Query psy11933
Match_columns 79
No_of_seqs 102 out of 164
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 22:41:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11933hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4118|consensus 100.0 1.7E-31 3.7E-36 168.5 6.6 74 1-77 1-74 (74)
2 PF12907 zf-met2: Zinc-binding 99.6 4.3E-16 9.3E-21 89.2 0.8 35 41-75 1-38 (40)
3 PF04419 4F5: 4F5 protein fami 98.0 7.8E-08 1.7E-12 54.2 -4.9 38 1-41 1-38 (38)
4 PF12874 zf-met: Zinc-finger o 97.2 0.0001 2.2E-09 36.4 0.6 23 42-64 1-23 (25)
5 PF13894 zf-C2H2_4: C2H2-type 97.1 0.00019 4.1E-09 34.0 0.7 24 42-65 1-24 (24)
6 PF00096 zf-C2H2: Zinc finger, 96.9 0.00031 6.6E-09 34.0 0.5 22 42-63 1-22 (23)
7 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0016 3.4E-08 32.6 1.1 25 42-66 2-26 (27)
8 smart00355 ZnF_C2H2 zinc finge 95.5 0.0076 1.6E-07 28.3 1.2 24 42-66 1-24 (26)
9 PF12171 zf-C2H2_jaz: Zinc-fin 95.4 0.0042 9E-08 31.4 0.1 23 42-64 2-24 (27)
10 PF09237 GAGA: GAGA factor; I 95.2 0.01 2.3E-07 36.0 1.3 28 42-69 25-52 (54)
11 smart00451 ZnF_U1 U1-like zinc 95.1 0.0088 1.9E-07 31.1 0.8 24 41-64 3-26 (35)
12 KOG4488|consensus 94.9 0.033 7.2E-07 35.3 3.0 26 1-26 1-26 (70)
13 PF12756 zf-C2H2_2: C2H2 type 94.1 0.025 5.3E-07 34.3 1.1 30 41-70 50-80 (100)
14 PF05605 zf-Di19: Drought indu 93.7 0.05 1.1E-06 31.5 1.8 28 41-69 2-29 (54)
15 PHA00616 hypothetical protein 93.6 0.039 8.4E-07 32.1 1.3 32 42-73 2-33 (44)
16 PF13909 zf-H2C2_5: C2H2-type 92.5 0.033 7.2E-07 27.1 -0.1 24 42-66 1-24 (24)
17 KOG1842|consensus 91.6 0.1 2.2E-06 43.1 1.6 29 41-69 15-43 (505)
18 PHA02768 hypothetical protein; 91.3 0.14 3E-06 31.0 1.6 26 40-66 4-29 (55)
19 PF12756 zf-C2H2_2: C2H2 type 89.4 0.11 2.4E-06 31.4 0.0 26 43-68 1-26 (100)
20 smart00734 ZnF_Rad18 Rad18-lik 89.2 0.23 5.1E-06 25.4 1.2 20 42-62 2-21 (26)
21 PF04780 DUF629: Protein of un 88.4 0.23 5.1E-06 40.7 1.3 32 42-74 58-89 (466)
22 PF13913 zf-C2HC_2: zinc-finge 88.3 0.27 5.9E-06 24.8 1.1 20 42-62 3-22 (25)
23 PF05605 zf-Di19: Drought indu 86.7 0.32 6.9E-06 28.0 0.9 24 40-65 30-53 (54)
24 PHA00732 hypothetical protein 85.9 0.63 1.4E-05 29.4 2.0 24 42-65 2-25 (79)
25 PF02892 zf-BED: BED zinc fing 85.9 0.34 7.4E-06 26.5 0.7 26 41-66 16-45 (45)
26 PHA00733 hypothetical protein 84.6 0.59 1.3E-05 31.7 1.5 21 42-62 74-94 (128)
27 PF04988 AKAP95: A-kinase anch 78.0 0.97 2.1E-05 32.8 0.7 23 42-64 1-23 (165)
28 PF04423 Rad50_zn_hook: Rad50 74.8 0.98 2.1E-05 26.0 0.0 21 43-63 22-44 (54)
29 smart00614 ZnF_BED BED zinc fi 73.5 1.7 3.6E-05 24.7 0.8 27 41-67 18-49 (50)
30 PTZ00448 hypothetical protein; 70.3 2.4 5.3E-05 34.1 1.3 24 41-64 314-337 (373)
31 PF09986 DUF2225: Uncharacteri 69.9 0.72 1.6E-05 33.5 -1.6 16 40-55 4-19 (214)
32 KOG2482|consensus 69.8 2.7 5.9E-05 34.2 1.5 25 41-65 195-220 (423)
33 PHA00733 hypothetical protein 69.1 2.9 6.3E-05 28.3 1.3 24 43-66 101-124 (128)
34 COG2879 Uncharacterized small 66.1 5.6 0.00012 24.9 2.0 22 49-70 20-41 (65)
35 KOG2785|consensus 64.7 4.1 8.8E-05 33.1 1.6 28 37-64 64-91 (390)
36 KOG1074|consensus 62.5 2 4.4E-05 38.1 -0.5 28 41-68 381-408 (958)
37 KOG2462|consensus 62.0 4.2 9.2E-05 31.6 1.2 23 41-63 215-237 (279)
38 PF12013 DUF3505: Protein of u 58.7 5.2 0.00011 25.6 1.0 25 41-65 80-108 (109)
39 PF07800 DUF1644: Protein of u 58.0 8.6 0.00019 27.8 2.1 32 38-69 77-136 (162)
40 PF13465 zf-H2C2_2: Zinc-finge 57.6 2.3 5.1E-05 21.2 -0.6 13 40-52 13-25 (26)
41 KOG0717|consensus 57.5 3.7 7.9E-05 34.3 0.1 25 42-66 293-318 (508)
42 KOG3608|consensus 57.1 7.2 0.00016 32.0 1.8 27 42-68 264-290 (467)
43 PLN02748 tRNA dimethylallyltra 56.0 5.4 0.00012 32.6 0.9 26 40-65 417-444 (468)
44 KOG1146|consensus 53.8 4.7 0.0001 37.3 0.3 29 40-68 464-492 (1406)
45 PF04959 ARS2: Arsenite-resist 52.6 4.1 9E-05 30.2 -0.2 26 41-66 77-102 (214)
46 smart00504 Ubox Modified RING 52.0 16 0.00034 20.5 2.2 12 42-53 2-13 (63)
47 PF05290 Baculo_IE-1: Baculovi 50.7 5.5 0.00012 28.3 0.1 15 40-54 120-134 (140)
48 PF03884 DUF329: Domain of unk 49.8 4.9 0.00011 24.3 -0.2 14 40-53 1-14 (57)
49 PF11931 DUF3449: Domain of un 49.7 5.5 0.00012 29.4 0.0 28 39-66 99-128 (196)
50 KOG3408|consensus 47.8 9.8 0.00021 26.7 1.0 24 42-65 58-82 (129)
51 PF13719 zinc_ribbon_5: zinc-r 47.1 5.3 0.00012 21.6 -0.3 14 40-53 1-14 (37)
52 COG4338 Uncharacterized protei 46.4 8.2 0.00018 23.3 0.4 21 42-62 13-33 (54)
53 TIGR02652 conserved hypothetic 44.9 8.6 0.00019 27.8 0.4 13 41-53 9-21 (163)
54 PF09654 DUF2396: Protein of u 44.9 8.7 0.00019 27.7 0.4 13 41-53 6-18 (161)
55 KOG1074|consensus 44.3 15 0.00033 32.9 1.8 25 42-67 880-904 (958)
56 KOG2462|consensus 44.2 7.3 0.00016 30.4 -0.1 29 39-67 241-269 (279)
57 PF07535 zf-DBF: DBF zinc fing 43.9 6.6 0.00014 23.0 -0.3 19 43-64 7-25 (49)
58 TIGR02098 MJ0042_CXXC MJ0042 f 43.3 6.4 0.00014 20.8 -0.4 15 40-54 1-15 (38)
59 PF10146 zf-C4H2: Zinc finger- 40.5 12 0.00026 27.9 0.6 18 42-69 209-226 (230)
60 COG4049 Uncharacterized protei 40.2 10 0.00022 23.6 0.2 24 42-65 18-41 (65)
61 TIGR01206 lysW lysine biosynth 39.6 8.9 0.00019 22.8 -0.2 13 41-53 2-14 (54)
62 COG5539 Predicted cysteine pro 38.8 11 0.00024 29.7 0.2 28 37-64 271-298 (306)
63 PF12230 PRP21_like_P: Pre-mRN 38.6 10 0.00022 27.3 0.0 23 39-62 166-188 (229)
64 COG1655 Uncharacterized protei 36.5 12 0.00025 29.1 -0.0 14 41-54 19-32 (267)
65 PTZ00417 lysine-tRNA ligase; P 36.4 15 0.00032 30.9 0.6 24 38-61 32-56 (585)
66 KOG3623|consensus 36.4 19 0.00041 32.2 1.2 30 37-67 277-306 (1007)
67 COG5246 PRP11 Splicing factor 36.0 16 0.00035 27.5 0.7 24 41-64 53-76 (222)
68 PRK11088 rrmA 23S rRNA methylt 35.5 12 0.00027 27.1 0.0 13 41-53 2-14 (272)
69 KOG3576|consensus 35.1 20 0.00044 27.6 1.1 32 39-70 210-241 (267)
70 PF03194 LUC7: LUC7 N_terminus 33.2 21 0.00045 26.8 0.9 23 42-64 191-216 (254)
71 PF06348 DUF1059: Protein of u 33.2 35 0.00076 20.0 1.7 24 54-77 26-49 (57)
72 KOG2893|consensus 33.2 20 0.00043 28.2 0.8 29 39-67 8-36 (341)
73 KOG1280|consensus 33.0 29 0.00062 28.2 1.7 30 40-69 78-107 (381)
74 PF05741 zf-nanos: Nanos RNA b 32.3 17 0.00037 21.8 0.3 11 41-51 33-43 (55)
75 PF13717 zinc_ribbon_4: zinc-r 31.8 13 0.00028 20.1 -0.3 14 40-53 1-14 (36)
76 KOG2505|consensus 30.8 27 0.00059 29.8 1.3 23 42-64 67-89 (591)
