Query 006644
Match_columns 637
No_of_seqs 241 out of 514
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 12:24:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006644.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006644hhsearch_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-41 6.4E-46 383.8 32.4 366 14-439 1-396 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 2.4E-21 5.2E-26 152.4 2.3 50 345-394 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.7 3.6E-17 7.7E-22 155.1 8.9 127 156-291 9-144 (144)
4 PF11789 zf-Nse: Zinc-finger o 98.5 6E-08 1.3E-12 78.7 1.5 52 337-390 2-53 (57)
5 PF02037 SAP: SAP domain; Int 97.9 1.5E-05 3.2E-10 58.5 3.5 35 13-47 1-35 (35)
6 smart00513 SAP Putative DNA-bi 97.7 4.5E-05 9.7E-10 55.8 4.0 34 14-47 2-35 (35)
7 KOG2979 Protein involved in DN 97.2 0.00017 3.8E-09 74.2 2.2 73 337-411 167-244 (262)
8 smart00504 Ubox Modified RING 97.2 0.0006 1.3E-08 55.0 4.9 59 347-410 2-60 (63)
9 KOG1973 Chromatin remodeling p 96.8 0.00066 1.4E-08 71.3 2.1 52 96-155 216-268 (274)
10 PF00628 PHD: PHD-finger; Int 96.5 0.00098 2.1E-08 52.0 0.8 48 101-153 1-49 (51)
11 PF04564 U-box: U-box domain; 96.0 0.0074 1.6E-07 51.1 3.8 63 346-412 4-66 (73)
12 COG5034 TNG2 Chromatin remodel 95.7 0.0054 1.2E-07 63.3 1.9 49 98-154 220-269 (271)
13 smart00249 PHD PHD zinc finger 94.8 0.03 6.4E-07 41.6 3.2 44 103-152 4-47 (47)
14 COG5627 MMS21 DNA repair prote 93.5 0.035 7.5E-07 56.9 1.5 70 337-408 180-251 (275)
15 COG5222 Uncharacterized conser 92.1 0.14 3E-06 54.2 3.7 61 342-405 270-331 (427)
16 PLN03208 E3 ubiquitin-protein 90.6 0.23 5E-06 49.9 3.5 55 346-401 18-84 (193)
17 PF13831 PHD_2: PHD-finger; PD 89.9 0.075 1.6E-06 39.4 -0.5 35 111-153 2-36 (36)
18 KOG2164 Predicted E3 ubiquitin 89.5 0.21 4.5E-06 56.4 2.3 56 346-402 186-242 (513)
19 PF14835 zf-RING_6: zf-RING of 89.4 0.39 8.4E-06 40.3 3.3 58 346-409 7-64 (65)
20 KOG1844 PHD Zn-finger proteins 88.1 0.27 5.8E-06 55.6 2.0 51 97-155 84-135 (508)
21 PF04641 Rtf2: Rtf2 RING-finge 87.5 0.53 1.2E-05 49.2 3.6 55 343-402 110-167 (260)
22 KOG4323 Polycomb-like PHD Zn-f 86.4 0.3 6.5E-06 54.9 1.1 54 98-154 170-223 (464)
23 TIGR00599 rad18 DNA repair pro 83.9 1.3 2.8E-05 49.4 4.5 66 343-414 23-89 (397)
24 cd00162 RING RING-finger (Real 80.1 1.5 3.2E-05 31.7 2.4 42 349-394 2-44 (45)
25 PF07498 Rho_N: Rho terminatio 79.0 2.5 5.5E-05 32.4 3.3 34 13-46 2-37 (43)
26 PF12949 HeH: HeH/LEM domain; 76.6 2.2 4.8E-05 31.7 2.3 28 14-41 2-31 (35)
27 KOG0311 Predicted E3 ubiquitin 68.9 0.57 1.2E-05 50.9 -3.3 70 341-413 38-108 (381)
28 PF13923 zf-C3HC4_2: Zinc fing 68.1 3.4 7.4E-05 30.5 1.7 39 349-391 1-39 (39)
29 PF14447 Prok-RING_4: Prokaryo 63.2 5.2 0.00011 32.7 1.9 36 353-399 18-53 (55)
30 KOG0978 E3 ubiquitin ligase in 60.9 4.1 8.8E-05 48.3 1.3 56 341-401 638-694 (698)
31 PF00097 zf-C3HC4: Zinc finger 56.4 7.6 0.00016 28.5 1.7 41 349-391 1-41 (41)
32 PF13445 zf-RING_UBOX: RING-ty 56.0 6.5 0.00014 30.3 1.3 39 349-389 1-43 (43)
33 KOG4259 Putative nucleic acid- 54.1 14 0.0003 38.3 3.6 36 14-49 7-42 (260)
34 KOG0957 PHD finger protein [Ge 53.7 8.4 0.00018 43.9 2.2 60 98-161 119-185 (707)
35 PF04810 zf-Sec23_Sec24: Sec23 53.3 1.9 4E-05 32.6 -2.0 16 379-394 18-33 (40)
36 KOG2169 Zn-finger transcriptio 52.0 12 0.00027 44.2 3.4 252 340-591 11-301 (636)
37 PF04423 Rad50_zn_hook: Rad50 51.1 4.5 9.7E-05 32.2 -0.3 34 374-410 10-43 (54)
38 PF10208 Armet: Degradation ar 49.4 14 0.00029 36.2 2.6 34 13-46 104-139 (154)
39 PF13920 zf-C3HC4_3: Zinc fing 49.2 7.9 0.00017 30.0 0.8 43 348-395 4-47 (50)
40 PF02837 Glyco_hydro_2_N: Glyc 48.3 56 0.0012 30.9 6.7 66 189-278 72-138 (167)
41 PF15227 zf-C3HC4_4: zinc fing 47.2 7.5 0.00016 29.6 0.4 42 349-391 1-42 (42)
42 PF08531 Bac_rhamnosid_N: Alph 45.5 13 0.00028 36.4 1.9 46 230-277 15-63 (172)
43 PF13894 zf-C2H2_4: C2H2-type 43.4 7.7 0.00017 24.5 -0.0 11 386-396 1-11 (24)
44 cd00350 rubredoxin_like Rubred 43.2 12 0.00026 27.0 0.9 11 384-394 16-26 (33)
45 KOG0801 Predicted E3 ubiquitin 42.3 13 0.00028 36.7 1.3 20 385-404 138-157 (205)
46 COG5574 PEX10 RING-finger-cont 41.2 14 0.00031 39.0 1.5 56 345-403 214-269 (271)
47 KOG2177 Predicted E3 ubiquitin 40.5 12 0.00025 37.3 0.7 62 346-414 13-74 (386)
48 PF02228 Gag_p19: Major core p 34.4 23 0.00049 31.1 1.4 40 372-413 45-87 (92)
49 smart00184 RING Ring finger. E 33.7 26 0.00056 24.0 1.4 25 363-391 14-39 (39)
50 KOG0957 PHD finger protein [Ge 32.9 24 0.00052 40.4 1.7 54 94-152 539-595 (707)
51 KOG3113 Uncharacterized conser 32.8 98 0.0021 32.9 5.9 112 284-402 48-164 (293)
52 COG5243 HRD1 HRD ubiquitin lig 32.7 46 0.00099 37.0 3.7 41 350-397 304-346 (491)
53 COG0723 QcrA Rieske Fe-S prote 32.5 17 0.00038 35.6 0.5 26 363-392 106-132 (177)
54 smart00531 TFIIE Transcription 32.3 51 0.0011 31.6 3.6 39 344-397 97-135 (147)
55 cd00730 rubredoxin Rubredoxin; 32.2 22 0.00048 28.4 0.9 12 383-394 32-43 (50)
56 KOG0320 Predicted E3 ubiquitin 32.1 28 0.00061 35.0 1.8 49 347-399 132-181 (187)
57 PF13639 zf-RING_2: Ring finge 32.0 25 0.00053 26.4 1.1 25 363-392 19-44 (44)
58 TIGR00570 cdk7 CDK-activating 32.0 56 0.0012 35.5 4.2 40 364-406 25-68 (309)
59 KOG0825 PHD Zn-finger protein 31.9 24 0.00051 42.5 1.5 52 98-156 214-267 (1134)
60 PF13670 PepSY_2: Peptidase pr 29.9 72 0.0016 27.3 3.8 32 406-437 31-62 (83)
61 PF00301 Rubredoxin: Rubredoxi 29.0 23 0.0005 27.9 0.6 13 382-394 31-43 (47)
62 TIGR00599 rad18 DNA repair pro 28.6 93 0.002 35.0 5.3 49 14-62 267-325 (397)
63 KOG3970 Predicted E3 ubiquitin 28.5 78 0.0017 33.0 4.3 58 357-414 57-123 (299)
64 smart00734 ZnF_Rad18 Rad18-lik 28.2 19 0.00042 24.8 -0.0 9 387-395 3-11 (26)
65 PF00096 zf-C2H2: Zinc finger, 26.8 17 0.00036 23.4 -0.5 11 386-396 1-11 (23)
66 COG5533 UBP5 Ubiquitin C-termi 26.1 25 0.00054 38.3 0.3 37 359-395 258-294 (415)
67 PHA02929 N1R/p28-like protein; 25.1 69 0.0015 33.5 3.4 44 347-395 175-226 (238)
68 PF14634 zf-RING_5: zinc-RING 24.2 47 0.001 25.1 1.5 41 349-393 2-44 (44)
69 PF05265 DUF723: Protein of un 24.0 1.2E+02 0.0026 25.4 3.8 36 309-355 3-41 (60)
70 PF05605 zf-Di19: Drought indu 23.3 27 0.00058 27.7 -0.0 11 385-395 2-12 (54)
71 PF13465 zf-H2C2_2: Zinc-finge 22.6 39 0.00084 23.0 0.7 16 380-395 9-24 (26)
72 PLN00162 transport protein sec 22.4 23 0.0005 42.8 -0.8 34 358-395 52-85 (761)
73 KOG0287 Postreplication repair 21.7 1.3E+02 0.0029 33.2 4.7 46 16-61 251-306 (442)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=3e-41 Score=383.77 Aligned_cols=366 Identities=21% Similarity=0.374 Sum_probs=263.2
Q ss_pred hhcChHHHHHHH-HHcCCCCCC--ChHHHHHHHHHhcCchh---HHHHHHHHHHH-hhc--ccchhhhhccCCCCccccc
Q 006644 14 VNFRMKELKDVL-TKLGLPKQG--KKQDLVDRIFHQLSDEG---VARIIDDTYRK-MQI--SEAADLAIMGQSGLDICNV 84 (637)
Q Consensus 14 ~sFRv~ELq~lL-~~lg~~KsG--rK~eL~~R~L~lL~~~~---v~~kI~elYr~-~~~--~~~~~~a~~~~~~~~~~~~ 84 (637)
|++|++|||.++ ++.++++.| +|++|+.|+|.++..+| ++++|+|+|++ +.+ ..+.++....
