Query 030304
Match_columns 179
No_of_seqs 148 out of 441
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:41:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030304.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030304hhsearch_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 9.9E-47 2.1E-51 306.9 10.5 153 22-179 14-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.6 1.1E-15 2.4E-20 89.4 2.4 25 23-47 1-25 (25)
3 smart00154 ZnF_AN1 AN1-like Zi 99.5 6.4E-15 1.4E-19 94.2 2.2 38 120-157 1-39 (39)
4 smart00259 ZnF_A20 A20-like zi 99.5 5.4E-15 1.2E-19 87.2 1.2 25 23-47 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.0 1.3E-10 2.9E-15 75.2 1.4 38 120-158 1-41 (43)
6 KOG3183 Predicted Zn-finger pr 96.6 0.00077 1.7E-08 58.5 0.9 40 118-158 9-51 (250)
7 COG3582 Predicted nucleic acid 96.4 0.0015 3.1E-08 53.8 1.7 38 119-157 96-137 (162)
8 PF01363 FYVE: FYVE zinc finge 93.7 0.035 7.7E-07 38.1 1.5 29 116-144 8-39 (69)
9 KOG3183 Predicted Zn-finger pr 92.7 0.022 4.8E-07 49.6 -0.9 43 112-154 93-139 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.2 0.065 1.4E-06 35.3 1.0 27 118-144 3-32 (57)
11 smart00064 FYVE Protein presen 92.2 0.082 1.8E-06 36.1 1.5 29 117-145 10-41 (68)
12 KOG1818 Membrane trafficking a 88.7 0.16 3.4E-06 49.6 0.6 45 116-160 164-222 (634)
13 KOG4345 NF-kappa B regulator A 88.5 0.22 4.7E-06 49.2 1.4 30 24-53 736-766 (774)
14 PF10571 UPF0547: Uncharacteri 84.4 0.5 1.1E-05 27.7 0.9 23 118-140 1-24 (26)
15 PF00130 C1_1: Phorbol esters/ 83.0 0.77 1.7E-05 29.7 1.5 24 116-139 10-37 (53)
16 PF15135 UPF0515: Uncharacteri 77.2 1.4 2.9E-05 39.1 1.6 31 112-142 127-167 (278)
17 PF14471 DUF4428: Domain of un 65.2 2.2 4.8E-05 28.5 0.1 19 119-137 1-27 (51)
18 PF02148 zf-UBP: Zn-finger in 60.0 5.3 0.00012 27.1 1.3 23 120-143 1-24 (63)
19 KOG1819 FYVE finger-containing 59.6 13 0.00029 36.4 4.3 30 115-144 899-931 (990)
20 PF13978 DUF4223: Protein of u 58.6 4.6 0.0001 27.7 0.8 18 140-157 19-36 (56)
21 PHA02768 hypothetical protein; 58.0 4.2 9.2E-05 27.9 0.5 16 128-143 2-18 (55)
22 cd00029 C1 Protein kinase C co 56.4 6 0.00013 24.6 1.0 24 116-139 10-37 (50)
23 PF01194 RNA_pol_N: RNA polyme 55.7 6.1 0.00013 27.6 1.0 13 117-129 4-16 (60)
24 smart00109 C1 Protein kinase C 55.1 7 0.00015 24.0 1.1 23 116-138 10-35 (49)
25 KOG1729 FYVE finger containing 53.7 3.4 7.4E-05 36.8 -0.6 33 115-148 166-202 (288)
26 PF08882 Acetone_carb_G: Aceto 52.8 6.5 0.00014 30.7 0.8 34 121-156 16-49 (112)
27 PF11781 RRN7: RNA polymerase 52.7 6.6 0.00014 24.5 0.7 22 118-139 9-34 (36)
28 COG1571 Predicted DNA-binding 51.8 8.5 0.00018 36.2 1.6 50 117-166 350-405 (421)
29 PRK04016 DNA-directed RNA poly 50.5 5.8 0.00012 28.0 0.2 13 117-129 4-16 (62)
30 KOG2807 RNA polymerase II tran 50.0 10 0.00022 34.9 1.7 41 114-154 327-372 (378)
31 COG1996 RPC10 DNA-directed RNA 49.7 6.9 0.00015 26.3 0.5 22 117-138 6-32 (49)
32 PF07649 C1_3: C1-like domain; 49.5 7.5 0.00016 22.7 0.6 22 119-140 2-25 (30)
33 PLN00032 DNA-directed RNA poly 49.3 6.4 0.00014 28.4 0.3 13 117-129 4-16 (71)
34 PF03107 C1_2: C1 domain; Int 46.2 15 0.00032 21.6 1.5 20 119-138 2-23 (30)
35 PF07975 C1_4: TFIIH C1-like d 44.6 11 0.00024 25.5 0.8 34 120-153 2-47 (51)
36 PTZ00303 phosphatidylinositol 43.7 12 0.00027 38.3 1.4 26 118-143 461-494 (1374)
37 KOG3497 DNA-directed RNA polym 43.5 8 0.00017 27.5 0.1 13 117-129 4-16 (69)
38 KOG1812 Predicted E3 ubiquitin 42.9 15 0.00032 33.8 1.7 31 115-145 304-338 (384)
39 PF05207 zf-CSL: CSL zinc fing 42.0 11 0.00024 25.4 0.6 14 129-142 16-29 (55)
40 PHA00626 hypothetical protein 41.2 14 0.0003 25.8 1.0 23 118-142 12-35 (59)
41 PF15549 PGC7_Stella: PGC7/Ste 41.1 14 0.00031 30.5 1.2 19 131-151 123-141 (160)
42 COG2888 Predicted Zn-ribbon RN 39.5 11 0.00024 26.5 0.3 21 116-138 37-58 (61)
43 KOG1842 FYVE finger-containing 38.9 7.4 0.00016 37.1 -0.9 25 118-142 181-208 (505)
44 PF02318 FYVE_2: FYVE-type zin 38.9 22 0.00049 27.0 1.9 30 117-146 54-87 (118)
45 COG1644 RPB10 DNA-directed RNA 37.4 11 0.00023 26.7 -0.0 13 117-129 4-16 (63)
46 smart00396 ZnF_UBR1 Putative z 37.4 18 0.00039 25.4 1.1 14 131-144 50-70 (71)
47 smart00659 RPOLCX RNA polymera 37.0 17 0.00036 23.6 0.8 19 119-137 4-26 (44)
48 PRK08402 replication factor A; 36.1 18 0.00039 33.1 1.2 29 117-146 212-245 (355)
49 PF03604 DNA_RNApol_7kD: DNA d 35.9 17 0.00036 22.2 0.6 18 120-137 3-24 (32)
50 PF02928 zf-C5HC2: C5HC2 zinc 35.8 18 0.00038 24.1 0.8 27 120-146 1-29 (54)
51 cd04476 RPA1_DBD_C RPA1_DBD_C: 35.0 18 0.00039 28.6 0.8 31 117-147 34-69 (166)
52 PF13717 zinc_ribbon_4: zinc-r 34.9 20 0.00043 22.1 0.9 11 119-129 4-14 (36)
53 PF14634 zf-RING_5: zinc-RING 34.7 14 0.0003 23.2 0.1 29 119-147 1-31 (44)
