Query 029070
Match_columns 199
No_of_seqs 222 out of 1305
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 07:00:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029070.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029070hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701 Focal adhesion adaptor 99.9 5.4E-27 1.2E-31 192.6 -1.4 127 9-177 274-402 (468)
2 KOG1701 Focal adhesion adaptor 99.9 2E-24 4.3E-29 177.6 2.5 121 9-170 334-465 (468)
3 KOG4577 Transcription factor L 99.9 5.3E-25 1.1E-29 172.7 -3.0 146 8-198 32-180 (383)
4 KOG2272 Focal adhesion protein 99.9 7.8E-24 1.7E-28 163.4 -1.7 165 8-173 11-258 (332)
5 KOG1700 Regulatory protein MLP 99.8 4.1E-21 8.8E-26 148.4 4.3 186 4-189 2-188 (200)
6 KOG2272 Focal adhesion protein 99.8 2.6E-21 5.5E-26 149.6 0.5 117 8-166 194-311 (332)
7 KOG1703 Adaptor protein Enigma 99.8 1E-19 2.2E-24 158.1 5.6 128 8-176 302-429 (479)
8 KOG1044 Actin-binding LIM Zn-f 99.8 1.8E-19 4E-24 153.1 2.9 134 8-183 132-266 (670)
9 KOG1703 Adaptor protein Enigma 99.8 1.7E-19 3.6E-24 156.7 1.6 116 8-164 362-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 8.5E-19 1.8E-23 149.1 4.8 162 10-173 17-196 (670)
11 PF00412 LIM: LIM domain; Int 99.6 5.4E-16 1.2E-20 96.8 3.9 57 12-68 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.5 1.9E-14 4.2E-19 89.7 4.7 57 112-168 1-58 (58)
13 KOG4577 Transcription factor L 99.1 5.4E-12 1.2E-16 99.8 -3.2 79 108-187 32-111 (383)
14 smart00132 LIM Zinc-binding do 98.9 1.4E-09 3.1E-14 61.7 2.5 37 11-47 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.6 2.7E-08 5.9E-13 56.3 2.5 37 111-147 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.3 2.2E-07 4.8E-12 72.0 0.3 67 6-72 105-171 (200)
17 KOG1702 Nebulin repeat protein 98.0 6E-07 1.3E-11 68.3 -2.4 62 9-70 4-65 (264)
18 KOG1702 Nebulin repeat protein 97.9 7.6E-07 1.7E-11 67.8 -3.3 59 110-168 5-63 (264)
19 KOG0490 Transcription factor, 97.8 3.3E-06 7.2E-11 66.7 -0.9 112 14-167 1-119 (235)
20 KOG0490 Transcription factor, 88.9 0.1 2.2E-06 41.0 -0.4 57 115-172 2-62 (235)
21 PF09943 DUF2175: Uncharacteri 86.6 0.21 4.6E-06 34.2 0.1 32 110-141 3-35 (101)
22 PF14446 Prok-RING_1: Prokaryo 86.2 0.48 1E-05 28.6 1.4 39 8-46 4-51 (54)
23 PF10367 Vps39_2: Vacuolar sor 79.4 1.5 3.2E-05 29.9 2.0 30 8-37 77-107 (109)
24 PF01258 zf-dskA_traR: Prokary 78.4 0.55 1.2E-05 25.7 -0.3 28 39-66 6-33 (36)
25 KOG0320 Predicted E3 ubiquitin 76.8 1.9 4E-05 32.7 2.0 37 33-69 128-165 (187)
26 COG2888 Predicted Zn-ribbon RN 76.4 2.9 6.3E-05 25.7 2.4 31 7-46 7-37 (61)
27 PF08394 Arc_trans_TRASH: Arch 76.0 1.6 3.4E-05 24.3 1.0 31 12-46 1-33 (37)
28 PF13240 zinc_ribbon_2: zinc-r 76.0 1.2 2.7E-05 21.8 0.6 8 12-19 2-9 (23)
29 PF10367 Vps39_2: Vacuolar sor 76.0 1.9 4E-05 29.4 1.7 29 110-138 79-108 (109)
30 PF10235 Cript: Microtubule-as 75.6 1.6 3.4E-05 29.3 1.2 28 32-65 40-67 (90)
31 PF14471 DUF4428: Domain of un 75.3 1.7 3.7E-05 26.0 1.2 29 38-67 1-30 (51)
32 smart00504 Ubox Modified RING 74.4 4 8.6E-05 24.8 2.8 32 37-69 2-33 (63)
33 PF11781 RRN7: RNA polymerase 73.6 1.6 3.6E-05 24.0 0.8 24 37-64 9-32 (36)
34 PF14835 zf-RING_6: zf-RING of 73.1 2.3 5E-05 26.7 1.4 33 37-69 8-40 (65)
35 PF06677 Auto_anti-p27: Sjogre 71.6 2.2 4.7E-05 24.3 1.0 22 38-63 19-40 (41)
36 PRK14890 putative Zn-ribbon RN 71.3 3.1 6.7E-05 25.6 1.6 30 8-46 6-35 (59)
37 COG1645 Uncharacterized Zn-fin 68.2 2.5 5.4E-05 30.5 0.9 22 38-64 30-51 (131)
38 COG4847 Uncharacterized protei 67.5 2.2 4.8E-05 28.8 0.5 35 110-144 7-42 (103)
39 COG2191 Formylmethanofuran deh 67.1 2 4.2E-05 33.3 0.2 31 137-167 173-203 (206)
40 PF14634 zf-RING_5: zinc-RING 66.2 5.2 0.00011 22.7 1.8 30 39-68 2-33 (44)
41 PF00645 zf-PARP: Poly(ADP-rib 65.8 3.3 7.1E-05 27.0 1.0 17 8-24 6-22 (82)
42 COG2191 Formylmethanofuran deh 64.3 2.5 5.4E-05 32.7 0.3 30 37-66 173-202 (206)
43 PF02069 Metallothio_Pro: Prok 63.6 4.1 8.8E-05 24.4 1.0 27 139-165 10-37 (52)
44 PF13923 zf-C3HC4_2: Zinc fing 61.5 8 0.00017 21.2 2.0 31 39-69 1-31 (39)
45 PF13920 zf-C3HC4_3: Zinc fing 60.4 7.9 0.00017 22.5 1.9 32 37-69 3-35 (50)
46 cd00162 RING RING-finger (Real 59.5 9.4 0.0002 20.7 2.1 31 39-69 2-32 (45)
47 KOG0978 E3 ubiquitin ligase in 55.3 5.3 0.00012 36.7 0.8 36 36-72 643-678 (698)
48 PRK00420 hypothetical protein; 54.9 6.6 0.00014 27.6 1.1 24 37-64 24-47 (112)
49 smart00531 TFIIE Transcription 53.3 4.4 9.6E-05 29.7 0.0 36 10-48 100-135 (147)
50 PF09943 DUF2175: Uncharacteri 52.6 14 0.0003 25.4 2.3 40 137-176 3-43 (101)
51 PF10083 DUF2321: Uncharacteri 50.2 12 0.00026 27.7 1.9 37 110-147 40-79 (158)
52 cd02249 ZZ Zinc finger, ZZ typ 49.7 14 0.0003 21.2 1.7 12 156-167 22-33 (46)
53 PF04502 DUF572: Family of unk 48.9 11 0.00023 31.6 1.6 39 9-47 40-88 (324)
54 PF06906 DUF1272: Protein of u 48.5 19 0.00042 21.8 2.2 31 39-69 8-41 (57)
55 KOG1813 Predicted E3 ubiquitin 46.6 9.8 0.00021 31.2 1.0 32 36-68 241-272 (313)
56 PF10886 DUF2685: Protein of u 46.5 14 0.00031 22.2 1.4 27 39-65 4-31 (54)
57 PF13248 zf-ribbon_3: zinc-rib 46.3 14 0.00031 18.4 1.2 10 110-119 3-12 (26)
58 TIGR02098 MJ0042_CXXC MJ0042 f 45.8 8.8 0.00019 20.9 0.5 31 11-46 4-35 (38)
59 TIGR00373 conserved hypothetic 45.8 6.2 0.00013 29.4 -0.2 31 10-48 110-140 (158)
60 PRK00398 rpoP DNA-directed RNA 45.5 12 0.00026 21.5 1.0 27 11-46 5-31 (46)
61 smart00291 ZnF_ZZ Zinc-binding 44.9 21 0.00046 20.2 2.0 10 157-166 27-36 (44)
62 COG5152 Uncharacterized conser 44.4 9.4 0.0002 29.5 0.6 33 36-69 196-228 (259)
63 TIGR02605 CxxC_CxxC_SSSS putat 43.5 11 0.00025 22.0 0.7 28 37-64 6-33 (52)
64 PRK06266 transcription initiat 43.4 8.4 0.00018 29.3 0.2 31 10-48 118-148 (178)
65 PF14569 zf-UDP: Zinc-binding 42.9 27 0.00058 22.8 2.4 40 8-68 8-47 (80)
66 PF09723 Zn-ribbon_8: Zinc rib 42.8 12 0.00025 21.2 0.7 27 37-63 6-32 (42)
67 PF04570 DUF581: Protein of un 42.5 13 0.00029 22.8 0.9 28 38-65 18-48 (58)
68 KOG0823 Predicted E3 ubiquitin 42.4 31 0.00068 27.3 3.2 40 29-69 40-79 (230)
69 PLN03208 E3 ubiquitin-protein 41.8 28 0.00061 26.9 2.8 33 35-68 17-49 (193)
70 PF13834 DUF4193: Domain of un 41.6 11 0.00024 25.7 0.5 29 35-63 69-98 (99)
71 smart00834 CxxC_CXXC_SSSS Puta 40.5 13 0.00028 20.4 0.6 10 37-46 6-15 (41)
72 COG4357 Zinc finger domain con 40.5 1.8 3.8E-05 29.3 -3.4 55 110-164 36-90 (105)
73 PF07754 DUF1610: Domain of un 40.5 25 0.00054 17.5 1.5 12 112-123 1-12 (24)
74 PF07191 zinc-ribbons_6: zinc- 39.7 6 0.00013 25.3 -0.9 10 110-119 31-40 (70)
75 COG4357 Zinc finger domain con 38.3 4.3 9.4E-05 27.5 -1.8 49 12-60 38-86 (105)
76 PRK00807 50S ribosomal protein 37.8 24 0.00051 21.1 1.5 23 11-33 3-28 (52)
77 PF14255 Cys_rich_CPXG: Cystei 36.5 20 0.00044 21.4 1.0 30 11-40 2-31 (52)
78 PF04810 zf-Sec23_Sec24: Sec23 36.0 25 0.00055 19.5 1.4 30 110-144 3-32 (40)
79 PF00097 zf-C3HC4: Zinc finger 35.9 40 0.00087 18.3 2.2 31 39-69 1-31 (41)
80 PRK14559 putative protein seri 35.5 18 0.00038 33.4 1.0 10 110-119 42-51 (645)
81 KOG3579 Predicted E3 ubiquitin 34.7 16 0.00034 30.0 0.4 32 110-141 269-300 (352)
82 PF12773 DZR: Double zinc ribb 34.1 41 0.00088 19.3 2.1 11 9-19 12-22 (50)
83 PLN02195 cellulose synthase A 33.8 42 0.0009 32.4 3.1 32 7-46 4-35 (977)
84 PF00096 zf-C2H2: Zinc finger, 33.6 19 0.00041 16.8 0.5 13 37-49 1-13 (23)
85 PF05502 Dynactin_p62: Dynacti 33.5 21 0.00046 31.7 1.1 38 110-148 27-64 (483)
86 cd02336 ZZ_RSC8 Zinc finger, Z 33.3 40 0.00086 19.5 1.9 29 138-166 2-32 (45)
87 PF01286 XPA_N: XPA protein N- 33.3 27 0.00059 18.9 1.1 10 10-19 4-13 (34)
88 KOG3002 Zn finger protein [Gen 32.9 29 0.00063 28.8 1.8 32 37-68 49-80 (299)
89 KOG4739 Uncharacterized protei 32.6 20 0.00044 28.5 0.8 28 41-68 8-36 (233)
90 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.6 42 0.00092 19.6 2.0 11 157-167 26-36 (48)
91 PRK12495 hypothetical protein; 31.1 24 0.00052 27.8 0.9 24 36-64 42-65 (226)
92 KOG3476 Microtubule-associated 30.6 4.2 9E-05 27.0 -2.8 13 110-122 80-92 (100)
93 KOG3970 Predicted E3 ubiquitin 30.4 44 0.00095 26.5 2.3 39 28-69 45-84 (299)
94 PRK04023 DNA polymerase II lar 30.2 38 0.00082 32.8 2.2 23 8-45 625-647 (1121)
95 smart00659 RPOLCX RNA polymera 30.1 31 0.00067 19.8 1.1 24 37-64 3-26 (44)
96 COG1813 Predicted transcriptio 29.6 85 0.0018 23.6 3.6 33 139-173 6-40 (165)
97 PF00130 C1_1: Phorbol esters/ 29.5 37 0.00081 19.7 1.4 13 7-19 9-21 (53)
98 PF02591 DUF164: Putative zinc 29.5 11 0.00024 22.6 -0.9 13 38-50 24-36 (56)
99 COG2075 RPL24A Ribosomal prote 29.4 36 0.00078 21.4 1.3 31 38-69 5-41 (66)
100 PF08209 Sgf11: Sgf11 (transcr 28.9 16 0.00035 19.6 -0.2 17 37-53 5-21 (33)
101 PF10122 Mu-like_Com: Mu-like 27.9 16 0.00035 21.8 -0.4 25 37-63 5-30 (51)
102 PLN02638 cellulose synthase A 27.9 57 0.0012 31.9 3.0 47 9-63 17-65 (1079)
103 cd02340 ZZ_NBR1_like Zinc fing 27.6 51 0.0011 18.7 1.7 9 158-166 24-32 (43)
