Query psy15163
Match_columns 176
No_of_seqs 174 out of 1208
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 22:11:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15163.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15163hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 1.8E-23 4E-28 167.3 -0.3 112 52-175 320-438 (468)
2 KOG1701|consensus 99.9 1.4E-23 3.1E-28 167.9 -3.0 97 73-176 276-372 (468)
3 KOG2272|consensus 99.8 1.5E-22 3.1E-27 152.4 -1.5 115 50-176 178-292 (332)
4 KOG2272|consensus 99.8 5.4E-22 1.2E-26 149.3 -3.9 101 70-176 11-111 (332)
5 KOG4577|consensus 99.8 5.5E-21 1.2E-25 146.3 -5.6 99 70-175 32-131 (383)
6 KOG1044|consensus 99.8 2.5E-19 5.4E-24 148.2 3.3 119 50-176 108-230 (670)
7 KOG1703|consensus 99.7 2.5E-18 5.5E-23 144.9 -0.3 111 54-175 350-461 (479)
8 KOG1703|consensus 99.6 8E-16 1.7E-20 129.8 3.5 98 72-176 304-401 (479)
9 PF00412 LIM: LIM domain; Int 99.6 3.6E-15 7.7E-20 90.6 4.3 58 74-135 1-58 (58)
10 KOG1044|consensus 99.2 7.1E-12 1.5E-16 104.5 4.2 86 72-175 17-102 (670)
11 KOG1700|consensus 99.2 1.7E-12 3.6E-17 97.7 -0.4 99 71-175 7-146 (200)
12 smart00132 LIM Zinc-binding do 99.0 3.6E-10 7.9E-15 62.6 2.5 38 139-176 1-39 (39)
13 PF00412 LIM: LIM domain; Int 98.9 7E-10 1.5E-14 67.0 2.7 37 140-176 1-38 (58)
14 KOG4577|consensus 98.7 1.7E-09 3.7E-14 83.6 -1.5 77 52-136 77-155 (383)
15 smart00132 LIM Zinc-binding do 98.7 2.1E-08 4.6E-13 55.3 2.8 38 73-114 1-38 (39)
16 KOG1700|consensus 98.0 1.3E-06 2.7E-11 66.0 -0.3 63 69-136 106-168 (200)
17 KOG1702|consensus 97.6 3.9E-06 8.5E-11 62.3 -3.0 59 73-136 6-64 (264)
18 KOG0490|consensus 97.5 7.6E-06 1.6E-10 62.8 -2.8 76 96-174 16-96 (235)
19 PF14446 Prok-RING_1: Prokaryo 91.3 0.14 3E-06 30.2 1.6 37 138-174 6-51 (54)
20 PF14446 Prok-RING_1: Prokaryo 90.9 0.16 3.4E-06 29.9 1.6 31 72-104 6-36 (54)
21 PF08394 Arc_trans_TRASH: Arch 89.0 0.17 3.7E-06 27.4 0.6 32 140-174 1-33 (37)
22 PF10367 Vps39_2: Vacuolar sor 85.6 0.58 1.3E-05 31.1 1.8 29 72-104 79-107 (109)
23 PF09943 DUF2175: Uncharacteri 85.5 0.31 6.7E-06 32.5 0.4 31 73-107 4-34 (101)
24 PF09943 DUF2175: Uncharacteri 85.2 0.25 5.3E-06 33.0 -0.1 28 139-166 4-32 (101)
25 PF14835 zf-RING_6: zf-RING of 80.1 1.6 3.5E-05 26.7 2.0 48 104-152 8-55 (65)
26 PF10367 Vps39_2: Vacuolar sor 79.9 1.1 2.4E-05 29.7 1.5 28 138-165 79-107 (109)
27 smart00504 Ubox Modified RING 79.8 1.4 3.1E-05 26.2 1.8 48 104-153 2-51 (63)
28 PF10235 Cript: Microtubule-as 79.2 1.3 2.8E-05 29.0 1.5 43 98-149 39-81 (90)
29 PF13240 zinc_ribbon_2: zinc-r 77.0 1.4 3.1E-05 21.1 0.9 9 140-148 2-10 (23)
30 PF13920 zf-C3HC4_3: Zinc fing 76.7 3.1 6.7E-05 23.7 2.5 42 105-148 4-48 (50)
31 PF10083 DUF2321: Uncharacteri 75.7 1.4 3E-05 31.8 1.0 49 123-174 27-78 (158)
32 KOG1813|consensus 74.7 1.7 3.6E-05 34.7 1.3 46 103-149 241-287 (313)
33 KOG0320|consensus 74.0 1.3 2.8E-05 32.7 0.5 53 100-152 128-182 (187)
34 PRK14890 putative Zn-ribbon RN 73.6 4.9 0.00011 24.1 2.8 14 72-85 8-21 (59)
35 COG4847 Uncharacterized protei 71.2 1.4 3E-05 29.0 0.1 29 138-166 7-36 (103)
36 COG5152 Uncharacterized conser 70.6 1.5 3.2E-05 33.0 0.1 49 101-150 194-243 (259)
37 PF00645 zf-PARP: Poly(ADP-rib 69.3 2.2 4.7E-05 27.1 0.7 17 72-88 8-24 (82)
38 COG0068 HypF Hydrogenase matur 67.0 8 0.00017 34.7 3.9 85 68-174 98-183 (750)
39 PLN03208 E3 ubiquitin-protein 67.0 8.2 0.00018 29.0 3.4 16 138-153 69-84 (193)
40 PF11781 RRN7: RNA polymerase 66.3 3.1 6.8E-05 22.3 0.8 23 105-131 10-32 (36)
41 PF10886 DUF2685: Protein of u 65.6 5.1 0.00011 23.5 1.7 25 138-162 2-26 (54)
42 COG2191 Formylmethanofuran deh 65.6 2.4 5.1E-05 32.0 0.4 31 104-134 173-203 (206)
43 PF06906 DUF1272: Protein of u 64.3 9.2 0.0002 22.7 2.6 26 124-150 29-54 (57)
44 KOG0978|consensus 62.9 1.8 3.8E-05 38.7 -0.9 16 138-153 679-694 (698)
45 PF14634 zf-RING_5: zinc-RING 62.5 8.1 0.00018 21.3 2.2 25 120-145 18-44 (44)
46 COG4847 Uncharacterized protei 61.6 3.8 8.3E-05 27.0 0.7 36 73-112 8-43 (103)
47 PF07754 DUF1610: Domain of un 61.1 6.9 0.00015 19.0 1.4 12 140-151 1-12 (24)
48 PF07191 zinc-ribbons_6: zinc- 60.5 2.5 5.4E-05 26.3 -0.2 10 138-147 31-40 (70)
49 cd00162 RING RING-finger (Real 59.1 5.9 0.00013 21.0 1.2 25 122-146 18-44 (45)
50 PF00096 zf-C2H2: Zinc finger, 58.3 5.3 0.00011 18.4 0.8 11 165-175 1-11 (23)
51 PF01258 zf-dskA_traR: Prokary 57.1 2.2 4.8E-05 22.6 -0.8 27 106-132 6-32 (36)
52 PF14471 DUF4428: Domain of un 55.4 9.5 0.00021 22.1 1.6 29 105-134 1-30 (51)
53 COG4357 Zinc finger domain con 52.4 1.2 2.6E-05 29.4 -2.7 52 73-129 37-88 (105)
54 PF11571 Med27: Mediator compl 51.7 4.3 9.3E-05 26.5 -0.3 18 129-147 47-64 (90)
55 COG2888 Predicted Zn-ribbon RN 50.5 20 0.00043 21.6 2.4 16 72-87 10-25 (61)
56 KOG2932|consensus 49.8 8.6 0.00019 31.0 1.1 43 105-148 92-134 (389)
57 PF02069 Metallothio_Pro: Prok 49.4 9.9 0.00021 22.2 1.0 28 105-132 9-37 (52)
58 PF13894 zf-C2H2_4: C2H2-type 49.1 9.6 0.00021 17.2 0.9 11 165-175 1-11 (24)
59 PF13923 zf-C3HC4_2: Zinc fing 48.9 6 0.00013 21.2 0.1 27 107-133 2-28 (39)
60 cd02336 ZZ_RSC8 Zinc finger, Z 46.4 20 0.00044 20.2 2.0 29 105-133 2-32 (45)
61 PF06677 Auto_anti-p27: Sjogre 46.2 10 0.00022 21.0 0.7 8 121-128 31-38 (41)
62 COG1645 Uncharacterized Zn-fin 45.2 9.8 0.00021 26.7 0.7 20 106-130 31-50 (131)
63 cd02249 ZZ Zinc finger, ZZ typ 44.8 19 0.0004 20.1 1.7 9 124-132 23-31 (46)
64 KOG3002|consensus 44.7 16 0.00034 29.5 1.9 43 104-148 49-91 (299)
65 PF12874 zf-met: Zinc-finger o 44.1 12 0.00026 17.5 0.8 12 165-176 1-12 (25)
66 PF13912 zf-C2H2_6: C2H2-type 43.8 12 0.00026 17.9 0.8 11 165-175 2-12 (27)
67 PF12171 zf-C2H2_jaz: Zinc-fin 43.0 16 0.00035 17.7 1.2 12 165-176 2-13 (27)
68 smart00291 ZnF_ZZ Zinc-binding 41.3 26 0.00056 19.3 2.0 10 124-133 27-36 (44)
69 KOG0823|consensus 41.3 40 0.00087 26.0 3.5 52 102-154 46-101 (230)
70 PF13248 zf-ribbon_3: zinc-rib 41.0 21 0.00045 17.3 1.4 7 73-79 18-24 (26)
71 PF12156 ATPase-cat_bd: Putati 40.8 12 0.00026 24.2 0.6 30 139-171 2-33 (88)
72 PRK00398 rpoP DNA-directed RNA 40.1 16 0.00036 20.3 1.0 10 138-147 22-31 (46)
73 KOG3579|consensus 39.0 17 0.00037 29.0 1.2 51 69-129 266-316 (352)
74 PF06827 zf-FPG_IleRS: Zinc fi 38.6 7.6 0.00017 19.5 -0.5 11 138-148 2-12 (30)
75 PF12674 Zn_ribbon_2: Putative 38.0 15 0.00033 23.5 0.7 28 106-133 3-35 (81)
76 COG4306 Uncharacterized protei 36.0 24 0.00051 24.6 1.4 46 126-174 30-78 (160)
77 PRK00420 hypothetical protein; 35.8 16 0.00035 25.0 0.6 10 73-82 25-34 (112)
78 KOG4739|consensus 35.5 27 0.00059 27.0 1.8 34 115-149 15-49 (233)
79 PF14569 zf-UDP: Zinc-binding 34.6 33 0.00071 21.8 1.8 23 124-146 36-60 (80)
80 KOG3476|consensus 34.2 5.2 0.00011 25.9 -1.9 37 104-149 55-91 (100)
81 PRK14873 primosome assembly pr 33.7 21 0.00045 32.1 1.1 36 107-146 396-431 (665)
82 PHA02775 E6; Provisional 33.7 10 0.00023 27.6 -0.6 14 73-86 45-58 (160)
83 PF12773 DZR: Double zinc ribb 33.2 39 0.00084 18.9 1.9 10 73-82 14-23 (50)
84 PF13465 zf-H2C2_2: Zinc-finge 31.7 26 0.00056 16.9 0.8 11 165-175 15-25 (26)
85 smart00249 PHD PHD zinc finger 31.5 37 0.0008 18.0 1.6 16 124-141 14-29 (47)
86 cd02341 ZZ_ZZZ3 Zinc finger, Z 31.3 49 0.0011 18.8 2.0 10 124-133 26-35 (48)
87 KOG4443|consensus 31.0 23 0.00051 31.5 0.9 18 157-174 108-125 (694)
88 PRK14559 putative protein seri 30.8 30 0.00066 31.0 1.6 11 73-83 3-13 (645)
89 PF00628 PHD: PHD-finger; Int 30.5 44 0.00095 18.6 1.8 29 74-105 2-30 (51)
90 PF04570 DUF581: Protein of un 30.3 35 0.00075 20.4 1.3 24 105-128 18-43 (58)
91 PF14149 YhfH: YhfH-like prote 30.0 17 0.00037 19.6 -0.0 18 131-148 7-24 (37)
92 COG0266 Nei Formamidopyrimidin 30.0 29 0.00064 27.6 1.3 28 135-164 244-271 (273)
93 PF05502 Dynactin_p62: Dynacti 29.9 35 0.00076 29.4 1.8 41 69-115 24-64 (483)
94 PF15135 UPF0515: Uncharacteri 29.7 65 0.0014 25.3 3.0 75 55-153 112-190 (278)
95 PF14255 Cys_rich_CPXG: Cystei 29.0 15 0.00032 21.4 -0.4 11 157-167 20-30 (52)
96 PHA02779 E6 protein; Provision 29.0 13 0.00029 26.7 -0.7 25 138-162 102-128 (150)
97 COG3813 Uncharacterized protei 28.8 53 0.0011 20.6 2.0 27 124-151 29-55 (84)
98 TIGR02420 dksA RNA polymerase- 28.6 11 0.00023 25.5 -1.2 10 139-148 82-91 (110)
99 cd02335 ZZ_ADA2 Zinc finger, Z 28.4 60 0.0013 18.3 2.1 9 125-133 25-33 (49)
100 PF00569 ZZ: Zinc finger, ZZ t 28.1 45 0.00097 18.6 1.5 10 124-133 28-37 (46)
101 PF04810 zf-Sec23_Sec24: Sec23 27.5 44 0.00095 18.1 1.4 30 138-172 3-32 (40)
102 KOG2462|consensus 27.4 33 0.00071 27.2 1.1 38 138-176 188-227 (279)
103 PF05502 Dynactin_p62: Dynacti 27.4 44 0.00096 28.8 2.0 12 163-174 51-62 (483)
