Query 038900
Match_columns 230
No_of_seqs 210 out of 735
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 04:24:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038900hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3002 Zn finger protein [Gen 100.0 3.1E-39 6.8E-44 281.5 11.4 204 1-210 65-279 (299)
2 PF03145 Sina: Seven in absent 100.0 8.4E-34 1.8E-38 236.1 7.2 188 30-219 1-198 (198)
3 cd03829 Sina Seven in absentia 99.5 5.7E-15 1.2E-19 111.4 2.0 101 122-222 23-127 (127)
4 KOG0297 TNF receptor-associate 99.1 1.7E-10 3.6E-15 105.3 5.9 99 2-104 39-143 (391)
5 PF02176 zf-TRAF: TRAF-type zi 98.3 3.1E-07 6.6E-12 61.6 1.8 50 42-94 8-60 (60)
6 PF14835 zf-RING_6: zf-RING of 97.3 0.00024 5.2E-09 48.1 2.7 37 2-39 25-65 (65)
7 PF02176 zf-TRAF: TRAF-type zi 97.2 0.00013 2.9E-09 48.6 1.0 43 66-108 1-43 (60)
8 PF13920 zf-C3HC4_3: Zinc fing 97.0 0.00013 2.8E-09 47.1 -0.4 28 2-29 19-49 (50)
9 PF14634 zf-RING_5: zinc-RING 96.9 0.00026 5.6E-09 44.4 0.5 24 2-25 19-44 (44)
10 COG5432 RAD18 RING-finger-cont 96.9 0.00038 8.2E-09 60.4 1.1 27 2-28 42-70 (391)
11 PLN03086 PRLI-interacting fact 96.8 0.00045 9.7E-09 65.7 1.1 47 45-95 408-454 (567)
12 KOG0287 Postreplication repair 96.5 0.00081 1.8E-08 59.5 0.6 42 2-43 40-86 (442)
13 TIGR00570 cdk7 CDK-activating 96.3 0.002 4.3E-08 56.9 2.0 27 2-28 25-54 (309)
14 TIGR00599 rad18 DNA repair pro 96.2 0.002 4.4E-08 58.9 1.6 41 2-42 43-88 (397)
15 smart00504 Ubox Modified RING 96.2 0.003 6.6E-08 42.2 2.0 40 2-41 18-62 (63)
16 PF13923 zf-C3HC4_2: Zinc fing 96.2 0.001 2.2E-08 40.5 -0.4 22 2-23 16-39 (39)
17 PLN03086 PRLI-interacting fact 96.0 0.019 4.1E-07 54.8 6.6 71 18-97 454-536 (567)
18 PF13639 zf-RING_2: Ring finge 95.9 0.00095 2.1E-08 41.7 -1.5 23 2-24 20-44 (44)
19 PF07800 DUF1644: Protein of u 95.7 0.014 3E-07 46.5 4.1 52 19-101 82-134 (162)
20 cd00162 RING RING-finger (Real 95.6 0.0045 9.6E-08 37.7 0.8 26 2-27 17-45 (45)
21 PLN03208 E3 ubiquitin-protein 95.6 0.0039 8.4E-08 51.5 0.6 27 2-28 35-79 (193)
22 PF15227 zf-C3HC4_4: zinc fing 94.9 0.0054 1.2E-07 38.1 -0.6 22 2-23 15-42 (42)
23 PF00097 zf-C3HC4: Zinc finger 94.5 0.0093 2E-07 36.4 -0.2 22 2-23 16-41 (41)
24 PF14570 zf-RING_4: RING/Ubox 94.4 0.01 2.2E-07 38.0 -0.2 27 1-27 18-47 (48)
25 PF14447 Prok-RING_4: Prokaryo 94.3 0.028 6E-07 36.9 1.7 27 2-28 24-50 (55)
26 KOG0311 Predicted E3 ubiquitin 94.1 0.0078 1.7E-07 53.7 -1.6 42 2-43 61-109 (381)
27 KOG0823 Predicted E3 ubiquitin 94.0 0.015 3.2E-07 49.1 -0.0 27 2-28 64-95 (230)
28 smart00184 RING Ring finger. E 93.9 0.017 3.7E-07 33.7 0.1 22 2-23 15-39 (39)
29 KOG4739 Uncharacterized protei 89.9 0.13 2.8E-06 43.8 0.8 27 2-28 22-48 (233)
30 KOG1785 Tyrosine kinase negati 89.0 0.1 2.3E-06 47.5 -0.4 27 2-28 386-416 (563)
31 KOG2164 Predicted E3 ubiquitin 88.9 0.098 2.1E-06 48.9 -0.6 28 2-29 203-237 (513)
32 PF05605 zf-Di19: Drought indu 88.1 0.54 1.2E-05 30.5 2.7 49 45-100 3-54 (54)
33 PF13445 zf-RING_UBOX: RING-ty 88.0 0.11 2.3E-06 32.5 -0.7 15 2-16 18-32 (43)
34 PF10083 DUF2321: Uncharacteri 86.6 0.18 3.9E-06 40.1 -0.3 27 1-28 10-50 (158)
35 PF04564 U-box: U-box domain; 85.6 0.46 9.9E-06 32.9 1.4 41 2-42 21-67 (73)
36 PF13909 zf-H2C2_5: C2H2-type 83.9 0.62 1.4E-05 24.7 1.1 23 76-100 2-24 (24)
37 COG4306 Uncharacterized protei 83.6 0.44 9.6E-06 36.7 0.6 25 1-27 10-49 (160)
38 PHA00616 hypothetical protein 82.8 1.2 2.6E-05 27.9 2.2 33 74-108 1-34 (44)
39 KOG2177 Predicted E3 ubiquitin 82.2 0.48 1E-05 40.1 0.4 46 2-48 30-78 (386)
40 COG2888 Predicted Zn-ribbon RN 81.0 1.5 3.2E-05 29.3 2.2 36 42-87 26-61 (61)
41 KOG2660 Locus-specific chromos 79.7 0.64 1.4E-05 41.4 0.3 41 3-43 34-83 (331)
42 PF13913 zf-C2HC_2: zinc-finge 79.3 1.1 2.4E-05 24.4 1.1 23 45-71 3-25 (25)
43 KOG2932 E3 ubiquitin ligase in 78.4 1 2.2E-05 39.9 1.1 59 2-67 108-167 (389)
44 KOG4185 Predicted E3 ubiquitin 77.7 1.1 2.4E-05 39.2 1.2 25 3-27 27-54 (296)
45 PF12861 zf-Apc11: Anaphase-pr 77.2 0.8 1.7E-05 32.9 0.1 27 2-28 51-82 (85)
46 COG5236 Uncharacterized conser 74.9 1.1 2.4E-05 40.3 0.4 91 2-101 78-179 (493)
47 PF04641 Rtf2: Rtf2 RING-finge 73.2 1.5 3.2E-05 38.0 0.8 27 2-28 134-161 (260)
48 PRK14890 putative Zn-ribbon RN 71.9 3.6 7.7E-05 27.5 2.2 13 73-87 47-59 (59)
49 PF04606 Ogr_Delta: Ogr/Delta- 71.5 2.2 4.7E-05 26.9 1.1 37 19-58 1-37 (47)
50 KOG4159 Predicted E3 ubiquitin 70.9 1.4 3.1E-05 40.5 0.2 27 2-28 101-129 (398)
51 COG5175 MOT2 Transcriptional r 70.9 0.84 1.8E-05 40.9 -1.3 27 1-27 34-63 (480)
52 KOG0824 Predicted E3 ubiquitin 70.4 2.3 5E-05 37.5 1.3 28 2-29 24-54 (324)
53 KOG4172 Predicted E3 ubiquitin 70.2 0.5 1.1E-05 31.0 -2.1 26 3-28 25-54 (62)
54 PF05253 zf-U11-48K: U11-48K-l 69.6 2.5 5.3E-05 23.5 0.9 24 45-71 3-26 (27)
55 KOG0802 E3 ubiquitin ligase [P 69.1 1.2 2.7E-05 42.6 -0.7 26 2-27 313-340 (543)
56 COG3813 Uncharacterized protei 64.0 2.8 6E-05 29.1 0.5 28 1-28 25-52 (84)
57 KOG3800 Predicted E3 ubiquitin 62.2 2.5 5.4E-05 37.1 -0.1 26 2-27 22-50 (300)
58 PF05605 zf-Di19: Drought indu 61.8 9 0.0002 24.6 2.6 28 74-103 2-29 (54)
59 PF13240 zinc_ribbon_2: zinc-r 61.4 4.8 0.0001 21.5 1.0 21 7-27 1-23 (23)
60 KOG0825 PHD Zn-finger protein 60.5 2.6 5.6E-05 41.9 -0.3 27 2-28 143-171 (1134)
61 KOG3608 Zn finger proteins [Ge 59.5 8.9 0.00019 34.8 2.9 92 5-101 237-347 (467)
62 PF08209 Sgf11: Sgf11 (transcr 58.8 6.1 0.00013 23.2 1.2 23 45-71 5-27 (33)
63 smart00734 ZnF_Rad18 Rad18-lik 58.0 5 0.00011 22.1 0.7 17 54-70 7-23 (26)
64 smart00301 DM Doublesex DNA-bi 57.4 5.8 0.00013 26.0 1.1 35 59-95 13-47 (54)
65 COG5222 Uncharacterized conser 57.3 5.9 0.00013 35.1 1.4 41 3-43 293-340 (427)
66 PF13894 zf-C2H2_4: C2H2-type 53.0 14 0.0003 18.6 2.0 22 76-99 2-24 (24)
67 PRK09678 DNA-binding transcrip 52.1 5.5 0.00012 27.7 0.3 45 19-66 3-47 (72)
68 PF13248 zf-ribbon_3: zinc-rib 51.5 8.8 0.00019 20.9 1.0 22 6-27 3-26 (26)
69 KOG1039 Predicted E3 ubiquitin 50.5 7.2 0.00016 35.3 0.9 27 2-28 186-221 (344)
70 COG5243 HRD1 HRD ubiquitin lig 50.0 6.2 0.00013 36.0 0.4 26 2-27 317-344 (491)
71 PF10426 zf-RAG1: Recombinatio 48.2 12 0.00025 21.5 1.2 21 45-67 3-23 (30)
72 PF07754 DUF1610: Domain of un 45.6 12 0.00025 20.4 0.9 6 19-24 18-23 (24)
73 PF06906 DUF1272: Protein of u 45.0 6.9 0.00015 25.8 -0.1 25 4-28 28-52 (57)
74 PF00096 zf-C2H2: Zinc finger, 44.0 10 0.00022 19.4 0.6 20 76-97 2-22 (23)
75 PRK04023 DNA polymerase II lar 43.6 25 0.00054 36.2 3.5 23 6-28 652-674 (1121)
76 PF03145 Sina: Seven in absent 43.5 23 0.0005 29.0 2.8 48 23-71 24-71 (198)
77 KOG1815 Predicted E3 ubiquitin 42.8 14 0.00031 34.4 1.6 23 1-23 182-205 (444)
78 PF06750 DiS_P_DiS: Bacterial 42.7 21 0.00045 25.9 2.1 25 4-28 32-69 (92)
79 PF09297 zf-NADH-PPase: NADH p 40.6 5.8 0.00013 22.7 -0.8 22 4-25 2-29 (32)
80 PF08882 Acetone_carb_G: Aceto 38.7 13 0.00028 28.0 0.6 10 1-10 27-36 (112)
81 COG5220 TFB3 Cdk activating ki 37.0 19 0.00042 30.9 1.4 39 18-59 11-64 (314)
82 KOG3002 Zn finger protein [Gen 34.4 17 0.00037 32.3 0.7 74 19-97 50-131 (299)
83 KOG1812 Predicted E3 ubiquitin 33.6 29 0.00062 31.9 2.1 62 2-65 167-252 (384)
84 KOG4628 Predicted E3 ubiquitin 33.5 23 0.00051 32.1 1.4 27 2-28 249-278 (348)
85 PF07191 zinc-ribbons_6: zinc- 33.5 8.5 0.00018 26.6 -1.1 26 3-28 15-41 (70)
86 KOG0297 TNF receptor-associate 33.3 26 0.00056 32.3 1.7 38 42-83 113-151 (391)
87 PRK06393 rpoE DNA-directed RNA 33.1 26 0.00056 23.8 1.2 24 4-27 4-27 (64)
88 PF00751 DM: DM DNA binding do 32.9 12 0.00027 23.7 -0.3 26 59-86 13-38 (47)
89 KOG3039 Uncharacterized conser 32.7 19 0.00042 31.0 0.7 27 2-28 242-270 (303)
90 PRK14714 DNA polymerase II lar 31.2 49 0.0011 35.0 3.4 22 7-28 694-720 (1337)
91 COG4357 Zinc finger domain con 31.1 21 0.00045 26.3 0.6 24 6-29 63-92 (105)
92 PF14334 DUF4390: Domain of un 30.5 34 0.00073 27.3 1.8 33 198-230 109-143 (165)
93 PRK08351 DNA-directed RNA poly 30.5 34 0.00073 23.0 1.5 22 6-27 4-25 (61)
94 PLN02248 cellulose synthase-li 30.4 21 0.00046 37.1 0.7 27 1-27 148-176 (1135)
95 COG2093 DNA-directed RNA polym 29.8 31 0.00068 23.3 1.2 21 6-26 5-27 (64)
96 KOG2462 C2H2-type Zn-finger pr 28.3 83 0.0018 27.6 3.8 72 19-97 163-237 (279)
97 PF10571 UPF0547: Uncharacteri 28.0 47 0.001 18.2 1.5 20 8-27 3-24 (26)
