Query psy2501
Match_columns 130
No_of_seqs 133 out of 1279
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 17:49:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.8 9.2E-21 2E-25 139.7 -3.9 115 10-125 286-407 (468)
2 KOG2272|consensus 99.7 1.3E-18 2.7E-23 121.1 0.1 121 10-130 147-272 (332)
3 KOG1701|consensus 99.7 9.7E-19 2.1E-23 129.1 -3.4 79 51-130 272-352 (468)
4 KOG1044|consensus 99.6 4.1E-17 8.9E-22 124.3 1.9 119 10-129 75-209 (670)
5 KOG2272|consensus 99.6 5.8E-16 1.2E-20 108.0 1.6 120 10-130 83-213 (332)
6 KOG1703|consensus 99.6 2.5E-16 5.5E-21 121.3 -1.6 122 9-130 312-442 (479)
7 PF00412 LIM: LIM domain; Int 99.6 5.4E-15 1.2E-19 82.9 4.2 56 56-111 1-58 (58)
8 KOG4577|consensus 99.4 1.5E-14 3.3E-19 102.5 -2.9 73 52-125 32-105 (383)
9 KOG1703|consensus 99.2 1.2E-11 2.6E-16 95.5 4.0 121 10-130 253-381 (479)
10 smart00132 LIM Zinc-binding do 98.7 7.6E-09 1.6E-13 52.8 2.5 36 55-90 1-38 (39)
11 KOG4577|consensus 98.7 8.8E-10 1.9E-14 78.6 -1.6 100 16-115 50-158 (383)
12 KOG1044|consensus 98.5 1.1E-08 2.4E-13 79.0 -1.6 96 12-107 146-247 (670)
13 KOG1700|consensus 98.0 2.4E-06 5.2E-11 59.2 0.7 61 53-113 7-68 (200)
14 KOG1700|consensus 97.8 3.8E-06 8.2E-11 58.2 0.2 59 53-111 108-167 (200)
15 KOG1702|consensus 97.7 3.6E-06 7.9E-11 57.8 -2.0 58 54-111 5-63 (264)
16 KOG0490|consensus 96.2 0.0013 2.9E-08 46.1 0.2 63 59-122 2-69 (235)
17 smart00132 LIM Zinc-binding do 93.2 0.089 1.9E-06 25.9 2.1 37 81-123 1-38 (39)
18 PF00412 LIM: LIM domain; Int 92.8 0.075 1.6E-06 28.9 1.6 39 82-126 1-40 (58)
19 PF14835 zf-RING_6: zf-RING of 83.4 1.2 2.6E-05 25.2 2.1 43 80-122 8-50 (65)
20 PF10235 Cript: Microtubule-as 82.5 0.95 2.1E-05 27.4 1.6 42 75-124 40-81 (90)
21 smart00504 Ubox Modified RING 76.4 4.2 9E-05 22.1 2.9 43 80-123 2-46 (63)
22 PF09943 DUF2175: Uncharacteri 74.7 0.97 2.1E-05 27.9 -0.0 31 54-84 3-35 (101)
23 COG2191 Formylmethanofuran deh 74.3 1.3 2.8E-05 30.8 0.5 31 80-110 173-203 (206)
24 PF10367 Vps39_2: Vacuolar sor 73.8 2.1 4.5E-05 26.1 1.4 28 53-80 78-107 (109)
25 PF14446 Prok-RING_1: Prokaryo 72.2 2.3 5E-05 23.2 1.1 28 53-80 5-36 (54)
26 KOG1813|consensus 71.2 2.3 4.9E-05 31.4 1.2 46 80-126 242-289 (313)
27 cd02336 ZZ_RSC8 Zinc finger, Z 70.8 4.5 9.8E-05 21.1 2.0 29 81-109 2-32 (45)
28 cd02249 ZZ Zinc finger, ZZ typ 70.7 4.5 9.7E-05 21.0 2.0 10 100-109 23-32 (46)
29 PF08394 Arc_trans_TRASH: Arch 70.6 2.4 5.3E-05 21.2 0.9 23 56-78 1-25 (37)
30 smart00291 ZnF_ZZ Zinc-binding 70.2 5 0.00011 20.6 2.1 10 100-109 27-36 (44)
31 PF00645 zf-PARP: Poly(ADP-rib 69.3 1.5 3.3E-05 25.7 -0.0 33 50-82 4-48 (82)
32 COG5152 Uncharacterized conser 68.8 1.9 4E-05 30.1 0.3 48 79-127 196-245 (259)
33 PF14634 zf-RING_5: zinc-RING 68.7 8.3 0.00018 19.6 2.8 23 98-120 20-44 (44)
34 PF11781 RRN7: RNA polymerase 68.6 3.2 7E-05 20.6 1.1 23 81-107 10-32 (36)
35 PF01258 zf-dskA_traR: Prokary 68.4 1.3 2.7E-05 21.8 -0.4 27 82-108 6-32 (36)
36 KOG2462|consensus 68.3 2.9 6.3E-05 30.5 1.2 37 54-90 162-198 (279)
37 PRK14873 primosome assembly pr 65.9 4 8.7E-05 33.6 1.7 38 81-121 394-431 (665)
38 KOG0320|consensus 65.4 4 8.7E-05 27.9 1.4 48 78-125 130-180 (187)
39 COG1645 Uncharacterized Zn-fin 63.5 3.3 7.2E-05 26.8 0.7 10 97-106 41-50 (131)
40 PF13920 zf-C3HC4_3: Zinc fing 63.0 8.3 0.00018 20.1 2.1 42 82-124 5-49 (50)
41 KOG4739|consensus 62.6 5.8 0.00012 28.3 1.8 34 91-124 15-49 (233)
42 PF12674 Zn_ribbon_2: Putative 61.9 4.6 0.0001 23.9 1.1 28 82-109 3-35 (81)
43 PF00569 ZZ: Zinc finger, ZZ t 61.2 6 0.00013 20.5 1.3 11 99-109 27-37 (46)
44 cd02341 ZZ_ZZZ3 Zinc finger, Z 61.0 10 0.00022 20.0 2.2 12 99-110 25-36 (48)
45 PF12773 DZR: Double zinc ribb 60.7 12 0.00026 19.5 2.5 9 82-90 15-23 (50)
46 PF04570 DUF581: Protein of un 60.1 7.7 0.00017 21.5 1.7 28 81-108 18-48 (58)
47 PF06906 DUF1272: Protein of u 57.8 18 0.00038 19.9 2.8 25 101-125 30-54 (57)
48 cd02340 ZZ_NBR1_like Zinc fing 56.9 12 0.00025 19.2 2.0 10 100-109 23-32 (43)
49 COG1644 RPB10 DNA-directed RNA 56.0 4.1 8.9E-05 22.8 0.1 13 112-124 4-16 (63)
50 PF14471 DUF4428: Domain of un 54.9 11 0.00023 20.2 1.7 29 81-110 1-30 (51)
51 PF13248 zf-ribbon_3: zinc-rib 54.6 8.9 0.00019 17.3 1.2 9 55-63 4-12 (26)
52 cd00162 RING RING-finger (Real 54.5 13 0.00029 17.9 2.0 24 98-121 18-44 (45)
53 COG4357 Zinc finger domain con 53.6 1.9 4E-05 26.4 -1.6 48 56-103 38-86 (105)
54 PRK14890 putative Zn-ribbon RN 53.5 18 0.0004 20.0 2.5 49 53-119 7-55 (59)
55 PF01194 RNA_pol_N: RNA polyme 53.1 7.4 0.00016 21.7 0.9 13 112-124 4-16 (60)
56 TIGR00595 priA primosomal prot 51.3 11 0.00023 30.0 1.9 38 81-121 224-262 (505)
57 cd02342 ZZ_UBA_plant Zinc fing 49.6 18 0.00038 18.8 1.9 11 99-109 23-33 (43)
58 PF02069 Metallothio_Pro: Prok 49.4 11 0.00025 20.3 1.2 28 81-108 9-37 (52)
59 PRK04016 DNA-directed RNA poly 49.0 7 0.00015 21.9 0.4 14 111-124 3-16 (62)
60 COG2888 Predicted Zn-ribbon RN 48.4 21 0.00045 19.9 2.1 27 53-88 9-36 (61)
61 PF13695 zf-3CxxC: Zinc-bindin 48.0 19 0.00042 21.9 2.3 10 55-64 7-16 (98)
62 PF01927 Mut7-C: Mut7-C RNAse 47.8 31 0.00067 22.6 3.4 39 51-89 89-134 (147)
63 COG1198 PriA Primosomal protei 47.7 57 0.0012 27.4 5.5 73 27-121 405-484 (730)
64 PF06677 Auto_anti-p27: Sjogre 47.5 7.1 0.00015 20.0 0.2 9 97-105 31-39 (41)
65 cd02335 ZZ_ADA2 Zinc finger, Z 47.1 23 0.00049 18.6 2.2 11 100-110 24-34 (49)
66 PF10083 DUF2321: Uncharacteri 46.7 8.4 0.00018 25.7 0.5 27 99-126 27-53 (158)
67 PRK11595 DNA utilization prote 44.8 25 0.00055 24.7 2.8 12 53-64 5-16 (227)
68 PF10892 DUF2688: Protein of u 44.8 5.2 0.00011 21.9 -0.5 36 81-121 12-47 (60)
69 cd02338 ZZ_PCMF_like Zinc fing 44.5 19 0.0004 19.0 1.6 11 100-110 24-34 (49)
70 PRK00420 hypothetical protein; 42.9 12 0.00027 23.6 0.8 11 54-64 24-34 (112)
71 PF02591 DUF164: Putative zinc 42.4 6.4 0.00014 21.3 -0.5 13 52-64 21-33 (56)
72 PRK04023 DNA polymerase II lar 42.1 35 0.00077 29.7 3.5 52 51-124 624-675 (1121)
73 cd02344 ZZ_HERC2 Zinc finger, 41.6 28 0.00061 18.1 1.9 11 99-109 23-33 (45)
74 PF14255 Cys_rich_CPXG: Cystei 40.9 14 0.0003 19.9 0.7 29 55-83 2-31 (52)
75 PF13923 zf-C3HC4_2: Zinc fing 40.6 19 0.0004 17.6 1.2 29 83-111 2-30 (39)
76 PF13240 zinc_ribbon_2: zinc-r 40.0 11 0.00023 16.6 0.2 9 82-90 2-10 (23)
77 cd02345 ZZ_dah Zinc finger, ZZ 38.2 26 0.00056 18.4 1.5 11 100-110 24-34 (49)
78 PRK14559 putative protein seri 37.9 28 0.0006 28.8 2.3 11 54-64 2-12 (645)
79 PF13834 DUF4193: Domain of un 37.8 9 0.00019 23.6 -0.3 29 78-106 69-98 (99)
80 PF05502 Dynactin_p62: Dynacti 37.7 14 0.00031 29.3 0.6 39 52-90 25-63 (483)
81 cd02334 ZZ_dystrophin Zinc fin 36.9 34 0.00073 18.1 1.8 11 100-110 24-34 (49)
82 KOG2932|consensus 35.5 23 0.00049 26.6 1.3 42 81-122 92-133 (389)
83 PF06689 zf-C4_ClpX: ClpX C4-t 35.1 33 0.00072 17.3 1.6 28 81-108 3-32 (41)
84 PLN03208 E3 ubiquitin-protein 33.9 62 0.0013 22.5 3.2 13 113-125 69-81 (193)
85 TIGR00373 conserved hypothetic 33.3 45 0.00097 22.2 2.4 31 52-90 108-139 (158)
86 KOG3476|consensus 33.0 8.7 0.00019 23.1 -0.9 25 98-124 67-91 (100)
87 KOG3039|consensus 31.0 65 0.0014 23.5 3.0 75 54-128 184-275 (303)
88 cd02339 ZZ_Mind_bomb Zinc fing 30.3 54 0.0012 16.9 1.9 9 100-108 24-32 (45)
89 KOG3002|consensus 29.8 50 0.0011 24.6 2.4 43 80-123 49-91 (299)
90 PF07754 DUF1610: Domain of un 29.8 29 0.00063 15.5 0.7 11 115-125 1-11 (24)
91 PRK00398 rpoP DNA-directed RNA 29.7 33 0.00071 17.6 1.1 26 55-89 5-31 (46)
92 PF10886 DUF2685: Protein of u 29.4 32 0.0007 18.7 1.0 13 113-125 2-14 (54)
93 PF04810 zf-Sec23_Sec24: Sec23 29.1 49 0.0011 16.5 1.6 29 54-87 3-32 (40)
94 PHA03082 DNA-dependent RNA pol 28.9 12 0.00027 20.6 -0.7 16 80-95 5-20 (63)
95 PF06827 zf-FPG_IleRS: Zinc fi 28.7 23 0.0005 16.3 0.3 12 54-65 2-13 (30)
96 PF05864 Chordopox_RPO7: Chord 28.6 13 0.00028 20.5 -0.6 16 80-95 5-20 (63)
97 cd01407 SIR2-fam SIR2 family o 27.7 42 0.00091 23.4 1.6 16 112-127 133-148 (218)
98 COG2174 RPL34A Ribosomal prote 27.7 26 0.00056 21.2 0.5 12 113-124 35-46 (93)
99 PF09723 Zn-ribbon_8: Zinc rib 27.5 19 0.00042 18.2 -0.1 9 55-63 7-15 (42)
100 KOG3579|consensus 26.4 41 0.00088 25.0 1.4 33 52-84 267-300 (352)
101 smart00834 CxxC_CXXC_SSSS Puta 26.1 22 0.00047 17.4 -0.1 9 55-63 7-15 (41)
102 PF00096 zf-C2H2: Zinc finger, 26.1 30 0.00066 14.4 0.4 11 80-90 1-11 (23)
103 PF04502 DUF572: Family of unk 24.8 23 0.0005 26.5 -0.1 10 113-122 78-87 (324)
104 PF11077 DUF2616: Protein of u 24.8 38 0.00082 23.1 0.9 36 76-111 136-171 (173)