104 smart00531 TFIIE Transcription 26.2 22 0.00048 25.3 -0.0 33 139-174 101-133 (147)
105 smart00355 ZnF_C2H2 zinc finge 25.5 33 0.00071 15.4 0.6 11 165-175 1-11 (26)
106 PF13834 DUF4193: Domain of un 25.5 20 0.00044 23.8 -0.3 31 100-130 67-98 (99)
107 PRK01103 formamidopyrimidine/5 25.1 37 0.00081 26.8 1.1 29 134-164 243-271 (274)
108 PF04641 Rtf2: Rtf2 RING-finge 24.8 1.1E+02 0.0023 24.0 3.6 55 99-154 109-167 (260)
109 PRK12495 hypothetical protein; 24.8 52 0.0011 25.3 1.7 11 104-114 43-53 (226)
110 cd02340 ZZ_NBR1_like Zinc fing 24.8 68 0.0015 17.7 1.8 7 126-132 25-31 (43)
111 PHA02610 uvsY.-2 hypothetical 24.5 57 0.0012 19.0 1.5 25 138-162 2-26 (53)
112 PRK14891 50S ribosomal protein 23.7 67 0.0015 22.5 2.0 20 72-91 5-24 (131)
113 TIGR00599 rad18 DNA repair pro 23.0 46 0.001 28.0 1.3 10 139-148 62-71 (397)
114 PHA02929 N1R/p28-like protein; 23.0 30 0.00066 26.9 0.2 25 122-147 200-226 (238)
115 PHA02768 hypothetical protein; 22.9 15 0.00033 21.7 -1.1 12 104-115 6-17 (55)
116 KOG3579|consensus 22.6 44 0.00096 26.8 1.0 53 104-168 269-321 (352)
117 COG1656 Uncharacterized conser 22.5 35 0.00075 25.0 0.4 36 138-173 98-139 (165)
118 KOG2114|consensus 22.0 36 0.00078 31.4 0.5 38 139-176 842-884 (933)
119 KOG2893|consensus 21.9 22 0.00049 27.7 -0.7 34 72-113 11-44 (341)
120 PF04564 U-box: U-box domain; 21.6 1.3E+02 0.0029 18.3 3.0 50 102-153 3-55 (73)
121 PRK14810 formamidopyrimidine-D 21.4 50 0.0011 26.1 1.1 28 135-164 243-270 (272)
122 PRK10445 endonuclease VIII; Pr 21.2 48 0.001 26.0 1.0 29 134-164 233-261 (263)
123 PF07649 C1_3: C1-like domain; 21.0 55 0.0012 16.2 0.9 11 105-115 2-12 (30)
124 PF11077 DUF2616: Protein of u 21.0 48 0.001 24.5 0.9 18 118-135 154-171 (173)
125 PF01286 XPA_N: XPA protein N- 20.7 43 0.00092 17.7 0.4 10 73-82 5-14 (34)
126 PRK14811 formamidopyrimidine-D 20.6 53 0.0011 25.9 1.1 11 138-148 236-246 (269)
127 PRK11595 DNA utilization prote 20.4 94 0.002 23.7 2.5 10 73-82 7-16 (227)
128 PF03854 zf-P11: P-11 zinc fin 20.2 1E+02 0.0022 17.7 1.9 27 122-148 19-46 (50)
No 1
>KOG1701|consensus
Probab=99.86 E-value=1.8e-23 Score=167.31 Aligned_cols=112 Identities=25% Similarity=0.643 Sum_probs=94.8
Q ss_pred CCCCcccCCCCCCccCCCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceee-eCCcccCHhH
Q psy15163 52 SGNGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFH-YKGNVYCLRD 130 (176)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~g~~yC~~~ 130 (176)
.+..+||+.||.. +..+|..|++.|. ++|+.|. |+.||+.||+|..|++.|.+..|.+ .++++||-.|
T Consensus 320 v~~k~~CE~cyq~-----tlekC~~Cg~~I~--d~iLrA~----GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~d 388 (468)
T KOG1701|consen 320 VDGKPYCEGCYQD-----TLEKCNKCGEPIM--DRILRAL----GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPD 388 (468)
T ss_pred cCCcccchHHHHH-----HHHHHhhhhhHHH--HHHHHhc----ccccCCCceEEEEeccccCCccccccCCCceeeehh
Confidence 3444666666553 2348999999997 4566775 8899999999999999999988876 7889999999
Q ss_pred HhhCCCcccccccccccccCc------eEEeCCCccccCCeecccCCcccC
Q psy15163 131 YATMLDIPRCHACDELIFVNE------YTLAENKTFHVKHFCCYECDKIIT 175 (176)
Q Consensus 131 y~~~~~~~~C~~C~~~I~~~~------~~~a~~~~~H~~CF~C~~C~~~l~ 175 (176)
|+++|+ |+|+.|+++|+..+ .|.++++.||.+||+|..|+..|+
T Consensus 389 fh~kfA-PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 389 FHKKFA-PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred hhhhcC-cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCcccc
Confidence 999999 99999999998642 256999999999999999999987
No 2
>KOG1701|consensus
Probab=99.85 E-value=1.4e-23 Score=167.94 Aligned_cols=97 Identities=31% Similarity=0.658 Sum_probs=90.0
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccccCce
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEY 152 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~~~~ 152 (176)
+|.+|+|.|...+..+.|+ ++.||..||+|..|++.|.+..||..++++||+.||.+.+ .||..|+++|++ .|
T Consensus 276 iC~~C~K~V~g~~~ac~Am----~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl--ekC~~Cg~~I~d-~i 348 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAM----DQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL--EKCNKCGEPIMD-RI 348 (468)
T ss_pred hhhhcCCcccCcchHHHHh----hhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--HHHhhhhhHHHH-HH
Confidence 8999999999888878887 8899999999999999999999999999999999998775 599999999965 58
Q ss_pred EEeCCCccccCCeecccCCcccCC
Q psy15163 153 TLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 153 ~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
++|+|+.||+.||+|..|.+.|++
T Consensus 349 LrA~GkayHp~CF~Cv~C~r~ldg 372 (468)
T KOG1701|consen 349 LRALGKAYHPGCFTCVVCARCLDG 372 (468)
T ss_pred HHhcccccCCCceEEEEeccccCC
Confidence 889999999999999999998864
No 3
>KOG2272|consensus
Probab=99.84 E-value=1.5e-22 Score=152.43 Aligned_cols=115 Identities=26% Similarity=0.614 Sum_probs=102.5
Q ss_pred cCCCCCcccCCCCCCccCCCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHh
Q psy15163 50 HGSGNGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLR 129 (176)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~ 129 (176)
+.-.+..||.+|.++++-+ +|+.|+++|. +.++.++ |+.||.++|+|+.|.+|+-+...|++.|..||+.
T Consensus 178 Revk~eLyClrChD~mgip----iCgaC~rpIe--ervi~am----gKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~ 247 (332)
T KOG2272|consen 178 REVKGELYCLRCHDKMGIP----ICGACRRPIE--ERVIFAM----GKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCET 247 (332)
T ss_pred hhhccceeccccccccCCc----ccccccCchH--HHHHHHh----ccccchhheeehhcCCcccchhhhhhcCchhHHH
Confidence 3345568999999998877 9999999997 4555665 8899999999999999998889999999999999
Q ss_pred HHhhCCCcccccccccccccCceEEeCCCccccCCeecccCCcccCC
Q psy15163 130 DYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 130 ~y~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
+|.++|+ ..|..|+..| ++++++|+++.|-++||.|+.|++.|.+
T Consensus 248 h~~qLfG-~~CF~C~~~i-~G~vv~al~KawCv~cf~Cs~Cdkkl~~ 292 (332)
T KOG2272|consen 248 HYHQLFG-NLCFICNRVI-GGDVVSALNKAWCVECFSCSTCDKKLTQ 292 (332)
T ss_pred HHHHHhh-hhheecCCcc-CccHHHHhhhhhcccccccccccccccc
Confidence 9999999 9999999999 5567789999999999999999998863
No 4
>KOG2272|consensus
Probab=99.81 E-value=5.4e-22 Score=149.35 Aligned_cols=101 Identities=29% Similarity=0.733 Sum_probs=93.0
Q ss_pred CCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCccccccccccccc
Q psy15163 70 SGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFV 149 (176)
Q Consensus 70 ~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~ 149 (176)
....|.+|...+.+.|.++... +..||..||.|.+|-+|+.+..||..+|+.||+.+|..+|+ |.|..|++.|.+
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~----ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~Lfa-PcC~kC~EFiiG 85 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSN----GELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFA-PCCGKCGEFIIG 85 (332)
T ss_pred HHHHHHHHhccCCchhhhhccC----chhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhc-hhhcccccchhh
Confidence 3458999999999899888776 88999999999999999999999999999999999999999 999999999987
Q ss_pred CceEEeCCCccccCCeecccCCcccCC
Q psy15163 150 NEYTLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 150 ~~~~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
+ +|.|++.+|||.||+|..|.+.|.+
T Consensus 86 r-VikamnnSwHp~CF~Cd~Cn~~Lad 111 (332)
T KOG2272|consen 86 R-VIKAMNNSWHPACFRCDLCNKHLAD 111 (332)
T ss_pred H-HHHhhccccCcccchhHHHHHHHhh
Confidence 6 5669999999999999999998864
No 5
>KOG4577|consensus
Probab=99.76 E-value=5.5e-21 Score=146.31 Aligned_cols=99 Identities=27% Similarity=0.680 Sum_probs=88.7
Q ss_pred CCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCccccccccccccc
Q psy15163 70 SGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFV 149 (176)
Q Consensus 70 ~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~ 149 (176)
+.+.|+.|++.|. ..+|..+. ++.||..|++|+.|+.+|.. .+|.+++.+||+.+|.++|+ .||..|...|.+
T Consensus 32 eip~CagC~q~Il-DrFilKvl----~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG-TKCsaC~~GIpP 104 (383)
T KOG4577|consen 32 EIPICAGCDQHIL-DRFILKVL----DRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG-TKCSACQEGIPP 104 (383)
T ss_pred ccccccchHHHHH-HHHHHHHH----hhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC-CcchhhcCCCCh
Confidence 4459999999998 45665665 88999999999999999987 68899999999999999999 999999999987
Q ss_pred CceE-EeCCCccccCCeecccCCcccC
Q psy15163 150 NEYT-LAENKTFHVKHFCCYECDKIIT 175 (176)
Q Consensus 150 ~~~~-~a~~~~~H~~CF~C~~C~~~l~ 175 (176)
..++ .|.+.+||.+||.|..|+.+|.
