Query 032800
Match_columns 133
No_of_seqs 107 out of 330
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:07:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032800hhsearch_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-53 1.8E-57 313.7 -2.9 118 1-122 1-120 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 4.2E-33 9.2E-38 196.2 6.5 89 13-107 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.4 0.0023 4.9E-08 47.6 2.2 90 13-104 4-95 (123)
4 PF01641 SelR: SelR domain; I 94.7 0.03 6.4E-07 42.3 2.8 71 12-89 36-106 (124)
5 TIGR00357 methionine-R-sulfoxi 94.6 0.037 8E-07 42.4 3.2 68 12-86 39-106 (134)
6 PRK00222 methionine sulfoxide 94.3 0.036 7.9E-07 42.8 2.6 68 12-86 42-109 (142)
7 PRK05508 methionine sulfoxide 93.6 0.078 1.7E-06 39.9 3.2 63 12-84 32-94 (119)
8 PRK05550 bifunctional methioni 91.4 0.14 3E-06 43.4 2.3 63 12-84 35-97 (283)
9 COG0229 Conserved domain frequ 91.4 0.26 5.7E-06 38.1 3.6 87 12-108 41-127 (140)
10 PRK14018 trifunctional thiored 91.0 0.22 4.8E-06 45.3 3.4 68 12-86 417-484 (521)
11 PF14976 FAM72: FAM72 protein 89.8 0.7 1.5E-05 36.1 4.7 63 12-86 14-88 (150)
12 KOG0856 Predicted pilin-like t 84.6 0.97 2.1E-05 35.2 2.8 67 10-84 51-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 71.7 6.4 0.00014 32.8 4.2 16 13-28 106-121 (354)
14 PRK02935 hypothetical protein; 54.8 8.5 0.00018 28.8 1.7 25 11-35 84-108 (110)
15 PF04828 GFA: Glutathione-depe 49.6 11 0.00024 24.6 1.5 31 52-82 31-61 (92)
16 PF02945 Endonuclease_7: Recom 48.5 5 0.00011 28.0 -0.4 16 67-82 50-65 (81)
17 TIGR01053 LSD1 zinc finger dom 47.2 17 0.00037 21.1 1.9 19 4-22 9-28 (31)
18 COG4416 Com Mu-like prophage p 45.6 9.3 0.0002 25.6 0.6 15 12-26 3-17 (60)
19 PF11023 DUF2614: Protein of u 43.4 9.8 0.00021 28.6 0.5 24 12-35 84-107 (114)
20 TIGR02820 formald_GSH S-(hydro 41.3 37 0.00079 27.1 3.5 33 50-83 71-103 (182)
21 PF03811 Zn_Tnp_IS1: InsA N-te 40.0 18 0.00039 21.7 1.2 27 68-94 4-31 (36)
22 COG3791 Uncharacterized conser 39.7 20 0.00043 26.6 1.6 21 66-86 66-86 (133)
23 PRK05417 glutathione-dependent 36.2 71 0.0015 25.6 4.4 55 50-109 75-129 (191)
24 PRK10123 wcaM putative colanic 33.0 76 0.0017 28.2 4.4 84 34-131 186-285 (464)
25 PF06943 zf-LSD1: LSD1 zinc fi 32.5 39 0.00084 18.9 1.7 19 3-21 5-24 (25)
26 TIGR00037 eIF_5A translation i 31.1 69 0.0015 23.9 3.4 31 35-65 35-65 (130)
27 COG1996 RPC10 DNA-directed RNA 30.4 42 0.00091 21.6 1.8 12 12-23 5-16 (49)
28 PLN03107 eukaryotic translatio 29.8 72 0.0016 24.8 3.4 31 35-65 49-79 (159)
29 PF00096 zf-C2H2: Zinc finger, 27.6 11 0.00024 19.1 -1.0 16 14-29 1-16 (23)
30 PF00412 LIM: LIM domain; Int 27.6 32 0.0007 20.8 0.9 16 12-27 25-40 (58)
31 PF10955 DUF2757: Protein of u 26.5 28 0.00062 24.3 0.6 16 13-28 4-19 (76)
32 PRK03999 translation initiatio 25.9 1E+02 0.0022 23.0 3.5 30 35-64 34-63 (129)
33 PF13912 zf-C2H2_6: C2H2-type 25.5 10 0.00022 20.0 -1.5 18 13-30 1-18 (27)
34 PF14803 Nudix_N_2: Nudix N-te 25.4 40 0.00087 19.9 1.0 14 71-84 2-15 (34)
35 smart00132 LIM Zinc-binding do 23.0 32 0.0007 18.7 0.3 13 12-24 26-38 (39)
36 PF13248 zf-ribbon_3: zinc-rib 22.3 29 0.00063 18.9 0.0 12 68-79 15-26 (26)
37 PF13842 Tnp_zf-ribbon_2: DDE_ 22.0 73 0.0016 18.4 1.7 15 12-26 15-29 (32)
38 PHA02565 49 recombination endo 20.2 28 0.0006 27.5 -0.5 20 61-82 49-68 (157)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=8.3e-53 Score=313.71 Aligned_cols=118 Identities=53% Similarity=0.927 Sum_probs=114.4
Q ss_pred CcceeeeecCC--ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCc
Q 032800 1 MGRIFVVELDG--RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQI 78 (133)
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 (133)
|||+|..+|++ +.|+|++|+|||+.++|||||+|+|++|+||||++|+||..|+.|+|.|+||+|+|+||+|+.|++.
