Query 030967
Match_columns 168
No_of_seqs 109 out of 325
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:15:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030967hhsearch_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 8.3E-50 1.8E-54 310.3 -4.0 109 1-109 1-111 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 1.7E-31 3.8E-36 194.7 6.9 89 13-107 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 95.7 0.0071 1.5E-07 46.9 2.2 88 13-102 4-93 (123)
4 TIGR00357 methionine-R-sulfoxi 93.4 0.078 1.7E-06 42.5 3.1 66 12-84 39-104 (134)
5 PRK00222 methionine sulfoxide 93.4 0.066 1.4E-06 43.3 2.7 67 12-85 42-108 (142)
6 PF01641 SelR: SelR domain; I 93.2 0.085 1.8E-06 41.7 2.9 70 12-88 36-105 (124)
7 PRK05508 methionine sulfoxide 92.7 0.13 2.8E-06 40.5 3.3 63 12-84 32-94 (119)
8 PRK05550 bifunctional methioni 90.2 0.23 4.9E-06 44.0 2.6 63 12-84 35-97 (283)
9 PRK14018 trifunctional thiored 88.9 0.4 8.6E-06 45.5 3.4 67 12-85 417-483 (521)
10 COG0229 Conserved domain frequ 84.7 1.3 2.7E-05 36.1 3.6 64 12-82 41-104 (140)
11 PF14976 FAM72: FAM72 protein 79.1 4.1 8.8E-05 33.5 4.7 79 12-102 14-105 (150)
12 KOG0856 Predicted pilin-like t 79.0 1.9 4.2E-05 35.2 2.8 67 10-84 51-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 61.9 12 0.00026 32.5 4.1 16 13-28 106-121 (354)
14 PRK02935 hypothetical protein; 42.4 17 0.00036 28.6 1.7 25 11-35 84-108 (110)
15 PF04828 GFA: Glutathione-depe 35.6 23 0.00051 24.0 1.4 19 64-82 43-61 (92)
16 PF11023 DUF2614: Protein of u 34.8 16 0.00035 28.8 0.5 25 12-36 84-108 (114)
17 PF02945 Endonuclease_7: Recom 30.7 16 0.00035 26.7 -0.1 16 67-82 50-65 (81)
18 PF14144 DOG1: Seed dormancy c 30.2 11 0.00023 27.4 -1.0 14 116-129 61-74 (80)
19 PF03811 Zn_Tnp_IS1: InsA N-te 29.2 33 0.00072 21.6 1.2 27 68-94 4-31 (36)
20 TIGR01053 LSD1 zinc finger dom 25.4 60 0.0013 19.8 1.8 19 4-22 9-28 (31)
21 PF10246 MRP-S35: Mitochondria 22.8 58 0.0013 25.4 1.7 49 44-97 11-65 (104)
22 COG3791 Uncharacterized conser 21.9 71 0.0015 24.7 2.1 21 65-85 65-85 (133)
23 TIGR00037 eIF_5A translation i 21.8 1E+02 0.0022 24.1 3.0 30 35-64 35-64 (130)
24 PF03242 LEA_3: Late embryogen 21.1 45 0.00098 25.1 0.8 20 107-129 60-79 (93)
25 COG5011 Uncharacterized protei 21.0 63 0.0014 28.2 1.8 29 119-147 38-66 (228)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=8.3e-50 Score=310.27 Aligned_cols=109 Identities=56% Similarity=1.015 Sum_probs=106.4
Q ss_pred CcceeeeecCC--ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCc
Q 030967 1 MGRIFVVELDG--RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQI 78 (168)
Q Consensus 1 MGr~F~~yL~g--~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~ 78 (168)
|||+|..+|++ +.|+|++|+||||.++|||||+|+|++|+||||++|+||..|+.|+|.|+||+|+|+||+|+.|++.
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 99999999999 5999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEecccCcceecCeEEEEecceeEee
Q 030967 79 VGWKYESAREKSQKYKEGKFVLERYMRYVSL 109 (168)
Q Consensus 79 LGWKYe~A~E~SQKYKEGKfILE~~~i~~~~ 109 (168)
||||||.|||+||||||||||||+++|....
