Query 011246
Match_columns 490
No_of_seqs 266 out of 524
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 23:13:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011246.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011246hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2169 Zn-finger transcriptio 100.0 9.6E-39 2.1E-43 352.1 23.1 368 1-422 5-396 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 3E-22 6.6E-27 151.3 1.8 50 328-377 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.7 7.7E-18 1.7E-22 154.2 9.8 126 140-274 10-144 (144)
4 PF11789 zf-Nse: Zinc-finger o 98.6 1.6E-08 3.5E-13 78.6 2.0 51 321-373 3-53 (57)
5 KOG1973 Chromatin remodeling p 98.1 1.7E-06 3.8E-11 87.4 2.9 55 76-138 213-268 (274)
6 PF00628 PHD: PHD-finger; Int 97.9 3E-06 6.5E-11 63.7 1.2 49 84-137 1-50 (51)
7 PF02037 SAP: SAP domain; Int 97.6 4.3E-05 9.3E-10 53.6 2.7 29 1-29 6-34 (35)
8 KOG2979 Protein involved in DN 97.6 3.2E-05 6.9E-10 76.5 2.4 75 320-396 167-246 (262)
9 smart00513 SAP Putative DNA-bi 97.5 0.00011 2.5E-09 51.3 3.3 30 1-30 6-35 (35)
10 smart00249 PHD PHD zinc finger 97.3 0.00025 5.5E-09 51.0 3.5 45 85-135 2-47 (47)
11 smart00504 Ubox Modified RING 97.3 0.00036 7.8E-09 54.2 4.5 59 330-393 2-60 (63)
12 COG5034 TNG2 Chromatin remodel 97.3 0.00021 4.6E-09 70.5 3.6 51 79-137 218-269 (271)
13 KOG1844 PHD Zn-finger proteins 96.9 0.00047 1E-08 75.2 2.4 52 80-139 84-136 (508)
14 PF04564 U-box: U-box domain; 96.2 0.0052 1.1E-07 49.9 3.5 63 329-395 4-66 (73)
15 PF13831 PHD_2: PHD-finger; PD 95.9 0.0019 4.1E-08 45.7 -0.2 35 94-136 2-36 (36)
16 COG5627 MMS21 DNA repair prote 94.6 0.014 3.1E-07 57.3 1.3 69 321-391 181-251 (275)
17 KOG0957 PHD finger protein [Ge 94.5 0.032 6.8E-07 60.0 3.5 67 72-142 110-183 (707)
18 KOG4323 Polycomb-like PHD Zn-f 92.9 0.054 1.2E-06 58.4 2.0 55 80-137 169-223 (464)
19 COG5222 Uncharacterized conser 92.7 0.095 2.1E-06 53.2 3.3 63 325-390 270-333 (427)
20 PF04641 Rtf2: Rtf2 RING-finge 89.8 0.3 6.5E-06 49.1 3.5 54 327-385 111-167 (260)
21 PLN03208 E3 ubiquitin-protein 89.4 0.34 7.3E-06 46.8 3.4 55 329-384 18-84 (193)
22 PF14835 zf-RING_6: zf-RING of 88.8 0.38 8.3E-06 38.4 2.7 58 329-392 7-64 (65)
23 KOG2164 Predicted E3 ubiquitin 84.8 0.56 1.2E-05 51.1 2.2 56 329-385 186-242 (513)
24 KOG0825 PHD Zn-finger protein 81.6 0.77 1.7E-05 52.2 1.7 53 79-138 212-266 (1134)
25 TIGR00599 rad18 DNA repair pro 80.6 2 4.4E-05 45.9 4.5 66 326-397 23-89 (397)
26 KOG0957 PHD finger protein [Ge 79.2 1.8 3.8E-05 47.2 3.4 55 76-135 538-595 (707)
27 cd00162 RING RING-finger (Real 78.2 1.7 3.8E-05 30.1 2.1 42 332-377 2-44 (45)
28 PF13923 zf-C3HC4_2: Zinc fing 68.8 2.8 6.1E-05 29.5 1.3 39 332-374 1-39 (39)
29 KOG1632 Uncharacterized PHD Zn 65.8 3 6.4E-05 44.0 1.3 51 82-138 60-113 (345)
30 PF04810 zf-Sec23_Sec24: Sec23 64.4 1.4 3E-05 31.7 -1.0 16 362-377 18-33 (40)
31 KOG3113 Uncharacterized conser 63.7 16 0.00035 36.8 5.8 112 267-385 48-164 (293)
32 PF13445 zf-RING_UBOX: RING-ty 63.7 4.1 8.8E-05 29.9 1.3 39 332-372 1-43 (43)
33 KOG0311 Predicted E3 ubiquitin 63.4 0.9 2E-05 47.4 -3.0 75 319-396 33-108 (381)
34 PF04423 Rad50_zn_hook: Rad50 62.7 2.1 4.6E-05 32.6 -0.3 38 356-396 9-46 (54)
35 KOG0955 PHD finger protein BR1 60.5 6.3 0.00014 47.0 2.8 52 79-139 217-270 (1051)
36 PF14447 Prok-RING_4: Prokaryo 59.8 6 0.00013 30.7 1.6 36 336-382 18-53 (55)
37 PF02837 Glyco_hydro_2_N: Glyc 59.1 29 0.00063 31.6 6.5 66 172-261 72-138 (167)
38 PF07498 Rho_N: Rho terminatio 58.1 8.6 0.00019 28.0 2.2 29 1-29 7-37 (43)
39 PF00097 zf-C3HC4: Zinc finger 58.0 5.5 0.00012 28.0 1.1 41 332-374 1-41 (41)
40 PF08531 Bac_rhamnosid_N: Alph 56.3 6.6 0.00014 36.9 1.7 46 213-260 15-63 (172)
41 KOG4259 Putative nucleic acid- 55.7 9.8 0.00021 37.7 2.7 32 1-32 11-42 (260)
42 KOG0956 PHD finger protein AF1 55.5 6.9 0.00015 44.3 1.9 37 83-119 7-45 (900)
43 cd00350 rubredoxin_like Rubred 54.1 6 0.00013 27.2 0.8 11 367-377 16-26 (33)
44 PF14446 Prok-RING_1: Prokaryo 53.9 8.8 0.00019 29.7 1.7 34 81-116 4-39 (54)
45 PF13894 zf-C2H2_4: C2H2-type 53.1 5.1 0.00011 24.1 0.3 11 369-379 1-11 (24)
46 KOG0978 E3 ubiquitin ligase in 52.9 6.4 0.00014 44.9 1.2 56 324-384 638-694 (698)
47 PF13920 zf-C3HC4_3: Zinc fing 49.5 8.2 0.00018 28.6 0.9 43 331-378 4-47 (50)
48 smart00531 TFIIE Transcription 49.2 29 0.00063 31.8 4.7 32 347-380 104-135 (147)
49 KOG1632 Uncharacterized PHD Zn 48.8 2.8 6E-05 44.1 -2.3 60 77-138 234-295 (345)
50 KOG0801 Predicted E3 ubiquitin 47.9 9.4 0.0002 36.0 1.2 22 368-389 138-159 (205)
51 PF07496 zf-CW: CW-type Zinc F 45.6 10 0.00022 28.5 0.9 34 96-136 3-36 (50)
52 PF15227 zf-C3HC4_4: zinc fing 43.3 11 0.00024 27.2 0.8 42 332-374 1-42 (42)
53 PF13670 PepSY_2: Peptidase pr 42.4 42 0.00092 27.4 4.2 33 389-421 31-63 (83)
54 PF12949 HeH: HeH/LEM domain; 42.3 26 0.00056 24.7 2.5 24 1-24 6-31 (35)
55 PF13832 zf-HC5HC2H_2: PHD-zin 41.9 15 0.00032 31.6 1.5 35 81-117 54-89 (110)
56 COG5574 PEX10 RING-finger-cont 41.4 13 0.00028 37.6 1.2 55 329-386 215-269 (271)
57 cd00730 rubredoxin Rubredoxin; 39.1 14 0.00029 28.2 0.7 12 366-377 32-43 (50)
58 PF00096 zf-C2H2: Zinc finger, 37.7 10 0.00022 23.2 -0.2 11 369-379 1-11 (23)
59 KOG1244 Predicted transcriptio 37.4 22 0.00048 36.2 2.1 43 86-135 286-328 (336)
60 KOG4443 Putative transcription 36.0 7 0.00015 44.0 -1.8 41 93-137 160-201 (694)
61 PF13639 zf-RING_2: Ring finge 35.9 17 0.00037 26.0 0.8 25 347-375 20-44 (44)
62 KOG4299 PHD Zn-finger protein 35.6 27 0.00058 39.3 2.6 52 82-138 253-305 (613)
63 PF00301 Rubredoxin: Rubredoxi 35.2 16 0.00034 27.4 0.5 13 365-377 31-43 (47)
64 PF02228 Gag_p19: Major core p 35.2 18 0.00039 30.2 0.9 21 354-374 44-64 (92)
65 smart00734 ZnF_Rad18 Rad18-lik 35.1 12 0.00026 24.5 -0.1 9 370-378 3-11 (26)
66 PF11793 FANCL_C: FANCL C-term 33.2 25 0.00053 28.3 1.4 31 349-380 32-67 (70)
67 COG5243 HRD1 HRD ubiquitin lig 33.0 30 0.00064 36.8 2.3 42 333-381 304-347 (491)
68 KOG2177 Predicted E3 ubiquitin 32.6 18 0.0004 34.8 0.7 62 329-397 13-74 (386)
69 KOG0287 Postreplication repair 32.4 60 0.0013 34.2 4.3 29 2-30 254-282 (442)
70 PF13465 zf-H2C2_2: Zinc-finge 31.7 26 0.00057 22.5 1.1 15 364-378 10-24 (26)
71 TIGR00599 rad18 DNA repair pro 31.5 42 0.00091 36.1 3.2 30 2-31 272-301 (397)
72 smart00184 RING Ring finger. E 30.4 29 0.00063 22.6 1.2 25 346-374 14-39 (39)
73 COG5533 UBP5 Ubiquitin C-termi 28.4 21 0.00046 37.2 0.3 37 342-378 258-294 (415)
74 PF05605 zf-Di19: Drought indu 28.1 16 0.00035 27.6 -0.5 11 368-378 2-12 (54)
75 COG3683 ABC-type uncharacteriz 28.0 1.2E+02 0.0025 30.0 5.2 61 212-275 89-155 (213)
76 KOG1245 Chromatin remodeling c 27.8 15 0.00033 45.5 -1.0 52 81-139 1107-1159(1404)
77 KOG1512 PHD Zn-finger protein 26.7 40 0.00086 34.7 1.9 50 86-145 319-369 (381)
78 PF07227 DUF1423: Protein of u 26.6 55 0.0012 35.7 3.0 58 86-145 133-200 (446)
79 PF13913 zf-C2HC_2: zinc-finge 26.5 15 0.00032 23.7 -0.8 15 369-383 3-17 (25)
80 PRK10613 hypothetical protein; 26.3 1.5E+02 0.0031 24.4 4.6 41 4-44 26-73 (74)
81 KOG0954 PHD finger protein [Ge 25.9 38 0.00081 39.0 1.7 49 81-138 270-321 (893)
82 KOG3970 Predicted E3 ubiquitin 25.4 89 0.0019 31.2 3.9 59 340-398 57-124 (299)
83 PHA02929 N1R/p28-like protein; 24.4 68 0.0015 32.2 3.1 44 330-378 175-226 (238)
84 PF00641 zf-RanBP: Zn-finger i 23.8 40 0.00087 22.3 0.9 10 366-375 2-11 (30)
85 PLN00162 transport protein sec 23.3 26 0.00057 40.8 -0.1 33 341-377 52-84 (761)
86 KOG0287 Postreplication repair 22.9 33 0.0007 36.1 0.5 62 329-396 23-85 (442)
87 PRK01343 zinc-binding protein; 22.9 42 0.0009 26.3 0.9 16 364-379 5-20 (57)
88 TIGR00570 cdk7 CDK-activating 22.7 96 0.0021 32.3 3.8 24 366-389 41-68 (309)
89 PF14634 zf-RING_5: zinc-RING 21.8 51 0.0011 23.7 1.2 32 341-376 13-44 (44)
90 cd00729 rubredoxin_SM Rubredox 20.5 52 0.0011 22.8 0.9 10 368-377 2-11 (34)
91 KOG0383 Predicted helicase [Ge 20.4 48 0.001 38.2 1.2 46 80-135 46-91 (696)
92 PF09889 DUF2116: Uncharacteri 20.3 49 0.0011 26.1 0.9 18 369-386 4-21 (59)
93 PF12874 zf-met: Zinc-finger o 20.1 32 0.00069 21.3 -0.2 11 369-379 1-11 (25)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=9.6e-39 Score=352.12 Aligned_cols=368 Identities=21% Similarity=0.343 Sum_probs=259.2
Q ss_pred ChhHHHHH-HHcCCCCCC--chHHHHHHHHHccChHh---HHHHHHHHHHHhhcccchhhhccCccCCCccccccccccc
