Query 046771
Match_columns 326
No_of_seqs 69 out of 71
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 04:20:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12874 zf-met: Zinc-finger o 98.3 2.6E-07 5.6E-12 56.9 1.5 25 223-247 1-25 (25)
2 smart00451 ZnF_U1 U1-like zinc 98.0 3E-06 6.5E-11 55.4 1.7 32 222-253 3-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.5 4.9E-05 1.1E-09 48.3 1.3 27 222-248 1-27 (27)
4 KOG0227 Splicing factor 3a, su 94.9 0.016 3.4E-07 54.2 2.3 40 220-259 51-90 (222)
5 PF13894 zf-C2H2_4: C2H2-type 93.1 0.053 1.2E-06 31.6 1.3 21 223-243 1-21 (24)
6 KOG4727 U1-like Zn-finger prot 93.0 0.067 1.5E-06 49.3 2.5 34 221-254 74-107 (193)
7 PF12756 zf-C2H2_2: C2H2 type 92.6 0.06 1.3E-06 40.5 1.3 32 221-252 49-80 (100)
8 PF06220 zf-U1: U1 zinc finger 92.1 0.13 2.7E-06 36.1 2.3 33 221-253 2-36 (38)
9 KOG3032 Uncharacterized conser 92.1 0.17 3.7E-06 48.6 3.9 43 213-256 26-68 (264)
10 PLN02748 tRNA dimethylallyltra 91.8 0.12 2.6E-06 52.8 2.7 39 221-259 417-456 (468)
11 COG5246 PRP11 Splicing factor 90.6 0.22 4.7E-06 46.6 3.0 38 217-254 47-85 (222)
12 PF00096 zf-C2H2: Zinc finger, 90.0 0.19 4.2E-06 30.0 1.5 21 223-243 1-21 (23)
13 smart00355 ZnF_C2H2 zinc finge 86.1 0.37 7.9E-06 28.0 0.9 21 223-243 1-21 (26)
14 PF13909 zf-H2C2_5: C2H2-type 84.9 0.52 1.1E-05 28.8 1.2 19 224-243 2-20 (24)
15 PF07535 zf-DBF: DBF zinc fing 84.0 0.47 1E-05 35.3 0.8 27 222-251 5-31 (49)
16 KOG4722 Zn-finger protein [Gen 83.1 0.62 1.3E-05 48.5 1.6 34 221-254 492-525 (672)
17 PF13912 zf-C2H2_6: C2H2-type 83.1 0.85 1.8E-05 28.2 1.6 21 223-243 2-22 (27)
18 smart00586 ZnF_DBF Zinc finger 81.5 0.56 1.2E-05 35.0 0.5 28 221-251 4-31 (49)
19 KOG0717 Molecular chaperone (D 77.9 1.2 2.7E-05 46.3 1.7 34 223-256 293-326 (508)
20 PF09237 GAGA: GAGA factor; I 76.5 2.5 5.3E-05 32.6 2.5 23 221-243 23-45 (54)
21 PF04988 AKAP95: A-kinase anch 75.0 2.3 5E-05 38.9 2.4 32 223-254 1-32 (165)
22 smart00734 ZnF_Rad18 Rad18-lik 69.4 2.7 5.8E-05 27.3 1.1 19 224-243 3-21 (26)
23 KOG3454 U1 snRNP-specific prot 66.4 3 6.5E-05 38.1 1.2 33 222-254 3-37 (165)
24 KOG3408 U1-like Zn-finger-cont 65.3 3.5 7.7E-05 36.4 1.4 35 221-255 56-90 (129)
25 PF12013 DUF3505: Protein of u 64.1 5.6 0.00012 32.2 2.3 34 220-254 9-42 (109)
26 KOG0150 Spliceosomal protein F 59.3 4.8 0.0001 40.3 1.3 32 222-253 10-42 (336)
27 KOG4167 Predicted DNA-binding 54.6 45 0.00098 37.2 7.6 32 221-254 791-822 (907)
28 PF03194 LUC7: LUC7 N_terminus 54.2 5.9 0.00013 37.5 1.0 30 220-249 188-220 (254)
29 KOG2391 Vacuolar sorting prote 53.2 85 0.0018 32.1 8.8 40 78-117 215-254 (365)
30 PF11830 DUF3350: Domain of un 52.3 43 0.00093 26.1 5.2 23 78-101 27-49 (56)
31 KOG1994 Predicted RNA binding 47.2 11 0.00025 36.5 1.7 25 221-245 238-262 (268)
32 PF12907 zf-met2: Zinc-binding 45.4 8.4 0.00018 27.8 0.4 30 223-252 2-34 (40)
33 COG5188 PRP9 Splicing factor 3 43.5 10 0.00022 39.1 0.7 32 222-253 238-269 (470)
34 KOG0796 Spliceosome subunit [R 43.0 8.1 0.00018 38.5 0.0 43 218-260 182-233 (319)
35 PF04959 ARS2: Arsenite-resist 42.9 19 0.00041 33.8 2.4 37 220-257 75-111 (214)
36 PF13049 DUF3910: Protein of u 38.2 22 0.00048 29.7 1.8 36 1-38 4-39 (93)
