Query 030824
Match_columns 171
No_of_seqs 149 out of 480
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:07:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173 Predicted Zn-finger pr 100.0 1.2E-46 2.6E-51 304.0 8.7 164 1-171 1-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.6 7.4E-16 1.6E-20 89.4 2.1 25 16-40 1-25 (25)
3 smart00259 ZnF_A20 A20-like zi 99.5 3.3E-15 7.1E-20 87.4 1.2 25 16-40 1-26 (26)
4 smart00154 ZnF_AN1 AN1-like Zi 99.5 1E-14 2.3E-19 92.4 2.4 38 112-149 1-39 (39)
5 PF01428 zf-AN1: AN1-like Zinc 99.0 8E-11 1.7E-15 75.5 1.2 38 112-150 1-41 (43)
6 KOG3183 Predicted Zn-finger pr 97.1 0.00017 3.6E-09 62.0 1.1 40 110-150 9-51 (250)
7 COG3582 Predicted nucleic acid 96.4 0.0017 3.7E-08 52.9 1.7 39 111-149 96-137 (162)
8 KOG3183 Predicted Zn-finger pr 94.7 0.0063 1.4E-07 52.4 -0.9 41 105-145 94-138 (250)
9 PF01363 FYVE: FYVE zinc finge 90.6 0.12 2.5E-06 35.2 0.9 29 108-136 8-39 (69)
10 cd00065 FYVE FYVE domain; Zinc 89.9 0.16 3.4E-06 33.1 1.1 28 109-136 2-32 (57)
11 smart00064 FYVE Protein presen 89.3 0.24 5.1E-06 33.5 1.6 29 109-137 10-41 (68)
12 PF10571 UPF0547: Uncharacteri 86.1 0.39 8.5E-06 27.9 1.0 23 110-132 1-24 (26)
13 KOG1818 Membrane trafficking a 84.4 0.41 9E-06 46.4 0.9 45 107-151 163-221 (634)
14 PF15135 UPF0515: Uncharacteri 72.9 2 4.3E-05 37.7 1.5 30 105-134 128-167 (278)
15 PF10122 Mu-like_Com: Mu-like 71.4 1.2 2.7E-05 29.9 -0.1 24 109-132 4-34 (51)
16 PF00130 C1_1: Phorbol esters/ 70.5 2.3 5E-05 27.2 1.0 24 108-131 10-37 (53)
17 PF07975 C1_4: TFIIH C1-like d 65.3 2.7 5.9E-05 28.1 0.6 34 112-145 2-47 (51)
18 PF02148 zf-UBP: Zn-finger in 65.3 3.6 7.9E-05 27.7 1.2 23 112-135 1-24 (63)
19 PHA02768 hypothetical protein; 62.6 3.1 6.7E-05 28.3 0.5 16 120-135 2-18 (55)
20 COG1996 RPC10 DNA-directed RNA 60.4 3.3 7.2E-05 27.6 0.3 23 109-131 6-33 (49)
21 PF13978 DUF4223: Protein of u 57.1 5.1 0.00011 27.2 0.8 18 132-149 19-36 (56)
22 COG1571 Predicted DNA-binding 56.5 6.6 0.00014 36.6 1.7 49 110-158 351-405 (421)
23 PHA00626 hypothetical protein 50.0 8.4 0.00018 26.6 1.0 23 110-134 12-35 (59)
24 KOG2807 RNA polymerase II tran 49.3 11 0.00024 34.4 1.8 40 106-145 327-371 (378)
25 PF13240 zinc_ribbon_2: zinc-r 49.1 11 0.00023 21.1 1.1 21 111-131 1-22 (23)
26 PF02928 zf-C5HC2: C5HC2 zinc 48.6 8.4 0.00018 25.4 0.8 27 112-138 1-29 (54)
27 smart00290 ZnF_UBP Ubiquitin C 44.7 7.8 0.00017 24.4 0.2 24 111-136 1-25 (50)
28 cd04476 RPA1_DBD_C RPA1_DBD_C: 44.0 10 0.00022 29.7 0.7 31 109-139 34-69 (166)
29 PF01194 RNA_pol_N: RNA polyme 43.8 12 0.00025 26.0 0.9 12 109-120 4-15 (60)
30 PF05207 zf-CSL: CSL zinc fing 43.7 9.9 0.00021 25.4 0.5 14 122-135 17-30 (55)
31 PRK00398 rpoP DNA-directed RNA 42.8 13 0.00029 23.4 1.0 29 110-138 4-37 (46)
32 PF04438 zf-HIT: HIT zinc fing 41.8 8.1 0.00018 22.9 -0.1 23 110-135 3-26 (30)
33 KOG1812 Predicted E3 ubiquitin 41.3 17 0.00036 33.2 1.8 31 107-137 304-338 (384)
34 smart00109 C1 Protein kinase C 40.9 16 0.00034 22.2 1.1 23 108-130 10-35 (49)
35 PF03107 C1_2: C1 domain; Int 40.7 20 0.00042 20.9 1.4 20 111-130 2-23 (30)
36 KOG1729 FYVE finger containing 39.8 6.4 0.00014 34.8 -1.1 33 107-140 166-202 (288)
37 smart00396 ZnF_UBR1 Putative z 39.6 16 0.00035 25.5 1.1 14 123-136 50-70 (71)
38 PF14369 zf-RING_3: zinc-finge 39.3 13 0.00029 22.7 0.6 22 111-132 4-31 (35)
39 PRK04016 DNA-directed RNA poly 38.7 11 0.00023 26.4 0.1 14 108-121 3-16 (62)
40 PF14471 DUF4428: Domain of un 38.5 11 0.00025 24.8 0.2 21 111-131 1-29 (51)
41 PLN00032 DNA-directed RNA poly 37.8 12 0.00026 26.8 0.2 13 109-121 4-16 (71)
42 KOG1819 FYVE finger-containing 37.5 16 0.00034 35.6 1.0 32 105-136 897-931 (990)
43 PF08882 Acetone_carb_G: Aceto 37.3 15 0.00033 28.4 0.8 33 113-147 16-48 (112)
44 PF02318 FYVE_2: FYVE-type zin 37.3 23 0.0005 26.7 1.8 31 108-138 53-87 (118)
45 cd00029 C1 Protein kinase C co 36.8 19 0.00042 22.1 1.0 24 108-131 10-37 (50)
46 PF08073 CHDNT: CHDNT (NUC034) 36.7 9.6 0.00021 26.0 -0.4 20 150-169 21-40 (55)
47 PF04236 Transp_Tc5_C: Tc5 tra 36.2 28 0.00062 24.1 1.9 33 109-144 27-63 (63)
48 PHA00616 hypothetical protein 35.5 10 0.00022 24.6 -0.4 11 124-134 2-13 (44)
49 PTZ00303 phosphatidylinositol 35.5 21 0.00044 36.5 1.5 26 110-135 461-494 (1374)
50 PRK14890 putative Zn-ribbon RN 34.5 17 0.00037 25.1 0.6 20 109-130 36-56 (59)
51 PF07649 C1_3: C1-like domain; 33.3 18 0.00039 20.8 0.5 22 111-132 2-25 (30)
52 PF13717 zinc_ribbon_4: zinc-r 33.2 20 0.00044 21.9 0.7 9 124-132 26-35 (36)
53 TIGR00373 conserved hypothetic 32.3 15 0.00032 29.3 -0.0 24 108-131 108-137 (158)
54 KOG3497 DNA-directed RNA polym 31.9 15 0.00032 25.9 -0.1 13 109-121 4-16 (69)
55 TIGR00627 tfb4 transcription f 31.7 23 0.0005 31.1 1.1 27 109-136 242-269 (279)
56 PF09538 FYDLN_acid: Protein o 31.3 28 0.0006 26.5 1.3 27 109-135 9-39 (108)
57 smart00647 IBR In Between Ring 30.7 34 0.00073 21.9 1.5 18 122-139 39-57 (64)
58 TIGR02098 MJ0042_CXXC MJ0042 f 29.2 30 0.00065 20.7 1.0 9 124-132 26-35 (38)
59 PRK06266 transcription initiat 28.3 20 0.00042 29.3 0.0 25 108-132 116-146 (178)
60 PF15549 PGC7_Stella: PGC7/Ste 28.1 30 0.00066 28.3 1.1 19 123-143 123-141 (160)
61 COG1439 Predicted nucleic acid 27.1 21 0.00045 29.7 -0.0 27 105-131 135-162 (177)
62 PF13842 Tnp_zf-ribbon_2: DDE_ 27.1 45 0.00097 19.9 1.5 26 111-136 2-30 (32)
63 PF01485 IBR: IBR domain; Int 27.0 25 0.00054 22.5 0.4 16 124-139 41-57 (64)
64 COG2888 Predicted Zn-ribbon RN 26.7 26 0.00056 24.4 0.4 22 107-130 36-58 (61)
65 COG1644 RPB10 DNA-directed RNA 25.5 21 0.00045 25.0 -0.2 12 109-120 4-15 (63)
66 PRK08402 replication factor A; 25.1 36 0.00078 30.8 1.2 28 110-138 213-245 (355)
67 smart00659 RPOLCX RNA polymera 24.9 34 0.00074 21.9 0.7 20 110-129 3-26 (44)
68 PF14446 Prok-RING_1: Prokaryo 24.9 42 0.00092 22.7 1.2 24 109-132 5-31 (54)
