Query 007048
Match_columns 620
No_of_seqs 238 out of 531
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 18:11:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007048.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007048hhsearch_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 7.1E-39 1.5E-43 363.2 31.2 366 1-422 5-396 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 9E-22 2E-26 154.4 2.2 50 328-377 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.7 1.5E-16 3.3E-21 150.4 7.1 127 139-274 9-144 (144)
4 PF11789 zf-Nse: Zinc-finger o 98.4 1E-07 2.2E-12 77.1 1.9 51 321-373 3-53 (57)
5 KOG1973 Chromatin remodeling p 97.9 6.6E-06 1.4E-10 86.0 2.5 52 79-138 216-268 (274)
6 PF00628 PHD: PHD-finger; Int 97.7 1.8E-05 3.9E-10 61.6 1.3 49 84-137 1-50 (51)
7 COG5034 TNG2 Chromatin remodel 97.6 2.3E-05 4.9E-10 80.1 2.1 49 81-137 220-269 (271)
8 PF02037 SAP: SAP domain; Int 97.4 0.0001 2.2E-09 53.9 2.9 30 1-30 6-35 (35)
9 smart00513 SAP Putative DNA-bi 97.3 0.00026 5.7E-09 51.6 3.4 30 1-30 6-35 (35)
10 smart00504 Ubox Modified RING 97.1 0.00086 1.9E-08 53.9 4.6 59 330-393 2-60 (63)
11 KOG2979 Protein involved in DN 97.0 0.00035 7.7E-09 71.8 2.2 74 320-395 167-245 (262)
12 smart00249 PHD PHD zinc finger 96.9 0.001 2.2E-08 49.4 3.3 44 86-135 4-47 (47)
13 PF04564 U-box: U-box domain; 95.5 0.015 3.4E-07 49.0 3.8 63 329-395 4-66 (73)
14 KOG1844 PHD Zn-finger proteins 95.5 0.0076 1.6E-07 67.7 2.4 52 80-139 84-136 (508)
15 PF13831 PHD_2: PHD-finger; PD 95.3 0.0043 9.4E-08 45.8 -0.2 35 94-136 2-36 (36)
16 KOG4323 Polycomb-like PHD Zn-f 92.7 0.051 1.1E-06 60.7 1.5 54 81-137 170-223 (464)
17 COG5627 MMS21 DNA repair prote 92.6 0.057 1.2E-06 55.2 1.5 70 320-391 180-251 (275)
18 COG5222 Uncharacterized conser 91.3 0.11 2.3E-06 54.9 1.8 61 325-388 270-331 (427)
19 KOG0957 PHD finger protein [Ge 90.0 0.29 6.3E-06 54.8 3.8 67 74-144 112-185 (707)
20 PLN03208 E3 ubiquitin-protein 89.8 0.29 6.3E-06 49.1 3.4 55 329-384 18-84 (193)
21 KOG2164 Predicted E3 ubiquitin 89.7 0.19 4E-06 56.6 2.1 57 329-386 186-243 (513)
22 PF14835 zf-RING_6: zf-RING of 89.2 0.34 7.4E-06 40.5 2.7 57 329-392 7-64 (65)
23 PF04641 Rtf2: Rtf2 RING-finge 86.9 0.6 1.3E-05 48.6 3.7 55 326-385 110-167 (260)
24 TIGR00599 rad18 DNA repair pro 84.7 1.1 2.3E-05 49.8 4.3 66 326-397 23-89 (397)
25 cd00162 RING RING-finger (Real 72.8 3 6.6E-05 29.9 2.3 42 332-377 2-44 (45)
26 PF13923 zf-C3HC4_2: Zinc fing 71.3 1.4 2.9E-05 32.5 0.1 39 332-374 1-39 (39)
27 KOG0956 PHD finger protein AF1 70.6 2.4 5.2E-05 49.5 1.9 48 82-136 6-55 (900)
28 KOG0311 Predicted E3 ubiquitin 61.8 0.84 1.8E-05 49.5 -3.7 70 324-396 38-108 (381)
29 KOG0957 PHD finger protein [Ge 61.3 12 0.00027 42.4 5.0 54 77-135 539-595 (707)
30 PF14447 Prok-RING_4: Prokaryo 60.6 5.4 0.00012 32.5 1.6 36 336-382 18-53 (55)
31 KOG0978 E3 ubiquitin ligase in 59.9 4.2 9.1E-05 48.0 1.2 56 324-384 638-694 (698)
32 PF04810 zf-Sec23_Sec24: Sec23 59.7 1.6 3.4E-05 32.9 -1.5 18 360-377 16-33 (40)
33 PF00097 zf-C3HC4: Zinc finger 57.5 6.2 0.00013 28.9 1.4 40 332-374 1-41 (41)
34 PF13445 zf-RING_UBOX: RING-ty 57.4 6.5 0.00014 30.2 1.5 39 332-372 1-43 (43)
35 PF04423 Rad50_zn_hook: Rad50 55.8 3.8 8.3E-05 32.5 -0.0 38 356-396 9-46 (54)
36 PF13920 zf-C3HC4_3: Zinc fing 53.9 6 0.00013 30.6 0.8 43 330-378 3-47 (50)
37 KOG2169 Zn-finger transcriptio 53.5 10 0.00023 44.6 3.1 252 323-574 11-301 (636)
38 KOG1632 Uncharacterized PHD Zn 53.1 6.2 0.00013 43.1 1.1 51 82-138 60-113 (345)
39 KOG0955 PHD finger protein BR1 52.1 11 0.00023 46.8 2.9 55 79-142 217-273 (1051)
40 PF08531 Bac_rhamnosid_N: Alph 51.3 9.4 0.0002 37.2 1.9 46 213-260 15-63 (172)
41 PF02837 Glyco_hydro_2_N: Glyc 49.1 54 0.0012 30.9 6.7 66 172-261 72-138 (167)
42 PF07498 Rho_N: Rho terminatio 49.1 14 0.00031 28.2 2.2 29 1-29 7-37 (43)
43 PF13894 zf-C2H2_4: C2H2-type 48.0 6.9 0.00015 24.6 0.3 11 369-379 1-11 (24)
44 PF14446 Prok-RING_1: Prokaryo 46.8 13 0.00027 30.3 1.6 33 82-116 5-39 (54)
45 PF15227 zf-C3HC4_4: zinc fing 45.3 8.9 0.00019 29.1 0.6 41 332-374 1-42 (42)
46 COG5574 PEX10 RING-finger-cont 44.3 11 0.00024 39.7 1.2 55 329-386 215-269 (271)
47 KOG4259 Putative nucleic acid- 43.9 19 0.00042 37.1 2.9 32 1-32 11-42 (260)
48 cd00350 rubredoxin_like Rubred 43.3 11 0.00024 27.1 0.8 11 367-377 16-26 (33)
49 KOG0801 Predicted E3 ubiquitin 42.6 12 0.00027 36.7 1.2 21 368-388 138-158 (205)
50 KOG0825 PHD Zn-finger protein 42.4 14 0.0003 44.1 1.8 66 79-151 212-282 (1134)
51 smart00531 TFIIE Transcription 42.2 37 0.00081 32.4 4.4 39 327-380 97-135 (147)
52 KOG4299 PHD Zn-finger protein 41.5 15 0.00032 42.8 1.8 51 83-138 254-305 (613)
53 KOG2177 Predicted E3 ubiquitin 41.1 10 0.00022 37.6 0.4 62 329-397 13-74 (386)
54 KOG1632 Uncharacterized PHD Zn 39.9 4.8 0.0001 43.9 -2.3 56 81-138 238-295 (345)
55 KOG0954 PHD finger protein [Ge 38.3 16 0.00035 43.3 1.5 44 86-138 276-321 (893)
56 KOG1512 PHD Zn-finger protein 37.9 19 0.00041 38.4 1.8 49 87-145 320-369 (381)
57 PF11793 FANCL_C: FANCL C-term 35.9 33 0.00071 28.9 2.6 31 349-380 32-67 (70)
58 COG0723 QcrA Rieske Fe-S prote 35.8 16 0.00035 35.7 0.8 26 346-376 106-132 (177)
59 PF12949 HeH: HeH/LEM domain; 35.2 37 0.00079 25.2 2.4 24 1-24 6-31 (35)
60 COG5243 HRD1 HRD ubiquitin lig 33.6 21 0.00045 39.4 1.3 28 347-381 320-347 (491)
61 PF00096 zf-C2H2: Zinc finger, 33.0 14 0.00029 23.7 -0.1 11 369-379 1-11 (23)
62 smart00184 RING Ring finger. E 32.9 26 0.00055 23.9 1.3 25 346-374 14-39 (39)
63 PF13639 zf-RING_2: Ring finge 32.5 21 0.00045 26.7 0.8 25 346-375 19-44 (44)
64 cd00730 rubredoxin Rubredoxin; 32.4 20 0.00043 28.6 0.7 12 366-377 32-43 (50)
65 KOG0287 Postreplication repair 31.5 69 0.0015 35.1 4.7 41 2-42 254-304 (442)
66 TIGR00570 cdk7 CDK-activating 31.4 53 0.0011 35.6 3.9 40 347-389 25-68 (309)
67 KOG3113 Uncharacterized conser 30.7 70 0.0015 33.8 4.5 112 267-385 48-164 (293)
68 PF13465 zf-H2C2_2: Zinc-finge 30.6 29 0.00064 23.5 1.2 17 362-378 8-24 (26)
69 PF02228 Gag_p19: Major core p 30.1 26 0.00055 30.7 1.0 40 355-396 45-87 (92)
70 smart00734 ZnF_Rad18 Rad18-lik 30.1 16 0.00036 25.1 -0.1 9 370-378 3-11 (26)
71 KOG3970 Predicted E3 ubiquitin 29.9 64 0.0014 33.5 4.0 59 340-398 57-124 (299)
72 PHA02929 N1R/p28-like protein; 29.8 48 0.001 34.6 3.2 44 330-378 175-226 (238)
73 PF13670 PepSY_2: Peptidase pr 29.2 80 0.0017 26.9 4.0 31 389-419 31-61 (83)
74 PF00301 Rubredoxin: Rubredoxi 29.2 23 0.00049 27.9 0.5 13 365-377 31-43 (47)
75 KOG0320 Predicted E3 ubiquitin 28.9 29 0.00063 34.7 1.3 48 330-382 132-181 (187)
76 PF13832 zf-HC5HC2H_2: PHD-zin 26.9 36 0.00077 30.4 1.5 31 85-117 59-89 (110)
77 PF14634 zf-RING_5: zinc-RING 26.3 38 0.00083 25.5 1.3 41 332-376 2-44 (44)
78 PLN00162 transport protein sec 25.7 20 0.00044 43.1 -0.4 33 342-378 53-85 (761)
79 PF07496 zf-CW: CW-type Zinc F 24.9 39 0.00085 26.6 1.2 32 96-134 3-34 (50)
80 PRK10613 hypothetical protein; 24.7 1.6E+02 0.0034 25.5 4.7 41 4-44 26-73 (74)
81 PF05265 DUF723: Protein of un 24.2 1.3E+02 0.0028 25.1 4.1 55 292-375 3-60 (60)
82 PF05605 zf-Di19: Drought indu 24.2 22 0.00047 28.1 -0.4 11 368-378 2-12 (54)
83 COG5533 UBP5 Ubiquitin C-termi 23.3 30 0.00066 37.5 0.3 41 337-377 252-293 (415)
84 KOG4443 Putative transcription 23.0 17 0.00037 42.6 -1.6 40 95-138 162-202 (694)
85 TIGR00599 rad18 DNA repair pro 22.9 73 0.0016 35.7 3.2 31 2-32 272-302 (397)
86 COG4068 Uncharacterized protei 21.4 63 0.0014 26.9 1.7 29 367-395 7-35 (64)
87 KOG1245 Chromatin remodeling c 20.7 28 0.0006 44.8 -0.7 52 81-139 1107-1159(1404)
88 KOG0287 Postreplication repair 20.0 40 0.00086 36.9 0.4 64 328-397 22-86 (442)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=7.1e-39 Score=363.15 Aligned_cols=366 Identities=22% Similarity=0.388 Sum_probs=256.9
Q ss_pred ChhHHHHH-HHcCCCCCC--chHHHHHHHHHhcChhH---HHHHHHHHHHH-hhcccchhhhhcccCCCccccceecccc
Q 007048 1 MKELKDVL-TKLGLPKQG--KKQDLVDRIFHQLSDEG---VARIIDDTYRK-MQISEAADLAIMGQSGLDICNVKVEMEA 73 (620)
Q Consensus 1 i~ELq~~L-~~~g~~K~G--kK~eL~~R~l~ll~~~~---v~~~I~e~y~~-~~~~~~~~~a~~~~~~~~~~~v~~~~~~ 73 (620)
+.||+.++ ++.++++.| +|.+|..|+|.++...+ ++.+|.++|++ +.+....... .+. ++.+...