T Consensus 1 m~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~--------- 71 (636)
T KOG2169|consen 1 MSLRVSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVK--------- 71 (636)
T ss_pred CCcccccccccchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccc---------
Confidence 589999999999 999999999 99999999999999998 79999999985 322 2222221111
Q ss_pred cccccccc-ccCCCCcccccCCCCCCCCCceeecCccccccccccccccCCCCcccc--cCCCCcccccccccccCCchh
Q 006644 85 KVEMEAED-SLNLGGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEI--RLLPPLFFCETCRIKRADPFW 161 (637)
Q Consensus 85 ~~~~~~~~-~~~~~~~~rC~C~ssl~~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~--p~~p~~f~C~~CRL~~~dPF~ 161 (637)
.+..... .+. .. |....|..-...+.-.+.+- +.++++ ++ +..|||
T Consensus 72 -~~~~~~~~~~~----------------~~-------~~~~~~~~~~~~~~~~l~g~~~~~~~~~------~~-~~~~~y 120 (636)
T KOG2169|consen 72 -LHPNVVPPFYP----------------LL-------WQLLRHPTQQPVTPSSLLGPPLPFHPDV------KL-KKLPFY 120 (636)
T ss_pred -cCCcccCcccc----------------ch-------hcccccCCCCCCCcccccCCCCcCCCcc------cc-cCCchh
Confidence 0000000 000 00 11111111000111000110 234444 44 469999
Q ss_pred HhhhhhcCceeeeeccccCCCCCCCceEEEEEEeCHhhHHhhcCC-C------ceEEEEEEecCCCccccccCCCceEEE
Q 006644 162 ITVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQNT-E------YDVQAWCILLNDKVSFRMQWPLHAELQ 234 (637)
Q Consensus 162 ~~i~~lL~Pv~L~~s~i~~~g~~~~Qs~~~~F~Lt~~q~~~L~~~-~------~~lqv~Ci~l~d~~~~~~~wP~~~~I~ 234 (637)
+++..+++|+.+.++.. ..++...+.|.|++++...+... + ..-.+ |.. ....+++.+||.++.++
T Consensus 121 ~~l~~~~~p~~~~~~~~-----~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~-~~s~p~e~~~p~~~~~~ 193 (636)
T KOG2169|consen 121 DVLSELIKPHVLHSSNS-----PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLM-ETSCPQEDHFPPNVQVK 193 (636)
T ss_pred eecccccCceeecCcCC-----CCcccccchhhcchhhhhhcccccccccccccccce-eec-cccCccccccCceeEEE
Confidence 99999999998876532 35567788999999998766431 1 11111 554 34567889999999999
Q ss_pred ECCeEeeecCCCCccc---C-CCCCCCCCCc-ccc--ccCCc-ccEEEEEEe--ccceEEEEEEEEeecCHHHHHHhccc
Q 006644 235 VNGLLVRTVNRPGTQL---L-GSNGRDDGAL-ITL--YIGEG-VNQISLSGC--DIRNFCFGVRLVKRQTVAQVLSLVPK 304 (637)
Q Consensus 235 VNg~~v~~~~RP~~~~---~-g~~gR~~~p~-IT~--~lk~g-~N~I~Is~~--d~~~y~~~V~lVk~~t~e~Ll~~I~~ 304 (637)
||+..+.... +... . -..+|...|. ||. ++..- .|.+.+.|. .++.|.+++|+|+.++.++||++++.
T Consensus 194 vn~~~~~l~~--~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~~llq~~~~ 271 (636)
T KOG2169|consen 194 VNNSPCQLPF--GYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSKDLLQRLKQ 271 (636)
T ss_pred ecCCcceeec--cccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHHHHHHHHhc
Confidence 9999888631 2211 1 1235666666 998 44433 377777664 57899999999999999999999986
Q ss_pred cCC-CCcHHHHHHHHHHhhCCccCCCCCCCCCcceeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccC
Q 006644 305 ETA-GEVFEDALTRVRRCFGGVATGNEDGDSDLEIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRT 383 (637)
Q Consensus 305 ~~~-~~~~edal~rIkr~l~~~~~~~~dsDdD~EIv~~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~ 383 (637)
..+ ...++.+.+.+++.+ ..+.|.||+++++.|||.|||+++||++|+|+..|+|+||||+.+||+||+++
T Consensus 272 ~~~~~~~~~~s~~~~~~~l--------~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~ 343 (636)
T KOG2169|consen 272 NGKINRNLSQSDALIKKKL--------TAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQK 343 (636)
T ss_pred cCCccCchhHhHHHhhccc--------ccCCcccceeccceeEecCCcccceeecCCcccccccceecchhhhHHhccCC
Confidence 432 223355666666433 34566689999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCCCCCCeeecHHHHHHHHHHhcCCCCccEEEEccCCceEEeccCCC
Q 006644 384 RKWQCPICMKNYSLEDLIIDPYFHRITTMMRNFADDLTEIEVKHDGSWRVKCKGEN 439 (637)
Q Consensus 384 ~~W~CPiC~k~~~~~dL~ID~y~~~IL~~l~~~~~dv~eV~v~~DGsW~~~~~~e~ 439 (637)
++|+||||++.+.+++|+||+||..||. +|..+++||++..||+|++...+.+
T Consensus 344 pTW~CPVC~~~~~~e~l~iD~~~~~iL~---~~~~~~~ev~~~~dGsw~pi~~~~~ 396 (636)
T KOG2169|consen 344 PTWRCPVCQKAAPFEGLIIDGYFLNILQ---SCQANVEEVEVSEDGSWKPIPEEAE 396 (636)
T ss_pred CeeeCccCCccccccchhhhHHHHHHHh---hccCCCcceEecCCCceecCccccc
Confidence 9999999999999999999999999974 5566799999999999999987655
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=99.82 E-value=2.4e-21 Score=152.43 Aligned_cols=50 Identities=62% Similarity=1.131 Sum_probs=36.6
Q ss_pred EeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCC
Q 006644 345 VNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKN 394 (637)
Q Consensus 345 vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 394 (637)
|||+||||++||++|+||+.|+|+|||||++||+++++++.|+||+|+++
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=99.70 E-value=3.6e-17 Score=155.14 Aligned_cols=127 Identities=25% Similarity=0.420 Sum_probs=83.0
Q ss_pred cCCchhHhhhhhcCceeeeeccccCCCCCCCceEEEEEEeCHhhHHhhcC--CCceEEEEEEecC---CCccccccCCCc
Q 006644 156 RADPFWITVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQN--TEYDVQAWCILLN---DKVSFRMQWPLH 230 (637)
Q Consensus 156 ~~dPF~~~i~~lL~Pv~L~~s~i~~~g~~~~Qs~~~~F~Lt~~q~~~L~~--~~~~lqv~Ci~l~---d~~~~~~~wP~~ 230 (637)
+.+|||+++ ++|.|+.+.+.. .+..++..+.|.|+++|+++|++ +.++|+|||...+ ....++++||.+
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 479999988 788887776532 12456788999999999999987 6799999999843 345788999999
Q ss_pred eEEEECCeEeeecCCCCcccCCCCCCCCCCccccccCCc---ccEEEEEEe-ccceEEEEEEEEe
Q 006644 231 AELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGEG---VNQISLSGC-DIRNFCFGVRLVK 291 (637)
Q Consensus 231 ~~I~VNg~~v~~~~RP~~~~~g~~gR~~~p~IT~~lk~g---~N~I~Is~~-d~~~y~~~V~lVk 291 (637)
++|+|||+.|++..| .+++++|...|++||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 83 ~evkvN~~~v~~~~~---glknKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 83 CEVKVNGKQVKLNNR---GLKNKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEEETTEE--S--S---S-TTS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred eEEEEeCEEcccCcc---CCCCCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 999999999998655 345667777788899999875 899999997 6789999999997
No 4
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.45 E-value=6e-08 Score=78.67 Aligned_cols=52 Identities=27% Similarity=0.585 Sum_probs=37.1
Q ss_pred ceeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCC
Q 006644 337 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI 390 (637)
Q Consensus 337 EIv~~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi 390 (637)
||+.+..+++++||||+..|+-|+++..|.|. ||-++.+++-.+...-+||+
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 35566789999999999999999999999996 99999999998888999999
No 5
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=97.85 E-value=1.5e-05 Score=58.48 Aligned_cols=35 Identities=37% Similarity=0.647 Sum_probs=31.0
Q ss_pred HhhcChHHHHHHHHHcCCCCCCChHHHHHHHHHhc
Q 006644 13 LVNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQL 47 (637)
Q Consensus 13 l~sFRv~ELq~lL~~lg~~KsGrK~eL~~R~L~lL 47 (637)
+..++|+|||.+|...|++.+|+|+||++|+.+.|
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 46789999999999999999999999999998753
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.71 E-value=4.5e-05 Score=55.80 Aligned_cols=34 Identities=44% Similarity=0.740 Sum_probs=31.5
Q ss_pred hhcChHHHHHHHHHcCCCCCCChHHHHHHHHHhc
Q 006644 14 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQL 47 (637)
Q Consensus 14 ~sFRv~ELq~lL~~lg~~KsGrK~eL~~R~L~lL 47 (637)
++++++||+..|...|++.+|+|+||++|+...+
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 5789999999999999999999999999998764
No 7
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=97.19 E-value=0.00017 Score=74.20 Aligned_cols=73 Identities=22% Similarity=0.374 Sum_probs=58.1
Q ss_pred ceeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCC--CCCCCCCC--Ceeec-HHHHHHHH
