Query 031253
Match_columns 163
No_of_seqs 148 out of 443
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 11:28:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031253.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031253hhsearch_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 4.6E-47 1E-51 304.0 9.1 151 5-163 14-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.6 6E-17 1.3E-21 93.3 1.9 25 6-30 1-25 (25)
3 smart00259 ZnF_A20 A20-like zi 99.6 2.5E-16 5.5E-21 91.4 1.2 25 6-30 1-26 (26)
4 smart00154 ZnF_AN1 AN1-like Zi 99.5 3.6E-15 7.7E-20 93.8 2.2 38 103-140 1-39 (39)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 4.9E-11 1.1E-15 76.0 1.2 38 103-141 1-41 (43)
6 COG3582 Predicted nucleic acid 96.5 0.0013 2.8E-08 53.1 1.7 38 102-140 99-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.5 0.00098 2.1E-08 56.9 0.8 40 101-141 9-51 (250)
8 PF01363 FYVE: FYVE zinc finge 93.5 0.041 8.8E-07 37.1 1.4 29 99-127 8-39 (69)
9 KOG3183 Predicted Zn-finger pr 92.5 0.03 6.5E-07 48.0 -0.5 41 96-136 94-138 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.4 0.055 1.2E-06 35.0 0.8 27 101-127 3-32 (57)
11 smart00064 FYVE Protein presen 92.0 0.086 1.9E-06 35.4 1.4 29 100-128 10-41 (68)
12 KOG1818 Membrane trafficking a 88.3 0.18 3.8E-06 48.5 0.6 44 99-142 164-221 (634)
13 PF10571 UPF0547: Uncharacteri 85.8 0.41 8.8E-06 27.6 1.0 22 102-123 2-24 (26)
14 PF00130 C1_1: Phorbol esters/ 84.6 0.53 1.1E-05 30.0 1.2 24 99-122 10-37 (53)
15 PF15135 UPF0515: Uncharacteri 77.2 1.3 2.9E-05 38.5 1.5 28 98-125 130-167 (278)
16 PF02148 zf-UBP: Zn-finger in 64.7 3.7 7.9E-05 27.5 1.1 23 103-126 1-24 (63)
17 PHA02768 hypothetical protein; 63.7 2.9 6.3E-05 28.2 0.5 16 111-126 2-18 (55)
18 KOG1729 FYVE finger containing 60.9 2.1 4.5E-05 37.6 -0.8 32 99-131 167-202 (288)
19 cd00029 C1 Protein kinase C co 60.5 4.6 0.0001 24.8 1.0 24 99-122 10-37 (50)
20 PF13978 DUF4223: Protein of u 59.7 4.2 9.2E-05 27.4 0.7 18 123-140 19-36 (56)
21 COG1571 Predicted DNA-binding 58.9 6.2 0.00013 36.5 1.9 54 101-156 351-410 (421)
22 smart00109 C1 Protein kinase C 58.6 5.4 0.00012 24.1 1.0 23 99-121 10-35 (49)
23 PF01194 RNA_pol_N: RNA polyme 58.0 4.9 0.00011 27.6 0.8 13 100-112 4-16 (60)
24 COG1996 RPC10 DNA-directed RNA 57.7 4.6 9.9E-05 26.7 0.6 22 100-121 6-32 (49)
25 PF08882 Acetone_carb_G: Aceto 55.1 5.9 0.00013 30.4 1.0 35 104-140 16-50 (112)
26 PRK04016 DNA-directed RNA poly 53.8 4.7 0.0001 27.9 0.2 13 100-112 4-16 (62)
27 KOG2807 RNA polymerase II tran 53.8 8 0.00017 35.0 1.7 29 98-126 328-358 (378)
28 PHA00626 hypothetical protein 53.7 6.9 0.00015 26.8 1.0 23 101-125 12-35 (59)
29 PTZ00303 phosphatidylinositol 53.2 9.4 0.0002 38.5 2.2 27 100-126 460-494 (1374)
30 PLN00032 DNA-directed RNA poly 52.8 5.2 0.00011 28.4 0.3 13 100-112 4-16 (71)
31 KOG1819 FYVE finger-containing 52.7 7.1 0.00015 37.6 1.2 29 99-127 900-931 (990)
32 PF05207 zf-CSL: CSL zinc fing 49.7 7.3 0.00016 25.8 0.6 14 112-125 16-29 (55)
33 PF07649 C1_3: C1-like domain; 49.7 7.2 0.00016 22.4 0.5 22 102-123 2-25 (30)
34 PF03604 DNA_RNApol_7kD: DNA d 48.8 7.8 0.00017 23.3 0.6 19 102-120 2-24 (32)
35 KOG3497 DNA-directed RNA polym 47.9 6.5 0.00014 27.5 0.1 13 100-112 4-16 (69)
36 COG1997 RPL43A Ribosomal prote 47.8 9.9 0.00021 28.1 1.1 33 97-130 32-70 (89)
37 smart00659 RPOLCX RNA polymera 47.7 9.1 0.0002 24.4 0.8 21 101-121 3-27 (44)
38 PF03107 C1_2: C1 domain; Int 46.7 13 0.00028 21.4 1.3 19 102-120 2-22 (30)
39 PF14471 DUF4428: Domain of un 45.2 10 0.00022 24.9 0.8 20 102-121 1-28 (51)
40 PF07975 C1_4: TFIIH C1-like d 44.9 9.2 0.0002 25.4 0.5 34 103-136 2-47 (51)
41 PF11781 RRN7: RNA polymerase 41.7 12 0.00025 22.9 0.6 22 101-122 9-34 (36)
42 COG1644 RPB10 DNA-directed RNA 40.9 8.9 0.00019 26.7 -0.0 13 100-112 4-16 (63)
43 PRK08402 replication factor A; 40.0 14 0.0003 33.2 1.0 28 101-129 213-245 (355)
44 KOG1812 Predicted E3 ubiquitin 40.0 17 0.00037 32.8 1.6 30 99-128 305-338 (384)
45 smart00290 ZnF_UBP Ubiquitin C 39.9 9.7 0.00021 23.8 0.0 24 102-127 1-25 (50)
46 PRK00398 rpoP DNA-directed RNA 38.5 17 0.00036 22.8 0.9 29 100-128 3-36 (46)
47 smart00396 ZnF_UBR1 Putative z 38.1 17 0.00037 25.1 1.1 14 114-127 50-70 (71)
48 cd04476 RPA1_DBD_C RPA1_DBD_C: 38.1 15 0.00032 28.5 0.8 32 99-130 33-69 (166)
49 PF02318 FYVE_2: FYVE-type zin 37.2 22 0.00048 26.6 1.6 31 99-129 53-87 (118)
50 PF06750 DiS_P_DiS: Bacterial 36.3 19 0.00042 26.1 1.1 14 99-112 32-45 (92)
51 COG2888 Predicted Zn-ribbon RN 35.6 15 0.00032 25.4 0.4 21 99-121 37-58 (61)
52 smart00647 IBR In Between Ring 35.6 24 0.00053 22.4 1.4 18 113-130 39-57 (64)
53 PF13842 Tnp_zf-ribbon_2: DDE_ 35.5 28 0.0006 20.7 1.5 26 102-127 2-30 (32)
54 PF13240 zinc_ribbon_2: zinc-r 34.7 22 0.00047 19.6 0.9 16 103-118 2-17 (23)
55 KOG1074 Transcriptional repres 34.1 30 0.00064 35.0 2.3 46 94-139 599-672 (958)
56 PF13717 zinc_ribbon_4: zinc-r 33.5 21 0.00045 21.6 0.8 9 115-123 26-35 (36)
57 KOG1842 FYVE finger-containing 33.4 10 0.00023 35.5 -0.8 26 100-125 180-208 (505)
58 PF14634 zf-RING_5: zinc-RING 32.3 15 0.00032 22.6 -0.0 29 102-130 1-31 (44)
59 PF01780 Ribosomal_L37ae: Ribo 31.1 16 0.00034 27.0 -0.1 32 98-130 33-70 (90)
60 PF15549 PGC7_Stella: PGC7/Ste 31.1 25 0.00054 28.6 1.1 19 114-134 123-141 (160)
61 PRK07218 replication factor A; 30.8 22 0.00049 32.7 0.9 21 100-122 297-318 (423)
62 PF08073 CHDNT: CHDNT (NUC034) 30.4 23 0.00049 24.0 0.6 20 141-160 21-40 (55)
63 PF01485 IBR: IBR domain; Int 29.9 22 0.00047 22.6 0.5 16 115-130 41-57 (64)
64 KOG3507 DNA-directed RNA polym 29.9 23 0.00051 24.4 0.6 24 98-121 18-45 (62)
65 PF02928 zf-C5HC2: C5HC2 zinc 29.7 25 0.00054 23.0 0.7 27 103-129 1-29 (54)
66 PF00096 zf-C2H2: Zinc finger, 29.6 22 0.00047 18.5 0.4 10 115-124 1-11 (23)
67 PF10367 Vps39_2: Vacuolar sor 29.4 34 0.00073 24.0 1.4 24 100-123 78-102 (109)
