Query 030726
Match_columns 172
No_of_seqs 150 out of 442
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:40:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030726.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030726hhsearch_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 1.7E-47 3.7E-52 309.7 9.9 164 1-172 1-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 1.9E-15 4.2E-20 96.2 2.3 38 113-150 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 2.8E-15 6.1E-20 87.4 2.1 25 15-39 1-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.5 1.2E-14 2.5E-19 85.5 1.1 25 15-39 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 4.1E-11 8.9E-16 77.2 1.3 38 113-151 1-41 (43)
6 COG3582 Predicted nucleic acid 96.6 0.0011 2.4E-08 54.2 1.6 38 112-150 99-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.5 0.001 2.2E-08 57.5 1.0 40 111-151 9-51 (250)
8 PF01363 FYVE: FYVE zinc finge 94.7 0.015 3.3E-07 39.7 1.2 29 109-137 8-39 (69)
9 cd00065 FYVE FYVE domain; Zinc 93.1 0.041 8.8E-07 36.0 0.9 27 111-137 3-32 (57)
10 KOG3183 Predicted Zn-finger pr 93.1 0.022 4.7E-07 49.4 -0.6 41 106-146 94-138 (250)
11 smart00064 FYVE Protein presen 92.7 0.063 1.4E-06 36.5 1.4 28 110-137 10-40 (68)
12 KOG1818 Membrane trafficking a 90.2 0.11 2.3E-06 50.5 0.6 46 109-154 164-223 (634)
13 PF10571 UPF0547: Uncharacteri 87.8 0.27 5.8E-06 28.7 1.0 23 111-133 1-24 (26)
14 PF15135 UPF0515: Uncharacteri 83.3 0.65 1.4E-05 40.9 1.6 30 106-135 128-167 (278)
15 PF00130 C1_1: Phorbol esters/ 83.0 0.71 1.5E-05 29.7 1.3 24 109-132 10-37 (53)
16 PF10122 Mu-like_Com: Mu-like 71.9 1.3 2.8E-05 30.0 0.1 24 110-133 4-34 (51)
17 PF02148 zf-UBP: Zn-finger in 67.2 3 6.4E-05 28.2 1.1 23 113-136 1-24 (63)
18 KOG1729 FYVE finger containing 64.9 1.8 3.9E-05 38.4 -0.5 33 109-142 167-203 (288)
19 PF14471 DUF4428: Domain of un 62.7 2.6 5.6E-05 28.1 0.1 22 112-133 1-30 (51)
20 KOG1819 FYVE finger-containing 59.3 4.7 0.0001 39.2 1.2 29 109-137 900-931 (990)
21 PHA00626 hypothetical protein 58.7 4.9 0.00011 28.0 0.9 23 111-135 12-35 (59)
22 PHA02768 hypothetical protein; 58.5 4 8.7E-05 27.9 0.5 15 121-135 2-17 (55)
23 KOG1812 Predicted E3 ubiquitin 58.0 6.3 0.00014 36.0 1.8 31 108-138 304-338 (384)
24 PF13978 DUF4223: Protein of u 56.7 5.1 0.00011 27.4 0.7 18 133-150 19-36 (56)
25 smart00109 C1 Protein kinase C 56.3 6.2 0.00013 24.1 1.0 24 109-132 10-36 (49)
26 PF11781 RRN7: RNA polymerase 56.2 5.3 0.00011 24.8 0.7 22 111-132 9-34 (36)
27 cd00029 C1 Protein kinase C co 55.9 6.1 0.00013 24.5 1.0 24 109-132 10-37 (50)
28 COG1996 RPC10 DNA-directed RNA 55.0 4.8 0.0001 27.0 0.4 23 110-132 6-33 (49)
29 PF01194 RNA_pol_N: RNA polyme 53.3 7.1 0.00015 27.2 1.0 13 110-122 4-16 (60)
30 PF05207 zf-CSL: CSL zinc fing 52.7 6.1 0.00013 26.5 0.6 13 122-134 16-28 (55)
31 PF08882 Acetone_carb_G: Aceto 49.4 8.6 0.00019 29.9 1.0 35 114-150 16-50 (112)
32 PTZ00303 phosphatidylinositol 48.9 9.1 0.0002 39.1 1.4 27 111-137 461-495 (1374)
33 PF07649 C1_3: C1-like domain; 48.0 7.8 0.00017 22.5 0.5 22 112-133 2-25 (30)
34 PRK04016 DNA-directed RNA poly 47.7 6.7 0.00015 27.5 0.2 13 110-122 4-16 (62)
35 PF03107 C1_2: C1 domain; Int 47.0 14 0.00029 21.7 1.4 20 112-131 2-23 (30)
36 PLN00032 DNA-directed RNA poly 46.6 7.5 0.00016 28.0 0.3 13 110-122 4-16 (71)
37 PF03604 DNA_RNApol_7kD: DNA d 45.4 9.3 0.0002 23.3 0.5 19 113-131 3-25 (32)
38 smart00659 RPOLCX RNA polymera 44.5 11 0.00023 24.4 0.7 20 112-131 4-27 (44)
39 PF02928 zf-C5HC2: C5HC2 zinc 44.2 11 0.00024 25.0 0.8 26 113-138 1-28 (54)
40 KOG2807 RNA polymerase II tran 43.4 14 0.00031 33.8 1.7 29 108-136 328-358 (378)
41 COG1571 Predicted DNA-binding 43.2 11 0.00023 35.3 0.9 25 111-135 351-379 (421)
42 smart00290 ZnF_UBP Ubiquitin C 42.7 8.5 0.00018 24.3 0.1 24 112-137 1-25 (50)
43 PF02318 FYVE_2: FYVE-type zin 40.6 18 0.0004 27.3 1.7 31 110-140 54-88 (118)
44 PF13842 Tnp_zf-ribbon_2: DDE_ 40.6 21 0.00047 21.4 1.6 26 112-137 2-30 (32)