Q 006644 337 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLE--DLIID-PYFHRITT 411 (637)
Q Consensus 337 EIv~~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~--dL~ID-~y~~~IL~ 411 (637)
++...+..+|++||+|+..|..|++++.|.|+ ||-.+.+++-....+-+||+ |...+... .|.-| .+..+|.+
T Consensus 167 e~~i~~e~fs~rdPis~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr~ 244 (262)
T KOG2979|consen 167 EELIGQEVFSNRDPISKKPIVNPVISKKCGHV--YDRDSIMQILCDEITIRCPVLGCENPYYIQPGHLDEDKELQQKIRQ 244 (262)
T ss_pred HHHhhhhhhcccCchhhhhhhchhhhcCcCcc--hhhhhHHHHhccCceeecccccCCccccccccccCchHHHHHHHHH
Confidence 45567789999999999999999999999998 99999999888888999999 77444433 44445 45555543
No 8
>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=97.19 E-value=0.0006 Score=55.03 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=50.4
Q ss_pred ecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeeecHHHHHHH
Q 006644 347 LRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRIT 410 (637)
Q Consensus 347 L~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~IL 410 (637)
|.|||++..|+.|+.. .|-|. |+.+.+.++-++ .-.||+|++.+..++|+-+..+.+.+
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 6899999999999986 56676 999988887765 46899999999999999998876654
No 9
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=96.76 E-value=0.00066 Score=71.34 Aligned_cols=52 Identities=25% Similarity=0.667 Sum_probs=43.4
Q ss_pred CCCcccccCCCCCCCCCceeecCcccc-ccccccccccCCCCcccccCCCCcccccccccc
Q 006644 96 LGGKIFCPCGTSLPSESKIQCVDPRCL-VQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 155 (637)
Q Consensus 96 ~~~~~rC~C~ssl~~~~~iqC~~~~C~-~~qH~~C~~~~~kp~~~~p~~p~~f~C~~CRL~ 155 (637)
+....+|+|. ....+.||.|.++.|. .|+|..||++-.+| .+.+||+.|+-.
T Consensus 216 ~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 216 PDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAE 268 (274)
T ss_pred CCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhh
Confidence 3457789999 5567899999999999 89999999997664 456999999854
No 10
>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=96.47 E-value=0.00098 Score=51.98 Aligned_cols=48 Identities=38% Similarity=0.706 Sum_probs=37.8
Q ss_pred cc-cCCCCCCCCCceeecCccccccccccccccCCCCcccccCCCCcccccccc
Q 006644 101 FC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 153 (637)
Q Consensus 101 rC-~C~ssl~~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~~p~~f~C~~CR 153 (637)
+| +|+.....+.||+|.. |+.|.|..|+.++.+..+. ....|+|+.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCc
Confidence 46 8888777889999998 9999999999987642211 22389999986
No 11
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.01 E-value=0.0074 Score=51.06 Aligned_cols=63 Identities=17% Similarity=0.254 Sum_probs=48.2
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeeecHHHHHHHHH
Q 006644 346 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTM 412 (637)
Q Consensus 346 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~IL~~ 412 (637)
.|.||||+..|+-|+....| |. ||-.+.....++ ..-.||+|++.+...+|+-+.-+...++.
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G-~t--yer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~ 66 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSG-HT--YERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEE 66 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTS-EE--EEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHH
T ss_pred ccCCcCcCcHhhCceeCCcC-CE--EcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHH
Confidence 37899999999999998777 76 999988876666 56789999999999999999888877654
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=95.66 E-value=0.0054 Score=63.30 Aligned_cols=49 Identities=22% Similarity=0.650 Sum_probs=40.0
Q ss_pred CcccccCCCCCCCCCceeecCccccc-cccccccccCCCCcccccCCCCccccccccc
Q 006644 98 GKIFCPCGTSLPSESKIQCVDPRCLV-QQHISCVIIPEKPMEEIRLLPPLFFCETCRI 154 (637)
Q Consensus 98 ~~~rC~C~ssl~~~~~iqC~~~~C~~-~qH~~C~~~~~kp~~~~p~~p~~f~C~~CRL 154 (637)
-..+|+|.+.. .+.||-|.++.|.. |+|..|+++...| ...+||+.|+-
T Consensus 220 e~lYCfCqqvS-yGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCFCQQVS-YGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKK 269 (271)
T ss_pred ceeEEEecccc-cccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHh
Confidence 35689997643 47899999999998 9999999997643 46899999984
No 13
>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 COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=93.47 E-value=0.035 Score=56.92 Aligned_cols=70 Identities=16% Similarity=0.293 Sum_probs=58.2
Q ss_pred ceeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCC--CCCCCCCCCeeecHHHHH
Q 006644 337 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLEDLIIDPYFHR 408 (637)
Q Consensus 337 EIv~~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~dL~ID~y~~~ 408 (637)
+|...+-.++++|||+...+..|.-+..|.|. ||.+.....-+--++--||. |........++=|..+.+
T Consensus 180 ~i~I~~~~~~nrCpitl~p~~~pils~kcnh~--~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~IlE~ 251 (275)
T COG5627 180 KILIHQELLSNRCPITLNPDFYPILSSKCNHK--PEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHILEK 251 (275)
T ss_pred hhhhhhhhhcccCCcccCcchhHHHHhhhccc--ccHHHHHHHhcCCceeecchhhcchheeccchhhhHHHHH
Confidence 35556678999999999999999999999998 99988887777778889997 988877777776666544
No 15
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.06 E-value=0.14 Score=54.20 Aligned_cols=61 Identities=25% Similarity=0.445 Sum_probs=44.3
Q ss_pred ceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCC-CCCCCCCeeecHH
Q 006644 342 SIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICM-KNYSLEDLIIDPY 405 (637)
Q Consensus 342 s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~-k~~~~~dL~ID~y 405 (637)
.-.|+|+||+....++.|+|..-|.|.-|=. -|+..---.-++||.|. +.+-++.|.-|.-
T Consensus 270 ~~~i~LkCplc~~Llrnp~kT~cC~~~fc~e---ci~~al~dsDf~CpnC~rkdvlld~l~pD~d 331 (427)
T COG5222 270 PPNISLKCPLCHCLLRNPMKTPCCGHTFCDE---CIGTALLDSDFKCPNCSRKDVLLDGLTPDID 331 (427)
T ss_pred CCCccccCcchhhhhhCcccCccccchHHHH---HHhhhhhhccccCCCcccccchhhccCccHH
Confidence 3468899999999999999999999985532 23322334569999996 4555666666644
No 16
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=90.65 E-value=0.23 Score=49.94 Aligned_cols=55 Identities=18% Similarity=0.436 Sum_probs=41.9
Q ss_pred eecCCCCccccccccCCCCcCcccccCH-HHHHHHH-----------ccCCccccCCCCCCCCCCCee
Q 006644 346 NLRCPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELN-----------QRTRKWQCPICMKNYSLEDLI 401 (637)
Q Consensus 346 sL~CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n-----------~~~~~W~CPiC~k~~~~~dL~ 401 (637)
.+.|||-...++.|+-. .|.|+-|..- ..|+... ......+||+|...+...+|+
T Consensus 18 ~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 18 DFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred ccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 58899999999999884 7999988864 4466532 134568999999998766554
No 17
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=89.86 E-value=0.075 Score=39.44 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=18.8
Q ss_pred CCceeecCccccccccccccccCCCCcccccCCCCcccccccc
Q 006644 111 ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 153 (637)
Q Consensus 111 ~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~~p~~f~C~~CR 153 (637)
..+|+|.. |.+..|.+||++...+ ..+.++|..|+
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 46899998 9999999999986542 23348998875
No 18
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.51 E-value=0.21 Score=56.40 Aligned_cols=56 Identities=25% Similarity=0.497 Sum_probs=48.2
Q ss_pred eecCCCCccccccccCCCCcCccccc-CHHHHHHHHccCCccccCCCCCCCCCCCeee
