Query 023002
Match_columns 289
No_of_seqs 281 out of 741
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:44:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023002hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1813 Predicted E3 ubiquitin 100.0 9.8E-64 2.1E-68 466.2 3.7 220 46-288 41-270 (313)
2 COG5152 Uncharacterized conser 100.0 1.8E-42 3.9E-47 311.1 3.2 99 173-288 127-225 (259)
3 PF15227 zf-C3HC4_4: zinc fing 98.9 7.8E-10 1.7E-14 76.7 1.4 27 262-288 1-27 (42)
4 KOG0823 Predicted E3 ubiquitin 98.7 1.4E-08 2.9E-13 93.6 3.5 33 256-288 44-76 (230)
5 PF13923 zf-C3HC4_2: Zinc fing 98.6 1.7E-08 3.6E-13 68.1 1.1 27 262-288 1-28 (39)
6 smart00504 Ubox Modified RING 98.4 9.2E-08 2E-12 68.9 1.8 29 260-288 2-30 (63)
7 PF13445 zf-RING_UBOX: RING-ty 98.4 9.7E-08 2.1E-12 67.1 0.9 26 262-288 1-30 (43)
8 KOG0320 Predicted E3 ubiquitin 98.4 1.6E-07 3.5E-12 84.0 2.4 32 257-288 129-162 (187)
9 PF00097 zf-C3HC4: Zinc finger 98.3 2.8E-07 6.2E-12 61.9 1.2 27 262-288 1-28 (41)
10 KOG0317 Predicted E3 ubiquitin 98.2 4.2E-07 9.1E-12 86.2 1.7 30 259-288 239-268 (293)
11 KOG2164 Predicted E3 ubiquitin 98.1 8.6E-07 1.9E-11 89.4 1.5 30 259-288 186-215 (513)
12 PF14634 zf-RING_5: zinc-RING 98.1 1.8E-06 3.8E-11 59.8 1.9 28 261-288 1-31 (44)
13 smart00184 RING Ring finger. E 98.0 3.4E-06 7.4E-11 53.3 2.2 26 262-287 1-26 (39)
14 COG5574 PEX10 RING-finger-cont 98.0 2.8E-06 6.1E-11 79.9 1.7 30 259-288 215-244 (271)
15 PF00642 zf-CCCH: Zinc finger 98.0 7.2E-07 1.6E-11 56.7 -1.6 27 185-211 1-27 (27)
16 smart00356 ZnF_C3H1 zinc finge 98.0 3.4E-06 7.4E-11 51.9 1.5 26 185-211 2-27 (27)
17 PF04564 U-box: U-box domain; 97.8 5.7E-06 1.2E-10 63.0 1.2 30 259-288 4-33 (73)
18 PF13920 zf-C3HC4_3: Zinc fing 97.8 6.2E-06 1.3E-10 58.1 1.2 29 260-288 3-32 (50)
19 cd00162 RING RING-finger (Real 97.7 1.4E-05 3E-10 52.2 1.5 27 261-287 1-28 (45)
20 PF13639 zf-RING_2: Ring finge 97.6 1.6E-05 3.6E-10 54.4 0.8 28 261-288 2-32 (44)
21 PF14835 zf-RING_6: zf-RING of 97.6 2.1E-05 4.5E-10 60.3 0.5 28 260-287 8-36 (65)
22 KOG0978 E3 ubiquitin ligase in 97.5 3E-05 6.5E-10 81.2 0.1 30 258-287 642-671 (698)
23 PHA02929 N1R/p28-like protein; 97.4 6.9E-05 1.5E-09 69.6 2.2 30 259-288 174-211 (238)
24 PF11789 zf-Nse: Zinc-finger o 97.3 8.9E-05 1.9E-09 54.9 1.4 33 256-288 8-41 (57)
25 COG5222 Uncharacterized conser 97.2 0.00036 7.9E-09 67.6 4.3 75 205-288 229-304 (427)
26 KOG4159 Predicted E3 ubiquitin 97.1 0.00016 3.5E-09 71.6 0.7 32 257-288 82-113 (398)
27 PHA02926 zinc finger-like prot 96.7 0.00071 1.5E-08 63.0 1.6 29 260-288 171-208 (242)
28 KOG0311 Predicted E3 ubiquitin 96.0 0.00073 1.6E-08 66.3 -2.6 32 257-288 41-73 (381)
29 KOG2879 Predicted E3 ubiquitin 95.7 0.0047 1E-07 59.1 1.6 31 258-288 238-269 (298)
30 PF12678 zf-rbx1: RING-H2 zinc 95.2 0.0086 1.9E-07 45.8 1.3 28 261-288 21-61 (73)
31 KOG1677 CCCH-type Zn-finger pr 95.0 0.011 2.4E-07 55.5 1.7 33 180-212 170-202 (332)
32 KOG3039 Uncharacterized conser 95.0 0.0095 2.1E-07 56.6 1.1 30 259-288 42-72 (303)
33 KOG1001 Helicase-like transcri 94.7 0.016 3.5E-07 61.0 1.9 29 260-289 455-483 (674)
34 KOG1002 Nucleotide excision re 94.4 0.015 3.2E-07 60.3 0.9 33 255-287 532-564 (791)
35 KOG0825 PHD Zn-finger protein 92.2 0.029 6.3E-07 60.3 -1.1 30 259-288 123-155 (1134)
36 KOG0802 E3 ubiquitin ligase [P 91.8 0.068 1.5E-06 54.5 1.1 29 260-288 292-325 (543)
37 KOG4692 Predicted E3 ubiquitin 90.3 0.13 2.8E-06 51.3 1.3 28 261-288 424-451 (489)
38 KOG1039 Predicted E3 ubiquitin 89.6 0.14 3.1E-06 50.3 1.0 30 259-288 161-198 (344)
39 KOG4172 Predicted E3 ubiquitin 89.6 0.1 2.2E-06 39.5 -0.0 28 261-288 9-37 (62)
40 KOG1814 Predicted E3 ubiquitin 89.0 0.18 3.9E-06 50.8 1.2 31 257-287 182-215 (445)
41 PF14608 zf-CCCH_2: Zinc finge 88.6 0.24 5.2E-06 29.3 1.1 19 189-210 1-19 (19)
42 PF04641 Rtf2: Rtf2 RING-finge 88.4 0.33 7.1E-06 45.1 2.5 35 255-289 109-147 (260)
43 KOG3039 Uncharacterized conser 88.3 0.23 4.9E-06 47.5 1.3 31 258-288 220-254 (303)
44 KOG1039 Predicted E3 ubiquitin 86.9 0.57 1.2E-05 46.1 3.2 15 196-210 101-115 (344)
45 PF12861 zf-Apc11: Anaphase-pr 85.5 0.48 1.1E-05 38.2 1.6 16 273-288 48-63 (85)
46 KOG0826 Predicted E3 ubiquitin 83.2 0.5 1.1E-05 46.6 0.9 32 257-288 298-330 (357)
47 KOG1677 CCCH-type Zn-finger pr 82.6 0.45 9.7E-06 44.8 0.3 29 185-213 130-159 (332)
48 PF10367 Vps39_2: Vacuolar sor 81.5 0.6 1.3E-05 36.3 0.7 27 261-287 80-108 (109)
49 PF03194 LUC7: LUC7 N_terminus 81.3 0.33 7.2E-06 45.5 -1.0 42 167-210 11-61 (254)
50 KOG1812 Predicted E3 ubiquitin 79.1 0.88 1.9E-05 45.0 1.1 33 256-288 143-179 (384)
51 KOG1815 Predicted E3 ubiquitin 78.0 1.4 3E-05 44.1 2.0 31 257-287 68-99 (444)
52 PF14447 Prok-RING_4: Prokaryo 77.9 0.83 1.8E-05 34.2 0.4 27 260-286 8-34 (55)
53 COG5236 Uncharacterized conser 77.9 1.4 3E-05 44.2 2.0 29 260-288 62-90 (493)
54 KOG1571 Predicted E3 ubiquitin 76.2 1.7 3.7E-05 43.1 2.1 30 253-282 299-328 (355)
55 KOG4265 Predicted E3 ubiquitin 75.0 2.4 5.2E-05 42.0 2.8 33 255-287 286-319 (349)
56 cd00065 FYVE FYVE domain; Zinc 73.7 1.8 3.9E-05 30.6 1.2 27 261-287 4-34 (57)
57 KOG4628 Predicted E3 ubiquitin 72.8 2.1 4.5E-05 42.4 1.8 30 258-287 228-260 (348)
58 KOG1785 Tyrosine kinase negati 72.7 1.6 3.4E-05 44.5 0.9 27 261-287 371-397 (563)
59 KOG2333 Uncharacterized conser 71.4 1.1 2.4E-05 46.5 -0.5 20 197-216 88-107 (614)
60 KOG0298 DEAD box-containing he 68.7 1.4 3.1E-05 49.8 -0.4 31 257-287 1151-1182(1394)
61 COG5540 RING-finger-containing 65.1 2.7 5.8E-05 41.5 0.7 32 257-288 321-355 (374)
62 KOG1763 Uncharacterized conser 64.7 1.7 3.7E-05 42.5 -0.6 29 183-212 88-116 (343)
63 PF13465 zf-H2C2_2: Zinc-finge 63.8 3.3 7.3E-05 25.7 0.8 14 258-271 13-26 (26)
64 KOG2185 Predicted RNA-processi 62.1 2.9 6.2E-05 42.6 0.3 23 188-211 141-163 (486)
65 smart00064 FYVE Protein presen 62.1 5.4 0.00012 29.2 1.7 28 260-287 11-42 (68)
66 KOG0804 Cytoplasmic Zn-finger 59.0 4.4 9.6E-05 41.6 1.1 32 256-288 173-208 (493)
67 PF01363 FYVE: FYVE zinc finge 58.8 2.1 4.6E-05 31.5 -0.9 28 260-287 10-41 (69)
68 KOG4275 Predicted E3 ubiquitin 58.6 3.4 7.5E-05 40.5 0.2 27 259-285 300-327 (350)
69 PF10235 Cript: Microtubule-as 52.7 6.6 0.00014 32.1 0.9 23 261-288 46-68 (90)
70 KOG1814 Predicted E3 ubiquitin 52.4 1.2 2.7E-05 45.1 -4.0 32 256-287 365-402 (445)
71 KOG2979 Protein involved in DN 51.4 5.6 0.00012 38.1 0.4 32 256-287 173-205 (262)
72 KOG2932 E3 ubiquitin ligase in 51.1 6.4 0.00014 39.0 0.7 28 260-287 91-119 (389)
73 KOG0796 Spliceosome subunit [R 48.7 3.7 8E-05 40.3 -1.3 41 168-210 13-62 (319)
74 KOG0828 Predicted E3 ubiquitin 45.5 8.7 0.00019 40.2 0.7 30 259-288 571-617 (636)
75 PF00096 zf-C2H2: Zinc finger, 45.4 7.6 0.00016 22.6 0.2 14 260-273 1-14 (23)
76 KOG1812 Predicted E3 ubiquitin 45.3 9.4 0.0002 37.9 0.9 29 259-287 306-339 (384)
77 KOG4445 Uncharacterized conser 43.9 9.2 0.0002 37.8 0.6 29 260-288 116-147 (368)
