Query 037934
Match_columns 141
No_of_seqs 129 out of 404
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:51:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037934.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037934hhsearch_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 5.7E-38 1.2E-42 246.0 7.9 138 3-141 15-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.6 9.5E-16 2.1E-20 86.9 2.0 25 3-27 1-25 (25)
3 smart00259 ZnF_A20 A20-like zi 99.5 4.2E-15 9.1E-20 85.0 1.3 25 3-27 1-26 (26)
4 smart00154 ZnF_AN1 AN1-like Zi 98.5 2.7E-08 5.9E-13 61.3 1.2 26 93-118 1-27 (39)
5 PF01428 zf-AN1: AN1-like Zinc 97.5 4.2E-05 9.2E-10 47.5 1.0 25 93-118 1-28 (43)
6 PF10571 UPF0547: Uncharacteri 87.6 0.27 6E-06 27.8 0.9 23 91-113 1-24 (26)
7 PF01363 FYVE: FYVE zinc finge 85.6 0.45 9.8E-06 31.2 1.3 30 89-118 8-40 (69)
8 PF15135 UPF0515: Uncharacteri 82.6 0.69 1.5E-05 39.4 1.4 30 87-116 129-168 (278)
9 cd00065 FYVE FYVE domain; Zinc 82.1 0.76 1.6E-05 28.9 1.2 28 91-118 3-33 (57)
10 smart00064 FYVE Protein presen 81.9 0.92 2E-05 29.6 1.6 29 90-118 10-41 (68)
11 PF01194 RNA_pol_N: RNA polyme 71.2 2 4.4E-05 29.0 0.9 14 89-102 3-16 (60)
12 PRK04016 DNA-directed RNA poly 67.9 1.9 4.1E-05 29.3 0.2 14 89-102 3-16 (62)
13 PLN00032 DNA-directed RNA poly 67.1 2.1 4.5E-05 29.9 0.3 14 89-102 3-16 (71)
14 KOG1818 Membrane trafficking a 66.1 2.2 4.8E-05 40.3 0.4 30 89-118 164-196 (634)
15 PF08882 Acetone_carb_G: Aceto 63.1 3.5 7.5E-05 31.1 0.9 23 94-118 16-38 (112)
16 PF00130 C1_1: Phorbol esters/ 62.1 4.4 9.6E-05 25.0 1.1 20 89-108 10-32 (53)
17 KOG3497 DNA-directed RNA polym 61.5 2.9 6.2E-05 28.8 0.1 14 89-102 3-16 (69)
18 COG1644 RPB10 DNA-directed RNA 60.7 2.8 6.2E-05 28.6 0.0 14 89-102 3-16 (63)
19 PF10122 Mu-like_Com: Mu-like 60.5 3.1 6.7E-05 27.3 0.2 23 90-112 4-33 (51)
20 COG1996 RPC10 DNA-directed RNA 56.4 4.8 0.0001 26.1 0.5 21 90-110 6-31 (49)
21 PF05207 zf-CSL: CSL zinc fing 55.0 5.4 0.00012 25.9 0.6 14 102-115 16-29 (55)
22 smart00109 C1 Protein kinase C 51.4 7.6 0.00016 22.9 0.8 20 89-108 10-31 (49)
23 cd00029 C1 Protein kinase C co 51.1 8.1 0.00018 23.1 0.9 20 89-108 10-32 (50)
24 PF14471 DUF4428: Domain of un 48.2 8.6 0.00019 24.7 0.8 13 92-104 1-13 (51)
25 PF08073 CHDNT: CHDNT (NUC034) 46.3 8.6 0.00019 25.5 0.5 19 120-138 22-40 (55)
26 KOG3183 Predicted Zn-finger pr 44.8 8.5 0.00018 32.6 0.4 26 92-118 10-38 (250)
27 PF03604 DNA_RNApol_7kD: DNA d 41.1 12 0.00026 22.0 0.6 10 90-99 17-26 (32)
28 KOG1819 FYVE finger-containing 38.7 14 0.0003 35.1 0.8 30 89-118 900-932 (990)
29 KOG1812 Predicted E3 ubiquitin 38.3 17 0.00036 32.1 1.2 30 88-117 304-337 (384)
30 PHA02768 hypothetical protein; 37.8 13 0.00028 24.6 0.4 15 100-114 1-16 (55)
31 smart00659 RPOLCX RNA polymera 37.7 16 0.00034 22.8 0.8 18 91-108 3-23 (44)
32 PF08600 Rsm1: Rsm1-like; Int 37.0 13 0.00028 26.3 0.3 17 90-106 19-35 (91)
33 COG3582 Predicted nucleic acid 34.7 18 0.0004 28.7 0.8 27 92-118 99-125 (162)
34 PF11781 RRN7: RNA polymerase 34.4 18 0.00039 21.7 0.6 22 91-112 9-34 (36)
