Query 007360
Match_columns 606
No_of_seqs 275 out of 555
Neff 5.5
Searched_HMMs 46136
Date Thu Mar 28 22:31:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007360.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007360hhsearch_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 1E-36 2.2E-41 344.9 24.2 374 12-454 1-396 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 2.8E-21 6.1E-26 150.9 2.3 50 360-409 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.7 2.6E-17 5.6E-22 155.2 10.0 127 170-305 9-144 (144)
4 KOG1973 Chromatin remodeling p 98.9 4.4E-10 9.6E-15 116.7 4.2 55 108-170 214-269 (274)
5 COG5034 TNG2 Chromatin remodel 98.9 7.1E-10 1.5E-14 111.8 2.7 51 111-169 219-270 (271)
6 PF11789 zf-Nse: Zinc-finger o 98.6 2.9E-08 6.3E-13 79.9 2.8 52 352-405 2-53 (57)
7 PF02037 SAP: SAP domain; Int 98.2 1.9E-06 4.1E-11 62.7 3.4 35 11-45 1-35 (35)
8 PF00628 PHD: PHD-finger; Int 98.0 1.3E-06 2.8E-11 67.8 0.6 49 115-168 1-50 (51)
9 smart00513 SAP Putative DNA-bi 98.0 6.9E-06 1.5E-10 59.6 3.6 34 12-45 2-35 (35)
10 smart00249 PHD PHD zinc finger 97.5 8E-05 1.7E-09 55.4 3.4 45 116-166 2-47 (47)
11 KOG2979 Protein involved in DN 97.4 7.8E-05 1.7E-09 76.2 2.7 72 352-425 167-243 (262)
12 smart00504 Ubox Modified RING 97.2 0.00052 1.1E-08 55.0 4.6 59 362-425 2-60 (63)
13 KOG1844 PHD Zn-finger proteins 96.4 0.0016 3.4E-08 73.1 2.2 52 111-170 84-136 (508)
14 PF04564 U-box: U-box domain; 96.2 0.0061 1.3E-07 51.2 4.2 63 361-427 4-66 (73)
15 PF13831 PHD_2: PHD-finger; PD 95.9 0.0021 4.6E-08 47.2 -0.1 35 125-167 2-36 (36)
16 COG5627 MMS21 DNA repair prote 95.3 0.009 2E-07 60.6 2.0 70 352-423 180-251 (275)
17 KOG4323 Polycomb-like PHD Zn-f 95.0 0.01 2.2E-07 65.8 1.5 57 110-169 168-224 (464)
18 KOG0957 PHD finger protein [Ge 93.3 0.096 2.1E-06 58.3 4.6 61 111-175 118-185 (707)
19 KOG2169 Zn-finger transcriptio 93.0 0.24 5.2E-06 57.8 7.6 236 355-592 11-264 (636)
20 COG5222 Uncharacterized conser 91.4 0.18 3.8E-06 53.1 3.5 64 356-422 269-333 (427)
21 PLN03208 E3 ubiquitin-protein 91.4 0.23 4.9E-06 49.6 4.1 55 361-416 18-84 (193)
22 PF12949 HeH: HeH/LEM domain; 90.8 0.16 3.4E-06 37.3 1.8 28 12-39 2-31 (35)
23 PF04641 Rtf2: Rtf2 RING-finge 88.8 0.4 8.7E-06 49.8 3.7 55 358-417 110-167 (260)
24 PF14835 zf-RING_6: zf-RING of 87.8 0.42 9.2E-06 39.7 2.4 58 361-424 7-64 (65)
25 PF07498 Rho_N: Rho terminatio 86.7 0.85 1.8E-05 34.7 3.4 36 11-46 2-39 (43)
26 KOG2164 Predicted E3 ubiquitin 85.3 0.53 1.1E-05 52.9 2.4 56 361-417 186-242 (513)
27 KOG4299 PHD Zn-finger protein 84.0 0.59 1.3E-05 53.6 2.0 53 113-170 253-306 (613)
28 TIGR00599 rad18 DNA repair pro 83.3 1.5 3.3E-05 48.4 4.8 66 358-429 23-89 (397)
29 KOG4259 Putative nucleic acid- 83.1 1.2 2.7E-05 45.3 3.6 67 11-78 6-73 (260)
30 KOG0957 PHD finger protein [Ge 80.3 3.3 7.1E-05 46.7 5.9 80 82-166 511-595 (707)
31 cd00162 RING RING-finger (Real 79.9 1.6 3.4E-05 31.4 2.4 42 364-409 2-44 (45)
32 KOG1632 Uncharacterized PHD Zn 79.5 0.89 1.9E-05 49.4 1.4 53 112-170 59-114 (345)
33 KOG0956 PHD finger protein AF1 77.5 1.3 2.8E-05 51.4 1.9 48 113-167 6-55 (900)
34 KOG0825 PHD Zn-finger protein 74.7 1.5 3.2E-05 51.6 1.4 52 112-170 214-267 (1134)
35 KOG0955 PHD finger protein BR1 74.5 2.4 5.1E-05 52.0 3.2 55 110-173 217-273 (1051)
36 KOG1244 Predicted transcriptio 72.8 2.5 5.5E-05 44.2 2.5 49 112-167 280-329 (336)
37 PF10208 Armet: Degradation ar 71.6 3.5 7.6E-05 39.9 2.9 38 10-47 103-142 (154)
38 KOG0978 E3 ubiquitin ligase in 70.4 1.4 3.1E-05 51.6 0.0 56 356-416 638-694 (698)
39 KOG1512 PHD Zn-finger protein 68.8 3 6.4E-05 44.0 1.9 50 117-176 319-369 (381)
40 KOG1245 Chromatin remodeling c 65.6 1.5 3.3E-05 55.3 -1.0 52 113-171 1108-1160(1404)
41 KOG0954 PHD finger protein [Ge 65.4 3.1 6.8E-05 48.8 1.4 49 112-169 270-321 (893)
42 PF13923 zf-C3HC4_2: Zinc fing 64.9 4 8.7E-05 29.8 1.5 39 364-406 1-39 (39)
43 PF04810 zf-Sec23_Sec24: Sec23 62.3 1.6 3.4E-05 32.7 -1.1 19 391-409 15-33 (40)
44 PF04423 Rad50_zn_hook: Rad50 61.3 2.5 5.4E-05 33.4 -0.2 37 389-428 10-46 (54)
45 PF14447 Prok-RING_4: Prokaryo 59.9 5.7 0.00012 32.1 1.6 36 369-415 19-54 (55)
46 PF13445 zf-RING_UBOX: RING-ty 59.2 6.4 0.00014 30.1 1.7 39 364-404 1-43 (43)
47 PF00097 zf-C3HC4: Zinc finger 55.4 7.1 0.00015 28.5 1.4 41 364-406 1-41 (41)
48 KOG0311 Predicted E3 ubiquitin 55.0 1.6 3.4E-05 47.3 -3.0 70 356-428 38-108 (381)
49 KOG1632 Uncharacterized PHD Zn 54.5 1.7 3.8E-05 47.2 -2.9 59 109-169 235-295 (345)
50 PF15227 zf-C3HC4_4: zinc fing 52.6 7.7 0.00017 29.2 1.2 42 364-406 1-42 (42)
51 PF13832 zf-HC5HC2H_2: PHD-zin 50.7 9.4 0.0002 34.1 1.7 34 113-148 55-89 (110)
52 PF13894 zf-C2H2_4: C2H2-type 50.3 6.1 0.00013 24.8 0.3 11 401-411 1-11 (24)
53 TIGR00599 rad18 DNA repair pro 46.2 23 0.0005 39.4 4.1 36 12-47 267-302 (397)
54 cd00350 rubredoxin_like Rubred 45.9 9.2 0.0002 27.4 0.7 12 399-410 16-27 (33)
55 PF13920 zf-C3HC4_3: Zinc fing 45.4 11 0.00025 28.9 1.2 43 363-410 4-47 (50)
56 PF14446 Prok-RING_1: Prokaryo 43.8 16 0.00035 29.5 1.8 34 111-146 3-38 (54)
57 smart00531 TFIIE Transcription 42.9 36 0.00078 32.4 4.4 69 307-412 67-135 (147)
58 PF08531 Bac_rhamnosid_N: Alph 42.5 13 0.00027 36.2 1.3 46 244-291 15-63 (172)
59 PLN03124 poly [ADP-ribose] pol 41.0 23 0.00049 41.8 3.2 38 12-49 3-40 (643)
60 COG5574 PEX10 RING-finger-cont 40.5 14 0.0003 38.7 1.3 54 361-418 215-269 (271)
61 KOG3113 Uncharacterized conser 40.3 54 0.0012 34.4 5.4 112 298-417 48-164 (293)
62 KOG2177 Predicted E3 ubiquitin 40.0 12 0.00026 37.1 0.7 62 361-429 13-74 (386)
63 PF02837 Glyco_hydro_2_N: Glyc 39.5 81 0.0018 29.6 6.3 66 203-292 72-138 (167)
64 cd04718 BAH_plant_2 BAH, or Br 37.6 22 0.00047 34.4 2.0 27 139-170 2-28 (148)
65 PF00096 zf-C2H2: Zinc finger, 35.2 12 0.00026 23.8 -0.1 11 401-411 1-11 (23)
66 PF13639 zf-RING_2: Ring finge 35.2 21 0.00045 26.6 1.2 24 378-406 19-43 (44)
67 KOG4443 Putative transcription 35.0 7 0.00015 45.5 -2.0 41 125-168 161-201 (694)
68 PF02228 Gag_p19: Major core p 34.8 18 0.0004 31.3 0.9 21 386-406 44-64 (92)
69 KOG0801 Predicted E3 ubiquitin 34.6 19 0.00042 35.3 1.1 21 400-420 138-158 (205)
70 COG5141 PHD zinc finger-contai 34.1 50 0.0011 37.6 4.3 48 114-170 194-244 (669)
71 PRK12678 transcription termina 34.1 35 0.00076 40.0 3.3 37 11-47 23-61 (672)
72 smart00734 ZnF_Rad18 Rad18-lik 33.2 13 0.00029 25.3 -0.1 9 402-410 3-11 (26)
73 cd00730 rubredoxin Rubredoxin; 32.9 19 0.0004 28.6 0.6 12 398-409 32-43 (50)
74 smart00184 RING Ring finger. E 32.9 28 0.0006 23.6 1.5 25 378-406 14-39 (39)
75 PF07496 zf-CW: CW-type Zinc F 31.7 28 0.0006 27.3 1.4 33 126-165 2-34 (50)
76 KOG0320 Predicted E3 ubiquitin 30.9 25 0.00055 35.0 1.3 49 362-414 132-181 (187)
77 TIGR00570 cdk7 CDK-activating 30.9 54 0.0012 35.3 3.9 40 379-421 25-68 (309)
78 PF00301 Rubredoxin: Rubredoxi 30.6 20 0.00044 28.0 0.4 12 398-409 32-43 (47)
79 COG5243 HRD1 HRD ubiquitin lig 29.7 36 0.00077 37.5 2.3 41 365-412 304-346 (491)
80 PF13670 PepSY_2: Peptidase pr 28.7 74 0.0016 27.0 3.7 33 421-453 31-64 (83)
81 PF13465 zf-H2C2_2: Zinc-finge 28.6 37 0.0008 22.8 1.4 15 396-410 10-24 (26)
82 PF13771 zf-HC5HC2H: PHD-like 28.4 37 0.00081 28.9 1.8 34 113-148 36-70 (90)
83 PHA02929 N1R/p28-like protein; 27.2 57 0.0012 33.9 3.2 44 362-410 175-226 (238)
84 COG5533 UBP5 Ubiquitin C-termi 26.8 24 0.00053 38.0 0.4 36 374-409 258-293 (415)
85 PF13913 zf-C2HC_2: zinc-finge 26.5 16 0.00034 24.7 -0.7 15 401-415 3-17 (25)
86 COG4068 Uncharacterized protei 26.4 49 0.0011 27.3 2.0 29 399-427 7-35 (64)
87 PLN00162 transport protein sec 25.4 21 0.00046 42.8 -0.3 34 373-410 52-85 (761)
88 KOG0287 Postreplication repair 25.4 79 0.0017 34.6 3.9 33 14-46 251-283 (442)
89 KOG0287 Postreplication repair 25.3 26 0.00055 38.1 0.3 63 360-428 22-85 (442)
90 KOG4661 Hsp27-ERE-TATA-binding 25.2 43 0.00094 38.7 2.0 40 9-48 28-67 (940)
91 KOG0383 Predicted helicase [Ge 24.8 35 0.00076 40.5 1.3 44 113-166 48-91 (696)
92 COG0723 QcrA Rieske Fe-S prote 24.4 33 0.00072 33.4 0.9 27 378-408 106-132 (177)
93 KOG3970 Predicted E3 ubiquitin 24.4 81 0.0018 32.6 3.6 58 372-429 57-123 (299)
94 PF04641 Rtf2: Rtf2 RING-finge 24.1 84 0.0018 32.7 3.8 31 362-394 35-65 (260)
95 PF14634 zf-RING_5: zinc-RING 23.6 50 0.0011 24.7 1.5 33 372-408 12-44 (44)
96 PF05605 zf-Di19: Drought indu 22.5 25 0.00054 27.7 -0.4 11 400-410 2-12 (54)
97 KOG2626 Histone H3 (Lys4) meth 21.6 74 0.0016 36.5 2.9 65 113-179 20-86 (544)
98 KOG2752 Uncharacterized conser 20.2 61 0.0013 35.0 1.9 34 112-147 127-167 (345)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=1e-36 Score=344.94 Aligned_cols=374 Identities=20% Similarity=0.366 Sum_probs=260.2
Q ss_pred HhccHHHHHHHH-HHhCCCCCC--ChHHHHHHHHHhccchhhhhhcccCCCCcHHHHHHHHHHHHHH-hhcc--CCCccC
Q 007360 12 AHFRIKELKDVL-TQLGLSKQG--KKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLVDDTHRK-LQVS--VAPDLA 85 (606)
Q Consensus 12 ~~fRi~ELk~vL-~~lglsk~G--~K~eL~~ril~~l~~~~~~~~~~~~~~~~~~~~~k~i~~~Y~~-m~~~--~~~~~~ 85 (606)
+++|+.||+.++ ...|+.+.| +|.+|.-|.+.++..++. +.++++|.+.|++ .... .+.+++
T Consensus 1 m~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~------------~~~q~~i~~~~~~~~~~~~~~~~~~~ 68 (636)
T KOG2169|consen 1 MSLRVSSLQVLLSGAIGRSFPGQVNKHKLAPRALTLVGSGCK------------PYLQMVIKELYQRQYPNGQQQPIDLP 68 (636)
T ss_pred CCcccccccccchhhhccccccccchhhhhhhhhcccccCCc------------hhhhhhhhhhhhhhcccccccccccc
Confidence 368999999998 788888888 899999999999988775 4588899999973 1111 111111
Q ss_pred CCCCCCCCCCCcccccccccccCCCCCceeccCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccc
Q 007360 86 SKGGQGVSNSSNIKIKGEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165 (606)
Q Consensus 86 s~~~~~~~~~~~~~p~~~~~~~~~~~~~~rCiC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~ 165 (606)
... ..|. .+...+.. ....+..|. =..++...+.+. ..-+=+.
