Query 025381
Match_columns 253
No_of_seqs 253 out of 806
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:13:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025381.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025381hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12428 DUF3675: Protein of u 100.0 6.6E-40 1.4E-44 267.3 6.9 115 113-241 1-118 (118)
2 KOG1609 Protein involved in mR 99.8 2E-20 4.4E-25 168.8 4.3 187 54-253 73-269 (323)
3 PHA02825 LAP/PHD finger-like p 99.8 3.9E-19 8.4E-24 151.5 4.7 68 54-124 3-70 (162)
4 PHA02862 5L protein; Provision 99.7 1.5E-17 3.3E-22 140.0 3.7 63 59-124 2-64 (156)
5 smart00744 RINGv The RING-vari 99.7 1.7E-17 3.8E-22 116.2 2.9 48 61-108 1-49 (49)
6 PF12906 RINGv: RING-variant d 99.6 2.9E-17 6.4E-22 114.1 1.4 46 62-107 1-47 (47)
7 KOG3053 Uncharacterized conser 99.5 5.8E-15 1.2E-19 134.3 3.7 67 54-120 15-90 (293)
8 COG5183 SSM4 Protein involved 99.5 1.6E-14 3.4E-19 146.8 4.0 58 56-113 9-67 (1175)
9 PF13639 zf-RING_2: Ring finge 97.7 1.5E-05 3.3E-10 53.5 1.5 41 61-108 2-44 (44)
10 KOG4628 Predicted E3 ubiquitin 97.4 0.00019 4.2E-09 68.6 4.4 48 60-113 230-279 (348)
11 PHA02929 N1R/p28-like protein; 97.1 0.00041 8.8E-09 63.3 3.3 50 57-113 172-228 (238)
12 cd00162 RING RING-finger (Real 97.1 0.00043 9.3E-09 44.4 2.5 44 61-110 1-44 (45)
13 COG5540 RING-finger-containing 96.8 0.00098 2.1E-08 63.1 3.2 51 57-113 321-373 (374)
14 PLN03208 E3 ubiquitin-protein 96.7 0.0016 3.5E-08 57.8 3.7 51 57-113 16-80 (193)
15 COG5243 HRD1 HRD ubiquitin lig 96.6 0.0031 6.7E-08 61.2 4.9 50 56-112 284-345 (491)
16 PF12678 zf-rbx1: RING-H2 zinc 96.5 0.0016 3.4E-08 48.9 1.9 41 61-108 21-73 (73)
17 PF00097 zf-C3HC4: Zinc finger 96.5 0.0016 3.4E-08 42.7 1.7 41 62-107 1-41 (41)
18 PF13920 zf-C3HC4_3: Zinc fing 96.5 0.0015 3.1E-08 45.1 1.5 46 59-112 2-48 (50)
19 smart00184 RING Ring finger. E 96.4 0.0026 5.6E-08 39.2 2.4 39 62-107 1-39 (39)
20 PF12861 zf-Apc11: Anaphase-pr 96.3 0.0031 6.7E-08 49.4 2.5 29 85-113 54-83 (85)
21 PF11793 FANCL_C: FANCL C-term 96.2 0.0017 3.6E-08 48.5 0.7 53 59-114 2-68 (70)
22 KOG0317 Predicted E3 ubiquitin 96.1 0.0086 1.9E-07 56.1 4.9 54 53-114 233-286 (293)
23 PHA02926 zinc finger-like prot 95.9 0.0066 1.4E-07 55.3 3.3 60 56-122 167-238 (242)
24 KOG0802 E3 ubiquitin ligase [P 95.6 0.0076 1.7E-07 60.3 2.6 49 57-112 289-341 (543)
25 KOG0828 Predicted E3 ubiquitin 95.3 0.015 3.3E-07 58.2 3.6 56 52-113 564-635 (636)
26 PF13923 zf-C3HC4_2: Zinc fing 94.8 0.013 2.8E-07 38.4 1.0 38 62-107 1-39 (39)
27 smart00504 Ubox Modified RING 94.4 0.045 9.8E-07 38.4 3.1 45 61-113 3-47 (63)
28 KOG1493 Anaphase-promoting com 93.9 0.018 3.9E-07 44.6 0.2 49 61-113 22-82 (84)
29 COG5219 Uncharacterized conser 93.6 0.019 4.2E-07 61.3 0.0 53 57-112 1467-1523(1525)
30 KOG0823 Predicted E3 ubiquitin 92.7 0.15 3.3E-06 46.5 4.2 53 55-113 43-96 (230)
31 KOG0827 Predicted E3 ubiquitin 92.6 0.096 2.1E-06 51.3 3.0 47 59-108 4-52 (465)
32 PF14634 zf-RING_5: zinc-RING 92.5 0.086 1.9E-06 35.4 1.9 42 61-109 1-44 (44)
33 COG5194 APC11 Component of SCF 91.4 0.11 2.3E-06 40.7 1.5 27 85-113 56-82 (88)
34 TIGR00599 rad18 DNA repair pro 91.4 0.13 2.8E-06 50.3 2.5 50 56-113 23-72 (397)
35 KOG1785 Tyrosine kinase negati 90.0 0.12 2.5E-06 51.0 0.7 50 57-112 367-416 (563)
36 PF14570 zf-RING_4: RING/Ubox 89.7 0.25 5.5E-06 34.9 2.1 45 62-112 1-48 (48)
37 PF05290 Baculo_IE-1: Baculovi 89.6 0.25 5.3E-06 42.0 2.3 56 58-114 79-134 (140)
38 PF05883 Baculo_RING: Baculovi 89.2 0.2 4.3E-06 42.4 1.4 42 56-99 23-69 (134)
39 KOG0804 Cytoplasmic Zn-finger 85.6 0.34 7.4E-06 48.2 0.9 51 55-112 171-222 (493)
40 KOG4265 Predicted E3 ubiquitin 84.4 1.1 2.4E-05 43.3 3.8 50 57-113 288-337 (349)
41 PF06210 DUF1003: Protein of u 84.2 5.6 0.00012 32.3 7.3 45 193-237 9-56 (108)
42 PLN02189 cellulose synthase 83.0 0.77 1.7E-05 49.8 2.3 52 57-112 32-87 (1040)
43 KOG2930 SCF ubiquitin ligase, 83.0 0.75 1.6E-05 37.6 1.7 27 85-113 83-109 (114)
44 PLN02436 cellulose synthase A 79.4 1.3 2.8E-05 48.3 2.5 52 57-112 34-89 (1094)
45 COG4420 Predicted membrane pro 78.5 8.4 0.00018 34.5 6.9 58 178-237 50-110 (191)
46 KOG4445 Uncharacterized conser 78.2 1.4 3.1E-05 42.1 2.1 53 57-114 113-188 (368)
47 PF15227 zf-C3HC4_4: zinc fing 78.1 1 2.3E-05 30.2 0.9 40 62-107 1-42 (42)
48 KOG0825 PHD Zn-finger protein 77.4 2.6 5.7E-05 44.9 3.9 30 76-112 142-171 (1134)
49 KOG1645 RING-finger-containing 75.6 2.1 4.6E-05 42.4 2.6 50 58-111 3-55 (463)
50 KOG2177 Predicted E3 ubiquitin 71.9 1.8 3.8E-05 36.7 0.9 46 56-109 10-55 (386)
51 TIGR00570 cdk7 CDK-activating 71.7 3.8 8.2E-05 39.1 3.2 50 59-114 3-56 (309)
52 PF13445 zf-RING_UBOX: RING-ty 70.9 2.4 5.2E-05 28.9 1.2 39 62-105 1-43 (43)
53 COG5432 RAD18 RING-finger-cont 70.3 2 4.3E-05 41.1 1.0 48 57-112 23-70 (391)
54 KOG1002 Nucleotide excision re 70.0 3.1 6.6E-05 42.7 2.2 58 55-118 532-592 (791)
55 PF04564 U-box: U-box domain; 68.8 2.6 5.7E-05 31.2 1.2 46 61-113 6-51 (73)
56 PF07800 DUF1644: Protein of u 68.5 5.9 0.00013 34.6 3.4 38 59-98 2-48 (162)
57 PLN02638 cellulose synthase A 64.7 5.4 0.00012 43.7 3.0 52 58-112 16-70 (1079)
58 PLN02195 cellulose synthase A 64.5 5.9 0.00013 43.0 3.2 52 58-112 5-59 (977)
59 KOG1734 Predicted RING-contain 64.1 2.2 4.7E-05 40.4 -0.1 65 55-135 220-293 (328)
60 KOG0320 Predicted E3 ubiquitin 63.4 6.4 0.00014 35.0 2.7 51 53-110 125-176 (187)
61 PF08746 zf-RING-like: RING-li 61.3 4.5 9.8E-05 27.4 1.1 22 86-107 22-43 (43)
62 PF10272 Tmpp129: Putative tra 58.3 11 0.00023 36.8 3.4 35 75-112 306-351 (358)
63 KOG0287 Postreplication repair 57.1 4 8.7E-05 39.8 0.4 47 58-112 22-68 (442)
64 PF10367 Vps39_2: Vacuolar sor 56.9 3.8 8.3E-05 31.2 0.2 33 57-94 76-109 (109)
65 PLN02915 cellulose synthase A 55.6 11 0.00023 41.5 3.2 54 56-112 12-68 (1044)
66 PF05191 ADK_lid: Adenylate ki 49.7 7.1 0.00015 25.7 0.5 19 102-120 2-20 (36)
67 KOG1941 Acetylcholine receptor 49.5 8.9 0.00019 38.1 1.4 48 57-109 363-413 (518)
68 KOG1039 Predicted E3 ubiquitin 48.3 14 0.0003 35.8 2.5 51 57-112 159-221 (344)
69 PLN02400 cellulose synthase 46.2 15 0.00032 40.5 2.5 53 57-112 34-89 (1085)
70 PF14569 zf-UDP: Zinc-binding 45.4 25 0.00054 27.4 3.0 55 57-114 7-64 (80)
71 KOG1952 Transcription factor N 45.2 14 0.00031 39.7 2.2 56 55-112 187-247 (950)
72 COG5574 PEX10 RING-finger-cont 43.7 27 0.00059 32.8 3.5 53 54-113 210-263 (271)
73 KOG2164 Predicted E3 ubiquitin 39.2 27 0.00058 35.6 3.0 50 59-114 186-238 (513)
74 COG5175 MOT2 Transcriptional r 35.0 35 0.00076 33.5 3.0 50 58-113 13-65 (480)
75 PF13894 zf-C2H2_4: C2H2-type 33.6 16 0.00035 19.9 0.3 11 103-113 2-12 (24)
76 PF11874 DUF3394: Domain of un 31.8 29 0.00063 30.8 1.7 21 230-250 162-182 (183)
77 PF00096 zf-C2H2: Zinc finger, 30.2 19 0.00042 20.2 0.2 12 103-114 2-13 (23)
78 KOG3899 Uncharacterized conser 29.0 36 0.00078 32.8 1.9 28 86-113 328-366 (381)
79 KOG0955 PHD finger protein BR1 28.7 18 0.00039 39.8 -0.1 51 57-109 217-268 (1051)
80 PF04423 Rad50_zn_hook: Rad50 28.6 34 0.00073 23.8 1.3 23 91-113 8-32 (54)
81 COG2322 Predicted membrane pro 27.7 2.5E+02 0.0054 25.0 6.7 61 183-243 78-144 (177)
82 PF05210 Sprouty: Sprouty prot 27.0 47 0.001 27.2 2.0 18 75-97 59-76 (108)
83 KOG0802 E3 ubiquitin ligase [P 26.8 28 0.00062 35.1 0.9 48 55-114 475-522 (543)
84 PF04641 Rtf2: Rtf2 RING-finge 26.0 59 0.0013 29.7 2.7 51 56-114 110-163 (260)
85 PF10571 UPF0547: Uncharacteri 25.7 33 0.00071 21.1 0.7 12 101-112 14-25 (26)
86 PF04532 DUF587: Protein of un 25.6 24 0.00052 32.0 0.1 17 74-90 105-121 (215)
87 KOG1428 Inhibitor of type V ad 24.3 72 0.0016 37.3 3.4 55 55-112 3482-3544(3738)
88 KOG4172 Predicted E3 ubiquitin 23.4 51 0.0011 24.3 1.4 43 60-112 8-54 (62)
89 KOG0801 Predicted E3 ubiquitin 23.1 44 0.00095 29.7 1.2 25 56-80 174-200 (205)
90 PRK12860 transcriptional activ 22.3 43 0.00094 29.9 1.1 28 75-108 134-161 (189)
91 COG5236 Uncharacterized conser 22.1 1E+02 0.0022 30.6 3.6 54 54-113 56-109 (493)
92 COG1983 PspC Putative stress-r 22.1 1E+02 0.0022 23.5 2.8 15 226-240 45-59 (70)
93 PF02891 zf-MIZ: MIZ/SP-RING z 22.1 59 0.0013 22.6 1.5 35 73-110 11-50 (50)
94 COG4846 CcdC Membrane protein 21.3 3.6E+02 0.0077 23.3 6.3 44 193-237 99-142 (163)
95 PF11431 Transport_MerF: Membr 21.3 1.9E+02 0.0042 20.3 3.9 21 230-250 24-46 (46)
96 smart00249 PHD PHD zinc finger 21.1 28 0.00061 21.9 -0.3 29 62-93 2-30 (47)
97 PRK11877 psaI photosystem I re 20.8 1.4E+02 0.0029 20.3 2.9 34 212-245 3-36 (38)
98 KOG0956 PHD finger protein AF1 20.6 50 0.0011 35.2 1.3 57 57-113 115-183 (900)
99 PRK12722 transcriptional activ 20.5 50 0.0011 29.4 1.1 29 75-109 134-162 (187)
No 1
>PF12428 DUF3675: Protein of unknown function (DUF3675) ; InterPro: IPR022143 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF00097 from PFAM. There are two completely conserved residues (R and L) that may be functionally important.
