Query psy3116
Match_columns 177
No_of_seqs 190 out of 752
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 16:50:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA02862 5L protein; Provision 99.9 3E-24 6.5E-29 170.2 4.2 89 38-132 2-93 (156)
2 PHA02825 LAP/PHD finger-like p 99.8 1.3E-21 2.8E-26 157.2 7.0 87 35-128 5-91 (162)
3 smart00744 RINGv The RING-vari 99.7 7.4E-19 1.6E-23 116.2 2.9 47 40-86 1-49 (49)
4 PF12906 RINGv: RING-variant d 99.7 6.4E-19 1.4E-23 115.6 0.9 45 41-85 1-47 (47)
5 COG5183 SSM4 Protein involved 99.6 6.3E-16 1.4E-20 148.2 7.5 60 35-94 9-70 (1175)
6 KOG3053|consensus 99.6 1.1E-15 2.3E-20 131.3 5.6 64 33-96 15-88 (293)
7 KOG1609|consensus 99.4 6E-14 1.3E-18 119.6 1.1 59 35-93 75-137 (323)
8 PF13639 zf-RING_2: Ring finge 97.4 5.9E-05 1.3E-09 47.7 0.8 41 39-86 1-44 (44)
9 PHA02929 N1R/p28-like protein; 96.9 0.0014 3.1E-08 56.2 4.5 55 35-96 171-233 (238)
10 PF12861 zf-Apc11: Anaphase-pr 96.8 0.0017 3.7E-08 47.7 4.0 52 37-92 20-84 (85)
11 PF11793 FANCL_C: FANCL C-term 96.5 0.00076 1.7E-08 47.3 0.6 52 38-92 2-68 (70)
12 cd00162 RING RING-finger (Real 96.1 0.0055 1.2E-07 36.9 2.6 43 40-88 1-44 (45)
13 PF13920 zf-C3HC4_3: Zinc fing 96.0 0.0028 6.2E-08 41.0 1.1 47 38-90 2-48 (50)
14 PLN03208 E3 ubiquitin-protein 95.9 0.0075 1.6E-07 50.5 3.4 52 35-91 15-80 (193)
15 smart00184 RING Ring finger. E 95.7 0.01 2.2E-07 34.3 2.5 39 41-85 1-39 (39)
16 KOG4628|consensus 95.5 0.018 4E-07 52.0 4.4 47 39-91 230-279 (348)
17 PF00097 zf-C3HC4: Zinc finger 95.2 0.014 3E-07 35.9 2.0 40 41-85 1-41 (41)
18 KOG0823|consensus 94.9 0.027 5.8E-07 48.3 3.6 53 35-92 44-97 (230)
19 smart00504 Ubox Modified RING 94.8 0.027 5.9E-07 37.3 2.6 45 40-91 3-47 (63)
20 COG5219 Uncharacterized conser 94.2 0.019 4.1E-07 58.0 1.0 53 36-91 1467-1524(1525)
21 COG5243 HRD1 HRD ubiquitin lig 94.2 0.067 1.5E-06 49.2 4.4 52 35-93 284-348 (491)
22 PHA02926 zinc finger-like prot 94.1 0.063 1.4E-06 46.2 4.0 57 35-96 167-236 (242)
23 KOG0802|consensus 93.8 0.04 8.8E-07 51.9 2.5 47 36-89 289-340 (543)
24 KOG1493|consensus 93.4 0.05 1.1E-06 39.6 1.7 49 40-92 22-83 (84)
25 KOG0317|consensus 92.8 0.11 2.4E-06 45.9 3.5 50 35-91 236-285 (293)
26 PF12678 zf-rbx1: RING-H2 zinc 92.7 0.067 1.5E-06 37.6 1.6 22 63-86 52-73 (73)
27 PF13923 zf-C3HC4_2: Zinc fing 92.3 0.074 1.6E-06 32.6 1.2 38 41-85 1-39 (39)
28 COG5540 RING-finger-containing 92.1 0.12 2.6E-06 46.4 2.7 50 35-90 320-372 (374)
29 KOG1785|consensus 90.1 0.11 2.4E-06 48.3 0.6 48 38-90 369-416 (563)
30 KOG0827|consensus 89.4 0.28 6E-06 45.4 2.6 46 38-86 4-52 (465)
31 PLN02189 cellulose synthase 87.6 0.44 9.6E-06 48.6 2.9 54 34-91 30-88 (1040)
32 PLN02436 cellulose synthase A 87.4 0.48 1E-05 48.5 3.0 54 34-91 32-90 (1094)
33 TIGR00599 rad18 DNA repair pro 87.1 0.46 9.9E-06 43.8 2.5 50 36-92 24-73 (397)
34 KOG4265|consensus 84.9 0.71 1.5E-05 41.9 2.6 47 34-90 286-336 (349)
35 COG5194 APC11 Component of SCF 84.4 1 2.3E-05 33.1 2.8 29 64-94 57-85 (88)
36 PF10272 Tmpp129: Putative tra 80.8 2.6 5.7E-05 38.4 4.6 56 34-92 267-353 (358)
37 KOG2930|consensus 80.8 1.8 4E-05 33.2 3.0 29 64-94 84-112 (114)
38 KOG1734|consensus 80.0 1.1 2.3E-05 39.9 1.7 58 36-96 222-287 (328)
39 PF14569 zf-UDP: Zinc-binding 79.9 1.7 3.6E-05 31.7 2.4 54 35-92 6-64 (80)
40 PF14570 zf-RING_4: RING/Ubox 77.3 1.7 3.6E-05 28.8 1.6 44 41-90 1-48 (48)
41 PLN02400 cellulose synthase 77.2 1.8 3.8E-05 44.6 2.5 54 34-91 32-90 (1085)
42 KOG1645|consensus 77.1 1.8 4E-05 40.3 2.4 49 37-89 3-55 (463)
43 PLN02195 cellulose synthase A 76.7 2.4 5.1E-05 43.3 3.3 52 35-90 3-59 (977)
44 PF05290 Baculo_IE-1: Baculovi 76.6 2 4.3E-05 34.3 2.2 56 37-94 79-136 (140)
45 PF14634 zf-RING_5: zinc-RING 76.1 2.3 5E-05 26.6 2.0 40 41-87 2-44 (44)
46 TIGR00570 cdk7 CDK-activating 75.6 2.3 5E-05 38.1 2.6 50 37-92 2-56 (309)
47 PF15227 zf-C3HC4_4: zinc fing 74.9 1 2.2E-05 28.4 0.1 40 41-85 1-42 (42)
48 PLN02915 cellulose synthase A 74.8 2.5 5.4E-05 43.4 2.9 60 28-91 5-69 (1044)
49 PLN02638 cellulose synthase A 74.8 3.3 7.1E-05 42.7 3.7 52 35-90 14-70 (1079)
50 KOG0828|consensus 73.0 2.6 5.7E-05 40.3 2.4 49 35-89 568-633 (636)
51 KOG1039|consensus 70.0 3.8 8.3E-05 37.2 2.7 63 28-95 151-226 (344)
52 PF08746 zf-RING-like: RING-li 66.4 3.1 6.8E-05 26.5 1.0 22 64-85 22-43 (43)
53 PF05883 Baculo_RING: Baculovi 66.3 2.6 5.6E-05 33.5 0.7 41 37-77 25-69 (134)
54 COG5432 RAD18 RING-finger-cont 64.4 3.8 8.2E-05 37.0 1.5 61 37-108 24-84 (391)
55 PF04564 U-box: U-box domain; 62.7 2.3 5E-05 29.5 -0.1 46 40-91 6-51 (73)
56 KOG0804|consensus 60.7 4.1 8.9E-05 38.4 1.1 46 35-89 172-221 (493)
57 KOG2164|consensus 59.8 7.6 0.00017 37.0 2.7 49 38-91 186-237 (513)
58 KOG2177|consensus 57.9 4.5 9.9E-05 32.2 0.8 45 35-86 10-54 (386)
59 KOG4445|consensus 55.2 6.4 0.00014 35.6 1.3 53 36-93 113-189 (368)
60 COG5175 MOT2 Transcriptional r 53.5 12 0.00026 34.6 2.7 61 27-92 4-66 (480)
61 PF10367 Vps39_2: Vacuolar sor 52.9 4.1 8.8E-05 29.2 -0.3 33 35-72 75-109 (109)
62 PF07800 DUF1644: Protein of u 46.3 27 0.00058 28.7 3.5 37 38-76 2-48 (162)
63 KOG4692|consensus 45.9 17 0.00036 33.8 2.5 48 35-92 419-469 (489)
64 PF13894 zf-C2H2_4: C2H2-type 43.0 11 0.00024 19.3 0.6 10 81-90 2-11 (24)
65 PF10571 UPF0547: Uncharacteri 42.5 12 0.00025 21.6 0.6 13 78-90 13-25 (26)
66 KOG0287|consensus 41.3 9.2 0.0002 35.2 0.1 48 38-92 23-70 (442)
67 KOG1100|consensus 41.0 16 0.00035 30.7 1.5 20 38-57 158-177 (207)
68 PF13445 zf-RING_UBOX: RING-ty 39.2 15 0.00033 23.4 0.8 38 41-83 1-43 (43)
69 KOG1002|consensus 37.0 22 0.00047 34.7 1.8 54 35-93 533-589 (791)
70 CHL00196 psbY photosystem II p 34.9 43 0.00093 20.9 2.3 20 125-144 5-24 (36)
71 PF15086 UPF0542: Uncharacteri 32.9 40 0.00087 24.3 2.2 20 126-145 27-46 (74)
72 KOG3899|consensus 32.0 39 0.00086 30.6 2.6 30 64-93 328-368 (381)
73 PF06750 DiS_P_DiS: Bacterial 31.6 89 0.0019 22.8 4.0 28 78-111 32-59 (92)
74 PRK13240 pbsY photosystem II p 31.0 57 0.0012 20.8 2.5 21 125-145 5-25 (40)
75 KOG0955|consensus 31.0 17 0.00038 37.5 0.2 40 30-71 211-252 (1051)
76 PF00096 zf-C2H2: Zinc finger, 30.6 20 0.00043 18.8 0.3 11 81-91 2-12 (23)
77 PF06298 PsbY: Photosystem II 29.8 57 0.0012 20.4 2.3 21 125-145 5-25 (36)
78 KOG2879|consensus 28.8 60 0.0013 29.0 3.1 55 31-90 232-287 (298)
79 KOG0956|consensus 28.8 31 0.00067 34.6 1.4 49 40-91 7-74 (900)
80 KOG0802|consensus 27.7 25 0.00054 33.3 0.6 47 36-93 477-523 (543)
81 KOG1952|consensus 27.3 65 0.0014 32.9 3.4 55 35-92 188-249 (950)
82 PF01440 Gemini_AL2: Geminivir 27.2 9.5 0.00021 30.3 -1.9 33 50-85 31-63 (134)
83 COG5236 Uncharacterized conser 26.9 76 0.0016 29.5 3.5 49 35-91 58-109 (493)
84 PF13764 E3_UbLigase_R4: E3 ub 26.7 49 0.0011 33.3 2.5 22 27-48 457-478 (802)
85 KOG0825|consensus 26.3 15 0.00032 37.3 -1.1 29 63-93 146-174 (1134)
86 smart00249 PHD PHD zinc finger 23.6 20 0.00043 21.1 -0.6 29 40-71 1-30 (47)
87 PF04423 Rad50_zn_hook: Rad50 23.5 75 0.0016 20.6 2.2 25 69-93 8-34 (54)
88 PF01363 FYVE: FYVE zinc finge 23.3 17 0.00037 24.4 -1.0 21 72-92 2-22 (69)
89 PF02891 zf-MIZ: MIZ/SP-RING z 22.5 57 0.0012 21.2 1.4 35 51-88 11-50 (50)
90 PF07787 DUF1625: Protein of u 22.4 78 0.0017 26.7 2.6 17 126-142 231-247 (248)
91 smart00451 ZnF_U1 U1-like zinc 22.0 85 0.0018 17.8 2.0 13 78-90 2-14 (35)
92 PF12874 zf-met: Zinc-finger o 22.0 35 0.00076 18.1 0.3 11 81-91 2-12 (25)
93 PF13465 zf-H2C2_2: Zinc-finge 21.6 42 0.0009 18.7 0.5 13 78-90 13-25 (26)
94 PF05417 Peptidase_C41: Hepati 20.7 27 0.00059 28.1 -0.5 23 54-76 24-48 (161)
95 PF01708 Gemini_mov: Geminivir 20.5 51 0.0011 24.6 1.0 19 127-145 41-59 (91)
No 1
>PHA02862 5L protein; Provisional
Probab=99.89 E-value=3e-24 Score=170.22 Aligned_cols=89 Identities=19% Similarity=0.447 Sum_probs=77.6
Q ss_pred CCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeecCccccccchHHHh---hccCChH
Q psy3116 38 MTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPTQTKLKSLLSWV---KHVDNRE 114 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~~~y~~~~~l~~W~---~~~~~~~ 114 (177)
+++||||+++++ +.++||+|+||.+|||++||++|++.+++..||+|+++|.+..+.+ |+++|. +.+.+..