68 PF09723 Zn-ribbon_8: Zinc rib 29.1 35 0.00076 21.1 1.3 20 112-131 3-23 (42)
69 PF10122 Mu-like_Com: Mu-like 29.0 20 0.00044 23.9 0.2 24 100-123 4-34 (51)
70 PF08600 Rsm1: Rsm1-like; Int 29.0 21 0.00045 25.8 0.3 18 100-117 19-36 (91)
71 PRK04136 rpl40e 50S ribosomal 28.2 30 0.00064 22.9 0.9 23 99-121 13-36 (48)
72 COG5432 RAD18 RING-finger-cont 28.0 20 0.00043 32.3 0.0 40 100-140 25-70 (391)
73 KOG0193 Serine/threonine prote 27.9 22 0.00047 34.7 0.3 51 101-156 190-244 (678)
74 PF14835 zf-RING_6: zf-RING of 27.8 33 0.00071 24.0 1.1 26 101-126 8-33 (65)
75 PF00869 Flavi_glycoprot: Flav 27.3 22 0.00049 31.4 0.2 10 11-20 103-112 (293)
76 PF14446 Prok-RING_1: Prokaryo 27.2 36 0.00077 22.9 1.1 24 100-123 5-31 (54)
77 PF13465 zf-H2C2_2: Zinc-finge 26.2 36 0.00078 18.8 0.9 11 113-123 13-24 (26)
78 PF00412 LIM: LIM domain; Int 25.6 29 0.00063 21.7 0.5 27 101-127 27-53 (58)
79 PRK14890 putative Zn-ribbon RN 24.9 31 0.00068 23.6 0.5 20 100-121 36-56 (59)
80 PF04438 zf-HIT: HIT zinc fing 24.7 29 0.00062 20.4 0.3 23 101-126 3-26 (30)
81 PF01529 zf-DHHC: DHHC palmito 24.4 64 0.0014 24.6 2.3 43 98-144 46-88 (174)
82 COG3357 Predicted transcriptio 24.2 28 0.0006 26.1 0.2 16 110-125 54-70 (97)
83 PTZ00218 40S ribosomal protein 24.1 43 0.00094 22.6 1.1 13 22-34 34-46 (54)
84 PRK12366 replication factor A; 24.0 33 0.00073 32.9 0.8 29 100-129 532-563 (637)
85 PF02704 GASA: Gibberellin reg 23.5 38 0.00083 23.3 0.8 19 15-34 34-52 (60)
86 COG3582 Predicted nucleic acid 23.5 43 0.00093 27.2 1.2 36 119-154 19-54 (162)
87 PF13894 zf-C2H2_4: C2H2-type 23.3 35 0.00076 17.1 0.4 8 116-123 2-10 (24)
88 COG1439 Predicted nucleic acid 22.6 31 0.00067 28.4 0.2 26 97-122 136-162 (177)
89 PF13923 zf-C3HC4_2: Zinc fing 22.4 39 0.00085 20.0 0.6 24 103-126 1-24 (39)
90 PF15288 zf-CCHC_6: Zinc knuck 22.2 47 0.001 21.1 0.9 15 12-26 6-20 (40)
91 smart00508 PostSET Cysteine-ri 21.9 46 0.001 19.2 0.8 12 114-125 2-13 (26)
92 smart00834 CxxC_CXXC_SSSS Puta 21.8 44 0.00096 19.7 0.7 14 113-126 4-18 (41)
93 PF14369 zf-RING_3: zinc-finge 21.1 44 0.00096 20.2 0.6 22 102-123 4-31 (35)
94 PF11722 zf-TRM13_CCCH: CCCH z 20.7 43 0.00093 19.9 0.5 10 119-128 21-30 (31)
95 TIGR02452 conserved hypothetic 20.7 48 0.001 28.7 1.0 26 7-34 210-235 (266)
96 PF12662 cEGF: Complement Clr- 20.6 91 0.002 17.5 1.8 20 114-136 1-20 (24)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.6e-47 Score=304.00 Aligned_cols=151 Identities=38% Similarity=0.796 Sum_probs=101.3
Q ss_pred cccccccCCCCCCcccCCCchhhhhhHHHHHHHHh-hhhhhhccccCCCCCCCCCCCCCCCCCCCchh-hhhhhcc-ccC
Q 031253 5 NVTMCIKGCGFYGSKENKNMCSKCYDDYLKAELIA-KSSKLLDAAKKPIGPTNAPNPSVLDKSWPPQW-IISAAKT-TNN 81 (163)
Q Consensus 5 ~p~LCaNgCGFFGS~aT~nmCSKCYrd~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~ 81 (163)
.++||+|||||||+|+|||||||||||++.++++. ...+.. +.+..++... +........ ..+.... ...
T Consensus 14 ~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~--~~~~~~~~~s-----~~~~~~~~~~~~~~~~~~~~~ 86 (167)
T KOG3173|consen 14 QDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPP--VESSLSSPRS-----VPSRDPPAVSLESTTESELKL 86 (167)
T ss_pred cccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCc--ccccccCccc-----cCccccccccccccccccccc
Confidence 35899999999999999999999999999888765 222211 1110000000 000000000 0000000 000
Q ss_pred CCCCCCccccCCCCCCccccccccccccccccceeeecCcccccCccCCCCCCCcccchHhhHHHHHHhCCccccccccc
Q 031253 82 SNAVDSRTIESGAAGSSVKRRCEICNKKVGLIEFKCRCGHLYCGTHRYPKEHACTFDFKKFDREMLVKDNPLIRADKLEG 161 (163)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~rC~~C~kk~gl~gf~CrCg~~fC~~HR~~~~H~C~~dyk~~~r~~l~k~np~v~~~k~~~ 161 (163)
.....+...+........++||+.|+|||||+||.||||++||+.|||+|.|+|+||||.+||+.|+++||+|+++||+
T Consensus 87 ~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~- 165 (167)
T KOG3173|consen 87 VSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQ- 165 (167)
T ss_pred cccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccc-
Confidence 0000011111112233567899999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q 031253 162 RI 163 (163)
Q Consensus 162 KI 163 (163)
||
T Consensus 166 ki 167 (167)
T KOG3173|consen 166 KI 167 (167)
T ss_pred cC
Confidence 98
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=99.64 E-value=6e-17 Score=93.27 Aligned_cols=25 Identities=52% Similarity=1.359 Sum_probs=21.0
Q ss_pred ccccccCCCCCCcccCCCchhhhhh
Q 031253 6 VTMCIKGCGFYGSKENKNMCSKCYD 30 (163)
Q Consensus 6 p~LCaNgCGFFGS~aT~nmCSKCYr 30 (163)
|+||++|||||||++|+||||||||
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 6799999999999999999999997
No 3
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.59 E-value=2.5e-16 Score=91.44 Aligned_cols=25 Identities=40% Similarity=1.162 Sum_probs=23.6
Q ss_pred ccccc-cCCCCCCcccCCCchhhhhh
Q 031253 6 VTMCI-KGCGFYGSKENKNMCSKCYD 30 (163)
Q Consensus 6 p~LCa-NgCGFFGS~aT~nmCSKCYr 30 (163)
|+||+ +||||||||+|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 56899 99999999999999999996
No 4
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.53 E-value=3.6e-15 Score=93.84 Aligned_cols=38 Identities=61% Similarity=1.434 Sum_probs=36.9
Q ss_pred cccccccccccceeee-cCcccccCccCCCCCCCcccch
Q 031253 103 CEICNKKVGLIEFKCR-CGHLYCGTHRYPKEHACTFDFK 140 (163)
Q Consensus 103 C~~C~kk~gl~gf~Cr-Cg~~fC~~HR~~~~H~C~~dyk 140 (163)
|+.|+++++|++|+|+ |+.+||..||+||.|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 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=99.05 E-value=4.9e-11 Score=75.99 Aligned_cols=38 Identities=45% Similarity=1.019 Sum_probs=28.2
Q ss_pred ccc--ccccccccceeee-cCcccccCccCCCCCCCcccchH
Q 031253 103 CEI--CNKKVGLIEFKCR-CGHLYCGTHRYPKEHACTFDFKK 141 (163)
Q Consensus 103 C~~--C~kk~gl~gf~Cr-Cg~~fC~~HR~~~~H~C~~dyk~ 141 (163)
|.. |++++. ++|.|+ |+..||..||+|+.|+|+.+++.