T Consensus 105 tqVVRkAqd~VYHl~CF~C~iC~R~L~ 131 (383)
T KOG4577|consen 105 TQVVRKAQDFVYHLHCFACFICKRQLA 131 (383)
T ss_pred HHHHHHhhcceeehhhhhhHhhhcccc
Confidence 6665 5999999999999999999885
No 6
>KOG1044|consensus
Probab=99.76 E-value=2.5e-19 Score=148.21 Aligned_cols=119 Identities=26% Similarity=0.625 Sum_probs=99.5
Q ss_pred cCCCCCcccCCCCCCccCC----CCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcc
Q psy15163 50 HGSGNGVTHGPCGNKLTQP----RSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNV 125 (176)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~----~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~ 125 (176)
+..+..+.|..|...+... .+...|++|++.|..++.++++ ++.||..||+|..|...|.+ .|..++|.+
T Consensus 108 t~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llal-----d~qwhv~cfkc~~c~~vL~g-ey~skdg~p 181 (670)
T KOG1044|consen 108 TFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLAL-----DKQWHVSCFKCKSCSAVLNG-EYMSKDGVP 181 (670)
T ss_pred eecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeee-----ccceeeeeeehhhhcccccc-eeeccCCCc
Confidence 3344445666665433221 2456899999999999888777 88999999999999999977 689999999
Q ss_pred cCHhHHhhCCCcccccccccccccCceEEeCCCccccCCeecccCCcccCC
Q psy15163 126 YCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 126 yC~~~y~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
||+.||.+.|+ -+|..|.+.|.+ .+++|.++.|||.|-+|+.|+.+|++
T Consensus 182 yce~dy~~~fg-vkc~~c~~fisg-kvLqag~kh~HPtCARCsRCgqmF~e 230 (670)
T KOG1044|consen 182 YCEKDYQAKFG-VKCEECEKFISG-KVLQAGDKHFHPTCARCSRCGQMFGE 230 (670)
T ss_pred chhhhhhhhcC-eehHHhhhhhhh-hhhhccCcccCcchhhhhhhcccccc
Confidence 99999999999 899999999965 46779999999999999999998863
No 7
>KOG1703|consensus
Probab=99.69 E-value=2.5e-18 Score=144.87 Aligned_cols=111 Identities=27% Similarity=0.639 Sum_probs=95.1
Q ss_pred CCcccCCCCCCccCCCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhh
Q psy15163 54 NGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYAT 133 (176)
Q Consensus 54 ~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~ 133 (176)
+..+|..|+.+...+ .|.+|+++|. ++.+ .+. +..||++||.|..|.++|.+..|+..++.+||+.||.+
T Consensus 350 g~~~c~~~~~~~~~p----~C~~C~~~i~-~~~v-~a~----~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~ 419 (479)
T KOG1703|consen 350 GKILCHECFHAPFRP----NCKRCLLPIL-EEGV-CAL----GRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKK 419 (479)
T ss_pred CCccHHHHHHHhhCc----cccccCCchH-HhHh-hhc----cCeechhceeeecccCCCCCCcccccCCccchhhhHhh
Confidence 334566666666555 9999999998 4555 554 88999999999999999999999999999999999999
Q ss_pred CCCccccccccccccc-CceEEeCCCccccCCeecccCCcccC
Q psy15163 134 MLDIPRCHACDELIFV-NEYTLAENKTFHVKHFCCYECDKIIT 175 (176)
Q Consensus 134 ~~~~~~C~~C~~~I~~-~~~~~a~~~~~H~~CF~C~~C~~~l~ 175 (176)
++. ++|..|.++|+. ...+.+++..||.+||+|+.|.+.|.
T Consensus 420 ~~~-~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~ 461 (479)
T KOG1703|consen 420 LFT-TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLT 461 (479)
T ss_pred hcc-ccchhccchhHhhhhHhhccCccccccceehhhhhcccc
Confidence 999 999999999863 34577999999999999999998876
No 8
>KOG1703|consensus
Probab=99.58 E-value=8e-16 Score=129.79 Aligned_cols=98 Identities=26% Similarity=0.560 Sum_probs=87.0
Q ss_pred cccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccccCc
Q psy15163 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNE 151 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~~~ 151 (176)
+.|..|++.|.....+ .++ ++.||+.+|.|..|...+....+...+|++||..||...+. +.|.+|+.+|.+ .
T Consensus 304 p~c~~c~~~i~~~~~i-~~~----~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~-p~C~~C~~~i~~-~ 376 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVI-VAL----GKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR-PNCKRCLLPILE-E 376 (479)
T ss_pred ccccccccCcccceeE-eec----cccccccceeeccccccccCCCccccCCCccHHHHHHHhhC-ccccccCCchHH-h
Confidence 6999999999843444 554 88999999999999999988888889999999999999999 999999999976 4
Q ss_pred eEEeCCCccccCCeecccCCcccCC
Q psy15163 152 YTLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 152 ~~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
+|.|+++.||++||+|..|+++|.+
T Consensus 377 ~v~a~~~~wH~~cf~C~~C~~~~~~ 401 (479)
T KOG1703|consen 377 GVCALGRLWHPECFVCADCGKPLKN 401 (479)
T ss_pred HhhhccCeechhceeeecccCCCCC
Confidence 6668899999999999999988764
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=99.56 E-value=3.6e-15 Score=90.61 Aligned_cols=58 Identities=29% Similarity=0.820 Sum_probs=52.8
Q ss_pred cccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCC
Q psy15163 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATML 135 (176)
Q Consensus 74 C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~ 135 (176)
|.+|+++|.+++.++.+. ++.||++||+|..|+++|.+..++..++++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~----~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAM----GKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEET----TEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeC----CcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 789999999888776676 8899999999999999998888999999999999998865
No 10
>KOG1044|consensus
Probab=99.23 E-value=7.1e-12 Score=104.50 Aligned_cols=86 Identities=23% Similarity=0.542 Sum_probs=72.6
Q ss_pred cccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccccCc
Q psy15163 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNE 151 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~~~ 151 (176)
..|..|.+.-. ++++... ++.||..||.|..|+..|....||.+++. ++++ + ..|.+.|.+ +
T Consensus 17 i~c~~c~~kc~-gevlrv~-----d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~yg-t--~~c~~~~~g-e 78 (670)
T KOG1044|consen 17 IKCDKCRKKCS-GEVLRVN-----DNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYG-T--DDCRAFVEG-E 78 (670)
T ss_pred eehhhhCCccc-cceeEee-----ccccceeeeeccccCCCcccccceecccc--------eeec-c--cchhhhccc-e
Confidence 48999999988 7766555 88999999999999999999899987665 4444 4 678888854 5
Q ss_pred eEEeCCCccccCCeecccCCcccC
Q psy15163 152 YTLAENKTFHVKHFCCYECDKIIT 175 (176)
Q Consensus 152 ~~~a~~~~~H~~CF~C~~C~~~l~ 175 (176)
++.++++.||++||.|+.|+.++.
T Consensus 79 vvsa~gktyh~~cf~cs~ck~pf~ 102 (670)
T KOG1044|consen 79 VVSTLGKTYHPKCFSCSTCKSPFK 102 (670)
T ss_pred eEecccceeccccceecccCCCCC
Confidence 778999999999999999999874
No 11
>KOG1700|consensus
Probab=99.21 E-value=1.7e-12 Score=97.74 Aligned_cols=99 Identities=24% Similarity=0.551 Sum_probs=83.4
Q ss_pred CcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCC---------------
Q psy15163 71 GKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATML--------------- 135 (176)
Q Consensus 71 ~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~--------------- 135 (176)
...|..|++.++..+.+. .+ +..||+.||.|..|...|....+..+++.+||+.+|...+
T Consensus 7 ~~kc~~c~k~vy~~e~~~-~~----g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~ 81 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQ-KD----GVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG 81 (200)
T ss_pred cchhhhccCcchHHHHHh-cc----CcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccC
Confidence 348999999999877765 43 8899999999999999999888999999999999654443
Q ss_pred --------------------------CcccccccccccccCceEEeCCCccccCCeecccCCcccC
Q psy15163 136 --------------------------DIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKIIT 175 (176)
Q Consensus 136 --------------------------~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~l~ 175 (176)
. ..|..|++.+.+-+-+...+..||..||+|..|+..|+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~-~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls 146 (200)
T KOG1700|consen 82 GLGKDGKSLNESKPNQSAKFQVFAGEK-EKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLS 146 (200)
T ss_pred CCCcccccccccccccchhHHhhhccc-cccccccceeeehHHHhhhhhhhhhhheeecccccccC
Confidence 3 47888888887655556789999999999999999886
No 12
>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=98.97 E-value=3.6e-10 Score=62.55 Aligned_cols=38 Identities=26% Similarity=0.472 Sum_probs=33.6
Q ss_pred cccccccccccC-ceEEeCCCccccCCeecccCCcccCC
Q psy15163 139 RCHACDELIFVN-EYTLAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 139 ~C~~C~~~I~~~-~~~~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
+|..|+++|.+. .++.+.++.||++||+|..|+.+|.+
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 39 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLGG 39 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCcc
Confidence 589999999876 56678999999999999999999864
No 13
>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=98.92 E-value=7e-10 Score=67.05 Aligned_cols=37 Identities=30% Similarity=0.618 Sum_probs=33.3
Q ss_pred ccccccccccCceE-EeCCCccccCCeecccCCcccCC
Q psy15163 140 CHACDELIFVNEYT-LAENKTFHVKHFCCYECDKIITQ 176 (176)
Q Consensus 140 C~~C~~~I~~~~~~-~a~~~~~H~~CF~C~~C~~~l~~ 176 (176)
|..|+++|.+++++ .++++.||++||+|..|+++|.+
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 38 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND 38 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC
Confidence 78999999877765 69999999999999999999864
No 14
>KOG4577|consensus
Probab=98.68 E-value=1.7e-09 Score=83.60 Aligned_cols=77 Identities=18% Similarity=0.380 Sum_probs=62.9
Q ss_pred CCCCcccCCCCCCccCCCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCcccc-CCCceee-eCCcccCHh
Q psy15163 52 SGNGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELL-VDLMYFH-YKGNVYCLR 129 (176)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~-~~g~~yC~~ 129 (176)
.++++||...+-+-+.. +|..|...|.+.+.|..|. +..||..||.|..|+++| .+..||. .++++.|+.
T Consensus 77 R~~s~yCkedFfKrfGT----KCsaC~~GIpPtqVVRkAq----d~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~ 148 (383)
T KOG4577|consen 77 REGSVYCKEDFFKRFGT----KCSACQEGIPPTQVVRKAQ----DFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKD 148 (383)
T ss_pred cCCceeehHHHHHHhCC----cchhhcCCCChHHHHHHhh----cceeehhhhhhHhhhcccccCCeeEEeccceeehhh
Confidence 45668887776655554 9999999999988887776 889999999999999999 4456765 788999999
Q ss_pred HHhhCCC
Q psy15163 130 DYATMLD 136 (176)
Q Consensus 130 ~y~~~~~ 136 (176)
+|++.-.
T Consensus 149 DYE~Ak~ 155 (383)
T KOG4577|consen 149 DYETAKQ 155 (383)
T ss_pred hHHHHHh
Confidence 9986433
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=98.66 E-value=2.1e-08 Score=55.28 Aligned_cols=38 Identities=39% Similarity=1.044 Sum_probs=31.7
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccccCccccC
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLV 114 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 114 (176)
+|..|+++|.+.+.++.+. ++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~----~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRAL----GKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeC----CccccccCCCCcccCCcCc
Confidence 4889999998664555554 8899999999999999885
No 16
>KOG1700|consensus
Probab=97.98 E-value=1.3e-06 Score=65.95 Aligned_cols=63 Identities=22% Similarity=0.566 Sum_probs=55.3
Q ss_pred CCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCC
Q psy15163 69 RSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD 136 (176)
Q Consensus 69 ~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~ 136 (176)
.+...|..|.+.+++.+.+... +..||..||+|..|+..|....+...++.+||..++.+++-
T Consensus 106 g~~~~c~~c~k~vy~~Ek~~~~-----~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 106 GEKEKCARCQKTVYPLEKVTGN-----GLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFK 168 (200)
T ss_pred ccccccccccceeeehHHHhhh-----hhhhhhhheeecccccccCCcchhhcCCccccchhhheeec
Confidence 4556899999999988887655 88999999999999999999999999999999988877654
No 17
>KOG1702|consensus
Probab=97.58 E-value=3.9e-06 Score=62.33 Aligned_cols=59 Identities=27% Similarity=0.585 Sum_probs=51.3
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCC
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD 136 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~ 136 (176)
.|..|++.+++.|.+... ++.||..||+|..|+.+|.-.++-..+.++||..+|....+
T Consensus 6 n~~~cgk~vYPvE~v~cl-----dk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCL-----DKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred hhhhhccccccHHHHhhH-----HHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 688899999988887666 88999999999999999987777778999999999976554
No 18
>KOG0490|consensus
Probab=97.49 E-value=7.6e-06 Score=62.78 Aligned_cols=76 Identities=33% Similarity=0.750 Sum_probs=63.0
Q ss_pred CcccCccCcccccCccccC--CCceeeeCCcccCHhHHhh--CCCcccccccccccccCc-eEEeCCCccccCCeecccC
Q psy15163 96 QVLWHPQCFVCSTCDELLV--DLMYFHYKGNVYCLRDYAT--MLDIPRCHACDELIFVNE-YTLAENKTFHVKHFCCYEC 170 (176)
Q Consensus 96 ~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~~y~~--~~~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C 170 (176)
+..||..|..|..|...|. ...|.. +|..||..+|.. .+. .+|.+|...|..-+ +..+..++ |.-||.|.+|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~-~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~ 92 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS-KRCARCKFTISQLDELERAFEKV-HLPCFACREC 92 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc-ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHH
Confidence 6789999999999999997 444445 999999999998 777 89999999996544 44577777 9999999998
Q ss_pred Cccc
Q psy15163 171 DKII 174 (176)
Q Consensus 171 ~~~l 174 (176)
...+
T Consensus 93 la~~ 96 (235)
T KOG0490|consen 93 LALL 96 (235)
T ss_pred Hhhc
Confidence 7654
No 19
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.34 E-value=0.14 Score=30.16 Aligned_cols=37 Identities=14% Similarity=0.434 Sum_probs=27.1
Q ss_pred ccccccccccc-cCceEE--eCCCccccCCe----eccc--CCccc
Q psy15163 138 PRCHACDELIF-VNEYTL--AENKTFHVKHF----CCYE--CDKII 174 (176)
Q Consensus 138 ~~C~~C~~~I~-~~~~~~--a~~~~~H~~CF----~C~~--C~~~l 174 (176)
.+|..|++.|. +++++. .=+..||.+|+ .|.. |+..+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 78999999996 345553 56888999998 4766 66554
No 20
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.93 E-value=0.16 Score=29.94 Aligned_cols=31 Identities=26% Similarity=0.649 Sum_probs=20.7
Q ss_pred cccccccccccCCCeEEEEeccCCCcccCccCc
Q psy15163 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCF 104 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf 104 (176)
.+|..|+++|.+++-++.--.. +..||++|.
