Query psy7602
Match_columns 95
No_of_seqs 109 out of 687
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 22:34:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7602hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814|consensus 99.6 3E-16 6.4E-21 120.1 6.5 80 4-93 198-283 (445)
2 KOG1815|consensus 99.6 3.4E-16 7.3E-21 121.4 4.9 80 5-94 83-169 (444)
3 KOG1812|consensus 99.3 8.3E-12 1.8E-16 95.8 5.3 72 9-93 166-243 (384)
4 smart00647 IBR In Between Ring 98.3 3.5E-07 7.6E-12 52.8 2.5 29 57-94 1-29 (64)
5 PF01485 IBR: IBR domain; Int 98.1 3.7E-07 8.1E-12 52.6 -1.5 29 57-94 1-29 (64)
6 PF15227 zf-C3HC4_4: zinc fing 97.9 4E-06 8.7E-11 45.7 1.3 33 4-41 9-41 (42)
7 PF13923 zf-C3HC4_2: Zinc fing 97.8 6.5E-06 1.4E-10 43.8 1.1 20 7-26 13-32 (39)
8 PF00097 zf-C3HC4: Zinc finger 97.8 1.3E-05 2.7E-10 42.7 1.4 20 7-26 13-32 (41)
9 PF13639 zf-RING_2: Ring finge 97.6 3.4E-05 7.4E-10 41.8 1.4 24 3-26 13-36 (44)
10 PF13445 zf-RING_UBOX: RING-ty 97.4 8E-05 1.7E-09 40.8 1.5 29 7-40 15-43 (43)
11 cd00162 RING RING-finger (Real 97.4 0.00015 3.2E-09 38.0 2.5 20 7-26 14-33 (45)
12 smart00184 RING Ring finger. E 97.2 0.00029 6.4E-09 35.5 2.3 22 4-25 9-30 (39)
13 PLN03208 E3 ubiquitin-protein 97.0 0.00041 8.9E-09 49.2 2.2 51 4-56 29-86 (193)
14 PF13920 zf-C3HC4_3: Zinc fing 97.0 0.00047 1E-08 38.3 1.6 35 4-49 13-48 (50)
15 KOG0320|consensus 96.8 0.0009 1.9E-08 47.0 2.1 36 7-53 147-182 (187)
16 PF14634 zf-RING_5: zinc-RING 96.8 0.001 2.2E-08 36.1 1.9 21 4-24 13-33 (44)
17 KOG0006|consensus 96.7 0.0027 5.8E-08 48.6 4.3 72 6-93 234-325 (446)
18 PF11789 zf-Nse: Zinc-finger o 96.5 0.0013 2.8E-08 38.0 1.3 33 6-45 25-57 (57)
19 smart00504 Ubox Modified RING 96.5 0.0047 1E-07 35.2 3.4 42 4-56 12-53 (63)
20 KOG0317|consensus 96.4 0.0028 6E-08 47.4 2.7 41 3-54 249-289 (293)
21 KOG1002|consensus 96.3 0.0031 6.6E-08 51.1 2.6 44 2-51 545-588 (791)
22 KOG2164|consensus 96.0 0.0038 8.2E-08 49.8 1.6 43 8-56 201-243 (513)
23 KOG0978|consensus 95.9 0.0035 7.7E-08 51.7 1.2 42 4-55 654-695 (698)
24 PHA02926 zinc finger-like prot 95.4 0.015 3.2E-07 42.4 2.7 36 8-48 194-229 (242)
25 TIGR00599 rad18 DNA repair pro 95.1 0.023 5E-07 44.4 3.3 34 7-51 40-73 (397)
26 KOG0823|consensus 95.1 0.011 2.3E-07 43.1 1.4 45 4-56 58-102 (230)
27 TIGR00570 cdk7 CDK-activating 95.1 0.02 4.4E-07 43.3 2.9 33 10-52 25-57 (309)
28 PHA02929 N1R/p28-like protein; 94.2 0.029 6.3E-07 41.0 1.8 31 8-49 197-227 (238)
29 KOG2177|consensus 93.0 0.054 1.2E-06 37.7 1.5 28 7-45 27-54 (386)
30 PF04564 U-box: U-box domain; 90.9 0.34 7.4E-06 28.8 3.1 57 4-71 15-71 (73)
31 PF12678 zf-rbx1: RING-H2 zinc 90.0 0.13 2.7E-06 30.8 0.6 18 9-26 48-65 (73)
32 COG5432 RAD18 RING-finger-cont 89.9 0.16 3.5E-06 38.6 1.3 38 9-52 41-78 (391)
33 KOG0287|consensus 87.9 0.31 6.7E-06 37.8 1.6 34 9-53 39-72 (442)
34 COG5574 PEX10 RING-finger-cont 85.8 0.67 1.4E-05 34.5 2.3 42 3-53 225-266 (271)
35 KOG4739|consensus 83.5 0.42 9.1E-06 34.9 0.4 18 4-21 16-33 (233)
36 KOG2660|consensus 82.6 0.44 9.6E-06 36.4 0.3 34 7-51 30-63 (331)
37 PF06844 DUF1244: Protein of u 81.2 1.3 2.9E-05 26.4 1.9 20 14-33 11-30 (68)
38 KOG0824|consensus 80.4 1.2 2.6E-05 33.9 1.9 40 7-56 21-60 (324)
39 KOG1428|consensus 79.1 5.5 0.00012 37.0 5.6 51 3-56 3499-3551(3738)
40 KOG0802|consensus 78.3 1.6 3.6E-05 35.1 2.2 21 6-26 309-329 (543)
41 PF14835 zf-RING_6: zf-RING of 78.2 0.23 5E-06 29.5 -2.0 32 9-53 24-55 (65)
42 PF11793 FANCL_C: FANCL C-term 75.3 1.2 2.6E-05 26.4 0.5 39 9-50 26-67 (70)
43 COG5152 Uncharacterized conser 75.2 1.4 2.9E-05 32.0 0.8 16 7-22 210-225 (259)
44 KOG0311|consensus 74.2 0.91 2E-05 35.2 -0.3 20 6-25 57-76 (381)
45 KOG1734|consensus 72.5 1.4 3E-05 33.3 0.3 41 4-53 245-285 (328)
46 KOG2979|consensus 71.9 6 0.00013 29.4 3.6 50 6-62 190-241 (262)
47 COG5540 RING-finger-containing 71.3 2.8 6.2E-05 32.2 1.8 37 4-50 337-373 (374)
48 KOG4159|consensus 69.7 8.4 0.00018 30.3 4.1 53 7-70 98-154 (398)
49 KOG1645|consensus 68.9 5.1 0.00011 31.8 2.8 44 4-56 20-63 (463)
50 PF12861 zf-Apc11: Anaphase-pr 67.8 5.4 0.00012 24.9 2.2 32 9-48 50-81 (85)
51 KOG1001|consensus 67.7 2.7 5.9E-05 35.0 1.1 41 4-53 464-504 (674)
52 COG3492 Uncharacterized protei 66.0 5.3 0.00012 25.4 2.0 19 14-32 42-60 (104)
53 KOG2932|consensus 63.2 3.2 6.8E-05 32.0 0.7 13 9-21 107-119 (389)
54 PF14447 Prok-RING_4: Prokaryo 60.2 2.6 5.6E-05 24.2 -0.2 35 5-52 19-53 (55)
55 PF07975 C1_4: TFIIH C1-like d 57.5 5.5 0.00012 22.4 0.9 12 9-20 25-36 (51)
56 COG5243 HRD1 HRD ubiquitin lig 55.7 7.7 0.00017 30.7 1.6 20 7-26 314-333 (491)
57 KOG1039|consensus 54.3 6.4 0.00014 30.4 1.0 34 9-46 185-218 (344)
58 KOG2879|consensus 53.8 8 0.00017 29.2 1.4 37 4-49 251-287 (298)
59 KOG1785|consensus 53.2 10 0.00022 30.4 1.9 35 4-45 380-414 (563)
60 KOG4692|consensus 51.8 9.7 0.00021 30.0 1.6 18 9-26 438-455 (489)
61 PF14570 zf-RING_4: RING/Ubox 50.4 11 0.00024 20.9 1.3 17 9-25 18-34 (48)
62 KOG4628|consensus 49.2 8 0.00017 29.9 0.8 24 4-27 243-266 (348)
63 KOG0297|consensus 46.6 8 0.00017 30.1 0.5 18 9-26 38-55 (391)
64 cd00065 FYVE FYVE domain; Zinc 46.2 8.6 0.00019 21.0 0.5 20 9-28 22-41 (57)
65 COG5112 UFD2 U1-like Zn-finger 45.9 10 0.00022 24.8 0.8 20 10-29 52-71 (126)
66 PHA03096 p28-like protein; Pro 43.1 19 0.00041 27.0 2.0 20 10-29 203-222 (284)
67 KOG1941|consensus 42.1 17 0.00037 29.0 1.7 38 3-49 379-416 (518)
68 KOG0006|consensus 41.1 15 0.00032 28.6 1.1 76 10-93 341-425 (446)
69 KOG3579|consensus 39.7 14 0.00031 28.1 0.9 32 12-47 291-323 (352)
70 PF01530 zf-C2HC: Zinc finger, 38.9 17 0.00038 18.4 0.9 10 86-95 4-13 (31)
71 KOG1813|consensus 37.5 13 0.00029 28.3 0.4 18 7-24 255-272 (313)
72 PF01776 Ribosomal_L22e: Ribos 36.0 59 0.0013 21.2 3.2 51 20-72 26-81 (112)
73 KOG2930|consensus 35.7 29 0.00063 22.6 1.7 19 10-28 80-98 (114)
74 KOG3408|consensus 34.7 17 0.00037 24.2 0.6 20 10-29 54-73 (129)
75 COG5194 APC11 Component of SCF 34.2 30 0.00064 21.5 1.5 17 10-26 53-69 (88)
76 KOG0828|consensus 33.8 33 0.00071 28.2 2.1 32 8-49 603-634 (636)
77 PF04891 NifQ: NifQ; InterPro 33.7 44 0.00096 23.2 2.5 27 57-93 132-158 (167)
78 KOG0827|consensus 33.3 32 0.00068 27.4 1.9 26 4-29 18-44 (465)
79 PF14353 CpXC: CpXC protein 33.1 35 0.00077 21.9 1.9 23 23-48 26-48 (128)
80 smart00064 FYVE Protein presen 33.0 20 0.00043 20.4 0.6 19 10-28 31-49 (68)
81 PF10426 zf-RAG1: Recombinatio 32.8 17 0.00037 18.3 0.2 15 36-50 2-16 (30)
82 KOG2594|consensus 32.6 47 0.001 26.1 2.7 23 7-29 26-48 (396)
83 COG5222 Uncharacterized conser 30.0 32 0.0007 26.6 1.4 29 8-46 290-318 (427)
84 KOG0825|consensus 30.0 31 0.00067 30.0 1.4 17 9-25 142-158 (1134)
85 KOG4185|consensus 29.8 28 0.0006 25.5 1.0 39 8-56 24-64 (296)
86 KOG3039|consensus 29.6 34 0.00073 25.7 1.4 20 10-29 60-79 (303)
87 PF04641 Rtf2: Rtf2 RING-finge 27.8 66 0.0014 23.4 2.8 36 9-56 133-168 (260)
88 KOG4445|consensus 27.8 49 0.0011 25.6 2.0 25 4-28 129-153 (368)
89 COG1996 RPC10 DNA-directed RNA 27.6 16 0.00036 20.4 -0.4 26 16-48 9-34 (49)
90 KOG3002|consensus 27.6 37 0.0008 25.7 1.4 10 12-21 68-77 (299)
91 KOG3434|consensus 26.0 80 0.0017 21.0 2.6 54 18-71 36-92 (125)
92 PF08882 Acetone_carb_G: Aceto 24.5 27 0.00058 22.9 0.1 23 7-29 25-49 (112)
93 KOG3268|consensus 22.8 1.5E+02 0.0032 21.3 3.6 40 7-49 186-228 (234)
94 PF01363 FYVE: FYVE zinc finge 22.4 11 0.00024 21.5 -1.8 17 10-26 30-46 (69)
95 PF14319 Zn_Tnp_IS91: Transpos 21.8 21 0.00046 22.9 -0.7 23 6-28 53-75 (111)
96 PF02748 PyrI_C: Aspartate car 21.7 38 0.00082 18.9 0.4 11 84-94 7-17 (52)
97 COG5220 TFB3 Cdk activating ki 21.4 30 0.00066 25.9 -0.1 31 10-48 33-63 (314)
98 PF10571 UPF0547: Uncharacteri 21.3 46 0.001 15.9 0.6 6 10-15 19-24 (26)
99 PF03854 zf-P11: P-11 zinc fin 20.1 19 0.00041 20.2 -1.1 9 13-21 2-10 (50)
No 1
>KOG1814|consensus
Probab=99.64 E-value=3e-16 Score=120.13 Aligned_cols=80 Identities=26% Similarity=0.458 Sum_probs=74.2
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH------HHHHHHHHHHHHhhCCCCCCC
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF------DVYQGILSNQVTNCRLASLVP 77 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l------~ky~~~l~~~~v~~~~~~~~~ 77 (95)
..++.++|+|+||+.|++.|.++.|+ +|++..++||+++|+...++.+++++ +||+++++++-++...