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 6999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEecccCcceecCeEEEEecceeeccccCcccccccccc
Q 032800 79 VGWKYESAREKSQKYKEGKFVLERFIFLSHIVSSNFCKHWVHEE 122 (133)
Q Consensus 79 LGWKY~~A~e~sqkYKEGkfILE~~~i~~~~~~~~~~~~~~~~~ 122 (133)
|||||+.|+|+||||||||||||+++|.+++ ++++ |+..+
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~-g~~~---~~~~~ 120 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPE-GWDL---EVGAL 120 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCC-Cchh---hcCCC
Confidence 9999999999999999999999999999999 9997 66544
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=4.2e-33 Score=196.17 Aligned_cols=89 Identities=56% Similarity=1.023 Sum_probs=85.6
Q ss_pred eEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeecc----EEEeeeeeccCCCceeeEEEEecc
Q 032800 13 SYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGM----HTVADIFCCSCGQIVGWKYESARE 88 (133)
Q Consensus 13 ~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~----H~V~DI~C~~C~~~LGWKY~~A~e 88 (133)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+||+|++|++.|||||++|++
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 8888889999999999 999999999999999999999999
Q ss_pred cCcceecCeEEEEecceee
Q 032800 89 KSQKYKEGKFVLERFIFLS 107 (133)
Q Consensus 89 ~sqkYKEGkfILE~~~i~~ 107 (133)
+ |+||||+||||++.|..
T Consensus 77 ~-~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASISS 94 (96)
T ss_pred h-HhhhCCEEEEEhhHEEE
Confidence 9 99999999999999864
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=96.36 E-value=0.0023 Score=47.61 Aligned_cols=90 Identities=16% Similarity=0.148 Sum_probs=61.4
Q ss_pred eEEecCCCCccCCCCCeeeeeecc--CCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEecccC
Q 032800 13 SYRCKFCRTHLALPEDLVSRAFHC--RRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREKS 90 (133)
Q Consensus 13 ~y~C~~C~thLa~~~~lISk~F~G--~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~LGWKY~~A~e~s 90 (133)
.+.|++|.+.++..+||-.-.-+. --.+. |...+.+...++.......+.+....|+|.+|++.+|-.+..---+=
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 478999999999999987652110 01222 33555555555553344558889999999999999999887665556
Q ss_pred cceecCeEEEEecc
Q 032800 91 QKYKEGKFVLERFI 104 (133)
Q Consensus 91 qkYKEGkfILE~~~ 104 (133)
.-.|.-.|.++...
T Consensus 82 P~L~iksfvv~~~~ 95 (123)
T PF11648_consen 82 PCLKIKSFVVELET 95 (123)
T ss_dssp EEE-GGGEEEEETT
T ss_pred cEEEeeeeeeeecC
Confidence 66777777755443
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=94.67 E-value=0.03 Score=42.30 Aligned_cols=71 Identities=21% Similarity=0.423 Sum_probs=44.7
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEeccc
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREK 89 (133)
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 (133)
-+|.|+.|+++|=+++. -|...+|=.-.++.+..-.+....|.++ |+.. ..|.|.+|+.+||=-......+
T Consensus 36 G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~v~~~~D~s~--g~~R-~Ev~C~~Cg~HLGHVF~DGp~~ 106 (124)
T PF01641_consen 36 GIYVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFSH--GMVR-TEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp EEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEECT--SSEE-EEEEETTTCCEEEEEESTSSTT
T ss_pred EEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEeccccC--CceE-EEEEecCCCCccccEeCCCCCC
Confidence 78999999999976552 4665556544344433323333344332 4443 6899999999999887755543
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=94.58 E-value=0.037 Score=42.39 Aligned_cols=68 Identities=19% Similarity=0.355 Sum_probs=43.3
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEe
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESA 86 (133)
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 86 (133)
-+|.|+.|+++|-++++ -|....|=.-.++.+-.-.+...+|++ -|+.. ..|.|.+|+.+||=-....
