Query 038787
Match_columns 153
No_of_seqs 146 out of 440
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:17:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038787hhsearch_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 8.4E-46 1.8E-50 294.4 8.9 148 3-153 15-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 1.7E-15 3.7E-20 94.9 2.2 38 93-130 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 2E-15 4.4E-20 86.8 1.9 25 3-27 1-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.5 9.1E-15 2E-19 84.8 1.2 25 3-27 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 2.3E-11 5E-16 77.0 1.6 38 93-131 1-41 (43)
6 COG3582 Predicted nucleic acid 96.4 0.0014 3E-08 52.7 1.5 38 92-130 96-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.3 0.0013 2.8E-08 55.9 0.6 41 90-131 8-51 (250)
8 PF01363 FYVE: FYVE zinc finge 93.9 0.039 8.5E-07 36.9 1.9 30 89-118 8-40 (69)
9 KOG3183 Predicted Zn-finger pr 92.9 0.023 4.9E-07 48.5 -0.7 41 87-127 95-139 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.3 0.055 1.2E-06 34.7 0.7 28 91-118 3-33 (57)
11 smart00064 FYVE Protein presen 91.2 0.082 1.8E-06 35.2 0.6 29 90-118 10-41 (68)
12 KOG1818 Membrane trafficking a 87.7 0.21 4.6E-06 47.6 0.7 42 89-130 164-219 (634)
13 PF10571 UPF0547: Uncharacteri 87.1 0.28 6.2E-06 28.2 0.8 23 91-113 1-24 (26)
14 PF00130 C1_1: Phorbol esters/ 86.3 0.44 9.5E-06 30.1 1.4 25 89-113 10-38 (53)
15 PF15135 UPF0515: Uncharacteri 80.4 0.89 1.9E-05 39.3 1.4 29 87-115 129-167 (278)
16 KOG1819 FYVE finger-containing 67.9 7.9 0.00017 37.1 4.3 30 89-118 900-932 (990)
17 PF02148 zf-UBP: Zn-finger in 66.8 3.3 7.2E-05 27.5 1.2 23 93-116 1-24 (63)
18 PHA02768 hypothetical protein; 63.0 3.2 6.9E-05 27.9 0.6 16 101-116 2-18 (55)
19 cd00029 C1 Protein kinase C co 61.2 4.1 8.8E-05 24.8 0.8 24 89-112 10-37 (50)
20 PF08882 Acetone_carb_G: Aceto 60.5 5 0.00011 30.7 1.3 35 94-130 16-50 (112)
21 smart00109 C1 Protein kinase C 59.2 4.2 9.2E-05 24.4 0.6 23 89-111 10-35 (49)
22 KOG1729 FYVE finger containing 59.0 2.2 4.8E-05 37.1 -0.9 33 89-122 167-203 (288)
23 COG1996 RPC10 DNA-directed RNA 58.7 4.1 8.9E-05 26.9 0.5 24 90-113 6-34 (49)
24 PF13978 DUF4223: Protein of u 53.9 6.1 0.00013 26.7 0.7 18 113-130 19-36 (56)
25 PF03604 DNA_RNApol_7kD: DNA d 51.4 6.4 0.00014 23.6 0.5 19 93-111 3-25 (32)
26 PHA00626 hypothetical protein 51.4 8.1 0.00018 26.4 1.0 23 91-115 12-35 (59)
27 PF01194 RNA_pol_N: RNA polyme 50.7 7.5 0.00016 26.6 0.8 13 90-102 4-16 (60)
28 PF05207 zf-CSL: CSL zinc fing 50.6 7.6 0.00016 25.6 0.8 14 102-115 16-29 (55)
29 smart00659 RPOLCX RNA polymera 48.4 8.4 0.00018 24.5 0.7 20 92-111 4-27 (44)
30 PRK04016 DNA-directed RNA poly 47.8 6.8 0.00015 27.0 0.2 13 90-102 4-16 (62)
31 PF07649 C1_3: C1-like domain; 47.4 7.9 0.00017 22.1 0.4 22 92-113 2-25 (30)
32 PF03107 C1_2: C1 domain; Int 47.3 14 0.0003 21.3 1.5 20 92-111 2-23 (30)
33 PF14471 DUF4428: Domain of un 46.1 9.5 0.00021 24.9 0.7 19 92-110 1-27 (51)
34 PLN00032 DNA-directed RNA poly 45.0 8.3 0.00018 27.3 0.3 13 90-102 4-16 (71)
35 PF02928 zf-C5HC2: C5HC2 zinc 42.7 13 0.00028 24.2 0.9 27 93-119 1-29 (54)
36 KOG1812 Predicted E3 ubiquitin 42.3 15 0.00032 32.9 1.6 31 88-118 304-338 (384)
37 PTZ00303 phosphatidylinositol 41.6 13 0.00028 37.5 1.1 27 91-117 461-495 (1374)
38 smart00647 IBR In Between Ring 40.9 19 0.00042 22.7 1.6 18 103-120 39-57 (64)
39 PF11781 RRN7: RNA polymerase 40.9 13 0.00028 22.7 0.7 22 91-112 9-34 (36)
40 PF02318 FYVE_2: FYVE-type zin 40.7 20 0.00042 26.7 1.8 32 89-120 53-88 (118)
41 KOG2807 RNA polymerase II tran 40.2 18 0.00039 32.7 1.7 28 89-116 329-358 (378)
42 PRK00398 rpoP DNA-directed RNA 39.9 16 0.00035 22.7 1.1 28 91-118 4-36 (46)
43 PF13842 Tnp_zf-ribbon_2: DDE_ 39.7 22 0.00047 21.1 1.5 26 92-117 2-30 (32)
44 smart00290 ZnF_UBP Ubiquitin C 39.6 9.2 0.0002 23.7 -0.1 24 92-117 1-25 (50)
45 KOG3497 DNA-directed RNA polym 39.5 11 0.00023 26.4 0.2 13 90-102 4-16 (69)
46 COG1571 Predicted DNA-binding 38.0 14 0.0003 34.0 0.7 54 90-145 350-409 (421)
47 PF13717 zinc_ribbon_4: zinc-r 36.8 19 0.00041 21.7 1.0 9 105-113 26-35 (36)
48 PF09723 Zn-ribbon_8: Zinc rib 36.6 25 0.00053 21.7 1.5 20 102-121 3-23 (42)
49 PF15549 PGC7_Stella: PGC7/Ste 36.4 21 0.00045 28.9 1.4 19 104-124 123-141 (160)
50 PF07975 C1_4: TFIIH C1-like d 36.4 14 0.00031 24.4 0.4 34 93-126 2-47 (51)
51 PF01485 IBR: IBR domain; Int 36.2 17 0.00037 22.9 0.8 16 105-120 41-57 (64)
52 COG1997 RPL43A Ribosomal prote 35.9 21 0.00046 26.3 1.3 33 87-120 32-70 (89)
53 PRK08402 replication factor A; 35.7 16 0.00034 32.6 0.7 21 91-111 213-238 (355)
54 cd04476 RPA1_DBD_C RPA1_DBD_C: 35.4 16 0.00034 28.1 0.6 32 89-120 33-69 (166)
55 PF10367 Vps39_2: Vacuolar sor 33.9 29 0.00063 24.0 1.7 24 90-113 78-102 (109)
56 COG1644 RPB10 DNA-directed RNA 33.7 14 0.00031 25.6 0.1 13 90-102 4-16 (63)
57 PF06750 DiS_P_DiS: Bacterial 33.0 22 0.00049 25.6 1.0 14 89-102 32-45 (92)
58 PF13240 zinc_ribbon_2: zinc-r 31.8 23 0.00051 19.4 0.7 16 93-108 2-17 (23)
59 PF08600 Rsm1: Rsm1-like; Int 31.0 19 0.0004 25.9 0.3 17 90-106 19-35 (91)
60 PF00096 zf-C2H2: Zinc finger, 29.2 26 0.00055 18.1 0.6 9 105-113 1-10 (23)
61 PF14634 zf-RING_5: zinc-RING 29.2 26 0.00057 21.4 0.7 29 92-120 1-31 (44)