35 PF07975 C1_4: TFIIH C1-like d 34.2 17 0.00037 23.6 0.5 23 93-115 2-33 (51)
36 PF00412 LIM: LIM domain; Int 33.4 25 0.00054 21.5 1.2 27 91-117 27-53 (58)
37 COG1571 Predicted DNA-binding 30.9 22 0.00048 32.2 0.8 26 91-116 351-380 (421)
38 PF14634 zf-RING_5: zinc-RING 29.8 26 0.00057 21.0 0.8 27 92-118 1-29 (44)
39 PTZ00218 40S ribosomal protein 29.2 28 0.0006 23.1 0.9 14 19-32 34-47 (54)
40 PF01485 IBR: IBR domain; Int 28.3 21 0.00045 22.2 0.1 27 92-118 20-55 (64)
41 smart00647 IBR In Between Ring 28.1 29 0.00063 21.5 0.8 17 102-118 38-55 (64)
42 PF11722 zf-TRM13_CCCH: CCCH z 27.9 24 0.00052 20.6 0.3 12 107-118 19-30 (31)
43 PF02928 zf-C5HC2: C5HC2 zinc 27.4 29 0.00063 22.1 0.7 26 93-118 1-28 (54)
44 PF14835 zf-RING_6: zf-RING of 26.8 33 0.00072 23.5 1.0 27 91-117 8-34 (65)
45 smart00396 ZnF_UBR1 Putative z 26.1 33 0.00072 23.1 0.9 14 104-117 50-70 (71)
46 PTZ00303 phosphatidylinositol 25.8 34 0.00074 34.2 1.1 28 91-118 461-496 (1374)
47 KOG1729 FYVE finger containing 25.4 21 0.00046 30.6 -0.3 31 89-120 167-201 (288)
48 PF15549 PGC7_Stella: PGC7/Ste 23.5 32 0.00069 27.4 0.4 13 104-118 123-135 (160)
49 smart00508 PostSET Cysteine-ri 22.6 45 0.00097 18.9 0.8 12 104-115 2-13 (26)
50 KOG0320 Predicted E3 ubiquitin 22.1 70 0.0015 26.1 2.1 41 87-130 128-169 (187)
51 PF15227 zf-C3HC4_4: zinc fing 21.5 35 0.00076 20.6 0.2 10 107-116 14-23 (42)
52 PRK06266 transcription initiat 20.9 40 0.00086 26.7 0.5 26 89-114 116-147 (178)
53 PF13923 zf-C3HC4_2: Zinc fing 20.4 46 0.001 19.3 0.6 12 105-116 13-24 (39)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.7e-38 Score=246.00 Aligned_cols=138 Identities=36% Similarity=0.728 Sum_probs=89.9
Q ss_pred ccccccCCCCCCcccCCCCchhhhhHHHhhhhcc-ccccCccccCCCCCCcc-ccCCC-CcccCCCCCCccccccccccc
Q 037934 3 PPLCTKGCGFYGTKEHKSMCSNCYNDFLEEQVTD-GVVKRPLKLMQPNPSIL-VFDPR-SLQSHSSSSSERTTIDSAAVE 79 (141)
Q Consensus 3 p~lC~ngCGFfGs~at~n~CSkCyr~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~-s~~~~~~~~~~~~~~~~~~~~ 79 (141)
+.||+|||||||+|+|+||||+||+|++.++++. ...+.........+..+ ..+.. ...+................+
T Consensus 15 ~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~~ 94 (167)
T KOG3173|consen 15 DLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLSSPRSVPSRDPPAVSLESTTESELKLVSDTPSTE 94 (167)
T ss_pred ccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCcccccccCccccCccccccccccccccccccccccCCccc
Confidence 5899999999999999999999999999888665 33222211100000000 00000 000000000000000000111
Q ss_pred ccccccCccccCccccccccccccceeeecCCcccchhh------------HhhHHHHHHhCCceeccccccCC
Q 037934 80 YSSAKTTSALEKRCEICDKKVGSIELKCRCGHLYCGTHR------------KFDRETLVEDNPLIRADKLEGRI 141 (141)
Q Consensus 80 ~~~~~~~~~~~~rC~~C~kkvgl~gf~CRCg~~fC~~HR------------~~~r~~lak~NP~v~~~Ki~~KI 141 (141)
+.+.......++||+.|+|||||+||.||||++||+.|| .+||+.|+++||+|+++||+ ||
T Consensus 95 ~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~-ki 167 (167)
T KOG3173|consen 95 EEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQ-KI 167 (167)
T ss_pred ccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccc-cC
