Query psy9235
Match_columns 317
No_of_seqs 260 out of 387
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:19:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1140|consensus 99.9 1.3E-22 2.8E-27 223.5 8.1 159 1-177 1039-1205(1738)
2 PF13639 zf-RING_2: Ring finge 97.0 0.00035 7.5E-09 48.2 1.7 22 113-134 14-35 (44)
3 KOG1139|consensus 96.9 0.0012 2.6E-08 69.7 5.4 77 1-95 648-724 (784)
4 KOG1139|consensus 96.7 0.0011 2.4E-08 70.0 3.1 69 240-317 644-719 (784)
5 cd00162 RING RING-finger (Real 96.2 0.0031 6.7E-08 41.8 2.0 21 114-134 12-32 (45)
6 PF12861 zf-Apc11: Anaphase-pr 95.9 0.0053 1.2E-07 49.1 2.2 24 113-136 45-68 (85)
7 KOG1940|consensus 95.2 0.014 3.1E-07 55.9 2.9 73 113-236 173-248 (276)
8 PF13923 zf-C3HC4_2: Zinc fing 94.9 0.015 3.2E-07 39.1 1.5 22 114-135 11-32 (39)
9 smart00184 RING Ring finger. E 94.8 0.026 5.7E-07 35.8 2.6 22 113-134 9-30 (39)
10 COG5243 HRD1 HRD ubiquitin lig 94.8 0.021 4.4E-07 56.8 2.9 17 118-134 316-332 (491)
11 PF12678 zf-rbx1: RING-H2 zinc 94.6 0.018 4E-07 44.2 1.6 21 114-134 44-64 (73)
12 PF00097 zf-C3HC4: Zinc finger 94.5 0.022 4.7E-07 38.3 1.6 20 116-135 13-32 (41)
13 PLN03208 E3 ubiquitin-protein 93.8 0.074 1.6E-06 48.6 4.0 55 115-176 31-87 (193)
14 PF14634 zf-RING_5: zinc-RING 93.5 0.073 1.6E-06 36.7 2.8 21 113-133 13-33 (44)
15 PF11793 FANCL_C: FANCL C-term 92.8 0.042 9E-07 42.1 0.7 39 118-168 26-64 (70)
16 PF09538 FYDLN_acid: Protein o 92.4 0.068 1.5E-06 44.5 1.5 26 261-286 8-36 (108)
17 PF13240 zinc_ribbon_2: zinc-r 92.4 0.07 1.5E-06 32.5 1.2 22 264-285 1-22 (23)
18 PF13920 zf-C3HC4_3: Zinc fing 92.3 0.15 3.3E-06 35.9 3.0 36 113-171 13-49 (50)
19 PF10571 UPF0547: Uncharacteri 91.9 0.077 1.7E-06 33.3 1.0 24 263-286 1-24 (26)
20 PHA02929 N1R/p28-like protein; 91.8 0.11 2.4E-06 48.9 2.3 36 116-174 196-231 (238)
21 PHA02926 zinc finger-like prot 90.4 0.22 4.8E-06 46.6 2.9 45 114-175 191-235 (242)
22 KOG4445|consensus 90.3 0.054 1.2E-06 52.5 -1.3 51 114-167 130-183 (368)
23 PF13248 zf-ribbon_3: zinc-rib 89.7 0.18 3.9E-06 31.3 1.1 24 262-285 2-25 (26)
24 TIGR02300 FYDLN_acid conserved 88.5 0.25 5.4E-06 42.3 1.6 26 261-286 8-36 (129)
25 PRK00415 rps27e 30S ribosomal 88.4 0.2 4.2E-06 37.6 0.8 30 259-288 8-42 (59)
26 PF01667 Ribosomal_S27e: Ribos 87.6 0.27 5.9E-06 36.3 1.1 30 259-288 4-38 (55)
27 PF13764 E3_UbLigase_R4: E3 ub 87.6 0.86 1.9E-05 49.8 5.4 66 54-135 465-530 (802)
28 COG2051 RPS27A Ribosomal prote 87.4 0.31 6.7E-06 37.3 1.4 31 259-289 16-51 (67)
29 PTZ00083 40S ribosomal protein 85.6 0.39 8.6E-06 38.4 1.1 30 260-289 33-67 (85)
30 PF15227 zf-C3HC4_4: zinc fing 85.3 0.65 1.4E-05 32.0 2.0 24 111-134 7-30 (42)
31 COG5194 APC11 Component of SCF 84.9 0.72 1.6E-05 36.7 2.3 23 113-135 47-69 (88)
32 KOG2930|consensus 81.8 1.2 2.5E-05 37.1 2.4 22 114-135 75-96 (114)
33 PLN00209 ribosomal protein S27 81.3 0.75 1.6E-05 36.9 1.1 31 259-289 33-68 (86)
34 COG5432 RAD18 RING-finger-cont 80.1 1.3 2.7E-05 43.2 2.4 23 111-133 34-56 (391)
35 KOG0823|consensus 79.5 1.7 3.7E-05 40.7 3.0 47 110-176 55-103 (230)
36 KOG1428|consensus 78.9 0.94 2E-05 52.2 1.3 104 118-270 3505-3610(3738)
37 PF02148 zf-UBP: Zn-finger in 78.1 1.4 2.9E-05 32.8 1.6 25 265-290 1-25 (63)
38 KOG0802|consensus 77.3 1.3 2.9E-05 46.1 1.8 19 117-135 311-329 (543)
39 KOG0827|consensus 76.8 1.4 3.1E-05 44.3 1.8 20 116-135 22-41 (465)
40 KOG1493|consensus 71.9 1.9 4.2E-05 34.0 1.1 34 114-167 45-78 (84)
41 KOG4172|consensus 69.6 2.1 4.5E-05 31.9 0.8 21 113-133 18-39 (62)
42 smart00744 RINGv The RING-vari 69.2 5.8 0.00013 28.2 3.0 22 115-136 14-40 (49)
43 PRK02935 hypothetical protein; 68.4 2.2 4.8E-05 35.6 0.8 30 258-288 66-98 (110)
44 smart00504 Ubox Modified RING 67.9 4.1 8.8E-05 29.3 2.0 22 113-134 12-33 (63)
45 PF08746 zf-RING-like: RING-li 67.5 3.5 7.6E-05 28.6 1.5 17 119-135 18-34 (43)
46 PF10367 Vps39_2: Vacuolar sor 65.0 1.7 3.7E-05 34.4 -0.5 15 117-131 95-109 (109)
47 TIGR00599 rad18 DNA repair pro 64.9 3.9 8.4E-05 41.4 1.9 18 116-133 40-57 (397)
48 smart00290 ZnF_UBP Ubiquitin C 63.1 5.7 0.00012 27.6 1.9 24 264-289 1-24 (50)
49 KOG1941|consensus 62.9 3.1 6.8E-05 42.0 0.8 22 113-134 380-401 (518)
50 KOG4628|consensus 62.3 4.7 0.0001 40.1 1.9 34 112-167 242-275 (348)
51 PF12773 DZR: Double zinc ribb 62.3 3.8 8.3E-05 28.6 0.9 24 262-285 12-38 (50)
52 PF08271 TF_Zn_Ribbon: TFIIB z 60.4 5.4 0.00012 27.3 1.4 24 263-286 1-29 (43)
53 PF06221 zf-C2HC5: Putative zi 60.1 3 6.6E-05 31.0 0.1 15 275-289 17-31 (57)
54 PF14599 zinc_ribbon_6: Zinc-r 58.5 2.8 6E-05 31.6 -0.4 36 197-236 9-44 (61)
55 KOG0828|consensus 58.4 5.4 0.00012 41.5 1.5 22 114-135 600-621 (636)
56 TIGR00570 cdk7 CDK-activating 58.1 6.8 0.00015 38.4 2.1 18 116-133 22-39 (309)
57 PF11023 DUF2614: Protein of u 57.1 3.6 7.9E-05 34.6 0.1 30 258-288 65-97 (114)
58 COG2888 Predicted Zn-ribbon RN 55.6 5.1 0.00011 30.1 0.7 26 258-283 23-57 (61)
59 PF07800 DUF1644: Protein of u 55.2 11 0.00023 33.7 2.7 53 123-175 36-96 (162)
60 PF05191 ADK_lid: Adenylate ki 55.1 3.6 7.7E-05 27.7 -0.2 24 262-285 1-30 (36)
61 PRK14890 putative Zn-ribbon RN 54.3 5.5 0.00012 29.9 0.7 13 259-271 22-34 (59)
62 PF13445 zf-RING_UBOX: RING-ty 52.8 10 0.00023 26.3 1.8 21 115-135 14-34 (43)
63 PF07754 DUF1610: Domain of un 51.7 6.3 0.00014 24.4 0.5 12 259-270 13-24 (24)
64 PF15616 TerY-C: TerY-C metal 50.3 12 0.00025 32.4 2.1 38 263-303 78-121 (131)
65 smart00154 ZnF_AN1 AN1-like Zi 50.3 12 0.00025 25.5 1.7 25 265-289 1-25 (39)
66 PF12773 DZR: Double zinc ribb 50.2 11 0.00023 26.3 1.5 25 259-283 26-50 (50)
67 COG4530 Uncharacterized protei 48.3 9.5 0.00021 32.2 1.2 26 261-286 8-36 (129)
68 COG5219 Uncharacterized conser 47.5 11 0.00024 42.2 1.9 24 113-136 1487-1510(1525)
69 PF14446 Prok-RING_1: Prokaryo 44.3 14 0.0003 27.3 1.4 26 260-285 3-30 (54)
70 KOG0309|consensus 43.2 12 0.00026 40.9 1.3 24 112-135 1040-1063(1081)
71 PF15353 HECA: Headcase protei 43.2 15 0.00033 30.6 1.7 18 120-137 40-57 (107)
72 COG2093 DNA-directed RNA polym 42.9 9.2 0.0002 29.1 0.3 23 262-284 4-26 (64)
73 PRK12286 rpmF 50S ribosomal pr 42.4 15 0.00033 27.1 1.4 24 261-285 26-49 (57)
74 PF11331 DUF3133: Protein of u 38.8 5.1 0.00011 28.6 -1.5 29 244-272 13-41 (46)
75 KOG0317|consensus 37.9 23 0.0005 34.4 2.2 23 112-134 249-271 (293)
76 COG5540 RING-finger-containing 37.1 24 0.00052 34.8 2.2 20 114-133 338-357 (374)
77 PRK00398 rpoP DNA-directed RNA 37.0 25 0.00054 24.3 1.8 25 262-286 3-31 (46)
78 PF03604 DNA_RNApol_7kD: DNA d 35.7 23 0.00049 23.3 1.3 21 264-284 2-25 (32)
79 PF01428 zf-AN1: AN1-like Zinc 35.2 24 0.00052 24.2 1.4 23 266-289 4-26 (43)
80 KOG2114|consensus 34.1 19 0.00042 39.7 1.2 29 113-167 852-880 (933)
81 TIGR01031 rpmF_bact ribosomal 33.6 26 0.00055 25.7 1.4 24 261-285 25-48 (55)
82 KOG0320|consensus 33.6 28 0.00061 31.7 1.9 21 115-135 146-166 (187)
83 COG4855 Uncharacterized protei 33.4 22 0.00047 27.6 1.0 23 265-288 13-35 (76)
84 TIGR02098 MJ0042_CXXC MJ0042 f 33.1 30 0.00064 22.7 1.6 25 262-286 2-35 (38)
85 KOG0287|consensus 32.1 34 0.00073 34.3 2.4 21 113-133 34-54 (442)
86 PRK00420 hypothetical protein; 31.7 32 0.00069 28.9 1.9 25 262-286 23-50 (112)
87 KOG2845|consensus 31.1 17 0.00038 37.7 0.2 13 278-290 172-184 (505)
88 cd00350 rubredoxin_like Rubred 30.0 29 0.00063 22.5 1.1 22 263-284 2-25 (33)
89 KOG1734|consensus 29.1 26 0.00056 34.0 1.0 21 113-133 245-265 (328)
90 KOG0269|consensus 28.2 33 0.00071 37.6 1.6 21 115-135 794-814 (839)
91 smart00647 IBR In Between Ring 27.8 46 0.001 23.6 2.0 29 261-289 17-53 (64)
92 COG4830 RPS26B Ribosomal prote 26.6 34 0.00074 28.3 1.2 19 263-281 21-39 (108)
93 KOG1814|consensus 26.2 34 0.00074 34.9 1.3 31 262-295 368-402 (445)
94 KOG3268|consensus 26.0 48 0.001 30.4 2.1 40 116-167 186-225 (234)
95 PF01363 FYVE: FYVE zinc finge 25.8 42 0.00091 24.7 1.4 32 261-294 8-41 (69)
96 TIGR00354 polC DNA polymerase, 25.7 27 0.00058 39.3 0.5 25 260-286 623-647 (1095)
97 PF09889 DUF2116: Uncharacteri 25.7 22 0.00047 26.6 -0.1 14 262-275 3-16 (59)
