Query 014025
Match_columns 432
No_of_seqs 239 out of 518
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 01:07:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014025.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014025hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2169 Zn-finger transcriptio 100.0 9.8E-37 2.1E-41 329.0 21.9 355 12-430 1-375 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.9 4.9E-24 1.1E-28 156.2 2.2 50 360-409 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.8 8.1E-20 1.8E-24 163.2 9.3 130 166-305 6-144 (144)
4 PF11789 zf-Nse: Zinc-finger o 98.6 2.4E-08 5.2E-13 75.2 2.9 54 352-407 2-57 (57)
5 PF02037 SAP: SAP domain; Int 98.6 4.2E-08 9.2E-13 66.5 3.6 35 11-45 1-35 (35)
6 smart00513 SAP Putative DNA-bi 98.5 2E-07 4.3E-12 63.2 4.0 34 12-45 2-35 (35)
7 KOG1973 Chromatin remodeling p 98.0 2.9E-06 6.2E-11 83.8 2.4 55 108-170 214-269 (274)
8 PF00628 PHD: PHD-finger; Int 97.7 5.1E-06 1.1E-10 60.7 -0.4 49 115-168 1-50 (51)
9 KOG2979 Protein involved in DN 97.3 0.00011 2.4E-09 70.6 2.2 75 352-428 167-246 (262)
10 smart00504 Ubox Modified RING 97.3 0.0004 8.8E-09 52.5 4.8 60 362-426 2-61 (63)
11 smart00249 PHD PHD zinc finger 97.1 0.00054 1.2E-08 48.1 3.2 44 117-166 4-47 (47)
12 COG5034 TNG2 Chromatin remodel 97.0 0.00025 5.5E-09 67.9 1.6 49 112-168 220-269 (271)
13 PF04564 U-box: U-box domain; 96.4 0.0036 7.8E-08 49.4 3.7 63 361-427 4-66 (73)
14 KOG1844 PHD Zn-finger proteins 96.0 0.004 8.8E-08 66.5 2.6 56 111-175 84-140 (508)
15 PF12949 HeH: HeH/LEM domain; 94.5 0.026 5.6E-07 38.2 1.9 29 11-39 1-31 (35)
16 KOG4323 Polycomb-like PHD Zn-f 94.4 0.015 3.3E-07 60.9 1.0 55 111-168 169-223 (464)
17 PLN03208 E3 ubiquitin-protein 94.4 0.044 9.5E-07 51.2 3.9 56 360-416 17-84 (193)
18 PF13831 PHD_2: PHD-finger; PD 94.3 0.01 2.2E-07 40.5 -0.3 35 125-167 2-36 (36)
19 COG5627 MMS21 DNA repair prote 94.3 0.024 5.2E-07 54.0 1.9 69 352-422 180-250 (275)
20 COG5222 Uncharacterized conser 93.8 0.055 1.2E-06 53.3 3.5 61 356-419 269-330 (427)
21 PF14835 zf-RING_6: zf-RING of 92.9 0.11 2.4E-06 39.9 3.1 59 361-425 7-65 (65)
22 KOG4259 Putative nucleic acid- 91.1 0.22 4.8E-06 47.2 3.6 36 12-47 7-42 (260)
23 PF07498 Rho_N: Rho terminatio 91.0 0.32 6.8E-06 34.4 3.5 35 11-45 2-38 (43)
24 TIGR00599 rad18 DNA repair pro 89.1 0.53 1.1E-05 49.0 4.7 67 358-430 23-90 (397)
25 KOG2164 Predicted E3 ubiquitin 88.2 0.3 6.6E-06 51.6 2.3 55 361-416 186-241 (513)
26 PF04641 Rtf2: Rtf2 RING-finge 87.2 0.65 1.4E-05 45.6 3.9 55 358-417 110-167 (260)
27 PF10208 Armet: Degradation ar 82.8 1.4 2.9E-05 39.8 3.5 38 11-48 104-143 (154)
28 cd00162 RING RING-finger (Real 81.2 1.6 3.4E-05 29.4 2.7 42 364-409 2-44 (45)
29 KOG0957 PHD finger protein [Ge 79.4 1.9 4E-05 45.6 3.5 68 104-175 111-185 (707)
30 PF13923 zf-C3HC4_2: Zinc fing 79.2 1.1 2.4E-05 30.5 1.3 39 364-406 1-39 (39)
31 TIGR00599 rad18 DNA repair pro 72.6 12 0.00027 39.0 7.4 64 12-78 267-330 (397)
32 KOG0825 PHD Zn-finger protein 71.8 1.8 4E-05 48.0 1.2 52 112-170 214-267 (1134)
33 PF13445 zf-RING_UBOX: RING-ty 71.5 2.8 6.1E-05 29.6 1.7 39 364-404 1-43 (43)
34 PF14447 Prok-RING_4: Prokaryo 70.7 3 6.5E-05 31.1 1.8 37 368-415 18-54 (55)
35 PF13920 zf-C3HC4_3: Zinc fing 69.3 3.2 6.8E-05 29.8 1.7 44 363-411 4-48 (50)
36 KOG0957 PHD finger protein [Ge 67.2 10 0.00022 40.4 5.3 53 109-166 540-595 (707)
37 PF15227 zf-C3HC4_4: zinc fing 67.2 3.5 7.6E-05 28.8 1.5 42 364-406 1-42 (42)
38 PF04423 Rad50_zn_hook: Rad50 66.5 3.1 6.7E-05 30.6 1.2 37 389-428 10-46 (54)
39 cd00350 rubredoxin_like Rubred 65.7 3 6.4E-05 27.6 0.8 11 399-409 16-26 (33)
40 KOG0978 E3 ubiquitin ligase in 64.5 2.4 5.1E-05 47.0 0.2 56 356-416 638-694 (698)
41 PF14446 Prok-RING_1: Prokaryo 63.2 5.5 0.00012 29.7 1.9 33 112-146 4-38 (54)
42 PF04810 zf-Sec23_Sec24: Sec23 63.2 1.3 2.8E-05 30.8 -1.4 16 394-409 18-33 (40)
43 PF13894 zf-C2H2_4: C2H2-type 61.7 3 6.5E-05 24.3 0.3 11 401-411 1-11 (24)
44 PF00097 zf-C3HC4: Zinc finger 61.6 6.5 0.00014 26.7 2.0 40 364-406 1-41 (41)
45 PF02837 Glyco_hydro_2_N: Glyc 61.4 28 0.00061 30.9 6.7 66 203-292 72-138 (167)
46 PF08531 Bac_rhamnosid_N: Alph 61.2 5 0.00011 36.8 1.7 47 244-292 15-64 (172)
47 KOG0801 Predicted E3 ubiquitin 60.9 4.4 9.5E-05 36.9 1.2 19 399-417 137-155 (205)
48 KOG0311 Predicted E3 ubiquitin 60.2 1.1 2.4E-05 45.4 -2.9 74 352-428 34-108 (381)
49 KOG2177 Predicted E3 ubiquitin 60.1 7.3 0.00016 37.1 2.8 63 360-429 12-74 (386)
50 PF02228 Gag_p19: Major core p 59.9 5.1 0.00011 32.1 1.3 39 387-427 45-86 (92)
51 KOG1244 Predicted transcriptio 57.8 7.1 0.00015 38.4 2.2 48 112-166 280-328 (336)
52 KOG1632 Uncharacterized PHD Zn 56.8 5.2 0.00011 41.0 1.1 50 115-170 62-114 (345)
53 PLN03124 poly [ADP-ribose] pol 56.7 8.2 0.00018 42.7 2.7 38 12-49 3-40 (643)
54 COG5243 HRD1 HRD ubiquitin lig 54.3 6.5 0.00014 40.3 1.4 28 379-413 320-347 (491)
55 cd00730 rubredoxin Rubredoxin; 52.8 6.4 0.00014 28.8 0.8 12 398-409 32-43 (50)
56 KOG0287 Postreplication repair 52.6 38 0.00082 34.5 6.3 56 12-69 249-304 (442)
57 KOG0955 PHD finger protein BR1 51.2 11 0.00024 43.9 2.7 55 110-173 217-273 (1051)
58 PRK12678 transcription termina 50.8 16 0.00036 40.1 3.8 38 11-48 23-62 (672)
59 COG5574 PEX10 RING-finger-cont 50.1 8.6 0.00019 37.7 1.4 55 361-418 215-269 (271)
60 PF00301 Rubredoxin: Rubredoxi 49.8 8.4 0.00018 27.8 1.0 14 396-409 30-43 (47)
61 KOG4299 PHD Zn-finger protein 49.6 10 0.00023 41.2 2.1 51 114-169 254-305 (613)
62 smart00184 RING Ring finger. E 48.8 13 0.00027 23.8 1.7 25 378-406 14-39 (39)
63 KOG0956 PHD finger protein AF1 47.5 11 0.00023 41.7 1.8 37 114-150 7-45 (900)
64 smart00734 ZnF_Rad18 Rad18-lik 45.9 6.6 0.00014 24.7 -0.1 10 402-411 3-12 (26)
65 COG4068 Uncharacterized protei 45.5 17 0.00037 27.5 2.0 30 399-428 7-36 (64)
66 PF00096 zf-C2H2: Zinc finger, 45.2 6.5 0.00014 23.1 -0.1 11 401-411 1-11 (23)
67 TIGR00570 cdk7 CDK-activating 44.8 16 0.00034 36.9 2.4 18 398-415 41-58 (309)
68 KOG4661 Hsp27-ERE-TATA-binding 43.9 14 0.00031 39.9 2.0 40 9-48 28-67 (940)
69 PF11793 FANCL_C: FANCL C-term 43.6 15 0.00033 28.5 1.7 31 381-412 32-67 (70)
70 PF11116 DUF2624: Protein of u 41.7 1.2E+02 0.0026 24.8 6.6 45 1-48 1-46 (85)
71 PF13639 zf-RING_2: Ring finge 41.5 16 0.00034 25.3 1.3 25 378-407 19-44 (44)
72 PF13832 zf-HC5HC2H_2: PHD-zin 41.1 18 0.00039 30.2 1.9 33 113-147 55-88 (110)
73 COG5533 UBP5 Ubiquitin C-termi 39.3 12 0.00026 37.7 0.6 35 375-409 259-293 (415)
74 COG0723 QcrA Rieske Fe-S prote 38.1 13 0.00028 34.1 0.5 26 378-408 106-132 (177)
75 PF14634 zf-RING_5: zinc-RING 36.4 25 0.00054 24.5 1.7 41 364-408 2-44 (44)
76 PF13465 zf-H2C2_2: Zinc-finge 36.3 30 0.00065 21.4 1.8 15 396-410 10-24 (26)
77 PF14000 Packaging_FI: DNA pac 36.2 54 0.0012 28.7 4.0 31 16-46 6-38 (125)
78 KOG1632 Uncharacterized PHD Zn 35.9 5.6 0.00012 40.8 -2.4 57 110-168 236-294 (345)
79 KOG3970 Predicted E3 ubiquitin 35.7 43 0.00094 32.2 3.6 58 371-428 56-122 (299)
80 PF07227 DUF1423: Protein of u 33.4 34 0.00073 36.1 2.8 52 115-168 131-191 (446)
81 PF00641 zf-RanBP: Zn-finger i 33.2 22 0.00048 22.7 0.9 10 398-407 2-11 (30)
82 PHA02929 N1R/p28-like protein; 33.2 28 0.00061 33.9 2.0 45 362-411 175-227 (238)
83 COG5141 PHD zinc finger-contai 31.8 51 0.0011 35.3 3.7 33 115-149 195-230 (669)
84 PF05605 zf-Di19: Drought indu 31.3 13 0.00028 27.2 -0.5 10 400-409 2-11 (54)
85 PF13913 zf-C2HC_2: zinc-finge 30.9 11 0.00025 23.2 -0.7 15 401-415 3-17 (25)
86 KOG0287 Postreplication repair 30.8 20 0.00042 36.5 0.5 65 359-429 21-86 (442)
87 KOG3113 Uncharacterized conser 30.7 73 0.0016 31.2 4.3 112 298-417 48-164 (293)
88 PRK01343 zinc-binding protein; 29.6 28 0.0006 26.3 1.0 16 396-411 5-20 (57)
89 PF12874 zf-met: Zinc-finger o 29.1 17 0.00037 21.7 -0.1 11 401-411 1-11 (25)
90 KOG1245 Chromatin remodeling c 28.9 13 0.00028 44.9 -1.3 53 112-171 1107-1160(1404)
91 PF13297 Telomere_Sde2_2: Telo 28.3 1.5E+02 0.0031 22.7 4.7 36 9-44 10-45 (60)
92 PF09889 DUF2116: Uncharacteri 28.1 51 0.0011 25.0 2.2 17 402-418 5-21 (59)
93 PF12861 zf-Apc11: Anaphase-pr 27.7 46 0.00099 27.2 2.1 31 379-413 51-84 (85)
94 cd00729 rubredoxin_SM Rubredox 27.5 29 0.00064 23.1 0.8 10 400-409 2-11 (34)
95 KOG0954 PHD finger protein [Ge 27.4 30 0.00066 38.6 1.3 49 112-169 270-321 (893)
96 TIGR03171 soxL2 Rieske iron-su 27.1 40 0.00088 34.1 2.0 9 377-385 182-190 (321)
97 PF13397 DUF4109: Domain of un 26.9 37 0.0008 28.8 1.4 42 355-413 22-63 (105)
98 PHA02926 zinc finger-like prot 26.4 38 0.00083 32.6 1.6 61 361-423 170-240 (242)
99 KOG2169 Zn-finger transcriptio 25.6 36 0.00079 37.8 1.5 43 6-48 14-56 (636)
100 KOG2266 Chromatin-associated p 25.2 85 0.0018 33.5 4.0 44 6-49 260-306 (594)
101 PF05265 DUF723: Protein of un 24.1 1.5E+02 0.0032 22.6 4.1 58 323-407 3-60 (60)
102 PRK00418 DNA gyrase inhibitor; 24.1 47 0.001 25.5 1.4 14 399-412 5-18 (62)
103 PF07496 zf-CW: CW-type Zinc F 24.0 40 0.00087 24.4 1.0 33 126-165 2-34 (50)
104 COG5432 RAD18 RING-finger-cont 23.9 33 0.00072 34.2 0.7 63 359-427 23-86 (391)
105 PF04780 DUF629: Protein of un 23.3 42 0.00092 35.8 1.4 35 387-425 44-78 (466)
106 COG5432 RAD18 RING-finger-cont 23.2 1.8E+02 0.0039 29.2 5.6 51 13-65 246-296 (391)
107 PF09943 DUF2175: Uncharacteri 22.7 34 0.00074 28.8 0.5 16 400-415 2-17 (101)
108 KOG0320 Predicted E3 ubiquitin 22.5 44 0.00094 31.1 1.1 47 362-413 132-180 (187)
109 PF14353 CpXC: CpXC protein 22.4 18 0.00038 31.3 -1.3 15 399-413 37-51 (128)
110 COG3024 Uncharacterized protei 22.3 40 0.00086 26.0 0.7 15 398-412 5-19 (65)
111 PF13771 zf-HC5HC2H: PHD-like 21.6 64 0.0014 25.7 1.9 32 114-147 37-69 (90)
112 PF11824 DUF3344: Protein of u 21.1 1.8E+02 0.0039 28.8 5.3 67 240-306 69-149 (271)
113 COG1592 Rubrerythrin [Energy p 21.1 70 0.0015 29.4 2.2 9 400-408 134-142 (166)
114 PLN00162 transport protein sec 21.0 28 0.0006 39.6 -0.5 19 391-409 66-84 (761)
115 TIGR00373 conserved hypothetic 20.1 1E+02 0.0023 27.8 3.1 66 307-414 77-142 (158)
116 PRK06266 transcription initiat 20.0 1.2E+02 0.0026 28.0 3.6 65 307-413 85-149 (178)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=9.8e-37 Score=328.99 Aligned_cols=355 Identities=19% Similarity=0.352 Sum_probs=246.4
Q ss_pred hhcCHHHHHHHH-HHhCCCCCC--ChHHHHHHHHHhcccccccccccCCCCCcHHHHHHHHHHHHHhccc-CCCCCcccC
Q 014025 12 AHFRIKELKDVL-TQLGLSKQG--KKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLVDDTHRKLQV-SVAPDLASK 87 (432)
Q Consensus 12 ~~fRv~ELk~vl-~~lgl~ksG--rK~eL~~Ril~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~y~~~~~-~~~~~~~~~ 87 (432)
+++|+.||+.++ .+.|+...| +|.+|.-|.+.++...+.+ ++..+|.+.|++... .......-.
