Query 030300
Match_columns 179
No_of_seqs 151 out of 444
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 11:38:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173 Predicted Zn-finger pr 100.0 3.3E-47 7.3E-52 310.0 10.2 164 8-179 1-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 2.5E-15 5.4E-20 96.3 2.3 38 120-157 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 4.4E-15 9.5E-20 87.3 2.3 25 22-46 1-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.4 1.9E-14 4.1E-19 85.3 1.1 25 22-46 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.0 5.9E-11 1.3E-15 77.0 1.3 38 120-158 1-41 (43)
6 KOG3183 Predicted Zn-finger pr 96.5 0.001 2.2E-08 57.9 1.0 40 118-158 9-51 (250)
7 COG3582 Predicted nucleic acid 96.2 0.0023 4.9E-08 52.7 1.7 37 120-157 100-137 (162)
8 PF01363 FYVE: FYVE zinc finge 94.0 0.025 5.4E-07 38.9 1.1 29 116-144 8-39 (69)
9 cd00065 FYVE FYVE domain; Zinc 92.7 0.051 1.1E-06 35.8 0.9 27 118-144 3-32 (57)
10 KOG3183 Predicted Zn-finger pr 92.7 0.027 5.8E-07 49.3 -0.6 41 113-153 94-138 (250)
11 smart00064 FYVE Protein presen 92.4 0.072 1.6E-06 36.5 1.5 28 117-144 10-40 (68)
12 KOG4345 NF-kappa B regulator A 90.5 0.12 2.6E-06 51.0 1.3 31 23-53 736-767 (774)
13 KOG1818 Membrane trafficking a 89.6 0.12 2.7E-06 50.4 0.6 46 116-161 164-223 (634)
14 PF10571 UPF0547: Uncharacteri 87.1 0.31 6.8E-06 28.7 1.0 23 118-140 1-24 (26)
15 PF15135 UPF0515: Uncharacteri 82.3 0.75 1.6E-05 40.8 1.6 30 113-142 128-167 (278)
16 PF00130 C1_1: Phorbol esters/ 82.1 0.8 1.7E-05 29.7 1.3 24 116-139 10-37 (53)
17 PF02148 zf-UBP: Zn-finger in 65.4 3.3 7.2E-05 28.2 1.1 23 120-143 1-24 (63)
18 KOG1729 FYVE finger containing 61.7 2.2 4.8E-05 38.1 -0.5 32 116-148 167-202 (288)
19 PF14471 DUF4428: Domain of un 59.4 3.2 7E-05 27.8 0.1 21 119-139 1-29 (51)
20 PHA02768 hypothetical protein; 56.0 4.7 0.0001 27.8 0.5 15 128-142 2-17 (55)
21 PF08882 Acetone_carb_G: Aceto 55.4 5.9 0.00013 31.0 1.0 33 121-155 16-48 (112)
22 PF13978 DUF4223: Protein of u 54.6 5.8 0.00013 27.4 0.7 18 140-157 19-36 (56)
23 PF01194 RNA_pol_N: RNA polyme 54.4 6.7 0.00014 27.6 1.0 13 117-129 4-16 (60)
24 smart00109 C1 Protein kinase C 54.2 7 0.00015 24.0 1.1 23 116-138 10-35 (49)
25 cd00029 C1 Protein kinase C co 54.2 6.8 0.00015 24.4 1.0 24 116-139 10-37 (50)
26 PF11781 RRN7: RNA polymerase 54.1 6.1 0.00013 24.7 0.7 22 118-139 9-34 (36)
27 KOG1812 Predicted E3 ubiquitin 54.0 8.1 0.00018 35.5 1.8 31 115-145 304-338 (384)
28 COG1996 RPC10 DNA-directed RNA 53.5 5.3 0.00012 27.0 0.4 23 117-139 6-33 (49)
29 KOG1819 FYVE finger-containing 53.5 6.5 0.00014 38.6 1.1 29 116-144 900-931 (990)
30 PHA00626 hypothetical protein 50.0 8.2 0.00018 27.0 0.9 22 118-141 12-34 (59)
31 PRK04016 DNA-directed RNA poly 48.2 6.6 0.00014 27.8 0.2 14 116-129 3-16 (62)
32 PLN00032 DNA-directed RNA poly 47.3 7.3 0.00016 28.3 0.3 14 116-129 3-16 (71)
33 PF05207 zf-CSL: CSL zinc fing 46.8 8.6 0.00019 26.0 0.6 14 128-141 15-28 (55)
34 PTZ00303 phosphatidylinositol 46.7 10 0.00023 39.0 1.4 27 118-144 461-495 (1374)
35 smart00659 RPOLCX RNA polymera 43.5 11 0.00025 24.5 0.8 20 119-138 4-27 (44)
36 PF07649 C1_3: C1-like domain; 43.4 10 0.00022 22.2 0.5 22 119-140 2-25 (30)
37 PF03604 DNA_RNApol_7kD: DNA d 43.4 10 0.00022 23.3 0.5 18 120-137 3-24 (32)
38 smart00290 ZnF_UBP Ubiquitin C 42.4 8.6 0.00019 24.5 0.1 24 119-144 1-25 (50)
39 PF03107 C1_2: C1 domain; Int 42.2 18 0.00039 21.3 1.4 20 119-138 2-23 (30)
40 COG1571 Predicted DNA-binding 41.2 12 0.00026 35.2 0.9 26 117-142 350-379 (421)
41 KOG3497 DNA-directed RNA polym 40.8 9.2 0.0002 27.3 0.0 13 117-129 4-16 (69)
42 KOG2807 RNA polymerase II tran 39.9 18 0.00039 33.5 1.7 29 115-143 328-358 (378)
43 PF02928 zf-C5HC2: C5HC2 zinc 38.6 15 0.00033 24.5 0.8 26 120-145 1-28 (54)
44 PF13842 Tnp_zf-ribbon_2: DDE_ 38.0 25 0.00054 21.3 1.6 26 119-144 2-30 (32)
45 PRK08402 replication factor A; 38.0 13 0.00029 33.9 0.6 29 117-146 212-245 (355)
46 PF07975 C1_4: TFIIH C1-like d 37.9 13 0.00028 25.2 0.4 34 120-153 2-47 (51)
47 PF02318 FYVE_2: FYVE-type zin 37.9 22 0.00047 27.1 1.7 31 117-147 54-88 (118)
48 PF15549 PGC7_Stella: PGC7/Ste 36.7 19 0.00041 29.8 1.3 19 131-151 123-141 (160)
49 COG1644 RPB10 DNA-directed RNA 35.8 12 0.00026 26.6 -0.0 13 117-129 4-16 (63)
50 smart00647 IBR In Between Ring 35.7 24 0.00053 22.9 1.5 18 130-147 39-57 (64)
51 cd04476 RPA1_DBD_C RPA1_DBD_C: 35.3 16 0.00035 28.9 0.6 32 116-147 33-69 (166)
52 PRK04136 rpl40e 50S ribosomal 35.0 20 0.00042 24.3 0.9 23 116-138 13-36 (48)
53 PF13717 zinc_ribbon_4: zinc-r 34.7 20 0.00043 22.2 0.8 9 132-140 26-35 (36)
54 KOG1842 FYVE finger-containing 34.2 9.9 0.00022 36.4 -0.8 25 118-142 181-208 (505)
55 PF13240 zinc_ribbon_2: zinc-r 33.4 24 0.00052 19.9 1.0 19 119-137 1-20 (23)
56 PF09723 Zn-ribbon_8: Zinc rib 32.6 26 0.00057 22.1 1.2 20 129-148 3-23 (42)
57 PF01485 IBR: IBR domain; Int 31.6 20 0.00043 23.2 0.5 16 132-147 41-57 (64)
58 PRK00398 rpoP DNA-directed RNA 30.9 26 0.00056 22.4 0.9 28 118-145 4-36 (46)
59 PF10122 Mu-like_Com: Mu-like 30.5 18 0.0004 24.7 0.2 24 117-140 4-34 (51)
60 PRK07218 replication factor A; 29.4 24 0.00052 33.1 0.8 21 117-139 297-318 (423)
61 PF10367 Vps39_2: Vacuolar sor 29.3 37 0.0008 24.2 1.7 24 117-140 78-102 (109)
62 PF06750 DiS_P_DiS: Bacterial 28.5 33 0.00072 25.4 1.3 15 116-130 32-46 (92)