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~ 111 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPE 111 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCC
Confidence 9999999999999999999999998887764
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=1.7e-31 Score=194.67 Aligned_cols=89 Identities=55% Similarity=1.001 Sum_probs=85.1
Q ss_pred eEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeec----EEEeeeeeccCCCceeeEEEEecc
Q 030967 13 SYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGM----HTVADIFCCSCGQIVGWKYESARE 88 (168)
Q Consensus 13 ~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~----H~V~DI~C~~C~t~LGWKYe~A~E 88 (168)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+|++|.+|++.|||||++|++
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 7778888899999999 999999999999999999999999
Q ss_pred cCcceecCeEEEEecceeE
Q 030967 89 KSQKYKEGKFVLERYMRYV 107 (168)
Q Consensus 89 ~SQKYKEGKfILE~~~i~~ 107 (168)
+ |+||||+||||++.|..
T Consensus 77 ~-~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASISS 94 (96)
T ss_pred h-HhhhCCEEEEEhhHEEE
Confidence 9 99999999999998864
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=95.68 E-value=0.0071 Score=46.87 Aligned_cols=88 Identities=16% Similarity=0.168 Sum_probs=58.3
Q ss_pred eEEecCCCCccCCCCCeeeeeecc--CCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEEEecccC
Q 030967 13 SYRCKFCRTHLALPEDLVSRAFHC--RRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREKS 90 (168)
Q Consensus 13 ~y~C~~C~thLA~~~eLISk~F~G--~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe~A~E~S 90 (168)
.+.|++|.+.++..+||-.-.-+. --.+. |...+.+...+++.....-+.+....|+|.+|++.+|-.+..---+=
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 478999999999999987642110 00122 33555666665554445568889999999999999998776544344
Q ss_pred cceecCeEEEEe
Q 030967 91 QKYKEGKFVLER 102 (168)
Q Consensus 91 QKYKEGKfILE~ 102 (168)
.-.|.-.|+++.
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 455666666443
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=93.43 E-value=0.078 Score=42.46 Aligned_cols=66 Identities=20% Similarity=0.360 Sum_probs=41.8
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe 84 (168)
-+|.|+.|+++|=.+++ .|....|=.-.+..+-.-.+...+|.. -|+.. ..|.|.+|+.+||--..
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----KFDSGCGWPSFYKPISEEVVAYERDES--HGMIR-TEVRCRNCDAHLGHVFD 104 (134)
T ss_pred eEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCceEEeecCC--CCcEE-EEEEecCCCCccCcccC
Confidence 78999999999987764 455555544444444111122233322 24444 57999999999997554
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=93.39 E-value=0.066 Score=43.26 Aligned_cols=67 Identities=16% Similarity=0.360 Sum_probs=42.4
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEEE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYES 85 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe~ 85 (168)
-+|.|+.|+++|=++++ .|....|=.-.+..+-.-.+...+|+. -|+.. ..|.|.+|+.+||-....
T Consensus 42 G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~D 108 (142)
T PRK00222 42 GIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDTS--HGMVR-TEVRCANCDSHLGHVFPD 108 (142)
T ss_pred eEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeeccC--CCceE-EEEEeCCCCCccCcccCC
Confidence 78999999999987743 466666655545544221222223321 13322 579999999999986643
No 6
>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=93.17 E-value=0.085 Score=41.66 Aligned_cols=70 Identities=21% Similarity=0.427 Sum_probs=43.2
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEEEecc
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESARE 88 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe~A~E 88 (168)
-+|.|+.|+++|=..+ ..|....|=.-.+..+..-.+...+|.. -|+. -..|.|.+|+.+||--......
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----TKFDSGCGWPSFWQPIPGDAVKEREDFS--HGMV-RTEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp EEEEETTTS-EEEEGG----GEETSSSSSSEESSCSSTTSEEEEEEEC--TSSE-EEEEEETTTCCEEEEEESTSST
T ss_pred EEEEcCCCCCccccCc----ccccCCcCCccccCcCChHHEEEecccc--CCce-EEEEEecCCCCccccEeCCCCC
Confidence 7899999999987655 3466666654444443332222233322 1444 4468999999999986664443
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=92.66 E-value=0.13 Score=40.53 Aligned_cols=63 Identities=27% Similarity=0.494 Sum_probs=42.7
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe 84 (168)
-+|.|+.|+++|=+.++ .|....|=.-.+..+-| .+...+|.. | + =..|.|.+|+.+||--..
