Query 029735
Match_columns 189
No_of_seqs 217 out of 1313
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 02:50:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029735hhsearch_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 1E-28 2.2E-33 201.8 -0.3 126 9-174 275-402 (468)
2 KOG1701 Focal adhesion adaptor 99.9 2.8E-24 6.1E-29 175.9 1.2 124 6-168 332-466 (468)
3 KOG2272 Focal adhesion protein 99.9 2.5E-23 5.4E-28 160.0 0.1 173 7-181 72-269 (332)
4 KOG4577 Transcription factor L 99.9 2.4E-23 5.1E-28 162.8 -2.7 142 7-189 32-176 (383)
5 KOG1700 Regulatory protein MLP 99.8 1.6E-21 3.4E-26 149.9 5.0 183 2-184 1-186 (200)
6 KOG2272 Focal adhesion protein 99.8 8.1E-22 1.8E-26 151.7 0.4 117 7-163 194-311 (332)
7 KOG1044 Actin-binding LIM Zn-f 99.8 1E-20 2.2E-25 159.9 3.8 165 9-175 17-201 (670)
8 KOG1703 Adaptor protein Enigma 99.8 2.8E-20 6E-25 160.4 5.6 127 7-172 302-428 (479)
9 KOG1703 Adaptor protein Enigma 99.8 6.8E-20 1.5E-24 158.1 1.7 116 7-161 362-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 4.5E-19 9.7E-24 150.1 2.1 115 7-161 132-247 (670)
11 PF00412 LIM: LIM domain; Int 99.6 4.2E-16 9.2E-21 96.8 4.6 57 11-67 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 2.6E-15 5.7E-20 93.2 4.5 57 109-165 1-58 (58)
13 KOG4577 Transcription factor L 99.3 1.4E-13 3E-18 108.3 -0.8 80 106-186 33-113 (383)
14 smart00132 LIM Zinc-binding do 98.9 1.5E-09 3.4E-14 61.2 2.4 37 10-46 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.7 1.2E-08 2.6E-13 57.5 2.5 37 108-144 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.4 1.6E-07 3.4E-12 72.4 1.8 69 106-174 7-76 (200)
17 KOG1702 Nebulin repeat protein 98.3 9.6E-08 2.1E-12 72.3 -1.2 75 107-186 5-79 (264)
18 KOG1702 Nebulin repeat protein 98.1 4E-07 8.6E-12 69.0 -1.7 61 8-68 4-64 (264)
19 KOG0490 Transcription factor, 97.8 4.9E-06 1.1E-10 65.3 -0.3 112 13-164 1-119 (235)
20 KOG0490 Transcription factor, 94.0 0.024 5.1E-07 44.3 1.2 74 112-186 2-81 (235)
21 PF14446 Prok-RING_1: Prokaryo 90.8 0.18 4E-06 30.3 1.8 37 107-143 6-51 (54)
22 PF08394 Arc_trans_TRASH: Arch 86.0 0.55 1.2E-05 26.0 1.5 32 11-45 1-33 (37)
23 PF10367 Vps39_2: Vacuolar sor 85.4 0.7 1.5E-05 31.4 2.2 29 8-36 78-107 (109)
24 PF13240 zinc_ribbon_2: zinc-r 84.6 0.52 1.1E-05 23.2 0.9 9 11-19 2-10 (23)
25 PF09943 DUF2175: Uncharacteri 84.4 0.4 8.6E-06 32.7 0.5 31 10-40 4-35 (101)
26 PF14471 DUF4428: Domain of un 83.6 0.61 1.3E-05 27.8 1.1 29 37-66 1-30 (51)
27 PF11781 RRN7: RNA polymerase 82.3 0.85 1.8E-05 25.1 1.3 24 36-63 9-32 (36)
28 PF14471 DUF4428: Domain of un 81.1 1.3 2.9E-05 26.3 1.9 29 135-164 1-30 (51)
29 PF10367 Vps39_2: Vacuolar sor 80.9 1.3 2.9E-05 29.9 2.2 29 107-135 79-108 (109)
30 PF10235 Cript: Microtubule-as 80.6 0.78 1.7E-05 30.7 0.8 30 31-66 40-69 (90)
31 PF14835 zf-RING_6: zf-RING of 79.2 1.6 3.6E-05 27.2 1.9 33 36-68 8-40 (65)
32 PF09943 DUF2175: Uncharacteri 77.8 0.62 1.3E-05 31.8 -0.3 29 108-136 4-33 (101)
33 PRK14890 putative Zn-ribbon RN 77.7 1.7 3.6E-05 26.6 1.6 31 6-45 5-35 (59)
34 PF01258 zf-dskA_traR: Prokary 77.5 0.44 9.6E-06 26.0 -0.9 28 38-65 6-33 (36)
35 PF06677 Auto_anti-p27: Sjogre 77.2 1.8 3.8E-05 24.5 1.5 22 37-62 19-40 (41)
36 smart00504 Ubox Modified RING 74.6 4.7 0.0001 24.3 3.1 32 36-68 2-33 (63)
37 COG1645 Uncharacterized Zn-fin 73.6 2.1 4.6E-05 30.7 1.5 22 38-64 31-52 (131)
38 PF00645 zf-PARP: Poly(ADP-rib 72.9 2.1 4.6E-05 27.8 1.3 16 7-22 6-21 (82)
39 PF12773 DZR: Double zinc ribb 70.2 2.3 5E-05 24.7 0.9 24 37-64 14-37 (50)
40 COG2888 Predicted Zn-ribbon RN 69.7 4.1 9E-05 25.0 1.9 46 8-62 9-56 (61)
41 COG2191 Formylmethanofuran deh 69.6 1.6 3.6E-05 33.5 0.2 31 36-66 173-203 (206)
42 KOG0320 Predicted E3 ubiquitin 68.3 3 6.6E-05 31.5 1.4 36 32-67 128-164 (187)
43 PF13248 zf-ribbon_3: zinc-rib 64.5 5.2 0.00011 20.0 1.4 12 107-118 3-14 (26)
44 PF02069 Metallothio_Pro: Prok 63.6 4.8 0.0001 24.0 1.4 27 37-63 9-36 (52)
45 COG4847 Uncharacterized protei 62.8 2.9 6.4E-05 28.1 0.4 30 10-39 8-38 (103)
46 COG2191 Formylmethanofuran deh 62.5 2.9 6.2E-05 32.3 0.3 31 134-164 173-203 (206)
47 PF07191 zinc-ribbons_6: zinc- 62.3 2.4 5.2E-05 27.0 -0.1 33 107-146 31-63 (70)
48 PF10083 DUF2321: Uncharacteri 61.9 5.2 0.00011 29.5 1.5 38 107-145 40-80 (158)
49 PF06906 DUF1272: Protein of u 61.1 9.4 0.0002 23.1 2.3 31 38-68 8-41 (57)
50 PRK00807 50S ribosomal protein 58.4 7.4 0.00016 23.2 1.6 32 9-43 2-36 (52)
51 PRK00420 hypothetical protein; 57.9 6.3 0.00014 27.5 1.4 25 36-64 24-48 (112)
52 PF13923 zf-C3HC4_2: Zinc fing 57.6 14 0.0003 20.1 2.5 31 38-68 1-31 (39)
53 PF05502 Dynactin_p62: Dynacti 57.4 4.9 0.00011 35.3 0.9 38 107-145 27-64 (483)
54 PF06750 DiS_P_DiS: Bacterial 56.3 4.6 9.9E-05 27.1 0.4 42 4-47 29-70 (92)
55 PF13920 zf-C3HC4_3: Zinc fing 55.2 14 0.00031 21.3 2.4 32 36-68 3-35 (50)
56 cd00162 RING RING-finger (Real 51.9 15 0.00033 19.7 2.2 30 38-67 2-31 (45)
57 smart00531 TFIIE Transcription 51.8 4.7 0.0001 29.4 -0.1 35 9-46 100-134 (147)
58 PF10886 DUF2685: Protein of u 51.1 10 0.00022 22.8 1.3 24 10-33 3-26 (54)
59 KOG4443 Putative transcription 51.1 6.5 0.00014 35.5 0.7 22 124-145 106-127 (694)
60 KOG3579 Predicted E3 ubiquitin 50.5 8.2 0.00018 31.4 1.1 30 10-39 270-299 (352)
61 COG4068 Uncharacterized protei 49.5 12 0.00026 22.9 1.4 22 2-23 2-23 (64)
62 COG5152 Uncharacterized conser 48.4 6.1 0.00013 30.4 0.1 32 36-68 197-228 (259)
63 KOG2893 Zn finger protein [Gen 48.0 6.5 0.00014 31.2 0.2 36 107-145 11-46 (341)
64 PF07754 DUF1610: Domain of un 47.1 12 0.00026 18.5 1.0 9 11-19 1-9 (24)
65 KOG1813 Predicted E3 ubiquitin 45.4 12 0.00025 30.7 1.2 31 36-67 242-272 (313)
66 PF07503 zf-HYPF: HypF finger; 43.6 4.8 0.0001 21.9 -0.8 30 11-45 2-31 (35)
67 cd02249 ZZ Zinc finger, ZZ typ 43.5 20 0.00044 20.4 1.8 11 154-164 23-33 (46)
68 KOG0978 E3 ubiquitin ligase in 42.8 8.1 0.00017 35.4 -0.0 49 36-120 644-692 (698)
69 COG4357 Zinc finger domain con 42.8 2.5 5.4E-05 28.5 -2.4 50 108-157 37-86 (105)
70 PF14634 zf-RING_5: zinc-RING 42.4 17 0.00036 20.4 1.3 30 38-67 2-33 (44)
71 PF04810 zf-Sec23_Sec24: Sec23 42.3 28 0.00061 19.3 2.2 30 107-141 3-32 (40)
72 PRK00398 rpoP DNA-directed RNA 42.3 12 0.00027 21.3 0.7 27 10-45 5-31 (46)
73 PRK14559 putative protein seri 41.8 15 0.00033 33.5 1.6 13 107-119 42-54 (645)
74 PF11023 DUF2614: Protein of u 41.6 10 0.00022 26.4 0.3 35 1-46 62-96 (114)
75 PRK02935 hypothetical protein; 41.2 12 0.00026 25.8 0.6 33 3-46 65-97 (110)
76 PF06827 zf-FPG_IleRS: Zinc fi 40.5 11 0.00023 19.4 0.3 12 107-118 2-13 (30)
77 PF13834 DUF4193: Domain of un 40.1 12 0.00026 25.4 0.5 29 34-62 69-98 (99)
78 COG4357 Zinc finger domain con 39.1 3.7 8E-05 27.7 -2.0 50 11-60 38-87 (105)
79 PRK04023 DNA polymerase II lar 38.4 30 0.00066 33.2 2.9 35 6-63 624-658 (1121)
80 COG0068 HypF Hydrogenase matur 38.2 11 0.00023 34.7 0.0 84 7-143 100-183 (750)
81 KOG3002 Zn finger protein [Gen 37.8 26 0.00056 28.9 2.2 32 36-67 49-80 (299)
82 PF14255 Cys_rich_CPXG: Cystei 37.7 17 0.00037 21.6 0.9 33 10-45 2-34 (52)
83 PRK06266 transcription initiat 37.2 11 0.00023 28.6 -0.1 30 9-46 118-147 (178)
84 smart00291 ZnF_ZZ Zinc-binding 37.1 33 0.00072 19.3 2.0 11 107-117 5-15 (44)
85 PF08271 TF_Zn_Ribbon: TFIIB z 36.1 26 0.00056 19.6 1.4 11 36-46 20-30 (43)
86 PF12674 Zn_ribbon_2: Putative 36.0 20 0.00043 23.5 1.0 28 136-163 3-35 (81)
87 PF00130 C1_1: Phorbol esters/ 35.9 24 0.00052 20.4 1.3 13 6-18 9-21 (53)
88 TIGR00570 cdk7 CDK-activating 35.4 35 0.00076 28.2 2.6 13 107-119 44-56 (309)
89 PF09723 Zn-ribbon_8: Zinc rib 35.4 15 0.00033 20.6 0.4 10 36-45 6-15 (42)
90 KOG2462 C2H2-type Zn-finger pr 34.7 22 0.00048 28.8 1.3 16 34-49 129-144 (279)
91 TIGR02098 MJ0042_CXXC MJ0042 f 34.4 16 0.00035 19.7 0.4 31 10-45 4-35 (38)
92 cd00472 Ribosomal_L24e_L24 Rib 34.1 27 0.00058 21.0 1.3 24 9-32 4-30 (54)
93 PF04502 DUF572: Family of unk 33.8 29 0.00062 28.9 1.9 39 8-46 40-88 (324)
94 PF04570 DUF581: Protein of un 33.5 29 0.00062 21.2 1.4 27 135-161 18-47 (58)
95 smart00834 CxxC_CXXC_SSSS Puta 32.6 18 0.00039 19.7 0.4 9 10-18 7-15 (41)
96 PRK14714 DNA polymerase II lar 32.6 35 0.00076 33.6 2.4 11 108-118 711-721 (1337)
97 PRK12775 putative trifunctiona 32.3 46 0.001 32.2 3.2 40 4-46 792-832 (1006)
98 PF01286 XPA_N: XPA protein N- 31.7 25 0.00055 19.0 0.8 11 9-19 4-14 (34)
99 TIGR02605 CxxC_CxxC_SSSS putat 31.4 20 0.00042 20.9 0.4 10 36-45 6-15 (52)
100 PF08746 zf-RING-like: RING-li 31.4 17 0.00038 20.6 0.2 11 11-21 1-11 (43)
101 TIGR01206 lysW lysine biosynth 31.1 40 0.00086 20.3 1.7 31 9-46 3-33 (54)
