Query 031015
Match_columns 167
No_of_seqs 163 out of 484
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:58:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031015.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031015hhsearch_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 4E-46 8.6E-51 300.1 9.4 163 1-167 1-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.5 1.6E-15 3.5E-20 87.9 1.9 25 13-37 1-25 (25)
3 smart00154 ZnF_AN1 AN1-like Zi 99.5 6.9E-15 1.5E-19 93.1 1.8 38 108-145 1-39 (39)
4 smart00259 ZnF_A20 A20-like zi 99.5 5.4E-15 1.2E-19 86.4 1.1 25 13-37 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 3.7E-11 8.1E-16 76.9 0.9 38 108-146 1-41 (43)
6 KOG3183 Predicted Zn-finger pr 97.2 9.7E-05 2.1E-09 63.3 0.9 40 105-145 8-50 (250)
7 COG3582 Predicted nucleic acid 96.8 0.00066 1.4E-08 55.2 1.8 39 107-145 96-137 (162)
8 KOG3183 Predicted Zn-finger pr 93.7 0.02 4.3E-07 49.4 0.2 42 101-142 94-139 (250)
9 PF01363 FYVE: FYVE zinc finge 92.3 0.054 1.2E-06 36.7 0.7 29 105-133 9-40 (69)
10 cd00065 FYVE FYVE domain; Zinc 91.8 0.076 1.7E-06 34.5 1.0 28 106-133 3-33 (57)
11 smart00064 FYVE Protein presen 91.3 0.11 2.4E-06 35.1 1.4 29 105-133 10-41 (68)
12 PF10571 UPF0547: Uncharacteri 89.5 0.17 3.7E-06 29.3 0.9 23 106-128 1-24 (26)
13 KOG1818 Membrane trafficking a 86.5 0.27 5.7E-06 47.6 0.7 47 103-149 163-223 (634)
14 PF00130 C1_1: Phorbol esters/ 73.0 1.6 3.5E-05 27.8 0.7 24 104-127 10-37 (53)
15 PF15135 UPF0515: Uncharacteri 68.9 2.5 5.4E-05 37.0 1.2 29 102-130 129-167 (278)
16 PF02148 zf-UBP: Zn-finger in 63.6 3.5 7.5E-05 27.7 0.9 23 108-131 1-24 (63)
17 PHA02768 hypothetical protein; 63.3 3.2 6.8E-05 28.2 0.6 16 116-131 2-18 (55)
18 PF13978 DUF4223: Protein of u 63.3 3.2 6.8E-05 28.3 0.6 18 128-145 19-36 (56)
19 PF07975 C1_4: TFIIH C1-like d 56.6 4.5 9.7E-05 27.0 0.4 34 108-141 2-47 (51)
20 COG1996 RPC10 DNA-directed RNA 53.9 4.9 0.00011 26.7 0.3 22 105-126 6-32 (49)
21 KOG2807 RNA polymerase II tran 50.1 8.7 0.00019 35.0 1.3 30 102-131 327-358 (378)
22 PF13240 zinc_ribbon_2: zinc-r 49.6 9.2 0.0002 21.3 0.9 20 107-126 1-21 (23)
23 smart00109 C1 Protein kinase C 49.5 10 0.00022 23.0 1.2 23 104-126 10-35 (49)
24 KOG1729 FYVE finger containing 49.4 4.3 9.3E-05 35.8 -0.7 32 104-136 167-202 (288)
25 PF14471 DUF4428: Domain of un 49.3 5.8 0.00013 26.2 0.1 22 107-128 1-30 (51)
26 PF07649 C1_3: C1-like domain; 45.3 8.4 0.00018 22.3 0.3 22 107-128 2-25 (30)
27 cd00029 C1 Protein kinase C co 45.3 12 0.00025 23.0 1.0 24 104-127 10-37 (50)
28 KOG1819 FYVE finger-containing 45.0 7.3 0.00016 37.7 0.1 28 105-132 901-931 (990)
29 PF05207 zf-CSL: CSL zinc fing 43.4 9.2 0.0002 25.5 0.3 14 117-130 16-29 (55)
30 KOG1812 Predicted E3 ubiquitin 42.5 11 0.00023 34.3 0.7 31 103-133 304-338 (384)
31 smart00290 ZnF_UBP Ubiquitin C 41.9 6.8 0.00015 24.6 -0.5 24 107-132 1-25 (50)
32 PF02928 zf-C5HC2: C5HC2 zinc 41.6 12 0.00026 24.6 0.7 27 108-134 1-29 (54)
33 PF09723 Zn-ribbon_8: Zinc rib 41.2 14 0.0003 23.1 0.9 21 116-136 2-23 (42)
34 cd04476 RPA1_DBD_C RPA1_DBD_C: 41.1 10 0.00023 29.6 0.4 32 104-135 33-69 (166)
35 PTZ00303 phosphatidylinositol 40.4 14 0.0003 37.6 1.2 27 106-132 461-495 (1374)
36 PF02318 FYVE_2: FYVE-type zin 39.9 18 0.00038 27.3 1.5 32 104-135 53-88 (118)
37 PF10122 Mu-like_Com: Mu-like 39.6 11 0.00023 25.4 0.2 24 105-128 4-34 (51)
38 PRK08402 replication factor A; 39.3 11 0.00024 34.0 0.3 29 105-134 212-245 (355)
39 PF08882 Acetone_carb_G: Aceto 39.0 14 0.0003 28.6 0.8 33 109-143 16-48 (112)
40 PF13842 Tnp_zf-ribbon_2: DDE_ 38.2 20 0.00042 21.5 1.2 26 107-132 2-30 (32)
41 PF03604 DNA_RNApol_7kD: DNA d 37.3 14 0.00031 22.3 0.5 18 108-125 3-24 (32)
42 PF01194 RNA_pol_N: RNA polyme 36.7 17 0.00037 25.2 0.8 12 105-116 4-15 (60)
43 smart00659 RPOLCX RNA polymera 36.2 15 0.00032 23.6 0.5 19 107-125 4-26 (44)
44 PF13248 zf-ribbon_3: zinc-rib 35.8 21 0.00046 20.1 1.0 21 106-126 3-24 (26)
45 PRK07218 replication factor A; 35.5 17 0.00036 33.7 0.8 22 104-127 296-318 (423)
46 PF03107 C1_2: C1 domain; Int 34.7 20 0.00044 20.8 0.8 20 107-126 2-23 (30)
47 PHA00626 hypothetical protein 34.4 17 0.00037 25.1 0.5 23 106-130 12-35 (59)
48 PRK04016 DNA-directed RNA poly 32.3 14 0.0003 25.8 -0.2 13 104-116 3-15 (62)
49 PF06750 DiS_P_DiS: Bacterial 32.1 26 0.00056 25.6 1.2 22 104-125 32-65 (92)
50 PF00096 zf-C2H2: Zinc finger, 32.0 17 0.00036 19.1 0.1 10 120-129 1-11 (23)
51 COG1571 Predicted DNA-binding 30.6 24 0.00051 32.9 1.0 26 105-130 350-379 (421)
52 PRK00398 rpoP DNA-directed RNA 30.3 21 0.00046 22.4 0.5 28 106-133 4-36 (46)
53 smart00834 CxxC_CXXC_SSSS Puta 30.0 23 0.0005 21.1 0.6 16 117-132 3-19 (41)
54 PF15549 PGC7_Stella: PGC7/Ste 29.9 25 0.00053 28.8 0.9 19 119-139 123-141 (160)
55 PLN00032 DNA-directed RNA poly 29.6 17 0.00038 26.0 -0.0 14 104-117 3-16 (71)
56 PF08073 CHDNT: CHDNT (NUC034) 29.2 22 0.00049 24.2 0.4 20 146-165 21-40 (55)
57 PF01485 IBR: IBR domain; Int 29.0 30 0.00065 22.1 1.0 29 107-135 20-57 (64)
58 PF04438 zf-HIT: HIT zinc fing 28.6 15 0.00033 21.7 -0.4 23 106-131 3-26 (30)
59 PF13465 zf-H2C2_2: Zinc-finge 28.4 25 0.00055 19.6 0.5 13 116-128 11-24 (26)
60 PRK12366 replication factor A; 27.2 24 0.00053 34.0 0.5 29 105-134 532-563 (637)
61 PF13717 zinc_ribbon_4: zinc-r 26.9 27 0.00058 21.3 0.5 9 120-128 26-35 (36)
62 KOG3507 DNA-directed RNA polym 26.9 25 0.00053 24.5 0.3 23 104-126 19-45 (62)
63 smart00647 IBR In Between Ring 26.9 36 0.00078 21.7 1.1 17 119-135 40-57 (64)
64 PRK14890 putative Zn-ribbon RN 26.7 31 0.00068 23.8 0.8 20 105-126 36-56 (59)
65 PF14835 zf-RING_6: zf-RING of 26.1 35 0.00076 24.0 1.0 28 105-132 7-34 (65)
66 COG3357 Predicted transcriptio 25.5 27 0.00058 26.3 0.3 16 115-130 54-70 (97)
