Query 023590
Match_columns 280
No_of_seqs 202 out of 791
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:11:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023590.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023590hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA02825 LAP/PHD finger-like p 99.8 2.6E-19 5.7E-24 154.9 7.9 74 49-129 3-76 (162)
2 PHA02862 5L protein; Provision 99.8 5.2E-20 1.1E-24 157.3 2.8 64 54-124 2-65 (156)
3 COG5183 SSM4 Protein involved 99.7 3E-17 6.6E-22 168.6 5.9 80 49-133 7-86 (1175)
4 smart00744 RINGv The RING-vari 99.7 2.7E-17 5.9E-22 116.9 2.8 49 56-108 1-49 (49)
5 PF12906 RINGv: RING-variant d 99.6 6.1E-17 1.3E-21 114.2 0.9 47 57-107 1-47 (47)
6 KOG3053 Uncharacterized conser 99.6 5.9E-16 1.3E-20 142.9 2.4 67 51-117 17-87 (293)
7 KOG1609 Protein involved in mR 99.4 8.1E-14 1.8E-18 127.5 1.5 76 49-127 73-150 (323)
8 PF13639 zf-RING_2: Ring finge 96.9 0.00023 4.9E-09 48.5 -0.3 44 55-108 1-44 (44)
9 PF11793 FANCL_C: FANCL C-term 96.2 0.0024 5.1E-08 48.5 1.7 58 54-114 2-68 (70)
10 PHA02929 N1R/p28-like protein; 95.9 0.0097 2.1E-07 55.3 4.3 54 52-115 172-230 (238)
11 PLN03208 E3 ubiquitin-protein 95.7 0.012 2.7E-07 53.1 4.1 57 50-114 14-81 (193)
12 KOG4628 Predicted E3 ubiquitin 95.6 0.01 2.2E-07 57.9 3.2 48 55-112 230-278 (348)
13 PF12861 zf-Apc11: Anaphase-pr 94.9 0.035 7.5E-07 44.3 3.9 55 54-114 21-84 (85)
14 COG5243 HRD1 HRD ubiquitin lig 94.8 0.027 5.8E-07 55.8 3.7 54 51-114 284-347 (491)
15 cd00162 RING RING-finger (Real 93.6 0.056 1.2E-06 34.8 2.3 43 56-110 1-44 (45)
16 PF12678 zf-rbx1: RING-H2 zinc 93.3 0.044 9.5E-07 41.7 1.5 45 54-108 19-73 (73)
17 COG5540 RING-finger-containing 93.2 0.057 1.2E-06 52.3 2.3 51 51-111 320-371 (374)
18 PHA02926 zinc finger-like prot 93.1 0.099 2.1E-06 48.6 3.8 62 49-115 165-233 (242)
19 KOG0802 E3 ubiquitin ligase [P 92.9 0.055 1.2E-06 55.1 1.9 52 50-111 287-340 (543)
20 PF13920 zf-C3HC4_3: Zinc fing 92.8 0.043 9.4E-07 38.3 0.8 45 55-112 3-48 (50)
21 smart00184 RING Ring finger. E 92.0 0.14 3E-06 31.7 2.3 39 57-107 1-39 (39)
22 KOG0823 Predicted E3 ubiquitin 91.8 0.42 9.2E-06 44.4 6.1 55 50-114 43-97 (230)
23 KOG0828 Predicted E3 ubiquitin 90.3 0.21 4.5E-06 51.2 2.8 57 46-111 563-633 (636)
24 PF00097 zf-C3HC4: Zinc finger 88.7 0.23 5E-06 32.8 1.2 40 57-107 1-41 (41)
25 KOG1493 Anaphase-promoting com 88.5 0.27 5.8E-06 38.9 1.6 53 56-114 22-83 (84)
26 smart00504 Ubox Modified RING 87.8 0.46 9.9E-06 33.8 2.4 45 56-113 3-47 (63)
27 KOG0825 PHD Zn-finger protein 87.3 0.89 1.9E-05 49.0 5.0 26 82-112 146-171 (1134)
28 PF13923 zf-C3HC4_2: Zinc fing 85.7 0.32 6.9E-06 32.2 0.6 38 57-107 1-39 (39)
29 KOG0317 Predicted E3 ubiquitin 85.4 0.87 1.9E-05 43.7 3.5 53 48-113 233-285 (293)
30 PLN02189 cellulose synthase 80.0 1.3 2.7E-05 49.0 2.7 54 52-112 32-87 (1040)
31 TIGR00599 rad18 DNA repair pro 76.8 1.6 3.5E-05 43.5 2.1 48 53-113 25-72 (397)
32 KOG0827 Predicted E3 ubiquitin 76.4 1.9 4.1E-05 43.2 2.5 47 54-108 4-52 (465)
33 PF14570 zf-RING_4: RING/Ubox 76.0 1.8 3.9E-05 31.2 1.6 48 57-112 1-48 (48)
34 PLN02436 cellulose synthase A 76.0 1.9 4.2E-05 47.8 2.6 53 53-112 35-89 (1094)
35 PF14634 zf-RING_5: zinc-RING 73.4 2.7 5.8E-05 28.6 2.0 43 57-109 2-44 (44)
36 COG5219 Uncharacterized conser 69.4 2.8 6E-05 46.4 1.9 55 53-113 1468-1524(1525)
37 KOG4265 Predicted E3 ubiquitin 69.2 5.5 0.00012 39.3 3.7 56 50-117 286-341 (349)
38 COG5194 APC11 Component of SCF 68.8 3.6 7.9E-05 32.9 2.0 28 82-114 56-83 (88)
39 PF14569 zf-UDP: Zinc-binding 68.0 4.2 9E-05 32.2 2.1 58 51-114 6-64 (80)
40 KOG0804 Cytoplasmic Zn-finger 64.6 3.7 7.9E-05 41.8 1.6 51 49-110 170-220 (493)
41 PF05883 Baculo_RING: Baculovi 63.7 2.4 5.2E-05 36.5 0.1 42 52-95 24-68 (134)
42 KOG2930 SCF ubiquitin ligase, 59.5 6.8 0.00015 32.7 2.0 28 82-114 83-110 (114)
43 KOG1785 Tyrosine kinase negati 55.3 5.1 0.00011 40.6 0.7 54 49-113 364-417 (563)
44 PLN02638 cellulose synthase A 54.9 11 0.00023 42.2 3.1 54 52-112 15-70 (1079)
45 KOG0802 E3 ubiquitin ligase [P 49.7 13 0.00028 38.1 2.7 49 49-114 474-522 (543)
46 KOG4445 Uncharacterized conser 49.3 11 0.00025 36.8 2.1 56 55-115 116-189 (368)
47 PLN02400 cellulose synthase 47.1 17 0.00036 40.8 3.2 54 53-112 35-89 (1085)
48 PLN02195 cellulose synthase A 44.9 19 0.00042 39.9 3.2 54 52-112 4-59 (977)
49 KOG1645 RING-finger-containing 42.6 20 0.00044 36.4 2.7 54 53-113 3-57 (463)
50 PF13445 zf-RING_UBOX: RING-ty 37.4 17 0.00037 25.2 1.0 42 57-104 1-42 (43)
51 PF15227 zf-C3HC4_4: zinc fing 36.2 14 0.00031 25.1 0.4 42 57-107 1-42 (42)
52 PF07800 DUF1644: Protein of u 35.2 60 0.0013 28.9 4.2 41 54-96 2-49 (162)
53 PLN02915 cellulose synthase A 33.3 37 0.0008 38.0 3.1 56 50-112 11-68 (1044)
54 PF05290 Baculo_IE-1: Baculovi 31.9 28 0.00061 30.3 1.6 56 53-114 79-134 (140)
55 KOG3268 Predicted E3 ubiquitin 30.1 49 0.0011 30.4 2.9 64 51-115 162-231 (234)
56 PF15050 SCIMP: SCIMP protein 29.6 12 0.00025 32.1 -1.1 37 182-223 8-44 (133)
57 TIGR00570 cdk7 CDK-activating 28.9 53 0.0012 32.0 3.1 51 55-114 4-56 (309)
58 PF10272 Tmpp129: Putative tra 28.6 66 0.0014 31.9 3.7 40 72-114 306-353 (358)
59 KOG0287 Postreplication repair 27.2 21 0.00045 35.6 0.0 46 54-112 23-68 (442)
60 TIGR02876 spore_yqfD sporulati 27.0 41 0.00089 33.2 2.0 31 173-203 67-106 (382)
61 PF02891 zf-MIZ: MIZ/SP-RING z 27.0 32 0.00069 24.4 0.9 39 69-110 10-50 (50)
62 KOG1039 Predicted E3 ubiquitin 25.7 58 0.0013 32.1 2.7 59 50-113 157-222 (344)
63 PF10367 Vps39_2: Vacuolar sor 25.4 26 0.00056 27.0 0.2 33 52-91 76-109 (109)
64 KOG0956 PHD finger protein AF1 24.8 42 0.00091 36.3 1.7 67 56-126 7-86 (900)
65 PF04423 Rad50_zn_hook: Rad50 24.7 57 0.0012 23.0 1.9 25 89-114 9-33 (54)
66 COG5175 MOT2 Transcriptional r 24.3 53 0.0012 32.9 2.2 53 53-114 13-66 (480)
67 PF11118 DUF2627: Protein of u 22.6 47 0.001 26.2 1.2 22 182-203 41-62 (77)
68 PF10571 UPF0547: Uncharacteri 22.0 38 0.00082 21.2 0.5 12 101-112 14-25 (26)
69 PF04564 U-box: U-box domain; 21.6 35 0.00076 25.5 0.3 46 56-113 6-51 (73)
70 PF13894 zf-C2H2_4: C2H2-type 21.2 44 0.00095 18.5 0.6 12 103-114 2-13 (24)
No 1
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.78 E-value=2.6e-19 Score=154.89 Aligned_cols=74 Identities=23% Similarity=0.580 Sum_probs=63.3
Q ss_pred cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeeeeeeccccccccce
Q 023590 49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKF 128 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~~~~~~~~W~~l~~ 128 (280)
+++...+.||||++++ +++.+||+|+||++|||++||++|+..++ ...||+|+++|.++...+++++|.--+.