T Consensus 5 ~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~--~~~------~~~~~~~ 76 (636)
T KOG2169|consen 5 VSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPID--LPA------VKLHPNV 76 (636)
T ss_pred cccccccchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhcccccccccc--ccc------cccCCcc
Confidence 46888888 899999999 99999999999999988 89999999995 4333321110 010 1111111
Q ss_pred cc-ccCCCCcccccCCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCcccccccccccCCChhHhhhhccC
Q 007048 74 ED-SLNLGGKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKRADPFWITVAHLVS 152 (620)
Q Consensus 74 ~~-~~~~~~~~rCiCg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~~~DPF~~~i~~lL~ 152 (620)
.. .+. . + |....|..=..+..-.+.+ +..-+-+.-|+. ..|||+.+..+++
T Consensus 77 ~~~~~~-~----------~------------~~~~~~~~~~~~~~~~l~g----~~~~~~~~~~~~-~~~~y~~l~~~~~ 128 (636)
T KOG2169|consen 77 VPPFYP-L----------L------------WQLLRHPTQQPVTPSSLLG----PPLPFHPDVKLK-KLPFYDVLSELIK 128 (636)
T ss_pred cCcccc-c----------h------------hcccccCCCCCCCcccccC----CCCcCCCccccc-CCchheecccccC
Confidence 11 111 0 0 0000010000011000001 001122233554 6899999999999
Q ss_pred ceeeeeccccCCCCCCcceEEEEEEecccccccccCC-C------ceEEEEEEeecCCccccccCCCceEEEECCeEeee
Q 007048 153 PMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQNT-E------YDVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRT 225 (620)
Q Consensus 153 Pv~l~~s~i~~~g~~~~qs~~~~F~Lt~~~~~~L~~~-~------~~lqv~Ci~l~d~~~~~~~wP~~~~I~VNg~~v~~ 225 (620)
|+.+.++.. ..++...+.|.|++++...+... + ..-.+ |+.. ...+++.+||.++.++||+..+.+
T Consensus 129 p~~~~~~~~-----~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~~-~s~p~e~~~p~~~~~~vn~~~~~l 201 (636)
T KOG2169|consen 129 PHVLHSSNS-----PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLME-TSCPQEDHFPPNVQVKVNNSPCQL 201 (636)
T ss_pred ceeecCcCC-----CCcccccchhhcchhhhhhcccccccccccccccce-eecc-ccCccccccCceeEEEecCCccee
Confidence 988875432 34567788999999987765321 1 11111 5553 456789999999999999998886
Q ss_pred cCCCCcc---cCC-CCCCCCCCc-ccc--cccCc-ccEEEEEEe--ccceEEEEEEEEeecCHHHHHHhccccCC-CCcH
Q 007048 226 VNRPGTQ---LLG-SNGRDDGAL-ITL--YIGEG-VNQISLSGC--DIRNFCFGVRLVKRQTVAQVLSLVPKETA-GEVF 294 (620)
Q Consensus 226 ~~rP~~~---~~g-~~~R~~~p~-IT~--~lk~g-~N~I~Is~~--d~~~y~~~V~lVk~~s~eqLl~~I~~~~~-~~~~ 294 (620)
.. +.. ..+ ..+|...|. ||. ++..- .|.+.+.|. ..+.|.+++|+|+.++.++||++++.... ...+
T Consensus 202 ~~--~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~~llq~~~~~~~~~~~~ 279 (636)
T KOG2169|consen 202 PF--GYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSKDLLQRLKQNGKINRNL 279 (636)
T ss_pred ec--cccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHHHHHHHHhccCCccCch
Confidence 41 221 111 135666666 998 55443 377777664 57899999999999999999999876422 2333
Q ss_pred HHHHHHHHHhhCCccCCCCCCCCCceeeeeceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCC
Q 007048 295 EDALTRVRRCFGGVATGNEDGDSDLEIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 374 (620)
Q Consensus 295 edal~rIkr~l~~~~~~~~dsDdD~eIv~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 374 (620)
+...+.+++.+ ..+.|.||+++++.|||.|||+++||++|+|+..|+|+||||+.+||+||+++++|+||||
T Consensus 280 ~~s~~~~~~~l--------~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC 351 (636)
T KOG2169|consen 280 SQSDALIKKKL--------TAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVC 351 (636)
T ss_pred hHhHHHhhccc--------ccCCcccceeccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccC
Confidence 55666666543 2345567999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCeeecHHHHHHHHHHhcCCCCceEEEEccCCcEEEeccCCC
Q 007048 375 MKNYSLEDLIIDPYFHRITTMMRNFADDLTEIEVKHDGSWRVKCKGEN 422 (620)
Q Consensus 375 ~k~~~~~~L~ID~y~~~IL~~l~~~~~dv~eV~v~~DGsW~~~~~~e~ 422 (620)
++.+.+++|+||+||+.|| .+|..+++||++..||+|++...+++
T Consensus 352 ~~~~~~e~l~iD~~~~~iL---~~~~~~~~ev~~~~dGsw~pi~~~~~ 396 (636)
T KOG2169|consen 352 QKAAPFEGLIIDGYFLNIL---QSCQANVEEVEVSEDGSWKPIPEEAE 396 (636)
T ss_pred CccccccchhhhHHHHHHH---hhccCCCcceEecCCCceecCccccc
Confidence 9999999999999999995 45667899999999999999877654
No 2
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.83 E-value=9e-22 Score=154.36 Aligned_cols=50 Identities=62% Similarity=1.131 Sum_probs=36.6
Q ss_pred EeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCC
Q 007048 328 VNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKN 377 (620)
Q Consensus 328 VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 377 (620)
|||+||||++||++|+||+.|+|+|||||++||++++++++|+||+|+++
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=99.65 E-value=1.5e-16 Score=150.37 Aligned_cols=127 Identities=25% Similarity=0.418 Sum_probs=82.5
Q ss_pred cCCChhHhhhhccCceeeeeccccCCCCCCcceEEEEEEecccccccccC--CCceEEEEEEeec---CCccccccCCCc
Q 007048 139 RADPFWITVAHLVSPMKLVASNIPTDGTNPLQKAEAAFHLTKAHSDLLQN--TEYDVQAWCILLN---DKVSFRMQWPLH 213 (620)
Q Consensus 139 ~~DPF~~~i~~lL~Pv~l~~s~i~~~g~~~~qs~~~~F~Lt~~~~~~L~~--~~~~lqv~Ci~l~---d~~~~~~~wP~~ 213 (620)
+.+|||+.+ .+|.|+.+.+.. .+..++..+.|.|+++|+++|++ +.++|+|||...+ ....+.++||.+
T Consensus 9 k~sPFY~~~-~~i~~~~~~~~~-----~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~FP~~ 82 (144)
T PF14324_consen 9 KPSPFYKVL-RLIHPTPLLPAS-----SSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIEFPPP 82 (144)
T ss_dssp --BTTEEEE-EEEEEEEEEE-------EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB-----SS
T ss_pred ccCCCccee-EEcCCccccccc-----cCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccccCCC
Confidence 368999988 788887766432 23456788999999999999976 6799999999843 345788999999
Q ss_pred eEEEECCeEeeecCCCCcccCCCCCCCCCCcccccccCc---ccEEEEEEe-ccceEEEEEEEEe
Q 007048 214 AELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGEG---VNQISLSGC-DIRNFCFGVRLVK 274 (620)
Q Consensus 214 ~~I~VNg~~v~~~~rP~~~~~g~~~R~~~p~IT~~lk~g---~N~I~Is~~-d~~~y~~~V~lVk 274 (620)
++|+|||+.|.+..|. +++++|...|++||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 83 ~evkvN~~~v~~~~~g---lknKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 83 CEVKVNGKQVKLNNRG---LKNKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEEETTEE--S--SS----TTS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred eEEEEeCEEcccCccC---CCCCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 9999999999986664 34556777788899999875 899999997 6789999999997
No 4
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.42 E-value=1e-07 Score=77.14 Aligned_cols=51 Identities=27% Similarity=0.578 Sum_probs=37.1
Q ss_pred eeeeceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccC
Q 007048 321 IIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI 373 (620)
Q Consensus 321 Iv~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi 373 (620)
|+++..+++++||||+..|+-|+++..|.|. ||-++.+++-.+...-+||+
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 5566689999999999999999999999997 99999999988889999999
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.86 E-value=6.6e-06 Score=85.96 Aligned_cols=52 Identities=25% Similarity=0.667 Sum_probs=45.5
Q ss_pred CCCcccccCCCCCCCCCeeeecCcccc-ccccccccccCCCCcccccCCCCcccccccccc
Q 007048 79 LGGKIFCPCGTSLPSESKIQCVDPRCL-VQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 79 ~~~~~rCiCg~sl~~~~mIqC~~~~C~-v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~ 138 (620)
++...+|+|. ...++.||-|+++.|. -|+|..||++-.+| .+.|||+.|+-.
