Query 033087
Match_columns 128
No_of_seqs 107 out of 329
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:39:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033087hhsearch_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 5.3E-52 1.1E-56 306.4 -3.3 111 1-111 1-113 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 5.3E-33 1.2E-37 194.3 6.5 89 13-107 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.2 0.0024 5.3E-08 47.0 1.4 87 13-103 4-94 (123)
4 PF01641 SelR: SelR domain; I 94.7 0.034 7.5E-07 41.5 3.3 70 12-88 36-105 (124)
5 TIGR00357 methionine-R-sulfoxi 94.4 0.043 9.4E-07 41.6 3.1 66 12-84 39-104 (134)
6 PRK00222 methionine sulfoxide 94.1 0.047 1E-06 41.8 2.9 67 12-85 42-108 (142)
7 PRK05508 methionine sulfoxide 93.3 0.092 2E-06 39.2 3.1 63 12-84 32-94 (119)
8 PRK05550 bifunctional methioni 91.3 0.16 3.5E-06 42.7 2.5 63 12-84 35-97 (283)
9 PRK14018 trifunctional thiored 90.5 0.28 6E-06 44.3 3.5 67 12-85 417-483 (521)
10 KOG0856 Predicted pilin-like t 85.9 1.3 2.7E-05 34.2 3.9 67 10-84 51-118 (146)
11 PF14976 FAM72: FAM72 protein 85.0 2.3 4.9E-05 33.0 5.0 77 12-100 14-103 (150)
12 COG0229 Conserved domain frequ 83.7 1.7 3.7E-05 33.3 3.8 63 12-81 41-103 (140)
13 PF09814 HECT_2: HECT-like Ubi 71.6 6.4 0.00014 32.5 4.2 16 13-28 106-121 (354)
14 PF04828 GFA: Glutathione-depe 54.6 10 0.00022 24.5 2.0 61 40-108 17-79 (92)
15 PRK02935 hypothetical protein; 53.8 8.9 0.00019 28.3 1.7 25 11-35 84-108 (110)
16 COG4416 Com Mu-like prophage p 46.9 9.3 0.0002 25.3 0.8 15 12-26 3-17 (60)
17 PF11023 DUF2614: Protein of u 46.5 8.2 0.00018 28.7 0.5 25 12-36 84-108 (114)
18 COG3791 Uncharacterized conser 46.2 14 0.00031 27.1 1.8 22 65-86 65-86 (133)
19 PLN03107 eukaryotic translatio 42.0 36 0.00078 26.2 3.5 31 35-65 49-79 (159)
20 TIGR01053 LSD1 zinc finger dom 40.6 25 0.00055 20.2 1.9 19 4-22 9-28 (31)
21 TIGR00037 eIF_5A translation i 40.0 29 0.00063 25.7 2.6 31 35-65 35-65 (130)
22 TIGR02820 formald_GSH S-(hydro 38.9 43 0.00094 26.5 3.6 31 52-83 73-103 (182)
23 PF14803 Nudix_N_2: Nudix N-te 37.7 19 0.00041 21.1 1.0 14 71-84 2-15 (34)
24 PF03811 Zn_Tnp_IS1: InsA N-te 34.9 25 0.00054 20.8 1.3 27 68-94 4-31 (36)
25 PF02945 Endonuclease_7: Recom 34.7 11 0.00025 25.9 -0.3 16 67-82 50-65 (81)
26 PF10955 DUF2757: Protein of u 32.4 23 0.0005 24.5 0.9 16 13-28 4-19 (76)
27 PF09855 DUF2082: Nucleic-acid 32.3 86 0.0019 20.8 3.7 12 66-77 33-44 (64)
28 COG1996 RPC10 DNA-directed RNA 31.5 39 0.00085 21.5 1.8 12 12-23 5-16 (49)
29 PRK05417 glutathione-dependent 29.6 67 0.0014 25.5 3.3 39 67-109 91-129 (191)
30 PF13248 zf-ribbon_3: zinc-rib 28.0 20 0.00042 19.4 -0.0 11 69-79 16-26 (26)
31 PF06943 zf-LSD1: LSD1 zinc fi 28.0 52 0.0011 18.2 1.7 19 3-21 5-24 (25)
32 PF13240 zinc_ribbon_2: zinc-r 25.5 23 0.00051 18.8 0.0 10 70-79 14-23 (23)
33 PF00412 LIM: LIM domain; Int 25.3 40 0.00086 20.2 1.0 16 12-27 25-40 (58)
34 PF00096 zf-C2H2: Zinc finger, 24.6 14 0.00031 18.5 -0.9 16 14-29 1-16 (23)
35 PRK03999 translation initiatio 24.1 98 0.0021 22.8 3.1 30 35-64 34-63 (129)
36 PF13842 Tnp_zf-ribbon_2: DDE_ 22.6 70 0.0015 18.2 1.6 15 12-26 15-29 (32)
37 PF13912 zf-C2H2_6: C2H2-type 22.5 13 0.00029 19.4 -1.3 17 13-29 1-17 (27)
