Query 036983
Match_columns 122
No_of_seqs 181 out of 344
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:24:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00744 RINGv The RING-vari 99.7 5.8E-17 1.2E-21 101.6 4.3 46 1-51 4-49 (49)
2 PF12906 RINGv: RING-variant d 99.6 3.3E-17 7.2E-22 101.9 1.2 45 1-50 3-47 (47)
3 PHA02825 LAP/PHD finger-like p 99.6 4.9E-16 1.1E-20 118.7 5.5 60 1-71 13-72 (162)
4 PHA02862 5L protein; Provision 99.6 1.1E-15 2.3E-20 115.8 3.4 59 1-70 7-65 (156)
5 KOG1609 Protein involved in mR 99.5 6E-15 1.3E-19 117.0 2.5 57 1-60 83-139 (323)
6 COG5183 SSM4 Protein involved 99.3 1.1E-12 2.4E-17 119.8 4.0 55 1-60 17-71 (1175)
7 KOG3053 Uncharacterized conser 98.1 1.7E-06 3.6E-11 71.3 2.0 43 17-59 38-86 (293)
8 PF13639 zf-RING_2: Ring finge 96.7 0.00076 1.6E-08 40.1 1.5 40 1-51 5-44 (44)
9 KOG4628 Predicted E3 ubiquitin 95.1 0.015 3.3E-07 49.6 2.6 42 12-59 240-282 (348)
10 PF12861 zf-Apc11: Anaphase-pr 93.4 0.055 1.2E-06 37.8 2.0 32 22-56 51-83 (85)
11 COG5219 Uncharacterized conser 93.1 0.067 1.5E-06 51.4 2.6 30 27-56 1495-1524(1525)
12 PF13920 zf-C3HC4_3: Zinc fing 92.4 0.21 4.6E-06 30.2 3.4 36 15-57 14-50 (50)
13 PHA02929 N1R/p28-like protein; 92.1 0.15 3.2E-06 41.4 3.1 36 17-59 196-231 (238)
14 PF12678 zf-rbx1: RING-H2 zinc 91.4 0.12 2.6E-06 34.2 1.6 22 28-51 52-73 (73)
15 smart00184 RING Ring finger. E 91.1 0.41 9E-06 25.6 3.3 30 15-50 10-39 (39)
16 cd00162 RING RING-finger (Real 91.0 0.22 4.9E-06 27.7 2.2 24 29-53 21-44 (45)
17 KOG1493 Anaphase-promoting com 89.3 0.23 5E-06 34.6 1.5 39 14-56 43-82 (84)
18 PF11793 FANCL_C: FANCL C-term 88.8 0.18 3.9E-06 33.3 0.7 48 1-55 7-66 (70)
19 PLN03208 E3 ubiquitin-protein 88.4 1 2.2E-05 35.8 4.8 36 15-55 30-79 (193)
20 smart00504 Ubox Modified RING 87.5 1.1 2.4E-05 27.5 3.8 33 15-54 13-45 (63)
21 PF00097 zf-C3HC4: Zinc finger 83.8 1.6 3.4E-05 24.9 2.9 28 18-50 14-41 (41)
22 KOG0802 E3 ubiquitin ligase [P 77.9 1.5 3.3E-05 38.7 2.1 31 16-53 309-339 (543)
23 PF13923 zf-C3HC4_2: Zinc fing 77.7 2.6 5.7E-05 24.1 2.4 28 16-50 11-39 (39)
24 COG5194 APC11 Component of SCF 73.8 2.7 5.9E-05 29.5 2.1 29 28-58 56-84 (88)
25 KOG0827 Predicted E3 ubiquitin 73.0 2.1 4.6E-05 37.7 1.7 24 28-51 28-52 (465)
26 PF08746 zf-RING-like: RING-li 67.7 2.9 6.3E-05 25.2 1.0 21 30-50 23-43 (43)
27 KOG0823 Predicted E3 ubiquitin 67.6 6.9 0.00015 31.9 3.4 38 14-56 58-96 (230)
28 PF13894 zf-C2H2_4: C2H2-type 66.0 2.6 5.6E-05 20.6 0.5 14 46-59 2-15 (24)
29 COG5243 HRD1 HRD ubiquitin lig 65.7 6.3 0.00014 34.8 3.0 33 15-54 312-344 (491)
30 PF10571 UPF0547: Uncharacteri 61.1 3.8 8.3E-05 22.4 0.6 14 42-55 12-25 (26)
31 PF14634 zf-RING_5: zinc-RING 60.2 16 0.00034 21.4 3.2 41 1-52 4-44 (44)
32 PHA02926 zinc finger-like prot 59.7 7.1 0.00015 32.0 2.2 32 28-59 199-234 (242)
33 KOG2930 SCF ubiquitin ligase, 55.8 10 0.00022 27.8 2.2 26 28-55 83-108 (114)
34 PF00096 zf-C2H2: Zinc finger, 55.3 4.9 0.00011 20.1 0.4 13 46-58 2-14 (23)
35 KOG0828 Predicted E3 ubiquitin 53.6 9 0.00019 34.9 1.9 35 13-53 598-632 (636)
36 smart00782 PhnA_Zn_Ribbon PhnA 49.9 8.7 0.00019 23.8 0.9 15 40-54 3-17 (47)
37 PF06170 DUF983: Protein of un 45.3 54 0.0012 22.5 4.4 17 42-58 6-22 (86)
38 PF13465 zf-H2C2_2: Zinc-finge 45.1 9.7 0.00021 20.2 0.5 12 45-56 15-26 (26)
39 PF13912 zf-C2H2_6: C2H2-type 44.3 7.7 0.00017 20.1 0.0 14 46-59 3-16 (27)
40 PF12874 zf-met: Zinc-finger o 43.6 9.7 0.00021 19.3 0.4 14 46-59 2-15 (25)
41 TIGR00599 rad18 DNA repair pro 43.5 23 0.00049 30.9 2.8 35 15-56 38-72 (397)
42 PF06305 DUF1049: Protein of u 41.8 35 0.00076 21.3 2.9 23 96-118 18-40 (68)
43 smart00451 ZnF_U1 U1-like zinc 40.0 14 0.00031 20.0 0.8 16 43-58 2-17 (35)
44 COG5540 RING-finger-containing 38.2 22 0.00047 30.7 1.8 35 14-54 337-371 (374)
45 PF01440 Gemini_AL2: Geminivir 33.8 5.6 0.00012 29.9 -2.1 34 15-51 31-64 (134)
46 PF12633 Adenyl_cycl_N: Adenyl 33.4 23 0.0005 28.3 1.2 11 111-121 37-47 (204)
47 PF06376 DUF1070: Protein of u 33.3 48 0.001 19.5 2.3 17 101-117 18-34 (34)
48 PF09777 OSTMP1: Osteopetrosis 32.8 14 0.0003 29.8 -0.2 84 29-118 106-208 (237)
49 PF12171 zf-C2H2_jaz: Zinc-fin 30.0 26 0.00056 18.4 0.7 14 46-59 3-16 (27)
50 PF15227 zf-C3HC4_4: zinc fing 29.7 38 0.00082 19.9 1.5 31 15-50 10-42 (42)
51 PF09607 BrkDBD: Brinker DNA-b 29.1 40 0.00086 22.0 1.6 21 22-42 23-49 (58)
52 smart00355 ZnF_C2H2 zinc finge 28.4 23 0.00051 17.0 0.3 13 46-58 2-14 (26)
53 PF03779 SPW: SPW repeat; Int 28.1 69 0.0015 19.9 2.5 19 99-119 4-22 (51)
54 PF06847 Arc_PepC_II: Archaeal 28.0 56 0.0012 22.7 2.3 21 92-112 67-89 (93)
55 PF04564 U-box: U-box domain; 27.9 47 0.001 21.5 1.8 36 15-56 16-51 (73)
56 PF14570 zf-RING_4: RING/Ubox 27.9 78 0.0017 19.8 2.7 33 17-55 14-48 (48)
57 COG5189 SFP1 Putative transcri 26.8 25 0.00055 30.6 0.5 16 45-60 399-414 (423)
58 PRK05978 hypothetical protein; 26.4 1.1E+02 0.0024 23.2 3.9 17 43-59 51-67 (148)
59 COG4698 Uncharacterized protei 24.5 28 0.00061 27.8 0.3 16 99-114 21-36 (197)
60 PF05210 Sprouty: Sprouty prot 22.7 57 0.0012 23.7 1.6 24 13-41 54-77 (108)
61 TIGR00270 conserved hypothetic 22.5 37 0.0008 25.6 0.6 12 46-57 2-13 (154)
62 PF03854 zf-P11: P-11 zinc fin 22.2 42 0.00091 21.3 0.7 25 28-54 21-45 (50)
63 PF12907 zf-met2: Zinc-binding 22.2 22 0.00047 21.5 -0.6 16 44-59 1-16 (40)
64 PF09630 DUF2024: Domain of un 21.5 57 0.0012 22.6 1.3 25 32-56 33-64 (81)