37 PHA00616 hypothetical protein 34.8 15 0.00033 27.0 0.4 20 223-242 2-21 (44)
38 COG5112 UFD2 U1-like Zn-finger 33.5 26 0.00056 30.8 1.6 38 221-258 54-91 (126)
39 PF11931 DUF3449: Domain of un 31.0 16 0.00035 34.0 0.0 37 222-258 101-138 (196)
40 PF12756 zf-C2H2_2: C2H2 type 29.8 18 0.00038 27.1 0.0 27 225-252 2-28 (100)
41 KOG1029 Endocytic adaptor prot 29.1 98 0.0021 35.1 5.3 7 31-37 260-266 (1118)
42 KOG2837 Protein containing a U 28.7 15 0.00033 36.4 -0.6 36 221-256 24-59 (309)
43 KOG3576 Ovo and related transc 28.6 39 0.00084 32.8 2.1 24 220-243 115-138 (267)
44 PF14968 CCDC84: Coiled coil p 28.6 29 0.00062 34.8 1.2 33 221-254 58-96 (336)
45 PHA00732 hypothetical protein 27.9 34 0.00073 27.3 1.3 22 223-244 2-23 (79)
46 PRK00888 ftsB cell division pr 27.5 1E+02 0.0022 25.7 4.1 35 80-114 37-75 (105)
47 KOG2893 Zn finger protein [Gen 26.6 37 0.00081 33.6 1.6 26 220-246 9-34 (341)
48 COG5136 U1 snRNP-specific prot 24.8 38 0.00083 31.6 1.2 33 222-254 3-37 (188)
49 PF05605 zf-Di19: Drought indu 24.6 47 0.001 24.0 1.5 21 222-243 2-22 (54)
50 KOG2505 Ankyrin repeat protein 24.4 42 0.00092 35.9 1.6 32 221-252 65-96 (591)
51 PF04810 zf-Sec23_Sec24: Sec23 22.9 37 0.0008 23.7 0.6 12 220-231 22-33 (40)
52 KOG3039 Uncharacterized conser 22.6 3.5E+02 0.0076 27.1 7.3 16 221-236 220-235 (303)
53 KOG3915 Transcription regulato 22.5 2E+02 0.0043 31.0 5.9 11 58-68 480-490 (641)
54 KOG3792 Transcription factor N 22.4 30 0.00065 38.3 0.1 31 221-251 192-222 (816)
55 KOG2482 Predicted C2H2-type Zn 21.7 42 0.0009 34.6 0.9 35 215-249 188-222 (423)
No 1
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.31 E-value=2.6e-07 Score=56.93 Aligned_cols=25 Identities=36% Similarity=0.748 Sum_probs=24.5
Q ss_pred eeeccccccccchhhHHhhhcccch
Q 046771 223 WSCALCQVSATTARGLYAHLQGKKH 247 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~GKrH 247 (326)
|.|.+|+++++++..|+.|++|++|
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 2
>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=98.00 E-value=3e-06 Score=55.36 Aligned_cols=32 Identities=44% Similarity=0.686 Sum_probs=29.8
Q ss_pred ceeeccccccccchhhHHhhhcccchHHHHHH
Q 046771 222 KWSCALCQVSATTARGLYAHLQGKKHKAKEKL 253 (326)
Q Consensus 222 eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~ 253 (326)
.|.|.+|+++++++..+.+|+.|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58899999999999999999999999998864
No 3
>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=97.47 E-value=4.9e-05 Score=48.29 Aligned_cols=27 Identities=30% Similarity=0.618 Sum_probs=25.2
Q ss_pred ceeeccccccccchhhHHhhhcccchH
Q 046771 222 KWSCALCQVSATTARGLYAHLQGKKHK 248 (326)
Q Consensus 222 eWsCalCqVttTSE~~LnsHL~GKrHk 248 (326)
.|.|.+|...+.++..|..|+.|++||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 378999999999999999999999997
No 4
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.95 E-value=0.016 Score=54.24 Aligned_cols=40 Identities=28% Similarity=0.403 Sum_probs=34.8
Q ss_pred CCceeeccccccccchhhHHhhhcccchHHHHHHhhHhhh
Q 046771 220 PTKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLRDLKM 259 (326)
Q Consensus 220 ~~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a~~~ 259 (326)
...+.|-||.-.-.+|.+.-.|++||||+.+++.-.++..
