Query 007373
Match_columns 606
No_of_seqs 272 out of 556
Neff 5.5
Searched_HMMs 46136
Date Thu Mar 28 22:42:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007373hhsearch_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 3E-38 6.6E-43 357.5 24.5 374 12-454 1-396 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 1.3E-21 2.9E-26 152.7 2.3 50 360-409 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.7 1.9E-17 4.1E-22 156.1 10.2 127 170-305 9-144 (144)
4 KOG1973 Chromatin remodeling p 98.7 1.2E-08 2.6E-13 106.1 4.0 54 108-169 214-268 (274)
5 COG5034 TNG2 Chromatin remodel 98.6 1.7E-08 3.6E-13 102.0 2.5 50 111-168 219-269 (271)
6 PF11789 zf-Nse: Zinc-finger o 98.5 6.8E-08 1.5E-12 77.7 2.7 52 352-405 2-53 (57)
7 PF02037 SAP: SAP domain; Int 98.1 2.6E-06 5.7E-11 61.9 3.7 35 11-45 1-35 (35)
8 smart00513 SAP Putative DNA-bi 97.9 1.4E-05 2.9E-10 58.0 3.8 34 12-45 2-35 (35)
9 PF00628 PHD: PHD-finger; Int 97.8 4.1E-06 8.9E-11 65.0 0.1 49 115-168 1-50 (51)
10 smart00249 PHD PHD zinc finger 97.2 0.00028 6.1E-09 52.4 3.3 45 116-166 2-47 (47)
11 KOG2979 Protein involved in DN 97.2 0.00023 4.9E-09 72.8 2.6 72 352-425 167-243 (262)
12 smart00504 Ubox Modified RING 97.0 0.00093 2E-08 53.6 4.6 59 362-425 2-60 (63)
13 KOG1844 PHD Zn-finger proteins 96.3 0.0019 4E-08 72.5 2.3 51 111-169 84-135 (508)
14 PF04564 U-box: U-box domain; 95.8 0.012 2.6E-07 49.4 4.1 63 361-427 4-66 (73)
15 PF13831 PHD_2: PHD-finger; PD 95.4 0.0046 1E-07 45.4 0.2 35 125-167 2-36 (36)
16 KOG4323 Polycomb-like PHD Zn-f 94.8 0.013 2.7E-07 65.1 1.4 55 111-168 169-223 (464)
17 COG5627 MMS21 DNA repair prote 94.4 0.022 4.7E-07 57.9 1.9 69 352-422 180-250 (275)
18 KOG2169 Zn-finger transcriptio 93.5 0.18 3.9E-06 58.8 7.6 236 355-592 11-264 (636)
19 COG5222 Uncharacterized conser 91.2 0.12 2.6E-06 54.2 2.1 62 356-420 269-331 (427)
20 PLN03208 E3 ubiquitin-protein 91.1 0.25 5.4E-06 49.3 4.1 55 361-416 18-84 (193)
21 PF12949 HeH: HeH/LEM domain; 90.0 0.24 5.1E-06 36.4 2.1 29 11-39 1-31 (35)
22 PF14835 zf-RING_6: zf-RING of 89.7 0.26 5.6E-06 40.9 2.4 58 361-424 7-64 (65)
23 KOG0957 PHD finger protein [Ge 89.7 0.38 8.3E-06 53.7 4.4 64 108-175 115-185 (707)
24 PF04641 Rtf2: Rtf2 RING-finge 87.1 0.6 1.3E-05 48.5 3.7 55 358-417 110-167 (260)
25 PF07498 Rho_N: Rho terminatio 86.6 0.85 1.8E-05 34.7 3.4 36 11-46 2-39 (43)
26 TIGR00599 rad18 DNA repair pro 84.9 1.1 2.5E-05 49.3 4.7 66 358-429 23-89 (397)
27 KOG2164 Predicted E3 ubiquitin 83.3 0.7 1.5E-05 51.9 2.2 56 361-417 186-242 (513)
28 cd00162 RING RING-finger (Real 80.5 1.4 3.1E-05 31.6 2.4 42 364-409 2-44 (45)
29 KOG4259 Putative nucleic acid- 79.6 1.9 4.2E-05 43.9 3.6 36 12-47 7-42 (260)
30 KOG4299 PHD Zn-finger protein 71.7 2.2 4.9E-05 49.0 2.0 52 113-169 253-305 (613)
31 KOG0825 PHD Zn-finger protein 71.6 1.9 4.1E-05 50.8 1.3 51 112-169 214-266 (1134)
32 PF10208 Armet: Degradation ar 70.4 4.2 9E-05 39.3 3.2 39 10-48 103-143 (154)
33 KOG1632 Uncharacterized PHD Zn 70.2 2.1 4.6E-05 46.5 1.3 51 113-169 60-113 (345)
34 KOG1244 Predicted transcriptio 68.6 3.7 7.9E-05 43.1 2.5 49 112-167 280-329 (336)
35 KOG0978 E3 ubiquitin ligase in 68.2 1.6 3.4E-05 51.2 -0.2 56 356-416 638-694 (698)
36 KOG1512 PHD Zn-finger protein 68.1 3.1 6.7E-05 43.9 1.9 50 117-176 319-369 (381)
37 KOG0955 PHD finger protein BR1 65.4 4.8 0.0001 49.5 3.0 55 110-173 217-273 (1051)
38 KOG0956 PHD finger protein AF1 63.6 4 8.6E-05 47.6 1.8 47 113-166 6-54 (900)
39 PF13923 zf-C3HC4_2: Zinc fing 63.4 3.3 7.2E-05 30.3 0.8 39 364-406 1-39 (39)
40 PF13445 zf-RING_UBOX: RING-ty 62.5 5.2 0.00011 30.6 1.7 39 364-404 1-43 (43)
41 PF14447 Prok-RING_4: Prokaryo 62.1 5 0.00011 32.4 1.7 36 369-415 19-54 (55)
42 PF04810 zf-Sec23_Sec24: Sec23 61.0 1.7 3.7E-05 32.5 -1.1 17 393-409 17-33 (40)
43 PF04423 Rad50_zn_hook: Rad50 59.9 2.7 5.9E-05 33.2 -0.2 38 388-428 9-46 (54)
44 KOG0957 PHD finger protein [Ge 58.5 11 0.00023 42.7 3.9 52 110-166 541-595 (707)
45 KOG0311 Predicted E3 ubiquitin 55.4 1.4 3.1E-05 47.5 -3.2 70 356-428 38-108 (381)
46 PF15227 zf-C3HC4_4: zinc fing 54.3 7 0.00015 29.4 1.2 42 364-406 1-42 (42)
47 PF00097 zf-C3HC4: Zinc finger 53.6 7.8 0.00017 28.2 1.4 40 364-406 1-41 (41)
48 KOG0954 PHD finger protein [Ge 52.0 7.3 0.00016 45.9 1.4 49 112-169 270-321 (893)
49 PF13894 zf-C2H2_4: C2H2-type 49.8 6.3 0.00014 24.7 0.3 11 401-411 1-11 (24)
50 KOG1245 Chromatin remodeling c 49.0 4.3 9.4E-05 51.5 -1.0 52 113-171 1108-1160(1404)
51 PF13920 zf-C3HC4_3: Zinc fing 47.9 9.8 0.00021 29.2 1.2 43 363-410 4-47 (50)
52 PF14446 Prok-RING_1: Prokaryo 46.1 15 0.00032 29.7 1.9 32 112-145 4-37 (54)
53 PF08531 Bac_rhamnosid_N: Alph 45.8 11 0.00024 36.6 1.5 46 244-291 15-63 (172)
54 KOG1632 Uncharacterized PHD Zn 45.7 3 6.6E-05 45.3 -2.7 58 110-169 236-295 (345)
55 cd00350 rubredoxin_like Rubred 44.4 10 0.00022 27.1 0.7 12 399-410 16-27 (33)
56 TIGR00599 rad18 DNA repair pro 44.3 25 0.00055 39.1 4.1 35 13-47 268-302 (397)
57 smart00531 TFIIE Transcription 43.1 36 0.00079 32.3 4.5 70 307-413 67-136 (147)
58 PF02837 Glyco_hydro_2_N: Glyc 42.9 64 0.0014 30.3 6.1 66 203-292 72-138 (167)
59 PF13832 zf-HC5HC2H_2: PHD-zin 42.1 16 0.00035 32.5 1.8 33 113-147 55-88 (110)
60 COG5574 PEX10 RING-finger-cont 41.7 13 0.00028 38.9 1.3 54 361-418 215-269 (271)
61 KOG2177 Predicted E3 ubiquitin 41.6 11 0.00024 37.4 0.8 62 361-429 13-74 (386)
62 PF02228 Gag_p19: Major core p 41.2 13 0.00027 32.3 0.9 21 386-406 44-64 (92)
63 KOG0801 Predicted E3 ubiquitin 39.1 15 0.00032 36.0 1.2 21 400-420 138-158 (205)
64 smart00184 RING Ring finger. E 34.6 25 0.00055 23.8 1.5 25 378-406 14-39 (39)
65 PF00096 zf-C2H2: Zinc finger, 33.9 13 0.00029 23.6 -0.1 11 401-411 1-11 (23)
66 COG5243 HRD1 HRD ubiquitin lig 33.1 44 0.00095 36.8 3.6 43 364-413 303-347 (491)
67 KOG3113 Uncharacterized conser 33.1 94 0.002 32.7 5.8 112 298-417 48-164 (293)
68 cd00730 rubredoxin Rubredoxin; 32.9 18 0.0004 28.5 0.6 12 398-409 32-43 (50)
69 PF13639 zf-RING_2: Ring finge 32.4 24 0.00053 26.2 1.2 25 378-407 19-44 (44)
70 KOG0320 Predicted E3 ubiquitin 32.3 23 0.0005 35.2 1.3 48 362-414 132-181 (187)
71 smart00734 ZnF_Rad18 Rad18-lik 31.4 15 0.00033 25.1 -0.1 9 402-410 3-11 (26)
72 PRK12678 transcription termina 31.1 43 0.00093 39.3 3.3 36 11-46 23-60 (672)
73 PLN03124 poly [ADP-ribose] pol 30.7 35 0.00076 40.2 2.6 38 12-49 3-40 (643)
74 PF00301 Rubredoxin: Rubredoxi 30.7 20 0.00043 28.0 0.5 13 397-409 31-43 (47)
75 PF13465 zf-H2C2_2: Zinc-finge 30.5 33 0.00071 23.1 1.4 16 395-410 9-24 (26)
76 PHA02929 N1R/p28-like protein; 30.0 33 0.00071 35.6 2.0 44 362-410 175-226 (238)
77 TIGR00570 cdk7 CDK-activating 29.8 58 0.0013 35.1 3.8 40 379-421 25-68 (309)
78 cd04718 BAH_plant_2 BAH, or Br 28.3 39 0.00084 32.7 2.0 27 139-170 2-28 (148)
79 PF14634 zf-RING_5: zinc-RING 27.8 38 0.00081 25.4 1.5 33 372-408 12-44 (44)
80 COG0723 QcrA Rieske Fe-S prote 27.5 27 0.00058 34.0 0.8 26 378-408 106-132 (177)
81 KOG0287 Postreplication repair 27.5 22 0.00047 38.6 0.2 63 360-428 22-85 (442)
82 PF13670 PepSY_2: Peptidase pr 27.4 80 0.0017 26.8 3.7 29 421-449 31-59 (83)
83 COG4068 Uncharacterized protei 27.4 42 0.0009 27.6 1.7 29 399-427 7-35 (64)
84 COG5533 UBP5 Ubiquitin C-termi 26.1 26 0.00056 37.8 0.5 36 374-409 258-293 (415)
85 PF07496 zf-CW: CW-type Zinc F 26.1 38 0.00082 26.5 1.3 33 126-165 2-34 (50)
86 PLN00162 transport protein sec 24.3 23 0.0005 42.5 -0.3 33 374-410 53-85 (761)
87 KOG4661 Hsp27-ERE-TATA-binding 23.9 50 0.0011 38.2 2.2 40 9-48 28-67 (940)
88 PF05605 zf-Di19: Drought indu 23.8 24 0.00052 27.7 -0.2 10 400-409 2-11 (54)
89 KOG4443 Putative transcription 23.0 15 0.00032 42.9 -2.1 40 125-168 161-201 (694)
90 PF05265 DUF723: Protein of un 22.7 1E+02 0.0022 25.5 3.1 37 323-371 3-42 (60)
91 KOG0287 Postreplication repair 22.2 1.1E+02 0.0024 33.4 4.3 34 13-46 250-283 (442)
92 PF13913 zf-C2HC_2: zinc-finge 22.0 21 0.00047 24.0 -0.7 15 401-415 3-17 (25)