69 PF00096 zf-C2H2: Zinc finger, 24.5 30 0.00064 18.1 0.3 11 124-134 1-12 (23)
70 TIGR00622 ssl1 transcription f 24.2 60 0.0013 25.0 2.1 37 110-146 56-108 (112)
71 PF03604 DNA_RNApol_7kD: DNA d 24.2 33 0.00071 20.7 0.5 16 112-127 3-21 (32)
72 PF01529 zf-DHHC: DHHC palmito 23.9 76 0.0016 24.4 2.6 45 105-153 44-88 (174)
73 PF10367 Vps39_2: Vacuolar sor 23.8 59 0.0013 22.9 1.9 24 109-132 78-102 (109)
74 KOG1074 Transcriptional repres 23.3 57 0.0012 33.3 2.2 31 104-134 600-645 (958)
75 COG1040 ComFC Predicted amidop 23.1 28 0.00061 29.2 0.1 48 110-157 25-83 (225)
76 PRK07218 replication factor A; 23.1 38 0.00083 31.5 0.9 20 109-130 297-317 (423)
77 KOG3362 Predicted BBOX Zn-fing 22.9 43 0.00094 27.3 1.1 28 105-135 114-142 (156)
78 PF06750 DiS_P_DiS: Bacterial 22.7 55 0.0012 23.9 1.5 14 109-122 33-46 (92)
79 PF11722 zf-TRM13_CCCH: CCCH z 22.6 37 0.00081 20.3 0.5 11 127-137 20-30 (31)
80 PRK12366 replication factor A; 22.4 38 0.00082 32.9 0.8 29 109-138 532-563 (637)
81 PRK04136 rpl40e 50S ribosomal 22.0 48 0.0011 22.0 1.0 22 109-130 14-36 (48)
82 PF13465 zf-H2C2_2: Zinc-finge 22.0 52 0.0011 18.3 1.0 13 120-132 11-24 (26)
83 PF13719 zinc_ribbon_5: zinc-r 22.0 42 0.0009 20.4 0.6 9 124-132 26-35 (37)
84 PF06524 NOA36: NOA36 protein; 21.7 31 0.00068 30.7 0.1 28 108-138 170-198 (314)
85 KOG1842 FYVE finger-containing 21.6 22 0.00047 33.7 -1.0 25 110-134 181-208 (505)
86 PF05458 Siva: Cd27 binding pr 21.2 83 0.0018 25.8 2.5 23 123-145 139-165 (175)
87 PF14835 zf-RING_6: zf-RING of 21.0 56 0.0012 23.0 1.2 26 110-135 8-33 (65)
88 PF07282 OrfB_Zn_ribbon: Putat 20.6 65 0.0014 21.5 1.5 24 108-131 27-55 (69)
89 PF00869 Flavi_glycoprot: Flav 20.5 36 0.00078 30.3 0.2 10 21-30 103-112 (293)
90 PF14634 zf-RING_5: zinc-RING 20.3 34 0.00073 21.2 -0.0 29 111-139 1-31 (44)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-46 Score=303.96 Aligned_cols=164 Identities=48% Similarity=0.893 Sum_probs=107.8
Q ss_pred CCCcccCCCccCCCCccchhcCCCCCCccccCCchhHHhHHHHHhHHHH-HHHHHhhhhhccCCCCCCCCCCchhhhccc
Q 030824 1 MGSEQSDGTSYTTSEPKLCVNGCAFFGTAANMGLCSKCYRDLRVKEDQA-ASAKAAMEKSLNLKSPKQIHQTPELETAKV 79 (171)
Q Consensus 1 M~~~~~~~~~~~~~~p~lC~n~CGFfGs~at~n~CSkCyrd~~~ke~~~-~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~ 79 (171)
|+ ++....+..+..++||+|||||||+|+|+||||+||||++.++++. ..+...+...+..+.+.+...+.. .....
T Consensus 1 M~-~e~~~~~~~~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~-~~~~~ 78 (167)
T KOG3173|consen 1 MA-SETNGSQTPPSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPRSVPSRDPPA-VSLES 78 (167)
T ss_pred Cc-ccccCCCCCCccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCccccCcccccc-ccccc
Confidence 55 2233333133456999999999999999999999999999877765 322221111111000000000000 00000
Q ss_pred cCCCcccCcccccccccCCC--CCCCCCCCCCCCCcccccccCCCceeeecCccccCCcCCCCCCCCcccchHhhHHHHH
Q 030824 80 AAEPFVGSSLSAAASQQLSV--EQPEPQAKGPTRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFKVTGRDAIA 157 (171)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~~--~~~~~~k~~~~rC~~C~kk~gl~gf~CrCg~~fC~~HR~~e~H~C~~Dyk~~~r~~l~ 157 (171)
.... +. ......++. .........++||..|+|+|||+||.||||++||+.|||+|.|+|+||||.+||+.|+
T Consensus 79 ~~~~-~~----~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~ 153 (167)
T KOG3173|consen 79 TTES-EL----KLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIA 153 (167)
T ss_pred cccc-cc----cccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHH
Confidence 0000 00 000011111 1112345668899999999999999999999999999999999999999999999999
Q ss_pred HhCCccccccccCC
Q 030824 158 RANPVVKADKLDRI 171 (171)
Q Consensus 158 k~np~vka~Ki~KI 171 (171)
|+||+|+|+||+||
T Consensus 154 k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 154 KANPVVKADKLQKI 167 (167)
T ss_pred HhCCeeeccccccC
Confidence 99999999999998
No 2
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.58 E-value=7.4e-16 Score=89.37 Aligned_cols=25 Identities=68% Similarity=1.576 Sum_probs=20.8
Q ss_pred ccchhcCCCCCCccccCCchhHHhH
Q 030824 16 PKLCVNGCAFFGTAANMGLCSKCYR 40 (171)
Q Consensus 16 p~lC~n~CGFfGs~at~n~CSkCyr 40 (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 3
>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=99.51 E-value=3.3e-15 Score=87.38 Aligned_cols=25 Identities=56% Similarity=1.327 Sum_probs=23.4
Q ss_pred ccchh-cCCCCCCccccCCchhHHhH
Q 030824 16 PKLCV-NGCAFFGTAANMGLCSKCYR 40 (171)
Q Consensus 16 p~lC~-n~CGFfGs~at~n~CSkCyr 40 (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 4
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.49 E-value=1e-14 Score=92.38 Aligned_cols=38 Identities=68% Similarity=1.446 Sum_probs=36.5
Q ss_pred CcccccccCCCceeee-cCccccCCcCCCCCCCCcccch
Q 030824 112 CLSCNKKVGLTGFKCK-CGSTFCGIHRYPEKHDCTFDFK 149 (171)
Q Consensus 112 C~~C~kk~gl~gf~Cr-Cg~~fC~~HR~~e~H~C~~Dyk 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 7899999999999997 9999999999999999999996
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=99.02 E-value=8e-11 Score=75.55 Aligned_cols=38 Identities=50% Similarity=0.930 Sum_probs=27.8
Q ss_pred Ccc--cccccCCCceeee-cCccccCCcCCCCCCCCcccchH
Q 030824 112 CLS--CNKKVGLTGFKCK-CGSTFCGIHRYPEKHDCTFDFKV 150 (171)
Q Consensus 112 C~~--C~kk~gl~gf~Cr-Cg~~fC~~HR~~e~H~C~~Dyk~ 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 454 999886 899997 99999999999999999999874
No 6
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=97.12 E-value=0.00017 Score=61.98 Aligned_cols=40 Identities=33% Similarity=0.822 Sum_probs=35.2
Q ss_pred CCCc--ccccccCCCceee-ecCccccCCcCCCCCCCCcccchH
Q 030824 110 TRCL--SCNKKVGLTGFKC-KCGSTFCGIHRYPEKHDCTFDFKV 150 (171)
Q Consensus 110 ~rC~--~C~kk~gl~gf~C-rCg~~fC~~HR~~e~H~C~~Dyk~ 150 (171)
..|. .|+. +..++|+| .|+..||..||.-+.|+|.+-|..