Probab=100.00 E-value=6.6e-40 Score=267.31 Aligned_cols=115 Identities=55% Similarity=1.064 Sum_probs=111.5
Q ss_pred cCccCCCCcccccc---ccCCCceeccccCCCCCeEEEEeeccccccccCCccccCCCCCcceehhhhhhhhhhhhhhhh
Q 025381 113 PGYTAPPPLFRYGG---NFRANWEISGRDLHHNPQLITMVTGEREFLDSDFDEYYTPSSRSLICCRIVAITVHLSLTLFG 189 (253)
Q Consensus 113 ~~yt~p~~~~~~~~---~~~~~W~i~~~dl~~~~~~iam~~~e~~~l~~~~~~~~~~~~~~~~~cR~~al~~~~~~t~~~ 189 (253)
|+||+|+|+++.++ ++|++|+++++|+++ +++++|+.+|++++|+||++|+.+|++|++||||+||
T Consensus 1 PgYTaPp~~~~~~~~~i~ir~~we~~~~d~~~-~~~~a~~~ae~~~l~~~y~e~~~~~~~~a~~CRsvAl---------- 69 (118)
T PF12428_consen 1 PGYTAPPKKFQPGETAIDIRGNWEISRRDLRD-PRFLAMAAAERQFLESEYDEYAASNTRGAACCRSVAL---------- 69 (118)
T ss_pred CCCCCCCCCCCcCccceEecCCccccccCccc-hhhhhhhhhhhhccccccccccccCCCceeHHHHHHH----------
Confidence 68999999999987 899999999999987 9999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhhheeecCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 025381 190 VRSLFMVLLVLRHTLPIIISGAGEYSLTLFTLLILRTIGILLPIYVMVKAFT 241 (253)
Q Consensus 190 v~~i~~~lLvlrh~l~l~~~~~~~~~~~~~t~~~lra~GillP~yi~~~~i~ 241 (253)
|||+||||||+++++.+|+|+|++++||+++||++||+||||||+|+|+
T Consensus 70 ---i~m~LLllRhal~l~~~~~~~~s~~lftl~~LRaaGilLP~Yim~rais 118 (118)
T PF12428_consen 70 ---IFMVLLLLRHALALVTGGAEDYSFTLFTLLLLRAAGILLPCYIMARAIS 118 (118)
T ss_pred ---HHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 9999999999999999999999999999999999999999999999984
No 2
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.80 E-value=2e-20 Score=168.75 Aligned_cols=187 Identities=29% Similarity=0.431 Sum_probs=134.6
Q ss_pred CCCCCCCeeeEeccCCCCC---CcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccCccCCCCcccccc---c
Q 025381 54 SSPSKLVECRICHEEDEDS---NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPGYTAPPPLFRYGG---N 127 (253)
Q Consensus 54 ~~~~~~~~CRIC~ee~~d~---~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~yt~p~~~~~~~~---~ 127 (253)
+.+.++..||||+++.++. .++.||.|+|+++|||+.|+++|+..|++..||+|++.|.+.++.+++...+.. .
T Consensus 73 ~~~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~~~~~~~~~~~~~~~ 152 (323)
T KOG1609|consen 73 ESPSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGTKLKPLIVISKVRSG 152 (323)
T ss_pred cCCCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecceeecceeehhhhhhH
Confidence 4566678999999987543 599999999999999999999999999999999999999998888777665433 1
Q ss_pred cCCCceeccccCCCCCeEEEEeeccccccccCCccccCCCCCcceehhhhh-hhhhhhhhhhhhHHHHHHHHHHHhhhhe
Q 025381 128 FRANWEISGRDLHHNPQLITMVTGEREFLDSDFDEYYTPSSRSLICCRIVA-ITVHLSLTLFGVRSLFMVLLVLRHTLPI 206 (253)
Q Consensus 128 ~~~~W~i~~~dl~~~~~~iam~~~e~~~l~~~~~~~~~~~~~~~~~cR~~a-l~~~~~~t~~~v~~i~~~lLvlrh~l~l 206 (253)
..+.|..........+..+++......++...++++....+..+..++.+. + .+.++.+.++.+++
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~i~~ 219 (323)
T KOG1609|consen 153 ALSERTLSGMILLKVALLVAIIVSVLPLLLGLLFELVLGVPSLVVESPLANPL-------------ALVALGLLGFKIWI 219 (323)
T ss_pred hhhheeeehhhhhhhhhhheeeEEeehhhhhhhHHHhccccccccCCCccCch-------------hheeecceechHHH
Confidence 223444444322222566677666677777666666666666667777766 3 44444445555544
Q ss_pred eecC---CCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhcC
Q 025381 207 IISG---AGEYSLTLFTLLILRTIGILLPIYVMVKAFTAIQRRRHQQVNY 253 (253)
Q Consensus 207 ~~~~---~~~~~~~~~t~~~lra~GillP~yi~~~~i~~~q~~r~q~~~~ 253 (253)
.... ...+..+.+.+.+.|+.+++++.+++++++...|.++.+.+.|
T Consensus 220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 (323)
T KOG1609|consen 220 FIILSGYIFILKSLKVKLVLIRAVIFLLLIKVVLAAVVILQLLLQRLVGY 269 (323)
T ss_pred HHHHHHHHHHHHHHHHHHhHhhhhccchhhhhhhhhHHHHHHHHhcceeE
Confidence 3211 1256777788899999999999999987777778887776654
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.76 E-value=3.9e-19 Score=151.50 Aligned_cols=68 Identities=24% Similarity=0.546 Sum_probs=57.3
Q ss_pred CCCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccCccCCCCcccc
Q 025381 54 SSPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPGYTAPPPLFRY 124 (253)
Q Consensus 54 ~~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~yt~p~~~~~~ 124 (253)
+.+...+.||||+++++ .+.+||+|+||+||||++||++|++.+++..||+|+++|.... ..+|+.+|
T Consensus 3 ~~s~~~~~CRIC~~~~~--~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~-~~kpl~~W 70 (162)
T PHA02825 3 DVSLMDKCCWICKDEYD--VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK-NYKKCTKW 70 (162)
T ss_pred CcCCCCCeeEecCCCCC--CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEE-ecCCCccc
Confidence 34567889999998864 4679999999999999999999999999999999999999763 44555443
No 4
>PHA02862 5L protein; Provisional
Probab=99.68 E-value=1.5e-17 Score=140.03 Aligned_cols=63 Identities=25% Similarity=0.602 Sum_probs=53.6
Q ss_pred CCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccCccCCCCcccc
Q 025381 59 LVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPGYTAPPPLFRY 124 (253)
Q Consensus 59 ~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~yt~p~~~~~~ 124 (253)
...||||++++++. .+||+|+||+||||++||++|++.+++..||+|+++|... +..+|+.+|
T Consensus 2 ~diCWIC~~~~~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik-~~yKpf~kW 64 (156)
T PHA02862 2 SDICWICNDVCDER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK-KTYVSFKKW 64 (156)
T ss_pred CCEEEEecCcCCCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE-EccccHHHh
Confidence 35899999997544 6999999999999999999999999999999999999864 344455555
No 5
>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=99.68 E-value=1.7e-17 Score=116.16 Aligned_cols=48 Identities=58% Similarity=1.342 Sum_probs=43.8
Q ss_pred eeeEeccC-CCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccc
Q 025381 61 ECRICHEE-DEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICR 108 (253)
Q Consensus 61 ~CRIC~ee-~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~ 108 (253)
.||||+++ +++++++.||+|+|+++|||++||++|+.++++.+||+|+
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 59999984 3456899999999999999999999999999999999996
No 6
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.65 E-value=2.9e-17 Score=114.09 Aligned_cols=46 Identities=52% Similarity=1.279 Sum_probs=37.6
Q ss_pred eeEeccCCCCC-CcccCcccCCCCccccHHHHHHHHHhcCCcccccc
Q 025381 62 CRICHEEDEDS-NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEIC 107 (253)
Q Consensus 62 CRIC~ee~~d~-~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC 107 (253)
||||+++++++ +|++||.|+||++|||++||++|+..+++.+||+|
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 89999987644 69999999999999999999999999999999998
No 7
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.52 E-value=5.8e-15 Score=134.29 Aligned_cols=67 Identities=31% Similarity=0.737 Sum_probs=58.3
Q ss_pred CCCCCCCeeeEeccCCCCCC---cccCcccCCCCccccHHHHHHHHHhcC------CccccccccccccCccCCCC
Q 025381 54 SSPSKLVECRICHEEDEDSN---MEIPCSCCGSLKYAHRKCVQRWCNEKG------DTTCEICREQYNPGYTAPPP 120 (253)
Q Consensus 54 ~~~~~~~~CRIC~ee~~d~~---L~~PC~C~GslkyvH~~CL~~W~~~k~------~~~CEiC~~~y~~~yt~p~~ 120 (253)
+..+.++.||||+..++|+. +++||.|+|+.||||+.||.+|+++|. ...|++|+++|...|+...+
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~ 90 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGP 90 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccCh
Confidence 45677899999999988763 899999999999999999999999874 57999999999988765544
No 8
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.48 E-value=1.6e-14 Score=146.76 Aligned_cols=58 Identities=40% Similarity=0.960 Sum_probs=52.8
Q ss_pred CCCCCeeeEeccCC-CCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 56 PSKLVECRICHEED-EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 56 ~~~~~~CRIC~ee~-~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
.++...||||+.|+ +|+||-+||+|+||+||+|++||.+|...+++++|++|+++|+.