38 smart00132 LIM Zinc-binding do 22.0 34 0.00074 18.4 0.3 13 12-24 26-38 (39)
39 PF06397 Desulfoferrod_N: Desu 21.7 51 0.0011 19.7 1.0 12 12-23 5-16 (36)
40 PF04246 RseC_MucC: Positive r 20.7 1.3E+02 0.0027 21.7 3.1 47 12-59 15-61 (135)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=5.3e-52 Score=306.43 Aligned_cols=111 Identities=56% Similarity=1.032 Sum_probs=109.0
Q ss_pred CcceeeeecCC--ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCc
Q 033087 1 MGRIFVVELDG--RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQI 78 (128)
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 (128)
|||+|..+|++ +.|+|++|+|||+.++|||||+|+|++|+||||++|+||..|++|+|.|+||+|+|+||+|+.|++.
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 eeeEEEEecccCcceecCeEEEEecceecccCC
Q 033087 79 VGWKYESAREKSQKYKEGKFVLERGRIVDEIDF 111 (128)
Q Consensus 79 lGWkY~~A~e~sqkYKEGkfILE~~~l~~~~~~ 111 (128)
|||||+.|||+||||||||||||+++|.+++++
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~ 113 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPEGW 113 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCCCc
Confidence 999999999999999999999999999999874
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=5.3e-33 Score=194.26 Aligned_cols=89 Identities=56% Similarity=1.048 Sum_probs=85.5
Q ss_pred eEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeec----EEEeeeeeccCCCceeeEEEEecc
Q 033087 13 SYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGM----HTVADIFCCSCGQIVGWKYESARE 88 (128)
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 (128)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..++++++.|+||. |+|+||+|++|++.|||||++|++
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 8888888999999999 999999999999999999999999
Q ss_pred cCcceecCeEEEEecceec
Q 033087 89 KSQKYKEGKFVLERGRIVD 107 (128)
Q Consensus 89 ~sqkYKEGkfILE~~~l~~ 107 (128)
+ |+||||+||||++.|..
T Consensus 77 ~-~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASISS 94 (96)
T ss_pred h-HhhhCCEEEEEhhHEEE
Confidence 9 99999999999999863
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=96.15 E-value=0.0024 Score=47.03 Aligned_cols=87 Identities=16% Similarity=0.195 Sum_probs=59.2
Q ss_pred eEEecCCCcccCCCCCeeeeeecCCC----CeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEEEecc
Q 033087 13 SYRCKFCRTHLALPEDLVSRAFHCRR----GKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESARE 88 (128)
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 (128)
.+.|++|.+.++..+||-.-. +.| .+. |...+.+...|+.......+.+....|+|.+|++.+|-.+..---
T Consensus 4 ~llC~kC~~~~C~~~DIr~ie--~~hhv~v~p~--F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m~yk~~ 79 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKIE--NSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMKYKGV 79 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEET--TTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEEETTE
T ss_pred EEECCCCCceeEchhheEEec--CCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheEECCc
Confidence 478999999999999987641 111 112 234555666555534445577889999999999999998766544
Q ss_pred cCcceecCeEEEEec
Q 033087 89 KSQKYKEGKFVLERG 103 (128)
Q Consensus 89 ~sqkYKEGkfILE~~ 103 (128)
+=.-.|.-.|+++..