98 KOG3161 Predicted E3 ubiquitin 27.8 19 0.00041 35.2 -0.1 20 2-21 32-51 (861)
99 PF12773 DZR: Double zinc ribb 26.4 42 0.00091 20.8 1.3 21 8-28 1-23 (50)
100 COG4647 AcxC Acetone carboxyla 26.4 24 0.00051 27.5 0.2 40 1-49 73-114 (165)
101 PF10235 Cript: Microtubule-as 26.1 38 0.00083 24.6 1.2 25 3-29 57-81 (90)
102 PF01363 FYVE: FYVE zinc finge 25.7 26 0.00057 23.4 0.3 14 2-15 30-43 (69)
103 KOG1002 Nucleotide excision re 25.1 20 0.00044 34.3 -0.4 27 2-28 553-586 (791)
104 PF10005 DUF2248: Uncharacteri 24.4 32 0.00068 31.1 0.6 55 8-63 2-73 (343)
105 PF01754 zf-A20: A20-like zinc 24.0 54 0.0012 17.9 1.3 15 74-89 1-15 (25)
106 PF09237 GAGA: GAGA factor; I 23.8 54 0.0012 21.3 1.4 28 72-101 22-50 (54)
107 PF12756 zf-C2H2_2: C2H2 type 23.6 49 0.0011 23.0 1.4 36 64-101 40-77 (100)
108 KOG2857 Predicted MYND Zn-fing 23.3 48 0.001 26.2 1.3 37 1-38 2-38 (157)
109 PRK14714 DNA polymerase II lar 22.8 55 0.0012 34.7 2.0 24 4-27 666-689 (1337)
110 PF12013 DUF3505: Protein of u 22.5 69 0.0015 23.5 2.1 26 75-100 81-109 (109)
111 PRK00398 rpoP DNA-directed RNA 22.3 13 0.00028 23.1 -1.7 22 7-28 5-32 (46)
112 COG2816 NPY1 NTP pyrophosphohy 21.2 51 0.0011 29.0 1.3 24 4-27 110-139 (279)
113 PF14353 CpXC: CpXC protein 21.2 1E+02 0.0022 23.2 2.8 10 19-28 3-12 (128)
114 PF11023 DUF2614: Protein of u 21.0 61 0.0013 24.5 1.5 28 6-33 70-101 (114)
115 PF07975 C1_4: TFIIH C1-like d 20.1 49 0.0011 21.3 0.7 25 19-48 23-47 (51)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=100.00 E-value=3.1e-39 Score=281.48 Aligned_cols=204 Identities=31% Similarity=0.546 Sum_probs=169.6
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCCC
Q 038900 1 CENGHMVCTTCRSKIKNDSCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPLS 80 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~~~~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~ 80 (230)
|++||++|++|+.++.+ +||.|+.+++++|+++||++++++. |||||+.+||++.++|.+..+||+.|.|+|+.||.+
T Consensus 65 C~nGHlaCssC~~~~~~-~CP~Cr~~~g~~R~~amEkV~e~~~-vpC~~~~~GC~~~~~Y~~~~~HE~~C~f~~~~CP~p 142 (299)
T KOG3002|consen 65 CDNGHLACSSCRTKVSN-KCPTCRLPIGNIRCRAMEKVAEAVL-VPCKNAKLGCTKSFPYGEKSKHEKVCEFRPCSCPVP 142 (299)
T ss_pred cCCCcEehhhhhhhhcc-cCCccccccccHHHHHHHHHHHhce-ecccccccCCceeeccccccccccccccCCcCCCCC
Confidence 89999999999999887 9999999999999999999999999 999999999999999999999999999999999999
Q ss_pred --CCCcccChhhHHHHHhhhcCCCce-----eEEecceEEEEEecCC--CCeEEEEEecCCeEEEEEEecCCCCceeEEE
Q 038900 81 --GCDFLGSSSQLYQHFRAQHQNSSV-----PFRYDQDFSIRLDAKN--DKFLVLLEGRDDNILFVLHNARSNQQQNGLS 151 (230)
Q Consensus 81 --~C~~~g~~~~L~~H~~~~H~~~~~-----~~~y~~~~~l~l~~~~--~~~~vl~~~~d~~~lFll~~~~~~~~g~~vs 151 (230)
.|+|+|.+++|..|+...|+..++ .|.+....+..+.... .+..+..+...+. +|+++.+. ++.|.+++
T Consensus 143 ~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~q~~~-~~~~~y~t 220 (299)
T KOG3002|consen 143 GAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFVATDENLLGAATWTLKTSVCFGREFGL-LFEVQCFR-EPHGVYVT 220 (299)
T ss_pred cccCCccCcHHHHHHHHHhhChhhhhhccccceecccCCccccccchhheeeeecCcEEEee-eeeehhhc-CCCceEEE
Confidence 899999999999999999999765 4444433322222221 1222233444555 88888866 77899999
Q ss_pred EEeecCCC--CCCCeEEEEEEeCCceEEEEEeecceecccccccCCCCCCcccccCcccCC
Q 038900 152 ISCISSSR--EARNEYKISVTFGSNNVSTLTFRSAISSSKKQLDNLPKLGFPLVPWLLDAT 210 (230)
Q Consensus 152 v~cigp~~--~~~f~Y~l~~~~~~~~l~~~s~~~~i~~s~~~~~~~~~~~fl~vp~~~~~~ 210 (230)
|++|.|.+ +.+|+|+|++.+++++|+|++.++++..+. ....|..+||++|.+++..
T Consensus 221 v~~i~~~~~e~~~fsy~L~~~~~~~klt~~s~~~s~~~kv--s~~~p~~dfm~ip~~~~~~ 279 (299)
T KOG3002|consen 221 VNRIAPSAPEAGEFSYSLALGGSGRKLTWQSPPRSIIQKV--SKVRPEDDFMLIPRSLLCL 279 (299)
T ss_pred eehhccCCCcccccceeeecCCCCceEeecCCcceeeccc--ceeccCCCceeccHHHhhc
Confidence 99999865 358999999999999999999988766532 2367889999999987654
No 2
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=100.00 E-value=8.4e-34 Score=236.05 Aligned_cols=188 Identities=27% Similarity=0.460 Sum_probs=112.0
Q ss_pred cchHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCC--CCCCcccChhhHHHHHhhhcCCCceeEE
Q 038900 30 TRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPL--SGCDFLGSSSQLYQHFRAQHQNSSVPFR 107 (230)
Q Consensus 30 ~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~--~~C~~~g~~~~L~~H~~~~H~~~~~~~~ 107 (230)
+||++||+++++++ +||+|+.+||++.++|.++.+||++|+|+|+.||. .+|+|+|+.++|..|+...|.+.++...
T Consensus 1 iR~~alE~v~~~~~-~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~~~~~ 79 (198)
T PF03145_consen 1 IRNRALEKVAESIK-FPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNVTDNG 79 (198)
T ss_dssp ---------------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSEEEES
T ss_pred CCcHHHHHHHhhce-ecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCccccCc
Confidence 58999999999999 99999999999999999999999999999999999 7899999999999999999999765432
Q ss_pred e-cceEEEEEecC--CCCeEEEEEecCCeEEEEEEecC--CCCceeEE-EEEeecCCC-CCCCeEEEEEEeCCceEEEEE
Q 038900 108 Y-DQDFSIRLDAK--NDKFLVLLEGRDDNILFVLHNAR--SNQQQNGL-SISCISSSR-EARNEYKISVTFGSNNVSTLT 180 (230)
Q Consensus 108 y-~~~~~l~l~~~--~~~~~vl~~~~d~~~lFll~~~~--~~~~g~~v-sv~cigp~~-~~~f~Y~l~~~~~~~~l~~~s 180 (230)
+ ...+......+ ...|++++...+|+ +|+|.... ....+.++ .|++||+++ +++|+|+|++.+++++|+||+
T Consensus 80 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~-~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~~~~rkl~~~~ 158 (198)
T PF03145_consen 80 TFSISFLHSDINSVESPDWVLVQFSCFGK-LFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVRSNGRKLTWQS 158 (198)
T ss_dssp S-EEEEEECTTT-SSSEEEEEEE-EETTE-EEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEEETTEEEEEEE
T ss_pred cceEEEeeecccccCCceEEEeecccCCc-cEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEecCCcEEEEEE
Confidence 2 11111111111 12455555245666 66666422 12334444 456678754 578999999999999999999
Q ss_pred eecceecccc-cccCCCCCCcccccCcccCCCCceEEEEE
Q 038900 181 FRSAISSSKK-QLDNLPKLGFPLVPWLLDATDGRLNLKIC 219 (230)
Q Consensus 181 ~~~~i~~s~~-~~~~~~~~~fl~vp~~~~~~~g~l~l~v~ 219 (230)
++++++.+.. ..++.+.+.++..-..+|.++|.|.++|+
T Consensus 159 ~p~si~~~~~~~~~~~d~li~~~~~~~~f~~~~~L~~~v~ 198 (198)
T PF03145_consen 159 FPRSIREDIDDAIESRDCLIINENAAQFFSEDGNLRYRVT 198 (198)
T ss_dssp --EETTT-SHHHHHCT-SEEEEHHHHHHHECTTEEEEEEE
T ss_pred cCcchhhhHHhhccCCcEEEEchHHHHhcCCCCeEEEEeC
Confidence 9999888543 22333333333334468899999998885
No 3
>cd03829 Sina Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-medi
Probab=99.50 E-value=5.7e-15 Score=111.37 Aligned_cols=101 Identities=15% Similarity=0.184 Sum_probs=79.8
Q ss_pred CeEEEEEecCCeEEEEEEecCC-C-CceeEEEEEeecCCCC-CCCeEEEEEEeCCceEEEEEeecceecccc-cccCCCC
Q 038900 122 KFLVLLEGRDDNILFVLHNARS-N-QQQNGLSISCISSSRE-ARNEYKISVTFGSNNVSTLTFRSAISSSKK-QLDNLPK 197 (230)
Q Consensus 122 ~~~vl~~~~d~~~lFll~~~~~-~-~~g~~vsv~cigp~~~-~~f~Y~l~~~~~~~~l~~~s~~~~i~~s~~-~~~~~~~ 197 (230)
.|++++.+++.+|+.+|.++.. + .....+.|+.||+..+ .+|+|.|++.+++|+|+||++|++|++|.. ..+..++
T Consensus 23 ~w~mv~sCfG~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~~n~RkL~we~~PRSIrds~~~~~~~~D~ 102 (127)
T cd03829 23 DWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELNGNRRRLTWEATPRSIREGHASVIDNSDC 102 (127)
T ss_pred eeeehhhhcCceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEcCCCcEEEeecCCccHHHhhHHHhhcCcc
Confidence 6777888888776666666432 1 1223577899998764 589999999999999999999999998764 3566677
Q ss_pred CCcccccCcccCCCCceEEEEEEEc
Q 038900 198 LGFPLVPWLLDATDGRLNLKICIFK 222 (230)
Q Consensus 198 ~~fl~vp~~~~~~~g~l~l~v~I~~ 222 (230)
+.|......+|+++|++.|+|+|+.
T Consensus 103 Lii~~~~A~~Fs~~g~l~l~v~It~ 127 (127)
T cd03829 103 LVFDTSIAQLFSENGNLGINVTISG 127 (127)
T ss_pred eEEechHhhhccCCCccEEEEEecC
Confidence 7777788899999999999999963
No 4
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=99.07 E-value=1.7e-10 Score=105.33 Aligned_cols=99 Identities=24% Similarity=0.499 Sum_probs=87.3
Q ss_pred CCCCccccccccccC--CCCCCCCCCCCCccc----hHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRSPIAYTR----NRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPC 75 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~~~~~~r----~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~ 75 (230)
.|||.||..|+.+.. +..||.|+..+..+. .+++.+++.++. +.|.++..||.+.+.+..+..|+..| .+.