93 PF13771 zf-HC5HC2H: PHD-like 21.7 61 0.0013 27.6 1.9 32 114-147 37-69 (90)
94 KOG3970 Predicted E3 ubiquitin 21.0 1E+02 0.0022 31.9 3.5 58 372-429 57-123 (299)
95 PF07227 DUF1423: Protein of u 20.8 78 0.0017 35.7 2.9 61 114-176 130-200 (446)
96 PF00641 zf-RanBP: Zn-finger i 20.0 54 0.0012 22.7 1.0 10 398-407 2-11 (30)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=3e-38 Score=357.48 Aligned_cols=374 Identities=21% Similarity=0.381 Sum_probs=263.7
Q ss_pred hhccHHHHHHHH-HHhCCCCCC--ChHHHHHHHHHhccccchhhccccCCCCcHHHHHHHHHHHHHh-hccc--CCcccc
Q 007373 12 AHFRIKELKDVL-TQLGLSKQG--KKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLVDDTHRK-LQVS--VAPDLA 85 (606)
Q Consensus 12 ~~fRi~ELk~lL-~~lglsk~G--kK~eL~~Ril~ll~~~~~~~~~~~~~~~~~~~v~k~I~~~Yr~-m~~~--~~~~~~ 85 (606)
+++|+.+|+.++ .+.|+.+.| +|.+|.-|+|.++...+. +++.++|.+.|++ .... .+.+++
T Consensus 1 m~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~------------~~~q~~i~~~~~~~~~~~~~~~~~~~ 68 (636)
T KOG2169|consen 1 MSLRVSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCK------------PYLQMVIKELYQRQYPNGQQQPIDLP 68 (636)
T ss_pred CCcccccccccchhhhccccccccchhhhhhhhhcccccCCc------------hhhhhhhhhhhhhhcccccccccccc
Confidence 478999999998 788888999 999999999999998876 4788899999974 1111 111211
Q ss_pred cCCCCCCCCCCcccccccccccCCCCCceeccCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccc
Q 007373 86 SKGGQGVSNSSNIKIKGEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165 (606)
Q Consensus 86 s~~~~~~~~~s~~~~~~~~~~~~q~~~~~rCiCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~ 165 (606)
... .... ..+ ..+.. . |....|..=..++...+.+ +..-+-+.
T Consensus 69 ~~~--~~~~---~~~-----~~~~~---------------~--------~~~~~~~~~~~~~~~~l~g----~~~~~~~~ 111 (636)
T KOG2169|consen 69 AVK--LHPN---VVP-----PFYPL---------------L--------WQLLRHPTQQPVTPSSLLG----PPLPFHPD 111 (636)
T ss_pred ccc--cCCc---ccC-----ccccc---------------h--------hcccccCCCCCCCcccccC----CCCcCCCc
Confidence 111 0000 000 00000 0 0000000000011111111 00123445
Q ss_pred cccccCCCceeeecccccceeeeeeccCCCCCCCceeeeEEEEeCHhhHhhhcCC-C------eeEEEEEEecCCCCccc
Q 007373 166 CRLSRADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSKQ-E------YDVQAWCMLLNDKVPFR 238 (606)
Q Consensus 166 CRl~r~dPF~~~i~~lL~Pv~l~~s~i~~~g~~~~Q~~~~~F~Lt~~~~~~L~~~-~------~~lql~C~~l~d~~~~~ 238 (606)
-|+ +..|||+++..+++|+.+..+.. ..++...+.|.|++.....+... + ..-.+ |+.. ...+++
T Consensus 112 ~~~-~~~~~y~~l~~~~~p~~~~~~~~-----~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~~-~s~p~e 183 (636)
T KOG2169|consen 112 VKL-KKLPFYDVLSELIKPHVLHSSNS-----PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLME-TSCPQE 183 (636)
T ss_pred ccc-cCCchheecccccCceeecCcCC-----CCcccccchhhcchhhhhhcccccccccccccccce-eecc-ccCccc
Confidence 566 67999999999999998876532 24556778899999988766431 1 11111 5543 355889
Q ss_pred ccCCCccEEEEcCeEeeccc-CCCCCCCCC-CCCCCCCC-ccc--CcCCC-ccEEEEEEe--cCceEEEEEEEEEecCHH
Q 007373 239 MQWPQYADLQVNGVPVRAIN-RPGSQLLGA-NGRDDGPI-ITP--WTKDG-INKIVLTGC--DARIFCLGVRIVKRRSVQ 310 (606)
Q Consensus 239 ~~wP~~~~I~VNg~~v~~~~-Rp~~~~~g~-~gR~~~pi-IT~--~lk~g-~N~I~is~~--d~~~y~~~V~lVk~~s~e 310 (606)
.+||..+.++||+..+.+.. .-..++.+. .+|...|. ||. ++... .|.+.+.|. ..+.|.+++|+|+.++.+
T Consensus 184 ~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~ 263 (636)
T KOG2169|consen 184 DHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSK 263 (636)
T ss_pred cccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHH
Confidence 99999999999999887741 111112222 26667777 999 44443 377777765 678999999999999999
Q ss_pred HHHhhcccCCC-CCCHHHHHHHHHHhhCCCCCCCCCCCCCCcceEeeeceeeecCCCCcccccccccCCCCCccccccHH
Q 007373 311 QVLNLIPKESE-GEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLD 389 (606)
Q Consensus 311 ~Ll~~I~~~~~-~~~~e~al~rIkr~l~~~~~~~~~d~DdD~eIv~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~ 389 (606)
+|+++++...+ ...++.+.+.+++.+ ..++|.||+++++.|||.|||+++||++|+|+..|+|+|||||.
T Consensus 264 ~llq~~~~~~~~~~~~~~s~~~~~~~l---------~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~ 334 (636)
T KOG2169|consen 264 DLLQRLKQNGKINRNLSQSDALIKKKL---------TAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDAL 334 (636)
T ss_pred HHHHHHhccCCccCchhHhHHHhhccc---------ccCCcccceeccceeEecCCcccceeecCCcccccccceecchh
Confidence 99999876432 233466677766544 23455679999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhhcCCCCeeEEEEccCCceEeccCCCc
Q 007373 390 VFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMRNCGEDITELEVKPDGSWRVKTRSES 454 (606)
Q Consensus 390 ~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L~~~~~dv~eV~v~~DGsW~~~~e~e~ 454 (606)
+||+||+++++|+||||.+.+.+++|+||+||+.|| .+|..+++||++..||+|++..+++.
T Consensus 335 ~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL---~~~~~~~~ev~~~~dGsw~pi~~~~~ 396 (636)
T KOG2169|consen 335 SYLQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNIL---QSCQANVEEVEVSEDGSWKPIPEEAE 396 (636)
T ss_pred hhHHhccCCCeeeCccCCccccccchhhhHHHHHHH---hhccCCCcceEecCCCceecCccccc
Confidence 999999999999999999999999999999999995 55677899999999999999887764
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=99.83 E-value=1.3e-21 Score=152.68 Aligned_cols=50 Identities=54% Similarity=1.107 Sum_probs=36.5
Q ss_pred eeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC
Q 007373 360 VNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 360 isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (606)
|||+||||++||++|+||+.|+|+|||||++||+++++++.|+||+|+++
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 79999999999999999999999999999999999999999999999874
No 3
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.72 E-value=1.9e-17 Score=156.07 Aligned_cols=127 Identities=21% Similarity=0.350 Sum_probs=83.7
Q ss_pred cCCCceeeecccccceeeeeeccCCCCCCCceeeeEEEEeCHhhHhhhcC--CCeeEEEEEEecC---CCCcccccCCCc
Q 007373 170 RADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSK--QEYDVQAWCMLLN---DKVPFRMQWPQY 244 (606)
Q Consensus 170 r~dPF~~~i~~lL~Pv~l~~s~i~~~g~~~~Q~~~~~F~Lt~~~~~~L~~--~~~~lql~C~~l~---d~~~~~~~wP~~ 244 (606)
+.+|||+++ .++.|+.+.+.. .+.++...+.|.|+++++++|++ +.++|+|||+..+ ....+.++||.+
T Consensus 9 k~sPFY~~~-~~i~~~~~~~~~-----~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~FP~~ 82 (144)
T PF14324_consen 9 KPSPFYKVL-RLIHPTPLLPAS-----SSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIEFPPP 82 (144)
T ss_dssp --BTTEEEE-EEEEEEEEEE-------EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB-----SS
T ss_pred ccCCCccee-EEcCCccccccc-----cCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccccCCC
Confidence 679999999 788888776532 23567889999999999999976 6899999999843 345778999999
Q ss_pred cEEEEcCeEeecccCCCCCCCCCCCCCCCCCcccCcCCC---ccEEEEEEe-cCceEEEEEEEEE
Q 007373 245 ADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKDG---INKIVLTGC-DARIFCLGVRIVK 305 (606)
Q Consensus 245 ~~I~VNg~~v~~~~Rp~~~~~g~~gR~~~piIT~~lk~g---~N~I~is~~-d~~~y~~~V~lVk 305 (606)
++|+|||+.|+++.|..+ +++|...|++||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 83 ~evkvN~~~v~~~~~glk---nKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 83 CEVKVNGKQVKLNNRGLK---NKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEEETTEE--S--SS-T---TS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred eEEEEeCEEcccCccCCC---CCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 999999999999887654 455666677799999865 799999997 6889999999997
No 4
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.68 E-value=1.2e-08 Score=106.08 Aligned_cols=54 Identities=33% Similarity=0.922 Sum_probs=48.0
Q ss_pred CCCCCceeccCCCCcCCCCeeeecCCCCC-CcccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 108 IQSDTKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 108 ~q~~~~~rCiCg~s~~~~~mI~C~~~~C~-~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
..++...||+|. ...+|.||.|+++.|. .|+|+.|||+..+| .++|||+.|+..