65 PF11298 DUF3099: Protein of u 21.4 37 0.0008 22.9 0.3 20 89-108 19-38 (73)
66 PRK08359 transcription factor; 21.2 46 0.001 25.9 0.9 14 45-58 7-20 (176)
67 PF10726 DUF2518: Protein of f 21.2 65 0.0014 24.6 1.7 20 100-119 19-38 (145)
68 PF13063 DUF3925: Protein of u 20.7 52 0.0011 21.7 0.9 15 105-119 19-33 (66)
69 PF13913 zf-C2HC_2: zinc-finge 20.6 41 0.00089 17.8 0.4 10 45-54 3-12 (25)
70 PF01363 FYVE: FYVE zinc finge 20.1 25 0.00054 22.1 -0.7 20 37-56 2-21 (69)
No 1
>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=99.67 E-value=5.8e-17 Score=101.63 Aligned_cols=46 Identities=46% Similarity=0.967 Sum_probs=41.5
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCC
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICG 51 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~ 51 (122)
||+++. +.++++++||.|+|+++++|++||++|+..+++++||||+
T Consensus 4 IC~~~~-----~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 4 ICHDEG-----DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CCCCCC-----CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 788732 3667899999999999999999999999999999999996
No 2
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.64 E-value=3.3e-17 Score=101.92 Aligned_cols=45 Identities=36% Similarity=0.891 Sum_probs=35.5
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecC
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEIC 50 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC 50 (122)
||+.+.+. +++|+.||.|+|+++|||++||++|+..+++++||+|
T Consensus 3 IC~~~~~~-----~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 3 ICLEGEEE-----DEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp TTTEE-SS-----SS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred EeCCcCCC-----CCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 78888753 2389999999999999999999999999999999998
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.62 E-value=4.9e-16 Score=118.70 Aligned_cols=60 Identities=28% Similarity=0.683 Sum_probs=51.5
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccCCCCCCchhhhcc
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAGANEADPMEQWTE 71 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~~~~~~~~e~w~~ 71 (122)
|||.+.+ ....||.|+|++++||++|+++|++.+++..||+|+++|...... +++.+|.-
T Consensus 13 IC~~~~~--------~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~---kpl~~W~~ 72 (162)
T PHA02825 13 ICKDEYD--------VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNY---KKCTKWRC 72 (162)
T ss_pred ecCCCCC--------CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEec---CCCccccc
Confidence 7876632 245899999999999999999999999999999999999888764 67889963
No 4
>PHA02862 5L protein; Provisional
Probab=99.57 E-value=1.1e-15 Score=115.76 Aligned_cols=59 Identities=22% Similarity=0.596 Sum_probs=51.5
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccCCCCCCchhhhc
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAGANEADPMEQWT 70 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~~~~~~~~e~w~ 70 (122)
|||.+.+. ...||.|+|++++|||+||++|++.++++.||+|+++|...+.. ++.++|.
T Consensus 7 IC~~~~~e--------~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~y---Kpf~kW~ 65 (156)
T PHA02862 7 ICNDVCDE--------RNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTY---VSFKKWN 65 (156)
T ss_pred EecCcCCC--------CcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEcc---ccHHHhh
Confidence 78876431 15999999999999999999999999999999999999877764 6899996
No 5
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.50 E-value=6e-15 Score=116.99 Aligned_cols=57 Identities=47% Similarity=0.879 Sum_probs=48.6
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccCC
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAGA 60 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~~ 60 (122)
|||...+..+ +.+++.||.|+|++++||+.|+++|+.+||+.+||+|++.|++....
T Consensus 83 Ic~~~~~~~~---~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~~ 139 (323)
T KOG1609|consen 83 ICHEEDEESN---GLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGTK 139 (323)
T ss_pred EEeccccccc---ccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceeccee
Confidence 6777654321 11799999999999999999999999999999999999999998663
No 6
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.31 E-value=1.1e-12 Score=119.82 Aligned_cols=55 Identities=24% Similarity=0.530 Sum_probs=49.0
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccCC
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAGA 60 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~~ 60 (122)
|||.+.. .|+||-.||+|+||++|+|++||..|...+++++||||||+|+.....
T Consensus 17 ICr~e~~-----~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY 71 (1175)
T COG5183 17 ICRTEDI-----RDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIY 71 (1175)
T ss_pred eecCCCC-----CCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeec
Confidence 5776543 788999999999999999999999999999999999999999776654
No 7
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.07 E-value=1.7e-06 Score=71.26 Aligned_cols=43 Identities=23% Similarity=0.474 Sum_probs=37.8
Q ss_pred eecCCCccchhhhhhHHHHHHHHhhcC------CCeeecCCcccccccC
Q 036983 17 IELGCSCKDDLAAAHKQCAEAWFKIKG------NKTCEICGTTASNVAG 59 (122)
Q Consensus 17 l~~pC~CkGsL~~vH~~Cl~~W~~~kg------~~~CEIC~~~~~n~~~ 59 (122)
-+.||.|+|+.+.|||+||.+|+..|. +-.|.-|..+|..+-.
