Query 033031
Match_columns 129
No_of_seqs 105 out of 328
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:58:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033031.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033031hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3399 Predicted Yippee-type 100.0 1.4E-52 3.1E-57 309.8 -2.9 117 1-117 1-119 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 1.6E-32 3.6E-37 192.0 6.1 88 13-106 2-93 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.7 0.0018 3.9E-08 47.8 3.5 88 13-102 4-93 (123)
4 TIGR00357 methionine-R-sulfoxi 94.2 0.056 1.2E-06 41.0 3.4 65 12-84 39-104 (134)
5 PRK00222 methionine sulfoxide 94.1 0.045 9.8E-07 41.9 2.8 67 12-85 42-108 (142)
6 PRK05508 methionine sulfoxide 93.4 0.1 2.2E-06 39.0 3.5 62 12-83 32-93 (119)
7 PF01641 SelR: SelR domain; I 93.3 0.077 1.7E-06 39.7 2.7 70 12-88 36-105 (124)
8 PRK05550 bifunctional methioni 91.4 0.17 3.7E-06 42.5 2.8 63 12-84 35-97 (283)
9 PRK14018 trifunctional thiored 90.1 0.33 7.1E-06 43.9 3.6 67 12-85 417-483 (521)
10 PF14976 FAM72: FAM72 protein 89.6 0.71 1.5E-05 35.8 4.6 63 12-86 14-88 (150)
11 KOG0856 Predicted pilin-like t 87.3 0.97 2.1E-05 34.9 4.0 67 10-84 51-118 (146)
12 COG0229 Conserved domain frequ 79.4 3.1 6.7E-05 31.9 3.9 64 12-82 41-104 (140)
13 PF09814 HECT_2: HECT-like Ubi 68.2 8.7 0.00019 31.8 4.3 17 13-29 106-122 (354)
14 PRK02935 hypothetical protein; 66.1 4.5 9.7E-05 29.9 1.9 25 11-35 84-108 (110)
15 PF11023 DUF2614: Protein of u 55.1 5.5 0.00012 29.7 0.7 25 11-35 83-107 (114)
16 PF04828 GFA: Glutathione-depe 51.6 14 0.0003 23.9 2.2 48 53-108 32-79 (92)
17 TIGR02820 formald_GSH S-(hydro 43.4 28 0.00061 27.5 3.1 30 53-83 74-103 (182)
18 TIGR01053 LSD1 zinc finger dom 42.1 24 0.00052 20.3 1.9 19 4-22 9-28 (31)
19 COG3791 Uncharacterized conser 33.8 28 0.00061 25.5 1.7 22 65-86 65-86 (133)
20 PF03811 Zn_Tnp_IS1: InsA N-te 33.6 27 0.00058 20.7 1.2 27 68-94 4-31 (36)
21 PF14803 Nudix_N_2: Nudix N-te 29.7 25 0.00054 20.6 0.7 14 71-84 2-15 (34)
22 PF06943 zf-LSD1: LSD1 zinc fi 28.8 51 0.0011 18.2 1.8 19 3-21 5-24 (25)
23 PF00412 LIM: LIM domain; Int 26.6 32 0.0007 20.7 0.8 15 13-27 26-40 (58)
24 TIGR00037 eIF_5A translation i 26.0 77 0.0017 23.5 2.9 30 35-64 35-64 (130)
25 PF10955 DUF2757: Protein of u 24.7 35 0.00075 23.6 0.8 16 13-28 4-19 (76)
26 PF13842 Tnp_zf-ribbon_2: DDE_ 23.6 65 0.0014 18.4 1.6 15 12-26 15-29 (32)
27 PF00096 zf-C2H2: Zinc finger, 23.4 13 0.00029 18.6 -1.2 16 14-29 1-16 (23)
28 PLN03107 eukaryotic translatio 23.0 93 0.002 24.0 2.9 30 35-64 49-78 (159)
29 smart00132 LIM Zinc-binding do 22.6 33 0.00071 18.5 0.3 11 14-24 28-38 (39)
30 PF13912 zf-C2H2_6: C2H2-type 22.5 12 0.00026 19.6 -1.6 18 13-30 1-18 (27)
31 PRK05417 glutathione-dependent 22.3 87 0.0019 24.9 2.7 41 65-109 89-129 (191)
32 PF10058 DUF2296: Predicted in 21.7 28 0.00061 22.3 -0.2 35 44-83 2-36 (54)