T Consensus 1 m~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~------------~~q~~i~~~~~~~~~~~~~~~~~~~ 68 (636)
T KOG2169|consen 1 MSLRVSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKP------------YLQMVIKELYQRQYPNGQQQPIDLP 68 (636)
T ss_pred CCcccccccccchhhhccccccccchhhhhhhhhcccccCCch------------hhhhhhhhhhhhhcccccccccccc
Confidence 368999999998 788888888 8899999999999888755 778888899885222 221111010
Q ss_pred CCCCcCCCCcccccccccccCCCCCccccCCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCccccccee
Q 014025 88 GGQGVSNSSNIKIKGEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (432)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~q~~~~~rC~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Cr 167 (432)
. ...+.+..+. .+.. . |....|..=..+....+.+ +..-+.+..+
T Consensus 69 ~---~~~~~~~~~~-----~~~~---------------~--------~~~~~~~~~~~~~~~~l~g----~~~~~~~~~~ 113 (636)
T KOG2169|consen 69 A---VKLHPNVVPP-----FYPL---------------L--------WQLLRHPTQQPVTPSSLLG----PPLPFHPDVK 113 (636)
T ss_pred c---cccCCcccCc-----cccc---------------h--------hcccccCCCCCCCcccccC----CCCcCCCccc
Confidence 0 0011111100 0000 0 0001111000011111111 0023456677
Q ss_pred ecccCcchhhccccccceeeeecccCCCCCCCceeeeEEEEeChhhHHhhccC-Ce------eEEEEEeecCCCCccccC
Q 014025 168 LSRADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSKQ-EY------DVQAWCMLLNDKVPFRMQ 240 (432)
Q Consensus 168 l~~~dPF~~~i~~ll~p~~l~~~~i~~~g~~~~q~~~~~F~Lt~~~~~~l~~~-~~------~l~v~C~~~~~~~~~~~~ 240 (432)
+ +..|||.++..+.+|+.+..+. + ..++...+.|.|+++....+... +. .-.+ |.. ..+.+++.+
T Consensus 114 ~-~~~~~y~~l~~~~~p~~~~~~~----~-~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~-~~s~p~e~~ 185 (636)
T KOG2169|consen 114 L-KKLPFYDVLSELIKPHVLHSSN----S-PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLM-ETSCPQEDH 185 (636)
T ss_pred c-cCCchheecccccCceeecCcC----C-CCcccccchhhcchhhhhhcccccccccccccccce-eec-cccCccccc
Confidence 7 5699999999999998887642 2 34455678899999998776532 10 0111 433 245678999
Q ss_pred CCceeeEEECCeeeecc-CCCCCCCCCC-CCCCCCCC-ccc--CcCCc-ccEEEEEEe--ccceEEEEEEEEEecCHHHH
Q 014025 241 WPQYADLQVNGVPVRAI-NRPGSQLLGA-NGRDDGPI-ITP--WTKDG-INKIVLTGC--DARIFCLGVRIVKRRSVQQV 312 (432)
Q Consensus 241 wP~~~~i~vNg~~v~~~-~r~~~~~~g~-~~r~~~~~-IT~--~l~~g-~N~I~i~~~--d~~~y~~~v~lVk~~s~~~l 312 (432)
||.++.++||+..+.+. ..-..++.+. .++...|. ||. ++... .|.+.+.|. .++.|.+++|+|+.++.++|
T Consensus 186 ~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~~l 265 (636)
T KOG2169|consen 186 FPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSKDL 265 (636)
T ss_pred cCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHHHH
Confidence 99999999999998875 2112222222 25655666 999 44443 377777664 48899999999999999999
Q ss_pred HhhcccCCC-CCCHHHHHHHHHHHhCCCCCCCCCCCCCCcceEeeceeeeecCCCccccccccccccCcCccccccHHHH
Q 014025 313 LNLIPKESE-GEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVF 391 (432)
Q Consensus 313 l~~I~~~~~-~~~~e~~~~~ik~~l~~~~~~~~~d~D~D~ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~f 391 (432)
+++++...+ ...++.+.+.|++.+. .|+|.||+++++.|||.|||+++||++|+|+..|+|+|||||.+|
T Consensus 266 lq~~~~~~~~~~~~~~s~~~~~~~l~---------~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~ 336 (636)
T KOG2169|consen 266 LQRLKQNGKINRNLSQSDALIKKKLT---------AGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSY 336 (636)
T ss_pred HHHHhccCCccCchhHhHHHhhcccc---------cCCcccceeccceeEecCCcccceeecCCcccccccceecchhhh
Confidence 999987542 2334778888876543 234557999999999999999999999999999999999999999
Q ss_pred HHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHHhhc
Q 014025 392 VELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKVLF 430 (432)
Q Consensus 392 L~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~~~ 430 (432)
|+||+++++|+||||++.+.+++|+||+||.+||..+..
T Consensus 337 lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL~~~~~ 375 (636)
T KOG2169|consen 337 LQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNILQSCQA 375 (636)
T ss_pred HHhccCCCeeeCccCCccccccchhhhHHHHHHHhhccC
Confidence 999999999999999999999999999999999988754
No 2
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.88 E-value=4.9e-24 Score=156.16 Aligned_cols=50 Identities=54% Similarity=1.107 Sum_probs=36.5
Q ss_pred eeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCC
Q 014025 360 VNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (432)
Q Consensus 360 isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (432)
|||+||||++||++||||+.|+|+|||||++||++++++++|+||||+++
T Consensus 1 vsL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 1 VSLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp EESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CeeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 79999999999999999999999999999999999999999999999974
No 3
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.81 E-value=8.1e-20 Score=163.18 Aligned_cols=130 Identities=22% Similarity=0.355 Sum_probs=84.4
Q ss_pred eeecccCcchhhccccccceeeeecccCCCCCCCceeeeEEEEeChhhHHhhcc--CCeeEEEEEeecC---CCCccccC
Q 014025 166 CRLSRADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSK--QEYDVQAWCMLLN---DKVPFRMQ 240 (432)
Q Consensus 166 Crl~~~dPF~~~i~~ll~p~~l~~~~i~~~g~~~~q~~~~~F~Lt~~~~~~l~~--~~~~l~v~C~~~~---~~~~~~~~ 240 (432)
-+| +.+|||+++ ++|.|+.+.+.. ....+...+.|.|+++++++|++ +.++|+|||+..+ .+..++++
T Consensus 6 ~~F-k~sPFY~~~-~~i~~~~~~~~~-----~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~ 78 (144)
T PF14324_consen 6 LRF-KPSPFYKVL-RLIHPTPLLPAS-----SSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIE 78 (144)
T ss_dssp --B---BTTEEEE-EEEEEEEEEE-------EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB---
T ss_pred cEe-ccCCCccee-EEcCCccccccc-----cCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccc
Confidence 345 779999977 788887776532 22355778999999999999987 6799999999853 34578999
Q ss_pred CCceeeEEECCeeeeccCCCCCCCCCCCCCCCCCCcccCcCCc---ccEEEEEEe-ccceEEEEEEEEE
Q 014025 241 WPQYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKDG---INKIVLTGC-DARIFCLGVRIVK 305 (432)
Q Consensus 241 wP~~~~i~vNg~~v~~~~r~~~~~~g~~~r~~~~~IT~~l~~g---~N~I~i~~~-d~~~y~~~v~lVk 305 (432)
||.+++|+|||+.|+++.|+++ +++|+..|+|||++++.. .|+|+|+|+ +.+.|+++|||||
T Consensus 79 FP~~~evkvN~~~v~~~~~glk---nKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 79 FPPPCEVKVNGKQVKLNNRGLK---NKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp --SSEEEEETTEE--S--SS-T---TS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred cCCCeEEEEeCEEcccCccCCC---CCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 9999999999999999988765 457778888899999975 899999997 5789999999997
No 4
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.61 E-value=2.4e-08 Score=75.18 Aligned_cols=54 Identities=24% Similarity=0.588 Sum_probs=37.3
Q ss_pred ceEeeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCC--CC
Q 014025 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CL 407 (432)
Q Consensus 352 ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~ 407 (432)
||+.+...++++||||...|+-|+++..|.|. ||-++.+++-.+...-+||+ |+
T Consensus 2 di~i~~~~~~~~CPiT~~~~~~PV~s~~C~H~--fek~aI~~~i~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 2 DIVIEGGTISLKCPITLQPFEDPVKSKKCGHT--FEKEAILQYIQRNGSKRCPVAGCN 57 (57)
T ss_dssp -----SSB--SB-TTTSSB-SSEEEESSS--E--EEHHHHHHHCTTTS-EE-SCCC-S
T ss_pred ceEEeccEeccCCCCcCChhhCCcCcCCCCCe--ecHHHHHHHHHhcCCCCCCCCCCC
Confidence 45666789999999999999999999999995 99999999988888999999 64
No 5
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=98.60 E-value=4.2e-08 Score=66.50 Aligned_cols=35 Identities=40% Similarity=0.676 Sum_probs=31.6
Q ss_pred HhhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 014025 11 LAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (432)
Q Consensus 11 l~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l 45 (432)
+++++|+|||..|+++||+.+|+|+||++|+.+++
T Consensus 1 l~~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 46899999999999999999999999999999875
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=98.46 E-value=2e-07 Score=63.17 Aligned_cols=34 Identities=50% Similarity=0.786 Sum_probs=32.0
Q ss_pred hhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 014025 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (432)
Q Consensus 12 ~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l 45 (432)
.+++++|||+.|++.||+.+|+|+||++|+..++
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999875
No 7
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.99 E-value=2.9e-06 Score=83.80 Aligned_cols=55 Identities=33% Similarity=0.907 Sum_probs=45.9
Q ss_pred CCCCCccccCCCCCCCCCCeeeecCCCCC-CcccccceecCCCCCCCCCCCCCcccccceeecc
Q 014025 108 IQSDTKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (432)
Q Consensus 108 ~q~~~~~rC~Cg~~~~~~~~i~C~~~~C~-~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~~ 170 (432)
.-++...+|+|. ....+.||-|+++.|. .|+|..||++..+| ...|||+.|+-..