63 KOG3507 DNA-directed RNA polym 27.8 27 0.00058 24.7 0.6 23 116-138 19-45 (62)
64 PF08073 CHDNT: CHDNT (NUC034) 27.6 23 0.0005 24.5 0.3 20 158-177 21-40 (55)
65 KOG1074 Transcriptional repres 27.5 41 0.0009 34.6 2.1 46 111-156 599-672 (958)
66 PF14634 zf-RING_5: zinc-RING 26.8 34 0.00075 21.4 1.0 29 119-147 1-31 (44)
67 PF04438 zf-HIT: HIT zinc fing 26.7 20 0.00043 21.5 -0.1 23 118-143 3-26 (30)
68 COG1997 RPL43A Ribosomal prote 26.2 37 0.00081 25.6 1.2 33 114-147 32-70 (89)
69 PF14835 zf-RING_6: zf-RING of 25.6 38 0.00083 24.2 1.1 27 117-143 7-33 (65)
70 PF08600 Rsm1: Rsm1-like; Int 25.5 27 0.00058 25.7 0.3 18 117-134 19-36 (91)
71 PF00096 zf-C2H2: Zinc finger, 24.2 31 0.00066 18.3 0.3 9 132-140 1-10 (23)
72 KOG0193 Serine/threonine prote 24.1 27 0.00059 34.7 0.2 50 118-172 190-243 (678)
73 PF00412 LIM: LIM domain; Int 23.2 31 0.00068 22.0 0.3 28 117-144 26-53 (58)
74 PRK12366 replication factor A; 22.0 35 0.00076 33.4 0.5 29 117-146 532-563 (637)
75 smart00396 ZnF_UBR1 Putative z 21.5 51 0.0011 23.2 1.1 14 131-144 50-70 (71)
76 COG3357 Predicted transcriptio 20.8 35 0.00077 26.1 0.2 16 127-142 54-70 (97)
77 PTZ00218 40S ribosomal protein 20.6 58 0.0013 22.5 1.2 13 38-50 34-46 (54)
78 PF05458 Siva: Cd27 binding pr 20.6 82 0.0018 26.1 2.3 38 116-153 110-165 (175)
79 PF07282 OrfB_Zn_ribbon: Putat 20.3 84 0.0018 21.1 2.0 24 116-139 27-55 (69)
80 smart00834 CxxC_CXXC_SSSS Puta 20.3 50 0.0011 19.8 0.8 14 130-143 4-18 (41)
81 PF13923 zf-C3HC4_2: Zinc fing 20.1 45 0.00098 20.2 0.5 23 120-142 1-23 (39)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.3e-47 Score=310.04 Aligned_cols=164 Identities=45% Similarity=0.853 Sum_probs=109.7
Q ss_pred CCCcccCCCCCCCCCcccccCCCCCCccccccchhhhhHHHHHHHhhhh-hhhhcccccccCCCCCCCCCcccccccccc
Q 030300 8 MDHDETGCQAPPEGPILCINNCGFFGSVATMNMCSKCYKDIMLKQDQAK-LAASSIGSIVNETSSSNGSESVAAATVDVQ 86 (179)
Q Consensus 8 M~~e~~~~q~~pe~p~LC~n~CGFfGs~at~n~CSkCyr~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (179)
|+++....+.+++.+.||+|||||||+|+|+||||+||++++.++++.. .....+..-+.. +.+ .+. ....
T Consensus 1 M~~e~~~~~~~~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~-~~s---~~~----~~~~ 72 (167)
T KOG3173|consen 1 MASETNGSQTPPSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSS-PRS---VPS----RDPP 72 (167)
T ss_pred CcccccCCCCCCccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccC-ccc---cCc----cccc
Confidence 6655444454234579999999999999999999999999998876652 222111110000 000 010 0000
Q ss_pred cCCCCcccc-cccCC-CCCCCcccccCCCCCCCCCcccccccccccceeeecCCccccCCCCCCCCCCcccchHHHHHHH
Q 030300 87 ASSVEPKII-SVQPS-CASELSESVEAKPKEGPSRCSSCKKRVGLTGFKCRCGNLYCVSHRYSDKHNCPFDYRTAARDAI 164 (179)
Q Consensus 87 ~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~~r~~l 164 (179)
+...+.... +...+ ..+...+.........++||+.|+|||||+||.||||++||+.|||||.|+|+||||.+||+.|
T Consensus 73 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i 152 (167)
T KOG3173|consen 73 AVSLESTTESELKLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKI 152 (167)
T ss_pred cccccccccccccccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHH
Confidence 000010000 00000 0001111222334557889999999999999999999999999999999999999999999999
Q ss_pred HHhCCcccccccccC
Q 030300 165 IKANPVIKAEKLDKI 179 (179)
Q Consensus 165 ~k~Np~v~~~Ki~KI 179 (179)
+++||+|+++||+||
T Consensus 153 ~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 153 AKANPVVKADKLQKI 167 (167)
T ss_pred HHhCCeeeccccccC
Confidence 999999999999998
No 2
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.54 E-value=2.5e-15 Score=96.33 Aligned_cols=38 Identities=63% Similarity=1.481 Sum_probs=36.9
Q ss_pred cccccccccccceeee-cCCccccCCCCCCCCCCcccch
Q 030300 120 CSSCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYR 157 (179)
Q Consensus 120 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 157 (179)
|+.|+++++|++|+|+ |+++||..|||||.|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 3
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.52 E-value=4.4e-15 Score=87.30 Aligned_cols=25 Identities=64% Similarity=1.420 Sum_probs=20.8
Q ss_pred CcccccCCCCCCccccccchhhhhH
Q 030300 22 PILCINNCGFFGSVATMNMCSKCYK 46 (179)
Q Consensus 22 p~LC~n~CGFfGs~at~n~CSkCyr 46 (179)
|.||++|||||||++|+||||+|||
T Consensus 1 ~~~C~~gCgf~Gs~~~~~~Cs~C~~ 25 (25)
T PF01754_consen 1 PSLCANGCGFYGSPATNGLCSKCYR 25 (25)
T ss_dssp SSB-TTTSSSB-BGGGTTS-HHHHH
T ss_pred CCcccCCCCCcccccccCcchhhcC
Confidence 5799999999999999999999997
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.45 E-value=1.9e-14 Score=85.28 Aligned_cols=25 Identities=60% Similarity=1.314 Sum_probs=23.4
Q ss_pred Ccccc-cCCCCCCccccccchhhhhH
Q 030300 22 PILCI-NNCGFFGSVATMNMCSKCYK 46 (179)
Q Consensus 22 p~LC~-n~CGFfGs~at~n~CSkCyr 46 (179)
|.||+ +||||||||+|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 46899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.04 E-value=5.9e-11 Score=76.96 Aligned_cols=38 Identities=42% Similarity=0.964 Sum_probs=28.1
Q ss_pred ccc--ccccccccceeee-cCCccccCCCCCCCCCCcccchH
Q 030300 120 CSS--CKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYRT 158 (179)
Q Consensus 120 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 158 (179)
|.. |++++. ++|.|+ |+..||..||||+.|+|+++++.