77 PF15227 zf-C3HC4_4: zinc fing 30.8 14 0.00031 20.3 -0.3 14 44-57 1-14 (42)
78 KOG2636|consensus 30.6 25 0.00055 29.4 1.0 23 40-62 400-423 (497)
79 PF04564 U-box: U-box domain; 28.5 47 0.001 19.9 1.8 29 42-70 5-44 (73)
80 smart00586 ZnF_DBF Zinc finger 28.5 18 0.0004 21.2 -0.1 19 43-64 7-25 (49)
81 COG5188 PRP9 Splicing factor 3 27.2 28 0.0006 28.7 0.7 34 35-68 232-266 (470)
82 KOG0227|consensus 27.2 32 0.00069 26.0 1.0 25 41-65 53-78 (222)
83 KOG1493|consensus 26.4 24 0.00051 23.1 0.1 11 42-52 71-81 (84)
84 PF04328 DUF466: Protein of un 26.1 42 0.00092 20.4 1.2 23 51-73 22-44 (65)
85 PRK00420 hypothetical protein; 26.0 44 0.00095 22.6 1.4 21 33-53 15-35 (112)
86 PF09538 FYDLN_acid: Protein o 25.6 25 0.00054 23.4 0.2 13 42-54 27-39 (108)
87 PF13445 zf-RING_UBOX: RING-ty 25.3 19 0.00041 20.2 -0.4 9 44-53 1-9 (43)
88 KOG4696|consensus 25.0 39 0.00086 27.3 1.2 21 41-62 2-22 (393)
89 KOG0717|consensus 25.0 40 0.00086 28.4 1.2 26 40-65 459-485 (508)
90 PF14357 DUF4404: Domain of un 24.9 41 0.0009 21.3 1.1 16 54-69 55-70 (85)
91 PLN00104 MYST -like histone ac 24.6 52 0.0011 27.2 1.8 23 40-62 197-219 (450)
92 PF13462 Thioredoxin_4: Thiore 24.6 21 0.00045 22.9 -0.4 22 40-61 20-41 (162)
93 PF10886 DUF2685: Protein of u 24.0 26 0.00057 21.2 0.0 22 43-64 3-36 (54)
94 PF14634 zf-RING_5: zinc-RING 23.5 27 0.00058 18.9 -0.0 10 40-49 35-44 (44)
95 PF02891 zf-MIZ: MIZ/SP-RING z 23.3 49 0.0011 18.8 1.1 18 32-49 32-49 (50)
96 PRK01343 zinc-binding protein; 23.3 29 0.00063 21.1 0.1 14 40-53 8-21 (57)
97 KOG3623|consensus 23.0 48 0.001 29.8 1.4 30 40-69 239-268 (1007)
98 PF14353 CpXC: CpXC protein 23.0 13 0.00028 24.4 -1.6 26 40-65 37-62 (128)
99 TIGR00373 conserved hypothetic 22.9 26 0.00057 24.3 -0.1 14 40-53 127-140 (158)
100 PF13920 zf-C3HC4_3: Zinc fing 22.9 38 0.00082 18.6 0.5 12 40-51 36-47 (50)
101 PF05443 ROS_MUCR: ROS/MUCR tr 22.5 37 0.0008 23.5 0.5 22 41-65 72-93 (132)
102 KOG4172|consensus 22.4 20 0.00044 22.1 -0.7 19 39-57 41-60 (62)
103 PF10013 DUF2256: Uncharacteri 22.3 37 0.00079 19.6 0.4 18 42-59 9-26 (42)
104 cd02970 PRX_like2 Peroxiredoxi 22.2 33 0.00072 21.6 0.2 20 43-62 35-54 (149)
105 cd03000 PDI_a_TMX3 PDIa family 21.9 53 0.0011 20.0 1.1 19 44-62 27-45 (104)
106 TIGR02738 TrbB type-F conjugat 21.7 28 0.0006 24.0 -0.2 18 44-61 62-79 (153)
107 PHA02610 uvsY.-2 hypothetical 21.2 28 0.00061 21.0 -0.2 11 43-53 3-13 (53)
108 PLN03239 histone acetyltransfe 20.8 64 0.0014 25.9 1.6 22 41-62 106-127 (351)
109 PF15176 LRR19-TM: Leucine-ric 20.4 25 0.00055 23.7 -0.6 22 39-60 35-58 (102)
110 PHA02929 N1R/p28-like protein; 20.2 33 0.00072 25.8 -0.1 13 41-53 216-228 (238)
111 COG5432 RAD18 RING-finger-cont 20.1 64 0.0014 26.1 1.5 22 42-64 161-182 (391)
112 cd00162 RING RING-finger (Real 20.1 38 0.00082 16.8 0.1 11 40-50 34-44 (45)
113 KOG3288|consensus 20.0 49 0.0011 26.1 0.8 28 37-64 272-299 (307)
No 1
>KOG4118|consensus
Probab=99.97 E-value=1.7e-31 Score=168.46 Aligned_cols=74 Identities=73% Similarity=1.079 Sum_probs=72.3
Q ss_pred CcchHHHHHHHHHHHHHHHHHHhhcCCChhhHHHHHHhhhhccchhhhhcCCChhhHhHHHHcCCCCCCCCchhhhh
Q psy11933 1 MARGQQKLQSQAKAQEKQAKAKKQQGHSLLDQKKAAQKALVHACVVCKAQMPDPKTYKQHFENKHPKNDLPEDLKDV 77 (79)
Q Consensus 1 M~rG~qK~q~q~r~~~k~~~~~~~~~~s~~sq~ka~~aA~~~~C~vC~~~f~~~k~l~~H~esKHpK~~~p~e~~~~ 77 (79)
|+||+||+|+|+||++++++++++.|+ ||++++.+||.++|.||+.+||++++|++||||||||++||+||.+|
T Consensus 1 MARGhQKiqSQqknaeKqAkakk~~G~---DQK~AA~~aL~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P~eL~~v 74 (74)
T KOG4118|consen 1 MARGHQKIQSQQKNAEKQAKAKKKQGH---DQKAAAMAALHHKCTVCMVQMPDPKTFKQHFENKHPKEPLPEELSEV 74 (74)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHcCc---cHHHHHHHHHHhhhHhhHhhCCCCchHHHHHhhcCCCCCCCHhhccC
Confidence 999999999999999999999999998 99999999999999999999999999999999999999999999876
No 2
>PF12907 zf-met2: Zinc-binding
Probab=99.57 E-value=4.3e-16 Score=89.15 Aligned_cols=35 Identities=34% Similarity=0.608 Sum_probs=31.5
Q ss_pred hccchhhhhcCCC---hhhHhHHHHcCCCCCCCCchhh
Q psy11933 41 VHACVVCKAQMPD---PKTYKQHFENKHPKNDLPEDLK 75 (79)
Q Consensus 41 ~~~C~vC~~~f~~---~k~l~~H~esKHpK~~~p~e~~ 75 (79)
+|+|+|||++||. +++|++|+||||||.+|++++=
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CFP 38 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECFP 38 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcCC
Confidence 5899999999998 8999999999999998887653
No 3
>PF04419 4F5: 4F5 protein family; InterPro: IPR007513 Members of this family are short proteins that are rich in aspartate, glutamate, lysine and arginine. Although the function of these proteins is unknown, they are found to be ubiquitously expressed [].; PDB: 1WVK_A.
Probab=98.00 E-value=7.8e-08 Score=54.17 Aligned_cols=38 Identities=53% Similarity=0.632 Sum_probs=18.0
Q ss_pred CcchHHHHHHHHHHHHHHHHHHhhcCCChhhHHHHHHhhhh
Q psy11933 1 MARGQQKLQSQAKAQEKQAKAKKQQGHSLLDQKKAAQKALV 41 (79)
Q Consensus 1 M~rG~qK~q~q~r~~~k~~~~~~~~~~s~~sq~ka~~aA~~ 41 (79)
|+||||+.++|+||.+++++.+++.++ ||++.++.+|+
T Consensus 1 MtRGnQr~~aRekn~Kk~~~~~~k~~~---s~l~~~~~~l~ 38 (38)
T PF04419_consen 1 MTRGNQREQAREKNQKKQAKQKKKGGK---SGLKAAQRALN 38 (38)
T ss_dssp ---SGGGTTTSTTT---SS---SS-SS----SS----TT--
T ss_pred CccHhHHHHHHHHHHHHhhccccCCCc---cchhHHHHhcC
Confidence 999999999999999999776555555 89999888764
No 4
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.24 E-value=0.0001 Score=36.40 Aligned_cols=23 Identities=22% Similarity=0.634 Sum_probs=21.4
Q ss_pred ccchhhhhcCCChhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK 64 (79)
+.|.||..+|.++.+|.+|+.++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999999876
No 5
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.09 E-value=0.00019 Score=34.01 Aligned_cols=24 Identities=21% Similarity=0.609 Sum_probs=20.1
Q ss_pred ccchhhhhcCCChhhHhHHHHcCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
++|++|..+|.+...|..|....|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 589999999999999999998765
No 6
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.90 E-value=0.00031 Score=34.00 Aligned_cols=22 Identities=18% Similarity=0.545 Sum_probs=20.5
Q ss_pred ccchhhhhcCCChhhHhHHHHc
Q psy11933 42 HACVVCKAQMPDPKTYKQHFEN 63 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~es 63 (79)
|+|++|...|.+...|..|...