62 PF08073 CHDNT: CHDNT (NUC034) 29.1 23 0.00049 23.9 0.4 20 131-150 21-40 (55)
63 PF13923 zf-C3HC4_2: Zinc fing 28.4 30 0.00066 20.4 0.9 22 94-115 2-23 (39)
64 PRK04136 rpl40e 50S ribosomal 28.3 31 0.00068 22.7 1.0 23 89-111 13-36 (48)
65 KOG1074 Transcriptional repres 28.2 30 0.00064 34.8 1.2 43 87-129 602-672 (958)
66 PF04438 zf-HIT: HIT zinc fing 28.1 23 0.00049 20.7 0.3 23 91-116 3-26 (30)
67 KOG3507 DNA-directed RNA polym 27.5 41 0.00088 23.3 1.5 22 90-111 20-45 (62)
68 PF01780 Ribosomal_L37ae: Ribo 27.3 27 0.00058 25.7 0.6 32 88-120 33-70 (90)
69 PRK07218 replication factor A; 27.2 27 0.00059 31.9 0.8 20 91-112 298-318 (423)
70 PF00412 LIM: LIM domain; Int 27.2 27 0.00059 21.7 0.5 27 91-117 27-53 (58)
71 COG5432 RAD18 RING-finger-cont 26.5 21 0.00046 32.0 -0.1 40 90-130 25-70 (391)
72 PF13465 zf-H2C2_2: Zinc-finge 25.7 40 0.00086 18.6 1.0 12 102-113 12-24 (26)
73 KOG0193 Serine/threonine prote 25.6 24 0.00053 34.2 0.2 50 91-146 190-244 (678)
74 PF14835 zf-RING_6: zf-RING of 25.4 36 0.00078 23.7 0.9 28 90-117 7-34 (65)
75 PF10122 Mu-like_Com: Mu-like 24.9 26 0.00057 23.3 0.2 24 90-113 4-34 (51)
76 smart00834 CxxC_CXXC_SSSS Puta 24.8 41 0.00089 19.7 1.0 16 102-117 3-19 (41)
77 PF12662 cEGF: Complement Clr- 24.1 70 0.0015 17.9 1.8 20 104-126 1-20 (24)
78 PF01529 zf-DHHC: DHHC palmito 23.8 75 0.0016 23.9 2.5 43 88-134 46-88 (174)
79 COG3357 Predicted transcriptio 22.8 30 0.00065 25.8 0.2 14 102-115 56-70 (97)
80 KOG1842 FYVE finger-containing 22.5 21 0.00045 33.4 -0.9 25 91-115 181-208 (505)
81 smart00396 ZnF_UBR1 Putative z 21.5 48 0.001 22.7 0.9 14 104-117 50-70 (71)
82 PRK12366 replication factor A; 20.8 38 0.00083 32.2 0.5 29 90-119 532-563 (637)
83 COG1773 Rubredoxin [Energy pro 20.7 46 0.00099 22.4 0.7 13 104-116 3-16 (55)
84 PTZ00218 40S ribosomal protein 20.6 51 0.0011 22.2 0.9 14 19-32 34-47 (54)
85 PF08646 Rep_fac-A_C: Replicat 20.1 36 0.00078 25.6 0.1 29 91-119 19-54 (146)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=8.4e-46 Score=294.42 Aligned_cols=148 Identities=36% Similarity=0.793 Sum_probs=101.0
Q ss_pred ccccccCCCCCCccccCCcchhhhhHHHHhhhcc-ccccCccccCCCCCCcccc-CCCCC--C-CCCCCCCCcccccccc
Q 038787 3 PPLCAKGCGFYGTKEHKSMCSKCYNDFLEEQVTD-GVVKRPLKLMQPNPSILVF-DPRSL--Q-SPSCSSSERTTIDSAA 77 (153)
Q Consensus 3 p~lC~n~CGFfGs~at~~~CSkCy~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~--~-~~~~~~~~~~~~~~~~ 77 (153)
++||+|||||||+|+|+||||+||++++.++++. ......+......+..... ..... . ....+.+... ..++.
T Consensus 15 ~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~-~~~s~ 93 (167)
T KOG3173|consen 15 DLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPRSVPSRDPPAVSLESTTESELKLVS-DTPST 93 (167)
T ss_pred ccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCccccCccccccccccccccccccccc-cCCcc
Confidence 4899999999999999999999999999988765 2222211110000000000 00000 0 0000000000 00111
Q ss_pred cccCCCCCccccccccccccccccccceeeecCceecCCCCCCCCCCCcccchhhhHHHHHHhCCceeccccccCC
Q 038787 78 VECSSGKTTSALEKRCEICDKKVGSIELKCRCGHLYCGTHRYPKEHACTFDFKKFDRETLVEDDPLIRADKLEGRI 153 (153)
Q Consensus 78 ~~~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~~r~~l~k~Np~v~~~Kl~~kI 153 (153)
..++.......++||..|+|||||+||.||||++||+.|||||.|+|+||||.+||+.|+++||+|+++||+ ||
T Consensus 94 -~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~-ki 167 (167)
T KOG3173|consen 94 -EEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQ-KI 167 (167)
T ss_pred -cccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccc-cC
Confidence 111112223467899999999999999999999999999999999999999999999999999999999999 98
No 2
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.55 E-value=1.7e-15 Score=94.85 Aligned_cols=38 Identities=55% Similarity=1.332 Sum_probs=36.8
Q ss_pred cccccccccccceeee-cCceecCCCCCCCCCCCcccch
Q 038787 93 CEICDKKVGSIELKCR-CGHLYCGTHRYPKEHACTFDFK 130 (153)
Q Consensus 93 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 130 (153)
|+.|+++++|++|+|+ |+++||+.||+||+|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 3
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.54 E-value=2e-15 Score=86.84 Aligned_cols=25 Identities=60% Similarity=1.516 Sum_probs=21.0
Q ss_pred ccccccCCCCCCccccCCcchhhhh
Q 038787 3 PPLCAKGCGFYGTKEHKSMCSKCYN 27 (153)
Q Consensus 3 p~lC~n~CGFfGs~at~~~CSkCy~ 27 (153)
|++|++|||||||++|+||||+|||
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 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.48 E-value=9.1e-15 Score=84.76 Aligned_cols=25 Identities=44% Similarity=1.263 Sum_probs=23.6
Q ss_pred ccccc-cCCCCCCccccCCcchhhhh
Q 038787 3 PPLCA-KGCGFYGTKEHKSMCSKCYN 27 (153)
Q Consensus 3 p~lC~-n~CGFfGs~at~~~CSkCy~ 27 (153)
|++|+ +||||||||+|+|||||||+
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 56899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.11 E-value=2.3e-11 Score=77.05 Aligned_cols=38 Identities=42% Similarity=0.973 Sum_probs=28.2
Q ss_pred ccc--ccccccccceeee-cCceecCCCCCCCCCCCcccchh
Q 038787 93 CEI--CDKKVGSIELKCR-CGHLYCGTHRYPKEHACTFDFKK 131 (153)
Q Consensus 93 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 131 (153)
|+. |++++. ++|.|+ |+..||..|||||.|+|+.+++.