Confidence 122233445688999999999999999999999999999 89999999999999999999 98
No 2
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.57 E-value=9.5e-16 Score=86.94 Aligned_cols=25 Identities=52% Similarity=1.460 Sum_probs=21.0
Q ss_pred ccccccCCCCCCcccCCCCchhhhh
Q 037934 3 PPLCTKGCGFYGTKEHKSMCSNCYN 27 (141)
Q Consensus 3 p~lC~ngCGFfGs~at~n~CSkCyr 27 (141)
|++|++|||||||++|+||||+||+
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 6899999999999999999999997
No 3
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.51 E-value=4.2e-15 Score=84.96 Aligned_cols=25 Identities=40% Similarity=1.237 Sum_probs=23.6
Q ss_pred ccccc-cCCCCCCcccCCCCchhhhh
Q 037934 3 PPLCT-KGCGFYGTKEHKSMCSNCYN 27 (141)
Q Consensus 3 p~lC~-ngCGFfGs~at~n~CSkCyr 27 (141)
|++|+ +|||||||++|+|||||||+
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 57899 99999999999999999996
No 4
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=98.54 E-value=2.7e-08 Score=61.34 Aligned_cols=26 Identities=62% Similarity=1.478 Sum_probs=25.3
Q ss_pred cccccccccccceeee-cCCcccchhh
Q 037934 93 CEICDKKVGSIELKCR-CGHLYCGTHR 118 (141)
Q Consensus 93 C~~C~kkvgl~gf~CR-Cg~~fC~~HR 118 (141)
|+.|+++++|++|+|+ |+.+||+.||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR 27 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHR 27 (39)
T ss_pred CcccCCcccccCeECCccCCccccccC
Confidence 7889999999999999 9999999999
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=97.48 E-value=4.2e-05 Score=47.54 Aligned_cols=25 Identities=44% Similarity=1.123 Sum_probs=17.3
Q ss_pred ccc--ccccccccceeee-cCCcccchhh
Q 037934 93 CEI--CDKKVGSIELKCR-CGHLYCGTHR 118 (141)
Q Consensus 93 C~~--C~kkvgl~gf~CR-Cg~~fC~~HR 118 (141)
|.. |++++. ++|.|+ |+..||..||
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTH
T ss_pred CccCcCcCccC-CCeECCCCCcccCcccc
Confidence 455 999998 799999 9999999999
No 6
>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=87.65 E-value=0.27 Score=27.78 Aligned_cols=23 Identities=30% Similarity=0.668 Sum_probs=20.7
Q ss_pred Cccccccccccccceeee-cCCcc
Q 037934 91 KRCEICDKKVGSIELKCR-CGHLY 113 (141)
Q Consensus 91 ~rC~~C~kkvgl~gf~CR-Cg~~f 113 (141)
.+|-.|++.|.+.--.|- ||+.|
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCCC
Confidence 368999999999999998 99988
No 7
>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=85.62 E-value=0.45 Score=31.20 Aligned_cols=30 Identities=33% Similarity=0.834 Sum_probs=17.7
Q ss_pred ccCcccccccccccc--ceeee-cCCcccchhh
Q 037934 89 LEKRCEICDKKVGSI--ELKCR-CGHLYCGTHR 118 (141)
Q Consensus 89 ~~~rC~~C~kkvgl~--gf~CR-Cg~~fC~~HR 118 (141)
....|..|+++.+|+ -..|| ||.+||+.+-
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 457999999999995 67786 8999998764
No 8
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=82.60 E-value=0.69 Score=39.40 Aligned_cols=30 Identities=33% Similarity=0.767 Sum_probs=24.9
Q ss_pred ccccCcccccccc---------ccccceee-ecCCcccch
Q 037934 87 SALEKRCEICDKK---------VGSIELKC-RCGHLYCGT 116 (141)
Q Consensus 87 ~~~~~rC~~C~kk---------vgl~gf~C-RCg~~fC~~ 116 (141)
.+..+||..|+|| .||--|.| .|++.|=|.