T Consensus 198 ~c~~~lpC~Hv~Ck~C~kdY~~~~i~-eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~ms----- 271 (445)
T KOG1814|consen 198 HCFKFLPCSHVFCKSCLKDYFTIQIQ-EGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELMS----- 271 (445)
T ss_pred ceeeecccchHHHHHHHHHHHHHhhh-cceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhhc-----
Confidence 34667899999999999999999998 79988999999999999999999988 9999999999999984
Q ss_pred CCCCCeeeCCCCCCcc
Q psy7602 78 CKCSWVRFPPGADFIL 93 (95)
Q Consensus 78 ~~~~~~~~CP~~~C~~ 93 (95)
++.|||++.|+.
T Consensus 272 ----dv~yCPr~~Cq~ 283 (445)
T KOG1814|consen 272 ----DVVYCPRACCQL 283 (445)
T ss_pred ----ccccCChhhccC
Confidence 999999999986
No 2
>KOG1815|consensus
Probab=99.62 E-value=3.4e-16 Score=121.44 Aligned_cols=80 Identities=34% Similarity=0.667 Sum_probs=71.2
Q ss_pred CcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH-------HHHHHHHHHHHHhhCCCCCCC
Q psy7602 5 LMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF-------DVYQGILSNQVTNCRLASLVP 77 (95)
Q Consensus 5 ~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l-------~ky~~~l~~~~v~~~~~~~~~ 77 (95)
++..+.|||.||..||..||..+|. +|....|+||..+|...+..++|..+ ++|++++.++||+++.
T Consensus 83 ~~~~~~c~H~~c~~cw~~yl~~kI~-~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~----- 156 (444)
T KOG1815|consen 83 EIIGLGCGHPFCPPCWTGYLGTKIH-EGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNV----- 156 (444)
T ss_pred hhhhcCCCcHHHHHHHHHHhhheee-ccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCC-----
Confidence 5777899999999999999999998 55533599999999999998888665 8999999999999996
Q ss_pred CCCCCeeeCCCCCCccC
Q psy7602 78 CKCSWVRFPPGADFILN 94 (95)
Q Consensus 78 ~~~~~~~~CP~~~C~~~ 94 (95)
.++|||+|+|++.
T Consensus 157 ----~lkwCP~~~C~~a 169 (444)
T KOG1815|consen 157 ----PLKWCPAPGCGLA 169 (444)
T ss_pred ----ccccCCCCCCCce
Confidence 6999999999873
No 3
>KOG1812|consensus
Probab=99.25 E-value=8.3e-12 Score=95.81 Aligned_cols=72 Identities=24% Similarity=0.499 Sum_probs=63.1
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH------HHHHHHHHHHHHhhCCCCCCCCCCCC
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF------DVYQGILSNQVTNCRLASLVPCKCSW 82 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l------~ky~~~l~~~~v~~~~~~~~~~~~~~ 82 (95)
+.|+|.||.+||++|++.+.. +| ..|+||+.+|+..++.+....+ +.|+..+.+.+|.... .
T Consensus 166 ~~C~H~fC~~C~k~~iev~~~-~~--~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~---------~ 233 (384)
T KOG1812|consen 166 LKCGHRFCKDCVKQHIEVKLL-SG--TVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLD---------R 233 (384)
T ss_pred hcccchhhhHHhHHHhhhhhc-cC--CCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhh---------c
Confidence 689999999999999999954 44 3799999999999999988777 8888999999998884 5
Q ss_pred eeeCCCCCCcc
Q psy7602 83 VRFPPGADFIL 93 (95)
Q Consensus 83 ~~~CP~~~C~~ 93 (95)
+ |||+|+|..
T Consensus 234 ~-ycp~~~C~~ 243 (384)
T KOG1812|consen 234 V-YCPYPRCSS 243 (384)
T ss_pred c-cCCCCCchH
Confidence 6 999999964
No 4
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.34 E-value=3.5e-07 Score=52.76 Aligned_cols=29 Identities=14% Similarity=0.255 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhhCCCCCCCCCCCCeeeCCCCCCccC
Q psy7602 57 DVYQGILSNQVTNCRLASLVPCKCSWVRFPPGADFILN 94 (95)
Q Consensus 57 ~ky~~~l~~~~v~~~~~~~~~~~~~~~~~CP~~~C~~~ 94 (95)
++|++++++++|+.++ +++|||+|+|+.+
T Consensus 1 ~~y~~~~~~~~i~~~~---------~~~~CP~~~C~~~ 29 (64)
T smart00647 1 EKYERLLLESYVESNP---------DLKWCPAPDCSAA 29 (64)
T ss_pred ChHHHHHHHHHHhcCC---------CccCCCCCCCcce
Confidence 4899999999999985 9999999999753
No 5
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.06 E-value=3.7e-07 Score=52.57 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHhhCCCCCCCCCCCCeeeCCCCCCccC
Q psy7602 57 DVYQGILSNQVTNCRLASLVPCKCSWVRFPPGADFILN 94 (95)
Q Consensus 57 ~ky~~~l~~~~v~~~~~~~~~~~~~~~~~CP~~~C~~~ 94 (95)
+||+++++++||+.++ +++|||+|||+.+
T Consensus 1 eky~~~~~~~~~~~~~---------~~~~Cp~~~C~~~ 29 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDP---------NIRWCPNPDCEYI 29 (64)
T ss_dssp HCHHHCCCHS---S------------CC--TTSST---
T ss_pred ChHHHHHHHHHHHCCC---------CccCCCCCCCccc
Confidence 5899999999998774 9999999999864
No 6
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.94 E-value=4e-06 Score=45.65 Aligned_cols=33 Identities=21% Similarity=0.464 Sum_probs=21.6
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCc
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAA 41 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~ 41 (95)
++-++|+|||.||.+|+..+.+..-. . .+.||.
T Consensus 9 ~~Pv~l~CGH~FC~~Cl~~~~~~~~~---~--~~~CP~ 41 (42)
T PF15227_consen 9 KDPVSLPCGHSFCRSCLERLWKEPSG---S--GFSCPE 41 (42)
T ss_dssp SSEEE-SSSSEEEHHHHHHHHCCSSS---S--T---SS
T ss_pred CCccccCCcCHHHHHHHHHHHHccCC---c--CCCCcC
Confidence 45567999999999999999876432 2 277874
No 7
>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=97.85 E-value=6.5e-06 Score=43.76 Aligned_cols=20 Identities=35% Similarity=0.876 Sum_probs=18.3
Q ss_pred ccCCCCchhhHHHHHHHHHh
Q psy7602 7 TGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~ 26 (95)
..+.|||.||.+||.+|++.
T Consensus 13 ~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 13 VVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EECTTSEEEEHHHHHHHHHC
T ss_pred EECCCCCchhHHHHHHHHHC
Confidence 57899999999999999876
No 8
>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=97.76 E-value=1.3e-05 Score=42.69 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=18.6
Q ss_pred ccCCCCchhhHHHHHHHHHh
Q psy7602 7 TGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~ 26 (95)
..++|||.||.+|+.+|++.
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHH
T ss_pred EEecCCCcchHHHHHHHHHh
Confidence 37899999999999999998
No 9
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=97.57 E-value=3.4e-05 Score=41.80 Aligned_cols=24 Identities=29% Similarity=0.588 Sum_probs=20.9
Q ss_pred CCCcccCCCCchhhHHHHHHHHHh
Q psy7602 3 STLMTGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 3 ~~~~~~l~CgH~FC~~C~~~yl~~ 26 (95)
.+....++|||.|+.+|+.+|++.
T Consensus 13 ~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 13 GEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp TSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CCeEEEccCCCeeCHHHHHHHHHh
Confidence 456677899999999999999966
No 10
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.42 E-value=8e-05 Score=40.84 Aligned_cols=29 Identities=24% Similarity=0.570 Sum_probs=18.0
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecC
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACA 40 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp 40 (95)
..|.|||.||++|+++.+..... ..++||
T Consensus 15 ~~L~CGH~~c~~cl~~l~~~~~~-----~~~kCP 43 (43)
T PF13445_consen 15 MVLPCGHVFCKDCLQKLSKKSDR-----NRFKCP 43 (43)
T ss_dssp EE-SSS-EEEHHHHHHHHHH-S------S-B--T
T ss_pred EEEeCccHHHHHHHHHHHhcCCC-----CeeeCc
Confidence 44889999999999999885432 257776
No 11
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.41 E-value=0.00015 Score=37.99 Aligned_cols=20 Identities=35% Similarity=0.848 Sum_probs=16.9
Q ss_pred ccCCCCchhhHHHHHHHHHh
Q psy7602 7 TGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~ 26 (95)
....|||.||.+|+..|++.