102 PF00569 ZZ: Zinc finger, ZZ t 29.9 42 0.00091 19.1 1.6 10 56-65 28-37 (46)
103 PF00096 zf-C2H2: Zinc finger, 29.5 24 0.00051 16.4 0.4 12 36-47 1-12 (23)
104 COG2075 RPL24A Ribosomal prote 29.4 48 0.001 20.8 1.9 22 37-58 5-29 (66)
105 PF02591 DUF164: Putative zinc 29.4 9.2 0.0002 22.9 -1.3 26 37-62 24-52 (56)
106 TIGR00373 conserved hypothetic 29.4 16 0.00034 27.1 -0.3 30 9-46 110-139 (158)
107 PLN02195 cellulose synthase A 29.0 55 0.0012 31.4 3.0 32 6-45 4-35 (977)
108 PF01246 Ribosomal_L24e: Ribos 28.1 31 0.00067 22.0 0.9 24 9-32 4-30 (71)
109 PF10080 DUF2318: Predicted me 27.0 52 0.0011 22.5 1.9 36 27-66 27-62 (102)
110 PF08792 A2L_zn_ribbon: A2L zi 27.0 54 0.0012 17.4 1.6 23 37-62 5-27 (33)
111 PRK12495 hypothetical protein; 26.6 36 0.00077 26.7 1.2 24 36-64 43-66 (226)
112 PLN02638 cellulose synthase A 26.5 59 0.0013 31.6 2.8 30 8-45 17-46 (1079)
113 PRK00085 recO DNA repair prote 26.0 32 0.0007 26.9 0.9 31 33-63 147-177 (247)
114 PRK14891 50S ribosomal protein 25.9 39 0.00084 24.1 1.2 25 9-33 5-32 (131)
115 cd02340 ZZ_NBR1_like Zinc fing 25.8 60 0.0013 18.3 1.8 11 108-118 2-12 (43)
116 TIGR02420 dksA RNA polymerase- 25.7 18 0.00038 25.0 -0.6 18 8-26 80-97 (110)
117 PF13717 zinc_ribbon_4: zinc-r 25.7 33 0.00072 18.6 0.6 30 10-44 4-34 (36)
118 PF12677 DUF3797: Domain of un 25.3 56 0.0012 19.2 1.6 27 9-35 14-42 (49)
119 smart00659 RPOLCX RNA polymera 25.2 47 0.001 18.9 1.3 8 11-18 5-12 (44)
120 PLN02436 cellulose synthase A 24.5 68 0.0015 31.2 2.8 19 9-31 37-55 (1094)
121 smart00249 PHD PHD zinc finger 24.4 51 0.0011 17.8 1.4 26 11-36 2-29 (47)
122 PF00628 PHD: PHD-finger; Int 24.0 69 0.0015 18.2 1.9 26 11-36 2-29 (51)
123 PF10122 Mu-like_Com: Mu-like 23.8 29 0.00062 20.6 0.2 26 36-63 5-31 (51)
124 PF07649 C1_3: C1-like domain; 23.8 40 0.00087 17.2 0.7 12 36-47 1-12 (30)
125 PF06689 zf-C4_ClpX: ClpX C4-t 23.7 1.2E+02 0.0025 16.9 2.7 30 135-164 3-34 (41)
126 COG1381 RecO Recombinational D 23.6 39 0.00084 26.9 1.0 31 33-63 152-182 (251)
127 cd02335 ZZ_ADA2 Zinc finger, Z 23.6 81 0.0017 18.2 2.1 10 155-164 25-34 (49)
128 PF13719 zinc_ribbon_5: zinc-r 23.4 43 0.00094 18.1 0.8 31 10-45 4-35 (37)
129 PF13894 zf-C2H2_4: C2H2-type 23.3 36 0.00079 15.4 0.5 11 36-46 1-11 (24)
130 COG0266 Nei Formamidopyrimidin 23.3 51 0.0011 26.8 1.6 28 105-133 244-271 (273)
131 PLN02189 cellulose synthase 23.2 74 0.0016 30.8 2.8 9 10-18 36-44 (1040)
132 PF09889 DUF2116: Uncharacteri 22.9 52 0.0011 20.1 1.2 13 32-47 3-15 (59)
133 COG1571 Predicted DNA-binding 22.8 53 0.0011 28.4 1.6 37 4-50 346-382 (421)
134 KOG3476 Microtubule-associated 22.5 14 0.00031 24.4 -1.4 25 36-66 55-79 (100)
135 PRK14873 primosome assembly pr 21.8 52 0.0011 30.3 1.5 25 37-64 394-418 (665)
136 COG3813 Uncharacterized protei 21.8 87 0.0019 20.0 2.0 31 38-68 8-41 (84)
137 PF12874 zf-met: Zinc-finger o 21.6 40 0.00087 15.9 0.4 13 36-48 1-13 (25)
138 cd02336 ZZ_RSC8 Zinc finger, Z 21.1 1.4E+02 0.003 17.1 2.7 28 136-163 3-32 (45)
139 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.9 97 0.0021 18.0 2.0 10 155-164 27-36 (48)
140 PF01927 Mut7-C: Mut7-C RNAse 20.8 68 0.0015 23.2 1.7 37 107-143 92-134 (147)
141 PF10764 Gin: Inhibitor of sig 20.6 88 0.0019 18.0 1.8 27 136-164 2-28 (46)
142 PF08209 Sgf11: Sgf11 (transcr 20.3 29 0.00063 18.6 -0.3 16 36-51 5-20 (33)
143 PRK13796 GTPase YqeH; Provisio 20.3 53 0.0012 27.7 1.2 10 55-64 33-42 (365)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.94 E-value=1e-28 Score=201.76 Aligned_cols=126 Identities=21% Similarity=0.559 Sum_probs=114.4
Q ss_pred CCcccCCccccccc-eEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcccccc
Q 029735 9 QKCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVE 87 (189)
Q Consensus 9 ~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~ 87 (189)
.+|.+|+|.|+... .+.||++.||..||+|..|++.|.++.||.+|+++||+.||....
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-------------------- 334 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-------------------- 334 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--------------------
Confidence 48999999997554 589999999999999999999999999999999999999998765
Q ss_pred CccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeee-cCCccccHhHHHhhhc
Q 029735 88 RSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVA-HEHRLYCRHHHNQLFK 166 (189)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~-~dg~~yC~~c~~~~~~ 166 (189)
.+|..|+++|.+. .+.+.|+.||+.||+|..|++.|++..|.. .++++||..||+++|+
T Consensus 335 -------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA 394 (468)
T KOG1701|consen 335 -------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA 394 (468)
T ss_pred -------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC
Confidence 7899999999864 379999999999999999999999987865 5799999999999999
Q ss_pred CCCCCCCC
Q 029735 167 QKGNFSQL 174 (189)
Q Consensus 167 ~k~~~~~~ 174 (189)
+||+.+..
T Consensus 395 PrCs~C~~ 402 (468)
T KOG1701|consen 395 PRCSVCGN 402 (468)
T ss_pred cchhhccC
Confidence 99986543
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.88 E-value=2.8e-24 Score=175.89 Aligned_cols=124 Identities=25% Similarity=0.622 Sum_probs=110.3
Q ss_pred CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeee-cCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735 6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCS-FEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV 84 (189)
Q Consensus 6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~ 84 (189)
....+|..|++.|+ +.+|.|+|+.||+.||+|-.|.+.|++..|.+ .++++||.+||++.|+
T Consensus 332 ~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA---------------- 394 (468)
T KOG1701|consen 332 DTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA---------------- 394 (468)
T ss_pred HHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC----------------
Confidence 34568999999995 78899999999999999999999999989975 5999999999999998
Q ss_pred cccCccCcCCcccccccCCCCCCCCccCCcccccCc------eeeccCccccccCceeCCCCCcCCC----CCeeecCCc
Q 029735 85 RVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE------KVAVDGTSYHKACFRCTHGGCVISP----SNYVAHEHR 154 (189)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~g~~~H~~Cf~C~~C~~~l~~----~~~~~~dg~ 154 (189)
++|+.|+++|.+.+ +|.++++.||.+|++|.+|+.+|+. ...|..||.
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 89999999998754 4789999999999999999999984 347889999
Q ss_pred cccHhHHHhhhcCC
Q 029735 155 LYCRHHHNQLFKQK 168 (189)
Q Consensus 155 ~yC~~c~~~~~~~k 168 (189)
++|+.|..++....
T Consensus 453 llCk~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 453 LLCKTCHLKRLQAG 466 (468)
T ss_pred eeechhhhhhhccc
Confidence 99999998876543
No 3
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.86 E-value=2.5e-23 Score=160.04 Aligned_cols=173 Identities=17% Similarity=0.253 Sum_probs=128.4
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhcc-----CCCCCCCCCCC
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMT-----GSLDKSFEGTP 81 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~-----~~~~~~~~~~~ 81 (189)
.+|.|++|++.| .+.++.+++.+||+.||+|..|++.|.+..|+-.+|+.+|..|.++..+.. |..+...+...
T Consensus 72 faPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~ 150 (332)
T KOG2272|consen 72 FAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ 150 (332)
T ss_pred hchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence 368899999999 599999999999999999999999999999999999999999998754321 12222222222
Q ss_pred ccccccCccCcCC-------------ccccc-ccC------CCCCCCCccCCcccccCceeeccCccccccCceeCCCCC
Q 029735 82 KTVRVERSADQVT-------------NSRVS-SMF------AGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGC 141 (189)
Q Consensus 82 ~~~~~~~~~~~~~-------------~~~~~-~~~------~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~ 141 (189)
-+...+.|+++.- ...+. +++ .-+.+.|..|.++|... .|.++|+.||.+.|+|+.|.+
T Consensus 151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~Cek 229 (332)
T KOG2272|consen 151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEK 229 (332)
T ss_pred cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHH-HHHHhccccchhheeehhcCC
Confidence 3333334443110 00000 110 01238999999999743 378999999999999999999
Q ss_pred cCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCChhHHH
Q 029735 142 VISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVE 181 (189)
Q Consensus 142 ~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~~~~~~ 181 (189)
|+-+-..+++.|.+||+.||.++||.-|-.+...-.-.|.