T Consensus 51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~e~ 90 (222)
T KOG0227|consen 51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAKEA 90 (222)
T ss_pred CcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHHHh
Confidence 4789999999999999999999999999999987544443
No 5
>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=93.08 E-value=0.053 Score=31.61 Aligned_cols=21 Identities=24% Similarity=0.624 Sum_probs=17.8
Q ss_pred eeeccccccccchhhHHhhhc
Q 046771 223 WSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~ 243 (326)
|.|.+|..++.+...|+.|+.
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 789999999999999999974
No 6
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=93.01 E-value=0.067 Score=49.33 Aligned_cols=34 Identities=21% Similarity=0.515 Sum_probs=31.2
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.-+-|.||..++-.-.++.+|++||+||-++..+
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred CceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 4789999999999999999999999999998754
No 7
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.56 E-value=0.06 Score=40.55 Aligned_cols=32 Identities=22% Similarity=0.582 Sum_probs=27.0
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHH
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEK 252 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e 252 (326)
..|.|.+|...+.+...|..|++.+.|+....
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 46999999999999999999999999987644
No 8
>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=92.10 E-value=0.13 Score=36.12 Aligned_cols=33 Identities=27% Similarity=0.377 Sum_probs=18.7
Q ss_pred Cceeeccccccccch--hhHHhhhcccchHHHHHH
Q 046771 221 TKWSCALCQVSATTA--RGLYAHLQGKKHKAKEKL 253 (326)
Q Consensus 221 ~eWsCalCqVttTSE--~~LnsHL~GKrHkAk~e~ 253 (326)
+.+-|..|.+..+.- ..=..|++|.+|+.+++.
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 357899999998543 345899999999999864
No 9
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.07 E-value=0.17 Score=48.60 Aligned_cols=43 Identities=23% Similarity=0.421 Sum_probs=37.2
Q ss_pred CCCCCCCCCceeeccccccccchhhHHhhhcccchHHHHHHhhH
Q 046771 213 PSKSSNKPTKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLRD 256 (326)
Q Consensus 213 p~~~~K~~~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a 256 (326)
|-...+.....+|.||.|-.- +.--.-|..||+|+.++++|+.
T Consensus 26 plakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs 68 (264)
T KOG3032|consen 26 PLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKS 68 (264)
T ss_pred HhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHh
Confidence 444455567899999999988 9999999999999999999984
No 10
>PLN02748 tRNA dimethylallyltransferase
Probab=91.76 E-value=0.12 Score=52.82 Aligned_cols=39 Identities=23% Similarity=0.432 Sum_probs=33.4
Q ss_pred Cceeeccccc-cccchhhHHhhhcccchHHHHHHhhHhhh
Q 046771 221 TKWSCALCQV-SATTARGLYAHLQGKKHKAKEKLLRDLKM 259 (326)
Q Consensus 221 ~eWsCalCqV-ttTSE~~LnsHL~GKrHkAk~e~L~a~~~ 259 (326)
+..+|.+|.- +...+..-+.|++||+|+..+..++.++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~~~ 456 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQKQT 456 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhhhh
Confidence 4558999998 89999999999999999999987765443
No 11
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=90.63 E-value=0.22 Score=46.64 Aligned_cols=38 Identities=32% Similarity=0.514 Sum_probs=33.2
Q ss_pred CCC-CCceeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 217 SNK-PTKWSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 217 ~K~-~~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.|. ..++.|-||.-+--+|.+...|++||||+.++..-
T Consensus 47 ~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 47 SKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred hhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 344 47999999999999999999999999999998753
No 12
>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=90.00 E-value=0.19 Score=30.03 Aligned_cols=21 Identities=24% Similarity=0.665 Sum_probs=19.7
Q ss_pred eeeccccccccchhhHHhhhc
Q 046771 223 WSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~ 243 (326)
|.|..|..++++...|+.|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 689999999999999999985
No 13
>smart00355 ZnF_C2H2 zinc finger.