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccC-CCeECCCCCcccCccccCccccCCcchhhc
Confidence 455 999888 699999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.49 E-value=0.0013 Score=53.14 Aligned_cols=38 Identities=29% Similarity=0.534 Sum_probs=30.0
Q ss_pred ccccccccccccceeee-cCcccccCccCCCCCCCcccch
Q 031253 102 RCEICNKKVGLIEFKCR-CGHLYCGTHRYPKEHACTFDFK 140 (163)
Q Consensus 102 rC~~C~kk~gl~gf~Cr-Cg~~fC~~HR~~~~H~C~~dyk 140 (163)
+|..|++..+| .++|. |++.||+.||+++.|+|.+...
T Consensus 99 ~~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 99 TPQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred cceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 34445555444 67999 9999999999999999998765
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.45 E-value=0.00098 Score=56.92 Aligned_cols=40 Identities=28% Similarity=0.869 Sum_probs=35.4
Q ss_pred cccc--cccccccccceeee-cCcccccCccCCCCCCCcccchH
Q 031253 101 RRCE--ICNKKVGLIEFKCR-CGHLYCGTHRYPKEHACTFDFKK 141 (163)
Q Consensus 101 ~rC~--~C~kk~gl~gf~Cr-Cg~~fC~~HR~~~~H~C~~dyk~ 141 (163)
..|. .|+. |.++.|+|. |+.+||..||--+.|+|.+-|..
T Consensus 9 kHCs~~~Ckq-lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCKQ-LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhhh-ccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4777 7865 799999999 99999999999999999998863
No 8
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=93.47 E-value=0.041 Score=37.14 Aligned_cols=29 Identities=38% Similarity=0.961 Sum_probs=17.5
Q ss_pred ccccccccccccccc--ceeee-cCcccccCc
Q 031253 99 VKRRCEICNKKVGLI--EFKCR-CGHLYCGTH 127 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~--gf~Cr-Cg~~fC~~H 127 (163)
....|..|+++.+|+ -..|| ||.+||+.+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCch
Confidence 457999999999995 48999 999999764
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=92.50 E-value=0.03 Score=48.00 Aligned_cols=41 Identities=32% Similarity=0.868 Sum_probs=35.0
Q ss_pred CCccccccc--ccccccccc-ceeee-cCcccccCccCCCCCCCc
Q 031253 96 GSSVKRRCE--ICNKKVGLI-EFKCR-CGHLYCGTHRYPKEHACT 136 (163)
Q Consensus 96 ~~~~~~rC~--~C~kk~gl~-gf~Cr-Cg~~fC~~HR~~~~H~C~ 136 (163)
.+..+++|. .|++++-+. .+.|+ ||..||-.||++-.|.|.
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 445677787 688988874 69999 999999999999999997
No 10
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=92.37 E-value=0.055 Score=35.01 Aligned_cols=27 Identities=33% Similarity=0.936 Sum_probs=23.5
Q ss_pred ccccccccccccc--ceeee-cCcccccCc
Q 031253 101 RRCEICNKKVGLI--EFKCR-CGHLYCGTH 127 (163)
Q Consensus 101 ~rC~~C~kk~gl~--gf~Cr-Cg~~fC~~H 127 (163)
..|..|.++.++. ...|| ||.+||+.+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHH
Confidence 5799999999994 68999 999999863
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=88.31 E-value=0.18 Score=48.46 Aligned_cols=44 Identities=27% Similarity=0.717 Sum_probs=34.7
Q ss_pred cccccccccccccccc--eeee-cCcccccCcc-----------CCCCCCCcccchHh
Q 031253 99 VKRRCEICNKKVGLIE--FKCR-CGHLYCGTHR-----------YPKEHACTFDFKKF 142 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~g--f~Cr-Cg~~fC~~HR-----------~~~~H~C~~dyk~~ 142 (163)
...+|..|+.+.|+++ ..|| ||.+||+.|- |-+.--|.-+|...
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l 221 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELL 221 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHh
Confidence 4579999999999975 7999 9999999873 34556677777533
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.77 E-value=0.41 Score=27.57 Aligned_cols=22 Identities=27% Similarity=0.591 Sum_probs=19.9
Q ss_pred ccccccccccccceeee-cCccc
Q 031253 102 RCEICNKKVGLIEFKCR-CGHLY 123 (163)
Q Consensus 102 rC~~C~kk~gl~gf~Cr-Cg~~f 123 (163)
+|-.|++.|.+.--.|- ||+.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 68899999999889999 99887
No 14
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=84.62 E-value=0.53 Score=29.98 Aligned_cols=24 Identities=29% Similarity=0.927 Sum_probs=18.6
Q ss_pred cccccccccccc---cccceeee-cCcc
Q 031253 99 VKRRCEICNKKV---GLIEFKCR-CGHL 122 (163)
Q Consensus 99 ~~~rC~~C~kk~---gl~gf~Cr-Cg~~ 122 (163)
.+..|..|++.| ++.|++|+ |+.+
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 66899999 7654
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=77.17 E-value=1.3 Score=38.48 Aligned_cols=28 Identities=39% Similarity=0.943 Sum_probs=23.0
Q ss_pred cccccccccccc---------ccccceeee-cCccccc
Q 031253 98 SVKRRCEICNKK---------VGLIEFKCR-CGHLYCG 125 (163)
Q Consensus 98 ~~~~rC~~C~kk---------~gl~gf~Cr-Cg~~fC~ 125 (163)
+..+||..|+|| .|+--|.|. |+++|=+
T Consensus 130 KeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccCCCccccccceeeeecccccccchh
Confidence 456899999988 677789995 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=64.67 E-value=3.7 Score=27.46 Aligned_cols=23 Identities=30% Similarity=0.898 Sum_probs=15.7
Q ss_pred cccccccccccceeee-cCcccccC
Q 031253 103 CEICNKKVGLIEFKCR-CGHLYCGT 126 (163)
Q Consensus 103 C~~C~kk~gl~gf~Cr-Cg~~fC~~ 126 (163)
|..|+.. +-.-+.|- ||.++|+.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 6677765 44567788 99999994
No 17
>PHA02768 hypothetical protein; Provisional
Probab=63.69 E-value=2.9 Score=28.23 Aligned_cols=16 Identities=31% Similarity=1.043 Sum_probs=13.0
Q ss_pred cccceeee-cCcccccC
Q 031253 111 GLIEFKCR-CGHLYCGT 126 (163)
Q Consensus 111 gl~gf~Cr-Cg~~fC~~ 126 (163)
.|+||.|. ||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 57899998 99988754
No 18
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=60.85 E-value=2.1 Score=37.57 Aligned_cols=32 Identities=25% Similarity=0.688 Sum_probs=26.0
Q ss_pred cccccccccc-ccccc--ceeee-cCcccccCccCCC
Q 031253 99 VKRRCEICNK-KVGLI--EFKCR-CGHLYCGTHRYPK 131 (163)
Q Consensus 99 ~~~rC~~C~k-k~gl~--gf~Cr-Cg~~fC~~HR~~~ 131 (163)
..++|..|.+ .-.|. --.|| ||.+||. |....