T Consensus 9 kHCs~~~Ckq-lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCKQ-LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhhh-ccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4687 8977 67899999 699999999999999999987764
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.38 E-value=0.0017 Score=52.91 Aligned_cols=39 Identities=36% Similarity=0.587 Sum_probs=29.5
Q ss_pred CCcccccccC--CCceee-ecCccccCCcCCCCCCCCcccch
Q 030824 111 RCLSCNKKVG--LTGFKC-KCGSTFCGIHRYPEKHDCTFDFK 149 (171)
Q Consensus 111 rC~~C~kk~g--l~gf~C-rCg~~fC~~HR~~e~H~C~~Dyk 149 (171)
+|..|-..++ -+.++| .|++.||+.||+++.|+|.+...
T Consensus 96 ~~a~~~~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 96 RCATPQCTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred eeecceeccCCccccccccCCCCcceeceecccccccccHHH
Confidence 5554433332 246899 69999999999999999998755
No 8
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=94.67 E-value=0.0063 Score=52.44 Aligned_cols=41 Identities=37% Similarity=0.852 Sum_probs=35.3
Q ss_pred CCCCCCCCc--ccccccCCC-ceee-ecCccccCCcCCCCCCCCc
Q 030824 105 QAKGPTRCL--SCNKKVGLT-GFKC-KCGSTFCGIHRYPEKHDCT 145 (171)
Q Consensus 105 ~k~~~~rC~--~C~kk~gl~-gf~C-rCg~~fC~~HR~~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 566778886 899988664 5999 5999999999999999997
No 9
>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=90.61 E-value=0.12 Score=35.17 Aligned_cols=29 Identities=31% Similarity=0.860 Sum_probs=17.2
Q ss_pred CCCCCcccccccCCC--ceeee-cCccccCCc
Q 030824 108 GPTRCLSCNKKVGLT--GFKCK-CGSTFCGIH 136 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~--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 356899999999987 48996 999999774
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=89.90 E-value=0.16 Score=33.08 Aligned_cols=28 Identities=36% Similarity=0.985 Sum_probs=23.5
Q ss_pred CCCCcccccccCCC--ceeee-cCccccCCc
Q 030824 109 PTRCLSCNKKVGLT--GFKCK-CGSTFCGIH 136 (171)
Q Consensus 109 ~~rC~~C~kk~gl~--gf~Cr-Cg~~fC~~H 136 (171)
...|..|.++.+++ ...|| ||.+||..+
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHH
Confidence 35799999999986 68995 999999863
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=86.14 E-value=0.39 Score=27.85 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=19.8
Q ss_pred CCCcccccccCCCceee-ecCccc
Q 030824 110 TRCLSCNKKVGLTGFKC-KCGSTF 132 (171)
Q Consensus 110 ~rC~~C~kk~gl~gf~C-rCg~~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 36899999998889999 499887
No 13
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=84.41 E-value=0.41 Score=46.37 Aligned_cols=45 Identities=31% Similarity=0.741 Sum_probs=33.9
Q ss_pred CCCCCCcccccccCCCc--eeee-cCccccCCcC-----------CCCCCCCcccchHh
Q 030824 107 KGPTRCLSCNKKVGLTG--FKCK-CGSTFCGIHR-----------YPEKHDCTFDFKVT 151 (171)
Q Consensus 107 ~~~~rC~~C~kk~gl~g--f~Cr-Cg~~fC~~HR-----------~~e~H~C~~Dyk~~ 151 (171)
.....|..|+.+.|+++ ..|| ||.+||+.|- |-+---|..+|...
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l 221 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELL 221 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHh
Confidence 34578999999999985 7897 9999999874 33345566676533
No 14
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=72.89 E-value=2 Score=37.71 Aligned_cols=30 Identities=43% Similarity=0.967 Sum_probs=23.4
Q ss_pred CCCCCCCCcccccc---------cCCCceee-ecCccccC
Q 030824 105 QAKGPTRCLSCNKK---------VGLTGFKC-KCGSTFCG 134 (171)
Q Consensus 105 ~k~~~~rC~~C~kk---------~gl~gf~C-rCg~~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 44557899999988 55567999 79999844
No 15
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=71.42 E-value=1.2 Score=29.94 Aligned_cols=24 Identities=33% Similarity=0.743 Sum_probs=18.8
Q ss_pred CCCCcccccccCCC------ceee-ecCccc
Q 030824 109 PTRCLSCNKKVGLT------GFKC-KCGSTF 132 (171)
Q Consensus 109 ~~rC~~C~kk~gl~------gf~C-rCg~~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 46999999988663 4789 898765
No 16
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=70.47 E-value=2.3 Score=27.19 Aligned_cols=24 Identities=42% Similarity=1.042 Sum_probs=17.6
Q ss_pred CCCCCccccccc---CCCceeee-cCcc
Q 030824 108 GPTRCLSCNKKV---GLTGFKCK-CGST 131 (171)
Q Consensus 108 ~~~rC~~C~kk~---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 467899999999 56799994 7654
No 17
>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=65.31 E-value=2.7 Score=28.14 Aligned_cols=34 Identities=29% Similarity=0.757 Sum_probs=17.4
Q ss_pred CcccccccCCC--------ceee-ecCccccCC---cCCCCCCCCc
Q 030824 112 CLSCNKKVGLT--------GFKC-KCGSTFCGI---HRYPEKHDCT 145 (171)
Q Consensus 112 C~~C~kk~gl~--------gf~C-rCg~~fC~~---HR~~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 66677766653 5999 799999965 3444467765
No 18
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=65.26 E-value=3.6 Score=27.70 Aligned_cols=23 Identities=30% Similarity=0.793 Sum_probs=15.9
Q ss_pred CcccccccCCCceee-ecCccccCC
Q 030824 112 CLSCNKKVGLTGFKC-KCGSTFCGI 135 (171)
Q Consensus 112 C~~C~kk~gl~gf~C-rCg~~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 6677765 4456889 799999995
No 19
>PHA02768 hypothetical protein; Provisional
Probab=62.55 E-value=3.1 Score=28.30 Aligned_cols=16 Identities=31% Similarity=0.910 Sum_probs=13.2
Q ss_pred CCCceee-ecCccccCC
Q 030824 120 GLTGFKC-KCGSTFCGI 135 (171)
Q Consensus 120 gl~gf~C-rCg~~fC~~ 135 (171)
.|+||.| .||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 4789999 699999765
No 20
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=60.40 E-value=3.3 Score=27.59 Aligned_cols=23 Identities=39% Similarity=1.051 Sum_probs=17.2
Q ss_pred CCCCcccccccCCC----ceee-ecCcc
Q 030824 109 PTRCLSCNKKVGLT----GFKC-KCGST 131 (171)
Q Consensus 109 ~~rC~~C~kk~gl~----gf~C-rCg~~ 131 (171)
..+|..|++.+.++ +..| +||.-
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 46899999999754 7889 47643
No 21
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=57.09 E-value=5.1 Score=27.24 Aligned_cols=18 Identities=22% Similarity=0.648 Sum_probs=15.9
Q ss_pred ccCCcCCCCCCCCcccch
Q 030824 132 FCGIHRYPEKHDCTFDFK 149 (171)
Q Consensus 132 fC~~HR~~e~H~C~~Dyk 149 (171)
=|--|.|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 467899999999999996
No 22
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.48 E-value=6.6 Score=36.56 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=34.4
Q ss_pred CCCcccccccCCC---ceee-ecCccccCCcCCCCCCCCc--ccchHhhHHHHHH
Q 030824 110 TRCLSCNKKVGLT---GFKC-KCGSTFCGIHRYPEKHDCT--FDFKVTGRDAIAR 158 (171)
Q Consensus 110 ~rC~~C~kk~gl~---gf~C-rCg~~fC~~HR~~e~H~C~--~Dyk~~~r~~l~k 158 (171)
-+|-.|+.++-.. ||+| +||..+=..-+..-.++-. +++-.-+|.+|.|
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk 405 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK 405 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC
Confidence 4899999887554 7999 5999887663333334333 5666778888876
No 23
>PHA00626 hypothetical protein
Probab=50.01 E-value=8.4 Score=26.60 Aligned_cols=23 Identities=13% Similarity=0.271 Sum_probs=16.2
Q ss_pred CCCcccccccCCCceee-ecCccccC
Q 030824 110 TRCLSCNKKVGLTGFKC-KCGSTFCG 134 (171)
Q Consensus 110 ~rC~~C~kk~gl~gf~C-rCg~~fC~ 134 (171)
.||..|++ ....|.| +||+.|-.
