG~i~C~~Cs~~~~~lp--~~-~~~~RVC~~C~~~l 131 (140)
||.|+.+||-.|+.-.-.+| .. ..+.|||+.|+..|
T Consensus 180 nR~~yg~~cra~~ilsg~vp~p~a~d~l~RVldS~~~nl 218 (473)
T KOG1843|consen 180 NRKFYGIFCRAKSILSGLVPVPFAADPLQRVLDSCAFNL 218 (473)
T ss_pred hhhhcCccchhhhhhccCCCCCcccCCHHHHHhhHhhcc
Confidence 99999999999988754444 33 78899999999988
No 11
>KOG1409|consensus
Probab=98.45 E-value=3.7e-08 Score=81.64 Aligned_cols=62 Identities=35% Similarity=0.961 Sum_probs=53.7
Q ss_pred CccccCcCCccccccccccc-----------cccccccccccCceEeCCCCCCeeeCCCC--CCCcccCcccHHHhhc
Q psy1895 69 AQWAKDKEAITCRACDKEFT-----------VTRRRHHCRNCGEIFCNMCSDNKMALPSA--AKPVRVCDECNVKLVE 133 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~-----------~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~--~~~~RVC~~C~~~l~~ 133 (140)
|.|..++ .|..|+.+|. +-.|.||||.||..+|..|++++...|.. +-.+|+|+.||..|..
T Consensus 277 pewl~s~---~cQ~c~qpffwn~~~m~~~k~~glr~h~crkcg~avc~~c~s~~~~~p~mg~e~~vR~~~~c~~~i~~ 351 (404)
T KOG1409|consen 277 PEWLDSD---SCQKCNQPFFWNFRQMWDRKQLGLRQHHCRKCGKAVCGKCSSNRSSYPTMGFEFSVRVCDSCYPTIKD 351 (404)
T ss_pred ccccccc---hhhhhCchHHHHHHHHHhhhhhhhhhhhhhhhhhhcCcccccCccccccccceeEEEEecccchhhhc
Confidence 8898876 8999999985 23578999999999999999998877764 7889999999999864
No 12
>KOG4424|consensus
Probab=98.30 E-value=2.1e-07 Score=81.18 Aligned_cols=65 Identities=28% Similarity=0.656 Sum_probs=55.7
Q ss_pred CCccccCcCCccccccccccc-cccccccccccCceEeCCCCCCeeeCCCC-CCCcccCcccHHHhhcc
Q psy1895 68 EAQWAKDKEAITCRACDKEFT-VTRRRHHCRNCGEIFCNMCSDNKMALPSA-AKPVRVCDECNVKLVEK 134 (140)
Q Consensus 68 ~~~W~~~~~~~~C~~C~~~F~-~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~-~~~~RVC~~C~~~l~~~ 134 (140)
.++| ++....|+.|+.+|+ ...++|||+.||.++|+.|+.+...+.+. ....|||..||....+.
T Consensus 408 ~~r~--~~k~~~c~~c~e~~~s~t~~R~~~k~~~~vlc~~cs~~~~~l~~~~s~ssrv~~~~~~~~~~a 474 (623)
T KOG4424|consen 408 APRR--DNKVTSCDSCEETFNSITFRRHRCKAKGAVLCDKCSDFMAKLSYDNSRSSRVCMDRYLTPSGA 474 (623)
T ss_pred Cccc--ccccccchhhcCchhhHHHhhhhhhhccceeeccccchhhhhcccccchhhhhhhhccCCCCC
Confidence 4567 777889999999998 67889999999999999999998877643 78889999999886653
No 13
>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=97.90 E-value=5.7e-05 Score=53.87 Aligned_cols=51 Identities=25% Similarity=0.657 Sum_probs=41.0
Q ss_pred CCccccccccccccc-cccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 76 EAITCRACDKEFTVT-RRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~-~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
....|..|..+|+++ ++.+.|..|+..||..|..+ ....+.-+|..|++.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-----~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-----SKKEPIWLCKVCQKQR 104 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-----TSSSCCEEEHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-----CCCCCCEEChhhHHHH
Confidence 345899999999976 57888999999999999876 2257889999999764
No 14
>KOG1811|consensus
Probab=97.57 E-value=4.4e-06 Score=74.26 Aligned_cols=63 Identities=30% Similarity=0.715 Sum_probs=51.0
Q ss_pred CCccccCc----CCcccccc-ccccccccccccccccCceEeCCCCCCeeeCCC--CCCCcccCcccHHH
Q psy1895 68 EAQWAKDK----EAITCRAC-DKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPS--AAKPVRVCDECNVK 130 (140)
Q Consensus 68 ~~~W~~~~----~~~~C~~C-~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~--~~~~~RVC~~C~~~ 130 (140)
..+|+||. .-..|+.| +..|..++||||||.||...|..|...+..... +..|.++|+.|+..
T Consensus 313 l~nfq~darrafs~a~~~a~~R~~~kd~~Rk~~~~g~Ga~e~aa~ea~kgiqEd~gse~~Adg~Dq~psv 382 (1141)
T KOG1811|consen 313 LHNFQPDARRAFSEAICMACCREHFKDFNRKHHCRGCGALECAACEAKKGIQEDCGSENPADGCDQCPSV 382 (1141)
T ss_pred hhhcChhhhhhhhhhHHHHHHHHHHHHHHHhhhccccchHHHhHHHHhhhhhhcccccCcccccccccch
Confidence 46799987 44567754 557999999999999999999999988765543 37899999999954
No 15
>KOG0230|consensus
Probab=97.32 E-value=0.00014 Score=69.46 Aligned_cols=49 Identities=43% Similarity=1.055 Sum_probs=40.2
Q ss_pred CccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhcc
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVEK 134 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~~ 134 (140)
...|..|+ +.++++|||+.||++||+.|... .....|||..|+......
T Consensus 5 ~~~~~~~~---t~~~~~~~~~~~g~~~~~~~~~~------~~~~i~~~~~~~~~~~~~ 53 (1598)
T KOG0230|consen 5 SNVCYDCD---TSVNRRHHCRVCGRVFCSKCQDS------PETSIRVCNECRGQWEQG 53 (1598)
T ss_pred ccchhccc---cccccCCCCcccCceeccccCCC------Cccceeehhhhhhhcccc
Confidence 45677787 78899999999999999999833 234899999999987653
No 16
>KOG0230|consensus
Probab=96.84 E-value=0.00067 Score=65.02 Aligned_cols=34 Identities=44% Similarity=1.199 Sum_probs=33.2
Q ss_pred ccCcCCccccccccccccccccccccccCceEeCCC
Q psy1895 72 AKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 72 ~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
.||.....|..|...|..++|+||| ||+|||..|
T Consensus 92 m~d~s~~ec~~~~~~~~t~Rr~~~~--~gqi~~ss~ 125 (1598)
T KOG0230|consen 92 MPDSSSKECYDCEQKFETFRRKHHC--CGQIFCSSC 125 (1598)
T ss_pred CCccccchhhhhccchhhhhccccc--CccccCCcc
Confidence 8889999999999999999999999 999999999
No 17
>KOG0993|consensus
Probab=95.53 E-value=0.0017 Score=55.50 Aligned_cols=65 Identities=23% Similarity=0.548 Sum_probs=55.7
Q ss_pred CccccCcCCccccccccccccccccccccc--cCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 69 AQWAKDKEAITCRACDKEFTVTRRRHHCRN--CGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~--CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
..|.-+.+...|..|..+|..++-.-||-+ |++|||-.|+...+|--.+..|..||..|+..+.+
T Consensus 460 le~ql~~~ve~c~~~~aS~~slk~e~erl~qq~eqi~~~~~~Katvp~l~~e~~akv~rlq~eL~~s 526 (542)
T KOG0993|consen 460 LEWQLDDDVEQCSNCDASFASLKVEPERLHQQCEQIFCMNCLKATVPSLPNERPAKVCRLQHELLNS 526 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhHHHhhcccccccchHHHHHHHHHHhhh
Confidence 567778888999999999999999999988 99999999998765544458999999999988764
No 18
>KOG1841|consensus
Probab=94.42 E-value=0.022 Score=53.75 Aligned_cols=56 Identities=30% Similarity=0.449 Sum_probs=46.9
Q ss_pred cCCccccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 67 TEAQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 67 ~~~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
.++.|++|..+..|+.|.+.|.++.++|||| |.++ .+-.+.+..|+|..|+..+..
T Consensus 647 ~ksVw~aDg~aPng~la~t~~~~~~e~~hsr--~~ls---------~~~~s~~~~~~~n~t~s~~rn 702 (1287)
T KOG1841|consen 647 VKSVWFADGIAPNGELAETRFTFTGERHHSR--GKLS---------LLYSSRKEARPCNITHSVLRN 702 (1287)
T ss_pred ecceeccCCcCCCceecccceeeeccccccc--cccc---------ccccccccCCCCcccCccchh
Confidence 4589999999999999999999999999999 8877 222235677999999887765
No 19
>KOG1729|consensus
Probab=93.04 E-value=0.018 Score=47.25 Aligned_cols=62 Identities=27% Similarity=0.628 Sum_probs=49.9
Q ss_pred CccccCcCCccccccccccccccccccccccCceEeCCCCC-Ce--eeC-CCC----CCCcccCcccHHH
Q psy1895 69 AQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSD-NK--MAL-PSA----AKPVRVCDECNVK 130 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~-~~--~~l-p~~----~~~~RVC~~C~~~ 130 (140)
+.|+.+.++..|..|...|.+..|.|||+.||+++|..|.. .. ..+ |.. ..+..+|..|+..
T Consensus 12 ~~~~~~~e~~s~~~~~~e~~~~~r~~~~~~~grv~~~q~~~~k~~rk~~q~r~~~l~~D~~~~~~~~~~~ 81 (288)
T KOG1729|consen 12 VDWQANSEANSCRNCKVEFCFGRRGHPCRECGRVLCRQGTLVKRCRKKLQSRSFFLFNDILVYGNIVSDN 81 (288)
T ss_pred HHHHHhccchhhhhhcccchhhhccCcccccchhhhhhhhhHHHHhcccccccccccccchhhcccccCH
Confidence 77899999999999999999999999999999999999987 11 111 111 5667788888766
No 20
>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=91.88 E-value=0.031 Score=34.39 Aligned_cols=43 Identities=28% Similarity=0.675 Sum_probs=24.7
Q ss_pred cccccccccccc------cccccccccCceEeCCCCCCeeeCCCCCCCcccCccc
Q psy1895 79 TCRACDKEFTVT------RRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDEC 127 (140)
Q Consensus 79 ~C~~C~~~F~~~------~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C 127 (140)
.|..|.++|... ..++.|..|+++||..|=.+- ......|.-|
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi------HE~LH~CPGC 49 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI------HETLHNCPGC 49 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT------TTTS-SSSTT
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcChhh------hccccCCcCC
Confidence 378899999875 367999999999999985441 2344555554
No 21
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.59 E-value=0.15 Score=36.37 Aligned_cols=35 Identities=26% Similarity=0.611 Sum_probs=28.1
Q ss_pred CCccccccccccccc----------cccccccccCceEeCCCCCC
Q psy1895 76 EAITCRACDKEFTVT----------RRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~----------~rkhhCr~CG~i~C~~Cs~~ 110 (140)
....|..|+.+|... ..++.|..|..+||.+|=.+
T Consensus 54 ~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f 98 (112)
T TIGR00622 54 GSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVF 98 (112)
T ss_pred CCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchh
Confidence 345699999999742 34678999999999999655
No 22
>KOG4275|consensus
Probab=90.60 E-value=0.03 Score=46.06 Aligned_cols=52 Identities=29% Similarity=0.784 Sum_probs=43.3
Q ss_pred ccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHH
Q psy1895 72 AKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVK 130 (140)
Q Consensus 72 ~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~ 130 (140)
-+...+.+|..|+..|..+.+||-|-.|.+-||..||.. ....|.|..|...
T Consensus 39 s~~~~~p~ckacg~~f~~~~~k~~c~dckk~fc~tcs~v-------~~~lr~c~~c~r~ 90 (350)
T KOG4275|consen 39 SSSSQAPHCKACGEEFEDAQSKSDCEDCKKEFCATCSRV-------SISLRTCTSCRRV 90 (350)
T ss_pred CcccccchhhhhchhHhhhhhhhhhhhhhHHHHHHHHHh-------cccchhhhHHHHH
Confidence 344556799999999999999999999999999999944 3456888888754
No 23
>KOG3799|consensus
Probab=88.89 E-value=1.3 Score=32.85 Aligned_cols=50 Identities=32% Similarity=0.766 Sum_probs=36.6
Q ss_pred Ccccccccc-ccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHH
Q psy1895 77 AITCRACDK-EFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNV 129 (140)
Q Consensus 77 ~~~C~~C~~-~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~ 129 (140)
...|.+|.+ +|.- .=-|.|..|.--||..|... +.+ .+++-..||+.|-.
T Consensus 65 datC~IC~KTKFAD-G~GH~C~YCq~r~CARCGGr-v~l-rsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 65 DATCGICHKTKFAD-GCGHNCSYCQTRFCARCGGR-VSL-RSNKVMWVCNLCRK 115 (169)
T ss_pred Ccchhhhhhccccc-ccCcccchhhhhHHHhcCCe-eee-ccCceEEeccCCcH
Confidence 347999988 3542 23488999999999999865 322 23677889999964
No 24
>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=88.37 E-value=0.33 Score=34.25 Aligned_cols=32 Identities=25% Similarity=0.622 Sum_probs=23.2
Q ss_pred CccccCcCCcccccccccccccccc-ccccccCceE
Q psy1895 69 AQWAKDKEAITCRACDKEFTVTRRR-HHCRNCGEIF 103 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~~~~rk-hhCr~CG~i~ 103 (140)
+-|--. ..|+.|+++|==|+|. ..|..||.+|
T Consensus 4 pelGtK---R~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 4 PELGTK---RTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cccCCc---ccCCCCcchhccCCCCCccCCCCCCcc
Confidence 455443 4899999999866554 4488888876
No 25
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=87.56 E-value=0.12 Score=30.22 Aligned_cols=42 Identities=29% Similarity=0.762 Sum_probs=27.3
Q ss_pred cccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCccc
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDEC 127 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C 127 (140)
+|..|...|+ -.++..=-.||++||..|..... ....+|..|
T Consensus 1 ~C~~C~~~~~-~~~~~~l~~CgH~~C~~C~~~~~------~~~~~CP~C 42 (44)
T PF14634_consen 1 HCNICFEKYS-EERRPRLTSCGHIFCEKCLKKLK------GKSVKCPIC 42 (44)
T ss_pred CCcCcCcccc-CCCCeEEcccCCHHHHHHHHhhc------CCCCCCcCC
Confidence 4778888882 12233345899999999987654 234555555
No 26
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.40 E-value=0.3 Score=36.55 Aligned_cols=25 Identities=40% Similarity=0.870 Sum_probs=19.4
Q ss_pred cccccccccc------------cccccccccccCceE
Q psy1895 79 TCRACDKEFT------------VTRRRHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~------------~~~rkhhCr~CG~i~ 103 (140)
.|+.|+.+++ ..+|+++|++||..|
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5888888772 355678999999877
No 27
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.60 E-value=0.41 Score=27.07 Aligned_cols=25 Identities=32% Similarity=1.063 Sum_probs=17.4
Q ss_pred cccccccccccc-------cccccccccCceE
Q psy1895 79 TCRACDKEFTVT-------RRRHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~~~-------~rkhhCr~CG~i~ 103 (140)
.|..|++.|.+- .++..|.+||++|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 588888888732 3456677887765
No 28
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=86.27 E-value=0.44 Score=27.49 Aligned_cols=26 Identities=38% Similarity=1.063 Sum_probs=19.0
Q ss_pred ccccccccccccccccccccCceEeCCC
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
|..|++.-.++ ...|+.|+.+||...
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCccccc--CeECCccCCcccccc
Confidence 55677765554 577999999998754
No 29
>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=85.77 E-value=0.26 Score=32.27 Aligned_cols=55 Identities=24% Similarity=0.588 Sum_probs=27.8
Q ss_pred cccccccccccccccccccccCce-----EeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI-----FCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i-----~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
.|+.|+.+........||..|+.- +|..|-..-..|-.-+..--.|..|+..++.
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiSK 62 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLISK 62 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE-T
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCceeec
Confidence 588888887777778888888764 5666655433222223334556666665543
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.73 E-value=0.4 Score=27.20 Aligned_cols=25 Identities=40% Similarity=1.079 Sum_probs=18.4
Q ss_pred cccccccccccc-------cccccccccCceE
Q psy1895 79 TCRACDKEFTVT-------RRRHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~~~-------~rkhhCr~CG~i~ 103 (140)
.|+.|+..|.+- .++..|..||.+|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 688899988743 3466788888776
No 31
>KOG2164|consensus
Probab=84.48 E-value=0.26 Score=43.18 Aligned_cols=51 Identities=29% Similarity=0.573 Sum_probs=39.1
Q ss_pred ccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
..|++|=.++.+-.+- +||+|||..|.-+....+ .....+-|..|+..+..