T Consensus 9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 34558999999887 67899999999999999999999999999999999999998863
No 9
>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=97.71 E-value=1.5e-05 Score=53.53 Aligned_cols=41 Identities=39% Similarity=1.066 Sum_probs=31.3
Q ss_pred eeeEeccCCC--CCCcccCcccCCCCccccHHHHHHHHHhcCCccccccc
Q 025381 61 ECRICHEEDE--DSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICR 108 (253)
Q Consensus 61 ~CRIC~ee~~--d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~ 108 (253)
.|-||+++.+ +.....||. +.+|.+|+++|++.+ .+|++|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCG-----HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTS-----EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCC-----CeeCHHHHHHHHHhC--CcCCccC
Confidence 6899999853 334566653 899999999999885 4999996
No 10
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=0.00019 Score=68.57 Aligned_cols=48 Identities=29% Similarity=0.773 Sum_probs=39.7
Q ss_pred CeeeEeccCCCCCC--cccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 60 VECRICHEEDEDSN--MEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 60 ~~CRIC~ee~~d~~--L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
..|-||+|+..++. -+.||+ +..|..|+..|+.+. .+.|++||+.-..
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 79999999975443 369998 789999999999877 5579999996553
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.09 E-value=0.00041 Score=63.29 Aligned_cols=50 Identities=32% Similarity=0.684 Sum_probs=37.7
Q ss_pred CCCCeeeEeccCCCCCC-------cccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 57 SKLVECRICHEEDEDSN-------MEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~-------L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+...+|-||+++..+.+ ...||. +..|..|+.+|+.. ..+||+|+.++..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~~--~~tCPlCR~~~~~ 228 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCN-----HVFCIECIDIWKKE--KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCC-----CcccHHHHHHHHhc--CCCCCCCCCEeeE
Confidence 34679999999743221 345564 88999999999965 4589999998873
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=97.08 E-value=0.00043 Score=44.42 Aligned_cols=44 Identities=36% Similarity=0.949 Sum_probs=33.3
Q ss_pred eeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccc
Q 025381 61 ECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQ 110 (253)
Q Consensus 61 ~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~ 110 (253)
.|-||++...+.....||. +.+|..|+.+|+.. +...|++|+..
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 4789988763333455565 67999999999976 56789999875
No 13
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.79 E-value=0.00098 Score=63.05 Aligned_cols=51 Identities=33% Similarity=0.725 Sum_probs=39.8
Q ss_pred CCCCeeeEeccCC--CCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 57 SKLVECRICHEED--EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~--~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
....+|-||.+.. .|.-++.||+ +-.|..|+.+|+..- ..+|++|+.+.+|
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~-----H~FH~~Cv~kW~~~y-~~~CPvCrt~iPP 373 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCD-----HRFHVGCVDKWLLGY-SNKCPVCRTAIPP 373 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccC-----ceechhHHHHHHhhh-cccCCccCCCCCC
Confidence 3458999999885 3445789998 789999999999732 2479999987653
No 14
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=96.69 E-value=0.0016 Score=57.84 Aligned_cols=51 Identities=16% Similarity=0.585 Sum_probs=40.3
Q ss_pred CCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHh--------------cCCcccccccccccc
Q 025381 57 SKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNE--------------KGDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~--------------k~~~~CEiC~~~y~~ 113 (253)
.+..+|-||++... .+.+.||. +.....||.+|+.. ++...|++|+.++..
T Consensus 16 ~~~~~CpICld~~~-dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVR-DPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCC-CcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 35678999998764 46778875 78999999999863 235689999998864
No 15
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0031 Score=61.20 Aligned_cols=50 Identities=30% Similarity=0.751 Sum_probs=38.6
Q ss_pred CCCCCeeeEeccCC--CC----------CCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 56 PSKLVECRICHEED--ED----------SNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 56 ~~~~~~CRIC~ee~--~d----------~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.+....|-||.+|- .+ .|-..||. +..|-+||+.|+..++ +|+||+.+..
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~ERqQ--TCPICr~p~i 345 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLERQQ--TCPICRRPVI 345 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHHhcc--CCCcccCccc
Confidence 45677999999982 11 23467887 7899999999997654 8999999844
No 16
>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=96.48 E-value=0.0016 Score=48.85 Aligned_cols=41 Identities=37% Similarity=0.918 Sum_probs=28.5
Q ss_pred eeeEeccCCCC-----------CC-cccCcccCCCCccccHHHHHHHHHhcCCccccccc
Q 025381 61 ECRICHEEDED-----------SN-MEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICR 108 (253)
Q Consensus 61 ~CRIC~ee~~d-----------~~-L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~ 108 (253)
.|-||+++-.+ -+ ...+|+ +..|..||.+|++.+. +|++|+
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~-----H~FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCG-----HIFHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTS-----EEEEHHHHHHHHTTSS--B-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccC-----CCEEHHHHHHHHhcCC--cCCCCC
Confidence 49999887421 11 234554 8899999999996554 999996
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=96.46 E-value=0.0016 Score=42.67 Aligned_cols=41 Identities=34% Similarity=0.944 Sum_probs=34.6
Q ss_pred eeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccc
Q 025381 62 CRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEIC 107 (253)
Q Consensus 62 CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC 107 (253)
|.||++...+.....||. +.+...|+.+|++.++...|++|
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 778988876544589987 78999999999998888889987
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=96.45 E-value=0.0015 Score=45.05 Aligned_cols=46 Identities=28% Similarity=0.689 Sum_probs=36.1
Q ss_pred CCeeeEeccCCCCCCcccCcccCCCCcc-ccHHHHHHHHHhcCCccccccccccc
Q 025381 59 LVECRICHEEDEDSNMEIPCSCCGSLKY-AHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 59 ~~~CRIC~ee~~d~~L~~PC~C~Gslky-vH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
...|.||++... +....||+ +. +-..|+.+|.+ +..+|++|+++++
T Consensus 2 ~~~C~iC~~~~~-~~~~~pCg-----H~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR-DVVLLPCG-----HLCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS-SEEEETTC-----EEEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred cCCCccCCccCC-ceEEeCCC-----ChHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 357999998864 36788987 56 89999999998 6679999998875
No 19
>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=96.43 E-value=0.0026 Score=39.22 Aligned_cols=39 Identities=38% Similarity=1.026 Sum_probs=30.1
Q ss_pred eeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccc
Q 025381 62 CRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEIC 107 (253)
Q Consensus 62 CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC 107 (253)
|.||++.. ......||. +..|..|+.+|++ ++...|++|
T Consensus 1 C~iC~~~~-~~~~~~~C~-----H~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL-KDPVVLPCG-----HTFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcCccCC-CCcEEecCC-----ChHHHHHHHHHHH-hCcCCCCCC
Confidence 67888773 346678876 5789999999998 455678877
No 20
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.27 E-value=0.0031 Score=49.36 Aligned_cols=29 Identities=21% Similarity=0.743 Sum_probs=25.4
Q ss_pred ccccHHHHHHHHHhc-CCcccccccccccc
Q 025381 85 KYAHRKCVQRWCNEK-GDTTCEICREQYNP 113 (253)
Q Consensus 85 kyvH~~CL~~W~~~k-~~~~CEiC~~~y~~ 113 (253)
+-+|..||.+|++.. .+..|++|+++|+.
T Consensus 54 H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 54 HNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred cHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 789999999999863 46799999999875
No 21
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.20 E-value=0.0017 Score=48.48 Aligned_cols=53 Identities=25% Similarity=0.387 Sum_probs=25.7
Q ss_pred CCeeeEeccCCC-C-CC--c-ccCcccCCCCccccHHHHHHHHHhc--C-------CccccccccccccC
Q 025381 59 LVECRICHEEDE-D-SN--M-EIPCSCCGSLKYAHRKCVQRWCNEK--G-------DTTCEICREQYNPG 114 (253)
Q Consensus 59 ~~~CRIC~ee~~-d-~~--L-~~PC~C~GslkyvH~~CL~~W~~~k--~-------~~~CEiC~~~y~~~ 114 (253)
+..|.||++... + .. + -....|. +..|..||.+|+... + ..+|+.|+++.+..
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 468999997642 2 22 2 2334674 689999999999752 1 23799999987643
No 22
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0086 Score=56.12 Aligned_cols=54 Identities=31% Similarity=0.897 Sum_probs=44.9
Q ss_pred CCCCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 53 GSSPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 53 ~~~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
.+.++....|-+|++.-+ ++--+||. +..=-.|++.|+.+|.. |++|+..++|.
T Consensus 233 ~~i~~a~~kC~LCLe~~~-~pSaTpCG-----HiFCWsCI~~w~~ek~e--CPlCR~~~~ps 286 (293)
T KOG0317|consen 233 SSIPEATRKCSLCLENRS-NPSATPCG-----HIFCWSCILEWCSEKAE--CPLCREKFQPS 286 (293)
T ss_pred ccCCCCCCceEEEecCCC-CCCcCcCc-----chHHHHHHHHHHccccC--CCcccccCCCc
Confidence 456788899999998864 36679987 67778999999988764 99999999874
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=95.93 E-value=0.0066 Score=55.33 Aligned_cols=60 Identities=25% Similarity=0.561 Sum_probs=43.5
Q ss_pred CCCCCeeeEeccCCC------CC--CcccCcccCCCCccccHHHHHHHHHhcC----CccccccccccccCccCCCCcc
Q 025381 56 PSKLVECRICHEEDE------DS--NMEIPCSCCGSLKYAHRKCVQRWCNEKG----DTTCEICREQYNPGYTAPPPLF 122 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~------d~--~L~~PC~C~GslkyvH~~CL~~W~~~k~----~~~CEiC~~~y~~~yt~p~~~~ 122 (253)
.+++.+|-||+|..- +. .+..||. +.....|+.+|.+.+. ...||+|+..|.. -.|.+.+
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~--I~pSrf~ 238 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRETGASDNCPICRTRFRN--ITMSKFY 238 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCC-----chHHHHHHHHHHHhccccCcCCcCCCCcceeee--eccccce
Confidence 456789999998731 11 3566776 7899999999998642 4679999999984 3444443
No 24
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.0076 Score=60.32 Aligned_cols=49 Identities=29% Similarity=0.657 Sum_probs=39.2
Q ss_pred CCCCeeeEeccCCCCC----CcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEEDEDS----NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~----~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.....|.||.|+-... +-..||. +-.|..||++|++. ..+|++|+..+.