T Consensus 216 ~~e~~yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 216 PDEPTYCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAE 268 (274)
T ss_pred CCCCEEEEec-ccccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhh
Confidence 5578999999 4448999999999999 79999999999876 567999999965
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=97.65 E-value=1.8e-05 Score=61.57 Aligned_cols=49 Identities=37% Similarity=0.674 Sum_probs=39.5
Q ss_pred cc-cCCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCccccccccc
Q 007048 84 FC-PCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (620)
Q Consensus 84 rC-iCg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL 137 (620)
+| +|+.....+.||+|+. |+.|+|..|++++.+..+. ....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCcC
Confidence 47 8999777899999999 9999999999998754221 223999999974
No 7
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.63 E-value=2.3e-05 Score=80.09 Aligned_cols=49 Identities=22% Similarity=0.650 Sum_probs=42.8
Q ss_pred CcccccCCCCCCCCCeeeecCccccc-cccccccccCCCCcccccCCCCccccccccc
Q 007048 81 GKIFCPCGTSLPSESKIQCVDPRCLV-QQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (620)
Q Consensus 81 ~~~rCiCg~sl~~~~mIqC~~~~C~v-~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL 137 (620)
...+|.|.+.. .|.||-|+++.|.. |+|..||++.+.| -..|||+.|+-
T Consensus 220 e~lYCfCqqvS-yGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCFCQQVS-YGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKK 269 (271)
T ss_pred ceeEEEecccc-cccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHh
Confidence 57899999655 78999999999999 9999999998755 46899999984
No 8
>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=97.45 E-value=0.0001 Score=53.91 Aligned_cols=30 Identities=40% Similarity=0.692 Sum_probs=26.5
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHhc
Q 007048 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQL 30 (620)
Q Consensus 1 i~ELq~~L~~~g~~K~GkK~eL~~R~l~ll 30 (620)
++|||..|...|++.+|+|++|++|+.+.|
T Consensus 6 v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 6 VAELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp HHHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 479999999999999999999999998753
No 9
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.28 E-value=0.00026 Score=51.58 Aligned_cols=30 Identities=50% Similarity=0.777 Sum_probs=27.5
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHhc
Q 007048 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQL 30 (620)
Q Consensus 1 i~ELq~~L~~~g~~K~GkK~eL~~R~l~ll 30 (620)
++|||..|.+.|++.+|+|++|++|+.+.+
T Consensus 6 ~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 6 VSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 479999999999999999999999998754
No 10
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.05 E-value=0.00086 Score=53.93 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=49.7
Q ss_pred ecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHH
Q 007048 330 LRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRIT 393 (620)
Q Consensus 330 L~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL 393 (620)
|.|||++..|+-|+.. .|-|. |+.+.+.++-.+ .-.||+|++.++.++|+-+..+.+.+
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 56776 998888887655 45899999999999999997776643
No 11
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=96.99 E-value=0.00035 Score=71.76 Aligned_cols=74 Identities=22% Similarity=0.363 Sum_probs=58.2
Q ss_pred eeeeeceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccC--CCCCCCCC--Ceeec-HHHHHHHH
Q 007048 320 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLE--DLIID-PYFHRITT 394 (620)
Q Consensus 320 eIv~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~--~L~ID-~y~~~IL~ 394 (620)
++...+..+|++||+|+..|.-|++++.|.|+ ||-.+-+++-....+-+||+ |..++... -|.-| .+..+|.+
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 45667789999999999999999999999998 99999999888888999999 76334433 34444 45555544
Q ss_pred H
Q 007048 395 M 395 (620)
Q Consensus 395 ~ 395 (620)
+
T Consensus 245 ~ 245 (262)
T KOG2979|consen 245 S 245 (262)
T ss_pred h
Confidence 3
No 12
>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 PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=95.51 E-value=0.015 Score=48.96 Aligned_cols=63 Identities=17% Similarity=0.254 Sum_probs=47.6
Q ss_pred eecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTM 395 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 395 (620)
.|.||||+..|+-|++...| |. ||-.+...-..+ ..-.||+|++++..++|+-+.-+...++.
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 47899999999999999777 76 998888776666 56789999999999999999888776653
No 14
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=95.47 E-value=0.0076 Score=67.71 Aligned_cols=52 Identities=27% Similarity=0.413 Sum_probs=45.6
Q ss_pred CCcccccCCCCCC-CCCeeeecCccccccccccccccCCCCcccccCCCCccccccccccc
Q 007048 80 GGKIFCPCGTSLP-SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 139 (620)
Q Consensus 80 ~~~~rCiCg~sl~-~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~~ 139 (620)
....+|+|+..-. .+.||+|+. |..|||.-|+++.... .|+.|.|+.|++..
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 4688999999887 899999999 9999999999987543 28999999999863
No 15
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.30 E-value=0.0043 Score=45.82 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=19.6
Q ss_pred CCeeeecCccccccccccccccCCCCcccccCCCCcccccccc
Q 007048 94 ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 136 (620)
Q Consensus 94 ~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CR 136 (620)
+.||+|.. |++..|..||++...+ ..+.|+|..|+
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 9999999999998754 23359999885
No 16
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=92.72 E-value=0.051 Score=60.68 Aligned_cols=54 Identities=22% Similarity=0.330 Sum_probs=42.3
Q ss_pred CcccccCCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCccccccccc
Q 007048 81 GKIFCPCGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRI 137 (620)
Q Consensus 81 ~~~rCiCg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL 137 (620)
...+|.||.+.....||+|.. |+.|+|..|+.-..+++. +...--+|+|-.|+-
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l-~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDEL-AGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhh-ccCccceEeehhhcc
Confidence 467788899877679999999 999999999998877643 222455778888774
No 17
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=92.57 E-value=0.057 Score=55.23 Aligned_cols=70 Identities=16% Similarity=0.293 Sum_probs=58.1
Q ss_pred eeeeeceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccC--CCCCCCCCCeeecHHHHH
Q 007048 320 EIIADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPI--CMKNYSLEDLIIDPYFHR 391 (620)
Q Consensus 320 eIv~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~~L~ID~y~~~ 391 (620)
+|+..+-.++++|||+...+..|.-+..|.|. ||.+..+..-+--++--||. |......+.++-|.-+.+
T Consensus 180 ~i~I~~~~~~nrCpitl~p~~~pils~kcnh~--~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~IlE~ 251 (275)
T COG5627 180 KILIHQELLSNRCPITLNPDFYPILSSKCNHK--PEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHILEK 251 (275)
T ss_pred hhhhhhhhhcccCCcccCcchhHHHHhhhccc--ccHHHHHHHhcCCceeecchhhcchheeccchhhhHHHHH
Confidence 35556678999999999999999999999998 99988887777778889997 988877777776666544
No 18
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.31 E-value=0.11 Score=54.93 Aligned_cols=61 Identities=25% Similarity=0.441 Sum_probs=43.7
Q ss_pred ceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCC-CCCCCCCeeecHH
Q 007048 325 SIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICM-KNYSLEDLIIDPY 388 (620)
Q Consensus 325 s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~-k~~~~~~L~ID~y 388 (620)
.-.|+|+|||....++-|+|..-|.|.-|=.. |+..---.-+.||.|. |.+-++.|.-|.-
T Consensus 270 ~~~i~LkCplc~~Llrnp~kT~cC~~~fc~ec---i~~al~dsDf~CpnC~rkdvlld~l~pD~d 331 (427)
T COG5222 270 PPNISLKCPLCHCLLRNPMKTPCCGHTFCDEC---IGTALLDSDFKCPNCSRKDVLLDGLTPDID 331 (427)
T ss_pred CCCccccCcchhhhhhCcccCccccchHHHHH---HhhhhhhccccCCCcccccchhhccCccHH
Confidence 34688999999999999999999999866432 2222233569999997 4555555555543
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=89.97 E-value=0.29 Score=54.84 Aligned_cols=67 Identities=24% Similarity=0.416 Sum_probs=48.2
Q ss_pred ccccCCCCcccccCCC--CCCCCCeeeecCccccccccccccccCCCCcccccC-----CCCcccccccccccCCChh
Q 007048 74 EDSLNLGGKIFCPCGT--SLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRL-----LPPLFFCETCRIKRADPFW 144 (620)
Q Consensus 74 ~~~~~~~~~~rCiCg~--sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~-----~P~~fyCe~CRL~~~DPF~ 144 (620)
..|+.-....-|+|-+ +...+.+|||+. |++..|-+||+..++. +|+. ....|||+.|+.--..|-.