T Consensus 187 ~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s-~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 187 MQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYS-AIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcccCCCCccccc----ccCceeeHHHHHHHHhhh-cccCCccCCchhhhccc
Confidence 5899999988865553 499999999987655444 35667889999988754
No 32
>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=83.46 E-value=0.79 Score=33.36 Aligned_cols=26 Identities=27% Similarity=0.353 Sum_probs=20.6
Q ss_pred ccccccccccccc-cccccccccCceE
Q psy1895 78 ITCRACDKEFTVT-RRRHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~-~rkhhCr~CG~i~ 103 (140)
..|+.|+++|=-| +.-..|..||.+|
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCcc
Confidence 4899999999854 5566788888876
No 33
>KOG0320|consensus
Probab=82.72 E-value=0.15 Score=39.16 Aligned_cols=47 Identities=23% Similarity=0.721 Sum_probs=33.2
Q ss_pred ccccccccccccccccc-cccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 78 ITCRACDKEFTVTRRRH-HCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkh-hCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
-.|.+|-.+|+ .+. ---.||+|||..|....+ +..++|..|.+.|..
T Consensus 132 ~~CPiCl~~~s---ek~~vsTkCGHvFC~~Cik~al------k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 132 YKCPICLDSVS---EKVPVSTKCGHVFCSQCIKDAL------KNTNKCPTCRKKITH 179 (187)
T ss_pred cCCCceecchh---hccccccccchhHHHHHHHHHH------HhCCCCCCcccccch
Confidence 35777766665 222 346899999999987643 467899999987754
No 34
>KOG3576|consensus
Probab=82.44 E-value=0.26 Score=38.97 Aligned_cols=32 Identities=44% Similarity=1.010 Sum_probs=23.7
Q ss_pred ccCcCCccccccccccc---cccc---------cccccccCceE
Q psy1895 72 AKDKEAITCRACDKEFT---VTRR---------RHHCRNCGEIF 103 (140)
Q Consensus 72 ~~~~~~~~C~~C~~~F~---~~~r---------khhCr~CG~i~ 103 (140)
-+|.+.-.|.+|++.|+ +++| ||-|..||+.|
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgf 155 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGF 155 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcc
Confidence 34566678999999998 3433 67788888876
No 35
>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=80.72 E-value=0.46 Score=27.42 Aligned_cols=33 Identities=24% Similarity=0.595 Sum_probs=24.3
Q ss_pred cccccccccccccccccccccCceEeCCCCCCee
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
.|.+|...|..-..-.-. .||++||..|...++
T Consensus 2 ~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWL 34 (44)
T ss_dssp CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHH
Confidence 689999999753333334 499999999987654
No 36
>PF12773 DZR: Double zinc ribbon
Probab=80.25 E-value=1.3 Score=26.25 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=18.7
Q ss_pred CcCCccccccccccc-cccccccccccCce
Q psy1895 74 DKEAITCRACDKEFT-VTRRRHHCRNCGEI 102 (140)
Q Consensus 74 ~~~~~~C~~C~~~F~-~~~rkhhCr~CG~i 102 (140)
+.++..|..|+.++. .......|..||..
T Consensus 9 ~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 344678888888877 23334567777664
No 37
>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=79.38 E-value=1.8 Score=26.34 Aligned_cols=33 Identities=24% Similarity=0.624 Sum_probs=20.5
Q ss_pred ccccc--ccccccccccc----ccccccCceEeCCCCCC
Q psy1895 78 ITCRA--CDKEFTVTRRR----HHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 78 ~~C~~--C~~~F~~~~rk----hhCr~CG~i~C~~Cs~~ 110 (140)
..|+. |+..|..-... ..|..||..||..|...
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 46765 88877643332 67999999999999764
No 38
>KOG0978|consensus
Probab=78.92 E-value=0.73 Score=42.04 Aligned_cols=44 Identities=25% Similarity=0.811 Sum_probs=31.8
Q ss_pred ccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHH
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVK 130 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~ 130 (140)
-.|+.|+..+-- --=..||++||..|...+. ....|-|..|...
T Consensus 644 LkCs~Cn~R~Kd----~vI~kC~H~FC~~Cvq~r~-----etRqRKCP~Cn~a 687 (698)
T KOG0978|consen 644 LKCSVCNTRWKD----AVITKCGHVFCEECVQTRY-----ETRQRKCPKCNAA 687 (698)
T ss_pred eeCCCccCchhh----HHHHhcchHHHHHHHHHHH-----HHhcCCCCCCCCC
Confidence 468999875541 0124799999999987643 5678999999754
No 39
>PRK00420 hypothetical protein; Validated
Probab=78.01 E-value=1.5 Score=31.12 Aligned_cols=25 Identities=16% Similarity=0.380 Sum_probs=16.1
Q ss_pred cccccccccccc-ccccccccccCce
Q psy1895 78 ITCRACDKEFTV-TRRRHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~~-~~rkhhCr~CG~i 102 (140)
.+|+.|+.+|.- -..+..|..||.+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 589999988764 3344445555554
No 40
>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=77.72 E-value=0.22 Score=27.71 Aligned_cols=42 Identities=31% Similarity=0.734 Sum_probs=25.9
Q ss_pred ccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHH
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNV 129 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~ 129 (140)
|.+|...| .....-..||+.||..|....... ....|..|..
T Consensus 2 C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~-----~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF---REPVVLLPCGHVFCRSCIDKWLKS-----GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh---hCceEecCCCChhcHHHHHHHHHh-----CcCCCCCCCC
Confidence 67777776 233344569999999998654321 2344666543
No 41
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.88 E-value=1.8 Score=25.46 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=17.0
Q ss_pred cccccccccccccc--cccccccCce
Q psy1895 79 TCRACDKEFTVTRR--RHHCRNCGEI 102 (140)
Q Consensus 79 ~C~~C~~~F~~~~r--khhCr~CG~i 102 (140)
.|..|+..|.+-.. ..+|..||.-
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCe
Confidence 58889998875444 4678877763
No 42
>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=73.70 E-value=2.2 Score=23.20 Aligned_cols=26 Identities=27% Similarity=0.629 Sum_probs=14.0
Q ss_pred eEeCCCCCCeeeCCCCCCCcccCcccHH
Q psy1895 102 IFCNMCSDNKMALPSAAKPVRVCDECNV 129 (140)
Q Consensus 102 i~C~~Cs~~~~~lp~~~~~~RVC~~C~~ 129 (140)
-||..|.....+.+ ....|+|..|-.
T Consensus 4 rfC~~CG~~t~~~~--~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAP--GGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-S--SSS-EEESSSS-
T ss_pred cccCcCCccccCCC--CcCEeECCCCcC
Confidence 36777776655544 478899998854
No 43
>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=73.12 E-value=2.2 Score=23.78 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=7.6
Q ss_pred cccccccccccc
Q psy1895 79 TCRACDKEFTVT 90 (140)
Q Consensus 79 ~C~~C~~~F~~~ 90 (140)
.|..|++.|.+-
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 477777766643
No 44
>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=72.85 E-value=2.1 Score=22.54 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=12.0
Q ss_pred cccccccccccccccccccccCceE
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~ 103 (140)
.|+.|++.-... -.-|.+||..|
T Consensus 2 ~CP~C~~~V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPES--AKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhh--cCcCCCCCCCC
Confidence 466666644322 23466666654
No 45
>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=72.12 E-value=0.91 Score=37.64 Aligned_cols=49 Identities=22% Similarity=0.498 Sum_probs=31.4
Q ss_pred ccccccccccccccc---cccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhhc
Q psy1895 78 ITCRACDKEFTVTRR---RHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVE 133 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r---khhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~~ 133 (140)
..|+.|...--+... -.+ .||+.||..|....... +...|..|...+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~l~~~-----~~~~CP~C~~~lrk 55 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDLLFVR-----GSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcCCCCCccCcccccccC--CCCCcccHHHHHHHhcC-----CCCCCCCCCCccch
Confidence 369999984222222 334 79999999998874322 22368888766543
No 46
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=71.18 E-value=2 Score=33.29 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=33.2
Q ss_pred cccccCceEeCCCCCC-eeeCCCC------CCCcccCcccHHHhhccc
Q psy1895 95 HCRNCGEIFCNMCSDN-KMALPSA------AKPVRVCDECNVKLVEKL 135 (140)
Q Consensus 95 hCr~CG~i~C~~Cs~~-~~~lp~~------~~~~RVC~~C~~~l~~~~ 135 (140)
.|...|+.||..|-.. ...+|.. -++..||+..+..|....
T Consensus 2 ~C~Y~G~yyC~~CH~~~~~vIParil~~WDf~~~pVs~~a~~~L~~~~ 49 (202)
T PF13901_consen 2 FCDYTGKYYCSSCHWNDTSVIPARILHNWDFRPYPVSRFAKQFLDQIW 49 (202)
T ss_pred ccCCCCCcCCCCCCCCCceeccHHHHHhcCCCccHHHHHHHHHHHHhc
Confidence 5889999999999887 4566654 688899999999886543
No 47
>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=71.14 E-value=1.4 Score=24.80 Aligned_cols=29 Identities=31% Similarity=0.769 Sum_probs=18.9
Q ss_pred ccccccccccccccccccccCceEeCCCCCCe
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMCSDNK 111 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~ 111 (140)
|.+|...+ .....--.||++||..|....
T Consensus 1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~~ 29 (39)
T PF13923_consen 1 CPICLDEL---RDPVVVTPCGHSFCKECIEKY 29 (39)
T ss_dssp ETTTTSB----SSEEEECTTSEEEEHHHHHHH
T ss_pred CCCCCCcc---cCcCEECCCCCchhHHHHHHH
Confidence 45564433 234456789999999997654
No 48
>PHA02768 hypothetical protein; Provisional
Probab=70.48 E-value=2.5 Score=26.32 Aligned_cols=25 Identities=24% Similarity=0.507 Sum_probs=16.8
Q ss_pred cccccccccccc------cc----cccccccCceE
Q psy1895 79 TCRACDKEFTVT------RR----RHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~~~------~r----khhCr~CG~i~ 103 (140)
.|..|++.|+.. .| .+.|-.||++|
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f 41 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRIS 41 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCccccee
Confidence 699999999722 22 33477777765
No 49
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=70.28 E-value=0.83 Score=35.45 Aligned_cols=56 Identities=16% Similarity=0.412 Sum_probs=36.7
Q ss_pred cCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCC----------CCCCcccCcccHHHhh
Q psy1895 73 KDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPS----------AAKPVRVCDECNVKLV 132 (140)
Q Consensus 73 ~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~----------~~~~~RVC~~C~~~l~ 132 (140)
+....-.|.+|...|.-- .--.||++||..|...+..... ..+....|..|...+.
T Consensus 14 ~~~~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 14 DSGGDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred cCCCccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 333456899999877521 2257999999999876432211 0234568999987764
No 50
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=68.73 E-value=1.6 Score=25.63 Aligned_cols=30 Identities=27% Similarity=0.830 Sum_probs=13.8
Q ss_pred ccccccccccccccccccccCceEeCCCCCC
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
|.+|.. |+.-...--=-.||++||..|...
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~ 30 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQK 30 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHH
Confidence 566666 654222222346999999888654
No 51
>KOG1814|consensus
Probab=68.53 E-value=9.3 Score=33.05 Aligned_cols=43 Identities=23% Similarity=0.773 Sum_probs=32.5
Q ss_pred CccccCcCCcccccccccccccc--ccccccccCceEeCCCCCCee
Q psy1895 69 AQWAKDKEAITCRACDKEFTVTR--RRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~F~~~~--rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
..|+..+ ...|+.|.....-.. -|.||-.||..||.-|+.--.
T Consensus 361 ekwl~~N-~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 361 EKWLESN-SKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHhc-CCCCCcccceeecCCCccceeeccccccceeehhhhcC
Confidence 3576543 568999988765443 478999999999999987544
No 52
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=67.46 E-value=2.9 Score=26.47 Aligned_cols=16 Identities=38% Similarity=0.999 Sum_probs=8.6
Q ss_pred ccccccccc--ccccCce
Q psy1895 87 FTVTRRRHH--CRNCGEI 102 (140)
Q Consensus 87 F~~~~rkhh--Cr~CG~i 102 (140)
|+-.+++.| ||.||+.
T Consensus 8 ~GKrnk~tH~~CRRCGr~ 25 (61)
T COG2126 8 FGKRNKKTHIRCRRCGRR 25 (61)
T ss_pred ccccCCcceehhhhccch
Confidence 444444444 7777654
No 53
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=65.36 E-value=7.6 Score=28.32 Aligned_cols=20 Identities=15% Similarity=0.293 Sum_probs=13.4
Q ss_pred ccccCcCCcccccccccccc
Q psy1895 70 QWAKDKEAITCRACDKEFTV 89 (140)
Q Consensus 70 ~W~~~~~~~~C~~C~~~F~~ 89 (140)
.+.++..-+.|..|+..+-.
T Consensus 84 ~~~~~~~~sRC~~CN~~L~~ 103 (147)
T PF01927_consen 84 KLRLDPIFSRCPKCNGPLRP 103 (147)
T ss_pred ccccCCCCCccCCCCcEeee
Confidence 33445556789999987653
No 54
>KOG0823|consensus
Probab=64.67 E-value=1.6 Score=34.69 Aligned_cols=32 Identities=22% Similarity=0.609 Sum_probs=21.7
Q ss_pred cccCceEeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 97 RNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 97 r~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
-.||+.||+.|.-++..+-. -...|..|...+
T Consensus 63 TlCGHLFCWpClyqWl~~~~---~~~~cPVCK~~V 94 (230)
T KOG0823|consen 63 TLCGHLFCWPCLYQWLQTRP---NSKECPVCKAEV 94 (230)
T ss_pred eecccceehHHHHHHHhhcC---CCeeCCcccccc
Confidence 48999999999987765433 234556665544
No 55
>KOG0317|consensus
Probab=64.58 E-value=1.9 Score=35.49 Aligned_cols=45 Identities=29% Similarity=0.614 Sum_probs=28.3
Q ss_pred ccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
..|..|=.. +.--.|-.||+|||+.|..-+.. .++. |..|.....
T Consensus 240 ~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~----ek~e--CPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLEN----RSNPSATPCGHIFCWSCILEWCS----EKAE--CPLCREKFQ 284 (293)
T ss_pred CceEEEecC----CCCCCcCcCcchHHHHHHHHHHc----cccC--CCcccccCC
Confidence 467777541 22334999999999999765432 1222 777766543
No 56
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=64.24 E-value=2.4 Score=26.62 Aligned_cols=15 Identities=40% Similarity=1.035 Sum_probs=12.0
Q ss_pred cccccccccCceEeC
Q psy1895 91 RRRHHCRNCGEIFCN 105 (140)
Q Consensus 91 ~rkhhCr~CG~i~C~ 105 (140)
.---+|-+||+|+|.
T Consensus 16 ~~~~NCl~CGkIiC~ 30 (57)
T PF06221_consen 16 PYAPNCLNCGKIICE 30 (57)
T ss_pred cccccccccChhhcc
Confidence 335789999999986
No 57
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=63.76 E-value=3.5 Score=24.55 Aligned_cols=14 Identities=36% Similarity=0.935 Sum_probs=10.0
Q ss_pred cccccccccccccc
Q psy1895 79 TCRACDKEFTVTRR 92 (140)
Q Consensus 79 ~C~~C~~~F~~~~r 92 (140)
.|..|+..|..+..
T Consensus 7 ~C~~Cg~~fe~~~~ 20 (52)
T TIGR02605 7 RCTACGHRFEVLQK 20 (52)
T ss_pred EeCCCCCEeEEEEe
Confidence 47788888876644
No 58
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.68 E-value=4.6 Score=36.75 Aligned_cols=33 Identities=24% Similarity=0.707 Sum_probs=25.3
Q ss_pred CcCCccccccccccccccccccccccCce------EeCCCCCC
Q psy1895 74 DKEAITCRACDKEFTVTRRRHHCRNCGEI------FCNMCSDN 110 (140)
Q Consensus 74 ~~~~~~C~~C~~~F~~~~rkhhCr~CG~i------~C~~Cs~~ 110 (140)
...+..|..|+.++.. ..|..||.. ||..|...
T Consensus 12 ~~~akFC~~CG~~l~~----~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 12 PNNNRFCQKCGTSLTH----KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCCccccccCCCCCC----CcCCCCCCCCCcccccccccCCc
Confidence 3456789999998853 369999987 88888765
No 59
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.06 E-value=3.8 Score=28.93 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=17.8
Q ss_pred CccccccccccccccccccccccCc
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
.-.|..|+..|........|..||.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcC
Confidence 3578999988887655555776664
No 60
>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=62.85 E-value=6.7 Score=24.59 Aligned_cols=28 Identities=29% Similarity=0.593 Sum_probs=21.4
Q ss_pred CCcccccccccccc--ccccccccccCceE
Q psy1895 76 EAITCRACDKEFTV--TRRRHHCRNCGEIF 103 (140)
Q Consensus 76 ~~~~C~~C~~~F~~--~~rkhhCr~CG~i~ 103 (140)
....|..|+..-.. ..|.+.|..||..+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 34579999987654 67788899999864
No 61
>KOG4739|consensus
Probab=62.70 E-value=2.5 Score=33.76 Aligned_cols=43 Identities=21% Similarity=0.580 Sum_probs=28.6
Q ss_pred cccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
+|..|...=+ ....+=-.|++|||..|..... .++|..|...+
T Consensus 5 hCn~C~~~~~--~~~f~LTaC~HvfC~~C~k~~~--------~~~C~lCkk~i 47 (233)
T KOG4739|consen 5 HCNKCFRFPS--QDPFFLTACRHVFCEPCLKASS--------PDVCPLCKKSI 47 (233)
T ss_pred EeccccccCC--CCceeeeechhhhhhhhcccCC--------cccccccccee
Confidence 5777766322 3333445899999999987532 12999998764
No 62
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=62.35 E-value=3.1 Score=23.51 Aligned_cols=16 Identities=44% Similarity=0.846 Sum_probs=10.7
Q ss_pred CCcccCcccHHHhhcc
Q psy1895 119 KPVRVCDECNVKLVEK 134 (140)
Q Consensus 119 ~~~RVC~~C~~~l~~~ 134 (140)
+..-+|+.|-..|.++
T Consensus 19 ~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 19 KVEGVCDNCGGELVQR 34 (36)
T ss_dssp SSTTBCTTTTEBEBEE
T ss_pred CCCCccCCCCCeeEeC
Confidence 4557788887766554
No 63
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=62.10 E-value=43 Score=22.12 Aligned_cols=33 Identities=21% Similarity=0.487 Sum_probs=23.0
Q ss_pred cCCccccccccccccccccccccccCceEeCCCCC
Q psy1895 75 KEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSD 109 (140)
Q Consensus 75 ~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~ 109 (140)
.+...|..|+++|+. ....--.||.+|-..|..