T Consensus 214 ~d~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 214 VDPDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAEN 269 (274)
T ss_pred cCCCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhhh
Confidence 345678999999 5567999999999999 99999999998664 3469999998643
No 8
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.75 E-value=5.1e-06 Score=60.70 Aligned_cols=49 Identities=41% Similarity=0.868 Sum_probs=38.9
Q ss_pred cc-CCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceee
Q 014025 115 CC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (432)
Q Consensus 115 rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl 168 (432)
+| +|+.....+.||+|+. |+.|+|..|++++.+..+. ....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCcC
Confidence 47 8999888899999999 9999999999987553221 123899998863
No 9
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=97.32 E-value=0.00011 Score=70.59 Aligned_cols=75 Identities=21% Similarity=0.303 Sum_probs=58.5
Q ss_pred ceEeeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCC--CCCCC--CCCCeeec-HHHHHHHH
Q 014025 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNY--SLENIIID-PYFNRITS 426 (432)
Q Consensus 352 ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~--~~~~L~ID-~y~~~Il~ 426 (432)
++...+..+|++||+|+..|.-|++++.|.|+ ||-++-++.-....+-.||+ |..++ .+..|.-| .+..+|-+
T Consensus 167 e~~i~~e~fs~rdPis~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr~ 244 (262)
T KOG2979|consen 167 EELIGQEVFSNRDPISKKPIVNPVISKKCGHV--YDRDSIMQILCDEITIRCPVLGCENPYYIQPGHLDEDKELQQKIRQ 244 (262)
T ss_pred HHHhhhhhhcccCchhhhhhhchhhhcCcCcc--hhhhhHHHHhccCceeecccccCCccccccccccCchHHHHHHHHH
Confidence 56667889999999999999999999999998 99999888877778999999 77333 33444445 45555554
Q ss_pred Hh
Q 014025 427 KV 428 (432)
Q Consensus 427 ~~ 428 (432)
.+
T Consensus 245 ~q 246 (262)
T KOG2979|consen 245 SQ 246 (262)
T ss_pred hc
Confidence 43
No 10
>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=97.30 E-value=0.0004 Score=52.55 Aligned_cols=60 Identities=13% Similarity=0.171 Sum_probs=49.6
Q ss_pred ecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHH
Q 014025 362 LRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITS 426 (432)
Q Consensus 362 L~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~ 426 (432)
|.|||++..|+-|+.. .|.|. |+.+.+.+.-.+ .-.||+|++.+..++|+-+..+.+.++
T Consensus 2 ~~Cpi~~~~~~~Pv~~-~~G~v--~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~~i~ 61 (63)
T smart00504 2 FLCPISLEVMKDPVIL-PSGQT--YERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKSAIQ 61 (63)
T ss_pred cCCcCCCCcCCCCEEC-CCCCE--EeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHHHHH
Confidence 7899999999999986 66675 998888877554 458999999999999999977666554
No 11
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.04 E-value=0.00025 Score=67.91 Aligned_cols=49 Identities=29% Similarity=0.818 Sum_probs=39.9
Q ss_pred CccccCCCCCCCCCCeeeecCCCCC-CcccccceecCCCCCCCCCCCCCcccccceee
Q 014025 112 TKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (432)
Q Consensus 112 ~~~rC~Cg~~~~~~~~i~C~~~~C~-~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl 168 (432)
...+|+|.+.. .+.||-|+++.|. -|+|..||++.+-| -..|||+.|+-
T Consensus 220 e~lYCfCqqvS-yGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCFCQQVS-YGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKK 269 (271)
T ss_pred ceeEEEecccc-cccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHh
Confidence 56899998764 4899999999994 79999999996322 34799999974
No 13
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.41 E-value=0.0036 Score=49.38 Aligned_cols=63 Identities=11% Similarity=0.223 Sum_probs=45.5
Q ss_pred eecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHH
Q 014025 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSK 427 (432)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~ 427 (432)
.|.||||+..|+-|++...+ |. ||-.+...-..+ ..-.||+|++++..++|+-+.=+...+++
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G-~t--yer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~ 66 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSG-HT--YERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEE 66 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTS-EE--EEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHH
T ss_pred ccCCcCcCcHhhCceeCCcC-CE--EcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHH
Confidence 37899999999999998777 54 998888776665 55689999999999999999665555543
No 14
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=95.97 E-value=0.004 Score=66.53 Aligned_cols=56 Identities=30% Similarity=0.625 Sum_probs=46.6
Q ss_pred CCccccCCCCCCC-CCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceeecccCcch
Q 014025 111 DTKVCCPCGSSLE-TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRADPFW 175 (432)
Q Consensus 111 ~~~~rC~Cg~~~~-~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~~~dPF~ 175 (432)
...++|.||.... .+.||+|+. |..|||..|+++.... .|..|+|+.|++ +.-+-+
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~~Wqh~~C~g~~~~~------~p~~y~c~~c~~-~~~~~~ 140 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CGRWQHKICCGSFKST------KPDKYVCEICTP-RNKEVE 140 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cCcccCceeeeecCCC------Cchhceeeeecc-ccccch
Confidence 3568999999988 999999999 9999999999986432 278999999999 434444
No 15
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=94.47 E-value=0.026 Score=38.22 Aligned_cols=29 Identities=28% Similarity=0.507 Sum_probs=20.6
Q ss_pred HhhcCHHHHHHHHHHhCCC--CCCChHHHHH
Q 014025 11 LAHFRIKELKDVLTQLGLS--KQGKKQDLVD 39 (432)
Q Consensus 11 l~~fRv~ELk~vl~~lgl~--ksGrK~eL~~ 39 (432)
+.+++|.|||.+|...|.. .+.+|+||++
T Consensus 1 p~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~ 31 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHGIEFPSNAKKAELVA 31 (35)
T ss_dssp STT--SHHHHHHHHHHT---SSS--SHHHHH
T ss_pred CCcCcHHHHHHHHHHcCCCCCCCCCHHHHHH
Confidence 3689999999999999986 8999999986
No 16
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.41 E-value=0.015 Score=60.88 Aligned_cols=55 Identities=22% Similarity=0.546 Sum_probs=43.5
Q ss_pred CCccccCCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceee
Q 014025 111 DTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (432)
Q Consensus 111 ~~~~rC~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl 168 (432)
.....|.||.....+.||+|.. |+.|+|..|++-..+++.-.. .-..|+|-.|.-
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l~~D-~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDELAGD-PFYEWFCDVCNR 223 (464)
T ss_pred ceeeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhhccC-ccceEeehhhcc
Confidence 3467888999988889999999 999999999998877644422 234788988865
No 17
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=94.39 E-value=0.044 Score=51.23 Aligned_cols=56 Identities=14% Similarity=0.376 Sum_probs=43.6
Q ss_pred eeecCCCccccccccccccCcCccccccHH-HHHHHh-----------cCCCceecCCCCCCCCCCCee
Q 014025 360 VNLRCPMSGSRIKVAGRFKPCVHMGCFDLD-VFVELN-----------QRSRKWQCPICLRNYSLENII 416 (432)
Q Consensus 360 isL~CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n-----------~~~~~W~CPiC~k~~~~~~L~ 416 (432)
=.+.|||-...++.|+-. .|.|+=|.+-- .|+... ......+||+|...+...+|+
T Consensus 17 ~~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred CccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 368999999999999884 79999888754 466542 134568999999999887764
No 18
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=94.35 E-value=0.01 Score=40.47 Aligned_cols=35 Identities=29% Similarity=0.729 Sum_probs=19.2
Q ss_pred CCeeeecCCCCCCcccccceecCCCCCCCCCCCCCccccccee
Q 014025 125 ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (432)
Q Consensus 125 ~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Cr 167 (432)
+.+|.|.. |+..-|..|+++...+ ....|+|..|+
T Consensus 2 n~ll~C~~--C~v~VH~~CYGv~~~~------~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CNVAVHQSCYGVSEVP------DGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S--EEEHHHHT-SS--------SS-----HHH-
T ss_pred CceEEeCC--CCCcCChhhCCcccCC------CCCcEECCcCC
Confidence 56899999 9999999999997553 23359998875
No 19
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=94.29 E-value=0.024 Score=54.00 Aligned_cols=69 Identities=16% Similarity=0.253 Sum_probs=55.7
Q ss_pred ceEeeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCC--CCCCCCCCCeeecHHHH
Q 014025 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNYSLENIIIDPYFN 422 (432)
Q Consensus 352 ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~~L~ID~y~~ 422 (432)
+|...+-.++++|||+...+.+|.=+..|.|. ||.+..+..-+--++--||. |+.....+.++-|.-++
T Consensus 180 ~i~I~~~~~~nrCpitl~p~~~pils~kcnh~--~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~IlE 250 (275)
T COG5627 180 KILIHQELLSNRCPITLNPDFYPILSSKCNHK--PEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHILE 250 (275)
T ss_pred hhhhhhhhhcccCCcccCcchhHHHHhhhccc--ccHHHHHHHhcCCceeecchhhcchheeccchhhhHHHH
Confidence 46667789999999999999999999999998 89887776666668889997 98876666666554443
No 20
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.84 E-value=0.055 Score=53.28 Aligned_cols=61 Identities=18% Similarity=0.446 Sum_probs=45.5
Q ss_pred eceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCC-CCCCCCCeeecH
Q 014025 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICL-RNYSLENIIIDP 419 (432)
Q Consensus 356 ~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~-k~~~~~~L~ID~ 419 (432)
..-.|||+||+......-|+|..-|.|.-|=. -|+..---.-+.||.|+ +++.++.|.-|.
T Consensus 269 ~~~~i~LkCplc~~Llrnp~kT~cC~~~fc~e---ci~~al~dsDf~CpnC~rkdvlld~l~pD~ 330 (427)
T COG5222 269 QPPNISLKCPLCHCLLRNPMKTPCCGHTFCDE---CIGTALLDSDFKCPNCSRKDVLLDGLTPDI 330 (427)
T ss_pred CCCCccccCcchhhhhhCcccCccccchHHHH---HHhhhhhhccccCCCcccccchhhccCccH
Confidence 34578899999999999999999999986533 23333334579999997 566666666653
No 21
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=92.93 E-value=0.11 Score=39.92 Aligned_cols=59 Identities=20% Similarity=0.375 Sum_probs=26.5
Q ss_pred eecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHH
Q 014025 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRIT 425 (432)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il 425 (432)
.|+|+.....|+.|+=--.|.|+=|=.-- ...-. -.||+|+.++-..|++|..-+.+++
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci-----~~~~~-~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI-----RDCIG-SECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG-----GGGTT-TB-SSS--B-S-SS----HHHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh-----HHhcC-CCCCCcCChHHHHHHHhhhhhhccC
Confidence 47999999999999988899998653221 11111 2599999999999999987776653
No 22
>KOG4259 consensus Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning]
Probab=91.13 E-value=0.22 Score=47.24 Aligned_cols=36 Identities=36% Similarity=0.595 Sum_probs=33.0
Q ss_pred hhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhccc
Q 014025 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSD 47 (432)
Q Consensus 12 ~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~ 47 (432)
..+.|.|||.=|..=||+..|.|.||++|+-+-+..
T Consensus 7 kklkVa~LkeeLa~rGL~~~GNK~EL~~RLtaa~e~ 42 (260)
T KOG4259|consen 7 KKLKVAELKEELAERGLSTAGNKAELVSRLTAATES 42 (260)
T ss_pred hhccHHHHHHHHHHhcccccCChHHHHHHHHHHHHH
Confidence 578999999999999999999999999999877655
No 23
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=91.03 E-value=0.32 Score=34.38 Aligned_cols=35 Identities=29% Similarity=0.500 Sum_probs=27.1
Q ss_pred HhhcCHHHHHHHHHHhCCC-C-CCChHHHHHHHHHhc
Q 014025 11 LAHFRIKELKDVLTQLGLS-K-QGKKQDLVDRILAIL 45 (432)
Q Consensus 11 l~~fRv~ELk~vl~~lgl~-k-sGrK~eL~~Ril~~l 45 (432)
|.+.-+.||+.+...+|+. . +=||+||+..|+.--
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~q 38 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAILKAQ 38 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHHHHH
Confidence 6788999999999999996 3 338999999998754
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.08 E-value=0.53 Score=48.98 Aligned_cols=67 Identities=16% Similarity=0.249 Sum_probs=53.7
Q ss_pred eeeeecCCCccccccccccccCcCccccccHHH-HHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHHhhc
Q 014025 358 IGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDV-FVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKVLF 430 (432)
Q Consensus 358 ~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~-fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~~~ 430 (432)
+.-.|.||+-...+.-|+- ..|.|.-|..--. |+.. .-.||+|...+....|+.+..+.+|++..+.
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~-----~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSN-----QPKCPLCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhC-----CCCCCCCCCccccccCccchHHHHHHHHHHH
Confidence 5667899999999999985 6899988766543 4432 2389999999988899999999999987654
No 25
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.18 E-value=0.3 Score=51.56 Aligned_cols=55 Identities=22% Similarity=0.513 Sum_probs=45.6
Q ss_pred eecCCCccccccccccccCcCcccccc-HHHHHHHhcCCCceecCCCCCCCCCCCee
Q 014025 361 NLRCPMSGSRIKVAGRFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNYSLENII 416 (432)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~~~~~L~ 416 (432)
...|||-.-.-.+|+|+. |-|+=||- +..|+.......--.||+|...+.+.||.
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~ 241 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLL 241 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhcccccee
Confidence 889999999999999999 99999986 45677766444445799999988887764
No 26
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.24 E-value=0.65 Score=45.58 Aligned_cols=55 Identities=24% Similarity=0.526 Sum_probs=39.4
Q ss_pred eeeeecCCCcccccc--ccccc-cCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeee
Q 014025 358 IGVNLRCPMSGSRIK--VAGRF-KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (432)
Q Consensus 358 ~~isL~CPls~~ri~--~P~Rg-~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (432)
......||+|+..|. ++.-. ..|-|.-+.+ ++=++. ..|.||+|++++.-+|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~--alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEK--ALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHH--HHHhhc---ccccccccCCccccCCEEE
Confidence 466789999999983 22222 5899974444 444442 5799999999999998774
No 27
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=82.83 E-value=1.4 Score=39.81 Aligned_cols=38 Identities=34% Similarity=0.550 Sum_probs=32.7
Q ss_pred HhhcCHHHHHHHHHHhCCCCCC--ChHHHHHHHHHhcccc
Q 014025 11 LAHFRIKELKDVLTQLGLSKQG--KKQDLVDRILAILSDD 48 (432)
Q Consensus 11 l~~fRv~ELk~vl~~lgl~ksG--rK~eL~~Ril~~l~~~ 48 (432)
|..+||+|||.+|..-|..=.| -|+|++.||.++-...