78 PHA03096 p28-like protein; Pro 43.3 12 0.00027 35.9 1.3 28 260-287 179-214 (284)
79 PF13912 zf-C2H2_6: C2H2-type 42.8 10 0.00023 22.8 0.5 13 259-271 1-13 (27)
80 KOG2817 Predicted E3 ubiquitin 42.3 13 0.00028 37.6 1.3 31 257-287 332-365 (394)
81 KOG1734 Predicted RING-contain 41.7 11 0.00024 36.7 0.8 27 261-287 226-262 (328)
82 PF05883 Baculo_RING: Baculovi 41.0 13 0.00028 32.4 1.0 31 258-288 25-64 (134)
83 PF02318 FYVE_2: FYVE-type zin 40.7 9.8 0.00021 31.4 0.2 28 260-287 55-87 (118)
84 KOG3579 Predicted E3 ubiquitin 39.2 10 0.00023 37.2 0.1 32 256-287 265-300 (352)
85 PF13894 zf-C2H2_4: C2H2-type 39.1 11 0.00025 21.2 0.2 13 260-272 1-13 (24)
86 KOG2034 Vacuolar sorting prote 38.1 13 0.00028 41.1 0.6 28 261-288 819-848 (911)
87 KOG1940 Zn-finger protein [Gen 37.6 12 0.00027 36.0 0.4 32 255-286 154-189 (276)
88 KOG3002 Zn finger protein [Gen 37.6 17 0.00036 35.3 1.3 31 258-288 47-78 (299)
89 PF10764 Gin: Inhibitor of sig 36.9 15 0.00033 26.3 0.6 26 261-287 1-26 (46)
90 KOG3476 Microtubule-associated 36.9 11 0.00024 31.0 -0.0 24 260-288 55-78 (100)
91 PF07975 C1_4: TFIIH C1-like d 36.7 21 0.00045 26.3 1.3 12 275-286 25-36 (51)
92 COG5243 HRD1 HRD ubiquitin lig 34.2 20 0.00044 36.5 1.2 27 261-287 289-328 (491)
93 PF10571 UPF0547: Uncharacteri 32.9 25 0.00053 22.4 1.1 21 261-281 2-24 (26)
94 smart00154 ZnF_AN1 AN1-like Zi 32.7 25 0.00055 24.1 1.2 11 259-269 12-22 (39)
95 PTZ00303 phosphatidylinositol 32.2 24 0.00052 39.2 1.5 28 260-287 461-497 (1374)
96 smart00647 IBR In Between Ring 31.3 14 0.0003 26.1 -0.3 12 276-287 45-56 (64)
97 KOG1040 Polyadenylation factor 31.2 15 0.00033 36.0 -0.1 41 167-210 59-99 (325)
98 smart00744 RINGv The RING-vari 31.2 36 0.00078 24.2 1.8 27 261-287 1-34 (49)
99 COG4647 AcxC Acetone carboxyla 30.6 22 0.00047 31.5 0.7 22 262-283 60-81 (165)
100 KOG2494 C3H1-type Zn-finger pr 30.1 10 0.00022 37.5 -1.6 26 203-228 85-110 (331)
101 KOG2114 Vacuolar assembly/sort 28.4 32 0.00069 38.1 1.6 27 261-287 842-869 (933)
102 KOG1729 FYVE finger containing 27.5 19 0.00041 34.8 -0.2 29 259-287 168-201 (288)
103 PF06827 zf-FPG_IleRS: Zinc fi 27.4 10 0.00022 24.1 -1.4 26 261-286 3-28 (30)
104 TIGR00622 ssl1 transcription f 27.3 29 0.00062 29.4 0.9 27 261-287 57-97 (112)
105 KOG0825 PHD Zn-finger protein 27.2 50 0.0011 36.7 2.8 28 261-288 98-132 (1134)
106 KOG1492 C3H1-type Zn-finger pr 27.2 26 0.00055 33.7 0.6 31 182-212 281-313 (377)
107 PF12874 zf-met: Zinc-finger o 26.5 24 0.00051 20.9 0.2 15 260-274 1-15 (25)
108 PF00412 LIM: LIM domain; Int 25.8 36 0.00077 23.6 1.0 31 258-288 25-56 (58)
109 KOG1100 Predicted E3 ubiquitin 24.1 29 0.00063 31.8 0.4 25 262-286 161-186 (207)
110 COG5063 CTH1 CCCH-type Zn-fing 23.7 38 0.00083 33.6 1.1 23 188-210 275-297 (351)
111 smart00451 ZnF_U1 U1-like zinc 23.4 39 0.00084 21.3 0.7 15 259-273 3-17 (35)
112 PF07191 zinc-ribbons_6: zinc- 23.3 17 0.00037 28.5 -1.1 13 273-285 42-56 (70)
113 PF08273 Prim_Zn_Ribbon: Zinc- 23.0 26 0.00057 24.5 -0.1 26 260-285 4-32 (40)
114 PF01485 IBR: IBR domain; Int 22.4 22 0.00047 25.0 -0.6 27 261-287 20-56 (64)
115 cd04707 otoconin_90 otoconin_9 21.8 21 0.00046 30.2 -0.9 20 193-212 17-46 (117)
116 KOG3777 Uncharacterized conser 21.8 62 0.0013 33.3 2.2 50 160-213 144-194 (443)
117 PF02891 zf-MIZ: MIZ/SP-RING z 21.4 43 0.00093 24.0 0.7 24 259-282 2-26 (50)
118 PF13719 zinc_ribbon_5: zinc-r 20.9 39 0.00085 22.7 0.4 11 259-269 25-35 (37)
119 cd00125 PLA2c PLA2c: Phospholi 20.5 16 0.00035 30.7 -1.9 20 192-211 19-48 (115)
120 PRK01103 formamidopyrimidine/5 20.0 32 0.00069 32.2 -0.2 26 261-286 247-272 (274)
No 1
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.8e-64 Score=466.18 Aligned_cols=220 Identities=47% Similarity=0.811 Sum_probs=179.7
Q ss_pred eeecccCCCCCCCCceeecCCCccCC--------CCCCCCCCCCCceeeeccchhccc--cccccccccccccchhhhHH
Q 023002 46 VLQNLKKPTKPDSKLYFSTGPSKRDT--------SADSNADSEKPIFQFESSKEIQVQ--HDSKATATLETETDFLRDSR 115 (289)
Q Consensus 46 v~~~~kkr~k~~~~~~~st~~~~~~~--------~~~~~~~~~~~~~~~~ssr~~~~~--~d~~AT~~~e~dt~~d~Da~ 115 (289)
+++..+.+++ ++|++|.+..+.... .+..+...+.+.|.|.|.+.+.+. .++|||+++|.+|+..+|||
T Consensus 41 s~r~ek~~k~-~~p~~q~~k~~~k~~~~~~~~s~~s~~~~~~ed~vv~y~s~~~~~~~g~~dsgat~t~e~~te~~~Daq 119 (313)
T KOG1813|consen 41 SSRLEKLEKK-IKPETQRKKETDKVLTGEEDDSALSICQNPFEDPVVTYCSCDKCALKGHTDSGATATLEEPTEGLRDAQ 119 (313)
T ss_pred hhhhhhhhhh-cchHhhhhhhhcccccccccccccccccCcccccceeeccccccccCCccccCceeEeecCcccchhHH
Confidence 3555555555 578877654322111 111223345799999998888765 59999999999999999999
Q ss_pred HHHHHHHHhhHHHhcCCCCCCccccccccccccccccccccccccccCCCCCCCCCcCCceeeeeeeeeecCCCcCCCcc
Q 023002 116 ALREKVLKRSEEALKGKASGDEKLYKGIHGYVDHKAGFRREHTVSSEKAGGSHGPLRASAHIRVTARFDYQPDICKDYKE 195 (289)
Q Consensus 116 ai~er~~~~~~~~l~g~~~~~d~~YrG~~~y~~~~~~~~~~~~~~~~~~~~~~GPirap~niR~t~~~DyqPDiCKDyke 195 (289)
+|+|++++..++.+.|+ .++.+|+|+|+|.+|.+ ..++..++...|.+=|||||++||++++|||||||||||+|
T Consensus 120 a~~er~~k~~~e~~~~k--~~~~lykg~~~ya~~~k---~~~~~~~n~s~g~~rpira~~~~r~~~~~d~qpDicKdyke 194 (313)
T KOG1813|consen 120 AIIERRIKEEREKLRGK--KDTKLYKGINTYADDAK---AQKVVKMNESIGTVRPIRAAMHTRAGERIDYQPDICKDYKE 194 (313)
T ss_pred HHhhhhHHHHHHhhcch--hHHHHHHHHHHHHhhhh---hhhhHhhhcccccccccchhhhhcccceeecCchhhhhhHh
Confidence 99999999778888886 48899999999999975 44445556666644499999999999999999999999999
Q ss_pred cccccCCCceeeeeecccccccchhhHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCCCceeccccccccCCceec
Q 023002 196 TGYCGYGDSCKFMHDRGDYKSGWQMEKEWEEAEKARKRNLALGGGDSDEEGVGQSDDDDEDSLPFACFICRKPFVDPVVT 275 (289)
Q Consensus 196 TG~CGfGDsCKFlHdR~dyk~GWqld~ewe~~~k~kk~~l~~g~~~~~~~~~~~~~~~~e~~~p~~C~IC~~~f~dPVvT 275 (289)
||||||||||||||+|+|||+||||++||++.+-. ......|++.+||.|.||++.|.+||||
T Consensus 195 Tgycg~gdSckFlh~r~DyK~GWqi~~e~d~~ke~-----------------~~~~~~D~~~~Pf~c~icr~~f~~pVvt 257 (313)
T KOG1813|consen 195 TGYCGYGDSCKFLHDRSDYKAGWQIEFEWDSAKEK-----------------KRVKIEDIELLPFKCFICRKYFYRPVVT 257 (313)
T ss_pred hCcccccchhhhhhhhhhccccceeehhhhccccc-----------------cceecCCcccCCccccccccccccchhh
Confidence 99999999999999999999999999999977511 1224456788999999999999999999
Q ss_pred CCCChhhHHhHhc
Q 023002 276 KCKHYFCEHCALK 288 (289)
Q Consensus 276 ~CGH~FC~~Ci~~ 288 (289)
.||||||+.|+++
T Consensus 258 ~c~h~fc~~ca~~ 270 (313)
T KOG1813|consen 258 KCGHYFCEVCALK 270 (313)
T ss_pred cCCceeehhhhcc
Confidence 9999999999975
No 2
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=100.00 E-value=1.8e-42 Score=311.15 Aligned_cols=99 Identities=48% Similarity=1.076 Sum_probs=86.9
Q ss_pred CCceeeeeeeeeecCCCcCCCcccccccCCCceeeeeecccccccchhhHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCC
Q 023002 173 ASAHIRVTARFDYQPDICKDYKETGYCGYGDSCKFMHDRGDYKSGWQMEKEWEEAEKARKRNLALGGGDSDEEGVGQSDD 252 (289)
Q Consensus 173 ap~niR~t~~~DyqPDiCKDykeTG~CGfGDsCKFlHdR~dyk~GWqld~ewe~~~k~kk~~l~~g~~~~~~~~~~~~~~ 252 (289)
.|++||++++|||||||||||++||||||||||||||+|+|||.||||++||...-. .+. -..