T Consensus 76 ~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 334579999999874 333444778888877754
No 64
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=61.83 E-value=2.7 Score=29.56 Aligned_cols=24 Identities=33% Similarity=0.855 Sum_probs=17.1
Q ss_pred ccccccccccccccccccccccCc
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
-.|..|+..|.+-.....|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGS 94 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCcC
Confidence 569999999987766677777775
No 65
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.82 E-value=4.7 Score=23.79 Aligned_cols=23 Identities=30% Similarity=0.859 Sum_probs=15.0
Q ss_pred cccccccccccc-cccccccccCc
Q psy1895 79 TCRACDKEFTVT-RRRHHCRNCGE 101 (140)
Q Consensus 79 ~C~~C~~~F~~~-~rkhhCr~CG~ 101 (140)
.|..|+..|.+- .....|+.||.
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCc
Confidence 488899988865 23344666653
No 66
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=61.70 E-value=7.5 Score=23.47 Aligned_cols=32 Identities=31% Similarity=0.697 Sum_probs=22.6
Q ss_pred ccc--cccccccc----ccccccccccCceEeCCCCCC
Q psy1895 79 TCR--ACDKEFTV----TRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 79 ~C~--~C~~~F~~----~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
-|+ .|+..... ......|..||..||..|...
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 355 66554433 345677999999999999764
No 67
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=60.97 E-value=3.9 Score=34.29 Aligned_cols=41 Identities=22% Similarity=0.575 Sum_probs=31.8
Q ss_pred ccccCcCCccccccccccc----------cccccccccccCceEeCCCCCC
Q psy1895 70 QWAKDKEAITCRACDKEFT----------VTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 70 ~W~~~~~~~~C~~C~~~F~----------~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
.|-.......|..|+-+|. +...++.|..|..-||..|-.+
T Consensus 355 p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvf 405 (421)
T COG5151 355 PEGTNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVF 405 (421)
T ss_pred cCCCCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHH
Confidence 4455555678999999885 3466899999999999999643
No 68
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=60.76 E-value=1.4 Score=25.60 Aligned_cols=15 Identities=33% Similarity=0.944 Sum_probs=12.4
Q ss_pred ccCceEeCCCCCCee
Q psy1895 98 NCGEIFCNMCSDNKM 112 (140)
Q Consensus 98 ~CG~i~C~~Cs~~~~ 112 (140)
.||++||..|.....
T Consensus 15 ~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 15 PCGHSFCRSCLERLW 29 (42)
T ss_dssp SSSSEEEHHHHHHHH
T ss_pred CCcCHHHHHHHHHHH
Confidence 799999999977643
No 69
>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=60.10 E-value=6.1 Score=24.43 Aligned_cols=26 Identities=23% Similarity=0.678 Sum_probs=15.3
Q ss_pred c-ccCcCCcccccccccccccccccc-ccccC
Q psy1895 71 W-AKDKEAITCRACDKEFTVTRRRHH-CRNCG 100 (140)
Q Consensus 71 W-~~~~~~~~C~~C~~~F~~~~rkhh-Cr~CG 100 (140)
| ........|..|+. +...|| |..||
T Consensus 19 ~kl~~p~l~~C~~cG~----~~~~H~vc~~cG 46 (55)
T TIGR01031 19 AKLTAPTLVVCPNCGE----FKLPHRVCPSCG 46 (55)
T ss_pred ccccCCcceECCCCCC----cccCeeECCccC
Confidence 5 44445556777777 334444 77776
No 70
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=59.86 E-value=6.9 Score=23.70 Aligned_cols=27 Identities=30% Similarity=0.619 Sum_probs=17.3
Q ss_pred Cccccccccccc-cccccccccccCceE
Q psy1895 77 AITCRACDKEFT-VTRRRHHCRNCGEIF 103 (140)
Q Consensus 77 ~~~C~~C~~~F~-~~~rkhhCr~CG~i~ 103 (140)
...|+.|+..|- .-..+.+|..||..+
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 347888888422 334467788887654
No 71
>KOG3173|consensus
Probab=58.38 E-value=5.2 Score=30.26 Aligned_cols=29 Identities=34% Similarity=0.878 Sum_probs=23.0
Q ss_pred CCccccccccccccccccccccccCceEeCCC
Q psy1895 76 EAITCRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
....|..|.++-++.. .+|| ||.+||...
T Consensus 104 ~~~rC~~C~kk~gltg--f~Cr-CG~~fC~~H 132 (167)
T KOG3173|consen 104 KKKRCFKCRKKVGLTG--FKCR-CGNTFCGTH 132 (167)
T ss_pred cchhhhhhhhhhcccc--cccc-cCCcccccc
Confidence 3456999999888877 8886 899998754
No 72
>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=58.22 E-value=3.5 Score=23.00 Aligned_cols=30 Identities=27% Similarity=0.612 Sum_probs=19.7
Q ss_pred ccccccccccccccccccccCceEeCCCCCCee
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
|.+|...|.... .=..||+.||..|....+
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHHHH
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHHHH
Confidence 456666555332 345899999999977644
No 73
>PF14353 CpXC: CpXC protein
Probab=57.76 E-value=5.2 Score=28.28 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.1
Q ss_pred cccccccCceE
Q psy1895 93 RHHCRNCGEIF 103 (140)
Q Consensus 93 khhCr~CG~i~ 103 (140)
.+.|..||..+
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 57788888765
No 74
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=57.56 E-value=9.9 Score=20.26 Aligned_cols=28 Identities=21% Similarity=0.509 Sum_probs=21.7
Q ss_pred cccccccccccccccccccccCceEeCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
.|..|++..+-+. -++|..|+-.+-..|
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCCCeEcCcc
Confidence 4888988887666 899998887666555
No 75
>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=56.96 E-value=7.2 Score=22.46 Aligned_cols=9 Identities=22% Similarity=0.719 Sum_probs=6.4
Q ss_pred ccccccccc
Q psy1895 79 TCRACDKEF 87 (140)
Q Consensus 79 ~C~~C~~~F 87 (140)
.|+.|+...
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 477787765
No 76
>PHA02926 zinc finger-like protein; Provisional
Probab=56.90 E-value=2 Score=34.33 Aligned_cols=54 Identities=19% Similarity=0.408 Sum_probs=32.8
Q ss_pred ccccccccccccccccccc------cccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 78 ITCRACDKEFTVTRRRHHC------RNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhC------r~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
..|.+|-....-- +...+ ..|+++||-.|-..+........-.+-|..|...+.
T Consensus 171 ~eCgICmE~I~eK-~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 171 KECGICYEVVYSK-RLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCccCccccccc-cccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 5788887532100 11122 489999999998876543222344677888876543
No 77
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=56.80 E-value=6.5 Score=21.29 Aligned_cols=23 Identities=26% Similarity=0.928 Sum_probs=15.3
Q ss_pred ccccccccccccccccccccccCceEeC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCN 105 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~ 105 (140)
..|.+|+. ..++.|..||..+|+
T Consensus 3 ~~C~vC~~-----~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-----PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-----EESEE-TTT--EESS
T ss_pred CCCccCcC-----CCEEECCCcCCceeC
Confidence 35778877 456889999999886
No 78
>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=56.71 E-value=5.6 Score=22.18 Aligned_cols=13 Identities=31% Similarity=0.871 Sum_probs=8.3
Q ss_pred ccccccccccccc
Q psy1895 79 TCRACDKEFTVTR 91 (140)
Q Consensus 79 ~C~~C~~~F~~~~ 91 (140)
.|..|+..|.++.
T Consensus 7 ~C~~Cg~~fe~~~ 19 (41)
T smart00834 7 RCEDCGHTFEVLQ 19 (41)
T ss_pred EcCCCCCEEEEEE
Confidence 4677777776543
No 79
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=55.25 E-value=6.1 Score=27.80 Aligned_cols=24 Identities=17% Similarity=0.598 Sum_probs=16.8
Q ss_pred ccccccccccccccccccccccCc
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
-.|..|+..|..-....-|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCC
Confidence 468888888877555555777764
No 80
>PF15616 TerY-C: TerY-C metal binding domain
Probab=54.46 E-value=8.6 Score=28.08 Aligned_cols=24 Identities=29% Similarity=0.989 Sum_probs=19.5
Q ss_pred ccccccccccccccccccccccCceEeCC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNM 106 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~ 106 (140)
..|+.|+..|.+. -| .||+++|..
T Consensus 78 PgCP~CGn~~~fa----~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 78 PGCPHCGNQYAFA----VC-GCGKLFCID 101 (131)
T ss_pred CCCCCCcChhcEE----Ee-cCCCEEEeC
Confidence 5799999998863 46 799999954
No 81
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=54.10 E-value=8.4 Score=21.53 Aligned_cols=27 Identities=26% Similarity=0.751 Sum_probs=12.1
Q ss_pred EeCCCCCC-eeeCCC-CCCCcccCcccHH
Q psy1895 103 FCNMCSDN-KMALPS-AAKPVRVCDECNV 129 (140)
Q Consensus 103 ~C~~Cs~~-~~~lp~-~~~~~RVC~~C~~ 129 (140)
||..|... ...+|. ...+-.||..|-.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 34444433 233443 3777789998854
No 82
>PRK12495 hypothetical protein; Provisional
Probab=53.70 E-value=17 Score=28.93 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=9.1
Q ss_pred Cccccccccccc
Q psy1895 77 AITCRACDKEFT 88 (140)
Q Consensus 77 ~~~C~~C~~~F~ 88 (140)
..+|..|+.+.-
T Consensus 42 a~hC~~CG~PIp 53 (226)
T PRK12495 42 NAHCDECGDPIF 53 (226)
T ss_pred hhhcccccCccc
Confidence 357999998755
No 83
>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=53.66 E-value=9.5 Score=21.03 Aligned_cols=23 Identities=26% Similarity=0.767 Sum_probs=13.4
Q ss_pred ccccccccccccc-ccccccccCc
Q psy1895 79 TCRACDKEFTVTR-RRHHCRNCGE 101 (140)
Q Consensus 79 ~C~~C~~~F~~~~-rkhhCr~CG~ 101 (140)
.|..|++.|.+-. ....|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 3777888877432 2345777774
No 84
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.81 E-value=7.2 Score=27.61 Aligned_cols=24 Identities=21% Similarity=0.678 Sum_probs=15.9
Q ss_pred ccccccccccccccccc-cccccCc
Q psy1895 78 ITCRACDKEFTVTRRRH-HCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkh-hCr~CG~ 101 (140)
-.|..|+..|.+..... +|..||.
T Consensus 72 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 72 LECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred EEhhhCCCccccCCccCCcCcCCCC
Confidence 46888888887754333 3766664
No 85
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.59 E-value=3.2 Score=33.79 Aligned_cols=44 Identities=30% Similarity=0.631 Sum_probs=27.6
Q ss_pred cccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHH
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVK 130 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~ 130 (140)
.|..|-..- ..--|..||++||..|.-.. ...+..-.|..|...
T Consensus 217 kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~----~t~~k~~~CplCRak 260 (271)
T COG5574 217 KCFLCLEEP----EVPSCTPCGHLFCLSCLLIS----WTKKKYEFCPLCRAK 260 (271)
T ss_pred ceeeeeccc----CCcccccccchhhHHHHHHH----HHhhccccCchhhhh
Confidence 577776632 23468999999999997541 112334446666544
No 86
>PRK01253 preprotein translocase subunit SecG; Reviewed
Probab=52.33 E-value=3.6 Score=25.49 Aligned_cols=24 Identities=33% Similarity=0.495 Sum_probs=20.5
Q ss_pred CCCCCCccchhhhHHHhhhhhhhc
Q psy1895 1 MTSGGLKRSFDDHVKMNKIAEHVK 24 (140)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~ 24 (140)
|+|+|+.+-||++..--|++|..-
T Consensus 11 ~ssAGL~ryy~ed~~~iKi~P~~V 34 (54)
T PRK01253 11 MSSAGLIRYFEEETEAIKIDPKTV 34 (54)
T ss_pred cccchhhhhhhcccCccccCCeee
Confidence 789999999999888888888743
No 87
>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=51.72 E-value=6.3 Score=24.86 Aligned_cols=27 Identities=26% Similarity=0.774 Sum_probs=17.1
Q ss_pred cccccccCceEeCCCCCCeeeCCCCCCCcccC-cccHHHhhc
Q psy1895 93 RHHCRNCGEIFCNMCSDNKMALPSAAKPVRVC-DECNVKLVE 133 (140)
Q Consensus 93 khhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC-~~C~~~l~~ 133 (140)
..||..||.. +|. ..+.| +.|-+.+..
T Consensus 3 HkHC~~CG~~-----------Ip~---~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 3 HKHCPVCGKP-----------IPP---DESFCSPKCREEYRK 30 (59)
T ss_pred CCcCCcCCCc-----------CCc---chhhhCHHHHHHHHH
Confidence 3678888874 232 46777 477766543
No 88
>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=50.89 E-value=7.4 Score=22.47 Aligned_cols=9 Identities=44% Similarity=1.280 Sum_probs=4.2
Q ss_pred ccccccccc
Q psy1895 80 CRACDKEFT 88 (140)
Q Consensus 80 C~~C~~~F~ 88 (140)
|..|+..|.
T Consensus 8 C~~Cg~~fe 16 (42)
T PF09723_consen 8 CEECGHEFE 16 (42)
T ss_pred eCCCCCEEE
Confidence 444444444
No 89
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=50.80 E-value=5.9 Score=22.03 Aligned_cols=8 Identities=50% Similarity=1.688 Sum_probs=2.5
Q ss_pred cccccCce
Q psy1895 95 HCRNCGEI 102 (140)
Q Consensus 95 hCr~CG~i 102 (140)
+|..||.+
T Consensus 13 rC~~Cg~~ 20 (37)
T PF12172_consen 13 RCRDCGRV 20 (37)
T ss_dssp E-TTT--E
T ss_pred EcCCCCCE
Confidence 35555554
No 90
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=50.50 E-value=9.8 Score=23.72 Aligned_cols=7 Identities=57% Similarity=1.550 Sum_probs=3.9
Q ss_pred ccccCce
Q psy1895 96 CRNCGEI 102 (140)
Q Consensus 96 Cr~CG~i 102 (140)
||.||..
T Consensus 18 CrRCG~~ 24 (55)
T PF01907_consen 18 CRRCGRR 24 (55)
T ss_dssp -TTTSSE
T ss_pred ecccCCe
Confidence 6666655
No 91
>KOG1829|consensus
Probab=49.12 E-value=9.3 Score=34.39 Aligned_cols=56 Identities=23% Similarity=0.567 Sum_probs=41.0
Q ss_pred CCccccccccccc--cccccccccccCceEeCCCCCCeeeC-CCC------CCCcccCcccHHHh
Q psy1895 76 EAITCRACDKEFT--VTRRRHHCRNCGEIFCNMCSDNKMAL-PSA------AKPVRVCDECNVKL 131 (140)
Q Consensus 76 ~~~~C~~C~~~F~--~~~rkhhCr~CG~i~C~~Cs~~~~~l-p~~------~~~~RVC~~C~~~l 131 (140)
..-.|..|+..++ ++.+-.-|+.+|.-||..|-.+...+ |.. -.+..||+.=+..|
T Consensus 339 Q~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~~y~Vs~~a~~~L 403 (580)
T KOG1829|consen 339 QNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFTKYPVSNFAKQFL 403 (580)
T ss_pred cCceecccCCCcccccccchhHhhhhhhhhCchhcccCcccccccceecccCcccccchhHHHHH
Confidence 3347999999998 45666679999999999998875544 543 46667776555444
No 92
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.12 E-value=8.4 Score=23.44 Aligned_cols=23 Identities=30% Similarity=0.862 Sum_probs=14.9
Q ss_pred cccccccccccc--cccccccccCc
Q psy1895 79 TCRACDKEFTVT--RRRHHCRNCGE 101 (140)
Q Consensus 79 ~C~~C~~~F~~~--~rkhhCr~CG~ 101 (140)
.|..|++.|.+. .+-..|..||.