T Consensus 3 ~~s~~~~~CRIC~~~~----~~~~~PC~CkGs~k~VH~sCL~rWi~~s~---~~~CeiC~~~Y~i~~~~kpl~~W~~~~~ 75 (162)
T PHA02825 3 DVSLMDKCCWICKDEY----DVVTNYCNCKNENKIVHKECLEEWINTSK---NKSCKICNGPYNIKKNYKKCTKWRCSFR 75 (162)
T ss_pred CcCCCCCeeEecCCCC----CCccCCcccCCCchHHHHHHHHHHHhcCC---CCcccccCCeEEEEEecCCCccccccCc
Confidence 4567788999999753 24679999999999999999999999875 5799999999999988899999976554
Q ss_pred e
Q 023590 129 R 129 (280)
Q Consensus 129 ~ 129 (280)
.
T Consensus 76 d 76 (162)
T PHA02825 76 D 76 (162)
T ss_pred c
Confidence 4
No 2
>PHA02862 5L protein; Provisional
Probab=99.78 E-value=5.2e-20 Score=157.27 Aligned_cols=64 Identities=22% Similarity=0.571 Sum_probs=56.3
Q ss_pred CCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeeeeeecccccc
Q 023590 54 LPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWR 124 (280)
Q Consensus 54 ~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~~~~~~~~W~ 124 (280)
.++||||+++++ +.++||+|+||.+|||++||++|++.++ +.+||+|+++|.++.+.++.++|+
T Consensus 2 ~diCWIC~~~~~----e~~~PC~C~GS~K~VHq~CL~~WIn~S~---k~~CeLCkteY~Ik~~yKpf~kW~ 65 (156)
T PHA02862 2 SDICWICNDVCD----ERNNFCGCNEEYKVVHIKCMQLWINYSK---KKECNLCKTKYNIKKTYVSFKKWN 65 (156)
T ss_pred CCEEEEecCcCC----CCcccccccCcchhHHHHHHHHHHhcCC---CcCccCCCCeEEEEEccccHHHhh
Confidence 468999997642 2369999999999999999999998764 589999999999999889999997
No 3
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.68 E-value=3e-17 Score=168.59 Aligned_cols=80 Identities=26% Similarity=0.740 Sum_probs=69.4
Q ss_pred cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeeeeeeccccccccce
Q 023590 49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKF 128 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~~~~~~~~W~~l~~ 128 (280)
+.+.+...||||+. |+.+++||.+||+|+||+||+|++||..|+..++ +.+|++||++|+++ +.+..++.+++++
T Consensus 7 ~mN~d~~~CRICr~-e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~---~~kCdiChy~~~Fk-~IY~e~mP~~IPf 81 (1175)
T COG5183 7 PMNEDKRSCRICRT-EDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSG---TKKCDICHYEYKFK-DIYKEDMPQIIPF 81 (1175)
T ss_pred CCCccchhceeecC-CCCCCCcCcccccccchhHHHHHHHHHHHHhcCC---Ccceeeecceeeee-eecccCCCcccce
Confidence 34555589999995 5668999999999999999999999999999764 68999999999998 4566799999999
Q ss_pred eEeee
Q 023590 129 RLFVA 133 (280)
Q Consensus 129 ~~~~~ 133 (280)
+++.+
T Consensus 82 siL~r 86 (1175)
T COG5183 82 SILIR 86 (1175)
T ss_pred ehhHH
Confidence 98764
No 4
>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=99.66 E-value=2.7e-17 Score=116.94 Aligned_cols=49 Identities=43% Similarity=1.112 Sum_probs=43.6
Q ss_pred cceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCcccccccccc
Q 023590 56 CCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108 (280)
Q Consensus 56 ~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk 108 (280)
+||||++ ++++++++++||+|+||++|||++||++|+..++ ..+||+|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~---~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESG---NKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC---CCcCCCCC
Confidence 6999998 4456789999999999999999999999999875 36999996
No 5
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.62 E-value=6.1e-17 Score=114.24 Aligned_cols=47 Identities=49% Similarity=1.180 Sum_probs=36.3
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccc
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTC 107 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElC 107 (280)
||||+++++ ++++|++||+|+||++|||++||++|+..++ ...||+|
T Consensus 1 CrIC~~~~~-~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~---~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEE-EDEPLISPCRCKGSMKYVHRSCLERWIRESG---NRKCEIC 47 (47)
T ss_dssp ETTTTEE-S-SSS-EE-SSS-SSCCGSEECCHHHHHHHHHT----SB-TTT
T ss_pred CeEeCCcCC-CCCceecccccCCCcchhHHHHHHHHHHhcC---CCcCCCC
Confidence 899998754 3458999999999999999999999999875 3679998
No 6
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.57 E-value=5.9e-16 Score=142.85 Aligned_cols=67 Identities=27% Similarity=0.779 Sum_probs=56.0
Q ss_pred CCCCCcceEeccCCCCCC-CccccccccCCCCcccchhhHHHHHHhhcC---ccccccccccceeeeeeee
Q 023590 51 NGSLPCCRICLENDGEPD-DELISPCMCKGTQQFVHRACLDHWRSVKEG---FAFSHCTTCKAQFHLRVEL 117 (280)
Q Consensus 51 ~~~~~~CRIC~~~~~e~~-~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~---~~~~~CElCk~~y~~~~~~ 117 (280)
...++.||||+.+++|.. ..+++||+|+||.|||||+||.+|+.+++. .++..|.+|+++|.+....
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~ 87 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQ 87 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccc
Confidence 455789999998765443 458999999999999999999999998753 4778999999999987533
No 7
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.39 E-value=8.1e-14 Score=127.55 Aligned_cols=76 Identities=41% Similarity=0.723 Sum_probs=59.0
Q ss_pred cCCCCCCcceEeccCCCCCC-CccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee-eeeecccccccc
Q 023590 49 IENGSLPCCRICLENDGEPD-DELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR-VELFEDNSWRKI 126 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~-~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~-~~~~~~~~W~~l 126 (280)
.++.+++.||||++..++.. .+++.||.|+|++++||+.||++|+..++ +..||+|++.|... ++.++...|.+.
T Consensus 73 ~~~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~---~~~CeiC~~~~~~~~~~~~~~~~~~~~ 149 (323)
T KOG1609|consen 73 ESPSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKG---NITCEICKSFFINVGTKLKPLIVISKV 149 (323)
T ss_pred cCCCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhcccc---Ceeeecccccceecceeecceeehhhh
Confidence 44555799999997554221 27999999999999999999999999775 48999999999987 344445556544
Q ss_pred c
Q 023590 127 K 127 (280)
Q Consensus 127 ~ 127 (280)
.