T Consensus 112 ~~Sapkk~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 112 TPSAPKKAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred ccCccccceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCCcc
Confidence 3444444557788844 455789999999 9999999999998654 4543 2356999999975544544
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=89.81 E-value=0.29 Score=49.07 Aligned_cols=55 Identities=18% Similarity=0.436 Sum_probs=41.4
Q ss_pred eecCCCCccceeccccCCCcCcccccCH-HHHHHHH-----------cCCCeeeccCCCCCCCCCCee
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELN-----------QRTRKWQCPICMKNYSLEDLI 384 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n-----------~~~~~W~CPiC~k~~~~~~L~ 384 (620)
.+.|||-...++.|+-. .|.|+=|..- ..|+... ......+||+|...+...+|+
T Consensus 18 ~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 18 DFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred ccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 58899999999999884 7999988764 4466532 134568999999998765553
No 21
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.75 E-value=0.19 Score=56.59 Aligned_cols=57 Identities=25% Similarity=0.471 Sum_probs=48.5
Q ss_pred eecCCCCccceeccccCCCcCccccc-CHHHHHHHHcCCCeeeccCCCCCCCCCCeeec
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCF-DLETFVELNQRTRKWQCPICMKNYSLEDLIID 386 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCF-Dl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID 386 (620)
.+.|||.+-.-.+|+|.. |-|+=|| -|-.|+.......--.||+|...+.+.+|.-=
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv 243 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPV 243 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeee
Confidence 788999999999999999 9999999 67888888755566689999988888766543
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=89.18 E-value=0.34 Score=40.49 Aligned_cols=57 Identities=19% Similarity=0.409 Sum_probs=26.2
Q ss_pred eecCCCCccceeccccCCCcCcccccCHH-HHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHH
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLE-TFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRI 392 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~I 392 (620)
.|+|+.-...|+.|+--..|.|+-|-.-- .++ . -.||+|+.++-..|++|-.-+..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~------~-~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCIRDCI------G-SECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTGGGGT------T-TB-SSS--B-S-SS----HHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHhHHhc------C-CCCCCcCChHHHHHHHhhhhhhcc
Confidence 47899999999999998899999664221 111 1 259999999999999998877654
No 23
>PF04641 Rtf2: Rtf2 RING-finger
Probab=86.93 E-value=0.6 Score=48.61 Aligned_cols=55 Identities=29% Similarity=0.663 Sum_probs=40.1
Q ss_pred eEEeecCCCCccceeccccC---CCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeee
Q 007048 326 IIVNLRCPMSGSRIRVAGRF---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 385 (620)
Q Consensus 326 ~~VSL~CPls~~ri~~P~Rg---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 385 (620)
....+.||+|+..|.==.|+ ..|-|+ |--.++=++. ..|.||+|++++.-.|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 35678899999999421222 488887 5555555552 6799999999999888874
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.71 E-value=1.1 Score=49.80 Aligned_cols=66 Identities=20% Similarity=0.300 Sum_probs=51.9
Q ss_pred eEEeecCCCCccceeccccCCCcCcccccCHH-HHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHHh
Q 007048 326 IIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLE-TFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 397 (620)
Q Consensus 326 ~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~-~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 397 (620)
+.-.|.||+-...+.-|+- ..|.|.-|..-- .|+.. .-.||+|...+....|+.+..+.+|++..+
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~-----~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSN-----QPKCPLCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhC-----CCCCCCCCCccccccCccchHHHHHHHHHH
Confidence 4567899999999999985 689999876433 34432 238999999998889999999988887554
No 25
>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=72.78 E-value=3 Score=29.94 Aligned_cols=42 Identities=26% Similarity=0.614 Sum_probs=28.1
Q ss_pred CCCCccceeccccCCCcCcccccCH-HHHHHHHcCCCeeeccCCCCC
Q 007048 332 CPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELNQRTRKWQCPICMKN 377 (620)
Q Consensus 332 CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC~k~ 377 (620)
||+-...+..|.....|.|.-|.+- ..|++. ...+||+|++.
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 6666666666777777999866653 334432 56789999875
No 26
>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=71.31 E-value=1.4 Score=32.51 Aligned_cols=39 Identities=26% Similarity=0.677 Sum_probs=26.7
Q ss_pred CCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCC
Q 007048 332 CPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPIC 374 (620)
Q Consensus 332 CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC 374 (620)
|||=+..++-|+....|.|+-|++ =+.++.+. ..+||+|
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 677788888898999999997774 23333333 2799998
No 27
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=70.63 E-value=2.4 Score=49.48 Aligned_cols=48 Identities=25% Similarity=0.590 Sum_probs=35.9
Q ss_pred cccccCCCCC--CCCCeeeecCccccccccccccccCCCCcccccCCCCcccccccc
Q 007048 82 KIFCPCGTSL--PSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCR 136 (620)
Q Consensus 82 ~~rCiCg~sl--~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CR 136 (620)
-..|+|-.-- ..+.+|.|+...|.|-.|-.||+|-.-| -..|||.-|-
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVP-------tGpWfCrKCe 55 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVP-------TGPWFCRKCE 55 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecC-------CCchhhhhhh
Confidence 3568996542 2568999999999999999999998654 3456665554
No 28
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.78 E-value=0.84 Score=49.47 Aligned_cols=70 Identities=27% Similarity=0.500 Sum_probs=55.9
Q ss_pred eceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCC-CCCeeecHHHHHHHHHH
Q 007048 324 DSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYS-LEDLIIDPYFHRITTMM 396 (620)
Q Consensus 324 ~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~-~~~L~ID~y~~~IL~~l 396 (620)
..+.+.|.||+-...|+.---.+.|-|--|||+-+ .+.+..--.||-|.|.+- =.+|++|.-|..|+..|
T Consensus 38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 56789999999999999888889999999998733 233444568999987664 45999999999987665
No 29
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=61.34 E-value=12 Score=42.45 Aligned_cols=54 Identities=20% Similarity=0.421 Sum_probs=40.2
Q ss_pred cCCCCccccc-CCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCc--cccccc
Q 007048 77 LNLGGKIFCP-CGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPL--FFCETC 135 (620)
Q Consensus 77 ~~~~~~~rCi-Cg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~--fyCe~C 135 (620)
+...+...|. |..+-.+.-+++|+. |+...|++|+..+.-- .|+.... |.|..|
T Consensus 539 ~~~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPLTR---~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 539 APKAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPLTR---LPKKNKNFGWQCSEC 595 (707)
T ss_pred cccccceeeeeeccchhhHHHhhcch--hhceeeccccCCcccc---CcccccCcceeeccc
Confidence 3345667786 988888888999999 9999999998876432 2443333 478888
No 30
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=60.59 E-value=5.4 Score=32.49 Aligned_cols=36 Identities=22% Similarity=0.558 Sum_probs=26.5
Q ss_pred ccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCC
Q 007048 336 GSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED 382 (620)
Q Consensus 336 ~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~ 382 (620)
..++..|+-..-|.+ |||++-|= -||+|++++.+.+
T Consensus 18 ~~~~~~pCgH~I~~~--~f~~~rYn---------gCPfC~~~~~~~~ 53 (55)
T PF14447_consen 18 TKGTVLPCGHLICDN--CFPGERYN---------GCPFCGTPFEFDD 53 (55)
T ss_pred cccccccccceeecc--ccChhhcc---------CCCCCCCcccCCC
Confidence 455566665555655 89999874 6999999987765
No 31
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=59.90 E-value=4.2 Score=48.03 Aligned_cols=56 Identities=25% Similarity=0.450 Sum_probs=41.8
Q ss_pred eceEEeecCCCCccceeccccCCCcCcccccC-HHHHHHHHcCCCeeeccCCCCCCCCCCee
Q 007048 324 DSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNYSLEDLI 384 (620)
Q Consensus 324 ~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~~~~~L~ 384 (620)
..++=-|+||+..+|-+--+= ..|-|+-||. ...++.+.+ =+||.|+..+.+.|+.
T Consensus 638 k~yK~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~etRq----RKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 638 KEYKELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYETRQ----RKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHHhceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHHhc----CCCCCCCCCCCccccc
Confidence 346778999999988764332 4799999984 456665544 4799999999888763
No 32
>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=59.66 E-value=1.6 Score=32.86 Aligned_cols=18 Identities=17% Similarity=0.746 Sum_probs=11.7
Q ss_pred HHHHcCCCeeeccCCCCC
Q 007048 360 VELNQRTRKWQCPICMKN 377 (620)
Q Consensus 360 L~~n~~~~~W~CPiC~k~ 377 (620)
.++.....+|.|++|+..
T Consensus 16 ~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 16 CQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp SEEETTTTEEEETTT--E
T ss_pred ceEcCCCCEEECcCCCCc
Confidence 334456789999999864
No 33
>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=57.48 E-value=6.2 Score=28.92 Aligned_cols=40 Identities=30% Similarity=0.701 Sum_probs=28.4
Q ss_pred CCCCccceeccccCCCcCcccccC-HHHHHHHHcCCCeeeccCC
Q 007048 332 CPMSGSRIRVAGRFKPCVHTGCFD-LETFVELNQRTRKWQCPIC 374 (620)
Q Consensus 332 CPls~~ri~~P~Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC 374 (620)
|||=...+..|.+...|.|.=|.+ +..+++. ...-+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~---~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN---SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH---TSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh---cCCccCCcC
Confidence 566777778888889999996654 3333333 666779998
No 34
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=57.37 E-value=6.5 Score=30.21 Aligned_cols=39 Identities=23% Similarity=0.581 Sum_probs=21.0
Q ss_pred CCCCccceec----cccCCCcCcccccCHHHHHHHHcCCCeeecc
Q 007048 332 CPMSGSRIRV----AGRFKPCVHTGCFDLETFVELNQRTRKWQCP 372 (620)
Q Consensus 332 CPls~~ri~~----P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CP 372 (620)
||+++. +.. |..- .|-|.=|.+.-.=|..+....+.+||
T Consensus 1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788887 766 6664 49999998877777666556789998
No 35
>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=55.79 E-value=3.8 Score=32.52 Aligned_cols=38 Identities=16% Similarity=0.442 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHH
Q 007048 356 LETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMM 396 (620)
Q Consensus 356 l~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l 396 (620)
+.-++..-..... .||+|++++.-+.- +.++.++-..+
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 44444443333
No 36
>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=53.94 E-value=6 Score=30.58 Aligned_cols=43 Identities=33% Similarity=0.644 Sum_probs=25.7
Q ss_pred ecCCCCccceeccccCCCcCcc-cccCH-HHHHHHHcCCCeeeccCCCCCC
Q 007048 330 LRCPMSGSRIRVAGRFKPCVHT-GCFDL-ETFVELNQRTRKWQCPICMKNY 378 (620)
Q Consensus 330 L~CPls~~ri~~P~Rg~~C~Hl-QCFDl-~~fL~~n~~~~~W~CPiC~k~~ 378 (620)
..|++=+.....+ -...|.|+ -|.+= ..++. ...+||+|.+++
T Consensus 3 ~~C~iC~~~~~~~-~~~pCgH~~~C~~C~~~~~~-----~~~~CP~Cr~~i 47 (50)
T PF13920_consen 3 EECPICFENPRDV-VLLPCGHLCFCEECAERLLK-----RKKKCPICRQPI 47 (50)
T ss_dssp SB-TTTSSSBSSE-EEETTCEEEEEHHHHHHHHH-----TTSBBTTTTBB-
T ss_pred CCCccCCccCCce-EEeCCCChHHHHHHhHHhcc-----cCCCCCcCChhh
Confidence 3466666655443 33469998 56542 23332 678999999876
No 37
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=53.55 E-value=10 Score=44.58 Aligned_cols=252 Identities=13% Similarity=0.012 Sum_probs=140.7
Q ss_pred eeceEEeecCCCCccceeccccCCCcCcccccC--HHHHHHHHc--CCCeeeccCCCCCCCCCCeeecHHHHHHHHHHhc
Q 007048 323 ADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFD--LETFVELNQ--RTRKWQCPICMKNYSLEDLIIDPYFHRITTMMRN 398 (620)
Q Consensus 323 ~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFD--l~~fL~~n~--~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~~ 398 (620)
..+.-+.+.+|.-..+.++.+|...|.+.+|+. ..-+=+..+ ....|.||+|-+.+...-.....++..+-..++.