Q 006644 346 NLRCPMSGSRIRVAGRFKPCVHTGCF-DLETFVELNQRTRKWQCPICMKNYSLEDLII 402 (637)
Q Consensus 346 sL~CPls~~ri~~P~Rg~~C~HlQCF-Dl~~fL~~n~~~~~W~CPiC~k~~~~~dL~I 402 (637)
.+.|||-+-.-.+|+|.. |-|+-|| -+-.|+........-.||+|...+++.+|.-
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 889999999999999999 9999999 5778888775556668999998888877655
No 19
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=89.44 E-value=0.39 Score=40.28 Aligned_cols=58 Identities=19% Similarity=0.380 Sum_probs=26.3
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeeecHHHHHH
Q 006644 346 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRI 409 (637)
Q Consensus 346 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~I 409 (637)
.|+|+.-...|+.|+--..|.|+-|=.-- ...-. -.||+|+.++-..|++|..-+..+
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 48999999999999998999998653221 11111 359999999999999998877655
No 20
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=88.11 E-value=0.27 Score=55.61 Aligned_cols=51 Identities=27% Similarity=0.419 Sum_probs=43.6
Q ss_pred CCcccccCCCCCC-CCCceeecCccccccccccccccCCCCcccccCCCCcccccccccc
Q 006644 97 GGKIFCPCGTSLP-SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 155 (637)
Q Consensus 97 ~~~~rC~C~ssl~-~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~~p~~f~C~~CRL~ 155 (637)
....+|+|+..-. .+.+++|.. |..|||.-|++..... .|+.|.|..|+..
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 4678999999877 899999999 9999999999875431 2799999999985
No 21
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.48 E-value=0.53 Score=49.20 Aligned_cols=55 Identities=29% Similarity=0.663 Sum_probs=40.9
Q ss_pred eEEeecCCCCccccccccCC---CCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeee
Q 006644 343 IIVNLRCPMSGSRIRVAGRF---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 402 (637)
Q Consensus 343 ~~vsL~CPls~~ri~~P~Rg---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~I 402 (637)
....+.||+|+..|.-=.|. ..|-|. |--.++=++. ..|.||+|++++.-.|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 35678899999999432233 589997 5555555552 6799999999999888886
No 22
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=86.37 E-value=0.3 Score=54.88 Aligned_cols=54 Identities=22% Similarity=0.335 Sum_probs=39.3
Q ss_pred CcccccCCCCCCCCCceeecCccccccccccccccCCCCcccccCCCCccccccccc
Q 006644 98 GKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 154 (637)
Q Consensus 98 ~~~rC~C~ssl~~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~~p~~f~C~~CRL 154 (637)
.+..|.|+.+.....||+|.. |+.|.|..|+....+++.- ...--+|+|-.|+-
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l~-~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDELA-GDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhhc-cCccceEeehhhcc
Confidence 367788888888779999999 9999999999877765321 11223566666653
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.86 E-value=1.3 Score=49.36 Aligned_cols=66 Identities=20% Similarity=0.300 Sum_probs=51.9
Q ss_pred eEEeecCCCCccccccccCCCCcCcccccCHH-HHHHHHccCCccccCCCCCCCCCCCeeecHHHHHHHHHHh
Q 006644 343 IIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLE-TFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 414 (637)
Q Consensus 343 ~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~IL~~l~ 414 (637)
+.-.|.||+-...+..|+- ..|.|.-|..-- .|+.. ...||+|...+....|+.+..+.+|++..+
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 4567899999999999985 689999877533 34431 238999999998889999988888887554
No 24
>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=80.09 E-value=1.5 Score=31.71 Aligned_cols=42 Identities=26% Similarity=0.614 Sum_probs=28.2
Q ss_pred CCCCccccccccCCCCcCcccccCH-HHHHHHHccCCccccCCCCCC
Q 006644 349 CPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELNQRTRKWQCPICMKN 394 (637)
Q Consensus 349 CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC~k~ 394 (637)
||+-...+..|.....|.|.-|.+- ..|++. ...+||+|++.
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 5666666666777777999866553 334332 56789999865
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=78.97 E-value=2.5 Score=32.39 Aligned_cols=34 Identities=26% Similarity=0.514 Sum_probs=25.5
Q ss_pred HhhcChHHHHHHHHHcCCCCC-C-ChHHHHHHHHHh
Q 006644 13 LVNFRMKELKDVLTKLGLPKQ-G-KKQDLVDRIFHQ 46 (637)
Q Consensus 13 l~sFRv~ELq~lL~~lg~~Ks-G-rK~eL~~R~L~l 46 (637)
|.+..+.||+.+-..+|+... + ||+||+..++.-
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~ 37 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAILKA 37 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHHHH
Confidence 456778999999999999543 3 799999998864
No 26
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=76.58 E-value=2.2 Score=31.69 Aligned_cols=28 Identities=32% Similarity=0.614 Sum_probs=20.3
Q ss_pred hhcChHHHHHHHHHcCC--CCCCChHHHHH
Q 006644 14 VNFRMKELKDVLTKLGL--PKQGKKQDLVD 41 (637)
Q Consensus 14 ~sFRv~ELq~lL~~lg~--~KsGrK~eL~~ 41 (637)
.+++|.||+.+|...|. +.+.||.||+.
T Consensus 2 ~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~ 31 (35)
T PF12949_consen 2 KSLTVAQLKRILDEHGIEFPSNAKKAELVA 31 (35)
T ss_dssp TT--SHHHHHHHHHHT---SSS--SHHHHH
T ss_pred CcCcHHHHHHHHHHcCCCCCCCCCHHHHHH
Confidence 67899999999999987 57789999984
No 27
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.87 E-value=0.57 Score=50.86 Aligned_cols=70 Identities=29% Similarity=0.515 Sum_probs=57.1
Q ss_pred eceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCC-CCCCeeecHHHHHHHHHH
Q 006644 341 DSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNY-SLEDLIIDPYFHRITTMM 413 (637)
Q Consensus 341 ~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~-~~~dL~ID~y~~~IL~~l 413 (637)
..+.+.+.||+-...|+.-.-.+.|-|--|||+-+ .+-+..--.||-|.|.+ .--+|++|.-|..|+..|
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 56789999999999999998899999999998733 23444556899998776 456999999999998766
No 28
>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=68.07 E-value=3.4 Score=30.47 Aligned_cols=39 Identities=26% Similarity=0.677 Sum_probs=26.9
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCC
Q 006644 349 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 391 (637)
Q Consensus 349 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 391 (637)
|||=+..++.|+....|.|+-|++ =+.++.++ ..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~--C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKE--CIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHH--HHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHH--HHHHHHHC--cCCCcCC
Confidence 677788888899999999997774 23333333 3799998
No 29
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=63.16 E-value=5.2 Score=32.69 Aligned_cols=36 Identities=22% Similarity=0.545 Sum_probs=25.6
Q ss_pred ccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCC
Q 006644 353 GSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED 399 (637)
Q Consensus 353 ~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~d 399 (637)
...+..|+--.-|.+ |||++.| =-||+|++++.+.+
T Consensus 18 ~~~~~~pCgH~I~~~--~f~~~rY---------ngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 18 TKGTVLPCGHLICDN--CFPGERY---------NGCPFCGTPFEFDD 53 (55)
T ss_pred cccccccccceeecc--ccChhhc---------cCCCCCCCcccCCC
Confidence 445555555555554 8999988 47999999987665
No 30
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=60.92 E-value=4.1 Score=48.28 Aligned_cols=56 Identities=25% Similarity=0.469 Sum_probs=41.9
Q ss_pred eceEEeecCCCCccccccccCCCCcCcccccC-HHHHHHHHccCCccccCCCCCCCCCCCee
Q 006644 341 DSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNYSLEDLI 401 (637)
Q Consensus 341 ~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~~~~dL~ 401 (637)
..++=-|+||...+|.+--+= ..|-|+-||. ...++.+ +.-+||.|+..+.+.|+.