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~C--gapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPEC--GAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCCCEEECCCC--CCcccHHHH
Confidence 4899999999633334333334 458888887
No 21
>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=89.03 E-value=0.17 Score=27.41 Aligned_cols=32 Identities=28% Similarity=0.580 Sum_probs=23.1
Q ss_pred ccccccccccCceE-EeCCCccccCCeecccCCccc
Q psy15163 140 CHACDELIFVNEYT-LAENKTFHVKHFCCYECDKII 174 (176)
Q Consensus 140 C~~C~~~I~~~~~~-~a~~~~~H~~CF~C~~C~~~l 174 (176)
|..|++.|.+++++ ...++.|| |.|..|...|
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 77899999887764 57888887 5555555443
No 22
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=85.59 E-value=0.58 Score=31.09 Aligned_cols=29 Identities=21% Similarity=0.553 Sum_probs=21.1
Q ss_pred cccccccccccCCCeEEEEeccCCCcccCccCc
Q psy15163 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCF 104 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf 104 (176)
..|..|+++|....+++... |..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~----~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPC----GHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCC----CeEEecccc
Confidence 47999999998665555543 666787775
No 23
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=85.54 E-value=0.31 Score=32.53 Aligned_cols=31 Identities=29% Similarity=0.621 Sum_probs=23.8
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccc
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCS 107 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~ 107 (176)
.|..|+++|+.++...... +..-|.+||+=.
T Consensus 4 kC~iCg~~I~~gqlFTF~~----kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTK----KGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEec----CCcEeHHHHHHH
Confidence 7999999999888764443 557899998744
No 24
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=85.23 E-value=0.25 Score=33.00 Aligned_cols=28 Identities=18% Similarity=0.502 Sum_probs=22.0
Q ss_pred cccccccccccCceE-EeCCCccccCCee
Q psy15163 139 RCHACDELIFVNEYT-LAENKTFHVKHFC 166 (176)
Q Consensus 139 ~C~~C~~~I~~~~~~-~a~~~~~H~~CF~ 166 (176)
+|..|+++|..++.. ...+..-|-+||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
Confidence 799999999877654 3556788888885
No 25
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=80.09 E-value=1.6 Score=26.69 Aligned_cols=48 Identities=15% Similarity=0.472 Sum_probs=21.0
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccccCce
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEY 152 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~~~~ 152 (176)
++|+.|..-|...-....=+..||..|-.+.++ ..|..|+.|--..++
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~-~~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG-SECPVCHTPAWIQDI 55 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTT-TB-SSS--B-S-SS-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC-CCCCCcCChHHHHHH
Confidence 456666666544222334456778888877888 789999987754443
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=79.91 E-value=1.1 Score=29.66 Aligned_cols=28 Identities=11% Similarity=0.348 Sum_probs=14.9
Q ss_pred ccccccccccccCceEE-eCCCccccCCe
Q psy15163 138 PRCHACDELIFVNEYTL-AENKTFHVKHF 165 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~~-a~~~~~H~~CF 165 (176)
..|..|+++|....++. -.+..+|-.|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46677777764443332 33455565554
No 27
>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=79.84 E-value=1.4 Score=26.16 Aligned_cols=48 Identities=17% Similarity=0.222 Sum_probs=34.1
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhCC--CcccccccccccccCceE
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATML--DIPRCHACDELIFVNEYT 153 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~--~~~~C~~C~~~I~~~~~~ 153 (176)
|.|..|...+.. ......|..||+.+..+.+ . ..|..|++++....++
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~-~~cP~~~~~~~~~~l~ 51 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSH-GTDPVTGQPLTHEDLI 51 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHC-CCCCCCcCCCChhhce
Confidence 567888887765 4556778999988876433 3 5799999888554444
No 28
>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=79.18 E-value=1.3 Score=29.04 Aligned_cols=43 Identities=21% Similarity=0.438 Sum_probs=29.6
Q ss_pred ccCccCcccccCccccCCCceeeeCCcccCHhHHhhCCCccccccccccccc
Q psy15163 98 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFV 149 (176)
Q Consensus 98 ~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~ 149 (176)
.|-+.--.|..|...+.. .|.-||..|..+. -+|+-|++.|.+
T Consensus 39 Py~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk---GiCamCGKki~d 81 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK---GICAMCGKKILD 81 (90)
T ss_pred cccccCcccccccccccc------CCCccChhhhccc---CcccccCCeecc
Confidence 344433467777766543 3567899997664 589999999964
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.02 E-value=1.4 Score=21.09 Aligned_cols=9 Identities=33% Similarity=0.704 Sum_probs=5.1
Q ss_pred ccccccccc
Q psy15163 140 CHACDELIF 148 (176)
Q Consensus 140 C~~C~~~I~ 148 (176)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555666653
No 30
>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=76.72 E-value=3.1 Score=23.67 Aligned_cols=42 Identities=21% Similarity=0.428 Sum_probs=26.3
Q ss_pred ccccCccccCCCceeeeCCcc-cCHhHHhhC--CCcccccccccccc
Q psy15163 105 VCSTCDELLVDLMYFHYKGNV-YCLRDYATM--LDIPRCHACDELIF 148 (176)
Q Consensus 105 ~C~~C~~~l~~~~~~~~~g~~-yC~~~y~~~--~~~~~C~~C~~~I~ 148 (176)
.|..|...... ..+..=|.. +|..|+.+. .. .+|..|+++|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~-~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRK-KKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTT-SBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccC-CCCCcCChhhc
Confidence 45555555443 334455666 888888765 34 79999999984
No 31
>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=75.68 E-value=1.4 Score=31.79 Aligned_cols=49 Identities=16% Similarity=0.354 Sum_probs=34.5
Q ss_pred CcccCHhHHhhCCCcccccccccccccCceE---EeCCCccccCCeecccCCccc
Q psy15163 123 GNVYCLRDYATMLDIPRCHACDELIFVNEYT---LAENKTFHVKHFCCYECDKII 174 (176)
Q Consensus 123 g~~yC~~~y~~~~~~~~C~~C~~~I~~~~~~---~a~~~~~H~~CF~C~~C~~~l 174 (176)
.+-||..|-.+... .|..|+-+|.+.-++ ...+..|++-= -|..|++++
T Consensus 27 ~~~fC~kCG~~tI~--~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpy 78 (158)
T PF10083_consen 27 REKFCSKCGAKTIT--SCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPY 78 (158)
T ss_pred HHHHHHHhhHHHHH--HCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCC
Confidence 35689999887764 999999999765322 34567777433 378888875
No 32
>KOG1813|consensus
Probab=74.65 E-value=1.7 Score=34.68 Aligned_cols=46 Identities=15% Similarity=0.311 Sum_probs=36.6
Q ss_pred CcccccCccccCCCceeeeCCcccCHhHHhhCCCc-cccccccccccc
Q psy15163 103 CFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDI-PRCHACDELIFV 149 (176)
Q Consensus 103 Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~-~~C~~C~~~I~~ 149 (176)
=|.|..|.+.+.. .....-+..+|+.|....|.. ++|..|++.+.+
T Consensus 241 Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred Ccccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 3788899888855 455567788999999887754 799999999965
No 33
>KOG0320|consensus
Probab=73.99 E-value=1.3 Score=32.73 Aligned_cols=53 Identities=17% Similarity=0.439 Sum_probs=38.3
Q ss_pred CccCcccccCccccCCCc-eeeeCCcccCHhHHhhCCCc-ccccccccccccCce
Q psy15163 100 HPQCFVCSTCDELLVDLM-YFHYKGNVYCLRDYATMLDI-PRCHACDELIFVNEY 152 (176)
Q Consensus 100 H~~Cf~C~~C~~~l~~~~-~~~~~g~~yC~~~y~~~~~~-~~C~~C~~~I~~~~~ 152 (176)
-..+|+|-.|-....... +..+=|.+||+.|-.+.... .+|..|++.|....+
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence 446788888877775543 45688999999998764321 699999998854433
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.56 E-value=4.9 Score=24.10 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=10.4
Q ss_pred cccccccccccCCC
Q psy15163 72 KTCKQCGQEVRSGD 85 (176)
Q Consensus 72 ~~C~~C~~~i~~~~ 85 (176)
..|..|+..|.+.+
T Consensus 8 ~~CtSCg~~i~~~~ 21 (59)
T PRK14890 8 PKCTSCGIEIAPRE 21 (59)
T ss_pred ccccCCCCcccCCC
Confidence 37888888887554
No 35
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.23 E-value=1.4 Score=28.97 Aligned_cols=29 Identities=17% Similarity=0.399 Sum_probs=21.0
Q ss_pred ccccccccccccCce-EEeCCCccccCCee
Q psy15163 138 PRCHACDELIFVNEY-TLAENKTFHVKHFC 166 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~-~~a~~~~~H~~CF~ 166 (176)
-+|..|+++|..++. +-.....-|-+||.
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~ 36 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLA 36 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHH
Confidence 479999998876654 33557778888875
No 36
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=70.59 E-value=1.5 Score=33.01 Aligned_cols=49 Identities=14% Similarity=0.316 Sum_probs=37.5
Q ss_pred ccCcccccCccccCCCceeeeCCcccCHhHHhhCCCc-ccccccccccccC
Q psy15163 101 PQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDI-PRCHACDELIFVN 150 (176)
Q Consensus 101 ~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~-~~C~~C~~~I~~~ 150 (176)
..=|.|..|.+-... .....-|..||..|+.+.+.. +.|..|++...+.
T Consensus 194 ~IPF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 194 KIPFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred CCceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 345899999887755 455567888999999877633 8999999887654
No 37
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=69.28 E-value=2.2 Score=27.10 Aligned_cols=17 Identities=29% Similarity=0.880 Sum_probs=12.8
Q ss_pred cccccccccccCCCeEE
Q psy15163 72 KTCKQCGQEVRSGDLAV 88 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~ 88 (176)
..|..|++.|..++.-+
T Consensus 8 a~Ck~C~~~I~kg~lRi 24 (82)
T PF00645_consen 8 AKCKGCKKKIAKGELRI 24 (82)
T ss_dssp EBETTTSCBE-TTSEEE
T ss_pred ccCcccCCcCCCCCEEE
Confidence 48999999998777643
No 38
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=67.00 E-value=8 Score=34.70 Aligned_cols=85 Identities=22% Similarity=0.503 Sum_probs=55.6
Q ss_pred CCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhHHh-hCCCcccccccccc
Q psy15163 68 PRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA-TMLDIPRCHACDEL 146 (176)
Q Consensus 68 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~-~~~~~~~C~~C~~~ 146 (176)
++....|..|.+.|.+.. ++.||--=-.|+.|+..+ -+.+.-||=..... ..| +-|..|.+
T Consensus 98 ~pD~a~C~~Cl~Ei~dp~----------~rrY~YPF~~CT~CGPRf-----TIi~alPYDR~nTsM~~F--~lC~~C~~- 159 (750)
T COG0068 98 PPDAATCEDCLEEIFDPN----------SRRYLYPFINCTNCGPRF-----TIIEALPYDRENTSMADF--PLCPFCDK- 159 (750)
T ss_pred CCchhhhHHHHHHhcCCC----------CcceeccccccCCCCcce-----eeeccCCCCcccCccccC--cCCHHHHH-
Confidence 456679999999997421 445665556788887654 34444454332221 222 67888875
Q ss_pred cccCceEEeCCCccccCCeecccCCccc
Q psy15163 147 IFVNEYTLAENKTFHVKHFCCYECDKII 174 (176)
Q Consensus 147 I~~~~~~~a~~~~~H~~CF~C~~C~~~l 174 (176)
+|....++.||.+=..|..|+-.+
T Consensus 160 ----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 160 ----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred ----HhcCccccccccccccCcccCCCe
Confidence 234457999999999999998754
No 39
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=66.99 E-value=8.2 Score=28.98 Aligned_cols=16 Identities=19% Similarity=0.563 Sum_probs=12.6
Q ss_pred ccccccccccccCceE
Q psy15163 138 PRCHACDELIFVNEYT 153 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~ 153 (176)
++|..|...|....++
T Consensus 69 ~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 69 PKCPVCKSDVSEATLV 84 (193)
T ss_pred CcCCCCCCcCChhcEE
Confidence 6899999999765554
No 40
>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=66.25 E-value=3.1 Score=22.28 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=15.4
Q ss_pred ccccCccccCCCceeeeCCcccCHhHH
Q psy15163 105 VCSTCDELLVDLMYFHYKGNVYCLRDY 131 (176)
Q Consensus 105 ~C~~C~~~l~~~~~~~~~g~~yC~~~y 131 (176)
.|..|+.. .|...+|..||..|-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCc
Confidence 46666553 466788888886664
No 41
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=65.63 E-value=5.1 Score=23.54 Aligned_cols=25 Identities=20% Similarity=0.216 Sum_probs=17.4
Q ss_pred ccccccccccccCceEEeCCCcccc
Q psy15163 138 PRCHACDELIFVNEYTLAENKTFHV 162 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~~a~~~~~H~ 162 (176)
.+|..|.++|.....+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 4799999999765445455556665
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=65.61 E-value=2.4 Score=32.00 Aligned_cols=31 Identities=23% Similarity=0.393 Sum_probs=25.2
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhC
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATM 134 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~ 134 (176)
-+|..|+..+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788888888776667789999999998754
No 43
>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=64.25 E-value=9.2 Score=22.65 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=19.7
Q ss_pred cccCHhHHhhCCCcccccccccccccC
Q psy15163 124 NVYCLRDYATMLDIPRCHACDELIFVN 150 (176)
Q Consensus 124 ~~yC~~~y~~~~~~~~C~~C~~~I~~~ 150 (176)
=-||..|....+. ..|..|++.+..+
T Consensus 29 CTFC~~C~e~~l~-~~CPNCgGelv~R 54 (57)
T PF06906_consen 29 CTFCADCAETMLN-GVCPNCGGELVRR 54 (57)
T ss_pred CcccHHHHHHHhc-CcCcCCCCccccC
Confidence 3468888888877 7999998876544
No 44
>KOG0978|consensus
Probab=62.93 E-value=1.8 Score=38.68 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=12.5
Q ss_pred ccccccccccccCceE
Q psy15163 138 PRCHACDELIFVNEYT 153 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~ 153 (176)
.+|..|+.+..++++.