T Consensus 32 G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~-~v~~~~D~~---~-~-RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 32 GTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKG-AVKRIPDAD---G-R-RTEIVCANCGGHLGHVFE 94 (119)
T ss_pred eEEEecCCCCccccccc----cccCCCCCcccCccccc-ceEEEecCC---C-c-EEEEEeCCCCCccCcccC
Confidence 78999999999987764 46666665444555533 233334443 2 2 467999999999997543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=90.18 E-value=0.23 Score=44.00 Aligned_cols=63 Identities=24% Similarity=0.438 Sum_probs=42.4
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe 84 (168)
-+|.|+.|+++|=++++ .|...+|=.-.++.+-|-.. ..++.. |+ =..|.|.+|+.+||--..
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 78999999999987654 46656665444665544322 222222 33 478999999999998654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=88.87 E-value=0.4 Score=45.54 Aligned_cols=67 Identities=9% Similarity=0.057 Sum_probs=43.2
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeEEEE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYES 85 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWKYe~ 85 (168)
-+|.|+.|+++|=+++ ..|....|=.-.+..+-+-.+...+|.+ -|++. ..|.|.+|+.+||-....
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 7899999999998875 3466666654444444322222233322 24444 479999999999986644
No 10
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=84.69 E-value=1.3 Score=36.06 Aligned_cols=64 Identities=23% Similarity=0.412 Sum_probs=42.1
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEeeeecEEEeeeeeccCCCceeeE
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWK 82 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~H~V~DI~C~~C~t~LGWK 82 (168)
-+|.|+.|+.+|=.+++ .|....|=--.+.-+.+-.+...+|+ .-|++.+ .|.|.+|+++||--
T Consensus 41 GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGHV 104 (140)
T COG0229 41 GIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGHV 104 (140)
T ss_pred ceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCccccc
Confidence 78999999999987764 45555554433444444344444443 2355443 68999999999963
No 11
>PF14976 FAM72: FAM72 protein
Probab=79.12 E-value=4.1 Score=33.49 Aligned_cols=79 Identities=27% Similarity=0.444 Sum_probs=47.6
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeeccc----CccceeEeeeec--------EEEeeeeeccCCCce
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITV----GASEERLMLSGM--------HTVADIFCCSCGQIV 79 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~----G~~e~r~m~TG~--------H~V~DI~C~~C~t~L 79 (168)
.+..|+.|++-|+... =||.|..+ .|+.. -||....-.+|. =.++|+-|..|+..|
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 5688999999887643 24555543 33321 122222223333 489999999999999
Q ss_pred eeEEEEeccc-CcceecCeEEEEe
Q 030967 80 GWKYESAREK-SQKYKEGKFVLER 102 (168)
Q Consensus 80 GWKYe~A~E~-SQKYKEGKfILE~ 102 (168)
|+.....=.. -+.-.-|.|-+=.
T Consensus 82 GYhV~~PC~~Cl~scNNGH~wmFh 105 (150)
T PF14976_consen 82 GYHVVVPCSRCLSSCNNGHFWMFH 105 (150)
T ss_pred eeEEEEEcchHhcCccCCceEEEe
Confidence 9998765321 1223467766633
No 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=79.02 E-value=1.9 Score=35.17 Aligned_cols=67 Identities=22% Similarity=0.395 Sum_probs=39.7
Q ss_pred CCceEEecCCCCccCCCCCeeeeeeccCCCceEEeceeeecccCccceeEe-eeecEEEeeeeeccCCCceeeEEE
Q 030967 10 DGRSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLM-LSGMHTVADIFCCSCGQIVGWKYE 84 (168)
Q Consensus 10 ~g~~y~C~~C~thLA~~~eLISk~F~G~~GrAyLF~~vvNV~~G~~e~r~m-~TG~H~V~DI~C~~C~t~LGWKYe 84 (168)
+.-+|.|+.|.++|-.+. .-|....|=--.|+.+- .|....+.+ .-|.| =.+|.|..|+.+||--.+
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----TKFDSGCGWPAFFEAIG---PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CCceEEEeecCCcccccc----ccccCCCCCchhhhccC---CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 337899999999997764 34665566433344331 221111111 01222 357899999999997553
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=61.93 E-value=12 Score=32.50 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=13.3
Q ss_pred eEEecCCCCccCCCCC
Q 030967 13 SYRCKFCRTHLALPED 28 (168)
Q Consensus 13 ~y~C~~C~thLA~~~e 28 (168)
.+.|++|++.|.....