T Consensus 38 WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P 86 (293)
T KOG3053|consen 38 WVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFP 86 (293)
T ss_pred hcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeecc
Confidence 479999999999999999999999864 2589999999987654
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=96.75 E-value=0.00076 Score=40.15 Aligned_cols=40 Identities=28% Similarity=0.813 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCC
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICG 51 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~ 51 (122)
||..+.+. +.....++|. ...|.+|+++|++.+ .+|-+|+
T Consensus 5 IC~~~~~~----~~~~~~l~C~-----H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFED----GEKVVKLPCG-----HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp TTTCBHHT----TSCEEEETTS-----EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCChhhcC----CCeEEEccCC-----CeeCHHHHHHHHHhC--CcCCccC
Confidence 66666643 4456788862 789999999999885 4898884
No 9
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.13 E-value=0.015 Score=49.57 Aligned_cols=42 Identities=26% Similarity=0.631 Sum_probs=33.6
Q ss_pred CCCCce-ecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccC
Q 036983 12 ESGVPI-ELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAG 59 (122)
Q Consensus 12 e~~~~l-~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~ 59 (122)
+.||.| ++||+ ..-|..|...|+... .+.|-+||+......+
T Consensus 240 ~~GdklRiLPC~-----H~FH~~CIDpWL~~~-r~~CPvCK~di~~~~~ 282 (348)
T KOG4628|consen 240 EKGDKLRILPCS-----HKFHVNCIDPWLTQT-RTFCPVCKRDIRTDSG 282 (348)
T ss_pred ccCCeeeEecCC-----CchhhccchhhHhhc-CccCCCCCCcCCCCCC
Confidence 466666 89997 678999999999987 5679999997755444
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=93.44 E-value=0.055 Score=37.80 Aligned_cols=32 Identities=19% Similarity=0.574 Sum_probs=26.6
Q ss_pred CccchhhhhhHHHHHHHHhh-cCCCeeecCCccccc
Q 036983 22 SCKDDLAAAHKQCAEAWFKI-KGNKTCEICGTTASN 56 (122)
Q Consensus 22 ~CkGsL~~vH~~Cl~~W~~~-kg~~~CEIC~~~~~n 56 (122)
.|+ ...|.+|+.+|++. +++..|-+|.++++.
T Consensus 51 ~C~---H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 51 KCS---HNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred cCc---cHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 555 46999999999998 467899999998864
No 11
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.06 E-value=0.067 Score=51.43 Aligned_cols=30 Identities=20% Similarity=0.595 Sum_probs=26.6
Q ss_pred hhhhhHHHHHHHHhhcCCCeeecCCccccc
Q 036983 27 LAAAHKQCAEAWFKIKGNKTCEICGTTASN 56 (122)
Q Consensus 27 L~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n 56 (122)
-.-.|..|+-+||+++++.+|.+|.+++..
T Consensus 1495 knKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1495 KNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred hhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 346899999999999999999999988753
No 12
>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=92.40 E-value=0.21 Score=30.22 Aligned_cols=36 Identities=31% Similarity=0.565 Sum_probs=29.0
Q ss_pred CceecCCCccchhhh-hhHHHHHHHHhhcCCCeeecCCcccccc
Q 036983 15 VPIELGCSCKDDLAA-AHKQCAEAWFKIKGNKTCEICGTTASNV 57 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~-vH~~Cl~~W~~~kg~~~CEIC~~~~~n~ 57 (122)
+.+..||. .. +-.+|+.+|++ ....|-+|+..+..|
T Consensus 14 ~~~~~pCg-----H~~~C~~C~~~~~~--~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 14 DVVLLPCG-----HLCFCEECAERLLK--RKKKCPICRQPIESV 50 (50)
T ss_dssp SEEEETTC-----EEEEEHHHHHHHHH--TTSBBTTTTBB-SEE
T ss_pred ceEEeCCC-----ChHHHHHHhHHhcc--cCCCCCcCChhhcCC
Confidence 47889986 44 77899999999 889999999987643
No 13
>PHA02929 N1R/p28-like protein; Provisional
Probab=92.07 E-value=0.15 Score=41.39 Aligned_cols=36 Identities=28% Similarity=0.564 Sum_probs=28.5
Q ss_pred eecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcccccccC
Q 036983 17 IELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASNVAG 59 (122)
Q Consensus 17 l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~~ 59 (122)
+..+|. ...|++|+.+|++. ..+|.+|+..+..+..
T Consensus 196 vl~~C~-----H~FC~~CI~~Wl~~--~~tCPlCR~~~~~v~~ 231 (238)
T PHA02929 196 ILSNCN-----HVFCIECIDIWKKE--KNTCPVCRTPFISVIK 231 (238)
T ss_pred ecCCCC-----CcccHHHHHHHHhc--CCCCCCCCCEeeEEee
Confidence 445664 67999999999875 5689999999887654
No 14
>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=91.44 E-value=0.12 Score=34.23 Aligned_cols=22 Identities=32% Similarity=0.851 Sum_probs=17.6
Q ss_pred hhhhHHHHHHHHhhcCCCeeecCC
Q 036983 28 AAAHKQCAEAWFKIKGNKTCEICG 51 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~kg~~~CEIC~ 51 (122)
...|.+|+++|++.+. +|-+|.
T Consensus 52 H~FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 52 HIFHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp EEEEHHHHHHHHTTSS--B-TTSS
T ss_pred CCEEHHHHHHHHhcCC--cCCCCC
Confidence 5689999999997655 999885
No 15
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=91.07 E-value=0.41 Score=25.56 Aligned_cols=30 Identities=40% Similarity=0.990 Sum_probs=22.5
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecC
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEIC 50 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC 50 (122)
++..+||.- ..|..|+++|++ .+...|.+|
T Consensus 10 ~~~~~~C~H-----~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 10 DPVVLPCGH-----TFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CcEEecCCC-----hHHHHHHHHHHH-hCcCCCCCC
Confidence 467788653 469999999998 566677765
No 16
>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=90.96 E-value=0.22 Score=27.71 Aligned_cols=24 Identities=33% Similarity=0.938 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHhhcCCCeeecCCcc
Q 036983 29 AAHKQCAEAWFKIKGNKTCEICGTT 53 (122)
Q Consensus 29 ~vH~~Cl~~W~~~kg~~~CEIC~~~ 53 (122)
..|..|+++|++. ++..|-+|+..
T Consensus 21 ~~c~~C~~~~~~~-~~~~Cp~C~~~ 44 (45)
T cd00162 21 VFCRSCIDKWLKS-GKNTCPLCRTP 44 (45)
T ss_pred hhcHHHHHHHHHh-CcCCCCCCCCc
Confidence 4799999999987 77789999875
No 17
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=89.26 E-value=0.23 Score=34.56 Aligned_cols=39 Identities=28% Similarity=0.652 Sum_probs=30.9
Q ss_pred CCceecCCCccchhhhhhHHHHHHHHhhcCC-CeeecCCccccc
Q 036983 14 GVPIELGCSCKDDLAAAHKQCAEAWFKIKGN-KTCEICGTTASN 56 (122)
Q Consensus 14 ~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~-~~CEIC~~~~~n 56 (122)
+=||+.+ .| +...|.+|+.+|+.++.+ ..|.+|.++|+.
T Consensus 43 dCPLv~G-~C---~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 43 DCPLVWG-YC---LHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCccHHH-HH---HHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 3466666 55 357999999999998776 589999999864
No 18
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=88.76 E-value=0.18 Score=33.26 Aligned_cols=48 Identities=27% Similarity=0.574 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCCCceecCC---CccchhhhhhHHHHHHHHhhc-CCC--------eeecCCcccc
Q 036983 1 ICHLSFDAANPESGVPIELGC---SCKDDLAAAHKQCAEAWFKIK-GNK--------TCEICGTTAS 55 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC---~CkGsL~~vH~~Cl~~W~~~k-g~~--------~CEIC~~~~~ 55 (122)
||..... +.++....-| .|+ ...|..||.+||... +++ .|-.|+...+
T Consensus 7 IC~~~~~----~~~~~p~~~C~n~~C~---~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 7 ICYSYRL----DDGEIPDVVCPNPSCG---KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp SS--SS-----TT-----B--S-TT-------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred cCCcEec----CCCCcCceEcCCcccC---CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 6665543 1222234445 455 478999999999963 222 5888877653
No 19
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=88.37 E-value=1 Score=35.76 Aligned_cols=36 Identities=19% Similarity=0.453 Sum_probs=27.7
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhc--------------CCCeeecCCcccc
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIK--------------GNKTCEICGTTAS 55 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~k--------------g~~~CEIC~~~~~ 55 (122)
++..++|. ......|+.+|+..+ +...|-+|+..+.