T Consensus 39 ~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~-i~c~~~~~GC~~~~~l~~~~~Hl~~c--~~~ 115 (391)
T KOG0297|consen 39 TCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLP-IRCIFASRGCRADLELEALQGHLSTC--DPL 115 (391)
T ss_pred CCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcc-cccccCCCCccccccHHHHHhHhccC--Ccc
Confidence 589999999999953 358999988876532 588999999999 99999999999999999999999999 999
Q ss_pred CCCCCCCCcccChhhHHHHHhhhcCCCce
Q 038900 76 SCPLSGCDFLGSSSQLYQHFRAQHQNSSV 104 (230)
Q Consensus 76 ~Cp~~~C~~~g~~~~L~~H~~~~H~~~~~ 104 (230)
.||. +|+..+..+++.+|+...+.....
T Consensus 116 ~C~~-~C~~~~~~~d~~~hl~~~C~~~~~ 143 (391)
T KOG0297|consen 116 KCPH-RCGVQVPRDDLEDHLEAECPRRSL 143 (391)
T ss_pred cCcc-ccccccchHHHHHHHhcccccccc
Confidence 9995 499999999999999887776543
No 5
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.30 E-value=3.1e-07 Score=61.59 Aligned_cols=50 Identities=36% Similarity=0.692 Sum_probs=37.9
Q ss_pred cceecCcCCCCCcceeeecCchhhHhh-cCCCCCCCCCC--CCCCcccChhhHHHH
Q 038900 42 VKSVSCKNAEYGCNEMLGYLEKNDHEK-ACKHSPCSCPL--SGCDFLGSSSQLYQH 94 (230)
Q Consensus 42 l~~v~C~n~~~GC~~~~~~~~~~~He~-~C~~~~~~Cp~--~~C~~~g~~~~L~~H 94 (230)
.. |+|+|. ||...+...++.+|++ +|+++++.||+ .||++.+.+.+|.+|
T Consensus 8 ~~-v~C~~~--cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RP-VPCPNG--CCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SE-EE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CE-eeCCCC--CcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 45 899984 7788899999999999 99999999998 489999999999887
No 6
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.26 E-value=0.00024 Score=48.10 Aligned_cols=37 Identities=24% Similarity=0.602 Sum_probs=19.5
Q ss_pred CCCCccccccccc-cCCCCCCCCCCCCC--cc-chHHHHHHH
Q 038900 2 ENGHMVCTTCRSK-IKNDSCPFDRSPIA--YT-RNRVIEKLL 39 (230)
Q Consensus 2 ~~GH~~C~~C~~~-l~~~~CP~C~~~~~--~~-r~~~~e~~~ 39 (230)
.|.|.||+.|+.+ ++. .||+|..|.- +. .|+.++.+|
T Consensus 25 ~CeH~fCs~Ci~~~~~~-~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 25 GCEHIFCSSCIRDCIGS-ECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp SSS--B-TTTGGGGTTT-B-SSS--B-S-SS----HHHHHHH
T ss_pred cCccHHHHHHhHHhcCC-CCCCcCChHHHHHHHhhhhhhccC
Confidence 4789999999988 443 7999999863 33 366666654
No 7
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.19 E-value=0.00013 Score=48.58 Aligned_cols=43 Identities=28% Similarity=0.640 Sum_probs=33.5
Q ss_pred HhhcCCCCCCCCCCCCCCcccChhhHHHHHhhhcCCCceeEEe
Q 038900 66 HEKACKHSPCSCPLSGCDFLGSSSQLYQHFRAQHQNSSVPFRY 108 (230)
Q Consensus 66 He~~C~~~~~~Cp~~~C~~~g~~~~L~~H~~~~H~~~~~~~~y 108 (230)
|++.|+++++.||..+|.-...+.+|.+|+...+....+...|
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 8899999999999766777788999999999999887766655
No 8
>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=97.02 E-value=0.00013 Score=47.05 Aligned_cols=28 Identities=32% Similarity=0.912 Sum_probs=22.9
Q ss_pred CCCCc-ccccccccc--CCCCCCCCCCCCCc
Q 038900 2 ENGHM-VCTTCRSKI--KNDSCPFDRSPIAY 29 (230)
Q Consensus 2 ~~GH~-~C~~C~~~l--~~~~CP~C~~~~~~ 29 (230)
++||. +|..|..++ ...+||.||.++..
T Consensus 19 pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 19 PCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp TTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 68999 999999997 33589999998753
No 9
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=96.94 E-value=0.00026 Score=44.45 Aligned_cols=24 Identities=38% Similarity=0.881 Sum_probs=20.7
Q ss_pred CCCCccccccccccC--CCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRS 25 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~ 25 (230)
++||+||.+|+.++. ...||.|++
T Consensus 19 ~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 19 SCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred ccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 589999999999976 458999984
No 10
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.88 E-value=0.00038 Score=60.40 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=22.6
Q ss_pred CCCCcccccccccc-C-CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI-K-NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~-~~~CP~C~~~~~ 28 (230)
+|||.||+-|+... + ++.||.||.+..
T Consensus 42 tCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 42 TCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred ccccchhHHHHHHHhcCCCCCccccccHH
Confidence 69999999999994 4 368999998764
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.80 E-value=0.00045 Score=65.67 Aligned_cols=47 Identities=26% Similarity=0.572 Sum_probs=41.7
Q ss_pred ecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCCCCCCcccChhhHHHHH
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPLSGCDFLGSSSQLYQHF 95 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~~C~~~g~~~~L~~H~ 95 (230)
+.|+| |+|.++..++..|+..|.|..+.||..+|+....++++.+|+
T Consensus 408 V~C~N----C~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~ 454 (567)
T PLN03086 408 VECRN----CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHV 454 (567)
T ss_pred EECCC----CCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCc
Confidence 89998 999999999999999999999999976777777777777775
No 12
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.51 E-value=0.00081 Score=59.52 Aligned_cols=42 Identities=24% Similarity=0.596 Sum_probs=32.9
Q ss_pred CCCCccccccccc-cCC-CCCCCCCCCCCcc--c-hHHHHHHHhhcc
Q 038900 2 ENGHMVCTTCRSK-IKN-DSCPFDRSPIAYT--R-NRVIEKLLESVK 43 (230)
Q Consensus 2 ~~GH~~C~~C~~~-l~~-~~CP~C~~~~~~~--r-~~~~e~~~~~l~ 43 (230)
+|||.||+-|+.+ |++ +.||.|+-++... | ++.++.++.++.
T Consensus 40 pCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 40 PCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred cccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHHH
Confidence 6999999999999 443 6899999887643 3 677888877764
No 13
>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=96.34 E-value=0.002 Score=56.87 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=22.4
Q ss_pred CCCCcccccccccc-C--CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI-K--NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~--~~~CP~C~~~~~ 28 (230)
+|||.+|.+|+..+ . .+.||.|+.++.
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 59999999999994 2 257999998775
No 14
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.24 E-value=0.002 Score=58.93 Aligned_cols=41 Identities=22% Similarity=0.503 Sum_probs=31.3
Q ss_pred CCCCcccccccccc-C-CCCCCCCCCCCCc---cchHHHHHHHhhc
Q 038900 2 ENGHMVCTTCRSKI-K-NDSCPFDRSPIAY---TRNRVIEKLLESV 42 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~-~~~CP~C~~~~~~---~r~~~~e~~~~~l 42 (230)
+|||.||+.|+... . ...||.|+.+++. .+|..++++++..
T Consensus 43 pCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 43 SCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred CCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence 69999999999974 2 2479999998864 3577777777654
No 15
>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=96.22 E-value=0.003 Score=42.16 Aligned_cols=40 Identities=13% Similarity=0.218 Sum_probs=31.4
Q ss_pred CCCCcccccccccc--CCCCCCCCCCCCCc---cchHHHHHHHhh
Q 038900 2 ENGHMVCTTCRSKI--KNDSCPFDRSPIAY---TRNRVIEKLLES 41 (230)
Q Consensus 2 ~~GH~~C~~C~~~l--~~~~CP~C~~~~~~---~r~~~~e~~~~~ 41 (230)
++||+||..|+.++ .+..||.|++++.. ..+..+++.++.
T Consensus 18 ~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 18 PSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 57999999999985 23589999999853 467888877653
No 16
>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=96.21 E-value=0.001 Score=40.54 Aligned_cols=22 Identities=41% Similarity=0.828 Sum_probs=17.3
Q ss_pred CCCCcccccccccc--CCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI--KNDSCPFD 23 (230)
Q Consensus 2 ~~GH~~C~~C~~~l--~~~~CP~C 23 (230)
++||+||.+|+.++ .+.+||.|
T Consensus 16 ~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 16 PCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp TTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCchhHHHHHHHHHCcCCCcCC
Confidence 68999999999984 23579987
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=95.95 E-value=0.019 Score=54.84 Aligned_cols=71 Identities=13% Similarity=0.202 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhh-cCCCCCCCCCCCCCCcccC---------
Q 038900 18 DSCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEK-ACKHSPCSCPLSGCDFLGS--------- 87 (230)
Q Consensus 18 ~~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~-~C~~~~~~Cp~~~C~~~g~--------- 87 (230)
..|+.|...+.. ....-...+-... +.|+ |+..+...++..|.. .|+.+++.|++ |+....
T Consensus 454 ~~C~~Cgk~f~~-s~LekH~~~~Hkp-v~Cp-----Cg~~~~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~ 524 (567)
T PLN03086 454 VHCEKCGQAFQQ-GEMEKHMKVFHEP-LQCP-----CGVVLEKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVR 524 (567)
T ss_pred ccCCCCCCccch-HHHHHHHHhcCCC-ccCC-----CCCCcchhHHHhhhhccCCCCceeCCC--CCCccccCccccchh
Confidence 356667665531 1111111111244 6776 666666677777765 68888888873 776653
Q ss_pred --hhhHHHHHhh
Q 038900 88 --SSQLYQHFRA 97 (230)
Q Consensus 88 --~~~L~~H~~~ 97 (230)
...|..|...
T Consensus 525 d~~s~Lt~HE~~ 536 (567)
T PLN03086 525 DRLRGMSEHESI 536 (567)
T ss_pred hhhhhHHHHHHh
Confidence 2367777665
No 18
>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=95.91 E-value=0.00095 Score=41.70 Aligned_cols=23 Identities=35% Similarity=0.687 Sum_probs=18.2
Q ss_pred CCCCccccccccccC--CCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDR 24 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~ 24 (230)
++||.||.+|+.++. +.+||.||
T Consensus 20 ~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 20 PCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp TTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred cCCCeeCHHHHHHHHHhCCcCCccC
Confidence 589999999999952 35899996
No 19
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=95.75 E-value=0.014 Score=46.53 Aligned_cols=52 Identities=31% Similarity=0.638 Sum_probs=38.6
Q ss_pred CCCCCCCCC-CccchHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCCCCCCcccChhhHHHHHhh
Q 038900 19 SCPFDRSPI-AYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPLSGCDFLGSSSQLYQHFRA 97 (230)
Q Consensus 19 ~CP~C~~~~-~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~~C~~~g~~~~L~~H~~~ 97 (230)
.||.||..+ +++--...++.++.-+ -.|+..+|.|.|.+.+|..|.+.
T Consensus 82 ~CPLCRG~V~GWtvve~AR~~LN~K~-------------------------------RsC~~e~C~F~GtY~eLrKHar~ 130 (162)
T PF07800_consen 82 ACPLCRGEVKGWTVVEPARRFLNAKK-------------------------------RSCSQESCSFSGTYSELRKHARS 130 (162)
T ss_pred cCccccCceeceEEchHHHHHhccCC-------------------------------ccCcccccccccCHHHHHHHHHh
Confidence 588888766 3444445566655444 25666789999999999999999
Q ss_pred hcCC
Q 038900 98 QHQN 101 (230)
Q Consensus 98 ~H~~ 101 (230)
.|+.
T Consensus 131 ~HP~ 134 (162)
T PF07800_consen 131 EHPS 134 (162)
T ss_pred hCCC
Confidence 9976
No 20
>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=95.65 E-value=0.0045 Score=37.69 Aligned_cols=26 Identities=38% Similarity=0.947 Sum_probs=20.6
Q ss_pred CCCCccccccccccC---CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK---NDSCPFDRSPI 27 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~---~~~CP~C~~~~ 27 (230)
++||.||..|+.++. +.+||.|+..+
T Consensus 17 ~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 17 PCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 489999999998742 34799998753
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=95.63 E-value=0.0039 Score=51.50 Aligned_cols=27 Identities=30% Similarity=0.646 Sum_probs=21.9
Q ss_pred CCCCccccccccccC------------------CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK------------------NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~------------------~~~CP~C~~~~~ 28 (230)
+|||+||..|+.++. ..+||.|+.++.
