Query psy7480
Match_columns 204
No_of_seqs 215 out of 1654
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 19:24:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7480.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7480hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 99.9 3E-28 6.5E-33 192.7 -2.5 145 50-199 32-204 (383)
2 KOG1701|consensus 99.9 3.5E-27 7.6E-32 195.6 -3.5 130 47-184 270-401 (468)
3 KOG1701|consensus 99.9 3.2E-25 6.8E-30 184.0 0.9 124 48-176 331-463 (468)
4 KOG2272|consensus 99.8 8.8E-22 1.9E-26 153.6 -1.1 126 42-174 186-311 (332)
5 KOG1044|consensus 99.8 6.2E-21 1.3E-25 163.6 2.6 118 49-173 131-248 (670)
6 KOG2272|consensus 99.8 4.6E-20 1E-24 144.0 0.3 129 47-184 133-261 (332)
7 KOG1703|consensus 99.7 8E-19 1.7E-23 154.0 3.1 122 49-177 301-422 (479)
8 KOG1703|consensus 99.7 2.8E-19 6.1E-24 156.8 0.1 119 48-172 360-478 (479)
9 PF00412 LIM: LIM domain; Int 99.6 1.9E-15 4E-20 95.2 5.7 58 118-176 1-58 (58)
10 KOG1044|consensus 99.6 4.7E-15 1E-19 127.8 6.2 126 48-180 13-195 (670)
11 PF00412 LIM: LIM domain; Int 99.4 7.8E-14 1.7E-18 87.7 3.5 57 54-112 1-58 (58)
12 KOG1700|consensus 99.4 8.1E-14 1.8E-18 108.9 -0.3 124 49-176 5-167 (200)
13 KOG4577|consensus 98.9 5.7E-11 1.2E-15 95.0 -3.0 74 117-193 35-110 (383)
14 smart00132 LIM Zinc-binding do 98.8 5.5E-09 1.2E-13 59.8 2.7 37 117-153 1-37 (39)
15 smart00132 LIM Zinc-binding do 98.6 3.8E-08 8.2E-13 56.2 2.6 37 53-89 1-38 (39)
16 KOG1702|consensus 98.4 1.7E-08 3.8E-13 77.3 -3.7 85 117-204 6-91 (264)
17 KOG0490|consensus 98.3 1.1E-07 2.4E-12 75.9 -1.0 116 56-175 1-119 (235)
18 KOG1700|consensus 97.5 2.7E-05 5.9E-10 61.0 0.2 65 47-113 104-168 (200)
19 KOG1702|consensus 97.3 2.9E-05 6.3E-10 59.8 -1.6 61 51-113 4-64 (264)
20 PF08394 Arc_trans_TRASH: Arch 91.6 0.12 2.5E-06 29.0 1.4 33 118-153 1-33 (37)
21 PF14446 Prok-RING_1: Prokaryo 88.8 0.32 7E-06 29.7 1.8 37 117-153 7-51 (54)
22 PF08394 Arc_trans_TRASH: Arch 87.8 0.37 7.9E-06 27.0 1.4 32 54-88 1-33 (37)
23 PF10367 Vps39_2: Vacuolar sor 87.1 0.45 9.9E-06 32.8 2.0 32 49-80 76-108 (109)
24 PF13920 zf-C3HC4_3: Zinc fing 86.9 0.51 1.1E-05 28.1 1.9 44 80-126 4-48 (50)
25 KOG0490|consensus 86.5 0.13 2.9E-06 40.7 -1.1 52 121-174 2-54 (235)
26 smart00504 Ubox Modified RING 85.0 0.48 1E-05 29.3 1.2 46 79-127 2-47 (63)
27 PF10367 Vps39_2: Vacuolar sor 84.5 0.79 1.7E-05 31.6 2.2 28 117-144 80-107 (109)
28 PF14835 zf-RING_6: zf-RING of 83.1 1.3 2.8E-05 28.1 2.4 46 79-129 8-54 (65)
29 KOG2462|consensus 82.4 0.41 8.9E-06 39.0 -0.0 16 74-89 183-198 (279)
30 PF14471 DUF4428: Domain of un 82.2 1.2 2.7E-05 26.8 2.0 30 145-175 1-30 (51)
31 PF09943 DUF2175: Uncharacteri 80.9 0.57 1.2E-05 32.4 0.3 31 52-82 3-34 (101)
32 KOG0320|consensus 78.7 0.62 1.4E-05 35.5 -0.1 51 76-127 129-179 (187)
33 PF12773 DZR: Double zinc ribb 76.2 2.1 4.5E-05 25.3 1.7 9 117-125 31-39 (50)
34 PF14634 zf-RING_5: zinc-RING 75.9 1.8 3.8E-05 25.0 1.3 43 81-123 2-44 (44)
35 PF09943 DUF2175: Uncharacteri 75.2 4.2 9.1E-05 28.2 3.2 32 144-175 3-34 (101)
36 PF07191 zinc-ribbons_6: zinc- 75.1 6.2 0.00013 25.4 3.8 60 80-155 3-62 (70)
37 PF11781 RRN7: RNA polymerase 74.5 2.3 4.9E-05 23.6 1.5 24 145-173 10-33 (36)
38 KOG1813|consensus 74.0 1.8 3.9E-05 35.8 1.3 47 78-127 241-287 (313)
39 COG1645 Uncharacterized Zn-fin 71.2 2.8 6.1E-05 30.4 1.7 23 80-109 30-52 (131)
40 PF06677 Auto_anti-p27: Sjogre 70.5 2.2 4.8E-05 24.5 0.8 21 146-171 20-40 (41)
41 COG1645 Uncharacterized Zn-fin 69.2 2.4 5.1E-05 30.8 1.0 22 146-173 31-52 (131)
42 COG2191 Formylmethanofuran deh 68.1 1.5 3.2E-05 34.2 -0.3 31 144-175 173-203 (206)
43 COG5152 Uncharacterized conser 67.3 1.2 2.5E-05 34.7 -1.0 48 77-127 195-242 (259)
44 PF01258 zf-dskA_traR: Prokary 67.1 0.8 1.7E-05 25.3 -1.5 28 146-174 6-33 (36)
45 KOG0978|consensus 66.3 0.91 2E-05 41.9 -2.0 48 79-129 644-692 (698)
46 PF13923 zf-C3HC4_2: Zinc fing 64.8 3.4 7.5E-05 23.0 0.9 38 81-121 1-39 (39)
47 COG4847 Uncharacterized protei 64.1 6.6 0.00014 26.8 2.2 29 144-172 7-35 (103)
48 PRK14890 putative Zn-ribbon RN 64.0 6.3 0.00014 24.5 2.0 29 50-87 6-34 (59)
49 PF06906 DUF1272: Protein of u 62.2 7.1 0.00015 23.9 1.9 45 80-126 7-52 (57)
50 PRK14559 putative protein seri 59.6 8.2 0.00018 35.8 2.8 22 104-125 30-51 (645)
51 COG0068 HypF Hydrogenase matur 57.8 12 0.00026 34.9 3.4 86 47-153 97-183 (750)
52 PRK00420 hypothetical protein; 57.1 4.5 9.7E-05 28.7 0.5 9 117-125 25-33 (112)
53 PF13240 zinc_ribbon_2: zinc-r 56.0 7 0.00015 19.3 1.0 8 118-125 2-9 (23)
54 cd02249 ZZ Zinc finger, ZZ typ 56.0 11 0.00023 21.9 2.0 12 164-175 22-33 (46)
55 PF10083 DUF2321: Uncharacteri 54.4 5.5 0.00012 29.8 0.6 51 100-155 27-80 (158)
56 PF00645 zf-PARP: Poly(ADP-rib 53.7 5.8 0.00013 26.0 0.6 13 117-129 9-21 (82)
57 PF13639 zf-RING_2: Ring finge 51.8 5.6 0.00012 22.6 0.3 11 99-109 21-31 (44)
58 smart00291 ZnF_ZZ Zinc-binding 50.9 14 0.00031 21.2 2.0 10 165-174 27-36 (44)
59 PF07754 DUF1610: Domain of un 50.4 11 0.00024 19.0 1.1 10 118-127 1-10 (24)
60 PF12674 Zn_ribbon_2: Putative 49.7 6.9 0.00015 26.0 0.5 29 145-173 2-34 (81)
61 PF10235 Cript: Microtubule-as 48.8 11 0.00025 25.5 1.4 37 79-127 45-81 (90)
62 PF06689 zf-C4_ClpX: ClpX C4-t 47.6 34 0.00074 19.4 3.1 31 145-175 3-34 (41)
63 PLN03208 E3 ubiquitin-protein 47.5 16 0.00034 28.5 2.2 11 117-127 70-80 (193)
64 cd00162 RING RING-finger (Real 47.4 8.8 0.00019 21.1 0.6 26 99-124 18-44 (45)
65 cd02335 ZZ_ADA2 Zinc finger, Z 46.0 20 0.00044 21.1 2.1 11 165-175 24-34 (49)
66 TIGR00599 rad18 DNA repair pro 45.7 7.7 0.00017 33.7 0.3 15 50-64 25-39 (397)
67 PF10886 DUF2685: Protein of u 45.4 16 0.00035 22.2 1.6 26 52-77 2-27 (54)
68 KOG3002|consensus 43.8 14 0.00031 30.8 1.6 43 79-126 49-91 (299)
69 PF00569 ZZ: Zinc finger, ZZ t 43.5 29 0.00064 20.1 2.5 10 165-174 28-37 (46)
70 PF14569 zf-UDP: Zinc-binding 43.0 27 0.00058 23.0 2.4 31 145-175 11-46 (80)
71 PF11571 Med27: Mediator compl 42.3 5.7 0.00012 26.8 -0.8 16 108-125 49-64 (90)
72 KOG4739|consensus 42.1 28 0.0006 28.0 2.9 33 93-127 17-49 (233)
73 COG2191 Formylmethanofuran deh 41.9 12 0.00026 29.4 0.8 31 79-111 173-203 (206)
74 cd02336 ZZ_RSC8 Zinc finger, Z 41.7 27 0.00058 20.4 2.1 31 144-175 1-33 (45)
75 PF02069 Metallothio_Pro: Prok 41.5 14 0.00031 22.3 0.9 27 145-172 9-36 (52)
76 COG3813 Uncharacterized protei 41.4 23 0.00049 23.0 1.9 44 81-126 8-52 (84)
77 PRK14873 primosome assembly pr 40.8 22 0.00048 33.2 2.5 38 80-124 394-431 (665)
78 KOG3579|consensus 39.0 36 0.00078 28.2 3.1 49 51-106 268-316 (352)
79 cd02341 ZZ_ZZZ3 Zinc finger, Z 38.8 28 0.0006 20.6 1.9 10 166-175 27-36 (48)
80 PF13834 DUF4193: Domain of un 38.7 9.2 0.0002 26.4 -0.2 28 143-171 70-98 (99)
81 cd02338 ZZ_PCMF_like Zinc fing 38.6 29 0.00063 20.5 2.0 11 165-175 24-34 (49)
82 TIGR03119 one_C_fhcD formylmet 37.8 14 0.00031 30.3 0.6 18 3-20 129-146 (287)
83 KOG4443|consensus 36.9 15 0.00033 33.7 0.8 89 47-154 31-126 (694)
84 COG2888 Predicted Zn-ribbon RN 36.0 13 0.00029 23.1 0.2 12 51-62 9-20 (61)
85 PRK02114 formylmethanofuran--t 35.3 16 0.00035 30.1 0.7 19 2-20 135-153 (297)
86 PF07503 zf-HYPF: HypF finger; 34.8 17 0.00038 20.0 0.5 31 54-89 2-32 (35)
87 cd02340 ZZ_NBR1_like Zinc fing 34.6 36 0.00078 19.5 1.9 11 117-127 2-12 (43)
88 PF04570 DUF581: Protein of un 34.6 30 0.00066 21.4 1.6 26 80-105 18-43 (58)
89 PF06827 zf-FPG_IleRS: Zinc fi 34.2 20 0.00042 18.6 0.7 10 117-126 3-12 (30)
90 KOG2462|consensus 33.8 20 0.00044 29.4 1.0 13 77-89 129-141 (279)
91 PF13248 zf-ribbon_3: zinc-rib 33.7 25 0.00053 17.7 1.0 9 117-125 4-12 (26)
92 PRK00807 50S ribosomal protein 33.2 33 0.00071 20.6 1.6 24 52-75 2-28 (52)
93 TIGR00595 priA primosomal prot 32.8 37 0.0008 30.5 2.5 29 95-124 234-262 (505)
94 COG1198 PriA Primosomal protei 31.6 37 0.00079 32.1 2.4 40 79-124 445-484 (730)
95 PF09723 Zn-ribbon_8: Zinc rib 31.5 9.5 0.00021 21.8 -0.9 9 117-125 7-15 (42)
96 PF10764 Gin: Inhibitor of sig 30.5 74 0.0016 18.6 2.8 28 146-176 2-29 (46)
97 COG5432 RAD18 RING-finger-cont 30.4 19 0.0004 29.9 0.3 44 79-125 26-69 (391)
98 PF07649 C1_3: C1-like domain; 30.4 22 0.00048 18.4 0.5 9 145-153 2-10 (30)
99 PF04564 U-box: U-box domain; 30.3 48 0.001 21.2 2.2 48 77-127 3-51 (73)
100 PF05502 Dynactin_p62: Dynacti 30.1 29 0.00062 31.1 1.4 36 117-154 28-63 (483)
101 KOG2932|consensus 30.0 21 0.00046 29.9 0.5 42 80-125 92-133 (389)
102 TIGR00570 cdk7 CDK-activating 29.6 26 0.00057 29.4 1.0 30 98-127 25-55 (309)
103 PRK14559 putative protein seri 29.3 52 0.0011 30.6 2.9 9 81-89 30-38 (645)
104 smart00547 ZnF_RBZ Zinc finger 28.6 33 0.00072 16.9 1.0 20 104-123 5-24 (26)
105 PF14570 zf-RING_4: RING/Ubox 28.5 23 0.0005 21.0 0.4 23 102-124 23-46 (48)
106 PF06750 DiS_P_DiS: Bacterial 28.3 21 0.00045 24.3 0.2 17 52-68 34-50 (92)
107 PF08792 A2L_zn_ribbon: A2L zi 28.2 44 0.00095 18.1 1.4 10 162-171 18-27 (33)
108 cd02345 ZZ_dah Zinc finger, ZZ 27.0 49 0.0011 19.5 1.6 10 166-175 25-34 (49)
109 KOG0823|consensus 26.5 59 0.0013 26.0 2.4 51 74-127 43-96 (230)
110 PF12677 DUF3797: Domain of un 26.0 45 0.00097 19.8 1.3 27 117-143 15-42 (49)
111 TIGR00143 hypF [NiFe] hydrogen 25.9 56 0.0012 30.8 2.5 86 47-153 64-150 (711)
112 PF04810 zf-Sec23_Sec24: Sec23 25.8 51 0.0011 18.4 1.5 30 52-86 3-32 (40)
113 PF00096 zf-C2H2: Zinc finger, 25.3 28 0.00062 16.3 0.3 10 144-153 1-10 (23)
114 cd02334 ZZ_dystrophin Zinc fin 25.2 64 0.0014 19.1 1.9 10 166-175 25-34 (49)
115 PF13717 zinc_ribbon_4: zinc-r 24.6 24 0.00053 19.4 -0.0 7 145-151 27-33 (36)
116 PRK00398 rpoP DNA-directed RNA 24.1 28 0.00061 20.1 0.2 27 117-153 5-31 (46)