105 PRK06266 transcription initiat 24.8 82 0.0018 21.5 2.6 31 52-90 116-147 (178)
106 cd02343 ZZ_EF Zinc finger, ZZ 24.5 85 0.0018 16.6 2.0 11 100-110 23-33 (48)
107 COG1571 Predicted DNA-binding 24.5 54 0.0012 25.6 1.8 34 51-93 348-381 (421)
108 PF07649 C1_3: C1-like domain; 24.4 45 0.00097 15.3 0.9 12 80-91 1-12 (30)
109 PF15135 UPF0515: Uncharacteri 24.1 77 0.0017 23.1 2.3 12 114-125 176-187 (278)
110 PRK14714 DNA polymerase II lar 23.9 66 0.0014 28.9 2.3 50 53-124 667-721 (1337)
111 PF13894 zf-C2H2_4: C2H2-type 23.9 39 0.00084 13.7 0.6 11 80-90 1-11 (24)
112 PF07503 zf-HYPF: HypF finger; 23.8 39 0.00086 16.5 0.6 31 56-90 2-32 (35)
113 PF08209 Sgf11: Sgf11 (transcr 22.9 21 0.00045 17.3 -0.5 16 80-95 5-20 (33)
114 PF06750 DiS_P_DiS: Bacterial 22.8 1.5E+02 0.0033 17.8 3.2 12 53-64 33-44 (92)
115 PF13717 zinc_ribbon_4: zinc-r 22.8 36 0.00079 16.6 0.4 8 56-63 5-12 (36)
116 PF11571 Med27: Mediator compl 22.7 25 0.00054 21.0 -0.2 18 105-122 47-64 (90)
117 PF14569 zf-UDP: Zinc-binding 22.7 68 0.0015 18.9 1.6 21 100-120 36-59 (80)
118 PF12898 Stc1: Stc1 domain; I 22.7 1.7E+02 0.0037 17.2 3.4 55 24-94 11-65 (84)
119 PF08271 TF_Zn_Ribbon: TFIIB z 22.7 37 0.00079 17.1 0.4 10 80-89 20-29 (43)
120 TIGR02605 CxxC_CxxC_SSSS putat 22.6 29 0.00064 18.1 0.1 10 54-63 6-15 (52)
121 PF00320 GATA: GATA zinc finge 22.4 77 0.0017 15.3 1.6 27 82-108 1-28 (36)
122 PF11331 DUF3133: Protein of u 22.1 54 0.0012 17.2 1.0 11 113-123 32-42 (46)
123 smart00531 TFIIE Transcription 22.0 86 0.0019 20.5 2.2 36 52-90 98-134 (147)
124 PRK00085 recO DNA repair prote 22.0 45 0.00097 23.5 0.9 32 76-107 146-177 (247)
125 PRK12495 hypothetical protein; 21.6 40 0.00086 24.0 0.5 28 52-89 41-68 (226)
126 PRK13796 GTPase YqeH; Provisio 21.3 63 0.0014 24.5 1.6 9 55-63 2-10 (365)
127 smart00659 RPOLCX RNA polymera 21.1 36 0.00078 17.6 0.2 9 55-63 4-12 (44)
128 COG1997 RPL43A Ribosomal prote 20.9 1.2E+02 0.0026 18.3 2.4 35 53-95 35-69 (89)
129 TIGR00270 conserved hypothetic 20.9 90 0.0019 20.8 2.1 9 82-90 3-11 (154)
130 KOG2186|consensus 20.7 23 0.00049 25.7 -0.8 41 55-95 5-45 (276)
131 PF08746 zf-RING-like: RING-li 20.6 20 0.00043 18.4 -0.9 8 56-63 1-8 (43)
132 PF10080 DUF2318: Predicted me 20.5 46 0.00099 20.6 0.6 27 80-110 36-62 (102)
133 COG1579 Zn-ribbon protein, pos 20.3 49 0.0011 23.8 0.8 15 51-65 195-209 (239)
134 COG4847 Uncharacterized protei 20.1 70 0.0015 19.6 1.3 35 54-88 7-43 (103)
135 KOG1829|consensus 20.0 42 0.00092 27.4 0.5 32 78-109 339-375 (580)
No 1
>KOG1701|consensus
Probab=99.76 E-value=9.2e-21 Score=139.75 Aligned_cols=115 Identities=26% Similarity=0.530 Sum_probs=93.2
Q ss_pred CCCCcccCCCCCCCCCCCchhHHHHHHHHHH------HHhhhcCCCCCCCccccccccccccceeeecCcccccCCcccC
Q psy2501 10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLT------AEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICT 83 (130)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~ 83 (130)
.....+.||++.+|..||.+..+...+..-. +.+++..+. ....+|..|++.|+++++.++|+.||+.||+|.
T Consensus 286 g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq-~tlekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv 364 (468)
T KOG1701|consen 286 GQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQ-DTLEKCNKCGEPIMDRILRALGKAYHPGCFTCV 364 (468)
T ss_pred CcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHH-HHHHHHhhhhhHHHHHHHHhcccccCCCceEEE
Confidence 3456788999999999998777776542211 111222332 122589999999999999999999999999999
Q ss_pred CCCcccCCCCee-ccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501 84 HCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDV 125 (130)
Q Consensus 84 ~C~~~l~~~~~~-~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~ 125 (130)
.|.+.|.+..|. ..++.+||..||.++|+++|+.|++||+++
T Consensus 365 ~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~ 407 (468)
T KOG1701|consen 365 VCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPR 407 (468)
T ss_pred EeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCC
Confidence 999999988887 778999999999999999999999999753
No 2
>KOG2272|consensus
Probab=99.71 E-value=1.3e-18 Score=121.15 Aligned_cols=121 Identities=27% Similarity=0.563 Sum_probs=99.2
Q ss_pred CCCCcccCCCCCCCCCCCchhHH----HHHHHHHHHHh-hhcCCCCCCCccccccccccccceeeecCcccccCCcccCC
Q psy2501 10 VTDSSSVSYSKPNQPVHQKGKQL----DCMLDSLTAEM-SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTH 84 (130)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~-~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~ 84 (130)
+.+..++-.+.++|+-+|.+..+ ++..-.+..++ .-..-...+.++|+.|.++|.++.+.++++.||.+.|+|+.
T Consensus 147 iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~ 226 (332)
T KOG2272|consen 147 IDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAK 226 (332)
T ss_pred cccccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehh
Confidence 45566777789999999955444 44333333332 22222345678999999999999999999999999999999
Q ss_pred CCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501 85 CNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT 130 (130)
Q Consensus 85 C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~ 130 (130)
|.+++-+.+.|.+.|..||+.+|.++|+-.|+.|+..|.|.++.||
T Consensus 227 CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al 272 (332)
T KOG2272|consen 227 CEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSAL 272 (332)
T ss_pred cCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHh
Confidence 9999988899999999999999999999999999999999998875
No 3
>KOG1701|consensus
Probab=99.68 E-value=9.7e-19 Score=129.14 Aligned_cols=79 Identities=30% Similarity=0.800 Sum_probs=72.7
Q ss_pred CCCcccccccccccc--ceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCcee
Q psy2501 51 TQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIR 128 (130)
Q Consensus 51 ~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~ 128 (130)
.++..|.+|+|.|.+ ..+++|++.||..||+|..|++.|.+..||..++++||+.||...+ ++|..|+++|+++||+
T Consensus 272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLr 350 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILR 350 (468)
T ss_pred hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHH
Confidence 344599999999974 4578999999999999999999999999999999999999998876 8999999999999999
Q ss_pred eC
Q psy2501 129 NT 130 (130)
Q Consensus 129 ~~ 130 (130)
||
T Consensus 351 A~ 352 (468)
T KOG1701|consen 351 AL 352 (468)
T ss_pred hc
Confidence 96
No 4
>KOG1044|consensus
Probab=99.64 E-value=4.1e-17 Score=124.33 Aligned_cols=119 Identities=24% Similarity=0.516 Sum_probs=94.3
Q ss_pred CCCCcccCCCCCCCCCCCchhHHHH---------------HHHHHHHHhhhcCCCCCCCcccccccccc-ccceeeecCc
Q psy2501 10 VTDSSSVSYSKPNQPVHQKGKQLDC---------------MLDSLTAEMSRQGVTTTQKGCCSSCDKPI-VGQVITALGK 73 (130)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~C~~C~~~i-~~~~~~~~~~ 73 (130)
+....+.++++++|+.+|.+..+.. +-+.....+...+....+...|++|+..| .++.+.++++
T Consensus 75 ~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~ 154 (670)
T KOG1044|consen 75 VEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDK 154 (670)
T ss_pred ccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeecc
Confidence 4456788999999999995443321 11112222222222334567899999999 5899999999
Q ss_pred ccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceee
Q psy2501 74 TWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRN 129 (130)
Q Consensus 74 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~ 129 (130)
.||..||+|..|+..|. ++|+..+|.+||+.+|...|+.+|..|.+.|.|++|.|
T Consensus 155 qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqa 209 (670)
T KOG1044|consen 155 QWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQA 209 (670)
T ss_pred ceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhc
Confidence 99999999999999996 47999999999999999999999999999999999987
No 5
>KOG2272|consensus
Probab=99.57 E-value=5.8e-16 Score=107.97 Aligned_cols=120 Identities=23% Similarity=0.352 Sum_probs=97.7
Q ss_pred CCCCcccCCCCCCCCCCCchhHHHHHHHHHHHHh------hhc-----CCCCCCCccccccccccccceeeecCcccccC
Q psy2501 10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEM------SRQ-----GVTTTQKGCCSSCDKPIVGQVITALGKTWHPE 78 (130)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~-----~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~ 78 (130)
+..+.+.+++..|||.+|.++.++..+.+..... .+. .....+..+|..|+..|.++.+...+..||+.