T Consensus 69 ~~~---------~~~~-~~~~~~~~------------~~~~~~~~~-----------~~~~~~~~l~g~----~~~~~~~ 111 (636)
T KOG2169|consen 69 AVK---------LHPN-VVPPFYPL------------LWQLLRHPT-----------QQPVTPSSLLGP----PLPFHPD 111 (636)
T ss_pred ccc---------cCCc-ccCccccc------------hhcccccCC-----------CCCCCcccccCC----CCcCCCc
Confidence 111 0110 00000000 000001000 000111111110 0112223
Q ss_pred cccccCCccceeecccccceeeeecccCCCCCCCceeeeEEEEeChhhHHhhcCC-C------eeEEEEEEecCCCCccc
Q 007360 166 CRLSRADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSKQ-E------YDVQAWCMLLNDKVPFR 238 (606)
Q Consensus 166 Crl~r~DPF~~~i~~ll~Pv~l~~s~i~~~G~~~~qs~~~~F~Lt~~~~~~L~~~-~------~~lql~C~~l~d~~~~~ 238 (606)
-++. ..|||+++..+++|+.+..... ...+...+.|.|+++....+... + ..-.+ |+.. ...+++
T Consensus 112 ~~~~-~~~~y~~l~~~~~p~~~~~~~~-----~~~~~~~~~f~lt~~~~~~i~~~~~~~~~~k~~~~~-~~~~-~s~p~e 183 (636)
T KOG2169|consen 112 VKLK-KLPFYDVLSELIKPHVLHSSNS-----PSLSESPFLFALTPEQVSGISSRPDVLPGSKSEGSV-CLME-TSCPQE 183 (636)
T ss_pred cccc-CCchheecccccCceeecCcCC-----CCcccccchhhcchhhhhhcccccccccccccccce-eecc-ccCccc
Confidence 3444 5999999999999998875432 24556778899999998776431 1 11111 5553 356888
Q ss_pred ccCCCceEEEEcCeEeecc-cCCCCCCCCC-CCCCCCCC-ccc--CcCCC-ccEEEEEEe--cCceEEEEEEEEEecCHH
Q 007360 239 MQWPQYADLQVNGVPVRAI-NRPGSQLLGA-NGRDDGPI-ITP--WTKDG-INKIVLTGC--DARIFCLGVRIVKRRSVQ 310 (606)
Q Consensus 239 ~~wP~~~~l~VNg~~v~~~-~Rp~~~~~g~-~gR~~~pi-IT~--~lk~g-~N~I~it~~--d~~~y~~~V~lVk~~s~e 310 (606)
.+||..+.++||+..+... ..-..++.+. .+|...|. ||. ++... .|.+.+.|. ..+.|.+++|+|+.++.+
T Consensus 184 ~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t~~ 263 (636)
T KOG2169|consen 184 DHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLTSK 263 (636)
T ss_pred cccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccCHH
Confidence 9999999999999988875 1111112222 25667777 998 44443 377777764 678999999999999999
Q ss_pred HHHHhcccCCC-CCCHHHHHHHHHHhhCCCCCCCCCCCCCCcceEeecceeeecCCCCcccccccccCCCCCccccccHH
Q 007360 311 QVLNLIPKESE-GEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLD 389 (606)
Q Consensus 311 ~Ll~~I~~~~~-~~~~e~al~rIkr~l~~~~~~~n~d~DdD~eIv~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~ 389 (606)
+|+++++...+ ...++...+.+++.+ ..++|.||+++++.|||.|||+++||++|+|+..|+|+||||+.
T Consensus 264 ~llq~~~~~~~~~~~~~~s~~~~~~~l---------~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~ 334 (636)
T KOG2169|consen 264 DLLQRLKQNGKINRNLSQSDALIKKKL---------TAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDAL 334 (636)
T ss_pred HHHHHHhccCCccCchhHhHHHhhccc---------ccCCcccceeccceeEecCCcccceeecCCcccccccceecchh
Confidence 99999876432 233466666666543 23456679999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhhcCCCCeeEEEEeeCCceEeccCCCc
Q 007360 390 VFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMRNCGEDITELEVKPDGSWRVKTRSES 454 (606)
Q Consensus 390 ~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~~~~~dv~eV~v~~DGsW~~~~~~e~ 454 (606)
+||+||+++++|+||||.+.+.+++|+||+||+.|| .+|..+++||++..||+|++...++.
T Consensus 335 ~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL---~~~~~~~~ev~~~~dGsw~pi~~~~~ 396 (636)
T KOG2169|consen 335 SYLQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNIL---QSCQANVEEVEVSEDGSWKPIPEEAE 396 (636)
T ss_pred hhHHhccCCCeeeCccCCccccccchhhhHHHHHHH---hhccCCCcceEecCCCceecCccccc
Confidence 999999999999999999999999999999999995 55677899999999999999887764
No 2
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.82 E-value=2.8e-21 Score=150.95 Aligned_cols=50 Identities=54% Similarity=1.107 Sum_probs=36.5
Q ss_pred eeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC
Q 007360 360 VNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 360 vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (606)
|||+||||++||++|+||+.|+|+|||||++||+++++++.|+||||+++
T Consensus 1 vsL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 1 VSLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp EESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CeeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 79999999999999999999999999999999999999999999999874
No 3
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.71 E-value=2.6e-17 Score=155.17 Aligned_cols=127 Identities=21% Similarity=0.350 Sum_probs=83.9
Q ss_pred cCCccceeecccccceeeeecccCCCCCCCceeeeEEEEeChhhHHhhcC--CCeeEEEEEEecC---CCCcccccCCCc
Q 007360 170 RADPFWVTIGHPLYPLKLTTTNIPTDGTNPARILEKTFPITRADKDLLSK--QEYDVQAWCMLLN---DKVPFRMQWPQY 244 (606)
Q Consensus 170 r~DPF~~~i~~ll~Pv~l~~s~i~~~G~~~~qs~~~~F~Lt~~~~~~L~~--~~~~lql~C~~l~---d~~~~~~~wP~~ 244 (606)
+.+|||+++ .++.|+.+.+.. .+.++...+.|.|+++++++|++ +.++|+|||+..+ ....+.++||.+
T Consensus 9 k~sPFY~~~-~~i~~~~~~~~~-----~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~FP~~ 82 (144)
T PF14324_consen 9 KPSPFYKVL-RLIHPTPLLPAS-----SSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIEFPPP 82 (144)
T ss_dssp --BTTEEEE-EEEEEEEEEE-------EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB-----SS
T ss_pred ccCCCccee-EEcCCccccccc-----cCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccccCCC
Confidence 579999999 788888776532 23567889999999999999987 6799999999843 345788999999
Q ss_pred eEEEEcCeEeecccCCCCCCCCCCCCCCCCCcccCcCCC---ccEEEEEEe-cCceEEEEEEEEE
Q 007360 245 ADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKDG---INKIVLTGC-DARIFCLGVRIVK 305 (606)
Q Consensus 245 ~~l~VNg~~v~~~~Rp~~~~~g~~gR~~~piIT~~lk~g---~N~I~it~~-d~~~y~~~V~lVk 305 (606)
++|+|||+.|+++.|..+ +++|+..|++||++++.. .|+|+|+|. +.+.|+++|||||
T Consensus 83 ~evkvN~~~v~~~~~glk---nKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 83 CEVKVNGKQVKLNNRGLK---NKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEEETTEE--S--SS-T---TS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred eEEEEeCEEcccCccCCC---CCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 999999999999887654 456666677799999865 799999997 6789999999997
No 4
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.95 E-value=4.4e-10 Score=116.65 Aligned_cols=55 Identities=33% Similarity=0.890 Sum_probs=48.7
Q ss_pred CCCCCceeccCCCCCCCCCeeeecCCCCC-CcccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 108 IQSDTKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 108 ~~~~~~~rCiC~~sl~~~~mI~C~~~~C~-~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
..++...||+|.+. .+|.||.||+++|. .|||+.||||..+| .+.|||+.|+...
T Consensus 214 ~d~~e~~yC~Cnqv-syg~Mi~CDn~~C~~eWFH~~CVGL~~~P-------kgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 214 VDPDEPTYCICNQV-SYGKMIGCDNPGCPIEWFHFTCVGLKTKP-------KGKWYCPRCKAEN 269 (274)
T ss_pred cCCCCCEEEEeccc-ccccccccCCCCCCcceEEEeccccccCC-------CCcccchhhhhhh
Confidence 44667999999955 59999999999999 79999999999887 7889999999764
No 5
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.88 E-value=7.1e-10 Score=111.82 Aligned_cols=51 Identities=27% Similarity=0.794 Sum_probs=45.5
Q ss_pred CCceeccCCCCCCCCCeeeecCCCCC-CcccccccccCCCCCCCCCCCCCcccccccccc
Q 007360 111 DTKVCCPCGSSLETESMIKCEDPRCP-VWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 111 ~~~~rCiC~~sl~~~~mI~C~~~~C~-~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~ 169 (606)
+...||+|++.. +|.||.||+++|+ .|||..|||+.+.| .+.|||+.|+-.
