Query psy6569
Match_columns 164
No_of_seqs 128 out of 298
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 21:27:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3454|consensus 100.0 3.2E-29 7E-34 202.9 13.3 71 1-71 1-71 (165)
2 PF06220 zf-U1: U1 zinc finger 99.8 9.5E-21 2.1E-25 120.7 2.8 38 1-38 1-38 (38)
3 COG5136 U1 snRNP-specific prot 99.7 8.3E-17 1.8E-21 132.0 6.1 49 1-49 1-49 (188)
4 KOG0150|consensus 99.2 3.8E-11 8.3E-16 106.3 5.3 43 2-45 9-51 (336)
5 smart00451 ZnF_U1 U1-like zinc 99.1 5.6E-11 1.2E-15 71.3 2.4 35 1-37 1-35 (35)
6 PF12171 zf-C2H2_jaz: Zinc-fin 98.6 4.3E-08 9.3E-13 57.0 2.2 27 3-31 1-27 (27)
7 KOG4727|consensus 98.3 5.2E-07 1.1E-11 75.1 4.6 33 2-36 74-106 (193)
8 PF12874 zf-met: Zinc-finger o 98.1 2E-06 4.4E-11 48.3 2.2 25 4-30 1-25 (25)
9 KOG0717|consensus 97.5 8.3E-05 1.8E-09 69.5 3.9 40 4-45 293-332 (508)
10 KOG1924|consensus 97.0 0.022 4.8E-07 57.0 14.0 9 5-13 438-446 (1102)
11 COG5188 PRP9 Splicing factor 3 96.9 0.0004 8.6E-09 63.8 2.0 34 2-37 237-270 (470)
12 KOG2893|consensus 96.7 0.02 4.3E-07 50.9 10.3 25 3-29 10-34 (341)
13 KOG3408|consensus 96.7 0.00091 2E-08 53.2 1.7 33 2-36 56-88 (129)
14 KOG0227|consensus 96.6 0.0014 3E-08 55.9 2.7 42 2-45 52-93 (222)
15 PF04988 AKAP95: A-kinase anch 96.2 0.013 2.9E-07 48.3 6.0 62 4-69 92-161 (165)
16 COG5246 PRP11 Splicing factor 96.0 0.011 2.5E-07 50.3 4.9 59 2-63 52-121 (222)
17 COG5112 UFD2 U1-like Zn-finger 95.5 0.0064 1.4E-07 48.0 1.3 33 3-37 55-87 (126)
18 PF13894 zf-C2H2_4: C2H2-type 95.2 0.015 3.2E-07 31.0 1.7 21 4-26 1-21 (24)
19 PF12756 zf-C2H2_2: C2H2 type 94.8 0.0089 1.9E-07 41.1 0.3 29 3-33 50-78 (100)
20 PF14968 CCDC84: Coiled coil p 94.8 0.05 1.1E-06 49.0 5.0 36 3-39 58-98 (336)
21 PF00096 zf-C2H2: Zinc finger, 94.7 0.024 5.1E-07 30.9 1.8 22 4-27 1-22 (23)
22 PF03194 LUC7: LUC7 N_terminus 94.4 0.056 1.2E-06 46.3 4.3 44 4-47 191-237 (254)
23 KOG2384|consensus 93.5 0.021 4.7E-07 48.9 -0.0 29 3-34 84-112 (223)
24 PF07535 zf-DBF: DBF zinc fing 93.2 0.071 1.5E-06 36.0 2.2 25 3-32 5-29 (49)
25 KOG3032|consensus 93.2 0.056 1.2E-06 47.4 2.1 32 4-38 36-67 (264)
26 PF13912 zf-C2H2_6: C2H2-type 93.1 0.068 1.5E-06 30.1 1.7 21 4-26 2-22 (27)
27 KOG2785|consensus 92.0 0.047 1E-06 50.2 0.1 36 3-40 68-103 (390)
28 KOG0796|consensus 92.0 0.23 4.9E-06 44.8 4.4 44 5-48 188-234 (319)
29 smart00586 ZnF_DBF Zinc finger 91.4 0.17 3.6E-06 34.3 2.3 25 3-32 5-29 (49)
30 smart00355 ZnF_C2H2 zinc finge 91.1 0.17 3.7E-06 26.7 1.7 21 4-26 1-21 (26)
31 PF14968 CCDC84: Coiled coil p 88.5 0.54 1.2E-05 42.5 3.8 34 5-43 1-34 (336)
32 KOG2837|consensus 87.9 0.19 4.1E-06 45.0 0.5 54 3-58 25-85 (309)
33 PTZ00448 hypothetical protein; 84.2 1 2.2E-05 41.5 3.2 37 3-41 314-350 (373)
34 PHA02768 hypothetical protein; 84.1 0.64 1.4E-05 32.2 1.5 22 3-26 5-26 (55)
35 COG5200 LUC7 U1 snRNP componen 83.2 0.85 1.8E-05 39.9 2.2 33 5-37 187-220 (258)
36 PF02892 zf-BED: BED zinc fing 83.0 0.78 1.7E-05 28.6 1.5 23 3-25 16-40 (45)
37 PF13909 zf-H2C2_5: C2H2-type 80.2 1.2 2.7E-05 24.5 1.5 20 4-26 1-20 (24)
38 KOG4849|consensus 78.2 18 0.0004 34.1 9.2 31 3-33 79-111 (498)
39 KOG4722|consensus 77.6 1.5 3.2E-05 42.1 2.0 34 3-38 493-526 (672)
40 smart00597 ZnF_TTF zinc finger 77.6 1.4 3E-05 32.7 1.4 32 3-34 25-72 (90)
41 PF13465 zf-H2C2_2: Zinc-finge 77.5 1.2 2.5E-05 25.6 0.8 12 3-14 14-25 (26)
42 KOG2785|consensus 74.5 2.4 5.2E-05 39.3 2.4 38 1-40 1-38 (390)
43 PF05605 zf-Di19: Drought indu 74.4 2.1 4.6E-05 28.1 1.6 22 3-27 2-23 (54)
44 smart00614 ZnF_BED BED zinc fi 71.5 1.8 3.9E-05 28.1 0.7 25 3-27 18-45 (50)
45 PF13913 zf-C2HC_2: zinc-finge 70.9 3.4 7.3E-05 23.9 1.7 20 4-26 3-22 (25)
46 KOG2505|consensus 68.5 4.2 9.2E-05 39.4 2.7 36 3-40 66-101 (591)
47 PF11931 DUF3449: Domain of un 66.3 1.9 4.2E-05 36.4 0.0 33 3-36 101-133 (196)
48 PF13821 DUF4187: Domain of un 66.2 3.2 6.9E-05 28.3 1.1 24 4-29 28-51 (55)
49 PF02748 PyrI_C: Aspartate car 66.1 1.6 3.6E-05 29.5 -0.4 13 3-15 35-47 (52)
50 PF05477 SURF2: Surfeit locus 64.8 4.9 0.00011 35.0 2.2 37 3-40 79-115 (244)
51 PF04988 AKAP95: A-kinase anch 63.6 12 0.00027 31.1 4.2 29 4-34 1-29 (165)
52 PF04746 DUF575: Protein of un 61.8 3.5 7.7E-05 31.8 0.7 52 11-67 48-100 (101)
53 PF04959 ARS2: Arsenite-resist 61.8 9 0.00019 32.6 3.2 30 3-35 77-106 (214)
54 COG1631 RPL42A Ribosomal prote 54.1 6.5 0.00014 30.1 1.0 18 3-20 8-25 (94)
55 PF14881 Tubulin_3: Tubulin do 49.2 9.8 0.00021 31.0 1.4 13 2-14 9-21 (180)
56 TIGR03830 CxxCG_CxxCG_HTH puta 49.1 55 0.0012 23.7 5.3 23 2-25 30-52 (127)
57 PF07975 C1_4: TFIIH C1-like d 48.5 2.9 6.2E-05 28.5 -1.5 16 3-19 29-44 (51)
58 PF14376 Haem_bd: Haem-binding 48.2 13 0.00028 29.0 1.9 62 5-68 43-113 (137)
59 PF15384 DUF4610: Domain of un 47.3 23 0.00051 30.3 3.4 46 11-61 34-79 (197)
60 KOG4849|consensus 44.2 2.7E+02 0.0059 26.6 10.0 10 152-161 338-347 (498)
61 KOG3792|consensus 44.0 4.4 9.5E-05 40.6 -1.6 32 2-35 358-389 (816)
62 KOG4167|consensus 43.5 20 0.00043 36.5 2.7 22 3-26 792-813 (907)
63 PHA00732 hypothetical protein 43.4 16 0.00036 26.3 1.7 21 4-26 2-22 (79)
64 PF13842 Tnp_zf-ribbon_2: DDE_ 42.5 10 0.00022 23.2 0.4 12 3-14 16-27 (32)
65 KOG2482|consensus 41.6 9.2 0.0002 35.7 0.2 35 3-39 195-231 (423)
66 PF11888 DUF3408: Protein of u 41.4 31 0.00066 26.8 3.0 27 33-59 106-132 (136)
67 COG4469 CoiA Competence protei 41.3 11 0.00023 34.7 0.5 50 3-52 25-88 (342)
68 PF08394 Arc_trans_TRASH: Arch 40.4 4.7 0.0001 25.9 -1.4 18 6-24 1-18 (37)
69 PF08349 DUF1722: Protein of u 40.3 39 0.00084 25.4 3.4 41 20-63 47-87 (117)
70 PF02701 zf-Dof: Dof domain, z 39.8 5.3 0.00012 28.6 -1.3 25 2-27 29-53 (63)
71 PF14616 DUF4451: Domain of un 39.7 14 0.00031 28.6 0.9 21 5-26 27-49 (124)
72 PHA03074 late transcription fa 38.9 14 0.00031 32.1 0.9 35 4-39 22-60 (225)
73 PHA00733 hypothetical protein 38.2 21 0.00045 27.7 1.6 22 3-26 73-94 (128)
74 TIGR00985 3a0801s04tom mitocho 36.5 94 0.002 25.2 5.2 26 5-31 23-49 (148)
75 PTZ00157 60S ribosomal protein 35.1 12 0.00026 28.0 -0.1 19 3-21 9-27 (84)
76 PF14369 zf-RING_3: zinc-finge 34.5 19 0.00041 22.4 0.7 12 3-14 2-13 (35)
77 KOG4594|consensus 34.2 1.8E+02 0.0039 26.9 7.1 13 99-111 141-153 (354)
78 KOG2893|consensus 34.1 3.7E+02 0.0079 24.5 9.2 22 3-26 34-55 (341)
79 PHA00616 hypothetical protein 33.6 17 0.00038 24.1 0.5 20 4-25 2-21 (44)
80 KOG3576|consensus 33.3 15 0.00033 32.3 0.2 21 3-25 145-165 (267)
81 PRK05767 rpl44e 50S ribosomal 32.8 14 0.0003 28.1 -0.1 18 3-20 8-25 (92)
82 PRK10167 hypothetical protein; 32.0 52 0.0011 27.0 3.1 42 19-63 87-128 (169)
83 PLN03238 probable histone acet 31.5 26 0.00056 31.5 1.3 22 3-26 48-69 (290)
84 PF00130 C1_1: Phorbol esters/ 31.5 23 0.0005 22.4 0.8 11 3-13 11-21 (53)
85 KOG3792|consensus 31.2 19 0.00042 36.2 0.6 29 4-34 194-222 (816)
86 KOG0545|consensus 30.5 30 0.00064 31.5 1.5 36 5-40 233-270 (329)
87 PF07909 DUF1663: Protein of u 30.3 57 0.0012 31.0 3.4 39 22-60 4-51 (497)
88 PF09441 Abp2: ARS binding pro 29.5 94 0.002 26.2 4.2 46 4-49 20-77 (175)
89 KOG4252|consensus 28.5 76 0.0016 27.8 3.6 57 7-63 39-95 (246)
90 KOG0132|consensus 28.4 3.6E+02 0.0078 28.0 8.6 10 130-139 632-641 (894)
91 PF13878 zf-C2H2_3: zinc-finge 28.3 51 0.0011 21.0 2.0 22 4-25 14-35 (41)
92 PTZ00064 histone acetyltransfe 28.2 28 0.0006 33.8 1.0 22 4-27 281-302 (552)
93 KOG3960|consensus 28.1 1.4E+02 0.003 27.0 5.2 38 4-43 104-142 (284)
94 KOG1365|consensus 27.9 1.4E+02 0.003 28.7 5.5 38 26-63 222-259 (508)
95 PF00643 zf-B_box: B-box zinc 27.8 26 0.00056 21.3 0.5 12 3-14 15-26 (42)
96 PF05766 NinG: Bacteriophage L 27.0 84 0.0018 26.5 3.5 12 3-14 6-17 (189)
97 PLN03239 histone acetyltransfe 26.8 26 0.00057 32.2 0.6 22 3-26 106-127 (351)
98 COG4049 Uncharacterized protei 26.7 34 0.00073 24.5 1.0 21 4-26 18-38 (65)
99 PLN00104 MYST -like histone ac 26.3 29 0.00064 32.8 0.8 22 3-26 198-219 (450)
100 PF10276 zf-CHCC: Zinc-finger 25.3 32 0.0007 22.3 0.6 10 4-13 30-39 (40)
101 COG3677 Transposase and inacti 25.2 50 0.0011 25.8 1.8 37 2-40 52-88 (129)
102 KOG3623|consensus 25.1 20 0.00042 36.7 -0.6 20 3-24 894-913 (1007)
103 KOG2554|consensus 24.3 1.1E+02 0.0025 28.9 4.2 38 3-41 315-355 (425)
104 COG3657 Uncharacterized protei 24.3 1.6E+02 0.0035 22.8 4.4 35 29-63 7-41 (100)
105 KOG0132|consensus 24.1 6.6E+02 0.014 26.2 9.6 11 145-155 688-698 (894)
106 TIGR02646 conserved hypothetic 23.6 16 0.00035 28.3 -1.2 29 3-33 24-52 (144)
107 PF05004 IFRD: Interferon-rela 22.8 1.3E+02 0.0028 26.3 4.1 46 16-62 55-100 (309)
108 PF00628 PHD: PHD-finger; Int 22.6 40 0.00086 21.1 0.7 11 4-15 15-25 (51)
109 PF13097 CENP-U: CENP-A nucleo 22.4 1.4E+02 0.003 25.2 4.0 34 16-49 115-148 (175)
110 PRK13264 3-hydroxyanthranilate 22.3 21 0.00045 29.8 -0.8 35 3-40 120-154 (177)
111 smart00249 PHD PHD zinc finger 22.3 33 0.00072 20.0 0.2 10 4-13 15-24 (47)
