Query 029213
Match_columns 197
No_of_seqs 145 out of 322
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:19:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3454 U1 snRNP-specific prot 99.9 5.6E-23 1.2E-27 170.4 10.6 59 1-59 1-59 (165)
2 PF06220 zf-U1: U1 zinc finger 99.8 5.7E-20 1.2E-24 119.7 2.9 38 1-38 1-38 (38)
3 KOG0150 Spliceosomal protein F 99.6 6.3E-16 1.4E-20 139.3 6.9 72 2-76 9-81 (336)
4 COG5136 U1 snRNP-specific prot 99.6 1.4E-15 3E-20 127.2 3.8 57 1-62 1-57 (188)
5 smart00451 ZnF_U1 U1-like zinc 99.1 5.3E-11 1.2E-15 73.5 2.6 35 1-37 1-35 (35)
6 KOG4727 U1-like Zn-finger prot 98.7 4E-08 8.6E-13 83.3 7.9 35 1-37 73-107 (193)
7 PF12171 zf-C2H2_jaz: Zinc-fin 98.5 4.6E-08 1E-12 58.3 2.3 27 3-31 1-27 (27)
8 KOG1924 RhoA GTPase effector D 98.3 2.4E-05 5.3E-10 78.7 15.4 19 103-121 542-560 (1102)
9 COG5188 PRP9 Splicing factor 3 98.1 2.5E-06 5.4E-11 79.5 4.5 61 2-65 237-298 (470)
10 PF12874 zf-met: Zinc-finger o 98.1 2.2E-06 4.8E-11 49.4 2.5 25 4-30 1-25 (25)
11 KOG2893 Zn finger protein [Gen 98.0 7.4E-05 1.6E-09 67.1 11.4 25 3-29 10-34 (341)
12 KOG3408 U1-like Zn-finger-cont 97.5 5.4E-05 1.2E-09 61.3 1.9 35 1-37 55-89 (129)
13 KOG0717 Molecular chaperone (D 97.5 9.4E-05 2E-09 70.8 3.6 40 4-45 293-332 (508)
14 COG5112 UFD2 U1-like Zn-finger 96.8 0.00051 1.1E-08 54.9 1.1 34 2-37 54-87 (126)
15 KOG1924 RhoA GTPase effector D 96.8 0.092 2E-06 53.9 16.8 9 5-13 438-446 (1102)
16 KOG0227 Splicing factor 3a, su 96.5 0.0018 3.9E-08 56.3 2.7 42 2-45 52-93 (222)
17 COG5246 PRP11 Splicing factor 95.8 0.0081 1.8E-07 52.1 3.3 34 2-37 52-85 (222)
18 PF04988 AKAP95: A-kinase anch 95.6 0.022 4.7E-07 48.2 5.0 41 4-45 92-132 (165)
19 PF14968 CCDC84: Coiled coil p 94.4 0.022 4.9E-07 52.6 1.9 38 3-41 58-100 (336)
20 PF13894 zf-C2H2_4: C2H2-type 94.4 0.033 7.2E-07 30.4 1.9 21 4-26 1-21 (24)
21 PF00096 zf-C2H2: Zinc finger, 94.0 0.046 1E-06 30.5 2.0 21 4-26 1-21 (23)
22 PF12756 zf-C2H2_2: C2H2 type 93.7 0.019 4.2E-07 41.0 0.1 30 3-34 50-79 (100)
23 PF13912 zf-C2H2_6: C2H2-type 93.3 0.067 1.5E-06 31.0 2.0 21 4-26 2-22 (27)
24 PF03194 LUC7: LUC7 N_terminus 93.0 0.15 3.2E-06 45.1 4.5 39 4-42 191-232 (254)
25 KOG3032 Uncharacterized conser 92.9 0.074 1.6E-06 47.6 2.5 33 3-38 35-67 (264)
26 KOG2384 Major histocompatibili 92.8 0.029 6.3E-07 49.1 -0.2 31 3-36 84-114 (223)
27 PF07535 zf-DBF: DBF zinc fing 92.1 0.091 2E-06 36.2 1.6 25 3-32 5-29 (49)
28 smart00586 ZnF_DBF Zinc finger 90.9 0.11 2.3E-06 36.0 1.0 25 3-32 5-29 (49)
29 PF14968 CCDC84: Coiled coil p 90.8 0.22 4.9E-06 46.1 3.2 35 5-44 1-35 (336)
30 smart00355 ZnF_C2H2 zinc finge 89.4 0.29 6.2E-06 26.6 1.8 21 4-26 1-21 (26)
31 KOG0796 Spliceosome subunit [R 88.3 0.68 1.5E-05 42.9 4.3 40 5-44 188-230 (319)
32 KOG2785 C2H2-type Zn-finger pr 87.7 0.21 4.6E-06 47.2 0.7 36 3-40 68-103 (390)
33 PF04988 AKAP95: A-kinase anch 83.6 2.1 4.5E-05 36.4 4.6 32 4-37 1-32 (165)
34 PF04959 ARS2: Arsenite-resist 83.2 2.3 5E-05 37.2 4.9 29 3-34 77-105 (214)
35 PTZ00448 hypothetical protein; 82.8 0.81 1.7E-05 43.2 2.1 38 3-42 314-351 (373)
36 PHA02768 hypothetical protein; 82.5 0.85 1.8E-05 32.2 1.6 21 3-25 5-25 (55)
37 PF02892 zf-BED: BED zinc fing 81.8 0.88 1.9E-05 29.2 1.4 23 3-25 16-40 (45)
38 KOG2505 Ankyrin repeat protein 80.6 0.94 2E-05 44.6 1.7 37 3-41 66-102 (591)
39 KOG2785 C2H2-type Zn-finger pr 79.7 2.1 4.5E-05 40.7 3.6 39 1-41 1-39 (390)
40 KOG2893 Zn finger protein [Gen 77.3 22 0.00047 32.7 9.2 31 3-36 34-64 (341)
41 PF13909 zf-H2C2_5: C2H2-type 77.0 1.9 4.2E-05 24.2 1.7 20 4-26 1-20 (24)
42 PF13465 zf-H2C2_2: Zinc-finge 75.2 1.5 3.3E-05 25.7 0.9 12 3-14 14-25 (26)
43 PF11931 DUF3449: Domain of un 75.0 0.94 2E-05 39.2 0.0 34 3-37 101-134 (196)
44 smart00597 ZnF_TTF zinc finger 73.5 2.2 4.7E-05 32.4 1.7 32 3-34 25-72 (90)
45 KOG4317 Predicted Zn-finger pr 72.7 2.8 6.1E-05 39.3 2.5 56 3-60 19-78 (383)
46 KOG3792 Transcription factor N 72.0 0.68 1.5E-05 47.1 -1.7 33 3-37 359-391 (816)
47 PF13913 zf-C2HC_2: zinc-finge 71.9 3.2 7E-05 24.4 1.8 20 4-26 3-22 (25)
48 KOG3623 Homeobox transcription 71.2 1.3 2.8E-05 45.6 -0.1 22 2-25 893-914 (1007)
49 KOG3960 Myogenic helix-loop-he 68.3 22 0.00048 32.5 7.1 71 4-76 104-183 (284)
50 KOG4722 Zn-finger protein [Gen 68.2 3.4 7.3E-05 40.4 2.0 34 3-38 493-526 (672)
51 PF02748 PyrI_C: Aspartate car 66.5 1.7 3.6E-05 30.1 -0.3 14 3-16 35-48 (52)
52 smart00614 ZnF_BED BED zinc fi 65.8 2.8 6.2E-05 27.9 0.8 25 3-27 18-45 (50)
53 PF05477 SURF2: Surfeit locus 64.3 5.2 0.00011 35.7 2.4 39 3-42 79-117 (244)
54 KOG2837 Protein containing a U 64.3 3.1 6.6E-05 38.3 0.9 32 3-36 25-56 (309)
55 COG5200 LUC7 U1 snRNP componen 62.2 5.8 0.00013 35.5 2.2 33 5-37 187-220 (258)
56 PF05605 zf-Di19: Drought indu 62.2 5.5 0.00012 26.8 1.7 21 3-26 2-22 (54)
57 KOG2636 Splicing factor 3a, su 60.3 2.8 6.2E-05 40.7 -0.0 28 4-33 272-299 (497)
58 KOG2482 Predicted C2H2-type Zn 60.0 2.9 6.4E-05 39.6 0.0 28 3-32 195-222 (423)
59 PF13821 DUF4187: Domain of un 58.5 5.5 0.00012 27.8 1.2 23 4-28 28-50 (55)
60 KOG4849 mRNA cleavage factor I 57.4 1.9E+02 0.0041 28.1 13.0 30 2-31 78-109 (498)
61 PF12756 zf-C2H2_2: C2H2 type 56.7 2.9 6.2E-05 29.6 -0.5 27 6-35 2-28 (100)
62 COG4469 CoiA Competence protei 52.7 5.9 0.00013 37.2 0.7 43 3-45 25-81 (342)
63 KOG3204 60S ribosomal protein 51.8 43 0.00094 29.3 5.8 57 19-76 132-191 (197)
64 KOG3576 Ovo and related transc 48.0 10 0.00022 34.0 1.4 22 3-26 145-166 (267)
65 PF14881 Tubulin_3: Tubulin do 47.2 10 0.00022 31.9 1.2 12 3-14 10-21 (180)
66 PF07975 C1_4: TFIIH C1-like d 43.4 4 8.7E-05 28.4 -1.4 15 3-18 29-43 (51)
67 TIGR00985 3a0801s04tom mitocho 41.1 79 0.0017 26.3 5.6 26 5-31 23-49 (148)
68 PF13842 Tnp_zf-ribbon_2: DDE_ 39.6 12 0.00025 23.4 0.4 12 3-14 16-27 (32)
69 KOG0545 Aryl-hydrocarbon recep 38.8 29 0.00063 32.2 2.9 38 5-42 233-272 (329)
70 KOG3792 Transcription factor N 38.7 8 0.00017 39.7 -0.7 29 4-34 194-222 (816)
71 PHA00732 hypothetical protein 37.0 24 0.00052 26.1 1.7 21 4-26 2-22 (79)
72 PHA03074 late transcription fa 36.6 17 0.00037 32.2 1.1 37 3-40 21-61 (225)
73 PF04746 DUF575: Protein of un 35.8 24 0.00053 27.8 1.7 34 11-44 48-82 (101)
74 TIGR00570 cdk7 CDK-activating 35.8 50 0.0011 30.6 4.0 15 3-17 43-57 (309)
75 PF02064 MAS20: MAS20 protein 34.3 34 0.00075 27.4 2.4 22 4-26 12-34 (121)
76 COG1631 RPL42A Ribosomal prote 34.3 23 0.00049 27.7 1.3 17 3-19 8-24 (94)
77 PF14291 DUF4371: Domain of un 34.2 56 0.0012 27.9 3.8 22 21-42 17-40 (235)
78 KOG4167 Predicted DNA-binding 34.1 27 0.00058 36.3 2.1 22 3-26 792-813 (907)
79 PF00191 Annexin: Annexin; In 33.8 50 0.0011 22.1 2.8 36 25-60 26-61 (66)
80 PHA00616 hypothetical protein 32.2 24 0.00051 23.9 0.9 20 4-25 2-21 (44)
81 PF14616 DUF4451: Domain of un 32.1 22 0.00048 28.3 0.9 21 5-26 27-49 (124)
82 PHA00733 hypothetical protein 31.2 32 0.00068 27.4 1.7 22 3-26 73-94 (128)
83 PF02701 zf-Dof: Dof domain, z 31.1 8.8 0.00019 28.0 -1.3 23 2-25 29-51 (63)
84 PRK00420 hypothetical protein; 30.6 1E+02 0.0022 24.6 4.4 13 2-14 39-51 (112)
85 PF14523 Syntaxin_2: Syntaxin- 30.4 2.1E+02 0.0046 20.7 7.8 27 47-73 69-96 (102)
86 PF10955 DUF2757: Protein of u 30.2 25 0.00053 26.4 0.8 11 3-13 4-14 (76)
87 PF14369 zf-RING_3: zinc-finge 30.1 25 0.00055 22.3 0.8 12 3-14 2-13 (35)
88 PF14279 HNH_5: HNH endonuclea 29.8 69 0.0015 23.3 3.1 47 6-58 1-52 (71)
89 PF11888 DUF3408: Protein of u 29.8 59 0.0013 25.9 3.0 56 6-61 65-122 (136)
90 PF00130 C1_1: Phorbol esters/ 27.8 29 0.00063 22.6 0.8 11 3-13 11-21 (53)
91 COG3105 Uncharacterized protei 27.4 2.7E+02 0.0059 23.2 6.5 39 26-66 31-69 (138)
92 TIGR03830 CxxCG_CxxCG_HTH puta 27.4 1.1E+02 0.0023 23.0 3.9 13 2-14 30-42 (127)
93 PF06295 DUF1043: Protein of u 27.2 3E+02 0.0064 21.8 6.6 15 50-64 44-58 (128)
94 PF09416 UPF1_Zn_bind: RNA hel 26.5 35 0.00076 28.6 1.2 13 4-16 15-27 (152)
95 PF08394 Arc_trans_TRASH: Arch 26.2 8.8 0.00019 25.1 -1.9 17 6-23 1-17 (37)
96 KOG4139 Protein kinase essenti 25.8 72 0.0016 31.7 3.4 23 3-30 299-321 (520)
97 PF11460 DUF3007: Protein of u 24.5 1.4E+02 0.003 23.8 4.1 31 30-60 67-97 (104)
98 KOG3576 Ovo and related transc 24.5 31 0.00068 31.0 0.6 37 3-41 173-212 (267)
99 PF05766 NinG: Bacteriophage L 24.4 1.1E+02 0.0025 26.3 4.0 26 5-31 125-150 (189)
100 KOG4330 Uncharacterized conser 24.1 2.8E+02 0.0062 24.3 6.3 51 17-67 133-188 (206)
101 PF10276 zf-CHCC: Zinc-finger 24.0 36 0.00079 22.5 0.7 10 4-13 30-39 (40)
102 PRK11677 hypothetical protein; 23.8 3.7E+02 0.008 22.0 6.7 45 30-76 30-78 (134)
103 KOG0956 PHD finger protein AF1 23.3 23 0.00049 36.7 -0.6 11 4-14 172-182 (900)
104 PF14410 GH-E: HNH/ENDO VII su 23.2 84 0.0018 22.8 2.5 34 2-38 4-37 (70)
105 KOG0819 Annexin [Intracellular 23.1 91 0.002 29.2 3.3 47 10-56 186-232 (321)
