Query 046120
Match_columns 381
No_of_seqs 257 out of 1721
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 08:58:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046120hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2084 Predicted histone tail 99.9 9.1E-22 2E-26 199.7 16.5 289 14-372 22-322 (482)
2 PF00856 SET: SET domain; Int 99.7 2.2E-16 4.7E-21 135.5 9.9 54 199-255 109-162 (162)
3 smart00317 SET SET (Su(var)3-9 99.4 4.5E-13 9.7E-18 109.2 7.5 48 204-254 69-116 (116)
4 KOG2589 Histone tail methylase 98.3 6.4E-07 1.4E-11 84.8 4.0 81 180-284 175-256 (453)
5 PF01753 zf-MYND: MYND finger; 98.1 3.3E-07 7.1E-12 59.4 -0.8 36 53-94 1-37 (37)
6 KOG4442 Clathrin coat binding 98.0 6.1E-06 1.3E-10 84.3 5.1 50 209-261 194-243 (729)
7 COG2940 Proteins containing SE 97.9 5.6E-06 1.2E-10 84.6 3.1 74 207-284 404-478 (480)
8 KOG1080 Histone H3 (Lys4) meth 97.9 6.9E-06 1.5E-10 88.8 3.8 47 208-258 939-986 (1005)
9 KOG1082 Histone H3 (Lys9) meth 97.2 0.00026 5.7E-09 69.8 3.0 51 209-259 273-324 (364)
10 KOG1141 Predicted histone meth 97.1 0.00027 5.8E-09 73.5 2.2 63 209-279 1190-1253(1262)
11 KOG1337 N-methyltransferase [G 96.8 0.0022 4.8E-08 65.5 6.0 95 167-275 197-291 (472)
12 KOG1338 Uncharacterized conser 96.6 0.016 3.4E-07 56.3 10.1 86 166-260 173-264 (466)
13 KOG1085 Predicted methyltransf 96.5 0.0017 3.6E-08 60.2 2.7 47 209-258 334-380 (392)
14 KOG1710 MYND Zn-finger and ank 95.7 0.0021 4.6E-08 59.8 -0.9 44 49-97 318-362 (396)
15 KOG1083 Putative transcription 95.7 0.0095 2.1E-07 64.0 3.7 45 209-256 1251-1295(1306)
16 PF13824 zf-Mss51: Zinc-finger 95.3 0.011 2.3E-07 41.4 1.8 46 53-100 2-48 (55)
17 KOG1079 Transcriptional repres 93.7 0.065 1.4E-06 55.4 3.8 45 209-257 666-711 (739)
18 PF04438 zf-HIT: HIT zinc fing 90.1 0.075 1.6E-06 32.5 -0.3 27 51-81 3-29 (30)
19 KOG2857 Predicted MYND Zn-fing 89.9 0.12 2.7E-06 43.0 0.7 31 50-83 5-35 (157)
20 KOG1085 Predicted methyltransf 88.8 0.46 1E-05 44.5 3.6 34 2-35 252-285 (392)
21 KOG1081 Transcription factor N 85.1 0.38 8.3E-06 48.9 1.1 54 202-258 364-418 (463)
22 PF04810 zf-Sec23_Sec24: Sec23 84.4 0.44 9.5E-06 31.1 0.8 32 333-367 3-34 (40)
23 PF08271 TF_Zn_Ribbon: TFIIB z 81.9 1 2.2E-05 29.8 1.8 37 333-375 1-37 (43)
24 PLN03158 methionine aminopepti 79.4 0.61 1.3E-05 46.6 0.1 36 49-89 8-51 (396)
25 PF09889 DUF2116: Uncharacteri 76.0 1.1 2.3E-05 32.0 0.5 27 50-85 3-29 (59)
26 PF02150 RNA_POL_M_15KD: RNA p 76.0 1.3 2.9E-05 28.0 0.9 32 334-371 3-34 (35)
27 PF08666 SAF: SAF domain; Int 74.6 2.1 4.5E-05 30.4 1.7 15 18-32 2-16 (63)
28 KOG4317 Predicted Zn-finger pr 74.3 1.7 3.8E-05 41.1 1.5 32 49-83 6-37 (383)
29 TIGR02059 swm_rep_I cyanobacte 70.6 6 0.00013 31.3 3.5 26 233-258 74-99 (101)
30 PRK00398 rpoP DNA-directed RNA 70.2 3.2 7E-05 27.8 1.7 31 331-368 2-32 (46)
31 PF10571 UPF0547: Uncharacteri 69.0 3.4 7.3E-05 24.3 1.4 23 52-75 2-24 (26)
32 PRK00418 DNA gyrase inhibitor; 68.5 2.6 5.6E-05 30.3 1.0 11 74-84 26-36 (62)
33 PRK01343 zinc-binding protein; 68.2 3 6.4E-05 29.5 1.2 11 74-84 25-35 (57)
34 PF07975 C1_4: TFIIH C1-like d 67.8 2 4.3E-05 29.7 0.3 30 52-82 1-37 (51)
35 KOG3612 PHD Zn-finger protein 67.8 1.1 2.4E-05 45.5 -1.3 42 49-98 526-568 (588)
36 PF03884 DUF329: Domain of unk 67.0 2.1 4.5E-05 30.3 0.3 11 74-84 22-32 (57)
37 COG3024 Uncharacterized protei 67.0 2.5 5.3E-05 30.5 0.6 11 74-84 27-37 (65)
38 KOG2461 Transcription factor B 63.8 4.7 0.0001 40.2 2.2 26 232-257 120-145 (396)
39 KOG4442 Clathrin coat binding 62.8 7.3 0.00016 41.0 3.4 30 6-35 120-149 (729)
40 smart00154 ZnF_AN1 AN1-like Zi 57.3 7 0.00015 25.3 1.4 24 53-77 1-24 (39)
41 PF08189 Meleagrin: Meleagrin/ 57.0 3.9 8.4E-05 25.9 0.2 19 71-89 6-25 (39)
42 PF07754 DUF1610: Domain of un 56.4 7.6 0.00016 22.4 1.3 21 53-73 1-24 (24)
43 KOG2807 RNA polymerase II tran 53.1 7 0.00015 37.4 1.3 40 49-89 329-368 (378)
44 PF08772 NOB1_Zn_bind: Nin one 53.1 6.2 0.00013 29.5 0.7 26 49-74 8-33 (73)
45 COG2051 RPS27A Ribosomal prote 52.9 7.5 0.00016 28.3 1.1 35 328-368 15-49 (67)
46 PRK00415 rps27e 30S ribosomal 52.6 7.6 0.00016 27.7 1.1 35 328-368 7-41 (59)
47 KOG3362 Predicted BBOX Zn-fing 51.4 5 0.00011 33.7 0.0 30 49-82 117-146 (156)
48 PF14949 ARF7EP_C: ARF7 effect 51.1 8.7 0.00019 30.7 1.3 19 65-83 74-92 (103)
49 smart00661 RPOL9 RNA polymeras 50.8 13 0.00029 25.2 2.1 31 334-369 2-32 (52)
50 smart00858 SAF This domain fam 50.6 9.9 0.00021 26.7 1.5 17 18-34 2-18 (64)
51 PF14570 zf-RING_4: RING/Ubox 50.2 5.3 0.00012 27.2 0.0 27 49-75 21-47 (48)
52 PF12855 Ecl1: Life-span regul 47.9 6.4 0.00014 26.2 0.1 30 50-86 6-36 (43)
53 PF01927 Mut7-C: Mut7-C RNAse 45.9 16 0.00034 31.1 2.2 32 334-367 93-134 (147)
54 PF10013 DUF2256: Uncharacteri 45.7 8.4 0.00018 25.4 0.4 31 50-82 8-40 (42)
55 TIGR03586 PseI pseudaminic aci 45.2 13 0.00029 36.1 1.9 21 16-36 274-294 (327)
56 smart00659 RPOLCX RNA polymera 44.0 18 0.0004 24.1 1.9 28 332-367 2-29 (44)
57 COG1594 RPB9 DNA-directed RNA 43.6 19 0.0004 29.3 2.2 32 334-370 4-35 (113)
58 COG4068 Uncharacterized protei 42.9 8.9 0.00019 27.1 0.2 25 50-83 8-32 (64)
59 cd02249 ZZ Zinc finger, ZZ typ 42.6 14 0.00029 24.7 1.1 35 52-89 2-37 (46)
60 cd02335 ZZ_ADA2 Zinc finger, Z 42.2 15 0.00032 25.0 1.2 32 52-84 2-34 (49)
61 PF01485 IBR: IBR domain; Int 42.1 16 0.00036 25.6 1.5 31 334-367 20-50 (64)
62 COG1998 RPS31 Ribosomal protei 41.8 15 0.00033 25.1 1.2 27 333-367 20-47 (51)
63 PF04570 DUF581: Protein of un 41.7 11 0.00025 26.7 0.6 35 49-84 15-50 (58)
64 PF13240 zinc_ribbon_2: zinc-r 41.3 16 0.00034 20.7 1.1 21 52-73 1-21 (23)
65 PF09538 FYDLN_acid: Protein o 40.9 19 0.00042 29.0 1.9 27 49-75 8-36 (108)
66 PF03604 DNA_RNApol_7kD: DNA d 40.8 17 0.00038 22.5 1.3 27 333-367 1-27 (32)
67 PF13719 zinc_ribbon_5: zinc-r 40.7 15 0.00033 23.4 1.0 33 332-367 2-35 (37)
68 TIGR02098 MJ0042_CXXC MJ0042 f 40.5 15 0.00033 23.2 1.0 34 332-368 2-36 (38)
69 PF14803 Nudix_N_2: Nudix N-te 40.4 18 0.0004 22.7 1.3 29 334-366 2-31 (34)
70 TIGR00622 ssl1 transcription f 40.3 29 0.00063 28.2 2.8 72 16-89 21-104 (112)
71 PF13717 zinc_ribbon_4: zinc-r 40.0 19 0.0004 22.9 1.3 33 332-367 2-35 (36)
72 TIGR03569 NeuB_NnaB N-acetylne 39.8 19 0.0004 35.1 2.0 21 16-36 276-296 (329)
73 PF13248 zf-ribbon_3: zinc-rib 39.2 17 0.00037 21.1 1.0 22 51-73 3-24 (26)
74 COG1656 Uncharacterized conser 38.7 17 0.00038 31.5 1.4 34 332-367 97-140 (165)
75 COG1579 Zn-ribbon protein, pos 37.4 18 0.00039 33.5 1.3 26 49-74 196-230 (239)
76 PF14169 YdjO: Cold-inducible 36.3 33 0.00071 24.5 2.2 35 331-369 17-51 (59)
77 PF09297 zf-NADH-PPase: NADH p 36.3 33 0.00072 20.9 2.0 26 334-366 5-30 (32)
78 PF12773 DZR: Double zinc ribb 35.2 30 0.00065 23.2 1.9 25 49-73 11-37 (50)
79 PHA00626 hypothetical protein 34.9 27 0.00059 24.5 1.6 19 356-374 22-40 (59)
80 COG1997 RPL43A Ribosomal prote 34.8 30 0.00064 26.7 1.9 34 329-370 32-66 (89)
81 PF01667 Ribosomal_S27e: Ribos 34.5 21 0.00046 25.1 1.0 34 328-368 3-37 (55)
82 PF12760 Zn_Tnp_IS1595: Transp 34.4 28 0.00061 23.2 1.6 32 329-366 15-46 (46)
83 PF14446 Prok-RING_1: Prokaryo 34.2 29 0.00064 24.2 1.7 28 49-76 4-32 (54)
84 PF01428 zf-AN1: AN1-like Zinc 33.5 16 0.00035 24.1 0.3 20 56-77 6-25 (43)
85 cd02340 ZZ_NBR1_like Zinc fing 32.1 28 0.0006 23.0 1.3 31 52-84 2-33 (43)
86 KOG2463 Predicted RNA-binding 31.7 20 0.00044 34.5 0.8 26 49-74 241-266 (376)
87 cd00729 rubredoxin_SM Rubredox 30.4 30 0.00064 21.6 1.1 10 356-365 17-26 (34)
88 COG2089 SpsE Sialic acid synth 30.1 27 0.00058 33.8 1.3 28 16-43 288-315 (347)
89 PRK00432 30S ribosomal protein 30.1 36 0.00077 23.4 1.6 26 333-367 21-47 (50)
90 PF00181 Ribosomal_L2: Ribosom 30.0 47 0.001 24.9 2.4 24 11-34 54-77 (77)
91 COG2888 Predicted Zn-ribbon RN 29.8 24 0.00051 25.2 0.6 35 50-84 9-48 (61)
92 PF06467 zf-FCS: MYM-type Zinc 29.7 23 0.0005 22.9 0.6 35 49-83 5-42 (43)
93 PF13894 zf-C2H2_4: C2H2-type 29.0 29 0.00063 18.6 0.9 12 358-369 1-12 (24)
94 KOG2155 Tubulin-tyrosine ligas 28.8 48 0.001 33.4 2.8 62 207-269 203-264 (631)
95 PF09538 FYDLN_acid: Protein o 28.1 42 0.00091 27.1 1.9 32 331-370 8-39 (108)
96 TIGR01053 LSD1 zinc finger dom 27.5 68 0.0015 19.7 2.3 27 333-366 2-28 (31)
97 COG5151 SSL1 RNA polymerase II 27.5 27 0.00059 33.3 0.8 52 36-89 349-411 (421)
98 COG1571 Predicted DNA-binding 27.4 35 0.00075 34.2 1.6 33 333-373 351-383 (421)
99 COG1779 C4-type Zn-finger prot 27.3 31 0.00068 30.8 1.1 46 329-376 11-62 (201)
100 TIGR01384 TFS_arch transcripti 27.2 39 0.00085 26.6 1.6 27 334-369 2-28 (104)
101 smart00291 ZnF_ZZ Zinc-binding 27.2 37 0.0008 22.4 1.2 33 49-83 3-36 (44)
102 PRK12618 flgA flagellar basal 26.8 37 0.00081 28.7 1.5 22 14-35 16-37 (141)
103 cd02343 ZZ_EF Zinc finger, ZZ 26.8 31 0.00068 23.5 0.8 31 52-84 2-33 (48)
104 COG1781 PyrI Aspartate carbamo 26.7 42 0.0009 28.7 1.7 44 331-374 105-152 (153)
105 smart00647 IBR In Between Ring 26.3 69 0.0015 22.3 2.7 31 333-367 19-50 (64)
106 cd00350 rubredoxin_like Rubred 26.2 38 0.00082 20.9 1.1 13 358-370 2-14 (33)
107 PLN03144 Carbon catabolite rep 25.6 30 0.00065 36.6 0.8 25 64-89 73-105 (606)
108 PLN00162 transport protein sec 24.5 42 0.00091 36.6 1.7 33 332-367 53-85 (761)
109 PLN00209 ribosomal protein S27 24.4 36 0.00078 26.1 0.8 35 328-368 32-66 (86)
110 COG1096 Predicted RNA-binding 24.2 62 0.0013 28.7 2.4 52 23-74 116-174 (188)
111 COG3357 Predicted transcriptio 23.4 81 0.0018 24.5 2.6 23 51-73 62-84 (97)
112 PF09151 DUF1936: Domain of un 22.9 35 0.00077 20.8 0.4 25 334-361 3-28 (36)
113 PF13453 zf-TFIIB: Transcripti 22.4 46 0.00099 21.5 1.0 27 335-366 2-28 (41)