104 PF06750 DiS_P_DiS: Bacterial 27.5 23 0.0005 23.8 0.3 42 4-47 28-69 (92)
105 PF12674 Zn_ribbon_2: Putative 27.0 32 0.0007 22.6 0.9 27 139-165 3-34 (81)
106 PF00569 ZZ: Zinc finger, ZZ t 26.9 48 0.001 19.0 1.5 9 158-166 29-37 (46)
107 KOG2462 C2H2-type Zn-finger pr 26.4 35 0.00076 27.8 1.2 28 34-61 128-155 (279)
108 PF08271 TF_Zn_Ribbon: TFIIB z 26.2 28 0.0006 19.6 0.4 12 37-48 20-31 (43)
109 PLN02436 cellulose synthase A 26.0 60 0.0013 31.7 2.7 28 11-46 38-65 (1094)
110 TIGR00570 cdk7 CDK-activating 25.9 71 0.0015 26.6 2.9 14 56-69 27-40 (309)
111 PF08746 zf-RING-like: RING-li 25.5 19 0.00042 20.4 -0.3 9 12-20 1-9 (43)
112 PF00628 PHD: PHD-finger; Int 24.8 61 0.0013 18.5 1.8 27 11-37 1-29 (51)
113 cd02335 ZZ_ADA2 Zinc finger, Z 24.7 45 0.00097 19.4 1.1 10 57-66 24-33 (49)
114 PF12874 zf-met: Zinc-finger o 24.4 34 0.00074 16.3 0.5 13 37-49 1-13 (25)
115 PF13894 zf-C2H2_4: C2H2-type 24.4 34 0.00073 15.6 0.5 12 37-48 1-12 (24)
116 PF13912 zf-C2H2_6: C2H2-type 24.1 35 0.00075 16.6 0.5 13 37-49 2-14 (27)
117 PRK00085 recO DNA repair prote 23.9 37 0.0008 26.8 0.9 31 34-64 147-177 (247)
118 KOG3579 Predicted E3 ubiquitin 23.7 35 0.00077 28.0 0.7 30 37-66 269-301 (352)
119 TIGR00270 conserved hypothetic 23.5 1.6E+02 0.0034 21.8 4.1 30 139-170 3-35 (154)
120 KOG3576 Ovo and related transc 23.3 9.1 0.0002 29.8 -2.5 16 34-49 115-130 (267)
121 TIGR02420 dksA RNA polymerase- 23.3 17 0.00036 25.3 -1.1 19 8-27 79-97 (110)
122 COG4068 Uncharacterized protei 23.2 46 0.001 20.4 1.0 14 10-23 9-22 (64)
123 PF01927 Mut7-C: Mut7-C RNAse 23.2 68 0.0015 23.4 2.1 37 110-146 92-134 (147)
124 PLN02189 cellulose synthase 23.2 73 0.0016 31.0 2.7 9 11-19 36-44 (1040)
125 PRK14891 50S ribosomal protein 22.1 55 0.0012 23.5 1.4 25 9-33 4-31 (131)
126 PRK13796 GTPase YqeH; Provisio 21.9 51 0.0011 28.0 1.4 10 56-65 33-42 (365)
127 PF07649 C1_3: C1-like domain; 21.7 40 0.00087 17.2 0.5 12 37-48 1-12 (30)
128 COG1381 RecO Recombinational D 21.4 42 0.00091 26.9 0.7 28 37-64 155-182 (251)
129 KOG1829 Uncharacterized conser 21.3 40 0.00086 30.6 0.6 31 35-65 339-374 (580)
130 cd02338 ZZ_PCMF_like Zinc fing 21.3 68 0.0015 18.7 1.5 11 157-167 24-34 (49)
131 cd00472 Ribosomal_L24e_L24 Rib 21.1 72 0.0016 19.2 1.5 23 10-32 4-29 (54)
132 cd02342 ZZ_UBA_plant Zinc fing 20.8 1E+02 0.0022 17.7 2.0 28 139-166 3-33 (43)
133 PF12171 zf-C2H2_jaz: Zinc-fin 20.6 64 0.0014 15.8 1.1 13 37-49 2-14 (27)
134 PF07503 zf-HYPF: HypF finger; 20.6 22 0.00047 19.4 -0.7 30 12-46 2-31 (35)
135 COG1571 Predicted DNA-binding 20.2 66 0.0014 28.0 1.7 37 5-51 346-382 (421)
136 PF10080 DUF2318: Predicted me 20.1 51 0.0011 22.7 0.8 35 29-67 28-62 (102)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.92 E-value=5.4e-27 Score=192.64 Aligned_cols=127 Identities=21% Similarity=0.533 Sum_probs=114.2
Q ss_pred CccccccCceeecce-eEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 9 QQKCMACDKTVYLVD-KLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
..+|.+|+|.|.... .+.||++.||..||+|..|++.|.++.||.+++++||+.||+...
T Consensus 274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl------------------- 334 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL------------------- 334 (468)
T ss_pred hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-------------------
Confidence 358999999997544 489999999999999999999999999999999999999999877
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeee-CCccccHhHHHh
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAH-EGRLYCKHHHNQ 166 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~yC~~c~~~ 166 (199)
.+|..|++.|++. ++.+.|+.||+.||+|.+|.+.|++..|.+. ++++||..||.+
T Consensus 335 ----------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~ 391 (468)
T KOG1701|consen 335 ----------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHK 391 (468)
T ss_pred ----------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhh
Confidence 6999999999743 3679999999999999999999999888654 799999999999
Q ss_pred HhcCCCCCCCc
Q 029070 167 LIKEKGNLSQL 177 (199)
Q Consensus 167 ~~~~k~~~~~~ 177 (199)
+|++||.....
T Consensus 392 kfAPrCs~C~~ 402 (468)
T KOG1701|consen 392 KFAPRCSVCGN 402 (468)
T ss_pred hcCcchhhccC
Confidence 99999986554
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.89 E-value=2e-24 Score=177.60 Aligned_cols=121 Identities=27% Similarity=0.655 Sum_probs=108.6
Q ss_pred CccccccCceeecceeEEeCCcccccccceeccCcccccCCccccc-CCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 9 QQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSF-EGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~-~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
..+|..|++.| .+..+.|+|+.||+.||+|..|++.|++..|.+. ++++||..||++.|+
T Consensus 334 lekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA------------------ 394 (468)
T KOG1701|consen 334 LEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA------------------ 394 (468)
T ss_pred HHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC------------------
Confidence 45799999999 4778999999999999999999999999999764 799999999999998
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCc------ceeecCccccccCeecccCCCCCCC----CCeeeeCCc
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTE------KVSVNGTPYHKSCFKCSHGGCVISP----SNYIAHEGR 157 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~~~~~H~~Cf~C~~C~~~l~~----~~~~~~~g~ 157 (199)
++|+.|+++|.+.+ +|+++++.||.+|++|..|+..|+. ...|..||.
T Consensus 395 ----------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~H 452 (468)
T KOG1701|consen 395 ----------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGH 452 (468)
T ss_pred ----------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCc
Confidence 99999999998753 4789999999999999999999983 357899999
Q ss_pred cccHhHHHhHhcC
Q 029070 158 LYCKHHHNQLIKE 170 (199)
Q Consensus 158 ~yC~~c~~~~~~~ 170 (199)
++|+.|+.++...
T Consensus 453 llCk~Ch~~Rl~~ 465 (468)
T KOG1701|consen 453 LLCKTCHLKRLQA 465 (468)
T ss_pred eeechhhhhhhcc
Confidence 9999999988654
No 3
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.88 E-value=5.3e-25 Score=172.66 Aligned_cols=146 Identities=26% Similarity=0.549 Sum_probs=121.6
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
+.++|++|++.|...-++.++++.||..|++|+.|..+|.+. .|.++|.+||+++|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhC------------------
Confidence 679999999999755567999999999999999999999854 5569999999999999998
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCccee-ecCccccccCeecccCCCCCC-CCCee-eeCCccccHhHH
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVS-VNGTPYHKSCFKCSHGGCVIS-PSNYI-AHEGRLYCKHHH 164 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~-~~~~~~H~~Cf~C~~C~~~l~-~~~~~-~~~g~~yC~~c~ 164 (199)
.+|..|...|.+.+.|. +.+..||..||.|..|+++|. +++|| +.|+++.|+.+|
T Consensus 93 ----------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DY 150 (383)
T KOG4577|consen 93 ----------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDY 150 (383)
T ss_pred ----------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhH
Confidence 89999999999998665 889999999999999999998 44565 558999999999
Q ss_pred HhHhcCCCCCCCcCCcccccccccccCCCCcccC
Q 029070 165 NQLIKEKGNLSQLEGEHEKTSVNANERVNGKQVD 198 (199)
Q Consensus 165 ~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (199)
++.....++ .+.+....+| .++.|..||++
T Consensus 151 E~Ak~k~~~--~l~gd~~nKR--PRTTItAKqLE 180 (383)
T KOG4577|consen 151 ETAKQKHCN--ELEGDASNKR--PRTTITAKQLE 180 (383)
T ss_pred HHHHhcccc--ccccccccCC--CcceeeHHHHH
Confidence 987655443 4444444443 46677777764
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.87 E-value=7.8e-24 Score=163.43 Aligned_cols=165 Identities=19% Similarity=0.330 Sum_probs=127.8
Q ss_pred CCccccccCceeeccee-EEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccC
Q 029070 8 TQQKCMACDKTVYLVDK-LTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAK 86 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 86 (199)
....|.+|..-..+.+. +...|..||..||+|++|-.+|.++.|++.+|+.||+.+|+.+|+|.+..+..|+....+..
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVika 90 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKA 90 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHh
Confidence 35689999998887774 68899999999999999999999999999999999999999999998766555543333333
Q ss_pred CCCCCCCC----------------------------------------------------------------CC-Ccc--
Q 029070 87 PEKPIDGE----------------------------------------------------------------KP-NVA-- 99 (199)
Q Consensus 87 ~~~~~~~~----------------------------------------------------------------~~-~~~-- 99 (199)
+.-+|+.. .. ...