117 PRK14714 DNA polymerase II lar 23.7 1E+02 0.0022 31.1 3.8 61 79-163 668-728 (1337)
118 KOG2893|consensus 23.6 19 0.00042 29.0 -0.8 37 50-89 9-45 (341)
119 PF00130 C1_1: Phorbol esters/ 23.5 42 0.00091 19.7 0.9 14 50-63 10-23 (53)
120 smart00531 TFIIE Transcription 23.3 25 0.00054 26.0 -0.2 38 49-89 97-134 (147)
121 cd02342 ZZ_UBA_plant Zinc fing 23.2 76 0.0016 18.4 1.8 10 166-175 25-34 (43)
122 PRK05580 primosome assembly pr 22.1 73 0.0016 29.8 2.5 57 66-124 369-430 (679)
123 COG4306 Uncharacterized protei 22.1 59 0.0013 23.5 1.5 48 103-154 30-79 (160)
124 smart00659 RPOLCX RNA polymera 21.8 33 0.00072 19.8 0.2 9 117-125 4-12 (44)
125 COG1813 Predicted transcriptio 21.8 1.1E+02 0.0024 23.3 3.0 34 146-181 6-40 (165)
126 PF10122 Mu-like_Com: Mu-like 21.7 17 0.00038 21.8 -1.0 9 117-125 6-14 (51)
127 PRK00085 recO DNA repair prote 21.5 43 0.00093 26.7 0.8 32 140-172 146-177 (247)
128 KOG0320|consensus 21.4 64 0.0014 24.9 1.6 35 142-176 130-164 (187)
129 KOG1705|consensus 21.1 75 0.0016 21.6 1.8 11 117-127 29-39 (110)
130 smart00184 RING Ring finger. E 20.9 44 0.00094 17.2 0.5 14 97-110 14-27 (39)
131 PF14255 Cys_rich_CPXG: Cystei 20.8 41 0.00089 20.3 0.4 9 54-62 3-11 (52)
132 PF05502 Dynactin_p62: Dynacti 20.7 53 0.0012 29.4 1.3 38 51-89 26-63 (483)
133 PRK03564 formate dehydrogenase 20.5 2.3E+02 0.005 23.8 4.9 13 49-61 185-197 (309)
134 COG1381 RecO Recombinational D 20.2 54 0.0012 26.5 1.2 31 141-172 152-182 (251)
No 1
>KOG4577|consensus
Probab=99.93 E-value=3e-28 Score=192.68 Aligned_cols=145 Identities=39% Similarity=0.880 Sum_probs=129.8
Q ss_pred CCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCCCc
Q psy7480 50 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 129 (204)
Q Consensus 50 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~~ 129 (204)
..++|++|.+.|.+.++++++++.||..|++|+.|..+|. ...|.++|.+||+++|.++|++ +|..|+..|.+..
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~---drCFsR~~s~yCkedFfKrfGT--KCsaC~~GIpPtq 106 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLA---DRCFSREGSVYCKEDFFKRFGT--KCSACQEGIPPTQ 106 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHH---HHHhhcCCceeehHHHHHHhCC--cchhhcCCCChHH
Confidence 6789999999999999999999999999999999999997 5689999999999999999999 9999999999865
Q ss_pred eEEecCCcccccCccccccCCccccCCCeEEE-eCCeeecHHHHHHHhh-------------------------hhcccC
Q psy7480 130 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILCEYDYEERQV-------------------------FANIAY 183 (204)
Q Consensus 130 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~~~-------------------------~~~~~~ 183 (204)
.+-.|.+.+||.+||.|..|++.|..|++||+ .|+++.|+.+|+..-. +...+|
T Consensus 107 VVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY 186 (383)
T KOG4577|consen 107 VVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY 186 (383)
T ss_pred HHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence 56678999999999999999999988999997 4799999999975421 223444
Q ss_pred C--CCchHHhhhccCccc
Q psy7480 184 N--PSSLAHLRRQVTLQV 199 (204)
Q Consensus 184 ~--~~~~~~~~~~~~~~~ 199 (204)
+ |+|++|||+||++.+
T Consensus 187 n~SpKPARHVREQLsseT 204 (383)
T KOG4577|consen 187 NTSPKPARHVREQLSSET 204 (383)
T ss_pred cCCCchhHHHHHHhhhcc
Confidence 4 999999999999875
No 2
>KOG1701|consensus
Probab=99.92 E-value=3.5e-27 Score=195.60 Aligned_cols=130 Identities=25% Similarity=0.570 Sum_probs=117.3
Q ss_pred CCCCCccccccccccccc-eeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCcc
Q psy7480 47 ASGGLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I 125 (204)
....+.+|.+|++.|++. ..+.||++.||..||+|..|++.|. ++.||..++++||+.||..... +|..|+++|
T Consensus 270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~--Gq~FY~v~~k~~CE~cyq~tle---kC~~Cg~~I 344 (468)
T KOG1701|consen 270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLA--GQSFYQVDGKPYCEGCYQDTLE---KCNKCGEPI 344 (468)
T ss_pred hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhc--cccccccCCcccchHHHHHHHH---HHhhhhhHH
Confidence 344566999999999988 5689999999999999999999998 6889999999999999998776 899999999
Q ss_pred CCCceEEecCCcccccCccccccCCccccCCCeEEE-eCCeeecHHHHHHHhhhhcccCC
Q psy7480 126 PAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILCEYDYEERQVFANIAYN 184 (204)
Q Consensus 126 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~~~~~~~~~~ 184 (204)
. |+++.|.|+.||+.||+|..|++.| +|..|++ .++++||..||.++|......+.
T Consensus 345 ~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~ 401 (468)
T KOG1701|consen 345 M--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCG 401 (468)
T ss_pred H--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCcchhhcc
Confidence 5 5999999999999999999999999 8999987 47999999999999876665555
No 3
>KOG1701|consensus
Probab=99.90 E-value=3.2e-25 Score=184.04 Aligned_cols=124 Identities=26% Similarity=0.621 Sum_probs=109.9
Q ss_pred CCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeE-EeeCCeecccccccccccCcccccccCCccC
Q psy7480 48 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 48 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~-~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
+..+.+|..|+++|.+. ++.++|+.||+.||+|..|.+.|+. -.| ...++.+||..||+++|++ +|+.|+++|+
T Consensus 331 q~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldg--ipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~ 405 (468)
T KOG1701|consen 331 QDTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDG--IPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPIL 405 (468)
T ss_pred HHHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCC--ccccccCCCceeeehhhhhhcCc--chhhccCCcc
Confidence 34577899999999999 7999999999999999999999983 344 5788999999999999999 9999999998
Q ss_pred CCc-----eEEecCCcccccCccccccCCcccc---CCCeEEEeCCeeecHHHHHHHh
Q psy7480 127 AFE-----MVMRAKNNVYHLECFACQQCNHRFC---VGDRFYLCDNKILCEYDYEERQ 176 (204)
Q Consensus 127 ~~~-----~~~~~~~~~~H~~Cf~C~~C~~~l~---~~~~~~~~~~~~~C~~c~~~~~ 176 (204)
+.+ ..|+++++.||.+|++|..|+..|+ ++...|..||+++|+.|+.++.
T Consensus 406 P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl 463 (468)
T KOG1701|consen 406 PRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRL 463 (468)
T ss_pred CCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhh
Confidence 732 2578999999999999999999996 4667999999999999998774
No 4
>KOG2272|consensus
Probab=99.82 E-value=8.8e-22 Score=153.56 Aligned_cols=126 Identities=31% Similarity=0.719 Sum_probs=115.6
Q ss_pred CCCCCCCCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCccccccc
Q psy7480 42 ALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAAC 121 (204)
Q Consensus 42 ~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C 121 (204)
.++....-+.++|+.|.++|.+. ++.++|+.||.+.|+|+.|.+++- |...|++.|..||+++|.++||. .|..|
T Consensus 186 ClrChD~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFl--GHrHYEkkGlaYCe~h~~qLfG~--~CF~C 260 (332)
T KOG2272|consen 186 CLRCHDKMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFL--GHRHYEKKGLAYCETHYHQLFGN--LCFIC 260 (332)
T ss_pred ccccccccCCcccccccCchHHH-HHHHhccccchhheeehhcCCccc--chhhhhhcCchhHHHHHHHHhhh--hheec
Confidence 45556777899999999999987 789999999999999999999975 56789999999999999999998 99999
Q ss_pred CCccCCCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHH
Q psy7480 122 TKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 174 (204)
Q Consensus 122 ~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 174 (204)
+.+|.| .++.|.++.|-++||.|+.|++.|.....|++.|-.|.|+.||.+
T Consensus 261 ~~~i~G--~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 261 NRVIGG--DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred CCccCc--cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 999976 789999999999999999999999777889999999999999984
No 5
>KOG1044|consensus
Probab=99.81 E-value=6.2e-21 Score=163.58 Aligned_cols=118 Identities=31% Similarity=0.687 Sum_probs=110.3
Q ss_pred CCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCCC
Q psy7480 49 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF 128 (204)
Q Consensus 49 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 128 (204)
.+...|++|++.|..+.++.++++.||..||+|..|+..|. ..|..++|.+||+.||.+.|+. +|..|.+.|.|
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~---gey~skdg~pyce~dy~~~fgv--kc~~c~~fisg- 204 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN---GEYMSKDGVPYCEKDYQAKFGV--KCEECEKFISG- 204 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc---ceeeccCCCcchhhhhhhhcCe--ehHHhhhhhhh-
Confidence 46778999999999988899999999999999999999997 5699999999999999999999 99999999987
Q ss_pred ceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHH
Q psy7480 129 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 173 (204)
Q Consensus 129 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 173 (204)
.++.|+|+.||+.|-+|+.|+.++.+|++.|+....++-..|-.
T Consensus 205 -kvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 205 -KVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred -hhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 89999999999999999999999999999999999988777753
No 6
>KOG2272|consensus
Probab=99.77 E-value=4.6e-20 Score=143.98 Aligned_cols=129 Identities=26% Similarity=0.430 Sum_probs=113.0
Q ss_pred CCCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccC
Q psy7480 47 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
...+.-+|.+|+..|.+. .+...+..||+..|+|..|++.|. +.-....|.+||..|+.++--+ .|..|.++|.