54 smart00290 ZnF_UBP Ubiquitin C 34.1 15 0.00033 23.2 0.2 24 119-144 1-25 (50)
55 PF13240 zinc_ribbon_2: zinc-r 32.3 26 0.00057 19.6 1.0 17 119-135 1-17 (23)
56 PF10367 Vps39_2: Vacuolar sor 32.1 32 0.00068 24.5 1.7 24 117-140 78-102 (109)
57 smart00647 IBR In Between Ring 31.1 32 0.00069 22.3 1.5 18 130-147 39-57 (64)
58 PF08073 CHDNT: CHDNT (NUC034) 30.2 20 0.00044 24.7 0.4 21 158-178 21-41 (55)
59 PF00412 LIM: LIM domain; Int 29.7 24 0.00052 22.5 0.7 27 118-144 27-53 (58)
60 PRK04136 rpl40e 50S ribosomal 29.6 28 0.0006 23.4 0.9 23 116-138 13-36 (48)
61 PRK00398 rpoP DNA-directed RNA 29.3 32 0.00069 21.8 1.2 28 118-145 4-36 (46)
62 COG5432 RAD18 RING-finger-cont 27.6 17 0.00037 33.2 -0.5 40 117-157 25-70 (391)
63 PF10122 Mu-like_Com: Mu-like 27.6 22 0.00048 24.1 0.2 24 117-140 4-34 (51)
64 PF13842 Tnp_zf-ribbon_2: DDE_ 27.5 47 0.001 20.0 1.6 26 119-144 2-30 (32)
65 PF14835 zf-RING_6: zf-RING of 26.8 36 0.00079 24.2 1.2 27 117-143 7-33 (65)
66 PRK07218 replication factor A; 26.6 29 0.00064 32.5 0.9 21 117-139 297-318 (423)
67 PF04438 zf-HIT: HIT zinc fing 26.0 22 0.00048 21.2 -0.0 23 118-143 3-26 (30)
68 PF05458 Siva: Cd27 binding pr 26.0 40 0.00086 27.9 1.4 38 116-153 110-165 (175)
69 PF00096 zf-C2H2: Zinc finger, 25.6 30 0.00064 18.3 0.4 10 132-141 1-11 (23)
70 COG1997 RPL43A Ribosomal prote 25.5 39 0.00085 25.4 1.2 34 113-147 31-70 (89)
71 PF08600 Rsm1: Rsm1-like; Int 24.1 28 0.00062 25.5 0.2 19 117-135 19-37 (91)
72 PF09723 Zn-ribbon_8: Zinc rib 24.1 46 0.001 20.9 1.2 20 129-148 3-23 (42)
73 KOG3507 DNA-directed RNA polym 22.9 39 0.00084 23.8 0.7 23 116-138 19-45 (62)
74 PF12662 cEGF: Complement Clr- 22.8 78 0.0017 18.1 1.9 20 131-153 1-20 (24)
75 PF01485 IBR: IBR domain; Int 22.7 38 0.00082 21.8 0.6 16 132-147 41-57 (64)
76 PF00869 Flavi_glycoprot: Flav 21.7 33 0.00071 30.9 0.2 10 28-37 103-112 (293)
77 PF13465 zf-H2C2_2: Zinc-finge 21.7 53 0.0012 18.4 1.0 12 129-140 12-24 (26)
78 KOG0193 Serine/threonine prote 21.3 34 0.00074 34.0 0.2 50 118-172 190-243 (678)
79 PTZ00218 40S ribosomal protein 21.2 58 0.0013 22.4 1.3 14 39-52 34-47 (54)
80 PRK12366 replication factor A; 20.9 43 0.00092 32.8 0.8 29 117-146 532-563 (637)
81 PF13923 zf-C3HC4_2: Zinc fing 20.6 46 0.001 20.1 0.7 24 120-143 1-24 (39)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=9.9e-47 Score=306.92 Aligned_cols=153 Identities=47% Similarity=0.842 Sum_probs=102.9
Q ss_pred CCcccccCCCCCCccccccchhHHHHHHHHHHHHH-hhhhccccccccCCCCCCCCCCccccccCCcCCcccccccccCC
Q 030304 22 GPILCVNNCGFFGSAATMNMCSKCHKAMILNQEQA-QLAASSIGSIVHGSSGGTGKEPIVAGSVDLQVGPVEIKKFSMEP 100 (179)
Q Consensus 22 ~p~lCaNgCGFfGs~at~nlCSkCyr~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (179)
.++||+|||||||+|+|+||||+||++++.++++. ..+...+..-+.++.+.....+. +...+..... +...+...+
T Consensus 14 ~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~-~~~~~~~~~~-~~~~~~~~~ 91 (167)
T KOG3173|consen 14 QDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPRSVPSRDPP-AVSLESTTES-ELKLVSDTP 91 (167)
T ss_pred cccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCccccCccccc-cccccccccc-cccccccCC
Confidence 46999999999999999999999999999888765 22222111100000000000000 0000000000 000000001
Q ss_pred CCCCCCCCCCCCCCCCCCcccccccccCccceeeecCccccCccccCCCCCCcccchHHHHHHHHHhCCcccccccccC
Q 030304 101 SSGSSFGFAGVKAKEGPKRCTTCNKRVGLTGFNCRCGNLFCAVHRYSDKHGCPFDYRTAAREAIAKANPVVKAEKLDKI 179 (179)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~rC~~C~kk~gl~gf~CrCg~~FC~~HRy~~~H~C~fDyk~~gre~l~k~Np~v~~~Ki~KI 179 (179)
+ .........+..++||..|+|||||+||.||||++||+.|||+|.|+|+||||.+||+.|+|+||+|+++||+||
T Consensus 92 s---~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 92 S---TEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQKI 167 (167)
T ss_pred c---ccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccccC
Confidence 0 001122234456889999999999999999999999999999999999999999999999999999999999998
No 2
>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=99.57 E-value=1.1e-15 Score=89.41 Aligned_cols=25 Identities=60% Similarity=1.327 Sum_probs=20.9
Q ss_pred CcccccCCCCCCccccccchhHHHH
Q 030304 23 PILCVNNCGFFGSAATMNMCSKCHK 47 (179)
Q Consensus 23 p~lCaNgCGFfGs~at~nlCSkCyr 47 (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 3
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.51 E-value=6.4e-15 Score=94.16 Aligned_cols=38 Identities=63% Similarity=1.456 Sum_probs=36.9
Q ss_pred ccccccccCccceeee-cCccccCccccCCCCCCcccch
Q 030304 120 CTTCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYR 157 (179)