T Consensus 91 mnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~ 170 (332)
T KOG2272|consen 91 MNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCG 170 (332)
T ss_pred hccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceeccccc
Confidence 33333221 00 000
Q ss_pred ---------------cccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHH
Q 029070 100 ---------------KVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHH 164 (199)
Q Consensus 100 ---------------~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~ 164 (199)
+.........++|..|.++|. ...|.+++++||.+.|+|+.|.+|+-+-+.+.+.|.+||+.+|
T Consensus 171 keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~ 249 (332)
T KOG2272|consen 171 KELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 249 (332)
T ss_pred ccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHH
Confidence 001111234689999999996 2236699999999999999999999988999999999999999
Q ss_pred HhHhcCCCC
Q 029070 165 NQLIKEKGN 173 (199)
Q Consensus 165 ~~~~~~k~~ 173 (199)
.++||.-+-
T Consensus 250 ~qLfG~~CF 258 (332)
T KOG2272|consen 250 HQLFGNLCF 258 (332)
T ss_pred HHHhhhhhe
Confidence 999987653
No 5
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=4.1e-21 Score=148.40 Aligned_cols=186 Identities=45% Similarity=0.848 Sum_probs=151.3
Q ss_pred ccCCCCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccC-CCCCCCCCCC
Q 029070 4 AFAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTG-SLDKSFEGTP 82 (199)
Q Consensus 4 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~-~~~~~~~~~~ 82 (199)
++.+....|..|++.|+..+.+...|..||..||+|..|.+.|....+..+++.+||..+|...+++.+ ...+++....
T Consensus 2 ~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~ 81 (200)
T KOG1700|consen 2 SFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG 81 (200)
T ss_pred CcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccC
Confidence 456677899999999999999999999999999999999999999999999999999998888888764 3344444322
Q ss_pred CccCCCCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHh
Q 029070 83 KIAKPEKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKH 162 (199)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~ 162 (199)
+......+.....+........+.+....|..|.+.+++.+.+...+..||..||+|..|+..|+...+....|.+||..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~ 161 (200)
T KOG1700|consen 82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKH 161 (200)
T ss_pred CCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccch
Confidence 22223333333333444455556677899999999999999999999999999999999999999989999999999999
Q ss_pred HHHhHhcCCCCCCCcCCcccccccccc
Q 029070 163 HHNQLIKEKGNLSQLEGEHEKTSVNAN 189 (199)
Q Consensus 163 c~~~~~~~k~~~~~~~~~~~~~~~~~~ 189 (199)
++.+++..++.+..+.+.....+....
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (200)
T KOG1700|consen 162 HFAQLFKGKGNYNEGFGARENKEAAAA 188 (200)
T ss_pred hhheeecCCCcccccchhhhhhhhhhh
Confidence 999999989988888777766654433
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=2.6e-21 Score=149.56 Aligned_cols=117 Identities=21% Similarity=0.467 Sum_probs=107.9
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
+.++|..|.++| ...+|.++|+.||.+.|+|+.|-+|+-+...|++.|.+||+.+|.++|+
T Consensus 194 gipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------ 254 (332)
T KOG2272|consen 194 GIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------ 254 (332)
T ss_pred CCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence 468999999999 4778999999999999999999999998899999999999999999998
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCC-CCeeeeCCccccHhHHHh
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISP-SNYIAHEGRLYCKHHHNQ 166 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~g~~yC~~c~~~ 166 (199)
..|-.|++.|- ++.|.+.++.|.++||.|+.|.+.|.. ..|+..|-.|.|+.||.+
T Consensus 255 ----------------------~~CF~C~~~i~-G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 255 ----------------------NLCFICNRVIG-GDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred ----------------------hhheecCCccC-ccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 89999999985 566889999999999999999999984 578899999999999973
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.79 E-value=1e-19 Score=158.08 Aligned_cols=128 Identities=23% Similarity=0.578 Sum_probs=116.7
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
..+.|..|++.|...+.+.++++.||+.+|.|..|...|....|...+|.+||..||.+.++
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~------------------ 363 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR------------------ 363 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhC------------------
Confidence 35899999999964389999999999999999999999999999999999999999999987
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHHHhH
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHHNQL 167 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 167 (199)
++|.+|.++|.+. .|.+.+..||++||.|..|+++|....|+..+|.+||+.||.++
T Consensus 364 ----------------------p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~ 420 (479)
T KOG1703|consen 364 ----------------------PNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKL 420 (479)
T ss_pred ----------------------ccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhh
Confidence 9999999999754 47788999999999999999999999999999999999999999
Q ss_pred hcCCCCCCC
Q 029070 168 IKEKGNLSQ 176 (199)
Q Consensus 168 ~~~k~~~~~ 176 (199)
++.++.+..
T Consensus 421 ~~~~~~~~~ 429 (479)
T KOG1703|consen 421 FTTKCDYCK 429 (479)
T ss_pred ccccchhcc
Confidence 997775443
No 8
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.76 E-value=1.8e-19 Score=153.13 Aligned_cols=134 Identities=20% Similarity=0.469 Sum_probs=113.4
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
+...|++|++.|..+..+.|+++.||..||+|..|...|. +.|..++|.+||+.||+..|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC------------------
Confidence 4678999999999999999999999999999999999996 789999999999999999998
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCC-CCCeeeeCCccccHhHHHh
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVIS-PSNYIAHEGRLYCKHHHNQ 166 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~c~~~ 166 (199)
.+|..|.+.|.+. .+.+.+++||+.|-+|+.|+..+. +++-|+.+..+|-+.|-..
T Consensus 193 ----------------------vkc~~c~~fisgk-vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa 249 (670)
T KOG1044|consen 193 ----------------------VKCEECEKFISGK-VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQA 249 (670)
T ss_pred ----------------------eehHHhhhhhhhh-hhhccCcccCcchhhhhhhccccccchheeeccccccCCccccc
Confidence 8999999999744 477999999999999999999998 5577888999999999765
Q ss_pred HhcCCCCCCCcCCcccc
Q 029070 167 LIKEKGNLSQLEGEHEK 183 (199)
Q Consensus 167 ~~~~k~~~~~~~~~~~~ 183 (199)
.-.++-....+....++
T Consensus 250 ~~tE~i~~~~rtst~Si 266 (670)
T KOG1044|consen 250 TKTEEILKPGRTSTESI 266 (670)
T ss_pred cchhhcccCCCCCcccc
Confidence 54444333333333333
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.75 E-value=1.7e-19 Score=156.70 Aligned_cols=116 Identities=27% Similarity=0.676 Sum_probs=107.2
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccCCCCCCCCCCCCccCC
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTGSLDKSFEGTPKIAKP 87 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (199)
..+.|.+|+++| .++.|.|.+..||++||+|..|+++|....|+..+|.+||+.||..++.
T Consensus 362 ~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~------------------ 422 (479)
T KOG1703|consen 362 FRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT------------------ 422 (479)
T ss_pred hCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc------------------
Confidence 368899999999 5899999999999999999999999999999999999999999999986
Q ss_pred CCCCCCCCCCcccccccCCCCCCCCcCCCceEecCcc-eeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHH
Q 029070 88 EKPIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEK-VSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHH 164 (199)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~ 164 (199)
.+|..|.++|..... +.+++..||..||+|..|.+.|.+..|+...++++|..|+
T Consensus 423 ----------------------~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 423 ----------------------TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred ----------------------ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 799999998875544 7799999999999999999999999999999999999875
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.75 E-value=8.5e-19 Score=149.12 Aligned_cols=162 Identities=21% Similarity=0.428 Sum_probs=114.4
Q ss_pred ccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccC-CcccccccHHHHhhccC--CCCCCCCCCCCc-c
Q 029070 10 QKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFE-GVLYCRPHFDQLFKRTG--SLDKSFEGTPKI-A 85 (199)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~-g~~yC~~c~~~~~~~~~--~~~~~~~~~~~~-~ 85 (199)
-.|..|.+.- .++++.+.++.||..||+|..|+..|..+.||.++ .++|+.........-.. ...+.+...-++ .
T Consensus 17 i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs 95 (670)
T KOG1044|consen 17 IKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 4699999999 59999999999999999999999999999988775 46677633222111000 111111111111 1
Q ss_pred CCCCCCCCCC--------------CCcccccccCCCCCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCe
Q 029070 86 KPEKPIDGEK--------------PNVAKVSTMFGGTREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNY 151 (199)
Q Consensus 86 ~~~~~~~~~~--------------~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~ 151 (199)
....|+.... .....+.+........|++|.+.|..++.+.++++.||..||+|..|...|.+ +|
T Consensus 96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey 174 (670)
T KOG1044|consen 96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EY 174 (670)
T ss_pred ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-ee
Confidence 1122221110 11111222222345799999999998888889999999999999999999987 88
Q ss_pred eeeCCccccHhHHHhHhcCCCC
Q 029070 152 IAHEGRLYCKHHHNQLIKEKGN 173 (199)
Q Consensus 152 ~~~~g~~yC~~c~~~~~~~k~~ 173 (199)
+..+|.|||+.+|.+.|+-||.
T Consensus 175 ~skdg~pyce~dy~~~fgvkc~ 196 (670)
T KOG1044|consen 175 MSKDGVPYCEKDYQAKFGVKCE 196 (670)
T ss_pred eccCCCcchhhhhhhhcCeehH
Confidence 9999999999999999998885
No 11
>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=99.61 E-value=5.4e-16 Score=96.78 Aligned_cols=57 Identities=28% Similarity=0.803 Sum_probs=52.9
Q ss_pred ccccCceeecceeE-EeCCcccccccceeccCcccccCCcccccCCcccccccHHHHh
Q 029070 12 CMACDKTVYLVDKL-TADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLF 68 (199)
Q Consensus 12 C~~C~~~I~~~~~~-~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (199)
|.+|+++|..++.+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
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 78999999877765 7999999999999999999999999999999999999998875
No 12
>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=99.51 E-value=1.9e-14 Score=89.70 Aligned_cols=57 Identities=32% Similarity=0.736 Sum_probs=52.8
Q ss_pred CcCCCceEecCcce-eecCccccccCeecccCCCCCCCCCeeeeCCccccHhHHHhHh
Q 029070 112 CVGCKNTVYPTEKV-SVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHHNQLI 168 (199)
Q Consensus 112 C~~C~~~I~~~~~v-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~ 168 (199)
|.+|+++|.+.+.+ .+.++.||++||+|..|+++|..+.++..+|++||..||.++|
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 78999999988865 5999999999999999999999888999999999999999876
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.07 E-value=5.4e-12 Score=99.80 Aligned_cols=79 Identities=20% Similarity=0.362 Sum_probs=70.4
Q ss_pred CCCCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHHHhHhcCCCC-CCCcCCccccccc
Q 029070 108 TREKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHHNQLIKEKGN-LSQLEGEHEKTSV 186 (199)
Q Consensus 108 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~k~~-~~~~~~~~~~~~~ 186 (199)
..++|++|.+.|.+...+.+++++||..|++|+.|+.+|.. ..+.++|.+||+.+|.++||.||. -++|+++..+.|.
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 45999999999987766679999999999999999999977 778999999999999999999998 7888888877664
Q ss_pred c
Q 029070 187 N 187 (199)
Q Consensus 187 ~ 187 (199)
.
T Consensus 111 A 111 (383)
T KOG4577|consen 111 A 111 (383)
T ss_pred h
Confidence 3
No 14
>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=98.87 E-value=1.4e-09 Score=61.69 Aligned_cols=37 Identities=32% Similarity=0.726 Sum_probs=33.5
Q ss_pred cccccCceeecc-eeEEeCCcccccccceeccCccccc
Q 029070 11 KCMACDKTVYLV-DKLTADNRIYHKACFRCHHCKGTLK 47 (199)
Q Consensus 11 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~ 47 (199)
+|.+|+++|..+ ..+.++++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999766 6789999999999999999999985
No 15
>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=98.61 E-value=2.7e-08 Score=56.29 Aligned_cols=37 Identities=32% Similarity=0.714 Sum_probs=32.7
Q ss_pred CCcCCCceEecC-cceeecCccccccCeecccCCCCCC
Q 029070 111 KCVGCKNTVYPT-EKVSVNGTPYHKSCFKCSHGGCVIS 147 (199)
Q Consensus 111 ~C~~C~~~I~~~-~~v~~~~~~~H~~Cf~C~~C~~~l~ 147 (199)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 588999999887 4467899999999999999999885
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.25 E-value=2.2e-07 Score=72.04 Aligned_cols=67 Identities=52% Similarity=1.077 Sum_probs=59.3
Q ss_pred CCCCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhccC
Q 029070 6 AGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTG 72 (199)
Q Consensus 6 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~ 72 (199)
.++...|..|.+.+++.+.+...+..||..||+|+.|+..|+.+.|...++.+||...+..++-...