T Consensus 39 G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~DG 106 (134)
T TIGR00357 39 GIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEVVAYERDES--HGMIR-TEVRCRNCDAHLGHVFDDG 106 (134)
T ss_pred eEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCceEEeecCC--CCcEE-EEEEecCCCCccCcccCCC
Confidence 78999999999987764 355555543334443122223344433 24444 6899999999999776543
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.30 E-value=0.036 Score=42.81 Aligned_cols=68 Identities=16% Similarity=0.351 Sum_probs=43.4
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEe
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESA 86 (133)
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 86 (133)
-+|.|+.|+++|=++++ -|.-.+|=.-.++.+-.-.+...+|+++ |+.. ..|.|..|+.+||=.....
T Consensus 42 G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~s~--gm~R-tEv~C~~Cg~HLGHVF~DG 109 (142)
T PRK00222 42 GIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDTSH--GMVR-TEVRCANCDSHLGHVFPDG 109 (142)
T ss_pred eEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeeccCC--CceE-EEEEeCCCCCccCcccCCC
Confidence 78999999999987753 4555566544444432222333333321 3322 5899999999999877543
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.63 E-value=0.078 Score=39.93 Aligned_cols=63 Identities=27% Similarity=0.494 Sum_probs=42.7
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEE
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (133)
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 (133)
-+|.|+.|+++|=++++ -|.-..|=.-.++.+-| .+...+|.. | + =..|.|..|+.+||=-..
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 46666665443554433 233444444 2 2 467999999999997664
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.39 E-value=0.14 Score=43.42 Aligned_cols=63 Identities=25% Similarity=0.459 Sum_probs=42.1
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEE
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (133)
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 (133)
-+|.|+.|+++|=++++ -|...+|=.-.++.+-|- .-..+|.. |+ =..|.|.+|+++||--..
T Consensus 35 G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~-~~~~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 35 GVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGA-VKRLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred cEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCc-cEEEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 78999999999988654 355555544435555432 22222222 33 478999999999998775
No 9
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=91.35 E-value=0.26 Score=38.11 Aligned_cols=87 Identities=17% Similarity=0.308 Sum_probs=52.0
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEecccCc
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREKSQ 91 (133)
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~sq 91 (133)
-+|.|..|..+|=++++ -|....|=--.++-+..-.+...+|++ -|++. ..|.|.+|+++||--...--.++-
T Consensus 41 GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~S--~gM~R-tEVrc~~c~sHLGHVF~DGP~~tg 113 (140)
T COG0229 41 GIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDRS--HGMVR-TEVRCANCDSHLGHVFPDGPPPTG 113 (140)
T ss_pred ceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeeccC--CCcEE-EEEEecCCCCccccccCCCCCCCC
Confidence 78999999999987664 355555543334444444445555543 35555 579999999999965433221111
Q ss_pred ceecCeEEEEecceeec
Q 032800 92 KYKEGKFVLERFIFLSH 108 (133)
Q Consensus 92 kYKEGkfILE~~~i~~~ 108 (133)
- =+|-|.-+-|.-.
T Consensus 114 g---lRYCINSasL~Fi 127 (140)
T COG0229 114 G---LRYCINSASLRFI 127 (140)
T ss_pred C---eeEeecchheeec
Confidence 0 1455555555444
No 10
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=91.02 E-value=0.22 Score=45.25 Aligned_cols=68 Identities=10% Similarity=0.091 Sum_probs=44.3
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEe
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESA 86 (133)
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 86 (133)
-+|.|+.|+++|=++++ -|....|=.-.++.+-+-.+....|.++ |++. ..|.|..|+++||-.....