T Consensus 150 ~ 150 (323)
T KOG1609|consen 150 R 150 (323)
T ss_pred h
Confidence 3
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=96.86 E-value=0.00023 Score=48.55 Aligned_cols=44 Identities=30% Similarity=0.829 Sum_probs=30.9
Q ss_pred CcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCcccccccccc
Q 023590 55 PCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108 (280)
Q Consensus 55 ~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk 108 (280)
+.|-||++.-.+.+.....|| .+..|.+|+.+|++.+ ..|++|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C-----~H~fh~~Ci~~~~~~~-----~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPC-----GHVFHRSCIKEWLKRN-----NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETT-----SEEEEHHHHHHHHHHS-----SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccC-----CCeeCHHHHHHHHHhC-----CcCCccC
Confidence 368899976533334455664 3789999999999874 4999985
No 9
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.23 E-value=0.0024 Score=48.46 Aligned_cols=58 Identities=21% Similarity=0.452 Sum_probs=27.7
Q ss_pred CCcceEeccCCCCCCC-c-cc-cccccCCCCcccchhhHHHHHHhhcCc------cccccccccceeeee
Q 023590 54 LPCCRICLENDGEPDD-E-LI-SPCMCKGTQQFVHRACLDHWRSVKEGF------AFSHCTTCKAQFHLR 114 (280)
Q Consensus 54 ~~~CRIC~~~~~e~~~-~-LI-sPC~CkGSlkyVH~~CL~~Wi~~s~~~------~~~~CElCk~~y~~~ 114 (280)
+..|.||++...+.++ | ++ ...+|. +..|..||.+|+....+. -.-.|+.|+.+..++
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 3579999975432222 2 23 335774 679999999999865321 234799999988764
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=95.89 E-value=0.0097 Score=55.26 Aligned_cols=54 Identities=24% Similarity=0.614 Sum_probs=38.4
Q ss_pred CCCCcceEeccCCCCCCC-----ccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeee
Q 023590 52 GSLPCCRICLENDGEPDD-----ELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRV 115 (280)
Q Consensus 52 ~~~~~CRIC~~~~~e~~~-----~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~ 115 (280)
+....|-||++.-.++.. ..+.||. +..|+.|+.+|+..+ ..|++|+.++...+
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~~~-----~tCPlCR~~~~~v~ 230 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCN-----HVFCIECIDIWKKEK-----NTCPVCRTPFISVI 230 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCC-----CcccHHHHHHHHhcC-----CCCCCCCCEeeEEe
Confidence 345799999975332211 2345563 779999999999753 58999999988543
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=95.70 E-value=0.012 Score=53.12 Aligned_cols=57 Identities=21% Similarity=0.567 Sum_probs=41.8
Q ss_pred CCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcC-----------ccccccccccceeeee
Q 023590 50 ENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEG-----------FAFSHCTTCKAQFHLR 114 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~-----------~~~~~CElCk~~y~~~ 114 (280)
..+..-.|-||++. ..+|.+++|. +..+..||.+|+..+.+ .....|++|+.++...
T Consensus 14 ~~~~~~~CpICld~---~~dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 14 DSGGDFDCNICLDQ---VRDPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred cCCCccCCccCCCc---CCCcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 34456789999974 3578888874 66889999999864321 1346899999988653
No 12
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.55 E-value=0.01 Score=57.90 Aligned_cols=48 Identities=38% Similarity=0.878 Sum_probs=38.2
Q ss_pred CcceEeccCCCCCCCcc-ccccccCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 55 PCCRICLENDGEPDDEL-ISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 55 ~~CRIC~~~~~e~~~~L-IsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
..|-||+|+- ++++.+ +-||+ +..|..|.+.||...+ +.|++||..-.
T Consensus 230 ~~CaIClEdY-~~GdklRiLPC~-----H~FH~~CIDpWL~~~r----~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDY-EKGDKLRILPCS-----HKFHVNCIDPWLTQTR----TFCPVCKRDIR 278 (348)
T ss_pred ceEEEeeccc-ccCCeeeEecCC-----CchhhccchhhHhhcC----ccCCCCCCcCC
Confidence 7999999764 345555 69987 6699999999998753 57999999544
No 13
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=94.91 E-value=0.035 Score=44.28 Aligned_cols=55 Identities=24% Similarity=0.552 Sum_probs=37.2
Q ss_pred CCcceEeccCCCC-------C--CCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 54 LPCCRICLENDGE-------P--DDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 54 ~~~CRIC~~~~~e-------~--~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
...|-||+..-+. + +-|++ =+.| .+-.|..|+.+|+++.++ +..|++|..+|+++
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv-~g~C---~H~FH~hCI~kWl~~~~~--~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLV-WGKC---SHNFHMHCILKWLSTQSS--KGQCPMCRQPWKFK 84 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCcee-eccC---ccHHHHHHHHHHHccccC--CCCCCCcCCeeeeC
Confidence 5577788753220 1 12332 3556 367999999999997532 46999999999875
No 14
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.82 E-value=0.027 Score=55.76 Aligned_cols=54 Identities=26% Similarity=0.640 Sum_probs=39.1
Q ss_pred CCCCCcceEeccCCCCCC----------CccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 51 NGSLPCCRICLENDGEPD----------DELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 51 ~~~~~~CRIC~~~~~e~~----------~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
..+..+|-||.++.-.++ .|---||. +..|-.||+.|++.+ ..|++|+.+-.+.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~ERq-----QTCPICr~p~ifd 347 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLERQ-----QTCPICRRPVIFD 347 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHHhc-----cCCCcccCccccc
Confidence 445679999997632222 23456775 569999999999865 4999999985544
No 15
>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=93.64 E-value=0.056 Score=34.84 Aligned_cols=43 Identities=30% Similarity=0.812 Sum_probs=30.3
Q ss_pred cceEeccCCCCCCCcc-ccccccCCCCcccchhhHHHHHHhhcCccccccccccce
Q 023590 56 CCRICLENDGEPDDEL-ISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQ 110 (280)
Q Consensus 56 ~CRIC~~~~~e~~~~L-IsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~ 110 (280)
.|-||++.. .++. +.||. ...|..||.+|++.. ...|++|+..
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~-----H~~c~~C~~~~~~~~----~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCG-----HVFCRSCIDKWLKSG----KNTCPLCRTP 44 (45)
T ss_pred CCCcCchhh---hCceEecCCC-----ChhcHHHHHHHHHhC----cCCCCCCCCc
Confidence 478998653 2333 45564 458999999999862 3589999865
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=93.33 E-value=0.044 Score=41.68 Aligned_cols=45 Identities=27% Similarity=0.729 Sum_probs=28.8
Q ss_pred CCcceEeccCCCCC-------C--Cc-cccccccCCCCcccchhhHHHHHHhhcCcccccccccc
Q 023590 54 LPCCRICLENDGEP-------D--DE-LISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108 (280)
Q Consensus 54 ~~~CRIC~~~~~e~-------~--~~-LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk 108 (280)
.+.|-||++.-.+. + -+ ...+| .+..|..||.+|++.+ ..|++|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C-----~H~FH~~Ci~~Wl~~~-----~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPC-----GHIFHFHCISQWLKQN-----NTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETT-----SEEEEHHHHHHHHTTS-----SB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEeccc-----CCCEEHHHHHHHHhcC-----CcCCCCC
Confidence 34599999655322 1 11 12344 3679999999999754 4999995
No 17
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.15 E-value=0.057 Score=52.27 Aligned_cols=51 Identities=25% Similarity=0.576 Sum_probs=37.6
Q ss_pred CCCCCcceEeccCCCCCCCc-cccccccCCCCcccchhhHHHHHHhhcCcccccccccccee
Q 023590 51 NGSLPCCRICLENDGEPDDE-LISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQF 111 (280)
Q Consensus 51 ~~~~~~CRIC~~~~~e~~~~-LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y 111 (280)
++.+-.|-||++.-. ..+. .+.||+ +-.|..|+++|+.-- ...|+.|.++.
T Consensus 320 a~~GveCaICms~fi-K~d~~~vlPC~-----H~FH~~Cv~kW~~~y----~~~CPvCrt~i 371 (374)
T COG5540 320 ADKGVECAICMSNFI-KNDRLRVLPCD-----HRFHVGCVDKWLLGY----SNKCPVCRTAI 371 (374)
T ss_pred cCCCceEEEEhhhhc-ccceEEEeccC-----ceechhHHHHHHhhh----cccCCccCCCC
Confidence 344589999997543 3333 579997 559999999999832 25999998864
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=93.15 E-value=0.099 Score=48.61 Aligned_cols=62 Identities=19% Similarity=0.413 Sum_probs=42.8
Q ss_pred cCCCCCCcceEeccCCCCC------CCccccccccCCCCcccchhhHHHHHHhhcC-ccccccccccceeeeee
Q 023590 49 IENGSLPCCRICLENDGEP------DDELISPCMCKGTQQFVHRACLDHWRSVKEG-FAFSHCTTCKAQFHLRV 115 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~------~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~-~~~~~CElCk~~y~~~~ 115 (280)
...+....|-||++.--+. .-.++.+|. +.....|+.+|.+.+.. .....|++|+.+|...+
T Consensus 165 ~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~ 233 (242)
T PHA02926 165 YRVSKEKECGICYEVVYSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRETGASDNCPICRTRFRNIT 233 (242)
T ss_pred HhccCCCCCccCccccccccccccccccccCCCC-----chHHHHHHHHHHHhccccCcCCcCCCCcceeeeec
Confidence 3445668999999753211 124567775 56888999999986532 13568999999998653
No 19
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.87 E-value=0.055 Score=55.09 Aligned_cols=52 Identities=29% Similarity=0.579 Sum_probs=39.0
Q ss_pred CCCCCCcceEeccCCCCCCC--ccccccccCCCCcccchhhHHHHHHhhcCcccccccccccee
Q 023590 50 ENGSLPCCRICLENDGEPDD--ELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQF 111 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e~~~--~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y 111 (280)
.......|.||.+......+ +-..||. +-.|..||.+|++.+ ..|++|+..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er~-----qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFERQ-----QTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHHh-----CcCCcchhhh
Confidence 34456799999986543222 6677774 779999999999875 5999999833
No 20
>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=92.82 E-value=0.043 Score=38.25 Aligned_cols=45 Identities=27% Similarity=0.704 Sum_probs=34.1
Q ss_pred CcceEeccCCCCCCCccccccccCCCCcc-cchhhHHHHHHhhcCccccccccccceee
Q 023590 55 PCCRICLENDGEPDDELISPCMCKGTQQF-VHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 55 ~~CRIC~~~~~e~~~~LIsPC~CkGSlky-VH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
..|.||++. ..+..+.||. +. +-..|+.+|++. ...|++|+.++.