T Consensus 14 ~~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 14 VLLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred EecCCCChhcHHHHHHHHHh
Confidence 33459999999999999875
No 12
>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=97.22 E-value=0.00029 Score=35.52 Aligned_cols=22 Identities=32% Similarity=0.712 Sum_probs=19.0
Q ss_pred CCcccCCCCchhhHHHHHHHHH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLT 25 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~ 25 (95)
+....+.|||.||.+|++.|++
T Consensus 9 ~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 9 KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcEEecCCChHHHHHHHHHHH
Confidence 4556678999999999999987
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.03 E-value=0.00041 Score=49.22 Aligned_cols=51 Identities=16% Similarity=0.308 Sum_probs=35.6
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhc-------CCceeeeecCccccCcccccchhhhH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQ-------EGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~-------~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
++-+.+.|||.||..|+.+|+...-.. .......+||. |+..|+...+..+
T Consensus 29 ~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPi 86 (193)
T PLN03208 29 RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPI 86 (193)
T ss_pred CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEe
Confidence 344557899999999999998753110 00112578996 9999988777665
No 14
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=96.96 E-value=0.00047 Score=38.26 Aligned_cols=35 Identities=26% Similarity=0.584 Sum_probs=25.9
Q ss_pred CCcccCCCCch-hhHHHHHHHHHhhhhcCCceeeeecCccccCcccc
Q psy7602 4 TLMTGLECSHR-FCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVD 49 (95)
Q Consensus 4 ~~~~~l~CgH~-FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~ 49 (95)
.+...++|||. ||.+|+..++. . ..+||. |+..|+
T Consensus 13 ~~~~~~pCgH~~~C~~C~~~~~~---~------~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 13 RDVVLLPCGHLCFCEECAERLLK---R------KKKCPI--CRQPIE 48 (50)
T ss_dssp SSEEEETTCEEEEEHHHHHHHHH---T------TSBBTT--TTBB-S
T ss_pred CceEEeCCCChHHHHHHhHHhcc---c------CCCCCc--CChhhc
Confidence 45566799999 99999999998 1 246775 766554
No 15
>KOG0320|consensus
Probab=96.77 E-value=0.0009 Score=47.03 Aligned_cols=36 Identities=28% Similarity=0.651 Sum_probs=25.4
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
++..|||.||+.|++.-+.. .-+||. |...|+..++
T Consensus 147 vsTkCGHvFC~~Cik~alk~---------~~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 147 VSTKCGHVFCSQCIKDALKN---------TNKCPT--CRKKITHKQF 182 (187)
T ss_pred cccccchhHHHHHHHHHHHh---------CCCCCC--cccccchhhh
Confidence 56789999999998875543 245876 6556665544
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=96.76 E-value=0.001 Score=36.08 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=17.9
Q ss_pred CCcccCCCCchhhHHHHHHHH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYL 24 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl 24 (95)
.....++|||.||.+|+.+..
T Consensus 13 ~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 13 RRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCeEEcccCCHHHHHHHHhhc
Confidence 456678999999999999876
No 17
>KOG0006|consensus
Probab=96.69 E-value=0.0027 Score=48.60 Aligned_cols=72 Identities=21% Similarity=0.338 Sum_probs=51.3
Q ss_pred cccCCCC--chhhHHHHHHHHHhhhhcCCce-------eeeecCccccCcccccchhhhH-----------HHHHHHHHH
Q psy7602 6 MTGLECS--HRFCTQCWCEYLTTKIIQEGMG-------QTIACAAHGCNILVDDGKPIEF-----------DVYQGILSN 65 (95)
Q Consensus 6 ~~~l~Cg--H~FC~~C~~~yl~~~I~~~g~~-------~~i~Cp~~~C~~~i~~~~i~~l-----------~ky~~~l~~ 65 (95)
...+.|. |.-|.+|++.|..+++. +-+. ..+.||+ +|.. +.|+.+ ++|+++-.+
T Consensus 234 vlvf~Cns~HvtC~dCFr~yc~~Rl~-~rqf~~~p~~gyslpc~a-gc~~----s~i~e~HHF~ilg~e~Y~rYQr~atE 307 (446)
T KOG0006|consen 234 VLVFQCNSRHVTCLDCFRLYCVTRLN-DRQFVHDPQLGYSLPCVA-GCPN----SLIKELHHFRILGEEQYNRYQRYATE 307 (446)
T ss_pred eEEEecCCceeehHHhhhhHhhhccc-ccccccCccccccccccC-CCch----HHHHhhhhheecchhHHHHHHHhhhh
Confidence 3446788 99999999999999996 4442 1356665 5653 333333 899999888
Q ss_pred HHHhhCCCCCCCCCCCCeeeCCCCCCcc
Q psy7602 66 QVTNCRLASLVPCKCSWVRFPPGADFIL 93 (95)
Q Consensus 66 ~~v~~~~~~~~~~~~~~~~~CP~~~C~~ 93 (95)
.+|.... .+ -||+|+|+.
T Consensus 308 e~vlq~g---------GV-lCP~pgCG~ 325 (446)
T KOG0006|consen 308 ECVLQMG---------GV-LCPRPGCGA 325 (446)
T ss_pred hheeecC---------CE-ecCCCCCCc
Confidence 8887773 34 499999874
No 18
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.53 E-value=0.0013 Score=38.04 Aligned_cols=33 Identities=24% Similarity=0.646 Sum_probs=22.1
Q ss_pred cccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccC
Q psy7602 6 MTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCN 45 (95)
Q Consensus 6 ~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~ 45 (95)
+.+..|||.|-++-+.+|| + .+ ..++||..||+
T Consensus 25 V~s~~C~H~fek~aI~~~i----~-~~--~~~~CPv~GC~ 57 (57)
T PF11789_consen 25 VKSKKCGHTFEKEAILQYI----Q-RN--GSKRCPVAGCN 57 (57)
T ss_dssp EEESSS--EEEHHHHHHHC----T-TT--S-EE-SCCC-S
T ss_pred cCcCCCCCeecHHHHHHHH----H-hc--CCCCCCCCCCC
Confidence 3456899999999999999 3 22 25899999995
No 19
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=96.45 E-value=0.0047 Score=35.17 Aligned_cols=42 Identities=7% Similarity=-0.059 Sum_probs=29.3
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
++-+.++|||.||++|+.+|++. + ..||. |+..++.+++...
T Consensus 12 ~~Pv~~~~G~v~~~~~i~~~~~~----~-----~~cP~--~~~~~~~~~l~~~ 53 (63)
T smart00504 12 KDPVILPSGQTYERRAIEKWLLS----H-----GTDPV--TGQPLTHEDLIPN 53 (63)
T ss_pred CCCEECCCCCEEeHHHHHHHHHH----C-----CCCCC--CcCCCChhhceeC
Confidence 34456789999999999999975 1 25665 5666665555443
No 20
>KOG0317|consensus
Probab=96.38 E-value=0.0028 Score=47.41 Aligned_cols=41 Identities=27% Similarity=0.573 Sum_probs=32.4
Q ss_pred CCCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhh
Q psy7602 3 STLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPI 54 (95)
Q Consensus 3 ~~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~ 54 (95)
.++-..++|||.||-.|+.+|+..+- | ||. |...+.++.+.
T Consensus 249 ~~~pSaTpCGHiFCWsCI~~w~~ek~-e--------CPl--CR~~~~pskvi 289 (293)
T KOG0317|consen 249 RSNPSATPCGHIFCWSCILEWCSEKA-E--------CPL--CREKFQPSKVI 289 (293)
T ss_pred CCCCCcCcCcchHHHHHHHHHHcccc-C--------CCc--ccccCCCccee
Confidence 34566789999999999999998866 2 875 88887777653
No 21
>KOG1002|consensus
Probab=96.29 E-value=0.0031 Score=51.07 Aligned_cols=44 Identities=25% Similarity=0.614 Sum_probs=34.7
Q ss_pred CCCCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccc
Q psy7602 2 PSTLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDG 51 (95)
Q Consensus 2 ~~~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~ 51 (95)
|+++.+..+|.|.||+.|+++|+..-.. |. .++||. |...++.+
T Consensus 545 ~aed~i~s~ChH~FCrlCi~eyv~~f~~--~~--nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 545 PAEDYIESSCHHKFCRLCIKEYVESFME--NN--NVTCPV--CHIGLSID 588 (791)
T ss_pred hhhhhHhhhhhHHHHHHHHHHHHHhhhc--cc--CCCCcc--cccccccc
Confidence 4566777899999999999999998773 33 489996 87665544
No 22
>KOG2164|consensus
Probab=95.95 E-value=0.0038 Score=49.83 Aligned_cols=43 Identities=23% Similarity=0.593 Sum_probs=34.3
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
.+.|||.||-.|+-+|+..... .+ ...||- |...|...++..+
T Consensus 201 ~t~CGHiFC~~CiLqy~~~s~~-~~---~~~CPi--C~s~I~~kdl~pv 243 (513)
T KOG2164|consen 201 RTNCGHIFCGPCILQYWNYSAI-KG---PCSCPI--CRSTITLKDLLPV 243 (513)
T ss_pred ccccCceeeHHHHHHHHhhhcc-cC---CccCCc--hhhhccccceeee
Confidence 3569999999999999998832 22 578986 9988888777665
No 23
>KOG0978|consensus
Probab=95.88 E-value=0.0035 Score=51.75 Aligned_cols=42 Identities=21% Similarity=0.427 Sum_probs=33.5
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhh
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIE 55 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~ 55 (95)
.+++...|||.||.+|.+..+.++-+ +||. |+.-+...+|..