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 998888 799999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.44 E-value=0.0014 Score=52.70 Aligned_cols=38 Identities=32% Similarity=0.641 Sum_probs=30.4
Q ss_pred ccc---cccccccccceeee-cCceecCCCCCCCCCCCcccch
Q 038787 92 RCE---ICDKKVGSIELKCR-CGHLYCGTHRYPKEHACTFDFK 130 (153)
Q Consensus 92 rC~---~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 130 (153)
+|. .|++..+| .++|- |++.||+.||.++.|+|.+...
T Consensus 96 ~~a~~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 96 RCATPQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred eeecceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 555 44444444 67999 9999999999999999998865
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.30 E-value=0.0013 Score=55.92 Aligned_cols=41 Identities=27% Similarity=0.764 Sum_probs=36.1
Q ss_pred ccccc--cccccccccceeee-cCceecCCCCCCCCCCCcccchh
Q 038787 90 EKRCE--ICDKKVGSIELKCR-CGHLYCGTHRYPKEHACTFDFKK 131 (153)
Q Consensus 90 ~~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 131 (153)
...|. .|+ ++.++.|+|- |+.+||..||--+.|.|.+-+..
T Consensus 8 GkHCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 8 GKHCSVPYCK-QLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred ccccCcchhh-hccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 35777 786 6689999999 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=93.89 E-value=0.039 Score=36.89 Aligned_cols=30 Identities=33% Similarity=0.834 Sum_probs=18.1
Q ss_pred ccccccccccccccc--ceeee-cCceecCCCC
Q 038787 89 LEKRCEICDKKVGSI--ELKCR-CGHLYCGTHR 118 (153)
Q Consensus 89 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 118 (153)
....|..|+++.+|+ -..|| ||.+||+.+-
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs 40 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCS 40 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchh
Confidence 467999999999995 58999 9999997653
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=92.91 E-value=0.023 Score=48.48 Aligned_cols=41 Identities=29% Similarity=0.839 Sum_probs=34.3
Q ss_pred cccccccc--ccccccccc-ceeee-cCceecCCCCCCCCCCCcc
Q 038787 87 SALEKRCE--ICDKKVGSI-ELKCR-CGHLYCGTHRYPKEHACTF 127 (153)
Q Consensus 87 ~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~f 127 (153)
+...++|. .|++++-|. .+.|+ ||..||-+||++-.|.|.-
T Consensus 95 k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~ 139 (250)
T KOG3183|consen 95 KVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNK 139 (250)
T ss_pred ccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhh
Confidence 34567777 688887774 69999 9999999999999999983
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=92.28 E-value=0.055 Score=34.72 Aligned_cols=28 Identities=29% Similarity=0.807 Sum_probs=24.0
Q ss_pred ccccccccccccc--ceeee-cCceecCCCC
Q 038787 91 KRCEICDKKVGSI--ELKCR-CGHLYCGTHR 118 (153)
Q Consensus 91 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 118 (153)
..|..|+++.++. ...|| ||.+||+.+-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~ 33 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCS 33 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHc
Confidence 5799999999994 69999 9999998543
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=87.66 E-value=0.21 Score=47.64 Aligned_cols=42 Identities=26% Similarity=0.683 Sum_probs=33.4
Q ss_pred cccccccccccccccc--eeee-cCceecCCCC-----------CCCCCCCcccch
Q 038787 89 LEKRCEICDKKVGSIE--LKCR-CGHLYCGTHR-----------YPKEHACTFDFK 130 (153)
Q Consensus 89 ~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk 130 (153)
....|..|+.+.|+++ ..|| ||.+||+.|- |-+.--|.-||.
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E 219 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYE 219 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHH
Confidence 4579999999999974 7999 9999999884 344456777765
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.05 E-value=0.28 Score=28.15 Aligned_cols=23 Identities=30% Similarity=0.668 Sum_probs=20.3
Q ss_pred cccccccccccccceeee-cCcee
Q 038787 91 KRCEICDKKVGSIELKCR-CGHLY 113 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~Cr-Cg~~F 113 (153)
.+|-.|++.|.+..-.|- ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 368899999999999999 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=86.28 E-value=0.44 Score=30.13 Aligned_cols=25 Identities=28% Similarity=0.841 Sum_probs=19.2
Q ss_pred cccccccccccc---cccceeee-cCcee
Q 038787 89 LEKRCEICDKKV---GSIELKCR-CGHLY 113 (153)
Q Consensus 89 ~~~rC~~C~kkv---gl~gf~Cr-Cg~~F 113 (153)
.+..|..|++.| ++.|++|+ |+.+.