Probab=86.06 E-value=0.37 Score=27.99 Aligned_cols=21 Identities=19% Similarity=0.510 Sum_probs=19.3
Q ss_pred eeeccccccccchhhHHhhhc
Q 046771 223 WSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~ 243 (326)
+.|..|..++.+...|+.|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 369999999999999999987
No 14
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=84.93 E-value=0.52 Score=28.77 Aligned_cols=19 Identities=32% Similarity=0.658 Sum_probs=15.6
Q ss_pred eeccccccccchhhHHhhhc
Q 046771 224 SCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 224 sCalCqVttTSE~~LnsHL~ 243 (326)
.|..|..+++ +.+|..|++
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 6999999999 999999985
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=83.97 E-value=0.47 Score=35.29 Aligned_cols=27 Identities=30% Similarity=0.482 Sum_probs=23.1
Q ss_pred ceeeccccccccchhhHHhhhcccchHHHH
Q 046771 222 KWSCALCQVSATTARGLYAHLQGKKHKAKE 251 (326)
Q Consensus 222 eWsCalCqVttTSE~~LnsHL~GKrHkAk~ 251 (326)
.=-|..|++.+. +|..|+.+++|+.=.
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CccCccccchhh---hHHHHhCCHHHHHHH
Confidence 446999999997 599999999999754
No 16
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=83.11 E-value=0.62 Score=48.50 Aligned_cols=34 Identities=32% Similarity=0.629 Sum_probs=29.9
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.+--|.+|+|--+||--|-+|..|++||-.+-.|
T Consensus 492 rkkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 492 RKKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 3557999999999999999999999999877554
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=83.06 E-value=0.85 Score=28.21 Aligned_cols=21 Identities=19% Similarity=0.475 Sum_probs=19.4
Q ss_pred eeeccccccccchhhHHhhhc
Q 046771 223 WSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~ 243 (326)
..|.+|+.++.+...|..|++
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 479999999999999999994
No 18
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=81.50 E-value=0.56 Score=35.04 Aligned_cols=28 Identities=25% Similarity=0.371 Sum_probs=23.4
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHH
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKE 251 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~ 251 (326)
+.--|..|.+.+. +|..|+.+++|+.=.
T Consensus 4 k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 4 KPGYCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred CCcccccHhHHHh---hHHHHhccHHHHHHH
Confidence 3456999999986 799999999999744
No 19
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=77.88 E-value=1.2 Score=46.28 Aligned_cols=34 Identities=32% Similarity=0.504 Sum_probs=32.5
Q ss_pred eeeccccccccchhhHHhhhcccchHHHHHHhhH
Q 046771 223 WSCALCQVSATTARGLYAHLQGKKHKAKEKLLRD 256 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a 256 (326)
.-|-+|.-+|-||..|..|-+-|+|+.+++.|+.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999999999973
No 20
>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=76.51 E-value=2.5 Score=32.57 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=16.8
Q ss_pred CceeeccccccccchhhHHhhhc
Q 046771 221 TKWSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~ 243 (326)
+.=+|.+|..+.++..+|..||.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHH
Confidence 45699999999999999999984
No 21
>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=74.97 E-value=2.3 Score=38.87 Aligned_cols=32 Identities=25% Similarity=0.594 Sum_probs=29.7
Q ss_pred eeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 223 WSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
++|.+|-+.+--+..+..||+++=|+....-+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 47999999999999999999999999888766
No 22
>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=69.36 E-value=2.7 Score=27.30 Aligned_cols=19 Identities=21% Similarity=0.534 Sum_probs=16.6
Q ss_pred eeccccccccchhhHHhhhc
Q 046771 224 SCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 224 sCalCqVttTSE~~LnsHL~ 243 (326)
.|.+|+-.. ++..+|+||-
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699998887 8899999985
No 23
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=66.42 E-value=3 Score=38.15 Aligned_cols=33 Identities=24% Similarity=0.477 Sum_probs=26.6
Q ss_pred ceeecccc--ccccchhhHHhhhcccchHHHHHHh
Q 046771 222 KWSCALCQ--VSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 222 eWsCalCq--VttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.+-|..|+ .|--|-+.=..||.|++|+.++...