T Consensus 12 vrcg~cr~--~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRG--WSDDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecc--cCcceEcCCCCCeech
Confidence 47778876 2346999 69888864
No 24
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=49.26 E-value=11 Score=34.43 Aligned_cols=40 Identities=23% Similarity=0.672 Sum_probs=27.6
Q ss_pred CCCCCCCccc-ccccCCCceeee-cCccccCC---cCCCCCCCCc
Q 030824 106 AKGPTRCLSC-NKKVGLTGFKCK-CGSTFCGI---HRYPEKHDCT 145 (171)
Q Consensus 106 k~~~~rC~~C-~kk~gl~gf~Cr-Cg~~fC~~---HR~~e~H~C~ 145 (171)
....++|+.| .+.++...|.|. |..+||.. -.+---|.|.
T Consensus 327 ~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~Cp 371 (378)
T KOG2807|consen 327 YNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCP 371 (378)
T ss_pred cCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCC
Confidence 3456789999 565666789995 99999975 2222345554
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.06 E-value=11 Score=21.06 Aligned_cols=21 Identities=24% Similarity=0.717 Sum_probs=13.3
Q ss_pred CCcccccccCCCceee-ecCcc
Q 030824 111 RCLSCNKKVGLTGFKC-KCGST 131 (171)
Q Consensus 111 rC~~C~kk~gl~gf~C-rCg~~ 131 (171)
+|..|++.+.-..-.| .||..
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 4677777776655556 46643
No 26
>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=48.58 E-value=8.4 Score=25.44 Aligned_cols=27 Identities=26% Similarity=0.630 Sum_probs=22.9
Q ss_pred CcccccccCCCceeeec--CccccCCcCC
Q 030824 112 CLSCNKKVGLTGFKCKC--GSTFCGIHRY 138 (171)
Q Consensus 112 C~~C~kk~gl~gf~CrC--g~~fC~~HR~ 138 (171)
|..|+.-.=|..+.|.| +.++|-.|-.
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~~ 29 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHAK 29 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccch
Confidence 67888888888999997 8999998854
No 27
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=44.72 E-value=7.8 Score=24.39 Aligned_cols=24 Identities=33% Similarity=0.789 Sum_probs=17.7
Q ss_pred CCcccccccCCCceee-ecCccccCCc
Q 030824 111 RCLSCNKKVGLTGFKC-KCGSTFCGIH 136 (171)
Q Consensus 111 rC~~C~kk~gl~gf~C-rCg~~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 6888886443 5678 6999999763
No 28
>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=44.04 E-value=10 Score=29.72 Aligned_cols=31 Identities=35% Similarity=0.662 Sum_probs=22.0
Q ss_pred CCCCcccccccCCC---ceee-ecCccc-cCCcCCC
Q 030824 109 PTRCLSCNKKVGLT---GFKC-KCGSTF-CGIHRYP 139 (171)
Q Consensus 109 ~~rC~~C~kk~gl~---gf~C-rCg~~f-C~~HR~~ 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 3899 688775 3446663
No 29
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=43.79 E-value=12 Score=25.97 Aligned_cols=12 Identities=50% Similarity=1.398 Sum_probs=9.2
Q ss_pred CCCCcccccccC
Q 030824 109 PTRCLSCNKKVG 120 (171)
Q Consensus 109 ~~rC~~C~kk~g 120 (171)
|-||++|+|-++
T Consensus 4 PVRCFTCGkvi~ 15 (60)
T PF01194_consen 4 PVRCFTCGKVIG 15 (60)
T ss_dssp SSS-STTTSBTC
T ss_pred ceecCCCCCChh
Confidence 679999999775
No 30
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=43.73 E-value=9.9 Score=25.40 Aligned_cols=14 Identities=29% Similarity=0.793 Sum_probs=11.0
Q ss_pred CceeeecCccccCC
Q 030824 122 TGFKCKCGSTFCGI 135 (171)
Q Consensus 122 ~gf~CrCg~~fC~~ 135 (171)
..+.||||+.|--.
T Consensus 17 ~~y~CRCG~~f~i~ 30 (55)
T PF05207_consen 17 YSYPCRCGGEFEIS 30 (55)
T ss_dssp EEEEETTSSEEEEE
T ss_pred EEEcCCCCCEEEEc
Confidence 46899999998644
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.80 E-value=13 Score=23.42 Aligned_cols=29 Identities=31% Similarity=0.716 Sum_probs=18.3
Q ss_pred CCCcccccccCCC----ceee-ecCccccCCcCC
Q 030824 110 TRCLSCNKKVGLT----GFKC-KCGSTFCGIHRY 138 (171)
Q Consensus 110 ~rC~~C~kk~gl~----gf~C-rCg~~fC~~HR~ 138 (171)
.+|..|+..+.+. .++| +||..+--.+|-
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKERP 37 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccCC
Confidence 4688888876442 5788 577666554443
No 32
>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=41.79 E-value=8.1 Score=22.93 Aligned_cols=23 Identities=26% Similarity=1.115 Sum_probs=15.2
Q ss_pred CCCcccccccCCCceee-ecCccccCC
Q 030824 110 TRCLSCNKKVGLTGFKC-KCGSTFCGI 135 (171)
Q Consensus 110 ~rC~~C~kk~gl~gf~C-rCg~~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 35788877 456899 799999985
No 33
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.25 E-value=17 Score=33.17 Aligned_cols=31 Identities=29% Similarity=0.762 Sum_probs=25.4
Q ss_pred CCCCCCcccccccCCCc----eeeecCccccCCcC
Q 030824 107 KGPTRCLSCNKKVGLTG----FKCKCGSTFCGIHR 137 (171)
Q Consensus 107 ~~~~rC~~C~kk~gl~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 44678999999888863 99999999997644
No 34
>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=40.86 E-value=16 Score=22.18 Aligned_cols=23 Identities=35% Similarity=0.931 Sum_probs=17.6
Q ss_pred CCCCCcccccccCCC--ceeee-cCc
Q 030824 108 GPTRCLSCNKKVGLT--GFKCK-CGS 130 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~--gf~Cr-Cg~ 130 (171)
.+..|..|++.+... |++|+ |+.