33 PF13465 zf-H2C2_2: Zinc-finge 21.6 59 0.0013 17.2 1.2 11 12-22 13-23 (26)
34 PF13248 zf-ribbon_3: zinc-rib 21.4 31 0.00067 18.6 -0.0 11 69-79 16-26 (26)
35 PF02945 Endonuclease_7: Recom 21.3 14 0.00031 25.5 -1.7 16 67-82 50-65 (81)
36 PF10238 Eapp_C: E2F-associate 20.7 64 0.0014 24.4 1.6 24 12-35 28-54 (136)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=1.4e-52 Score=309.77 Aligned_cols=117 Identities=60% Similarity=1.018 Sum_probs=114.1
Q ss_pred CCceeEEccCCc--eEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCc
Q 033031 1 MGRLFVVNLEGK--IYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSI 78 (129)
Q Consensus 1 MGr~f~~~l~g~--~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~ 78 (129)
|||+|..+|.++ .|+|++|+|||+.++|||||+|+|++|+||||++|+||..|+.++|.|+||+|+|+||+|+.|++.
T Consensus 1 mgR~F~~~l~~~~~~y~C~~C~thla~~~dliSksf~gr~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~~ 80 (122)
T KOG3399|consen 1 MGRLFEAMLEANHRLYSCAHCKTHLARHDDLISKSFRGRTGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGTG 80 (122)
T ss_pred CcchHHHHhccCCceEeccCCcccccchhhccccccccCCCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCCC
Confidence 999999999984 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeEEeecccCcceecCeEEEEeeeeeCCCCCCccccc
Q 033031 79 VGWKYETAHEKSQKYKEGKSVLERFKVSGPDGSNYWVSH 117 (129)
Q Consensus 79 LGWkY~~A~e~sqkYKEGKfILE~~~i~~~~g~~~~~~~ 117 (129)
|||||+.|||+||||||||||||+++|.+++|+|.+++.
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~~~~~~~ 119 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPEGWDLEVGA 119 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCCCchhhcCC
Confidence 999999999999999999999999999999999988743
No 2
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=99.97 E-value=1.6e-32 Score=192.04 Aligned_cols=88 Identities=58% Similarity=1.050 Sum_probs=84.4
Q ss_pred eEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeecc----EEEEeeeeecCCCceeeeEEeecc
Q 033031 13 IYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGM----HTVADIFCVGCGSIVGWKYETAHE 88 (129)
Q Consensus 13 ~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~----h~V~DI~C~~C~~~LGWkY~~A~e 88 (129)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+||+|++|++.|||||+.|++
T Consensus 2 vf~C~~C~t~l~ds~~lvs--~~g~~~~a~l~~---~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~~a~~ 76 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVS--FHGREGKAYLFN---NVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKYESAPE 76 (96)
T ss_pred EEECCCCCCCcCCHHHhee--cCCCCccEEEEe---eeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEEEEcCH
Confidence 7999999999999999999 999999999998 7777888999999999 999999999999999999999999
Q ss_pred cCcceecCeEEEEeeeee
Q 033031 89 KSQKYKEGKSVLERFKVS 106 (129)
Q Consensus 89 ~sqkYKEGKfILE~~~i~ 106 (129)
+ |+||||+||||++.|.