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 46799998 3445777888999999999998754
No 24
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=65.30 E-value=3.5 Score=36.40 Aligned_cols=35 Identities=31% Similarity=0.487 Sum_probs=32.1
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHhh
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLR 255 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~ 255 (326)
...-|-.|.-.+.+++.|..|+.+|.||--+..|+
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 47889999999999999999999999999887775
No 25
>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=64.05 E-value=5.6 Score=32.24 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=27.4
Q ss_pred CCceeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 220 PTKWSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 220 ~~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.+-|.|..|++.... ..+.+||+.+-|.-+.+..
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~ 42 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQER 42 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHH
Confidence 368999999987777 8999999998877655433
No 26
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=59.27 E-value=4.8 Score=40.27 Aligned_cols=32 Identities=25% Similarity=0.431 Sum_probs=25.7
Q ss_pred ceeecccccccc-chhhHHhhhcccchHHHHHH
Q 046771 222 KWSCALCQVSAT-TARGLYAHLQGKKHKAKEKL 253 (326)
Q Consensus 222 eWsCalCqVttT-SE~~LnsHL~GKrHkAk~e~ 253 (326)
.--|.+|++=.. .-.+...|-+|+|||+++++
T Consensus 10 kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 10 KKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred chhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 446999988665 45677889999999999874
No 27
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=54.55 E-value=45 Score=37.19 Aligned_cols=32 Identities=22% Similarity=0.388 Sum_probs=25.2
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHh
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L 254 (326)
.-+-|..|.--|--=+++|-|+ |+|+-+.++-
T Consensus 791 giFpCreC~kvF~KiKSrNAHM--K~Hr~q~~~~ 822 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHM--KTHRQQEEQQ 822 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHH--HHHHHHHHHH
Confidence 5678999999898899999998 5666655443
No 28
>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=54.21 E-value=5.9 Score=37.51 Aligned_cols=30 Identities=27% Similarity=0.478 Sum_probs=23.7
Q ss_pred CCceeecccc---ccccchhhHHhhhcccchHH
Q 046771 220 PTKWSCALCQ---VSATTARGLYAHLQGKKHKA 249 (326)
Q Consensus 220 ~~eWsCalCq---VttTSE~~LnsHL~GKrHkA 249 (326)
++-=+|.||. +..-++.-|.+|+.||-|..
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 3456899995 45566788999999999964
No 29
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.15 E-value=85 Score=32.13 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHH
Q 046771 78 LLYTLQREIEKEIIRREIIAAEIERRRLPEEEASRELMIE 117 (326)
Q Consensus 78 ~~~~L~Releke~IR~eiI~~E~a~rr~LEaEvrREl~~E 117 (326)
-+|.||+.+++|.-|..-..+++.|+.|--.+-..||.+|
T Consensus 215 ~~eklR~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~ 254 (365)
T KOG2391|consen 215 VREKLRRRREEEMERLQAEQESLKRTEEELNIGKQKLVAM 254 (365)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHH
Confidence 3477888888888887777777776655544444555444
No 30
>PF11830 DUF3350: Domain of unknown function (DUF3350); InterPro: IPR021785 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.
Probab=52.30 E-value=43 Score=26.10 Aligned_cols=23 Identities=26% Similarity=0.383 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 046771 78 LLYTLQREIEKEIIRREIIAAEIE 101 (326)
Q Consensus 78 ~~~~L~Releke~IR~eiI~~E~a 101 (326)
++++| |+||+-+|.|.||--=|+
T Consensus 27 t~eel-R~LWrkAI~QqIlL~RME 49 (56)
T PF11830_consen 27 TREEL-RELWRKAIHQQILLLRME 49 (56)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHH
Confidence 55665 589999999999976555
No 31
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=47.16 E-value=11 Score=36.53 Aligned_cols=25 Identities=24% Similarity=0.627 Sum_probs=23.2
Q ss_pred CceeeccccccccchhhHHhhhccc
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGK 245 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GK 245 (326)
..|-|-+|.+.+.++-+|.+||-|-
T Consensus 238 eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred cceEEEEeccccCCHHHHHHhCCCC
Confidence 4799999999999999999999884
No 32
>PF12907 zf-met2: Zinc-binding
Probab=45.41 E-value=8.4 Score=27.80 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=23.8
Q ss_pred eeecccc---ccccchhhHHhhhcccchHHHHH
Q 046771 223 WSCALCQ---VSATTARGLYAHLQGKKHKAKEK 252 (326)
Q Consensus 223 WsCalCq---VttTSE~~LnsHL~GKrHkAk~e 252 (326)
-.|.||- +.++++..|.+|-..|-=|...+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~ 34 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFE 34 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHH
Confidence 3699998 89999999999998775554343
No 33
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=43.49 E-value=10 Score=39.06 Aligned_cols=32 Identities=25% Similarity=0.397 Sum_probs=27.8
Q ss_pred ceeeccccccccchhhHHhhhcccchHHHHHH
Q 046771 222 KWSCALCQVSATTARGLYAHLQGKKHKAKEKL 253 (326)
Q Consensus 222 eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~ 253 (326)
..-|.+|+--+..-+-+..||-||+|..+...