T Consensus 35 ~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 35 LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 589999999997631 147999999886
No 22
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=94.87 E-value=0.0054 Score=38.13 Aligned_cols=22 Identities=32% Similarity=0.658 Sum_probs=15.5
Q ss_pred CCCCccccccccccC----C--CCCCCC
Q 038900 2 ENGHMVCTTCRSKIK----N--DSCPFD 23 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~----~--~~CP~C 23 (230)
++||.||.+|+.++. . ..||.|
T Consensus 15 ~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 15 PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 589999999999852 1 258877
No 23
>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=94.48 E-value=0.0093 Score=36.37 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=17.7
Q ss_pred CCCCcccccccccc-C---CCCCCCC
Q 038900 2 ENGHMVCTTCRSKI-K---NDSCPFD 23 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~---~~~CP~C 23 (230)
++||.||..|+.++ . ..+||.|
T Consensus 16 ~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 16 PCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred cCCCcchHHHHHHHHHhcCCccCCcC
Confidence 58999999999984 2 2479987
No 24
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.42 E-value=0.01 Score=37.99 Aligned_cols=27 Identities=37% Similarity=0.811 Sum_probs=15.5
Q ss_pred CCCCCccccccccccC---CCCCCCCCCCC
Q 038900 1 CENGHMVCTTCRSKIK---NDSCPFDRSPI 27 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~---~~~CP~C~~~~ 27 (230)
|++|+.+|..|..++. +++||.||++.
T Consensus 18 C~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 18 CECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp STTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 8999999999988853 36899999863
No 25
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.31 E-value=0.028 Score=36.93 Aligned_cols=27 Identities=30% Similarity=0.851 Sum_probs=22.6
Q ss_pred CCCCccccccccccCCCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
+|||++|..|..-....-||.|..++.
T Consensus 24 pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 24 PCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred cccceeeccccChhhccCCCCCCCccc
Confidence 699999999998754346999999875
No 26
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.13 E-value=0.0078 Score=53.70 Aligned_cols=42 Identities=26% Similarity=0.466 Sum_probs=33.1
Q ss_pred CCCCcccccccccc---CCCCCCCCCCCCCccc----hHHHHHHHhhcc
Q 038900 2 ENGHMVCTTCRSKI---KNDSCPFDRSPIAYTR----NRVIEKLLESVK 43 (230)
Q Consensus 2 ~~GH~~C~~C~~~l---~~~~CP~C~~~~~~~r----~~~~e~~~~~l~ 43 (230)
.|+|+||.+|+-+. .+..||+||+.+...| +.....++.++.
T Consensus 61 eClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i~ 109 (381)
T KOG0311|consen 61 ECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKIY 109 (381)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHHHHHh
Confidence 48999999999883 3458999999887654 567777877776
No 27
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.99 E-value=0.015 Score=49.08 Aligned_cols=27 Identities=26% Similarity=0.642 Sum_probs=21.8
Q ss_pred CCCCccccccccccC----C-CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK----N-DSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~----~-~~CP~C~~~~~ 28 (230)
.|||+||-.|+-++. + ..||+|+..++
T Consensus 64 lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 64 LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred ecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 389999999999963 1 35899998775
No 28
>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=93.88 E-value=0.017 Score=33.70 Aligned_cols=22 Identities=36% Similarity=0.851 Sum_probs=17.5
Q ss_pred CCCCcccccccccc---CCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI---KNDSCPFD 23 (230)
Q Consensus 2 ~~GH~~C~~C~~~l---~~~~CP~C 23 (230)
++||.||..|+.++ ...+||.|
T Consensus 15 ~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 15 PCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred cCCChHHHHHHHHHHHhCcCCCCCC
Confidence 58999999999875 23479987
No 29
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=89.88 E-value=0.13 Score=43.81 Aligned_cols=27 Identities=26% Similarity=0.630 Sum_probs=22.3
Q ss_pred CCCCccccccccccCCCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
.|+|+||..|...-....||.|+.++.
T Consensus 22 aC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 22 ACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred echhhhhhhhcccCCccccccccceee
Confidence 489999999998754447999999864
No 30
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=89.01 E-value=0.1 Score=47.45 Aligned_cols=27 Identities=37% Similarity=0.931 Sum_probs=22.9
Q ss_pred CCCCccccccccccCC----CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIKN----DSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~----~~CP~C~~~~~ 28 (230)
+|||+.|.+|...++. ..||.||..|.
T Consensus 386 PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 386 PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred cccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 6999999999998752 47999998774
No 31
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.91 E-value=0.098 Score=48.93 Aligned_cols=28 Identities=36% Similarity=0.714 Sum_probs=22.0
Q ss_pred CCCCcccccccccc-C------CCCCCCCCCCCCc
Q 038900 2 ENGHMVCTTCRSKI-K------NDSCPFDRSPIAY 29 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~------~~~CP~C~~~~~~ 29 (230)
.|||+||..|+-.. + ..+||.|+..|..
T Consensus 203 ~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 38999999999872 2 1479999987763
No 32
>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=88.06 E-value=0.54 Score=30.52 Aligned_cols=49 Identities=20% Similarity=0.492 Sum_probs=32.0
Q ss_pred ecCcCCCCCcceeeecCchhhHhhcCCC---CCCCCCCCCCCcccChhhHHHHHhhhcC
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHEKACKH---SPCSCPLSGCDFLGSSSQLYQHFRAQHQ 100 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He~~C~~---~~~~Cp~~~C~~~g~~~~L~~H~~~~H~ 100 (230)
+.||| |.+.+....+..|...--. ..+.||. |... ...+|..|+...|.
T Consensus 3 f~CP~----C~~~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~-~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPY----CGKGFSESSLVEHCEDEHRSESKNVVCPI--CSSR-VTDNLIRHLNSQHR 54 (54)
T ss_pred cCCCC----CCCccCHHHHHHHHHhHCcCCCCCccCCC--chhh-hhhHHHHHHHHhcC
Confidence 67776 6666666677777543221 2578884 7654 33589999988874
No 33
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=87.97 E-value=0.11 Score=32.53 Aligned_cols=15 Identities=33% Similarity=0.871 Sum_probs=12.3
Q ss_pred CCCCccccccccccC
Q 038900 2 ENGHMVCTTCRSKIK 16 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~ 16 (230)
+|||+||.+|+.++.
T Consensus 18 ~CGH~~c~~cl~~l~ 32 (43)
T PF13445_consen 18 PCGHVFCKDCLQKLS 32 (43)
T ss_dssp SSS-EEEHHHHHHHH
T ss_pred eCccHHHHHHHHHHH
Confidence 589999999999963
No 34
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=86.58 E-value=0.18 Score=40.12 Aligned_cols=27 Identities=44% Similarity=0.984 Sum_probs=21.6
Q ss_pred CCCCCc--------------cccccccccCCCCCCCCCCCCC
Q 038900 1 CENGHM--------------VCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 1 C~~GH~--------------~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
|.|||+ ||+.|-.+.-. .||.|..+|.
T Consensus 10 C~NGH~~t~~~~~~p~~~~~fC~kCG~~tI~-~Cp~C~~~Ir 50 (158)
T PF10083_consen 10 CLNGHVITDSYDKNPELREKFCSKCGAKTIT-SCPNCSTPIR 50 (158)
T ss_pred ccCccccccccccCchHHHHHHHHhhHHHHH-HCcCCCCCCC
Confidence 788887 89999888433 6999998874
No 35
>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=85.56 E-value=0.46 Score=32.89 Aligned_cols=41 Identities=22% Similarity=0.417 Sum_probs=29.1
Q ss_pred CCCCcccccccccc-C--CCCCCCCCCCCCc---cchHHHHHHHhhc
Q 038900 2 ENGHMVCTTCRSKI-K--NDSCPFDRSPIAY---TRNRVIEKLLESV 42 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~--~~~CP~C~~~~~~---~r~~~~e~~~~~l 42 (230)
+.||+|+.+++.++ . +..||.++.++.. ..|.+|.+.|+..
T Consensus 21 ~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~ 67 (73)
T PF04564_consen 21 PSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 57999999999984 2 3579999999874 4688888887654
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=83.90 E-value=0.62 Score=24.74 Aligned_cols=23 Identities=35% Similarity=0.832 Sum_probs=17.5
Q ss_pred CCCCCCCCcccChhhHHHHHhhhcC
Q 038900 76 SCPLSGCDFLGSSSQLYQHFRAQHQ 100 (230)
Q Consensus 76 ~Cp~~~C~~~g~~~~L~~H~~~~H~ 100 (230)
.|+ .|+|.....+|..|+...|+
T Consensus 2 ~C~--~C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCP--HCSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp E-S--SSS-EESHHHHHHHHHHHHS
T ss_pred CCC--CCCCcCCHHHHHHHHHhhCc
Confidence 466 59998888899999998874
No 37
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.65 E-value=0.44 Score=36.66 Aligned_cols=25 Identities=40% Similarity=1.022 Sum_probs=20.3
Q ss_pred CCCCCc--------------cccccccc-cCCCCCCCCCCCC
Q 038900 1 CENGHM--------------VCTTCRSK-IKNDSCPFDRSPI 27 (230)
Q Consensus 1 C~~GH~--------------~C~~C~~~-l~~~~CP~C~~~~ 27 (230)
|.|||+ |||.|-.. +. .||.|..+|
T Consensus 10 c~ngh~attaadq~pel~eafcskcgeati~--qcp~csasi 49 (160)
T COG4306 10 CLNGHVATTAADQSPELMEAFCSKCGEATIT--QCPICSASI 49 (160)
T ss_pred cCCCceeeccccCCHHHHHHHHhhhchHHHh--cCCccCCcc
Confidence 789996 79999876 44 499998876
No 38
>PHA00616 hypothetical protein
Probab=82.77 E-value=1.2 Score=27.95 Aligned_cols=33 Identities=15% Similarity=0.415 Sum_probs=25.9
Q ss_pred CCCCCCCCCCccc-ChhhHHHHHhhhcCCCceeEEe
Q 038900 74 PCSCPLSGCDFLG-SSSQLYQHFRAQHQNSSVPFRY 108 (230)
Q Consensus 74 ~~~Cp~~~C~~~g-~~~~L~~H~~~~H~~~~~~~~y 108 (230)
|+.|| .|+... ..++|..|+...|.....+..|
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 56787 688776 5689999999999887655554
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.18 E-value=0.48 Score=40.13 Aligned_cols=46 Identities=26% Similarity=0.476 Sum_probs=32.3
Q ss_pred CCCCccccccccccCC--CCCCCCCCCCC-ccchHHHHHHHhhcceecCc
Q 038900 2 ENGHMVCTTCRSKIKN--DSCPFDRSPIA-YTRNRVIEKLLESVKSVSCK 48 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~--~~CP~C~~~~~-~~r~~~~e~~~~~l~~v~C~ 48 (230)
+|||.||..|+..+.. ..||.||.+.. ..+|..+.+++..+. ....
T Consensus 30 ~C~H~~c~~C~~~~~~~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~-~~~~ 78 (386)
T KOG2177|consen 30 PCGHNFCRACLTRSWEGPLSCPVCRPPSRNLRPNVLLANLVERLR-QLRL 78 (386)
T ss_pred cccchHhHHHHHHhcCCCcCCcccCCchhccCccHHHHHHHHHHH-hcCC
Confidence 5999999999998542 37999995211 225777777777766 4443
No 40
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.00 E-value=1.5 Score=29.31 Aligned_cols=36 Identities=36% Similarity=0.725 Sum_probs=20.0
Q ss_pred cceecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCCCCCCcccC
Q 038900 42 VKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPLSGCDFLGS 87 (230)
Q Consensus 42 l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~~C~~~g~ 87 (230)
.. ++||| |.+.+.+.-..--+ .-.++.|| .|+|.|+
T Consensus 26 v~-F~CPn----CGe~~I~Rc~~CRk---~g~~Y~Cp--~CGF~GP 61 (61)
T COG2888 26 VK-FPCPN----CGEVEIYRCAKCRK---LGNPYRCP--KCGFEGP 61 (61)
T ss_pred eE-eeCCC----CCceeeehhhhHHH---cCCceECC--CcCccCC
Confidence 45 78885 66544443221111 12578887 6998874
No 41
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=79.72 E-value=0.64 Score=41.37 Aligned_cols=41 Identities=22% Similarity=0.415 Sum_probs=29.4
Q ss_pred CCCcccccccccc--CCCCCCCCCCCCCcc-------chHHHHHHHhhcc
Q 038900 3 NGHMVCTTCRSKI--KNDSCPFDRSPIAYT-------RNRVIEKLLESVK 43 (230)
Q Consensus 3 ~GH~~C~~C~~~l--~~~~CP~C~~~~~~~-------r~~~~e~~~~~l~ 43 (230)
|=|.||.+|+-+. .+..||.|...+... .++.|..++.+|-
T Consensus 34 CLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVyKLV 83 (331)
T KOG2660|consen 34 CLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLNIRSDRTLQDIVYKLV 83 (331)
T ss_pred HHHHHHHHHHHHHHHHhccCCccceeccCccccccCCcchHHHHHHHHHc
Confidence 3499999999883 234899998776532 3677777777663
No 42
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.28 E-value=1.1 Score=24.42 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=17.4
Q ss_pred ecCcCCCCCcceeeecCchhhHhhcCC
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHEKACK 71 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He~~C~ 71 (230)
++|+ -|+-++....++.|++.|.