67 PF09538 FYDLN_acid: Protein o 25.5 38 0.00083 25.7 1.2 27 104-130 8-38 (108)
68 PRK04136 rpl40e 50S ribosomal 25.4 38 0.00082 22.5 1.0 23 104-126 13-36 (48)
69 KOG3497 DNA-directed RNA polym 25.2 22 0.00047 25.1 -0.2 13 105-117 4-16 (69)
70 PF09416 UPF1_Zn_bind: RNA hel 24.9 32 0.0007 27.8 0.7 26 107-132 2-28 (152)
71 COG1040 ComFC Predicted amidop 24.8 30 0.00064 29.0 0.5 49 106-154 25-84 (225)
72 COG2888 Predicted Zn-ribbon RN 24.0 34 0.00075 23.8 0.6 19 105-126 38-58 (61)
73 COG1933 Archaeal DNA polymeras 24.0 32 0.0007 30.0 0.6 24 104-127 166-192 (253)
74 PF14369 zf-RING_3: zinc-finge 23.9 36 0.00078 20.7 0.6 21 108-128 5-31 (35)
75 PF13894 zf-C2H2_4: C2H2-type 23.9 30 0.00064 17.5 0.2 9 120-128 1-10 (24)
76 KOG0193 Serine/threonine prote 23.3 32 0.00069 33.8 0.5 50 106-160 190-243 (678)
77 KOG3362 Predicted BBOX Zn-fing 23.2 43 0.00093 27.2 1.1 29 100-131 113-142 (156)
78 COG3582 Predicted nucleic acid 23.0 45 0.00097 27.3 1.2 41 118-158 12-53 (162)
79 PF11781 RRN7: RNA polymerase 22.9 31 0.00067 21.2 0.2 22 106-127 9-34 (36)
80 PF11722 zf-TRM13_CCCH: CCCH z 22.8 37 0.00079 20.3 0.5 10 124-133 21-30 (31)
81 COG1644 RPB10 DNA-directed RNA 22.4 25 0.00054 24.6 -0.3 13 104-116 3-15 (63)
82 PF15288 zf-CCHC_6: Zinc knuck 22.1 47 0.001 21.2 0.9 17 18-34 5-21 (40)
83 TIGR02452 conserved hypothetic 22.1 42 0.00091 29.2 0.9 26 14-41 210-235 (266)
84 TIGR02605 CxxC_CxxC_SSSS putat 22.0 39 0.00085 21.4 0.6 21 116-136 2-23 (52)
85 PF14634 zf-RING_5: zinc-RING 21.9 40 0.00087 20.8 0.6 29 107-135 1-31 (44)
86 PF00869 Flavi_glycoprot: Flav 21.8 31 0.00067 30.7 0.0 10 18-27 103-112 (293)
87 PF13912 zf-C2H2_6: C2H2-type 21.2 36 0.00077 18.5 0.2 11 120-130 2-13 (27)
88 PF08600 Rsm1: Rsm1-like; Int 21.0 34 0.00074 24.8 0.1 19 105-123 19-37 (91)
89 TIGR00622 ssl1 transcription f 20.9 70 0.0015 24.6 1.8 35 106-142 56-108 (112)
90 KOG1074 Transcriptional repres 20.9 46 0.00099 33.9 1.0 45 100-144 600-672 (958)
91 KOG1842 FYVE finger-containing 20.8 26 0.00057 33.2 -0.6 25 106-130 181-208 (505)
92 smart00396 ZnF_UBR1 Putative z 20.2 48 0.001 23.0 0.8 14 119-132 50-70 (71)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4e-46 Score=300.10 Aligned_cols=163 Identities=48% Similarity=0.873 Sum_probs=108.8
Q ss_pred Cchhhhcccc--ccccchhccCCCCCccccCCcchhhhHHHHHHHhhh-hhcchhhccccCCCCCCCCCCCCCCCCCCCC
Q 031015 1 MAEEHRFQAQ--EGHRLCANNCGFFGSTATMNLCSKCYRDHCLKEQQQ-ASIKTTVENSLSASPPSSSAPFLGSVPDPPA 77 (167)
Q Consensus 1 M~~e~~~q~p--~~p~lC~ngCGFFGs~aT~nlCSkCyr~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (167)
|++++....+ +.+.||.|||||||+|+|+||||+||++++.++++. ...+..+...++.+... +..........
T Consensus 1 M~~e~~~~~~~~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~s~---~~~~~~~~~~~ 77 (167)
T KOG3173|consen 1 MASETNGSQTPPSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPRSV---PSRDPPAVSLE 77 (167)
T ss_pred CcccccCCCCCCccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCcccc---Ccccccccccc
Confidence 6655543332 235899999999999999999999999999887765 33332222111100000 10000000000
Q ss_pred CCCCCcCCC-CCcchhhhhhhccCCCCCCCCcchhhhcccccccccccCcccccCCCCCCCCCCcchhhHhhHHHHHHhC
Q 031015 78 LALPEVNGD-KDADVAVVLEQQQQQPPQPNRCSVCRKRIGLTGFKCRCGTIFCGTHRYPEKHGCSFDFKKVGREEIARAN 156 (167)
Q Consensus 78 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~rC~~C~kk~~l~~f~CrCg~~FC~~HR~~e~H~C~~dyk~~~r~~i~k~N 156 (167)
..... +.. ..........+.......++||..|+|+|||+||.||||++||+.|||||.|+|+||||.+||+.|+++|
T Consensus 78 ~~~~~-~~~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~n 156 (167)
T KOG3173|consen 78 STTES-ELKLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKAN 156 (167)
T ss_pred ccccc-cccccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhC
Confidence 00000 000 0000001112223445667899999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccC
Q 031015 157 PLIKAEKLEKI 167 (167)
Q Consensus 157 p~v~~~K~~kI 167 (167)
|+|+++||+||
T Consensus 157 P~v~a~k~~ki 167 (167)
T KOG3173|consen 157 PVVKADKLQKI 167 (167)
T ss_pred CeeeccccccC
Confidence 99999999998
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=99.55 E-value=1.6e-15 Score=87.92 Aligned_cols=25 Identities=72% Similarity=1.436 Sum_probs=20.7
Q ss_pred ccchhccCCCCCccccCCcchhhhH
Q 031015 13 HRLCANNCGFFGSTATMNLCSKCYR 37 (167)
Q Consensus 13 p~lC~ngCGFFGs~aT~nlCSkCyr 37 (167)
|.+|++|||||||++|+||||||||
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 4699999999999999999999997
No 3
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.50 E-value=6.9e-15 Score=93.06 Aligned_cols=38 Identities=66% Similarity=1.552 Sum_probs=36.6
Q ss_pred cchhhhcccccccccc-cCcccccCCCCCCCCCCcchhh
Q 031015 108 CSVCRKRIGLTGFKCR-CGTIFCGTHRYPEKHGCSFDFK 145 (167)
Q Consensus 108 C~~C~kk~~l~~f~Cr-Cg~~FC~~HR~~e~H~C~~dyk 145 (167)
|+.|+++++|++|+|+ |+++||..|||||.|+|++|||
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 7889999999999999 9999999999999999999996
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.49 E-value=5.4e-15 Score=86.43 Aligned_cols=25 Identities=52% Similarity=1.172 Sum_probs=23.3
Q ss_pred ccchh-ccCCCCCccccCCcchhhhH
Q 031015 13 HRLCA-NNCGFFGSTATMNLCSKCYR 37 (167)
Q Consensus 13 p~lC~-ngCGFFGs~aT~nlCSkCyr 37 (167)
|.+|+ +||||||||+|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 35899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.06 E-value=3.7e-11 Score=76.94 Aligned_cols=38 Identities=53% Similarity=1.017 Sum_probs=27.9
Q ss_pred cch--hhhcccccccccc-cCcccccCCCCCCCCCCcchhhH
Q 031015 108 CSV--CRKRIGLTGFKCR-CGTIFCGTHRYPEKHGCSFDFKK 146 (167)
Q Consensus 108 C~~--C~kk~~l~~f~Cr-Cg~~FC~~HR~~e~H~C~~dyk~ 146 (167)
|+. |++++. ++|.|+ |+..||..|||||.|+|+.+++.