T Consensus 219 ~e~lYCfCqqvS-yGqMVaCDn~nCkrEWFH~~CVGLk~pP-------KG~WYC~eCk~~ 270 (271)
T COG5034 219 GEELYCFCQQVS-YGQMVACDNANCKREWFHLECVGLKEPP-------KGKWYCPECKKA 270 (271)
T ss_pred CceeEEEecccc-cccceecCCCCCchhheeccccccCCCC-------CCcEeCHHhHhc
Confidence 358999999986 9999999999999 49999999998876 789999999853
No 6
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.58 E-value=2.9e-08 Score=79.88 Aligned_cols=52 Identities=23% Similarity=0.556 Sum_probs=37.2
Q ss_pred ceEeecceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC
Q 007360 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI 405 (606)
Q Consensus 352 eIv~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPi 405 (606)
||+.+...++++||||+..|+-|++++.|.|. ||-++++++-.+...-+||+
T Consensus 2 di~i~~~~~~~~CPiT~~~~~~PV~s~~C~H~--fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 2 DIVIEGGTISLKCPITLQPFEDPVKSKKCGHT--FEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -----SSB--SB-TTTSSB-SSEEEESSS--E--EEHHHHHHHCTTTS-EE-SC
T ss_pred ceEEeccEeccCCCCcCChhhCCcCcCCCCCe--ecHHHHHHHHHhcCCCCCCC
Confidence 35667789999999999999999999999996 99999999988889999999
No 7
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=98.15 E-value=1.9e-06 Score=62.71 Aligned_cols=35 Identities=40% Similarity=0.676 Sum_probs=31.3
Q ss_pred HHhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 007360 11 LAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (606)
Q Consensus 11 l~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l 45 (606)
+..++++|||..|.++||+.+|+|++|++||..+|
T Consensus 1 l~~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 35789999999999999999999999999998864
No 8
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.03 E-value=1.3e-06 Score=67.80 Aligned_cols=49 Identities=41% Similarity=0.868 Sum_probs=39.7
Q ss_pred ec-cCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccc
Q 007360 115 CC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (606)
Q Consensus 115 rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl 168 (606)
+| +|++....+.||+|+. |..|+|..|++++.+..+. ....|+|+.|+-
T Consensus 1 ~C~vC~~~~~~~~~i~C~~--C~~~~H~~C~~~~~~~~~~---~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDS--CNRWYHQECVGPPEKAEEI---PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBST--TSCEEETTTSTSSHSHHSH---HSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCC--CChhhCcccCCCChhhccC---CCCcEECcCCcC
Confidence 58 8999888899999999 9999999999998653111 123899999974
No 9
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.98 E-value=6.9e-06 Score=59.59 Aligned_cols=34 Identities=50% Similarity=0.786 Sum_probs=31.6
Q ss_pred HhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhc
Q 007360 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAIL 45 (606)
Q Consensus 12 ~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l 45 (606)
..+.++|||++|.++||+.+|+|++|++||..++
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 4688999999999999999999999999998875
No 10
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=97.42 E-value=7.8e-05 Score=76.17 Aligned_cols=72 Identities=22% Similarity=0.335 Sum_probs=57.6
Q ss_pred ceEeecceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC--CCCCCCC--CCeeec-HHHHHHH
Q 007360 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNYSL--ENIIID-PYFNRIT 425 (606)
Q Consensus 352 eIv~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPi--C~k~~~~--~~L~ID-~y~~~IL 425 (606)
++...+..+|++||+|+..|..|++++.|.|+ ||-++.+++-....+-.||+ |...+.. .-|.-| .+..+|.
T Consensus 167 e~~i~~e~fs~rdPis~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr 243 (262)
T KOG2979|consen 167 EELIGQEVFSNRDPISKKPIVNPVISKKCGHV--YDRDSIMQILCDEITIRCPVLGCENPYYIQPGHLDEDKELQQKIR 243 (262)
T ss_pred HHHhhhhhhcccCchhhhhhhchhhhcCcCcc--hhhhhHHHHhccCceeecccccCCccccccccccCchHHHHHHHH
Confidence 56667889999999999999999999999998 99999999888788999999 8744443 334444 4444443
No 12
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.20 E-value=0.00052 Score=55.04 Aligned_cols=59 Identities=14% Similarity=0.173 Sum_probs=50.1
Q ss_pred ecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHH
Q 007360 362 LRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRIT 425 (606)
Q Consensus 362 L~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL 425 (606)
|.|||++..|+.|+.. .|-|. |+.+.+.++... .-.||+|++.++.++|+-+..+.+.+
T Consensus 2 ~~Cpi~~~~~~~Pv~~-~~G~v--~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~~i 60 (63)
T smart00504 2 FLCPISLEVMKDPVIL-PSGQT--YERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKSAI 60 (63)
T ss_pred cCCcCCCCcCCCCEEC-CCCCE--EeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHHHH
Confidence 6899999999999986 67776 999988887655 45899999999999999998777653
No 13
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=96.41 E-value=0.0016 Score=73.08 Aligned_cols=52 Identities=31% Similarity=0.680 Sum_probs=46.0
Q ss_pred CCceeccCCCCCC-CCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 111 DTKVCCPCGSSLE-TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 111 ~~~~rCiC~~sl~-~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
...++|+|+.... .+.||+|+. |..|||..|+++.... . |+.|+|+.|++..
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~--c~~Wqh~~C~g~~~~~----~--p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDW--CGRWQHKICCGSFKST----K--PDKYVCEICTPRN 136 (508)
T ss_pred CcccccccccccCCCceeeCCcc--cCcccCceeeeecCCC----C--chhceeeeecccc
Confidence 4589999999988 999999999 9999999999987654 1 7999999999874
No 14
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.19 E-value=0.0061 Score=51.19 Aligned_cols=63 Identities=11% Similarity=0.223 Sum_probs=48.0
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSK 427 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 427 (606)
.|.||||+..|+-|+....| |. ||-.+......+ ..-.||+|++++...+|+-+.-+...++.
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G-~t--yer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~ 66 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSG-HT--YERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEE 66 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTS-EE--EEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHH
T ss_pred ccCCcCcCcHhhCceeCCcC-CE--EcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHH
Confidence 47899999999999998777 75 999998876655 56789999999999999999888877654
No 15
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.88 E-value=0.0021 Score=47.21 Aligned_cols=35 Identities=29% Similarity=0.729 Sum_probs=19.7
Q ss_pred CCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccc
Q 007360 125 ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (606)
Q Consensus 125 ~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Cr 167 (606)
..||.|+. |.+..|..|+|+...+ ....|+|..|+
T Consensus 2 n~ll~C~~--C~v~VH~~CYGv~~~~------~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDN--CNVAVHQSCYGVSEVP------DGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SS--S--EEEHHHHT-SS--------SS-----HHH-
T ss_pred CceEEeCC--CCCcCChhhCCcccCC------CCCcEECCcCC
Confidence 46899999 9999999999998765 23359999885
No 16
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=95.30 E-value=0.009 Score=60.60 Aligned_cols=70 Identities=16% Similarity=0.263 Sum_probs=59.3
Q ss_pred ceEeecceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccC--CCCCCCCCCeeecHHHHH
Q 007360 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPI--CLRNYSLENIIIDPYFNR 423 (606)
Q Consensus 352 eIv~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPi--C~k~~~~~~L~ID~y~~~ 423 (606)
+|...+..++++|||+..++..|.=+..|.|. ||.+.....-+--++--||. |.+......++-|..+++
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 46667789999999999999999999999998 99988887777678889998 988877777777766654
No 17
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.97 E-value=0.01 Score=65.77 Aligned_cols=57 Identities=21% Similarity=0.523 Sum_probs=43.6
Q ss_pred CCCceeccCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007360 110 SDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 110 ~~~~~rCiC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~ 169 (606)
+....+|.||.......||+|+. |+-|+|-.|+.-..+++.- ...-..|||-.|+-.
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~--C~~~fHq~Chqp~i~~~l~-~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDK--CRQWYHQACHQPLIKDELA-GDPFYEWFCDVCNRG 224 (464)
T ss_pred cceeeeeecCCcCccceeeeecc--cccHHHHHhccCCCCHhhc-cCccceEeehhhccc
Confidence 33488999999987779999999 9999999999877665322 122456888888754
No 18
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.29 E-value=0.096 Score=58.25 Aligned_cols=61 Identities=21% Similarity=0.635 Sum_probs=45.8
Q ss_pred CCceeccCCCC--CCCCCeeeecCCCCCCcccccccccCCCCCCCCCCC-----CCcccccccccccCCccc
Q 007360 111 DTKVCCPCGSS--LETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPV-----PELFYCEICRLSRADPFW 175 (606)
Q Consensus 111 ~~~~rCiC~~s--l~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~-----P~~fyCe~Crl~r~DPF~ 175 (606)
...+.|+|-+. ...+++|+|+. |++-.|-+|+|..+.. +||.. ...|||+.|+.--..|-.
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~--CGi~VHEgCYGv~dn~--si~s~~s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDK--CGINVHEGCYGVLDNV--SIPSGSSDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred cceEEEEeecCccccccceeeccc--cCceeccccccccccc--ccCCCCccCCCCchhhhhHhcCCCCCcc
Confidence 34578899654 34689999999 9999999999988554 44432 256999999977655644
No 19
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=93.03 E-value=0.24 Score=57.78 Aligned_cols=236 Identities=17% Similarity=0.063 Sum_probs=166.3
Q ss_pred eecceeeecCCCCcccccccccCCCCCcccccc--HHHHHHHhc--CCCeeeccCCCCCCCCCCeeecHHHHHHHHHhhc
Q 007360 355 ADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFD--LDVFVELNQ--RSRKWQCPICLRNYSLENIIIDPYFNRITSKMRN 430 (606)
Q Consensus 355 ~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFD--l~~fL~~n~--~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~~ 430 (606)
..+.-+.+.+|.-..+.+..+|...|.+..|+. ..-+=+..+ ....|.||+|-+.+...-.....++..+-..++.
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~q~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (636)
T KOG2169|consen 11 LLSGAIGRSFPGQVNKHKLAPRALTLVGSGCKPYLQMVIKELYQRQYPNGQQQPIDLPAVKLHPNVVPPFYPLLWQLLRH 90 (636)
T ss_pred cchhhhccccccccchhhhhhhhhcccccCCchhhhhhhhhhhhhhccccccccccccccccCCcccCccccchhccccc
Confidence 334456778898889999999999999999998 444434333 4578999999888887777777777765344443
Q ss_pred CCC-CeeEEEEee---CCceEeccCCCcccccccccCCCCCCCCCCccCCCCCCCchhhhhhhhhccccCCCCCcceeee
Q 007360 431 CGE-DITELEVKP---DGSWRVKTRSESDRREIGDLASWHFPDGSLCAPAGGEDKPKVEMLKHVRQEGVSEGHIGLKLGI 506 (606)
Q Consensus 431 ~~~-dv~eV~v~~---DGsW~~~~~~e~~~~~~~~~~~~~~~dg~~~~~~~~~~~~~~~~~~~~~~e~~s~~~~~~~~~~ 506 (606)
.-. -+....+.. +..|+++....+...-++.+.+|+.......... -...-.+... .-+.+..+.++.-+..+.
T Consensus 91 ~~~~~~~~~~l~g~~~~~~~~~~~~~~~~y~~l~~~~~p~~~~~~~~~~~-~~~~~~f~lt-~~~~~~i~~~~~~~~~~k 168 (636)
T KOG2169|consen 91 PTQQPVTPSSLLGPPLPFHPDVKLKKLPFYDVLSELIKPHVLHSSNSPSL-SESPFLFALT-PEQVSGISSRPDVLPGSK 168 (636)
T ss_pred CCCCCCCcccccCCCCcCCCcccccCCchheecccccCceeecCcCCCCc-ccccchhhcc-hhhhhhcccccccccccc
Confidence 222 355555655 7899998888777666678888987766666211 1111122221 223344555554444444
Q ss_pred ee------CCCCceeecCCCCCCCCCCcc-cccccccCCcceeecccCCCCCCCCCCC---CccccCCCceeeeccCCcc
Q 007360 507 RK------NRNGLWEVSKPEDMNGSSGSR-LQEKFENHDLKVIPMSSSATGSGRDGED---ASVNQDVGGTFDFTNNGIE 576 (606)
Q Consensus 507 ~~------~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 576 (606)
+. ..++.||...|.....+..|. .+--+.+...+..++....++..++..+ .++..++...+.|..++..