T Consensus 2 ~diCWIC~~~~~-e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~yK-----pf~kW~~~f~d~k~~l 75 (156)
T PHA02862 2 SDICWICNDVCD-ERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTYV-----SFKKWNWCFNDKKTTL 75 (156)
T ss_pred CCEEEEecCcCC-CCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEccc-----cHHHhhccCCCCCCch
Confidence 579999998873 3369999999999999999999999999999999999999988776 999996 5666778
Q ss_pred HHHHHhhhhhHHHHHHHH
Q psy3116 115 DMEEMLTDFAATFLFSPF 132 (177)
Q Consensus 115 ~~r~i~~d~l~~l~ltpi 132 (177)
+++-++++.++++++||-
T Consensus 76 ~ki~fI~~~v~fi~it~s 93 (156)
T PHA02862 76 SKIFFILFALVFIFLTIS 93 (156)
T ss_pred heeeeHhhhhhheeeecc
Confidence 888888888888777764
No 2
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.85 E-value=1.3e-21 Score=157.22 Aligned_cols=87 Identities=17% Similarity=0.447 Sum_probs=70.8
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeecCccccccchHHHhhccCChH
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPTQTKLKSLLSWVKHVDNRE 114 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~~~y~~~~~l~~W~~~~~~~~ 114 (177)
+..++.||||++++ +++.+||+|+||+++||++||++|++.++..+||+|+++|++.+..+ |+.+|...+....
T Consensus 5 s~~~~~CRIC~~~~-~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~k-----pl~~W~~~~~dc~ 78 (162)
T PHA02825 5 SLMDKCCWICKDEY-DVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNYK-----KCTKWRCSFRDCH 78 (162)
T ss_pred CCCCCeeEecCCCC-CCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEecC-----CCccccccCcchh
Confidence 56789999999887 35779999999999999999999999999999999999999998877 9999965544322
Q ss_pred HHHHHhhhhhHHHH
Q psy3116 115 DMEEMLTDFAATFL 128 (177)
Q Consensus 115 ~~r~i~~d~l~~l~ 128 (177)
.+.+..+.+++++
T Consensus 79 -~~~l~~~llcl~~ 91 (162)
T PHA02825 79 -DSAIVNSLLCLIV 91 (162)
T ss_pred -hHHHHHHHHHHHH
Confidence 3445555554433
No 3
>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=99.74 E-value=7.4e-19 Score=116.20 Aligned_cols=47 Identities=53% Similarity=1.251 Sum_probs=43.9
Q ss_pred eeEEcccCC--CCcccccccccCccccccHHHHHHHHHHcCCCccCCCC
Q psy3116 40 ICRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCK 86 (177)
Q Consensus 40 ~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~ 86 (177)
+||||++++ +++|++||+|+|+++|||++||++|+..+++.+||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 599999833 88999999999999999999999999999999999996
No 4
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.73 E-value=6.4e-19 Score=115.59 Aligned_cols=45 Identities=51% Similarity=1.305 Sum_probs=37.1
Q ss_pred eEEcccCC--CCcccccccccCccccccHHHHHHHHHHcCCCccCCC
Q psy3116 41 CRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 41 CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC 85 (177)
||||++++ +++|++||+|+||++|||++||++|+..++..+||+|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 89999887 5579999999999999999999999999999999998
No 5
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.62 E-value=6.3e-16 Score=148.19 Aligned_cols=60 Identities=40% Similarity=1.032 Sum_probs=55.6
Q ss_pred CCCCCeeEEcccCC--CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeec
Q psy3116 35 DEDMTICRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERL 94 (177)
Q Consensus 35 ~~~~~~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~ 94 (177)
+++...||||+.++ ++||-+||+|+||++|+|++||..|+..+++.+||+|+++|+++..
T Consensus 9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 34558999999887 9999999999999999999999999999999999999999998764
No 6
>KOG3053|consensus
Probab=99.59 E-value=1.1e-15 Score=131.27 Aligned_cols=64 Identities=25% Similarity=0.693 Sum_probs=55.3
Q ss_pred CCCCCCCeeEEcccCC-CC---cccccccccCccccccHHHHHHHHHHcC------CCccCCCCCeeEeeecCc
Q psy3116 33 SDDEDMTICRICYGAD-QQ---NLLSICQCKGSIAYVHIECIERWLQECG------VDKCDLCKYQFTTERLPT 96 (177)
Q Consensus 33 ~~~~~~~~CRIC~~~~-~~---~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~------~~~CelC~~~y~~~~~~~ 96 (177)
.+.+.++.||||+..+ ++ .+++||+|+||.+|||++||.+|++++. ...|..|+++|.+..++.
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l 88 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQL 88 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeecccc
Confidence 3457789999999777 33 4899999999999999999999998873 578999999999987765
No 7
>KOG1609|consensus
Probab=99.40 E-value=6e-14 Score=119.59 Aligned_cols=59 Identities=42% Similarity=0.887 Sum_probs=52.4
Q ss_pred CCCCCeeEEcccCC--CC--cccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeee
Q psy3116 35 DEDMTICRICYGAD--QQ--NLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTER 93 (177)
Q Consensus 35 ~~~~~~CRIC~~~~--~~--~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~ 93 (177)
+.+++.||||+++. .+ +++.||.|+|+.++||+.|+++|+..+++..||+|++.|....
T Consensus 75 ~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~ 137 (323)
T KOG1609|consen 75 PSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVG 137 (323)
T ss_pred CCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecc
Confidence 34468999999766 22 7999999999999999999999999999999999999998774
No 8
>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=97.37 E-value=5.9e-05 Score=47.70 Aligned_cols=41 Identities=27% Similarity=0.733 Sum_probs=29.4
Q ss_pred CeeEEcccCC-C--CcccccccccCccccccHHHHHHHHHHcCCCccCCCC
Q psy3116 39 TICRICYGAD-Q--QNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCK 86 (177)
Q Consensus 39 ~~CRIC~~~~-~--~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~ 86 (177)
+.|-||+++. . .....| |. ...|.+|+.+|++.+ ..|++|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~--C~---H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP--CG---HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET--TS---EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc--CC---CeeCHHHHHHHHHhC--CcCCccC
Confidence 4688998776 3 333445 53 689999999999886 4999995
No 9
>PHA02929 N1R/p28-like protein; Provisional
Probab=96.86 E-value=0.0014 Score=56.23 Aligned_cols=55 Identities=27% Similarity=0.625 Sum_probs=40.9
Q ss_pred CCCCCeeEEcccCC-CCc-------ccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeecCc
Q psy3116 35 DEDMTICRICYGAD-QQN-------LLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPT 96 (177)
Q Consensus 35 ~~~~~~CRIC~~~~-~~~-------Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~~~ 96 (177)
.+.+..|-||++.. +.+ .+.||. ...|..|+.+|+.. ...|++|+.++....+.+
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~~--~~tCPlCR~~~~~v~~~r 233 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCN-----HVFCIECIDIWKKE--KNTCPVCRTPFISVIKSR 233 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCC-----CcccHHHHHHHHhc--CCCCCCCCCEeeEEeeee
Confidence 35578999999864 221 345553 57999999999975 458999999998766554
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.81 E-value=0.0017 Score=47.74 Aligned_cols=52 Identities=23% Similarity=0.632 Sum_probs=37.0
Q ss_pred CCCeeEEcccCC------------CCcccccccccCccccccHHHHHHHHHHc-CCCccCCCCCeeEee
Q psy3116 37 DMTICRICYGAD------------QQNLLSICQCKGSIAYVHIECIERWLQEC-GVDKCDLCKYQFTTE 92 (177)
Q Consensus 37 ~~~~CRIC~~~~------------~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s-~~~~CelC~~~y~~~ 92 (177)
+++.|-||+... +-|++ =+.|. ...|..|+.+|+++. .+..|++|+.+|.+.