T Consensus 129 rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 129 RKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 3456899999887 89999999 999999554
No 9
>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=82.12 E-value=0.76 Score=28.86 Aligned_cols=28 Identities=29% Similarity=0.807 Sum_probs=23.0
Q ss_pred Ccccccccccccc--ceeee-cCCcccchhh
Q 037934 91 KRCEICDKKVGSI--ELKCR-CGHLYCGTHR 118 (141)
Q Consensus 91 ~rC~~C~kkvgl~--gf~CR-Cg~~fC~~HR 118 (141)
..|..|.++.++. ...|| ||.+||+.+-
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 66774 8999998765
No 10
>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 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=71.20 E-value=2 Score=28.97 Aligned_cols=14 Identities=36% Similarity=0.857 Sum_probs=10.5
Q ss_pred ccCccccccccccc
Q 037934 89 LEKRCEICDKKVGS 102 (141)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (141)
.|-||++|+|-||-
T Consensus 3 iPVRCFTCGkvi~~ 16 (60)
T PF01194_consen 3 IPVRCFTCGKVIGN 16 (60)
T ss_dssp -SSS-STTTSBTCG
T ss_pred CceecCCCCCChhH
Confidence 37899999999973
No 12
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=67.88 E-value=1.9 Score=29.31 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=11.9
Q ss_pred ccCccccccccccc
Q 037934 89 LEKRCEICDKKVGS 102 (141)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (141)
.|-||++|+|-||=
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 47899999999874
No 13
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=67.11 E-value=2.1 Score=29.85 Aligned_cols=14 Identities=36% Similarity=0.857 Sum_probs=11.8
Q ss_pred ccCccccccccccc
Q 037934 89 LEKRCEICDKKVGS 102 (141)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (141)
.|-||++|+|-||=
T Consensus 3 iPVRCFTCGkvig~ 16 (71)
T PLN00032 3 IPVRCFTCGKVIGN 16 (71)
T ss_pred CceeecCCCCCcHH
Confidence 37899999999874
No 14
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=66.10 E-value=2.2 Score=40.28 Aligned_cols=30 Identities=33% Similarity=0.885 Sum_probs=25.8
Q ss_pred ccCcccccccccccc--ceeee-cCCcccchhh
Q 037934 89 LEKRCEICDKKVGSI--ELKCR-CGHLYCGTHR 118 (141)
Q Consensus 89 ~~~rC~~C~kkvgl~--gf~CR-Cg~~fC~~HR 118 (141)
+...|..|+.+.|++ -..|| ||.+||+.|-
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcs 196 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCS 196 (634)
T ss_pred cccccceeeeeeeeccccccccccchhhccCcc
Confidence 356999999999997 45677 9999999987
No 15
>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=63.12 E-value=3.5 Score=31.06 Aligned_cols=23 Identities=39% Similarity=0.810 Sum_probs=17.3
Q ss_pred ccccccccccceeeecCCcccchhh
Q 037934 94 EICDKKVGSIELKCRCGHLYCGTHR 118 (141)
Q Consensus 94 ~~C~kkvgl~gf~CRCg~~fC~~HR 118 (141)
+.|+++- .-.+|+||+.||+.+.
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~ 38 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARE 38 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhc
Confidence 4455544 2689999999999877
No 16
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=62.14 E-value=4.4 Score=25.03 Aligned_cols=20 Identities=25% Similarity=0.760 Sum_probs=16.6
Q ss_pred ccCccccccccc---cccceeee
Q 037934 89 LEKRCEICDKKV---GSIELKCR 108 (141)
Q Consensus 89 ~~~rC~~C~kkv---gl~gf~CR 108 (141)
.+..|..|++.| ++.|++|+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~ 32 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCS 32 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEET
T ss_pred CCCCCcccCcccCCCCCCeEEEC
Confidence 577999999999 66899997
No 17
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=61.49 E-value=2.9 Score=28.75 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=11.7
Q ss_pred ccCccccccccccc
Q 037934 89 LEKRCEICDKKVGS 102 (141)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (141)
.|.||++|+|-||-
T Consensus 3 iPiRCFtCGKvig~ 16 (69)
T KOG3497|consen 3 IPIRCFTCGKVIGD 16 (69)
T ss_pred eeeEeeeccccccc
Confidence 36899999998874
No 18
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=60.72 E-value=2.8 Score=28.58 Aligned_cols=14 Identities=36% Similarity=0.802 Sum_probs=11.8
Q ss_pred ccCccccccccccc
Q 037934 89 LEKRCEICDKKVGS 102 (141)
Q Consensus 89 ~~~rC~~C~kkvgl 102 (141)
-|.||++|+|-||-
T Consensus 3 iPiRCFsCGkvi~~ 16 (63)
T COG1644 3 IPVRCFSCGKVIGH 16 (63)
T ss_pred CceEeecCCCCHHH
Confidence 37899999998874
No 19