114 PF09723 Zn-ribbon_8: Zinc rib 22.0 56 0.0012 21.3 1.3 27 333-366 6-35 (42)
115 cd00065 FYVE FYVE domain; Zinc 21.5 71 0.0015 21.8 1.9 30 51-81 3-33 (57)
116 PF11781 RRN7: RNA polymerase 21.5 60 0.0013 20.6 1.3 27 333-367 9-35 (36)
117 PF01599 Ribosomal_S27: Riboso 21.4 57 0.0012 22.1 1.2 30 331-366 17-47 (47)
118 PTZ00083 40S ribosomal protein 21.1 46 0.001 25.5 0.8 35 328-368 31-65 (85)
119 COG1996 RPC10 DNA-directed RNA 21.0 52 0.0011 22.6 1.0 26 49-74 5-33 (49)
120 TIGR02300 FYDLN_acid conserved 20.8 78 0.0017 26.3 2.2 34 331-372 8-41 (129)
121 TIGR01206 lysW lysine biosynth 20.5 1E+02 0.0022 21.6 2.4 32 332-368 2-33 (54)
122 TIGR03170 flgA_cterm flagella 20.0 55 0.0012 26.5 1.2 15 20-34 2-16 (122)
No 1
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=99.88 E-value=9.1e-22 Score=199.72 Aligned_cols=289 Identities=21% Similarity=0.332 Sum_probs=168.5
Q ss_pred CCCccEEEEcccCCCCcEEEEcCcceeccccccccCcccccccccccCCCCCccCCCCCCC-cCccccchhhhhcCCchh
Q 046120 14 EGRGRGLVSTQSLKAGQIVLRDSPILLYSALPFINSSSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSHSPY 92 (381)
Q Consensus 14 ~~~GRglvAtrdi~~GevIl~e~P~v~~p~~~l~~~~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H~~~ 92 (381)
+..|||++|+++|++|++|++|.|++.+|.. ..|..|+.. ....|..|... +|.. |....|...| .+
T Consensus 22 ~~~Gr~~~a~~~i~~g~~i~~e~p~~~~p~~------~~~~~c~~~----~~~~C~~~~~~~~~~~-~~~~~~~~~~-~~ 89 (482)
T KOG2084|consen 22 PELGRGLVATQAIEAGEVILEEEPLVVGPAS------KSCSRCLGC----SCDHCRRCLEAIECNK-CQQRGWALCG-KF 89 (482)
T ss_pred cccCcceeeecccCCCceEEecCcceeeecc------cCCcccccc----chhhhhcCCccHhhhh-hhccCccccc-hh
Confidence 4789999999999999999999999998875 344444432 23456666666 7753 3333333444 44
Q ss_pred hhHhHHHhhhcCCCCCCCCChhHHHHHHHHHHHhhhccCCchhHHH--HHH---hcCCCCCCchhHHHH---HHhhCCC-
Q 046120 93 VCQALTRLLNLNSPDAANLPLDRQLQARFLIAAYNLAVVNPSQFQI--LLA---FQGTVTDNDTSAAHY---LSSLCPP- 163 (381)
Q Consensus 93 EC~~l~~~~~~~~~~~~~~~~~~~~~~R~l~~~~~l~~~~~~~~~~--l~~---L~~~~~~~~~~~~~~---l~~l~~~- 163 (381)
+|....... ... +......-..+..........+..+.. +.. +..+..........+ .......
T Consensus 90 ~~~~~~~~~-~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (482)
T KOG2084|consen 90 ACSADLAKL-ECE------PLKLVGAPEECLALSSLHEESREAIVLLSLLEECSLSAEKPRLRLDLSYLEHGATEDDQSH 162 (482)
T ss_pred hcchhhccc-ccc------chhhccchHHHHHhhcCCccccchHHHHHHHHHhhhhcccccHhHHHhhHHHHhhHHhhcc
Confidence 444311100 000 000000000001100111111111110 111 111110000000000 0000000
Q ss_pred -CCCCCHHHHHHHHHHhhccccccccCCcCCCCCCccceeEEeccccccccCCCCCCceeeeccccccCCCceEEEEEcc
Q 046120 164 -PASTTIELTAALLAKDRLNAFGLMEPYIEGQDGRRSVRAYGIYLKASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIH 242 (381)
Q Consensus 164 -~~~~~~~~i~~ll~~l~~Nsf~i~~~~~~~~~~~~~~~g~gLyp~~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r 242 (381)
........+..++..+..|++.+...... ......+.|+||..+++||||.||+.. .| .+....+++..
T Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~hsC~pn~~~-~~------~~~~~~~~~~~ 232 (482)
T KOG2084|consen 163 LLLVLAADCISKLFPSLLCNSITNASSLRV---PEPLFLGRGLFPGSSLFNHSCFPNISV-IF------DGRGLALLVPA 232 (482)
T ss_pred ccchhHHHHHHHHHHHHHHhhhhhhhhhhc---cccccceeeecccchhcccCCCCCeEE-EE------CCceeEEEeec
Confidence 01112333444555555666655432110 001148999999999999999999984 34 35566777778
Q ss_pred CCCCCC-eeEEeecCCCCCHHHHHHHHhcCCCeeeeCccccCcccCCCCCCCCccchhhcchhhHHhhhcCccccccCCC
Q 046120 243 DVPQGR-EICLSYFPVNYDYSTRQKRLLYDYDFACDCDRCKVEANWSDNDNDDENNEEVMDEDQDEQMVASDDDAEVHGD 321 (381)
Q Consensus 243 ~I~~Ge-El~isY~~~~~~~~~Rr~~L~~~y~F~C~C~rC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 321 (381)
.+.+++ +|+++|++..+++..||.+|+..|.|.|.|+||.++++ .
T Consensus 233 ~~~~~~~~l~~~y~~~~~~~~~r~~~l~~~~~f~c~c~rc~d~~~-----------------------------~----- 278 (482)
T KOG2084|consen 233 GIDAGEEELTISYTDPLLSTASRQKQLRQSKLFSCQCPRCLDPTE-----------------------------L----- 278 (482)
T ss_pred ccCCCCCEEEEeecccccCHHHHHHHHhhccceeeecCCCCCCCc-----------------------------c-----
Confidence 888776 99999999999999999999999999999999998663 2
Q ss_pred CCCchhhHhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCcccccCc
Q 046120 322 TNFPHAYFFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDAIG 372 (381)
Q Consensus 322 ~~~~~~~~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~~~ 372 (381)
++++..++|..++|.+.+.+..+.... ..|.|..|.......++
T Consensus 279 -----~~~~~~~~c~~~~~~~~~~~~~~~~~~--~~w~~~~~~~~~~~~~~ 322 (482)
T KOG2084|consen 279 -----GTFLSSLRCENCTCGGLLGTSFLDKED--LQWPCTECALVRLKAYV 322 (482)
T ss_pred -----ccchhhhhhcCCCCCCccCCCcccccC--CCccccccccchhHHHH
Confidence 268899999999998777666555421 47999999998875433
No 2
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.67 E-value=2.2e-16 Score=135.53 Aligned_cols=54 Identities=30% Similarity=0.435 Sum_probs=43.1
Q ss_pred cceeEEeccccccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeec
Q 046120 199 SVRAYGIYLKASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYF 255 (381)
Q Consensus 199 ~~~g~gLyp~~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~ 255 (381)
...+.+|||.++||||||.||+......+ ..+..++|+|.|+|++||||+|||+
T Consensus 109 ~~~~~~l~p~~d~~NHsc~pn~~~~~~~~---~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 109 DRDGIALYPFADMLNHSCDPNCEVSFDFD---GDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEEETGGGGSEEESSTSEEEEEEEE---TTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccCcHhHheccccccccceeeEee---cccceEEEEECCccCCCCEEEEEEC
Confidence 45689999999999999999998532111 1368999999999999999999996
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.42 E-value=4.5e-13 Score=109.23 Aligned_cols=48 Identities=25% Similarity=0.423 Sum_probs=38.4
Q ss_pred EeccccccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEee
Q 046120 204 GIYLKASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSY 254 (381)
Q Consensus 204 gLyp~~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY 254 (381)
.++|.++++||||.||+....... .+...+.++|+|+|++|||||++|
T Consensus 69 ~~~~~~~~iNHsc~pN~~~~~~~~---~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 69 RKGNIARFINHSCEPNCELLFVEV---NGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred ccCcHHHeeCCCCCCCEEEEEEEE---CCCcEEEEEECCCcCCCCEEeecC
Confidence 378899999999999998532211 122269999999999999999999
No 4
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=98.27 E-value=6.4e-07 Score=84.85 Aligned_cols=81 Identities=27% Similarity=0.472 Sum_probs=59.5
Q ss_pred hccccccccCCcCCCCCCccceeEEeccc-cccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecCCC
Q 046120 180 RLNAFGLMEPYIEGQDGRRSVRAYGIYLK-ASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVN 258 (381)
Q Consensus 180 ~~Nsf~i~~~~~~~~~~~~~~~g~gLyp~-~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~ 258 (381)
.-|-|.|+-+... .-..||.. ++++||.|.||+..+.. ++.++.|+++|||++|||||.=|+..+
T Consensus 175 g~nDFSvmyStRk--------~caqLwLGPaafINHDCrpnCkFvs~------g~~tacvkvlRDIePGeEITcFYgs~f 240 (453)
T KOG2589|consen 175 GGNDFSVMYSTRK--------RCAQLWLGPAAFINHDCRPNCKFVST------GRDTACVKVLRDIEPGEEITCFYGSGF 240 (453)
T ss_pred cCCceeeeeeccc--------chhhheeccHHhhcCCCCCCceeecC------CCceeeeehhhcCCCCceeEEeecccc
Confidence 3477777644221 23355654 68899999999974321 357899999999999999999999987
Q ss_pred CCHHHHHHHHhcCCCeeeeCccccCc
Q 046120 259 YDYSTRQKRLLYDYDFACDCDRCKVE 284 (381)
Q Consensus 259 ~~~~~Rr~~L~~~y~F~C~C~rC~~~ 284 (381)
.+. ..-.|.|.-|...
T Consensus 241 FG~----------~N~~CeC~TCER~ 256 (453)
T KOG2589|consen 241 FGE----------NNEECECVTCERR 256 (453)
T ss_pred cCC----------CCceeEEeecccc
Confidence 654 2358999999764
No 5
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=98.14 E-value=3.3e-07 Score=59.41 Aligned_cols=36 Identities=28% Similarity=0.778 Sum_probs=29.7
Q ss_pred ccccccccCCCCCccCCCCCCC-cCccccchhhhhcCCchhhh
Q 046120 53 CHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSHSPYVC 94 (381)
Q Consensus 53 C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H~~~EC 94 (381)
|.+|++. ...+|++|+.+ |||++||+++| ..| +.+|
T Consensus 1 C~~C~~~----~~~~C~~C~~~~YCs~~Cq~~~w-~~H-k~~C 37 (37)
T PF01753_consen 1 CAVCGKP----ALKRCSRCKSVYYCSEECQRADW-PYH-KFEC 37 (37)
T ss_dssp -TTTSSC----SSEEETTTSSSEESSHHHHHHHH-HHH-CCTH
T ss_pred CcCCCCC----cCCcCCCCCCEEecCHHHHHHHH-HHH-hhhC
Confidence 6788883 33499999999 99999999999 788 7776
No 6
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.01 E-value=6.1e-06 Score=84.34 Aligned_cols=50 Identities=26% Similarity=0.362 Sum_probs=37.9
Q ss_pred cccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecCCCCCH
Q 046120 209 ASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVNYDY 261 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~~~~ 261 (381)
+-++||||+||+..-.|.- .+-.+|-|.|.|+|++|||||..|--...++
T Consensus 194 aRFiNHSC~PNa~~~KWtV---~~~lRvGiFakk~I~~GEEITFDYqf~rYGr 243 (729)
T KOG4442|consen 194 ARFINHSCDPNAEVQKWTV---PDELRVGIFAKKVIKPGEEITFDYQFDRYGR 243 (729)
T ss_pred HHhhcCCCCCCceeeeeee---CCeeEEEEeEecccCCCceeeEecccccccc
Confidence 4578999999987422210 1346788899999999999999998776554
No 7
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=97.92 E-value=5.6e-06 Score=84.63 Aligned_cols=74 Identities=31% Similarity=0.422 Sum_probs=58.2
Q ss_pred cccccccCCCCCCceeeeccccccCCC-ceEEEEEccCCCCCCeeEEeecCCCCCHHHHHHHHhcCCCeeeeCccccCc
Q 046120 207 LKASFFNHDCLPNACRFDYVDAAAENN-TDIIVRMIHDVPQGREICLSYFPVNYDYSTRQKRLLYDYDFACDCDRCKVE 284 (381)
Q Consensus 207 p~~Sl~NHSC~PN~~~~~~~d~~~~~~-~~l~vrA~r~I~~GeEl~isY~~~~~~~~~Rr~~L~~~y~F~C~C~rC~~~ 284 (381)
..+.++||||.||+..+.... .| ..+.++|+|||++||||++.|....+....+...+...++..|.|.+|...