45 PF07975 C1_4: TFIIH C1-like d 40.1 11 0.00025 25.3 0.4 34 113-146 2-47 (51)
46 KOG3497 DNA-directed RNA polym 39.8 9.7 0.00021 27.0 0.0 13 110-122 4-16 (69)
47 PRK04136 rpl40e 50S ribosomal 39.6 15 0.00032 24.6 0.9 23 109-131 13-36 (48)
48 cd04476 RPA1_DBD_C RPA1_DBD_C: 39.1 13 0.00028 29.2 0.6 32 109-140 33-69 (166)
49 PRK08402 replication factor A; 39.1 13 0.00027 33.9 0.6 29 110-139 212-245 (355)
50 PF13240 zinc_ribbon_2: zinc-r 38.7 17 0.00038 20.3 0.9 20 112-131 1-21 (23)
51 smart00647 IBR In Between Ring 37.1 22 0.00048 22.9 1.4 18 123-140 39-57 (64)
52 PF15549 PGC7_Stella: PGC7/Ste 36.9 19 0.00041 29.6 1.3 19 124-144 123-141 (160)
53 PF08073 CHDNT: CHDNT (NUC034) 36.7 11 0.00023 25.9 -0.2 20 151-170 21-40 (55)
54 PF09723 Zn-ribbon_8: Zinc rib 36.6 21 0.00045 22.4 1.2 20 122-141 3-23 (42)
55 KOG1842 FYVE finger-containing 36.4 8.8 0.00019 36.4 -0.8 25 111-135 181-208 (505)
56 PF13717 zinc_ribbon_4: zinc-r 36.1 18 0.00039 22.2 0.8 22 112-133 4-35 (36)
57 COG1644 RPB10 DNA-directed RNA 35.6 12 0.00026 26.4 -0.0 13 110-122 4-16 (63)
58 PRK00398 rpoP DNA-directed RNA 33.8 21 0.00046 22.6 0.9 28 111-138 4-36 (46)
59 PF01485 IBR: IBR domain; Int 33.7 18 0.00038 23.3 0.5 16 125-140 41-57 (64)
60 PF10367 Vps39_2: Vacuolar sor 31.3 33 0.00071 24.3 1.6 24 110-133 78-102 (109)
61 PF06750 DiS_P_DiS: Bacterial 31.2 28 0.0006 25.6 1.3 15 109-123 32-46 (92)
62 PF04438 zf-HIT: HIT zinc fing 30.8 18 0.00038 21.6 0.1 23 111-136 3-26 (30)
63 PRK07218 replication factor A; 29.8 23 0.00051 32.9 0.8 21 110-132 297-318 (423)
64 KOG3507 DNA-directed RNA polym 29.6 23 0.00051 24.8 0.6 23 109-131 19-45 (62)
65 PHA00616 hypothetical protein 28.5 16 0.00034 23.9 -0.4 11 125-135 2-13 (44)
66 KOG0193 Serine/threonine prote 28.3 21 0.00045 35.3 0.2 50 111-165 190-243 (678)
67 PF14634 zf-RING_5: zinc-RING 28.2 31 0.00068 21.4 1.0 29 112-140 1-31 (44)
68 COG1997 RPL43A Ribosomal prote 27.7 34 0.00073 25.7 1.2 33 107-140 32-70 (89)
69 PF14835 zf-RING_6: zf-RING of 27.5 34 0.00073 24.3 1.1 26 111-136 8-33 (65)
70 PF00096 zf-C2H2: Zinc finger, 25.9 27 0.00059 18.3 0.3 9 125-133 1-10 (23)
71 PF08600 Rsm1: Rsm1-like; Int 25.6 27 0.00058 25.6 0.3 18 110-127 19-36 (91)
72 KOG1074 Transcriptional repres 25.6 47 0.001 34.0 2.1 46 104-149 599-672 (958)
73 PF00412 LIM: LIM domain; Int 24.9 27 0.00059 22.1 0.3 27 111-137 27-53 (58)
74 PF07282 OrfB_Zn_ribbon: Putat 23.7 52 0.0011 22.0 1.5 24 109-132 27-55 (69)
75 smart00834 CxxC_CXXC_SSSS Puta 23.4 40 0.00086 20.1 0.8 14 123-136 4-18 (41)
76 COG3357 Predicted transcriptio 23.2 29 0.00064 26.3 0.2 16 120-135 54-70 (97)
77 PRK12366 replication factor A; 23.2 32 0.00069 33.5 0.4 29 110-139 532-563 (637)
78 smart00396 ZnF_UBR1 Putative z 23.2 44 0.00096 23.3 1.1 14 124-137 50-70 (71)
79 PTZ00218 40S ribosomal protein 22.8 48 0.001 22.7 1.1 13 31-43 34-46 (54)
80 PF13923 zf-C3HC4_2: Zinc fing 22.3 38 0.00082 20.4 0.5 23 113-135 1-23 (39)
81 COG1773 Rubredoxin [Energy pro 21.3 39 0.00085 23.1 0.5 13 124-136 3-16 (55)
82 PF13465 zf-H2C2_2: Zinc-finge 21.0 50 0.0011 18.5 0.8 11 123-133 13-24 (26)
83 PF08646 Rep_fac-A_C: Replicat 20.9 30 0.00064 26.6 -0.2 29 111-139 19-54 (146)
84 PF05458 Siva: Cd27 binding pr 20.4 83 0.0018 25.9 2.3 38 109-146 110-165 (175)
85 PF11722 zf-TRM13_CCCH: CCCH z 20.3 44 0.00095 20.1 0.5 10 129-138 21-30 (31)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.7e-47 Score=309.70 Aligned_cols=164 Identities=45% Similarity=0.856 Sum_probs=110.5
Q ss_pred CCCCccCCCCCCCCccccccCCCCCCccccCCcchhhhHHHHHHHhhhh-hhhhcccccccCCCCCCCCCcccccccccc
Q 030726 1 MDHDETGCQAPPEGPILCINNCGFFGSVATMNMCSKCYKDIMLKQDQAK-LAASSIGSIVNETSSSNGSESVAAATVDVQ 79 (172)
Q Consensus 1 M~~~~~~~q~~~e~p~lC~n~CGFfGs~at~n~CSkCyr~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (172)
|+++....+.+++.++||+|||||||+|+|+||||+||++++.++++.. .....+..-+. .+.+ .+. ....