T Consensus 30 dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 30 DPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred CcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 46778773 467899999998743 3468999999884
No 20
>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=87.47 E-value=1.1 Score=27.51 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=27.3
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCccc
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTA 54 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~ 54 (122)
+|..+||+ ...-++|+++|++. +.+|.+|++.+
T Consensus 13 ~Pv~~~~G-----~v~~~~~i~~~~~~--~~~cP~~~~~~ 45 (63)
T smart00504 13 DPVILPSG-----QTYERRAIEKWLLS--HGTDPVTGQPL 45 (63)
T ss_pred CCEECCCC-----CEEeHHHHHHHHHH--CCCCCCCcCCC
Confidence 47788764 66889999999987 56899999877
No 21
>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=83.76 E-value=1.6 Score=24.93 Aligned_cols=28 Identities=25% Similarity=0.809 Sum_probs=23.5
Q ss_pred ecCCCccchhhhhhHHHHHHHHhhcCCCeeecC
Q 036983 18 ELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEIC 50 (122)
Q Consensus 18 ~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC 50 (122)
.++|. ......|+.+|++.++...|-+|
T Consensus 14 ~~~C~-----H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 14 LLPCG-----HSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTS-----EEEEHHHHHHHHHHTSSSBTTTT
T ss_pred EecCC-----CcchHHHHHHHHHhcCCccCCcC
Confidence 77775 55899999999999888888776
No 22
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.87 E-value=1.5 Score=38.74 Aligned_cols=31 Identities=35% Similarity=0.891 Sum_probs=26.9
Q ss_pred ceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcc
Q 036983 16 PIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTT 53 (122)
Q Consensus 16 ~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~ 53 (122)
+-.+||. ...|..|+..||+. ..+|-+|+..
T Consensus 309 ~~rL~C~-----Hifh~~CL~~W~er--~qtCP~CR~~ 339 (543)
T KOG0802|consen 309 PKRLPCG-----HIFHDSCLRSWFER--QQTCPTCRTV 339 (543)
T ss_pred cceeecc-----cchHHHHHHHHHHH--hCcCCcchhh
Confidence 5678884 78999999999998 6799999993
No 23
>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=77.69 E-value=2.6 Score=24.12 Aligned_cols=28 Identities=29% Similarity=0.802 Sum_probs=20.6
Q ss_pred c-eecCCCccchhhhhhHHHHHHHHhhcCCCeeecC
Q 036983 16 P-IELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEIC 50 (122)
Q Consensus 16 ~-l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC 50 (122)
+ ..++|. ....++|+++|++. +..|-+|
T Consensus 11 ~~~~~~CG-----H~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 11 PVVVTPCG-----HSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp EEEECTTS-----EEEEHHHHHHHHHC--TSB-TTT
T ss_pred cCEECCCC-----CchhHHHHHHHHHC--cCCCcCC
Confidence 5 567775 45799999999988 4688766
No 24
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=73.82 E-value=2.7 Score=29.47 Aligned_cols=29 Identities=28% Similarity=0.513 Sum_probs=24.0
Q ss_pred hhhhHHHHHHHHhhcCCCeeecCCccccccc
Q 036983 28 AAAHKQCAEAWFKIKGNKTCEICGTTASNVA 58 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n~~ 58 (122)
...|.+|+.+|+++|| .|.++.++|+.-.
T Consensus 56 HaFH~HCI~rWL~Tk~--~CPld~q~w~~~~ 84 (88)
T COG5194 56 HAFHDHCIYRWLDTKG--VCPLDRQTWVLAD 84 (88)
T ss_pred hHHHHHHHHHHHhhCC--CCCCCCceeEEec
Confidence 3689999999999955 7999999886543
No 25
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.99 E-value=2.1 Score=37.69 Aligned_cols=24 Identities=33% Similarity=0.832 Sum_probs=20.7
Q ss_pred hhhhHHHHHHHHhhcC-CCeeecCC
Q 036983 28 AAAHKQCAEAWFKIKG-NKTCEICG 51 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~kg-~~~CEIC~ 51 (122)
...|..|+.+||..-- ||.|+||+
T Consensus 28 hifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 28 HIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred hHHHHHHHHHHHccCCccCCCCcee
Confidence 3689999999999754 48999999
No 26
>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=67.72 E-value=2.9 Score=25.19 Aligned_cols=21 Identities=29% Similarity=0.855 Sum_probs=15.4
Q ss_pred hhHHHHHHHHhhcCCCeeecC
Q 036983 30 AHKQCAEAWFKIKGNKTCEIC 50 (122)
Q Consensus 30 vH~~Cl~~W~~~kg~~~CEIC 50 (122)
.|..|+++.|+.+.+..|..|
T Consensus 23 ~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 23 LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp E-HHHHHHHTTT-SS-B-TTT
T ss_pred HHHHHHHHHHhcCCCCCCcCC
Confidence 899999999999998888766
No 27
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.62 E-value=6.9 Score=31.90 Aligned_cols=38 Identities=21% Similarity=0.490 Sum_probs=28.2
Q ss_pred CCceecCCCccchhhhhhHHHHHHHHhhcCCCe-eecCCccccc
Q 036983 14 GVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKT-CEICGTTASN 56 (122)
Q Consensus 14 ~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~-CEIC~~~~~n 56 (122)
-||+++.|. .+.==-|+-||+.++.++. |-+||.+..-
T Consensus 58 kdPVvTlCG-----HLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 58 KDPVVTLCG-----HLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCEEeecc-----cceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 357888875 2333579999999987765 5999998843
No 28
>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=65.96 E-value=2.6 Score=20.60 Aligned_cols=14 Identities=29% Similarity=0.755 Sum_probs=9.4
Q ss_pred eeecCCcccccccC
Q 036983 46 TCEICGTTASNVAG 59 (122)
Q Consensus 46 ~CEIC~~~~~n~~~ 59 (122)
.|++|++.|.+...
T Consensus 2 ~C~~C~~~~~~~~~ 15 (24)
T PF13894_consen 2 QCPICGKSFRSKSE 15 (24)
T ss_dssp E-SSTS-EESSHHH
T ss_pred CCcCCCCcCCcHHH
Confidence 59999999977653
No 29
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=65.69 E-value=6.3 Score=34.82 Aligned_cols=33 Identities=30% Similarity=0.797 Sum_probs=27.1
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCccc
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTA 54 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~ 54 (122)
.|-.+||. ...|-+||..|+.- ..+|.||+...
T Consensus 312 ~pKrLpCG-----HilHl~CLknW~ER--qQTCPICr~p~ 344 (491)
T COG5243 312 TPKRLPCG-----HILHLHCLKNWLER--QQTCPICRRPV 344 (491)
T ss_pred Cccccccc-----ceeeHHHHHHHHHh--ccCCCcccCcc
Confidence 35578886 67999999999975 45899999983
No 30
>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=61.14 E-value=3.8 Score=22.45 Aligned_cols=14 Identities=29% Similarity=0.601 Sum_probs=11.6
Q ss_pred cCCCeeecCCcccc
Q 036983 42 KGNKTCEICGTTAS 55 (122)
Q Consensus 42 kg~~~CEIC~~~~~ 55 (122)
...+.|..|||+|.