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~ 171 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKG 171 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCC
Confidence 3556789999999999999999999999999999999999999999999999999888777665443
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.95 E-value=6e-07 Score=68.31 Aligned_cols=62 Identities=32% Similarity=0.795 Sum_probs=55.9
Q ss_pred CccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHhhc
Q 029070 9 QQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKR 70 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~ 70 (199)
...|..|++.+++.+.+..+++.||..||.|..|+.+|.-..|-..+.++||..+|....++
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence 45688999999999999999999999999999999999988888889999999999765544
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.86 E-value=7.6e-07 Score=67.75 Aligned_cols=59 Identities=32% Similarity=0.648 Sum_probs=53.6
Q ss_pred CCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHHHhHh
Q 029070 110 EKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHHNQLI 168 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~ 168 (199)
..|..|++.+++.|.|..+++.||..||+|..|+-+|....+.-.+.++||..+|.+..
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 67889999999999999999999999999999999999878878899999999997643
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.79 E-value=3.3e-06 Score=66.75 Aligned_cols=112 Identities=18% Similarity=0.477 Sum_probs=86.1
Q ss_pred ccCceeecceeEEeCCcccccccceeccCccccc--CCcccccCCcccccccHHH--HhhccCCCCCCCCCCCCccCCCC
Q 029070 14 ACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLK--LGNYNSFEGVLYCRPHFDQ--LFKRTGSLDKSFEGTPKIAKPEK 89 (199)
Q Consensus 14 ~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~ 89 (199)
.|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.. .+.
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~-------------------- 59 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS-------------------- 59 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc--------------------
Confidence 3677775444567779999999999999999997 445666 999999999987 332
Q ss_pred CCCCCCCCcccccccCCCCCCCCcCCCceEecCccee-ecCccccccCeecccCCCCCC-CCCeeee-CCccccHhHHHh
Q 029070 90 PIDGEKPNVAKVSTMFGGTREKCVGCKNTVYPTEKVS-VNGTPYHKSCFKCSHGGCVIS-PSNYIAH-EGRLYCKHHHNQ 166 (199)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~-~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~-~g~~yC~~c~~~ 166 (199)
.+|.+|...+...+.|. +..+. |.-||.|..|...+. ...+.+. +.+.+|..++.+
T Consensus 60 --------------------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 60 --------------------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred --------------------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 78999999987666665 55555 999999999988665 4455444 558889888865
Q ss_pred H
Q 029070 167 L 167 (199)
Q Consensus 167 ~ 167 (199)
.
T Consensus 119 ~ 119 (235)
T KOG0490|consen 119 E 119 (235)
T ss_pred h
Confidence 4
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=88.93 E-value=0.1 Score=40.98 Aligned_cols=57 Identities=19% Similarity=0.494 Sum_probs=44.1
Q ss_pred CCceEecCcceeecCccccccCeecccCCCCCC--CCCeeeeCCccccHhHHHh--HhcCCC
Q 029070 115 CKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVIS--PSNYIAHEGRLYCKHHHNQ--LIKEKG 172 (199)
Q Consensus 115 C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~--~~~~k~ 172 (199)
|+..|.+...+...+..||..|..|..|...+. ...+.. +|..||...+.. .+..++
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr 62 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRC 62 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccc
Confidence 566676655556679999999999999999997 434555 999999999987 555444
No 21
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=86.62 E-value=0.21 Score=34.17 Aligned_cols=32 Identities=25% Similarity=0.556 Sum_probs=24.2
Q ss_pred CCCcCCCceEecCccee-ecCccccccCeeccc
Q 029070 110 EKCVGCKNTVYPTEKVS-VNGTPYHKSCFKCSH 141 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~-~~~~~~H~~Cf~C~~ 141 (199)
-+|..|+++|..++.++ ..+..-|..||+=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 47889999998888776 455778888887443
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.19 E-value=0.48 Score=28.63 Aligned_cols=39 Identities=26% Similarity=0.548 Sum_probs=27.3
Q ss_pred CCccccccCceeecce-eE--EeCCcccccccc----eecc--Ccccc
Q 029070 8 TQQKCMACDKTVYLVD-KL--TADNRIYHKACF----RCHH--CKGTL 46 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~-~~--~~~~~~~H~~CF----~C~~--C~~~L 46 (199)
...+|..|+++|.+++ .| ..=+..||.+|. .|.. |+..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 4678999999996443 44 345788999997 5655 55544
No 23
>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=79.37 E-value=1.5 Score=29.90 Aligned_cols=30 Identities=20% Similarity=0.394 Sum_probs=18.5
Q ss_pred CCccccccCceeecceeEE-eCCcccccccc
Q 029070 8 TQQKCMACDKTVYLVDKLT-ADNRIYHKACF 37 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~-~~~~~~H~~CF 37 (199)
....|..|+++|.....+. -.|..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 3566888888885444333 33566777775
No 24
>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=78.38 E-value=0.55 Score=25.73 Aligned_cols=28 Identities=14% Similarity=0.407 Sum_probs=16.4
Q ss_pred eccCcccccCCcccccCCcccccccHHH
Q 029070 39 CHHCKGTLKLGNYNSFEGVLYCRPHFDQ 66 (199)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~ 66 (199)
|..|+.++.........+..+|..|+..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 6666666665555556666777776654
No 25
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.75 E-value=1.9 Score=32.71 Aligned_cols=37 Identities=14% Similarity=0.427 Sum_probs=30.0
Q ss_pred ccccceeccCcccccCCc-ccccCCcccccccHHHHhh
Q 029070 33 HKACFRCHHCKGTLKLGN-YNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 33 H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~c~~~~~~ 69 (199)
-..++.|-.|-....... +..+=|.+||..|......
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 347899999988887665 6677899999999987765
No 26
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.41 E-value=2.9 Score=25.69 Aligned_cols=31 Identities=16% Similarity=0.474 Sum_probs=22.4
Q ss_pred CCCccccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 7 GTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 7 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
...++|..|+..|..++.... |.|-.|+..+
T Consensus 7 ~~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~ 37 (61)
T COG2888 7 KDPPVCTSCGREIAPGETAVK---------FPCPNCGEVE 37 (61)
T ss_pred cCCceeccCCCEeccCCceeE---------eeCCCCCcee
Confidence 336899999999976665433 7788887544
No 27
>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=76.02 E-value=1.6 Score=24.26 Aligned_cols=31 Identities=19% Similarity=0.550 Sum_probs=20.3
Q ss_pred ccccCceeecce--eEEeCCcccccccceeccCcccc
Q 029070 12 CMACDKTVYLVD--KLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 12 C~~C~~~I~~~~--~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
|.-|+.+|. ++ ++...++.||.-| ..|...|
T Consensus 1 Cd~CG~~I~-~eP~~~k~~~~~y~fCC---~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVVKIGNKVYYFCC---PTCLSQF 33 (37)
T ss_pred CCccCCccc-CCEEEEEECCeEEEEEC---HHHHHHH
Confidence 677899995 44 3577888887544 4454433
No 28
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.00 E-value=1.2 Score=21.84 Aligned_cols=8 Identities=25% Similarity=0.957 Sum_probs=4.4
Q ss_pred ccccCcee
Q 029070 12 CMACDKTV 19 (199)
Q Consensus 12 C~~C~~~I 19 (199)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 55555555
No 29
>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=75.98 E-value=1.9 Score=29.41 Aligned_cols=29 Identities=31% Similarity=0.447 Sum_probs=20.5
Q ss_pred CCCcCCCceEecCccee-ecCccccccCee
Q 029070 110 EKCVGCKNTVYPTEKVS-VNGTPYHKSCFK 138 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~-~~~~~~H~~Cf~ 138 (199)
..|+.|+++|.....+. ..+..+|..|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 78999999997544333 456778888863
No 30
>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=75.60 E-value=1.6 Score=29.35 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=17.8
Q ss_pred cccccceeccCcccccCCcccccCCcccccccHH
Q 029070 32 YHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFD 65 (199)
Q Consensus 32 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~ 65 (199)
|-+.=-.|..|+..+. ..|..||..|..
T Consensus 40 y~~~~~~C~~CK~~v~------q~g~~YCq~CAY 67 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVH------QPGAKYCQTCAY 67 (90)
T ss_pred ccccCccccccccccc------cCCCccChhhhc
Confidence 4333346788877663 337789999953
No 31
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=75.35 E-value=1.7 Score=25.95 Aligned_cols=29 Identities=21% Similarity=0.592 Sum_probs=22.0
Q ss_pred eeccCcccccCCc-ccccCCcccccccHHHH
Q 029070 38 RCHHCKGTLKLGN-YNSFEGVLYCRPHFDQL 67 (199)
Q Consensus 38 ~C~~C~~~L~~~~-f~~~~g~~yC~~c~~~~ 67 (199)
.|+.|+..+.-.. +-..|| ..|..|+.++
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 4788988886443 556677 7999999887
No 32
>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=74.38 E-value=4 Score=24.82 Aligned_cols=32 Identities=19% Similarity=0.179 Sum_probs=25.4
Q ss_pred ceeccCcccccCCcccccCCcccccccHHHHhh
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
|.|..|+..+.+. .....|..||+.|..+.+.
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHH
Confidence 6788999888753 4556789999999988775
No 33
>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=73.60 E-value=1.6 Score=23.98 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=17.1
Q ss_pred ceeccCcccccCCcccccCCcccccccH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
+.|..|+.. .|...+|..||..|-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCc
Confidence 347777654 467788999997763
No 34
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=73.13 E-value=2.3 Score=26.68 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=13.8
Q ss_pred ceeccCcccccCCcccccCCcccccccHHHHhh
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
++|+.|...|...-....=..+||..|....++
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~ 40 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG 40 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC
Confidence 567888777754333334457788888655554
No 35
>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=71.64 E-value=2.2 Score=24.26 Aligned_cols=22 Identities=27% Similarity=0.723 Sum_probs=14.7
Q ss_pred eeccCcccccCCcccccCCccccccc
Q 029070 38 RCHHCKGTLKLGNYNSFEGVLYCRPH 63 (199)
Q Consensus 38 ~C~~C~~~L~~~~f~~~~g~~yC~~c 63 (199)
.|..|+.+|- -.++|+.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4566777773 246788888766
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.26 E-value=3.1 Score=25.59 Aligned_cols=30 Identities=23% Similarity=0.598 Sum_probs=20.7
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
..++|..|+..|.+.+.... |.|-.|+..+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~---------F~CPnCG~~~ 35 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVK---------FLCPNCGEVI 35 (59)
T ss_pred cCccccCCCCcccCCCccCE---------eeCCCCCCee
Confidence 45689999999975553222 7788887763
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=68.20 E-value=2.5 Score=30.46 Aligned_cols=22 Identities=23% Similarity=0.655 Sum_probs=18.0
Q ss_pred eeccCcccccCCcccccCCcccccccH
Q 029070 38 RCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
.|..|+.|| | .++|.+||+.|-
T Consensus 30 hCp~Cg~PL----F-~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----F-RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----e-eeCCeEECCCCC
Confidence 368888888 3 399999999995
No 38
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=67.45 E-value=2.2 Score=28.78 Aligned_cols=35 Identities=23% Similarity=0.350 Sum_probs=26.5
Q ss_pred CCCcCCCceEecCccee-ecCccccccCeecccCCC
Q 029070 110 EKCVGCKNTVYPTEKVS-VNGTPYHKSCFKCSHGGC 144 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~-~~~~~~H~~Cf~C~~C~~ 144 (199)
-+|+.|+..|..++.++ .....-|-+||.=+.-++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 58999999999888877 445667888887655444
No 39
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=67.14 E-value=2 Score=33.30 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=25.6
Q ss_pred eecccCCCCCCCCCeeeeCCccccHhHHHhH
Q 029070 137 FKCSHGGCVISPSNYIAHEGRLYCKHHHNQL 167 (199)
Q Consensus 137 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 167 (199)
-+|+.|+..+....-...+|+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788898888776667889999999999754
No 40
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=66.17 E-value=5.2 Score=22.71 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=19.3
Q ss_pred eccCcccccC-Cccc-ccCCcccccccHHHHh
Q 029070 39 CHHCKGTLKL-GNYN-SFEGVLYCRPHFDQLF 68 (199)
Q Consensus 39 C~~C~~~L~~-~~f~-~~~g~~yC~~c~~~~~ 68 (199)
|..|...+.+ ..+. ..=|.++|..|..++.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 5667777732 2333 3348899999987765
No 41
>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=65.79 E-value=3.3 Score=27.01 Aligned_cols=17 Identities=24% Similarity=0.499 Sum_probs=12.4
Q ss_pred CCccccccCceeeccee
Q 029070 8 TQQKCMACDKTVYLVDK 24 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~ 24 (199)
+-..|..|++.|..++.