T Consensus 417 G~y~c~~c~~pLf~s~~----Kf~sg~GWPsF~~~i~~~~v~~~~d~s~--g~~R-~Ev~c~~c~~HLGHvf~dg 484 (521)
T PRK14018 417 GIYVDVVSGEPLFSSAD----KYDSGCGWPSFTRPIDAKVVTEHDDFSY--NMRR-TEVRSRAADSHLGHVFPDG 484 (521)
T ss_pred EEEEecCCCCccccCcc----cccCCCCCcccCcccCcCceEEeeccCC--CceE-EEEEECCCCCcCCcccCCC
Confidence 78999999999988753 4655566444344333222333344322 4444 4899999999999877554
No 11
>PF14976 FAM72: FAM72 protein
Probab=89.78 E-value=0.7 Score=36.14 Aligned_cols=63 Identities=30% Similarity=0.497 Sum_probs=41.1
Q ss_pred ceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccC----CCcceeEeeecc--------EEEeeeeeccCCCce
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITV----GASEERLMLSGM--------HTVADIFCCSCGQIV 79 (133)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~vvNv~~----g~~e~r~m~TG~--------H~V~DI~C~~C~~~L 79 (133)
.+..|+.|.+-|+... =||.|..+ +|+.+ -+|....-.+|. =.++|+-|.+|+..|
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 5689999999887643 24555554 34432 223323323333 259999999999999
Q ss_pred eeEEEEe
Q 032800 80 GWKYESA 86 (133)
Q Consensus 80 GWKY~~A 86 (133)
|+.....
T Consensus 82 GYhV~~P 88 (150)
T PF14976_consen 82 GYHVVVP 88 (150)
T ss_pred eeEEEEE
Confidence 9988654
No 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=84.57 E-value=0.97 Score=35.20 Aligned_cols=67 Identities=22% Similarity=0.413 Sum_probs=39.1
Q ss_pred CCceEEecCCCCccCCCCCeeeeeeccCCCceEEecceeeccCCCcceeEe-eeccEEEeeeeeccCCCceeeEEE
Q 032800 10 DGRSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLM-LSGMHTVADIFCCSCGQIVGWKYE 84 (133)
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~ 84 (133)
+.-+|.|..|.++|-.+. .-|....|=--.|+.+ + .|....+.+ .-|.| =.+|.|..|+.+||--.+
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 347899999999997764 3455555532223332 1 122111111 11222 368999999999997664
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=71.67 E-value=6.4 Score=32.82 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=13.4
Q ss_pred eEEecCCCCccCCCCC
Q 032800 13 SYRCKFCRTHLALPED 28 (133)
Q Consensus 13 ~y~C~~C~thLa~~~~ 28 (133)
.+.|++|++.|.....
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=54.77 E-value=8.5 Score=28.76 Aligned_cols=25 Identities=32% Similarity=0.654 Sum_probs=21.0
Q ss_pred CceEEecCCCCccCCCCCeeeeeec
Q 032800 11 GRSYRCKFCRTHLALPEDLVSRAFH 35 (133)
Q Consensus 11 g~~y~C~~C~thLa~~~~lISk~F~ 35 (133)
|++..|-+|++||+...++--|.|+
T Consensus 84 GrvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 84 GRVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred cceeecCcCCCcCCcCccccccCcC
Confidence 4889999999999998887766664
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=49.60 E-value=11 Score=24.59 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=17.2
Q ss_pred CCCcceeEeeeccEEEeeeeeccCCCceeeE
Q 032800 52 VGASEERLMLSGMHTVADIFCCSCGQIVGWK 82 (133)
Q Consensus 52 ~g~~e~r~m~TG~H~V~DI~C~~C~~~LGWK 82 (133)
.|+..-+........+.-.+|..|++.|.+.
T Consensus 31 ~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 31 SGSENLKEYQFSGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp E-GGGEEEC--TTSSCEEEEETTT--EEEEE
T ss_pred eccccceEEEeCCCcCcCcccCCCCCeeecc
Confidence 3544444444234445669999999999977
No 16
>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=48.47 E-value=5 Score=28.03 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=14.8
Q ss_pred EeeeeeccCCCceeeE
Q 032800 67 VADIFCCSCGQIVGWK 82 (133)
Q Consensus 67 V~DI~C~~C~~~LGWK 82 (133)
||-+-|..|++.||+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 8999999999999975
No 17
>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=47.18 E-value=17 Score=21.13 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=14.3
Q ss_pred eeeeecCC-ceEEecCCCCc
Q 032800 4 IFVVELDG-RSYRCKFCRTH 22 (133)
Q Consensus 4 ~f~~yl~g-~~y~C~~C~th 22 (133)
.-+.|..| +.+.|+.|++.