T Consensus 214 ~d~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 214 VDPDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAE 268 (274)
T ss_pred cCCCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhh
Confidence 446679999999 5789999999999999 99999999999877 568999999864
No 5
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.60 E-value=1.7e-08 Score=102.03 Aligned_cols=50 Identities=28% Similarity=0.836 Sum_probs=44.5
Q ss_pred CCceeccCCCCcCCCCeeeecCCCCC-CcccccccccCCCCCCCCCCCCCccccccccc
Q 007373 111 DTKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (606)
Q Consensus 111 ~~~~rCiCg~s~~~~~mI~C~~~~C~-~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl 168 (606)
+...||+|.+ ..+|.||.|+++.|. .|+|+.|||+.+.| .+.|||+.|+-
T Consensus 219 ~e~lYCfCqq-vSyGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~ 269 (271)
T COG5034 219 GEELYCFCQQ-VSYGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKK 269 (271)
T ss_pred CceeEEEecc-cccccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHh
Confidence 3589999997 578999999999999 99999999998765 56999999985
No 6
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.49 E-value=6.8e-08 Score=77.69 Aligned_cols=52 Identities=23% Similarity=0.556 Sum_probs=37.1
Q ss_pred ceEeeeceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC
Q 007373 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI 405 (606)
Q Consensus 352 eIv~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi 405 (606)
||+.+...++++||||+..|+-|+++..|.|. ||-++.+++-.+...-+||+
T Consensus 2 di~i~~~~~~~~CPiT~~~~~~PV~s~~C~H~--fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 2 DIVIEGGTISLKCPITLQPFEDPVKSKKCGHT--FEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -----SSB--SB-TTTSSB-SSEEEESSS--E--EEHHHHHHHCTTTS-EE-SC
T ss_pred ceEEeccEeccCCCCcCChhhCCcCcCCCCCe--ecHHHHHHHHHhcCCCCCCC
Confidence 35556689999999999999999999999997 99999999988889999999
No 7
>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=98.12 E-value=2.6e-06 Score=61.90 Aligned_cols=35 Identities=40% Similarity=0.676 Sum_probs=31.4
Q ss_pred HhhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 007373 11 LAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (606)
Q Consensus 11 L~~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll 45 (606)
|+.+++.|||..|.++||+.+|+|++|++|+.++|
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 46789999999999999999999999999998864
No 8
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.89 E-value=1.4e-05 Score=58.00 Aligned_cols=34 Identities=50% Similarity=0.786 Sum_probs=31.6
Q ss_pred hhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 007373 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (606)
Q Consensus 12 ~~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll 45 (606)
+.+.+.|||..|.++|++.+|+|++|++|+..++
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 4688999999999999999999999999998864
No 9
>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=97.82 E-value=4.1e-06 Score=64.98 Aligned_cols=49 Identities=41% Similarity=0.881 Sum_probs=39.6
Q ss_pred ec-cCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccc
Q 007373 115 CC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (606)
Q Consensus 115 rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl 168 (606)
+| +|++....+.||+|+. |..|+|..|++++.+..+ .....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~---~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEE---IPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHS---HHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhcc---CCCCcEECcCCcC
Confidence 57 8999888899999999 999999999998865321 1233899999974
No 10
>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 KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=97.16 E-value=0.00023 Score=72.85 Aligned_cols=72 Identities=22% Similarity=0.335 Sum_probs=57.0
Q ss_pred ceEeeeceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC--CCCCCCC--CCeeec-HHHHHHH
Q 007373 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNYSL--ENIIID-PYFNRIT 425 (606)
Q Consensus 352 eIv~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~--~~L~ID-~y~~~IL 425 (606)
++...+..+|++||+|+..|..|++++.|.|+ ||-.+-.++-....+-.||+ |..++.. ..|.-| .+...|.
T Consensus 167 e~~i~~e~fs~rdPis~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr 243 (262)
T KOG2979|consen 167 EELIGQEVFSNRDPISKKPIVNPVISKKCGHV--YDRDSIMQILCDEITIRCPVLGCENPYYIQPGHLDEDKELQQKIR 243 (262)
T ss_pred HHHhhhhhhcccCchhhhhhhchhhhcCcCcc--hhhhhHHHHhccCceeecccccCCccccccccccCchHHHHHHHH
Confidence 56667889999999999999999999999999 99999998887788999999 7744443 334444 4444443
No 12
>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=97.03 E-value=0.00093 Score=53.56 Aligned_cols=59 Identities=14% Similarity=0.173 Sum_probs=49.5
Q ss_pred ecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHH
Q 007373 362 LRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRIT 425 (606)
Q Consensus 362 L~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL 425 (606)
|.|||++..|+.|+.. .|-|. |+.+.+.++-+. .-.||+|++++..++|+-+..+.+.+
T Consensus 2 ~~Cpi~~~~~~~Pv~~-~~G~v--~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~~i 60 (63)
T smart00504 2 FLCPISLEVMKDPVIL-PSGQT--YERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKSAI 60 (63)
T ss_pred cCCcCCCCcCCCCEEC-CCCCE--EeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHHHH
Confidence 7899999999999986 67776 898888877655 45899999999999999987776653
No 13
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=96.33 E-value=0.0019 Score=72.50 Aligned_cols=51 Identities=31% Similarity=0.684 Sum_probs=44.7
Q ss_pred CCceeccCCCCcC-CCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 111 DTKVCCPCGSSLE-TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 111 ~~~~rCiCg~s~~-~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
...++|.|+.... .+.||+|+. |..|||..|+++.... -|+.|+|+.|++.
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~~Wqh~~C~g~~~~~------~p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CGRWQHKICCGSFKST------KPDKYVCEICTPR 135 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cCcccCceeeeecCCC------Cchhceeeeeccc
Confidence 3579999999888 899999999 9999999999987544 1789999999884
No 14
>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=95.77 E-value=0.012 Score=49.38 Aligned_cols=63 Identities=11% Similarity=0.223 Sum_probs=47.5
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSK 427 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 427 (606)
.|.||||+..|+-|+....| |. ||-.+.....++ ..-.||+|++++...+|+-+.-+...++.
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 47899999999999998777 76 998888776555 56789999999999999999888776553
No 15
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.39 E-value=0.0046 Score=45.37 Aligned_cols=35 Identities=29% Similarity=0.729 Sum_probs=19.7
Q ss_pred CCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccc
Q 007373 125 ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (606)
Q Consensus 125 ~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CR 167 (606)
+.||+|+. |++..|..|||+...+ ....|+|..|+
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 57999999 9999999999998654 23359999885
No 16
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.76 E-value=0.013 Score=65.12 Aligned_cols=55 Identities=22% Similarity=0.534 Sum_probs=42.6
Q ss_pred CCceeccCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccc
Q 007373 111 DTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (606)
Q Consensus 111 ~~~~rCiCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl 168 (606)
....+|.||.+.....||+|+. |+.|+|..|+.-..+++.- ...-.+|||-.|.-
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l~-~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDELA-GDPFYEWFCDVCNR 223 (464)
T ss_pred ceeeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhhc-cCccceEeehhhcc
Confidence 3488899999988889999999 9999999999877665332 22334788888854
No 17
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=94.37 E-value=0.022 Score=57.89 Aligned_cols=69 Identities=16% Similarity=0.253 Sum_probs=56.6
Q ss_pred ceEeeeceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC--CCCCCCCCCeeecHHHH
Q 007373 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNYSLENIIIDPYFN 422 (606)
Q Consensus 352 eIv~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~~L~ID~y~~ 422 (606)
+|+..+-.++++|||+..++..|.=+..|.|. ||....+..-+--++--||. |.+....+.++-|..+.
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 45667779999999999999999999999998 99888777666668889997 98877666666565543
No 18
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=93.52 E-value=0.18 Score=58.83 Aligned_cols=236 Identities=17% Similarity=0.060 Sum_probs=167.1
Q ss_pred eeeceeeecCCCCcccccccccCCCCCcccccc--HHHHHHHhc--CCCeeeccCCCCCCCCCCeeecHHHHHHHHHhhc
Q 007373 355 ADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFD--LDVFVELNQ--RSRKWQCPICLRNYSLENIIIDPYFNRITSKMRN 430 (606)
Q Consensus 355 ~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFD--l~~fL~~n~--~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L~~ 430 (606)
..+.-+.+.+|.-..+.+..+|...|.+..|+. ..-+=+..+ ....|.||+|-+.+...-..+..|+..+-..++.
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (636)
T KOG2169|consen 11 LLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVKLHPNVVPPFYPLLWQLLRH 90 (636)
T ss_pred cchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccccCCcccCccccchhccccc
Confidence 334456778999899999999999999999998 443333333 4578999999888887777777777665344443
Q ss_pred CCC-CeeEEEEcc---CCceEeccCCCcccccccccCCCCCCCCCCccCCCCCCCchhhhhhhhhccccCCCCCcceeee
Q 007373 431 CGE-DITELEVKP---DGSWRVKTRSESDRREIGDLASWHFPDGSLCAPAGGEDKPKVEMLKHVRQEGVSEGHIGLKLGI 506 (606)
Q Consensus 431 ~~~-dv~eV~v~~---DGsW~~~~e~e~~~~d~~~~~~~~~~dg~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~ 506 (606)
.-. -+....+.. +..|++.....+.-.-++.+.+|+........ ..-...-.+... .-+.+..+.++.-+..+.
T Consensus 91 ~~~~~~~~~~l~g~~~~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~~~-~~~~~~~~f~lt-~~~~~~i~~~~~~~~~~k 168 (636)
T KOG2169|consen 91 PTQQPVTPSSLLGPPLPFHPDVKLKKLPFYDVLSELIKPHVLHSSNSP-SLSESPFLFALT-PEQVSGISSRPDVLPGSK 168 (636)
T ss_pred CCCCCCCcccccCCCCcCCCcccccCCchheecccccCceeecCcCCC-Ccccccchhhcc-hhhhhhcccccccccccc
Confidence 322 355555665 78999988887776666788899877666662 111222122221 223344555554454444
Q ss_pred ee------CCCCceeecCCCCCCCCCCcc-cccccccCCcceeecccCCCCCCCCCCC---CccccCCCceeeeccCCcc
Q 007373 507 RK------NRNGLWEVSKPEDMNGSSGSR-LQEKFENHDLKVIPMSSSATGSGRDGED---ASVNQDVGGTFDFTNNGIE 576 (606)
Q Consensus 507 ~~------~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 576 (606)
+. ..++.||...|.....+..|. .+--+.+...+..++....++..++..+ .++..++...+.|..++..