T Consensus 106 ~~~C~~C~~~li~~~~ 121 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRN 121 (354)
T ss_pred EEECCCCCCcccCccc
Confidence 6999999999976644
No 14
>PRK02935 hypothetical protein; Provisional
Probab=42.37 E-value=17 Score=28.57 Aligned_cols=25 Identities=32% Similarity=0.654 Sum_probs=21.2
Q ss_pred CceEEecCCCCccCCCCCeeeeeec
Q 030967 11 GRSYRCKFCRTHLALPEDLVSRAFH 35 (168)
Q Consensus 11 g~~y~C~~C~thLA~~~eLISk~F~ 35 (168)
|++..|-+|+++|+...++--|.|+
T Consensus 84 GrvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 84 GRVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred cceeecCcCCCcCCcCccccccCcC
Confidence 3789999999999999888777664
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=35.62 E-value=23 Score=23.97 Aligned_cols=19 Identities=26% Similarity=0.448 Sum_probs=13.2
Q ss_pred cEEEeeeeeccCCCceeeE
Q 030967 64 MHTVADIFCCSCGQIVGWK 82 (168)
Q Consensus 64 ~H~V~DI~C~~C~t~LGWK 82 (168)
...+.-.+|.+|++.|.+.
T Consensus 43 ~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 43 GKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TSSCEEEEETTT--EEEEE
T ss_pred CCcCcCcccCCCCCeeecc
Confidence 3445568999999999976
No 16
>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=34.79 E-value=16 Score=28.84 Aligned_cols=25 Identities=28% Similarity=0.545 Sum_probs=21.4
Q ss_pred ceEEecCCCCccCCCCCeeeeeecc
Q 030967 12 RSYRCKFCRTHLALPEDLVSRAFHC 36 (168)
Q Consensus 12 ~~y~C~~C~thLA~~~eLISk~F~G 36 (168)
+...|-+|+++|+...++--|.|+-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 6789999999999999988887753
No 17
>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=30.68 E-value=16 Score=26.70 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=14.8
Q ss_pred EeeeeeccCCCceeeE
Q 030967 67 VADIFCCSCGQIVGWK 82 (168)
Q Consensus 67 V~DI~C~~C~t~LGWK 82 (168)
||-+-|..|++.||+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 9999999999999974
No 18
>PF14144 DOG1: Seed dormancy control
Probab=30.17 E-value=11 Score=27.41 Aligned_cols=14 Identities=50% Similarity=1.569 Sum_probs=10.9
Q ss_pred ceeccCCccCCcce
Q 030967 116 FFFWLGGWHPAGSF 129 (168)
Q Consensus 116 ~~~~~~~~~~~~~~ 129 (168)
.|-|+|||.|.-.+
T Consensus 61 ~flWiGG~RPS~~~ 74 (80)
T PF14144_consen 61 CFLWIGGWRPSELF 74 (80)
T ss_pred HHHHHhcCCHHHHH
Confidence 57899999996543
No 19
>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=29.17 E-value=33 Score=21.57 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=22.2
Q ss_pred eeeeeccCCCce-eeEEEEecccCccee
Q 030967 68 ADIFCCSCGQIV-GWKYESAREKSQKYK 94 (168)
Q Consensus 68 ~DI~C~~C~t~L-GWKYe~A~E~SQKYK 94 (168)
-||.|..|++.- --|+-+.-.-.|+|.