>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=60.49 E-value=3.1 Score=27.32 Aligned_cols=23 Identities=43% Similarity=1.063 Sum_probs=16.4
Q ss_pred cCccccccccccc------cceee-ecCCc
Q 037934 90 EKRCEICDKKVGS------IELKC-RCGHL 112 (141)
Q Consensus 90 ~~rC~~C~kkvgl------~gf~C-RCg~~ 112 (141)
..||..|+|.+.. ..++| |||.+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 4699999998877 35666 56544
No 20
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=56.39 E-value=4.8 Score=26.12 Aligned_cols=21 Identities=33% Similarity=0.956 Sum_probs=16.8
Q ss_pred cCccccccccccc----cceeee-cC
Q 037934 90 EKRCEICDKKVGS----IELKCR-CG 110 (141)
Q Consensus 90 ~~rC~~C~kkvgl----~gf~CR-Cg 110 (141)
..+|..|+++|-| .+..|. ||
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg 31 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCG 31 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCC
Confidence 4689999999985 488998 54
No 21
>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=55.00 E-value=5.4 Score=25.92 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=11.1
Q ss_pred ccceeeecCCcccc
Q 037934 102 SIELKCRCGHLYCG 115 (141)
Q Consensus 102 l~gf~CRCg~~fC~ 115 (141)
...+.||||..|--
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 46789999999853
No 22
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=51.41 E-value=7.6 Score=22.88 Aligned_cols=20 Identities=25% Similarity=0.685 Sum_probs=16.8
Q ss_pred ccCccccccccccc--cceeee
Q 037934 89 LEKRCEICDKKVGS--IELKCR 108 (141)
Q Consensus 89 ~~~rC~~C~kkvgl--~gf~CR 108 (141)
.+..|..|++.+.. .|++|+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~ 31 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCS 31 (49)
T ss_pred CCCCccccccccCcCCCCcCCC
Confidence 46789999999987 489888
No 23
>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=51.14 E-value=8.1 Score=23.05 Aligned_cols=20 Identities=25% Similarity=0.682 Sum_probs=17.0
Q ss_pred ccCccccccccccc---cceeee
Q 037934 89 LEKRCEICDKKVGS---IELKCR 108 (141)
Q Consensus 89 ~~~rC~~C~kkvgl---~gf~CR 108 (141)
.+..|..|++.+.. .|++|+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~ 32 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCS 32 (50)
T ss_pred CCCChhhcchhhhccccceeEcC
Confidence 46789999999984 799998
No 24
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=48.20 E-value=8.6 Score=24.68 Aligned_cols=13 Identities=46% Similarity=1.178 Sum_probs=11.3
Q ss_pred ccccccccccccc
Q 037934 92 RCEICDKKVGSIE 104 (141)
Q Consensus 92 rC~~C~kkvgl~g 104 (141)
+|..|++++||++
T Consensus 1 ~C~iCg~kigl~~ 13 (51)
T PF14471_consen 1 KCAICGKKIGLFK 13 (51)
T ss_pred CCCcccccccccc
Confidence 5899999999964
No 25
>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=46.27 E-value=8.6 Score=25.52 Aligned_cols=19 Identities=32% Similarity=0.309 Sum_probs=15.8
Q ss_pred hhHHHHHHhCCceeccccc
Q 037934 120 FDRETLVEDNPLIRADKLE 138 (141)
Q Consensus 120 ~~r~~lak~NP~v~~~Ki~ 138 (141)
.=|-+|+++||++.-.||.
T Consensus 22 ~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 22 HVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHCCCCcHHHHH
Confidence 3488999999999888774
No 26
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=44.82 E-value=8.5 Score=32.59 Aligned_cols=26 Identities=31% Similarity=1.003 Sum_probs=21.2
Q ss_pred ccc--cccccccccceee-ecCCcccchhh
Q 037934 92 RCE--ICDKKVGSIELKC-RCGHLYCGTHR 118 (141)
Q Consensus 92 rC~--~C~kkvgl~gf~C-RCg~~fC~~HR 118 (141)
.|. .|+ .+-++-|+| .|+.+||.-||
T Consensus 10 HCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHr 38 (250)
T KOG3183|consen 10 HCSVPYCK-QLDFLPFKCDGCSGIFCLEHR 38 (250)
T ss_pred ccCcchhh-hccccceeeCCccchhhhccc
Confidence 566 664 466788999 69999999999
No 27
>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=41.07 E-value=12 Score=22.01 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=4.3
Q ss_pred cCcccccccc
Q 037934 90 EKRCEICDKK 99 (141)
Q Consensus 90 ~~rC~~C~kk 99 (141)
+.||..|+-+
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 3455555443
No 28
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=38.73 E-value=14 Score=35.05 Aligned_cols=30 Identities=27% Similarity=0.817 Sum_probs=21.9
Q ss_pred ccCccccccccccc--cceeee-cCCcccchhh
Q 037934 89 LEKRCEICDKKVGS--IELKCR-CGHLYCGTHR 118 (141)
Q Consensus 89 ~~~rC~~C~kkvgl--~gf~CR-Cg~~fC~~HR 118 (141)