Q Consensus 120 C~~C~kk~gl~gf~Cr-Cg~~FC~~HRy~~~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 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=99.50 E-value=5.4e-15 Score=87.24 Aligned_cols=25 Identities=60% Similarity=1.278 Sum_probs=23.4
Q ss_pred Ccccc-cCCCCCCccccccchhHHHH
Q 030304 23 PILCV-NNCGFFGSAATMNMCSKCHK 47 (179)
Q Consensus 23 p~lCa-NgCGFfGs~at~nlCSkCyr 47 (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=98.99 E-value=1.3e-10 Score=75.16 Aligned_cols=38 Identities=34% Similarity=0.866 Sum_probs=28.1
Q ss_pred ccc--cccccCccceeee-cCccccCccccCCCCCCcccchH
Q 030304 120 CTT--CNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYRT 158 (179)
Q Consensus 120 C~~--C~kk~gl~gf~Cr-Cg~~FC~~HRy~~~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 999887 799999 99999999999999999999874
No 6
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.59 E-value=0.00077 Score=58.50 Aligned_cols=40 Identities=35% Similarity=0.945 Sum_probs=35.1
Q ss_pred Cccc--ccccccCccceeee-cCccccCccccCCCCCCcccchH
Q 030304 118 KRCT--TCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYRT 158 (179)
Q Consensus 118 ~rC~--~C~kk~gl~gf~Cr-Cg~~FC~~HRy~~~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 4676 787 6789999999 99999999999999999988763
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.44 E-value=0.0015 Score=53.76 Aligned_cols=38 Identities=34% Similarity=0.667 Sum_probs=30.2
Q ss_pred ccc---ccccccCccceeee-cCccccCccccCCCCCCcccch
Q 030304 119 RCT---TCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYR 157 (179)
Q Consensus 119 rC~---~C~kk~gl~gf~Cr-Cg~~FC~~HRy~~~H~C~fDyk 157 (179)
+|. .|++..+|+ ++|. |++.||+.||+++.|+|.+...
T Consensus 96 ~~a~~~~~g~~s~l~-~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 96 RCATPQCTGKGSTLA-GKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred eeecceeccCCcccc-ccccCCCCcceeceecccccccccHHH
Confidence 555 455555444 8898 9999999999999999998854
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=93.73 E-value=0.035 Score=38.07 Aligned_cols=29 Identities=31% Similarity=0.887 Sum_probs=17.9
Q ss_pred CCCcccccccccCcc--ceeee-cCccccCcc
Q 030304 116 GPKRCTTCNKRVGLT--GFNCR-CGNLFCAVH 144 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~--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 457899999999997 49999 999999874
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=92.74 E-value=0.022 Score=49.57 Aligned_cols=43 Identities=35% Similarity=0.745 Sum_probs=36.1
Q ss_pred CCCCCCCccc--ccccccCcc-ceeee-cCccccCccccCCCCCCcc
Q 030304 112 KAKEGPKRCT--TCNKRVGLT-GFNCR-CGNLFCAVHRYSDKHGCPF 154 (179)
Q Consensus 112 ~~~~~~~rC~--~C~kk~gl~-gf~Cr-Cg~~FC~~HRy~~~H~C~f 154 (179)
..+..+++|. .|+|++-+. .+.|+ ||..||-+||++-.|.|.-
T Consensus 93 ~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~ 139 (250)
T KOG3183|consen 93 KRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNK 139 (250)
T ss_pred hcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhh
Confidence 3455677886 799998775 69999 9999999999999999973
No 10
>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=92.24 E-value=0.065 Score=35.26 Aligned_cols=27 Identities=41% Similarity=1.030 Sum_probs=23.9
Q ss_pred CcccccccccCcc--ceeee-cCccccCcc
Q 030304 118 KRCTTCNKRVGLT--GFNCR-CGNLFCAVH 144 (179)
Q Consensus 118 ~rC~~C~kk~gl~--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 5799999999996 69999 999999863
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 KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=88.68 E-value=0.16 Score=49.60 Aligned_cols=45 Identities=29% Similarity=0.710 Sum_probs=35.1
Q ss_pred CCCcccccccccCccc--eeee-cCccccCccc-----------cCCCCCCcccchHHH
Q 030304 116 GPKRCTTCNKRVGLTG--FNCR-CGNLFCAVHR-----------YSDKHGCPFDYRTAA 160 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~g--f~Cr-Cg~~FC~~HR-----------y~~~H~C~fDyk~~g 160 (179)
...+|..|+.+.|+++ ..|| ||.+||+.|- |-..--|.-+|...-
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~ 222 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLT 222 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhh
Confidence 3578999999999985 8999 9999999873 344556777776433
No 13
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=88.53 E-value=0.22 Score=49.22 Aligned_cols=30 Identities=30% Similarity=0.698 Sum_probs=26.6
Q ss_pred ccc-ccCCCCCCccccccchhHHHHHHHHHH
Q 030304 24 ILC-VNNCGFFGSAATMNMCSKCHKAMILNQ 53 (179)
Q Consensus 24 ~lC-aNgCGFfGs~at~nlCSkCyr~~~~~~ 53 (179)
.+| .-||.|||++.|+++||-|||+.+..-
T Consensus 736 ~rck~~nc~~Yg~~~~~~~c~~c~r~el~~~ 766 (774)
T KOG4345|consen 736 MRCKWPNCDHYGRAETNGYCSECYREELRRG 766 (774)
T ss_pred hHhhcccchhhccccccccchhhhhHHHhcc
Confidence 478 889999999999999999999977543
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=84.43 E-value=0.5 Score=27.66 Aligned_cols=23 Identities=35% Similarity=0.743 Sum_probs=20.2