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChH
Confidence 467999999999 66899999 86653
No 15
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=80.43 E-value=0.89 Score=39.35 Aligned_cols=29 Identities=34% Similarity=0.818 Sum_probs=23.6
Q ss_pred ccccccccccccc---------ccccceee-ecCceecC
Q 038787 87 SALEKRCEICDKK---------VGSIELKC-RCGHLYCG 115 (153)
Q Consensus 87 ~~~~~rC~~C~kk---------vgl~gf~C-rCg~~FC~ 115 (153)
.+.-+||..|+|| .|+--|+| .|+++|=+
T Consensus 129 rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 129 RKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ccccccccccccccCCCccccccceeeeecccccccchh
Confidence 3456899999988 67788999 59999954
No 16
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=67.91 E-value=7.9 Score=37.14 Aligned_cols=30 Identities=27% Similarity=0.817 Sum_probs=22.0
Q ss_pred cccccccccccccc--cceeee-cCceecCCCC
Q 038787 89 LEKRCEICDKKVGS--IELKCR-CGHLYCGTHR 118 (153)
Q Consensus 89 ~~~rC~~C~kkvgl--~gf~Cr-Cg~~FC~~HR 118 (153)
+.-+|..|...... .--.|| ||++||++--
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs 932 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCS 932 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeecccc
Confidence 35689999765444 346899 9999998743
No 17
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=66.84 E-value=3.3 Score=27.48 Aligned_cols=23 Identities=35% Similarity=0.894 Sum_probs=15.2
Q ss_pred cccccccccccceeee-cCceecCC
Q 038787 93 CEICDKKVGSIELKCR-CGHLYCGT 116 (153)
Q Consensus 93 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 116 (153)
|..|+.. +-.-+.|- ||.++|+.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5667755 44457787 99999994
No 18
>PHA02768 hypothetical protein; Provisional
Probab=62.99 E-value=3.2 Score=27.92 Aligned_cols=16 Identities=25% Similarity=0.810 Sum_probs=12.6
Q ss_pred cccceeee-cCceecCC
Q 038787 101 GSIELKCR-CGHLYCGT 116 (153)
Q Consensus 101 gl~gf~Cr-Cg~~FC~~ 116 (153)
.|+||.|. ||..|-..
T Consensus 2 ~~~~y~C~~CGK~Fs~~ 18 (55)
T PHA02768 2 ALLGYECPICGEIYIKR 18 (55)
T ss_pred cccccCcchhCCeeccH
Confidence 57899998 98888653
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=61.22 E-value=4.1 Score=24.80 Aligned_cols=24 Identities=25% Similarity=0.656 Sum_probs=19.3
Q ss_pred cccccccccccccc---cceeee-cCce
Q 038787 89 LEKRCEICDKKVGS---IELKCR-CGHL 112 (153)
Q Consensus 89 ~~~rC~~C~kkvgl---~gf~Cr-Cg~~ 112 (153)
.+..|..|++.+.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 36789999999984 799998 7543
No 20
>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=60.55 E-value=5 Score=30.69 Aligned_cols=35 Identities=31% Similarity=0.467 Sum_probs=25.8
Q ss_pred ccccccccccceeeecCceecCCCCCCCCCCCcccch
Q 038787 94 EICDKKVGSIELKCRCGHLYCGTHRYPKEHACTFDFK 130 (153)
Q Consensus 94 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk 130 (153)
+.|+++- .-.+|+||+.||+-+..-+.|.=-++-.
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 5566554 2679999999999988877777655543
No 21
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=59.22 E-value=4.2 Score=24.40 Aligned_cols=23 Identities=26% Similarity=0.717 Sum_probs=18.4
Q ss_pred cccccccccccccc--cceeee-cCc
Q 038787 89 LEKRCEICDKKVGS--IELKCR-CGH 111 (153)
Q Consensus 89 ~~~rC~~C~kkvgl--~gf~Cr-Cg~ 111 (153)
.+..|..|++.+.. .|++|+ |+.
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 22
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=58.98 E-value=2.2 Score=37.12 Aligned_cols=33 Identities=21% Similarity=0.586 Sum_probs=26.8
Q ss_pred cccccccccc-ccccc--ceeee-cCceecCCCCCCCC
Q 038787 89 LEKRCEICDK-KVGSI--ELKCR-CGHLYCGTHRYPKE 122 (153)
Q Consensus 89 ~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e~ 122 (153)
..+.|..|.+ .-.|. --+|| ||.+||. |.....
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n~ 203 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRNR 203 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhcCc
Confidence 4689999999 77873 57899 9999999 876543
No 23
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=58.73 E-value=4.1 Score=26.86 Aligned_cols=24 Identities=29% Similarity=0.794 Sum_probs=18.8
Q ss_pred ccccccccccccc----cceeee-cCcee
Q 038787 90 EKRCEICDKKVGS----IELKCR-CGHLY 113 (153)
Q Consensus 90 ~~rC~~C~kkvgl----~gf~Cr-Cg~~F 113 (153)
.-+|..|++++.+ .+..|. ||+-.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 4689999999985 489998 76543
No 24
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=53.91 E-value=6.1 Score=26.66 Aligned_cols=18 Identities=33% Similarity=0.748 Sum_probs=16.0
Q ss_pred ecCCCCCCCCCCCcccch
Q 038787 113 YCGTHRYPKEHACTFDFK 130 (153)
Q Consensus 113 FC~~HRy~e~H~C~fDyk 130 (153)
-|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999995
No 25
>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=51.40 E-value=6.4 Score=23.60 Aligned_cols=19 Identities=37% Similarity=0.996 Sum_probs=9.9
Q ss_pred cccccccccc---cceeee-cCc
Q 038787 93 CEICDKKVGS---IELKCR-CGH 111 (153)
Q Consensus 93 C~~C~kkvgl---~gf~Cr-Cg~ 111 (153)
|..|+..+.| ...+|+ ||+
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCcCCCeeEcCCCCcEECCcCCC
Confidence 5566666666 245666 543
No 26
>PHA00626 hypothetical protein
Probab=51.38 E-value=8.1 Score=26.44 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=15.7
Q ss_pred cccccccccccccceeee-cCceecC
Q 038787 91 KRCEICDKKVGSIELKCR-CGHLYCG 115 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~ 115 (153)
.||.+|++.. .-|+|. ||+.|-.