T Consensus 83 iiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~y 162 (332)
T KOG2272|consen 83 IIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPY 162 (332)
T ss_pred hhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCcc
Confidence 4457788999999999999998887766544333 111 22345667899999999888899999999999
Q ss_pred CcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501 79 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT 130 (130)
Q Consensus 79 Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~ 130 (130)
.|+|..|++.|.. .-....+.+||..|+.+.--|+|++|.+||++++|.||
T Consensus 163 HFkCt~C~keL~s-daRevk~eLyClrChD~mgipiCgaC~rpIeervi~am 213 (332)
T KOG2272|consen 163 HFKCTTCGKELTS-DAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAM 213 (332)
T ss_pred ceecccccccccc-hhhhhccceeccccccccCCcccccccCchHHHHHHHh
Confidence 9999999999964 33477789999999877666999999999999999875
No 6
>KOG1703|consensus
Probab=99.55 E-value=2.5e-16 Score=121.31 Aligned_cols=122 Identities=29% Similarity=0.657 Sum_probs=98.6
Q ss_pred CCCC-CcccCCCCCCCCCCCchhHHHHHHHHHHHH------hhhcCCCCCCCccccccccccccceeeecCcccccCCcc
Q psy2501 9 SVTD-SSSVSYSKPNQPVHQKGKQLDCMLDSLTAE------MSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFI 81 (130)
Q Consensus 9 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~ 81 (130)
+... ..++++++.||+.+|.+......+...... +....+.....+.|.+|+++|.++.|.++++.||++||.
T Consensus 312 ~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~ 391 (479)
T KOG1703|consen 312 KIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFV 391 (479)
T ss_pred CcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhcee
Confidence 4556 888999999999999666655443322221 122223345668999999999999999999999999999
Q ss_pred cCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccc--cCceeeC
Q psy2501 82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DVSIRNT 130 (130)
Q Consensus 82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~ 130 (130)
|..|..++....|+..++.+||+.||.+++..+|..|.++|+ +..+.|+
T Consensus 392 C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~ 442 (479)
T KOG1703|consen 392 CADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEAD 442 (479)
T ss_pred eecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhcc
Confidence 999999999999999999999999999999999999999987 7666653
No 7
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.55 E-value=5.4e-15 Score=82.89 Aligned_cols=56 Identities=46% Similarity=1.178 Sum_probs=50.1
Q ss_pred cccccccccc-ce-eeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501 56 CSSCDKPIVG-QV-ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111 (130)
Q Consensus 56 C~~C~~~i~~-~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 111 (130)
|..|+++|.+ .. +.+.++.||++||+|..|+.+|.+..++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7899999974 33 36999999999999999999998888999999999999998875
No 8
>KOG4577|consensus
Probab=99.38 E-value=1.5e-14 Score=102.55 Aligned_cols=73 Identities=27% Similarity=0.773 Sum_probs=66.2
Q ss_pred CCccccccccccccce-eeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501 52 QKGCCSSCDKPIVGQV-ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV 125 (130)
Q Consensus 52 ~~~~C~~C~~~i~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~ 125 (130)
..++|+.|.+.|.+.+ +.++++.||..|++|+.|..+|.+ ..+.+++.+||+.+|.++|+-+|++|++.|.+.
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt 105 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPT 105 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChH
Confidence 5578999999998765 579999999999999999999975 578999999999999999999999999999753
No 9
>KOG1703|consensus
Probab=99.20 E-value=1.2e-11 Score=95.55 Aligned_cols=121 Identities=26% Similarity=0.437 Sum_probs=91.4
Q ss_pred CCCCcccCCCCCCCCCCCchhHHHHHHHHHHHH--hh-----hcCCCCCCCcccccccccccc-ceeeecCcccccCCcc
Q psy2501 10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAE--MS-----RQGVTTTQKGCCSSCDKPIVG-QVITALGKTWHPEHFI 81 (130)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-----~~~~~~~~~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~ 81 (130)
.....+.+....|++..+...+.-.+....... +. ...+.....+.|..|...|.+ +.+.++++.||+.+|.
T Consensus 253 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~ 332 (479)
T KOG1703|consen 253 ECQPLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKEWHPEHFS 332 (479)
T ss_pred ccCcceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeecccccccccee
Confidence 333555666777777776444222222111111 11 111222344899999999998 8899999999999999
Q ss_pred cCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501 82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT 130 (130)
Q Consensus 82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~ 130 (130)
|..|...+..+.+...+|.+||..||...+.+.|.+|+++|++++|.|+
T Consensus 333 c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~ 381 (479)
T KOG1703|consen 333 CEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL 381 (479)
T ss_pred eccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc
Confidence 9999999988888899999999999999999999999999999999875
No 10
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.74 E-value=7.6e-09 Score=52.80 Aligned_cols=36 Identities=56% Similarity=1.238 Sum_probs=32.1
Q ss_pred ccccccccccc--ceeeecCcccccCCcccCCCCcccC
Q psy2501 55 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 55 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
+|..|++.|.+ ..+.+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 48899999975 6678999999999999999999885
No 11
>KOG4577|consensus
Probab=98.73 E-value=8.8e-10 Score=78.63 Aligned_cols=100 Identities=21% Similarity=0.360 Sum_probs=72.2
Q ss_pred cCCCCCCCCCCCchhHHHHHHHHHHHHh-----hhcCCCCCCCccccccccccc-ccee-eecCcccccCCcccCCCCcc
Q psy2501 16 VSYSKPNQPVHQKGKQLDCMLDSLTAEM-----SRQGVTTTQKGCCSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQE 88 (130)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~C~~C~~~i~-~~~~-~~~~~~~H~~Cf~C~~C~~~ 88 (130)
..+++.||..|..++.+...+..--... ++...-..++.+|..|...|. .+++ .+.+..||..||.|..|++.
T Consensus 50 Kvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~ 129 (383)
T KOG4577|consen 50 KVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQ 129 (383)
T ss_pred HHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcc
Confidence 4567899999997777765554433222 222222346679999999995 5554 47889999999999999999
Q ss_pred cC-CCCee-ccCCcccCHHhhhhhcCCCC
Q psy2501 89 LG-TRNFF-ERDSRPYCEPDYHNLFSPRC 115 (130)
Q Consensus 89 l~-~~~~~-~~~~~~~C~~~~~~~~~~~C 115 (130)
|. +.+|| ..++++.|+.+|..--..-|
T Consensus 130 L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 130 LATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred cccCCeeEEeccceeehhhhHHHHHhccc
Confidence 96 44777 67889999999985443434
No 12
>KOG1044|consensus
Probab=98.50 E-value=1.1e-08 Score=78.95 Aligned_cols=96 Identities=20% Similarity=0.303 Sum_probs=77.6
Q ss_pred CCcccCCCCCCCCCCCchhHHHHHHHHHHHH-----hhhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCC
Q psy2501 12 DSSSVSYSKPNQPVHQKGKQLDCMLDSLTAE-----MSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCN 86 (130)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~ 86 (130)
.++..++.+.||-.||.+..+...+...... .+...+...++.+|..|.+-|.+.++.+.++.||+.|-+|+.|+
T Consensus 146 gq~llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HPtCARCsRCg 225 (670)
T KOG1044|consen 146 GQALLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHPTCARCSRCG 225 (670)
T ss_pred cceeeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccCcccCcchhhhhhhc
Confidence 3677899999999999888777666543322 24555666778899999999999999999999999999999999
Q ss_pred cccCCC-CeeccCCcccCHHhh
Q psy2501 87 QELGTR-NFFERDSRPYCEPDY 107 (130)
Q Consensus 87 ~~l~~~-~~~~~~~~~~C~~~~ 107 (130)
..++++ +.|..+..++-..|-
T Consensus 226 qmF~eGEEMYlQGs~iWHP~C~ 247 (670)
T KOG1044|consen 226 QMFGEGEEMYLQGSEIWHPDCK 247 (670)
T ss_pred cccccchheeeccccccCCccc
Confidence 999866 567777777776664
No 13
>KOG1700|consensus
Probab=97.95 E-value=2.4e-06 Score=59.21 Aligned_cols=61 Identities=26% Similarity=0.614 Sum_probs=52.6
Q ss_pred Cccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCC
Q psy2501 53 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113 (130)
Q Consensus 53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~ 113 (130)
...|..|++.++ .+.+...+..||..||+|..|...|....+...++.+||+.+|...+++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~ 68 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGP 68 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCc
Confidence 358999999996 5556688999999999999999999888888999999999977777765
No 14
>KOG1700|consensus
Probab=97.84 E-value=3.8e-06 Score=58.24 Aligned_cols=59 Identities=31% Similarity=0.712 Sum_probs=51.2
Q ss_pred Cccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501 53 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111 (130)
Q Consensus 53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 111 (130)
...|..|.+.++ .+.+...+..||..||+|+.|+..|+.+.+....+.+||+.++..++
T Consensus 108 ~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 108 KEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred ccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 357999999996 46677889999999999999999999989999999999987776654
No 15
>KOG1702|consensus
Probab=97.67 E-value=3.6e-06 Score=57.77 Aligned_cols=58 Identities=29% Similarity=0.707 Sum_probs=50.3
Q ss_pred ccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501 54 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111 (130)
Q Consensus 54 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 111 (130)
..|..|++.++ .+.+..+++.||..||+|..|+.+|.-..+-..+.++||..+|.+..
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 45778999886 46688999999999999999999998777878999999999997654
No 16
>KOG0490|consensus
Probab=96.20 E-value=0.0013 Score=46.10 Aligned_cols=63 Identities=33% Similarity=0.829 Sum_probs=50.3
Q ss_pred cccccccce-eeecCcccccCCcccCCCCcccC--CCCeeccCCcccCHHhhhh--hcCCCCccCcccc
Q psy2501 59 CDKPIVGQV-ITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHN--LFSPRCSYCNGPI 122 (130)
Q Consensus 59 C~~~i~~~~-~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~--~~~~~C~~C~~~I 122 (130)
|+..|.+.+ +...+..||..|..|..|...+. ...+.. +|..||..+|.+ .+..+|.+|...|
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 555665443 45568999999999999999997 444445 999999999998 7778999998876
No 17
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=93.17 E-value=0.089 Score=25.85 Aligned_cols=37 Identities=16% Similarity=0.471 Sum_probs=25.4
Q ss_pred ccCCCCcccCCC-CeeccCCcccCHHhhhhhcCCCCccCccccc
Q psy2501 81 ICTHCNQELGTR-NFFERDSRPYCEPDYHNLFSPRCSYCNGPIL 123 (130)
Q Consensus 81 ~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~ 123 (130)
+|..|+.++.+. ......++.|...|| +|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf------~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECF------KCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCC------CCcccCCcCc
Confidence 477888888765 444556677776664 6777877764
No 18
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=92.84 E-value=0.075 Score=28.87 Aligned_cols=39 Identities=18% Similarity=0.514 Sum_probs=30.6
Q ss_pred cCCCCcccCCCCee-ccCCcccCHHhhhhhcCCCCccCccccccCc
Q psy2501 82 CTHCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDVS 126 (130)
Q Consensus 82 C~~C~~~l~~~~~~-~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~ 126 (130)
|..|+.++.+.... ...++.|...|| +|..|+++|.+..
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECF------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTS------BETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEEEEeCCcEEEcccc------ccCCCCCccCCCe
Confidence 67889998766655 578888888885 7999999987653
No 19
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.41 E-value=1.2 Score=25.22 Aligned_cols=43 Identities=16% Similarity=0.444 Sum_probs=18.6
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccc
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI 122 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I 122 (130)
.+|+.|..-|...-....=+..||..|-...++..|-.|+.|-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Pa 50 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPA 50 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChH
Confidence 4566666665433223334567788777777777788887764
No 20
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=82.52 E-value=0.95 Score=27.39 Aligned_cols=42 Identities=24% Similarity=0.543 Sum_probs=28.2
Q ss_pred cccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccccc
Q psy2501 75 WHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124 (130)
Q Consensus 75 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~ 124 (130)
|-..--.|..|...+.. .|.-||..|..+. .+|+-|++.|++
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 43333466667665532 2467899996654 799999999854
No 21
>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=76.45 E-value=4.2 Score=22.13 Aligned_cols=43 Identities=9% Similarity=0.193 Sum_probs=30.1
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhhc--CCCCccCccccc
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLF--SPRCSYCNGPIL 123 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~--~~~C~~C~~~I~ 123 (130)
|.|..|...+.+. .....|..||+.+..+.+ ...|-.|++++.