Q ss_pred CcccccccccCccceeee-cCccc
Q 030304 118 KRCTTCNKRVGLTGFNCR-CGNLF 140 (179)
Q Consensus 118 ~rC~~C~kk~gl~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 368899999999999998 99887
No 15
>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=83.01 E-value=0.77 Score=29.71 Aligned_cols=24 Identities=38% Similarity=1.054 Sum_probs=18.4
Q ss_pred CCCccccccccc---Cccceeee-cCcc
Q 030304 116 GPKRCTTCNKRV---GLTGFNCR-CGNL 139 (179)
Q Consensus 116 ~~~rC~~C~kk~---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 7654
No 16
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=77.24 E-value=1.4 Score=39.06 Aligned_cols=31 Identities=32% Similarity=0.815 Sum_probs=24.2
Q ss_pred CCCCCCCcccccccc---------cCccceeee-cCccccC
Q 030304 112 KAKEGPKRCTTCNKR---------VGLTGFNCR-CGNLFCA 142 (179)
Q Consensus 112 ~~~~~~~rC~~C~kk---------~gl~gf~Cr-Cg~~FC~ 142 (179)
+..+...||..|+|| .|+.-|+|. |+++|=+
T Consensus 127 p~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 127 PQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred CcccccccccccccccCCCccccccceeeeecccccccchh
Confidence 344557999999998 577779994 9999854
No 17
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=65.16 E-value=2.2 Score=28.53 Aligned_cols=19 Identities=42% Similarity=1.291 Sum_probs=15.5
Q ss_pred cccccccccCcc-------ceeee-cC
Q 030304 119 RCTTCNKRVGLT-------GFNCR-CG 137 (179)
Q Consensus 119 rC~~C~kk~gl~-------gf~Cr-Cg 137 (179)
+|..|++++||+ ||.|. |-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~ 27 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCL 27 (51)
T ss_pred CCCccccccccccceeccCccchHHHH
Confidence 599999999997 57777 64
No 18
>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=60.04 E-value=5.3 Score=27.12 Aligned_cols=23 Identities=26% Similarity=0.759 Sum_probs=15.4
Q ss_pred ccccccccCccceeee-cCccccCc
Q 030304 120 CTTCNKRVGLTGFNCR-CGNLFCAV 143 (179)
Q Consensus 120 C~~C~kk~gl~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 44457888 99999995
No 19
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=59.63 E-value=13 Score=36.40 Aligned_cols=30 Identities=30% Similarity=0.875 Sum_probs=21.9
Q ss_pred CCCCcccccccccCcc--ceeee-cCccccCcc
Q 030304 115 EGPKRCTTCNKRVGLT--GFNCR-CGNLFCAVH 144 (179)
Q Consensus 115 ~~~~rC~~C~kk~gl~--gf~Cr-Cg~~FC~~H 144 (179)
....+|..|.-..... --.|| ||++||++-
T Consensus 899 ~~a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 899 EDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred CcchhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 3457899997554432 46899 999999874
No 20
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=58.64 E-value=4.6 Score=27.75 Aligned_cols=18 Identities=28% Similarity=0.717 Sum_probs=16.1
Q ss_pred ccCccccCCCCCCcccch
Q 030304 140 FCAVHRYSDKHGCPFDYR 157 (179)
Q Consensus 140 FC~~HRy~~~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 21
>PHA02768 hypothetical protein; Provisional
Probab=58.04 E-value=4.2 Score=27.92 Aligned_cols=16 Identities=31% Similarity=1.036 Sum_probs=13.2
Q ss_pred Cccceeee-cCccccCc
Q 030304 128 GLTGFNCR-CGNLFCAV 143 (179)
Q Consensus 128 gl~gf~Cr-Cg~~FC~~ 143 (179)
.|+||.|. ||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 47899999 99998764
No 22
>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=56.44 E-value=6 Score=24.64 Aligned_cols=24 Identities=29% Similarity=0.704 Sum_probs=19.0
Q ss_pred CCCcccccccccCc---cceeee-cCcc
Q 030304 116 GPKRCTTCNKRVGL---TGFNCR-CGNL 139 (179)
Q Consensus 116 ~~~rC~~C~kk~gl---~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 7543
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=55.66 E-value=6.1 Score=27.63 Aligned_cols=13 Identities=54% Similarity=1.081 Sum_probs=10.0
Q ss_pred CCcccccccccCc
Q 030304 117 PKRCTTCNKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kk~gl 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 6799999998863
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=55.06 E-value=7 Score=24.03 Aligned_cols=23 Identities=30% Similarity=0.865 Sum_probs=18.2
Q ss_pred CCCcccccccccCcc--ceeee-cCc
Q 030304 116 GPKRCTTCNKRVGLT--GFNCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~--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 357899999999873 88888 644
No 25
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=53.74 E-value=3.4 Score=36.83 Aligned_cols=33 Identities=27% Similarity=0.761 Sum_probs=26.9
Q ss_pred CCCCccccccc-ccCcc--ceeee-cCccccCccccCC
Q 030304 115 EGPKRCTTCNK-RVGLT--GFNCR-CGNLFCAVHRYSD 148 (179)
Q Consensus 115 ~~~~rC~~C~k-k~gl~--gf~Cr-Cg~~FC~~HRy~~ 148 (179)
...++|..|.+ .-.|. --+|| ||.+||. |....