T Consensus 6 ~Ra~Ck~C~~~I~kg~l 22 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGEL 22 (82)
T ss_dssp STEBETTTSCBE-TTSE
T ss_pred CCccCcccCCcCCCCCE
Confidence 45689999999976653
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=64.31 E-value=2.5 Score=32.72 Aligned_cols=30 Identities=20% Similarity=0.477 Sum_probs=26.1
Q ss_pred ceeccCcccccCCcccccCCcccccccHHH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHFDQ 66 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~ 66 (199)
-+|+.|+..+....-...+|++.|..||..
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccc
Confidence 689999999987777778999999999864
No 43
>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=63.62 E-value=4.1 Score=24.43 Aligned_cols=27 Identities=33% Similarity=0.821 Sum_probs=15.9
Q ss_pred cccCCCCCCCCCeeeeCCcccc-HhHHH
Q 029070 139 CSHGGCVISPSNYIAHEGRLYC-KHHHN 165 (199)
Q Consensus 139 C~~C~~~l~~~~~~~~~g~~yC-~~c~~ 165 (199)
|..|...++...-+..||+.|| ..|..
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-TTTSEESSS-EESSHHHHH
T ss_pred CCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 6777888876677889999998 56654
No 44
>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=61.54 E-value=8 Score=21.19 Aligned_cols=31 Identities=16% Similarity=0.391 Sum_probs=21.0
Q ss_pred eccCcccccCCcccccCCcccccccHHHHhh
Q 029070 39 CHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
|..|...+.+......=|..||.+|..+...
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 4567666665334556688999999888765
No 45
>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=60.36 E-value=7.9 Score=22.51 Aligned_cols=32 Identities=22% Similarity=0.289 Sum_probs=20.0
Q ss_pred ceeccCcccccCCcccccCCcc-cccccHHHHhh
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVL-YCRPHFDQLFK 69 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~-yC~~c~~~~~~ 69 (199)
+.|..|.....+. .+..=|.. +|..|+.+...
T Consensus 3 ~~C~iC~~~~~~~-~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRDV-VLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSSE-EEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCce-EEeCCCChHHHHHHhHHhcc
Confidence 3566776665432 23344677 99999988765
No 46
>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=59.52 E-value=9.4 Score=20.73 Aligned_cols=31 Identities=23% Similarity=0.434 Sum_probs=17.5
Q ss_pred eccCcccccCCcccccCCcccccccHHHHhh
Q 029070 39 CHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
|..|...+........=|..||..|....+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH
Confidence 5566666632222222467788888776654
No 47
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=55.34 E-value=5.3 Score=36.74 Aligned_cols=36 Identities=14% Similarity=0.356 Sum_probs=24.4
Q ss_pred cceeccCcccccCCcccccCCcccccccHHHHhhccC
Q 029070 36 CFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFKRTG 72 (199)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~ 72 (199)
=++|..|+....+ .-..+=+.+||..|-..++.++-
T Consensus 643 ~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRq 678 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQ 678 (698)
T ss_pred ceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhc
Confidence 3688999855432 12334578899999998887543
No 48
>PRK00420 hypothetical protein; Validated
Probab=54.90 E-value=6.6 Score=27.56 Aligned_cols=24 Identities=25% Similarity=0.474 Sum_probs=16.6
Q ss_pred ceeccCcccccCCcccccCCcccccccH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
-.|..|+.+| |-.++|..||+.|-
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCC
Confidence 4567787766 33378888888874
No 49
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=53.31 E-value=4.4 Score=29.72 Aligned_cols=36 Identities=19% Similarity=0.450 Sum_probs=25.7
Q ss_pred ccccccCceeecceeEEeCCcccccccceeccCcccccC
Q 029070 10 QKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKL 48 (199)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 48 (199)
=.|..|+..+...+.+...+. ..=|+|..|+..|..
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEEE
Confidence 469999988876665544332 333999999999853
No 50
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=52.60 E-value=14 Score=25.43 Aligned_cols=40 Identities=13% Similarity=-0.018 Sum_probs=30.8
Q ss_pred eecccCCCCCC-CCCeeeeCCccccHhHHHhHhcCCCCCCC
Q 029070 137 FKCSHGGCVIS-PSNYIAHEGRLYCKHHHNQLIKEKGNLSQ 176 (199)
Q Consensus 137 f~C~~C~~~l~-~~~~~~~~g~~yC~~c~~~~~~~k~~~~~ 176 (199)
++|..|+.++. ++.|....+.+..-.||.+....+...+.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k~~~~~ 43 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKASKKLYGDV 43 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHhhhcccCh
Confidence 47999999987 55777777788999999887766665443
No 51
>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=50.16 E-value=12 Score=27.73 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=24.6
Q ss_pred CCCcCCCceEecCcc---eeecCccccccCeecccCCCCCC
Q 029070 110 EKCVGCKNTVYPTEK---VSVNGTPYHKSCFKCSHGGCVIS 147 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~---v~~~~~~~H~~Cf~C~~C~~~l~ 147 (199)
..|..|+.+|.+... |...+..|+.- --|..|+++..
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCc
Confidence 689999999986543 34445666622 23777888764
No 52
>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=49.71 E-value=14 Score=21.22 Aligned_cols=12 Identities=8% Similarity=-0.064 Sum_probs=8.2
Q ss_pred CccccHhHHHhH
Q 029070 156 GRLYCKHHHNQL 167 (199)
Q Consensus 156 g~~yC~~c~~~~ 167 (199)
+--+|..||...
T Consensus 22 d~dLC~~Cf~~~ 33 (46)
T cd02249 22 DFDLCSSCYAKG 33 (46)
T ss_pred CCcCHHHHHCcC
Confidence 345688888753
No 53
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=48.87 E-value=11 Score=31.62 Aligned_cols=39 Identities=18% Similarity=0.471 Sum_probs=28.6
Q ss_pred CccccccCceeecceeEEe-----CC-----cccccccceeccCccccc
Q 029070 9 QQKCMACDKTVYLVDKLTA-----DN-----RIYHKACFRCHHCKGTLK 47 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~~-----~~-----~~~H~~CF~C~~C~~~L~ 47 (199)
+-.|..|+..|+-|..+.| .+ ...+.--++|..|...|.
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 5689999999987766533 23 334557788999988875
No 54
>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=48.47 E-value=19 Score=21.85 Aligned_cols=31 Identities=16% Similarity=0.430 Sum_probs=17.5
Q ss_pred eccCcccccCCc---ccccCCcccccccHHHHhh
Q 029070 39 CHHCKGTLKLGN---YNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 39 C~~C~~~L~~~~---f~~~~g~~yC~~c~~~~~~ 69 (199)
|..|++.|.... +.-.-.-.||..|...++.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~ 41 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLN 41 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc
Confidence 455666665433 2222345577788777765
No 55
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.63 E-value=9.8 Score=31.25 Aligned_cols=32 Identities=16% Similarity=0.349 Sum_probs=23.0
Q ss_pred cceeccCcccccCCcccccCCcccccccHHHHh
Q 029070 36 CFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLF 68 (199)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (199)
=|.|..|++.+. ..-...-+..+|+.|..+.+
T Consensus 241 Pf~c~icr~~f~-~pVvt~c~h~fc~~ca~~~~ 272 (313)
T KOG1813|consen 241 PFKCFICRKYFY-RPVVTKCGHYFCEVCALKPY 272 (313)
T ss_pred Cccccccccccc-cchhhcCCceeehhhhcccc
Confidence 477888888775 33455678889999976655
No 56
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=46.53 E-value=14 Score=22.23 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=13.5
Q ss_pred eccCcccccCCcccccCCcccc-cccHH
Q 029070 39 CHHCKGTLKLGNYNSFEGVLYC-RPHFD 65 (199)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC-~~c~~ 65 (199)
|..|++++.....+..++.+.| ..|++
T Consensus 4 CvVCKqpi~~a~~v~T~~G~VH~g~C~~ 31 (54)
T PF10886_consen 4 CVVCKQPIDDALVVETESGPVHPGVCAQ 31 (54)
T ss_pred eeeeCCccCcceEEEcCCCccCcHHHHH
Confidence 5666666665444444444444 34443
No 57
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.35 E-value=14 Score=18.45 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=5.6
Q ss_pred CCCcCCCceE
Q 029070 110 EKCVGCKNTV 119 (199)
Q Consensus 110 ~~C~~C~~~I 119 (199)
..|..|+..|
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 4566666544
No 58
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=45.82 E-value=8.8 Score=20.92 Aligned_cols=31 Identities=29% Similarity=0.662 Sum_probs=18.2
Q ss_pred cccccCceeecce-eEEeCCcccccccceeccCcccc
Q 029070 11 KCMACDKTVYLVD-KLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 11 ~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
.|..|+..+...+ .+...+. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 5888888764332 2322221 37788887766
No 59
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=45.80 E-value=6.2 Score=29.41 Aligned_cols=31 Identities=16% Similarity=0.331 Sum_probs=24.3
Q ss_pred ccccccCceeecceeEEeCCcccccccceeccCcccccC
Q 029070 10 QKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKL 48 (199)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 48 (199)
=.|..|+..+...+.+.. =|+|..|+..|..
T Consensus 110 Y~Cp~c~~r~tf~eA~~~--------~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMEL--------NFTCPRCGAMLDY 140 (158)
T ss_pred EECCCCCcEeeHHHHHHc--------CCcCCCCCCEeee
Confidence 369999988877666642 4999999999863
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=45.54 E-value=12 Score=21.48 Aligned_cols=27 Identities=33% Similarity=0.594 Sum_probs=15.7
Q ss_pred cccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 11 KCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
+|..|+..+...+... =++|..|+.++
T Consensus 5 ~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYGT---------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCCC---------ceECCCCCCeE
Confidence 5777777664322211 26777777655
No 61
>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=44.90 E-value=21 Score=20.24 Aligned_cols=10 Identities=10% Similarity=0.228 Sum_probs=7.1
Q ss_pred ccccHhHHHh
Q 029070 157 RLYCKHHHNQ 166 (199)
Q Consensus 157 ~~yC~~c~~~ 166 (199)
--+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 3468888875
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=44.41 E-value=9.4 Score=29.53 Aligned_cols=33 Identities=18% Similarity=0.308 Sum_probs=24.6
Q ss_pred cceeccCcccccCCcccccCCcccccccHHHHhh
Q 029070 36 CFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
=|.|..|.+... ......=|..+|..|+.+.+.
T Consensus 196 PF~C~iCKkdy~-spvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 196 PFLCGICKKDYE-SPVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred ceeehhchhhcc-chhhhhcchhHHHHHHHHHhc
Confidence 488899988775 334455688899999887764
No 63
>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=43.45 E-value=11 Score=22.01 Aligned_cols=28 Identities=18% Similarity=0.324 Sum_probs=14.5
Q ss_pred ceeccCcccccCCcccccCCcccccccH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
|+|..|+..+....-...+..+-|..|-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECG 33 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCC
Confidence 5677777655433211223455566663
No 64
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.45 E-value=8.4 Score=29.32 Aligned_cols=31 Identities=23% Similarity=0.488 Sum_probs=24.1
Q ss_pred ccccccCceeecceeEEeCCcccccccceeccCcccccC
Q 029070 10 QKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKL 48 (199)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 48 (199)
=.|..|+..+...+.+. .=|+|..|+..|..
T Consensus 118 Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 36999998887766553 24999999999964
No 65
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=42.92 E-value=27 Score=22.78 Aligned_cols=40 Identities=30% Similarity=0.679 Sum_probs=13.7
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccccccHHHHh
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLF 68 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (199)
...+|..|+..|- +.+.|..| --|..|+- +.|..||+-..