T Consensus 1 M~~e~~~~~~~~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~-~~~s---~~~----~~~~ 72 (167)
T KOG3173|consen 1 MASETNGSQTPPSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLS-SPRS---VPS----RDPP 72 (167)
T ss_pred CcccccCCCCCCccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCccccccc-Cccc---cCc----cccc
Confidence 6766555555344579999999999999999999999999998876652 22211111000 0000 110 0000
Q ss_pred cCCCCcccc-cccCC-CCCCCcccccCCCCCCCCCcccccccccccceeeecCCccccCCCCCCCCCCcccchHHHHHHH
Q 030726 80 ASSVEPKII-SVQPS-CASELSESVEAKPKEGPSRCSSCKKRVGLTGFKCRCGNLYCVSHRYSDKHNCPFDYRTAARDAI 157 (172)
Q Consensus 80 ~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~~r~~l 157 (172)
....+.+.. +...+ ..+...+.........++||+.|+|||||+||.||||++||+.|||+|.|+|+||||.+||+.|
T Consensus 73 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i 152 (167)
T KOG3173|consen 73 AVSLESTTESELKLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKI 152 (167)
T ss_pred cccccccccccccccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHH
Confidence 000110000 00000 0011111222334556889999999999999999999999999999999999999999999999
Q ss_pred HHhCCcccccccccC
Q 030726 158 IKANPVIKAEKLDKI 172 (172)
Q Consensus 158 ~k~Np~v~~~Kl~kI 172 (172)
+++||+|+++||+||
T Consensus 153 ~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 153 AKANPVVKADKLQKI 167 (167)
T ss_pred HHhCCeeeccccccC
Confidence 999999999999998
No 2
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.55 E-value=1.9e-15 Score=96.16 Aligned_cols=38 Identities=63% Similarity=1.481 Sum_probs=36.9
Q ss_pred cccccccccccceeee-cCCccccCCCCCCCCCCcccch
Q 030726 113 CSSCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYR 150 (172)
Q Consensus 113 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 150 (172)
|+.|+++++|++|+|+ |+++||..|||+|.|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 3
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.54 E-value=2.8e-15 Score=87.45 Aligned_cols=25 Identities=64% Similarity=1.420 Sum_probs=20.8
Q ss_pred ccccccCCCCCCccccCCcchhhhH
Q 030726 15 PILCINNCGFFGSVATMNMCSKCYK 39 (172)
Q Consensus 15 p~lC~n~CGFfGs~at~n~CSkCyr 39 (172)
|.+|++|||||||++|+||||+|||
T Consensus 1 ~~~C~~gCgf~Gs~~~~~~Cs~C~~ 25 (25)
T PF01754_consen 1 PSLCANGCGFYGSPATNGLCSKCYR 25 (25)
T ss_dssp SSB-TTTSSSB-BGGGTTS-HHHHH
T ss_pred CCcccCCCCCcccccccCcchhhcC
Confidence 5799999999999999999999997
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.47 E-value=1.2e-14 Score=85.54 Aligned_cols=25 Identities=60% Similarity=1.314 Sum_probs=23.3
Q ss_pred ccccc-cCCCCCCccccCCcchhhhH
Q 030726 15 PILCI-NNCGFFGSVATMNMCSKCYK 39 (172)
Q Consensus 15 p~lC~-n~CGFfGs~at~n~CSkCyr 39 (172)
|.+|+ +||||||||+|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 45899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.07 E-value=4.1e-11 Score=77.18 Aligned_cols=38 Identities=42% Similarity=0.964 Sum_probs=28.0
Q ss_pred ccc--ccccccccceeee-cCCccccCCCCCCCCCCcccchH
Q 030726 113 CSS--CKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYRT 151 (172)
Q Consensus 113 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 151 (172)
|.. |++++. ++|.|+ |+..||..|||++.|+|+++++.
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccC-CCeECCCCCcccCccccCccccCCcchhhc
Confidence 455 998887 799999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.56 E-value=0.0011 Score=54.22 Aligned_cols=38 Identities=26% Similarity=0.505 Sum_probs=30.0
Q ss_pred Ccccccccccccceeee-cCCccccCCCCCCCCCCcccch
Q 030726 112 RCSSCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYR 150 (172)
Q Consensus 112 rC~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 150 (172)
+|..|++..+| .++|- |++.||+.||+++.|+|.+...
T Consensus 99 ~~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 99 TPQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred cceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 34455555444 58997 9999999999999999998655
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.47 E-value=0.001 Score=57.48 Aligned_cols=40 Identities=38% Similarity=1.013 Sum_probs=35.1
Q ss_pred CCcc--cccccccccceeee-cCCccccCCCCCCCCCCcccchH
Q 030726 111 SRCS--SCKKRVGLTGFKCR-CGNLYCVSHRYSDKHNCPFDYRT 151 (172)
Q Consensus 111 ~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 151 (172)
..|. .|+ .|.++.|+|- |+.+||..||--+.|+|.+-|..
T Consensus 9 kHCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCK-QLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhh-hccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4677 787 5799999996 99999999999999999988764
No 8
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=94.69 E-value=0.015 Score=39.71 Aligned_cols=29 Identities=38% Similarity=0.863 Sum_probs=17.5
Q ss_pred CCCCccccccccccc--ceeee-cCCccccCC
Q 030726 109 GPSRCSSCKKRVGLT--GFKCR-CGNLYCVSH 137 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 137 (172)
....|..|+++.+|+ -..|| ||.+||+.+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCch
Confidence 357899999999997 49999 999999754
No 9
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=93.08 E-value=0.041 Score=36.02 Aligned_cols=27 Identities=41% Similarity=1.011 Sum_probs=23.5
Q ss_pred CCccccccccccc--ceeee-cCCccccCC
Q 030726 111 SRCSSCKKRVGLT--GFKCR-CGNLYCVSH 137 (172)
Q Consensus 111 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 137 (172)
..|..|+++++++ ...|| ||.+||..+
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 69998 999999754
No 10
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=93.06 E-value=0.022 Score=49.41 Aligned_cols=41 Identities=34% Similarity=0.826 Sum_probs=34.9
Q ss_pred CCCCCCCcc--ccccccccc-ceeee-cCCccccCCCCCCCCCCc
Q 030726 106 PKEGPSRCS--SCKKRVGLT-GFKCR-CGNLYCVSHRYSDKHNCP 146 (172)
Q Consensus 106 ~~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~ 146 (172)
.+...++|. .|+|++-|. .+.|+ ||..||-+||++-.|.|.
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 445567777 788888875 69998 999999999999999998
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=90.17 E-value=0.11 Score=50.52 Aligned_cols=46 Identities=28% Similarity=0.707 Sum_probs=35.9
Q ss_pred CCCCcccccccccccc--eeee-cCCccccCCC-----------CCCCCCCcccchHHHH
Q 030726 109 GPSRCSSCKKRVGLTG--FKCR-CGNLYCVSHR-----------YSDKHNCPFDYRTAAR 154 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~~r 154 (172)
....|..|+.+.|+++ ..|| ||.+||+.|= |-+.--|..||...-|
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTR 223 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhh
Confidence 3578999999999985 8999 9999999874 3455667777764433
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.84 E-value=0.27 Score=28.72 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=20.5
Q ss_pred CCcccccccccccceeee-cCCcc
Q 030726 111 SRCSSCKKRVGLTGFKCR-CGNLY 133 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~Cr-Cg~~F 133 (172)
.+|-.|++.|.+..-.|- ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 368999999999999997 99887
No 14
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=83.31 E-value=0.65 Score=40.86 Aligned_cols=30 Identities=33% Similarity=0.868 Sum_probs=24.1
Q ss_pred CCCCCCCccccccc---------ccccceee-ecCCcccc
Q 030726 106 PKEGPSRCSSCKKR---------VGLTGFKC-RCGNLYCV 135 (172)
Q Consensus 106 ~~~~~~rC~~C~kk---------vgl~gf~C-rCg~~FC~ 135 (172)
..+..+||..|+|| .|+.-|+| .|+++|=+
T Consensus 128 ~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 128 QRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccccCCCccccccceeeeecccccccchh
Confidence 34557899999988 67778999 59999954
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=82.98 E-value=0.71 Score=29.72 Aligned_cols=24 Identities=38% Similarity=1.079 Sum_probs=18.3
Q ss_pred CCCCcccccccc---cccceeee-cCCc
Q 030726 109 GPSRCSSCKKRV---GLTGFKCR-CGNL 132 (172)
Q Consensus 109 ~~~rC~~C~kkv---gl~gf~Cr-Cg~~ 132 (172)
.+..|..|++.| ++.|++|+ |+.+
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 56799998 8765
No 16
>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=71.91 E-value=1.3 Score=29.98 Aligned_cols=24 Identities=33% Similarity=0.834 Sum_probs=18.6
Q ss_pred CCCccccccccccc------ceee-ecCCcc
Q 030726 110 PSRCSSCKKRVGLT------GFKC-RCGNLY 133 (172)
Q Consensus 110 ~~rC~~C~kkvgl~------gf~C-rCg~~F 133 (172)
.-||..|+|.|... ..+| |||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 46999999998774 4788 688664
No 17
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=67.16 E-value=3 Score=28.24 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=15.2
Q ss_pred cccccccccccceeee-cCCccccC
Q 030726 113 CSSCKKRVGLTGFKCR-CGNLYCVS 136 (172)
Q Consensus 113 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 136 (172)
|..|+.. +-.-+.|- ||.++|+.