T Consensus 133 ~~~g~YvC~KCh~~iD~~-~l~fr~d~yH~yHFkCt~C~keL~---sdaRevk~eLyClrChD~mgip--iCgaC~rpIe 206 (332)
T KOG2272|consen 133 KGRGRYVCQKCHAHIDEQ-PLTFRGDPYHPYHFKCTTCGKELT---SDAREVKGELYCLRCHDKMGIP--ICGACRRPIE 206 (332)
T ss_pred cccceeehhhhhhhcccc-cccccCCCCCccceeccccccccc---chhhhhccceeccccccccCCc--ccccccCchH
Confidence 344567899999999885 688999999999999999999997 3446778899999999988777 9999999995
Q ss_pred CCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHHHhhhhcccCC
Q psy7480 127 AFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYN 184 (204)
Q Consensus 127 ~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~ 184 (204)
+++|.++|+.||.++|+|+.|.+|+ .|.+.|+..|.+||+.+|.++|.......+
T Consensus 207 --ervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG~~CF~C~ 261 (332)
T KOG2272|consen 207 --ERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFGNLCFICN 261 (332)
T ss_pred --HHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhhhhheecC
Confidence 5899999999999999999999999 888999999999999999999865554444
No 7
>KOG1703|consensus
Probab=99.74 E-value=8e-19 Score=153.96 Aligned_cols=122 Identities=24% Similarity=0.493 Sum_probs=111.5
Q ss_pred CCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCCC
Q psy7480 49 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF 128 (204)
Q Consensus 49 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 128 (204)
...+.|..|+..|.+..++.++++.||+.+|.|..|+..+.. ..+...+|++||..||...+.+ .|.+|+++|.+
T Consensus 301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~--~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~- 375 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILD--GGPRELDGKILCHECFHAPFRP--NCKRCLLPILE- 375 (479)
T ss_pred cccccccccccCcccceeEeeccccccccceeeccccccccC--CCccccCCCccHHHHHHHhhCc--cccccCCchHH-
Confidence 355899999999999447999999999999999999999875 3468899999999999999998 99999999976
Q ss_pred ceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHHHhh
Q psy7480 129 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV 177 (204)
Q Consensus 129 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~ 177 (204)
.+|.|.++.||++||.|..|++.| .+..|+..++.+||..||.+++.
T Consensus 376 -~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 376 -EGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred -hHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhcc
Confidence 789999999999999999999999 78889999999999999999865
No 8
>KOG1703|consensus
Probab=99.73 E-value=2.8e-19 Score=156.82 Aligned_cols=119 Identities=26% Similarity=0.585 Sum_probs=109.2
Q ss_pred CCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 48 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 48 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
....+.|.+|+++|.+. .|.+++..||++||.|..|++.|. ...|+..++.+||+.||.+++.+ +|..|.++|..
T Consensus 360 ~~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~--~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~ 434 (479)
T KOG1703|consen 360 APFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLK--NSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEF 434 (479)
T ss_pred HhhCccccccCCchHHh-HhhhccCeechhceeeecccCCCC--CCcccccCCccchhhhHhhhccc--cchhccchhHh
Confidence 46788999999999999 577889999999999999999997 46799999999999999999998 99999999875
Q ss_pred CceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHH
Q psy7480 128 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 172 (204)
Q Consensus 128 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 172 (204)
.+..+.+++..||..||+|..|.+.| .+..|+...+.++|..|+
T Consensus 435 ~~~~ie~~~~~~h~~~F~c~~c~~~l-~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 435 GSRQIEADGSPFHGDCFRCANCMKKL-TKKTFFETLDKPLCQKHF 478 (479)
T ss_pred hhhHhhccCccccccceehhhhhccc-cCCceeecCCccccccCC
Confidence 56889999999999999999999999 788999999999999885
No 9
>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=99.60 E-value=1.9e-15 Score=95.20 Aligned_cols=58 Identities=36% Similarity=0.745 Sum_probs=52.4
Q ss_pred ccccCCccCCCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHHHh
Q psy7480 118 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 176 (204)
Q Consensus 118 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 176 (204)
|.+|+++|.+.+.++.+.|+.||++||+|..|+++| .+..|+..+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPL-NDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBT-TTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCcc-CCCeeEeECCEEECHHHHhhhC
Confidence 789999999877777899999999999999999999 5555999999999999999875
No 10
>KOG1044|consensus
Probab=99.56 E-value=4.7e-15 Score=127.78 Aligned_cols=126 Identities=23% Similarity=0.528 Sum_probs=97.9
Q ss_pred CCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEee-CCeecccccccc----------------
Q psy7480 48 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQK-ANLILCKRDYLR---------------- 110 (204)
Q Consensus 48 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~-~g~~~C~~cy~~---------------- 110 (204)
......|.+|.+.-.+. ++.+.++.||..||+|..|+..|++. . ||.+ +..+|+......
T Consensus 13 ~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~-g-ff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~ 89 (670)
T KOG1044|consen 13 GKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEG-G-FFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHP 89 (670)
T ss_pred cccceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccc-c-ceecccceeecccchhhhccceeEecccceecc
Confidence 34456799999998887 89999999999999999999999963 3 5544 445666432211
Q ss_pred ----------------------------------------cccCcccccccCCccCCCceEEecCCcccccCccccccCC
Q psy7480 111 ----------------------------------------LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 150 (204)
Q Consensus 111 ----------------------------------------~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~ 150 (204)
..++ ..|++|+..|.. +..+.|+++.||..||+|..|+
T Consensus 90 ~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~p-s~cagc~~~lk~-gq~llald~qwhv~cfkc~~c~ 167 (670)
T KOG1044|consen 90 KCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGP-STCAGCGEELKN-GQALLALDKQWHVSCFKCKSCS 167 (670)
T ss_pred ccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCC-ccccchhhhhhc-cceeeeeccceeeeeeehhhhc
Confidence 0000 138899988864 4788899999999999999999
Q ss_pred ccccCCCeEEEeCCeeecHHHHHHHhhhhc
Q psy7480 151 HRFCVGDRFYLCDNKILCEYDYEERQVFAN 180 (204)
Q Consensus 151 ~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~ 180 (204)
..| . .+|..++|.+||..||.++|...+
T Consensus 168 ~vL-~-gey~skdg~pyce~dy~~~fgvkc 195 (670)
T KOG1044|consen 168 AVL-N-GEYMSKDGVPYCEKDYQAKFGVKC 195 (670)
T ss_pred ccc-c-ceeeccCCCcchhhhhhhhcCeeh
Confidence 999 4 479999999999999999885443
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=99.44 E-value=7.8e-14 Score=87.71 Aligned_cols=57 Identities=39% Similarity=0.864 Sum_probs=50.8
Q ss_pred ccccccccccceeE-eecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccc
Q psy7480 54 CASCGKRITERFLL-KALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 112 (204)
Q Consensus 54 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~ 112 (204)
|.+|+++|.+..++ .++|+.||++||+|..|+..|.. ..++..+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND--GDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT--SSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC--CeeEeECCEEECHHHHhhhC
Confidence 78999999988544 79999999999999999999984 44899999999999998765
No 12
>KOG1700|consensus
Probab=99.36 E-value=8.1e-14 Score=108.85 Aligned_cols=124 Identities=22% Similarity=0.528 Sum_probs=102.5
Q ss_pred CCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccccccCc-------------
Q psy7480 49 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTT------------- 115 (204)
Q Consensus 49 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~------------- 115 (204)
.....|..|++.++-.+.+...|..||+.||+|..|.+.|.. ..+..+++.+||+.||...+++.
T Consensus 5 ~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~--~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~ 82 (200)
T KOG1700|consen 5 GTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTL--SGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGG 82 (200)
T ss_pred cccchhhhccCcchHHHHHhccCcchhhhHHhcccccccccc--ccccccccccccccchHhhhCcccccccccccccCC
Confidence 445689999999998866778899999999999999999984 55778999999999765543321
Q ss_pred --------------------------ccccccCCccCCCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecH
Q psy7480 116 --------------------------GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 169 (204)
Q Consensus 116 --------------------------~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~ 169 (204)
..|..|++.+.+.+ -+...+..||..||+|+.|+..| ....+....+.+||.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~~l-s~~~~~~~~g~l~~~ 160 (200)
T KOG1700|consen 83 LGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGKKL-SPKNYAALEGVLYCK 160 (200)
T ss_pred CCcccccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccccc-CCcchhhcCCccccc
Confidence 13999999998754 45677999999999999999999 667888889999999
Q ss_pred HHHHHHh
Q psy7480 170 YDYEERQ 176 (204)
Q Consensus 170 ~c~~~~~ 176 (204)
.++..++
T Consensus 161 ~~~~~~~ 167 (200)
T KOG1700|consen 161 HHFAQLF 167 (200)
T ss_pred hhhheee
Confidence 9887764
No 13
>KOG4577|consensus
Probab=98.92 E-value=5.7e-11 Score=94.97 Aligned_cols=74 Identities=20% Similarity=0.533 Sum_probs=64.8
Q ss_pred cccccCCccCCCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHHHhhhhcccCC--CCchHHhhh
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYN--PSSLAHLRR 193 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~--~~~~~~~~~ 193 (204)
.|++|.+.|.. ..++.+.++.||..|.+|+.|..+| ++..+.++|.+||+++|.++|.++..+++ ..|...||+
T Consensus 35 ~CagC~q~IlD-rFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 35 ICAGCDQHILD-RFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred cccchHHHHHH-HHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 89999999964 4578899999999999999999999 66788899999999999999999999999 445555554
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=98.76 E-value=5.5e-09 Score=59.77 Aligned_cols=37 Identities=43% Similarity=0.909 Sum_probs=33.7
Q ss_pred cccccCCccCCCceEEecCCcccccCccccccCCccc
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 153 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 153 (204)
+|.+|+++|.+.+..+.+.++.||++||+|..|+++|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 5899999998765788899999999999999999998
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=98.58 E-value=3.8e-08 Score=56.21 Aligned_cols=37 Identities=46% Similarity=1.076 Sum_probs=33.5
Q ss_pred cccccccccccc-eeEeecCccccccCccccCCCcccC
Q psy7480 53 ECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLG 89 (204)
Q Consensus 53 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~ 89 (204)
+|.+|+++|.+. ..+.+.+..||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999987 6788899999999999999999885
No 16
>KOG1702|consensus
Probab=98.35 E-value=1.7e-08 Score=77.30 Aligned_cols=85 Identities=21% Similarity=0.381 Sum_probs=72.2
Q ss_pred cccccCCccCCCceEEecCCcccccCccccccCCccccCCCeEEEeCCeeecHHHHHHHhhhhcccCCCCchHH-hhhcc
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAH-LRRQV 195 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~-~~~~~ 195 (204)
.|..|++.+.+.+ -+.-.++.||..||+|..|+..| .-.+|-..+.++||..+|.+. +++.++.+|+.++. ...++
T Consensus 6 n~~~cgk~vYPvE-~v~cldk~whk~cfkce~c~mtl-nmKnyKgy~kkpycn~hYpkq-~at~~adTPEm~Rik~n~en 82 (264)
T KOG1702|consen 6 NREDCGKTVYPVE-EVKCLDKVWHKQCFKCEVCGMTL-NMKNYKGYDKKPYCNPHYPKQ-VATVMADTPEMRRIKENTEN 82 (264)
T ss_pred hhhhhccccccHH-HHhhHHHHHHHHhheeeeccCCh-hhhhccccccCCCcCcccccc-eeeeecCCHHHHHHHhhhcc
Confidence 5788999888754 45778999999999999999999 666787789999999999877 48888899999866 66788
Q ss_pred CcccccccC
Q psy7480 196 TLQVLWIRE 204 (204)
Q Consensus 196 ~~~~~~~~~ 204 (204)
.+||.|.+|
T Consensus 83 qS~vkY~~e 91 (264)
T KOG1702|consen 83 QSNVKYHAE 91 (264)
T ss_pred chhhhhHHH
Confidence 999998775
No 17
>KOG0490|consensus
Probab=98.27 E-value=1.1e-07 Score=75.94 Aligned_cols=116 Identities=41% Similarity=0.823 Sum_probs=96.9
Q ss_pred ccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccccc--cccCcccccccCCccCCCceEEe
Q psy7480 56 SCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR--LFGTTGYCAACTKVIPAFEMVMR 133 (204)
Q Consensus 56 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~--~~~~~~~C~~C~~~I~~~~~~~~ 133 (204)
.|+..|.+...+.+.+..||..|..|..|...+.. ....+..+|..||..+|.. .+.. +|.+|...|...+.+..
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler 77 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGV-GDTCFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELER 77 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhcc-CCCcccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHH
Confidence 36778888866777799999999999999999873 2344555999999999998 6665 99999999977777888
Q ss_pred cCCcccccCccccccCCccccCCCeEEEeCC-eeecHHHHHHH
Q psy7480 134 AKNNVYHLECFACQQCNHRFCVGDRFYLCDN-KILCEYDYEER 175 (204)
Q Consensus 134 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~-~~~C~~c~~~~ 175 (204)
+..+. |..||.|..|...+..+..+.+... +.+|.+.+.+.