98 PRK14714 DNA polymerase II lar 25.6 31 0.00068 39.8 1.0 23 262-286 667-689 (1337)
99 PF05883 Baculo_RING: Baculovi 25.1 68 0.0015 27.9 2.8 22 112-133 39-66 (134)
100 PRK14715 DNA polymerase II lar 24.7 30 0.00066 40.2 0.7 24 260-285 672-695 (1627)
101 PRK09335 30S ribosomal protein 23.9 48 0.001 27.2 1.5 21 262-282 20-40 (95)
102 cd00729 rubredoxin_SM Rubredox 23.8 35 0.00076 22.4 0.6 22 263-284 3-26 (34)
103 PRK12495 hypothetical protein; 23.4 70 0.0015 30.1 2.7 27 260-286 40-68 (226)
104 PF04423 Rad50_zn_hook: Rad50 23.2 31 0.00067 24.6 0.3 7 161-167 22-28 (54)
105 COG0333 RpmF Ribosomal protein 22.8 49 0.0011 24.6 1.3 23 261-284 26-48 (57)
106 smart00659 RPOLCX RNA polymera 22.7 51 0.0011 23.0 1.3 22 263-284 3-27 (44)
107 KOG1785|consensus 22.7 41 0.00088 34.4 1.1 43 112-175 379-421 (563)
108 PHA00626 hypothetical protein 22.3 64 0.0014 24.2 1.7 8 264-271 2-9 (59)
109 KOG0804|consensus 22.2 46 0.001 34.4 1.4 24 110-133 187-210 (493)
110 PF14206 Cys_rich_CPCC: Cystei 22.2 44 0.00096 26.4 1.0 22 262-283 1-27 (78)
111 KOG1002|consensus 22.2 62 0.0014 34.3 2.3 72 112-207 546-621 (791)
112 PF01783 Ribosomal_L32p: Ribos 22.1 35 0.00076 24.9 0.4 23 261-284 25-47 (56)
113 PF04641 Rtf2: Rtf2 RING-finge 22.1 68 0.0015 30.3 2.4 21 112-132 127-147 (260)
114 KOG2164|consensus 21.3 55 0.0012 34.2 1.7 46 113-176 197-244 (513)
115 KOG0804|consensus 20.9 45 0.00098 34.5 1.0 25 262-288 228-252 (493)
116 COG2023 RPR2 RNase P subunit R 20.3 84 0.0018 26.2 2.3 24 262-285 56-91 (105)
117 PRK14892 putative transcriptio 20.2 45 0.00097 27.4 0.7 23 261-285 20-51 (99)
118 PRK12496 hypothetical protein; 20.1 53 0.0012 29.0 1.2 24 262-285 127-152 (164)
No 1
>KOG1140|consensus
Probab=99.87 E-value=1.3e-22 Score=223.49 Aligned_cols=159 Identities=28% Similarity=0.429 Sum_probs=110.0
Q ss_pred CHHHHHHHHHHhHHhhhhhhcccccccCCcCccCCCCCC-------ccccCCCCCCCCCCCCCccceeecCCCccccc-C
Q psy9235 1 MQAQQNSFMKENAQLFEANATIKLEEEEPESSCMDVVEH-------PVALGPNQTPRPNTGPVYYTCILCQEEQALTK-Q 72 (317)
Q Consensus 1 ms~~Qk~Fm~~N~~l~~~~~~~~~e~~~~~~~~md~~~~-------~valGp~~~~~~~~~~~~~tCILCqE~~~~~~-~ 72 (317)
|++||.+||++|.+-|++.. +..++..+ ......+.. .-.+-+..+..........+|++|++...+.. .
T Consensus 1039 ~s~qq~kfm~~~e~e~d~~~-~~~~~~~~-~~~~~~d~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~i~~e~e~~~~~~ 1116 (1738)
T KOG1140|consen 1039 FSNQQTKFMAENEDEFDEQE-NQTPSSGS-KTYEEEDFTCALCQDNSCTDFQVKPASHLVKPIFRECIICDENEDVPNWD 1116 (1738)
T ss_pred HHHHHHHHHHhcccccCccc-ccCccccc-cchhhhhccchhhhccchhccccccchhhhcccccccccCChhccCCCcc
Confidence 68999999999976665521 11111111 000000000 00001111222212345679999999998865 5
Q ss_pred CCcEEEEEeeecCcccccccCCCCCCCcccccccCCCCCCCCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCc
Q psy9235 73 NDALVLAAFVQQSTVMFRNRNADRTDFKVNSLYISLEHQGPAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTS 152 (317)
Q Consensus 73 ~~p~g~~a~vQ~S~Vl~~~~~~~~~~~~D~~l~~~~~~~~~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~ 152 (317)
+..++..+|+|+++.... +++.+. ....|+++++|||.||+.||++|+++.+.+++.+....+.+..
T Consensus 1117 ~~~~v~~~f~~~s~~~sd------------~l~~p~-~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~s 1183 (1738)
T KOG1140|consen 1117 GRYSVSSAFAQKSDDVSD------------ALTEPG-SLSCGTVLSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYS 1183 (1738)
T ss_pred ccchhhhHhhhhcccccc------------cccCCC-CCcccceeeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccc
Confidence 689999999999987751 344454 6778999999999999999999999999888887776666544
Q ss_pred cCCCCCeeeccCCccccceEeccCC
Q psy9235 153 FDIEKNEFLCPLCECLSNAALPLIP 177 (317)
Q Consensus 153 ~d~~~~EFlCPLCrsLsN~vLP~ip 177 (317)
++++|+||+|++|+|+.||.++
T Consensus 1184 ---e~~l~lCp~c~slsn~~lp~~~ 1205 (1738)
T KOG1140|consen 1184 ---ENGLFLCPLCKSLSNVSLPMFL 1205 (1738)
T ss_pred ---cCCcccCCchHhhhhccCCcCC
Confidence 7899999999999999999654
No 2
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=97.01 E-value=0.00035 Score=48.19 Aligned_cols=22 Identities=27% Similarity=0.718 Sum_probs=18.6
Q ss_pred CCceeecCCchhhHHHHHHHhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
..++.-.|||..|.+|+++|++
T Consensus 14 ~~~~~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 14 EKVVKLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp SCEEEETTSEEEEHHHHHHHHH
T ss_pred CeEEEccCCCeeCHHHHHHHHH
Confidence 3566777999999999999984
No 3
>KOG1139|consensus
Probab=96.92 E-value=0.0012 Score=69.75 Aligned_cols=77 Identities=13% Similarity=0.232 Sum_probs=49.6
Q ss_pred CHHHHHHHHHHhHHhhhhhhcccccccCCcCccCCCCCCccccCCCCCCCCCCCCCccceeecCCCcccccCCCcEEEEE
Q psy9235 1 MQAQQNSFMKENAQLFEANATIKLEEEEPESSCMDVVEHPVALGPNQTPRPNTGPVYYTCILCQEEQALTKQNDALVLAA 80 (317)
Q Consensus 1 ms~~Qk~Fm~~N~~l~~~~~~~~~e~~~~~~~~md~~~~~valGp~~~~~~~~~~~~~tCILCqE~~~~~~~~~p~g~~a 80 (317)
|+++|+-||.+|..-=.. . . ..|+ +....-+||.+ ..+..|.|++|+.... .+.++|+|+++
T Consensus 648 fa~~~~~~~~q~~a~~s~-~---~-------~g~e-d~~~~~~~~~q-----~~~k~y~C~icg~n~p-~T~~np~G~~~ 709 (784)
T KOG1139|consen 648 FAKRRMEAIMQNSAKKSA-Q---T-------EGME-DAEVNKVDPSQ-----QNRKVYECPICGQNAP-NTVENPFGMLA 709 (784)
T ss_pred HHHHHHHHHHHHHHHhhh-c---c-------cCCC-hHHHhhhCccc-----CCccCCcCCcCCCCCC-cccCCCceEEE
Confidence 567888888888542111 0 1 1121 11112236665 3456899999995544 47899999999
Q ss_pred eeecCcccccccCCC
Q psy9235 81 FVQQSTVMFRNRNAD 95 (317)
Q Consensus 81 ~vQ~S~Vl~~~~~~~ 95 (317)
++.++.|+.+.....
T Consensus 710 l~~~~~I~~~r~~~~ 724 (784)
T KOG1139|consen 710 LLSTNFICEERIDAS 724 (784)
T ss_pred EEeecchHHHHHhhc
Confidence 999999998766543
No 4
>KOG1139|consensus
Probab=96.69 E-value=0.0011 Score=69.99 Aligned_cols=69 Identities=6% Similarity=-0.103 Sum_probs=58.1
Q ss_pred ccccccccCCChhHHHHHHhhccccCCCCCCCCCCCceeeceeCceecC--CCccccccc-----cccccceEEEEEeee
Q psy9235 240 PLEINRLINLPDDYSELINTVSLFTCPNSDREDSRNPALCLICGDMLCS--QSYCCQTEL-----FFKMSARSFFTVNKT 312 (317)
Q Consensus 240 p~~~~~l~~LP~~y~~L~~~~~~~~C~~c~~~~~~~P~lCL~CG~~~C~--~~~CC~~~~-----~~~~~~~~~~~~~~~ 312 (317)
|+..|.+..+|--|+++.++..+. +.+ +|+.|+.||. .|. +.|||...+ .|++|+|+|++|.++
T Consensus 644 ~~~~fa~~~~~~~~q~~a~~s~~~-------~g~-ed~~~~~~~~-~q~~~k~y~C~icg~n~p~T~~np~G~~~l~~~~ 714 (784)
T KOG1139|consen 644 AAKEFAKRRMEAIMQNSAKKSAQT-------EGM-EDAEVNKVDP-SQQNRKVYECPICGQNAPNTVENPFGMLALLSTN 714 (784)
T ss_pred HhHHHHHHHHHHHHHHHHHhhhcc-------cCC-ChHHHhhhCc-ccCCccCCcCCcCCCCCCcccCCCceEEEEEeec
Confidence 888899999999999999976554 434 8999999998 566 899997543 599999999999999
Q ss_pred EEeeC
Q psy9235 313 LFLVH 317 (317)
Q Consensus 313 ~~~~~ 317 (317)
+|+-|
T Consensus 715 ~I~~~ 719 (784)
T KOG1139|consen 715 FICEE 719 (784)
T ss_pred chHHH
Confidence 99754
No 5
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=96.20 E-value=0.0031 Score=41.76 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=16.9
Q ss_pred CceeecCCchhhHHHHHHHhh
Q psy9235 114 APHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~ 134 (317)
...+..|||.+|..|++.|++
T Consensus 12 ~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 12 PVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred ceEecCCCChhcHHHHHHHHH
Confidence 344555999999999999974
No 6
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.88 E-value=0.0053 Score=49.06 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=20.1
Q ss_pred CCceeecCCchhhHHHHHHHhhhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDNI 136 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s~ 136 (317)
..++...|||.-|..|..+.+++.
T Consensus 45 Cplv~g~C~H~FH~hCI~kWl~~~ 68 (85)
T PF12861_consen 45 CPLVWGKCSHNFHMHCILKWLSTQ 68 (85)
T ss_pred CceeeccCccHHHHHHHHHHHccc
Confidence 356778899999999999998653
No 7
>KOG1940|consensus
Probab=95.19 E-value=0.014 Score=55.85 Aligned_cols=73 Identities=22% Similarity=0.498 Sum_probs=49.9
Q ss_pred CCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEeccCCCCCCCCCCCCccccc
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALPLIPALSSIQTTTPTENAE 192 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP~ip~~~~~~~~~~~e~~~ 192 (317)
..+.+-.|||.||+.||+.|.. .+ |.||+|..+.|...