T Consensus 3 ~~C~----~CgR~F~~~~l~~H~~~C~ 25 (25)
T PF13913_consen 3 VPCP----ICGRKFNPDRLEKHEKICK 25 (25)
T ss_pred CcCC----CCCCEECHHHHHHHHHhcC
Confidence 6776 4788888888888887774
No 43
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=78.38 E-value=1 Score=39.88 Aligned_cols=59 Identities=22% Similarity=0.450 Sum_probs=39.1
Q ss_pred CCCCccccccccccCCCCCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcce-eeecCchhhHh
Q 038900 2 ENGHMVCTTCRSKIKNDSCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNE-MLGYLEKNDHE 67 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~~~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~-~~~~~~~~~He 67 (230)
+|-|+||-.|-..-..+.||.|...+ .-+|.....-. |-|. ...||.- ++.-.+++.|.
T Consensus 108 PCkHvFCl~CAr~~~dK~Cp~C~d~V-----qrIeq~~~g~i-FmC~-~~~GC~RTyLsqrDlqAHI 167 (389)
T KOG2932|consen 108 PCKHVFCLECARSDSDKICPLCDDRV-----QRIEQIMMGGI-FMCA-APHGCLRTYLSQRDLQAHI 167 (389)
T ss_pred ccchhhhhhhhhcCccccCcCcccHH-----HHHHHhcccce-EEee-cchhHHHHHhhHHHHHHHh
Confidence 57899999998765544799997644 34555555555 7787 5667754 44455555554
No 44
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.72 E-value=1.1 Score=39.22 Aligned_cols=25 Identities=44% Similarity=0.899 Sum_probs=21.3
Q ss_pred CCCccccccccccC-C--CCCCCCCCCC
Q 038900 3 NGHMVCTTCRSKIK-N--DSCPFDRSPI 27 (230)
Q Consensus 3 ~GH~~C~~C~~~l~-~--~~CP~C~~~~ 27 (230)
|||.+|..|..++. + ..||.||.+.
T Consensus 27 c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 27 CGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred cCceehHhHHHHHhcCceeeccCCCCcc
Confidence 89999999999963 2 4699999985
No 45
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=77.24 E-value=0.8 Score=32.89 Aligned_cols=27 Identities=26% Similarity=0.481 Sum_probs=21.0
Q ss_pred CCCCcccccccccc-C----CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI-K----NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-~----~~~CP~C~~~~~ 28 (230)
.|+|.|=..|+.+. + ++.||.||++..
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred cCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 68899999998883 2 257999998764
No 46
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.93 E-value=1.1 Score=40.27 Aligned_cols=91 Identities=23% Similarity=0.441 Sum_probs=47.1
Q ss_pred CCCCccccccccccC----CCCCCCCCCCCCcc-----chHHHHHH-HhhcceecCcCCCCCcceeeecCchhhHhhcCC
Q 038900 2 ENGHMVCTTCRSKIK----NDSCPFDRSPIAYT-----RNRVIEKL-LESVKSVSCKNAEYGCNEMLGYLEKNDHEKACK 71 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~----~~~CP~C~~~~~~~-----r~~~~e~~-~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~ 71 (230)
||||..|.-|--++. ...||.||...... ....+... .... ++..+| +.|..-+.-++.=.
T Consensus 78 PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~~~~~DI~D~~~~k~-----~~EK~G----I~y~~E~v~~E~~~ 148 (493)
T COG5236 78 PCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDRRQWKG-----REEKVG----IFYEGEDVRDEMED 148 (493)
T ss_pred cCCchHHHHHHHHHHHHHhccCCCccccccceEEEecCCCCcchhHhhhcc-----ccccee----eeecchHHHHHHHH
Confidence 799999999988753 24799999865311 11111111 1111 133333 33333322222222
Q ss_pred CCCCCCCCCCCCcc-cChhhHHHHHhhhcCC
Q 038900 72 HSPCSCPLSGCDFL-GSSSQLYQHFRAQHQN 101 (230)
Q Consensus 72 ~~~~~Cp~~~C~~~-g~~~~L~~H~~~~H~~ 101 (230)
.-...||...|... +..++|..|+...|..
T Consensus 149 LL~F~CP~skc~~~C~~~k~lk~H~K~~H~~ 179 (493)
T COG5236 149 LLSFKCPKSKCHRRCGSLKELKKHYKAQHGF 179 (493)
T ss_pred HHHhcCCchhhhhhhhhHHHHHHHHHhhcCc
Confidence 33355665544332 2357888888887764
No 47
>PF04641 Rtf2: Rtf2 RING-finger
Probab=73.23 E-value=1.5 Score=37.99 Aligned_cols=27 Identities=19% Similarity=0.448 Sum_probs=24.1
Q ss_pred CCCCccccccccccC-CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK-NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~-~~~CP~C~~~~~ 28 (230)
+|||+|+..++..+. ...||.|.+++.
T Consensus 134 ~cG~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 134 PCGCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred CCCCEeeHHHHHhhcccccccccCCccc
Confidence 699999999999987 457999999986
No 48
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.89 E-value=3.6 Score=27.45 Aligned_cols=13 Identities=46% Similarity=1.288 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCcccC
Q 038900 73 SPCSCPLSGCDFLGS 87 (230)
Q Consensus 73 ~~~~Cp~~~C~~~g~ 87 (230)
.++.|| .|+|.|+
T Consensus 47 ~~Y~CP--~CGF~GP 59 (59)
T PRK14890 47 NPYTCP--KCGFEGP 59 (59)
T ss_pred CceECC--CCCCcCc
Confidence 567887 6888874
No 49
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=71.54 E-value=2.2 Score=26.93 Aligned_cols=37 Identities=24% Similarity=0.509 Sum_probs=28.7
Q ss_pred CCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcceee
Q 038900 19 SCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEML 58 (230)
Q Consensus 19 ~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~ 58 (230)
+||.|...........+.+.+..+. ..|.|.+ |...+
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y-~qC~N~~--Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELY-CQCTNPE--CGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEE-EEECCCc--CCCEE
Confidence 4999988765555778888889999 9999984 54444
No 50
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.95 E-value=1.4 Score=40.51 Aligned_cols=27 Identities=26% Similarity=0.671 Sum_probs=22.1
Q ss_pred CCCCccccccccccC--CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~~~~ 28 (230)
++||.+|..|+.+.. ...||.|+.++.
T Consensus 101 pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 101 PCGHSFCLECLDRSLDQETECPLCRDELV 129 (398)
T ss_pred cccccccHHHHHHHhccCCCCcccccccc
Confidence 699999999987742 257999999875
No 51
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=70.88 E-value=0.84 Score=40.91 Aligned_cols=27 Identities=33% Similarity=0.785 Sum_probs=23.1
Q ss_pred CCCCCccccccccccC---CCCCCCCCCCC
Q 038900 1 CENGHMVCTTCRSKIK---NDSCPFDRSPI 27 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~---~~~CP~C~~~~ 27 (230)
|+||-.+|.-|+..+. +++||.||.-.
T Consensus 34 c~cgy~ic~fc~~~irq~lngrcpacrr~y 63 (480)
T COG5175 34 CPCGYQICQFCYNNIRQNLNGRCPACRRKY 63 (480)
T ss_pred CCcccHHHHHHHHHHHhhccCCChHhhhhc
Confidence 8999999999998863 47999999754
No 52
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.39 E-value=2.3 Score=37.51 Aligned_cols=28 Identities=25% Similarity=0.370 Sum_probs=22.5
Q ss_pred CCCCccccccccccC---CCCCCCCCCCCCc
Q 038900 2 ENGHMVCTTCRSKIK---NDSCPFDRSPIAY 29 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~---~~~CP~C~~~~~~ 29 (230)
+|+|.||--|++-.. ...|+.||.+|..
T Consensus 24 ~C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 24 YCFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred cccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 589999999998732 2459999999863
No 53
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.19 E-value=0.5 Score=31.01 Aligned_cols=26 Identities=42% Similarity=1.016 Sum_probs=19.9
Q ss_pred CCCc-cccccccccC---CCCCCCCCCCCC
Q 038900 3 NGHM-VCTTCRSKIK---NDSCPFDRSPIA 28 (230)
Q Consensus 3 ~GH~-~C~~C~~~l~---~~~CP~C~~~~~ 28 (230)
|||. .|-.|-.++. ++.||.||.|+.
T Consensus 25 CGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 25 CGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 7886 7888977742 368999998864
No 54
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=69.57 E-value=2.5 Score=23.50 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=16.7
Q ss_pred ecCcCCCCCcceeeecCchhhHhhcCC
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHEKACK 71 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He~~C~ 71 (230)
+.|||. =.-.++-.+++.|...|+
T Consensus 3 v~CPyn---~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 3 VRCPYN---PSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EE-TTT---SS-EEEGGGHHHHHHHHH
T ss_pred eeCCCC---CCcCcCHHHHHHHHHHcC
Confidence 678873 466888888888888774
No 55
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.12 E-value=1.2 Score=42.57 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=21.2
Q ss_pred CCCCccccccccccC--CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRSPI 27 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~~~ 27 (230)
+|||+|+..|+.++- ...||.||..+
T Consensus 313 ~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 313 PCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred ecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 589999999999962 23799999844
No 56
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.04 E-value=2.8 Score=29.13 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=21.5
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCC
Q 038900 1 CENGHMVCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
|.-.|.||..|-....++.||.|...+.
T Consensus 25 CtfEcTFCadCae~~l~g~CPnCGGelv 52 (84)
T COG3813 25 CTFECTFCADCAENRLHGLCPNCGGELV 52 (84)
T ss_pred EEEeeehhHhHHHHhhcCcCCCCCchhh
Confidence 4456889999998643458999988775
No 57
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=62.22 E-value=2.5 Score=37.10 Aligned_cols=26 Identities=31% Similarity=0.661 Sum_probs=21.8
Q ss_pred CCCCcccccccccc---CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI---KNDSCPFDRSPI 27 (230)
Q Consensus 2 ~~GH~~C~~C~~~l---~~~~CP~C~~~~ 27 (230)
+|||..|.+|...+ +.+.||.|...+
T Consensus 22 ~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 22 ECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred cccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 69999999999996 335799998866
No 58
>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=61.76 E-value=9 Score=24.63 Aligned_cols=28 Identities=32% Similarity=0.549 Sum_probs=22.8
Q ss_pred CCCCCCCCCCcccChhhHHHHHhhhcCCCc
Q 038900 74 PCSCPLSGCDFLGSSSQLYQHFRAQHQNSS 103 (230)
Q Consensus 74 ~~~Cp~~~C~~~g~~~~L~~H~~~~H~~~~ 103 (230)
.+.||+ |+...+..+|..|+...|....
T Consensus 2 ~f~CP~--C~~~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPY--CGKGFSESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCC--CCCccCHHHHHHHHHhHCcCCC
Confidence 367884 8885678999999999998754
No 59
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=61.41 E-value=4.8 Score=21.49 Aligned_cols=21 Identities=29% Similarity=0.835 Sum_probs=14.4
Q ss_pred cccccccccCC--CCCCCCCCCC
Q 038900 7 VCTTCRSKIKN--DSCPFDRSPI 27 (230)
Q Consensus 7 ~C~~C~~~l~~--~~CP~C~~~~ 27 (230)
+|..|-.++.. ..||.|..++
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCcC
Confidence 57788777643 3688887654
No 60
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=60.54 E-value=2.6 Score=41.88 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=22.4
Q ss_pred CCCCccccccccccCC--CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIKN--DSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~--~~CP~C~~~~~ 28 (230)
+++|.||..|+..+.. ..||+||..++
T Consensus 143 ~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 143 HTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred ccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 5899999999998742 48999998764
No 61
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=59.52 E-value=8.9 Score=34.79 Aligned_cols=92 Identities=14% Similarity=0.369 Sum_probs=62.4
Q ss_pred CccccccccccC--------------CCCCCCCCCCCCcc---chHHHHHHHhhcceecCcCCCCCcce-eeecCchhhH
Q 038900 5 HMVCTTCRSKIK--------------NDSCPFDRSPIAYT---RNRVIEKLLESVKSVSCKNAEYGCNE-MLGYLEKNDH 66 (230)
Q Consensus 5 H~~C~~C~~~l~--------------~~~CP~C~~~~~~~---r~~~~e~~~~~l~~v~C~n~~~GC~~-~~~~~~~~~H 66 (230)
|--|+.|.++.. .-+||.|....+.. ++..+-+-.++-. +.|. -|.. -+...++.+|
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkp-fKCd----~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKP-FKCD----ECDTRCVRESDLAKH 311 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCC-cccc----chhhhhccHHHHHHH
Confidence 556777766521 14799998766532 3455555566666 7776 4544 4556688888
Q ss_pred hhcCCCCCCCCCCCCCCccc-ChhhHHHHHhhhcCC
Q 038900 67 EKACKHSPCSCPLSGCDFLG-SSSQLYQHFRAQHQN 101 (230)
Q Consensus 67 e~~C~~~~~~Cp~~~C~~~g-~~~~L~~H~~~~H~~ 101 (230)
...=.-.-+.|-.+.|.+.. .+.+|..|+...|..