T Consensus 654 Kd~vI~kC~H~FC~~Cvq~r~etRqR--------KCP~--Cn~aFganDv~~ 695 (698)
T KOG0978|consen 654 KDAVITKCGHVFCEECVQTRYETRQR--------KCPK--CNAAFGANDVHR 695 (698)
T ss_pred hhHHHHhcchHHHHHHHHHHHHHhcC--------CCCC--CCCCCCcccccc
Confidence 45667789999999999999887653 5884 888888877754
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=95.37 E-value=0.015 Score=42.44 Aligned_cols=36 Identities=25% Similarity=0.563 Sum_probs=27.2
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCccc
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILV 48 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i 48 (95)
..+|+|.||..|++++-.++- +.|. .-.||. |+..+
T Consensus 194 L~~CnHsFCl~CIr~Wr~~r~-~~~~--~rsCPi--CR~~f 229 (242)
T PHA02926 194 LDSCNHIFCITCINIWHRTRR-ETGA--SDNCPI--CRTRF 229 (242)
T ss_pred cCCCCchHHHHHHHHHHHhcc-ccCc--CCcCCC--Cccee
Confidence 348999999999999999865 2343 468997 77543
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.12 E-value=0.023 Score=44.35 Aligned_cols=34 Identities=26% Similarity=0.605 Sum_probs=25.1
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccc
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDG 51 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~ 51 (95)
+.++|||.||..|++.|+.. . ..||. |...+..+
T Consensus 40 vitpCgH~FCs~CI~~~l~~------~---~~CP~--Cr~~~~~~ 73 (397)
T TIGR00599 40 VLTSCSHTFCSLCIRRCLSN------Q---PKCPL--CRAEDQES 73 (397)
T ss_pred cCCCCCCchhHHHHHHHHhC------C---CCCCC--CCCccccc
Confidence 45799999999999999853 1 26874 77665543
No 26
>KOG0823|consensus
Probab=95.12 E-value=0.011 Score=43.08 Aligned_cols=45 Identities=22% Similarity=0.444 Sum_probs=35.1
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
++-+...|||-||=-|+.+|+..+-. .-.||. |+..|+.+.|-.|
T Consensus 58 kdPVvTlCGHLFCWpClyqWl~~~~~------~~~cPV--CK~~Vs~~~vvPl 102 (230)
T KOG0823|consen 58 KDPVVTLCGHLFCWPCLYQWLQTRPN------SKECPV--CKAEVSIDTVVPL 102 (230)
T ss_pred CCCEEeecccceehHHHHHHHhhcCC------CeeCCc--cccccccceEEee
Confidence 44555679999999999999998764 134665 9998888887666
No 27
>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=95.09 E-value=0.02 Score=43.30 Aligned_cols=33 Identities=21% Similarity=0.653 Sum_probs=24.4
Q ss_pred CCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccch
Q psy7602 10 ECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGK 52 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~ 52 (95)
.|||.||..|+...+ . .|. ..|| .|+..+....
T Consensus 25 ~CGH~~C~sCv~~l~----~-~~~---~~CP--~C~~~lrk~~ 57 (309)
T TIGR00570 25 VCGHTLCESCVDLLF----V-RGS---GSCP--ECDTPLRKNN 57 (309)
T ss_pred CCCCcccHHHHHHHh----c-CCC---CCCC--CCCCccchhh
Confidence 799999999999986 2 232 4799 6877655544
No 28
>PHA02929 N1R/p28-like protein; Provisional
Probab=94.18 E-value=0.029 Score=41.02 Aligned_cols=31 Identities=23% Similarity=0.551 Sum_probs=23.1
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccc
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVD 49 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~ 49 (95)
..+|+|.||.+|+.++++. .-.||. |+..+.
T Consensus 197 l~~C~H~FC~~CI~~Wl~~---------~~tCPl--CR~~~~ 227 (238)
T PHA02929 197 LSNCNHVFCIECIDIWKKE---------KNTCPV--CRTPFI 227 (238)
T ss_pred cCCCCCcccHHHHHHHHhc---------CCCCCC--CCCEee
Confidence 3589999999999999753 136886 776543
No 29
>KOG2177|consensus
Probab=93.02 E-value=0.054 Score=37.70 Aligned_cols=28 Identities=29% Similarity=0.834 Sum_probs=23.1
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccC
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCN 45 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~ 45 (95)
..+.|||.||..|+..... ..+.||. |.
T Consensus 27 ~~l~C~H~~c~~C~~~~~~---------~~~~Cp~--cr 54 (386)
T KOG2177|consen 27 VLLPCGHNFCRACLTRSWE---------GPLSCPV--CR 54 (386)
T ss_pred ccccccchHhHHHHHHhcC---------CCcCCcc--cC
Confidence 5678999999999999888 2378886 66
No 30
>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=90.94 E-value=0.34 Score=28.76 Aligned_cols=57 Identities=7% Similarity=-0.075 Sum_probs=32.3
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhHHHHHHHHHHHHHhhC
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQGILSNQVTNCR 71 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l~ky~~~l~~~~v~~~ 71 (95)
.+-+.+++||.|.+.++.+|++. . ...||. ++..++.+++..-...++ .++.|++.|
T Consensus 15 ~dPVi~~~G~tyer~~I~~~l~~--~------~~~~P~--t~~~l~~~~l~pn~~Lk~-~I~~~~~~~ 71 (73)
T PF04564_consen 15 RDPVILPSGHTYERSAIERWLEQ--N------GGTDPF--TRQPLSESDLIPNRALKS-AIEEWCAEN 71 (73)
T ss_dssp SSEEEETTSEEEEHHHHHHHHCT--T------SSB-TT--T-SB-SGGGSEE-HHHHH-HHHHHHHHC
T ss_pred hCceeCCcCCEEcHHHHHHHHHc--C------CCCCCC--CCCcCCcccceECHHHHH-HHHHHHHHc
Confidence 44456789999999999999987 1 234554 456666655433222222 233555554
No 31
>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=89.99 E-value=0.13 Score=30.80 Aligned_cols=18 Identities=28% Similarity=0.648 Sum_probs=16.1
Q ss_pred CCCCchhhHHHHHHHHHh
Q psy7602 9 LECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~ 26 (95)
..|||.|-..|++++|+.
T Consensus 48 ~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp ETTSEEEEHHHHHHHHTT
T ss_pred cccCCCEEHHHHHHHHhc
Confidence 479999999999999954
No 32
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=89.89 E-value=0.16 Score=38.60 Aligned_cols=38 Identities=24% Similarity=0.552 Sum_probs=27.2
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccch
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGK 52 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~ 52 (95)
..|||.||.-|++.||..+-+ --.|-++-|...+..+.
T Consensus 41 TtCgHtFCslCIR~hL~~qp~------CP~Cr~~~~esrlr~~s 78 (391)
T COG5432 41 TTCGHTFCSLCIRRHLGTQPF------CPVCREDPCESRLRGSS 78 (391)
T ss_pred cccccchhHHHHHHHhcCCCC------CccccccHHhhhcccch
Confidence 579999999999999976442 23566666766555443
No 33
>KOG0287|consensus
Probab=87.85 E-value=0.31 Score=37.81 Aligned_cols=34 Identities=32% Similarity=0.792 Sum_probs=24.6
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
.+|+|.||.-|++.||..+-+ ||. |-..+.++.+
T Consensus 39 tpCsHtfCSlCIR~~L~~~p~---------CP~--C~~~~~Es~L 72 (442)
T KOG0287|consen 39 TPCSHTFCSLCIRKFLSYKPQ---------CPT--CCVTVTESDL 72 (442)
T ss_pred ccccchHHHHHHHHHhccCCC---------CCc--eecccchhhh
Confidence 479999999999999976542 543 6655555544
No 34
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.82 E-value=0.67 Score=34.54 Aligned_cols=42 Identities=26% Similarity=0.406 Sum_probs=26.5
Q ss_pred CCCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 3 STLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 3 ~~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
+.....+.|||.||..|+-...+.+- .-.||. |.....+..+
T Consensus 225 ~~~ps~t~CgHlFC~~Cl~~~~t~~k-------~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 225 PEVPSCTPCGHLFCLSCLLISWTKKK-------YEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cCCcccccccchhhHHHHHHHHHhhc-------cccCch--hhhhccchhh
Confidence 34455578999999999987532221 234765 7766555443
No 35
>KOG4739|consensus
Probab=83.53 E-value=0.42 Score=34.94 Aligned_cols=18 Identities=28% Similarity=0.610 Sum_probs=14.8
Q ss_pred CCcccCCCCchhhHHHHH
Q psy7602 4 TLMTGLECSHRFCTQCWC 21 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~ 21 (95)
..++.++|+|+||..|.+
T Consensus 16 ~~f~LTaC~HvfC~~C~k 33 (233)
T KOG4739|consen 16 DPFFLTACRHVFCEPCLK 33 (233)
T ss_pred Cceeeeechhhhhhhhcc
Confidence 456667999999999965
No 36
>KOG2660|consensus
Probab=82.64 E-value=0.44 Score=36.42 Aligned_cols=34 Identities=35% Similarity=0.870 Sum_probs=25.7
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccc
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDG 51 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~ 51 (95)
....|-|.||+.|+-.|++. ...||. |+..|..+
T Consensus 30 TI~eCLHTFCkSCivk~l~~---------~~~CP~--C~i~ih~t 63 (331)
T KOG2660|consen 30 TITECLHTFCKSCIVKYLEE---------SKYCPT--CDIVIHKT 63 (331)
T ss_pred hHHHHHHHHHHHHHHHHHHH---------hccCCc--cceeccCc
Confidence 34579999999999999987 135775 77665554
No 37
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=81.19 E-value=1.3 Score=26.38 Aligned_cols=20 Identities=20% Similarity=0.687 Sum_probs=14.2
Q ss_pred hhhHHHHHHHHHhhhhcCCc
Q psy7602 14 RFCTQCWCEYLTTKIIQEGM 33 (95)
Q Consensus 14 ~FC~~C~~~yl~~~I~~~g~ 33 (95)
.||++|+..++.....+.|.
T Consensus 11 gFCRNCLskWy~~aA~~~g~ 30 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEERGI 30 (68)
T ss_dssp S--HHHHHHHHHHHHHHCT-
T ss_pred HHHHHHHHHHHHHHHHhcCC
Confidence 49999999999998875453
No 38
>KOG0824|consensus
Probab=80.38 E-value=1.2 Score=33.90 Aligned_cols=40 Identities=28% Similarity=0.559 Sum_probs=29.0
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
+.|.|+|.||--|+++-+.. + ...|+. |...|+++.+.+.