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 5677777777653 445668899988876554 347888888774
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=74.68 E-value=0.97 Score=27.93 Aligned_cols=31 Identities=35% Similarity=0.417 Sum_probs=22.9
Q ss_pred ccccccccccc-cceeeec-CcccccCCcccCC
Q psy2501 54 GCCSSCDKPIV-GQVITAL-GKTWHPEHFICTH 84 (130)
Q Consensus 54 ~~C~~C~~~i~-~~~~~~~-~~~~H~~Cf~C~~ 84 (130)
..|..|++.|. |+.+.+. ...-|..||+-..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 46999999995 7777653 3567999987543
No 23
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=74.28 E-value=1.3 Score=30.81 Aligned_cols=31 Identities=16% Similarity=0.425 Sum_probs=24.6
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhh
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNL 110 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~ 110 (130)
-+|+.|+-......-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 4788888877666666888999999998754
No 24
>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=73.84 E-value=2.1 Score=26.05 Aligned_cols=28 Identities=29% Similarity=0.526 Sum_probs=14.1
Q ss_pred Cccccccccccccce-ee-ecCcccccCCc
Q psy2501 53 KGCCSSCDKPIVGQV-IT-ALGKTWHPEHF 80 (130)
Q Consensus 53 ~~~C~~C~~~i~~~~-~~-~~~~~~H~~Cf 80 (130)
...|..|++.|.... +. ..+..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 345777777774322 22 22344565554
No 25
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.25 E-value=2.3 Score=23.19 Aligned_cols=28 Identities=18% Similarity=0.533 Sum_probs=18.6
Q ss_pred Cccccccccccc--cceee--ecCcccccCCc
Q psy2501 53 KGCCSSCDKPIV--GQVIT--ALGKTWHPEHF 80 (130)
Q Consensus 53 ~~~C~~C~~~i~--~~~~~--~~~~~~H~~Cf 80 (130)
+.+|..|++.|. +.++. .-+..||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 467999999983 44443 34566777775
No 26
>KOG1813|consensus
Probab=71.24 E-value=2.3 Score=31.36 Aligned_cols=46 Identities=15% Similarity=0.346 Sum_probs=33.9
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhhcC--CCCccCccccccCc
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFS--PRCSYCNGPILDVS 126 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~--~~C~~C~~~I~~~~ 126 (130)
|.|..|.+..-. .....-+.-+|..|..+.|. ++|..|++.|.|.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~ 289 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSF 289 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccccc
Confidence 677778777632 23344567789999988775 59999999988765
No 27
>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=70.78 E-value=4.5 Score=21.12 Aligned_cols=29 Identities=14% Similarity=0.450 Sum_probs=18.1
Q ss_pred ccCCCCcccCCCCeec--cCCcccCHHhhhh
Q psy2501 81 ICTHCNQELGTRNFFE--RDSRPYCEPDYHN 109 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~--~~~~~~C~~~~~~ 109 (130)
.|..|+..+....|.. ..+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 4666777776444441 2246779999874
No 28
>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=70.68 E-value=4.5 Score=20.98 Aligned_cols=10 Identities=20% Similarity=0.428 Sum_probs=6.4
Q ss_pred cccCHHhhhh
Q psy2501 100 RPYCEPDYHN 109 (130)
Q Consensus 100 ~~~C~~~~~~ 109 (130)
..+|..||..
T Consensus 23 ~dLC~~Cf~~ 32 (46)
T cd02249 23 FDLCSSCYAK 32 (46)
T ss_pred CcCHHHHHCc
Confidence 4557777764
No 29
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=70.59 E-value=2.4 Score=21.23 Aligned_cols=23 Identities=26% Similarity=0.472 Sum_probs=14.7
Q ss_pred ccccccccccc--eeeecCcccccC
Q psy2501 56 CSSCDKPIVGQ--VITALGKTWHPE 78 (130)
Q Consensus 56 C~~C~~~i~~~--~~~~~~~~~H~~ 78 (130)
|..|+.+|.++ .+...++.|+.-
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fC 25 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFC 25 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEE
Confidence 56688888643 345677777733
No 30
>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=70.18 E-value=5 Score=20.62 Aligned_cols=10 Identities=10% Similarity=0.434 Sum_probs=7.0
Q ss_pred cccCHHhhhh
Q psy2501 100 RPYCEPDYHN 109 (130)
Q Consensus 100 ~~~C~~~~~~ 109 (130)
..+|..||..
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 4568888864
No 31
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=69.28 E-value=1.5 Score=25.67 Aligned_cols=33 Identities=27% Similarity=0.625 Sum_probs=20.1
Q ss_pred CCCCccccccccccc-cce-----eeec-C-----cccccCCccc
Q psy2501 50 TTQKGCCSSCDKPIV-GQV-----ITAL-G-----KTWHPEHFIC 82 (130)
Q Consensus 50 ~~~~~~C~~C~~~i~-~~~-----~~~~-~-----~~~H~~Cf~C 82 (130)
.++...|..|+..|. +.. +... + ..||..||.=
T Consensus 4 ks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~~ 48 (82)
T PF00645_consen 4 KSGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFFK 48 (82)
T ss_dssp SSSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHHH
T ss_pred CCCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECcccccc
Confidence 345568999999994 322 1122 1 3578888763
No 32
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=68.82 E-value=1.9 Score=30.06 Aligned_cols=48 Identities=13% Similarity=0.396 Sum_probs=35.0
Q ss_pred CcccCCCCcccCCCCeeccCCcccCHHhhhhhcC--CCCccCccccccCce
Q psy2501 79 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS--PRCSYCNGPILDVSI 127 (130)
Q Consensus 79 Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~--~~C~~C~~~I~~~~~ 127 (130)
=|.|..|...... ..+..=|.-||..|+.+.+. +.|..|++.--|.+-
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~ 245 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFW 245 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhcccee
Confidence 3788888876532 23344577889999988875 699999998766653
No 33
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=68.67 E-value=8.3 Score=19.62 Aligned_cols=23 Identities=26% Similarity=0.561 Sum_probs=16.5
Q ss_pred CCcccCHHhhhhhc--CCCCccCcc
Q psy2501 98 DSRPYCEPDYHNLF--SPRCSYCNG 120 (130)
Q Consensus 98 ~~~~~C~~~~~~~~--~~~C~~C~~ 120 (130)
=|..+|..|..+.. ...|-.|++
T Consensus 20 CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 20 CGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 36788888887776 457777753
No 34
>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=68.58 E-value=3.2 Score=20.57 Aligned_cols=23 Identities=26% Similarity=0.589 Sum_probs=15.0
Q ss_pred ccCCCCcccCCCCeeccCCcccCHHhh
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYCEPDY 107 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~ 107 (130)
.|..|+.. .+...+|..||..|-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCc
Confidence 35666553 455778888887664
No 35
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=68.41 E-value=1.3 Score=21.83 Aligned_cols=27 Identities=11% Similarity=0.379 Sum_probs=12.0
Q ss_pred cCCCCcccCCCCeeccCCcccCHHhhh
Q psy2501 82 CTHCNQELGTRNFFERDSRPYCEPDYH 108 (130)
Q Consensus 82 C~~C~~~l~~~~~~~~~~~~~C~~~~~ 108 (130)
|..|+.++...+.....+..+|..|+.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhC
Confidence 444444444333334455556666654
No 36
>KOG2462|consensus
Probab=68.28 E-value=2.9 Score=30.47 Aligned_cols=37 Identities=19% Similarity=0.305 Sum_probs=20.0
Q ss_pred ccccccccccccceeeecCcccccCCcccCCCCcccC
Q psy2501 54 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 54 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
..|..|++.-..+-...+-..-|.--+.|..|++.++
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCCCccccccccccc
Confidence 4566666654322112233334665667777777764
No 37
>PRK14873 primosome assembly protein PriA; Provisional
Probab=65.86 E-value=4 Score=33.59 Aligned_cols=38 Identities=26% Similarity=0.499 Sum_probs=25.1
Q ss_pred ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccc
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP 121 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~ 121 (130)
+|..|+.+|. ++...+.+.|.-|-......+|-.|+..
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 5566666663 3444567778888665555589999764
No 38
>KOG0320|consensus
Probab=65.45 E-value=4 Score=27.91 Aligned_cols=48 Identities=13% Similarity=0.421 Sum_probs=35.3
Q ss_pred CCcccCCCCcccCCCC-eeccCCcccCHHhhhhhc--CCCCccCccccccC
Q psy2501 78 EHFICTHCNQELGTRN-FFERDSRPYCEPDYHNLF--SPRCSYCNGPILDV 125 (130)
Q Consensus 78 ~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~~~~~~~--~~~C~~C~~~I~~~ 125 (130)
.+++|..|-....... +.-.=|.+||..|-...+ +.+|-.|++.|+-+
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 5678888777765543 446668999999987544 46999999988743
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.46 E-value=3.3 Score=26.84 Aligned_cols=10 Identities=20% Similarity=0.584 Sum_probs=5.5
Q ss_pred cCCcccCHHh
Q psy2501 97 RDSRPYCEPD 106 (130)
Q Consensus 97 ~~~~~~C~~~ 106 (130)
.+|.+||..|
T Consensus 41 KdG~v~CPvC 50 (131)
T COG1645 41 KDGEVFCPVC 50 (131)
T ss_pred eCCeEECCCC
Confidence 5555555555
No 40
>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=63.02 E-value=8.3 Score=20.12 Aligned_cols=42 Identities=21% Similarity=0.503 Sum_probs=25.4
Q ss_pred cCCCCcccCCCCeeccCCcc-cCHHhhhhhc--CCCCccCcccccc
Q psy2501 82 CTHCNQELGTRNFFERDSRP-YCEPDYHNLF--SPRCSYCNGPILD 124 (130)
Q Consensus 82 C~~C~~~l~~~~~~~~~~~~-~C~~~~~~~~--~~~C~~C~~~I~~ 124 (130)
|..|...... ..+..=|.. +|..|..+.+ ..+|-.|.++|+.
T Consensus 5 C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 5 CPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp -TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 4444444322 122344566 8999987764 4689999999863
No 41
>KOG4739|consensus
Probab=62.60 E-value=5.8 Score=28.33 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=25.5
Q ss_pred CCCeeccC-CcccCHHhhhhhcCCCCccCcccccc
Q psy2501 91 TRNFFERD-SRPYCEPDYHNLFSPRCSYCNGPILD 124 (130)
Q Consensus 91 ~~~~~~~~-~~~~C~~~~~~~~~~~C~~C~~~I~~ 124 (130)
...||... ..++|..|.....++.|..|.+.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 44566443 67889999877777799999998754
No 42
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=61.86 E-value=4.6 Score=23.90 Aligned_cols=28 Identities=32% Similarity=0.675 Sum_probs=16.2
Q ss_pred cCCCCcccCCCCee-----ccCCcccCHHhhhh
Q psy2501 82 CTHCNQELGTRNFF-----ERDSRPYCEPDYHN 109 (130)
Q Consensus 82 C~~C~~~l~~~~~~-----~~~~~~~C~~~~~~ 109 (130)
|..|+.||.....+ ...+.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 56677776533322 33346788888753
No 43
>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=61.24 E-value=6 Score=20.54 Aligned_cols=11 Identities=18% Similarity=0.452 Sum_probs=7.5
Q ss_pred CcccCHHhhhh
Q psy2501 99 SRPYCEPDYHN 109 (130)
Q Consensus 99 ~~~~C~~~~~~ 109 (130)
+.-+|..||.+
T Consensus 27 d~dLC~~C~~~ 37 (46)
T PF00569_consen 27 DYDLCEDCFSK 37 (46)
T ss_dssp S-EEEHHHHHH
T ss_pred CCchhhHHHhC
Confidence 35678888875
No 44
>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=60.98 E-value=10 Score=20.02 Aligned_cols=12 Identities=8% Similarity=-0.020 Sum_probs=8.3
Q ss_pred CcccCHHhhhhh
Q psy2501 99 SRPYCEPDYHNL 110 (130)
Q Consensus 99 ~~~~C~~~~~~~ 110 (130)
+.-+|..||.+.