T Consensus 77 ~-~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASIS 93 (96)
T ss_pred h-HhhhCCEEEEEhhHEE
Confidence 9 9999999999999885
No 3
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=96.71 E-value=0.0018 Score=47.77 Aligned_cols=88 Identities=16% Similarity=0.138 Sum_probs=59.1
Q ss_pred eEEeccCCCCCCCCCCccccccc--CCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeEEeecccC
Q 033031 13 IYSCKHCRTHLALCEDVVSKSFH--CRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYETAHEKS 90 (129)
Q Consensus 13 ~y~C~~C~thLa~~~~lISk~F~--G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~~A~e~s 90 (129)
.+.|++|.+.++..+||-.-.-+ =--.+. |...+.+...+++.....-+......|+|..|+..+|-.+..---+=
T Consensus 4 ~llC~kC~~~~C~~~DIr~ie~~hhv~v~p~--F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m~yk~~~L 81 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKIENSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMKYKGVEL 81 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEETTTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEEETTEEE
T ss_pred EEECCCCCceeEchhheEEecCCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheEECCccc
Confidence 47899999999999999443111 000111 33555555555554455568889999999999999998876654445
Q ss_pred cceecCeEEEEe
Q 033031 91 QKYKEGKSVLER 102 (129)
Q Consensus 91 qkYKEGKfILE~ 102 (129)
+-.|.-.|+++.
T Consensus 82 P~L~iksfvv~~ 93 (123)
T PF11648_consen 82 PCLKIKSFVVEL 93 (123)
T ss_dssp EEE-GGGEEEEE
T ss_pred cEEEeeeeeeee
Confidence 667777777544
No 4
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=94.22 E-value=0.056 Score=41.02 Aligned_cols=65 Identities=23% Similarity=0.460 Sum_probs=40.7
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeee-eecccCcccceeeeeccEEEEeeeeecCCCceeeeEE
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKV-VNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYE 84 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v-~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~ 84 (129)
-+|.|+.|+++|-++++ .|....|=.-.+..+ -|. +...++.. -|+.. ..|.|..|+.+||--..
T Consensus 39 G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~-V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~ 104 (134)
T TIGR00357 39 GIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEV-VAYERDES--HGMIR-TEVRCRNCDAHLGHVFD 104 (134)
T ss_pred eEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCc-eEEeecCC--CCcEE-EEEEecCCCCccCcccC
Confidence 67999999999987764 455555544444444 222 22233322 13333 58999999999996554
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.14 E-value=0.045 Score=41.91 Aligned_cols=67 Identities=21% Similarity=0.417 Sum_probs=41.1
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeEEe
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYET 85 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~~ 85 (129)
-+|.|+.|.++|=+++ ..|.-..|=.-.+..+-.-.+...+++. -|+. =..|.|..|+.+||-....
T Consensus 42 G~Y~C~~Cg~pLF~S~----~Kf~Sg~GWPSF~~~i~~~~V~~~~D~s--~gm~-RtEv~C~~Cg~HLGHVF~D 108 (142)
T PRK00222 42 GIYVCIVCGEPLFSSD----TKFDSGCGWPSFTKPIDEEAIRELRDTS--HGMV-RTEVRCANCDSHLGHVFPD 108 (142)
T ss_pred eEEEecCCCchhcCCc----ccccCCCCCcCcCcccCCCceEEeeccC--CCce-EEEEEeCCCCCccCcccCC
Confidence 6799999999998774 3466556655445444211122222221 1222 2589999999999966543
No 6
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.42 E-value=0.1 Score=38.99 Aligned_cols=62 Identities=26% Similarity=0.519 Sum_probs=41.1
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeE
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKY 83 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY 83 (129)
-+|.|+.|.++|=++++ .|.-..|=.-.+..+-|. +...++.. | .=..|.|..|+.+||--.