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~ 269 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGKRHCKEGQG 269 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhh
Confidence 34799999999999999999999999876653
No 34
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=43.00 E-value=8.1 Score=38.53 Aligned_cols=43 Identities=26% Similarity=0.336 Sum_probs=31.5
Q ss_pred CCCCceeeccc---cccccchhhHHhhhcccchH------HHHHHhhHhhhh
Q 046771 218 NKPTKWSCALC---QVSATTARGLYAHLQGKKHK------AKEKLLRDLKMF 260 (326)
Q Consensus 218 K~~~eWsCalC---qVttTSE~~LnsHL~GKrHk------Ak~e~L~a~~~~ 260 (326)
..|+-=.|.|| .+-.-...-|.+|+.||=|- .+++.|++....
T Consensus 182 ~~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~~~~ 233 (319)
T KOG0796|consen 182 QQQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKEKAK 233 (319)
T ss_pred hhhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhH
Confidence 34456689999 45566788899999999995 566666655544
No 35
>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=42.85 E-value=19 Score=33.82 Aligned_cols=37 Identities=24% Similarity=0.438 Sum_probs=29.6
Q ss_pred CCceeeccccccccchhhHHhhhcccchHHHHHHhhHh
Q 046771 220 PTKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLRDL 257 (326)
Q Consensus 220 ~~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a~ 257 (326)
-.+|-|.+|+--|-.+.-...|+. +||-.+++.++..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~e 111 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKE 111 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHH
Confidence 358999999999999999999997 6799999987644
No 36
>PF13049 DUF3910: Protein of unknown function (DUF3910)
Probab=38.21 E-value=22 Score=29.69 Aligned_cols=36 Identities=31% Similarity=0.645 Sum_probs=27.8
Q ss_pred CCcccccCCCcceeeeeeeeEEEeecccccccccCCCC
Q 046771 1 QTKTHWTGSPTSYIARRQHALTFLSQSMESKFGRIDDR 38 (326)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~f~~~sMEFkfRAgD~R 38 (326)
|.|..|.|.|-.||-. -.||+=.+|.+|..-..|+|
T Consensus 4 ~akvdwigtpkpyiyk--ddvtyda~~idfsl~~ddnr 39 (93)
T PF13049_consen 4 QAKVDWIGTPKPYIYK--DDVTYDATSIDFSLENDDNR 39 (93)
T ss_pred cceeeeccCCCceEec--ccceeeeeEEEEEeccCCCe
Confidence 5688999999999977 45777677888876555555
No 37
>PHA00616 hypothetical protein
Probab=34.79 E-value=15 Score=26.98 Aligned_cols=20 Identities=20% Similarity=0.467 Sum_probs=18.8
Q ss_pred eeeccccccccchhhHHhhh
Q 046771 223 WSCALCQVSATTARGLYAHL 242 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL 242 (326)
..|..|+..+.....|+.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CccchhhHHHhhHHHHHHHH
Confidence 46999999999999999999
No 38
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=33.48 E-value=26 Score=30.79 Aligned_cols=38 Identities=32% Similarity=0.504 Sum_probs=33.1
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHhhHhh
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLRDLK 258 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a~~ 258 (326)
...-|--|---+-++..|-.|+.||=|+-....|+..-
T Consensus 54 GqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRevp 91 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKGKVHKRRAKELREVP 91 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcCc
Confidence 46789999999999999999999999999888776543
No 39
>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=31.02 E-value=16 Score=34.04 Aligned_cols=37 Identities=19% Similarity=0.347 Sum_probs=0.0
Q ss_pred ceeeccc-cccccchhhHHhhhcccchHHHHHHhhHhh
Q 046771 222 KWSCALC-QVSATTARGLYAHLQGKKHKAKEKLLRDLK 258 (326)
Q Consensus 222 eWsCalC-qVttTSE~~LnsHL~GKrHkAk~e~L~a~~ 258 (326)
+..|.|| +.+.-..+.+..|.+.-||.--+..|+--+
T Consensus 101 ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~n 138 (196)
T PF11931_consen 101 EYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIPN 138 (196)
T ss_dssp --------------------------------------
T ss_pred eeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCCC
Confidence 7889999 677789999999999999999888886654
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=29.78 E-value=18 Score=27.14 Aligned_cols=27 Identities=30% Similarity=0.567 Sum_probs=0.0
Q ss_pred eccccccccchhhHHhhhcccchHHHHH
Q 046771 225 CALCQVSATTARGLYAHLQGKKHKAKEK 252 (326)
Q Consensus 225 CalCqVttTSE~~LnsHL~GKrHkAk~e 252 (326)
|.+|..++++...|..||. ..|...+.
