Query 043013
Match_columns 179
No_of_seqs 83 out of 85
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:56:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2785 C2H2-type Zn-finger pr 99.0 6.6E-11 1.4E-15 107.9 -0.7 69 30-98 22-102 (390)
2 PF12874 zf-met: Zinc-finger o 98.6 1.6E-08 3.4E-13 57.5 1.7 25 65-89 1-25 (25)
3 smart00451 ZnF_U1 U1-like zinc 98.5 9.6E-08 2.1E-12 57.5 2.2 32 64-95 3-34 (35)
4 PF12171 zf-C2H2_jaz: Zinc-fin 98.1 9.4E-07 2E-11 51.8 1.3 26 65-90 2-27 (27)
5 PF06220 zf-U1: U1 zinc finger 96.3 0.0033 7.1E-08 40.6 2.4 33 63-95 2-36 (38)
6 KOG0717 Molecular chaperone (D 96.0 0.0041 8.9E-08 59.2 2.6 37 65-101 293-329 (508)
7 PF13894 zf-C2H2_4: C2H2-type 95.9 0.0058 1.2E-07 32.8 1.7 21 65-85 1-21 (24)
8 PF12756 zf-C2H2_2: C2H2 type 95.6 0.0047 1E-07 42.5 0.8 35 60-94 46-80 (100)
9 PF00096 zf-C2H2: Zinc finger, 95.1 0.014 3E-07 32.2 1.6 22 65-86 1-22 (23)
10 KOG0227 Splicing factor 3a, su 95.1 0.013 2.8E-07 50.9 2.1 32 64-95 53-84 (222)
11 PLN02748 tRNA dimethylallyltra 95.0 0.019 4E-07 53.8 2.9 36 64-99 418-454 (468)
12 KOG4727 U1-like Zn-finger prot 94.3 0.036 7.7E-07 47.4 2.9 37 60-96 71-107 (193)
13 COG5246 PRP11 Splicing factor 94.2 0.044 9.6E-07 47.5 3.1 34 63-96 52-85 (222)
14 smart00355 ZnF_C2H2 zinc finge 93.1 0.051 1.1E-06 29.0 1.2 21 65-85 1-21 (26)
15 PF07535 zf-DBF: DBF zinc fing 92.9 0.054 1.2E-06 37.1 1.3 28 63-93 4-31 (49)
16 PTZ00448 hypothetical protein; 92.8 0.013 2.9E-07 54.1 -2.3 26 31-56 334-359 (373)
17 PF13912 zf-C2H2_6: C2H2-type 92.8 0.072 1.6E-06 30.4 1.6 21 65-85 2-22 (27)
18 smart00586 ZnF_DBF Zinc finger 92.8 0.043 9.4E-07 37.8 0.7 30 62-94 3-32 (49)
19 KOG3032 Uncharacterized conser 92.7 0.25 5.3E-06 44.1 5.4 45 53-98 24-68 (264)
20 KOG4722 Zn-finger protein [Gen 88.4 0.25 5.4E-06 47.8 1.7 34 64-97 493-526 (672)
21 KOG3408 U1-like Zn-finger-cont 88.3 0.28 6E-06 39.9 1.7 35 64-98 57-91 (129)
22 PF13909 zf-H2C2_5: C2H2-type 85.8 0.53 1.2E-05 26.3 1.4 19 66-85 2-20 (24)
23 PF04988 AKAP95: A-kinase anch 85.8 0.61 1.3E-05 39.3 2.4 33 65-97 1-33 (165)
24 smart00734 ZnF_Rad18 Rad18-lik 83.2 0.7 1.5E-05 27.6 1.2 19 66-85 3-21 (26)
25 PF09237 GAGA: GAGA factor; I 83.1 0.75 1.6E-05 32.7 1.5 25 61-85 21-45 (54)
26 KOG2837 Protein containing a U 82.5 0.23 5E-06 45.1 -1.5 36 63-98 24-59 (309)
27 COG5112 UFD2 U1-like Zn-finger 76.0 1.8 3.9E-05 35.0 1.8 35 64-98 55-89 (126)
28 KOG0150 Spliceosomal protein F 74.9 1.5 3.3E-05 40.4 1.3 35 61-95 7-42 (336)
29 KOG3454 U1 snRNP-specific prot 73.9 2 4.2E-05 36.3 1.6 34 63-96 2-37 (165)
30 PF04959 ARS2: Arsenite-resist 72.1 4.3 9.4E-05 34.9 3.3 40 60-100 73-112 (214)
31 KOG1994 Predicted RNA binding 71.2 2.4 5.3E-05 38.0 1.6 24 64-87 239-262 (268)
32 PF12756 zf-C2H2_2: C2H2 type 63.8 2.3 4.9E-05 29.1 0.0 27 67-94 2-28 (100)
33 PHA02768 hypothetical protein; 63.4 4 8.8E-05 28.7 1.2 25 64-90 5-29 (55)
34 KOG2505 Ankyrin repeat protein 61.1 5.5 0.00012 39.1 2.0 33 63-95 65-97 (591)
35 PHA00732 hypothetical protein 60.2 5.7 0.00012 29.0 1.6 22 65-86 2-23 (79)
36 COG5188 PRP9 Splicing factor 3 56.9 5.7 0.00012 37.8 1.3 32 63-94 237-268 (470)
37 PF05605 zf-Di19: Drought indu 56.5 7.1 0.00015 25.8 1.4 20 65-85 3-22 (54)