T Consensus 169 ~~~~~~~~~~s~p~e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~ 248 (636)
T KOG2169|consen 169 SEGSVCLMETSCPQEDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLEPKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGK 248 (636)
T ss_pred cccceeeccccCccccccCceeEEEecCCcceeeccccCCCCcccccCCCCCCCcCcccccccccccccceEEEEeccCc
Confidence 43 458999999998887777544 3333367778888888899999999988 8899889999999999999
Q ss_pred cccccccCCcccccCC
Q 007360 577 HDSMSLNVDPTYAFAD 592 (606)
Q Consensus 577 ~~~~~~~~~~~~~~~~ 592 (606)
-.|+..+|...|...+
T Consensus 249 ~ysl~~~~v~~~t~~~ 264 (636)
T KOG2169|consen 249 SYSLSVYFVEGLTSKD 264 (636)
T ss_pred ccceEEEEecccCHHH
Confidence 9999999999887654
No 20
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.36 E-value=0.18 Score=53.06 Aligned_cols=64 Identities=17% Similarity=0.394 Sum_probs=46.0
Q ss_pred ecceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCC-CCCCCCCeeecHHHH
Q 007360 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICL-RNYSLENIIIDPYFN 422 (606)
Q Consensus 356 ~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~-k~~~~~~L~ID~y~~ 422 (606)
..-.|+|+|||....++.|+|..-|.|.-|=.. |+...--.-+.||.|. +.+-++.|.-|.-.+
T Consensus 269 ~~~~i~LkCplc~~Llrnp~kT~cC~~~fc~ec---i~~al~dsDf~CpnC~rkdvlld~l~pD~dk~ 333 (427)
T COG5222 269 QPPNISLKCPLCHCLLRNPMKTPCCGHTFCDEC---IGTALLDSDFKCPNCSRKDVLLDGLTPDIDKK 333 (427)
T ss_pred CCCCccccCcchhhhhhCcccCccccchHHHHH---HhhhhhhccccCCCcccccchhhccCccHHHH
Confidence 345788999999999999999999999855332 2222223468999997 466666666665443
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=91.36 E-value=0.23 Score=49.62 Aligned_cols=55 Identities=15% Similarity=0.402 Sum_probs=42.2
Q ss_pred eecCCCCcccccccccCCCCCccccccHH-HHHHHh-----------cCCCeeeccCCCCCCCCCCee
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLD-VFVELN-----------QRSRKWQCPICLRNYSLENII 416 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFDl~-~fL~~n-----------~~~~~W~CPiC~k~~~~~~L~ 416 (606)
.+.|||-...++.|+-. .|.|+-|..-- .|+... ......+||+|...+...+|+
T Consensus 18 ~~~CpICld~~~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 79999888754 466532 134568999999998766654
No 22
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=90.80 E-value=0.16 Score=37.33 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=20.2
Q ss_pred HhccHHHHHHHHHHhCCC--CCCChHHHHH
Q 007360 12 AHFRIKELKDVLTQLGLS--KQGKKQDLVD 39 (606)
Q Consensus 12 ~~fRi~ELk~vL~~lgls--k~G~K~eL~~ 39 (606)
++++|.|||.+|...|+. .+.||.||+.
T Consensus 2 ~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~ 31 (35)
T PF12949_consen 2 KSLTVAQLKRILDEHGIEFPSNAKKAELVA 31 (35)
T ss_dssp TT--SHHHHHHHHHHT---SSS--SHHHHH
T ss_pred CcCcHHHHHHHHHHcCCCCCCCCCHHHHHH
Confidence 578999999999999987 8999999985
No 23
>PF04641 Rtf2: Rtf2 RING-finger
Probab=88.83 E-value=0.4 Score=49.77 Aligned_cols=55 Identities=27% Similarity=0.663 Sum_probs=39.8
Q ss_pred ceeeecCCCCcccccccccC---CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007360 358 IGVNLRCPMSGSRIKVAGRF---KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 358 ~~vSL~CPls~~ri~~P~Rg---~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
....+.||+|+..|.-=.|+ ..|-|. |--.++=++. ..|.||+|++++.-.|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 35678999999999422222 689998 4444444442 5799999999999888874
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=87.78 E-value=0.42 Score=39.71 Aligned_cols=58 Identities=21% Similarity=0.385 Sum_probs=26.1
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHH
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRI 424 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~I 424 (606)
.|+|+.-...|+.|+--..|.|+-|=.-- ..... -.||+|+.++...|++|..-+..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci-----~~~~~-~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI-----RDCIG-SECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG-----GGGTT-TB-SSS--B-S-SS----HHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh-----HHhcC-CCCCCcCChHHHHHHHhhhhhhcc
Confidence 48999999999999998899998553211 11111 359999999999999998777654
No 25
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=86.65 E-value=0.85 Score=34.69 Aligned_cols=36 Identities=28% Similarity=0.517 Sum_probs=27.5
Q ss_pred HHhccHHHHHHHHHHhCCC--CCCChHHHHHHHHHhcc
Q 007360 11 LAHFRIKELKDVLTQLGLS--KQGKKQDLVDRILAILS 46 (606)
Q Consensus 11 l~~fRi~ELk~vL~~lgls--k~G~K~eL~~ril~~l~ 46 (606)
|...-+.||+.+...+|+. .+=||+||+..|+..-.
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il~~q~ 39 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAILKAQA 39 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHHHHHC
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHHHHHH
Confidence 6778899999999999996 34489999999987543
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.30 E-value=0.53 Score=52.88 Aligned_cols=56 Identities=21% Similarity=0.489 Sum_probs=45.9
Q ss_pred eecCCCCcccccccccCCCCCcccccc-HHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFD-l~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
...|||-+-.-.+|+|.. |-|+-||- +-.|+.......--.||+|...+++.+|.-
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p 242 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP 242 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence 789999999999999998 99999885 566777664555568999998887766654
No 27
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=83.95 E-value=0.59 Score=53.61 Aligned_cols=53 Identities=30% Similarity=0.758 Sum_probs=41.7
Q ss_pred ceecc-CCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 113 KVCCP-CGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 113 ~~rCi-C~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
..+|. |+++-....+|.|+. |...||..|.--|-.+ +.+| ++.|+|+.|..+-
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~--Cp~sFH~~CLePPl~~-eniP--~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDG--CPRSFHQTCLEPPLEP-ENIP--PGSWFCPECKIKS 306 (613)
T ss_pred HHHHHHhCCccccccceeecC--CchHHHHhhcCCCCCc-ccCC--CCccccCCCeeee
Confidence 45895 998866677799999 9999999999876322 4454 5689999998773
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.30 E-value=1.5 Score=48.44 Aligned_cols=66 Identities=17% Similarity=0.300 Sum_probs=51.4
Q ss_pred ceeeecCCCCcccccccccCCCCCccccccHHH-HHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007360 358 IGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDV-FVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 358 ~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~-fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 429 (606)
+.-.|.||+-...+..|+- ..|.|.-|..--. |+.. .-.||+|...+....|..+..+.+|++..+
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~-----~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSN-----QPKCPLCRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhC-----CCCCCCCCCccccccCccchHHHHHHHHHH
Confidence 4556899999999999985 6899998765433 3331 238999999998888998888888887554
No 29
>KOG4259 consensus Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning]
Probab=83.06 E-value=1.2 Score=45.27 Aligned_cols=67 Identities=24% Similarity=0.355 Sum_probs=48.8
Q ss_pred HHhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccchhhhhhcccCCCCcHHHHHHHHHHH-HHHhhc
Q 007360 11 LAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSPVSKEEVAKLVDDT-HRKLQV 78 (606)
Q Consensus 11 l~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l~~~~~~~~~~~~~~~~~~~~~k~i~~~-Y~~m~~ 78 (606)
..++.|.|||.=|..-||+..|+|.|||+|+.+-+..- .+-..+..+.++.+....+.+|+ |.-|..
T Consensus 6 ~kklkVa~LkeeLa~rGL~~~GNK~EL~~RLtaa~e~i-aDe~~~~d~~tt~~d~h~l~ddi~~dd~l~ 73 (260)
T KOG4259|consen 6 YKKLKVAELKEELAERGLSTAGNKAELVSRLTAATESI-ADENTSNDNATTLGDLHPLEDDIDWDDMLN 73 (260)
T ss_pred hhhccHHHHHHHHHHhcccccCChHHHHHHHHHHHHHH-HHHhhcCccccccccccccccccchhhhhc
Confidence 46789999999999999999999999999998877651 11123445556666666666665 555533
No 30
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=80.33 E-value=3.3 Score=46.67 Aligned_cols=80 Identities=21% Similarity=0.406 Sum_probs=48.4
Q ss_pred CccCCCCCCCCCCCCccccc--ccccccCCCCCceec-cCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCC-
Q 007360 82 PDLASKGGQGVSNSSNIKIK--GEMDDYIQSDTKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPV- 157 (606)
Q Consensus 82 ~~~~s~~~~~~~~~~~~~p~--~~~~~~~~~~~~~rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~- 157 (606)
+.++.+++...+++++.+-- .....++..-..+.| +|..+-....+++|+. |+..+|.+|+..+-.. .|.-
T Consensus 511 ~e~~pks~~p~~~~~~rk~g~~st~~~s~~~a~~ysCgiCkks~dQHll~~CDt--C~lhYHlGCL~PPLTR---~Pkk~ 585 (707)
T KOG0957|consen 511 TELGPKSGLPLSDFNNRKSGSRSTPAISAPKAMNYSCGICKKSTDQHLLTQCDT--CHLHYHLGCLSPPLTR---LPKKN 585 (707)
T ss_pred hhcCCccCCcCcccccccccccCCcccccccccceeeeeeccchhhHHHhhcch--hhceeeccccCCcccc---Ccccc
Confidence 34445544555555432210 111122233345667 7999888888999999 9999999999865322 1221
Q ss_pred -CCccccccc
Q 007360 158 -PELFYCEIC 166 (606)
Q Consensus 158 -P~~fyCe~C 166 (606)
.--|.|..|
T Consensus 586 kn~gWqCsEC 595 (707)
T KOG0957|consen 586 KNFGWQCSEC 595 (707)
T ss_pred cCcceeeccc
Confidence 234789999
No 31
>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=79.92 E-value=1.6 Score=31.39 Aligned_cols=42 Identities=26% Similarity=0.606 Sum_probs=27.9
Q ss_pred CCCCcccccccccCCCCCccccccH-HHHHHHhcCCCeeeccCCCCC
Q 007360 364 CPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlqCFDl-~~fL~~n~~~~~W~CPiC~k~ 409 (606)
||+-...+..|.....|.|.-|.+- ..|++. ....||+|.+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKS----GKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHh----CcCCCCCCCCc
Confidence 5566666666777777999866553 233332 56789999875
No 32
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=79.54 E-value=0.89 Score=49.36 Aligned_cols=53 Identities=28% Similarity=0.644 Sum_probs=41.2
Q ss_pred CceeccCCCCCC-CCCeeeecCCCCCCcccccc--cccCCCCCCCCCCCCCccccccccccc
Q 007360 112 TKVCCPCGSSLE-TESMIKCEDPRCPVWQHMSC--VIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 112 ~~~rCiC~~sl~-~~~mI~C~~~~C~~wqH~~C--v~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
+..+|.|..... .+.|++|+. |..|.|+.| |+++.+. -+.+..|||..|....
T Consensus 59 ~~~~~~~~~~~~p~~~~~~cd~--C~~~~~~ec~~v~~~~~e----~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 59 TQRYCKCYKPCDPDDLMEQCDL--CEDWYHGECWEVGTAEKE----APKEDPKVCDECKEAQ 114 (345)
T ss_pred hhchhhcccccCchhhhhcccc--ccccccccccccCchhhc----CCccccccccccchhh
Confidence 355898887753 348999999 999999999 9998765 2236789998887653
No 33
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=77.47 E-value=1.3 Score=51.36 Aligned_cols=48 Identities=25% Similarity=0.724 Sum_probs=37.0
Q ss_pred ceeccCCCCCC--CCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccc
Q 007360 113 KVCCPCGSSLE--TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (606)
Q Consensus 113 ~~rCiC~~sl~--~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Cr 167 (606)
--.|+|-.-.. -.-+|-||...|.|..|-.||+|..-| -+.|||--|-
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVP-------tGpWfCrKCe 55 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVP-------TGPWFCRKCE 55 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecC-------CCchhhhhhh
Confidence 35789975432 245899999999999999999998776 4667777664
No 34
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=74.71 E-value=1.5 Score=51.62 Aligned_cols=52 Identities=23% Similarity=0.600 Sum_probs=40.1
Q ss_pred Cceec-cCCCCCCCCCeeeecCCCCCC-cccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 112 TKVCC-PCGSSLETESMIKCEDPRCPV-WQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 112 ~~~rC-iC~~sl~~~~mI~C~~~~C~~-wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
..+.| +|+....-.-|+-|+. |+. ++|+.|+..+-.. +| ...|||..|-+..