T Consensus 8 ~~qiCqiCGD~VG----l~~~Ge~F----VAC~eC~f-------------PvCr~CyEYEr 47 (80)
T PF14569_consen 8 NGQICQICGDDVG----LTENGEVF----VACHECAF-------------PVCRPCYEYER 47 (80)
T ss_dssp SS-B-SSS--B------B-SSSSB------S-SSS------------------HHHHHHHH
T ss_pred CCcccccccCccc----cCCCCCEE----EEEcccCC-------------ccchhHHHHHh
Confidence 3566777776663 23444444 23455543 44777776443
No 66
>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=42.81 E-value=12 Score=21.17 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=13.3
Q ss_pred ceeccCcccccCCcccccCCccccccc
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPH 63 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c 63 (199)
|+|..|+..+....-...+..+-|+.|
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~C 32 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPEC 32 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCC
Confidence 566666655543321222445556655
No 67
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=42.49 E-value=13 Score=22.79 Aligned_cols=28 Identities=25% Similarity=0.390 Sum_probs=20.0
Q ss_pred eeccCcccccCC--cccccCCccccc-ccHH
Q 029070 38 RCHHCKGTLKLG--NYNSFEGVLYCR-PHFD 65 (199)
Q Consensus 38 ~C~~C~~~L~~~--~f~~~~g~~yC~-~c~~ 65 (199)
.|..|++.|..+ .|..++.+.+|. +|-.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 367888899853 376788899995 5543
No 68
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.39 E-value=31 Score=27.32 Aligned_cols=40 Identities=23% Similarity=0.446 Sum_probs=27.7
Q ss_pred CcccccccceeccCcccccCCcccccCCcccccccHHHHhh
Q 029070 29 NRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 29 ~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
+..---..|.|..|-.. +...-...=|.+||-.|..+-..
T Consensus 40 ~~~~~~~~FdCNICLd~-akdPVvTlCGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 40 GRNRDGGFFDCNICLDL-AKDPVVTLCGHLFCWPCLYQWLQ 79 (230)
T ss_pred CccCCCCceeeeeeccc-cCCCEEeecccceehHHHHHHHh
Confidence 33345678999999443 33445566799999999877554
No 69
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=41.82 E-value=28 Score=26.89 Aligned_cols=33 Identities=21% Similarity=0.506 Sum_probs=23.3
Q ss_pred ccceeccCcccccCCcccccCCcccccccHHHHh
Q 029070 35 ACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLF 68 (199)
Q Consensus 35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (199)
.-|.|..|...+.+. ....=|..||..|..+..
T Consensus 17 ~~~~CpICld~~~dP-VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 17 GDFDCNICLDQVRDP-VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred CccCCccCCCcCCCc-EEcCCCchhHHHHHHHHH
Confidence 358888888877533 344568999999987543
No 70
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=41.59 E-value=11 Score=25.68 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=19.0
Q ss_pred ccceeccCcccccCCc-ccccCCccccccc
Q 029070 35 ACFRCHHCKGTLKLGN-YNSFEGVLYCRPH 63 (199)
Q Consensus 35 ~CF~C~~C~~~L~~~~-f~~~~g~~yC~~c 63 (199)
.=|+|+.|-..-.... -...+|.+||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 4499999954432222 2356799999987
No 71
>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=40.52 E-value=13 Score=20.39 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=4.7
Q ss_pred ceeccCcccc
Q 029070 37 FRCHHCKGTL 46 (199)
Q Consensus 37 F~C~~C~~~L 46 (199)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 3445554444
No 72
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=40.50 E-value=1.8 Score=29.33 Aligned_cols=55 Identities=11% Similarity=0.233 Sum_probs=38.3
Q ss_pred CCCcCCCceEecCcceeecCccccccCeecccCCCCCCCCCeeeeCCccccHhHH
Q 029070 110 EKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISPSNYIAHEGRLYCKHHH 164 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~ 164 (199)
.-|..|+..+.......+.-..++..+.-|..|.+.|.-.+|.+.+.=|||..-|
T Consensus 36 YaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 36 YACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred hhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCCCC
Confidence 3466777666544323466677899999999999999877777777666665433
No 73
>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=40.48 E-value=25 Score=17.48 Aligned_cols=12 Identities=33% Similarity=0.960 Sum_probs=6.5
Q ss_pred CcCCCceEecCc
Q 029070 112 CVGCKNTVYPTE 123 (199)
Q Consensus 112 C~~C~~~I~~~~ 123 (199)
|..|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 445666665544
No 74
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=39.70 E-value=6 Score=25.26 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=4.1
Q ss_pred CCCcCCCceE
Q 029070 110 EKCVGCKNTV 119 (199)
Q Consensus 110 ~~C~~C~~~I 119 (199)
..|..|++++
T Consensus 31 a~CPdC~~~L 40 (70)
T PF07191_consen 31 AFCPDCGQPL 40 (70)
T ss_dssp EE-TTT-SB-
T ss_pred ccCCCcccHH
Confidence 4566666554
No 75
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=38.29 E-value=4.3 Score=27.48 Aligned_cols=49 Identities=16% Similarity=0.353 Sum_probs=26.6
Q ss_pred ccccCceeecceeEEeCCcccccccceeccCcccccCCcccccCCcccc
Q 029070 12 CMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNYNSFEGVLYC 60 (199)
Q Consensus 12 C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC 60 (199)
|..|+..+..-......-..+|+.+..|-.|++.|.-..|.....-+||
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 4445555432223334445567777777777777765555544444444
No 76
>PRK00807 50S ribosomal protein L24e; Validated
Probab=37.76 E-value=24 Score=21.08 Aligned_cols=23 Identities=22% Similarity=0.356 Sum_probs=13.6
Q ss_pred cccccCceeeccee---EEeCCcccc
Q 029070 11 KCMACDKTVYLVDK---LTADNRIYH 33 (199)
Q Consensus 11 ~C~~C~~~I~~~~~---~~~~~~~~H 33 (199)
.|.-|+..|+++.- +..+|+.|.
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 57777777765442 445566654
No 77
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=36.54 E-value=20 Score=21.42 Aligned_cols=30 Identities=20% Similarity=0.548 Sum_probs=20.8
Q ss_pred cccccCceeecceeEEeCCcccccccceec
Q 029070 11 KCMACDKTVYLVDKLTADNRIYHKACFRCH 40 (199)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~ 40 (199)
.|+-|+..|...--....++.|=..|-.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 488999998532234566788888885553
No 78
>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=36.04 E-value=25 Score=19.54 Aligned_cols=30 Identities=20% Similarity=0.544 Sum_probs=14.8
Q ss_pred CCCcCCCceEecCcceeecCccccccCeecccCCC
Q 029070 110 EKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGC 144 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~ 144 (199)
.+|..|+-.|.+--.+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 68999988887654455545554 6777765
No 79
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.92 E-value=40 Score=18.28 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=20.9
Q ss_pred eccCcccccCCcccccCCcccccccHHHHhh
Q 029070 39 CHHCKGTLKLGNYNSFEGVLYCRPHFDQLFK 69 (199)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (199)
|..|...+........=|..||..|..+.+.
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHH
Confidence 4566666654443444578899999888775
No 80
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.49 E-value=18 Score=33.37 Aligned_cols=10 Identities=20% Similarity=0.690 Sum_probs=5.8
Q ss_pred CCCcCCCceE
Q 029070 110 EKCVGCKNTV 119 (199)
Q Consensus 110 ~~C~~C~~~I 119 (199)
..|..|+..+
T Consensus 42 ~fC~~CG~~~ 51 (645)
T PRK14559 42 AHCPNCGAET 51 (645)
T ss_pred ccccccCCcc
Confidence 4566666554
No 81
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.72 E-value=16 Score=30.00 Aligned_cols=32 Identities=34% Similarity=0.622 Sum_probs=27.5
Q ss_pred CCCcCCCceEecCcceeecCccccccCeeccc
Q 029070 110 EKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSH 141 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~ 141 (199)
-.|.-|++.+.+...|..-.-.-|+-||-|++
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH
Confidence 57899999998887677778889999999985
No 82
>PF12773 DZR: Double zinc ribbon
Probab=34.08 E-value=41 Score=19.34 Aligned_cols=11 Identities=18% Similarity=0.603 Sum_probs=6.1
Q ss_pred CccccccCcee
Q 029070 9 QQKCMACDKTV 19 (199)
Q Consensus 9 ~~~C~~C~~~I 19 (199)
...|..|+.++
T Consensus 12 ~~fC~~CG~~l 22 (50)
T PF12773_consen 12 AKFCPHCGTPL 22 (50)
T ss_pred ccCChhhcCCh
Confidence 44555555555
No 83
>PLN02195 cellulose synthase A
Probab=33.82 E-value=42 Score=32.38 Aligned_cols=32 Identities=22% Similarity=0.621 Sum_probs=21.1
Q ss_pred CCCccccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 7 GTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 7 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
++..+|..|+..|. +..+|..| --|..|+-++
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~pv 35 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSYPL 35 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCCcc
Confidence 34678999988874 34666666 4466775544
No 84
>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=33.60 E-value=19 Score=16.84 Aligned_cols=13 Identities=15% Similarity=0.659 Sum_probs=9.2
Q ss_pred ceeccCcccccCC
Q 029070 37 FRCHHCKGTLKLG 49 (199)
Q Consensus 37 F~C~~C~~~L~~~ 49 (199)
|+|..|++.+...
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 5788888777543
No 85
>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=33.49 E-value=21 Score=31.66 Aligned_cols=38 Identities=21% Similarity=0.365 Sum_probs=23.6
Q ss_pred CCCcCCCceEecCcceeecCccccccCeecccCCCCCCC
Q 029070 110 EKCVGCKNTVYPTEKVSVNGTPYHKSCFKCSHGGCVISP 148 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~ 148 (199)
..|..|-..+...+ +...+...-++||.|..|..+|..
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 45666655554333 344445555688888888887763
No 86
>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=33.29 E-value=40 Score=19.46 Aligned_cols=29 Identities=14% Similarity=0.174 Sum_probs=16.7
Q ss_pred ecccCCCCCCCCCeeee--CCccccHhHHHh
Q 029070 138 KCSHGGCVISPSNYIAH--EGRLYCKHHHNQ 166 (199)
Q Consensus 138 ~C~~C~~~l~~~~~~~~--~g~~yC~~c~~~ 166 (199)
.|..|+..+..-.|... .+.-+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 35556665554333211 246679999975
No 87
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.26 E-value=27 Score=18.92 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=4.1
Q ss_pred ccccccCcee
Q 029070 10 QKCMACDKTV 19 (199)
Q Consensus 10 ~~C~~C~~~I 19 (199)
+.|..|++++
T Consensus 4 ~~C~eC~~~f 13 (34)
T PF01286_consen 4 PKCDECGKPF 13 (34)
T ss_dssp EE-TTT--EE
T ss_pred chHhHhCCHH
Confidence 4566666665
No 88
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=32.90 E-value=29 Score=28.77 Aligned_cols=32 Identities=19% Similarity=0.341 Sum_probs=25.2
Q ss_pred ceeccCcccccCCcccccCCcccccccHHHHh
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHFDQLF 68 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (199)
+-|-.|...|....|.-.+|.+.|..|-.++.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 66788888888777888889999999875544
No 89
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=32.64 E-value=20 Score=28.49 Aligned_cols=28 Identities=11% Similarity=0.218 Sum_probs=16.3
Q ss_pred cCcccccCCcccccC-CcccccccHHHHh
Q 029070 41 HCKGTLKLGNYNSFE-GVLYCRPHFDQLF 68 (199)
Q Consensus 41 ~C~~~L~~~~f~~~~-g~~yC~~c~~~~~ 68 (199)
.|...-....|+... ..++|..|...-.
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~ 36 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASS 36 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCC
Confidence 333333344566554 7889999965433
No 90
>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=32.57 E-value=42 Score=19.61 Aligned_cols=11 Identities=9% Similarity=-0.064 Sum_probs=7.8
Q ss_pred ccccHhHHHhH
Q 029070 157 RLYCKHHHNQL 167 (199)
Q Consensus 157 ~~yC~~c~~~~ 167 (199)
-=+|..||...