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccC--cceEcCCCCCeech
Confidence 4788887532 358888 8887753
No 27
>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=50.65 E-value=7.5 Score=26.64 Aligned_cols=13 Identities=38% Similarity=0.851 Sum_probs=10.2
Q ss_pred ccccccccccccc
Q 038787 90 EKRCEICDKKVGS 102 (153)
Q Consensus 90 ~~rC~~C~kkvgl 102 (153)
|-||++|+|-||-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 5799999999874
No 28
>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=50.62 E-value=7.6 Score=25.61 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=10.8
Q ss_pred ccceeeecCceecC
Q 038787 102 SIELKCRCGHLYCG 115 (153)
Q Consensus 102 l~gf~CrCg~~FC~ 115 (153)
...+.||||..|--
T Consensus 16 ~~~y~CRCG~~f~i 29 (55)
T PF05207_consen 16 VYSYPCRCGGEFEI 29 (55)
T ss_dssp EEEEEETTSSEEEE
T ss_pred EEEEcCCCCCEEEE
Confidence 35789999998753
No 29
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.45 E-value=8.4 Score=24.47 Aligned_cols=20 Identities=30% Similarity=0.786 Sum_probs=14.3
Q ss_pred ccccccccccc---cceeee-cCc
Q 038787 92 RCEICDKKVGS---IELKCR-CGH 111 (153)
Q Consensus 92 rC~~C~kkvgl---~gf~Cr-Cg~ 111 (153)
+|..|+..+.+ .+.+|+ ||+
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCc
Confidence 68888888777 357776 654
No 30
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=47.75 E-value=6.8 Score=27.05 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 038787 90 EKRCEICDKKVGS 102 (153)
Q Consensus 90 ~~rC~~C~kkvgl 102 (153)
|-||++|+|-+|-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6799999998875
No 31
>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=47.43 E-value=7.9 Score=22.12 Aligned_cols=22 Identities=27% Similarity=0.783 Sum_probs=8.8
Q ss_pred ccccccccccc-cceeee-cCcee
Q 038787 92 RCEICDKKVGS-IELKCR-CGHLY 113 (153)
Q Consensus 92 rC~~C~kkvgl-~gf~Cr-Cg~~F 113 (153)
+|..|++.+.. ..|.|. |...+
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 32
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=47.32 E-value=14 Score=21.27 Aligned_cols=20 Identities=25% Similarity=0.913 Sum_probs=16.5
Q ss_pred cccccccccccc-ceeee-cCc
Q 038787 92 RCEICDKKVGSI-ELKCR-CGH 111 (153)
Q Consensus 92 rC~~C~kkvgl~-gf~Cr-Cg~ 111 (153)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 488999999888 89997 653
No 33
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=46.11 E-value=9.5 Score=24.88 Aligned_cols=19 Identities=42% Similarity=1.107 Sum_probs=15.0
Q ss_pred cccccccccccc-------ceeee-cC
Q 038787 92 RCEICDKKVGSI-------ELKCR-CG 110 (153)
Q Consensus 92 rC~~C~kkvgl~-------gf~Cr-Cg 110 (153)
+|..|++++||+ ||.|. |-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~ 27 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCL 27 (51)
T ss_pred CCCccccccccccceeccCccchHHHH
Confidence 599999999994 56776 54
No 34
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=44.97 E-value=8.3 Score=27.32 Aligned_cols=13 Identities=38% Similarity=0.851 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 038787 90 EKRCEICDKKVGS 102 (153)
Q Consensus 90 ~~rC~~C~kkvgl 102 (153)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998875
No 35
>PF02928 zf-C5HC2: C5HC2 zinc finger; InterPro: IPR004198 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [], and may have a DNA binding function. The mouse jumonji protein is required for neural tube formation, and is essential for normal heart development. It also plays a role in the down-regulation of cell proliferation signalling. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005634 nucleus
Probab=42.74 E-value=13 Score=24.21 Aligned_cols=27 Identities=26% Similarity=0.662 Sum_probs=22.2
Q ss_pred cccccccccccceeeec--CceecCCCCC
Q 038787 93 CEICDKKVGSIELKCRC--GHLYCGTHRY 119 (153)
Q Consensus 93 C~~C~kkvgl~gf~CrC--g~~FC~~HRy 119 (153)
|..|+.-.=|..+.|.| +.++|-.|--
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 66788777788899997 8999999953
No 36
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.34 E-value=15 Score=32.91 Aligned_cols=31 Identities=26% Similarity=0.673 Sum_probs=25.5
Q ss_pred ccccccccccccccc----cceeeecCceecCCCC
Q 038787 88 ALEKRCEICDKKVGS----IELKCRCGHLYCGTHR 118 (153)
Q Consensus 88 ~~~~rC~~C~kkvgl----~gf~CrCg~~FC~~HR 118 (153)
+.-.+|..|+--+-| .-+.||||+.||..=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 345799999998888 3499999999997765
No 37
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=41.59 E-value=13 Score=37.49 Aligned_cols=27 Identities=30% Similarity=0.644 Sum_probs=21.1
Q ss_pred cccccccccccc-------cceeee-cCceecCCC
Q 038787 91 KRCEICDKKVGS-------IELKCR-CGHLYCGTH 117 (153)
Q Consensus 91 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 117 (153)
..|..|+++-+. .--+|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 579999999863 245699 999998654
No 38
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=40.94 E-value=19 Score=22.72 Aligned_cols=18 Identities=28% Similarity=0.901 Sum_probs=15.0
Q ss_pred cceee-ecCceecCCCCCC
Q 038787 103 IELKC-RCGHLYCGTHRYP 120 (153)
Q Consensus 103 ~gf~C-rCg~~FC~~HRy~ 120 (153)
..+.| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 46789 7999999998865
No 39
>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=40.93 E-value=13 Score=22.67 Aligned_cols=22 Identities=32% Similarity=0.804 Sum_probs=17.1
Q ss_pred ccccccccccccc--c-eee-ecCce
Q 038787 91 KRCEICDKKVGSI--E-LKC-RCGHL 112 (153)
Q Consensus 91 ~rC~~C~kkvgl~--g-f~C-rCg~~ 112 (153)
.+|..|+-+.... | |.| +||++
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999996663 4 889 79875
No 40
>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=40.65 E-value=20 Score=26.65 Aligned_cols=32 Identities=28% Similarity=0.567 Sum_probs=24.5
Q ss_pred ccccccccccccccc---ceeee-cCceecCCCCCC
Q 038787 89 LEKRCEICDKKVGSI---ELKCR-CGHLYCGTHRYP 120 (153)
Q Consensus 89 ~~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 120 (153)
....|..|.+.+|++ |..|. |.+.+|..=+.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 356999999999984 78999 999999876553
No 41
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=40.20 E-value=18 Score=32.67 Aligned_cols=28 Identities=21% Similarity=0.635 Sum_probs=23.4
Q ss_pred cccccccc-cccccccceeee-cCceecCC
Q 038787 89 LEKRCEIC-DKKVGSIELKCR-CGHLYCGT 116 (153)
Q Consensus 89 ~~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 116 (153)
..++|+.| .+.++-..|.|+ |-++||..
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeecc
Confidence 56789999 666677889999 99999964
No 42
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.92 E-value=16 Score=22.68 Aligned_cols=28 Identities=25% Similarity=0.606 Sum_probs=18.3
Q ss_pred cccccccccccc----cceeee-cCceecCCCC
Q 038787 91 KRCEICDKKVGS----IELKCR-CGHLYCGTHR 118 (153)
Q Consensus 91 ~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HR 118 (153)
-+|..|+..+.+ ..+.|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 478888887755 257887 7665544444
No 43
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=39.67 E-value=22 Score=21.07 Aligned_cols=26 Identities=31% Similarity=0.769 Sum_probs=18.3
Q ss_pred ccccccccccc--cceeee-cCceecCCC
Q 038787 92 RCEICDKKVGS--IELKCR-CGHLYCGTH 117 (153)
Q Consensus 92 rC~~C~kkvgl--~gf~Cr-Cg~~FC~~H 117 (153)
||..|.++--. +.|.|. |+-..|..|
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 67777765222 789998 887777766
No 44
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=39.63 E-value=9.2 Score=23.68 Aligned_cols=24 Identities=33% Similarity=0.890 Sum_probs=17.3
Q ss_pred ccccccccccccceeee-cCceecCCC
Q 038787 92 RCEICDKKVGSIELKCR-CGHLYCGTH 117 (153)
Q Consensus 92 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 117 (153)
||..|..... -+.|- |+.++|+..
