Query 030810
Match_columns 171
No_of_seqs 150 out of 441
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:54:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030810.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030810hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173 Predicted Zn-finger pr 100.0 3.5E-47 7.6E-52 307.5 10.5 162 1-171 1-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.6 1.7E-15 3.8E-20 96.3 2.3 38 112-149 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 2.4E-15 5.2E-20 87.7 2.3 25 15-39 1-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.5 1E-14 2.2E-19 85.7 1.1 25 15-39 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 3.6E-11 7.8E-16 77.4 1.6 38 112-150 1-41 (43)
6 COG3582 Predicted nucleic acid 96.8 0.00066 1.4E-08 55.4 1.6 38 111-149 99-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.5 0.0011 2.4E-08 57.2 1.1 40 110-150 9-51 (250)
8 PF01363 FYVE: FYVE zinc finge 94.3 0.024 5.3E-07 38.6 1.6 29 108-136 8-39 (69)
9 KOG3183 Predicted Zn-finger pr 93.3 0.019 4.1E-07 49.7 -0.6 41 105-145 94-138 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.9 0.045 9.8E-07 35.8 0.9 27 110-136 3-32 (57)
11 smart00064 FYVE Protein presen 92.6 0.067 1.4E-06 36.3 1.4 29 109-137 10-41 (68)
12 KOG1818 Membrane trafficking a 89.5 0.13 2.8E-06 49.9 0.6 45 108-152 164-222 (634)
13 PF10571 UPF0547: Uncharacteri 87.7 0.27 5.9E-06 28.7 0.9 23 110-132 1-24 (26)
14 PF00130 C1_1: Phorbol esters/ 84.3 0.64 1.4E-05 29.9 1.5 24 108-131 10-37 (53)
15 PF15135 UPF0515: Uncharacteri 81.6 0.81 1.8E-05 40.2 1.5 30 105-134 128-167 (278)
16 PF02148 zf-UBP: Zn-finger in 68.2 3 6.5E-05 28.2 1.3 23 112-135 1-24 (63)
17 PF14471 DUF4428: Domain of un 66.4 2 4.3E-05 28.6 0.1 22 111-132 1-30 (51)
18 KOG1729 FYVE finger containing 59.6 2.6 5.6E-05 37.3 -0.4 33 107-140 166-202 (288)
19 PF13978 DUF4223: Protein of u 58.4 4.7 0.0001 27.6 0.8 18 132-149 19-36 (56)
20 smart00109 C1 Protein kinase C 58.3 5.5 0.00012 24.3 1.1 24 108-131 10-36 (49)
21 cd00029 C1 Protein kinase C co 58.1 5.5 0.00012 24.6 1.0 24 108-131 10-37 (50)
22 PHA02768 hypothetical protein; 57.5 4.3 9.3E-05 27.7 0.5 16 120-135 2-18 (55)
23 KOG1819 FYVE finger-containing 55.8 6.4 0.00014 38.3 1.5 30 108-137 900-932 (990)
24 PF01194 RNA_pol_N: RNA polyme 55.0 6.4 0.00014 27.4 1.0 13 109-121 4-16 (60)
25 COG1996 RPC10 DNA-directed RNA 54.3 5.3 0.00011 26.8 0.5 22 109-130 6-32 (49)
26 PF08882 Acetone_carb_G: Aceto 52.9 6.9 0.00015 30.4 1.0 33 113-147 16-48 (112)
27 PF07649 C1_3: C1-like domain; 51.1 6.9 0.00015 22.7 0.6 22 111-132 2-25 (30)
28 KOG1812 Predicted E3 ubiquitin 50.3 8.6 0.00019 35.1 1.4 31 107-137 304-338 (384)
29 PRK04016 DNA-directed RNA poly 50.3 5.9 0.00013 27.8 0.3 14 108-121 3-16 (62)
30 PLN00032 DNA-directed RNA poly 48.9 6.7 0.00015 28.2 0.4 13 109-121 4-16 (71)
31 PF05207 zf-CSL: CSL zinc fing 48.4 8 0.00017 25.9 0.7 13 121-133 16-28 (55)
32 PF03107 C1_2: C1 domain; Int 46.0 15 0.00032 21.5 1.5 20 111-130 2-23 (30)
33 smart00290 ZnF_UBP Ubiquitin C 45.7 7.5 0.00016 24.6 0.2 24 111-136 1-25 (50)
34 PTZ00303 phosphatidylinositol 44.5 12 0.00026 38.3 1.4 27 110-136 461-495 (1374)
35 PF02318 FYVE_2: FYVE-type zin 42.9 17 0.00038 27.4 1.9 31 109-139 54-88 (118)
36 PF02928 zf-C5HC2: C5HC2 zinc 42.4 12 0.00027 24.7 0.8 26 112-137 1-28 (54)
37 KOG3497 DNA-directed RNA polym 42.2 8.6 0.00019 27.2 0.1 13 109-121 4-16 (69)
38 PF03604 DNA_RNApol_7kD: DNA d 42.2 12 0.00025 22.8 0.6 18 112-129 3-24 (32)
39 PRK08402 replication factor A; 42.1 12 0.00026 33.9 1.0 28 110-138 213-245 (355)
40 KOG2807 RNA polymerase II tran 42.1 16 0.00034 33.6 1.7 29 107-135 328-358 (378)
41 smart00659 RPOLCX RNA polymera 41.7 13 0.00028 24.0 0.8 20 110-129 3-26 (44)
42 PF07975 C1_4: TFIIH C1-like d 40.0 12 0.00026 25.1 0.5 34 112-145 2-47 (51)