T Consensus 3 ~~C~iC~~~---~~~~~~~pCg-----H~~~C~~C~~~~~~~-----~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFEN---PRDVVLLPCG-----HLCFCEECAERLLKR-----KKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSS---BSSEEEETTC-----EEEEEHHHHHHHHHT-----TSBBTTTTBB-S
T ss_pred CCCccCCcc---CCceEEeCCC-----ChHHHHHHhHHhccc-----CCCCCcCChhhc
Confidence 579999975 3467889986 34 788999999983 369999998764
No 21
>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=91.99 E-value=0.14 Score=31.75 Aligned_cols=39 Identities=33% Similarity=0.885 Sum_probs=28.1
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccc
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTC 107 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElC 107 (280)
|.||++. ..++.+.||. ...|..|+.+|++.. ...|++|
T Consensus 1 C~iC~~~---~~~~~~~~C~-----H~~c~~C~~~~~~~~----~~~CP~C 39 (39)
T smart00184 1 CPICLEE---LKDPVVLPCG-----HTFCRSCIRKWLKSG----NNTCPIC 39 (39)
T ss_pred CCcCccC---CCCcEEecCC-----ChHHHHHHHHHHHhC----cCCCCCC
Confidence 6789865 3466778865 348999999999822 3578776
No 22
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.80 E-value=0.42 Score=44.41 Aligned_cols=55 Identities=25% Similarity=0.683 Sum_probs=43.8
Q ss_pred CCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 50 ENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
+.+..-.|-||++. ..+|.+++|. +..==.||-||+..+.+ ...|++||..-...
T Consensus 43 ~~~~~FdCNICLd~---akdPVvTlCG-----HLFCWpClyqWl~~~~~--~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 43 RDGGFFDCNICLDL---AKDPVVTLCG-----HLFCWPCLYQWLQTRPN--SKECPVCKAEVSID 97 (230)
T ss_pred CCCCceeeeeeccc---cCCCEEeecc-----cceehHHHHHHHhhcCC--CeeCCccccccccc
Confidence 45677899999975 4689999996 33445899999998764 57899999998876
No 23
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.30 E-value=0.21 Score=51.19 Aligned_cols=57 Identities=21% Similarity=0.529 Sum_probs=39.8
Q ss_pred ccccCCCCCCcceEeccCCC-----CC---------CCccccccccCCCCcccchhhHHHHHHhhcCcccccccccccee
Q 023590 46 DEDIENGSLPCCRICLENDG-----EP---------DDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQF 111 (280)
Q Consensus 46 ~~~~~~~~~~~CRIC~~~~~-----e~---------~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y 111 (280)
+.+.....+..|-||.+.-. .+ .+=+++||+ +..|+.||++|.... +..|+.|..+.
T Consensus 563 h~~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~y----kl~CPvCR~pL 633 (636)
T KOG0828|consen 563 HLEAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDTY----KLICPVCRCPL 633 (636)
T ss_pred cccchhhccccceEeccccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhhh----cccCCccCCCC
Confidence 34556677889999996432 01 123456887 679999999999853 26899997653
No 24
>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=88.68 E-value=0.23 Score=32.79 Aligned_cols=40 Identities=35% Similarity=0.821 Sum_probs=29.7
Q ss_pred ceEeccCCCCCCCcc-ccccccCCCCcccchhhHHHHHHhhcCccccccccc
Q 023590 57 CRICLENDGEPDDEL-ISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTC 107 (280)
Q Consensus 57 CRIC~~~~~e~~~~L-IsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElC 107 (280)
|.||++.. .++. +.||. +-++..||.+|++.++ ...|++|
T Consensus 1 C~iC~~~~---~~~~~~~~C~-----H~fC~~C~~~~~~~~~---~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF---EDPVILLPCG-----HSFCRDCLRKWLENSG---SVKCPLC 41 (41)
T ss_dssp ETTTSSBC---SSEEEETTTS-----EEEEHHHHHHHHHHTS---SSBTTTT
T ss_pred CCcCCccc---cCCCEEecCC-----CcchHHHHHHHHHhcC---CccCCcC
Confidence 67888643 3455 78886 6699999999999632 4678887
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=88.51 E-value=0.27 Score=38.92 Aligned_cols=53 Identities=21% Similarity=0.554 Sum_probs=37.9
Q ss_pred cceEeccCCC---------CCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 56 CCRICLENDG---------EPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 56 ~CRIC~~~~~---------e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
.|-||++.-+ .++-||+-- .| ....|.-|+.+|+..+.+ +..|+.|..+|++.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C---~h~fh~hCI~~wl~~~ts--q~~CPmcRq~~~~~ 83 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWG-YC---LHAFHAHCILKWLNTPTS--QGQCPMCRQTWQFK 83 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHH-HH---HHHHHHHHHHHHhcCccc--cccCCcchheeEec
Confidence 7888875321 123466533 55 367999999999998653 57999999999874
No 26
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=87.76 E-value=0.46 Score=33.80 Aligned_cols=45 Identities=22% Similarity=0.320 Sum_probs=35.1
Q ss_pred cceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 56 CCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 56 ~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
.|.||.+-- .+|.+.||. +-+-+.|+.+|++.. ..|++|+.++..
T Consensus 3 ~Cpi~~~~~---~~Pv~~~~G-----~v~~~~~i~~~~~~~-----~~cP~~~~~~~~ 47 (63)
T smart00504 3 LCPISLEVM---KDPVILPSG-----QTYERRAIEKWLLSH-----GTDPVTGQPLTH 47 (63)
T ss_pred CCcCCCCcC---CCCEECCCC-----CEEeHHHHHHHHHHC-----CCCCCCcCCCCh
Confidence 688998653 468888863 668999999999762 589999987753
No 27
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.27 E-value=0.89 Score=49.05 Aligned_cols=26 Identities=15% Similarity=0.653 Sum_probs=18.3
Q ss_pred cccchhhHHHHHHhhcCccccccccccceee
Q 023590 82 QFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 82 kyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
.|.|..|+..|-... ..|.+|..+|-
T Consensus 146 H~FC~~Ci~sWsR~a-----qTCPiDR~EF~ 171 (1134)
T KOG0825|consen 146 HYFCEECVGSWSRCA-----QTCPVDRGEFG 171 (1134)
T ss_pred cccHHHHhhhhhhhc-----ccCchhhhhhh
Confidence 467777777776543 47888877776
No 28
>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=85.72 E-value=0.32 Score=32.24 Aligned_cols=38 Identities=26% Similarity=0.878 Sum_probs=27.2
Q ss_pred ceEeccCCCCCCCc-cccccccCCCCcccchhhHHHHHHhhcCccccccccc
Q 023590 57 CRICLENDGEPDDE-LISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTC 107 (280)
Q Consensus 57 CRIC~~~~~e~~~~-LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElC 107 (280)
|-||++. ..++ .+.||. +...++|+++|++.+ ..|++|
T Consensus 1 C~iC~~~---~~~~~~~~~CG-----H~fC~~C~~~~~~~~-----~~CP~C 39 (39)
T PF13923_consen 1 CPICLDE---LRDPVVVTPCG-----HSFCKECIEKYLEKN-----PKCPVC 39 (39)
T ss_dssp ETTTTSB----SSEEEECTTS-----EEEEHHHHHHHHHCT-----SB-TTT
T ss_pred CCCCCCc---ccCcCEECCCC-----CchhHHHHHHHHHCc-----CCCcCC
Confidence 6688864 3457 468875 678999999999862 588877
No 29
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=85.37 E-value=0.87 Score=43.69 Aligned_cols=53 Identities=26% Similarity=0.648 Sum_probs=40.8
Q ss_pred ccCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 48 DIENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 48 ~~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
...+...+.|-+|++. ..+|--+||. +..==+|+..|.+++ ..|++|..+++-
T Consensus 233 ~~i~~a~~kC~LCLe~---~~~pSaTpCG-----HiFCWsCI~~w~~ek-----~eCPlCR~~~~p 285 (293)
T KOG0317|consen 233 SSIPEATRKCSLCLEN---RSNPSATPCG-----HIFCWSCILEWCSEK-----AECPLCREKFQP 285 (293)
T ss_pred ccCCCCCCceEEEecC---CCCCCcCcCc-----chHHHHHHHHHHccc-----cCCCcccccCCC
Confidence 3445666899999975 4578889986 345568999999876 469999988874
No 30
>PLN02189 cellulose synthase
Probab=80.00 E-value=1.3 Score=48.99 Aligned_cols=54 Identities=28% Similarity=0.579 Sum_probs=39.6
Q ss_pred CCCCcceEeccCCC-CCCCccccccc-cCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 52 GSLPCCRICLENDG-EPDDELISPCM-CKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 52 ~~~~~CRIC~~~~~-e~~~~LIsPC~-CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
.+..+|+||-+.-+ +.++++.-.|+ |. --|=+.|.+.=+++- +..|++||++|+
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~---fpvCr~Cyeyer~eg----~q~CpqCkt~Y~ 87 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECG---FPVCRPCYEYERREG----TQNCPQCKTRYK 87 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCC---CccccchhhhhhhcC----CccCcccCCchh
Confidence 34569999987644 23466778888 72 238899997766543 479999999999
No 31
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.85 E-value=1.6 Score=43.54 Aligned_cols=48 Identities=21% Similarity=0.461 Sum_probs=37.2
Q ss_pred CCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 53 SLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 53 ~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
....|.||++.- .+|.+.||. +.....|+.+|+... ..|++|+.++..