T Consensus 404 ~~~r~~nHS~~pN~~~~~~~~----~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 404 DVARFINHSCTPNCEASPIEV----NGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred cccceeecCCCCCcceecccc----cccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 346699999999998542211 12 488999999999999999999998766554566677778999999999853
No 8
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=97.92 E-value=6.9e-06 Score=88.83 Aligned_cols=47 Identities=28% Similarity=0.498 Sum_probs=38.8
Q ss_pred ccccccCCCCCCce-eeeccccccCCCceEEEEEccCCCCCCeeEEeecCCC
Q 046120 208 KASFFNHDCLPNAC-RFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVN 258 (381)
Q Consensus 208 ~~Sl~NHSC~PN~~-~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~ 258 (381)
.|.++||||.||+. ++..++ +..+|+|.|.|+|.+|||||..|--..
T Consensus 939 iAr~InHsC~PNCyakvi~V~----g~~~IvIyakr~I~~~EElTYDYkF~~ 986 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVE----GDKRIVIYSKRDIAAGEELTYDYKFPT 986 (1005)
T ss_pred hhheeecccCCCceeeEEEec----CeeEEEEEEecccccCceeeeeccccc
Confidence 47899999999987 444443 557999999999999999999997553
No 9
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=97.16 E-value=0.00026 Score=69.84 Aligned_cols=51 Identities=27% Similarity=0.356 Sum_probs=37.9
Q ss_pred cccccCCCCCCceeee-ccccccCCCceEEEEEccCCCCCCeeEEeecCCCC
Q 046120 209 ASFFNHDCLPNACRFD-YVDAAAENNTDIIVRMIHDVPQGREICLSYFPVNY 259 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~~~-~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~~ 259 (381)
+=++||||.||+.++. +.+.....-.++.+.|+++|++|+|||..|+....
T Consensus 273 ~RfinHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~ 324 (364)
T KOG1082|consen 273 ARFINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYK 324 (364)
T ss_pred cccccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhccccc
Confidence 4578999999998532 21211112357889999999999999999998754
No 10
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=97.07 E-value=0.00027 Score=73.49 Aligned_cols=63 Identities=22% Similarity=0.336 Sum_probs=45.7
Q ss_pred cccccCCCCCCcee-eeccccccCCCceEEEEEccCCCCCCeeEEeecCCCCCHHHHHHHHhcCCCeeeeCc
Q 046120 209 ASFFNHDCLPNACR-FDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVNYDYSTRQKRLLYDYDFACDCD 279 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~-~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~~~~~~Rr~~L~~~y~F~C~C~ 279 (381)
+-++||||.||+.. ..|+|+.+-+-.-+.+.|.+-|++|.|||..|....-.+. .+-..|.|-
T Consensus 1190 GRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~--------~keL~C~CG 1253 (1262)
T KOG1141|consen 1190 GRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVA--------TKELTCHCG 1253 (1262)
T ss_pred hhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccc--------cceEEEecC
Confidence 45899999999873 2366765434456678899999999999999998753332 244678874
No 11
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=96.77 E-value=0.0022 Score=65.54 Aligned_cols=95 Identities=18% Similarity=0.142 Sum_probs=65.6
Q ss_pred CCHHHHHHHHHHhhccccccccCCcCCCCCCccceeEEeccccccccCCCCCCceeeeccccccCCCceEEEEEccCCCC
Q 046120 167 TTIELTAALLAKDRLNAFGLMEPYIEGQDGRRSVRAYGIYLKASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQ 246 (381)
Q Consensus 167 ~~~~~i~~ll~~l~~Nsf~i~~~~~~~~~~~~~~~g~gLyp~~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~ 246 (381)
++.+.+......+...+|.+....+.. ......-.+|.|..-++||++.+.... +.. .+..+.+++.++|++
T Consensus 197 ~~~~~~~w~~~~~~sr~~~~~~~~~~~--~~~~~~~~~L~P~~D~~NH~~~~~~~~--~~~----~d~~~~l~~~~~v~~ 268 (472)
T KOG1337|consen 197 FTFSAFKWAYSIVNSRAFYLPSLQRLT--AGDPDDNEALAPLIDLLNHSPEVIKAG--YNQ----EDEAVELVAERDVSA 268 (472)
T ss_pred cchHHHHHHHHHHhhhhhccccccccc--cCCCCcchhhhhhHHhhccCchhcccc--ccC----CCCcEEEEEeeeecC
Confidence 555666677777777777665432100 011123358999999999999994432 211 234889999999999
Q ss_pred CCeeEEeecCCCCCHHHHHHHHhcCCCee
Q 046120 247 GREICLSYFPVNYDYSTRQKRLLYDYDFA 275 (381)
Q Consensus 247 GeEl~isY~~~~~~~~~Rr~~L~~~y~F~ 275 (381)
||||+|+|++.. - ..|...|||.
T Consensus 269 geevfi~YG~~~--N----~eLL~~YGFv 291 (472)
T KOG1337|consen 269 GEEVFINYGPKS--N----AELLLHYGFV 291 (472)
T ss_pred CCeEEEecCCCc--h----HHHHHhcCCC
Confidence 999999999943 2 2367789997
No 12
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.62 E-value=0.016 Score=56.30 Aligned_cols=86 Identities=15% Similarity=0.060 Sum_probs=61.5
Q ss_pred CCCHHHHHHHHHHhhccccccccCCcCC---CCCCccceeEEeccccccccCC---CCCCceeeeccccccCCCceEEEE
Q 046120 166 STTIELTAALLAKDRLNAFGLMEPYIEG---QDGRRSVRAYGIYLKASFFNHD---CLPNACRFDYVDAAAENNTDIIVR 239 (381)
Q Consensus 166 ~~~~~~i~~ll~~l~~Nsf~i~~~~~~~---~~~~~~~~g~gLyp~~Sl~NHS---C~PN~~~~~~~d~~~~~~~~l~vr 239 (381)
.++.+.++.+.+.+..=+|.|.-..+.. ...+....|-..-|.+-++||. |..|.. + ..+.+.++
T Consensus 173 ~~slEdF~y~~Al~laysfdve~~~s~~~~eee~e~e~ngk~m~p~ad~lNhd~~k~nanl~---y------~~NcL~mv 243 (466)
T KOG1338|consen 173 RPSLEDFMYAYALGLAYSFDVEFLLSLDNLEEESEIECNGKLMTPIADFLNHDGLKANANLR---Y------EDNCLEMV 243 (466)
T ss_pred ccCHHHHHHHHHHHHHHheeeehhcchhhhhhhhccccCcccccchhhhhccchhhccccee---c------cCcceeee
Confidence 4677888888888877788765331111 0122345678889999999996 555542 3 35788999
Q ss_pred EccCCCCCCeeEEeecCCCCC
Q 046120 240 MIHDVPQGREICLSYFPVNYD 260 (381)
Q Consensus 240 A~r~I~~GeEl~isY~~~~~~ 260 (381)
|.|+|++|+|++.+|+-..++
T Consensus 244 a~r~iekgdev~n~dg~~p~~ 264 (466)
T KOG1338|consen 244 ADRNIEKGDEVDNSDGLKPMG 264 (466)
T ss_pred ecCCCCCccccccccccCcch
Confidence 999999999999999855444
No 13
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=96.52 E-value=0.0017 Score=60.21 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=37.9
Q ss_pred cccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecCCC
Q 046120 209 ASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVN 258 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~ 258 (381)
.-|+|||=.+|+..- .++. ++...|++.|.|+|.+||||+..|+|-.
T Consensus 334 GRLINHS~~gNl~TK-vv~I--dg~pHLiLvA~rdIa~GEELlYDYGDRS 380 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTK-VVEI--DGSPHLILVARRDIAQGEELLYDYGDRS 380 (392)
T ss_pred hhhhcccccCcceee-EEEe--cCCceEEEEeccccccchhhhhhccccc
Confidence 348999999998731 2222 2567999999999999999999999964
No 14
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=95.66 E-value=0.0021 Score=59.79 Aligned_cols=44 Identities=25% Similarity=0.654 Sum_probs=37.1
Q ss_pred CcccccccccccCCCCCccCCCCCCC-cCccccchhhhhcCCchhhhHhH
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSHSPYVCQAL 97 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H~~~EC~~l 97 (381)
....|+.|..+- ...+|+.|+.+ ||+++||+..| ..| +-.|..|
T Consensus 318 d~~fCstCG~~g---a~KrCs~CKav~YCdqeCQk~hW-f~H-KK~C~~L 362 (396)
T KOG1710|consen 318 DCQFCSTCGHPG---AKKRCSQCKAVAYCDQECQKFHW-FIH-KKVCSFL 362 (396)
T ss_pred ecccccccCCCC---ccchhhhhHHHHHHHHHHHHhhh-HHH-HHHHHHH
Confidence 456788887763 46899999988 99999999999 788 7889877
No 15
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=95.65 E-value=0.0095 Score=64.01 Aligned_cols=45 Identities=27% Similarity=0.507 Sum_probs=34.6
Q ss_pred cccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecC
Q 046120 209 ASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFP 256 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~ 256 (381)
+-+.||||.||+.-..| ..+ +-.++.|.|.|||.+||||+.-|--
T Consensus 1251 ~RfinhscKPNc~~qkw-SVN--G~~Rv~L~A~rDi~kGEELtYDYN~ 1295 (1306)
T KOG1083|consen 1251 ARFINHSCKPNCEMQKW-SVN--GEYRVGLFALRDLPKGEELTYDYNF 1295 (1306)
T ss_pred ccccccccCCCCccccc-ccc--ceeeeeeeecCCCCCCceEEEeccc
Confidence 34679999999884333 111 3468899999999999999999854
No 16
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=95.31 E-value=0.011 Score=41.38 Aligned_cols=46 Identities=22% Similarity=0.553 Sum_probs=34.9
Q ss_pred ccccccccCCCCCccCCCCCCC-cCccccchhhhhcCCchhhhHhHHHh
Q 046120 53 CHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSHSPYVCQALTRL 100 (381)
Q Consensus 53 C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H~~~EC~~l~~~ 100 (381)
|..|.........+.||.|+++ |||++=...+. .+| +..|..|+..
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~-e~H-~~~c~~LRqv 48 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDY-EEH-RQLCERLRQV 48 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccCHHHHHHhH-HHH-HHHHHHHHHh
Confidence 6666665544457899999999 99987766664 678 6689988764
No 17
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=93.68 E-value=0.065 Score=55.39 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=35.7
Q ss_pred cccccCCCCCCcee-eeccccccCCCceEEEEEccCCCCCCeeEEeecCC
Q 046120 209 ASFFNHDCLPNACR-FDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPV 257 (381)
Q Consensus 209 ~Sl~NHSC~PN~~~-~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~ 257 (381)
+-+.|||=.||+-. +.++. +..+|-|+|.|.|.+|||||..|...
T Consensus 666 ~rFANHS~nPNCYAkvm~V~----GdhRIGifAkRaIeagEELffDYrYs 711 (739)
T KOG1079|consen 666 IRFANHSFNPNCYAKVMMVA----GDHRIGIFAKRAIEAGEELFFDYRYS 711 (739)
T ss_pred hhhccCCCCCCcEEEEEEec----CCcceeeeehhhcccCceeeeeeccC
Confidence 45679999999873 32332 35678899999999999999999864
No 18
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=90.05 E-value=0.075 Score=32.49 Aligned_cols=27 Identities=30% Similarity=0.873 Sum_probs=18.9
Q ss_pred ccccccccccCCCCCccCCCCCCCcCccccc
Q 046120 51 SFCHNCFRKTMHSSSSICPSCSVAFCSPKCS 81 (381)
Q Consensus 51 ~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~ 81 (381)
..|..|.. . ..+.|++|+..|||-+|.
T Consensus 3 ~~C~vC~~-~---~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 3 KLCSVCGN-P---AKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EEETSSSS-E---ESEE-TTT--EESSHHHH
T ss_pred CCCccCcC-C---CEEECCCcCCceeCcEeE
Confidence 46777776 2 478999999999999885
No 19
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=89.95 E-value=0.12 Score=42.98 Aligned_cols=31 Identities=32% Similarity=0.819 Sum_probs=25.6
Q ss_pred cccccccccccCCCCCccCCCCCCCcCccccchh
Q 046120 50 SSFCHNCFRKTMHSSSSICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 50 ~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~~ 83 (381)
...|.-|++.. ..++||.|..+|||-.|.+.