T Consensus 26 ~DlC~~C~~~~ 36 (48)
T cd02341 26 FDLCQDCVVKG 36 (48)
T ss_pred CccCHHHHhCc
Confidence 34688998764
No 91
>PRK12495 hypothetical protein; Provisional
Probab=31.14 E-value=24 Score=27.78 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=13.6
Q ss_pred cceeccCcccccCCcccccCCcccccccH
Q 029070 36 CFRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
=+.|..|+.+|. ...|..+|..|-
T Consensus 42 a~hC~~CG~PIp-----a~pG~~~Cp~CQ 65 (226)
T PRK12495 42 NAHCDECGDPIF-----RHDGQEFCPTCQ 65 (226)
T ss_pred hhhcccccCccc-----CCCCeeECCCCC
Confidence 355566666663 235666666664
No 92
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=30.62 E-value=4.2 Score=26.98 Aligned_cols=13 Identities=23% Similarity=0.544 Sum_probs=10.3
Q ss_pred CCCcCCCceEecC
Q 029070 110 EKCVGCKNTVYPT 122 (199)
Q Consensus 110 ~~C~~C~~~I~~~ 122 (199)
..|+.|++.|...
T Consensus 80 giCAMCGKki~nT 92 (100)
T KOG3476|consen 80 GICAMCGKKILNT 92 (100)
T ss_pred hHHHHhhhHhhcc
Confidence 5899999988754
No 93
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.44 E-value=44 Score=26.52 Aligned_cols=39 Identities=15% Similarity=0.290 Sum_probs=22.6
Q ss_pred CCcccccccceeccCcccccCCcccc-cCCcccccccHHHHhh
Q 029070 28 DNRIYHKACFRCHHCKGTLKLGNYNS-FEGVLYCRPHFDQLFK 69 (199)
Q Consensus 28 ~~~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~c~~~~~~ 69 (199)
.+.-|-++| ..|+.+|..+.-.. .==.++.-.|+..+-+
T Consensus 45 ~DsDY~pNC---~LC~t~La~gdt~RLvCyhlfHW~ClneraA 84 (299)
T KOG3970|consen 45 QDSDYNPNC---RLCNTPLASGDTTRLVCYHLFHWKCLNERAA 84 (299)
T ss_pred hhcCCCCCC---ceeCCccccCcceeehhhhhHHHHHhhHHHh
Confidence 355677776 77888998765321 1113344566655544
No 94
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.18 E-value=38 Score=32.80 Aligned_cols=23 Identities=35% Similarity=0.922 Sum_probs=14.5
Q ss_pred CCccccccCceeecceeEEeCCcccccccceeccCccc
Q 029070 8 TQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGT 45 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~ 45 (199)
+...|..|+.... + |+|..|+..
T Consensus 625 g~RfCpsCG~~t~-----------~----frCP~CG~~ 647 (1121)
T PRK04023 625 GRRKCPSCGKETF-----------Y----RRCPFCGTH 647 (1121)
T ss_pred cCccCCCCCCcCC-----------c----ccCCCCCCC
Confidence 3567777777631 1 677777665
No 95
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.08 E-value=31 Score=19.79 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=11.8
Q ss_pred ceeccCcccccCCcccccCCcccccccH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
+.|..|+..+... ..+.+.|+.|-
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG 26 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECG 26 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCC
Confidence 3455665554422 23455565553
No 96
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=29.58 E-value=85 Score=23.63 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=22.2
Q ss_pred cccCCCCCCCCCeeeeCC--ccccHhHHHhHhcCCCC
Q 029070 139 CSHGGCVISPSNYIAHEG--RLYCKHHHNQLIKEKGN 173 (199)
Q Consensus 139 C~~C~~~l~~~~~~~~~g--~~yC~~c~~~~~~~k~~ 173 (199)
|..|++.+........+| .-.|..|+ .|+.+..
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~ 40 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAK 40 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCcc
Confidence 788888887434444454 34599999 7875554
No 97
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=29.54 E-value=37 Score=19.70 Aligned_cols=13 Identities=23% Similarity=0.577 Sum_probs=9.5
Q ss_pred CCCccccccCcee
Q 029070 7 GTQQKCMACDKTV 19 (199)
Q Consensus 7 ~~~~~C~~C~~~I 19 (199)
.....|..|++.|
T Consensus 9 ~~~~~C~~C~~~i 21 (53)
T PF00130_consen 9 SKPTYCDVCGKFI 21 (53)
T ss_dssp SSTEB-TTSSSBE
T ss_pred CCCCCCcccCccc
Confidence 3467899999998
No 98
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.47 E-value=11 Score=22.60 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=6.2
Q ss_pred eeccCcccccCCc
Q 029070 38 RCHHCKGTLKLGN 50 (199)
Q Consensus 38 ~C~~C~~~L~~~~ 50 (199)
+|..|+..|..+.
T Consensus 24 ~C~gC~~~l~~~~ 36 (56)
T PF02591_consen 24 TCSGCHMELPPQE 36 (56)
T ss_pred ccCCCCEEcCHHH
Confidence 4455555554443
No 99
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=29.40 E-value=36 Score=21.42 Aligned_cols=31 Identities=29% Similarity=0.638 Sum_probs=20.1
Q ss_pred eeccCcccccCCc---ccccCCccc--cc-ccHHHHhh
Q 029070 38 RCHHCKGTLKLGN---YNSFEGVLY--CR-PHFDQLFK 69 (199)
Q Consensus 38 ~C~~C~~~L~~~~---f~~~~g~~y--C~-~c~~~~~~ 69 (199)
+|+-|+..+..+. |...||.++ |. .|.. +++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k-~~~ 41 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK-LFK 41 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHHH-HHH
Confidence 5778888887664 666677764 63 5554 554
No 100
>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=28.94 E-value=16 Score=19.65 Aligned_cols=17 Identities=12% Similarity=0.544 Sum_probs=11.7
Q ss_pred ceeccCcccccCCcccc
Q 029070 37 FRCHHCKGTLKLGNYNS 53 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~ 53 (199)
|.|..|++++....|..
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 67888888887776653
No 101
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=27.89 E-value=16 Score=21.75 Aligned_cols=25 Identities=28% Similarity=0.495 Sum_probs=15.7
Q ss_pred ceeccCcccccCC-cccccCCccccccc
Q 029070 37 FRCHHCKGTLKLG-NYNSFEGVLYCRPH 63 (199)
Q Consensus 37 F~C~~C~~~L~~~-~f~~~~g~~yC~~c 63 (199)
++|..|++.|... .|. ..++-|..|
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC 30 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRC 30 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCC
Confidence 5777888877653 332 445667666
No 102
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.87 E-value=57 Score=31.86 Aligned_cols=47 Identities=23% Similarity=0.405 Sum_probs=26.6
Q ss_pred CccccccCceeecceeEEeCCcccccccceeccCcccccCCc--ccccCCccccccc
Q 029070 9 QQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGN--YNSFEGVLYCRPH 63 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~--f~~~~g~~yC~~c 63 (199)
..+|..|+..|. +.++|..| --|..|+-++=... |-.++|.-.|.+|
T Consensus 17 ~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPVCrpCYEYEr~eG~q~CPqC 65 (1079)
T PLN02638 17 GQVCQICGDNVG----KTVDGEPF----VACDVCAFPVCRPCYEYERKDGNQSCPQC 65 (1079)
T ss_pred CceeeecccccC----cCCCCCEE----EEeccCCCccccchhhhhhhcCCccCCcc
Confidence 348999988774 34667766 45677766553222 2233444444444
No 103
>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=27.57 E-value=51 Score=18.66 Aligned_cols=9 Identities=11% Similarity=0.327 Sum_probs=5.9
Q ss_pred cccHhHHHh
Q 029070 158 LYCKHHHNQ 166 (199)
Q Consensus 158 ~yC~~c~~~ 166 (199)
-+|..||..
T Consensus 24 dLC~~C~~~ 32 (43)
T cd02340 24 DLCESCEAK 32 (43)
T ss_pred cchHHhhCc
Confidence 357777764
No 104
>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=27.53 E-value=23 Score=23.81 Aligned_cols=42 Identities=14% Similarity=0.293 Sum_probs=28.1
Q ss_pred ccCCCCccccccCceeecceeEEeCCcccccccceeccCccccc
Q 029070 4 AFAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLK 47 (199)
Q Consensus 4 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 47 (199)
++......|..|++++..-+.+-+.+-.+. =-+|..|+.++.
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~l--rGrCr~C~~~I~ 69 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLL--RGRCRYCGAPIP 69 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHh--CCCCcccCCCCC
Confidence 344456789999999876666655544333 346788888885
No 105
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=27.05 E-value=32 Score=22.55 Aligned_cols=27 Identities=19% Similarity=0.407 Sum_probs=15.4
Q ss_pred cccCCCCCCCCC-ee-eeC---CccccHhHHH
Q 029070 139 CSHGGCVISPSN-YI-AHE---GRLYCKHHHN 165 (199)
Q Consensus 139 C~~C~~~l~~~~-~~-~~~---g~~yC~~c~~ 165 (199)
|..|+-||.... +. ..| ..-||.-||.
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 666777776443 21 122 3557888875
No 106
>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=26.91 E-value=48 Score=18.97 Aligned_cols=9 Identities=11% Similarity=0.375 Sum_probs=7.1
Q ss_pred cccHhHHHh
Q 029070 158 LYCKHHHNQ 166 (199)
Q Consensus 158 ~yC~~c~~~ 166 (199)
=+|..||.+
T Consensus 29 dLC~~C~~~ 37 (46)
T PF00569_consen 29 DLCEDCFSK 37 (46)
T ss_dssp EEEHHHHHH
T ss_pred chhhHHHhC
Confidence 369999976
No 107
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.42 E-value=35 Score=27.81 Aligned_cols=28 Identities=11% Similarity=0.177 Sum_probs=16.7
Q ss_pred cccceeccCcccccCCcccccCCccccc
Q 029070 34 KACFRCHHCKGTLKLGNYNSFEGVLYCR 61 (199)
Q Consensus 34 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~ 61 (199)
...++|..|++.+....=..+..+..|.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~ 155 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRS 155 (279)
T ss_pred CCceeccccccccccccccchhhccccc
Confidence 4568888898888654433333344443
No 108
>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=26.16 E-value=28 Score=19.58 Aligned_cols=12 Identities=25% Similarity=0.556 Sum_probs=6.6
Q ss_pred ceeccCcccccC
Q 029070 37 FRCHHCKGTLKL 48 (199)
Q Consensus 37 F~C~~C~~~L~~ 48 (199)
+.|..|+..|.+
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 567777666653
No 109
>PLN02436 cellulose synthase A
Probab=25.96 E-value=60 Score=31.71 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=14.4
Q ss_pred cccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 11 KCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
+|..|+..|. +.++|..| --|..|+-++
T Consensus 38 iCqICGD~Vg----~t~dGe~F----VACn~C~fpv 65 (1094)
T PLN02436 38 TCQICGDEIE----LTVDGEPF----VACNECAFPV 65 (1094)
T ss_pred cccccccccC----cCCCCCEE----EeeccCCCcc
Confidence 6777766552 23555555 3345554444
No 110
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.89 E-value=71 Score=26.60 Aligned_cols=14 Identities=36% Similarity=0.638 Sum_probs=11.2
Q ss_pred CcccccccHHHHhh
Q 029070 56 GVLYCRPHFDQLFK 69 (199)
Q Consensus 56 g~~yC~~c~~~~~~ 69 (199)
|..+|..|....|.
T Consensus 27 GH~~C~sCv~~l~~ 40 (309)
T TIGR00570 27 GHTLCESCVDLLFV 40 (309)
T ss_pred CCcccHHHHHHHhc
Confidence 77788888888774
No 111
>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=25.48 E-value=19 Score=20.45 Aligned_cols=9 Identities=44% Similarity=0.962 Sum_probs=2.9
Q ss_pred ccccCceee
Q 029070 12 CMACDKTVY 20 (199)
Q Consensus 12 C~~C~~~I~ 20 (199)
|..|++.|.