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er--~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFER--QQTCPTCRTVLY 341 (543)
T ss_pred hcCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHH--hCcCCcchhhhh
Confidence 3477999999985432 6678887 78999999999987 458999999443
No 25
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.31 E-value=0.015 Score=58.19 Aligned_cols=56 Identities=27% Similarity=0.684 Sum_probs=42.3
Q ss_pred CCCCCCCCCeeeEeccCCC------C----------CCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 52 IGSSPSKLVECRICHEEDE------D----------SNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 52 ~~~~~~~~~~CRIC~ee~~------d----------~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+|..-+....|-||...-+ + +.+.+||. +..|+.||++|.+.. +..|++|+.+..+
T Consensus 564 ~~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~y-kl~CPvCR~pLPp 635 (636)
T KOG0828|consen 564 LEAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDTY-KLICPVCRCPLPP 635 (636)
T ss_pred ccchhhccccceEeccccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhhh-cccCCccCCCCCC
Confidence 3455678899999987631 1 24677998 789999999999743 2689999987643
No 26
>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=94.80 E-value=0.013 Score=38.39 Aligned_cols=38 Identities=26% Similarity=0.877 Sum_probs=29.0
Q ss_pred eeEeccCCCCCC-cccCcccCCCCccccHHHHHHHHHhcCCcccccc
Q 025381 62 CRICHEEDEDSN-MEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEIC 107 (253)
Q Consensus 62 CRIC~ee~~d~~-L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC 107 (253)
|-||++...+ + ...||. +...+.|+++|++. +.+|++|
T Consensus 1 C~iC~~~~~~-~~~~~~CG-----H~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD-PVVVTPCG-----HSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS-EEEECTTS-----EEEEHHHHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccC-cCEECCCC-----CchhHHHHHHHHHC--cCCCcCC
Confidence 6789887654 5 578887 78999999999977 3689987
No 27
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=94.38 E-value=0.045 Score=38.43 Aligned_cols=45 Identities=18% Similarity=0.351 Sum_probs=36.3
Q ss_pred eeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 61 ECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 61 ~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
.|.||.+.-.+ +...||. +-+-+.|+.+|+++ +.+|++|++++..
T Consensus 3 ~Cpi~~~~~~~-Pv~~~~G-----~v~~~~~i~~~~~~--~~~cP~~~~~~~~ 47 (63)
T smart00504 3 LCPISLEVMKD-PVILPSG-----QTYERRAIEKWLLS--HGTDPVTGQPLTH 47 (63)
T ss_pred CCcCCCCcCCC-CEECCCC-----CEEeHHHHHHHHHH--CCCCCCCcCCCCh
Confidence 58899887654 7788864 78999999999977 4589999998854
No 28
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=93.90 E-value=0.018 Score=44.63 Aligned_cols=49 Identities=27% Similarity=0.693 Sum_probs=36.0
Q ss_pred eeeEeccCC-----------CCCCcccCcccCCCCccccHHHHHHHHHhcC-Ccccccccccccc
Q 025381 61 ECRICHEED-----------EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKG-DTTCEICREQYNP 113 (253)
Q Consensus 61 ~CRIC~ee~-----------~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~-~~~CEiC~~~y~~ 113 (253)
.|-||..+. ++-||+-. .| .+.+|..|+.+|++.+. ...|+.|+++|+.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C---~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWG-YC---LHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHH-HH---HHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 677776553 23355444 55 37899999999999754 5799999999875
No 29
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.64 E-value=0.019 Score=61.26 Aligned_cols=53 Identities=26% Similarity=0.725 Sum_probs=38.9
Q ss_pred CCCCeeeEeccCCC--CCCc-ccCcc-cCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEEDE--DSNM-EIPCS-CCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~~--d~~L-~~PC~-C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
+.-.+|-||..--. |..+ ..-|. |+ .-.|..||-+|+++++..+||+|+.++.
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCk---nKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCK---NKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhh---hhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 55678999975421 2222 23444 43 4699999999999999999999998775
No 30
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.67 E-value=0.15 Score=46.55 Aligned_cols=53 Identities=17% Similarity=0.579 Sum_probs=43.2
Q ss_pred CCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcC-Ccccccccccccc
Q 025381 55 SPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKG-DTTCEICREQYNP 113 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~-~~~CEiC~~~y~~ 113 (253)
.+...-.|-||++...| +.+++|. +..==-||-+|+..+. ...|++||.+...
T Consensus 43 ~~~~~FdCNICLd~akd-PVvTlCG-----HLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAKD-PVVTLCG-----HLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCCceeeeeeccccCC-CEEeecc-----cceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 46778899999998865 8999997 5666789999998764 5677999997763
No 31
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.58 E-value=0.096 Score=51.28 Aligned_cols=47 Identities=26% Similarity=0.706 Sum_probs=32.5
Q ss_pred CCeeeEeccCCCCCCcccCcc-cCCCCccccHHHHHHHHHhcCC-ccccccc
Q 025381 59 LVECRICHEEDEDSNMEIPCS-CCGSLKYAHRKCVQRWCNEKGD-TTCEICR 108 (253)
Q Consensus 59 ~~~CRIC~ee~~d~~L~~PC~-C~GslkyvH~~CL~~W~~~k~~-~~CEiC~ 108 (253)
+..|.||-+..+...-..|=. | -+.+|..||++|+..... +.||||+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~c---Ghifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTC---GHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEeccCCccccccccccch---hhHHHHHHHHHHHccCCccCCCCcee
Confidence 568999944433222233333 4 278999999999986554 6999999
No 32
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=92.49 E-value=0.086 Score=35.43 Aligned_cols=42 Identities=29% Similarity=0.665 Sum_probs=34.3
Q ss_pred eeeEeccCC--CCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccc
Q 025381 61 ECRICHEED--EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICRE 109 (253)
Q Consensus 61 ~CRIC~ee~--~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~ 109 (253)
.|-||++.. +..+++.+|. +.+..+|++++. .....|++|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~Cg-----H~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCG-----HIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccC-----CHHHHHHHHhhc--CCCCCCcCCCC
Confidence 377898886 3346889987 889999999998 66789999985
No 33
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=91.44 E-value=0.11 Score=40.70 Aligned_cols=27 Identities=30% Similarity=0.755 Sum_probs=24.1
Q ss_pred ccccHHHHHHHHHhcCCcccccccccccc
Q 025381 85 KYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 85 kyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+-.|..|+.+|++.|+ .|++++++|+.
T Consensus 56 HaFH~HCI~rWL~Tk~--~CPld~q~w~~ 82 (88)
T COG5194 56 HAFHDHCIYRWLDTKG--VCPLDRQTWVL 82 (88)
T ss_pred hHHHHHHHHHHHhhCC--CCCCCCceeEE
Confidence 6799999999999966 79999999975
No 34
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.43 E-value=0.13 Score=50.34 Aligned_cols=50 Identities=20% Similarity=0.519 Sum_probs=40.0
Q ss_pred CCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 56 PSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
.+....|.||++... .+.+.||. +.+...|+.+|+..+ ..|++|+..+..
T Consensus 23 Le~~l~C~IC~d~~~-~PvitpCg-----H~FCs~CI~~~l~~~--~~CP~Cr~~~~~ 72 (397)
T TIGR00599 23 LDTSLRCHICKDFFD-VPVLTSCS-----HTFCSLCIRRCLSNQ--PKCPLCRAEDQE 72 (397)
T ss_pred cccccCCCcCchhhh-CccCCCCC-----CchhHHHHHHHHhCC--CCCCCCCCcccc
Confidence 346679999988764 46678887 788999999999764 389999998864
No 35
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=89.99 E-value=0.12 Score=51.01 Aligned_cols=50 Identities=30% Similarity=0.721 Sum_probs=41.1
Q ss_pred CCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
+.-..|.||-|.+.+ .-+.||. +..-..||..|..+.+...|+.|+.+.+
T Consensus 367 sTFeLCKICaendKd-vkIEPCG-----HLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 367 STFELCKICAENDKD-VKIEPCG-----HLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred chHHHHHHhhccCCC-ccccccc-----chHHHHHHHhhcccCCCCCCCceeeEec
Confidence 455689999777653 4578987 5777899999999888889999998887
No 36
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=89.72 E-value=0.25 Score=34.85 Aligned_cols=45 Identities=29% Similarity=0.671 Sum_probs=20.4
Q ss_pred eeEeccCCC-CCCcccCcccCCCCccccHHHHHHHHHhc--CCccccccccccc
Q 025381 62 CRICHEEDE-DSNMEIPCSCCGSLKYAHRKCVQRWCNEK--GDTTCEICREQYN 112 (253)
Q Consensus 62 CRIC~ee~~-d~~L~~PC~C~GslkyvH~~CL~~W~~~k--~~~~CEiC~~~y~ 112 (253)
|.+|.++.+ ...-..||.|. ++-|+.=|.+-+ ++..|+-|+++|+
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 556766642 33457999994 456666666544 4789999999985
No 37
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=89.64 E-value=0.25 Score=41.96 Aligned_cols=56 Identities=25% Similarity=0.637 Sum_probs=46.4
Q ss_pred CCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 58 KLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 58 ~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
..-+|-||+|...|+.+..|=.|.| -+.---=|.+-|.-.+-.-.||+|++.|+..
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCg-Y~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCG-YSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred CceeccCcccccchhhcCCcccccc-hHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 5678999999988889999999998 3445555678898777788999999999864
No 38
>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=89.19 E-value=0.2 Score=42.39 Aligned_cols=42 Identities=31% Similarity=0.657 Sum_probs=29.4
Q ss_pred CCCCCeeeEeccCCCC--CCcccCcccCCCC---ccccHHHHHHHHHhc
Q 025381 56 PSKLVECRICHEEDED--SNMEIPCSCCGSL---KYAHRKCVQRWCNEK 99 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~d--~~L~~PC~C~Gsl---kyvH~~CL~~W~~~k 99 (253)
+....+|+||++.-.+ +-...+| .|.+ |..|..|+++|-+++
T Consensus 23 ~~~~~EC~IC~~~I~~~~GvV~vt~--~g~lnLEkmfc~~C~~rw~~~~ 69 (134)
T PF05883_consen 23 PRCTVECQICFDRIDNNDGVVYVTD--GGTLNLEKMFCADCDKRWRRER 69 (134)
T ss_pred cccCeeehhhhhhhhcCCCEEEEec--CCeehHHHHHHHHHHHHHHhhc
Confidence 3457899999988544 4444554 4544 569999999996543
No 39
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=85.61 E-value=0.34 Score=48.21 Aligned_cols=51 Identities=22% Similarity=0.596 Sum_probs=35.7
Q ss_pred CCCCCCeeeEeccCCC-CCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 55 SPSKLVECRICHEEDE-DSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~-d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
...+.+.|-+|+|--+ +...+.|=.| .+-.|-.|+++|-+. +|++|++.-.
T Consensus 171 ~~tELPTCpVCLERMD~s~~gi~t~~c---~Hsfh~~cl~~w~~~----scpvcR~~q~ 222 (493)
T KOG0804|consen 171 GLTELPTCPVCLERMDSSTTGILTILC---NHSFHCSCLMKWWDS----SCPVCRYCQS 222 (493)
T ss_pred CcccCCCcchhHhhcCccccceeeeec---ccccchHHHhhcccC----cChhhhhhcC
Confidence 4578899999998743 3334444444 278999999999754 6888876544
No 40
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.37 E-value=1.1 Score=43.26 Aligned_cols=50 Identities=26% Similarity=0.566 Sum_probs=32.8
Q ss_pred CCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 57 SKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+..++|=||+.+..+ -++.||+= --.=..|.+.-. -..+.|+||++++..
T Consensus 288 ~~gkeCVIClse~rd-t~vLPCRH----LCLCs~Ca~~Lr--~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSESRD-TVVLPCRH----LCLCSGCAKSLR--YQTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCCcc-eEEecchh----hehhHhHHHHHH--HhhcCCCccccchHh
Confidence 668999999998754 46677660 012234655554 224579999998863
No 41
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=84.17 E-value=5.6 Score=32.27 Aligned_cols=45 Identities=22% Similarity=0.401 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhhheeec---CCCchhHHHHHHHHHHHHhhhHHHHHHH
Q 025381 193 LFMVLLVLRHTLPIIIS---GAGEYSLTLFTLLILRTIGILLPIYVMV 237 (253)
Q Consensus 193 i~~~lLvlrh~l~l~~~---~~~~~~~~~~t~~~lra~GillP~yi~~ 237 (253)
++++++++|-++.+... .-|.|+|.++++++-=.|.++-|+..|.