T Consensus 104 l~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~el~~k~ 143 (154)
T PF10208_consen 104 LKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEELKPKY 143 (154)
T ss_dssp TTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHCCCCCC
T ss_pred HhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHHHhhhc
Confidence 6789999999999999999888 6999999999965544
No 28
>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=81.24 E-value=1.6 Score=29.43 Aligned_cols=42 Identities=24% Similarity=0.539 Sum_probs=28.3
Q ss_pred CCCccccccccccccCcCccccccHH-HHHHHhcCCCceecCCCCCC
Q 014025 364 CPMSGSRIKVAGRFKPCVHMGCFDLD-VFVELNQRSRKWQCPICLRN 409 (432)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n~~~~~W~CPiC~k~ 409 (432)
||+-...+..|.....|.|.-|.+-. .|++. ...+||+|++.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKS----GKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHh----CcCCCCCCCCc
Confidence 56666666667777779998666633 34432 56789999875
No 29
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=79.42 E-value=1.9 Score=45.64 Aligned_cols=68 Identities=19% Similarity=0.536 Sum_probs=44.8
Q ss_pred ccccCCCCCccccCCCCCC--CCCCeeeecCCCCCCcccccceecCCCCCCCCCC-----CCCcccccceeecccCcch
Q 014025 104 MDDYIQSDTKVCCPCGSSL--ETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPP-----VPELFYCEICRLSRADPFW 175 (432)
Q Consensus 104 ~~~~~q~~~~~rC~Cg~~~--~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~-----~p~~f~C~~Crl~~~dPF~ 175 (432)
...|+.-...+.|+|-+.. .-+.+|+|+. |+..-|-+||+..+.. +++. -...|||+.|+.--..|-.
T Consensus 111 ~~~Sapkk~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 111 RTPSAPKKAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred cccCccccceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCCcc
Confidence 3344444455788996653 3588999999 9999999999986321 2211 1236899988874444543
No 30
>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=79.16 E-value=1.1 Score=30.53 Aligned_cols=39 Identities=23% Similarity=0.627 Sum_probs=26.9
Q ss_pred CCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCC
Q 014025 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (432)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 406 (432)
|||=...+.-|+....|.|+=|++= +.+..+. ..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C--~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKEC--IEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHH--HHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHH--HHHHHHC--cCCCcCC
Confidence 6777788888989999999977753 3333333 3799998
No 31
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.56 E-value=12 Score=39.01 Aligned_cols=64 Identities=23% Similarity=0.246 Sum_probs=46.3
Q ss_pred hhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccccccccccCCCCCcHHHHHHHHHHHHHhccc
Q 014025 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLVDDTHRKLQV 78 (432)
Q Consensus 12 ~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~y~~~~~ 78 (432)
..|..++||..|..|||+.+|-|++|+.|--+++.---++ ....++.++.++.+- .+.|++-++
T Consensus 267 ~~l~~~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l~Nan--~Ds~~p~s~~~L~~~-l~~wE~t~~ 330 (397)
T TIGR00599 267 SLLTDSQIRKKLSELGLSTNGTRQLLQKRHNEWETLWNSN--CDSLEPVDKRELLRQ-LDSWERTQG 330 (397)
T ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhc--cccCCCCCHHHHHHH-HHHHHHHhc
Confidence 4688999999999999999999999999999987654322 344556666666551 124444444
No 32
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=71.83 E-value=1.8 Score=48.00 Aligned_cols=52 Identities=23% Similarity=0.520 Sum_probs=40.0
Q ss_pred Ccccc-CCCCCCCCCCeeeecCCCCCCc-ccccceecCCCCCCCCCCCCCcccccceeecc
Q 014025 112 TKVCC-PCGSSLETESMIKCEDPRCPVW-QHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (432)
Q Consensus 112 ~~~rC-~Cg~~~~~~~~i~C~~~~C~~~-qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~~ 170 (432)
..++| +|+.....+-||-|+. |+.- .|+.|+..+-. +. -...|||.-|-+..
T Consensus 214 E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~--ei---P~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLS--ES---PVNEWYCTNCSLLE 267 (1134)
T ss_pred ccccceeeccCChHHhheeecc--cccceeeccccCcccc--cc---cccceecCcchhhh
Confidence 55788 5999988899999999 9888 99999876421 11 13479999998754
No 33
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=71.51 E-value=2.8 Score=29.64 Aligned_cols=39 Identities=23% Similarity=0.539 Sum_probs=21.9
Q ss_pred CCCccccccc----cccccCcCccccccHHHHHHHhcCCCceecC
Q 014025 364 CPMSGSRIKV----AGRFKPCVHMGCFDLDVFVELNQRSRKWQCP 404 (432)
Q Consensus 364 CPls~~ri~~----P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CP 404 (432)
||+++. +.. |.. ..|.|.=|.|...=|..+....+.+||
T Consensus 1 CpIc~e-~~~~~n~P~~-L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMV-LPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEE-EeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788877 666 666 459999999988877776667789998
No 34
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=70.72 E-value=3 Score=31.13 Aligned_cols=37 Identities=16% Similarity=0.452 Sum_probs=25.1
Q ss_pred cccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCe
Q 014025 368 GSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENI 415 (432)
Q Consensus 368 ~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L 415 (432)
......|+-..-|.+ |||++-| =-||+|++++.+.+.
T Consensus 18 ~~~~~~pCgH~I~~~--~f~~~rY---------ngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 18 TKGTVLPCGHLICDN--CFPGERY---------NGCPFCGTPFEFDDP 54 (55)
T ss_pred cccccccccceeecc--ccChhhc---------cCCCCCCCcccCCCC
Confidence 344455544444443 8999987 469999999887663
No 35
>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=69.26 E-value=3.2 Score=29.83 Aligned_cols=44 Identities=30% Similarity=0.606 Sum_probs=25.3
Q ss_pred cCCCccccccccccccCcCcc-ccccHHHHHHHhcCCCceecCCCCCCCC
Q 014025 363 RCPMSGSRIKVAGRFKPCVHM-GCFDLDVFVELNQRSRKWQCPICLRNYS 411 (432)
Q Consensus 363 ~CPls~~ri~~P~Rg~~C~Hl-QCFDl~~fL~~n~~~~~W~CPiC~k~~~ 411 (432)
.|++=+.....+ -...|.|+ -|++-.. .+.. ...+||+|.+++.
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C~~--~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEECAE--RLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHHHH--HHHH--TTSBBTTTTBB-S
T ss_pred CCccCCccCCce-EEeCCCChHHHHHHhH--Hhcc--cCCCCCcCChhhc
Confidence 455555554432 33469997 5555332 2222 6789999998763
No 36
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=67.18 E-value=10 Score=40.40 Aligned_cols=53 Identities=21% Similarity=0.537 Sum_probs=37.3
Q ss_pred CCCCcccc-CCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCC--Ccccccce
Q 014025 109 QSDTKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVP--ELFYCEIC 166 (432)
Q Consensus 109 q~~~~~rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p--~~f~C~~C 166 (432)
..-....| +|..+-.....++|+. |+..+|.+|+..|-.. .|.-. ..|.|..|
T Consensus 540 ~~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPLTR---~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 540 PKAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPLTR---LPKKNKNFGWQCSEC 595 (707)
T ss_pred ccccceeeeeeccchhhHHHhhcch--hhceeeccccCCcccc---CcccccCcceeeccc
Confidence 34456778 5988888888999999 9999999999865221 11112 24567777
No 37
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=67.15 E-value=3.5 Score=28.80 Aligned_cols=42 Identities=24% Similarity=0.411 Sum_probs=24.4
Q ss_pred CCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCC
Q 014025 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (432)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 406 (432)
|||=..-++-|+. ..|.|.=|++--.=+........+.||+|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 5777777777776 68999988775443333333334999998
No 38
>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=66.45 E-value=3.1 Score=30.59 Aligned_cols=37 Identities=19% Similarity=0.458 Sum_probs=18.1
Q ss_pred HHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHHh
Q 014025 389 DVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKV 428 (432)
Q Consensus 389 ~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~ 428 (432)
.-++..-..... .||+|++++..+.- +.++.++-+.+
T Consensus 10 ~k~i~~l~~~~~-~CPlC~r~l~~e~~--~~li~~~~~~i 46 (54)
T PF04423_consen 10 KKYIEELKEAKG-CCPLCGRPLDEEHR--QELIKKYKSEI 46 (54)
T ss_dssp HHHHHHHTT-SE-E-TTT--EE-HHHH--HHHHHHHHHHH
T ss_pred HHHHHHHhcCCC-cCCCCCCCCCHHHH--HHHHHHHHHHH
Confidence 445555555555 99999998875543 44444444333
No 39
>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=65.75 E-value=3 Score=27.63 Aligned_cols=11 Identities=36% Similarity=1.189 Sum_probs=9.5
Q ss_pred CceecCCCCCC
Q 014025 399 RKWQCPICLRN 409 (432)
Q Consensus 399 ~~W~CPiC~k~ 409 (432)
+.|.||+|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 78999999864
No 40
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=64.49 E-value=2.4 Score=47.04 Aligned_cols=56 Identities=23% Similarity=0.416 Sum_probs=42.6
Q ss_pred eceeeeecCCCccccccccccccCcCccccccH-HHHHHHhcCCCceecCCCCCCCCCCCee
Q 014025 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPICLRNYSLENII 416 (432)
Q Consensus 356 ~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC~k~~~~~~L~ 416 (432)
....=-|+||.-.+|.+--+= ..|-|+=||+. ..++.+.+ =+||.|+..+.+.|+.
T Consensus 638 k~yK~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~etRq----RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 638 KEYKELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYETRQ----RKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHHhceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHHhc----CCCCCCCCCCCccccc
Confidence 346778999999999763222 47999999974 45666655 4899999999988853
No 41
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=63.18 E-value=5.5 Score=29.67 Aligned_cols=33 Identities=24% Similarity=0.692 Sum_probs=27.5
Q ss_pred CccccC-CCCCCC-CCCeeeecCCCCCCcccccceec
Q 014025 112 TKVCCP-CGSSLE-TESMIKCEDPRCPVWQHMSCVII 146 (432)
Q Consensus 112 ~~~rC~-Cg~~~~-~~~~i~C~~~~C~~~qH~~Cv~~ 146 (432)
...+|. ||..+. .+..|.|-. |+...|..|...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~--CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPE--CGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCC--CCCcccHHHHhh
Confidence 346785 898874 789999999 999999999754
No 42
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=63.17 E-value=1.3 Score=30.76 Aligned_cols=16 Identities=19% Similarity=0.810 Sum_probs=10.9
Q ss_pred HhcCCCceecCCCCCC
Q 014025 394 LNQRSRKWQCPICLRN 409 (432)
Q Consensus 394 ~n~~~~~W~CPiC~k~ 409 (432)
......+|.||+|+..
T Consensus 18 ~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 18 FDDGGKTWICNFCGTK 33 (40)
T ss_dssp EETTTTEEEETTT--E
T ss_pred EcCCCCEEECcCCCCc
Confidence 4456789999999863
No 43
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=61.69 E-value=3 Score=24.30 Aligned_cols=11 Identities=45% Similarity=1.361 Sum_probs=7.2
Q ss_pred eecCCCCCCCC
Q 014025 401 WQCPICLRNYS 411 (432)
Q Consensus 401 W~CPiC~k~~~ 411 (432)
|+||+|++.+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 89999998654
No 44
>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=61.56 E-value=6.5 Score=26.66 Aligned_cols=40 Identities=30% Similarity=0.623 Sum_probs=28.1
Q ss_pred CCCccccccccccccCcCccccccH-HHHHHHhcCCCceecCCC
Q 014025 364 CPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPIC 406 (432)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC 406 (432)
||+=...+..|.+...|.|.=|.+= ..+++. ...-+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~---~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN---SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH---TSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh---cCCccCCcC
Confidence 5666777777888899999966653 333333 556779998
No 45
>PF02837 Glyco_hydro_2_N: Glycosyl hydrolases family 2, sugar binding domain; InterPro: IPR006104 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This domain has a jelly-roll fold [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3FN9_C 2VZU_A 2X09_A 2VZO_A 2X05_A 2VZV_B ....
Probab=61.40 E-value=28 Score=30.91 Aligned_cols=66 Identities=21% Similarity=0.101 Sum_probs=43.7
Q ss_pred eeEEEEeChhhHHhhccCCeeEEEEEeecCCCCccccCCCceeeEEECCeeeeccCCCCCCCCCCCCCCCCCCcccCcCC
Q 014025 203 LEKTFPITRADKDLLSKQEYDVQAWCMLLNDKVPFRMQWPQYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKD 282 (432)
Q Consensus 203 ~~~~F~Lt~~~~~~l~~~~~~l~v~C~~~~~~~~~~~~wP~~~~i~vNg~~v~~~~r~~~~~~g~~~r~~~~~IT~~l~~ 282 (432)
.+.+|.++++. ...++.|....++ ...+|.|||+.|-.. ..+ -+....+||++|+.
T Consensus 72 Yr~~f~lp~~~------~~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~~~-------~~~~~~dIt~~l~~ 127 (167)
T PF02837_consen 72 YRRTFTLPADW------KGKRVFLRFEGVD----------YAAEVYVNGKLVGSH-EGG-------YTPFEFDITDYLKP 127 (167)
T ss_dssp EEEEEEESGGG------TTSEEEEEESEEE----------SEEEEEETTEEEEEE-EST-------TS-EEEECGGGSSS
T ss_pred EEEEEEeCchh------cCceEEEEeccce----------EeeEEEeCCeEEeee-CCC-------cCCeEEeChhhccC
Confidence 46789998864 2345555543332 347899999998652 111 12234669999999
Q ss_pred cc-cEEEEEEe
Q 014025 283 GI-NKIVLTGC 292 (432)
Q Consensus 283 g~-N~I~i~~~ 292 (432)
|. |.|.|...
T Consensus 128 g~~N~l~V~v~ 138 (167)
T PF02837_consen 128 GEENTLAVRVD 138 (167)
T ss_dssp EEEEEEEEEEE
T ss_pred CCCEEEEEEEe
Confidence 97 99999875
No 46
>PF08531 Bac_rhamnosid_N: Alpha-L-rhamnosidase N-terminal domain; InterPro: IPR013737 This domain is found in bacterial rhamnosidase A and B enzymes and is probably involved in substrate recognition. ; PDB: 2OKX_B.
Probab=61.25 E-value=5 Score=36.75 Aligned_cols=47 Identities=28% Similarity=0.220 Sum_probs=26.4
Q ss_pred eeeEEECCeeeecc-CCCCCCCCCCCCC--CCCCCcccCcCCcccEEEEEEe
Q 014025 244 YADLQVNGVPVRAI-NRPGSQLLGANGR--DDGPIITPWTKDGINKIVLTGC 292 (432)
Q Consensus 244 ~~~i~vNg~~v~~~-~r~~~~~~g~~~r--~~~~~IT~~l~~g~N~I~i~~~ 292 (432)
..+++|||+.|-.- ..|++. ...+| -...|||++|+.|.|.|-+...