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv-~g~C~---H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLV-WGKCS---HNFHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCcee-eccCc---cHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 367788886543 11222 23454 469999999999874 568999999999864
No 11
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.55 E-value=0.00076 Score=47.34 Aligned_cols=52 Identities=19% Similarity=0.506 Sum_probs=25.6
Q ss_pred CCeeEEcccCC---CCccccc---ccccCccccccHHHHHHHHHHcC---------CCccCCCCCeeEee
Q psy3116 38 MTICRICYGAD---QQNLLSI---CQCKGSIAYVHIECIERWLQECG---------VDKCDLCKYQFTTE 92 (177)
Q Consensus 38 ~~~CRIC~~~~---~~~Li~P---C~C~Gs~~~VH~~CL~~Wi~~s~---------~~~CelC~~~y~~~ 92 (177)
+..|.||++.. ++....- ..|. +..|..||.+|+.... .-.|+.|+.+..++
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~---~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCG---KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT-------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccC---CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 45799998653 2222333 4676 6899999999997642 13599999998754
No 12
>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=96.12 E-value=0.0055 Score=36.87 Aligned_cols=43 Identities=30% Similarity=0.764 Sum_probs=31.5
Q ss_pred eeEEcccCC-CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCe
Q psy3116 40 ICRICYGAD-QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQ 88 (177)
Q Consensus 40 ~CRIC~~~~-~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~ 88 (177)
.|-||++.. ....+.||. ...|..|+.+|++. +...|++|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~-----H~~c~~C~~~~~~~-~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCG-----HVFCRSCIDKWLKS-GKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCC-----ChhcHHHHHHHHHh-CcCCCCCCCCc
Confidence 377888766 333445564 35899999999987 56779999875
No 13
>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=96.03 E-value=0.0028 Score=41.00 Aligned_cols=47 Identities=28% Similarity=0.594 Sum_probs=37.0
Q ss_pred CCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 38 MTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
...|.||++...+.++.||+= ..+-..|+.+|++ +...|++|+.++.
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH----~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGH----LCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCE----EEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeCCCC----hHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 457999998876788899863 2378899999999 7789999998764
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=95.93 E-value=0.0075 Score=50.46 Aligned_cols=52 Identities=21% Similarity=0.567 Sum_probs=40.7
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHc--------------CCCccCCCCCeeEe
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQEC--------------GVDKCDLCKYQFTT 91 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s--------------~~~~CelC~~~y~~ 91 (177)
..+.-.|-||++....+.+.||. ...+..||.+|+..+ +...|++|+..+..
T Consensus 15 ~~~~~~CpICld~~~dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCCccCCccCCCcCCCcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 45678999999877788888873 456789999998642 34689999998754
No 15
>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=95.68 E-value=0.01 Score=34.31 Aligned_cols=39 Identities=28% Similarity=0.818 Sum_probs=29.5
Q ss_pred eEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCC
Q psy3116 41 CRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 41 CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC 85 (177)
|.||++......+.||.- ..|..|+.+|++ .+...|++|
T Consensus 1 C~iC~~~~~~~~~~~C~H-----~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGH-----TFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCC-----hHHHHHHHHHHH-hCcCCCCCC
Confidence 678877765667778654 479999999998 455678876
No 16
>KOG4628|consensus
Probab=95.48 E-value=0.018 Score=51.99 Aligned_cols=47 Identities=30% Similarity=0.743 Sum_probs=37.2
Q ss_pred CeeEEcccCC--CCcc-cccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 39 TICRICYGAD--QQNL-LSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 39 ~~CRIC~~~~--~~~L-i~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
..|-||+|+. ++.| +-||+ ...|..|...||... ...|++||..-..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~-----H~FH~~CIDpWL~~~-r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCS-----HKFHVNCIDPWLTQT-RTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeEecCC-----CchhhccchhhHhhc-CccCCCCCCcCCC
Confidence 6999999988 3444 56875 468999999999887 5569999986443
No 17
>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=95.22 E-value=0.014 Score=35.85 Aligned_cols=40 Identities=33% Similarity=0.844 Sum_probs=32.3
Q ss_pred eEEcccCCCCcc-cccccccCccccccHHHHHHHHHHcCCCccCCC
Q psy3116 41 CRICYGADQQNL-LSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 41 CRIC~~~~~~~L-i~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC 85 (177)
|.||++....+. +.||. ..++..|+.+|++.++...|++|
T Consensus 1 C~iC~~~~~~~~~~~~C~-----H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCG-----HSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTS-----EEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCC-----CcchHHHHHHHHHhcCCccCCcC
Confidence 678887775555 78875 35888999999998888889988
No 18
>KOG0823|consensus
Probab=94.95 E-value=0.027 Score=48.29 Aligned_cols=53 Identities=23% Similarity=0.657 Sum_probs=41.8
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHc-CCCccCCCCCeeEee
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQEC-GVDKCDLCKYQFTTE 92 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s-~~~~CelC~~~y~~~ 92 (177)
+.+.-.|-||++...+|.+++|. ...==.||-+|+..+ ++..|++||.+...+
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCG-----HLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCG-----HLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCCceeeeeeccccCCCEEeecc-----cceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 34566899999988899999997 122238999999886 567789999987755
No 19
>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=94.77 E-value=0.027 Score=37.26 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=36.7
Q ss_pred eeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 40 ICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 40 ~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
.|.||.+.-.+|.+.||. ..+-+.|+.+|+.. ...|++|+..+..
T Consensus 3 ~Cpi~~~~~~~Pv~~~~G-----~v~~~~~i~~~~~~--~~~cP~~~~~~~~ 47 (63)
T smart00504 3 LCPISLEVMKDPVILPSG-----QTYERRAIEKWLLS--HGTDPVTGQPLTH 47 (63)
T ss_pred CCcCCCCcCCCCEECCCC-----CEEeHHHHHHHHHH--CCCCCCCcCCCCh
Confidence 688997766778888873 56889999999987 5689999988753
No 20
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.16 E-value=0.019 Score=57.96 Aligned_cols=53 Identities=28% Similarity=0.752 Sum_probs=40.1
Q ss_pred CCCCeeEEcccCC---CCccc-cccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 36 EDMTICRICYGAD---QQNLL-SICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 36 ~~~~~CRIC~~~~---~~~Li-~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
++...|-||+.-- +..|- .-|. |+ .-.|-.||-+|.++++..+|++|+.++++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCk---nKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCK---NKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhh---hhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 5678899998533 34443 2343 44 46999999999999999999999988753
No 21
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.15 E-value=0.067 Score=49.20 Aligned_cols=52 Identities=19% Similarity=0.616 Sum_probs=38.0
Q ss_pred CCCCCeeEEcccCC---C-C---------cccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeee
Q psy3116 35 DEDMTICRICYGAD---Q-Q---------NLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTER 93 (177)
Q Consensus 35 ~~~~~~CRIC~~~~---~-~---------~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~ 93 (177)
..+..+|-||.++- + + |=.-||. ...|..||+.|++.+ .+|++|+.+.....
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~ERq--QTCPICr~p~ifd~ 348 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLERQ--QTCPICRRPVIFDQ 348 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHHhc--cCCCcccCcccccc
Confidence 45678999999883 1 1 2344664 468999999999764 68999999855443
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=94.15 E-value=0.063 Score=46.17 Aligned_cols=57 Identities=26% Similarity=0.627 Sum_probs=41.9
Q ss_pred CCCCCeeEEcccCC-C--------CcccccccccCccccccHHHHHHHHHHc----CCCccCCCCCeeEeeecCc
Q psy3116 35 DEDMTICRICYGAD-Q--------QNLLSICQCKGSIAYVHIECIERWLQEC----GVDKCDLCKYQFTTERLPT 96 (177)
Q Consensus 35 ~~~~~~CRIC~~~~-~--------~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s----~~~~CelC~~~y~~~~~~~ 96 (177)
.+.+..|-||++.- + -.++.||. ......|+.+|.+.+ ....|++|+..|....+.+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSr 236 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSK 236 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCC-----chHHHHHHHHHHHhccccCcCCcCCCCcceeeeecccc
Confidence 34578999999763 1 13566765 346679999999864 2567999999999777665
No 23
>KOG0802|consensus
Probab=93.84 E-value=0.04 Score=51.90 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=37.2
Q ss_pred CCCCeeEEcccCC-CC----cccccccccCccccccHHHHHHHHHHcCCCccCCCCCee
Q psy3116 36 EDMTICRICYGAD-QQ----NLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQF 89 (177)
Q Consensus 36 ~~~~~CRIC~~~~-~~----~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y 89 (177)
.....|.||.|+. .. +-.-||. .-.|..||.+|++. ...|++|+..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er--~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFER--QQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHH--hCcCCcchhhh
Confidence 3478999999887 33 5566663 57999999999988 67899999943
No 24
>KOG1493|consensus
Probab=93.36 E-value=0.05 Score=39.64 Aligned_cols=49 Identities=24% Similarity=0.560 Sum_probs=35.6
Q ss_pred eeEEcccCC------------CCcccccccccCccccccHHHHHHHHHHc-CCCccCCCCCeeEee
Q psy3116 40 ICRICYGAD------------QQNLLSICQCKGSIAYVHIECIERWLQEC-GVDKCDLCKYQFTTE 92 (177)
Q Consensus 40 ~CRIC~~~~------------~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s-~~~~CelC~~~y~~~ 92 (177)
.|-||+... +-||+-- .|. .-.|..|+.+|+..+ ....|++|+.+|++.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C~---h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~ 83 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWG-YCL---HAFHAHCILKWLNTPTSQGQCPMCRQTWQFK 83 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHH-HHH---HHHHHHHHHHHhcCccccccCCcchheeEec
Confidence 777776543 3355433 443 468999999999876 467899999999864
No 25
>KOG0317|consensus
Probab=92.79 E-value=0.11 Score=45.89 Aligned_cols=50 Identities=24% Similarity=0.574 Sum_probs=39.9
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
.+....|-+|++.-.+|=-.||. ...=-.|+..|..++.. |++|+.+++-
T Consensus 236 ~~a~~kC~LCLe~~~~pSaTpCG-----HiFCWsCI~~w~~ek~e--CPlCR~~~~p 285 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPSATPCG-----HIFCWSCILEWCSEKAE--CPLCREKFQP 285 (293)
T ss_pred CCCCCceEEEecCCCCCCcCcCc-----chHHHHHHHHHHccccC--CCcccccCCC
Confidence 45568999999888888889997 12224899999988755 9999999873
No 26
>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=92.66 E-value=0.067 Score=37.59 Aligned_cols=22 Identities=36% Similarity=1.094 Sum_probs=17.9
Q ss_pred ccccHHHHHHHHHHcCCCccCCCC
Q psy3116 63 AYVHIECIERWLQECGVDKCDLCK 86 (177)
Q Consensus 63 ~~VH~~CL~~Wi~~s~~~~CelC~ 86 (177)
...|..||.+|++.+. .|++|+
T Consensus 52 H~FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 52 HIFHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp EEEEHHHHHHHHTTSS--B-TTSS
T ss_pred CCEEHHHHHHHHhcCC--cCCCCC
Confidence 4689999999997665 999996
No 27
>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=92.30 E-value=0.074 Score=32.63 Aligned_cols=38 Identities=32% Similarity=0.802 Sum_probs=27.4
Q ss_pred eEEcccCCCCc-ccccccccCccccccHHHHHHHHHHcCCCccCCC
Q psy3116 41 CRICYGADQQN-LLSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 41 CRIC~~~~~~~-Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC 85 (177)
|-||++...++ .+.||. .....+|+++|++. ..+|++|
T Consensus 1 C~iC~~~~~~~~~~~~CG-----H~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCG-----HSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTS-----EEEEHHHHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCC-----CchhHHHHHHHHHC--cCCCcCC
Confidence 66887766566 467774 45788999999988 3689887
No 28
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.08 E-value=0.12 Score=46.44 Aligned_cols=50 Identities=22% Similarity=0.644 Sum_probs=38.2
Q ss_pred CCCCCeeEEcccCC---CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 35 DEDMTICRICYGAD---QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 35 ~~~~~~CRIC~~~~---~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
...+-.|-||.+.- +.-.+.||+ .-.|..|+++|+..- +..|++|+++.+
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~-----H~FH~~Cv~kW~~~y-~~~CPvCrt~iP 372 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCD-----HRFHVGCVDKWLLGY-SNKCPVCRTAIP 372 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccC-----ceechhHHHHHHhhh-cccCCccCCCCC
Confidence 45678999998877 344568986 368999999999732 257999998753
No 29
>KOG1785|consensus
Probab=90.12 E-value=0.11 Score=48.30 Aligned_cols=48 Identities=19% Similarity=0.654 Sum_probs=39.5
Q ss_pred CCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 38 MTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
...|.||-+.+.+.-|.||. ...-..||..|..++....|+.|+.+..