Q 011246 1 MKELKDVL-TKLGLPKQG--KKQDLVDRIFHQLSDEG---VARIIDDTYRKMQISEAADLAIMGQSGLDICNVKVEMEAE 74 (490)
Q Consensus 1 ~~eL~~~L-~~~g~~k~G--~K~~L~~r~l~ll~~~~---~~~~i~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (490)
+.||+.++ ++.++++.| +|.+|.-|+|.++...+ +..+|.++|++...-+.....- .+... .++ ..+.
T Consensus 5 ~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~-~~~~~----~~~-~~~~ 78 (636)
T KOG2169|consen 5 VSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPID-LPAVK----LHP-NVVP 78 (636)
T ss_pred cccccccchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhcccccccccc-ccccc----cCC-cccC
Confidence 35788887 889999999 99999999999999999 7999999999533322221110 00000 010 0001
Q ss_pred cccCCCCceeccCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccc--cCCCCceecccceeccCCccceeeecccc
Q 011246 75 DSLNLGGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEI--RLLPPLFFCETCRIKRADPFWITVAHLVS 152 (490)
Q Consensus 75 ~~~~~~~~~rCiCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~--p~~p~~f~C~~Crl~~~dPF~~~i~~ll~ 152 (490)
..+.. . |....|..=..+....+.+- +.+++ -|+. ..|||+++..+.+
T Consensus 79 ~~~~~-~----------------------~~~~~~~~~~~~~~~~l~g~~~~~~~~------~~~~-~~~~y~~l~~~~~ 128 (636)
T KOG2169|consen 79 PFYPL-L----------------------WQLLRHPTQQPVTPSSLLGPPLPFHPD------VKLK-KLPFYDVLSELIK 128 (636)
T ss_pred ccccc-h----------------------hcccccCCCCCCCcccccCCCCcCCCc------cccc-CCchheecccccC
Confidence 01110 0 00111100000111111110 11222 2665 5999999999999
Q ss_pred cceeeecccCCCCCCCcceeeEEEEeCHhhHHhhcCC-Cc------eEEEEEEeecCCCccccCCCcceEEEEcCeEEee
Q 011246 153 PMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQNT-EY------DVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRT 225 (490)
Q Consensus 153 P~~l~~s~i~~~g~~~~q~~~~~F~Lt~~~~~~l~~~-~~------~lql~C~~l~d~~~~~~~wP~~~~i~VNg~~v~~ 225 (490)
|+.+.++.. ..++...+.|.|+++....+... +. .-.+ |+. ....+++.+||.++.++||+..+.+
T Consensus 129 p~~~~~~~~-----~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~-~~s~p~e~~~p~~~~~~vn~~~~~l 201 (636)
T KOG2169|consen 129 PHVLHSSNS-----PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLM-ETSCPQEDHFPPNVQVKVNNSPCQL 201 (636)
T ss_pred ceeecCcCC-----CCcccccchhhcchhhhhhcccccccccccccccce-eec-cccCccccccCceeEEEecCCccee
Confidence 998876532 34566778899999988765431 11 1111 554 3467899999999999999998887
Q ss_pred c-CCCCcccCCC-CCCCCCCc-ccc--cccCc-ccEEEEEEe--ccceEEEEEEEEeecCHHHHHHhcccCCC-CCcHHH
Q 011246 226 V-NRPGTQLLGS-NGRDDGAL-ITL--YIGEG-VNQISLSGC--DIRNFCFGVRLVKRQTVAQVLSLVPKETA-GEVFED 296 (490)
Q Consensus 226 ~-~rp~~~~~g~-~~r~~~p~-IT~--~lk~g-~N~I~is~~--d~~~y~~~V~lVk~~t~e~ll~~I~~~~~-~~~~e~ 296 (490)
. ..-..++.+. .+|...|. ||. ++... .|.+.+.|. ..+.|.+++|+|+.++.+.|+++++...+ ...++.
T Consensus 202 ~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~~llq~~~~~~~~~~~~~~ 281 (636)
T KOG2169|consen 202 PFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSKDLLQRLKQNGKINRNLSQ 281 (636)
T ss_pred eccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHHHHHHHHhccCCccCchhH
Confidence 5 2111222232 36666666 998 44433 377777664 57899999999999999999999876532 234467
Q ss_pred HHHHHHHhhCCccCCCCCCCCCceeeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCC
Q 011246 297 ALTRVRRCFGGVATGNEDGDSDLEIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMK 376 (490)
Q Consensus 297 al~rik~~l~~~~~~~~d~DdD~eIv~~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k 376 (490)
+.+.+++.+. .++|.||+++++.|||.|||+++||++|+|+..|+|+||||+.+||+||+++++|+||||.+
T Consensus 282 s~~~~~~~l~--------~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~ 353 (636)
T KOG2169|consen 282 SDALIKKKLT--------AGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQK 353 (636)
T ss_pred hHHHhhcccc--------cCCcccceeccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccCCc
Confidence 7777776543 34455689999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeecHHHHHHHHHHhcCCCCeeEEEEeeCCcEEEeecCCC
Q 011246 377 NYSLEDLIIDPYFHRITTMMRNFADDLTEIEVKHDGSWRVKCKGEN 422 (490)
Q Consensus 377 ~~~~~~L~ID~y~~~il~~l~~~~~dv~eV~v~~DGsW~~~~e~e~ 422 (490)
.+.+++|+||+||..|| .++..++++|++..||+|+++.++++
T Consensus 354 ~~~~e~l~iD~~~~~iL---~~~~~~~~ev~~~~dGsw~pi~~~~~ 396 (636)
T KOG2169|consen 354 AAPFEGLIIDGYFLNIL---QSCQANVEEVEVSEDGSWKPIPEEAE 396 (636)
T ss_pred cccccchhhhHHHHHHH---hhccCCCcceEecCCCceecCccccc
Confidence 99999999999999995 55667899999999999999987764
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=99.84 E-value=3e-22 Score=151.32 Aligned_cols=50 Identities=62% Similarity=1.131 Sum_probs=36.5
Q ss_pred EeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCC
Q 011246 328 VNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKN 377 (490)
Q Consensus 328 vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~ 377 (490)
|||+||||++||++|+||+.|+|+|||||++||+++++++.|+||+|+++
T Consensus 1 vsL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 1 VSLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp EESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CeeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 79999999999999999999999999999999999999999999999974
No 3
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.74 E-value=7.7e-18 Score=154.24 Aligned_cols=126 Identities=25% Similarity=0.393 Sum_probs=82.7
Q ss_pred CCccceeeecccccceeeecccCCCCCCCcceeeEEEEeCHhhHHhhcC--CCceEEEEEEeec---CCCccccCCCcce
Q 011246 140 ADPFWITVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQN--TEYDVQAWCILLN---DKVSFRMQWPLHA 214 (490)
Q Consensus 140 ~dPF~~~i~~ll~P~~l~~s~i~~~g~~~~q~~~~~F~Lt~~~~~~l~~--~~~~lql~C~~l~---d~~~~~~~wP~~~ 214 (490)
..|||+++ +++.|+.+.+.. .+..+...+.|.|+++|+++|++ +.++|+|||...+ ....++++||.++
T Consensus 10 ~sPFY~~~-~~i~~~~~~~~~-----~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~FP~~~ 83 (144)
T PF14324_consen 10 PSPFYKVL-RLIHPTPLLPAS-----SSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIEFPPPC 83 (144)
T ss_dssp -BTTEEEE-EEEEEEEEEE-------EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB-----SSE
T ss_pred cCCCccee-EEcCCccccccc-----cCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccccCCCe
Confidence 59999999 778887775432 22356788999999999999977 6799999999843 3457899999999
Q ss_pred EEEEcCeEEeecCCCCcccCCCCCCCCCCcccccccCc---ccEEEEEEe-ccceEEEEEEEEe
Q 011246 215 ELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGEG---VNQISLSGC-DIRNFCFGVRLVK 274 (490)
Q Consensus 215 ~i~VNg~~v~~~~rp~~~~~g~~~r~~~p~IT~~lk~g---~N~I~is~~-d~~~y~~~V~lVk 274 (490)
+|+|||+.|+++.|.++++ +|...|++||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 84 evkvN~~~v~~~~~glknK---pGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 84 EVKVNGKQVKLNNRGLKNK---PGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEETTEE--S--SS-TTS----GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred EEEEeCEEcccCccCCCCC---CCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 9999999999988876654 4556678899999875 799999996 6789999999997
No 4
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.61 E-value=1.6e-08 Score=78.61 Aligned_cols=51 Identities=27% Similarity=0.578 Sum_probs=37.2
Q ss_pred eeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCC
Q 011246 321 IIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI 373 (490)
Q Consensus 321 Iv~~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPi 373 (490)
|+.+..+++++||||...|+-|++++.|.|. ||-++.+++-.+...-+||+
T Consensus 3 i~i~~~~~~~~CPiT~~~~~~PV~s~~C~H~--fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 3 IVIEGGTISLKCPITLQPFEDPVKSKKCGHT--FEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp ----SSB--SB-TTTSSB-SSEEEESSS--E--EEHHHHHHHCTTTS-EE-SC
T ss_pred eEEeccEeccCCCCcCChhhCCcCcCCCCCe--ecHHHHHHHHHhcCCCCCCC
Confidence 5556689999999999999999999999997 99999999988888999999
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.09 E-value=1.7e-06 Score=87.45 Aligned_cols=55 Identities=24% Similarity=0.662 Sum_probs=47.8
Q ss_pred ccCCCCceeccCCCCCCCCCeeeeeCCCcC-ccccccccccCCCCCccccCCCCceecccceec
Q 011246 76 SLNLGGKIFCPCGTSLPSESKIQCVDPRCL-VQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 76 ~~~~~~~~rCiCg~s~~~~~mIqC~~~~C~-v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
...++...+|+|. ....|.||.|+++.|. -|+|..|||+..+| .+.+||+.|+-.