T Consensus 25 ~~l~C~IC~d~~---~~PvitpCg-----H~FCs~CI~~~l~~~-----~~CP~Cr~~~~~ 72 (397)
T TIGR00599 25 TSLRCHICKDFF---DVPVLTSCS-----HTFCSLCIRRCLSNQ-----PKCPLCRAEDQE 72 (397)
T ss_pred cccCCCcCchhh---hCccCCCCC-----CchhHHHHHHHHhCC-----CCCCCCCCcccc
Confidence 346899999643 467888875 567789999999753 489999998764
No 32
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.40 E-value=1.9 Score=43.23 Aligned_cols=47 Identities=30% Similarity=0.781 Sum_probs=31.8
Q ss_pred CCcceEeccCCCCCCCcc--ccccccCCCCcccchhhHHHHHHhhcCcccccccccc
Q 023590 54 LPCCRICLENDGEPDDEL--ISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108 (280)
Q Consensus 54 ~~~CRIC~~~~~e~~~~L--IsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk 108 (280)
...|-||-+.- ..+.++ |+.|. +..|..||.+|+..-.+ ++.|++|+
T Consensus 4 ~A~C~Ic~d~~-p~~~~l~~i~~cG-----hifh~~cl~qwfe~~Ps--~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHICIDGR-PNDHELGPIGTCG-----HIFHTTCLTQWFEGDPS--NRGCPICQ 52 (465)
T ss_pred cceeeEeccCC-ccccccccccchh-----hHHHHHHHHHHHccCCc--cCCCCcee
Confidence 45899995432 222333 34443 56999999999986543 37999998
No 33
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=76.01 E-value=1.8 Score=31.15 Aligned_cols=48 Identities=23% Similarity=0.642 Sum_probs=22.0
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
|.+|.+.. +..+.-+.||.|. +|-|+.=|.....+ ..-.|+-|+.+|.
T Consensus 1 cp~C~e~~-d~~d~~~~PC~Cg------f~IC~~C~~~i~~~-~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCECG------FQICRFCYHDILEN-EGGRCPGCREPYK 48 (48)
T ss_dssp -TTTS-B---CCCTT--SSTTS----------HHHHHHHTTS-S-SB-TTT--B--
T ss_pred CCCccccc-ccCCCccccCcCC------CcHHHHHHHHHHhc-cCCCCCCCCCCCC
Confidence 45666433 4456678999993 56677777766532 2469999999984
No 34
>PLN02436 cellulose synthase A
Probab=76.01 E-value=1.9 Score=47.79 Aligned_cols=53 Identities=28% Similarity=0.538 Sum_probs=39.0
Q ss_pred CCCcceEeccCCC-CCCCccccccc-cCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 53 SLPCCRICLENDG-EPDDELISPCM-CKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 53 ~~~~CRIC~~~~~-e~~~~LIsPC~-CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
+..+|+||-++-+ +.++++.-.|+ |. --|=+.|.+.=+++- ...|.+||++|+
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~---fpvCr~Cyeyer~eg----~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECA---FPVCRPCYEYERREG----NQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCC---CccccchhhhhhhcC----CccCcccCCchh
Confidence 4469999987543 23566778888 72 238899997666543 479999999999
No 35
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=73.44 E-value=2.7 Score=28.59 Aligned_cols=43 Identities=23% Similarity=0.648 Sum_probs=32.2
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccc
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKA 109 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~ 109 (280)
|-||++.-.+...+.+.+|. ..+.++|+.+.. . ....|++|+.
T Consensus 2 C~~C~~~~~~~~~~~l~~Cg-----H~~C~~C~~~~~--~---~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCG-----HIFCEKCLKKLK--G---KSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccC-----CHHHHHHHHhhc--C---CCCCCcCCCC
Confidence 77898765334467889985 678999999988 1 2479999973
No 36
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.36 E-value=2.8 Score=46.42 Aligned_cols=55 Identities=27% Similarity=0.606 Sum_probs=34.8
Q ss_pred CCCcceEeccCCCCCCCccc-ccc-ccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 53 SLPCCRICLENDGEPDDELI-SPC-MCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 53 ~~~~CRIC~~~~~e~~~~LI-sPC-~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
....|-||+.--..-+..|- .-| .|+ .-.|-.||-+|.++++ ...|++|..++.+
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCk---nKFH~~CLyKWf~Ss~---~s~CPlCRseitf 1524 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCK---NKFHTRCLYKWFASSA---RSNCPLCRSEITF 1524 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhh---hhhhHHHHHHHHHhcC---CCCCCcccccccc
Confidence 34789999853210111221 111 222 3389999999999875 4799999987764
No 37
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.22 E-value=5.5 Score=39.27 Aligned_cols=56 Identities=25% Similarity=0.539 Sum_probs=38.2
Q ss_pred CCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeeeee
Q 023590 50 ENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVEL 117 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~~~ 117 (280)
.+++.+.|=||+.+ ..+-++.|||= -..=..|-+.-+-. +..|++|..++.-..+.
T Consensus 286 ~~~~gkeCVIClse---~rdt~vLPCRH----LCLCs~Ca~~Lr~q-----~n~CPICRqpi~~ll~i 341 (349)
T KOG4265|consen 286 ESESGKECVICLSE---SRDTVVLPCRH----LCLCSGCAKSLRYQ-----TNNCPICRQPIEELLEI 341 (349)
T ss_pred cccCCCeeEEEecC---CcceEEecchh----hehhHhHHHHHHHh-----hcCCCccccchHhhhee
Confidence 34678999999964 35678889871 22445677666532 35899999988754433
No 38
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=68.76 E-value=3.6 Score=32.88 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=24.4
Q ss_pred cccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 82 QFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 82 kyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
.-.|--|+.+|++.+ ..|+++..+|++.
T Consensus 56 HaFH~HCI~rWL~Tk-----~~CPld~q~w~~~ 83 (88)
T COG5194 56 HAFHDHCIYRWLDTK-----GVCPLDRQTWVLA 83 (88)
T ss_pred hHHHHHHHHHHHhhC-----CCCCCCCceeEEe
Confidence 558999999999986 3899999999875
No 39
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=67.95 E-value=4.2 Score=32.24 Aligned_cols=58 Identities=24% Similarity=0.442 Sum_probs=23.8
Q ss_pred CCCCCcceEeccCCC-CCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 51 NGSLPCCRICLENDG-EPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 51 ~~~~~~CRIC~~~~~-e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
..+..+|.||-+.-+ +.++++.--|+=- --.|=+.|.+.=+++. ...|..||++|...