T Consensus 173 ~~~~~~~CgH~~h~~cf~e~~~----------------------~~-y~CP~C~~~~d~~~------------------- 210 (276)
T KOG1940|consen 173 EDAGVLKCGHYMHSRCFEEMIC----------------------EG-YTCPICSKPGDMSH------------------- 210 (276)
T ss_pred ccCCccCcccchHHHHHHHHhc----------------------cC-CCCCcccchHHHHH-------------------
Confidence 5678889999999999999961 24 99999987444332
Q ss_pred cccccCHHHHHHHHHHHHHH---HHHhhhhccCCcccCCCCCCcccc
Q psy9235 193 VFVHMDFDAWLSIVEMVLEH---KKRLKKSKATSECQDSTSSKQVPQ 236 (317)
Q Consensus 193 ~~~~~~~~~w~~~~~~~~~~---~~~~~~~~~~~~~~~s~~~~~v~~ 236 (317)
-.+.+.+.|++ --+...+++-..|+||.....++.
T Consensus 211 ---------~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~ 248 (276)
T KOG1940|consen 211 ---------YFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKY 248 (276)
T ss_pred ---------HHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccce
Confidence 22334444443 122355777888999888777653
No 8
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=94.88 E-value=0.015 Score=39.08 Aligned_cols=22 Identities=27% Similarity=0.726 Sum_probs=19.0
Q ss_pred CceeecCCchhhHHHHHHHhhh
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s 135 (317)
..++..|||....+|+++|++.
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHHC
T ss_pred cCEECCCCCchhHHHHHHHHHC
Confidence 3478999999999999999843
No 9
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=94.85 E-value=0.026 Score=35.78 Aligned_cols=22 Identities=27% Similarity=0.723 Sum_probs=19.0
Q ss_pred CCceeecCCchhhHHHHHHHhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
..+.+..|||..|..|++.|++
T Consensus 9 ~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 9 KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcEEecCCChHHHHHHHHHHH
Confidence 4567778999999999999985
No 10
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.81 E-value=0.021 Score=56.80 Aligned_cols=17 Identities=29% Similarity=1.021 Sum_probs=15.4
Q ss_pred ecCCchhhHHHHHHHhh
Q psy9235 118 STCGHVMHSTCWSKYFD 134 (317)
Q Consensus 118 ssCGH~mH~~C~~~Y~~ 134 (317)
-.|||..|.+|++.+++
T Consensus 316 LpCGHilHl~CLknW~E 332 (491)
T COG5243 316 LPCGHILHLHCLKNWLE 332 (491)
T ss_pred ccccceeeHHHHHHHHH
Confidence 36999999999999985
No 11
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=94.58 E-value=0.018 Score=44.25 Aligned_cols=21 Identities=29% Similarity=0.705 Sum_probs=17.2
Q ss_pred CceeecCCchhhHHHHHHHhh
Q psy9235 114 APHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~ 134 (317)
.+....|||.-|..|..+.++
T Consensus 44 ~i~~~~C~H~FH~~Ci~~Wl~ 64 (73)
T PF12678_consen 44 PIVWGPCGHIFHFHCISQWLK 64 (73)
T ss_dssp -EEEETTSEEEEHHHHHHHHT
T ss_pred ceEecccCCCEEHHHHHHHHh
Confidence 346678999999999999983
No 12
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=94.47 E-value=0.022 Score=38.25 Aligned_cols=20 Identities=30% Similarity=0.735 Sum_probs=18.3
Q ss_pred eeecCCchhhHHHHHHHhhh
Q psy9235 116 HTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~~s 135 (317)
.+..|||..+..|+.+|+++
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHH
T ss_pred EEecCCCcchHHHHHHHHHh
Confidence 58999999999999999864
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=93.77 E-value=0.074 Score=48.57 Aligned_cols=55 Identities=24% Similarity=0.533 Sum_probs=35.7
Q ss_pred ceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCcccc--ceEeccC
Q psy9235 115 PHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLS--NAALPLI 176 (317)
Q Consensus 115 ~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLs--N~vLP~i 176 (317)
+++..|||.-...|+.+|+....... .+. +. .+...+...||+||+.- +.++|++
T Consensus 31 PVvT~CGH~FC~~CI~~wl~~s~~s~-~~~---~~---~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 31 PVVTLCGHLFCWPCIHKWTYASNNSR-QRV---DQ---YDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred cEEcCCCchhHHHHHHHHHHhccccc-ccc---cc---ccccCCCCcCCCCCCcCChhcEEEee
Confidence 46678999999999999975432110 000 00 01135678999999865 4588886
No 14
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=93.55 E-value=0.073 Score=36.75 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=18.9
Q ss_pred CCceeecCCchhhHHHHHHHh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~ 133 (317)
....+.+|||.+..+|+++..
T Consensus 13 ~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 13 RRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCeEEcccCCHHHHHHHHhhc
Confidence 468999999999999999886
No 15
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=92.76 E-value=0.042 Score=42.06 Aligned_cols=39 Identities=33% Similarity=0.645 Sum_probs=19.6
Q ss_pred ecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccc
Q psy9235 118 STCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECL 168 (317)
Q Consensus 118 ssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsL 168 (317)
..||+..|..|+.+|+.+.... |. .|++-.| .||.|+..
T Consensus 26 ~~C~~~fH~~CL~~wf~~~~~~--------~~--~~~~~~G--~CP~C~~~ 64 (70)
T PF11793_consen 26 PSCGKKFHLLCLSEWFLSLEKS--------RQ--SFIPIFG--ECPYCSSP 64 (70)
T ss_dssp TT----B-SGGGHHHHHHHHSS--------S---TTT--EE--E-TTT-SE
T ss_pred cccCCHHHHHHHHHHHHHcccC--------Ce--eeccccc--CCcCCCCe
Confidence 3799999999999999877532 11 1233233 49999863
No 16
>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=92.42 E-value=0.068 Score=44.54 Aligned_cols=26 Identities=27% Similarity=0.706 Sum_probs=22.7
Q ss_pred ccccCCCCCCC---CCCCceeeceeCcee
Q psy9235 261 SLFTCPNSDRE---DSRNPALCLICGDML 286 (317)
Q Consensus 261 ~~~~C~~c~~~---~~~~P~lCL~CG~~~ 286 (317)
.+|.||+||+- +.++|++|-.||+.+
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 68999999975 678999999999865
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.36 E-value=0.07 Score=32.49 Aligned_cols=22 Identities=32% Similarity=0.705 Sum_probs=19.9
Q ss_pred cCCCCCCCCCCCceeeceeCce
Q psy9235 264 TCPNSDREDSRNPALCLICGDM 285 (317)
Q Consensus 264 ~C~~c~~~~~~~P~lCL~CG~~ 285 (317)
+||+||.+++++-..|..||+-
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 5999999999999999999974
No 18
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=92.30 E-value=0.15 Score=35.87 Aligned_cols=36 Identities=19% Similarity=0.526 Sum_probs=28.0
Q ss_pred CCceeecCCch-hhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccce
Q psy9235 113 PAPHTSTCGHV-MHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNA 171 (317)
Q Consensus 113 ~g~~vssCGH~-mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~ 171 (317)
..+.+..|||. +-..|+.++++. .-.||+||+--+.
T Consensus 13 ~~~~~~pCgH~~~C~~C~~~~~~~-----------------------~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 13 RDVVLLPCGHLCFCEECAERLLKR-----------------------KKKCPICRQPIES 49 (50)
T ss_dssp SSEEEETTCEEEEEHHHHHHHHHT-----------------------TSBBTTTTBB-SE
T ss_pred CceEEeCCCChHHHHHHhHHhccc-----------------------CCCCCcCChhhcC
Confidence 35788899999 999999999851 1179999986553
No 19
>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=91.90 E-value=0.077 Score=33.33 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCCCceeeceeCcee
Q psy9235 263 FTCPNSDREDSRNPALCLICGDML 286 (317)
Q Consensus 263 ~~C~~c~~~~~~~P~lCL~CG~~~ 286 (317)
++||.|++++|..-..|-.||-.+
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 479999999999999999999654
No 20
>PHA02929 N1R/p28-like protein; Provisional
Probab=91.78 E-value=0.11 Score=48.90 Aligned_cols=36 Identities=22% Similarity=0.469 Sum_probs=27.7
Q ss_pred eeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEec
Q psy9235 116 HTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALP 174 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP 174 (317)
++..|||..|..|+..+++.. =.||+||..--.|++
T Consensus 196 vl~~C~H~FC~~CI~~Wl~~~-----------------------~tCPlCR~~~~~v~~ 231 (238)
T PHA02929 196 ILSNCNHVFCIECIDIWKKEK-----------------------NTCPVCRTPFISVIK 231 (238)
T ss_pred ecCCCCCcccHHHHHHHHhcC-----------------------CCCCCCCCEeeEEee
Confidence 566899999999999986311 169999987666665
No 21
>PHA02926 zinc finger-like protein; Provisional
Probab=90.37 E-value=0.22 Score=46.56 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=34.8
Q ss_pred CceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEecc
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALPL 175 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP~ 175 (317)
..++..|||.-...|..+..++... ...+-.||+||.-...++|-
T Consensus 191 FGIL~~CnHsFCl~CIr~Wr~~r~~-----------------~~~~rsCPiCR~~f~~I~pS 235 (242)
T PHA02926 191 FGLLDSCNHIFCITCINIWHRTRRE-----------------TGASDNCPICRTRFRNITMS 235 (242)
T ss_pred ccccCCCCchHHHHHHHHHHHhccc-----------------cCcCCcCCCCcceeeeeccc
Confidence 3478899999999999999754210 12356899999999988874
No 22
>KOG4445|consensus
Probab=90.28 E-value=0.054 Score=52.52 Aligned_cols=51 Identities=29% Similarity=0.603 Sum_probs=33.4
Q ss_pred CceeecCCchhhHHHHHHHhhhhhhhccCC---ccccCCCCccCCCCCeeeccCCcc
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDNILAKENRR---PYRLRQPTSFDIEKNEFLCPLCEC 167 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr---~q~~R~~~~~d~~~~EFlCPLCrs 167 (317)
...++-|-|+||+.||.+|+......-+.- .+.-|.|.- +.-+-+||.||-
T Consensus 130 ~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~---~~~eavcpVcre 183 (368)
T KOG4445|consen 130 AFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMK---EQVEAVCPVCRE 183 (368)
T ss_pred ceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---hhHhhhhhHhhh
Confidence 467889999999999999998764322110 112233332 345667999985
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.67 E-value=0.18 Score=31.35 Aligned_cols=24 Identities=29% Similarity=0.631 Sum_probs=21.0
Q ss_pred cccCCCCCCCCCCCceeeceeCce
Q psy9235 262 LFTCPNSDREDSRNPALCLICGDM 285 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P~lCL~CG~~ 285 (317)
.+.||+||..++.+-..|-.||+-
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCC
Confidence 467999999988899999999974
No 24
>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=88.45 E-value=0.25 Score=42.35 Aligned_cols=26 Identities=27% Similarity=0.535 Sum_probs=22.7
Q ss_pred ccccCCCCCCC---CCCCceeeceeCcee
Q psy9235 261 SLFTCPNSDRE---DSRNPALCLICGDML 286 (317)
Q Consensus 261 ~~~~C~~c~~~---~~~~P~lCL~CG~~~ 286 (317)
.+|.||+||+- +.++|++|-.||+.+
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCcc
Confidence 68999999975 568999999999874
No 25
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=88.38 E-value=0.2 Score=37.56 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=25.5
Q ss_pred hhccccCCCCCCCC-----CCCceeeceeCceecC
Q psy9235 259 TVSLFTCPNSDRED-----SRNPALCLICGDMLCS 288 (317)
Q Consensus 259 ~~~~~~C~~c~~~~-----~~~P~lCL~CG~~~C~ 288 (317)
++.+.+||.|+.+- +..++.|+.||+.++-
T Consensus 8 ~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 8 RFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred eEEEEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 36788999999874 5689999999999975
No 26
>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=87.64 E-value=0.27 Score=36.31 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=20.1
Q ss_pred hhccccCCCCCCC-----CCCCceeeceeCceecC
Q psy9235 259 TVSLFTCPNSDRE-----DSRNPALCLICGDMLCS 288 (317)
Q Consensus 259 ~~~~~~C~~c~~~-----~~~~P~lCL~CG~~~C~ 288 (317)
++.+.+||.|+.+ -+..++.|+.||.++|-
T Consensus 4 ~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 4 YFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp -EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred cEEEEECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 3678899999976 13579999999999985
No 27
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=87.59 E-value=0.86 Score=49.81 Aligned_cols=66 Identities=15% Similarity=0.232 Sum_probs=46.4
Q ss_pred CCCccceeecCCCcccccCCCcEEEEEeeecCcccccccCCCCCCCcccccccCCCCCCCCceeecCCchhhHHHHHHHh
Q psy9235 54 GPVYYTCILCQEEQALTKQNDALVLAAFVQQSTVMFRNRNADRTDFKVNSLYISLEHQGPAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 54 ~~~~~tCILCqE~~~~~~~~~p~g~~a~vQ~S~Vl~~~~~~~~~~~~D~~l~~~~~~~~~g~~vssCGH~mH~~C~~~Y~ 133 (317)
++.-.+|.+|+|.-.. ..++++|+-+|.-+.++-..... . ....|.-+.|=..++|++|.++-.
