Query 033435
Match_columns 119
No_of_seqs 115 out of 326
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 13:51:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033435.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033435hhsearch_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 1.9E-52 4.1E-57 304.4 -3.7 115 1-116 1-118 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 4.9E-33 1.1E-37 191.8 5.8 88 15-108 3-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.4 0.0019 4.1E-08 46.9 1.7 89 14-104 4-94 (123)
4 PF01641 SelR: SelR domain; I 94.3 0.041 9E-07 40.5 2.8 70 12-89 36-105 (124)
5 TIGR00357 methionine-R-sulfoxi 94.2 0.052 1.1E-06 40.5 3.2 67 12-86 39-105 (134)
6 PRK00222 methionine sulfoxide 93.8 0.053 1.2E-06 40.9 2.6 67 12-86 42-108 (142)
7 PRK05508 methionine sulfoxide 93.0 0.11 2.3E-06 38.2 3.0 63 12-85 32-94 (119)
8 PRK05550 bifunctional methioni 91.1 0.18 3.9E-06 41.7 2.7 63 12-85 35-97 (283)
9 PF14976 FAM72: FAM72 protein 90.6 0.67 1.5E-05 35.3 5.1 61 15-87 16-88 (150)
10 PRK14018 trifunctional thiored 89.4 0.36 7.8E-06 42.9 3.2 82 12-101 417-500 (521)
11 COG0229 Conserved domain frequ 85.1 1.2 2.6E-05 33.6 3.5 65 12-84 41-105 (140)
12 KOG0856 Predicted pilin-like t 81.8 1.6 3.4E-05 33.2 2.9 67 10-85 51-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 70.6 6.6 0.00014 32.0 4.0 17 14-30 106-122 (354)
14 PRK02935 hypothetical protein; 56.5 8 0.00017 28.1 1.8 25 11-36 84-108 (110)
15 PF04828 GFA: Glutathione-depe 49.4 17 0.00037 23.1 2.3 47 54-108 32-78 (92)
16 TIGR02820 formald_GSH S-(hydro 48.9 21 0.00045 27.8 3.1 31 53-84 73-103 (182)
17 PF11023 DUF2614: Protein of u 43.9 9.9 0.00022 27.8 0.6 26 11-37 83-108 (114)
18 PF03811 Zn_Tnp_IS1: InsA N-te 41.3 15 0.00033 21.4 1.0 27 69-95 4-31 (36)
19 PRK05417 glutathione-dependent 40.6 29 0.00064 27.1 2.8 40 66-109 89-128 (191)
20 TIGR01053 LSD1 zinc finger dom 38.9 26 0.00056 19.8 1.7 19 4-23 9-28 (31)
21 PF10955 DUF2757: Protein of u 35.0 20 0.00044 24.4 1.0 17 13-29 3-19 (76)
22 PF06943 zf-LSD1: LSD1 zinc fi 32.6 35 0.00076 18.6 1.5 19 3-22 5-24 (25)
23 COG1996 RPC10 DNA-directed RNA 31.4 37 0.0008 21.3 1.7 10 15-24 7-16 (49)
24 PF00412 LIM: LIM domain; Int 30.4 30 0.00064 20.5 1.1 14 15-28 27-40 (58)
25 PF00096 zf-C2H2: Zinc finger, 28.2 12 0.00025 18.5 -0.8 16 15-30 1-16 (23)
26 PF14803 Nudix_N_2: Nudix N-te 27.1 28 0.0006 20.1 0.5 14 72-85 2-15 (34)
27 PF10058 DUF2296: Predicted in 27.0 19 0.00042 22.6 -0.2 39 45-88 2-40 (54)
28 COG4187 RocB Arginine degradat 25.3 50 0.0011 29.8 2.0 43 24-84 200-244 (553)
29 COG3791 Uncharacterized conser 25.3 56 0.0012 23.5 2.0 22 66-87 65-86 (133)
30 TIGR00037 eIF_5A translation i 25.0 85 0.0018 22.8 2.9 30 36-65 35-64 (130)
31 smart00132 LIM Zinc-binding do 23.6 32 0.0007 18.2 0.4 11 15-25 28-38 (39)
32 PF02945 Endonuclease_7: Recom 23.5 9.2 0.0002 26.0 -2.3 16 68-83 50-65 (81)
33 PF13842 Tnp_zf-ribbon_2: DDE_ 23.2 61 0.0013 18.2 1.5 15 13-27 15-29 (32)
34 PF10246 MRP-S35: Mitochondria 23.2 48 0.001 23.9 1.2 51 44-99 10-66 (104)