T Consensus 15 ~Y~l~vNG~~V~~~~l~P~~t--~y~~~~~Y~tyDVt~~L~~G~N~iav~lg 64 (172)
T PF08531_consen 15 RYELYVNGERVGDGPLAPGWT--DYDKRVYYQTYDVTPYLRPGENVIAVWLG 64 (172)
T ss_dssp EEEEEETTEEEEEE----------BTTEEEEEEEE-TTT--TTEEEEEEEEE
T ss_pred eEEEEECCEEeeCCccccccc--cCCCceEEEEEeChHHhCCCCCEEEEEEe
Confidence 46899999999642 123321 11121 2355799999999999988753
No 47
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.87 E-value=4.4 Score=36.86 Aligned_cols=19 Identities=21% Similarity=0.599 Sum_probs=16.2
Q ss_pred CceecCCCCCCCCCCCeee
Q 014025 399 RKWQCPICLRNYSLENIII 417 (432)
Q Consensus 399 ~~W~CPiC~k~~~~~~L~I 417 (432)
.-.+||||+|.+..+|+.|
T Consensus 137 ~g~KCPvC~K~V~sDd~e~ 155 (205)
T KOG0801|consen 137 SGMKCPVCHKVVPSDDAEI 155 (205)
T ss_pred CCccCCccccccCCCcceE
Confidence 3579999999999999765
No 48
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.21 E-value=1.1 Score=45.43 Aligned_cols=74 Identities=31% Similarity=0.517 Sum_probs=56.7
Q ss_pred ceEeeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCC-CCCCeeecHHHHHHHHHh
Q 014025 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNY-SLENIIIDPYFNRITSKV 428 (432)
Q Consensus 352 ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~-~~~~L~ID~y~~~Il~~~ 428 (432)
+|--..+.+++.||+-...|+----.+.|-|-=|||+-+ .+-+..--.||-|.+.+ .--+|++|.-|..++.+|
T Consensus 34 ~~~l~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 34 MVDLAMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred eecHHHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 333356789999999998888777778999999998744 23344456899998654 445799999999988776
No 49
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.13 E-value=7.3 Score=37.12 Aligned_cols=63 Identities=17% Similarity=0.313 Sum_probs=45.1
Q ss_pred eeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHHhh
Q 014025 360 VNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKVL 429 (432)
Q Consensus 360 isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~~ 429 (432)
--|.|||....++-| +...|.|.-|.....=+.- ....||.|..... +|.=...+..+++..+
T Consensus 12 ~~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~----~~~~Cp~cr~~~~--~~~~n~~l~~~~~~~~ 74 (386)
T KOG2177|consen 12 EELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE----GPLSCPVCRPPSR--NLRPNVLLANLVERLR 74 (386)
T ss_pred ccccChhhHHHhhcC-ccccccchHhHHHHHHhcC----CCcCCcccCCchh--ccCccHHHHHHHHHHH
Confidence 346899999999999 8889999999876654433 5699999995222 5554455555555444
No 50
>PF02228 Gag_p19: Major core protein p19; InterPro: IPR003139 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from delta-retroviruses such as Human T-lymphotropic virus 1 and Human T-cell leukemia virus 2 (HTLV-2), both members of the human oncovirus subclass of retroviruses [, ].; GO: 0005198 structural molecule activity, 0019013 viral nucleocapsid; PDB: 1JVR_A.
Probab=59.94 E-value=5.1 Score=32.05 Aligned_cols=39 Identities=28% Similarity=0.478 Sum_probs=24.2
Q ss_pred cHHHHHHHhcCCCceecCCCCCCCCCCCeeecHH---HHHHHHH
Q 014025 387 DLDVFVELNQRSRKWQCPICLRNYSLENIIIDPY---FNRITSK 427 (432)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y---~~~Il~~ 427 (432)
||..||.+.-+++.|-|||=-.- +.+|+--+| +.||++.
T Consensus 45 qLr~flk~alkTpvwl~pi~ysl--la~lipkgypgrv~ei~~i 86 (92)
T PF02228_consen 45 QLRNFLKLALKTPVWLNPINYSL--LASLIPKGYPGRVNEIINI 86 (92)
T ss_dssp HHHHHHHHHHT-TTSTTTT-TTT--HHHHS-SS-STTHHHHHHH
T ss_pred HHHHHHHHHHcCCeeeccccHHH--HHHHccCCCCchHHHHHHH
Confidence 68999999999999999984321 223443333 5566554
No 51
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=57.81 E-value=7.1 Score=38.39 Aligned_cols=48 Identities=31% Similarity=0.779 Sum_probs=34.8
Q ss_pred Ccccc-CCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccce
Q 014025 112 TKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEIC 166 (432)
Q Consensus 112 ~~~rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~C 166 (432)
..-+| +||.+...+.++-|++ |..-.|+.|+..| |.. |+ ...|-|..|
T Consensus 280 eck~csicgtsenddqllfcdd--cdrgyhmyclspp---m~e-pp-egswsc~KO 328 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDD--CDRGYHMYCLSPP---MVE-PP-EGSWSCHLC 328 (336)
T ss_pred ecceeccccCcCCCceeEeecc--cCCceeeEecCCC---cCC-CC-CCchhHHHH
Confidence 34455 5999988899999999 9999999998865 222 11 235667665
No 52
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=56.83 E-value=5.2 Score=41.04 Aligned_cols=50 Identities=26% Similarity=0.618 Sum_probs=37.8
Q ss_pred ccCCCCCCCC-CCeeeecCCCCCCcccccc--eecCCCCCCCCCCCCCcccccceeecc
Q 014025 115 CCPCGSSLET-ESMIKCEDPRCPVWQHMSC--VIIPEKPTEGNPPVPELFYCEICRLSR 170 (432)
Q Consensus 115 rC~Cg~~~~~-~~~i~C~~~~C~~~qH~~C--v~~~~k~~~~~~~~p~~f~C~~Crl~~ 170 (432)
+|.|-..... +.|++|+. |..|.|..| ++++.+... .+..+||..|....
T Consensus 62 ~~~~~~~~~p~~~~~~cd~--C~~~~~~ec~~v~~~~~e~p----~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 62 YCKCYKPCDPDDLMEQCDL--CEDWYHGECWEVGTAEKEAP----KEDPKVCDECKEAQ 114 (345)
T ss_pred hhhcccccCchhhhhcccc--ccccccccccccCchhhcCC----ccccccccccchhh
Confidence 6666665443 48999999 999999999 999866422 35689999888743
No 53
>PLN03124 poly [ADP-ribose] polymerase; Provisional
Probab=56.70 E-value=8.2 Score=42.70 Aligned_cols=38 Identities=29% Similarity=0.541 Sum_probs=35.4
Q ss_pred hhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhccccc
Q 014025 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQ 49 (432)
Q Consensus 12 ~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~~ 49 (432)
..++|.||++-|..=||+..|.|++|+.|.-+.+....
T Consensus 3 ~~~~v~~l~~~l~~~~~~~~g~k~~l~~rl~~~~~~e~ 40 (643)
T PLN03124 3 NKLKVDELRAALAKRGLDTTGLKAALVRRLDDAIAEDA 40 (643)
T ss_pred ccchhHHHHHHHHhcCCcccccchHHHHHHHhhhhhhh
Confidence 57899999999999999999999999999999988765
No 54
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=54.29 E-value=6.5 Score=40.29 Aligned_cols=28 Identities=36% Similarity=0.821 Sum_probs=20.2
Q ss_pred CcCccccccHHHHHHHhcCCCceecCCCCCCCCCC
Q 014025 379 PCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLE 413 (432)
Q Consensus 379 ~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (432)
+|-|+.| |++|++.++ .||||..++-++
T Consensus 320 HilHl~C--LknW~ERqQ-----TCPICr~p~ifd 347 (491)
T COG5243 320 HILHLHC--LKNWLERQQ-----TCPICRRPVIFD 347 (491)
T ss_pred ceeeHHH--HHHHHHhcc-----CCCcccCccccc
Confidence 4556666 688888655 699999986544
No 55
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=52.79 E-value=6.4 Score=28.81 Aligned_cols=12 Identities=33% Similarity=1.176 Sum_probs=9.6
Q ss_pred CCceecCCCCCC
Q 014025 398 SRKWQCPICLRN 409 (432)
Q Consensus 398 ~~~W~CPiC~k~ 409 (432)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 458999999854
No 56
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=52.55 E-value=38 Score=34.55 Aligned_cols=56 Identities=27% Similarity=0.362 Sum_probs=41.2
Q ss_pred hhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccccccccccCCCCCcHHHHHHHH
Q 014025 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLV 69 (432)
Q Consensus 12 ~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~~~~~~~~~~~~~~~~~~~~~i 69 (432)
+.+-=.++|.=|..+||+.+|.||.|+.|-.++..-.-++ -....++++.++..-+
T Consensus 249 ~lls~s~ik~KLse~GLst~G~kQ~likRh~~~v~lyNsn--cD~l~Pvs~ael~rql 304 (442)
T KOG0287|consen 249 NLLSDSDIKKKLSEHGLSTQGNKQQLIKRHQEFVHLYNSN--CDALHPVSAAELVRQL 304 (442)
T ss_pred hhccHHHHHHHHHHcCCCCcchHHHHHHHHHHHHHHHhcc--ccccCCcCHHHHHHHH
Confidence 3455678999999999999999999999998887654322 3345666666654433
No 57
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=51.21 E-value=11 Score=43.87 Aligned_cols=55 Identities=27% Similarity=0.633 Sum_probs=40.5
Q ss_pred CCCccccCCCCCCC--CCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceeecccCc
Q 014025 110 SDTKVCCPCGSSLE--TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRADP 173 (432)
Q Consensus 110 ~~~~~rC~Cg~~~~--~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~~~dP 173 (432)
.++...|+|-.-.. .+..+.|++ |+...|..||+++.-| ...|.|-.|-+...-|
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~--Cnl~VHq~Cygi~~ip-------eg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG--CNLAVHQECYGIPFIP-------EGQWLCRRCLQSPQRP 273 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC--CcchhhhhccCCCCCC-------CCcEeehhhccCcCcc
Confidence 34556678976543 478999999 9999999999975322 2368888888866555
No 58
>PRK12678 transcription termination factor Rho; Provisional
Probab=50.84 E-value=16 Score=40.10 Aligned_cols=38 Identities=29% Similarity=0.515 Sum_probs=32.3
Q ss_pred HhhcCHHHHHHHHHHhCCC-CCC-ChHHHHHHHHHhcccc
Q 014025 11 LAHFRIKELKDVLTQLGLS-KQG-KKQDLVDRILAILSDD 48 (432)
Q Consensus 11 l~~fRv~ELk~vl~~lgl~-ksG-rK~eL~~Ril~~l~~~ 48 (432)
|..+++.|||.+..+||+. .++ ||.||+.-|-+--..+
T Consensus 23 LsamkL~ELr~lA~~lGI~Gts~mrK~eLI~AI~~~~gg~ 62 (672)
T PRK12678 23 LAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKEARGGG 62 (672)
T ss_pred cccCcHHHHHHHHHHcCCcccccccHHHHHHHHHHhhcCC
Confidence 6789999999999999999 555 8999999997765443
No 59
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.09 E-value=8.6 Score=37.69 Aligned_cols=55 Identities=22% Similarity=0.425 Sum_probs=41.1
Q ss_pred eecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeeec
Q 014025 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIID 418 (432)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID 418 (432)
+-+|+|-..-+..|++. .|.|+ |-+.--+.+-.....=.||.|.....+.+++|+
T Consensus 215 d~kC~lC~e~~~~ps~t-~CgHl--FC~~Cl~~~~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 215 DYKCFLCLEEPEVPSCT-PCGHL--FCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred ccceeeeecccCCcccc-cccch--hhHHHHHHHHHhhccccCchhhhhccchhhhee
Confidence 56899999999999885 79999 545555554333333349999999999888765
No 60
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=49.77 E-value=8.4 Score=27.83 Aligned_cols=14 Identities=29% Similarity=0.947 Sum_probs=8.1
Q ss_pred cCCCceecCCCCCC
Q 014025 396 QRSRKWQCPICLRN 409 (432)
Q Consensus 396 ~~~~~W~CPiC~k~ 409 (432)
.....|.||+|+..
T Consensus 30 ~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 30 DLPDDWVCPVCGAP 43 (47)
T ss_dssp GS-TT-B-TTTSSB
T ss_pred HCCCCCcCcCCCCc
Confidence 34568999999853
No 61
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=49.57 E-value=10 Score=41.25 Aligned_cols=51 Identities=29% Similarity=0.733 Sum_probs=37.4
Q ss_pred cccC-CCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceeec
Q 014025 114 VCCP-CGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (432)
Q Consensus 114 ~rC~-Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~ 169 (432)
..|. |+++-.-...|.|+. |...+|..|+-.|-. .+.+| +..|+|+.|..+
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~--Cp~sFH~~CLePPl~-~eniP--~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDG--CPRSFHQTCLEPPLE-PENIP--PGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccccccceeecC--CchHHHHhhcCCCCC-cccCC--CCccccCCCeee
Confidence 4785 888744356699999 999999999887622 23333 348999999874
No 62
>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=48.82 E-value=13 Score=23.75 Aligned_cols=25 Identities=36% Similarity=0.784 Sum_probs=15.5
Q ss_pred cCcCccccccH-HHHHHHhcCCCceecCCC
Q 014025 378 KPCVHMGCFDL-DVFVELNQRSRKWQCPIC 406 (432)
Q Consensus 378 ~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC 406 (432)
..|.|.-|++- +.|++ ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 45999866553 34444 344679987
No 63
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=47.51 E-value=11 Score=41.67 Aligned_cols=37 Identities=27% Similarity=0.710 Sum_probs=29.5
Q ss_pred cccCCCCCC--CCCCeeeecCCCCCCcccccceecCCCC
Q 014025 114 VCCPCGSSL--ETESMIKCEDPRCPVWQHMSCVIIPEKP 150 (432)
Q Consensus 114 ~rC~Cg~~~--~~~~~i~C~~~~C~~~qH~~Cv~~~~k~ 150 (432)
-.|+|-.-. ...-+|-|+...|.+.-|-.||+|-.-|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVP 45 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVP 45 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcceeEecC
Confidence 468886643 2467899999999999999999996543
No 64
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=45.91 E-value=6.6 Score=24.66 Aligned_cols=10 Identities=50% Similarity=1.441 Sum_probs=8.3
Q ss_pred ecCCCCCCCC
Q 014025 402 QCPICLRNYS 411 (432)
Q Consensus 402 ~CPiC~k~~~ 411 (432)
.||||++.+.