T Consensus 213 ~~d~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 213 AVDPDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAE 268 (274)
T ss_pred ccCCCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhh
Confidence 3557789999999 5557899999999999 99999999998776 477999999865
No 6
>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=97.94 E-value=3e-06 Score=63.68 Aligned_cols=49 Identities=37% Similarity=0.674 Sum_probs=39.8
Q ss_pred ec-cCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceeccccee
Q 011246 84 FC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (490)
Q Consensus 84 rC-iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl 137 (490)
+| +|+...+.+.||+|+. |+.|+|..|++++.+..+. ....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCcC
Confidence 57 8999888999999999 9999999999998653222 223999999963
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=97.62 E-value=4.3e-05 Score=53.60 Aligned_cols=29 Identities=38% Similarity=0.670 Sum_probs=26.0
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHc
Q 011246 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQ 29 (490)
Q Consensus 1 ~~eL~~~L~~~g~~k~G~K~~L~~r~l~l 29 (490)
++|||..|...|++.+|+|++|++|+.+.
T Consensus 6 v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~ 34 (35)
T PF02037_consen 6 VAELKEELKERGLSTSGKKAELIERLKEH 34 (35)
T ss_dssp HHHHHHHHHHTTS-STSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHh
Confidence 47999999999999999999999999864
No 8
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=97.59 E-value=3.2e-05 Score=76.48 Aligned_cols=75 Identities=21% Similarity=0.353 Sum_probs=59.6
Q ss_pred eeeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCC--CCCCCCCC--Ceeec-HHHHHHHH
Q 011246 320 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLE--DLIID-PYFHRITT 394 (490)
Q Consensus 320 eIv~~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPi--C~k~~~~~--~L~ID-~y~~~il~ 394 (490)
++...+.++|++||+|+..|..|++++.|.|+ ||-.+-+++-....+-.||+ |...+... -|.-| .+..+|.+
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 45667889999999999999999999999998 99999999887788999999 77444433 44444 45666554
Q ss_pred HH
Q 011246 395 MM 396 (490)
Q Consensus 395 ~l 396 (490)
..
T Consensus 245 ~q 246 (262)
T KOG2979|consen 245 SQ 246 (262)
T ss_pred hc
Confidence 43
No 9
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.48 E-value=0.00011 Score=51.32 Aligned_cols=30 Identities=50% Similarity=0.777 Sum_probs=27.4
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHcc
Q 011246 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQL 30 (490)
Q Consensus 1 ~~eL~~~L~~~g~~k~G~K~~L~~r~l~ll 30 (490)
++||+..|.+.|++.+|+|++|++|+...+
T Consensus 6 ~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 6 VSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 479999999999999999999999998753
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 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=97.28 E-value=0.00036 Score=54.22 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=50.2
Q ss_pred ecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHH
Q 011246 330 LRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRIT 393 (490)
Q Consensus 330 L~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il 393 (490)
|.||+++..|+.|+.. .|.|. |+.+.+.++.++ .-.||+|++.++.++|+-+..+.+.+
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 67786 999998887655 46899999999999999997776653
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.26 E-value=0.00021 Score=70.52 Aligned_cols=51 Identities=24% Similarity=0.650 Sum_probs=42.9
Q ss_pred CCCceeccCCCCCCCCCeeeeeCCCcC-ccccccccccCCCCCccccCCCCceeccccee
Q 011246 79 LGGKIFCPCGTSLPSESKIQCVDPRCL-VQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (490)
Q Consensus 79 ~~~~~rCiCg~s~~~~~mIqC~~~~C~-v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl 137 (490)
++...+|+|.+.. .|.||-|+++.|. -|+|..|||+..-| -..+||+.|+-
T Consensus 218 e~e~lYCfCqqvS-yGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYCFCQQVS-YGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKK 269 (271)
T ss_pred cCceeEEEecccc-cccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHh
Confidence 5678999998743 6889999999995 69999999997654 36899999975
No 13
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=96.90 E-value=0.00047 Score=75.17 Aligned_cols=52 Identities=27% Similarity=0.413 Sum_probs=46.7
Q ss_pred CCceeccCCCCCC-CCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceecc
Q 011246 80 GGKIFCPCGTSLP-SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 139 (490)
Q Consensus 80 ~~~~rCiCg~s~~-~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~~ 139 (490)
...++|+|+.... .+.||+|+. |..|||..|+++.... -|+.|+|+.|++..
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~~Wqh~~C~g~~~~~------~p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CGRWQHKICCGSFKST------KPDKYVCEICTPRN 136 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cCcccCceeeeecCCC------Cchhceeeeecccc
Confidence 4789999999988 999999999 9999999999988654 28999999999864
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=96.17 E-value=0.0052 Score=49.90 Aligned_cols=63 Identities=17% Similarity=0.254 Sum_probs=47.7
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHHHH
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTM 395 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il~~ 395 (490)
.|.||||+..|+-|++...+ |. ||-.+...-..+ ..-.||+|++.+...+|+-+.-+...++.
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 36899999999999998777 76 999998876655 56789999999999999999888776653
No 15
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.89 E-value=0.0019 Score=45.67 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=19.7
Q ss_pred CCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccce
Q 011246 94 ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 136 (490)
Q Consensus 94 ~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Cr 136 (490)
+.||+|.. |++.-|..||++...+ ..+.++|..|+
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 46899999 9999999999998765 23459999885
No 16
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=94.62 E-value=0.014 Score=57.26 Aligned_cols=69 Identities=16% Similarity=0.291 Sum_probs=58.8
Q ss_pred eeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCC--CCCCCCCCCeeecHHHHH
Q 011246 321 IIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLEDLIIDPYFHR 391 (490)
Q Consensus 321 Iv~~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPi--C~k~~~~~~L~ID~y~~~ 391 (490)
|+..+-.++++|||+...+..|.-+..|.|. ||.+..+..-+--++--||. |......+.++-|..+++
T Consensus 181 i~I~~~~~~nrCpitl~p~~~pils~kcnh~--~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~IlE~ 251 (275)
T COG5627 181 ILIHQELLSNRCPITLNPDFYPILSSKCNHK--PEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHILEK 251 (275)
T ss_pred hhhhhhhhcccCCcccCcchhHHHHhhhccc--ccHHHHHHHhcCCceeecchhhcchheeccchhhhHHHHH
Confidence 5566778999999999999999999999998 99988887766678889998 998887777877776654
No 17
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.48 E-value=0.032 Score=60.04 Aligned_cols=67 Identities=25% Similarity=0.425 Sum_probs=47.6
Q ss_pred ccccccCCCCceeccCCC--CCCCCCeeeeeCCCcCccccccccccCCCCCccccCC-----CCceecccceeccCCc
Q 011246 72 EAEDSLNLGGKIFCPCGT--SLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLL-----PPLFFCETCRIKRADP 142 (490)
Q Consensus 72 ~~~~~~~~~~~~rCiCg~--s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~-----p~~f~C~~Crl~~~dP 142 (490)
+...|++-...+-|+|-+ +.+-+.+|||+. |++-.|-+|||..++. ++|.. -..+||+.|+.--..|
T Consensus 110 e~~~Sapkk~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P 183 (707)
T KOG0957|consen 110 ERTPSAPKKAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLP 183 (707)
T ss_pred ccccCccccceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCC
Confidence 434455545567889965 567889999999 9999999999987544 44432 2568999887643334
No 18
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=92.92 E-value=0.054 Score=58.40 Aligned_cols=55 Identities=22% Similarity=0.302 Sum_probs=42.4
Q ss_pred CCceeccCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceeccccee
Q 011246 80 GGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (490)
Q Consensus 80 ~~~~rCiCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl 137 (490)
.....|.||.+.+.+.||+|.. |+-|+|-.|+....+++.- ..--.+|||-.|.-
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 3467788899888779999999 9999999999977665321 22346788888854
No 19
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.73 E-value=0.095 Score=53.25 Aligned_cols=63 Identities=24% Similarity=0.413 Sum_probs=46.9
Q ss_pred ceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCC-CCCCCCCeeecHHHH
Q 011246 325 SIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICM-KNYSLEDLIIDPYFH 390 (490)
Q Consensus 325 s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~-k~~~~~~L~ID~y~~ 390 (490)
.-.|+|+|||.....+.|+|..-|.|.-|=.. |+..---.-+.||.|. +++-++.|.-|.-..