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 4689999999 77773 46899 9999999 76544
No 19
>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=60.47 E-value=4.6 Score=24.76 Aligned_cols=24 Identities=21% Similarity=0.570 Sum_probs=19.2
Q ss_pred cccccccccccccc---cceeee-cCcc
Q 031253 99 VKRRCEICNKKVGL---IEFKCR-CGHL 122 (163)
Q Consensus 99 ~~~rC~~C~kk~gl---~gf~Cr-Cg~~ 122 (163)
.+..|..|++.+.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 35689999999984 899999 7543
No 20
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=59.71 E-value=4.2 Score=27.43 Aligned_cols=18 Identities=33% Similarity=0.748 Sum_probs=15.9
Q ss_pred cccCccCCCCCCCcccch
Q 031253 123 YCGTHRYPKEHACTFDFK 140 (163)
Q Consensus 123 fC~~HR~~~~H~C~~dyk 140 (163)
=|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 467899999999999995
No 21
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=58.89 E-value=6.2 Score=36.47 Aligned_cols=54 Identities=24% Similarity=0.472 Sum_probs=37.9
Q ss_pred cccccccccccc---cceeee-cCcccccCcc--CCCCCCCcccchHhhHHHHHHhCCcccc
Q 031253 101 RRCEICNKKVGL---IEFKCR-CGHLYCGTHR--YPKEHACTFDFKKFDREMLVKDNPLIRA 156 (163)
Q Consensus 101 ~rC~~C~kk~gl---~gf~Cr-Cg~~fC~~HR--~~~~H~C~~dyk~~~r~~l~k~np~v~~ 156 (163)
-+|-.|++++-. .||+|+ ||..+=..-+ ++..-.=.+++-..+|.+|.| |.+..
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk--P~~~~ 410 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK--PLVLE 410 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC--Ccchh
Confidence 499999998866 489999 9998866532 222333345666788899988 66543
No 22
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=58.56 E-value=5.4 Score=24.12 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=18.4
Q ss_pred cccccccccccccc--cceeee-cCc
Q 031253 99 VKRRCEICNKKVGL--IEFKCR-CGH 121 (163)
Q Consensus 99 ~~~rC~~C~kk~gl--~gf~Cr-Cg~ 121 (163)
.+..|..|++.+.. .|++|+ |+.
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCc
Confidence 36789999999987 489998 654
No 23
>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=57.98 E-value=4.9 Score=27.65 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=10.2
Q ss_pred ccccccccccccc
Q 031253 100 KRRCEICNKKVGL 112 (163)
Q Consensus 100 ~~rC~~C~kk~gl 112 (163)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6799999998874
No 24
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=57.71 E-value=4.6 Score=26.72 Aligned_cols=22 Identities=32% Similarity=0.948 Sum_probs=18.0
Q ss_pred ccccccccccccc----cceeee-cCc
Q 031253 100 KRRCEICNKKVGL----IEFKCR-CGH 121 (163)
Q Consensus 100 ~~rC~~C~kk~gl----~gf~Cr-Cg~ 121 (163)
..+|..|++++.+ .+..|. ||+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 5799999999985 578998 654
No 25
>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=55.13 E-value=5.9 Score=30.40 Aligned_cols=35 Identities=31% Similarity=0.449 Sum_probs=26.5
Q ss_pred ccccccccccceeeecCcccccCccCCCCCCCcccch
Q 031253 104 EICNKKVGLIEFKCRCGHLYCGTHRYPKEHACTFDFK 140 (163)
Q Consensus 104 ~~C~kk~gl~gf~CrCg~~fC~~HR~~~~H~C~~dyk 140 (163)
+.|+++- .-.+|+||+.||+.+..-..|.--++-.
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~vRd 50 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYVRD 50 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEecC
Confidence 4566654 2679999999999988888887766654
No 26
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=53.82 E-value=4.7 Score=27.94 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 031253 100 KRRCEICNKKVGL 112 (163)
Q Consensus 100 ~~rC~~C~kk~gl 112 (163)
|-||++|+|-+|-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6799999998875
No 27
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=53.80 E-value=8 Score=35.00 Aligned_cols=29 Identities=21% Similarity=0.670 Sum_probs=24.2
Q ss_pred ccccccccc-cccccccceeee-cCcccccC
Q 031253 98 SVKRRCEIC-NKKVGLIEFKCR-CGHLYCGT 126 (163)
Q Consensus 98 ~~~~rC~~C-~kk~gl~gf~Cr-Cg~~fC~~ 126 (163)
...++|+.| .+.++...|.|+ |-++||-.
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeecc
Confidence 356789999 666777889999 99999975
No 28
>PHA00626 hypothetical protein
Probab=53.73 E-value=6.9 Score=26.82 Aligned_cols=23 Identities=13% Similarity=0.208 Sum_probs=16.7
Q ss_pred cccccccccccccceeee-cCccccc
Q 031253 101 RRCEICNKKVGLIEFKCR-CGHLYCG 125 (163)
Q Consensus 101 ~rC~~C~kk~gl~gf~Cr-Cg~~fC~ 125 (163)
.||.+|++-. .-|+|. ||+.|-.
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccC--cceEcCCCCCeech
Confidence 4788888732 458998 9888864
No 29
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=53.21 E-value=9.4 Score=38.52 Aligned_cols=27 Identities=26% Similarity=0.624 Sum_probs=21.5
Q ss_pred ccccccccccccc-------cceeee-cCcccccC
Q 031253 100 KRRCEICNKKVGL-------IEFKCR-CGHLYCGT 126 (163)
Q Consensus 100 ~~rC~~C~kk~gl-------~gf~Cr-Cg~~fC~~ 126 (163)
...|..|+++-+. .--.|| ||.+||+.
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCcc
Confidence 3579999999864 245699 99999876
No 30
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=52.83 E-value=5.2 Score=28.44 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 031253 100 KRRCEICNKKVGL 112 (163)
Q Consensus 100 ~~rC~~C~kk~gl 112 (163)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998875
No 31
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=52.70 E-value=7.1 Score=37.57 Aligned_cols=29 Identities=28% Similarity=0.839 Sum_probs=21.6
Q ss_pred cccccccccccccc--cceeee-cCcccccCc
Q 031253 99 VKRRCEICNKKVGL--IEFKCR-CGHLYCGTH 127 (163)
Q Consensus 99 ~~~rC~~C~kk~gl--~gf~Cr-Cg~~fC~~H 127 (163)
..-+|..|...... .-..|| ||++||++-
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 35699999865444 245899 999999864
No 32
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=49.72 E-value=7.3 Score=25.83 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=10.8
Q ss_pred ccceeeecCccccc
Q 031253 112 LIEFKCRCGHLYCG 125 (163)
Q Consensus 112 l~gf~CrCg~~fC~ 125 (163)
..-+.||||..|--
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 35689999998753
No 33
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=49.69 E-value=7.2 Score=22.39 Aligned_cols=22 Identities=27% Similarity=0.792 Sum_probs=8.8
Q ss_pred ccccccccccc-cceeee-cCccc
Q 031253 102 RCEICNKKVGL-IEFKCR-CGHLY 123 (163)
Q Consensus 102 rC~~C~kk~gl-~gf~Cr-Cg~~f 123 (163)
+|..|++.+.. ..|.|. |...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 68999999888 789998 76543
No 34
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=48.80 E-value=7.8 Score=23.27 Aligned_cols=19 Identities=37% Similarity=0.929 Sum_probs=10.7
Q ss_pred ccccccccccc---cceeee-cC
Q 031253 102 RCEICNKKVGL---IEFKCR-CG 120 (163)
Q Consensus 102 rC~~C~kk~gl---~gf~Cr-Cg 120 (163)
.|..|+..+.| ...+|+ ||
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCcCCCeeEcCCCCcEECCcCC
Confidence 36666666666 345666 54
No 35
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=47.86 E-value=6.5 Score=27.48 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 031253 100 KRRCEICNKKVGL 112 (163)
Q Consensus 100 ~~rC~~C~kk~gl 112 (163)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998875
No 36
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=47.81 E-value=9.9 Score=28.10 Aligned_cols=33 Identities=30% Similarity=0.811 Sum_probs=25.1
Q ss_pred Cccccccccccccccc----cc-eeee-cCcccccCccCC
Q 031253 97 SSVKRRCEICNKKVGL----IE-FKCR-CGHLYCGTHRYP 130 (163)
Q Consensus 97 ~~~~~rC~~C~kk~gl----~g-f~Cr-Cg~~fC~~HR~~ 130 (163)
+..+..|..|+++ .+ +| ..|+ ||++|=+---.|
T Consensus 32 ~~~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 32 QRAKHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HhcCCcCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 3467899999987 33 44 6999 999998776555
