Query 030772
Match_columns 171
No_of_seqs 149 out of 444
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:20:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173 Predicted Zn-finger pr 100.0 9.6E-47 2.1E-51 305.3 9.3 149 20-171 14-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 1.7E-15 3.8E-20 96.5 2.2 38 112-149 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 4.3E-15 9.4E-20 86.9 1.9 25 21-45 1-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.4 1.9E-14 4.2E-19 84.8 1.1 25 21-45 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 2.7E-11 5.8E-16 78.1 1.1 38 112-150 1-41 (43)
6 COG3582 Predicted nucleic acid 96.4 0.0017 3.7E-08 53.1 1.7 39 111-149 96-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.4 0.0013 2.8E-08 57.0 0.9 40 110-150 9-51 (250)
8 PF01363 FYVE: FYVE zinc finge 94.6 0.016 3.5E-07 39.6 1.2 29 108-136 8-39 (69)
9 KOG3183 Predicted Zn-finger pr 93.2 0.02 4.4E-07 49.7 -0.6 43 103-145 92-138 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.8 0.048 1E-06 35.7 0.9 28 109-136 2-32 (57)
11 smart00064 FYVE Protein presen 92.4 0.072 1.6E-06 36.2 1.4 28 109-136 10-40 (68)
12 KOG4345 NF-kappa B regulator A 91.1 0.1 2.2E-06 51.2 1.3 30 22-51 736-766 (774)
13 KOG1818 Membrane trafficking a 89.7 0.14 2.9E-06 49.8 0.9 45 107-151 163-221 (634)
14 PF10571 UPF0547: Uncharacteri 87.6 0.29 6.4E-06 28.6 1.0 23 110-132 1-24 (26)
15 PF15135 UPF0515: Uncharacteri 81.4 0.79 1.7E-05 40.4 1.4 31 104-134 127-167 (278)
16 PF00130 C1_1: Phorbol esters/ 81.0 0.84 1.8E-05 29.4 1.1 24 108-131 10-37 (53)
17 KOG1729 FYVE finger containing 70.4 1.2 2.6E-05 39.5 -0.4 33 108-141 167-203 (288)
18 PF02148 zf-UBP: Zn-finger in 66.2 3.1 6.6E-05 28.2 1.0 23 112-135 1-24 (63)
19 PF14471 DUF4428: Domain of un 60.3 3 6.4E-05 27.8 0.0 22 111-132 1-30 (51)
20 PHA02768 hypothetical protein; 56.7 4.6 0.0001 27.7 0.5 16 120-135 2-18 (55)
21 smart00109 C1 Protein kinase C 55.1 6.5 0.00014 24.0 1.0 23 108-130 10-35 (49)
22 PF13978 DUF4223: Protein of u 55.0 5.8 0.00013 27.3 0.8 18 132-149 19-36 (56)
23 COG1996 RPC10 DNA-directed RNA 54.7 5 0.00011 27.0 0.4 22 109-130 6-32 (49)
24 KOG1812 Predicted E3 ubiquitin 54.0 6.4 0.00014 36.0 1.1 31 107-137 304-338 (384)
25 cd00029 C1 Protein kinase C co 53.8 6.6 0.00014 24.3 0.9 24 108-131 10-37 (50)
26 PF01194 RNA_pol_N: RNA polyme 52.3 7.1 0.00015 27.3 0.9 13 109-121 4-16 (60)
27 PF11781 RRN7: RNA polymerase 51.3 6.4 0.00014 24.5 0.5 22 110-131 9-34 (36)
28 PRK04016 DNA-directed RNA poly 48.5 6.4 0.00014 27.7 0.2 14 108-121 3-16 (62)
29 PF08882 Acetone_carb_G: Aceto 48.4 9.1 0.0002 29.9 1.0 33 113-147 16-48 (112)
30 PTZ00303 phosphatidylinositol 47.6 9.6 0.00021 39.0 1.3 27 110-136 461-495 (1374)
31 KOG1819 FYVE finger-containing 47.1 5.9 0.00013 38.7 -0.2 30 108-137 900-932 (990)
32 PF05207 zf-CSL: CSL zinc fing 46.8 7.8 0.00017 26.0 0.4 13 121-133 16-28 (55)
33 PLN00032 DNA-directed RNA poly 46.6 7.5 0.00016 28.1 0.3 13 109-121 4-16 (71)
34 PF03604 DNA_RNApol_7kD: DNA d 45.2 10 0.00022 23.2 0.7 20 111-130 2-25 (32)
35 PF02928 zf-C5HC2: C5HC2 zinc 43.0 12 0.00026 24.8 0.8 26 112-137 1-28 (54)
36 PHA00626 hypothetical protein 42.8 12 0.00026 26.1 0.8 22 110-133 12-34 (59)
37 PF07649 C1_3: C1-like domain; 42.7 9.7 0.00021 22.2 0.3 22 111-132 2-25 (30)
38 smart00659 RPOLCX RNA polymera 42.2 12 0.00025 24.3 0.7 20 110-129 3-26 (44)
39 smart00290 ZnF_UBP Ubiquitin C 41.6 8.6 0.00019 24.3 -0.0 24 111-136 1-25 (50)
40 KOG3497 DNA-directed RNA polym 40.5 9.7 0.00021 27.1 0.1 13 109-121 4-16 (69)
41 cd04476 RPA1_DBD_C RPA1_DBD_C: 40.2 13 0.00027 29.3 0.7 32 108-139 33-69 (166)