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC--~fPvCr~CyEYErkeg----~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHEC--AFPVCRPCYEYERKEG----NQVCPQCKTRYKRH 64 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-------HHHHHHHHHTS-----SB-TTT--B----
T ss_pred hcCCcccccccCccccCCCCCEEEEEccc--CCccchhHHHHHhhcC----cccccccCCCcccc
Confidence 356679999986543 2234455555422 1238899998887763 47999999999854
No 40
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=64.55 E-value=3.7 Score=41.84 Aligned_cols=51 Identities=29% Similarity=0.661 Sum_probs=34.9
Q ss_pred cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccce
Q 023590 49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQ 110 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~ 110 (280)
...-+.|+|-+|++... ++-.-|.|=.| .+-.|.+||.+|=. ..|++|.+-
T Consensus 170 ~~~tELPTCpVCLERMD-~s~~gi~t~~c---~Hsfh~~cl~~w~~-------~scpvcR~~ 220 (493)
T KOG0804|consen 170 TGLTELPTCPVCLERMD-SSTTGILTILC---NHSFHCSCLMKWWD-------SSCPVCRYC 220 (493)
T ss_pred CCcccCCCcchhHhhcC-ccccceeeeec---ccccchHHHhhccc-------CcChhhhhh
Confidence 44566799999997643 33223444444 25589999999964 689999764
No 41
>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=63.71 E-value=2.4 Score=36.52 Aligned_cols=42 Identities=21% Similarity=0.423 Sum_probs=28.1
Q ss_pred CCCCcceEeccCCCCCCCccccccccCCCC---cccchhhHHHHHHh
Q 023590 52 GSLPCCRICLENDGEPDDELISPCMCKGTQ---QFVHRACLDHWRSV 95 (280)
Q Consensus 52 ~~~~~CRIC~~~~~e~~~~LIsPC~CkGSl---kyVH~~CL~~Wi~~ 95 (280)
.....|+||++.-.+.++-..-+|. |++ +..|..|+++|...
T Consensus 24 ~~~~EC~IC~~~I~~~~GvV~vt~~--g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 24 RCTVECQICFDRIDNNDGVVYVTDG--GTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred ccCeeehhhhhhhhcCCCEEEEecC--CeehHHHHHHHHHHHHHHhh
Confidence 3467899999765542344445544 444 34899999999644
No 42
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=59.46 E-value=6.8 Score=32.72 Aligned_cols=28 Identities=14% Similarity=0.529 Sum_probs=23.9
Q ss_pred cccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 82 QFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 82 kyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
+-.|.-|+.+||+.+ ..|+||..+..+.
T Consensus 83 HaFH~hCisrWlktr-----~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 83 HAFHFHCISRWLKTR-----NVCPLDNKEWVFQ 110 (114)
T ss_pred hHHHHHHHHHHHhhc-----CcCCCcCcceeEe
Confidence 558999999999986 4999999888765
No 43
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=55.29 E-value=5.1 Score=40.58 Aligned_cols=54 Identities=31% Similarity=0.784 Sum_probs=40.0
Q ss_pred cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
...+.-..|.||-+.+ .+--|.||. +..-..||..|..++++ ..|+.|..+.+-
T Consensus 364 eMgsTFeLCKICaend---KdvkIEPCG-----HLlCt~CLa~WQ~sd~g---q~CPFCRcEIKG 417 (563)
T KOG1785|consen 364 EMGSTFELCKICAEND---KDVKIEPCG-----HLLCTSCLAAWQDSDEG---QTCPFCRCEIKG 417 (563)
T ss_pred HccchHHHHHHhhccC---CCccccccc-----chHHHHHHHhhcccCCC---CCCCceeeEecc
Confidence 3555667999998653 466789986 34556899999987654 589999887663
No 44
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=54.91 E-value=11 Score=42.25 Aligned_cols=54 Identities=31% Similarity=0.624 Sum_probs=36.2
Q ss_pred CCCCcceEeccCCC-CCCCccccccc-cCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 52 GSLPCCRICLENDG-EPDDELISPCM-CKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 52 ~~~~~CRIC~~~~~-e~~~~LIsPC~-CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
.+..+|+||-+.-+ +.++++.--|+ |. --|=+.|.+-=+++- ...|++||++|+
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~---FPVCrpCYEYEr~eG----~q~CPqCktrYk 70 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCA---FPVCRPCYEYERKDG----NQSCPQCKTKYK 70 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCC---CccccchhhhhhhcC----CccCCccCCchh
Confidence 34569999986543 22344444554 31 228899997666553 479999999999
No 45
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.66 E-value=13 Score=38.12 Aligned_cols=49 Identities=27% Similarity=0.630 Sum_probs=35.6
Q ss_pred cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
.-....+.|+||.+.- ..-+.||. |..||.+|...+ ..|++|+......
T Consensus 474 ~l~~~~~~~~~~~~~~----~~~~~~~~--------~~~~l~~~~~~~-----~~~pl~~~~~~~~ 522 (543)
T KOG0802|consen 474 QLREPNDVCAICYQEM----SARITPCS--------HALCLRKWLYVQ-----EVCPLCHTYMKED 522 (543)
T ss_pred hhhcccCcchHHHHHH----Hhcccccc--------chhHHHhhhhhc-----cccCCCchhhhcc
Confidence 3345568999999753 23456666 999999999865 4899997766554
No 46
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=49.34 E-value=11 Score=36.80 Aligned_cols=56 Identities=20% Similarity=0.438 Sum_probs=36.5
Q ss_pred CcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhc------------------Cccccccccccceeeeee
Q 023590 55 PCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKE------------------GFAFSHCTTCKAQFHLRV 115 (280)
Q Consensus 55 ~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~------------------~~~~~~CElCk~~y~~~~ 115 (280)
.+|-||+=+-.+.+.-.+++|. +|.|-.||.+.|..-. ..-...|.+|..+..++.
T Consensus 116 gqCvICLygfa~~~~ft~T~C~-----Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~ 189 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACD-----HYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE 189 (368)
T ss_pred CceEEEEEeecCCCceeeehhH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence 4666666443222223458875 8999999998876421 112357999999888774
No 47
>PLN02400 cellulose synthase
Probab=47.13 E-value=17 Score=40.76 Aligned_cols=54 Identities=22% Similarity=0.471 Sum_probs=35.6
Q ss_pred CCCcceEeccCCC-CCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 53 SLPCCRICLENDG-EPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 53 ~~~~CRIC~~~~~-e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
+..+|+||-++-+ +.++++.--|+=-| --|=+.|.+-=+++- ...|++||++|+
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCa--FPVCRpCYEYERkeG----nq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECA--FPVCRPCYEYERKDG----TQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCC--CccccchhheecccC----CccCcccCCccc
Confidence 4569999987544 22344555554211 228889986655542 479999999999
No 48
>PLN02195 cellulose synthase A
Probab=44.87 E-value=19 Score=39.93 Aligned_cols=54 Identities=24% Similarity=0.524 Sum_probs=35.7
Q ss_pred CCCCcceEeccCCCC-CCCccccccc-cCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 52 GSLPCCRICLENDGE-PDDELISPCM-CKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 52 ~~~~~CRIC~~~~~e-~~~~LIsPC~-CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
++..+|+||-+.-+- .++++.--|+ | ---|=+.|.+-=+++- +..|++||++|+
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC---~~pvCrpCyeyer~eg----~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHEC---SYPLCKACLEYEIKEG----RKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccC---CCccccchhhhhhhcC----CccCCccCCccc
Confidence 345699999864432 2333444443 3 1238899997666543 479999999999
No 49
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.60 E-value=20 Score=36.35 Aligned_cols=54 Identities=20% Similarity=0.590 Sum_probs=37.7
Q ss_pred CCCcceEeccCCCCCCCc-cccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 53 SLPCCRICLENDGEPDDE-LISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 53 ~~~~CRIC~~~~~e~~~~-LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
...+|-||++.-..+++. +++| .| -...-..|.++|+- +. -...|++|+.+=..