T Consensus 369 FeLCKICaendKdvkIEPCG-----HLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 369 FELCKICAENDKDVKIEPCG-----HLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHHHhhccCCCccccccc-----chHHHHHHHhhcccCCCCCCCceeeEec
Confidence 37899998888777789996 1333489999999998999999998865
No 30
>KOG0827|consensus
Probab=89.38 E-value=0.28 Score=45.39 Aligned_cols=46 Identities=26% Similarity=0.731 Sum_probs=32.4
Q ss_pred CCeeEEcccCC--CCcccccccccCccccccHHHHHHHHHHcCC-CccCCCC
Q psy3116 38 MTICRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQECGV-DKCDLCK 86 (177)
Q Consensus 38 ~~~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~-~~CelC~ 86 (177)
..+|-||-++. +..|-.-=.|- ...|..||.+|+..... +.|++|+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cG---hifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCG---HIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchh---hHHHHHHHHHHHccCCccCCCCcee
Confidence 46899995544 33342221132 35899999999998876 7999999
No 31
>PLN02189 cellulose synthase
Probab=87.62 E-value=0.44 Score=48.58 Aligned_cols=54 Identities=24% Similarity=0.581 Sum_probs=41.4
Q ss_pred CCCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 34 DDEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 34 ~~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
...++.+|+||.++- ++++.-+|. |. --|=+.|. ..-+..++..|+.||++|.-
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~---fpvCr~Cy-eyer~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECG---FPVCRPCY-EYERREGTQNCPQCKTRYKR 88 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCC---Cccccchh-hhhhhcCCccCcccCCchhh
Confidence 345677999998653 677778888 74 23778999 55566688999999999983
No 32
>PLN02436 cellulose synthase A
Probab=87.37 E-value=0.48 Score=48.49 Aligned_cols=54 Identities=20% Similarity=0.486 Sum_probs=41.8
Q ss_pred CCCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 34 DDEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 34 ~~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
...++.+|+||-++- ++++.-.|+ |. --|=+.|. ..-+..++..|+.||++|.-
T Consensus 32 ~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~---fpvCr~Cy-eyer~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 32 QELSGQTCQICGDEIELTVDGEPFVACNECA---FPVCRPCY-EYERREGNQACPQCKTRYKR 90 (1094)
T ss_pred cccCCccccccccccCcCCCCCEEEeeccCC---Cccccchh-hhhhhcCCccCcccCCchhh
Confidence 355677999997653 777888888 64 23778999 55566688999999999983
No 33
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.14 E-value=0.46 Score=43.79 Aligned_cols=50 Identities=26% Similarity=0.484 Sum_probs=39.1
Q ss_pred CCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 36 EDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 36 ~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
.....|.||++....+.+.||. ......|+.+|+... ..|++|+..+...
T Consensus 24 e~~l~C~IC~d~~~~PvitpCg-----H~FCs~CI~~~l~~~--~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPVLTSCS-----HTFCSLCIRRCLSNQ--PKCPLCRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhhCccCCCCC-----CchhHHHHHHHHhCC--CCCCCCCCccccc
Confidence 4567999998766778888875 245568999999764 4799999998744
No 34
>KOG4265|consensus
Probab=84.88 E-value=0.71 Score=41.90 Aligned_cols=47 Identities=19% Similarity=0.629 Sum_probs=35.7
Q ss_pred CCCCCCeeEEcccCCCCccccccc----ccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 34 DDEDMTICRICYGADQQNLLSICQ----CKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 34 ~~~~~~~CRIC~~~~~~~Li~PC~----C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
.+++++.|=||..+..+-++-||+ |+ .|-+.-.- ....|++|+..+.
T Consensus 286 ~~~~gkeCVIClse~rdt~vLPCRHLCLCs--------~Ca~~Lr~--q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 286 ESESGKECVICLSESRDTVVLPCRHLCLCS--------GCAKSLRY--QTNNCPICRQPIE 336 (349)
T ss_pred cccCCCeeEEEecCCcceEEecchhhehhH--------hHHHHHHH--hhcCCCccccchH
Confidence 447799999998888778888887 65 57766552 2357999998865
No 35
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=84.38 E-value=1 Score=33.09 Aligned_cols=29 Identities=28% Similarity=0.505 Sum_probs=24.9
Q ss_pred cccHHHHHHHHHHcCCCccCCCCCeeEeeec
Q psy3116 64 YVHIECIERWLQECGVDKCDLCKYQFTTERL 94 (177)
Q Consensus 64 ~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~ 94 (177)
-.|..|+.+||++ +..|++++.+|++.+.
T Consensus 57 aFH~HCI~rWL~T--k~~CPld~q~w~~~~~ 85 (88)
T COG5194 57 AFHDHCIYRWLDT--KGVCPLDRQTWVLADG 85 (88)
T ss_pred HHHHHHHHHHHhh--CCCCCCCCceeEEecc
Confidence 4799999999999 4679999999987653
No 36
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=80.77 E-value=2.6 Score=38.41 Aligned_cols=56 Identities=23% Similarity=0.650 Sum_probs=37.9
Q ss_pred CCCCCCeeEEcccCC-CCccc-------------------ccccccCccccccHHHHHHHHHHc-----------CCCcc
Q psy3116 34 DDEDMTICRICYGAD-QQNLL-------------------SICQCKGSIAYVHIECIERWLQEC-----------GVDKC 82 (177)
Q Consensus 34 ~~~~~~~CRIC~~~~-~~~Li-------------------~PC~C~Gs~~~VH~~CL~~Wi~~s-----------~~~~C 82 (177)
..++.+.|-=|.... +-.|. .+|.|+- -==.+||-+|+..+ ++..|
T Consensus 267 ~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRP---mWC~~Cm~kwFasrQd~~~~~~Wl~~~~~C 343 (358)
T PF10272_consen 267 SGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRP---MWCLECMGKWFASRQDQQHPETWLSGKCPC 343 (358)
T ss_pred CccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccc---hHHHHHHHHHhhhcCCCCChhhhhcCCCCC
Confidence 456778888887554 22222 2566652 22458999999875 46789
Q ss_pred CCCCCeeEee
Q psy3116 83 DLCKYQFTTE 92 (177)
Q Consensus 83 elC~~~y~~~ 92 (177)
+.|+.+|-+.
T Consensus 344 PtCRa~FCil 353 (358)
T PF10272_consen 344 PTCRAKFCIL 353 (358)
T ss_pred CCCcccceee
Confidence 9999999764
No 37
>KOG2930|consensus
Probab=80.77 E-value=1.8 Score=33.22 Aligned_cols=29 Identities=31% Similarity=0.729 Sum_probs=24.7
Q ss_pred cccHHHHHHHHHHcCCCccCCCCCeeEeeec
Q psy3116 64 YVHIECIERWLQECGVDKCDLCKYQFTTERL 94 (177)
Q Consensus 64 ~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~ 94 (177)
-.|.-|+.+||+++ ..|+||..++.+.+.
T Consensus 84 aFH~hCisrWlktr--~vCPLdn~eW~~qr~ 112 (114)
T KOG2930|consen 84 AFHFHCISRWLKTR--NVCPLDNKEWVFQRY 112 (114)
T ss_pred HHHHHHHHHHHhhc--CcCCCcCcceeEeec
Confidence 47999999999986 579999999887653
No 38
>KOG1734|consensus
Probab=79.98 E-value=1.1 Score=39.91 Aligned_cols=58 Identities=19% Similarity=0.451 Sum_probs=40.4
Q ss_pred CCCCeeEEcccCC-----CCccc---ccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeecCc
Q psy3116 36 EDMTICRICYGAD-----QQNLL---SICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPT 96 (177)
Q Consensus 36 ~~~~~CRIC~~~~-----~~~Li---~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~~~ 96 (177)
.+..+|-+|-+.- ++.+| .-=.|. ...|+-|++-|--.-++.+|+-||.+...++-++
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCn---HvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfs 287 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCN---HVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFS 287 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecc---cchHHHhhhhheeecCCCCCchHHHHhhHhhhcc
Confidence 4567899996432 11121 122243 4689999999999999999999999987765443
No 39
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=79.86 E-value=1.7 Score=31.71 Aligned_cols=54 Identities=26% Similarity=0.540 Sum_probs=23.3
Q ss_pred CCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 35 DEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 35 ~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
+.++.+|.||-+.- ++.+.-.|. |. --|=+.|.+-=+++ ++..|..|+++|...