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 444 999886 899999 99999999999999999999874
No 6
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=97.24 E-value=9.7e-05 Score=63.33 Aligned_cols=40 Identities=38% Similarity=0.897 Sum_probs=36.4
Q ss_pred CCCcc--hhhhcccccccccc-cCcccccCCCCCCCCCCcchhh
Q 031015 105 PNRCS--VCRKRIGLTGFKCR-CGTIFCGTHRYPEKHGCSFDFK 145 (167)
Q Consensus 105 ~~rC~--~C~kk~~l~~f~Cr-Cg~~FC~~HR~~e~H~C~~dyk 145 (167)
-.+|+ .|+. +..++|+|- |+.+||..||.-+.|+|.+-|.
T Consensus 8 GkHCs~~~Ckq-lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 8 GKHCSVPYCKQ-LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLR 50 (250)
T ss_pred ccccCcchhhh-ccccceeeCCccchhhhccchHhhcCCCcccc
Confidence 35888 8988 889999999 9999999999999999998876
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.78 E-value=0.00066 Score=55.15 Aligned_cols=39 Identities=33% Similarity=0.605 Sum_probs=30.3
Q ss_pred Ccchhhhcc--cccccccc-cCcccccCCCCCCCCCCcchhh
Q 031015 107 RCSVCRKRI--GLTGFKCR-CGTIFCGTHRYPEKHGCSFDFK 145 (167)
Q Consensus 107 rC~~C~kk~--~l~~f~Cr-Cg~~FC~~HR~~e~H~C~~dyk 145 (167)
+|..|...+ +-+.++|. |++.||+.||+++.|+|.+...
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 555333333 24579999 9999999999999999998854
No 8
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=93.74 E-value=0.02 Score=49.38 Aligned_cols=42 Identities=36% Similarity=0.844 Sum_probs=35.1
Q ss_pred CCCCCCCcc--hhhhccccc-ccccc-cCcccccCCCCCCCCCCcc
Q 031015 101 QPPQPNRCS--VCRKRIGLT-GFKCR-CGTIFCGTHRYPEKHGCSF 142 (167)
Q Consensus 101 ~~~~~~rC~--~C~kk~~l~-~f~Cr-Cg~~FC~~HR~~e~H~C~~ 142 (167)
.+...++|. .|++++-+. .+.|+ |+..||-+||++-.|.|.-
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~ 139 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNK 139 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhh
Confidence 345567787 799988664 59999 9999999999999999983
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=92.34 E-value=0.054 Score=36.70 Aligned_cols=29 Identities=31% Similarity=0.953 Sum_probs=17.8
Q ss_pred CCCcchhhhccccc--ccccc-cCcccccCCC
Q 031015 105 PNRCSVCRKRIGLT--GFKCR-CGTIFCGTHR 133 (167)
Q Consensus 105 ~~rC~~C~kk~~l~--~f~Cr-Cg~~FC~~HR 133 (167)
...|..|+++.+++ -..|| ||.+||+.+-
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs 40 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCS 40 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchh
Confidence 57999999999987 49999 9999997654
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=91.83 E-value=0.076 Score=34.51 Aligned_cols=28 Identities=43% Similarity=0.973 Sum_probs=24.2
Q ss_pred CCcchhhhccccc--ccccc-cCcccccCCC
Q 031015 106 NRCSVCRKRIGLT--GFKCR-CGTIFCGTHR 133 (167)
Q Consensus 106 ~rC~~C~kk~~l~--~f~Cr-Cg~~FC~~HR 133 (167)
..|..|.++.+++ ...|+ ||.+||+.+-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~ 33 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCS 33 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHc
Confidence 5799999999996 69999 9999998553
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=89.46 E-value=0.17 Score=29.33 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=20.6
Q ss_pred CCcchhhhcccccccccc-cCccc
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGTIF 128 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~~F 128 (167)
++|-.|++.|.+..-.|. ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 378999999999999999 99888
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=86.46 E-value=0.27 Score=47.55 Aligned_cols=47 Identities=32% Similarity=0.766 Sum_probs=36.3
Q ss_pred CCCCCcchhhhcccccc--cccc-cCcccccCCC-----------CCCCCCCcchhhHhhH
Q 031015 103 PQPNRCSVCRKRIGLTG--FKCR-CGTIFCGTHR-----------YPEKHGCSFDFKKVGR 149 (167)
Q Consensus 103 ~~~~rC~~C~kk~~l~~--f~Cr-Cg~~FC~~HR-----------~~e~H~C~~dyk~~~r 149 (167)
.....|..|+.+.|+++ ..|| ||.+||+.|- |-+---|..+|...-|
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTR 223 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhh
Confidence 34579999999999984 8999 9999999884 3455667777764433
No 14
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=73.01 E-value=1.6 Score=27.84 Aligned_cols=24 Identities=46% Similarity=1.218 Sum_probs=18.4
Q ss_pred CCCCcchhhhcc---cccccccc-cCcc
Q 031015 104 QPNRCSVCRKRI---GLTGFKCR-CGTI 127 (167)
Q Consensus 104 ~~~rC~~C~kk~---~l~~f~Cr-Cg~~ 127 (167)
.+..|..|++.+ ++.|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 467999999999 56699999 8654
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=68.90 E-value=2.5 Score=37.05 Aligned_cols=29 Identities=41% Similarity=0.943 Sum_probs=22.6
Q ss_pred CCCCCCcchhhhc---------ccccccccc-cCccccc
Q 031015 102 PPQPNRCSVCRKR---------IGLTGFKCR-CGTIFCG 130 (167)
Q Consensus 102 ~~~~~rC~~C~kk---------~~l~~f~Cr-Cg~~FC~ 130 (167)
.+...||..|+++ .|+.-|.|. |++.|=+
T Consensus 129 rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 129 RKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ccccccccccccccCCCccccccceeeeecccccccchh
Confidence 3456899999988 556679996 9999854
No 16
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=63.62 E-value=3.5 Score=27.74 Aligned_cols=23 Identities=39% Similarity=0.937 Sum_probs=15.5
Q ss_pred cchhhhcccccccccc-cCcccccC
Q 031015 108 CSVCRKRIGLTGFKCR-CGTIFCGT 131 (167)
Q Consensus 108 C~~C~kk~~l~~f~Cr-Cg~~FC~~ 131 (167)
|..|+.. +-.-+.|- ||.++|+.
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 5667765 44557788 99999995
No 17
>PHA02768 hypothetical protein; Provisional
Probab=63.35 E-value=3.2 Score=28.24 Aligned_cols=16 Identities=38% Similarity=1.070 Sum_probs=13.1
Q ss_pred cccccccc-cCcccccC
Q 031015 116 GLTGFKCR-CGTIFCGT 131 (167)
Q Consensus 116 ~l~~f~Cr-Cg~~FC~~ 131 (167)
.|+||.|. ||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 47899999 99998754
No 18
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=63.27 E-value=3.2 Score=28.25 Aligned_cols=18 Identities=28% Similarity=0.691 Sum_probs=16.2
Q ss_pred cccCCCCCCCCCCcchhh
Q 031015 128 FCGTHRYPEKHGCSFDFK 145 (167)
Q Consensus 128 FC~~HR~~e~H~C~~dyk 145 (167)
=|.-|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999996
No 19
>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=56.56 E-value=4.5 Score=27.05 Aligned_cols=34 Identities=26% Similarity=0.647 Sum_probs=16.7
Q ss_pred cchhhhccccc--------ccccc-cCcccccC---CCCCCCCCCc
Q 031015 108 CSVCRKRIGLT--------GFKCR-CGTIFCGT---HRYPEKHGCS 141 (167)
Q Consensus 108 C~~C~kk~~l~--------~f~Cr-Cg~~FC~~---HR~~e~H~C~ 141 (167)
|+.|.+.+... .|+|. |+..||-. .-+-.-|+|+
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 66677766663 59998 99999853 2333456665
No 20
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=53.93 E-value=4.9 Score=26.74 Aligned_cols=22 Identities=32% Similarity=1.087 Sum_probs=17.0
Q ss_pred CCCcchhhhccccc----ccccc-cCc
Q 031015 105 PNRCSVCRKRIGLT----GFKCR-CGT 126 (167)
Q Consensus 105 ~~rC~~C~kk~~l~----~f~Cr-Cg~ 126 (167)
.-+|..|++.+.++ +..|. ||+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 35899999999754 78998 753
No 21
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=50.13 E-value=8.7 Score=34.98 Aligned_cols=30 Identities=20% Similarity=0.640 Sum_probs=23.2
Q ss_pred CCCCCCcchh-hhcccccccccc-cCcccccC
Q 031015 102 PPQPNRCSVC-RKRIGLTGFKCR-CGTIFCGT 131 (167)
Q Consensus 102 ~~~~~rC~~C-~kk~~l~~f~Cr-Cg~~FC~~ 131 (167)
....++|+.| .+.++-..|.|+ |.++||..