T Consensus 270 ~~~i~LkCplc~~Llrnp~kT~cC~~~fc~ec---i~~al~dsDf~CpnC~rkdvlld~l~pD~dk~ 333 (427)
T COG5222 270 PPNISLKCPLCHCLLRNPMKTPCCGHTFCDEC---IGTALLDSDFKCPNCSRKDVLLDGLTPDIDKK 333 (427)
T ss_pred CCCccccCcchhhhhhCcccCccccchHHHHH---HhhhhhhccccCCCcccccchhhccCccHHHH
Confidence 34678999999999999999999999855332 2222223469999999 677777777775443
No 20
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.78 E-value=0.3 Score=49.15 Aligned_cols=54 Identities=30% Similarity=0.686 Sum_probs=41.2
Q ss_pred EEeecCCCCccccccccCC---CCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeee
Q 011246 327 IVNLRCPMSGSRIRVAGRF---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 385 (490)
Q Consensus 327 ~vsL~CPls~~ri~~P~R~---~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~I 385 (490)
...+.||+|+..|.-=.|+ ..|-|. |-..++=++. ..|.||+|++++.-.|+++
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 5567899999999422232 589997 6666666662 5799999999999999885
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=89.43 E-value=0.34 Score=46.80 Aligned_cols=55 Identities=18% Similarity=0.417 Sum_probs=41.8
Q ss_pred eecCCCCccccccccCCCCcCcccccCHH-HHHHHH-----------cCCCeeecCCCCCCCCCCCee
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLE-TFVELN-----------QRTRKWQCPICMKNYSLEDLI 384 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFDl~-~fL~~~-----------~~~~~W~CPiC~k~~~~~~L~ 384 (490)
.+.|||-...++.|+-. .|.|+=|..-- .|+... ......+||+|...+...+|+
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 57899999999999884 79999877744 466532 133568999999998776664
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=88.80 E-value=0.38 Score=38.42 Aligned_cols=58 Identities=19% Similarity=0.380 Sum_probs=25.9
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHH
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRI 392 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~i 392 (490)
.|+|+.-...|+.|+--..|.|+-|-.-- ...-. -.||+|+.++-..|++|..-+..+
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 47899999999999998899998654321 11111 259999999999999998776654
No 23
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.84 E-value=0.56 Score=51.05 Aligned_cols=56 Identities=25% Similarity=0.511 Sum_probs=46.3
Q ss_pred eecCCCCccccccccCCCCcCcccccC-HHHHHHHHcCCCeeecCCCCCCCCCCCeee
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNYSLEDLII 385 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFD-l~~fL~~~~~~~~W~CPiC~k~~~~~~L~I 385 (490)
...|||-+-.-.+|+|.. |-|+=||- +-.|+........-.||+|...+++.||.-
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 778999999999999999 99998885 566776665555668999999888877654
No 24
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=81.55 E-value=0.77 Score=52.21 Aligned_cols=53 Identities=17% Similarity=0.421 Sum_probs=42.9
Q ss_pred CCCceec-cCCCCCCCCCeeeeeCCCcCcc-ccccccccCCCCCccccCCCCceecccceec
Q 011246 79 LGGKIFC-PCGTSLPSESKIQCVDPRCLVQ-QHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 79 ~~~~~rC-iCg~s~~~~~mIqC~~~~C~v~-qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
....++| ||+...+..-|+-|+. |+.. .|..|+..+... + --..|||.-|-+.
T Consensus 212 ~~E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~e---i--P~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 212 SQEEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSE---S--PVNEWYCTNCSLL 266 (1134)
T ss_pred ccccccceeeccCChHHhheeecc--cccceeeccccCccccc---c--cccceecCcchhh
Confidence 4567888 6999999899999999 9988 999999976432 1 1368999999775
No 25
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.64 E-value=2 Score=45.94 Aligned_cols=66 Identities=20% Similarity=0.300 Sum_probs=50.7
Q ss_pred eEEeecCCCCccccccccCCCCcCcccccCHHH-HHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHHHHHh
Q 011246 326 IIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLET-FVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 397 (490)
Q Consensus 326 ~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~-fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il~~l~ 397 (490)
+.-.|.||+=...+..|+- ..|.|.-|..--. |+.. .-.||+|...+....|..+..+.+|++..+
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 3456799999999999985 6899987765433 3321 238999999998888998888888887543
No 26
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=79.21 E-value=1.8 Score=47.17 Aligned_cols=55 Identities=22% Similarity=0.393 Sum_probs=40.3
Q ss_pred ccCCCCceec-cCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCC--Cceecccc
Q 011246 76 SLNLGGKIFC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLP--PLFFCETC 135 (490)
Q Consensus 76 ~~~~~~~~rC-iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p--~~f~C~~C 135 (490)
+........| ||..+-++..+++|+. |+..+|.+|...+-..+ |.-. .-+.|..|
T Consensus 538 s~~~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPLTR~---Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 538 SAPKAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPLTRL---PKKNKNFGWQCSEC 595 (707)
T ss_pred ccccccceeeeeeccchhhHHHhhcch--hhceeeccccCCccccC---cccccCcceeeccc
Confidence 3445566778 6999999999999999 99999999999774321 2222 22368888
No 27
>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=78.18 E-value=1.7 Score=30.07 Aligned_cols=42 Identities=26% Similarity=0.614 Sum_probs=26.7
Q ss_pred CCCCccccccccCCCCcCcccccCH-HHHHHHHcCCCeeecCCCCCC
Q 011246 332 CPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELNQRTRKWQCPICMKN 377 (490)
Q Consensus 332 CPls~~ri~~P~R~~~C~HlQCFDl-~~fL~~~~~~~~W~CPiC~k~ 377 (490)
||+-...+..|.....|.|.-|.+- ..|++. ...+||+|++.
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 5555555566666667999855552 233332 56789999865
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=68.85 E-value=2.8 Score=29.49 Aligned_cols=39 Identities=26% Similarity=0.677 Sum_probs=26.3
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCC
Q 011246 332 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 374 (490)
Q Consensus 332 CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC 374 (490)
|||=+..+..|+....|.|+=|++ =+.++.+. ..+||+|
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 566677788888899999996664 34444444 3799998
No 29
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=65.81 E-value=3 Score=43.95 Aligned_cols=51 Identities=25% Similarity=0.435 Sum_probs=40.0
Q ss_pred ceeccCCCCC-CCCCeeeeeCCCcCccccccc--cccCCCCCccccCCCCceecccceec
Q 011246 82 KIFCPCGTSL-PSESKIQCVDPRCLVQQHISC--VIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 82 ~~rCiCg~s~-~~~~mIqC~~~~C~v~qH~~C--v~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
..+|.|-..- +...|++|+. |..|.|..| ++++.+.. ..++.|+|..|...
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 4477777653 3458999999 999999999 99986652 25689999999665
No 30
>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=64.43 E-value=1.4 Score=31.73 Aligned_cols=16 Identities=19% Similarity=0.804 Sum_probs=10.9
Q ss_pred HHcCCCeeecCCCCCC
Q 011246 362 LNQRTRKWQCPICMKN 377 (490)
Q Consensus 362 ~~~~~~~W~CPiC~k~ 377 (490)
+.....+|.||+|+..
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 3456789999999964
No 31
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.71 E-value=16 Score=36.85 Aligned_cols=112 Identities=17% Similarity=0.281 Sum_probs=64.2
Q ss_pred EEEEEEEeecCHHHHHHhcccCC-CCCcHHHHHHHHHHhhCCccCCCCCCCCCc-eeeeeceEEeecCCCCccccccccC
Q 011246 267 CFGVRLVKRQTVAQVLSLVPKET-AGEVFEDALTRVRRCFGGVATGNEDGDSDL-EIIADSIIVNLRCPMSGSRIRVAGR 344 (490)
Q Consensus 267 ~~~V~lVk~~t~e~ll~~I~~~~-~~~~~e~al~rik~~l~~~~~~~~d~DdD~-eIv~~s~~vsL~CPls~~ri~~P~R 344 (490)
+++..+=+-++-+.|++.|.... .+.++. -+.-++....-..+.|.+...|. +--.+....-..||++...|.=--|
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks~~pksaS-hIKslKDvveLklt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~~ 126 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKSSLPKSAS-HIKSLKDVVELKLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKYR 126 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcccCCcchh-hhcchhhHhheecccCcccccccCccccccccceeecccccceecceEE
Confidence 44555666678888998876542 222221 12222322222222232221110 0112445778899999999975444
Q ss_pred C---CCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeee
Q 011246 345 F---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 385 (490)
Q Consensus 345 ~---~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~I 385 (490)
+ ..|-|. |...+.=++ ..-.|++|+..+.-+|.+|
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 457776 666664443 3567999999999998877
No 32
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=63.66 E-value=4.1 Score=29.91 Aligned_cols=39 Identities=21% Similarity=0.511 Sum_probs=20.3
Q ss_pred CCCCcccccc----ccCCCCcCcccccCHHHHHHHHcCCCeeecC
Q 011246 332 CPMSGSRIRV----AGRFKPCVHTGCFDLETFVELNQRTRKWQCP 372 (490)
Q Consensus 332 CPls~~ri~~----P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CP 372 (490)
||+++. +.. |..-. |.|.=|.|.-.=|..+....+.+||
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 788888 766 77654 9999888877666655556789998
No 33
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.40 E-value=0.9 Score=47.43 Aligned_cols=75 Identities=25% Similarity=0.462 Sum_probs=57.7
Q ss_pred ceeeeeceEEeecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCC-CCCeeecHHHHHHHHHH
Q 011246 319 LEIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYS-LEDLIIDPYFHRITTMM 396 (490)
Q Consensus 319 ~eIv~~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~-~~~L~ID~y~~~il~~l 396 (490)
++|--..+.+++.||+-...|+.-.-.+.|.|--|||+-+ .+-+..--.||-|.+.+- --+|++|.-|..++..|
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 4444466788999999999999988889999998988743 233444568999997765 44899999888777654
No 34
>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=62.71 E-value=2.1 Score=32.55 Aligned_cols=38 Identities=16% Similarity=0.442 Sum_probs=18.8
Q ss_pred HHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHHHHH
Q 011246 356 LETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMM 396 (490)
Q Consensus 356 l~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il~~l 396 (490)
+.-++.+-..... .||+|++++..+.- +.++.++-+.+
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 99999999876543 44544443333
No 35
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=60.51 E-value=6.3 Score=47.01 Aligned_cols=52 Identities=23% Similarity=0.452 Sum_probs=38.0
Q ss_pred CCCceeccCCCCCC--CCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceecc
Q 011246 79 LGGKIFCPCGTSLP--SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 139 (490)
Q Consensus 79 ~~~~~rCiCg~s~~--~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~~ 139 (490)
+++..-|||..-.- .+..|.|+. |++..|-.|||++..+ -..+.|-.|-...