T Consensus 230 PFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv 269 (332)
T KOG2272|consen 230 PFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVV 269 (332)
T ss_pred cccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHH
Confidence 9988889999999999999999999998765544444443
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.85 E-value=2.4e-23 Score=162.79 Aligned_cols=142 Identities=24% Similarity=0.511 Sum_probs=117.0
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
..++|++|.+.|.+.-++.++++.||..|++|+.|..+|.. ..+.+++.+||+.+|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC------------------
Confidence 56899999999987778999999999999999999999975 46689999999999999998
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCcee-eccCccccccCceeCCCCCcCCCC-Cee-ecCCccccHhHHHh
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPS-NYV-AHEHRLYCRHHHNQ 163 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~-~~~-~~dg~~yC~~c~~~ 163 (189)
.+|..|.+.|.+...| .+.+.+||..||.|..|+++|..+ .|| +.|+++.|+.+|+.
T Consensus 93 --------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~ 152 (383)
T KOG4577|consen 93 --------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET 152 (383)
T ss_pred --------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence 8999999999987755 688999999999999999999874 465 56899999999998
Q ss_pred hhcCCCCCCCCCChhHHHHHhhccCC
Q 029735 164 LFKQKGNFSQLDNHEQVEAVTENATA 189 (189)
Q Consensus 164 ~~~~k~~~~~~~~~~~~~~~~~~~~~ 189 (189)
.-..-+. +..+.....|.+..|||
T Consensus 153 Ak~k~~~--~l~gd~~nKRPRTTItA 176 (383)
T KOG4577|consen 153 AKQKHCN--ELEGDASNKRPRTTITA 176 (383)
T ss_pred HHhcccc--ccccccccCCCcceeeH
Confidence 8665554 22222333444444443
No 5
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.84 E-value=1.6e-21 Score=149.86 Aligned_cols=183 Identities=44% Similarity=0.824 Sum_probs=145.4
Q ss_pred CcCCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC-CCCCCCCC
Q 029735 2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS-LDKSFEGT 80 (189)
Q Consensus 2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~-~~~~~~~~ 80 (189)
|++......|..|++.|+..+.+...|..||+.||+|..|.+.|....+...++.+||..+|...+++... ....++..
T Consensus 1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~ 80 (200)
T KOG1700|consen 1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKA 80 (200)
T ss_pred CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccccc
Confidence 45677788999999999999998899999999999999999999999999999999999998888877653 33433322
Q ss_pred CccccccCccC--cCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccH
Q 029735 81 PKTVRVERSAD--QVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158 (189)
Q Consensus 81 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~ 158 (189)
..+.....+.. .+........+.++...|.+|.+.+++.+.+...+..||..||+|+.|+..|....+...+|.+||.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~ 160 (200)
T KOG1700|consen 81 GGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCK 160 (200)
T ss_pred CCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccc
Confidence 22222222222 1222234455667779999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhcCCCCCCCCCChhHHHHHh
Q 029735 159 HHHNQLFKQKGNFSQLDNHEQVEAVT 184 (189)
Q Consensus 159 ~c~~~~~~~k~~~~~~~~~~~~~~~~ 184 (189)
.++..++-.+..+..+..+....+.+
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (200)
T KOG1700|consen 161 HHFAQLFKGKGNYNEGFGARENKEAA 186 (200)
T ss_pred hhhheeecCCCcccccchhhhhhhhh
Confidence 99998887777777666655544443
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=8.1e-22 Score=151.73 Aligned_cols=117 Identities=20% Similarity=0.506 Sum_probs=108.0
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
+.++|+.|.++| .+.++.++|+.||.+.|+|+.|-+|+-+...|++.|..||+.+|.++++
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 4678899999999999999999999988899999999999999999998
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCC-CCeeecCCccccHhHHHh
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHHNQ 163 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~dg~~yC~~c~~~ 163 (189)
..|-.|+.+|.+ +.+.++++.|.++||+|+.|.+.|.. ..|++.|-.|.|+.||.+
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 --------------------NLCFICNRVIGG-DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred --------------------hhheecCCccCc-cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 899999999974 55899999999999999999999987 468999999999999974
No 7
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=1e-20 Score=159.92 Aligned_cols=165 Identities=18% Similarity=0.354 Sum_probs=114.9
Q ss_pred CCcccCCccccccceEeeCCccccccccccccccccccCCCeeecC-CeeeecccHHHHh------------hccCCC--
Q 029735 9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE-GVLYCKPHFDQLF------------KMTGSL-- 73 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~-g~~yC~~cy~~~~------------~~~~~~-- 73 (189)
-.|.+|.+... +++|.+.+++||..||.|..|+..|..+.|+.++ .++|+........ .++|..
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 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 46999999994 9999999999999999999999999999988774 4677763322211 111110
Q ss_pred --CCCCCCCCccccccCccC-c--CCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCe
Q 029735 74 --DKSFEGTPKTVRVERSAD-Q--VTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNY 148 (189)
Q Consensus 74 --~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~ 148 (189)
..+|....+++..++... + +.+.........++..|++|++.|..+..+.++++.||..||+|..|...|.+ .|
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 111111111111111110 0 00000111111234789999999998888899999999999999999999986 58
Q ss_pred eecCCccccHhHHHhhhcCCCCCCCCC
Q 029735 149 VAHEHRLYCRHHHNQLFKQKGNFSQLD 175 (189)
Q Consensus 149 ~~~dg~~yC~~c~~~~~~~k~~~~~~~ 175 (189)
+..||.|||+.+|++.||-||..++.+
T Consensus 175 ~skdg~pyce~dy~~~fgvkc~~c~~f 201 (670)
T KOG1044|consen 175 MSKDGVPYCEKDYQAKFGVKCEECEKF 201 (670)
T ss_pred eccCCCcchhhhhhhhcCeehHHhhhh
Confidence 999999999999999999999755443
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.80 E-value=2.8e-20 Score=160.44 Aligned_cols=127 Identities=24% Similarity=0.536 Sum_probs=116.9
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
..+.|..|.+.|.....+.++++.||+.+|.|..|...|....|...+|.+||..|+.+.++
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 45899999999953388999999999999999999999998899999999999999999987
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK 166 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~ 166 (189)
+.|.+|+++|.+. .|.+.++.||++||.|..|+++|....|+..||.+||+.||+++++
T Consensus 364 --------------------p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 364 --------------------PNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred --------------------ccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc
Confidence 8999999999864 4888899999999999999999999999999999999999999999
Q ss_pred CCCCCC
Q 029735 167 QKGNFS 172 (189)
Q Consensus 167 ~k~~~~ 172 (189)
+++.++
T Consensus 423 ~~~~~~ 428 (479)
T KOG1703|consen 423 TKCDYC 428 (479)
T ss_pred ccchhc
Confidence 888655
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.77 E-value=6.8e-20 Score=158.05 Aligned_cols=116 Identities=28% Similarity=0.671 Sum_probs=106.7
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
..++|.+|+++|. ++.|.+.++.||++||.|..|+++|.+..|+..++.+||+.||.+++.
T Consensus 362 ~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~------------------ 422 (479)
T KOG1703|consen 362 FRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT------------------ 422 (479)
T ss_pred hCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc------------------
Confidence 4689999999994 888999999999999999999999999999999999999999999986
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCce-eeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHH
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~ 161 (189)
++|..|.++|..... +.+++..||..||+|..|.+.|..+.|+...++|+|..|+
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 689999998874433 7999999999999999999999999999999999999875
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.74 E-value=4.5e-19 Score=150.06 Aligned_cols=115 Identities=23% Similarity=0.560 Sum_probs=104.6
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
+...|++|++.|..+..|.|+++.||..||+|..|+..| .+.|..++|.+||+.||++.|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcC------------------
Confidence 467899999999999999999999999999999999999 5789999999999999999998
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCC-CCeeecCCccccHhHH
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHH 161 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~dg~~yC~~c~ 161 (189)
.+|..|.+.|.+. .+.+.|++||+.|-+|+.|+.+++. +.+|..+..+|-..|-
T Consensus 193 --------------------vkc~~c~~fisgk-vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~ 247 (670)
T KOG1044|consen 193 --------------------VKCEECEKFISGK-VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCK 247 (670)
T ss_pred --------------------eehHHhhhhhhhh-hhhccCcccCcchhhhhhhccccccchheeeccccccCCccc
Confidence 8999999999864 3789999999999999999999987 4578888888887775
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=99.62 E-value=4.2e-16 Score=96.78 Aligned_cols=57 Identities=30% Similarity=0.771 Sum_probs=52.7
Q ss_pred cccCCccccccceE-eeCCccccccccccccccccccCCCeeecCCeeeecccHHHHh
Q 029735 11 CKACEKTVYLVDQL-TADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 11 C~~C~~~I~~~~~~-~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 67 (189)
|.+|+++|.+++.+ .++|+.||++||+|..|+++|.+..|+..+|++||..||.++|
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 7999999999999999999999888999999999999998875
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=99.57 E-value=2.6e-15 Score=93.18 Aligned_cols=57 Identities=26% Similarity=0.708 Sum_probs=52.9
Q ss_pred CccCCcccccCcee-eccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhh
Q 029735 109 CVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165 (189)
Q Consensus 109 C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~ 165 (189)
|.+|+++|.+.+.+ .+.|+.||++||+|..|+++|..+.++..+|++||+.||.++|
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 78999999988765 6999999999999999999999988999999999999999886
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.33 E-value=1.4e-13 Score=108.32 Aligned_cols=80 Identities=16% Similarity=0.337 Sum_probs=73.3
Q ss_pred CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCCCChhHHHHHh
Q 029735 106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQLDNHEQVEAVT 184 (189)
Q Consensus 106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~~~~~~~~~~~ 184 (189)
.++|++|.+.|.+...+.++++.||..|++|+.|+.+|.. ..+.++|.+||+++|.++||+||+ ...|+.+.+|.|.+
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 3899999999998776789999999999999999999986 578899999999999999999999 68899999999987
Q ss_pred hc
Q 029735 185 EN 186 (189)
Q Consensus 185 ~~ 186 (189)
++
T Consensus 112 qd 113 (383)
T KOG4577|consen 112 QD 113 (383)
T ss_pred hc
Confidence 75
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=98.86 E-value=1.5e-09 Score=61.25 Aligned_cols=37 Identities=38% Similarity=0.730 Sum_probs=33.5
Q ss_pred CcccCCcccccc-ceEeeCCcccccccccccccccccc
Q 029735 10 KCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 10 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
+|.+|+++|.++ ..+.++++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999876 6788999999999999999999985
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=98.69 E-value=1.2e-08 Score=57.48 Aligned_cols=37 Identities=27% Similarity=0.633 Sum_probs=32.9
Q ss_pred CCccCCcccccC-ceeeccCccccccCceeCCCCCcCC
Q 029735 108 KCVACKKTVYPI-EKVAVDGTSYHKACFRCTHGGCVIS 144 (189)
Q Consensus 108 ~C~~C~~~I~~~-~~v~~~g~~~H~~Cf~C~~C~~~l~ 144 (189)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 488999999986 4578899999999999999999885
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.36 E-value=1.6e-07 Score=72.45 Aligned_cols=69 Identities=43% Similarity=0.809 Sum_probs=62.0
Q ss_pred CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCC
Q 029735 106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQL 174 (189)
Q Consensus 106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~ 174 (189)
...|..|++.|+..+++...|..||+.||+|..|.+.|..+.+...++.+||..++...++++.. +..+
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~ 76 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG 76 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence 36899999999998888899999999999999999999998888999999999988888888876 5554
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.27 E-value=9.6e-08 Score=72.32 Aligned_cols=75 Identities=28% Similarity=0.585 Sum_probs=62.0
Q ss_pred CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCChhHHHHHhhc
Q 029735 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEAVTEN 186 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~~~~~~~~~~~ 186 (189)
..|..|++.+++.|.|.-+++.||..||+|..|+.+|...++...|.++||..+|.+.. +.-...-+...|+.+|
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~-----at~~adTPEm~Rik~n 79 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV-----ATVMADTPEMRRIKEN 79 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce-----eeeecCCHHHHHHHhh
Confidence 57889999999999999999999999999999999999888888999999999997654 3333444555555554
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.06 E-value=4e-07 Score=69.01 Aligned_cols=61 Identities=36% Similarity=0.811 Sum_probs=55.5
Q ss_pred CCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735 8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 68 (189)
...|..|++.+++.|.|.-+++.||..||+|..|+-+|.-..|-..+.++||..+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 4678999999999999999999999999999999999988888888999999999976654
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.76 E-value=4.9e-06 Score=65.31 Aligned_cols=112 Identities=18% Similarity=0.502 Sum_probs=86.2
Q ss_pred cCCccccccceEeeCCcccccccccccccccccc--CCCeeecCCeeeecccHHH--HhhccCCCCCCCCCCCccccccC
Q 029735 13 ACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK--LSNYCSFEGVLYCKPHFDQ--LFKMTGSLDKSFEGTPKTVRVER 88 (189)
Q Consensus 13 ~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~--~~~~~~~~~~~~~~~~~~~~~~~ 88 (189)
.|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.+ .+.