T Consensus 32 G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~-v~~~~D~~---~--~RtEv~C~~C~~HLGHVF 93 (119)
T PRK05508 32 GTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKGA-VKRIPDAD---G--RRTEIVCANCGGHLGHVF 93 (119)
T ss_pred eEEEecCCCCccccccc----cccCCCCCcccCcccccc-eEEEecCC---C--cEEEEEeCCCCCccCccc
Confidence 67999999999987754 466556654445544332 22333433 2 246899999999999554
No 7
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=93.28 E-value=0.077 Score=39.73 Aligned_cols=70 Identities=26% Similarity=0.509 Sum_probs=41.6
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeEEeecc
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYETAHE 88 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~~A~e 88 (129)
-+|.|+.|+++|=+++ ..|....|=.-.+..+..-.+....+..+ |+ .-..|.|..|+.+||=-......
T Consensus 36 G~Y~C~~Cg~pLF~S~----~Kf~Sg~GWPSF~~~i~~~~v~~~~D~s~--g~-~R~Ev~C~~Cg~HLGHVF~DGp~ 105 (124)
T PF01641_consen 36 GIYVCAVCGTPLFSSD----TKFDSGCGWPSFWQPIPGDAVKEREDFSH--GM-VRTEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp EEEEETTTS-EEEEGG----GEETSSSSSSEESSCSSTTSEEEEEEECT--SS-EEEEEEETTTCCEEEEEESTSST
T ss_pred EEEEcCCCCCccccCc----ccccCCcCCccccCcCChHHEEEeccccC--Cc-eEEEEEecCCCCccccEeCCCCC
Confidence 6799999999997665 34555555444444333212222222221 33 34589999999999976655444
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.43 E-value=0.17 Score=42.53 Aligned_cols=63 Identities=24% Similarity=0.509 Sum_probs=41.8
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeEE
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYE 84 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~ 84 (129)
-+|.|+.|+++|=++++ .|.-.+|=.-.++.+-|-.. ..++.. |+ =..|.|..|+.+||--..
T Consensus 35 G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~~-~~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 35 GVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAVK-RLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred cEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccE-EEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 67999999999987653 46655665444655544322 222222 32 479999999999996654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.13 E-value=0.33 Score=43.85 Aligned_cols=67 Identities=13% Similarity=0.125 Sum_probs=42.1
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeEEe
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYET 85 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~~ 85 (129)
-+|.|+.|+++|=++. ..|....|=.-.+..+-+-.+....+.. -|+.. ..|.|..|+.+||-....
T Consensus 417 G~y~c~~c~~pLf~s~----~Kf~sg~GWPsF~~~i~~~~v~~~~d~s--~g~~R-~Ev~c~~c~~HLGHvf~d 483 (521)
T PRK14018 417 GIYVDVVSGEPLFSSA----DKYDSGCGWPSFTRPIDAKVVTEHDDFS--YNMRR-TEVRSRAADSHLGHVFPD 483 (521)
T ss_pred EEEEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeeccC--CCceE-EEEEECCCCCcCCcccCC
Confidence 6799999999998875 4466555544444444322222223321 13333 489999999999966644
No 10
>PF14976 FAM72: FAM72 protein
Probab=89.61 E-value=0.71 Score=35.76 Aligned_cols=63 Identities=30% Similarity=0.572 Sum_probs=41.1
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeeccc---C-cccceeeeecc--------EEEEeeeeecCCCce
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSV---G-EKEERLMMTGM--------HTVADIFCVGCGSIV 79 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~---g-~~~~r~m~TG~--------h~V~DI~C~~C~~~L 79 (129)
.+..|+.|.+-|+... =||.|..+ +|+.+ . ||....-.+|. =.++||-|.+|+..|
T Consensus 14 ~~L~C~~C~~~l~~Rg-----------MkAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~v 81 (150)
T PF14976_consen 14 YILCCKFCDQVLCNRG-----------MKAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIV 81 (150)
T ss_pred EEEECCCCCchhccch-----------hhheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCee
Confidence 4588999999887543 25666554 33332 1 23323323333 389999999999999
Q ss_pred eeeEEee
Q 033031 80 GWKYETA 86 (129)
Q Consensus 80 GWkY~~A 86 (129)
|+.++..