T Consensus 465 ee~gl~C~ICrEGy~~-~p~~~lGiY~f~kr~~l~~~~~~--------------~-~~~~~~sTVs~fn~iH~~CH~~A~ 528 (802)
T PF13764_consen 465 EEDGLTCCICREGYKF-RPDEVLGIYAFSKRVNLEEFEGK--------------S-RKTYGYSTVSHFNIIHFSCHQSAV 528 (802)
T ss_pred ccCCCeEEEcCCcccc-CCccceeeEEEeecccchhhccC--------------C-CCCcceeeeeeeeeeeHHhhHHHH
Confidence 4556799999998754 35788999999987766431100 0 122466666777899999999887
Q ss_pred hh
Q psy9235 134 DN 135 (317)
Q Consensus 134 ~s 135 (317)
++
T Consensus 529 ra 530 (802)
T PF13764_consen 529 RA 530 (802)
T ss_pred Hh
Confidence 64
No 28
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=87.45 E-value=0.31 Score=37.29 Aligned_cols=31 Identities=29% Similarity=0.662 Sum_probs=25.0
Q ss_pred hhccccCCCCCCC-----CCCCceeeceeCceecCC
Q psy9235 259 TVSLFTCPNSDRE-----DSRNPALCLICGDMLCSQ 289 (317)
Q Consensus 259 ~~~~~~C~~c~~~-----~~~~P~lCL~CG~~~C~~ 289 (317)
++.+.+||.|+.+ -+...+.|+.||++++-.
T Consensus 16 ~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred eEEEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 4678899999976 245789999999999863
No 29
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=85.57 E-value=0.39 Score=38.39 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=24.9
Q ss_pred hccccCCCCCCCC-----CCCceeeceeCceecCC
Q psy9235 260 VSLFTCPNSDRED-----SRNPALCLICGDMLCSQ 289 (317)
Q Consensus 260 ~~~~~C~~c~~~~-----~~~P~lCL~CG~~~C~~ 289 (317)
+...+||.|+.+- ...++.|+.||.++|--
T Consensus 33 Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 33 FMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred EEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 6889999999871 24799999999999863
No 30
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=85.30 E-value=0.65 Score=31.96 Aligned_cols=24 Identities=21% Similarity=0.555 Sum_probs=19.1
Q ss_pred CCCCceeecCCchhhHHHHHHHhh
Q psy9235 111 QGPAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 111 ~~~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
....+++-.|||..=.+|+.++.+
T Consensus 7 ~~~~Pv~l~CGH~FC~~Cl~~~~~ 30 (42)
T PF15227_consen 7 LFKDPVSLPCGHSFCRSCLERLWK 30 (42)
T ss_dssp B-SSEEE-SSSSEEEHHHHHHHHC
T ss_pred hhCCccccCCcCHHHHHHHHHHHH
Confidence 345678899999999999999974
No 31
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=84.89 E-value=0.72 Score=36.71 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=20.0
Q ss_pred CCceeecCCchhhHHHHHHHhhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s 135 (317)
.-++...|.|.-|..|..+++++
T Consensus 47 C~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 47 CPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred ceEEEEecchHHHHHHHHHHHhh
Confidence 45677889999999999999865
No 32
>KOG2930|consensus
Probab=81.84 E-value=1.2 Score=37.14 Aligned_cols=22 Identities=23% Similarity=0.593 Sum_probs=18.2
Q ss_pred CceeecCCchhhHHHHHHHhhh
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s 135 (317)
-+.=..|.|.-|+.|..+++++
T Consensus 75 ~VaWG~CNHaFH~hCisrWlkt 96 (114)
T KOG2930|consen 75 TVAWGVCNHAFHFHCISRWLKT 96 (114)
T ss_pred EEEeeecchHHHHHHHHHHHhh
Confidence 3455679999999999999854
No 33
>PLN00209 ribosomal protein S27; Provisional
Probab=81.27 E-value=0.75 Score=36.88 Aligned_cols=31 Identities=19% Similarity=0.375 Sum_probs=25.3
Q ss_pred hhccccCCCCCCCC-----CCCceeeceeCceecCC
Q psy9235 259 TVSLFTCPNSDRED-----SRNPALCLICGDMLCSQ 289 (317)
Q Consensus 259 ~~~~~~C~~c~~~~-----~~~P~lCL~CG~~~C~~ 289 (317)
++...+||.|+.+- +..++.|+.||.++|--
T Consensus 33 ~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 33 FFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred EEEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 36889999999871 34799999999999863
No 34
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=80.06 E-value=1.3 Score=43.22 Aligned_cols=23 Identities=30% Similarity=0.639 Sum_probs=20.0
Q ss_pred CCCCceeecCCchhhHHHHHHHh
Q psy9235 111 QGPAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 111 ~~~g~~vssCGH~mH~~C~~~Y~ 133 (317)
...-+..++|||.--+=|.++|+
T Consensus 34 ~i~ip~~TtCgHtFCslCIR~hL 56 (391)
T COG5432 34 RISIPCETTCGHTFCSLCIRRHL 56 (391)
T ss_pred eeecceecccccchhHHHHHHHh
Confidence 33567899999999999999998
No 35
>KOG0823|consensus
Probab=79.48 E-value=1.7 Score=40.75 Aligned_cols=47 Identities=21% Similarity=0.563 Sum_probs=35.9
Q ss_pred CCCCCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccc--cceEeccC
Q psy9235 110 HQGPAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECL--SNAALPLI 176 (317)
Q Consensus 110 ~~~~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsL--sN~vLP~i 176 (317)
+....++++-|||.-=--|+.+++....+ -=.||.||+- ..+|||++
T Consensus 55 d~akdPVvTlCGHLFCWpClyqWl~~~~~--------------------~~~cPVCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 55 DLAKDPVVTLCGHLFCWPCLYQWLQTRPN--------------------SKECPVCKAEVSIDTVVPLY 103 (230)
T ss_pred cccCCCEEeecccceehHHHHHHHhhcCC--------------------CeeCCccccccccceEEeee
Confidence 45578999999999988888888744211 1268999986 57899995
No 36
>KOG1428|consensus
Probab=78.92 E-value=0.94 Score=52.18 Aligned_cols=104 Identities=21% Similarity=0.413 Sum_probs=60.8
Q ss_pred ecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEec--cCCCCCCCCCCCCcccccccc
Q psy9235 118 STCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALP--LIPALSSIQTTTPTENAEVFV 195 (317)
Q Consensus 118 ssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP--~ip~~~~~~~~~~~e~~~~~~ 195 (317)
-.|||..|+.|-.+-++.-+.- | ....+...||+|+.--|-++- ++.|...+
T Consensus 3505 L~C~HiFHlqC~R~vLE~RW~G-----------P--RItF~FisCPiC~n~InH~~LkDLldPiKel------------- 3558 (3738)
T KOG1428|consen 3505 LDCSHIFHLQCCRRVLENRWLG-----------P--RITFGFISCPICKNKINHIVLKDLLDPIKEL------------- 3558 (3738)
T ss_pred cCCccchhHHHHHHHHHhcccC-----------C--eeEEeeeecccccchhhhHHHHHHHHHHHHH-------------
Confidence 3699999999999998765421 1 124678899999986665431 11111111
Q ss_pred ccCHHHHHHHHHHHHHHHHHhhhhccCCcccCCCCCCcccccCCccccccccCCChhHHHHHHhhccccCCCCCC
Q psy9235 196 HMDFDAWLSIVEMVLEHKKRLKKSKATSECQDSTSSKQVPQDRKPLEINRLINLPDDYSELINTVSLFTCPNSDR 270 (317)
Q Consensus 196 ~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~v~~~~~p~~~~~l~~LP~~y~~L~~~~~~~~C~~c~~ 270 (317)
+++-.+...|++|+. ++ .+ -|.+++|.. ++.+=|..|. +++|....|-+|.+
T Consensus 3559 ---~edV~~KA~MRLEYe-GL---~k------------s~AiT~P~~--~FYNdPa~YA--mnRY~Y~vC~KCrK 3610 (3738)
T KOG1428|consen 3559 ---YEDVRRKALMRLEYE-GL---HK------------SEAITTPGV--RFYNDPAGYA--MNRYAYYVCYKCRK 3610 (3738)
T ss_pred ---HHHHHHHHhhhhhhc-cc---cc------------cccccCCCc--eeccChhhhh--hhhhhhhhhhhhhh
Confidence 223333444455541 11 11 234454554 4566777775 78888888877754
No 37
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=78.12 E-value=1.4 Score=32.75 Aligned_cols=25 Identities=32% Similarity=0.681 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCceeeceeCceecCCC
Q psy9235 265 CPNSDREDSRNPALCLICGDMLCSQS 290 (317)
Q Consensus 265 C~~c~~~~~~~P~lCL~CG~~~C~~~ 290 (317)
|..|+.. .++.-+||.||.+.|...
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~~ 25 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGRY 25 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETTT
T ss_pred CCCCCCc-CCceEEeCCCCcccccCC
Confidence 5667765 568999999999999953
No 38
>KOG0802|consensus
Probab=77.26 E-value=1.3 Score=46.05 Aligned_cols=19 Identities=32% Similarity=1.041 Sum_probs=16.3
Q ss_pred eecCCchhhHHHHHHHhhh
Q psy9235 117 TSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 117 vssCGH~mH~~C~~~Y~~s 135 (317)
.-.|||.-|..|++++++-
T Consensus 311 rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 311 RLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred eeecccchHHHHHHHHHHH
Confidence 3469999999999999953
No 39
>KOG0827|consensus
Probab=76.84 E-value=1.4 Score=44.32 Aligned_cols=20 Identities=40% Similarity=1.132 Sum_probs=17.5
Q ss_pred eeecCCchhhHHHHHHHhhh
Q psy9235 116 HTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~~s 135 (317)
-+++|||+.|..|+..+++.
T Consensus 22 ~i~~cGhifh~~cl~qwfe~ 41 (465)
T KOG0827|consen 22 PIGTCGHIFHTTCLTQWFEG 41 (465)
T ss_pred cccchhhHHHHHHHHHHHcc
Confidence 36789999999999999954
No 40
>KOG1493|consensus
Probab=71.86 E-value=1.9 Score=34.04 Aligned_cols=34 Identities=24% Similarity=0.545 Sum_probs=26.3
Q ss_pred CceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCcc
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCEC 167 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrs 167 (317)
-++..-|-|..|..|..+.+.+.. +.=+||+||+
T Consensus 45 PLv~G~C~h~fh~hCI~~wl~~~t--------------------sq~~CPmcRq 78 (84)
T KOG1493|consen 45 PLVWGYCLHAFHAHCILKWLNTPT--------------------SQGQCPMCRQ 78 (84)
T ss_pred ccHHHHHHHHHHHHHHHHHhcCcc--------------------ccccCCcchh
Confidence 346678999999999999985432 1248999996
No 41
>KOG4172|consensus
Probab=69.58 E-value=2.1 Score=31.86 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=15.9
Q ss_pred CCceeecCCch-hhHHHHHHHh
Q psy9235 113 PAPHTSTCGHV-MHSTCWSKYF 133 (317)
Q Consensus 113 ~g~~vssCGH~-mH~~C~~~Y~ 133 (317)
...++-+|||. |-|.|--+..