112 PF10955 DUF2757: Protein of u 22.2 38 0.00082 24.9 0.6 11 3-13 4-14 (76)
113 KOG4317|consensus 22.0 62 0.0014 30.1 2.0 36 3-40 19-57 (383)
114 PF09416 UPF1_Zn_bind: RNA hel 21.8 53 0.0012 26.9 1.4 13 4-16 15-27 (152)
115 smart00238 BIR Baculoviral inh 21.7 52 0.0011 22.0 1.2 13 3-15 36-48 (71)
116 PF04423 Rad50_zn_hook: Rad50 21.5 1.9E+02 0.0042 18.7 3.8 9 5-13 22-30 (54)
117 PF14659 Phage_int_SAM_3: Phag 21.2 68 0.0015 19.8 1.5 28 7-40 4-31 (58)
118 PF08209 Sgf11: Sgf11 (transcr 21.0 53 0.0012 20.5 1.0 20 3-25 4-23 (33)
119 PF12548 DUF3740: Sulfatase pr 20.3 1.3E+02 0.0028 24.3 3.3 34 8-42 92-126 (145)
120 PF06881 Elongin_A: RNA polyme 20.2 2E+02 0.0042 21.3 4.0 39 11-49 32-80 (109)
No 1
>KOG3454|consensus
Probab=99.96 E-value=3.2e-29 Score=202.93 Aligned_cols=71 Identities=72% Similarity=1.173 Sum_probs=68.1
Q ss_pred CCcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCCC
Q psy6569 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFGNKG 71 (164)
Q Consensus 1 MPRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~~~p~~~~p 71 (164)
|+||||||||+||||||+||||+|+.|+||++||+.||++|.||+||.+||+++++|..+++...+|.+..
T Consensus 1 MpRYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY~k~~eeqAq~liD~~~~~~~~~~g~~~~~~~~~ 71 (165)
T KOG3454|consen 1 MPRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYYQKWMEEQAQKLIDETILRFIGKKGQKVPFSNAR 71 (165)
T ss_pred CCcchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccCCcccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999988888543
No 2
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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 motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=99.81 E-value=9.5e-21 Score=120.68 Aligned_cols=38 Identities=74% Similarity=1.416 Sum_probs=26.4
Q ss_pred CCcccccCCcceeccCChHHHHhhhchhhHHHHHHHHH
Q psy6569 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYY 38 (164)
Q Consensus 1 MPRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY 38 (164)
|+||||||||+||++|++++|++|+.|++|++||++||
T Consensus 1 m~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~y 38 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRYY 38 (38)
T ss_dssp --S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHHT
T ss_pred CcCeecccccceecCCChHHHHHhhccHHHHHHHHHhC
Confidence 79999999999999999999999999999999999997
No 3
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=99.67 E-value=8.3e-17 Score=132.02 Aligned_cols=49 Identities=49% Similarity=0.926 Sum_probs=44.6
Q ss_pred CCcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHH
Q psy6569 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNL 49 (164)
Q Consensus 1 MPRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~i 49 (164)
|+|||||||++|||||+.||||.|+.|++|..++++||.+..++.+.+.
T Consensus 1 MpRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY~~~a~di~~e~ 49 (188)
T COG5136 1 MPRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYMEMAEDIAAEM 49 (188)
T ss_pred CcchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999887444443
No 4
>KOG0150|consensus
Probab=99.15 E-value=3.8e-11 Score=106.25 Aligned_cols=43 Identities=33% Similarity=0.749 Sum_probs=38.5
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQ 45 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeq 45 (164)
+++|||||++||. |+..++..|++|++|++||+++++..++..
T Consensus 9 ~kkfCdyCKiWi~-dN~~Sv~~He~GkrHke~V~Kritdi~rks 51 (336)
T KOG0150|consen 9 PKKFCDYCKIWIK-DNPASVRFHERGKRHKENVAKRITDIHRKS 51 (336)
T ss_pred cchhhhhhhhhhc-CChHHHHhHhhhhHHHHHHHHHHHHHHHhh
Confidence 6899999999995 888888999999999999999998876643
No 5
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=99.09 E-value=5.6e-11 Score=71.27 Aligned_cols=35 Identities=34% Similarity=0.652 Sum_probs=30.2
Q ss_pred CCcccccCCcceeccCChHHHHhhhchhhHHHHHHHH
Q psy6569 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFY 37 (164)
Q Consensus 1 MPRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkry 37 (164)
+++|||++|+++|+ +.+.+++|+.|++|++|++++
T Consensus 1 ~~~~~C~~C~~~~~--~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 1 TGGFYCKLCNVTFT--DEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred CcCeEccccCCccC--CHHHHHHHHChHHHHHHHHcC
Confidence 46899999999994 566679999999999999864
No 6
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.55 E-value=4.3e-08 Score=56.99 Aligned_cols=27 Identities=44% Similarity=0.977 Sum_probs=24.3
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHK 31 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk 31 (164)
+|||++||++| .+.+.+++|++|++|+
T Consensus 1 q~~C~~C~k~f--~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYF--SSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBB--SSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCc--CCHHHHHHHHccCCCC
Confidence 59999999999 5788999999999996
No 7
>KOG4727|consensus
Probab=98.34 E-value=5.2e-07 Score=75.14 Aligned_cols=33 Identities=39% Similarity=0.771 Sum_probs=28.7
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKF 36 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkr 36 (164)
.+||||.||+.+ .||.. +.+|++|++|+.|+..
T Consensus 74 ~GyyCdVCdcvv-KDSin-flDHiNgKkHqrnlgm 106 (193)
T KOG4727|consen 74 GGYYCDVCDCVV-KDSIN-FLDHINGKKHQRNLGM 106 (193)
T ss_pred Cceeeeecceee-hhhHH-HHHHhccHHHHHHHhh
Confidence 479999999999 58877 6999999999999543
No 8
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.10 E-value=2e-06 Score=48.35 Aligned_cols=25 Identities=32% Similarity=0.842 Sum_probs=23.3
Q ss_pred ccccCCcceeccCChHHHHhhhchhhH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKH 30 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKH 30 (164)
|+|+.|++.| .+...+++|++|++|
T Consensus 1 ~~C~~C~~~f--~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSF--SSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEE--SSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCc--CCHHHHHHHHCcCCC
Confidence 7999999999 578889999999998
No 9
>KOG0717|consensus
Probab=97.51 E-value=8.3e-05 Score=69.50 Aligned_cols=40 Identities=35% Similarity=0.537 Sum_probs=36.3
Q ss_pred ccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQ 45 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeq 45 (164)
+||..|++.| .|...+++|+++++|++||.+--+++.++.
T Consensus 293 lyC~vCnKsF--KseKq~kNHEnSKKHkenv~eLrqemEEEe 332 (508)
T KOG0717|consen 293 LYCVVCNKSF--KSEKQLKNHENSKKHKENVAELRQEMEEEE 332 (508)
T ss_pred eEEeeccccc--cchHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 7999999999 689999999999999999999888776664
No 10
>KOG1924|consensus
Probab=96.95 E-value=0.022 Score=56.97 Aligned_cols=9 Identities=11% Similarity=-0.193 Sum_probs=6.1
Q ss_pred cccCCccee
Q psy6569 5 YCDYCDTYL 13 (164)
Q Consensus 5 YCDYCdk~f 13 (164)
.|.+||--|
T Consensus 438 Hr~~~DPdf 446 (1102)
T KOG1924|consen 438 HRTGMDPDF 446 (1102)
T ss_pred hcCCCCCCc
Confidence 477777665
No 11
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=96.95 E-value=0.0004 Score=63.83 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=30.4
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFY 37 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkry 37 (164)
+++||..|.+|| .+.+|+..|+.|++|.+|+++.
T Consensus 237 ~~~YC~~C~r~f--~~~~VFe~Hl~gK~H~k~~~~~ 270 (470)
T COG5188 237 PKVYCVKCGREF--SRSKVFEYHLEGKRHCKEGQGK 270 (470)
T ss_pred cceeeHhhhhHh--hhhHHHHHHHhhhhhhhhhhhh
Confidence 579999999999 5789999999999999997654
No 12
>KOG2893|consensus
Probab=96.68 E-value=0.02 Score=50.88 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=20.5
Q ss_pred cccccCCcceeccCChHHHHhhhchhh
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRK 29 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkK 29 (164)
|-||=|||+-| |...++.+|..-+.
T Consensus 10 kpwcwycnref--ddekiliqhqkakh 34 (341)
T KOG2893|consen 10 KPWCWYCNREF--DDEKILIQHQKAKH 34 (341)
T ss_pred Cceeeeccccc--chhhhhhhhhhhcc
Confidence 56999999999 77888888876554
No 13
>KOG3408|consensus
Probab=96.65 E-value=0.00091 Score=53.22 Aligned_cols=33 Identities=33% Similarity=0.584 Sum_probs=28.2
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKF 36 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkr 36 (164)
.-|||-.|.+|| ++.++++.|..++.|++-|++
T Consensus 56 GqfyCi~CaRyF--i~~~~l~~H~ktK~HKrRvK~ 88 (129)
T KOG3408|consen 56 GQFYCIECARYF--IDAKALKTHFKTKVHKRRVKE 88 (129)
T ss_pred ceeehhhhhhhh--cchHHHHHHHhccHHHHHHHh
Confidence 358999999999 578889999999999965553
No 14
>KOG0227|consensus
Probab=96.62 E-value=0.0014 Score=55.90 Aligned_cols=42 Identities=33% Similarity=0.498 Sum_probs=35.0
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQ 45 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeq 45 (164)
.+|-|+-|.+. |.+-.++..|..|+||+.|+.++-.+..++.