T Consensus 327 ~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 327 YNGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred cCCCcceeeeccccCCCCcEEchhccceeecc
Confidence 3456789999 555555689999 99999964
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.58 E-value=9.2 Score=21.31 Aligned_cols=20 Identities=35% Similarity=0.712 Sum_probs=12.9
Q ss_pred Ccchhhhcccccccccc-cCc
Q 031015 107 RCSVCRKRIGLTGFKCR-CGT 126 (167)
Q Consensus 107 rC~~C~kk~~l~~f~Cr-Cg~ 126 (167)
+|..|++.+.-..-.|. ||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 46677777766655566 654
No 23
>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=49.49 E-value=10 Score=23.01 Aligned_cols=23 Identities=43% Similarity=1.109 Sum_probs=18.2
Q ss_pred CCCCcchhhhccccc--ccccc-cCc
Q 031015 104 QPNRCSVCRKRIGLT--GFKCR-CGT 126 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~--~f~Cr-Cg~ 126 (167)
.+..|..|++.+... +++|+ |+.
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCc
Confidence 467899999998764 88888 754
No 24
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=49.37 E-value=4.3 Score=35.81 Aligned_cols=32 Identities=31% Similarity=0.777 Sum_probs=25.1
Q ss_pred CCCCcchhhh-ccccc--ccccc-cCcccccCCCCCC
Q 031015 104 QPNRCSVCRK-RIGLT--GFKCR-CGTIFCGTHRYPE 136 (167)
Q Consensus 104 ~~~rC~~C~k-k~~l~--~f~Cr-Cg~~FC~~HR~~e 136 (167)
..++|..|.+ .-.|+ --.|| ||.+||. |....
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 3589999999 66665 47899 9999999 76533
No 25
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=49.33 E-value=5.8 Score=26.18 Aligned_cols=22 Identities=41% Similarity=1.182 Sum_probs=17.1
Q ss_pred Ccchhhhccccc-------ccccc-cCccc
Q 031015 107 RCSVCRKRIGLT-------GFKCR-CGTIF 128 (167)
Q Consensus 107 rC~~C~kk~~l~-------~f~Cr-Cg~~F 128 (167)
+|..|++++|++ ||.|. |-...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 589999999997 57888 75444
No 26
>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=45.34 E-value=8.4 Score=22.25 Aligned_cols=22 Identities=32% Similarity=0.717 Sum_probs=8.9
Q ss_pred Ccchhhhcccc-cccccc-cCccc
Q 031015 107 RCSVCRKRIGL-TGFKCR-CGTIF 128 (167)
Q Consensus 107 rC~~C~kk~~l-~~f~Cr-Cg~~F 128 (167)
+|..|++.+.. ..|.|. |...+
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 68899999988 789998 86554
No 27
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=45.28 E-value=12 Score=23.03 Aligned_cols=24 Identities=42% Similarity=0.937 Sum_probs=18.9
Q ss_pred CCCCcchhhhcccc---cccccc-cCcc
Q 031015 104 QPNRCSVCRKRIGL---TGFKCR-CGTI 127 (167)
Q Consensus 104 ~~~rC~~C~kk~~l---~~f~Cr-Cg~~ 127 (167)
.+..|..|++.+.. .+++|+ |+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 46789999999884 689999 7543
No 28
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=44.98 E-value=7.3 Score=37.71 Aligned_cols=28 Identities=36% Similarity=0.978 Sum_probs=20.9
Q ss_pred CCCcchhhhccccc--ccccc-cCcccccCC
Q 031015 105 PNRCSVCRKRIGLT--GFKCR-CGTIFCGTH 132 (167)
Q Consensus 105 ~~rC~~C~kk~~l~--~f~Cr-Cg~~FC~~H 132 (167)
..+|..|....... --.|| ||++||++-
T Consensus 901 a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 46888887654443 46899 999999864
No 29
>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=43.42 E-value=9.2 Score=25.50 Aligned_cols=14 Identities=36% Similarity=0.828 Sum_probs=10.9
Q ss_pred ccccccccCccccc
Q 031015 117 LTGFKCRCGTIFCG 130 (167)
Q Consensus 117 l~~f~CrCg~~FC~ 130 (167)
...+.||||..|--
T Consensus 16 ~~~y~CRCG~~f~i 29 (55)
T PF05207_consen 16 VYSYPCRCGGEFEI 29 (55)
T ss_dssp EEEEEETTSSEEEE
T ss_pred EEEEcCCCCCEEEE
Confidence 35789999998753
No 30
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.46 E-value=11 Score=34.30 Aligned_cols=31 Identities=32% Similarity=0.750 Sum_probs=25.2
Q ss_pred CCCCCcchhhhccccc----ccccccCcccccCCC
Q 031015 103 PQPNRCSVCRKRIGLT----GFKCRCGTIFCGTHR 133 (167)
Q Consensus 103 ~~~~rC~~C~kk~~l~----~f~CrCg~~FC~~HR 133 (167)
+.-.+|..|+-.+.+. -+.||||..||-.=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 3457999999998886 399999999996544
No 31
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=41.91 E-value=6.8 Score=24.61 Aligned_cols=24 Identities=42% Similarity=0.913 Sum_probs=17.6
Q ss_pred Ccchhhhcccccccccc-cCcccccCC
Q 031015 107 RCSVCRKRIGLTGFKCR-CGTIFCGTH 132 (167)
Q Consensus 107 rC~~C~kk~~l~~f~Cr-Cg~~FC~~H 132 (167)
||..|..... -+.|- |+.++|+..