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6899999999999999999876
No 7
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.42 E-value=0.0016 Score=32.57 Aligned_cols=25 Identities=12% Similarity=0.343 Sum_probs=22.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
+.|.+|..+|.+...|..|-...|+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhcC
Confidence 6899999999999999999976665
No 8
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.51 E-value=0.0076 Score=28.33 Aligned_cols=24 Identities=21% Similarity=0.490 Sum_probs=21.2
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
+.|++|..+|.....|..|.. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 579999999999999999998 554
No 9
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.43 E-value=0.0042 Score=31.45 Aligned_cols=23 Identities=26% Similarity=0.550 Sum_probs=21.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK 64 (79)
+.|.+|.-.|.+...|.+|..+|
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 68999999999999999999875
No 10
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.20 E-value=0.01 Score=35.96 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=21.9
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
.+|++|...+.....|+.|.|..|-+.|
T Consensus 25 atCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCcchhhccchhhHHHHHHHHhcccC
Confidence 5899999999999999999999996653
No 11
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.14 E-value=0.0088 Score=31.14 Aligned_cols=24 Identities=21% Similarity=0.506 Sum_probs=22.2
Q ss_pred hccchhhhhcCCChhhHhHHHHcC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
.+.|.+|...|.+...+..|..++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 478999999999999999999987
No 12
>KOG4488|consensus
Probab=94.89 E-value=0.033 Score=35.30 Aligned_cols=26 Identities=31% Similarity=0.385 Sum_probs=20.9
Q ss_pred CcchHHHHHHHHHHHHHHHHHHhhcC
Q psy11933 1 MARGQQKLQSQAKAQEKQAKAKKQQG 26 (79)
Q Consensus 1 M~rG~qK~q~q~r~~~k~~~~~~~~~ 26 (79)
|+||||.--++++|.++.+...++..
T Consensus 1 MtRGNQRdLaRqKN~KK~~d~~K~kr 26 (70)
T KOG4488|consen 1 MTRGNQRDLARQKNMKKQQDIAKGKR 26 (70)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhccc
Confidence 99999988779999999885554433
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.14 E-value=0.025 Score=34.27 Aligned_cols=30 Identities=20% Similarity=0.503 Sum_probs=24.0
Q ss_pred hccchhhhhcCCChhhHhHHHHcC-CCCCCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK-HPKNDL 70 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK-HpK~~~ 70 (79)
.+.|.+|...|.+...|.+|..++ |.+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 589999999999999999999988 655433
No 14
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=93.69 E-value=0.05 Score=31.47 Aligned_cols=28 Identities=18% Similarity=0.373 Sum_probs=23.9
Q ss_pred hccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
.|.||.|.. -.+...|..|.+..|+...
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC
Confidence 488999999 6778899999999998653
No 15
>PHA00616 hypothetical protein
Probab=93.64 E-value=0.039 Score=32.05 Aligned_cols=32 Identities=22% Similarity=0.415 Sum_probs=28.0
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCCCCCCch
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPKNDLPED 73 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK~~~p~e 73 (79)
++|+-|...|...+.|..|..+.|--.+|--|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 68999999999999999999988877776544
No 16
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=92.52 E-value=0.033 Score=27.12 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=19.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
|.|+.|--... +..|..|....||
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 57999998887 9999999998886
No 17
>KOG1842|consensus
Probab=91.60 E-value=0.1 Score=43.14 Aligned_cols=29 Identities=21% Similarity=0.560 Sum_probs=26.6
Q ss_pred hccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
.|.||||+.-|++...|..|++.-|+-+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 48999999999999999999999998654
No 18
>PHA02768 hypothetical protein; Provisional
Probab=91.34 E-value=0.14 Score=30.97 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=23.6
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
+.|.|++|...|.....|..|... |.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~-H~ 29 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRK-HN 29 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHh-cC
Confidence 568999999999999999999997 55
No 19
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.38 E-value=0.11 Score=31.37 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=0.0
Q ss_pred cchhhhhcCCChhhHhHHHHcCCCCC
Q psy11933 43 ACVVCKAQMPDPKTYKQHFENKHPKN 68 (79)
Q Consensus 43 ~C~vC~~~f~~~k~l~~H~esKHpK~ 68 (79)
.|.+|...|.+...|.+|....|.-.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~ 26 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD 26 (100)
T ss_dssp --------------------------
T ss_pred Cccccccccccccccccccccccccc
Confidence 59999999999999999999999643
No 20
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=89.20 E-value=0.23 Score=25.44 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=16.6
Q ss_pred ccchhhhhcCCChhhHhHHHH
Q psy11933 42 HACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~e 62 (79)
+.||||.+.+ ....+..|.+
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999998 6677888877
No 21
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=88.37 E-value=0.23 Score=40.70 Aligned_cols=32 Identities=28% Similarity=0.628 Sum_probs=27.3
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCCCCCCchh
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPKNDLPEDL 74 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK~~~p~e~ 74 (79)
-+|++|-..|++...+..|.+++|+-. ++|.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~-l~P~l 89 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG-LKPKL 89 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh-cChhh
Confidence 469999999999999999999999865 44444
No 22
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.30 E-value=0.27 Score=24.84 Aligned_cols=20 Identities=20% Similarity=0.669 Sum_probs=16.7
Q ss_pred ccchhhhhcCCChhhHhHHHH
Q psy11933 42 HACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~e 62 (79)
+.|++|..+| .+..|..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 5799999999 7778888864
No 23
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=86.69 E-value=0.32 Score=28.03 Aligned_cols=24 Identities=21% Similarity=0.617 Sum_probs=19.8
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
.+++||||-..+.+ .|..|+...|
T Consensus 30 ~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 30 KNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CCccCCCchhhhhh--HHHHHHHHhc
Confidence 46999999987664 8899998877
No 24
>PHA00732 hypothetical protein
Probab=85.89 E-value=0.63 Score=29.39 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=14.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
+.|.+|...|.....|..|....|
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H 25 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNH 25 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhccc
Confidence 456666666666666666665434
No 25
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=85.88 E-value=0.34 Score=26.47 Aligned_cols=26 Identities=27% Similarity=0.585 Sum_probs=19.9
Q ss_pred hccchhhhhcCCC----hhhHhHHHHcCCC
Q psy11933 41 VHACVVCKAQMPD----PKTYKQHFENKHP 66 (79)
Q Consensus 41 ~~~C~vC~~~f~~----~k~l~~H~esKHp 66 (79)
...|..|...+.. -..|..|...+||
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHHTTH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhhhCc
Confidence 4689999999887 5899999999997
No 26
>PHA00733 hypothetical protein
Probab=84.65 E-value=0.59 Score=31.67 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=12.3
Q ss_pred ccchhhhhcCCChhhHhHHHH
Q psy11933 42 HACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~e 62 (79)
+.|+.|...|.....|..|..
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHh
Confidence 556666666666555555554
No 27
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=78.01 E-value=0.97 Score=32.76 Aligned_cols=23 Identities=30% Similarity=0.632 Sum_probs=21.2
Q ss_pred ccchhhhhcCCChhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK 64 (79)
|.|++|+-..-....+..|++|+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~ 23 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESK 23 (165)
T ss_pred CccceeeeecccHHHHHHHHccc
Confidence 68999999888899999999998
No 28
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=74.81 E-value=0.98 Score=26.01 Aligned_cols=21 Identities=10% Similarity=0.542 Sum_probs=11.7
Q ss_pred cchhhhhcCCC--hhhHhHHHHc
Q psy11933 43 ACVVCKAQMPD--PKTYKQHFEN 63 (79)
Q Consensus 43 ~C~vC~~~f~~--~k~l~~H~es 63 (79)
.||||...|.. ...|..++.+
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~ 44 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKS 44 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHH
Confidence 89999999988 4455555543
No 29
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=73.45 E-value=1.7 Score=24.67 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=23.2
Q ss_pred hccchhhhhcCCCh-----hhHhHHHHcCCCC
Q psy11933 41 VHACVVCKAQMPDP-----KTYKQHFENKHPK 67 (79)
Q Consensus 41 ~~~C~vC~~~f~~~-----k~l~~H~esKHpK 67 (79)
..+|..|...+... ..|..|..++||.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 46899999998664 6999999999985
No 30
>PTZ00448 hypothetical protein; Provisional
Probab=70.33 E-value=2.4 Score=34.11 Aligned_cols=24 Identities=29% Similarity=0.701 Sum_probs=22.0
Q ss_pred hccchhhhhcCCChhhHhHHHHcC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
.+.|..|..+|.+....++||.|-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 477999999999999999999986
No 31
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=69.85 E-value=0.72 Score=33.53 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.2
Q ss_pred hhccchhhhhcCCChh
Q psy11933 40 LVHACVVCKAQMPDPK 55 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k 55 (79)
.+++||||.+.|....