35 PLN03107 eukaryotic translatio 22.0 1E+02 0.0022 23.4 2.9 36 36-71 49-85 (159)
36 PF13248 zf-ribbon_3: zinc-rib 22.0 26 0.00057 18.6 -0.2 11 70-80 16-26 (26)
37 PF04246 RseC_MucC: Positive r 21.0 1.3E+02 0.0028 21.3 3.1 43 15-58 17-59 (135)
38 smart00714 LITAF Possible memb 20.3 52 0.0011 20.8 0.9 12 72-83 54-65 (67)
39 PRK11586 napB nitrate reductas 20.3 66 0.0014 24.6 1.6 32 7-39 114-145 (149)
40 PRK03999 translation initiatio 20.1 1.2E+02 0.0026 22.0 2.9 31 35-65 33-63 (129)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=1.9e-52 Score=304.42 Aligned_cols=115 Identities=53% Similarity=0.929 Sum_probs=110.2
Q ss_pred Ccceeeeeecc--eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCC
Q 033435 1 MGRIFLVELKG--RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQ 78 (119)
Q Consensus 1 MGr~f~~yl~g--~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~ 78 (119)
|||+|.++|++ +. |+|++|+||||+++||||++|+|++|+||||++|+||..|+.|+|.|+||+|+|+||+|+.|++
T Consensus 1 mgR~F~~~l~~~~~~-y~C~~C~thla~~~dliSksf~gr~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~ 79 (122)
T KOG3399|consen 1 MGRLFEAMLEANHRL-YSCAHCKTHLARHDDLISKSFRGRTGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGT 79 (122)
T ss_pred CcchHHHHhccCCce-EeccCCcccccchhhccccccccCCCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCC
Confidence 99999999999 58 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeEEEEeccCCcceecCeEEEEeehhhhh-hhheeee
Q 033435 79 IVGWKYVAAHDKNQKYKEGKFVLERYRIGKY-VFELLVS 116 (119)
Q Consensus 79 ~lGWkY~~A~e~sqkYKEGkfILE~~~i~k~-~~~~~~~ 116 (119)
.|||||+.|||+||||||||||||+++|.+. -+++.++
T Consensus 80 ~~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~~~~~~ 118 (122)
T KOG3399|consen 80 GLGWKYEHAYEKSQKYKEGKFILELAEIFKPEGWDLEVG 118 (122)
T ss_pred CcceeeeeccCchhhhcCcchHHHHHHhcCCCCchhhcC
Confidence 9999999999999999999999999999986 4666554
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=99.98 E-value=4.9e-33 Score=191.85 Aligned_cols=88 Identities=45% Similarity=0.940 Sum_probs=84.6
Q ss_pred EecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeec----EEEeeeeeeeCCCeeeeEEEEeccC
Q 033435 15 YKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGM----HTVEDIFCCCCGQIVGWKYVAAHDK 90 (119)
Q Consensus 15 y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~----H~V~DI~C~~C~~~lGWkY~~A~e~ 90 (119)
|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+||+|++|++.|||||+.|+++
T Consensus 3 f~C~~C~t~l~ds~~lvs--~~g~~~~a~l~~---~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~~a~~~ 77 (96)
T PF03226_consen 3 FQCKNCKTILADSNELVS--FHGREGKAYLFN---NVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKYESAPEE 77 (96)
T ss_pred EECCCCCCCcCCHHHhee--cCCCCccEEEEe---eeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEEEEcCHh
Confidence 999999999999999999 999999999998 8888889999999999 9999999999999999999999999
Q ss_pred CcceecCeEEEEeehhhh
Q 033435 91 NQKYKEGKFVLERYRIGK 108 (119)
Q Consensus 91 sqkYKEGkfILE~~~i~k 108 (119)
|+||||+||||++.|..