106 PLN03238 probable histone acet 23.0 47 0.001 30.6 1.5 22 3-26 48-69 (290)
107 PTZ00046 rifin; Provisional 22.7 1.1E+02 0.0023 29.1 3.7 10 3-13 39-48 (358)
108 PF06319 DUF1052: Protein of u 22.7 37 0.0008 28.7 0.7 13 4-16 82-94 (157)
109 PF00643 zf-B_box: B-box zinc 21.9 40 0.00086 21.0 0.6 12 3-14 15-26 (42)
110 KOG3623 Homeobox transcription 21.9 20 0.00044 37.3 -1.2 34 4-42 951-984 (1007)
111 KOG1146 Homeobox protein [Gene 21.9 11 0.00025 40.9 -3.0 53 4-57 735-798 (1406)
112 COG3677 Transposase and inacti 21.8 61 0.0013 26.0 1.8 36 3-40 53-88 (129)
113 PF13878 zf-C2H2_3: zinc-finge 21.8 83 0.0018 20.4 2.1 24 3-26 13-36 (41)
114 KOG0352 ATP-dependent DNA heli 21.7 1.7E+02 0.0037 29.3 5.0 52 7-67 353-404 (641)
115 PF12940 RAG1: Recombination-a 21.1 25 0.00054 33.9 -0.7 34 3-37 216-249 (442)
116 PF10186 Atg14: UV radiation r 20.8 2.1E+02 0.0046 24.2 5.0 9 3-11 11-19 (302)
117 PF00628 PHD: PHD-finger; Int 20.8 46 0.001 21.4 0.7 11 3-13 14-24 (51)
118 PRK10780 periplasmic chaperone 20.7 4.6E+02 0.01 21.2 7.7 29 16-44 30-58 (165)
119 PTZ00064 histone acetyltransfe 20.7 49 0.0011 33.0 1.1 23 3-27 280-302 (552)
120 TIGR01477 RIFIN variant surfac 20.6 1.2E+02 0.0025 28.8 3.5 10 3-13 42-51 (353)
121 COG4049 Uncharacterized protei 20.4 69 0.0015 23.3 1.6 21 4-26 18-38 (65)
122 PLN00064 photosystem II protei 20.2 1E+02 0.0022 26.4 2.8 38 30-67 126-164 (166)
123 PF04837 MbeB_N: MbeB-like, N- 20.2 3.2E+02 0.0068 19.1 5.7 35 34-69 7-41 (52)
124 KOG0579 Ste20-like serine/thre 20.1 1.1E+02 0.0023 32.3 3.4 61 9-76 1118-1178(1187)
125 KOG2314 Translation initiation 20.1 2.8E+02 0.006 28.4 6.1 22 23-44 599-620 (698)
No 1
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=99.89 E-value=5.6e-23 Score=170.44 Aligned_cols=59 Identities=66% Similarity=1.151 Sum_probs=55.6
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLG 59 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~ 59 (197)
|+||||||||+||+|||+||||.|+.|++|++||+.||+.|.+|++|.+||+..+..+.
T Consensus 1 MpRYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY~k~~eeqAq~liD~~~~~~~~ 59 (165)
T KOG3454|consen 1 MPRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYYQKWMEEQAQKLIDETILRFIG 59 (165)
T ss_pred CCcchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 89999999999999999999999999999999999999999999999999997777654
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=99.78 E-value=5.7e-20 Score=119.68 Aligned_cols=38 Identities=76% Similarity=1.521 Sum_probs=26.3
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYY 38 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy 38 (197)
|+||||||||+||++|+.++|++|+.|++|++||++||
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 89999999999999999999999999999999999986
No 3
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=99.62 E-value=6.3e-16 Score=139.26 Aligned_cols=72 Identities=25% Similarity=0.584 Sum_probs=65.8
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHhhHHHHHHhHHhhhhhh
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQ-TQSLIDQRIKEHLGQTAAFQQVGAAYNQHLL 76 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek-~Q~l~dk~lkk~l~~teaf~~ag~~y~~dla 76 (197)
+++|||||+|||. |+..+++.|++|+||+.||+++++.+++.. .+.+.++.|.+.|++||+. |-++|++||.
T Consensus 9 ~kkfCdyCKiWi~-dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEaa--A~~syaedl~ 81 (336)
T KOG0150|consen 9 PKKFCDYCKIWIK-DNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEAA--ASASYAEDLS 81 (336)
T ss_pred cchhhhhhhhhhc-CChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHHH--HHHHHHHhhh
Confidence 6899999999995 778778999999999999999999999884 5777999999999999995 8999999997
No 4
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=99.57 E-value=1.4e-15 Score=127.22 Aligned_cols=57 Identities=42% Similarity=0.799 Sum_probs=48.0
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQTA 62 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~te 62 (197)
|+|||||||++||+||++||||.|+.|++|..++++||..+-++ |.++..+.|..|.
T Consensus 1 MpRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY~~~a~d-----i~~e~~~~lr~i~ 57 (188)
T COG5136 1 MPRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYMEMAED-----IAAEMASILRDIK 57 (188)
T ss_pred CcchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHh
Confidence 89999999999999999999999999999999999999987653 3344444455554
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=5.3e-11 Score=73.53 Aligned_cols=35 Identities=31% Similarity=0.586 Sum_probs=29.9
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
+++|||++|+++|. +.+.+++|+.|++|++|++++
T Consensus 1 ~~~~~C~~C~~~~~--~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 1 TGGFYCKLCNVTFT--DEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred CcCeEccccCCccC--CHHHHHHHHChHHHHHHHHcC
Confidence 57899999999994 455569999999999999864
No 6
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=98.73 E-value=4e-08 Score=83.33 Aligned_cols=35 Identities=37% Similarity=0.603 Sum_probs=30.1
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
+++||||+|||.+ .||.. +.+|++|++|++|+...
T Consensus 73 ~~GyyCdVCdcvv-KDSin-flDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 73 KGGYYCDVCDCVV-KDSIN-FLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCceeeeecceee-hhhHH-HHHHhccHHHHHHHhhh
Confidence 4689999999999 59888 59999999999995443
No 7
>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=98.54 E-value=4.6e-08 Score=58.27 Aligned_cols=27 Identities=48% Similarity=0.912 Sum_probs=23.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHK 31 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk 31 (197)
+|||++||++| .+...+++|++|++||
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 58999999999 4678889999999997
No 8
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=98.28 E-value=2.4e-05 Score=78.70 Aligned_cols=19 Identities=37% Similarity=0.646 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCCCCCCCCC
Q 029213 103 RPPVLPRPGPSPPGYVSAP 121 (197)
Q Consensus 103 ~pp~~p~~~p~~pg~~~~p 121 (197)
+||+.++|+||.+|.+++|
T Consensus 542 pppPppPPlpggag~PPPP 560 (1102)
T KOG1924|consen 542 PPPPPPPPLPGGAGPPPPP 560 (1102)
T ss_pred CCCCCCCCCCCCCCCCccC
Confidence 3344456677776644433
No 9
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=98.13 E-value=2.5e-06 Score=79.48 Aligned_cols=61 Identities=15% Similarity=0.246 Sum_probs=45.6
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHhhHHHH
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQ-QTQSLIDQRIKEHLGQTAAFQ 65 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~e-k~Q~l~dk~lkk~l~~teaf~ 65 (197)
+++||.+|.+|| ...+|+..|+.||+|.+|+++.-...+.| .+++ +.+.+.+.+..|++||
T Consensus 237 ~~~YC~~C~r~f--~~~~VFe~Hl~gK~H~k~~~~~~~~v~~Ey~l~r-~~kyl~d~~s~trs~V 298 (470)
T COG5188 237 PKVYCVKCGREF--SRSKVFEYHLEGKRHCKEGQGKEEFVYSEYVLHR-YLKYLGDPVSETRSLV 298 (470)
T ss_pred cceeeHhhhhHh--hhhHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHH-HHHHhCChhHHHHHHH
Confidence 478999999999 56799999999999999998876655555 4444 4555555555555553
No 10
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.11 E-value=2.2e-06 Score=49.44 Aligned_cols=25 Identities=36% Similarity=0.766 Sum_probs=22.8
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKH 30 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrH 30 (197)
|+|+.|++.| .+...+++|++|++|
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 567788999999998
No 11
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=98.01 E-value=7.4e-05 Score=67.14 Aligned_cols=25 Identities=24% Similarity=0.563 Sum_probs=20.3
Q ss_pred cccccCCcceeccCCHHHHHHhhcchH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYK 29 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~Gkr 29 (197)
|-||=|||+-| |...++.+|..-|.
T Consensus 10 kpwcwycnref--ddekiliqhqkakh 34 (341)
T KOG2893|consen 10 KPWCWYCNREF--DDEKILIQHQKAKH 34 (341)
T ss_pred Cceeeeccccc--chhhhhhhhhhhcc
Confidence 45999999999 77788899877554
No 12
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=97.48 E-value=5.4e-05 Score=61.28 Aligned_cols=35 Identities=26% Similarity=0.440 Sum_probs=29.3
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
++-|||-.|++|| .+.++++.|..++.||+.|++.
T Consensus 55 ~GqfyCi~CaRyF--i~~~~l~~H~ktK~HKrRvK~l 89 (129)
T KOG3408|consen 55 GGQFYCIECARYF--IDAKALKTHFKTKVHKRRVKEL 89 (129)
T ss_pred Cceeehhhhhhhh--cchHHHHHHHhccHHHHHHHhc
Confidence 4579999999999 4567789999999999776653
No 13
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=9.4e-05 Score=70.78 Aligned_cols=40 Identities=35% Similarity=0.589 Sum_probs=36.6
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQ 45 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek 45 (197)
+||..|++.| .|...+++|+++|+|++||++.-+.++++.