T Consensus 12 ~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 12 ESAKFCPHCGYDFE 25 (26)
T ss_pred hhcCcCCCCCCCCc
Confidence 45689999999985
No 31
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=60.25 E-value=16 Score=21.43 Aligned_cols=41 Identities=22% Similarity=0.487 Sum_probs=29.6
Q ss_pred CCCCCCCCCCCCCCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCc
Q 036983 1 ICHLSFDAANPESGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGT 52 (122)
Q Consensus 1 ICh~~~~~~~~e~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~ 52 (122)
||+.... +...+.+++|. ..+-++|+++.. .....|-+|++
T Consensus 4 ~C~~~~~----~~~~~~l~~Cg-----H~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 4 ICFEKYS----EERRPRLTSCG-----HIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CcCcccc----CCCCeEEcccC-----CHHHHHHHHhhc--CCCCCCcCCCC
Confidence 4555551 23447788884 578899999988 77789999974
No 32
>PHA02926 zinc finger-like protein; Provisional
Probab=59.66 E-value=7.1 Score=32.03 Aligned_cols=32 Identities=22% Similarity=0.564 Sum_probs=25.7
Q ss_pred hhhhHHHHHHHHhhc----CCCeeecCCcccccccC
Q 036983 28 AAAHKQCAEAWFKIK----GNKTCEICGTTASNVAG 59 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~k----g~~~CEIC~~~~~n~~~ 59 (122)
......|+.+|.+.+ +.+.|.+|...|..+..
T Consensus 199 HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~p 234 (242)
T PHA02926 199 HIFCITCINIWHRTRRETGASDNCPICRTRFRNITM 234 (242)
T ss_pred chHHHHHHHHHHHhccccCcCCcCCCCcceeeeecc
Confidence 346779999999975 35779999999987764
No 33
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=55.83 E-value=10 Score=27.77 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=20.8
Q ss_pred hhhhHHHHHHHHhhcCCCeeecCCcccc
Q 036983 28 AAAHKQCAEAWFKIKGNKTCEICGTTAS 55 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~kg~~~CEIC~~~~~ 55 (122)
...|.+|..+|+|.+ ..|.+|.++..
T Consensus 83 HaFH~hCisrWlktr--~vCPLdn~eW~ 108 (114)
T KOG2930|consen 83 HAFHFHCISRWLKTR--NVCPLDNKEWV 108 (114)
T ss_pred hHHHHHHHHHHHhhc--CcCCCcCccee
Confidence 358999999999985 47888887653
No 34
>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=55.33 E-value=4.9 Score=20.07 Aligned_cols=13 Identities=38% Similarity=0.897 Sum_probs=10.6
Q ss_pred eeecCCccccccc
Q 036983 46 TCEICGTTASNVA 58 (122)
Q Consensus 46 ~CEIC~~~~~n~~ 58 (122)
.|++|+..|....
T Consensus 2 ~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 2 KCPICGKSFSSKS 14 (23)
T ss_dssp EETTTTEEESSHH
T ss_pred CCCCCCCccCCHH
Confidence 5999999997654
No 35
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.60 E-value=9 Score=34.94 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=26.9
Q ss_pred CCCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCcc
Q 036983 13 SGVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTT 53 (122)
Q Consensus 13 ~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~ 53 (122)
+.+.+.+||. ...|++||++|..... -.|.+|...
T Consensus 598 ~~nYm~tPC~-----HifH~~CL~~WMd~yk-l~CPvCR~p 632 (636)
T KOG0828|consen 598 RRNYMLTPCH-----HIFHRQCLLQWMDTYK-LICPVCRCP 632 (636)
T ss_pred hccccccchH-----HHHHHHHHHHHHhhhc-ccCCccCCC
Confidence 4467888997 6899999999998321 478888764
No 36
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=49.88 E-value=8.7 Score=23.85 Aligned_cols=15 Identities=27% Similarity=0.833 Sum_probs=11.0
Q ss_pred hhcCCCeeecCCccc
Q 036983 40 KIKGNKTCEICGTTA 54 (122)
Q Consensus 40 ~~kg~~~CEIC~~~~ 54 (122)
+.+.+.+||+|+.+.
T Consensus 3 ~~Rs~~kCELC~a~~ 17 (47)
T smart00782 3 LARCESKCELCGSDS 17 (47)
T ss_pred hHHcCCcccCcCCCC
Confidence 345566799999765
No 37
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=45.25 E-value=54 Score=22.55 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=13.1
Q ss_pred cCCCeeecCCccccccc
Q 036983 42 KGNKTCEICGTTASNVA 58 (122)
Q Consensus 42 kg~~~CEIC~~~~~n~~ 58 (122)
|=+..|+.||.+|.-.+
T Consensus 6 k~~~~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 6 KVAPRCPHCGLDYSHAR 22 (86)
T ss_pred cCCCcccccCCccccCC
Confidence 34678999999996654
No 38
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=45.15 E-value=9.7 Score=20.21 Aligned_cols=12 Identities=42% Similarity=0.880 Sum_probs=9.8
Q ss_pred CeeecCCccccc
Q 036983 45 KTCEICGTTASN 56 (122)
Q Consensus 45 ~~CEIC~~~~~n 56 (122)
=.|++|++.|.+
T Consensus 15 ~~C~~C~k~F~~ 26 (26)
T PF13465_consen 15 YKCPYCGKSFSN 26 (26)
T ss_dssp EEESSSSEEESS
T ss_pred CCCCCCcCeeCc
Confidence 489999998863
No 39
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=44.26 E-value=7.7 Score=20.12 Aligned_cols=14 Identities=36% Similarity=0.864 Sum_probs=12.2
Q ss_pred eeecCCcccccccC
Q 036983 46 TCEICGTTASNVAG 59 (122)
Q Consensus 46 ~CEIC~~~~~n~~~ 59 (122)
.|++|+..|.+...
T Consensus 3 ~C~~C~~~F~~~~~ 16 (27)
T PF13912_consen 3 ECDECGKTFSSLSA 16 (27)
T ss_dssp EETTTTEEESSHHH
T ss_pred CCCccCCccCChhH
Confidence 69999999988765
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=43.65 E-value=9.7 Score=19.33 Aligned_cols=14 Identities=29% Similarity=0.686 Sum_probs=11.3
Q ss_pred eeecCCcccccccC
Q 036983 46 TCEICGTTASNVAG 59 (122)
Q Consensus 46 ~CEIC~~~~~n~~~ 59 (122)
.|+||+..|.+...
T Consensus 2 ~C~~C~~~f~s~~~ 15 (25)
T PF12874_consen 2 YCDICNKSFSSENS 15 (25)
T ss_dssp EETTTTEEESSHHH
T ss_pred CCCCCCCCcCCHHH
Confidence 59999999977653
No 41
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.46 E-value=23 Score=30.92 Aligned_cols=35 Identities=20% Similarity=0.517 Sum_probs=25.8
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCccccc
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASN 56 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n 56 (122)
++.++||. ......|+..|+..+ ..|-+|+..+..