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 78877665
No 41
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.12 E-value=98 Score=35.13 Aligned_cols=7 Identities=0% Similarity=-0.439 Sum_probs=3.8
Q ss_pred ccccCCC
Q 046771 31 KFGRIDD 37 (326)
Q Consensus 31 kfRAgD~ 37 (326)
+|-+|+.
T Consensus 260 ma~sGq~ 266 (1118)
T KOG1029|consen 260 MAKSGQP 266 (1118)
T ss_pred HHhcCCC
Confidence 4556654
No 42
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=28.65 E-value=15 Score=36.43 Aligned_cols=36 Identities=22% Similarity=0.541 Sum_probs=32.7
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHHHhhH
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEKLLRD 256 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e~L~a 256 (326)
..|-|-.||-.|..|-++..|+.---|+-.+..+..
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 489999999999999999999999999998876643
No 43
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=28.62 E-value=39 Score=32.80 Aligned_cols=24 Identities=25% Similarity=0.506 Sum_probs=21.7
Q ss_pred CCceeeccccccccchhhHHhhhc
Q 046771 220 PTKWSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 220 ~~eWsCalCqVttTSE~~LnsHL~ 243 (326)
+...+|.||+-+++=.+-||.||.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k 138 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK 138 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh
Confidence 458999999999999999999984
No 44
>PF14968 CCDC84: Coiled coil protein 84
Probab=28.61 E-value=29 Score=34.79 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=25.9
Q ss_pred Cceeeccccccccch------hhHHhhhcccchHHHHHHh
Q 046771 221 TKWSCALCQVSATTA------RGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 221 ~eWsCalCqVttTSE------~~LnsHL~GKrHkAk~e~L 254 (326)
.-| |.+|..-..-- .++..||.+..|+.++..-
T Consensus 58 ~fW-C~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F 96 (336)
T PF14968_consen 58 RFW-CVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKF 96 (336)
T ss_pred eeE-eeCccchhhhccchhhhccHHhhcCCHHHHHHHHHH
Confidence 466 99996544332 5899999999999999865
No 45
>PHA00732 hypothetical protein
Probab=27.92 E-value=34 Score=27.33 Aligned_cols=22 Identities=23% Similarity=0.555 Sum_probs=19.8
Q ss_pred eeeccccccccchhhHHhhhcc
Q 046771 223 WSCALCQVSATTARGLYAHLQG 244 (326)
Q Consensus 223 WsCalCqVttTSE~~LnsHL~G 244 (326)
..|..|.-++++..+|..|++.