T Consensus 214 E~~~C~IC~~~DpEdVLLLCDs--CN~~~YH~YCLDPdl~e---iP--~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCDS--CNKVYYHVYCLDPDLSE---SP--VNEWYCTNCSLLE 267 (1134)
T ss_pred ccccceeeccCChHHhheeecc--cccceeeccccCccccc---cc--ccceecCcchhhh
Confidence 36788 6998877788999999 996 5999999864311 11 4679999998763
No 35
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=74.52 E-value=2.4 Score=52.01 Aligned_cols=55 Identities=27% Similarity=0.633 Sum_probs=44.0
Q ss_pred CCCceeccCCCCCC--CCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccccCCc
Q 007360 110 SDTKVCCPCGSSLE--TESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRADP 173 (606)
Q Consensus 110 ~~~~~rCiC~~sl~--~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r~DP 173 (606)
+++...|+|-..-. ....|.|+. |++..|-.|||++.-| -+.|.|-.|-....-|
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~--Cnl~VHq~Cygi~~ip-------eg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDG--CNLAVHQECYGIPFIP-------EGQWLCRRCLQSPQRP 273 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCC--CcchhhhhccCCCCCC-------CCcEeehhhccCcCcc
Confidence 44567779987644 378999999 9999999999976544 5689999999887666
No 36
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=72.78 E-value=2.5 Score=44.24 Aligned_cols=49 Identities=29% Similarity=0.682 Sum_probs=36.9
Q ss_pred Cceec-cCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccc
Q 007360 112 TKVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICR 167 (606)
Q Consensus 112 ~~~rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Cr 167 (606)
...+| +||.+.-.+.++-|++ |...+|+.|+..+-. ..| -+.|-|..|-
T Consensus 280 eck~csicgtsenddqllfcdd--cdrgyhmyclsppm~---epp--egswsc~KOG 329 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDD--CDRGYHMYCLSPPMV---EPP--EGSWSCHLCL 329 (336)
T ss_pred ecceeccccCcCCCceeEeecc--cCCceeeEecCCCcC---CCC--CCchhHHHHH
Confidence 35566 6888876788999999 999999999986521 111 3678898885
No 37
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=71.58 E-value=3.5 Score=39.88 Aligned_cols=38 Identities=34% Similarity=0.579 Sum_probs=32.4
Q ss_pred HHHhccHHHHHHHHHHhCCCCCC--ChHHHHHHHHHhccc
Q 007360 10 KLAHFRIKELKDVLTQLGLSKQG--KKQDLVDRILAILSD 47 (606)
Q Consensus 10 ~l~~fRi~ELk~vL~~lglsk~G--~K~eL~~ril~~l~~ 47 (606)
-|..+||+|||.||..-|..=.| -|.|++.||..+-..
T Consensus 103 Dl~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~el~~k 142 (154)
T PF10208_consen 103 DLKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEELKPK 142 (154)
T ss_dssp STTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHCCCCC
T ss_pred HHhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHHHhhh
Confidence 36789999999999999999888 699999999985544
No 38
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=70.41 E-value=1.4 Score=51.62 Aligned_cols=56 Identities=21% Similarity=0.409 Sum_probs=42.1
Q ss_pred ecceeeecCCCCcccccccccCCCCCccccccH-HHHHHHhcCCCeeeccCCCCCCCCCCee
Q 007360 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDL-DVFVELNQRSRKWQCPICLRNYSLENII 416 (606)
Q Consensus 356 ~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl-~~fL~~n~~~~~W~CPiC~k~~~~~~L~ 416 (606)
..++=-|+||.-..|-+--+= ..|-|+-||.- ..++.+. .=+||.|+..+.+.|+.
T Consensus 638 k~yK~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~Cvq~r~etR----qRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 638 KEYKELLKCSVCNTRWKDAVI-TKCGHVFCEECVQTRYETR----QRKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHHhceeCCCccCchhhHHH-HhcchHHHHHHHHHHHHHh----cCCCCCCCCCCCccccc
Confidence 346778999999988764332 57999999873 4555544 45899999999998864
No 39
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=68.81 E-value=3 Score=44.00 Aligned_cols=50 Identities=20% Similarity=0.407 Sum_probs=40.5
Q ss_pred cCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccc-cccccCCccce
Q 007360 117 PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI-CRLSRADPFWV 176 (606)
Q Consensus 117 iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~-Crl~r~DPF~~ 176 (606)
||++...-.+|+-|+- |...+|.-|||+..-| -+.|+|.+ |+.. ..||.+
T Consensus 319 IC~~P~~E~E~~FCD~--CDRG~HT~CVGL~~lP-------~G~WICD~~C~~~-~~~t~R 369 (381)
T KOG1512|consen 319 ICLGPVIESEHLFCDV--CDRGPHTLCVGLQDLP-------RGEWICDMRCREA-TLNTTR 369 (381)
T ss_pred ccCCcccchheecccc--ccCCCCcccccccccc-------CccchhhhHHHHh-cCCCCh
Confidence 6888877789999999 9999999999998765 57899985 7765 355553
No 40
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=65.65 E-value=1.5 Score=55.34 Aligned_cols=52 Identities=23% Similarity=0.541 Sum_probs=38.9
Q ss_pred ceec-cCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccccC
Q 007360 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRA 171 (606)
Q Consensus 113 ~~rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r~ 171 (606)
..+| +|........|+-|+. |..|+|+.|....-. .. .+..|+|+.||..+-
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~--c~~~~h~~C~rp~~~---~~--~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDE--CLSGFHLFCLRPALS---SV--PPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHh--hhhhHHHHhhhhhhc---cC--CcCCccCCccchhhh
Confidence 4556 4655555568999999 999999999975422 22 267899999999863
No 41
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=65.36 E-value=3.1 Score=48.77 Aligned_cols=49 Identities=33% Similarity=0.733 Sum_probs=40.5
Q ss_pred Cceec-cCCCC--CCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007360 112 TKVCC-PCGSS--LETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 112 ~~~rC-iC~~s--l~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~ 169 (606)
..+-| +|.+. .+..+||-|+. |+.=-|..|+||-+-| -+.|.|-+|-+.
T Consensus 270 edviCDvCrspD~e~~neMVfCd~--Cn~cVHqaCyGIle~p-------~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDK--CNICVHQACYGILEVP-------EGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEecc--chhHHHHhhhceeecC-------CCCeeehhcccc
Confidence 34556 67665 45789999999 9999999999998765 478999999988
No 42
>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=64.93 E-value=4 Score=29.84 Aligned_cols=39 Identities=23% Similarity=0.627 Sum_probs=26.5
Q ss_pred CCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCC
Q 007360 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC 406 (606)
|||=+..++.|+....|.|+-|++= +.++.+. ..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C--~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKEC--IEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHH--HHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHH--HHHHHHC--cCCCcCC
Confidence 5677778888989999999977653 3333333 3799998
No 43
>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=62.26 E-value=1.6 Score=32.70 Aligned_cols=19 Identities=21% Similarity=0.835 Sum_probs=12.1
Q ss_pred HHHHhcCCCeeeccCCCCC
Q 007360 391 FVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 391 fL~~n~~~~~W~CPiC~k~ 409 (606)
|.++.....+|.||+|+..
T Consensus 15 ~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 15 FCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp TSEEETTTTEEEETTT--E
T ss_pred cceEcCCCCEEECcCCCCc
Confidence 3334456789999999864
No 44
>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=61.28 E-value=2.5 Score=33.39 Aligned_cols=37 Identities=19% Similarity=0.452 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHh
Q 007360 389 DVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 389 ~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l 428 (606)
.-++..-..... .||+|++++..+.- +.++.++-..+
T Consensus 10 ~k~i~~l~~~~~-~CPlC~r~l~~e~~--~~li~~~~~~i 46 (54)
T PF04423_consen 10 KKYIEELKEAKG-CCPLCGRPLDEEHR--QELIKKYKSEI 46 (54)
T ss_dssp HHHHHHHTT-SE-E-TTT--EE-HHHH--HHHHHHHHHHH
T ss_pred HHHHHHHhcCCC-cCCCCCCCCCHHHH--HHHHHHHHHHH
Confidence 345555555555 99999999877654 55555544433
No 45
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=59.85 E-value=5.7 Score=32.15 Aligned_cols=36 Identities=17% Similarity=0.475 Sum_probs=24.9
Q ss_pred ccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCe
Q 007360 369 SRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENI 415 (606)
Q Consensus 369 ~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L 415 (606)
.++..|+--.-|.+ |||++-| =-||+|++++.+.+.
T Consensus 19 ~~~~~pCgH~I~~~--~f~~~rY---------ngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 19 KGTVLPCGHLICDN--CFPGERY---------NGCPFCGTPFEFDDP 54 (55)
T ss_pred ccccccccceeecc--ccChhhc---------cCCCCCCCcccCCCC
Confidence 34445544444444 8999987 479999999877653
No 46
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=59.15 E-value=6.4 Score=30.07 Aligned_cols=39 Identities=21% Similarity=0.504 Sum_probs=20.8
Q ss_pred CCCCcccccc----cccCCCCCccccccHHHHHHHhcCCCeeecc
Q 007360 364 CPMSGSRIKV----AGRFKPCVHMGCFDLDVFVELNQRSRKWQCP 404 (606)
Q Consensus 364 CPls~~ri~~----P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CP 404 (606)
||+++. +.. |..-. |.|.-|.|.-.=|..+....+.+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788877 666 77755 9999888877766665556789998
No 47
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=55.42 E-value=7.1 Score=28.46 Aligned_cols=41 Identities=27% Similarity=0.583 Sum_probs=27.9
Q ss_pred CCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCC
Q 007360 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC 406 (606)
||+=...+..|.+...|.|.-|.+ =+.++.+....-+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~--C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRD--CLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHH--HHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHH--HHHHHHHhcCCccCCcC
Confidence 566667777788889999996555 33333332666779988
No 48
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.01 E-value=1.6 Score=47.29 Aligned_cols=70 Identities=31% Similarity=0.552 Sum_probs=56.6
Q ss_pred ecceeeecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC-CCCCCeeecHHHHHHHHHh
Q 007360 356 DSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN-YSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 356 ~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~-~~~~~L~ID~y~~~IL~~l 428 (606)
..+.+.+.||+-+..|+.-.-...|-|--|||+-+ .+.+..--.||-|.+. ..--+|++|.-|..|+..|
T Consensus 38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i 108 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKI 108 (381)
T ss_pred HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHH
Confidence 46888999999999999988899999999998744 2334445689999765 4567999999999988766
No 49
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=54.45 E-value=1.7 Score=47.15 Aligned_cols=59 Identities=32% Similarity=0.603 Sum_probs=41.2
Q ss_pred CCCCceec-cCCCCCCC-CCeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccccccc
Q 007360 109 QSDTKVCC-PCGSSLET-ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLS 169 (606)
Q Consensus 109 ~~~~~~rC-iC~~sl~~-~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~ 169 (606)
.+-....| .||..... ..+|.|+. |..|||..|+.+.+.+...+......|+|+.|.+.
T Consensus 235 ~~~~~~~~~~cg~~~~~~~~~~~~~~--~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 235 PDYSKLICDPCGLSDANKKFEICCDL--CESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred cccccccccccCcchHHHHHHHHHHH--HHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 33345677 47765433 66888888 99999999999987653333222345999999875
No 50
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=52.55 E-value=7.7 Score=29.22 Aligned_cols=42 Identities=24% Similarity=0.411 Sum_probs=24.0
Q ss_pred CCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCC
Q 007360 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 364 CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC 406 (606)
|||=..-++-|+. ..|.|.-|+.=-.=+........+.||+|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 5677777777877 58999988765333332333334899998
No 51
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=50.74 E-value=9.4 Score=34.05 Aligned_cols=34 Identities=35% Similarity=0.717 Sum_probs=28.7
Q ss_pred ceec-cCCCCCCCCCeeeecCCCCCCcccccccccCC
Q 007360 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPE 148 (606)
Q Consensus 113 ~~rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~ 148 (606)
..+| +|+++ .|..|+|..++|..++|..|-....
T Consensus 55 ~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~g 89 (110)
T PF13832_consen 55 KLKCSICGKS--GGACIKCSHPGCSTAFHPTCARKAG 89 (110)
T ss_pred CCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHCC
Confidence 4556 79988 6889999999999999999986543
No 52
>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=50.34 E-value=6.1 Score=24.75 Aligned_cols=11 Identities=45% Similarity=1.361 Sum_probs=7.3
Q ss_pred eeccCCCCCCC
Q 007360 401 WQCPICLRNYS 411 (606)
Q Consensus 401 W~CPiC~k~~~ 411 (606)
|+||+|++.+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 89999997653
No 53
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.16 E-value=23 Score=39.38 Aligned_cols=36 Identities=25% Similarity=0.294 Sum_probs=32.3
Q ss_pred HhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccc
Q 007360 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSD 47 (606)
Q Consensus 12 ~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l~~ 47 (606)
..+..+.||..|..|||+.+|-|++|+.|--.|..-
T Consensus 267 ~~l~~~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l 302 (397)
T TIGR00599 267 SLLTDSQIRKKLSELGLSTNGTRQLLQKRHNEWETL 302 (397)
T ss_pred hhcCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHH
Confidence 357789999999999999999999999999888764
No 54
>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=45.95 E-value=9.2 Score=27.36 Aligned_cols=12 Identities=33% Similarity=1.032 Sum_probs=9.9
Q ss_pred CeeeccCCCCCC
Q 007360 399 RKWQCPICLRNY 410 (606)
Q Consensus 399 ~~W~CPiC~k~~ 410 (606)
..|.||+|+...