T Consensus 679 RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVH 694 (698)
T ss_pred CCCCCCCCCCCccccc
Confidence 5899999988766653
No 45
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=62.54 E-value=8.1 Score=21.30 Aligned_cols=25 Identities=16% Similarity=0.574 Sum_probs=16.0
Q ss_pred eeCCcccCHhHHhhCC--Cccccccccc
Q psy15163 120 HYKGNVYCLRDYATML--DIPRCHACDE 145 (176)
Q Consensus 120 ~~~g~~yC~~~y~~~~--~~~~C~~C~~ 145 (176)
..=|..+|..|..+.. . ..|..|++
T Consensus 18 ~~CgH~~C~~C~~~~~~~~-~~CP~C~k 44 (44)
T PF14634_consen 18 TSCGHIFCEKCLKKLKGKS-VKCPICRK 44 (44)
T ss_pred cccCCHHHHHHHHhhcCCC-CCCcCCCC
Confidence 3456677777777665 3 56776653
No 46
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=61.64 E-value=3.8 Score=26.96 Aligned_cols=36 Identities=22% Similarity=0.427 Sum_probs=25.8
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccccCccc
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDEL 112 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 112 (176)
.|..|+++|..+++..... ....|-+||.-+.-+++
T Consensus 8 kC~VCg~~iieGqkFTF~~----kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTK----KGSVHYECLAESKRKKP 43 (103)
T ss_pred eEeeeCCEeeeccEEEEee----CCcchHHHHHHHHhcCc
Confidence 7999999998888764432 34679899876654443
No 47
>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=61.13 E-value=6.9 Score=19.00 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=7.2
Q ss_pred ccccccccccCc
Q psy15163 140 CHACDELIFVNE 151 (176)
Q Consensus 140 C~~C~~~I~~~~ 151 (176)
|..|+..|.+++
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 556776775543
No 48
>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=60.51 E-value=2.5 Score=26.29 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=4.1
Q ss_pred cccccccccc
Q psy15163 138 PRCHACDELI 147 (176)
Q Consensus 138 ~~C~~C~~~I 147 (176)
+.|..|++++
T Consensus 31 a~CPdC~~~L 40 (70)
T PF07191_consen 31 AFCPDCGQPL 40 (70)
T ss_dssp EE-TTT-SB-
T ss_pred ccCCCcccHH
Confidence 4566666655
No 49
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=59.08 E-value=5.9 Score=21.01 Aligned_cols=25 Identities=24% Similarity=0.491 Sum_probs=10.7
Q ss_pred CCcccCHhHHhhCCC--cccccccccc
Q psy15163 122 KGNVYCLRDYATMLD--IPRCHACDEL 146 (176)
Q Consensus 122 ~g~~yC~~~y~~~~~--~~~C~~C~~~ 146 (176)
=+..||..|..+.+. ..+|..|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 344455555432221 0356555543
No 50
>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=58.31 E-value=5.3 Score=18.41 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=8.0
Q ss_pred eecccCCcccC
Q psy15163 165 FCCYECDKIIT 175 (176)
Q Consensus 165 F~C~~C~~~l~ 175 (176)
|.|..|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 67888887764
No 51
>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=57.10 E-value=2.2 Score=22.65 Aligned_cols=27 Identities=19% Similarity=0.452 Sum_probs=12.9
Q ss_pred cccCccccCCCceeeeCCcccCHhHHh
Q psy15163 106 CSTCDELLVDLMYFHYKGNVYCLRDYA 132 (176)
Q Consensus 106 C~~C~~~l~~~~~~~~~g~~yC~~~y~ 132 (176)
|..|+.++.........+..+|..|..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhC
Confidence 555555554444444455556655543
No 52
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=55.36 E-value=9.5 Score=22.09 Aligned_cols=29 Identities=14% Similarity=0.327 Sum_probs=18.6
Q ss_pred ccccCccccCCCc-eeeeCCcccCHhHHhhC
Q psy15163 105 VCSTCDELLVDLM-YFHYKGNVYCLRDYATM 134 (176)
Q Consensus 105 ~C~~C~~~l~~~~-~~~~~g~~yC~~~y~~~ 134 (176)
.|..|+..++-.. +-..|| ..|..|+.+.
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 3677777775533 445666 5788888654
No 53
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=52.35 E-value=1.2 Score=29.36 Aligned_cols=52 Identities=21% Similarity=0.545 Sum_probs=31.7
Q ss_pred ccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHh
Q psy15163 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLR 129 (176)
Q Consensus 73 ~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~ 129 (176)
.|..|+..+..--+.-+. -..+++.+..|-.|...|.-..|.....=+||..
T Consensus 37 aCy~CHdel~~Hpf~p~~-----~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 37 ACYHCHDELEDHPFEPWG-----LQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred hHHHHHhHHhcCCCccCC-----hhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 577787777643332222 2356778888888888886655555555455543
No 54
>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=51.65 E-value=4.3 Score=26.48 Aligned_cols=18 Identities=22% Similarity=0.811 Sum_probs=15.0
Q ss_pred hHHhhCCCccccccccccc
Q psy15163 129 RDYATMLDIPRCHACDELI 147 (176)
Q Consensus 129 ~~y~~~~~~~~C~~C~~~I 147 (176)
.-|...|. .+|..|++.+
T Consensus 47 ~sY~~lfs-~pC~~C~klL 64 (90)
T PF11571_consen 47 SSYRNLFS-TPCKKCGKLL 64 (90)
T ss_pred HHHhhhcc-chhhHHHhHh
Confidence 44677888 8999999988
No 55
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=50.53 E-value=20 Score=21.55 Aligned_cols=16 Identities=38% Similarity=0.993 Sum_probs=11.2
Q ss_pred cccccccccccCCCeE
Q psy15163 72 KTCKQCGQEVRSGDLA 87 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~ 87 (176)
..|..|+..|.+++..
T Consensus 10 ~~CtSCg~~i~p~e~~ 25 (61)
T COG2888 10 PVCTSCGREIAPGETA 25 (61)
T ss_pred ceeccCCCEeccCCce
Confidence 3788888888656543
No 56
>KOG2932|consensus
Probab=49.77 E-value=8.6 Score=31.05 Aligned_cols=43 Identities=23% Similarity=0.406 Sum_probs=29.1
Q ss_pred ccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccc
Q psy15163 105 VCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIF 148 (176)
Q Consensus 105 ~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~ 148 (176)
.|..|..+|.-....+.=...||.+|....-. +.|..|...|.
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~d-K~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSD-KICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCcc-ccCcCcccHHH
Confidence 46777777755444445556778788755545 68999998874
No 57
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=49.39 E-value=9.9 Score=22.21 Aligned_cols=28 Identities=18% Similarity=0.460 Sum_probs=15.0
Q ss_pred ccccCccccCCCceeeeCCcccCH-hHHh
Q psy15163 105 VCSTCDELLVDLMYFHYKGNVYCL-RDYA 132 (176)
Q Consensus 105 ~C~~C~~~l~~~~~~~~~g~~yC~-~~y~ 132 (176)
.|..|...+....-+.++|+.||. .|..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 356677777655677889999984 5543
No 58
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=49.10 E-value=9.6 Score=17.21 Aligned_cols=11 Identities=36% Similarity=0.730 Sum_probs=6.1
Q ss_pred eecccCCcccC
Q psy15163 165 FCCYECDKIIT 175 (176)
Q Consensus 165 F~C~~C~~~l~ 175 (176)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 56777777654
No 59
>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=48.87 E-value=6 Score=21.15 Aligned_cols=27 Identities=19% Similarity=0.296 Sum_probs=12.6
Q ss_pred ccCccccCCCceeeeCCcccCHhHHhh
Q psy15163 107 STCDELLVDLMYFHYKGNVYCLRDYAT 133 (176)
Q Consensus 107 ~~C~~~l~~~~~~~~~g~~yC~~~y~~ 133 (176)
..|...+.+......=|..||..|..+
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHHHHHH
T ss_pred CCCCCcccCcCEECCCCCchhHHHHHH
Confidence 344444443223345556666666543
No 60
>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=46.38 E-value=20 Score=20.17 Aligned_cols=29 Identities=24% Similarity=0.390 Sum_probs=16.1
Q ss_pred ccccCccccCCCceee--eCCcccCHhHHhh
Q psy15163 105 VCSTCDELLVDLMYFH--YKGNVYCLRDYAT 133 (176)
Q Consensus 105 ~C~~C~~~l~~~~~~~--~~g~~yC~~~y~~ 133 (176)
.|..|+..+....|.- ..+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 3555666655322221 2245679999875
No 61
>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=46.18 E-value=10 Score=20.99 Aligned_cols=8 Identities=38% Similarity=1.248 Sum_probs=3.9
Q ss_pred eCCcccCH
Q psy15163 121 YKGNVYCL 128 (176)
Q Consensus 121 ~~g~~yC~ 128 (176)
++++.||.
T Consensus 31 k~g~~~Cv 38 (41)
T PF06677_consen 31 KDGKIYCV 38 (41)
T ss_pred cCCCEECC
Confidence 44555553
No 62
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.18 E-value=9.8 Score=26.72 Aligned_cols=20 Identities=35% Similarity=0.853 Sum_probs=11.4
Q ss_pred cccCccccCCCceeeeCCcccCHhH
Q psy15163 106 CSTCDELLVDLMYFHYKGNVYCLRD 130 (176)
Q Consensus 106 C~~C~~~l~~~~~~~~~g~~yC~~~ 130 (176)
|..|+.|| |.++|.+||..|
T Consensus 31 Cp~Cg~PL-----F~KdG~v~CPvC 50 (131)
T COG1645 31 CPKCGTPL-----FRKDGEVFCPVC 50 (131)
T ss_pred CcccCCcc-----eeeCCeEECCCC
Confidence 55565555 336677766444
No 63
>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=44.82 E-value=19 Score=20.12 Aligned_cols=9 Identities=33% Similarity=0.379 Sum_probs=4.9
Q ss_pred cccCHhHHh
Q psy15163 124 NVYCLRDYA 132 (176)
Q Consensus 124 ~~yC~~~y~ 132 (176)
.-+|..||.