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCeeehhhccCceeCCCCCc
Confidence 588999999744 33344666654
No 93
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=48.91 E-value=7 Score=26.57 Aligned_cols=25 Identities=28% Similarity=0.671 Sum_probs=18.0
Q ss_pred ccccccccccc---------cccccccccccCce
Q psy1895 78 ITCRACDKEFT---------VTRRRHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~---------~~~rkhhCr~CG~i 102 (140)
+.|..|+++.. .+.-|.+||.|+.-
T Consensus 34 S~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~ 67 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAP 67 (92)
T ss_pred CcCcCCCCcCcccccchHHHHHHhCCCCcccCCC
Confidence 57888888754 44557888888763
No 94
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=48.63 E-value=5.4 Score=27.85 Aligned_cols=52 Identities=23% Similarity=0.572 Sum_probs=32.5
Q ss_pred CCccccccccccccccccccc------ccc---CceEeCCCCCCeeeCCC---CCCCcccCcccHH
Q psy1895 76 EAITCRACDKEFTVTRRRHHC------RNC---GEIFCNMCSDNKMALPS---AAKPVRVCDECNV 129 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~~rkhhC------r~C---G~i~C~~Cs~~~~~lp~---~~~~~RVC~~C~~ 129 (140)
....|..|..+-. ..+..| ..| ...||..|...+...-. ...+..+|..|..
T Consensus 6 ~g~~CHqCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 6 NGKTCHQCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCchhhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 3457888888533 222334 555 89999999877543211 1456778888765
No 95
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=47.82 E-value=12 Score=30.38 Aligned_cols=35 Identities=29% Similarity=0.636 Sum_probs=26.8
Q ss_pred ccccCcCCccccccccccccc-------cccccccccCceEe
Q psy1895 70 QWAKDKEAITCRACDKEFTVT-------RRRHHCRNCGEIFC 104 (140)
Q Consensus 70 ~W~~~~~~~~C~~C~~~F~~~-------~rkhhCr~CG~i~C 104 (140)
.|-.-++++.|..|.++|... .-..||..|++.|=
T Consensus 125 rvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 125 RVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccCcccccccccccccccCCCccccccceeeeecccccccch
Confidence 345667788999999998743 33689999999873
No 96
>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=47.45 E-value=9.7 Score=21.24 Aligned_cols=26 Identities=27% Similarity=0.623 Sum_probs=13.4
Q ss_pred eEeCCCCCCeeeCCCCCCCcccCcccH
Q psy1895 102 IFCNMCSDNKMALPSAAKPVRVCDECN 128 (140)
Q Consensus 102 i~C~~Cs~~~~~lp~~~~~~RVC~~C~ 128 (140)
.||..|.+-..+-......+ +|..|-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~-~C~~C~ 27 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRV-ACRTCG 27 (35)
T ss_dssp -BETTTTSBEEEEEETTTTE-EESSSS
T ss_pred eeCCCCCccceEcCCCccCc-CCCCCC
Confidence 47777776543322223333 677773
No 97
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.64 E-value=10 Score=27.53 Aligned_cols=13 Identities=31% Similarity=1.071 Sum_probs=8.3
Q ss_pred ccccccccccccc
Q psy1895 78 ITCRACDKEFTVT 90 (140)
Q Consensus 78 ~~C~~C~~~F~~~ 90 (140)
-.|..|+..|.+-
T Consensus 71 ~~C~~CG~~~~~~ 83 (135)
T PRK03824 71 LKCRNCGNEWSLK 83 (135)
T ss_pred EECCCCCCEEecc
Confidence 4577777666654
No 98
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.12 E-value=14 Score=29.13 Aligned_cols=26 Identities=27% Similarity=0.718 Sum_probs=19.4
Q ss_pred cCCccccccccccccccccccccccCceE
Q psy1895 75 KEAITCRACDKEFTVTRRRHHCRNCGEIF 103 (140)
Q Consensus 75 ~~~~~C~~C~~~F~~~~rkhhCr~CG~i~ 103 (140)
.....|..|+. +..|...|..||..+
T Consensus 307 ~tS~~C~~cg~---~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH---LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC---ccceeEECCCCCCee
Confidence 44478999999 446677888888764
No 99
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.75 E-value=12 Score=19.24 Aligned_cols=7 Identities=29% Similarity=0.918 Sum_probs=3.5
Q ss_pred ccccccc
Q psy1895 79 TCRACDK 85 (140)
Q Consensus 79 ~C~~C~~ 85 (140)
.|..|++
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3555555
No 100
>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=45.74 E-value=10 Score=28.15 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=20.5
Q ss_pred CCcccccccccccc---ccccccccccCceE
Q psy1895 76 EAITCRACDKEFTV---TRRRHHCRNCGEIF 103 (140)
Q Consensus 76 ~~~~C~~C~~~F~~---~~rkhhCr~CG~i~ 103 (140)
.-=.|+.|+..|++ +.--.+|..||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 34469999999984 44567788888763
No 101
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=45.24 E-value=12 Score=25.92 Aligned_cols=34 Identities=26% Similarity=0.518 Sum_probs=26.5
Q ss_pred cccccccCceEeCC--CCCCeeeCCCCCCCcccCcccHHHhhcc
Q psy1895 93 RHHCRNCGEIFCNM--CSDNKMALPSAAKPVRVCDECNVKLVEK 134 (140)
Q Consensus 93 khhCr~CG~i~C~~--Cs~~~~~lp~~~~~~RVC~~C~~~l~~~ 134 (140)
--+|..||+.+|.. ||-+. ..|.|..|...-...
T Consensus 49 Ga~CS~C~~~VC~~~~CSlFY--------tkrFC~pC~~~~~~~ 84 (97)
T PF10170_consen 49 GAPCSICGKPVCVGQDCSLFY--------TKRFCLPCVKRNLKA 84 (97)
T ss_pred CccccccCCceEcCCCccEEe--------eCceeHHHHHHHHHH
Confidence 46899999999964 98774 459999998765543
No 102
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.23 E-value=11 Score=26.56 Aligned_cols=24 Identities=25% Similarity=0.695 Sum_probs=15.0
Q ss_pred cccccccccccccccc-ccccccCc
Q psy1895 78 ITCRACDKEFTVTRRR-HHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rk-hhCr~CG~ 101 (140)
-.|..|+..|...... ..|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCC
Confidence 4588888877764332 34666664
No 103
>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=44.56 E-value=2.7 Score=24.80 Aligned_cols=44 Identities=20% Similarity=0.563 Sum_probs=28.4
Q ss_pred ccccccccccccccccccccccCce-EeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEI-FCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i-~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
..|.+|...+.. ..-..||+. ||..|...... ....|..|.+.+
T Consensus 3 ~~C~iC~~~~~~----~~~~pCgH~~~C~~C~~~~~~------~~~~CP~Cr~~i 47 (50)
T PF13920_consen 3 EECPICFENPRD----VVLLPCGHLCFCEECAERLLK------RKKKCPICRQPI 47 (50)
T ss_dssp SB-TTTSSSBSS----EEEETTCEEEEEHHHHHHHHH------TTSBBTTTTBB-
T ss_pred CCCccCCccCCc----eEEeCCCChHHHHHHhHHhcc------cCCCCCcCChhh
Confidence 368888886542 344579999 99999876543 445666665544
No 104
>PRK12496 hypothetical protein; Provisional
Probab=44.45 E-value=14 Score=27.71 Aligned_cols=11 Identities=27% Similarity=0.984 Sum_probs=5.6
Q ss_pred cccccccCceE
Q psy1895 93 RHHCRNCGEIF 103 (140)
Q Consensus 93 khhCr~CG~i~ 103 (140)
++.|..||+.|
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 44455555544
No 105
>KOG1314|consensus
Probab=43.96 E-value=10 Score=32.35 Aligned_cols=33 Identities=27% Similarity=0.819 Sum_probs=23.1
Q ss_pred cCCccccCcCCc-----cccccccccccccccccccccCc
Q psy1895 67 TEAQWAKDKEAI-----TCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 67 ~~~~W~~~~~~~-----~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
..+.|.|....+ .|..|+. | ---|.||||.|.+
T Consensus 76 vp~~wkPe~~~D~~~lqfCk~Cqg-Y-KapRSHHCrkCnr 113 (414)
T KOG1314|consen 76 VPLGWKPENPKDEMFLQFCKKCQG-Y-KAPRSHHCRKCNR 113 (414)
T ss_pred CCCCCCCCCChhHHHHHHHhhccC-c-CCCccccchHHHH
Confidence 347899865554 5888876 2 2367899999865
No 106
>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=43.85 E-value=14 Score=25.07 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=17.9
Q ss_pred cccccccccccccccccccccCceEe
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFC 104 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C 104 (140)
.|..|+..+........|+.||...=
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccc
Confidence 57888887765545667888876643
No 107
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=43.65 E-value=13 Score=27.18 Aligned_cols=8 Identities=38% Similarity=1.734 Sum_probs=4.6
Q ss_pred ccccCceE
Q psy1895 96 CRNCGEIF 103 (140)
Q Consensus 96 Cr~CG~i~ 103 (140)
|..||.+|
T Consensus 32 C~~CG~v~ 39 (140)
T COG1545 32 CKKCGRVY 39 (140)
T ss_pred cCCCCeEE
Confidence 55666554
No 108
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=43.61 E-value=21 Score=22.44 Aligned_cols=15 Identities=40% Similarity=0.767 Sum_probs=11.9
Q ss_pred CCCcccCcccHHHhh
Q psy1895 118 AKPVRVCDECNVKLV 132 (140)
Q Consensus 118 ~~~~RVC~~C~~~l~ 132 (140)
.++..||..|..+..
T Consensus 41 p~~~PVCP~Ck~iye 55 (58)
T PF11238_consen 41 PKPFPVCPECKEIYE 55 (58)
T ss_pred CCCCCCCcCHHHHHH
Confidence 566899999988754
No 109
>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=42.62 E-value=15 Score=21.24 Aligned_cols=15 Identities=33% Similarity=1.006 Sum_probs=9.5
Q ss_pred cccccccCceEeCCC
Q psy1895 93 RHHCRNCGEIFCNMC 107 (140)
Q Consensus 93 khhCr~CG~i~C~~C 107 (140)
...|+.||..||...
T Consensus 13 ~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH 27 (43)
T ss_dssp HEE-TTTS-EE-TTT
T ss_pred CeECCCCCcccCccc
Confidence 467999999998765
No 110
>KOG3896|consensus
Probab=42.24 E-value=13 Score=31.55 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=25.5
Q ss_pred ccccccccccccccccccCceEeCCCCCCeee
Q psy1895 82 ACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMA 113 (140)
Q Consensus 82 ~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~ 113 (140)
.|+ .|..+..-..||.|-++-|..|+.+.+.
T Consensus 14 ~cg-~~~pl~~L~FCRyC~klrc~~Cv~hEvd 44 (449)
T KOG3896|consen 14 TCG-KFRPLPDLVFCRYCFKLRCDDCVLHEVD 44 (449)
T ss_pred ecc-ccccccceeeeecccccccccccccccc
Confidence 355 6888888899999999999999887654
No 111
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=41.23 E-value=6.6 Score=22.10 Aligned_cols=16 Identities=44% Similarity=0.949 Sum_probs=6.5
Q ss_pred cccccccc-cccccccc
Q psy1895 80 CRACDKEF-TVTRRRHH 95 (140)
Q Consensus 80 C~~C~~~F-~~~~rkhh 95 (140)
|..|.+.+ +...|++|
T Consensus 2 C~~C~~Ey~~p~~RR~~ 18 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFH 18 (35)
T ss_dssp -HHHHHHHCSTTSTTTT
T ss_pred CHHHHHHHcCCCCCccc
Confidence 34444443 34444444
No 112
>COG1773 Rubredoxin [Energy production and conversion]
Probab=41.18 E-value=13 Score=23.15 Aligned_cols=37 Identities=24% Similarity=0.579 Sum_probs=20.4
Q ss_pred ccccccccCceEeCCCCCCeeeCCCC-----CCCcccCcccH
Q psy1895 92 RRHHCRNCGEIFCNMCSDNKMALPSA-----AKPVRVCDECN 128 (140)
Q Consensus 92 rkhhCr~CG~i~C~~Cs~~~~~lp~~-----~~~~RVC~~C~ 128 (140)
+++.|+.||.||=..=-.....++.. ...-.+|..|-
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg 43 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECG 43 (55)
T ss_pred CceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCC
Confidence 46889999999843322222222221 23346777775
No 113
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=41.04 E-value=13 Score=28.49 Aligned_cols=15 Identities=40% Similarity=0.933 Sum_probs=7.6
Q ss_pred cccccccccccCceE
Q psy1895 89 VTRRRHHCRNCGEIF 103 (140)
Q Consensus 89 ~~~rkhhCr~CG~i~ 103 (140)
.+..+..|..|+++|
T Consensus 135 v~~w~~rC~GC~~~f 149 (177)
T COG1439 135 VRKWRLRCHGCKRIF 149 (177)
T ss_pred EeeeeEEEecCceec
Confidence 344445555555554
No 114
>PRK04023 DNA polymerase II large subunit; Validated
Probab=40.73 E-value=24 Score=34.04 Aligned_cols=46 Identities=24% Similarity=0.528 Sum_probs=31.1
Q ss_pred cCCccccccccccccccccccccccCce-----EeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 75 KEAITCRACDKEFTVTRRRHHCRNCGEI-----FCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 75 ~~~~~C~~C~~~F~~~~rkhhCr~CG~i-----~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
.....|..|+... -...|..||.. ||..|-.... .-.|..|-..+.
T Consensus 624 Vg~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~~~--------~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIEVE--------EDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC----CcccCCCCCCCCCcceeCccccCcCC--------CCcCCCCCCCCC
Confidence 3456899999974 33679999964 8999954321 134877765544
No 115
>KOG3362|consensus
Probab=40.66 E-value=11 Score=28.08 Aligned_cols=26 Identities=27% Similarity=0.783 Sum_probs=20.3
Q ss_pred CCccccccccccccccccccccccCceEeCC
Q psy1895 76 EAITCRACDKEFTVTRRRHHCRNCGEIFCNM 106 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~ 106 (140)
....|.+|+ +-.++-|-+||.-+|+-
T Consensus 117 ~r~fCaVCG-----~~S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 117 LRKFCAVCG-----YDSKYSCVNCGTKYCSV 142 (156)
T ss_pred cchhhhhcC-----CCchhHHHhcCCceeec
Confidence 457899999 24468999999988863
No 116
>PF06741 LsmAD: LsmAD domain; InterPro: IPR009604 This entry represents a conserved region approximately 250 residues long located on eukaryotic ataxin-2 []. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].
Probab=40.58 E-value=24 Score=23.07 Aligned_cols=36 Identities=17% Similarity=0.314 Sum_probs=24.0
Q ss_pred CCccchhhhHHHhhhhhhhcchhhhhHHHHHHHHHHHH
Q psy1895 5 GLKRSFDDHVKMNKIAEHVKDNVSDDKYKESELALEEL 42 (140)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~l~~~ 42 (140)
|.+.+||+..+|-+++..-. .-++.+.++++--.++
T Consensus 2 GV~stydE~lYTT~Ld~~~~--~~k~~~~~A~riA~EI 37 (72)
T PF06741_consen 2 GVKSTYDENLYTTPLDRSDP--DYKEREAEAERIAREI 37 (72)
T ss_pred CCCCccCchhceeeccCCCc--chHHHHHHHHHHHHHH
Confidence 78999999999999988643 3344444444433343
No 117
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.50 E-value=12 Score=28.49 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=19.8
Q ss_pred CCcccccccccccc---ccccccccccCceE
Q psy1895 76 EAITCRACDKEFTV---TRRRHHCRNCGEIF 103 (140)
Q Consensus 76 ~~~~C~~C~~~F~~---~~rkhhCr~CG~i~ 103 (140)
.-=.|+.|+..|++ +.--.+|..||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 34469999999984 44456788887653
No 118
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=40.25 E-value=16 Score=26.52 Aligned_cols=28 Identities=32% Similarity=0.703 Sum_probs=19.2
Q ss_pred cCcCCccccccccccccccccccccccCce
Q psy1895 73 KDKEAITCRACDKEFTVTRRRHHCRNCGEI 102 (140)
Q Consensus 73 ~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i 102 (140)
.......|..|... .-.|-|||+.||+-
T Consensus 44 ~~~~~~~C~~C~~~--kp~Rs~HC~~C~~C 71 (174)
T PF01529_consen 44 ENGELKYCSTCKII--KPPRSHHCRVCNRC 71 (174)
T ss_pred cCCCCEECcccCCc--CCCcceeccccccc
Confidence 33445678888764 44578999988764
No 119
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=39.99 E-value=21 Score=20.87 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=4.1
Q ss_pred cccCcccH
Q psy1895 121 VRVCDECN 128 (140)
Q Consensus 121 ~RVC~~C~ 128 (140)
..||..|-
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 45555553
No 120
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=39.35 E-value=18 Score=21.97 Aligned_cols=22 Identities=32% Similarity=0.794 Sum_probs=16.5
Q ss_pred ccccccccccccccccccccccCc
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
..|..|++.-. .+-.+||.||.