T Consensus 169 ~~~~~~~~~~s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~ 248 (636)
T KOG2169|consen 169 SEGSVCLMETSCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGK 248 (636)
T ss_pred cccceeeccccCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCc
Confidence 43 458999999998887776544 3333367778888888899999999988 8899889999999999999
Q ss_pred cccccccCCcccccCC
Q 007373 577 HDSMSLNVDPTYAFAD 592 (606)
Q Consensus 577 ~~~~~~~~~~~~~~~~ 592 (606)
-.|+..+|...|...+
T Consensus 249 ~ysl~~~~v~~~t~~~ 264 (636)
T KOG2169|consen 249 SYSLSVYFVEGLTSKD 264 (636)
T ss_pred ccceEEEEecccCHHH
Confidence 9999999999887654
No 19
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.17 E-value=0.12 Score=54.23 Aligned_cols=62 Identities=19% Similarity=0.431 Sum_probs=44.3
Q ss_pred eeceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCC-CCCCCCeeecHH
Q 007373 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR-NYSLENIIIDPY 420 (606)
Q Consensus 356 ~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k-~~~~~~L~ID~y 420 (606)
..-.|+|+|||.+..++.|+|..-|.|.-|=.. |+...--.-+.||.|.. .+.++.|.-|.=
T Consensus 269 ~~~~i~LkCplc~~Llrnp~kT~cC~~~fc~ec---i~~al~dsDf~CpnC~rkdvlld~l~pD~d 331 (427)
T COG5222 269 QPPNISLKCPLCHCLLRNPMKTPCCGHTFCDEC---IGTALLDSDFKCPNCSRKDVLLDGLTPDID 331 (427)
T ss_pred CCCCccccCcchhhhhhCcccCccccchHHHHH---HhhhhhhccccCCCcccccchhhccCccHH
Confidence 345788999999999999999999999966443 22222234599999974 555555555543
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=91.07 E-value=0.25 Score=49.29 Aligned_cols=55 Identities=15% Similarity=0.416 Sum_probs=42.1
Q ss_pred eecCCCCcccccccccCCCCCccccccHH-HHHHHh-----------cCCCeeeccCCCCCCCCCCee
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLD-VFVELN-----------QRSRKWQCPICLRNYSLENII 416 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n-----------~~~~~W~CPiC~k~~~~~~L~ 416 (606)
.+.|||-...++.|+- ..|.|+-|..-- .|+... ......+||+|...+...+|+
T Consensus 18 ~~~CpICld~~~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 18 DFDCNICLDQVRDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred ccCCccCCCcCCCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 5889999999999988 479999888744 466532 134568999999998766654
No 21
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=90.03 E-value=0.24 Score=36.36 Aligned_cols=29 Identities=28% Similarity=0.507 Sum_probs=20.7
Q ss_pred HhhccHHHHHHHHHHhCCC--CCCChHHHHH
Q 007373 11 LAHFRIKELKDVLTQLGLS--KQGKKQDLVD 39 (606)
Q Consensus 11 L~~fRi~ELk~lL~~lgls--k~GkK~eL~~ 39 (606)
+++++|.|||.+|...|+. .+.||.||+.
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 3578999999999999987 8999999985
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=89.75 E-value=0.26 Score=40.90 Aligned_cols=58 Identities=21% Similarity=0.385 Sum_probs=26.5
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHH
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRI 424 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~I 424 (606)
.|+|+.-...|+.|+--..|.|+-|-.-- ..... -.||+|+.++...|++|..-+..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci-----~~~~~-~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI-----RDCIG-SECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG-----GGGTT-TB-SSS--B-S-SS----HHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh-----HHhcC-CCCCCcCChHHHHHHHhhhhhhcc
Confidence 48999999999999998999999664321 11111 359999999999999998877665
No 23
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=89.66 E-value=0.38 Score=53.68 Aligned_cols=64 Identities=20% Similarity=0.612 Sum_probs=45.8
Q ss_pred CCCCCceeccCCCC--cCCCCeeeecCCCCCCcccccccccCCCCCCCCCC-----CCCcccccccccccCCCce
Q 007373 108 IQSDTKVCCPCGSS--LETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPP-----VPELFYCEICRLSRADPFW 175 (606)
Q Consensus 108 ~q~~~~~rCiCg~s--~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~-----~p~~fyCe~CRl~r~dPF~ 175 (606)
+.-...+.|+|-+. ...+++|||+. |++.-|-+|||..++. +||. -...|||+.|+.--..|-.
T Consensus 115 apkk~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 115 APKKAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred ccccceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCCcc
Confidence 33344578899653 44699999999 9999999999988554 3332 2246999999875555644
No 24
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.09 E-value=0.6 Score=48.50 Aligned_cols=55 Identities=25% Similarity=0.581 Sum_probs=39.2
Q ss_pred ceeeecCCCCcccccccccC---CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007373 358 IGVNLRCPMSGSRIKVAGRF---KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 358 ~~isL~CPls~~ri~~P~Rg---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
....+.||+|+..|.-=.|+ ..|-|.-+. .++=++. ..|.||+|++++.-.|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~--~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSE--KALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeH--HHHHhhc---ccccccccCCccccCCEEE
Confidence 35678999999999322222 689998444 4444442 5799999999999888874
No 25
>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=86.63 E-value=0.85 Score=34.67 Aligned_cols=36 Identities=28% Similarity=0.517 Sum_probs=27.5
Q ss_pred HhhccHHHHHHHHHHhCCC--CCCChHHHHHHHHHhcc
Q 007373 11 LAHFRIKELKDVLTQLGLS--KQGKKQDLVDRILAILS 46 (606)
Q Consensus 11 L~~fRi~ELk~lL~~lgls--k~GkK~eL~~Ril~ll~ 46 (606)
|...-+.||+.+...+|+. ..=||+||+..|+.--.
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~q~ 39 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAILKAQA 39 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHHHC
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHHHHHH
Confidence 6678899999999999996 34489999999987543
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.86 E-value=1.1 Score=49.35 Aligned_cols=66 Identities=17% Similarity=0.300 Sum_probs=51.6
Q ss_pred ceeeecCCCCcccccccccCCCCCccccccHHH-HHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007373 358 IGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDV-FVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 358 ~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~-fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L~ 429 (606)
+.-.|.||+-...+..|+- ..|.|.-|..--. |+.. .-.||+|...+....|+.+..+.+|++..+
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~-----~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSN-----QPKCPLCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhC-----CCCCCCCCCccccccCccchHHHHHHHHHH
Confidence 4456899999999999985 7999998765433 4432 238999999998889998888888887544
No 27
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.33 E-value=0.7 Score=51.94 Aligned_cols=56 Identities=21% Similarity=0.489 Sum_probs=45.6
Q ss_pred eecCCCCcccccccccCCCCCcccccc-HHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
...|||-+-.-.+|+|.. |-|+-||- |-.|+.......-=.||+|...+++.+|.-
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p 242 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP 242 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence 789999999999999999 99999885 566777664445557999998887766653
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=80.50 E-value=1.4 Score=31.57 Aligned_cols=42 Identities=26% Similarity=0.606 Sum_probs=28.2
Q ss_pred CCCCcccccccccCCCCCccccccH-HHHHHHhcCCCeeeccCCCCC
Q 007373 364 CPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC~k~ 409 (606)
||+-...+..|.....|.|.-|.+- ..|++. ....||+|.+.
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 5666666666777777999866663 334432 56789999875
No 29
>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=79.55 E-value=1.9 Score=43.89 Aligned_cols=36 Identities=36% Similarity=0.595 Sum_probs=32.8
Q ss_pred hhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccc
Q 007373 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSD 47 (606)
Q Consensus 12 ~~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll~~ 47 (606)
..+.|.|||.=|..=||+..|+|.||++|+.+-+..
T Consensus 7 kklkVa~LkeeLa~rGL~~~GNK~EL~~RLtaa~e~ 42 (260)
T KOG4259|consen 7 KKLKVAELKEELAERGLSTAGNKAELVSRLTAATES 42 (260)
T ss_pred hhccHHHHHHHHHHhcccccCChHHHHHHHHHHHHH
Confidence 467899999999999999999999999999887765
No 30
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=71.74 E-value=2.2 Score=49.04 Aligned_cols=52 Identities=29% Similarity=0.726 Sum_probs=39.0
Q ss_pred ceecc-CCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 113 KVCCP-CGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 113 ~~rCi-Cg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
..+|. |+++-.....|.|+. |...+|..|.--+-. .+.+| ++-|+|+.|...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~--Cp~sFH~~CLePPl~-~eniP--~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG--CPRSFHQTCLEPPLE-PENIP--PGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecC--CchHHHHhhcCCCCC-cccCC--CCccccCCCeee
Confidence 34885 998755566799999 999999999875522 24444 458999999874
No 31
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=71.62 E-value=1.9 Score=50.75 Aligned_cols=51 Identities=24% Similarity=0.565 Sum_probs=38.5
Q ss_pred Cceec-cCCCCcCCCCeeeecCCCCCCc-ccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 112 TKVCC-PCGSSLETESMIKCEDPRCPVW-QHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 112 ~~~rC-iCg~s~~~~~mI~C~~~~C~~w-qH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
..++| +|+....-.-||-|+. |+.. .|+.|+..+-.. +| ...|||.-|-+.
T Consensus 214 E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~e---iP--~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSE---SP--VNEWYCTNCSLL 266 (1134)
T ss_pred ccccceeeccCChHHhheeecc--cccceeeccccCccccc---cc--ccceecCcchhh
Confidence 36788 6998877788999999 9955 999998753211 11 358999999764
No 32
>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=70.36 E-value=4.2 Score=39.35 Aligned_cols=39 Identities=33% Similarity=0.540 Sum_probs=33.0
Q ss_pred HHhhccHHHHHHHHHHhCCCCCC--ChHHHHHHHHHhcccc
Q 007373 10 KLAHFRIKELKDVLTQLGLSKQG--KKQDLVDRILAILSDD 48 (606)
Q Consensus 10 ~L~~fRi~ELk~lL~~lglsk~G--kK~eL~~Ril~ll~~~ 48 (606)
-|..+||+|||.||..-|..=.| -|.|++.||.++-...
T Consensus 103 Dl~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~el~~k~ 143 (154)
T PF10208_consen 103 DLKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEELKPKY 143 (154)
T ss_dssp STTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHCCCCCC
T ss_pred HHhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHHHhhhc
Confidence 36789999999999999999887 6999999999865543
No 33
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=70.20 E-value=2.1 Score=46.50 Aligned_cols=51 Identities=27% Similarity=0.646 Sum_probs=39.8
Q ss_pred ceeccCCCCcCC-CCeeeecCCCCCCcccccc--cccCCCCCCCCCCCCCcccccccccc
Q 007373 113 KVCCPCGSSLET-ESMIKCEDPRCPVWQHMSC--VIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 113 ~~rCiCg~s~~~-~~mI~C~~~~C~~wqH~~C--v~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
..+|.|.....- ..|++|+. |..|.|+.| |+++.+.. +.+..|||..|...