42 PF02318 FYVE_2: FYVE-type zin 39.9 19 0.00041 27.3 1.6 32 108-139 53-88 (118)
43 PF03107 C1_2: C1 domain; Int 39.4 18 0.0004 21.2 1.2 20 111-130 2-23 (30)
44 COG1571 Predicted DNA-binding 38.7 14 0.0003 34.6 0.9 50 109-158 350-405 (421)
45 PRK08402 replication factor A; 38.5 13 0.00028 33.8 0.6 29 109-138 212-245 (355)
46 PF08073 CHDNT: CHDNT (NUC034) 38.3 9.6 0.00021 26.2 -0.2 20 150-169 21-40 (55)
47 PF07975 C1_4: TFIIH C1-like d 38.0 12 0.00026 25.2 0.3 23 112-134 2-33 (51)
48 KOG1842 FYVE finger-containing 38.0 8.5 0.00018 36.6 -0.6 26 109-134 180-208 (505)
49 KOG2807 RNA polymerase II tran 37.3 20 0.00043 33.0 1.6 29 107-135 328-358 (378)
50 PF13240 zinc_ribbon_2: zinc-r 36.8 19 0.00042 20.2 1.0 20 111-130 1-21 (23)
51 COG1644 RPB10 DNA-directed RNA 35.6 12 0.00027 26.4 0.0 13 109-121 4-16 (63)
52 PRK04136 rpl40e 50S ribosomal 35.0 20 0.00043 24.1 0.9 23 108-130 13-36 (48)
53 PF13717 zinc_ribbon_4: zinc-r 33.0 20 0.00043 22.1 0.6 11 111-121 4-14 (36)
54 PF13842 Tnp_zf-ribbon_2: DDE_ 31.5 35 0.00075 20.6 1.5 26 111-136 2-30 (32)
55 PF15549 PGC7_Stella: PGC7/Ste 31.4 24 0.00052 29.1 1.0 19 123-143 123-141 (160)
56 PF09723 Zn-ribbon_8: Zinc rib 31.3 26 0.00055 22.1 1.0 20 121-140 3-23 (42)
57 PF06750 DiS_P_DiS: Bacterial 30.8 29 0.00063 25.5 1.3 15 108-122 32-46 (92)
58 PRK07218 replication factor A; 29.3 25 0.00054 32.8 0.9 21 109-131 297-318 (423)
59 KOG3507 DNA-directed RNA polym 29.2 23 0.0005 24.9 0.5 23 108-130 19-45 (62)
60 smart00647 IBR In Between Ring 29.1 35 0.00075 21.9 1.3 17 123-139 40-57 (64)
61 PF10367 Vps39_2: Vacuolar sor 28.1 36 0.00077 24.1 1.4 24 109-132 78-102 (109)
62 PF01485 IBR: IBR domain; Int 28.0 27 0.00059 22.4 0.7 29 111-139 20-57 (64)
63 COG1997 RPL43A Ribosomal prote 27.7 31 0.00067 25.9 1.0 34 106-139 32-70 (89)
64 PF04438 zf-HIT: HIT zinc fing 27.6 19 0.00042 21.5 -0.1 23 110-135 3-26 (30)
65 PF10122 Mu-like_Com: Mu-like 27.4 21 0.00046 24.2 0.1 24 109-132 4-34 (51)
66 PRK00398 rpoP DNA-directed RNA 27.0 29 0.00063 22.0 0.7 27 110-136 4-35 (46)
67 KOG0193 Serine/threonine prote 25.6 26 0.00056 34.7 0.3 50 110-164 190-243 (678)
68 PF14835 zf-RING_6: zf-RING of 25.4 38 0.00083 24.1 1.1 27 109-135 7-33 (65)
69 KOG1074 Transcriptional repres 25.3 40 0.00087 34.5 1.6 44 105-148 601-672 (958)
70 PF00096 zf-C2H2: Zinc finger, 24.8 29 0.00063 18.2 0.3 9 124-132 1-10 (23)
71 PRK12366 replication factor A; 24.6 30 0.00065 33.6 0.6 29 109-138 532-563 (637)
72 PF08600 Rsm1: Rsm1-like; Int 23.6 30 0.00065 25.3 0.3 18 109-126 19-36 (91)
73 PF14634 zf-RING_5: zinc-RING 23.6 38 0.00082 21.0 0.7 29 111-139 1-31 (44)
74 PF00412 LIM: LIM domain; Int 23.0 29 0.00064 22.0 0.1 27 110-136 27-53 (58)
75 PF05458 Siva: Cd27 binding pr 21.9 76 0.0016 26.1 2.3 37 109-145 111-165 (175)
76 COG3357 Predicted transcriptio 21.5 35 0.00076 26.0 0.3 13 122-134 57-70 (97)
77 smart00396 ZnF_UBR1 Putative z 20.9 49 0.0011 23.1 0.9 13 124-136 51-70 (71)
78 PTZ00218 40S ribosomal protein 20.5 57 0.0012 22.4 1.1 13 37-49 34-46 (54)
79 smart00834 CxxC_CXXC_SSSS Puta 20.3 46 0.001 19.9 0.6 11 123-133 5-16 (41)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=9.6e-47 Score=305.28 Aligned_cols=149 Identities=46% Similarity=0.900 Sum_probs=104.2
Q ss_pred CccccccCCCCCCCcCCCcchhhhhHHHHhhhcCC-CCCCCcccccccCCcccccCCCCCCcccccCCCCccccccc--c
Q 030772 20 TPIYCANNCGFFGSANTNNLCSKCYKDYLLKQSKN-PNPSPIEEEKNKNKTNIEQNEANPVGGVVENRDPAAQVVVV--D 96 (171)
Q Consensus 20 ~p~lC~ngCGFfGs~at~nlCSkCyr~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~ 96 (171)
.++||+|||||||+|+|+||||+||++++.++++. ..++..+...++.+. +.....+.+...+..... +.+.. .