T Consensus 78 -~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 78 -QKYKEGKFILEKASISS 94 (96)
T ss_pred -HhhhCCEEEEEhhHEEE
Confidence 99999999999998853
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=96.38 E-value=0.0019 Score=46.95 Aligned_cols=89 Identities=17% Similarity=0.143 Sum_probs=61.5
Q ss_pred EEecCCCCccccCCCCeeeecccc--CCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEEeccCC
Q 033435 14 YYKCRFCNSHLALADSVLSWSFNC--RRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHDKN 91 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~lISk~F~G--~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e~s 91 (119)
.+.|++|.+.++..+||-.-.-+. --.+. |...+.+...|.+.....-+.+....|+|.+|++.+|-.+..---+=
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 388999999999999987652110 01122 33555566665554445568889999999999999999887665556
Q ss_pred cceecCeEEEEee
Q 033435 92 QKYKEGKFVLERY 104 (119)
Q Consensus 92 qkYKEGkfILE~~ 104 (119)
+-.|.-.|+++..
T Consensus 82 P~L~iksfvv~~~ 94 (123)
T PF11648_consen 82 PCLKIKSFVVELE 94 (123)
T ss_dssp EEE-GGGEEEEET
T ss_pred cEEEeeeeeeeec
Confidence 6777777875543
No 4
>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=94.31 E-value=0.041 Score=40.51 Aligned_cols=70 Identities=20% Similarity=0.423 Sum_probs=42.8
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEEecc
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHD 89 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e 89 (119)
-+ |.|+.|+++|=+++. .|....|=.-.++.+..-.+....|..+ |+. -..|.|.+|+.+||--......
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 GI-YVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFSH--GMV-RTEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp EE-EEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEECT--SSE-EEEEEETTTCCEEEEEESTSST
T ss_pred EE-EEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEeccccC--Cce-EEEEEecCCCCccccEeCCCCC
Confidence 45 999999999976653 4665566443344333323333333321 443 4579999999999977765544
No 5
>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=94.20 E-value=0.052 Score=40.53 Aligned_cols=67 Identities=15% Similarity=0.330 Sum_probs=41.5
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEE
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVA 86 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~ 86 (119)
-+ |.|+.|+++|=++++ .|....|=.-.++.+-.-.+...+|.. -|+.. ..|.|.+|+.+||--...
T Consensus 39 G~-Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~D 105 (134)
T TIGR00357 39 GI-YVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEVVAYERDES--HGMIR-TEVRCRNCDAHLGHVFDD 105 (134)
T ss_pred eE-EEccCCCCccccccc----hhcCCCCCcCcCcccCCCceEEeecCC--CCcEE-EEEEecCCCCccCcccCC
Confidence 45 999999999987765 355555543333444111223333322 24433 589999999999976543
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=93.80 E-value=0.053 Score=40.85 Aligned_cols=67 Identities=18% Similarity=0.376 Sum_probs=41.4
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEE
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVA 86 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~ 86 (119)
-+ |.|+.|+++|=++++ .|....|=.-.++.+-.-.+...+|+. -|+. =..|.|..|+.+||--...
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 GI-YVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDTS--HGMV-RTEVRCANCDSHLGHVFPD 108 (142)
T ss_pred eE-EEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeeccC--CCce-EEEEEeCCCCCccCcccCC
Confidence 45 999999999987743 466666644434443222222223321 1222 2579999999999977654
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=92.97 E-value=0.11 Score=38.21 Aligned_cols=63 Identities=19% Similarity=0.450 Sum_probs=41.8
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEE
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYV 85 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~ 85 (119)
-+ |.|+.|+++|=++++ .|....|=.-.+..+-| .+...+|.. | .=..|.|++|+.+||--..
T Consensus 32 G~-Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~-~v~~~~D~~---~--~RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 32 GT-YVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKG-AVKRIPDAD---G--RRTEIVCANCGGHLGHVFE 94 (119)
T ss_pred eE-EEecCCCCccccccc----cccCCCCCcccCccccc-ceEEEecCC---C--cEEEEEeCCCCCccCcccC
Confidence 45 999999999987764 46666664443444433 233344443 2 2467999999999996654
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.13 E-value=0.18 Score=41.71 Aligned_cols=63 Identities=22% Similarity=0.453 Sum_probs=41.6
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEE
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYV 85 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~ 85 (119)
-+ |.|+.|+++|=++++ .|....|=.-.++.+-|-. -..++.. |+ =..|.|.+|+++||--..