T Consensus 21 v~l~C~HkFCyiCiKGsy~n-----d---k~~Cav--CR~pids~i~~~p 60 (324)
T KOG0824|consen 21 VNLYCFHKFCYICIKGSYKN-----D---KKTCAV--CRFPIDSTIDFEP 60 (324)
T ss_pred ccccccchhhhhhhcchhhc-----C---CCCCce--ecCCCCcchhcch
Confidence 56899999999998764432 2 235775 8888888876544
No 39
>KOG1428|consensus
Probab=79.11 E-value=5.5 Score=37.00 Aligned_cols=51 Identities=22% Similarity=0.359 Sum_probs=41.3
Q ss_pred CCCcccCCCCchhhHHHHHHHHHhhhhcCCc--eeeeecCccccCcccccchhhhH
Q psy7602 3 STLMTGLECSHRFCTQCWCEYLTTKIIQEGM--GQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 3 ~~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~--~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
....+.|.|+|.|=..|-+.-|+.+-. +.+ ..-|.||- |...|....++.|
T Consensus 3499 AAP~IqL~C~HiFHlqC~R~vLE~RW~-GPRItF~FisCPi--C~n~InH~~LkDL 3551 (3738)
T KOG1428|consen 3499 AAPAIQLDCSHIFHLQCCRRVLENRWL-GPRITFGFISCPI--CKNKINHIVLKDL 3551 (3738)
T ss_pred CCcceecCCccchhHHHHHHHHHhccc-CCeeEEeeeeccc--ccchhhhHHHHHH
Confidence 345678999999999999999999986 444 23689996 9999988877766
No 40
>KOG0802|consensus
Probab=78.29 E-value=1.6 Score=35.07 Aligned_cols=21 Identities=24% Similarity=0.575 Sum_probs=18.9
Q ss_pred cccCCCCchhhHHHHHHHHHh
Q psy7602 6 MTGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 6 ~~~l~CgH~FC~~C~~~yl~~ 26 (95)
...|.|||.|+..|++.|++.
T Consensus 309 ~~rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 309 PKRLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred cceeecccchHHHHHHHHHHH
Confidence 456899999999999999987
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=78.17 E-value=0.23 Score=29.49 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=14.0
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
-.|.|.||..|.++ .+. ..||. |....-..++
T Consensus 24 ~~CeH~fCs~Ci~~----~~~-------~~CPv--C~~Paw~qD~ 55 (65)
T PF14835_consen 24 GGCEHIFCSSCIRD----CIG-------SECPV--CHTPAWIQDI 55 (65)
T ss_dssp -SSS--B-TTTGGG----GTT-------TB-SS--S--B-S-SS-
T ss_pred ccCccHHHHHHhHH----hcC-------CCCCC--cCChHHHHHH
Confidence 47999999999854 331 13775 7765554444
No 42
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=75.30 E-value=1.2 Score=26.37 Aligned_cols=39 Identities=18% Similarity=0.396 Sum_probs=20.5
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCcee-ee--ecCccccCccccc
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQ-TI--ACAAHGCNILVDD 50 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~-~i--~Cp~~~C~~~i~~ 50 (95)
..|++.|=..|+.+|+++.-. +.+.+ +| .||. |+..|+-
T Consensus 26 ~~C~~~fH~~CL~~wf~~~~~-~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 26 PSCGKKFHLLCLSEWFLSLEK-SRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp TT----B-SGGGHHHHHHHHS-SS-TTT--EEE-TT--T-SEEEG
T ss_pred cccCCHHHHHHHHHHHHHccc-CCeeecccccCCcC--CCCeeeE
Confidence 368999999999999987664 32212 33 7885 8877764
No 43
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=75.21 E-value=1.4 Score=32.02 Aligned_cols=16 Identities=38% Similarity=0.881 Sum_probs=12.9
Q ss_pred ccCCCCchhhHHHHHH
Q psy7602 7 TGLECSHRFCTQCWCE 22 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~ 22 (95)
+...|||.||..|.-.
T Consensus 210 vvt~CGH~FC~~Cai~ 225 (259)
T COG5152 210 VVTECGHSFCSLCAIR 225 (259)
T ss_pred hhhhcchhHHHHHHHH
Confidence 4468999999999753
No 44
>KOG0311|consensus
Probab=74.17 E-value=0.91 Score=35.23 Aligned_cols=20 Identities=50% Similarity=0.933 Sum_probs=15.0
Q ss_pred cccCCCCchhhHHHHHHHHH
Q psy7602 6 MTGLECSHRFCTQCWCEYLT 25 (95)
Q Consensus 6 ~~~l~CgH~FC~~C~~~yl~ 25 (95)
|....|.|+||.+|+-.-++
T Consensus 57 mttkeClhrfc~~ci~~a~r 76 (381)
T KOG0311|consen 57 MTTKECLHRFCFDCIWKALR 76 (381)
T ss_pred cccHHHHHHHHHHHHHHHHH
Confidence 44568999999999865443
No 45
>KOG1734|consensus
Probab=72.45 E-value=1.4 Score=33.28 Aligned_cols=41 Identities=24% Similarity=0.408 Sum_probs=31.6
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
++++.|+|+|+|=..|.+++... |+ .-+||= |+..++.+.+
T Consensus 245 enty~LsCnHvFHEfCIrGWciv-----GK--kqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 245 ENTYKLSCNHVFHEFCIRGWCIV-----GK--KQTCPY--CKEKVDLKRM 285 (328)
T ss_pred hhheeeecccchHHHhhhhheee-----cC--CCCCch--HHHHhhHhhh
Confidence 46889999999999999999753 43 357885 8888876543
No 46
>KOG2979|consensus
Probab=71.91 E-value=6 Score=29.45 Aligned_cols=50 Identities=22% Similarity=0.354 Sum_probs=32.5
Q ss_pred cccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccC--cccccchhhhHHHHHHH
Q psy7602 6 MTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCN--ILVDDGKPIEFDVYQGI 62 (95)
Q Consensus 6 ~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~--~~i~~~~i~~l~ky~~~ 62 (95)
+.+-.|||+|=++=..+|+.. . ..|+||..||. ..+....+...+-+++-
T Consensus 190 viSkkC~HvydrDsI~~~l~~------~-~~i~CPv~gC~~~~~~~~~~l~~d~el~~k 241 (262)
T KOG2979|consen 190 VISKKCGHVYDRDSIMQILCD------E-ITIRCPVLGCENPYYIQPGHLDEDKELQQK 241 (262)
T ss_pred hhhcCcCcchhhhhHHHHhcc------C-ceeecccccCCccccccccccCchHHHHHH
Confidence 455679999877766666543 2 35999999999 45555544444344333
No 47
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.27 E-value=2.8 Score=32.15 Aligned_cols=37 Identities=27% Similarity=0.631 Sum_probs=28.4
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCccccc
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDD 50 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~ 50 (95)
++...|+|.|+|-..|...|+. |. ..+||. |+..+++
T Consensus 337 d~~~vlPC~H~FH~~Cv~kW~~------~y--~~~CPv--Crt~iPP 373 (374)
T COG5540 337 DRLRVLPCDHRFHVGCVDKWLL------GY--SNKCPV--CRTAIPP 373 (374)
T ss_pred ceEEEeccCceechhHHHHHHh------hh--cccCCc--cCCCCCC
Confidence 4456689999999999999874 33 467886 8887765
No 48
>KOG4159|consensus
Probab=69.69 E-value=8.4 Score=30.29 Aligned_cols=53 Identities=15% Similarity=0.329 Sum_probs=30.5
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCccccc-chhhh---HHHHHHHHHHHHHhh
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDD-GKPIE---FDVYQGILSNQVTNC 70 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~-~~i~~---l~ky~~~l~~~~v~~ 70 (95)
+.++|||.||..|+.+ .. + + .-.||. |...+.. ....+ +.++...++.+|++.
T Consensus 98 v~tpcghs~c~~Cl~r----~l-d--~--~~~cp~--Cr~~l~e~~~~~~~~~~~r~~~~li~~F~~~ 154 (398)
T KOG4159|consen 98 VVTPCGHSFCLECLDR----SL-D--Q--ETECPL--CRDELVELPALEQALSLNRLLCKLITKFLEG 154 (398)
T ss_pred ccccccccccHHHHHH----Hh-c--c--CCCCcc--cccccccchHHHHHHHHHHHHHHHHHHhhhh
Confidence 4569999999999555 22 1 2 345665 7765553 22221 255555555555544
No 49
>KOG1645|consensus
Probab=68.91 E-value=5.1 Score=31.84 Aligned_cols=44 Identities=23% Similarity=0.432 Sum_probs=32.0
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
..+.++.|||-|=.+|.+.+|- |+. ...||. |+..-...+|...
T Consensus 20 hr~vsl~cghlFgs~cie~wl~-k~~------~~~cp~--c~~katkr~i~~e 63 (463)
T KOG1645|consen 20 HRIVSLQCGHLFGSQCIEKWLG-KKT------KMQCPL--CSGKATKRQIRPE 63 (463)
T ss_pred eEEeeecccccccHHHHHHHHh-hhh------hhhCcc--cCChhHHHHHHHH
Confidence 4567899999999999999994 442 478886 7765555554433
No 50
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=67.83 E-value=5.4 Score=24.86 Aligned_cols=32 Identities=28% Similarity=0.570 Sum_probs=23.4
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCccc
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILV 48 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i 48 (95)
-.|+|.|-..|+.++|+++- ++ =.||. |+...