T Consensus 82 GYhV~~P 88 (150)
T PF14976_consen 82 GYHVVVP 88 (150)
T ss_pred eeEEEEE
Confidence 9888754
No 11
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=87.31 E-value=0.97 Score=34.86 Aligned_cols=67 Identities=22% Similarity=0.459 Sum_probs=38.1
Q ss_pred CCceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceee-eeccEEEEeeeeecCCCceeeeEE
Q 033031 10 EGKIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLM-MTGMHTVADIFCVGCGSIVGWKYE 84 (129)
Q Consensus 10 ~g~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m-~TG~h~V~DI~C~~C~~~LGWkY~ 84 (129)
+.-+|.|..|.++|-.+. ..|....|=--.|+.+ + .|....+.. .-|.+ =.+|.|..|+.+||--.+
T Consensus 51 e~GvY~C~~C~~pLykS~----tKfdsgcGWPAF~e~i-~--~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 51 EEGVYVCAGCGTPLYKST----TKFDSGCGWPAFFEAI-G--PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CCceEEEeecCCcccccc----ccccCCCCCchhhhcc-C--CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 457899999999997764 3455555543333332 0 111111111 01111 248999999999995543
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=79.45 E-value=3.1 Score=31.95 Aligned_cols=64 Identities=28% Similarity=0.482 Sum_probs=39.0
Q ss_pred ceEEeccCCCCCCCCCCcccccccCCCCeeeeeeeeeecccCcccceeeeeccEEEEeeeeecCCCceeee
Q 033031 12 KIYSCKHCRTHLALCEDVVSKSFHCRHGKAYLFSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWK 82 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWk 82 (129)
-+|.|..|..+|-++++ .|.-..|=--.+..+..-.+...++++ -|++. ..|.|..|+++||--
T Consensus 41 GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~S--~gM~R-tEVrc~~c~sHLGHV 104 (140)
T COG0229 41 GIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDRS--HGMVR-TEVRCANCDSHLGHV 104 (140)
T ss_pred ceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeeccC--CCcEE-EEEEecCCCCccccc
Confidence 68999999999987764 344444433333333332333333322 23333 479999999999943
No 13
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=68.19 E-value=8.7 Score=31.81 Aligned_cols=17 Identities=18% Similarity=0.608 Sum_probs=13.7
Q ss_pred eEEeccCCCCCCCCCCc
Q 033031 13 IYSCKHCRTHLALCEDV 29 (129)
Q Consensus 13 ~y~C~~C~thLa~~~~l 29 (129)
.+.|++|++.|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766443
No 14
>PRK02935 hypothetical protein; Provisional
Probab=66.12 E-value=4.5 Score=29.92 Aligned_cols=25 Identities=32% Similarity=0.732 Sum_probs=21.8
Q ss_pred CceEEeccCCCCCCCCCCccccccc
Q 033031 11 GKIYSCKHCRTHLALCEDVVSKSFH 35 (129)
Q Consensus 11 g~~y~C~~C~thLa~~~~lISk~F~ 35 (129)
||+..|-+|++||+...++--|.|.