No 37
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.72 E-value=9.1 Score=24.40 Aligned_cols=21 Identities=29% Similarity=0.771 Sum_probs=15.2
Q ss_pred cccccccccccc---cceeee-cCc
Q 031253 101 RRCEICNKKVGL---IEFKCR-CGH 121 (163)
Q Consensus 101 ~rC~~C~kk~gl---~gf~Cr-Cg~ 121 (163)
.+|..|+..+.+ .+..|+ ||+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 478888888887 357776 643
No 38
>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=46.74 E-value=13 Score=21.45 Aligned_cols=19 Identities=26% Similarity=0.978 Sum_probs=16.0
Q ss_pred cccccccccccc-ceeee-cC
Q 031253 102 RCEICNKKVGLI-EFKCR-CG 120 (163)
Q Consensus 102 rC~~C~kk~gl~-gf~Cr-Cg 120 (163)
.|..|++++.-. .|.|. |+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 488999999888 89997 65
No 39
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=45.18 E-value=10 Score=24.85 Aligned_cols=20 Identities=45% Similarity=1.253 Sum_probs=15.5
Q ss_pred cccccccccccc-------ceeee-cCc
Q 031253 102 RCEICNKKVGLI-------EFKCR-CGH 121 (163)
Q Consensus 102 rC~~C~kk~gl~-------gf~Cr-Cg~ 121 (163)
+|..|++++||+ ||.|. |-.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~ 28 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLK 28 (51)
T ss_pred CCCccccccccccceeccCccchHHHHH
Confidence 599999999994 46777 543
No 40
>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=44.85 E-value=9.2 Score=25.37 Aligned_cols=34 Identities=24% Similarity=0.568 Sum_probs=16.8
Q ss_pred ccccccccccc--------ceeee-cCcccccC---ccCCCCCCCc
Q 031253 103 CEICNKKVGLI--------EFKCR-CGHLYCGT---HRYPKEHACT 136 (163)
Q Consensus 103 C~~C~kk~gl~--------gf~Cr-Cg~~fC~~---HR~~~~H~C~ 136 (163)
|+.|.+.+.-. .|.|. |+..||.. -.+-.-|+|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 56666666653 58887 99999864 3344567765
No 41
>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=41.72 E-value=12 Score=22.92 Aligned_cols=22 Identities=32% Similarity=0.902 Sum_probs=16.8
Q ss_pred ccccccccccccc--c-eee-ecCcc
Q 031253 101 RRCEICNKKVGLI--E-FKC-RCGHL 122 (163)
Q Consensus 101 ~rC~~C~kk~gl~--g-f~C-rCg~~ 122 (163)
-+|..|+-+.... | |.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 3699999986663 4 789 79875
No 42
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=40.90 E-value=8.9 Score=26.65 Aligned_cols=13 Identities=38% Similarity=0.746 Sum_probs=10.9
Q ss_pred ccccccccccccc
Q 031253 100 KRRCEICNKKVGL 112 (163)
Q Consensus 100 ~~rC~~C~kk~gl 112 (163)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6799999998764
No 43
>PRK08402 replication factor A; Reviewed
Probab=40.03 E-value=14 Score=33.24 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=18.6
Q ss_pred cccccccccccc----cceeee-cCcccccCccC
Q 031253 101 RRCEICNKKVGL----IEFKCR-CGHLYCGTHRY 129 (163)
Q Consensus 101 ~rC~~C~kk~gl----~gf~Cr-Cg~~fC~~HR~ 129 (163)
.+|..|+|||-. ..+.|. ||.+-+ .|||
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 699999999963 347777 554333 4554
No 44
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.99 E-value=17 Score=32.81 Aligned_cols=30 Identities=33% Similarity=0.791 Sum_probs=24.5
Q ss_pred cccccccccccccc----cceeeecCcccccCcc
Q 031253 99 VKRRCEICNKKVGL----IEFKCRCGHLYCGTHR 128 (163)
Q Consensus 99 ~~~rC~~C~kk~gl----~gf~CrCg~~fC~~HR 128 (163)
.-.+|..|+--+.| .-++||||+-||..=.
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred hcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 35799999998888 3489999999997644
No 45
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=39.93 E-value=9.7 Score=23.75 Aligned_cols=24 Identities=33% Similarity=0.953 Sum_probs=17.7
Q ss_pred ccccccccccccceeee-cCcccccCc
Q 031253 102 RCEICNKKVGLIEFKCR-CGHLYCGTH 127 (163)
Q Consensus 102 rC~~C~kk~gl~gf~Cr-Cg~~fC~~H 127 (163)
||..|..... -+.|- |+.++|+..
T Consensus 1 ~C~~C~~~~~--l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN--LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC--eEEecCCCCcccCCC
Confidence 6888886554 45666 999999763
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=38.53 E-value=17 Score=22.79 Aligned_cols=29 Identities=28% Similarity=0.656 Sum_probs=19.0
Q ss_pred ccccccccccccc----cceeee-cCcccccCcc
Q 031253 100 KRRCEICNKKVGL----IEFKCR-CGHLYCGTHR 128 (163)
Q Consensus 100 ~~rC~~C~kk~gl----~gf~Cr-Cg~~fC~~HR 128 (163)
..+|..|+..+.+ ..++|. ||..+--.+|
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 3578888887755 357888 7665544444
No 47
>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=38.14 E-value=17 Score=25.09 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=12.1
Q ss_pred ceeeecCcc-------cccCc
Q 031253 114 EFKCRCGHL-------YCGTH 127 (163)
Q Consensus 114 gf~CrCg~~-------fC~~H 127 (163)
||.|.||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999998 88887
No 48
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=38.11 E-value=15 Score=28.55 Aligned_cols=32 Identities=31% Similarity=0.518 Sum_probs=22.6
Q ss_pred ccccccccccccccc---ceeee-cCccc-ccCccCC
Q 031253 99 VKRRCEICNKKVGLI---EFKCR-CGHLY-CGTHRYP 130 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~---gf~Cr-Cg~~f-C~~HR~~ 130 (163)
.=..|..|+|||-.. .|.|. |+..+ =-.+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 346788999999875 48888 87765 3346663
No 49
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=37.22 E-value=22 Score=26.57 Aligned_cols=31 Identities=29% Similarity=0.670 Sum_probs=23.5
Q ss_pred ccccccccccccccc---ceeee-cCcccccCccC
Q 031253 99 VKRRCEICNKKVGLI---EFKCR-CGHLYCGTHRY 129 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~---gf~Cr-Cg~~fC~~HR~ 129 (163)
....|..|.+.+|++ |..|. |...+|..=+.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 356999999999984 68999 99999987444
No 50
>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=36.30 E-value=19 Score=26.12 Aligned_cols=14 Identities=14% Similarity=0.560 Sum_probs=11.9
Q ss_pred cccccccccccccc
Q 031253 99 VKRRCEICNKKVGL 112 (163)
Q Consensus 99 ~~~rC~~C~kk~gl 112 (163)
.+++|..|++++..
T Consensus 32 ~rS~C~~C~~~L~~ 45 (92)
T PF06750_consen 32 PRSHCPHCGHPLSW 45 (92)
T ss_pred CCCcCcCCCCcCcc
Confidence 36899999999886
No 51
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.60 E-value=15 Score=25.42 Aligned_cols=21 Identities=38% Similarity=1.020 Sum_probs=14.4
Q ss_pred cccccccccccccccceee-ecCc
Q 031253 99 VKRRCEICNKKVGLIEFKC-RCGH 121 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~gf~C-rCg~ 121 (163)
.-.||..|||- |. .|+| .||.
T Consensus 37 ~I~Rc~~CRk~-g~-~Y~Cp~CGF 58 (61)
T COG2888 37 EIYRCAKCRKL-GN-PYRCPKCGF 58 (61)
T ss_pred eeehhhhHHHc-CC-ceECCCcCc
Confidence 35789999873 33 5788 4775
No 52
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=35.58 E-value=24 Score=22.44 Aligned_cols=18 Identities=28% Similarity=0.870 Sum_probs=14.7
Q ss_pred cceee-ecCcccccCccCC
Q 031253 113 IEFKC-RCGHLYCGTHRYP 130 (163)
Q Consensus 113 ~gf~C-rCg~~fC~~HR~~ 130 (163)
....| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 46789 7999999988765
No 53
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=35.49 E-value=28 Score=20.67 Aligned_cols=26 Identities=31% Similarity=0.815 Sum_probs=17.8
Q ss_pred cccccccccc-c-cceeee-cCcccccCc
Q 031253 102 RCEICNKKVG-L-IEFKCR-CGHLYCGTH 127 (163)
Q Consensus 102 rC~~C~kk~g-l-~gf~Cr-Cg~~fC~~H 127 (163)
||..|.++-- - +-|.|. |+-..|..|
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 6777766422 2 678898 887777666
No 54
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.71 E-value=22 Score=19.62 Aligned_cols=16 Identities=19% Similarity=0.405 Sum_probs=8.4
Q ss_pred cccccccccccceeee
Q 031253 103 CEICNKKVGLIEFKCR 118 (163)
Q Consensus 103 C~~C~kk~gl~gf~Cr 118 (163)
|..|++++.-..-.|.