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCc
Confidence 367899999998763 88885 654
No 35
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=40.68 E-value=20 Score=20.87 Aligned_cols=20 Identities=25% Similarity=0.652 Sum_probs=16.2
Q ss_pred CCcccccccCCC-ceee-ecCc
Q 030824 111 RCLSCNKKVGLT-GFKC-KCGS 130 (171)
Q Consensus 111 rC~~C~kk~gl~-gf~C-rCg~ 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 8999 4663
No 36
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=39.77 E-value=6.4 Score=34.82 Aligned_cols=33 Identities=24% Similarity=0.699 Sum_probs=25.3
Q ss_pred CCCCCCccccc-ccCCC--ceeee-cCccccCCcCCCC
Q 030824 107 KGPTRCLSCNK-KVGLT--GFKCK-CGSTFCGIHRYPE 140 (171)
Q Consensus 107 ~~~~rC~~C~k-k~gl~--gf~Cr-Cg~~fC~~HR~~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 66665 47796 9999999 76543
No 37
>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=39.64 E-value=16 Score=25.45 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=12.1
Q ss_pred ceeeecCcc-------ccCCc
Q 030824 123 GFKCKCGST-------FCGIH 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 489999998 88887
No 38
>PF14369 zf-RING_3: zinc-finger
Probab=39.34 E-value=13 Score=22.70 Aligned_cols=22 Identities=32% Similarity=0.810 Sum_probs=14.6
Q ss_pred CCcccccccCCC----cee-e-ecCccc
Q 030824 111 RCLSCNKKVGLT----GFK-C-KCGSTF 132 (171)
Q Consensus 111 rC~~C~kk~gl~----gf~-C-rCg~~f 132 (171)
=|+.|++.|.+. ... | +|++.|
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 378888777653 344 7 687766
No 39
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=38.66 E-value=11 Score=26.38 Aligned_cols=14 Identities=36% Similarity=0.880 Sum_probs=10.9
Q ss_pred CCCCCcccccccCC
Q 030824 108 GPTRCLSCNKKVGL 121 (171)
Q Consensus 108 ~~~rC~~C~kk~gl 121 (171)
.|-||++|+|-+|-
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 36799999997743
No 40
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=38.54 E-value=11 Score=24.83 Aligned_cols=21 Identities=43% Similarity=1.108 Sum_probs=15.7
Q ss_pred CCcccccccCCC-------ceee-ecCcc
Q 030824 111 RCLSCNKKVGLT-------GFKC-KCGST 131 (171)
Q Consensus 111 rC~~C~kk~gl~-------gf~C-rCg~~ 131 (171)
+|..|++++||+ |+-| .|-..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHH
Confidence 589999999997 5777 36433
No 41
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=37.84 E-value=12 Score=26.83 Aligned_cols=13 Identities=46% Similarity=1.214 Sum_probs=10.5
Q ss_pred CCCCcccccccCC
Q 030824 109 PTRCLSCNKKVGL 121 (171)
Q Consensus 109 ~~rC~~C~kk~gl 121 (171)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999997753
No 42
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=37.51 E-value=16 Score=35.61 Aligned_cols=32 Identities=25% Similarity=0.817 Sum_probs=21.2
Q ss_pred CCCCCCCCcccccccCCC--ceeee-cCccccCCc
Q 030824 105 QAKGPTRCLSCNKKVGLT--GFKCK-CGSTFCGIH 136 (171)
Q Consensus 105 ~k~~~~rC~~C~kk~gl~--gf~Cr-Cg~~fC~~H 136 (171)
+-....+|-.|....... .-.|| ||++||++-
T Consensus 897 pd~~a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 897 PDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred CCCcchhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 334567898886533221 35797 999999863
No 43
>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=37.35 E-value=15 Score=28.41 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=25.0
Q ss_pred cccccccCCCceeeecCccccCCcCCCCCCCCccc
Q 030824 113 LSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFD 147 (171)
Q Consensus 113 ~~C~kk~gl~gf~CrCg~~fC~~HR~~e~H~C~~D 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 5566655 26899999999999888777776544
No 44
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=37.30 E-value=23 Score=26.67 Aligned_cols=31 Identities=29% Similarity=0.723 Sum_probs=23.0
Q ss_pred CCCCCcccccccCCC---ceee-ecCccccCCcCC
Q 030824 108 GPTRCLSCNKKVGLT---GFKC-KCGSTFCGIHRY 138 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~---gf~C-rCg~~fC~~HR~ 138 (171)
....|..|.+.+|++ |..| .|+..+|..=+.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 346899999998886 6899 599999987444
No 45
>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=36.78 E-value=19 Score=22.07 Aligned_cols=24 Identities=33% Similarity=0.757 Sum_probs=18.4
Q ss_pred CCCCCcccccccCC---Cceeee-cCcc
Q 030824 108 GPTRCLSCNKKVGL---TGFKCK-CGST 131 (171)
Q Consensus 108 ~~~rC~~C~kk~gl---~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 35689999999884 689995 7544
No 46
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=36.73 E-value=9.6 Score=25.98 Aligned_cols=20 Identities=35% Similarity=0.355 Sum_probs=16.2
Q ss_pred HhhHHHHHHhCCcccccccc
Q 030824 150 VTGRDAIARANPVVKADKLD 169 (171)
Q Consensus 150 ~~~r~~l~k~np~vka~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 34478899999999888875
No 47
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=36.18 E-value=28 Score=24.08 Aligned_cols=33 Identities=30% Similarity=0.623 Sum_probs=24.7
Q ss_pred CCCCcc--cccccCCCceee-ecCccccCCcCCC-CCCCC
Q 030824 109 PTRCLS--CNKKVGLTGFKC-KCGSTFCGIHRYP-EKHDC 144 (171)
Q Consensus 109 ~~rC~~--C~kk~gl~gf~C-rCg~~fC~~HR~~-e~H~C 144 (171)
...|.. |+. +.=..| +|...+|-.|-.. +.|.|
T Consensus 27 ~~~C~~~gC~~---~s~I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 27 AGDCDITGCNN---TSFIRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred cCcCCCCCCCC---cCEEEccccCCcccccceeeeeeEcC
Confidence 445665 754 344788 8999999999995 77877
No 48
>PHA00616 hypothetical protein
Probab=35.50 E-value=10 Score=24.65 Aligned_cols=11 Identities=36% Similarity=1.283 Sum_probs=8.7
Q ss_pred eee-ecCccccC
Q 030824 124 FKC-KCGSTFCG 134 (171)
Q Consensus 124 f~C-rCg~~fC~ 134 (171)
|+| +||..|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 678 89988864
No 49
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=35.46 E-value=21 Score=36.53 Aligned_cols=26 Identities=27% Similarity=0.770 Sum_probs=20.4
Q ss_pred CCCcccccccCCC-------ceeee-cCccccCC
Q 030824 110 TRCLSCNKKVGLT-------GFKCK-CGSTFCGI 135 (171)
Q Consensus 110 ~rC~~C~kk~gl~-------gf~Cr-Cg~~fC~~ 135 (171)
..|..|+++-..+ --.|| ||.+||+.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCcc
Confidence 5799999988632 35597 99999876
No 50
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=34.49 E-value=17 Score=25.12 Aligned_cols=20 Identities=40% Similarity=0.916 Sum_probs=14.8
Q ss_pred CCCCcccccccCCCceee-ecCc
Q 030824 109 PTRCLSCNKKVGLTGFKC-KCGS 130 (171)
Q Consensus 109 ~~rC~~C~kk~gl~gf~C-rCg~ 130 (171)
-.||..||| ....++| .||.