T Consensus 166 ~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 166 SEATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred ccceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 35799999999 77776 47899 9999999 76544
No 26
>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=52.82 E-value=6.5 Score=30.74 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=25.9
Q ss_pred cccccccCccceeeecCccccCccccCCCCCCcccc
Q 030304 121 TTCNKRVGLTGFNCRCGNLFCAVHRYSDKHGCPFDY 156 (179)
Q Consensus 121 ~~C~kk~gl~gf~CrCg~~FC~~HRy~~~H~C~fDy 156 (179)
+.|+++- .-.+|+||+.||+.+..-..|.--++=
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~vR 49 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYVR 49 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEec
Confidence 5666655 258999999999998888888766653
No 27
>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=52.73 E-value=6.6 Score=24.47 Aligned_cols=22 Identities=36% Similarity=1.007 Sum_probs=17.3
Q ss_pred CcccccccccCcc--c-eee-ecCcc
Q 030304 118 KRCTTCNKRVGLT--G-FNC-RCGNL 139 (179)
Q Consensus 118 ~rC~~C~kk~gl~--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 4 889 79875
No 28
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.79 E-value=8.5 Score=36.18 Aligned_cols=50 Identities=22% Similarity=0.424 Sum_probs=34.3
Q ss_pred CCcccccccccCcc---ceeee-cCccccCccccCCCCC--CcccchHHHHHHHHH
Q 030304 117 PKRCTTCNKRVGLT---GFNCR-CGNLFCAVHRYSDKHG--CPFDYRTAAREAIAK 166 (179)
Q Consensus 117 ~~rC~~C~kk~gl~---gf~Cr-Cg~~FC~~HRy~~~H~--C~fDyk~~gre~l~k 166 (179)
.-+|-.|++++... ||+|+ ||..+=..-+-.=.++ =.+++-.-+|.+|.|
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk 405 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK 405 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC
Confidence 35899999998765 79999 9988866632222232 234556777888865
No 29
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=50.47 E-value=5.8 Score=27.97 Aligned_cols=13 Identities=46% Similarity=0.930 Sum_probs=11.0
Q ss_pred CCcccccccccCc
Q 030304 117 PKRCTTCNKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kk~gl 129 (179)
|-||++|+|-+|-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6799999998864
No 30
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=49.96 E-value=10 Score=34.94 Aligned_cols=41 Identities=27% Similarity=0.699 Sum_probs=29.3
Q ss_pred CCCCCccccc-ccccCccceeee-cCccccCc---cccCCCCCCcc
Q 030304 114 KEGPKRCTTC-NKRVGLTGFNCR-CGNLFCAV---HRYSDKHGCPF 154 (179)
Q Consensus 114 ~~~~~rC~~C-~kk~gl~gf~Cr-Cg~~FC~~---HRy~~~H~C~f 154 (179)
....++|+.| .+.++...|.|. |-++||.. -.+---|.|.+
T Consensus 327 ~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~Cpg 372 (378)
T KOG2807|consen 327 YNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPG 372 (378)
T ss_pred cCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCC
Confidence 3456889999 666777789999 99999975 22223466653
No 31
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.70 E-value=6.9 Score=26.34 Aligned_cols=22 Identities=36% Similarity=1.076 Sum_probs=17.2
Q ss_pred CCcccccccccCcc----ceeee-cCc
Q 030304 117 PKRCTTCNKRVGLT----GFNCR-CGN 138 (179)
Q Consensus 117 ~~rC~~C~kk~gl~----gf~Cr-Cg~ 138 (179)
.-+|..|++++-++ +..|. ||+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 46899999999854 78898 754
No 32
>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=49.47 E-value=7.5 Score=22.70 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=8.8
Q ss_pred cccccccccCc-cceeee-cCccc
Q 030304 119 RCTTCNKRVGL-TGFNCR-CGNLF 140 (179)
Q Consensus 119 rC~~C~kk~gl-~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 68999999988 789998 75543
No 33
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=49.28 E-value=6.4 Score=28.44 Aligned_cols=13 Identities=54% Similarity=1.081 Sum_probs=11.0
Q ss_pred CCcccccccccCc
Q 030304 117 PKRCTTCNKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kk~gl 129 (179)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998864
No 34
>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=46.25 E-value=15 Score=21.64 Aligned_cols=20 Identities=20% Similarity=0.708 Sum_probs=16.5
Q ss_pred cccccccccCcc-ceeee-cCc
Q 030304 119 RCTTCNKRVGLT-GFNCR-CGN 138 (179)
Q Consensus 119 rC~~C~kk~gl~-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 35
>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=44.61 E-value=11 Score=25.47 Aligned_cols=34 Identities=32% Similarity=0.756 Sum_probs=17.4
Q ss_pred ccccccccCcc--------ceeee-cCccccCc---cccCCCCCCc
Q 030304 120 CTTCNKRVGLT--------GFNCR-CGNLFCAV---HRYSDKHGCP 153 (179)
Q Consensus 120 C~~C~kk~gl~--------gf~Cr-Cg~~FC~~---HRy~~~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 66677666653 48898 99999864 4444567775
No 36
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=43.68 E-value=12 Score=38.32 Aligned_cols=26 Identities=27% Similarity=0.837 Sum_probs=21.2
Q ss_pred CcccccccccCc-------cceeee-cCccccCc
Q 030304 118 KRCTTCNKRVGL-------TGFNCR-CGNLFCAV 143 (179)
Q Consensus 118 ~rC~~C~kk~gl-------~gf~Cr-Cg~~FC~~ 143 (179)
..|..|+++-+. .--+|| ||.+||+.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCcc
Confidence 579999999864 245699 99999876
No 37
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=43.54 E-value=8 Score=27.49 Aligned_cols=13 Identities=54% Similarity=1.045 Sum_probs=11.0
Q ss_pred CCcccccccccCc
Q 030304 117 PKRCTTCNKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kk~gl 129 (179)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998874
No 38
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.90 E-value=15 Score=33.77 Aligned_cols=31 Identities=32% Similarity=0.907 Sum_probs=25.6
Q ss_pred CCCCcccccccccCcc-c---eeeecCccccCccc
Q 030304 115 EGPKRCTTCNKRVGLT-G---FNCRCGNLFCAVHR 145 (179)
Q Consensus 115 ~~~~rC~~C~kk~gl~-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 4468999999998886 3 99999999997644
No 39
>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=42.03 E-value=11 Score=25.36 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=10.7
Q ss_pred ccceeeecCccccC
Q 030304 129 LTGFNCRCGNLFCA 142 (179)
Q Consensus 129 l~gf~CrCg~~FC~ 142 (179)
..-+.||||..|--
T Consensus 16 ~~~y~CRCG~~f~i 29 (55)
T PF05207_consen 16 VYSYPCRCGGEFEI 29 (55)
T ss_dssp EEEEEETTSSEEEE
T ss_pred EEEEcCCCCCEEEE
Confidence 34589999998753
No 40
>PHA00626 hypothetical protein
Probab=41.16 E-value=14 Score=25.79 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=15.5
Q ss_pred CcccccccccCccceeee-cCccccC
Q 030304 118 KRCTTCNKRVGLTGFNCR-CGNLFCA 142 (179)
Q Consensus 118 ~rC~~C~kk~gl~gf~Cr-Cg~~FC~ 142 (179)
-||.+|++.. .-|+|. ||+.|-.
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccC--cceEcCCCCCeech
Confidence 4777777632 248888 8887754
No 41
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=41.11 E-value=14 Score=30.48 Aligned_cols=19 Identities=32% Similarity=0.968 Sum_probs=15.8
Q ss_pred ceeeecCccccCccccCCCCC
Q 030304 131 GFNCRCGNLFCAVHRYSDKHG 151 (179)
Q Consensus 131 gf~CrCg~~FC~~HRy~~~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 399999 8999999776655
No 42
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.54 E-value=11 Score=26.48 Aligned_cols=21 Identities=38% Similarity=1.028 Sum_probs=13.9
Q ss_pred CCCcccccccccCccceee-ecCc
Q 030304 116 GPKRCTTCNKRVGLTGFNC-RCGN 138 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~gf~C-rCg~ 138 (179)
.-.||..||| +|- .|+| .||.