T Consensus 15 ~ICrkC~ARnp--~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARNP--WRATKCRKCGY 36 (48)
T ss_pred cchhcccCCCC--ccccccccCCC
Confidence 46899988654 45678998885
No 121
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=39.20 E-value=18 Score=23.27 Aligned_cols=41 Identities=24% Similarity=0.759 Sum_probs=16.5
Q ss_pred cccccccccccccccccc-cccCceEeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 79 TCRACDKEFTVTRRRHHC-RNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhC-r~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
.|..|.. ++ +.-.| -.|.++||+.|.+..+ +. -|..|+...
T Consensus 9 rCs~C~~---~l-~~pv~l~~CeH~fCs~Ci~~~~-----~~---~CPvC~~Pa 50 (65)
T PF14835_consen 9 RCSICFD---IL-KEPVCLGGCEHIFCSSCIRDCI-----GS---ECPVCHTPA 50 (65)
T ss_dssp S-SSS-S------SS-B---SSS--B-TTTGGGGT-----TT---B-SSS--B-
T ss_pred CCcHHHH---Hh-cCCceeccCccHHHHHHhHHhc-----CC---CCCCcCChH
Confidence 3555544 33 34445 7899999999986532 11 277776543
No 122
>PHA02929 N1R/p28-like protein; Provisional
Probab=39.06 E-value=6.2 Score=31.55 Aligned_cols=51 Identities=20% Similarity=0.444 Sum_probs=32.5
Q ss_pred CCcccccccccccccc---c-cccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 76 EAITCRACDKEFTVTR---R-RHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~~---r-khhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
....|.+|...|.--. + -..=..||++||..|...+.. ....|..|...+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~------~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK------EKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh------cCCCCCCCCCEee
Confidence 3468999999765211 0 011237999999999876542 2346777766554
No 123
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.03 E-value=22 Score=22.02 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=13.4
Q ss_pred ccccccccccccccccccccccCce
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i 102 (140)
..|..|+.+|..-.-..-|.-||.+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCc
Confidence 4577777777543333444444443
No 124
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=38.88 E-value=5.9 Score=20.40 Aligned_cols=13 Identities=31% Similarity=0.917 Sum_probs=9.7
Q ss_pred ccccccccccccc
Q psy1895 79 TCRACDKEFTVTR 91 (140)
Q Consensus 79 ~C~~C~~~F~~~~ 91 (140)
.|..|+++|..-.
T Consensus 4 ~C~~CgR~F~~~~ 16 (25)
T PF13913_consen 4 PCPICGRKFNPDR 16 (25)
T ss_pred cCCCCCCEECHHH
Confidence 5888888887433
No 125
>PRK11595 DNA utilization protein GntX; Provisional
Probab=38.79 E-value=7.7 Score=30.23 Aligned_cols=29 Identities=24% Similarity=0.779 Sum_probs=20.0
Q ss_pred cccccccccccccccccccccCce------EeCCCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI------FCNMCSD 109 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i------~C~~Cs~ 109 (140)
.|..|...|.++ .++|..||.. +|..|..
T Consensus 22 lC~~C~~~l~~~--~~~C~~Cg~~~~~~~~~C~~C~~ 56 (227)
T PRK11595 22 ICSVCSRALRTL--KTCCPQCGLPATHPHLPCGRCLQ 56 (227)
T ss_pred ccHHHHhhCCcc--cCcCccCCCcCCCCCCCcHHHHc
Confidence 678887777764 4678888864 3666644
No 126
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=38.59 E-value=18 Score=21.88 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=8.6
Q ss_pred ccCcccHHHhh
Q psy1895 122 RVCDECNVKLV 132 (140)
Q Consensus 122 RVC~~C~~~l~ 132 (140)
-||..|+..+.
T Consensus 21 ~iC~~C~~Kl~ 31 (51)
T PF14471_consen 21 YICKDCLKKLS 31 (51)
T ss_pred cchHHHHHHhc
Confidence 58888888873
No 127
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=38.44 E-value=16 Score=27.45 Aligned_cols=15 Identities=53% Similarity=1.134 Sum_probs=9.7
Q ss_pred cccccccccccCceE
Q psy1895 89 VTRRRHHCRNCGEIF 103 (140)
Q Consensus 89 ~~~rkhhCr~CG~i~ 103 (140)
.++|+.+|..||.-|
T Consensus 24 aIRRRReC~~C~~RF 38 (156)
T COG1327 24 AIRRRRECLECGERF 38 (156)
T ss_pred hhhhhhccccccccc
Confidence 456666777777654
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.34 E-value=20 Score=33.15 Aligned_cols=32 Identities=28% Similarity=0.808 Sum_probs=18.4
Q ss_pred cccccccccccccc--cccccccCce-----EeCCCCCC
Q psy1895 79 TCRACDKEFTVTRR--RHHCRNCGEI-----FCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~~~r--khhCr~CG~i-----~C~~Cs~~ 110 (140)
.|..|...+++-.. .-.|+.||.- .|..|.+.
T Consensus 446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 46677776665433 3336666665 55555554
No 129
>KOG0119|consensus
Probab=37.15 E-value=54 Score=29.22 Aligned_cols=40 Identities=18% Similarity=0.128 Sum_probs=24.0
Q ss_pred cchhhhHHHhhhhhhhcchhhhhHHHHHHHHHHHHHhhhh
Q psy1895 8 RSFDDHVKMNKIAEHVKDNVSDDKYKESELALEELGAQLS 47 (140)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~l~~~~~~l~ 47 (140)
++-|+.-.+.+..|.|.-.|.-+..|.++.+++.+...++
T Consensus 190 ~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~ 229 (554)
T KOG0119|consen 190 GRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQ 229 (554)
T ss_pred cCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHH
Confidence 3444444555666667777777766666666665554443
No 130
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=37.00 E-value=14 Score=22.18 Aligned_cols=30 Identities=27% Similarity=0.706 Sum_probs=19.9
Q ss_pred cccccccccccccccccccccC---ceEeCCCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCG---EIFCNMCSD 109 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG---~i~C~~Cs~ 109 (140)
.|..|+. ..+...|+||..|. --+|..|-.
T Consensus 2 ~Cd~C~~-~pI~G~R~~C~~C~~~d~DlC~~C~~ 34 (48)
T cd02341 2 KCDSCGI-EPIPGTRYHCSECDDGDFDLCQDCVV 34 (48)
T ss_pred CCCCCCC-CccccceEECCCCCCCCCccCHHHHh
Confidence 3777877 22447789999987 446666643
No 131
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=36.56 E-value=19 Score=20.24 Aligned_cols=32 Identities=19% Similarity=0.413 Sum_probs=20.7
Q ss_pred CccccccccccccccccccccccCceEeCCCC
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGEIFCNMCS 108 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs 108 (140)
...|..|++.+..+..-..|+.|+.++=..|.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~ 42 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCA 42 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHH
Confidence 45799999887654335668887765444443
No 132
>KOG2462|consensus
Probab=36.18 E-value=13 Score=30.52 Aligned_cols=54 Identities=20% Similarity=0.611 Sum_probs=31.9
Q ss_pred Cccccccccccc---cc---------cccccccccCceEeCCCCCCeeeCCC-CCCCcccCcccHHHh
Q psy1895 77 AITCRACDKEFT---VT---------RRRHHCRNCGEIFCNMCSDNKMALPS-AAKPVRVCDECNVKL 131 (140)
Q Consensus 77 ~~~C~~C~~~F~---~~---------~rkhhCr~CG~i~C~~Cs~~~~~lp~-~~~~~RVC~~C~~~l 131 (140)
.-.|.+|++.|+ +| .+-..|..||+.|=++ |+-++-+-. ++...--|..|.+..
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADR-SNLRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADR-SNLRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcch-HHHHHHHHhhcCCccccCcchhhHH
Confidence 457999999998 33 2344588888877332 111211111 134467788887654
No 133
>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=36.08 E-value=25 Score=18.20 Aligned_cols=8 Identities=50% Similarity=1.265 Sum_probs=4.9
Q ss_pred cccccccC
Q psy1895 93 RHHCRNCG 100 (140)
Q Consensus 93 khhCr~CG 100 (140)
.+.|.+||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35577776
No 134
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=36.07 E-value=50 Score=23.99 Aligned_cols=30 Identities=23% Similarity=0.686 Sum_probs=18.1
Q ss_pred CcCCccccccccccccccc--------cccccccCceE
Q psy1895 74 DKEAITCRACDKEFTVTRR--------RHHCRNCGEIF 103 (140)
Q Consensus 74 ~~~~~~C~~C~~~F~~~~r--------khhCr~CG~i~ 103 (140)
+...=.|+.|+..|++..- ...|..||..+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 3344579999999985322 24555665543
No 135
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=35.71 E-value=14 Score=20.72 Aligned_cols=29 Identities=24% Similarity=0.611 Sum_probs=18.5
Q ss_pred ccccccccccccccccccccccCceEeCCCCCC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
..|..+.... -...|..|+..+|..|...
T Consensus 4 ~~C~~H~~~~----~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEP----LSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSB----EEEEETTTTEEEEHHHHHT
T ss_pred ccCccCCccc----eEEEecCCCCccCccCCCC
Confidence 4566666531 2356888888888888543
No 136
>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=34.74 E-value=16 Score=26.13 Aligned_cols=24 Identities=29% Similarity=0.675 Sum_probs=21.2
Q ss_pred cccccccccccccccccccccCce
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI 102 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i 102 (140)
.|+.|++..-.+.|-.-|-+|++.
T Consensus 71 ~CP~C~K~TKmLGr~D~CM~C~~p 94 (114)
T PF11023_consen 71 ECPNCGKQTKMLGRVDACMHCKEP 94 (114)
T ss_pred ECCCCCChHhhhchhhccCcCCCc
Confidence 699999999899998889998875
No 137
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=34.72 E-value=29 Score=20.34 Aligned_cols=35 Identities=20% Similarity=0.548 Sum_probs=25.8
Q ss_pred CCcccccccccc-ccccccccccccCceEeCCCCCC
Q psy1895 76 EAITCRACDKEF-TVTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 76 ~~~~C~~C~~~F-~~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
....|..|++.. ++...-..|..|+.++=..|...
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 456899999987 56677788999999887777665
No 138
>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=34.53 E-value=8.8 Score=19.93 Aligned_cols=15 Identities=33% Similarity=0.864 Sum_probs=11.1
Q ss_pred cccCceEeCCCCCCe
Q psy1895 97 RNCGEIFCNMCSDNK 111 (140)
Q Consensus 97 r~CG~i~C~~Cs~~~ 111 (140)
..||++||..|....
T Consensus 14 ~~C~H~~c~~C~~~~ 28 (39)
T smart00184 14 LPCGHTFCRSCIRKW 28 (39)
T ss_pred ecCCChHHHHHHHHH
Confidence 458888888887643
No 139
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=34.31 E-value=21 Score=20.01 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=4.7
Q ss_pred ccccccccccc
Q psy1895 78 ITCRACDKEFT 88 (140)
Q Consensus 78 ~~C~~C~~~F~ 88 (140)
..|..|+++|.
T Consensus 4 ~~C~eC~~~f~ 14 (34)
T PF01286_consen 4 PKCDECGKPFM 14 (34)
T ss_dssp EE-TTT--EES
T ss_pred chHhHhCCHHH
Confidence 45666666664
No 140
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=34.27 E-value=6.7 Score=24.21 Aligned_cols=43 Identities=26% Similarity=0.744 Sum_probs=31.6
Q ss_pred cccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
.|..|+..|.+ ..-..|..||+--|+.|-.. ..-.|..|..++
T Consensus 9 ~CDLCn~~~p~-~~LRQCvlCGRWaC~sCW~d---------eYY~CksC~Gii 51 (57)
T PF14445_consen 9 SCDLCNSSHPI-SELRQCVLCGRWACNSCWQD---------EYYTCKSCNGII 51 (57)
T ss_pred hHHhhcccCcH-HHHHHHhhhchhhhhhhhhh---------hHhHHHhhhchh
Confidence 58889998874 34468999999999999754 335666776554
No 141
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=33.92 E-value=20 Score=21.41 Aligned_cols=13 Identities=23% Similarity=0.759 Sum_probs=10.2
Q ss_pred cccccccCceEeC
Q psy1895 93 RHHCRNCGEIFCN 105 (140)
Q Consensus 93 khhCr~CG~i~C~ 105 (140)
|+.|+.||.|+=.
T Consensus 1 ky~C~~CgyvYd~ 13 (47)
T PF00301_consen 1 KYQCPVCGYVYDP 13 (47)
T ss_dssp EEEETTTSBEEET
T ss_pred CcCCCCCCEEEcC
Confidence 5789999998743
No 142
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=33.68 E-value=19 Score=20.93 Aligned_cols=30 Identities=23% Similarity=0.682 Sum_probs=21.4
Q ss_pred cccccccccccccccccccccC-ceEeCCCCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCG-EIFCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG-~i~C~~Cs~~ 110 (140)
.|..|+. .+...+++|..|- --+|..|-..
T Consensus 2 ~Cd~C~~--~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQG--PIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCC--cCcCCeEECCCCCCccchHHhhCc
Confidence 4788888 4566788999884 5577777443
No 143
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.48 E-value=25 Score=20.68 Aligned_cols=15 Identities=27% Similarity=0.718 Sum_probs=11.8
Q ss_pred Ccccccccccccccc
Q psy1895 77 AITCRACDKEFTVTR 91 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~ 91 (140)
...|..|+++|+...
T Consensus 8 ~K~C~~C~rpf~WRK 22 (42)
T PF10013_consen 8 SKICPVCGRPFTWRK 22 (42)
T ss_pred CCcCcccCCcchHHH
Confidence 358999999998543
No 144
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=33.37 E-value=22 Score=24.36 Aligned_cols=7 Identities=57% Similarity=1.588 Sum_probs=3.5
Q ss_pred ccccCce
Q psy1895 96 CRNCGEI 102 (140)
Q Consensus 96 Cr~CG~i 102 (140)
|+.||..
T Consensus 19 CrRCG~~ 25 (91)
T PTZ00073 19 CRRCGKR 25 (91)
T ss_pred hcccCcc
Confidence 5555543
No 145
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=33.19 E-value=24 Score=25.32 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=5.0
Q ss_pred cccccccccc
Q psy1895 79 TCRACDKEFT 88 (140)
Q Consensus 79 ~C~~C~~~F~ 88 (140)
.|..|+..+.
T Consensus 125 ~C~~C~~~~~ 134 (157)
T PF10263_consen 125 RCPSCGREYK 134 (157)
T ss_pred EcCCCCCEee
Confidence 4555554443
No 146
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.08 E-value=33 Score=23.78 Aligned_cols=43 Identities=23% Similarity=0.492 Sum_probs=26.2
Q ss_pred CccccccccccccccccccccccCceEeCCCCCCe-eeCCCCCCCcc
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNK-MALPSAAKPVR 122 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~-~~lp~~~~~~R 122 (140)
.-.|..|+. ..+...+.+ .=+++.|..|..+. ..++....|+-
T Consensus 21 ~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epID 64 (99)
T PRK14892 21 IFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVD 64 (99)
T ss_pred EeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchh
Confidence 456888884 454433333 56788999998774 33444455543
No 147
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=32.98 E-value=19 Score=20.85 Aligned_cols=21 Identities=33% Similarity=0.833 Sum_probs=14.8
Q ss_pred ccccccccccccccccccccccC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCG 100 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG 100 (140)
..|..|++. +...+++|..|.
T Consensus 5 ~~C~~C~~~--i~g~ry~C~~C~ 25 (44)
T smart00291 5 YSCDTCGKP--IVGVRYHCLVCP 25 (44)
T ss_pred cCCCCCCCC--CcCCEEECCCCC
Confidence 368889884 445677888774
No 148
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=32.89 E-value=15 Score=17.65 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=7.2
Q ss_pred cccccccccc
Q psy1895 79 TCRACDKEFT 88 (140)
Q Consensus 79 ~C~~C~~~F~ 88 (140)
.|..|++.|.
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 3777887776
No 149
>KOG4080|consensus
Probab=32.50 E-value=21 Score=27.19 Aligned_cols=14 Identities=29% Similarity=0.619 Sum_probs=10.5
Q ss_pred CCcccCcccHHHhh
Q psy1895 119 KPVRVCDECNVKLV 132 (140)
Q Consensus 119 ~~~RVC~~C~~~l~ 132 (140)
...-.|+.||..+.
T Consensus 104 ~a~~LC~~Cy~kV~ 117 (176)
T KOG4080|consen 104 PAHTLCDYCYAKVH 117 (176)
T ss_pred cccccHHHHHHHHH
Confidence 45678999998764
No 150
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.47 E-value=20 Score=30.82 Aligned_cols=48 Identities=21% Similarity=0.605 Sum_probs=31.9
Q ss_pred cCCccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 75 KEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 75 ~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
...-.|.+|...|..- .--.||+.||..|...... ....|..|...+.
T Consensus 24 e~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~------~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 24 DTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLS------NQPKCPLCRAEDQ 71 (397)
T ss_pred ccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHh------CCCCCCCCCCccc
Confidence 3446899999877521 1358999999999875432 1236777766543
No 151
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=32.22 E-value=29 Score=19.91 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=6.8
Q ss_pred ccccccccccc
Q psy1895 78 ITCRACDKEFT 88 (140)
Q Consensus 78 ~~C~~C~~~F~ 88 (140)
..|..|+..|.