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~--Cnl~VHq~Cygi~~ip-------eg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG--CNLAVHQECYGIPFIP-------EGQWLCRRCLQSP 270 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC--CcchhhhhccCCCCCC-------CCcEeehhhccCc
Confidence 46677779977543 478999999 9999999999976543 1455666665544
No 36
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=59.83 E-value=6 Score=30.74 Aligned_cols=36 Identities=22% Similarity=0.545 Sum_probs=25.6
Q ss_pred ccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCC
Q 011246 336 GSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED 382 (490)
Q Consensus 336 ~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~ 382 (490)
...+..|+-..-|.+ |||++.| =-||+|++++.+.+
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 445555655555555 8999876 36999999987765
No 37
>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=59.14 E-value=29 Score=31.60 Aligned_cols=66 Identities=24% Similarity=0.150 Sum_probs=41.8
Q ss_pred eeEEEEeCHhhHHhhcCCCceEEEEEEeecCCCccccCCCcceEEEEcCeEEeecCCCCcccCCCCCCCCCCcccccccC
Q 011246 172 AEAAFHLTKAHSDLLQNTEYDVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGE 251 (490)
Q Consensus 172 ~~~~F~Lt~~~~~~l~~~~~~lql~C~~l~d~~~~~~~wP~~~~i~VNg~~v~~~~rp~~~~~g~~~r~~~p~IT~~lk~ 251 (490)
.+..|.|..+. ...++.|..-.++ ...+|.|||+.|-.. ..+ -..-..+||++|+.
T Consensus 72 Yr~~f~lp~~~------~~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~~~-------~~~~~~dIt~~l~~ 127 (167)
T PF02837_consen 72 YRRTFTLPADW------KGKRVFLRFEGVD----------YAAEVYVNGKLVGSH-EGG-------YTPFEFDITDYLKP 127 (167)
T ss_dssp EEEEEEESGGG------TTSEEEEEESEEE----------SEEEEEETTEEEEEE-EST-------TS-EEEECGGGSSS
T ss_pred EEEEEEeCchh------cCceEEEEeccce----------EeeEEEeCCeEEeee-CCC-------cCCeEEeChhhccC
Confidence 45678888764 1334444443332 458999999988652 111 11234569999999
Q ss_pred cc-cEEEEEEe
Q 011246 252 GV-NQISLSGC 261 (490)
Q Consensus 252 g~-N~I~is~~ 261 (490)
|. |.|.|...
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 99988653
No 38
>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=58.10 E-value=8.6 Score=28.03 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=22.3
Q ss_pred ChhHHHHHHHcCCCCCC--chHHHHHHHHHc
Q 011246 1 MKELKDVLTKLGLPKQG--KKQDLVDRIFHQ 29 (490)
Q Consensus 1 ~~eL~~~L~~~g~~k~G--~K~~L~~r~l~l 29 (490)
+.||+.+=..+|.+.-+ +|+||+..|+.-
T Consensus 7 ~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~ 37 (43)
T PF07498_consen 7 LSELREIAKELGIEGYSKMRKQELIFAILKA 37 (43)
T ss_dssp HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCcCCHHHHHHHHHHH
Confidence 46999999999996443 799999999864
No 39
>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=57.98 E-value=5.5 Score=27.98 Aligned_cols=41 Identities=24% Similarity=0.591 Sum_probs=27.3
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCC
Q 011246 332 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 374 (490)
Q Consensus 332 CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC 374 (490)
||+=...+..|.+...|.|.=|.+ =+.++.+....-+||+|
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 455566677777888999995544 44443333666789988
No 40
>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=56.31 E-value=6.6 Score=36.93 Aligned_cols=46 Identities=30% Similarity=0.209 Sum_probs=25.6
Q ss_pred ceEEEEcCeEEeec-CCCCcccCCCCCC--CCCCcccccccCcccEEEEEE
Q 011246 213 HAELQVNGLLVRTV-NRPGTQLLGSNGR--DDGALITLYIGEGVNQISLSG 260 (490)
Q Consensus 213 ~~~i~VNg~~v~~~-~rp~~~~~g~~~r--~~~p~IT~~lk~g~N~I~is~ 260 (490)
..+++|||+.|-.- ..|+... -.+| -...+||++|+.|.|.|.+..
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 47899999999642 2343321 1122 224569999999999998764
No 41
>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=55.70 E-value=9.8 Score=37.65 Aligned_cols=32 Identities=34% Similarity=0.542 Sum_probs=28.4
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHccCh
Q 011246 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQLSD 32 (490)
Q Consensus 1 ~~eL~~~L~~~g~~k~G~K~~L~~r~l~ll~~ 32 (490)
|.||+.=|..-||+--|.|.||++|+.+-+..
T Consensus 11 Va~LkeeLa~rGL~~~GNK~EL~~RLtaa~e~ 42 (260)
T KOG4259|consen 11 VAELKEELAERGLSTAGNKAELVSRLTAATES 42 (260)
T ss_pred HHHHHHHHHHhcccccCChHHHHHHHHHHHHH
Confidence 46899999999999999999999999876543
No 42
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=55.53 E-value=6.9 Score=44.33 Aligned_cols=37 Identities=24% Similarity=0.499 Sum_probs=30.7
Q ss_pred eeccCCCCC--CCCCeeeeeCCCcCccccccccccCCCC
Q 011246 83 IFCPCGTSL--PSESKIQCVDPRCLVQQHISCVIIPEKP 119 (490)
Q Consensus 83 ~rCiCg~s~--~~~~mIqC~~~~C~v~qH~~Cv~~~~k~ 119 (490)
-.|+|-..- +.+.+|-|+...|.|-.|-.||+|-.-|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVP 45 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVP 45 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcceeEecC
Confidence 468897643 4678999999999999999999997654
No 43
>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=54.07 E-value=6 Score=27.16 Aligned_cols=11 Identities=36% Similarity=1.222 Sum_probs=9.6
Q ss_pred CeeecCCCCCC
Q 011246 367 RKWQCPICMKN 377 (490)
Q Consensus 367 ~~W~CPiC~k~ 377 (490)
..|.||+|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 78999999964
No 44
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.90 E-value=8.8 Score=29.74 Aligned_cols=34 Identities=24% Similarity=0.606 Sum_probs=28.0
Q ss_pred Cceecc-CCCCCC-CCCeeeeeCCCcCccccccccccC
Q 011246 81 GKIFCP-CGTSLP-SESKIQCVDPRCLVQQHISCVIIP 116 (490)
Q Consensus 81 ~~~rCi-Cg~s~~-~~~mIqC~~~~C~v~qH~~Cv~~~ 116 (490)
...+|. ||..+. .+..|.|.. |+...|..|+...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~--CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPE--CGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCC--CCCcccHHHHhhC
Confidence 456774 898874 788999999 9999999999643
No 45
>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=53.10 E-value=5.1 Score=24.11 Aligned_cols=11 Identities=55% Similarity=1.404 Sum_probs=7.3
Q ss_pred eecCCCCCCCC
Q 011246 369 WQCPICMKNYS 379 (490)
Q Consensus 369 W~CPiC~k~~~ 379 (490)
|+||+|++.++
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 46
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=52.86 E-value=6.4 Score=44.93 Aligned_cols=56 Identities=25% Similarity=0.449 Sum_probs=41.0
Q ss_pred eceEEeecCCCCccccccccCCCCcCcccccCH-HHHHHHHcCCCeeecCCCCCCCCCCCee
Q 011246 324 DSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELNQRTRKWQCPICMKNYSLEDLI 384 (490)
Q Consensus 324 ~s~~vsL~CPls~~ri~~P~R~~~C~HlQCFDl-~~fL~~~~~~~~W~CPiC~k~~~~~~L~ 384 (490)
...+=-|+||.-.+|.+--+= ..|-|+-||+- ..++.+ +.-+||.|+..+.+.|+.
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 345677999999988765332 47999988863 445544 455899999999988763
No 47
>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=49.52 E-value=8.2 Score=28.55 Aligned_cols=43 Identities=33% Similarity=0.598 Sum_probs=24.1
Q ss_pred cCCCCccccccccCCCCcCcc-cccCHHHHHHHHcCCCeeecCCCCCCC
Q 011246 331 RCPMSGSRIRVAGRFKPCVHT-GCFDLETFVELNQRTRKWQCPICMKNY 378 (490)
Q Consensus 331 ~CPls~~ri~~P~R~~~C~Hl-QCFDl~~fL~~~~~~~~W~CPiC~k~~ 378 (490)
.|++=+.....+ -...|.|+ -|++ =+..+.. ...+||+|.+++
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~--C~~~~~~--~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEE--CAERLLK--RKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHH--HHHHHHH--TTSBBTTTTBB-
T ss_pred CCccCCccCCce-EEeCCCChHHHHH--HhHHhcc--cCCCCCcCChhh
Confidence 355555544432 23469998 4444 3333333 678999999876
No 48
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=49.22 E-value=29 Score=31.82 Aligned_cols=32 Identities=16% Similarity=0.392 Sum_probs=20.7
Q ss_pred CcCcccccCHHHHHHHHcCCCeeecCCCCCCCCC
Q 011246 347 PCVHTGCFDLETFVELNQRTRKWQCPICMKNYSL 380 (490)
Q Consensus 347 ~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~ 380 (490)
.|.+. |++.-.+........+.||.|+..+..