T Consensus 84 GrvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 84 GRVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred cceeecCcCCCcCCcCccccccCcC
Confidence 6889999999999999988777664
No 15
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=55.11 E-value=5.5 Score=29.65 Aligned_cols=25 Identities=32% Similarity=0.751 Sum_probs=21.9
Q ss_pred CceEEeccCCCCCCCCCCccccccc
Q 033031 11 GKIYSCKHCRTHLALCEDVVSKSFH 35 (129)
Q Consensus 11 g~~y~C~~C~thLa~~~~lISk~F~ 35 (129)
|+...|-+|++||+...++--|.|+
T Consensus 83 Gr~D~CM~C~~pLTLd~~legkef~ 107 (114)
T PF11023_consen 83 GRVDACMHCKEPLTLDPSLEGKEFD 107 (114)
T ss_pred chhhccCcCCCcCccCchhhcchhh
Confidence 5778999999999999999887775
No 16
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=51.62 E-value=14 Score=23.94 Aligned_cols=48 Identities=19% Similarity=0.202 Sum_probs=24.3
Q ss_pred CcccceeeeeccEEEEeeeeecCCCceeeeEEeecccCcceecCeEEEEeeeeeCC
Q 033031 53 GEKEERLMMTGMHTVADIFCVGCGSIVGWKYETAHEKSQKYKEGKSVLERFKVSGP 108 (129)
Q Consensus 53 g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY~~A~e~sqkYKEGKfILE~~~i~~~ 108 (129)
|+..-+........+.-.+|..|++.|.+... -..+.+.|-...|-++
T Consensus 32 g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~~~--------~~~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 32 GSENLKEYQFSGKGVERYFCPTCGSPLFSEDE--------RDPDLVGVNAGTLDDP 79 (92)
T ss_dssp -GGGEEEC--TTSSCEEEEETTT--EEEEEES--------STTTEEEEEGGGBTT-
T ss_pred ccccceEEEeCCCcCcCcccCCCCCeeecccC--------CCCCEEEEEeEeeCCC
Confidence 54444443324445666999999999997622 2234555555544443
No 17
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=43.41 E-value=28 Score=27.55 Aligned_cols=30 Identities=13% Similarity=0.284 Sum_probs=18.0
Q ss_pred CcccceeeeeccEEEEeeeeecCCCceeeeE
Q 033031 53 GEKEERLMMTGMHTVADIFCVGCGSIVGWKY 83 (129)
Q Consensus 53 g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY 83 (129)
|+...+....|.+. .--||..|++.|-++.
T Consensus 74 G~~~l~~Y~ss~~~-~R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 74 NGDKLKVVDASATI-QRHACKGCGTHMYGRI 103 (182)
T ss_pred CCcceEEEeCCCCE-EeecCCCCCCcccccc
Confidence 54443333334444 4449999999995544
No 18
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=42.10 E-value=24 Score=20.29 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=14.1
Q ss_pred eeEEccCC-ceEEeccCCCC
Q 033031 4 LFVVNLEG-KIYSCKHCRTH 22 (129)
Q Consensus 4 ~f~~~l~g-~~y~C~~C~th 22 (129)
.-+.|+.| +.+.|..|++.
T Consensus 9 t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cEeecCCCCCeEECCCCCeE
Confidence 45677777 77888888763
No 19
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=33.83 E-value=28 Score=25.53 Aligned_cols=22 Identities=27% Similarity=0.579 Sum_probs=16.7
Q ss_pred EEEEeeeeecCCCceeeeEEee
Q 033031 65 HTVADIFCVGCGSIVGWKYETA 86 (129)
Q Consensus 65 h~V~DI~C~~C~~~LGWkY~~A 86 (129)
..+.-.||..|+++|-|+....
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCCeecccCCCceEEecCCC
Confidence 3344449999999999997654
No 20
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=33.58 E-value=27 Score=20.70 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=21.9
Q ss_pred EeeeeecCCCce-eeeEEeecccCccee
Q 033031 68 ADIFCVGCGSIV-GWKYETAHEKSQKYK 94 (129)
Q Consensus 68 ~DI~C~~C~~~L-GWkY~~A~e~sqkYK 94 (129)
.+|.|..|++.- --|.-+.-.-.|+|.
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryr 31 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYR 31 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEe
Confidence 479999999988 777777777778774
No 21
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.74 E-value=25 Score=20.59 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=7.2
Q ss_pred eeecCCCceeeeEE
Q 033031 71 FCVGCGSIVGWKYE 84 (129)
Q Consensus 71 ~C~~C~~~LGWkY~ 84 (129)
||..|++.|-++..