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccC-CCeECCCCCcccCccccCccccCCcchhhc
Confidence 455 998887 799999 99999999999999999999874
No 6
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.47 E-value=0.001 Score=57.87 Aligned_cols=40 Identities=38% Similarity=1.013 Sum_probs=35.4
Q ss_pred CCcc--cccccccccceeee-cCCccccCCCCCCCCCCcccchH
Q 030300 118 SRCS--SCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYRT 158 (179)
Q Consensus 118 ~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 158 (179)
..|. .|+ ++.++.|+|- |+.+||..||-.+.|+|.+-|..
T Consensus 9 kHCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCK-QLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhh-hccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4677 787 5799999998 99999999999999999987763
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.22 E-value=0.0023 Score=52.75 Aligned_cols=37 Identities=27% Similarity=0.520 Sum_probs=28.9
Q ss_pred cccccccccccceeee-cCCccccCCCCCCCCCCcccch
Q 030300 120 CSSCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYR 157 (179)
Q Consensus 120 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 157 (179)
|..|++..+| .++|- |++.||+.||.++.|+|.+...
T Consensus 100 ~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 100 PQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred ceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 3344444333 68898 9999999999999999998765
No 8
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=94.00 E-value=0.025 Score=38.89 Aligned_cols=29 Identities=38% Similarity=0.863 Sum_probs=17.7
Q ss_pred CCCCccccccccccc--ceeee-cCCccccCC
Q 030300 116 GPSRCSSCKKRVGLT--GFKCR-CGNLYCVSH 144 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 144 (179)
....|..|+++.+|+ -..|| ||.+||+.+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCch
Confidence 357899999999997 49999 999999764
No 9
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=92.68 E-value=0.051 Score=35.82 Aligned_cols=27 Identities=41% Similarity=1.011 Sum_probs=23.7
Q ss_pred CCccccccccccc--ceeee-cCCccccCC
Q 030300 118 SRCSSCKKRVGLT--GFKCR-CGNLYCVSH 144 (179)
Q Consensus 118 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 144 (179)
..|..|.++.+++ ...|| ||.+||..+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHH
Confidence 5799999999997 69999 999999754
No 10
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=92.66 E-value=0.027 Score=49.25 Aligned_cols=41 Identities=34% Similarity=0.826 Sum_probs=34.9
Q ss_pred CCCCCCCcc--ccccccccc-ceeee-cCCccccCCCCCCCCCCc
Q 030300 113 PKEGPSRCS--SCKKRVGLT-GFKCR-CGNLYCVSHRYSDKHNCP 153 (179)
Q Consensus 113 ~~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~ 153 (179)
.+...++|. .|+|++-|. .+.|+ ||..||-+||++-.|.|.
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 444567777 788888775 69999 999999999999999998
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=90.51 E-value=0.12 Score=51.02 Aligned_cols=31 Identities=29% Similarity=0.843 Sum_probs=27.5
Q ss_pred ccc-ccCCCCCCccccccchhhhhHHHHHHHh
Q 030300 23 ILC-INNCGFFGSVATMNMCSKCYKDIMLKQD 53 (179)
Q Consensus 23 ~LC-~n~CGFfGs~at~n~CSkCyr~~~~~~~ 53 (179)
.+| .-+|.|||++.|+++||-|||+.+....
T Consensus 736 ~rck~~nc~~Yg~~~~~~~c~~c~r~el~~~~ 767 (774)
T KOG4345|consen 736 MRCKWPNCDHYGRAETNGYCSECYREELRRGE 767 (774)
T ss_pred hHhhcccchhhccccccccchhhhhHHHhccc
Confidence 588 6899999999999999999999887553
No 13
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=89.62 E-value=0.12 Score=50.42 Aligned_cols=46 Identities=28% Similarity=0.707 Sum_probs=36.0
Q ss_pred CCCCcccccccccccc--eeee-cCCccccCCC-----------CCCCCCCcccchHHHH
Q 030300 116 GPSRCSSCKKRVGLTG--FKCR-CGNLYCVSHR-----------YSDKHNCPFDYRTAAR 161 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~~r 161 (179)
....|..|+.+.|+++ ..|| ||.+||+.|= |-+.--|.-||...-|
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTR 223 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhh
Confidence 4578999999999985 8999 9999999874 3455667777764433
No 14
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.14 E-value=0.31 Score=28.66 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=20.6
Q ss_pred CCcccccccccccceeee-cCCcc
Q 030300 118 SRCSSCKKRVGLTGFKCR-CGNLY 140 (179)
Q Consensus 118 ~rC~~C~kkvgl~gf~Cr-Cg~~F 140 (179)
.+|-.|++.|.+..-.|- ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 368999999999999999 99887
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=82.26 E-value=0.75 Score=40.77 Aligned_cols=30 Identities=33% Similarity=0.868 Sum_probs=24.1
Q ss_pred CCCCCCCccccccc---------ccccceee-ecCCcccc
Q 030300 113 PKEGPSRCSSCKKR---------VGLTGFKC-RCGNLYCV 142 (179)
Q Consensus 113 ~~~~~~rC~~C~kk---------vgl~gf~C-rCg~~FC~ 142 (179)
..+..+||..|+|| .|+.-|.| .|+++|=+
T Consensus 128 ~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 128 QRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccccCCCccccccceeeeecccccccchh
Confidence 34557999999988 67778999 59999854
No 16
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=82.06 E-value=0.8 Score=29.69 Aligned_cols=24 Identities=38% Similarity=1.079 Sum_probs=18.5
Q ss_pred CCCCcccccccc---cccceeee-cCCc
Q 030300 116 GPSRCSSCKKRV---GLTGFKCR-CGNL 139 (179)
Q Consensus 116 ~~~rC~~C~kkv---gl~gf~Cr-Cg~~ 139 (179)
.+..|..|++.| ++.|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 467899999999 66799999 7665
No 17
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=65.43 E-value=3.3 Score=28.20 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=15.3
Q ss_pred cccccccccccceeee-cCCccccC
Q 030300 120 CSSCKKRVGLTGFKCR-CGNLYCVS 143 (179)
Q Consensus 120 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 143 (179)
|..|+.. +-.-+.|- ||.++|+.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5667755 44457787 99999994
No 18
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=61.74 E-value=2.2 Score=38.11 Aligned_cols=32 Identities=25% Similarity=0.720 Sum_probs=26.8
Q ss_pred CCCCcccccc-ccccc--ceeee-cCCccccCCCCCC
Q 030300 116 GPSRCSSCKK-RVGLT--GFKCR-CGNLYCVSHRYSD 148 (179)
Q Consensus 116 ~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e 148 (179)
..++|..|.+ .-.|+ --.|| ||.+||. |.-..