+.-+|..|...... .--.|| ||.+||++--
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs 932 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCS 932 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeecccc
Confidence 45699999866544 245677 9999998754
No 29
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=17 Score=32.12 Aligned_cols=30 Identities=27% Similarity=0.707 Sum_probs=24.3
Q ss_pred cccCccccccccccc----cceeeecCCcccchh
Q 037934 88 ALEKRCEICDKKVGS----IELKCRCGHLYCGTH 117 (141)
Q Consensus 88 ~~~~rC~~C~kkvgl----~gf~CRCg~~fC~~H 117 (141)
+.-.+|..|+-.+-| .-+.||||+-||-.=
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C 337 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMC 337 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhc
Confidence 345799999998877 468999999999653
No 30
>PHA02768 hypothetical protein; Provisional
Probab=37.83 E-value=13 Score=24.58 Aligned_cols=15 Identities=27% Similarity=0.928 Sum_probs=10.3
Q ss_pred ccccceeee-cCCccc
Q 037934 100 VGSIELKCR-CGHLYC 114 (141)
Q Consensus 100 vgl~gf~CR-Cg~~fC 114 (141)
+.|+||+|- ||..|=
T Consensus 1 ~~~~~y~C~~CGK~Fs 16 (55)
T PHA02768 1 MALLGYECPICGEIYI 16 (55)
T ss_pred CcccccCcchhCCeec
Confidence 357889884 666664
No 31
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.72 E-value=16 Score=22.82 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=11.7
Q ss_pred Ccccccccccccc---ceeee
Q 037934 91 KRCEICDKKVGSI---ELKCR 108 (141)
Q Consensus 91 ~rC~~C~kkvgl~---gf~CR 108 (141)
.+|..|+..+-+. +.+|+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~ 23 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCR 23 (44)
T ss_pred EECCCCCCEeecCCCCceECC
Confidence 3677777777763 56664
No 32
>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=36.98 E-value=13 Score=26.29 Aligned_cols=17 Identities=24% Similarity=0.511 Sum_probs=14.1
Q ss_pred cCcccccccccccccee
Q 037934 90 EKRCEICDKKVGSIELK 106 (141)
Q Consensus 90 ~~rC~~C~kkvgl~gf~ 106 (141)
--.|..|.+||||=.|+
T Consensus 19 ~~~C~~C~Rr~GLW~f~ 35 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFK 35 (91)
T ss_pred eEEccccCcEeeeeecc
Confidence 46899999999996554
No 33
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=34.75 E-value=18 Score=28.72 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=20.0
Q ss_pred ccccccccccccceeeecCCcccchhh
Q 037934 92 RCEICDKKVGSIELKCRCGHLYCGTHR 118 (141)
Q Consensus 92 rC~~C~kkvgl~gf~CRCg~~fC~~HR 118 (141)
+|..|++..+|.+--=-|++.||+.||
T Consensus 99 ~~~~~g~~s~l~~~c~~c~g~fc~~h~ 125 (162)
T COG3582 99 TPQCTGKGSTLAGKCNYCTGYFCAEHR 125 (162)
T ss_pred cceeccCCccccccccCCCCcceecee
Confidence 455666666766544469999999999
No 34
>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=34.43 E-value=18 Score=21.67 Aligned_cols=22 Identities=32% Similarity=0.757 Sum_probs=17.5
Q ss_pred Ccccccccccccc---ceee-ecCCc
Q 037934 91 KRCEICDKKVGSI---ELKC-RCGHL 112 (141)
Q Consensus 91 ~rC~~C~kkvgl~---gf~C-RCg~~ 112 (141)
.+|..|+-+.... -|.| +||++
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999997774 5789 99875
No 35
>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=34.19 E-value=17 Score=23.62 Aligned_cols=23 Identities=26% Similarity=0.749 Sum_probs=9.5
Q ss_pred ccccccccccc--------ceee-ecCCcccc
Q 037934 93 CEICDKKVGSI--------ELKC-RCGHLYCG 115 (141)
Q Consensus 93 C~~C~kkvgl~--------gf~C-RCg~~fC~ 115 (141)
|+.|.+.+.-. .|+| +|+..||-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCI 33 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-H
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCcccc
Confidence 55555555542 4666 57777774
No 36
>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=33.36 E-value=25 Score=21.51 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=21.5
Q ss_pred CccccccccccccceeeecCCcccchh
Q 037934 91 KRCEICDKKVGSIELKCRCGHLYCGTH 117 (141)
Q Consensus 91 ~rC~~C~kkvgl~gf~CRCg~~fC~~H 117 (141)
-+|..|++.+...+|.=+=|.+||..|
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 578899999988777777777888765
No 37
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.86 E-value=22 Score=32.23 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=20.1
Q ss_pred Cccccccccccc---cceeee-cCCcccch
Q 037934 91 KRCEICDKKVGS---IELKCR-CGHLYCGT 116 (141)
Q Consensus 91 ~rC~~C~kkvgl---~gf~CR-Cg~~fC~~ 116 (141)
-+|..|++++-- .||+|+ ||..+=..