T Consensus 25 d~DlC~~C~~~~ 36 (48)
T cd02341 25 DFDLCQDCVVKG 36 (48)
T ss_pred CCccCHHHHhCc
Confidence 355688888754
No 45
>PF12773 DZR: Double zinc ribbon
Probab=60.69 E-value=12 Score=19.45 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=4.3
Q ss_pred cCCCCcccC
Q psy2501 82 CTHCNQELG 90 (130)
Q Consensus 82 C~~C~~~l~ 90 (130)
|..|+..|.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444555443
No 46
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=60.10 E-value=7.7 Score=21.48 Aligned_cols=28 Identities=21% Similarity=0.695 Sum_probs=18.7
Q ss_pred ccCCCCcccC-CCC-eeccCCcccC-HHhhh
Q psy2501 81 ICTHCNQELG-TRN-FFERDSRPYC-EPDYH 108 (130)
Q Consensus 81 ~C~~C~~~l~-~~~-~~~~~~~~~C-~~~~~ 108 (130)
.|..|++.|. +.. |..++.+.+| ..|-.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 4667778886 344 4478888888 46644
No 47
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=57.75 E-value=18 Score=19.90 Aligned_cols=25 Identities=16% Similarity=0.592 Sum_probs=18.6
Q ss_pred ccCHHhhhhhcCCCCccCccccccC
Q psy2501 101 PYCEPDYHNLFSPRCSYCNGPILDV 125 (130)
Q Consensus 101 ~~C~~~~~~~~~~~C~~C~~~I~~~ 125 (130)
-||..|....+...|-.|+..+..+
T Consensus 30 TFC~~C~e~~l~~~CPNCgGelv~R 54 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGGELVRR 54 (57)
T ss_pred cccHHHHHHHhcCcCcCCCCccccC
Confidence 4688888888788888887765443
No 48
>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=56.89 E-value=12 Score=19.22 Aligned_cols=10 Identities=20% Similarity=0.238 Sum_probs=5.9
Q ss_pred cccCHHhhhh
Q psy2501 100 RPYCEPDYHN 109 (130)
Q Consensus 100 ~~~C~~~~~~ 109 (130)
..+|..||..
T Consensus 23 ~dLC~~C~~~ 32 (43)
T cd02340 23 YDLCESCEAK 32 (43)
T ss_pred ccchHHhhCc
Confidence 4457777654
No 49
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=55.95 E-value=4.1 Score=22.80 Aligned_cols=13 Identities=31% Similarity=0.491 Sum_probs=10.1
Q ss_pred CCCCccCcccccc
Q psy2501 112 SPRCSYCNGPILD 124 (130)
Q Consensus 112 ~~~C~~C~~~I~~ 124 (130)
..+|++|+++|..
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 3489999998853
No 50
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=54.89 E-value=11 Score=20.21 Aligned_cols=29 Identities=24% Similarity=0.544 Sum_probs=18.9
Q ss_pred ccCCCCcccCCCC-eeccCCcccCHHhhhhh
Q psy2501 81 ICTHCNQELGTRN-FFERDSRPYCEPDYHNL 110 (130)
Q Consensus 81 ~C~~C~~~l~~~~-~~~~~~~~~C~~~~~~~ 110 (130)
.|..|+..++--. +-..+| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 3677777775332 446666 5799998665
No 51
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.64 E-value=8.9 Score=17.29 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy2501 55 CCSSCDKPI 63 (130)
Q Consensus 55 ~C~~C~~~i 63 (130)
.|..|+..+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 355555543
No 52
>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=54.55 E-value=13 Score=17.94 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=13.2
Q ss_pred CCcccCHHhhhhhc---CCCCccCccc
Q psy2501 98 DSRPYCEPDYHNLF---SPRCSYCNGP 121 (130)
Q Consensus 98 ~~~~~C~~~~~~~~---~~~C~~C~~~ 121 (130)
=+..||..|..+.+ ..+|-.|...
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 34556666654333 2357777654
No 53
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=53.60 E-value=1.9 Score=26.41 Aligned_cols=48 Identities=23% Similarity=0.490 Sum_probs=28.0
Q ss_pred ccccccccccce-eeecCcccccCCcccCCCCcccCCCCeeccCCcccC
Q psy2501 56 CSSCDKPIVGQV-ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103 (130)
Q Consensus 56 C~~C~~~i~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C 103 (130)
|..|+..+.... ..+.-..+++.+-.|..|...|.-.+|...+.=+||
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 556666664322 334445677777788888887765555544443333
No 54
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=53.48 E-value=18 Score=20.04 Aligned_cols=49 Identities=22% Similarity=0.505 Sum_probs=27.5
Q ss_pred CccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCc
Q psy2501 53 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCN 119 (130)
Q Consensus 53 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~ 119 (130)
.++|..|+..|.+.- +---|.|..|+..+-. -|..|-.....-+|-.|+
T Consensus 7 ~~~CtSCg~~i~~~~--------~~~~F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 7 PPKCTSCGIEIAPRE--------KAVKFLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred CccccCCCCcccCCC--------ccCEeeCCCCCCeeEe----------echhHHhcCCceECCCCC
Confidence 457999999885321 1112777777775311 166664433334666665
No 55
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=53.12 E-value=7.4 Score=21.70 Aligned_cols=13 Identities=31% Similarity=0.537 Sum_probs=9.2
Q ss_pred CCCCccCcccccc
Q psy2501 112 SPRCSYCNGPILD 124 (130)
Q Consensus 112 ~~~C~~C~~~I~~ 124 (130)
..+|++|++.|..
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 4589999998853
No 56
>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=51.33 E-value=11 Score=30.02 Aligned_cols=38 Identities=16% Similarity=0.519 Sum_probs=22.8
Q ss_pred ccCCCCcccCCCCeeccCCcccCHHhhhhh-cCCCCccCccc
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYCEPDYHNL-FSPRCSYCNGP 121 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~-~~~~C~~C~~~ 121 (130)
+|..|+.+| .|+..++.+.|.-|-... +...|-.|+..
T Consensus 224 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 445555554 344556677788775433 33488888763
No 57
>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=49.60 E-value=18 Score=18.76 Aligned_cols=11 Identities=9% Similarity=0.268 Sum_probs=6.7
Q ss_pred CcccCHHhhhh
Q psy2501 99 SRPYCEPDYHN 109 (130)
Q Consensus 99 ~~~~C~~~~~~ 109 (130)
+.-+|..||.+
T Consensus 23 dyDLC~~C~~~ 33 (43)
T cd02342 23 DYDLCTICFSR 33 (43)
T ss_pred CCccHHHHhhh
Confidence 34567777654
No 58
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=49.36 E-value=11 Score=20.32 Aligned_cols=28 Identities=21% Similarity=0.583 Sum_probs=15.2
Q ss_pred ccCCCCcccCCCCeeccCCcccC-HHhhh
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYC-EPDYH 108 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C-~~~~~ 108 (130)
.|..|.-.++...-...+|+.|| +.|..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 45667777765566788999998 56643
No 59
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=49.01 E-value=7 Score=21.94 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=10.7
Q ss_pred cCCCCccCcccccc
Q psy2501 111 FSPRCSYCNGPILD 124 (130)
Q Consensus 111 ~~~~C~~C~~~I~~ 124 (130)
+..+|++|++.|..
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 34589999998854
No 60
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.37 E-value=21 Score=19.90 Aligned_cols=27 Identities=30% Similarity=0.838 Sum_probs=16.8
Q ss_pred Cccccccccccc-cceeeecCcccccCCcccCCCCcc
Q psy2501 53 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQE 88 (130)
Q Consensus 53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~ 88 (130)
.+.|..|+..|. ++... -|.|..|+..
T Consensus 9 ~~~CtSCg~~i~p~e~~v---------~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGETAV---------KFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCcee---------EeeCCCCCce
Confidence 468999999883 33211 1667777743
No 61
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=48.02 E-value=19 Score=21.88 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=6.2
Q ss_pred cccccccccc
Q psy2501 55 CCSSCDKPIV 64 (130)
Q Consensus 55 ~C~~C~~~i~ 64 (130)
.|..|+....
T Consensus 7 ~C~~C~~~W~ 16 (98)
T PF13695_consen 7 QCSKCSRGWT 16 (98)
T ss_pred ECCCCCCCCc
Confidence 5667766654
No 62
>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=47.81 E-value=31 Score=22.57 Aligned_cols=39 Identities=18% Similarity=0.418 Sum_probs=23.3
Q ss_pred CCCccccccccccc--c-c-e---eeecCcccccCCcccCCCCccc
Q psy2501 51 TQKGCCSSCDKPIV--G-Q-V---ITALGKTWHPEHFICTHCNQEL 89 (130)
Q Consensus 51 ~~~~~C~~C~~~i~--~-~-~---~~~~~~~~H~~Cf~C~~C~~~l 89 (130)
....+|..|+..+. . + . +...-...+...+.|..|++-.
T Consensus 89 ~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 34578999999873 1 1 1 1112222355677889888854
No 63
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.69 E-value=57 Score=27.44 Aligned_cols=73 Identities=16% Similarity=0.341 Sum_probs=42.8
Q ss_pred CchhHHHHHHHHHHHHh------hhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCc
Q psy2501 27 QKGKQLDCMLDSLTAEM------SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSR 100 (130)
Q Consensus 27 ~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~ 100 (130)
|+..-++.+...+.... .+.+|. ..-.|..|+.. +.|..|+..| .++-..+.
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys--~~l~C~~Cg~v-----------------~~Cp~Cd~~l---t~H~~~~~ 462 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYA--PLLLCRDCGYI-----------------AECPNCDSPL---TLHKATGQ 462 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCcc--ceeecccCCCc-----------------ccCCCCCcce---EEecCCCe
Confidence 45555555555444332 333332 22357777653 4666777766 35555678
Q ss_pred ccCHHhhhh-hcCCCCccCccc
Q psy2501 101 PYCEPDYHN-LFSPRCSYCNGP 121 (130)
Q Consensus 101 ~~C~~~~~~-~~~~~C~~C~~~ 121 (130)
+.|.-|-.. .....|-.|+..
T Consensus 463 L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 463 LRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eEeCCCCCCCCCCCCCCCCCCC
Confidence 888877655 344589999876
No 64
>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=47.46 E-value=7.1 Score=19.98 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=4.5
Q ss_pred cCCcccCHH
Q psy2501 97 RDSRPYCEP 105 (130)
Q Consensus 97 ~~~~~~C~~ 105 (130)
++++.||..
T Consensus 31 k~g~~~Cv~ 39 (41)
T PF06677_consen 31 KDGKIYCVS 39 (41)
T ss_pred cCCCEECCC
Confidence 445555543
No 65
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=47.14 E-value=23 Score=18.58 Aligned_cols=11 Identities=9% Similarity=0.042 Sum_probs=6.6
Q ss_pred cccCHHhhhhh
Q psy2501 100 RPYCEPDYHNL 110 (130)
Q Consensus 100 ~~~C~~~~~~~ 110 (130)
..+|..||...
T Consensus 24 ~dLC~~Cf~~g 34 (49)
T cd02335 24 FDLCLECFSAG 34 (49)
T ss_pred cchhHHhhhCc
Confidence 44577777643
No 66
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.66 E-value=8.4 Score=25.73 Aligned_cols=27 Identities=19% Similarity=0.429 Sum_probs=19.8
Q ss_pred CcccCHHhhhhhcCCCCccCccccccCc
Q psy2501 99 SRPYCEPDYHNLFSPRCSYCNGPILDVS 126 (130)
Q Consensus 99 ~~~~C~~~~~~~~~~~C~~C~~~I~~~~ 126 (130)
..-||..|-.+.. -.|-.|+-+|.|.+
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y 53 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIRGDY 53 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCCCce
Confidence 4567888876655 67888888888764
No 67
>PRK11595 DNA utilization protein GntX; Provisional
Probab=44.83 E-value=25 Score=24.70 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=8.5
Q ss_pred Cccccccccccc
Q psy2501 53 KGCCSSCDKPIV 64 (130)
Q Consensus 53 ~~~C~~C~~~i~ 64 (130)
.++|..|+..+.