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~---fPvCr~CyEYErke-g~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECA---FPVCRPCYEYERKE-GNQVCPQCKTRYKRH 64 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS--------HHHHHHHHHT-S-SB-TTT--B----
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccC---CccchhHHHHHhhc-CcccccccCCCcccc
Confidence 56789999997643 566666665 42 34778998865544 677899999999843
No 40
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=77.31 E-value=1.7 Score=28.80 Aligned_cols=44 Identities=16% Similarity=0.417 Sum_probs=20.3
Q ss_pred eEEcccCC--CCcccccccccCccccccHHHHHHHHHHc--CCCccCCCCCeeE
Q psy3116 41 CRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQEC--GVDKCDLCKYQFT 90 (177)
Q Consensus 41 CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s--~~~~CelC~~~y~ 90 (177)
|.+|-+.. .+.-+.||.|. ++-|+.=|.+.. ....|+-|+.+|.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cg------f~IC~~C~~~i~~~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECG------FQICRFCYHDILENEGGRCPGCREPYK 48 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----------HHHHHHHTTSS-SB-TTT--B--
T ss_pred CCCcccccccCCCccccCcCC------CcHHHHHHHHHHhccCCCCCCCCCCCC
Confidence 44565433 45567899996 456666666555 4788999999984
No 41
>PLN02400 cellulose synthase
Probab=77.21 E-value=1.8 Score=44.59 Aligned_cols=54 Identities=24% Similarity=0.571 Sum_probs=37.8
Q ss_pred CCCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 34 DDEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 34 ~~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
.+.++.+|+||-++- ++++.-.|. |. --|=+.|.+ .=+..++..|+.||++|.-
T Consensus 32 ~~~~gqiCqICGD~VG~t~dGe~FVAC~eCa---FPVCRpCYE-YERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 32 KNLNGQICQICGDDVGVTETGDVFVACNECA---FPVCRPCYE-YERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred cccCCceeeecccccCcCCCCCEEEEEccCC---Cccccchhh-eecccCCccCcccCCcccc
Confidence 356778999997653 566666665 32 226679984 3334478899999999983
No 42
>KOG1645|consensus
Probab=77.09 E-value=1.8 Score=40.27 Aligned_cols=49 Identities=31% Similarity=0.661 Sum_probs=37.7
Q ss_pred CCCeeEEcccCC----CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCee
Q psy3116 37 DMTICRICYGAD----QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQF 89 (177)
Q Consensus 37 ~~~~CRIC~~~~----~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y 89 (177)
.+.+|-||+++- +..+++| .|. ...-..|+++||-.+-...|++|+.+=
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl-~cg---hlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSL-QCG---HLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccccCceeeeeeeecCceEEeee-ccc---ccccHHHHHHHHhhhhhhhCcccCChh
Confidence 467899999876 4556666 443 467789999999766678999999864
No 43
>PLN02195 cellulose synthase A
Probab=76.71 E-value=2.4 Score=43.26 Aligned_cols=52 Identities=19% Similarity=0.469 Sum_probs=36.9
Q ss_pred CCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 35 DEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 35 ~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
++++.+|+||.+.- ++++.-.|+ |. --|=+.|.+ .=+..++..|+.||++|+
T Consensus 3 ~~~~~~c~~cgd~~~~~~~g~~fvaC~eC~---~pvCrpCye-yer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 3 ESGAPICATCGEEVGVDSNGEAFVACHECS---YPLCKACLE-YEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cCCCccceecccccCcCCCCCeEEEeccCC---Cccccchhh-hhhhcCCccCCccCCccc
Confidence 45678999997643 455555565 32 237779994 444557889999999999
No 44
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=76.62 E-value=2 Score=34.33 Aligned_cols=56 Identities=20% Similarity=0.405 Sum_probs=43.7
Q ss_pred CCCeeEEcccCC-CCcccccccccCccccccHH-HHHHHHHHcCCCccCCCCCeeEeeec
Q psy3116 37 DMTICRICYGAD-QQNLLSICQCKGSIAYVHIE-CIERWLQECGVDKCDLCKYQFTTERL 94 (177)
Q Consensus 37 ~~~~CRIC~~~~-~~~Li~PC~C~Gs~~~VH~~-CL~~Wi~~s~~~~CelC~~~y~~~~~ 94 (177)
.--.|-||.|.. ++..+.|=.|-| .-+-.. |..-|--.+--..|++|++.|.....
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCg--Y~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCG--YSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhhcCCcccccc--hHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 557899999988 899999999988 224444 45667776777899999999986543
No 45
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=76.09 E-value=2.3 Score=26.62 Aligned_cols=40 Identities=23% Similarity=0.630 Sum_probs=30.6
Q ss_pred eEEcccCC---CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCC
Q psy3116 41 CRICYGAD---QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKY 87 (177)
Q Consensus 41 CRIC~~~~---~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~ 87 (177)
|-||++.. ..+.+.+|. ..+..+|+.+.. .....|++|+.
T Consensus 2 C~~C~~~~~~~~~~~l~~Cg-----H~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCG-----HIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccC-----CHHHHHHHHhhc--CCCCCCcCCCC
Confidence 67887655 456788874 457789999998 67788999974
No 46
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.60 E-value=2.3 Score=38.07 Aligned_cols=50 Identities=16% Similarity=0.458 Sum_probs=34.6
Q ss_pred CCCeeEEcccCC--CC---cccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 37 DMTICRICYGAD--QQ---NLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 37 ~~~~CRIC~~~~--~~---~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
++..|-+|.... .. -+++||. .-.=.+|+.+.+.. +...|+.|+..++..
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CG-----H~~C~sCv~~l~~~-~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCG-----HTLCESCVDLLFVR-GSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCC-----CcccHHHHHHHhcC-CCCCCCCCCCccchh
Confidence 346899998765 22 2678774 22445999997643 566899999877654
No 47
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=74.88 E-value=1 Score=28.38 Aligned_cols=40 Identities=25% Similarity=0.474 Sum_probs=25.2
Q ss_pred eEEcccCCCCcccccccccCccccccHHHHHHHHHHcCC--CccCCC
Q psy3116 41 CRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGV--DKCDLC 85 (177)
Q Consensus 41 CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~--~~CelC 85 (177)
|-||++-..+|..-+|. .-.=+.||.+|.+..+. ..|++|
T Consensus 1 CpiC~~~~~~Pv~l~CG-----H~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCG-----HSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSS-----SEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCc-----CHHHHHHHHHHHHccCCcCCCCcCC
Confidence 56776665778888885 12345999999987654 488887
No 48
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=74.83 E-value=2.5 Score=43.37 Aligned_cols=60 Identities=22% Similarity=0.556 Sum_probs=41.2
Q ss_pred CCCCCCCCCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 28 DKPDSSDDEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 28 ~~~~~~~~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
+++....+-++.+|.||-++- ++++.-.|+ |. --|-+.|. ..=+..++..|+.||++|..
T Consensus 5 ~~~~~~~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~---fpvCr~cy-eye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 5 DRPPTRQSADAKTCRVCGDEVGVKEDGQPFVACHVCG---FPVCKPCY-EYERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred cCCccccCCCcchhhccccccCcCCCCCEEEEeccCC---Cccccchh-hhhhhcCCccCCccCCchhh
Confidence 344444566789999997653 556656665 32 23667999 44445578899999999983
No 49
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=74.78 E-value=3.3 Score=42.65 Aligned_cols=52 Identities=23% Similarity=0.552 Sum_probs=37.4
Q ss_pred CCCCCeeEEcccCC----CCccccccc-ccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 35 DEDMTICRICYGAD----QQNLLSICQ-CKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 35 ~~~~~~CRIC~~~~----~~~Li~PC~-C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
+.++.+|+||.++- ++++.-.|+ |. --|=+.|.+ .=+..++..|+.||++|+
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~---FPVCrpCYE-YEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCA---FPVCRPCYE-YERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCC---Cccccchhh-hhhhcCCccCCccCCchh
Confidence 55677999997653 566666665 32 227779994 334457889999999998
No 50
>KOG0828|consensus
Probab=73.01 E-value=2.6 Score=40.31 Aligned_cols=49 Identities=20% Similarity=0.594 Sum_probs=35.1
Q ss_pred CCCCCeeEEcccCC-----------------CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCee
Q psy3116 35 DEDMTICRICYGAD-----------------QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQF 89 (177)
Q Consensus 35 ~~~~~~CRIC~~~~-----------------~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y 89 (177)
......|-||...- .+=+++||. ...|+.||++|.+.. +..|+.|+.+.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~y-kl~CPvCR~pL 633 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDTY-KLICPVCRCPL 633 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhhh-cccCCccCCCC
Confidence 35568899997542 123455876 478999999999853 26799998764
No 51
>KOG1039|consensus
Probab=70.04 E-value=3.8 Score=37.16 Aligned_cols=63 Identities=17% Similarity=0.472 Sum_probs=40.0
Q ss_pred CCCCCCCCCCCCeeEEcccCC-CCc-------ccccccccCccccccHHHHHHHHHHcC-----CCccCCCCCeeEeeec
Q psy3116 28 DKPDSSDDEDMTICRICYGAD-QQN-------LLSICQCKGSIAYVHIECIERWLQECG-----VDKCDLCKYQFTTERL 94 (177)
Q Consensus 28 ~~~~~~~~~~~~~CRIC~~~~-~~~-------Li~PC~C~Gs~~~VH~~CL~~Wi~~s~-----~~~CelC~~~y~~~~~ 94 (177)
++.-......+..|=||.+.- +-. .+.+|. ...=.+|+.+|-.... ...|++|+..=.....
T Consensus 151 e~~~a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~-----H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~p 225 (344)
T KOG1039|consen 151 ERSFALQKSSEKECGICMETINEKAASERRFGILPNCN-----HSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNP 225 (344)
T ss_pred hhccCcCccccccceehhhhccccchhhhhcccCCCcc-----hhhhhcHhHhhhhhhccccccccCCCcccCccccccc
Confidence 333333356789999999876 211 123454 1122378999997766 6899999987554444
Q ss_pred C
Q psy3116 95 P 95 (177)
Q Consensus 95 ~ 95 (177)
.
T Consensus 226 S 226 (344)
T KOG1039|consen 226 S 226 (344)
T ss_pred c
Confidence 3
No 52
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=66.40 E-value=3.1 Score=26.46 Aligned_cols=22 Identities=23% Similarity=0.714 Sum_probs=16.0
Q ss_pred cccHHHHHHHHHHcCCCccCCC
Q psy3116 64 YVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 64 ~VH~~CL~~Wi~~s~~~~CelC 85 (177)
-+|..|+++.++......|+.|
T Consensus 22 r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 22 RLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp EE-HHHHHHHTTT-SS-B-TTT
T ss_pred hHHHHHHHHHHhcCCCCCCcCC
Confidence 4999999999999887789877
No 53
>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=66.30 E-value=2.6 Score=33.55 Aligned_cols=41 Identities=17% Similarity=0.347 Sum_probs=27.8
Q ss_pred CCCeeEEcccCC---CCcccccccccCcc-ccccHHHHHHHHHHc
Q psy3116 37 DMTICRICYGAD---QQNLLSICQCKGSI-AYVHIECIERWLQEC 77 (177)
Q Consensus 37 ~~~~CRIC~~~~---~~~Li~PC~C~Gs~-~~VH~~CL~~Wi~~s 77 (177)
....|+||++.- ++-+.-+|.-.-.+ +..|.+|+++|-+..