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 44457885 99999994
No 18
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=64.91 E-value=1.8 Score=38.39 Aligned_cols=33 Identities=24% Similarity=0.725 Sum_probs=27.0
Q ss_pred CCCCcccccc-ccccc--ceeee-cCCccccCCCCCCC
Q 030726 109 GPSRCSSCKK-RVGLT--GFKCR-CGNLYCVSHRYSDK 142 (172)
Q Consensus 109 ~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e~ 142 (172)
..++|..|.+ .-.|. --.|| ||.+||. |.-..+
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n~ 203 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRNR 203 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhcCc
Confidence 4689999999 77776 48899 9999999 875543
No 19
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=62.74 E-value=2.6 Score=28.08 Aligned_cols=22 Identities=36% Similarity=1.073 Sum_probs=16.7
Q ss_pred Cccccccccccc-------ceeee-cCCcc
Q 030726 112 RCSSCKKRVGLT-------GFKCR-CGNLY 133 (172)
Q Consensus 112 rC~~C~kkvgl~-------gf~Cr-Cg~~F 133 (172)
+|..|++++||+ ||.|. |-...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 599999999996 57776 64433
No 20
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=59.31 E-value=4.7 Score=39.19 Aligned_cols=29 Identities=24% Similarity=0.807 Sum_probs=21.7
Q ss_pred CCCCccccccccccc--ceeee-cCCccccCC
Q 030726 109 GPSRCSSCKKRVGLT--GFKCR-CGNLYCVSH 137 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 137 (172)
+.-+|..|....... -..|| ||++||++-
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 457899998654442 46899 999999864
No 21
>PHA00626 hypothetical protein
Probab=58.71 E-value=4.9 Score=27.95 Aligned_cols=23 Identities=13% Similarity=0.330 Sum_probs=15.2
Q ss_pred CCcccccccccccceeee-cCCcccc
Q 030726 111 SRCSSCKKRVGLTGFKCR-CGNLYCV 135 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~ 135 (172)
.||.+|++... -|+|. ||+.|-.
T Consensus 12 vrcg~cr~~sn--rYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWSD--DYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccCc--ceEcCCCCCeech
Confidence 47777776333 38886 8877753
No 22
>PHA02768 hypothetical protein; Provisional
Probab=58.51 E-value=4 Score=27.90 Aligned_cols=15 Identities=40% Similarity=1.187 Sum_probs=12.0
Q ss_pred cccceeee-cCCcccc
Q 030726 121 GLTGFKCR-CGNLYCV 135 (172)
Q Consensus 121 gl~gf~Cr-Cg~~FC~ 135 (172)
.|+||.|- ||..|-.
T Consensus 2 ~~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 2 ALLGYECPICGEIYIK 17 (55)
T ss_pred cccccCcchhCCeecc
Confidence 57899996 9988864
No 23
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.95 E-value=6.3 Score=35.96 Aligned_cols=31 Identities=32% Similarity=0.860 Sum_probs=26.1
Q ss_pred CCCCCccccccccccc-c---eeeecCCccccCCC
Q 030726 108 EGPSRCSSCKKRVGLT-G---FKCRCGNLYCVSHR 138 (172)
Q Consensus 108 ~~~~rC~~C~kkvgl~-g---f~CrCg~~FC~~HR 138 (172)
+.-.+|..|+-.+.|. | ++||||+-||..=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 3457899999999886 3 99999999998766
No 24
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=56.71 E-value=5.1 Score=27.44 Aligned_cols=18 Identities=33% Similarity=0.839 Sum_probs=16.0
Q ss_pred cccCCCCCCCCCCcccch
Q 030726 133 YCVSHRYSDKHNCPFDYR 150 (172)
Q Consensus 133 FC~~HRy~e~H~C~fDyk 150 (172)
-|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999996
No 25
>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=56.33 E-value=6.2 Score=24.12 Aligned_cols=24 Identities=29% Similarity=0.880 Sum_probs=18.5
Q ss_pred CCCCccccccccccc--ceeee-cCCc
Q 030726 109 GPSRCSSCKKRVGLT--GFKCR-CGNL 132 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~ 132 (172)
.+..|..|++.+... |++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCch
Confidence 356899999999873 88887 6543
No 26
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=56.20 E-value=5.3 Score=24.81 Aligned_cols=22 Identities=36% Similarity=0.948 Sum_probs=17.5
Q ss_pred CCccccccccccc--c-eee-ecCCc
Q 030726 111 SRCSSCKKRVGLT--G-FKC-RCGNL 132 (172)
Q Consensus 111 ~rC~~C~kkvgl~--g-f~C-rCg~~ 132 (172)
-+|..|+-+...+ | |.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999997765 4 899 89875
No 27
>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=55.88 E-value=6.1 Score=24.45 Aligned_cols=24 Identities=29% Similarity=0.783 Sum_probs=19.0
Q ss_pred CCCCcccccccccc---cceeee-cCCc
Q 030726 109 GPSRCSSCKKRVGL---TGFKCR-CGNL 132 (172)
Q Consensus 109 ~~~rC~~C~kkvgl---~gf~Cr-Cg~~ 132 (172)
.+..|..|++.+.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 35689999999985 689998 7554
No 28
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=55.05 E-value=4.8 Score=26.97 Aligned_cols=23 Identities=35% Similarity=1.021 Sum_probs=17.9
Q ss_pred CCCccccccccccc----ceeee-cCCc
Q 030726 110 PSRCSSCKKRVGLT----GFKCR-CGNL 132 (172)
Q Consensus 110 ~~rC~~C~kkvgl~----gf~Cr-Cg~~ 132 (172)
.-+|..|++++.|. +..|. ||+-
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 35899999999854 79997 7654
No 29
>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=53.29 E-value=7.1 Score=27.20 Aligned_cols=13 Identities=46% Similarity=1.020 Sum_probs=10.1
Q ss_pred CCCcccccccccc
Q 030726 110 PSRCSSCKKRVGL 122 (172)
Q Consensus 110 ~~rC~~C~kkvgl 122 (172)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6799999998874
No 30
>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=52.68 E-value=6.1 Score=26.53 Aligned_cols=13 Identities=31% Similarity=0.994 Sum_probs=10.5
Q ss_pred ccceeeecCCccc
Q 030726 122 LTGFKCRCGNLYC 134 (172)
Q Consensus 122 l~gf~CrCg~~FC 134 (172)
..-+.||||..|-
T Consensus 16 ~~~y~CRCG~~f~ 28 (55)
T PF05207_consen 16 VYSYPCRCGGEFE 28 (55)
T ss_dssp EEEEEETTSSEEE
T ss_pred EEEEcCCCCCEEE
Confidence 3568999999874
No 31
>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=49.42 E-value=8.6 Score=29.94 Aligned_cols=35 Identities=17% Similarity=0.304 Sum_probs=25.7
Q ss_pred ccccccccccceeeecCCccccCCCCCCCCCCcccch
Q 030726 114 SSCKKRVGLTGFKCRCGNLYCVSHRYSDKHNCPFDYR 150 (172)
Q Consensus 114 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk 150 (172)
+.|+++- .-.+|+||+.||+-+.--..|.--++-.