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl-~c---ghlFgs~cie~wl~-k~--~~~~cp~c~~katk 57 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSL-QC---GHLFGSQCIEKWLG-KK--TKMQCPLCSGKATK 57 (463)
T ss_pred ccccCceeeeeeeecCceEEeee-cc---cccccHHHHHHHHh-hh--hhhhCcccCChhHH
Confidence 456899999866555544 5555 44 34577899999995 32 35899999876443
No 50
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=37.37 E-value=17 Score=25.16 Aligned_cols=42 Identities=24% Similarity=0.555 Sum_probs=20.2
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCcccccc
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHC 104 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~C 104 (280)
|-||.+-.++...|.+.||. +-+=++||+++.+.+. .+..+|
T Consensus 1 CpIc~e~~~~~n~P~~L~CG-----H~~c~~cl~~l~~~~~-~~~~kC 42 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCG-----HVFCKDCLQKLSKKSD-RNRFKC 42 (43)
T ss_dssp -TTT----TTSS-EEE-SSS------EEEHHHHHHHHHH-S--S-B--
T ss_pred CCccccccCCCCCCEEEeCc-----cHHHHHHHHHHHhcCC-CCeeeC
Confidence 55677622223346889965 4588999999998653 123455
No 51
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=36.23 E-value=14 Score=25.12 Aligned_cols=42 Identities=31% Similarity=0.667 Sum_probs=25.5
Q ss_pred ceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccc
Q 023590 57 CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTC 107 (280)
Q Consensus 57 CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElC 107 (280)
|-||++- ..+|...+|. +-.=+.||.+|.+...+ ....|++|
T Consensus 1 CpiC~~~---~~~Pv~l~CG-----H~FC~~Cl~~~~~~~~~-~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL---FKDPVSLPCG-----HSFCRSCLERLWKEPSG-SGFSCPEC 42 (42)
T ss_dssp ETTTTSB----SSEEE-SSS-----SEEEHHHHHHHHCCSSS-ST---SSS
T ss_pred CCccchh---hCCccccCCc-----CHHHHHHHHHHHHccCC-cCCCCcCC
Confidence 5677753 3578888875 34668999999976543 22678877
No 52
>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=35.15 E-value=60 Score=28.95 Aligned_cols=41 Identities=27% Similarity=0.677 Sum_probs=25.9
Q ss_pred CCcceEeccCCCC-------CCCccccccccCCCCcccchhhHHHHHHhh
Q 023590 54 LPCCRICLENDGE-------PDDELISPCMCKGTQQFVHRACLDHWRSVK 96 (280)
Q Consensus 54 ~~~CRIC~~~~~e-------~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s 96 (280)
...|-||++-.-. +-+.=-.|=.|. ..|-|.+||+|..+..
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~--Ts~rhSNCLdqfkka~ 49 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCD--TSYRHSNCLDQFKKAY 49 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccC--CccchhHHHHHHHHHh
Confidence 4579999975421 111222344476 4578999999998764
No 53
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=33.35 E-value=37 Score=38.05 Aligned_cols=56 Identities=23% Similarity=0.570 Sum_probs=37.0
Q ss_pred CCCCCCcceEeccCCCC-CCCccccccc-cCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 50 ENGSLPCCRICLENDGE-PDDELISPCM-CKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e-~~~~LIsPC~-CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
++.+..+|.||-+.-+- .++++.--|+ | ---|=+.|.+-=+++- ...|.+||++|.
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC---~fpvCr~cyeye~~~g----~~~cp~c~t~y~ 68 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVC---GFPVCKPCYEYERSEG----NQCCPQCNTRYK 68 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccC---CCccccchhhhhhhcC----CccCCccCCchh
Confidence 34567799999865442 2344444443 3 1228889997665542 479999999999
No 54
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=31.86 E-value=28 Score=30.29 Aligned_cols=56 Identities=23% Similarity=0.634 Sum_probs=39.6
Q ss_pred CCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 53 SLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 53 ~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
.--+|-||.+.. .++.++.|=.|-|- +.---=|..-|--.+ -...|+.||+.|+..
T Consensus 79 ~lYeCnIC~etS--~ee~FLKPneCCgY-~iCn~Cya~LWK~~~---~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 79 KLYECNICKETS--AEERFLKPNECCGY-SICNACYANLWKFCN---LYPVCPVCKTSFKSS 134 (140)
T ss_pred CceeccCccccc--chhhcCCcccccch-HHHHHHHHHHHHHcc---cCCCCCccccccccc
Confidence 556899999754 45789999999773 223333456676544 247999999999865
No 55
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.13 E-value=49 Score=30.37 Aligned_cols=64 Identities=22% Similarity=0.503 Sum_probs=36.5
Q ss_pred CCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHh----hcCc--cccccccccceeeeee
Q 023590 51 NGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSV----KEGF--AFSHCTTCKAQFHLRV 115 (280)
Q Consensus 51 ~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~----s~~~--~~~~CElCk~~y~~~~ 115 (280)
+.....|-||+.-.- ++..--.-|.-.---+-.|+-||-.|+.. +++. -+-.|+-|..+..++.
T Consensus 162 dd~~~~cgicyayql-dGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm 231 (234)
T KOG3268|consen 162 DDELGACGICYAYQL-DGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM 231 (234)
T ss_pred chhhhcccceeeeec-CCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence 344456777773110 01011123333223477999999999864 2322 3468999998887664
No 56
>PF15050 SCIMP: SCIMP protein
Probab=29.57 E-value=12 Score=32.13 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=23.6
Q ss_pred hhhhhHHHHHHHHhccceeeeecccccceeecccceeeeeee
Q 023590 182 FYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSL 223 (280)
Q Consensus 182 F~~~~gv~~Ffvlvg~~G~iv~~~~c~vY~~~~~~~~~W~~l 223 (280)
||++++|-.-+|-+ -+|+|++| |||-..++=+.|.+-
T Consensus 8 FWiiLAVaII~vS~-~lglIlyC----vcR~~lRqGkkweia 44 (133)
T PF15050_consen 8 FWIILAVAIILVSV-VLGLILYC----VCRWQLRQGKKWEIA 44 (133)
T ss_pred hHHHHHHHHHHHHH-HHHHHHHH----HHHHHHHccccceec
Confidence 99999986544444 34777775 555444445677764
No 57
>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=28.95 E-value=53 Score=31.99 Aligned_cols=51 Identities=16% Similarity=0.382 Sum_probs=32.8
Q ss_pred CcceEeccCCCC-CCC-ccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590 55 PCCRICLENDGE-PDD-ELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 55 ~~CRIC~~~~~e-~~~-~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
..|-||....-- +.. -++++|. +-.=++|+.+.+... ...|+.|+..+...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CG-----H~~C~sCv~~l~~~~----~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCG-----HTLCESCVDLLFVRG----SGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCC-----CcccHHHHHHHhcCC----CCCCCCCCCccchh
Confidence 589999964321 121 2677663 335569999966432 35899998877643
No 58
>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=28.59 E-value=66 Score=31.92 Aligned_cols=40 Identities=23% Similarity=0.674 Sum_probs=28.8
Q ss_pred ccccccCCCCcccchhhHHHHHHhhcC--------ccccccccccceeeee
Q 023590 72 ISPCMCKGTQQFVHRACLDHWRSVKEG--------FAFSHCTTCKAQFHLR 114 (280)
Q Consensus 72 IsPC~CkGSlkyVH~~CL~~Wi~~s~~--------~~~~~CElCk~~y~~~ 114 (280)
=.+|.|+- -==.+||-||+.+++. +.+-.|+.|..+|=+.
T Consensus 306 C~~C~CRP---mWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil 353 (358)
T PF10272_consen 306 CQQCYCRP---MWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL 353 (358)
T ss_pred Cccccccc---hHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence 45777751 1246899999998863 2467999999998654
No 59
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=27.19 E-value=21 Score=35.62 Aligned_cols=46 Identities=30% Similarity=0.658 Sum_probs=33.4
Q ss_pred CCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceee
Q 023590 54 LPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFH 112 (280)
Q Consensus 54 ~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~ 112 (280)
.--|-||++- ..-|+|.||. +-.-.-|+...++.+ ..|++|.++++
T Consensus 23 lLRC~IC~ey---f~ip~itpCs-----HtfCSlCIR~~L~~~-----p~CP~C~~~~~ 68 (442)
T KOG0287|consen 23 LLRCGICFEY---FNIPMITPCS-----HTFCSLCIRKFLSYK-----PQCPTCCVTVT 68 (442)
T ss_pred HHHHhHHHHH---hcCceecccc-----chHHHHHHHHHhccC-----CCCCceecccc
Confidence 3479999964 3578999964 223445777877654 69999998887
No 60
>TIGR02876 spore_yqfD sporulation protein YqfD. YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter.