T Consensus 4 k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK 19 (214)
T ss_pred CceECCCCCCeeeeeE
Confidence 3589999999999843
No 32
>KOG2482|consensus
Probab=69.84 E-value=2.7 Score=34.17 Aligned_cols=25 Identities=32% Similarity=0.655 Sum_probs=23.3
Q ss_pred hccchhhhhcCCChhhHhHHHHcC-C
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK-H 65 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK-H 65 (79)
.+.|=-|-..|++.++|++|...| |
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~H 220 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRH 220 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccC
Confidence 478999999999999999999998 6
No 33
>PHA00733 hypothetical protein
Probab=69.06 E-value=2.9 Score=28.27 Aligned_cols=24 Identities=25% Similarity=0.542 Sum_probs=21.5
Q ss_pred cchhhhhcCCChhhHhHHHHcCCC
Q psy11933 43 ACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 43 ~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
.|++|...|.....|..|..-+|.
T Consensus 101 ~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 101 VCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCCccCCHHHHHHHHHHhcC
Confidence 799999999999999999988885
No 34
>COG2879 Uncharacterized small protein [Function unknown]
Probab=66.14 E-value=5.6 Score=24.95 Aligned_cols=22 Identities=32% Similarity=0.646 Sum_probs=19.5
Q ss_pred hcCCChhhHhHHHHcCCCCCCC
Q psy11933 49 AQMPDPKTYKQHFENKHPKNDL 70 (79)
Q Consensus 49 ~~f~~~k~l~~H~esKHpK~~~ 70 (79)
...||...|.+|...+||..|.
T Consensus 20 vGvpdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 20 VGVPDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred cCCCcHHHHHHHHHHhCcCCCc
Confidence 4678999999999999998875
No 35
>KOG2785|consensus
Probab=64.73 E-value=4.1 Score=33.06 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=24.7
Q ss_pred HhhhhccchhhhhcCCChhhHhHHHHcC
Q psy11933 37 QKALVHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 37 ~aA~~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
++-+-+.|.||+..|..+....+|.-||
T Consensus 64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk 91 (390)
T KOG2785|consen 64 EAESVVYCEACNKSFASPKAHENHLKSK 91 (390)
T ss_pred hcccceehHHhhccccChhhHHHHHHHh
Confidence 4456688999999999999999999887
No 36
>KOG1074|consensus
Probab=62.48 E-value=2 Score=38.08 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=20.0
Q ss_pred hccchhhhhcCCChhhHhHHHHcCCCCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENKHPKN 68 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esKHpK~ 68 (79)
-|+|.||...|..+-.|+-||.-.|-|.
T Consensus 381 PfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 381 PFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred CeeecccccccccccceeeeeeeccccC
Confidence 3778888888888777777777555443
No 37
>KOG2462|consensus
Probab=62.00 E-value=4.2 Score=31.64 Aligned_cols=23 Identities=17% Similarity=0.512 Sum_probs=19.5
Q ss_pred hccchhhhhcCCChhhHhHHHHc
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFEN 63 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~es 63 (79)
-|.|++|...|-|+..|+-|..-
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred CccCCcccchhcchHHHHHHHHh
Confidence 38899999999998888888763
No 38
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=58.74 E-value=5.2 Score=25.65 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=22.8
Q ss_pred hccc----hhhhhcCCChhhHhHHHHcCC
Q psy11933 41 VHAC----VVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 41 ~~~C----~vC~~~f~~~k~l~~H~esKH 65 (79)
-+.| ..|.-.+.+..++..||..+|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3789 999998889999999999988
No 39
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=57.98 E-value=8.6 Score=27.84 Aligned_cols=32 Identities=19% Similarity=0.498 Sum_probs=25.6
Q ss_pred hhhhccchhhhhc---------------------------CCC-hhhHhHHHHcCCCCCC
Q psy11933 38 KALVHACVVCKAQ---------------------------MPD-PKTYKQHFENKHPKND 69 (79)
Q Consensus 38 aA~~~~C~vC~~~---------------------------f~~-~k~l~~H~esKHpK~~ 69 (79)
......|+.||-. |.. +..|.-|...+||-..
T Consensus 77 ~~~~L~CPLCRG~V~GWtvve~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~r 136 (162)
T PF07800_consen 77 EQPELACPLCRGEVKGWTVVEPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSAR 136 (162)
T ss_pred ccccccCccccCceeceEEchHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCC
Confidence 3456889999876 444 8999999999999653
No 40
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=57.63 E-value=2.3 Score=21.18 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=10.6
Q ss_pred hhccchhhhhcCC
Q psy11933 40 LVHACVVCKAQMP 52 (79)
Q Consensus 40 ~~~~C~vC~~~f~ 52 (79)
..|.|++|...|.
T Consensus 13 k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 13 KPYKCPYCGKSFS 25 (26)
T ss_dssp SSEEESSSSEEES
T ss_pred CCCCCCCCcCeeC
Confidence 3489999998885
No 41
>KOG0717|consensus
Probab=57.45 E-value=3.7 Score=34.32 Aligned_cols=25 Identities=36% Similarity=0.626 Sum_probs=23.1
Q ss_pred ccchhhhhcCCChhhHhHHHHcC-CC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK-HP 66 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK-Hp 66 (79)
+-|.||--+|-+.++|+-|-.|| |-
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHk 318 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHK 318 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHH
Confidence 78999999999999999999998 63
No 42
>KOG3608|consensus
Probab=57.09 E-value=7.2 Score=32.04 Aligned_cols=27 Identities=19% Similarity=0.528 Sum_probs=25.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPKN 68 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK~ 68 (79)
|+|+.|-.+.+++..|.-|..-+|++.
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~d 290 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKD 290 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccC
Confidence 899999999999999999999999984
No 43
>PLN02748 tRNA dimethylallyltransferase
Probab=55.96 E-value=5.4 Score=32.60 Aligned_cols=26 Identities=19% Similarity=0.484 Sum_probs=23.1
Q ss_pred hhccchhhhh-cCCChhhHhHHHHcC-C
Q psy11933 40 LVHACVVCKA-QMPDPKTYKQHFENK-H 65 (79)
Q Consensus 40 ~~~~C~vC~~-~f~~~k~l~~H~esK-H 65 (79)
..++|.||.- +|....+-.+|..++ |
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~H 444 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGH 444 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHH
Confidence 4578999997 899999999999987 6
No 44
>KOG1146|consensus
Probab=53.78 E-value=4.7 Score=37.27 Aligned_cols=29 Identities=24% Similarity=0.440 Sum_probs=26.5
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCCCCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKHPKN 68 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKHpK~ 68 (79)
..++|++|...|....+|..|.++|||-.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~ 492 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPES 492 (1406)
T ss_pred ccccCCccchhhhhHHHhhhccccccccc
Confidence 56899999999999999999999999853
No 45
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=52.64 E-value=4.1 Score=30.22 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=21.2
Q ss_pred hccchhhhhcCCChhhHhHHHHcCCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENKHP 66 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esKHp 66 (79)
++-|++|..-|-.+.=..-|..+||+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 57899999999999999999999998
No 46
>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=52.05 E-value=16 Score=20.53 Aligned_cols=12 Identities=25% Similarity=0.456 Sum_probs=6.1
Q ss_pred ccchhhhhcCCC
Q psy11933 42 HACVVCKAQMPD 53 (79)
Q Consensus 42 ~~C~vC~~~f~~ 53 (79)
+.|+||+..|-+
T Consensus 2 ~~Cpi~~~~~~~ 13 (63)
T smart00504 2 FLCPISLEVMKD 13 (63)
T ss_pred cCCcCCCCcCCC
Confidence 345555555443
No 47
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=50.72 E-value=5.5 Score=28.27 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=12.1
Q ss_pred hhccchhhhhcCCCh
Q psy11933 40 LVHACVVCKAQMPDP 54 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~ 54 (79)
+--+||||+++|-+.