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 34565 999999764
No 45
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=39.54 E-value=11 Score=26.40 Aligned_cols=13 Identities=38% Similarity=0.830 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 038787 90 EKRCEICDKKVGS 102 (153)
Q Consensus 90 ~~rC~~C~kkvgl 102 (153)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 5799999998875
No 46
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.01 E-value=14 Score=34.03 Aligned_cols=54 Identities=20% Similarity=0.378 Sum_probs=33.9
Q ss_pred ccccccccccccc---cceeee-cCceecCCCCCCCCCC--CcccchhhhHHHHHHhCCcee
Q 038787 90 EKRCEICDKKVGS---IELKCR-CGHLYCGTHRYPKEHA--CTFDFKKFDRETLVEDDPLIR 145 (153)
Q Consensus 90 ~~rC~~C~kkvgl---~gf~Cr-Cg~~FC~~HRy~e~H~--C~fDyk~~~r~~l~k~Np~v~ 145 (153)
..+|..|++++-- .||+|+ ||..+=..-+-.=.++ =.+++-..+|..|.| |.+-
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk--P~~~ 409 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK--PLVL 409 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC--Ccch
Confidence 3599999988755 489999 9887644332211222 223455667777766 5553
No 47
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=36.76 E-value=19 Score=21.71 Aligned_cols=9 Identities=44% Similarity=1.730 Sum_probs=4.0
Q ss_pred eeee-cCcee
Q 038787 105 LKCR-CGHLY 113 (153)
Q Consensus 105 f~Cr-Cg~~F 113 (153)
.+|. ||++|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 3444 44444
No 48
>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=36.62 E-value=25 Score=21.72 Aligned_cols=20 Identities=25% Similarity=0.607 Sum_probs=16.4
Q ss_pred ccceeee-cCceecCCCCCCC
Q 038787 102 SIELKCR-CGHLYCGTHRYPK 121 (153)
Q Consensus 102 l~gf~Cr-Cg~~FC~~HRy~e 121 (153)
+-.|+|. ||+.|=-.+...+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4578999 9999988887776
No 49
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=36.45 E-value=21 Score=28.87 Aligned_cols=19 Identities=42% Similarity=1.158 Sum_probs=15.6
Q ss_pred ceeeecCceecCCCCCCCCCC
Q 038787 104 ELKCRCGHLYCGTHRYPKEHA 124 (153)
Q Consensus 104 gf~CrCg~~FC~~HRy~e~H~ 124 (153)
-|+|.| .||-.||.|.+-+
T Consensus 123 ~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 123 RFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred ceeeee--eeecccCCCcccc
Confidence 589998 7999999776665
No 50
>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=36.44 E-value=14 Score=24.36 Aligned_cols=34 Identities=24% Similarity=0.591 Sum_probs=14.5
Q ss_pred cccccccccc--------cceeee-cCceecCC---CCCCCCCCCc
Q 038787 93 CEICDKKVGS--------IELKCR-CGHLYCGT---HRYPKEHACT 126 (153)
Q Consensus 93 C~~C~kkvgl--------~gf~Cr-Cg~~FC~~---HRy~e~H~C~ 126 (153)
|+.|.+.+.- ..|.|. |+..||.. --+-.-|+|+
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 5555555555 358887 88999852 2222356654
No 51
>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=36.19 E-value=17 Score=22.91 Aligned_cols=16 Identities=31% Similarity=0.866 Sum_probs=13.9
Q ss_pred eeee-cCceecCCCCCC
Q 038787 105 LKCR-CGHLYCGTHRYP 120 (153)
Q Consensus 105 f~Cr-Cg~~FC~~HRy~ 120 (153)
+.|. |+..||..++-+
T Consensus 41 ~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CCTTSCCSEECSSSTSE
T ss_pred eECCCCCCcCccccCcc
Confidence 7899 999999998854
No 52
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=35.90 E-value=21 Score=26.31 Aligned_cols=33 Identities=27% Similarity=0.699 Sum_probs=24.9
Q ss_pred cccccccccccccccc----cc-eeee-cCceecCCCCCC
Q 038787 87 SALEKRCEICDKKVGS----IE-LKCR-CGHLYCGTHRYP 120 (153)
Q Consensus 87 ~~~~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~ 120 (153)
+..+-.|..|+++ .+ +| ..|+ ||.+|=+---.|
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 3457799999988 33 34 7899 999998766655
No 53
>PRK08402 replication factor A; Reviewed
Probab=35.74 E-value=16 Score=32.63 Aligned_cols=21 Identities=29% Similarity=0.580 Sum_probs=15.3
Q ss_pred cccccccccccc----cceeee-cCc
Q 038787 91 KRCEICDKKVGS----IELKCR-CGH 111 (153)
Q Consensus 91 ~rC~~C~kkvgl----~gf~Cr-Cg~ 111 (153)
.+|..|+|||-. ..+.|. ||.
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 699999999963 346676 443
No 54
>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=35.43 E-value=16 Score=28.14 Aligned_cols=32 Identities=28% Similarity=0.497 Sum_probs=22.5
Q ss_pred ccccccccccccccc---ceeee-cCcee-cCCCCCC
Q 038787 89 LEKRCEICDKKVGSI---ELKCR-CGHLY-CGTHRYP 120 (153)
Q Consensus 89 ~~~rC~~C~kkvgl~---gf~Cr-Cg~~F-C~~HRy~ 120 (153)
.=..|..|+|||-.. .|.|. |+..+ =-.+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 346788999999875 38887 77665 3455663
No 55
>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=33.93 E-value=29 Score=24.04 Aligned_cols=24 Identities=29% Similarity=0.826 Sum_probs=16.8
Q ss_pred ccccccccccccccceeee-cCcee
Q 038787 90 EKRCEICDKKVGSIELKCR-CGHLY 113 (153)
Q Consensus 90 ~~rC~~C~kkvgl~gf~Cr-Cg~~F 113 (153)
...|..|+|++|...|.=- ||.+|
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 55544
No 56
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=33.74 E-value=14 Score=25.62 Aligned_cols=13 Identities=38% Similarity=0.792 Sum_probs=10.9
Q ss_pred ccccccccccccc
Q 038787 90 EKRCEICDKKVGS 102 (153)
Q Consensus 90 ~~rC~~C~kkvgl 102 (153)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 5799999998874
No 57
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=33.02 E-value=22 Score=25.60 Aligned_cols=14 Identities=14% Similarity=0.432 Sum_probs=11.7
Q ss_pred cccccccccccccc
Q 038787 89 LEKRCEICDKKVGS 102 (153)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (153)
.+++|..|++++..
T Consensus 32 ~rS~C~~C~~~L~~ 45 (92)
T PF06750_consen 32 PRSHCPHCGHPLSW 45 (92)
T ss_pred CCCcCcCCCCcCcc
Confidence 36899999999876
No 58
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.78 E-value=23 Score=19.45 Aligned_cols=16 Identities=19% Similarity=0.517 Sum_probs=7.7
Q ss_pred cccccccccccceeee
Q 038787 93 CEICDKKVGSIELKCR 108 (153)
Q Consensus 93 C~~C~kkvgl~gf~Cr 108 (153)
|..|++++.-..-.|.