T Consensus 23 ~dLC~~Cf~ 31 (46)
T cd02249 23 FDLCSSCYA 31 (46)
T ss_pred CcCHHHHHC
Confidence 335666664
No 64
>KOG3002|consensus
Probab=44.65 E-value=16 Score=29.50 Aligned_cols=43 Identities=19% Similarity=0.372 Sum_probs=27.8
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccc
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIF 148 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~ 148 (176)
+.|..|-..|..-.+.-.+|.+.|..|-.++. .+|..|..+|.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~--~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS--NKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhc--ccCCccccccc
Confidence 44555556665545555677777877765444 48888888874
No 65
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=44.08 E-value=12 Score=17.52 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=8.3
Q ss_pred eecccCCcccCC
Q psy15163 165 FCCYECDKIITQ 176 (176)
Q Consensus 165 F~C~~C~~~l~~ 176 (176)
|.|..|++.+.+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 678888776653
No 66
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=43.81 E-value=12 Score=17.91 Aligned_cols=11 Identities=45% Similarity=0.999 Sum_probs=7.4
Q ss_pred eecccCCcccC
Q psy15163 165 FCCYECDKIIT 175 (176)
Q Consensus 165 F~C~~C~~~l~ 175 (176)
|.|..|++.+.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 56777777654
No 67
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=43.01 E-value=16 Score=17.66 Aligned_cols=12 Identities=42% Similarity=1.016 Sum_probs=7.9
Q ss_pred eecccCCcccCC
Q psy15163 165 FCCYECDKIITQ 176 (176)
Q Consensus 165 F~C~~C~~~l~~ 176 (176)
|.|..|++.|.+
T Consensus 2 ~~C~~C~k~f~~ 13 (27)
T PF12171_consen 2 FYCDACDKYFSS 13 (27)
T ss_dssp CBBTTTTBBBSS
T ss_pred CCcccCCCCcCC
Confidence 567777776653
No 68
>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=41.31 E-value=26 Score=19.34 Aligned_cols=10 Identities=20% Similarity=0.328 Sum_probs=6.5
Q ss_pred cccCHhHHhh
Q psy15163 124 NVYCLRDYAT 133 (176)
Q Consensus 124 ~~yC~~~y~~ 133 (176)
.-+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 3458888764
No 69
>KOG0823|consensus
Probab=41.31 E-value=40 Score=26.03 Aligned_cols=52 Identities=19% Similarity=0.436 Sum_probs=35.8
Q ss_pred cCcccccCccccCCCceeeeCCcccCHhHHhhCC----CcccccccccccccCceEE
Q psy15163 102 QCFVCSTCDELLVDLMYFHYKGNVYCLRDYATML----DIPRCHACDELIFVNEYTL 154 (176)
Q Consensus 102 ~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~----~~~~C~~C~~~I~~~~~~~ 154 (176)
..|.|..|=....+ .....=|.+||..|.++-+ +...|.+|+..|....+|-
T Consensus 46 ~~FdCNICLd~akd-PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP 101 (230)
T KOG0823|consen 46 GFFDCNICLDLAKD-PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP 101 (230)
T ss_pred CceeeeeeccccCC-CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence 44777777554433 5667788999999986532 2157899999997766653
No 70
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.98 E-value=21 Score=17.33 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=3.2
Q ss_pred ccccccc
Q psy15163 73 TCKQCGQ 79 (176)
Q Consensus 73 ~C~~C~~ 79 (176)
.|..|+.
T Consensus 18 fC~~CG~ 24 (26)
T PF13248_consen 18 FCPNCGA 24 (26)
T ss_pred cChhhCC
Confidence 4444444
No 71
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=40.84 E-value=12 Score=24.23 Aligned_cols=30 Identities=23% Similarity=0.638 Sum_probs=14.9
Q ss_pred cccccccccccC-ceE-EeCCCccccCCeecccCC
Q psy15163 139 RCHACDELIFVN-EYT-LAENKTFHVKHFCCYECD 171 (176)
Q Consensus 139 ~C~~C~~~I~~~-~~~-~a~~~~~H~~CF~C~~C~ 171 (176)
.|..|+.+|..+ .++ ...+. ..=|.|..|.
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~---~~~FCC~GC~ 33 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGE---ERPFCCPGCQ 33 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCC---ccccccHHHH
Confidence 477777777432 222 22332 2446666664
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.14 E-value=16 Score=20.32 Aligned_cols=10 Identities=40% Similarity=0.727 Sum_probs=6.0
Q ss_pred cccccccccc
Q psy15163 138 PRCHACDELI 147 (176)
Q Consensus 138 ~~C~~C~~~I 147 (176)
.+|..|+..+
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 4666666655
No 73
>KOG3579|consensus
Probab=39.05 E-value=17 Score=29.02 Aligned_cols=51 Identities=25% Similarity=0.512 Sum_probs=34.7
Q ss_pred CCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHh
Q psy15163 69 RSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLR 129 (176)
Q Consensus 69 ~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~ 129 (176)
.....|.-|++.+.+..+|-.. ...-|+-||-|+. ..|..+ -.-+.+||..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCP-----SVp~HKFCFPCSR--esIK~Q---g~sgevYCPS 316 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCP-----SVPSHKFCFPCSR--ESIKQQ---GASGEVYCPS 316 (352)
T ss_pred CCceeehhhhhhhccCceeecC-----CCcccceecccCH--HHHHhh---cCCCceeCCC
Confidence 3446899999999988777655 6678999999874 222221 1345778853
No 74
>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=38.57 E-value=7.6 Score=19.53 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=6.1
Q ss_pred ccccccccccc
Q psy15163 138 PRCHACDELIF 148 (176)
Q Consensus 138 ~~C~~C~~~I~ 148 (176)
.+|..|...|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 57888988884
No 75
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=37.99 E-value=15 Score=23.46 Aligned_cols=28 Identities=29% Similarity=0.486 Sum_probs=15.8
Q ss_pred cccCccccCCCceee-----eCCcccCHhHHhh
Q psy15163 106 CSTCDELLVDLMYFH-----YKGNVYCLRDYAT 133 (176)
Q Consensus 106 C~~C~~~l~~~~~~~-----~~g~~yC~~~y~~ 133 (176)
|..|+.||.....+- ..+.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 666777765443211 2334588888854
No 76
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.03 E-value=24 Score=24.65 Aligned_cols=46 Identities=20% Similarity=0.509 Sum_probs=24.9
Q ss_pred cCHhHHhhCCCcccccccccccccCceE---EeCCCccccCCeecccCCccc
Q psy15163 126 YCLRDYATMLDIPRCHACDELIFVNEYT---LAENKTFHVKHFCCYECDKII 174 (176)
Q Consensus 126 yC~~~y~~~~~~~~C~~C~~~I~~~~~~---~a~~~~~H~~CF~C~~C~~~l 174 (176)
||..|-.... ..|..|+.+|.+..++ -.+|..|-+-=| |..|++++
T Consensus 30 fcskcgeati--~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~f 78 (160)
T COG4306 30 FCSKCGEATI--TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRF 78 (160)
T ss_pred HHhhhchHHH--hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCC
Confidence 4555554433 3677777777655433 244555555433 56666654
No 77
>PRK00420 hypothetical protein; Validated
Probab=35.77 E-value=16 Score=24.96 Aligned_cols=10 Identities=30% Similarity=0.790 Sum_probs=5.7
Q ss_pred cccccccccc
Q psy15163 73 TCKQCGQEVR 82 (176)
Q Consensus 73 ~C~~C~~~i~ 82 (176)
.|..|+.++.
T Consensus 25 ~CP~Cg~pLf 34 (112)
T PRK00420 25 HCPVCGLPLF 34 (112)
T ss_pred CCCCCCCcce
Confidence 5666655543
No 78
>KOG4739|consensus
Probab=35.52 E-value=27 Score=27.05 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=25.2
Q ss_pred CCceee-eCCcccCHhHHhhCCCccccccccccccc
Q psy15163 115 DLMYFH-YKGNVYCLRDYATMLDIPRCHACDELIFV 149 (176)
Q Consensus 115 ~~~~~~-~~g~~yC~~~y~~~~~~~~C~~C~~~I~~ 149 (176)
...||+ -=..++|..|...-.+ +.|..|++.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~-~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSP-DVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCc-cccccccceeee
Confidence 445554 4567889999877776 799999999854
No 79
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=34.56 E-value=33 Score=21.81 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=9.7
Q ss_pred cccCHhHHh--hCCCcccccccccc
Q psy15163 124 NVYCLRDYA--TMLDIPRCHACDEL 146 (176)
Q Consensus 124 ~~yC~~~y~--~~~~~~~C~~C~~~ 146 (176)
.|.|+.||. ++-+...|.+|+-+
T Consensus 36 fPvCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 36 FPVCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp ----HHHHHHHHHTS-SB-TTT--B
T ss_pred CccchhHHHHHhhcCcccccccCCC
Confidence 356888884 33443678888744
No 80
>KOG3476|consensus
Probab=34.23 E-value=5.2 Score=25.88 Aligned_cols=37 Identities=24% Similarity=0.533 Sum_probs=26.8
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhCCCccccccccccccc
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFV 149 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~ 149 (176)
-+|-.|...+.+ .|--||..|..+. ..|+-|++.|..
T Consensus 55 ~kC~iCk~~vHQ------~GshYC~tCAY~K---giCAMCGKki~n 91 (100)
T KOG3476|consen 55 AKCRICKQLVHQ------PGSHYCQTCAYKK---GICAMCGKKILN 91 (100)
T ss_pred chhHHHHHHhcC------CcchhHhHhhhhh---hHHHHhhhHhhc
Confidence 456666655432 4567899998765 699999999964
No 81
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.75 E-value=21 Score=32.11 Aligned_cols=36 Identities=22% Similarity=0.225 Sum_probs=24.2
Q ss_pred ccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccc
Q psy15163 107 STCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDEL 146 (176)
Q Consensus 107 ~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~ 146 (176)
..|+.+| .|+...+.+.|..|-..... ..|..|+..
T Consensus 396 ~~C~~~L---~~h~~~~~l~Ch~CG~~~~p-~~Cp~Cgs~ 431 (665)
T PRK14873 396 RHCTGPL---GLPSAGGTPRCRWCGRAAPD-WRCPRCGSD 431 (665)
T ss_pred CCCCCce---eEecCCCeeECCCCcCCCcC-ccCCCCcCC
Confidence 3444444 34445667889888766555 799999875
No 82
>PHA02775 E6; Provisional
Probab=33.66 E-value=10 Score=27.58 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=10.1
Q ss_pred ccccccccccCCCe
Q psy15163 73 TCKQCGQEVRSGDL 86 (176)
Q Consensus 73 ~C~~C~~~i~~~~~ 86 (176)
.|..|++.+...|.
T Consensus 45 ~CvFCk~~Lt~~E~ 58 (160)
T PHA02775 45 CCHYCKKCLSLLDI 58 (160)
T ss_pred EeeccCCcCCHHHH
Confidence 68899988854443
No 83
>PF12773 DZR: Double zinc ribbon
Probab=33.19 E-value=39 Score=18.91 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=5.4
Q ss_pred cccccccccc
Q psy15163 73 TCKQCGQEVR 82 (176)
Q Consensus 73 ~C~~C~~~i~ 82 (176)
.|..|+..+.
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 5555555554
No 84
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=31.69 E-value=26 Score=16.89 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=6.7
Q ss_pred eecccCCcccC
Q psy15163 165 FCCYECDKIIT 175 (176)
Q Consensus 165 F~C~~C~~~l~ 175 (176)
|.|..|++.+.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 56666666553
No 85
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=31.28 E-value=49 Score=18.84 Aligned_cols=10 Identities=10% Similarity=-0.014 Sum_probs=6.4
Q ss_pred cccCHhHHhh
Q psy15163 124 NVYCLRDYAT 133 (176)
Q Consensus 124 ~~yC~~~y~~ 133 (176)
.-+|..||..
T Consensus 26 ~DlC~~C~~~ 35 (48)
T cd02341 26 FDLCQDCVVK 35 (48)
T ss_pred CccCHHHHhC
Confidence 3457777764
No 87
>KOG4443|consensus
Probab=31.01 E-value=23 Score=31.48 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=8.9
Q ss_pred CCccccCCeecccCCccc
Q psy15163 157 NKTFHVKHFCCYECDKII 174 (176)
Q Consensus 157 ~~~~H~~CF~C~~C~~~l 174 (176)
+..+-++||.|..|+..|
T Consensus 108 g~~~ckk~~~c~qc~~~l 125 (694)
T KOG4443|consen 108 GPWLCKKCTRCRQCDSTL 125 (694)
T ss_pred cccccHHHHhhhhccccc
Confidence 344445555555555443
No 88
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.80 E-value=30 Score=30.98 Aligned_cols=11 Identities=36% Similarity=0.676 Sum_probs=8.2
Q ss_pred ccccccccccC
Q psy15163 73 TCKQCGQEVRS 83 (176)
Q Consensus 73 ~C~~C~~~i~~ 83 (176)
+|..|+..+..
T Consensus 3 ~Cp~Cg~~n~~ 13 (645)
T PRK14559 3 ICPQCQFENPN 13 (645)
T ss_pred cCCCCCCcCCC
Confidence 68888887753
No 89
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=30.48 E-value=44 Score=18.64 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=16.3
Q ss_pred cccccccccCCCeEEEEeccCCCcccCccCcc
Q psy15163 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFV 105 (176)
Q Consensus 74 C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~ 105 (176)
|..|++.-. .+.++.-+.. +..||..|..