T Consensus 9 t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cEeecCCCCCeEECCCCCeE
Confidence 45677778 88888888764
No 18
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=45.56 E-value=9.3 Score=25.59 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=11.0
Q ss_pred ceEEecCCCCccCCC
Q 032800 12 RSYRCKFCRTHLALP 26 (133)
Q Consensus 12 ~~y~C~~C~thLa~~ 26 (133)
+..+|++|..-||-.
T Consensus 3 ~tiRC~~CnKlLa~a 17 (60)
T COG4416 3 QTIRCAKCNKLLAEA 17 (60)
T ss_pred eeeehHHHhHHHHhc
Confidence 467888888877653
No 19
>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=43.40 E-value=9.8 Score=28.60 Aligned_cols=24 Identities=29% Similarity=0.609 Sum_probs=20.8
Q ss_pred ceEEecCCCCccCCCCCeeeeeec
Q 032800 12 RSYRCKFCRTHLALPEDLVSRAFH 35 (133)
Q Consensus 12 ~~y~C~~C~thLa~~~~lISk~F~ 35 (133)
+...|-+|++||+...++--|.|+
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~ 107 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFD 107 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhh
Confidence 678999999999999888777765
No 20
>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=41.28 E-value=37 Score=27.15 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=20.2
Q ss_pred ccCCCcceeEeeeccEEEeeeeeccCCCceeeEE
Q 032800 50 ITVGASEERLMLSGMHTVADIFCCSCGQIVGWKY 83 (133)
Q Consensus 50 v~~g~~e~r~m~TG~H~V~DI~C~~C~~~LGWKY 83 (133)
+..|+...+....|.+..+ -||..|++.|-++.
T Consensus 71 i~~G~~~l~~Y~ss~~~~R-~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 71 VTANGDKLKVVDASATIQR-HACKGCGTHMYGRI 103 (182)
T ss_pred EecCCcceEEEeCCCCEEe-ecCCCCCCcccccc
Confidence 4345544333344555444 49999999996654
No 21
>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=39.98 E-value=18 Score=21.68 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=22.5
Q ss_pred eeeeeccCCCce-eeEEEEecccCccee
Q 032800 68 ADIFCCSCGQIV-GWKYESAREKSQKYK 94 (133)
Q Consensus 68 ~DI~C~~C~~~L-GWKY~~A~e~sqkYK 94 (133)
-||.|..|++.- --|+-+...-.|+|.
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 489999999998 778888887888874
No 22
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=39.66 E-value=20 Score=26.60 Aligned_cols=21 Identities=24% Similarity=0.626 Sum_probs=16.3
Q ss_pred EEeeeeeccCCCceeeEEEEe
Q 032800 66 TVADIFCCSCGQIVGWKYESA 86 (133)
Q Consensus 66 ~V~DI~C~~C~~~LGWKY~~A 86 (133)
.+.-.+|..|+++|-|+....
T Consensus 66 ~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 66 SAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCeecccCCCceEEecCCC
Confidence 344449999999999997554
No 23
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=36.21 E-value=71 Score=25.64 Aligned_cols=55 Identities=13% Similarity=0.112 Sum_probs=32.4
Q ss_pred ccCCCcceeEeeeccEEEeeeeeccCCCceeeEEEEecccCcceecCeEEEEecceeecc
Q 032800 50 ITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREKSQKYKEGKFVLERFIFLSHI 109 (133)
Q Consensus 50 v~~g~~e~r~m~TG~H~V~DI~C~~C~~~LGWKY~~A~e~sqkYKEGkfILE~~~i~~~~ 109 (133)
++.|+...+...+|. .++--+|..|++.|-++++....+ -.|..+|-...+-.+.