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 4689999999 77776 47899 9999999 87544
No 19
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=59.35 E-value=3.2 Score=27.80 Aligned_cols=21 Identities=38% Similarity=1.124 Sum_probs=16.3
Q ss_pred Cccccccccccc-------ceeee-cCCc
Q 030300 119 RCSSCKKRVGLT-------GFKCR-CGNL 139 (179)
Q Consensus 119 rC~~C~kkvgl~-------gf~Cr-Cg~~ 139 (179)
+|..|++++||+ ||.|. |-.-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHH
Confidence 599999999997 57777 6433
No 20
>PHA02768 hypothetical protein; Provisional
Probab=55.95 E-value=4.7 Score=27.79 Aligned_cols=15 Identities=40% Similarity=1.187 Sum_probs=12.2
Q ss_pred cccceeee-cCCcccc
Q 030300 128 GLTGFKCR-CGNLYCV 142 (179)
Q Consensus 128 gl~gf~Cr-Cg~~FC~ 142 (179)
.|+||.|- ||..|-.
T Consensus 2 ~~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 2 ALLGYECPICGEIYIK 17 (55)
T ss_pred cccccCcchhCCeecc
Confidence 57899998 9888864
No 21
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=55.41 E-value=5.9 Score=31.05 Aligned_cols=33 Identities=18% Similarity=0.344 Sum_probs=25.1
Q ss_pred ccccccccccceeeecCCccccCCCCCCCCCCccc
Q 030300 121 SSCKKRVGLTGFKCRCGNLYCVSHRYSDKHNCPFD 155 (179)
Q Consensus 121 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fD 155 (179)
+.|+++- .-.+|+||+.||+-+..-..|.--++
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEe
Confidence 5666654 27899999999999887777765554
No 22
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=54.62 E-value=5.8 Score=27.40 Aligned_cols=18 Identities=33% Similarity=0.839 Sum_probs=16.0
Q ss_pred cccCCCCCCCCCCcccch
Q 030300 140 YCVSHRYSDKHNCPFDYR 157 (179)
Q Consensus 140 FC~~HRy~e~H~C~fDyk 157 (179)
=|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999996
No 23
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=54.39 E-value=6.7 Score=27.56 Aligned_cols=13 Identities=46% Similarity=1.020 Sum_probs=10.1
Q ss_pred CCCcccccccccc
Q 030300 117 PSRCSSCKKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kkvgl 129 (179)
|-||++|+|-||-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6799999998873
No 24
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=54.24 E-value=7 Score=24.04 Aligned_cols=23 Identities=30% Similarity=0.948 Sum_probs=18.3
Q ss_pred CCCCccccccccccc--ceeee-cCC
Q 030300 116 GPSRCSSCKKRVGLT--GFKCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~--gf~Cr-Cg~ 138 (179)
.+..|..|++.+... |++|+ |+.
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCc
Confidence 467899999999873 88888 654
No 25
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=54.24 E-value=6.8 Score=24.43 Aligned_cols=24 Identities=29% Similarity=0.783 Sum_probs=19.1
Q ss_pred CCCCcccccccccc---cceeee-cCCc
Q 030300 116 GPSRCSSCKKRVGL---TGFKCR-CGNL 139 (179)
Q Consensus 116 ~~~rC~~C~kkvgl---~gf~Cr-Cg~~ 139 (179)
.+..|..|++.+.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 35789999999985 689998 7554
No 26
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=54.12 E-value=6.1 Score=24.75 Aligned_cols=22 Identities=36% Similarity=0.948 Sum_probs=17.5
Q ss_pred CCccccccccccc--c-eee-ecCCc
Q 030300 118 SRCSSCKKRVGLT--G-FKC-RCGNL 139 (179)
Q Consensus 118 ~rC~~C~kkvgl~--g-f~C-rCg~~ 139 (179)
-+|..|+-+...+ | |.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999997775 4 899 89875
No 27
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.97 E-value=8.1 Score=35.54 Aligned_cols=31 Identities=29% Similarity=0.781 Sum_probs=26.2
Q ss_pred CCCCCcccccccccccc----eeeecCCccccCCC
Q 030300 115 EGPSRCSSCKKRVGLTG----FKCRCGNLYCVSHR 145 (179)
Q Consensus 115 ~~~~rC~~C~kkvgl~g----f~CrCg~~FC~~HR 145 (179)
+.-.+|..|+-.+.|.+ +.||||+-||..=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 34689999999998873 99999999997765
No 28
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=53.55 E-value=5.3 Score=26.98 Aligned_cols=23 Identities=35% Similarity=1.021 Sum_probs=18.0
Q ss_pred CCCccccccccccc----ceeee-cCCc
Q 030300 117 PSRCSSCKKRVGLT----GFKCR-CGNL 139 (179)
Q Consensus 117 ~~rC~~C~kkvgl~----gf~Cr-Cg~~ 139 (179)
.-+|..|++++.|. +..|. ||+-
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 35899999999854 79998 7653