T Consensus 312 ~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg 347 (467)
T KOG3608|consen 312 VQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEG 347 (467)
T ss_pred HHhccccceecCCCCCcHHHHHHHHHHHHHHHhccC
Confidence 87444455788888898877 568999999988843
No 62
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=58.79 E-value=6.1 Score=23.17 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=16.7
Q ss_pred ecCcCCCCCcceeeecCchhhHhhcCC
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHEKACK 71 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He~~C~ 71 (230)
+.|+| |.-.+.-.....|++.|.
T Consensus 5 ~~C~n----C~R~v~a~RfA~HLekCm 27 (33)
T PF08209_consen 5 VECPN----CGRPVAASRFAPHLEKCM 27 (33)
T ss_dssp EE-TT----TSSEEEGGGHHHHHHHHT
T ss_pred EECCC----CcCCcchhhhHHHHHHHH
Confidence 77774 777888888888887774
No 63
>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=58.00 E-value=5 Score=22.07 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=8.4
Q ss_pred cceeeecCchhhHhhcC
Q 038900 54 CNEMLGYLEKNDHEKAC 70 (230)
Q Consensus 54 C~~~~~~~~~~~He~~C 70 (230)
|.+.++...+.+|.+.|
T Consensus 7 C~~~v~~~~in~HLD~C 23 (26)
T smart00734 7 CFREVPENLINSHLDSC 23 (26)
T ss_pred CcCcccHHHHHHHHHHh
Confidence 44444444445555544
No 64
>smart00301 DM Doublesex DNA-binding motif.
Probab=57.35 E-value=5.8 Score=25.99 Aligned_cols=35 Identities=17% Similarity=0.438 Sum_probs=27.7
Q ss_pred ecCchhhHhhcCCCCCCCCCCCCCCcccChhhHHHHH
Q 038900 59 GYLEKNDHEKACKHSPCSCPLSGCDFLGSSSQLYQHF 95 (230)
Q Consensus 59 ~~~~~~~He~~C~~~~~~Cp~~~C~~~g~~~~L~~H~ 95 (230)
....+..|-..|+|+.|.|+ .|.....+..++...
T Consensus 13 ~~~~lKGHKr~C~~r~C~C~--kC~Li~~Rq~vma~q 47 (54)
T smart00301 13 VKVPLKGHKPECPFRDCECE--KCTLVEKRRALMALQ 47 (54)
T ss_pred CeeccCCcCCCCCCCCCcCC--CCcChHHHHHHHHHH
Confidence 45567889999999999997 798887776666543
No 65
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.30 E-value=5.9 Score=35.07 Aligned_cols=41 Identities=20% Similarity=0.355 Sum_probs=28.1
Q ss_pred CCCccccccccc-c--CCCCCCCCCC-CC---CccchHHHHHHHhhcc
Q 038900 3 NGHMVCTTCRSK-I--KNDSCPFDRS-PI---AYTRNRVIEKLLESVK 43 (230)
Q Consensus 3 ~GH~~C~~C~~~-l--~~~~CP~C~~-~~---~~~r~~~~e~~~~~l~ 43 (230)
|||.||..|+.. | +..+||.|.. .+ +...+..+++.++.+.
T Consensus 293 C~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~dk~~EvE~~l 340 (427)
T COG5222 293 CGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDIDKKLEVEKAL 340 (427)
T ss_pred ccchHHHHHHhhhhhhccccCCCcccccchhhccCccHHHHHHHHHHH
Confidence 799999999997 3 2368999965 22 2345666666666554
No 66
>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=52.96 E-value=14 Score=18.59 Aligned_cols=22 Identities=45% Similarity=0.712 Sum_probs=15.2
Q ss_pred CCCCCCCCccc-ChhhHHHHHhhhc
Q 038900 76 SCPLSGCDFLG-SSSQLYQHFRAQH 99 (230)
Q Consensus 76 ~Cp~~~C~~~g-~~~~L~~H~~~~H 99 (230)
.|+ -|+... ...+|..|+...|
T Consensus 2 ~C~--~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCP--ICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-S--STS-EESSHHHHHHHHHHHS
T ss_pred CCc--CCCCcCCcHHHHHHHHHhhC
Confidence 466 488776 5789999998776
No 67
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=52.10 E-value=5.5 Score=27.69 Aligned_cols=45 Identities=18% Similarity=0.332 Sum_probs=30.9
Q ss_pred CCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcceeeecCchhhH
Q 038900 19 SCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDH 66 (230)
Q Consensus 19 ~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~H 66 (230)
+||.|+........+.+...+..+. ..|.|- .|..++...+--.|
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y-~qC~N~--eCg~tF~t~es~s~ 47 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERY-HQCQNV--NCSATFITYESVQR 47 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheee-eecCCC--CCCCEEEEEEEEEE
Confidence 5999988763334677777788888 999987 46665555544444
No 68
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.51 E-value=8.8 Score=20.92 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=13.5
Q ss_pred ccccccccccCC--CCCCCCCCCC
Q 038900 6 MVCTTCRSKIKN--DSCPFDRSPI 27 (230)
Q Consensus 6 ~~C~~C~~~l~~--~~CP~C~~~~ 27 (230)
++|.+|-..+.. ..||.|..++
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCcccccChhhCCCC
Confidence 367777776432 3588776653
No 69
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.48 E-value=7.2 Score=35.30 Aligned_cols=27 Identities=37% Similarity=0.802 Sum_probs=22.1
Q ss_pred CCCCccccccccccC---------CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK---------NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~---------~~~CP~C~~~~~ 28 (230)
+|-|.+|-+|+.+++ ...||.||.+..
T Consensus 186 nC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 186 NCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred CcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 377999999999975 157999998765
No 70
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=50.00 E-value=6.2 Score=35.98 Aligned_cols=26 Identities=27% Similarity=0.682 Sum_probs=21.1
Q ss_pred CCCCccccccccccC--CCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRSPI 27 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~~~ 27 (230)
||||.+=-+|.+.+- ...||.||.|+
T Consensus 317 pCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 317 PCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred cccceeeHHHHHHHHHhccCCCcccCcc
Confidence 689999999988852 24899999994
No 71
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=48.17 E-value=12 Score=21.48 Aligned_cols=21 Identities=24% Similarity=0.450 Sum_probs=8.3
Q ss_pred ecCcCCCCCcceeeecCchhhHh
Q 038900 45 VSCKNAEYGCNEMLGYLEKNDHE 67 (230)
Q Consensus 45 v~C~n~~~GC~~~~~~~~~~~He 67 (230)
+.||=+ +|.+.+.+++...|.
T Consensus 3 vrCPvk--dC~EEv~lgKY~~H~ 23 (30)
T PF10426_consen 3 VRCPVK--DCDEEVSLGKYSHHL 23 (30)
T ss_dssp EE--ST--T---EEEHHHHHHHH
T ss_pred cccccc--cCcchhhhhhhcccc
Confidence 455543 555555555555554
No 72
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=45.62 E-value=12 Score=20.36 Aligned_cols=6 Identities=33% Similarity=0.678 Sum_probs=4.0
Q ss_pred CCCCCC
Q 038900 19 SCPFDR 24 (230)
Q Consensus 19 ~CP~C~ 24 (230)
.||.|.
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 577774
No 73
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=44.96 E-value=6.9 Score=25.80 Aligned_cols=25 Identities=20% Similarity=0.515 Sum_probs=19.1
Q ss_pred CCccccccccccCCCCCCCCCCCCC
Q 038900 4 GHMVCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 4 GH~~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
--.||..|...+.++.||.|...+.
T Consensus 28 ECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 28 ECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred eCcccHHHHHHHhcCcCcCCCCccc
Confidence 3469999999863348999987664
No 74
>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=44.01 E-value=10 Score=19.39 Aligned_cols=20 Identities=40% Similarity=0.600 Sum_probs=14.2
Q ss_pred CCCCCCCCccc-ChhhHHHHHhh
Q 038900 76 SCPLSGCDFLG-SSSQLYQHFRA 97 (230)
Q Consensus 76 ~Cp~~~C~~~g-~~~~L~~H~~~ 97 (230)
.|| .|+... ...+|..|++.
T Consensus 2 ~C~--~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCP--ICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EET--TTTEEESSHHHHHHHHHH
T ss_pred CCC--CCCCccCCHHHHHHHHhH
Confidence 465 587766 46788888876
No 75
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.58 E-value=25 Score=36.23 Aligned_cols=23 Identities=17% Similarity=0.436 Sum_probs=13.6
Q ss_pred ccccccccccCCCCCCCCCCCCC
Q 038900 6 MVCTTCRSKIKNDSCPFDRSPIA 28 (230)
Q Consensus 6 ~~C~~C~~~l~~~~CP~C~~~~~ 28 (230)
.+|..|........||.|.....
T Consensus 652 ~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 652 YRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred eeCccccCcCCCCcCCCCCCCCC
Confidence 36777766554335777765553
No 76
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=43.48 E-value=23 Score=29.03 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=30.0
Q ss_pred CCCCCCccchHHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCC
Q 038900 23 DRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACK 71 (230)
Q Consensus 23 C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~ 71 (230)
|...+.+..-..=|+.-.-.. ..||....||.|...+.++..|...--
T Consensus 24 C~~~~~~~~~~~HE~~C~~~p-~~CP~~~~~C~~~G~~~~l~~Hl~~~H 71 (198)
T PF03145_consen 24 CTETFPYSEKREHEEECPFRP-CSCPFPGSGCDWQGSYKELLDHLRDKH 71 (198)
T ss_dssp ---EE-GGGHHHHHHT-TTSE-EE-SSSSTT---EEECCCHHHHHHHHT
T ss_pred CcccccccChhhHhccCCCcC-CcCCCCCCCccccCCHHHHHHHHHHHC
Confidence 666555555555566666777 999986679999999999999998744
No 77
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.81 E-value=14 Score=34.43 Aligned_cols=23 Identities=35% Similarity=0.782 Sum_probs=16.9
Q ss_pred CCCCCccccccccccCC-CCCCCC
Q 038900 1 CENGHMVCTTCRSKIKN-DSCPFD 23 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~~-~~CP~C 23 (230)
|.+||.||..|...... ..|+..
T Consensus 182 C~~g~~FC~~C~~~~H~p~~C~~~ 205 (444)
T KOG1815|consen 182 CGCGHEFCFACGEESHSPVSCPGA 205 (444)
T ss_pred CCCCchhHhhccccccCCCcccch
Confidence 89999999999887542 245444
No 78
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=42.66 E-value=21 Score=25.91 Aligned_cols=25 Identities=20% Similarity=0.590 Sum_probs=18.9
Q ss_pred CCccccccccccC-------------CCCCCCCCCCCC
Q 038900 4 GHMVCTTCRSKIK-------------NDSCPFDRSPIA 28 (230)
Q Consensus 4 GH~~C~~C~~~l~-------------~~~CP~C~~~~~ 28 (230)
+...|.+|..++. .++|..|+.+++
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred CCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCC
Confidence 4568888888863 268999988875
No 79
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=40.61 E-value=5.8 Score=22.71 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=12.5
Q ss_pred CCccccccccccC--C----CCCCCCCC
Q 038900 4 GHMVCTTCRSKIK--N----DSCPFDRS 25 (230)
Q Consensus 4 GH~~C~~C~~~l~--~----~~CP~C~~ 25 (230)
-|.||+.|-..+. . ..||.|..
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcC
Confidence 3889999988742 1 35888864
No 80
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=38.71 E-value=13 Score=28.01 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=8.1
Q ss_pred CCCCCccccc
Q 038900 1 CENGHMVCTT 10 (230)
Q Consensus 1 C~~GH~~C~~ 10 (230)
|.|||.||+.
T Consensus 27 c~CGh~f~d~ 36 (112)
T PF08882_consen 27 CDCGHEFCDA 36 (112)
T ss_pred ccCCCeecCh
Confidence 7889988864
No 81
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=37.02 E-value=19 Score=30.92 Aligned_cols=39 Identities=18% Similarity=0.485 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCccc---------h------HHHHHHHhhcceecCcCCCCCcceeee
Q 038900 18 DSCPFDRSPIAYTR---------N------RVIEKLLESVKSVSCKNAEYGCNEMLG 59 (230)
Q Consensus 18 ~~CP~C~~~~~~~r---------~------~~~e~~~~~l~~v~C~n~~~GC~~~~~ 59 (230)
.+||.|..+.-..+ | ..+.++...=. .+||+. ||...+.