T Consensus 75 it~g~~~l~~y~ss~-~i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllDd~~ 129 (191)
T PRK05417 75 VTANGDKLKVVDESA-TIQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQEQG 129 (191)
T ss_pred EEeCCcceEEEeCCC-CeEeeeCCCCCCccccccccccCC----CCCeEEEehhhcCCCC
Confidence 333544433333333 355559999999998887633111 2377777777765543
No 24
>PRK10123 wcaM putative colanic acid biosynthesis protein; Provisional
Probab=33.01 E-value=76 Score=28.22 Aligned_cols=84 Identities=27% Similarity=0.408 Sum_probs=56.7
Q ss_pred eccCCCceEEecceeeccCCCcceeEeeeccEEEeeeeeccCCCcee-------eEEEEecccCcceecCeEEEEe----
Q 032800 34 FHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVG-------WKYESAREKSQKYKEGKFVLER---- 102 (133)
Q Consensus 34 F~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~LG-------WKY~~A~e~sqkYKEGkfILE~---- 102 (133)
|+.-.|.|.-.+-++| ||..+---|++..|.|.+=+..+| =.|+.+|-++|..| .|++-.
T Consensus 186 fs~lqgdaiewnvain-------dr~ilisdhvie~inctngkinwgigiglagstydn~ype~q~vk--nfvvanitgs 256 (464)
T PRK10123 186 FSDLQGDAIEWNVAIN-------DRDILISDHVIERINCTNGKINWGIGIGLAGSTYDNNYPEDQAVK--NFVVANITGS 256 (464)
T ss_pred cccccCceEEEEEEec-------ccceeeehheheeecccCCcccceeeeeeccccccCCCchhhhhh--hEEEEeccCc
Confidence 4445555655444443 677888889999999998877765 37899999999888 466532
Q ss_pred ---cceeeccccCcccccccc--cccccccccce
Q 032800 103 ---FIFLSHIVSSNFCKHWVH--EESHNVVPAFL 131 (133)
Q Consensus 103 ---~~i~~~~~~~~~~~~~~~--~~~~~~~~~~~ 131 (133)
..+..+| | +|+++ -.|+||.|.|-
T Consensus 257 ~crqlvhven-g----khfvirnvkaknitpdfs 285 (464)
T PRK10123 257 DCRQLIHVEN-G----KHFVIRNIKAKNITPDFS 285 (464)
T ss_pred ChhheEEecC-C----cEEEEEeeeccccCCCch
Confidence 2222233 3 35555 57899999884
No 25
>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=32.51 E-value=39 Score=18.95 Aligned_cols=19 Identities=37% Similarity=0.712 Sum_probs=14.6
Q ss_pred ceeeeecCC-ceEEecCCCC
Q 032800 3 RIFVVELDG-RSYRCKFCRT 21 (133)
Q Consensus 3 r~f~~yl~g-~~y~C~~C~t 21 (133)
|..+.|..| +.-.|+.|++
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 26
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=31.08 E-value=69 Score=23.91 Aligned_cols=31 Identities=23% Similarity=0.111 Sum_probs=25.9
Q ss_pred ccCCCceEEecceeeccCCCcceeEeeeccE
Q 032800 35 HCRRGKAYLFNSAVNITVGASEERLMLSGMH 65 (133)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H 65 (133)
.|+||.|+.--++.|+..|...+..+.++--
T Consensus 35 pGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ 65 (130)
T TIGR00037 35 PGKHGHAKARVVAIGIFTGKKLEFVSPSTSK 65 (130)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEECCCCE
Confidence 6999999999999999999988877665543
No 27
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.38 E-value=42 Score=21.63 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=10.4
Q ss_pred ceEEecCCCCcc
Q 032800 12 RSYRCKFCRTHL 23 (133)
Q Consensus 12 ~~y~C~~C~thL 23 (133)
..|.|..|+..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 579999999888
No 28
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=29.78 E-value=72 Score=24.83 Aligned_cols=31 Identities=23% Similarity=0.256 Sum_probs=26.9
Q ss_pred ccCCCceEEecceeeccCCCcceeEeeeccE
Q 032800 35 HCRRGKAYLFNSAVNITVGASEERLMLSGMH 65 (133)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~H 65 (133)
.|+||.|+.--.+.|+..|...++...++--
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ 79 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSHN 79 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCCE
Confidence 7999999999999999999998888766653
No 29
>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=27.58 E-value=11 Score=19.11 Aligned_cols=16 Identities=25% Similarity=0.825 Sum_probs=12.2
Q ss_pred EEecCCCCccCCCCCe