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~-------------------- 59 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS-------------------- 59 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc--------------------
Confidence 3677886666678889999999999999999997 445555 999999999987 332
Q ss_pred ccCcCCcccccccCCCCCCCCccCCcccccCcee-eccCccccccCceeCCCCCcCCC-CCeeec-CCccccHhHHHhh
Q 029735 89 SADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISP-SNYVAH-EHRLYCRHHHNQL 164 (189)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~-dg~~yC~~c~~~~ 164 (189)
.+|.+|...+...+.+ .+..+. |..||.|..|...+.. ..+.+. +.+.+|.+++.+.
T Consensus 60 ------------------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 ------------------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ------------------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 6899999988665544 455555 9999999999886655 345444 4589998887654
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.04 E-value=0.024 Score=44.31 Aligned_cols=74 Identities=14% Similarity=0.362 Sum_probs=53.6
Q ss_pred CCcccccCceeeccCccccccCceeCCCCCcCC--CCCeeecCCccccHhHHHh--hhcCCCCC-CCCC-ChhHHHHHhh
Q 029735 112 CKKTVYPIEKVAVDGTSYHKACFRCTHGGCVIS--PSNYVAHEHRLYCRHHHNQ--LFKQKGNF-SQLD-NHEQVEAVTE 185 (189)
Q Consensus 112 C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~--~~~~~~~dg~~yC~~c~~~--~~~~k~~~-~~~~-~~~~~~~~~~ 185 (189)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..++.+ .+..++.- .-.. +-..++++++
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~ 80 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFE 80 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhc
Confidence 566676655566679999999999999999997 444555 999999999998 77777763 3332 3334666554
Q ss_pred c
Q 029735 186 N 186 (189)
Q Consensus 186 ~ 186 (189)
+
T Consensus 81 ~ 81 (235)
T KOG0490|consen 81 K 81 (235)
T ss_pred C
Confidence 3
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.78 E-value=0.18 Score=30.31 Aligned_cols=37 Identities=27% Similarity=0.626 Sum_probs=25.7
Q ss_pred CCCccCCcccccCceee---ccCccccccCc----eeCC--CCCcC
Q 029735 107 DKCVACKKTVYPIEKVA---VDGTSYHKACF----RCTH--GGCVI 143 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~---~~g~~~H~~Cf----~C~~--C~~~l 143 (189)
.+|..|+++|.+.+.+. .-+..||++|+ .|.. |+..+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 78999999997544332 45788999887 4554 55443
No 22
>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=85.99 E-value=0.55 Score=26.00 Aligned_cols=32 Identities=25% Similarity=0.476 Sum_probs=22.3
Q ss_pred cccCCccccccc-eEeeCCccccccccccccccccc
Q 029735 11 CKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 11 C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
|.-|+++|.+.. .+...++.||. -|..|...|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~f---CC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYF---CCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEE---ECHHHHHHH
Confidence 678999996443 47889999994 445555554
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=85.44 E-value=0.7 Score=31.37 Aligned_cols=29 Identities=24% Similarity=0.417 Sum_probs=15.7
Q ss_pred CCCcccCCccccccce-EeeCCcccccccc
Q 029735 8 TQKCKACEKTVYLVDQ-LTADNKVYHKACF 36 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF 36 (189)
...|..|+++|..... +...|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4457777777754333 2334455666654
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.61 E-value=0.52 Score=23.16 Aligned_cols=9 Identities=22% Similarity=0.785 Sum_probs=6.1
Q ss_pred cccCCcccc
Q 029735 11 CKACEKTVY 19 (189)
Q Consensus 11 C~~C~~~I~ 19 (189)
|+.|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 667777774
No 25
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=84.37 E-value=0.4 Score=32.74 Aligned_cols=31 Identities=32% Similarity=0.568 Sum_probs=19.6
Q ss_pred CcccCCccccccceEeeC-Ccccccccccccc
Q 029735 10 KCKACEKTVYLVDQLTAD-NKVYHKACFRCHH 40 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~-~~~~H~~CF~C~~ 40 (189)
+|..|+++|+.|+.+.+. +..-|-.||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 577777777777765443 3456777776543
No 26
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=83.56 E-value=0.61 Score=27.76 Aligned_cols=29 Identities=24% Similarity=0.584 Sum_probs=22.4
Q ss_pred ccccccccccCCC-eeecCCeeeecccHHHH
Q 029735 37 RCHHCKGTLKLSN-YCSFEGVLYCKPHFDQL 66 (189)
Q Consensus 37 ~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~ 66 (189)
.|+.|+..++--. +-..|| +.|..|+.++
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 4888999885433 557787 7999999887
No 27
>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=82.28 E-value=0.85 Score=25.05 Aligned_cols=24 Identities=25% Similarity=0.483 Sum_probs=17.7
Q ss_pred cccccccccccCCCeeecCCeeeecccH
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHF 63 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy 63 (189)
+.|..|+.. .|...+|..||..|-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCc
Confidence 347777665 467889999998775
No 28
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=81.14 E-value=1.3 Score=26.30 Aligned_cols=29 Identities=17% Similarity=0.423 Sum_probs=22.4
Q ss_pred eeCCCCCcCCC-CCeeecCCccccHhHHHhh
Q 029735 135 RCTHGGCVISP-SNYVAHEHRLYCRHHHNQL 164 (189)
Q Consensus 135 ~C~~C~~~l~~-~~~~~~dg~~yC~~c~~~~ 164 (189)
.|..|+..++. ..+-..|| ..|..|+.++
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 37888888876 33567788 6899999887
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=80.86 E-value=1.3 Score=29.93 Aligned_cols=29 Identities=28% Similarity=0.437 Sum_probs=20.4
Q ss_pred CCCccCCcccccCce-eeccCccccccCce
Q 029735 107 DKCVACKKTVYPIEK-VAVDGTSYHKACFR 135 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~ 135 (189)
..|..|+++|..... +...|..+|..|++
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 679999999876443 34567778887753
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=80.60 E-value=0.78 Score=30.69 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=19.3
Q ss_pred ccccccccccccccccCCCeeecCCeeeecccHHHH
Q 029735 31 YHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66 (189)
Q Consensus 31 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 66 (189)
|-..=-.|..|...+.. .|..||..|..+.
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk 69 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK 69 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc
Confidence 44433467888777743 2567999996544
No 31
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=79.15 E-value=1.6 Score=27.22 Aligned_cols=33 Identities=18% Similarity=0.326 Sum_probs=14.7
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 68 (189)
++|+.|...|...--...=...||..|..+.++
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 578888887754433344557788888766554
No 32
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=77.78 E-value=0.62 Score=31.81 Aligned_cols=29 Identities=31% Similarity=0.627 Sum_probs=19.0
Q ss_pred CCccCCcccccCceeec-cCccccccCcee
Q 029735 108 KCVACKKTVYPIEKVAV-DGTSYHKACFRC 136 (189)
Q Consensus 108 ~C~~C~~~I~~~~~v~~-~g~~~H~~Cf~C 136 (189)
+|..|+++|+.++.+++ .+..-|..||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 57788888877776543 335567777754
No 33
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.67 E-value=1.7 Score=26.64 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=21.3
Q ss_pred CCCCCcccCCccccccceEeeCCccccccccccccccccc
Q 029735 6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
...+.|..|+..|.+.+.- -=|.|-.|+..+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~~ 35 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKA---------VKFLCPNCGEVI 35 (59)
T ss_pred ccCccccCCCCcccCCCcc---------CEeeCCCCCCee
Confidence 3456899999998655421 128888888873
No 34
>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=77.48 E-value=0.44 Score=26.03 Aligned_cols=28 Identities=14% Similarity=0.449 Sum_probs=13.9
Q ss_pred cccccccccCCCeeecCCeeeecccHHH
Q 029735 38 CHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65 (189)
Q Consensus 38 C~~C~~~L~~~~f~~~~g~~yC~~cy~~ 65 (189)
|..|+.++.........+..+|..|..+
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 5555555554444445555566655543
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=77.20 E-value=1.8 Score=24.54 Aligned_cols=22 Identities=27% Similarity=0.690 Sum_probs=15.2
Q ss_pred ccccccccccCCCeeecCCeeeeccc
Q 029735 37 RCHHCKGTLKLSNYCSFEGVLYCKPH 62 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~~~g~~yC~~c 62 (189)
.|..|+.+|- ..++|+.||..|
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 3566777773 357888888776
No 36
>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=74.64 E-value=4.7 Score=24.34 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=24.9
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 68 (189)
|.|..|+..+.+ ......|..||..|..+...
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 578889888865 45567789999999987664
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.62 E-value=2.1 Score=30.66 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=18.1
Q ss_pred cccccccccCCCeeecCCeeeecccHH
Q 029735 38 CHHCKGTLKLSNYCSFEGVLYCKPHFD 64 (189)
Q Consensus 38 C~~C~~~L~~~~f~~~~g~~yC~~cy~ 64 (189)
|..|+.+| |. ++|.+||.-|-.
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCCc
Confidence 67888888 43 999999999963
No 38
>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=72.88 E-value=2.1 Score=27.79 Aligned_cols=16 Identities=31% Similarity=0.648 Sum_probs=11.6
Q ss_pred CCCCcccCCccccccc
Q 029735 7 TTQKCKACEKTVYLVD 22 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~ 22 (189)
+-..|..|++.|..++
T Consensus 6 ~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGE 21 (82)
T ss_dssp STEBETTTSCBE-TTS
T ss_pred CCccCcccCCcCCCCC
Confidence 3458999999997555
No 39
>PF12773 DZR: Double zinc ribbon
Probab=70.16 E-value=2.3 Score=24.72 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=12.2
Q ss_pred ccccccccccCCCeeecCCeeeecccHH
Q 029735 37 RCHHCKGTLKLSNYCSFEGVLYCKPHFD 64 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 64 (189)
.|..|+..|. .......+|..|-.
T Consensus 14 fC~~CG~~l~----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 14 FCPHCGTPLP----PPDQSKKICPNCGA 37 (50)
T ss_pred CChhhcCChh----hccCCCCCCcCCcC
Confidence 3556666664 22233455666643
No 40
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=69.67 E-value=4.1 Score=24.96 Aligned_cols=46 Identities=13% Similarity=0.332 Sum_probs=28.2
Q ss_pred CCCcccCCccccccceEeeCCccccccccccccccccccCC--CeeecCCeeeeccc
Q 029735 8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLS--NYCSFEGVLYCKPH 62 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~--~f~~~~g~~yC~~c 62 (189)
.+.|..|+..|..++.-. =|.|-.|+..+-.. ......+.+-|..|
T Consensus 9 ~~~CtSCg~~i~p~e~~v---------~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~C 56 (61)
T COG2888 9 PPVCTSCGREIAPGETAV---------KFPCPNCGEVEIYRCAKCRKLGNPYRCPKC 56 (61)
T ss_pred CceeccCCCEeccCCcee---------EeeCCCCCceeeehhhhHHHcCCceECCCc
Confidence 689999999996665322 27888888544222 22333445556665
No 41
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=69.57 E-value=1.6 Score=33.53 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=26.6
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHH
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 66 (189)
-+|..|+..+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999999777777889999999999653
No 42
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.30 E-value=3 Score=31.45 Aligned_cols=36 Identities=11% Similarity=0.416 Sum_probs=28.2
Q ss_pred cccccccccccccccCCC-eeecCCeeeecccHHHHh
Q 029735 32 HKACFRCHHCKGTLKLSN-YCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 32 H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~~ 67 (189)
-..+++|-.|-....... +..+=|.+||..|.....