43 COG1571 Predicted DNA-binding 39.9 13 0.00028 34.8 0.9 26 109-134 350-379 (421)
44 PHA00626 hypothetical protein 39.7 15 0.00033 25.5 0.9 22 110-133 12-34 (59)
45 cd04476 RPA1_DBD_C RPA1_DBD_C: 38.8 14 0.0003 29.0 0.8 31 109-139 34-69 (166)
46 PF13240 zinc_ribbon_2: zinc-r 38.7 17 0.00037 20.3 0.9 20 111-130 1-21 (23)
47 COG1644 RPB10 DNA-directed RNA 38.5 10 0.00023 26.7 0.0 13 109-121 4-16 (63)
48 PF11781 RRN7: RNA polymerase 37.0 16 0.00034 22.6 0.7 22 110-131 9-34 (36)
49 PF13717 zinc_ribbon_4: zinc-r 34.7 21 0.00045 21.9 0.9 9 124-132 26-35 (36)
50 KOG1842 FYVE finger-containing 34.0 10 0.00022 35.9 -0.7 25 110-134 181-208 (505)
51 PF10367 Vps39_2: Vacuolar sor 32.5 31 0.00066 24.4 1.7 24 109-132 78-102 (109)
52 PF13842 Tnp_zf-ribbon_2: DDE_ 32.5 35 0.00075 20.5 1.6 26 111-136 2-30 (32)
53 PF09723 Zn-ribbon_8: Zinc rib 32.3 27 0.00059 21.9 1.2 20 121-140 3-23 (42)
54 PF15549 PGC7_Stella: PGC7/Ste 31.8 25 0.00054 28.9 1.2 19 123-143 123-141 (160)
55 smart00647 IBR In Between Ring 31.3 32 0.0007 22.1 1.5 18 122-139 39-57 (64)
56 PF13248 zf-ribbon_3: zinc-rib 31.2 28 0.0006 19.7 1.0 21 110-130 3-24 (26)
57 PRK04136 rpl40e 50S ribosomal 30.8 25 0.00055 23.5 0.9 23 108-130 13-36 (48)
58 PF04438 zf-HIT: HIT zinc fing 29.9 18 0.00039 21.5 0.1 23 110-135 3-26 (30)
59 PRK00398 rpoP DNA-directed RNA 29.4 28 0.00061 21.9 0.9 28 110-137 4-36 (46)
60 PF06750 DiS_P_DiS: Bacterial 29.1 32 0.00069 25.2 1.3 14 109-122 33-46 (92)
61 PRK07218 replication factor A; 29.1 25 0.00054 32.7 0.9 21 109-131 297-318 (423)
62 PF08073 CHDNT: CHDNT (NUC034) 28.6 22 0.00049 24.3 0.4 20 150-169 21-40 (55)
63 PF01485 IBR: IBR domain; Int 28.1 25 0.00055 22.5 0.6 16 124-139 41-57 (64)
64 PF10122 Mu-like_Com: Mu-like 27.0 24 0.00051 23.9 0.2 24 109-132 4-34 (51)
65 PF08600 Rsm1: Rsm1-like; Int 26.6 25 0.00053 25.7 0.3 18 109-126 19-36 (91)
66 PF00096 zf-C2H2: Zinc finger, 26.6 28 0.0006 18.3 0.5 9 124-132 1-10 (23)
67 KOG0193 Serine/threonine prote 26.0 24 0.00052 34.8 0.2 50 110-164 190-243 (678)
68 PF14835 zf-RING_6: zf-RING of 25.5 40 0.00086 23.9 1.2 26 110-135 8-33 (65)
69 PF00412 LIM: LIM domain; Int 25.5 29 0.00063 22.0 0.5 27 110-136 27-53 (58)
70 PF14634 zf-RING_5: zinc-RING 25.3 40 0.00088 20.9 1.1 29 111-139 1-31 (44)
71 KOG3507 DNA-directed RNA polym 24.5 34 0.00074 24.0 0.7 23 108-130 19-45 (62)
72 PRK12366 replication factor A; 24.5 32 0.00068 33.4 0.7 29 109-138 532-563 (637)
73 COG2888 Predicted Zn-ribbon RN 23.8 28 0.00061 24.4 0.2 21 108-130 37-58 (61)
74 KOG1074 Transcriptional repres 23.1 42 0.00091 34.3 1.3 45 104-148 600-672 (958)
75 smart00396 ZnF_UBR1 Putative z 22.9 46 0.00099 23.2 1.1 14 123-136 50-70 (71)
76 PTZ00218 40S ribosomal protein 22.0 54 0.0012 22.4 1.3 13 31-43 34-46 (54)
77 smart00834 CxxC_CXXC_SSSS Puta 21.1 47 0.001 19.8 0.8 12 122-133 4-16 (41)
78 PF13923 zf-C3HC4_2: Zinc fing 20.8 46 0.00099 20.0 0.7 23 112-134 1-23 (39)
79 COG3357 Predicted transcriptio 20.2 37 0.0008 25.8 0.2 13 122-134 57-70 (97)
80 PF07282 OrfB_Zn_ribbon: Putat 20.2 70 0.0015 21.4 1.5 23 109-131 28-55 (69)
81 PF12662 cEGF: Complement Clr- 20.1 98 0.0021 17.6 1.9 20 123-145 1-20 (24)
82 PF11722 zf-TRM13_CCCH: CCCH z 20.1 44 0.00096 20.1 0.5 11 127-137 20-30 (31)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.5e-47 Score=307.54 Aligned_cols=162 Identities=45% Similarity=0.805 Sum_probs=107.8
Q ss_pred CCCccccCCCCC-CCccchhcCCCCCCccccCCchhHHHHHHHHHHHHH-hhhhccccccccCCCCCCCCCCcccCCccc
Q 030810 1 MESHDETGCQAP-EGPILCVNNCGFFGSAATMNMCSKCHKAMILNQEQA-QLAASSIGSIVHGSSGGTGKEPIVAGSVDL 78 (171)
Q Consensus 1 M~~~~~~~~q~p-~~p~lC~n~CGFfGs~at~n~CSkCyr~~~~~~~~~-~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~ 78 (171)
|+ ++....+.+ ..++||+|||||||+|+|+||||+||++++.++++. ..+...+...+.+ + ...+ ..+.