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 678889999999999999999998888763
No 14
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=96.78 E-value=0.00051 Score=54.94 Aligned_cols=34 Identities=24% Similarity=0.471 Sum_probs=29.6
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
+.+||-.|++|| ++..++..|..|+-|++.+++.
T Consensus 54 GqhYCieCaryf--~t~~aL~~HkkgkvHkRR~Kel 87 (126)
T COG5112 54 GQHYCIECARYF--ITEKALMEHKKGKVHKRRAKEL 87 (126)
T ss_pred ceeeeehhHHHH--HHHHHHHHHhccchhHHHHHHH
Confidence 368999999999 7888889999999999877654
No 15
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=96.75 E-value=0.092 Score=53.86 Aligned_cols=9 Identities=11% Similarity=-0.193 Sum_probs=6.5
Q ss_pred cccCCccee
Q 029213 5 YCDYCDTYL 13 (197)
Q Consensus 5 YCdYCd~~f 13 (197)
.|++||--|
T Consensus 438 Hr~~~DPdf 446 (1102)
T KOG1924|consen 438 HRTGMDPDF 446 (1102)
T ss_pred hcCCCCCCc
Confidence 577887766
No 16
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.51 E-value=0.0018 Score=56.33 Aligned_cols=42 Identities=24% Similarity=0.441 Sum_probs=35.0
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHH
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQ 45 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek 45 (197)
++|-|..|.+. |.+-.++..|..||||+.|+.++-....+++
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 58999999986 5677778999999999999999877655543
No 17
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.84 E-value=0.0081 Score=52.11 Aligned_cols=34 Identities=29% Similarity=0.415 Sum_probs=29.8
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
++|-|..|++.- -+-+++..|..||||+.|+.++
T Consensus 52 Gk~vC~LC~T~H--~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 52 GKYVCLLCKTKH--LTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred CcEEeeeecccc--ccHHHHHHhhccchhhhhHHHH
Confidence 589999999874 5667779999999999999998
No 18
>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=95.61 E-value=0.022 Score=48.15 Aligned_cols=41 Identities=22% Similarity=0.382 Sum_probs=37.3
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQ 45 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek 45 (197)
..|--||.+|- ...++...|+.+..|.+|++.+..+++++.
T Consensus 92 ~hCsACd~~IP-~~~~~vQ~Hl~S~~H~~Nrr~~~eq~Kr~s 132 (165)
T PF04988_consen 92 AHCSACDVFIP-MQHSSVQKHLKSQDHNKNRRAMMEQSKRSS 132 (165)
T ss_pred hhhhHhhhhcc-CcHHHHHHHhccHHHHhhHHHHHHHHHHHH
Confidence 47999999995 778888999999999999999999999885
No 19
>PF14968 CCDC84: Coiled coil protein 84
Probab=94.39 E-value=0.022 Score=52.61 Aligned_cols=38 Identities=24% Similarity=0.590 Sum_probs=30.2
Q ss_pred cccccCCcceeccCCH-----HHHHHhhcchHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSP-----SVRKQHNAGYKHKANVRSYYQQF 41 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~-----SvRk~H~~GkrHk~NVk~yy~~~ 41 (197)
+|||-+||.-+. |.. .....|+.+..|++||++++...
T Consensus 58 ~fWC~fC~~ev~-~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~~ 100 (336)
T PF14968_consen 58 RFWCVFCDCEVR-EHDSSFACGGAIEHLASPEHRKNVKKFWWKN 100 (336)
T ss_pred eeEeeCccchhh-hccchhhhccHHhhcCCHHHHHHHHHHHHHc
Confidence 789999999994 442 12468999999999999996554
No 20
>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=94.37 E-value=0.033 Score=30.40 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=15.9
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|-|++|++.| ++...++.|+.
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 67788888875
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=93.95 E-value=0.046 Score=30.50 Aligned_cols=21 Identities=33% Similarity=0.562 Sum_probs=17.5
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|-|++|++.| .+.+.++.|..
T Consensus 1 y~C~~C~~~f--~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSF--SSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEE--SSHHHHHHHHH
T ss_pred CCCCCCCCcc--CCHHHHHHHHh
Confidence 6799999999 56777888875
No 22
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.70 E-value=0.019 Score=40.97 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=24.4
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANV 34 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NV 34 (197)
.+.|.+|++.| ++...++.|++.+.|++..
T Consensus 50 ~~~C~~C~~~f--~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTF--RSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EE--SSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCC--cCHHHHHHHHcCccCCCcc
Confidence 38999999999 6788889999999998654
No 23
>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=93.31 E-value=0.067 Score=30.96 Aligned_cols=21 Identities=29% Similarity=0.616 Sum_probs=18.1
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|.|+.|++.| .+.+.+..|..
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 67888898874
No 24
>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=92.98 E-value=0.15 Score=45.10 Aligned_cols=39 Identities=21% Similarity=0.483 Sum_probs=27.4
Q ss_pred ccccCCcceec-cCCHHHHHHhhcchHHHHH--HHHHHHHHH
Q 029213 4 YYCDYCDTYLT-HDSPSVRKQHNAGYKHKAN--VRSYYQQFE 42 (197)
Q Consensus 4 yYCdYCd~~ft-~Ds~SvRk~H~~GkrHk~N--Vk~yy~~~~ 42 (197)
--||+|+.||+ +|+.+=+.+|..||.|..= +++.|..+.
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~IR~~l~el~ 232 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAKIREKLKELK 232 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccchhhhHHHHHHHHHHHH
Confidence 46999999984 4766655779999999853 333344444
No 25
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.90 E-value=0.074 Score=47.59 Aligned_cols=33 Identities=24% Similarity=0.503 Sum_probs=28.6
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYY 38 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy 38 (197)
..-|-+|++-| . .++|..|.+|++|+.+|....
T Consensus 35 ql~C~vCn~pi--K-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 35 QLVCRVCNVPI--K-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred CeeEEEecCcc--c-HHHHHHHhccHHHHHHHHHHH
Confidence 45799999999 3 899999999999998887655
No 26
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=92.81 E-value=0.029 Score=49.13 Aligned_cols=31 Identities=26% Similarity=0.684 Sum_probs=24.4
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRS 36 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~ 36 (197)
-+||+.||+||. |+.+ -.|..+..|+-|.+.
T Consensus 84 lfyCE~Cd~~ip-~~~~--snH~tSttHllsl~~ 114 (223)
T KOG2384|consen 84 LFYCEVCDIYIP-NSKK--SNHFTSTTHLLSLQH 114 (223)
T ss_pred cchhhhhhhhcc-CCCC--ccchhhHHHHhhhcc
Confidence 589999999994 6554 478888888877654
No 27
>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=92.10 E-value=0.091 Score=36.19 Aligned_cols=25 Identities=28% Similarity=0.573 Sum_probs=20.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKA 32 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~ 32 (197)
.-||+.|.+.| |+ +..|+.+.+|++
T Consensus 5 ~GYCE~C~~ky--~~---l~~Hi~s~~Hr~ 29 (49)
T PF07535_consen 5 PGYCENCRVKY--DD---LEEHIQSEKHRK 29 (49)
T ss_pred CccCccccchh--hh---HHHHhCCHHHHH
Confidence 45999999999 32 588999999983
No 28
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=90.89 E-value=0.11 Score=35.97 Aligned_cols=25 Identities=28% Similarity=0.530 Sum_probs=20.7
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKA 32 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~ 32 (197)
.-||+-|...| |+ +..|+.+++|++
T Consensus 5 ~GYCE~Cr~kf--d~---l~~Hi~s~~Hr~ 29 (49)
T smart00586 5 PGYCENCREKY--DD---LETHLLSEKHRR 29 (49)
T ss_pred CcccccHhHHH--hh---HHHHhccHHHHH
Confidence 35999999999 42 578999999983
No 29
>PF14968 CCDC84: Coiled coil protein 84
Probab=90.75 E-value=0.22 Score=46.13 Aligned_cols=35 Identities=23% Similarity=0.623 Sum_probs=30.0
Q ss_pred cccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHH
Q 029213 5 YCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQ 44 (197)
Q Consensus 5 YCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~e 44 (197)
||+.|.+.. |. ++.|.-+++|+++++..+..|+..
T Consensus 1 yC~vCr~~h--~~---gr~H~Y~~~Hq~~L~~~L~rf~~K 35 (336)
T PF14968_consen 1 YCEVCRRNH--DQ---GRRHVYSPKHQKSLSAFLSRFRSK 35 (336)
T ss_pred CcchhhCcc--cc---cCCCccCHHHHHHHHHHHHHHHHH
Confidence 899999875 53 699999999999999998888744
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=89.43 E-value=0.29 Score=26.59 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=16.1
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|-|+.|++.| .+.+.++.|..
T Consensus 1 ~~C~~C~~~f--~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVF--KSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchh--CCHHHHHHHHH
Confidence 5799999999 34566677775
No 31
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=88.31 E-value=0.68 Score=42.86 Aligned_cols=40 Identities=20% Similarity=0.497 Sum_probs=28.5
Q ss_pred cccCCcceec-cCCHHHHHHhhcchHHHHH--HHHHHHHHHHH
Q 029213 5 YCDYCDTYLT-HDSPSVRKQHNAGYKHKAN--VRSYYQQFEEQ 44 (197)
Q Consensus 5 YCdYCd~~ft-~Ds~SvRk~H~~GkrHk~N--Vk~yy~~~~~e 44 (197)
.|++|+.||. +|+.+=...|++||-|..- ++..|..++++
T Consensus 188 VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~ 230 (319)
T KOG0796|consen 188 VCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKE 230 (319)
T ss_pred HHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHH
Confidence 5999999985 4555545569999999965 34445555544
No 32
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=87.69 E-value=0.21 Score=47.16 Aligned_cols=36 Identities=25% Similarity=0.513 Sum_probs=31.7
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQ 40 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~ 40 (197)
-+||..|++.| .+....++|+..++|+.|+.++++.
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 47999999999 4666679999999999999999973
No 33
>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=83.61 E-value=2.1 Score=36.42 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=24.2
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
|.|.+|+-... .......|+.++.|++-++.-
T Consensus 1 F~Cs~CKfrtf--~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 1 FTCSFCKFRTF--EEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred Cccceeeeecc--cHHHHHHHHccchHHHHHHHH
Confidence 67999997764 334569999999999765544
No 34
>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=83.19 E-value=2.3 Score=37.17 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=18.2
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANV 34 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NV 34 (197)
||.|..|.|-| .....++.|+. .||.+-|
T Consensus 77 K~~C~lc~KlF--kg~eFV~KHI~-nKH~e~v 105 (214)
T PF04959_consen 77 KWRCPLCGKLF--KGPEFVRKHIF-NKHPEKV 105 (214)
T ss_dssp EEEE-SSS-EE--SSHHHHHHHHH-HH-HHHH
T ss_pred EECCCCCCccc--CChHHHHHHHh-hcCHHHH
Confidence 78999999999 44555577776 4566444
No 35
>PTZ00448 hypothetical protein; Provisional
Probab=82.78 E-value=0.81 Score=43.17 Aligned_cols=38 Identities=24% Similarity=0.296 Sum_probs=33.3
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFE 42 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~ 42 (197)
.|.|--|+..| ++...++.|..+--|+-|++++++.+-
T Consensus 314 ~~tC~~C~v~F--~~~~~qR~H~KSDwHrYNLKRkl~gLp 351 (373)
T PTZ00448 314 MLLCRKCNIQL--MDHNAFKQHYRSEWHIFNTKRNARKME 351 (373)
T ss_pred Ccccccccccc--CCHHHHHHHhhhhHHHHHHHHHhcCCC
Confidence 37799999999 567778999999999999999998864
No 36
>PHA02768 hypothetical protein; Provisional
Probab=82.49 E-value=0.85 Score=32.24 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=14.6
Q ss_pred cccccCCcceeccCCHHHHHHhh
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHN 25 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~ 25 (197)
+|.|+.|++.|+ . .+.+..|.