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~ 69 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRER 69 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhc
Confidence 467899999765 34555565544333 248999999996443
No 54
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=64.43 E-value=3.8 Score=36.96 Aligned_cols=61 Identities=25% Similarity=0.319 Sum_probs=43.0
Q ss_pred CCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeeecCccccccchHHHhh
Q psy3116 37 DMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPTQTKLKSLLSWVK 108 (177)
Q Consensus 37 ~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~~~~y~~~~~l~~W~~ 108 (177)
....||||++--.-|++.||.= -.-.-|+.+-+... ..|++|.+++...+.+. ..+..|+.
T Consensus 24 s~lrC~IC~~~i~ip~~TtCgH-----tFCslCIR~hL~~q--p~CP~Cr~~~~esrlr~----~s~~~ei~ 84 (391)
T COG5432 24 SMLRCRICDCRISIPCETTCGH-----TFCSLCIRRHLGTQ--PFCPVCREDPCESRLRG----SSGSREIN 84 (391)
T ss_pred hHHHhhhhhheeecceeccccc-----chhHHHHHHHhcCC--CCCccccccHHhhhccc----chhHHHHH
Confidence 4568999976667788888861 12247888877653 57999999998777654 24566753
No 55
>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=62.72 E-value=2.3 Score=29.51 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=31.6
Q ss_pred eeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEe
Q psy3116 40 ICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 40 ~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
.|-|+++-..+|.+.|+. ...=+.|+++|+.. +...|++|+.....
T Consensus 6 ~CpIt~~lM~dPVi~~~G-----~tyer~~I~~~l~~-~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 6 LCPITGELMRDPVILPSG-----HTYERSAIERWLEQ-NGGTDPFTRQPLSE 51 (73)
T ss_dssp B-TTTSSB-SSEEEETTS-----EEEEHHHHHHHHCT-TSSB-TTT-SB-SG
T ss_pred CCcCcCcHhhCceeCCcC-----CEEcHHHHHHHHHc-CCCCCCCCCCcCCc
Confidence 466665444778888854 46788999999988 66789999887664
No 56
>KOG0804|consensus
Probab=60.68 E-value=4.1 Score=38.41 Aligned_cols=46 Identities=22% Similarity=0.693 Sum_probs=33.1
Q ss_pred CCCCCeeEEcccCC----CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCee
Q psy3116 35 DEDMTICRICYGAD----QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQF 89 (177)
Q Consensus 35 ~~~~~~CRIC~~~~----~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y 89 (177)
-.+.|.|-+|++.. .+.+..+|. .-.|-.||.+|=.. +|++|++--
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~-----Hsfh~~cl~~w~~~----scpvcR~~q 221 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCN-----HSFHCSCLMKWWDS----SCPVCRYCQ 221 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecc-----cccchHHHhhcccC----cChhhhhhc
Confidence 35679999998654 444555654 35899999999766 588887653
No 57
>KOG2164|consensus
Probab=59.79 E-value=7.6 Score=37.01 Aligned_cols=49 Identities=20% Similarity=0.435 Sum_probs=34.7
Q ss_pred CCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHc---CCCccCCCCCeeEe
Q psy3116 38 MTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQEC---GVDKCDLCKYQFTT 91 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s---~~~~CelC~~~y~~ 91 (177)
...|-||++...-+...-|. ...=-.||.+.++.+ +-..|++|...+..
T Consensus 186 ~~~CPICL~~~~~p~~t~CG-----HiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCG-----HIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCcccccccC-----ceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 78999999887333333343 112348998888776 56789999998776
No 58
>KOG2177|consensus
Probab=57.94 E-value=4.5 Score=32.22 Aligned_cols=45 Identities=22% Similarity=0.501 Sum_probs=34.4
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCC
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCK 86 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~ 86 (177)
..+.-.|-||++....+.+-||. ...=..|+..+.. ....|+.|+
T Consensus 10 ~~~~~~C~iC~~~~~~p~~l~C~-----H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREPVLLPCG-----HNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhhcCcccccc-----chHhHHHHHHhcC--CCcCCcccC
Confidence 35678999999887566788886 1223489999888 678899999
No 59
>KOG4445|consensus
Probab=55.24 E-value=6.4 Score=35.57 Aligned_cols=53 Identities=26% Similarity=0.649 Sum_probs=36.8
Q ss_pred CCCCeeEEcccCC-CC--cccccccccCccccccHHHHHHHHHHc---------------------CCCccCCCCCeeEe
Q psy3116 36 EDMTICRICYGAD-QQ--NLLSICQCKGSIAYVHIECIERWLQEC---------------------GVDKCDLCKYQFTT 91 (177)
Q Consensus 36 ~~~~~CRIC~~~~-~~--~Li~PC~C~Gs~~~VH~~CL~~Wi~~s---------------------~~~~CelC~~~y~~ 91 (177)
-....|-||+=+. ++ -.+.||. .|.|..||.|.|.+- -...|++|+++...
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~-----Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACD-----HYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3445677766554 33 3456764 599999999988762 13569999999887
Q ss_pred ee
Q psy3116 92 ER 93 (177)
Q Consensus 92 ~~ 93 (177)
+.
T Consensus 188 e~ 189 (368)
T KOG4445|consen 188 EE 189 (368)
T ss_pred cc
Confidence 64
No 60
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=53.47 E-value=12 Score=34.56 Aligned_cols=61 Identities=15% Similarity=0.463 Sum_probs=40.2
Q ss_pred cCCCCCCCCCCCCeeEEcccCC--CCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 27 LDKPDSSDDEDMTICRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 27 ~~~~~~~~~~~~~~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
-|+-++|. .+++.|-.|.++- .+.-.-||.|- .-|-+-|-.. |++.-.-+|+-|+..|.-+
T Consensus 4 ~qei~~se-deed~cplcie~mditdknf~pc~cg---y~ic~fc~~~-irq~lngrcpacrr~y~de 66 (480)
T COG5175 4 VQEIHNSE-DEEDYCPLCIEPMDITDKNFFPCPCG---YQICQFCYNN-IRQNLNGRCPACRRKYDDE 66 (480)
T ss_pred hhhccccc-cccccCcccccccccccCCcccCCcc---cHHHHHHHHH-HHhhccCCChHhhhhcccc
Confidence 45555544 4556699998876 56667899995 2254555332 3333466899999999754
No 61
>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=52.89 E-value=4.1 Score=29.16 Aligned_cols=33 Identities=27% Similarity=0.513 Sum_probs=23.2
Q ss_pred CCCCCeeEEcccCC-CCc-ccccccccCccccccHHHHHH
Q psy3116 35 DEDMTICRICYGAD-QQN-LLSICQCKGSIAYVHIECIER 72 (177)
Q Consensus 35 ~~~~~~CRIC~~~~-~~~-Li~PC~C~Gs~~~VH~~CL~~ 72 (177)
-+++..|.+|...- .+. .+.||. ..||..|+.|
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCC-----eEEecccccC
Confidence 35677899998766 333 356764 5899999864
No 62
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=46.30 E-value=27 Score=28.67 Aligned_cols=37 Identities=24% Similarity=0.770 Sum_probs=25.7
Q ss_pred CCeeEEcccCCCCcccccc-------c---ccCccccccHHHHHHHHHH
Q psy3116 38 MTICRICYGADQQNLLSIC-------Q---CKGSIAYVHIECIERWLQE 76 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC-------~---C~Gs~~~VH~~CL~~Wi~~ 76 (177)
+..|-||.+-.-+..+--| + |.. .|-|..||++.-+.
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~T--s~rhSNCLdqfkka 48 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDT--SYRHSNCLDQFKKA 48 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCC--ccchhHHHHHHHHH
Confidence 5679999887733333333 2 653 58899999999865
No 63
>KOG4692|consensus
Probab=45.90 E-value=17 Score=33.79 Aligned_cols=48 Identities=27% Similarity=0.692 Sum_probs=36.0
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccH---HHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHI---ECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~---~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
++++..|-||+.++-+..+.||+ |+ .|+.+=+ -+...|=.||+....+
T Consensus 419 ~sEd~lCpICyA~pi~Avf~PC~--------H~SC~~CI~qHl--mN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPINAVFAPCS--------HRSCYGCITQHL--MNCKRCFFCKTTVIDV 469 (489)
T ss_pred CcccccCcceecccchhhccCCC--------CchHHHHHHHHH--hcCCeeeEecceeeeh
Confidence 46788999999998788999996 33 3555444 2557899999987753
No 64
>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=42.97 E-value=11 Score=19.32 Aligned_cols=10 Identities=30% Similarity=1.012 Sum_probs=6.9
Q ss_pred ccCCCCCeeE
Q psy3116 81 KCDLCKYQFT 90 (177)
Q Consensus 81 ~CelC~~~y~ 90 (177)
.|++|+..|.
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 5999999986
No 65
>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=42.50 E-value=12 Score=21.57 Aligned_cols=13 Identities=31% Similarity=0.836 Sum_probs=10.6
Q ss_pred CCCccCCCCCeeE
Q psy3116 78 GVDKCDLCKYQFT 90 (177)
Q Consensus 78 ~~~~CelC~~~y~ 90 (177)
....|+.||+.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 3568999999985
No 66
>KOG0287|consensus
Probab=41.30 E-value=9.2 Score=35.20 Aligned_cols=48 Identities=21% Similarity=0.490 Sum_probs=36.2
Q ss_pred CCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEee
Q psy3116 38 MTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~ 92 (177)
.-.|-||++=..-|+|.||.= -.-.-|+...++. ...|+.|.++|+=.