T Consensus 52 G~yeCkLClT~--H~ne~Syl~HtqGKKHq~Nlarraa~e~k~s 93 (222)
T KOG0227|consen 52 GKYECKLCLTL--HNNEGSYLAHTQGKKHQTNLARRAAKEAKES 93 (222)
T ss_pred cceeehhhhhh--hcchhhhhhhhccchhhHHHHHHHHHHhhcC
Confidence 47899999985 5788889999999999999999887654433
No 15
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.19 E-value=0.013 Score=48.33 Aligned_cols=62 Identities=21% Similarity=0.446 Sum_probs=49.2
Q ss_pred ccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHH---HHHHHH-----HHHHHHHHcCCCCCCCCCC
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEE---QAQNLI-----DATTAAYKAGKIANNPFGN 69 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~ee---qaq~ii-----D~~tra~~~G~~~~~p~~~ 69 (164)
..|-.||++|. ...++..+|+.+.-|..|++.+..++.++ .|++++ .+.-..|.+|. |||..
T Consensus 92 ~hCsACd~~IP-~~~~~vQ~Hl~S~~H~~Nrr~~~eq~Kr~sl~vA~Silnnk~Ik~~le~ylKGe---nPF~~ 161 (165)
T PF04988_consen 92 AHCSACDVFIP-MQHSSVQKHLKSQDHNKNRRAMMEQSKRSSLSVARSILNNKHIKKRLEKYLKGE---NPFTD 161 (165)
T ss_pred hhhhHhhhhcc-CcHHHHHHHhccHHHHhhHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHhcCC---CCCcC
Confidence 47999999995 78888899999999999999999988774 455553 33466677787 66753
No 16
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.01 E-value=0.011 Score=50.30 Aligned_cols=59 Identities=31% Similarity=0.438 Sum_probs=42.1
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK-----------WMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~-----------~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
.+|-|.-|++. |-+-+++..|..|+||+.|+.++-.. .+-.+-|++|++...-...| |+
T Consensus 52 Gk~vC~LC~T~--H~~e~Sy~~H~~GKKH~~n~~rrs~eksslgrEnqtthdfrqqQkiieaKqSlk~~G-iP 121 (222)
T COG5246 52 GKYVCLLCKTK--HLTEMSYVKHREGKKHKENSSRRSEEKSSLGRENQTTHDFRQQQKIIEAKQSLKRSG-IP 121 (222)
T ss_pred CcEEeeeeccc--cccHHHHHHhhccchhhhhHHHHHHHhhcccccCCchhhhhhHHHHHHHHHHHHhcC-CC
Confidence 47899999986 56888889999999999999998321 11234456666665555555 44
No 17
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=95.48 E-value=0.0064 Score=47.98 Aligned_cols=33 Identities=27% Similarity=0.481 Sum_probs=28.7
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFY 37 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkry 37 (164)
-+||-.|++|| +|..+.+.|..|+-|++-+++-
T Consensus 55 qhYCieCaryf--~t~~aL~~HkkgkvHkRR~Kel 87 (126)
T COG5112 55 QHYCIECARYF--ITEKALMEHKKGKVHKRRAKEL 87 (126)
T ss_pred eeeeehhHHHH--HHHHHHHHHhccchhHHHHHHH
Confidence 48999999999 7999999999999999665543
No 18
>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=95.17 E-value=0.015 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=16.2
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
|-|++|++.| ++...+++|+.
T Consensus 1 ~~C~~C~~~~--~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSF--RSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EE--SSHHHHHHHHH
T ss_pred CCCcCCCCcC--CcHHHHHHHHH
Confidence 6799999999 67888899875
No 19
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.83 E-value=0.0089 Score=41.08 Aligned_cols=29 Identities=24% Similarity=0.652 Sum_probs=24.2
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDN 33 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~N 33 (164)
.+.|.+|++.| ++.+.++.|.+...|++.
T Consensus 50 ~~~C~~C~~~f--~s~~~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 50 SFRCPYCNKTF--RSREALQEHMRSKHHKKR 78 (100)
T ss_dssp SEEBSSSS-EE--SSHHHHHHHHHHTTTTC-
T ss_pred CCCCCccCCCC--cCHHHHHHHHcCccCCCc
Confidence 48999999999 688889999999999864
No 20
>PF14968 CCDC84: Coiled coil protein 84
Probab=94.78 E-value=0.05 Score=48.98 Aligned_cols=36 Identities=22% Similarity=0.594 Sum_probs=29.5
Q ss_pred cccccCCcceeccCCh-----HHHHhhhchhhHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSP-----SVRKTHCQGRKHKDNVKFYYQ 39 (164)
Q Consensus 3 RYYCDYCdk~fthDS~-----SvRK~H~~GkKHk~NVkryY~ 39 (164)
+|||.+|+.-+. |.. .....|+.+..|++||++|+.
T Consensus 58 ~fWC~fC~~ev~-~~~s~~~~~~ai~HLaS~eH~k~vk~F~w 98 (336)
T PF14968_consen 58 RFWCVFCDCEVR-EHDSSFACGGAIEHLASPEHRKNVKKFWW 98 (336)
T ss_pred eeEeeCccchhh-hccchhhhccHHhhcCCHHHHHHHHHHHH
Confidence 799999999994 442 234679999999999999974
No 21
>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=94.73 E-value=0.024 Score=30.92 Aligned_cols=22 Identities=32% Similarity=0.547 Sum_probs=18.4
Q ss_pred ccccCCcceeccCChHHHHhhhch
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQG 27 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~G 27 (164)
|-|++|++.| .+.+.++.|..-
T Consensus 1 y~C~~C~~~f--~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSF--SSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEE--SSHHHHHHHHHH
T ss_pred CCCCCCCCcc--CCHHHHHHHHhH
Confidence 6799999999 578888888753
No 22
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=94.42 E-value=0.056 Score=46.31 Aligned_cols=44 Identities=18% Similarity=0.445 Sum_probs=32.9
Q ss_pred ccccCCcceec-cCChHHHHhhhchhhHH--HHHHHHHHHHHHHHHH
Q psy6569 4 YYCDYCDTYLT-HDSPSVRKTHCQGRKHK--DNVKFYYQKWMEEQAQ 47 (164)
Q Consensus 4 YYCDYCdk~ft-hDS~SvRK~H~~GkKHk--~NVkryY~~~~eeqaq 47 (164)
--||.|+.||+ +|+.+=+.+|..|+.|. ..+++.|..+.+...+
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~IR~~l~el~e~~~~ 237 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAKIREKLKELKEKREE 237 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccchhhhHHHHHHHHHHHHHHHHH
Confidence 36999999984 46666566799999999 5667777776665554
No 23
>KOG2384|consensus
Probab=93.46 E-value=0.021 Score=48.94 Aligned_cols=29 Identities=28% Similarity=0.722 Sum_probs=23.1
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNV 34 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NV 34 (164)
-|||+.||+||. ||.+ .+|.++.-|+-|.
T Consensus 84 lfyCE~Cd~~ip-~~~~--snH~tSttHllsl 112 (223)
T KOG2384|consen 84 LFYCEVCDIYIP-NSKK--SNHFTSTTHLLSL 112 (223)
T ss_pred cchhhhhhhhcc-CCCC--ccchhhHHHHhhh
Confidence 589999999994 6655 4799999998543
No 24
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=93.21 E-value=0.071 Score=35.97 Aligned_cols=25 Identities=32% Similarity=0.660 Sum_probs=20.8
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKD 32 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~ 32 (164)
.-||+-|.+.|. | +..|+.+.+|++
T Consensus 5 ~GYCE~C~~ky~-~----l~~Hi~s~~Hr~ 29 (49)
T PF07535_consen 5 PGYCENCRVKYD-D----LEEHIQSEKHRK 29 (49)
T ss_pred CccCccccchhh-h----HHHHhCCHHHHH
Confidence 359999999993 2 678999999994
No 25
>KOG3032|consensus
Probab=93.19 E-value=0.056 Score=47.37 Aligned_cols=32 Identities=22% Similarity=0.586 Sum_probs=27.7
Q ss_pred ccccCCcceeccCChHHHHhhhchhhHHHHHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYY 38 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY 38 (164)
.-|-.|++-| . .++|..|.+|++|+++|..--
T Consensus 36 l~C~vCn~pi--K-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 36 LVCRVCNVPI--K-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred eeEEEecCcc--c-HHHHHHHhccHHHHHHHHHHH
Confidence 4699999999 3 999999999999998886544
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.12 E-value=0.068 Score=30.12 Aligned_cols=21 Identities=29% Similarity=0.564 Sum_probs=18.3
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
|.|+.|++.| .+.+.+.+|..
T Consensus 2 ~~C~~C~~~F--~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTF--SSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEE--SSHHHHHHHHC
T ss_pred CCCCccCCcc--CChhHHHHHhH
Confidence 7899999999 67888899974
No 27
>KOG2785|consensus
Probab=92.02 E-value=0.047 Score=50.24 Aligned_cols=36 Identities=25% Similarity=0.579 Sum_probs=32.5
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
-+||..|++.| .|....++|+.+++|++|+++++++
T Consensus 68 ~~~c~~c~k~~--~s~~a~~~hl~Sk~h~~~~~~~~r~ 103 (390)
T KOG2785|consen 68 VVYCEACNKSF--ASPKAHENHLKSKKHVENLSNHQRS 103 (390)
T ss_pred ceehHHhhccc--cChhhHHHHHHHhhcchhhhhhhcc
Confidence 37999999999 5788889999999999999999983
No 28
>KOG0796|consensus
Probab=91.97 E-value=0.23 Score=44.80 Aligned_cols=44 Identities=20% Similarity=0.417 Sum_probs=32.3
Q ss_pred cccCCcceec-cCChHHHHhhhchhhHH--HHHHHHHHHHHHHHHHH
Q psy6569 5 YCDYCDTYLT-HDSPSVRKTHCQGRKHK--DNVKFYYQKWMEEQAQN 48 (164)
Q Consensus 5 YCDYCdk~ft-hDS~SvRK~H~~GkKHk--~NVkryY~~~~eeqaq~ 48 (164)
.|+.|+.||. +|+.+=..+|++|+-|. ..++..|.++.++.+..
T Consensus 188 VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~~~~~ 234 (319)
T KOG0796|consen 188 VCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKEKAKR 234 (319)
T ss_pred HHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhHH
Confidence 5999999985 45555445699999999 45677777776655554
No 29
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=91.41 E-value=0.17 Score=34.32 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=20.5
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKD 32 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~ 32 (164)
.-||+-|...| | .+.+|+.+.+|++
T Consensus 5 ~GYCE~Cr~kf--d---~l~~Hi~s~~Hr~ 29 (49)
T smart00586 5 PGYCENCREKY--D---DLETHLLSEKHRR 29 (49)
T ss_pred CcccccHhHHH--h---hHHHHhccHHHHH
Confidence 34999999999 3 2678999999994
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=91.05 E-value=0.17 Score=26.71 Aligned_cols=21 Identities=33% Similarity=0.613 Sum_probs=16.7
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
|-|+.|++.| .+.+.+..|..