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~vRd 50 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYVRD 50 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEecC
Confidence 5666654 2689999999999888777776555543
No 32
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=48.95 E-value=9.1 Score=39.08 Aligned_cols=27 Identities=33% Similarity=0.757 Sum_probs=20.9
Q ss_pred CCcccccccccc-------cceeee-cCCccccCC
Q 030726 111 SRCSSCKKRVGL-------TGFKCR-CGNLYCVSH 137 (172)
Q Consensus 111 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 137 (172)
..|..|+++-.. .--.|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 569999999863 246699 999998643
No 33
>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=47.97 E-value=7.8 Score=22.53 Aligned_cols=22 Identities=27% Similarity=0.670 Sum_probs=8.7
Q ss_pred Ccccccccccc-cceeee-cCCcc
Q 030726 112 RCSSCKKRVGL-TGFKCR-CGNLY 133 (172)
Q Consensus 112 rC~~C~kkvgl-~gf~Cr-Cg~~F 133 (172)
+|..|++.+.. ..|.|. |...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 68999999888 789997 76554
No 34
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=47.68 E-value=6.7 Score=27.52 Aligned_cols=13 Identities=38% Similarity=0.869 Sum_probs=11.1
Q ss_pred CCCcccccccccc
Q 030726 110 PSRCSSCKKRVGL 122 (172)
Q Consensus 110 ~~rC~~C~kkvgl 122 (172)
|-||++|+|-+|-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6799999998865
No 35
>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=47.01 E-value=14 Score=21.67 Aligned_cols=20 Identities=20% Similarity=0.730 Sum_probs=16.6
Q ss_pred Cccccccccccc-ceeee-cCC
Q 030726 112 RCSSCKKRVGLT-GFKCR-CGN 131 (172)
Q Consensus 112 rC~~C~kkvgl~-gf~Cr-Cg~ 131 (172)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 489999999988 99996 653
No 36
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=46.57 E-value=7.5 Score=27.99 Aligned_cols=13 Identities=46% Similarity=1.020 Sum_probs=11.1
Q ss_pred CCCcccccccccc
Q 030726 110 PSRCSSCKKRVGL 122 (172)
Q Consensus 110 ~~rC~~C~kkvgl 122 (172)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998864
No 37
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=45.45 E-value=9.3 Score=23.27 Aligned_cols=19 Identities=37% Similarity=1.073 Sum_probs=10.1
Q ss_pred ccccccccccc---ceeee-cCC
Q 030726 113 CSSCKKRVGLT---GFKCR-CGN 131 (172)
Q Consensus 113 C~~C~kkvgl~---gf~Cr-Cg~ 131 (172)
|..|+..+.|. ..+|+ ||+
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCcCCCeeEcCCCCcEECCcCCC
Confidence 56666666663 35666 543
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.45 E-value=11 Score=24.44 Aligned_cols=20 Identities=30% Similarity=0.924 Sum_probs=14.6
Q ss_pred Cccccccccccc---ceeee-cCC
Q 030726 112 RCSSCKKRVGLT---GFKCR-CGN 131 (172)
Q Consensus 112 rC~~C~kkvgl~---gf~Cr-Cg~ 131 (172)
+|..|+..+.+. +.+|+ ||+
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCc
Confidence 688888888875 57776 654
No 39
>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=44.25 E-value=11 Score=24.96 Aligned_cols=26 Identities=35% Similarity=0.890 Sum_probs=22.4
Q ss_pred cccccccccccceeeec--CCccccCCC
Q 030726 113 CSSCKKRVGLTGFKCRC--GNLYCVSHR 138 (172)
Q Consensus 113 C~~C~kkvgl~gf~CrC--g~~FC~~HR 138 (172)
|..|+.-.=|..+.|.| +.++|-.|-
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~ 28 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHA 28 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccc
Confidence 67888888888999997 899999884
No 40
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=43.40 E-value=14 Score=33.82 Aligned_cols=29 Identities=24% Similarity=0.877 Sum_probs=23.2
Q ss_pred CCCCCcccc-cccccccceeee-cCCccccC
Q 030726 108 EGPSRCSSC-KKRVGLTGFKCR-CGNLYCVS 136 (172)
Q Consensus 108 ~~~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 136 (172)
...++|+.| .+.++-..|.|+ |-++||..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeecc
Confidence 456789999 666666789998 99999963
No 41
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.22 E-value=11 Score=35.33 Aligned_cols=25 Identities=32% Similarity=0.849 Sum_probs=19.8
Q ss_pred CCccccccccccc---ceeee-cCCcccc
Q 030726 111 SRCSSCKKRVGLT---GFKCR-CGNLYCV 135 (172)
Q Consensus 111 ~rC~~C~kkvgl~---gf~Cr-Cg~~FC~ 135 (172)
-+|..|++++.-. ||+|+ ||..+=.
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCc
Confidence 4899999987654 79998 9886643
No 42
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=42.66 E-value=8.5 Score=24.31 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=17.8
Q ss_pred Ccccccccccccceeee-cCCccccCC
Q 030726 112 RCSSCKKRVGLTGFKCR-CGNLYCVSH 137 (172)
Q Consensus 112 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 137 (172)
||..|..... -+.|- |+.++|+..