Q 032800 14 YRCKFCRTHLALPEDL 29 (133)
Q Consensus 14 y~C~~C~thLa~~~~l 29 (133)
|.|..|+..+...++|
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 7899999887766554
No 30
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=27.56 E-value=32 Score=20.82 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=13.1
Q ss_pred ceEEecCCCCccCCCC
Q 032800 12 RSYRCKFCRTHLALPE 27 (133)
Q Consensus 12 ~~y~C~~C~thLa~~~ 27 (133)
.-|.|..|+.+|...+
T Consensus 25 ~Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGD 40 (58)
T ss_dssp TTSBETTTTCBTTTSS
T ss_pred cccccCCCCCccCCCe
Confidence 5588999999987766
No 31
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=26.47 E-value=28 Score=24.31 Aligned_cols=16 Identities=25% Similarity=0.735 Sum_probs=13.2
Q ss_pred eEEecCCCCccCCCCC
Q 032800 13 SYRCKFCRTHLALPED 28 (133)
Q Consensus 13 ~y~C~~C~thLa~~~~ 28 (133)
.|.|++|++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999876655
No 32
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=25.87 E-value=1e+02 Score=23.02 Aligned_cols=30 Identities=17% Similarity=0.065 Sum_probs=24.9
Q ss_pred ccCCCceEEecceeeccCCCcceeEeeecc
Q 032800 35 HCRRGKAYLFNSAVNITVGASEERLMLSGM 64 (133)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~ 64 (133)
.|+||.|+.--++.|+..|...++...++-
T Consensus 34 pGkhg~a~vr~k~knL~tG~~~e~~~~s~d 63 (129)
T PRK03999 34 PGKHGSAKARIVAIGIFDGQKRSLVQPVDA 63 (129)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 688999998889999999988777766654
No 33
>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=25.49 E-value=10 Score=20.04 Aligned_cols=18 Identities=17% Similarity=0.462 Sum_probs=13.3
Q ss_pred eEEecCCCCccCCCCCee
Q 032800 13 SYRCKFCRTHLALPEDLV 30 (133)
Q Consensus 13 ~y~C~~C~thLa~~~~lI 30 (133)
+|.|..|+.-+.+.+.++
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 589999998777655543
No 34
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.43 E-value=40 Score=19.92 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=7.2
Q ss_pred eeccCCCceeeEEE
Q 032800 71 FCCSCGQIVGWKYE 84 (133)
Q Consensus 71 ~C~~C~~~LGWKY~ 84 (133)
||..|++.|-++..
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 35
>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=23.03 E-value=32 Score=18.73 Aligned_cols=13 Identities=23% Similarity=0.784 Sum_probs=10.9
Q ss_pred ceEEecCCCCccC
Q 032800 12 RSYRCKFCRTHLA 24 (133)
Q Consensus 12 ~~y~C~~C~thLa 24 (133)
.-|.|..|+..|+
T Consensus 26 ~Cf~C~~C~~~L~ 38 (39)
T smart00132 26 ECFKCSKCGKPLG 38 (39)
T ss_pred cCCCCcccCCcCc
Confidence 4589999999886
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.27 E-value=29 Score=18.88 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=7.3
Q ss_pred eeeeeccCCCce
Q 032800 68 ADIFCCSCGQIV 79 (133)
Q Consensus 68 ~DI~C~~C~~~L 79 (133)
.+-+|..|++.|
T Consensus 15 ~~~fC~~CG~~L 26 (26)
T PF13248_consen 15 DAKFCPNCGAKL 26 (26)
T ss_pred ccccChhhCCCC
Confidence 355677776654
No 37
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=22.04 E-value=73 Score=18.37 Aligned_cols=15 Identities=27% Similarity=0.665 Sum_probs=12.5
Q ss_pred ceEEecCCCCccCCC
Q 032800 12 RSYRCKFCRTHLALP 26 (133)
Q Consensus 12 ~~y~C~~C~thLa~~ 26 (133)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 569999999888764
No 38
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=20.20 E-value=28 Score=27.53 Aligned_cols=20 Identities=25% Similarity=0.557 Sum_probs=17.2
Q ss_pred eeccEEEeeeeeccCCCceeeE
Q 032800 61 LSGMHTVADIFCCSCGQIVGWK 82 (133)
Q Consensus 61 ~TG~H~V~DI~C~~C~~~LGWK 82 (133)
.||. ||-+-|..|+..+|+-
T Consensus 49 ~TG~--VRGLLC~~CN~~lG~~ 68 (157)
T PHA02565 49 NAGR--VRGLLCNLCNALEGQM 68 (157)
T ss_pred cccc--ccccCchhhhhhhhhh
Confidence 3565 8999999999999986
Done!