T Consensus 38 ~PvitpCg-----H~FCs~CI~~~l~~~--~~CP~Cr~~~~~ 72 (397)
T TIGR00599 38 VPVLTSCS-----HTFCSLCIRRCLSNQ--PKCPLCRAEDQE 72 (397)
T ss_pred CccCCCCC-----CchhHHHHHHHHhCC--CCCCCCCCcccc
Confidence 35566764 345678999999764 489999998854
No 42
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.82 E-value=35 Score=21.28 Aligned_cols=23 Identities=13% Similarity=0.449 Sum_probs=18.9
Q ss_pred chHHHHHHHHHHHHHHHHHhhhc
Q 036983 96 HRFLNFLLACMVFAFVISWLFHF 118 (122)
Q Consensus 96 ~~flnfllacmv~afvi~W~f~~ 118 (122)
.|.-..+++++++++++.|++.+
T Consensus 18 ~pl~l~il~~f~~G~llg~l~~~ 40 (68)
T PF06305_consen 18 LPLGLLILIAFLLGALLGWLLSL 40 (68)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH
Confidence 67778888999999999988753
No 43
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=40.00 E-value=14 Score=20.01 Aligned_cols=16 Identities=25% Similarity=0.634 Sum_probs=12.4
Q ss_pred CCCeeecCCccccccc
Q 036983 43 GNKTCEICGTTASNVA 58 (122)
Q Consensus 43 g~~~CEIC~~~~~n~~ 58 (122)
|.-.|++|...|.+..
T Consensus 2 ~~~~C~~C~~~~~~~~ 17 (35)
T smart00451 2 GGFYCKLCNVTFTDEI 17 (35)
T ss_pred cCeEccccCCccCCHH
Confidence 5668999999987443
No 44
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.20 E-value=22 Score=30.72 Aligned_cols=35 Identities=23% Similarity=0.530 Sum_probs=25.5
Q ss_pred CCceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCccc
Q 036983 14 GVPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTA 54 (122)
Q Consensus 14 ~~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~ 54 (122)
+....+||. .-.|..|+++|+.-- ...|.+|....
T Consensus 337 d~~~vlPC~-----H~FH~~Cv~kW~~~y-~~~CPvCrt~i 371 (374)
T COG5540 337 DRLRVLPCD-----HRFHVGCVDKWLLGY-SNKCPVCRTAI 371 (374)
T ss_pred ceEEEeccC-----ceechhHHHHHHhhh-cccCCccCCCC
Confidence 345678886 468999999999832 23799997653
No 45
>PF01440 Gemini_AL2: Geminivirus AL2 protein; InterPro: IPR000942 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=33.77 E-value=5.6 Score=29.90 Aligned_cols=34 Identities=26% Similarity=0.582 Sum_probs=28.7
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCC
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICG 51 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~ 51 (122)
..+-++|.|.= |+|-.|....|..+|+-.|-=-.
T Consensus 31 RRIDL~CGCSy---yihinC~~hGFTHRGthhCsS~~ 64 (134)
T PF01440_consen 31 RRIDLPCGCSY---YIHINCHNHGFTHRGTHHCSSSR 64 (134)
T ss_pred CccccCCCCEE---EeecccCCCCcCCCcCccCCCcC
Confidence 45789999985 89999999999999999986443
No 46
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=33.35 E-value=23 Score=28.27 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=9.9
Q ss_pred HHHHhhhccCC
Q 036983 111 VISWLFHFNIP 121 (122)
Q Consensus 111 vi~W~f~~~~~ 121 (122)
+||+|||+|.|
T Consensus 37 LlPlLlH~Nhp 47 (204)
T PF12633_consen 37 LLPLLLHYNHP 47 (204)
T ss_pred HHHHHHhcCCC
Confidence 49999999987
No 47
>PF06376 DUF1070: Protein of unknown function (DUF1070); InterPro: IPR009424 This entry represents the arabinogalactan peptide family found in plants [].
Probab=33.28 E-value=48 Score=19.47 Aligned_cols=17 Identities=35% Similarity=0.731 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHhhh
Q 036983 101 FLLACMVFAFVISWLFH 117 (122)
Q Consensus 101 fllacmv~afvi~W~f~ 117 (122)
+.+.+|+.|.++-.+||
T Consensus 18 iay~Lm~~Al~~tyl~H 34 (34)
T PF06376_consen 18 IAYMLMLVALVVTYLFH 34 (34)
T ss_pred HHHHHHHHHHHHHhhcC
Confidence 57788899999998887
No 48
>PF09777 OSTMP1: Osteopetrosis-associated transmembrane protein 1 precursor; InterPro: IPR019172 Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease [, ].
Probab=32.78 E-value=14 Score=29.78 Aligned_cols=84 Identities=18% Similarity=0.279 Sum_probs=48.5
Q ss_pred hhhHHHHHHHHh--------hcCCCeeecCCcccccccCCCCCCchhhhcccCCCCCCCCCCCCCcccccccccc-----
Q 036983 29 AAHKQCAEAWFK--------IKGNKTCEICGTTASNVAGANEADPMEQWTESNDATPTASAVPIHQAETRNFWQG----- 95 (122)
Q Consensus 29 ~vH~~Cl~~W~~--------~kg~~~CEIC~~~~~n~~~~~~~~~~e~w~~~~~~~~~~~~~~~~~~e~r~~W~~----- 95 (122)
.....|+++=++ ..++..|..|+..|..+.++ ..+..+.++...= --.+-.+..+|..|-.
T Consensus 106 ~~~~~Cf~~~~~~~~~~~~~~n~s~vC~~C~~~Y~~L~~~-----Y~~l~~~~~~~~C-~DveD~MN~Tr~lWs~~~~C~ 179 (237)
T PF09777_consen 106 NQTLTCFENNQQGSTSSSLSTNNSSVCKNCKTAYNDLNDF-----YWSLEKTNNGAVC-FDVEDAMNRTRHLWSKTFNCS 179 (237)
T ss_pred HHHHHHHHHhccCccccccccCCCchhHHHHHHHHHHHHH-----HHHHHhhccCcee-hhHHHHHHHHHHHhcccccCC
Confidence 355678776432 25788999999999888763 2222221110000 0011134455666643
Q ss_pred ------chHHHHHHHHHHHHHHHHHhhhc
Q 036983 96 ------HRFLNFLLACMVFAFVISWLFHF 118 (122)
Q Consensus 96 ------~~flnfllacmv~afvi~W~f~~ 118 (122)
++-..+++|..++++++|=+|.+
T Consensus 180 ~~~~~~~~~~~~~i~v~~~vl~lpv~FY~ 208 (237)
T PF09777_consen 180 VPCKDEVPSETAVIAVSVFVLFLPVLFYL 208 (237)
T ss_pred CcccccccchhHHHHHHHHHHHHHHHHHH
Confidence 45556778888888888877754
No 49
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=30.04 E-value=26 Score=18.37 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=11.5
Q ss_pred eeecCCcccccccC
Q 036983 46 TCEICGTTASNVAG 59 (122)
Q Consensus 46 ~CEIC~~~~~n~~~ 59 (122)
.|++|+..|.+...
T Consensus 3 ~C~~C~k~f~~~~~ 16 (27)
T PF12171_consen 3 YCDACDKYFSSENQ 16 (27)
T ss_dssp BBTTTTBBBSSHHH
T ss_pred CcccCCCCcCCHHH
Confidence 69999999987754
No 50
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=29.75 E-value=38 Score=19.91 Aligned_cols=31 Identities=26% Similarity=0.648 Sum_probs=19.7
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCC--eeecC
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNK--TCEIC 50 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~--~CEIC 50 (122)
+|+.++|. .-.=++|+++|.+..+.. .|-+|
T Consensus 10 ~Pv~l~CG-----H~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 10 DPVSLPCG-----HSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp SEEE-SSS-----SEEEHHHHHHHHCCSSSST---SSS
T ss_pred CccccCCc-----CHHHHHHHHHHHHccCCcCCCCcCC
Confidence 47777774 234478999999887665 67665
No 51
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=29.14 E-value=40 Score=21.99 Aligned_cols=21 Identities=24% Similarity=0.531 Sum_probs=14.5
Q ss_pred Cccchhhh------hhHHHHHHHHhhc
Q 036983 22 SCKDDLAA------AHKQCAEAWFKIK 42 (122)
Q Consensus 22 ~CkGsL~~------vH~~Cl~~W~~~k 42 (122)
.|+|+.+. |++.|..+|++.+
T Consensus 23 nc~~~~RAaarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 23 NCKGNQRAAARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp TTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred chhhhHHHHHHHhCccHHHHHHHHHHH
Confidence 46766555 6999999999864
No 52
>smart00355 ZnF_C2H2 zinc finger.