T Consensus 1 M~-~e~~~~~~~~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~-~---~s~~----~~~~ 71 (167)
T KOG3173|consen 1 MA-SETNGSQTPPSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSS-P---RSVP----SRDP 71 (167)
T ss_pred Cc-ccccCCCCCCccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccC-c---cccC----cccc
Confidence 55 444444432 346999999999999999999999999999887765 2222211110000 0 0000 0000
Q ss_pred cCCccccccc-ccCCC--CCCCCCCCCCCCCCCCCccccccccccccceeeecCccccCCCCCCCCCCCCccchHHHHHH
Q 030810 79 QVGPVEIKKF-SMEPS--SGSSFGFAGVKAKEGPKRCTTCNKRVGLTGFNCRCGNLFCAVHRYSDKHGCPFDYRTAAREA 155 (171)
Q Consensus 79 ~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~~r~~ 155 (171)
.....+.... +...+ ..+............++||..|+|||||+||.||||++||+.|||||.|+|+||||.+||+.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~ 151 (167)
T KOG3173|consen 72 PAVSLESTTESELKLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREK 151 (167)
T ss_pred ccccccccccccccccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHH
Confidence 0000000000 00000 00011112233445688999999999999999999999999999999999999999999999
Q ss_pred HHHhCCcccccccccC
Q 030810 156 IAKANPVVKAEKLDKI 171 (171)
Q Consensus 156 i~k~Np~v~~~Ki~KI 171 (171)
|+++||+|+++||+||
T Consensus 152 i~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 152 IAKANPVVKADKLQKI 167 (167)
T ss_pred HHHhCCeeeccccccC
Confidence 9999999999999998
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=96.27 Aligned_cols=38 Identities=63% Similarity=1.456 Sum_probs=36.9
Q ss_pred cccccccccccceeee-cCccccCCCCCCCCCCCCccch
Q 030810 112 CTTCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYR 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=99.54 E-value=2.4e-15 Score=87.66 Aligned_cols=25 Identities=60% Similarity=1.327 Sum_probs=20.8
Q ss_pred ccchhcCCCCCCccccCCchhHHHH
Q 030810 15 PILCVNNCGFFGSAATMNMCSKCHK 39 (171)
Q Consensus 15 p~lC~n~CGFfGs~at~n~CSkCyr 39 (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 5799999999999999999999997
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.47 E-value=1e-14 Score=85.73 Aligned_cols=25 Identities=60% Similarity=1.278 Sum_probs=23.4
Q ss_pred ccchh-cCCCCCCccccCCchhHHHH
Q 030810 15 PILCV-NNCGFFGSAATMNMCSKCHK 39 (171)
Q Consensus 15 p~lC~-n~CGFfGs~at~n~CSkCyr 39 (171)
|++|+ +||||||||+|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 46899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.08 E-value=3.6e-11 Score=77.36 Aligned_cols=38 Identities=34% Similarity=0.866 Sum_probs=28.1
Q ss_pred ccc--ccccccccceeee-cCccccCCCCCCCCCCCCccchH
Q 030810 112 CTT--CNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYRT 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 998887 799999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.76 E-value=0.00066 Score=55.43 Aligned_cols=38 Identities=29% Similarity=0.491 Sum_probs=30.2
Q ss_pred ccccccccccccceeee-cCccccCCCCCCCCCCCCccch
Q 030810 111 RCTTCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYR 149 (171)
Q Consensus 111 rC~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 149 (171)
+|..|++..+|. ++|- |++.||+.||+++.|+|.+...
T Consensus 99 ~~~~~g~~s~l~-~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 99 TPQCTGKGSTLA-GKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred cceeccCCcccc-ccccCCCCcceeceecccccccccHHH
Confidence 344555555554 8898 9999999999999999998854
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.47 E-value=0.0011 Score=57.25 Aligned_cols=40 Identities=35% Similarity=0.945 Sum_probs=35.1
Q ss_pred Cccc--cccccccccceeee-cCccccCCCCCCCCCCCCccchH
Q 030810 110 KRCT--TCNKRVGLTGFNCR-CGNLFCAVHRYSDKHGCPFDYRT 150 (171)
Q Consensus 110 ~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 150 (171)
..|. .|+ .+.++.|+|- |+.+||..||-.+.|+|.+.|..
T Consensus 9 kHCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCK-QLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhh-hccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4676 787 6788999999 99999999999999999998763
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=94.32 E-value=0.024 Score=38.62 Aligned_cols=29 Identities=31% Similarity=0.887 Sum_probs=17.7
Q ss_pred CCCcccccccccccc--ceeee-cCccccCCC
Q 030810 108 GPKRCTTCNKRVGLT--GFNCR-CGNLFCAVH 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 457899999999997 49999 999999764
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=93.28 E-value=0.019 Score=49.74 Aligned_cols=41 Identities=34% Similarity=0.782 Sum_probs=34.8
Q ss_pred CCCCCCccc--ccccccccc-ceeee-cCccccCCCCCCCCCCCC
Q 030810 105 AKEGPKRCT--TCNKRVGLT-GFNCR-CGNLFCAVHRYSDKHGCP 145 (171)
Q Consensus 105 ~~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~ 145 (171)
.+...++|. .|++++-|. .+.|+ ||..||-+||++-.|.|.