T Consensus 1 ~C~~C~~~~~--l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN--LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC--eEEecCCCCcccCCC
Confidence 6888886554 36774 999999764
No 43
>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=40.64 E-value=18 Score=27.33 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=23.9
Q ss_pred CCCccccccccccc---ceeee-cCCccccCCCCC
Q 030726 110 PSRCSSCKKRVGLT---GFKCR-CGNLYCVSHRYS 140 (172)
Q Consensus 110 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 140 (172)
...|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 46899999999986 68997 999999876653
No 44
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=40.60 E-value=21 Score=21.45 Aligned_cols=26 Identities=35% Similarity=0.841 Sum_probs=18.6
Q ss_pred Cccccccccc-c-cceeee-cCCccccCC
Q 030726 112 RCSSCKKRVG-L-TGFKCR-CGNLYCVSH 137 (172)
Q Consensus 112 rC~~C~kkvg-l-~gf~Cr-Cg~~FC~~H 137 (172)
||..|.++-- - +.|.|. |+-..|..|
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 679997 987778776
No 45
>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=40.09 E-value=11 Score=25.27 Aligned_cols=34 Identities=32% Similarity=0.882 Sum_probs=15.2
Q ss_pred ccccccccccc--------ceeee-cCCccccC---CCCCCCCCCc
Q 030726 113 CSSCKKRVGLT--------GFKCR-CGNLYCVS---HRYSDKHNCP 146 (172)
Q Consensus 113 C~~C~kkvgl~--------gf~Cr-Cg~~FC~~---HRy~e~H~C~ 146 (172)
|+.|.+.+.-. .|.|. |+..||.. -=+-.-|+|+
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 56666666553 58994 99999852 2223456654
No 46
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=39.82 E-value=9.7 Score=27.00 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=10.9
Q ss_pred CCCcccccccccc
Q 030726 110 PSRCSSCKKRVGL 122 (172)
Q Consensus 110 ~~rC~~C~kkvgl 122 (172)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 5799999998774
No 47
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=39.55 E-value=15 Score=24.62 Aligned_cols=23 Identities=35% Similarity=0.778 Sum_probs=19.4
Q ss_pred CCCCcccccccccccceeee-cCC
Q 030726 109 GPSRCSSCKKRVGLTGFKCR-CGN 131 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~gf~Cr-Cg~ 131 (172)
.+.-|..|+-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 35679999999999999998 876
No 48
>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=39.07 E-value=13 Score=29.24 Aligned_cols=32 Identities=25% Similarity=0.559 Sum_probs=23.0
Q ss_pred CCCCccccccccccc---ceeee-cCCcc-ccCCCCC
Q 030726 109 GPSRCSSCKKRVGLT---GFKCR-CGNLY-CVSHRYS 140 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~---gf~Cr-Cg~~F-C~~HRy~ 140 (172)
.-..|..|+|||-.. .|.|. |+..+ =..+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 346788999999875 38885 87765 4566664
No 49
>PRK08402 replication factor A; Reviewed
Probab=39.06 E-value=13 Score=33.88 Aligned_cols=29 Identities=17% Similarity=0.457 Sum_probs=19.0
Q ss_pred CCCcccccccccc----cceeee-cCCccccCCCC
Q 030726 110 PSRCSSCKKRVGL----TGFKCR-CGNLYCVSHRY 139 (172)
Q Consensus 110 ~~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 139 (172)
-.+|..|+|||-. -.+.|. ||.+-+ .|||
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 3699999999963 247776 554433 4554
No 50
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.73 E-value=17 Score=20.32 Aligned_cols=20 Identities=25% Similarity=0.713 Sum_probs=11.4
Q ss_pred Ccccccccccccceeee-cCC
Q 030726 112 RCSSCKKRVGLTGFKCR-CGN 131 (172)
Q Consensus 112 rC~~C~kkvgl~gf~Cr-Cg~ 131 (172)
+|..|++++.-..-.|. ||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 36666666665544454 553
No 51
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=37.14 E-value=22 Score=22.90 Aligned_cols=18 Identities=22% Similarity=0.815 Sum_probs=14.9
Q ss_pred cceee-ecCCccccCCCCC
Q 030726 123 TGFKC-RCGNLYCVSHRYS 140 (172)
Q Consensus 123 ~gf~C-rCg~~FC~~HRy~ 140 (172)
....| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 35889 7999999998865
No 52
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=36.89 E-value=19 Score=29.64 Aligned_cols=19 Identities=47% Similarity=1.149 Sum_probs=15.4
Q ss_pred ceeeecCCccccCCCCCCCCC
Q 030726 124 GFKCRCGNLYCVSHRYSDKHN 144 (172)
Q Consensus 124 gf~CrCg~~FC~~HRy~e~H~ 144 (172)
-|+|.| .||-.||.+.+-+
T Consensus 123 ~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 123 RFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred ceeeee--eeecccCCCcccc
Confidence 389998 7999999776655
No 53
>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=36.70 E-value=11 Score=25.90 Aligned_cols=20 Identities=35% Similarity=0.363 Sum_probs=16.2
Q ss_pred HHHHHHHHHhCCcccccccc
Q 030726 151 TAARDAIIKANPVIKAEKLD 170 (172)
Q Consensus 151 ~~~r~~l~k~Np~v~~~Kl~ 170 (172)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34478899999999888875
No 54
>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=36.58 E-value=21 Score=22.44 Aligned_cols=20 Identities=25% Similarity=0.748 Sum_probs=16.4
Q ss_pred ccceeee-cCCccccCCCCCC
Q 030726 122 LTGFKCR-CGNLYCVSHRYSD 141 (172)
Q Consensus 122 l~gf~Cr-Cg~~FC~~HRy~e 141 (172)
+-.|+|. ||..|=-.+.+.+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4579997 9999988888777
No 55
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=36.37 E-value=8.8 Score=36.43 Aligned_cols=25 Identities=40% Similarity=1.055 Sum_probs=22.0
Q ss_pred CCccccccccccc--ceeee-cCCcccc
Q 030726 111 SRCSSCKKRVGLT--GFKCR-CGNLYCV 135 (172)
Q Consensus 111 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 135 (172)
.-|..|.++.||+ --.|| ||.+.|.
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHH
Confidence 4799999999997 59999 9999873
No 56
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=36.12 E-value=18 Score=22.21 Aligned_cols=22 Identities=23% Similarity=1.029 Sum_probs=11.4
Q ss_pred Cccccccccccc---------ceeee-cCCcc
Q 030726 112 RCSSCKKRVGLT---------GFKCR-CGNLY 133 (172)
Q Consensus 112 rC~~C~kkvgl~---------gf~Cr-Cg~~F 133 (172)
+|..|+++..+. -.+|. ||.+|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 455555554442 25664 66655
No 57
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=35.58 E-value=12 Score=26.38 Aligned_cols=13 Identities=54% Similarity=1.066 Sum_probs=10.8
Q ss_pred CCCcccccccccc
Q 030726 110 PSRCSSCKKRVGL 122 (172)
Q Consensus 110 ~~rC~~C~kkvgl 122 (172)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6799999998764
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=33.80 E-value=21 Score=22.57 Aligned_cols=28 Identities=32% Similarity=0.844 Sum_probs=18.1
Q ss_pred CCccccccccccc----ceeee-cCCccccCCC
Q 030726 111 SRCSSCKKRVGLT----GFKCR-CGNLYCVSHR 138 (172)
Q Consensus 111 ~rC~~C~kkvgl~----gf~Cr-Cg~~FC~~HR 138 (172)
-+|..|+..+.+. .++|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 4688888877552 47886 7765544444
No 59
>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=33.73 E-value=18 Score=23.33 Aligned_cols=16 Identities=25% Similarity=0.808 Sum_probs=13.9
Q ss_pred eeee-cCCccccCCCCC
Q 030726 125 FKCR-CGNLYCVSHRYS 140 (172)
Q Consensus 125 f~Cr-Cg~~FC~~HRy~ 140 (172)
+.|. |+..||..++-+
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 7898 999999998854
No 60
>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=31.29 E-value=33 Score=24.28 Aligned_cols=24 Identities=33% Similarity=0.805 Sum_probs=16.8
Q ss_pred CCCcccccccccccceee-ecCCcc
Q 030726 110 PSRCSSCKKRVGLTGFKC-RCGNLY 133 (172)
Q Consensus 110 ~~rC~~C~kkvgl~gf~C-rCg~~F 133 (172)
...|..|+|++|...|.= -||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 457999999999865443 255554
No 61
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=31.21 E-value=28 Score=25.60 Aligned_cols=15 Identities=20% Similarity=0.448 Sum_probs=12.1
Q ss_pred CCCCccccccccccc
Q 030726 109 GPSRCSSCKKRVGLT 123 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~ 123 (172)
.+++|..|++++...