T Consensus 18 vdsVlYtCGHMCmCy~Cg~rl~ 39 (62)
T KOG4172|consen 18 VDSVLYTCGHMCMCYACGLRLK 39 (62)
T ss_pred chHHHHHcchHHhHHHHHHHHH
Confidence 46678899996 7788876664
No 42
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=69.16 E-value=5.8 Score=28.19 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=16.6
Q ss_pred ceeecCC-----chhhHHHHHHHhhhh
Q psy9235 115 PHTSTCG-----HVMHSTCWSKYFDNI 136 (317)
Q Consensus 115 ~~vssCG-----H~mH~~C~~~Y~~s~ 136 (317)
+.+.-|. |++|.+|+++++...
T Consensus 14 ~l~~PC~C~G~~~~vH~~Cl~~W~~~~ 40 (49)
T smart00744 14 PLVSPCRCKGSLKYVHQECLERWINES 40 (49)
T ss_pred eeEeccccCCchhHHHHHHHHHHHHHc
Confidence 3455564 999999999998543
No 43
>PRK02935 hypothetical protein; Provisional
Probab=68.39 E-value=2.2 Score=35.56 Aligned_cols=30 Identities=17% Similarity=0.531 Sum_probs=23.6
Q ss_pred HhhccccCCCCCCCCCC---CceeeceeCceecC
Q psy9235 258 NTVSLFTCPNSDREDSR---NPALCLICGDMLCS 288 (317)
Q Consensus 258 ~~~~~~~C~~c~~~~~~---~P~lCL~CG~~~C~ 288 (317)
.++.+..||+|+++ .+ .--+|..|++.+=.
T Consensus 66 tkavqV~CP~C~K~-TKmLGrvD~CM~C~~PLTL 98 (110)
T PRK02935 66 TKAVQVICPSCEKP-TKMLGRVDACMHCNQPLTL 98 (110)
T ss_pred ccceeeECCCCCch-hhhccceeecCcCCCcCCc
Confidence 45778899999987 54 46699999997644
No 44
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=67.89 E-value=4.1 Score=29.27 Aligned_cols=22 Identities=14% Similarity=0.214 Sum_probs=19.1
Q ss_pred CCceeecCCchhhHHHHHHHhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
..+++..|||+.-..|+.+|++
T Consensus 12 ~~Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 12 KDPVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred CCCEECCCCCEEeHHHHHHHHH
Confidence 3468889999999999999984
No 45
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=67.52 E-value=3.5 Score=28.62 Aligned_cols=17 Identities=35% Similarity=1.005 Sum_probs=11.3
Q ss_pred cCCchhhHHHHHHHhhh
Q psy9235 119 TCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 119 sCGH~mH~~C~~~Y~~s 135 (317)
.|+=-||..|+++|+..
T Consensus 18 ~C~~r~H~~C~~~y~r~ 34 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRH 34 (43)
T ss_dssp -S--EE-HHHHHHHTTT
T ss_pred ccCchHHHHHHHHHHhc
Confidence 57778999999999843
No 46
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=65.02 E-value=1.7 Score=34.42 Aligned_cols=15 Identities=40% Similarity=0.988 Sum_probs=11.8
Q ss_pred eecCCchhhHHHHHH
Q psy9235 117 TSTCGHVMHSTCWSK 131 (317)
Q Consensus 117 vssCGH~mH~~C~~~ 131 (317)
+--|||++|+.|.++
T Consensus 95 ~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 95 VFPCGHVVHYSCIKR 109 (109)
T ss_pred EeCCCeEEecccccC
Confidence 345899999999864
No 47
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.88 E-value=3.9 Score=41.38 Aligned_cols=18 Identities=22% Similarity=0.602 Sum_probs=16.0
Q ss_pred eeecCCchhhHHHHHHHh
Q psy9235 116 HTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~ 133 (317)
++..|||.-...|+..|+
T Consensus 40 vitpCgH~FCs~CI~~~l 57 (397)
T TIGR00599 40 VLTSCSHTFCSLCIRRCL 57 (397)
T ss_pred cCCCCCCchhHHHHHHHH
Confidence 356899999999999997
No 48
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=63.08 E-value=5.7 Score=27.57 Aligned_cols=24 Identities=33% Similarity=0.742 Sum_probs=19.2
Q ss_pred cCCCCCCCCCCCceeeceeCceecCC
Q psy9235 264 TCPNSDREDSRNPALCLICGDMLCSQ 289 (317)
Q Consensus 264 ~C~~c~~~~~~~P~lCL~CG~~~C~~ 289 (317)
+|..|+.. . +--+||.||.+.|..
T Consensus 1 ~C~~C~~~-~-~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTI-E-NLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCc-C-CeEEecCCCCcccCC
Confidence 58899976 3 578999999888754
No 49
>KOG1941|consensus
Probab=62.87 E-value=3.1 Score=42.02 Aligned_cols=22 Identities=18% Similarity=0.590 Sum_probs=18.7
Q ss_pred CCceeecCCchhhHHHHHHHhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
.....--|.|+.|..|.+.|++
T Consensus 380 e~LqALpCsHIfH~rCl~e~L~ 401 (518)
T KOG1941|consen 380 ERLQALPCSHIFHLRCLQEILE 401 (518)
T ss_pred ccccccchhHHHHHHHHHHHHH
Confidence 4566778999999999999983
No 50
>KOG4628|consensus
Probab=62.32 E-value=4.7 Score=40.09 Aligned_cols=34 Identities=26% Similarity=0.768 Sum_probs=27.6
Q ss_pred CCCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCcc
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCEC 167 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrs 167 (317)
+..+.+=.|+|.-|..|...++-.. |. .||+||+
T Consensus 242 GdklRiLPC~H~FH~~CIDpWL~~~-----------r~-----------~CPvCK~ 275 (348)
T KOG4628|consen 242 GDKLRILPCSHKFHVNCIDPWLTQT-----------RT-----------FCPVCKR 275 (348)
T ss_pred CCeeeEecCCCchhhccchhhHhhc-----------Cc-----------cCCCCCC
Confidence 3567788999999999999998332 32 7999999
No 51
>PF12773 DZR: Double zinc ribbon
Probab=62.27 E-value=3.8 Score=28.56 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=13.3
Q ss_pred cccCCCCCCCCC---CCceeeceeCce
Q psy9235 262 LFTCPNSDREDS---RNPALCLICGDM 285 (317)
Q Consensus 262 ~~~C~~c~~~~~---~~P~lCL~CG~~ 285 (317)
...|++||..++ ....+|-.||+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 344666666544 234566666664
No 52
>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=60.42 E-value=5.4 Score=27.31 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.0
Q ss_pred ccCCCCCCCC----C-CCceeeceeCcee
Q psy9235 263 FTCPNSDRED----S-RNPALCLICGDML 286 (317)
Q Consensus 263 ~~C~~c~~~~----~-~~P~lCL~CG~~~ 286 (317)
++||+||... + +--.+|-.||.++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 4799999751 1 2356899998875
No 53
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=60.13 E-value=3 Score=31.00 Aligned_cols=15 Identities=40% Similarity=1.048 Sum_probs=12.8
Q ss_pred CceeeceeCceecCC
Q psy9235 275 NPALCLICGDMLCSQ 289 (317)
Q Consensus 275 ~P~lCL~CG~~~C~~ 289 (317)
....||.||+|+|.+
T Consensus 17 ~~~NCl~CGkIiC~~ 31 (57)
T PF06221_consen 17 YAPNCLNCGKIICEQ 31 (57)
T ss_pred ccccccccChhhccc
Confidence 356899999999985
No 54
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=58.46 E-value=2.8 Score=31.57 Aligned_cols=36 Identities=25% Similarity=0.293 Sum_probs=12.7
Q ss_pred cCHHHHHHHHHHHHHHHHHhhhhccCCcccCCCCCCcccc
Q psy9235 197 MDFDAWLSIVEMVLEHKKRLKKSKATSECQDSTSSKQVPQ 236 (317)
Q Consensus 197 ~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~v~~ 236 (317)
..||+.|....|.-++ ..++..+.||||+.++.|+.
T Consensus 9 ~~LD~~i~~~pmP~~Y----~~~~v~IlCNDC~~~s~v~f 44 (61)
T PF14599_consen 9 RMLDAEIAATPMPEEY----RNKKVWILCNDCNAKSEVPF 44 (61)
T ss_dssp -----------------------EEEEEESSS--EEEEE-
T ss_pred HHHHHHHHhCCCCHHH----hCCEEEEECCCCCCccceee
Confidence 4567777777777776 45688999999999998874
No 55
>KOG0828|consensus
Probab=58.39 E-value=5.4 Score=41.49 Aligned_cols=22 Identities=23% Similarity=0.656 Sum_probs=18.9
Q ss_pred CceeecCCchhhHHHHHHHhhh
Q psy9235 114 APHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~~s 135 (317)
...++-|.|++|..|+++.++.
T Consensus 600 nYm~tPC~HifH~~CL~~WMd~ 621 (636)
T KOG0828|consen 600 NYMLTPCHHIFHRQCLLQWMDT 621 (636)
T ss_pred cccccchHHHHHHHHHHHHHhh
Confidence 4567789999999999999964
No 56
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.14 E-value=6.8 Score=38.40 Aligned_cols=18 Identities=28% Similarity=0.763 Sum_probs=15.5
Q ss_pred eeecCCchhhHHHHHHHh
Q psy9235 116 HTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~ 133 (317)
.++.|||.|=-+|..+.+
T Consensus 22 ~i~~CGH~~C~sCv~~l~ 39 (309)
T TIGR00570 22 MVNVCGHTLCESCVDLLF 39 (309)
T ss_pred ccCCCCCcccHHHHHHHh
Confidence 344799999999999987
No 57
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=57.12 E-value=3.6 Score=34.64 Aligned_cols=30 Identities=20% Similarity=0.567 Sum_probs=22.0
Q ss_pred HhhccccCCCCCCCCCC---CceeeceeCceecC
Q psy9235 258 NTVSLFTCPNSDREDSR---NPALCLICGDMLCS 288 (317)
Q Consensus 258 ~~~~~~~C~~c~~~~~~---~P~lCL~CG~~~C~ 288 (317)
.++...+||+|+++ ++ .--.|..||+.+=.
T Consensus 65 tkav~V~CP~C~K~-TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 65 TKAVQVECPNCGKQ-TKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred ccceeeECCCCCCh-HhhhchhhccCcCCCcCcc
Confidence 34677789999987 42 33599999987643
No 58
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.64 E-value=5.1 Score=30.15 Aligned_cols=26 Identities=42% Similarity=0.773 Sum_probs=17.1
Q ss_pred HhhccccCCCCCCC-CCC--------CceeeceeC
Q psy9235 258 NTVSLFTCPNSDRE-DSR--------NPALCLICG 283 (317)
Q Consensus 258 ~~~~~~~C~~c~~~-~~~--------~P~lCL~CG 283 (317)
+.|..+.||+||++ +-| .|-.|--||
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred CceeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 56788888888854 221 566666666
No 59
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=55.19 E-value=11 Score=33.73 Aligned_cols=53 Identities=19% Similarity=0.291 Sum_probs=28.8
Q ss_pred hhhHHHHHHHhhhhhhhccCCcccc----CCC----CccCCCCCeeeccCCccccceEecc
Q psy9235 123 VMHSTCWSKYFDNILAKENRRPYRL----RQP----TSFDIEKNEFLCPLCECLSNAALPL 175 (317)
Q Consensus 123 ~mH~~C~~~Y~~s~~~~e~rr~q~~----R~~----~~~d~~~~EFlCPLCrsLsN~vLP~ 175 (317)
+-|.+|+..|-++-........+.. +.. ..-.....+-.|||||.--.--..+
T Consensus 36 ~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~V~GWtvv 96 (162)
T PF07800_consen 36 YRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGEVKGWTVV 96 (162)
T ss_pred cchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCceeceEEc
Confidence 3589999999777543221111100 000 0012355689999999865544444
No 60
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=55.12 E-value=3.6 Score=27.68 Aligned_cols=24 Identities=25% Similarity=0.542 Sum_probs=17.9
Q ss_pred cccCCCCCCC------CCCCceeeceeCce
Q psy9235 262 LFTCPNSDRE------DSRNPALCLICGDM 285 (317)
Q Consensus 262 ~~~C~~c~~~------~~~~P~lCL~CG~~ 285 (317)
++.|++||++ -|+.+.+|-.||.-
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPPKVEGVCDNCGGE 30 (36)
T ss_dssp EEEETTTTEEEETTTB--SSTTBCTTTTEB
T ss_pred CcCcCCCCCccccccCCCCCCCccCCCCCe
Confidence 4679999965 26788999999974
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.34 E-value=5.5 Score=29.87 Aligned_cols=13 Identities=31% Similarity=0.626 Sum_probs=9.3
Q ss_pred hhccccCCCCCCC
Q psy9235 259 TVSLFTCPNSDRE 271 (317)
Q Consensus 259 ~~~~~~C~~c~~~ 271 (317)
.+.++.||+||++
T Consensus 22 ~~~~F~CPnCG~~ 34 (59)
T PRK14890 22 KAVKFLCPNCGEV 34 (59)
T ss_pred ccCEeeCCCCCCe
Confidence 3677777777776
No 62
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=52.76 E-value=10 Score=26.34 Aligned_cols=21 Identities=33% Similarity=0.713 Sum_probs=16.0
Q ss_pred ceeecCCchhhHHHHHHHhhh
Q psy9235 115 PHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 115 ~~vssCGH~mH~~C~~~Y~~s 135 (317)
+.+-.|||++=.+|.++..+.