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (636)
T KOG2169|consen 11 LLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVKLHPNVVPPFYPLLWQLLRH 90 (636)
T ss_pred cchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccccCCcccCccccchhccccc
Confidence 334466788999999999999999999999998 333333333 4578999999988887777788777765344544
Q ss_pred CCC-CceEEEEcc---CCcEEEeccCCC-----CCCccccCCCCCcccccccccccccceeeeccC----CceeeeEec-
Q 007048 399 FAD-DLTEIEVKH---DGSWRVKCKGEN-----NNLAEWHSPDGSTYAARSEVVSNSETKQLVNSG----QTIIARIKK- 464 (620)
Q Consensus 399 ~~~-dv~eV~v~~---DGsW~~~~~~e~-----~~~~~w~~p~g~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~- 464 (620)
... -+....+.- +..|+++..... ..+.+|+....+.+.............+.+.++ +.+.-|.|.
T Consensus 91 ~~~~~~~~~~l~g~~~~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~~~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~ 170 (636)
T KOG2169|consen 91 PTQQPVTPSSLLGPPLPFHPDVKLKKLPFYDVLSELIKPHVLHSSNSPSLSESPFLFALTPEQVSGISSRPDVLPGSKSE 170 (636)
T ss_pred CCCCCCCcccccCCCCcCCCcccccCCchheecccccCceeecCcCCCCcccccchhhcchhhhhhcccccccccccccc
Confidence 322 355555555 688998776655 677788887766662221111112212222222 233334444
Q ss_pred ------CCCCceeeecCCCCCC-Cccccccc--cCCcceeeeccccCCCCCCCCCC---CcccCCCCC-------cccCC
Q 007048 465 ------NLSANVDVSKYWSTSP-NKHMSYHV--ENNSEKIITMSSSASGCSRDEED---PTVNQDTNS-------RKDLN 525 (620)
Q Consensus 465 ------~~~g~~~~s~~~~~~~-~~~~~~~~--~~~~~~~~~~ss~~~~~~~~~~~---~~~~~~~~~-------~~~~~ 525 (620)
..++.||-..|..... -|.-.-.+ .+...+..++....++..++..+ .++...... +..-.
T Consensus 171 ~~~~~~~~s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~y 250 (636)
T KOG2169|consen 171 GSVCLMETSCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSY 250 (636)
T ss_pred cceeeccccCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCccc
Confidence 3356666555433222 11101111 23333444444444444444443 233332221 22333
Q ss_pred CCCCCCCCccCCCCC-CCCCCCCCcEEEecCCCcCCCccC-CCcccCCCcc
Q 007048 526 DIPHRIDPIFGTGNQ-TDGLIGDTDIIVLSDSEEDNDHLA-PSTSYQSYHP 574 (620)
Q Consensus 526 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~lsds~~~~~~~~-~~~~~~~~~~ 574 (620)
++...+..+++.... .---.......+++.|+......+ .+..++-.++
T Consensus 251 sl~~~~v~~~t~~~llq~~~~~~~~~~~~~~s~~~~~~~l~~~~d~~i~tt 301 (636)
T KOG2169|consen 251 SLSVYFVEGLTSKDLLQRLKQNGKINRNLSQSDALIKKKLTAGPDSEIATT 301 (636)
T ss_pred ceEEEEecccCHHHHHHHHhccCCccCchhHhHHHhhcccccCCcccceec
Confidence 445566666665554 212225566667788888766666 5555555444
No 38
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=53.06 E-value=6.2 Score=43.10 Aligned_cols=51 Identities=25% Similarity=0.436 Sum_probs=39.6
Q ss_pred cccccCCCCC-CCCCeeeecCccccccccccc--cccCCCCcccccCCCCcccccccccc
Q 007048 82 KIFCPCGTSL-PSESKIQCVDPRCLVQQHISC--VIIPEKPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 82 ~~rCiCg~sl-~~~~mIqC~~~~C~v~qH~~C--v~i~~kp~~~~p~~P~~fyCe~CRL~ 138 (620)
..+|.|-..- +...|++|+. |..|.|..| ++++.+. -.....|+|..|...
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~--C~~~~~~ec~~v~~~~~e----~p~~~~~~c~~c~~~ 113 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDL--CEDWYHGECWEVGTAEKE----APKEDPKVCDECKEA 113 (345)
T ss_pred hchhhcccccCchhhhhcccc--ccccccccccccCchhhc----CCccccccccccchh
Confidence 4467776653 2347999999 999999999 9998764 345788999988864
No 39
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=52.14 E-value=11 Score=46.77 Aligned_cols=55 Identities=24% Similarity=0.470 Sum_probs=41.2
Q ss_pred CCCcccccCCCCCC--CCCeeeecCccccccccccccccCCCCcccccCCCCcccccccccccCCC
Q 007048 79 LGGKIFCPCGTSLP--SESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKRADP 142 (620)
Q Consensus 79 ~~~~~rCiCg~sl~--~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~~~DP 142 (620)
.++..-|+|-..-- .+..|.|+. |++-.|..||+++..| -..|.|-.|-....-|
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~--Cnl~VHq~Cygi~~ip-------eg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG--CNLAVHQECYGIPFIP-------EGQWLCRRCLQSPQRP 273 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC--CcchhhhhccCCCCCC-------CCcEeehhhccCcCcc
Confidence 45667788976533 367999999 9999999999966433 4578888888765544
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=51.26 E-value=9.4 Score=37.25 Aligned_cols=46 Identities=30% Similarity=0.209 Sum_probs=25.2
Q ss_pred ceEEEECCeEeeec-CCCCcccCCCCCC--CCCCcccccccCcccEEEEEE
Q 007048 213 HAELQVNGLLVRTV-NRPGTQLLGSNGR--DDGALITLYIGEGVNQISLSG 260 (620)
Q Consensus 213 ~~~I~VNg~~v~~~-~rP~~~~~g~~~R--~~~p~IT~~lk~g~N~I~Is~ 260 (620)
..+++|||+.|-.- ..|+... ..+| -...+||++|+.|.|.|.+..
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 56899999998742 2354421 1111 234569999999999988764
No 41
>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=49.11 E-value=54 Score=30.88 Aligned_cols=66 Identities=24% Similarity=0.168 Sum_probs=41.5
Q ss_pred EEEEEEecccccccccCCCceEEEEEEeecCCccccccCCCceEEEECCeEeeecCCCCcccCCCCCCCCCCcccccccC
Q 007048 172 AEAAFHLTKAHSDLLQNTEYDVQAWCILLNDKVSFRMQWPLHAELQVNGLLVRTVNRPGTQLLGSNGRDDGALITLYIGE 251 (620)
Q Consensus 172 ~~~~F~Lt~~~~~~L~~~~~~lqv~Ci~l~d~~~~~~~wP~~~~I~VNg~~v~~~~rP~~~~~g~~~R~~~p~IT~~lk~ 251 (620)
.+..|.|.++. + +.++.|..-.++ ....|.|||+.|-.. ..+. +.-..+||++|+.
T Consensus 72 Yr~~f~lp~~~----~--~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~~~~-------~~~~~dIt~~l~~ 127 (167)
T PF02837_consen 72 YRRTFTLPADW----K--GKRVFLRFEGVD----------YAAEVYVNGKLVGSH-EGGY-------TPFEFDITDYLKP 127 (167)
T ss_dssp EEEEEEESGGG----T--TSEEEEEESEEE----------SEEEEEETTEEEEEE-ESTT-------S-EEEECGGGSSS
T ss_pred EEEEEEeCchh----c--CceEEEEeccce----------EeeEEEeCCeEEeee-CCCc-------CCeEEeChhhccC
Confidence 56678887754 1 234444443332 467899999988742 2111 2233569999999
Q ss_pred cc-cEEEEEEe
Q 007048 252 GV-NQISLSGC 261 (620)
Q Consensus 252 g~-N~I~Is~~ 261 (620)
|. |.|.|...
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 42
>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=49.07 E-value=14 Score=28.15 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=22.4
Q ss_pred ChhHHHHHHHcCCCCCC--chHHHHHHHHHh
Q 007048 1 MKELKDVLTKLGLPKQG--KKQDLVDRIFHQ 29 (620)
Q Consensus 1 i~ELq~~L~~~g~~K~G--kK~eL~~R~l~l 29 (620)
+.||+.+=..+|.+..+ ||+||+..|+.-
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 43
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=47.98 E-value=6.9 Score=24.63 Aligned_cols=11 Identities=55% Similarity=1.404 Sum_probs=7.2
Q ss_pred eeccCCCCCCC
Q 007048 369 WQCPICMKNYS 379 (620)
Q Consensus 369 W~CPiC~k~~~ 379 (620)
|+||+|++.+.
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 44
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.83 E-value=13 Score=30.29 Aligned_cols=33 Identities=24% Similarity=0.633 Sum_probs=27.6
Q ss_pred ccccc-CCCCCC-CCCeeeecCccccccccccccccC
Q 007048 82 KIFCP-CGTSLP-SESKIQCVDPRCLVQQHISCVIIP 116 (620)
Q Consensus 82 ~~rCi-Cg~sl~-~~~mIqC~~~~C~v~qH~~Cv~i~ 116 (620)
..+|. ||..+. .++.|.|-. |....|..|+...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~--CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPE--CGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCCCCEEECCC--CCCcccHHHHhhC
Confidence 45676 898875 789999999 9999999998654
No 45
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=45.27 E-value=8.9 Score=29.06 Aligned_cols=41 Identities=24% Similarity=0.572 Sum_probs=23.1
Q ss_pred CCCCccceeccccCCCcCcccccCH-HHHHHHHcCCCeeeccCC
Q 007048 332 CPMSGSRIRVAGRFKPCVHTGCFDL-ETFVELNQRTRKWQCPIC 374 (620)
Q Consensus 332 CPls~~ri~~P~Rg~~C~HlQCFDl-~~fL~~n~~~~~W~CPiC 374 (620)
|||-...++-|+. ..|.|.=|+.- ..|.. ......+.||+|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~-~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWK-EPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHC-CSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHH-ccCCcCCCCcCC
Confidence 6777777777776 58999988754 33332 222334999998
No 46
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.32 E-value=11 Score=39.68 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=41.4
Q ss_pred eecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeeec
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIID 386 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID 386 (620)
+.+|+|-..-+..|++. .|-|+ |-+.-.+.|-.....=.||.|.....+..++|+
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 67899999999999885 79999 555555655333334449999999988877665
No 47
>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=43.95 E-value=19 Score=37.10 Aligned_cols=32 Identities=34% Similarity=0.542 Sum_probs=28.3
Q ss_pred ChhHHHHHHHcCCCCCCchHHHHHHHHHhcCh
Q 007048 1 MKELKDVLTKLGLPKQGKKQDLVDRIFHQLSD 32 (620)
Q Consensus 1 i~ELq~~L~~~g~~K~GkK~eL~~R~l~ll~~ 32 (620)
|.||+.=|..-||+--|.|.||++|+.+-+..