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~--C~~~~~~ec~~v~~~~~e~----p~~~~~~c~~c~~~ 113 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDL--CEDWYHGECWEVGTAEKEA----PKEDPKVCDECKEA 113 (345)
T ss_pred hchhhcccccCchhhhhcccc--ccccccccccccCchhhcC----Cccccccccccchh
Confidence 458888776443 48999999 999999999 99986642 23678999999764
No 34
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=68.60 E-value=3.7 Score=43.08 Aligned_cols=49 Identities=31% Similarity=0.748 Sum_probs=36.2
Q ss_pred Cceec-cCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccc
Q 007373 112 TKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (606)
Q Consensus 112 ~~~rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CR 167 (606)
..-+| +||.+.--+.++-|++ |....||.|...+ |.. |+ .+.|-|.+|-
T Consensus 280 eck~csicgtsenddqllfcdd--cdrgyhmyclspp---m~e-pp-egswsc~KOG 329 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDD--CDRGYHMYCLSPP---MVE-PP-EGSWSCHLCL 329 (336)
T ss_pred ecceeccccCcCCCceeEeecc--cCCceeeEecCCC---cCC-CC-CCchhHHHHH
Confidence 35566 6888776788999999 9999999998754 222 11 3478888883
No 35
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=68.22 E-value=1.6 Score=51.21 Aligned_cols=56 Identities=23% Similarity=0.435 Sum_probs=42.7
Q ss_pred eeceeeecCCCCcccccccccCCCCCccccccH-HHHHHHhcCCCeeeccCCCCCCCCCCee
Q 007373 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPICLRNYSLENII 416 (606)
Q Consensus 356 ~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC~k~~~~~~L~ 416 (606)
..++=-|+||.-.+|.+--+= ..|-|+-||.- ..++.+ +.=+||.|+..+.+.|+.
T Consensus 638 k~yK~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~et----RqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 638 KEYKELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYET----RQRKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHHhceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHH----hcCCCCCCCCCCCccccc
Confidence 346778999999988775443 58999999874 455554 455899999999988864
No 36
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=68.07 E-value=3.1 Score=43.85 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=40.0
Q ss_pred cCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccc-ccccccCCCcee
Q 007373 117 PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCE-ICRLSRADPFWV 176 (606)
Q Consensus 117 iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe-~CRl~r~dPF~~ 176 (606)
+|++...-.+|+-|+. |...+|..|||+..-| -+.|+|. .|+. +..||.+
T Consensus 319 IC~~P~~E~E~~FCD~--CDRG~HT~CVGL~~lP-------~G~WICD~~C~~-~~~~t~R 369 (381)
T KOG1512|consen 319 ICLGPVIESEHLFCDV--CDRGPHTLCVGLQDLP-------RGEWICDMRCRE-ATLNTTR 369 (381)
T ss_pred ccCCcccchheecccc--ccCCCCcccccccccc-------CccchhhhHHHH-hcCCCCh
Confidence 6888877889999999 9999999999997654 3589996 4776 4566654
No 37
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=65.36 E-value=4.8 Score=49.49 Aligned_cols=55 Identities=27% Similarity=0.633 Sum_probs=42.2
Q ss_pred CCCceeccCCCCcC--CCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccccCCC
Q 007373 110 SDTKVCCPCGSSLE--TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRADP 173 (606)
Q Consensus 110 ~~~~~rCiCg~s~~--~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~r~dP 173 (606)
.+....|+|-.--. ....|.|+. |+...|..|||++..| .+.|.|-.|-....-|
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 34467779976543 378999999 9999999999976543 3588999987766555
No 38
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=63.61 E-value=4 Score=47.60 Aligned_cols=47 Identities=26% Similarity=0.743 Sum_probs=35.2
Q ss_pred ceeccCCCCc--CCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccc
Q 007373 113 KVCCPCGSSL--ETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEIC 166 (606)
Q Consensus 113 ~~rCiCg~s~--~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~C 166 (606)
--.|+|-.-- .-.-+|-||...|.|.-|-.||+|-+-| .+.|||--|
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVP-------tGpWfCrKC 54 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVP-------TGPWFCRKC 54 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecC-------CCchhhhhh
Confidence 3578997532 1356899999999999999999998765 246777555
No 39
>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=63.39 E-value=3.3 Score=30.26 Aligned_cols=39 Identities=23% Similarity=0.627 Sum_probs=26.5
Q ss_pred CCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCC
Q 007373 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 406 (606)
|||=+..+..|+....|.|+-|++= +.++.+. ..+||+|
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 5777778888989999999977753 3333333 3799998
No 40
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=62.55 E-value=5.2 Score=30.57 Aligned_cols=39 Identities=21% Similarity=0.504 Sum_probs=21.4
Q ss_pred CCCCcccccc----cccCCCCCccccccHHHHHHHhcCCCeeecc
Q 007373 364 CPMSGSRIKV----AGRFKPCVHMGCFDLDVFVELNQRSRKWQCP 404 (606)
Q Consensus 364 CPls~~ri~~----P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CP 404 (606)
||+++. +.. |..-. |-|.-|.|.-.=|..+....+.+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788877 666 77744 9999999988777766556789998
No 41
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=62.13 E-value=5 Score=32.40 Aligned_cols=36 Identities=17% Similarity=0.475 Sum_probs=24.8
Q ss_pred ccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCe
Q 007373 369 SRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENI 415 (606)
Q Consensus 369 ~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L 415 (606)
.++..|+--.-|.+ |||++-| =-||+|++++.+.+.
T Consensus 19 ~~~~~pCgH~I~~~--~f~~~rY---------ngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 19 KGTVLPCGHLICDN--CFPGERY---------NGCPFCGTPFEFDDP 54 (55)
T ss_pred ccccccccceeecc--ccChhhc---------cCCCCCCCcccCCCC
Confidence 34445544444444 8999987 569999999877653
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=60.95 E-value=1.7 Score=32.48 Aligned_cols=17 Identities=18% Similarity=0.796 Sum_probs=11.3
Q ss_pred HHhcCCCeeeccCCCCC
Q 007373 393 ELNQRSRKWQCPICLRN 409 (606)
Q Consensus 393 ~~n~~~~~W~CPiC~k~ 409 (606)
++.....+|.||+|+..
T Consensus 17 ~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 17 QFDDGGKTWICNFCGTK 33 (40)
T ss_dssp EEETTTTEEEETTT--E
T ss_pred eEcCCCCEEECcCCCCc
Confidence 34456789999999864
No 43
>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=59.90 E-value=2.7 Score=33.19 Aligned_cols=38 Identities=21% Similarity=0.475 Sum_probs=19.5
Q ss_pred HHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHh
Q 007373 388 LDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 388 l~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L 428 (606)
+.-+|..-..... .||+|++++..+.- +.++.++-..+
T Consensus 9 ~~k~i~~l~~~~~-~CPlC~r~l~~e~~--~~li~~~~~~i 46 (54)
T PF04423_consen 9 LKKYIEELKEAKG-CCPLCGRPLDEEHR--QELIKKYKSEI 46 (54)
T ss_dssp HHHHHHHHTT-SE-E-TTT--EE-HHHH--HHHHHHHHHHH
T ss_pred HHHHHHHHhcCCC-cCCCCCCCCCHHHH--HHHHHHHHHHH
Confidence 3445555555555 99999999876654 55555443333
No 44
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=58.51 E-value=11 Score=42.74 Aligned_cols=52 Identities=21% Similarity=0.579 Sum_probs=37.1
Q ss_pred CCCceec-cCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCC--ccccccc
Q 007373 110 SDTKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPE--LFYCEIC 166 (606)
Q Consensus 110 ~~~~~rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~--~fyCe~C 166 (606)
+-..+.| +|..+-....+++|+. |+..+|.+|+..+- .-.|.-.. -|.|..|
T Consensus 541 ~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPL---TR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 541 KAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPL---TRLPKKNKNFGWQCSEC 595 (707)
T ss_pred cccceeeeeeccchhhHHHhhcch--hhceeeccccCCcc---ccCcccccCcceeeccc
Confidence 3345677 7998888888999999 99999999987542 22232222 3578888
No 45
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.37 E-value=1.4 Score=47.49 Aligned_cols=70 Identities=31% Similarity=0.552 Sum_probs=56.8
Q ss_pred eeceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC-CCCCCeeecHHHHHHHHHh
Q 007373 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN-YSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 356 ~s~~isL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~-~~~~~L~ID~y~~~IL~~L 428 (606)
..+.+.+.||+-...|+.-.-...|.|--|||+-+ .+.+..--.||-|.|. ..-..|++|.-|..|+..|
T Consensus 38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 46889999999999999988889999999999754 2334455689999765 4567999999999888765
No 46
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=54.26 E-value=7 Score=29.45 Aligned_cols=42 Identities=24% Similarity=0.411 Sum_probs=24.3
Q ss_pred CCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCC
Q 007373 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 406 (606)
|||=..-++-|+. ..|-|.-|+.--.=+........+.||+|
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 5777777778877 68999988775433332333334999998
No 47
>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=53.57 E-value=7.8 Score=28.22 Aligned_cols=40 Identities=33% Similarity=0.669 Sum_probs=28.0
Q ss_pred CCCCcccccccccCCCCCcccccc-HHHHHHHhcCCCeeeccCC
Q 007373 364 CPMSGSRIKVAGRFKPCVHMGCFD-LDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC 406 (606)
||+=...+..|.+...|.|.-|.+ +..+++. ...-+||+|
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 566667777788889999996665 3333332 566779988
No 48
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=52.04 E-value=7.3 Score=45.87 Aligned_cols=49 Identities=33% Similarity=0.733 Sum_probs=39.6
Q ss_pred Cceec-cCCCC--cCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 112 TKVCC-PCGSS--LETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 112 ~~~rC-iCg~s--~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
..+-| +|... .+..+||-|+. |+.=-|..||||-+-| ...|.|-.|-+.
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 34566 67654 45789999999 9999999999998765 357999999885
No 49
>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=49.78 E-value=6.3 Score=24.67 Aligned_cols=11 Identities=45% Similarity=1.361 Sum_probs=7.2
Q ss_pred eeccCCCCCCC
Q 007373 401 WQCPICLRNYS 411 (606)
Q Consensus 401 W~CPiC~k~~~ 411 (606)
|+||+|++.+.