No 29
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=53.52 E-value=6.5 Score=38.59 Aligned_cols=29 Identities=24% Similarity=0.807 Sum_probs=21.8
Q ss_pred CCCCccccccccccc--ceeee-cCCccccCC
Q 030300 116 GPSRCSSCKKRVGLT--GFKCR-CGNLYCVSH 144 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 144 (179)
..-+|..|....... -..|| ||++||++-
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 457899998654443 46899 999999864
No 30
>PHA00626 hypothetical protein
Probab=50.03 E-value=8.2 Score=27.05 Aligned_cols=22 Identities=14% Similarity=0.369 Sum_probs=14.5
Q ss_pred CCcccccccccccceeee-cCCccc
Q 030300 118 SRCSSCKKRVGLTGFKCR-CGNLYC 141 (179)
Q Consensus 118 ~rC~~C~kkvgl~gf~Cr-Cg~~FC 141 (179)
.||.+|++.. .-|+|. ||+.|-
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft 34 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDS 34 (59)
T ss_pred eeeceecccC--cceEcCCCCCeec
Confidence 4777777632 248887 877764
No 31
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=48.20 E-value=6.6 Score=27.80 Aligned_cols=14 Identities=36% Similarity=0.700 Sum_probs=11.4
Q ss_pred CCCCcccccccccc
Q 030300 116 GPSRCSSCKKRVGL 129 (179)
Q Consensus 116 ~~~rC~~C~kkvgl 129 (179)
.|-||++|+|-+|-
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 36799999998764
No 32
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=47.31 E-value=7.3 Score=28.30 Aligned_cols=14 Identities=43% Similarity=0.840 Sum_probs=11.4
Q ss_pred CCCCcccccccccc
Q 030300 116 GPSRCSSCKKRVGL 129 (179)
Q Consensus 116 ~~~rC~~C~kkvgl 129 (179)
.|-||++|+|-+|-
T Consensus 3 iPVRCFTCGkvig~ 16 (71)
T PLN00032 3 IPVRCFTCGKVIGN 16 (71)
T ss_pred CceeecCCCCCcHH
Confidence 36799999998764
No 33
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=46.82 E-value=8.6 Score=26.01 Aligned_cols=14 Identities=36% Similarity=1.080 Sum_probs=10.9
Q ss_pred cccceeeecCCccc
Q 030300 128 GLTGFKCRCGNLYC 141 (179)
Q Consensus 128 gl~gf~CrCg~~FC 141 (179)
+..-+.||||..|-
T Consensus 15 ~~~~y~CRCG~~f~ 28 (55)
T PF05207_consen 15 GVYSYPCRCGGEFE 28 (55)
T ss_dssp TEEEEEETTSSEEE
T ss_pred CEEEEcCCCCCEEE
Confidence 34578999999874
No 34
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=46.68 E-value=10 Score=38.95 Aligned_cols=27 Identities=33% Similarity=0.757 Sum_probs=21.0
Q ss_pred CCcccccccccc-------cceeee-cCCccccCC
Q 030300 118 SRCSSCKKRVGL-------TGFKCR-CGNLYCVSH 144 (179)
Q Consensus 118 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 144 (179)
..|..|+++-.. .--.|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 579999999863 246699 999998643
No 35
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=43.51 E-value=11 Score=24.49 Aligned_cols=20 Identities=30% Similarity=0.924 Sum_probs=14.7
Q ss_pred Cccccccccccc---ceeee-cCC
Q 030300 119 RCSSCKKRVGLT---GFKCR-CGN 138 (179)
Q Consensus 119 rC~~C~kkvgl~---gf~Cr-Cg~ 138 (179)
+|..|+..+.+. +.+|+ ||+
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCc
Confidence 688888888875 57776 653
No 36
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=43.38 E-value=10 Score=22.22 Aligned_cols=22 Identities=27% Similarity=0.670 Sum_probs=8.7
Q ss_pred Ccccccccccc-cceeee-cCCcc
Q 030300 119 RCSSCKKRVGL-TGFKCR-CGNLY 140 (179)
Q Consensus 119 rC~~C~kkvgl-~gf~Cr-Cg~~F 140 (179)
+|..|++.+.. ..|.|. |...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 68999999888 789998 76543
No 37
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=43.36 E-value=10 Score=23.27 Aligned_cols=18 Identities=39% Similarity=1.110 Sum_probs=9.8
Q ss_pred ccccccccccc---ceeee-cC
Q 030300 120 CSSCKKRVGLT---GFKCR-CG 137 (179)
Q Consensus 120 C~~C~kkvgl~---gf~Cr-Cg 137 (179)
|..|+..+.|. ..+|+ ||
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCcCCCeeEcCCCCcEECCcCC
Confidence 55666666653 35666 54
No 38
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=42.40 E-value=8.6 Score=24.47 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=17.6
Q ss_pred Ccccccccccccceeee-cCCccccCC
Q 030300 119 RCSSCKKRVGLTGFKCR-CGNLYCVSH 144 (179)
Q Consensus 119 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 144 (179)
||..|..... -+.|- |+.++|+..