T Consensus 80 ~LP~L~iksfvv~~~ 94 (123)
T PF11648_consen 80 ELPCLKIKSFVVELE 94 (123)
T ss_dssp EEEEE-GGGEEEEET
T ss_pred cccEEEeeeeeeeec
Confidence 455666677775443
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=94.75 E-value=0.034 Score=41.55 Aligned_cols=70 Identities=21% Similarity=0.436 Sum_probs=43.5
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEEEecc
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYESARE 88 (128)
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 88 (128)
-+|.|+.|.++|=.++ ..|....|=.-.+..+..-.+...+|.. -|+.. ..|.|.+|+.+||--......
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--HGMVR-TEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp EEEEETTTS-EEEEGG----GEETSSSSSSEESSCSSTTSEEEEEEEC--TSSEE-EEEEETTTCCEEEEEESTSST
T ss_pred EEEEcCCCCCccccCc----ccccCCcCCccccCcCChHHEEEecccc--CCceE-EEEEecCCCCccccEeCCCCC
Confidence 7899999999987655 3466566654444444332333333322 24444 468999999999986664443
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=94.36 E-value=0.043 Score=41.57 Aligned_cols=66 Identities=20% Similarity=0.360 Sum_probs=41.4
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (128)
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 (128)
-+|.|+.|.++|-.+++ .|....|=.-.+..+-.-.+...+|.. -|+.. ..|.|.+|+.+||--..
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 355555544334444111122333322 24444 57999999999998554
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.11 E-value=0.047 Score=41.77 Aligned_cols=67 Identities=16% Similarity=0.360 Sum_probs=42.0
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEEE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYES 85 (128)
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 (128)
-+|.|+.|.++|=++++ .|....|=.-.+..+-.-.+...+|+. -|+.. ..|.|..|+.+||-....
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 466666654444444222222222321 13332 579999999999986643
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.28 E-value=0.092 Score=39.16 Aligned_cols=63 Identities=27% Similarity=0.490 Sum_probs=42.1
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (128)
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 (128)
-+|.|+.|.++|=.+++ .|....|=.-.+..+-| .+...+|.. | .=..|.|..|+.+||--..
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--RRTEIVCANCGGHLGHVFE 94 (119)
T ss_pred eEEEecCCCCccccccc----cccCCCCCcccCccccc-ceEEEecCC---C--cEEEEEeCCCCCccCcccC
Confidence 78999999999987754 46666665444554433 233333433 2 2467999999999998543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.26 E-value=0.16 Score=42.65 Aligned_cols=63 Identities=24% Similarity=0.438 Sum_probs=41.7
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYE 84 (128)
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 (128)
-+|.|+.|+++|=++++ .|....|=.-.++.+-|-.. ..++.. |+ -..|.|..|+.+||--..
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 46555555444555544222 222222 33 478999999999998654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.53 E-value=0.28 Score=44.26 Aligned_cols=67 Identities=9% Similarity=0.057 Sum_probs=42.7
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceeeEEEE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGWKYES 85 (128)
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 (128)
-+|.|+.|+++|=++. ..|....|=.-.+..+-+-.+...+|.. -|++. ..|.|..|+.+||-....
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 3466666654434433222222223322 24444 379999999999986643
No 10
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=85.85 E-value=1.3 Score=34.22 Aligned_cols=67 Identities=22% Similarity=0.409 Sum_probs=38.6
Q ss_pred CCceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEee-eecEEEeeeeeccCCCceeeEEE
Q 033087 10 DGRSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLML-SGMHTVADIFCCSCGQIVGWKYE 84 (128)
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 (128)
+.-+|.|..|.++|-.+. .-|....|=--.|+.+ + .|....+.+. -|.+ =.+|.|..|+.+||--.+
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 3455555532223322 1 2221111111 1222 357899999999997543
No 11