T Consensus 14 P~~L~CGH~~c~~cl~~l~~~ 34 (43)
T PF13445_consen 14 PMVLPCGHVFCKDCLQKLSKK 34 (43)
T ss_dssp EEE-SSS-EEEHHHHHHHHHH
T ss_pred CEEEeCccHHHHHHHHHHHhc
Confidence 556669999999999999864
No 63
>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=51.68 E-value=6.3 Score=24.40 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=9.7
Q ss_pred hhccccCCCCCC
Q psy9235 259 TVSLFTCPNSDR 270 (317)
Q Consensus 259 ~~~~~~C~~c~~ 270 (317)
++..+.||+||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 477889999984
No 64
>PF15616 TerY-C: TerY-C metal binding domain
Probab=50.32 E-value=12 Score=32.42 Aligned_cols=38 Identities=29% Similarity=0.698 Sum_probs=27.7
Q ss_pred ccCCCCCCCCCCCceeeceeCceecCCC----cc--ccccccccccc
Q psy9235 263 FTCPNSDREDSRNPALCLICGDMLCSQS----YC--CQTELFFKMSA 303 (317)
Q Consensus 263 ~~C~~c~~~~~~~P~lCL~CG~~~C~~~----~C--C~~~~~~~~~~ 303 (317)
-.||.||.. .--++| -||+|+|... .| |-.+..++++.
T Consensus 78 PgCP~CGn~--~~fa~C-~CGkl~Ci~g~~~~~CPwCg~~g~~~~~~ 121 (131)
T PF15616_consen 78 PGCPHCGNQ--YAFAVC-GCGKLFCIDGEGEVTCPWCGNEGSFGAGD 121 (131)
T ss_pred CCCCCCcCh--hcEEEe-cCCCEEEeCCCCCEECCCCCCeeeecccC
Confidence 679999997 477999 8999999633 23 55555666654
No 65
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=50.27 E-value=12 Score=25.49 Aligned_cols=25 Identities=20% Similarity=0.622 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceeeceeCceecCC
Q psy9235 265 CPNSDREDSRNPALCLICGDMLCSQ 289 (317)
Q Consensus 265 C~~c~~~~~~~P~lCL~CG~~~C~~ 289 (317)
|-.|++.+.-.|..|-.||..+|++
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 5568877563499999999999984
No 66
>PF12773 DZR: Double zinc ribbon
Probab=50.19 E-value=11 Score=26.30 Aligned_cols=25 Identities=36% Similarity=0.703 Sum_probs=20.9
Q ss_pred hhccccCCCCCCCCCCCceeeceeC
Q psy9235 259 TVSLFTCPNSDREDSRNPALCLICG 283 (317)
Q Consensus 259 ~~~~~~C~~c~~~~~~~P~lCL~CG 283 (317)
......|++||...+.+-..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3456789999999888888999888
No 67
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.31 E-value=9.5 Score=32.22 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=22.2
Q ss_pred ccccCCCCCCC---CCCCceeeceeCcee
Q psy9235 261 SLFTCPNSDRE---DSRNPALCLICGDML 286 (317)
Q Consensus 261 ~~~~C~~c~~~---~~~~P~lCL~CG~~~ 286 (317)
.+|.||.||+. +.|+|++|-.||+-.
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCccccchhhccCCCccccCcccccc
Confidence 57889999975 578999999999854
No 68
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.47 E-value=11 Score=42.22 Aligned_cols=24 Identities=29% Similarity=0.731 Sum_probs=20.0
Q ss_pred CCceeecCCchhhHHHHHHHhhhh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDNI 136 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s~ 136 (317)
+..--.||-|--|..|+-+++++.
T Consensus 1487 PskrC~TCknKFH~~CLyKWf~Ss 1510 (1525)
T COG5219 1487 PSKRCATCKNKFHTRCLYKWFASS 1510 (1525)
T ss_pred CccccchhhhhhhHHHHHHHHHhc
Confidence 455567899999999999999775
No 69
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.29 E-value=14 Score=27.26 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=22.1
Q ss_pred hccccCCCCCCCC--CCCceeeceeCce
Q psy9235 260 VSLFTCPNSDRED--SRNPALCLICGDM 285 (317)
Q Consensus 260 ~~~~~C~~c~~~~--~~~P~lCL~CG~~ 285 (317)
|...+|+-||+.+ .+|-++|--||+.
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCc
Confidence 5678899999987 5688999999985
No 70
>KOG0309|consensus
Probab=43.22 E-value=12 Score=40.89 Aligned_cols=24 Identities=38% Similarity=0.890 Sum_probs=19.4
Q ss_pred CCCceeecCCchhhHHHHHHHhhh
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y~~s 135 (317)
+...+-.+|||+||.+|...+++.
T Consensus 1040 gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1040 GSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ccchhhccccccccHHHHHHHHhc
Confidence 345566789999999999999843
No 71
>PF15353 HECA: Headcase protein family homologue
Probab=43.21 E-value=15 Score=30.62 Aligned_cols=18 Identities=44% Similarity=0.892 Sum_probs=15.3
Q ss_pred CCchhhHHHHHHHhhhhh
Q psy9235 120 CGHVMHSTCWSKYFDNIL 137 (317)
Q Consensus 120 CGH~mH~~C~~~Y~~s~~ 137 (317)
.|++||..||+.+=+++.
T Consensus 40 ~~~~MH~~CF~~wE~~iL 57 (107)
T PF15353_consen 40 FGQYMHRECFEKWEDSIL 57 (107)
T ss_pred CCCchHHHHHHHHHHHHH
Confidence 399999999999977664
No 72
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=42.92 E-value=9.2 Score=29.06 Aligned_cols=23 Identities=26% Similarity=0.703 Sum_probs=20.2
Q ss_pred cccCCCCCCCCCCCceeeceeCc
Q psy9235 262 LFTCPNSDREDSRNPALCLICGD 284 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P~lCL~CG~ 284 (317)
.+.|.+|+...+.|--+|-+||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 45799999998889999999996
No 73
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=42.41 E-value=15 Score=27.13 Aligned_cols=24 Identities=29% Similarity=0.653 Sum_probs=18.5
Q ss_pred ccccCCCCCCCCCCCceeeceeCce
Q psy9235 261 SLFTCPNSDREDSRNPALCLICGDM 285 (317)
Q Consensus 261 ~~~~C~~c~~~~~~~P~lCL~CG~~ 285 (317)
....||+||.. -.-=-+|+.||..
T Consensus 26 ~l~~C~~CG~~-~~~H~vC~~CG~Y 49 (57)
T PRK12286 26 GLVECPNCGEP-KLPHRVCPSCGYY 49 (57)
T ss_pred cceECCCCCCc-cCCeEECCCCCcC
Confidence 44679999998 3356899999953
No 74
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=38.84 E-value=5.1 Score=28.59 Aligned_cols=29 Identities=17% Similarity=0.246 Sum_probs=24.0
Q ss_pred ccccCCChhHHHHHHhhccccCCCCCCCC
Q psy9235 244 NRLINLPDDYSELINTVSLFTCPNSDRED 272 (317)
Q Consensus 244 ~~l~~LP~~y~~L~~~~~~~~C~~c~~~~ 272 (317)
++|+.||.++.-.=....+.+|-.|.+++
T Consensus 13 ~~lLqlP~~~~~~~k~~~klrCGaCs~vl 41 (46)
T PF11331_consen 13 FELLQLPAKFSLSKKNQQKLRCGACSEVL 41 (46)
T ss_pred HHHHcCCCccCCCccceeEEeCCCCceeE
Confidence 89999999998775558888899998773
No 75
>KOG0317|consensus
Probab=37.92 E-value=23 Score=34.45 Aligned_cols=23 Identities=22% Similarity=0.681 Sum_probs=18.6
Q ss_pred CCCceeecCCchhhHHHHHHHhh
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKYFD 134 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y~~ 134 (317)
+..+-..-|||.-=-+|...+..
T Consensus 249 ~~~pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 249 RSNPSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred CCCCCcCcCcchHHHHHHHHHHc
Confidence 45677889999998888888863
No 76
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.12 E-value=24 Score=34.82 Aligned_cols=20 Identities=25% Similarity=0.592 Sum_probs=18.4
Q ss_pred CceeecCCchhhHHHHHHHh
Q psy9235 114 APHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 114 g~~vssCGH~mH~~C~~~Y~ 133 (317)
...+.-|.|.-|..|..+++
T Consensus 338 ~~~vlPC~H~FH~~Cv~kW~ 357 (374)
T COG5540 338 RLRVLPCDHRFHVGCVDKWL 357 (374)
T ss_pred eEEEeccCceechhHHHHHH
Confidence 47888999999999999998
No 77
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.04 E-value=25 Score=24.29 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=17.4
Q ss_pred cccCCCCCCCC---CC-CceeeceeCcee
Q psy9235 262 LFTCPNSDRED---SR-NPALCLICGDML 286 (317)
Q Consensus 262 ~~~C~~c~~~~---~~-~P~lCL~CG~~~ 286 (317)
..+|++||.+. +. ...-|-.||.-+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 46799999763 22 267888888643
No 78
>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=35.72 E-value=23 Score=23.29 Aligned_cols=21 Identities=29% Similarity=0.716 Sum_probs=15.2
Q ss_pred cCCCCCCC---CCCCceeeceeCc
Q psy9235 264 TCPNSDRE---DSRNPALCLICGD 284 (317)
Q Consensus 264 ~C~~c~~~---~~~~P~lCL~CG~ 284 (317)
.|..||.+ .+.+|.-|-.||-
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 47788866 3458899999984
No 79
>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=35.24 E-value=24 Score=24.19 Aligned_cols=23 Identities=30% Similarity=0.752 Sum_probs=14.8
Q ss_pred CCCCCCCCCCceeeceeCceecCC
Q psy9235 266 PNSDREDSRNPALCLICGDMLCSQ 289 (317)
Q Consensus 266 ~~c~~~~~~~P~lCL~CG~~~C~~ 289 (317)
+.|++.+. .|..|-.||..+|..
T Consensus 4 ~~C~~~~~-~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 4 PGCKKKDF-LPFKCKHCGKSFCLK 26 (43)
T ss_dssp TTT--BCT-SHEE-TTTS-EE-TT
T ss_pred CcCcCccC-CCeECCCCCcccCcc
Confidence 34888766 899999999999984
No 80
>KOG2114|consensus
Probab=34.11 E-value=19 Score=39.69 Aligned_cols=29 Identities=31% Similarity=0.558 Sum_probs=23.0
Q ss_pred CCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCcc
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCEC 167 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrs 167 (317)
.-.+--.|||..|-.|+. .+|+-||-|+.
T Consensus 852 lP~VhF~CgHsyHqhC~e--------------------------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 852 LPFVHFLCGHSYHQHCLE--------------------------DKEDKCPKCLP 880 (933)
T ss_pred cceeeeecccHHHHHhhc--------------------------cCcccCCccch
Confidence 345566799999999997 13789999987
No 81
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=33.65 E-value=26 Score=25.70 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=18.1
Q ss_pred ccccCCCCCCCCCCCceeeceeCce
Q psy9235 261 SLFTCPNSDREDSRNPALCLICGDM 285 (317)
Q Consensus 261 ~~~~C~~c~~~~~~~P~lCL~CG~~ 285 (317)
....|++||+. -.-=-+|+.||..