T Consensus 23 lLRC~IC~eyf~ip~itpCsH-----tfCSlCIR~~L~~--~p~CP~C~~~~~Es 70 (442)
T KOG0287|consen 23 LLRCGICFEYFNIPMITPCSH-----TFCSLCIRKFLSY--KPQCPTCCVTVTES 70 (442)
T ss_pred HHHHhHHHHHhcCceeccccc-----hHHHHHHHHHhcc--CCCCCceecccchh
Confidence 357999998778899999751 2234788888866 46799999998743
No 67
>KOG1100|consensus
Probab=41.05 E-value=16 Score=30.71 Aligned_cols=20 Identities=35% Similarity=0.652 Sum_probs=15.8
Q ss_pred CCeeEEcccCCCCccccccc
Q psy3116 38 MTICRICYGADQQNLLSICQ 57 (177)
Q Consensus 38 ~~~CRIC~~~~~~~Li~PC~ 57 (177)
...||.|.+.+..-++.||+
T Consensus 158 ~~~Cr~C~~~~~~VlllPCr 177 (207)
T KOG1100|consen 158 MRSCRKCGEREATVLLLPCR 177 (207)
T ss_pred cccceecCcCCceEEeeccc
Confidence 34499998888667888987
No 68
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=39.16 E-value=15 Score=23.37 Aligned_cols=38 Identities=18% Similarity=0.528 Sum_probs=19.3
Q ss_pred eEEccc--CC-CCcccccccccCccccccHHHHHHHHHHc--CCCccC
Q psy3116 41 CRICYG--AD-QQNLLSICQCKGSIAYVHIECIERWLQEC--GVDKCD 83 (177)
Q Consensus 41 CRIC~~--~~-~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s--~~~~Ce 83 (177)
|-||.+ ++ .-|.+-||.- -+=++||+++.+.+ +..+|+
T Consensus 1 CpIc~e~~~~~n~P~~L~CGH-----~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCGH-----VFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS------EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCccccccCCCCCCEEEeCcc-----HHHHHHHHHHHhcCCCCeeeCc
Confidence 445655 22 3467888653 46679999999876 455553
No 69
>KOG1002|consensus
Probab=36.95 E-value=22 Score=34.73 Aligned_cols=54 Identities=15% Similarity=0.439 Sum_probs=41.6
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHH---cCCCccCCCCCeeEeee
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQE---CGVDKCDLCKYQFTTER 93 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~---s~~~~CelC~~~y~~~~ 93 (177)
+.+...|-+|++..++.+.+-|.= -.-+.|+...+.. +....|+.|.-...+..
T Consensus 533 nk~~~~C~lc~d~aed~i~s~ChH-----~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 533 NKGEVECGLCHDPAEDYIESSCHH-----KFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred ccCceeecccCChhhhhHhhhhhH-----HHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 467789999998887788888862 2334899999865 35689999999887763
No 70
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=34.92 E-value=43 Score=20.95 Aligned_cols=20 Identities=5% Similarity=0.069 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHhhhhhcc
Q psy3116 125 ATFLFSPFIILLTLSGYQTF 144 (177)
Q Consensus 125 ~~l~ltpi~i~~~~L~~~~f 144 (177)
.++++.|+++..+|..|--.
T Consensus 5 lliVl~Pil~A~~Wa~fNIg 24 (36)
T CHL00196 5 LLVIAAPVLAAASWALFNIG 24 (36)
T ss_pred HHHHHHHHHHHHHHHHHHhH
Confidence 45788999999999877653
No 71
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=32.92 E-value=40 Score=24.26 Aligned_cols=20 Identities=10% Similarity=0.419 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhhhhhccc
Q psy3116 126 TFLFSPFIILLTLSGYQTFS 145 (177)
Q Consensus 126 ~l~ltpi~i~~~~L~~~~fs 145 (177)
++.+||++|+++.+.|.+.-
T Consensus 27 ll~LtPlfiisa~lSwkLaK 46 (74)
T PF15086_consen 27 LLILTPLFIISAVLSWKLAK 46 (74)
T ss_pred HHHHhHHHHHHHHHHHHHHH
Confidence 46689999999888887754
No 72
>KOG3899|consensus
Probab=31.99 E-value=39 Score=30.60 Aligned_cols=30 Identities=17% Similarity=0.447 Sum_probs=24.1
Q ss_pred cccHHHHHHHHHHc-----------CCCccCCCCCeeEeee
Q psy3116 64 YVHIECIERWLQEC-----------GVDKCDLCKYQFTTER 93 (177)
Q Consensus 64 ~VH~~CL~~Wi~~s-----------~~~~CelC~~~y~~~~ 93 (177)
.--++||.+|+..+ ++..|+.|+..|-+..
T Consensus 328 ~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 328 LWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred HHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 44579999999654 5789999999998764
No 73
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=31.63 E-value=89 Score=22.81 Aligned_cols=28 Identities=18% Similarity=0.247 Sum_probs=19.0
Q ss_pred CCCccCCCCCeeEeeecCccccccchHHHhhccC
Q psy3116 78 GVDKCDLCKYQFTTERLPTQTKLKSLLSWVKHVD 111 (177)
Q Consensus 78 ~~~~CelC~~~y~~~~~~~y~~~~~l~~W~~~~~ 111 (177)
....|+-|+++.+.-..- |+.-|+.+.+
T Consensus 32 ~rS~C~~C~~~L~~~~lI------Pi~S~l~lrG 59 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLI------PILSYLLLRG 59 (92)
T ss_pred CCCcCcCCCCcCcccccc------hHHHHHHhCC
Confidence 457899999987644322 7788875443
No 74
>PRK13240 pbsY photosystem II protein Y; Reviewed
Probab=31.01 E-value=57 Score=20.83 Aligned_cols=21 Identities=5% Similarity=0.124 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHhhhhhccc
Q psy3116 125 ATFLFSPFIILLTLSGYQTFS 145 (177)
Q Consensus 125 ~~l~ltpi~i~~~~L~~~~fs 145 (177)
.++++.|+++..+|..|-.-.
T Consensus 5 lliVl~Pil~A~~Wa~fNIg~ 25 (40)
T PRK13240 5 LLIVLAPILAAAGWAVFNIGK 25 (40)
T ss_pred HHHHHHHHHHHHHHHHHHhhH
Confidence 457889999999998776543
No 75
>KOG0955|consensus
Probab=30.99 E-value=17 Score=37.54 Aligned_cols=40 Identities=30% Similarity=0.664 Sum_probs=28.1
Q ss_pred CCCCCCCCCCeeEEcccCC--CCcccccccccCccccccHHHHH
Q psy3116 30 PDSSDDEDMTICRICYGAD--QQNLLSICQCKGSIAYVHIECIE 71 (177)
Q Consensus 30 ~~~~~~~~~~~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~ 71 (177)
++.+..+....|-||.+++ ....|--| .|=-..||++|.-
T Consensus 211 ~~~~~~~~D~~C~iC~~~~~~n~n~ivfC--D~Cnl~VHq~Cyg 252 (1051)
T KOG0955|consen 211 PKDALLEEDAVCCICLDGECQNSNVIVFC--DGCNLAVHQECYG 252 (1051)
T ss_pred CCccccCCCccceeecccccCCCceEEEc--CCCcchhhhhccC
Confidence 3334457889999999988 33444454 3434799999997
No 76
>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=30.61 E-value=20 Score=18.78 Aligned_cols=11 Identities=36% Similarity=1.068 Sum_probs=9.2
Q ss_pred ccCCCCCeeEe
Q psy3116 81 KCDLCKYQFTT 91 (177)
Q Consensus 81 ~CelC~~~y~~ 91 (177)
.|+.|+..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 59999999973
No 77
>PF06298 PsbY: Photosystem II protein Y (PsbY); InterPro: IPR009388 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants []. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea []. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.; GO: 0030145 manganese ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0016021 integral to membrane
Probab=29.79 E-value=57 Score=20.39 Aligned_cols=21 Identities=5% Similarity=0.023 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHhhhhhccc
Q psy3116 125 ATFLFSPFIILLTLSGYQTFS 145 (177)
Q Consensus 125 ~~l~ltpi~i~~~~L~~~~fs 145 (177)
.++++.|+++..+|..|--..
T Consensus 5 ~liVl~Pil~A~gWa~fNIg~ 25 (36)
T PF06298_consen 5 LLIVLLPILPAAGWALFNIGR 25 (36)
T ss_pred hHHHHHHHHHHHHHHHHHhHH
Confidence 357889999999998776543
No 78
>KOG2879|consensus
Probab=28.83 E-value=60 Score=28.99 Aligned_cols=55 Identities=20% Similarity=0.246 Sum_probs=39.2
Q ss_pred CCCCCCCCCeeEEcccCCCCcc-cccccccCccccccHHHHHHHHHHcCCCccCCCCCeeE
Q psy3116 31 DSSDDEDMTICRICYGADQQNL-LSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFT 90 (177)
Q Consensus 31 ~~~~~~~~~~CRIC~~~~~~~L-i~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~ 90 (177)
+++..++...|-+|.+....|. +.||.= ..=..|+..=...+..-+|+.|+..-.
T Consensus 232 sss~~t~~~~C~~Cg~~PtiP~~~~~C~H-----iyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 232 SSSTGTSDTECPVCGEPPTIPHVIGKCGH-----IYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ccccccCCceeeccCCCCCCCeeeccccc-----eeehhhhhhhhcchhhcccCccCCCCc
Confidence 4555688899999977665554 567762 222467777776667789999999865
No 79
>KOG0956|consensus
Probab=28.78 E-value=31 Score=34.57 Aligned_cols=49 Identities=24% Similarity=0.588 Sum_probs=34.6
Q ss_pred eeEEcccCC---CCcccccccccCccc--cccHHHH-------HHHHHHc-------CCCccCCCCCeeEe
Q psy3116 40 ICRICYGAD---QQNLLSICQCKGSIA--YVHIECI-------ERWLQEC-------GVDKCDLCKYQFTT 91 (177)
Q Consensus 40 ~CRIC~~~~---~~~Li~PC~C~Gs~~--~VH~~CL-------~~Wi~~s-------~~~~CelC~~~y~~ 91 (177)
-|-.|-++. ++||+. |+|--- -||+.|- -.|+=.+ ...+||||-+++--
T Consensus 7 GCCVCSDErGWaeNPLVY---CDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGA 74 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVY---CDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGA 74 (900)
T ss_pred ceeeecCcCCCccCceee---ecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccc
Confidence 488897665 889884 555333 5999997 4677332 35789999988753
No 80
>KOG0802|consensus
Probab=27.69 E-value=25 Score=33.31 Aligned_cols=47 Identities=28% Similarity=0.747 Sum_probs=34.6
Q ss_pred CCCCeeEEcccCCCCcccccccccCccccccHHHHHHHHHHcCCCccCCCCCeeEeee
Q psy3116 36 EDMTICRICYGADQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTER 93 (177)
Q Consensus 36 ~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~ 93 (177)
...+.|+||.+.. ..-+.||. |-.||.+|+..+ ..|++|+.......
T Consensus 477 ~~~~~~~~~~~~~-~~~~~~~~--------~~~~l~~~~~~~--~~~pl~~~~~~~~~ 523 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-SARITPCS--------HALCLRKWLYVQ--EVCPLCHTYMKEDD 523 (543)
T ss_pred cccCcchHHHHHH-Hhcccccc--------chhHHHhhhhhc--cccCCCchhhhccc
Confidence 4468999998766 34455665 999999999764 46999987765544
No 81
>KOG1952|consensus
Probab=27.30 E-value=65 Score=32.93 Aligned_cols=55 Identities=22% Similarity=0.495 Sum_probs=38.9
Q ss_pred CCCCCeeEEcccCC--CCcccccccccCccccccHHHHHHHHHHc-----CCCccCCCCCeeEee
Q psy3116 35 DEDMTICRICYGAD--QQNLLSICQCKGSIAYVHIECIERWLQEC-----GVDKCDLCKYQFTTE 92 (177)
Q Consensus 35 ~~~~~~CRIC~~~~--~~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s-----~~~~CelC~~~y~~~ 92 (177)
+.+.-.|-||.+.- ..+.- .|+-=....|..|+++|-+.+ +.|+|+-|++.+...