38 PF11931 DUF3449: Domain of un 56.3 3.7 8E-05 35.1 0.0 36 64-99 101-137 (196)
39 PHA00616 hypothetical protein 55.7 5 0.00011 27.1 0.6 21 65-85 2-22 (44)
40 KOG3792 Transcription factor N 55.1 6.4 0.00014 40.0 1.4 65 27-93 151-222 (816)
41 PTZ00448 hypothetical protein; 52.9 9.6 0.00021 35.7 2.1 32 64-95 314-345 (373)
42 PF14968 CCDC84: Coiled coil p 51.3 10 0.00022 34.8 2.0 42 61-102 55-102 (336)
43 PF12013 DUF3505: Protein of u 49.7 18 0.0004 26.7 2.8 32 62-94 9-40 (109)
44 KOG3576 Ovo and related transc 48.8 27 0.00058 31.4 4.1 25 61-85 114-138 (267)
45 PHA00733 hypothetical protein 48.6 13 0.00028 29.1 1.9 25 62-86 71-95 (128)
46 smart00614 ZnF_BED BED zinc fi 48.2 8.2 0.00018 25.2 0.7 26 64-90 18-48 (50)
47 PF13913 zf-C2HC_2: zinc-finge 47.0 13 0.00029 21.7 1.4 19 66-85 4-22 (25)
48 KOG2482 Predicted C2H2-type Zn 46.7 9.3 0.0002 36.2 1.0 28 64-91 195-222 (423)
49 PF12907 zf-met2: Zinc-binding 46.5 8.9 0.00019 25.4 0.6 25 66-90 3-30 (40)
50 PF03194 LUC7: LUC7 N_terminus 42.7 12 0.00025 32.6 1.0 30 62-91 188-220 (254)
51 PF02892 zf-BED: BED zinc fing 41.6 19 0.00041 22.5 1.5 24 61-84 13-40 (45)
52 KOG2462 C2H2-type Zn-finger pr 39.4 16 0.00034 33.2 1.2 22 64-85 215-236 (279)
53 KOG1146 Homeobox protein [Gene 36.6 21 0.00045 38.6 1.8 39 60-98 514-552 (1406)
54 PF12013 DUF3505: Protein of u 33.1 73 0.0016 23.5 3.8 33 54-86 70-106 (109)
55 PHA00733 hypothetical protein 33.0 26 0.00057 27.4 1.5 25 64-89 99-123 (128)
56 KOG2893 Zn finger protein [Gen 31.2 28 0.0006 32.0 1.5 29 60-88 6-34 (341)
57 PF04780 DUF629: Protein of un 27.6 37 0.00079 32.7 1.7 30 63-93 56-85 (466)
58 PF14968 CCDC84: Coiled coil p 27.6 28 0.00061 32.0 0.9 30 66-98 1-30 (336)
59 KOG1074 Transcriptional repres 27.4 22 0.00048 36.9 0.3 56 63-124 632-690 (958)
60 PF13465 zf-H2C2_2: Zinc-finge 26.4 43 0.00093 19.3 1.3 14 63-76 13-26 (26)
61 KOG2462 C2H2-type Zn-finger pr 21.7 74 0.0016 29.0 2.4 24 62-85 159-182 (279)
62 KOG2636 Splicing factor 3a, su 20.8 46 0.001 32.4 1.0 33 64-96 401-434 (497)
63 KOG3576 Ovo and related transc 20.4 32 0.00069 30.9 -0.2 29 63-91 172-203 (267)
64 KOG0796 Spliceosome subunit [R 20.2 42 0.00092 31.0 0.6 39 61-99 183-230 (319)
No 1
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=98.98 E-value=6.6e-11 Score=107.85 Aligned_cols=69 Identities=20% Similarity=0.269 Sum_probs=60.9
Q ss_pred eeccCCCCCCCcccccCCCCCCCCCCcCCC------------cCCCeeeeccccccccchHHHHHhhcccchHHHHHHhH
Q 043013 30 QVKPYPNLCGSKQEATTLPADSGKPCSTGS------------KKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLE 97 (179)
Q Consensus 30 l~Kpd~n~ygvKRKaktlp~~s~Ev~~~k~------------K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ 97 (179)
=+|++||+||+|||++.+||++.|.|..++ ...+.-.|.+|...+.|+.+..+||.+++|+.++..+.
T Consensus 22 HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~ 101 (390)
T KOG2785|consen 22 HYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQ 101 (390)
T ss_pred HhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhhHHHHHHHhhcchhhhhhh
Confidence 379999999999999999999988886665 34457899999999999999999999999999988755
Q ss_pred H
Q 043013 98 R 98 (179)
Q Consensus 98 a 98 (179)
.