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al 164 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL 164 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHH
Confidence 456799999987776554 557889999999998765
No 43
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=64.48 E-value=5.2 Score=20.02 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=7.9
Q ss_pred CCCccCCccccc
Q 029735 107 DKCVACKKTVYP 118 (189)
Q Consensus 107 ~~C~~C~~~I~~ 118 (189)
..|+.|+..|..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 467778776544
No 44
>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=4.8 Score=24.03 Aligned_cols=27 Identities=19% Similarity=0.454 Sum_probs=15.3
Q ss_pred ccccccccccCCCeeecCCeeeec-ccH
Q 029735 37 RCHHCKGTLKLSNYCSFEGVLYCK-PHF 63 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~~~g~~yC~-~cy 63 (189)
-|..|...++...-+.+||++||. .|.
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA 36 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACA 36 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHh
Confidence 366777788766778899999994 454
No 45
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.75 E-value=2.9 Score=28.08 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=15.4
Q ss_pred CcccCCccccccceEeeCC-ccccccccccc
Q 029735 10 KCKACEKTVYLVDQLTADN-KVYHKACFRCH 39 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~~-~~~H~~CF~C~ 39 (189)
.|..|+++|..|+.+..-. ..-|-+||.=+
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s 38 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAES 38 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHH
Confidence 4666666665555543322 24555555443
No 46
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=62.49 E-value=2.9 Score=32.25 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=24.3
Q ss_pred ceeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735 134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQL 164 (189)
Q Consensus 134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~ 164 (189)
-+|..|+-.+-...-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788888877665556778999999998753
No 47
>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=62.27 E-value=2.4 Score=26.96 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=14.1
Q ss_pred CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCC
Q 029735 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPS 146 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~ 146 (189)
..|+.|++++. .+.+-|.. =|-|..|+-.++..
T Consensus 31 a~CPdC~~~Le---~LkACGAv----dYFC~~c~gLiSKk 63 (70)
T PF07191_consen 31 AFCPDCGQPLE---VLKACGAV----DYFCNHCHGLISKK 63 (70)
T ss_dssp EE-TTT-SB-E---EEEETTEE----EEE-TTTT-EE-TT
T ss_pred ccCCCcccHHH---HHHHhccc----ceeeccCCceeecc
Confidence 46777777764 34444421 13466666655543
No 48
>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=61.86 E-value=5.2 Score=29.51 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=26.9
Q ss_pred CCCccCCcccccCce---eeccCccccccCceeCCCCCcCCC
Q 029735 107 DKCVACKKTVYPIEK---VAVDGTSYHKACFRCTHGGCVISP 145 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~---v~~~g~~~H~~Cf~C~~C~~~l~~ 145 (189)
..|+.|+-+|.+... +...|..|+.- --|..|+++...
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPW 80 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPW 80 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCch
Confidence 689999999987543 44556667643 348888888765
No 49
>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=61.06 E-value=9.4 Score=23.12 Aligned_cols=31 Identities=16% Similarity=0.455 Sum_probs=16.6
Q ss_pred cccccccccCCC---eeecCCeeeecccHHHHhh
Q 029735 38 CHHCKGTLKLSN---YCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 38 C~~C~~~L~~~~---f~~~~g~~yC~~cy~~~~~ 68 (189)
|..|++.|.... +.-.-.=-||.+|....+.
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 455666664432 2222234567777777654
No 50
>PRK00807 50S ribosomal protein L24e; Validated
Probab=58.42 E-value=7.4 Score=23.17 Aligned_cols=32 Identities=19% Similarity=0.442 Sum_probs=21.0
Q ss_pred CCcccCCccccccc---eEeeCCccccccccccccccc
Q 029735 9 QKCKACEKTVYLVD---QLTADNKVYHKACFRCHHCKG 43 (189)
Q Consensus 9 ~~C~~C~~~I~~~~---~~~~~~~~~H~~CF~C~~C~~ 43 (189)
..|..|+..|+++. ++..+|+.|. |-+..|.+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~ 36 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEK 36 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHH
Confidence 36888888888665 2566777777 44445544
No 51
>PRK00420 hypothetical protein; Validated
Probab=57.92 E-value=6.3 Score=27.52 Aligned_cols=25 Identities=24% Similarity=0.414 Sum_probs=17.0
Q ss_pred cccccccccccCCCeeecCCeeeecccHH
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 64 (189)
-.|..|+.+| |..++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 3466777766 334788888888754
No 52
>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=57.65 E-value=14 Score=20.12 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=20.7
Q ss_pred cccccccccCCCeeecCCeeeecccHHHHhh
Q 029735 38 CHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 38 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 68 (189)
|..|...+.+......=|..||.+|..+...
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 4566666655334567788899999877654
No 53
>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=57.41 E-value=4.9 Score=35.32 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=25.8
Q ss_pred CCCccCCcccccCceeeccCccccccCceeCCCCCcCCC
Q 029735 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP 145 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~ 145 (189)
..|+.|...+...+ +...+...-++||.|-.|..+|..
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 45777776665444 444555556688888888888765
No 54
>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=56.30 E-value=4.6 Score=27.11 Aligned_cols=42 Identities=14% Similarity=0.293 Sum_probs=30.3
Q ss_pred CCCCCCCcccCCccccccceEeeCCccccccccccccccccccC
Q 029735 4 FAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL 47 (189)
Q Consensus 4 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 47 (189)
+....+.|..|++++..-+.+.+.+-.+.+ -+|..|+.+++.
T Consensus 29 i~~~rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~ 70 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPP 70 (92)
T ss_pred ccCCCCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCCh
Confidence 444568899999999776766665555444 478889998854
No 55
>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=55.23 E-value=14 Score=21.30 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=20.1
Q ss_pred cccccccccccCCCeeecCCee-eecccHHHHhh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVL-YCKPHFDQLFK 68 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~-yC~~cy~~~~~ 68 (189)
+.|..|...... ..+..=|.. +|..|+.+...
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc
Confidence 356667666543 233456677 99999988753
No 56
>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=51.93 E-value=15 Score=19.71 Aligned_cols=30 Identities=17% Similarity=0.430 Sum_probs=14.7
Q ss_pred cccccccccCCCeeecCCeeeecccHHHHh
Q 029735 38 CHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 38 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 67 (189)
|..|...+........=+..||..|..+.+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~ 31 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWL 31 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHH
Confidence 455555552222222245566777766554
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.84 E-value=4.7 Score=29.40 Aligned_cols=35 Identities=20% Similarity=0.519 Sum_probs=24.2
Q ss_pred CCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
-.|+.|+..+...+.+...+. ..=|.|..|+..|.
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 369999988865555443332 23399999999984
No 58
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=51.13 E-value=10 Score=22.79 Aligned_cols=24 Identities=13% Similarity=0.283 Sum_probs=13.1
Q ss_pred CcccCCccccccceEeeCCccccc
Q 029735 10 KCKACEKTVYLVDQLTADNKVYHK 33 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~~~~~H~ 33 (189)
+|..|+++|.+...+...+..-|+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCc
Confidence 466666666544444444445554
No 59
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=51.11 E-value=6.5 Score=35.51 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=15.4
Q ss_pred ccCccccccCceeCCCCCcCCC
Q 029735 124 VDGTSYHKACFRCTHGGCVISP 145 (189)
Q Consensus 124 ~~g~~~H~~Cf~C~~C~~~l~~ 145 (189)
..|..+.++|++|..|...|.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 3455667778888888877765
No 60
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.48 E-value=8.2 Score=31.41 Aligned_cols=30 Identities=23% Similarity=0.515 Sum_probs=15.9
Q ss_pred CcccCCccccccceEeeCCccccccccccc
Q 029735 10 KCKACEKTVYLVDQLTADNKVYHKACFRCH 39 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~ 39 (189)
.|-.|++.+.+..+|..-.-.-|+-||-|+
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccC
Confidence 355555555544455444444555555555
No 61
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=49.52 E-value=12 Score=22.86 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=13.6
Q ss_pred CcCCCCCCCcccCCccccccce
Q 029735 2 ASFAGTTQKCKACEKTVYLVDQ 23 (189)
Q Consensus 2 ~~~~~~~~~C~~C~~~I~~~~~ 23 (189)
+.-......|..|+++|..++.
T Consensus 2 ~~~v~PH~HC~VCg~aIp~de~ 23 (64)
T COG4068 2 MPGVVPHRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CCCCCCCccccccCCcCCCccc
Confidence 3444456677788887765553
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=48.38 E-value=6.1 Score=30.42 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=23.1
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 68 (189)
|.|..|.+.... ..+..=|..||..|+.+.+.
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhc
Confidence 788888887743 33445678889999887764
No 63
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=47.96 E-value=6.5 Score=31.19 Aligned_cols=36 Identities=17% Similarity=0.321 Sum_probs=22.9
Q ss_pred CCCccCCcccccCceeeccCccccccCceeCCCCCcCCC
Q 029735 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP 145 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~ 145 (189)
+-|+.|+...-+ |.|.+. +-....|+|..|++.|-+
T Consensus 11 pwcwycnrefdd-ekiliq--hqkakhfkchichkkl~s 46 (341)
T KOG2893|consen 11 PWCWYCNREFDD-EKILIQ--HQKAKHFKCHICHKKLFS 46 (341)
T ss_pred ceeeecccccch-hhhhhh--hhhhccceeeeehhhhcc
Confidence 569999987654 333221 112356999999988754
No 64
>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=47.07 E-value=12 Score=18.53 Aligned_cols=9 Identities=22% Similarity=1.003 Sum_probs=4.1
Q ss_pred cccCCcccc
Q 029735 11 CKACEKTVY 19 (189)
Q Consensus 11 C~~C~~~I~ 19 (189)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 344444443
No 65
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.42 E-value=12 Score=30.69 Aligned_cols=31 Identities=16% Similarity=0.413 Sum_probs=23.0
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 67 (189)
|.|..|++.... .-...-+..+|+.|..+.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~ 272 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPY 272 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhcccc
Confidence 778888888753 3455678889999987665
No 66
>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=43.65 E-value=4.8 Score=21.93 Aligned_cols=30 Identities=23% Similarity=0.661 Sum_probs=18.6
Q ss_pred cccCCccccccceEeeCCccccccccccccccccc
Q 029735 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 11 C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
|..|.+++ ....++.||..=..|..||-.+
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 55665555 3556899999999999998766
No 67
>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=43.54 E-value=20 Score=20.41 Aligned_cols=11 Identities=9% Similarity=-0.082 Sum_probs=7.5
Q ss_pred ccccHhHHHhh
Q 029735 154 RLYCRHHHNQL 164 (189)
Q Consensus 154 ~~yC~~c~~~~ 164 (189)
--+|..||...
T Consensus 23 ~dLC~~Cf~~~ 33 (46)
T cd02249 23 FDLCSSCYAKG 33 (46)
T ss_pred CcCHHHHHCcC
Confidence 34688888754
No 68
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=42.84 E-value=8.1 Score=35.40 Aligned_cols=49 Identities=16% Similarity=0.429 Sum_probs=35.0
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcc
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKT 115 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 115 (189)
++|..|+....+ .-..+=+..||..|...++.++- .+|+.|+.+
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRq-----------------------------------RKCP~Cn~a 687 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQ-----------------------------------RKCPKCNAA 687 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhc-----------------------------------CCCCCCCCC
Confidence 688888865532 22345567899999988886322 789999988
Q ss_pred cccCc
Q 029735 116 VYPIE 120 (189)
Q Consensus 116 I~~~~ 120 (189)
..+.+
T Consensus 688 FganD 692 (698)
T KOG0978|consen 688 FGAND 692 (698)
T ss_pred CCccc
Confidence 86655
No 69
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=42.78 E-value=2.5 Score=28.51 Aligned_cols=50 Identities=12% Similarity=0.244 Sum_probs=34.0
Q ss_pred CCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCcccc
Q 029735 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157 (189)
Q Consensus 108 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC 157 (189)
.|..|...+..-...-+.-..+++.+.-|.+|.+.|....|.....=|||
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 47778777765443344446788888889999888877656655555555
No 70
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=42.38 E-value=17 Score=20.44 Aligned_cols=30 Identities=17% Similarity=0.386 Sum_probs=16.6
Q ss_pred cccccccccC--CCeeecCCeeeecccHHHHh
Q 029735 38 CHHCKGTLKL--SNYCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 38 C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~ 67 (189)
|..|...+.+ ..+...=|..+|..|..++.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 4455555521 12334456777888876654
No 71
>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=42.28 E-value=28 Score=19.28 Aligned_cols=30 Identities=20% Similarity=0.567 Sum_probs=15.5
Q ss_pred CCCccCCcccccCceeeccCccccccCceeCCCCC
Q 029735 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGC 141 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~ 141 (189)
.+|..|+-.|.+--.+...++.| +|..|+.