T Consensus 5 P~~C~~C~~~~~ 16 (227)
T PRK11595 5 PGLCWLCRMPLA 16 (227)
T ss_pred CCcCccCCCccC
Confidence 356888887763
No 68
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=44.81 E-value=5.2 Score=21.92 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=20.0
Q ss_pred ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccc
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP 121 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~ 121 (130)
.|..|++++..... .+|=-+.-..+|+.+|..|--|
T Consensus 12 ~CrRCGk~i~tl~~-----SL~Gad~lr~klG~IC~~Citp 47 (60)
T PF10892_consen 12 PCRRCGKSIRTLSR-----SLIGADDLRVKLGGICGDCITP 47 (60)
T ss_pred hhhhhCccHHHHHH-----HhhChHHHHHHHcchhhccCCH
Confidence 45566666543221 1222334457788899988655
No 69
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=44.48 E-value=19 Score=18.99 Aligned_cols=11 Identities=18% Similarity=0.298 Sum_probs=6.7
Q ss_pred cccCHHhhhhh
Q psy2501 100 RPYCEPDYHNL 110 (130)
Q Consensus 100 ~~~C~~~~~~~ 110 (130)
..+|..||...
T Consensus 24 ~dlC~~Cf~~~ 34 (49)
T cd02338 24 YDLCADCYDSG 34 (49)
T ss_pred CccchhHHhCC
Confidence 44577777644
No 70
>PRK00420 hypothetical protein; Validated
Probab=42.93 E-value=12 Score=23.57 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=7.0
Q ss_pred ccccccccccc
Q psy2501 54 GCCSSCDKPIV 64 (130)
Q Consensus 54 ~~C~~C~~~i~ 64 (130)
..|..|+.+++
T Consensus 24 ~~CP~Cg~pLf 34 (112)
T PRK00420 24 KHCPVCGLPLF 34 (112)
T ss_pred CCCCCCCCcce
Confidence 45777776663
No 71
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=42.42 E-value=6.4 Score=21.29 Aligned_cols=13 Identities=31% Similarity=0.815 Sum_probs=8.3
Q ss_pred CCccccccccccc
Q psy2501 52 QKGCCSSCDKPIV 64 (130)
Q Consensus 52 ~~~~C~~C~~~i~ 64 (130)
....|.+|+..|.
T Consensus 21 ~~~~C~gC~~~l~ 33 (56)
T PF02591_consen 21 EGGTCSGCHMELP 33 (56)
T ss_pred eCCccCCCCEEcC
Confidence 3456777777764
No 72
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.11 E-value=35 Score=29.74 Aligned_cols=52 Identities=17% Similarity=0.309 Sum_probs=34.8
Q ss_pred CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccccc
Q psy2501 51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124 (130)
Q Consensus 51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~ 124 (130)
.+...|..|+... .-|+|..|+.. .....+|..|-...-...|-.|+..+.+
T Consensus 624 Vg~RfCpsCG~~t--------------~~frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 624 IGRRKCPSCGKET--------------FYRRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred ccCccCCCCCCcC--------------CcccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 4567899998863 11788888876 1223468888655545679999887654
No 73
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=41.62 E-value=28 Score=18.12 Aligned_cols=11 Identities=18% Similarity=0.573 Sum_probs=7.4
Q ss_pred CcccCHHhhhh
Q psy2501 99 SRPYCEPDYHN 109 (130)
Q Consensus 99 ~~~~C~~~~~~ 109 (130)
+.-+|..||..
T Consensus 23 dyDLC~~Cf~~ 33 (45)
T cd02344 23 DFDFCENCFKT 33 (45)
T ss_pred CccchHHhhCC
Confidence 35568888765
No 74
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=40.88 E-value=14 Score=19.94 Aligned_cols=29 Identities=21% Similarity=0.458 Sum_probs=18.5
Q ss_pred cccccccccccce-eeecCcccccCCcccC
Q psy2501 55 CCSSCDKPIVGQV-ITALGKTWHPEHFICT 83 (130)
Q Consensus 55 ~C~~C~~~i~~~~-~~~~~~~~H~~Cf~C~ 83 (130)
.|..|+..+.-.. .+..++.|-.+|-.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 4788888874222 3445677877776664
No 75
>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=40.60 E-value=19 Score=17.64 Aligned_cols=29 Identities=14% Similarity=0.287 Sum_probs=15.2
Q ss_pred CCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501 83 THCNQELGTRNFFERDSRPYCEPDYHNLF 111 (130)
Q Consensus 83 ~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 111 (130)
..|...+.+......=|..||..|..+.+
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~C~~~~~ 30 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKECIEKYL 30 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHHHHHHHH
T ss_pred CCCCCcccCcCEECCCCCchhHHHHHHHH
Confidence 34444444322334556778888876544
No 76
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.01 E-value=11 Score=16.61 Aligned_cols=9 Identities=33% Similarity=1.114 Sum_probs=5.0
Q ss_pred cCCCCcccC
Q psy2501 82 CTHCNQELG 90 (130)
Q Consensus 82 C~~C~~~l~ 90 (130)
|..|+..+.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 455666554
No 77
>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=38.21 E-value=26 Score=18.44 Aligned_cols=11 Identities=18% Similarity=0.196 Sum_probs=6.6
Q ss_pred cccCHHhhhhh
Q psy2501 100 RPYCEPDYHNL 110 (130)
Q Consensus 100 ~~~C~~~~~~~ 110 (130)
..+|..||...
T Consensus 24 ydLC~~Cf~~~ 34 (49)
T cd02345 24 YSLCLGCYTKG 34 (49)
T ss_pred cCchHHHHhCC
Confidence 34577777643
No 78
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.89 E-value=28 Score=28.76 Aligned_cols=11 Identities=18% Similarity=0.323 Sum_probs=8.1
Q ss_pred ccccccccccc
Q psy2501 54 GCCSSCDKPIV 64 (130)
Q Consensus 54 ~~C~~C~~~i~ 64 (130)
.+|..|+..+.
T Consensus 2 ~~Cp~Cg~~n~ 12 (645)
T PRK14559 2 LICPQCQFENP 12 (645)
T ss_pred CcCCCCCCcCC
Confidence 36888888763
No 79
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=37.79 E-value=9 Score=23.59 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=17.5
Q ss_pred CCcccCCCCcccCCCCee-ccCCcccCHHh
Q psy2501 78 EHFICTHCNQELGTRNFF-ERDSRPYCEPD 106 (130)
Q Consensus 78 ~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~~ 106 (130)
+=|.|+.|-.---..+.+ ..+|+++|..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 347787776432222222 66788999877
No 80
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=37.73 E-value=14 Score=29.29 Aligned_cols=39 Identities=15% Similarity=0.278 Sum_probs=27.6
Q ss_pred CCccccccccccccceeeecCcccccCCcccCCCCcccC
Q psy2501 52 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 52 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
....|..|-..+...-+...+......||.|..|...|.
T Consensus 25 ~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 25 DSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ceeECccccccCChhhheeccceeccccccCCCCCCcce
Confidence 345688887766432234555666789999999999985
No 81
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=36.87 E-value=34 Score=18.12 Aligned_cols=11 Identities=9% Similarity=0.286 Sum_probs=6.9
Q ss_pred cccCHHhhhhh
Q psy2501 100 RPYCEPDYHNL 110 (130)
Q Consensus 100 ~~~C~~~~~~~ 110 (130)
.-+|..||...
T Consensus 24 ~DLC~~Cf~~g 34 (49)
T cd02334 24 YDLCQSCFFSG 34 (49)
T ss_pred cCchHHHHhCC
Confidence 44577777643
No 82
>KOG2932|consensus
Probab=35.45 E-value=23 Score=26.59 Aligned_cols=42 Identities=12% Similarity=0.347 Sum_probs=20.4
Q ss_pred ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccc
Q psy2501 81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI 122 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I 122 (130)
-|..|+.++.--...+.=+.+||.+|.-.--.+.|-.|+.+|
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH
Confidence 355565555311122333456666664322234677776654
No 83
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=35.11 E-value=33 Score=17.29 Aligned_cols=28 Identities=11% Similarity=0.292 Sum_probs=13.0
Q ss_pred ccCCCCcccCCCCee--ccCCcccCHHhhh
Q psy2501 81 ICTHCNQELGTRNFF--ERDSRPYCEPDYH 108 (130)
Q Consensus 81 ~C~~C~~~l~~~~~~--~~~~~~~C~~~~~ 108 (130)
+|+.|+++-...... ..++...|..|-.
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 577777776544322 3334555777654
No 84
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=33.91 E-value=62 Score=22.50 Aligned_cols=13 Identities=23% Similarity=0.945 Sum_probs=9.5
Q ss_pred CCCccCccccccC
Q psy2501 113 PRCSYCNGPILDV 125 (130)
Q Consensus 113 ~~C~~C~~~I~~~ 125 (130)
.+|-.|..+|...
T Consensus 69 ~~CPvCR~~Is~~ 81 (193)
T PLN03208 69 PKCPVCKSDVSEA 81 (193)
T ss_pred CcCCCCCCcCChh
Confidence 4788888887543
No 85
>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=33.32 E-value=45 Score=22.21 Aligned_cols=31 Identities=16% Similarity=0.344 Sum_probs=22.3
Q ss_pred CCccccccccccc-cceeeecCcccccCCcccCCCCcccC
Q psy2501 52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
....|..|+..+. .+.+. .-|.|..|+..|.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 3457999998774 44332 2599999999884
No 86
>KOG3476|consensus
Probab=33.01 E-value=8.7 Score=23.06 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=19.4
Q ss_pred CCcccCHHhhhhhcCCCCccCcccccc
Q psy2501 98 DSRPYCEPDYHNLFSPRCSYCNGPILD 124 (130)
Q Consensus 98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~ 124 (130)
.|.-||..|..+. .+|+-|++.|..
T Consensus 67 ~GshYC~tCAY~K--giCAMCGKki~n 91 (100)
T KOG3476|consen 67 PGSHYCQTCAYKK--GICAMCGKKILN 91 (100)
T ss_pred CcchhHhHhhhhh--hHHHHhhhHhhc
Confidence 4556899997654 799999998864
No 87
>KOG3039|consensus
Probab=30.96 E-value=65 Score=23.46 Aligned_cols=75 Identities=16% Similarity=0.214 Sum_probs=52.4
Q ss_pred ccccccccccc--c---ceeeecCc-------ccccCCcccCCCCcccCCC-Cee--ccCCcccCHHhhhhhcCC--CCc
Q psy2501 54 GCCSSCDKPIV--G---QVITALGK-------TWHPEHFICTHCNQELGTR-NFF--ERDSRPYCEPDYHNLFSP--RCS 116 (130)
Q Consensus 54 ~~C~~C~~~i~--~---~~~~~~~~-------~~H~~Cf~C~~C~~~l~~~-~~~--~~~~~~~C~~~~~~~~~~--~C~ 116 (130)
..|..-+++|. + -.+..++. .-|..-|.|..+...|... ..+ ...|.++|..|..+++.. .|.
T Consensus 184 v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~p 263 (303)
T KOG3039|consen 184 VVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDP 263 (303)
T ss_pred eeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccccccc
Confidence 57888888873 1 11222221 3466778999999999755 333 567899999999888764 899
Q ss_pred cCccccccCcee
Q psy2501 117 YCNGPILDVSIR 128 (130)
Q Consensus 117 ~C~~~I~~~~~~ 128 (130)
.|+++..++=|.
T Consensus 264 v~d~plkdrdiI 275 (303)
T KOG3039|consen 264 VTDKPLKDRDII 275 (303)
T ss_pred CCCCcCcccceE
Confidence 999998765544
No 88
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=30.31 E-value=54 Score=16.95 Aligned_cols=9 Identities=33% Similarity=0.726 Sum_probs=5.4
Q ss_pred cccCHHhhh
Q psy2501 100 RPYCEPDYH 108 (130)
Q Consensus 100 ~~~C~~~~~ 108 (130)
.-+|..||.