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 46
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=27.47 E-value=1e+02 Score=25.74 Aligned_cols=35 Identities=31% Similarity=0.275 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh----ccHHHHHHHH
Q 046771 80 YTLQREIEKEIIRREIIAAEIERRR----LPEEEASREL 114 (326)
Q Consensus 80 ~~L~Releke~IR~eiI~~E~a~rr----~LEaEvrREl 114 (326)
++++.|+++-+-+.+-|.+|+.+-+ -||+-+|+||
T Consensus 37 ~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~L 75 (105)
T PRK00888 37 AAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNEL 75 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHc
Confidence 4555556665666666667666332 2444444444
No 47
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=26.60 E-value=37 Score=33.58 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=22.1
Q ss_pred CCceeeccccccccchhhHHhhhcccc
Q 046771 220 PTKWSCALCQVSATTARGLYAHLQGKK 246 (326)
Q Consensus 220 ~~eWsCalCqVttTSE~~LnsHL~GKr 246 (326)
.+-| |..|+--+-.|+-|+.|..-|-
T Consensus 9 ~kpw-cwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhcc
Confidence 4777 9999999999999999976554
No 48
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=24.76 E-value=38 Score=31.56 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=25.5
Q ss_pred ceeecccccccc--chhhHHhhhcccchHHHHHHh
Q 046771 222 KWSCALCQVSAT--TARGLYAHLQGKKHKAKEKLL 254 (326)
Q Consensus 222 eWsCalCqVttT--SE~~LnsHL~GKrHkAk~e~L 254 (326)
.+-|..|++--| +-+.-..||.|++|--..+..
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dY 37 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDY 37 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHH
Confidence 357999987554 456678999999998877755
No 49
>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=24.61 E-value=47 Score=23.98 Aligned_cols=21 Identities=19% Similarity=0.555 Sum_probs=16.9
Q ss_pred ceeeccccccccchhhHHhhhc
Q 046771 222 KWSCALCQVSATTARGLYAHLQ 243 (326)
Q Consensus 222 eWsCalCqVttTSE~~LnsHL~ 243 (326)
...|++|.- .-++.+|.+|+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~ 22 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCE 22 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHH
Confidence 467999988 677888998875
No 50
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=24.42 E-value=42 Score=35.92 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=30.1
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHHH
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKEK 252 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~e 252 (326)
..|.|..||+++.+-....+|.+--=|+-++.
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~K 96 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTK 96 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999998885
No 51
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=22.95 E-value=37 Score=23.67 Aligned_cols=12 Identities=25% Similarity=0.966 Sum_probs=8.3
Q ss_pred CCceeecccccc
Q 046771 220 PTKWSCALCQVS 231 (326)
Q Consensus 220 ~~eWsCalCqVt 231 (326)
.+.|+|.+|+..
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 368999999753
No 52
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.62 E-value=3.5e+02 Score=27.06 Aligned_cols=16 Identities=13% Similarity=0.428 Sum_probs=12.5
Q ss_pred Cceeeccccccccchh
Q 046771 221 TKWSCALCQVSATTAR 236 (326)
Q Consensus 221 ~eWsCalCqVttTSE~ 236 (326)
+.+.|++|.++-|.-.
T Consensus 220 ~ryiCpvtrd~LtNt~ 235 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTT 235 (303)
T ss_pred cceecccchhhhcCcc
Confidence 7899999987766544
No 53
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=22.52 E-value=2e+02 Score=31.04 Aligned_cols=11 Identities=27% Similarity=0.350 Sum_probs=8.7
Q ss_pred ccccccCCCCC
Q 046771 58 DDQARRGNYSM 68 (326)
Q Consensus 58 ~~~~~~Gg~~~ 68 (326)
..+++.|||++
T Consensus 480 ~~~al~gG~~g 490 (641)
T KOG3915|consen 480 HGQALPGGFPG 490 (641)
T ss_pred CCCcCCCCCCC
Confidence 35789999994
No 54
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=22.43 E-value=30 Score=38.26 Aligned_cols=31 Identities=35% Similarity=0.622 Sum_probs=28.7
Q ss_pred CceeeccccccccchhhHHhhhcccchHHHH
Q 046771 221 TKWSCALCQVSATTARGLYAHLQGKKHKAKE 251 (326)
Q Consensus 221 ~eWsCalCqVttTSE~~LnsHL~GKrHkAk~ 251 (326)
.---|.+||+.|..-.+...||+|-||..+.
T Consensus 192 qL~~~kw~k~~a~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 192 QLHYCKWCKISAAGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred HhhhhHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 4568999999999999999999999999987
No 55
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=21.70 E-value=42 Score=34.56 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=29.7
Q ss_pred CCCCCCCceeeccccccccchhhHHhhhcccchHH
Q 046771 215 KSSNKPTKWSCALCQVSATTARGLYAHLQGKKHKA 249 (326)
Q Consensus 215 ~~~K~~~eWsCalCqVttTSE~~LnsHL~GKrHkA 249 (326)
..+++....-|-.|.+.+....+|.+|++-|+|+.
T Consensus 188 hLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 188 HLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred HHHHHHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 33445567789999999999999999999999983
Done!