T Consensus 127 ~Pt~~r~~~viD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~KtGWkLn~EWnA~~E-------e~~----------v~~ 189 (259)
T COG5152 127 QPTMFRDGEVIDTQPDVCKDYKETGYCGYGDSCKFLHDRSDFKTGWKLNQEWNAEYE-------EAP----------VIS 189 (259)
T ss_pred CCceeeccceeecCcccccchhhcccccCCchhhhhhhhhhhhcccccchhhcchhh-------hcc----------ccc
Confidence 369999999999999999999999999999999999999999999999999983310 111 123
Q ss_pred CCCCCCceeccccccccCCceecCCCChhhHHhHhc
Q 023002 253 DDEDSLPFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 253 ~~e~~~p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
.+-++|||.|.||.+.|..||||.|||+||+.|+++
T Consensus 190 ~~~e~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~ 225 (259)
T COG5152 190 GPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIR 225 (259)
T ss_pred CCCCCCceeehhchhhccchhhhhcchhHHHHHHHH
Confidence 445789999999999999999999999999999974
No 3
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.86 E-value=7.8e-10 Score=76.74 Aligned_cols=27 Identities=44% Similarity=0.995 Sum_probs=23.9
Q ss_pred ccccccccCCceecCCCChhhHHhHhc
Q 023002 262 CFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 262 C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
|+||++.|++||++.|||.||..||.+
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~ 27 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRSCLER 27 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHHHHHH
T ss_pred CCccchhhCCccccCCcCHHHHHHHHH
Confidence 899999999999999999999999964
No 4
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=1.4e-08 Score=93.60 Aligned_cols=33 Identities=45% Similarity=0.811 Sum_probs=30.7
Q ss_pred CCCceeccccccccCCceecCCCChhhHHhHhc
Q 023002 256 DSLPFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
+.--|.|.||++.-++||||.|||.|||.||.+
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyq 76 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQ 76 (230)
T ss_pred CCCceeeeeeccccCCCEEeecccceehHHHHH
Confidence 566899999999999999999999999999975
No 5
>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=98.58 E-value=1.7e-08 Score=68.08 Aligned_cols=27 Identities=52% Similarity=1.081 Sum_probs=24.4
Q ss_pred ccccccccCCc-eecCCCChhhHHhHhc
Q 023002 262 CFICRKPFVDP-VVTKCKHYFCEHCALK 288 (289)
Q Consensus 262 C~IC~~~f~dP-VvT~CGH~FC~~Ci~~ 288 (289)
|+||.+.+.+| |++.|||.||..|+.+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHH
Confidence 89999999999 6899999999999974
No 6
>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=98.43 E-value=9.2e-08 Score=68.93 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=27.5
Q ss_pred eeccccccccCCceecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
|.|+||++.+.+||+++|||.||..||.+
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~ 30 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEK 30 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHH
Confidence 68999999999999999999999999974
No 7
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.38 E-value=9.7e-08 Score=67.11 Aligned_cols=26 Identities=46% Similarity=1.166 Sum_probs=17.8
Q ss_pred ccccccccCC----ceecCCCChhhHHhHhc
Q 023002 262 CFICRKPFVD----PVVTKCKHYFCEHCALK 288 (289)
Q Consensus 262 C~IC~~~f~d----PVvT~CGH~FC~~Ci~~ 288 (289)
|+||++ |.+ |+++.|||.||+.|+.+
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~ 30 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQK 30 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHH
Confidence 899999 988 99999999999999965
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.37 E-value=1.6e-07 Score=84.02 Aligned_cols=32 Identities=38% Similarity=0.812 Sum_probs=27.7
Q ss_pred CCceecccccccc--CCceecCCCChhhHHhHhc
Q 023002 257 SLPFACFICRKPF--VDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 257 ~~p~~C~IC~~~f--~dPVvT~CGH~FC~~Ci~~ 288 (289)
+.-|.||||+..+ +-||.|+|||.||..||..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~ 162 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKD 162 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHH
Confidence 3459999999999 4688899999999999964
No 9
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.27 E-value=2.8e-07 Score=61.87 Aligned_cols=27 Identities=52% Similarity=1.179 Sum_probs=25.7
Q ss_pred ccccccccCCce-ecCCCChhhHHhHhc
Q 023002 262 CFICRKPFVDPV-VTKCKHYFCEHCALK 288 (289)
Q Consensus 262 C~IC~~~f~dPV-vT~CGH~FC~~Ci~~ 288 (289)
|+||++.+.+|+ ++.|||.||..|+.+
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~ 28 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRK 28 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHH
Confidence 899999999999 999999999999974
No 10
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=4.2e-07 Score=86.25 Aligned_cols=30 Identities=33% Similarity=0.775 Sum_probs=28.1
Q ss_pred ceeccccccccCCceecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
-++|.||++...||..|+|||.|||.||+.
T Consensus 239 ~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~ 268 (293)
T KOG0317|consen 239 TRKCSLCLENRSNPSATPCGHIFCWSCILE 268 (293)
T ss_pred CCceEEEecCCCCCCcCcCcchHHHHHHHH
Confidence 478999999999999999999999999974
No 11
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.12 E-value=8.6e-07 Score=89.38 Aligned_cols=30 Identities=43% Similarity=0.928 Sum_probs=28.5
Q ss_pred ceeccccccccCCceecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
+..||||+..+.-|+.|.|||.||..||++
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHHHHHH
Confidence 569999999999999999999999999985
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.08 E-value=1.8e-06 Score=59.79 Aligned_cols=28 Identities=43% Similarity=0.988 Sum_probs=25.2
Q ss_pred ecccccccc---CCceecCCCChhhHHhHhc
Q 023002 261 ACFICRKPF---VDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f---~dPVvT~CGH~FC~~Ci~~ 288 (289)
.|+||.+.| ..|++|.|||.||..|+.+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 389999999 5799999999999999975
No 13
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.01 E-value=3.4e-06 Score=53.26 Aligned_cols=26 Identities=46% Similarity=1.036 Sum_probs=24.9
Q ss_pred ccccccccCCceecCCCChhhHHhHh
Q 023002 262 CFICRKPFVDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 262 C~IC~~~f~dPVvT~CGH~FC~~Ci~ 287 (289)
|+||++...+|+++.|||.||..|+.
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~ 26 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIR 26 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHH
Confidence 89999999999999999999999985
No 14
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=2.8e-06 Score=79.93 Aligned_cols=30 Identities=37% Similarity=0.880 Sum_probs=28.1
Q ss_pred ceeccccccccCCceecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
-|.|+||.+...+|+.|.|||.||+.||+.
T Consensus 215 d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~ 244 (271)
T COG5574 215 DYKCFLCLEEPEVPSCTPCGHLFCLSCLLI 244 (271)
T ss_pred ccceeeeecccCCcccccccchhhHHHHHH
Confidence 367999999999999999999999999975
No 15
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=97.96 E-value=7.2e-07 Score=56.65 Aligned_cols=27 Identities=37% Similarity=1.074 Sum_probs=21.1
Q ss_pred ecCCCcCCCcccccccCCCceeeeeec
Q 023002 185 YQPDICKDYKETGYCGYGDSCKFMHDR 211 (289)
Q Consensus 185 yqPDiCKDykeTG~CGfGDsCKFlHdR 211 (289)
|..-+|+.|.++|+|.||++|.|+|++
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred CccccChhhccCCccCCCCCcCccCCC
Confidence 345689999999999999999999985
No 16
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.96 E-value=3.4e-06 Score=51.93 Aligned_cols=26 Identities=50% Similarity=1.261 Sum_probs=23.3
Q ss_pred ecCCCcCCCcccccccCCCceeeeeec
Q 023002 185 YQPDICKDYKETGYCGYGDSCKFMHDR 211 (289)
Q Consensus 185 yqPDiCKDykeTG~CGfGDsCKFlHdR 211 (289)
|++-+|++| ++|+|.+|++|.|+|+.
T Consensus 2 ~k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 567789999 99999999999999973
No 17
>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=97.84 E-value=5.7e-06 Score=62.97 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=26.2
Q ss_pred ceeccccccccCCceecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
.|.|+||.+.|+|||+++|||.|+..||.+
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G~tyer~~I~~ 33 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSGHTYERSAIER 33 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTSEEEEHHHHHH
T ss_pred ccCCcCcCcHhhCceeCCcCCEEcHHHHHH
Confidence 489999999999999999999999999974
No 18
>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=97.84 E-value=6.2e-06 Score=58.10 Aligned_cols=29 Identities=41% Similarity=0.799 Sum_probs=26.3
Q ss_pred eeccccccccCCceecCCCCh-hhHHhHhc
Q 023002 260 FACFICRKPFVDPVVTKCKHY-FCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~-FC~~Ci~~ 288 (289)
+.|.||++.+.++++++|||. ||..|+.+
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~ 32 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCEECAER 32 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEHHHHHH
T ss_pred CCCccCCccCCceEEeCCCChHHHHHHhHH
Confidence 589999999999999999999 99999864
No 19
>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=97.73 E-value=1.4e-05 Score=52.24 Aligned_cols=27 Identities=44% Similarity=1.000 Sum_probs=24.2
Q ss_pred eccccccccCCceecC-CCChhhHHhHh
Q 023002 261 ACFICRKPFVDPVVTK-CKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~-CGH~FC~~Ci~ 287 (289)
.|+||++.+.+|+++. |||.||..|+.
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~ 28 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCID 28 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHH
Confidence 4999999998888776 99999999985
No 20
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=97.64 E-value=1.6e-05 Score=54.44 Aligned_cols=28 Identities=32% Similarity=0.670 Sum_probs=25.0
Q ss_pred ecccccccc---CCceecCCCChhhHHhHhc
Q 023002 261 ACFICRKPF---VDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f---~dPVvT~CGH~FC~~Ci~~ 288 (289)
.|+||++.| ..++++.|||.||..||.+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~ 32 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKE 32 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHH
Confidence 599999999 4688899999999999864
No 21
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.56 E-value=2.1e-05 Score=60.28 Aligned_cols=28 Identities=36% Similarity=0.938 Sum_probs=16.5
Q ss_pred eeccccccccCCce-ecCCCChhhHHhHh
Q 023002 260 FACFICRKPFVDPV-VTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~dPV-vT~CGH~FC~~Ci~ 287 (289)
+.|++|...++.|| ++.|.|.||+.||-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~ 36 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIR 36 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGG
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhH
Confidence 57999999999998 59999999999985
No 22
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.45 E-value=3e-05 Score=81.17 Aligned_cols=30 Identities=40% Similarity=0.957 Sum_probs=28.1
Q ss_pred CceeccccccccCCceecCCCChhhHHhHh
Q 023002 258 LPFACFICRKPFVDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 258 ~p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~ 287 (289)
--+.|++|..-|+|-|+++|||.||..|+.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq 671 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITKCGHVFCEECVQ 671 (698)
T ss_pred hceeCCCccCchhhHHHHhcchHHHHHHHH
Confidence 467899999999999999999999999985
No 23
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.42 E-value=6.9e-05 Score=69.64 Aligned_cols=30 Identities=30% Similarity=0.754 Sum_probs=25.4
Q ss_pred ceeccccccccCCc--------eecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDP--------VVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dP--------VvT~CGH~FC~~Ci~~ 288 (289)
...|+||++.+.++ |++.|||.||..||.+
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~ 211 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHH
Confidence 35899999998763 7889999999999963
No 24
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.33 E-value=8.9e-05 Score=54.87 Aligned_cols=33 Identities=36% Similarity=0.743 Sum_probs=24.0
Q ss_pred CCCceeccccccccCCceec-CCCChhhHHhHhc
Q 023002 256 DSLPFACFICRKPFVDPVVT-KCKHYFCEHCALK 288 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dPVvT-~CGH~FC~~Ci~~ 288 (289)
..+.+.|||.+..|++||.. .|||.|....|++
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~ 41 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQ 41 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHH
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHH
Confidence 55789999999999999995 9999999998864
No 25
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.19 E-value=0.00036 Score=67.60 Aligned_cols=75 Identities=20% Similarity=0.449 Sum_probs=51.6
Q ss_pred eeeeeecccccccchhhHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCCCCCceeccccccccCCceec-CCCChhhH
Q 023002 205 CKFMHDRGDYKSGWQMEKEWEEAEKARKRNLALGGGDSDEEGVGQSDDDDEDSLPFACFICRKPFVDPVVT-KCKHYFCE 283 (289)
Q Consensus 205 CKFlHdR~dyk~GWqld~ewe~~~k~kk~~l~~g~~~~~~~~~~~~~~~~e~~~p~~C~IC~~~f~dPVvT-~CGH~FC~ 283 (289)
-..+.+-++|.---.--++||.=|..++.....|. +- + .---.+++++|+.|...+++|+-| -|||.||.
T Consensus 229 ~imit~EG~yVv~qpdvqsWe~Yq~r~~a~~~~~D------qv-~--k~~~~~i~LkCplc~~Llrnp~kT~cC~~~fc~ 299 (427)
T COG5222 229 AIMITPEGGYVVAQPDVQSWEKYQQRTKAVAEIPD------QV-Y--KMQPPNISLKCPLCHCLLRNPMKTPCCGHTFCD 299 (427)
T ss_pred ceEEcCCCCeEEeccchHHHHHHHHHHHhhhhCch------hh-h--ccCCCCccccCcchhhhhhCcccCccccchHHH
Confidence 34566677776655555889988765544222111 00 0 011257899999999999999999 78999999
Q ss_pred HhHhc
Q 023002 284 HCALK 288 (289)
Q Consensus 284 ~Ci~~ 288 (289)
.||..