T Consensus 120 ~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 120 LYPVCPVCKTSFKSS 134 (140)
T ss_pred cCCCCCccccccccc
Confidence 445899999999874
No 48
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=49.79 E-value=4.9 Score=24.31 Aligned_cols=14 Identities=14% Similarity=0.451 Sum_probs=7.3
Q ss_pred hhccchhhhhcCCC
Q psy11933 40 LVHACVVCKAQMPD 53 (79)
Q Consensus 40 ~~~~C~vC~~~f~~ 53 (79)
+++.|++|+..+.-
T Consensus 1 m~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 1 MTVKCPICGKPVEW 14 (57)
T ss_dssp -EEE-TTT--EEE-
T ss_pred CcccCCCCCCeecc
Confidence 46889999987654
No 49
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=49.65 E-value=5.5 Score=29.38 Aligned_cols=28 Identities=21% Similarity=0.608 Sum_probs=0.0
Q ss_pred hhhccchhhh-hcCCChhhHhHHHH-cCCC
Q psy11933 39 ALVHACVVCK-AQMPDPKTYKQHFE-NKHP 66 (79)
Q Consensus 39 A~~~~C~vC~-~~f~~~k~l~~H~e-sKHp 66 (79)
...|.|.||. +++..++.+..||. .+|.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~ 128 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHA 128 (196)
T ss_dssp ------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHH
Confidence 3458999998 45667999999995 3463
No 50
>KOG3408|consensus
Probab=47.80 E-value=9.8 Score=26.65 Aligned_cols=24 Identities=38% Similarity=0.751 Sum_probs=22.7
Q ss_pred ccchhhhhcCCChhhHhHHHHcC-C
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK-H 65 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK-H 65 (79)
|-|-.|---|.+.+.|..||.+| |
T Consensus 58 fyCi~CaRyFi~~~~l~~H~ktK~H 82 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKTKVH 82 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhccHH
Confidence 78999999999999999999998 5
No 51
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.08 E-value=5.3 Score=21.59 Aligned_cols=14 Identities=14% Similarity=0.589 Sum_probs=11.0
Q ss_pred hhccchhhhhcCCC
Q psy11933 40 LVHACVVCKAQMPD 53 (79)
Q Consensus 40 ~~~~C~vC~~~f~~ 53 (79)
+.|.|+-|.+.|-.
T Consensus 1 M~i~CP~C~~~f~v 14 (37)
T PF13719_consen 1 MIITCPNCQTRFRV 14 (37)
T ss_pred CEEECCCCCceEEc
Confidence 45788888888876
No 52
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.42 E-value=8.2 Score=23.28 Aligned_cols=21 Identities=19% Similarity=0.548 Sum_probs=16.0
Q ss_pred ccchhhhhcCCChhhHhHHHH
Q psy11933 42 HACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~e 62 (79)
-||+||.-.|.-.+...+-|+
T Consensus 13 KICpvCqRPFsWRkKW~~cWD 33 (54)
T COG4338 13 KICPVCQRPFSWRKKWARCWD 33 (54)
T ss_pred hhhhhhcCchHHHHHHHHHHH
Confidence 489999999987666655554
No 53
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=44.91 E-value=8.6 Score=27.76 Aligned_cols=13 Identities=23% Similarity=0.705 Sum_probs=11.3
Q ss_pred hccchhhhhcCCC
Q psy11933 41 VHACVVCKAQMPD 53 (79)
Q Consensus 41 ~~~C~vC~~~f~~ 53 (79)
.|.|+.|||+.|-
T Consensus 9 ei~CPhCRQ~ipA 21 (163)
T TIGR02652 9 EIRCPHCRQNIPA 21 (163)
T ss_pred cCcCchhhcccch
Confidence 4789999999876
No 54
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=44.86 E-value=8.7 Score=27.70 Aligned_cols=13 Identities=23% Similarity=0.698 Sum_probs=11.2
Q ss_pred hccchhhhhcCCC
Q psy11933 41 VHACVVCKAQMPD 53 (79)
Q Consensus 41 ~~~C~vC~~~f~~ 53 (79)
-|.|+.|||+.|-
T Consensus 6 ei~CPhCRq~ipA 18 (161)
T PF09654_consen 6 EIQCPHCRQTIPA 18 (161)
T ss_pred cCcCchhhcccch
Confidence 4789999999876
No 55
>KOG1074|consensus
Probab=44.29 E-value=15 Score=32.89 Aligned_cols=25 Identities=28% Similarity=0.627 Sum_probs=20.1
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPK 67 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK 67 (79)
..|.||+.+|.....|+.|.. -|++
T Consensus 880 h~C~vCgk~FsSSsALqiH~r-THtg 904 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMR-THTG 904 (958)
T ss_pred hhhccchhcccchHHHHHhhh-cCCC
Confidence 679999999999888888877 4544
No 56
>KOG2462|consensus
Probab=44.23 E-value=7.3 Score=30.35 Aligned_cols=29 Identities=21% Similarity=0.285 Sum_probs=24.8
Q ss_pred hhhccchhhhhcCCChhhHhHHHHcCCCC
Q psy11933 39 ALVHACVVCKAQMPDPKTYKQHFENKHPK 67 (79)
Q Consensus 39 A~~~~C~vC~~~f~~~k~l~~H~esKHpK 67 (79)
-.+|.|+.|..+|-...-|.-|.|+.=.+
T Consensus 241 ~K~~qC~~C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred CccccCcchhhHHHHHHHHHHhhhhcccc
Confidence 34799999999999999999999986444
No 57
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=43.86 E-value=6.6 Score=23.00 Aligned_cols=19 Identities=21% Similarity=0.676 Sum_probs=15.4
Q ss_pred cchhhhhcCCChhhHhHHHHcC
Q psy11933 43 ACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 43 ~C~vC~~~f~~~k~l~~H~esK 64 (79)
-|.+|+..|-+ |.+|..|.
T Consensus 7 YCE~C~~ky~~---l~~Hi~s~ 25 (49)
T PF07535_consen 7 YCENCRVKYDD---LEEHIQSE 25 (49)
T ss_pred cCccccchhhh---HHHHhCCH
Confidence 59999999975 77787775
No 58
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=43.26 E-value=6.4 Score=20.77 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=11.2
Q ss_pred hhccchhhhhcCCCh
Q psy11933 40 LVHACVVCKAQMPDP 54 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~ 54 (79)
+.+.|+-|.+.|...
T Consensus 1 M~~~CP~C~~~~~v~ 15 (38)
T TIGR02098 1 MRIQCPNCKTSFRVV 15 (38)
T ss_pred CEEECCCCCCEEEeC
Confidence 457888888887763
No 59
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=40.47 E-value=12 Score=27.94 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=11.7
Q ss_pred ccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
-||++|++ =.+|||||.+
T Consensus 209 PiCPlCK~----------KsRSrnpKk~ 226 (230)
T PF10146_consen 209 PICPLCKA----------KSRSRNPKKP 226 (230)
T ss_pred CCCccccc----------ccccCCCCCc
Confidence 36666655 3467888865
No 60
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=40.22 E-value=10 Score=23.56 Aligned_cols=24 Identities=25% Similarity=0.511 Sum_probs=21.3
Q ss_pred ccchhhhhcCCChhhHhHHHHcCC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
+.|+-|..-|-+.+.|..|.---|
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHh
Confidence 679999999999999999986555
No 61
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=39.56 E-value=8.9 Score=22.84 Aligned_cols=13 Identities=23% Similarity=0.455 Sum_probs=8.8
Q ss_pred hccchhhhhcCCC
Q psy11933 41 VHACVVCKAQMPD 53 (79)
Q Consensus 41 ~~~C~vC~~~f~~ 53 (79)
.+.|++|.+.+--
T Consensus 2 ~~~CP~CG~~iev 14 (54)
T TIGR01206 2 QFECPDCGAEIEL 14 (54)
T ss_pred ccCCCCCCCEEec
Confidence 4678888876643
No 62
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=38.79 E-value=11 Score=29.70 Aligned_cols=28 Identities=18% Similarity=0.311 Sum_probs=23.8
Q ss_pred HhhhhccchhhhhcCCChhhHhHHHHcC
Q psy11933 37 QKALVHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 37 ~aA~~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
-+...++|.+|...|-....+..|..+-
T Consensus 271 T~~~~ik~n~c~~~~~~e~~~~~Ha~a~ 298 (306)
T COG5539 271 TASPSIKCNICGTGFVGEKDYYAHALAT 298 (306)
T ss_pred cCCceEEeeccccccchhhHHHHHHHhh
Confidence 3456789999999999999999998764
No 63
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=38.60 E-value=10 Score=27.33 Aligned_cols=23 Identities=13% Similarity=0.374 Sum_probs=0.0
Q ss_pred hhhccchhhhhcCCChhhHhHHHH
Q psy11933 39 ALVHACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 39 A~~~~C~vC~~~f~~~k~l~~H~e 62 (79)
..-++|+||++..|.. .|.+|.+
T Consensus 166 ~~~~~cPitGe~IP~~-e~~eHmR 188 (229)
T PF12230_consen 166 EKMIICPITGEMIPAD-EMDEHMR 188 (229)
T ss_dssp ------------------------
T ss_pred cccccccccccccccc-ccccccc
Confidence 3448899999999873 3555544
No 64
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.50 E-value=12 Score=29.06 Aligned_cols=14 Identities=21% Similarity=0.627 Sum_probs=11.7
Q ss_pred hccchhhhhcCCCh
Q psy11933 41 VHACVVCKAQMPDP 54 (79)
Q Consensus 41 ~~~C~vC~~~f~~~ 54 (79)
.|.||||.+.|-.+
T Consensus 19 ~ieCPvC~tkFkke 32 (267)
T COG1655 19 TIECPVCNTKFKKE 32 (267)
T ss_pred eeccCcccchhhhh
Confidence 48899999999763
No 65
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=36.41 E-value=15 Score=30.92 Aligned_cols=24 Identities=29% Similarity=0.378 Sum_probs=18.6
Q ss_pred hhhhccchh-hhhcCCChhhHhHHH
Q psy11933 38 KALVHACVV-CKAQMPDPKTYKQHF 61 (79)
Q Consensus 38 aA~~~~C~v-C~~~f~~~k~l~~H~ 61 (79)
+..||+|+| |++-|...+.-++|.