T Consensus 3 ~~C~~Cg~~l~ 13 (47)
T PF13005_consen 3 RACPDCGGELK 13 (47)
T ss_pred CcCCCCCceee
Confidence 35666666665
No 152
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=31.78 E-value=17 Score=22.29 Aligned_cols=29 Identities=31% Similarity=0.613 Sum_probs=15.1
Q ss_pred ccccccccccccccccccccCceEeCCCCCC
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
|..|+..++..-|+.- .=+..+|+.|.-+
T Consensus 2 C~~C~~~~Tp~WR~g~--~~~~~LCNaCgl~ 30 (54)
T cd00202 2 CSNCGTTTTPLWRRGP--SGGSTLCNACGLY 30 (54)
T ss_pred CCCCCCCCCcccccCC--CCcchHHHHHHHH
Confidence 6666666665444432 3344555555444
No 153
>KOG1812|consensus
Probab=31.59 E-value=21 Score=30.42 Aligned_cols=32 Identities=31% Similarity=0.890 Sum_probs=22.6
Q ss_pred ccccccccccccccc--cccccccCceEeCCCCCC
Q psy1895 78 ITCRACDKEFTVTRR--RHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r--khhCr~CG~i~C~~Cs~~ 110 (140)
..|+.|+...-+... .-+|| ||.-||..|-..
T Consensus 307 r~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~ 340 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGD 340 (384)
T ss_pred CcCcccceeeeecCCcceEEee-ccccchhhcCcc
Confidence 468888775444333 34499 999999999843
No 154
>PF07130 YebG: YebG protein; InterPro: IPR009813 This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS [].; PDB: 3ERM_E.
Probab=31.41 E-value=86 Score=20.73 Aligned_cols=43 Identities=26% Similarity=0.272 Sum_probs=30.3
Q ss_pred hhhHHHhhhhhhhcchhhhhHHHHHHHHHHHHHhhhhhhHHHH
Q psy1895 11 DDHVKMNKIAEHVKDNVSDDKYKESELALEELGAQLSKSKLQV 53 (140)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~r~~~~~~~~~l~~~~~~l~~s~~~~ 53 (140)
|..=||..+++++.+.+.......-+...++++.-|...+..+
T Consensus 26 DAyDKmLd~Ad~L~~~L~~~~~~lde~~~E~l~l~LA~~kd~~ 68 (75)
T PF07130_consen 26 DAYDKMLDLADNLTDFLEQSVLGLDEAQAEELALYLAENKDEL 68 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSTT--HHHHHHHHHHHHTTHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCHHHH
Confidence 4556889999999998888777666777777777666555433
No 155
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=31.41 E-value=20 Score=30.24 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=4.0
Q ss_pred Ccccccccc
Q psy1895 77 AITCRACDK 85 (140)
Q Consensus 77 ~~~C~~C~~ 85 (140)
+..|..|..
T Consensus 252 av~C~~C~y 260 (344)
T PF09332_consen 252 AVTCKQCKY 260 (344)
T ss_dssp EEEETTT--
T ss_pred EEEcCCCCC
Confidence 345666643
No 156
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.32 E-value=28 Score=21.03 Aligned_cols=25 Identities=36% Similarity=0.747 Sum_probs=16.4
Q ss_pred ccccccccccc-----cc---cccccccccCce
Q psy1895 78 ITCRACDKEFT-----VT---RRRHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~-----~~---~rkhhCr~CG~i 102 (140)
..|..|+-..+ -+ ....+|.+||+|
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 47999988765 11 234667787776
No 157
>KOG1311|consensus
Probab=31.06 E-value=22 Score=28.60 Aligned_cols=23 Identities=26% Similarity=0.598 Sum_probs=16.7
Q ss_pred CccccccccccccccccccccccCc
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGE 101 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~ 101 (140)
...|..|+.- .-.|-|||+.|+.
T Consensus 113 ~~~C~~C~~~--rPpRs~HCsvC~~ 135 (299)
T KOG1311|consen 113 WKYCDTCQLY--RPPRSSHCSVCNN 135 (299)
T ss_pred eEEcCcCccc--CCCCcccchhhcc
Confidence 4678888774 5577888888765
No 158
>KOG2807|consensus
Probab=31.02 E-value=32 Score=29.08 Aligned_cols=51 Identities=24% Similarity=0.595 Sum_probs=32.8
Q ss_pred cccCcCCccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccH
Q psy1895 71 WAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECN 128 (140)
Q Consensus 71 W~~~~~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~ 128 (140)
|........|..|+... .-..++.|..|-.+||.+|-.+- ......|..|-
T Consensus 324 ~~~~~~~~~Cf~C~~~~-~~~~~y~C~~Ck~~FCldCDv~i------HesLh~CpgCe 374 (378)
T KOG2807|consen 324 ETEYNGSRFCFACQGEL-LSSGRYRCESCKNVFCLDCDVFI------HESLHNCPGCE 374 (378)
T ss_pred ccccCCCcceeeecccc-CCCCcEEchhccceeeccchHHH------HhhhhcCCCcC
Confidence 33333344699994322 34557889999999999996542 24456666664
No 159
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=30.88 E-value=23 Score=25.77 Aligned_cols=25 Identities=28% Similarity=0.725 Sum_probs=17.6
Q ss_pred ccccccccccccccc-----cccccccCce
Q psy1895 78 ITCRACDKEFTVTRR-----RHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r-----khhCr~CG~i 102 (140)
-.|..|+.+-+.+.+ -.+|..||..
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 369999999886655 2357777653
No 160
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=30.58 E-value=30 Score=25.76 Aligned_cols=15 Identities=47% Similarity=0.933 Sum_probs=9.7
Q ss_pred cccccccccccCceE
Q psy1895 89 VTRRRHHCRNCGEIF 103 (140)
Q Consensus 89 ~~~rkhhCr~CG~i~ 103 (140)
.++|+..|..||+-|
T Consensus 24 ~IRRRReC~~C~~RF 38 (147)
T TIGR00244 24 SIRRRRECLECHERF 38 (147)
T ss_pred eeeecccCCccCCcc
Confidence 456666777777655
No 161
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=29.94 E-value=16 Score=23.69 Aligned_cols=39 Identities=31% Similarity=0.638 Sum_probs=25.2
Q ss_pred ccccccCceEeCCCCCCe-e-------eCCC--C--CCCcccCcccHHHhh
Q psy1895 94 HHCRNCGEIFCNMCSDNK-M-------ALPS--A--AKPVRVCDECNVKLV 132 (140)
Q Consensus 94 hhCr~CG~i~C~~Cs~~~-~-------~lp~--~--~~~~RVC~~C~~~l~ 132 (140)
--|..||..+|...+... . |+|. . .-|--+|..|+..+.
T Consensus 17 avCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~a~~ 67 (68)
T PF09947_consen 17 AVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHAALK 67 (68)
T ss_pred ehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHHHhh
Confidence 458889999988877642 1 1221 1 345568999998653
No 162
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=29.61 E-value=21 Score=20.79 Aligned_cols=30 Identities=30% Similarity=0.724 Sum_probs=20.1
Q ss_pred cccccccccccccccccccccC-ceEeCCCCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCG-EIFCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG-~i~C~~Cs~~ 110 (140)
.|..|.++ +...+.+|..|. -.+|..|-..
T Consensus 2 ~C~~C~~~--i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 2 SCDGCLKP--IVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCcCCCCC--CcCCEEECCCCCCCcCHHHHHCc
Confidence 47888883 445788888886 4466666443
No 163
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=29.50 E-value=31 Score=24.53 Aligned_cols=26 Identities=27% Similarity=0.647 Sum_probs=19.7
Q ss_pred ccccccccccccccccccccCceEeCCC
Q psy1895 80 CRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 80 C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
|+.|+.++. ..+.+|.+||-.+-+.-
T Consensus 1 CPvCg~~l~--vt~l~C~~C~t~i~G~F 26 (113)
T PF09862_consen 1 CPVCGGELV--VTRLKCPSCGTEIEGEF 26 (113)
T ss_pred CCCCCCceE--EEEEEcCCCCCEEEeee
Confidence 888998655 56788999998876543
No 164
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=29.00 E-value=15 Score=26.73 Aligned_cols=20 Identities=35% Similarity=0.796 Sum_probs=11.5
Q ss_pred CcCCccccccccccccccccc
Q psy1895 74 DKEAITCRACDKEFTVTRRRH 94 (140)
Q Consensus 74 ~~~~~~C~~C~~~F~~~~rkh 94 (140)
..+.-.|..|+++|..+ +||
T Consensus 69 ~~d~i~clecGk~~k~L-krH 88 (132)
T PF05443_consen 69 TPDYIICLECGKKFKTL-KRH 88 (132)
T ss_dssp -SS-EE-TBT--EESBH-HHH
T ss_pred ccCeeEEccCCcccchH-HHH
Confidence 34456899999999998 444
No 165
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=28.79 E-value=28 Score=19.54 Aligned_cols=24 Identities=21% Similarity=0.591 Sum_probs=14.3
Q ss_pred cccccccccc-cccccccccccCce
Q psy1895 79 TCRACDKEFT-VTRRRHHCRNCGEI 102 (140)
Q Consensus 79 ~C~~C~~~F~-~~~rkhhCr~CG~i 102 (140)
.|..|+..|. .-...+-|..||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 4888888744 33445556666654
No 166
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=28.42 E-value=45 Score=27.73 Aligned_cols=55 Identities=27% Similarity=0.581 Sum_probs=35.4
Q ss_pred Cccccccccc--cccc-------cccccccccCc------eEeCCCCCCeeeC-----CCC--CCCcccCcccHHHhh
Q psy1895 77 AITCRACDKE--FTVT-------RRRHHCRNCGE------IFCNMCSDNKMAL-----PSA--AKPVRVCDECNVKLV 132 (140)
Q Consensus 77 ~~~C~~C~~~--F~~~-------~rkhhCr~CG~------i~C~~Cs~~~~~l-----p~~--~~~~RVC~~C~~~l~ 132 (140)
...|+.|+.. .+++ .|..||..|+. +-|..|-... .+ ... ...+-+|+.|..-+.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~-~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSG-KLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCC-ceeeeeecCCCcceEeeecccccccce
Confidence 4689999986 2322 46678999984 5788887642 22 211 234578999976553
No 167
>KOG3795|consensus
Probab=28.09 E-value=29 Score=26.95 Aligned_cols=23 Identities=30% Similarity=0.772 Sum_probs=16.9
Q ss_pred cccccccccccccCc---eEeCCCCC
Q psy1895 87 FTVTRRRHHCRNCGE---IFCNMCSD 109 (140)
Q Consensus 87 F~~~~rkhhCr~CG~---i~C~~Cs~ 109 (140)
|.....||.|+.||. .||-.|.-
T Consensus 9 ~d~ieGRs~C~~C~~SRkFfCY~C~V 34 (230)
T KOG3795|consen 9 FDPIEGRSTCPGCKSSRKFFCYDCRV 34 (230)
T ss_pred cCcccccccCCCCCCcceEEEEeecc
Confidence 455667788888885 48988864
No 168
>PHA00733 hypothetical protein
Probab=28.03 E-value=1.2e+02 Score=21.57 Aligned_cols=26 Identities=27% Similarity=0.671 Sum_probs=16.8
Q ss_pred cccccccccccccc----------ccccccccCceE
Q psy1895 78 ITCRACDKEFTVTR----------RRHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~~----------rkhhCr~CG~i~ 103 (140)
-.|..|++.|.... ..+.|..||+.|
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F 109 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEF 109 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCcc
Confidence 47999999987221 234566666665
No 169
>PHA00732 hypothetical protein
Probab=27.97 E-value=47 Score=21.88 Aligned_cols=9 Identities=22% Similarity=0.586 Sum_probs=4.7
Q ss_pred ccccccccc
Q psy1895 80 CRACDKEFT 88 (140)
Q Consensus 80 C~~C~~~F~ 88 (140)
|..|++.|.
T Consensus 4 C~~Cgk~F~ 12 (79)
T PHA00732 4 CPICGFTTV 12 (79)
T ss_pred CCCCCCccC
Confidence 555555554
No 170
>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=27.66 E-value=40 Score=29.60 Aligned_cols=33 Identities=27% Similarity=0.745 Sum_probs=19.9
Q ss_pred cccccccccccc--cccccccccCce-----EeCCCCCCe
Q psy1895 79 TCRACDKEFTVT--RRRHHCRNCGEI-----FCNMCSDNK 111 (140)
Q Consensus 79 ~C~~C~~~F~~~--~rkhhCr~CG~i-----~C~~Cs~~~ 111 (140)
.|..|..+.+.- ...-.|..||.. .|..|.+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSED 263 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCe
Confidence 366666655532 334558888766 577776643
No 171
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=27.65 E-value=40 Score=20.85 Aligned_cols=16 Identities=25% Similarity=0.594 Sum_probs=11.1
Q ss_pred cccccccccCceEeCC
Q psy1895 91 RRRHHCRNCGEIFCNM 106 (140)
Q Consensus 91 ~rkhhCr~CG~i~C~~ 106 (140)
.+..-|-.||.++|.+
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 3445688999999885
No 172
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=27.46 E-value=49 Score=27.43 Aligned_cols=56 Identities=25% Similarity=0.618 Sum_probs=34.1
Q ss_pred Ccccccccccc--ccc--------cccccccccCc------eEeCCCCCCe----eeCCC--CCCCcc--cCcccHHHhh
Q psy1895 77 AITCRACDKEF--TVT--------RRRHHCRNCGE------IFCNMCSDNK----MALPS--AAKPVR--VCDECNVKLV 132 (140)
Q Consensus 77 ~~~C~~C~~~F--~~~--------~rkhhCr~CG~------i~C~~Cs~~~----~~lp~--~~~~~R--VC~~C~~~l~ 132 (140)
...|++|+..= +++ .|..||..|+. +-|..|-... ..+.. ....+| +|+.|..-+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchh
Confidence 45899999853 222 35678998884 5788886642 11111 112345 9999976553
No 173
>KOG2593|consensus
Probab=27.40 E-value=93 Score=27.16 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=26.3
Q ss_pred Cccccccccccccc---------cccccccccCceEeCCCCCC
Q psy1895 77 AITCRACDKEFTVT---------RRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 77 ~~~C~~C~~~F~~~---------~rkhhCr~CG~i~C~~Cs~~ 110 (140)
.=.|+.|+++|+.| ....||-+||.-+=..|+..
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~ 170 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKL 170 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccC
Confidence 34799999999832 35889999998887777653
No 174
>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=27.40 E-value=44 Score=19.36 Aligned_cols=30 Identities=20% Similarity=0.805 Sum_probs=18.5
Q ss_pred CccccCcCCccccccccc--ccccc-ccccccccCc
Q psy1895 69 AQWAKDKEAITCRACDKE--FTVTR-RRHHCRNCGE 101 (140)
Q Consensus 69 ~~W~~~~~~~~C~~C~~~--F~~~~-rkhhCr~CG~ 101 (140)
..|... ..|+.|+.. +.+.. .++.|+.|++
T Consensus 13 ~RW~~g---~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 13 IRWPDG---FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred hcCCCC---CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 457655 469999873 22222 5667888764
No 175
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=27.16 E-value=20 Score=20.98 Aligned_cols=22 Identities=32% Similarity=0.803 Sum_probs=12.4
Q ss_pred ccccccccccccccccccccccC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCG 100 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG 100 (140)
..|..|+.. .+...|++|..|.
T Consensus 5 ~~C~~C~~~-~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTD-PIIGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SS-SEESSEEEESSSS
T ss_pred eECcCCCCC-cCcCCeEECCCCC
Confidence 468888873 3334567777764
No 176
>KOG0153|consensus
Probab=26.84 E-value=29 Score=29.47 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=18.0
Q ss_pred ccCcCCccccccccccccccccc
Q psy1895 72 AKDKEAITCRACDKEFTVTRRRH 94 (140)
Q Consensus 72 ~~~~~~~~C~~C~~~F~~~~rkh 94 (140)
.......+|.+|.++|++|+.+-
T Consensus 36 tK~~~gkECKICtrPfT~Frw~p 58 (377)
T KOG0153|consen 36 TKEPYGKECKICTRPFTIFRWCP 58 (377)
T ss_pred eccccCCccceecCcceEEEecc
Confidence 45556689999999999986643
No 177
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=26.21 E-value=61 Score=28.24 Aligned_cols=40 Identities=18% Similarity=0.372 Sum_probs=23.4
Q ss_pred ccccccccccCceEeCCCCCCeeeCCCC-----CCCcccCcccHH
Q psy1895 90 TRRRHHCRNCGEIFCNMCSDNKMALPSA-----AKPVRVCDECNV 129 (140)
Q Consensus 90 ~~rkhhCr~CG~i~C~~Cs~~~~~lp~~-----~~~~RVC~~C~~ 129 (140)
-..++.|+.||.++=..=......+|.. -..--+|..|-.
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCC
Confidence 4567889999999854322222223332 122468888853
No 178
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=26.05 E-value=2e+02 Score=25.45 Aligned_cols=44 Identities=27% Similarity=0.408 Sum_probs=26.5
Q ss_pred CCCc-cchhhhHHHhhhhhh-hcchhhhhHHHHHHHHHHHHHhhhh
Q psy1895 4 GGLK-RSFDDHVKMNKIAEH-VKDNVSDDKYKESELALEELGAQLS 47 (140)
Q Consensus 4 ~~~~-~~~~~~~~~~~~~~~-~~~~~~r~~~~~~~~~l~~~~~~l~ 47 (140)
||++ ..|+++|-..++.++ .+..-++++++.+.+.++.+..++.