T Consensus 1 ~~C~~C~~~f--~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVF--KSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchh--CCHHHHHHHHH
Confidence 5799999999 45677788876
No 31
>PF14968 CCDC84: Coiled coil protein 84
Probab=88.46 E-value=0.54 Score=42.47 Aligned_cols=34 Identities=21% Similarity=0.595 Sum_probs=28.2
Q ss_pred cccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHH
Q psy6569 5 YCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWME 43 (164)
Q Consensus 5 YCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~e 43 (164)
||+.|.+.. |. ++.|.-+.+|+++++.++..|..
T Consensus 1 yC~vCr~~h--~~---gr~H~Y~~~Hq~~L~~~L~rf~~ 34 (336)
T PF14968_consen 1 YCEVCRRNH--DQ---GRRHVYSPKHQKSLSAFLSRFRS 34 (336)
T ss_pred CcchhhCcc--cc---cCCCccCHHHHHHHHHHHHHHHH
Confidence 899999875 43 79999999999999888877543
No 32
>KOG2837|consensus
Probab=87.89 E-value=0.19 Score=44.98 Aligned_cols=54 Identities=13% Similarity=0.357 Sum_probs=38.4
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKF-------YYQKWMEEQAQNLIDATTAAYK 58 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkr-------yY~~~~eeqaq~iiD~~tra~~ 58 (164)
||||.-|.+-+ + +.+.++-|+.+-.|++.... +.+.|..+.++++.+-..+++.
T Consensus 25 RwyCqmCQkQc-r-DeNGFkCH~~SeSHqRql~~~~~Np~~~~~~fs~eF~~dFl~LLr~~~g 85 (309)
T KOG2837|consen 25 RWYCQMCQKQC-R-DENGFKCHTMSESHQRQLLLFALNPGRSLERFSNEFEKDFLSLLRQRHG 85 (309)
T ss_pred HHHHHHHHHHh-c-cccccccccCCHHHHHHHHHHHhCcchhHHHhHHHHHHHHHHHHHHHhc
Confidence 79999999999 3 47889999999999976543 3445555555555555444443
No 33
>PTZ00448 hypothetical protein; Provisional
Probab=84.16 E-value=1 Score=41.50 Aligned_cols=37 Identities=24% Similarity=0.255 Sum_probs=33.1
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKW 41 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~ 41 (164)
.|-|--|+..| ++...++.|..+--|+-|+++....+
T Consensus 314 ~~tC~~C~v~F--~~~~~qR~H~KSDwHrYNLKRkl~gL 350 (373)
T PTZ00448 314 MLLCRKCNIQL--MDHNAFKQHYRSEWHIFNTKRNARKM 350 (373)
T ss_pred Ccccccccccc--CCHHHHHHHhhhhHHHHHHHHHhcCC
Confidence 37799999999 57888999999999999999999864
No 34
>PHA02768 hypothetical protein; Provisional
Probab=84.07 E-value=0.64 Score=32.19 Aligned_cols=22 Identities=23% Similarity=0.415 Sum_probs=15.6
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
.|.|+.|++.|+ ..+.++.|..
T Consensus 5 ~y~C~~CGK~Fs--~~~~L~~H~r 26 (55)
T PHA02768 5 GYECPICGEIYI--KRKSMITHLR 26 (55)
T ss_pred ccCcchhCCeec--cHHHHHHHHH
Confidence 689999999995 3444455543
No 35
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=83.16 E-value=0.85 Score=39.90 Aligned_cols=33 Identities=24% Similarity=0.509 Sum_probs=23.9
Q ss_pred cccCCcceecc-CChHHHHhhhchhhHHHHHHHH
Q psy6569 5 YCDYCDTYLTH-DSPSVRKTHCQGRKHKDNVKFY 37 (164)
Q Consensus 5 YCDYCdk~fth-DS~SvRK~H~~GkKHk~NVkry 37 (164)
-|+.|..||+. |+..-..+|.+|+-|..-+.-+
T Consensus 187 vC~iCgayLsrlDtdrrladHf~GklHlGy~~~R 220 (258)
T COG5200 187 VCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVR 220 (258)
T ss_pred hhhhhhhHHHhcchhhHHHHHhccchhhhHHHHH
Confidence 59999999864 4444445699999999654433
No 36
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=83.01 E-value=0.78 Score=28.59 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=15.0
Q ss_pred cccccCCcceeccC--ChHHHHhhh
Q psy6569 3 KYYCDYCDTYLTHD--SPSVRKTHC 25 (164)
Q Consensus 3 RYYCDYCdk~fthD--S~SvRK~H~ 25 (164)
+..|.||++.|..+ +.+..+.|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 56899999999764 666777787
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=80.19 E-value=1.2 Score=24.45 Aligned_cols=20 Identities=40% Similarity=0.687 Sum_probs=13.2
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
|-|++|+ |.+ . .+..++|+.
T Consensus 1 y~C~~C~-y~t-~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCS-YST-S-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS--EE-S-HHHHHHHHH
T ss_pred CCCCCCC-CcC-C-HHHHHHHHH
Confidence 6799999 665 3 667777864
No 38
>KOG4849|consensus
Probab=78.23 E-value=18 Score=34.09 Aligned_cols=31 Identities=19% Similarity=0.436 Sum_probs=18.0
Q ss_pred cccccCCc--ceeccCChHHHHhhhchhhHHHH
Q psy6569 3 KYYCDYCD--TYLTHDSPSVRKTHCQGRKHKDN 33 (164)
Q Consensus 3 RYYCDYCd--k~fthDS~SvRK~H~~GkKHk~N 33 (164)
|.||-|-+ .|.|-|....-.-|.+|.....-
T Consensus 79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~d 111 (498)
T KOG4849|consen 79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFAD 111 (498)
T ss_pred ceEEEEecceeEEeccHHHHHHHHhhhHHHHhh
Confidence 45676665 47765544443338788775433
No 39
>KOG4722|consensus
Probab=77.57 E-value=1.5 Score=42.10 Aligned_cols=34 Identities=26% Similarity=0.518 Sum_probs=27.8
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYY 38 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY 38 (164)
+..|..|++.| .|--+.-.|..|++|+++|....
T Consensus 493 kkqcslcnvli--ssevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 493 KKQCSLCNVLI--SSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhccchhhhhh--hhhhhhhhhhcchhHHHHHHHHh
Confidence 45799999999 45566667999999999987765
No 40
>smart00597 ZnF_TTF zinc finger in transposases and transcription factors.
Probab=77.56 E-value=1.4 Score=32.69 Aligned_cols=32 Identities=25% Similarity=0.553 Sum_probs=21.7
Q ss_pred cccccCCcceec---cCCh-------------HHHHhhhchhhHHHHH
Q psy6569 3 KYYCDYCDTYLT---HDSP-------------SVRKTHCQGRKHKDNV 34 (164)
Q Consensus 3 RYYCDYCdk~ft---hDS~-------------SvRK~H~~GkKHk~NV 34 (164)
+-||-||..|-. ..+. +.++.|+.+..|..+.
T Consensus 25 ~~fC~~C~lF~~~~~~~~~~f~~~Gf~nwk~~~~l~~H~~s~~H~~a~ 72 (90)
T smart00597 25 KAFCKACYLFRPGRDGDSDLFVTEGFCSWNVERILKQHEVSKRHRNAF 72 (90)
T ss_pred cEEEEEEEeeccCCCCCcCcccccCcCcchhhhhHHhhcCCHHHHhHH
Confidence 469999999820 1111 1278899999999776
No 41
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=77.54 E-value=1.2 Score=25.63 Aligned_cols=12 Identities=33% Similarity=1.027 Sum_probs=10.5
Q ss_pred cccccCCcceec
Q psy6569 3 KYYCDYCDTYLT 14 (164)
Q Consensus 3 RYYCDYCdk~ft 14 (164)
.|.|++|++.|+
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 589999999984
No 42
>KOG2785|consensus
Probab=74.46 E-value=2.4 Score=39.33 Aligned_cols=38 Identities=18% Similarity=0.407 Sum_probs=34.1
Q ss_pred CCcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 1 MPRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
|..|-|--|++.| |+....+.|-.+-=|+-|++|...+
T Consensus 1 st~ftC~tC~v~F--~~ad~Qr~HyKSdWHRYNLKRkVA~ 38 (390)
T KOG2785|consen 1 STGFTCNTCNVEF--DDADEQRAHYKSDWHRYNLKRKVAS 38 (390)
T ss_pred CCcceeeceeeee--ccHHHHHHHhhhhHHHhhHHhHhhc
Confidence 5679999999999 6788889999999999999999864
No 43
>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=74.37 E-value=2.1 Score=28.08 Aligned_cols=22 Identities=32% Similarity=0.754 Sum_probs=16.6
Q ss_pred cccccCCcceeccCChHHHHhhhch
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQG 27 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~G 27 (164)
.|-|.||++.| +.+.+..|..-
T Consensus 2 ~f~CP~C~~~~---~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGKGF---SESSLVEHCED 23 (54)
T ss_pred CcCCCCCCCcc---CHHHHHHHHHh
Confidence 58899999976 35667778654
No 44
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=71.49 E-value=1.8 Score=28.07 Aligned_cols=25 Identities=28% Similarity=0.561 Sum_probs=16.8
Q ss_pred cccccCCcceeccCC---hHHHHhhhch
Q psy6569 3 KYYCDYCDTYLTHDS---PSVRKTHCQG 27 (164)
Q Consensus 3 RYYCDYCdk~fthDS---~SvRK~H~~G 27 (164)
+-.|.||++-|+.++ -+.++.|+..
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 467999999997553 3445555544
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=70.88 E-value=3.4 Score=23.86 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=14.7
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
.-|.+|++.| ..+.+..|+.
T Consensus 3 ~~C~~CgR~F---~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF---NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE---CHHHHHHHHH
Confidence 4699999999 3555677753
No 46
>KOG2505|consensus
Probab=68.52 E-value=4.2 Score=39.36 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=32.9
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
+.+|-.|++-| ++..+++.|...--|+-|+++.++.
T Consensus 66 ~~~CstCq~~F--~s~~eqr~HyksD~HR~N~Krkl~~ 101 (591)
T KOG2505|consen 66 SDQCSTCQIPF--GSRQEQREHYKSDWHRFNTKRKLRG 101 (591)
T ss_pred cccccccCCcc--ccHHHHHHHHHHHHHHHHHHHHhcC
Confidence 57899999999 7899999999999999999999863
No 47
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=66.26 E-value=1.9 Score=36.39 Aligned_cols=33 Identities=18% Similarity=0.407 Sum_probs=0.0
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKF 36 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkr 36 (164)
.|.|+.|+=+.. --..+|..|.+.+||..-++.
T Consensus 101 ey~CEICGN~~Y-~GrkaFekHF~E~rH~~Glrc 133 (196)
T PF11931_consen 101 EYKCEICGNQSY-KGRKAFEKHFQEWRHAYGLRC 133 (196)
T ss_dssp ----------------------------------
T ss_pred eeeeEeCCCcce-ecHHHHHHhcChhHHHccChh
Confidence 589999998875 568889999999999876553
No 48
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=66.22 E-value=3.2 Score=28.34 Aligned_cols=24 Identities=29% Similarity=0.675 Sum_probs=19.6
Q ss_pred ccccCCcceeccCChHHHHhhhchhh
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRK 29 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkK 29 (164)
+||-||++.+ ++.....+|+-|..
T Consensus 28 ~YC~~Cg~~Y--~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 28 NYCFWCGTKY--DDEEDLERNCPGPT 51 (55)
T ss_pred ceeeeeCCcc--CCHHHHHhCCCCCC
Confidence 7999999999 67777778887753
No 49
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=66.10 E-value=1.6 Score=29.49 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=9.1
Q ss_pred cccccCCcceecc
Q psy6569 3 KYYCDYCDTYLTH 15 (164)
Q Consensus 3 RYYCDYCdk~fth 15 (164)
+|-|.||++.++.