T Consensus 3 ~CPiC~~~v~ 12 (26)
T smart00734 3 QCPVCFREVP 12 (26)
T ss_pred cCCCCcCccc
Confidence 6999999873
No 65
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=45.45 E-value=17 Score=27.49 Aligned_cols=30 Identities=13% Similarity=0.278 Sum_probs=24.3
Q ss_pred CceecCCCCCCCCCCCeeecHHHHHHHHHh
Q 014025 399 RKWQCPICLRNYSLENIIIDPYFNRITSKV 428 (432)
Q Consensus 399 ~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~ 428 (432)
|.=.||+|++.+++++-.-.+--.|||+.=
T Consensus 7 PH~HC~VCg~aIp~de~~CSe~C~eil~ke 36 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQVCSEECGEILNKE 36 (64)
T ss_pred CCccccccCCcCCCccchHHHHHHHHHHHH
Confidence 456799999999999888777777887643
No 66
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=45.24 E-value=6.5 Score=23.11 Aligned_cols=11 Identities=45% Similarity=1.413 Sum_probs=8.9
Q ss_pred eecCCCCCCCC
Q 014025 401 WQCPICLRNYS 411 (432)
Q Consensus 401 W~CPiC~k~~~ 411 (432)
|+||+|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 78999998654
No 67
>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=44.84 E-value=16 Score=36.86 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=14.3
Q ss_pred CCceecCCCCCCCCCCCe
Q 014025 398 SRKWQCPICLRNYSLENI 415 (432)
Q Consensus 398 ~~~W~CPiC~k~~~~~~L 415 (432)
.+.-.||+|++.++..++
T Consensus 41 ~~~~~CP~C~~~lrk~~f 58 (309)
T TIGR00570 41 RGSGSCPECDTPLRKNNF 58 (309)
T ss_pred CCCCCCCCCCCccchhhc
Confidence 344599999999988883
No 68
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=43.86 E-value=14 Score=39.88 Aligned_cols=40 Identities=25% Similarity=0.474 Sum_probs=37.1
Q ss_pred HHHhhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccc
Q 014025 9 EKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDD 48 (432)
Q Consensus 9 ~~l~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~ 48 (432)
.+|..|||-+|+.-|.--+|...|.|+-|++|+..-|...
T Consensus 28 rrlseLRViDLraEL~KRnldt~GnKsVLmERLkKal~~E 67 (940)
T KOG4661|consen 28 RRLSELRVIDLRAELEKRNLDTVGNKSVLMERLKKALRAE 67 (940)
T ss_pred chhhheeeeehhhHHhhhcccccCcHHHHHHHHHHHHHhc
Confidence 4688999999999999999999999999999999888775
No 69
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=43.56 E-value=15 Score=28.54 Aligned_cols=31 Identities=26% Similarity=0.544 Sum_probs=16.8
Q ss_pred CccccccHHHHHHHhcCC-----CceecCCCCCCCCC
Q 014025 381 VHMGCFDLDVFVELNQRS-----RKWQCPICLRNYSL 412 (432)
Q Consensus 381 ~HlQCFDl~~fL~~n~~~-----~~W~CPiC~k~~~~ 412 (432)
-|+.|. .+||+...... -.++||.|++++..
T Consensus 32 fH~~CL-~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 32 FHLLCL-SEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp B-SGGG-HHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred HHHHHH-HHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 477775 45555543321 25899999998754
No 70
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=41.66 E-value=1.2e+02 Score=24.75 Aligned_cols=45 Identities=24% Similarity=0.322 Sum_probs=34.7
Q ss_pred CccHHH-HHHHHhhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccc
Q 014025 1 MDSVAS-CKEKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDD 48 (432)
Q Consensus 1 ~~~~~~-~~~~l~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~ 48 (432)
|-++.. +..+|+++-..||-..+++.|.+.+.+-++.+ +.++...
T Consensus 1 M~i~qqiVn~Kln~iT~~eLlkyskqy~i~it~~QA~~I---~~~lr~k 46 (85)
T PF11116_consen 1 MKIIQQIVNQKLNNITAKELLKYSKQYNISITKKQAEQI---ANILRGK 46 (85)
T ss_pred ChHHHHHHHHHHhcCCHHHHHHHHHHhCCCCCHHHHHHH---HHHHhcC
Confidence 434444 66789999999999999999999998877664 4555554
No 71
>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=41.50 E-value=16 Score=25.31 Aligned_cols=25 Identities=28% Similarity=0.664 Sum_probs=14.1
Q ss_pred cCcCcccccc-HHHHHHHhcCCCceecCCCC
Q 014025 378 KPCVHMGCFD-LDVFVELNQRSRKWQCPICL 407 (432)
Q Consensus 378 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~ 407 (432)
..|.|.=|.+ +..||+.+ ..||+|.
T Consensus 19 l~C~H~fh~~Ci~~~~~~~-----~~CP~CR 44 (44)
T PF13639_consen 19 LPCGHVFHRSCIKEWLKRN-----NSCPVCR 44 (44)
T ss_dssp ETTSEEEEHHHHHHHHHHS-----SB-TTTH
T ss_pred ccCCCeeCHHHHHHHHHhC-----CcCCccC
Confidence 4477764443 44566543 2999993
No 72
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=41.06 E-value=18 Score=30.24 Aligned_cols=33 Identities=36% Similarity=0.746 Sum_probs=27.4
Q ss_pred cccc-CCCCCCCCCCeeeecCCCCCCcccccceecC
Q 014025 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIP 147 (432)
Q Consensus 113 ~~rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~ 147 (432)
..+| +|+.+ .+..|+|..++|..+.|..|....
T Consensus 55 ~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 55 KLKCSICGKS--GGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHC
Confidence 3456 69988 677999999999999999997654
No 73
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=39.32 E-value=12 Score=37.70 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=26.3
Q ss_pred ccccCcCccccccHHHHHHHhcCCCceecCCCCCC
Q 014025 375 GRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (432)
Q Consensus 375 ~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (432)
-|-+.|.-..|||--+=-+.-+-...|.||.|.+.
T Consensus 259 ~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 259 YEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK 293 (415)
T ss_pred chheeecHHHHHHHhhhHHhhcCcccccCchhccc
Confidence 46688887779986655555566789999999854
No 74
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=38.06 E-value=13 Score=34.12 Aligned_cols=26 Identities=31% Similarity=0.647 Sum_probs=18.4
Q ss_pred cCcCccccccHHHHHHHhc-CCCceecCCCCC
Q 014025 378 KPCVHMGCFDLDVFVELNQ-RSRKWQCPICLR 408 (432)
Q Consensus 378 ~~C~HlQCFDl~~fL~~n~-~~~~W~CPiC~k 408 (432)
..|+||.|.=.-. +. ....|.|| |+-
T Consensus 106 ~iCtHlGC~~~~~----~~~~~~~~~CP-CHG 132 (177)
T COG0723 106 AICTHLGCTVPWN----NAGAEGGFFCP-CHG 132 (177)
T ss_pred eeccCCCCccCcc----cCCCCCeEEcc-CCC
Confidence 4699999975443 33 34799999 763
No 75
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=36.40 E-value=25 Score=24.45 Aligned_cols=41 Identities=22% Similarity=0.519 Sum_probs=24.8
Q ss_pred CCCccccc--cccccccCcCccccccHHHHHHHhcCCCceecCCCCC
Q 014025 364 CPMSGSRI--KVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408 (432)
Q Consensus 364 CPls~~ri--~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k 408 (432)
||+=+.+. ..+.+-..|.|.=|-.-..=+. ...-.||+|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 34334444 3456778899986543332222 56789999985
No 76
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=36.30 E-value=30 Score=21.37 Aligned_cols=15 Identities=20% Similarity=0.913 Sum_probs=11.1
Q ss_pred cCCCceecCCCCCCC
Q 014025 396 QRSRKWQCPICLRNY 410 (432)
Q Consensus 396 ~~~~~W~CPiC~k~~ 410 (432)
.....+.||+|++..
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 344569999999753
No 77
>PF14000 Packaging_FI: DNA packaging protein FI
Probab=36.21 E-value=54 Score=28.73 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCC--CCCChHHHHHHHHHhcc
Q 014025 16 IKELKDVLTQLGLS--KQGKKQDLVDRILAILS 46 (432)
Q Consensus 16 v~ELk~vl~~lgl~--ksGrK~eL~~Ril~~l~ 46 (432)
++=|++|-..||+- .||-++||-.|+.++=+
T Consensus 6 l~RL~eLa~~LGRE~d~SGSaAeiaqRVAEwEE 38 (125)
T PF14000_consen 6 LARLRELAAQLGREPDMSGSAAEIAQRVAEWEE 38 (125)
T ss_pred HHHHHHHHHHhCcCCCccccHHHHHHHHHHHHH
Confidence 45577778888885 89999999999987633
No 78
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=35.89 E-value=5.6 Score=40.78 Aligned_cols=57 Identities=32% Similarity=0.589 Sum_probs=38.0
Q ss_pred CCCccccC-CCCCCCC-CCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceee
Q 014025 110 SDTKVCCP-CGSSLET-ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (432)
Q Consensus 110 ~~~~~rC~-Cg~~~~~-~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl 168 (432)
......|. ||.+..+ ..+|.|+. |..|+|..|+++.+.+..........|+|+.|.+
T Consensus 236 ~~~~~~~~~cg~~~~~~~~~~~~~~--~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 236 DYSKLICDPCGLSDANKKFEICCDL--CESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccCcchHHHHHHHHHHH--HHHHhcccccccccchhhhhhhhccceecCceee
Confidence 33445664 7776543 78888999 9999999999986443221111113499999988
No 79
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.65 E-value=43 Score=32.20 Aligned_cols=58 Identities=17% Similarity=0.339 Sum_probs=40.0
Q ss_pred ccccccccCcCccccccHHHHHHHhcCC---------CceecCCCCCCCCCCCeeecHHHHHHHHHh
Q 014025 371 IKVAGRFKPCVHMGCFDLDVFVELNQRS---------RKWQCPICLRNYSLENIIIDPYFNRITSKV 428 (432)
Q Consensus 371 i~~P~Rg~~C~HlQCFDl~~fL~~n~~~---------~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~ 428 (432)
-++|--+..|.-+-|+||-.|==+|++. .-++||-|+..+-|--=.+......+.+.+
T Consensus 56 C~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L 122 (299)
T KOG3970|consen 56 CNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQL 122 (299)
T ss_pred eCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHH
Confidence 3566677889999999999988777752 479999999776554433444444443333
No 80
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=33.44 E-value=34 Score=36.15 Aligned_cols=52 Identities=31% Similarity=0.741 Sum_probs=34.3
Q ss_pred ccCCCCC---CCCCCeeeecCCCCCCcccccceecCC-----CCCCCC-CCCCCcccccceee
Q 014025 115 CCPCGSS---LETESMIKCEDPRCPVWQHMSCVIIPE-----KPTEGN-PPVPELFYCEICRL 168 (432)
Q Consensus 115 rC~Cg~~---~~~~~~i~C~~~~C~~~qH~~Cv~~~~-----k~~~~~-~~~p~~f~C~~Crl 168 (432)
.|+|..- ..+..+|.|+. |+.|-|..|-.-.. ....|. ....-.|+|-.|--
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd~--CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~ 191 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCDV--CGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGK 191 (446)
T ss_pred ccccCCcccCCCCeeEEeccC--CCceehhhhhcccccccCCccCCCCCccCceEEEccCCCC
Confidence 3356553 24789999999 99999999975432 112221 12344899999965
No 81
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=33.21 E-value=22 Score=22.68 Aligned_cols=10 Identities=40% Similarity=1.428 Sum_probs=8.3
Q ss_pred CCceecCCCC
Q 014025 398 SRKWQCPICL 407 (432)
Q Consensus 398 ~~~W~CPiC~ 407 (432)
...|.|+.|.
T Consensus 2 ~g~W~C~~C~ 11 (30)
T PF00641_consen 2 EGDWKCPSCT 11 (30)
T ss_dssp SSSEEETTTT
T ss_pred CcCccCCCCc
Confidence 3579999997
No 82
>PHA02929 N1R/p28-like protein; Provisional
Probab=33.18 E-value=28 Score=33.85 Aligned_cols=45 Identities=18% Similarity=0.540 Sum_probs=28.3
Q ss_pred ecCCCcccccccc-c------cccCcCcccccc-HHHHHHHhcCCCceecCCCCCCCC
Q 014025 362 LRCPMSGSRIKVA-G------RFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNYS 411 (432)
Q Consensus 362 L~CPls~~ri~~P-~------Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~~ 411 (432)
..||+-...+.-+ + .-..|.|.=|.+ +..|+..+ =.||+|...+.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~-----~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK-----NTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC-----CCCCCCCCEee
Confidence 5789888876533 2 224799875555 23465432 27999998654
No 83
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=31.82 E-value=51 Score=35.26 Aligned_cols=33 Identities=27% Similarity=0.669 Sum_probs=25.5
Q ss_pred ccC-CCCCC--CCCCeeeecCCCCCCcccccceecCCC
Q 014025 115 CCP-CGSSL--ETESMIKCEDPRCPVWQHMSCVIIPEK 149 (432)
Q Consensus 115 rC~-Cg~~~--~~~~~i~C~~~~C~~~qH~~Cv~~~~k 149 (432)
+|. |.+.. ..+.+|-|++ |+..-|-+|+|++.-
T Consensus 195 ~C~~c~~t~~eN~naiVfCdg--C~i~VHq~CYGI~f~ 230 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDG--CEICVHQSCYGIQFL 230 (669)
T ss_pred hhHhccccccCCcceEEEecC--cchhhhhhcccceec
Confidence 553 65543 3577899999 999999999999743
No 84
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=31.34 E-value=13 Score=27.25 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=6.0
Q ss_pred ceecCCCCCC
Q 014025 400 KWQCPICLRN 409 (432)
Q Consensus 400 ~W~CPiC~k~ 409 (432)
++.||.|++.