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 789999998643
No 55
>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=45.39 E-value=11 Score=28.89 Aligned_cols=43 Identities=30% Similarity=0.603 Sum_probs=24.8
Q ss_pred cCCCCcccccccccCCCCCcc-ccccHHHHHHHhcCCCeeeccCCCCCC
Q 007360 363 RCPMSGSRIKVAGRFKPCVHM-GCFDLDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 363 ~CPls~~ri~~P~Rg~~C~Hl-qCFDl~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
.|++=+.....+ -...|.|+ -|++= +..+.. ...+||+|.+++
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C--~~~~~~--~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEEC--AERLLK--RKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHH--HHHHHH--TTSBBTTTTBB-
T ss_pred CCccCCccCCce-EEeCCCChHHHHHH--hHHhcc--cCCCCCcCChhh
Confidence 455555554443 33479998 55543 223222 678999999876
No 56
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=43.82 E-value=16 Score=29.51 Aligned_cols=34 Identities=21% Similarity=0.553 Sum_probs=27.9
Q ss_pred CCceec-cCCCCCC-CCCeeeecCCCCCCccccccccc
Q 007360 111 DTKVCC-PCGSSLE-TESMIKCEDPRCPVWQHMSCVII 146 (606)
Q Consensus 111 ~~~~rC-iC~~sl~-~~~mI~C~~~~C~~wqH~~Cv~i 146 (606)
.+..+| .|+..+. .++.|.|-. |+...|..|...
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~--CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPE--CGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCC--CCCcccHHHHhh
Confidence 345678 4888874 789999999 999999999854
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.86 E-value=36 Score=32.35 Aligned_cols=69 Identities=13% Similarity=0.328 Sum_probs=40.1
Q ss_pred cCHHHHHHhcccCCCCCCHHHHHHHHHHhhCCCCCCCCCCCCCCcceEeecceeeecCCCCcccccccccCCCCCccccc
Q 007360 307 RSVQQVLNLIPKESEGEHFEDALTRVCRCVGGGNAADNADSDSDLEVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCF 386 (606)
Q Consensus 307 ~s~e~Ll~~I~~~~~~~~~e~al~rIkr~l~~~~~~~n~d~DdD~eIv~~~~~vSL~CPls~~ri~~P~Rg~~C~HlqCF 386 (606)
+..+.+++-|+.+ +...+++++..+.. +.-.....|| .|.+. |
T Consensus 67 i~y~~~~~vik~r-----~~~~~~~L~~~l~~-----------------e~~~~~Y~Cp-------------~C~~~--y 109 (147)
T smart00531 67 INYDTLLDVVKYK-----LDKMRKRLEDKLED-----------------ETNNAYYKCP-------------NCQSK--Y 109 (147)
T ss_pred ecHHHHHHHHHHH-----HHHHHHHHHHHHhc-----------------ccCCcEEECc-------------CCCCE--e
Confidence 3667777766542 34455666554421 1123467898 35543 5
Q ss_pred cHHHHHHHhcCCCeeeccCCCCCCCC
Q 007360 387 DLDVFVELNQRSRKWQCPICLRNYSL 412 (606)
Q Consensus 387 Dl~~fL~~n~~~~~W~CPiC~k~~~~ 412 (606)
.....+........+.||.|+..+..
T Consensus 110 ~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 110 TFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred eHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 55555554333667999999987744
No 58
>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=42.47 E-value=13 Score=36.24 Aligned_cols=46 Identities=28% Similarity=0.209 Sum_probs=25.1
Q ss_pred ceEEEEcCeEeecc-cCCCCCCCCCCCC--CCCCCcccCcCCCccEEEEEE
Q 007360 244 YADLQVNGVPVRAI-NRPGSQLLGANGR--DDGPIITPWTKDGINKIVLTG 291 (606)
Q Consensus 244 ~~~l~VNg~~v~~~-~Rp~~~~~g~~gR--~~~piIT~~lk~g~N~I~it~ 291 (606)
..+++|||+.|-.- ..|+... ..+| -...+||++|+.|.|.|.+..
T Consensus 15 ~Y~l~vNG~~V~~~~l~P~~t~--y~~~~~Y~tyDVt~~L~~G~N~iav~l 63 (172)
T PF08531_consen 15 RYELYVNGERVGDGPLAPGWTD--YDKRVYYQTYDVTPYLRPGENVIAVWL 63 (172)
T ss_dssp EEEEEETTEEEEEE----------BTTEEEEEEEE-TTT--TTEEEEEEEE
T ss_pred eEEEEECCEEeeCCcccccccc--CCCceEEEEEeChHHhCCCCCEEEEEE
Confidence 47899999998642 2343321 1111 124569999999999998764
No 59
>PLN03124 poly [ADP-ribose] polymerase; Provisional
Probab=41.00 E-value=23 Score=41.76 Aligned_cols=38 Identities=29% Similarity=0.541 Sum_probs=35.1
Q ss_pred HhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccchh
Q 007360 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQ 49 (606)
Q Consensus 12 ~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l~~~~ 49 (606)
..++|.||++-|..=||+..|.|++|+.|+-..+..+.
T Consensus 3 ~~~~v~~l~~~l~~~~~~~~g~k~~l~~rl~~~~~~e~ 40 (643)
T PLN03124 3 NKLKVDELRAALAKRGLDTTGLKAALVRRLDDAIAEDA 40 (643)
T ss_pred ccchhHHHHHHHHhcCCcccccchHHHHHHHhhhhhhh
Confidence 46899999999999999999999999999999988655
No 60
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.46 E-value=14 Score=38.74 Aligned_cols=54 Identities=24% Similarity=0.531 Sum_probs=41.2
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeee-ccCCCCCCCCCCeeec
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQ-CPICLRNYSLENIIID 418 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~-CPiC~k~~~~~~L~ID 418 (606)
+-+|+|-...+..|.+. .|-|+ |=+.-.+.+ ..+.+.. ||.|.....+..++|+
T Consensus 215 d~kC~lC~e~~~~ps~t-~CgHl--FC~~Cl~~~-~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 215 DYKCFLCLEEPEVPSCT-PCGHL--FCLSCLLIS-WTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred ccceeeeecccCCcccc-cccch--hhHHHHHHH-HHhhccccCchhhhhccchhhhee
Confidence 56899999999999984 89999 555555554 3444455 9999999988877654
No 61
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.25 E-value=54 Score=34.39 Aligned_cols=112 Identities=16% Similarity=0.299 Sum_probs=62.1
Q ss_pred EEEEEEEEecCHHHHHHhcccCC-CCCCHHHHHHHHHHhhCCCCCCCCCCCCCCcc-eEeecceeeecCCCCcccccccc
Q 007360 298 CLGVRIVKRRSVQQVLNLIPKES-EGEHFEDALTRVCRCVGGGNAADNADSDSDLE-VVADSIGVNLRCPMSGSRIKVAG 375 (606)
Q Consensus 298 ~~~V~lVk~~s~e~Ll~~I~~~~-~~~~~e~al~rIkr~l~~~~~~~n~d~DdD~e-Iv~~~~~vSL~CPls~~ri~~P~ 375 (606)
+++..+=+-++-+.|++.|..++ ...++.. ++-+|.... -..+.|.+...|.. --.+....-.+||++...|.=--
T Consensus 48 iv~c~lGrLYNKe~vi~~LL~Ks~~pksaSh-IKslKDvve-Lklt~n~~~~gD~~~~~~D~~~a~fiCPvtgleMng~~ 125 (293)
T KOG3113|consen 48 IVACGLGRLYNKESVIEFLLDKSSLPKSASH-IKSLKDVVE-LKLTLNPAFEGDKGNKHDDTQRARFICPVTGLEMNGKY 125 (293)
T ss_pred eeeehhhccccHHHHHHHHHhcccCCcchhh-hcchhhHhh-eecccCcccccccCccccccccceeecccccceecceE
Confidence 34555666678888998886542 1222211 111221110 00112211111110 11234577889999999997555
Q ss_pred cC---CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeee
Q 007360 376 RF---KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIII 417 (606)
Q Consensus 376 Rg---~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~I 417 (606)
|+ ..|-|. |...+.=++ ..-.|++|+..+.-+|.+|
T Consensus 126 ~F~~l~~CGcV--~SerAlKei----kas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 126 RFCALRCCGCV--FSERALKEI----KASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred EEEEEecccee--ccHHHHHHh----hhccccccCCcccccCeEe
Confidence 54 457776 666654433 3568999999998888775
No 62
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.99 E-value=12 Score=37.05 Aligned_cols=62 Identities=19% Similarity=0.371 Sum_probs=44.2
Q ss_pred eecCCCCcccccccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007360 361 NLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 361 SL~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 429 (606)
-|.||+....++-| +...|.|.-|..-..=+.- ....||.|..... +|.-...+..+++.++
T Consensus 13 ~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~----~~~~Cp~cr~~~~--~~~~n~~l~~~~~~~~ 74 (386)
T KOG2177|consen 13 ELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE----GPLSCPVCRPPSR--NLRPNVLLANLVERLR 74 (386)
T ss_pred cccChhhHHHhhcC-ccccccchHhHHHHHHhcC----CCcCCcccCCchh--ccCccHHHHHHHHHHH
Confidence 47899999999999 8888999988765543332 5689999995222 5555555555555443
No 63
>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=39.51 E-value=81 Score=29.58 Aligned_cols=66 Identities=21% Similarity=0.111 Sum_probs=41.5
Q ss_pred eeEEEEeChhhHHhhcCCCeeEEEEEEecCCCCcccccCCCceEEEEcCeEeecccCCCCCCCCCCCCCCCCCcccCcCC
Q 007360 203 LEKTFPITRADKDLLSKQEYDVQAWCMLLNDKVPFRMQWPQYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWTKD 282 (606)
Q Consensus 203 ~~~~F~Lt~~~~~~L~~~~~~lql~C~~l~d~~~~~~~wP~~~~l~VNg~~v~~~~Rp~~~~~g~~gR~~~piIT~~lk~ 282 (606)
.+.+|.|.++. ...++.|....++ ...+|.|||+.|-.. ..+. +.-..+||++|+.
T Consensus 72 Yr~~f~lp~~~------~~~~~~L~f~gv~----------~~a~v~vNG~~vg~~-~~~~-------~~~~~dIt~~l~~ 127 (167)
T PF02837_consen 72 YRRTFTLPADW------KGKRVFLRFEGVD----------YAAEVYVNGKLVGSH-EGGY-------TPFEFDITDYLKP 127 (167)
T ss_dssp EEEEEEESGGG------TTSEEEEEESEEE----------SEEEEEETTEEEEEE-ESTT-------S-EEEECGGGSSS
T ss_pred EEEEEEeCchh------cCceEEEEeccce----------EeeEEEeCCeEEeee-CCCc-------CCeEEeChhhccC
Confidence 46678887764 2334444333322 258999999988652 1111 1223559999999
Q ss_pred Cc-cEEEEEEe
Q 007360 283 GI-NKIVLTGC 292 (606)
Q Consensus 283 g~-N~I~it~~ 292 (606)
|. |.|.|...