T Consensus 2 fC~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FCPQCGGPLERRIP 15 (34)
T ss_dssp B-TTT--B-EEE--
T ss_pred ccccccChhhhhcC
Confidence 79999999988876
No 22
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.84 E-value=51 Score=18.23 Aligned_cols=19 Identities=26% Similarity=0.576 Sum_probs=14.4
Q ss_pred ceeEEccCC-ceEEeccCCC
Q 033031 3 RLFVVNLEG-KIYSCKHCRT 21 (129)
Q Consensus 3 r~f~~~l~g-~~y~C~~C~t 21 (129)
|..+.|+.| +.-.|..|++
T Consensus 5 r~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CceEEcCCCCCCeECCccCc
Confidence 456778888 7788888875
No 23
>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=26.62 E-value=32 Score=20.66 Aligned_cols=15 Identities=20% Similarity=0.583 Sum_probs=12.2
Q ss_pred eEEeccCCCCCCCCC
Q 033031 13 IYSCKHCRTHLALCE 27 (129)
Q Consensus 13 ~y~C~~C~thLa~~~ 27 (129)
-|.|..|+.+|...+
T Consensus 26 Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGD 40 (58)
T ss_dssp TSBETTTTCBTTTSS
T ss_pred ccccCCCCCccCCCe
Confidence 388999999987765
No 24
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=25.95 E-value=77 Score=23.46 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=24.6
Q ss_pred cCCCCeeeeeeeeeecccCcccceeeeecc
Q 033031 35 HCRHGKAYLFSKVVNVSVGEKEERLMMTGM 64 (129)
Q Consensus 35 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 64 (129)
.|+||.|+.--.+.|+..|...+..+.++-
T Consensus 35 pGkhG~A~vr~k~knl~tG~~~e~~f~s~~ 64 (130)
T TIGR00037 35 PGKHGHAKARVVAIGIFTGKKLEFVSPSTS 64 (130)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEECCCC
Confidence 588999999999999999988776665544
No 25
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=24.75 E-value=35 Score=23.62 Aligned_cols=16 Identities=31% Similarity=0.850 Sum_probs=13.2
Q ss_pred eEEeccCCCCCCCCCC
Q 033031 13 IYSCKHCRTHLALCED 28 (129)
Q Consensus 13 ~y~C~~C~thLa~~~~ 28 (129)
.|.|++|++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 3999999999877654
No 26
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=23.56 E-value=65 Score=18.38 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=12.4
Q ss_pred ceEEeccCCCCCCCC
Q 033031 12 KIYSCKHCRTHLALC 26 (129)
Q Consensus 12 ~~y~C~~C~thLa~~ 26 (129)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 459999999988764
No 27
>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=23.42 E-value=13 Score=18.63 Aligned_cols=16 Identities=19% Similarity=0.613 Sum_probs=12.0
Q ss_pred EEeccCCCCCCCCCCc
Q 033031 14 YSCKHCRTHLALCEDV 29 (129)
Q Consensus 14 y~C~~C~thLa~~~~l 29 (129)
|.|..|+..+...++|
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 7899998877766554
No 28
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=22.96 E-value=93 Score=23.98 Aligned_cols=30 Identities=20% Similarity=0.308 Sum_probs=25.4
Q ss_pred cCCCCeeeeeeeeeecccCcccceeeeecc
Q 033031 35 HCRHGKAYLFSKVVNVSVGEKEERLMMTGM 64 (129)
Q Consensus 35 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 64 (129)
.|+||.|+.--.+.|+..|...++.+.++-
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~ 78 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSH 78 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 599999999999999999998877766554
No 29
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=22.63 E-value=33 Score=18.53 Aligned_cols=11 Identities=27% Similarity=0.951 Sum_probs=9.9
Q ss_pred EEeccCCCCCC
Q 033031 14 YSCKHCRTHLA 24 (129)
Q Consensus 14 y~C~~C~thLa 24 (129)
|.|..|+..|+
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 89999999886
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=22.53 E-value=12 Score=19.60 Aligned_cols=18 Identities=11% Similarity=0.456 Sum_probs=13.1
Q ss_pred eEEeccCCCCCCCCCCcc
Q 033031 13 IYSCKHCRTHLALCEDVV 30 (129)
Q Consensus 13 ~y~C~~C~thLa~~~~lI 30 (129)
+|.|..|+.-+.+...++
T Consensus 1 ~~~C~~C~~~F~~~~~l~ 18 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALR 18 (27)
T ss_dssp SEEETTTTEEESSHHHHH
T ss_pred CCCCCccCCccCChhHHH
Confidence 588999988776655543
No 31
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=22.29 E-value=87 Score=24.90 Aligned_cols=41 Identities=15% Similarity=0.117 Sum_probs=27.2
Q ss_pred EEEEeeeeecCCCceeeeEEeecccCcceecCeEEEEeeeeeCCC
Q 033031 65 HTVADIFCVGCGSIVGWKYETAHEKSQKYKEGKSVLERFKVSGPD 109 (129)
Q Consensus 65 h~V~DI~C~~C~~~LGWkY~~A~e~sqkYKEGKfILE~~~i~~~~ 109 (129)
..+.--+|..|++.|-+.++..-. --.|..+|-...+-++.