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 3566666663
No 85
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.89 E-value=11 Score=23.24 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=11.4
Q ss_pred eecCCCCCCCCCCCe
Q 014025 401 WQCPICLRNYSLENI 415 (432)
Q Consensus 401 W~CPiC~k~~~~~~L 415 (432)
-.||+|++...++.|
T Consensus 3 ~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 3 VPCPICGRKFNPDRL 17 (25)
T ss_pred CcCCCCCCEECHHHH
Confidence 479999998766544
No 86
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=30.79 E-value=20 Score=36.53 Aligned_cols=65 Identities=20% Similarity=0.358 Sum_probs=52.3
Q ss_pred eeeecCCCccccccccccccCcCcccc-ccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHHhh
Q 014025 359 GVNLRCPMSGSRIKVAGRFKPCVHMGC-FDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKVL 429 (432)
Q Consensus 359 ~isL~CPls~~ri~~P~Rg~~C~HlQC-FDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~~~ 429 (432)
--.|+|-|-+.=+++|.=.- |.|.-| |-...||.. +=+||.|--..+-.+|+=...+.||++.+.
T Consensus 21 D~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~-----~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSY-----KPQCPTCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhcc-----CCCCCceecccchhhhhhhhHHHHHHHHHH
Confidence 34689999988888887765 999876 667777753 348999999999999999999999988654
No 87
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.69 E-value=73 Score=31.25 Aligned_cols=112 Identities=16% Similarity=0.299 Sum_probs=60.7
Q ss_pred EEEEEEEEecCHHHHHhhcccCCCCCCHH-HHHHHHHHHhCCCCCCCCCCCCCCc-ceEeeceeeeecCCCccccccccc
Q 014025 298 CLGVRIVKRRSVQQVLNLIPKESEGEHFE-DALTRVCRCVGGGNAADNADSDSDL-EVVADSIGVNLRCPMSGSRIKVAG 375 (432)
Q Consensus 298 ~~~v~lVk~~s~~~ll~~I~~~~~~~~~e-~~~~~ik~~l~~~~~~~~~d~D~D~-ev~~~~~~isL~CPls~~ri~~P~ 375 (432)
+++..+=+-++-+.|++.|.... ..+.. .-+.-++..+.= .-..|.+...|. +=-.+....-.+||++...|.=--
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks-~~pksaShIKslKDvveL-klt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~ 125 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKS-SLPKSASHIKSLKDVVEL-KLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKY 125 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcc-cCCcchhhhcchhhHhhe-ecccCcccccccCccccccccceeecccccceecceE
Confidence 45566667779999999988753 22221 112222221110 011121121110 011234688899999999887433
Q ss_pred cc---cCcCccccccHHHHHHHhcCCCceecCCCCCCCCCCCeee
Q 014025 376 RF---KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (432)
Q Consensus 376 Rg---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (432)
|+ ..|-|. |...+.=+. .-=.|++|+..+.-+|.+|
T Consensus 126 ~F~~l~~CGcV--~SerAlKei----kas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 126 RFCALRCCGCV--FSERALKEI----KASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred EEEEEecccee--ccHHHHHHh----hhccccccCCcccccCeEe
Confidence 33 235554 554443332 2458999999999988765
No 88
>PRK01343 zinc-binding protein; Provisional
Probab=29.64 E-value=28 Score=26.27 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=12.3
Q ss_pred cCCCceecCCCCCCCC
Q 014025 396 QRSRKWQCPICLRNYS 411 (432)
Q Consensus 396 ~~~~~W~CPiC~k~~~ 411 (432)
...+.-+||+|+++..
T Consensus 5 ~~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 5 PLRPTRPCPECGKPST 20 (57)
T ss_pred cCCCCCcCCCCCCcCc
Confidence 3457789999999864
No 89
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=29.12 E-value=17 Score=21.75 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=8.7
Q ss_pred eecCCCCCCCC
Q 014025 401 WQCPICLRNYS 411 (432)
Q Consensus 401 W~CPiC~k~~~ 411 (432)
|.|.+|++.+.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 89999987543
No 90
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=28.92 E-value=13 Score=44.89 Aligned_cols=53 Identities=23% Similarity=0.532 Sum_probs=39.0
Q ss_pred Ccccc-CCCCCCCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceeeccc
Q 014025 112 TKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRA 171 (432)
Q Consensus 112 ~~~rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~~~ 171 (432)
...+| +|........|+-|.. |..|.|..|+...- ... .+..|+|+.|+..+-
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~--c~~~~h~~C~rp~~---~~~--~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDE--CLSGFHLFCLRPAL---SSV--PPGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHh--hhhhHHHHhhhhhh---ccC--CcCCccCCccchhhh
Confidence 34566 3666666678999999 99999999987532 121 245799999999763
No 91
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=28.27 E-value=1.5e+02 Score=22.69 Aligned_cols=36 Identities=31% Similarity=0.518 Sum_probs=28.5
Q ss_pred HHHhhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHh
Q 014025 9 EKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAI 44 (432)
Q Consensus 9 ~~l~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~ 44 (432)
+.|+.+=+..||.-|.++||.-.|.=+|=.+|+..+
T Consensus 10 ~eLe~lGldrLK~~L~a~GLKcGGTl~ERA~RLfs~ 45 (60)
T PF13297_consen 10 EELEALGLDRLKSALMALGLKCGGTLQERAARLFSV 45 (60)
T ss_pred HHHHHhCHHHHHHHHHHcCCccCCCHHHHHHHHHHh
Confidence 446789999999999999999999866655555443
No 92
>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=28.11 E-value=51 Score=25.02 Aligned_cols=17 Identities=18% Similarity=0.626 Sum_probs=14.1
Q ss_pred ecCCCCCCCCCCCeeec
Q 014025 402 QCPICLRNYSLENIIID 418 (432)
Q Consensus 402 ~CPiC~k~~~~~~L~ID 418 (432)
.||+|+++++++...=|
T Consensus 5 HC~~CG~~Ip~~~~fCS 21 (59)
T PF09889_consen 5 HCPVCGKPIPPDESFCS 21 (59)
T ss_pred cCCcCCCcCCcchhhhC
Confidence 69999999998766554
No 93
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=27.74 E-value=46 Score=27.20 Aligned_cols=31 Identities=29% Similarity=0.761 Sum_probs=19.5
Q ss_pred CcCccccccHH---HHHHHhcCCCceecCCCCCCCCCC
Q 014025 379 PCVHMGCFDLD---VFVELNQRSRKWQCPICLRNYSLE 413 (432)
Q Consensus 379 ~C~HlQCFDl~---~fL~~n~~~~~W~CPiC~k~~~~~ 413 (432)
.|.| +|-+- .||+.+ ..+=+||.|.+...+.
T Consensus 51 ~C~H--~FH~hCI~kWl~~~--~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 51 KCSH--NFHMHCILKWLSTQ--SSKGQCPMCRQPWKFK 84 (85)
T ss_pred cCcc--HHHHHHHHHHHccc--cCCCCCCCcCCeeeeC
Confidence 3777 46654 455443 3345999999876654
No 94
>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=27.50 E-value=29 Score=23.10 Aligned_cols=10 Identities=40% Similarity=1.188 Sum_probs=7.1
Q ss_pred ceecCCCCCC
Q 014025 400 KWQCPICLRN 409 (432)
Q Consensus 400 ~W~CPiC~k~ 409 (432)
.|+|++|+-.
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 4888888743
No 95
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=27.40 E-value=30 Score=38.61 Aligned_cols=49 Identities=33% Similarity=0.733 Sum_probs=37.4
Q ss_pred Ccccc-CCCCC--CCCCCeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccceeec
Q 014025 112 TKVCC-PCGSS--LETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (432)
Q Consensus 112 ~~~rC-~Cg~~--~~~~~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~Crl~ 169 (432)
..+-| +|... .+...||-|+. |+.=-|..|+++-+-| ...|.|-.|-+.
T Consensus 270 edviCDvCrspD~e~~neMVfCd~--Cn~cVHqaCyGIle~p-------~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDK--CNICVHQACYGILEVP-------EGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEecc--chhHHHHhhhceeecC-------CCCeeehhcccc
Confidence 34455 46554 56789999999 9999999999997554 136889999884
No 96
>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2. This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.
Probab=27.10 E-value=40 Score=34.10 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=6.8
Q ss_pred ccCcCcccc
Q 014025 377 FKPCVHMGC 385 (432)
Q Consensus 377 g~~C~HlQC 385 (432)
+.-|.|+.|
T Consensus 182 S~IC~H~GC 190 (321)
T TIGR03171 182 SAICQHLGC 190 (321)
T ss_pred ecccCcCCC
Confidence 456888888
No 97
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=26.91 E-value=37 Score=28.81 Aligned_cols=42 Identities=24% Similarity=0.514 Sum_probs=27.8
Q ss_pred eeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCC
Q 014025 355 ADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLE 413 (432)
Q Consensus 355 ~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (432)
+.-..|+-.||-+. .+.+| |-.+ .+-..+|.||.|+.++..+
T Consensus 22 apR~~v~Y~C~~Gh-~~~v~-----------Fa~e-----AevP~~WeC~~cG~~A~~~ 63 (105)
T PF13397_consen 22 APRQRVSYWCPNGH-ETEVP-----------FAAE-----AEVPATWECPRCGLPAGRD 63 (105)
T ss_pred cCceEEEEECCCCC-EEecc-----------cccc-----CCCCCceeCCCCCCccccc
Confidence 45679999999753 33333 3222 2445799999999987654
No 98
>PHA02926 zinc finger-like protein; Provisional
Probab=26.38 E-value=38 Score=32.62 Aligned_cols=61 Identities=18% Similarity=0.522 Sum_probs=39.6
Q ss_pred eecCCCcccccccc--------ccccCcCccccccH-HHHHHHh-cCCCceecCCCCCCCCCCCeeecHHHHH
Q 014025 361 NLRCPMSGSRIKVA--------GRFKPCVHMGCFDL-DVFVELN-QRSRKWQCPICLRNYSLENIIIDPYFNR 423 (432)
Q Consensus 361 sL~CPls~~ri~~P--------~Rg~~C~HlQCFDl-~~fL~~n-~~~~~W~CPiC~k~~~~~~L~ID~y~~~ 423 (432)
...|++-...+--+ +--..|.|.=|++- ..|-... +......||+|..... .+.-..||..
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~--~I~pSrf~~~ 240 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR--NITMSKFYKL 240 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee--eeccccceec
Confidence 57899998776322 22358999988874 4455432 2334678999998654 4666666544
No 99
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=25.65 E-value=36 Score=37.82 Aligned_cols=43 Identities=16% Similarity=0.028 Sum_probs=37.7
Q ss_pred HHHHHHhhcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccc
Q 014025 6 SCKEKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDD 48 (432)
Q Consensus 6 ~~~~~l~~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~ 48 (432)
.+..+-...++.++|.+.+++++..+|.|+.|+++|.++++..
T Consensus 14 ~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~ 56 (636)
T KOG2169|consen 14 GAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQ 56 (636)
T ss_pred hhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhh
Confidence 3455556778899999999999999999999999999999963
No 100
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=25.20 E-value=85 Score=33.53 Aligned_cols=44 Identities=25% Similarity=0.331 Sum_probs=38.9
Q ss_pred HHHHHHhhcCHHHHHHHHHHhCCCCCCChH---HHHHHHHHhccccc
Q 014025 6 SCKEKLAHFRIKELKDVLTQLGLSKQGKKQ---DLVDRILAILSDDQ 49 (432)
Q Consensus 6 ~~~~~l~~fRv~ELk~vl~~lgl~ksGrK~---eL~~Ril~~l~~~~ 49 (432)
..+++|..++=.-|..+|--|-|+.+|-+. ||+-|+|.||....