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 4555555544433344
No 59
>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=30.96 E-value=19 Score=25.89 Aligned_cols=17 Identities=24% Similarity=0.511 Sum_probs=14.0
Q ss_pred cccccccccccccccee
Q 038787 90 EKRCEICDKKVGSIELK 106 (153)
Q Consensus 90 ~~rC~~C~kkvgl~gf~ 106 (153)
--.|..|.+||||=.|+
T Consensus 19 ~~~C~~C~Rr~GLW~f~ 35 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFK 35 (91)
T ss_pred eEEccccCcEeeeeecc
Confidence 45899999999996554
No 60
>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=29.20 E-value=26 Score=18.09 Aligned_cols=9 Identities=44% Similarity=1.313 Sum_probs=4.6
Q ss_pred eeee-cCcee
Q 038787 105 LKCR-CGHLY 113 (153)
Q Consensus 105 f~Cr-Cg~~F 113 (153)
|.|. ||..|
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 3455 55555
No 61
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=29.16 E-value=26 Score=21.36 Aligned_cols=29 Identities=28% Similarity=0.651 Sum_probs=19.8
Q ss_pred ccccccccccc--cceeeecCceecCCCCCC
Q 038787 92 RCEICDKKVGS--IELKCRCGHLYCGTHRYP 120 (153)
Q Consensus 92 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 120 (153)
+|..|.++... ..+.=.||++||..+...
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47777777722 345556999999876543
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=29.09 E-value=23 Score=23.91 Aligned_cols=20 Identities=25% Similarity=0.292 Sum_probs=15.8
Q ss_pred hhhHHHHHHhCCceeccccc
Q 038787 131 KFDRETLVEDDPLIRADKLE 150 (153)
Q Consensus 131 ~~~r~~l~k~Np~v~~~Kl~ 150 (153)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 33477899999999888774
No 63
>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=28.36 E-value=30 Score=20.41 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=11.9
Q ss_pred ccccccccccceeeecCceecC
Q 038787 94 EICDKKVGSIELKCRCGHLYCG 115 (153)
Q Consensus 94 ~~C~kkvgl~gf~CrCg~~FC~ 115 (153)
..|...+.-.-..-.||++||.
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~ 23 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCK 23 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEH
T ss_pred CCCCCcccCcCEECCCCCchhH
Confidence 3444333332245569999985
No 64
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=28.25 E-value=31 Score=22.71 Aligned_cols=23 Identities=35% Similarity=0.675 Sum_probs=19.6
Q ss_pred cccccccccccccccceeee-cCc
Q 038787 89 LEKRCEICDKKVGSIELKCR-CGH 111 (153)
Q Consensus 89 ~~~rC~~C~kkvgl~gf~Cr-Cg~ 111 (153)
+..-|..|.-+.....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 45689999999999999999 775
No 65
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=28.22 E-value=30 Score=34.78 Aligned_cols=43 Identities=26% Similarity=0.682 Sum_probs=30.7
Q ss_pred cccccccccccccc--------------cccceeee-cCceecC---------CCC----CCCCCCCcccc
Q 038787 87 SALEKRCEICDKKV--------------GSIELKCR-CGHLYCG---------THR----YPKEHACTFDF 129 (153)
Q Consensus 87 ~~~~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC~---------~HR----y~e~H~C~fDy 129 (153)
...+|.|-.|.|-| |-..|+|+ ||.-|-- .|| +.-.|.|.+-|
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 45789999998754 33679999 9999963 343 33577888544
No 66
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=28.06 E-value=23 Score=20.74 Aligned_cols=23 Identities=35% Similarity=1.097 Sum_probs=14.9
Q ss_pred cccccccccccccceeee-cCceecCC
Q 038787 91 KRCEICDKKVGSIELKCR-CGHLYCGT 116 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 116 (153)
..|..|+. .--+.|. |+..||+.
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 47888886 4458887 99999985
No 67
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=27.46 E-value=41 Score=23.25 Aligned_cols=22 Identities=27% Similarity=0.614 Sum_probs=17.7
Q ss_pred ccccccccccccc---cceeee-cCc
Q 038787 90 EKRCEICDKKVGS---IELKCR-CGH 111 (153)
Q Consensus 90 ~~rC~~C~kkvgl---~gf~Cr-Cg~ 111 (153)
.--|.-|+-+.-| ..+.|| ||+
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEeccccccccccCCCcEehhhcch
Confidence 4689999999888 369999 864
No 68
>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=27.35 E-value=27 Score=25.71 Aligned_cols=32 Identities=28% Similarity=0.707 Sum_probs=22.3
Q ss_pred ccccccccccccccc----cc-eeee-cCceecCCCCCC
Q 038787 88 ALEKRCEICDKKVGS----IE-LKCR-CGHLYCGTHRYP 120 (153)
Q Consensus 88 ~~~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~ 120 (153)
..+-.|..|++.. + +| .+|+ ||.+|-+-=..|
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 4567899999874 4 33 8999 999998765443
No 69
>PRK07218 replication factor A; Provisional
Probab=27.24 E-value=27 Score=31.91 Aligned_cols=20 Identities=30% Similarity=0.810 Sum_probs=15.5
Q ss_pred cccccccccccccceeee-cCce
Q 038787 91 KRCEICDKKVGSIELKCR-CGHL 112 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~Cr-Cg~~ 112 (153)
.||..|+|+|.. +.|+ ||.+
T Consensus 298 ~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC--CcCCCCCCc
Confidence 799999999955 6777 5543
No 70
>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=27.21 E-value=27 Score=21.70 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=19.6
Q ss_pred cccccccccccccceeeecCceecCCC
Q 038787 91 KRCEICDKKVGSIELKCRCGHLYCGTH 117 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~CrCg~~FC~~H 117 (153)
-+|..|++.|...+|.=+=|..||..|
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 578889988888666666666777654
No 71
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=26.49 E-value=21 Score=31.99 Aligned_cols=40 Identities=30% Similarity=0.648 Sum_probs=25.7
Q ss_pred ccccccccccccccceeeecCceecCC--CCCCCCC----CCcccch
Q 038787 90 EKRCEICDKKVGSIELKCRCGHLYCGT--HRYPKEH----ACTFDFK 130 (153)
Q Consensus 90 ~~rC~~C~kkvgl~gf~CrCg~~FC~~--HRy~e~H----~C~fDyk 130 (153)
.-||..|.-++.+ ...=-||++||+. -||-..| .|.||+.