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~Gp-AqCP~~--gC~kILR 64 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGP-AQCPYK--GCGKILR 64 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCC-CCCCCc--cHHHHHH
Confidence 37999998753211 1 24555555556 889986 9977554
No 82
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=34.36 E-value=17 Score=32.28 Aligned_cols=74 Identities=18% Similarity=0.296 Sum_probs=50.9
Q ss_pred CCCCCCCCCCc---cch---HHHHHHHhhcceecCcCCCCCcceeeecCchhhHhhcCCCCCCCCCCC--CCCcccChhh
Q 038900 19 SCPFDRSPIAY---TRN---RVIEKLLESVKSVSCKNAEYGCNEMLGYLEKNDHEKACKHSPCSCPLS--GCDFLGSSSQ 90 (230)
Q Consensus 19 ~CP~C~~~~~~---~r~---~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~~~He~~C~~~~~~Cp~~--~C~~~g~~~~ 90 (230)
.||.|..++.. .++ .+...=-.++. ..|| .|...++...-..=|+.+.-..++||+. ||.+.+++..
T Consensus 50 eCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~-~~CP----~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 50 DCPVCFNPLSPPIFQCDNGHLACSSCRTKVS-NKCP----TCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred cCchhhccCcccceecCCCcEehhhhhhhhc-ccCC----ccccccccHHHHHHHHHHHhceecccccccCCceeecccc
Confidence 59999998862 121 23333333666 8898 4888887443344556899999999975 8999998766
Q ss_pred HHHHHhh
Q 038900 91 LYQHFRA 97 (230)
Q Consensus 91 L~~H~~~ 97 (230)
-..|.+.
T Consensus 125 ~~~HE~~ 131 (299)
T KOG3002|consen 125 KSKHEKV 131 (299)
T ss_pred ccccccc
Confidence 6777554
No 83
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.61 E-value=29 Score=31.90 Aligned_cols=62 Identities=23% Similarity=0.484 Sum_probs=38.3
Q ss_pred CCCCccccccccccC--------CCCCCC--CCCCCCccc--------------hHHHHHHHhhcceecCcCCCCCccee
Q 038900 2 ENGHMVCTTCRSKIK--------NDSCPF--DRSPIAYTR--------------NRVIEKLLESVKSVSCKNAEYGCNEM 57 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--------~~~CP~--C~~~~~~~r--------------~~~~e~~~~~l~~v~C~n~~~GC~~~ 57 (230)
.|||.||..|..+.- ..+||. |...+.... ...-|.++.+...+.|||. .|...
T Consensus 167 ~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~~~ycp~~--~C~~l 244 (384)
T KOG1812|consen 167 KCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLDRVYCPYP--RCSSL 244 (384)
T ss_pred cccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhhcccCCCC--CchHh
Confidence 589999999998731 146765 444443221 1233444444433788886 88888
Q ss_pred eecCchhh
Q 038900 58 LGYLEKND 65 (230)
Q Consensus 58 ~~~~~~~~ 65 (230)
+...++.+
T Consensus 245 ~~~~el~~ 252 (384)
T KOG1812|consen 245 MSKTELSS 252 (384)
T ss_pred hhhhhhcc
Confidence 88777764
No 84
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.52 E-value=23 Score=32.05 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=21.5
Q ss_pred CCCCccccccccccC--CC-CCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--ND-SCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~-~CP~C~~~~~ 28 (230)
||+|.|=..|+.++- +. .||.|+.++.
T Consensus 249 PC~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 249 PCSHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred cCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence 689999999999952 22 4999998764
No 85
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=33.51 E-value=8.5 Score=26.60 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=14.6
Q ss_pred CCCccccccccccC-CCCCCCCCCCCC
Q 038900 3 NGHMVCTTCRSKIK-NDSCPFDRSPIA 28 (230)
Q Consensus 3 ~GH~~C~~C~~~l~-~~~CP~C~~~~~ 28 (230)
.||..|..|-.... .+.||.|..++.
T Consensus 15 ~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 15 GGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp TTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CCEEECccccccceecccCCCcccHHH
Confidence 46788888887743 246999988764
No 86
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=33.27 E-value=26 Score=32.27 Aligned_cols=38 Identities=21% Similarity=0.457 Sum_probs=31.6
Q ss_pred cceecCcCCCCCcceeeecCchhhHh-hcCCCCCCCCCCCCCC
Q 038900 42 VKSVSCKNAEYGCNEMLGYLEKNDHE-KACKHSPCSCPLSGCD 83 (230)
Q Consensus 42 l~~v~C~n~~~GC~~~~~~~~~~~He-~~C~~~~~~Cp~~~C~ 83 (230)
-. ++|+| +|...++-.++.+|. ++|+++...|...++.
T Consensus 113 ~~-~~C~~---~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~ 151 (391)
T KOG0297|consen 113 DP-LKCPH---RCGVQVPRDDLEDHLEAECPRRSLKCSLCQSD 151 (391)
T ss_pred Cc-ccCcc---ccccccchHHHHHHHhcccccccccchhhcCc
Confidence 46 88998 499999999999998 5999999988754443
No 87
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.08 E-value=26 Score=23.79 Aligned_cols=24 Identities=17% Similarity=0.515 Sum_probs=18.2
Q ss_pred CCccccccccccCCCCCCCCCCCC
Q 038900 4 GHMVCTTCRSKIKNDSCPFDRSPI 27 (230)
Q Consensus 4 GH~~C~~C~~~l~~~~CP~C~~~~ 27 (230)
...+|..|..-.....||.|...-
T Consensus 4 ~~~AC~~C~~i~~~~~Cp~Cgs~~ 27 (64)
T PRK06393 4 QYRACKKCKRLTPEKTCPVHGDEK 27 (64)
T ss_pred hhhhHhhCCcccCCCcCCCCCCCc
Confidence 457899998776545899998753
No 88
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=32.91 E-value=12 Score=23.73 Aligned_cols=26 Identities=19% Similarity=0.662 Sum_probs=15.0
Q ss_pred ecCchhhHhhcCCCCCCCCCCCCCCccc
Q 038900 59 GYLEKNDHEKACKHSPCSCPLSGCDFLG 86 (230)
Q Consensus 59 ~~~~~~~He~~C~~~~~~Cp~~~C~~~g 86 (230)
....+..|...|+|+.|.|. .|....
T Consensus 13 ~~~~lKgHk~~C~~~~C~C~--kC~li~ 38 (47)
T PF00751_consen 13 VIVPLKGHKRYCPFRDCQCD--KCALIA 38 (47)
T ss_dssp ---TTTT-GGG-TTTT--SH--HHHHHH
T ss_pred cccchhhhccccCcCCCcCC--CCcCcH
Confidence 35567889999999999996 576544
No 89
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.71 E-value=19 Score=31.05 Aligned_cols=27 Identities=26% Similarity=0.539 Sum_probs=21.1
Q ss_pred CCCCccccccccccC--CCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKIK--NDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~--~~~CP~C~~~~~ 28 (230)
++||+||-.|..++- ...||+|..++.
T Consensus 242 ~sg~Vv~~ecvEklir~D~v~pv~d~plk 270 (303)
T KOG3039|consen 242 PSGHVVTKECVEKLIRKDMVDPVTDKPLK 270 (303)
T ss_pred cCCcEeeHHHHHHhccccccccCCCCcCc
Confidence 579999999999863 246898888765
No 90
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.17 E-value=49 Score=35.02 Aligned_cols=22 Identities=27% Similarity=0.736 Sum_probs=14.1
Q ss_pred cccccccccCCC-----CCCCCCCCCC
Q 038900 7 VCTTCRSKIKND-----SCPFDRSPIA 28 (230)
Q Consensus 7 ~C~~C~~~l~~~-----~CP~C~~~~~ 28 (230)
.|.+|-.++... .||.|..++.
T Consensus 694 ~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 694 VCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred eCccCCCccCCCccccccCCCCCCccc
Confidence 377776665322 6888887764
No 91
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=31.09 E-value=21 Score=26.27 Aligned_cols=24 Identities=33% Similarity=0.881 Sum_probs=17.0
Q ss_pred ccccccccccC------CCCCCCCCCCCCc
Q 038900 6 MVCTTCRSKIK------NDSCPFDRSPIAY 29 (230)
Q Consensus 6 ~~C~~C~~~l~------~~~CP~C~~~~~~ 29 (230)
+.|+.|+..|. ...||.|+++++.
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp 92 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNP 92 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCc
Confidence 57888887763 1468888888753
No 92
>PF14334 DUF4390: Domain of unknown function (DUF4390)
Probab=30.54 E-value=34 Score=27.32 Aligned_cols=33 Identities=21% Similarity=0.350 Sum_probs=24.8
Q ss_pred CCcccccCcccCCCC--ceEEEEEEEccCCCcCCC
Q 038900 198 LGFPLVPWLLDATDG--RLNLKICIFKDRLPHWLR 230 (230)
Q Consensus 198 ~~fl~vp~~~~~~~g--~l~l~v~I~~~~~~~~~~ 230 (230)
..+-++|...+.++. .+.++++.+..+||-||+
T Consensus 109 ~~~~l~~~~~L~~g~~Y~~~lr~~Ld~~~LP~plq 143 (165)
T PF14334_consen 109 RNWPLAPLSDLEPGEDYQVRLRFRLDRSQLPKPLQ 143 (165)
T ss_pred CCcEeccHHHCCCCCeEEEEEEEEEEhHHCCHhHh
Confidence 466677777776654 377888888999999985
No 93
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=30.46 E-value=34 Score=22.99 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=16.5
Q ss_pred ccccccccccCCCCCCCCCCCC
Q 038900 6 MVCTTCRSKIKNDSCPFDRSPI 27 (230)
Q Consensus 6 ~~C~~C~~~l~~~~CP~C~~~~ 27 (230)
.+|..|..-.....||.|...-
T Consensus 4 kAC~~C~~i~~~~~CP~Cgs~~ 25 (61)
T PRK08351 4 KACRHCHYITTEDRCPVCGSRD 25 (61)
T ss_pred hhhhhCCcccCCCcCCCCcCCc
Confidence 4788998776545799998753
No 94
>PLN02248 cellulose synthase-like protein
Probab=30.41 E-value=21 Score=37.11 Aligned_cols=27 Identities=33% Similarity=0.775 Sum_probs=21.5
Q ss_pred CCCCCcccccccccc-C-CCCCCCCCCCC
Q 038900 1 CENGHMVCTTCRSKI-K-NDSCPFDRSPI 27 (230)
Q Consensus 1 C~~GH~~C~~C~~~l-~-~~~CP~C~~~~ 27 (230)
|+|++..|..|.... . .+.||-|+++.