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (585)
T PTZ00417 32 KNKNIICPVHCKQCFVTMSEKKEHV 56 (585)
T ss_pred CCCceecccchhhheeehhhhhHHH
Confidence 456799997 888888866667775
No 66
>KOG3623|consensus
Probab=36.35 E-value=19 Score=32.19 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=24.7
Q ss_pred HhhhhccchhhhhcCCChhhHhHHHHcCCCC
Q psy11933 37 QKALVHACVVCKAQMPDPKTYKQHFENKHPK 67 (79)
Q Consensus 37 ~aA~~~~C~vC~~~f~~~k~l~~H~esKHpK 67 (79)
+.--+|+|+.|...|--...|++|.+. |+.
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRI-HSG 306 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRI-HSG 306 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhhee-ecC
Confidence 334459999999999999999999986 543
No 67
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=35.99 E-value=16 Score=27.49 Aligned_cols=24 Identities=29% Similarity=0.580 Sum_probs=22.4
Q ss_pred hccchhhhhcCCChhhHhHHHHcC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
++.|..|.++-+...++.-|-+-|
T Consensus 53 k~vC~LC~T~H~~e~Sy~~H~~GK 76 (222)
T COG5246 53 KYVCLLCKTKHLTEMSYVKHREGK 76 (222)
T ss_pred cEEeeeeccccccHHHHHHhhccc
Confidence 589999999999999999999987
No 68
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=35.48 E-value=12 Score=27.11 Aligned_cols=13 Identities=15% Similarity=0.480 Sum_probs=10.6
Q ss_pred hccchhhhhcCCC
Q psy11933 41 VHACVVCKAQMPD 53 (79)
Q Consensus 41 ~~~C~vC~~~f~~ 53 (79)
.+.||||++.+..
T Consensus 2 ~~~CP~C~~~l~~ 14 (272)
T PRK11088 2 SYQCPLCHQPLTL 14 (272)
T ss_pred cccCCCCCcchhc
Confidence 4789999998853
No 69
>KOG3576|consensus
Probab=35.07 E-value=20 Score=27.56 Aligned_cols=32 Identities=25% Similarity=0.435 Sum_probs=28.0
Q ss_pred hhhccchhhhhcCCChhhHhHHHHcCCCCCCC
Q psy11933 39 ALVHACVVCKAQMPDPKTYKQHFENKHPKNDL 70 (79)
Q Consensus 39 A~~~~C~vC~~~f~~~k~l~~H~esKHpK~~~ 70 (79)
+.-|+|.-|.-+-..+..|..|..+-||-.++
T Consensus 210 ~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 210 AKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred hheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 56699999999999999999999999996553
No 70
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=33.23 E-value=21 Score=26.82 Aligned_cols=23 Identities=30% Similarity=0.611 Sum_probs=18.4
Q ss_pred ccchhhhhcCCC---hhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPD---PKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~---~k~l~~H~esK 64 (79)
.+|.||++-... ..=|..||.-|
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK 216 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGK 216 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccc
Confidence 689999976655 56689999877
No 71
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=33.18 E-value=35 Score=20.05 Aligned_cols=24 Identities=21% Similarity=0.450 Sum_probs=20.9
Q ss_pred hhhHhHHHHcCCCCCCCCchhhhh
Q psy11933 54 PKTYKQHFENKHPKNDLPEDLKDV 77 (79)
Q Consensus 54 ~k~l~~H~esKHpK~~~p~e~~~~ 77 (79)
...+.+|...-|.-..+|+++.+-
T Consensus 26 l~~~~~Ha~~~Hg~~~~~~el~~~ 49 (57)
T PF06348_consen 26 LEAVVEHAREVHGMTEIPEELREK 49 (57)
T ss_pred HHHHHHHHHHhcCCccCCHHHHHH
Confidence 678999999999999899998763
No 72
>KOG2893|consensus
Probab=33.18 E-value=20 Score=28.24 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=25.2
Q ss_pred hhhccchhhhhcCCChhhHhHHHHcCCCC
Q psy11933 39 ALVHACVVCKAQMPDPKTYKQHFENKHPK 67 (79)
Q Consensus 39 A~~~~C~vC~~~f~~~k~l~~H~esKHpK 67 (79)
-++--|=.|-.-|-|++.|.||..+||=|
T Consensus 8 ~~kpwcwycnrefddekiliqhqkakhfk 36 (341)
T KOG2893|consen 8 VDKPWCWYCNREFDDEKILIQHQKAKHFK 36 (341)
T ss_pred cCCceeeecccccchhhhhhhhhhhccce
Confidence 34467999999999999999999999954
No 73
>KOG1280|consensus
Probab=32.98 E-value=29 Score=28.22 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=27.0
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
..|.|+.|..+=....+|..|..+-||-..
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccC
Confidence 379999999998889999999999999776
No 74
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=32.30 E-value=17 Score=21.81 Aligned_cols=11 Identities=27% Similarity=0.555 Sum_probs=3.6
Q ss_pred hccchhhhhcC
Q psy11933 41 VHACVVCKAQM 51 (79)
Q Consensus 41 ~~~C~vC~~~f 51 (79)
.++|++|.++=
T Consensus 33 ~y~Cp~CgAtG 43 (55)
T PF05741_consen 33 KYVCPICGATG 43 (55)
T ss_dssp G---TTT---G
T ss_pred cCcCCCCcCcC
Confidence 48899998873
No 75
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=31.80 E-value=13 Score=20.06 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=9.9
Q ss_pred hhccchhhhhcCCC
Q psy11933 40 LVHACVVCKAQMPD 53 (79)
Q Consensus 40 ~~~~C~vC~~~f~~ 53 (79)
+.|.|+-|.+.|-.
T Consensus 1 M~i~Cp~C~~~y~i 14 (36)
T PF13717_consen 1 MIITCPNCQAKYEI 14 (36)
T ss_pred CEEECCCCCCEEeC
Confidence 35778888777765
No 76
>KOG2505|consensus
Probab=30.81 E-value=27 Score=29.76 Aligned_cols=23 Identities=13% Similarity=0.582 Sum_probs=20.7
Q ss_pred ccchhhhhcCCChhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK 64 (79)
..|++|..+|.+.-..+.||.+-
T Consensus 67 ~~CstCq~~F~s~~eqr~HyksD 89 (591)
T KOG2505|consen 67 DQCSTCQIPFGSRQEQREHYKSD 89 (591)
T ss_pred ccccccCCccccHHHHHHHHHHH
Confidence 57999999999999999999874
No 77
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=30.80 E-value=14 Score=20.26 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=9.3
Q ss_pred chhhhhcCCChhhH
Q psy11933 44 CVVCKAQMPDPKTY 57 (79)
Q Consensus 44 C~vC~~~f~~~k~l 57 (79)
|+||..-|-++.+|
T Consensus 1 CpiC~~~~~~Pv~l 14 (42)
T PF15227_consen 1 CPICLDLFKDPVSL 14 (42)
T ss_dssp ETTTTSB-SSEEE-
T ss_pred CCccchhhCCcccc
Confidence 88999888885443
No 78
>KOG2636|consensus
Probab=30.55 E-value=25 Score=29.41 Aligned_cols=23 Identities=22% Similarity=0.595 Sum_probs=20.4
Q ss_pred hhccchhhh-hcCCChhhHhHHHH
Q psy11933 40 LVHACVVCK-AQMPDPKTYKQHFE 62 (79)
Q Consensus 40 ~~~~C~vC~-~~f~~~k~l~~H~e 62 (79)
..|.|.||. .+...++++.-||.
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cccceeeccCccccCcHHHHHHhH
Confidence 348899999 89999999999995
No 79
>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=28.50 E-value=47 Score=19.87 Aligned_cols=29 Identities=14% Similarity=0.290 Sum_probs=15.8
Q ss_pred ccchhhhhcCCC-----------hhhHhHHHHcCCCCCCC
Q psy11933 42 HACVVCKAQMPD-----------PKTYKQHFENKHPKNDL 70 (79)
Q Consensus 42 ~~C~vC~~~f~~-----------~k~l~~H~esKHpK~~~ 70 (79)
|.|+||+.-|-+ ...+..+++..++..|+
T Consensus 5 f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~ 44 (73)
T PF04564_consen 5 FLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPF 44 (73)
T ss_dssp GB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TT
T ss_pred cCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCC
Confidence 678888887777 44555555553544444
No 80
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=28.47 E-value=18 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.583 Sum_probs=14.7
Q ss_pred cchhhhhcCCChhhHhHHHHcC
Q psy11933 43 ACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 43 ~C~vC~~~f~~~k~l~~H~esK 64 (79)
-|.+|+.-|-+ |.+|..++
T Consensus 7 YCE~Cr~kfd~---l~~Hi~s~ 25 (49)
T smart00586 7 YCENCREKYDD---LETHLLSE 25 (49)
T ss_pred ccccHhHHHhh---HHHHhccH
Confidence 59999999864 66677665
No 81
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.23 E-value=28 Score=28.73 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=29.0
Q ss_pred HHHhhhhccchhhhhcCCChhhHhHHHHcC-CCCC
Q psy11933 35 AAQKALVHACVVCKAQMPDPKTYKQHFENK-HPKN 68 (79)
Q Consensus 35 a~~aA~~~~C~vC~~~f~~~k~l~~H~esK-HpK~ 68 (79)
.+.-+..|-|++|..-|-..+.++-|.++| |.|.