T Consensus 128 g~~N~l~V~v~ 138 (167)
T PF02837_consen 128 GEENTLAVRVD 138 (167)
T ss_dssp EEEEEEEEEEE
T ss_pred CCCEEEEEEEe
Confidence 98 99988764
No 64
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=37.63 E-value=22 Score=34.39 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=20.3
Q ss_pred ccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 139 QHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 139 qH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
+|..|+..+ +..+|. +.|+||.|+..+
T Consensus 2 ~H~~CL~Pp---l~~~P~--g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPP---LKEVPE--GDWICPFCEVEK 28 (148)
T ss_pred cccccCCCC---CCCCCC--CCcCCCCCcCCC
Confidence 699998754 444443 689999999875
No 65
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=35.24 E-value=12 Score=23.79 Aligned_cols=11 Identities=45% Similarity=1.413 Sum_probs=9.1
Q ss_pred eeccCCCCCCC
Q 007360 401 WQCPICLRNYS 411 (606)
Q Consensus 401 W~CPiC~k~~~ 411 (606)
|+||+|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 68999998764
No 66
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=35.22 E-value=21 Score=26.58 Aligned_cols=24 Identities=29% Similarity=0.722 Sum_probs=13.0
Q ss_pred CCCCcccccc-HHHHHHHhcCCCeeeccCC
Q 007360 378 KPCVHMGCFD-LDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 378 ~~C~HlqCFD-l~~fL~~n~~~~~W~CPiC 406 (606)
..|.|.-|.+ +..||+.+ ..||+|
T Consensus 19 l~C~H~fh~~Ci~~~~~~~-----~~CP~C 43 (44)
T PF13639_consen 19 LPCGHVFHRSCIKEWLKRN-----NSCPVC 43 (44)
T ss_dssp ETTSEEEEHHHHHHHHHHS-----SB-TTT
T ss_pred ccCCCeeCHHHHHHHHHhC-----CcCCcc
Confidence 3488874333 34444432 399999
No 67
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=34.98 E-value=7 Score=45.46 Aligned_cols=41 Identities=27% Similarity=0.542 Sum_probs=29.7
Q ss_pred CCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccc
Q 007360 125 ESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRL 168 (606)
Q Consensus 125 ~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl 168 (606)
--|+.|+. |.+|+|..|-++.......+ .+...|-|-.||.
T Consensus 161 ~~~~~c~~--c~rwsh~~c~~~sdd~~~q~-~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 161 LPMVCCSI--CQRWSHGGCDGISDDKYMQA-QVDLQYKCSTCRG 201 (694)
T ss_pred hhhHHHHH--hcccccCCCCccchHHHHHH-hhhhhcccceeeh
Confidence 34799999 99999999999874321111 1124799999993
No 68
>PF02228 Gag_p19: Major core protein p19; InterPro: IPR003139 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from delta-retroviruses such as Human T-lymphotropic virus 1 and Human T-cell leukemia virus 2 (HTLV-2), both members of the human oncovirus subclass of retroviruses [, ].; GO: 0005198 structural molecule activity, 0019013 viral nucleocapsid; PDB: 1JVR_A.
Probab=34.76 E-value=18 Score=31.33 Aligned_cols=21 Identities=29% Similarity=0.582 Sum_probs=17.4
Q ss_pred ccHHHHHHHhcCCCeeeccCC
Q 007360 386 FDLDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 386 FDl~~fL~~n~~~~~W~CPiC 406 (606)
-+|..||.+..+++.|-|||=
T Consensus 44 ~qLr~flk~alkTpvwl~pi~ 64 (92)
T PF02228_consen 44 HQLRNFLKLALKTPVWLNPIN 64 (92)
T ss_dssp HHHHHHHHHHHT-TTSTTTT-
T ss_pred HHHHHHHHHHHcCCeeecccc
Confidence 468999999999999999983
No 69
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.62 E-value=19 Score=35.26 Aligned_cols=21 Identities=19% Similarity=0.498 Sum_probs=17.7
Q ss_pred eeeccCCCCCCCCCCeeecHH
Q 007360 400 KWQCPICLRNYSLENIIIDPY 420 (606)
Q Consensus 400 ~W~CPiC~k~~~~~~L~ID~y 420 (606)
-.+||||+|.+..+++.|--.
T Consensus 138 g~KCPvC~K~V~sDd~e~Hlv 158 (205)
T KOG0801|consen 138 GMKCPVCHKVVPSDDAEIHLV 158 (205)
T ss_pred CccCCccccccCCCcceEEEE
Confidence 478999999999999887643
No 70
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=34.13 E-value=50 Score=37.63 Aligned_cols=48 Identities=25% Similarity=0.654 Sum_probs=35.6
Q ss_pred eec-cCCCCC--CCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccccccc
Q 007360 114 VCC-PCGSSL--ETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSR 170 (606)
Q Consensus 114 ~rC-iC~~sl--~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~Crl~r 170 (606)
-+| +|-++. -...+|-|++ |..--|-.|+||+.-| -+.|+|--|.+..
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdg--C~i~VHq~CYGI~f~p-------eG~WlCrkCi~~~ 244 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDG--CEICVHQSCYGIQFLP-------EGFWLCRKCIYGE 244 (669)
T ss_pred hhhHhccccccCCcceEEEecC--cchhhhhhcccceecC-------cchhhhhhhcccc
Confidence 355 466553 2356899999 9999999999998765 3478888777654
No 71
>PRK12678 transcription termination factor Rho; Provisional
Probab=34.06 E-value=35 Score=40.01 Aligned_cols=37 Identities=30% Similarity=0.528 Sum_probs=31.2
Q ss_pred HHhccHHHHHHHHHHhCCC-CCC-ChHHHHHHHHHhccc
Q 007360 11 LAHFRIKELKDVLTQLGLS-KQG-KKQDLVDRILAILSD 47 (606)
Q Consensus 11 l~~fRi~ELk~vL~~lgls-k~G-~K~eL~~ril~~l~~ 47 (606)
|..+++.|||.+..+||+. -++ ||.||+.-|-+--..
T Consensus 23 LsamkL~ELr~lA~~lGI~Gts~mrK~eLI~AI~~~~gg 61 (672)
T PRK12678 23 LAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKEARGG 61 (672)
T ss_pred cccCcHHHHHHHHHHcCCcccccccHHHHHHHHHHhhcC
Confidence 7789999999999999999 444 899999999765543
No 72
>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=33.24 E-value=13 Score=25.32 Aligned_cols=9 Identities=56% Similarity=1.586 Sum_probs=8.0
Q ss_pred eccCCCCCC
Q 007360 402 QCPICLRNY 410 (606)
Q Consensus 402 ~CPiC~k~~ 410 (606)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
No 73
>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=32.88 E-value=19 Score=28.57 Aligned_cols=12 Identities=33% Similarity=1.176 Sum_probs=9.4
Q ss_pred CCeeeccCCCCC
Q 007360 398 SRKWQCPICLRN 409 (606)
Q Consensus 398 ~~~W~CPiC~k~ 409 (606)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 347999999854
No 74
>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=32.88 E-value=28 Score=23.63 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=15.1
Q ss_pred CCCCcccccc-HHHHHHHhcCCCeeeccCC
Q 007360 378 KPCVHMGCFD-LDVFVELNQRSRKWQCPIC 406 (606)
Q Consensus 378 ~~C~HlqCFD-l~~fL~~n~~~~~W~CPiC 406 (606)
..|.|.-|+. +..|++ ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 4599986555 233443 344679987
No 75
>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=31.70 E-value=28 Score=27.28 Aligned_cols=33 Identities=18% Similarity=0.740 Sum_probs=16.2
Q ss_pred CeeeecCCCCCCcccccccccCCCCCCCCCCCCCcccccc
Q 007360 126 SMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165 (606)
Q Consensus 126 ~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~ 165 (606)
..|||+. |.+|-... .++... ...+|+.|+|.+
T Consensus 2 ~WVQCd~--C~KWR~lp-~~~~~~----~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDS--CLKWRRLP-EEVDPI----REELPDPWYCSM 34 (50)
T ss_dssp EEEE-TT--T--EEEE--CCHHCT----SCCSSTT--GGG
T ss_pred eEEECCC--CCceeeCC-hhhCcc----cccCCCeEEcCC
Confidence 3699998 99999776 222211 123577999865
No 76
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.92 E-value=25 Score=34.95 Aligned_cols=49 Identities=16% Similarity=0.438 Sum_probs=31.8
Q ss_pred ecCCCCcccccccc-cCCCCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCC
Q 007360 362 LRCPMSGSRIKVAG-RFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLEN 414 (606)
Q Consensus 362 L~CPls~~ri~~P~-Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~ 414 (606)
.+||+-+....-=+ -+..|-|+-|= .-|. ...+.+-+||+|+|.++-.+
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvFC~---~Cik-~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVFCS---QCIK-DALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cCCCceecchhhccccccccchhHHH---HHHH-HHHHhCCCCCCcccccchhh
Confidence 78999887774322 45789998441 1111 23346789999999776544
No 77
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.91 E-value=54 Score=35.32 Aligned_cols=40 Identities=28% Similarity=0.398 Sum_probs=24.9
Q ss_pred CCCccccccHHHHHHHhcCCCeeeccCCCCCCCCCC----eeecHHH
Q 007360 379 PCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLEN----IIIDPYF 421 (606)
Q Consensus 379 ~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~~~----L~ID~y~ 421 (606)
.|-|.-|- +-|...-..+.-.||+|++.++..+ +..|..+
T Consensus 25 ~CGH~~C~---sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D~~v 68 (309)
T TIGR00570 25 VCGHTLCE---SCVDLLFVRGSGSCPECDTPLRKNNFRVQLFEDPTV 68 (309)
T ss_pred CCCCcccH---HHHHHHhcCCCCCCCCCCCccchhhccccccccHHH
Confidence 47776553 2222222345569999999998888 5556555
No 78
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=30.56 E-value=20 Score=28.03 Aligned_cols=12 Identities=33% Similarity=1.140 Sum_probs=7.1
Q ss_pred CCeeeccCCCCC
Q 007360 398 SRKWQCPICLRN 409 (606)
Q Consensus 398 ~~~W~CPiC~k~ 409 (606)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 457999999854
No 79
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=29.67 E-value=36 Score=37.51 Aligned_cols=41 Identities=27% Similarity=0.557 Sum_probs=24.7
Q ss_pred CCCcccccccccC--CCCCccccccHHHHHHHhcCCCeeeccCCCCCCCC
Q 007360 365 PMSGSRIKVAGRF--KPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSL 412 (606)
Q Consensus 365 Pls~~ri~~P~Rg--~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~~~ 412 (606)
|+-+..=..|-|- -+|-|+.| |+.|++.+ =.||||..++-+
T Consensus 304 ~~~~~~~~~pKrLpCGHilHl~C--LknW~ERq-----QTCPICr~p~if 346 (491)
T COG5243 304 PLPRGLDMTPKRLPCGHILHLHC--LKNWLERQ-----QTCPICRRPVIF 346 (491)
T ss_pred cCcccccCCcccccccceeeHHH--HHHHHHhc-----cCCCcccCcccc
Confidence 3333333344442 35666666 67888754 369999998644
No 80
>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=28.69 E-value=74 Score=26.99 Aligned_cols=33 Identities=21% Similarity=0.474 Sum_probs=24.4
Q ss_pred HHHHHHHhhcCCCCeeEEEEeeCCceEec-cCCC
Q 007360 421 FNRITSKMRNCGEDITELEVKPDGSWRVK-TRSE 453 (606)
Q Consensus 421 ~~~IL~~l~~~~~dv~eV~v~~DGsW~~~-~~~e 453 (606)
..++++.++..+-+|.+|+++.||.|.+. .+.+
T Consensus 31 ~~~~~~~l~~~G~~v~~ve~~~~g~yev~~~~~d 64 (83)
T PF13670_consen 31 IEQAVAKLEAQGYQVREVEFDDDGCYEVEARDKD 64 (83)
T ss_pred HHHHHHHHHhcCCceEEEEEcCCCEEEEEEEECC
Confidence 44555556665669999999999999998 3443
No 81
>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=28.62 E-value=37 Score=22.82 Aligned_cols=15 Identities=20% Similarity=0.913 Sum_probs=11.3
Q ss_pred cCCCeeeccCCCCCC
Q 007360 396 QRSRKWQCPICLRNY 410 (606)
Q Consensus 396 ~~~~~W~CPiC~k~~ 410 (606)
.....+.||+|++.+
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 344569999999765
No 82
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=28.36 E-value=37 Score=28.92 Aligned_cols=34 Identities=26% Similarity=0.591 Sum_probs=27.6
Q ss_pred ceec-cCCCCCCCCCeeeecCCCCCCcccccccccCC
Q 007360 113 KVCC-PCGSSLETESMIKCEDPRCPVWQHMSCVIIPE 148 (606)
Q Consensus 113 ~~rC-iC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~ 148 (606)
...| +|+.. .|-.|+|..+.|...+|..|-....