T Consensus 37 ~I~Rc~~CRk-~g~-~Y~Cp~CGF 58 (61)
T COG2888 37 EIYRCAKCRK-LGN-PYRCPKCGF 58 (61)
T ss_pred eeehhhhHHH-cCC-ceECCCcCc
Confidence 4578888885 333 4788 4774
No 43
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=38.95 E-value=7.4 Score=37.09 Aligned_cols=25 Identities=40% Similarity=1.116 Sum_probs=22.2
Q ss_pred CcccccccccCcc--ceeee-cCccccC
Q 030304 118 KRCTTCNKRVGLT--GFNCR-CGNLFCA 142 (179)
Q Consensus 118 ~rC~~C~kk~gl~--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 4699999999997 58999 9999884
No 44
>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=38.88 E-value=22 Score=27.00 Aligned_cols=30 Identities=27% Similarity=0.695 Sum_probs=23.3
Q ss_pred CCcccccccccCcc---ceeee-cCccccCcccc
Q 030304 117 PKRCTTCNKRVGLT---GFNCR-CGNLFCAVHRY 146 (179)
Q Consensus 117 ~~rC~~C~kk~gl~---gf~Cr-Cg~~FC~~HRy 146 (179)
...|..|.+.+|++ |..|. |...+|..=+.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 46899999999986 68999 99999987544
No 45
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=37.39 E-value=11 Score=26.70 Aligned_cols=13 Identities=46% Similarity=1.083 Sum_probs=10.7
Q ss_pred CCcccccccccCc
Q 030304 117 PKRCTTCNKRVGL 129 (179)
Q Consensus 117 ~~rC~~C~kk~gl 129 (179)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6799999998753
No 46
>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=37.37 E-value=18 Score=25.42 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=12.1
Q ss_pred ceeeecCcc-------ccCcc
Q 030304 131 GFNCRCGNL-------FCAVH 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 489999998 88887
No 47
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.99 E-value=17 Score=23.59 Aligned_cols=19 Identities=32% Similarity=0.950 Sum_probs=13.5
Q ss_pred cccccccccCcc---ceeee-cC
Q 030304 119 RCTTCNKRVGLT---GFNCR-CG 137 (179)
Q Consensus 119 rC~~C~kk~gl~---gf~Cr-Cg 137 (179)
+|..|+..+.+. +.+|+ ||
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCC
Confidence 688888887775 46776 54
No 48
>PRK08402 replication factor A; Reviewed
Probab=36.08 E-value=18 Score=33.06 Aligned_cols=29 Identities=17% Similarity=0.457 Sum_probs=18.8
Q ss_pred CCcccccccccCc----cceeee-cCccccCcccc
Q 030304 117 PKRCTTCNKRVGL----TGFNCR-CGNLFCAVHRY 146 (179)
Q Consensus 117 ~~rC~~C~kk~gl----~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 3799999999953 247777 554333 4554
No 49
>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=35.88 E-value=17 Score=22.24 Aligned_cols=18 Identities=39% Similarity=1.060 Sum_probs=9.1
Q ss_pred ccccccccCcc---ceeee-cC
Q 030304 120 CTTCNKRVGLT---GFNCR-CG 137 (179)
Q Consensus 120 C~~C~kk~gl~---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 55566666553 35555 53
No 50
>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=35.76 E-value=18 Score=24.09 Aligned_cols=27 Identities=26% Similarity=0.769 Sum_probs=22.4
Q ss_pred ccccccccCccceeeec--CccccCcccc
Q 030304 120 CTTCNKRVGLTGFNCRC--GNLFCAVHRY 146 (179)
Q Consensus 120 C~~C~kk~gl~gf~CrC--g~~FC~~HRy 146 (179)
|..|+.-.=|..+.|.| +.++|-.|-.
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~~ 29 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHAK 29 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccch
Confidence 67788888788999997 8999988853
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=35.01 E-value=18 Score=28.60 Aligned_cols=31 Identities=29% Similarity=0.609 Sum_probs=21.8
Q ss_pred CCcccccccccCcc---ceeee-cCccc-cCccccC
Q 030304 117 PKRCTTCNKRVGLT---GFNCR-CGNLF-CAVHRYS 147 (179)
Q Consensus 117 ~~rC~~C~kk~gl~---gf~Cr-Cg~~F-C~~HRy~ 147 (179)
=..|..|+|||-.. .|.|. |+..+ =-.+||.
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 45688999999765 38888 87765 3446664
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.94 E-value=20 Score=22.11 Aligned_cols=11 Identities=18% Similarity=0.827 Sum_probs=5.5
Q ss_pred cccccccccCc
Q 030304 119 RCTTCNKRVGL 129 (179)
Q Consensus 119 rC~~C~kk~gl 129 (179)
+|..|+++..+
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 35555555444
No 53
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=34.66 E-value=14 Score=23.21 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=20.0
Q ss_pred cccccccccC--ccceeeecCccccCccccC
Q 030304 119 RCTTCNKRVG--LTGFNCRCGNLFCAVHRYS 147 (179)
Q Consensus 119 rC~~C~kk~g--l~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 4777888872 2345556999999886543
No 54
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=34.10 E-value=15 Score=23.25 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=17.4
Q ss_pred cccccccccCccceeee-cCccccCcc
Q 030304 119 RCTTCNKRVGLTGFNCR-CGNLFCAVH 144 (179)
Q Consensus 119 rC~~C~kk~gl~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 6888885543 35666 999999763
No 55
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=32.28 E-value=26 Score=19.63 Aligned_cols=17 Identities=18% Similarity=0.495 Sum_probs=8.7
Q ss_pred cccccccccCccceeee
Q 030304 119 RCTTCNKRVGLTGFNCR 135 (179)
Q Consensus 119 rC~~C~kk~gl~gf~Cr 135 (179)
+|..|++++.-..-.|.
T Consensus 1 ~Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCP 17 (23)
T ss_pred CCcccCCCCCCcCcchh
Confidence 35566666654443344
No 56
>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=32.06 E-value=32 Score=24.52 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=16.4
Q ss_pred CCcccccccccCccceeee-cCccc
Q 030304 117 PKRCTTCNKRVGLTGFNCR-CGNLF 140 (179)
Q Consensus 117 ~~rC~~C~kk~gl~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 44443
No 57
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.05 E-value=32 Score=22.26 Aligned_cols=18 Identities=28% Similarity=0.779 Sum_probs=14.7
Q ss_pred cceee-ecCccccCccccC
Q 030304 130 TGFNC-RCGNLFCAVHRYS 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 45889 7999999988765
No 58
>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=30.20 E-value=20 Score=24.66 Aligned_cols=21 Identities=38% Similarity=0.392 Sum_probs=16.9
Q ss_pred HHHHHHHHHhCCccccccccc
Q 030304 158 TAAREAIAKANPVVKAEKLDK 178 (179)
Q Consensus 158 ~~gre~l~k~Np~v~~~Ki~K 178 (179)
..=|-.|+++||++.-.||..