T Consensus 9 ~~~~~~~~Wi~~N~~~~~~~~fDpyPFilLnl~lS~~Aa~~ap~Ilms 56 (108)
T PF06210_consen 9 IFTVFLAVWILLNILAPPRPAFDPYPFILLNLVLSLEAAYQAPLILMS 56 (108)
T ss_pred HHHHHHHHHHHHHhhccccCCCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666677777766532 3478999999999888899998986554
No 42
>PLN02189 cellulose synthase
Probab=83.03 E-value=0.77 Score=49.82 Aligned_cols=52 Identities=25% Similarity=0.638 Sum_probs=39.5
Q ss_pred CCCCeeeEeccCC---CCCCcccCcc-cCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEED---EDSNMEIPCS-CCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~---~d~~L~~PC~-C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.....|+||-++. .++.+...|+ |. --|=+.|. +.=.+.|+..|+.||+.|+
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~---fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECG---FPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCC---Cccccchh-hhhhhcCCccCcccCCchh
Confidence 3455899998884 4567778898 62 34888998 4444568899999999998
No 43
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=82.98 E-value=0.75 Score=37.63 Aligned_cols=27 Identities=19% Similarity=0.586 Sum_probs=23.3
Q ss_pred ccccHHHHHHHHHhcCCcccccccccccc
Q 025381 85 KYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 85 kyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+-+|..|+.+|++.++ .||+|+++...
T Consensus 83 HaFH~hCisrWlktr~--vCPLdn~eW~~ 109 (114)
T KOG2930|consen 83 HAFHFHCISRWLKTRN--VCPLDNKEWVF 109 (114)
T ss_pred hHHHHHHHHHHHhhcC--cCCCcCcceeE
Confidence 6799999999997764 89999998764
No 44
>PLN02436 cellulose synthase A
Probab=79.41 E-value=1.3 Score=48.31 Aligned_cols=52 Identities=25% Similarity=0.643 Sum_probs=39.9
Q ss_pred CCCCeeeEeccCC---CCCCcccCcc-cCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEED---EDSNMEIPCS-CCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~---~d~~L~~PC~-C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.....|+||-++. .++.+...|+ |. --|=+.|. +.-.+.|+..|+.||+.|+
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~---fpvCr~Cy-eyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECA---FPVCRPCY-EYERREGNQACPQCKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCC---Cccccchh-hhhhhcCCccCcccCCchh
Confidence 4556999998884 4677888888 62 34888998 4444568899999999998
No 45
>COG4420 Predicted membrane protein [Function unknown]
Probab=78.50 E-value=8.4 Score=34.48 Aligned_cols=58 Identities=22% Similarity=0.257 Sum_probs=43.9
Q ss_pred hhhhhhhhhhhhhHHHHHHHHHHHhhhheee--cC-CCchhHHHHHHHHHHHHhhhHHHHHHH
Q 025381 178 AITVHLSLTLFGVRSLFMVLLVLRHTLPIII--SG-AGEYSLTLFTLLILRTIGILLPIYVMV 237 (253)
Q Consensus 178 al~~~~~~t~~~v~~i~~~lLvlrh~l~l~~--~~-~~~~~~~~~t~~~lra~GillP~yi~~ 237 (253)
.|+.|++.|.|-+.+ ++++++|-.+.+.+ +. -+.|+|.++.+++--.|.|--|+..|.
T Consensus 50 ~ia~f~Gsw~fil~~--~~~ll~Wi~lNl~~~~~~~wDpyPFi~LnLllS~~AaiqAp~IlmS 110 (191)
T COG4420 50 KIARFGGSWAFILTF--TLLLLLWIVLNLFLVPGLAWDPYPFILLNLLLSTLAAIQAPLILMS 110 (191)
T ss_pred HHHHHcCChHHHHHH--HHHHHHHHHHHHhhhcCCcCCCccHHHHHHHHHHHHHHHHhHHHHH
Confidence 566688888885544 46777888888752 23 377999999999999999999986654
No 46
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=78.23 E-value=1.4 Score=42.12 Aligned_cols=53 Identities=26% Similarity=0.533 Sum_probs=38.2
Q ss_pred CCCCeeeEeccCCCCCC--cccCcccCCCCccccHHHHHHHHHhc---------------------CCcccccccccccc
Q 025381 57 SKLVECRICHEEDEDSN--MEIPCSCCGSLKYAHRKCVQRWCNEK---------------------GDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~--L~~PC~C~GslkyvH~~CL~~W~~~k---------------------~~~~CEiC~~~y~~ 113 (253)
-...+|-||+=...+++ .++||- +|.|..||.|.+++- -...|++|+...+.
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 44557778776654443 578886 899999999998641 14679999987764
Q ss_pred C
Q 025381 114 G 114 (253)
Q Consensus 114 ~ 114 (253)
.
T Consensus 188 e 188 (368)
T KOG4445|consen 188 E 188 (368)
T ss_pred c
Confidence 3
No 47
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=78.14 E-value=1 Score=30.23 Aligned_cols=40 Identities=28% Similarity=0.715 Sum_probs=26.8
Q ss_pred eeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCC--cccccc
Q 025381 62 CRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGD--TTCEIC 107 (253)
Q Consensus 62 CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~--~~CEiC 107 (253)
|-||++--. +|...+|. +-+=+.||.+|.++.+. ..|++|
T Consensus 1 CpiC~~~~~-~Pv~l~CG-----H~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK-DPVSLPCG-----HSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S-SEEE-SSS-----SEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC-CccccCCc-----CHHHHHHHHHHHHccCCcCCCCcCC
Confidence 667877654 47778886 57788999999987654 589887
No 48
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=77.43 E-value=2.6 Score=44.93 Aligned_cols=30 Identities=23% Similarity=0.572 Sum_probs=24.8
Q ss_pred cCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 76 IPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 76 ~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.+|.| |+|..|+..|.+. ..+|++|+.+|.
T Consensus 142 k~c~H-----~FC~~Ci~sWsR~--aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 142 KHTAH-----YFCEECVGSWSRC--AQTCPVDRGEFG 171 (1134)
T ss_pred ccccc-----ccHHHHhhhhhhh--cccCchhhhhhh
Confidence 45665 9999999999855 458999999996
No 49
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.64 E-value=2.1 Score=42.36 Aligned_cols=50 Identities=18% Similarity=0.535 Sum_probs=37.7
Q ss_pred CCCeeeEeccCCC---CCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccc
Q 025381 58 KLVECRICHEEDE---DSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQY 111 (253)
Q Consensus 58 ~~~~CRIC~ee~~---d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y 111 (253)
....|-||+++-. +..++.| .| -+..-..|+++|+-.+-...|++|+.+-
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl-~c---ghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSL-QC---GHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccccCceeeeeeeecCceEEeee-cc---cccccHHHHHHHHhhhhhhhCcccCChh
Confidence 4568999999842 3456666 34 3688999999999766678999998643
No 50
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.89 E-value=1.8 Score=36.73 Aligned_cols=46 Identities=28% Similarity=0.678 Sum_probs=38.0
Q ss_pred CCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccc
Q 025381 56 PSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICRE 109 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~ 109 (253)
..+...|.||++...+. .+.||. +.+=+.|+..+.. ....|+.|+.
T Consensus 10 ~~~~~~C~iC~~~~~~p-~~l~C~-----H~~c~~C~~~~~~--~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP-VLLPCG-----HNFCRACLTRSWE--GPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHhhcC-cccccc-----chHhHHHHHHhcC--CCcCCcccCC
Confidence 45788999999987653 788887 6777899999998 7789999994
No 51
>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=71.74 E-value=3.8 Score=39.09 Aligned_cols=50 Identities=18% Similarity=0.368 Sum_probs=36.1
Q ss_pred CCeeeEeccCCCCC----CcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 59 LVECRICHEEDEDS----NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 59 ~~~CRIC~ee~~d~----~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
...|-+|....-.+ -+++||. +-+=..|+.+.+. ++...|+.|+..+...
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CG-----H~~C~sCv~~l~~-~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCG-----HTLCESCVDLLFV-RGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCC-----CcccHHHHHHHhc-CCCCCCCCCCCccchh
Confidence 35799999874222 2577775 5677899999663 4667999999988754
No 52
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=70.87 E-value=2.4 Score=28.93 Aligned_cols=39 Identities=26% Similarity=0.705 Sum_probs=21.0
Q ss_pred eeEeccCCC-CC-CcccCcccCCCCccccHHHHHHHHHhc--CCcccc
Q 025381 62 CRICHEEDE-DS-NMEIPCSCCGSLKYAHRKCVQRWCNEK--GDTTCE 105 (253)
Q Consensus 62 CRIC~ee~~-d~-~L~~PC~C~GslkyvH~~CL~~W~~~k--~~~~CE 105 (253)
|-||.+-.+ ++ ++..||. +-+=++||+++.+.+ +..+|+
T Consensus 1 CpIc~e~~~~~n~P~~L~CG-----H~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCG-----HVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS------EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCccccccCCCCCCEEEeCc-----cHHHHHHHHHHHhcCCCCeeeCc
Confidence 567777322 22 5789976 688999999999865 456664
No 53
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=70.30 E-value=2 Score=41.11 Aligned_cols=48 Identities=25% Similarity=0.571 Sum_probs=37.2
Q ss_pred CCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
..+-.||||++--. -++++||. +-+-.-|+.+.+.+.. .|++|.+++.
T Consensus 23 Ds~lrC~IC~~~i~-ip~~TtCg-----HtFCslCIR~hL~~qp--~CP~Cr~~~~ 70 (391)
T COG5432 23 DSMLRCRICDCRIS-IPCETTCG-----HTFCSLCIRRHLGTQP--FCPVCREDPC 70 (391)
T ss_pred hhHHHhhhhhheee-cceecccc-----cchhHHHHHHHhcCCC--CCccccccHH
Confidence 45678999977653 37888887 5667789999886644 8999999876
No 54
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=69.98 E-value=3.1 Score=42.75 Aligned_cols=58 Identities=26% Similarity=0.651 Sum_probs=45.1
Q ss_pred CCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHh---cCCccccccccccccCccCC
Q 025381 55 SPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNE---KGDTTCEICREQYNPGYTAP 118 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~---k~~~~CEiC~~~y~~~yt~p 118 (253)
......+|-+|+++.+| ..++-|. +-.-+.|+..++.. ..+.+|+.|.......-+.|
T Consensus 532 enk~~~~C~lc~d~aed-~i~s~Ch-----H~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~ 592 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAED-YIESSCH-----HKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEP 592 (791)
T ss_pred cccCceeecccCChhhh-hHhhhhh-----HHHHHHHHHHHHHhhhcccCCCCccccccccccccch
Confidence 34567899999988764 7788887 46778999999874 45799999999888765554
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=68.82 E-value=2.6 Score=31.15 Aligned_cols=46 Identities=20% Similarity=0.362 Sum_probs=30.7
Q ss_pred eeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 61 ECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 61 ~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
.|-|+.+--. .+.+.|+. +..=+.|+++|++. +..+|++|+++...