T Consensus 35 G~-y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~-~~~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 35 GV-YLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAV-KRLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred cE-EEcCCCCchhcCChh----hccCCCCCcCcCcccCCcc-EEEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 45 999999999988654 4666666444455554432 2222222 33 488999999999997664
No 9
>PF14976 FAM72: FAM72 protein
Probab=90.56 E-value=0.67 Score=35.33 Aligned_cols=61 Identities=34% Similarity=0.646 Sum_probs=40.8
Q ss_pred EecCCCCccccCCCCeeeeccccCCceEEEeeccccccc----Cccceeeeeeec--------EEEeeeeeeeCCCeeee
Q 033435 15 YKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIML----GPQEERLMLSGM--------HTVEDIFCCCCGQIVGW 82 (119)
Q Consensus 15 y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~----g~~e~r~m~TG~--------H~V~DI~C~~C~~~lGW 82 (119)
..|+.|.+-|+... =||.|..+ +|+.+ -||....-.+|. =.++|+-|..|+..||+
T Consensus 16 L~C~~C~~~l~~Rg-----------MkAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~vGY 83 (150)
T PF14976_consen 16 LCCKFCDQVLCNRG-----------MKAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIVGY 83 (150)
T ss_pred EECCCCCchhccch-----------hhheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCeeee
Confidence 78999999887643 24666555 44443 123333333343 26999999999999999
Q ss_pred EEEEe
Q 033435 83 KYVAA 87 (119)
Q Consensus 83 kY~~A 87 (119)
-++..
T Consensus 84 hV~~P 88 (150)
T PF14976_consen 84 HVVVP 88 (150)
T ss_pred EEEEE
Confidence 88754
No 10
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=89.37 E-value=0.36 Score=42.90 Aligned_cols=82 Identities=9% Similarity=0.059 Sum_probs=48.7
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEEecc--
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHD-- 89 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e-- 89 (119)
-+ |.|+.|+++|=+++ ..|....|=.-.++.+-+-.+...+|.. -|++. ..|.|++|+++||-.......
T Consensus 417 G~-y~c~~c~~pLf~s~----~Kf~sg~GWPsF~~~i~~~~v~~~~d~s--~g~~R-~Ev~c~~c~~HLGHvf~dgp~~~ 488 (521)
T PRK14018 417 GI-YVDVVSGEPLFSSA----DKYDSGCGWPSFTRPIDAKVVTEHDDFS--YNMRR-TEVRSRAADSHLGHVFPDGPRDK 488 (521)
T ss_pred EE-EEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeeccC--CCceE-EEEEECCCCCcCCcccCCCCCCC
Confidence 55 99999999998875 3466666643333333222223333322 24443 489999999999987755331
Q ss_pred CCcceecCeEEE
Q 033435 90 KNQKYKEGKFVL 101 (119)
Q Consensus 90 ~sqkYKEGkfIL 101 (119)
..++|=.+---|
T Consensus 489 ~g~RyCiNs~~l 500 (521)
T PRK14018 489 GGLRYCINGASL 500 (521)
T ss_pred CCCEeeeceeEE
Confidence 234554444333
No 11
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=85.06 E-value=1.2 Score=33.60 Aligned_cols=65 Identities=20% Similarity=0.430 Sum_probs=41.3
Q ss_pred eeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEE
Q 033435 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 84 (119)
-+ |.|..|+.+|=++++ .|....|=--.+.-+.+-.+...+|+ .-|++. ..|.|.+|+++||--.