T Consensus 1 ~C~~C~~~~~--l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN--LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC--eEEecCCCCcccCCC
Confidence 6888886544 45666 999999764
No 39
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=42.21 E-value=18 Score=21.33 Aligned_cols=20 Identities=20% Similarity=0.730 Sum_probs=16.5
Q ss_pred Cccccccccccc-ceeee-cCC
Q 030300 119 RCSSCKKRVGLT-GFKCR-CGN 138 (179)
Q Consensus 119 rC~~C~kkvgl~-gf~Cr-Cg~ 138 (179)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 488999999888 89997 653
No 40
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.21 E-value=12 Score=35.25 Aligned_cols=26 Identities=31% Similarity=0.805 Sum_probs=20.2
Q ss_pred CCCccccccccccc---ceeee-cCCcccc
Q 030300 117 PSRCSSCKKRVGLT---GFKCR-CGNLYCV 142 (179)
Q Consensus 117 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~ 142 (179)
.-+|..|++++.-. ||+|+ ||..+=.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCc
Confidence 34899999987654 79999 9876643
No 41
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=40.76 E-value=9.2 Score=27.33 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=11.0
Q ss_pred CCCcccccccccc
Q 030300 117 PSRCSSCKKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kkvgl 129 (179)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998774
No 42
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=39.87 E-value=18 Score=33.51 Aligned_cols=29 Identities=24% Similarity=0.877 Sum_probs=23.4
Q ss_pred CCCCCcccc-cccccccceeee-cCCccccC
Q 030300 115 EGPSRCSSC-KKRVGLTGFKCR-CGNLYCVS 143 (179)
Q Consensus 115 ~~~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 143 (179)
...++|+.| .+.++-..|.|+ |-++||..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeecc
Confidence 356789999 666666789999 99999963
No 43
>PF02928 zf-C5HC2: C5HC2 zinc finger; InterPro: IPR004198 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [], and may have a DNA binding function. The mouse jumonji protein is required for neural tube formation, and is essential for normal heart development. It also plays a role in the down-regulation of cell proliferation signalling. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005634 nucleus
Probab=38.62 E-value=15 Score=24.47 Aligned_cols=26 Identities=35% Similarity=0.890 Sum_probs=22.2
Q ss_pred cccccccccccceeeec--CCccccCCC
Q 030300 120 CSSCKKRVGLTGFKCRC--GNLYCVSHR 145 (179)
Q Consensus 120 C~~C~kkvgl~gf~CrC--g~~FC~~HR 145 (179)
|..|+.-.=|..+.|.| +.++|-.|-
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~ 28 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHA 28 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccc
Confidence 67888888888999997 899999884
No 44
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=38.03 E-value=25 Score=21.34 Aligned_cols=26 Identities=35% Similarity=0.841 Sum_probs=18.4
Q ss_pred Cccccccccc-c-cceeee-cCCccccCC
Q 030300 119 RCSSCKKRVG-L-TGFKCR-CGNLYCVSH 144 (179)
Q Consensus 119 rC~~C~kkvg-l-~gf~Cr-Cg~~FC~~H 144 (179)
||..|.++-- - |.|.|. |+-..|..|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 6777776422 2 679998 887777766
No 45
>PRK08402 replication factor A; Reviewed
Probab=37.97 E-value=13 Score=33.94 Aligned_cols=29 Identities=17% Similarity=0.457 Sum_probs=18.8
Q ss_pred CCCcccccccccc----cceeee-cCCccccCCCC
Q 030300 117 PSRCSSCKKRVGL----TGFKCR-CGNLYCVSHRY 146 (179)
Q Consensus 117 ~~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 146 (179)
-.+|..|+|||-. -.+.|. ||.+-+ .|||
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 3699999999963 247777 554333 4553
No 46
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=37.91 E-value=13 Score=25.21 Aligned_cols=34 Identities=32% Similarity=0.882 Sum_probs=15.1
Q ss_pred ccccccccccc--------ceeee-cCCccccC---CCCCCCCCCc
Q 030300 120 CSSCKKRVGLT--------GFKCR-CGNLYCVS---HRYSDKHNCP 153 (179)
Q Consensus 120 C~~C~kkvgl~--------gf~Cr-Cg~~FC~~---HRy~e~H~C~ 153 (179)
|+.|.+.+.-. .|.|. |+..||.. -=+-.-|+|+
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 55666666553 58887 99999852 2223456654
No 47
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=37.87 E-value=22 Score=27.12 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=24.1
Q ss_pred CCCccccccccccc---ceeee-cCCccccCCCCC
Q 030300 117 PSRCSSCKKRVGLT---GFKCR-CGNLYCVSHRYS 147 (179)
Q Consensus 117 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 147 (179)
...|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 46899999999986 68999 999999876654
No 48
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=36.71 E-value=19 Score=29.84 Aligned_cols=19 Identities=47% Similarity=1.149 Sum_probs=15.5
Q ss_pred ceeeecCCccccCCCCCCCCC
Q 030300 131 GFKCRCGNLYCVSHRYSDKHN 151 (179)
Q Consensus 131 gf~CrCg~~FC~~HRy~e~H~ 151 (179)
-|+|.| .||-.||.|.+-+
T Consensus 123 ~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 123 RFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred ceeeee--eeecccCCCcccc
Confidence 489998 7999999776665
No 49
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=35.81 E-value=12 Score=26.61 Aligned_cols=13 Identities=54% Similarity=1.066 Sum_probs=10.8
Q ss_pred CCCcccccccccc
Q 030300 117 PSRCSSCKKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kkvgl 129 (179)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6799999998763
No 50
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=35.66 E-value=24 Score=22.87 Aligned_cols=18 Identities=22% Similarity=0.815 Sum_probs=14.9
Q ss_pred cceee-ecCCccccCCCCC
Q 030300 130 TGFKC-RCGNLYCVSHRYS 147 (179)
Q Consensus 130 ~gf~C-rCg~~FC~~HRy~ 147 (179)
....| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 35889 7999999998865
No 51
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=35.30 E-value=16 Score=28.89 Aligned_cols=32 Identities=28% Similarity=0.639 Sum_probs=22.5
Q ss_pred CCCCcccccccccccc---eeee-cCCcc-ccCCCCC
Q 030300 116 GPSRCSSCKKRVGLTG---FKCR-CGNLY-CVSHRYS 147 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~g---f~Cr-Cg~~F-C~~HRy~ 147 (179)
.=..|..|+|||-..+ |.|. |+..+ =-.+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 3467889999997753 8887 77665 4456664
No 52
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=35.00 E-value=20 Score=24.27 Aligned_cols=23 Identities=35% Similarity=0.778 Sum_probs=19.5
Q ss_pred CCCCcccccccccccceeee-cCC
Q 030300 116 GPSRCSSCKKRVGLTGFKCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~gf~Cr-Cg~ 138 (179)
...-|..|.-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 35679999999999999999 775
No 53
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.67 E-value=20 Score=22.20 Aligned_cols=9 Identities=33% Similarity=1.490 Sum_probs=4.7
Q ss_pred eeee-cCCcc
Q 030300 132 FKCR-CGNLY 140 (179)
Q Consensus 132 f~Cr-Cg~~F 140 (179)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4554 55554
No 54
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=34.25 E-value=9.9 Score=36.36 Aligned_cols=25 Identities=40% Similarity=1.055 Sum_probs=22.1
Q ss_pred CCccccccccccc--ceeee-cCCcccc
Q 030300 118 SRCSSCKKRVGLT--GFKCR-CGNLYCV 142 (179)
Q Consensus 118 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 142 (179)
.-|..|.++.||+ --.|| ||.+.|.