T Consensus 25 ~lrC~IC~~~i~i-p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRISI-PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheeec-ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence 4699999877665 1111399999985 2443333 4667764
No 72
>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=25.70 E-value=40 Score=18.56 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=6.9
Q ss_pred ccceeee-cCcee
Q 038787 102 SIELKCR-CGHLY 113 (153)
Q Consensus 102 l~gf~Cr-Cg~~F 113 (153)
-..|.|. |+..|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 3456666 66555
No 73
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=25.64 E-value=24 Score=34.21 Aligned_cols=50 Identities=28% Similarity=0.616 Sum_probs=33.8
Q ss_pred cccccccccccccceeee-cCcee---cCCCCCCCCCCCc-ccchhhhHHHHHHhCCceec
Q 038787 91 KRCEICDKKVGSIELKCR-CGHLY---CGTHRYPKEHACT-FDFKKFDRETLVEDDPLIRA 146 (153)
Q Consensus 91 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~-fDyk~~~r~~l~k~Np~v~~ 146 (153)
.-|..|.+++=++||+|+ |++.| |+.|- | -.|. +|. .|+.+...+|-+..
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~v-p--~~C~~~~~---~~~~~~~~~~~~~~ 244 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRV-P--TSCVNPDH---LRQLLVFEFPAVGG 244 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCC-C--CCCCCcch---Hhhhhhhccccccc
Confidence 457777888888999999 99866 55443 2 3344 333 46777777777643
No 74
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=25.37 E-value=36 Score=23.72 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=11.3
Q ss_pred ccccccccccccccceeeecCceecCCC
Q 038787 90 EKRCEICDKKVGSIELKCRCGHLYCGTH 117 (153)
Q Consensus 90 ~~rC~~C~kkvgl~gf~CrCg~~FC~~H 117 (153)
--||..|.--+..---.-.|+++||+.-
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHH
Confidence 4688888765443212235899999863
No 75
>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=24.94 E-value=26 Score=23.32 Aligned_cols=24 Identities=38% Similarity=0.922 Sum_probs=17.3
Q ss_pred ccccccccccccc------cceeee-cCcee
Q 038787 90 EKRCEICDKKVGS------IELKCR-CGHLY 113 (153)
Q Consensus 90 ~~rC~~C~kkvgl------~gf~Cr-Cg~~F 113 (153)
.-||..|+|.|.. +..+|- ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 4699999998876 356774 76554
No 76
>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=24.78 E-value=41 Score=19.70 Aligned_cols=16 Identities=31% Similarity=0.775 Sum_probs=9.4
Q ss_pred ccceeee-cCceecCCC
Q 038787 102 SIELKCR-CGHLYCGTH 117 (153)
Q Consensus 102 l~gf~Cr-Cg~~FC~~H 117 (153)
+-.|+|. ||..|=..+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQ 19 (41)
T ss_pred CEEEEcCCCCCEEEEEE
Confidence 3456777 777664433
No 77
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=24.08 E-value=70 Score=17.94 Aligned_cols=20 Identities=25% Similarity=0.688 Sum_probs=13.1
Q ss_pred ceeeecCceecCCCCCCCCCCCc
Q 038787 104 ELKCRCGHLYCGTHRYPKEHACT 126 (153)
Q Consensus 104 gf~CrCg~~FC~~HRy~e~H~C~ 126 (153)
+|.|.|..-| ..-++.|.|.
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 5889986554 3445777774
No 78
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=23.84 E-value=75 Score=23.91 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=31.8
Q ss_pred ccccccccccccccccceeeecCceecCCCCCCCCCCCcccchhhhH
Q 038787 88 ALEKRCEICDKKVGSIELKCRCGHLYCGTHRYPKEHACTFDFKKFDR 134 (153)
Q Consensus 88 ~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~~r 134 (153)
....-|.+|+...++....|+ .|+.=-+.=+|-|.+--.=.|+
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 356899999999999999999 4444333448999987665554
No 79
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.76 E-value=30 Score=25.83 Aligned_cols=14 Identities=21% Similarity=0.714 Sum_probs=9.5
Q ss_pred ccceeee-cCceecC
Q 038787 102 SIELKCR-CGHLYCG 115 (153)
Q Consensus 102 l~gf~Cr-Cg~~FC~ 115 (153)
+..-.|| ||++|=.
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 3566777 8887754
No 80
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=22.46 E-value=21 Score=33.43 Aligned_cols=25 Identities=32% Similarity=0.917 Sum_probs=21.9
Q ss_pred ccccccccccccc--ceeee-cCceecC
Q 038787 91 KRCEICDKKVGSI--ELKCR-CGHLYCG 115 (153)
Q Consensus 91 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 115 (153)
.-|..|.++.||+ --+|| ||.+.|.
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHH
Confidence 5799999999995 58999 9999883
No 81
>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=21.47 E-value=48 Score=22.72 Aligned_cols=14 Identities=36% Similarity=0.861 Sum_probs=11.8
Q ss_pred ceeeecCce-------ecCCC
Q 038787 104 ELKCRCGHL-------YCGTH 117 (153)
Q Consensus 104 gf~CrCg~~-------FC~~H 117 (153)
||.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999988 88887
No 82
>PRK12366 replication factor A; Reviewed
Probab=20.80 E-value=38 Score=32.24 Aligned_cols=29 Identities=28% Similarity=0.597 Sum_probs=20.1
Q ss_pred cccccccccccccc--ceeee-cCceecCCCCC
Q 038787 90 EKRCEICDKKVGSI--ELKCR-CGHLYCGTHRY 119 (153)
Q Consensus 90 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 119 (153)
-.+|..|+|||-.. .|.|. ||.+ =..|||
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 37999999999653 27886 7776 224554
No 83
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.69 E-value=46 Score=22.44 Aligned_cols=13 Identities=31% Similarity=0.879 Sum_probs=8.8
Q ss_pred ceeee-cCceecCC
Q 038787 104 ELKCR-CGHLYCGT 116 (153)
Q Consensus 104 gf~Cr-Cg~~FC~~ 116 (153)
-++|+ ||++|=..
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 36787 88887443
No 84
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.56 E-value=51 Score=22.16 Aligned_cols=14 Identities=21% Similarity=0.698 Sum_probs=11.6
Q ss_pred CCcchhhhhHHHHh
Q 038787 19 KSMCSKCYNDFLEE 32 (153)
Q Consensus 19 ~~~CSkCy~~~~~~ 32 (153)
.|||..|||+....
T Consensus 34 L~~CRqCFRe~A~~ 47 (54)
T PTZ00218 34 LNVCRQCFRENAEL 47 (54)
T ss_pred cchhhHHHHHhhHh
Confidence 57999999998653
No 85
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.08 E-value=36 Score=25.62 Aligned_cols=29 Identities=31% Similarity=0.683 Sum_probs=18.0
Q ss_pred cccc--ccccccccc---ceeee-cCcee-cCCCCC
Q 038787 91 KRCE--ICDKKVGSI---ELKCR-CGHLY-CGTHRY 119 (153)
Q Consensus 91 ~rC~--~C~kkvgl~---gf~Cr-Cg~~F-C~~HRy 119 (153)
.-|. .|+|||-.. .+.|. |+..+ =-.+||
T Consensus 19 ~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry 54 (146)
T PF08646_consen 19 PACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRY 54 (146)
T ss_dssp EE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEE
T ss_pred CCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEE
Confidence 4688 999998874 37894 88775 346676
Done!