T Consensus 104 ~C~~~--y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 104 NCQSK--YTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CCCCE--eeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 36543 665555555334567999999987644
No 49
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=48.80 E-value=2.8 Score=44.14 Aligned_cols=60 Identities=25% Similarity=0.388 Sum_probs=41.6
Q ss_pred cCCCCceecc-CCCCCCC-CCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceec
Q 011246 77 LNLGGKIFCP-CGTSLPS-ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 77 ~~~~~~~rCi-Cg~s~~~-~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
+.......|. ||.++.. .++|.|.. |..|+|..|+.+...........-..|+|+.|.+.
T Consensus 234 ~~~~~~~~~~~cg~~~~~~~~~~~~~~--~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 234 APDYSKLICDPCGLSDANKKFEICCDL--CESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred ccccccccccccCcchHHHHHHHHHHH--HHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 4444556664 7776543 78999999 99999999999886543332212245999999874
No 50
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.91 E-value=9.4 Score=35.99 Aligned_cols=22 Identities=27% Similarity=0.548 Sum_probs=18.5
Q ss_pred eeecCCCCCCCCCCCeeecHHH
Q 011246 368 KWQCPICMKNYSLEDLIIDPYF 389 (490)
Q Consensus 368 ~W~CPiC~k~~~~~~L~ID~y~ 389 (490)
-.+||||+|.+..+|+.|--.|
T Consensus 138 g~KCPvC~K~V~sDd~e~HlvM 159 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDDAEIHLVM 159 (205)
T ss_pred CccCCccccccCCCcceEEEEE
Confidence 4799999999999999887443
No 51
>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=45.61 E-value=10 Score=28.55 Aligned_cols=34 Identities=21% Similarity=0.431 Sum_probs=17.5
Q ss_pred eeeeeCCCcCccccccccccCCCCCccccCCCCceecccce
Q 011246 96 KIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 136 (490)
Q Consensus 96 mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Cr 136 (490)
.|||+. |.+|-... ..+... ...+|+.|+|.+-.
T Consensus 3 WVQCd~--C~KWR~lp-~~~~~~----~~~~~d~W~C~~n~ 36 (50)
T PF07496_consen 3 WVQCDS--CLKWRRLP-EEVDPI----REELPDPWYCSMNP 36 (50)
T ss_dssp EEE-TT--T--EEEE--CCHHCT----SCCSSTT--GGGSS
T ss_pred EEECCC--CCceeeCC-hhhCcc----cccCCCeEEcCCCC
Confidence 689998 99999977 222220 12367899997643
No 52
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=43.28 E-value=11 Score=27.24 Aligned_cols=42 Identities=21% Similarity=0.442 Sum_probs=22.1
Q ss_pred CCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCC
Q 011246 332 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 374 (490)
Q Consensus 332 CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC 374 (490)
||+=...++-|+. ..|.|.=|+.--.=+........+.||+|
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 5666667777776 57999977664332222222333899998
No 53
>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=42.37 E-value=42 Score=27.45 Aligned_cols=33 Identities=15% Similarity=0.386 Sum_probs=25.3
Q ss_pred HHHHHHHHhcCCCCeeEEEEeeCCcEEEeecCC
Q 011246 389 FHRITTMMRNFADDLTEIEVKHDGSWRVKCKGE 421 (490)
Q Consensus 389 ~~~il~~l~~~~~dv~eV~v~~DGsW~~~~e~e 421 (490)
..++++.++..+-+|.+|+++.||.|++..-..
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~yev~~~~~ 63 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGCYEVEARDK 63 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCEEEEEEEEC
Confidence 455666666666799999999999999984443
No 54
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=42.28 E-value=26 Score=24.74 Aligned_cols=24 Identities=38% Similarity=0.702 Sum_probs=18.2
Q ss_pred ChhHHHHHHHcCC--CCCCchHHHHH
Q 011246 1 MKELKDVLTKLGL--PKQGKKQDLVD 24 (490)
Q Consensus 1 ~~eL~~~L~~~g~--~k~G~K~~L~~ 24 (490)
|.||+.+|...|. +.+.||.||++
T Consensus 6 V~~Lk~iL~~~~I~~ps~AkKaeLv~ 31 (35)
T PF12949_consen 6 VAQLKRILDEHGIEFPSNAKKAELVA 31 (35)
T ss_dssp SHHHHHHHHHHT---SSS--SHHHHH
T ss_pred HHHHHHHHHHcCCCCCCCCCHHHHHH
Confidence 5799999999885 68899999985
No 55
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=41.90 E-value=15 Score=31.64 Aligned_cols=35 Identities=31% Similarity=0.627 Sum_probs=28.9
Q ss_pred Cceec-cCCCCCCCCCeeeeeCCCcCccccccccccCC
Q 011246 81 GKIFC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPE 117 (490)
Q Consensus 81 ~~~rC-iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~ 117 (490)
...+| +|+.+ .|..|+|..+.|..+.|..|.....
T Consensus 54 ~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~g 89 (110)
T PF13832_consen 54 FKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARKAG 89 (110)
T ss_pred cCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHCC
Confidence 35566 69987 5779999999999999999987653
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.43 E-value=13 Score=37.63 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=41.5
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeeec
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIID 386 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID 386 (490)
+.+|+|-...+..|++. .|.|+ |-+.-.+.|-.....-.||.|.....+.+++|+
T Consensus 215 d~kC~lC~e~~~~ps~t-~CgHl--FC~~Cl~~~~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 215 DYKCFLCLEEPEVPSCT-PCGHL--FCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred ccceeeeecccCCcccc-cccch--hhHHHHHHHHHhhccccCchhhhhccchhhhee
Confidence 55799999999999875 79999 666666665333334449999999988877664
No 57
>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=39.08 E-value=14 Score=28.16 Aligned_cols=12 Identities=33% Similarity=1.198 Sum_probs=9.5
Q ss_pred CCeeecCCCCCC
Q 011246 366 TRKWQCPICMKN 377 (490)
Q Consensus 366 ~~~W~CPiC~k~ 377 (490)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 457999999954
No 58
>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=37.68 E-value=10 Score=23.17 Aligned_cols=11 Identities=55% Similarity=1.455 Sum_probs=9.1
Q ss_pred eecCCCCCCCC
Q 011246 369 WQCPICMKNYS 379 (490)
Q Consensus 369 W~CPiC~k~~~ 379 (490)
|+||+|++.++
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 59
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=37.41 E-value=22 Score=36.24 Aligned_cols=43 Identities=28% Similarity=0.529 Sum_probs=32.4
Q ss_pred cCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccc
Q 011246 86 PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETC 135 (490)
Q Consensus 86 iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~C 135 (490)
|||.|.-...++-|++ |....|+.|...+--. .| -..+-|.+|
T Consensus 286 icgtsenddqllfcdd--cdrgyhmyclsppm~e---pp--egswsc~KO 328 (336)
T KOG1244|consen 286 ICGTSENDDQLLFCDD--CDRGYHMYCLSPPMVE---PP--EGSWSCHLC 328 (336)
T ss_pred cccCcCCCceeEeecc--cCCceeeEecCCCcCC---CC--CCchhHHHH
Confidence 6888877778999999 9999999999976321 11 145667776
No 60
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=36.05 E-value=7 Score=44.02 Aligned_cols=41 Identities=29% Similarity=0.435 Sum_probs=31.0
Q ss_pred CCCeeeeeCCCcCccccccccccCC-CCCccccCCCCceeccccee
Q 011246 93 SESKIQCVDPRCLVQQHISCVIIPE-KPMEEIRLLPPLFFCETCRI 137 (490)
Q Consensus 93 ~~~mIqC~~~~C~v~qH~~Cv~~~~-k~~~~~p~~p~~f~C~~Crl 137 (490)
.-.|+.|.. |.+|+|.+|-++.. +.++-. +...|-|-+||.
T Consensus 160 ~~~~~~c~~--c~rwsh~~c~~~sdd~~~q~~--vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 160 SLPMVCCSI--CQRWSHGGCDGISDDKYMQAQ--VDLQYKCSTCRG 201 (694)
T ss_pred chhhHHHHH--hcccccCCCCccchHHHHHHh--hhhhcccceeeh
Confidence 345799999 99999999999874 333322 115899999995
No 61
>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=35.93 E-value=17 Score=25.99 Aligned_cols=25 Identities=36% Similarity=0.816 Sum_probs=12.6
Q ss_pred CcCcccccCHHHHHHHHcCCCeeecCCCC
Q 011246 347 PCVHTGCFDLETFVELNQRTRKWQCPICM 375 (490)
Q Consensus 347 ~C~HlQCFDl~~fL~~~~~~~~W~CPiC~ 375 (490)
.|.|. |-.+=+.+..++. .+||+|.
T Consensus 20 ~C~H~--fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 20 PCGHV--FHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp TTSEE--EEHHHHHHHHHHS--SB-TTTH
T ss_pred cCCCe--eCHHHHHHHHHhC--CcCCccC
Confidence 47876 4443333333222 3999993
No 62
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=35.62 E-value=27 Score=39.34 Aligned_cols=52 Identities=37% Similarity=0.742 Sum_probs=39.3
Q ss_pred ceecc-CCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceec
Q 011246 82 KIFCP-CGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 82 ~~rCi-Cg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
...|. |+++.--..+|+|+. |..-+|..|...|..+ +.+| ++-++|+.|...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~--Cp~sFH~~CLePPl~~-eniP--~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG--CPRSFHQTCLEPPLEP-ENIP--PGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecC--CchHHHHhhcCCCCCc-ccCC--CCccccCCCeee
Confidence 44784 888654456799999 9999999999987322 2344 468999999876
No 63
>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=35.19 E-value=16 Score=27.45 Aligned_cols=13 Identities=31% Similarity=1.017 Sum_probs=7.4
Q ss_pred CCCeeecCCCCCC
Q 011246 365 RTRKWQCPICMKN 377 (490)
Q Consensus 365 ~~~~W~CPiC~k~ 377 (490)
-...|.||+|+..