T Consensus 14 ~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~--s~~~~~~~~~~~~~~~~~-~~~~~~~~ 90 (167)
T KOG3173|consen 14 QDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPR--SVPSRDPPAVSLESTTES-ELKLVSDT 90 (167)
T ss_pred cccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCcc--ccCccccccccccccccc-cccccccC
Confidence 46999999999999999999999999999887665 333322221111001 000011111111111110 11000 0
Q ss_pred CC--CCCCCCCCCCCCcccccccccccccceeecCccccCCcCCCCCCCCCccchHhhHHHHHHhCCcccccccccC
Q 030772 97 EG--ASSENPEKRPANRCSFCRKRIGLTGFKCRCEQTFCSLHRYSDKHNCVFDYKSAGQDAIAKANPVVKADKIEKI 171 (171)
Q Consensus 97 ~~--~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~gr~~l~k~NP~v~~~Kl~kI 171 (171)
+. ..........++||+.|+|||||+||.||||++||+.|||||.|+|+||||.+||+.|+++||+|+++||+||
T Consensus 91 ~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 91 PSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQKI 167 (167)
T ss_pred CcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccccC
Confidence 10 0112344566889999999999999999999999999999999999999999999999999999999999998
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=1.7e-15 Score=96.50 Aligned_cols=38 Identities=61% Similarity=1.388 Sum_probs=36.9
Q ss_pred ccccccccccccceee-cCccccCCcCCCCCCCCCccch
Q 030772 112 CSFCRKRIGLTGFKCR-CEQTFCSLHRYSDKHNCVFDYK 149 (171)
Q Consensus 112 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 149 (171)
|+.|+++++|++|+|+ |+++||..|||||.|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 3
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.52 E-value=4.3e-15 Score=86.91 Aligned_cols=25 Identities=68% Similarity=1.497 Sum_probs=20.8
Q ss_pred ccccccCCCCCCCcCCCcchhhhhH
Q 030772 21 PIYCANNCGFFGSANTNNLCSKCYK 45 (171)
Q Consensus 21 p~lC~ngCGFfGs~at~nlCSkCyr 45 (171)
|++|++|||||||++|+||||+|||
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 5699999999999999999999997
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.45 E-value=1.9e-14 Score=84.83 Aligned_cols=25 Identities=60% Similarity=1.384 Sum_probs=23.3
Q ss_pred ccccc-cCCCCCCCcCCCcchhhhhH
Q 030772 21 PIYCA-NNCGFFGSANTNNLCSKCYK 45 (171)
Q Consensus 21 p~lC~-ngCGFfGs~at~nlCSkCyr 45 (171)
|++|+ +|||||||++|+||||+||+
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=99.09 E-value=2.7e-11 Score=78.10 Aligned_cols=38 Identities=45% Similarity=0.966 Sum_probs=28.2
Q ss_pred ccc--cccccccccceee-cCccccCCcCCCCCCCCCccchH
Q 030772 112 CSF--CRKRIGLTGFKCR-CEQTFCSLHRYSDKHNCVFDYKS 150 (171)
Q Consensus 112 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 150 (171)
|.. |++++. ++|.|+ |+..||..|||||.|+|+++++.
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccC-CCeECCCCCcccCccccCccccCCcchhhc
Confidence 455 999887 799999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.38 E-value=0.0017 Score=53.15 Aligned_cols=39 Identities=28% Similarity=0.461 Sum_probs=30.1
Q ss_pred ccccccccccc--ccceee-cCccccCCcCCCCCCCCCccch
Q 030772 111 RCSFCRKRIGL--TGFKCR-CEQTFCSLHRYSDKHNCVFDYK 149 (171)
Q Consensus 111 rC~~C~kkvgl--~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 149 (171)
+|..|-..++- +.++|- |++.||+.||+++.|+|.+...
T Consensus 96 ~~a~~~~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 96 RCATPQCTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred eeecceeccCCccccccccCCCCcceeceecccccccccHHH
Confidence 56544444333 358898 9999999999999999998854
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.35 E-value=0.0013 Score=56.99 Aligned_cols=40 Identities=33% Similarity=0.894 Sum_probs=35.2
Q ss_pred Cccc--ccccccccccceee-cCccccCCcCCCCCCCCCccchH
Q 030772 110 NRCS--FCRKRIGLTGFKCR-CEQTFCSLHRYSDKHNCVFDYKS 150 (171)
Q Consensus 110 ~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 150 (171)
..|. .|+. |.++.|+|- |+.+||..||--+.|+|.+.|..
T Consensus 9 kHCs~~~Ckq-lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCKQ-LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhhh-ccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4677 7776 799999999 99999999999999999988763
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=94.61 E-value=0.016 Score=39.55 Aligned_cols=29 Identities=34% Similarity=0.828 Sum_probs=17.7
Q ss_pred CCCcccccccccccc--cceee-cCccccCCc
Q 030772 108 PANRCSFCRKRIGLT--GFKCR-CEQTFCSLH 136 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 136 (171)
....|..|+++.+|+ -..|| ||.+||+.+
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 358999999999997 49999 999999754
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=93.20 E-value=0.02 Score=49.68 Aligned_cols=43 Identities=33% Similarity=0.753 Sum_probs=36.1
Q ss_pred CCCCCCCCccc--ccccccccc-cceee-cCccccCCcCCCCCCCCC
Q 030772 103 NPEKRPANRCS--FCRKRIGLT-GFKCR-CEQTFCSLHRYSDKHNCV 145 (171)
Q Consensus 103 ~~~~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~ 145 (171)
...+...++|. .|++++-|. .+.|+ ||..||-+||++-.|.|.
T Consensus 92 ~~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 92 KKRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred hhcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 33455667787 788988775 69999 999999999999999998
No 10
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=92.84 E-value=0.048 Score=35.69 Aligned_cols=28 Identities=43% Similarity=0.854 Sum_probs=24.0
Q ss_pred CCcccccccccccc--cceee-cCccccCCc
Q 030772 109 ANRCSFCRKRIGLT--GFKCR-CEQTFCSLH 136 (171)
Q Consensus 109 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 136 (171)
...|..|+++++++ ...|| ||.+||..+
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHH
Confidence 36799999999996 69999 999999754
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=91.06 E-value=0.1 Score=51.23 Aligned_cols=30 Identities=40% Similarity=0.943 Sum_probs=26.7
Q ss_pred ccc-ccCCCCCCCcCCCcchhhhhHHHHhhh
Q 030772 22 IYC-ANNCGFFGSANTNNLCSKCYKDYLLKQ 51 (171)
Q Consensus 22 ~lC-~ngCGFfGs~at~nlCSkCyr~~~~~~ 51 (171)
.+| .-+|.|||++.|+++||-|||+.+..-
T Consensus 736 ~rck~~nc~~Yg~~~~~~~c~~c~r~el~~~ 766 (774)
T KOG4345|consen 736 MRCKWPNCDHYGRAETNGYCSECYREELRRG 766 (774)
T ss_pred hHhhcccchhhccccccccchhhhhHHHhcc
Confidence 478 679999999999999999999998654
No 13
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=89.70 E-value=0.14 Score=49.83 Aligned_cols=45 Identities=31% Similarity=0.628 Sum_probs=35.5
Q ss_pred CCCCccccccccccccc--ceee-cCccccCCcC-----------CCCCCCCCccchHh
Q 030772 107 RPANRCSFCRKRIGLTG--FKCR-CEQTFCSLHR-----------YSDKHNCVFDYKSA 151 (171)
Q Consensus 107 ~~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~ 151 (171)
.....|..|+.+.|+++ ..|| ||.+||+.|= |-+.--|.-||...