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 444567786 789888775 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=92.90 E-value=0.045 Score=35.76 Aligned_cols=27 Identities=41% Similarity=1.030 Sum_probs=23.7
Q ss_pred Ccccccccccccc--ceeee-cCccccCCC
Q 030810 110 KRCTTCNKRVGLT--GFNCR-CGNLFCAVH 136 (171)
Q Consensus 110 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 136 (171)
..|..|+++.+++ ...|| ||.+||+.+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHH
Confidence 5799999999996 69999 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 KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=89.50 E-value=0.13 Score=49.87 Aligned_cols=45 Identities=29% Similarity=0.710 Sum_probs=35.2
Q ss_pred CCCccccccccccccc--eeee-cCccccCCCC-----------CCCCCCCCccchHHH
Q 030810 108 GPKRCTTCNKRVGLTG--FNCR-CGNLFCAVHR-----------YSDKHGCPFDYRTAA 152 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~~ 152 (171)
....|..|+.+.|+++ ..|| ||.+||+.|= |.+.--|.-||...-
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~ 222 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLT 222 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhh
Confidence 3578999999999985 8999 9999999884 344566777776433
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.71 E-value=0.27 Score=28.67 Aligned_cols=23 Identities=35% Similarity=0.743 Sum_probs=20.4
Q ss_pred Cccccccccccccceeee-cCccc
Q 030810 110 KRCTTCNKRVGLTGFNCR-CGNLF 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 14
>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=84.27 E-value=0.64 Score=29.90 Aligned_cols=24 Identities=38% Similarity=1.054 Sum_probs=18.5
Q ss_pred CCCccccccccc---cccceeee-cCcc
Q 030810 108 GPKRCTTCNKRV---GLTGFNCR-CGNL 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 467999999999 56799999 7654
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=81.57 E-value=0.81 Score=40.22 Aligned_cols=30 Identities=33% Similarity=0.849 Sum_probs=23.9
Q ss_pred CCCCCCcccccccc---------ccccceeee-cCccccC
Q 030810 105 AKEGPKRCTTCNKR---------VGLTGFNCR-CGNLFCA 134 (171)
Q Consensus 105 ~~~~~~rC~~C~kk---------vgl~gf~Cr-Cg~~FC~ 134 (171)
..+..+||..|+|| .|+.-|+|. |+++|=+
T Consensus 128 ~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 128 QRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccccCCCccccccceeeeecccccccchh
Confidence 34557999999988 677789994 9999854
No 16
>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=68.21 E-value=3 Score=28.18 Aligned_cols=23 Identities=26% Similarity=0.759 Sum_probs=15.1
Q ss_pred cccccccccccceeee-cCccccCC
Q 030810 112 CTTCNKRVGLTGFNCR-CGNLFCAV 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 34457788 99999994
No 17
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=66.45 E-value=2 Score=28.60 Aligned_cols=22 Identities=36% Similarity=1.126 Sum_probs=17.0
Q ss_pred cccccccccccc-------ceeee-cCccc
Q 030810 111 RCTTCNKRVGLT-------GFNCR-CGNLF 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 599999999997 57787 65443
No 18
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=59.60 E-value=2.6 Score=37.34 Aligned_cols=33 Identities=27% Similarity=0.761 Sum_probs=27.1
Q ss_pred CCCCccccccc-ccccc--ceeee-cCccccCCCCCCC
Q 030810 107 EGPKRCTTCNK-RVGLT--GFNCR-CGNLFCAVHRYSD 140 (171)
Q Consensus 107 ~~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e 140 (171)
...++|..|.+ .-.|. --+|| ||.+||. |.-..
T Consensus 166 ~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 166 SEATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred ccceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 35689999999 77776 47899 9999999 87544
No 19
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=58.36 E-value=4.7 Score=27.57 Aligned_cols=18 Identities=28% Similarity=0.717 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCCCCccch
Q 030810 132 FCAVHRYSDKHGCPFDYR 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 20
>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=58.32 E-value=5.5 Score=24.33 Aligned_cols=24 Identities=29% Similarity=0.800 Sum_probs=18.6
Q ss_pred CCCcccccccccccc--ceeee-cCcc
Q 030810 108 GPKRCTTCNKRVGLT--GFNCR-CGNL 131 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~ 131 (171)
.+..|..|++.+... |++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCch
Confidence 357899999999873 88888 6543
No 21
>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=58.11 E-value=5.5 Score=24.64 Aligned_cols=24 Identities=29% Similarity=0.704 Sum_probs=19.1
Q ss_pred CCCccccccccccc---cceeee-cCcc
Q 030810 108 GPKRCTTCNKRVGL---TGFNCR-CGNL 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 35689999999985 689999 7554
No 22
>PHA02768 hypothetical protein; Provisional
Probab=57.48 E-value=4.3 Score=27.74 Aligned_cols=16 Identities=31% Similarity=1.036 Sum_probs=12.6
Q ss_pred cccceeee-cCccccCC
Q 030810 120 GLTGFNCR-CGNLFCAV 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 47899998 98888653
No 23
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=55.80 E-value=6.4 Score=38.31 Aligned_cols=30 Identities=27% Similarity=0.833 Sum_probs=22.1
Q ss_pred CCCcccccccccccc--ceeee-cCccccCCCC
Q 030810 108 GPKRCTTCNKRVGLT--GFNCR-CGNLFCAVHR 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 457899997655442 46899 9999998643
No 24
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=54.95 E-value=6.4 Score=27.40 Aligned_cols=13 Identities=54% Similarity=1.081 Sum_probs=10.0
Q ss_pred CCccccccccccc
Q 030810 109 PKRCTTCNKRVGL 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 6799999998863
No 25
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=54.35 E-value=5.3 Score=26.76 Aligned_cols=22 Identities=36% Similarity=1.076 Sum_probs=17.4
Q ss_pred CCcccccccccccc----ceeee-cCc
Q 030810 109 PKRCTTCNKRVGLT----GFNCR-CGN 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 26