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 5556666555443444
No 55
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=34.13 E-value=30 Score=34.95 Aligned_cols=46 Identities=26% Similarity=0.660 Sum_probs=31.7
Q ss_pred CCCCccccccccccccc--------------cccceeee-cCccccc---------CccC----CCCCCCcccc
Q 031253 94 AAGSSVKRRCEICNKKV--------------GLIEFKCR-CGHLYCG---------THRY----PKEHACTFDF 139 (163)
Q Consensus 94 ~~~~~~~~rC~~C~kk~--------------gl~gf~Cr-Cg~~fC~---------~HR~----~~~H~C~~dy 139 (163)
..+...+|.|-.|.|-| |-..|+|+ ||.-|-- .||- --+|.|.+-|
T Consensus 599 ~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 599 ENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 34456799999998754 34679999 9999963 3443 2567777544
No 56
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=33.55 E-value=21 Score=21.61 Aligned_cols=9 Identities=44% Similarity=1.667 Sum_probs=3.9
Q ss_pred eeee-cCccc
Q 031253 115 FKCR-CGHLY 123 (163)
Q Consensus 115 f~Cr-Cg~~f 123 (163)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3444 44443
No 57
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=33.36 E-value=10 Score=35.51 Aligned_cols=26 Identities=35% Similarity=0.961 Sum_probs=22.4
Q ss_pred cccccccccccccc--ceeee-cCccccc
Q 031253 100 KRRCEICNKKVGLI--EFKCR-CGHLYCG 125 (163)
Q Consensus 100 ~~rC~~C~kk~gl~--gf~Cr-Cg~~fC~ 125 (163)
..-|..|.++.||+ --.|| ||.+.|.
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchHHHH
Confidence 35899999999995 58999 9999884
No 58
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=32.31 E-value=15 Score=22.62 Aligned_cols=29 Identities=28% Similarity=0.628 Sum_probs=19.5
Q ss_pred cccccccccc--ccceeeecCcccccCccCC
Q 031253 102 RCEICNKKVG--LIEFKCRCGHLYCGTHRYP 130 (163)
Q Consensus 102 rC~~C~kk~g--l~gf~CrCg~~fC~~HR~~ 130 (163)
+|..|.++.. ...+.=.||++||..+...
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 4777777772 2345556999999876543
No 59
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=31.10 E-value=16 Score=27.02 Aligned_cols=32 Identities=31% Similarity=0.828 Sum_probs=22.3
Q ss_pred ccccccccccccccc----cc-eeee-cCcccccCccCC
Q 031253 98 SVKRRCEICNKKVGL----IE-FKCR-CGHLYCGTHRYP 130 (163)
Q Consensus 98 ~~~~rC~~C~kk~gl----~g-f~Cr-Cg~~fC~~HR~~ 130 (163)
..+..|..|+|.. + +| .+|+ ||.+|-+-=..|
T Consensus 33 ~~ky~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy~~ 70 (90)
T PF01780_consen 33 HAKYTCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAYTP 70 (90)
T ss_dssp HS-BEESSSSSSE-EEEEETTEEEETTTTEEEE-BSSSS
T ss_pred hCCCcCCCCCCce-eEEeeeEEeecCCCCCEEeCCCccc
Confidence 3568899999864 4 34 7999 999998764443
No 60
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=31.09 E-value=25 Score=28.55 Aligned_cols=19 Identities=47% Similarity=1.246 Sum_probs=15.3
Q ss_pred ceeeecCcccccCccCCCCCC
Q 031253 114 EFKCRCGHLYCGTHRYPKEHA 134 (163)
Q Consensus 114 gf~CrCg~~fC~~HR~~~~H~ 134 (163)
-|+|.| .||-.||.+.+-+
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 61
>PRK07218 replication factor A; Provisional
Probab=30.76 E-value=22 Score=32.69 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=16.1
Q ss_pred ccccccccccccccceeee-cCcc
Q 031253 100 KRRCEICNKKVGLIEFKCR-CGHL 122 (163)
Q Consensus 100 ~~rC~~C~kk~gl~gf~Cr-Cg~~ 122 (163)
-.||..|+++|.. +.|+ ||.+
T Consensus 297 i~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred eecCcCccccccC--CcCCCCCCc
Confidence 4799999999855 6788 5543
No 62
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=30.40 E-value=23 Score=23.96 Aligned_cols=20 Identities=35% Similarity=0.419 Sum_probs=15.9
Q ss_pred HhhHHHHHHhCCcccccccc
Q 031253 141 KFDREMLVKDNPLIRADKLE 160 (163)
Q Consensus 141 ~~~r~~l~k~np~v~~~k~~ 160 (163)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 33477899999999888874
No 63
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=29.91 E-value=22 Score=22.60 Aligned_cols=16 Identities=31% Similarity=0.831 Sum_probs=13.7
Q ss_pred eeee-cCcccccCccCC
Q 031253 115 FKCR-CGHLYCGTHRYP 130 (163)
Q Consensus 115 f~Cr-Cg~~fC~~HR~~ 130 (163)
+.|. |+..||..++-+
T Consensus 41 ~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CCTTSCCSEECSSSTSE
T ss_pred eECCCCCCcCccccCcc
Confidence 7899 999999998753
No 64
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.86 E-value=23 Score=24.45 Aligned_cols=24 Identities=29% Similarity=0.682 Sum_probs=18.9
Q ss_pred ccccccccccccccc---cceeee-cCc
Q 031253 98 SVKRRCEICNKKVGL---IEFKCR-CGH 121 (163)
Q Consensus 98 ~~~~rC~~C~kk~gl---~gf~Cr-Cg~ 121 (163)
.-..-|.-|+.+.-| ..|.|| ||+
T Consensus 18 ~miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 18 TMIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred cEEEEeccccccccccCCCcEehhhcch
Confidence 346789999999888 359999 864
No 65
>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=29.68 E-value=25 Score=22.96 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=22.0
Q ss_pred cccccccccccceeeec--CcccccCccC
Q 031253 103 CEICNKKVGLIEFKCRC--GHLYCGTHRY 129 (163)
Q Consensus 103 C~~C~kk~gl~gf~CrC--g~~fC~~HR~ 129 (163)
|..|+.-.=|..+.|.| +.++|=.|-.