T Consensus 78 ~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 78 AFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 88888 9999999999998878888888765 89999888654
No 18
>KOG1700|consensus
Probab=97.48 E-value=2.7e-05 Score=60.98 Aligned_cols=65 Identities=23% Similarity=0.556 Sum_probs=55.0
Q ss_pred CCCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeeccccccccccc
Q psy7480 47 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 113 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~ 113 (204)
.......|..|++.++..+.+...+..||..||+|..|+..|.. ..+....+.+||...+..++-
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~--~~~~~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSP--KNYAALEGVLYCKHHFAQLFK 168 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCC--cchhhcCCccccchhhheeec
Confidence 44567789999999998877888999999999999999999984 567888999999877766543
No 19
>KOG1702|consensus
Probab=97.29 E-value=2.9e-05 Score=59.83 Aligned_cols=61 Identities=25% Similarity=0.506 Sum_probs=51.7
Q ss_pred CccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeeccccccccccc
Q psy7480 51 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 113 (204)
Q Consensus 51 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~ 113 (204)
...|..|++.++..+.+.-+++.||..||+|..|+..|.. ..+-..+.++||..+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCccccccee
Confidence 4567889999998777888999999999999999999974 556678999999999987544
No 20
>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=91.60 E-value=0.12 Score=29.03 Aligned_cols=33 Identities=33% Similarity=0.748 Sum_probs=24.7
Q ss_pred ccccCCccCCCceEEecCCcccccCccccccCCccc
Q psy7480 118 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 153 (204)
Q Consensus 118 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 153 (204)
|..|++.|.+...++...++.|| |.|..|.+.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 77899999876667888888888 5556665554
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.82 E-value=0.32 Score=29.66 Aligned_cols=37 Identities=24% Similarity=0.652 Sum_probs=25.1
Q ss_pred cccccCCccCCCceEEe--cCCcccccCcc----cccc--CCccc
Q psy7480 117 YCAACTKVIPAFEMVMR--AKNNVYHLECF----ACQQ--CNHRF 153 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 153 (204)
+|..|+++|...+.++. .-+..||.+|+ .|.. |+..+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 89999999975444444 34667888887 3655 55543
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=87.79 E-value=0.37 Score=27.04 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=23.3
Q ss_pred ccccccccccc-eeEeecCccccccCccccCCCccc
Q psy7480 54 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRL 88 (204)
Q Consensus 54 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~L 88 (204)
|..|+.+|.+. .++...++.|| |-|..|...+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 77899999988 56778888898 4445554443
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=87.06 E-value=0.45 Score=32.84 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=22.7
Q ss_pred CCCccccccccccccc-eeEeecCccccccCcc
Q psy7480 49 GGLKECASCGKRITER-FLLKALDLFWHEDCLK 80 (204)
Q Consensus 49 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~ 80 (204)
.....|..|+++|... .++...|..+|..|++
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3355699999999876 4455567778888763
No 24
>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=86.92 E-value=0.51 Score=28.06 Aligned_cols=44 Identities=18% Similarity=0.392 Sum_probs=31.2
Q ss_pred cccCCCcccCcCCCeEEeeCCee-cccccccccccCcccccccCCccC
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLI-LCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~-~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
.|..|..... ...+..-|.. +|..|..+......+|..|.++|.
T Consensus 4 ~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4666766654 4567778888 999999887543348999999984
No 25
>KOG0490|consensus
Probab=86.51 E-value=0.13 Score=40.67 Aligned_cols=52 Identities=27% Similarity=0.706 Sum_probs=40.2
Q ss_pred cCCccCCCceEEecCCcccccCccccccCCccccC-CCeEEEeCCeeecHHHHHH
Q psy7480 121 CTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEE 174 (204)
Q Consensus 121 C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~ 174 (204)
|+..|.+ ...+.+.+..||..|..|..|...+.. ...|.. +|..||...+..
T Consensus 2 ~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~ 54 (235)
T KOG0490|consen 2 CGRQILD-RYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR 54 (235)
T ss_pred CCccccc-hHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh
Confidence 5666654 235566689999999999999999942 334555 999999999987
No 26
>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=85.02 E-value=0.48 Score=29.33 Aligned_cols=46 Identities=7% Similarity=0.030 Sum_probs=32.8
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
|.|..|+..+. .......|..||..|..+.+...+.|..|++++..
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 56788888876 34667788999988887654333378888887743
No 27
>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=84.51 E-value=0.79 Score=31.60 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=18.1
Q ss_pred cccccCCccCCCceEEecCCcccccCcc
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECF 144 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf 144 (204)
.|..|+++|.....++.-.|..+|..|+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 6888888886533344444666777775
No 28
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.12 E-value=1.3 Score=28.06 Aligned_cols=46 Identities=22% Similarity=0.403 Sum_probs=24.6
Q ss_pred ccccCCCcccCcCCCeE-EeeCCeecccccccccccCcccccccCCccCCCc
Q psy7480 79 LKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 129 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~-~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~~ 129 (204)
++|+.|...|.. .+ ...-+.+||..|-...++. .|..|+.|.+..|
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 578888888862 32 4566789999999988887 8999999887644
No 29
>KOG2462|consensus
Probab=82.37 E-value=0.41 Score=39.02 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=7.7
Q ss_pred ccccCccccCCCcccC
Q psy7480 74 WHEDCLKCGCCDCRLG 89 (204)
Q Consensus 74 ~H~~Cf~C~~C~~~L~ 89 (204)
-|.-=+.|..||+.+.
T Consensus 183 TH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 183 THTLPCECGICGKAFS 198 (279)
T ss_pred ccCCCccccccccccc
Confidence 3443445555555543
No 30
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=82.18 E-value=1.2 Score=26.81 Aligned_cols=30 Identities=20% Similarity=0.490 Sum_probs=23.4
Q ss_pred ccccCCccccCCCeEEEeCCeeecHHHHHHH
Q psy7480 145 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 175 (204)
Q Consensus 145 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 175 (204)
.|..|+..++.-..+-+.|| ..|..|+.+.
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 48889999854445667788 6999999876
No 31
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=80.92 E-value=0.57 Score=32.39 Aligned_cols=31 Identities=29% Similarity=0.401 Sum_probs=22.5
Q ss_pred ccccccccccccceeEee-cCccccccCcccc
Q psy7480 52 KECASCGKRITERFLLKA-LDLFWHEDCLKCG 82 (204)
Q Consensus 52 ~~C~~C~~~I~~~~~~~~-~~~~~H~~Cf~C~ 82 (204)
-.|..|+++|+.++.+++ .+..-|..||+=.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 368889999888865555 4467788888744
No 32
>KOG0320|consensus
Probab=78.71 E-value=0.62 Score=35.55 Aligned_cols=51 Identities=24% Similarity=0.436 Sum_probs=37.2
Q ss_pred ccCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 76 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 76 ~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
..+++|..|=....+ ...+.-+-|++||..|.........+|..|++.|..
T Consensus 129 ~~~~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSE-KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhh-ccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 457888888777653 123457899999999987654433489999998853
No 33
>PF12773 DZR: Double zinc ribbon
Probab=76.17 E-value=2.1 Score=25.31 Aligned_cols=9 Identities=22% Similarity=0.597 Sum_probs=4.2
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 344554443
No 34
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=75.87 E-value=1.8 Score=24.98 Aligned_cols=43 Identities=23% Similarity=0.491 Sum_probs=26.1
Q ss_pred ccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCC
Q psy7480 81 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTK 123 (204)
Q Consensus 81 C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~ 123 (204)
|..|...+......+...=|.++|..|..+..+....|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 4555555532234456677888888888877621127877764
No 35
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=75.15 E-value=4.2 Score=28.16 Aligned_cols=32 Identities=16% Similarity=0.361 Sum_probs=21.1
Q ss_pred cccccCCccccCCCeEEEeCCeeecHHHHHHH
Q psy7480 144 FACQQCNHRFCVGDRFYLCDNKILCEYDYEER 175 (204)
Q Consensus 144 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 175 (204)
++|..|+.++-.|+.|+...+.+.--.||.+.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 35677777766666776665566667776654
No 36
>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=75.13 E-value=6.2 Score=25.44 Aligned_cols=60 Identities=18% Similarity=0.433 Sum_probs=30.8
Q ss_pred cccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCCCceEEecCCcccccCccccccCCccccC
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 155 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 155 (204)
.|..|..+|. ..++..+|..|...... ...|..|++++ .++.|-|.. =|.|..|+..++.
T Consensus 3 ~CP~C~~~L~-------~~~~~~~C~~C~~~~~~-~a~CPdC~~~L----e~LkACGAv----dYFC~~c~gLiSK 62 (70)
T PF07191_consen 3 TCPKCQQELE-------WQGGHYHCEACQKDYKK-EAFCPDCGQPL----EVLKACGAV----DYFCNHCHGLISK 62 (70)
T ss_dssp B-SSS-SBEE-------EETTEEEETTT--EEEE-EEE-TTT-SB-----EEEEETTEE----EEE-TTTT-EE-T
T ss_pred cCCCCCCccE-------EeCCEEECcccccccee-cccCCCcccHH----HHHHHhccc----ceeeccCCceeec
Confidence 4666766664 23467777777654221 23899999988 566766531 2468888888743
No 37
>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=74.52 E-value=2.3 Score=23.65 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=16.6
Q ss_pred ccccCCccccCCCeEEEeCCeeecHHHHH
Q psy7480 145 ACQQCNHRFCVGDRFYLCDNKILCEYDYE 173 (204)
Q Consensus 145 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 173 (204)
.|..|+.. .|...+|..||..|..
T Consensus 10 ~C~~C~~~-----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR-----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe-----EeEccCCEEEhhhCce
Confidence 36777553 4667889999977743
No 38
>KOG1813|consensus
Probab=73.98 E-value=1.8 Score=35.75 Aligned_cols=47 Identities=17% Similarity=0.335 Sum_probs=35.2
Q ss_pred CccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 78 CLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 78 Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
-|.|..|..... ......-+.-+|+.|..+.+...++|..|++.+.+
T Consensus 241 Pf~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred Cccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 467777877775 45667778888999988776543489999988866
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=71.25 E-value=2.8 Score=30.45 Aligned_cols=23 Identities=22% Similarity=0.520 Sum_probs=17.4
Q ss_pred cccCCCcccCcCCCeEEeeCCeeccccccc
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLILCKRDYL 109 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~ 109 (204)
.|..|+.+| |.++|.+||..|-.
T Consensus 30 hCp~Cg~PL-------F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL-------FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc-------eeeCCeEECCCCCc
Confidence 467787776 44999999988864
No 40
>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=70.48 E-value=2.2 Score=24.45 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=11.7
Q ss_pred cccCCccccCCCeEEEeCCeeecHHH
Q psy7480 146 CQQCNHRFCVGDRFYLCDNKILCEYD 171 (204)
Q Consensus 146 C~~C~~~l~~~~~~~~~~~~~~C~~c 171 (204)
|..|+.+| |-..+|+.||..|
T Consensus 20 Cp~C~~PL-----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL-----MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee-----EEecCCCEECCCC
Confidence 55566665 3345666666544
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=69.21 E-value=2.4 Score=30.84 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=18.5
Q ss_pred cccCCccccCCCeEEEeCCeeecHHHHH
Q psy7480 146 CQQCNHRFCVGDRFYLCDNKILCEYDYE 173 (204)
Q Consensus 146 C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 173 (204)
|..|+.+| |- .+|.+||..|-.
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 88899988 55 899999999963
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=68.06 E-value=1.5 Score=34.24 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=25.2
Q ss_pred cccccCCccccCCCeEEEeCCeeecHHHHHHH
Q psy7480 144 FACQQCNHRFCVGDRFYLCDNKILCEYDYEER 175 (204)
Q Consensus 144 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 175 (204)
-+|+.|+..+ ....-...||+++|..|+.+.
T Consensus 173 v~C~kCGE~~-~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELF-MEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCccc-ccchhhhcCCceecccccccc
Confidence 5799999998 555566689999999999754
No 43
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=67.33 E-value=1.2 Score=34.69 Aligned_cols=48 Identities=19% Similarity=0.376 Sum_probs=36.3
Q ss_pred cCccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 77 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 77 ~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
.-|.|..|.+... ++....-|.-+|..|+.+.+...+.|..|++...|
T Consensus 195 IPF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 195 IPFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred Cceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 3578888888775 45667788889999988776443489999888766
No 44
>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=67.07 E-value=0.8 Score=25.30 Aligned_cols=28 Identities=21% Similarity=0.474 Sum_probs=15.0
Q ss_pred cccCCccccCCCeEEEeCCeeecHHHHHH
Q psy7480 146 CQQCNHRFCVGDRFYLCDNKILCEYDYEE 174 (204)
Q Consensus 146 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 174 (204)
|..|+.++ ...+.....+..+|..|...