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 3457999999853
No 64
>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=35.17 E-value=18 Score=30.17 Aligned_cols=21 Identities=33% Similarity=0.651 Sum_probs=17.3
Q ss_pred cCHHHHHHHHcCCCeeecCCC
Q 011246 354 FDLETFVELNQRTRKWQCPIC 374 (490)
Q Consensus 354 FDl~~fL~~~~~~~~W~CPiC 374 (490)
-||..||.+.-+++-|-|||=
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 368899999999999999983
No 65
>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=35.13 E-value=12 Score=24.46 Aligned_cols=9 Identities=44% Similarity=1.497 Sum_probs=8.0
Q ss_pred ecCCCCCCC
Q 011246 370 QCPICMKNY 378 (490)
Q Consensus 370 ~CPiC~k~~ 378 (490)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
No 66
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=33.24 E-value=25 Score=28.34 Aligned_cols=31 Identities=29% Similarity=0.514 Sum_probs=16.1
Q ss_pred CcccccCHHHHHHHHcC-----CCeeecCCCCCCCCC
Q 011246 349 VHTGCFDLETFVELNQR-----TRKWQCPICMKNYSL 380 (490)
Q Consensus 349 ~HlQCFDl~~fL~~~~~-----~~~W~CPiC~k~~~~ 380 (490)
-|+.|. .++|+..... .-.++||.|.+++..
T Consensus 32 fH~~CL-~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 32 FHLLCL-SEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp B-SGGG-HHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred HHHHHH-HHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 377775 3455544322 125899999988754
No 67
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=33.03 E-value=30 Score=36.84 Aligned_cols=42 Identities=24% Similarity=0.546 Sum_probs=24.8
Q ss_pred CCCccccccccCC--CCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCC
Q 011246 333 PMSGSRIRVAGRF--KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLE 381 (490)
Q Consensus 333 Pls~~ri~~P~R~--~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~ 381 (490)
|+-+..=+.|-|- -+|-|+.| |++|++.+ =.||||..++-++
T Consensus 304 ~~~~~~~~~pKrLpCGHilHl~C--LknW~ERq-----QTCPICr~p~ifd 347 (491)
T COG5243 304 PLPRGLDMTPKRLPCGHILHLHC--LKNWLERQ-----QTCPICRRPVIFD 347 (491)
T ss_pred cCcccccCCcccccccceeeHHH--HHHHHHhc-----cCCCcccCccccc
Confidence 3333333344443 24666666 67888754 3599999986443
No 68
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.61 E-value=18 Score=34.85 Aligned_cols=62 Identities=23% Similarity=0.390 Sum_probs=43.7
Q ss_pred eecCCCCccccccccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHHHHHh
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 397 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il~~l~ 397 (490)
-|.||+-...++-| +...|.|.-|..-..=+.- ....||.|..... +|.-...+..+++.++
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 35799999999999 8888999988765543322 5699999995222 5555555555555443
No 69
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=32.37 E-value=60 Score=34.25 Aligned_cols=29 Identities=34% Similarity=0.547 Sum_probs=25.3
Q ss_pred hhHHHHHHHcCCCCCCchHHHHHHHHHcc
Q 011246 2 KELKDVLTKLGLPKQGKKQDLVDRIFHQL 30 (490)
Q Consensus 2 ~eL~~~L~~~g~~k~G~K~~L~~r~l~ll 30 (490)
+.+|.=|..+|||-+|.||-|+.|-.+..
T Consensus 254 s~ik~KLse~GLst~G~kQ~likRh~~~v 282 (442)
T KOG0287|consen 254 SDIKKKLSEHGLSTQGNKQQLIKRHQEFV 282 (442)
T ss_pred HHHHHHHHHcCCCCcchHHHHHHHHHHHH
Confidence 36788999999999999999999976654
No 70
>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=31.70 E-value=26 Score=22.53 Aligned_cols=15 Identities=27% Similarity=0.937 Sum_probs=11.3
Q ss_pred cCCCeeecCCCCCCC
Q 011246 364 QRTRKWQCPICMKNY 378 (490)
Q Consensus 364 ~~~~~W~CPiC~k~~ 378 (490)
.....++||+|++.+
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 344569999999764
No 71
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.54 E-value=42 Score=36.15 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=26.7
Q ss_pred hhHHHHHHHcCCCCCCchHHHHHHHHHccC
Q 011246 2 KELKDVLTKLGLPKQGKKQDLVDRIFHQLS 31 (490)
Q Consensus 2 ~eL~~~L~~~g~~k~G~K~~L~~r~l~ll~ 31 (490)
+.|+..|..+||+-+|-|+.|+.|--+...
T Consensus 272 ~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~ 301 (397)
T TIGR00599 272 SQIRKKLSELGLSTNGTRQLLQKRHNEWET 301 (397)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence 579999999999999999999999876544
No 72
>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=30.37 E-value=29 Score=22.64 Aligned_cols=25 Identities=36% Similarity=0.906 Sum_probs=14.6
Q ss_pred CCcCcccccC-HHHHHHHHcCCCeeecCCC
Q 011246 346 KPCVHTGCFD-LETFVELNQRTRKWQCPIC 374 (490)
Q Consensus 346 ~~C~HlQCFD-l~~fL~~~~~~~~W~CPiC 374 (490)
..|.|.-|++ ++.|++ ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 3588885544 233443 344679987
No 73
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=28.36 E-value=21 Score=37.15 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=27.1
Q ss_pred ccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCCC
Q 011246 342 AGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNY 378 (490)
Q Consensus 342 P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~~ 378 (490)
|-+-+.|.-..|||--+=-+.-+-...|.||.|++.-
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 3466788877799876655555667789999999553
No 74
>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=28.12 E-value=16 Score=27.63 Aligned_cols=11 Identities=36% Similarity=1.174 Sum_probs=8.6
Q ss_pred eeecCCCCCCC
Q 011246 368 KWQCPICMKNY 378 (490)
Q Consensus 368 ~W~CPiC~k~~ 378 (490)
++.||.|++.+
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 57899999843
No 75
>COG3683 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=28.04 E-value=1.2e+02 Score=30.03 Aligned_cols=61 Identities=20% Similarity=0.240 Sum_probs=36.2
Q ss_pred cceEEEEcCeEEeecCCCCcccCCCCCCCCCCcccc------cccCcccEEEEEEeccceEEEEEEEEee
Q 011246 212 LHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITL------YIGEGVNQISLSGCDIRNFCFGVRLVKR 275 (490)
Q Consensus 212 ~~~~i~VNg~~v~~~~rp~~~~~g~~~r~~~p~IT~------~lk~g~N~I~is~~d~~~y~~~V~lVk~ 275 (490)
..-.|+.||+.|+..+|| ...|++..++...+.= ......+++.|...|+ .|+.++...+-
T Consensus 89 yFt~I~~~gk~vk~~~~p--~~~~~~~~d~ql~~~F~i~la~p~~l~~~~l~~~~YDp-TyY~amdY~~d 155 (213)
T COG3683 89 YFTFIRDNGKKVKYSPRP--THYGAKRKDNQLLIYFSIPLAEPQPLKGATLSFGTYDP-TYYVAMDYAKD 155 (213)
T ss_pred hhhhheeCCceeeccCCC--chhcccccCCEEEEEEecCcccccccCCceEEEEecCC-eeEEEEeeccc
Confidence 345788899999876665 3345554444443321 1222345787776665 46667777765
No 76
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=27.79 E-value=15 Score=45.47 Aligned_cols=52 Identities=23% Similarity=0.578 Sum_probs=40.4
Q ss_pred Cceec-cCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceecc
Q 011246 81 GKIFC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 139 (490)
Q Consensus 81 ~~~rC-iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~~ 139 (490)
...+| +|........|+-|+. |..|.|..|....... ..+..++|+.||..+
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~--c~~~~h~~C~rp~~~~-----~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDE--CLSGFHLFCLRPALSS-----VPPGDWMCPSCRKEH 1159 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHh--hhhhHHHHhhhhhhcc-----CCcCCccCCccchhh
Confidence 35566 4666555678999999 9999999999976432 246789999999986
No 77
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=26.75 E-value=40 Score=34.69 Aligned_cols=50 Identities=20% Similarity=0.351 Sum_probs=38.7
Q ss_pred cCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceeccc-ceeccCCccce
Q 011246 86 PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCET-CRIKRADPFWI 145 (490)
Q Consensus 86 iCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~-Crl~~~dPF~~ 145 (490)
||++......|+-|+. |....|.-|||+..-| -..++|.+ |+.. .-||..