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 48
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=43.25 E-value=11 Score=27.12 Aligned_cols=11 Identities=36% Similarity=1.222 Sum_probs=9.5
Q ss_pred CeeeccCCCCC
Q 007048 367 RKWQCPICMKN 377 (620)
Q Consensus 367 ~~W~CPiC~k~ 377 (620)
..|.||+|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 78999999864
No 49
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.61 E-value=12 Score=36.74 Aligned_cols=21 Identities=29% Similarity=0.548 Sum_probs=17.6
Q ss_pred eeeccCCCCCCCCCCeeecHH
Q 007048 368 KWQCPICMKNYSLEDLIIDPY 388 (620)
Q Consensus 368 ~W~CPiC~k~~~~~~L~ID~y 388 (620)
-.+||||+|.+..+++.|--.
T Consensus 138 g~KCPvC~K~V~sDd~e~Hlv 158 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDDAEIHLV 158 (205)
T ss_pred CccCCccccccCCCcceEEEE
Confidence 478999999999999887643
No 50
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=42.44 E-value=14 Score=44.13 Aligned_cols=66 Identities=17% Similarity=0.418 Sum_probs=46.9
Q ss_pred CCCccccc-CCCCCCCCCeeeecCcccccc-ccccccccCCCCcccccCCCCcccccccccccC---CChhHhhhhcc
Q 007048 79 LGGKIFCP-CGTSLPSESKIQCVDPRCLVQ-QHISCVIIPEKPMEEIRLLPPLFFCETCRIKRA---DPFWITVAHLV 151 (620)
Q Consensus 79 ~~~~~rCi-Cg~sl~~~~mIqC~~~~C~v~-qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~~~---DPF~~~i~~lL 151 (620)
.....+|. |+.+-...-||-|+. |+.- .|.-|+..+.. ...-..|||.-|-+..+ .=|+..++.++
T Consensus 212 ~~E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~-----eiP~~eWYC~NC~dL~~~eh~~~~~~~~~~~ 282 (1134)
T KOG0825|consen 212 SQEEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLS-----ESPVNEWYCTNCSLLEITEHKDFTLKTEELI 282 (1134)
T ss_pred ccccccceeeccCChHHhheeecc--cccceeeccccCcccc-----cccccceecCcchhhhhhhhhHHHHHHHHHh
Confidence 34567786 998877788999999 9997 99999886542 12346899999998532 24555555444
No 51
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.23 E-value=37 Score=32.37 Aligned_cols=39 Identities=18% Similarity=0.462 Sum_probs=24.9
Q ss_pred EEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCC
Q 007048 327 IVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSL 380 (620)
Q Consensus 327 ~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~ 380 (620)
.....||- |.+- |.+.-.+........+.||.|+..+..
T Consensus 97 ~~~Y~Cp~-------------C~~~--y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 97 NAYYKCPN-------------CQSK--YTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CcEEECcC-------------CCCE--eeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 45778984 5433 555555544333567999999987644
No 52
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=41.51 E-value=15 Score=42.80 Aligned_cols=51 Identities=37% Similarity=0.740 Sum_probs=39.3
Q ss_pred cccc-CCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCcccccccccc
Q 007048 83 IFCP-CGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 83 ~rCi-Cg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~ 138 (620)
.+|. |+++-....+|+|+. |..-+|..|.-.+..+ +.+ .++-|+|..|..+
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~--Cp~sFH~~CLePPl~~-eni--P~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDG--CPRSFHQTCLEPPLEP-ENI--PPGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccccccceeecC--CchHHHHhhcCCCCCc-ccC--CCCccccCCCeee
Confidence 3777 888744467899999 9999999998876322 334 3568999999976
No 53
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.07 E-value=10 Score=37.60 Aligned_cols=62 Identities=23% Similarity=0.390 Sum_probs=44.5
Q ss_pred eecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHHh
Q 007048 329 NLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 397 (620)
Q Consensus 329 SL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 397 (620)
-|.|||....++-| +...|.|.-|..-..=+.- ....||.|..... +|.--..+..+.+.++
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 46799999999999 8888999999854433322 5699999995222 6665555666655554
No 54
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=39.86 E-value=4.8 Score=43.95 Aligned_cols=56 Identities=27% Similarity=0.475 Sum_probs=39.7
Q ss_pred Cccccc-CCCCCCC-CCeeeecCccccccccccccccCCCCcccccCCCCcccccccccc
Q 007048 81 GKIFCP-CGTSLPS-ESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 81 ~~~rCi-Cg~sl~~-~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~ 138 (620)
....|. ||.++.+ ..+|.|.. |..|+|..|+.+..............|+|+.|.+.
T Consensus 238 ~~~~~~~cg~~~~~~~~~~~~~~--~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 238 SKLICDPCGLSDANKKFEICCDL--CESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred ccccccccCcchHHHHHHHHHHH--HHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 445565 6765443 67899999 99999999999986553333333355999999873
No 55
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=38.33 E-value=16 Score=43.33 Aligned_cols=44 Identities=25% Similarity=0.576 Sum_probs=35.9
Q ss_pred cCCCC--CCCCCeeeecCccccccccccccccCCCCcccccCCCCcccccccccc
Q 007048 86 PCGTS--LPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 86 iCg~s--l~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~ 138 (620)
+|.+. -+...||-|+. |+.-.|..||+|-+-| -..|.|..|-|.
T Consensus 276 vCrspD~e~~neMVfCd~--Cn~cVHqaCyGIle~p-------~gpWlCr~Calg 321 (893)
T KOG0954|consen 276 VCRSPDSEEANEMVFCDK--CNICVHQACYGILEVP-------EGPWLCRTCALG 321 (893)
T ss_pred eecCCCccccceeEEecc--chhHHHHhhhceeecC-------CCCeeehhcccc
Confidence 36544 45678999999 9999999999998654 267899999986
No 56
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.92 E-value=19 Score=38.40 Aligned_cols=49 Identities=20% Similarity=0.376 Sum_probs=39.0
Q ss_pred CCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCcccccc-cccccCCChhH
Q 007048 87 CGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCET-CRIKRADPFWI 145 (620)
Q Consensus 87 Cg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~-CRL~~~DPF~~ 145 (620)
|++......|+-|+. |....|.-||++..-| ...|+|.+ |+.. ..||.+
T Consensus 320 C~~P~~E~E~~FCD~--CDRG~HT~CVGL~~lP-------~G~WICD~~C~~~-~~~t~R 369 (381)
T KOG1512|consen 320 CLGPVIESEHLFCDV--CDRGPHTLCVGLQDLP-------RGEWICDMRCREA-TLNTTR 369 (381)
T ss_pred cCCcccchheecccc--ccCCCCcccccccccc-------CccchhhhHHHHh-cCCCCh
Confidence 887776778999999 9999999999997543 46899986 7764 456654
No 57
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=35.86 E-value=33 Score=28.86 Aligned_cols=31 Identities=29% Similarity=0.510 Sum_probs=16.5
Q ss_pred CcccccCHHHHHHHHcCC-----CeeeccCCCCCCCC
Q 007048 349 VHTGCFDLETFVELNQRT-----RKWQCPICMKNYSL 380 (620)
Q Consensus 349 ~HlQCFDl~~fL~~n~~~-----~~W~CPiC~k~~~~ 380 (620)
-|+.|. .++|+...... -.++||.|.+++..
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 477774 34555443321 26899999988754
No 58
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=35.84 E-value=16 Score=35.71 Aligned_cols=26 Identities=31% Similarity=0.643 Sum_probs=18.4
Q ss_pred CCcCcccccCHHHHHHHHc-CCCeeeccCCCC
Q 007048 346 KPCVHTGCFDLETFVELNQ-RTRKWQCPICMK 376 (620)
Q Consensus 346 ~~C~HlQCFDl~~fL~~n~-~~~~W~CPiC~k 376 (620)
..|+|+.|.=... +. ....|.|| |+-
T Consensus 106 ~iCtHlGC~~~~~----~~~~~~~~~CP-CHG 132 (177)
T COG0723 106 AICTHLGCTVPWN----NAGAEGGFFCP-CHG 132 (177)
T ss_pred eeccCCCCccCcc----cCCCCCeEEcc-CCC
Confidence 4599999985544 33 34799999 763
No 59
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=35.20 E-value=37 Score=25.23 Aligned_cols=24 Identities=38% Similarity=0.702 Sum_probs=18.2
Q ss_pred ChhHHHHHHHcCC--CCCCchHHHHH
Q 007048 1 MKELKDVLTKLGL--PKQGKKQDLVD 24 (620)
Q Consensus 1 i~ELq~~L~~~g~--~K~GkK~eL~~ 24 (620)
|.||+.+|...|. +.+.||.||+.
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 5799999999886 68889999985
No 60
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=33.62 E-value=21 Score=39.42 Aligned_cols=28 Identities=32% Similarity=0.795 Sum_probs=19.5
Q ss_pred CcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCC
Q 007048 347 PCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLE 381 (620)
Q Consensus 347 ~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~ 381 (620)
+|-|+.| |++|++.++ .||||..++-++
T Consensus 320 HilHl~C--LknW~ERqQ-----TCPICr~p~ifd 347 (491)
T COG5243 320 HILHLHC--LKNWLERQQ-----TCPICRRPVIFD 347 (491)
T ss_pred ceeeHHH--HHHHHHhcc-----CCCcccCccccc
Confidence 4666666 678886543 599999986443
No 61
>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=32.95 E-value=14 Score=23.71 Aligned_cols=11 Identities=55% Similarity=1.455 Sum_probs=9.0
Q ss_pred eeccCCCCCCC
Q 007048 369 WQCPICMKNYS 379 (620)
Q Consensus 369 W~CPiC~k~~~ 379 (620)
|+||+|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 78999998764
No 62
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=32.93 E-value=26 Score=23.93 Aligned_cols=25 Identities=36% Similarity=0.906 Sum_probs=15.4
Q ss_pred CCcCcccccC-HHHHHHHHcCCCeeeccCC
Q 007048 346 KPCVHTGCFD-LETFVELNQRTRKWQCPIC 374 (620)
Q Consensus 346 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC 374 (620)
..|.|.-|.. +..|++ ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 4599986654 334444 344679987
No 63
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=32.53 E-value=21 Score=26.71 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=13.7
Q ss_pred CCcCcccccC-HHHHHHHHcCCCeeeccCCC
Q 007048 346 KPCVHTGCFD-LETFVELNQRTRKWQCPICM 375 (620)
Q Consensus 346 ~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~ 375 (620)
..|.|.-|.+ +..||+.+ .+||+|.