T Consensus 6 C~~CGe~I-~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPI-PEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBE-EHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChH-HHHHHHhCCCcEECHHHhCc
Confidence 66666666 33344445666777777654
No 45
>KOG0978|consensus
Probab=66.33 E-value=0.91 Score=41.91 Aligned_cols=48 Identities=23% Similarity=0.540 Sum_probs=33.1
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccC-cccccccCCccCCCc
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPAFE 129 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~-~~~C~~C~~~I~~~~ 129 (204)
++|+.|+.... ......-+++||..|...++.. +-+|+.|+.+..++|
T Consensus 644 LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 57777775554 2345667788888888776653 237999999886654
No 46
>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=64.78 E-value=3.4 Score=22.95 Aligned_cols=38 Identities=18% Similarity=0.431 Sum_probs=21.8
Q ss_pred ccCCCcccCcCCCe-EEeeCCeecccccccccccCccccccc
Q psy7480 81 CGCCDCRLGEVGST-LYQKANLILCKRDYLRLFGTTGYCAAC 121 (204)
Q Consensus 81 C~~C~~~L~~~~~~-~~~~~g~~~C~~cy~~~~~~~~~C~~C 121 (204)
|..|...+. .. ....-|..||..|..+......+|..|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 445656554 34 467788889988877654432255443
No 47
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=64.13 E-value=6.6 Score=26.78 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=14.3
Q ss_pred cccccCCccccCCCeEEEeCCeeecHHHH
Q psy7480 144 FACQQCNHRFCVGDRFYLCDNKILCEYDY 172 (204)
Q Consensus 144 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 172 (204)
|+|..|+.++..|+.|......+.--+|+
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl 35 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECL 35 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHH
Confidence 45555555555555555433333334444
No 48
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=64.02 E-value=6.3 Score=24.47 Aligned_cols=29 Identities=28% Similarity=0.446 Sum_probs=17.1
Q ss_pred CCccccccccccccceeEeecCccccccCccccCCCcc
Q psy7480 50 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCR 87 (204)
Q Consensus 50 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~ 87 (204)
..++|..|+..|.+.+.. --|.|..|+..
T Consensus 6 ~~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKA---------VKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCCcccCCCcc---------CEeeCCCCCCe
Confidence 345677887777654211 11677777665
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=62.17 E-value=7.1 Score=23.95 Aligned_cols=45 Identities=18% Similarity=0.424 Sum_probs=27.0
Q ss_pred cccCCCcccCcCC-CeEEeeCCeecccccccccccCcccccccCCccC
Q psy7480 80 KCGCCDCRLGEVG-STLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 80 ~C~~C~~~L~~~~-~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
.|..|++.|.... ..+.-.-.=.||.+|....+.. .|..|+..+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~--~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG--VCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC--cCcCCCCccc
Confidence 3555666665221 2333233345788888877665 8999987664
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.63 E-value=8.2 Score=35.79 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=10.8
Q ss_pred ccccccccccCcccccccCCcc
Q psy7480 104 CKRDYLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 104 C~~cy~~~~~~~~~C~~C~~~I 125 (204)
|..|-...-.....|..|+..+
T Consensus 30 Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 30 CPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCCCCCCCcccccccccCCcc
Confidence 5555544332223566666654
No 51
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=57.79 E-value=12 Score=34.87 Aligned_cols=86 Identities=19% Similarity=0.372 Sum_probs=57.4
Q ss_pred CCCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccccc-cccccCcccccccCCcc
Q psy7480 47 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY-LRLFGTTGYCAACTKVI 125 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy-~~~~~~~~~C~~C~~~I 125 (204)
..+...+|..|-+.|.+. .++.||--=-.|..||-.+. +....||=..-. .+.|. .|..|.+
T Consensus 97 I~pD~a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRfT-------Ii~alPYDR~nTsM~~F~---lC~~C~~-- 159 (750)
T COG0068 97 IPPDAATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRFT-------IIEALPYDRENTSMADFP---LCPFCDK-- 159 (750)
T ss_pred cCCchhhhHHHHHHhcCC-----CCcceeccccccCCCCccee-------eeccCCCCcccCccccCc---CCHHHHH--
Confidence 456778999999988876 36778877778999987653 222233221111 12222 6888865
Q ss_pred CCCceEEecCCcccccCccccccCCccc
Q psy7480 126 PAFEMVMRAKNNVYHLECFACQQCNHRF 153 (204)
Q Consensus 126 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 153 (204)
++-...++.||.+=..|..|+-.+
T Consensus 160 ----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 160 ----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred ----HhcCccccccccccccCcccCCCe
Confidence 344556888999999999998876
No 52
>PRK00420 hypothetical protein; Validated
Probab=57.10 E-value=4.5 Score=28.67 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=4.1
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
.|..|+.++
T Consensus 25 ~CP~Cg~pL 33 (112)
T PRK00420 25 HCPVCGLPL 33 (112)
T ss_pred CCCCCCCcc
Confidence 444454444
No 53
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=56.05 E-value=7 Score=19.30 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=3.6
Q ss_pred ccccCCcc
Q psy7480 118 CAACTKVI 125 (204)
Q Consensus 118 C~~C~~~I 125 (204)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 54
>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=55.99 E-value=11 Score=21.92 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=7.9
Q ss_pred CeeecHHHHHHH
Q psy7480 164 NKILCEYDYEER 175 (204)
Q Consensus 164 ~~~~C~~c~~~~ 175 (204)
+--+|..||...
T Consensus 22 d~dLC~~Cf~~~ 33 (46)
T cd02249 22 DFDLCSSCYAKG 33 (46)
T ss_pred CCcCHHHHHCcC
Confidence 344788887753
No 55
>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=54.38 E-value=5.5 Score=29.78 Aligned_cols=51 Identities=16% Similarity=0.320 Sum_probs=35.2
Q ss_pred CeecccccccccccCcccccccCCccCCCc---eEEecCCcccccCccccccCCccccC
Q psy7480 100 NLILCKRDYLRLFGTTGYCAACTKVIPAFE---MVMRAKNNVYHLECFACQQCNHRFCV 155 (204)
Q Consensus 100 g~~~C~~cy~~~~~~~~~C~~C~~~I~~~~---~~~~~~~~~~H~~Cf~C~~C~~~l~~ 155 (204)
..-||..|-.+... .|..|+.+|.|.. .++.. +..|+.-- -|..||+++..
T Consensus 27 ~~~fC~kCG~~tI~---~Cp~C~~~IrG~y~v~gv~~~-g~~~~~Ps-YC~~CGkpyPW 80 (158)
T PF10083_consen 27 REKFCSKCGAKTIT---SCPNCSTPIRGDYHVEGVFGL-GGHYEAPS-YCHNCGKPYPW 80 (158)
T ss_pred HHHHHHHhhHHHHH---HCcCCCCCCCCceecCCeeee-CCCCCCCh-hHHhCCCCCch
Confidence 35589999888776 7999999998742 23323 45566332 38889998843
No 56
>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=53.69 E-value=5.8 Score=26.03 Aligned_cols=13 Identities=38% Similarity=0.639 Sum_probs=9.3
Q ss_pred cccccCCccCCCc
Q psy7480 117 YCAACTKVIPAFE 129 (204)
Q Consensus 117 ~C~~C~~~I~~~~ 129 (204)
+|..|++.|.-++
T Consensus 9 ~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 9 KCKGCKKKIAKGE 21 (82)
T ss_dssp BETTTSCBE-TTS
T ss_pred cCcccCCcCCCCC
Confidence 7999999986533
No 57
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=51.80 E-value=5.6 Score=22.64 Aligned_cols=11 Identities=0% Similarity=-0.019 Sum_probs=5.1
Q ss_pred CCeeccccccc
Q psy7480 99 ANLILCKRDYL 109 (204)
Q Consensus 99 ~g~~~C~~cy~ 109 (204)
=|..||..|..
T Consensus 21 C~H~fh~~Ci~ 31 (44)
T PF13639_consen 21 CGHVFHRSCIK 31 (44)
T ss_dssp TSEEEEHHHHH
T ss_pred CCCeeCHHHHH
Confidence 44444444443
No 58
>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=50.91 E-value=14 Score=21.15 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=7.2
Q ss_pred eeecHHHHHH
Q psy7480 165 KILCEYDYEE 174 (204)
Q Consensus 165 ~~~C~~c~~~ 174 (204)
.-+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 3478888875
No 59
>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=50.38 E-value=11 Score=18.95 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=5.7
Q ss_pred ccccCCccCC
Q psy7480 118 CAACTKVIPA 127 (204)
Q Consensus 118 C~~C~~~I~~ 127 (204)
|..|+..|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 4556666654
No 60
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=49.73 E-value=6.9 Score=25.97 Aligned_cols=29 Identities=28% Similarity=0.640 Sum_probs=18.1
Q ss_pred ccccCCccccCCCeEEE-eC---CeeecHHHHH
Q psy7480 145 ACQQCNHRFCVGDRFYL-CD---NKILCEYDYE 173 (204)
Q Consensus 145 ~C~~C~~~l~~~~~~~~-~~---~~~~C~~c~~ 173 (204)
.|..|+.||.....+.. .| +.-||.-||.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 48888888843332322 22 4568999985
No 61
>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=48.75 E-value=11 Score=25.50 Aligned_cols=37 Identities=27% Similarity=0.582 Sum_probs=25.3
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
-.|..|...+.. .|.-||..|-.+. +.|+-|++.|..
T Consensus 45 ~~C~~CK~~v~q--------~g~~YCq~CAYkk----GiCamCGKki~d 81 (90)
T PF10235_consen 45 SKCKICKTKVHQ--------PGAKYCQTCAYKK----GICAMCGKKILD 81 (90)
T ss_pred cccccccccccc--------CCCccChhhhccc----CcccccCCeecc
Confidence 356777666642 2556899995543 289999999854
No 62
>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=47.60 E-value=34 Score=19.37 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=18.0
Q ss_pred ccccCCccccCCCeEEE-eCCeeecHHHHHHH
Q psy7480 145 ACQQCNHRFCVGDRFYL-CDNKILCEYDYEER 175 (204)
Q Consensus 145 ~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~ 175 (204)
.|+-|+++......... .++...|..|....
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 58888888744444444 33777899997754
No 63
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=47.50 E-value=16 Score=28.53 Aligned_cols=11 Identities=18% Similarity=0.670 Sum_probs=8.7
Q ss_pred cccccCCccCC
Q psy7480 117 YCAACTKVIPA 127 (204)
Q Consensus 117 ~C~~C~~~I~~ 127 (204)
+|..|...|..
T Consensus 70 ~CPvCR~~Is~ 80 (193)
T PLN03208 70 KCPVCKSDVSE 80 (193)
T ss_pred cCCCCCCcCCh
Confidence 78888888854
No 64
>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=47.38 E-value=8.8 Score=21.06 Aligned_cols=26 Identities=12% Similarity=0.429 Sum_probs=11.9
Q ss_pred CCeecccccccccccC-cccccccCCc
Q psy7480 99 ANLILCKRDYLRLFGT-TGYCAACTKV 124 (204)
Q Consensus 99 ~g~~~C~~cy~~~~~~-~~~C~~C~~~ 124 (204)
-|..||..|....+.. ..+|..|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 4455555555433221 1256666543
No 65
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=45.99 E-value=20 Score=21.08 Aligned_cols=11 Identities=18% Similarity=0.123 Sum_probs=7.9
Q ss_pred eeecHHHHHHH
Q psy7480 165 KILCEYDYEER 175 (204)
Q Consensus 165 ~~~C~~c~~~~ 175 (204)
--+|..||...
T Consensus 24 ~dLC~~Cf~~g 34 (49)
T cd02335 24 FDLCLECFSAG 34 (49)
T ss_pred cchhHHhhhCc
Confidence 44788888754
No 66
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.70 E-value=7.7 Score=33.71 Aligned_cols=15 Identities=13% Similarity=0.222 Sum_probs=8.7
Q ss_pred CCccccccccccccc
Q psy7480 50 GLKECASCGKRITER 64 (204)
Q Consensus 50 ~~~~C~~C~~~I~~~ 64 (204)
....|..|...+...
T Consensus 25 ~~l~C~IC~d~~~~P 39 (397)
T TIGR00599 25 TSLRCHICKDFFDVP 39 (397)
T ss_pred cccCCCcCchhhhCc
Confidence 345677776655443
No 67
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=45.44 E-value=16 Score=22.21 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=18.4
Q ss_pred ccccccccccccceeEeecCcccccc
Q psy7480 52 KECASCGKRITERFLLKALDLFWHED 77 (204)
Q Consensus 52 ~~C~~C~~~I~~~~~~~~~~~~~H~~ 77 (204)
.+|..|+.+|.....+...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 46888999988875555555566655
No 68
>KOG3002|consensus
Probab=43.79 E-value=14 Score=30.81 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=30.7
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccC
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
+-|..|...|.. -.++-.+|.+.|..|-.++.. +|..|..+|.
T Consensus 49 leCPvC~~~l~~--Pi~QC~nGHlaCssC~~~~~~---~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSP--PIFQCDNGHLACSSCRTKVSN---KCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcc--cceecCCCcEehhhhhhhhcc---cCCccccccc
Confidence 566677777752 345667888888888765554 7888888885
No 69
>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=43.48 E-value=29 Score=20.07 Aligned_cols=10 Identities=30% Similarity=0.458 Sum_probs=7.5
Q ss_pred eeecHHHHHH
Q psy7480 165 KILCEYDYEE 174 (204)
Q Consensus 165 ~~~C~~c~~~ 174 (204)
-=+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 3489999986
No 70
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=43.02 E-value=27 Score=23.00 Aligned_cols=31 Identities=29% Similarity=0.601 Sum_probs=10.0
Q ss_pred ccccCCcccc---CCCeEEEe-C-CeeecHHHHHHH
Q psy7480 145 ACQQCNHRFC---VGDRFYLC-D-NKILCEYDYEER 175 (204)
Q Consensus 145 ~C~~C~~~l~---~~~~~~~~-~-~~~~C~~c~~~~ 175 (204)
.|..|+..++ .|+-|+.- + +.|.|+.||+-.