T Consensus 41 Gi-Y~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~R-tEVrc~~c~sHLGHVF 105 (140)
T COG0229 41 GI-YVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVR-TEVRCANCDSHLGHVF 105 (140)
T ss_pred ce-EEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEE-EEEEecCCCCcccccc
Confidence 56 999999999977764 45555553333444433334444443 234443 4789999999999543
No 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=81.82 E-value=1.6 Score=33.18 Aligned_cols=67 Identities=19% Similarity=0.384 Sum_probs=39.1
Q ss_pred cceeEEecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccceeee-eeecEEEeeeeeeeCCCeeeeEEE
Q 033435 10 KGRSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLM-LSGMHTVEDIFCCCCGQIVGWKYV 85 (119)
Q Consensus 10 ~g~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m-~TG~H~V~DI~C~~C~~~lGWkY~ 85 (119)
+.-+ |.|..|+++|-+++ ..|....|=--.|+.+ + .|....+.. .-|.| =.+|.|..|+.+||--.+
T Consensus 51 e~Gv-Y~C~~C~~pLykS~----tKfdsgcGWPAF~e~i-~--~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 51 EEGV-YVCAGCGTPLYKST----TKFDSGCGWPAFFEAI-G--PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CCce-EEEeecCCcccccc----ccccCCCCCchhhhcc-C--CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 3366 99999999997764 3466555542223332 1 222111111 11122 458999999999997654
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=70.56 E-value=6.6 Score=31.98 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=13.5
Q ss_pred EEecCCCCccccCCCCe
Q 033435 14 YYKCRFCNSHLALADSV 30 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~l 30 (119)
.+.|++|++.|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 39999999999766543
No 14
>PRK02935 hypothetical protein; Provisional
Probab=56.51 E-value=8 Score=28.14 Aligned_cols=25 Identities=36% Similarity=0.623 Sum_probs=21.1
Q ss_pred ceeEEecCCCCccccCCCCeeeeccc
Q 033435 11 GRSYYKCRFCNSHLALADSVLSWSFN 36 (119)
Q Consensus 11 g~~~y~C~~C~thLa~~~~lISk~F~ 36 (119)
|++ ..|-+|++||+...++--|.|+
T Consensus 84 Grv-D~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 84 GRV-DACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred cce-eecCcCCCcCCcCccccccCcC
Confidence 477 8999999999999888777664
No 15
>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=49.42 E-value=17 Score=23.15 Aligned_cols=47 Identities=15% Similarity=0.138 Sum_probs=24.7
Q ss_pred CccceeeeeeecEEEeeeeeeeCCCeeeeEEEEeccCCcceecCeEEEEeehhhh
Q 033435 54 GPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHDKNQKYKEGKFVLERYRIGK 108 (119)
Q Consensus 54 g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~i~k 108 (119)
|+..-+........+.-.+|.+|++.|.+... -..+.+.|-...|..
T Consensus 32 g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~~~--------~~~~~~~V~~g~ld~ 78 (92)
T PF04828_consen 32 GSENLKEYQFSGKGVERYFCPTCGSPLFSEDE--------RDPDLVGVNAGTLDD 78 (92)
T ss_dssp -GGGEEEC--TTSSCEEEEETTT--EEEEEES--------STTTEEEEEGGGBTT
T ss_pred ccccceEEEeCCCcCcCcccCCCCCeeecccC--------CCCCEEEEEeEeeCC
Confidence 44433333323444666999999999997621 123456666555544
No 16
>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=48.91 E-value=21 Score=27.81 Aligned_cols=31 Identities=10% Similarity=0.153 Sum_probs=18.6
Q ss_pred cCccceeeeeeecEEEeeeeeeeCCCeeeeEE
Q 033435 53 LGPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (119)
Q Consensus 53 ~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 84 (119)
.|+...+....|.+. .--+|..|++.|-+..
T Consensus 73 ~G~~~l~~Y~ss~~~-~R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 73 ANGDKLKVVDASATI-QRHACKGCGTHMYGRI 103 (182)
T ss_pred cCCcceEEEeCCCCE-EeecCCCCCCcccccc
Confidence 354443333334444 4449999999996654
No 17
>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=43.86 E-value=9.9 Score=27.83 Aligned_cols=26 Identities=31% Similarity=0.518 Sum_probs=21.5
Q ss_pred ceeEEecCCCCccccCCCCeeeecccc
Q 033435 11 GRSYYKCRFCNSHLALADSVLSWSFNC 37 (119)
Q Consensus 11 g~~~y~C~~C~thLa~~~~lISk~F~G 37 (119)
|+. ..|-+|++||+...++--|.|+-
T Consensus 83 Gr~-D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 83 GRV-DACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred chh-hccCcCCCcCccCchhhcchhhH
Confidence 366 78999999999999988777753
No 18
>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=41.28 E-value=15 Score=21.39 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=22.3
Q ss_pred eeeeeeeCCCee-eeEEEEeccCCccee
Q 033435 69 EDIFCCCCGQIV-GWKYVAAHDKNQKYK 95 (119)
Q Consensus 69 ~DI~C~~C~~~l-GWkY~~A~e~sqkYK 95 (119)
.||.|..|++.- --|.-+.-.-.|+|.