T Consensus 36 I~RC~~CRk--~~~~Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRK--QSNPYTCPKCGF 56 (59)
T ss_pred EeechhHHh--cCCceECCCCCC
Confidence 568999988 2357888 7875
No 51
>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=33.31 E-value=18 Score=20.83 Aligned_cols=22 Identities=27% Similarity=0.745 Sum_probs=8.3
Q ss_pred CCcccccccCC-Cceee-ecCccc
Q 030824 111 RCLSCNKKVGL-TGFKC-KCGSTF 132 (171)
Q Consensus 111 rC~~C~kk~gl-~gf~C-rCg~~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 68999998887 78888 476543
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=33.23 E-value=20 Score=21.85 Aligned_cols=9 Identities=56% Similarity=1.567 Sum_probs=4.9
Q ss_pred eee-ecCccc
Q 030824 124 FKC-KCGSTF 132 (171)
Q Consensus 124 f~C-rCg~~f 132 (171)
.+| +||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 555 465554
No 53
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=32.34 E-value=15 Score=29.34 Aligned_cols=24 Identities=21% Similarity=0.532 Sum_probs=18.9
Q ss_pred CCCCCcccccccCCC-----ceee-ecCcc
Q 030824 108 GPTRCLSCNKKVGLT-----GFKC-KCGST 131 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~-----gf~C-rCg~~ 131 (171)
.-..|..|+.|.... +|.| +||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 346788999888664 8999 79987
No 54
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=31.95 E-value=15 Score=25.91 Aligned_cols=13 Identities=46% Similarity=1.173 Sum_probs=10.6
Q ss_pred CCCCcccccccCC
Q 030824 109 PTRCLSCNKKVGL 121 (171)
Q Consensus 109 ~~rC~~C~kk~gl 121 (171)
|-||++|+|-+|.
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999997764
No 55
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.74 E-value=23 Score=31.08 Aligned_cols=27 Identities=30% Similarity=0.816 Sum_probs=22.3
Q ss_pred CCCCcccccccCCCceee-ecCccccCCc
Q 030824 109 PTRCLSCNKKVGLTGFKC-KCGSTFCGIH 136 (171)
Q Consensus 109 ~~rC~~C~kk~gl~gf~C-rCg~~fC~~H 136 (171)
+..|+ |-+++-..||.| +|...||...
T Consensus 242 ra~Cf-Ch~k~v~~GyvCs~Clsi~C~~p 269 (279)
T TIGR00627 242 RASCF-CHHQLVSIGFVCSVCLSVLCQYT 269 (279)
T ss_pred cceee-ecCccccceEECCCccCCcCCCC
Confidence 34666 788888899999 8999999865
No 56
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.28 E-value=28 Score=26.46 Aligned_cols=27 Identities=33% Similarity=0.602 Sum_probs=19.7
Q ss_pred CCCCcccccccCC---Cceee-ecCccccCC
Q 030824 109 PTRCLSCNKKVGL---TGFKC-KCGSTFCGI 135 (171)
Q Consensus 109 ~~rC~~C~kk~gl---~gf~C-rCg~~fC~~ 135 (171)
+..|..|++|--- .+..| +||..|=-.
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 5679999998543 36889 788877544
No 57
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=30.70 E-value=34 Score=21.95 Aligned_cols=18 Identities=39% Similarity=0.925 Sum_probs=14.8
Q ss_pred Cceee-ecCccccCCcCCC
Q 030824 122 TGFKC-KCGSTFCGIHRYP 139 (171)
Q Consensus 122 ~gf~C-rCg~~fC~~HR~~ 139 (171)
..+.| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 45889 8999999988765
No 58
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=29.17 E-value=30 Score=20.65 Aligned_cols=9 Identities=44% Similarity=1.442 Sum_probs=4.6
Q ss_pred eee-ecCccc
Q 030824 124 FKC-KCGSTF 132 (171)
Q Consensus 124 f~C-rCg~~f 132 (171)
+.| +||..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 455 455544
No 59
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.26 E-value=20 Score=29.32 Aligned_cols=25 Identities=28% Similarity=0.809 Sum_probs=19.5
Q ss_pred CCCCCcccccccCCC-----ceee-ecCccc
Q 030824 108 GPTRCLSCNKKVGLT-----GFKC-KCGSTF 132 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~-----gf~C-rCg~~f 132 (171)
.-..|..|++|.... +|.| .||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 356799999988664 8999 798764
No 60
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=28.14 E-value=30 Score=28.29 Aligned_cols=19 Identities=37% Similarity=1.165 Sum_probs=15.3
Q ss_pred ceeeecCccccCCcCCCCCCC
Q 030824 123 GFKCKCGSTFCGIHRYPEKHD 143 (171)
Q Consensus 123 gf~CrCg~~fC~~HR~~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 488987 7999999776665
No 61
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=27.14 E-value=21 Score=29.67 Aligned_cols=27 Identities=30% Similarity=0.485 Sum_probs=21.6
Q ss_pred CCCCCCCCcccccccCCCceee-ecCcc
Q 030824 105 QAKGPTRCLSCNKKVGLTGFKC-KCGST 131 (171)
Q Consensus 105 ~k~~~~rC~~C~kk~gl~gf~C-rCg~~ 131 (171)
...+..||+.|++......-.| .||..
T Consensus 135 v~~w~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 135 VRKWRLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred EeeeeEEEecCceecCCCCCcCCCCCCc
Confidence 4557899999999888667888 68865
No 62
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.08 E-value=45 Score=19.91 Aligned_cols=26 Identities=38% Similarity=0.821 Sum_probs=18.3
Q ss_pred CCcccccccC-C-Cceee-ecCccccCCc
Q 030824 111 RCLSCNKKVG-L-TGFKC-KCGSTFCGIH 136 (171)
Q Consensus 111 rC~~C~kk~g-l-~gf~C-rCg~~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 67999 5988888776
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=27.01 E-value=25 Score=22.51 Aligned_cols=16 Identities=38% Similarity=0.924 Sum_probs=13.5
Q ss_pred eeee-cCccccCCcCCC
Q 030824 124 FKCK-CGSTFCGIHRYP 139 (171)
Q Consensus 124 f~Cr-Cg~~fC~~HR~~ 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 7896 999999997754
No 64
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.67 E-value=26 Score=24.44 Aligned_cols=22 Identities=36% Similarity=0.866 Sum_probs=15.0
Q ss_pred CCCCCCcccccccCCCceee-ecCc
Q 030824 107 KGPTRCLSCNKKVGLTGFKC-KCGS 130 (171)
Q Consensus 107 ~~~~rC~~C~kk~gl~gf~C-rCg~ 130 (171)
+.-.||..||| + -..+.| .||.