T Consensus 11 iCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE 46 (80)
T PF14569_consen 11 ICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE 46 (80)
T ss_dssp B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH
T ss_pred ccccccCccccCCCCCEEEEEcccCCccchhHHHHH
Confidence 3555555543 24445442 2 667899999743
No 71
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=42.29 E-value=5.7 Score=26.85 Aligned_cols=16 Identities=44% Similarity=0.949 Sum_probs=13.0
Q ss_pred ccccccCcccccccCCcc
Q psy7480 108 YLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 108 y~~~~~~~~~C~~C~~~I 125 (204)
|...|.. .|.+|++.+
T Consensus 49 Y~~lfs~--pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFST--PCKKCGKLL 64 (90)
T ss_pred Hhhhccc--hhhHHHhHh
Confidence 5667777 899999988
No 72
>KOG4739|consensus
Probab=42.09 E-value=28 Score=27.99 Aligned_cols=33 Identities=15% Similarity=0.292 Sum_probs=26.1
Q ss_pred CeEEeeCCeecccccccccccCcccccccCCccCC
Q psy7480 93 STLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 127 (204)
Q Consensus 93 ~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~ 127 (204)
..|..--..++|..|.....+. .|..|++.|..
T Consensus 17 ~f~LTaC~HvfC~~C~k~~~~~--~C~lCkk~ir~ 49 (233)
T KOG4739|consen 17 PFFLTACRHVFCEPCLKASSPD--VCPLCKKSIRI 49 (233)
T ss_pred ceeeeechhhhhhhhcccCCcc--ccccccceeee
Confidence 3445667889999998888876 89999998843
No 73
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=41.92 E-value=12 Score=29.36 Aligned_cols=31 Identities=16% Similarity=0.215 Sum_probs=23.0
Q ss_pred ccccCCCcccCcCCCeEEeeCCeeccccccccc
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 111 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~ 111 (204)
-+|+.|+..+.+ ..-...+|+++|..||.+.
T Consensus 173 v~C~kCGE~~~e--~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFME--PRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCccccc--chhhhcCCceecccccccc
Confidence 578888887753 3346778999999998754
No 74
>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=41.69 E-value=27 Score=20.37 Aligned_cols=31 Identities=23% Similarity=0.436 Sum_probs=19.5
Q ss_pred cccccCCccccCCCeEEE-e-CCeeecHHHHHHH
Q psy7480 144 FACQQCNHRFCVGDRFYL-C-DNKILCEYDYEER 175 (204)
Q Consensus 144 f~C~~C~~~l~~~~~~~~-~-~~~~~C~~c~~~~ 175 (204)
+.|..|+..+ ...+|.- + .+..+|..||.+-
T Consensus 1 y~C~~Cg~D~-t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 1 YHCFTCGNDC-TRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred CcccCCCCcc-CceEEEecCCCccccChHHHhCc
Confidence 3577777777 3444432 1 2467899999853
No 75
>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=41.48 E-value=14 Score=22.29 Aligned_cols=27 Identities=26% Similarity=0.397 Sum_probs=13.4
Q ss_pred ccccCCccccCCCeEEEeCCeeec-HHHH
Q psy7480 145 ACQQCNHRFCVGDRFYLCDNKILC-EYDY 172 (204)
Q Consensus 145 ~C~~C~~~l~~~~~~~~~~~~~~C-~~c~ 172 (204)
.|..|...+ ....-+..||+.|| ..|.
T Consensus 9 aC~~C~C~V-~~~~Ai~~dGk~YCS~aCA 36 (52)
T PF02069_consen 9 ACPSCSCVV-SEEEAIQKDGKYYCSEACA 36 (52)
T ss_dssp SSTT----B--TTTSEESSS-EESSHHHH
T ss_pred cCCCCEeEE-CchHhHHhCCEeeecHHHh
Confidence 377788887 33445558999998 4443
No 76
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.36 E-value=23 Score=22.96 Aligned_cols=44 Identities=18% Similarity=0.381 Sum_probs=26.5
Q ss_pred ccCCCcccCc-CCCeEEeeCCeecccccccccccCcccccccCCccC
Q psy7480 81 CGCCDCRLGE-VGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 126 (204)
Q Consensus 81 C~~C~~~L~~-~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~ 126 (204)
|..|++.|.. .+....-.-.-.||.+|....+.. .|..|+..+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g--~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHG--LCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC--cCCCCCchhh
Confidence 4556666652 122222223345788888877776 8999987654
No 77
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.82 E-value=22 Score=33.17 Aligned_cols=38 Identities=21% Similarity=0.333 Sum_probs=24.4
Q ss_pred cccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCc
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 124 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~ 124 (204)
+|..|+.+|. |....+.+.|.-|-...... .|..|+..
T Consensus 394 ~C~~C~~~L~-----~h~~~~~l~Ch~CG~~~~p~--~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG-----LPSAGGTPRCRWCGRAAPDW--RCPRCGSD 431 (665)
T ss_pred ECCCCCCcee-----EecCCCeeECCCCcCCCcCc--cCCCCcCC
Confidence 3444544443 33446688899996655444 89999875
No 78
>KOG3579|consensus
Probab=39.00 E-value=36 Score=28.19 Aligned_cols=49 Identities=14% Similarity=0.391 Sum_probs=32.0
Q ss_pred CccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeecccc
Q psy7480 51 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 106 (204)
Q Consensus 51 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~ 106 (204)
.-.|..|++.+.+.-.+.--.-.-|+-||-|+. ..|.. ....|.+||..
T Consensus 268 pLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~-----Qg~sgevYCPS 316 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQ-----QGASGEVYCPS 316 (352)
T ss_pred ceeehhhhhhhccCceeecCCCcccceecccCH--HHHHh-----hcCCCceeCCC
Confidence 346888999998885465666678888888753 23321 23356778853
No 79
>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=38.84 E-value=28 Score=20.61 Aligned_cols=10 Identities=20% Similarity=0.155 Sum_probs=7.5
Q ss_pred eecHHHHHHH
Q psy7480 166 ILCEYDYEER 175 (204)
Q Consensus 166 ~~C~~c~~~~ 175 (204)
=+|..||...
T Consensus 27 DlC~~C~~~~ 36 (48)
T cd02341 27 DLCQDCVVKG 36 (48)
T ss_pred ccCHHHHhCc
Confidence 3789998764
No 80
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=38.66 E-value=9.2 Score=26.36 Aligned_cols=28 Identities=18% Similarity=0.320 Sum_probs=17.0
Q ss_pred ccccccCCccccCCCeEE-EeCCeeecHHH
Q psy7480 143 CFACQQCNHRFCVGDRFY-LCDNKILCEYD 171 (204)
Q Consensus 143 Cf~C~~C~~~l~~~~~~~-~~~~~~~C~~c 171 (204)
=|+|+.|--.- .-.+.. ..+|++||..|
T Consensus 70 EFTCssCFLV~-HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVH-HRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEe-chhhhccccCCCEecccc
Confidence 37787775443 222222 45789999887
No 81
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=38.56 E-value=29 Score=20.47 Aligned_cols=11 Identities=27% Similarity=0.404 Sum_probs=8.0
Q ss_pred eeecHHHHHHH
Q psy7480 165 KILCEYDYEER 175 (204)
Q Consensus 165 ~~~C~~c~~~~ 175 (204)
--+|..||...
T Consensus 24 ~dlC~~Cf~~~ 34 (49)
T cd02338 24 YDLCADCYDSG 34 (49)
T ss_pred CccchhHHhCC
Confidence 34799998854
No 82
>TIGR03119 one_C_fhcD formylmethanofuran--tetrahydromethanopterin N-formyltransferase. Members of this protein family are the FhcD protein of tetrahydromethanopterin (H4MPT)-dependent C-1 carrier metabolism. In the archaea, FhcD is designated formylmethanofuran--tetrahydromethanopterin N-formyltransferase, while in bacteria it is commonly designated as formyltransferase/hydrolase complex subunit D. FhcD is essential for one-carbon metabolism in at least three groups of prokaryotes: methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria.
Probab=37.76 E-value=14 Score=30.30 Aligned_cols=18 Identities=28% Similarity=0.495 Sum_probs=15.3
Q ss_pred ccceeeeccCCccccccc
Q psy7480 3 TRRMWYIDICDYRSYFDS 20 (204)
Q Consensus 3 ~~~~~~~~~~~~~~~~~s 20 (204)
.||+||+++||=....+.
T Consensus 129 Grr~wrIPVMdGEFl~E~ 146 (287)
T TIGR03119 129 GRRYWRIPVMDGEFLCED 146 (287)
T ss_pred CEEEEEEEeccCcEEEEE
Confidence 599999999998877744
No 83
>KOG4443|consensus
Probab=36.86 E-value=15 Score=33.74 Aligned_cols=89 Identities=25% Similarity=0.567 Sum_probs=46.8
Q ss_pred CCCCCccccccccccccceeEe------ecCccc-cccCccccCCCcccCcCCCeEEeeCCeecccccccccccCccccc
Q psy7480 47 ASGGLKECASCGKRITERFLLK------ALDLFW-HEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA 119 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~~~~~------~~~~~~-H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~ 119 (204)
....+..|.-|++.-... .+. .+.+.| =+.|-.|..|+. .++ ...-++|+.|-.... .
T Consensus 31 ~ag~m~ac~~c~~~yH~~-cvt~~~~~~~l~~gWrC~~crvCe~c~~-~gD-------~~kf~~Ck~cDvsyh------~ 95 (694)
T KOG4443|consen 31 RAGRLLACSDCGQKYHPY-CVTSWAQHAVLSGGWRCPSCRVCEACGT-TGD-------PKKFLLCKRCDVSYH------C 95 (694)
T ss_pred ccCcchhhhhhcccCCcc-hhhHHHhHHHhcCCcccCCceeeeeccc-cCC-------ccccccccccccccc------c
Confidence 444566677776543332 111 112223 234555666652 221 123456777755432 2
Q ss_pred ccCCccCCCceEEecCCcccccCccccccCCcccc
Q psy7480 120 ACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 154 (204)
Q Consensus 120 ~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 154 (204)
.|.+|.. +.++ .+..+-++|+.|..|+..+.
T Consensus 96 yc~~P~~--~~v~--sg~~~ckk~~~c~qc~~~lp 126 (694)
T KOG4443|consen 96 YCQKPPN--DKVP--SGPWLCKKCTRCRQCDSTLP 126 (694)
T ss_pred cccCCcc--cccc--CcccccHHHHhhhhcccccc
Confidence 3555553 2332 36677889999999998883
No 84
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.99 E-value=13 Score=23.07 Aligned_cols=12 Identities=42% Similarity=0.980 Sum_probs=7.6
Q ss_pred Cccccccccccc
Q psy7480 51 LKECASCGKRIT 62 (204)
Q Consensus 51 ~~~C~~C~~~I~ 62 (204)
.+.|..|+..|.
T Consensus 9 ~~~CtSCg~~i~ 20 (61)
T COG2888 9 PPVCTSCGREIA 20 (61)
T ss_pred CceeccCCCEec
Confidence 456777776663
No 85
>PRK02114 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional
Probab=35.34 E-value=16 Score=30.13 Aligned_cols=19 Identities=32% Similarity=0.483 Sum_probs=15.9
Q ss_pred CccceeeeccCCccccccc
Q psy7480 2 PTRRMWYIDICDYRSYFDS 20 (204)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~s 20 (204)
-.|++||+++||=....+.
T Consensus 135 ~grr~wriPVMdGEFl~Ee 153 (297)
T PRK02114 135 GGRRYWRIPIMDGEFLIEE 153 (297)
T ss_pred CCEEEEEeeeccccEEEEE
Confidence 3599999999998887754
No 86
>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=34.76 E-value=17 Score=19.95 Aligned_cols=31 Identities=23% Similarity=0.518 Sum_probs=18.3
Q ss_pred ccccccccccceeEeecCccccccCccccCCCcccC
Q psy7480 54 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 89 (204)
Q Consensus 54 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 89 (204)
|..|.+.+.+. .++.||..=..|..||-.+.