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 446778999999988774432 4799999985 4555554 445899999999888763
No 31
>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=56.35 E-value=7.6 Score=28.55 Aligned_cols=41 Identities=24% Similarity=0.591 Sum_probs=28.5
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCC
Q 006644 349 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 391 (637)
Q Consensus 349 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 391 (637)
||+=...+..|.+...|.|.-|.+ =+.++.+....-+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~--C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRD--CLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHH--HHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHH--HHHHHHHhcCCccCCcC
Confidence 566677777788889999995554 33333333667789998
No 32
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=56.01 E-value=6.5 Score=30.34 Aligned_cols=39 Identities=23% Similarity=0.581 Sum_probs=20.4
Q ss_pred CCCCcccccc----ccCCCCcCcccccCHHHHHHHHccCCccccC
Q 006644 349 CPMSGSRIRV----AGRFKPCVHTGCFDLETFVELNQRTRKWQCP 389 (637)
Q Consensus 349 CPls~~ri~~----P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CP 389 (637)
||+++. +.. |..- .|-|.-|.+.-.=|..+....+.+||
T Consensus 1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788887 666 6664 49999888877666655556789998
No 33
>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=54.06 E-value=14 Score=38.27 Aligned_cols=36 Identities=31% Similarity=0.517 Sum_probs=32.0
Q ss_pred hhcChHHHHHHHHHcCCCCCCChHHHHHHHHHhcCc
Q 006644 14 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLSD 49 (637)
Q Consensus 14 ~sFRv~ELq~lL~~lg~~KsGrK~eL~~R~L~lL~~ 49 (637)
..+.|.||+.=|..-||+--|.|.||++|..+-+..
T Consensus 7 kklkVa~LkeeLa~rGL~~~GNK~EL~~RLtaa~e~ 42 (260)
T KOG4259|consen 7 KKLKVAELKEELAERGLSTAGNKAELVSRLTAATES 42 (260)
T ss_pred hhccHHHHHHHHHHhcccccCChHHHHHHHHHHHHH
Confidence 567899999999999999999999999998776543
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=53.71 E-value=8.4 Score=43.87 Aligned_cols=60 Identities=25% Similarity=0.485 Sum_probs=43.1
Q ss_pred CcccccCCC--CCCCCCceeecCccccccccccccccCCCCcccccC-----CCCcccccccccccCCchh
Q 006644 98 GKIFCPCGT--SLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRL-----LPPLFFCETCRIKRADPFW 161 (637)
Q Consensus 98 ~~~rC~C~s--sl~~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~-----~p~~f~C~~CRL~~~dPF~ 161 (637)
...-|+|-+ +...+.+|||.+ |++..|-+||+.... .+||- ....++|+.|+.--..|-.
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn--~si~s~~s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDN--VSIPSGSSDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred ceEEEEeecCccccccceeeccc--cCceecccccccccc--cccCCCCccCCCCchhhhhHhcCCCCCcc
Confidence 345678844 456788999999 999999999997642 23322 3356899999976555654
No 35
>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=53.26 E-value=1.9 Score=32.61 Aligned_cols=16 Identities=19% Similarity=0.804 Sum_probs=10.8
Q ss_pred HHccCCccccCCCCCC
Q 006644 379 LNQRTRKWQCPICMKN 394 (637)
Q Consensus 379 ~n~~~~~W~CPiC~k~ 394 (637)
+.....+|.|++|+..
T Consensus 18 ~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 18 FDDGGKTWICNFCGTK 33 (40)
T ss_dssp EETTTTEEEETTT--E
T ss_pred EcCCCCEEECcCCCCc
Confidence 3456789999999864
No 36
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=51.96 E-value=12 Score=44.15 Aligned_cols=252 Identities=13% Similarity=0.012 Sum_probs=140.4
Q ss_pred eeceEEeecCCCCccccccccCCCCcCcccccC--HHHHHHHHc--cCCccccCCCCCCCCCCCeeecHHHHHHHHHHhc
Q 006644 340 ADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFD--LETFVELNQ--RTRKWQCPICMKNYSLEDLIIDPYFHRITTMMRN 415 (637)
Q Consensus 340 ~~s~~vsL~CPls~~ri~~P~Rg~~C~HlQCFD--l~~fL~~n~--~~~~W~CPiC~k~~~~~dL~ID~y~~~IL~~l~~ 415 (637)
..+.-+.+.+|.-..+.+..+|...|.+..|+. ..-+=+..+ ....|.||+|-+.+...-.....++..+-..++.
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (636)
T KOG2169|consen 11 LLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVKLHPNVVPPFYPLLWQLLRH 90 (636)
T ss_pred cchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccccCCcccCccccchhccccc
Confidence 334467788999899999999999999999998 444444433 4578999999888887777777777665344444
Q ss_pred CCC-CccEEEEcc---CCceEEeccCCC-----CCCccccCCCCCccccccccccccccceeeccC----CceeeeEec-
Q 006644 416 FAD-DLTEIEVKH---DGSWRVKCKGEN-----NNLAEWHSPDGSTYAARSEVVSNSETKQLVNSG----QTIIARIKK- 481 (637)
Q Consensus 416 ~~~-dv~eV~v~~---DGsW~~~~~~e~-----~~~~~w~~p~g~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~- 481 (637)
.-. -+....+.- +..|+++..... ..+.+|+....+.+.............+.+.++ +.+.-|.|.
T Consensus 91 ~~~~~~~~~~l~g~~~~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~~~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~ 170 (636)
T KOG2169|consen 91 PTQQPVTPSSLLGPPLPFHPDVKLKKLPFYDVLSELIKPHVLHSSNSPSLSESPFLFALTPEQVSGISSRPDVLPGSKSE 170 (636)
T ss_pred CCCCCCCcccccCCCCcCCCcccccCCchheecccccCceeecCcCCCCcccccchhhcchhhhhhcccccccccccccc
Confidence 322 355555555 688998877655 677788877766662221111111111222222 233334444
Q ss_pred ------CCCCceeeecCCCCCC-Cccccccc--cCCccceeeccccCCCCCCCCCC---CcccCCCCC-------cccCC
Q 006644 482 ------NLSANVDVSKYWSTSP-NKHMSYHV--ENNSEKIITMSSSASGCSRDEED---PTVNQDTNS-------RKDLN 542 (637)
Q Consensus 482 ------~~~g~~~~s~~~~~~~-~~~~~~~~--~~~~~~~~~~ss~~~~~~~~~~~---~~~~~~~~~-------~~~~~ 542 (637)
..++.||-..|..... -|.-.-.+ .+...+..++....++..++..+ .++...... +..-.