Probab=28.40 E-value=23 Score=16.96 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=10.1
Q ss_pred eeecCCccccccc
Q 036983 46 TCEICGTTASNVA 58 (122)
Q Consensus 46 ~CEIC~~~~~n~~ 58 (122)
.|+.|++.|.+..
T Consensus 2 ~C~~C~~~f~~~~ 14 (26)
T smart00355 2 RCPECGKVFKSKS 14 (26)
T ss_pred CCCCCcchhCCHH
Confidence 5889999887654
No 53
>PF03779 SPW: SPW repeat; InterPro: IPR005530 A short repeat found in a small family of membrane-bound proteins. This repeat contains a conserved SPW motif in the first of two transmembrane helices [].
Probab=28.09 E-value=69 Score=19.92 Aligned_cols=19 Identities=37% Similarity=0.877 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHhhhcc
Q 036983 99 LNFLLACMVFAFVISWLFHFN 119 (122)
Q Consensus 99 lnfllacmv~afvi~W~f~~~ 119 (122)
.|+++. +|.++-||+++|.
T Consensus 4 ~~~llG--lwli~SPWvlgf~ 22 (51)
T PF03779_consen 4 LNLLLG--LWLIVSPWVLGFS 22 (51)
T ss_pred HHHHHH--HHHHHhHHHcccC
Confidence 455553 4788899999985
No 54
>PF06847 Arc_PepC_II: Archaeal Peptidase A24 C-terminus Type II; InterPro: IPR009655 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This region is of unknown function, which is found at the C terminus of archaeal preflagellin aspartic acid signal peptidases []. The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes utilizing the same catalytic mechanism []. The preflagellin peptidase is required for the removal of the leader peptide from archaeal flagellin []. Preflagellin aspartic acid signal peptidases belong to the MEROPS peptidase family A24B (preflagellin peptidase, clan AD).; GO: 0008233 peptidase activity; PDB: 3S0X_B.
Probab=28.02 E-value=56 Score=22.73 Aligned_cols=21 Identities=29% Similarity=0.559 Sum_probs=15.0
Q ss_pred cc--ccchHHHHHHHHHHHHHHH
Q 036983 92 FW--QGHRFLNFLLACMVFAFVI 112 (122)
Q Consensus 92 ~W--~~~~flnfllacmv~afvi 112 (122)
+| -|.||++++.+-+++|+++
T Consensus 67 VWVTpgiPFlvpIt~G~iial~~ 89 (93)
T PF06847_consen 67 VWVTPGIPFLVPITAGYIIALIY 89 (93)
T ss_dssp EEE-----THHHHHHHHHHHHHH
T ss_pred EEEeCCCcCHHHHHHHHHHHHHh
Confidence 56 4789999999999999875
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=27.92 E-value=47 Score=21.47 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=25.7
Q ss_pred CceecCCCccchhhhhhHHHHHHHHhhcCCCeeecCCccccc
Q 036983 15 VPIELGCSCKDDLAAAHKQCAEAWFKIKGNKTCEICGTTASN 56 (122)
Q Consensus 15 ~~l~~pC~CkGsL~~vH~~Cl~~W~~~kg~~~CEIC~~~~~n 56 (122)
+|.++|+. ...=+.++++|++. ++.+|-+|+.....
T Consensus 16 dPVi~~~G-----~tyer~~I~~~l~~-~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 16 DPVILPSG-----HTYERSAIERWLEQ-NGGTDPFTRQPLSE 51 (73)
T ss_dssp SEEEETTS-----EEEEHHHHHHHHCT-TSSB-TTT-SB-SG
T ss_pred CceeCCcC-----CEEcHHHHHHHHHc-CCCCCCCCCCcCCc
Confidence 46777754 46779999999998 78899999877643
No 56
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=27.86 E-value=78 Score=19.76 Aligned_cols=33 Identities=18% Similarity=0.399 Sum_probs=17.6
Q ss_pred eecCCCccchhhhhhHHHHHHHHhhc--CCCeeecCCcccc
Q 036983 17 IELGCSCKDDLAAAHKQCAEAWFKIK--GNKTCEICGTTAS 55 (122)
Q Consensus 17 l~~pC~CkGsL~~vH~~Cl~~W~~~k--g~~~CEIC~~~~~ 55 (122)
-..||.|. +|-|..=|.+++ ++..|--|+..|.
T Consensus 14 ~~~PC~Cg------f~IC~~C~~~i~~~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 14 DFYPCECG------FQICRFCYHDILENEGGRCPGCREPYK 48 (48)
T ss_dssp T--SSTTS----------HHHHHHHTTSS-SB-TTT--B--
T ss_pred ccccCcCC------CcHHHHHHHHHHhccCCCCCCCCCCCC
Confidence 46899996 567888888887 4789999998874
No 57
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=26.81 E-value=25 Score=30.56 Aligned_cols=16 Identities=31% Similarity=0.750 Sum_probs=14.5
Q ss_pred CeeecCCcccccccCC
Q 036983 45 KTCEICGTTASNVAGA 60 (122)
Q Consensus 45 ~~CEIC~~~~~n~~~~ 60 (122)
-.||+|+..|+|+-|+
T Consensus 399 YrCevC~KRYKNlNGL 414 (423)
T COG5189 399 YRCEVCDKRYKNLNGL 414 (423)
T ss_pred eeccccchhhccCccc
Confidence 4899999999999886
No 58
>PRK05978 hypothetical protein; Provisional
Probab=26.41 E-value=1.1e+02 Score=23.16 Aligned_cols=17 Identities=18% Similarity=0.460 Sum_probs=13.0
Q ss_pred CCCeeecCCcccccccC
Q 036983 43 GNKTCEICGTTASNVAG 59 (122)
Q Consensus 43 g~~~CEIC~~~~~n~~~ 59 (122)
=+..|+.|+.+|.-.+.
T Consensus 51 v~~~C~~CG~~~~~~~a 67 (148)
T PRK05978 51 PVDHCAACGEDFTHHRA 67 (148)
T ss_pred cCCCccccCCccccCCc
Confidence 46689999998877654
No 59
>COG4698 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.54 E-value=28 Score=27.75 Aligned_cols=16 Identities=50% Similarity=0.600 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 036983 99 LNFLLACMVFAFVISW 114 (122)
Q Consensus 99 lnfllacmv~afvi~W 114 (122)
+|+|+|..+.+||++|
T Consensus 21 ln~l~~~~i~~~vlsp 36 (197)
T COG4698 21 LNTLLAVLIALFVLSP 36 (197)
T ss_pred HHHHHHHHhheeeccC
Confidence 6888898888899987
No 60
>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=22.69 E-value=57 Score=23.68 Aligned_cols=24 Identities=25% Similarity=0.769 Sum_probs=18.8
Q ss_pred CCCceecCCCccchhhhhhHHHHHHHHhh
Q 036983 13 SGVPIELGCSCKDDLAAAHKQCAEAWFKI 41 (122)
Q Consensus 13 ~~~~l~~pC~CkGsL~~vH~~Cl~~W~~~ 41 (122)
+|+--..||+|.. +.+|..+|.-.