T Consensus 232 g~~~~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~ 266 (470)
T COG5188 232 GAEWFPKVYCVKCGREFSRSKVFEYHLEGKRHCKE 266 (470)
T ss_pred hhhhccceeeHhhhhHhhhhHHHHHHHhhhhhhhh
Confidence 345566799999999999999999999999 8765
No 82
>KOG0227|consensus
Probab=27.22 E-value=32 Score=26.02 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=22.2
Q ss_pred hccchhhhhcCCChhhHhHHHHcC-C
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENK-H 65 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esK-H 65 (79)
++.|..|.+.-++..+|.-|-+-| |
T Consensus 53 ~yeCkLClT~H~ne~Syl~HtqGKKH 78 (222)
T KOG0227|consen 53 KYECKLCLTLHNNEGSYLAHTQGKKH 78 (222)
T ss_pred ceeehhhhhhhcchhhhhhhhccchh
Confidence 489999999999999999998876 5
No 83
>KOG1493|consensus
Probab=26.37 E-value=24 Score=23.11 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=9.4
Q ss_pred ccchhhhhcCC
Q psy11933 42 HACVVCKAQMP 52 (79)
Q Consensus 42 ~~C~vC~~~f~ 52 (79)
-.|+.|||+|.
T Consensus 71 ~~CPmcRq~~~ 81 (84)
T KOG1493|consen 71 GQCPMCRQTWQ 81 (84)
T ss_pred ccCCcchheeE
Confidence 47999999985
No 84
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=26.11 E-value=42 Score=20.43 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=18.5
Q ss_pred CCChhhHhHHHHcCCCCCCCCch
Q psy11933 51 MPDPKTYKQHFENKHPKNDLPED 73 (79)
Q Consensus 51 f~~~k~l~~H~esKHpK~~~p~e 73 (79)
-+++-.|-+|....||-.|...+
T Consensus 22 ~~~Ye~Yv~H~~~~HP~~p~ms~ 44 (65)
T PF04328_consen 22 EPDYERYVEHMRRHHPDEPPMSE 44 (65)
T ss_pred cHHHHHHHHHHHHHCcCCCCCCH
Confidence 34578899999999998887654
No 85
>PRK00420 hypothetical protein; Validated
Probab=25.95 E-value=44 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=15.4
Q ss_pred HHHHHhhhhccchhhhhcCCC
Q psy11933 33 KKAAQKALVHACVVCKAQMPD 53 (79)
Q Consensus 33 ~ka~~aA~~~~C~vC~~~f~~ 53 (79)
|-..+.-+...||+|...|..
T Consensus 15 Ll~Ga~ml~~~CP~Cg~pLf~ 35 (112)
T PRK00420 15 LLKGAKMLSKHCPVCGLPLFE 35 (112)
T ss_pred HHhHHHHccCCCCCCCCccee
Confidence 333556688899999988764
No 86
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.62 E-value=25 Score=23.43 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=10.9
Q ss_pred ccchhhhhcCCCh
Q psy11933 42 HACVVCKAQMPDP 54 (79)
Q Consensus 42 ~~C~vC~~~f~~~ 54 (79)
|+|+-|.+.|+-.
T Consensus 27 ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 27 IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCCccCcc
Confidence 7899999998875
No 87
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=25.28 E-value=19 Score=20.19 Aligned_cols=9 Identities=33% Similarity=1.091 Sum_probs=3.3
Q ss_pred chhhhhcCCC
Q psy11933 44 CVVCKAQMPD 53 (79)
Q Consensus 44 C~vC~~~f~~ 53 (79)
|+||+. |.+
T Consensus 1 CpIc~e-~~~ 9 (43)
T PF13445_consen 1 CPICKE-FST 9 (43)
T ss_dssp -TTT-----T
T ss_pred CCcccc-ccC
Confidence 889998 755
No 88
>KOG4696|consensus
Probab=24.98 E-value=39 Score=27.30 Aligned_cols=21 Identities=24% Similarity=0.339 Sum_probs=14.9
Q ss_pred hccchhhhhcCCChhhHhHHHH
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~e 62 (79)
.++||+|+-+ .....+.-|.+
T Consensus 2 e~iCP~CkLs-v~~~~m~~Hie 22 (393)
T KOG4696|consen 2 EIICPFCKLS-VNYDEMCFHIE 22 (393)
T ss_pred cccccceecc-cCHHHHHHHHH
Confidence 4799999999 45555555555
No 89
>KOG0717|consensus
Probab=24.95 E-value=40 Score=28.38 Aligned_cols=26 Identities=15% Similarity=0.506 Sum_probs=22.1
Q ss_pred hhccchhhhhcCCChhhHhHHHHcC-C
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENK-H 65 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esK-H 65 (79)
..++|..|+..|+++.-|-.|...- |
T Consensus 459 a~~~C~tCr~~FdSRnkLF~Hlk~tgH 485 (508)
T KOG0717|consen 459 ALISCTTCRESFDSRNKLFAHLKKTGH 485 (508)
T ss_pred hhHhhhhhhhhccchhHHHHHhhhcCC
Confidence 3589999999999999999998754 5
No 90
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=24.85 E-value=41 Score=21.27 Aligned_cols=16 Identities=31% Similarity=0.432 Sum_probs=12.6
Q ss_pred hhhHhHHHHcCCCCCC
Q psy11933 54 PKTYKQHFENKHPKND 69 (79)
Q Consensus 54 ~k~l~~H~esKHpK~~ 69 (79)
...+..|||..||+..
T Consensus 55 l~~av~~FE~~HP~l~ 70 (85)
T PF14357_consen 55 LNEAVERFEASHPKLA 70 (85)
T ss_pred HHHHHHHHHHhCCcHH
Confidence 4557899999999753
No 91
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=24.64 E-value=52 Score=27.21 Aligned_cols=23 Identities=17% Similarity=0.394 Sum_probs=20.9
Q ss_pred hhccchhhhhcCCChhhHhHHHH
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~e 62 (79)
.-|+|.-|..-|....+|..|..
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHh
Confidence 35899999999999999999986
No 92
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=24.60 E-value=21 Score=22.94 Aligned_cols=22 Identities=9% Similarity=0.298 Sum_probs=16.9
Q ss_pred hhccchhhhhcCCChhhHhHHH
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHF 61 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~ 61 (79)
..+.|+.|+..+.....+..++
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 3578999999888866777776
No 93
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=23.97 E-value=26 Score=21.15 Aligned_cols=22 Identities=41% Similarity=0.739 Sum_probs=15.7
Q ss_pred cchhhhhcCCC------------hhhHhHHHHcC
Q psy11933 43 ACVVCKAQMPD------------PKTYKQHFENK 64 (79)
Q Consensus 43 ~C~vC~~~f~~------------~k~l~~H~esK 64 (79)
+|-||++.... +-.-.+|.+.+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~g~C~~y~~e~ 36 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHPGVCAQYLEEL 36 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCcHHHHHHHHhc
Confidence 79999998776 34455666655
No 94
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=23.51 E-value=27 Score=18.93 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=7.7
Q ss_pred hhccchhhhh
Q psy11933 40 LVHACVVCKA 49 (79)
Q Consensus 40 ~~~~C~vC~~ 49 (79)
..+.|+||++
T Consensus 35 ~~~~CP~C~k 44 (44)
T PF14634_consen 35 KSVKCPICRK 44 (44)
T ss_pred CCCCCcCCCC
Confidence 3578999974
No 95
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=23.28 E-value=49 Score=18.84 Aligned_cols=18 Identities=17% Similarity=0.423 Sum_probs=7.8
Q ss_pred HHHHHHhhhhccchhhhh
Q psy11933 32 QKKAAQKALVHACVVCKA 49 (79)
Q Consensus 32 q~ka~~aA~~~~C~vC~~ 49 (79)
=+..+...-...|+||.+
T Consensus 32 fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 32 FLESNQRTPKWKCPICNK 49 (50)
T ss_dssp HHHHHHHS---B-TTT--
T ss_pred HHHHhhccCCeECcCCcC
Confidence 344455555589999975
No 96
>PRK01343 zinc-binding protein; Provisional
Probab=23.28 E-value=29 Score=21.06 Aligned_cols=14 Identities=14% Similarity=0.349 Sum_probs=11.0
Q ss_pred hhccchhhhhcCCC
Q psy11933 40 LVHACVVCKAQMPD 53 (79)
Q Consensus 40 ~~~~C~vC~~~f~~ 53 (79)
....|+||+..|..
T Consensus 8 p~~~CP~C~k~~~~ 21 (57)
T PRK01343 8 PTRPCPECGKPSTR 21 (57)
T ss_pred CCCcCCCCCCcCcC
Confidence 34789999998763
No 97
>KOG3623|consensus
Probab=23.04 E-value=48 Score=29.77 Aligned_cols=30 Identities=17% Similarity=0.455 Sum_probs=24.9
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCCCCCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKHPKND 69 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKHpK~~ 69 (79)
-+|-|..|-.+|..+.+|++|....-|-.+
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~hkpg~d 268 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQLHKPGGD 268 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHhhcCCCc
Confidence 357799999999999999999997666543
No 98
>PF14353 CpXC: CpXC protein
Probab=23.02 E-value=13 Score=24.38 Aligned_cols=26 Identities=15% Similarity=0.225 Sum_probs=17.9
Q ss_pred hhccchhhhhcCCChhhHhHHHHcCC
Q psy11933 40 LVHACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 40 ~~~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
+.++|+-|+..|.-.-.+.-|...++
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~~ 62 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEKK 62 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCCC
Confidence 45899999999987544444544444
No 99
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.90 E-value=26 Score=24.29 Aligned_cols=14 Identities=29% Similarity=0.503 Sum_probs=10.1
Q ss_pred hhccchhhhhcCCC
Q psy11933 40 LVHACVVCKAQMPD 53 (79)
Q Consensus 40 ~~~~C~vC~~~f~~ 53 (79)
..|.|++|+.++..