T Consensus 5 t~tC~ic~e~~---~KYKCpkC~vPYCSl~CfKi 35 (157)
T KOG2857|consen 5 TTTCVICLESE---IKYKCPKCSVPYCSLPCFKI 35 (157)
T ss_pred eeeehhhhcch---hhccCCCCCCccccchhhhh
Confidence 46788888754 37899999999999999854
No 20
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=88.79 E-value=0.46 Score=44.46 Aligned_cols=34 Identities=21% Similarity=0.414 Sum_probs=29.8
Q ss_pred CCCCCceEEEEeCCCccEEEEcccCCCCcEEEEc
Q 046120 2 SAVSETVTVAEIEGRGRGLVSTQSLKAGQIVLRD 35 (381)
Q Consensus 2 ~~~s~~i~v~~~~~~GRglvAtrdi~~GevIl~e 35 (381)
.+..+++.+....++||||+|++.++.||-|.+-
T Consensus 252 ~g~~egl~~~~~dgKGRGv~a~~~F~rgdFVVEY 285 (392)
T KOG1085|consen 252 KGTNEGLLEVYKDGKGRGVRAKVNFERGDFVVEY 285 (392)
T ss_pred hccccceeEEeeccccceeEeecccccCceEEEE
Confidence 3566889999999999999999999999988754
No 21
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=85.13 E-value=0.38 Score=48.94 Aligned_cols=54 Identities=22% Similarity=0.276 Sum_probs=39.3
Q ss_pred eEEeccccc-cccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecCCC
Q 046120 202 AYGIYLKAS-FFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVN 258 (381)
Q Consensus 202 g~gLyp~~S-l~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~ 258 (381)
-.+.+...| ++||||.||+..-.+.. -....+.+.|.+.|+.|+|+|.+|.-.-
T Consensus 364 d~~~~~n~sr~~nh~~~~~v~~~k~~~---~~~t~~~~~a~~~i~~g~e~t~~~n~~~ 418 (463)
T KOG1081|consen 364 DAGPKGNYSRFLNHSCQPNVETEKWQV---IGDTRVGLFAPRQIEAGEELTFNYNGNC 418 (463)
T ss_pred ccccccchhhhhcccCCCceeechhhe---ecccccccccccccccchhhhheeeccc
Confidence 345566554 57999999997321110 1346788999999999999999998764
No 22
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=84.42 E-value=0.44 Score=31.15 Aligned_cols=32 Identities=31% Similarity=0.621 Sum_probs=17.7
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
++|.+ |.++|-|.-..+... ..|.|+.|+...
T Consensus 3 ~rC~~--C~aylNp~~~~~~~~-~~w~C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRR--CRAYLNPFCQFDDGG-KTWICNFCGTKN 34 (40)
T ss_dssp -B-TT--T--BS-TTSEEETTT-TEEEETTT--EE
T ss_pred cccCC--CCCEECCcceEcCCC-CEEECcCCCCcC
Confidence 57876 889988776554432 479999999753
No 23
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=81.87 E-value=1 Score=29.78 Aligned_cols=37 Identities=22% Similarity=0.435 Sum_probs=22.7
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCcccccCccCC
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDAIGRED 375 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~~~~~~ 375 (381)
|+||. |++..+-.++.. ....|..||.++.+..+.++
T Consensus 1 m~Cp~--Cg~~~~~~D~~~----g~~vC~~CG~Vl~e~~i~~~ 37 (43)
T PF08271_consen 1 MKCPN--CGSKEIVFDPER----GELVCPNCGLVLEENIIDEG 37 (43)
T ss_dssp ESBTT--TSSSEEEEETTT----TEEEETTT-BBEE-TTBSCC
T ss_pred CCCcC--CcCCceEEcCCC----CeEECCCCCCEeecccccCC
Confidence 57987 654322233222 46899999999998877654
No 24
>PLN03158 methionine aminopeptidase; Provisional
Probab=79.40 E-value=0.61 Score=46.56 Aligned_cols=36 Identities=44% Similarity=0.809 Sum_probs=27.8
Q ss_pred CcccccccccccCCCCCccCCCCCC-------C-cCccccchhhhhcCC
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSV-------A-FCSPKCSTAAASSSH 89 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~-------~-yCS~~C~~~a~~~~H 89 (381)
....|..|.+. ..+.||.|.. . |||++|.+.+| ..|
T Consensus 8 ~~~~c~~c~~~----a~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w-~~H 51 (396)
T PLN03158 8 SPLACARCSKP----AHLQCPKCLELKLPREGASFCSQDCFKAAW-SSH 51 (396)
T ss_pred CcccccCCCCc----ccccCccchhcCCCCCCceeECHHHHHHHH-HHH
Confidence 45569999874 3478998864 4 99999999999 455
No 25
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=76.05 E-value=1.1 Score=32.05 Aligned_cols=27 Identities=30% Similarity=0.641 Sum_probs=20.6
Q ss_pred cccccccccccCCCCCccCCCCCCCcCccccchhhh
Q 046120 50 SSFCHNCFRKTMHSSSSICPSCSVAFCSPKCSTAAA 85 (381)
Q Consensus 50 ~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~~a~ 85 (381)
..+|..|.+++++ ...|||++|++..+
T Consensus 3 HkHC~~CG~~Ip~---------~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 3 HKHCPVCGKPIPP---------DESFCSPKCREEYR 29 (59)
T ss_pred CCcCCcCCCcCCc---------chhhhCHHHHHHHH
Confidence 4689999888873 23499999998754
No 26
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=76.02 E-value=1.3 Score=28.00 Aligned_cols=32 Identities=25% Similarity=0.548 Sum_probs=20.7
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCcccccC
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDAI 371 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~~ 371 (381)
.||. |++.|.|...... .. .|..|+.....++
T Consensus 3 FCp~--C~nlL~p~~~~~~---~~-~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 3 FCPE--CGNLLYPKEDKEK---RV-ACRTCGYEEPISQ 34 (35)
T ss_dssp BETT--TTSBEEEEEETTT---TE-EESSSS-EEE-SS
T ss_pred eCCC--CCccceEcCCCcc---Cc-CCCCCCCccCCCC
Confidence 3887 8999987643321 23 8999998876554
No 27
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=74.61 E-value=2.1 Score=30.39 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=11.7
Q ss_pred cEEEEcccCCCCcEE
Q 046120 18 RGLVSTQSLKAGQIV 32 (381)
Q Consensus 18 RglvAtrdi~~GevI 32 (381)
+.+||+++|++|++|
T Consensus 2 ~vvVA~~di~~G~~i 16 (63)
T PF08666_consen 2 RVVVAARDIPAGTVI 16 (63)
T ss_dssp SEEEESSTB-TT-BE
T ss_pred cEEEEeCccCCCCEE
Confidence 468999999999998
No 28
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=74.28 E-value=1.7 Score=41.15 Aligned_cols=32 Identities=31% Similarity=0.676 Sum_probs=25.9
Q ss_pred CcccccccccccCCCCCccCCCCCCCcCccccchh
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~~ 83 (381)
....|+-|..... .+.||+|+..|||-.|.+.
T Consensus 6 ~~~~C~ic~vq~~---~YtCPRCn~~YCsl~CYr~ 37 (383)
T KOG4317|consen 6 SFLACGICGVQKR---EYTCPRCNLLYCSLKCYRN 37 (383)
T ss_pred ceeeccccccccc---cccCCCCCccceeeeeecC
Confidence 4567888877654 4899999999999999854
No 29
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=70.65 E-value=6 Score=31.27 Aligned_cols=26 Identities=35% Similarity=0.485 Sum_probs=23.1
Q ss_pred CceEEEEEccCCCCCCeeEEeecCCC
Q 046120 233 NTDIIVRMIHDVPQGREICLSYFPVN 258 (381)
Q Consensus 233 ~~~l~vrA~r~I~~GeEl~isY~~~~ 258 (381)
...+.+...++|..|++++++|.++.
T Consensus 74 ~ktVTLTL~~~V~~Gq~VTVsYt~ps 99 (101)
T TIGR02059 74 NTTITLTLAQVVEDGDEVTLSYTKNS 99 (101)
T ss_pred ccEEEEEecccccCCCEEEEEeeCCC
Confidence 34889999999999999999999874
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.17 E-value=3.2 Score=27.80 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=21.1
Q ss_pred hhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 331 MRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 331 ~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.-|+|++ |+..+. +++.. ..+.|+.||....
T Consensus 2 ~~y~C~~--CG~~~~-~~~~~----~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCAR--CGREVE-LDEYG----TGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCC--CCCEEE-ECCCC----CceECCCCCCeEE
Confidence 3488987 877664 43332 2589999997654
No 31
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=68.96 E-value=3.4 Score=24.31 Aligned_cols=23 Identities=30% Similarity=0.791 Sum_probs=17.7
Q ss_pred cccccccccCCCCCccCCCCCCCc
Q 046120 52 FCHNCFRKTMHSSSSICPSCSVAF 75 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~~y 75 (381)
.|-.|.+.++ .....||.|+..|
T Consensus 2 ~CP~C~~~V~-~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVP-ESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCch-hhcCcCCCCCCCC
Confidence 5788888877 4567899998764
No 32
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=68.50 E-value=2.6 Score=30.35 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=9.2
Q ss_pred CcCccccchhh
Q 046120 74 AFCSPKCSTAA 84 (381)
Q Consensus 74 ~yCS~~C~~~a 84 (381)
+|||+.|+..+
T Consensus 26 PFCS~RCk~ID 36 (62)
T PRK00418 26 PFCSKRCQLID 36 (62)
T ss_pred CcccHHHHhhh
Confidence 49999999775
No 33
>PRK01343 zinc-binding protein; Provisional
Probab=68.16 E-value=3 Score=29.50 Aligned_cols=11 Identities=36% Similarity=1.011 Sum_probs=9.3
Q ss_pred CcCccccchhh
Q 046120 74 AFCSPKCSTAA 84 (381)
Q Consensus 74 ~yCS~~C~~~a 84 (381)
+|||+.|+..+
T Consensus 25 PFCS~RC~~iD 35 (57)
T PRK01343 25 PFCSERCRDID 35 (57)
T ss_pred cccCHHHhhhh
Confidence 39999999775
No 34
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=67.83 E-value=2 Score=29.69 Aligned_cols=30 Identities=30% Similarity=0.866 Sum_probs=17.6
Q ss_pred cccccccccCCC-------CCccCCCCCCCcCccccch
Q 046120 52 FCHNCFRKTMHS-------SSSICPSCSVAFCSPKCST 82 (381)
Q Consensus 52 ~C~~C~~~~~~~-------~~~~C~~C~~~yCS~~C~~ 82 (381)
.|..|.++++.. ..++|++|+..|| -+|-.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC-~dCD~ 37 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFC-IDCDV 37 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B--HHHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccc-cCcCh
Confidence 378888888743 3589999999999 47754
No 35
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.81 E-value=1.1 Score=45.47 Aligned_cols=42 Identities=24% Similarity=0.661 Sum_probs=30.4
Q ss_pred CcccccccccccCCCCCccCCCCCCC-cCccccchhhhhcCCchhhhHhHH
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSHSPYVCQALT 98 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H~~~EC~~l~ 98 (381)
...=|.+|.+.. .+.| |.-. |||-+||+..| ..| +.-|..-+
T Consensus 526 kKQWC~nC~~EA----iy~C--CWNTSYCsveCQQ~HW-~~H-~ksCrrk~ 568 (588)
T KOG3612|consen 526 KKQWCYNCLDEA----IYHC--CWNTSYCSVECQQGHW-PEH-RKSCRRKK 568 (588)
T ss_pred HHHHHHhhhHHH----HHHh--hccccccCcchhhccc-hhH-hhhhcccC
Confidence 456788998743 3443 4555 99999999999 588 77886443
No 36
>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=67.03 E-value=2.1 Score=30.33 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=9.4
Q ss_pred CcCccccchhh
Q 046120 74 AFCSPKCSTAA 84 (381)
Q Consensus 74 ~yCS~~C~~~a 84 (381)
+|||+.|+..+
T Consensus 22 PFCS~RCk~iD 32 (57)
T PF03884_consen 22 PFCSERCKLID 32 (57)
T ss_dssp SSSSHHHHHHH
T ss_pred CcccHhhcccC
Confidence 39999999876
No 37
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.95 E-value=2.5 Score=30.45 Aligned_cols=11 Identities=36% Similarity=0.978 Sum_probs=8.9
Q ss_pred CcCccccchhh
Q 046120 74 AFCSPKCSTAA 84 (381)
Q Consensus 74 ~yCS~~C~~~a 84 (381)
+|||+.|+..+
T Consensus 27 PFCSkRCklID 37 (65)
T COG3024 27 PFCSKRCKLID 37 (65)
T ss_pred cchhHhhhhcc
Confidence 38999999765
No 38
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=63.79 E-value=4.7 Score=40.23 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=23.9
Q ss_pred CCceEEEEEccCCCCCCeeEEeecCC
Q 046120 232 NNTDIIVRMIHDVPQGREICLSYFPV 257 (381)
Q Consensus 232 ~~~~l~vrA~r~I~~GeEl~isY~~~ 257 (381)
.+..|.++|+|+|++||||.+=|++.