T Consensus 36 ~~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 36 KLKCSICKKK--GGACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred CCCCcCCCCC--CCeEEEEeCCCCCcEEChHHHccCC
Confidence 3456 58865 5789999999999999999987653
No 83
>PHA02929 N1R/p28-like protein; Provisional
Probab=27.22 E-value=57 Score=33.91 Aligned_cols=44 Identities=20% Similarity=0.612 Sum_probs=28.1
Q ss_pred ecCCCCcccccccc-------cCCCCCcccccc-HHHHHHHhcCCCeeeccCCCCCC
Q 007360 362 LRCPMSGSRIKVAG-------RFKPCVHMGCFD-LDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 362 L~CPls~~ri~~P~-------Rg~~C~HlqCFD-l~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
..||+-...+.-+. .-..|.|.-|.+ +..|+.. .=.||+|...+
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-----~~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-----KNTCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-----CCCCCCCCCEe
Confidence 57999888775432 234799975554 2245542 23799998765
No 84
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=26.84 E-value=24 Score=38.04 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=26.8
Q ss_pred cccCCCCCccccccHHHHHHHhcCCCeeeccCCCCC
Q 007360 374 AGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRN 409 (606)
Q Consensus 374 P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~ 409 (606)
|-+-++|.-.+|||--.=-+.-+-...|.||.|++.
T Consensus 258 ~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 258 PYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK 293 (415)
T ss_pred cchheeecHHHHHHHhhhHHhhcCcccccCchhccc
Confidence 446688887779987655555566778999999865
No 85
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.46 E-value=16 Score=24.67 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=11.7
Q ss_pred eeccCCCCCCCCCCe
Q 007360 401 WQCPICLRNYSLENI 415 (606)
Q Consensus 401 W~CPiC~k~~~~~~L 415 (606)
-.||+|++.+.++.|
T Consensus 3 ~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 3 VPCPICGRKFNPDRL 17 (25)
T ss_pred CcCCCCCCEECHHHH
Confidence 479999999866544
No 86
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=26.43 E-value=49 Score=27.30 Aligned_cols=29 Identities=14% Similarity=0.310 Sum_probs=23.6
Q ss_pred CeeeccCCCCCCCCCCeeecHHHHHHHHH
Q 007360 399 RKWQCPICLRNYSLENIIIDPYFNRITSK 427 (606)
Q Consensus 399 ~~W~CPiC~k~~~~~~L~ID~y~~~IL~~ 427 (606)
|.-.||+|++.+.+++-.-.+--.+||+.
T Consensus 7 PH~HC~VCg~aIp~de~~CSe~C~eil~k 35 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQVCSEECGEILNK 35 (64)
T ss_pred CCccccccCCcCCCccchHHHHHHHHHHH
Confidence 45579999999999988877777777764
No 87
>PLN00162 transport protein sec23; Provisional
Probab=25.41 E-value=21 Score=42.81 Aligned_cols=34 Identities=21% Similarity=0.694 Sum_probs=21.6
Q ss_pred ccccCCCCCccccccHHHHHHHhcCCCeeeccCCCCCC
Q 007360 373 VAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNY 410 (606)
Q Consensus 373 ~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k~~ 410 (606)
-|+|-..|+-. +.-|.+...+.++|.||+|+..-
T Consensus 52 ~pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N 85 (761)
T PLN00162 52 DPLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRN 85 (761)
T ss_pred CCCccCCCcCE----ECCceEEecCCCEEEccCCCCCC
Confidence 36665556543 33344445667899999998653
No 88
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=25.37 E-value=79 Score=34.56 Aligned_cols=33 Identities=33% Similarity=0.524 Sum_probs=27.6
Q ss_pred ccHHHHHHHHHHhCCCCCCChHHHHHHHHHhcc
Q 007360 14 FRIKELKDVLTQLGLSKQGKKQDLVDRILAILS 46 (606)
Q Consensus 14 fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l~ 46 (606)
+-=.++|.=|..+||+.+|.||.|+-|--.+.-
T Consensus 251 ls~s~ik~KLse~GLst~G~kQ~likRh~~~v~ 283 (442)
T KOG0287|consen 251 LSDSDIKKKLSEHGLSTQGNKQQLIKRHQEFVH 283 (442)
T ss_pred ccHHHHHHHHHHcCCCCcchHHHHHHHHHHHHH
Confidence 334678999999999999999999999776643
No 89
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=25.29 E-value=26 Score=38.15 Aligned_cols=63 Identities=21% Similarity=0.390 Sum_probs=50.5
Q ss_pred eeecCCCCcccccccccCCCCCcccc-ccHHHHHHHhcCCCeeeccCCCCCCCCCCeeecHHHHHHHHHh
Q 007360 360 VNLRCPMSGSRIKVAGRFKPCVHMGC-FDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKM 428 (606)
Q Consensus 360 vSL~CPls~~ri~~P~Rg~~C~HlqC-FDl~~fL~~n~~~~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l 428 (606)
-.|+|-|-+.=+++|+=.- |.|.-| |-...||.. +=+||.|-..++-.+|+-...+.+|++.+
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~-----~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSY-----KPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhcc-----CCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 3689999988888888765 999865 566666653 35799999999999999888888888754
No 90
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=25.16 E-value=43 Score=38.70 Aligned_cols=40 Identities=25% Similarity=0.474 Sum_probs=37.0
Q ss_pred HHHHhccHHHHHHHHHHhCCCCCCChHHHHHHHHHhccch
Q 007360 9 EKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDD 48 (606)
Q Consensus 9 ~~l~~fRi~ELk~vL~~lglsk~G~K~eL~~ril~~l~~~ 48 (606)
.+|..|||=+|+.-|.--.|-..|+|..||+|+-..|.++
T Consensus 28 rrlseLRViDLraEL~KRnldt~GnKsVLmERLkKal~~E 67 (940)
T KOG4661|consen 28 RRLSELRVIDLRAELEKRNLDTVGNKSVLMERLKKALRAE 67 (940)
T ss_pred chhhheeeeehhhHHhhhcccccCcHHHHHHHHHHHHHhc
Confidence 5789999999999999999999999999999999888754
No 91
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=24.83 E-value=35 Score=40.55 Aligned_cols=44 Identities=32% Similarity=0.787 Sum_probs=33.5
Q ss_pred ceeccCCCCCCCCCeeeecCCCCCCcccccccccCCCCCCCCCCCCCccccccc
Q 007360 113 KVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEIC 166 (606)
Q Consensus 113 ~~rCiC~~sl~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~p~~P~~fyCe~C 166 (606)
...|+|+. +|..+-|+. |..|+|..|.+.+..+ .+ ...|.|+.|
T Consensus 48 e~c~ic~~---~g~~l~c~t--C~~s~h~~cl~~pl~~----~p-~~~~~c~Rc 91 (696)
T KOG0383|consen 48 EACRICAD---GGELLWCDT--CPASFHASCLGPPLTP----QP-NGEFICPRC 91 (696)
T ss_pred hhhhhhcC---CCcEEEecc--ccHHHHHHccCCCCCc----CC-ccceeeeee
Confidence 45668874 568899999 9999999999876543 11 233999988
No 92
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=24.40 E-value=33 Score=33.36 Aligned_cols=27 Identities=26% Similarity=0.525 Sum_probs=18.2
Q ss_pred CCCCccccccHHHHHHHhcCCCeeeccCCCC
Q 007360 378 KPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408 (606)
Q Consensus 378 ~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k 408 (606)
..|+|+.|.=... -......|.|| |+-
T Consensus 106 ~iCtHlGC~~~~~---~~~~~~~~~CP-CHG 132 (177)
T COG0723 106 AICTHLGCTVPWN---NAGAEGGFFCP-CHG 132 (177)
T ss_pred eeccCCCCccCcc---cCCCCCeEEcc-CCC
Confidence 4699999975443 11344799999 653
No 93
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.35 E-value=81 Score=32.62 Aligned_cols=58 Identities=17% Similarity=0.366 Sum_probs=40.6
Q ss_pred cccccCCCCCccccccHHHHHHHhcCC---------CeeeccCCCCCCCCCCeeecHHHHHHHHHhh
Q 007360 372 KVAGRFKPCVHMGCFDLDVFVELNQRS---------RKWQCPICLRNYSLENIIIDPYFNRITSKMR 429 (606)
Q Consensus 372 ~~P~Rg~~C~HlqCFDl~~fL~~n~~~---------~~W~CPiC~k~~~~~~L~ID~y~~~IL~~l~ 429 (606)
.+|--...|.-+-||++-.|=-+|++. .-++||-|+..+-+--=.+......+.+.|+
T Consensus 57 ~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~ 123 (299)
T KOG3970|consen 57 NTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLK 123 (299)
T ss_pred CCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHH
Confidence 456667788889999998887777542 4799999998776544445555555544454
No 94
>PF04641 Rtf2: Rtf2 RING-finger
Probab=24.11 E-value=84 Score=32.69 Aligned_cols=31 Identities=10% Similarity=0.107 Sum_probs=24.3
Q ss_pred ecCCCCcccccccccCCCCCccccccHHHHHHH
Q 007360 362 LRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVEL 394 (606)
Q Consensus 362 L~CPls~~ri~~P~Rg~~C~HlqCFDl~~fL~~ 394 (606)
-.|+||+.+++.|+=+ |..-.=|+.++.|+.
T Consensus 35 ~~CaLS~~pL~~PiV~--d~~G~LynKeaile~ 65 (260)
T PF04641_consen 35 THCALSQQPLEDPIVS--DRLGRLYNKEAILEF 65 (260)
T ss_pred CcccCcCCccCCCeee--CCCCeeEcHHHHHHH
Confidence 3699999999999944 444445999998875
No 95
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=23.65 E-value=50 Score=24.75 Aligned_cols=33 Identities=27% Similarity=0.604 Sum_probs=20.9
Q ss_pred cccccCCCCCccccccHHHHHHHhcCCCeeeccCCCC
Q 007360 372 KVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408 (606)
Q Consensus 372 ~~P~Rg~~C~HlqCFDl~~fL~~n~~~~~W~CPiC~k 408 (606)
..+.+-..|.|+-|-.=.. .+. ...-.||+|++
T Consensus 12 ~~~~~l~~CgH~~C~~C~~--~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 12 ERRPRLTSCGHIFCEKCLK--KLK--GKSVKCPICRK 44 (44)
T ss_pred CCCeEEcccCCHHHHHHHH--hhc--CCCCCCcCCCC
Confidence 3456678899985543222 222 56789999975
No 96
>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=22.53 E-value=25 Score=27.67 Aligned_cols=11 Identities=27% Similarity=1.132 Sum_probs=8.7
Q ss_pred eeeccCCCCCC
Q 007360 400 KWQCPICLRNY 410 (606)
Q Consensus 400 ~W~CPiC~k~~ 410 (606)
++.||.|++.+
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 57899999843
No 97
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=21.58 E-value=74 Score=36.55 Aligned_cols=65 Identities=17% Similarity=0.281 Sum_probs=45.1
Q ss_pred ceeccCCCCC-CCCCeeeecCCCCCCcccccccccCCCCCCCC-CCCCCcccccccccccCCccceeec
Q 007360 113 KVCCPCGSSL-ETESMIKCEDPRCPVWQHMSCVIIPEKPTEGN-PPVPELFYCEICRLSRADPFWVTIG 179 (606)
Q Consensus 113 ~~rCiC~~sl-~~~~mI~C~~~~C~~wqH~~Cv~i~~k~~~~~-p~~P~~fyCe~Crl~r~DPF~~~i~ 179 (606)
.+.|+|+..- ..-..++|.. |..|+|..|.-...--.++. ......|.|-.|++...-=|-..+.
T Consensus 20 ~~~~y~e~~r~l~~~elqcs~--clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~~~e~f~~~~a 86 (544)
T KOG2626|consen 20 ATVCYCEGERNLGIVELQCST--CLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPSGREHFERKQA 86 (544)
T ss_pred ccccccccccccCceeeEeee--cccccccccccccccccccCCcccceeEEeccccCcchhhhhhccc
Confidence 5789999763 3567899999 99999987765443222233 3456789999999885445555443
No 98
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=20.25 E-value=61 Score=34.97 Aligned_cols=34 Identities=26% Similarity=0.740 Sum_probs=26.8
Q ss_pred CceeccCCCCC------CCCCeeeecCCCCCCccc-ccccccC
Q 007360 112 TKVCCPCGSSL------ETESMIKCEDPRCPVWQH-MSCVIIP 147 (606)
Q Consensus 112 ~~~rCiC~~sl------~~~~mI~C~~~~C~~wqH-~~Cv~i~ 147 (606)
.-.+|.|.-.- ..+.|+||.. |.=||| -+|+...
T Consensus 127 qG~~C~Cd~~Ypdp~~~~e~~m~QC~i--CEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 127 QGLFCKCDTPYPDPVRTEEGEMLQCVI--CEDWFHCEGCMQAK 167 (345)
T ss_pred cceeEEecCCCCCccccccceeeeEEe--ccchhcccccCccc
Confidence 36788886542 3588999999 999999 8888764
Done!