T Consensus 351 p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 351 PVCPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCCccCCchhhcCCCCcccccccccCCcc
Confidence 389999988744 599999 98876544
No 38
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=29.82 E-value=26 Score=21.01 Aligned_cols=27 Identities=30% Similarity=0.712 Sum_probs=18.3
Q ss_pred ccccccccc--cccceeeecCCcccchhh
Q 037934 92 RCEICDKKV--GSIELKCRCGHLYCGTHR 118 (141)
Q Consensus 92 rC~~C~kkv--gl~gf~CRCg~~fC~~HR 118 (141)
+|..|.++. ....+-=.||++||..+-
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~ 29 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCL 29 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHH
Confidence 366677666 223555679999998765
No 39
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=29.22 E-value=28 Score=23.06 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=11.5
Q ss_pred CCCchhhhhHHHhh
Q 037934 19 KSMCSNCYNDFLEE 32 (141)
Q Consensus 19 ~n~CSkCyr~~~~~ 32 (141)
.|||..|||+....
T Consensus 34 L~~CRqCFRe~A~~ 47 (54)
T PTZ00218 34 LNVCRQCFRENAEL 47 (54)
T ss_pred cchhhHHHHHhhHh
Confidence 57999999998653
No 40
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=28.29 E-value=21 Score=22.16 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=15.4
Q ss_pred cccc--ccccccc----c--ceeee-cCCcccchhh
Q 037934 92 RCEI--CDKKVGS----I--ELKCR-CGHLYCGTHR 118 (141)
Q Consensus 92 rC~~--C~kkvgl----~--gf~CR-Cg~~fC~~HR 118 (141)
.|.. |..-+-. . -+.|. |+..||..++
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~ 55 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCG 55 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSST
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccC
Confidence 5544 6555544 1 27899 9999998776
No 41
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=28.09 E-value=29 Score=21.52 Aligned_cols=17 Identities=24% Similarity=0.829 Sum_probs=13.3
Q ss_pred ccceee-ecCCcccchhh
Q 037934 102 SIELKC-RCGHLYCGTHR 118 (141)
Q Consensus 102 l~gf~C-RCg~~fC~~HR 118 (141)
.....| .||..||-.++
T Consensus 38 ~~~v~C~~C~~~fC~~C~ 55 (64)
T smart00647 38 CNRVTCPKCGFSFCFRCK 55 (64)
T ss_pred CCeeECCCCCCeECCCCC
Confidence 346788 89999998765
No 42
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=27.85 E-value=24 Score=20.61 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=8.4
Q ss_pred eecCCcccchhh
Q 037934 107 CRCGHLYCGTHR 118 (141)
Q Consensus 107 CRCg~~fC~~HR 118 (141)
-+=|..||+.|.
T Consensus 19 ~~~g~~fC~~H~ 30 (31)
T PF11722_consen 19 RKPGSRFCGEHM 30 (31)
T ss_pred ecCcCCccccCC
Confidence 344678999883
No 43
>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=27.44 E-value=29 Score=22.15 Aligned_cols=26 Identities=27% Similarity=0.714 Sum_probs=21.9
Q ss_pred cccccccccccceeeec--CCcccchhh
Q 037934 93 CEICDKKVGSIELKCRC--GHLYCGTHR 118 (141)
Q Consensus 93 C~~C~kkvgl~gf~CRC--g~~fC~~HR 118 (141)
|..|+.-.=|..+.|.| +.++|=.|-
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~ 28 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHA 28 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccc
Confidence 67788888888999998 889998885
No 44
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=26.84 E-value=33 Score=23.50 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=10.2
Q ss_pred CccccccccccccceeeecCCcccchh
Q 037934 91 KRCEICDKKVGSIELKCRCGHLYCGTH 117 (141)
Q Consensus 91 ~rC~~C~kkvgl~gf~CRCg~~fC~~H 117 (141)
-||+.|.--+-.-----.|+++||+.=
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHH
Confidence 477777654433211235889999864
No 45
>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=26.12 E-value=33 Score=23.12 Aligned_cols=14 Identities=36% Similarity=0.861 Sum_probs=12.0
Q ss_pred ceeeecCCc-------ccchh
Q 037934 104 ELKCRCGHL-------YCGTH 117 (141)
Q Consensus 104 gf~CRCg~~-------fC~~H 117 (141)
||.|-||.. ||..|
T Consensus 50 ~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 50 SGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CEEECCCChhccCCCcccccc
Confidence 389999987 89888
No 46
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=25.82 E-value=34 Score=34.16 Aligned_cols=28 Identities=29% Similarity=0.654 Sum_probs=20.9
Q ss_pred Ccccccccccccc-------ceeee-cCCcccchhh
Q 037934 91 KRCEICDKKVGSI-------ELKCR-CGHLYCGTHR 118 (141)
Q Consensus 91 ~rC~~C~kkvgl~-------gf~CR-Cg~~fC~~HR 118 (141)
..|..|+++-+.. --.|| ||.+||+..-
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCcccc
Confidence 5799999998742 33497 8999987543
No 47
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=25.36 E-value=21 Score=30.61 Aligned_cols=31 Identities=23% Similarity=0.608 Sum_probs=24.9
Q ss_pred ccCccccccc-ccccc--ceeee-cCCcccchhhHh
Q 037934 89 LEKRCEICDK-KVGSI--ELKCR-CGHLYCGTHRKF 120 (141)
Q Consensus 89 ~~~rC~~C~k-kvgl~--gf~CR-Cg~~fC~~HR~~ 120 (141)
..+.|..|.+ .-.|. --.|| ||.+||. |...