T Consensus 50 g~C~H~FH~hCI~kWl~~~~---~~---~~CPm--CR~~w 81 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQS---SK---GQCPM--CRQPW 81 (85)
T ss_pred ccCccHHHHHHHHHHHcccc---CC---CCCCC--cCCee
Confidence 36999999999999999852 12 26775 65543
No 51
>KOG1001|consensus
Probab=67.71 E-value=2.7 Score=35.03 Aligned_cols=41 Identities=20% Similarity=0.474 Sum_probs=27.4
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchh
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKP 53 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i 53 (95)
+..+...|||.||.+||..+++..-. . .|| .|...+....+
T Consensus 464 ~~~~it~c~h~~c~~c~~~~i~~~~~--~-----~~~--~cr~~l~~~~l 504 (674)
T KOG1001|consen 464 DSFFITRCGHDFCVECLKKSIQQSEN--A-----PCP--LCRNVLKEKKL 504 (674)
T ss_pred ccceeecccchHHHHHHHhccccccC--C-----CCc--HHHHHHHHHHH
Confidence 34455789999999999999876432 1 444 47655554443
No 52
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.96 E-value=5.3 Score=25.41 Aligned_cols=19 Identities=21% Similarity=0.663 Sum_probs=15.7
Q ss_pred hhhHHHHHHHHHhhhhcCC
Q psy7602 14 RFCTQCWCEYLTTKIIQEG 32 (95)
Q Consensus 14 ~FC~~C~~~yl~~~I~~~g 32 (95)
-||++|+..|++......|
T Consensus 42 gFCRNCLs~Wy~eaae~~g 60 (104)
T COG3492 42 GFCRNCLSNWYREAAEAQG 60 (104)
T ss_pred HHHHHHHHHHHHHHHhccC
Confidence 5999999999999885334
No 53
>KOG2932|consensus
Probab=63.25 E-value=3.2 Score=32.00 Aligned_cols=13 Identities=38% Similarity=1.088 Sum_probs=11.6
Q ss_pred CCCCchhhHHHHH
Q psy7602 9 LECSHRFCTQCWC 21 (95)
Q Consensus 9 l~CgH~FC~~C~~ 21 (95)
..|.|+||.+|-+
T Consensus 107 IPCkHvFCl~CAr 119 (389)
T KOG2932|consen 107 IPCKHVFCLECAR 119 (389)
T ss_pred cccchhhhhhhhh
Confidence 5899999999976
No 54
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=60.22 E-value=2.6 Score=24.22 Aligned_cols=35 Identities=26% Similarity=0.546 Sum_probs=23.9
Q ss_pred CcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccch
Q psy7602 5 LMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGK 52 (95)
Q Consensus 5 ~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~ 52 (95)
.-..++|||.-|.+||- |. ..-.||- |...++.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~----------~~-rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFP----------GE-RYNGCPF--CGTPFEFDD 53 (55)
T ss_pred ccccccccceeeccccC----------hh-hccCCCC--CCCcccCCC
Confidence 34568999999999993 22 2346775 777666554
No 55
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=57.54 E-value=5.5 Score=22.43 Aligned_cols=12 Identities=33% Similarity=1.038 Sum_probs=7.3
Q ss_pred CCCCchhhHHHH
Q psy7602 9 LECSHRFCTQCW 20 (95)
Q Consensus 9 l~CgH~FC~~C~ 20 (95)
-.|++.||.+|=
T Consensus 25 ~~C~~~FC~dCD 36 (51)
T PF07975_consen 25 PKCKNHFCIDCD 36 (51)
T ss_dssp TTTT--B-HHHH
T ss_pred CCCCCccccCcC
Confidence 469999999993
No 56
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=55.74 E-value=7.7 Score=30.70 Aligned_cols=20 Identities=25% Similarity=0.591 Sum_probs=17.8
Q ss_pred ccCCCCchhhHHHHHHHHHh
Q psy7602 7 TGLECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~ 26 (95)
..|+|||.+-..|++.|++-
T Consensus 314 KrLpCGHilHl~CLknW~ER 333 (491)
T COG5243 314 KRLPCGHILHLHCLKNWLER 333 (491)
T ss_pred ccccccceeeHHHHHHHHHh
Confidence 45899999999999999874
No 57
>KOG1039|consensus
Probab=54.27 E-value=6.4 Score=30.36 Aligned_cols=34 Identities=24% Similarity=0.712 Sum_probs=24.1
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCc
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNI 46 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~ 46 (95)
.+|.|.||..|.+.+=..+-. +.. ..-.||. |..
T Consensus 185 pnC~H~~Cl~Cir~wr~~~q~-~~~-~sksCP~--CRv 218 (344)
T KOG1039|consen 185 PNCNHSFCLNCIRKWRQATQF-ESK-TSKSCPF--CRV 218 (344)
T ss_pred CCcchhhhhcHhHhhhhhhcc-ccc-cccCCCc--ccC
Confidence 469999999999988765553 222 3457886 653
No 58
>KOG2879|consensus
Probab=53.79 E-value=8 Score=29.20 Aligned_cols=37 Identities=19% Similarity=0.393 Sum_probs=24.9
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccc
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVD 49 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~ 49 (95)
-.+....|||.||--|.+.-+...+ ..+||. |+....
T Consensus 251 iP~~~~~C~HiyCY~Ci~ts~~~~a-------sf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 251 IPHVIGKCGHIYCYYCIATSRLWDA-------SFTCPL--CGENVE 287 (298)
T ss_pred CCeeeccccceeehhhhhhhhcchh-------hcccCc--cCCCCc
Confidence 3445566999999999876544322 478885 776544
No 59
>KOG1785|consensus
Probab=53.16 E-value=10 Score=30.38 Aligned_cols=35 Identities=26% Similarity=0.643 Sum_probs=25.6
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccC
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCN 45 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~ 45 (95)
.+....+|||-.|..|+..|-.+ ++|+ .||--.|.
T Consensus 380 KdvkIEPCGHLlCt~CLa~WQ~s---d~gq----~CPFCRcE 414 (563)
T KOG1785|consen 380 KDVKIEPCGHLLCTSCLAAWQDS---DEGQ----TCPFCRCE 414 (563)
T ss_pred CCcccccccchHHHHHHHhhccc---CCCC----CCCceeeE
Confidence 45667799999999999988654 4454 47765554
No 60
>KOG4692|consensus
Probab=51.85 E-value=9.7 Score=29.99 Aligned_cols=18 Identities=39% Similarity=0.761 Sum_probs=15.7
Q ss_pred CCCCchhhHHHHHHHHHh
Q psy7602 9 LECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~ 26 (95)
.+|+|+-|.+|+.+|+-.
T Consensus 438 ~PC~H~SC~~CI~qHlmN 455 (489)
T KOG4692|consen 438 APCSHRSCYGCITQHLMN 455 (489)
T ss_pred cCCCCchHHHHHHHHHhc
Confidence 589999999999998753
No 61
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=50.40 E-value=11 Score=20.94 Aligned_cols=17 Identities=29% Similarity=0.888 Sum_probs=10.2
Q ss_pred CCCCchhhHHHHHHHHH
Q psy7602 9 LECSHRFCTQCWCEYLT 25 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~ 25 (95)
=.||+..|+.||..-++
T Consensus 18 C~Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 18 CECGFQICRFCYHDILE 34 (48)
T ss_dssp STTS----HHHHHHHTT
T ss_pred CcCCCcHHHHHHHHHHh
Confidence 36999999999987655
No 62
>KOG4628|consensus
Probab=49.20 E-value=8 Score=29.93 Aligned_cols=24 Identities=33% Similarity=0.625 Sum_probs=20.5
Q ss_pred CCcccCCCCchhhHHHHHHHHHhh
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTK 27 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~ 27 (95)
+.+..|+|+|.|-.+|..-||...
T Consensus 243 dklRiLPC~H~FH~~CIDpWL~~~ 266 (348)
T KOG4628|consen 243 DKLRILPCSHKFHVNCIDPWLTQT 266 (348)
T ss_pred CeeeEecCCCchhhccchhhHhhc
Confidence 455669999999999999999874
No 63
>KOG0297|consensus
Probab=46.57 E-value=8 Score=30.07 Aligned_cols=18 Identities=44% Similarity=1.041 Sum_probs=16.0
Q ss_pred CCCCchhhHHHHHHHHHh
Q psy7602 9 LECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~ 26 (95)
..|||.||..|....++.
T Consensus 38 ~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 38 TTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CCCCCcccccccchhhcc
Confidence 689999999999887776
No 64
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=46.24 E-value=8.6 Score=21.03 Aligned_cols=20 Identities=20% Similarity=0.615 Sum_probs=15.9
Q ss_pred CCCCchhhHHHHHHHHHhhh
Q psy7602 9 LECSHRFCTQCWCEYLTTKI 28 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I 28 (95)
-.||+.||.+|.........
T Consensus 22 r~Cg~~~C~~C~~~~~~~~~ 41 (57)
T cd00065 22 RNCGRIFCSKCSSNRIPLPS 41 (57)
T ss_pred CcCcCCcChHHcCCeeecCc
Confidence 36999999999998766443
No 65
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=45.92 E-value=10 Score=24.85 Aligned_cols=20 Identities=20% Similarity=0.602 Sum_probs=17.1
Q ss_pred CCCchhhHHHHHHHHHhhhh
Q psy7602 10 ECSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~ 29 (95)
.=||.||.+|-+.++++++.
T Consensus 52 GlGqhYCieCaryf~t~~aL 71 (126)
T COG5112 52 GLGQHYCIECARYFITEKAL 71 (126)
T ss_pred CCceeeeehhHHHHHHHHHH
Confidence 46899999999999987764
No 66
>PHA03096 p28-like protein; Provisional
Probab=43.11 E-value=19 Score=27.05 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=18.2
Q ss_pred CCCchhhHHHHHHHHHhhhh
Q psy7602 10 ECSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~ 29 (95)
.|.|.||..|.+.+..++..