T Consensus 19 l~C~H~fh~~Ci~~~~~~~-----~~CP~CR 44 (44)
T PF13639_consen 19 LPCGHVFHRSCIKEWLKRN-----NSCPVCR 44 (44)
T ss_dssp ETTSEEEEHHHHHHHHHHS-----SB-TTTH
T ss_pred ccCCCeeCHHHHHHHHHhC-----CcCCccC
Confidence 3488874432 45555442 3999993
No 64
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=32.40 E-value=20 Score=28.57 Aligned_cols=12 Identities=33% Similarity=1.198 Sum_probs=9.5
Q ss_pred CCeeeccCCCCC
Q 007048 366 TRKWQCPICMKN 377 (620)
Q Consensus 366 ~~~W~CPiC~k~ 377 (620)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 457999999854
No 65
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=31.51 E-value=69 Score=35.15 Aligned_cols=41 Identities=27% Similarity=0.400 Sum_probs=32.6
Q ss_pred hhHHHHHHHcCCCCCCchHHHHHHHHHhcChhH----------HHHHHHHH
Q 007048 2 KELKDVLTKLGLPKQGKKQDLVDRIFHQLSDEG----------VARIIDDT 42 (620)
Q Consensus 2 ~ELq~~L~~~g~~K~GkK~eL~~R~l~ll~~~~----------v~~~I~e~ 42 (620)
+.+|.=|..+||+-+|.||-|+.|-.+...-.. .+.+|++|
T Consensus 254 s~ik~KLse~GLst~G~kQ~likRh~~~v~lyNsncD~l~Pvs~ael~rql 304 (442)
T KOG0287|consen 254 SDIKKKLSEHGLSTQGNKQQLIKRHQEFVHLYNSNCDALHPVSAAELVRQL 304 (442)
T ss_pred HHHHHHHHHcCCCCcchHHHHHHHHHHHHHHHhccccccCCcCHHHHHHHH
Confidence 468899999999999999999999876654422 66667666
No 66
>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=31.43 E-value=53 Score=35.58 Aligned_cols=40 Identities=30% Similarity=0.452 Sum_probs=24.2
Q ss_pred CcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCC----eeecHHH
Q 007048 347 PCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED----LIIDPYF 389 (620)
Q Consensus 347 ~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~----L~ID~y~ 389 (620)
.|-|.-|- +-|...-..+.-.||+|++.++..+ +.-|..+
T Consensus 25 ~CGH~~C~---sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D~~v 68 (309)
T TIGR00570 25 VCGHTLCE---SCVDLLFVRGSGSCPECDTPLRKNNFRVQLFEDPTV 68 (309)
T ss_pred CCCCcccH---HHHHHHhcCCCCCCCCCCCccchhhccccccccHHH
Confidence 46676554 2222211334559999999998887 5555554
No 67
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.69 E-value=70 Score=33.79 Aligned_cols=112 Identities=17% Similarity=0.279 Sum_probs=60.8
Q ss_pred EEEEEEEeecCHHHHHHhccccC-CCCcHHHHHHHHHHhhCCccCCCCCCCCCc-eeeeeceEEeecCCCCccceecccc
Q 007048 267 CFGVRLVKRQTVAQVLSLVPKET-AGEVFEDALTRVRRCFGGVATGNEDGDSDL-EIIADSIIVNLRCPMSGSRIRVAGR 344 (620)
Q Consensus 267 ~~~V~lVk~~s~eqLl~~I~~~~-~~~~~edal~rIkr~l~~~~~~~~dsDdD~-eIv~~s~~VSL~CPls~~ri~~P~R 344 (620)
+++..|=+-++-+.|++.|..+. -+.++.. ++-++..+.-..+.|.+...|. +--.+....-..||++...|.==-|
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks~~pksaSh-IKslKDvveLklt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~~ 126 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKSSLPKSASH-IKSLKDVVELKLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKYR 126 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcccCCcchhh-hcchhhHhheecccCcccccccCccccccccceeecccccceecceEE
Confidence 34555556678888998886542 1222211 1122222211112222211110 0122445788999999998873333
Q ss_pred C---CCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCCeee
Q 007048 345 F---KPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLEDLII 385 (620)
Q Consensus 345 g---~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 385 (620)
+ ..|-|+ |...+.=++- .=.|++|+..+.-+|.+|
T Consensus 127 F~~l~~CGcV--~SerAlKeik----as~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 127 FCALRCCGCV--FSERALKEIK----ASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred EEEEecccee--ccHHHHHHhh----hccccccCCcccccCeEe
Confidence 3 245554 5555544433 457999999999888775
No 68
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=30.63 E-value=29 Score=23.46 Aligned_cols=17 Identities=24% Similarity=0.825 Sum_probs=12.3
Q ss_pred HHcCCCeeeccCCCCCC
Q 007048 362 LNQRTRKWQCPICMKNY 378 (620)
Q Consensus 362 ~n~~~~~W~CPiC~k~~ 378 (620)
.-.....++||+|++.+
T Consensus 8 ~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 8 THTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHSSSSSEEESSSSEEE
T ss_pred hcCCCCCCCCCCCcCee
Confidence 33445679999999764
No 69
>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=30.12 E-value=26 Score=30.70 Aligned_cols=40 Identities=30% Similarity=0.554 Sum_probs=25.1
Q ss_pred CHHHHHHHHcCCCeeeccCCCCCCCCCCeeecHH---HHHHHHHH
Q 007048 355 DLETFVELNQRTRKWQCPICMKNYSLEDLIIDPY---FHRITTMM 396 (620)
Q Consensus 355 Dl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y---~~~IL~~l 396 (620)
+|..||.+.-+++-|-|||=-. -+.+|+--+| +.+|++.|
T Consensus 45 qLr~flk~alkTpvwl~pi~ys--lla~lipkgypgrv~ei~~il 87 (92)
T PF02228_consen 45 QLRNFLKLALKTPVWLNPINYS--LLASLIPKGYPGRVNEIINIL 87 (92)
T ss_dssp HHHHHHHHHHT-TTSTTTT-TT--THHHHS-SS-STTHHHHHHHH
T ss_pred HHHHHHHHHHcCCeeeccccHH--HHHHHccCCCCchHHHHHHHH
Confidence 7899999999999999998321 1234444444 55666544
No 70
>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=30.07 E-value=16 Score=25.08 Aligned_cols=9 Identities=44% Similarity=1.497 Sum_probs=8.0
Q ss_pred eccCCCCCC
Q 007048 370 QCPICMKNY 378 (620)
Q Consensus 370 ~CPiC~k~~ 378 (620)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
No 71
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.86 E-value=64 Score=33.51 Aligned_cols=59 Identities=17% Similarity=0.324 Sum_probs=42.4
Q ss_pred eccccCCCcCcccccCHHHHHHHHcC---------CCeeeccCCCCCCCCCCeeecHHHHHHHHHHhc
Q 007048 340 RVAGRFKPCVHTGCFDLETFVELNQR---------TRKWQCPICMKNYSLEDLIIDPYFHRITTMMRN 398 (620)
Q Consensus 340 ~~P~Rg~~C~HlQCFDl~~fL~~n~~---------~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~~ 398 (620)
.+|--...|.-+-|++|-.|--+|++ ..-++||.|+..+-+--=.+......+.+.|++
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 45666788999999999998888775 247999999988765544455555555555543
No 72
>PHA02929 N1R/p28-like protein; Provisional
Probab=29.82 E-value=48 Score=34.57 Aligned_cols=44 Identities=16% Similarity=0.542 Sum_probs=27.9
Q ss_pred ecCCCCccceeccc-------cCCCcCcccccC-HHHHHHHHcCCCeeeccCCCCCC
Q 007048 330 LRCPMSGSRIRVAG-------RFKPCVHTGCFD-LETFVELNQRTRKWQCPICMKNY 378 (620)
Q Consensus 330 L~CPls~~ri~~P~-------Rg~~C~HlQCFD-l~~fL~~n~~~~~W~CPiC~k~~ 378 (620)
..||+-...+.-+. .-..|.|.-|.+ +..|+.. . =.||+|...+
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 56999988765432 224799975554 3345532 2 2799999765
No 73
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=29.21 E-value=80 Score=26.91 Aligned_cols=31 Identities=16% Similarity=0.397 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCCceEEEEccCCcEEEecc
Q 007048 389 FHRITTMMRNFADDLTEIEVKHDGSWRVKCK 419 (620)
Q Consensus 389 ~~~IL~~l~~~~~dv~eV~v~~DGsW~~~~~ 419 (620)
..+|+..++.-+-+|.+|+++.||.|++..-
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~yev~~~ 61 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGCYEVEAR 61 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCEEEEEEE
Confidence 4556666666666999999999999999843
No 74
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.19 E-value=23 Score=27.92 Aligned_cols=13 Identities=31% Similarity=1.017 Sum_probs=7.4
Q ss_pred CCCeeeccCCCCC
Q 007048 365 RTRKWQCPICMKN 377 (620)
Q Consensus 365 ~~~~W~CPiC~k~ 377 (620)
-...|.||+|+..
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 3568999999853
No 75
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.94 E-value=29 Score=34.73 Aligned_cols=48 Identities=21% Similarity=0.517 Sum_probs=31.5
Q ss_pred ecCCCCcccee--ccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCCCCCC
Q 007048 330 LRCPMSGSRIR--VAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNYSLED 382 (620)
Q Consensus 330 L~CPls~~ri~--~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~ 382 (620)
.+||+-+.... .| =+..|-|+-|= .-|. +..+.+-+||+|+|.++-.+
T Consensus 132 ~~CPiCl~~~sek~~-vsTkCGHvFC~---~Cik-~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVP-VSTKCGHVFCS---QCIK-DALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhhccc-cccccchhHHH---HHHH-HHHHhCCCCCCcccccchhh
Confidence 78998877764 44 34789999552 1111 22356789999999776543
No 76
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=26.95 E-value=36 Score=30.42 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=26.1
Q ss_pred ccCCCCCCCCCeeeecCccccccccccccccCC
Q 007048 85 CPCGTSLPSESKIQCVDPRCLVQQHISCVIIPE 117 (620)
Q Consensus 85 CiCg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~ 117 (620)
++|+.+ .|..|+|..+.|..+.|..|-....