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 67788887788899997 8899988853
No 66
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=29.58 E-value=22 Score=18.46 Aligned_cols=10 Identities=40% Similarity=1.354 Sum_probs=5.2
Q ss_pred eeee-cCcccc
Q 031253 115 FKCR-CGHLYC 124 (163)
Q Consensus 115 f~Cr-Cg~~fC 124 (163)
|.|. ||..|=
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 4555 555553
No 67
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=29.36 E-value=34 Score=23.95 Aligned_cols=24 Identities=33% Similarity=0.840 Sum_probs=16.5
Q ss_pred ccccccccccccccceeee-cCccc
Q 031253 100 KRRCEICNKKVGLIEFKCR-CGHLY 123 (163)
Q Consensus 100 ~~rC~~C~kk~gl~gf~Cr-Cg~~f 123 (163)
...|..|+|++|...|.=- ||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 4689999999998554332 55444
No 68
>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=29.14 E-value=35 Score=21.11 Aligned_cols=20 Identities=25% Similarity=0.768 Sum_probs=15.7
Q ss_pred ccceeee-cCcccccCccCCC
Q 031253 112 LIEFKCR-CGHLYCGTHRYPK 131 (163)
Q Consensus 112 l~gf~Cr-Cg~~fC~~HR~~~ 131 (163)
+-.|+|. ||..|=-.+...+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4468998 9999988777666
No 69
>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=29.01 E-value=20 Score=23.91 Aligned_cols=24 Identities=38% Similarity=0.851 Sum_probs=17.3
Q ss_pred ccccccccccccc------cceeee-cCccc
Q 031253 100 KRRCEICNKKVGL------IEFKCR-CGHLY 123 (163)
Q Consensus 100 ~~rC~~C~kk~gl------~gf~Cr-Cg~~f 123 (163)
.-||..|+|.|.. +..+|- ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 4699999998877 245775 76553
No 70
>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=28.97 E-value=21 Score=25.82 Aligned_cols=18 Identities=33% Similarity=0.726 Sum_probs=14.6
Q ss_pred ccccccccccccccceee
Q 031253 100 KRRCEICNKKVGLIEFKC 117 (163)
Q Consensus 100 ~~rC~~C~kk~gl~gf~C 117 (163)
.-.|..|.+||||=.|+=
T Consensus 19 ~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred eEEccccCcEeeeeeccc
Confidence 568999999999966543
No 71
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=28.17 E-value=30 Score=22.87 Aligned_cols=23 Identities=39% Similarity=0.756 Sum_probs=19.3
Q ss_pred cccccccccccccccceeee-cCc
Q 031253 99 VKRRCEICNKKVGLIEFKCR-CGH 121 (163)
Q Consensus 99 ~~~rC~~C~kk~gl~gf~Cr-Cg~ 121 (163)
...-|..|.-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 35679999999999889999 876
No 72
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=27.98 E-value=20 Score=32.26 Aligned_cols=40 Identities=28% Similarity=0.658 Sum_probs=27.1
Q ss_pred ccccccccccccccceeeecCcccccC--ccCCCCC----CCcccch
Q 031253 100 KRRCEICNKKVGLIEFKCRCGHLYCGT--HRYPKEH----ACTFDFK 140 (163)
Q Consensus 100 ~~rC~~C~kk~gl~gf~CrCg~~fC~~--HR~~~~H----~C~~dyk 140 (163)
.-||..|.-++.+. -.=-||++||+. -||-..| .|.||+.
T Consensus 25 ~lrC~IC~~~i~ip-~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISIP-CETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeecc-eecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 57999999887661 111399999997 4554444 4667764
No 73
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=27.94 E-value=22 Score=34.71 Aligned_cols=51 Identities=27% Similarity=0.705 Sum_probs=33.4
Q ss_pred cccccccccccccceeee-cCccc---ccCccCCCCCCCcccchHhhHHHHHHhCCcccc
Q 031253 101 RRCEICNKKVGLIEFKCR-CGHLY---CGTHRYPKEHACTFDFKKFDREMLVKDNPLIRA 156 (163)
Q Consensus 101 ~rC~~C~kk~gl~gf~Cr-Cg~~f---C~~HR~~~~H~C~~dyk~~~r~~l~k~np~v~~ 156 (163)
--|..|.+++=.+||+|+ ||+.| |+.|- |. -|. ++ .-.|+.+...+|-+..
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~v-p~--~C~-~~-~~~~~~~~~~~~~~~~ 244 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRV-PT--SCV-NP-DHLRQLLVFEFPAVGG 244 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCC-CC--CCC-Cc-chHhhhhhhccccccc
Confidence 357777788888999999 99866 54433 22 333 33 2356677777776653
No 74
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=27.78 E-value=33 Score=23.99 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=11.1
Q ss_pred cccccccccccccceeeecCcccccC
Q 031253 101 RRCEICNKKVGLIEFKCRCGHLYCGT 126 (163)
Q Consensus 101 ~rC~~C~kk~gl~gf~CrCg~~fC~~ 126 (163)
-||..|.--+...--.=.|+++||+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHH
Confidence 58888887655533334588999987
No 75
>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=27.33 E-value=22 Score=31.37 Aligned_cols=10 Identities=40% Similarity=1.278 Sum_probs=6.2
Q ss_pred cCCCCCCccc
Q 031253 11 KGCGFYGSKE 20 (163)
Q Consensus 11 NgCGFFGS~a 20 (163)
||||+||--.
T Consensus 103 NGCgLFGKGS 112 (293)
T PF00869_consen 103 NGCGLFGKGS 112 (293)
T ss_dssp GT-SS-EEEE
T ss_pred cccEEEeCCc
Confidence 8999998643
No 76
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=27.25 E-value=36 Score=22.93 Aligned_cols=24 Identities=38% Similarity=0.830 Sum_probs=18.4
Q ss_pred ccccccccccc--cccceeee-cCccc
Q 031253 100 KRRCEICNKKV--GLIEFKCR-CGHLY 123 (163)
Q Consensus 100 ~~rC~~C~kk~--gl~gf~Cr-Cg~~f 123 (163)
..+|..|++++ +-....|- ||..|
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcc
Confidence 46999999999 55667888 76654
No 77
>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=26.25 E-value=36 Score=18.80 Aligned_cols=11 Identities=36% Similarity=1.150 Sum_probs=6.3
Q ss_pred cceeee-cCccc
Q 031253 113 IEFKCR-CGHLY 123 (163)
Q Consensus 113 ~gf~Cr-Cg~~f 123 (163)
..|.|. |+..|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 356666 65555
No 78
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=25.62 E-value=29 Score=21.74 Aligned_cols=27 Identities=26% Similarity=0.534 Sum_probs=19.1
Q ss_pred cccccccccccccceeeecCcccccCc
Q 031253 101 RRCEICNKKVGLIEFKCRCGHLYCGTH 127 (163)
Q Consensus 101 ~rC~~C~kk~gl~gf~CrCg~~fC~~H 127 (163)
-+|..|++.|...+|.=+=|..||..|
T Consensus 27 f~C~~C~~~l~~~~~~~~~~~~~C~~c 53 (58)
T PF00412_consen 27 FKCSKCGKPLNDGDFYEKDGKPYCKDC 53 (58)
T ss_dssp SBETTTTCBTTTSSEEEETTEEEEHHH
T ss_pred cccCCCCCccCCCeeEeECCEEECHHH
Confidence 578889998887666656566666554
No 79
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.91 E-value=31 Score=23.65 Aligned_cols=20 Identities=40% Similarity=1.079 Sum_probs=14.6
Q ss_pred ccccccccccccccceee-ecCc
Q 031253 100 KRRCEICNKKVGLIEFKC-RCGH 121 (163)
Q Consensus 100 ~~rC~~C~kk~gl~gf~C-rCg~ 121 (163)
-.||..|||- + ..|+| .||.
T Consensus 36 I~RC~~CRk~-~-~~Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRKQ-S-NPYTCPKCGF 56 (59)
T ss_pred EeechhHHhc-C-CceECCCCCC
Confidence 5689999884 2 46888 5875
No 80
>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=24.66 E-value=29 Score=20.36 Aligned_cols=23 Identities=30% Similarity=1.129 Sum_probs=14.4
Q ss_pred cccccccccccccceeee-cCcccccC
Q 031253 101 RRCEICNKKVGLIEFKCR-CGHLYCGT 126 (163)
Q Consensus 101 ~rC~~C~kk~gl~gf~Cr-Cg~~fC~~ 126 (163)
..|..|+. .--++|. |+..||+.
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 46777877 3457887 88888885
No 81
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=24.37 E-value=64 Score=24.56 Aligned_cols=43 Identities=19% Similarity=0.359 Sum_probs=32.3
Q ss_pred ccccccccccccccccceeeecCcccccCccCCCCCCCcccchHhhH
Q 031253 98 SVKRRCEICNKKVGLIEFKCRCGHLYCGTHRYPKEHACTFDFKKFDR 144 (163)
Q Consensus 98 ~~~~rC~~C~kk~gl~gf~CrCg~~fC~~HR~~~~H~C~~dyk~~~r 144 (163)
....-|.+|+...+.....|+ .|+.=-+--+|.|.+--.=.|+
T Consensus 46 ~~~~~C~~C~~~kp~Rs~HC~----~C~~CV~~~DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 46 GELKYCSTCKIIKPPRSHHCR----VCNRCVLRFDHHCPWLGNCIGR 88 (174)
T ss_pred CCCEECcccCCcCCCcceecc----ccccccccccccchhhcccccc
Confidence 456799999999999999999 5555444448999987655444
No 82
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.20 E-value=28 Score=26.09 Aligned_cols=16 Identities=19% Similarity=0.607 Sum_probs=10.6
Q ss_pred ccccceeee-cCccccc
Q 031253 110 VGLIEFKCR-CGHLYCG 125 (163)
Q Consensus 110 ~gl~gf~Cr-Cg~~fC~ 125 (163)
|-+..-.|| ||++|=.