T Consensus 35 ~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 35 KLRCHYCERIITE 47 (52)
T ss_dssp EEEETTT--EEEH
T ss_pred EEEeeCCCCEecc
Confidence 5789999999954
No 50
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=64.81 E-value=4.9 Score=34.96 Aligned_cols=37 Identities=19% Similarity=0.478 Sum_probs=30.2
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
.+||..-...| +.+......|++|+|-+++++.|=..
T Consensus 79 ~LfCkLT~~~i-Nk~pe~V~rHv~GKRf~kaLek~ee~ 115 (244)
T PF05477_consen 79 KLFCKLTGRHI-NKSPEHVERHVNGKRFQKALEKYEEC 115 (244)
T ss_pred eeEEechHhHh-ccCHHHHHHHhhhHHHHHHHHHHHHH
Confidence 57888888999 46677779999999999888776554
No 51
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=63.56 E-value=12 Score=31.12 Aligned_cols=29 Identities=17% Similarity=0.481 Sum_probs=22.7
Q ss_pred ccccCCcceeccCChHHHHhhhchhhHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKHKDNV 34 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKHk~NV 34 (164)
|.|.+|+-... ......+|+.++.|++-+
T Consensus 1 F~Cs~CKfrtf--~~~ei~~HleS~~H~E~~ 29 (165)
T PF04988_consen 1 FTCSFCKFRTF--EEKEIEKHLESKFHKETL 29 (165)
T ss_pred Cccceeeeecc--cHHHHHHHHccchHHHHH
Confidence 67999997763 455668999999999654
No 52
>PF04746 DUF575: Protein of unknown function (DUF575); InterPro: IPR006835 This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Probab=61.81 E-value=3.5 Score=31.83 Aligned_cols=52 Identities=25% Similarity=0.388 Sum_probs=34.7
Q ss_pred ceeccCChHHHHh-hhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCC
Q psy6569 11 TYLTHDSPSVRKT-HCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPF 67 (164)
Q Consensus 11 k~fthDS~SvRK~-H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~~~p~ 67 (164)
-.|+.|-.++.|. |..|..|+.-|++|++++....+.+-.|+ -.|+.+.+||
T Consensus 48 p~f~SDV~~ivKvEk~~G~dhisrve~~Lk~~R~~i~~ed~~K-----VHGk~p~~pf 100 (101)
T PF04746_consen 48 PMFTSDVASIVKVEKTRGRDHISRVEEYLKSLRVTIEPEDLGK-----VHGKYPEDPF 100 (101)
T ss_pred CCCchHHHHHHHHHHhhCCCchHHHHHHHHHhcCCCCcccccc-----ccCcCCCCCC
Confidence 3455566666555 99999999988888887654433333332 3577777776
No 53
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=61.79 E-value=9 Score=32.64 Aligned_cols=30 Identities=27% Similarity=0.653 Sum_probs=17.9
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVK 35 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVk 35 (164)
||-|..|.|-| +. ..-++.|+. .||.+.|+
T Consensus 77 K~~C~lc~KlF-kg-~eFV~KHI~-nKH~e~ve 106 (214)
T PF04959_consen 77 KWRCPLCGKLF-KG-PEFVRKHIF-NKHPEKVE 106 (214)
T ss_dssp EEEE-SSS-EE-SS-HHHHHHHHH-HH-HHHHH
T ss_pred EECCCCCCccc-CC-hHHHHHHHh-hcCHHHHH
Confidence 79999999999 34 444566765 35655443
No 54
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=54.07 E-value=6.5 Score=30.14 Aligned_cols=18 Identities=33% Similarity=0.803 Sum_probs=13.0
Q ss_pred cccccCCcceeccCChHH
Q psy6569 3 KYYCDYCDTYLTHDSPSV 20 (164)
Q Consensus 3 RYYCDYCdk~fthDS~Sv 20 (164)
+-||.||+++-.|.-..+
T Consensus 8 ~tyCp~CkkhT~H~V~~~ 25 (94)
T COG1631 8 RTYCPYCKKHTIHKVERV 25 (94)
T ss_pred eecCcccccceeeeeeeh
Confidence 469999999976554443
No 55
>PF14881 Tubulin_3: Tubulin domain
Probab=49.23 E-value=9.8 Score=31.01 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=11.3
Q ss_pred CcccccCCcceec
Q psy6569 2 PKYYCDYCDTYLT 14 (164)
Q Consensus 2 PRYYCDYCdk~ft 14 (164)
-|||.||+..++-
T Consensus 9 vryWSDy~r~~yh 21 (180)
T PF14881_consen 9 VRYWSDYNRVHYH 21 (180)
T ss_pred CEECCCCCcceeC
Confidence 3899999999983
No 56
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=49.12 E-value=55 Score=23.74 Aligned_cols=23 Identities=26% Similarity=0.703 Sum_probs=14.8
Q ss_pred CcccccCCcceeccCChHHHHhhh
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHC 25 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~ 25 (164)
+.++|+-|+-.+. |.......|.
T Consensus 30 ~~~~C~~CGe~~~-~~e~~~~~~~ 52 (127)
T TIGR03830 30 PGWYCPACGEELL-DPEESKRNSA 52 (127)
T ss_pred eeeECCCCCCEEE-cHHHHHHHHH
Confidence 5689999998885 4344333333
No 57
>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=48.51 E-value=2.9 Score=28.51 Aligned_cols=16 Identities=25% Similarity=0.841 Sum_probs=9.4
Q ss_pred cccccCCcceeccCChH
Q psy6569 3 KYYCDYCDTYLTHDSPS 19 (164)
Q Consensus 3 RYYCDYCdk~fthDS~S 19 (164)
.+||..||+|+ |++..
T Consensus 29 ~~FC~dCD~fi-HE~LH 44 (51)
T PF07975_consen 29 NHFCIDCDVFI-HETLH 44 (51)
T ss_dssp --B-HHHHHTT-TTTS-
T ss_pred CccccCcChhh-hcccc
Confidence 46888888888 77653
No 58
>PF14376 Haem_bd: Haem-binding domain
Probab=48.25 E-value=13 Score=29.02 Aligned_cols=62 Identities=13% Similarity=0.260 Sum_probs=35.7
Q ss_pred cccCCcceecc----CC---h-HHHHhhh-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Q psy6569 5 YCDYCDTYLTH----DS---P-SVRKTHC-QGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFG 68 (164)
Q Consensus 5 YCDYCdk~fth----DS---~-SvRK~H~-~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~~~p~~ 68 (164)
-|.+|+..=|+ +. . -.-..|. .|++|. |+..+... .+..-+...+++....+.|+.+..-|.
T Consensus 43 ~CydCHSn~T~~PwYa~i~p~s~l~~~dI~~Gr~~l-Nfs~~~~~-~~~~~~~~l~~i~~~I~~g~MP~~~Y~ 113 (137)
T PF14376_consen 43 SCYDCHSNNTRYPWYANIAPASWLMEKDIKEGRRHL-NFSEWGSY-SKRKQEAKLAKIEEVIEDGEMPPPSYT 113 (137)
T ss_pred cccccCCCCCCCccceecCchHHHHHHHHHHHHHHh-Ccchhhhc-CcccCHHHHHHHHHHHHcCCCChHHHh
Confidence 49999864321 00 1 1124465 777777 77766554 222223336777778888888765443
No 59
>PF15384 DUF4610: Domain of unknown function (DUF4610)
Probab=47.25 E-value=23 Score=30.28 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=23.5
Q ss_pred ceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Q psy6569 11 TYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGK 61 (164)
Q Consensus 11 k~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~ 61 (164)
+++| |-..+|+.|..-- .+..+.+.+.-..++++.-+...|+++|.
T Consensus 34 i~vT-Dg~dvW~t~~t~d----sL~~~k~~~~L~~~Edy~~rfR~Ac~~~~ 79 (197)
T PF15384_consen 34 IYVT-DGADVWSTCFTPD----SLAALKARFGLSSAEDYFSRFRAACEQQA 79 (197)
T ss_pred EEec-ccHHhhhhccCHH----HHHHHHhhcccchHHHHHHHHHHHhhcCe
Confidence 5576 7888999877532 22233333333333444444444555544
No 60
>KOG4849|consensus
Probab=44.21 E-value=2.7e+02 Score=26.55 Aligned_cols=10 Identities=50% Similarity=0.777 Sum_probs=6.1
Q ss_pred CCCCCCCCCC
Q psy6569 152 MRPPMMQDHP 161 (164)
Q Consensus 152 ~~~~~~~~~~ 161 (164)
||||+...++
T Consensus 338 ~~pPyn~~~~ 347 (498)
T KOG4849|consen 338 MRPPYNGLPP 347 (498)
T ss_pred CCCCCCCCCc
Confidence 6777655443
No 61
>KOG3792|consensus
Probab=43.99 E-value=4.4 Score=40.58 Aligned_cols=32 Identities=31% Similarity=0.793 Sum_probs=25.7
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVK 35 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVk 35 (164)
-+|.|+.||+-| +| +....-|++|+||.-..+
T Consensus 358 ~~f~cKlcdckf-~d-~nak~mhl~grRhrLQYk 389 (816)
T KOG3792|consen 358 LRFHCKLCDCKF-ND-PNAKEMHLKGRRHRLQYK 389 (816)
T ss_pred HhhhhhhhcCCC-CC-cchHHhhhhcccccceec
Confidence 379999999999 35 555567999999996655
No 62
>KOG4167|consensus
Probab=43.53 E-value=20 Score=36.45 Aligned_cols=22 Identities=18% Similarity=0.392 Sum_probs=18.2
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
-|-|..|+|-| +...+|+.|-.
T Consensus 792 iFpCreC~kvF--~KiKSrNAHMK 813 (907)
T KOG4167|consen 792 IFPCRECGKVF--FKIKSRNAHMK 813 (907)
T ss_pred eeehHHHHHHH--HHHhhhhHHHH
Confidence 36799999999 67888898874
No 63
>PHA00732 hypothetical protein
Probab=43.37 E-value=16 Score=26.30 Aligned_cols=21 Identities=19% Similarity=0.395 Sum_probs=16.5
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
|-|+.|++.|+ +.+..+.|..
T Consensus 2 y~C~~Cgk~F~--s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTV--TLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccC--CHHHHHHHhh
Confidence 67999999994 5666788865
No 64
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=42.50 E-value=10 Score=23.22 Aligned_cols=12 Identities=42% Similarity=1.021 Sum_probs=10.8
Q ss_pred cccccCCcceec
Q psy6569 3 KYYCDYCDTYLT 14 (164)
Q Consensus 3 RYYCDYCdk~ft 14 (164)
+|+|.-|+++|-
T Consensus 16 ~~~C~~C~v~lC 27 (32)
T PF13842_consen 16 RYMCSKCDVPLC 27 (32)
T ss_pred EEEccCCCCccc
Confidence 799999999984
No 65
>KOG2482|consensus
Probab=41.56 E-value=9.2 Score=35.69 Aligned_cols=35 Identities=23% Similarity=0.544 Sum_probs=26.4
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHH--HHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDN--VKFYYQ 39 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~N--VkryY~ 39 (164)
++-|-||.|-| +|... .|.|-+-++|++- ..++|+
T Consensus 195 r~~CLyCekif-rdknt-LkeHMrkK~HrrinPknreYD 231 (423)
T KOG2482|consen 195 RLRCLYCEKIF-RDKNT-LKEHMRKKRHRRINPKNREYD 231 (423)
T ss_pred hheeeeecccc-CCcHH-HHHHHHhccCcccCCCccccc
Confidence 57899999999 46555 6999999999852 334444
No 66
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=41.40 E-value=31 Score=26.76 Aligned_cols=27 Identities=7% Similarity=0.245 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHc
Q psy6569 33 NVKFYYQKWMEEQAQNLIDATTAAYKA 59 (164)
Q Consensus 33 NVkryY~~~~eeqaq~iiD~~tra~~~ 59 (164)
.|..|.++++++......|.+.+.|.+
T Consensus 106 si~~yidNIL~~Hle~~~eeI~~l~~~ 132 (136)
T PF11888_consen 106 SISGYIDNILRHHLEEYREEINELYEK 132 (136)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888899888888888888777765
No 67
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=41.32 E-value=11 Score=34.67 Aligned_cols=50 Identities=16% Similarity=0.359 Sum_probs=28.3
Q ss_pred cccccCCccee------------ccCChHHHHh--hhchhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYL------------THDSPSVRKT--HCQGRKHKDNVKFYYQKWMEEQAQNLIDA 52 (164)
Q Consensus 3 RYYCDYCdk~f------------thDS~SvRK~--H~~GkKHk~NVkryY~~~~eeqaq~iiD~ 52 (164)
||||..|+.-+ .|.+....+- -+.+..|..+.+.-|..+.++.++-.+|.