T Consensus 36 ~~I~Rc~~CRk-~-g~~Y~Cp~CGF 58 (61)
T COG2888 36 VEIYRCAKCRK-L-GNPYRCPKCGF 58 (61)
T ss_pred eeeehhhhHHH-c-CCceECCCcCc
Confidence 34578888887 2 246888 6874
No 65
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=25.54 E-value=21 Score=25.02 Aligned_cols=12 Identities=58% Similarity=1.417 Sum_probs=9.9
Q ss_pred CCCCcccccccC
Q 030824 109 PTRCLSCNKKVG 120 (171)
Q Consensus 109 ~~rC~~C~kk~g 120 (171)
|-||++|+|-+|
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 679999999764
No 66
>PRK08402 replication factor A; Reviewed
Probab=25.14 E-value=36 Score=30.84 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=18.1
Q ss_pred CCCcccccccCC----Cceeee-cCccccCCcCC
Q 030824 110 TRCLSCNKKVGL----TGFKCK-CGSTFCGIHRY 138 (171)
Q Consensus 110 ~rC~~C~kk~gl----~gf~Cr-Cg~~fC~~HR~ 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 689999999952 247774 554333 4554
No 67
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.95 E-value=34 Score=21.91 Aligned_cols=20 Identities=25% Similarity=0.841 Sum_probs=13.4
Q ss_pred CCCcccccccCCC---ceeee-cC
Q 030824 110 TRCLSCNKKVGLT---GFKCK-CG 129 (171)
Q Consensus 110 ~rC~~C~kk~gl~---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 3678888877664 47774 54
No 68
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.93 E-value=42 Score=22.75 Aligned_cols=24 Identities=33% Similarity=0.844 Sum_probs=18.2
Q ss_pred CCCCccccccc--CCCceee-ecCccc
Q 030824 109 PTRCLSCNKKV--GLTGFKC-KCGSTF 132 (171)
Q Consensus 109 ~~rC~~C~kk~--gl~gf~C-rCg~~f 132 (171)
..+|..|++++ +--...| .||..|
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcc
Confidence 46899999999 5556888 577664
No 69
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=24.55 E-value=30 Score=18.07 Aligned_cols=11 Identities=45% Similarity=1.358 Sum_probs=6.2
Q ss_pred eee-ecCccccC
Q 030824 124 FKC-KCGSTFCG 134 (171)
Q Consensus 124 f~C-rCg~~fC~ 134 (171)
|.| .||..|-.
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 456 46666643
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.24 E-value=60 Score=25.04 Aligned_cols=37 Identities=22% Similarity=0.492 Sum_probs=24.3
Q ss_pred CCCcccccccCC------------Cceee-ecCccccCC---cCCCCCCCCcc
Q 030824 110 TRCLSCNKKVGL------------TGFKC-KCGSTFCGI---HRYPEKHDCTF 146 (171)
Q Consensus 110 ~rC~~C~kk~gl------------~gf~C-rCg~~fC~~---HR~~e~H~C~~ 146 (171)
..|+.|.+.+.. ..|.| +|+..||-. -.+-.-|+|..
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPG 108 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPG 108 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcC
Confidence 459999886542 25899 799999933 22223566653
No 71
>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=24.23 E-value=33 Score=20.71 Aligned_cols=16 Identities=31% Similarity=0.827 Sum_probs=7.6
Q ss_pred CcccccccCCC---ceeee
Q 030824 112 CLSCNKKVGLT---GFKCK 127 (171)
Q Consensus 112 C~~C~kk~gl~---gf~Cr 127 (171)
|..|+..+.|. ...|+
T Consensus 3 C~~Cg~~~~~~~~~~irC~ 21 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCP 21 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBS
T ss_pred CCcCCCeeEcCCCCcEECC
Confidence 55555555543 34553
No 72
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=23.89 E-value=76 Score=24.36 Aligned_cols=45 Identities=18% Similarity=0.369 Sum_probs=32.1
Q ss_pred CCCCCCCCcccccccCCCceeeecCccccCCcCCCCCCCCcccchHhhH
Q 030824 105 QAKGPTRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFKVTGR 153 (171)
Q Consensus 105 ~k~~~~rC~~C~kk~gl~gf~CrCg~~fC~~HR~~e~H~C~~Dyk~~~r 153 (171)
......-|.+|+...+.....|+ .|+.=-+--+|.|.+--.=.|+
T Consensus 44 ~~~~~~~C~~C~~~kp~Rs~HC~----~C~~CV~~~DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 44 ENGELKYCSTCKIIKPPRSHHCR----VCNRCVLRFDHHCPWLGNCIGR 88 (174)
T ss_pred cCCCCEECcccCCcCCCcceecc----ccccccccccccchhhcccccc
Confidence 34456789999998888899997 5555334448999976655444
No 73
>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=23.79 E-value=59 Score=22.85 Aligned_cols=24 Identities=33% Similarity=0.724 Sum_probs=16.8
Q ss_pred CCCCcccccccCCCceeee-cCccc
Q 030824 109 PTRCLSCNKKVGLTGFKCK-CGSTF 132 (171)
Q Consensus 109 ~~rC~~C~kk~gl~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 4579999999988655543 54443
No 74
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=23.27 E-value=57 Score=33.32 Aligned_cols=31 Identities=35% Similarity=0.907 Sum_probs=23.3
Q ss_pred CCCCCCCCCccccccc--------------CCCceeee-cCccccC
Q 030824 104 PQAKGPTRCLSCNKKV--------------GLTGFKCK-CGSTFCG 134 (171)
Q Consensus 104 ~~k~~~~rC~~C~kk~--------------gl~gf~Cr-Cg~~fC~ 134 (171)
.+...+|.|-.|.+-| |-..|+|+ ||+-|--
T Consensus 600 ~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtT 645 (958)
T KOG1074|consen 600 NKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTT 645 (958)
T ss_pred cccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhcc
Confidence 3566789999887743 33479997 9999973
No 75
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=23.14 E-value=28 Score=29.24 Aligned_cols=48 Identities=21% Similarity=0.331 Sum_probs=31.1
Q ss_pred CCCcccccccCCCceee-ecCccccCCcC----------CCCCCCCcccchHhhHHHHH
Q 030824 110 TRCLSCNKKVGLTGFKC-KCGSTFCGIHR----------YPEKHDCTFDFKVTGRDAIA 157 (171)
Q Consensus 110 ~rC~~C~kk~gl~gf~C-rCg~~fC~~HR----------~~e~H~C~~Dyk~~~r~~l~ 157 (171)
-.|..|.+.+.+.+..| +||..+=..|- +-++|.+.|+|...-|+.|.
T Consensus 25 ~~C~~C~~~~~~~~~~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~l~~~i~ 83 (225)
T COG1040 25 GLCSGCQADLPLIGNLCPLCGLPLSSHACRCGECLAKPPPFERLRSLGSYNGPLRELIS 83 (225)
T ss_pred CcChhhhhchhHHHhhhHhhhChhccccccCHHHhcCCCcceeEEEEEEccHHHHHHHH
Confidence 35677777666665566 46655544311 13467899999998888775
No 76
>PRK07218 replication factor A; Provisional
Probab=23.08 E-value=38 Score=31.47 Aligned_cols=20 Identities=25% Similarity=0.687 Sum_probs=15.1
Q ss_pred CCCCcccccccCCCceeee-cCc
Q 030824 109 PTRCLSCNKKVGLTGFKCK-CGS 130 (171)
Q Consensus 109 ~~rC~~C~kk~gl~gf~Cr-Cg~ 130 (171)
-.||..|+++|.. +.|+ ||.
T Consensus 297 i~rCP~C~r~v~~--~~C~~hG~ 317 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRSHGA 317 (423)
T ss_pred eecCcCccccccC--CcCCCCCC
Confidence 4899999998854 6776 543
No 77
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=22.92 E-value=43 Score=27.25 Aligned_cols=28 Identities=21% Similarity=0.724 Sum_probs=21.2
Q ss_pred CCCCCCCCcccccccCCCceee-ecCccccCC
Q 030824 105 QAKGPTRCLSCNKKVGLTGFKC-KCGSTFCGI 135 (171)
Q Consensus 105 ~k~~~~rC~~C~kk~gl~gf~C-rCg~~fC~~ 135 (171)
-++...-|..|+- ..-+.| .||..||+.
T Consensus 114 ~KP~r~fCaVCG~---~S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 114 FKPLRKFCAVCGY---DSKYSCVNCGTKYCSV 142 (156)
T ss_pred CCCcchhhhhcCC---CchhHHHhcCCceeec
Confidence 3455678999962 345888 799999986
No 78
>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=22.75 E-value=55 Score=23.91 Aligned_cols=14 Identities=14% Similarity=0.480 Sum_probs=11.5
Q ss_pred CCCCcccccccCCC
Q 030824 109 PTRCLSCNKKVGLT 122 (171)
Q Consensus 109 ~~rC~~C~kk~gl~ 122 (171)
+.+|..|++++...