T Consensus 102 r 102 (390)
T KOG2785|consen 102 R 102 (390)
T ss_pred c
Confidence 3
No 2
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.62 E-value=1.6e-08 Score=57.55 Aligned_cols=25 Identities=44% Similarity=0.861 Sum_probs=24.6
Q ss_pred eeeccccccccchHHHHHhhcccch
Q 043013 65 WSCALCQVSSTSKRNLDEHLRGKKH 89 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~GKKH 89 (179)
|.|.+|+++|+|+..|..|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 8999999999999999999999998
No 3
>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=98.46 E-value=9.6e-08 Score=57.51 Aligned_cols=32 Identities=38% Similarity=0.733 Sum_probs=29.9
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aa 95 (179)
.|.|.+|++.|+++..|.+|+.|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58999999999999999999999999998764
No 4
>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=98.13 E-value=9.4e-07 Score=51.83 Aligned_cols=26 Identities=35% Similarity=0.735 Sum_probs=25.3
Q ss_pred eeeccccccccchHHHHHhhcccchH
Q 043013 65 WSCALCQVSSTSKRNLDEHLRGKKHK 90 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~GKKHK 90 (179)
|.|.+|++.|.++..|.+|+.|++||
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 78999999999999999999999997
No 5
>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=96.30 E-value=0.0033 Score=40.60 Aligned_cols=33 Identities=30% Similarity=0.430 Sum_probs=20.2
Q ss_pred Ceeeecccccccc--chHHHHHhhcccchHHHHHH
Q 043013 63 MHWSCALCQVSST--SKRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 63 ~eWsCalCqvt~T--SE~~L~nHL~GKKHKAk~aa 95 (179)
+.++|..|++-++ +-..-.+|++|.+|+.+++.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred cCeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 5689999999994 34566899999999999864
No 6
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.0041 Score=59.18 Aligned_cols=37 Identities=32% Similarity=0.540 Sum_probs=34.0
Q ss_pred eeeccccccccchHHHHHhhcccchHHHHHHhHHHhh
Q 043013 65 WSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLEREKK 101 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ak~K 101 (179)
-.|-+|.++|-||.+|.||-++|+|+-+++.|+.+-.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqemE 329 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQEME 329 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999876443
No 7
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.86 E-value=0.0058 Score=32.82 Aligned_cols=21 Identities=38% Similarity=0.816 Sum_probs=17.9
Q ss_pred eeeccccccccchHHHHHhhc
Q 043013 65 WSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~ 85 (179)
|.|.+|+.+|.+..+|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 789999999999999999985
No 8
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.57 E-value=0.0047 Score=42.52 Aligned_cols=35 Identities=31% Similarity=0.636 Sum_probs=27.1
Q ss_pred cCCCeeeeccccccccchHHHHHhhcccchHHHHH
Q 043013 60 KKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEE 94 (179)
Q Consensus 60 K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~a 94 (179)
+....|.|.+|+..|.|..+|..|++.+.|+....
T Consensus 46 ~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 46 KVKESFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp ---SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred ccCCCCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 33347999999999999999999999999988644
No 9
>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=95.12 E-value=0.014 Score=32.20 Aligned_cols=22 Identities=41% Similarity=0.831 Sum_probs=20.2
Q ss_pred eeeccccccccchHHHHHhhcc
Q 043013 65 WSCALCQVSSTSKRNLDEHLRG 86 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~G 86 (179)
|.|..|...|.+...|..|++-
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6799999999999999999863
No 10
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.11 E-value=0.013 Score=50.89 Aligned_cols=32 Identities=25% Similarity=0.526 Sum_probs=30.3
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aa 95 (179)
..-|-+|...--+|..+..|++||||+.|++.
T Consensus 53 ~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlar 84 (222)
T KOG0227|consen 53 KYECKLCLTLHNNEGSYLAHTQGKKHQTNLAR 84 (222)
T ss_pred ceeehhhhhhhcchhhhhhhhccchhhHHHHH
Confidence 78999999999999999999999999999874
No 11
>PLN02748 tRNA dimethylallyltransferase
Probab=94.95 E-value=0.019 Score=53.81 Aligned_cols=36 Identities=17% Similarity=0.520 Sum_probs=31.1
Q ss_pred eeeeccccc-cccchHHHHHhhcccchHHHHHHhHHH
Q 043013 64 HWSCALCQV-SSTSKRNLDEHLRGKKHKAKEEGLERE 99 (179)
Q Consensus 64 eWsCalCqv-t~TSE~~L~nHL~GKKHKAk~aaL~ak 99 (179)
...|.+|+. +...+..++.|+.||+||-++..++.+
T Consensus 418 ~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 418 QYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred cccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 347999997 899999999999999999998866543
No 12
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=94.34 E-value=0.036 Score=47.40 Aligned_cols=37 Identities=22% Similarity=0.407 Sum_probs=32.4
Q ss_pred cCCCeeeeccccccccchHHHHHhhcccchHHHHHHh
Q 043013 60 KKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGL 96 (179)
Q Consensus 60 K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL 96 (179)
....-+.|.+|.-.+---.+|..||+||+|+-|+..+
T Consensus 71 sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 71 SQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 3445789999999999999999999999999998754
No 13
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.18 E-value=0.044 Score=47.50 Aligned_cols=34 Identities=26% Similarity=0.498 Sum_probs=31.4
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHHHHh
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGL 96 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL 96 (179)
-...|-+|..+--+|..+..|++||||+.|+.+-
T Consensus 52 Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 52 GKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred CcEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 3889999999999999999999999999998754
No 14
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.15 E-value=0.051 Score=29.01 Aligned_cols=21 Identities=38% Similarity=0.706 Sum_probs=19.3
Q ss_pred eeeccccccccchHHHHHhhc
Q 043013 65 WSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~ 85 (179)
+.|..|..+|.+...|+.|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 369999999999999999987
No 15
>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=92.87 E-value=0.054 Score=37.08 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=24.6
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKE 93 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~ 93 (179)
..-.|..|++.|. +|..|+.+++|+.-.