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 176 (1135)
T PLN02248 148 CECGFKICRDCYIDAVKSGGICPGCKEPY 176 (1135)
T ss_pred ccccchhHHhHhhhhhhcCCCCCCCcccc
Confidence 889999999998874 2 26899998875
No 95
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=29.77 E-value=31 Score=23.27 Aligned_cols=21 Identities=29% Similarity=0.676 Sum_probs=15.5
Q ss_pred ccccccccccCCC--CCCCCCCC
Q 038900 6 MVCTTCRSKIKND--SCPFDRSP 26 (230)
Q Consensus 6 ~~C~~C~~~l~~~--~CP~C~~~ 26 (230)
.+|..|..-.... .||.|..+
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred HHHhhccccCCCCCccCCCCCCc
Confidence 5789997665433 49999886
No 96
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=28.26 E-value=83 Score=27.60 Aligned_cols=72 Identities=18% Similarity=0.295 Sum_probs=37.1
Q ss_pred CCCCCCCCCCccchHHHHHHHhhcceecCcCCCCCcceeeecCch-hhHhh-cCCCCCCCCCCCCCCccc-ChhhHHHHH
Q 038900 19 SCPFDRSPIAYTRNRVIEKLLESVKSVSCKNAEYGCNEMLGYLEK-NDHEK-ACKHSPCSCPLSGCDFLG-SSSQLYQHF 95 (230)
Q Consensus 19 ~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~n~~~GC~~~~~~~~~-~~He~-~C~~~~~~Cp~~~C~~~g-~~~~L~~H~ 95 (230)
.|+.|.+.........|.-..-.|. ..|. =|.+.+..--| +.|.+ -=.-.|+.|| -|+-.. .+..|..|+
T Consensus 163 ~C~~C~K~YvSmpALkMHirTH~l~-c~C~----iCGKaFSRPWLLQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 163 SCKYCGKVYVSMPALKMHIRTHTLP-CECG----ICGKAFSRPWLLQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAHM 235 (279)
T ss_pred cCCCCCceeeehHHHhhHhhccCCC-cccc----cccccccchHHhhcccccccCCCCccCC--cccchhcchHHHHHHH
Confidence 4666654332233344444444444 4444 36555554332 33443 1223577777 576555 467888887
Q ss_pred hh
Q 038900 96 RA 97 (230)
Q Consensus 96 ~~ 97 (230)
++
T Consensus 236 QT 237 (279)
T KOG2462|consen 236 QT 237 (279)
T ss_pred Hh
Confidence 76
No 97
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=27.99 E-value=47 Score=18.23 Aligned_cols=20 Identities=20% Similarity=0.624 Sum_probs=10.7
Q ss_pred ccccccccC--CCCCCCCCCCC
Q 038900 8 CTTCRSKIK--NDSCPFDRSPI 27 (230)
Q Consensus 8 C~~C~~~l~--~~~CP~C~~~~ 27 (230)
|-.|...+. ...||.|.-.+
T Consensus 3 CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 3 CPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CCCCcCCchhhcCcCCCCCCCC
Confidence 556666543 13577775443
No 98
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.80 E-value=19 Score=35.22 Aligned_cols=20 Identities=40% Similarity=0.969 Sum_probs=17.5
Q ss_pred CCCCccccccccccCCCCCC
Q 038900 2 ENGHMVCTTCRSKIKNDSCP 21 (230)
Q Consensus 2 ~~GH~~C~~C~~~l~~~~CP 21 (230)
.|||+.|..|.+++-+..||
T Consensus 32 ~cghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 32 QCGHTICGHCVQLLYNASCP 51 (861)
T ss_pred cccchHHHHHHHhHhhccCC
Confidence 48999999999998766788
No 99
>PF12773 DZR: Double zinc ribbon
Probab=26.43 E-value=42 Score=20.84 Aligned_cols=21 Identities=24% Similarity=0.733 Sum_probs=9.8
Q ss_pred ccccccccCC--CCCCCCCCCCC
Q 038900 8 CTTCRSKIKN--DSCPFDRSPIA 28 (230)
Q Consensus 8 C~~C~~~l~~--~~CP~C~~~~~ 28 (230)
|..|-..+.. ..||.|..++.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 3444444321 24666655544
No 100
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=26.37 E-value=24 Score=27.46 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=20.8
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCccch--HHHHHHHhhcceecCcC
Q 038900 1 CENGHMVCTTCRSKIKNDSCPFDRSPIAYTRN--RVIEKLLESVKSVSCKN 49 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~~~~CP~C~~~~~~~r~--~~~e~~~~~l~~v~C~n 49 (230)
|.|||.||.-=..--.+ ..-+.|+ ..|+.+.-++. +|=++
T Consensus 73 cecghsf~d~r~nwkl~--------a~i~vrdtee~lreiyp~s~-ipdp~ 114 (165)
T COG4647 73 CECGHSFGDYRENWKLH--------ANIYVRDTEEKLREIYPKSD-IPDPQ 114 (165)
T ss_pred EeccccccChhhCceee--------eEEEEcchHHHHHHhCcccC-CCCch
Confidence 88999998642221111 1113454 34666665665 55554
No 101
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=26.08 E-value=38 Score=24.59 Aligned_cols=25 Identities=28% Similarity=0.432 Sum_probs=18.5
Q ss_pred CCCccccccccccCCCCCCCCCCCCCc
Q 038900 3 NGHMVCTTCRSKIKNDSCPFDRSPIAY 29 (230)
Q Consensus 3 ~GH~~C~~C~~~l~~~~CP~C~~~~~~ 29 (230)
.||-+|..|--+-. .|..|...+.+
T Consensus 57 ~g~~YCq~CAYkkG--iCamCGKki~d 81 (90)
T PF10235_consen 57 PGAKYCQTCAYKKG--ICAMCGKKILD 81 (90)
T ss_pred CCCccChhhhcccC--cccccCCeecc
Confidence 47888888866544 69999887744
No 102
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=25.69 E-value=26 Score=23.36 Aligned_cols=14 Identities=36% Similarity=0.914 Sum_probs=8.8
Q ss_pred CCCCcccccccccc
Q 038900 2 ENGHMVCTTCRSKI 15 (230)
Q Consensus 2 ~~GH~~C~~C~~~l 15 (230)
.+|++||++|....
T Consensus 30 ~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 30 NCGRVVCSSCSSQR 43 (69)
T ss_dssp TT--EEECCCS-EE
T ss_pred CCCCEECCchhCCE
Confidence 37999999998763
No 103
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=25.13 E-value=20 Score=34.28 Aligned_cols=27 Identities=22% Similarity=0.515 Sum_probs=20.7
Q ss_pred CCCCcccccccccc-------CCCCCCCCCCCCC
Q 038900 2 ENGHMVCTTCRSKI-------KNDSCPFDRSPIA 28 (230)
Q Consensus 2 ~~GH~~C~~C~~~l-------~~~~CP~C~~~~~ 28 (230)
.|.|.||.-|+... .+..||+|..++.
T Consensus 553 ~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 553 SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred hhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 37899999999763 1257999987765
No 104
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=24.43 E-value=32 Score=31.14 Aligned_cols=55 Identities=22% Similarity=0.366 Sum_probs=36.7
Q ss_pred cccccccc--CCCCCCCCCCCCCccch----HHHHHH----------HhhcceecCcCCCC-CcceeeecCch
Q 038900 8 CTTCRSKI--KNDSCPFDRSPIAYTRN----RVIEKL----------LESVKSVSCKNAEY-GCNEMLGYLEK 63 (230)
Q Consensus 8 C~~C~~~l--~~~~CP~C~~~~~~~r~----~~~e~~----------~~~l~~v~C~n~~~-GC~~~~~~~~~ 63 (230)
|..|-+.+ .|..|-.|...+++.+. .+++.. -.... .+|.|..+ +|+|.++-.+-
T Consensus 2 C~~Cg~~v~FeNt~C~~Cg~~LGf~p~~~~~~al~~~~~~~~~~~~~~~~~~-~~C~N~~~~~CNWlvp~~~~ 73 (343)
T PF10005_consen 2 CPNCGQPVFFENTRCLSCGSALGFDPDRREMVALEPDGDGRWRAPAAPGRRY-RRCANAEHAVCNWLVPADDP 73 (343)
T ss_pred CCCCCCcceeCCCccccCCccccCCCCCCcEEeeccCCCCcccccCCCCcee-eeCCCCCccccceeecCCCC
Confidence 77888876 34579999998886542 123321 11245 79999654 79999987765
No 105
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=24.04 E-value=54 Score=17.92 Aligned_cols=15 Identities=47% Similarity=1.161 Sum_probs=8.9
Q ss_pred CCCCCCCCCCcccChh
Q 038900 74 PCSCPLSGCDFLGSSS 89 (230)
Q Consensus 74 ~~~Cp~~~C~~~g~~~ 89 (230)
|..| .++|+|-|+..
T Consensus 1 ~~~C-~~gCgf~Gs~~ 15 (25)
T PF01754_consen 1 PSLC-ANGCGFYGSPA 15 (25)
T ss_dssp SSB--TTTSSSB-BGG
T ss_pred CCcc-cCCCCCccccc
Confidence 3467 57899988643
No 106
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=23.79 E-value=54 Score=21.32 Aligned_cols=28 Identities=29% Similarity=0.611 Sum_probs=18.1
Q ss_pred CCCCCCCCCCCCccc-ChhhHHHHHhhhcCC
Q 038900 72 HSPCSCPLSGCDFLG-SSSQLYQHFRAQHQN 101 (230)
Q Consensus 72 ~~~~~Cp~~~C~~~g-~~~~L~~H~~~~H~~ 101 (230)
..|-.|| -|+-+. +..+|..|+...|..
T Consensus 22 ~~PatCP--~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCP--ICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-T--TT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCC--cchhhccchhhHHHHHHHHhcc
Confidence 3456788 588876 568999999999865
No 107
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=23.55 E-value=49 Score=23.04 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=19.9
Q ss_pred hhHhhcCCCCCCCCCCCCCCccc-ChhhHHHHHhhh-cCC
Q 038900 64 NDHEKACKHSPCSCPLSGCDFLG-SSSQLYQHFRAQ-HQN 101 (230)
Q Consensus 64 ~~He~~C~~~~~~Cp~~~C~~~g-~~~~L~~H~~~~-H~~ 101 (230)
..+.+.-......|+ -|+... +..+|..|++.. |..
T Consensus 40 ~~~~~~~~~~~~~C~--~C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 40 LNYLRKKVKESFRCP--YCNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp ---------SSEEBS--SSS-EESSHHHHHHHHHHTTTTC
T ss_pred ccccccccCCCCCCC--ccCCCCcCHHHHHHHHcCccCCC
Confidence 334444444467887 587766 689999999975 544
No 108
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=23.27 E-value=48 Score=26.18 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=24.7
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCccchHHHHHH
Q 038900 1 CENGHMVCTTCRSKIKNDSCPFDRSPIAYTRNRVIEKL 38 (230)
Q Consensus 1 C~~GH~~C~~C~~~l~~~~CP~C~~~~~~~r~~~~e~~ 38 (230)
|+| -..|.-|..+-..-+||.|+.|.-...|.-+.+.
T Consensus 2 ~kc-t~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 2 CKC-TTTCVICLESEIKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred Ccc-eeeehhhhcchhhccCCCCCCccccchhhhhccC
Confidence 455 6789999987532389999987654445444443
No 109
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.76 E-value=55 Score=34.69 Aligned_cols=24 Identities=21% Similarity=0.559 Sum_probs=15.0
Q ss_pred CCccccccccccCCCCCCCCCCCC
Q 038900 4 GHMVCTTCRSKIKNDSCPFDRSPI 27 (230)
Q Consensus 4 GH~~C~~C~~~l~~~~CP~C~~~~ 27 (230)
|.+.|.+|-.......||.|....
T Consensus 666 ~~rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 666 GRRRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EEEECCCCCCccccccCcccCCcC
Confidence 446677777664334677777654
No 110
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.55 E-value=69 Score=23.51 Aligned_cols=26 Identities=23% Similarity=0.650 Sum_probs=20.5
Q ss_pred CCC--CCCCCCccc-ChhhHHHHHhhhcC
Q 038900 75 CSC--PLSGCDFLG-SSSQLYQHFRAQHQ 100 (230)
Q Consensus 75 ~~C--p~~~C~~~g-~~~~L~~H~~~~H~ 100 (230)
+.| ....|+|.. +.+.|..|+...|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 555 445899977 67899999999984
No 111
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.34 E-value=13 Score=23.10 Aligned_cols=22 Identities=23% Similarity=0.656 Sum_probs=13.7
Q ss_pred cccccccccC------CCCCCCCCCCCC
Q 038900 7 VCTTCRSKIK------NDSCPFDRSPIA 28 (230)
Q Consensus 7 ~C~~C~~~l~------~~~CP~C~~~~~ 28 (230)
.|.+|-..+. ..+||.|..++.
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 4777766641 146888877664
No 112
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=21.24 E-value=51 Score=28.98 Aligned_cols=24 Identities=25% Similarity=0.473 Sum_probs=17.5
Q ss_pred CCccccccccccCC------CCCCCCCCCC
Q 038900 4 GHMVCTTCRSKIKN------DSCPFDRSPI 27 (230)
Q Consensus 4 GH~~C~~C~~~l~~------~~CP~C~~~~ 27 (230)
.|+||+.|-.++.. ..||.|+...
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 58899999888531 3588887654
No 113
>PF14353 CpXC: CpXC protein
Probab=21.17 E-value=1e+02 Score=23.25 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=8.2
Q ss_pred CCCCCCCCCC
Q 038900 19 SCPFDRSPIA 28 (230)
Q Consensus 19 ~CP~C~~~~~ 28 (230)
+||.|...+.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 6999998765
No 114
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=20.98 E-value=61 Score=24.53 Aligned_cols=28 Identities=18% Similarity=0.516 Sum_probs=19.6
Q ss_pred cccccccccc---C-CCCCCCCCCCCCccchH
Q 038900 6 MVCTTCRSKI---K-NDSCPFDRSPIAYTRNR 33 (230)
Q Consensus 6 ~~C~~C~~~l---~-~~~CP~C~~~~~~~r~~ 33 (230)
+.|.+|-... . ...|+.|++|++-.++.
T Consensus 70 V~CP~C~K~TKmLGr~D~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 70 VECPNCGKQTKMLGRVDACMHCKEPLTLDPSL 101 (114)
T ss_pred eECCCCCChHhhhchhhccCcCCCcCccCchh
Confidence 4688887763 2 14799999998765543
No 115
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.08 E-value=49 Score=21.35 Aligned_cols=25 Identities=12% Similarity=0.292 Sum_probs=9.4
Q ss_pred CCCCCCCCCCccchHHHHHHHhhcceecCc
Q 038900 19 SCPFDRSPIAYTRNRVIEKLLESVKSVSCK 48 (230)
Q Consensus 19 ~CP~C~~~~~~~r~~~~e~~~~~l~~v~C~ 48 (230)
.||.|+..+ +..-+..|-... -.||
T Consensus 23 ~C~~C~~~F----C~dCD~fiHE~L-H~CP 47 (51)
T PF07975_consen 23 RCPKCKNHF----CIDCDVFIHETL-HNCP 47 (51)
T ss_dssp --TTTT--B-----HHHHHTTTTTS--SSS
T ss_pred ECCCCCCcc----ccCcChhhhccc-cCCc
Confidence 477776532 344444444444 4555
Done!