T Consensus 33 rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 33 RSHCPHCGHPLSWW 46 (92)
T ss_pred CCcCcCCCCcCccc
Confidence 67999999988754
No 79
>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=22.62 E-value=37 Score=20.31 Aligned_cols=11 Identities=64% Similarity=1.071 Sum_probs=8.2
Q ss_pred ecCccccCCcC
Q 030824 127 KCGSTFCGIHR 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 34678999985
No 80
>PRK12366 replication factor A; Reviewed
Probab=22.41 E-value=38 Score=32.85 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=20.7
Q ss_pred CCCCcccccccCCC--ceee-ecCccccCCcCC
Q 030824 109 PTRCLSCNKKVGLT--GFKC-KCGSTFCGIHRY 138 (171)
Q Consensus 109 ~~rC~~C~kk~gl~--gf~C-rCg~~fC~~HR~ 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 2789 68877 224555
No 81
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=22.04 E-value=48 Score=22.04 Aligned_cols=22 Identities=32% Similarity=0.848 Sum_probs=18.3
Q ss_pred CCCCcccccccCCCceeee-cCc
Q 030824 109 PTRCLSCNKKVGLTGFKCK-CGS 130 (171)
Q Consensus 109 ~~rC~~C~kk~gl~gf~Cr-Cg~ 130 (171)
..-|..|.-++....-.|| ||+
T Consensus 14 k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCccccccccCCC
Confidence 4568999999998899996 875
No 82
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.99 E-value=52 Score=18.28 Aligned_cols=13 Identities=46% Similarity=1.196 Sum_probs=8.3
Q ss_pred CCCceee-ecCccc
Q 030824 120 GLTGFKC-KCGSTF 132 (171)
Q Consensus 120 gl~gf~C-rCg~~f 132 (171)
|.-.|.| .|+..|
T Consensus 11 ~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 11 GEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSEEESSSSEEE
T ss_pred CCCCCCCCCCcCee
Confidence 4446778 477666
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=21.97 E-value=42 Score=20.44 Aligned_cols=9 Identities=56% Similarity=1.567 Sum_probs=4.4
Q ss_pred eee-ecCccc
Q 030824 124 FKC-KCGSTF 132 (171)
Q Consensus 124 f~C-rCg~~f 132 (171)
.+| +|+.+|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 445 455444
No 84
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.67 E-value=31 Score=30.72 Aligned_cols=28 Identities=36% Similarity=0.908 Sum_probs=22.5
Q ss_pred CCCCCcccccccCCCceee-ecCccccCCcCC
Q 030824 108 GPTRCLSCNKKVGLTGFKC-KCGSTFCGIHRY 138 (171)
Q Consensus 108 ~~~rC~~C~kk~gl~gf~C-rCg~~fC~~HR~ 138 (171)
...+|..|++ |-.+.| ||..-||..|--
T Consensus 170 E~~KC~SCNr---lGq~sCLRCK~cfCddHvr 198 (314)
T PF06524_consen 170 ETFKCQSCNR---LGQYSCLRCKICFCDDHVR 198 (314)
T ss_pred cccccccccc---ccchhhhheeeeehhhhhh
Confidence 3578999988 556889 899999999853
No 85
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=21.56 E-value=22 Score=33.74 Aligned_cols=25 Identities=36% Similarity=1.002 Sum_probs=21.6
Q ss_pred CCCcccccccCCC--ceeee-cCccccC
Q 030824 110 TRCLSCNKKVGLT--GFKCK-CGSTFCG 134 (171)
Q Consensus 110 ~rC~~C~kk~gl~--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 58898 9999884
No 86
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=21.20 E-value=83 Score=25.77 Aligned_cols=23 Identities=22% Similarity=0.678 Sum_probs=15.0
Q ss_pred ceee-ecCccccCC---cCCCCCCCCc
Q 030824 123 GFKC-KCGSTFCGI---HRYPEKHDCT 145 (171)
Q Consensus 123 gf~C-rCg~~fC~~---HR~~e~H~C~ 145 (171)
.+.| -|+..||+. ..|.+.++..
T Consensus 139 ~~~C~~C~~~~Cs~Cs~~~y~~~~e~~ 165 (175)
T PF05458_consen 139 IRSCSSCSEVFCSLCSTVNYSDQYERV 165 (175)
T ss_pred HhhhhchhhhhhcCccccccCCccccc
Confidence 4556 477777654 7777777644
No 87
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=21.00 E-value=56 Score=23.01 Aligned_cols=26 Identities=23% Similarity=0.431 Sum_probs=10.6
Q ss_pred CCCcccccccCCCceeeecCccccCC
Q 030824 110 TRCLSCNKKVGLTGFKCKCGSTFCGI 135 (171)
Q Consensus 110 ~rC~~C~kk~gl~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 58888877543322223688999987
No 88
>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=20.64 E-value=65 Score=21.47 Aligned_cols=24 Identities=25% Similarity=0.685 Sum_probs=16.5
Q ss_pred CCCCCcccccccCC--C--ceeee-cCcc
Q 030824 108 GPTRCLSCNKKVGL--T--GFKCK-CGST 131 (171)
Q Consensus 108 ~~~rC~~C~kk~gl--~--gf~Cr-Cg~~ 131 (171)
.+..|..|+.++.. . .|.|. ||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 35679999887766 2 48884 7654
No 89
>PF00869 Flavi_glycoprot: Flavivirus glycoprotein, central and dimerisation domains; InterPro: IPR011999 Flaviviruses are small, enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Yellow fever virus (YFV), West Nile virus (WNV), Tick-borne encephalitis virus, Japanese encephalitis virus and Dengue virus 2 viruses []. Flaviviruses consist of three structural proteins: the core nucleocapsid protein C (IPR001122 from INTERPRO), and the envelope glycoproteins M (IPR000069 from INTERPRO) and E. Glycoprotein E is a class II viral fusion protein that mediates both receptor binding and fusion. Class II viral fusion proteins are found in flaviviruses and alphaviruses, and are structurally distinct from class I fusion proteins from influenza virus and HIV. Glycoprotein E is comprised of three domains: domain I (dimerisation domain) is an 8-stranded beta barrel, domain II (central domain) is an elongated domain composed of twelve beta strands and two alpha helices, and domain III (immunoglobulin-like domain) is an IgC-like module with ten beta strands. This entry represents domains I and II, which are intertwined []. The glycoprotein E dimers on the viral surface re-cluster irreversibly into fusion-competent trimers upon exposure to low pH, as found in the acidic environment of the endosome. The formation of trimers results in a conformational change in the hinge region of domain II, a key structural element that opens a ligand-binding hydrophobic pocket at the interface between domains I and II. The conformational change results in the exposure of a fusion peptide loop at the tip of domain II, which is required in the fusion step to drive the cellular and viral membranes together by inserting into the membrane [].; GO: 0016021 integral to membrane, 0019031 viral envelope; PDB: 3P54_A 1OK8_A 1OAN_A 1OKE_B 3C5X_A 3C6E_A 2JSF_A 1URZ_B 3IYW_A 2JV6_A ....
Probab=20.49 E-value=36 Score=30.34 Aligned_cols=10 Identities=50% Similarity=1.321 Sum_probs=6.2
Q ss_pred cCCCCCCccc
Q 030824 21 NGCAFFGTAA 30 (171)
Q Consensus 21 n~CGFfGs~a 30 (171)
||||+||--.
T Consensus 103 NGCgLFGKGS 112 (293)
T PF00869_consen 103 NGCGLFGKGS 112 (293)
T ss_dssp GT-SS-EEEE
T ss_pred cccEEEeCCc
Confidence 8999999643
No 90
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=20.28 E-value=34 Score=21.15 Aligned_cols=29 Identities=24% Similarity=0.413 Sum_probs=18.8
Q ss_pred CCcccccccCC--CceeeecCccccCCcCCC
Q 030824 111 RCLSCNKKVGL--TGFKCKCGSTFCGIHRYP 139 (171)
Q Consensus 111 rC~~C~kk~gl--~gf~CrCg~~fC~~HR~~ 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 47778777722 233347999999876543
Done!