T Consensus 25 ~l~~C~~cG~~-~~~H~vc~~cG~Y 48 (55)
T TIGR01031 25 TLVVCPNCGEF-KLPHRVCPSCGYY 48 (55)
T ss_pred cceECCCCCCc-ccCeeECCccCeE
Confidence 34679999997 3356899999953
No 82
>KOG0320|consensus
Probab=33.57 E-value=28 Score=31.72 Aligned_cols=21 Identities=38% Similarity=0.843 Sum_probs=18.0
Q ss_pred ceeecCCchhhHHHHHHHhhh
Q psy9235 115 PHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 115 ~~vssCGH~mH~~C~~~Y~~s 135 (317)
++..-|||+-=-.|.+.-++.
T Consensus 146 ~vsTkCGHvFC~~Cik~alk~ 166 (187)
T KOG0320|consen 146 PVSTKCGHVFCSQCIKDALKN 166 (187)
T ss_pred ccccccchhHHHHHHHHHHHh
Confidence 466899999999999998754
No 83
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.43 E-value=22 Score=27.57 Aligned_cols=23 Identities=26% Similarity=0.925 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCceeeceeCceecC
Q psy9235 265 CPNSDREDSRNPALCLICGDMLCS 288 (317)
Q Consensus 265 C~~c~~~~~~~P~lCL~CG~~~C~ 288 (317)
|..=|++ ++.-+||.+||.=+|.
T Consensus 13 C~eeGKD-tdAV~iCIVCG~GlC~ 35 (76)
T COG4855 13 CAEEGKD-TDAVGICIVCGMGLCM 35 (76)
T ss_pred HHHhCCC-cccEEEEEEeCchHHH
Confidence 3334554 7788999999998875
No 84
>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=33.15 E-value=30 Score=22.72 Aligned_cols=25 Identities=28% Similarity=0.582 Sum_probs=14.4
Q ss_pred cccCCCCCCC--CCC-----C--ceeeceeCcee
Q psy9235 262 LFTCPNSDRE--DSR-----N--PALCLICGDML 286 (317)
Q Consensus 262 ~~~C~~c~~~--~~~-----~--P~lCL~CG~~~ 286 (317)
+.+||+|+.. ++. . -+-|-.||..+
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 3578888872 121 1 25677777643
No 85
>KOG0287|consensus
Probab=32.11 E-value=34 Score=34.31 Aligned_cols=21 Identities=29% Similarity=0.706 Sum_probs=18.2
Q ss_pred CCceeecCCchhhHHHHHHHh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~ 133 (317)
.-+.+..|||..-.=|..+|+
T Consensus 34 ~ip~itpCsHtfCSlCIR~~L 54 (442)
T KOG0287|consen 34 NIPMITPCSHTFCSLCIRKFL 54 (442)
T ss_pred cCceeccccchHHHHHHHHHh
Confidence 346778899999999999998
No 86
>PRK00420 hypothetical protein; Validated
Probab=31.68 E-value=32 Score=28.95 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=18.4
Q ss_pred cccCCCCCCCCC---CCceeeceeCcee
Q psy9235 262 LFTCPNSDREDS---RNPALCLICGDML 286 (317)
Q Consensus 262 ~~~C~~c~~~~~---~~P~lCL~CG~~~ 286 (317)
...||.||.... .-...|..||+.+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCee
Confidence 367999997654 3578888888754
No 87
>KOG2845|consensus
Probab=31.13 E-value=17 Score=37.71 Aligned_cols=13 Identities=46% Similarity=1.165 Sum_probs=11.5
Q ss_pred eeceeCceecCCC
Q psy9235 278 LCLICGDMLCSQS 290 (317)
Q Consensus 278 lCL~CG~~~C~~~ 290 (317)
=||.||+|+|.|-
T Consensus 172 NCL~CGkIVCeQE 184 (505)
T KOG2845|consen 172 NCLGCGKIVCEQE 184 (505)
T ss_pred cccccceeEEEec
Confidence 6999999999874
No 88
>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=30.01 E-value=29 Score=22.47 Aligned_cols=22 Identities=32% Similarity=0.890 Sum_probs=15.3
Q ss_pred ccCCCCCCC-CCC-CceeeceeCc
Q psy9235 263 FTCPNSDRE-DSR-NPALCLICGD 284 (317)
Q Consensus 263 ~~C~~c~~~-~~~-~P~lCL~CG~ 284 (317)
.+|..||-+ +++ +|-.|-+||.
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCC
Confidence 368888865 343 6778888875
No 89
>KOG1734|consensus
Probab=29.13 E-value=26 Score=34.03 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=18.2
Q ss_pred CCceeecCCchhhHHHHHHHh
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~ 133 (317)
...|.-+|+|+-|--|.+-..
T Consensus 245 enty~LsCnHvFHEfCIrGWc 265 (328)
T KOG1734|consen 245 ENTYKLSCNHVFHEFCIRGWC 265 (328)
T ss_pred hhheeeecccchHHHhhhhhe
Confidence 356788999999999999885
No 90
>KOG0269|consensus
Probab=28.23 E-value=33 Score=37.58 Aligned_cols=21 Identities=24% Similarity=0.446 Sum_probs=17.5
Q ss_pred ceeecCCchhhHHHHHHHhhh
Q psy9235 115 PHTSTCGHVMHSTCWSKYFDN 135 (317)
Q Consensus 115 ~~vssCGH~mH~~C~~~Y~~s 135 (317)
.+-..|||.+|.+|.++|+..
T Consensus 794 ~~c~~C~H~gH~sh~~sw~~~ 814 (839)
T KOG0269|consen 794 VWCQVCGHGGHDSHLKSWFFK 814 (839)
T ss_pred eecccccccccHHHHHHHHhc
Confidence 445679999999999999843
No 91
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=27.85 E-value=46 Score=23.57 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=20.4
Q ss_pred ccccCC--CCCCCCC------CCceeeceeCceecCC
Q psy9235 261 SLFTCP--NSDREDS------RNPALCLICGDMLCSQ 289 (317)
Q Consensus 261 ~~~~C~--~c~~~~~------~~P~lCL~CG~~~C~~ 289 (317)
..+.|| +|+..+. ...+.|-.||..+|..
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 455698 8875422 2368888899999975
No 92
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=26.60 E-value=34 Score=28.33 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=16.4
Q ss_pred ccCCCCCCCCCCCceeece
Q psy9235 263 FTCPNSDREDSRNPALCLI 281 (317)
Q Consensus 263 ~~C~~c~~~~~~~P~lCL~ 281 (317)
.+|.+||+..|+|.+||-.
T Consensus 21 v~CdnCg~~vPkdKAikr~ 39 (108)
T COG4830 21 VRCDNCGKAVPKDKAIKRT 39 (108)
T ss_pred eeeccccccCCccceeeEe
Confidence 4699999999999999864
No 93
>KOG1814|consensus
Probab=26.21 E-value=34 Score=34.93 Aligned_cols=31 Identities=29% Similarity=0.714 Sum_probs=25.4
Q ss_pred cccCCCCCCCCCC----CceeeceeCceecCCCccccc
Q psy9235 262 LFTCPNSDREDSR----NPALCLICGDMLCSQSYCCQT 295 (317)
Q Consensus 262 ~~~C~~c~~~~~~----~P~lCL~CG~~~C~~~~CC~~ 295 (317)
-.+||+|+.++.+ ..+-|..||..+| ++|..
T Consensus 368 ~krCP~C~v~IEr~eGCnKM~C~~c~~~fc---~~c~~ 402 (445)
T KOG1814|consen 368 SKRCPKCKVVIERSEGCNKMHCTKCGTYFC---WICAE 402 (445)
T ss_pred CCCCCcccceeecCCCccceeeccccccce---eehhh
Confidence 4679999988765 5899999999998 56765
No 94
>KOG3268|consensus
Probab=26.03 E-value=48 Score=30.43 Aligned_cols=40 Identities=40% Similarity=0.848 Sum_probs=30.1
Q ss_pred eeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCcc
Q psy9235 116 HTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCEC 167 (317)
Q Consensus 116 ~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrs 167 (317)
.-..||...|.-|+-.++.++... |+ +||+-.|| ||.|.-
T Consensus 186 dN~qCgkpFHqiCL~dWLRgilTs--------RQ--SFdiiFGe--CPYCS~ 225 (234)
T KOG3268|consen 186 DNIQCGKPFHQICLTDWLRGILTS--------RQ--SFDIIFGE--CPYCSD 225 (234)
T ss_pred cccccCCcHHHHHHHHHHHHHhhc--------cc--eeeeeecc--CCCCCC
Confidence 457899999999999999887532 32 36666664 999964
No 95
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=25.75 E-value=42 Score=24.69 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=16.5
Q ss_pred ccccCCCCCCCC--CCCceeeceeCceecCCCcccc
Q psy9235 261 SLFTCPNSDRED--SRNPALCLICGDMLCSQSYCCQ 294 (317)
Q Consensus 261 ~~~~C~~c~~~~--~~~P~lCL~CG~~~C~~~~CC~ 294 (317)
....|..|++.- .+..--|-.||.++|.. |..
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~--Cs~ 41 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSS--CSS 41 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECC--CS-
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCc--hhC
Confidence 345688888762 34678899999999976 554
No 96
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=25.74 E-value=27 Score=39.26 Aligned_cols=25 Identities=28% Similarity=0.741 Sum_probs=20.9
Q ss_pred hccccCCCCCCCCCCCceeeceeCcee
Q psy9235 260 VSLFTCPNSDREDSRNPALCLICGDML 286 (317)
Q Consensus 260 ~~~~~C~~c~~~~~~~P~lCL~CG~~~ 286 (317)
...|+||+||+. + --..|..||+-.
T Consensus 623 v~~RKCPkCG~y-T-lk~rCP~CG~~T 647 (1095)
T TIGR00354 623 IAIRKCPQCGKE-S-FWLKCPVCGELT 647 (1095)
T ss_pred EEEEECCCCCcc-c-ccccCCCCCCcc
Confidence 457899999998 4 678999999864
No 97
>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=25.71 E-value=22 Score=26.64 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=11.1
Q ss_pred cccCCCCCCCCCCC
Q psy9235 262 LFTCPNSDREDSRN 275 (317)
Q Consensus 262 ~~~C~~c~~~~~~~ 275 (317)
++.|+.||+.+|.+
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 57899999887754
No 98
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.58 E-value=31 Score=39.77 Aligned_cols=23 Identities=26% Similarity=0.506 Sum_probs=18.6
Q ss_pred cccCCCCCCCCCCCceeeceeCcee
Q psy9235 262 LFTCPNSDREDSRNPALCLICGDML 286 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P~lCL~CG~~~ 286 (317)
+++||+||.+.+. ..|..||.-.