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~ 201 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSR 201 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhc
Confidence 4689999999 88884 45586 9999999 8833
No 48
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=23.49 E-value=32 Score=27.41 Aligned_cols=13 Identities=46% Similarity=1.461 Sum_probs=11.2
Q ss_pred ceeeecCCcccchhh
Q 037934 104 ELKCRCGHLYCGTHR 118 (141)
Q Consensus 104 gf~CRCg~~fC~~HR 118 (141)
-|+|.| .||-.||
T Consensus 123 ~FrC~C--~yC~~~~ 135 (160)
T PF15549_consen 123 RFRCEC--HYCQSHR 135 (160)
T ss_pred ceeeee--eeecccC
Confidence 488998 7999998
No 49
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=22.57 E-value=45 Score=18.91 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=9.9
Q ss_pred ceeeecCCcccc
Q 037934 104 ELKCRCGHLYCG 115 (141)
Q Consensus 104 gf~CRCg~~fC~ 115 (141)
.|.|+||...|-
T Consensus 2 ~~~C~CGs~~CR 13 (26)
T smart00508 2 KQPCLCGAPNCR 13 (26)
T ss_pred CeeeeCCCcccc
Confidence 378999998885
No 50
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.15 E-value=70 Score=26.12 Aligned_cols=41 Identities=24% Similarity=0.614 Sum_probs=26.3
Q ss_pred ccccCcccccccccccc-ceeeecCCcccchhhHhhHHHHHHhCC
Q 037934 87 SALEKRCEICDKKVGSI-ELKCRCGHLYCGTHRKFDRETLVEDNP 130 (141)
Q Consensus 87 ~~~~~rC~~C~kkvgl~-gf~CRCg~~fC~~HR~~~r~~lak~NP 130 (141)
+.....|..|--.+--- -|.=.||++||.. =-|++|.+.|+
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~---Cik~alk~~~~ 169 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQ---CIKDALKNTNK 169 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHH---HHHHHHHhCCC
Confidence 33446677774333332 2667899999985 45677777775
No 51
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=21.48 E-value=35 Score=20.63 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=7.1
Q ss_pred eecCCcccch
Q 037934 107 CRCGHLYCGT 116 (141)
Q Consensus 107 CRCg~~fC~~ 116 (141)
-.||++||-.
T Consensus 14 l~CGH~FC~~ 23 (42)
T PF15227_consen 14 LPCGHSFCRS 23 (42)
T ss_dssp -SSSSEEEHH
T ss_pred cCCcCHHHHH
Confidence 4689999953
No 52
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.92 E-value=40 Score=26.65 Aligned_cols=26 Identities=19% Similarity=0.562 Sum_probs=20.9
Q ss_pred ccCccccccccccc-----cceee-ecCCccc
Q 037934 89 LEKRCEICDKKVGS-----IELKC-RCGHLYC 114 (141)
Q Consensus 89 ~~~rC~~C~kkvgl-----~gf~C-RCg~~fC 114 (141)
.-..|..|.++.-. .+|.| +||...=
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 45689999999987 49999 8887653
No 53
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=20.36 E-value=46 Score=19.27 Aligned_cols=12 Identities=33% Similarity=1.002 Sum_probs=8.8
Q ss_pred eeeecCCcccch
Q 037934 105 LKCRCGHLYCGT 116 (141)
Q Consensus 105 f~CRCg~~fC~~ 116 (141)
..-.||++||..
T Consensus 13 ~~~~CGH~fC~~ 24 (39)
T PF13923_consen 13 VVTPCGHSFCKE 24 (39)
T ss_dssp EECTTSEEEEHH
T ss_pred EECCCCCchhHH
Confidence 456799999863
Done!