T Consensus 32 ~rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWW 46 (92)
T ss_pred CCCcCcCCCCcCccc
Confidence 368999999998864
No 62
>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=30.79 E-value=18 Score=21.60 Aligned_cols=23 Identities=35% Similarity=1.002 Sum_probs=15.2
Q ss_pred CCcccccccccccceeee-cCCccccC
Q 030726 111 SRCSSCKKRVGLTGFKCR-CGNLYCVS 136 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 136 (172)
..|..|+. ..-++|. ||..||++
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 46888887 4568994 99999985
No 63
>PRK07218 replication factor A; Provisional
Probab=29.77 E-value=23 Score=32.94 Aligned_cols=21 Identities=29% Similarity=0.711 Sum_probs=16.3
Q ss_pred CCCcccccccccccceeee-cCCc
Q 030726 110 PSRCSSCKKRVGLTGFKCR-CGNL 132 (172)
Q Consensus 110 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 132 (172)
-.||..|+++|.. +.|+ ||.+
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 4799999999855 6787 6544
No 64
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.65 E-value=23 Score=24.81 Aligned_cols=23 Identities=30% Similarity=0.702 Sum_probs=17.7
Q ss_pred CCCCccccccccccc---ceeee-cCC
Q 030726 109 GPSRCSSCKKRVGLT---GFKCR-CGN 131 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~---gf~Cr-Cg~ 131 (172)
-.--|.-|+.+.-|. .+.|| ||+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcch
Confidence 346799999888884 49999 864
No 65
>PHA00616 hypothetical protein
Probab=28.53 E-value=16 Score=23.95 Aligned_cols=11 Identities=36% Similarity=1.370 Sum_probs=7.7
Q ss_pred eee-ecCCcccc
Q 030726 125 FKC-RCGNLYCV 135 (172)
Q Consensus 125 f~C-rCg~~FC~ 135 (172)
|+| |||.+|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 567 58888863
No 66
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=28.26 E-value=21 Score=35.29 Aligned_cols=50 Identities=26% Similarity=0.704 Sum_probs=32.7
Q ss_pred CCcccccccccccceeee-cCCcc---ccCCCCCCCCCCcccchHHHHHHHHHhCCccc
Q 030726 111 SRCSSCKKRVGLTGFKCR-CGNLY---CVSHRYSDKHNCPFDYRTAARDAIIKANPVIK 165 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~fDyk~~~r~~l~k~Np~v~ 165 (172)
--|..|.+++=.+||+|+ ||+.| |+.| -|. -|. ++ .-.|+.+...+|-|.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~-vp~--~C~-~~-~~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPR-VPT--SCV-NP-DHLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCC-CCC--CCC-Cc-chHhhhhhhcccccc
Confidence 457777888888999999 99876 4443 232 343 33 234667777777654
No 67
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=28.22 E-value=31 Score=21.41 Aligned_cols=29 Identities=17% Similarity=0.500 Sum_probs=19.7
Q ss_pred Ccccccccccc--cceeeecCCccccCCCCC
Q 030726 112 RCSSCKKRVGL--TGFKCRCGNLYCVSHRYS 140 (172)
Q Consensus 112 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 140 (172)
+|..|.++... ..+.=.||++||..+-..
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47788888722 245556999999876543
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=27.67 E-value=34 Score=25.66 Aligned_cols=33 Identities=27% Similarity=0.694 Sum_probs=24.5
Q ss_pred CCCCCCcccccccccc----cc-eeee-cCCccccCCCCC
Q 030726 107 KEGPSRCSSCKKRVGL----TG-FKCR-CGNLYCVSHRYS 140 (172)
Q Consensus 107 ~~~~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~ 140 (172)
+..+-.|..|+++ .+ +| ..|+ ||.+|=+---.|
T Consensus 32 ~~~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 32 QRAKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HhcCCcCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 3456789999987 33 13 8998 999998776655
No 69
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=27.53 E-value=34 Score=24.27 Aligned_cols=26 Identities=27% Similarity=0.540 Sum_probs=10.6
Q ss_pred CCcccccccccccceeeecCCccccC
Q 030726 111 SRCSSCKKRVGLTGFKCRCGNLYCVS 136 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~CrCg~~FC~~ 136 (172)
-||..|.--+..---.=.|+++||+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHH
Confidence 58888886544432334689999985
No 70
>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=25.86 E-value=27 Score=18.31 Aligned_cols=9 Identities=44% Similarity=1.508 Sum_probs=4.4
Q ss_pred eeee-cCCcc
Q 030726 125 FKCR-CGNLY 133 (172)
Q Consensus 125 f~Cr-Cg~~F 133 (172)
|.|. ||..|
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 3454 55544
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=25.63 E-value=27 Score=25.56 Aligned_cols=18 Identities=44% Similarity=0.713 Sum_probs=14.7
Q ss_pred CCCcccccccccccceee
Q 030726 110 PSRCSSCKKRVGLTGFKC 127 (172)
Q Consensus 110 ~~rC~~C~kkvgl~gf~C 127 (172)
--.|..|.+||||=.|+=
T Consensus 19 ~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred eEEccccCcEeeeeeccc
Confidence 457999999999976653
No 72
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=25.60 E-value=47 Score=34.00 Aligned_cols=46 Identities=26% Similarity=0.770 Sum_probs=31.3
Q ss_pred CCCCCCCCCcccccccc--------------cccceeee-cCCccc---------cCCCCC----CCCCCcccc
Q 030726 104 AKPKEGPSRCSSCKKRV--------------GLTGFKCR-CGNLYC---------VSHRYS----DKHNCPFDY 149 (172)
Q Consensus 104 ~~~~~~~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC---------~~HRy~----e~H~C~fDy 149 (172)
..+...+|.|-+|.|-| |-..|+|+ ||.-|- +.||-. -.|.|.+-|
T Consensus 599 ~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 599 ENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 34455689999998754 33369999 999996 345432 567787544
No 73
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=24.90 E-value=27 Score=22.11 Aligned_cols=27 Identities=30% Similarity=0.580 Sum_probs=18.5
Q ss_pred CCcccccccccccceeeecCCccccCC
Q 030726 111 SRCSSCKKRVGLTGFKCRCGNLYCVSH 137 (172)
Q Consensus 111 ~rC~~C~kkvgl~gf~CrCg~~FC~~H 137 (172)
-+|..|++.|...+|.=+=|..||..|
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 577788888877666555566666544
No 74
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.73 E-value=52 Score=22.01 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=17.5
Q ss_pred CCCCcccccccccc--c--ceeee-cCCc
Q 030726 109 GPSRCSSCKKRVGL--T--GFKCR-CGNL 132 (172)
Q Consensus 109 ~~~rC~~C~kkvgl--~--gf~Cr-Cg~~ 132 (172)
+...|..|+.++.- . .|.|. ||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 35679999888776 2 58887 7765
No 75
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.40 E-value=40 Score=20.15 Aligned_cols=14 Identities=29% Similarity=0.914 Sum_probs=7.8
Q ss_pred cceeee-cCCccccC
Q 030726 123 TGFKCR-CGNLYCVS 136 (172)
Q Consensus 123 ~gf~Cr-Cg~~FC~~ 136 (172)
-.|+|. ||..|=..