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pHFAHk~l~~C~~~~EnES~~HL~~Kr~Lyqwlk~q~~~VelE~ 88 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPHFAHKSLKACAFFNENESEEHLKGKRQLYQWLKRQGCKVELEP 88 (342)
T ss_pred ccccCCCCCeeeeecCccccchhhhhhhhhccccCCCCCHHHHHhHHHHHHHHHhcCCceeeec
Confidence 68999999644 3333222111 13566777777777776666534433333
No 68
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=40.37 E-value=4.7 Score=25.93 Aligned_cols=18 Identities=44% Similarity=0.848 Sum_probs=13.0
Q ss_pred ccCCcceeccCChHHHHhh
Q psy6569 6 CDYCDTYLTHDSPSVRKTH 24 (164)
Q Consensus 6 CDYCdk~fthDS~SvRK~H 24 (164)
||||+.-|+ +.+-+.|.+
T Consensus 1 Cd~CG~~I~-~eP~~~k~~ 18 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVVKIG 18 (37)
T ss_pred CCccCCccc-CCEEEEEEC
Confidence 999999995 555554543
No 69
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=40.30 E-value=39 Score=25.35 Aligned_cols=41 Identities=22% Similarity=0.331 Sum_probs=27.8
Q ss_pred HHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 20 VRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 20 vRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
.+++|.+-..|. --||++...+.+++...+...+|++|+++
T Consensus 47 ~~~~~~Nvl~Hi---~Gyfk~~ls~~EK~~~~~~i~~yr~g~i~ 87 (117)
T PF08349_consen 47 TRGSHINVLQHI---FGYFKKKLSSEEKQHFLDLIEDYREGKIP 87 (117)
T ss_pred CchhHHHHHHHH---HHHHHHhCCHHHHHHHHHHHHHHHcCCcc
Confidence 345566655555 55666666666777777778888888876
No 70
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=39.76 E-value=5.3 Score=28.63 Aligned_cols=25 Identities=36% Similarity=0.955 Sum_probs=17.3
Q ss_pred CcccccCCcceeccCChHHHHhhhch
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQG 27 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~G 27 (164)
|||||.-|..|+|+. -+.|+--..|
T Consensus 29 PR~~Ck~C~rywT~G-G~lRnVPvgg 53 (63)
T PF02701_consen 29 PRYFCKSCRRYWTHG-GTLRNVPVGG 53 (63)
T ss_pred cchhhHHHHHHHHhc-ceecCCccCC
Confidence 799999999999853 4444443333
No 71
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=39.66 E-value=14 Score=28.56 Aligned_cols=21 Identities=33% Similarity=0.548 Sum_probs=13.7
Q ss_pred cccCCc--ceeccCChHHHHhhhc
Q psy6569 5 YCDYCD--TYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 5 YCDYCd--k~fthDS~SvRK~H~~ 26 (164)
+|.||. +||. =.-|++-.|++
T Consensus 27 lCp~C~~~~wl~-lKnSsY~~Hl~ 49 (124)
T PF14616_consen 27 LCPYCPGGNWLK-LKNSSYWYHLQ 49 (124)
T ss_pred ECCCCCCCcEee-ecccchhhhhh
Confidence 799999 9983 22344456653
No 72
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=38.85 E-value=14 Score=32.07 Aligned_cols=35 Identities=26% Similarity=0.431 Sum_probs=23.0
Q ss_pred ccccCCcceeccCChHHHHh---hh-chhhHHHHHHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKT---HC-QGRKHKDNVKFYYQ 39 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~---H~-~GkKHk~NVkryY~ 39 (164)
|||-.|...|+..+. +-+. |. +-.-|.+||-++..
T Consensus 22 efC~fC~~~f~~~sK-~~kks~fhvsNKlIHlrNVLrrll 60 (225)
T PHA03074 22 EFCIFCESVFQTSSK-VQKKSNFHVSNKLIHLRNVLRRLL 60 (225)
T ss_pred EEeecHHHHHhhhhh-hhhhcccccccceeeHHHHHHHHH
Confidence 789999999964433 3233 55 34458888777664
No 73
>PHA00733 hypothetical protein
Probab=38.23 E-value=21 Score=27.65 Aligned_cols=22 Identities=27% Similarity=0.474 Sum_probs=17.1
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
.|-|+.|++.| .+.+.++.|..
T Consensus 73 Py~C~~Cgk~F--ss~s~L~~H~r 94 (128)
T PHA00733 73 PYVCPLCLMPF--SSSVSLKQHIR 94 (128)
T ss_pred CccCCCCCCcC--CCHHHHHHHHh
Confidence 47899999999 46666777765
No 74
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=36.46 E-value=94 Score=25.25 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=15.9
Q ss_pred cccCCcceeccCChHHHHh-hhchhhHH
Q psy6569 5 YCDYCDTYLTHDSPSVRKT-HCQGRKHK 31 (164)
Q Consensus 5 YCDYCdk~fthDS~SvRK~-H~~GkKHk 31 (164)
||.|.|.-= +.++.-||+ |++-+|..
T Consensus 23 YciYFD~KR-R~dPdFRkkLr~rr~k~~ 49 (148)
T TIGR00985 23 YAIYFDYKR-RNDPDFRKKLRRRRKKQA 49 (148)
T ss_pred HHHhhhhhh-ccCHHHHHHHHHHHHHHH
Confidence 899998775 345665544 55554433
No 75
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=35.08 E-value=12 Score=28.03 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=14.4
Q ss_pred cccccCCcceeccCChHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVR 21 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvR 21 (164)
+-||.+|++.-.|.-..++
T Consensus 9 ~tyC~~C~kHt~HkV~qyK 27 (84)
T PTZ00157 9 KTYCKKCGKHTSHKVSQYK 27 (84)
T ss_pred cccCcCCCCCccEEEEEec
Confidence 5699999999877655543
No 76
>PF14369 zf-RING_3: zinc-finger
Probab=34.52 E-value=19 Score=22.43 Aligned_cols=12 Identities=25% Similarity=1.248 Sum_probs=10.5
Q ss_pred cccccCCcceec
Q psy6569 3 KYYCDYCDTYLT 14 (164)
Q Consensus 3 RYYCDYCdk~ft 14 (164)
+|||--|++++.
T Consensus 2 ~ywCh~C~~~V~ 13 (35)
T PF14369_consen 2 RYWCHQCNRFVR 13 (35)
T ss_pred CEeCccCCCEeE
Confidence 799999998884
No 77
>KOG4594|consensus
Probab=34.17 E-value=1.8e+02 Score=26.86 Aligned_cols=13 Identities=46% Similarity=0.853 Sum_probs=7.7
Q ss_pred CCCCCCCCCCCCC
Q psy6569 99 GPPPGMMPGMMPP 111 (164)
Q Consensus 99 ~p~~~~~p~~~~~ 111 (164)
.++++.+||.-|+
T Consensus 141 ~~Ppg~~pG~qPl 153 (354)
T KOG4594|consen 141 MQPPGGVPGSQPL 153 (354)
T ss_pred CCCCCCCCCCCcc
Confidence 4556666666444
No 78
>KOG2893|consensus
Probab=34.05 E-value=3.7e+02 Score=24.52 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=13.5
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
-|.|..|+|.|. |--.+.-|+-
T Consensus 34 hfkchichkkl~--sgpglsihcm 55 (341)
T KOG2893|consen 34 HFKCHICHKKLF--SGPGLSIHCM 55 (341)
T ss_pred cceeeeehhhhc--cCCCceeehh
Confidence 478999998874 2222344553
No 79
>PHA00616 hypothetical protein
Probab=33.62 E-value=17 Score=24.11 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=16.4
Q ss_pred ccccCCcceeccCChHHHHhhh
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHC 25 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~ 25 (164)
|-|.-|++.|. ..+..+.|+
T Consensus 2 YqC~~CG~~F~--~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFR--KKKEVIEHL 21 (44)
T ss_pred CccchhhHHHh--hHHHHHHHH
Confidence 78999999994 566678888
No 80
>KOG3576|consensus
Probab=33.25 E-value=15 Score=32.30 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=10.7
Q ss_pred cccccCCcceeccCChHHHHhhh
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHC 25 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~ 25 (164)
||.|-+|++-| ||+.. .|.|.
T Consensus 145 r~lct~cgkgf-ndtfd-lkrh~ 165 (267)
T KOG3576|consen 145 RHLCTFCGKGF-NDTFD-LKRHT 165 (267)
T ss_pred HHHHhhccCcc-cchhh-hhhhh
Confidence 45566666665 45443 24443
No 81
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=32.80 E-value=14 Score=28.11 Aligned_cols=18 Identities=39% Similarity=0.903 Sum_probs=13.9
Q ss_pred cccccCCcceeccCChHH
Q psy6569 3 KYYCDYCDTYLTHDSPSV 20 (164)
Q Consensus 3 RYYCDYCdk~fthDS~Sv 20 (164)
+-||.+|++.-.|.-..+
T Consensus 8 ~tyCp~CkkHt~HkV~qy 25 (92)
T PRK05767 8 RTYCPYCKTHTEHEVEKV 25 (92)
T ss_pred cccCcCCCCcccEEEEEE
Confidence 569999999987665444
No 82
>PRK10167 hypothetical protein; Provisional
Probab=32.01 E-value=52 Score=27.04 Aligned_cols=42 Identities=14% Similarity=0.306 Sum_probs=27.8
Q ss_pred HHHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 19 SVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 19 SvRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
..+++|.+=..|. .-||++.....+++..-+...+|++|+++
T Consensus 87 ~t~~~~~NvL~Hi---~GYFKk~Ls~~EKq~l~~lI~~Yr~g~vp 128 (169)
T PRK10167 87 ANVRDHTNVLMHV---QGYFRPHIDSTERQQLAALIDSYRRGEQP 128 (169)
T ss_pred CCcchhHHHHHHH---HHHHHhhCCHHHHHHHHHHHHHHHcCCCC
Confidence 3456666666665 56666665566655566667788888887
No 83
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=31.53 E-value=26 Score=31.51 Aligned_cols=22 Identities=27% Similarity=0.656 Sum_probs=18.0
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
-|.||||=+|+ ++...+..|..
T Consensus 48 lyiCe~Clky~--~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYM--RKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchh--CCHHHHHHHHH
Confidence 38899999999 57777788865
No 84
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=31.49 E-value=23 Score=22.44 Aligned_cols=11 Identities=36% Similarity=1.210 Sum_probs=8.5
Q ss_pred cccccCCccee
Q psy6569 3 KYYCDYCDTYL 13 (164)
Q Consensus 3 RYYCDYCdk~f 13 (164)
.-||++|++.|
T Consensus 11 ~~~C~~C~~~i 21 (53)
T PF00130_consen 11 PTYCDVCGKFI 21 (53)
T ss_dssp TEB-TTSSSBE
T ss_pred CCCCcccCccc
Confidence 35899999999
No 85
>KOG3792|consensus
Probab=31.23 E-value=19 Score=36.22 Aligned_cols=29 Identities=28% Similarity=0.682 Sum_probs=25.0
Q ss_pred ccccCCcceeccCChHHHHhhhchhhHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQGRKHKDNV 34 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~GkKHk~NV 34 (164)
.|||.|++.- ...+++..|+.+.||+.+.