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHH
Confidence 4799999999998 59999 9999873
No 55
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.39 E-value=24 Score=19.90 Aligned_cols=19 Identities=26% Similarity=0.742 Sum_probs=10.1
Q ss_pred Ccccccccccccceeee-cC
Q 030300 119 RCSSCKKRVGLTGFKCR-CG 137 (179)
Q Consensus 119 rC~~C~kkvgl~gf~Cr-Cg 137 (179)
+|..|++++.-..-.|. ||
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCCcCcchhhhC
Confidence 35566666655444454 44
No 56
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.55 E-value=26 Score=22.14 Aligned_cols=20 Identities=25% Similarity=0.748 Sum_probs=16.4
Q ss_pred ccceeee-cCCccccCCCCCC
Q 030300 129 LTGFKCR-CGNLYCVSHRYSD 148 (179)
Q Consensus 129 l~gf~Cr-Cg~~FC~~HRy~e 148 (179)
+-.|+|. ||..|=-.+.+.+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4578999 9999988887776
No 57
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=31.55 E-value=20 Score=23.22 Aligned_cols=16 Identities=25% Similarity=0.808 Sum_probs=13.9
Q ss_pred eeee-cCCccccCCCCC
Q 030300 132 FKCR-CGNLYCVSHRYS 147 (179)
Q Consensus 132 f~Cr-Cg~~FC~~HRy~ 147 (179)
+.|. |+..||..++-+
T Consensus 41 ~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CCTTSCCSEECSSSTSE
T ss_pred eECCCCCCcCccccCcc
Confidence 7899 999999998854
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.85 E-value=26 Score=22.36 Aligned_cols=28 Identities=32% Similarity=0.844 Sum_probs=17.7
Q ss_pred CCccccccccccc----ceeee-cCCccccCCC
Q 030300 118 SRCSSCKKRVGLT----GFKCR-CGNLYCVSHR 145 (179)
Q Consensus 118 ~rC~~C~kkvgl~----gf~Cr-Cg~~FC~~HR 145 (179)
-+|..|+..+.+. .++|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 4688888877553 47787 7665544443
No 59
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=30.46 E-value=18 Score=24.65 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=17.6
Q ss_pred CCCccccccccccc------ceeee-cCCcc
Q 030300 117 PSRCSSCKKRVGLT------GFKCR-CGNLY 140 (179)
Q Consensus 117 ~~rC~~C~kkvgl~------gf~Cr-Cg~~F 140 (179)
.-||..|+|.|... ..+|- ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 46999999988774 36774 77654
No 60
>PRK07218 replication factor A; Provisional
Probab=29.44 E-value=24 Score=33.11 Aligned_cols=21 Identities=29% Similarity=0.711 Sum_probs=16.2
Q ss_pred CCCcccccccccccceeee-cCCc
Q 030300 117 PSRCSSCKKRVGLTGFKCR-CGNL 139 (179)
Q Consensus 117 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 139 (179)
-.||..|+++|.. +.|+ ||.+
T Consensus 297 i~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred eecCcCccccccC--CcCCCCCCc
Confidence 4899999999855 7788 6544
No 61
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=29.35 E-value=37 Score=24.18 Aligned_cols=24 Identities=33% Similarity=0.773 Sum_probs=16.7
Q ss_pred CCCcccccccccccceeee-cCCcc
Q 030300 117 PSRCSSCKKRVGLTGFKCR-CGNLY 140 (179)
Q Consensus 117 ~~rC~~C~kkvgl~gf~Cr-Cg~~F 140 (179)
...|..|+|++|...|.=- ||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 4679999999998654333 55544
No 62
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=28.53 E-value=33 Score=25.39 Aligned_cols=15 Identities=20% Similarity=0.448 Sum_probs=12.1
Q ss_pred CCCCccccccccccc
Q 030300 116 GPSRCSSCKKRVGLT 130 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~ 130 (179)
.+++|..|++++...
T Consensus 32 ~rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWW 46 (92)
T ss_pred CCCcCcCCCCcCccc
Confidence 368999999998864
No 63
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=27.76 E-value=27 Score=24.73 Aligned_cols=23 Identities=30% Similarity=0.702 Sum_probs=17.8
Q ss_pred CCCCccccccccccc---ceeee-cCC
Q 030300 116 GPSRCSSCKKRVGLT---GFKCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~---gf~Cr-Cg~ 138 (179)
-.--|.-|..+.-|. .+.|| ||+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcch
Confidence 356799999888885 49999 864
No 64
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.56 E-value=23 Score=24.49 Aligned_cols=20 Identities=35% Similarity=0.363 Sum_probs=16.4
Q ss_pred HHHHHHHHHhCCcccccccc
Q 030300 158 TAARDAIIKANPVIKAEKLD 177 (179)
Q Consensus 158 ~~~r~~l~k~Np~v~~~Ki~ 177 (179)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34578899999999888875
No 65
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=27.52 E-value=41 Score=34.64 Aligned_cols=46 Identities=26% Similarity=0.777 Sum_probs=31.3
Q ss_pred CCCCCCCCCcccccccc--------------cccceeee-cCCcccc---------CCCCC----CCCCCcccc
Q 030300 111 AKPKEGPSRCSSCKKRV--------------GLTGFKCR-CGNLYCV---------SHRYS----DKHNCPFDY 156 (179)
Q Consensus 111 ~~~~~~~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC~---------~HRy~----e~H~C~fDy 156 (179)
..+...+|.|-.|.|-| |-..|+|+ ||.-|-- .||-. -.|.|.+-|
T Consensus 599 ~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 599 ENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 33445689999998744 33469999 9999963 35432 567788544
No 66
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=26.81 E-value=34 Score=21.38 Aligned_cols=29 Identities=17% Similarity=0.500 Sum_probs=19.9
Q ss_pred Ccccccccccc--cceeeecCCccccCCCCC
Q 030300 119 RCSSCKKRVGL--TGFKCRCGNLYCVSHRYS 147 (179)
Q Consensus 119 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 147 (179)
+|..|.++... ..+.=.||++||..+-..
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47788888722 345556999999876543
No 67
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=26.74 E-value=20 Score=21.53 Aligned_cols=23 Identities=35% Similarity=1.002 Sum_probs=15.0
Q ss_pred CCcccccccccccceeee-cCCccccC
Q 030300 118 SRCSSCKKRVGLTGFKCR-CGNLYCVS 143 (179)
Q Consensus 118 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 143 (179)
..|..|+. ..-++|. |+..||+.
T Consensus 3 ~~C~vC~~---~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 3 KLCSVCGN---PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EEETSSSS---EESEE-TTT--EESSH
T ss_pred CCCccCcC---CCEEECCCcCCceeCc
Confidence 46788886 4568887 99999985
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.24 E-value=37 Score=25.64 Aligned_cols=33 Identities=24% Similarity=0.670 Sum_probs=24.7
Q ss_pred CCCCCCccccccccccc----c-eeee-cCCccccCCCCC
Q 030300 114 KEGPSRCSSCKKRVGLT----G-FKCR-CGNLYCVSHRYS 147 (179)
Q Consensus 114 ~~~~~rC~~C~kkvgl~----g-f~Cr-Cg~~FC~~HRy~ 147 (179)
+..+-.|..|+++ .+- | ..|+ ||.+|=+---.|
T Consensus 32 ~~~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 32 QRAKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HhcCCcCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 4457789999987 331 3 8999 999998776655
No 69
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=25.64 E-value=38 Score=24.19 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=10.8
Q ss_pred CCCcccccccccccceeeecCCccccC
Q 030300 117 PSRCSSCKKRVGLTGFKCRCGNLYCVS 143 (179)
Q Consensus 117 ~~rC~~C~kkvgl~gf~CrCg~~FC~~ 143 (179)
--||..|.--+..---.=.|+++||+.