T Consensus 300 eci~~ 304 (427)
T COG5222 300 ECIGT 304 (427)
T ss_pred HHHhh
Confidence 99963
No 26
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00016 Score=71.58 Aligned_cols=32 Identities=38% Similarity=0.920 Sum_probs=29.7
Q ss_pred CCceeccccccccCCceecCCCChhhHHhHhc
Q 023002 257 SLPFACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 257 ~~p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
..+|.|-||...|.+||+|+|||.||..||.+
T Consensus 82 ~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r 113 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTPCGHSFCLECLDR 113 (398)
T ss_pred cchhhhhhhHhhcCCCccccccccccHHHHHH
Confidence 45899999999999999999999999999764
No 27
>PHA02926 zinc finger-like protein; Provisional
Probab=96.71 E-value=0.00071 Score=63.02 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=24.4
Q ss_pred eeccccccccC---------CceecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFV---------DPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~---------dPVvT~CGH~FC~~Ci~~ 288 (289)
..|+||++... -+|+..|+|.||..||.+
T Consensus 171 ~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~ 208 (242)
T PHA02926 171 KECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINI 208 (242)
T ss_pred CCCccCccccccccccccccccccCCCCchHHHHHHHH
Confidence 48999998753 268999999999999963
No 28
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.01 E-value=0.00073 Score=66.29 Aligned_cols=32 Identities=31% Similarity=0.721 Sum_probs=28.8
Q ss_pred CCceeccccccccCCceec-CCCChhhHHhHhc
Q 023002 257 SLPFACFICRKPFVDPVVT-KCKHYFCEHCALK 288 (289)
Q Consensus 257 ~~p~~C~IC~~~f~dPVvT-~CGH~FC~~Ci~~ 288 (289)
.+.|.|+||+..++..++| .|+|-||..||..
T Consensus 41 ~~~v~c~icl~llk~tmttkeClhrfc~~ci~~ 73 (381)
T KOG0311|consen 41 DIQVICPICLSLLKKTMTTKECLHRFCFDCIWK 73 (381)
T ss_pred hhhhccHHHHHHHHhhcccHHHHHHHHHHHHHH
Confidence 5689999999999998877 7999999999975
No 29
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.0047 Score=59.09 Aligned_cols=31 Identities=29% Similarity=0.665 Sum_probs=27.7
Q ss_pred CceeccccccccCCceecC-CCChhhHHhHhc
Q 023002 258 LPFACFICRKPFVDPVVTK-CKHYFCEHCALK 288 (289)
Q Consensus 258 ~p~~C~IC~~~f~dPVvT~-CGH~FC~~Ci~~ 288 (289)
....|++|.+.++.|.+.. |||.||..||..
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIAT 269 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhh
Confidence 3568999999999999987 999999999864
No 30
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=95.23 E-value=0.0086 Score=45.81 Aligned_cols=28 Identities=46% Similarity=0.987 Sum_probs=22.8
Q ss_pred eccccccccCCc-------------eecCCCChhhHHhHhc
Q 023002 261 ACFICRKPFVDP-------------VVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f~dP-------------VvT~CGH~FC~~Ci~~ 288 (289)
.|.||++.|.+| ++..|||.|-..||.+
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~ 61 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQ 61 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHH
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHH
Confidence 399999999443 4568999999999963
No 31
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=95.04 E-value=0.011 Score=55.54 Aligned_cols=33 Identities=30% Similarity=0.899 Sum_probs=28.1
Q ss_pred eeeeeecCCCcCCCcccccccCCCceeeeeecc
Q 023002 180 TARFDYQPDICKDYKETGYCGYGDSCKFMHDRG 212 (289)
Q Consensus 180 t~~~DyqPDiCKDykeTG~CGfGDsCKFlHdR~ 212 (289)
....-|.=.+|..|..||+|-||..|+|.|...
T Consensus 170 ~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 170 GNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEP 202 (332)
T ss_pred cCCCCCCCcCCCccccCCCCCCCCcCeecCCCc
Confidence 334557778999999999999999999999854
No 32
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.01 E-value=0.0095 Score=56.56 Aligned_cols=30 Identities=33% Similarity=0.599 Sum_probs=27.7
Q ss_pred ce-eccccccccCCceecCCCChhhHHhHhc
Q 023002 259 PF-ACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~-~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
|| .|.+|++++.|||+++=||.||..|||+
T Consensus 42 ~FdcCsLtLqPc~dPvit~~GylfdrEaILe 72 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDPVITPDGYLFDREAILE 72 (303)
T ss_pred CcceeeeecccccCCccCCCCeeeeHHHHHH
Confidence 45 5899999999999999999999999985
No 33
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=94.67 E-value=0.016 Score=60.97 Aligned_cols=29 Identities=34% Similarity=0.766 Sum_probs=27.2
Q ss_pred eeccccccccCCceecCCCChhhHHhHhcC
Q 023002 260 FACFICRKPFVDPVVTKCKHYFCEHCALKV 289 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~v 289 (289)
+.|+||.+ ...+|+|.|||.||..|+..+
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~ 483 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHDFCVECLKKS 483 (674)
T ss_pred cccccccc-cccceeecccchHHHHHHHhc
Confidence 89999999 999999999999999999753
No 34
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.41 E-value=0.015 Score=60.27 Aligned_cols=33 Identities=30% Similarity=0.729 Sum_probs=29.1
Q ss_pred CCCCceeccccccccCCceecCCCChhhHHhHh
Q 023002 255 EDSLPFACFICRKPFVDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 255 e~~~p~~C~IC~~~f~dPVvT~CGH~FC~~Ci~ 287 (289)
+..-...|.+|.++-.+||++.|.|.||..|+-
T Consensus 532 enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~ 564 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYIESSCHHKFCRLCIK 564 (791)
T ss_pred cccCceeecccCChhhhhHhhhhhHHHHHHHHH
Confidence 344467899999999999999999999999983
No 35
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=92.22 E-value=0.029 Score=60.26 Aligned_cols=30 Identities=33% Similarity=0.654 Sum_probs=25.4
Q ss_pred ceeccccccccCCcee---cCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPVV---TKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPVv---T~CGH~FC~~Ci~~ 288 (289)
.-.|++|+..|.+-++ .+|+||||..||..
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s 155 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS 155 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence 4579999999988665 58999999999863
No 36
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.85 E-value=0.068 Score=54.50 Aligned_cols=29 Identities=28% Similarity=0.644 Sum_probs=26.6
Q ss_pred eeccccccccCC-----ceecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFVD-----PVVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~d-----PVvT~CGH~FC~~Ci~~ 288 (289)
-.|+||++.+.. |-..+|||.||..|+.+
T Consensus 292 ~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~ 325 (543)
T KOG0802|consen 292 ELCIICLEELHSGHNITPKRLPCGHIFHDSCLRS 325 (543)
T ss_pred CeeeeechhhccccccccceeecccchHHHHHHH
Confidence 489999999998 89999999999999864
No 37
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.27 E-value=0.13 Score=51.29 Aligned_cols=28 Identities=29% Similarity=0.653 Sum_probs=26.7
Q ss_pred eccccccccCCceecCCCChhhHHhHhc
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
.|+||--.+.+.|.++|+|--|..||.+
T Consensus 424 lCpICyA~pi~Avf~PC~H~SC~~CI~q 451 (489)
T KOG4692|consen 424 LCPICYAGPINAVFAPCSHRSCYGCITQ 451 (489)
T ss_pred cCcceecccchhhccCCCCchHHHHHHH
Confidence 8999999999999999999999999964
No 38
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.59 E-value=0.14 Score=50.26 Aligned_cols=30 Identities=30% Similarity=0.718 Sum_probs=26.1
Q ss_pred ceeccccccccCCce-----e---cCCCChhhHHhHhc
Q 023002 259 PFACFICRKPFVDPV-----V---TKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f~dPV-----v---T~CGH~FC~~Ci~~ 288 (289)
...|-||++....++ . -.|-|.||..||..
T Consensus 161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~ 198 (344)
T KOG1039|consen 161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRK 198 (344)
T ss_pred cccceehhhhccccchhhhhcccCCCcchhhhhcHhHh
Confidence 578999999998887 3 78999999999853
No 39
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.57 E-value=0.1 Score=39.51 Aligned_cols=28 Identities=39% Similarity=0.901 Sum_probs=24.8
Q ss_pred eccccccccCCceecCCCCh-hhHHhHhc
Q 023002 261 ACFICRKPFVDPVVTKCKHY-FCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~-FC~~Ci~~ 288 (289)
.|.||.+.+.|.|+-.|||. .|..|.++
T Consensus 9 ECTICye~pvdsVlYtCGHMCmCy~Cg~r 37 (62)
T KOG4172|consen 9 ECTICYEHPVDSVLYTCGHMCMCYACGLR 37 (62)
T ss_pred ceeeeccCcchHHHHHcchHHhHHHHHHH
Confidence 69999999999999999996 68888764
No 40
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.03 E-value=0.18 Score=50.84 Aligned_cols=31 Identities=29% Similarity=0.676 Sum_probs=26.2
Q ss_pred CCceeccccccccCC---ceecCCCChhhHHhHh
Q 023002 257 SLPFACFICRKPFVD---PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 257 ~~p~~C~IC~~~f~d---PVvT~CGH~FC~~Ci~ 287 (289)
..-|.|-||.+...- =+.++|+|+||..|+.
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~k 215 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLK 215 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHH
Confidence 347899999999854 5679999999999974
No 41
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=88.65 E-value=0.24 Score=29.27 Aligned_cols=19 Identities=42% Similarity=0.822 Sum_probs=14.5
Q ss_pred CcCCCcccccccCCCceeeeee
Q 023002 189 ICKDYKETGYCGYGDSCKFMHD 210 (289)
Q Consensus 189 iCKDykeTG~CGfGDsCKFlHd 210 (289)
+||-+.. |.+|++|.|+|-
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 3674443 999999999993
No 42
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.39 E-value=0.33 Score=45.15 Aligned_cols=35 Identities=20% Similarity=0.365 Sum_probs=27.6
Q ss_pred CCCCceeccccccccCC--c--eecCCCChhhHHhHhcC
Q 023002 255 EDSLPFACFICRKPFVD--P--VVTKCKHYFCEHCALKV 289 (289)
Q Consensus 255 e~~~p~~C~IC~~~f~d--P--VvT~CGH~FC~~Ci~~v 289 (289)
....+|.|||+...|.. + .+-+|||.|++.++.++
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~ 147 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL 147 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh
Confidence 34579999999999943 2 34699999999998654
No 43
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.26 E-value=0.23 Score=47.49 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=27.5
Q ss_pred CceeccccccccCC----ceecCCCChhhHHhHhc
Q 023002 258 LPFACFICRKPFVD----PVVTKCKHYFCEHCALK 288 (289)
Q Consensus 258 ~p~~C~IC~~~f~d----PVvT~CGH~FC~~Ci~~ 288 (289)
..|.||||+..+.| .|+-+|||.||..|+.+
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEk 254 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEK 254 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHH
Confidence 57999999999988 46789999999999865
No 44
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.86 E-value=0.57 Score=46.12 Aligned_cols=15 Identities=20% Similarity=0.587 Sum_probs=9.7
Q ss_pred cccccCCCceeeeee
Q 023002 196 TGYCGYGDSCKFMHD 210 (289)
Q Consensus 196 TG~CGfGDsCKFlHd 210 (289)
-|-|-||.+|.++|.