T Consensus 24 yDLC~~C~~ 32 (45)
T cd02339 24 YDLCTTCYH 32 (45)
T ss_pred ccchHHHhC
Confidence 345777765
No 89
>KOG3002|consensus
Probab=29.84 E-value=50 Score=24.58 Aligned_cols=43 Identities=23% Similarity=0.427 Sum_probs=28.3
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccc
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL 123 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~ 123 (130)
+.|..|...|.-..+--.+|.+.|..|..++ ..+|-.|.++|.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 4555666666544444667788888885433 468888888865
No 90
>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=29.82 E-value=29 Score=15.54 Aligned_cols=11 Identities=36% Similarity=0.899 Sum_probs=7.5
Q ss_pred CccCccccccC
Q psy2501 115 CSYCNGPILDV 125 (130)
Q Consensus 115 C~~C~~~I~~~ 125 (130)
|.+|+..|.++
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 66777777654
No 91
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.67 E-value=33 Score=17.57 Aligned_cols=26 Identities=19% Similarity=0.544 Sum_probs=15.2
Q ss_pred cccccccccc-cceeeecCcccccCCcccCCCCccc
Q psy2501 55 CCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQEL 89 (130)
Q Consensus 55 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l 89 (130)
+|..|+..+. +.... -++|..|+..+
T Consensus 5 ~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYGT---------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCCC---------ceECCCCCCeE
Confidence 5788887663 22110 36777777655
No 92
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=29.42 E-value=32 Score=18.72 Aligned_cols=13 Identities=38% Similarity=0.774 Sum_probs=10.1
Q ss_pred CCCccCccccccC
Q psy2501 113 PRCSYCNGPILDV 125 (130)
Q Consensus 113 ~~C~~C~~~I~~~ 125 (130)
.+|..|.+||..-
T Consensus 2 ~~CvVCKqpi~~a 14 (54)
T PF10886_consen 2 EICVVCKQPIDDA 14 (54)
T ss_pred CeeeeeCCccCcc
Confidence 4788999998753
No 93
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.06 E-value=49 Score=16.49 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=12.3
Q ss_pred ccccccccccccc-eeeecCcccccCCcccCCCCc
Q psy2501 54 GCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQ 87 (130)
Q Consensus 54 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~ 87 (130)
.+|..|+.-|... .+...++. ++|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~-----w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKT-----WICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTE-----EEETTT--
T ss_pred cccCCCCCEECCcceEcCCCCE-----EECcCCCC
Confidence 4688888877532 23333344 46777765
No 94
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=28.86 E-value=12 Score=20.59 Aligned_cols=16 Identities=19% Similarity=0.850 Sum_probs=13.0
Q ss_pred cccCCCCcccCCCCee
Q psy2501 80 FICTHCNQELGTRNFF 95 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~ 95 (130)
..|+.||+.|+..+|.
T Consensus 5 lVCsTCGrDlSeeRy~ 20 (63)
T PHA03082 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCcchhHHHHH
Confidence 4799999999877665
No 95
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=28.72 E-value=23 Score=16.31 Aligned_cols=12 Identities=25% Similarity=0.399 Sum_probs=5.3
Q ss_pred cccccccccccc
Q psy2501 54 GCCSSCDKPIVG 65 (130)
Q Consensus 54 ~~C~~C~~~i~~ 65 (130)
.+|..|+..|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 357777777643
No 96
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=28.61 E-value=13 Score=20.51 Aligned_cols=16 Identities=19% Similarity=0.850 Sum_probs=13.2
Q ss_pred cccCCCCcccCCCCee
Q psy2501 80 FICTHCNQELGTRNFF 95 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~ 95 (130)
..|+.||+.++..+|.
T Consensus 5 lvCSTCGrDlSeeRy~ 20 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCCcchHHHHH
Confidence 4799999999877765
No 97
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=27.67 E-value=42 Score=23.37 Aligned_cols=16 Identities=31% Similarity=0.758 Sum_probs=12.4
Q ss_pred CCCCccCccccccCce
Q psy2501 112 SPRCSYCNGPILDVSI 127 (130)
Q Consensus 112 ~~~C~~C~~~I~~~~~ 127 (130)
.|+|-.|+.++.+.++
T Consensus 133 ~p~C~~Cg~~lrP~Vv 148 (218)
T cd01407 133 VPRCPKCGGLLRPDVV 148 (218)
T ss_pred CCcCCCCCCccCCCeE
Confidence 4788899888877665
No 98
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=27.66 E-value=26 Score=21.23 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=8.6
Q ss_pred CCCccCcccccc
Q psy2501 113 PRCSYCNGPILD 124 (130)
Q Consensus 113 ~~C~~C~~~I~~ 124 (130)
++|+.|+.++-|
T Consensus 35 p~C~~cg~pL~G 46 (93)
T COG2174 35 PKCAICGRPLGG 46 (93)
T ss_pred CcccccCCccCC
Confidence 578888887643
No 99
>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=27.55 E-value=19 Score=18.20 Aligned_cols=9 Identities=22% Similarity=0.829 Sum_probs=4.5
Q ss_pred ccccccccc
Q psy2501 55 CCSSCDKPI 63 (130)
Q Consensus 55 ~C~~C~~~i 63 (130)
+|..|+...
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 455555443
No 100
>KOG3579|consensus
Probab=26.42 E-value=41 Score=24.98 Aligned_cols=33 Identities=18% Similarity=0.473 Sum_probs=25.8
Q ss_pred CCcccccccccccc-ceeeecCcccccCCcccCC
Q psy2501 52 QKGCCSSCDKPIVG-QVITALGKTWHPEHFICTH 84 (130)
Q Consensus 52 ~~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~ 84 (130)
....|.-|++.+.+ .+|..-.-.-|.-||-|+.
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCH
Confidence 33689999999974 6677777778999999874
No 101
>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=26.10 E-value=22 Score=17.44 Aligned_cols=9 Identities=22% Similarity=0.863 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy2501 55 CCSSCDKPI 63 (130)
Q Consensus 55 ~C~~C~~~i 63 (130)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 455565544
No 102
>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=26.06 E-value=30 Score=14.40 Aligned_cols=11 Identities=18% Similarity=0.860 Sum_probs=6.7
Q ss_pred cccCCCCcccC
Q psy2501 80 FICTHCNQELG 90 (130)
Q Consensus 80 f~C~~C~~~l~ 90 (130)
|.|..|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 45666766654
No 103
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=24.82 E-value=23 Score=26.50 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=6.1
Q ss_pred CCCccCcccc
Q psy2501 113 PRCSYCNGPI 122 (130)
Q Consensus 113 ~~C~~C~~~I 122 (130)
-+|..|+..|
T Consensus 78 ~kC~~C~~~i 87 (324)
T PF04502_consen 78 IKCPRCSNEI 87 (324)
T ss_pred EEcCCCCCEE
Confidence 4666666655
No 104
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=24.80 E-value=38 Score=23.13 Aligned_cols=36 Identities=17% Similarity=0.337 Sum_probs=22.5
Q ss_pred ccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501 76 HPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111 (130)
Q Consensus 76 H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 111 (130)
|..|++|..--...+...++.-+-.++|..|+..+|
T Consensus 136 ~~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 136 YDKCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred ccccCcCCCCcccccceeEEecChhhcccccCcccc
Confidence 345666655433333333667788899999987665
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.79 E-value=82 Score=21.45 Aligned_cols=31 Identities=19% Similarity=0.483 Sum_probs=22.3
Q ss_pred CCccccccccccc-cceeeecCcccccCCcccCCCCcccC
Q psy2501 52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
....|..|+..+. .+.+. .-|.|..|+..|.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 3457999998774 33322 3599999999984
No 106
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.52 E-value=85 Score=16.60 Aligned_cols=11 Identities=9% Similarity=0.196 Sum_probs=6.5
Q ss_pred cccCHHhhhhh
Q psy2501 100 RPYCEPDYHNL 110 (130)
Q Consensus 100 ~~~C~~~~~~~ 110 (130)
..+|..||.+-
T Consensus 23 ~DlC~~Cf~~g 33 (48)
T cd02343 23 MDLCKTCFLGG 33 (48)
T ss_pred chhHHHHHhCC
Confidence 44577777643
No 107
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.50 E-value=54 Score=25.64 Aligned_cols=34 Identities=18% Similarity=0.523 Sum_probs=22.1
Q ss_pred CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCC
Q psy2501 51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRN 93 (130)
Q Consensus 51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~ 93 (130)
..+++|..|+... ...|+. -|+|..|+..+....
T Consensus 348 ~~~p~Cp~Cg~~m-----~S~G~~----g~rC~kCg~~~~~~~ 381 (421)
T COG1571 348 RVNPVCPRCGGRM-----KSAGRN----GFRCKKCGTRARETL 381 (421)
T ss_pred EcCCCCCccCCch-----hhcCCC----CcccccccccCCccc
Confidence 3457888888754 333443 488888888775443
No 108
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=24.35 E-value=45 Score=15.32 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=2.6
Q ss_pred cccCCCCcccCC
Q psy2501 80 FICTHCNQELGT 91 (130)
Q Consensus 80 f~C~~C~~~l~~ 91 (130)
|.|..|+.++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 345555555543
No 109
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.09 E-value=77 Score=23.08 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=8.1
Q ss_pred CCccCccccccC
Q psy2501 114 RCSYCNGPILDV 125 (130)
Q Consensus 114 ~C~~C~~~I~~~ 125 (130)
-|..|+.++.+.
T Consensus 176 PCy~C~~~v~P~ 187 (278)
T PF15135_consen 176 PCYGCGNPVYPS 187 (278)
T ss_pred CccCCCCccCcc
Confidence 577787776543
No 110
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.93 E-value=66 Score=28.89 Aligned_cols=50 Identities=16% Similarity=0.361 Sum_probs=26.8
Q ss_pred CccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcC-----CCCccCcccccc
Q psy2501 53 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS-----PRCSYCNGPILD 124 (130)
Q Consensus 53 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~-----~~C~~C~~~I~~ 124 (130)
..+|..|+..+.. +.|..|+.++.. ...|..|-...-. ..|..|+.+...
T Consensus 667 ~rkCPkCG~~t~~--------------~fCP~CGs~te~--------vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 667 RRRCPSCGTETYE--------------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEECCCCCCcccc--------------ccCcccCCcCCC--------ceeCccCCCccCCCccccccCCCCCCcccc
Confidence 4678888875421 145556655421 1145555443222 268888776543
No 111
>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=23.90 E-value=39 Score=13.74 Aligned_cols=11 Identities=27% Similarity=0.881 Sum_probs=5.0
Q ss_pred cccCCCCcccC
Q psy2501 80 FICTHCNQELG 90 (130)
Q Consensus 80 f~C~~C~~~l~ 90 (130)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 45666666553
No 112
>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=23.82 E-value=39 Score=16.53 Aligned_cols=31 Identities=23% Similarity=0.626 Sum_probs=16.3
Q ss_pred ccccccccccceeeecCcccccCCcccCCCCcccC
Q psy2501 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 56 C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
|..|.+.+. ...++.||-.-..|..||-.+.
T Consensus 2 C~~C~~Ey~----~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYF----DPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHC----STTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHc----CCCCCcccCcCccCCCCCCCEE
Confidence 444544332 3356788888888888887653
No 113
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.91 E-value=21 Score=17.35 Aligned_cols=16 Identities=19% Similarity=0.642 Sum_probs=10.5
Q ss_pred cccCCCCcccCCCCee
Q psy2501 80 FICTHCNQELGTRNFF 95 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~ 95 (130)
|.|..|++++....|+
T Consensus 5 ~~C~nC~R~v~a~RfA 20 (33)
T PF08209_consen 5 VECPNCGRPVAASRFA 20 (33)
T ss_dssp EE-TTTSSEEEGGGHH
T ss_pred EECCCCcCCcchhhhH
Confidence 5677788877666654
No 114
>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=22.82 E-value=1.5e+02 Score=17.76 Aligned_cols=12 Identities=25% Similarity=0.974 Sum_probs=8.0
Q ss_pred Cccccccccccc
Q psy2501 53 KGCCSSCDKPIV 64 (130)
Q Consensus 53 ~~~C~~C~~~i~ 64 (130)
..+|..|++++.