T Consensus 1 C~~C~~iv~ 9 (43)
T PF08746_consen 1 CEACKEIVT 9 (43)
T ss_dssp -TTT-SB-S
T ss_pred CcccchhHe
Confidence 344555554
No 112
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=24.79 E-value=61 Score=18.54 Aligned_cols=27 Identities=33% Similarity=0.662 Sum_probs=14.9
Q ss_pred cccccCceeecceeEEeC--Ccccccccc
Q 029070 11 KCMACDKTVYLVDKLTAD--NRIYHKACF 37 (199)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~--~~~~H~~CF 37 (199)
+|..|++.-..++.|.-. +..||..|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 366777744333444333 466787774
No 113
>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=24.65 E-value=45 Score=19.38 Aligned_cols=10 Identities=20% Similarity=0.364 Sum_probs=6.7
Q ss_pred cccccccHHH
Q 029070 57 VLYCRPHFDQ 66 (199)
Q Consensus 57 ~~yC~~c~~~ 66 (199)
--+|..||..
T Consensus 24 ~dLC~~Cf~~ 33 (49)
T cd02335 24 FDLCLECFSA 33 (49)
T ss_pred cchhHHhhhC
Confidence 3468888864
No 114
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=24.41 E-value=34 Score=16.29 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=9.4
Q ss_pred ceeccCcccccCC
Q 029070 37 FRCHHCKGTLKLG 49 (199)
Q Consensus 37 F~C~~C~~~L~~~ 49 (199)
|.|..|+..+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 5788888877653
No 115
>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=24.38 E-value=34 Score=15.62 Aligned_cols=12 Identities=25% Similarity=0.836 Sum_probs=6.5
Q ss_pred ceeccCcccccC
Q 029070 37 FRCHHCKGTLKL 48 (199)
Q Consensus 37 F~C~~C~~~L~~ 48 (199)
|.|..|+..+..
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 567778776653
No 116
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=24.06 E-value=35 Score=16.64 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=9.7
Q ss_pred ceeccCcccccCC
Q 029070 37 FRCHHCKGTLKLG 49 (199)
Q Consensus 37 F~C~~C~~~L~~~ 49 (199)
|+|..|++.+...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 6788888887654
No 117
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.88 E-value=37 Score=26.81 Aligned_cols=31 Identities=16% Similarity=0.171 Sum_probs=22.2
Q ss_pred cccceeccCcccccCCcccccCCcccccccH
Q 029070 34 KACFRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 34 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
++=..|..|+.++....|...+|.++|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3335678888887644466778888888885
No 118
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.68 E-value=35 Score=28.00 Aligned_cols=30 Identities=17% Similarity=0.432 Sum_probs=14.2
Q ss_pred ceeccCcccccCCcccc---cCCcccccccHHH
Q 029070 37 FRCHHCKGTLKLGNYNS---FEGVLYCRPHFDQ 66 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~---~~g~~yC~~c~~~ 66 (199)
++|..|+..|.+..|+. +....||-.|-.+
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 44555555555555432 3344444444433
No 119
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=23.50 E-value=1.6e+02 Score=21.82 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=21.5
Q ss_pred cccCCCCCCCCCe-eeeCC--ccccHhHHHhHhcC
Q 029070 139 CSHGGCVISPSNY-IAHEG--RLYCKHHHNQLIKE 170 (199)
Q Consensus 139 C~~C~~~l~~~~~-~~~~g--~~yC~~c~~~~~~~ 170 (199)
|..|++.+.+..+ ...+| ...|..|+ +||.
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH--hcCC
Confidence 8889999887644 34455 44599999 6665
No 120
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.33 E-value=9.1 Score=29.85 Aligned_cols=16 Identities=25% Similarity=0.656 Sum_probs=11.4
Q ss_pred cccceeccCcccccCC
Q 029070 34 KACFRCHHCKGTLKLG 49 (199)
Q Consensus 34 ~~CF~C~~C~~~L~~~ 49 (199)
..=|+|..|++.+.-+
T Consensus 115 ~d~ftCrvCgK~F~lQ 130 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQ 130 (267)
T ss_pred CCeeeeehhhhhhhHH
Confidence 4568888888877533
No 121
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=23.28 E-value=17 Score=25.27 Aligned_cols=19 Identities=21% Similarity=0.473 Sum_probs=11.7
Q ss_pred CCccccccCceeecceeEEe
Q 029070 8 TQQKCMACDKTVYLVDKLTA 27 (199)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~ 27 (199)
+-..|..|+++|. -+++.|
T Consensus 79 ~yG~C~~Cge~I~-~~RL~a 97 (110)
T TIGR02420 79 EYGYCEECGEEIG-LRRLEA 97 (110)
T ss_pred CCCchhccCCccc-HHHHhh
Confidence 3467888888883 444433
No 122
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=23.23 E-value=46 Score=20.42 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=6.9
Q ss_pred ccccccCceeecce
Q 029070 10 QKCMACDKTVYLVD 23 (199)
Q Consensus 10 ~~C~~C~~~I~~~~ 23 (199)
..|..|+++|..++
T Consensus 9 ~HC~VCg~aIp~de 22 (64)
T COG4068 9 RHCVVCGKAIPPDE 22 (64)
T ss_pred ccccccCCcCCCcc
Confidence 44555555554433
No 123
>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=23.22 E-value=68 Score=23.38 Aligned_cols=37 Identities=19% Similarity=0.425 Sum_probs=23.9
Q ss_pred CCCcCCCceEecCcc--e----eecCccccccCeecccCCCCC
Q 029070 110 EKCVGCKNTVYPTEK--V----SVNGTPYHKSCFKCSHGGCVI 146 (199)
Q Consensus 110 ~~C~~C~~~I~~~~~--v----~~~~~~~H~~Cf~C~~C~~~l 146 (199)
.+|..|+..+.+... + ...-...+..-+.|..|++..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 699999998865432 1 111222345577899998853
No 124
>PLN02189 cellulose synthase
Probab=23.20 E-value=73 Score=31.04 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=5.1
Q ss_pred cccccCcee
Q 029070 11 KCMACDKTV 19 (199)
Q Consensus 11 ~C~~C~~~I 19 (199)
+|..|+..|
T Consensus 36 ~C~iCgd~v 44 (1040)
T PLN02189 36 VCEICGDEI 44 (1040)
T ss_pred ccccccccc
Confidence 566665554
No 125
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=22.05 E-value=55 Score=23.48 Aligned_cols=25 Identities=12% Similarity=0.206 Sum_probs=16.9
Q ss_pred CccccccCceeecce---eEEeCCcccc
Q 029070 9 QQKCMACDKTVYLVD---KLTADNRIYH 33 (199)
Q Consensus 9 ~~~C~~C~~~I~~~~---~~~~~~~~~H 33 (199)
..+|..|+..|++|. +|...|+.|+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 346888888888765 3555666664
No 126
>PRK13796 GTPase YqeH; Provisional
Probab=21.88 E-value=51 Score=28.02 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=5.9
Q ss_pred CcccccccHH
Q 029070 56 GVLYCRPHFD 65 (199)
Q Consensus 56 g~~yC~~c~~ 65 (199)
+.++|+.||.
T Consensus 33 ~~~~C~RC~~ 42 (365)
T PRK13796 33 EEVYCQRCFR 42 (365)
T ss_pred CCeEchhhhh
Confidence 3566666663
No 127
>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=21.68 E-value=40 Score=17.25 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=3.4
Q ss_pred ceeccCcccccC
Q 029070 37 FRCHHCKGTLKL 48 (199)
Q Consensus 37 F~C~~C~~~L~~ 48 (199)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 467777777654
No 128
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.42 E-value=42 Score=26.93 Aligned_cols=28 Identities=14% Similarity=0.350 Sum_probs=23.2
Q ss_pred ceeccCcccccCCcccccCCcccccccH
Q 029070 37 FRCHHCKGTLKLGNYNSFEGVLYCRPHF 64 (199)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (199)
..|+.|+.+.....|+...+...|.+|+
T Consensus 155 ~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 155 TSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHhCcCCcCCCcceeeccCcccchhcc
Confidence 4688888888877788888888888886
No 129
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=21.33 E-value=40 Score=30.62 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=23.7
Q ss_pred ccceeccCcccccCCc-----ccccCCcccccccHH
Q 029070 35 ACFRCHHCKGTLKLGN-----YNSFEGVLYCRPHFD 65 (199)
Q Consensus 35 ~CF~C~~C~~~L~~~~-----f~~~~g~~yC~~c~~ 65 (199)
.-|+|+.|+..|.... |....|+.||..|..
T Consensus 339 Q~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~ 374 (580)
T KOG1829|consen 339 QNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQ 374 (580)
T ss_pred cCceecccCCCcccccccchhHhhhhhhhhCchhcc
Confidence 5689999999997432 445689999998864
No 130
>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=21.31 E-value=68 Score=18.66 Aligned_cols=11 Identities=9% Similarity=0.008 Sum_probs=7.7
Q ss_pred ccccHhHHHhH
Q 029070 157 RLYCKHHHNQL 167 (199)
Q Consensus 157 ~~yC~~c~~~~ 167 (199)
--+|..||...
T Consensus 24 ~dlC~~Cf~~~ 34 (49)
T cd02338 24 YDLCADCYDSG 34 (49)
T ss_pred CccchhHHhCC
Confidence 34688898754
No 131
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.07 E-value=72 Score=19.21 Aligned_cols=23 Identities=22% Similarity=0.626 Sum_probs=12.6
Q ss_pred ccccccCceeecce---eEEeCCccc
Q 029070 10 QKCMACDKTVYLVD---KLTADNRIY 32 (199)
Q Consensus 10 ~~C~~C~~~I~~~~---~~~~~~~~~ 32 (199)
..|.-|+..|++|. +|..+|+.+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~ 29 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVF 29 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEE
Confidence 35666777776654 234444444
No 132
>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=20.77 E-value=1e+02 Score=17.70 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=13.6
Q ss_pred cccCCC-CCCCCCeeee--CCccccHhHHHh
Q 029070 139 CSHGGC-VISPSNYIAH--EGRLYCKHHHNQ 166 (199)
Q Consensus 139 C~~C~~-~l~~~~~~~~--~g~~yC~~c~~~ 166 (199)
|..|+. +|.+.+|.-. .+-=+|..||.+
T Consensus 3 CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 3 CDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 444443 3444343322 234468888765
No 133
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=20.61 E-value=64 Score=15.84 Aligned_cols=13 Identities=23% Similarity=0.628 Sum_probs=9.6
Q ss_pred ceeccCcccccCC
Q 029070 37 FRCHHCKGTLKLG 49 (199)
Q Consensus 37 F~C~~C~~~L~~~ 49 (199)
|.|..|++.+.+.
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 6788888887654
No 134
>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=20.58 E-value=22 Score=19.38 Aligned_cols=30 Identities=27% Similarity=0.627 Sum_probs=17.5
Q ss_pred ccccCceeecceeEEeCCcccccccceeccCcccc
Q 029070 12 CMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTL 46 (199)
Q Consensus 12 C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 46 (199)
|..|.+.+ ....++.||..=..|..|+-.+
T Consensus 2 C~~C~~Ey-----~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEY-----FDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHH-----CSTTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHH-----cCCCCCcccCcCccCCCCCCCE
Confidence 55564444 3456888999988999997665
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.21 E-value=66 Score=28.01 Aligned_cols=37 Identities=19% Similarity=0.468 Sum_probs=24.1
Q ss_pred cCCCCccccccCceeecceeEEeCCcccccccceeccCcccccCCcc
Q 029070 5 FAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCKGTLKLGNY 51 (199)
Q Consensus 5 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f 51 (199)
++..+|+|..|+... ...|+. =|+|..|+..+....+
T Consensus 346 ~~~~~p~Cp~Cg~~m------~S~G~~----g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 346 YERVNPVCPRCGGRM------KSAGRN----GFRCKKCGTRARETLI 382 (421)
T ss_pred eEEcCCCCCccCCch------hhcCCC----CcccccccccCCcccc
Confidence 445578888887655 344544 3888888887765543
No 136
>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=20.07 E-value=51 Score=22.68 Aligned_cols=35 Identities=20% Similarity=0.292 Sum_probs=24.4
Q ss_pred CcccccccceeccCcccccCCcccccCCcccccccHHHH
Q 029070 29 NRIYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHFDQL 67 (199)
Q Consensus 29 ~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~ 67 (199)
+..+...==.|..| .+..|+..++.+.|..|-.+.
T Consensus 28 dg~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 28 DGSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred CCCEEEEEEecccc----CCCceEEECCEEEEecCCCEE
Confidence 33444433457777 557899999999999995443
Done!