T Consensus 2 C~~C~~Ey~~p-----~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDP-----SNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCST-----TSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHcCC-----CCCcccCcCccCCCCCCCEE
Confidence 56666655443 47889999999999987764
No 87
>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=34.64 E-value=36 Score=19.51 Aligned_cols=11 Identities=27% Similarity=0.676 Sum_probs=6.6
Q ss_pred cccccCCccCC
Q psy7480 117 YCAACTKVIPA 127 (204)
Q Consensus 117 ~C~~C~~~I~~ 127 (204)
.|.+|+++|.|
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 46666666544
No 88
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=34.55 E-value=30 Score=21.40 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=12.4
Q ss_pred cccCCCcccCcCCCeEEeeCCeeccc
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLILCK 105 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~~C~ 105 (204)
.|..|++.|......|..+..+.+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 34455566653223333444566664
No 89
>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=34.15 E-value=20 Score=18.62 Aligned_cols=10 Identities=30% Similarity=0.677 Sum_probs=4.9
Q ss_pred cccccCCccC
Q psy7480 117 YCAACTKVIP 126 (204)
Q Consensus 117 ~C~~C~~~I~ 126 (204)
+|..|+..|.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 6778887773
No 90
>KOG2462|consensus
Probab=33.80 E-value=20 Score=29.40 Aligned_cols=13 Identities=23% Similarity=0.416 Sum_probs=9.4
Q ss_pred cCccccCCCcccC
Q psy7480 77 DCLKCGCCDCRLG 89 (204)
Q Consensus 77 ~Cf~C~~C~~~L~ 89 (204)
..++|..|++...
T Consensus 129 ~r~~c~eCgk~ys 141 (279)
T KOG2462|consen 129 PRYKCPECGKSYS 141 (279)
T ss_pred Cceeccccccccc
Confidence 4567788887775
No 91
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=33.73 E-value=25 Score=17.71 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=4.9
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455565544
No 92
>PRK00807 50S ribosomal protein L24e; Validated
Probab=33.15 E-value=33 Score=20.65 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=15.1
Q ss_pred ccccccccccccc---eeEeecCcccc
Q psy7480 52 KECASCGKRITER---FLLKALDLFWH 75 (204)
Q Consensus 52 ~~C~~C~~~I~~~---~~~~~~~~~~H 75 (204)
..|..|+..|..+ ..+..+|+.|.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 3578888888743 22455666665
No 93
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.82 E-value=37 Score=30.55 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=20.5
Q ss_pred EEeeCCeecccccccccccCcccccccCCc
Q psy7480 95 LYQKANLILCKRDYLRLFGTTGYCAACTKV 124 (204)
Q Consensus 95 ~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~ 124 (204)
|....+.+.|..|-...-.+ ..|..|+..
T Consensus 234 ~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C~s~ 262 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQEPIP-KTCPQCGSE 262 (505)
T ss_pred EecCCCeEEcCCCcCcCCCC-CCCCCCCCC
Confidence 55667889999996554322 289999874
No 94
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.63 E-value=37 Score=32.10 Aligned_cols=40 Identities=20% Similarity=0.338 Sum_probs=26.6
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCc
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 124 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~ 124 (204)
++|..|+..|. |....+.+.|.-|-...--+ ..|..|+..
T Consensus 445 ~~Cp~Cd~~lt-----~H~~~~~L~CH~Cg~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT-----LHKATGQLRCHYCGYQEPIP-QSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE-----EecCCCeeEeCCCCCCCCCC-CCCCCCCCC
Confidence 35555665553 55667889999997653332 289999876
No 95
>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=31.49 E-value=9.5 Score=21.76 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=4.9
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
+|..|+...
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 466666544
No 96
>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=30.55 E-value=74 Score=18.61 Aligned_cols=28 Identities=18% Similarity=0.215 Sum_probs=17.3
Q ss_pred cccCCccccCCCeEEEeCCeeecHHHHHHHh
Q psy7480 146 CQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 176 (204)
Q Consensus 146 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 176 (204)
|..|+++... .. ...|...|..|-.+++
T Consensus 2 CiiC~~~~~~--GI-~I~~~fIC~~CE~~iv 29 (46)
T PF10764_consen 2 CIICGKEKEE--GI-HIYGKFICSDCEKEIV 29 (46)
T ss_pred eEeCCCcCCC--CE-EEECeEehHHHHHHhc
Confidence 6667776522 22 2457788888866654
No 97
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=30.43 E-value=19 Score=29.93 Aligned_cols=44 Identities=27% Similarity=0.651 Sum_probs=27.6
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCcc
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I 125 (204)
++|..|...|. -...-.-|.-||.-|.....+.++.|..|....
T Consensus 26 lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 45666666554 234445566677777777766666788777643
No 98
>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=30.41 E-value=22 Score=18.44 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=2.1
Q ss_pred ccccCCccc
Q psy7480 145 ACQQCNHRF 153 (204)
Q Consensus 145 ~C~~C~~~l 153 (204)
.|..|++++
T Consensus 2 ~C~~C~~~~ 10 (30)
T PF07649_consen 2 RCDACGKPI 10 (30)
T ss_dssp --TTTS---
T ss_pred cCCcCCCcC
Confidence 455555554
No 99
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=30.30 E-value=48 Score=21.16 Aligned_cols=48 Identities=8% Similarity=0.048 Sum_probs=29.7
Q ss_pred cCccccCCCcccCcCCCeEEeeCCeecccccccccccC-cccccccCCccCC
Q psy7480 77 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPA 127 (204)
Q Consensus 77 ~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~-~~~C~~C~~~I~~ 127 (204)
+=|.|..++..+. ......+|..|...+..+-+.. ...|..++.++..
T Consensus 3 ~~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 3478888887776 5677888899988776554332 2378888888764
No 100
>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=30.13 E-value=29 Score=31.11 Aligned_cols=36 Identities=31% Similarity=0.748 Sum_probs=20.8
Q ss_pred cccccCCccCCCceEEecCCcccccCccccccCCcccc
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 154 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 154 (204)
.|..|-..+...+ +.+.+..-..+||.|-.|...|.
T Consensus 28 yCp~CL~~~p~~e--~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 28 YCPNCLFEVPSSE--ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ECccccccCChhh--heeccceeccccccCCCCCCcce
Confidence 4666665554321 22333333448888888888883
No 101
>KOG2932|consensus
Probab=29.96 E-value=21 Score=29.86 Aligned_cols=42 Identities=17% Similarity=0.356 Sum_probs=26.6
Q ss_pred cccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCcc
Q psy7480 80 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 80 ~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I 125 (204)
-|..|+.+|.-.+ -.+.-+.+||.+|....--. .|..|...|
T Consensus 92 fCd~Cd~PI~IYG--RmIPCkHvFCl~CAr~~~dK--~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYG--RMIPCKHVFCLECARSDSDK--ICPLCDDRV 133 (389)
T ss_pred eecccCCcceeee--cccccchhhhhhhhhcCccc--cCcCcccHH
Confidence 4777888775222 23556677888876544333 688887776
No 102
>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=29.58 E-value=26 Score=29.35 Aligned_cols=30 Identities=23% Similarity=0.440 Sum_probs=18.8
Q ss_pred eCCeecccccccccccC-cccccccCCccCC
Q psy7480 98 KANLILCKRDYLRLFGT-TGYCAACTKVIPA 127 (204)
Q Consensus 98 ~~g~~~C~~cy~~~~~~-~~~C~~C~~~I~~ 127 (204)
.-|+.+|..|....|.. .+.|..|++++..
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 45666777777665421 1268888877754
No 103
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.31 E-value=52 Score=30.64 Aligned_cols=9 Identities=22% Similarity=0.711 Sum_probs=4.6
Q ss_pred ccCCCcccC
Q psy7480 81 CGCCDCRLG 89 (204)
Q Consensus 81 C~~C~~~L~ 89 (204)
|..|+..+.
T Consensus 30 Cp~CG~~~~ 38 (645)
T PRK14559 30 CPQCGTEVP 38 (645)
T ss_pred CCCCCCCCC
Confidence 455555543
No 104
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=28.58 E-value=33 Score=16.89 Aligned_cols=20 Identities=25% Similarity=0.512 Sum_probs=9.5
Q ss_pred ccccccccccCcccccccCC
Q psy7480 104 CKRDYLRLFGTTGYCAACTK 123 (204)
Q Consensus 104 C~~cy~~~~~~~~~C~~C~~ 123 (204)
|..|....+.....|..|+.
T Consensus 5 C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 5 CPACTFLNFASRSKCFACGA 24 (26)
T ss_pred CCCCCCcChhhhccccccCC
Confidence 44454444433335666654
No 105
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=28.53 E-value=23 Score=21.02 Aligned_cols=23 Identities=22% Similarity=0.651 Sum_probs=10.2
Q ss_pred eccccccccccc-CcccccccCCc
Q psy7480 102 ILCKRDYLRLFG-TTGYCAACTKV 124 (204)
Q Consensus 102 ~~C~~cy~~~~~-~~~~C~~C~~~ 124 (204)
-.|..||.+... ..++|.+|.++
T Consensus 23 ~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 23 QICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp ---HHHHHHHTTSS-SB-TTT--B
T ss_pred cHHHHHHHHHHhccCCCCCCCCCC
Confidence 357777765542 22488888765
No 106
>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=28.33 E-value=21 Score=24.26 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=8.9
Q ss_pred ccccccccccccceeEe
Q psy7480 52 KECASCGKRITERFLLK 68 (204)
Q Consensus 52 ~~C~~C~~~I~~~~~~~ 68 (204)
..|..|++++.-.+.+.
T Consensus 34 S~C~~C~~~L~~~~lIP 50 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIP 50 (92)
T ss_pred CcCcCCCCcCcccccch
Confidence 45666666655443333
No 107
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.23 E-value=44 Score=18.05 Aligned_cols=10 Identities=20% Similarity=0.388 Sum_probs=4.4
Q ss_pred eCCeeecHHH
Q psy7480 162 CDNKILCEYD 171 (204)
Q Consensus 162 ~~~~~~C~~c 171 (204)
.++..+|..|
T Consensus 18 ~~~~~~C~~C 27 (33)
T PF08792_consen 18 EDDYEVCIFC 27 (33)
T ss_pred cCCeEEcccC
Confidence 3444444444
No 108
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=26.96 E-value=49 Score=19.49 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=7.4
Q ss_pred eecHHHHHHH
Q psy7480 166 ILCEYDYEER 175 (204)
Q Consensus 166 ~~C~~c~~~~ 175 (204)
-+|..||...
T Consensus 25 dLC~~Cf~~~ 34 (49)
T cd02345 25 SLCLGCYTKG 34 (49)
T ss_pred CchHHHHhCC
Confidence 3789998754
No 109
>KOG0823|consensus
Probab=26.48 E-value=59 Score=26.02 Aligned_cols=51 Identities=12% Similarity=0.284 Sum_probs=35.7
Q ss_pred ccccCccccCCCcccCcCCCeEEeeCCeecccccccccccC---cccccccCCccCC
Q psy7480 74 WHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT---TGYCAACTKVIPA 127 (204)
Q Consensus 74 ~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~---~~~C~~C~~~I~~ 127 (204)
---..|.|..|-..-. ......-|++||-.|..+-... ...|..|+-.|..
T Consensus 43 ~~~~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCCceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 4455788888866654 5678889999999998653211 1257889888764
No 110
>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=26.01 E-value=45 Score=19.82 Aligned_cols=27 Identities=15% Similarity=0.383 Sum_probs=20.2
Q ss_pred cccccCCccCCC-ceEEecCCcccccCc
Q psy7480 117 YCAACTKVIPAF-EMVMRAKNNVYHLEC 143 (204)
Q Consensus 117 ~C~~C~~~I~~~-~~~~~~~~~~~H~~C 143 (204)
.|..|+.-..++ +..+.+.+..|+..|
T Consensus 15 ~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 15 KCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred cCcccCCcEeecCcceEEEeccceeeee
Confidence 788998887664 345677788888776
No 111
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=25.88 E-value=56 Score=30.82 Aligned_cols=86 Identities=17% Similarity=0.433 Sum_probs=54.2
Q ss_pred CCCCCccccccccccccceeEeecCccccccCccccCCCcccCcCCCeEEeeCCeeccccc-ccccccCcccccccCCcc
Q psy7480 47 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD-YLRLFGTTGYCAACTKVI 125 (204)
Q Consensus 47 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~~~g~~~C~~c-y~~~~~~~~~C~~C~~~I 125 (204)
......+|..|-+.+.+. .++.|+--=..|..||-... +....+|=..- ....|. .|..|.+-.
T Consensus 64 ippD~a~C~~Cl~E~~dp-----~~Rry~YpF~nCt~CGPr~~-------i~~~lpydr~~t~m~~f~---~C~~C~~ey 128 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDK-----NDRRYLYPFISCTHCGPRFT-------IIEALPYDRENTSMADFP---LCPDCAKEY 128 (711)
T ss_pred cCCchhhHHHHHHHhcCC-----CcccccCCcccccCCCCCeE-------EeecCCCCCCCcCCCCCc---CCHHHHHHh
Confidence 456778999999888765 36778877778999986643 11222221110 112233 677776544
Q ss_pred CCCceEEecCCcccccCccccccCCccc
Q psy7480 126 PAFEMVMRAKNNVYHLECFACQQCNHRF 153 (204)
Q Consensus 126 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 153 (204)
-.-.++.||-.=..|..|+-.|
T Consensus 129 ------~~p~~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 129 ------KDPLDRRFHAQPIACPRCGPQL 150 (711)
T ss_pred ------cCCccccCCCCCccCCCCCcEE
Confidence 2335777888888888888777
No 112
>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=25.79 E-value=51 Score=18.44 Aligned_cols=30 Identities=17% Similarity=0.476 Sum_probs=11.4
Q ss_pred ccccccccccccceeEeecCccccccCccccCCCc
Q psy7480 52 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDC 86 (204)
Q Consensus 52 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~ 86 (204)
.+|..|+-.|..--.+...++.| +|..|+.