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 89999997653
No 50
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=48.97 E-value=4.3 Score=51.50 Aligned_cols=52 Identities=23% Similarity=0.541 Sum_probs=38.1
Q ss_pred ceec-cCCCCcCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccccC
Q 007373 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRA 171 (606)
Q Consensus 113 ~~rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~r~ 171 (606)
.++| +|........|+-|+. |..|.|+.|....-. .. -+..|+|+.||..+-
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~--c~~~~h~~C~rp~~~---~~--~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDE--CLSGFHLFCLRPALS---SV--PPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHh--hhhhHHHHhhhhhhc---cC--CcCCccCCccchhhh
Confidence 4556 4655555578999999 999999999865422 11 256899999999763
No 51
>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=47.87 E-value=9.8 Score=29.23 Aligned_cols=43 Identities=30% Similarity=0.618 Sum_probs=25.0
Q ss_pred cCCCCcccccccccCCCCCcc-ccccHHHHHHHhcCCCeeeccCCCCCC
Q 007373 363 RCPMSGSRIKVAGRFKPCVHM-GCFDLDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 363 ~CPls~~ri~~P~Rg~~C~Hl-QCFDl~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
.|++=+.....+ -...|.|+ -|.+=. ..+.. ...+||+|.+++
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C~--~~~~~--~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEECA--ERLLK--RKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHHH--HHHHH--TTSBBTTTTBB-
T ss_pred CCccCCccCCce-EEeCCCChHHHHHHh--HHhcc--cCCCCCcCChhh
Confidence 455555554443 33579998 555532 22222 678999999876
No 52
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.12 E-value=15 Score=29.68 Aligned_cols=32 Identities=22% Similarity=0.638 Sum_probs=27.1
Q ss_pred Cceec-cCCCCcC-CCCeeeecCCCCCCcccccccc
Q 007373 112 TKVCC-PCGSSLE-TESMIKCEDPRCPVWQHMSCVI 145 (606)
Q Consensus 112 ~~~rC-iCg~s~~-~~~mI~C~~~~C~~wqH~~Cv~ 145 (606)
+..+| .||..+. .+..|.|-. |+...|..|+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~--CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPE--CGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCCEEECCC--CCCcccHHHHh
Confidence 45678 4898875 789999999 99999999984
No 53
>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=45.82 E-value=11 Score=36.57 Aligned_cols=46 Identities=28% Similarity=0.223 Sum_probs=24.5
Q ss_pred ccEEEEcCeEeec-ccCCCCCCCCCCCC--CCCCCcccCcCCCccEEEEEE
Q 007373 244 YADLQVNGVPVRA-INRPGSQLLGANGR--DDGPIITPWTKDGINKIVLTG 291 (606)
Q Consensus 244 ~~~I~VNg~~v~~-~~Rp~~~~~g~~gR--~~~piIT~~lk~g~N~I~is~ 291 (606)
..+++|||+.|-. ...|+... ..+| -...+||++|+.|.|.|.+..
T Consensus 15 ~Y~l~vNG~~V~~~~l~P~~t~--y~~~~~Y~tyDVt~~L~~G~N~iav~l 63 (172)
T PF08531_consen 15 RYELYVNGERVGDGPLAPGWTD--YDKRVYYQTYDVTPYLRPGENVIAVWL 63 (172)
T ss_dssp EEEEEETTEEEEEE----------BTTEEEEEEEE-TTT--TTEEEEEEEE
T ss_pred eEEEEECCEEeeCCcccccccc--CCCceEEEEEeChHHhCCCCCEEEEEE
Confidence 3679999999864 22344321 1111 124569999999999988764
No 54
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=45.65 E-value=3 Score=45.28 Aligned_cols=58 Identities=33% Similarity=0.615 Sum_probs=39.6
Q ss_pred CCCceec-cCCCCcCC-CCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007373 110 SDTKVCC-PCGSSLET-ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 110 ~~~~~rC-iCg~s~~~-~~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~ 169 (606)
+-....| .||.+... ..+|.|+. |..|+|..|+.+.......+......|+|+.|.+.
T Consensus 236 ~~~~~~~~~cg~~~~~~~~~~~~~~--~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 236 DYSKLICDPCGLSDANKKFEICCDL--CESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred ccccccccccCcchHHHHHHHHHHH--HHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 3345667 47765444 67898998 99999999999876552222111234999999873
No 55
>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=44.37 E-value=10 Score=27.13 Aligned_cols=12 Identities=33% Similarity=1.032 Sum_probs=9.9
Q ss_pred CeeeccCCCCCC
Q 007373 399 RKWQCPICLRNY 410 (606)
Q Consensus 399 ~~W~CPiC~k~~ 410 (606)
..|.||+|+...
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 789999998643
No 56
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.26 E-value=25 Score=39.07 Aligned_cols=35 Identities=26% Similarity=0.292 Sum_probs=32.1
Q ss_pred hccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccc
Q 007373 13 HFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSD 47 (606)
Q Consensus 13 ~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll~~ 47 (606)
.+..+.||..|..|||+.+|-|++|+.|--++..-
T Consensus 268 ~l~~~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l 302 (397)
T TIGR00599 268 LLTDSQIRKKLSELGLSTNGTRQLLQKRHNEWETL 302 (397)
T ss_pred hcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHH
Confidence 67889999999999999999999999999887764
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.10 E-value=36 Score=32.30 Aligned_cols=70 Identities=13% Similarity=0.330 Sum_probs=39.9
Q ss_pred cCHHHHHhhcccCCCCCCHHHHHHHHHHhhCCCCCCCCCCCCCCcceEeeeceeeecCCCCcccccccccCCCCCccccc
Q 007373 307 RSVQQVLNLIPKESEGEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCF 386 (606)
Q Consensus 307 ~s~e~Ll~~I~~~~~~~~~e~al~rIkr~l~~~~~~~~~d~DdD~eIv~~s~~isL~CPls~~ri~~P~Rg~~C~HlQCF 386 (606)
+..+.+++-|+.+ +..++++++..+.. + .-.....||- |.+. |
T Consensus 67 i~y~~~~~vik~r-----~~~~~~~L~~~l~~---------e--------~~~~~Y~Cp~-------------C~~~--y 109 (147)
T smart00531 67 INYDTLLDVVKYK-----LDKMRKRLEDKLED---------E--------TNNAYYKCPN-------------CQSK--Y 109 (147)
T ss_pred ecHHHHHHHHHHH-----HHHHHHHHHHHHhc---------c--------cCCcEEECcC-------------CCCE--e
Confidence 3667777766542 34455566554421 1 1134678983 5433 5
Q ss_pred cHHHHHHHhcCCCeeeccCCCCCCCCC
Q 007373 387 DLDVFVELNQRSRKWQCPICLRNYSLE 413 (606)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (606)
.....+........+.||.|+..+...
T Consensus 110 ~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 110 TFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred eHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 555555543336679999999887543
No 58
>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=42.90 E-value=64 Score=30.31 Aligned_cols=66 Identities=21% Similarity=0.111 Sum_probs=41.4
Q ss_pred eeEEEEeCHhhHhhhcCCCeeEEEEEEecCCCCcccccCCCccEEEEcCeEeecccCCCCCCCCCCCCCCCCCcccCcCC
Q 007373 203 LEKTFPITRADKDLLSKQEYDVQAWCMLLNDKVPFRMQWPQYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKD 282 (606)
Q Consensus 203 ~~~~F~Lt~~~~~~L~~~~~~lql~C~~l~d~~~~~~~wP~~~~I~VNg~~v~~~~Rp~~~~~g~~gR~~~piIT~~lk~ 282 (606)
.+.+|.|+++. ...++.|....++ ...+|.|||+.|-.. ..+. +.-..+||++|+.
T Consensus 72 Yr~~f~lp~~~------~~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~~~~-------~~~~~dIt~~l~~ 127 (167)
T PF02837_consen 72 YRRTFTLPADW------KGKRVFLRFEGVD----------YAAEVYVNGKLVGSH-EGGY-------TPFEFDITDYLKP 127 (167)
T ss_dssp EEEEEEESGGG------TTSEEEEEESEEE----------SEEEEEETTEEEEEE-ESTT-------S-EEEECGGGSSS
T ss_pred EEEEEEeCchh------cCceEEEEeccce----------EeeEEEeCCeEEeee-CCCc-------CCeEEeChhhccC
Confidence 46778887765 2334444433322 237899999988642 1111 1223459999999
Q ss_pred Cc-cEEEEEEe
Q 007373 283 GI-NKIVLTGC 292 (606)
Q Consensus 283 g~-N~I~is~~ 292 (606)
|. |.|.|...
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 98 99988764
No 59
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=42.11 E-value=16 Score=32.52 Aligned_cols=33 Identities=36% Similarity=0.746 Sum_probs=27.8
Q ss_pred ceec-cCCCCcCCCCeeeecCCCCCCcccccccccC
Q 007373 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIP 147 (606)
Q Consensus 113 ~~rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~ 147 (606)
..+| +|+.+ .|..|+|..++|..++|..|-...
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 4556 79986 688999999999999999997654
No 60
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.68 E-value=13 Score=38.93 Aligned_cols=54 Identities=24% Similarity=0.546 Sum_probs=41.3
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeee-ccCCCCCCCCCCeeec
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQ-CPICLRNYSLENIIID 418 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~-CPiC~k~~~~~~L~ID 418 (606)
+-+|+|-...+..|.+ ..|-|+ |-+.-.+.+ ..+.+.. ||.|.....+..++|+
T Consensus 215 d~kC~lC~e~~~~ps~-t~CgHl--FC~~Cl~~~-~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 215 DYKCFLCLEEPEVPSC-TPCGHL--FCLSCLLIS-WTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred ccceeeeecccCCccc-ccccch--hhHHHHHHH-HHhhccccCchhhhhccchhhhee
Confidence 5689999999999998 589999 545555554 3444555 9999999988887654
No 61
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.65 E-value=11 Score=37.37 Aligned_cols=62 Identities=19% Similarity=0.371 Sum_probs=44.3
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007373 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 361 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L~ 429 (606)
-|.||+-...++-| +...|.|.-|..-..=+.- ....||.|..... +|.-...+..+++.++
T Consensus 13 ~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~----~~~~Cp~cr~~~~--~~~~n~~l~~~~~~~~ 74 (386)
T KOG2177|consen 13 ELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE----GPLSCPVCRPPSR--NLRPNVLLANLVERLR 74 (386)
T ss_pred cccChhhHHHhhcC-ccccccchHhHHHHHHhcC----CCcCCcccCCchh--ccCccHHHHHHHHHHH
Confidence 47899999999999 8888999988876544332 5699999995222 5555555555555443
No 62
>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=41.25 E-value=13 Score=32.27 Aligned_cols=21 Identities=29% Similarity=0.582 Sum_probs=17.4
Q ss_pred ccHHHHHHHhcCCCeeeccCC
Q 007373 386 FDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 386 FDl~~fL~~n~~~~~W~CPiC 406 (606)
-+|..||.+.-+++.|.|||=
T Consensus 44 ~qLr~flk~alkTpvwl~pi~ 64 (92)
T PF02228_consen 44 HQLRNFLKLALKTPVWLNPIN 64 (92)
T ss_dssp HHHHHHHHHHHT-TTSTTTT-
T ss_pred HHHHHHHHHHHcCCeeecccc
Confidence 368999999999999999984
No 63
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.08 E-value=15 Score=35.96 Aligned_cols=21 Identities=19% Similarity=0.498 Sum_probs=17.8
Q ss_pred eeeccCCCCCCCCCCeeecHH
Q 007373 400 KWQCPICLRNYSLENIIIDPY 420 (606)
Q Consensus 400 ~W~CPiC~k~~~~~~L~ID~y 420 (606)
-.+||||+|.+..+++.|--.