T Consensus 33 rS~C~~C~~~L~ 44 (92)
T PF06750_consen 33 RSHCPHCGHPLS 44 (92)
T ss_pred CCcCcCCCCcCc
Confidence 456777777763
No 115
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=22.78 E-value=36 Score=16.62 Aligned_cols=8 Identities=25% Similarity=0.978 Sum_probs=4.2
Q ss_pred cccccccc
Q psy2501 56 CSSCDKPI 63 (130)
Q Consensus 56 C~~C~~~i 63 (130)
|..|+...
T Consensus 5 Cp~C~~~y 12 (36)
T PF13717_consen 5 CPNCQAKY 12 (36)
T ss_pred CCCCCCEE
Confidence 55555544
No 116
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=22.74 E-value=25 Score=21.04 Aligned_cols=18 Identities=39% Similarity=0.857 Sum_probs=14.0
Q ss_pred HhhhhhcCCCCccCcccc
Q psy2501 105 PDYHNLFSPRCSYCNGPI 122 (130)
Q Consensus 105 ~~~~~~~~~~C~~C~~~I 122 (130)
.-|..+|...|..|++-+
T Consensus 47 ~sY~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 47 SSYRNLFSTPCKKCGKLL 64 (90)
T ss_pred HHHhhhccchhhHHHhHh
Confidence 346677888999998876
No 117
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.73 E-value=68 Score=18.90 Aligned_cols=21 Identities=29% Similarity=0.635 Sum_probs=7.5
Q ss_pred cccCHHhhhh--hcC-CCCccCcc
Q psy2501 100 RPYCEPDYHN--LFS-PRCSYCNG 120 (130)
Q Consensus 100 ~~~C~~~~~~--~~~-~~C~~C~~ 120 (130)
.+.|+.||.. +-+ ..|..|.-
T Consensus 36 fPvCr~CyEYErkeg~q~CpqCkt 59 (80)
T PF14569_consen 36 FPVCRPCYEYERKEGNQVCPQCKT 59 (80)
T ss_dssp ----HHHHHHHHHTS-SB-TTT--
T ss_pred CccchhHHHHHhhcCcccccccCC
Confidence 4457777752 222 25666653
No 118
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=22.72 E-value=1.7e+02 Score=17.20 Aligned_cols=55 Identities=16% Similarity=0.276 Sum_probs=30.7
Q ss_pred CCCCchhHHHHHHHHHHHHhhhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCe
Q psy2501 24 PVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF 94 (130)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~ 94 (130)
.+.|+..+++.....+... ........-.|..|...-..+ +.|..|++.++-..|
T Consensus 11 ~~~FS~~Ql~~~~~~~~~~---~~~~~~~~i~C~~ct~~q~~E-------------l~C~~C~~~k~ld~F 65 (84)
T PF12898_consen 11 LSAFSKNQLEKLRKQIRAN---RVDPANSGIRCRECTGGQVVE-------------LTCSPCGKTKPLDEF 65 (84)
T ss_pred hHHcCHHHHHHHHHHHhhc---cCccCCCCCCCccCCCCCcCc-------------CEeccCCCCcCHHHH
Confidence 3467888888877766555 111223334676665432111 277788877653334
No 119
>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=22.72 E-value=37 Score=17.13 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=5.0
Q ss_pred cccCCCCccc
Q psy2501 80 FICTHCNQEL 89 (130)
Q Consensus 80 f~C~~C~~~l 89 (130)
+.|..|+.-|
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 4556665554
No 120
>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=22.61 E-value=29 Score=18.10 Aligned_cols=10 Identities=20% Similarity=0.674 Sum_probs=5.9
Q ss_pred cccccccccc
Q psy2501 54 GCCSSCDKPI 63 (130)
Q Consensus 54 ~~C~~C~~~i 63 (130)
-+|..|+...
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 3566666644
No 121
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=22.36 E-value=77 Score=15.35 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=11.8
Q ss_pred cCCCCcccCCCCeeccCCcc-cCHHhhh
Q psy2501 82 CTHCNQELGTRNFFERDSRP-YCEPDYH 108 (130)
Q Consensus 82 C~~C~~~l~~~~~~~~~~~~-~C~~~~~ 108 (130)
|..|+..-+..-....++.. +|..|+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 34444443322222445555 8888865
No 122
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.13 E-value=54 Score=17.20 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=8.2
Q ss_pred CCCccCccccc
Q psy2501 113 PRCSYCNGPIL 123 (130)
Q Consensus 113 ~~C~~C~~~I~ 123 (130)
-+|++|++-|.
T Consensus 32 lrCGaCs~vl~ 42 (46)
T PF11331_consen 32 LRCGACSEVLS 42 (46)
T ss_pred EeCCCCceeEE
Confidence 36999988764
No 123
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.02 E-value=86 Score=20.46 Aligned_cols=36 Identities=22% Similarity=0.447 Sum_probs=22.7
Q ss_pred CCccccccccccc-cceeeecCcccccCCcccCCCCcccC
Q psy2501 52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELG 90 (130)
Q Consensus 52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~ 90 (130)
..-.|..|+..+. ...+...+. ..=|.|..|+..|.
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 3457999998874 332222221 22399999999873
No 124
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.97 E-value=45 Score=23.49 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=18.0
Q ss_pred ccCCcccCCCCcccCCCCeeccCCcccCHHhh
Q psy2501 76 HPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107 (130)
Q Consensus 76 H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~ 107 (130)
-++-..|..|+..+....|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 33444666777665422333566666676663
No 125
>PRK12495 hypothetical protein; Provisional
Probab=21.58 E-value=40 Score=23.96 Aligned_cols=28 Identities=29% Similarity=0.770 Sum_probs=18.6
Q ss_pred CCccccccccccccceeeecCcccccCCcccCCCCccc
Q psy2501 52 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 89 (130)
Q Consensus 52 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l 89 (130)
....|..|+.+|. -++.+-.|..|....
T Consensus 41 sa~hC~~CG~PIp----------a~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIF----------RHDGQEFCPTCQQPV 68 (226)
T ss_pred chhhcccccCccc----------CCCCeeECCCCCCcc
Confidence 3457888998886 124556677777654
No 126
>PRK13796 GTPase YqeH; Provisional
Probab=21.28 E-value=63 Score=24.54 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=5.6
Q ss_pred ccccccccc
Q psy2501 55 CCSSCDKPI 63 (130)
Q Consensus 55 ~C~~C~~~i 63 (130)
+|.+||..+
T Consensus 2 ~C~GCG~~l 10 (365)
T PRK13796 2 RCIGCGAAI 10 (365)
T ss_pred cccCCCcee
Confidence 466666655
No 127
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.12 E-value=36 Score=17.55 Aligned_cols=9 Identities=22% Similarity=0.815 Sum_probs=5.0
Q ss_pred ccccccccc
Q psy2501 55 CCSSCDKPI 63 (130)
Q Consensus 55 ~C~~C~~~i 63 (130)
+|+.|+..+
T Consensus 4 ~C~~Cg~~~ 12 (44)
T smart00659 4 ICGECGREN 12 (44)
T ss_pred ECCCCCCEe
Confidence 455665544
No 128
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.94 E-value=1.2e+02 Score=18.29 Aligned_cols=35 Identities=20% Similarity=0.590 Sum_probs=23.3
Q ss_pred CccccccccccccceeeecCcccccCCcccCCCCcccCCCCee
Q psy2501 53 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95 (130)
Q Consensus 53 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 95 (130)
...|..|+....- ......| .|..|+..+.++.|.
T Consensus 35 ~~~Cp~C~~~~Vk---R~a~GIW-----~C~kCg~~fAGgay~ 69 (89)
T COG1997 35 KHVCPFCGRTTVK---RIATGIW-----KCRKCGAKFAGGAYT 69 (89)
T ss_pred CCcCCCCCCccee---eeccCeE-----EcCCCCCeecccccc
Confidence 3579999998421 2223334 788999998877664
No 129
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.88 E-value=90 Score=20.76 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=4.1
Q ss_pred cCCCCcccC
Q psy2501 82 CTHCNQELG 90 (130)
Q Consensus 82 C~~C~~~l~ 90 (130)
|..|++.+.
T Consensus 3 CEiCG~~i~ 11 (154)
T TIGR00270 3 CEICGRKIK 11 (154)
T ss_pred cccCCCccC
Confidence 444444443
No 130
>KOG2186|consensus
Probab=20.67 E-value=23 Score=25.73 Aligned_cols=41 Identities=12% Similarity=0.390 Sum_probs=24.9
Q ss_pred cccccccccccceeeecCcccccCCcccCCCCcccCCCCee
Q psy2501 55 CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95 (130)
Q Consensus 55 ~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 95 (130)
.|..|+..|--..+.----..|..+|.|-.|+..+.+..|.
T Consensus 5 tCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sYk 45 (276)
T KOG2186|consen 5 TCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSYK 45 (276)
T ss_pred ehhhhhhhccccchHHHHHhccCCeeEEeecccccccchhh
Confidence 47778887731111111112466889999999998766554
No 131
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=20.57 E-value=20 Score=18.37 Aligned_cols=8 Identities=25% Similarity=1.103 Sum_probs=2.6
Q ss_pred cccccccc
Q psy2501 56 CSSCDKPI 63 (130)
Q Consensus 56 C~~C~~~i 63 (130)
|..|++.+
T Consensus 1 C~~C~~iv 8 (43)
T PF08746_consen 1 CEACKEIV 8 (43)
T ss_dssp -TTT-SB-
T ss_pred CcccchhH
Confidence 34455555
No 132
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=20.50 E-value=46 Score=20.61 Aligned_cols=27 Identities=15% Similarity=0.508 Sum_probs=19.5
Q ss_pred cccCCCCcccCCCCeeccCCcccCHHhhhhh
Q psy2501 80 FICTHCNQELGTRNFFERDSRPYCEPDYHNL 110 (130)
Q Consensus 80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~ 110 (130)
=.|..| ++..|+..++.+.|..|-.+.
T Consensus 36 daCeiC----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 36 DACEIC----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred Eecccc----CCCceEEECCEEEEecCCCEE
Confidence 356666 456788889999999886543
No 133
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.26 E-value=49 Score=23.82 Aligned_cols=15 Identities=13% Similarity=0.488 Sum_probs=10.9
Q ss_pred CCCcccccccccccc
Q psy2501 51 TQKGCCSSCDKPIVG 65 (130)
Q Consensus 51 ~~~~~C~~C~~~i~~ 65 (130)
..+.+|++|+-.|..
T Consensus 195 l~g~~C~GC~m~l~~ 209 (239)
T COG1579 195 LEGRVCGGCHMKLPS 209 (239)
T ss_pred ecCCcccCCeeeecH
Confidence 455789999888753
No 134
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.06 E-value=70 Score=19.62 Aligned_cols=35 Identities=23% Similarity=0.228 Sum_probs=23.7
Q ss_pred cccccccccc-ccceeeec-CcccccCCcccCCCCcc
Q psy2501 54 GCCSSCDKPI-VGQVITAL-GKTWHPEHFICTHCNQE 88 (130)
Q Consensus 54 ~~C~~C~~~i-~~~~~~~~-~~~~H~~Cf~C~~C~~~ 88 (130)
.+|..|++.| .|+.+.+- ..+-|-+||.-+.-+++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 4688999988 47776643 34568888876654443
No 135
>KOG1829|consensus
Probab=20.04 E-value=42 Score=27.36 Aligned_cols=32 Identities=19% Similarity=0.545 Sum_probs=20.7
Q ss_pred CCcccCCCCcccCCC-----CeeccCCcccCHHhhhh
Q psy2501 78 EHFICTHCNQELGTR-----NFFERDSRPYCEPDYHN 109 (130)
Q Consensus 78 ~Cf~C~~C~~~l~~~-----~~~~~~~~~~C~~~~~~ 109 (130)
.-|+|+.|+..+... ++-...|+.||..|...
T Consensus 339 Q~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~ 375 (580)
T KOG1829|consen 339 QNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQN 375 (580)
T ss_pred cCceecccCCCcccccccchhHhhhhhhhhCchhccc
Confidence 457899999998632 12244567777777653
Done!