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=52.89 E-value=6.9 Score=30.40 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=24.7
Q ss_pred ccccccccccceeeecCccccCCCCCCCCCCCCcc
Q 030810 113 TTCNKRVGLTGFNCRCGNLFCAVHRYSDKHGCPFD 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 5666655 25899999999999887777765554
No 27
>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=51.12 E-value=6.9 Score=22.73 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=8.9
Q ss_pred ccccccccccc-cceeee-cCccc
Q 030810 111 RCTTCNKRVGL-TGFNCR-CGNLF 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 68999999988 789998 76554
No 28
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.32 E-value=8.6 Score=35.09 Aligned_cols=31 Identities=32% Similarity=0.907 Sum_probs=25.7
Q ss_pred CCCCcccccccccccc-c---eeeecCccccCCCC
Q 030810 107 EGPKRCTTCNKRVGLT-G---FNCRCGNLFCAVHR 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 4468999999998886 3 99999999997655
No 29
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=50.31 E-value=5.9 Score=27.76 Aligned_cols=14 Identities=43% Similarity=0.757 Sum_probs=11.4
Q ss_pred CCCccccccccccc
Q 030810 108 GPKRCTTCNKRVGL 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 36799999998864
No 30
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=48.88 E-value=6.7 Score=28.21 Aligned_cols=13 Identities=54% Similarity=1.081 Sum_probs=11.0
Q ss_pred CCccccccccccc
Q 030810 109 PKRCTTCNKRVGL 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 6799999998864
No 31
>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=48.36 E-value=8 Score=25.92 Aligned_cols=13 Identities=38% Similarity=1.035 Sum_probs=10.3
Q ss_pred ccceeeecCcccc
Q 030810 121 LTGFNCRCGNLFC 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 3468999999874
No 32
>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=45.99 E-value=15 Score=21.48 Aligned_cols=20 Identities=20% Similarity=0.708 Sum_probs=16.5
Q ss_pred cccccccccccc-ceeee-cCc
Q 030810 111 RCTTCNKRVGLT-GFNCR-CGN 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 33
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=45.68 E-value=7.5 Score=24.55 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=17.6
Q ss_pred ccccccccccccceeee-cCccccCCC
Q 030810 111 RCTTCNKRVGLTGFNCR-CGNLFCAVH 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 6888886554 35666 999999764
No 34
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=44.48 E-value=12 Score=38.27 Aligned_cols=27 Identities=26% Similarity=0.790 Sum_probs=21.0
Q ss_pred Cccccccccccc-------cceeee-cCccccCCC
Q 030810 110 KRCTTCNKRVGL-------TGFNCR-CGNLFCAVH 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 569999999863 245699 999998643
No 35
>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=42.94 E-value=17 Score=27.41 Aligned_cols=31 Identities=26% Similarity=0.652 Sum_probs=24.1
Q ss_pred CCcccccccccccc---ceeee-cCccccCCCCCC
Q 030810 109 PKRCTTCNKRVGLT---GFNCR-CGNLFCAVHRYS 139 (171)
Q Consensus 109 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 139 (171)
...|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 46899999999986 68999 999999876653
No 36
>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=42.39 E-value=12 Score=24.69 Aligned_cols=26 Identities=27% Similarity=0.825 Sum_probs=22.2
Q ss_pred cccccccccccceeeec--CccccCCCC
Q 030810 112 CTTCNKRVGLTGFNCRC--GNLFCAVHR 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 67788888888999997 899999885
No 37
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=42.25 E-value=8.6 Score=27.22 Aligned_cols=13 Identities=54% Similarity=1.045 Sum_probs=11.0
Q ss_pred CCccccccccccc
Q 030810 109 PKRCTTCNKRVGL 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 38
>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=42.24 E-value=12 Score=22.83 Aligned_cols=18 Identities=39% Similarity=1.060 Sum_probs=9.5
Q ss_pred ccccccccccc---ceeee-cC
Q 030810 112 CTTCNKRVGLT---GFNCR-CG 129 (171)
Q Consensus 112 C~~C~kkvgl~---gf~Cr-Cg 129 (171)
|..|+..+.|. ..+|+ ||
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCcCCCeeEcCCCCcEECCcCC
Confidence 55566666653 35666 54
No 39
>PRK08402 replication factor A; Reviewed
Probab=42.06 E-value=12 Score=33.93 Aligned_cols=28 Identities=18% Similarity=0.510 Sum_probs=18.6
Q ss_pred Cccccccccccc----cceeee-cCccccCCCCC
Q 030810 110 KRCTTCNKRVGL----TGFNCR-CGNLFCAVHRY 138 (171)
Q Consensus 110 ~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 138 (171)
.+|..|+|||-. -.+.|. ||.+-+ .|||
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 699999999953 247777 554333 4554
No 40
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=42.05 E-value=16 Score=33.56 Aligned_cols=29 Identities=28% Similarity=0.849 Sum_probs=23.4
Q ss_pred CCCCccccc-cccccccceeee-cCccccCC
Q 030810 107 EGPKRCTTC-NKRVGLTGFNCR-CGNLFCAV 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 666666789999 99999963
No 41
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.73 E-value=13 Score=23.97 Aligned_cols=20 Identities=30% Similarity=0.868 Sum_probs=14.2
Q ss_pred Ccccccccccccc---ceeee-cC
Q 030810 110 KRCTTCNKRVGLT---GFNCR-CG 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 3688888888775 57776 64
No 42
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=40.04 E-value=12 Score=25.11 Aligned_cols=34 Identities=32% Similarity=0.756 Sum_probs=15.8
Q ss_pred ccccccccccc--------ceeee-cCccccCC---CCCCCCCCCC
Q 030810 112 CTTCNKRVGLT--------GFNCR-CGNLFCAV---HRYSDKHGCP 145 (171)
Q Consensus 112 C~~C~kkvgl~--------gf~Cr-Cg~~FC~~---HRy~e~H~C~ 145 (171)
|+.|.+.+.-. .|.|. |+..||.. -=+-.-|+|+
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 56666666653 48897 99999852 2223456664
No 43
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.90 E-value=13 Score=34.77 Aligned_cols=26 Identities=31% Similarity=0.800 Sum_probs=20.2
Q ss_pred CCcccccccccccc---ceeee-cCccccC