T Consensus 171 ~~~~~~~~s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~y 250 (636)
T KOG2169|consen 171 GSVCLMETSCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSY 250 (636)
T ss_pred cceeeccccCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCccc
Confidence 3356666555433222 11101111 23333444444444444444443 333332221 22333
Q ss_pred CCCCCCCCccCCCCC-CCCCCCCCcEEEecCCCcCCCccC-CCcccCCCcc
Q 006644 543 DIPHRIDPIFGTGNQ-TDGLIGDTDIIVLSDSEEDNDHLA-PSTSYQSYHP 591 (637)
Q Consensus 543 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~lsds~~~~~~~~-~~~~~~~~~~ 591 (637)
++...+..+++.... .---.......+++.|+......+ .+..++-.++
T Consensus 251 sl~~~~v~~~t~~~llq~~~~~~~~~~~~~~s~~~~~~~l~~~~d~~i~tt 301 (636)
T KOG2169|consen 251 SLSVYFVEGLTSKDLLQRLKQNGKINRNLSQSDALIKKKLTAGPDSEIATT 301 (636)
T ss_pred ceEEEEecccCHHHHHHHHhccCCccCchhHhHHHhhcccccCCcccceec
Confidence 445566666665554 212225566667788888766666 5555555444
No 37
>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=51.14 E-value=4.5 Score=32.23 Aligned_cols=34 Identities=15% Similarity=0.435 Sum_probs=17.1
Q ss_pred HHHHHHHccCCccccCCCCCCCCCCCeeecHHHHHHH
Q 006644 374 ETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRIT 410 (637)
Q Consensus 374 ~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~IL 410 (637)
.-++..-..... .||+|++++..+.- +.++.++-
T Consensus 10 ~k~i~~l~~~~~-~CPlC~r~l~~e~~--~~li~~~~ 43 (54)
T PF04423_consen 10 KKYIEELKEAKG-CCPLCGRPLDEEHR--QELIKKYK 43 (54)
T ss_dssp HHHHHHHTT-SE-E-TTT--EE-HHHH--HHHHHHHH
T ss_pred HHHHHHHhcCCC-cCCCCCCCCCHHHH--HHHHHHHH
Confidence 445555555555 99999999876543 44444443
No 38
>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=49.36 E-value=14 Score=36.24 Aligned_cols=34 Identities=38% Similarity=0.523 Sum_probs=28.7
Q ss_pred HhhcChHHHHHHHHHcCCCCCCC--hHHHHHHHHHh
Q 006644 13 LVNFRMKELKDVLTKLGLPKQGK--KQDLVDRIFHQ 46 (637)
Q Consensus 13 l~sFRv~ELq~lL~~lg~~KsGr--K~eL~~R~L~l 46 (637)
|.-+||+||+.||..-|..=.|. |.|++.||-+|
T Consensus 104 l~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~el 139 (154)
T PF10208_consen 104 LKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEEL 139 (154)
T ss_dssp TTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHCC
T ss_pred HhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHHH
Confidence 67789999999999999999996 89999887764
No 39
>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=49.23 E-value=7.9 Score=30.03 Aligned_cols=43 Identities=33% Similarity=0.590 Sum_probs=24.8
Q ss_pred cCCCCccccccccCCCCcCcc-cccCHHHHHHHHccCCccccCCCCCCC
Q 006644 348 RCPMSGSRIRVAGRFKPCVHT-GCFDLETFVELNQRTRKWQCPICMKNY 395 (637)
Q Consensus 348 ~CPls~~ri~~P~Rg~~C~Hl-QCFDl~~fL~~n~~~~~W~CPiC~k~~ 395 (637)
.|++=+.....+ -...|.|+ -|++= +..+.+ ...+||+|.+++
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C--~~~~~~--~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEEC--AERLLK--RKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHH--HHHHHH--TTSBBTTTTBB-
T ss_pred CCccCCccCCce-EEeCCCChHHHHHH--hHHhcc--cCCCCCcCChhh
Confidence 455555554443 33469998 55542 222222 778999999876
No 40
>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=48.32 E-value=56 Score=30.91 Aligned_cols=66 Identities=24% Similarity=0.161 Sum_probs=42.2
Q ss_pred EEEEEEeCHhhHHhhcCCCceEEEEEEecCCCccccccCCCceEEEECCeEeeecCCCCcccCCCCCCCCCCccccccCC
Q 006644 189 AEAAFHLTKAHSDLLQNTEYDVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGE 268 (637)
Q Consensus 189 ~~~~F~Lt~~q~~~L~~~~~~lqv~Ci~l~d~~~~~~~wP~~~~I~VNg~~v~~~~RP~~~~~g~~gR~~~p~IT~~lk~ 268 (637)
.+.+|.|.++. .+.++.|..-.++ ....|.|||+.|-.. ..+. +.-..+||.+|+.
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 56789987764 2334544443332 457899999988742 1111 1223469999999
Q ss_pred cc-cEEEEEEe
Q 006644 269 GV-NQISLSGC 278 (637)
Q Consensus 269 g~-N~I~Is~~ 278 (637)
|. |.|.|...
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 99988753
No 41
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=47.24 E-value=7.5 Score=29.56 Aligned_cols=42 Identities=21% Similarity=0.442 Sum_probs=23.4
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCC
Q 006644 349 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 391 (637)
Q Consensus 349 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 391 (637)
|||=...++-|+. ..|.|.-|+.--.=+........+.||+|
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 6777777888876 68999988754322222222334899998
No 42
>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=45.50 E-value=13 Score=36.41 Aligned_cols=46 Identities=30% Similarity=0.209 Sum_probs=25.2
Q ss_pred ceEEEECCeEeeec-CCCCcccCCCCCC--CCCCccccccCCcccEEEEEE
Q 006644 230 HAELQVNGLLVRTV-NRPGTQLLGSNGR--DDGALITLYIGEGVNQISLSG 277 (637)
Q Consensus 230 ~~~I~VNg~~v~~~-~RP~~~~~g~~gR--~~~p~IT~~lk~g~N~I~Is~ 277 (637)
..+++|||+.|-.- ..|+... ..+| -...+||.+|+.|.|.|.+..
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 46899999998742 2344321 1111 234569999999999998764
No 43
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=43.37 E-value=7.7 Score=24.50 Aligned_cols=11 Identities=55% Similarity=1.404 Sum_probs=7.2
Q ss_pred cccCCCCCCCC
Q 006644 386 WQCPICMKNYS 396 (637)
Q Consensus 386 W~CPiC~k~~~ 396 (637)
|+||+|++.+.
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 78999997653
No 44
>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=43.18 E-value=12 Score=27.03 Aligned_cols=11 Identities=36% Similarity=1.222 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 006644 384 RKWQCPICMKN 394 (637)
Q Consensus 384 ~~W~CPiC~k~ 394 (637)
..|.||+|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 78999999864
No 45
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.27 E-value=13 Score=36.69 Aligned_cols=20 Identities=30% Similarity=0.594 Sum_probs=17.3
Q ss_pred ccccCCCCCCCCCCCeeecH
Q 006644 385 KWQCPICMKNYSLEDLIIDP 404 (637)
Q Consensus 385 ~W~CPiC~k~~~~~dL~ID~ 404 (637)
-.+||||+|.+..+|+.|--
T Consensus 138 g~KCPvC~K~V~sDd~e~Hl 157 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDDAEIHL 157 (205)
T ss_pred CccCCccccccCCCcceEEE
Confidence 47999999999999988763
No 46
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.20 E-value=14 Score=39.00 Aligned_cols=56 Identities=21% Similarity=0.379 Sum_probs=41.2
Q ss_pred EeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeeec
Q 006644 345 VNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIID 403 (637)
Q Consensus 345 vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID 403 (637)
-+.+|+|-..-+..|.+. .|-|+ |-+.-.+.+-.....-.||.|.....+.+++|+
T Consensus 214 ~d~kC~lC~e~~~~ps~t-~CgHl--FC~~Cl~~~~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCT-PCGHL--FCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred cccceeeeecccCCcccc-cccch--hhHHHHHHHHHhhccccCchhhhhccchhhhee
Confidence 367899999999999885 79999 555555555333334449999999888777654
No 47
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.47 E-value=12 Score=37.32 Aligned_cols=62 Identities=23% Similarity=0.390 Sum_probs=44.4
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeeecHHHHHHHHHHh
Q 006644 346 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 414 (637)
Q Consensus 346 sL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y~~~IL~~l~ 414 (637)
-|.|||....++-| +...|.|.-|..-..=+.- ....||.|..... +|.-...+..+++..+
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 56799999999999 8888999988854333222 5699999995222 6665556666665554
No 48
>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=34.44 E-value=23 Score=31.11 Aligned_cols=40 Identities=30% Similarity=0.547 Sum_probs=24.9
Q ss_pred CHHHHHHHHccCCccccCCCCCCCCCCCeeecHH---HHHHHHHH
Q 006644 372 DLETFVELNQRTRKWQCPICMKNYSLEDLIIDPY---FHRITTMM 413 (637)
Q Consensus 372 Dl~~fL~~n~~~~~W~CPiC~k~~~~~dL~ID~y---~~~IL~~l 413 (637)
+|..||.+.-+++-|-|||=-.- +..|+--+| +.+|++.|
T Consensus 45 qLr~flk~alkTpvwl~pi~ysl--la~lipkgypgrv~ei~~il 87 (92)
T PF02228_consen 45 QLRNFLKLALKTPVWLNPINYSL--LASLIPKGYPGRVNEIINIL 87 (92)
T ss_dssp HHHHHHHHHHT-TTSTTTT-TTT--HHHHS-SS-STTHHHHHHHH
T ss_pred HHHHHHHHHHcCCeeeccccHHH--HHHHccCCCCchHHHHHHHH
Confidence 78999999999999999984211 234444444 55565544
No 49