T Consensus 5 ~y~C~~CGK~Fs-~-~~~L~~H~ 25 (55)
T PHA02768 5 GYECPICGEIYI-K-RKSMITHL 25 (55)
T ss_pred ccCcchhCCeec-c-HHHHHHHH
Confidence 689999999995 3 33344444
No 37
>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=81.76 E-value=0.88 Score=29.18 Aligned_cols=23 Identities=26% Similarity=0.522 Sum_probs=15.1
Q ss_pred cccccCCcceeccC--CHHHHHHhh
Q 029213 3 RYYCDYCDTYLTHD--SPSVRKQHN 25 (197)
Q Consensus 3 ryYCdYCd~~ft~D--s~SvRk~H~ 25 (197)
+..|.||++.|..+ +.+.++.|+
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 56899999999765 666777787
No 38
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=80.63 E-value=0.94 Score=44.60 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.6
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQF 41 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~ 41 (197)
+.+|-.|++-| ++...++.|...--|+-|+++.++.+
T Consensus 66 ~~~CstCq~~F--~s~~eqr~HyksD~HR~N~Krkl~~~ 102 (591)
T KOG2505|consen 66 SDQCSTCQIPF--GSRQEQREHYKSDWHRFNTKRKLRGK 102 (591)
T ss_pred cccccccCCcc--ccHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 56899999999 78999999999999999999998764
No 39
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=79.70 E-value=2.1 Score=40.69 Aligned_cols=39 Identities=15% Similarity=0.390 Sum_probs=34.3
Q ss_pred CCcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHH
Q 029213 1 MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQF 41 (197)
Q Consensus 1 MPryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~ 41 (197)
|..|-|.-|++.| |+....+.|-..-=|+-|++++..++
T Consensus 1 st~ftC~tC~v~F--~~ad~Qr~HyKSdWHRYNLKRkVA~l 39 (390)
T KOG2785|consen 1 STGFTCNTCNVEF--DDADEQRAHYKSDWHRYNLKRKVASL 39 (390)
T ss_pred CCcceeeceeeee--ccHHHHHHHhhhhHHHhhHHhHhhcC
Confidence 6789999999999 66667799999999999999997764
No 40
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=77.26 E-value=22 Score=32.67 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=16.6
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRS 36 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~ 36 (197)
-|.|..|+|.|... -.+.-|+. .-||+-+.+
T Consensus 34 hfkchichkkl~sg--pglsihcm-qvhketid~ 64 (341)
T KOG2893|consen 34 HFKCHICHKKLFSG--PGLSIHCM-QVHKETIDK 64 (341)
T ss_pred cceeeeehhhhccC--CCceeehh-hhhhhhhhc
Confidence 36799998877422 11233554 335555443
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=77.01 E-value=1.9 Score=24.25 Aligned_cols=20 Identities=40% Similarity=0.658 Sum_probs=13.1
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|-|++|+ |.+ . .+.++.|+.
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 666788864
No 42
>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=75.19 E-value=1.5 Score=25.71 Aligned_cols=12 Identities=33% Similarity=1.018 Sum_probs=10.5
Q ss_pred cccccCCcceec
Q 029213 3 RYYCDYCDTYLT 14 (197)
Q Consensus 3 ryYCdYCd~~ft 14 (197)
.|-|++|++.|.
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 588999999984
No 43
>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=75.01 E-value=0.94 Score=39.23 Aligned_cols=34 Identities=18% Similarity=0.440 Sum_probs=0.0
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
.|.|+.|+=+.. --..++..|.+.+||..-++..
T Consensus 101 ey~CEICGN~~Y-~GrkaFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 101 EYKCEICGNQSY-KGRKAFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp -----------------------------------
T ss_pred eeeeEeCCCcce-ecHHHHHHhcChhHHHccChhc
Confidence 589999998875 5567789999999999887654
No 44
>smart00597 ZnF_TTF zinc finger in transposases and transcription factors.
Probab=73.55 E-value=2.2 Score=32.45 Aligned_cols=32 Identities=25% Similarity=0.537 Sum_probs=20.3
Q ss_pred cccccCCcceec---cCCHH-------------HHHHhhcchHHHHHH
Q 029213 3 RYYCDYCDTYLT---HDSPS-------------VRKQHNAGYKHKANV 34 (197)
Q Consensus 3 ryYCdYCd~~ft---~Ds~S-------------vRk~H~~GkrHk~NV 34 (197)
+.||-||..|-. ..+.+ .++.|+.+..|..+.
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 469999999830 11111 257777777777665
No 45
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=72.65 E-value=2.8 Score=39.32 Aligned_cols=56 Identities=13% Similarity=0.263 Sum_probs=39.5
Q ss_pred cccccCCcceeccCCHHHHHHh---hcchHHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHh
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQH---NAGYKHKANVRSYYQQFEEQ-QTQSLIDQRIKEHLGQ 60 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H---~~GkrHk~NVk~yy~~~~~e-k~Q~l~dk~lkk~l~~ 60 (197)
+|.|.-||--++ |..-+++| +..+.-++||+.-+.++|.. +..++..+++++.+++
T Consensus 19 ~YtCPRCn~~YC--sl~CYr~h~~~CsE~FyrdqV~~eL~~~r~d~s~k~km~e~lkr~~q~ 78 (383)
T KOG4317|consen 19 EYTCPRCNLLYC--SLKCYRNHKHSCSEKFYRDQVKQELSGKRADISQKRKMGEELKRKMQK 78 (383)
T ss_pred cccCCCCCccce--eeeeecCCCccchHHHHHHHHHHHhhhccccccchhHHHHHHHHHHhh
Confidence 688988887774 56666665 56788888888888887765 3444566666666655
No 46
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=72.05 E-value=0.68 Score=47.05 Aligned_cols=33 Identities=24% Similarity=0.633 Sum_probs=26.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
+|.|+.||+-| +|-.+ ..-|++|+||.-.+++.
T Consensus 359 ~f~cKlcdckf-~d~na-k~mhl~grRhrLQYk~k 391 (816)
T KOG3792|consen 359 RFHCKLCDCKF-NDPNA-KEMHLKGRRHRLQYKQK 391 (816)
T ss_pred hhhhhhhcCCC-CCcch-HHhhhhcccccceeccc
Confidence 78999999999 57555 47799999999776633
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=71.94 E-value=3.2 Score=24.41 Aligned_cols=20 Identities=20% Similarity=0.514 Sum_probs=14.3
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
.-|.+|++.|. .+.+..|+.
T Consensus 3 ~~C~~CgR~F~---~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKFN---PDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEEC---HHHHHHHHH
Confidence 46999999993 344577753
No 48
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=71.20 E-value=1.3 Score=45.55 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=15.3
Q ss_pred CcccccCCcceeccCCHHHHHHhh
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHN 25 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~ 25 (197)
+-|-||-|||.|. + .|++..|-
T Consensus 893 gmyaCDqCDK~Fq-K-qSSLaRHK 914 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQ-K-QSSLARHK 914 (1007)
T ss_pred ccchHHHHHHHHH-h-hHHHHHhh
Confidence 3689999999995 3 34445553
No 49
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=68.32 E-value=22 Score=32.52 Aligned_cols=71 Identities=17% Similarity=0.230 Sum_probs=43.7
Q ss_pred ccccCCcceeccCCHHHHHH-hhcchHHHHHHHHHHHHHHHHH----hhHH-HHHHHH---HHHHhhHHHHHHhHHhhhh
Q 029213 4 YYCDYCDTYLTHDSPSVRKQ-HNAGYKHKANVRSYYQQFEEQQ----TQSL-IDQRIK---EHLGQTAAFQQVGAAYNQH 74 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~-H~~GkrHk~NVk~yy~~~~~ek----~Q~l-~dk~lk---k~l~~teaf~~ag~~y~~d 74 (197)
+-|+.|+++.+ +.--||. -.+.+|-.+.|.+.|+.+++.. .|+| ..++|. +++++.+++.+....-+++
T Consensus 104 wackackrks~--svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~ 181 (284)
T KOG3960|consen 104 WACKACKRKST--SVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKG 181 (284)
T ss_pred Hhhhhcccccc--chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchh
Confidence 45999998874 3333555 5688888888888898888652 3554 334444 4455555554444444445
Q ss_pred hh
Q 029213 75 LL 76 (197)
Q Consensus 75 la 76 (197)
|+
T Consensus 182 ~~ 183 (284)
T KOG3960|consen 182 LA 183 (284)
T ss_pred hh
Confidence 54
No 50
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=68.18 E-value=3.4 Score=40.44 Aligned_cols=34 Identities=21% Similarity=0.431 Sum_probs=26.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYY 38 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy 38 (197)
+..|..|++.|+ |--.+-.|..|++|++.|...+
T Consensus 493 kkqcslcnvlis--sevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 493 KKQCSLCNVLIS--SEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhccchhhhhhh--hhhhhhhhhcchhHHHHHHHHh
Confidence 457999999993 4444556999999999988763
No 51
>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=66.51 E-value=1.7 Score=30.14 Aligned_cols=14 Identities=36% Similarity=1.054 Sum_probs=9.7
Q ss_pred cccccCCcceeccC
Q 029213 3 RYYCDYCDTYLTHD 16 (197)
Q Consensus 3 ryYCdYCd~~ft~D 16 (197)
+|-|.||++.++.|
T Consensus 35 ~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 35 KLRCHYCERIITED 48 (52)
T ss_dssp EEEETTT--EEEHH
T ss_pred EEEeeCCCCEeccc
Confidence 68899999999644
No 52
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=65.79 E-value=2.8 Score=27.88 Aligned_cols=25 Identities=32% Similarity=0.562 Sum_probs=17.0
Q ss_pred cccccCCcceeccCC---HHHHHHhhcc
Q 029213 3 RYYCDYCDTYLTHDS---PSVRKQHNAG 27 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds---~SvRk~H~~G 27 (197)
+..|.||++-|+.++ .+.++.|+..
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 467999999997653 3445556554
No 53
>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=64.33 E-value=5.2 Score=35.71 Aligned_cols=39 Identities=15% Similarity=0.402 Sum_probs=30.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFE 42 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~ 42 (197)
.+||..-.+.| +.+......|.+|+|-++.+++|-....
T Consensus 79 ~LfCkLT~~~i-Nk~pe~V~rHv~GKRf~kaLek~ee~~~ 117 (244)
T PF05477_consen 79 KLFCKLTGRHI-NKSPEHVERHVNGKRFQKALEKYEECQK 117 (244)
T ss_pred eeEEechHhHh-ccCHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence 57899999999 4666666999999999988877755544
No 54
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=64.28 E-value=3.1 Score=38.30 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=26.6
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRS 36 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~ 36 (197)
||||.-|.+-+ +| .+.++-|+.+-.|++....
T Consensus 25 RwyCqmCQkQc-rD-eNGFkCH~~SeSHqRql~~ 56 (309)
T KOG2837|consen 25 RWYCQMCQKQC-RD-ENGFKCHTMSESHQRQLLL 56 (309)
T ss_pred HHHHHHHHHHh-cc-ccccccccCCHHHHHHHHH
Confidence 79999999998 45 5557999999999976543
No 55
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=62.21 E-value=5.8 Score=35.51 Aligned_cols=33 Identities=24% Similarity=0.428 Sum_probs=24.5
Q ss_pred cccCCcceecc-CCHHHHHHhhcchHHHHHHHHH
Q 029213 5 YCDYCDTYLTH-DSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 5 YCdYCd~~ft~-Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
-|+.|..||.. |+.+-...|.+||-|..-+..+
T Consensus 187 vC~iCgayLsrlDtdrrladHf~GklHlGy~~~R 220 (258)
T COG5200 187 VCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVR 220 (258)
T ss_pred hhhhhhhHHHhcchhhHHHHHhccchhhhHHHHH
Confidence 59999999864 4444445699999999765544
No 56
>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=62.17 E-value=5.5 Score=26.83 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=15.6
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
.|-|.||++.| | ...+..|..