T Consensus 4 k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 4 KPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 4568999999997 699999999999874
No 16
>PTZ00448 hypothetical protein; Provisional
Probab=92.82 E-value=0.013 Score=54.08 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=23.0
Q ss_pred eccCCCCCCCcccccCCCCCCCCCCc
Q 043013 31 VKPYPNLCGSKQEATTLPADSGKPCS 56 (179)
Q Consensus 31 ~Kpd~n~ygvKRKaktlp~~s~Ev~~ 56 (179)
+|+|||+||+|||+..+||++.+.|.
T Consensus 334 ~KSDwHrYNLKRkl~gLppvse~eF~ 359 (373)
T PTZ00448 334 YRSEWHIFNTKRNARKMEPISEEEFL 359 (373)
T ss_pred hhhhHHHHHHHHHhcCCCCCCHHHHH
Confidence 79999999999999999999866553
No 17
>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=92.82 E-value=0.072 Score=30.36 Aligned_cols=21 Identities=33% Similarity=0.583 Sum_probs=19.4
Q ss_pred eeeccccccccchHHHHHhhc
Q 043013 65 WSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~ 85 (179)
..|..|+.+|.+..+|..|++
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 469999999999999999994
No 18
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=92.75 E-value=0.043 Score=37.76 Aligned_cols=30 Identities=27% Similarity=0.430 Sum_probs=25.3
Q ss_pred CCeeeeccccccccchHHHHHhhcccchHHHHH
Q 043013 62 PMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEE 94 (179)
Q Consensus 62 ~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~a 94 (179)
++.-.|..|.+.|. +|..|+.|++|+.-..
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLLSEKHRRFAE 32 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhccHHHHHHHc
Confidence 34678999999987 8999999999998643
No 19
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.69 E-value=0.25 Score=44.09 Aligned_cols=45 Identities=20% Similarity=0.339 Sum_probs=37.2
Q ss_pred CCCcCCCcCCCeeeeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 53 KPCSTGSKKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 53 Ev~~~k~K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
+++-.+.+..-.-+|.+|++--- +.-+.-|..||+|+.+++.|+.
T Consensus 24 ~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs 68 (264)
T KOG3032|consen 24 DSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKS 68 (264)
T ss_pred ccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHh
Confidence 33334445555789999999988 9999999999999999999984
No 20
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=88.44 E-value=0.25 Score=47.79 Aligned_cols=34 Identities=32% Similarity=0.542 Sum_probs=30.8
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHHhH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLE 97 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ 97 (179)
..-|++|+|--+||--|-+|..|+||++.+..+.
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 6689999999999999999999999999876553
No 21
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=88.33 E-value=0.28 Score=39.92 Aligned_cols=35 Identities=23% Similarity=0.452 Sum_probs=32.9
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
.+.|-.|-..|.++.+|.-|..||.||-.+.+|+.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 78999999999999999999999999999988864
No 22
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=85.80 E-value=0.53 Score=26.32 Aligned_cols=19 Identities=42% Similarity=0.880 Sum_probs=15.6
Q ss_pred eeccccccccchHHHHHhhc
Q 043013 66 SCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 66 sCalCqvt~TSE~~L~nHL~ 85 (179)
.|..|.-+++ +.+|..|++
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHH
Confidence 6999999998 999999986
No 23
>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=85.76 E-value=0.61 Score=39.26 Aligned_cols=33 Identities=21% Similarity=0.632 Sum_probs=29.8
Q ss_pred eeeccccccccchHHHHHhhcccchHHHHHHhH
Q 043013 65 WSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLE 97 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ 97 (179)
+.|++|...+.-+.....||+++=|+..+.-+.
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~ 33 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQ 33 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHH
Confidence 479999999999999999999999998777663
No 24
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=83.25 E-value=0.7 Score=27.61 Aligned_cols=19 Identities=21% Similarity=0.592 Sum_probs=17.3
Q ss_pred eeccccccccchHHHHHhhc
Q 043013 66 SCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 66 sCalCqvt~TSE~~L~nHL~ 85 (179)
.|.+|+... ++..+|+||.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999998 8899999997
No 25
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=83.15 E-value=0.75 Score=32.68 Aligned_cols=25 Identities=28% Similarity=0.546 Sum_probs=17.8
Q ss_pred CCCeeeeccccccccchHHHHHhhc
Q 043013 61 KPMHWSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 61 ~~~eWsCalCqvt~TSE~~L~nHL~ 85 (179)
....-+|.+|..++.+..+|..||.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHH
Confidence 3346799999999999999999995
No 26
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=82.47 E-value=0.23 Score=45.09 Aligned_cols=36 Identities=17% Similarity=0.438 Sum_probs=31.9
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
..|+|..||..|.-|+.|.-|+.+.-|+-.+.....
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 489999999999999999999999999988765443
No 27
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=75.98 E-value=1.8 Score=35.02 Aligned_cols=35 Identities=29% Similarity=0.489 Sum_probs=32.6
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
...|--|-.-|-++.+|..|+.|+=|+-.+..|+.