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 489999999988 778877777788875
No 19
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=40.59 E-value=29 Score=27.13 Aligned_cols=40 Identities=13% Similarity=0.027 Sum_probs=26.0
Q ss_pred EEEeeeeeeeCCCeeeeEEEEeccCCcceecCeEEEEeehhhhh
Q 033435 66 HTVEDIFCCCCGQIVGWKYVAAHDKNQKYKEGKFVLERYRIGKY 109 (119)
Q Consensus 66 H~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~i~k~ 109 (119)
..+.--+|..|++.|-+..+..-.+ -.|..+|-...+...
T Consensus 89 ~~i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllDd~ 128 (191)
T PRK05417 89 ATIQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQEQ 128 (191)
T ss_pred CCeEeeeCCCCCCccccccccccCC----CCCeEEEehhhcCCC
Confidence 3355569999999998887632111 237777776666544
No 20
>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=38.87 E-value=26 Score=19.80 Aligned_cols=19 Identities=26% Similarity=0.693 Sum_probs=12.7
Q ss_pred eeeeeecc-eeEEecCCCCcc
Q 033435 4 IFLVELKG-RSYYKCRFCNSH 23 (119)
Q Consensus 4 ~f~~yl~g-~~~y~C~~C~th 23 (119)
.-+.|..| +. +.|+.|++.
T Consensus 9 t~L~yP~gA~~-vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASS-VRCALCQTV 28 (31)
T ss_pred cEeecCCCCCe-EECCCCCeE
Confidence 34567777 55 888888764
No 21
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=34.97 E-value=20 Score=24.38 Aligned_cols=17 Identities=29% Similarity=0.761 Sum_probs=13.7
Q ss_pred eEEecCCCCccccCCCC
Q 033435 13 SYYKCRFCNSHLALADS 29 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~~ 29 (119)
+.|.|++|++.+..-+.
T Consensus 3 i~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 3 IHYYCRHCGTKIGTIDA 19 (76)
T ss_pred eEEEecCCCCEEEEeec
Confidence 35999999999876554
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=32.60 E-value=35 Score=18.58 Aligned_cols=19 Identities=32% Similarity=0.758 Sum_probs=13.5
Q ss_pred ceeeeeecc-eeEEecCCCCc
Q 033435 3 RIFLVELKG-RSYYKCRFCNS 22 (119)
Q Consensus 3 r~f~~yl~g-~~~y~C~~C~t 22 (119)
|..+.|..| +. -.|+.|++
T Consensus 5 r~~L~yp~GA~s-VrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPS-VRCACCHT 24 (25)
T ss_pred CceEEcCCCCCC-eECCccCc
Confidence 455677777 65 78888875
No 23
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.40 E-value=37 Score=21.29 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=9.2
Q ss_pred EecCCCCccc
Q 033435 15 YKCRFCNSHL 24 (119)
Q Consensus 15 y~C~~C~thL 24 (119)
|.|..|+..+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 9999999888
No 24
>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=30.43 E-value=30 Score=20.47 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=12.0
Q ss_pred EecCCCCccccCCC
Q 033435 15 YKCRFCNSHLALAD 28 (119)
Q Consensus 15 y~C~~C~thLa~~~ 28 (119)
|.|..|+.+|...+
T Consensus 27 f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 27 FKCSKCGKPLNDGD 40 (58)
T ss_dssp SBETTTTCBTTTSS
T ss_pred cccCCCCCccCCCe
Confidence 88999999987766
No 25
>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=28.19 E-value=12 Score=18.51 Aligned_cols=16 Identities=25% Similarity=0.796 Sum_probs=12.2
Q ss_pred EecCCCCccccCCCCe
Q 033435 15 YKCRFCNSHLALADSV 30 (119)
Q Consensus 15 y~C~~C~thLa~~~~l 30 (119)
|.|..|+....+.++|
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 7899998887766554
No 26
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.05 E-value=28 Score=20.05 Aligned_cols=14 Identities=29% Similarity=0.646 Sum_probs=7.2
Q ss_pred eeeeCCCeeeeEEE
Q 033435 72 FCCCCGQIVGWKYV 85 (119)
Q Consensus 72 ~C~~C~~~lGWkY~ 85 (119)
||.+|++.|-++..