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 478999999988 777877777788875
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=25.43 E-value=60 Score=19.82 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=13.2
Q ss_pred eeeeecCC-ceEEecCCCCc
Q 030967 4 IFVVELDG-RSYRCKFCRTH 22 (168)
Q Consensus 4 ~F~~yL~g-~~y~C~~C~th 22 (168)
.-+.|..| +.+.|+.|++.
T Consensus 9 t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cEeecCCCCCeEECCCCCeE
Confidence 34567777 77888888764
No 21
>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=22.82 E-value=58 Score=25.35 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=29.8
Q ss_pred eceeeecccCccceeEeeeec--EEEeeeeeccCCCceeeEEE----EecccCcceecCe
Q 030967 44 FNSAVNITVGASEERLMLSGM--HTVADIFCCSCGQIVGWKYE----SAREKSQKYKEGK 97 (168)
Q Consensus 44 F~~vvNV~~G~~e~r~m~TG~--H~V~DI~C~~C~t~LGWKYe----~A~E~SQKYKEGK 97 (168)
+++--=+..|+++++. ++|. |+|.|-- ---.|||.. +.-.++++|.+|-
T Consensus 11 LR~S~fi~lG~~~gk~-V~G~I~hvv~ddL----YIDfG~KFhcVc~rp~~~~~~y~~G~ 65 (104)
T PF10246_consen 11 LRNSPFIQLGDPEGKI-VIGKIFHVVDDDL----YIDFGGKFHCVCKRPAVNGEKYVRGS 65 (104)
T ss_pred hcCChhhhcCCccCCE-EEEEEEEEecCce----EEEeCCceeEEEecccccccccccCC
Confidence 3333335578888766 5565 7776521 123588873 3445778899984
No 22
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=21.95 E-value=71 Score=24.66 Aligned_cols=21 Identities=24% Similarity=0.604 Sum_probs=15.8
Q ss_pred EEEeeeeeccCCCceeeEEEE
Q 030967 65 HTVADIFCCSCGQIVGWKYES 85 (168)
Q Consensus 65 H~V~DI~C~~C~t~LGWKYe~ 85 (168)
+.+.-.+|.+|+++|-|+...
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~ 85 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPD 85 (133)
T ss_pred CCCCCeecccCCCceEEecCC
Confidence 334444999999999997644
No 23
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=21.82 E-value=1e+02 Score=24.08 Aligned_cols=30 Identities=23% Similarity=0.108 Sum_probs=24.5
Q ss_pred ccCCCceEEeceeeecccCccceeEeeeec
Q 030967 35 HCRRGKAYLFNSAVNITVGASEERLMLSGM 64 (168)
Q Consensus 35 ~G~~GrAyLF~~vvNV~~G~~e~r~m~TG~ 64 (168)
.|+||.|+.--.+.|+..|..-+..+.++-
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 688999999899999999988776655544
No 24
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=21.08 E-value=45 Score=25.12 Aligned_cols=20 Identities=20% Similarity=0.404 Sum_probs=15.5
Q ss_pred EeeeeecccceeccCCccCCcce
Q 030967 107 VSLLYIQIPFFFWLGGWHPAGSF 129 (168)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~ 129 (168)
...-|+.||-- |||.|+.-+
T Consensus 60 ~~~~W~pDPvT---GyyrPen~~ 79 (93)
T PF03242_consen 60 EKSSWMPDPVT---GYYRPENHF 79 (93)
T ss_pred cccccccCCCC---ccccCCCCC
Confidence 34569999975 899999754
No 25
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.02 E-value=63 Score=28.21 Aligned_cols=29 Identities=34% Similarity=0.704 Sum_probs=27.0
Q ss_pred ccCCccCCcceeEeeeEEeeecceeeEee
Q 030967 119 WLGGWHPAGSFIYTVTICVSIYNRGRIVD 147 (168)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 147 (168)
.-||.||--++.+.-+.-|.+||.|.|+|
T Consensus 38 yT~GFhP~prmsia~alpvG~~ssge~fd 66 (228)
T COG5011 38 YTGGFHPHPRMSIAQALPVGIYSSGEIFD 66 (228)
T ss_pred ecCCCCCCCceeeccccccccccCceEEE
Confidence 35899999999999999999999999998
Done!