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 67888988887654455555564 6777765
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.25 E-value=12 Score=21.31 Aligned_cols=27 Identities=33% Similarity=0.592 Sum_probs=16.4
Q ss_pred CcccCCccccccceEeeCCccccccccccccccccc
Q 029735 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
.|..|+..+...+... =++|..|+.++
T Consensus 5 ~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYGT---------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCCC---------ceECCCCCCeE
Confidence 5888888774322211 26777887765
No 73
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=41.76 E-value=15 Score=33.51 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=9.2
Q ss_pred CCCccCCcccccC
Q 029735 107 DKCVACKKTVYPI 119 (189)
Q Consensus 107 ~~C~~C~~~I~~~ 119 (189)
..|..||.++...
T Consensus 42 ~fC~~CG~~~~~~ 54 (645)
T PRK14559 42 AHCPNCGAETGTI 54 (645)
T ss_pred ccccccCCcccch
Confidence 5788888876543
No 74
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=41.62 E-value=10 Score=26.43 Aligned_cols=35 Identities=31% Similarity=0.558 Sum_probs=24.3
Q ss_pred CCcCCCCCCCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 1 MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 1 ~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
|.|.+.....|+.|+++. ...|+. =.|-.|+.+|.
T Consensus 62 mlStkav~V~CP~C~K~T------KmLGr~-----D~CM~C~~pLT 96 (114)
T PF11023_consen 62 MLSTKAVQVECPNCGKQT------KMLGRV-----DACMHCKEPLT 96 (114)
T ss_pred hhcccceeeECCCCCChH------hhhchh-----hccCcCCCcCc
Confidence 345555667899999986 244554 26788999884
No 75
>PRK02935 hypothetical protein; Provisional
Probab=41.18 E-value=12 Score=25.77 Aligned_cols=33 Identities=30% Similarity=0.555 Sum_probs=22.1
Q ss_pred cCCCCCCCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 3 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
|-+.....|+.|+|+.. .+|+.- .|-.|+.+|.
T Consensus 65 StkavqV~CP~C~K~TK------mLGrvD-----~CM~C~~PLT 97 (110)
T PRK02935 65 STKAVQVICPSCEKPTK------MLGRVD-----ACMHCNQPLT 97 (110)
T ss_pred cccceeeECCCCCchhh------hcccee-----ecCcCCCcCC
Confidence 33444568999999863 334432 6888999984
No 76
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=40.53 E-value=11 Score=19.38 Aligned_cols=12 Identities=25% Similarity=0.601 Sum_probs=6.7
Q ss_pred CCCccCCccccc
Q 029735 107 DKCVACKKTVYP 118 (189)
Q Consensus 107 ~~C~~C~~~I~~ 118 (189)
..|.+|+..|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 579999988754
No 77
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=40.11 E-value=12 Score=25.41 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=18.5
Q ss_pred cccccccccccccCCCe-eecCCeeeeccc
Q 029735 34 ACFRCHHCKGTLKLSNY-CSFEGVLYCKPH 62 (189)
Q Consensus 34 ~CF~C~~C~~~L~~~~f-~~~~g~~yC~~c 62 (189)
.=|+|+.|-..--.... ...+|.+||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 34899988543322222 256899999988
No 78
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=39.09 E-value=3.7 Score=27.71 Aligned_cols=50 Identities=16% Similarity=0.341 Sum_probs=31.5
Q ss_pred cccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeec
Q 029735 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60 (189)
Q Consensus 11 C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~ 60 (189)
|..|...+..-..+...-..+++.+..|-.|.+.|.-..|.+...-+||.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 55566666433445555566788888888888888655665555544444
No 79
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.41 E-value=30 Score=33.21 Aligned_cols=35 Identities=29% Similarity=0.533 Sum_probs=22.0
Q ss_pred CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccH
Q 029735 6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63 (189)
Q Consensus 6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy 63 (189)
.+...|..|+.... =|+|..|+..- ....+|..|-
T Consensus 624 Vg~RfCpsCG~~t~---------------~frCP~CG~~T--------e~i~fCP~CG 658 (1121)
T PRK04023 624 IGRRKCPSCGKETF---------------YRRCPFCGTHT--------EPVYRCPRCG 658 (1121)
T ss_pred ccCccCCCCCCcCC---------------cccCCCCCCCC--------CcceeCcccc
Confidence 34567888887631 17888888761 2234677773
No 80
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.21 E-value=11 Score=34.66 Aligned_cols=84 Identities=18% Similarity=0.403 Sum_probs=53.4
Q ss_pred CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735 7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV 86 (189)
Q Consensus 7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 86 (189)
...+|..|-+.|. .-.++.||--=-.|+.||-.+ .+...-|| ++.+. ...+
T Consensus 100 D~a~C~~Cl~Ei~-----dp~~rrY~YPF~~CT~CGPRf-----TIi~alPY-----DR~nT----sM~~---------- 150 (750)
T COG0068 100 DAATCEDCLEEIF-----DPNSRRYLYPFINCTNCGPRF-----TIIEALPY-----DRENT----SMAD---------- 150 (750)
T ss_pred chhhhHHHHHHhc-----CCCCcceeccccccCCCCcce-----eeeccCCC-----CcccC----cccc----------
Confidence 3467888888775 445677777777888886544 34444443 11110 0000
Q ss_pred cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcC
Q 029735 87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVI 143 (189)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l 143 (189)
-+.|..|.+ +.-...++.||..=..|-.|+..+
T Consensus 151 -------------------F~lC~~C~~-----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 151 -------------------FPLCPFCDK-----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred -------------------CcCCHHHHH-----HhcCccccccccccccCcccCCCe
Confidence 167888865 224567899999988899998765
No 81
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=37.80 E-value=26 Score=28.89 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=26.7
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHHh
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 67 (189)
+-|-.|...|....|.=.+|.+.|..|-.++.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 67888888998888888899999999986553
No 82
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=37.70 E-value=17 Score=21.64 Aligned_cols=33 Identities=18% Similarity=0.524 Sum_probs=22.4
Q ss_pred CcccCCccccccceEeeCCccccccccccccccccc
Q 029735 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 10 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
.|+-|+.+|...--....+..|=..|-.| -+++
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC---C~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC---CRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc---CCcc
Confidence 58999999853333455667888887555 4566
No 83
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.24 E-value=11 Score=28.56 Aligned_cols=30 Identities=23% Similarity=0.557 Sum_probs=22.6
Q ss_pred CCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
-.|+.|+......+.+. .=|.|..|+..|.
T Consensus 118 Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 118 FFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred EECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 36999998886555443 1399999999995
No 84
>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=37.13 E-value=33 Score=19.31 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=7.6
Q ss_pred CCCccCCcccc
Q 029735 107 DKCVACKKTVY 117 (189)
Q Consensus 107 ~~C~~C~~~I~ 117 (189)
..|..|+.+|.
T Consensus 5 ~~C~~C~~~i~ 15 (44)
T smart00291 5 YSCDTCGKPIV 15 (44)
T ss_pred cCCCCCCCCCc
Confidence 56888877554
No 85
>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=36.09 E-value=26 Score=19.64 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=5.7
Q ss_pred ccccccccccc
Q 029735 36 FRCHHCKGTLK 46 (189)
Q Consensus 36 F~C~~C~~~L~ 46 (189)
+.|..|+..|.
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 45666665554
No 86
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=36.01 E-value=20 Score=23.46 Aligned_cols=28 Identities=18% Similarity=0.349 Sum_probs=16.2
Q ss_pred eCCCCCcCCCCCee--ecC---CccccHhHHHh
Q 029735 136 CTHGGCVISPSNYV--AHE---HRLYCRHHHNQ 163 (189)
Q Consensus 136 C~~C~~~l~~~~~~--~~d---g~~yC~~c~~~ 163 (189)
|+.|+-||.....+ ..| ..-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 66677776654321 223 35688888753
No 87
>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=35.93 E-value=24 Score=20.43 Aligned_cols=13 Identities=23% Similarity=0.652 Sum_probs=9.0
Q ss_pred CCCCCcccCCccc
Q 029735 6 GTTQKCKACEKTV 18 (189)
Q Consensus 6 ~~~~~C~~C~~~I 18 (189)
.....|..|++.|
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 3456788898888
No 88
>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=35.42 E-value=35 Score=28.23 Aligned_cols=13 Identities=15% Similarity=0.480 Sum_probs=9.7
Q ss_pred CCCccCCcccccC
Q 029735 107 DKCVACKKTVYPI 119 (189)
Q Consensus 107 ~~C~~C~~~I~~~ 119 (189)
..|+.|++++...
T Consensus 44 ~~CP~C~~~lrk~ 56 (309)
T TIGR00570 44 GSCPECDTPLRKN 56 (309)
T ss_pred CCCCCCCCccchh
Confidence 5799998887654
No 89
>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=35.37 E-value=15 Score=20.58 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=5.2
Q ss_pred cccccccccc
Q 029735 36 FRCHHCKGTL 45 (189)
Q Consensus 36 F~C~~C~~~L 45 (189)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 4555555444
No 90
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=34.70 E-value=22 Score=28.80 Aligned_cols=16 Identities=19% Similarity=0.613 Sum_probs=11.0
Q ss_pred cccccccccccccCCC
Q 029735 34 ACFRCHHCKGTLKLSN 49 (189)
Q Consensus 34 ~CF~C~~C~~~L~~~~ 49 (189)
..++|..|++.+....
T Consensus 129 ~r~~c~eCgk~ysT~s 144 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSS 144 (279)
T ss_pred Cceecccccccccccc
Confidence 4577888888776443
No 91
>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=34.40 E-value=16 Score=19.72 Aligned_cols=31 Identities=32% Similarity=0.700 Sum_probs=18.4
Q ss_pred CcccCCccccccc-eEeeCCccccccccccccccccc
Q 029735 10 KCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 10 ~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
.|+.|+..+...+ .+...+. -++|..|+..|
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 2332222 36778887766
No 92
>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=34.09 E-value=27 Score=20.98 Aligned_cols=24 Identities=29% Similarity=0.634 Sum_probs=16.7
Q ss_pred CCcccCCccccccc---eEeeCCcccc
Q 029735 9 QKCKACEKTVYLVD---QLTADNKVYH 32 (189)
Q Consensus 9 ~~C~~C~~~I~~~~---~~~~~~~~~H 32 (189)
..|.-|+..|+++. +|..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 46888888888775 3566666665
No 93
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=33.76 E-value=29 Score=28.87 Aligned_cols=39 Identities=15% Similarity=0.467 Sum_probs=27.2
Q ss_pred CCCcccCCccccccceEe-----eCC-----cccccccccccccccccc
Q 029735 8 TQKCKACEKTVYLVDQLT-----ADN-----KVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~~~-----~~~-----~~~H~~CF~C~~C~~~L~ 46 (189)
+..|..|+..|+-|..++ +.+ -....--++|..|...|.