>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=33.75 E-value=26 Score=24.02 Aligned_cols=25 Identities=36% Similarity=0.906 Sum_probs=15.5
Q ss_pred CCcCcccccC-HHHHHHHHccCCccccCCC
Q 006644 363 KPCVHTGCFD-LETFVELNQRTRKWQCPIC 391 (637)
Q Consensus 363 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC 391 (637)
..|.|.-|+. +..|++ ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 4599986654 334443 345679987
No 50
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=32.89 E-value=24 Score=40.39 Aligned_cols=54 Identities=20% Similarity=0.415 Sum_probs=40.5
Q ss_pred cCCCCcccc-cCCCCCCCCCceeecCccccccccccccccCCCCcccccCCCCc--cccccc
Q 006644 94 LNLGGKIFC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPL--FFCETC 152 (637)
Q Consensus 94 ~~~~~~~rC-~C~ssl~~~~~iqC~~~~C~~~qH~~C~~~~~kp~~~~p~~p~~--f~C~~C 152 (637)
....+.+.| +|.-+-.+..+++|.. |+..-|.+|+..|-.. .|+...+ +.|..|
T Consensus 539 ~~~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPLTR---~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 539 APKAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPLTR---LPKKNKNFGWQCSEC 595 (707)
T ss_pred cccccceeeeeeccchhhHHHhhcch--hhceeeccccCCcccc---CcccccCcceeeccc
Confidence 345577888 8998888889999999 9999999999876432 2443333 468888
No 51
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.84 E-value=98 Score=32.86 Aligned_cols=112 Identities=17% Similarity=0.285 Sum_probs=62.1
Q ss_pred EEEEEEEeecCHHHHHHhccccC-CCCcHHHHHHHHHHhhCCccCCCCCCCCCc-ceeeeceEEeecCCCCccccccccC
Q 006644 284 CFGVRLVKRQTVAQVLSLVPKET-AGEVFEDALTRVRRCFGGVATGNEDGDSDL-EIIADSIIVNLRCPMSGSRIRVAGR 361 (637)
Q Consensus 284 ~~~V~lVk~~t~e~Ll~~I~~~~-~~~~~edal~rIkr~l~~~~~~~~dsDdD~-EIv~~s~~vsL~CPls~~ri~~P~R 361 (637)
+++..|=|-++-+.|++.|...+ -+.++.. ++-++....-....|.+...|. +--.+....-..||++...|.==-|
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks~~pksaSh-IKslKDvveLklt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~~ 126 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKSSLPKSASH-IKSLKDVVELKLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKYR 126 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcccCCcchhh-hcchhhHhheecccCcccccccCccccccccceeecccccceecceEE
Confidence 45556666778899999887542 1111111 1112222111111121110110 0112345788999999999875444
Q ss_pred C---CCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCCeee
Q 006644 362 F---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 402 (637)
Q Consensus 362 g---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~dL~I 402 (637)
+ ..|-|. |...+.=++ ..=.|++|+..+.-+|.+|
T Consensus 127 F~~l~~CGcV--~SerAlKei----kas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 127 FCALRCCGCV--FSERALKEI----KASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred EEEEecccee--ccHHHHHHh----hhccccccCCcccccCeEe
Confidence 4 456665 665554433 3557999999999888876
No 52
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=32.70 E-value=46 Score=37.00 Aligned_cols=41 Identities=27% Similarity=0.581 Sum_probs=24.3
Q ss_pred CCCccccccccCC--CCcCcccccCHHHHHHHHccCCccccCCCCCCCCC
Q 006644 350 PMSGSRIRVAGRF--KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSL 397 (637)
Q Consensus 350 Pls~~ri~~P~Rg--~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~ 397 (637)
|+-+..=..|-|- -+|-|+.| |++|++-++ .||||..++-+
T Consensus 304 ~~~~~~~~~pKrLpCGHilHl~C--LknW~ERqQ-----TCPICr~p~if 346 (491)
T COG5243 304 PLPRGLDMTPKRLPCGHILHLHC--LKNWLERQQ-----TCPICRRPVIF 346 (491)
T ss_pred cCcccccCCcccccccceeeHHH--HHHHHHhcc-----CCCcccCcccc
Confidence 3333333344442 24566666 788887433 59999998644
No 53
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=32.48 E-value=17 Score=35.60 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=18.1
Q ss_pred CCcCcccccCHHHHHHHHc-cCCccccCCCC
Q 006644 363 KPCVHTGCFDLETFVELNQ-RTRKWQCPICM 392 (637)
Q Consensus 363 ~~C~HlQCFDl~~fL~~n~-~~~~W~CPiC~ 392 (637)
..|+|+.|.=... +. ....|.||.-+
T Consensus 106 ~iCtHlGC~~~~~----~~~~~~~~~CPCHG 132 (177)
T COG0723 106 AICTHLGCTVPWN----NAGAEGGFFCPCHG 132 (177)
T ss_pred eeccCCCCccCcc----cCCCCCeEEccCCC
Confidence 4599999985544 33 34789999433
No 54
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.34 E-value=51 Score=31.57 Aligned_cols=39 Identities=18% Similarity=0.462 Sum_probs=25.0
Q ss_pred EEeecCCCCccccccccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCC
Q 006644 344 IVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSL 397 (637)
Q Consensus 344 ~vsL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~ 397 (637)
.....||- |.+- |.+.-.+........+.||.|+..+..
T Consensus 97 ~~~Y~Cp~-------------C~~~--y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 97 NAYYKCPN-------------CQSK--YTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CcEEECcC-------------CCCE--eeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 45678983 5433 555555554333566999999987644
No 55
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=32.17 E-value=22 Score=28.42 Aligned_cols=12 Identities=33% Similarity=1.198 Sum_probs=9.4
Q ss_pred CCccccCCCCCC
Q 006644 383 TRKWQCPICMKN 394 (637)
Q Consensus 383 ~~~W~CPiC~k~ 394 (637)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 457999999854
No 56
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.13 E-value=28 Score=34.96 Aligned_cols=49 Identities=18% Similarity=0.443 Sum_probs=31.7
Q ss_pred ecCCCCcccccccc-CCCCcCcccccCHHHHHHHHccCCccccCCCCCCCCCCC
Q 006644 347 LRCPMSGSRIRVAG-RFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED 399 (637)
Q Consensus 347 L~CPls~~ri~~P~-Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~d 399 (637)
.+||+-+....-=+ =+..|-|+-|= .-|. +..+.+-+||+|+|.+.-.+
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvFC~---~Cik-~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVFCS---QCIK-DALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhhccccccccchhHHH---HHHH-HHHHhCCCCCCcccccchhh
Confidence 78999887774333 35789998441 1111 23356789999999775443
No 57
>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=32.04 E-value=25 Score=26.43 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=13.6
Q ss_pred CCcCcccccC-HHHHHHHHccCCccccCCCC
Q 006644 363 KPCVHTGCFD-LETFVELNQRTRKWQCPICM 392 (637)
Q Consensus 363 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~ 392 (637)
..|.|.-|.+ +..|++. . ..||+|.
T Consensus 19 l~C~H~fh~~Ci~~~~~~---~--~~CP~CR 44 (44)
T PF13639_consen 19 LPCGHVFHRSCIKEWLKR---N--NSCPVCR 44 (44)
T ss_dssp ETTSEEEEHHHHHHHHHH---S--SB-TTTH
T ss_pred ccCCCeeCHHHHHHHHHh---C--CcCCccC
Confidence 3488874442 4445543 2 3999993
No 58
>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=32.02 E-value=56 Score=35.52 Aligned_cols=40 Identities=30% Similarity=0.452 Sum_probs=25.2
Q ss_pred CcCcccccCHHHHHHHHccCCccccCCCCCCCCCCC----eeecHHH
Q 006644 364 PCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED----LIIDPYF 406 (637)
Q Consensus 364 ~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~d----L~ID~y~ 406 (637)
.|-|.-|- +-|...-..+.-.||+|++.++..+ +..|..+
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 47776654 2222222345569999999998887 4556554
No 59
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=31.91 E-value=24 Score=42.49 Aligned_cols=52 Identities=19% Similarity=0.477 Sum_probs=39.5
Q ss_pred Ccccc-cCCCCCCCCCceeecCcccccc-ccccccccCCCCcccccCCCCccccccccccc
Q 006644 98 GKIFC-PCGTSLPSESKIQCVDPRCLVQ-QHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 156 (637)
Q Consensus 98 ~~~rC-~C~ssl~~~~~iqC~~~~C~~~-qH~~C~~~~~kp~~~~p~~p~~f~C~~CRL~~ 156 (637)
-...| +|+..-.-..||.|.. |+.- -|.-|+..+.- .+ -...|||.-|.+..
T Consensus 214 E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~---ei--P~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLS---ES--PVNEWYCTNCSLLE 267 (1134)
T ss_pred ccccceeeccCChHHhheeecc--cccceeeccccCcccc---cc--cccceecCcchhhh
Confidence 34566 7887777788999999 9997 89999976431 12 24689999999864
No 60
>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=29.87 E-value=72 Score=27.28 Aligned_cols=32 Identities=16% Similarity=0.386 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCCCccEEEEccCCceEEeccC
Q 006644 406 FHRITTMMRNFADDLTEIEVKHDGSWRVKCKG 437 (637)
Q Consensus 406 ~~~IL~~l~~~~~dv~eV~v~~DGsW~~~~~~ 437 (637)
..+++..++..+-+|.+|+++.||.|++..-.