T Consensus 120 ~~~~Ifyrt~r~I~p~eELlVWY~~e 145 (396)
T KOG2461|consen 120 IGENIFYRTIRDIRPNEELLVWYGSE 145 (396)
T ss_pred ccCceEEEecccCCCCCeEEEEeccc
Confidence 46889999999999999999999985
No 39
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.80 E-value=7.3 Score=41.03 Aligned_cols=30 Identities=30% Similarity=0.438 Sum_probs=27.2
Q ss_pred CceEEEEeCCCccEEEEcccCCCCcEEEEc
Q 046120 6 ETVTVAEIEGRGRGLVSTQSLKAGQIVLRD 35 (381)
Q Consensus 6 ~~i~v~~~~~~GRglvAtrdi~~GevIl~e 35 (381)
-+++|..++.+|-||.|..||++|+-|++=
T Consensus 120 A~vevF~Te~KG~GLRA~~dI~~g~FI~EY 149 (729)
T KOG4442|consen 120 AKVEVFLTEKKGCGLRAEEDIPKGQFILEY 149 (729)
T ss_pred CceeEEEecCcccceeeccccCCCcEEeee
Confidence 368999999999999999999999999863
No 40
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=57.30 E-value=7 Score=25.33 Aligned_cols=24 Identities=33% Similarity=0.805 Sum_probs=18.2
Q ss_pred ccccccccCCCCCccCCCCCCCcCc
Q 046120 53 CHNCFRKTMHSSSSICPSCSVAFCS 77 (381)
Q Consensus 53 C~~C~~~~~~~~~~~C~~C~~~yCS 77 (381)
|+.|-+.... .++.|..|+..||+
T Consensus 1 C~~C~~~~~l-~~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGL-TGFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccc-cCeECCccCCcccc
Confidence 5667776552 27889999999996
No 41
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=56.97 E-value=3.9 Score=25.88 Aligned_cols=19 Identities=32% Similarity=0.716 Sum_probs=14.9
Q ss_pred CCCC-cCccccchhhhhcCC
Q 046120 71 CSVA-FCSPKCSTAAASSSH 89 (381)
Q Consensus 71 C~~~-yCS~~C~~~a~~~~H 89 (381)
|..+ |||..|.+++-..+|
T Consensus 6 cpkiGYCS~~CsKt~vWa~s 25 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVWAFS 25 (39)
T ss_pred Ccccceecccccccceeeec
Confidence 6678 999999988644666
No 42
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=56.37 E-value=7.6 Score=22.41 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=13.7
Q ss_pred ccccccccCCC---CCccCCCCCC
Q 046120 53 CHNCFRKTMHS---SSSICPSCSV 73 (381)
Q Consensus 53 C~~C~~~~~~~---~~~~C~~C~~ 73 (381)
|..|...+.+. ..+.||+|++
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 55666655532 3578999974
No 43
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=53.13 E-value=7 Score=37.44 Aligned_cols=40 Identities=33% Similarity=0.692 Sum_probs=29.9
Q ss_pred CcccccccccccCCCCCccCCCCCCCcCccccchhhhhcCC
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVAFCSPKCSTAAASSSH 89 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~~a~~~~H 89 (381)
....|..|+..+.+...++|..|+.+||. .|-.-.-.+.|
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCl-dCDv~iHesLh 368 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCL-DCDVFIHESLH 368 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeec-cchHHHHhhhh
Confidence 56679999776665668999999999996 78755433444
No 44
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=53.11 E-value=6.2 Score=29.48 Aligned_cols=26 Identities=35% Similarity=0.780 Sum_probs=13.3
Q ss_pred CcccccccccccCCCCCccCCCCCCC
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA 74 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~ 74 (381)
....|+.||+........-||.|+..
T Consensus 8 ~vlrC~aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 8 WVLRCHACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp EEEE-SSS--EES-SS--S-SSS--S
T ss_pred eeEEccccccCcCCCCceeCcccCCC
Confidence 45689999998886667889888864
No 45
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=52.94 E-value=7.5 Score=28.26 Aligned_cols=35 Identities=29% Similarity=0.562 Sum_probs=23.5
Q ss_pred hHhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 328 YFFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 328 ~~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+|.+++|+. |++...-... . ++...|..||.++-
T Consensus 15 s~Fl~VkCpd--C~N~q~vFsh-a---st~V~C~~CG~~l~ 49 (67)
T COG2051 15 SRFLRVKCPD--CGNEQVVFSH-A---STVVTCLICGTTLA 49 (67)
T ss_pred ceEEEEECCC--CCCEEEEecc-C---ceEEEecccccEEE
Confidence 4789999997 7644332211 1 25789999998753
No 46
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=52.65 E-value=7.6 Score=27.66 Aligned_cols=35 Identities=29% Similarity=0.554 Sum_probs=23.5
Q ss_pred hHhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 328 YFFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 328 ~~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+|.+++|+. |.....-..- . ++...|..||....
T Consensus 7 S~F~~VkCp~--C~n~q~vFsh-a---~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 7 SRFLKVKCPD--CGNEQVVFSH-A---STVVRCLVCGKTLA 41 (59)
T ss_pred CeEEEEECCC--CCCeEEEEec-C---CcEEECcccCCCcc
Confidence 4789999997 7644321211 1 25689999998874
No 47
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=51.38 E-value=5 Score=33.74 Aligned_cols=30 Identities=30% Similarity=0.758 Sum_probs=25.5
Q ss_pred CcccccccccccCCCCCccCCCCCCCcCccccch
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVAFCSPKCST 82 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~ 82 (381)
....|.-|.- .+.+.|..|+-.|||..|..
T Consensus 117 ~r~fCaVCG~----~S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 117 LRKFCAVCGY----DSKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred cchhhhhcCC----CchhHHHhcCCceeechhhh
Confidence 6779999982 25789999999999999984
No 48
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=51.12 E-value=8.7 Score=30.69 Aligned_cols=19 Identities=32% Similarity=0.924 Sum_probs=16.3
Q ss_pred CccCCCCCCCcCccccchh
Q 046120 65 SSICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 65 ~~~C~~C~~~yCS~~C~~~ 83 (381)
.++|+.|+..-|+.+|+..
T Consensus 74 ~~PC~~C~S~KCG~~CR~n 92 (103)
T PF14949_consen 74 HYPCPKCGSRKCGPECRCN 92 (103)
T ss_pred cccCCCCCCCccChhhCcC
Confidence 4689999999999999754
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=50.81 E-value=13 Score=25.18 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=19.5
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCcccc
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKND 369 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~ 369 (381)
.||. |+..|.+. ..+.+ ..|.|..||.....
T Consensus 2 FCp~--Cg~~l~~~-~~~~~--~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPK--CGNMLIPK-EGKEK--RRFVCRKCGYEEPI 32 (52)
T ss_pred CCCC--CCCccccc-cCCCC--CEEECCcCCCeEEC
Confidence 3886 87777543 22211 26999999987543
No 50
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=50.63 E-value=9.9 Score=26.74 Aligned_cols=17 Identities=29% Similarity=0.563 Sum_probs=13.9
Q ss_pred cEEEEcccCCCCcEEEE
Q 046120 18 RGLVSTQSLKAGQIVLR 34 (381)
Q Consensus 18 RglvAtrdi~~GevIl~ 34 (381)
+-+||+++|++|++|-.
T Consensus 2 ~v~va~~~i~~G~~i~~ 18 (64)
T smart00858 2 RVVVAARDLPAGEVITA 18 (64)
T ss_pred CEEEEeCccCCCCCcch
Confidence 46889999999998864
No 51
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=50.24 E-value=5.3 Score=27.23 Aligned_cols=27 Identities=19% Similarity=0.764 Sum_probs=13.9
Q ss_pred CcccccccccccCCCCCccCCCCCCCc
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVAF 75 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~y 75 (381)
...+|..|+..+.....-+||+|+.+|
T Consensus 21 gf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 21 GFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp S----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 678999999887743456899998775
No 52
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=47.94 E-value=6.4 Score=26.17 Aligned_cols=30 Identities=17% Similarity=0.494 Sum_probs=20.7
Q ss_pred cccccccccccCCCCCccCCCCCCC-cCccccchhhhh
Q 046120 50 SSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAAS 86 (381)
Q Consensus 50 ~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~ 86 (381)
...|..|-+.+.. .-... |||++|+..++.
T Consensus 6 ~~yC~~Cdk~~~~-------~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 6 NDYCIVCDKQIDP-------PDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hhHHHHhhccccC-------CCCCccccCHHHHhHhhh
Confidence 4578888877631 11334 999999988764
No 53
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=45.88 E-value=16 Score=31.13 Aligned_cols=32 Identities=25% Similarity=0.686 Sum_probs=22.1
Q ss_pred ccCCCCcceeeecCCCCCCC----------CCceeeeCCccCcc
Q 046120 334 MCDRDNCWGTLAPLPPSDAT----------PSTVMECNVCGNLK 367 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~----------~~~~~~C~~C~~~~ 367 (381)
+|+. |+|.|.|+++.+-. ....|+|+.||+..
T Consensus 93 RC~~--CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 93 RCPK--CNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred ccCC--CCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 7987 88998887543110 01369999999864
No 54
>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=45.69 E-value=8.4 Score=25.37 Aligned_cols=31 Identities=26% Similarity=0.576 Sum_probs=17.7
Q ss_pred cccccccccccCCCCCccCCCCC-CC-cCccccch
Q 046120 50 SSFCHNCFRKTMHSSSSICPSCS-VA-FCSPKCST 82 (381)
Q Consensus 50 ~~~C~~C~~~~~~~~~~~C~~C~-~~-yCS~~C~~ 82 (381)
...|..|.+++.-.. .=..|- .+ |||+.|+.
T Consensus 8 ~K~C~~C~rpf~WRK--KW~~~Wd~VkYCS~rCR~ 40 (42)
T PF10013_consen 8 SKICPVCGRPFTWRK--KWARCWDEVKYCSDRCRR 40 (42)
T ss_pred CCcCcccCCcchHHH--HHHHhchhhccHHHHhcc
Confidence 457888877765110 001122 25 99999985
No 55
>TIGR03586 PseI pseudaminic acid synthase.
Probab=45.19 E-value=13 Score=36.10 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=18.4
Q ss_pred CccEEEEcccCCCCcEEEEcC
Q 046120 16 RGRGLVSTQSLKAGQIVLRDS 36 (381)
Q Consensus 16 ~GRglvAtrdi~~GevIl~e~ 36 (381)
..|.|||+|||++|++|=.+.
T Consensus 274 ~rrsl~a~~di~~G~~it~~~ 294 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEEN 294 (327)
T ss_pred eeEEEEEccCcCCCCEecHHh
Confidence 479999999999999987665
No 56
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.01 E-value=18 Score=24.07 Aligned_cols=28 Identities=25% Similarity=0.640 Sum_probs=18.4
Q ss_pred hcccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 332 RYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 332 ~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
.|.|.+ |+..+- +.+. ...+|..||..+
T Consensus 2 ~Y~C~~--Cg~~~~-~~~~-----~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGE--CGRENE-IKSK-----DVVRCRECGYRI 29 (44)
T ss_pred EEECCC--CCCEee-cCCC-----CceECCCCCceE
Confidence 478987 765553 3322 248999999764
No 57
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=43.58 E-value=19 Score=29.35 Aligned_cols=32 Identities=22% Similarity=0.588 Sum_probs=23.4
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCccccc
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDA 370 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~ 370 (381)
.|+. |+++|+|-..... ..++|.+||.....+
T Consensus 4 FCp~--Cgsll~p~~~~~~---~~l~C~kCgye~~~~ 35 (113)
T COG1594 4 FCPK--CGSLLYPKKDDEG---GKLVCRKCGYEEEAS 35 (113)
T ss_pred ccCC--ccCeeEEeEcCCC---cEEECCCCCcchhcc
Confidence 3887 8999987643222 469999999877655
No 58
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=42.87 E-value=8.9 Score=27.10 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=18.1
Q ss_pred cccccccccccCCCCCccCCCCCCCcCccccchh
Q 046120 50 SSFCHNCFRKTMHSSSSICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 50 ~~~C~~C~~~~~~~~~~~C~~C~~~yCS~~C~~~ 83 (381)
..+|.-|.+.++. +..+||++|+..
T Consensus 8 H~HC~VCg~aIp~---------de~~CSe~C~ei 32 (64)
T COG4068 8 HRHCVVCGKAIPP---------DEQVCSEECGEI 32 (64)
T ss_pred CccccccCCcCCC---------ccchHHHHHHHH
Confidence 4688888888773 234899999843
No 59
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=42.60 E-value=14 Score=24.73 Aligned_cols=35 Identities=20% Similarity=0.632 Sum_probs=27.0
Q ss_pred cccccccccCCCCCccCCCCCCC-cCccccchhhhhcCC
Q 046120 52 FCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAAASSSH 89 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a~~~~H 89 (381)
.|+.|.+++. ...+.|..|... .| .+|..... ..|
T Consensus 2 ~C~~C~~~i~-g~r~~C~~C~d~dLC-~~Cf~~~~-~~H 37 (46)
T cd02249 2 SCDGCLKPIV-GVRYHCLVCEDFDLC-SSCYAKGK-KGH 37 (46)
T ss_pred CCcCCCCCCc-CCEEECCCCCCCcCH-HHHHCcCc-CCC
Confidence 5999999776 367899999988 99 48877653 344
No 60
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=42.16 E-value=15 Score=24.96 Aligned_cols=32 Identities=22% Similarity=0.620 Sum_probs=25.7
Q ss_pred cccccccccCCCCCccCCCCCCC-cCccccchhh
Q 046120 52 FCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAA 84 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a 84 (381)
.|++|.+.+.....+.|..|... .| .+|....
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC-~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLC-LECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchh-HHhhhCc
Confidence 69999998875467899999888 99 4887654
No 61
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=42.05 E-value=16 Score=25.55 Aligned_cols=31 Identities=16% Similarity=0.398 Sum_probs=15.0
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
.||..+|.+++.... .... ..+.|..|+...
T Consensus 20 ~Cp~~~C~~~~~~~~-~~~~--~~~~C~~C~~~f 50 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDD-GCNS--PIVTCPSCGTEF 50 (64)
T ss_dssp --TTSST---ECS-S-STTS----CCTTSCCSEE
T ss_pred CCCCCCCcccEEecC-CCCC--CeeECCCCCCcC
Confidence 899999988876433 2221 137788887643
No 62
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=41.80 E-value=15 Score=25.07 Aligned_cols=27 Identities=30% Similarity=0.714 Sum_probs=18.1
Q ss_pred cccCCCCcc-eeeecCCCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCW-GTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~-g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
=.||+ |+ |++.. +-.+ -|.|-.||.+.
T Consensus 20 ~~CPr--CG~gvfmA-~H~d-----R~~CGkCgyTe 47 (51)
T COG1998 20 RFCPR--CGPGVFMA-DHKD-----RWACGKCGYTE 47 (51)
T ss_pred ccCCC--CCCcchhh-hcCc-----eeEeccccceE
Confidence 35998 76 67652 2222 49999999764
No 63
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=41.70 E-value=11 Score=26.73 Aligned_cols=35 Identities=29% Similarity=0.460 Sum_probs=23.0
Q ss_pred CcccccccccccCCCCCccCCCCCCC-cCccccchhh
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAA 84 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a 84 (381)
-...|..|-+.|....- ..---+.. |||.+|+...