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 567999999998765543 333 223455688999988874
No 94
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=33.53 E-value=29 Score=21.23 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=17.0
Q ss_pred eeCCCCCcCCC--CCeeecCCccccH-hHH
Q 029735 135 RCTHGGCVISP--SNYVAHEHRLYCR-HHH 161 (189)
Q Consensus 135 ~C~~C~~~l~~--~~~~~~dg~~yC~-~c~ 161 (189)
.|..|++.|.. ..|+-++.+.+|. .|-
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 36667777774 2355567788884 443
No 95
>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=32.60 E-value=18 Score=19.68 Aligned_cols=9 Identities=33% Similarity=1.073 Sum_probs=4.2
Q ss_pred CcccCCccc
Q 029735 10 KCKACEKTV 18 (189)
Q Consensus 10 ~C~~C~~~I 18 (189)
.|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 345555443
No 96
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.59 E-value=35 Score=33.60 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=5.8
Q ss_pred CCccCCccccc
Q 029735 108 KCVACKKTVYP 118 (189)
Q Consensus 108 ~C~~C~~~I~~ 118 (189)
.|+.|+.++..
T Consensus 711 ~CP~CGtplv~ 721 (1337)
T PRK14714 711 ECPRCDVELTP 721 (1337)
T ss_pred cCCCCCCcccc
Confidence 46666555443
No 97
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=32.31 E-value=46 Score=32.16 Aligned_cols=40 Identities=13% Similarity=0.366 Sum_probs=27.1
Q ss_pred CCCCCCCcccCCccccccc-eEeeCCcccccccccccccccccc
Q 029735 4 FAGTTQKCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 4 ~~~~~~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
+..+..+|++|++|+..++ ++-..+.... .+|..|++.-.
T Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 832 (1006)
T PRK12775 792 AETGVATCPKCHRPLEGDEEYVCCATSELQ---WRCDDCGKVSE 832 (1006)
T ss_pred ccCCCccCcccCCCCCCCceeEEecCccee---eehhhhccccc
Confidence 4556778999999997655 4544444433 46788888654
No 98
>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=31.65 E-value=25 Score=18.97 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=4.6
Q ss_pred CCcccCCcccc
Q 029735 9 QKCKACEKTVY 19 (189)
Q Consensus 9 ~~C~~C~~~I~ 19 (189)
+.|-.|++++.
T Consensus 4 ~~C~eC~~~f~ 14 (34)
T PF01286_consen 4 PKCDECGKPFM 14 (34)
T ss_dssp EE-TTT--EES
T ss_pred chHhHhCCHHH
Confidence 45666666663
No 99
>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=31.43 E-value=20 Score=20.88 Aligned_cols=10 Identities=30% Similarity=1.032 Sum_probs=5.2
Q ss_pred cccccccccc
Q 029735 36 FRCHHCKGTL 45 (189)
Q Consensus 36 F~C~~C~~~L 45 (189)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 4555555544
No 100
>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=31.41 E-value=17 Score=20.56 Aligned_cols=11 Identities=36% Similarity=0.758 Sum_probs=3.9
Q ss_pred cccCCcccccc
Q 029735 11 CKACEKTVYLV 21 (189)
Q Consensus 11 C~~C~~~I~~~ 21 (189)
|..|++.+.-|
T Consensus 1 C~~C~~iv~~G 11 (43)
T PF08746_consen 1 CEACKEIVTQG 11 (43)
T ss_dssp -TTT-SB-SSS
T ss_pred CcccchhHeee
Confidence 44555555433
No 101
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.08 E-value=40 Score=20.25 Aligned_cols=31 Identities=19% Similarity=0.494 Sum_probs=20.0
Q ss_pred CCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
..|+.|+..|.-.+... |. -..|..|+..|.
T Consensus 3 ~~CP~CG~~iev~~~~~--Ge-----iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--GE-----LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCcc--CC-----EEeCCCCCCEEE
Confidence 37999999885333221 22 357888988874
No 102
>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=29.91 E-value=42 Score=19.13 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=7.3
Q ss_pred eeeecccHHH
Q 029735 56 VLYCKPHFDQ 65 (189)
Q Consensus 56 ~~yC~~cy~~ 65 (189)
--+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 4579999976
No 103
>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=29.49 E-value=24 Score=16.42 Aligned_cols=12 Identities=17% Similarity=0.744 Sum_probs=8.4
Q ss_pred cccccccccccC
Q 029735 36 FRCHHCKGTLKL 47 (189)
Q Consensus 36 F~C~~C~~~L~~ 47 (189)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 567788777754
No 104
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=29.41 E-value=48 Score=20.76 Aligned_cols=22 Identities=18% Similarity=0.533 Sum_probs=13.9
Q ss_pred ccccccccccCCC---eeecCCeee
Q 029735 37 RCHHCKGTLKLSN---YCSFEGVLY 58 (189)
Q Consensus 37 ~C~~C~~~L~~~~---f~~~~g~~y 58 (189)
+|+-|+..|.++. |...||.++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~ 29 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVL 29 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEE
Confidence 5677777776653 455677643
No 105
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.39 E-value=9.2 Score=22.89 Aligned_cols=26 Identities=15% Similarity=0.439 Sum_probs=13.9
Q ss_pred ccccccccccCCCeee---cCCeeeeccc
Q 029735 37 RCHHCKGTLKLSNYCS---FEGVLYCKPH 62 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~---~~g~~yC~~c 62 (189)
+|..|+..|+++.+.. .++-.+|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 5666666665554331 1345666655
No 106
>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=29.38 E-value=16 Score=27.08 Aligned_cols=30 Identities=17% Similarity=0.367 Sum_probs=22.8
Q ss_pred CCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735 9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK 46 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~ 46 (189)
-.|+.|+..+...+.+. .=|.|..||..|.
T Consensus 110 Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 110 FICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred EECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 36999998886666553 1399999999984
No 107
>PLN02195 cellulose synthase A
Probab=29.01 E-value=55 Score=31.43 Aligned_cols=32 Identities=25% Similarity=0.653 Sum_probs=20.1
Q ss_pred CCCCCcccCCccccccceEeeCCccccccccccccccccc
Q 029735 6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
+....|..|+..|- +..+|..| .. |..|+-++
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f-va---C~eC~~pv 35 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF-VA---CHECSYPL 35 (977)
T ss_pred CCCccceecccccC----cCCCCCeE-EE---eccCCCcc
Confidence 34568999999884 34567665 44 45554443
No 108
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=28.07 E-value=31 Score=22.00 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=13.0
Q ss_pred CCcccCCccccccc---eEeeCCcccc
Q 029735 9 QKCKACEKTVYLVD---QLTADNKVYH 32 (189)
Q Consensus 9 ~~C~~C~~~I~~~~---~~~~~~~~~H 32 (189)
..|.-|+..|++|. +|..+|+.++
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred EEecccCCccCCCCCeEEEecCCCeEE
Confidence 46888888888775 3555666665
No 109
>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=27.03 E-value=52 Score=22.54 Aligned_cols=36 Identities=22% Similarity=0.308 Sum_probs=26.6
Q ss_pred CCccccccccccccccccccCCCeeecCCeeeecccHHHH
Q 029735 27 DNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66 (189)
Q Consensus 27 ~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 66 (189)
.+..+...==.|..| .+..|+..++.+.|..|-.+.
T Consensus 27 ~dg~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 27 PDGSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred CCCCEEEEEEecccc----CCCceEEECCEEEEecCCCEE
Confidence 344555555567888 567899999999999997544
No 110
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.96 E-value=54 Score=17.45 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=12.7
Q ss_pred ccccccccccCCCeeecCCeeeeccc
Q 029735 37 RCHHCKGTLKLSNYCSFEGVLYCKPH 62 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~~~g~~yC~~c 62 (189)
+|..|+..+ -+...++..+|..|
T Consensus 5 ~C~~C~~~~---i~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNG---IVNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCe---EEEecCCeEEcccC
Confidence 355566554 23355666666666
No 111
>PRK12495 hypothetical protein; Provisional
Probab=26.62 E-value=36 Score=26.72 Aligned_cols=24 Identities=17% Similarity=0.535 Sum_probs=14.4
Q ss_pred cccccccccccCCCeeecCCeeeecccHH
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 64 (189)
+.|..|+.+|. ...|..+|..|-.
T Consensus 43 ~hC~~CG~PIp-----a~pG~~~Cp~CQ~ 66 (226)
T PRK12495 43 AHCDECGDPIF-----RHDGQEFCPTCQQ 66 (226)
T ss_pred hhcccccCccc-----CCCCeeECCCCCC
Confidence 45666666663 2366666766653
No 112
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=26.49 E-value=59 Score=31.58 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=19.5
Q ss_pred CCCcccCCccccccceEeeCCccccccccccccccccc
Q 029735 8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
..+|..|+..|- +.++|..| .-|..|+-++
T Consensus 17 ~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPV 46 (1079)
T PLN02638 17 GQVCQICGDNVG----KTVDGEPF----VACDVCAFPV 46 (1079)
T ss_pred CceeeecccccC----cCCCCCEE----EEeccCCCcc
Confidence 348999988873 45677766 3445565555
No 113
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=25.98 E-value=32 Score=26.92 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=23.5
Q ss_pred ccccccccccccccCCCeeecCCeeeecccH
Q 029735 33 KACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63 (189)
Q Consensus 33 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy 63 (189)
++=..|..|++++....|...+|..+|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3335788999888644566789999999986
No 114
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=25.95 E-value=39 Score=24.14 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=19.1
Q ss_pred CCcccCCccccccc---eEeeCCccccc
Q 029735 9 QKCKACEKTVYLVD---QLTADNKVYHK 33 (189)
Q Consensus 9 ~~C~~C~~~I~~~~---~~~~~~~~~H~ 33 (189)
.+|..|+.+|++|. +|...|+.|+.
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~F 32 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHF 32 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEE
Confidence 57999999998875 46667777773
No 115
>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=25.81 E-value=60 Score=18.30 Aligned_cols=11 Identities=18% Similarity=0.588 Sum_probs=6.9
Q ss_pred CCccCCccccc
Q 029735 108 KCVACKKTVYP 118 (189)
Q Consensus 108 ~C~~C~~~I~~ 118 (189)
.|.+|+++|.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 47777776543
No 116
>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=25.71 E-value=18 Score=24.97 Aligned_cols=18 Identities=22% Similarity=0.510 Sum_probs=12.5
Q ss_pred CCCcccCCccccccceEee
Q 029735 8 TQKCKACEKTVYLVDQLTA 26 (189)
Q Consensus 8 ~~~C~~C~~~I~~~~~~~~ 26 (189)
-..|-.|+++| +.+++.+
T Consensus 80 yG~C~~Cge~I-~~~RL~a 97 (110)
T TIGR02420 80 YGYCEECGEEI-GLRRLEA 97 (110)
T ss_pred CCchhccCCcc-cHHHHhh
Confidence 36788888888 4555554
No 117
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=25.70 E-value=33 Score=18.56 Aligned_cols=30 Identities=17% Similarity=0.608 Sum_probs=16.5
Q ss_pred CcccCCcccccc-ceEeeCCcccccccccccccccc
Q 029735 10 KCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGT 44 (189)
Q Consensus 10 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~ 44 (189)
.|+.|+...... +.|...+.. ++|..|+..