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l 221 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELL 221 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHh
Confidence 34689999999999985 8999 9999999874 34556677776543
No 14
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.60 E-value=0.29 Score=28.62 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=20.6
Q ss_pred Ccccccccccccccceee-cCccc
Q 030772 110 NRCSFCRKRIGLTGFKCR-CEQTF 132 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~~F 132 (171)
.+|-.|++.|.+..-.|- ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 368999999999999999 99887
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=81.38 E-value=0.79 Score=40.40 Aligned_cols=31 Identities=39% Similarity=1.074 Sum_probs=24.5
Q ss_pred CCCCCCCcccccccc---------ccccccee-ecCccccC
Q 030772 104 PEKRPANRCSFCRKR---------IGLTGFKC-RCEQTFCS 134 (171)
Q Consensus 104 ~~~~~~~rC~~C~kk---------vgl~gf~C-rCg~~FC~ 134 (171)
+..+..+||..|+|| .||.-|.| .|+++|=+
T Consensus 127 p~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 127 PQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred CcccccccccccccccCCCccccccceeeeecccccccchh
Confidence 334567999999988 67778999 59999854
No 16
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=80.99 E-value=0.84 Score=29.38 Aligned_cols=24 Identities=33% Similarity=0.892 Sum_probs=18.5
Q ss_pred CCCccccccccc---ccccceee-cCcc
Q 030772 108 PANRCSFCRKRI---GLTGFKCR-CEQT 131 (171)
Q Consensus 108 ~~~rC~~C~kkv---gl~gf~Cr-Cg~~ 131 (171)
.+..|..|++.| ++.|++|+ |+.+
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 468999999999 56799999 7654
No 17
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=70.39 E-value=1.2 Score=39.47 Aligned_cols=33 Identities=24% Similarity=0.661 Sum_probs=27.3
Q ss_pred CCCccccccc-ccccc--cceee-cCccccCCcCCCCC
Q 030772 108 PANRCSFCRK-RIGLT--GFKCR-CEQTFCSLHRYSDK 141 (171)
Q Consensus 108 ~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e~ 141 (171)
..++|..|.+ .-.|+ --.|| ||.+||. |.-..+
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 4699999999 88886 48899 9999999 876543
No 18
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=66.21 E-value=3.1 Score=28.20 Aligned_cols=23 Identities=26% Similarity=0.622 Sum_probs=15.1
Q ss_pred ccccccccccccceee-cCccccCC
Q 030772 112 CSFCRKRIGLTGFKCR-CEQTFCSL 135 (171)
Q Consensus 112 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 135 (171)
|..|+.. +-.-+.|- ||.++|+.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5667755 44457787 99999994
No 19
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=60.28 E-value=3 Score=27.84 Aligned_cols=22 Identities=41% Similarity=1.228 Sum_probs=16.8
Q ss_pred cccccccccccc-------cceee-cCccc
Q 030772 111 RCSFCRKRIGLT-------GFKCR-CEQTF 132 (171)
Q Consensus 111 rC~~C~kkvgl~-------gf~Cr-Cg~~F 132 (171)
+|..|++++||+ ||.|. |-.-.
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 57787 64433
No 20
>PHA02768 hypothetical protein; Provisional
Probab=56.69 E-value=4.6 Score=27.69 Aligned_cols=16 Identities=25% Similarity=0.841 Sum_probs=12.6
Q ss_pred ccccceee-cCccccCC
Q 030772 120 GLTGFKCR-CEQTFCSL 135 (171)
Q Consensus 120 gl~gf~Cr-Cg~~FC~~ 135 (171)
.|+||.|- ||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 57899998 98888653
No 21
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=55.13 E-value=6.5 Score=24.03 Aligned_cols=23 Identities=35% Similarity=0.937 Sum_probs=18.4
Q ss_pred CCCcccccccccccc--cceee-cCc
Q 030772 108 PANRCSFCRKRIGLT--GFKCR-CEQ 130 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~--gf~Cr-Cg~ 130 (171)
.+..|..|++.|... |++|+ |+.
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCc
Confidence 467899999999873 88888 654
No 22
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=54.97 E-value=5.8 Score=27.28 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=16.2
Q ss_pred ccCCcCCCCCCCCCccch
Q 030772 132 FCSLHRYSDKHNCVFDYK 149 (171)
Q Consensus 132 FC~~HRy~e~H~C~fDyk 149 (171)
-|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999996
No 23
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=54.67 E-value=5 Score=26.99 Aligned_cols=22 Identities=27% Similarity=0.945 Sum_probs=17.6
Q ss_pred CCcccccccccccc----cceee-cCc
Q 030772 109 ANRCSFCRKRIGLT----GFKCR-CEQ 130 (171)
Q Consensus 109 ~~rC~~C~kkvgl~----gf~Cr-Cg~ 130 (171)
.-+|..|++++.|. +..|. ||+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 46899999999854 79998 754
No 24
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.96 E-value=6.4 Score=35.95 Aligned_cols=31 Identities=32% Similarity=0.860 Sum_probs=25.7
Q ss_pred CCCCcccccccccccc-c---ceeecCccccCCcC
Q 030772 107 RPANRCSFCRKRIGLT-G---FKCRCEQTFCSLHR 137 (171)
Q Consensus 107 ~~~~rC~~C~kkvgl~-g---f~CrCg~~FC~~HR 137 (171)
+.-.+|..|+--+.|. | ++||||+.||-.=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 3468999999999996 3 99999999996654
No 25
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=53.77 E-value=6.6 Score=24.31 Aligned_cols=24 Identities=33% Similarity=0.802 Sum_probs=19.2
Q ss_pred CCCccccccccccc---ccceee-cCcc
Q 030772 108 PANRCSFCRKRIGL---TGFKCR-CEQT 131 (171)
Q Consensus 108 ~~~rC~~C~kkvgl---~gf~Cr-Cg~~ 131 (171)
.+..|..|++.|.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 36789999999985 689998 7544
No 26
>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=52.30 E-value=7.1 Score=27.28 Aligned_cols=13 Identities=46% Similarity=0.733 Sum_probs=10.2