T Consensus 2 C~vC~~~~~-~~~~i~C~~C--~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQSDD-DGDMIQCDSC--NRWYHQECVG 30 (51)
T ss_dssp BTTTTSSCT-TSSEEEBSTT--SCEEETTTST
T ss_pred CcCCCCcCC-CCCeEEcCCC--ChhhCcccCC
Confidence 556666443 3334444444 4478888864
No 90
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=30.28 E-value=35 Score=20.40 Aligned_cols=24 Identities=17% Similarity=0.423 Sum_probs=14.0
Q ss_pred ccccCccccC-CCcee-eeCCcccCH
Q psy15163 105 VCSTCDELLV-DLMYF-HYKGNVYCL 128 (176)
Q Consensus 105 ~C~~C~~~l~-~~~~~-~~~g~~yC~ 128 (176)
.|..|++.|. +...| .+..+.+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 4556777775 33334 355677774
No 91
>PF14149 YhfH: YhfH-like protein
Probab=30.04 E-value=17 Score=19.63 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=13.2
Q ss_pred HhhCCCcccccccccccc
Q psy15163 131 YATMLDIPRCHACDELIF 148 (176)
Q Consensus 131 y~~~~~~~~C~~C~~~I~ 148 (176)
|.+.+....|..||+.|.
T Consensus 7 FfrnLp~K~C~~CG~~i~ 24 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIE 24 (37)
T ss_pred HHHhCCCcccHHHHHHHH
Confidence 445554479999999994
No 92
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.97 E-value=29 Score=27.55 Aligned_cols=28 Identities=11% Similarity=0.059 Sum_probs=17.4
Q ss_pred CCcccccccccccccCceEEeCCCccccCC
Q psy15163 135 LDIPRCHACDELIFVNEYTLAENKTFHVKH 164 (176)
Q Consensus 135 ~~~~~C~~C~~~I~~~~~~~a~~~~~H~~C 164 (176)
-+ ..|..|+.+|.. ..+.-++..|.|.|
T Consensus 244 ~G-epC~~CGt~I~k-~~~~gR~t~~CP~C 271 (273)
T COG0266 244 AG-EPCRRCGTPIEK-IKLGGRSTFYCPVC 271 (273)
T ss_pred CC-CCCCccCCEeEE-EEEcCCcCEeCCCC
Confidence 35 799999999943 23334455555554
No 93
>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=29.86 E-value=35 Score=29.43 Aligned_cols=41 Identities=27% Similarity=0.431 Sum_probs=28.4
Q ss_pred CCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCC
Q psy15163 69 RSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVD 115 (176)
Q Consensus 69 ~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 115 (176)
.....|..|-..+...+.. ++ +....+.||.|-.|..+|..
T Consensus 24 i~~~yCp~CL~~~p~~e~~--~~----~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 24 IDSYYCPNCLFEVPSSEAR--SE----KNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred cceeECccccccCChhhhe--ec----cceeccccccCCCCCCccee
Confidence 4556888888877644422 21 34556799999999999854
No 94
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=29.71 E-value=65 Score=25.31 Aligned_cols=75 Identities=13% Similarity=0.464 Sum_probs=47.9
Q ss_pred CcccCCCCC----CccCCCCCcccccccccccCCCeEEEEeccCCCcccCccCcccccCccccCCCceeeeCCcccCHhH
Q psy15163 55 GVTHGPCGN----KLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRD 130 (176)
Q Consensus 55 ~~~~~~~~~----~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~ 130 (176)
.+.|..|.. .+....+-.+|.+|.+.-.+ |- . ++.|-..=|.|..|+..+.+ |...
T Consensus 112 qFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDP---VP-~-----dkmwG~aef~C~~C~h~F~G--~~qm--------- 171 (278)
T PF15135_consen 112 QFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDP---VP-C-----DKMWGIAEFHCPKCRHNFRG--FAQM--------- 171 (278)
T ss_pred eeeccccchHHHhccCcccccccccccccccCC---Cc-c-----ccccceeeeecccccccchh--hhhc---------
Confidence 356777743 23334556689999887642 22 1 55676667999999998876 2111
Q ss_pred HhhCCCcccccccccccccCceE
Q psy15163 131 YATMLDIPRCHACDELIFVNEYT 153 (176)
Q Consensus 131 y~~~~~~~~C~~C~~~I~~~~~~ 153 (176)
... ..|..|+.++.+..++
T Consensus 172 ---~v~-sPCy~C~~~v~P~~Il 190 (278)
T PF15135_consen 172 ---GVP-SPCYGCGNPVYPSRIL 190 (278)
T ss_pred ---CCC-CCccCCCCccCccccc
Confidence 112 5888999988765443
No 95
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=29.04 E-value=15 Score=21.44 Aligned_cols=11 Identities=9% Similarity=0.386 Sum_probs=4.8
Q ss_pred CCccccCCeec
Q psy15163 157 NKTFHVKHFCC 167 (176)
Q Consensus 157 ~~~~H~~CF~C 167 (176)
++.|-.+|-.|
T Consensus 20 ~Q~yiEDC~vC 30 (52)
T PF14255_consen 20 DQEYIEDCQVC 30 (52)
T ss_pred CeeEEeehhhc
Confidence 44444444443
No 96
>PHA02779 E6 protein; Provisional
Probab=28.96 E-value=13 Score=26.72 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=15.4
Q ss_pred ccccccccccccCce--EEeCCCcccc
Q psy15163 138 PRCHACDELIFVNEY--TLAENKTFHV 162 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~--~~a~~~~~H~ 162 (176)
-+|..|.+++...|- ....++.||.
T Consensus 102 IRC~~C~k~L~~~EK~~~~~~~~~F~~ 128 (150)
T PHA02779 102 IRCYLCHKPLCPVEKVNHILKKARFIK 128 (150)
T ss_pred EEHhHcCCcCCHHHHHHHHHcCCCEEE
Confidence 488899988865431 2245555554
No 97
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.76 E-value=53 Score=20.58 Aligned_cols=27 Identities=15% Similarity=0.349 Sum_probs=20.4
Q ss_pred cccCHhHHhhCCCcccccccccccccCc
Q psy15163 124 NVYCLRDYATMLDIPRCHACDELIFVNE 151 (176)
Q Consensus 124 ~~yC~~~y~~~~~~~~C~~C~~~I~~~~ 151 (176)
--||..|...+++ ..|..|++.+..++
T Consensus 29 cTFCadCae~~l~-g~CPnCGGelv~RP 55 (84)
T COG3813 29 CTFCADCAENRLH-GLCPNCGGELVARP 55 (84)
T ss_pred eehhHhHHHHhhc-CcCCCCCchhhcCc
Confidence 3468888888888 89999998765544
No 98
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=28.61 E-value=11 Score=25.49 Aligned_cols=10 Identities=40% Similarity=0.710 Sum_probs=7.2
Q ss_pred cccccccccc
Q psy15163 139 RCHACDELIF 148 (176)
Q Consensus 139 ~C~~C~~~I~ 148 (176)
.|..|+++|.
T Consensus 82 ~C~~Cge~I~ 91 (110)
T TIGR02420 82 YCEECGEEIG 91 (110)
T ss_pred chhccCCccc
Confidence 7777777773
No 99
>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=28.42 E-value=60 Score=18.32 Aligned_cols=9 Identities=22% Similarity=0.615 Sum_probs=5.4
Q ss_pred ccCHhHHhh
Q psy15163 125 VYCLRDYAT 133 (176)
Q Consensus 125 ~yC~~~y~~ 133 (176)
-+|..||..
T Consensus 25 dLC~~Cf~~ 33 (49)
T cd02335 25 DLCLECFSA 33 (49)
T ss_pred chhHHhhhC
Confidence 357777653
No 100
>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=28.07 E-value=45 Score=18.59 Aligned_cols=10 Identities=10% Similarity=0.242 Sum_probs=6.6
Q ss_pred cccCHhHHhh
Q psy15163 124 NVYCLRDYAT 133 (176)
Q Consensus 124 ~~yC~~~y~~ 133 (176)
.-+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 4468888865
No 101
>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=27.47 E-value=44 Score=18.05 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=12.9
Q ss_pred ccccccccccccCceEEeCCCccccCCeecccCCc
Q psy15163 138 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDK 172 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~ 172 (176)
.+|..|+..|-.-..+...++. ++|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~-----w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKT-----WICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTE-----EEETTT--
T ss_pred cccCCCCCEECCcceEcCCCCE-----EECcCCCC
Confidence 5888999888443223333333 56776654
No 102
>KOG2462|consensus
Probab=27.41 E-value=33 Score=27.24 Aligned_cols=38 Identities=24% Similarity=0.536 Sum_probs=22.2
Q ss_pred ccccccccccccCceEEeCCCcccc--CCeecccCCcccCC
Q psy15163 138 PRCHACDELIFVNEYTLAENKTFHV--KHFCCYECDKIITQ 176 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~~a~~~~~H~--~CF~C~~C~~~l~~ 176 (176)
-+|..|++.. .+.++--.--..|- +=|.|..|++.|.|
T Consensus 188 c~C~iCGKaF-SRPWLLQGHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 188 CECGICGKAF-SRPWLLQGHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred cccccccccc-cchHHhhcccccccCCCCccCCcccchhcc
Confidence 4788888877 44543101111222 44888899888764
No 103
>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=27.39 E-value=44 Score=28.85 Aligned_cols=12 Identities=25% Similarity=0.453 Sum_probs=7.1
Q ss_pred CCeecccCCccc
Q psy15163 163 KHFCCYECDKII 174 (176)
Q Consensus 163 ~CF~C~~C~~~l 174 (176)
+||.|..|..+|
T Consensus 51 ~Cf~CP~C~~~L 62 (483)
T PF05502_consen 51 NCFDCPICFSPL 62 (483)
T ss_pred ccccCCCCCCcc
Confidence 566666665554
No 104
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.21 E-value=22 Score=25.29 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=17.8
Q ss_pred cccccccccccCceEEeCCCccccCCeecccCCccc
Q psy15163 139 RCHACDELIFVNEYTLAENKTFHVKHFCCYECDKII 174 (176)
Q Consensus 139 ~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~l 174 (176)
.|..|+..+...+.+...+. ..=|.|..|+..|
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l 133 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEEL 133 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEE
Confidence 56667666644333222221 2337788887766
No 105
>smart00355 ZnF_C2H2 zinc finger.
Probab=25.49 E-value=33 Score=15.40 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=5.8
Q ss_pred eecccCCcccC
Q psy15163 165 FCCYECDKIIT 175 (176)
Q Consensus 165 F~C~~C~~~l~ 175 (176)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 34566665543
No 106
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=25.49 E-value=20 Score=23.82 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=17.6
Q ss_pred CccCcccccCccccCCC-ceeeeCCcccCHhH
Q psy15163 100 HPQCFVCSTCDELLVDL-MYFHYKGNVYCLRD 130 (176)
Q Consensus 100 H~~Cf~C~~C~~~l~~~-~~~~~~g~~yC~~~ 130 (176)
-..=|+|+.|-.--.-. .-...+|+++|..|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 33457887774433111 12246788888776
No 107
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=25.10 E-value=37 Score=26.80 Aligned_cols=29 Identities=14% Similarity=0.107 Sum_probs=16.5
Q ss_pred CCCcccccccccccccCceEEeCCCccccCC
Q psy15163 134 MLDIPRCHACDELIFVNEYTLAENKTFHVKH 164 (176)
Q Consensus 134 ~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~C 164 (176)
+.+ ..|..|+.+|.. ..+..+...|.|.|
T Consensus 243 R~g-~pC~~Cg~~I~~-~~~~gR~t~~CP~C 271 (274)
T PRK01103 243 REG-EPCRRCGTPIEK-IKQGGRSTFFCPRC 271 (274)
T ss_pred CCC-CCCCCCCCeeEE-EEECCCCcEECcCC
Confidence 345 689999999942 23323344444443
No 108
>PF04641 Rtf2: Rtf2 RING-finger
Probab=24.82 E-value=1.1e+02 Score=24.04 Aligned_cols=55 Identities=11% Similarity=0.271 Sum_probs=41.0
Q ss_pred cCccCcccccCccccCCC-ce--eeeCCcccCHhHHhhCC-CcccccccccccccCceEE
Q psy15163 99 WHPQCFVCSTCDELLVDL-MY--FHYKGNVYCLRDYATML-DIPRCHACDELIFVNEYTL 154 (176)
Q Consensus 99 ~H~~Cf~C~~C~~~l~~~-~~--~~~~g~~yC~~~y~~~~-~~~~C~~C~~~I~~~~~~~ 154 (176)
....-|.|......|.+. .| ...-|.+|++....+.- . ..|..|+++....++|.