T Consensus 54 Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 54 LLVRPARCKKCGFEFRD 70 (97)
T ss_pred EEecChhhcccCccccc
Confidence 334566787 8888755
No 83
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=24.06 E-value=43 Score=22.56 Aligned_cols=13 Identities=23% Similarity=0.864 Sum_probs=11.1
Q ss_pred CCchhhhhhHHHH
Q 031253 22 KNMCSKCYDDYLK 34 (163)
Q Consensus 22 ~nmCSKCYrd~~~ 34 (163)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 6899999999854
No 84
>PRK12366 replication factor A; Reviewed
Probab=24.01 E-value=33 Score=32.93 Aligned_cols=29 Identities=28% Similarity=0.639 Sum_probs=20.6
Q ss_pred cccccccccccccc--ceeee-cCcccccCccC
Q 031253 100 KRRCEICNKKVGLI--EFKCR-CGHLYCGTHRY 129 (163)
Q Consensus 100 ~~rC~~C~kk~gl~--gf~Cr-Cg~~fC~~HR~ 129 (163)
-.+|..|+|||-.. .|.|. ||.+ =..|||
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 37999999999652 27896 8877 224555
No 85
>PF02704 GASA: Gibberellin regulated protein; InterPro: IPR003854 This is the GASA gibberellin regulated cysteine rich protein family. The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.
Probab=23.50 E-value=38 Score=23.29 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=14.3
Q ss_pred CCCcccCCCchhhhhhHHHH
Q 031253 15 FYGSKENKNMCSKCYDDYLK 34 (163)
Q Consensus 15 FFGS~aT~nmCSKCYrd~~~ 34 (163)
=-|...+.+.| .||+|...
T Consensus 34 P~GT~gn~~~C-pCY~~m~t 52 (60)
T PF02704_consen 34 PPGTYGNKEEC-PCYRDMKT 52 (60)
T ss_pred CCCCCCCCccC-CChhhhhc
Confidence 34666677999 99999853
No 86
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=23.50 E-value=43 Score=27.19 Aligned_cols=36 Identities=11% Similarity=0.071 Sum_probs=22.4
Q ss_pred cCcccccCccCCCCCCCcccchHhhHHHHHHhCCcc
Q 031253 119 CGHLYCGTHRYPKEHACTFDFKKFDREMLVKDNPLI 154 (163)
Q Consensus 119 Cg~~fC~~HR~~~~H~C~~dyk~~~r~~l~k~np~v 154 (163)
|+.+||..|+..-.|.|.+--....|-.|++.-|.+
T Consensus 19 ~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~~ 54 (162)
T COG3582 19 TAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPGQ 54 (162)
T ss_pred eeeeccCccccccccccchhhhhhhhhccccCCCcc
Confidence 445677788877777777764444455555544443
No 87
>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=23.28 E-value=35 Score=17.11 Aligned_cols=8 Identities=38% Similarity=1.406 Sum_probs=2.5
Q ss_pred eee-cCccc
Q 031253 116 KCR-CGHLY 123 (163)
Q Consensus 116 ~Cr-Cg~~f 123 (163)
.|. ||.+|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 444 44433
No 88
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.57 E-value=31 Score=28.43 Aligned_cols=26 Identities=23% Similarity=0.456 Sum_probs=20.4
Q ss_pred Cccccccccccccccccceeee-cCcc
Q 031253 97 SSVKRRCEICNKKVGLIEFKCR-CGHL 122 (163)
Q Consensus 97 ~~~~~rC~~C~kk~gl~gf~Cr-Cg~~ 122 (163)
..+..||+.|++......-.|- ||.-
T Consensus 136 ~~w~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 136 RKWRLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred eeeeEEEecCceecCCCCCcCCCCCCc
Confidence 4578899999999886666777 7754
No 89
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=22.38 E-value=39 Score=20.02 Aligned_cols=24 Identities=29% Similarity=0.721 Sum_probs=13.1
Q ss_pred cccccccccccceeeecCcccccC
Q 031253 103 CEICNKKVGLIEFKCRCGHLYCGT 126 (163)
Q Consensus 103 C~~C~kk~gl~gf~CrCg~~fC~~ 126 (163)
|..|...+.-.-..-.||++||..
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~ 24 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKE 24 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHH
T ss_pred CCCCCCcccCcCEECCCCCchhHH
Confidence 344544333322455699999964
No 90
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=22.20 E-value=47 Score=21.09 Aligned_cols=15 Identities=27% Similarity=0.866 Sum_probs=13.1
Q ss_pred CCCCCCcccCCCchh
Q 031253 12 GCGFYGSKENKNMCS 26 (163)
Q Consensus 12 gCGFFGS~aT~nmCS 26 (163)
+||=||.-.|+-.|-
T Consensus 6 ~CG~~GH~~t~k~CP 20 (40)
T PF15288_consen 6 NCGAFGHMRTNKRCP 20 (40)
T ss_pred ccccccccccCccCC
Confidence 699999999998875
No 91
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=21.95 E-value=46 Score=19.19 Aligned_cols=12 Identities=33% Similarity=0.872 Sum_probs=10.3
Q ss_pred ceeeecCccccc
Q 031253 114 EFKCRCGHLYCG 125 (163)
Q Consensus 114 gf~CrCg~~fC~ 125 (163)
.|.|+||...|-
T Consensus 2 ~~~C~CGs~~CR 13 (26)
T smart00508 2 KQPCLCGAPNCR 13 (26)
T ss_pred CeeeeCCCcccc
Confidence 478999999886
No 92
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.80 E-value=44 Score=19.68 Aligned_cols=14 Identities=36% Similarity=1.020 Sum_probs=7.6
Q ss_pred cceeee-cCcccccC
Q 031253 113 IEFKCR-CGHLYCGT 126 (163)
Q Consensus 113 ~gf~Cr-Cg~~fC~~ 126 (163)
-.|+|. ||..|=-.
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 346666 66655433
No 93
>PF14369 zf-RING_3: zinc-finger
Probab=21.11 E-value=44 Score=20.18 Aligned_cols=22 Identities=27% Similarity=0.629 Sum_probs=12.7
Q ss_pred cccccccccccc----cee-ee-cCccc
Q 031253 102 RCEICNKKVGLI----EFK-CR-CGHLY 123 (163)
Q Consensus 102 rC~~C~kk~gl~----gf~-Cr-Cg~~f 123 (163)
=|+.|++.|-+. ... |- |+.-|
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 477777777652 333 55 55544
No 94
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=20.71 E-value=43 Score=19.89 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=7.9
Q ss_pred cCcccccCcc
Q 031253 119 CGHLYCGTHR 128 (163)
Q Consensus 119 Cg~~fC~~HR 128 (163)
=|..||+.|.
T Consensus 21 ~g~~fC~~H~ 30 (31)
T PF11722_consen 21 PGSRFCGEHM 30 (31)
T ss_pred CcCCccccCC
Confidence 4678999985
No 95
>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=20.71 E-value=48 Score=28.72 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=22.2
Q ss_pred cccccCCCCCCcccCCCchhhhhhHHHH
Q 031253 7 TMCIKGCGFYGSKENKNMCSKCYDDYLK 34 (163)
Q Consensus 7 ~LCaNgCGFFGS~aT~nmCSKCYrd~~~ 34 (163)
+|=+=|||-|||+.. +=.+||++.+.
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 455779999999996 67999999986
No 96
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=20.59 E-value=91 Score=17.49 Aligned_cols=20 Identities=25% Similarity=0.773 Sum_probs=12.3
Q ss_pred ceeeecCcccccCccCCCCCCCc
Q 031253 114 EFKCRCGHLYCGTHRYPKEHACT 136 (163)
Q Consensus 114 gf~CrCg~~fC~~HR~~~~H~C~ 136 (163)
+|+|.|..-| ...++.|.|.
T Consensus 1 sy~C~C~~Gy---~l~~d~~~C~ 20 (24)
T PF12662_consen 1 SYTCSCPPGY---QLSPDGRSCE 20 (24)
T ss_pred CEEeeCCCCC---cCCCCCCccc
Confidence 5888886544 3335666663
Done!