Q ss_pred CCccccccccccc
Q 030772 109 ANRCSFCRKRIGL 121 (171)
Q Consensus 109 ~~rC~~C~kkvgl 121 (171)
|-||++|+|-||-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6899999998874
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=51.31 E-value=6.4 Score=24.49 Aligned_cols=22 Identities=32% Similarity=0.901 Sum_probs=17.6
Q ss_pred Ccccccccccccc--c-cee-ecCcc
Q 030772 110 NRCSFCRKRIGLT--G-FKC-RCEQT 131 (171)
Q Consensus 110 ~rC~~C~kkvgl~--g-f~C-rCg~~ 131 (171)
-+|..|+-+...+ | |.| +||.+
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 79875
No 28
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=48.55 E-value=6.4 Score=27.69 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=11.6
Q ss_pred CCCccccccccccc
Q 030772 108 PANRCSFCRKRIGL 121 (171)
Q Consensus 108 ~~~rC~~C~kkvgl 121 (171)
.|-||++|+|-||-
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 36899999998864
No 29
>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=48.37 E-value=9.1 Score=29.86 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=24.2
Q ss_pred cccccccccccceeecCccccCCcCCCCCCCCCcc
Q 030772 113 SFCRKRIGLTGFKCRCEQTFCSLHRYSDKHNCVFD 147 (171)
Q Consensus 113 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fD 147 (171)
+.|+++- .-.+|+||+.||+-+.-=..|.--++
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEe
Confidence 5566654 26899999999998887777765544
No 30
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=47.57 E-value=9.6 Score=39.01 Aligned_cols=27 Identities=22% Similarity=0.703 Sum_probs=21.1
Q ss_pred Cccccccccccc-------ccceee-cCccccCCc
Q 030772 110 NRCSFCRKRIGL-------TGFKCR-CEQTFCSLH 136 (171)
Q Consensus 110 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 136 (171)
..|..|+++-+. .-..|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 579999999863 246699 999998643
No 31
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=47.14 E-value=5.9 Score=38.67 Aligned_cols=30 Identities=27% Similarity=0.675 Sum_probs=22.7
Q ss_pred CCCcccccccccccc--cceee-cCccccCCcC
Q 030772 108 PANRCSFCRKRIGLT--GFKCR-CEQTFCSLHR 137 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 137 (171)
+.-+|..|....... -..|| ||++||++--
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs 932 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCS 932 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeecccc
Confidence 457899998765543 47899 9999998643
No 32
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=46.84 E-value=7.8 Score=26.05 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.4
Q ss_pred cccceeecCcccc
Q 030772 121 LTGFKCRCEQTFC 133 (171)
Q Consensus 121 l~gf~CrCg~~FC 133 (171)
...+.||||..|-
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 33
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=46.58 E-value=7.5 Score=28.06 Aligned_cols=13 Identities=46% Similarity=0.733 Sum_probs=11.2
Q ss_pred CCccccccccccc
Q 030772 109 ANRCSFCRKRIGL 121 (171)
Q Consensus 109 ~~rC~~C~kkvgl 121 (171)
|-||++|+|-||-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6899999998764
No 34
>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=45.20 E-value=10 Score=23.15 Aligned_cols=20 Identities=25% Similarity=0.785 Sum_probs=11.6
Q ss_pred cccccccccccc---cceee-cCc
Q 030772 111 RCSFCRKRIGLT---GFKCR-CEQ 130 (171)
Q Consensus 111 rC~~C~kkvgl~---gf~Cr-Cg~ 130 (171)
.|..|+..+.|. ..+|+ ||+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 366777777764 46777 653
No 35
>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=43.02 E-value=12 Score=24.84 Aligned_cols=26 Identities=31% Similarity=0.865 Sum_probs=22.5
Q ss_pred ccccccccccccceeec--CccccCCcC
Q 030772 112 CSFCRKRIGLTGFKCRC--EQTFCSLHR 137 (171)
Q Consensus 112 C~~C~kkvgl~gf~CrC--g~~FC~~HR 137 (171)
|..|+.-.=|..+.|.| +.++|-.|-
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 36
>PHA00626 hypothetical protein
Probab=42.84 E-value=12 Score=26.11 Aligned_cols=22 Identities=14% Similarity=0.221 Sum_probs=14.3
Q ss_pred Ccccccccccccccceee-cCcccc
Q 030772 110 NRCSFCRKRIGLTGFKCR-CEQTFC 133 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~~FC 133 (171)
.||.+|++-. .-|+|. ||+.|-
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft 34 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDS 34 (59)
T ss_pred eeeceecccC--cceEcCCCCCeec
Confidence 4777777632 248887 877764
No 37
>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=42.73 E-value=9.7 Score=22.17 Aligned_cols=22 Identities=32% Similarity=0.771 Sum_probs=8.7
Q ss_pred ccccccccccc-ccceee-cCccc
Q 030772 111 RCSFCRKRIGL-TGFKCR-CEQTF 132 (171)
Q Consensus 111 rC~~C~kkvgl-~gf~Cr-Cg~~F 132 (171)
+|..|++.+.. ..|.|. |...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 68999999888 789998 76553
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.25 E-value=12 Score=24.28 Aligned_cols=20 Identities=25% Similarity=0.725 Sum_probs=14.9
Q ss_pred Ccccccccccccc---cceee-cC
Q 030772 110 NRCSFCRKRIGLT---GFKCR-CE 129 (171)
Q Consensus 110 ~rC~~C~kkvgl~---gf~Cr-Cg 129 (171)
-+|..|+..+.+. +.+|+ ||
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCC
Confidence 4688898888885 57776 64
No 39
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=41.63 E-value=8.6 Score=24.30 Aligned_cols=24 Identities=33% Similarity=0.646 Sum_probs=17.4
Q ss_pred cccccccccccccceee-cCccccCCc
Q 030772 111 RCSFCRKRIGLTGFKCR-CEQTFCSLH 136 (171)
Q Consensus 111 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 136 (171)
||..|..... -+.|- |+.++|+..