T Consensus 101 ~~~~~~g~~~~~~~~ 115 (344)
T KOG1039|consen 101 HGQCRFGNGDVTLNG 115 (344)
T ss_pred ccccccCCccccccc
Confidence 466666677776663
No 45
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=85.53 E-value=0.48 Score=38.21 Aligned_cols=16 Identities=56% Similarity=0.972 Sum_probs=13.7
Q ss_pred eecCCCChhhHHhHhc
Q 023002 273 VVTKCKHYFCEHCALK 288 (289)
Q Consensus 273 VvT~CGH~FC~~Ci~~ 288 (289)
|.-.|+|.|=..||++
T Consensus 48 v~g~C~H~FH~hCI~k 63 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILK 63 (85)
T ss_pred eeccCccHHHHHHHHH
Confidence 5569999999999975
No 46
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=83.24 E-value=0.5 Score=46.56 Aligned_cols=32 Identities=25% Similarity=0.479 Sum_probs=26.5
Q ss_pred CCceeccccccccCCceecCC-CChhhHHhHhc
Q 023002 257 SLPFACFICRKPFVDPVVTKC-KHYFCEHCALK 288 (289)
Q Consensus 257 ~~p~~C~IC~~~f~dPVvT~C-GH~FC~~Ci~~ 288 (289)
...-.||||++.-.||.+..= |-.||..|+.+
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~ 330 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFS 330 (357)
T ss_pred CccccChhHHhccCCCceEEecceEEeHHHHHH
Confidence 344579999999999977655 99999999964
No 47
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=82.56 E-value=0.45 Score=44.83 Aligned_cols=29 Identities=31% Similarity=1.095 Sum_probs=24.0
Q ss_pred ecCCCcCCCcccccccC-CCceeeeeeccc
Q 023002 185 YQPDICKDYKETGYCGY-GDSCKFMHDRGD 213 (289)
Q Consensus 185 yqPDiCKDykeTG~CGf-GDsCKFlHdR~d 213 (289)
|.=..|..|.++|+|.| |++|+|-|-..-
T Consensus 130 ~kt~lc~~~~~~g~c~y~ge~crfah~~~e 159 (332)
T KOG1677|consen 130 YKTPLCRSFRKSGTCKYRGEQCRFAHGLEE 159 (332)
T ss_pred ccCCcceeeecCccccccCchhhhcCCccc
Confidence 44467999999999999 999999775544
No 48
>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=81.54 E-value=0.6 Score=36.30 Aligned_cols=27 Identities=33% Similarity=0.714 Sum_probs=23.3
Q ss_pred eccccccccCCce--ecCCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPV--VTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPV--vT~CGH~FC~~Ci~ 287 (289)
.|++|.+.+-+++ +.+|||.|-..|+.
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 5999999998765 47999999999975
No 49
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=81.27 E-value=0.33 Score=45.50 Aligned_cols=42 Identities=29% Similarity=0.642 Sum_probs=30.1
Q ss_pred CCCCCcCCceeeeeeeeeecCCCcCCCcccccccCC---------Cceeeeee
Q 023002 167 SHGPLRASAHIRVTARFDYQPDICKDYKETGYCGYG---------DSCKFMHD 210 (289)
Q Consensus 167 ~~GPirap~niR~t~~~DyqPDiCKDykeTG~CGfG---------DsCKFlHd 210 (289)
+.|+-|...+-+.+..|+ -|||||.|-- |||++- ..|..+|+
T Consensus 11 LMG~~Rn~~~~~~~~~f~-D~~VCk~~L~-g~CPhdLF~nTK~DLG~C~kiHd 61 (254)
T PF03194_consen 11 LMGSNRNGDPSKRKVHFT-DPDVCKYFLV-GFCPHDLFVNTKSDLGPCPKIHD 61 (254)
T ss_pred HcCCccCCCccccCCCCC-CcccCHHHHh-CCCcHHHHhhcccccchhhhhcC
Confidence 346666554434446674 4999999986 999985 57999997
No 50
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.08 E-value=0.88 Score=45.03 Aligned_cols=33 Identities=30% Similarity=0.553 Sum_probs=24.2
Q ss_pred CCCceeccccccccCCc----eecCCCChhhHHhHhc
Q 023002 256 DSLPFACFICRKPFVDP----VVTKCKHYFCEHCALK 288 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dP----VvT~CGH~FC~~Ci~~ 288 (289)
...+..|.||..-...+ .+..|+|.||..|+.+
T Consensus 143 ~~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~ 179 (384)
T KOG1812|consen 143 KLPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQ 179 (384)
T ss_pred ccccccCccCccccccHhhhHHHhcccchhhhHHhHH
Confidence 34577899999333222 3789999999999864
No 51
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.01 E-value=1.4 Score=44.07 Aligned_cols=31 Identities=26% Similarity=0.540 Sum_probs=27.1
Q ss_pred CCceeccccccccCC-ceecCCCChhhHHhHh
Q 023002 257 SLPFACFICRKPFVD-PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 257 ~~p~~C~IC~~~f~d-PVvT~CGH~FC~~Ci~ 287 (289)
.....|.||...+.. .+...|||.||..|..
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~ 99 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWT 99 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcHHHHHHHH
Confidence 456899999999996 7778999999999975
No 52
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=77.95 E-value=0.83 Score=34.25 Aligned_cols=27 Identities=26% Similarity=0.653 Sum_probs=24.4
Q ss_pred eeccccccccCCceecCCCChhhHHhH
Q 023002 260 FACFICRKPFVDPVVTKCKHYFCEHCA 286 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~FC~~Ci 286 (289)
..|..|...-...++.+|||..|..|.
T Consensus 8 ~~~~~~~~~~~~~~~~pCgH~I~~~~f 34 (55)
T PF14447_consen 8 QPCVFCGFVGTKGTVLPCGHLICDNCF 34 (55)
T ss_pred eeEEEccccccccccccccceeecccc
Confidence 468899999899999999999999886
No 53
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.89 E-value=1.4 Score=44.24 Aligned_cols=29 Identities=28% Similarity=0.697 Sum_probs=27.1
Q ss_pred eeccccccccCCceecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
..|.||-....=..+++|+|-.|-.|+++
T Consensus 62 ~~C~ICA~~~TYs~~~PC~H~~CH~Ca~R 90 (493)
T COG5236 62 MNCQICAGSTTYSARYPCGHQICHACAVR 90 (493)
T ss_pred ceeEEecCCceEEEeccCCchHHHHHHHH
Confidence 48999999999999999999999999875
No 54
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.16 E-value=1.7 Score=43.13 Aligned_cols=30 Identities=27% Similarity=0.486 Sum_probs=26.8
Q ss_pred CCCCCCceeccccccccCCceecCCCChhh
Q 023002 253 DDEDSLPFACFICRKPFVDPVVTKCKHYFC 282 (289)
Q Consensus 253 ~~e~~~p~~C~IC~~~f~dPVvT~CGH~FC 282 (289)
..+...|-.|.||...+.+-+..+|||.-|
T Consensus 299 ~~~~~~p~lcVVcl~e~~~~~fvpcGh~cc 328 (355)
T KOG1571|consen 299 FRELPQPDLCVVCLDEPKSAVFVPCGHVCC 328 (355)
T ss_pred ccccCCCCceEEecCCccceeeecCCcEEE
Confidence 345678999999999999999999999976
No 55
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.02 E-value=2.4 Score=42.01 Aligned_cols=33 Identities=36% Similarity=0.717 Sum_probs=28.6
Q ss_pred CCCCceeccccccccCCceecCCCCh-hhHHhHh
Q 023002 255 EDSLPFACFICRKPFVDPVVTKCKHY-FCEHCAL 287 (289)
Q Consensus 255 e~~~p~~C~IC~~~f~dPVvT~CGH~-FC~~Ci~ 287 (289)
+.+-.-.|-||+.-.+|-||++|-|. -|..|+.
T Consensus 286 ~~~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~ 319 (349)
T KOG4265|consen 286 ESESGKECVICLSESRDTVVLPCRHLCLCSGCAK 319 (349)
T ss_pred cccCCCeeEEEecCCcceEEecchhhehhHhHHH
Confidence 44557799999999999999999996 7888875
No 56
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=73.72 E-value=1.8 Score=30.59 Aligned_cols=27 Identities=33% Similarity=0.929 Sum_probs=21.5
Q ss_pred eccccccccC----CceecCCCChhhHHhHh
Q 023002 261 ACFICRKPFV----DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~----dPVvT~CGH~FC~~Ci~ 287 (289)
.|.+|...|. ..--..||+.||..|+.
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~ 34 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSS 34 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcC
Confidence 6888988773 44557899999999975
No 57
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.84 E-value=2.1 Score=42.38 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=24.8
Q ss_pred CceeccccccccCC---ceecCCCChhhHHhHh
Q 023002 258 LPFACFICRKPFVD---PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 258 ~p~~C~IC~~~f~d---PVvT~CGH~FC~~Ci~ 287 (289)
.++.|.||++.|.. -.+++|.|.|=-.||-
T Consensus 228 ~~~~CaIClEdY~~GdklRiLPC~H~FH~~CID 260 (348)
T KOG4628|consen 228 ATDTCAICLEDYEKGDKLRILPCSHKFHVNCID 260 (348)
T ss_pred CCceEEEeecccccCCeeeEecCCCchhhccch
Confidence 34899999999963 5679999999888873
No 58
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=72.67 E-value=1.6 Score=44.48 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=25.5
Q ss_pred eccccccccCCceecCCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci~ 287 (289)
.|-||-+.=+|--+-+|||..|..|+.
T Consensus 371 LCKICaendKdvkIEPCGHLlCt~CLa 397 (563)
T KOG1785|consen 371 LCKICAENDKDVKIEPCGHLLCTSCLA 397 (563)
T ss_pred HHHHhhccCCCcccccccchHHHHHHH
Confidence 599999999999999999999999984
No 59
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=71.38 E-value=1.1 Score=46.50 Aligned_cols=20 Identities=40% Similarity=1.071 Sum_probs=17.7
Q ss_pred ccccCCCceeeeeecccccc
Q 023002 197 GYCGYGDSCKFMHDRGDYKS 216 (289)
Q Consensus 197 G~CGfGDsCKFlHdR~dyk~ 216 (289)
--|.|||.|+|.||-+-|++
T Consensus 88 ~~C~f~d~Crf~HDi~ayLa 107 (614)
T KOG2333|consen 88 SKCSFGDNCRFVHDIEAYLA 107 (614)
T ss_pred ccCcccccccccccHHHHHh
Confidence 37999999999999988865
No 60
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=68.70 E-value=1.4 Score=49.84 Aligned_cols=31 Identities=29% Similarity=0.523 Sum_probs=28.0
Q ss_pred CCceeccccccccC-CceecCCCChhhHHhHh
Q 023002 257 SLPFACFICRKPFV-DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 257 ~~p~~C~IC~~~f~-dPVvT~CGH~FC~~Ci~ 287 (289)
..++.|.||++..+ -=.++.|||.+|-.|..
T Consensus 1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~ 1182 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDE 1182 (1394)
T ss_pred hcccchHHHHHHHHhcCCeeeechhHhhhHHH
Confidence 45889999999998 78899999999999975
No 61
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.13 E-value=2.7 Score=41.49 Aligned_cols=32 Identities=31% Similarity=0.579 Sum_probs=26.4
Q ss_pred CCceeccccccccC---CceecCCCChhhHHhHhc
Q 023002 257 SLPFACFICRKPFV---DPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 257 ~~p~~C~IC~~~f~---dPVvT~CGH~FC~~Ci~~ 288 (289)
..-..|.||+..|. .-++++|.|.|=..|+.+
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~k 355 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDK 355 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHH
Confidence 34578999999993 368899999999999853
No 62
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=64.69 E-value=1.7 Score=42.49 Aligned_cols=29 Identities=41% Similarity=0.851 Sum_probs=22.8
Q ss_pred eeecCCCcCCCcccccccCCCceeeeeecc
Q 023002 183 FDYQPDICKDYKETGYCGYGDSCKFMHDRG 212 (289)
Q Consensus 183 ~DyqPDiCKDykeTG~CGfGDsCKFlHdR~ 212 (289)
+|=.--+|--|++ |.|+=|+-|||+||-.