T Consensus 15 FL~~C~~C~k~L~~~~D-iymYrGd~aFCS~ECR~~q 50 (58)
T PF04570_consen 15 FLSFCYLCKKKLDPGKD-IYMYRGDKAFCSEECRSQQ 50 (58)
T ss_pred HHHHHHccCCCCCCCCC-eeeeccccccccHHHHHHH
Confidence 45689999999873211 11123555 9999999764
No 64
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.34 E-value=16 Score=20.72 Aligned_cols=21 Identities=29% Similarity=0.929 Sum_probs=14.3
Q ss_pred cccccccccCCCCCccCCCCCC
Q 046120 52 FCHNCFRKTMHSSSSICPSCSV 73 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~ 73 (381)
.|.+|.+.+.. ...-|+.|+.
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCC-cCcchhhhCC
Confidence 37788888773 4556777765
No 65
>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=40.89 E-value=19 Score=28.99 Aligned_cols=27 Identities=26% Similarity=0.714 Sum_probs=19.9
Q ss_pred CcccccccccccCC--CCCccCCCCCCCc
Q 046120 49 SSSFCHNCFRKTMH--SSSSICPSCSVAF 75 (381)
Q Consensus 49 ~~~~C~~C~~~~~~--~~~~~C~~C~~~y 75 (381)
...+|..|.+++-. ..++.||.|+..|
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 67899999988662 3567788777654
No 66
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=40.84 E-value=17 Score=22.46 Aligned_cols=27 Identities=33% Similarity=0.899 Sum_probs=15.8
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
|.|.+ |+..+. +.+.+ ..+|..||..+
T Consensus 1 Y~C~~--Cg~~~~-~~~~~-----~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGE--CGAEVE-LKPGD-----PIRCPECGHRI 27 (32)
T ss_dssp EBESS--SSSSE--BSTSS-----TSSBSSSS-SE
T ss_pred CCCCc--CCCeeE-cCCCC-----cEECCcCCCeE
Confidence 56776 754443 44433 37899999754
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=40.75 E-value=15 Score=23.37 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=19.2
Q ss_pred hcccCCCCcce-eeecCCCCCCCCCceeeeCCccCcc
Q 046120 332 RYMCDRDNCWG-TLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 332 ~~~C~~~~C~g-~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
.+.||+ |+. +-+|....... ....+|..|+.+.
T Consensus 2 ~i~CP~--C~~~f~v~~~~l~~~-~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPN--CQTRFRVPDDKLPAG-GRKVRCPKCGHVF 35 (37)
T ss_pred EEECCC--CCceEEcCHHHcccC-CcEEECCCCCcEe
Confidence 467987 764 33333222222 2468999999865
No 68
>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=40.53 E-value=15 Score=23.21 Aligned_cols=34 Identities=21% Similarity=0.432 Sum_probs=19.2
Q ss_pred hcccCCCCcceee-ecCCCCCCCCCceeeeCCccCccc
Q 046120 332 RYMCDRDNCWGTL-APLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 332 ~~~C~~~~C~g~~-~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+.||. |+... ++..+..... ....|..||....
T Consensus 2 ~~~CP~--C~~~~~v~~~~~~~~~-~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPN--CKTSFRVVDSQLGANG-GKVRCGKCGHVWY 36 (38)
T ss_pred EEECCC--CCCEEEeCHHHcCCCC-CEEECCCCCCEEE
Confidence 467987 75432 2222222221 3589999998754
No 69
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=40.41 E-value=18 Score=22.67 Aligned_cols=29 Identities=31% Similarity=0.781 Sum_probs=14.2
Q ss_pred ccCCCCcceeeecC-CCCCCCCCceeeeCCccCc
Q 046120 334 MCDRDNCWGTLAPL-PPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 334 ~C~~~~C~g~~~p~-~~~~~~~~~~~~C~~C~~~ 366 (381)
.|++ |++.|... ++++.. .-+.|..||.+
T Consensus 2 fC~~--CG~~l~~~ip~gd~r--~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQ--CGGPLERRIPEGDDR--ERLVCPACGFI 31 (34)
T ss_dssp B-TT--T--B-EEE--TT-SS---EEEETTTTEE
T ss_pred cccc--ccChhhhhcCCCCCc--cceECCCCCCE
Confidence 3877 87665433 333432 35899999975
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.33 E-value=29 Score=28.16 Aligned_cols=72 Identities=21% Similarity=0.383 Sum_probs=39.6
Q ss_pred CccEEEEcccCCCC-cEEEEcCcceeccccccccCcccccccccccCCC-----------CCccCCCCCCCcCccccchh
Q 046120 16 RGRGLVSTQSLKAG-QIVLRDSPILLYSALPFINSSSFCHNCFRKTMHS-----------SSSICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 16 ~GRglvAtrdi~~G-evIl~e~P~v~~p~~~l~~~~~~C~~C~~~~~~~-----------~~~~C~~C~~~yCS~~C~~~ 83 (381)
-|-.||..-.|..- --||--+||+-++... ......|..|..+++.. ..+.|+.|+..|| .+|-.-
T Consensus 21 CgLtLVss~HLARSyHHLfPl~~f~ev~~~~-~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC-~dCD~f 98 (112)
T TIGR00622 21 CGLTLILSTHLARSYHHLFPLKAFQEIPLEE-YNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFC-VDCDVF 98 (112)
T ss_pred CCCEEeccchHHHhhhccCCCcccccccccc-cCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccc-cccchh
Confidence 35555555444333 1223234443333221 11345799999987631 2467999999999 578654
Q ss_pred hhhcCC
Q 046120 84 AASSSH 89 (381)
Q Consensus 84 a~~~~H 89 (381)
.-...|
T Consensus 99 iHe~Lh 104 (112)
T TIGR00622 99 VHESLH 104 (112)
T ss_pred hhhhcc
Confidence 333444
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.98 E-value=19 Score=22.85 Aligned_cols=33 Identities=15% Similarity=0.291 Sum_probs=18.7
Q ss_pred hcccCCCCcc-eeeecCCCCCCCCCceeeeCCccCcc
Q 046120 332 RYMCDRDNCW-GTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 332 ~~~C~~~~C~-g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
.+.|++ |. -+-+|-....... ...+|..||.+.
T Consensus 2 ~i~Cp~--C~~~y~i~d~~ip~~g-~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPN--CQAKYEIDDEKIPPKG-RKVRCSKCGHVF 35 (36)
T ss_pred EEECCC--CCCEEeCCHHHCCCCC-cEEECCCCCCEe
Confidence 467987 75 3433322122221 468999999864
No 72
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=39.75 E-value=19 Score=35.13 Aligned_cols=21 Identities=29% Similarity=0.561 Sum_probs=18.4
Q ss_pred CccEEEEcccCCCCcEEEEcC
Q 046120 16 RGRGLVSTQSLKAGQIVLRDS 36 (381)
Q Consensus 16 ~GRglvAtrdi~~GevIl~e~ 36 (381)
..|.|||++||++|++|-.+.
T Consensus 276 ~rrsl~a~~di~~G~~lt~~~ 296 (329)
T TIGR03569 276 ARKSLVAAKDIKKGEIFTEDN 296 (329)
T ss_pred cceEEEEccCcCCCCEecHHh
Confidence 379999999999999997665
No 73
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.24 E-value=17 Score=21.10 Aligned_cols=22 Identities=32% Similarity=0.881 Sum_probs=15.2
Q ss_pred ccccccccccCCCCCccCCCCCC
Q 046120 51 SFCHNCFRKTMHSSSSICPSCSV 73 (381)
Q Consensus 51 ~~C~~C~~~~~~~~~~~C~~C~~ 73 (381)
..|.+|.+.+. ....-|+.|+.
T Consensus 3 ~~Cp~Cg~~~~-~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEID-PDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCC-cccccChhhCC
Confidence 46888888665 34567777765
No 74
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=38.75 E-value=17 Score=31.47 Aligned_cols=34 Identities=21% Similarity=0.518 Sum_probs=22.7
Q ss_pred hcccCCCCcceeeecCCCCCC----------CCCceeeeCCccCcc
Q 046120 332 RYMCDRDNCWGTLAPLPPSDA----------TPSTVMECNVCGNLK 367 (381)
Q Consensus 332 ~~~C~~~~C~g~~~p~~~~~~----------~~~~~~~C~~C~~~~ 367 (381)
.-+||. |+|.|.+++...- +....|.|.+||+..
T Consensus 97 ~~RCp~--CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPE--CNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcc--cCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 458998 8899987753320 111258899999863
No 75
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=37.44 E-value=18 Score=33.51 Aligned_cols=26 Identities=23% Similarity=0.580 Sum_probs=21.2
Q ss_pred CcccccccccccCC---------CCCccCCCCCCC
Q 046120 49 SSSFCHNCFRKTMH---------SSSSICPSCSVA 74 (381)
Q Consensus 49 ~~~~C~~C~~~~~~---------~~~~~C~~C~~~ 74 (381)
...+|.+|+-.++. ...+.||.|+..
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 67899999998883 356889999876
No 76
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=36.28 E-value=33 Score=24.47 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=24.8
Q ss_pred hhcccCCCCcceeeecCCCCCCCCCceeeeCCccCcccc
Q 046120 331 MRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKND 369 (381)
Q Consensus 331 ~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~ 369 (381)
.-+.|...+|.|++. -+-.-. ..=.|..|+..+..
T Consensus 17 ~VW~Ct~e~C~gWmR-~nFs~~---~~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 17 KVWECTSEDCNGWMR-DNFSFE---EEPVCPLCKSPMVS 51 (59)
T ss_pred eeEEeCCCCCCcccc-cccccC---CCccCCCcCCcccc
Confidence 557899999999997 433222 13579999987654
No 77
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=36.26 E-value=33 Score=20.88 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=14.4
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCc
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
.|++ |++.+.+.+.. ...+|..||..
T Consensus 5 fC~~--CG~~t~~~~~g-----~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGR--CGAPTKPAPGG-----WARRCPSCGHE 30 (32)
T ss_dssp B-TT--T--BEEE-SSS-----S-EEESSSS-E
T ss_pred ccCc--CCccccCCCCc-----CEeECCCCcCE
Confidence 4887 88888766432 34799999864
No 78
>PF12773 DZR: Double zinc ribbon
Probab=35.22 E-value=30 Score=23.23 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=19.1
Q ss_pred CcccccccccccC--CCCCccCCCCCC
Q 046120 49 SSSFCHNCFRKTM--HSSSSICPSCSV 73 (381)
Q Consensus 49 ~~~~C~~C~~~~~--~~~~~~C~~C~~ 73 (381)
...+|.+|...+. ....+.|+.|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcC
Confidence 5678999988887 445677888875
No 79
>PHA00626 hypothetical protein
Probab=34.91 E-value=27 Score=24.54 Aligned_cols=19 Identities=21% Similarity=0.242 Sum_probs=15.6
Q ss_pred ceeeeCCccCcccccCccC
Q 046120 356 TVMECNVCGNLKNDAIGRE 374 (381)
Q Consensus 356 ~~~~C~~C~~~~~~~~~~~ 374 (381)
...+|..||...+.+.|-|
T Consensus 22 nrYkCkdCGY~ft~~~~~~ 40 (59)
T PHA00626 22 DDYVCCDCGYNDSKDAFGE 40 (59)
T ss_pred cceEcCCCCCeechhhhhh
Confidence 4589999999999887733
No 80
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=34.83 E-value=30 Score=26.69 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=22.1
Q ss_pred HhhhcccCCCCcce-eeecCCCCCCCCCceeeeCCccCccccc
Q 046120 329 FFMRYMCDRDNCWG-TLAPLPPSDATPSTVMECNVCGNLKNDA 370 (381)
Q Consensus 329 ~~~~~~C~~~~C~g-~~~p~~~~~~~~~~~~~C~~C~~~~~~~ 370 (381)
.-..+.||. |+- .+.-+ . ...|+|.+||.+...-
T Consensus 32 ~~~~~~Cp~--C~~~~VkR~---a---~GIW~C~kCg~~fAGg 66 (89)
T COG1997 32 QRAKHVCPF--CGRTTVKRI---A---TGIWKCRKCGAKFAGG 66 (89)
T ss_pred HhcCCcCCC--CCCcceeee---c---cCeEEcCCCCCeeccc
Confidence 346788998 653 33222 1 1579999999986543
No 81
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=34.51 E-value=21 Score=25.06 Aligned_cols=34 Identities=29% Similarity=0.675 Sum_probs=18.2
Q ss_pred hHhhhcccCCCCcceeee-cCCCCCCCCCceeeeCCccCccc
Q 046120 328 YFFMRYMCDRDNCWGTLA-PLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 328 ~~~~~~~C~~~~C~g~~~-p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+|+.++|+. |...-. -..+ ++...|..||.++-
T Consensus 3 S~Fm~VkCp~--C~~~q~vFSha-----~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 3 SYFMDVKCPG--CYNIQTVFSHA-----QTVVKCVVCGTVLA 37 (55)
T ss_dssp --EEEEE-TT--T-SEEEEETT------SS-EE-SSSTSEEE
T ss_pred ccEEEEECCC--CCCeeEEEecC-----CeEEEcccCCCEec
Confidence 4789999997 764322 1222 25689999998763
No 82
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=34.40 E-value=28 Score=23.18 Aligned_cols=32 Identities=13% Similarity=0.265 Sum_probs=19.1
Q ss_pred HhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCc
Q 046120 329 FFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 329 ~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
|-..+.||.++.. ....+.. ...|+|..|++.