T Consensus 194 ~~~kw~k~~a--~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 194 HYCKWCKISA--AGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred hhhHHHHHhc--cccHHHHHHHHHHHHHHhc
Confidence 4899999997 5777789999999999765
No 86
>KOG0545|consensus
Probab=30.48 E-value=30 Score=31.49 Aligned_cols=36 Identities=31% Similarity=0.647 Sum_probs=24.5
Q ss_pred cccCCcceeccCChHHHHhhhch--hhHHHHHHHHHHH
Q psy6569 5 YCDYCDTYLTHDSPSVRKTHCQG--RKHKDNVKFYYQK 40 (164)
Q Consensus 5 YCDYCdk~fthDS~SvRK~H~~G--kKHk~NVkryY~~ 40 (164)
+-.||.++|.....-.-..|++. ++|-.||+.||+.
T Consensus 233 llNy~QC~L~~~e~yevleh~seiL~~~~~nvKA~frR 270 (329)
T KOG0545|consen 233 LLNYCQCLLKKEEYYEVLEHCSEILRHHPGNVKAYFRR 270 (329)
T ss_pred HHhHHHHHhhHHHHHHHHHHHHHHHhcCCchHHHHHHH
Confidence 34588888854444444667755 5777899999864
No 87
>PF07909 DUF1663: Protein of unknown function (DUF1663); InterPro: IPR012457 The members of this family are hypothetical proteins expressed by Trypanosoma cruzi, a eukaryotic parasite that causes Chagas, disease in humans. This region is found as multiple copies per protein.
Probab=30.29 E-value=57 Score=31.01 Aligned_cols=39 Identities=31% Similarity=0.528 Sum_probs=31.6
Q ss_pred HhhhchhhHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHcC
Q psy6569 22 KTHCQGRKHKDNVKFYYQKWMEEQAQ---------NLIDATTAAYKAG 60 (164)
Q Consensus 22 K~H~~GkKHk~NVkryY~~~~eeqaq---------~iiD~~tra~~~G 60 (164)
..|..|+|.+-||+++..+|.+-+.. ++|++..++|...
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (497)
T PF07909_consen 4 QRHAVGKKERVNVQRRVSSWRKLQLREAEHARSGREIIEAARAAYEDE 51 (497)
T ss_pred hhhhcchhhhhhHhhhhhhhHhhhhhhhccccchHHHHHHHHHhhccc
Confidence 56999999999999999998775543 4678888888864
No 88
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=29.50 E-value=94 Score=26.24 Aligned_cols=46 Identities=17% Similarity=0.283 Sum_probs=24.7
Q ss_pred ccccCCccee--ccCChHHHHhhh-----chhhH-----HHHHHHHHHHHHHHHHHHH
Q psy6569 4 YYCDYCDTYL--THDSPSVRKTHC-----QGRKH-----KDNVKFYYQKWMEEQAQNL 49 (164)
Q Consensus 4 YYCDYCdk~f--thDS~SvRK~H~-----~GkKH-----k~NVkryY~~~~eeqaq~i 49 (164)
-||-|||-++ .-|+...|+.-. .|+.. -+.++++.++..+-|+|-+
T Consensus 20 ~FilyCNP~vP~~tdT~~Lr~aFr~pPkS~Gk~Fs~~~Lf~LI~k~~~keikTW~~La 77 (175)
T PF09441_consen 20 AFILYCNPAVPLDTDTSELREAFRSPPKSDGKSFSTFTLFELIRKLESKEIKTWAQLA 77 (175)
T ss_pred eeeeecCCCCCCCCCHHHHHHHhcCCCCcCCccchHHHHHHHHHHHhhhhHhHHHHHH
Confidence 3789999998 225555555532 22221 2345555555555555444
No 89
>KOG4252|consensus
Probab=28.52 E-value=76 Score=27.77 Aligned_cols=57 Identities=25% Similarity=0.245 Sum_probs=35.8
Q ss_pred cCCcceeccCChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 7 DYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 7 DYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
.||+--||.|-....-.-..-++-+-+.++-...+-+..-|+..|++|.||-.|..+
T Consensus 39 ryCkgifTkdykktIgvdflerqi~v~~Edvr~mlWdtagqeEfDaItkAyyrgaqa 95 (246)
T KOG4252|consen 39 RYCKGIFTKDYKKTIGVDFLERQIKVLIEDVRSMLWDTAGQEEFDAITKAYYRGAQA 95 (246)
T ss_pred HHhccccccccccccchhhhhHHHHhhHHHHHHHHHHhccchhHHHHHHHHhccccc
Confidence 377666666644433334444455555555555555666777789999998887755
No 90
>KOG0132|consensus
Probab=28.42 E-value=3.6e+02 Score=27.96 Aligned_cols=10 Identities=30% Similarity=0.118 Sum_probs=4.0
Q ss_pred CCCCCCCCCC
Q psy6569 130 MMGGMGGMGP 139 (164)
Q Consensus 130 ~~~~~~~~~~ 139 (164)
.++|-+.|+|
T Consensus 632 ~~pPpg~~pP 641 (894)
T KOG0132|consen 632 YPPPPGFMPP 641 (894)
T ss_pred CCCCcccCCC
Confidence 3333344443
No 91
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=28.29 E-value=51 Score=20.96 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=18.9
Q ss_pred ccccCCcceeccCChHHHHhhh
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHC 25 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~ 25 (164)
-.|..|+..++.++....+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~ 35 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHK 35 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHH
Confidence 4799999999888888888885
No 92
>PTZ00064 histone acetyltransferase; Provisional
Probab=28.15 E-value=28 Score=33.84 Aligned_cols=22 Identities=18% Similarity=0.467 Sum_probs=18.2
Q ss_pred ccccCCcceeccCChHHHHhhhch
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQG 27 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~G 27 (164)
|.|+||=+|| ++...+..|...
T Consensus 281 YICEfCLkY~--~s~~~l~rH~~~ 302 (552)
T PTZ00064 281 HFCEYCLDFF--CFEDELIRHLSR 302 (552)
T ss_pred EEccchhhhh--CCHHHHHHHHhc
Confidence 8899999999 577778888753
No 93
>KOG3960|consensus
Probab=28.07 E-value=1.4e+02 Score=26.98 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=27.8
Q ss_pred ccccCCcceeccCChHHHHh-hhchhhHHHHHHHHHHHHHH
Q psy6569 4 YYCDYCDTYLTHDSPSVRKT-HCQGRKHKDNVKFYYQKWME 43 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~-H~~GkKHk~NVkryY~~~~e 43 (164)
+=|+.|+++.+ +.--||. -.+-+|-.+.|.+-|+.+++
T Consensus 104 wackackrks~--svDRRKAATMRERRRLkKVNEAFE~LKR 142 (284)
T KOG3960|consen 104 WACKACKRKST--SVDRRKAATMRERRRLKKVNEAFETLKR 142 (284)
T ss_pred Hhhhhcccccc--chhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45999999874 4554555 55778888888888877665
No 94
>KOG1365|consensus
Probab=27.86 E-value=1.4e+02 Score=28.68 Aligned_cols=38 Identities=18% Similarity=0.222 Sum_probs=30.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 26 QGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 26 ~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
.=+||++|+-++|=++.+..++++.....|....+.|+
T Consensus 222 aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~ 259 (508)
T KOG1365|consen 222 ALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIP 259 (508)
T ss_pred HHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccC
Confidence 34689999999999999999999877777766666665
No 95
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=27.79 E-value=26 Score=21.28 Aligned_cols=12 Identities=25% Similarity=0.850 Sum_probs=10.6
Q ss_pred cccccCCcceec
Q psy6569 3 KYYCDYCDTYLT 14 (164)
Q Consensus 3 RYYCDYCdk~ft 14 (164)
.|||..|+..|-
T Consensus 15 ~~~C~~C~~~~C 26 (42)
T PF00643_consen 15 SLFCEDCNEPLC 26 (42)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEecCCCCccC
Confidence 689999999986
No 96
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=26.98 E-value=84 Score=26.49 Aligned_cols=12 Identities=17% Similarity=0.758 Sum_probs=10.2
Q ss_pred cccccCCcceec
Q psy6569 3 KYYCDYCDTYLT 14 (164)
Q Consensus 3 RYYCDYCdk~ft 14 (164)
+.-|+.|..||+
T Consensus 6 ~rKCKvCg~~F~ 17 (189)
T PF05766_consen 6 RRKCKVCGEWFV 17 (189)
T ss_pred CCcCcccCCccc
Confidence 457999999995
No 97
>PLN03239 histone acetyltransferase; Provisional
Probab=26.76 E-value=26 Score=32.22 Aligned_cols=22 Identities=14% Similarity=0.267 Sum_probs=16.4
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
-|.|+||=+|+ ++.+....|..
T Consensus 106 lYiCE~Clky~--~~~~~l~~H~~ 127 (351)
T PLN03239 106 LYVCEFSFGFF--ARKSELLRFQA 127 (351)
T ss_pred EEEeccchhhh--cCHHHHHHHHH
Confidence 37899999999 46666666653
No 98
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.69 E-value=34 Score=24.55 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=14.8
Q ss_pred ccccCCcceeccCChHHHHhhhc
Q psy6569 4 YYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 4 YYCDYCdk~fthDS~SvRK~H~~ 26 (164)
+-|.-|+..| +|+.+ +..|.+
T Consensus 18 lrCPRC~~~F-R~~K~-Y~RHVN 38 (65)
T COG4049 18 LRCPRCGMVF-RRRKD-YIRHVN 38 (65)
T ss_pred eeCCchhHHH-HHhHH-HHHHhh
Confidence 4699999999 56655 355553
No 99
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=26.35 E-value=29 Score=32.82 Aligned_cols=22 Identities=18% Similarity=0.753 Sum_probs=18.1
Q ss_pred cccccCCcceeccCChHHHHhhhc
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQ 26 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~ 26 (164)
-|.|+||=+|| .+...+..|..
T Consensus 198 lyiCe~Cl~y~--~~~~~~~~H~~ 219 (450)
T PLN00104 198 LYFCEFCLKFM--KRKEQLQRHMK 219 (450)
T ss_pred EEEchhhhhhh--cCHHHHHHHHh
Confidence 38899999999 46777888875
No 100
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=25.27 E-value=32 Score=22.25 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=8.5
Q ss_pred ccccCCccee
Q psy6569 4 YYCDYCDTYL 13 (164)
Q Consensus 4 YYCDYCdk~f 13 (164)
-.|.||++.|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 5799999876
No 101
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.22 E-value=50 Score=25.77 Aligned_cols=37 Identities=22% Similarity=0.257 Sum_probs=23.1
Q ss_pred CcccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 2 PRYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
.||-|.-|++.|+..+-+.+.. .-.+=+..+..+|..