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~-~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKS-KKCPVCGKPFTEEDIIP 167 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhccc-ccccccCCccccCCEEE
Confidence 346678888888888653 22 23678899999987775 4 68999999998767764
No 109
>PRK12495 hypothetical protein; Provisional
Probab=24.80 E-value=52 Score=25.30 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=6.2
Q ss_pred cccccCccccC
Q psy15163 104 FVCSTCDELLV 114 (176)
Q Consensus 104 f~C~~C~~~l~ 114 (176)
+.|..|+.+|.
T Consensus 43 ~hC~~CG~PIp 53 (226)
T PRK12495 43 AHCDECGDPIF 53 (226)
T ss_pred hhcccccCccc
Confidence 45566666553
No 110
>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=24.80 E-value=68 Score=17.67 Aligned_cols=7 Identities=29% Similarity=0.240 Sum_probs=3.7
Q ss_pred cCHhHHh
Q psy15163 126 YCLRDYA 132 (176)
Q Consensus 126 yC~~~y~ 132 (176)
+|..||.
T Consensus 25 LC~~C~~ 31 (43)
T cd02340 25 LCESCEA 31 (43)
T ss_pred chHHhhC
Confidence 4555553
No 111
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=24.54 E-value=57 Score=18.96 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=15.0
Q ss_pred ccccccccccccCceEEeCCCcccc
Q psy15163 138 PRCHACDELIFVNEYTLAENKTFHV 162 (176)
Q Consensus 138 ~~C~~C~~~I~~~~~~~a~~~~~H~ 162 (176)
.+|-.|.+||...-.+......-|+
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~ 26 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHP 26 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCC
Confidence 4788888888543334444555554
No 112
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=23.68 E-value=67 Score=22.48 Aligned_cols=20 Identities=25% Similarity=0.679 Sum_probs=15.4
Q ss_pred cccccccccccCCCeEEEEe
Q psy15163 72 KTCKQCGQEVRSGDLAVYTE 91 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~ 91 (176)
..|..|+..|+++.-++..+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR 24 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVR 24 (131)
T ss_pred eeecCcCCcccCCCCcEEEe
Confidence 37999999998887665554
No 113
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.05 E-value=46 Score=27.98 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=6.2
Q ss_pred cccccccccc
Q psy15163 139 RCHACDELIF 148 (176)
Q Consensus 139 ~C~~C~~~I~ 148 (176)
.|..|...+.
T Consensus 62 ~CP~Cr~~~~ 71 (397)
T TIGR00599 62 KCPLCRAEDQ 71 (397)
T ss_pred CCCCCCCccc
Confidence 5666666653
No 114
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.05 E-value=30 Score=26.90 Aligned_cols=25 Identities=16% Similarity=0.442 Sum_probs=13.3
Q ss_pred CCcccCHhHHhhC--CCccccccccccc
Q psy15163 122 KGNVYCLRDYATM--LDIPRCHACDELI 147 (176)
Q Consensus 122 ~g~~yC~~~y~~~--~~~~~C~~C~~~I 147 (176)
=+..||..|..+- .. ..|..|+..+
T Consensus 200 C~H~FC~~CI~~Wl~~~-~tCPlCR~~~ 226 (238)
T PHA02929 200 CNHVFCIECIDIWKKEK-NTCPVCRTPF 226 (238)
T ss_pred CCCcccHHHHHHHHhcC-CCCCCCCCEe
Confidence 3556666665321 12 4666666665
No 115
>PHA02768 hypothetical protein; Provisional
Probab=22.89 E-value=15 Score=21.66 Aligned_cols=12 Identities=25% Similarity=1.002 Sum_probs=8.5
Q ss_pred cccccCccccCC
Q psy15163 104 FVCSTCDELLVD 115 (176)
Q Consensus 104 f~C~~C~~~l~~ 115 (176)
|.|..|++.+..
T Consensus 6 y~C~~CGK~Fs~ 17 (55)
T PHA02768 6 YECPICGEIYIK 17 (55)
T ss_pred cCcchhCCeecc
Confidence 677788777654
No 116
>KOG3579|consensus
Probab=22.63 E-value=44 Score=26.75 Aligned_cols=53 Identities=17% Similarity=0.308 Sum_probs=27.5
Q ss_pred cccccCccccCCCceeeeCCcccCHhHHhhCCCcccccccccccccCceEEeCCCccccCCeecc
Q psy15163 104 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCY 168 (176)
Q Consensus 104 f~C~~C~~~l~~~~~~~~~g~~yC~~~y~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~ 168 (176)
+.|..|+..|.++-|..--..+. + ..|.-|+..-+-. -.+.+..|.|.-=+|.
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~---------H-KFCFPCSResIK~--Qg~sgevYCPSGdkCP 321 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPS---------H-KFCFPCSRESIKQ--QGASGEVYCPSGDKCP 321 (352)
T ss_pred eeehhhhhhhccCceeecCCCcc---------c-ceecccCHHHHHh--hcCCCceeCCCCCcCc
Confidence 67888888887754443222111 1 4555565432111 1245666776655554
No 117
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.54 E-value=35 Score=24.99 Aligned_cols=36 Identities=22% Similarity=0.413 Sum_probs=22.8
Q ss_pred cccccccccccc---CceE-EeC--CCccccCCeecccCCcc
Q psy15163 138 PRCHACDELIFV---NEYT-LAE--NKTFHVKHFCCYECDKI 173 (176)
Q Consensus 138 ~~C~~C~~~I~~---~~~~-~a~--~~~~H~~CF~C~~C~~~ 173 (176)
.+|..|+..+.. +++. ..- -...|-+.++|..|++.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 589999988853 1111 011 22457788999999874
No 118
>KOG2114|consensus
Probab=22.01 E-value=36 Score=31.37 Aligned_cols=38 Identities=16% Similarity=0.405 Sum_probs=0.0
Q ss_pred cccccccccccCceEEeCCCccccCCee-----cccCCcccCC
Q psy15163 139 RCHACDELIFVNEYTLAENKTFHVKHFC-----CYECDKIITQ 176 (176)
Q Consensus 139 ~C~~C~~~I~~~~~~~a~~~~~H~~CF~-----C~~C~~~l~~ 176 (176)
+|..|+..+.--.+----+..||..||. |..|...+++
T Consensus 842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~~~ 884 (933)
T KOG2114|consen 842 KCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPELRG 884 (933)
T ss_pred eecccCCccccceeeeecccHHHHHhhccCcccCCccchhhhh
No 119
>KOG2893|consensus
Probab=21.87 E-value=22 Score=27.65 Aligned_cols=34 Identities=21% Similarity=0.467 Sum_probs=24.2
Q ss_pred cccccccccccCCCeEEEEeccCCCcccCccCcccccCcccc
Q psy15163 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELL 113 (176)
Q Consensus 72 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 113 (176)
.-|--|+..+. +|+++.. .-...+|+|..|++.|
T Consensus 11 pwcwycnrefd-dekiliq-------hqkakhfkchichkkl 44 (341)
T KOG2893|consen 11 PWCWYCNREFD-DEKILIQ-------HQKAKHFKCHICHKKL 44 (341)
T ss_pred ceeeecccccc-hhhhhhh-------hhhhccceeeeehhhh
Confidence 37999999987 4555322 2234679999999988
No 120
>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=21.60 E-value=1.3e+02 Score=18.33 Aligned_cols=50 Identities=14% Similarity=0.134 Sum_probs=29.7
Q ss_pred cCcccccCccccCCCceeeeCCcccCHhHHh---hCCCcccccccccccccCceE
Q psy15163 102 QCFVCSTCDELLVDLMYFHYKGNVYCLRDYA---TMLDIPRCHACDELIFVNEYT 153 (176)
Q Consensus 102 ~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~y~---~~~~~~~C~~C~~~I~~~~~~ 153 (176)
+-|.|..++..+.+ ......|..|.+..-. +..+ ..|..++++|....++
T Consensus 3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~~~~-~~~P~t~~~l~~~~l~ 55 (73)
T PF04564_consen 3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLEQNG-GTDPFTRQPLSESDLI 55 (73)
T ss_dssp GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHCTTS-SB-TTT-SB-SGGGSE
T ss_pred cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHHcCC-CCCCCCCCcCCcccce
Confidence 44777777776655 5566778888876554 3334 6898999888665544
No 121
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.38 E-value=50 Score=26.12 Aligned_cols=28 Identities=11% Similarity=0.166 Sum_probs=16.7
Q ss_pred CCcccccccccccccCceEEeCCCccccCC
Q psy15163 135 LDIPRCHACDELIFVNEYTLAENKTFHVKH 164 (176)
Q Consensus 135 ~~~~~C~~C~~~I~~~~~~~a~~~~~H~~C 164 (176)
-+ ..|..|+.+|.. ..+..+...|.|.|
T Consensus 243 ~g-~pCprCG~~I~~-~~~~gR~t~~CP~C 270 (272)
T PRK14810 243 TG-EPCLNCKTPIRR-VVVAGRSSHYCPHC 270 (272)
T ss_pred CC-CcCCCCCCeeEE-EEECCCccEECcCC
Confidence 35 689999999942 23333444454444
No 122
>PRK10445 endonuclease VIII; Provisional
Probab=21.24 E-value=48 Score=26.05 Aligned_cols=29 Identities=10% Similarity=0.056 Sum_probs=16.8
Q ss_pred CCCcccccccccccccCceEEeCCCccccCC
Q psy15163 134 MLDIPRCHACDELIFVNEYTLAENKTFHVKH 164 (176)
Q Consensus 134 ~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~C 164 (176)
+.+ ..|..|+.+|.. ..+..+...|.|.|
T Consensus 233 r~g-~~Cp~Cg~~I~~-~~~~gR~t~~CP~C 261 (263)
T PRK10445 233 RDG-EACERCGGIIEK-TTLSSRPFYWCPGC 261 (263)
T ss_pred CCC-CCCCCCCCEeEE-EEECCCCcEECCCC
Confidence 345 789999999942 22323344444444
No 123
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.04 E-value=55 Score=16.25 Aligned_cols=11 Identities=18% Similarity=0.640 Sum_probs=2.5
Q ss_pred ccccCccccCC
Q psy15163 105 VCSTCDELLVD 115 (176)
Q Consensus 105 ~C~~C~~~l~~ 115 (176)
.|..|++++.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 44555555443
No 124
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=21.01 E-value=48 Score=24.51 Aligned_cols=18 Identities=11% Similarity=0.393 Sum_probs=13.0
Q ss_pred eeeeCCcccCHhHHhhCC
Q psy15163 118 YFHYKGNVYCLRDYATML 135 (176)
Q Consensus 118 ~~~~~g~~yC~~~y~~~~ 135 (176)
++-.+..++|..|+.-+|
T Consensus 154 ~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 154 FTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred EEecChhhcccccCcccc
Confidence 555677888888877665
No 125
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.65 E-value=43 Score=17.70 Aligned_cols=10 Identities=30% Similarity=1.042 Sum_probs=3.8
Q ss_pred cccccccccc
Q psy15163 73 TCKQCGQEVR 82 (176)
Q Consensus 73 ~C~~C~~~i~ 82 (176)
.|..|++++.
T Consensus 5 ~C~eC~~~f~ 14 (34)
T PF01286_consen 5 KCDECGKPFM 14 (34)
T ss_dssp E-TTT--EES
T ss_pred hHhHhCCHHH
Confidence 5555555554
No 126
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.63 E-value=53 Score=25.93 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=9.6
Q ss_pred ccccccccccc
Q psy15163 138 PRCHACDELIF 148 (176)
Q Consensus 138 ~~C~~C~~~I~ 148 (176)
..|..|+.+|.
T Consensus 236 ~pC~~Cg~~I~ 246 (269)
T PRK14811 236 QPCPRCGTPIE 246 (269)
T ss_pred CCCCcCCCeeE
Confidence 68999999994
No 127
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.38 E-value=94 Score=23.69 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=6.0
Q ss_pred cccccccccc
Q psy15163 73 TCKQCGQEVR 82 (176)
Q Consensus 73 ~C~~C~~~i~ 82 (176)
.|..|++.+.
T Consensus 7 ~C~~C~~~~~ 16 (227)
T PRK11595 7 LCWLCRMPLA 16 (227)
T ss_pred cCccCCCccC
Confidence 5666666553
No 128
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=20.15 E-value=1e+02 Score=17.67 Aligned_cols=27 Identities=26% Similarity=0.515 Sum_probs=15.9
Q ss_pred CCcccCHhHHhhCCCc-ccccccccccc
Q psy15163 122 KGNVYCLRDYATMLDI-PRCHACDELIF 148 (176)
Q Consensus 122 ~g~~yC~~~y~~~~~~-~~C~~C~~~I~ 148 (176)
.+..+|..|-..++.. +.|..|++++.
T Consensus 19 ~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 19 SDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cchhHHHHHHHHHhccccCCCcccCcCc
Confidence 4455677776655543 78999988873
Done!