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 45676 999999764
No 32
>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=41.56 E-value=12 Score=24.60 Aligned_cols=27 Identities=30% Similarity=0.818 Sum_probs=22.6
Q ss_pred cchhhhccccccccccc--CcccccCCCC
Q 031015 108 CSVCRKRIGLTGFKCRC--GTIFCGTHRY 134 (167)
Q Consensus 108 C~~C~kk~~l~~f~CrC--g~~FC~~HR~ 134 (167)
|..|+.-.=|..+.|+| +.++|=.|--
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 67788888888999997 8999998853
No 33
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=41.24 E-value=14 Score=23.14 Aligned_cols=21 Identities=24% Similarity=0.588 Sum_probs=16.8
Q ss_pred cccccccc-cCcccccCCCCCC
Q 031015 116 GLTGFKCR-CGTIFCGTHRYPE 136 (167)
Q Consensus 116 ~l~~f~Cr-Cg~~FC~~HR~~e 136 (167)
.+-.|+|. ||..|=-.+.+.+
T Consensus 2 P~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 2 PIYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CCEEEEeCCCCCEEEEEEEcCC
Confidence 35579999 9999988877766
No 34
>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=41.14 E-value=10 Score=29.56 Aligned_cols=32 Identities=22% Similarity=0.511 Sum_probs=23.3
Q ss_pred CCCCcchhhhccccc---ccccc-cCccc-ccCCCCC
Q 031015 104 QPNRCSVCRKRIGLT---GFKCR-CGTIF-CGTHRYP 135 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~---~f~Cr-Cg~~F-C~~HR~~ 135 (167)
.=.-|..|+|||... .|.|. |+..+ =-.+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 346788999999765 38888 87765 4566663
No 35
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=40.35 E-value=14 Score=37.63 Aligned_cols=27 Identities=26% Similarity=0.711 Sum_probs=20.7
Q ss_pred CCcchhhhccccc-------ccccc-cCcccccCC
Q 031015 106 NRCSVCRKRIGLT-------GFKCR-CGTIFCGTH 132 (167)
Q Consensus 106 ~rC~~C~kk~~l~-------~f~Cr-Cg~~FC~~H 132 (167)
..|..|+++-..+ --.|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 5699999988632 45699 999998654
No 36
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=39.95 E-value=18 Score=27.25 Aligned_cols=32 Identities=25% Similarity=0.564 Sum_probs=24.4
Q ss_pred CCCCcchhhhccccc---ccccc-cCcccccCCCCC
Q 031015 104 QPNRCSVCRKRIGLT---GFKCR-CGTIFCGTHRYP 135 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~---~f~Cr-Cg~~FC~~HR~~ 135 (167)
....|..|.+.+|++ +..|. |...+|..=+.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 356999999999886 68899 999999876653
No 37
>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=39.61 E-value=11 Score=25.43 Aligned_cols=24 Identities=38% Similarity=0.746 Sum_probs=17.9
Q ss_pred CCCcchhhhccccc------ccccc-cCccc
Q 031015 105 PNRCSVCRKRIGLT------GFKCR-CGTIF 128 (167)
Q Consensus 105 ~~rC~~C~kk~~l~------~f~Cr-Cg~~F 128 (167)
.-||..|+|.|... ..+|. ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 46999999988763 47787 87654
No 38
>PRK08402 replication factor A; Reviewed
Probab=39.29 E-value=11 Score=33.98 Aligned_cols=29 Identities=17% Similarity=0.476 Sum_probs=19.7
Q ss_pred CCCcchhhhcccc----cccccc-cCcccccCCCC
Q 031015 105 PNRCSVCRKRIGL----TGFKCR-CGTIFCGTHRY 134 (167)
Q Consensus 105 ~~rC~~C~kk~~l----~~f~Cr-Cg~~FC~~HR~ 134 (167)
-.+|..|+|||-. -.+.|. ||.+-+ .|||
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 3699999999963 247777 665433 5554
No 39
>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=38.99 E-value=14 Score=28.59 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=23.6
Q ss_pred chhhhcccccccccccCcccccCCCCCCCCCCcch
Q 031015 109 SVCRKRIGLTGFKCRCGTIFCGTHRYPEKHGCSFD 143 (167)
Q Consensus 109 ~~C~kk~~l~~f~CrCg~~FC~~HR~~e~H~C~~d 143 (167)
+.|+++- . -.+|+||+.||+-+..-+.|.-.++
T Consensus 16 ~i~~~~~-k-~vkc~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 16 WIVQKKD-K-VVKCDCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred EEEEecC-c-eeeccCCCeecChhcChhhCcEEEe
Confidence 3455544 2 6799999999998887777765544
No 40
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=38.21 E-value=20 Score=21.48 Aligned_cols=26 Identities=35% Similarity=0.847 Sum_probs=19.1
Q ss_pred Ccchhhhcccc--cccccc-cCcccccCC
Q 031015 107 RCSVCRKRIGL--TGFKCR-CGTIFCGTH 132 (167)
Q Consensus 107 rC~~C~kk~~l--~~f~Cr-Cg~~FC~~H 132 (167)
||..|.++-.. +.|.|. |+-..|..|
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 67777764322 689999 988888776
No 41
>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=37.25 E-value=14 Score=22.29 Aligned_cols=18 Identities=33% Similarity=1.067 Sum_probs=9.9
Q ss_pred cchhhhccccc---ccccc-cC
Q 031015 108 CSVCRKRIGLT---GFKCR-CG 125 (167)
Q Consensus 108 C~~C~kk~~l~---~f~Cr-Cg 125 (167)
|..|+..+.+. ..+|+ ||
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCcCCCeeEcCCCCcEECCcCC
Confidence 55666666553 35666 54
No 42
>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=36.70 E-value=17 Score=25.17 Aligned_cols=12 Identities=58% Similarity=1.140 Sum_probs=9.3
Q ss_pred CCCcchhhhccc
Q 031015 105 PNRCSVCRKRIG 116 (167)
Q Consensus 105 ~~rC~~C~kk~~ 116 (167)
|-||++|+|-++
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 43
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.16 E-value=15 Score=23.57 Aligned_cols=19 Identities=32% Similarity=0.952 Sum_probs=13.2
Q ss_pred Ccchhhhccccc---ccccc-cC
Q 031015 107 RCSVCRKRIGLT---GFKCR-CG 125 (167)
Q Consensus 107 rC~~C~kk~~l~---~f~Cr-Cg 125 (167)
+|..|+..+.+. +.+|+ ||
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCC
Confidence 577888877664 57776 64
No 44
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.83 E-value=21 Score=20.10 Aligned_cols=21 Identities=29% Similarity=0.632 Sum_probs=13.9
Q ss_pred CCcchhhhcccccccccc-cCc
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGT 126 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~ 126 (167)
..|..|++.+....-.|. ||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 467788886655566666 654
No 45
>PRK07218 replication factor A; Provisional
Probab=35.54 E-value=17 Score=33.72 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=17.2
Q ss_pred CCCCcchhhhcccccccccc-cCcc
Q 031015 104 QPNRCSVCRKRIGLTGFKCR-CGTI 127 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~~f~Cr-Cg~~ 127 (167)
--.||..|+++|.. +.|+ ||.+
T Consensus 296 li~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 296 LIERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred ceecCcCccccccC--CcCCCCCCc
Confidence 34899999999855 7888 6654
No 46
>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=34.75 E-value=20 Score=20.78 Aligned_cols=20 Identities=35% Similarity=0.866 Sum_probs=16.5
Q ss_pred Ccchhhhccccc-ccccc-cCc
Q 031015 107 RCSVCRKRIGLT-GFKCR-CGT 126 (167)
Q Consensus 107 rC~~C~kk~~l~-~f~Cr-Cg~ 126 (167)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 488999999888 89998 653
No 47
>PHA00626 hypothetical protein
Probab=34.40 E-value=17 Score=25.12 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=14.8
Q ss_pred CCcchhhhcccccccccc-cCccccc
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGTIFCG 130 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~~FC~ 130 (167)
.||..|++.. .-|+|+ ||+.|--
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccC--cceEcCCCCCeech
Confidence 3666766622 358888 8877753
No 48
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=32.27 E-value=14 Score=25.76 Aligned_cols=13 Identities=46% Similarity=0.848 Sum_probs=10.6
Q ss_pred CCCCcchhhhccc
Q 031015 104 QPNRCSVCRKRIG 116 (167)
Q Consensus 104 ~~~rC~~C~kk~~ 116 (167)
.|-||++|+|-++
T Consensus 3 iPvRCFTCGkvi~ 15 (62)
T PRK04016 3 IPVRCFTCGKVIA 15 (62)
T ss_pred CCeEecCCCCChH
Confidence 3679999999774
No 49
>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=32.13 E-value=26 Score=25.58 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=16.9
Q ss_pred CCCCcchhhhccccc-----------ccccc-cC
Q 031015 104 QPNRCSVCRKRIGLT-----------GFKCR-CG 125 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~-----------~f~Cr-Cg 125 (167)
.+.+|..|++++... -++|| |+
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~ 65 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCG 65 (92)
T ss_pred CCCcCcCCCCcCcccccchHHHHHHhCCCCcccC
Confidence 368999999998764 47888 53
No 50
>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=31.96 E-value=17 Score=19.08 Aligned_cols=10 Identities=50% Similarity=1.411 Sum_probs=5.9
Q ss_pred cccc-cCcccc
Q 031015 120 FKCR-CGTIFC 129 (167)
Q Consensus 120 f~Cr-Cg~~FC 129 (167)
|.|. ||..|=
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 4566 666663
No 51
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.61 E-value=24 Score=32.92 Aligned_cols=26 Identities=35% Similarity=0.813 Sum_probs=19.6
Q ss_pred CCCcchhhhcccc---cccccc-cCccccc
Q 031015 105 PNRCSVCRKRIGL---TGFKCR-CGTIFCG 130 (167)