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~W---SC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~ 249 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVW---SCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTV 249 (950)
T ss_pred hcCceEEEEeeeeccccCCce---ecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccC
Confidence 34557899998765 22222 244334669999999998765 478999999888743
No 82
>PF01440 Gemini_AL2: Geminivirus AL2 protein; InterPro: IPR000942 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=27.24 E-value=9.5 Score=30.33 Aligned_cols=33 Identities=24% Similarity=0.629 Sum_probs=27.7
Q ss_pred CcccccccccCccccccHHHHHHHHHHcCCCccCCC
Q psy3116 50 QNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85 (177)
Q Consensus 50 ~~Li~PC~C~Gs~~~VH~~CL~~Wi~~s~~~~CelC 85 (177)
..+--||.|. .|+|.+|-...+.++|+..|.--
T Consensus 31 RRIDL~CGCS---yyihinC~~hGFTHRGthhCsS~ 63 (134)
T PF01440_consen 31 RRIDLPCGCS---YYIHINCHNHGFTHRGTHHCSSS 63 (134)
T ss_pred CccccCCCCE---EEeecccCCCCcCCCcCccCCCc
Confidence 3455799998 79999999999999998888653
No 83
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=26.89 E-value=76 Score=29.53 Aligned_cols=49 Identities=27% Similarity=0.485 Sum_probs=33.0
Q ss_pred CCCCCeeEEcccCCCCcccccccccCccccccHH---HHHHHHHHcCCCccCCCCCeeEe
Q psy3116 35 DEDMTICRICYGADQQNLLSICQCKGSIAYVHIE---CIERWLQECGVDKCDLCKYQFTT 91 (177)
Q Consensus 35 ~~~~~~CRIC~~~~~~~Li~PC~C~Gs~~~VH~~---CL~~Wi~~s~~~~CelC~~~y~~ 91 (177)
+++..+|-||-++-.-.-+.||. |+- |-.+-..-=.+..|.+|+++...
T Consensus 58 DEen~~C~ICA~~~TYs~~~PC~--------H~~CH~Ca~RlRALY~~K~C~~CrTE~e~ 109 (493)
T COG5236 58 DEENMNCQICAGSTTYSARYPCG--------HQICHACAVRLRALYMQKGCPLCRTETEA 109 (493)
T ss_pred ccccceeEEecCCceEEEeccCC--------chHHHHHHHHHHHHHhccCCCccccccce
Confidence 46678999997766444567876 444 44444444467889999998653
No 84
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=26.71 E-value=49 Score=33.35 Aligned_cols=22 Identities=27% Similarity=0.495 Sum_probs=16.5
Q ss_pred cCCCCCCCCCCCCeeEEcccCC
Q psy3116 27 LDKPDSSDDEDMTICRICYGAD 48 (177)
Q Consensus 27 ~~~~~~~~~~~~~~CRIC~~~~ 48 (177)
.++..+..++.+..|.||+||.
T Consensus 457 l~~~~~l~ee~gl~C~ICrEGy 478 (802)
T PF13764_consen 457 LQNMEDLEEEDGLTCCICREGY 478 (802)
T ss_pred hcCcccccccCCCeEEEcCCcc
Confidence 3344445578899999999997
No 85
>KOG0825|consensus
Probab=26.33 E-value=15 Score=37.30 Aligned_cols=29 Identities=21% Similarity=0.557 Sum_probs=22.6
Q ss_pred ccccHHHHHHHHHHcCCCccCCCCCeeEeee
Q psy3116 63 AYVHIECIERWLQECGVDKCDLCKYQFTTER 93 (177)
Q Consensus 63 ~~VH~~CL~~Wi~~s~~~~CelC~~~y~~~~ 93 (177)
.|.|..|+..|-+. ..+|++|+.+|--..
T Consensus 146 H~FC~~Ci~sWsR~--aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 146 HYFCEECVGSWSRC--AQTCPVDRGEFGEVK 174 (1134)
T ss_pred cccHHHHhhhhhhh--cccCchhhhhhheee
Confidence 38889999999654 468999999997443
No 86
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.54 E-value=75 Score=20.56 Aligned_cols=25 Identities=20% Similarity=0.543 Sum_probs=12.3
Q ss_pred HHHHHHHHc-CCC-ccCCCCCeeEeee
Q psy3116 69 CIERWLQEC-GVD-KCDLCKYQFTTER 93 (177)
Q Consensus 69 CL~~Wi~~s-~~~-~CelC~~~y~~~~ 93 (177)
=+.+.+..- +.. .|++|+.+|.-..
T Consensus 8 ~~~k~i~~l~~~~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 8 ELKKYIEELKEAKGCCPLCGRPLDEEH 34 (54)
T ss_dssp HHHHHHHHHTT-SEE-TTT--EE-HHH
T ss_pred HHHHHHHHHhcCCCcCCCCCCCCCHHH
Confidence 355666442 223 8999999997543
No 88
>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=23.28 E-value=17 Score=24.40 Aligned_cols=21 Identities=19% Similarity=0.702 Sum_probs=12.1
Q ss_pred HHHHHcCCCccCCCCCeeEee
Q psy3116 72 RWLQECGVDKCDLCKYQFTTE 92 (177)
Q Consensus 72 ~Wi~~s~~~~CelC~~~y~~~ 92 (177)
.|...+....|.+|+..|.+.
T Consensus 2 ~W~~d~~~~~C~~C~~~F~~~ 22 (69)
T PF01363_consen 2 HWVPDSEASNCMICGKKFSLF 22 (69)
T ss_dssp -SSSGGG-SB-TTT--B-BSS
T ss_pred CcCCCCCCCcCcCcCCcCCCc
Confidence 577777888999999999764
No 89
>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=22.49 E-value=57 Score=21.16 Aligned_cols=35 Identities=23% Similarity=0.481 Sum_probs=14.7
Q ss_pred cccccccccCccccccHHHH--HHHHHH---cCCCccCCCCCe
Q psy3116 51 NLLSICQCKGSIAYVHIECI--ERWLQE---CGVDKCDLCKYQ 88 (177)
Q Consensus 51 ~Li~PC~C~Gs~~~VH~~CL--~~Wi~~---s~~~~CelC~~~ 88 (177)
.+..|.+=+ ...|..|+ +.|+.. .+.+.|++|+.+
T Consensus 11 ~i~~P~Rg~---~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 11 RIRIPVRGK---NCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-SSEEEET---T--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred EEEeCccCC---cCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 444565533 46788884 567754 467999999863
No 90
>PF07787 DUF1625: Protein of unknown function (DUF1625); InterPro: IPR012430 Sequences making up this family are derived from hypothetical proteins expressed by both prokaryotic and eukaryotic species. The region in question is approximately 250 residues long.
Probab=22.38 E-value=78 Score=26.74 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHhhhhh
Q psy3116 126 TFLFSPFIILLTLSGYQ 142 (177)
Q Consensus 126 ~l~ltpi~i~~~~L~~~ 142 (177)
.+.++.++|+.+|+.|+
T Consensus 231 s~~lsl~~Ia~aW~~yR 247 (248)
T PF07787_consen 231 SFSLSLLTIALAWLFYR 247 (248)
T ss_pred HHHHHHHHHHHhheeeC
Confidence 33444445555565544
No 91
>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=21.99 E-value=85 Score=17.83 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=10.3
Q ss_pred CCCccCCCCCeeE
Q psy3116 78 GVDKCDLCKYQFT 90 (177)
Q Consensus 78 ~~~~CelC~~~y~ 90 (177)
+...|++|+..|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 3467999999876
No 92
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.99 E-value=35 Score=18.15 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=9.1
Q ss_pred ccCCCCCeeEe
Q psy3116 81 KCDLCKYQFTT 91 (177)
Q Consensus 81 ~CelC~~~y~~ 91 (177)
.|++|+..|.-
T Consensus 2 ~C~~C~~~f~s 12 (25)
T PF12874_consen 2 YCDICNKSFSS 12 (25)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCCcCC
Confidence 69999998863
No 93
>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=21.57 E-value=42 Score=18.66 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=10.3
Q ss_pred CCCccCCCCCeeE
Q psy3116 78 GVDKCDLCKYQFT 90 (177)
Q Consensus 78 ~~~~CelC~~~y~ 90 (177)
+.-.|+.|+..|.
T Consensus 13 k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 13 KPYKCPYCGKSFS 25 (26)
T ss_dssp SSEEESSSSEEES
T ss_pred CCCCCCCCcCeeC
Confidence 3568999999884
No 94
>PF05417 Peptidase_C41: Hepatitis E cysteine protease; InterPro: IPR008748 This entry represents the cysteine proteinase of hepatitis E virus, which is a papain-like protease that cleaves the viral polyprotein encoded by ORF1 of the hepatitis E virus (Porcine hemagglutinating encephalomyelitis virus) [, , ].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=20.67 E-value=27 Score=28.10 Aligned_cols=23 Identities=26% Similarity=0.780 Sum_probs=18.6
Q ss_pred ccccccCccccccHH--HHHHHHHH
Q psy3116 54 SICQCKGSIAYVHIE--CIERWLQE 76 (177)
Q Consensus 54 ~PC~C~Gs~~~VH~~--CL~~Wi~~ 76 (177)
.||+|..-++-+-.+ |+.+|+.+
T Consensus 24 ~~CrCr~~~r~~~~k~CCfmrwLgQ 48 (161)
T PF05417_consen 24 VPCRCRSFLRKAAKKFCCFMRWLGQ 48 (161)
T ss_pred cccccHHHHHHHhhCceehhhhhcc
Confidence 799999877766554 79999976
No 95
>PF01708 Gemini_mov: Geminivirus putative movement protein ; InterPro: IPR002621 This family consists of putative movement proteins from Maize streak virus and Wheat dwarf virus [].; GO: 0046740 spread of virus in host, cell to cell, 0016021 integral to membrane
Probab=20.50 E-value=51 Score=24.62 Aligned_cols=19 Identities=16% Similarity=0.168 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHhhhhhccc
Q psy3116 127 FLFSPFIILLTLSGYQTFS 145 (177)
Q Consensus 127 l~ltpi~i~~~~L~~~~fs 145 (177)
++++.+++++.||.|..|-
T Consensus 41 ~i~~lvaVg~~YL~y~~fL 59 (91)
T PF01708_consen 41 AIFTLVAVGCLYLAYTWFL 59 (91)
T ss_pred eehHHHHHHHHHHHHHHHH
Confidence 4555678888999998887
Done!