Q 030810 109 PKRCTTCNKRVGLT---GFNCR-CGNLFCA 134 (171)
Q Consensus 109 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~ 134 (171)
.-+|-.|++++.-. ||+|+ ||..+=.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCc
Confidence 35899999988654 79999 9876643
No 44
>PHA00626 hypothetical protein
Probab=39.73 E-value=15 Score=25.52 Aligned_cols=22 Identities=18% Similarity=0.292 Sum_probs=13.8
Q ss_pred Cccccccccccccceeee-cCcccc
Q 030810 110 KRCTTCNKRVGLTGFNCR-CGNLFC 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 3677776522 248887 877764
No 45
>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=38.84 E-value=14 Score=28.98 Aligned_cols=31 Identities=29% Similarity=0.609 Sum_probs=22.4
Q ss_pred CCcccccccccccc---ceeee-cCccc-cCCCCCC
Q 030810 109 PKRCTTCNKRVGLT---GFNCR-CGNLF-CAVHRYS 139 (171)
Q Consensus 109 ~~rC~~C~kkvgl~---gf~Cr-Cg~~F-C~~HRy~ 139 (171)
=..|..|+|||-.. .|.|. |+..+ =-.+||-
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 45688999999765 38888 77765 4566764
No 46
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.66 E-value=17 Score=20.31 Aligned_cols=20 Identities=25% Similarity=0.730 Sum_probs=10.9
Q ss_pred ccccccccccccceeee-cCc
Q 030810 111 RCTTCNKRVGLTGFNCR-CGN 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 36666666655444455 443
No 47
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=38.52 E-value=10 Score=26.66 Aligned_cols=13 Identities=46% Similarity=1.083 Sum_probs=10.8
Q ss_pred CCccccccccccc
Q 030810 109 PKRCTTCNKRVGL 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 6799999998853
No 48
>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=37.01 E-value=16 Score=22.63 Aligned_cols=22 Identities=36% Similarity=1.007 Sum_probs=17.4
Q ss_pred Ccccccccccccc--c-eee-ecCcc
Q 030810 110 KRCTTCNKRVGLT--G-FNC-RCGNL 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 49
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.66 E-value=21 Score=21.91 Aligned_cols=9 Identities=44% Similarity=1.471 Sum_probs=4.9
Q ss_pred eeee-cCccc
Q 030810 124 FNCR-CGNLF 132 (171)
Q Consensus 124 f~Cr-Cg~~F 132 (171)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 5555 65554
No 50
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=34.00 E-value=10 Score=35.94 Aligned_cols=25 Identities=40% Similarity=1.116 Sum_probs=22.0
Q ss_pred Ccccccccccccc--ceeee-cCccccC
Q 030810 110 KRCTTCNKRVGLT--GFNCR-CGNLFCA 134 (171)
Q Consensus 110 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 134 (171)
.-|..|.++.||+ --.|| ||.+.|.
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHH
Confidence 4799999999997 68999 9999884
No 51
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=32.51 E-value=31 Score=24.40 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=16.5
Q ss_pred CCccccccccccccceeee-cCccc
Q 030810 109 PKRCTTCNKRVGLTGFNCR-CGNLF 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 4579999999998654333 55444
No 52
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=32.46 E-value=35 Score=20.50 Aligned_cols=26 Identities=31% Similarity=0.810 Sum_probs=18.5
Q ss_pred cccccccccc-c-cceeee-cCccccCCC
Q 030810 111 RCTTCNKRVG-L-TGFNCR-CGNLFCAVH 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 6777776432 2 679998 887777766
No 53
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.27 E-value=27 Score=21.87 Aligned_cols=20 Identities=25% Similarity=0.750 Sum_probs=16.4
Q ss_pred ccceeee-cCccccCCCCCCC
Q 030810 121 LTGFNCR-CGNLFCAVHRYSD 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 4569999 9999988887776
No 54
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=31.76 E-value=25 Score=28.91 Aligned_cols=19 Identities=32% Similarity=0.968 Sum_probs=15.2
Q ss_pred ceeeecCccccCCCCCCCCCC
Q 030810 123 GFNCRCGNLFCAVHRYSDKHG 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 7999999766555
No 55
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.30 E-value=32 Score=22.07 Aligned_cols=18 Identities=28% Similarity=0.779 Sum_probs=14.9
Q ss_pred cceee-ecCccccCCCCCC
Q 030810 122 TGFNC-RCGNLFCAVHRYS 139 (171)
Q Consensus 122 ~gf~C-rCg~~FC~~HRy~ 139 (171)
....| .||..||-.++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 35889 7999999988865
No 56
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.20 E-value=28 Score=19.70 Aligned_cols=21 Identities=24% Similarity=0.680 Sum_probs=12.5
Q ss_pred Cccccccccccccceeee-cCc
Q 030810 110 KRCTTCNKRVGLTGFNCR-CGN 130 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~ 130 (171)
..|..|++.+.-..-.|. ||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 467777776555555555 543
No 57
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=30.78 E-value=25 Score=23.49 Aligned_cols=23 Identities=39% Similarity=0.843 Sum_probs=19.2
Q ss_pred CCCccccccccccccceeee-cCc
Q 030810 108 GPKRCTTCNKRVGLTGFNCR-CGN 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 35678999999999999999 775
No 58
>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=29.94 E-value=18 Score=21.52 Aligned_cols=23 Identities=30% Similarity=1.086 Sum_probs=15.4
Q ss_pred Cccccccccccccceeee-cCccccCC
Q 030810 110 KRCTTCNKRVGLTGFNCR-CGNLFCAV 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 46888887 5568998 99999985
No 59
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.41 E-value=28 Score=21.95 Aligned_cols=28 Identities=32% Similarity=0.795 Sum_probs=17.6
Q ss_pred Ccccccccccccc----ceeee-cCccccCCCC
Q 030810 110 KRCTTCNKRVGLT----GFNCR-CGNLFCAVHR 137 (171)
Q Consensus 110 ~rC~~C~kkvgl~----gf~Cr-Cg~~FC~~HR 137 (171)
-+|..|+..+-+. .++|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 4788888877552 47787 6655443333
No 60
>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=29.14 E-value=32 Score=25.24 Aligned_cols=14 Identities=14% Similarity=0.494 Sum_probs=11.7
Q ss_pred CCcccccccccccc
Q 030810 109 PKRCTTCNKRVGLT 122 (171)
Q Consensus 109 ~~rC~~C~kkvgl~ 122 (171)
+++|..|++++...