T Consensus 2 ~f~CP~C~~~~--~-~~~L~~H~~ 22 (54)
T PF05605_consen 2 SFTCPYCGKGF--S-ESSLVEHCE 22 (54)
T ss_pred CcCCCCCCCcc--C-HHHHHHHHH
Confidence 58899999976 4 455677765
No 57
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=60.32 E-value=2.8 Score=40.72 Aligned_cols=28 Identities=11% Similarity=0.026 Sum_probs=12.5
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKAN 33 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~N 33 (197)
-+|..|++||. +.+....|+.++-|.+|
T Consensus 272 t~~~ra~rlf~--Tk~~~l~~L~~~~~~kn 299 (497)
T KOG2636|consen 272 TLHERAQRLFS--TKSKSLSHLDTKLFAKN 299 (497)
T ss_pred eecHHHHhhhh--hcCcchhhhhhhhhccC
Confidence 34555555552 33333445544444444
No 58
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=60.04 E-value=2.9 Score=39.64 Aligned_cols=28 Identities=29% Similarity=0.635 Sum_probs=23.8
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKA 32 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~ 32 (197)
|+-|-||.|.| +|... .+.|-+-|+|++
T Consensus 195 r~~CLyCekif-rdknt-LkeHMrkK~Hrr 222 (423)
T KOG2482|consen 195 RLRCLYCEKIF-RDKNT-LKEHMRKKRHRR 222 (423)
T ss_pred hheeeeecccc-CCcHH-HHHHHHhccCcc
Confidence 57899999999 57655 599999999986
No 59
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=58.52 E-value=5.5 Score=27.81 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=18.2
Q ss_pred ccccCCcceeccCCHHHHHHhhcch
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGY 28 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~Gk 28 (197)
+||-||.+.+ ++......|.-|.
T Consensus 28 ~YC~~Cg~~Y--~d~~dL~~~CPG~ 50 (55)
T PF13821_consen 28 NYCFWCGTKY--DDEEDLERNCPGP 50 (55)
T ss_pred ceeeeeCCcc--CCHHHHHhCCCCC
Confidence 6999999999 5666667777664
No 60
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=57.36 E-value=1.9e+02 Score=28.06 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=19.5
Q ss_pred CcccccCCc--ceeccCCHHHHHHhhcchHHH
Q 029213 2 PRYYCDYCD--TYLTHDSPSVRKQHNAGYKHK 31 (197)
Q Consensus 2 PryYCdYCd--~~ft~Ds~SvRk~H~~GkrHk 31 (197)
+|.||-|-+ .|+|.|..-...-|..|....
T Consensus 78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~ 109 (498)
T KOG4849|consen 78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQF 109 (498)
T ss_pred CceEEEEecceeEEeccHHHHHHHHhhhHHHH
Confidence 477888876 588767544433388887644
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=56.72 E-value=2.9 Score=29.60 Aligned_cols=27 Identities=30% Similarity=0.460 Sum_probs=0.0
Q ss_pred ccCCcceeccCCHHHHHHhhcchHHHHHHH
Q 029213 6 CDYCDTYLTHDSPSVRKQHNAGYKHKANVR 35 (197)
Q Consensus 6 CdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk 35 (197)
|.+|+..| ++......|+. ..|.-++.
T Consensus 2 C~~C~~~f--~~~~~l~~H~~-~~H~~~~~ 28 (100)
T PF12756_consen 2 CLFCDESF--SSVDDLLQHMK-KKHGFDIP 28 (100)
T ss_dssp ------------------------------
T ss_pred cccccccc--ccccccccccc-cccccccc
Confidence 99999999 45666788985 66665554
No 62
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=52.73 E-value=5.9 Score=37.15 Aligned_cols=43 Identities=26% Similarity=0.511 Sum_probs=26.0
Q ss_pred cccccCCcceeccCCHHHHHHh--------------hcchHHHHHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQH--------------NAGYKHKANVRSYYQQFEEQQ 45 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H--------------~~GkrHk~NVk~yy~~~~~ek 45 (197)
||||..|+.-+.=..-..+.-| +.+-.|..+.+..|..+.+++
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pHFAHk~l~~C~~~~EnES~~HL~~Kr~Lyqwlk~q~ 81 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPHFAHKSLKACAFFNENESEEHLKGKRQLYQWLKRQG 81 (342)
T ss_pred ccccCCCCCeeeeecCccccchhhhhhhhhccccCCCCCHHHHHhHHHHHHHHHhcC
Confidence 7899999975422222222223 345667777777777777653
No 63
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=51.79 E-value=43 Score=29.32 Aligned_cols=57 Identities=14% Similarity=0.135 Sum_probs=30.8
Q ss_pred HHHHHhhcchHHHHHHHHHHHHHHHHH--hhHHHHHHHHHHHHhhHHHHHH-hHHhhhhhh
Q 029213 19 SVRKQHNAGYKHKANVRSYYQQFEEQQ--TQSLIDQRIKEHLGQTAAFQQV-GAAYNQHLL 76 (197)
Q Consensus 19 SvRk~H~~GkrHk~NVk~yy~~~~~ek--~Q~l~dk~lkk~l~~teaf~~a-g~~y~~dla 76 (197)
..|..|+-||+|+ .|...++.-++++ ++....+.+.+...+.|..+.. -..|.+-|+
T Consensus 132 lG~L~~eVGWkyq-~vtatLEeKRKeK~~~~y~kKkql~kl~~~Aekn~~kkidky~e~l~ 191 (197)
T KOG3204|consen 132 LGRLSHEVGWKYQ-AVTATLEEKRKEKAKIHYQKKKQLMRLRKQAEKNVEKKIDKYTEVLK 191 (197)
T ss_pred eccchhhhcchhH-HHHHHHHHHHhHhhhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 3467899999998 5566666666664 3332233344444444433211 124655554
No 64
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=48.03 E-value=10 Score=33.98 Aligned_cols=22 Identities=27% Similarity=0.686 Sum_probs=14.9
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
||.|-+|++-| ||+... |.|.+
T Consensus 145 r~lct~cgkgf-ndtfdl-krh~r 166 (267)
T KOG3576|consen 145 RHLCTFCGKGF-NDTFDL-KRHTR 166 (267)
T ss_pred HHHHhhccCcc-cchhhh-hhhhc
Confidence 67788888887 576654 66653
No 65
>PF14881 Tubulin_3: Tubulin domain
Probab=47.15 E-value=10 Score=31.91 Aligned_cols=12 Identities=33% Similarity=0.683 Sum_probs=11.0
Q ss_pred cccccCCcceec
Q 029213 3 RYYCDYCDTYLT 14 (197)
Q Consensus 3 ryYCdYCd~~ft 14 (197)
|||.||+..+|-
T Consensus 10 ryWSDy~r~~yh 21 (180)
T PF14881_consen 10 RYWSDYNRVHYH 21 (180)
T ss_pred EECCCCCcceeC
Confidence 899999999993
No 66
>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=43.39 E-value=4 Score=28.36 Aligned_cols=15 Identities=27% Similarity=0.890 Sum_probs=9.4
Q ss_pred cccccCCcceeccCCH
Q 029213 3 RYYCDYCDTYLTHDSP 18 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~ 18 (197)
.+||..||+|+ |+++
T Consensus 29 ~~FC~dCD~fi-HE~L 43 (51)
T PF07975_consen 29 NHFCIDCDVFI-HETL 43 (51)
T ss_dssp --B-HHHHHTT-TTTS
T ss_pred CccccCcChhh-hccc
Confidence 46888888887 7765
No 67
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=41.11 E-value=79 Score=26.31 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=15.3
Q ss_pred cccCCcceeccCCHHHHHH-hhcchHHH
Q 029213 5 YCDYCDTYLTHDSPSVRKQ-HNAGYKHK 31 (197)
Q Consensus 5 YCdYCd~~ft~Ds~SvRk~-H~~GkrHk 31 (197)
||.|-|.-=. .+...||+ |++-+|..
T Consensus 23 YciYFD~KRR-~dPdFRkkLr~rr~k~~ 49 (148)
T TIGR00985 23 YAIYFDYKRR-NDPDFRKKLRRRRKKQA 49 (148)
T ss_pred HHHhhhhhhc-cCHHHHHHHHHHHHHHH
Confidence 8999987753 44554444 55444333
No 68
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=39.56 E-value=12 Score=23.39 Aligned_cols=12 Identities=50% Similarity=1.076 Sum_probs=10.8
Q ss_pred cccccCCcceec
Q 029213 3 RYYCDYCDTYLT 14 (197)
Q Consensus 3 ryYCdYCd~~ft 14 (197)
+|+|.-||++|-
T Consensus 16 ~~~C~~C~v~lC 27 (32)
T PF13842_consen 16 RYMCSKCDVPLC 27 (32)
T ss_pred EEEccCCCCccc
Confidence 699999999985
No 69
>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]
Probab=38.82 E-value=29 Score=32.16 Aligned_cols=38 Identities=21% Similarity=0.472 Sum_probs=27.5
Q ss_pred cccCCcceeccCCHHHHHHhhcc--hHHHHHHHHHHHHHH
Q 029213 5 YCDYCDTYLTHDSPSVRKQHNAG--YKHKANVRSYYQQFE 42 (197)
Q Consensus 5 YCdYCd~~ft~Ds~SvRk~H~~G--krHk~NVk~yy~~~~ 42 (197)
|-.||.|+|.....-....|++. ++|-.||+.||+.-+
T Consensus 233 llNy~QC~L~~~e~yevleh~seiL~~~~~nvKA~frRak 272 (329)
T KOG0545|consen 233 LLNYCQCLLKKEEYYEVLEHCSEILRHHPGNVKAYFRRAK 272 (329)
T ss_pred HHhHHHHHhhHHHHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence 45789999854444444667755 578899999998765
No 70
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=38.74 E-value=8 Score=39.69 Aligned_cols=29 Identities=28% Similarity=0.614 Sum_probs=24.7
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKANV 34 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NV 34 (197)
.||+.|++.- +..+.+..|+.+.||+.+.
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 5999999996 5666789999999999765
No 71
>PHA00732 hypothetical protein
Probab=37.04 E-value=24 Score=26.12 Aligned_cols=21 Identities=24% Similarity=0.392 Sum_probs=16.0
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
|-|+.|++.|. +.+.++.|..
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 4566677865
No 72
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=36.59 E-value=17 Score=32.21 Aligned_cols=37 Identities=24% Similarity=0.421 Sum_probs=22.3
Q ss_pred cccccCCcceeccCCHHHHHH---hh-cchHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQ---HN-AGYKHKANVRSYYQQ 40 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~---H~-~GkrHk~NVk~yy~~ 40 (197)
-+||-+|.-.|+.-+. +-+. |. +-.-|.+||-+++..
T Consensus 21 ~efC~fC~~~f~~~sK-~~kks~fhvsNKlIHlrNVLrrlls 61 (225)
T PHA03074 21 YEFCIFCESVFQTSSK-VQKKSNFHVSNKLIHLRNVLRRLLS 61 (225)
T ss_pred EEEeecHHHHHhhhhh-hhhhcccccccceeeHHHHHHHHHH
Confidence 3689999999864433 2233 44 333477777666443
No 73
>PF04746 DUF575: Protein of unknown function (DUF575); InterPro: IPR006835 This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Probab=35.84 E-value=24 Score=27.77 Aligned_cols=34 Identities=24% Similarity=0.408 Sum_probs=25.7
Q ss_pred ceeccCCHHHHH-HhhcchHHHHHHHHHHHHHHHH
Q 029213 11 TYLTHDSPSVRK-QHNAGYKHKANVRSYYQQFEEQ 44 (197)
Q Consensus 11 ~~ft~Ds~SvRk-~H~~GkrHk~NVk~yy~~~~~e 44 (197)
-.|+.|-.++.| +|..|+.|...|+++++++|..