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-------RGEWICDMRCREA-TLNTTR 369 (381)
T ss_pred ccCCcccchheecccc--ccCCCCcccccccccc-------CccchhhhHHHHh-cCCCCh
Confidence 7898877788999999 9999999999997544 25788874 6664 355553
No 78
>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=26.65 E-value=55 Score=35.66 Aligned_cols=58 Identities=22% Similarity=0.291 Sum_probs=36.6
Q ss_pred cCCCCC---CCCCeeeeeCCCcCccccccccccCCC--C---Cccc-cCCCCceeccccee-ccCCccce
Q 011246 86 PCGTSL---PSESKIQCVDPRCLVQQHISCVIIPEK--P---MEEI-RLLPPLFFCETCRI-KRADPFWI 145 (490)
Q Consensus 86 iCg~s~---~~~~mIqC~~~~C~v~qH~~Cv~~~~k--~---~~~~-p~~p~~f~C~~Crl-~~~dPF~~ 145 (490)
+|..-. .+-.+|.|+. |..|-|..|-.-... + ..|. ..+--.|+|-.|-- ..+..|++
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~--CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk 200 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDV--CGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVK 200 (446)
T ss_pred ccCCcccCCCCeeEEeccC--CCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhHHHHHH
Confidence 565522 2456999999 999999999875431 1 1121 12456899999944 33444443
No 79
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.53 E-value=15 Score=23.71 Aligned_cols=15 Identities=33% Similarity=0.930 Sum_probs=11.4
Q ss_pred eecCCCCCCCCCCCe
Q 011246 369 WQCPICMKNYSLEDL 383 (490)
Q Consensus 369 W~CPiC~k~~~~~~L 383 (490)
-.||+|++.+.++.|
T Consensus 3 ~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 3 VPCPICGRKFNPDRL 17 (25)
T ss_pred CcCCCCCCEECHHHH
Confidence 479999998766544
No 80
>PRK10613 hypothetical protein; Provisional
Probab=26.26 E-value=1.5e+02 Score=24.42 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=34.7
Q ss_pred HHHHHHHcCCCCCCchHHHHHHHHHccChHh-------HHHHHHHHHH
Q 011246 4 LKDVLTKLGLPKQGKKQDLVDRIFHQLSDEG-------VARIIDDTYR 44 (490)
Q Consensus 4 L~~~L~~~g~~k~G~K~~L~~r~l~ll~~~~-------~~~~i~~~y~ 44 (490)
|--+|.++|.---||-=-=++|-++-++|+. -.+.|+..||
T Consensus 26 lTlmLkamGQADAGkVii~mEr~ia~meD~~QA~vf~nTv~QIK~aYR 73 (74)
T PRK10613 26 LTLMLKAMGQADAGRVILKMEKQIAQIEDETQAAVFSNTVKQIKQAYR 73 (74)
T ss_pred HHHHHHHhcccccchHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhc
Confidence 3456889999999999999999999999998 4567777787
No 81
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=25.93 E-value=38 Score=39.02 Aligned_cols=49 Identities=24% Similarity=0.605 Sum_probs=38.2
Q ss_pred Cceec-cCCCC--CCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccceec
Q 011246 81 GKIFC-PCGTS--LPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (490)
Q Consensus 81 ~~~rC-iCg~s--~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~Crl~ 138 (490)
..+-| +|... .+-..||-|+. |++=-|..||||-+-| . ..+.|-.|-+-
T Consensus 270 edviCDvCrspD~e~~neMVfCd~--Cn~cVHqaCyGIle~p-----~--gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDK--CNICVHQACYGILEVP-----E--GPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEecc--chhHHHHhhhceeecC-----C--CCeeehhcccc
Confidence 34455 57654 45678999999 9999999999997654 2 67899999886
No 82
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.37 E-value=89 Score=31.18 Aligned_cols=59 Identities=17% Similarity=0.324 Sum_probs=40.4
Q ss_pred ccccCCCCcCcccccCHHHHHHHHcC---------CCeeecCCCCCCCCCCCeeecHHHHHHHHHHhc
Q 011246 340 RVAGRFKPCVHTGCFDLETFVELNQR---------TRKWQCPICMKNYSLEDLIIDPYFHRITTMMRN 398 (490)
Q Consensus 340 ~~P~R~~~C~HlQCFDl~~fL~~~~~---------~~~W~CPiC~k~~~~~~L~ID~y~~~il~~l~~ 398 (490)
.+|--...|.-+-|+|+-.|==+|++ ..-++||.|+..+-+.-=.+......+.+.|++
T Consensus 57 ~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~q 124 (299)
T KOG3970|consen 57 NTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQ 124 (299)
T ss_pred CCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHh
Confidence 55666778888999999888777764 236999999977655443445555554455543
No 83
>PHA02929 N1R/p28-like protein; Provisional
Probab=24.42 E-value=68 Score=32.16 Aligned_cols=44 Identities=16% Similarity=0.542 Sum_probs=26.8
Q ss_pred ecCCCCcccccccc-------CCCCcCcccccC-HHHHHHHHcCCCeeecCCCCCCC
Q 011246 330 LRCPMSGSRIRVAG-------RFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNY 378 (490)
Q Consensus 330 L~CPls~~ri~~P~-------R~~~C~HlQCFD-l~~fL~~~~~~~~W~CPiC~k~~ 378 (490)
..||+-...+.-+. .-..|.|.=|.+ +..|+.. . =.||+|...+
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~---~--~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE---K--NTCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc---C--CCCCCCCCEe
Confidence 36888888765432 224799874443 2245532 2 3799999765
No 84
>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=23.78 E-value=40 Score=22.33 Aligned_cols=10 Identities=40% Similarity=1.441 Sum_probs=8.4
Q ss_pred CCeeecCCCC
Q 011246 366 TRKWQCPICM 375 (490)
Q Consensus 366 ~~~W~CPiC~ 375 (490)
...|.|+.|.
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 4579999997
No 85
>PLN00162 transport protein sec23; Provisional
Probab=23.35 E-value=26 Score=40.79 Aligned_cols=33 Identities=21% Similarity=0.710 Sum_probs=20.3
Q ss_pred cccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCCC
Q 011246 341 VAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKN 377 (490)
Q Consensus 341 ~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k~ 377 (490)
-|+|-+.|.-. +.-|.+...+.++|.||+|+..
T Consensus 52 ~pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~ 84 (761)
T PLN00162 52 DPLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQR 84 (761)
T ss_pred CCCccCCCcCE----ECCceEEecCCCEEEccCCCCC
Confidence 36665555532 2233334456789999999854
No 86
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=22.90 E-value=33 Score=36.12 Aligned_cols=62 Identities=26% Similarity=0.436 Sum_probs=49.7
Q ss_pred eecCCCCccccccccCCCCcCcccc-cCHHHHHHHHcCCCeeecCCCCCCCCCCCeeecHHHHHHHHHH
Q 011246 329 NLRCPMSGSRIRVAGRFKPCVHTGC-FDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMM 396 (490)
Q Consensus 329 sL~CPls~~ri~~P~R~~~C~HlQC-FDl~~fL~~~~~~~~W~CPiC~k~~~~~~L~ID~y~~~il~~l 396 (490)
.|+|-|-+.-+++|+=.- |.|.-| |-...||. .+=+||.|-..++-.+|+=...+.+|++.+
T Consensus 23 lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~-----~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 23 LLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLS-----YKPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHhHHHHHhcCceecc-ccchHHHHHHHHHhc-----cCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 689999998888888776 999865 45566663 345799999999999999888888888754
No 87
>PRK01343 zinc-binding protein; Provisional
Probab=22.86 E-value=42 Score=26.34 Aligned_cols=16 Identities=25% Similarity=0.441 Sum_probs=12.5
Q ss_pred cCCCeeecCCCCCCCC
Q 011246 364 QRTRKWQCPICMKNYS 379 (490)
Q Consensus 364 ~~~~~W~CPiC~k~~~ 379 (490)
...+.-+||+|++.+.
T Consensus 5 ~~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 5 PLRPTRPCPECGKPST 20 (57)
T ss_pred cCCCCCcCCCCCCcCc
Confidence 3456789999999864
No 88
>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=22.74 E-value=96 Score=32.33 Aligned_cols=24 Identities=25% Similarity=0.456 Sum_probs=17.1
Q ss_pred CCeeecCCCCCCCCCCC----eeecHHH
Q 011246 366 TRKWQCPICMKNYSLED----LIIDPYF 389 (490)
Q Consensus 366 ~~~W~CPiC~k~~~~~~----L~ID~y~ 389 (490)
.+.-.||+|++.++..+ +..|..+
T Consensus 41 ~~~~~CP~C~~~lrk~~fr~q~F~D~~v 68 (309)
T TIGR00570 41 RGSGSCPECDTPLRKNNFRVQLFEDPTV 68 (309)
T ss_pred CCCCCCCCCCCccchhhccccccccHHH
Confidence 34569999999988877 4445444
No 89
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.84 E-value=51 Score=23.70 Aligned_cols=32 Identities=31% Similarity=0.605 Sum_probs=20.3
Q ss_pred cccCCCCcCcccccCHHHHHHHHcCCCeeecCCCCC
Q 011246 341 VAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMK 376 (490)
Q Consensus 341 ~P~R~~~C~HlQCFDl~~fL~~~~~~~~W~CPiC~k 376 (490)
.+.+-..|.|+=|-.=.. .+. ...-.||+|++
T Consensus 13 ~~~~l~~CgH~~C~~C~~--~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 13 RRPRLTSCGHIFCEKCLK--KLK--GKSVKCPICRK 44 (44)
T ss_pred CCeEEcccCCHHHHHHHH--hhc--CCCCCCcCCCC
Confidence 356667899985543222 222 56789999985
No 90
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.46 E-value=52 Score=22.82 Aligned_cols=10 Identities=40% Similarity=1.208 Sum_probs=7.5
Q ss_pred eeecCCCCCC
Q 011246 368 KWQCPICMKN 377 (490)
Q Consensus 368 ~W~CPiC~k~ 377 (490)
.|+|++|+-.
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 5888888844
No 91
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=20.42 E-value=48 Score=38.18 Aligned_cols=46 Identities=24% Similarity=0.475 Sum_probs=34.7
Q ss_pred CCceeccCCCCCCCCCeeeeeCCCcCccccccccccCCCCCccccCCCCceecccc
Q 011246 80 GGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETC 135 (490)
Q Consensus 80 ~~~~rCiCg~s~~~~~mIqC~~~~C~v~qH~~Cv~~~~k~~~~~p~~p~~f~C~~C 135 (490)
+....|+|+. +|..+-|+. |..|.|..|.+.+..+. | . ..|.|+.|
T Consensus 46 ~~e~c~ic~~---~g~~l~c~t--C~~s~h~~cl~~pl~~~---p-~-~~~~c~Rc 91 (696)
T KOG0383|consen 46 EQEACRICAD---GGELLWCDT--CPASFHASCLGPPLTPQ---P-N-GEFICPRC 91 (696)
T ss_pred hhhhhhhhcC---CCcEEEecc--ccHHHHHHccCCCCCcC---C-c-cceeeeee
Confidence 3455568876 677899999 99999999999875431 1 2 33999988
No 92
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.34 E-value=49 Score=26.11 Aligned_cols=18 Identities=22% Similarity=0.580 Sum_probs=14.1
Q ss_pred eecCCCCCCCCCCCeeec
Q 011246 369 WQCPICMKNYSLEDLIID 386 (490)
Q Consensus 369 W~CPiC~k~~~~~~L~ID 386 (490)
=.||+|++++.++...=|
T Consensus 4 kHC~~CG~~Ip~~~~fCS 21 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCS 21 (59)
T ss_pred CcCCcCCCcCCcchhhhC
Confidence 469999999998765554
No 93
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.15 E-value=32 Score=21.33 Aligned_cols=11 Identities=45% Similarity=1.132 Sum_probs=8.7
Q ss_pred eecCCCCCCCC
Q 011246 369 WQCPICMKNYS 379 (490)
Q Consensus 369 W~CPiC~k~~~ 379 (490)
|.|.+|++.+.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 88999987653
Done!