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 27
>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=26.99 E-value=19 Score=22.63 Aligned_cols=39 Identities=15% Similarity=0.355 Sum_probs=25.9
Q ss_pred eecccccccCccceeeeeeecEEEeeeeeeeCCCeeeeEEEEec
Q 033435 45 FSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAH 88 (119)
Q Consensus 45 f~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~ 88 (119)
|++++++..|..+ |+...--.+-|++|.++=|---..++
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~~~~~ 40 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAPKEEF 40 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccccccC
Confidence 5678888888766 33333444569999999887543333
No 28
>COG4187 RocB Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]
Probab=25.33 E-value=50 Score=29.85 Aligned_cols=43 Identities=23% Similarity=0.315 Sum_probs=32.6
Q ss_pred ccCCCCeeeeccccCCceEEEeecccccccCccceeeeeeec--EEEeeeeeeeCCCeeeeEE
Q 033435 24 LALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGM--HTVEDIFCCCCGQIVGWKY 84 (119)
Q Consensus 24 La~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~--H~V~DI~C~~C~~~lGWkY 84 (119)
++-..|.+++.|.|..||++ .||. -.+.--+|.+|.+++|.-.
T Consensus 200 ~~IN~D~~~~~~dGd~~ryv------------------YtGtiGKLLp~f~vvG~etHvG~~f 244 (553)
T COG4187 200 AAINLDVTSDQGDGDQGRYV------------------YTGTIGKLLPFFFVVGCETHVGYPF 244 (553)
T ss_pred EEeccccccCCCCCccceEE------------------EeccchhhcceeEEEeeccccCCcc
Confidence 34567888999999999875 4554 4567788999999999654
No 29
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=25.25 E-value=56 Score=23.53 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=16.8
Q ss_pred EEEeeeeeeeCCCeeeeEEEEe
Q 033435 66 HTVEDIFCCCCGQIVGWKYVAA 87 (119)
Q Consensus 66 H~V~DI~C~~C~~~lGWkY~~A 87 (119)
+.+.-.+|..|+++|-|+....
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCCeecccCCCceEEecCCC
Confidence 3444459999999999997554
No 30
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=24.98 E-value=85 Score=22.84 Aligned_cols=30 Identities=20% Similarity=0.118 Sum_probs=25.3
Q ss_pred ccCCceEEEeecccccccCccceeeeeeec
Q 033435 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (119)
Q Consensus 36 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~ 65 (119)
+|+||.|+.--.+.|+..|...+..+.++-
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 799999999889999999998777666554
No 31
>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=23.63 E-value=32 Score=18.25 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=9.8
Q ss_pred EecCCCCcccc
Q 033435 15 YKCRFCNSHLA 25 (119)
Q Consensus 15 y~C~~C~thLa 25 (119)
|.|..|+..|+
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 89999999886
No 32
>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=23.48 E-value=9.2 Score=26.00 Aligned_cols=16 Identities=25% Similarity=0.675 Sum_probs=14.8
Q ss_pred EeeeeeeeCCCeeeeE
Q 033435 68 VEDIFCCCCGQIVGWK 83 (119)
Q Consensus 68 V~DI~C~~C~~~lGWk 83 (119)
||-+-|..|++.+|+-
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 33
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=23.22 E-value=61 Score=18.16 Aligned_cols=15 Identities=27% Similarity=0.711 Sum_probs=12.2
Q ss_pred eEEecCCCCccccCC
Q 033435 13 SYYKCRFCNSHLALA 27 (119)
Q Consensus 13 ~~y~C~~C~thLa~~ 27 (119)
+.|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 449999999988764
No 34
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=23.22 E-value=48 Score=23.93 Aligned_cols=51 Identities=27% Similarity=0.382 Sum_probs=31.7
Q ss_pred EeecccccccCccceeeeeeec--EEEeeeeeeeCCCeeeeEEE----EeccCCcceecCeE
Q 033435 44 LFSDVVNIMLGPQEERLMLSGM--HTVEDIFCCCCGQIVGWKYV----AAHDKNQKYKEGKF 99 (119)