Q Consensus 105 ~~rC~~C~kk~~l---~~f~Cr-Cg~~FC~ 130 (167)
..+|..|+.++.- .||+|+ ||..+=.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCc
Confidence 4589999987744 389999 9876643
No 52
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.29 E-value=21 Score=22.41 Aligned_cols=28 Identities=29% Similarity=0.775 Sum_probs=17.6
Q ss_pred CCcchhhhccccc----ccccc-cCcccccCCC
Q 031015 106 NRCSVCRKRIGLT----GFKCR-CGTIFCGTHR 133 (167)
Q Consensus 106 ~rC~~C~kk~~l~----~f~Cr-Cg~~FC~~HR 133 (167)
-+|..|+..+.+. .+.|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 4688888876442 57788 7665544443
No 53
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.03 E-value=23 Score=21.10 Aligned_cols=16 Identities=25% Similarity=0.783 Sum_probs=9.9
Q ss_pred ccccccc-cCcccccCC
Q 031015 117 LTGFKCR-CGTIFCGTH 132 (167)
Q Consensus 117 l~~f~Cr-Cg~~FC~~H 132 (167)
+..|+|. ||..|=-.+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQ 19 (41)
T ss_pred CEEEEcCCCCCEEEEEE
Confidence 4467777 777664433
No 54
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=29.86 E-value=25 Score=28.78 Aligned_cols=19 Identities=37% Similarity=1.144 Sum_probs=15.4
Q ss_pred ccccccCcccccCCCCCCCCC
Q 031015 119 GFKCRCGTIFCGTHRYPEKHG 139 (167)
Q Consensus 119 ~f~CrCg~~FC~~HR~~e~H~ 139 (167)
.|+|.| .||-.||.|.+-+
T Consensus 123 ~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 123 RFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred ceeeee--eeecccCCCcccc
Confidence 489998 7999999776655
No 55
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=29.64 E-value=17 Score=25.96 Aligned_cols=14 Identities=50% Similarity=0.861 Sum_probs=10.9
Q ss_pred CCCCcchhhhcccc
Q 031015 104 QPNRCSVCRKRIGL 117 (167)
Q Consensus 104 ~~~rC~~C~kk~~l 117 (167)
.|-||++|+|-+|-
T Consensus 3 iPVRCFTCGkvig~ 16 (71)
T PLN00032 3 IPVRCFTCGKVIGN 16 (71)
T ss_pred CceeecCCCCCcHH
Confidence 36799999997743
No 56
>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=29.21 E-value=22 Score=24.17 Aligned_cols=20 Identities=35% Similarity=0.343 Sum_probs=16.5
Q ss_pred HhhHHHHHHhCCcccccccc
Q 031015 146 KVGREEIARANPLIKAEKLE 165 (167)
Q Consensus 146 ~~~r~~i~k~Np~v~~~K~~ 165 (167)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34578899999999988875
No 57
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=28.95 E-value=30 Score=22.06 Aligned_cols=29 Identities=34% Similarity=0.709 Sum_probs=17.4
Q ss_pred Ccch--hhhccccc----c--cccc-cCcccccCCCCC
Q 031015 107 RCSV--CRKRIGLT----G--FKCR-CGTIFCGTHRYP 135 (167)
Q Consensus 107 rC~~--C~kk~~l~----~--f~Cr-Cg~~FC~~HR~~ 135 (167)
.|.. |..-+... . +.|. |+..||..++-+
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 5654 66655442 2 7899 999999998854
No 58
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=28.58 E-value=15 Score=21.72 Aligned_cols=23 Identities=35% Similarity=1.080 Sum_probs=15.4
Q ss_pred CCcchhhhcccccccccc-cCcccccC
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGTIFCGT 131 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~~FC~~ 131 (167)
..|..|+. ..-+.|. |+..||+.
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 46778877 5568998 99999985
No 59
>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=28.45 E-value=25 Score=19.57 Aligned_cols=13 Identities=46% Similarity=1.142 Sum_probs=8.5
Q ss_pred cccccccc-cCccc
Q 031015 116 GLTGFKCR-CGTIF 128 (167)
Q Consensus 116 ~l~~f~Cr-Cg~~F 128 (167)
|.-.|.|. |+..|
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 34467777 77666
No 60
>PRK12366 replication factor A; Reviewed
Probab=27.16 E-value=24 Score=34.03 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=21.4
Q ss_pred CCCcchhhhccccc--ccccc-cCcccccCCCC
Q 031015 105 PNRCSVCRKRIGLT--GFKCR-CGTIFCGTHRY 134 (167)
Q Consensus 105 ~~rC~~C~kk~~l~--~f~Cr-Cg~~FC~~HR~ 134 (167)
-.+|..|+|||-.. .|.|. ||.+ =..|||
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 47999999999653 27897 8877 335665
No 61
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.90 E-value=27 Score=21.28 Aligned_cols=9 Identities=44% Similarity=1.553 Sum_probs=4.6
Q ss_pred cccc-cCccc
Q 031015 120 FKCR-CGTIF 128 (167)
Q Consensus 120 f~Cr-Cg~~F 128 (167)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4555 55544
No 62
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=26.88 E-value=25 Score=24.53 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=17.5
Q ss_pred CCCCcchhhhccccc---ccccc-cCc
Q 031015 104 QPNRCSVCRKRIGLT---GFKCR-CGT 126 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~---~f~Cr-Cg~ 126 (167)
-.--|..|+.+..|- .+.|| ||+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcch
Confidence 346799999888774 59999 863
No 63
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.86 E-value=36 Score=21.74 Aligned_cols=17 Identities=35% Similarity=0.950 Sum_probs=14.3
Q ss_pred cccc-ccCcccccCCCCC
Q 031015 119 GFKC-RCGTIFCGTHRYP 135 (167)
Q Consensus 119 ~f~C-rCg~~FC~~HR~~ 135 (167)
...| .||..||-.++.+
T Consensus 40 ~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred eeECCCCCCeECCCCCCc
Confidence 5889 6999999988865
No 64
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.70 E-value=31 Score=23.83 Aligned_cols=20 Identities=40% Similarity=1.001 Sum_probs=14.1
Q ss_pred CCCcchhhhcccccccccc-cCc
Q 031015 105 PNRCSVCRKRIGLTGFKCR-CGT 126 (167)
Q Consensus 105 ~~rC~~C~kk~~l~~f~Cr-Cg~ 126 (167)
-.||..|||- -..|+|. ||.
T Consensus 36 I~RC~~CRk~--~~~Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRKQ--SNPYTCPKCGF 56 (59)
T ss_pred EeechhHHhc--CCceECCCCCC
Confidence 4689999882 1478885 875
No 65
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=26.09 E-value=35 Score=24.01 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=11.3
Q ss_pred CCCcchhhhcccccccccccCcccccCC
Q 031015 105 PNRCSVCRKRIGLTGFKCRCGTIFCGTH 132 (167)
Q Consensus 105 ~~rC~~C~kk~~l~~f~CrCg~~FC~~H 132 (167)
--||+.|..-+..-.-.-.|+++||+.-
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHH
Confidence 3588888875433223345889999864
No 66
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.53 E-value=27 Score=26.34 Aligned_cols=16 Identities=25% Similarity=0.648 Sum_probs=11.1
Q ss_pred ccccccccc-cCccccc
Q 031015 115 IGLTGFKCR-CGTIFCG 130 (167)
Q Consensus 115 ~~l~~f~Cr-Cg~~FC~ 130 (167)
|-+.+-.|+ ||+.|=.
T Consensus 54 Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 54 LLVRPARCKKCGFEFRD 70 (97)
T ss_pred EEecChhhcccCccccc
Confidence 434478888 8888854
No 67
>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=25.49 E-value=38 Score=25.66 Aligned_cols=27 Identities=26% Similarity=0.552 Sum_probs=19.4
Q ss_pred CCCCcchhhhcccc---cccccc-cCccccc
Q 031015 104 QPNRCSVCRKRIGL---TGFKCR-CGTIFCG 130 (167)
Q Consensus 104 ~~~rC~~C~kk~~l---~~f~Cr-Cg~~FC~ 130 (167)
.+..|..|++|.-- .+..|. ||..|=-
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 36789999998543 368898 7776643
No 68
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=25.42 E-value=38 Score=22.55 Aligned_cols=23 Identities=35% Similarity=0.743 Sum_probs=19.7
Q ss_pred CCCCcchhhhcccccccccc-cCc
Q 031015 104 QPNRCSVCRKRIGLTGFKCR-CGT 126 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~~f~Cr-Cg~ 126 (167)
.+.-|..|.-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 45679999999999999999 875
No 69
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=25.17 E-value=22 Score=25.08 Aligned_cols=13 Identities=54% Similarity=0.935 Sum_probs=10.5
Q ss_pred CCCcchhhhcccc
Q 031015 105 PNRCSVCRKRIGL 117 (167)
Q Consensus 105 ~~rC~~C~kk~~l 117 (167)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999997753
No 70
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=24.89 E-value=32 Score=27.81 Aligned_cols=26 Identities=27% Similarity=0.671 Sum_probs=16.7
Q ss_pred Ccchhhhcccccccccc-cCcccccCC
Q 031015 107 RCSVCRKRIGLTGFKCR-CGTIFCGTH 132 (167)
Q Consensus 107 rC~~C~kk~~l~~f~Cr-Cg~~FC~~H 132 (167)
.|..|+-.-.-.-.+|. |++.||..-
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~ 28 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGR 28 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--
T ss_pred CccccCCCCcccEeEcCCCCcEeecCC
Confidence 58889877777788999 999999874
No 71
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=24.84 E-value=30 Score=29.00 Aligned_cols=49 Identities=24% Similarity=0.351 Sum_probs=32.7
Q ss_pred CCcchhhhcccccccccc-cCcccccCCC----------CCCCCCCcchhhHhhHHHHHH
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGTIFCGTHR----------YPEKHGCSFDFKKVGREEIAR 154 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~~FC~~HR----------~~e~H~C~~dyk~~~r~~i~k 154 (167)
..|..|.+.+.+++..|. |+..+=..|- +-+.|.+-|+|...-|+.|..