T Consensus 55 qhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 67999999999999999999999999999888875
No 28
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=74.88 E-value=1.5 Score=40.42 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=27.3
Q ss_pred CCCeeeeccccccccc-hHHHHHhhcccchHHHHHH
Q 043013 61 KPMHWSCALCQVSSTS-KRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 61 ~~~eWsCalCqvt~TS-E~~L~nHL~GKKHKAk~aa 95 (179)
.++..+|.+|++=+.- ...-..|-+|+|||.+++.
T Consensus 7 S~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 7 SQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred hccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 3556799999886543 4457789999999999874
No 29
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=73.92 E-value=2 Score=36.28 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=26.8
Q ss_pred Ceeeeccccccc--cchHHHHHhhcccchHHHHHHh
Q 043013 63 MHWSCALCQVSS--TSKRNLDEHLRGKKHKAKEEGL 96 (179)
Q Consensus 63 ~eWsCalCqvt~--TSE~~L~nHL~GKKHKAk~aaL 96 (179)
+...|..|++-- -|-+.=..|+.|++|+.+++..
T Consensus 2 pRYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 2 PRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred CcchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 356899999544 4677788999999999987654
No 30
>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=72.06 E-value=4.3 Score=34.91 Aligned_cols=40 Identities=25% Similarity=0.493 Sum_probs=31.7
Q ss_pred cCCCeeeeccccccccchHHHHHhhcccchHHHHHHhHHHh
Q 043013 60 KKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLEREK 100 (179)
Q Consensus 60 K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ak~ 100 (179)
...-.|-|.+|++-|-.+.-...|+. .||-.++++++.+-
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 44558999999999999999999998 68999999876543
No 31
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=71.17 E-value=2.4 Score=37.97 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=22.6
Q ss_pred eeeeccccccccchHHHHHhhccc
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGK 87 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GK 87 (179)
.|.|-.|.+.|.++.+|..|.-|-
T Consensus 239 h~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ceEEEEeccccCCHHHHHHhCCCC
Confidence 799999999999999999999874
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=63.85 E-value=2.3 Score=29.10 Aligned_cols=27 Identities=33% Similarity=0.564 Sum_probs=0.0
Q ss_pred eccccccccchHHHHHhhcccchHHHHH
Q 043013 67 CALCQVSSTSKRNLDEHLRGKKHKAKEE 94 (179)
Q Consensus 67 CalCqvt~TSE~~L~nHL~GKKHKAk~a 94 (179)
|.+|..++.+...|..||. ..|.....
T Consensus 2 C~~C~~~f~~~~~l~~H~~-~~H~~~~~ 28 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK-KKHGFDIP 28 (100)
T ss_dssp ----------------------------
T ss_pred ccccccccccccccccccc-cccccccc
Confidence 9999999999999999995 88887654
No 33
>PHA02768 hypothetical protein; Provisional
Probab=63.37 E-value=4 Score=28.71 Aligned_cols=25 Identities=24% Similarity=0.634 Sum_probs=21.6
Q ss_pred eeeeccccccccchHHHHHhhcccchH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHK 90 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHK 90 (179)
-..|..|+..|+...+|..|++- |-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC
Confidence 35799999999999999999854 65
No 34
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=61.10 E-value=5.5 Score=39.12 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=30.7
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHHHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aa 95 (179)
-.|+|..||..|-|-.....|.+.-=|+-|+..
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Kr 97 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKR 97 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999753
No 35
>PHA00732 hypothetical protein
Probab=60.24 E-value=5.7 Score=29.03 Aligned_cols=22 Identities=23% Similarity=0.644 Sum_probs=19.8
Q ss_pred eeeccccccccchHHHHHhhcc
Q 043013 65 WSCALCQVSSTSKRNLDEHLRG 86 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~G 86 (179)
..|..|...|.+..+|..|+..
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 4699999999999999999863
No 36
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=56.85 E-value=5.7 Score=37.80 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=28.1
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKEE 94 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~a 94 (179)
+...|..|+.-|..-.-|..||.||+|.-+..
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~ 268 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQ 268 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhh
Confidence 35589999999999999999999999987654
No 37
>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=56.49 E-value=7.1 Score=25.84 Aligned_cols=20 Identities=30% Similarity=0.627 Sum_probs=17.4
Q ss_pred eeeccccccccchHHHHHhhc
Q 043013 65 WSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~ 85 (179)
..|.+|+. ..++..|..|+.
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~ 22 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCE 22 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHH
Confidence 57999999 788999999986
No 38
>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=56.33 E-value=3.7 Score=35.13 Aligned_cols=36 Identities=17% Similarity=0.441 Sum_probs=0.0
Q ss_pred eeeeccc-cccccchHHHHHhhcccchHHHHHHhHHH
Q 043013 64 HWSCALC-QVSSTSKRNLDEHLRGKKHKAKEEGLERE 99 (179)
Q Consensus 64 eWsCalC-qvt~TSE~~L~nHL~GKKHKAk~aaL~ak 99 (179)
+..|.|| +.+|-...+|..|.+..||.--+..|.-.