T Consensus 15 W~~g~~CP~Cg~~-~~~~~~~-----~~~~~C~~C~~q 46 (46)
T PF12760_consen 15 WPDGFVCPHCGST-KHYRLKT-----RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCCCe-eeEEeCC-----CCeEECCCCCCc
Confidence 4556789984332 2222322 146999999863
No 83
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=34.24 E-value=29 Score=24.25 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=21.3
Q ss_pred CcccccccccccC-CCCCccCCCCCCCcC
Q 046120 49 SSSFCHNCFRKTM-HSSSSICPSCSVAFC 76 (381)
Q Consensus 49 ~~~~C~~C~~~~~-~~~~~~C~~C~~~yC 76 (381)
....|..|...+. ....+.|+.|+.+|=
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCccc
Confidence 4678999999885 346789998887753
No 84
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=33.48 E-value=16 Score=24.05 Aligned_cols=20 Identities=30% Similarity=0.791 Sum_probs=11.4
Q ss_pred cccccCCCCCccCCCCCCCcCc
Q 046120 56 CFRKTMHSSSSICPSCSVAFCS 77 (381)
Q Consensus 56 C~~~~~~~~~~~C~~C~~~yCS 77 (381)
|.+... .++.|+.|+..||.
T Consensus 6 C~~~~~--~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 6 CKKKDF--LPFKCKHCGKSFCL 25 (43)
T ss_dssp T--BCT--SHEE-TTTS-EE-T
T ss_pred CcCccC--CCeECCCCCcccCc
Confidence 655544 46899999999995
No 85
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=32.11 E-value=28 Score=23.00 Aligned_cols=31 Identities=19% Similarity=0.617 Sum_probs=24.2
Q ss_pred cccccccccCCCCCccCCCCCCC-cCccccchhh
Q 046120 52 FCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAA 84 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a 84 (381)
.|++|-+++. ...++|..|... +| .+|....
T Consensus 2 ~Cd~C~~~i~-G~ry~C~~C~d~dLC-~~C~~~~ 33 (43)
T cd02340 2 ICDGCQGPIV-GVRYKCLVCPDYDLC-ESCEAKG 33 (43)
T ss_pred CCCCCCCcCc-CCeEECCCCCCccch-HHhhCcC
Confidence 5899998765 467899999877 99 4787653
No 86
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=31.73 E-value=20 Score=34.47 Aligned_cols=26 Identities=35% Similarity=0.744 Sum_probs=21.5
Q ss_pred CcccccccccccCCCCCccCCCCCCC
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA 74 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~ 74 (381)
....|+.||+........-|+.|+.-
T Consensus 241 ~iLRCh~Cfsit~~m~k~FCp~CG~~ 266 (376)
T KOG2463|consen 241 YILRCHGCFSITSEMPKDFCPSCGHK 266 (376)
T ss_pred heeEeeeeeEecCccchhcccccCCC
Confidence 55699999999886667889999875
No 87
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=30.36 E-value=30 Score=21.61 Aligned_cols=10 Identities=30% Similarity=0.983 Sum_probs=5.1
Q ss_pred ceeeeCCccC
Q 046120 356 TVMECNVCGN 365 (381)
Q Consensus 356 ~~~~C~~C~~ 365 (381)
....|..||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3345555554
No 88
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=30.07 E-value=27 Score=33.78 Aligned_cols=28 Identities=32% Similarity=0.484 Sum_probs=21.6
Q ss_pred CccEEEEcccCCCCcEEEEcCcceeccc
Q 046120 16 RGRGLVSTQSLKAGQIVLRDSPILLYSA 43 (381)
Q Consensus 16 ~GRglvAtrdi~~GevIl~e~P~v~~p~ 43 (381)
.-|+||+++||++||++-++.=.+.-|.
T Consensus 288 ~~Rsl~~~kdikkGe~ls~~Nl~~~RP~ 315 (347)
T COG2089 288 ARRSLVATKDIKKGEILSEDNLKVLRPG 315 (347)
T ss_pred HhhheeeecccccCccccccceEEeCCC
Confidence 3599999999999999877765444333
No 89
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=30.05 E-value=36 Score=23.36 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=17.1
Q ss_pred cccCCCCcce-eeecCCCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCWG-TLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~g-~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
-.||+ |+. .|++-. .-|.|..||.+.
T Consensus 21 ~fCP~--Cg~~~m~~~~-------~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPR--CGSGFMAEHL-------DRWHCGKCGYTE 47 (50)
T ss_pred CcCcC--CCcchheccC-------CcEECCCcCCEE
Confidence 36998 764 554321 249999999753
No 90
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=29.96 E-value=47 Score=24.90 Aligned_cols=24 Identities=21% Similarity=0.423 Sum_probs=18.4
Q ss_pred EEeCCCccEEEEcccCCCCcEEEE
Q 046120 11 AEIEGRGRGLVSTQSLKAGQIVLR 34 (381)
Q Consensus 11 ~~~~~~GRglvAtrdi~~GevIl~ 34 (381)
+...+.=++++|+..+++||+|..
T Consensus 54 ~~~~g~~~yiiA~eg~~vGd~I~s 77 (77)
T PF00181_consen 54 KYEDGEKRYIIAPEGMKVGDIIES 77 (77)
T ss_dssp EETTSEEEEEEEBTTEBTTEEEEE
T ss_pred EecCCcEEEEEeECCCcCCCEEEC
Confidence 333334589999999999999863
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.84 E-value=24 Score=25.16 Aligned_cols=35 Identities=23% Similarity=0.612 Sum_probs=25.6
Q ss_pred cccccccccccCCC---CCccCCCCCCC--cCccccchhh
Q 046120 50 SSFCHNCFRKTMHS---SSSICPSCSVA--FCSPKCSTAA 84 (381)
Q Consensus 50 ~~~C~~C~~~~~~~---~~~~C~~C~~~--yCS~~C~~~a 84 (381)
...|..|...+.+. ..++||+|+.+ |=...|++..
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g 48 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLG 48 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcC
Confidence 57899999988432 35899999954 5447898653
No 92
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=29.75 E-value=23 Score=22.89 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=19.0
Q ss_pred CcccccccccccCCCCC---ccCCCCCCCcCccccchh
Q 046120 49 SSSFCHNCFRKTMHSSS---SICPSCSVAFCSPKCSTA 83 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~---~~C~~C~~~yCS~~C~~~ 83 (381)
....|.+|.+.+..... +.=.+-...|||..|..+
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~ 42 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSS 42 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHHhh
Confidence 45789999988763331 221233445999999753
No 93
>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=28.98 E-value=29 Score=18.61 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=7.4
Q ss_pred eeeCCccCcccc
Q 046120 358 MECNVCGNLKND 369 (381)
Q Consensus 358 ~~C~~C~~~~~~ 369 (381)
|.|+.|+...+.
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 679999887654
No 94
>KOG2155 consensus Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.80 E-value=48 Score=33.39 Aligned_cols=62 Identities=19% Similarity=0.044 Sum_probs=42.7
Q ss_pred cccccccCCCCCCceeeeccccccCCCceEEEEEccCCCCCCeeEEeecCCCCCHHHHHHHHh
Q 046120 207 LKASFFNHDCLPNACRFDYVDAAAENNTDIIVRMIHDVPQGREICLSYFPVNYDYSTRQKRLL 269 (381)
Q Consensus 207 p~~Sl~NHSC~PN~~~~~~~d~~~~~~~~l~vrA~r~I~~GeEl~isY~~~~~~~~~Rr~~L~ 269 (381)
-.+|.+.||=.||.....|.--+ .+-.--++..+|++..||||+-.+....-....|...|.
T Consensus 203 efGsrvrHsdePnf~~aPf~fmP-q~vaYsimwp~k~~~tgeE~trDfasg~~~p~~Rk~~l~ 264 (631)
T KOG2155|consen 203 EFGSRVRHSDEPNFRIAPFMFMP-QNVAYSIMWPTKPVNTGEEITRDFASGVIHPEWRKYILQ 264 (631)
T ss_pred hhhhhhccCCCCcceeeeheecc-hhcceeEEeeccCCCCchHHHHHHhhcCCCHHHHHHHhc
Confidence 45799999999998742221101 012234578899999999999888776555667777664
No 95
>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=28.08 E-value=42 Score=27.08 Aligned_cols=32 Identities=19% Similarity=0.408 Sum_probs=23.4
Q ss_pred hhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccccc
Q 046120 331 MRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDA 370 (381)
Q Consensus 331 ~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~ 370 (381)
.+-.|+. |+--++=++-. -..|.+||.....+
T Consensus 8 tKR~Cp~--CG~kFYDLnk~------PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPS--CGAKFYDLNKD------PIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCC--CcchhccCCCC------CccCCCCCCccCcc
Confidence 6678987 77666645431 27899999998877
No 96
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=27.51 E-value=68 Score=19.66 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=17.6
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCc
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
+.|.. |. +++..|++. ..++|..|..+
T Consensus 2 ~~C~~--C~-t~L~yP~gA----~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVCGG--CR-TLLMYPRGA----SSVRCALCQTV 28 (31)
T ss_pred cCcCC--CC-cEeecCCCC----CeEECCCCCeE
Confidence 34654 64 444477765 46999999764
No 97
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=27.49 E-value=27 Score=33.30 Aligned_cols=52 Identities=23% Similarity=0.436 Sum_probs=34.2
Q ss_pred CcceeccccccccCcccccccccccCC-----------CCCccCCCCCCCcCccccchhhhhcCC
Q 046120 36 SPILLYSALPFINSSSFCHNCFRKTMH-----------SSSSICPSCSVAFCSPKCSTAAASSSH 89 (381)
Q Consensus 36 ~P~v~~p~~~l~~~~~~C~~C~~~~~~-----------~~~~~C~~C~~~yCS~~C~~~a~~~~H 89 (381)
+||+-.|... .-...+|..|..+.+. ...+.|+.|+..||+ .|-.-.....|
T Consensus 349 k~f~E~p~~~-~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~-dCdvfiHe~Lh 411 (421)
T COG5151 349 KPFVEKPEGT-NPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCS-DCDVFIHETLH 411 (421)
T ss_pred cccccccCCC-CCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhh-hhHHHHHHHHh
Confidence 4555444431 1267899999987662 235899999999996 78765443444
No 98
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.36 E-value=35 Score=34.24 Aligned_cols=33 Identities=21% Similarity=0.606 Sum_probs=24.8
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCcccccCcc
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDAIGR 373 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~~~~ 373 (381)
=+||. |+|.|-.. +. ..|+|.+||...+...+.
T Consensus 351 p~Cp~--Cg~~m~S~--G~----~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 351 PVCPR--CGGRMKSA--GR----NGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCc--cCCchhhc--CC----CCcccccccccCCccccc
Confidence 37988 89999532 22 259999999998877664
No 99
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=27.30 E-value=31 Score=30.82 Aligned_cols=46 Identities=28% Similarity=0.382 Sum_probs=28.8
Q ss_pred HhhhcccCCCCcceeeecCCCCCCCC------CceeeeCCccCcccccCccCCC
Q 046120 329 FFMRYMCDRDNCWGTLAPLPPSDATP------STVMECNVCGNLKNDAIGREDT 376 (381)
Q Consensus 329 ~~~~~~C~~~~C~g~~~p~~~~~~~~------~~~~~C~~C~~~~~~~~~~~~~ 376 (381)
+...+-||. |++.|.-..-...-+ -+.|.|..||...++....|.+
T Consensus 11 ~~~~~~CPv--Cg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~ 62 (201)
T COG1779 11 FETRIDCPV--CGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEER 62 (201)
T ss_pred eeeeecCCc--ccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccC
Confidence 456678998 777654221111110 1469999999999887765543
No 100
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=27.18 E-value=39 Score=26.64 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=19.3
Q ss_pred ccCCCCcceeeecCCCCCCCCCceeeeCCccCcccc
Q 046120 334 MCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKND 369 (381)
Q Consensus 334 ~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~ 369 (381)
.|+. |++.|.|.. ..+.|..|+.+...
T Consensus 2 fC~~--Cg~~l~~~~-------~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPK--CGSLMTPKN-------GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcc--cCcccccCC-------CeEECcCCCCcccc
Confidence 4876 888886531 25899999977553
No 101
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=27.18 E-value=37 Score=22.37 Aligned_cols=33 Identities=21% Similarity=0.521 Sum_probs=25.7
Q ss_pred CcccccccccccCCCCCccCCCCCCC-cCccccchh
Q 046120 49 SSSFCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTA 83 (381)
Q Consensus 49 ~~~~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~ 83 (381)
....|+.|.+++. ...+.|..|... .| .+|...
T Consensus 3 ~~~~C~~C~~~i~-g~ry~C~~C~d~dlC-~~Cf~~ 36 (44)
T smart00291 3 HSYSCDTCGKPIV-GVRYHCLVCPDYDLC-QSCFAK 36 (44)
T ss_pred CCcCCCCCCCCCc-CCEEECCCCCCccch-HHHHhC
Confidence 3567999999665 456789999888 99 588754
No 102
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.84 E-value=37 Score=28.70 Aligned_cols=22 Identities=9% Similarity=0.252 Sum_probs=18.2
Q ss_pred CCCccEEEEcccCCCCcEEEEc
Q 046120 14 EGRGRGLVSTQSLKAGQIVLRD 35 (381)
Q Consensus 14 ~~~GRglvAtrdi~~GevIl~e 35 (381)
+..+..+||+|+|.+|++|-.+
T Consensus 16 ~~~~~VvVA~r~L~rGevIt~~ 37 (141)
T PRK12618 16 PAAAETVVAARTIRALTVIGAE 37 (141)
T ss_pred cceeEEEEEccCcCCCCCcCHH
Confidence 4568889999999999998543
No 103
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.77 E-value=31 Score=23.49 Aligned_cols=31 Identities=19% Similarity=0.494 Sum_probs=23.9
Q ss_pred cccccccccCCCCCccCCCCCCC-cCccccchhh
Q 046120 52 FCHNCFRKTMHSSSSICPSCSVA-FCSPKCSTAA 84 (381)
Q Consensus 52 ~C~~C~~~~~~~~~~~C~~C~~~-yCS~~C~~~a 84 (381)
.|++|-+.+. ...++|-.|... +|. +|....