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHH
Confidence 357888876544432334689999985
No 70
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=25.50 E-value=27 Score=25.75 Aligned_cols=18 Identities=44% Similarity=0.713 Sum_probs=14.8
Q ss_pred CCCcccccccccccceee
Q 030300 117 PSRCSSCKKRVGLTGFKC 134 (179)
Q Consensus 117 ~~rC~~C~kkvgl~gf~C 134 (179)
--.|..|.+||||=.|+=
T Consensus 19 ~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred eEEccccCcEeeeeeccc
Confidence 467999999999976653
No 71
>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=24.22 E-value=31 Score=18.26 Aligned_cols=9 Identities=44% Similarity=1.508 Sum_probs=4.2
Q ss_pred eeee-cCCcc
Q 030300 132 FKCR-CGNLY 140 (179)
Q Consensus 132 f~Cr-Cg~~F 140 (179)
|.|. ||..|
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 3444 54444
No 72
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=24.13 E-value=27 Score=34.73 Aligned_cols=50 Identities=26% Similarity=0.704 Sum_probs=32.7
Q ss_pred CCcccccccccccceeee-cCCcc---ccCCCCCCCCCCcccchHHHHHHHHHhCCccc
Q 030300 118 SRCSSCKKRVGLTGFKCR-CGNLY---CVSHRYSDKHNCPFDYRTAARDAIIKANPVIK 172 (179)
Q Consensus 118 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~fDyk~~~r~~l~k~Np~v~ 172 (179)
--|..|.+++=.+||+|+ |++.| |+.| -|. .|. +| .-.|+.+...+|-|.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~-vp~--~C~-~~-~~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPR-VPT--SCV-NP-DHLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCC-CCC--CCC-Cc-chHhhhhhhcccccc
Confidence 457777788888999999 99876 4443 222 343 33 234566777777654
No 73
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=23.23 E-value=31 Score=22.00 Aligned_cols=28 Identities=29% Similarity=0.522 Sum_probs=19.0
Q ss_pred CCCcccccccccccceeeecCCccccCC
Q 030300 117 PSRCSSCKKRVGLTGFKCRCGNLYCVSH 144 (179)
Q Consensus 117 ~~rC~~C~kkvgl~gf~CrCg~~FC~~H 144 (179)
=-+|..|++.|...+|.=+=|..||..|
T Consensus 26 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c 53 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYEKDGKPYCKDC 53 (58)
T ss_dssp TSBETTTTCBTTTSSEEEETTEEEEHHH
T ss_pred ccccCCCCCccCCCeeEeECCEEECHHH
Confidence 3577888888877666655566666544
No 74
>PRK12366 replication factor A; Reviewed
Probab=22.02 E-value=35 Score=33.40 Aligned_cols=29 Identities=28% Similarity=0.661 Sum_probs=20.6
Q ss_pred CCCccccccccccc--ceeee-cCCccccCCCC
Q 030300 117 PSRCSSCKKRVGLT--GFKCR-CGNLYCVSHRY 146 (179)
Q Consensus 117 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 146 (179)
-.+|..|+|||-.. .|.|. ||.+ =..|||
T Consensus 532 y~aCp~CnkKv~~~~g~~~C~~c~~~-~p~~~~ 563 (637)
T PRK12366 532 LYLCPNCRKRVEEVDGEYICEFCGEV-EPNELL 563 (637)
T ss_pred EecccccCeEeEcCCCcEECCCCCCC-CCcEEE
Confidence 37899999999653 27896 8877 235555
No 75
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=21.49 E-value=51 Score=23.19 Aligned_cols=14 Identities=36% Similarity=0.888 Sum_probs=11.8
Q ss_pred ceeeecCCc-------cccCC
Q 030300 131 GFKCRCGNL-------YCVSH 144 (179)
Q Consensus 131 gf~CrCg~~-------FC~~H 144 (179)
||.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999988 88887
No 76
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.78 E-value=35 Score=26.09 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=10.0
Q ss_pred ccccceeee-cCCcccc
Q 030300 127 VGLTGFKCR-CGNLYCV 142 (179)
Q Consensus 127 vgl~gf~Cr-Cg~~FC~ 142 (179)
|=+..-.|| ||++|=.
T Consensus 54 Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 54 LLVRPARCKKCGFEFRD 70 (97)
T ss_pred EEecChhhcccCccccc
Confidence 333467777 8877744
No 77
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.57 E-value=58 Score=22.46 Aligned_cols=13 Identities=23% Similarity=0.940 Sum_probs=11.1
Q ss_pred ccchhhhhHHHHH
Q 030300 38 MNMCSKCYKDIML 50 (179)
Q Consensus 38 ~n~CSkCyr~~~~ 50 (179)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 5799999999864
No 78
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=20.56 E-value=82 Score=26.11 Aligned_cols=38 Identities=24% Similarity=0.643 Sum_probs=24.1
Q ss_pred CCCCccccccccccc--------------ceeee-cCCccc---cCCCCCCCCCCc
Q 030300 116 GPSRCSSCKKRVGLT--------------GFKCR-CGNLYC---VSHRYSDKHNCP 153 (179)
Q Consensus 116 ~~~rC~~C~kkvgl~--------------gf~Cr-Cg~~FC---~~HRy~e~H~C~ 153 (179)
.+..|+.|.+.+... .+.|- |+.+|| +..+|.+.++..
T Consensus 110 ~~~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~y~~~~e~~ 165 (175)
T PF05458_consen 110 ASRACSVCQRTQRIKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVNYSDQYERV 165 (175)
T ss_pred cCccCcCCcCCCCCCccccccCcHHHHHHHhhhhchhhhhhcCccccccCCccccc
Confidence 455688887665443 35555 777665 567887777654
No 79
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.31 E-value=84 Score=21.14 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=17.5
Q ss_pred CCCCcccccccccc--c--ceeee-cCCc
Q 030300 116 GPSRCSSCKKRVGL--T--GFKCR-CGNL 139 (179)
Q Consensus 116 ~~~rC~~C~kkvgl--~--gf~Cr-Cg~~ 139 (179)
....|..|+.++.- . .|.|. ||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45679999888776 2 58888 7665
No 80
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.30 E-value=50 Score=19.85 Aligned_cols=14 Identities=29% Similarity=0.914 Sum_probs=8.0
Q ss_pred cceeee-cCCccccC
Q 030300 130 TGFKCR-CGNLYCVS 143 (179)
Q Consensus 130 ~gf~Cr-Cg~~FC~~ 143 (179)
-.|+|. ||..|=..
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 356666 66666433
No 81
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=20.10 E-value=45 Score=20.17 Aligned_cols=23 Identities=22% Similarity=0.625 Sum_probs=12.3
Q ss_pred cccccccccccceeeecCCcccc
Q 030300 120 CSSCKKRVGLTGFKCRCGNLYCV 142 (179)
Q Consensus 120 C~~C~kkvgl~gf~CrCg~~FC~ 142 (179)
|..|...+.-.-..-.||++||.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~ 23 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCK 23 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEH
T ss_pred CCCCCCcccCcCEECCCCCchhH
Confidence 34454433332245669999985
Done!