T Consensus 48 p~f~SDV~~ivKvEk~~G~dhisrve~~Lk~~R~~ 82 (101)
T PF04746_consen 48 PMFTSDVASIVKVEKTRGRDHISRVEEYLKSLRVT 82 (101)
T ss_pred CCCchHHHHHHHHHHhhCCCchHHHHHHHHHhcCC
Confidence 345566666555 4999999999999999887743
No 74
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.77 E-value=50 Score=30.60 Aligned_cols=15 Identities=33% Similarity=0.558 Sum_probs=10.4
Q ss_pred cccccCCcceeccCC
Q 029213 3 RYYCDYCDTYLTHDS 17 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds 17 (197)
..-|..|++.|..++
T Consensus 43 ~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 43 SGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCCCCCccchhh
Confidence 457999988775443
No 75
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=34.34 E-value=34 Score=27.41 Aligned_cols=22 Identities=32% Similarity=0.551 Sum_probs=0.0
Q ss_pred ccccCCcceeccCCHHHHHH-hhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQ-HNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~-H~~ 26 (197)
-||.|-|.-=. .+...||. |++
T Consensus 12 gYciYFD~KRR-~dP~frkkL~~r 34 (121)
T PF02064_consen 12 GYCIYFDYKRR-SDPDFRKKLRER 34 (121)
T ss_dssp ------------------------
T ss_pred HHHhhcccccc-cChHHHHHHHHH
Confidence 48999988753 33444333 443
No 76
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=34.28 E-value=23 Score=27.74 Aligned_cols=17 Identities=35% Similarity=0.823 Sum_probs=12.5
Q ss_pred cccccCCcceeccCCHH
Q 029213 3 RYYCDYCDTYLTHDSPS 19 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~S 19 (197)
+-||.||+++-.|.-..
T Consensus 8 ~tyCp~CkkhT~H~V~~ 24 (94)
T COG1631 8 RTYCPYCKKHTIHKVER 24 (94)
T ss_pred eecCcccccceeeeeee
Confidence 56999999997654333
No 77
>PF14291 DUF4371: Domain of unknown function (DUF4371)
Probab=34.21 E-value=56 Score=27.92 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=18.5
Q ss_pred HHHhhc--chHHHHHHHHHHHHHH
Q 029213 21 RKQHNA--GYKHKANVRSYYQQFE 42 (197)
Q Consensus 21 Rk~H~~--GkrHk~NVk~yy~~~~ 42 (197)
++.|+. ...|+++++.|.+...
T Consensus 17 ~~~He~~~s~~H~~a~~~~~~~~~ 40 (235)
T PF14291_consen 17 FKKHEKSVSSSHKNAMEAWKEFKQ 40 (235)
T ss_pred HHhhCCCCCHHHHHHHHHHHHHhc
Confidence 689999 9999999988766543
No 78
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=34.06 E-value=27 Score=36.28 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=18.1
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
-|-|..|||-| +...+|+.|-.
T Consensus 792 iFpCreC~kvF--~KiKSrNAHMK 813 (907)
T KOG4167|consen 792 IFPCRECGKVF--FKIKSRNAHMK 813 (907)
T ss_pred eeehHHHHHHH--HHHhhhhHHHH
Confidence 57899999999 67777888864
No 79
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=33.85 E-value=50 Score=22.13 Aligned_cols=36 Identities=6% Similarity=0.095 Sum_probs=21.5
Q ss_pred hcchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Q 029213 25 NAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQ 60 (197)
Q Consensus 25 ~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~ 60 (197)
.+...|.+.++..|+......+.+.+.++++..+++
T Consensus 26 ~rs~~ql~~i~~~Y~~~~g~~L~~~i~~e~sGd~~~ 61 (66)
T PF00191_consen 26 TRSPAQLRAIKQAYKKKYGKDLEEDIKKETSGDFEK 61 (66)
T ss_dssp HSTHHHHHHHHHHHHHHHSS-HHHHHHHHSTHHHHH
T ss_pred hhcccccceeehhhhhhhHHHHHHHHHHhCCHHHHH
Confidence 355678888888887776555444455555544443
No 80
>PHA00616 hypothetical protein
Probab=32.25 E-value=24 Score=23.94 Aligned_cols=20 Identities=20% Similarity=0.363 Sum_probs=15.9
Q ss_pred ccccCCcceeccCCHHHHHHhh
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHN 25 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~ 25 (197)
|-|.-|++.|. ..+..+.|+
T Consensus 2 YqC~~CG~~F~--~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFR--KKKEVIEHL 21 (44)
T ss_pred CccchhhHHHh--hHHHHHHHH
Confidence 67999999994 456668888
No 81
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=32.12 E-value=22 Score=28.31 Aligned_cols=21 Identities=29% Similarity=0.521 Sum_probs=14.5
Q ss_pred cccCCc--ceeccCCHHHHHHhhc
Q 029213 5 YCDYCD--TYLTHDSPSVRKQHNA 26 (197)
Q Consensus 5 YCdYCd--~~ft~Ds~SvRk~H~~ 26 (197)
+|.||+ +||.=. .|.+..|+.
T Consensus 27 lCp~C~~~~wl~lK-nSsY~~Hl~ 49 (124)
T PF14616_consen 27 LCPYCPGGNWLKLK-NSSYWYHLQ 49 (124)
T ss_pred ECCCCCCCcEeeec-ccchhhhhh
Confidence 899999 998323 344567764
No 82
>PHA00733 hypothetical protein
Probab=31.21 E-value=32 Score=27.42 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=16.5
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
.|-|+.|++.| .+.+.++.|..
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 45566677765
No 83
>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=31.14 E-value=8.8 Score=28.01 Aligned_cols=23 Identities=39% Similarity=0.933 Sum_probs=16.1
Q ss_pred CcccccCCcceeccCCHHHHHHhh
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHN 25 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~ 25 (197)
|||||.-|.+|+|+. -+.|+--.
T Consensus 29 PR~~Ck~C~rywT~G-G~lRnVPv 51 (63)
T PF02701_consen 29 PRYFCKSCRRYWTHG-GTLRNVPV 51 (63)
T ss_pred cchhhHHHHHHHHhc-ceecCCcc
Confidence 699999999999744 34444333
No 84
>PRK00420 hypothetical protein; Validated
Probab=30.55 E-value=1e+02 Score=24.56 Aligned_cols=13 Identities=8% Similarity=0.092 Sum_probs=10.0
Q ss_pred CcccccCCcceec
Q 029213 2 PRYYCDYCDTYLT 14 (197)
Q Consensus 2 PryYCdYCd~~ft 14 (197)
+..||.-|+..+.
T Consensus 39 g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 39 GEVVCPVHGKVYI 51 (112)
T ss_pred CceECCCCCCeee
Confidence 3678999998774
No 85
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=30.41 E-value=2.1e+02 Score=20.71 Aligned_cols=27 Identities=19% Similarity=0.421 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHHHhh-HHHHHHhHHhhh
Q 029213 47 QSLIDQRIKEHLGQT-AAFQQVGAAYNQ 73 (197)
Q Consensus 47 Q~l~dk~lkk~l~~t-eaf~~ag~~y~~ 73 (197)
+.+..++|..+|... .+|.++++.|.+
T Consensus 69 ~k~~~~KL~~df~~~l~~fq~~q~~~~~ 96 (102)
T PF14523_consen 69 QKLQREKLSRDFKEALQEFQKAQRRYAE 96 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334555666665554 667666666643
No 86
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=30.19 E-value=25 Score=26.42 Aligned_cols=11 Identities=45% Similarity=1.210 Sum_probs=10.4
Q ss_pred cccccCCccee
Q 029213 3 RYYCDYCDTYL 13 (197)
Q Consensus 3 ryYCdYCd~~f 13 (197)
+|||.+|+..+
T Consensus 4 ~Y~CRHCg~~I 14 (76)
T PF10955_consen 4 HYYCRHCGTKI 14 (76)
T ss_pred EEEecCCCCEE
Confidence 79999999998
No 87
>PF14369 zf-RING_3: zinc-finger
Probab=30.06 E-value=25 Score=22.31 Aligned_cols=12 Identities=33% Similarity=1.303 Sum_probs=10.5
Q ss_pred cccccCCcceec
Q 029213 3 RYYCDYCDTYLT 14 (197)
Q Consensus 3 ryYCdYCd~~ft 14 (197)
+|||--|++++.
T Consensus 2 ~ywCh~C~~~V~ 13 (35)
T PF14369_consen 2 RYWCHQCNRFVR 13 (35)
T ss_pred CEeCccCCCEeE
Confidence 699999998884
No 88
>PF14279 HNH_5: HNH endonuclease
Probab=29.81 E-value=69 Score=23.27 Aligned_cols=47 Identities=19% Similarity=0.301 Sum_probs=28.7
Q ss_pred ccCCcceeccCCHHHHHHhh-----cchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 029213 6 CDYCDTYLTHDSPSVRKQHN-----AGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHL 58 (197)
Q Consensus 6 CdYCd~~ft~Ds~SvRk~H~-----~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l 58 (197)
|-||++-+..++.+ .+|. .|+.+..+|.+.-.++.-. .+|..+.+.+
T Consensus 1 Ci~C~~~~~~~~~s--~EHIIP~sLGG~~~~~~vC~~CN~~~g~----~vD~~l~~~~ 52 (71)
T PF14279_consen 1 CIYCNKEKSESNFS--EEHIIPESLGGKLKINNVCDKCNNKFGS----KVDAELANQF 52 (71)
T ss_pred CccCCCCCCccCCC--ccccCchhcCCcccccchhHHHhHHHhH----HHHHHHHHhH
Confidence 89999998655433 5674 6777776666665554322 2455544443
No 89
>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=29.76 E-value=59 Score=25.94 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=38.1
Q ss_pred ccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHH--HhhHHHHHHHHHHHHhh
Q 029213 6 CDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQ--QTQSLIDQRIKEHLGQT 61 (197)
Q Consensus 6 CdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~e--k~Q~l~dk~lkk~l~~t 61 (197)
-||..+||.......|+.=-..+.+++.+.+-.+.+... .+-..+++.|..+|+.=
T Consensus 65 ~~Y~~~FL~~~~~~~R~~vyI~~e~h~~l~~Iv~~ig~~~~si~~yidNIL~~Hle~~ 122 (136)
T PF11888_consen 65 EDYRETFLKRPKIKARKGVYISRETHERLSRIVRVIGERKMSISGYIDNILRHHLEEY 122 (136)
T ss_pred HHHHHHhCCCCCCCCCeeeEECHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHH
Confidence 367788886666666555334555666777777777744 46667888888888764
No 90
>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=27.82 E-value=29 Score=22.64 Aligned_cols=11 Identities=36% Similarity=1.201 Sum_probs=8.4
Q ss_pred cccccCCccee
Q 029213 3 RYYCDYCDTYL 13 (197)
Q Consensus 3 ryYCdYCd~~f 13 (197)
.-||++|++.|
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 35899999998
No 91
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.39 E-value=2.7e+02 Score=23.18 Aligned_cols=39 Identities=13% Similarity=0.261 Sum_probs=21.6
Q ss_pred cchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhHHHHH
Q 029213 26 AGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQTAAFQQ 66 (197)
Q Consensus 26 ~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~teaf~~ 66 (197)
+..+|+.++++-++..+.+- .+ +.+++.++|.++.+.++
T Consensus 31 ~~~k~q~~~q~ELe~~K~~l-d~-~rqel~~HFa~sAeLlk 69 (138)
T COG3105 31 RKLKQQQKLQYELEKVKAQL-DE-YRQELVKHFARSAELLK 69 (138)
T ss_pred hhhhhHHHHHHHHHHHHHHH-HH-HHHHHHHHHHHHHHHHH
Confidence 44566666666665554331 11 44566677777655543
No 92
>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=27.36 E-value=1.1e+02 Score=23.03 Aligned_cols=13 Identities=38% Similarity=0.989 Sum_probs=10.8
Q ss_pred CcccccCCcceec
Q 029213 2 PRYYCDYCDTYLT 14 (197)
Q Consensus 2 PryYCdYCd~~ft 14 (197)
+.++|+-|+-.+.