T Consensus 6 ~CpIt~~lM~-dPVi~~~G-----~tyer~~I~~~l~~-~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 6 LCPITGELMR-DPVILPSG-----HTYERSAIERWLEQ-NGGTDPFTRQPLSE 51 (73)
T ss_dssp B-TTTSSB-S-SEEEETTS-----EEEEHHHHHHHHCT-TSSB-TTT-SB-SG
T ss_pred CCcCcCcHhh-CceeCCcC-----CEEcHHHHHHHHHc-CCCCCCCCCCcCCc
Confidence 5666655543 36777754 68999999999977 56789999887764
No 56
>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=68.49 E-value=5.9 Score=34.57 Aligned_cols=38 Identities=29% Similarity=0.704 Sum_probs=25.9
Q ss_pred CCeeeEeccCCCCC------CcccCcc---cCCCCccccHHHHHHHHHh
Q 025381 59 LVECRICHEEDEDS------NMEIPCS---CCGSLKYAHRKCVQRWCNE 98 (253)
Q Consensus 59 ~~~CRIC~ee~~d~------~L~~PC~---C~GslkyvH~~CL~~W~~~ 98 (253)
...|-||+|-.-.. .-...|+ |.. .|-|..||.+..+.
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 56899998875221 1234443 654 58899999999875
No 57
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=64.71 E-value=5.4 Score=43.73 Aligned_cols=52 Identities=23% Similarity=0.637 Sum_probs=36.7
Q ss_pred CCCeeeEeccCC---CCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 58 KLVECRICHEED---EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 58 ~~~~CRIC~ee~---~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
....|+||-++. .++.+.--|+=+| --|=+.|.+ .=..-|+..|++||+.|+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~--FPVCrpCYE-YEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCA--FPVCRPCYE-YERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCC--Cccccchhh-hhhhcCCccCCccCCchh
Confidence 456999998884 3566666676322 237788873 333457889999999998
No 58
>PLN02195 cellulose synthase A
Probab=64.46 E-value=5.9 Score=43.05 Aligned_cols=52 Identities=21% Similarity=0.533 Sum_probs=35.9
Q ss_pred CCCeeeEeccCC---CCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 58 KLVECRICHEED---EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 58 ~~~~CRIC~ee~---~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
....|+||-++. .++.+..-|+=+| --|=+.|.+ .=.+-|+..|++||++|+
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~--~pvCrpCye-yer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECS--YPLCKACLE-YEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCC--Cccccchhh-hhhhcCCccCCccCCccc
Confidence 455899998874 3455656666322 247788873 333457899999999998
No 59
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.14 E-value=2.2 Score=40.38 Aligned_cols=65 Identities=23% Similarity=0.619 Sum_probs=44.5
Q ss_pred CCCCCCeeeEeccCC-----CCC----CcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccCccCCCCccccc
Q 025381 55 SPSKLVECRICHEED-----EDS----NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPGYTAPPPLFRYG 125 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~-----~d~----~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~yt~p~~~~~~~ 125 (253)
...+...|-+|-..- +++ .-..-|+ +-.|+-|+.-|+---++.+||-||+.-..+
T Consensus 220 khl~d~vCaVCg~~~~~s~~eegvienty~LsCn-----HvFHEfCIrGWcivGKkqtCPYCKekVdl~----------- 283 (328)
T KOG1734|consen 220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCN-----HVFHEFCIRGWCIVGKKQTCPYCKEKVDLK----------- 283 (328)
T ss_pred CCCCcchhHhhcchheeecchhhhhhhheeeecc-----cchHHHhhhhheeecCCCCCchHHHHhhHh-----------
Confidence 335567899996541 221 2234555 689999999999887788999999876643
Q ss_pred cccCCCceec
Q 025381 126 GNFRANWEIS 135 (253)
Q Consensus 126 ~~~~~~W~i~ 135 (253)
+-|+..||.+
T Consensus 284 rmfsnpWekp 293 (328)
T KOG1734|consen 284 RMFSNPWEKP 293 (328)
T ss_pred hhccCccccc
Confidence 1345678764
No 60
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.44 E-value=6.4 Score=35.04 Aligned_cols=51 Identities=18% Similarity=0.482 Sum_probs=36.9
Q ss_pred CCCCCCCCeeeEeccCCCCC-CcccCcccCCCCccccHHHHHHHHHhcCCccccccccc
Q 025381 53 GSSPSKLVECRICHEEDEDS-NMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQ 110 (253)
Q Consensus 53 ~~~~~~~~~CRIC~ee~~d~-~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~ 110 (253)
+..++....|-||++..++. +.-+-|. +.+=.+|++.-+ |...+|++|++.
T Consensus 125 ~~~~~~~~~CPiCl~~~sek~~vsTkCG-----HvFC~~Cik~al--k~~~~CP~C~kk 176 (187)
T KOG0320|consen 125 PLRKEGTYKCPICLDSVSEKVPVSTKCG-----HVFCSQCIKDAL--KNTNKCPTCRKK 176 (187)
T ss_pred ccccccccCCCceecchhhccccccccc-----hhHHHHHHHHHH--HhCCCCCCcccc
Confidence 45566778999999997643 3334443 667789988887 446799999973
No 61
>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=61.30 E-value=4.5 Score=27.45 Aligned_cols=22 Identities=18% Similarity=0.730 Sum_probs=15.9
Q ss_pred cccHHHHHHHHHhcCCcccccc
Q 025381 86 YAHRKCVQRWCNEKGDTTCEIC 107 (253)
Q Consensus 86 yvH~~CL~~W~~~k~~~~CEiC 107 (253)
-.|..|+++++..+.+.+|+.|
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 3999999999998877789987
No 62
>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=58.27 E-value=11 Score=36.79 Aligned_cols=35 Identities=23% Similarity=0.714 Sum_probs=26.4
Q ss_pred ccCcccCCCCccccHHHHHHHHHhc-----------CCccccccccccc
Q 025381 75 EIPCSCCGSLKYAHRKCVQRWCNEK-----------GDTTCEICREQYN 112 (253)
Q Consensus 75 ~~PC~C~GslkyvH~~CL~~W~~~k-----------~~~~CEiC~~~y~ 112 (253)
-.+|.|+- .==.+|+-+|+.++ |+..|+.|++.|=
T Consensus 306 C~~C~CRP---mWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 306 CQQCYCRP---MWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred Cccccccc---hHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 35777752 34578999999765 4679999999884
No 63
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=57.14 E-value=4 Score=39.80 Aligned_cols=47 Identities=28% Similarity=0.581 Sum_probs=37.5
Q ss_pred CCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 58 KLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 58 ~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
..-.|-||++=.. -+++.||. +-.-.-|+...++.+ ..|+.|..++.
T Consensus 22 ~lLRC~IC~eyf~-ip~itpCs-----HtfCSlCIR~~L~~~--p~CP~C~~~~~ 68 (442)
T KOG0287|consen 22 DLLRCGICFEYFN-IPMITPCS-----HTFCSLCIRKFLSYK--PQCPTCCVTVT 68 (442)
T ss_pred HHHHHhHHHHHhc-Cceecccc-----chHHHHHHHHHhccC--CCCCceecccc
Confidence 4568999998764 48999976 566678888888664 58999999886
No 64
>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=56.93 E-value=3.8 Score=31.20 Aligned_cols=33 Identities=24% Similarity=0.700 Sum_probs=23.9
Q ss_pred CCCCeeeEeccCCCCCC-cccCcccCCCCccccHHHHHH
Q 025381 57 SKLVECRICHEEDEDSN-MEIPCSCCGSLKYAHRKCVQR 94 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~-L~~PC~C~GslkyvH~~CL~~ 94 (253)
.....|.+|...-..+. .+-||. +.+|..|++|
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCC-----eEEecccccC
Confidence 34567999988865444 467875 6899999864
No 65
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=55.62 E-value=11 Score=41.46 Aligned_cols=54 Identities=26% Similarity=0.710 Sum_probs=37.5
Q ss_pred CCCCCeeeEeccCC---CCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 56 PSKLVECRICHEED---EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 56 ~~~~~~CRIC~ee~---~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.-....|.||-++. .++.+..-|+=+| --|=+.|. +.=.+.|+..|+.||+.|+
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~--fpvCr~cy-eye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCG--FPVCKPCY-EYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCC--Cccccchh-hhhhhcCCccCCccCCchh
Confidence 34677899998874 3455666666222 23778887 3333457889999999998
No 66
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=49.70 E-value=7.1 Score=25.71 Aligned_cols=19 Identities=21% Similarity=0.593 Sum_probs=14.1
Q ss_pred ccccccccccccCccCCCC
Q 025381 102 TTCEICREQYNPGYTAPPP 120 (253)
Q Consensus 102 ~~CEiC~~~y~~~yt~p~~ 120 (253)
..|+.|+..|...|.+|+.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~ 20 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKV 20 (36)
T ss_dssp EEETTTTEEEETTTB--SS
T ss_pred cCcCCCCCccccccCCCCC
Confidence 4799999999988877643
No 67
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=49.48 E-value=8.9 Score=38.13 Aligned_cols=48 Identities=27% Similarity=0.723 Sum_probs=38.7
Q ss_pred CCCCeeeEeccCC--CCCCc-ccCcccCCCCccccHHHHHHHHHhcCCcccccccc
Q 025381 57 SKLVECRICHEED--EDSNM-EIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICRE 109 (253)
Q Consensus 57 ~~~~~CRIC~ee~--~d~~L-~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~ 109 (253)
+.+-.|-.|-+.- .+++| -.||+ +..|..|++..+..+++.+||-|++
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCs-----HIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCS-----HIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchh-----HHHHHHHHHHHHHhCCCCCCccHHH
Confidence 4567788996653 23445 58998 7999999999999999999999994
No 68
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.33 E-value=14 Score=35.78 Aligned_cols=51 Identities=24% Similarity=0.579 Sum_probs=36.2
Q ss_pred CCCCeeeEeccCCCCCC-----c-c-cCcccCCCCccccHHHHHHHHHhcC-----Cccccccccccc
Q 025381 57 SKLVECRICHEEDEDSN-----M-E-IPCSCCGSLKYAHRKCVQRWCNEKG-----DTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~-----L-~-~PC~C~GslkyvH~~CL~~W~~~k~-----~~~CEiC~~~y~ 112 (253)
...+.|-||++...+.. + + .+|. +..=.+|+.+|...+. ...|++|+..-+
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~-----H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCN-----HSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcc-----hhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 56889999998864322 2 2 4465 4555789999997655 689999996543
No 69
>PLN02400 cellulose synthase
Probab=46.18 E-value=15 Score=40.54 Aligned_cols=53 Identities=23% Similarity=0.623 Sum_probs=35.8
Q ss_pred CCCCeeeEeccCC---CCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccc
Q 025381 57 SKLVECRICHEED---EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 57 ~~~~~CRIC~ee~---~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~ 112 (253)
.....|+||-++. .++++..-|+=+| --|=+.|.+ .=..-|+..|++||+.|+
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCa--FPVCRpCYE-YERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECA--FPVCRPCYE-YERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCC--Cccccchhh-eecccCCccCcccCCccc
Confidence 3556999998884 3566666665222 236677762 222347889999999998
No 70
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=45.40 E-value=25 Score=27.43 Aligned_cols=55 Identities=22% Similarity=0.548 Sum_probs=22.9
Q ss_pred CCCCeeeEeccCC---CCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 57 SKLVECRICHEED---EDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 57 ~~~~~CRIC~ee~---~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
.....|.||-++. .++.+..-|.=.+ --|=+.|.+-=.+ -|+..|+.|+++|+..