T Consensus 88 vDPKSvvCafFk~-g~C~KG~kCKFsHdl~ 116 (343)
T KOG1763|consen 88 VDPKSVVCAFFKQ-GTCTKGDKCKFSHDLA 116 (343)
T ss_pred CCchHHHHHHHhc-cCCCCCCcccccchHH
Confidence 4444457887887 9999999999999843
No 63
>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=63.84 E-value=3.3 Score=25.68 Aligned_cols=14 Identities=36% Similarity=0.940 Sum_probs=12.1
Q ss_pred CceeccccccccCC
Q 023002 258 LPFACFICRKPFVD 271 (289)
Q Consensus 258 ~p~~C~IC~~~f~d 271 (289)
.||.|++|...|.+
T Consensus 13 k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 13 KPYKCPYCGKSFSN 26 (26)
T ss_dssp SSEEESSSSEEESS
T ss_pred CCCCCCCCcCeeCc
Confidence 68999999998863
No 64
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=62.14 E-value=2.9 Score=42.59 Aligned_cols=23 Identities=39% Similarity=0.999 Sum_probs=19.7
Q ss_pred CCcCCCcccccccCCCceeeeeec
Q 023002 188 DICKDYKETGYCGYGDSCKFMHDR 211 (289)
Q Consensus 188 DiCKDykeTG~CGfGDsCKFlHdR 211 (289)
-+|+-|-+ |-|.||.+|.|.|--
T Consensus 141 kpC~ffLe-g~CRF~enCRfSHG~ 163 (486)
T KOG2185|consen 141 KPCKFFLE-GRCRFGENCRFSHGL 163 (486)
T ss_pred ccchHhhc-cccccCcccccccCc
Confidence 35988887 899999999999954
No 65
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=59.02 E-value=4.4 Score=41.60 Aligned_cols=32 Identities=28% Similarity=0.676 Sum_probs=25.4
Q ss_pred CCCceeccccccccCCce----ecCCCChhhHHhHhc
Q 023002 256 DSLPFACFICRKPFVDPV----VTKCKHYFCEHCALK 288 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dPV----vT~CGH~FC~~Ci~~ 288 (289)
-++| +||||++-+-..| .+.|-|.|=-.|+.+
T Consensus 173 tELP-TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~ 208 (493)
T KOG0804|consen 173 TELP-TCPVCLERMDSSTTGILTILCNHSFHCSCLMK 208 (493)
T ss_pred ccCC-CcchhHhhcCccccceeeeecccccchHHHhh
Confidence 3577 9999999996654 579999998888753
No 67
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=58.80 E-value=2.1 Score=31.52 Aligned_cols=28 Identities=29% Similarity=0.698 Sum_probs=14.6
Q ss_pred eeccccccccCC----ceecCCCChhhHHhHh
Q 023002 260 FACFICRKPFVD----PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~d----PVvT~CGH~FC~~Ci~ 287 (289)
-.|.+|...|.- -.=-.||+.||..|..
T Consensus 10 ~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp SB-TTT--B-BSSS-EEE-TTT--EEECCCS-
T ss_pred CcCcCcCCcCCCceeeEccCCCCCEECCchhC
Confidence 389999999921 1125799999999864
No 68
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.60 E-value=3.4 Score=40.50 Aligned_cols=27 Identities=33% Similarity=0.710 Sum_probs=22.8
Q ss_pred ceeccccccccCCceecCCCChh-hHHh
Q 023002 259 PFACFICRKPFVDPVVTKCKHYF-CEHC 285 (289)
Q Consensus 259 p~~C~IC~~~f~dPVvT~CGH~F-C~~C 285 (289)
..+|.||++.++|=|.+.|||.. |-.|
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~C 327 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKC 327 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhh
Confidence 67999999999999999999963 4444
No 69
>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=52.73 E-value=6.6 Score=32.09 Aligned_cols=23 Identities=35% Similarity=0.915 Sum_probs=19.4
Q ss_pred eccccccccCCceecCCCChhhHHhHhc
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
.|.||......| ||.||..|+.+
T Consensus 46 ~C~~CK~~v~q~-----g~~YCq~CAYk 68 (90)
T PF10235_consen 46 KCKICKTKVHQP-----GAKYCQTCAYK 68 (90)
T ss_pred cccccccccccC-----CCccChhhhcc
Confidence 699999877665 89999999864
No 70
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.41 E-value=1.2 Score=45.05 Aligned_cols=32 Identities=34% Similarity=0.582 Sum_probs=25.1
Q ss_pred CCCceeccccccccCC------ceecCCCChhhHHhHh
Q 023002 256 DSLPFACFICRKPFVD------PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~d------PVvT~CGH~FC~~Ci~ 287 (289)
+.-.-.||-|.-+... =+-|.||||||+-|..
T Consensus 365 ~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~ 402 (445)
T KOG1814|consen 365 ESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAE 402 (445)
T ss_pred HhcCCCCCcccceeecCCCccceeeccccccceeehhh
Confidence 3456689999988743 3569999999999975
No 71
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=51.40 E-value=5.6 Score=38.08 Aligned_cols=32 Identities=28% Similarity=0.574 Sum_probs=26.4
Q ss_pred CCCceeccccccccCCcee-cCCCChhhHHhHh
Q 023002 256 DSLPFACFICRKPFVDPVV-TKCKHYFCEHCAL 287 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dPVv-T~CGH~FC~~Ci~ 287 (289)
+.+.+.|||-..++.+||+ ++|||.|-..=+.
T Consensus 173 e~fs~rdPis~~~I~nPviSkkC~HvydrDsI~ 205 (262)
T KOG2979|consen 173 EVFSNRDPISKKPIVNPVISKKCGHVYDRDSIM 205 (262)
T ss_pred hhhcccCchhhhhhhchhhhcCcCcchhhhhHH
Confidence 3567899999999999998 6999999765443
No 72
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=51.13 E-value=6.4 Score=39.03 Aligned_cols=28 Identities=36% Similarity=0.717 Sum_probs=20.2
Q ss_pred eeccccccccC-CceecCCCChhhHHhHh
Q 023002 260 FACFICRKPFV-DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~-dPVvT~CGH~FC~~Ci~ 287 (289)
.-|--|..+.. -=-+..|.|.||..|+.
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr 119 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECAR 119 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhh
Confidence 45777766442 23358999999999986
No 73
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=48.74 E-value=3.7 Score=40.31 Aligned_cols=41 Identities=34% Similarity=0.758 Sum_probs=29.0
Q ss_pred CCCCcCCceeeeeeeeeecCCCcCCCcccccccCC---------Cceeeeee
Q 023002 168 HGPLRASAHIRVTARFDYQPDICKDYKETGYCGYG---------DSCKFMHD 210 (289)
Q Consensus 168 ~GPirap~niR~t~~~DyqPDiCKDykeTG~CGfG---------DsCKFlHd 210 (289)
.||-|..--=|..+.||= ||||+.|-. |||++- ..|--.|+
T Consensus 13 MGs~r~~~~~~~~v~~~D-~~VC~~fLv-g~CPHDlF~nTk~dlg~C~kvHd 62 (319)
T KOG0796|consen 13 MGSNRDGDETRQRVKFDD-PDVCKSFLV-GFCPHDLFQNTKMDLGPCPKVHD 62 (319)
T ss_pred hCCCcCCCcccCCCCCCc-hhHHHHHHh-CCCcHHHhhhhhcccCcccchhh
Confidence 455554433233456776 999999987 999974 77888887
No 74
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.54 E-value=8.7 Score=40.18 Aligned_cols=30 Identities=33% Similarity=0.818 Sum_probs=22.6
Q ss_pred ceecccccccc-----------------CCceecCCCChhhHHhHhc
Q 023002 259 PFACFICRKPF-----------------VDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 259 p~~C~IC~~~f-----------------~dPVvT~CGH~FC~~Ci~~ 288 (289)
--.|.||+.+. +|=++|+|-|.|=..|+++
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~ 617 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQ 617 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHH
Confidence 34699998765 2456789999999999864
No 75
>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=45.39 E-value=7.6 Score=22.58 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=11.8
Q ss_pred eeccccccccCCce
Q 023002 260 FACFICRKPFVDPV 273 (289)
Q Consensus 260 ~~C~IC~~~f~dPV 273 (289)
|.|++|...|.++.
T Consensus 1 y~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 1 YKCPICGKSFSSKS 14 (23)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCCCCCccCCHH
Confidence 68999999998764
No 76
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.30 E-value=9.4 Score=37.91 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=22.8
Q ss_pred ceecccccccc-----CCceecCCCChhhHHhHh
Q 023002 259 PFACFICRKPF-----VDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 259 p~~C~IC~~~f-----~dPVvT~CGH~FC~~Ci~ 287 (289)
-..|++|+-.. -+.++=.|||-||+.|..
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~ 339 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGG 339 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCc
Confidence 35699998776 367776799999999973
No 77
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=43.93 E-value=9.2 Score=37.78 Aligned_cols=29 Identities=38% Similarity=0.801 Sum_probs=24.4
Q ss_pred eeccccccccCC-c--eecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFVD-P--VVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~d-P--VvT~CGH~FC~~Ci~~ 288 (289)
-.|.||+.-|.+ | ++|.|-|||=..|+.+
T Consensus 116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaR 147 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACDHYMHFACLAR 147 (368)
T ss_pred CceEEEEEeecCCCceeeehhHHHHHHHHHHH
Confidence 479999999965 3 6899999999999853
No 78
>PHA03096 p28-like protein; Provisional
Probab=43.29 E-value=12 Score=35.91 Aligned_cols=28 Identities=25% Similarity=0.414 Sum_probs=23.1
Q ss_pred eeccccccccC--------CceecCCCChhhHHhHh
Q 023002 260 FACFICRKPFV--------DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~--------dPVvT~CGH~FC~~Ci~ 287 (289)
..|.||++.-. .-++..|-|.||..|+.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~ 214 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIK 214 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHH
Confidence 57999998763 35668999999999985
No 79
>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=42.76 E-value=10 Score=22.85 Aligned_cols=13 Identities=46% Similarity=1.004 Sum_probs=11.4
Q ss_pred ceeccccccccCC
Q 023002 259 PFACFICRKPFVD 271 (289)
Q Consensus 259 p~~C~IC~~~f~d 271 (289)
||.|.+|...|.+
T Consensus 1 ~~~C~~C~~~F~~ 13 (27)
T PF13912_consen 1 PFECDECGKTFSS 13 (27)
T ss_dssp SEEETTTTEEESS
T ss_pred CCCCCccCCccCC
Confidence 6899999999965
No 80
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.26 E-value=13 Score=37.56 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=24.7
Q ss_pred CCceeccccccccCC---ceecCCCChhhHHhHh
Q 023002 257 SLPFACFICRKPFVD---PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 257 ~~p~~C~IC~~~f~d---PVvT~CGH~FC~~Ci~ 287 (289)
..-|.|||=++--.+ |+...|||..|..-+.
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAln 365 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALN 365 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHH
Confidence 346899998887753 9999999999886553
No 81
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.75 E-value=11 Score=36.73 Aligned_cols=27 Identities=30% Similarity=0.682 Sum_probs=23.2
Q ss_pred eccccccccCCce----------ecCCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPV----------VTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPV----------vT~CGH~FC~~Ci~ 287 (289)
.|.||.+.+-..| ...|+|.|=+.||.
T Consensus 226 vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIr 262 (328)
T KOG1734|consen 226 VCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIR 262 (328)
T ss_pred hhHhhcchheeecchhhhhhhheeeecccchHHHhhh
Confidence 7999999986655 57999999999984
No 82
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=40.99 E-value=13 Score=32.42 Aligned_cols=31 Identities=23% Similarity=0.510 Sum_probs=23.9
Q ss_pred CceeccccccccCC--ce-ecCCC------ChhhHHhHhc
Q 023002 258 LPFACFICRKPFVD--PV-VTKCK------HYFCEHCALK 288 (289)
Q Consensus 258 ~p~~C~IC~~~f~d--PV-vT~CG------H~FC~~Ci~~ 288 (289)
....|.||.+..-+ -| ...|| |.||..|+.+
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~r 64 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKR 64 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHH
Confidence 35789999999977 33 34565 8999999864
No 83
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=40.69 E-value=9.8 Score=31.41 Aligned_cols=28 Identities=39% Similarity=0.916 Sum_probs=19.7
Q ss_pred eeccccccccC-----CceecCCCChhhHHhHh
Q 023002 260 FACFICRKPFV-----DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~-----dPVvT~CGH~FC~~Ci~ 287 (289)
-.|.+|..+|. .-+-..|+|.+|..|-.