T Consensus 1 ~C~~C~~~~~--l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN--LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC--eEEecCCCCcccCCC
Confidence 6888886544 35666 999999764
No 40
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=40.54 E-value=9.7 Score=27.09 Aligned_cols=13 Identities=46% Similarity=0.692 Sum_probs=11.1
Q ss_pred CCccccccccccc
Q 030772 109 ANRCSFCRKRIGL 121 (171)
Q Consensus 109 ~~rC~~C~kkvgl 121 (171)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998874
No 41
>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=40.23 E-value=13 Score=29.27 Aligned_cols=32 Identities=25% Similarity=0.612 Sum_probs=23.1
Q ss_pred CCCccccccccccccc---ceee-cCccc-cCCcCCC
Q 030772 108 PANRCSFCRKRIGLTG---FKCR-CEQTF-CSLHRYS 139 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~g---f~Cr-Cg~~F-C~~HRy~ 139 (171)
.=..|..|+|||-..+ |.|. |+..+ =..+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 3467889999998753 8887 77665 4566774
No 42
>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=39.87 E-value=19 Score=27.26 Aligned_cols=32 Identities=25% Similarity=0.615 Sum_probs=24.7
Q ss_pred CCCcccccccccccc---cceee-cCccccCCcCCC
Q 030772 108 PANRCSFCRKRIGLT---GFKCR-CEQTFCSLHRYS 139 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 139 (171)
....|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 457999999999986 68999 999999876653
No 43
>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=39.38 E-value=18 Score=21.15 Aligned_cols=20 Identities=30% Similarity=0.788 Sum_probs=16.3
Q ss_pred cccccccccccc-cceee-cCc
Q 030772 111 RCSFCRKRIGLT-GFKCR-CEQ 130 (171)
Q Consensus 111 rC~~C~kkvgl~-gf~Cr-Cg~ 130 (171)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 488999999888 89997 653
No 44
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.75 E-value=14 Score=34.64 Aligned_cols=50 Identities=16% Similarity=0.353 Sum_probs=29.6
Q ss_pred CCcccccccccccc---cceee-cCccccCCcCCCCCCCC--CccchHhhHHHHHH
Q 030772 109 ANRCSFCRKRIGLT---GFKCR-CEQTFCSLHRYSDKHNC--VFDYKSAGQDAIAK 158 (171)
Q Consensus 109 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~e~H~C--~fDyk~~gr~~l~k 158 (171)
.-+|..|++++.-. ||+|+ ||..+=..-+-.=.++= .+++-..+|..|.|
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk 405 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK 405 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC
Confidence 35999999987654 79999 98766443222111111 13344556666654
No 45
>PRK08402 replication factor A; Reviewed
Probab=38.54 E-value=13 Score=33.84 Aligned_cols=29 Identities=14% Similarity=0.402 Sum_probs=18.8
Q ss_pred CCccccccccccc----ccceee-cCccccCCcCC
Q 030772 109 ANRCSFCRKRIGL----TGFKCR-CEQTFCSLHRY 138 (171)
Q Consensus 109 ~~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 138 (171)
-.+|..|+|||-. -.+.|. ||.+-+ .|||
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 3799999999963 246676 554333 4554
No 46
>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=38.27 E-value=9.6 Score=26.21 Aligned_cols=20 Identities=30% Similarity=0.326 Sum_probs=16.3
Q ss_pred HhhHHHHHHhCCcccccccc
Q 030772 150 SAGQDAIAKANPVVKADKIE 169 (171)
Q Consensus 150 ~~gr~~l~k~NP~v~~~Kl~ 169 (171)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34478899999999888874
No 47
>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=38.04 E-value=12 Score=25.18 Aligned_cols=23 Identities=30% Similarity=0.873 Sum_probs=11.5
Q ss_pred ccccccccccc--------cceee-cCccccC
Q 030772 112 CSFCRKRIGLT--------GFKCR-CEQTFCS 134 (171)
Q Consensus 112 C~~C~kkvgl~--------gf~Cr-Cg~~FC~ 134 (171)
|+.|.+.+.-. .|.|. |+..||.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCI 33 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-H
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCcccc
Confidence 66666666653 48887 9999984
No 48
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=37.99 E-value=8.5 Score=36.59 Aligned_cols=26 Identities=35% Similarity=0.922 Sum_probs=22.6
Q ss_pred CCcccccccccccc--cceee-cCccccC
Q 030772 109 ANRCSFCRKRIGLT--GFKCR-CEQTFCS 134 (171)
Q Consensus 109 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 134 (171)
..-|..|.++.||+ -..|| ||.+.|.
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchHHHH
Confidence 36799999999997 59999 9999883
No 49
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=37.29 E-value=20 Score=33.02 Aligned_cols=29 Identities=21% Similarity=0.659 Sum_probs=23.2
Q ss_pred CCCCccccc-ccccccccceee-cCccccCC
Q 030772 107 RPANRCSFC-RKRIGLTGFKCR-CEQTFCSL 135 (171)
Q Consensus 107 ~~~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 135 (171)
...++|+.| .+.++-..|.|. |-++||..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeecc
Confidence 356789999 555666689999 99999963
No 50
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=36.83 E-value=19 Score=20.18 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=11.1
Q ss_pred cccccccccccccceee-cCc
Q 030772 111 RCSFCRKRIGLTGFKCR-CEQ 130 (171)
Q Consensus 111 rC~~C~kkvgl~gf~Cr-Cg~ 130 (171)
+|..|+++|.-..-.|. ||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 36666666655544455 443
No 51
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=35.60 E-value=12 Score=26.40 Aligned_cols=13 Identities=46% Similarity=0.746 Sum_probs=10.9
Q ss_pred CCccccccccccc
Q 030772 109 ANRCSFCRKRIGL 121 (171)
Q Consensus 109 ~~rC~~C~kkvgl 121 (171)
|-||++|+|-||-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6899999998764
No 52
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=34.99 E-value=20 Score=24.13 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=19.7
Q ss_pred CCCcccccccccccccceee-cCc
Q 030772 108 PANRCSFCRKRIGLTGFKCR-CEQ 130 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~gf~Cr-Cg~ 130 (171)
++.-|..|+-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 45779999999999999999 775
No 53
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=33.04 E-value=20 Score=22.08 Aligned_cols=11 Identities=18% Similarity=0.764 Sum_probs=5.6
Q ss_pred ccccccccccc
Q 030772 111 RCSFCRKRIGL 121 (171)
Q Consensus 111 rC~~C~kkvgl 121 (171)
+|..|+++..+
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 45555555444
No 54
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=31.51 E-value=35 Score=20.57 Aligned_cols=26 Identities=31% Similarity=0.850 Sum_probs=18.5
Q ss_pred cccccccccc-c-ccceee-cCccccCCc
Q 030772 111 RCSFCRKRIG-L-TGFKCR-CEQTFCSLH 136 (171)
Q Consensus 111 rC~~C~kkvg-l-~gf~Cr-Cg~~FC~~H 136 (171)
||..|.++-- - |.|.|. |+-.+|..|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 6777776422 2 679998 887777766
No 55
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=31.42 E-value=24 Score=29.10 Aligned_cols=19 Identities=37% Similarity=1.085 Sum_probs=15.2
Q ss_pred cceeecCccccCCcCCCCCCC
Q 030772 123 GFKCRCEQTFCSLHRYSDKHN 143 (171)
Q Consensus 123 gf~CrCg~~FC~~HRy~e~H~ 143 (171)
-|+|.| .||-.||.|.+-+
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 56
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.35 E-value=26 Score=22.07 Aligned_cols=20 Identities=25% Similarity=0.730 Sum_probs=16.2
Q ss_pred cccceee-cCccccCCcCCCC
Q 030772 121 LTGFKCR-CEQTFCSLHRYSD 140 (171)
Q Consensus 121 l~gf~Cr-Cg~~FC~~HRy~e 140 (171)
+-.|+|. ||..|=-.+.+.+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4568999 9999988887776
No 57
>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=30.78 E-value=29 Score=25.49 Aligned_cols=15 Identities=20% Similarity=0.656 Sum_probs=12.2
Q ss_pred CCCcccccccccccc
Q 030772 108 PANRCSFCRKRIGLT 122 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~ 122 (171)
.+++|..|++++...