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCcC
Confidence 4899999998553 5999999764
No 99
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=25.11 E-value=68 Score=27.89 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=18.6
Q ss_pred CCCceeecCC------chhhHHHHHHHh
Q psy9235 112 GPAPHTSTCG------HVMHSTCWSKYF 133 (317)
Q Consensus 112 ~~g~~vssCG------H~mH~~C~~~Y~ 133 (317)
..|++.-+|| |+||.+|+++|-
T Consensus 39 ~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 39 NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 4588888887 899999999994
No 100
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=24.70 E-value=30 Score=40.21 Aligned_cols=24 Identities=25% Similarity=0.779 Sum_probs=20.0
Q ss_pred hccccCCCCCCCCCCCceeeceeCce
Q psy9235 260 VSLFTCPNSDREDSRNPALCLICGDM 285 (317)
Q Consensus 260 ~~~~~C~~c~~~~~~~P~lCL~CG~~ 285 (317)
...++||+||++ + --..|.+||+-
T Consensus 672 i~~~~Cp~Cg~~-~-~~~~Cp~CG~~ 695 (1627)
T PRK14715 672 IAFFKCPKCGKV-G-LYHVCPFCGTR 695 (1627)
T ss_pred EEeeeCCCCCCc-c-ccccCcccCCc
Confidence 457899999998 3 56899999975
No 101
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=23.94 E-value=48 Score=27.20 Aligned_cols=21 Identities=29% Similarity=0.602 Sum_probs=17.3
Q ss_pred cccCCCCCCCCCCCceeecee
Q psy9235 262 LFTCPNSDREDSRNPALCLIC 282 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P~lCL~C 282 (317)
..+|.+||...|+|.||+.+=
T Consensus 20 ~V~C~nCgr~vPKDKAIkrf~ 40 (95)
T PRK09335 20 YVQCDNCGRRVPRDKAVCVTK 40 (95)
T ss_pred cEEeCCCCCcCcCCceEEEEE
Confidence 456999999989999998763
No 102
>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=23.84 E-value=35 Score=22.43 Aligned_cols=22 Identities=32% Similarity=0.847 Sum_probs=15.2
Q ss_pred ccCCCCCCC-CCC-CceeeceeCc
Q psy9235 263 FTCPNSDRE-DSR-NPALCLICGD 284 (317)
Q Consensus 263 ~~C~~c~~~-~~~-~P~lCL~CG~ 284 (317)
.+|..||-. +.+ .|..|-+||.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCC
Confidence 468888865 222 4778888885
No 103
>PRK12495 hypothetical protein; Provisional
Probab=23.38 E-value=70 Score=30.11 Aligned_cols=27 Identities=15% Similarity=0.354 Sum_probs=17.8
Q ss_pred hccccCCCCCCCCCCCc--eeeceeCcee
Q psy9235 260 VSLFTCPNSDREDSRNP--ALCLICGDML 286 (317)
Q Consensus 260 ~~~~~C~~c~~~~~~~P--~lCL~CG~~~ 286 (317)
...+.|+.||..||..| ..|..|++++
T Consensus 40 msa~hC~~CG~PIpa~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQEFCPTCQQPV 68 (226)
T ss_pred cchhhcccccCcccCCCCeeECCCCCCcc
Confidence 45678999999988543 3355555443
No 104
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.24 E-value=31 Score=24.61 Aligned_cols=7 Identities=57% Similarity=1.431 Sum_probs=3.9
Q ss_pred eccCCcc
Q psy9235 161 LCPLCEC 167 (317)
Q Consensus 161 lCPLCrs 167 (317)
.||||.+
T Consensus 22 ~CPlC~r 28 (54)
T PF04423_consen 22 CCPLCGR 28 (54)
T ss_dssp E-TTT--
T ss_pred cCCCCCC
Confidence 9999987
No 105
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=22.82 E-value=49 Score=24.64 Aligned_cols=23 Identities=35% Similarity=0.715 Sum_probs=17.7
Q ss_pred ccccCCCCCCCCCCCceeeceeCc
Q psy9235 261 SLFTCPNSDREDSRNPALCLICGD 284 (317)
Q Consensus 261 ~~~~C~~c~~~~~~~P~lCL~CG~ 284 (317)
....|++||+. -.---+|+.||.
T Consensus 26 ~~~~c~~cG~~-~l~Hrvc~~cg~ 48 (57)
T COG0333 26 TLSVCPNCGEY-KLPHRVCLKCGY 48 (57)
T ss_pred cceeccCCCCc-ccCceEcCCCCC
Confidence 45679999987 334589999995
No 106
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.72 E-value=51 Score=23.02 Aligned_cols=22 Identities=32% Similarity=0.748 Sum_probs=15.9
Q ss_pred ccCCCCCCC---CCCCceeeceeCc
Q psy9235 263 FTCPNSDRE---DSRNPALCLICGD 284 (317)
Q Consensus 263 ~~C~~c~~~---~~~~P~lCL~CG~ 284 (317)
..|.+||.+ ++.+++-|-.||-
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 568888865 2357888888884
No 107
>KOG1785|consensus
Probab=22.69 E-value=41 Score=34.44 Aligned_cols=43 Identities=23% Similarity=0.679 Sum_probs=30.2
Q ss_pred CCCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEecc
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALPL 175 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP~ 175 (317)
...+-+--|||.|-..|+-.+-.+- +-=-||.||.-----=|+
T Consensus 379 dKdvkIEPCGHLlCt~CLa~WQ~sd---------------------~gq~CPFCRcEIKGte~v 421 (563)
T KOG1785|consen 379 DKDVKIEPCGHLLCTSCLAAWQDSD---------------------EGQTCPFCRCEIKGTEPV 421 (563)
T ss_pred CCCcccccccchHHHHHHHhhcccC---------------------CCCCCCceeeEeccccce
Confidence 3567788999999999998885332 122799999764433343
No 108
>PHA00626 hypothetical protein
Probab=22.26 E-value=64 Score=24.16 Aligned_cols=8 Identities=25% Similarity=0.858 Sum_probs=6.8
Q ss_pred cCCCCCCC
Q psy9235 264 TCPNSDRE 271 (317)
Q Consensus 264 ~C~~c~~~ 271 (317)
.||+||+.
T Consensus 2 ~CP~CGS~ 9 (59)
T PHA00626 2 SCPKCGSG 9 (59)
T ss_pred CCCCCCCc
Confidence 69999985
No 109
>KOG0804|consensus
Probab=22.24 E-value=46 Score=34.39 Aligned_cols=24 Identities=25% Similarity=0.567 Sum_probs=20.6
Q ss_pred CCCCCceeecCCchhhHHHHHHHh
Q psy9235 110 HQGPAPHTSTCGHVMHSTCWSKYF 133 (317)
Q Consensus 110 ~~~~g~~vssCGH~mH~~C~~~Y~ 133 (317)
.-..|+...-|.|.-|..|..++-
T Consensus 187 ~s~~gi~t~~c~Hsfh~~cl~~w~ 210 (493)
T KOG0804|consen 187 SSTTGILTILCNHSFHCSCLMKWW 210 (493)
T ss_pred ccccceeeeecccccchHHHhhcc
Confidence 345789999999999999998874
No 110
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=22.22 E-value=44 Score=26.36 Aligned_cols=22 Identities=18% Similarity=0.498 Sum_probs=14.7
Q ss_pred cccCCCCCCC-CCCCce----eeceeC
Q psy9235 262 LFTCPNSDRE-DSRNPA----LCLICG 283 (317)
Q Consensus 262 ~~~C~~c~~~-~~~~P~----lCL~CG 283 (317)
+.+||=||.. +...+. ||.+|+
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCC
Confidence 4679999954 233444 898886
No 111
>KOG1002|consensus
Probab=22.16 E-value=62 Score=34.33 Aligned_cols=72 Identities=21% Similarity=0.485 Sum_probs=45.2
Q ss_pred CCCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccceEeccCCCCCCC----CCCCC
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNAALPLIPALSSI----QTTTP 187 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~vLP~ip~~~~~----~~~~~ 187 (317)
......++|-|.----|.+.|+.+... ..+ ..||.|. ||+.-+++.. ..-..
T Consensus 546 aed~i~s~ChH~FCrlCi~eyv~~f~~-----------------~~n-vtCP~C~------i~LsiDlse~alek~~l~~ 601 (791)
T KOG1002|consen 546 AEDYIESSCHHKFCRLCIKEYVESFME-----------------NNN-VTCPVCH------IGLSIDLSEPALEKTDLKG 601 (791)
T ss_pred hhhhHhhhhhHHHHHHHHHHHHHhhhc-----------------ccC-CCCcccc------ccccccccchhhhhcchhh
Confidence 346788999999999999999977531 223 7999995 4443222211 11122
Q ss_pred ccccccccccCHHHHHHHHH
Q psy9235 188 TENAEVFVHMDFDAWLSIVE 207 (317)
Q Consensus 188 ~e~~~~~~~~~~~~w~~~~~ 207 (317)
..+++...-.++++|=.+..
T Consensus 602 Fk~sSIlnRinm~~~qsSTK 621 (791)
T KOG1002|consen 602 FKASSILNRINMDDWQSSTK 621 (791)
T ss_pred hhhHHHhhhcchhhhcchhH
Confidence 33444445588999976543
No 112
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=22.07 E-value=35 Score=24.89 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=17.0
Q ss_pred ccccCCCCCCCCCCCceeeceeCc
Q psy9235 261 SLFTCPNSDREDSRNPALCLICGD 284 (317)
Q Consensus 261 ~~~~C~~c~~~~~~~P~lCL~CG~ 284 (317)
....||+||.. ..--.+|.-||.
T Consensus 25 ~l~~c~~cg~~-~~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEP-KLPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSE-ESTTSBCTTTBB
T ss_pred ceeeeccCCCE-ecccEeeCCCCe
Confidence 44679999976 335588999984
No 113
>PF04641 Rtf2: Rtf2 RING-finger
Probab=22.05 E-value=68 Score=30.26 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=18.1
Q ss_pred CCCceeecCCchhhHHHHHHH
Q psy9235 112 GPAPHTSTCGHVMHSTCWSKY 132 (317)
Q Consensus 112 ~~g~~vssCGH~mH~~C~~~Y 132 (317)
..-+++.+|||++=+.+++..
T Consensus 127 ~~fv~l~~cG~V~s~~alke~ 147 (260)
T PF04641_consen 127 HKFVYLRPCGCVFSEKALKEL 147 (260)
T ss_pred eeEEEEcCCCCEeeHHHHHhh
Confidence 356889999999999999887
No 114
>KOG2164|consensus
Probab=21.35 E-value=55 Score=34.24 Aligned_cols=46 Identities=26% Similarity=0.689 Sum_probs=34.4
Q ss_pred CCceeecCCchhhHHHHHHHhhhhhhhccCCccccCCCCccCCCCCeeeccCCccccce--EeccC
Q psy9235 113 PAPHTSTCGHVMHSTCWSKYFDNILAKENRRPYRLRQPTSFDIEKNEFLCPLCECLSNA--ALPLI 176 (317)
Q Consensus 113 ~g~~vssCGH~mH~~C~~~Y~~s~~~~e~rr~q~~R~~~~~d~~~~EFlCPLCrsLsN~--vLP~i 176 (317)
.-+..+.|||+-=..|+-.|+..-. -.+-=.||||++---. |.|+.
T Consensus 197 ~~p~~t~CGHiFC~~CiLqy~~~s~------------------~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 197 SVPVRTNCGHIFCGPCILQYWNYSA------------------IKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred CcccccccCceeeHHHHHHHHhhhc------------------ccCCccCCchhhhccccceeeee
Confidence 3456667999999999999986541 1234479999998777 77774
No 115
>KOG0804|consensus
Probab=20.92 E-value=45 Score=34.46 Aligned_cols=25 Identities=28% Similarity=0.654 Sum_probs=21.3
Q ss_pred cccCCCCCCCCCCCceeeceeCceecC
Q psy9235 262 LFTCPNSDREDSRNPALCLICGDMLCS 288 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P~lCL~CG~~~C~ 288 (317)
...|..||.. .+-.|||+||-+.|+
T Consensus 228 ~~~c~~c~~~--~~LwicliCg~vgcg 252 (493)
T KOG0804|consen 228 SSLCLACGCT--EDLWICLICGNVGCG 252 (493)
T ss_pred hhhhhhhccc--ccEEEEEEccceecc
Confidence 3468889886 688999999999997
No 116
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.32 E-value=84 Score=26.23 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=16.6
Q ss_pred cccCCCCCCCC-C-----------CCceeeceeCce
Q psy9235 262 LFTCPNSDRED-S-----------RNPALCLICGDM 285 (317)
Q Consensus 262 ~~~C~~c~~~~-~-----------~~P~lCL~CG~~ 285 (317)
+..|.+|...+ | ..-..||-||.+
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~ 91 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTI 91 (105)
T ss_pred HHhccccCcccccCcceEEEEcCCeEEEEecCCCcE
Confidence 34588998741 2 145789999986
No 117
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.19 E-value=45 Score=27.44 Aligned_cols=23 Identities=26% Similarity=0.590 Sum_probs=16.7
Q ss_pred ccccCCCCCCCCCCC---------ceeeceeCce
Q psy9235 261 SLFTCPNSDREDSRN---------PALCLICGDM 285 (317)
Q Consensus 261 ~~~~C~~c~~~~~~~---------P~lCL~CG~~ 285 (317)
..+.||+||.. .. -..|..||..
T Consensus 20 t~f~CP~Cge~--~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGKV--SISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCCe--EeeeecCCCcceEECCCCCCc
Confidence 45779999953 23 4789999874
No 118
>PRK12496 hypothetical protein; Provisional
Probab=20.08 E-value=53 Score=29.05 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=18.3
Q ss_pred cccCCCCCCCCCCCc--eeeceeCce
Q psy9235 262 LFTCPNSDREDSRNP--ALCLICGDM 285 (317)
Q Consensus 262 ~~~C~~c~~~~~~~P--~lCL~CG~~ 285 (317)
+.+|+.||+.-+.++ -.|-.||.-
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSP 152 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCCh
Confidence 467999999865443 679999964
Done!