T Consensus 127 ~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 127 LNFTCPRCGAMLDY 140 (158)
T ss_pred cCCcCCCCCCEeee
Confidence 46888888877544
No 100
>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=22.86 E-value=38 Score=18.60 Aligned_cols=12 Identities=17% Similarity=0.706 Sum_probs=8.8
Q ss_pred hhccchhhhhcC
Q psy11933 40 LVHACVVCKAQM 51 (79)
Q Consensus 40 ~~~~C~vC~~~f 51 (79)
....|++|++..
T Consensus 36 ~~~~CP~Cr~~i 47 (50)
T PF13920_consen 36 RKKKCPICRQPI 47 (50)
T ss_dssp TTSBBTTTTBB-
T ss_pred cCCCCCcCChhh
Confidence 457899999865
No 101
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=22.46 E-value=37 Score=23.49 Aligned_cols=22 Identities=23% Similarity=0.606 Sum_probs=11.9
Q ss_pred hccchhhhhcCCChhhHhHHHHcCC
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFENKH 65 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~esKH 65 (79)
.|+|=+|+..|-. |+-|....|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT
T ss_pred eeEEccCCcccch---HHHHHHHcc
Confidence 3889999999855 455555444
No 102
>KOG4172|consensus
Probab=22.43 E-value=20 Score=22.13 Aligned_cols=19 Identities=47% Similarity=0.880 Sum_probs=13.2
Q ss_pred hhhccchhhhhcCCC-hhhH
Q psy11933 39 ALVHACVVCKAQMPD-PKTY 57 (79)
Q Consensus 39 A~~~~C~vC~~~f~~-~k~l 57 (79)
++.-.|+|||...-+ .++|
T Consensus 41 ~~~g~CPiCRapi~dvIkTY 60 (62)
T KOG4172|consen 41 ALHGCCPICRAPIKDVIKTY 60 (62)
T ss_pred ccCCcCcchhhHHHHHHHhh
Confidence 356789999987655 4444
No 103
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.27 E-value=37 Score=19.56 Aligned_cols=18 Identities=22% Similarity=0.494 Sum_probs=13.3
Q ss_pred ccchhhhhcCCChhhHhH
Q psy11933 42 HACVVCKAQMPDPKTYKQ 59 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~ 59 (79)
-+|.||.-.|.-.+-...
T Consensus 9 K~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWAR 26 (42)
T ss_pred CcCcccCCcchHHHHHHH
Confidence 379999999987554443
No 104
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=22.17 E-value=33 Score=21.56 Aligned_cols=20 Identities=10% Similarity=0.419 Sum_probs=15.0
Q ss_pred cchhhhhcCCChhhHhHHHH
Q psy11933 43 ACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 43 ~C~vC~~~f~~~k~l~~H~e 62 (79)
-|++|+..++....+.+-+.
T Consensus 35 ~Cp~C~~~~~~l~~~~~~~~ 54 (149)
T cd02970 35 GCPFCREYLRALSKLLPELD 54 (149)
T ss_pred CChhHHHHHHHHHHHHHHHH
Confidence 59999999888666655554
No 105
>cd03000 PDI_a_TMX3 PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase.
Probab=21.85 E-value=53 Score=19.97 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=15.8
Q ss_pred chhhhhcCCChhhHhHHHH
Q psy11933 44 CVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 44 C~vC~~~f~~~k~l~~H~e 62 (79)
|+.|+...|....|..++.
T Consensus 27 C~~C~~~~p~l~~l~~~~~ 45 (104)
T cd03000 27 CGHCKKLEPVWNEVGAELK 45 (104)
T ss_pred CHHHHhhChHHHHHHHHHH
Confidence 9999999998667777764
No 106
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.
Probab=21.67 E-value=28 Score=23.96 Aligned_cols=18 Identities=33% Similarity=0.717 Sum_probs=14.9
Q ss_pred chhhhhcCCChhhHhHHH
Q psy11933 44 CVVCKAQMPDPKTYKQHF 61 (79)
Q Consensus 44 C~vC~~~f~~~k~l~~H~ 61 (79)
|+.|+..+|....|.+.+
T Consensus 62 CppCr~e~P~L~~l~~~~ 79 (153)
T TIGR02738 62 CPYCHQFAPVLKRFSQQF 79 (153)
T ss_pred ChhHHHHHHHHHHHHHHc
Confidence 999999999976666654
No 107
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=21.19 E-value=28 Score=20.99 Aligned_cols=11 Identities=45% Similarity=1.038 Sum_probs=8.9
Q ss_pred cchhhhhcCCC
Q psy11933 43 ACVVCKAQMPD 53 (79)
Q Consensus 43 ~C~vC~~~f~~ 53 (79)
+|.||++.+-.
T Consensus 3 iCvvCK~Pi~~ 13 (53)
T PHA02610 3 ICVVCKQPIEK 13 (53)
T ss_pred eeeeeCCchhh
Confidence 79999998743
No 108
>PLN03239 histone acetyltransferase; Provisional
Probab=20.78 E-value=64 Score=25.90 Aligned_cols=22 Identities=5% Similarity=0.030 Sum_probs=19.6
Q ss_pred hccchhhhhcCCChhhHhHHHH
Q psy11933 41 VHACVVCKAQMPDPKTYKQHFE 62 (79)
Q Consensus 41 ~~~C~vC~~~f~~~k~l~~H~e 62 (79)
-++|.-|..-|.+...|..|..
T Consensus 106 lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 106 LYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred EEEeccchhhhcCHHHHHHHHH
Confidence 4899999999999999999865
No 109
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=20.41 E-value=25 Score=23.72 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=16.5
Q ss_pred hhhccchhhhhcCCC--hhhHhHH
Q psy11933 39 ALVHACVVCKAQMPD--PKTYKQH 60 (79)
Q Consensus 39 A~~~~C~vC~~~f~~--~k~l~~H 60 (79)
++.++|++|+.-|.+ -.-|.+|
T Consensus 35 alaaKC~~~~k~~~SY~H~rL~e~ 58 (102)
T PF15176_consen 35 ALAAKCPVWYKYLASYRHHRLPET 58 (102)
T ss_pred HHHHHhHHHHHHHhccccccCCcc
Confidence 566899999999988 3345555
No 110
>PHA02929 N1R/p28-like protein; Provisional
Probab=20.17 E-value=33 Score=25.82 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=10.6
Q ss_pred hccchhhhhcCCC
Q psy11933 41 VHACVVCKAQMPD 53 (79)
Q Consensus 41 ~~~C~vC~~~f~~ 53 (79)
+..||+||..|..
T Consensus 216 ~~tCPlCR~~~~~ 228 (238)
T PHA02929 216 KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCCCEeeE
Confidence 3589999998875
No 111
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=20.14 E-value=64 Score=26.06 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=16.5
Q ss_pred ccchhhhhcCCChhhHhHHHHcC
Q psy11933 42 HACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 42 ~~C~vC~~~f~~~k~l~~H~esK 64 (79)
+.|++|- +|--.+++.+|.++=
T Consensus 161 ~~CP~C~-~~~P~~~i~~HLD~C 182 (391)
T COG5432 161 VHCPACS-NLVPHNQINQHLDSC 182 (391)
T ss_pred hcCchhh-ccCchHHHHHHHHHH
Confidence 6899995 455567888998753
No 112
>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=20.07 E-value=38 Score=16.78 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=8.1
Q ss_pred hhccchhhhhc
Q psy11933 40 LVHACVVCKAQ 50 (79)
Q Consensus 40 ~~~~C~vC~~~ 50 (79)
..+.|++|+..
T Consensus 34 ~~~~Cp~C~~~ 44 (45)
T cd00162 34 GKNTCPLCRTP 44 (45)
T ss_pred CcCCCCCCCCc
Confidence 35679999865
No 113
>KOG3288|consensus
Probab=20.04 E-value=49 Score=26.09 Aligned_cols=28 Identities=18% Similarity=0.409 Sum_probs=24.4
Q ss_pred HhhhhccchhhhhcCCChhhHhHHHHcC
Q psy11933 37 QKALVHACVVCKAQMPDPKTYKQHFENK 64 (79)
Q Consensus 37 ~aA~~~~C~vC~~~f~~~k~l~~H~esK 64 (79)
-+-+.+.|.||...|...+.-.+|.++-
T Consensus 272 t~~ftlRC~~Cq~glvGq~ea~eHA~~T 299 (307)
T KOG3288|consen 272 TAKFTLRCMVCQMGLVGQKEAAEHAKAT 299 (307)
T ss_pred ccceEEEeeecccceeeHHHHHHHHHhc
Confidence 4456788999999999999999999875
Done!