T Consensus 33 rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 33 RSHCPHCGHPLSWW 46 (92)
T ss_pred CCcCcCCCCcCccc
Confidence 58999999998764
No 61
>PRK07218 replication factor A; Provisional
Probab=29.07 E-value=25 Score=32.74 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=15.9
Q ss_pred CCccccccccccccceeee-cCcc
Q 030810 109 PKRCTTCNKRVGLTGFNCR-CGNL 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 4799999999954 6777 5543
No 62
>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=28.56 E-value=22 Score=24.31 Aligned_cols=20 Identities=40% Similarity=0.434 Sum_probs=16.4
Q ss_pred HHHHHHHHHhCCcccccccc
Q 030810 150 TAAREAIAKANPVVKAEKLD 169 (171)
Q Consensus 150 ~~~r~~i~k~Np~v~~~Ki~ 169 (171)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34578899999999888875
No 63
>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=28.11 E-value=25 Score=22.51 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=14.0
Q ss_pred eeee-cCccccCCCCCC
Q 030810 124 FNCR-CGNLFCAVHRYS 139 (171)
Q Consensus 124 f~Cr-Cg~~FC~~HRy~ 139 (171)
+.|. |+..||..++-+
T Consensus 41 ~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CCTTSCCSEECSSSTSE
T ss_pred eECCCCCCcCccccCcc
Confidence 7899 999999998854
No 64
>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=26.96 E-value=24 Score=23.90 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=17.2
Q ss_pred CCcccccccccccc------ceeee-cCccc
Q 030810 109 PKRCTTCNKRVGLT------GFNCR-CGNLF 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 65
>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=26.62 E-value=25 Score=25.71 Aligned_cols=18 Identities=33% Similarity=0.660 Sum_probs=14.6
Q ss_pred CCccccccccccccceee
Q 030810 109 PKRCTTCNKRVGLTGFNC 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 457999999999976653
No 66
>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=26.61 E-value=28 Score=18.26 Aligned_cols=9 Identities=44% Similarity=1.490 Sum_probs=4.5
Q ss_pred eeee-cCccc
Q 030810 124 FNCR-CGNLF 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 3455 55554
No 67
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=26.03 E-value=24 Score=34.82 Aligned_cols=50 Identities=28% Similarity=0.663 Sum_probs=32.5
Q ss_pred Cccccccccccccceeee-cCccc---cCCCCCCCCCCCCccchHHHHHHHHHhCCccc
Q 030810 110 KRCTTCNKRVGLTGFNCR-CGNLF---CAVHRYSDKHGCPFDYRTAAREAIAKANPVVK 164 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~fDyk~~~r~~i~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 457777788878999999 99866 54443 2 2343 332 34566777777654
No 68
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=25.48 E-value=40 Score=23.89 Aligned_cols=26 Identities=23% Similarity=0.548 Sum_probs=10.4
Q ss_pred CccccccccccccceeeecCccccCC
Q 030810 110 KRCTTCNKRVGLTGFNCRCGNLFCAV 135 (171)
Q Consensus 110 ~rC~~C~kkvgl~gf~CrCg~~FC~~ 135 (171)
-||..|.--+...--.-.|+++||+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHH
Confidence 57888876544432334689999985
No 69
>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=25.48 E-value=29 Score=21.97 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=18.7
Q ss_pred CccccccccccccceeeecCccccCCC
Q 030810 110 KRCTTCNKRVGLTGFNCRCGNLFCAVH 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 577888888877666655566666554
No 70
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=25.34 E-value=40 Score=20.87 Aligned_cols=29 Identities=21% Similarity=0.524 Sum_probs=19.7
Q ss_pred ccccccccccc--cceeeecCccccCCCCCC
Q 030810 111 RCTTCNKRVGL--TGFNCRCGNLFCAVHRYS 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 47778877722 245556999999876543
No 71
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=24.54 E-value=34 Score=23.97 Aligned_cols=23 Identities=30% Similarity=0.657 Sum_probs=17.7
Q ss_pred CCCcccccccccccc---ceeee-cCc
Q 030810 108 GPKRCTTCNKRVGLT---GFNCR-CGN 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 456789999888884 49999 864
No 72
>PRK12366 replication factor A; Reviewed
Probab=24.48 E-value=32 Score=33.43 Aligned_cols=29 Identities=28% Similarity=0.604 Sum_probs=20.9
Q ss_pred CCcccccccccccc--ceeee-cCccccCCCCC
Q 030810 109 PKRCTTCNKRVGLT--GFNCR-CGNLFCAVHRY 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 37899999999653 27896 8877 335665
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.81 E-value=28 Score=24.36 Aligned_cols=21 Identities=38% Similarity=1.083 Sum_probs=13.6
Q ss_pred CCCccccccccccccceee-ecCc
Q 030810 108 GPKRCTTCNKRVGLTGFNC-RCGN 130 (171)
Q Consensus 108 ~~~rC~~C~kkvgl~gf~C-rCg~ 130 (171)
.-.||..||| +| ..|.| .||.