T Consensus 55 ~~vV~~~FddkVnqSALteqQ~kasELEKqLaaLrqElq~~saq~~ 100 (475)
T PRK13729 55 TGVVDTTFDDKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRG 100 (475)
T ss_pred cceecchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3444 478888888877766 4666666666665555554434333
No 179
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.88 E-value=38 Score=24.76 Aligned_cols=24 Identities=33% Similarity=0.870 Sum_probs=17.1
Q ss_pred ccccccccccccccccccccccCceEeCCCCC
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSD 109 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~ 109 (140)
.+|+.|+.+. |. .=|.|||.-|-.
T Consensus 29 ~hCp~Cg~PL--F~------KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPL--FR------KDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcc--ee------eCCeEECCCCCc
Confidence 3799999963 32 347888888873
No 180
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.71 E-value=50 Score=22.56 Aligned_cols=26 Identities=35% Similarity=0.878 Sum_probs=18.0
Q ss_pred ccccccccccccccc----cccccccCceEeC
Q psy1895 78 ITCRACDKEFTVTRR----RHHCRNCGEIFCN 105 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r----khhCr~CG~i~C~ 105 (140)
..|+.|.++ . ..| .-.|+.||..|=.
T Consensus 36 ~~Cp~C~~~-~-VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 36 HVCPFCGRT-T-VKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CcCCCCCCc-c-eeeeccCeEEcCCCCCeecc
Confidence 479999997 3 222 3458899988744
No 181
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.66 E-value=22 Score=21.72 Aligned_cols=15 Identities=20% Similarity=0.749 Sum_probs=12.0
Q ss_pred ccccccccccccccc
Q psy1895 78 ITCRACDKEFTVTRR 92 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r 92 (140)
..|..|+++|+..++
T Consensus 13 KICpvCqRPFsWRkK 27 (54)
T COG4338 13 KICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhhcCchHHHHH
Confidence 489999999996543
No 182
>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=25.55 E-value=23 Score=33.40 Aligned_cols=32 Identities=34% Similarity=0.994 Sum_probs=0.0
Q ss_pred ccccccccCce----EeCCCCCCeeeCCCCCCCcccCcccHHH
Q psy1895 92 RRHHCRNCGEI----FCNMCSDNKMALPSAAKPVRVCDECNVK 130 (140)
Q Consensus 92 rkhhCr~CG~i----~C~~Cs~~~~~lp~~~~~~RVC~~C~~~ 130 (140)
-...|..||.. .|..|..++ .|+++|..|-..
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T-------~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHT-------EPVYVCPDCGIE 689 (900)
T ss_dssp -------------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCcc-------ccceeccccccc
Confidence 34556666654 566665553 345555555443
No 183
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=25.45 E-value=38 Score=20.28 Aligned_cols=16 Identities=31% Similarity=0.532 Sum_probs=12.7
Q ss_pred CCCcccCcccHHHhhc
Q psy1895 118 AKPVRVCDECNVKLVE 133 (140)
Q Consensus 118 ~~~~RVC~~C~~~l~~ 133 (140)
+.|.-+|..|++.|+=
T Consensus 3 GAPFv~C~~C~~lLql 18 (46)
T PF11331_consen 3 GAPFVVCSSCFELLQL 18 (46)
T ss_pred CCCEeECccHHHHHcC
Confidence 4578899999998863
No 184
>KOG1356|consensus
Probab=25.31 E-value=32 Score=32.44 Aligned_cols=34 Identities=24% Similarity=0.530 Sum_probs=26.6
Q ss_pred CccccccccccccccccccccccCceEeCCCCCCee
Q psy1895 77 AITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
...|..|.+ ++|+-.--|+.||..||-.|...+.
T Consensus 229 ~~mC~~C~~--tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 229 REMCDRCET--TLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred chhhhhhcc--cccceeEEccccCCeeeecchhhcc
Confidence 357999998 3444445599999999999998875
No 185
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.30 E-value=38 Score=17.17 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=3.9
Q ss_pred ccccccCce
Q psy1895 94 HHCRNCGEI 102 (140)
Q Consensus 94 hhCr~CG~i 102 (140)
+.|..||+.
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 344444443
No 186
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.14 E-value=40 Score=30.82 Aligned_cols=32 Identities=28% Similarity=0.798 Sum_probs=17.7
Q ss_pred ccccccccccccc--ccccccccCce----EeCCCCCC
Q psy1895 79 TCRACDKEFTVTR--RRHHCRNCGEI----FCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~~~--rkhhCr~CG~i----~C~~Cs~~ 110 (140)
.|..|..+.++-. ..-.|+.||.. .|..|.+.
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4556666665432 23457777753 45555554
No 187
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=25.10 E-value=34 Score=25.07 Aligned_cols=24 Identities=25% Similarity=0.639 Sum_probs=16.9
Q ss_pred ccccccccccccccc-----cccccccCc
Q psy1895 78 ITCRACDKEFTVTRR-----RHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r-----khhCr~CG~ 101 (140)
-.|..|+.+-+.+.+ -.+|..||.
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 369999999886655 234666665
No 188
>KOG1813|consensus
Probab=25.10 E-value=38 Score=28.17 Aligned_cols=28 Identities=32% Similarity=0.825 Sum_probs=21.0
Q ss_pred cccccccccccccccccccccCceEeCCCCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~ 110 (140)
.|.+|.+.|--= -=-.||+.||..|...
T Consensus 243 ~c~icr~~f~~p----Vvt~c~h~fc~~ca~~ 270 (313)
T KOG1813|consen 243 KCFICRKYFYRP----VVTKCGHYFCEVCALK 270 (313)
T ss_pred cccccccccccc----hhhcCCceeehhhhcc
Confidence 499999987521 1247999999999865
No 189
>KOG3183|consensus
Probab=24.93 E-value=26 Score=28.18 Aligned_cols=51 Identities=22% Similarity=0.538 Sum_probs=29.2
Q ss_pred cccc--ccccccccccccccccccCceEeCCCCCCeeeC-CCC---CCCcccCcccHHHh
Q psy1895 78 ITCR--ACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMAL-PSA---AKPVRVCDECNVKL 131 (140)
Q Consensus 78 ~~C~--~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~l-p~~---~~~~RVC~~C~~~l 131 (140)
.+|. .|..- .|+ -.+|-.|+.+||...-++...- |.. ...+.+|..|...+
T Consensus 9 kHCs~~~Ckql-DFL--Pf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv 65 (250)
T KOG3183|consen 9 KHCSVPYCKQL-DFL--PFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPV 65 (250)
T ss_pred cccCcchhhhc-ccc--ceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCC
Confidence 4565 56552 222 2478888888887766553221 211 56677787776543
No 190
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=24.91 E-value=37 Score=24.84 Aligned_cols=26 Identities=19% Similarity=0.585 Sum_probs=19.9
Q ss_pred cccccccccccccc-ccccccccCceE
Q psy1895 78 ITCRACDKEFTVTR-RRHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~~-rkhhCr~CG~i~ 103 (140)
..|..|+++..... ....|..|+..+
T Consensus 35 ~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcccEeCCCCcEECCCCCCcC
Confidence 47999999876554 678888888764
No 191
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.78 E-value=44 Score=20.42 Aligned_cols=24 Identities=29% Similarity=0.693 Sum_probs=10.3
Q ss_pred cccccccc-ccc-cccccccccccCc
Q psy1895 78 ITCRACDK-EFT-VTRRRHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~-~F~-~~~rkhhCr~CG~ 101 (140)
..|+.|+. .|= .-..|.+|-.||.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 34666653 221 1223444555543
No 192
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.75 E-value=34 Score=24.98 Aligned_cols=24 Identities=25% Similarity=0.653 Sum_probs=15.0
Q ss_pred ccccccccccccc--cccccccccCc
Q psy1895 78 ITCRACDKEFTVT--RRRHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~--~rkhhCr~CG~ 101 (140)
+.|..|++.|--- .=...|..||.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCC
Confidence 4688888887622 22345777774
No 193
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=24.68 E-value=34 Score=24.05 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=17.3
Q ss_pred ccccccccccccccc-----cccccccCc
Q psy1895 78 ITCRACDKEFTVTRR-----RHHCRNCGE 101 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r-----khhCr~CG~ 101 (140)
-.|..|+.+-+.+.+ -.+|..||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 379999999886665 344777774
No 194
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.50 E-value=42 Score=18.16 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=8.0
Q ss_pred ccccccCceE
Q psy1895 94 HHCRNCGEIF 103 (140)
Q Consensus 94 hhCr~CG~i~ 103 (140)
+.|..||.++
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 5688999886
No 195
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=24.44 E-value=32 Score=20.48 Aligned_cols=27 Identities=33% Similarity=0.946 Sum_probs=16.8
Q ss_pred ccccccc-ccccccccccccccCce-EeCCC
Q psy1895 79 TCRACDK-EFTVTRRRHHCRNCGEI-FCNMC 107 (140)
Q Consensus 79 ~C~~C~~-~F~~~~rkhhCr~CG~i-~C~~C 107 (140)
.|..|.+ ++. ..|.+|-.|... +|..|
T Consensus 2 ~C~~C~~~~i~--g~R~~C~~C~dydLC~~C 30 (49)
T cd02345 2 SCSACRKQDIS--GIRFPCQVCRDYSLCLGC 30 (49)
T ss_pred cCCCCCCCCce--EeeEECCCCCCcCchHHH
Confidence 4778887 555 456778777543 44444
No 196
>PRK06260 threonine synthase; Validated
Probab=24.41 E-value=48 Score=27.95 Aligned_cols=24 Identities=29% Similarity=0.772 Sum_probs=18.8
Q ss_pred cccccccccccccccccccccCce
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI 102 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i 102 (140)
.|..|++.|..-...+.|..||..
T Consensus 5 ~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 5 KCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred EECCCCCCCCCCCccccCCCCCCe
Confidence 688999999866566779888764
No 197
>PRK05978 hypothetical protein; Provisional
Probab=24.40 E-value=42 Score=24.95 Aligned_cols=26 Identities=38% Similarity=0.866 Sum_probs=18.7
Q ss_pred ccccccccc--cc-cccccccccccCceE
Q psy1895 78 ITCRACDKE--FT-VTRRRHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~--F~-~~~rkhhCr~CG~i~ 103 (140)
..|+.|++. |. +++=+.+|..||.-|
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCcc
Confidence 468999873 44 455577799998865
No 198
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.32 E-value=60 Score=29.67 Aligned_cols=45 Identities=22% Similarity=0.654 Sum_probs=30.0
Q ss_pred cccccccccccccccccccccCce----EeCCCCCCeeeCCCCCCCcccCcccHHHh
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI----FCNMCSDNKMALPSAAKPVRVCDECNVKL 131 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i----~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l 131 (140)
.|+.|+..-. ..-..|..||.. +|..|... + ....+.|..|-..+
T Consensus 3 ~Cp~Cg~~n~--~~akFC~~CG~~l~~~~Cp~CG~~---~---~~~~~fC~~CG~~~ 51 (645)
T PRK14559 3 ICPQCQFENP--NNNRFCQKCGTSLTHKPCPQCGTE---V---PVDEAHCPNCGAET 51 (645)
T ss_pred cCCCCCCcCC--CCCccccccCCCCCCCcCCCCCCC---C---CcccccccccCCcc
Confidence 6888888633 333468888876 47777654 2 24567899886554
No 199
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.23 E-value=44 Score=32.98 Aligned_cols=28 Identities=43% Similarity=1.108 Sum_probs=0.0
Q ss_pred cccccccC----ceEeCCCCCCeeeCCCCCCCcccCccc
Q psy1895 93 RHHCRNCG----EIFCNMCSDNKMALPSAAKPVRVCDEC 127 (140)
Q Consensus 93 khhCr~CG----~i~C~~Cs~~~~~lp~~~~~~RVC~~C 127 (140)
+..|..|| ..||..|... ..++.+|..|
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~-------te~vy~CPsC 698 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTH-------TEPVYVCPDC 698 (1337)
T ss_pred EEECCCCCCccccccCcccCCc-------CCCceeCccC
No 200
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.16 E-value=63 Score=20.51 Aligned_cols=32 Identities=28% Similarity=0.732 Sum_probs=21.8
Q ss_pred Ccccccccccccccc--ccccccccCceEeCCCC
Q psy1895 77 AITCRACDKEFTVTR--RRHHCRNCGEIFCNMCS 108 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~--rkhhCr~CG~i~C~~Cs 108 (140)
...|..|+....... -++-|.+||.+.=.+|.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhh
Confidence 467999999875433 35669999976544443
No 201
>PF01190 Pollen_Ole_e_I: Pollen proteins Ole e I like; InterPro: IPR006041 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ole e 1. A number of plant pollen proteins, whose biological function is not yet known, are structurally related []. These proteins are most probably secreted and consist of about 145 residues. There are six cysteines which are conserved in the sequence of these proteins. They seem to be involved in disulphide bonds.
Probab=24.07 E-value=48 Score=22.08 Aligned_cols=10 Identities=40% Similarity=1.258 Sum_probs=8.9
Q ss_pred CceEeCCCCC
Q psy1895 100 GEIFCNMCSD 109 (140)
Q Consensus 100 G~i~C~~Cs~ 109 (140)
|.|+|..|..
T Consensus 3 G~V~C~~C~~ 12 (97)
T PF01190_consen 3 GVVYCDDCSS 12 (97)
T ss_pred EEEEeCCCCC
Confidence 7899999988
No 202
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.05 E-value=41 Score=24.10 Aligned_cols=26 Identities=15% Similarity=0.088 Sum_probs=19.1
Q ss_pred cccccccccccccccc-ccccccCceE
Q psy1895 78 ITCRACDKEFTVTRRR-HHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rk-hhCr~CG~i~ 103 (140)
..|+.|+++|--++|. ..|..||+.|
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccCccccchhhccCCCccccCcccccc
Confidence 4689999999866664 4477777765
No 203
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.97 E-value=27 Score=20.97 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=6.0
Q ss_pred ccccccccccc
Q psy1895 79 TCRACDKEFTV 89 (140)
Q Consensus 79 ~C~~C~~~F~~ 89 (140)
.|+.|+++|+-
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999999973
No 204
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=23.96 E-value=36 Score=20.38 Aligned_cols=30 Identities=7% Similarity=0.062 Sum_probs=19.9
Q ss_pred cccccccccccccccccccccCceEeCCCCCCee
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
.|.+|...|.- -....||++||..|....+
T Consensus 3 ~Cpi~~~~~~~----Pv~~~~G~v~~~~~i~~~~ 32 (63)
T smart00504 3 LCPISLEVMKD----PVILPSGQTYERRAIEKWL 32 (63)
T ss_pred CCcCCCCcCCC----CEECCCCCEEeHHHHHHHH
Confidence 46777776542 2345789999988876543
No 205
>KOG1315|consensus
Probab=23.91 E-value=39 Score=28.07 Aligned_cols=10 Identities=30% Similarity=0.909 Sum_probs=4.6
Q ss_pred CcccCcccHH
Q psy1895 120 PVRVCDECNV 129 (140)
Q Consensus 120 ~~RVC~~C~~ 129 (140)
-.+||..|+-
T Consensus 125 HCsvC~rCvL 134 (307)
T KOG1315|consen 125 HCSVCNRCVL 134 (307)
T ss_pred cchhhhhhhh
Confidence 3445555543
No 206
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=23.85 E-value=39 Score=16.99 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy1895 80 CRACDKEFT 88 (140)
Q Consensus 80 C~~C~~~F~ 88 (140)
|..|+++..
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 344444433
No 207
>PRK03954 ribonuclease P protein component 4; Validated
Probab=23.48 E-value=2.3e+02 Score=20.26 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=7.5
Q ss_pred cccccccccc
Q psy1895 78 ITCRACDKEF 87 (140)
Q Consensus 78 ~~C~~C~~~F 87 (140)
..|..|...+
T Consensus 65 ~~CK~C~t~L 74 (121)
T PRK03954 65 RYCKRCHSFL 74 (121)
T ss_pred HHhhcCCCee
Confidence 4788888765
No 208
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=23.39 E-value=31 Score=24.33 Aligned_cols=11 Identities=55% Similarity=1.503 Sum_probs=9.6
Q ss_pred cccccccCceE
Q psy1895 93 RHHCRNCGEIF 103 (140)
Q Consensus 93 khhCr~CG~i~ 103 (140)
-|.|-+||.+|
T Consensus 2 pH~CtrCG~vf 12 (112)
T COG3364 2 PHQCTRCGEVF 12 (112)
T ss_pred Cceeccccccc
Confidence 37899999998
No 209
>PRK07591 threonine synthase; Validated
Probab=23.34 E-value=50 Score=28.18 Aligned_cols=25 Identities=28% Similarity=0.776 Sum_probs=19.5
Q ss_pred ccccccccccccccccccccccCceE
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~ 103 (140)
-.|..|++.|..-.. ..|..||..+
T Consensus 19 l~C~~Cg~~~~~~~~-~~C~~cg~~l 43 (421)
T PRK07591 19 LKCRECGAEYPLGPI-HVCEECFGPL 43 (421)
T ss_pred EEeCCCCCcCCCCCC-ccCCCCCCeE
Confidence 479999999986544 7898888654
No 210
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.30 E-value=55 Score=20.27 Aligned_cols=8 Identities=63% Similarity=1.506 Sum_probs=3.5
Q ss_pred CcccCccc
Q psy1895 120 PVRVCDEC 127 (140)
Q Consensus 120 ~~RVC~~C 127 (140)
+.+||..|
T Consensus 39 ~H~vC~~C 46 (57)
T PRK12286 39 PHRVCPSC 46 (57)
T ss_pred CeEECCCC
Confidence 34444444
No 211
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.07 E-value=84 Score=19.83 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=19.8
Q ss_pred Ccccccccccccccc--ccccccccCceE
Q psy1895 77 AITCRACDKEFTVTR--RRHHCRNCGEIF 103 (140)
Q Consensus 77 ~~~C~~C~~~F~~~~--rkhhCr~CG~i~ 103 (140)
...|..|+....... -+..|.+||.+.