T Consensus 25 ~~C~~C~~~~~~~~~~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~l~~~i~~ 84 (225)
T COG1040 25 GLCSGCQADLPLIGNLCPLCGLPLSSHACRCGECLAKPPPFERLRSLGSYNGPLRELISQ 84 (225)
T ss_pred CcChhhhhchhHHHhhhHhhhChhccccccCHHHhcCCCcceeEEEEEEccHHHHHHHHH
Confidence 467777777777666676 6665544321 134577899999888888753
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.05 E-value=34 Score=23.79 Aligned_cols=19 Identities=47% Similarity=1.195 Sum_probs=13.8
Q ss_pred CCCcchhhhcccc-cccccc-cCc
Q 031015 105 PNRCSVCRKRIGL-TGFKCR-CGT 126 (167)
Q Consensus 105 ~~rC~~C~kk~~l-~~f~Cr-Cg~ 126 (167)
-.||..||| | ..|.|. ||.
T Consensus 38 I~Rc~~CRk---~g~~Y~Cp~CGF 58 (61)
T COG2888 38 IYRCAKCRK---LGNPYRCPKCGF 58 (61)
T ss_pred eehhhhHHH---cCCceECCCcCc
Confidence 468888888 4 468884 774
No 73
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=24.03 E-value=32 Score=30.01 Aligned_cols=24 Identities=33% Similarity=0.677 Sum_probs=19.6
Q ss_pred CCCCcchhhhccccc--ccccc-cCcc
Q 031015 104 QPNRCSVCRKRIGLT--GFKCR-CGTI 127 (167)
Q Consensus 104 ~~~rC~~C~kk~~l~--~f~Cr-Cg~~ 127 (167)
..-||..|++|.+.. ..+|+ ||+.
T Consensus 166 q~~rc~~c~~k~rr~pl~g~c~kcg~~ 192 (253)
T COG1933 166 QEFRCVKCNTKFRRPPLDGKCPICGGK 192 (253)
T ss_pred heeehHhhhhhhcCCCccccccccCCe
Confidence 457999999999885 68888 8873
No 74
>PF14369 zf-RING_3: zinc-finger
Probab=23.93 E-value=36 Score=20.71 Aligned_cols=21 Identities=24% Similarity=0.681 Sum_probs=13.9
Q ss_pred cchhhhccccc----ccc-cc-cCccc
Q 031015 108 CSVCRKRIGLT----GFK-CR-CGTIF 128 (167)
Q Consensus 108 C~~C~kk~~l~----~f~-Cr-Cg~~F 128 (167)
|..|++.|.+. ... |. |++.|
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 77788777653 344 77 77666
No 75
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.90 E-value=30 Score=17.51 Aligned_cols=9 Identities=56% Similarity=1.571 Sum_probs=3.3
Q ss_pred cccc-cCccc
Q 031015 120 FKCR-CGTIF 128 (167)
Q Consensus 120 f~Cr-Cg~~F 128 (167)
|.|. |+..|
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 3455 55444
No 76
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=23.31 E-value=32 Score=33.82 Aligned_cols=50 Identities=26% Similarity=0.607 Sum_probs=32.3
Q ss_pred CCcchhhhcccccccccc-cCccc---ccCCCCCCCCCCcchhhHhhHHHHHHhCCccc
Q 031015 106 NRCSVCRKRIGLTGFKCR-CGTIF---CGTHRYPEKHGCSFDFKKVGREEIARANPLIK 160 (167)
Q Consensus 106 ~rC~~C~kk~~l~~f~Cr-Cg~~F---C~~HR~~e~H~C~~dyk~~~r~~i~k~Np~v~ 160 (167)
.-|..|.+++-.++|+|+ |++.| |+.|-- --|. +|. -.|+.+...+|-|.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~vp---~~C~-~~~-~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRVP---TSCV-NPD-HLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCCC---CCCC-Ccc-hHhhhhhhcccccc
Confidence 457767777878899999 99866 555432 2344 332 34666677777654
No 77
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=23.16 E-value=43 Score=27.25 Aligned_cols=29 Identities=31% Similarity=0.812 Sum_probs=22.4
Q ss_pred CCCCCCCCcchhhhcccccccccc-cCcccccC
Q 031015 100 QQPPQPNRCSVCRKRIGLTGFKCR-CGTIFCGT 131 (167)
Q Consensus 100 ~~~~~~~rC~~C~kk~~l~~f~Cr-Cg~~FC~~ 131 (167)
+-++...-|..|+- ..-+.|- ||..||+.
T Consensus 113 ~~KP~r~fCaVCG~---~S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 113 SFKPLRKFCAVCGY---DSKYSCVNCGTKYCSV 142 (156)
T ss_pred CCCCcchhhhhcCC---CchhHHHhcCCceeec
Confidence 34456678999982 4568998 99999986
No 78
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=22.97 E-value=45 Score=27.27 Aligned_cols=41 Identities=7% Similarity=0.037 Sum_probs=24.8
Q ss_pred cccccc-cCcccccCCCCCCCCCCcchhhHhhHHHHHHhCCc
Q 031015 118 TGFKCR-CGTIFCGTHRYPEKHGCSFDFKKVGREEIARANPL 158 (167)
Q Consensus 118 ~~f~Cr-Cg~~FC~~HR~~e~H~C~~dyk~~~r~~i~k~Np~ 158 (167)
+++.|. |+.+||..|++.-.|.|.+--..-.|-.|++.-|.
T Consensus 12 lP~r~~~~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~ 53 (162)
T COG3582 12 LPSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPG 53 (162)
T ss_pred CCccccceeeeccCccccccccccchhhhhhhhhccccCCCc
Confidence 355555 66678888888888888776333334444444443
No 79
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=22.94 E-value=31 Score=21.18 Aligned_cols=22 Identities=41% Similarity=1.011 Sum_probs=16.8
Q ss_pred CCcchhhhccccc--c-ccc-ccCcc
Q 031015 106 NRCSVCRKRIGLT--G-FKC-RCGTI 127 (167)
Q Consensus 106 ~rC~~C~kk~~l~--~-f~C-rCg~~ 127 (167)
.+|..|+.....+ | +.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999986665 3 889 69865
No 80
>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=22.85 E-value=37 Score=20.34 Aligned_cols=10 Identities=50% Similarity=1.062 Sum_probs=7.8
Q ss_pred cCcccccCCC
Q 031015 124 CGTIFCGTHR 133 (167)
Q Consensus 124 Cg~~FC~~HR 133 (167)
=|..||+.|.
T Consensus 21 ~g~~fC~~H~ 30 (31)
T PF11722_consen 21 PGSRFCGEHM 30 (31)
T ss_pred CcCCccccCC
Confidence 4678999985
No 81
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=22.39 E-value=25 Score=24.62 Aligned_cols=13 Identities=54% Similarity=0.979 Sum_probs=10.4
Q ss_pred CCCCcchhhhccc
Q 031015 104 QPNRCSVCRKRIG 116 (167)
Q Consensus 104 ~~~rC~~C~kk~~ 116 (167)
.|-||++|+|-+|
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 3679999999774
No 82
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=22.10 E-value=47 Score=21.24 Aligned_cols=17 Identities=41% Similarity=0.823 Sum_probs=14.8
Q ss_pred ccCCCCCccccCCcchh
Q 031015 18 NNCGFFGSTATMNLCSK 34 (167)
Q Consensus 18 ngCGFFGs~aT~nlCSk 34 (167)
.+||=||.-.|+-.|..