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred cchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 38999998873 23457899999999853
No 84
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.16 E-value=10 Score=37.18 Aligned_cols=32 Identities=31% Similarity=0.820 Sum_probs=26.9
Q ss_pred CCCceeccccccccCCceecCC----CChhhHHhHh
Q 023002 256 DSLPFACFICRKPFVDPVVTKC----KHYFCEHCAL 287 (289)
Q Consensus 256 ~~~p~~C~IC~~~f~dPVvT~C----GH~FC~~Ci~ 287 (289)
...|+.|.+|.+-+.|--.-.| .|-||-.|-.
T Consensus 265 ~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred CCCceeehhhhhhhccCceeecCCCcccceecccCH
Confidence 4568999999999998777777 7999999954
No 85
>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=39.12 E-value=11 Score=21.18 Aligned_cols=13 Identities=46% Similarity=0.961 Sum_probs=8.8
Q ss_pred eeccccccccCCc
Q 023002 260 FACFICRKPFVDP 272 (289)
Q Consensus 260 ~~C~IC~~~f~dP 272 (289)
|.|++|...|.+.
T Consensus 1 ~~C~~C~~~~~~~ 13 (24)
T PF13894_consen 1 FQCPICGKSFRSK 13 (24)
T ss_dssp EE-SSTS-EESSH
T ss_pred CCCcCCCCcCCcH
Confidence 6899999888764
No 86
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.13 E-value=13 Score=41.06 Aligned_cols=28 Identities=32% Similarity=0.923 Sum_probs=22.9
Q ss_pred ecccccccc-CCc-eecCCCChhhHHhHhc
Q 023002 261 ACFICRKPF-VDP-VVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f-~dP-VvT~CGH~FC~~Ci~~ 288 (289)
.|-+|..++ ..| ++-+|||.|=+.|+++
T Consensus 819 ~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~ 848 (911)
T KOG2034|consen 819 SCDHCGRPLLIKPFYVFPCGHCFHRDCLIR 848 (911)
T ss_pred chHHhcchhhcCcceeeeccchHHHHHHHH
Confidence 699999887 334 5679999999999975
No 87
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=37.65 E-value=12 Score=35.96 Aligned_cols=32 Identities=41% Similarity=0.783 Sum_probs=24.4
Q ss_pred CCCCceecccccccc----CCceecCCCChhhHHhH
Q 023002 255 EDSLPFACFICRKPF----VDPVVTKCKHYFCEHCA 286 (289)
Q Consensus 255 e~~~p~~C~IC~~~f----~dPVvT~CGH~FC~~Ci 286 (289)
|...++.||||.+.+ .+|.+.+|||+-=..|+
T Consensus 154 e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf 189 (276)
T KOG1940|consen 154 ERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCF 189 (276)
T ss_pred hhcccCCCchhHHHhccccccCCccCcccchHHHHH
Confidence 345677799999866 68999999998644444
No 88
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=37.56 E-value=17 Score=35.27 Aligned_cols=31 Identities=26% Similarity=0.641 Sum_probs=24.9
Q ss_pred CceeccccccccCCceec-CCCChhhHHhHhc
Q 023002 258 LPFACFICRKPFVDPVVT-KCKHYFCEHCALK 288 (289)
Q Consensus 258 ~p~~C~IC~~~f~dPVvT-~CGH~FC~~Ci~~ 288 (289)
.-+.||||...+.-|+.- .=||.-|..|-.+
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~ 78 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTK 78 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhh
Confidence 357899999999988753 3399999999743
No 89
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=36.92 E-value=15 Score=26.30 Aligned_cols=26 Identities=23% Similarity=0.652 Sum_probs=21.0
Q ss_pred eccccccccCCceecCCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci~ 287 (289)
.|.||.+...+ =+.-.|+..|..|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48999998887 556689999999954
No 90
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=36.87 E-value=11 Score=31.03 Aligned_cols=24 Identities=33% Similarity=0.849 Sum_probs=20.1
Q ss_pred eeccccccccCCceecCCCChhhHHhHhc
Q 023002 260 FACFICRKPFVDPVVTKCKHYFCEHCALK 288 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~CGH~FC~~Ci~~ 288 (289)
-.|.||......| |-++|..|+.+
T Consensus 55 ~kC~iCk~~vHQ~-----GshYC~tCAY~ 78 (100)
T KOG3476|consen 55 AKCRICKQLVHQP-----GSHYCQTCAYK 78 (100)
T ss_pred chhHHHHHHhcCC-----cchhHhHhhhh
Confidence 4699999998888 77889999864
No 91
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=36.74 E-value=21 Score=26.29 Aligned_cols=12 Identities=50% Similarity=1.231 Sum_probs=6.7
Q ss_pred cCCCChhhHHhH
Q 023002 275 TKCKHYFCEHCA 286 (289)
Q Consensus 275 T~CGH~FC~~Ci 286 (289)
..|+++||..|=
T Consensus 25 ~~C~~~FC~dCD 36 (51)
T PF07975_consen 25 PKCKNHFCIDCD 36 (51)
T ss_dssp TTTT--B-HHHH
T ss_pred CCCCCccccCcC
Confidence 467888998884
No 92
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=34.15 E-value=20 Score=36.48 Aligned_cols=27 Identities=30% Similarity=0.682 Sum_probs=21.8
Q ss_pred eccccccccC-------------CceecCCCChhhHHhHh
Q 023002 261 ACFICRKPFV-------------DPVVTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~-------------dPVvT~CGH~FC~~Ci~ 287 (289)
.|.||++.+. .|--.+|||.|=-.|+.
T Consensus 289 ~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLk 328 (491)
T COG5243 289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLK 328 (491)
T ss_pred eEEEecccccCCCCccCcccccCCcccccccceeeHHHHH
Confidence 8999999843 24678999999888873
No 93
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=32.95 E-value=25 Score=22.41 Aligned_cols=21 Identities=19% Similarity=0.474 Sum_probs=11.8
Q ss_pred eccccccccCCce--ecCCCChh
Q 023002 261 ACFICRKPFVDPV--VTKCKHYF 281 (289)
Q Consensus 261 ~C~IC~~~f~dPV--vT~CGH~F 281 (289)
.||-|......-. --.|||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 4666666552211 24588887
No 94
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.69 E-value=25 Score=24.09 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=6.4
Q ss_pred ceecccccccc
Q 023002 259 PFACFICRKPF 269 (289)
Q Consensus 259 p~~C~IC~~~f 269 (289)
||.|..|...|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 66666555555
No 95
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=32.22 E-value=24 Score=39.16 Aligned_cols=28 Identities=25% Similarity=0.752 Sum_probs=21.4
Q ss_pred eeccccccccCC---ce------ecCCCChhhHHhHh
Q 023002 260 FACFICRKPFVD---PV------VTKCKHYFCEHCAL 287 (289)
Q Consensus 260 ~~C~IC~~~f~d---PV------vT~CGH~FC~~Ci~ 287 (289)
-.|.+|...|.. ++ --.||+.||..|-.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSS 497 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCIT 497 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccC
Confidence 479999999942 12 24699999999963
No 96
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.26 E-value=14 Score=26.09 Aligned_cols=12 Identities=42% Similarity=1.101 Sum_probs=10.3
Q ss_pred CCCChhhHHhHh
Q 023002 276 KCKHYFCEHCAL 287 (289)
Q Consensus 276 ~CGH~FC~~Ci~ 287 (289)
.|||.||..|..
T Consensus 45 ~C~~~fC~~C~~ 56 (64)
T smart00647 45 KCGFSFCFRCKV 56 (64)
T ss_pred CCCCeECCCCCC
Confidence 789999999864
No 97
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=31.25 E-value=15 Score=36.03 Aligned_cols=41 Identities=32% Similarity=0.750 Sum_probs=26.4
Q ss_pred CCCCCcCCceeeeeeeeeecCCCcCCCcccccccCCCceeeeee
Q 023002 167 SHGPLRASAHIRVTARFDYQPDICKDYKETGYCGYGDSCKFMHD 210 (289)
Q Consensus 167 ~~GPirap~niR~t~~~DyqPDiCKDykeTG~CGfGDsCKFlHd 210 (289)
..|||---.+++.. .-++ -.|||.|-. |-|--||.|=|||.
T Consensus 59 ~~~~~~~~~~~~~~-~~~~-~~vcK~~l~-glC~kgD~C~Flhe 99 (325)
T KOG1040|consen 59 ERGPICPKSHNDVS-DSRG-KVVCKHWLR-GLCKKGDQCEFLHE 99 (325)
T ss_pred cCCCCCccccCCcc-ccCC-ceeehhhhh-hhhhccCcCcchhh
Confidence 34554443444321 1233 577998887 89999999999995
No 98
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=31.21 E-value=36 Score=24.23 Aligned_cols=27 Identities=33% Similarity=0.810 Sum_probs=21.0
Q ss_pred ecccccc--ccCCceecCCC-----ChhhHHhHh
Q 023002 261 ACFICRK--PFVDPVVTKCK-----HYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~--~f~dPVvT~CG-----H~FC~~Ci~ 287 (289)
.|.||+. ...+|++.+|. |+|=..|+.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~ 34 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLE 34 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHH
Confidence 4899997 55789999995 777777764
No 99
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=30.60 E-value=22 Score=31.48 Aligned_cols=22 Identities=27% Similarity=0.614 Sum_probs=17.4
Q ss_pred ccccccccCCceecCCCChhhH
Q 023002 262 CFICRKPFVDPVVTKCKHYFCE 283 (289)
Q Consensus 262 C~IC~~~f~dPVvT~CGH~FC~ 283 (289)
=+||...-+.-+--.|||.||-
T Consensus 60 lfi~qs~~~rv~rcecghsf~d 81 (165)
T COG4647 60 LFICQSAQKRVIRCECGHSFGD 81 (165)
T ss_pred EEEEecccccEEEEeccccccC
Confidence 3688888877566789999995
No 100
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=30.07 E-value=10 Score=37.49 Aligned_cols=26 Identities=15% Similarity=0.349 Sum_probs=16.5
Q ss_pred CceeeeeecccccccchhhHHHHHHH
Q 023002 203 DSCKFMHDRGDYKSGWQMEKEWEEAE 228 (289)
Q Consensus 203 DsCKFlHdR~dyk~GWqld~ewe~~~ 228 (289)
|+|||||-=.+.|-+..|..|..-..
T Consensus 85 ~nCkylHpp~hlkdql~ingrn~l~l 110 (331)
T KOG2494|consen 85 ENCKYLHPPQHLKDQLKINGRNNLIL 110 (331)
T ss_pred ccceecCCChhhhhhhhhcccccHHH
Confidence 66888887777666666655544433
No 101
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.37 E-value=32 Score=38.14 Aligned_cols=27 Identities=30% Similarity=0.688 Sum_probs=25.0
Q ss_pred eccccccccCCceec-CCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPVVT-KCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT-~CGH~FC~~Ci~ 287 (289)
+|..|...+-=|+|- .|||.|=+.|+.