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 45666666555442233334444 5666654
No 113
>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=25.28 E-value=28 Score=16.34 Aligned_cols=10 Identities=30% Similarity=1.112 Sum_probs=7.8
Q ss_pred cccccCCccc
Q psy7480 144 FACQQCNHRF 153 (204)
Q Consensus 144 f~C~~C~~~l 153 (204)
|.|..|++.+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 5788888877
No 114
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=25.20 E-value=64 Score=19.11 Aligned_cols=10 Identities=20% Similarity=0.291 Sum_probs=7.7
Q ss_pred eecHHHHHHH
Q psy7480 166 ILCEYDYEER 175 (204)
Q Consensus 166 ~~C~~c~~~~ 175 (204)
-+|..||...
T Consensus 25 DLC~~Cf~~g 34 (49)
T cd02334 25 DLCQSCFFSG 34 (49)
T ss_pred CchHHHHhCC
Confidence 3799998865
No 115
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.60 E-value=24 Score=19.36 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=3.0
Q ss_pred ccccCCc
Q psy7480 145 ACQQCNH 151 (204)
Q Consensus 145 ~C~~C~~ 151 (204)
+|..|+.
T Consensus 27 ~C~~C~~ 33 (36)
T PF13717_consen 27 RCSKCGH 33 (36)
T ss_pred ECCCCCC
Confidence 3444443
No 116
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.12 E-value=28 Score=20.05 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=16.1
Q ss_pred cccccCCccCCCceEEecCCcccccCccccccCCccc
Q psy7480 117 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 153 (204)
Q Consensus 117 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 153 (204)
+|..|+..+...+.. . -++|..|+..+
T Consensus 5 ~C~~CG~~~~~~~~~----~------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG----T------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC----C------ceECCCCCCeE
Confidence 688888766321111 1 35788887766
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.72 E-value=1e+02 Score=31.11 Aligned_cols=61 Identities=16% Similarity=0.265 Sum_probs=0.0
Q ss_pred ccccCCCcccCcCCCeEEeeCCeecccccccccccCcccccccCCccCCCceEEecCCcccccCccccccCCccccCCCe
Q psy7480 79 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDR 158 (204)
Q Consensus 79 f~C~~C~~~L~~~~~~~~~~~g~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~ 158 (204)
++|..|+.... ..+|..|-...-.. ..|..|+..+.+.+.. .. .|..|+.++ ....
T Consensus 668 rkCPkCG~~t~-----------~~fCP~CGs~te~v-y~CPsCGaev~~des~-a~----------~CP~CGtpl-v~~~ 723 (1337)
T PRK14714 668 RRCPSCGTETY-----------ENRCPDCGTHTEPV-YVCPDCGAEVPPDESG-RV----------ECPRCDVEL-TPYQ 723 (1337)
T ss_pred EECCCCCCccc-----------cccCcccCCcCCCc-eeCccCCCccCCCccc-cc----------cCCCCCCcc-cccc
Q ss_pred EEEeC
Q psy7480 159 FYLCD 163 (204)
Q Consensus 159 ~~~~~ 163 (204)
....+
T Consensus 724 ~~~i~ 728 (1337)
T PRK14714 724 RRTIN 728 (1337)
T ss_pred eEEec
No 118
>KOG2893|consensus
Probab=23.64 E-value=19 Score=28.99 Aligned_cols=37 Identities=19% Similarity=0.364 Sum_probs=24.1
Q ss_pred CCccccccccccccceeEeecCccccccCccccCCCcccC
Q psy7480 50 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 89 (204)
Q Consensus 50 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 89 (204)
..+-|-.|+..+.+..++..-.+ ..+|+|..|.+.|-
T Consensus 9 ~kpwcwycnrefddekiliqhqk---akhfkchichkkl~ 45 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILIQHQK---AKHFKCHICHKKLF 45 (341)
T ss_pred CCceeeecccccchhhhhhhhhh---hccceeeeehhhhc
Confidence 34568889888877743322222 34588888888774
No 119
>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=23.55 E-value=42 Score=19.66 Aligned_cols=14 Identities=36% Similarity=0.525 Sum_probs=9.1
Q ss_pred CCcccccccccccc
Q psy7480 50 GLKECASCGKRITE 63 (204)
Q Consensus 50 ~~~~C~~C~~~I~~ 63 (204)
....|..|++.|.+
T Consensus 10 ~~~~C~~C~~~i~g 23 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG 23 (53)
T ss_dssp STEB-TTSSSBECS
T ss_pred CCCCCcccCcccCC
Confidence 35578888888833
No 120
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.31 E-value=25 Score=25.96 Aligned_cols=38 Identities=21% Similarity=0.437 Sum_probs=22.4
Q ss_pred CCCccccccccccccceeEeecCccccccCccccCCCcccC
Q psy7480 49 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 89 (204)
Q Consensus 49 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 89 (204)
...-.|..|+......+.+...+. ..-|.|..|+..|.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 345568888876665433322221 23388888888775
No 121
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=23.22 E-value=76 Score=18.37 Aligned_cols=10 Identities=20% Similarity=0.391 Sum_probs=6.6
Q ss_pred eecHHHHHHH
Q psy7480 166 ILCEYDYEER 175 (204)
Q Consensus 166 ~~C~~c~~~~ 175 (204)
=+|..||.+.
T Consensus 25 DLC~~C~~~~ 34 (43)
T cd02342 25 DLCTICFSRM 34 (43)
T ss_pred ccHHHHhhhh
Confidence 3678887653
No 122
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.10 E-value=73 Score=29.83 Aligned_cols=57 Identities=18% Similarity=0.213 Sum_probs=30.9
Q ss_pred eEeecCccccccCccccCCCcccC----cCCCeEEeeCCeeccccccccc-ccCcccccccCCc
Q psy7480 66 LLKALDLFWHEDCLKCGCCDCRLG----EVGSTLYQKANLILCKRDYLRL-FGTTGYCAACTKV 124 (204)
Q Consensus 66 ~~~~~~~~~H~~Cf~C~~C~~~L~----~~~~~~~~~~g~~~C~~cy~~~-~~~~~~C~~C~~~ 124 (204)
++...++.-+..-+.|..|+..+. +..-.|....+.+.|..|-... ... .|..|+..
T Consensus 369 vll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~--~Cp~Cg~~ 430 (679)
T PRK05580 369 VLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPK--ACPECGST 430 (679)
T ss_pred EEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCC--CCCCCcCC
Confidence 444444443334444555544332 1111244457788899996554 333 89999775
No 123
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.07 E-value=59 Score=23.49 Aligned_cols=48 Identities=21% Similarity=0.418 Sum_probs=29.8
Q ss_pred cccccccccccCcccccccCCccCCCce--EEecCCcccccCccccccCCcccc
Q psy7480 103 LCKRDYLRLFGTTGYCAACTKVIPAFEM--VMRAKNNVYHLECFACQQCNHRFC 154 (204)
Q Consensus 103 ~C~~cy~~~~~~~~~C~~C~~~I~~~~~--~~~~~~~~~H~~Cf~C~~C~~~l~ 154 (204)
||..|-..... .|..|+.+|.|... -+...|.-|-+--| |..|++++.
T Consensus 30 fcskcgeati~---qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fp 79 (160)
T COG4306 30 FCSKCGEATIT---QCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFP 79 (160)
T ss_pred HHhhhchHHHh---cCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCC
Confidence 56666655554 68889999987421 12234555655443 778888774
No 124
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.84 E-value=33 Score=19.83 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=4.2
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
+|..|+..+
T Consensus 4 ~C~~Cg~~~ 12 (44)
T smart00659 4 ICGECGREN 12 (44)
T ss_pred ECCCCCCEe
Confidence 355555433
No 125
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=21.75 E-value=1.1e+02 Score=23.26 Aligned_cols=34 Identities=12% Similarity=0.153 Sum_probs=19.7
Q ss_pred cccCCccccCCCeEEEeC-CeeecHHHHHHHhhhhcc
Q psy7480 146 CQQCNHRFCVGDRFYLCD-NKILCEYDYEERQVFANI 181 (204)
Q Consensus 146 C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~~~~~~ 181 (204)
|.-|++.+.........+ ..-.|..|+ +|.....
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~ 40 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAK 40 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCcc
Confidence 889999984222222223 234599998 5543333
No 126
>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=21.73 E-value=17 Score=21.80 Aligned_cols=9 Identities=33% Similarity=1.080 Sum_probs=4.7
Q ss_pred cccccCCcc
Q psy7480 117 YCAACTKVI 125 (204)
Q Consensus 117 ~C~~C~~~I 125 (204)
+|..|++.+
T Consensus 6 RC~~CnklL 14 (51)
T PF10122_consen 6 RCGHCNKLL 14 (51)
T ss_pred eccchhHHH
Confidence 455555544
No 127
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.53 E-value=43 Score=26.66 Aligned_cols=32 Identities=16% Similarity=0.124 Sum_probs=22.1
Q ss_pred ccCccccccCCccccCCCeEEEeCCeeecHHHH
Q psy7480 140 HLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 172 (204)
Q Consensus 140 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 172 (204)
=++=..|..|++++ ....|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~-~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPG-DHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCC-CceEEecccCCccccccc
Confidence 34445688888887 334455678888888885
No 128
>KOG0320|consensus
Probab=21.42 E-value=64 Score=24.86 Aligned_cols=35 Identities=9% Similarity=0.189 Sum_probs=24.8
Q ss_pred CccccccCCccccCCCeEEEeCCeeecHHHHHHHh
Q psy7480 142 ECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 176 (204)
Q Consensus 142 ~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 176 (204)
.+|+|-.|-........+...=|++||+.|.....
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al 164 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL 164 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHH
Confidence 56888888777633334555668999999987764
No 129
>KOG1705|consensus
Probab=21.12 E-value=75 Score=21.56 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=4.9
Q ss_pred cccccCCccCC
Q psy7480 117 YCAACTKVIPA 127 (204)
Q Consensus 117 ~C~~C~~~I~~ 127 (204)
+|..|.-.+.+
T Consensus 29 kC~ICDS~VRP 39 (110)
T KOG1705|consen 29 KCVICDSYVRP 39 (110)
T ss_pred ccccccccccc
Confidence 44444444433
No 130
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=20.94 E-value=44 Score=17.20 Aligned_cols=14 Identities=7% Similarity=0.211 Sum_probs=6.9
Q ss_pred eeCCeecccccccc
Q psy7480 97 QKANLILCKRDYLR 110 (204)
Q Consensus 97 ~~~g~~~C~~cy~~ 110 (204)
..-+..+|..|...
T Consensus 14 ~~C~H~~c~~C~~~ 27 (39)
T smart00184 14 LPCGHTFCRSCIRK 27 (39)
T ss_pred ecCCChHHHHHHHH
Confidence 34445555555543
No 131
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.76 E-value=41 Score=20.30 Aligned_cols=9 Identities=44% Similarity=1.191 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy7480 54 CASCGKRIT 62 (204)
Q Consensus 54 C~~C~~~I~ 62 (204)
|..|++.|.
T Consensus 3 CPyCge~~~ 11 (52)
T PF14255_consen 3 CPYCGEPIE 11 (52)
T ss_pred CCCCCCeeE
Confidence 555555554
No 132
>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=20.75 E-value=53 Score=29.42 Aligned_cols=38 Identities=16% Similarity=0.336 Sum_probs=27.9
Q ss_pred CccccccccccccceeEeecCccccccCccccCCCcccC
Q psy7480 51 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 89 (204)
Q Consensus 51 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 89 (204)
...|..|-..+...+ +...+..-..+||.|..|...|.
T Consensus 26 ~~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred eeECccccccCChhh-heeccceeccccccCCCCCCcce
Confidence 456777777666553 45566677779999999998886
No 133
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.50 E-value=2.3e+02 Score=23.85 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=9.3
Q ss_pred CCCcccccccccc
Q psy7480 49 GGLKECASCGKRI 61 (204)
Q Consensus 49 ~~~~~C~~C~~~I 61 (204)
.....|..||..-
T Consensus 185 ~~~~~CPvCGs~P 197 (309)
T PRK03564 185 EQRQFCPVCGSMP 197 (309)
T ss_pred cCCCCCCCCCCcc
Confidence 3567899998753
No 134
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=20.25 E-value=54 Score=26.51 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=20.7
Q ss_pred cCccccccCCccccCCCeEEEeCCeeecHHHH
Q psy7480 141 LECFACQQCNHRFCVGDRFYLCDNKILCEYDY 172 (204)
Q Consensus 141 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 172 (204)
++=-.|..|+.+. ....|+...|...|.+|+
T Consensus 152 ~~l~~Ca~cg~~~-~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPV-DPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcC-CCcceeeccCcccchhcc
Confidence 3334577777777 444666677777777775
Done!