T Consensus 2 ~CdgC~~~~~-~~RykCl~C~d~DlC~-~Cf~~g 33 (48)
T cd02343 2 SCDGCDEIAP-WHRYRCLQCTDMDLCK-TCFLGG 33 (48)
T ss_pred CCCCCCCcCC-CceEECCCCCCchhHH-HHHhCC
Confidence 5899988654 457899999988 994 787654
No 104
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=26.67 E-value=42 Score=28.69 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=28.3
Q ss_pred hhcccCCCCcc-eeeecCCCC---CCCCCceeeeCCccCcccccCccC
Q 046120 331 MRYMCDRDNCW-GTLAPLPPS---DATPSTVMECNVCGNLKNDAIGRE 374 (381)
Q Consensus 331 ~~~~C~~~~C~-g~~~p~~~~---~~~~~~~~~C~~C~~~~~~~~~~~ 374 (381)
.-++|++.+|- ..=.|+.+. ........+|-.|++..+.+++.+
T Consensus 105 gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~~~~~~v~~ 152 (153)
T COG1781 105 GVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKTFSEDEVLE 152 (153)
T ss_pred cEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcEechhhhhc
Confidence 44899999994 222255442 110113589999999999887753
No 105
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.27 E-value=69 Score=22.25 Aligned_cols=31 Identities=16% Similarity=0.340 Sum_probs=19.3
Q ss_pred cccCCCCcceeeecC-CCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCWGTLAPL-PPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~-~~~~~~~~~~~~C~~C~~~~ 367 (381)
.+||..+|...+... .++. ....|..|+...
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~----~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGC----NRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcceEEecCCCCC----CeeECCCCCCeE
Confidence 369988897666533 1122 357888887543
No 106
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=26.22 E-value=38 Score=20.86 Aligned_cols=13 Identities=31% Similarity=0.810 Sum_probs=8.8
Q ss_pred eeeCCccCccccc
Q 046120 358 MECNVCGNLKNDA 370 (381)
Q Consensus 358 ~~C~~C~~~~~~~ 370 (381)
|+|..||.+...+
T Consensus 2 ~~C~~CGy~y~~~ 14 (33)
T cd00350 2 YVCPVCGYIYDGE 14 (33)
T ss_pred EECCCCCCEECCC
Confidence 7777777775543
No 107
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=25.58 E-value=30 Score=36.59 Aligned_cols=25 Identities=36% Similarity=0.810 Sum_probs=18.5
Q ss_pred CCccCCCCC---C----C-cCccccchhhhhcCC
Q 046120 64 SSSICPSCS---V----A-FCSPKCSTAAASSSH 89 (381)
Q Consensus 64 ~~~~C~~C~---~----~-yCS~~C~~~a~~~~H 89 (381)
....|+.|- . . |||++|.+.+| ..|
T Consensus 73 a~lqCp~C~k~~~~~~~s~fCsq~CFk~~w-~~H 105 (606)
T PLN03144 73 ATLQCVGCVKAKLPVSKSYHCSPKCFSDAW-RHH 105 (606)
T ss_pred ccccCccchhcCCCcCcceeeCHHHHHHHH-HHH
Confidence 346777764 2 3 99999999999 455
No 108
>PLN00162 transport protein sec23; Provisional
Probab=24.55 E-value=42 Score=36.64 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=23.8
Q ss_pred hcccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 332 RYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 332 ~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
-++|.+ |.++|-|.-.-+... ..|.|+.|+...
T Consensus 53 pvRC~~--CraylNPf~~~d~~~-~~W~C~~C~~~N 85 (761)
T PLN00162 53 PLRCRT--CRAVLNPYCRVDFQA-KIWICPFCFQRN 85 (761)
T ss_pred CCccCC--CcCEECCceEEecCC-CEEEccCCCCCC
Confidence 378976 999998765444332 479999998764
No 109
>PLN00209 ribosomal protein S27; Provisional
Probab=24.39 E-value=36 Score=26.13 Aligned_cols=35 Identities=26% Similarity=0.626 Sum_probs=23.4
Q ss_pred hHhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 328 YFFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 328 ~~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+|+.++|+. |...-.-.. -. ++...|..||.+..
T Consensus 32 S~Fm~VkCp~--C~n~q~VFS-hA---~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 32 SFFMDVKCQG--CFNITTVFS-HS---QTVVVCGSCQTVLC 66 (86)
T ss_pred CEEEEEECCC--CCCeeEEEe-cC---ceEEEccccCCEee
Confidence 5889999997 764432121 11 25689999998774
No 110
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.16 E-value=62 Score=28.74 Aligned_cols=52 Identities=21% Similarity=0.416 Sum_probs=31.9
Q ss_pred cccCCCCcEEEE-----cCcceeccc-cccccCcccccccccccCC-CCCccCCCCCCC
Q 046120 23 TQSLKAGQIVLR-----DSPILLYSA-LPFINSSSFCHNCFRKTMH-SSSSICPSCSVA 74 (381)
Q Consensus 23 trdi~~GevIl~-----e~P~v~~p~-~~l~~~~~~C~~C~~~~~~-~~~~~C~~C~~~ 74 (381)
+..|++||+|-- ..|+..... ..|.-....|+.|...+.. .....||.|+..
T Consensus 116 ~d~f~~GDivrA~Vis~~~~~~Lst~~~dlGVI~A~CsrC~~~L~~~~~~l~Cp~Cg~t 174 (188)
T COG1096 116 SDAFRIGDIVRARVISTGDPIQLSTKGNDLGVIYARCSRCRAPLVKKGNMLKCPNCGNT 174 (188)
T ss_pred ccccccccEEEEEEEecCCCeEEEecCCcceEEEEEccCCCcceEEcCcEEECCCCCCE
Confidence 468999997742 134332212 1122356799999988763 235789888864
No 111
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.39 E-value=81 Score=24.54 Aligned_cols=23 Identities=30% Similarity=0.574 Sum_probs=13.0
Q ss_pred ccccccccccCCCCCccCCCCCC
Q 046120 51 SFCHNCFRKTMHSSSSICPSCSV 73 (381)
Q Consensus 51 ~~C~~C~~~~~~~~~~~C~~C~~ 73 (381)
.-|.+=|+......+.+||.|+.
T Consensus 62 kkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 62 KKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred cccCccccccccCCcccCCcchh
Confidence 34555555533234678887763
No 112
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.86 E-value=35 Score=20.81 Aligned_cols=25 Identities=28% Similarity=0.760 Sum_probs=13.7
Q ss_pred ccCCCCcc-eeeecCCCCCCCCCceeeeC
Q 046120 334 MCDRDNCW-GTLAPLPPSDATPSTVMECN 361 (381)
Q Consensus 334 ~C~~~~C~-g~~~p~~~~~~~~~~~~~C~ 361 (381)
+||+ |+ |+|.|+-.-..+ ...+.|.
T Consensus 3 lcpk--cgvgvl~pvy~~kge-ikvfrcs 28 (36)
T PF09151_consen 3 LCPK--CGVGVLEPVYNQKGE-IKVFRCS 28 (36)
T ss_dssp B-TT--TSSSBEEEEE-TTS--EEEEEES
T ss_pred cCCc--cCceEEEEeecCCCc-EEEEEcC
Confidence 6887 65 999887322111 2456775
No 113
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.45 E-value=46 Score=21.51 Aligned_cols=27 Identities=33% Similarity=0.803 Sum_probs=14.4
Q ss_pred cCCCCcceeeecCCCCCCCCCceeeeCCccCc
Q 046120 335 CDRDNCWGTLAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 335 C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
||+ |+..|.+..-.+ -....|..|+-.
T Consensus 2 CP~--C~~~l~~~~~~~---~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPR--CGTELEPVRLGD---VEIDVCPSCGGI 28 (41)
T ss_pred cCC--CCcccceEEECC---EEEEECCCCCeE
Confidence 666 655554443211 135678888743
No 114
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.96 E-value=56 Score=21.34 Aligned_cols=27 Identities=26% Similarity=0.732 Sum_probs=17.4
Q ss_pred cccCCCCccee---eecCCCCCCCCCceeeeCCccCc
Q 046120 333 YMCDRDNCWGT---LAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 333 ~~C~~~~C~g~---~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
|+|.. |+.. +.++.. . ....|..||..
T Consensus 6 y~C~~--Cg~~fe~~~~~~~---~--~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEE--CGHEFEVLQSISE---D--DPVPCPECGST 35 (42)
T ss_pred EEeCC--CCCEEEEEEEcCC---C--CCCcCCCCCCC
Confidence 78986 7644 444432 1 35789999983
No 115
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=21.53 E-value=71 Score=21.83 Aligned_cols=30 Identities=37% Similarity=0.784 Sum_probs=22.5
Q ss_pred ccccccccccCCC-CCccCCCCCCCcCccccc
Q 046120 51 SFCHNCFRKTMHS-SSSICPSCSVAFCSPKCS 81 (381)
Q Consensus 51 ~~C~~C~~~~~~~-~~~~C~~C~~~yCS~~C~ 81 (381)
..|..|-+.+... ....|..|+.+||+ .|.
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~-~C~ 33 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCS-KCS 33 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcCh-HHc
Confidence 5788888776632 35689999999996 665
No 116
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.50 E-value=60 Score=20.57 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=18.2
Q ss_pred cccCCCCcceeeecCCCCCCCCCceeeeCCccCcc
Q 046120 333 YMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLK 367 (381)
Q Consensus 333 ~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~ 367 (381)
+.|+. |++...... + ..+.|..||.+.
T Consensus 9 ~~C~~--C~~~~~~~~--d----G~~yC~~cG~~~ 35 (36)
T PF11781_consen 9 EPCPV--CGSRWFYSD--D----GFYYCDRCGHQS 35 (36)
T ss_pred CcCCC--CCCeEeEcc--C----CEEEhhhCceEc
Confidence 34988 877754221 1 469999999764
No 117
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=21.41 E-value=57 Score=22.14 Aligned_cols=30 Identities=27% Similarity=0.554 Sum_probs=17.4
Q ss_pred hhcccCCCCcc-eeeecCCCCCCCCCceeeeCCccCc
Q 046120 331 MRYMCDRDNCW-GTLAPLPPSDATPSTVMECNVCGNL 366 (381)
Q Consensus 331 ~~~~C~~~~C~-g~~~p~~~~~~~~~~~~~C~~C~~~ 366 (381)
.+-.||.+.|+ |++.-. ..+ -|.|-+||.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~-H~d-----R~~CGKCg~T 47 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAE-HKD-----RHYCGKCGYT 47 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE--SS-----EEEETTTSS-
T ss_pred hhhcCCCcccCCceEeee-cCC-----CccCCCcccC
Confidence 34569977786 664323 222 4899999863
No 118
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=21.08 E-value=46 Score=25.51 Aligned_cols=35 Identities=23% Similarity=0.461 Sum_probs=23.3
Q ss_pred hHhhhcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 328 YFFMRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 328 ~~~~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+|+.++|+. |...-.-.. -. ++...|..||.+.-
T Consensus 31 S~Fm~VkCp~--C~n~q~VFS-hA---~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 31 SYFMDVKCPG--CSQITTVFS-HA---QTVVLCGGCSSQLC 65 (85)
T ss_pred CeEEEEECCC--CCCeeEEEe-cC---ceEEEccccCCEee
Confidence 5889999997 764422121 11 25789999998764
No 119
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.02 E-value=52 Score=22.55 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=18.3
Q ss_pred CcccccccccccCC---CCCccCCCCCCC
Q 046120 49 SSSFCHNCFRKTMH---SSSSICPSCSVA 74 (381)
Q Consensus 49 ~~~~C~~C~~~~~~---~~~~~C~~C~~~ 74 (381)
..-.|..|.+.+.. ...++||.|+.-
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 34578999888762 246889988753
No 120
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=20.82 E-value=78 Score=26.26 Aligned_cols=34 Identities=9% Similarity=0.032 Sum_probs=24.0
Q ss_pred hhcccCCCCcceeeecCCCCCCCCCceeeeCCccCcccccCc
Q 046120 331 MRYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKNDAIG 372 (381)
Q Consensus 331 ~~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~~~~~ 372 (381)
.+-.|+. |+-.++-++.. -..|.+||.....+.+
T Consensus 8 tKr~Cp~--cg~kFYDLnk~------p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 8 TKRICPN--TGSKFYDLNRR------PAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccccCCC--cCccccccCCC------CccCCCcCCccCcchh
Confidence 6678987 76666545431 3789999999877744
No 121
>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=20.50 E-value=1e+02 Score=21.56 Aligned_cols=32 Identities=19% Similarity=0.578 Sum_probs=20.3
Q ss_pred hcccCCCCcceeeecCCCCCCCCCceeeeCCccCccc
Q 046120 332 RYMCDRDNCWGTLAPLPPSDATPSTVMECNVCGNLKN 368 (381)
Q Consensus 332 ~~~C~~~~C~g~~~p~~~~~~~~~~~~~C~~C~~~~~ 368 (381)
.+.||. |+..+. ++..... -...|..||...-
T Consensus 2 ~~~CP~--CG~~ie-v~~~~~G--eiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPD--CGAEIE-LENPELG--ELVICDECGAELE 33 (54)
T ss_pred ccCCCC--CCCEEe-cCCCccC--CEEeCCCCCCEEE
Confidence 468998 776664 4433222 3579999997643
No 122
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=20.02 E-value=55 Score=26.49 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=11.3
Q ss_pred EEEcccCCCCcEEEE
Q 046120 20 LVSTQSLKAGQIVLR 34 (381)
Q Consensus 20 lvAtrdi~~GevIl~ 34 (381)
++|+++|++|++|-.
T Consensus 2 ~Va~r~I~~G~~i~~ 16 (122)
T TIGR03170 2 VVAKRPLKRGEVISP 16 (122)
T ss_pred EEECcccCCCCCcCH
Confidence 678888888887743
Done!