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~yev~~~~ 62 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGCYEVEARD 62 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCEEEEEEEE
Confidence 34555556666669999999999999998443
No 61
>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=29.04 E-value=23 Score=27.95 Aligned_cols=13 Identities=31% Similarity=1.017 Sum_probs=7.3
Q ss_pred cCCccccCCCCCC
Q 006644 382 RTRKWQCPICMKN 394 (637)
Q Consensus 382 ~~~~W~CPiC~k~ 394 (637)
-...|.||+|+..
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 3567999999743
No 62
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.61 E-value=93 Score=35.00 Aligned_cols=49 Identities=16% Similarity=0.131 Sum_probs=39.0
Q ss_pred hhcChHHHHHHHHHcCCCCCCChHHHHHHHHHhcCchh----------HHHHHHHHHHH
Q 006644 14 VNFRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLSDEG----------VARIIDDTYRK 62 (637)
Q Consensus 14 ~sFRv~ELq~lL~~lg~~KsGrK~eL~~R~L~lL~~~~----------v~~kI~elYr~ 62 (637)
..+..+.|+..|..+||+-+|-|+.|+.|--++..--. -....+||+.+
T Consensus 267 ~~l~~~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l~Nan~Ds~~p~s~~~L~~~l~~w 325 (397)
T TIGR00599 267 SLLTDSQIRKKLSELGLSTNGTRQLLQKRHNEWETLWNSNCDSLEPVDKRELLRQLDSW 325 (397)
T ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHHH
Confidence 56788999999999999999999999999888766322 34566666654
No 63
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.48 E-value=78 Score=33.02 Aligned_cols=58 Identities=17% Similarity=0.326 Sum_probs=41.4
Q ss_pred ccccCCCCcCcccccCHHHHHHHHcc---------CCccccCCCCCCCCCCCeeecHHHHHHHHHHh
Q 006644 357 RVAGRFKPCVHTGCFDLETFVELNQR---------TRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 414 (637)
Q Consensus 357 ~~P~Rg~~C~HlQCFDl~~fL~~n~~---------~~~W~CPiC~k~~~~~dL~ID~y~~~IL~~l~ 414 (637)
.+|--...|.-+-|++|-.|=-+|++ ..-++||.|+..+-+--=.+......+.+.|+
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 45666788999999999999888765 24699999998875554445555555444454
No 64
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=28.20 E-value=19 Score=24.81 Aligned_cols=9 Identities=44% Similarity=1.497 Sum_probs=7.9
Q ss_pred ccCCCCCCC
Q 006644 387 QCPICMKNY 395 (637)
Q Consensus 387 ~CPiC~k~~ 395 (637)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
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=26.79 E-value=17 Score=23.36 Aligned_cols=11 Identities=55% Similarity=1.455 Sum_probs=8.9
Q ss_pred cccCCCCCCCC
Q 006644 386 WQCPICMKNYS 396 (637)
Q Consensus 386 W~CPiC~k~~~ 396 (637)
|+||+|++...
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 68999998764
No 66
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=26.09 E-value=25 Score=38.28 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=26.7
Q ss_pred ccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCC
Q 006644 359 AGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNY 395 (637)
Q Consensus 359 P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~ 395 (637)
|-+-++|.-..|||--.=-+.-+-...|.||.|++.-
T Consensus 258 ~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k~ 294 (415)
T COG5533 258 PYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRKE 294 (415)
T ss_pred cchheeecHHHHHHHhhhHHhhcCcccccCchhcccc
Confidence 3466788877798865554555667889999998653
No 67
>PHA02929 N1R/p28-like protein; Provisional
Probab=25.14 E-value=69 Score=33.54 Aligned_cols=44 Identities=16% Similarity=0.566 Sum_probs=27.9
Q ss_pred ecCCCCcccccccc-------CCCCcCcccccC-HHHHHHHHccCCccccCCCCCCC
Q 006644 347 LRCPMSGSRIRVAG-------RFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNY 395 (637)
Q Consensus 347 L~CPls~~ri~~P~-------Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~ 395 (637)
..||+-...+.-+. .-..|.|.-|.+ +..|+. +. =.||+|...+
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~---~~--~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK---EK--NTCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh---cC--CCCCCCCCEe
Confidence 56999988766432 224799975554 234543 22 3799998765
No 68
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=24.16 E-value=47 Score=25.13 Aligned_cols=41 Identities=24% Similarity=0.504 Sum_probs=24.2
Q ss_pred CCCCcccc--ccccCCCCcCcccccCHHHHHHHHccCCccccCCCCC
Q 006644 349 CPMSGSRI--RVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMK 393 (637)
Q Consensus 349 CPls~~ri--~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k 393 (637)
|++=+.+. +.+.+-..|.|+-|-.=..=+ . ...-.||+|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~--~--~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKL--K--GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhh--c--CCCCCCcCCCC
Confidence 34444444 345666789998554222211 1 56789999985
No 69
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=24.03 E-value=1.2e+02 Score=25.38 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=22.0
Q ss_pred CcHHHHHHHHHHhhCCccCCCCCCCCCccee---eeceEEeecCCCCccc
Q 006644 309 EVFEDALTRVRRCFGGVATGNEDGDSDLEII---ADSIIVNLRCPMSGSR 355 (637)
Q Consensus 309 ~~~edal~rIkr~l~~~~~~~~dsDdD~EIv---~~s~~vsL~CPls~~r 355 (637)
.+++++..+....++ |.+++ -....+.++||+-+..
T Consensus 3 ~t~~~~~~r~~e~Fp-----------~~slvef~g~~~PvtI~CP~HG~~ 41 (60)
T PF05265_consen 3 MTFESAASRFEEKFP-----------HYSLVEFSGVATPVTIRCPKHGNF 41 (60)
T ss_pred eeHHHHHHHHHHHCC-----------CceEEEEeCCCCceEEECCCCCcE
Confidence 367777777776653 12333 2345788888876554
No 70
>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=23.28 E-value=27 Score=27.72 Aligned_cols=11 Identities=36% Similarity=1.174 Sum_probs=8.5
Q ss_pred ccccCCCCCCC
Q 006644 385 KWQCPICMKNY 395 (637)
Q Consensus 385 ~W~CPiC~k~~ 395 (637)
++.||.|++.+
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 57899999843
No 71
>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=22.61 E-value=39 Score=22.95 Aligned_cols=16 Identities=25% Similarity=0.903 Sum_probs=11.8
Q ss_pred HccCCccccCCCCCCC
Q 006644 380 NQRTRKWQCPICMKNY 395 (637)
Q Consensus 380 n~~~~~W~CPiC~k~~ 395 (637)
-.....++||+|++..
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 3445679999999754
No 72
>PLN00162 transport protein sec23; Provisional
Probab=22.43 E-value=23 Score=42.83 Aligned_cols=34 Identities=21% Similarity=0.676 Sum_probs=20.8
Q ss_pred cccCCCCcCcccccCHHHHHHHHccCCccccCCCCCCC
Q 006644 358 VAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNY 395 (637)
Q Consensus 358 ~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~ 395 (637)
-|+|-+.|+-. +.-|.+...+.++|.||+|+..-
T Consensus 52 ~pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N 85 (761)
T PLN00162 52 DPLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRN 85 (761)
T ss_pred CCCccCCCcCE----ECCceEEecCCCEEEccCCCCCC
Confidence 35665555543 33344445567899999997553
No 73
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=21.67 E-value=1.3e+02 Score=33.16 Aligned_cols=46 Identities=24% Similarity=0.340 Sum_probs=35.8
Q ss_pred cChHHHHHHHHHcCCCCCCChHHHHHHHHHhcCc---hh-------HHHHHHHHHH
Q 006644 16 FRMKELKDVLTKLGLPKQGKKQDLVDRIFHQLSD---EG-------VARIIDDTYR 61 (637)
Q Consensus 16 FRv~ELq~lL~~lg~~KsGrK~eL~~R~L~lL~~---~~-------v~~kI~elYr 61 (637)
+-=+.++.=|..+||+-+|.||-|+.|-.+...- .| .+..|++|-.
T Consensus 251 ls~s~ik~KLse~GLst~G~kQ~likRh~~~v~lyNsncD~l~Pvs~ael~rql~~ 306 (442)
T KOG0287|consen 251 LSDSDIKKKLSEHGLSTQGNKQQLIKRHQEFVHLYNSNCDALHPVSAAELVRQLEN 306 (442)
T ss_pred ccHHHHHHHHHHcCCCCcchHHHHHHHHHHHHHHHhccccccCCcCHHHHHHHHHH
Confidence 3447899999999999999999999998776542 22 4677777754
Done!