T Consensus 260 K~kEkl~K~~kekL~~fCdvLdi~~~kst~kkeelv~rvleFL~~P~ 306 (594)
T KOG2266|consen 260 KKKEKLKKCDKEKLISFCDVLDIPRSKSTVKKEELVVRVLEFLEKPK 306 (594)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccccccccchHHHHHHHHHHHHhCCc
Confidence 467889999999999999999999888666 99999999998754
No 101
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=24.13 E-value=1.5e+02 Score=22.63 Aligned_cols=58 Identities=29% Similarity=0.449 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHhCCCCCCCCCCCCCCcceEeeceeeeecCCCccccccccccccCcCccccccHHHHHHHhcCCCcee
Q 014025 323 EHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQ 402 (432)
Q Consensus 323 ~~~e~~~~~ik~~l~~~~~~~~~d~D~D~ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~ 402 (432)
.+++++..+....++. -+-+|-......+.++||+-+.-..-| | .+|+. .+|=
T Consensus 3 ~t~~~~~~r~~e~Fp~---------~slvef~g~~~PvtI~CP~HG~~~~s~-----------~--~~~~~-----sk~G 55 (60)
T PF05265_consen 3 MTFESAASRFEEKFPH---------YSLVEFSGVATPVTIRCPKHGNFTCST-----------F--NSFIK-----SKHG 55 (60)
T ss_pred eeHHHHHHHHHHHCCC---------ceEEEEeCCCCceEEECCCCCcEEecc-----------H--Hhhhh-----hccC
Confidence 4678888888776642 011222334468999999877654433 2 23332 4578
Q ss_pred cCCCC
Q 014025 403 CPICL 407 (432)
Q Consensus 403 CPiC~ 407 (432)
||-|+
T Consensus 56 CP~Cg 60 (60)
T PF05265_consen 56 CPECG 60 (60)
T ss_pred CCCCC
Confidence 99995
No 102
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.07 E-value=47 Score=25.51 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=10.9
Q ss_pred CceecCCCCCCCCC
Q 014025 399 RKWQCPICLRNYSL 412 (432)
Q Consensus 399 ~~W~CPiC~k~~~~ 412 (432)
.+-+||+|+|.+.+
T Consensus 5 ~~v~CP~C~k~~~w 18 (62)
T PRK00418 5 ITVNCPTCGKPVEW 18 (62)
T ss_pred ccccCCCCCCcccc
Confidence 45789999998753
No 103
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=23.99 E-value=40 Score=24.39 Aligned_cols=33 Identities=18% Similarity=0.740 Sum_probs=15.7
Q ss_pred CeeeecCCCCCCcccccceecCCCCCCCCCCCCCcccccc
Q 014025 126 SMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165 (432)
Q Consensus 126 ~~i~C~~~~C~~~qH~~Cv~~~~k~~~~~~~~p~~f~C~~ 165 (432)
..|||+. |.+|-.+. ..+... ...+|..|+|.+
T Consensus 2 ~WVQCd~--C~KWR~lp-~~~~~~----~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDS--CLKWRRLP-EEVDPI----REELPDPWYCSM 34 (50)
T ss_dssp EEEE-TT--T--EEEE--CCHHCT----SCCSSTT--GGG
T ss_pred eEEECCC--CCceeeCC-hhhCcc----cccCCCeEEcCC
Confidence 4799998 99998875 222110 023566888765
No 104
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=23.89 E-value=33 Score=34.22 Aligned_cols=63 Identities=19% Similarity=0.348 Sum_probs=47.3
Q ss_pred eeeecCCCccccccccccccCcCcccc-ccHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHHHH
Q 014025 359 GVNLRCPMSGSRIKVAGRFKPCVHMGC-FDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSK 427 (432)
Q Consensus 359 ~isL~CPls~~ri~~P~Rg~~C~HlQC-FDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il~~ 427 (432)
--.|+|-|-..+|++|+-. .|.|.-| |-...+|. ..=.||+|..+-...-|+=..-..+|++.
T Consensus 23 Ds~lrC~IC~~~i~ip~~T-tCgHtFCslCIR~hL~-----~qp~CP~Cr~~~~esrlr~~s~~~ei~es 86 (391)
T COG5432 23 DSMLRCRICDCRISIPCET-TCGHTFCSLCIRRHLG-----TQPFCPVCREDPCESRLRGSSGSREINES 86 (391)
T ss_pred hhHHHhhhhhheeecceec-ccccchhHHHHHHHhc-----CCCCCccccccHHhhhcccchhHHHHHHh
Confidence 4468999999999999975 7999876 33444443 33479999998887778777777777654
No 105
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=23.33 E-value=42 Score=35.79 Aligned_cols=35 Identities=20% Similarity=0.594 Sum_probs=24.5
Q ss_pred cHHHHHHHhcCCCceecCCCCCCCCCCCeeecHHHHHHH
Q 014025 387 DLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRIT 425 (432)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~Il 425 (432)
|+.+|..-|....-|.||.|.+.. .+ -+.|..-+.
T Consensus 44 eal~fak~n~sWrFWiCp~CskkF--~d--~~~~~~H~~ 78 (466)
T PF04780_consen 44 EALSFAKENKSWRFWICPRCSKKF--SD--AESCLSHME 78 (466)
T ss_pred HHHHHHHhcCceeEeeCCccccee--CC--HHHHHHHHH
Confidence 567888888888999999999643 22 345554444
No 106
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=23.19 E-value=1.8e+02 Score=29.21 Aligned_cols=51 Identities=25% Similarity=0.352 Sum_probs=38.1
Q ss_pred hcCHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccccccccccCCCCCcHHHH
Q 014025 13 HFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSPVSKEEV 65 (432)
Q Consensus 13 ~fRv~ELk~vl~~lgl~ksGrK~eL~~Ril~~l~~~~~~~~~~~~~~~~~~~~ 65 (432)
++--+..+.-|..|||+..|-||-|+.|-..+...-- .+...++++.+.++
T Consensus 246 ~lseSkIr~KLS~mGL~T~G~kQ~l~rR~~~~~~L~N--SN~D~~qPV~~~~L 296 (391)
T COG5432 246 LLSESKIRSKLSEMGLPTDGHKQLLQRRHAKWVTLYN--SNLDQKQPVSKRNL 296 (391)
T ss_pred hhhHHHHHHHHHHcCCCCccHHHHHHHHhhhhhhhhc--cCccccCCccHHHH
Confidence 3445667888999999999999999999988765432 23456677776554
No 107
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.72 E-value=34 Score=28.82 Aligned_cols=16 Identities=31% Similarity=0.781 Sum_probs=12.8
Q ss_pred ceecCCCCCCCCCCCe
Q 014025 400 KWQCPICLRNYSLENI 415 (432)
Q Consensus 400 ~W~CPiC~k~~~~~~L 415 (432)
+|+|-||++++.-.++
T Consensus 2 kWkC~iCg~~I~~gql 17 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQL 17 (101)
T ss_pred ceEEEecCCeeeecce
Confidence 6999999998765543
No 108
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.47 E-value=44 Score=31.08 Aligned_cols=47 Identities=21% Similarity=0.539 Sum_probs=30.8
Q ss_pred ecCCCccccc--cccccccCcCccccccHHHHHHHhcCCCceecCCCCCCCCCC
Q 014025 362 LRCPMSGSRI--KVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLE 413 (432)
Q Consensus 362 L~CPls~~ri--~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (432)
..||+-.... +.| =+..|.|+-|= .-|. +..+.+-+||+|+|.+.-.
T Consensus 132 ~~CPiCl~~~sek~~-vsTkCGHvFC~---~Cik-~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVP-VSTKCGHVFCS---QCIK-DALKNTNKCPTCRKKITHK 180 (187)
T ss_pred cCCCceecchhhccc-cccccchhHHH---HHHH-HHHHhCCCCCCcccccchh
Confidence 6899887776 355 45789998542 1121 2334678999999966543
No 109
>PF14353 CpXC: CpXC protein
Probab=22.43 E-value=18 Score=31.28 Aligned_cols=15 Identities=33% Similarity=0.862 Sum_probs=11.8
Q ss_pred CceecCCCCCCCCCC
Q 014025 399 RKWQCPICLRNYSLE 413 (432)
Q Consensus 399 ~~W~CPiC~k~~~~~ 413 (432)
-.+.||-|+....++
T Consensus 37 ~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLE 51 (128)
T ss_pred CEEECCCCCCceecC
Confidence 489999999776543
No 110
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.34 E-value=40 Score=26.00 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=11.7
Q ss_pred CCceecCCCCCCCCC
Q 014025 398 SRKWQCPICLRNYSL 412 (432)
Q Consensus 398 ~~~W~CPiC~k~~~~ 412 (432)
..+-+||+|+|++..
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 456789999998765
No 111
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=21.61 E-value=64 Score=25.67 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=26.0
Q ss_pred ccc-CCCCCCCCCCeeeecCCCCCCcccccceecC
Q 014025 114 VCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIP 147 (432)
Q Consensus 114 ~rC-~Cg~~~~~~~~i~C~~~~C~~~qH~~Cv~~~ 147 (432)
..| +|+.. .|-.|+|..+.|....|..|....
T Consensus 37 ~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 37 LKCSICKKK--GGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred CCCcCCCCC--CCeEEEEeCCCCCcEEChHHHccC
Confidence 355 58865 478999999999999999997654
No 112
>PF11824 DUF3344: Protein of unknown function (DUF3344); InterPro: IPR021779 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 amino acids in length.
Probab=21.13 E-value=1.8e+02 Score=28.77 Aligned_cols=67 Identities=21% Similarity=0.231 Sum_probs=42.6
Q ss_pred CCCceeeEEECCeeeec-----cCCCCCCCCCCCCCCC-----C-CCcccCcCCcccEEEEEE-e--ccceEEEEEEEEE
Q 014025 240 QWPQYADLQVNGVPVRA-----INRPGSQLLGANGRDD-----G-PIITPWTKDGINKIVLTG-C--DARIFCLGVRIVK 305 (432)
Q Consensus 240 ~wP~~~~i~vNg~~v~~-----~~r~~~~~~g~~~r~~-----~-~~IT~~l~~g~N~I~i~~-~--d~~~y~~~v~lVk 305 (432)
..+..+.+.+||..+.. ...+-...+++-.|-+ - -++|++++.|.|++.|+- . |++.|-+.+.+|=
T Consensus 69 ~~~~~~~~~fNg~~~~~~~l~~~~~~Y~d~~~~g~~~~~~yg~~vYDVT~~i~~g~n~~~v~~~~~~dg~iyg~tLvvvY 148 (271)
T PF11824_consen 69 GYYPSFTVTFNGNTLEEFNLETPEAPYVDQKGHGNYVDYDYGMWVYDVTDLIKSGENTVTVTTGSSFDGRIYGITLVVVY 148 (271)
T ss_pred CCCceEEEEECCccceeeeccCCCCceEEecCccceeccceEEEEEECcccccCCceEEEEEeCCCCCCCEeeEEEEEEE
Confidence 45788999999988742 1111111333333311 1 458999999999999987 2 6788876666653
Q ss_pred e
Q 014025 306 R 306 (432)
Q Consensus 306 ~ 306 (432)
.
T Consensus 149 e 149 (271)
T PF11824_consen 149 E 149 (271)
T ss_pred E
Confidence 3
No 113
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=21.08 E-value=70 Score=29.40 Aligned_cols=9 Identities=44% Similarity=1.423 Sum_probs=6.4
Q ss_pred ceecCCCCC
Q 014025 400 KWQCPICLR 408 (432)
Q Consensus 400 ~W~CPiC~k 408 (432)
.|.||+|+-
T Consensus 134 ~~vC~vCGy 142 (166)
T COG1592 134 VWVCPVCGY 142 (166)
T ss_pred EEEcCCCCC
Confidence 677777763
No 114
>PLN00162 transport protein sec23; Provisional
Probab=20.98 E-value=28 Score=39.59 Aligned_cols=19 Identities=21% Similarity=1.013 Sum_probs=13.8
Q ss_pred HHHHhcCCCceecCCCCCC
Q 014025 391 FVELNQRSRKWQCPICLRN 409 (432)
Q Consensus 391 fL~~n~~~~~W~CPiC~k~ 409 (432)
|.+...+.++|.||+|+..
T Consensus 66 f~~~d~~~~~W~C~~C~~~ 84 (761)
T PLN00162 66 YCRVDFQAKIWICPFCFQR 84 (761)
T ss_pred ceEEecCCCEEEccCCCCC
Confidence 3344556789999999854
No 115
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.12 E-value=1e+02 Score=27.81 Aligned_cols=66 Identities=15% Similarity=0.336 Sum_probs=39.8
Q ss_pred cCHHHHHhhcccCCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCCcceEeeceeeeecCCCccccccccccccCcCccccc
Q 014025 307 RSVQQVLNLIPKESEGEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCF 386 (432)
Q Consensus 307 ~s~~~ll~~I~~~~~~~~~e~~~~~ik~~l~~~~~~~~~d~D~D~ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCF 386 (432)
+..+++.+.|+.+ ....++.+++.+.. +. -..--.||-...|+.
T Consensus 77 i~~~~i~d~Ik~~-----~~~~~~~lk~~l~~---------e~--------~~~~Y~Cp~c~~r~t-------------- 120 (158)
T TIGR00373 77 INYEKALDVLKRK-----LEETAKKLREKLEF---------ET--------NNMFFICPNMCVRFT-------------- 120 (158)
T ss_pred eCHHHHHHHHHHH-----HHHHHHHHHHHHhh---------cc--------CCCeEECCCCCcEee--------------
Confidence 4889999888863 45566677765521 11 133446776555543
Q ss_pred cHHHHHHHhcCCCceecCCCCCCCCCCC
Q 014025 387 DLDVFVELNQRSRKWQCPICLRNYSLEN 414 (432)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~~~ 414 (432)
|++..+ --+.||.|+..+...|
T Consensus 121 ----f~eA~~--~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 121 ----FNEAME--LNFTCPRCGAMLDYLD 142 (158)
T ss_pred ----HHHHHH--cCCcCCCCCCEeeecc
Confidence 333332 2699999998765433
No 116
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.04 E-value=1.2e+02 Score=28.00 Aligned_cols=65 Identities=15% Similarity=0.271 Sum_probs=39.1
Q ss_pred cCHHHHHhhcccCCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCCcceEeeceeeeecCCCccccccccccccCcCccccc
Q 014025 307 RSVQQVLNLIPKESEGEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCF 386 (432)
Q Consensus 307 ~s~~~ll~~I~~~~~~~~~e~~~~~ik~~l~~~~~~~~~d~D~D~ev~~~~~~isL~CPls~~ri~~P~Rg~~C~HlQCF 386 (432)
++.+++.+.|+.+ ....++.++..+.. +. -..--.||-...|...
T Consensus 85 l~~~~i~d~ik~~-----~~~~~~klk~~l~~---------e~--------~~~~Y~Cp~C~~rytf------------- 129 (178)
T PRK06266 85 PELEKLPEIIKKK-----KMEELKKLKEQLEE---------EE--------NNMFFFCPNCHIRFTF------------- 129 (178)
T ss_pred eCHHHHHHHHHHH-----HHHHHHHHHHHhhh---------cc--------CCCEEECCCCCcEEeH-------------
Confidence 6889998888863 34566677665521 11 1234567765555432
Q ss_pred cHHHHHHHhcCCCceecCCCCCCCCCC
Q 014025 387 DLDVFVELNQRSRKWQCPICLRNYSLE 413 (432)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (432)
++..+ .-+.||+|+..+...
T Consensus 130 -----~eA~~--~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 130 -----DEAME--YGFRCPQCGEMLEEY 149 (178)
T ss_pred -----HHHhh--cCCcCCCCCCCCeec
Confidence 22222 369999999887653
Done!