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 356665 66655433
No 76
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.25 E-value=29 Score=26.31 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=10.1
Q ss_pred ccccceeee-cCCcccc
Q 030726 120 VGLTGFKCR-CGNLYCV 135 (172)
Q Consensus 120 vgl~gf~Cr-Cg~~FC~ 135 (172)
|-+..-.|| ||++|=.
T Consensus 54 Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 54 LLVRPARCKKCGFEFRD 70 (97)
T ss_pred EEecChhhcccCccccc
Confidence 333467777 8877744
No 77
>PRK12366 replication factor A; Reviewed
Probab=23.23 E-value=32 Score=33.45 Aligned_cols=29 Identities=28% Similarity=0.661 Sum_probs=20.7
Q ss_pred CCCccccccccccc--ceeee-cCCccccCCCC
Q 030726 110 PSRCSSCKKRVGLT--GFKCR-CGNLYCVSHRY 139 (172)
Q Consensus 110 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 139 (172)
-.+|..|+|||-.. .|.|. ||.+ =..|||
T Consensus 532 y~aCp~CnkKv~~~~g~~~C~~c~~~-~p~~~~ 563 (637)
T PRK12366 532 LYLCPNCRKRVEEVDGEYICEFCGEV-EPNELL 563 (637)
T ss_pred EecccccCeEeEcCCCcEECCCCCCC-CCcEEE
Confidence 37899999999653 27895 8877 235555
No 78
>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=23.21 E-value=44 Score=23.29 Aligned_cols=14 Identities=36% Similarity=0.888 Sum_probs=11.8
Q ss_pred ceeeecCCc-------cccCC
Q 030726 124 GFKCRCGNL-------YCVSH 137 (172)
Q Consensus 124 gf~CrCg~~-------FC~~H 137 (172)
||.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999988 88887
No 79
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=22.76 E-value=48 Score=22.65 Aligned_cols=13 Identities=23% Similarity=0.940 Sum_probs=11.1
Q ss_pred CCcchhhhHHHHH
Q 030726 31 MNMCSKCYKDIML 43 (172)
Q Consensus 31 ~n~CSkCyr~~~~ 43 (172)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 5799999999854
No 80
>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=22.26 E-value=38 Score=20.35 Aligned_cols=23 Identities=22% Similarity=0.625 Sum_probs=12.4
Q ss_pred cccccccccccceeeecCCcccc
Q 030726 113 CSSCKKRVGLTGFKCRCGNLYCV 135 (172)
Q Consensus 113 C~~C~kkvgl~gf~CrCg~~FC~ 135 (172)
|..|...+.-.-..-.||++||.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~ 23 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCK 23 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEH
T ss_pred CCCCCCcccCcCEECCCCCchhH
Confidence 34454433332244569999985
No 81
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.35 E-value=39 Score=23.13 Aligned_cols=13 Identities=31% Similarity=0.976 Sum_probs=9.0
Q ss_pred ceeee-cCCccccC
Q 030726 124 GFKCR-CGNLYCVS 136 (172)
Q Consensus 124 gf~Cr-Cg~~FC~~ 136 (172)
-++|+ ||++|=..
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 37887 88887443
No 82
>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=21.02 E-value=50 Score=18.47 Aligned_cols=11 Identities=36% Similarity=1.189 Sum_probs=6.6
Q ss_pred cceeee-cCCcc
Q 030726 123 TGFKCR-CGNLY 133 (172)
Q Consensus 123 ~gf~Cr-Cg~~F 133 (172)
..|.|. |+..|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 356675 66655
No 83
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.85 E-value=30 Score=26.62 Aligned_cols=29 Identities=28% Similarity=0.799 Sum_probs=18.1
Q ss_pred CCcc--ccccccccc---ceee-ecCCcc-ccCCCC
Q 030726 111 SRCS--SCKKRVGLT---GFKC-RCGNLY-CVSHRY 139 (172)
Q Consensus 111 ~rC~--~C~kkvgl~---gf~C-rCg~~F-C~~HRy 139 (172)
.-|. .|+|||-.. .+.| +|+..+ =-.+||
T Consensus 19 ~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry 54 (146)
T PF08646_consen 19 PACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRY 54 (146)
T ss_dssp EE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEE
T ss_pred CCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEE
Confidence 3577 999998775 2799 598775 446777
No 84
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=20.40 E-value=83 Score=25.87 Aligned_cols=38 Identities=24% Similarity=0.643 Sum_probs=23.8
Q ss_pred CCCCccccccccccc--------------ceeee-cCCccc---cCCCCCCCCCCc
Q 030726 109 GPSRCSSCKKRVGLT--------------GFKCR-CGNLYC---VSHRYSDKHNCP 146 (172)
Q Consensus 109 ~~~rC~~C~kkvgl~--------------gf~Cr-Cg~~FC---~~HRy~e~H~C~ 146 (172)
.+..|+.|.+.+... .+.|. |+.+|| +..+|.+.++..
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 345688887664432 35564 777665 567887777654
No 85
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=20.34 E-value=44 Score=20.13 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=7.9
Q ss_pred cCCccccCCC
Q 030726 129 CGNLYCVSHR 138 (172)
Q Consensus 129 Cg~~FC~~HR 138 (172)
=|..||+.|.
T Consensus 21 ~g~~fC~~H~ 30 (31)
T PF11722_consen 21 PGSRFCGEHM 30 (31)
T ss_pred CcCCccccCC
Confidence 4778999985
Done!