T Consensus 54 e~d~ad~PCSC~~-----~~~c~~RW~~L 77 (108)
T PF05210_consen 54 EGDCADHPCSCDT-----PSRCCARWLAL 77 (108)
T ss_pred CcccCCCccccCC-----ccchHHHHHHH
Confidence 3444566999998 88999999865
No 61
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.53 E-value=37 Score=25.61 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=9.6
Q ss_pred eeecCCcccccc
Q 036983 46 TCEICGTTASNV 57 (122)
Q Consensus 46 ~CEIC~~~~~n~ 57 (122)
.|||||.+....
T Consensus 2 ~CEiCG~~i~~~ 13 (154)
T TIGR00270 2 NCEICGRKIKGK 13 (154)
T ss_pred ccccCCCccCCC
Confidence 499999887655
No 62
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=22.19 E-value=42 Score=21.34 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=15.5
Q ss_pred hhhhHHHHHHHHhhcCCCeeecCCccc
Q 036983 28 AAAHKQCAEAWFKIKGNKTCEICGTTA 54 (122)
Q Consensus 28 ~~vH~~Cl~~W~~~kg~~~CEIC~~~~ 54 (122)
.|.=..|+..-+ +.+..||||+++.
T Consensus 21 HYLCl~CLt~ml--~~s~~C~iC~~~L 45 (50)
T PF03854_consen 21 HYLCLNCLTLML--SRSDRCPICGKPL 45 (50)
T ss_dssp -EEEHHHHHHT---SSSSEETTTTEE-
T ss_pred hhHHHHHHHHHh--ccccCCCcccCcC
Confidence 355556765444 4567999999875
No 63
>PF12907 zf-met2: Zinc-binding
Probab=22.16 E-value=22 Score=21.49 Aligned_cols=16 Identities=31% Similarity=0.601 Sum_probs=12.3
Q ss_pred CCeeecCCcccccccC
Q 036983 44 NKTCEICGTTASNVAG 59 (122)
Q Consensus 44 ~~~CEIC~~~~~n~~~ 59 (122)
+..|.||+++|...+.
T Consensus 1 ~i~C~iC~qtF~~t~~ 16 (40)
T PF12907_consen 1 NIICKICRQTFMQTTN 16 (40)
T ss_pred CcCcHHhhHHHHhcCC
Confidence 3579999999966554
No 64
>PF09630 DUF2024: Domain of unknown function (DUF2024); InterPro: IPR018592 This protein of 86 residues is expressed in bacteria. It consists of two alpha helices and four beta strands. Its function is unknown.; PDB: 2HFQ_A.
Probab=21.47 E-value=57 Score=22.62 Aligned_cols=25 Identities=24% Similarity=0.575 Sum_probs=19.5
Q ss_pred HHHHHHHHhhcC-------CCeeecCCccccc
Q 036983 32 KQCAEAWFKIKG-------NKTCEICGTTASN 56 (122)
Q Consensus 32 ~~Cl~~W~~~kg-------~~~CEIC~~~~~n 56 (122)
.+++.+||+++| .+.|--|+++-.+
T Consensus 33 ~~yaK~yL~sig~~~~~vt~~eC~FCHse~A~ 64 (81)
T PF09630_consen 33 IEYAKEYLKSIGEEDADVTQKECRFCHSEEAP 64 (81)
T ss_dssp HHHHHHHHHHHT---S---TTTEEEEEEEE--
T ss_pred HHHHHHHHHhcCCCCCccccccCcccccccCC
Confidence 468999999987 5789999988433
No 65
>PF11298 DUF3099: Protein of unknown function (DUF3099); InterPro: IPR021449 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=21.39 E-value=37 Score=22.90 Aligned_cols=20 Identities=30% Similarity=0.431 Sum_probs=14.3
Q ss_pred cccccccchHHHHHHHHHHH
Q 036983 89 TRNFWQGHRFLNFLLACMVF 108 (122)
Q Consensus 89 ~r~~W~~~~flnfllacmv~ 108 (122)
++.+.++.++.-|++|.++.
T Consensus 19 ~Y~i~M~~Ri~~fvlA~~~~ 38 (73)
T PF11298_consen 19 RYLIMMGIRIPCFVLAAVVY 38 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33457788888888877666
No 66
>PRK08359 transcription factor; Validated
Probab=21.21 E-value=46 Score=25.89 Aligned_cols=14 Identities=36% Similarity=0.871 Sum_probs=10.9
Q ss_pred CeeecCCccccccc
Q 036983 45 KTCEICGTTASNVA 58 (122)
Q Consensus 45 ~~CEIC~~~~~n~~ 58 (122)
..|||||.+....+
T Consensus 7 ~~CEiCG~~i~g~~ 20 (176)
T PRK08359 7 RYCEICGAEIRGPG 20 (176)
T ss_pred ceeecCCCccCCCC
Confidence 45999999986553
No 67
>PF10726 DUF2518: Protein of function (DUF2518); InterPro: IPR019664 This entry contains the Ycf51 protein family, which is conserved in Cyanobacteria. The function is not known.
Probab=21.19 E-value=65 Score=24.64 Aligned_cols=20 Identities=25% Similarity=0.552 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHhhhcc
Q 036983 100 NFLLACMVFAFVISWLFHFN 119 (122)
Q Consensus 100 nfllacmv~afvi~W~f~~~ 119 (122)
.++....+.||+.-|=|+|-
T Consensus 19 i~~~~lTilaFi~~WG~RFR 38 (145)
T PF10726_consen 19 IALAVLTILAFIFKWGIRFR 38 (145)
T ss_pred HHHHHHHHHHHHhccCceEE
Confidence 34556789999999998884
No 68
>PF13063 DUF3925: Protein of unknown function (DUF3925)
Probab=20.65 E-value=52 Score=21.66 Aligned_cols=15 Identities=33% Similarity=0.833 Sum_probs=12.3
Q ss_pred HHHHHHHHHHhhhcc
Q 036983 105 CMVFAFVISWLFHFN 119 (122)
Q Consensus 105 cmv~afvi~W~f~~~ 119 (122)
-|...||+-|+.++|
T Consensus 19 ymmll~v~gw~idvn 33 (66)
T PF13063_consen 19 YMMLLFVAGWVIDVN 33 (66)
T ss_pred HHHHHHHhhheEecc
Confidence 366789999998876
No 69
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.65 E-value=41 Score=17.82 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=8.8
Q ss_pred CeeecCCccc
Q 036983 45 KTCEICGTTA 54 (122)
Q Consensus 45 ~~CEIC~~~~ 54 (122)
..|.+|+..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 4799999999
No 70
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=20.13 E-value=25 Score=22.11 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=10.4
Q ss_pred HHHhhcCCCeeecCCccccc
Q 036983 37 AWFKIKGNKTCEICGTTASN 56 (122)
Q Consensus 37 ~W~~~kg~~~CEIC~~~~~n 56 (122)
.|...+....|.+|+..|..
T Consensus 2 ~W~~d~~~~~C~~C~~~F~~ 21 (69)
T PF01363_consen 2 HWVPDSEASNCMICGKKFSL 21 (69)
T ss_dssp -SSSGGG-SB-TTT--B-BS
T ss_pred CcCCCCCCCcCcCcCCcCCC
Confidence 46777778888888888843
Done!