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~--fPvCr~CyEYErk-eg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECA--FPVCRPCYEYERK-EGNQVCPQCKTRYKRH 64 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-------HHHHHHHHH-TS-SB-TTT--B----
T ss_pred cCCcccccccCccccCCCCCEEEEEcccC--CccchhHHHHHhh-cCcccccccCCCcccc
Confidence 4567899998874 3456666665222 3477888765543 4678999999999843
No 71
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=45.21 E-value=14 Score=39.72 Aligned_cols=56 Identities=20% Similarity=0.514 Sum_probs=40.0
Q ss_pred CCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhc-----CCccccccccccc
Q 025381 55 SPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEK-----GDTTCEICREQYN 112 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k-----~~~~CEiC~~~y~ 112 (253)
......+|-||.+.-....-+=- |+.=.+.+|-.|+++|-..+ ..+.|+-|+..++
T Consensus 187 l~~~~yeCmIC~e~I~~t~~~WS--C~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 187 LSNRKYECMICTERIKRTAPVWS--CKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred HhcCceEEEEeeeeccccCCcee--cchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 45678899999988542221222 33335779999999998753 3689999998877
No 72
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.66 E-value=27 Score=32.84 Aligned_cols=53 Identities=28% Similarity=0.595 Sum_probs=40.0
Q ss_pred CCCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHH-HHHhcCCcccccccccccc
Q 025381 54 SSPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQR-WCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 54 ~~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~-W~~~k~~~~CEiC~~~y~~ 113 (253)
-.|.....|-||.+..+ .+.-+||. +..--.||.. |...| ...|++|++.-.|
T Consensus 210 fip~~d~kC~lC~e~~~-~ps~t~Cg-----HlFC~~Cl~~~~t~~k-~~~CplCRak~~p 263 (271)
T COG5574 210 FIPLADYKCFLCLEEPE-VPSCTPCG-----HLFCLSCLLISWTKKK-YEFCPLCRAKVYP 263 (271)
T ss_pred cccccccceeeeecccC-Cccccccc-----chhhHHHHHHHHHhhc-cccCchhhhhccc
Confidence 35677889999988764 47778886 6777889999 88554 4469999976544
No 73
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.18 E-value=27 Score=35.56 Aligned_cols=50 Identities=26% Similarity=0.574 Sum_probs=35.9
Q ss_pred CCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHh---cCCccccccccccccC
Q 025381 59 LVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNE---KGDTTCEICREQYNPG 114 (253)
Q Consensus 59 ~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~---k~~~~CEiC~~~y~~~ 114 (253)
..+|-||+++..- +..+-|. +..=-.||.+..+. ++-..|++|...+.++
T Consensus 186 ~~~CPICL~~~~~-p~~t~CG-----HiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k 238 (513)
T KOG2164|consen 186 DMQCPICLEPPSV-PVRTNCG-----HIFCGPCILQYWNYSAIKGPCSCPICRSTITLK 238 (513)
T ss_pred CCcCCcccCCCCc-ccccccC-----ceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence 7899999998753 3333354 55667888777764 4678999999887763
No 74
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=35.01 E-value=35 Score=33.54 Aligned_cols=50 Identities=26% Similarity=0.641 Sum_probs=32.8
Q ss_pred CCCeeeEeccCCC-CCCcccCcccCCCCccccHHHHHHHHHhc--CCcccccccccccc
Q 025381 58 KLVECRICHEEDE-DSNMEIPCSCCGSLKYAHRKCVQRWCNEK--GDTTCEICREQYNP 113 (253)
Q Consensus 58 ~~~~CRIC~ee~~-d~~L~~PC~C~GslkyvH~~CL~~W~~~k--~~~~CEiC~~~y~~ 113 (253)
++..|-.|.|+-+ ...-..||.|. | +-|---|-+-+ -+.+|+-|+..|.-
T Consensus 13 eed~cplcie~mditdknf~pc~cg----y--~ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCG----Y--QICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred ccccCcccccccccccCCcccCCcc----c--HHHHHHHHHHHhhccCCChHhhhhccc
Confidence 4456999999854 22446799983 3 33433454433 36699999998874
No 75
>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=33.59 E-value=16 Score=19.94 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=7.4
Q ss_pred ccccccccccc
Q 025381 103 TCEICREQYNP 113 (253)
Q Consensus 103 ~CEiC~~~y~~ 113 (253)
.|++|++.|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 59999998874
No 76
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=31.77 E-value=29 Score=30.81 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhh
Q 025381 230 LLPIYVMVKAFTAIQRRRHQQ 250 (253)
Q Consensus 230 llP~yi~~~~i~~~q~~r~q~ 250 (253)
.+|-.+++-.|..+||||+++
T Consensus 162 yiPAlLLL~lv~~lQrRR~~~ 182 (183)
T PF11874_consen 162 YIPALLLLGLVAWLQRRRRRK 182 (183)
T ss_pred eHHHHHHHHHHHHHhhhhccC
Confidence 357777888888999999875
No 77
>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=30.20 E-value=19 Score=20.18 Aligned_cols=12 Identities=25% Similarity=0.897 Sum_probs=9.8
Q ss_pred cccccccccccC
Q 025381 103 TCEICREQYNPG 114 (253)
Q Consensus 103 ~CEiC~~~y~~~ 114 (253)
.|+.|++.|...
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 599999999753
No 78
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.04 E-value=36 Score=32.81 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=22.2
Q ss_pred cccHHHHHHHHHhc-----------CCcccccccccccc
Q 025381 86 YAHRKCVQRWCNEK-----------GDTTCEICREQYNP 113 (253)
Q Consensus 86 yvH~~CL~~W~~~k-----------~~~~CEiC~~~y~~ 113 (253)
.--++||.+|+..+ |+-.|+.|++.|-.
T Consensus 328 ~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci 366 (381)
T KOG3899|consen 328 LWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI 366 (381)
T ss_pred HHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence 45689999999643 57799999998853
No 79
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=28.67 E-value=18 Score=39.79 Aligned_cols=51 Identities=24% Similarity=0.444 Sum_probs=35.4
Q ss_pred CCCCeeeEeccCCCC-CCcccCcccCCCCccccHHHHHHHHHhcCCcccccccc
Q 025381 57 SKLVECRICHEEDED-SNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICRE 109 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d-~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~ 109 (253)
+....|-||.+.+.+ .+.+.-|. |=-.+||+.|.-.=...-|.+.|.-|.+
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYGIPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred CCCccceeecccccCCCceEEEcC--CCcchhhhhccCCCCCCCCcEeehhhcc
Confidence 567799999998755 35566665 2247999999873333446677777764
No 80
>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=28.64 E-value=34 Score=23.79 Aligned_cols=23 Identities=17% Similarity=0.570 Sum_probs=11.5
Q ss_pred HHHHHHHh-c-CCcccccccccccc
Q 025381 91 CVQRWCNE-K-GDTTCEICREQYNP 113 (253)
Q Consensus 91 CL~~W~~~-k-~~~~CEiC~~~y~~ 113 (253)
-++++++. + ....||+|+.+|..
T Consensus 8 ~~~k~i~~l~~~~~~CPlC~r~l~~ 32 (54)
T PF04423_consen 8 ELKKYIEELKEAKGCCPLCGRPLDE 32 (54)
T ss_dssp HHHHHHHHHTT-SEE-TTT--EE-H
T ss_pred HHHHHHHHHhcCCCcCCCCCCCCCH
Confidence 35566653 2 23399999999875
No 81
>COG2322 Predicted membrane protein [Function unknown]
Probab=27.71 E-value=2.5e+02 Score=24.96 Aligned_cols=61 Identities=33% Similarity=0.542 Sum_probs=44.1
Q ss_pred hhhhhhhhHHHHHHHHHHHhhhheee--cCCCc----hhHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 025381 183 LSLTLFGVRSLFMVLLVLRHTLPIII--SGAGE----YSLTLFTLLILRTIGILLPIYVMVKAFTAI 243 (253)
Q Consensus 183 ~~~t~~~v~~i~~~lLvlrh~l~l~~--~~~~~----~~~~~~t~~~lra~GillP~yi~~~~i~~~ 243 (253)
+-++.+-...+|.++-+-||.+.=.. ++++. |-+-+++=.+|=++++.|-.|.+.++++-.
T Consensus 78 aMltA~~l~l~FlvlYltr~~l~~~t~f~~~G~~k~~Y~~iL~~Hi~LA~i~vPLal~al~~a~~~~ 144 (177)
T COG2322 78 AMLTAFTLALVFLVLYLTRHGLGGETAFGGTGIYKGIYFFILITHIILAAINVPLALYALILAWKGL 144 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccccCCCCeeeehHHHHHHHHHHHHHHHhhhHHHHHHHHHhcch
Confidence 33444455556777777788776654 66655 566777777889999999999999999843
No 82
>PF05210 Sprouty: Sprouty protein (Spry); InterPro: IPR007875 Sprouty (Spry) and Spred (Sprouty related EVH1 domain) proteins have been identified as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases [1,2]. These proteins share a conserved, C-terminal cysteine-rich region, the SPR domain. This domain has been defined as a novel cytosol to membrane translocation domain [, , , ]. It has been found to be a PtdIns(4,5)P2-binding domain that targets the proteins to a cellular localization that maximizes their inhibitory potential [, ]. It also mediates homodimer formation of these proteins [, ]. The SPR domain can occur in association with the WH1 domain (see IPR000697 from INTERPRO) (located in the N-terminal part of the proteins) in the Spred proteins.; GO: 0007275 multicellular organismal development, 0009966 regulation of signal transduction, 0016020 membrane
Probab=26.99 E-value=47 Score=27.22 Aligned_cols=18 Identities=39% Similarity=1.088 Sum_probs=15.2
Q ss_pred ccCcccCCCCccccHHHHHHHHH
Q 025381 75 EIPCSCCGSLKYAHRKCVQRWCN 97 (253)
Q Consensus 75 ~~PC~C~GslkyvH~~CL~~W~~ 97 (253)
..||+|.. +..|..||.-
T Consensus 59 d~PCSC~~-----~~~c~~RW~~ 76 (108)
T PF05210_consen 59 DHPCSCDT-----PSRCCARWLA 76 (108)
T ss_pred CCccccCC-----ccchHHHHHH
Confidence 46999975 8899999974
No 83
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.81 E-value=28 Score=35.08 Aligned_cols=48 Identities=27% Similarity=0.616 Sum_probs=35.6
Q ss_pred CCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 55 SPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
.......|+||.++. ..-+.||. |..|+.+|...+. .|+.|+......
T Consensus 475 l~~~~~~~~~~~~~~--~~~~~~~~--------~~~~l~~~~~~~~--~~pl~~~~~~~~ 522 (543)
T KOG0802|consen 475 LREPNDVCAICYQEM--SARITPCS--------HALCLRKWLYVQE--VCPLCHTYMKED 522 (543)
T ss_pred hhcccCcchHHHHHH--Hhcccccc--------chhHHHhhhhhcc--ccCCCchhhhcc
Confidence 346677899998776 23345665 9999999997654 799998776644
No 84
>PF04641 Rtf2: Rtf2 RING-finger
Probab=25.98 E-value=59 Score=29.65 Aligned_cols=51 Identities=16% Similarity=0.421 Sum_probs=34.1
Q ss_pred CCCCCeeeEeccCCCC-CC--cccCcccCCCCccccHHHHHHHHHhcCCccccccccccccC
Q 025381 56 PSKLVECRICHEEDED-SN--MEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNPG 114 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~d-~~--L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~~ 114 (253)
....-.|-|...+-.. .. .+.||.| -+-..+|++-- ....|++|+.+|...
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~-----V~s~~alke~k---~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGC-----VFSEKALKELK---KSKKCPVCGKPFTEE 163 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCC-----EeeHHHHHhhc---ccccccccCCccccC
Confidence 3445566666555422 12 4789998 67788877762 355799999999843
No 85
>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=25.72 E-value=33 Score=21.09 Aligned_cols=12 Identities=17% Similarity=0.587 Sum_probs=9.9
Q ss_pred Cccccccccccc
Q 025381 101 DTTCEICREQYN 112 (253)
Q Consensus 101 ~~~CEiC~~~y~ 112 (253)
...|+.|++.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 468999999885
No 86
>PF04532 DUF587: Protein of unknown function (DUF587); InterPro: IPR007618 This domain is found at the N-termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N-terminal to the UL87 (IPR004285 from INTERPRO), which has no known function.