T Consensus 52 qRyrC~~C~~tf~~~~~~~~~~--~~~~~~~~~~~~~~~ 88 (129)
T COG3677 52 QRYKCKSCGSTFTVETGSPLSK--ALYKIKLQAVTLYML 88 (129)
T ss_pred cccccCCcCcceeeeccCcccc--cchHHHHHHHHHHHc
Confidence 4899999999998666655333 223334444555543
No 102
>KOG3623|consensus
Probab=25.06 E-value=20 Score=36.65 Aligned_cols=20 Identities=35% Similarity=0.660 Sum_probs=13.7
Q ss_pred cccccCCcceeccCChHHHHhh
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTH 24 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H 24 (164)
-|-||-|||.|.. .|++..|
T Consensus 894 myaCDqCDK~FqK--qSSLaRH 913 (1007)
T KOG3623|consen 894 MYACDQCDKAFQK--QSSLARH 913 (1007)
T ss_pred cchHHHHHHHHHh--hHHHHHh
Confidence 4889999999953 3334444
No 103
>KOG2554|consensus
Probab=24.35 E-value=1.1e+02 Score=28.86 Aligned_cols=38 Identities=24% Similarity=0.210 Sum_probs=24.4
Q ss_pred cccccC--CcceeccCChHHHHhhhchhhHH-HHHHHHHHHH
Q psy6569 3 KYYCDY--CDTYLTHDSPSVRKTHCQGRKHK-DNVKFYYQKW 41 (164)
Q Consensus 3 RYYCDY--Cdk~fthDS~SvRK~H~~GkKHk-~NVkryY~~~ 41 (164)
-|.|+| |+.-+.+|+.+. ..-....+|. +|+..+|+.-
T Consensus 315 LydC~f~~e~~ew~~~~~sd-~~a~~~l~~t~~~L~~~~q~~ 355 (425)
T KOG2554|consen 315 LYDCDFHRENVEWRHDTESD-QIAPKILKITWENLVEHLQNG 355 (425)
T ss_pred EEecCCCCcccccccccccc-ccchhHHHHHHHHHHHHHHhH
Confidence 388999 998877777665 3333333333 6777777653
No 104
>COG3657 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.27 E-value=1.6e+02 Score=22.85 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Q psy6569 29 KHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIA 63 (164)
Q Consensus 29 KHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~~ 63 (164)
+-.+-+.+|++++.+..|+..|.+.....+.|...
T Consensus 7 ~~~d~F~~W~~kLkD~~Aka~I~~Rl~rl~~GN~G 41 (100)
T COG3657 7 KGTDTFSEWLKKLKDRRAKAKIAARLDRLALGNFG 41 (100)
T ss_pred cchHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCCc
Confidence 34567889999999999999999999998888754
No 105
>KOG0132|consensus
Probab=24.15 E-value=6.6e+02 Score=26.16 Aligned_cols=11 Identities=55% Similarity=0.960 Sum_probs=4.9
Q ss_pred CCCCCCCCCCC
Q psy6569 145 PMGPMGPMRPP 155 (164)
Q Consensus 145 ~~~~~~~~~~~ 155 (164)
+.|++-+|+|+
T Consensus 688 p~~~~~~m~P~ 698 (894)
T KOG0132|consen 688 PRGGMRHMPPP 698 (894)
T ss_pred CCCCCCCCCCC
Confidence 34444445544
No 106
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=23.57 E-value=16 Score=28.32 Aligned_cols=29 Identities=14% Similarity=0.274 Sum_probs=19.2
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDN 33 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~N 33 (164)
.+.|-||...+.. ...-.+|..-+.+-..
T Consensus 24 ~~~C~YC~~~~~~--~~~~ieH~~Pk~~~~~ 52 (144)
T TIGR02646 24 GGLCAYCEREIEL--LGSHIEHFRPKGAYPP 52 (144)
T ss_pred CCCcCccCCCcCC--CCcceeeecccCCChh
Confidence 5789999998842 2334678877654333
No 107
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=22.81 E-value=1.3e+02 Score=26.31 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=29.3
Q ss_pred CChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Q psy6569 16 DSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKI 62 (164)
Q Consensus 16 DS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~iiD~~tra~~~G~~ 62 (164)
.+.+.|..-+.+..+. -..+|..+|.+++...+.|...+..++|+-
T Consensus 55 K~~~~Re~aL~~l~~~-l~~~~~~d~v~~~~~tL~~~~~k~lkkg~~ 100 (309)
T PF05004_consen 55 KSSSTREAALEALIRA-LSSRYLPDFVEDRRETLLDALLKSLKKGKS 100 (309)
T ss_pred cCHHHHHHHHHHHHHH-HHhcccHHHHHHHHHHHHHHHHHHhccCCH
Confidence 4455555555555555 334455566777777788888888887763
No 108
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=22.57 E-value=40 Score=21.07 Aligned_cols=11 Identities=36% Similarity=1.074 Sum_probs=9.4
Q ss_pred ccccCCcceecc
Q psy6569 4 YYCDYCDTYLTH 15 (164)
Q Consensus 4 YYCDYCdk~fth 15 (164)
..||.|+.|+ |
T Consensus 15 i~C~~C~~~~-H 25 (51)
T PF00628_consen 15 IQCDSCNRWY-H 25 (51)
T ss_dssp EEBSTTSCEE-E
T ss_pred EEcCCCChhh-C
Confidence 5799999998 5
No 109
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=22.36 E-value=1.4e+02 Score=25.17 Aligned_cols=34 Identities=9% Similarity=0.243 Sum_probs=27.9
Q ss_pred CChHHHHhhhchhhHHHHHHHHHHHHHHHHHHHH
Q psy6569 16 DSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNL 49 (164)
Q Consensus 16 DS~SvRK~H~~GkKHk~NVkryY~~~~eeqaq~i 49 (164)
++...+++-+....++++|..||..|.++.+.-|
T Consensus 115 k~~~eYkq~ieS~~cr~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 115 KTALEYKQSIESKICRKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566788899999999999999999887665554
No 110
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=22.32 E-value=21 Score=29.83 Aligned_cols=35 Identities=17% Similarity=0.410 Sum_probs=20.7
Q ss_pred cccccCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
+|||+-|+..+ |. ..+.-...|+.=+..+++||.+
T Consensus 120 ~wyc~~c~~~~-~e--~~f~~~d~~~~~~~~~~~f~~~ 154 (177)
T PRK13264 120 QWYCDECNHKV-HE--VEVQLTDIETDLPPVFAAFYAS 154 (177)
T ss_pred EEECCCCCCeE-EE--EEEEecChhhhhHHHHHHHhcC
Confidence 68999999888 32 1112233555555555666554
No 111
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=22.20 E-value=38 Score=24.90 Aligned_cols=11 Identities=45% Similarity=1.210 Sum_probs=10.3
Q ss_pred cccccCCccee
Q psy6569 3 KYYCDYCDTYL 13 (164)
Q Consensus 3 RYYCDYCdk~f 13 (164)
.|+|.+|+..+
T Consensus 4 ~Y~CRHCg~~I 14 (76)
T PF10955_consen 4 HYYCRHCGTKI 14 (76)
T ss_pred EEEecCCCCEE
Confidence 69999999998
No 113
>KOG4317|consensus
Probab=22.00 E-value=62 Score=30.06 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=23.8
Q ss_pred cccccCCcceeccCChHHHHhhh---chhhHHHHHHHHHHH
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHC---QGRKHKDNVKFYYQK 40 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~---~GkKHk~NVkryY~~ 40 (164)
+|-|.-||.-+. |...+++|- .-+.-++||+.-+.+
T Consensus 19 ~YtCPRCn~~YC--sl~CYr~h~~~CsE~FyrdqV~~eL~~ 57 (383)
T KOG4317|consen 19 EYTCPRCNLLYC--SLKCYRNHKHSCSEKFYRDQVKQELSG 57 (383)
T ss_pred cccCCCCCccce--eeeeecCCCccchHHHHHHHHHHHhhh
Confidence 688999998874 777788864 344455555444443
No 114
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=21.81 E-value=53 Score=26.93 Aligned_cols=13 Identities=15% Similarity=0.751 Sum_probs=9.9
Q ss_pred ccccCCcceeccC
Q psy6569 4 YYCDYCDTYLTHD 16 (164)
Q Consensus 4 YYCDYCdk~fthD 16 (164)
..|..|++||.+.
T Consensus 15 v~C~~c~kWFCNg 27 (152)
T PF09416_consen 15 VKCNTCNKWFCNG 27 (152)
T ss_dssp EEETTTTEEEES-
T ss_pred eEcCCCCcEeecC
Confidence 4688999999753
No 115
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=21.72 E-value=52 Score=21.95 Aligned_cols=13 Identities=23% Similarity=0.593 Sum_probs=10.0
Q ss_pred cccccCCcceecc
Q psy6569 3 KYYCDYCDTYLTH 15 (164)
Q Consensus 3 RYYCDYCdk~fth 15 (164)
+.-|.||+..|.+
T Consensus 36 ~v~C~~C~~~l~~ 48 (71)
T smart00238 36 EVKCFFCGGELDN 48 (71)
T ss_pred EEEeCCCCCCcCC
Confidence 4579999998843
No 116
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.53 E-value=1.9e+02 Score=18.71 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=5.2
Q ss_pred cccCCccee
Q psy6569 5 YCDYCDTYL 13 (164)
Q Consensus 5 YCDYCdk~f 13 (164)
-|..|+.-|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 599999999
No 117
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=21.25 E-value=68 Score=19.85 Aligned_cols=28 Identities=14% Similarity=0.190 Sum_probs=14.6
Q ss_pred cCCcceeccCChHHHHhhhchhhHHHHHHHHHHH
Q psy6569 7 DYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQK 40 (164)
Q Consensus 7 DYCdk~fthDS~SvRK~H~~GkKHk~NVkryY~~ 40 (164)
++|+.||. . ++ ........++.+..++.
T Consensus 4 ~~~~~wl~--~---~~-~~~~~~T~~~y~~~~~~ 31 (58)
T PF14659_consen 4 EFFEEWLE--E---YK-SNLKPSTYKNYKSIIKN 31 (58)
T ss_dssp HHHHHHHH--H---HT-CTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHH--H---hc-ccCCHHHHHHHHHHHHH
Confidence 56677772 1 12 34444555555555555
No 118
>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=20.97 E-value=53 Score=20.50 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=14.4
Q ss_pred cccccCCcceeccCChHHHHhhh
Q psy6569 3 KYYCDYCDTYLTHDSPSVRKTHC 25 (164)
Q Consensus 3 RYYCDYCdk~fthDS~SvRK~H~ 25 (164)
-+.|..|++.+. .+-+..|+
T Consensus 4 ~~~C~nC~R~v~---a~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVA---ASRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEE---GGGHHHHH
T ss_pred eEECCCCcCCcc---hhhhHHHH
Confidence 468999999993 55566776
No 119
>PF12548 DUF3740: Sulfatase protein; InterPro: IPR024609 This uncharacterised domain is found in the C-terminal region of extracellular sulphatase proteins.
Probab=20.30 E-value=1.3e+02 Score=24.25 Aligned_cols=34 Identities=15% Similarity=0.268 Sum_probs=23.5
Q ss_pred CCcceeccCChHHHHhhhchhhHH-HHHHHHHHHHH
Q psy6569 8 YCDTYLTHDSPSVRKTHCQGRKHK-DNVKFYYQKWM 42 (164)
Q Consensus 8 YCdk~fthDS~SvRK~H~~GkKHk-~NVkryY~~~~ 42 (164)
-|+.-|. ++..+||+|-.-.-|+ ++++..+.++.
T Consensus 92 nCs~~iY-~d~~aWk~hr~~ID~eIe~Lq~Ki~~LK 126 (145)
T PF12548_consen 92 NCSNVIY-QDPKAWKDHRLHIDHEIETLQDKIKNLK 126 (145)
T ss_pred eccHhhh-cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777775 5688899998777776 55555555543
No 120
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=20.15 E-value=2e+02 Score=21.27 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=21.5
Q ss_pred ceeccCChHHHHhhhchhh----------HHHHHHHHHHHHHHHHHHHH
Q psy6569 11 TYLTHDSPSVRKTHCQGRK----------HKDNVKFYYQKWMEEQAQNL 49 (164)
Q Consensus 11 k~fthDS~SvRK~H~~GkK----------Hk~NVkryY~~~~eeqaq~i 49 (164)
..|..||...|+.|+.=.. ..+.-+++|..+.+++++.+
T Consensus 32 p~l~~~tdeLW~~~i~rdFp~~~~~~~~~~~~~Wr~~Y~~~~~e~e~~~ 80 (109)
T PF06881_consen 32 PHLIEDTDELWKKLIKRDFPEESKRQKPKEPESWRELYEKLKKEREEKL 80 (109)
T ss_pred CCcchhhHHHHHHHHHhHCcChhhcccccccchHHHHHHHHHHHHHHHH
Confidence 3344456666666553222 22456677777766666655
Done!