T Consensus 89 ~~i~R~FC~~CGS~L~~~~e~~~~----~~pgl~fV~~gllDd~~ 129 (191)
T PRK05417 89 ATIQRHACKECGVHMYGRIENKDH----PFYGLDFVHTELSQEQG 129 (191)
T ss_pred CCeEeeeCCCCCCccccccccccC----CCCCeEEEehhhcCCCC
Confidence 345556999999999887762201 12377888777766654
No 32
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.74 E-value=28 Score=22.27 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=24.1
Q ss_pred eeeeeecccCcccceeeeeccEEEEeeeeecCCCceeeeE
Q 033031 44 FSKVVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKY 83 (129)
Q Consensus 44 f~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~LGWkY 83 (129)
|++++++..|..+ |+...---+-|.+|.++=|---
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~ 36 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAP 36 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccc
Confidence 5677788887666 3333334566999999999654
No 33
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.60 E-value=59 Score=17.25 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=9.2
Q ss_pred ceEEeccCCCC
Q 033031 12 KIYSCKHCRTH 22 (129)
Q Consensus 12 ~~y~C~~C~th 22 (129)
++|.|..|..-
T Consensus 13 k~~~C~~C~k~ 23 (26)
T PF13465_consen 13 KPYKCPYCGKS 23 (26)
T ss_dssp SSEEESSSSEE
T ss_pred CCCCCCCCcCe
Confidence 88999999753
No 34
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.43 E-value=31 Score=18.58 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=5.8
Q ss_pred eeeeecCCCce
Q 033031 69 DIFCVGCGSIV 79 (129)
Q Consensus 69 DI~C~~C~~~L 79 (129)
+-||..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 44566665543
No 35
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=21.34 E-value=14 Score=25.51 Aligned_cols=16 Identities=25% Similarity=0.696 Sum_probs=14.8
Q ss_pred EEeeeeecCCCceeee
Q 033031 67 VADIFCVGCGSIVGWK 82 (129)
Q Consensus 67 V~DI~C~~C~~~LGWk 82 (129)
||-+-|..|++.||+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 9999999999999975
No 36
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=20.69 E-value=64 Score=24.43 Aligned_cols=24 Identities=25% Similarity=0.455 Sum_probs=18.7
Q ss_pred ceEEeccCCCCCCCCCC---ccccccc
Q 033031 12 KIYSCKHCRTHLALCED---VVSKSFH 35 (129)
Q Consensus 12 ~~y~C~~C~thLa~~~~---lISk~F~ 35 (129)
-+.+|..|-|.|+...+ .....|+
T Consensus 28 avLsCp~Cft~lc~dcQrHe~y~~QYR 54 (136)
T PF10238_consen 28 AVLSCPACFTTLCLDCQRHEKYKNQYR 54 (136)
T ss_pred ceEeCccccceeeecccccchhcceee
Confidence 67999999999998766 5555554
Done!