Probab=25.59 E-value=24 Score=31.99 Aligned_cols=17 Identities=47% Similarity=0.761 Sum_probs=15.2
Q ss_pred cccCcccCCCCccccHH
Q 025381 74 MEIPCSCCGSLKYAHRK 90 (253)
Q Consensus 74 L~~PC~C~GslkyvH~~ 90 (253)
.+.|+.|.|.+-|||++
T Consensus 105 ~~~~~~C~GP~LYVhr~ 121 (215)
T PF04532_consen 105 AECAYFCRGPLLYVHRK 121 (215)
T ss_pred hhCCcccCCceEEEEcc
Confidence 37999999999999994
No 87
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=24.35 E-value=72 Score=37.34 Aligned_cols=55 Identities=24% Similarity=0.459 Sum_probs=38.9
Q ss_pred CCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhc--------CCccccccccccc
Q 025381 55 SPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEK--------GDTTCEICREQYN 112 (253)
Q Consensus 55 ~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k--------~~~~CEiC~~~y~ 112 (253)
.......|-||+.|.-. -.||---|--+..|-.|..+-+..+ +-..|+||+.+..
T Consensus 3482 kQD~DDmCmICFTE~L~---AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALS---AAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hcccCceEEEEehhhhC---CCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 34567789999887422 2555433435899999998777654 4679999998765
No 88
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.41 E-value=51 Score=24.34 Aligned_cols=43 Identities=33% Similarity=0.555 Sum_probs=26.7
Q ss_pred CeeeEeccCCCCCCc---ccCcccCCCCccccHHHHH-HHHHhcCCccccccccccc
Q 025381 60 VECRICHEEDEDSNM---EIPCSCCGSLKYAHRKCVQ-RWCNEKGDTTCEICREQYN 112 (253)
Q Consensus 60 ~~CRIC~ee~~d~~L---~~PC~C~GslkyvH~~CL~-~W~~~k~~~~CEiC~~~y~ 112 (253)
.+|-||.|..-++-+ -+-|-| ..|-. .|.. ....|+||+.+.+
T Consensus 8 dECTICye~pvdsVlYtCGHMCmC--------y~Cg~rl~~~--~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMC--------YACGLRLKKA--LHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhH--------HHHHHHHHHc--cCCcCcchhhHHH
Confidence 689999988644322 233444 34533 3332 5668999998765
No 89
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.11 E-value=44 Score=29.70 Aligned_cols=25 Identities=40% Similarity=0.826 Sum_probs=19.2
Q ss_pred CCCCCeeeEeccCCC--CCCcccCccc
Q 025381 56 PSKLVECRICHEEDE--DSNMEIPCSC 80 (253)
Q Consensus 56 ~~~~~~CRIC~ee~~--d~~L~~PC~C 80 (253)
..+.-+|-||+|+-+ +..-..||.|
T Consensus 174 ~ddkGECvICLEdL~~GdtIARLPCLC 200 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTIARLPCLC 200 (205)
T ss_pred cccCCcEEEEhhhccCCCceeccceEE
Confidence 356779999999864 3456799999
No 90
>PRK12860 transcriptional activator FlhC; Provisional
Probab=22.27 E-value=43 Score=29.90 Aligned_cols=28 Identities=21% Similarity=0.604 Sum_probs=21.5
Q ss_pred ccCcccCCCCccccHHHHHHHHHhcCCccccccc
Q 025381 75 EIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICR 108 (253)
Q Consensus 75 ~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~ 108 (253)
..||.|+|+--.+|.. ..+.+-.|++|+
T Consensus 134 l~~C~~Cgg~fv~~~~------e~~~~f~CplC~ 161 (189)
T PRK12860 134 LARCCRCGGKFVTHAH------DLRHNFVCGLCQ 161 (189)
T ss_pred eccCCCCCCCeecccc------ccCCCCcCCCCC
Confidence 6999988875555755 446688999999
No 91
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.12 E-value=1e+02 Score=30.57 Aligned_cols=54 Identities=19% Similarity=0.469 Sum_probs=33.6
Q ss_pred CCCCCCCeeeEeccCCCCCCcccCcccCCCCccccHHHHHHHHHhcCCcccccccccccc
Q 025381 54 SSPSKLVECRICHEEDEDSNMEIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICREQYNP 113 (253)
Q Consensus 54 ~~~~~~~~CRIC~ee~~d~~L~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~~y~~ 113 (253)
+..++...|-||-+.-. -.-..||.= -.-..|--+-..--.+..|.+|+.+...
T Consensus 56 dtDEen~~C~ICA~~~T-Ys~~~PC~H-----~~CH~Ca~RlRALY~~K~C~~CrTE~e~ 109 (493)
T COG5236 56 DTDEENMNCQICAGSTT-YSARYPCGH-----QICHACAVRLRALYMQKGCPLCRTETEA 109 (493)
T ss_pred ccccccceeEEecCCce-EEEeccCCc-----hHHHHHHHHHHHHHhccCCCccccccce
Confidence 34567789999976642 134689871 2222344444444456689999998864
No 92
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=22.11 E-value=1e+02 Score=23.49 Aligned_cols=15 Identities=13% Similarity=0.304 Sum_probs=12.4
Q ss_pred HHhhhHHHHHHHHHH
Q 025381 226 TIGILLPIYVMVKAF 240 (253)
Q Consensus 226 a~GillP~yi~~~~i 240 (253)
.+|+.++.||+++.|
T Consensus 45 ~~~~~ii~Yiia~~i 59 (70)
T COG1983 45 LTGFGIIAYIIAALI 59 (70)
T ss_pred chhHHHHHHHHHHHH
Confidence 578889999999865
No 93
>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=22.07 E-value=59 Score=22.59 Aligned_cols=35 Identities=20% Similarity=0.546 Sum_probs=14.3
Q ss_pred CcccCcccCCCCccccHHH--HHHHHH---hcCCccccccccc
Q 025381 73 NMEIPCSCCGSLKYAHRKC--VQRWCN---EKGDTTCEICREQ 110 (253)
Q Consensus 73 ~L~~PC~C~GslkyvH~~C--L~~W~~---~k~~~~CEiC~~~ 110 (253)
.+..|++= ..-.|-+| |..|+. +++...|++|+++
T Consensus 11 ~i~~P~Rg---~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 11 RIRIPVRG---KNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-SSEEEE---TT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred EEEeCccC---CcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 45566552 24578888 456765 3567899999874
No 94
>COG4846 CcdC Membrane protein involved in cytochrome C biogenesis [Posttranslational modification, protein turnover, chaperones]
Probab=21.33 E-value=3.6e+02 Score=23.35 Aligned_cols=44 Identities=23% Similarity=0.487 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhhheeecCCCchhHHHHHHHHHHHHhhhHHHHHHH
Q 025381 193 LFMVLLVLRHTLPIIISGAGEYSLTLFTLLILRTIGILLPIYVMV 237 (253)
Q Consensus 193 i~~~lLvlrh~l~l~~~~~~~~~~~~~t~~~lra~GillP~yi~~ 237 (253)
|++-||++|..+...+++.-++. .+--+|.+-|.|.+.|-=+.+
T Consensus 99 ILigLLiiRi~~K~~is~sid~g-eLsGMF~ilAf~MIvPWRiaM 142 (163)
T COG4846 99 ILIGLLIIRIVMKYIISGSIDVG-ELSGMFWILAFGMIVPWRIAM 142 (163)
T ss_pred HHHHHHHHHHHHHHHHcCCccHH-HhhhHHHHHHHHhhhHHHHHH
Confidence 88999999999999988886553 233355567888888865443
No 95
>PF11431 Transport_MerF: Membrane transport protein MerF; InterPro: IPR021091 This entry represents Mercury ion transport protein MerF, which has a core helix-loop-helix domain. It also has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm []. ; PDB: 1WAZ_A 2LJ2_A 2H3O_A.
Probab=21.31 E-value=1.9e+02 Score=20.34 Aligned_cols=21 Identities=38% Similarity=0.580 Sum_probs=11.3
Q ss_pred hHHHHHHHHHH--HHHHHHHHhh
Q 025381 230 LLPIYVMVKAF--TAIQRRRHQQ 250 (253)
Q Consensus 230 llP~yi~~~~i--~~~q~~r~q~ 250 (253)
|+|...+.-++ +++.|+|++|
T Consensus 24 L~PaLa~fi~lt~yal~r~~~~~ 46 (46)
T PF11431_consen 24 LLPALAVFIGLTIYALWRRRRKQ 46 (46)
T ss_dssp TTTTHHHHHHHHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHHHHHHHHhccC
Confidence 66766554444 4555655554
No 96
>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 PRK11877 psaI photosystem I reaction center subunit VIII; Reviewed
Probab=20.75 E-value=1.4e+02 Score=20.29 Aligned_cols=34 Identities=18% Similarity=0.370 Sum_probs=24.7
Q ss_pred CchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 025381 212 GEYSLTLFTLLILRTIGILLPIYVMVKAFTAIQR 245 (253)
Q Consensus 212 ~~~~~~~~t~~~lra~GillP~yi~~~~i~~~q~ 245 (253)
++|+-+.+--++.=..|+++|...|+-...-||+
T Consensus 3 g~~aas~LPsI~VPlVGlvfPai~Mallf~yIe~ 36 (38)
T PRK11877 3 GDFAASWLPWIFVPLVGWVFPAVFMVLLGRYITA 36 (38)
T ss_pred chHhHHhCchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4565555555667789999999999887666654
No 98
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=20.59 E-value=50 Score=35.20 Aligned_cols=57 Identities=26% Similarity=0.571 Sum_probs=39.4
Q ss_pred CCCCeeeEeccCCCCCC----cccCcccCCCCccccHHHHHHH---HHhc-----CCcccccccccccc
Q 025381 57 SKLVECRICHEEDEDSN----MEIPCSCCGSLKYAHRKCVQRW---CNEK-----GDTTCEICREQYNP 113 (253)
Q Consensus 57 ~~~~~CRIC~ee~~d~~----L~~PC~C~GslkyvH~~CL~~W---~~~k-----~~~~CEiC~~~y~~ 113 (253)
.--+.|.||.|++.++. --.-|+=.|=-+-+|..|-|+- |.|- +...|--|++-|..
T Consensus 115 RfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~HfsK 183 (900)
T KOG0956|consen 115 RFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFSK 183 (900)
T ss_pred hhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHHH
Confidence 45689999998864432 2355654444478999999875 3343 35689999998873
No 99
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.50 E-value=50 Score=29.44 Aligned_cols=29 Identities=28% Similarity=0.797 Sum_probs=22.0
Q ss_pred ccCcccCCCCccccHHHHHHHHHhcCCcccccccc
Q 025381 75 EIPCSCCGSLKYAHRKCVQRWCNEKGDTTCEICRE 109 (253)
Q Consensus 75 ~~PC~C~GslkyvH~~CL~~W~~~k~~~~CEiC~~ 109 (253)
..||.|+|+--.+|.. ..+.+-.|++|+-
T Consensus 134 l~~C~~Cgg~fv~~~~------e~~~~f~CplC~~ 162 (187)
T PRK12722 134 LSSCNCCGGHFVTHAH------DPVGSFVCGLCQP 162 (187)
T ss_pred eccCCCCCCCeecccc------ccCCCCcCCCCCC
Confidence 6899988875555775 3456789999995
Done!