T Consensus 203 ~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 203 EIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred cCCcHHHHHHHHHHHHhhhh
Confidence 79999999999999998763
No 67
>KOG1941|consensus
Probab=42.06 E-value=17 Score=28.98 Aligned_cols=38 Identities=34% Similarity=0.673 Sum_probs=27.0
Q ss_pred CCCcccCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccc
Q psy7602 3 STLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVD 49 (95)
Q Consensus 3 ~~~~~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~ 49 (95)
++.+-.|+|.|.|=..|...||+. +| +=.||. |+.+++
T Consensus 379 ~e~LqALpCsHIfH~rCl~e~L~~----n~---~rsCP~--CrklrS 416 (518)
T KOG1941|consen 379 NERLQALPCSHIFHLRCLQEILEN----NG---TRSCPN--CRKLRS 416 (518)
T ss_pred cccccccchhHHHHHHHHHHHHHh----CC---CCCCcc--HHHHHh
Confidence 456678999999999999999943 23 235764 664433
No 68
>KOG0006|consensus
Probab=41.06 E-value=15 Score=28.63 Aligned_cols=76 Identities=14% Similarity=0.280 Sum_probs=40.8
Q ss_pred CCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhHHHHHHHHHHHHHhhCCCCCCC---------CCC
Q psy7602 10 ECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQGILSNQVTNCRLASLVP---------CKC 80 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l~ky~~~l~~~~v~~~~~~~~~---------~~~ 80 (95)
.||-.||++|.+.|-+-.-. .+-.. =-...|.+.+++...++ ++|+.+... -|+.. +.-|| .++
T Consensus 341 gCgf~FCR~C~e~yh~geC~-~~~~a---s~t~tc~y~vde~~a~~-arwd~as~~-TIk~t-TkpCPkChvptErnGGC 413 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECS-AVFEA---SGTTTCAYRVDERAAEQ-ARWDAASKE-TIKKT-TKPCPKCHVPTERNGGC 413 (446)
T ss_pred CchhHhHHHHHhhhccccce-eeecc---ccccceeeecChhhhhh-hhhhhhhhh-hhhhc-cCCCCCccCccccCCce
Confidence 59999999999998653332 11100 01124666666644333 455544322 23322 23343 244
Q ss_pred CCeeeCCCCCCcc
Q psy7602 81 SWVRFPPGADFIL 93 (95)
Q Consensus 81 ~~~~~CP~~~C~~ 93 (95)
..++ ||.|.|++
T Consensus 414 mHm~-Ct~~~Cg~ 425 (446)
T KOG0006|consen 414 MHMK-CTQPQCGL 425 (446)
T ss_pred EEee-cCCCCCCc
Confidence 4555 88888876
No 69
>KOG3579|consensus
Probab=39.71 E-value=14 Score=28.14 Aligned_cols=32 Identities=28% Similarity=0.698 Sum_probs=25.6
Q ss_pred CchhhHHHHHHHHHhhhhcCCceeeeecCcc-ccCcc
Q psy7602 12 SHRFCTQCWCEYLTTKIIQEGMGQTIACAAH-GCNIL 47 (95)
Q Consensus 12 gH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~-~C~~~ 47 (95)
.|.||.-|-++.|+.+=. .| .++||.. +|..+
T Consensus 291 ~HKFCFPCSResIK~Qg~-sg---evYCPSGdkCPLv 323 (352)
T KOG3579|consen 291 SHKFCFPCSRESIKQQGA-SG---EVYCPSGDKCPLV 323 (352)
T ss_pred ccceecccCHHHHHhhcC-CC---ceeCCCCCcCccc
Confidence 699999999999998775 44 5899986 57643
No 70
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=38.89 E-value=17 Score=18.41 Aligned_cols=10 Identities=20% Similarity=0.079 Sum_probs=6.1
Q ss_pred CCCCCCccCC
Q psy7602 86 PPGADFILNG 95 (95)
Q Consensus 86 CP~~~C~~~~ 95 (95)
||.|+|.=.|
T Consensus 4 CPtpGCdg~G 13 (31)
T PF01530_consen 4 CPTPGCDGSG 13 (31)
T ss_dssp SSSTT--SCS
T ss_pred CCCCCCCccc
Confidence 9999997443
No 71
>KOG1813|consensus
Probab=37.47 E-value=13 Score=28.27 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=14.0
Q ss_pred ccCCCCchhhHHHHHHHH
Q psy7602 7 TGLECSHRFCTQCWCEYL 24 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl 24 (95)
+...|+|.||..|-...+
T Consensus 255 Vvt~c~h~fc~~ca~~~~ 272 (313)
T KOG1813|consen 255 VVTKCGHYFCEVCALKPY 272 (313)
T ss_pred hhhcCCceeehhhhcccc
Confidence 456899999999976544
No 72
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=35.96 E-value=59 Score=21.23 Aligned_cols=51 Identities=16% Similarity=0.236 Sum_probs=27.5
Q ss_pred HHHHHHhhhhcCCceee----eecCccccCcccccchhhhH-HHHHHHHHHHHHhhCC
Q psy7602 20 WCEYLTTKIIQEGMGQT----IACAAHGCNILVDDGKPIEF-DVYQGILSNQVTNCRL 72 (95)
Q Consensus 20 ~~~yl~~~I~~~g~~~~----i~Cp~~~C~~~i~~~~i~~l-~ky~~~l~~~~v~~~~ 72 (95)
+..||+.+|+=+|.... +..-..+=...++. .+ .+ .+|.+.|-+.|+..+.
T Consensus 26 fe~fL~erIKV~gk~gnlg~~V~i~~~~~ki~V~s-~v-~fsKrYLKYLTKKyLKK~~ 81 (112)
T PF01776_consen 26 FEKFLQERIKVNGKTGNLGNKVTISRDKNKITVTS-EV-PFSKRYLKYLTKKYLKKNN 81 (112)
T ss_dssp HHHHHHHHHHHHSCSSSSTTTEEEEE-SSEEEEEE-SS-S-SHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHheEeCCcccccCCeEEEEecCCEEEEEe-cc-cccHHHHHHHHHHHHhhcc
Confidence 56788887764443222 22211111111211 12 33 9999999999998773
No 73
>KOG2930|consensus
Probab=35.67 E-value=29 Score=22.59 Aligned_cols=19 Identities=32% Similarity=0.726 Sum_probs=17.1
Q ss_pred CCCchhhHHHHHHHHHhhh
Q psy7602 10 ECSHRFCTQCWCEYLTTKI 28 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I 28 (95)
.|.|.|=..|+..+|.++-
T Consensus 80 ~CNHaFH~hCisrWlktr~ 98 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRN 98 (114)
T ss_pred ecchHHHHHHHHHHHhhcC
Confidence 5999999999999998864
No 74
>KOG3408|consensus
Probab=34.69 E-value=17 Score=24.24 Aligned_cols=20 Identities=15% Similarity=0.501 Sum_probs=17.4
Q ss_pred CCCchhhHHHHHHHHHhhhh
Q psy7602 10 ECSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~ 29 (95)
+=|+.||..|-+.++.+++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l 73 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKAL 73 (129)
T ss_pred CCceeehhhhhhhhcchHHH
Confidence 36899999999999988876
No 75
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=34.16 E-value=30 Score=21.54 Aligned_cols=17 Identities=35% Similarity=0.843 Sum_probs=16.0
Q ss_pred CCCchhhHHHHHHHHHh
Q psy7602 10 ECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~ 26 (95)
-|.|.|=..|+..+|.+
T Consensus 53 ~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 49999999999999998
No 76
>KOG0828|consensus
Probab=33.84 E-value=33 Score=28.22 Aligned_cols=32 Identities=22% Similarity=0.594 Sum_probs=23.2
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccc
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVD 49 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~ 49 (95)
..+|.|.|=+.|++++.. +. .+.||. |+..++
T Consensus 603 ~tPC~HifH~~CL~~WMd------~y--kl~CPv--CR~pLP 634 (636)
T KOG0828|consen 603 LTPCHHIFHRQCLLQWMD------TY--KLICPV--CRCPLP 634 (636)
T ss_pred ccchHHHHHHHHHHHHHh------hh--cccCCc--cCCCCC
Confidence 358999999999999865 22 366776 555554
No 77
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=33.67 E-value=44 Score=23.18 Aligned_cols=27 Identities=4% Similarity=-0.084 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhhCCCCCCCCCCCCeeeCCCCCCcc
Q psy7602 57 DVYQGILSNQVTNCRLASLVPCKCSWVRFPPGADFIL 93 (95)
Q Consensus 57 ~ky~~~l~~~~v~~~~~~~~~~~~~~~~~CP~~~C~~ 93 (95)
-||+||+-++.=++. .+.=|+.|.|..
T Consensus 132 MrWKKFfYrqlCe~e----------G~~~C~aPsC~~ 158 (167)
T PF04891_consen 132 MRWKKFFYRQLCERE----------GLYLCRAPSCEE 158 (167)
T ss_pred CcHHHHHHHHHHHHc----------CCCcCCCCCCCC
Confidence 678888887766666 455588988863
No 78
>KOG0827|consensus
Probab=33.33 E-value=32 Score=27.42 Aligned_cols=26 Identities=19% Similarity=0.459 Sum_probs=21.0
Q ss_pred CCcccCC-CCchhhHHHHHHHHHhhhh
Q psy7602 4 TLMTGLE-CSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 4 ~~~~~l~-CgH~FC~~C~~~yl~~~I~ 29 (95)
.++-..+ |||.|=..|+.+|.+..-.
T Consensus 18 ~~l~~i~~cGhifh~~cl~qwfe~~Ps 44 (465)
T KOG0827|consen 18 HELGPIGTCGHIFHTTCLTQWFEGDPS 44 (465)
T ss_pred cccccccchhhHHHHHHHHHHHccCCc
Confidence 3445555 9999999999999988765
No 79
>PF14353 CpXC: CpXC protein
Probab=33.07 E-value=35 Score=21.88 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=17.2
Q ss_pred HHHhhhhcCCceeeeecCccccCccc
Q psy7602 23 YLTTKIIQEGMGQTIACAAHGCNILV 48 (95)
Q Consensus 23 yl~~~I~~~g~~~~i~Cp~~~C~~~i 48 (95)
=+..+|. +|..+..+||. |+..+
T Consensus 26 ~l~e~il-~g~l~~~~CP~--Cg~~~ 48 (128)
T PF14353_consen 26 ELKEKIL-DGSLFSFTCPS--CGHKF 48 (128)
T ss_pred HHHHHHH-cCCcCEEECCC--CCCce
Confidence 3577887 68878999997 76543
No 80
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=32.83 E-value=17 Score=18.33 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=7.7
Q ss_pred eeecCccccCccccc
Q psy7602 36 TIACAAHGCNILVDD 50 (95)
Q Consensus 36 ~i~Cp~~~C~~~i~~ 50 (95)
.++||.-+|...|..
T Consensus 2 ~vrCPvkdC~EEv~l 16 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSL 16 (30)
T ss_dssp EEE--STT---EEEH
T ss_pred ccccccccCcchhhh
Confidence 489999999987764
No 82
>KOG2594|consensus
Probab=32.58 E-value=47 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.439 Sum_probs=18.7
Q ss_pred ccCCCCchhhHHHHHHHHHhhhh
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~ 29 (95)
+.++=.-.||.+|+.+|++.|++
T Consensus 26 ~v~~~k~~~C~eCFv~~v~~KfR 48 (396)
T KOG2594|consen 26 TVDGKKDAFCDECFVNNVRNKFR 48 (396)
T ss_pred cccccchhHHHHHHHHHHHHHHH
Confidence 33444558999999999999998
No 83
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.01 E-value=32 Score=26.59 Aligned_cols=29 Identities=28% Similarity=0.769 Sum_probs=19.9
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCc
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNI 46 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~ 46 (95)
.-.|+|.||.+|+..-| .| ....||. |..