T Consensus 30 ~~~~C~~CGe~~~ 42 (127)
T TIGR03830 30 PGWYCPACGEELL 42 (127)
T ss_pred eeeECCCCCCEEE
Confidence 4689999998885
No 93
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.16 E-value=3e+02 Score=21.80 Aligned_cols=15 Identities=33% Similarity=0.614 Sum_probs=9.0
Q ss_pred HHHHHHHHHHhhHHH
Q 029213 50 IDQRIKEHLGQTAAF 64 (197)
Q Consensus 50 ~dk~lkk~l~~teaf 64 (197)
+.+.+.++|.+|..+
T Consensus 44 yk~~V~~HF~~ta~L 58 (128)
T PF06295_consen 44 YKQEVNDHFAQTAEL 58 (128)
T ss_pred HHHHHHHHHHHHHHH
Confidence 555666666666443
No 94
>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=26.48 E-value=35 Score=28.63 Aligned_cols=13 Identities=15% Similarity=0.751 Sum_probs=10.1
Q ss_pred ccccCCcceeccC
Q 029213 4 YYCDYCDTYLTHD 16 (197)
Q Consensus 4 yYCdYCd~~ft~D 16 (197)
..|..|+|||.|.
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 4688999999854
No 95
>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=26.18 E-value=8.8 Score=25.14 Aligned_cols=17 Identities=47% Similarity=0.900 Sum_probs=11.5
Q ss_pred ccCCcceeccCCHHHHHH
Q 029213 6 CDYCDTYLTHDSPSVRKQ 23 (197)
Q Consensus 6 CdYCd~~ft~Ds~SvRk~ 23 (197)
||||+.-|. +..-++|.
T Consensus 1 Cd~CG~~I~-~eP~~~k~ 17 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVVKI 17 (37)
T ss_pred CCccCCccc-CCEEEEEE
Confidence 999999995 44433343
No 96
>KOG4139 consensus Protein kinase essential for the initiation of DNA replication [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=25.75 E-value=72 Score=31.67 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=14.7
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKH 30 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrH 30 (197)
+-||++|.-.+ +.+++ |+....|
T Consensus 299 ~GrCpfc~~~~--~~L~~---hk~s~~h 321 (520)
T KOG4139|consen 299 KGRCPFCGERY--YDLSI---HKQSVQH 321 (520)
T ss_pred ccccccccchH--HHhHH---Hhhhhhh
Confidence 35899998887 44655 4444444
No 97
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=24.51 E-value=1.4e+02 Score=23.79 Aligned_cols=31 Identities=13% Similarity=0.223 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Q 029213 30 HKANVRSYYQQFEEQQTQSLIDQRIKEHLGQ 60 (197)
Q Consensus 30 Hk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~ 60 (197)
.++++++.|+.+.+++.|..+++-..+++++
T Consensus 67 Q~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~ 97 (104)
T PF11460_consen 67 QRKDYEEAVDQLTNEELQKRLEELSPEELEA 97 (104)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHhCCHHHHHH
Confidence 4455666666666665555455444444433
No 98
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=24.47 E-value=31 Score=30.99 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=27.4
Q ss_pred cccccCCcceeccCCHHHHHHhh---cchHHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHN---AGYKHKANVRSYYQQF 41 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~---~GkrHk~NVk~yy~~~ 41 (197)
-|.|..|++-|+.. -| ++.|+ -|..|+-+++++-+.+
T Consensus 173 pykc~~c~kaftqr-cs-leshl~kvhgv~~~yaykerr~kl 212 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQR-CS-LESHLKKVHGVQHQYAYKERRAKL 212 (267)
T ss_pred ccchhhhhHHHHhh-cc-HHHHHHHHcCchHHHHHHHhhhhe
Confidence 38899999999743 33 47777 5888888887776654
No 99
>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=24.39 E-value=1.1e+02 Score=26.34 Aligned_cols=26 Identities=12% Similarity=0.121 Sum_probs=15.3
Q ss_pred cccCCcceeccCCHHHHHHhhcchHHH
Q 029213 5 YCDYCDTYLTHDSPSVRKQHNAGYKHK 31 (197)
Q Consensus 5 YCdYCd~~ft~Ds~SvRk~H~~GkrHk 31 (197)
-|..||.|++ ++.-.++.++..+-=.
T Consensus 125 qC~~CN~~~s-gn~~~Yr~~Li~kiG~ 150 (189)
T PF05766_consen 125 QCKHCNRHLS-GNIVEYRIGLIEKIGQ 150 (189)
T ss_pred cCCccccccc-cCHHHHHHHHHHHHhH
Confidence 4888888885 4454455555444333
No 100
>KOG4330 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.11 E-value=2.8e+02 Score=24.35 Aligned_cols=51 Identities=14% Similarity=0.107 Sum_probs=26.5
Q ss_pred CHHHHHHh-hcchHHHHHHHHHHHHHHH---HHhhHHHHHHHHHHH-HhhHHHHHH
Q 029213 17 SPSVRKQH-NAGYKHKANVRSYYQQFEE---QQTQSLIDQRIKEHL-GQTAAFQQV 67 (197)
Q Consensus 17 s~SvRk~H-~~GkrHk~NVk~yy~~~~~---ek~Q~l~dk~lkk~l-~~teaf~~a 67 (197)
+.+++..| +.--.-.+||..--+.+.+ .++.+.++..|.+.| ++-++||+|
T Consensus 133 s~s~~mr~~ek~~FTlrqVqmICErllKerE~klReeyE~vLttKLaEQydafVkF 188 (206)
T KOG4330|consen 133 STSSTMRKSEKPLFTLRQVQMICERLLKEREIKLREEYEMVLTTKLAEQYDAFVKF 188 (206)
T ss_pred CccchhhccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555 4444555666555444432 245555666555443 344777754
No 101
>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=23.97 E-value=36 Score=22.45 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=8.6
Q ss_pred ccccCCccee
Q 029213 4 YYCDYCDTYL 13 (197)
Q Consensus 4 yYCdYCd~~f 13 (197)
..|.||++.|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 5799999877
No 102
>PRK11677 hypothetical protein; Provisional
Probab=23.84 E-value=3.7e+02 Score=21.97 Aligned_cols=45 Identities=13% Similarity=0.284 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhHHHHH-HhHHhh---hhhh
Q 029213 30 HKANVRSYYQQFEEQQTQSLIDQRIKEHLGQTAAFQQ-VGAAYN---QHLL 76 (197)
Q Consensus 30 Hk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~teaf~~-ag~~y~---~dla 76 (197)
.++++++-++..+.+ -+.+.+++.++|.+|...+. -.+.|+ +|||
T Consensus 30 ~q~~le~eLe~~k~e--le~YkqeV~~HFa~TA~Ll~~L~~~Y~~Ly~HlA 78 (134)
T PRK11677 30 QQQALQYELEKNKAE--LEEYRQELVSHFARSAELLDTMAKDYRQLYQHMA 78 (134)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444443333 12266777888877755433 244453 3555
No 103
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=23.25 E-value=23 Score=36.66 Aligned_cols=11 Identities=36% Similarity=1.105 Sum_probs=9.4
Q ss_pred ccccCCcceec
Q 029213 4 YYCDYCDTYLT 14 (197)
Q Consensus 4 yYCdYCd~~ft 14 (197)
.||-||+-+|.
T Consensus 172 KYCGYCk~Hfs 182 (900)
T KOG0956|consen 172 KYCGYCKYHFS 182 (900)
T ss_pred eechhHHHHHH
Confidence 69999998883
No 104
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=23.19 E-value=84 Score=22.77 Aligned_cols=34 Identities=12% Similarity=-0.084 Sum_probs=24.4
Q ss_pred CcccccCCcceeccCCHHHHHHhhcchHHHHHHHHHH
Q 029213 2 PRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYY 38 (197)
Q Consensus 2 PryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy 38 (197)
+.|+|+-|..-|. + .-- ..|..|+.|.+.+.++.
T Consensus 4 G~~~~~~~~~~i~-~-~~d-mgH~~~~e~~~~~~~~~ 37 (70)
T PF14410_consen 4 GKVRDPNTGYPIE-G-PWD-MGHKPGVEYWRLVGRAE 37 (70)
T ss_pred CeEecCCCCCCCC-C-CCC-ccCchHHHHHHHHHHHH
Confidence 4789999999983 2 222 46888888887766653
No 105
>KOG0819 consensus Annexin [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.09 E-value=91 Score=29.19 Aligned_cols=47 Identities=13% Similarity=0.134 Sum_probs=32.2
Q ss_pred cceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Q 029213 10 DTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKE 56 (197)
Q Consensus 10 d~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk 56 (197)
++|-++++.-++.-+.+.+.|.+.|-..|+...-..+.+.++++++.
T Consensus 186 ~k~gtde~~~~~Il~tRs~~qL~~vf~~y~~~~g~diek~I~~e~~g 232 (321)
T KOG0819|consen 186 KKWGTDEDKFIRILTTRSKAQLRLVFEEYQRISGKDIEKSIKEEFSG 232 (321)
T ss_pred hhccCcHHHHHHHHHhCCHHHHHHHHHHHHHhcchhHHHHHhhccCc
Confidence 45556666667778999999999999999887654433334444443
No 106
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.03 E-value=47 Score=30.62 Aligned_cols=22 Identities=32% Similarity=0.697 Sum_probs=17.5
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
-|.|+||=+|| ++...+..|..
T Consensus 48 lyiCe~Clky~--~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYM--RKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchh--CCHHHHHHHHH
Confidence 37899999999 56677788865
No 107
>PTZ00046 rifin; Provisional
Probab=22.73 E-value=1.1e+02 Score=29.13 Aligned_cols=10 Identities=40% Similarity=1.248 Sum_probs=5.0
Q ss_pred cccccCCccee
Q 029213 3 RYYCDYCDTYL 13 (197)
Q Consensus 3 ryYCdYCd~~f 13 (197)
|-.|+ ||.|-
T Consensus 39 R~LcE-CeLY~ 48 (358)
T PTZ00046 39 RLLCE-CELYS 48 (358)
T ss_pred hhhhh-hhcCC
Confidence 34453 66654
No 108
>PF06319 DUF1052: Protein of unknown function (DUF1052); InterPro: IPR009394 This entry is represented by Ralstonia phage RSL1, Orf212. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of unknown function.; PDB: 3DNX_A.
Probab=22.68 E-value=37 Score=28.74 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=9.1
Q ss_pred ccccCCcceeccC
Q 029213 4 YYCDYCDTYLTHD 16 (197)
Q Consensus 4 yYCdYCd~~ft~D 16 (197)
-|-+|||+||.-.
T Consensus 82 dY~~~CDRfyfAv 94 (157)
T PF06319_consen 82 DYLDWCDRFYFAV 94 (157)
T ss_dssp GGGGG-SEEEEEE
T ss_pred HHHHhhceeEEec
Confidence 4889999988633
No 109
>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=21.88 E-value=40 Score=21.01 Aligned_cols=12 Identities=25% Similarity=0.841 Sum_probs=10.6
Q ss_pred cccccCCcceec
Q 029213 3 RYYCDYCDTYLT 14 (197)
Q Consensus 3 ryYCdYCd~~ft 14 (197)
+|||.-|+..|-
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 110
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=21.86 E-value=20 Score=37.27 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=20.8
Q ss_pred ccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFE 42 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~ 42 (197)
|-||-|.|.|.|. -| +-+|-+ |+-.+.+.|+.-+
T Consensus 951 fQCdKClKRFSHS-GS-YSQHMN---HRYSYCKpyrEer 984 (1007)
T KOG3623|consen 951 FQCDKCLKRFSHS-GS-YSQHMN---HRYSYCKPYREER 984 (1007)
T ss_pred chhhhhhhhcccc-cc-hHhhhc---cchhcccchhhcc
Confidence 6677777777533 33 466665 7666666665543
No 111
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=21.85 E-value=11 Score=40.88 Aligned_cols=53 Identities=21% Similarity=0.369 Sum_probs=0.0
Q ss_pred ccccCCcceeccCCHHHHHHhhc----------chHHHHHHHHHHHHHHHH-HhhHHHHHHHHHH
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA----------GYKHKANVRSYYQQFEEQ-QTQSLIDQRIKEH 57 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~----------GkrHk~NVk~yy~~~~~e-k~Q~l~dk~lkk~ 57 (197)
+-|.+||+|.+ |++-....|+. |-.|...++.|.++.+.. +++++.|+++.|+
T Consensus 735 ~~civcd~~st-~~l~~l~~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kanfqlh~Ktdkh~qk~ 798 (1406)
T KOG1146|consen 735 FDCIVCDVFST-DRLDQLWFHNTRERSRKEQVPGDVPSCKLKPYATNTKANFQLHNKTDKHVQKY 798 (1406)
T ss_pred HHHhhhhhhhh-hhHHHHhhcchhhhhhhhcccCCCCcceecccccccchhhhhhcccchhhhcc
No 112
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.81 E-value=61 Score=25.97 Aligned_cols=36 Identities=31% Similarity=0.464 Sum_probs=22.0
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQ 40 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~ 40 (197)
||-|.-|++.|+..+-+.+. | .=.+=++-+..+|..