T Consensus 101 ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~ 137 (196)
T PF11931_consen 101 EYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIP 137 (196)
T ss_dssp -------------------------------------
T ss_pred eeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCC
Confidence 5699999 67777999999999999999888777554
No 39
>PHA00616 hypothetical protein
Probab=55.73 E-value=5 Score=27.15 Aligned_cols=21 Identities=29% Similarity=0.494 Sum_probs=19.2
Q ss_pred eeeccccccccchHHHHHhhc
Q 043013 65 WSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 65 WsCalCqvt~TSE~~L~nHL~ 85 (179)
..|..|+..|...+.|..|++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH
Confidence 369999999999999999993
No 40
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=55.12 E-value=6.4 Score=39.98 Aligned_cols=65 Identities=31% Similarity=0.418 Sum_probs=42.5
Q ss_pred cceeeccC---CCCCCCcccccCCCCCCCCCCcCCCcCCC----eeeeccccccccchHHHHHhhcccchHHHH
Q 043013 27 QAQQVKPY---PNLCGSKQEATTLPADSGKPCSTGSKKPM----HWSCALCQVSSTSKRNLDEHLRGKKHKAKE 93 (179)
Q Consensus 27 V~~l~Kpd---~n~ygvKRKaktlp~~s~Ev~~~k~K~~~----eWsCalCqvt~TSE~~L~nHL~GKKHKAk~ 93 (179)
-+.|-.|. .+.+..+-.+....++.+-. .++|..+ -..|.+||+.|..-+.+..||+|+||..+.
T Consensus 151 ~~~lqsP~~r~e~~~~~~~~a~s~~dppd~l--dR~K~~~~laqL~~~kw~k~~a~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 151 GIPLQSPNGRAENEKQRKMEATSVKDPPDVL--DRPKAPPRLAQLHYCKWCKISAAGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred CCcCCCCCCccchhcccCccccCCCCchhhc--ccccCchHHHHhhhhHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 45555554 45555443333322221111 3445554 458999999999999999999999999987
No 41
>PTZ00448 hypothetical protein; Provisional
Probab=52.86 E-value=9.6 Score=35.73 Aligned_cols=32 Identities=16% Similarity=0.357 Sum_probs=29.3
Q ss_pred eeeeccccccccchHHHHHhhcccchHHHHHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKAKEEG 95 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aa 95 (179)
..+|..|++.|.+......|..+-=|+-|+..
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKR 345 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKR 345 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHH
Confidence 46799999999999999999999999999864
No 42
>PF14968 CCDC84: Coiled coil protein 84
Probab=51.30 E-value=10 Score=34.82 Aligned_cols=42 Identities=14% Similarity=0.288 Sum_probs=32.3
Q ss_pred CCCeeeeccccccccch------HHHHHhhcccchHHHHHHhHHHhhh
Q 043013 61 KPMHWSCALCQVSSTSK------RNLDEHLRGKKHKAKEEGLEREKKH 102 (179)
Q Consensus 61 ~~~eWsCalCqvt~TSE------~~L~nHL~GKKHKAk~aaL~ak~Ka 102 (179)
....|+|.+|.....-- .++..||.+..|+.++.++..+.++
T Consensus 55 ~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~~g~ 102 (336)
T PF14968_consen 55 HRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFWWKNGA 102 (336)
T ss_pred ccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHHHHcCC
Confidence 34567799996544332 6889999999999999999776643
No 43
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=49.73 E-value=18 Score=26.69 Aligned_cols=32 Identities=25% Similarity=0.456 Sum_probs=25.7
Q ss_pred CCeeeeccccccccchHHHHHhhcccchHHHHH
Q 043013 62 PMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEE 94 (179)
Q Consensus 62 ~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~a 94 (179)
..-|.|..|+....- +.+..||+.+-|..+-.
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~ 40 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQ 40 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHH
Confidence 357999999987766 99999999987766443
No 44
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=48.82 E-value=27 Score=31.39 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=22.0
Q ss_pred CCCeeeeccccccccchHHHHHhhc
Q 043013 61 KPMHWSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 61 ~~~eWsCalCqvt~TSE~~L~nHL~ 85 (179)
..-.++|.+|++.|+=.+-||.||.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~k 138 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLK 138 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhh
Confidence 3458899999999999999999984
No 45
>PHA00733 hypothetical protein
Probab=48.55 E-value=13 Score=29.07 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=21.1
Q ss_pred CCeeeeccccccccchHHHHHhhcc
Q 043013 62 PMHWSCALCQVSSTSKRNLDEHLRG 86 (179)
Q Consensus 62 ~~eWsCalCqvt~TSE~~L~nHL~G 86 (179)
..+|.|..|...|.+...|..|..-
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhc
Confidence 4478899999999999999988874
No 46
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=48.17 E-value=8.2 Score=25.25 Aligned_cols=26 Identities=35% Similarity=0.595 Sum_probs=20.7
Q ss_pred eeeeccccccccch-----HHHHHhhcccchH
Q 043013 64 HWSCALCQVSSTSK-----RNLDEHLRGKKHK 90 (179)
Q Consensus 64 eWsCalCqvt~TSE-----~~L~nHL~GKKHK 90 (179)
.-.|..|...++.. ++|..||.. +|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~-~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR-KHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh-HCc
Confidence 45799998888766 699999987 553
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=47.00 E-value=13 Score=21.70 Aligned_cols=19 Identities=21% Similarity=0.613 Sum_probs=15.4
Q ss_pred eeccccccccchHHHHHhhc
Q 043013 66 SCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 66 sCalCqvt~TSE~~L~nHL~ 85 (179)
.|.+|+.+| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 599999999 6777888853