T Consensus 290 T~cC~~~fc~eci~~al----~d----sDf~Cpn--C~r 318 (427)
T COG5222 290 TPCCGHTFCDECIGTAL----LD----SDFKCPN--CSR 318 (427)
T ss_pred CccccchHHHHHHhhhh----hh----ccccCCC--ccc
Confidence 34799999999987543 32 1467885 764
No 84
>KOG0825|consensus
Probab=29.97 E-value=31 Score=30.02 Aligned_cols=17 Identities=24% Similarity=0.630 Sum_probs=13.9
Q ss_pred CCCCchhhHHHHHHHHH
Q psy7602 9 LECSHRFCTQCWCEYLT 25 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~ 25 (95)
..|+|.||..|+..|-+
T Consensus 142 k~c~H~FC~~Ci~sWsR 158 (1134)
T KOG0825|consen 142 KHTAHYFCEECVGSWSR 158 (1134)
T ss_pred cccccccHHHHhhhhhh
Confidence 46999999999887654
No 85
>KOG4185|consensus
Probab=29.82 E-value=28 Score=25.47 Aligned_cols=39 Identities=28% Similarity=0.644 Sum_probs=27.8
Q ss_pred cCCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcc--cccchhhhH
Q psy7602 8 GLECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNIL--VDDGKPIEF 56 (95)
Q Consensus 8 ~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~--i~~~~i~~l 56 (95)
.|.|||.+|..|....+.. + .|.|| -|... ++...++.+
T Consensus 24 ~l~c~h~~c~~c~~~l~~~-----~---~i~cp--fcR~~~~~~~~~~~~l 64 (296)
T KOG4185|consen 24 VLKCGHTICQNCASKLLGN-----S---RILCP--FCRETTEIPDGDVKSL 64 (296)
T ss_pred ccccCceehHhHHHHHhcC-----c---eeecc--CCCCcccCCchhHhhh
Confidence 3679999999998876543 2 35664 47766 777777777
No 86
>KOG3039|consensus
Probab=29.61 E-value=34 Score=25.72 Aligned_cols=20 Identities=15% Similarity=0.095 Sum_probs=17.4
Q ss_pred CCCchhhHHHHHHHHHhhhh
Q psy7602 10 ECSHRFCTQCWCEYLTTKII 29 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~ 29 (95)
.=||.||++|+-+||.++=+
T Consensus 60 ~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 60 PDGYLFDREAILEYILAQKK 79 (303)
T ss_pred CCCeeeeHHHHHHHHHHHHH
Confidence 44899999999999998776
No 87
>PF04641 Rtf2: Rtf2 RING-finger
Probab=27.82 E-value=66 Score=23.40 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=26.0
Q ss_pred CCCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCcccccchhhhH
Q psy7602 9 LECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEF 56 (95)
Q Consensus 9 l~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i~~~~i~~l 56 (95)
-+|||+|....+++. + . + -.||. |+..+..++|..|
T Consensus 133 ~~cG~V~s~~alke~---k-~-~-----~~Cp~--c~~~f~~~DiI~L 168 (260)
T PF04641_consen 133 RPCGCVFSEKALKEL---K-K-S-----KKCPV--CGKPFTEEDIIPL 168 (260)
T ss_pred cCCCCEeeHHHHHhh---c-c-c-----ccccc--cCCccccCCEEEe
Confidence 389999999999887 1 2 1 22775 8887777766555
No 88
>KOG4445|consensus
Probab=27.78 E-value=49 Score=25.57 Aligned_cols=25 Identities=28% Similarity=0.513 Sum_probs=20.8
Q ss_pred CCcccCCCCchhhHHHHHHHHHhhh
Q psy7602 4 TLMTGLECSHRFCTQCWCEYLTTKI 28 (95)
Q Consensus 4 ~~~~~l~CgH~FC~~C~~~yl~~~I 28 (95)
..++...|-|+|=..|+..||+...
T Consensus 129 ~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 129 PAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred CceeeehhHHHHHHHHHHHHHHHHH
Confidence 3467789999999999999987644
No 89
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.60 E-value=16 Score=20.39 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=15.7
Q ss_pred hHHHHHHHHHhhhhcCCceeeeecCccccCccc
Q psy7602 16 CTQCWCEYLTTKIIQEGMGQTIACAAHGCNILV 48 (95)
Q Consensus 16 C~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i 48 (95)
|..|++.+ ..+. .+ ..|+||. |+..|
T Consensus 9 C~~Cg~~~--~~~~-~~--~~irCp~--Cg~rI 34 (49)
T COG1996 9 CARCGREV--ELDQ-ET--RGIRCPY--CGSRI 34 (49)
T ss_pred hhhcCCee--ehhh-cc--CceeCCC--CCcEE
Confidence 66777777 3232 22 3699996 77643
No 90
>KOG3002|consensus
Probab=27.60 E-value=37 Score=25.68 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=7.9
Q ss_pred CchhhHHHHH
Q psy7602 12 SHRFCTQCWC 21 (95)
Q Consensus 12 gH~FC~~C~~ 21 (95)
||--|..|-.
T Consensus 68 GHlaCssC~~ 77 (299)
T KOG3002|consen 68 GHLACSSCRT 77 (299)
T ss_pred CcEehhhhhh
Confidence 7888888873
No 91
>KOG3434|consensus
Probab=25.97 E-value=80 Score=21.03 Aligned_cols=54 Identities=9% Similarity=0.018 Sum_probs=29.1
Q ss_pred HHHHHHHHhhhhcCCceeeeecCcc--ccCccccc-chhhhHHHHHHHHHHHHHhhC
Q psy7602 18 QCWCEYLTTKIIQEGMGQTIACAAH--GCNILVDD-GKPIEFDVYQGILSNQVTNCR 71 (95)
Q Consensus 18 ~C~~~yl~~~I~~~g~~~~i~Cp~~--~C~~~i~~-~~i~~l~ky~~~l~~~~v~~~ 71 (95)
+=+.+||.++|+-+|..-++.=... .=+..|+- +......+|.++|.+.|++.|
T Consensus 36 A~fe~fLqerIKv~GK~gnLg~vv~ie~~kskitV~s~~~Fs~rylKyltkkYLkk~ 92 (125)
T KOG3434|consen 36 ADLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYLKYLTKKYLKKN 92 (125)
T ss_pred HHHHHHHHHHhhhcccccccCCeEEEecCCcEEEEEecCCccHHHHHHHHHHHHhhh
Confidence 4478899999886665433310000 00001111 011111899999999999887
No 92
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=24.47 E-value=27 Score=22.85 Aligned_cols=23 Identities=22% Similarity=0.544 Sum_probs=15.1
Q ss_pred ccCCCCchhhH--HHHHHHHHhhhh
Q psy7602 7 TGLECSHRFCT--QCWCEYLTTKII 29 (95)
Q Consensus 7 ~~l~CgH~FC~--~C~~~yl~~~I~ 29 (95)
+.-.|||.||. +=|+.+....++
T Consensus 25 vkc~CGh~f~d~r~NwK~~alv~vR 49 (112)
T PF08882_consen 25 VKCDCGHEFCDARENWKLGALVYVR 49 (112)
T ss_pred eeccCCCeecChhcChhhCcEEEec
Confidence 33469999996 556666555444
No 93
>KOG3268|consensus
Probab=22.79 E-value=1.5e+02 Score=21.32 Aligned_cols=40 Identities=18% Similarity=0.492 Sum_probs=29.9
Q ss_pred ccCCCCchhhHHHHHHHHHhhhhcCCceeee---ecCccccCcccc
Q psy7602 7 TGLECSHRFCTQCWCEYLTTKIIQEGMGQTI---ACAAHGCNILVD 49 (95)
Q Consensus 7 ~~l~CgH~FC~~C~~~yl~~~I~~~g~~~~i---~Cp~~~C~~~i~ 49 (95)
....||..|=.-|+..||+.-.. .-+++.| .||- |...|.
T Consensus 186 dN~qCgkpFHqiCL~dWLRgilT-sRQSFdiiFGeCPY--CS~Pia 228 (234)
T KOG3268|consen 186 DNIQCGKPFHQICLTDWLRGILT-SRQSFDIIFGECPY--CSDPIA 228 (234)
T ss_pred cccccCCcHHHHHHHHHHHHHhh-ccceeeeeeccCCC--CCCcce
Confidence 34679999999999999998886 5676666 5664 655443
No 94
>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=22.36 E-value=11 Score=21.50 Aligned_cols=17 Identities=18% Similarity=0.676 Sum_probs=10.4
Q ss_pred CCCchhhHHHHHHHHHh
Q psy7602 10 ECSHRFCTQCWCEYLTT 26 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~ 26 (95)
.||+.||.+|....+..
T Consensus 30 ~CG~~vC~~Cs~~~~~~ 46 (69)
T PF01363_consen 30 NCGRVVCSSCSSQRIPL 46 (69)
T ss_dssp TT--EEECCCS-EEEEE
T ss_pred CCCCEECCchhCCEEcc
Confidence 49999999998665543
No 95
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.85 E-value=21 Score=22.87 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=16.3
Q ss_pred cccCCCCchhhHHHHHHHHHhhh
Q psy7602 6 MTGLECSHRFCTQCWCEYLTTKI 28 (95)
Q Consensus 6 ~~~l~CgH~FC~~C~~~yl~~~I 28 (95)
....+|+|++|..|=..+-+.=+
T Consensus 53 ~~~~SCk~R~CP~C~~~~~~~W~ 75 (111)
T PF14319_consen 53 IVYNSCKNRHCPSCQAKATEQWI 75 (111)
T ss_pred EecCcccCcCCCCCCChHHHHHH
Confidence 45578999999999765444333
No 96
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=21.71 E-value=38 Score=18.94 Aligned_cols=11 Identities=27% Similarity=0.232 Sum_probs=7.1
Q ss_pred eeCCCCCCccC
Q psy7602 84 RFPPGADFILN 94 (95)
Q Consensus 84 ~~CP~~~C~~~ 94 (95)
--||+|+|.=+
T Consensus 7 l~C~Np~CITn 17 (52)
T PF02748_consen 7 LKCPNPNCITN 17 (52)
T ss_dssp SE-SSTTBTTT
T ss_pred EEcCCCCcccC
Confidence 34999999643
No 97
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=21.41 E-value=30 Score=25.88 Aligned_cols=31 Identities=35% Similarity=0.945 Sum_probs=23.4
Q ss_pred CCCchhhHHHHHHHHHhhhhcCCceeeeecCccccCccc
Q psy7602 10 ECSHRFCTQCWCEYLTTKIIQEGMGQTIACAAHGCNILV 48 (95)
Q Consensus 10 ~CgH~FC~~C~~~yl~~~I~~~g~~~~i~Cp~~~C~~~i 48 (95)
.|-|+.|-.|.- +|...| +-.||-.+|+.++
T Consensus 33 ECyHrmCESCvd-----RIFs~G---pAqCP~~gC~kIL 63 (314)
T COG5220 33 ECYHRMCESCVD-----RIFSRG---PAQCPYKGCGKIL 63 (314)
T ss_pred HHHHHHHHHHHH-----HHhcCC---CCCCCCccHHHHH
Confidence 499999999975 455334 5789999998654
No 98
>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=21.27 E-value=46 Score=15.91 Aligned_cols=6 Identities=33% Similarity=0.932 Sum_probs=3.5
Q ss_pred CCCchh
Q psy7602 10 ECSHRF 15 (95)
Q Consensus 10 ~CgH~F 15 (95)
.|||.|
T Consensus 19 ~CG~~F 24 (26)
T PF10571_consen 19 HCGYDF 24 (26)
T ss_pred CCCCCC
Confidence 366655
No 99
>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=20.10 E-value=19 Score=20.20 Aligned_cols=9 Identities=33% Similarity=1.198 Sum_probs=1.8
Q ss_pred chhhHHHHH
Q psy7602 13 HRFCTQCWC 21 (95)
Q Consensus 13 H~FC~~C~~ 21 (95)
-.+|+.||.
T Consensus 2 r~nCKsCWf 10 (50)
T PF03854_consen 2 RYNCKSCWF 10 (50)
T ss_dssp -----SS-S
T ss_pred CccChhhhh
Confidence 345666664
Done!