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVI 35 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCee
Confidence 347999998776444 367799999873
No 212
>PF01147 Crust_neurohorm: Crustacean CHH/MIH/GIH neurohormone family; InterPro: IPR001166 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. ; GO: 0005184 neuropeptide hormone activity, 0005576 extracellular region; PDB: 1J0T_A.
Probab=23.05 E-value=22 Score=23.32 Aligned_cols=16 Identities=44% Similarity=0.708 Sum_probs=12.0
Q ss_pred CCCcccCcccHHHhhc
Q psy1895 118 AKPVRVCDECNVKLVE 133 (140)
Q Consensus 118 ~~~~RVC~~C~~~l~~ 133 (140)
.+-.|||+.||...-.
T Consensus 17 ~kldrVC~DCyNl~R~ 32 (73)
T PF01147_consen 17 KKLDRVCDDCYNLFRE 32 (73)
T ss_dssp HHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHHHcC
Confidence 4557999999998643
No 213
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=22.95 E-value=32 Score=15.98 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=6.2
Q ss_pred ccccccccccc
Q psy1895 79 TCRACDKEFTV 89 (140)
Q Consensus 79 ~C~~C~~~F~~ 89 (140)
.|..|+..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 47788887763
No 214
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=22.74 E-value=57 Score=23.50 Aligned_cols=10 Identities=20% Similarity=0.963 Sum_probs=5.8
Q ss_pred cccccccccc
Q psy1895 79 TCRACDKEFT 88 (140)
Q Consensus 79 ~C~~C~~~F~ 88 (140)
.|..|+..+.
T Consensus 114 ~C~~C~~~~~ 123 (146)
T smart00731 114 RCTGCGQRYL 123 (146)
T ss_pred ECCCCCCCCc
Confidence 4666666554
No 215
>PRK04351 hypothetical protein; Provisional
Probab=22.71 E-value=51 Score=24.34 Aligned_cols=13 Identities=31% Similarity=0.570 Sum_probs=7.1
Q ss_pred CCcccCcccHHHh
Q psy1895 119 KPVRVCDECNVKL 131 (140)
Q Consensus 119 ~~~RVC~~C~~~l 131 (140)
...-+|..|...|
T Consensus 130 ~~~yrCg~C~g~L 142 (149)
T PRK04351 130 TKRYRCGKCRGKL 142 (149)
T ss_pred CCcEEeCCCCcEe
Confidence 3445666665554
No 216
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=22.50 E-value=36 Score=20.11 Aligned_cols=28 Identities=21% Similarity=0.685 Sum_probs=16.0
Q ss_pred cccccccccccccccccccccCce-EeCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEI-FCNMC 107 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i-~C~~C 107 (140)
.|-.|+. +.+.-.|++|..|... +|..|
T Consensus 2 ~CDgCg~-~PI~G~RykC~~C~dyDLC~~C 30 (43)
T cd02342 2 QCDGCGV-LPITGPRYKSKVKEDYDLCTIC 30 (43)
T ss_pred CCCCCCC-CcccccceEeCCCCCCccHHHH
Confidence 3666665 3455667777766443 44444
No 217
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.49 E-value=44 Score=23.78 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=8.4
Q ss_pred cccccccccccc
Q psy1895 78 ITCRACDKEFTV 89 (140)
Q Consensus 78 ~~C~~C~~~F~~ 89 (140)
-.| .|+..|.+
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 468 89988765
No 218
>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=22.46 E-value=55 Score=20.54 Aligned_cols=14 Identities=21% Similarity=0.669 Sum_probs=6.5
Q ss_pred ccccccccccCceE
Q psy1895 90 TRRRHHCRNCGEIF 103 (140)
Q Consensus 90 ~~rkhhCr~CG~i~ 103 (140)
....-.|..||+.|
T Consensus 50 ~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 50 VEGELICPECGREY 63 (68)
T ss_dssp TTTEEEETTTTEEE
T ss_pred cCCEEEcCCCCCEE
Confidence 33344455555544
No 219
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.40 E-value=41 Score=19.07 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=6.1
Q ss_pred cccccccCceE
Q psy1895 93 RHHCRNCGEIF 103 (140)
Q Consensus 93 khhCr~CG~i~ 103 (140)
-+.|..||.|+
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 46799999886
No 220
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=22.34 E-value=42 Score=21.40 Aligned_cols=7 Identities=57% Similarity=1.559 Sum_probs=3.5
Q ss_pred ccccCce
Q psy1895 96 CRNCGEI 102 (140)
Q Consensus 96 Cr~CG~i 102 (140)
||.||..
T Consensus 20 CrRCG~~ 26 (62)
T PRK04179 20 CRRCGRH 26 (62)
T ss_pred hcccCcc
Confidence 5555543
No 221
>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=21.99 E-value=55 Score=18.96 Aligned_cols=22 Identities=32% Similarity=0.951 Sum_probs=12.6
Q ss_pred cccccccccccccccccccccCceEeCCC
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMC 107 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~C~~C 107 (140)
.|..|+.+. ++-+ =|.+||..|
T Consensus 19 ~Cp~C~~PL--~~~k-----~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL--MRDK-----DGKIYCVSC 40 (41)
T ss_pred ccCCCCCee--EEec-----CCCEECCCC
Confidence 688896543 2211 256677666
No 222
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=21.83 E-value=61 Score=21.15 Aligned_cols=14 Identities=43% Similarity=1.087 Sum_probs=8.7
Q ss_pred cccccccc--ccCceE
Q psy1895 90 TRRRHHCR--NCGEIF 103 (140)
Q Consensus 90 ~~rkhhCr--~CG~i~ 103 (140)
..+.+.|. .||..|
T Consensus 24 ~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 24 KERYHQCQNVNCSATF 39 (72)
T ss_pred heeeeecCCCCCCCEE
Confidence 34455577 777766
No 223
>KOG4323|consensus
Probab=21.82 E-value=46 Score=29.26 Aligned_cols=53 Identities=21% Similarity=0.475 Sum_probs=32.0
Q ss_pred cccccccc-ccccccccccccccCceEeCCCCCCee--eCCCCCCCcccCcccHHH
Q psy1895 78 ITCRACDK-EFTVTRRRHHCRNCGEIFCNMCSDNKM--ALPSAAKPVRVCDECNVK 130 (140)
Q Consensus 78 ~~C~~C~~-~F~~~~rkhhCr~CG~i~C~~Cs~~~~--~lp~~~~~~RVC~~C~~~ 130 (140)
.+|..|+. .++.++|...|+.|+.-|=..|..-.+ .+-....-+-.|+.|...
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 35888884 677888999999999875444432211 111113445667777543
No 224
>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=21.74 E-value=62 Score=20.07 Aligned_cols=27 Identities=22% Similarity=0.674 Sum_probs=13.6
Q ss_pred cccccccc---cccccccccccccCceEeC
Q psy1895 79 TCRACDKE---FTVTRRRHHCRNCGEIFCN 105 (140)
Q Consensus 79 ~C~~C~~~---F~~~~rkhhCr~CG~i~C~ 105 (140)
.|..|... |+--.....|..||.++|.
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 46777664 5544455567777777663
No 225
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=21.66 E-value=32 Score=17.15 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=8.8
Q ss_pred ccccccccccc
Q psy1895 79 TCRACDKEFTV 89 (140)
Q Consensus 79 ~C~~C~~~F~~ 89 (140)
.|..|++.|..
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 58889998873
No 226
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=21.57 E-value=47 Score=22.46 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=10.8
Q ss_pred ccccCceEeCCCC
Q psy1895 96 CRNCGEIFCNMCS 108 (140)
Q Consensus 96 Cr~CG~i~C~~Cs 108 (140)
|+.||++++-.+.
T Consensus 76 C~~Cg~i~~~~~~ 88 (116)
T cd07153 76 CTKCGKVIDFEDC 88 (116)
T ss_pred eCCCCCEEEecCc
Confidence 9999999986654
No 227
>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=21.36 E-value=47 Score=26.79 Aligned_cols=55 Identities=33% Similarity=0.684 Sum_probs=27.2
Q ss_pred Ccccccccccc--ccc-------cccccccccCc------eEeCCCCCCee-eCC-----CC-CCCcccCcccHHHh
Q psy1895 77 AITCRACDKEF--TVT-------RRRHHCRNCGE------IFCNMCSDNKM-ALP-----SA-AKPVRVCDECNVKL 131 (140)
Q Consensus 77 ~~~C~~C~~~F--~~~-------~rkhhCr~CG~------i~C~~Cs~~~~-~lp-----~~-~~~~RVC~~C~~~l 131 (140)
...|++|+..= +.+ .|..||..||. +-|..|.+... .+. .. ...+-||+.|..-+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence 35899999952 222 36678999985 47888876421 111 11 45678999997654
No 228
>PF07776 zf-AD: Zinc-finger associated domain (zf-AD) ; InterPro: IPR012934 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 zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 1PZW_A.
Probab=20.98 E-value=30 Score=20.86 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=12.6
Q ss_pred CCCcccCcccHHHhhc
Q psy1895 118 AKPVRVCDECNVKLVE 133 (140)
Q Consensus 118 ~~~~RVC~~C~~~l~~ 133 (140)
..|..||..|+..|..
T Consensus 42 ~lp~~IC~~C~~~l~~ 57 (75)
T PF07776_consen 42 DLPQQICSSCWEKLQQ 57 (75)
T ss_dssp SS-SEEEHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHH
Confidence 5677899999998864
No 229
>KOG2932|consensus
Probab=20.95 E-value=45 Score=28.13 Aligned_cols=46 Identities=22% Similarity=0.629 Sum_probs=34.0
Q ss_pred CCccccccccccccccccccccccCceEeCCCCCCeeeCCCCCCCcccCcccHHHhh
Q psy1895 76 EAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132 (140)
Q Consensus 76 ~~~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~~lp~~~~~~RVC~~C~~~l~ 132 (140)
.+..|..|..+.-++-|..- |.+|||-.|... .+.+.|..|-+.++
T Consensus 89 ~VHfCd~Cd~PI~IYGRmIP---CkHvFCl~CAr~--------~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 89 RVHFCDRCDFPIAIYGRMIP---CKHVFCLECARS--------DSDKICPLCDDRVQ 134 (389)
T ss_pred ceEeecccCCcceeeecccc---cchhhhhhhhhc--------CccccCcCcccHHH
Confidence 36789999999888888764 567999999764 24567777766553
No 230
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=20.90 E-value=40 Score=22.39 Aligned_cols=30 Identities=27% Similarity=0.656 Sum_probs=16.0
Q ss_pred ccccccccccccccc---cccccccCce---EeCCC
Q psy1895 78 ITCRACDKEFTVTRR---RHHCRNCGEI---FCNMC 107 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r---khhCr~CG~i---~C~~C 107 (140)
..|.+|+.++....+ .-||..+|.| .|..|
T Consensus 23 ~~C~iC~~~~~~~~~~~~vDHdH~tG~vRGlLC~~C 58 (81)
T PF02945_consen 23 GRCAICGKPLPGESRKLVVDHDHKTGRVRGLLCRSC 58 (81)
T ss_dssp TE-TTT-SEEETTCGGCEEEE-TTTTBEEEEEEHHH
T ss_pred CcCcCCCCCcccCCCcceecCCCCCCCchhhhhhHH
Confidence 379999995543233 3468888775 44444
No 231
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=20.75 E-value=41 Score=19.85 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=6.0
Q ss_pred cccCcccHHH
Q psy1895 121 VRVCDECNVK 130 (140)
Q Consensus 121 ~RVC~~C~~~ 130 (140)
.-+|..||..
T Consensus 23 ~dLC~~CF~~ 32 (45)
T cd02336 23 YDLCPSCYQE 32 (45)
T ss_pred cccChHHHhC
Confidence 4566666653
No 232
>PRK10061 DNA damage-inducible protein YebG; Provisional
Probab=20.70 E-value=95 Score=21.50 Aligned_cols=43 Identities=19% Similarity=0.135 Sum_probs=32.8
Q ss_pred hhhHHHhhhhhhhcchhhhhHHHHHHHHHHHHHhhhhhhHHHH
Q psy1895 11 DDHVKMNKIAEHVKDNVSDDKYKESELALEELGAQLSKSKLQV 53 (140)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~r~~~~~~~~~l~~~~~~l~~s~~~~ 53 (140)
|..-||..+++++.+.+.......-++..++++.-|...+..+
T Consensus 26 DAyDKMLD~Ad~L~~~L~~s~~~ldE~q~E~L~l~LA~nKd~l 68 (96)
T PRK10061 26 DAYDKMLDTADLLDTWLTNSPVQMEDEQREALSLWLAEQKDVL 68 (96)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 5566899999999999988877666777788877776655544
No 233
>PRK02935 hypothetical protein; Provisional
Probab=20.33 E-value=48 Score=23.45 Aligned_cols=25 Identities=24% Similarity=0.687 Sum_probs=21.1
Q ss_pred cccccccccccccccccccccCceE
Q psy1895 79 TCRACDKEFTVTRRRHHCRNCGEIF 103 (140)
Q Consensus 79 ~C~~C~~~F~~~~rkhhCr~CG~i~ 103 (140)
.|+.|++.=..+.|-.-|-+|++..
T Consensus 72 ~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 72 ICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred ECCCCCchhhhccceeecCcCCCcC
Confidence 7999999888888888888888753
No 234
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.24 E-value=54 Score=19.77 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=9.6
Q ss_pred cccccccCceEe
Q psy1895 93 RHHCRNCGEIFC 104 (140)
Q Consensus 93 khhCr~CG~i~C 104 (140)
++.|..||.|+=
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 467999999883
No 235
>PRK08197 threonine synthase; Validated
Probab=20.22 E-value=61 Score=27.28 Aligned_cols=24 Identities=21% Similarity=0.832 Sum_probs=18.4
Q ss_pred ccccccccccccccccccccccCce
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEI 102 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i 102 (140)
-.|..|++.|..-.....| .||..
T Consensus 8 ~~C~~Cg~~~~~~~~~~~C-~cg~~ 31 (394)
T PRK08197 8 LECSKCGETYDADQVHNLC-KCGKP 31 (394)
T ss_pred EEECCCCCCCCCCCcceec-CCCCe
Confidence 3699999999876666678 78754
No 236
>PHA02942 putative transposase; Provisional
Probab=20.22 E-value=82 Score=26.74 Aligned_cols=28 Identities=25% Similarity=0.777 Sum_probs=18.4
Q ss_pred CCccccccccccc-cccccccccccCceE
Q psy1895 76 EAITCRACDKEFT-VTRRRHHCRNCGEIF 103 (140)
Q Consensus 76 ~~~~C~~C~~~F~-~~~rkhhCr~CG~i~ 103 (140)
....|+.|+..-. +-.|.+.|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 3456888886422 334667898898864
No 237
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.14 E-value=47 Score=25.63 Aligned_cols=26 Identities=23% Similarity=0.498 Sum_probs=18.8
Q ss_pred ccccccccccccccc-----cccccccCceE
Q psy1895 78 ITCRACDKEFTVTRR-----RHHCRNCGEIF 103 (140)
Q Consensus 78 ~~C~~C~~~F~~~~r-----khhCr~CG~i~ 103 (140)
-.|..|+.+-+.+.+ -.+|..||..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 379999999986655 23577777653
No 238
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.07 E-value=67 Score=29.29 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=18.9
Q ss_pred ccccccccccc--ccccccccccCce-----EeCCCCCC
Q psy1895 79 TCRACDKEFTV--TRRRHHCRNCGEI-----FCNMCSDN 110 (140)
Q Consensus 79 ~C~~C~~~F~~--~~rkhhCr~CG~i-----~C~~Cs~~ 110 (140)
.|..|..+++. ..+.-.|+.||.. .|..|.+.
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 45666665553 2344458888765 47777554
No 239
>KOG2177|consensus
Probab=20.01 E-value=22 Score=26.89 Aligned_cols=31 Identities=29% Similarity=0.668 Sum_probs=23.9
Q ss_pred ccccccccccccccccccccccCceEeCCCCCCee
Q psy1895 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKM 112 (140)
Q Consensus 78 ~~C~~C~~~F~~~~rkhhCr~CG~i~C~~Cs~~~~ 112 (140)
-.|.+|-..|..- .--.||+.||..|.....
T Consensus 14 ~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~ 44 (386)
T KOG2177|consen 14 LTCPICLEYFREP----VLLPCGHNFCRACLTRSW 44 (386)
T ss_pred ccChhhHHHhhcC----ccccccchHhHHHHHHhc
Confidence 4799999988754 556799999999976543
Done!