T Consensus 138 g~KCPvC~K~V~sDd~e~Hlv 158 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDDAEIHLV 158 (205)
T ss_pred CccCCccccccCCCcceEEEE
Confidence 478999999999999887643
No 64
>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=34.60 E-value=25 Score=23.84 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=15.4
Q ss_pred CCCCcccccc-HHHHHHHhcCCCeeeccCC
Q 007373 378 KPCVHMGCFD-LDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 378 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC 406 (606)
..|.|.-|.. +..|++ .....||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 4699986655 333444 344679987
No 65
>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=33.95 E-value=13 Score=23.60 Aligned_cols=11 Identities=45% Similarity=1.413 Sum_probs=9.0
Q ss_pred eeccCCCCCCC
Q 007373 401 WQCPICLRNYS 411 (606)
Q Consensus 401 W~CPiC~k~~~ 411 (606)
|+||+|++.+.
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 78999998764
No 66
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=33.12 E-value=44 Score=36.83 Aligned_cols=43 Identities=26% Similarity=0.529 Sum_probs=26.5
Q ss_pred CCCCcccccccccC--CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCC
Q 007373 364 CPMSGSRIKVAGRF--KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLE 413 (606)
Q Consensus 364 CPls~~ri~~P~Rg--~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~ 413 (606)
-|+-+..=+.|-|- -+|-|+.| |+.|++.+ =.||||..++-++
T Consensus 303 ~~~~~~~~~~pKrLpCGHilHl~C--LknW~ERq-----QTCPICr~p~ifd 347 (491)
T COG5243 303 EPLPRGLDMTPKRLPCGHILHLHC--LKNWLERQ-----QTCPICRRPVIFD 347 (491)
T ss_pred ccCcccccCCcccccccceeeHHH--HHHHHHhc-----cCCCcccCccccc
Confidence 34443333444442 36777767 78888754 4699999986443
No 67
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.06 E-value=94 Score=32.68 Aligned_cols=112 Identities=16% Similarity=0.291 Sum_probs=60.3
Q ss_pred EEEEEEEEecCHHHHHhhcccCC-CCCCHHHHHHHHHHhhCCCCCCCCCCCCCCc-ceEeeeceeeecCCCCcccccccc
Q 007373 298 CLGVRIVKRRSVQQVLNLIPKES-EGEHFEDALTRVCRCVGGGNAADNADSDSDL-EVVADSIGVNLRCPMSGSRIKVAG 375 (606)
Q Consensus 298 ~~~V~lVk~~s~e~Ll~~I~~~~-~~~~~e~al~rIkr~l~~~~~~~~~d~DdD~-eIv~~s~~isL~CPls~~ri~~P~ 375 (606)
+++..+=+-++-+.|++.|..++ ...++.. ++-+|..+.= ..+.|.+...|. +--.+....-.+||++...|.=--
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks~~pksaSh-IKslKDvveL-klt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~ 125 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKSSLPKSASH-IKSLKDVVEL-KLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKY 125 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcccCCcchhh-hcchhhHhhe-ecccCcccccccCccccccccceeecccccceecceE
Confidence 44555666678888998886542 1222211 1111111100 011221111111 011234577889999999997544
Q ss_pred cC---CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007373 376 RF---KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 376 Rg---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
|+ ..|-|. |...+.=+ ...-.|++|+..+.-+|.+|
T Consensus 126 ~F~~l~~CGcV--~SerAlKe----ikas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 126 RFCALRCCGCV--FSERALKE----IKASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred EEEEEecccee--ccHHHHHH----hhhccccccCCcccccCeEe
Confidence 44 345554 55544333 34678999999999888775
No 68
>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=32.90 E-value=18 Score=28.54 Aligned_cols=12 Identities=33% Similarity=1.176 Sum_probs=9.4
Q ss_pred CCeeeccCCCCC
Q 007373 398 SRKWQCPICLRN 409 (606)
Q Consensus 398 ~~~W~CPiC~k~ 409 (606)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 457999999854
No 69
>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=32.42 E-value=24 Score=26.19 Aligned_cols=25 Identities=28% Similarity=0.664 Sum_probs=13.8
Q ss_pred CCCCcccccc-HHHHHHHhcCCCeeeccCCC
Q 007373 378 KPCVHMGCFD-LDVFVELNQRSRKWQCPICL 407 (606)
Q Consensus 378 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~ 407 (606)
..|.|.-|.+ +..||+.+ ..||+|.
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 3488874443 44555442 3999993
No 70
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.29 E-value=23 Score=35.21 Aligned_cols=48 Identities=19% Similarity=0.528 Sum_probs=31.8
Q ss_pred ecCCCCccccc--ccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCC
Q 007373 362 LRCPMSGSRIK--VAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLEN 414 (606)
Q Consensus 362 L~CPls~~ri~--~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~ 414 (606)
.+||+-+.... .| -+..|-|+-|=- -|. ...+.+-+||+|+|.+.-.+
T Consensus 132 ~~CPiCl~~~sek~~-vsTkCGHvFC~~---Cik-~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVP-VSTKCGHVFCSQ---CIK-DALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhhccc-cccccchhHHHH---HHH-HHHHhCCCCCCcccccchhh
Confidence 68998877763 44 457899995521 111 23456789999999776443
No 71
>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=31.42 E-value=15 Score=25.06 Aligned_cols=9 Identities=56% Similarity=1.586 Sum_probs=8.0
Q ss_pred eccCCCCCC
Q 007373 402 QCPICLRNY 410 (606)
Q Consensus 402 ~CPiC~k~~ 410 (606)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
No 72
>PRK12678 transcription termination factor Rho; Provisional
Probab=31.07 E-value=43 Score=39.33 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=30.4
Q ss_pred HhhccHHHHHHHHHHhCCCCCC--ChHHHHHHHHHhcc
Q 007373 11 LAHFRIKELKDVLTQLGLSKQG--KKQDLVDRILAILS 46 (606)
Q Consensus 11 L~~fRi~ELk~lL~~lglsk~G--kK~eL~~Ril~ll~ 46 (606)
|+..++.|||.|..+||+...+ ||.||+.-|-+--.
T Consensus 23 LsamkL~ELr~lA~~lGI~Gts~mrK~eLI~AI~~~~g 60 (672)
T PRK12678 23 LAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKEARG 60 (672)
T ss_pred cccCcHHHHHHHHHHcCCcccccccHHHHHHHHHHhhc
Confidence 6788999999999999999444 79999998866544
No 73
>PLN03124 poly [ADP-ribose] polymerase; Provisional
Probab=30.71 E-value=35 Score=40.21 Aligned_cols=38 Identities=29% Similarity=0.541 Sum_probs=35.1
Q ss_pred hhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccccc
Q 007373 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQ 49 (606)
Q Consensus 12 ~~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll~~~~ 49 (606)
+.++|.||++-|..=||+-.|.|.+|+.|.-+.+..+.
T Consensus 3 ~~~~v~~l~~~l~~~~~~~~g~k~~l~~rl~~~~~~e~ 40 (643)
T PLN03124 3 NKLKVDELRAALAKRGLDTTGLKAALVRRLDDAIAEDA 40 (643)
T ss_pred ccchhHHHHHHHHhcCCcccccchHHHHHHHhhhhhhh
Confidence 56899999999999999999999999999999988665
No 74
>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=30.70 E-value=20 Score=28.01 Aligned_cols=13 Identities=31% Similarity=0.997 Sum_probs=7.4
Q ss_pred CCCeeeccCCCCC
Q 007373 397 RSRKWQCPICLRN 409 (606)
Q Consensus 397 ~~~~W~CPiC~k~ 409 (606)
-...|.||+|+..
T Consensus 31 Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 31 LPDDWVCPVCGAP 43 (47)
T ss_dssp S-TT-B-TTTSSB
T ss_pred CCCCCcCcCCCCc
Confidence 3457999999854
No 75
>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=30.53 E-value=33 Score=23.05 Aligned_cols=16 Identities=19% Similarity=0.881 Sum_probs=11.8
Q ss_pred hcCCCeeeccCCCCCC
Q 007373 395 NQRSRKWQCPICLRNY 410 (606)
Q Consensus 395 n~~~~~W~CPiC~k~~ 410 (606)
-.....+.||+|++.+
T Consensus 9 H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HSSSSSEEESSSSEEE
T ss_pred cCCCCCCCCCCCcCee
Confidence 3445679999999764
No 76
>PHA02929 N1R/p28-like protein; Provisional
Probab=30.05 E-value=33 Score=35.61 Aligned_cols=44 Identities=20% Similarity=0.612 Sum_probs=28.5
Q ss_pred ecCCCCcccccccc-------cCCCCCcccccc-HHHHHHHhcCCCeeeccCCCCCC
Q 007373 362 LRCPMSGSRIKVAG-------RFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 362 L~CPls~~ri~~P~-------Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
..||+-...+.-+. .-..|.|.-|.+ +..|+.. .=.||+|...+
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-----~~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-----KNTCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-----CCCCCCCCCEe
Confidence 57999888765432 234799976555 2345542 22799998765
No 77
>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=29.76 E-value=58 Score=35.09 Aligned_cols=40 Identities=28% Similarity=0.398 Sum_probs=24.4
Q ss_pred CCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCC----eeecHHH
Q 007373 379 PCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLEN----IIIDPYF 421 (606)
Q Consensus 379 ~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~----L~ID~y~ 421 (606)
.|-|.-|- +-|...-..+.-.||+|++.++..+ +.-|..+
T Consensus 25 ~CGH~~C~---sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D~~v 68 (309)
T TIGR00570 25 VCGHTLCE---SCVDLLFVRGSGSCPECDTPLRKNNFRVQLFEDPTV 68 (309)
T ss_pred CCCCcccH---HHHHHHhcCCCCCCCCCCCccchhhccccccccHHH
Confidence 46776554 2222222334569999999998887 5555554
No 78
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=28.26 E-value=39 Score=32.67 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=19.3
Q ss_pred ccccccccCCCCCCCCCCCCCccccccccccc
Q 007373 139 QHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 139 qH~~Cv~i~~k~~~g~p~~p~~fyCe~CRl~r 170 (606)
+|+.|+.- |+..+|+ +.|+||.|+..+
T Consensus 2 ~H~~CL~P---pl~~~P~--g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRP---PLKEVPE--GDWICPFCEVEK 28 (148)
T ss_pred cccccCCC---CCCCCCC--CCcCCCCCcCCC
Confidence 69999764 3444443 589999999854
No 79
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=27.77 E-value=38 Score=25.41 Aligned_cols=33 Identities=24% Similarity=0.541 Sum_probs=21.7
Q ss_pred cccccCCCCCccccccHHHHHHHhcCCCeeeccCCCC
Q 007373 372 KVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408 (606)
Q Consensus 372 ~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k 408 (606)
..+.+-..|.|+-|-.=..=+. ...-.||+|++
T Consensus 12 ~~~~~l~~CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 12 ERRPRLTSCGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred CCCeEEcccCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 3456678899986644322222 56789999975
No 80
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=27.53 E-value=27 Score=34.01 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=18.3
Q ss_pred CCCCccccccHHHHHHHh-cCCCeeeccCCCC
Q 007373 378 KPCVHMGCFDLDVFVELN-QRSRKWQCPICLR 408 (606)
Q Consensus 378 ~~C~HlQCFDl~~fL~~n-~~~~~W~CPiC~k 408 (606)
..|+|+.|.=... + .....|.|| |+.