T Consensus 21 q~vRP~l~~~NPk~~~sKl~~ 41 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLMM 41 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHHH
Confidence 345888999999998888753
No 59
>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=29.69 E-value=24 Score=22.52 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=19.8
Q ss_pred CcccccccccCccceeeecCccccCcc
Q 030304 118 KRCTTCNKRVGLTGFNCRCGNLFCAVH 144 (179)
Q Consensus 118 ~rC~~C~kk~gl~gf~CrCg~~FC~~H 144 (179)
-+|..|++.|+..+|.=+=|..||..|
T Consensus 27 f~C~~C~~~l~~~~~~~~~~~~~C~~c 53 (58)
T PF00412_consen 27 FKCSKCGKPLNDGDFYEKDGKPYCKDC 53 (58)
T ss_dssp SBETTTTCBTTTSSEEEETTEEEEHHH
T ss_pred cccCCCCCccCCCeeEeECCEEECHHH
Confidence 578889988887766666666777654
No 60
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=29.56 E-value=28 Score=23.43 Aligned_cols=23 Identities=39% Similarity=0.843 Sum_probs=19.3
Q ss_pred CCCcccccccccCccceeee-cCc
Q 030304 116 GPKRCTTCNKRVGLTGFNCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~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 35668999999999999999 876
No 61
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.30 E-value=32 Score=21.85 Aligned_cols=28 Identities=32% Similarity=0.795 Sum_probs=17.5
Q ss_pred CcccccccccCcc----ceeee-cCccccCccc
Q 030304 118 KRCTTCNKRVGLT----GFNCR-CGNLFCAVHR 145 (179)
Q Consensus 118 ~rC~~C~kk~gl~----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 4688888877542 47787 6655544443
No 62
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=27.65 E-value=17 Score=33.23 Aligned_cols=40 Identities=28% Similarity=0.641 Sum_probs=26.9
Q ss_pred CCcccccccccCccceeeecCccccCc--cccCCCC----CCcccch
Q 030304 117 PKRCTTCNKRVGLTGFNCRCGNLFCAV--HRYSDKH----GCPFDYR 157 (179)
Q Consensus 117 ~~rC~~C~kk~gl~gf~CrCg~~FC~~--HRy~~~H----~C~fDyk 157 (179)
.-||..|.-++.+. -.=-||++||+. -||-..| .|.||+.
T Consensus 25 ~lrC~IC~~~i~ip-~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISIP-CETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeecc-eecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 57999998877553 122499999997 4554444 3566654
No 63
>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=27.63 E-value=22 Score=24.14 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=17.0
Q ss_pred CCcccccccccCcc------ceeee-cCccc
Q 030304 117 PKRCTTCNKRVGLT------GFNCR-CGNLF 140 (179)
Q Consensus 117 ~~rC~~C~kk~gl~------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 46999999998764 36664 66543
No 64
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.53 E-value=47 Score=20.02 Aligned_cols=26 Identities=31% Similarity=0.810 Sum_probs=18.2
Q ss_pred cccccccccC-c-cceeee-cCccccCcc
Q 030304 119 RCTTCNKRVG-L-TGFNCR-CGNLFCAVH 144 (179)
Q Consensus 119 rC~~C~kk~g-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 65
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=26.83 E-value=36 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.500 Sum_probs=11.7
Q ss_pred CCcccccccccCccceeeecCccccCc
Q 030304 117 PKRCTTCNKRVGLTGFNCRCGNLFCAV 143 (179)
Q Consensus 117 ~~rC~~C~kk~gl~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 358888887665543445699999987
No 66
>PRK07218 replication factor A; Provisional
Probab=26.55 E-value=29 Score=32.49 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=16.0
Q ss_pred CCcccccccccCccceeee-cCcc
Q 030304 117 PKRCTTCNKRVGLTGFNCR-CGNL 139 (179)
Q Consensus 117 ~~rC~~C~kk~gl~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 4899999999954 6777 5543
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=26.04 E-value=22 Score=21.23 Aligned_cols=23 Identities=30% Similarity=1.086 Sum_probs=15.1
Q ss_pred CcccccccccCccceeee-cCccccCc
Q 030304 118 KRCTTCNKRVGLTGFNCR-CGNLFCAV 143 (179)
Q Consensus 118 ~rC~~C~kk~gl~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 46888886 4568897 99999986
No 68
>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=25.96 E-value=40 Score=27.91 Aligned_cols=38 Identities=24% Similarity=0.694 Sum_probs=24.0
Q ss_pred CCCcccccccccCcc--------------ceeee-cCccccCc---cccCCCCCCc
Q 030304 116 GPKRCTTCNKRVGLT--------------GFNCR-CGNLFCAV---HRYSDKHGCP 153 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~--------------gf~Cr-Cg~~FC~~---HRy~~~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 445677776554332 45566 77777654 8887777654
No 69
>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=25.57 E-value=30 Score=18.25 Aligned_cols=10 Identities=40% Similarity=1.344 Sum_probs=5.3
Q ss_pred eeee-cCcccc
Q 030304 132 FNCR-CGNLFC 141 (179)
Q Consensus 132 f~Cr-Cg~~FC 141 (179)
|.|. ||..|-
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 4555 555553
No 70
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.45 E-value=39 Score=25.44 Aligned_cols=34 Identities=24% Similarity=0.670 Sum_probs=25.1
Q ss_pred CCCCCCcccccccccCcc----c-eeee-cCccccCccccC
Q 030304 113 AKEGPKRCTTCNKRVGLT----G-FNCR-CGNLFCAVHRYS 147 (179)
Q Consensus 113 ~~~~~~rC~~C~kk~gl~----g-f~Cr-Cg~~FC~~HRy~ 147 (179)
.+..+-.|..|+++ .+- | -.|+ ||.+|=+---.|
T Consensus 31 ~~~~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 31 QQRAKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HHhcCCcCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 34567889999987 331 3 8999 999998776555
No 71
>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=24.11 E-value=28 Score=25.54 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=15.3
Q ss_pred CCcccccccccCccceeee
Q 030304 117 PKRCTTCNKRVGLTGFNCR 135 (179)
Q Consensus 117 ~~rC~~C~kk~gl~gf~Cr 135 (179)
.-.|..|.+||||=.|+=+
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~ 37 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSK 37 (91)
T ss_pred eEEccccCcEeeeeecccC
Confidence 5679999999999766543
No 72
>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=24.06 E-value=46 Score=20.93 Aligned_cols=20 Identities=25% Similarity=0.750 Sum_probs=15.7
Q ss_pred ccceeee-cCccccCccccCC
Q 030304 129 LTGFNCR-CGNLFCAVHRYSD 148 (179)
Q Consensus 129 l~gf~Cr-Cg~~FC~~HRy~~ 148 (179)
+-.|+|. ||.+|=-.+...+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4468999 9999988777666
No 73
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=22.86 E-value=39 Score=23.80 Aligned_cols=23 Identities=30% Similarity=0.657 Sum_probs=17.8
Q ss_pred CCCcccccccccCcc---ceeee-cCc
Q 030304 116 GPKRCTTCNKRVGLT---GFNCR-CGN 138 (179)
Q Consensus 116 ~~~rC~~C~kk~gl~---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 356799999888884 49999 864
No 74
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=22.82 E-value=78 Score=18.09 Aligned_cols=20 Identities=20% Similarity=0.668 Sum_probs=12.3
Q ss_pred ceeeecCccccCccccCCCCCCc
Q 030304 131 GFNCRCGNLFCAVHRYSDKHGCP 153 (179)
Q Consensus 131 gf~CrCg~~FC~~HRy~~~H~C~ 153 (179)
+|+|.|..-| ...++.|.|.