T Consensus 53 RyrC~~C~~tf~~~~~~~~~-~-~~~~~~~~~~~~~~~ 88 (129)
T COG3677 53 RYKCKSCGSTFTVETGSPLS-K-ALYKIKLQAVTLYML 88 (129)
T ss_pred ccccCCcCcceeeeccCccc-c-cchHHHHHHHHHHHc
Confidence 79999999999766655533 3 223334444444444
No 113
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.76 E-value=83 Score=20.42 Aligned_cols=24 Identities=25% Similarity=0.439 Sum_probs=19.2
Q ss_pred cccccCCcceeccCCHHHHHHhhc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
...|..|+-.++.++..-.+.|.+
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~ 36 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKK 36 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHH
Confidence 457999999998888887777753
No 114
>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=21.67 E-value=1.7e+02 Score=29.32 Aligned_cols=52 Identities=15% Similarity=0.274 Sum_probs=30.1
Q ss_pred cCCcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhHHHHHH
Q 029213 7 DYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQTAAFQQV 67 (197)
Q Consensus 7 dYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~teaf~~a 67 (197)
-||..|+.+......+.-+++--|+ +++....++.++.+...|+.+-.||..
T Consensus 353 SyCRLYYsR~D~~~i~FLi~~e~ak---------lrek~~ke~~~k~~I~~F~k~~eFCE~ 404 (641)
T KOG0352|consen 353 SYCRLYYSRQDKNALNFLVSGELAK---------LREKAKKEMQIKSIITGFAKMLEFCES 404 (641)
T ss_pred cceeeeecccchHHHHHHHhhHHHH---------HHHhcchhhhHHHHHHHHHHHHHHHHH
Confidence 4888888765555434444444444 222223445666677777777777753
No 115
>PF12940 RAG1: Recombination-activation protein 1 (RAG1); InterPro: IPR024627 This entry represents recombination activating protein 1 (RAG1), which is the catalytic component of the RAG complex. The RAG complex is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination []. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) []. Many of the proteins recognised by this entry are fragments.; GO: 0043565 sequence-specific DNA binding, 0033151 V(D)J recombination
Probab=21.14 E-value=25 Score=33.90 Aligned_cols=34 Identities=26% Similarity=0.569 Sum_probs=28.5
Q ss_pred cccccCCcceeccCCHHHHHHhhcchHHHHHHHHH
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY 37 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~GkrHk~NVk~y 37 (197)
.|.|..||..-+..+++. -.|...+.|.+|+++|
T Consensus 216 tYiCTLCdstraeAsqnm-vlhsItrsh~Enlery 249 (442)
T PF12940_consen 216 TYICTLCDSTRAEASQNM-VLHSITRSHEENLERY 249 (442)
T ss_pred eEEEeeccCcchhhhhcc-ccccccCCchhhhhhc
Confidence 699999999986555553 7799999999999877
No 116
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=20.83 E-value=2.1e+02 Score=24.22 Aligned_cols=9 Identities=44% Similarity=1.350 Sum_probs=5.9
Q ss_pred cccccCCcc
Q 029213 3 RYYCDYCDT 11 (197)
Q Consensus 3 ryYCdYCd~ 11 (197)
++||..|=.
T Consensus 11 ~~~C~~C~~ 19 (302)
T PF10186_consen 11 RFYCANCVN 19 (302)
T ss_pred CeECHHHHH
Confidence 567777743
No 117
>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=20.76 E-value=46 Score=21.40 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=9.3
Q ss_pred cccccCCccee
Q 029213 3 RYYCDYCDTYL 13 (197)
Q Consensus 3 ryYCdYCd~~f 13 (197)
...||.|+.||
T Consensus 14 ~i~C~~C~~~~ 24 (51)
T PF00628_consen 14 MIQCDSCNRWY 24 (51)
T ss_dssp EEEBSTTSCEE
T ss_pred eEEcCCCChhh
Confidence 35799999998
No 118
>PRK10780 periplasmic chaperone; Provisional
Probab=20.68 E-value=4.6e+02 Score=21.20 Aligned_cols=29 Identities=7% Similarity=0.020 Sum_probs=23.1
Q ss_pred CCHHHHHHhhcchHHHHHHHHHHHHHHHH
Q 029213 16 DSPSVRKQHNAGYKHKANVRSYYQQFEEQ 44 (197)
Q Consensus 16 Ds~SvRk~H~~GkrHk~NVk~yy~~~~~e 44 (197)
|...+..+|..+++-...+++.++.+.++
T Consensus 30 d~q~il~~~p~~k~~~~~le~~~~~~q~e 58 (165)
T PRK10780 30 NMGSIFQQVPQRTGVSKQLENEFKGRASE 58 (165)
T ss_pred eHHHHHHHCHHHHHHHHHHHHHHHHHHHH
Confidence 77788888999998888888888766544
No 119
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.67 E-value=49 Score=32.97 Aligned_cols=23 Identities=17% Similarity=0.431 Sum_probs=18.0
Q ss_pred cccccCCcceeccCCHHHHHHhhcc
Q 029213 3 RYYCDYCDTYLTHDSPSVRKQHNAG 27 (197)
Q Consensus 3 ryYCdYCd~~ft~Ds~SvRk~H~~G 27 (197)
-|.|+||=+|| ++...+..|...
T Consensus 280 LYICEfCLkY~--~s~~~l~rH~~~ 302 (552)
T PTZ00064 280 LHFCEYCLDFF--CFEDELIRHLSR 302 (552)
T ss_pred EEEccchhhhh--CCHHHHHHHHhc
Confidence 37899999999 566777888663
No 120
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=20.56 E-value=1.2e+02 Score=28.82 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=4.8
Q ss_pred cccccCCccee
Q 029213 3 RYYCDYCDTYL 13 (197)
Q Consensus 3 ryYCdYCd~~f 13 (197)
|-+|+ ||.|-
T Consensus 42 R~LcE-CeLy~ 51 (353)
T TIGR01477 42 RSLCE-CELYS 51 (353)
T ss_pred ehhhh-hhccc
Confidence 34453 55553
No 121
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=20.37 E-value=69 Score=23.32 Aligned_cols=21 Identities=14% Similarity=0.333 Sum_probs=15.0
Q ss_pred ccccCCcceeccCCHHHHHHhhc
Q 029213 4 YYCDYCDTYLTHDSPSVRKQHNA 26 (197)
Q Consensus 4 yYCdYCd~~ft~Ds~SvRk~H~~ 26 (197)
+-|.-|+..| +|+.+. ..|.+
T Consensus 18 lrCPRC~~~F-R~~K~Y-~RHVN 38 (65)
T COG4049 18 LRCPRCGMVF-RRRKDY-IRHVN 38 (65)
T ss_pred eeCCchhHHH-HHhHHH-HHHhh
Confidence 4699999999 576664 55553
No 122
>PLN00064 photosystem II protein Psb27; Provisional
Probab=20.24 E-value=1e+02 Score=26.41 Aligned_cols=38 Identities=16% Similarity=0.107 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHH-HHHhhHHHHHHHHHHHHhhHHHHHH
Q 029213 30 HKANVRSYYQQFE-EQQTQSLIDQRIKEHLGQTAAFQQV 67 (197)
Q Consensus 30 Hk~NVk~yy~~~~-~ek~Q~l~dk~lkk~l~~teaf~~a 67 (197)
-...+.-||..|. ..=+.++..++|.++|+++|..+.-
T Consensus 126 ALNaLAGHY~SfgpnrPlPeKlK~RL~qE~~~AEkal~R 164 (166)
T PLN00064 126 ALNAVSGHYISFGPTAPIPAKRKARILEEMDTAEKALLR 164 (166)
T ss_pred HHHHHHHHhhccCCCCCCcHHHHHHHHHHHHHHHHHHHc
Confidence 3444666676664 2234556778889999998876543
No 123
>PF04837 MbeB_N: MbeB-like, N-term conserved region; InterPro: IPR006922 This family consists of Mbe/Mob proteins defined by an N-terminal conserved region. These proteins are essential for specific plasmid transfer.
Probab=20.19 E-value=3.2e+02 Score=19.10 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHhhHHHHHHhH
Q 029213 34 VRSYYQQFEEQQTQSLIDQRIKEHLGQTAAFQQVGA 69 (197)
Q Consensus 34 Vk~yy~~~~~ek~Q~l~dk~lkk~l~~teaf~~ag~ 69 (197)
+.+-|++--++++++ +++.++.+|.+-|.++.+..
T Consensus 7 LA~~feqkskeqa~s-te~~vk~af~~~E~~l~~~L 41 (52)
T PF04837_consen 7 LAKDFEQKSKEQAES-TEQMVKNAFEQHEKSLSAAL 41 (52)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 344444433444444 78888888888887765543
No 124
>KOG0579 consensus Ste20-like serine/threonine protein kinase [Signal transduction mechanisms]
Probab=20.09 E-value=1.1e+02 Score=32.34 Aligned_cols=61 Identities=15% Similarity=0.424 Sum_probs=39.9
Q ss_pred CcceeccCCHHHHHHhhcchHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhHHHHHHhHHhhhhhh
Q 029213 9 CDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQTAAFQQVGAAYNQHLL 76 (197)
Q Consensus 9 Cd~~ft~Ds~SvRk~H~~GkrHk~NVk~yy~~~~~ek~Q~l~dk~lkk~l~~teaf~~ag~~y~~dla 76 (197)
|+..+.|.+... |.| -.+|.++++.|-+.+...+ .++++.++.++..+|-| +|-+|..-.+
T Consensus 1118 chlLvEhEtqkl-Kel--de~h~~~~~~w~e~l~~rk--~~lee~~~~~~reqE~f--~~ms~~~~~~ 1178 (1187)
T KOG0579|consen 1118 CHLLVEHETQKL-KEL--DEKHHEMRELWQENLIARK--TVLEEKFEDELREQEVF--YGMSYTSSQA 1178 (1187)
T ss_pred HHHHHHHHHHHH-HHH--HHHHHHHHHHHHHhhhhhh--hHHHHHHHHHHHHHHHH--hccccccCCC
Confidence 555555444432 433 3467778888877776553 34777788888888888 6888865444
No 125
>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]
Probab=20.07 E-value=2.8e+02 Score=28.44 Aligned_cols=22 Identities=41% Similarity=0.539 Sum_probs=17.1
Q ss_pred HhhcchHHHHHHHHHHHHHHHH
Q 029213 23 QHNAGYKHKANVRSYYQQFEEQ 44 (197)
Q Consensus 23 ~H~~GkrHk~NVk~yy~~~~~e 44 (197)
..+.=|+-|+|+++|++.|+++
T Consensus 599 S~e~~KkIkKnLKky~a~Feeq 620 (698)
T KOG2314|consen 599 SEEKQKKIKKNLKKYSAQFEEQ 620 (698)
T ss_pred CHHHHHHHHHHHHHHHHHHhhh
Confidence 3445577889999999999865
Done!