T Consensus 106 ~iCtHlGC~~~~~----~~~~~~~~~CP-CHG 132 (177)
T COG0723 106 AICTHLGCTVPWN----NAGAEGGFFCP-CHG 132 (177)
T ss_pred eeccCCCCccCcc----cCCCCCeEEcc-CCC
Confidence 4699999975443 2 344799999 653
No 81
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=27.51 E-value=22 Score=38.65 Aligned_cols=63 Identities=21% Similarity=0.390 Sum_probs=51.1
Q ss_pred eeecCCCCcccccccccCCCCCcccc-ccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHh
Q 007373 360 VNLRCPMSGSRIKVAGRFKPCVHMGC-FDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 360 isL~CPls~~ri~~P~Rg~~C~HlQC-FDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L 428 (606)
-.|||-|-+.=+++|.=.- |.|.-| |-...||.. +=+||.|-..++-.+|+=...+.+|++.+
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~-----~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSY-----KPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhcc-----CCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 3689999988888888765 999876 566777753 45799999999999999888888888654
No 82
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=27.44 E-value=80 Score=26.77 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=23.0
Q ss_pred HHHHHHHhhcCCCCeeEEEEccCCceEec
Q 007373 421 FNRITSKMRNCGEDITELEVKPDGSWRVK 449 (606)
Q Consensus 421 ~~~IL~~L~~~~~dv~eV~v~~DGsW~~~ 449 (606)
..+|++.++..+-+|.+|+++.||.|++.
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~yev~ 59 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGCYEVE 59 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCEEEEE
Confidence 35556666665669999999999999998
No 83
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=27.41 E-value=42 Score=27.64 Aligned_cols=29 Identities=14% Similarity=0.310 Sum_probs=23.6
Q ss_pred CeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007373 399 RKWQCPICLRNYSLENIIIDPYFNRITSK 427 (606)
Q Consensus 399 ~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 427 (606)
|.--||+|++.+.+++-.-.+--.+||+.
T Consensus 7 PH~HC~VCg~aIp~de~~CSe~C~eil~k 35 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQVCSEECGEILNK 35 (64)
T ss_pred CCccccccCCcCCCccchHHHHHHHHHHH
Confidence 45579999999999988887777777753
No 84
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=26.11 E-value=26 Score=37.82 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=26.1
Q ss_pred cccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC
Q 007373 374 AGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 374 P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (606)
|-+-++|.-..|||--+=-+.-+-...|.||.|++.
T Consensus 258 ~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 258 PYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK 293 (415)
T ss_pred cchheeecHHHHHHHhhhHHhhcCcccccCchhccc
Confidence 346688887779886554444556678999999864
No 85
>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=26.08 E-value=38 Score=26.48 Aligned_cols=33 Identities=18% Similarity=0.740 Sum_probs=16.3
Q ss_pred CeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccc
Q 007373 126 SMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165 (606)
Q Consensus 126 ~mI~C~~~~C~~wqH~~Cv~i~~k~~~g~p~~p~~fyCe~ 165 (606)
..|||+. |.+|-... ..+... ...+|+.|||.+
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 4689998 99999876 222210 023577999976
No 86
>PLN00162 transport protein sec23; Provisional
Probab=24.28 E-value=23 Score=42.52 Aligned_cols=33 Identities=21% Similarity=0.744 Sum_probs=20.7
Q ss_pred cccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCC
Q 007373 374 AGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 374 P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
|+|-..|+-. +.-|.+...+.++|.||+|+..-
T Consensus 53 pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N 85 (761)
T PLN00162 53 PLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRN 85 (761)
T ss_pred CCccCCCcCE----ECCceEEecCCCEEEccCCCCCC
Confidence 5665555543 33344445567899999998653
No 87
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=23.87 E-value=50 Score=38.19 Aligned_cols=40 Identities=25% Similarity=0.474 Sum_probs=37.2
Q ss_pred HHHhhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhcccc
Q 007373 9 EKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDD 48 (606)
Q Consensus 9 ~~L~~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll~~~ 48 (606)
.+|..+||.+|+.-|.--.|-..|.|+-||+|+-..|.++
T Consensus 28 rrlseLRViDLraEL~KRnldt~GnKsVLmERLkKal~~E 67 (940)
T KOG4661|consen 28 RRLSELRVIDLRAELEKRNLDTVGNKSVLMERLKKALRAE 67 (940)
T ss_pred chhhheeeeehhhHHhhhcccccCcHHHHHHHHHHHHHhc
Confidence 5789999999999999999999999999999999888764
No 88
>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=23.75 E-value=24 Score=27.74 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=8.3
Q ss_pred eeeccCCCCC
Q 007373 400 KWQCPICLRN 409 (606)
Q Consensus 400 ~W~CPiC~k~ 409 (606)
++.||.|++.
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 5789999984
No 89
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=23.05 E-value=15 Score=42.91 Aligned_cols=40 Identities=28% Similarity=0.612 Sum_probs=29.4
Q ss_pred CCeeeecCCCCCCcccccccccCCCC-CCCCCCCCCccccccccc
Q 007373 125 ESMIKCEDPRCPVWQHMSCVIIPEKP-TEGNPPVPELFYCEICRL 168 (606)
Q Consensus 125 ~~mI~C~~~~C~~wqH~~Cv~i~~k~-~~g~p~~p~~fyCe~CRl 168 (606)
--|+.|.. |.+|+|..|-++.... |+- .+...|-|..||-
T Consensus 161 ~~~~~c~~--c~rwsh~~c~~~sdd~~~q~--~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 161 LPMVCCSI--CQRWSHGGCDGISDDKYMQA--QVDLQYKCSTCRG 201 (694)
T ss_pred hhhHHHHH--hcccccCCCCccchHHHHHH--hhhhhcccceeeh
Confidence 34799999 9999999999886432 221 1224899999993
No 90
>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=22.65 E-value=1e+02 Score=25.54 Aligned_cols=37 Identities=27% Similarity=0.400 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHhhCCCCCCCCCCCCCCcceE---eeeceeeecCCCCcccc
Q 007373 323 EHFEDALTRVCRCVGGGNAADNADSDSDLEVV---ADSIGVNLRCPMSGSRI 371 (606)
Q Consensus 323 ~~~e~al~rIkr~l~~~~~~~~~d~DdD~eIv---~~s~~isL~CPls~~ri 371 (606)
.+++++..|....++ |..++ -....+.++||+-+.-.
T Consensus 3 ~t~~~~~~r~~e~Fp------------~~slvef~g~~~PvtI~CP~HG~~~ 42 (60)
T PF05265_consen 3 MTFESAASRFEEKFP------------HYSLVEFSGVATPVTIRCPKHGNFT 42 (60)
T ss_pred eeHHHHHHHHHHHCC------------CceEEEEeCCCCceEEECCCCCcEE
Confidence 467888888776664 12332 23467888999876543
No 91
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=22.17 E-value=1.1e+02 Score=33.40 Aligned_cols=34 Identities=32% Similarity=0.490 Sum_probs=28.4
Q ss_pred hccHHHHHHHHHHhCCCCCCChHHHHHHHHHhcc
Q 007373 13 HFRIKELKDVLTQLGLSKQGKKQDLVDRILAILS 46 (606)
Q Consensus 13 ~fRi~ELk~lL~~lglsk~GkK~eL~~Ril~ll~ 46 (606)
.+-=.++|.=|..+||+.+|.||.|+-|--++.-
T Consensus 250 lls~s~ik~KLse~GLst~G~kQ~likRh~~~v~ 283 (442)
T KOG0287|consen 250 LLSDSDIKKKLSEHGLSTQGNKQQLIKRHQEFVH 283 (442)
T ss_pred hccHHHHHHHHHHcCCCCcchHHHHHHHHHHHHH
Confidence 3444688999999999999999999999776654
No 92
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.02 E-value=21 Score=23.98 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=11.6
Q ss_pred eeccCCCCCCCCCCe
Q 007373 401 WQCPICLRNYSLENI 415 (606)
Q Consensus 401 W~CPiC~k~~~~~~L 415 (606)
-.||+|++.+.++.|
T Consensus 3 ~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 3 VPCPICGRKFNPDRL 17 (25)
T ss_pred CcCCCCCCEECHHHH
Confidence 579999998866544
No 93
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=21.70 E-value=61 Score=27.57 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=26.3
Q ss_pred eec-cCCCCcCCCCeeeecCCCCCCcccccccccC
Q 007373 114 VCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIP 147 (606)
Q Consensus 114 ~rC-iCg~s~~~~~mI~C~~~~C~~wqH~~Cv~i~ 147 (606)
..| +|+.. .|-.|+|..+.|...+|..|-...
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 455 58864 579999999999999999997654
No 94
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.01 E-value=1e+02 Score=31.89 Aligned_cols=58 Identities=17% Similarity=0.362 Sum_probs=40.5
Q ss_pred cccccCCCCCccccccHHHHHHHhcC---------CCeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007373 372 KVAGRFKPCVHMGCFDLDVFVELNQR---------SRKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 372 ~~P~Rg~~C~HlQCFDl~~fL~~n~~---------~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~L~ 429 (606)
.+|--...|.-+-|+||-.|==+|++ ..-++||-|+..+-+--=.+......+.+.|+
T Consensus 57 ~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~ 123 (299)
T KOG3970|consen 57 NTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLK 123 (299)
T ss_pred CCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHH
Confidence 55666778888889998888766654 24699999998776555455665555544454
No 95
>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=20.83 E-value=78 Score=35.70 Aligned_cols=61 Identities=30% Similarity=0.624 Sum_probs=37.7
Q ss_pred eeccCCCC---cCCCCeeeecCCCCCCcccccccccCCC-----CCCCC-CCCCCccccccccc-ccCCCcee
Q 007373 114 VCCPCGSS---LETESMIKCEDPRCPVWQHMSCVIIPEK-----PTEGN-PPVPELFYCEICRL-SRADPFWV 176 (606)
Q Consensus 114 ~rCiCg~s---~~~~~mI~C~~~~C~~wqH~~Cv~i~~k-----~~~g~-p~~p~~fyCe~CRl-~r~dPF~~ 176 (606)
..|+|..- ..+-.+|.|+. |+.|-|..|-.-... ...|- ..+...|||-.|-- ..+..|++
T Consensus 130 ~C~iC~kfD~~~n~~~Wi~Cd~--CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk 200 (446)
T PF07227_consen 130 MCCICSKFDDNKNTCSWIGCDV--CGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVK 200 (446)
T ss_pred CccccCCcccCCCCeeEEeccC--CCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhHHHHHH
Confidence 33456552 23567999999 999999999754321 12222 23456899999953 33344443
No 96
>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=20.05 E-value=54 Score=22.65 Aligned_cols=10 Identities=40% Similarity=1.428 Sum_probs=8.2
Q ss_pred CCeeeccCCC
Q 007373 398 SRKWQCPICL 407 (606)
Q Consensus 398 ~~~W~CPiC~ 407 (606)
...|.|+.|.
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 4579999996
Done!