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~ 34 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV 34 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence 477787764333 335444432 566766654
No 118
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=25.32 E-value=56 Score=19.17 Aligned_cols=27 Identities=19% Similarity=0.533 Sum_probs=20.5
Q ss_pred CCcccCCccccc-cc-eEeeCCccccccc
Q 029735 9 QKCKACEKTVYL-VD-QLTADNKVYHKAC 35 (189)
Q Consensus 9 ~~C~~C~~~I~~-~~-~~~~~~~~~H~~C 35 (189)
..|+.|+-.... ++ .|.+.+..|++.|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 579999987643 33 5888899999887
No 119
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=25.21 E-value=47 Score=18.92 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=3.6
Q ss_pred cccCCccc
Q 029735 11 CKACEKTV 18 (189)
Q Consensus 11 C~~C~~~I 18 (189)
|+.|+..+
T Consensus 5 C~~Cg~~~ 12 (44)
T smart00659 5 CGECGREN 12 (44)
T ss_pred CCCCCCEe
Confidence 44444443
No 120
>PLN02436 cellulose synthase A
Probab=24.55 E-value=68 Score=31.18 Aligned_cols=19 Identities=32% Similarity=0.749 Sum_probs=11.4
Q ss_pred CCcccCCccccccceEeeCCccc
Q 029735 9 QKCKACEKTVYLVDQLTADNKVY 31 (189)
Q Consensus 9 ~~C~~C~~~I~~~~~~~~~~~~~ 31 (189)
.+|..|+..|- +.++|..|
T Consensus 37 ~iCqICGD~Vg----~t~dGe~F 55 (1094)
T PLN02436 37 QTCQICGDEIE----LTVDGEPF 55 (1094)
T ss_pred ccccccccccC----cCCCCCEE
Confidence 36777777663 23556655
No 121
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=23.97 E-value=69 Score=18.18 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=14.4
Q ss_pred cccCCccccccceEee--CCcccccccc
Q 029735 11 CKACEKTVYLVDQLTA--DNKVYHKACF 36 (189)
Q Consensus 11 C~~C~~~I~~~~~~~~--~~~~~H~~CF 36 (189)
|..|++.-..++.|.- =++.||..|.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 6777774433344433 3356787764
No 123
>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=23.76 E-value=29 Score=20.61 Aligned_cols=26 Identities=27% Similarity=0.468 Sum_probs=13.7
Q ss_pred cccccccccccCC-CeeecCCeeeecccH
Q 029735 36 FRCHHCKGTLKLS-NYCSFEGVLYCKPHF 63 (189)
Q Consensus 36 F~C~~C~~~L~~~-~f~~~~g~~yC~~cy 63 (189)
++|..|++.|... .+. ..++-|..|-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCC
Confidence 4666676666542 222 3345566553
No 124
>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=23.76 E-value=40 Score=17.17 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=3.5
Q ss_pred cccccccccccC
Q 029735 36 FRCHHCKGTLKL 47 (189)
Q Consensus 36 F~C~~C~~~L~~ 47 (189)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 567777777754
No 125
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=23.69 E-value=1.2e+02 Score=16.87 Aligned_cols=30 Identities=20% Similarity=0.319 Sum_probs=15.6
Q ss_pred eeCCCCCcCCCCC-eee-cCCccccHhHHHhh
Q 029735 135 RCTHGGCVISPSN-YVA-HEHRLYCRHHHNQL 164 (189)
Q Consensus 135 ~C~~C~~~l~~~~-~~~-~dg~~yC~~c~~~~ 164 (189)
+|+.|+++..... .+. .++...|..|-...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 4777887766533 222 33677788886543
No 126
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=23.62 E-value=39 Score=26.93 Aligned_cols=31 Identities=13% Similarity=0.310 Sum_probs=25.8
Q ss_pred ccccccccccccccCCCeeecCCeeeecccH
Q 029735 33 KACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63 (189)
Q Consensus 33 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy 63 (189)
++=..|+.|+.+.....|+...+...|..|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3445789999999887888899999999987
No 127
>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=23.61 E-value=81 Score=18.19 Aligned_cols=10 Identities=10% Similarity=0.022 Sum_probs=7.1
Q ss_pred cccHhHHHhh
Q 029735 155 LYCRHHHNQL 164 (189)
Q Consensus 155 ~yC~~c~~~~ 164 (189)
-+|..||...
T Consensus 25 dLC~~Cf~~g 34 (49)
T cd02335 25 DLCLECFSAG 34 (49)
T ss_pred chhHHhhhCc
Confidence 3588888754
No 128
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.42 E-value=43 Score=18.15 Aligned_cols=31 Identities=26% Similarity=0.703 Sum_probs=16.6
Q ss_pred CcccCCcccccc-ceEeeCCccccccccccccccccc
Q 029735 10 KCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTL 45 (189)
Q Consensus 10 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L 45 (189)
+|+.|+....-. +.|...+. . ++|..|+..+
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~--~---vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGR--K---VRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCc--E---EECCCCCcEe
Confidence 577887764322 34544444 2 5666666543
No 129
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.33 E-value=36 Score=15.43 Aligned_cols=11 Identities=27% Similarity=0.975 Sum_probs=5.8
Q ss_pred ccccccccccc
Q 029735 36 FRCHHCKGTLK 46 (189)
Q Consensus 36 F~C~~C~~~L~ 46 (189)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 46777777664
No 130
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.32 E-value=51 Score=26.80 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=15.9
Q ss_pred CCCCCccCCcccccCceeeccCccccccC
Q 029735 105 TQDKCVACKKTVYPIEKVAVDGTSYHKAC 133 (189)
Q Consensus 105 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~C 133 (189)
...-|.+|+.+|... .+.-.+..|.+.|
T Consensus 244 ~GepC~~CGt~I~k~-~~~gR~t~~CP~C 271 (273)
T COG0266 244 AGEPCRRCGTPIEKI-KLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCCccCCEeEEE-EEcCCcCEeCCCC
Confidence 346788888888532 2344444554444
No 131
>PLN02189 cellulose synthase
Probab=23.23 E-value=74 Score=30.80 Aligned_cols=9 Identities=22% Similarity=0.903 Sum_probs=5.9
Q ss_pred CcccCCccc
Q 029735 10 KCKACEKTV 18 (189)
Q Consensus 10 ~C~~C~~~I 18 (189)
.|..|+..|
T Consensus 36 ~C~iCgd~v 44 (1040)
T PLN02189 36 VCEICGDEI 44 (1040)
T ss_pred ccccccccc
Confidence 666666666
No 132
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.95 E-value=52 Score=20.15 Aligned_cols=13 Identities=31% Similarity=0.600 Sum_probs=6.8
Q ss_pred cccccccccccccccC
Q 029735 32 HKACFRCHHCKGTLKL 47 (189)
Q Consensus 32 H~~CF~C~~C~~~L~~ 47 (189)
|.+|. .||+++..
T Consensus 3 HkHC~---~CG~~Ip~ 15 (59)
T PF09889_consen 3 HKHCP---VCGKPIPP 15 (59)
T ss_pred CCcCC---cCCCcCCc
Confidence 45543 34666653
No 133
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.79 E-value=53 Score=28.40 Aligned_cols=37 Identities=16% Similarity=0.466 Sum_probs=26.2
Q ss_pred CCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCe
Q 029735 4 FAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY 50 (189)
Q Consensus 4 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f 50 (189)
|...+|+|+.|+.... ..|+. =|+|..|+.......+
T Consensus 346 ~~~~~p~Cp~Cg~~m~------S~G~~----g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 346 YERVNPVCPRCGGRMK------SAGRN----GFRCKKCGTRARETLI 382 (421)
T ss_pred eEEcCCCCCccCCchh------hcCCC----CcccccccccCCcccc
Confidence 4556889999988763 33443 3899999998866544
No 134
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=22.49 E-value=14 Score=24.38 Aligned_cols=25 Identities=24% Similarity=0.529 Sum_probs=16.0
Q ss_pred cccccccccccCCCeeecCCeeeecccHHHH
Q 029735 36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 66 (189)
-+|..|...+- ..|.-||..|.-+.
T Consensus 55 ~kC~iCk~~vH------Q~GshYC~tCAY~K 79 (100)
T KOG3476|consen 55 AKCRICKQLVH------QPGSHYCQTCAYKK 79 (100)
T ss_pred chhHHHHHHhc------CCcchhHhHhhhhh
Confidence 45666765542 35677899886554
No 135
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.81 E-value=52 Score=30.28 Aligned_cols=25 Identities=36% Similarity=0.599 Sum_probs=14.4
Q ss_pred ccccccccccCCCeeecCCeeeecccHH
Q 029735 37 RCHHCKGTLKLSNYCSFEGVLYCKPHFD 64 (189)
Q Consensus 37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 64 (189)
+|..|+.+|. |....+.+.|.-|-.
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGR 418 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcC
Confidence 3444555552 334566788888854
No 136
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.80 E-value=87 Score=20.05 Aligned_cols=31 Identities=13% Similarity=0.310 Sum_probs=15.4
Q ss_pred cccccccccCCCe---eecCCeeeecccHHHHhh
Q 029735 38 CHHCKGTLKLSNY---CSFEGVLYCKPHFDQLFK 68 (189)
Q Consensus 38 C~~C~~~L~~~~f---~~~~g~~yC~~cy~~~~~ 68 (189)
|.-|.+-|.+.+- .-.-.--||.+|....+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~ 41 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLH 41 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc
Confidence 4555666654321 111123467777776665
No 137
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.64 E-value=40 Score=15.95 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=8.9
Q ss_pred cccccccccccCC
Q 029735 36 FRCHHCKGTLKLS 48 (189)
Q Consensus 36 F~C~~C~~~L~~~ 48 (189)
|.|..|+..+.+.
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 5678887777543
No 138
>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=21.13 E-value=1.4e+02 Score=17.07 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=15.5
Q ss_pred eCCCCCcCCCCCeee--cCCccccHhHHHh
Q 029735 136 CTHGGCVISPSNYVA--HEHRLYCRHHHNQ 163 (189)
Q Consensus 136 C~~C~~~l~~~~~~~--~dg~~yC~~c~~~ 163 (189)
|..|+..+....|.. ..+.-+|..||.+
T Consensus 3 C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 3 CFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred ccCCCCccCceEEEecCCCccccChHHHhC
Confidence 555555554322221 1246689999976
No 139
>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=20.88 E-value=97 Score=17.98 Aligned_cols=10 Identities=10% Similarity=0.036 Sum_probs=7.3
Q ss_pred cccHhHHHhh
Q 029735 155 LYCRHHHNQL 164 (189)
Q Consensus 155 ~yC~~c~~~~ 164 (189)
=+|..||...
T Consensus 27 DlC~~C~~~~ 36 (48)
T cd02341 27 DLCQDCVVKG 36 (48)
T ss_pred ccCHHHHhCc
Confidence 3688998764
No 140
>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=20.80 E-value=68 Score=23.22 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=23.1
Q ss_pred CCCccCCcccccCceeec------cCccccccCceeCCCCCcC
Q 029735 107 DKCVACKKTVYPIEKVAV------DGTSYHKACFRCTHGGCVI 143 (189)
Q Consensus 107 ~~C~~C~~~I~~~~~v~~------~g~~~H~~Cf~C~~C~~~l 143 (189)
.+|..|+.++.....-.+ .-...+..-+.|..|++..
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 699999998865432111 1122344567899998753
No 141
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=20.64 E-value=88 Score=18.03 Aligned_cols=27 Identities=11% Similarity=0.282 Sum_probs=12.5
Q ss_pred eCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735 136 CTHGGCVISPSNYVAHEHRLYCRHHHNQL 164 (189)
Q Consensus 136 C~~C~~~l~~~~~~~~dg~~yC~~c~~~~ 164 (189)
|..|+++...+ ....|...|..|-.++
T Consensus 2 CiiC~~~~~~G--I~I~~~fIC~~CE~~i 28 (46)
T PF10764_consen 2 CIICGKEKEEG--IHIYGKFICSDCEKEI 28 (46)
T ss_pred eEeCCCcCCCC--EEEECeEehHHHHHHh
Confidence 44455444332 2234455566664444
No 142
>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=20.34 E-value=29 Score=18.59 Aligned_cols=16 Identities=19% Similarity=0.623 Sum_probs=10.4
Q ss_pred cccccccccccCCCee
Q 029735 36 FRCHHCKGTLKLSNYC 51 (189)
Q Consensus 36 F~C~~C~~~L~~~~f~ 51 (189)
|.|..|++++....|.
T Consensus 5 ~~C~nC~R~v~a~RfA 20 (33)
T PF08209_consen 5 VECPNCGRPVAASRFA 20 (33)
T ss_dssp EE-TTTSSEEEGGGHH
T ss_pred EECCCCcCCcchhhhH
Confidence 5677777777766664
No 143
>PRK13796 GTPase YqeH; Provisional
Probab=20.30 E-value=53 Score=27.68 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=7.3
Q ss_pred CeeeecccHH
Q 029735 55 GVLYCKPHFD 64 (189)
Q Consensus 55 g~~yC~~cy~ 64 (189)
+.++|.+||.
T Consensus 33 ~~~~C~RC~~ 42 (365)
T PRK13796 33 EEVYCQRCFR 42 (365)
T ss_pred CCeEchhhhh
Confidence 4678888884
Done!