T Consensus 59 ~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~g 89 (110)
T PF13832_consen 59 SICGKS--GGACIKCSHPGCSTAFHPTCARKAG 89 (110)
T ss_pred cCCCCC--CceeEEcCCCCCCcCCCHHHHHHCC
Confidence 459877 5679999999999999999977654
No 77
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=26.31 E-value=38 Score=25.52 Aligned_cols=41 Identities=24% Similarity=0.507 Sum_probs=25.0
Q ss_pred CCCCccce--eccccCCCcCcccccCHHHHHHHHcCCCeeeccCCCC
Q 007048 332 CPMSGSRI--RVAGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMK 376 (620)
Q Consensus 332 CPls~~ri--~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k 376 (620)
|++=+.+. ..+.+-..|.|+=|-.=..=+. ...-.||+|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 44444444 3456677899986543222222 66789999985
No 78
>PLN00162 transport protein sec23; Provisional
Probab=25.67 E-value=20 Score=43.10 Aligned_cols=33 Identities=21% Similarity=0.725 Sum_probs=20.7
Q ss_pred cccCCCcCcccccCHHHHHHHHcCCCeeeccCCCCCC
Q 007048 342 AGRFKPCVHTGCFDLETFVELNQRTRKWQCPICMKNY 378 (620)
Q Consensus 342 P~Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~~ 378 (620)
|+|-..|+-. +.-|.+...+.++|.||+|+..-
T Consensus 53 pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N 85 (761)
T PLN00162 53 PLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRN 85 (761)
T ss_pred CCccCCCcCE----ECCceEEecCCCEEEccCCCCCC
Confidence 5554555443 33344455677899999997553
No 79
>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=24.88 E-value=39 Score=26.57 Aligned_cols=32 Identities=22% Similarity=0.480 Sum_probs=15.9
Q ss_pred eeeecCccccccccccccccCCCCcccccCCCCcccccc
Q 007048 96 KIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCET 134 (620)
Q Consensus 96 mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~ 134 (620)
.|||+. |.+|-.+. ..+.. .....|+.|+|.+
T Consensus 3 WVQCd~--C~KWR~lp-~~~~~----~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 3 WVQCDS--CLKWRRLP-EEVDP----IREELPDPWYCSM 34 (50)
T ss_dssp EEE-TT--T--EEEE--CCHHC----TSCCSSTT--GGG
T ss_pred EEECCC--CCceeeCC-hhhCc----ccccCCCeEEcCC
Confidence 689998 99999765 22211 1134677999975
No 80
>PRK10613 hypothetical protein; Provisional
Probab=24.74 E-value=1.6e+02 Score=25.48 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=34.9
Q ss_pred HHHHHHHcCCCCCCchHHHHHHHHHhcChhH-------HHHHHHHHHH
Q 007048 4 LKDVLTKLGLPKQGKKQDLVDRIFHQLSDEG-------VARIIDDTYR 44 (620)
Q Consensus 4 Lq~~L~~~g~~K~GkK~eL~~R~l~ll~~~~-------v~~~I~e~y~ 44 (620)
|--+|.++|.---||-=-=++|.++-++|+. -.+.|+..||
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 3456889999999999999999999999988 4567777887
No 81
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=24.24 E-value=1.3e+02 Score=25.06 Aligned_cols=55 Identities=27% Similarity=0.566 Sum_probs=32.8
Q ss_pred CcHHHHHHHHHHhhCCccCCCCCCCCCceee---eeceEEeecCCCCccceeccccCCCcCcccccCHHHHHHHHcCCCe
Q 007048 292 EVFEDALTRVRRCFGGVATGNEDGDSDLEII---ADSIIVNLRCPMSGSRIRVAGRFKPCVHTGCFDLETFVELNQRTRK 368 (620)
Q Consensus 292 ~~~edal~rIkr~l~~~~~~~~dsDdD~eIv---~~s~~VSL~CPls~~ri~~P~Rg~~C~HlQCFDl~~fL~~n~~~~~ 368 (620)
.+++++..+....+. |.+++ -....+.++||+-+.-.--| +.+|+. .+
T Consensus 3 ~t~~~~~~r~~e~Fp-----------~~slvef~g~~~PvtI~CP~HG~~~~s~-------------~~~~~~-----sk 53 (60)
T PF05265_consen 3 MTFESAASRFEEKFP-----------HYSLVEFSGVATPVTIRCPKHGNFTCST-------------FNSFIK-----SK 53 (60)
T ss_pred eeHHHHHHHHHHHCC-----------CceEEEEeCCCCceEEECCCCCcEEecc-------------HHhhhh-----hc
Confidence 467778777776653 23333 24458889999876543322 233332 45
Q ss_pred eeccCCC
Q 007048 369 WQCPICM 375 (620)
Q Consensus 369 W~CPiC~ 375 (620)
|-||.|+
T Consensus 54 ~GCP~Cg 60 (60)
T PF05265_consen 54 HGCPECG 60 (60)
T ss_pred cCCCCCC
Confidence 7899995
No 82
>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=24.22 E-value=22 Score=28.13 Aligned_cols=11 Identities=36% Similarity=1.174 Sum_probs=8.6
Q ss_pred eeeccCCCCCC
Q 007048 368 KWQCPICMKNY 378 (620)
Q Consensus 368 ~W~CPiC~k~~ 378 (620)
++.||.|++.+
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 57899999843
No 83
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=23.26 E-value=30 Score=37.53 Aligned_cols=41 Identities=22% Similarity=0.343 Sum_probs=28.3
Q ss_pred cceeccc-cCCCcCcccccCHHHHHHHHcCCCeeeccCCCCC
Q 007048 337 SRIRVAG-RFKPCVHTGCFDLETFVELNQRTRKWQCPICMKN 377 (620)
Q Consensus 337 ~ri~~P~-Rg~~C~HlQCFDl~~fL~~n~~~~~W~CPiC~k~ 377 (620)
+.+.+|. |-+.|.-..|||--.=-+.-+....|.||.|++.
T Consensus 252 s~l~vp~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 252 STLLVPPYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK 293 (415)
T ss_pred ceeeeccchheeecHHHHHHHhhhHHhhcCcccccCchhccc
Confidence 3344444 5678887779876555555566789999999855
No 84
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=23.03 E-value=17 Score=42.59 Aligned_cols=40 Identities=28% Similarity=0.461 Sum_probs=30.2
Q ss_pred CeeeecCccccccccccccccCC-CCcccccCCCCcccccccccc
Q 007048 95 SKIQCVDPRCLVQQHISCVIIPE-KPMEEIRLLPPLFFCETCRIK 138 (620)
Q Consensus 95 ~mIqC~~~~C~v~qH~~Cv~i~~-kp~~~~p~~P~~fyCe~CRL~ 138 (620)
.|+.|.. |.+|+|..|-++.. +.|+.. ..-.|-|..||-.
T Consensus 162 ~~~~c~~--c~rwsh~~c~~~sdd~~~q~~--vD~~~~CS~CR~e 202 (694)
T KOG4443|consen 162 PMVCCSI--CQRWSHGGCDGISDDKYMQAQ--VDLQYKCSTCRGE 202 (694)
T ss_pred hhHHHHH--hcccccCCCCccchHHHHHHh--hhhhcccceeehh
Confidence 4799999 99999999999874 333322 2258999999943
No 85
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.89 E-value=73 Score=35.68 Aligned_cols=31 Identities=26% Similarity=0.340 Sum_probs=27.9
Q ss_pred hhHHHHHHHcCCCCCCchHHHHHHHHHhcCh
Q 007048 2 KELKDVLTKLGLPKQGKKQDLVDRIFHQLSD 32 (620)
Q Consensus 2 ~ELq~~L~~~g~~K~GkK~eL~~R~l~ll~~ 32 (620)
+.|+..|..+||+-+|-|+.|+.|--+...-
T Consensus 272 ~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l 302 (397)
T TIGR00599 272 SQIRKKLSELGLSTNGTRQLLQKRHNEWETL 302 (397)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHH
Confidence 5799999999999999999999998876654
No 86
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=21.36 E-value=63 Score=26.86 Aligned_cols=29 Identities=14% Similarity=0.272 Sum_probs=23.1
Q ss_pred CeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007048 367 RKWQCPICMKNYSLEDLIIDPYFHRITTM 395 (620)
Q Consensus 367 ~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 395 (620)
|.=.||+|++.+.+++-.-.+--.+||+.
T Consensus 7 PH~HC~VCg~aIp~de~~CSe~C~eil~k 35 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQVCSEECGEILNK 35 (64)
T ss_pred CCccccccCCcCCCccchHHHHHHHHHHH
Confidence 45579999999999888777777777753
No 87
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=20.74 E-value=28 Score=44.77 Aligned_cols=52 Identities=23% Similarity=0.586 Sum_probs=39.3
Q ss_pred Cccccc-CCCCCCCCCeeeecCccccccccccccccCCCCcccccCCCCccccccccccc
Q 007048 81 GKIFCP-CGTSLPSESKIQCVDPRCLVQQHISCVIIPEKPMEEIRLLPPLFFCETCRIKR 139 (620)
Q Consensus 81 ~~~rCi-Cg~sl~~~~mIqC~~~~C~v~qH~~Cv~i~~kp~~~~p~~P~~fyCe~CRL~~ 139 (620)
.+.+|. |.-.-+...|+-|.. |..|.|..|....... ..+..|+|+.||..+
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 445554 655555568999999 9999999998865432 356779999999975
No 88
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=20.00 E-value=40 Score=36.93 Aligned_cols=64 Identities=25% Similarity=0.409 Sum_probs=50.7
Q ss_pred EeecCCCCccceeccccCCCcCcccc-cCHHHHHHHHcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHHh
Q 007048 328 VNLRCPMSGSRIRVAGRFKPCVHTGC-FDLETFVELNQRTRKWQCPICMKNYSLEDLIIDPYFHRITTMMR 397 (620)
Q Consensus 328 VSL~CPls~~ri~~P~Rg~~C~HlQC-FDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 397 (620)
=.|+|-|.+.=+++|.-.- |.|.-| |-...||. .+=+||.|-..++-.+|+=...+.+|++.++
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~-----~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLS-----YKPQCPTCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhc-----cCCCCCceecccchhhhhhhhHHHHHHHHHH
Confidence 3689999988888888766 999876 46666663 3457999999999899998888888887553
Done!