T Consensus 32 ~rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWW 46 (92)
T ss_pred CCCcCcCCCCcCccc
Confidence 368999999998764
No 58
>PRK07218 replication factor A; Provisional
Probab=29.31 E-value=25 Score=32.79 Aligned_cols=21 Identities=29% Similarity=0.558 Sum_probs=16.1
Q ss_pred CCcccccccccccccceee-cCcc
Q 030772 109 ANRCSFCRKRIGLTGFKCR-CEQT 131 (171)
Q Consensus 109 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 131 (171)
-.||..|+++|.. +.|+ ||.+
T Consensus 297 i~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred eecCcCccccccC--CcCCCCCCc
Confidence 4899999999855 7787 5543
No 59
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.19 E-value=23 Score=24.92 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=18.2
Q ss_pred CCCcccccccccccc---cceee-cCc
Q 030772 108 PANRCSFCRKRIGLT---GFKCR-CEQ 130 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~---gf~Cr-Cg~ 130 (171)
-.--|..|+.+..|. .+.|| ||+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcch
Confidence 357899999998884 49999 864
No 60
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=29.07 E-value=35 Score=21.95 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=14.5
Q ss_pred ccee-ecCccccCCcCCC
Q 030772 123 GFKC-RCEQTFCSLHRYS 139 (171)
Q Consensus 123 gf~C-rCg~~FC~~HRy~ 139 (171)
...| .||..||-.++.+
T Consensus 40 ~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred eeECCCCCCeECCCCCCc
Confidence 5889 7999999988865
No 61
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=28.09 E-value=36 Score=24.06 Aligned_cols=24 Identities=29% Similarity=0.689 Sum_probs=16.5
Q ss_pred CCcccccccccccccceee-cCccc
Q 030772 109 ANRCSFCRKRIGLTGFKCR-CEQTF 132 (171)
Q Consensus 109 ~~rC~~C~kkvgl~gf~Cr-Cg~~F 132 (171)
...|..|+|++|...|.=- ||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 4779999999998644322 45444
No 62
>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=28.04 E-value=27 Score=22.41 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=17.0
Q ss_pred cccc--cccccccc----c--ceee-cCccccCCcCCC
Q 030772 111 RCSF--CRKRIGLT----G--FKCR-CEQTFCSLHRYS 139 (171)
Q Consensus 111 rC~~--C~kkvgl~----g--f~Cr-Cg~~FC~~HRy~ 139 (171)
.|.. |..-+... . +.|. |+..||..++-+
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 5544 65544442 2 7899 999999998854
No 63
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=27.66 E-value=31 Score=25.94 Aligned_cols=34 Identities=32% Similarity=0.719 Sum_probs=25.0
Q ss_pred CCCCCccccccccccc---cc-ceee-cCccccCCcCCC
Q 030772 106 KRPANRCSFCRKRIGL---TG-FKCR-CEQTFCSLHRYS 139 (171)
Q Consensus 106 ~~~~~rC~~C~kkvgl---~g-f~Cr-Cg~~FC~~HRy~ 139 (171)
+..+-.|..|+++.-. +| ..|+ ||++|=+---.|
T Consensus 32 ~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 32 QRAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HhcCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccc
Confidence 4557899999987222 13 8999 999998776655
No 64
>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=27.58 E-value=19 Score=21.47 Aligned_cols=23 Identities=35% Similarity=1.048 Sum_probs=15.1
Q ss_pred Ccccccccccccccceee-cCccccCC
Q 030772 110 NRCSFCRKRIGLTGFKCR-CEQTFCSL 135 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 135 (171)
..|..|+. ..-++|. |+..||+.
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 46788877 4568887 99889985
No 65
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=27.37 E-value=21 Score=24.23 Aligned_cols=24 Identities=29% Similarity=0.713 Sum_probs=17.4
Q ss_pred CCcccccccccccc------cceee-cCccc
Q 030772 109 ANRCSFCRKRIGLT------GFKCR-CEQTF 132 (171)
Q Consensus 109 ~~rC~~C~kkvgl~------gf~Cr-Cg~~F 132 (171)
.-||..|+|.|... ..+|- ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 46999999988774 36674 76553
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.05 E-value=29 Score=21.95 Aligned_cols=27 Identities=22% Similarity=0.672 Sum_probs=17.3
Q ss_pred Ccccccccccccc----cceee-cCccccCCc
Q 030772 110 NRCSFCRKRIGLT----GFKCR-CEQTFCSLH 136 (171)
Q Consensus 110 ~rC~~C~kkvgl~----gf~Cr-Cg~~FC~~H 136 (171)
-+|..|+..+.+. .+.|. ||..+--.+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 5788888877553 47787 665444333
No 67
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=25.55 E-value=26 Score=34.69 Aligned_cols=50 Identities=28% Similarity=0.620 Sum_probs=32.8
Q ss_pred Ccccccccccccccceee-cCccc---cCCcCCCCCCCCCccchHhhHHHHHHhCCccc
Q 030772 110 NRCSFCRKRIGLTGFKCR-CEQTF---CSLHRYSDKHNCVFDYKSAGQDAIAKANPVVK 164 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~fDyk~~gr~~l~k~NP~v~ 164 (171)
--|..|.+++=.+||+|+ |++.| |+.|= | -.|. +|. -.|+.+...+|-+.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~v-p--~~C~-~~~-~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRV-P--TSCV-NPD-HLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCC-C--CCCC-Ccc-hHhhhhhhcccccc
Confidence 457777888888999999 99866 55443 2 2343 332 34566777777664
No 68
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=25.42 E-value=38 Score=24.05 Aligned_cols=27 Identities=33% Similarity=0.565 Sum_probs=11.2
Q ss_pred CCcccccccccccccceeecCccccCC
Q 030772 109 ANRCSFCRKRIGLTGFKCRCEQTFCSL 135 (171)
Q Consensus 109 ~~rC~~C~kkvgl~gf~CrCg~~FC~~ 135 (171)
--||..|.--+..---.-.|+++||+.