T Consensus 5 ~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 5 KNCGAFGHMRTNKRCPM 21 (40)
T ss_pred cccccccccccCccCCC
Confidence 47999999999988874
No 83
>TIGR02452 conserved hypothetical protein TIGR02452. Members of this uncharacterized protein family are found in Streptomyces, Nostoc sp. PCC 7120, Clostridium acetobutylicum, Lactobacillus johnsonii NCC 533, Deinococcus radiodurans, and Pirellula sp. for a broad but sparse phylogenetic distibution that at least suggests lateral gene transfer.
Probab=22.10 E-value=42 Score=29.24 Aligned_cols=26 Identities=31% Similarity=0.489 Sum_probs=22.2
Q ss_pred cchhccCCCCCccccCCcchhhhHHHHH
Q 031015 14 RLCANNCGFFGSTATMNLCSKCYRDHCL 41 (167)
Q Consensus 14 ~lC~ngCGFFGs~aT~nlCSkCyr~~~~ 41 (167)
+|=+=|||-|||+.. .=.+||++++.
T Consensus 210 VLGA~GCG~f~N~p~--~VA~~f~evL~ 235 (266)
T TIGR02452 210 VLGAWGCGVFGNDPA--EVAKIFHDLLS 235 (266)
T ss_pred EECCccccccCCCHH--HHHHHHHHHhc
Confidence 355789999999996 67999999986
No 84
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=21.98 E-value=39 Score=21.37 Aligned_cols=21 Identities=19% Similarity=0.623 Sum_probs=14.9
Q ss_pred cccccccc-cCcccccCCCCCC
Q 031015 116 GLTGFKCR-CGTIFCGTHRYPE 136 (167)
Q Consensus 116 ~l~~f~Cr-Cg~~FC~~HR~~e 136 (167)
.+..|+|. ||..|=..+.+.+
T Consensus 2 P~Yey~C~~Cg~~fe~~~~~~~ 23 (52)
T TIGR02605 2 PIYEYRCTACGHRFEVLQKMSD 23 (52)
T ss_pred CCEEEEeCCCCCEeEEEEecCC
Confidence 34568888 8888877766543
No 85
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.92 E-value=40 Score=20.76 Aligned_cols=29 Identities=24% Similarity=0.591 Sum_probs=19.2
Q ss_pred Ccchhhhccc--ccccccccCcccccCCCCC
Q 031015 107 RCSVCRKRIG--LTGFKCRCGTIFCGTHRYP 135 (167)
Q Consensus 107 rC~~C~kk~~--l~~f~CrCg~~FC~~HR~~ 135 (167)
+|..|.++.. ...+.=.||.+||..+...
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 4677777772 2244555999999876543
No 86
>PF00869 Flavi_glycoprot: Flavivirus glycoprotein, central and dimerisation domains; InterPro: IPR011999 Flaviviruses are small, enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Yellow fever virus (YFV), West Nile virus (WNV), Tick-borne encephalitis virus, Japanese encephalitis virus and Dengue virus 2 viruses []. Flaviviruses consist of three structural proteins: the core nucleocapsid protein C (IPR001122 from INTERPRO), and the envelope glycoproteins M (IPR000069 from INTERPRO) and E. Glycoprotein E is a class II viral fusion protein that mediates both receptor binding and fusion. Class II viral fusion proteins are found in flaviviruses and alphaviruses, and are structurally distinct from class I fusion proteins from influenza virus and HIV. Glycoprotein E is comprised of three domains: domain I (dimerisation domain) is an 8-stranded beta barrel, domain II (central domain) is an elongated domain composed of twelve beta strands and two alpha helices, and domain III (immunoglobulin-like domain) is an IgC-like module with ten beta strands. This entry represents domains I and II, which are intertwined []. The glycoprotein E dimers on the viral surface re-cluster irreversibly into fusion-competent trimers upon exposure to low pH, as found in the acidic environment of the endosome. The formation of trimers results in a conformational change in the hinge region of domain II, a key structural element that opens a ligand-binding hydrophobic pocket at the interface between domains I and II. The conformational change results in the exposure of a fusion peptide loop at the tip of domain II, which is required in the fusion step to drive the cellular and viral membranes together by inserting into the membrane [].; GO: 0016021 integral to membrane, 0019031 viral envelope; PDB: 3P54_A 1OK8_A 1OAN_A 1OKE_B 3C5X_A 3C6E_A 2JSF_A 1URZ_B 3IYW_A 2JV6_A ....
Probab=21.78 E-value=31 Score=30.70 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=6.3
Q ss_pred ccCCCCCccc
Q 031015 18 NNCGFFGSTA 27 (167)
Q Consensus 18 ngCGFFGs~a 27 (167)
||||+||--.
T Consensus 103 NGCgLFGKGS 112 (293)
T PF00869_consen 103 NGCGLFGKGS 112 (293)
T ss_dssp GT-SS-EEEE
T ss_pred cccEEEeCCc
Confidence 8999999654
No 87
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=21.19 E-value=36 Score=18.46 Aligned_cols=11 Identities=45% Similarity=1.346 Sum_probs=7.9
Q ss_pred cccc-cCccccc
Q 031015 120 FKCR-CGTIFCG 130 (167)
Q Consensus 120 f~Cr-Cg~~FC~ 130 (167)
|.|. |+..|-.
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 6777 8777754
No 88
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=21.03 E-value=34 Score=24.83 Aligned_cols=19 Identities=42% Similarity=0.740 Sum_probs=15.3
Q ss_pred CCCcchhhhcccccccccc
Q 031015 105 PNRCSVCRKRIGLTGFKCR 123 (167)
Q Consensus 105 ~~rC~~C~kk~~l~~f~Cr 123 (167)
--.|..|.++|||-.|+=+
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~ 37 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSK 37 (91)
T ss_pred eEEccccCcEeeeeecccC
Confidence 4689999999999776543
No 89
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.92 E-value=70 Score=24.64 Aligned_cols=35 Identities=26% Similarity=0.632 Sum_probs=24.6
Q ss_pred CCcchhhhcccc------------cccccc-cCcccc-----cCCCCCCCCCCcc
Q 031015 106 NRCSVCRKRIGL------------TGFKCR-CGTIFC-----GTHRYPEKHGCSF 142 (167)
Q Consensus 106 ~rC~~C~kk~~l------------~~f~Cr-Cg~~FC-----~~HR~~e~H~C~~ 142 (167)
..|+.|.+.+.- ..|.|. |...|| -.|- .-|+|.+
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe--~Lh~CPG 108 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE--SLHCCPG 108 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh--hccCCcC
Confidence 469999886542 258899 999999 4443 4566654
No 90
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=20.87 E-value=46 Score=33.88 Aligned_cols=45 Identities=31% Similarity=0.825 Sum_probs=29.5
Q ss_pred CCCCCCCCcchhhhcc--------------cccccccc-cCcccccC---------CCC----CCCCCCcchh
Q 031015 100 QQPPQPNRCSVCRKRI--------------GLTGFKCR-CGTIFCGT---------HRY----PEKHGCSFDF 144 (167)
Q Consensus 100 ~~~~~~~rC~~C~kk~--------------~l~~f~Cr-Cg~~FC~~---------HR~----~e~H~C~~dy 144 (167)
.+...+|.|-.|.+-| |-..|+|+ ||.-|--+ ||- --.|.|.+.|
T Consensus 600 ~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 600 NKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred cccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 3445689999887633 23379999 99999743 432 2467777444
No 91
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=20.78 E-value=26 Score=33.15 Aligned_cols=25 Identities=40% Similarity=1.091 Sum_probs=21.8
Q ss_pred CCcchhhhccccc--ccccc-cCccccc
Q 031015 106 NRCSVCRKRIGLT--GFKCR-CGTIFCG 130 (167)
Q Consensus 106 ~rC~~C~kk~~l~--~f~Cr-Cg~~FC~ 130 (167)
.-|..|.++.||+ --.|| ||.+.|.
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHH
Confidence 5799999999997 58999 9998773
No 92
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=20.24 E-value=48 Score=22.97 Aligned_cols=14 Identities=36% Similarity=0.809 Sum_probs=11.7
Q ss_pred ccccccCcc-------cccCC
Q 031015 119 GFKCRCGTI-------FCGTH 132 (167)
Q Consensus 119 ~f~CrCg~~-------FC~~H 132 (167)
+|.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 388999988 88887
Done!