T Consensus 842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e 869 (933)
T KOG2114|consen 842 KCSACEGTLDLPFVHFLCGHSYHQHCLE 869 (933)
T ss_pred eecccCCccccceeeeecccHHHHHhhc
Confidence 799999999999995 999999999985
No 102
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=27.49 E-value=19 Score=34.81 Aligned_cols=29 Identities=17% Similarity=0.539 Sum_probs=21.4
Q ss_pred ceeccccccccCC-----ceecCCCChhhHHhHh
Q 023002 259 PFACFICRKPFVD-----PVVTKCKHYFCEHCAL 287 (289)
Q Consensus 259 p~~C~IC~~~f~d-----PVvT~CGH~FC~~Ci~ 287 (289)
--.|.+|...... --.-.||++||..|-.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~ 201 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSR 201 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhhhhhc
Confidence 3479999994322 2357899999999954
No 103
>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=27.44 E-value=10 Score=24.09 Aligned_cols=26 Identities=23% Similarity=0.554 Sum_probs=17.9
Q ss_pred eccccccccCCceecCCCChhhHHhH
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCA 286 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci 286 (289)
.|+.|...+.+-.+-.-..+||..|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 68888888888888788888888885
No 104
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.32 E-value=29 Score=29.44 Aligned_cols=27 Identities=41% Similarity=1.065 Sum_probs=21.1
Q ss_pred eccccccccCCce--------------ecCCCChhhHHhHh
Q 023002 261 ACFICRKPFVDPV--------------VTKCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~IC~~~f~dPV--------------vT~CGH~FC~~Ci~ 287 (289)
.|.-|+..|..+. -..|.+.||..|-+
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 5999999887652 47899999988843
No 105
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=27.20 E-value=50 Score=36.72 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=19.8
Q ss_pred eccccccccCCc-------eecCCCChhhHHhHhc
Q 023002 261 ACFICRKPFVDP-------VVTKCKHYFCEHCALK 288 (289)
Q Consensus 261 ~C~IC~~~f~dP-------VvT~CGH~FC~~Ci~~ 288 (289)
.|.||..-|.+| .+..|+|.||..||+.
T Consensus 98 Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s 132 (1134)
T KOG0825|consen 98 TSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKS 132 (1134)
T ss_pred ccchhheecCCcccccCcCchhhhhhhhhhHHHHH
Confidence 466665555553 3467999999999974
No 106
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=27.16 E-value=26 Score=33.67 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=24.8
Q ss_pred eeee--cCCCcCCCcccccccCCCceeeeeecc
Q 023002 182 RFDY--QPDICKDYKETGYCGYGDSCKFMHDRG 212 (289)
Q Consensus 182 ~~Dy--qPDiCKDykeTG~CGfGDsCKFlHdR~ 212 (289)
.+.| .--||-.|..-|||-.|-|||-.|+-.
T Consensus 281 hihysenapicfefakygfcelgtscknqhilq 313 (377)
T KOG1492|consen 281 HIHYSENAPICFEFAKYGFCELGTSCKNQHILQ 313 (377)
T ss_pred EEeecCCCceeeeehhcceeccccccccceeee
Confidence 3444 245899999999999999999999753
No 107
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.45 E-value=24 Score=20.85 Aligned_cols=15 Identities=40% Similarity=0.755 Sum_probs=12.1
Q ss_pred eeccccccccCCcee
Q 023002 260 FACFICRKPFVDPVV 274 (289)
Q Consensus 260 ~~C~IC~~~f~dPVv 274 (289)
|.|.||...|.++..
T Consensus 1 ~~C~~C~~~f~s~~~ 15 (25)
T PF12874_consen 1 FYCDICNKSFSSENS 15 (25)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCCcCCHHH
Confidence 679999999987643
No 108
>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=25.78 E-value=36 Score=23.58 Aligned_cols=31 Identities=32% Similarity=0.601 Sum_probs=24.7
Q ss_pred CceeccccccccCCc-eecCCCChhhHHhHhc
Q 023002 258 LPFACFICRKPFVDP-VVTKCKHYFCEHCALK 288 (289)
Q Consensus 258 ~p~~C~IC~~~f~dP-VvT~CGH~FC~~Ci~~ 288 (289)
.=|.|.+|...+.+. ....=|..+|..|..+
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 368999999999765 5666678999998754
No 109
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.05 E-value=29 Score=31.80 Aligned_cols=25 Identities=24% Similarity=0.733 Sum_probs=22.4
Q ss_pred ccccccccCCceecCCCCh-hhHHhH
Q 023002 262 CFICRKPFVDPVVTKCKHY-FCEHCA 286 (289)
Q Consensus 262 C~IC~~~f~dPVvT~CGH~-FC~~Ci 286 (289)
|.+|+..-..-++.+|-|+ +|..|-
T Consensus 161 Cr~C~~~~~~VlllPCrHl~lC~~C~ 186 (207)
T KOG1100|consen 161 CRKCGEREATVLLLPCRHLCLCGICD 186 (207)
T ss_pred ceecCcCCceEEeecccceEeccccc
Confidence 9999999999899999985 788886
No 110
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=23.72 E-value=38 Score=33.60 Aligned_cols=23 Identities=39% Similarity=1.080 Sum_probs=20.1
Q ss_pred CCcCCCcccccccCCCceeeeee
Q 023002 188 DICKDYKETGYCGYGDSCKFMHD 210 (289)
Q Consensus 188 DiCKDykeTG~CGfGDsCKFlHd 210 (289)
.-|+..-..|||+||--|-|-|-
T Consensus 275 ePcinwe~sGyc~yg~Rc~F~hg 297 (351)
T COG5063 275 EPCINWEKSGYCPYGLRCCFKHG 297 (351)
T ss_pred CCccchhhcccCccccccccccC
Confidence 44889988999999999999883
No 111
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=23.44 E-value=39 Score=21.31 Aligned_cols=15 Identities=33% Similarity=0.859 Sum_probs=12.7
Q ss_pred ceeccccccccCCce
Q 023002 259 PFACFICRKPFVDPV 273 (289)
Q Consensus 259 p~~C~IC~~~f~dPV 273 (289)
+|.|.+|...|.++.
T Consensus 3 ~~~C~~C~~~~~~~~ 17 (35)
T smart00451 3 GFYCKLCNVTFTDEI 17 (35)
T ss_pred CeEccccCCccCCHH
Confidence 689999999998654
No 112
>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=23.26 E-value=17 Score=28.49 Aligned_cols=13 Identities=54% Similarity=1.546 Sum_probs=6.8
Q ss_pred eecCCC--ChhhHHh
Q 023002 273 VVTKCK--HYFCEHC 285 (289)
Q Consensus 273 VvT~CG--H~FC~~C 285 (289)
|+-.|| -|||..|
T Consensus 42 ~LkACGAvdYFC~~c 56 (70)
T PF07191_consen 42 VLKACGAVDYFCNHC 56 (70)
T ss_dssp EEEETTEEEEE-TTT
T ss_pred HHHHhcccceeeccC
Confidence 445666 5666655
No 113
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=22.96 E-value=26 Score=24.49 Aligned_cols=26 Identities=19% Similarity=0.430 Sum_probs=13.4
Q ss_pred eeccccccccCCceecC---CCChhhHHh
Q 023002 260 FACFICRKPFVDPVVTK---CKHYFCEHC 285 (289)
Q Consensus 260 ~~C~IC~~~f~dPVvT~---CGH~FC~~C 285 (289)
-.||+|...=+--|.+. =||++|..|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCC
Confidence 35888876543333332 499999888
No 114
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=22.41 E-value=22 Score=24.97 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=14.8
Q ss_pred eccc--cccccC-----Cc--eec-CCCChhhHHhHh
Q 023002 261 ACFI--CRKPFV-----DP--VVT-KCKHYFCEHCAL 287 (289)
Q Consensus 261 ~C~I--C~~~f~-----dP--VvT-~CGH~FC~~Ci~ 287 (289)
-||- |...+. +. |.= .|||.||..|-.
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 56 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGE 56 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCc
Confidence 6776 777663 12 333 499999999864
No 115
>cd04707 otoconin_90 otoconin_90: Phospholipase A2-like domains present in otoconin-90 and otoconin-95, mammal proteins that are principal matrix proteins of calcitic otoconia. Interactions involving otoconin-90 may trigger or constitute key events in otoconia formation. The PLA2-like domains in otoconins may have lost their metal-binding sites.
Probab=21.84 E-value=21 Score=30.21 Aligned_cols=20 Identities=40% Similarity=0.963 Sum_probs=14.7
Q ss_pred Ccccc-cccCC---------Cceeeeeecc
Q 023002 193 YKETG-YCGYG---------DSCKFMHDRG 212 (289)
Q Consensus 193 ykeTG-~CGfG---------DsCKFlHdR~ 212 (289)
|..=| |||+| |.|-|.||.=
T Consensus 17 Y~~YGCyCG~GG~G~PvD~~DrCC~~HD~C 46 (117)
T cd04707 17 FEDYGCYCGQEGEGLPVDELDRCCFQHRCC 46 (117)
T ss_pred HcccCCcccCCCCCCCcccchhHHHHhHHH
Confidence 33447 99999 5788888764
No 116
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.80 E-value=62 Score=33.32 Aligned_cols=50 Identities=24% Similarity=0.526 Sum_probs=32.7
Q ss_pred cccCCCCCCCCCcCCceeee-eeeeeecCCCcCCCcccccccCCCceeeeeeccc
Q 023002 160 SSEKAGGSHGPLRASAHIRV-TARFDYQPDICKDYKETGYCGYGDSCKFMHDRGD 213 (289)
Q Consensus 160 ~~~~~~~~~GPirap~niR~-t~~~DyqPDiCKDykeTG~CGfGDsCKFlHdR~d 213 (289)
.+..+.|+.||--.- .||. ...|-+.++.|- |.. +|.||.-|||+|--..
T Consensus 144 pPDdplgr~GPsl~~-fL~k~p~~~aq~~q~Cp-ygk--kctyg~kck~~h~~~~ 194 (443)
T KOG3777|consen 144 PPDDPLGREGPSLDN-FLSKKPLLWAQNKQPCP-YGK--KCTYGGKCKFYHPEIA 194 (443)
T ss_pred CCCCcccccCcchhh-hhhhccchhhhcccCCC-ccc--ccCCCCceeecccccc
Confidence 345567788974432 2343 346777788784 322 8999999999996433
No 117
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=21.36 E-value=43 Score=23.98 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=15.7
Q ss_pred ceeccccccccCCcee-cCCCChhh
Q 023002 259 PFACFICRKPFVDPVV-TKCKHYFC 282 (289)
Q Consensus 259 p~~C~IC~~~f~dPVv-T~CGH~FC 282 (289)
.+.|||....+..||- ..|.|.-|
T Consensus 2 sL~CPls~~~i~~P~Rg~~C~H~~C 26 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRGKNCKHLQC 26 (50)
T ss_dssp ESB-TTTSSB-SSEEEETT--SS--
T ss_pred eeeCCCCCCEEEeCccCCcCcccce
Confidence 4789999999999998 48999876
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.92 E-value=39 Score=22.70 Aligned_cols=11 Identities=27% Similarity=0.630 Sum_probs=5.0
Q ss_pred ceecccccccc
Q 023002 259 PFACFICRKPF 269 (289)
Q Consensus 259 p~~C~IC~~~f 269 (289)
.+.|+-|...|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 44454444443
No 119
>cd00125 PLA2c PLA2c: Phospholipase A2, a family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in
Probab=20.52 E-value=16 Score=30.71 Aligned_cols=20 Identities=55% Similarity=1.172 Sum_probs=13.5
Q ss_pred CCcccc-cccCC---------Cceeeeeec
Q 023002 192 DYKETG-YCGYG---------DSCKFMHDR 211 (289)
Q Consensus 192 DykeTG-~CGfG---------DsCKFlHdR 211 (289)
+|..-| |||+| |.|-|.||.
T Consensus 19 ~Y~~YGCyCG~GG~G~PvD~~DrCC~~HD~ 48 (115)
T cd00125 19 DYNGYGCYCGLGGSGTPVDDTDRCCQVHDC 48 (115)
T ss_pred HHhhcCCccCCCCCCCCcccHHHHHHHHHh
Confidence 344458 99999 466666664
No 120
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=20.02 E-value=32 Score=32.25 Aligned_cols=26 Identities=23% Similarity=0.623 Sum_probs=23.6
Q ss_pred eccccccccCCceecCCCChhhHHhH
Q 023002 261 ACFICRKPFVDPVVTKCKHYFCEHCA 286 (289)
Q Consensus 261 ~C~IC~~~f~dPVvT~CGH~FC~~Ci 286 (289)
.|+.|......-++-..+-|||..|-
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEECcCCC
Confidence 59999999988888899999999994
Done!