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHH
Confidence 368888887654433344688999985
No 69
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=25.34 E-value=40 Score=34.54 Aligned_cols=44 Identities=23% Similarity=0.702 Sum_probs=30.4
Q ss_pred CCCCCCcccccccccc--------------cccceee-cCccccC---------CcCC----CCCCCCCccc
Q 030772 105 EKRPANRCSFCRKRIG--------------LTGFKCR-CEQTFCS---------LHRY----SDKHNCVFDY 148 (171)
Q Consensus 105 ~~~~~~rC~~C~kkvg--------------l~gf~Cr-Cg~~FC~---------~HRy----~e~H~C~fDy 148 (171)
+...+|.|-.|.|-|. -..|+|+ ||.-|-- .||- --.|.|.+-|
T Consensus 601 ~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 601 KRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 3457899999987543 3369999 9999963 3443 2567787544
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=24.79 E-value=29 Score=18.23 Aligned_cols=9 Identities=44% Similarity=1.464 Sum_probs=4.4
Q ss_pred ceee-cCccc
Q 030772 124 FKCR-CEQTF 132 (171)
Q Consensus 124 f~Cr-Cg~~F 132 (171)
|.|. ||..|
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 55555
No 71
>PRK12366 replication factor A; Reviewed
Probab=24.65 E-value=30 Score=33.63 Aligned_cols=29 Identities=24% Similarity=0.537 Sum_probs=21.1
Q ss_pred CCcccccccccccc--cceee-cCccccCCcCC
Q 030772 109 ANRCSFCRKRIGLT--GFKCR-CEQTFCSLHRY 138 (171)
Q Consensus 109 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 138 (171)
-.+|..|+|||-.. .|.|. ||.+ =..|||
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 48999999999653 27896 8877 335665
No 72
>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=23.64 E-value=30 Score=25.31 Aligned_cols=18 Identities=44% Similarity=0.866 Sum_probs=14.9
Q ss_pred CCccccccccccccccee
Q 030772 109 ANRCSFCRKRIGLTGFKC 126 (171)
Q Consensus 109 ~~rC~~C~kkvgl~gf~C 126 (171)
--.|..|.+||||=.|+=
T Consensus 19 ~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred eEEccccCcEeeeeeccc
Confidence 578999999999976653
No 73
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=23.60 E-value=38 Score=21.04 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=19.8
Q ss_pred ccccccccccc--ccceeecCccccCCcCCC
Q 030772 111 RCSFCRKRIGL--TGFKCRCEQTFCSLHRYS 139 (171)
Q Consensus 111 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 139 (171)
+|..|.+++.- ..+.=.||.+||..+-..
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47778888722 245556999999876543
No 74
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=23.02 E-value=29 Score=21.96 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=18.2
Q ss_pred CcccccccccccccceeecCccccCCc
Q 030772 110 NRCSFCRKRIGLTGFKCRCEQTFCSLH 136 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~CrCg~~FC~~H 136 (171)
-+|..|++.|...+|.=.=|..||..|
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 577788888877665555556666544
No 75
>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=21.86 E-value=76 Score=26.13 Aligned_cols=37 Identities=32% Similarity=0.730 Sum_probs=22.7
Q ss_pred CCcccccccccccc--------------cceee-cCcccc---CCcCCCCCCCCC
Q 030772 109 ANRCSFCRKRIGLT--------------GFKCR-CEQTFC---SLHRYSDKHNCV 145 (171)
Q Consensus 109 ~~rC~~C~kkvgl~--------------gf~Cr-Cg~~FC---~~HRy~e~H~C~ 145 (171)
+..|+.|.+.+... .+.|. |+.+|| +..+|.+.++..
T Consensus 111 ~~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~y~~~~e~~ 165 (175)
T PF05458_consen 111 SRACSVCQRTQRIKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVNYSDQYERV 165 (175)
T ss_pred CccCcCCcCCCCCCccccccCcHHHHHHHhhhhchhhhhhcCccccccCCccccc
Confidence 44577776554332 45566 777665 567887777654
No 76
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=21.54 E-value=35 Score=25.99 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=8.5
Q ss_pred ccceee-cCccccC
Q 030772 122 TGFKCR-CEQTFCS 134 (171)
Q Consensus 122 ~gf~Cr-Cg~~FC~ 134 (171)
..-.|| ||+.|=.
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 356677 7777744
No 77
>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=20.92 E-value=49 Score=23.09 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=11.2
Q ss_pred ceeecCcc-------ccCCc
Q 030772 124 FKCRCEQT-------FCSLH 136 (171)
Q Consensus 124 f~CrCg~~-------FC~~H 136 (171)
+.|-||.. ||..|
T Consensus 51 ~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 51 GICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred EEECCCChhccCCCcccccc
Confidence 88999987 88887
No 78
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.50 E-value=57 Score=22.37 Aligned_cols=13 Identities=23% Similarity=0.820 Sum_probs=11.1
Q ss_pred CcchhhhhHHHHh
Q 030772 37 NNLCSKCYKDYLL 49 (171)
Q Consensus 37 ~nlCSkCyr~~~~ 49 (171)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 5799999999853
No 79
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.29 E-value=46 Score=19.87 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=6.2
Q ss_pred cceee-cCcccc
Q 030772 123 GFKCR-CEQTFC 133 (171)
Q Consensus 123 gf~Cr-Cg~~FC 133 (171)
.|+|. ||..|=
T Consensus 5 ~y~C~~Cg~~fe 16 (41)
T smart00834 5 EYRCEDCGHTFE 16 (41)
T ss_pred EEEcCCCCCEEE
Confidence 45666 666553
Done!