Q Consensus 44 Lf~~vvNv~~g~~e~r~m~TG~--H~V~DI~C~~C~~~lGWkY~----~A~e~sqkYKEGkf 99 (119)
|+++--=+..|+++++. ++|. |+|.|--= --.|||.. +.-.++++|.+|-=
T Consensus 10 lLR~S~fi~lG~~~gk~-V~G~I~hvv~ddLY----IDfG~KFhcVc~rp~~~~~~y~~G~r 66 (104)
T PF10246_consen 10 LLRNSPFIQLGDPEGKI-VIGKIFHVVDDDLY----IDFGGKFHCVCKRPAVNGEKYVRGSR 66 (104)
T ss_pred HhcCChhhhcCCccCCE-EEEEEEEEecCceE----EEeCCceeEEEecccccccccccCCE
Confidence 34444445679988865 6666 87776211 23588864 34457788999853
No 35
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=22.05 E-value=1e+02 Score=23.40 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=28.3
Q ss_pred ccCCceEEEeecccccccCccceeeeeeecEE-Eeee
Q 033435 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGMHT-VEDI 71 (119)
Q Consensus 36 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~-V~DI 71 (119)
+|+||.|+.--.+.|+..|...+....++--. +.+|
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ve~~~v 85 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCDVPHV 85 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCCEEEEEEE
Confidence 79999999988999999999888777665532 4444
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.04 E-value=26 Score=18.55 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=6.2
Q ss_pred eeeeeeCCCee
Q 033435 70 DIFCCCCGQIV 80 (119)
Q Consensus 70 DI~C~~C~~~l 80 (119)
+-+|.+|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45566666543
No 37
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=20.96 E-value=1.3e+02 Score=21.32 Aligned_cols=43 Identities=14% Similarity=0.273 Sum_probs=32.0
Q ss_pred EecCCCCccccCCCCeeeeccccCCceEEEeecccccccCccce
Q 033435 15 YKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEE 58 (119)
Q Consensus 15 y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~ 58 (119)
=.|.+|+..=.-...++++.+.++. ..+...+-.|...|+..+
T Consensus 17 saC~~C~~~~~Cg~~~~~~~~~~~~-~~~~~~~~~~~~~GD~V~ 59 (135)
T PF04246_consen 17 SACGSCSASGGCGTGLLAKLFSGKP-ITFRAPNPIGAKVGDRVE 59 (135)
T ss_pred CcCcccCCCCCCCcchhhhhcCCCc-EEEEecCCCCCCCCCEEE
Confidence 4688888766667778888888877 566667777888887644
No 38
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.33 E-value=52 Score=20.79 Aligned_cols=12 Identities=33% Similarity=0.927 Sum_probs=10.0
Q ss_pred eeeeCCCeeeeE
Q 033435 72 FCCCCGQIVGWK 83 (119)
Q Consensus 72 ~C~~C~~~lGWk 83 (119)
+|.+|+..||-+
T Consensus 54 ~Cp~C~~~lg~~ 65 (67)
T smart00714 54 YCPNCGAFLGTY 65 (67)
T ss_pred ECCCCCCEeEEe
Confidence 599999999853
No 39
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=20.29 E-value=66 Score=24.58 Aligned_cols=32 Identities=22% Similarity=0.391 Sum_probs=25.9
Q ss_pred eeecceeEEecCCCCccccCCCCeeeeccccCC
Q 033435 7 VELKGRSYYKCRFCNSHLALADSVLSWSFNCRR 39 (119)
Q Consensus 7 ~yl~g~~~y~C~~C~thLa~~~~lISk~F~G~~ 39 (119)
.-++.+. |-|..|+.+=+...-|+.-.|....
T Consensus 114 ~~vsprR-YfCtQCHVPQada~PLV~N~F~~~~ 145 (149)
T PRK11586 114 AEVAPRR-YFCLQCHVPQADTAPIVGNTFTPSK 145 (149)
T ss_pred cccCccc-eeeccccCccccCccCCCCCccchh
Confidence 3344566 9999999999999999999887544
No 40
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=20.13 E-value=1.2e+02 Score=22.01 Aligned_cols=31 Identities=13% Similarity=0.036 Sum_probs=24.7
Q ss_pred cccCCceEEEeecccccccCccceeeeeeec
Q 033435 35 FNCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (119)
Q Consensus 35 F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~ 65 (119)
=+|+||.|+.--.+.|+..|...++...++-
T Consensus 33 kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d 63 (129)
T PRK03999 33 KPGKHGSAKARIVAIGIFDGQKRSLVQPVDA 63 (129)
T ss_pred cCCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 3788899998889999999987766665554
Done!