T Consensus 1 sy~C~C~~Gy---~l~~d~~~C~ 20 (24)
T PF12662_consen 1 SYTCSCPPGY---QLSPDGRSCE 20 (24)
T ss_pred CEEeeCCCCC---cCCCCCCccc
Confidence 5888885444 3345667774
No 75
>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=22.73 E-value=38 Score=21.84 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=13.8
Q ss_pred eeee-cCccccCccccC
Q 030304 132 FNCR-CGNLFCAVHRYS 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 999999997754
No 76
>PF00869 Flavi_glycoprot: Flavivirus glycoprotein, central and dimerisation domains; InterPro: IPR011999 Flaviviruses are small, enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Yellow fever virus (YFV), West Nile virus (WNV), Tick-borne encephalitis virus, Japanese encephalitis virus and Dengue virus 2 viruses []. Flaviviruses consist of three structural proteins: the core nucleocapsid protein C (IPR001122 from INTERPRO), and the envelope glycoproteins M (IPR000069 from INTERPRO) and E. Glycoprotein E is a class II viral fusion protein that mediates both receptor binding and fusion. Class II viral fusion proteins are found in flaviviruses and alphaviruses, and are structurally distinct from class I fusion proteins from influenza virus and HIV. Glycoprotein E is comprised of three domains: domain I (dimerisation domain) is an 8-stranded beta barrel, domain II (central domain) is an elongated domain composed of twelve beta strands and two alpha helices, and domain III (immunoglobulin-like domain) is an IgC-like module with ten beta strands. This entry represents domains I and II, which are intertwined []. The glycoprotein E dimers on the viral surface re-cluster irreversibly into fusion-competent trimers upon exposure to low pH, as found in the acidic environment of the endosome. The formation of trimers results in a conformational change in the hinge region of domain II, a key structural element that opens a ligand-binding hydrophobic pocket at the interface between domains I and II. The conformational change results in the exposure of a fusion peptide loop at the tip of domain II, which is required in the fusion step to drive the cellular and viral membranes together by inserting into the membrane [].; GO: 0016021 integral to membrane, 0019031 viral envelope; PDB: 3P54_A 1OK8_A 1OAN_A 1OKE_B 3C5X_A 3C6E_A 2JSF_A 1URZ_B 3IYW_A 2JV6_A ....
Probab=21.69 E-value=33 Score=30.86 Aligned_cols=10 Identities=50% Similarity=1.318 Sum_probs=6.4
Q ss_pred cCCCCCCccc
Q 030304 28 NNCGFFGSAA 37 (179)
Q Consensus 28 NgCGFfGs~a 37 (179)
||||+||--.
T Consensus 103 NGCgLFGKGS 112 (293)
T PF00869_consen 103 NGCGLFGKGS 112 (293)
T ss_dssp GT-SS-EEEE
T ss_pred cccEEEeCCc
Confidence 9999999654
No 77
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.68 E-value=53 Score=18.43 Aligned_cols=12 Identities=33% Similarity=0.999 Sum_probs=7.1
Q ss_pred ccceeee-cCccc
Q 030304 129 LTGFNCR-CGNLF 140 (179)
Q Consensus 129 l~gf~Cr-Cg~~F 140 (179)
...|.|. |+..|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 3346776 66655
No 78
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=21.27 E-value=34 Score=34.02 Aligned_cols=50 Identities=28% Similarity=0.663 Sum_probs=32.2
Q ss_pred CcccccccccCccceeee-cCccc---cCccccCCCCCCcccchHHHHHHHHHhCCccc
Q 030304 118 KRCTTCNKRVGLTGFNCR-CGNLF---CAVHRYSDKHGCPFDYRTAAREAIAKANPVVK 172 (179)
Q Consensus 118 ~rC~~C~kk~gl~gf~Cr-Cg~~F---C~~HRy~~~H~C~fDyk~~gre~l~k~Np~v~ 172 (179)
--|..|.+++=.+||+|+ |++.| |+.|- | --|. +|. -.|+.+...+|-|.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~v-p--~~C~-~~~-~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRV-P--TSCV-NPD-HLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCC-C--CCCC-Ccc-hHhhhhhhcccccc
Confidence 457767778878899999 99866 44433 2 2333 333 35667777777664
No 79
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.19 E-value=58 Score=22.36 Aligned_cols=14 Identities=21% Similarity=0.627 Sum_probs=11.5
Q ss_pred ccchhHHHHHHHHH
Q 030304 39 MNMCSKCHKAMILN 52 (179)
Q Consensus 39 ~nlCSkCyr~~~~~ 52 (179)
.|||..|||+....
T Consensus 34 L~~CRqCFRe~A~~ 47 (54)
T PTZ00218 34 LNVCRQCFRENAEL 47 (54)
T ss_pred cchhhHHHHHhhHh
Confidence 57999999998643
No 80
>PRK12366 replication factor A; Reviewed
Probab=20.89 E-value=43 Score=32.79 Aligned_cols=29 Identities=28% Similarity=0.604 Sum_probs=20.8
Q ss_pred CCcccccccccCcc--ceeee-cCccccCcccc
Q 030304 117 PKRCTTCNKRVGLT--GFNCR-CGNLFCAVHRY 146 (179)
Q Consensus 117 ~~rC~~C~kk~gl~--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 37899999999543 27896 8877 234666
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=20.59 E-value=46 Score=20.07 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=13.5
Q ss_pred ccccccccCccceeeecCccccCc
Q 030304 120 CTTCNKRVGLTGFNCRCGNLFCAV 143 (179)
Q Consensus 120 C~~C~kk~gl~gf~CrCg~~FC~~ 143 (179)
|..|...+.-.-..-.||++||..
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~ 24 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKE 24 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHH
T ss_pred CCCCCCcccCcCEECCCCCchhHH
Confidence 344544333322456699999964
Done!