No 48
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=46.73 E-value=9.3 Score=36.20 Aligned_cols=28 Identities=32% Similarity=0.663 Sum_probs=25.8
Q ss_pred eeeeccccccccchHHHHHhhcccchHH
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKHKA 91 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKHKA 91 (179)
..-|-.|.+.|.-.++|..|++-|+|+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcc
Confidence 5689999999999999999999999973
No 49
>PF12907 zf-met2: Zinc-binding
Probab=46.52 E-value=8.9 Score=25.43 Aligned_cols=25 Identities=32% Similarity=0.699 Sum_probs=21.0
Q ss_pred eecccc---ccccchHHHHHhhcccchH
Q 043013 66 SCALCQ---VSSTSKRNLDEHLRGKKHK 90 (179)
Q Consensus 66 sCalCq---vt~TSE~~L~nHL~GKKHK 90 (179)
.|.+|- ..++++..|..|...|-=|
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 599998 7889999999999876544
No 50
>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=42.70 E-value=12 Score=32.56 Aligned_cols=30 Identities=27% Similarity=0.544 Sum_probs=23.6
Q ss_pred CCeeeecccc---ccccchHHHHHhhcccchHH
Q 043013 62 PMHWSCALCQ---VSSTSKRNLDEHLRGKKHKA 91 (179)
Q Consensus 62 ~~eWsCalCq---vt~TSE~~L~nHL~GKKHKA 91 (179)
+.--.|.+|. ...-++.-|.+|+.||-|-.
T Consensus 188 qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 188 QKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cCccchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 3456899996 45567888999999999954
No 51
>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=41.61 E-value=19 Score=22.48 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=16.0
Q ss_pred CCCeeeeccccccccch----HHHHHhh
Q 043013 61 KPMHWSCALCQVSSTSK----RNLDEHL 84 (179)
Q Consensus 61 ~~~eWsCalCqvt~TSE----~~L~nHL 84 (179)
......|.+|...+... ..|..||
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34578999998877665 8999999
No 52
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=39.37 E-value=16 Score=33.20 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=17.2
Q ss_pred eeeeccccccccchHHHHHhhc
Q 043013 64 HWSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~ 85 (179)
.++|..|.+.|--.++|..|+|
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred CccCCcccchhcchHHHHHHHH
Confidence 4578888888888888888875
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=36.62 E-value=21 Score=38.57 Aligned_cols=39 Identities=28% Similarity=0.459 Sum_probs=33.2
Q ss_pred cCCCeeeeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 60 KKPMHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 60 K~~~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
-.....-|..|.+++|....|-.||+.=+|+.+++.+..
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~ 552 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEE 552 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHh
Confidence 344577899999999999999999999999999765544
No 54
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=33.13 E-value=73 Score=23.50 Aligned_cols=33 Identities=24% Similarity=0.419 Sum_probs=28.2
Q ss_pred CCcCCCcCCCeeee----ccccccccchHHHHHhhcc
Q 043013 54 PCSTGSKKPMHWSC----ALCQVSSTSKRNLDEHLRG 86 (179)
Q Consensus 54 v~~~k~K~~~eWsC----alCqvt~TSE~~L~nHL~G 86 (179)
.|..+.....-+.| ..|.-.+++...+.+|++-
T Consensus 70 ~Pi~gLp~~~G~~C~~~~~~C~y~~~~~~~m~~H~~~ 106 (109)
T PF12013_consen 70 PPIPGLPVYDGYRCQCDPPHCGYITRSKKTMRKHWRK 106 (109)
T ss_pred CcCCCCCCCCCeeeecCCCCCCcEeccHHHHHHHHHH
Confidence 45567777789999 9999999999999999873
No 55
>PHA00733 hypothetical protein
Probab=33.01 E-value=26 Score=27.35 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.2
Q ss_pred eeeeccccccccchHHHHHhhcccch
Q 043013 64 HWSCALCQVSSTSKRNLDEHLRGKKH 89 (179)
Q Consensus 64 eWsCalCqvt~TSE~~L~nHL~GKKH 89 (179)
.+.|..|...|.....|..|+. ++|
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~-~~h 123 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVC-KKH 123 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHH-Hhc
Confidence 4799999999999999999864 444
No 56
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=31.16 E-value=28 Score=31.97 Aligned_cols=29 Identities=24% Similarity=0.281 Sum_probs=21.6
Q ss_pred cCCCeeeeccccccccchHHHHHhhcccc
Q 043013 60 KKPMHWSCALCQVSSTSKRNLDEHLRGKK 88 (179)
Q Consensus 60 K~~~eWsCalCqvt~TSE~~L~nHL~GKK 88 (179)
|.+..-||.+|+..|--|.-|..|..-|-
T Consensus 6 kk~~kpwcwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 6 KKVDKPWCWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred cccCCceeeecccccchhhhhhhhhhhcc
Confidence 33444569999999999999999876543
No 57
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=27.63 E-value=37 Score=32.66 Aligned_cols=30 Identities=20% Similarity=0.455 Sum_probs=25.7
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKE 93 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~ 93 (179)
.=|.|.+|...|++-..|.+|+. .+|-++.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~-~eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHME-QEHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHH-Hhhhhhc
Confidence 37899999999999999999998 4677765
No 58
>PF14968 CCDC84: Coiled coil protein 84
Probab=27.61 E-value=28 Score=32.03 Aligned_cols=30 Identities=17% Similarity=0.358 Sum_probs=24.9
Q ss_pred eeccccccccchHHHHHhhcccchHHHHHHhHH
Q 043013 66 SCALCQVSSTSKRNLDEHLRGKKHKAKEEGLER 98 (179)
Q Consensus 66 sCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~a 98 (179)
+|.+|..+... -..|.=+++||.++.+++.