Probab=26.99 E-value=41 Score=33.17 Aligned_cols=31 Identities=19% Similarity=0.456 Sum_probs=25.5
Q ss_pred ccccCCCcchh---------hhhHHHHHHHHhccceeeee
Q 023590 173 RILSKHPIPFY---------YCIELLLWVGSLGLFPCIYG 203 (280)
Q Consensus 173 r~L~~~~~~F~---------~~~gv~~Ffvlvg~~G~iv~ 203 (280)
++++|+.+||+ ..+|+++|++++=++-.+||
T Consensus 67 ~I~~r~GlpF~~~r~~kRk~~~~G~~~f~~ll~~lS~fIW 106 (382)
T TIGR02876 67 KIIARKGLPFLFKRLRKRPGILIGILLFLAIVYFLSNFIW 106 (382)
T ss_pred EEECCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhheEE
Confidence 56677899998 67899999998877777777
No 61
>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=26.97 E-value=32 Score=24.39 Aligned_cols=39 Identities=15% Similarity=0.360 Sum_probs=18.4
Q ss_pred CccccccccCCCCcccchhh--HHHHHHhhcCccccccccccce
Q 023590 69 DELISPCMCKGTQQFVHRAC--LDHWRSVKEGFAFSHCTTCKAQ 110 (280)
Q Consensus 69 ~~LIsPC~CkGSlkyVH~~C--L~~Wi~~s~~~~~~~CElCk~~ 110 (280)
..+..|++= ....|-+| |+.|+........+.|++|+.+
T Consensus 10 ~~i~~P~Rg---~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 10 QRIRIPVRG---KNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-SSEEEE---TT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CEEEeCccC---CcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 345567653 35688888 5678887654456999999863
No 62
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.68 E-value=58 Score=32.13 Aligned_cols=59 Identities=24% Similarity=0.562 Sum_probs=35.8
Q ss_pred CCCCCCcceEeccCCCCCC---Ccc-ccc-cccCCCCcccchhhHHHHHHhhc--Cccccccccccceeee
Q 023590 50 ENGSLPCCRICLENDGEPD---DEL-ISP-CMCKGTQQFVHRACLDHWRSVKE--GFAFSHCTTCKAQFHL 113 (280)
Q Consensus 50 ~~~~~~~CRIC~~~~~e~~---~~L-IsP-C~CkGSlkyVH~~CL~~Wi~~s~--~~~~~~CElCk~~y~~ 113 (280)
.......|=||++...+.- ..+ |.| |. ...=.+|..+|.+.++ ..-.+.|++|...=..
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~-----H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCN-----HSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcc-----hhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 3466899999998765432 001 333 43 2234578899996553 1124799999765443
No 63
>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=25.42 E-value=26 Score=26.99 Aligned_cols=33 Identities=24% Similarity=0.620 Sum_probs=22.0
Q ss_pred CCCCcceEeccCCCCCCCc-cccccccCCCCcccchhhHHH
Q 023590 52 GSLPCCRICLENDGEPDDE-LISPCMCKGTQQFVHRACLDH 91 (280)
Q Consensus 52 ~~~~~CRIC~~~~~e~~~~-LIsPC~CkGSlkyVH~~CL~~ 91 (280)
.+...|.+|...-+. .. .+.||. ..||..|+.|
T Consensus 76 ~~~~~C~vC~k~l~~--~~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN--SVFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred CCCCCccCcCCcCCC--ceEEEeCCC-----eEEecccccC
Confidence 345679999976532 33 356763 5799999764
No 64
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=24.82 E-value=42 Score=36.33 Aligned_cols=67 Identities=24% Similarity=0.574 Sum_probs=43.5
Q ss_pred cceEeccCCCCCCCccccccccCCCCc--ccchhhH-------HHHHHhh---c-Cccccccccccceeeeeeeeecccc
Q 023590 56 CCRICLENDGEPDDELISPCMCKGTQQ--FVHRACL-------DHWRSVK---E-GFAFSHCTTCKAQFHLRVELFEDNS 122 (280)
Q Consensus 56 ~CRIC~~~~~e~~~~LIsPC~CkGSlk--yVH~~CL-------~~Wi~~s---~-~~~~~~CElCk~~y~~~~~~~~~~~ 122 (280)
=|-.|-++.+=.++|||. |+|-.- -|||.|- -.|+=.+ + .....+||||-+++--- |.-+...
T Consensus 7 GCCVCSDErGWaeNPLVY---CDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGAL-KkTDn~G 82 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVY---CDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGAL-KKTDNGG 82 (900)
T ss_pred ceeeecCcCCCccCceee---ecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccce-ecccCCC
Confidence 388998766656789984 666443 3999996 3566322 1 12457999998887643 3334577
Q ss_pred cccc
Q 023590 123 WRKI 126 (280)
Q Consensus 123 W~~l 126 (280)
|...
T Consensus 83 WAHV 86 (900)
T KOG0956|consen 83 WAHV 86 (900)
T ss_pred ceEE
Confidence 8654
No 65
>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=24.74 E-value=57 Score=23.04 Aligned_cols=25 Identities=12% Similarity=0.264 Sum_probs=12.4
Q ss_pred HHHHHHhhcCccccccccccceeeee
Q 023590 89 LDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 89 L~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
+.+.+..-...+ ..|++|+.+|.-.
T Consensus 9 ~~k~i~~l~~~~-~~CPlC~r~l~~e 33 (54)
T PF04423_consen 9 LKKYIEELKEAK-GCCPLCGRPLDEE 33 (54)
T ss_dssp HHHHHHHHTT-S-EE-TTT--EE-HH
T ss_pred HHHHHHHHhcCC-CcCCCCCCCCCHH
Confidence 556666543322 3999999998743
No 66
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=24.31 E-value=53 Score=32.89 Aligned_cols=53 Identities=19% Similarity=0.701 Sum_probs=35.8
Q ss_pred CCCcceEeccCCCCCCCccccccccCCCCcc-cchhhHHHHHHhhcCccccccccccceeeee
Q 023590 53 SLPCCRICLENDGEPDDELISPCMCKGTQQF-VHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114 (280)
Q Consensus 53 ~~~~CRIC~~~~~e~~~~LIsPC~CkGSlky-VH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~ 114 (280)
+.+.|-.|.+. -+-.+.-.-||.| .| |-|-| |-..+++. .-+|+-|...|.-+
T Consensus 13 eed~cplcie~-mditdknf~pc~c----gy~ic~fc---~~~irq~l-ngrcpacrr~y~de 66 (480)
T COG5175 13 EEDYCPLCIEP-MDITDKNFFPCPC----GYQICQFC---YNNIRQNL-NGRCPACRRKYDDE 66 (480)
T ss_pred ccccCcccccc-cccccCCcccCCc----ccHHHHHH---HHHHHhhc-cCCChHhhhhcccc
Confidence 44579999964 3445677899999 33 55666 55444331 35899999988754
No 67
>PF11118 DUF2627: Protein of unknown function (DUF2627); InterPro: IPR020138 This entry represents uncharacterised membrane proteins with no known function.
Probab=22.56 E-value=47 Score=26.24 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=18.7
Q ss_pred hhhhhHHHHHHHHhccceeeee
Q 023590 182 FYYCIELLLWVGSLGLFPCIYG 203 (280)
Q Consensus 182 F~~~~gv~~Ffvlvg~~G~iv~ 203 (280)
.+...|.+.|..-+||+|+.++
T Consensus 41 lqfl~G~~lf~~G~~Fi~GfI~ 62 (77)
T PF11118_consen 41 LQFLAGLLLFAIGVGFIAGFIL 62 (77)
T ss_pred HHHHHHHHHHHHHHHHHHhHhh
Confidence 3466799999999999999887
No 68
>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=21.96 E-value=38 Score=21.23 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=10.3
Q ss_pred ccccccccceee
Q 023590 101 FSHCTTCKAQFH 112 (280)
Q Consensus 101 ~~~CElCk~~y~ 112 (280)
...|+.|++.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 579999999885
No 69
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=21.60 E-value=35 Score=25.55 Aligned_cols=46 Identities=17% Similarity=0.252 Sum_probs=30.3
Q ss_pred cceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeee
Q 023590 56 CCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113 (280)
Q Consensus 56 ~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~ 113 (280)
.|-|+++-- .+|.+.|+. +..=+.|+++|+.... ..|++|+.+...
T Consensus 6 ~CpIt~~lM---~dPVi~~~G-----~tyer~~I~~~l~~~~----~~~P~t~~~l~~ 51 (73)
T PF04564_consen 6 LCPITGELM---RDPVILPSG-----HTYERSAIERWLEQNG----GTDPFTRQPLSE 51 (73)
T ss_dssp B-TTTSSB----SSEEEETTS-----EEEEHHHHHHHHCTTS----SB-TTT-SB-SG
T ss_pred CCcCcCcHh---hCceeCCcC-----CEEcHHHHHHHHHcCC----CCCCCCCCcCCc
Confidence 566776432 478888843 5688999999998732 689999876654
No 70
>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=21.21 E-value=44 Score=18.46 Aligned_cols=12 Identities=25% Similarity=0.849 Sum_probs=7.8
Q ss_pred ccccccceeeee
Q 023590 103 HCTTCKAQFHLR 114 (280)
Q Consensus 103 ~CElCk~~y~~~ 114 (280)
.|++|+..|.-.
T Consensus 2 ~C~~C~~~~~~~ 13 (24)
T PF13894_consen 2 QCPICGKSFRSK 13 (24)
T ss_dssp E-SSTS-EESSH
T ss_pred CCcCCCCcCCcH
Confidence 699999988743
Done!