T Consensus 37 ~I~Rc~~CRk-~g-~~Y~Cp~CGF 58 (61)
T COG2888 37 EIYRCAKCRK-LG-NPYRCPKCGF 58 (61)
T ss_pred eeehhhhHHH-cC-CceECCCcCc
Confidence 3578888885 22 24788 5775
No 74
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=23.12 E-value=42 Score=34.31 Aligned_cols=45 Identities=29% Similarity=0.836 Sum_probs=30.6
Q ss_pred CCCCCCCccccccccc--------------cccceeee-cCccccC---------CCCCC----CCCCCCccc
Q 030810 104 KAKEGPKRCTTCNKRV--------------GLTGFNCR-CGNLFCA---------VHRYS----DKHGCPFDY 148 (171)
Q Consensus 104 ~~~~~~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC~---------~HRy~----e~H~C~fDy 148 (171)
.+...+|.|-.|.|-| |-..|+|+ ||+-|-- .||-. -.|.|.+-|
T Consensus 600 ~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 600 NKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred cccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 3445789999998744 33369999 9999973 34432 567787544
No 75
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=22.89 E-value=46 Score=23.20 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=11.9
Q ss_pred ceeeecCcc-------ccCCC
Q 030810 123 GFNCRCGNL-------FCAVH 136 (171)
Q Consensus 123 gf~CrCg~~-------FC~~H 136 (171)
||.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999988 88887
No 76
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.97 E-value=54 Score=22.37 Aligned_cols=13 Identities=23% Similarity=0.751 Sum_probs=11.0
Q ss_pred CCchhHHHHHHHH
Q 030810 31 MNMCSKCHKAMIL 43 (171)
Q Consensus 31 ~n~CSkCyr~~~~ 43 (171)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 5799999999854
No 77
>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=21.09 E-value=47 Score=19.79 Aligned_cols=12 Identities=33% Similarity=1.016 Sum_probs=7.2
Q ss_pred cceeee-cCcccc
Q 030810 122 TGFNCR-CGNLFC 133 (171)
Q Consensus 122 ~gf~Cr-Cg~~FC 133 (171)
-.|+|. ||..|=
T Consensus 4 Y~y~C~~Cg~~fe 16 (41)
T smart00834 4 YEYRCEDCGHTFE 16 (41)
T ss_pred EEEEcCCCCCEEE
Confidence 356666 666554
No 78
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=20.82 E-value=46 Score=19.96 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=12.3
Q ss_pred cccccccccccceeeecCccccC
Q 030810 112 CTTCNKRVGLTGFNCRCGNLFCA 134 (171)
Q Consensus 112 C~~C~kkvgl~gf~CrCg~~FC~ 134 (171)
|..|...+.-.-..-.||++||.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~ 23 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCK 23 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEH
T ss_pred CCCCCCcccCcCEECCCCCchhH
Confidence 34454433332245569999985
No 79
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.20 E-value=37 Score=25.76 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=8.6
Q ss_pred cceeee-cCccccC
Q 030810 122 TGFNCR-CGNLFCA 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 356777 7777744
No 80
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.18 E-value=70 Score=21.36 Aligned_cols=23 Identities=30% Similarity=0.774 Sum_probs=16.8
Q ss_pred CCccccccccccc--c--ceeee-cCcc
Q 030810 109 PKRCTTCNKRVGL--T--GFNCR-CGNL 131 (171)
Q Consensus 109 ~~rC~~C~kkvgl--~--gf~Cr-Cg~~ 131 (171)
...|..|+.++.- . .|.|. ||..
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCE
Confidence 4579999888776 2 58888 7655
No 81
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=20.13 E-value=98 Score=17.60 Aligned_cols=20 Identities=20% Similarity=0.668 Sum_probs=12.8
Q ss_pred ceeeecCccccCCCCCCCCCCCC
Q 030810 123 GFNCRCGNLFCAVHRYSDKHGCP 145 (171)
Q Consensus 123 gf~CrCg~~FC~~HRy~e~H~C~ 145 (171)
+|.|.|..-| ..-++.|.|.
T Consensus 1 sy~C~C~~Gy---~l~~d~~~C~ 20 (24)
T PF12662_consen 1 SYTCSCPPGY---QLSPDGRSCE 20 (24)
T ss_pred CEEeeCCCCC---cCCCCCCccc
Confidence 5889986544 3345677774
No 82
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=20.09 E-value=44 Score=20.10 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=8.3
Q ss_pred ecCccccCCCC
Q 030810 127 RCGNLFCAVHR 137 (171)
Q Consensus 127 rCg~~FC~~HR 137 (171)
+=|..||+.|.
T Consensus 20 ~~g~~fC~~H~ 30 (31)
T PF11722_consen 20 KPGSRFCGEHM 30 (31)
T ss_pred cCcCCccccCC
Confidence 44678999985
Done!