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L~ 30 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFLS 30 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHHH
Confidence 59999888766 7789999999999987754
No 59
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=27.41 E-value=22 Score=36.89 Aligned_cols=56 Identities=30% Similarity=0.364 Sum_probs=38.9
Q ss_pred CeeeeccccccccchHHHHHhhcccchHHHHHHhHHHhhhhhcC---cCCcccccceeeeeeeee
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLRGKKHKAKEEGLEREKKHMARS---NESKKNDEAVSLTTSTTI 124 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~GKKHKAk~aaL~ak~Kama~~---~~skk~~~~~kl~~s~~~ 124 (179)
..+.|.||+..|+.+.+|.-|+.+ ||++= .++.... -. -+-+|+..++.|+--|.+
T Consensus 632 RPFkCKiCgRAFtTkGNLkaH~~v--Hka~p-~~R~q~S---cP~~~ic~~kftn~V~lpQhIri 690 (958)
T KOG1074|consen 632 RPFKCKICGRAFTTKGNLKAHMSV--HKAKP-PARVQFS---CPSTFICQKKFTNAVTLPQHIRI 690 (958)
T ss_pred Cccccccccchhccccchhhcccc--cccCc-ccccccc---CCchhhhcccccccccccceEEe
Confidence 378999999999999999999988 66653 2232221 01 123888888887766555
No 60
>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=26.38 E-value=43 Score=19.30 Aligned_cols=14 Identities=21% Similarity=0.574 Sum_probs=11.3
Q ss_pred Ceeeeccccccccc
Q 043013 63 MHWSCALCQVSSTS 76 (179)
Q Consensus 63 ~eWsCalCqvt~TS 76 (179)
..+.|.+|..+|..
T Consensus 13 k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 13 KPYKCPYCGKSFSN 26 (26)
T ss_dssp SSEEESSSSEEESS
T ss_pred CCCCCCCCcCeeCc
Confidence 45899999998863
No 61
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.69 E-value=74 Score=29.00 Aligned_cols=24 Identities=29% Similarity=0.495 Sum_probs=16.7
Q ss_pred CCeeeeccccccccchHHHHHhhc
Q 043013 62 PMHWSCALCQVSSTSKRNLDEHLR 85 (179)
Q Consensus 62 ~~eWsCalCqvt~TSE~~L~nHL~ 85 (179)
++..+|.+|.+.|.|-.+|.-||+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHir 182 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIR 182 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhh
Confidence 446677777777777777777764
No 62
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.75 E-value=46 Score=32.43 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=27.7
Q ss_pred eeeecccc-ccccchHHHHHhhcccchHHHHHHh
Q 043013 64 HWSCALCQ-VSSTSKRNLDEHLRGKKHKAKEEGL 96 (179)
Q Consensus 64 eWsCalCq-vt~TSE~~L~nHL~GKKHKAk~aaL 96 (179)
+..|.||. .+|..-.+|+.|..-.||.--+..|
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCL 434 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCL 434 (497)
T ss_pred ccceeeccCccccCcHHHHHHhHHHHHhhcceec
Confidence 45999997 9999999999999999997554444
No 63
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=20.39 E-value=32 Score=30.91 Aligned_cols=29 Identities=31% Similarity=0.726 Sum_probs=23.8
Q ss_pred CeeeeccccccccchHHHHHhhc---ccchHH
Q 043013 63 MHWSCALCQVSSTSKRNLDEHLR---GKKHKA 91 (179)
Q Consensus 63 ~eWsCalCqvt~TSE~~L~nHL~---GKKHKA 91 (179)
..+.|.+|.+.||-.-.|.+||. |..|+-
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~y 203 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQY 203 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHH
Confidence 36789999999999999999986 555544
No 64
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=20.24 E-value=42 Score=30.98 Aligned_cols=39 Identities=28% Similarity=0.530 Sum_probs=27.9
Q ss_pred CCCeeeeccccc---cccchHHHHHhhcccchH------HHHHHhHHH
Q 043013 61 KPMHWSCALCQV---SSTSKRNLDEHLRGKKHK------AKEEGLERE 99 (179)
Q Consensus 61 ~~~eWsCalCqv---t~TSE~~L~nHL~GKKHK------Ak~aaL~ak 99 (179)
.++--.|.+|.. -.-...-|..|+.||-|- .+++.|+..
T Consensus 183 ~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~ 230 (319)
T KOG0796|consen 183 QQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKE 230 (319)
T ss_pred hhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHH
Confidence 344568999954 456788899999999995 455555443
Done!