>PF14976 FAM72: FAM72 protein
Probab=84.96 E-value=2.3 Score=32.98 Aligned_cols=77 Identities=27% Similarity=0.469 Sum_probs=47.4
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEeccccccc----CccceeEeeeec--------EEEeeeeeccCCCce
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITV----GASEERLMLSGM--------HTVADIFCCSCGQIV 79 (128)
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 (128)
.+..|+.|.+-|+... =||.|... .|+.+ -||....-.+|. =.++|+-|..|+..|
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 5688999999887543 24555554 33332 123322223333 459999999999999
Q ss_pred eeEEEEeccc-CcceecCeEEE
Q 033087 80 GWKYESAREK-SQKYKEGKFVL 100 (128)
Q Consensus 80 GWkY~~A~e~-sqkYKEGkfIL 100 (128)
|+-+...-.. -+.-.-|.|-+
T Consensus 82 GYhV~~PC~~Cl~scNNGH~wm 103 (150)
T PF14976_consen 82 GYHVVVPCSRCLSSCNNGHFWM 103 (150)
T ss_pred eeEEEEEcchHhcCccCCceEE
Confidence 9998875432 12234666665
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=83.75 E-value=1.7 Score=33.31 Aligned_cols=63 Identities=24% Similarity=0.428 Sum_probs=40.7
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeEeeeecEEEeeeeeccCCCceee
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERLMLSGMHTVADIFCCSCGQIVGW 81 (128)
Q Consensus 12 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGW 81 (128)
-+|.|+.|..+|-.+++ .|....|=--.+.-+..-.+...+|+ .-|++.+ .|.|.+|+++||-
T Consensus 41 GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGH 103 (140)
T COG0229 41 GIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGH 103 (140)
T ss_pred ceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCcccc
Confidence 78999999999977654 35555554333343333333333332 2355544 6899999999997
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=71.56 E-value=6.4 Score=32.54 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=13.3
Q ss_pred eEEecCCCcccCCCCC
Q 033087 13 SYRCKFCRTHLALPED 28 (128)
Q Consensus 13 ~y~C~~C~thLa~~~~ 28 (128)
.+.|++|++.|.....
T Consensus 106 ~~~C~~C~~~li~~~~ 121 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRN 121 (354)
T ss_pred EEECCCCCCcccCccc
Confidence 6999999999976644
No 14
>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=54.56 E-value=10 Score=24.54 Aligned_cols=61 Identities=15% Similarity=0.190 Sum_probs=28.4
Q ss_pred eEEEEecccccc--cCccceeEeeeecEEEeeeeeccCCCceeeEEEEecccCcceecCeEEEEecceecc
Q 033087 40 KAYLFNSAVNIT--VGASEERLMLSGMHTVADIFCCSCGQIVGWKYESAREKSQKYKEGKFVLERGRIVDE 108 (128)
Q Consensus 40 ~AyLf~~vvNv~--~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~l~~~ 108 (128)
.+++.-..-++. .|...-+........+.-.+|..|+++|.+.. .-..+.+.|-...|-..
T Consensus 17 ~~~~~~~~~~~~~~~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~~--------~~~~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 17 SAWAIVPKDDFRWTSGSENLKEYQFSGKGVERYFCPTCGSPLFSED--------ERDPDLVGVNAGTLDDP 79 (92)
T ss_dssp EEEEEEEGGGEEEEE-GGGEEEC--TTSSCEEEEETTT--EEEEEE--------SSTTTEEEEEGGGBTT-
T ss_pred eeEEEEcccceEEeeccccceEEEeCCCcCcCcccCCCCCeeeccc--------CCCCCEEEEEeEeeCCC
Confidence 333333333444 34333333331333455689999999999862 12234555555555443
No 15
>PRK02935 hypothetical protein; Provisional
Probab=53.76 E-value=8.9 Score=28.33 Aligned_cols=25 Identities=32% Similarity=0.654 Sum_probs=21.0
Q ss_pred CceEEecCCCcccCCCCCeeeeeec
Q 033087 11 GRSYRCKFCRTHLALPEDLVSRAFH 35 (128)
Q Consensus 11 g~~y~C~~C~thLa~~~~liSk~f~ 35 (128)
|++..|-+|++||+...++--|.|+
T Consensus 84 GrvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 84 GRVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred cceeecCcCCCcCCcCccccccCcC
Confidence 3889999999999998887766664
No 16
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=46.89 E-value=9.3 Score=25.28 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=10.9
Q ss_pred ceEEecCCCcccCCC
Q 033087 12 RSYRCKFCRTHLALP 26 (128)
Q Consensus 12 ~~y~C~~C~thLa~~ 26 (128)
+..+|++|..-||-.
T Consensus 3 ~tiRC~~CnKlLa~a 17 (60)
T COG4416 3 QTIRCAKCNKLLAEA 17 (60)
T ss_pred eeeehHHHhHHHHhc
Confidence 467888888777754
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=46.49 E-value=8.2 Score=28.71 Aligned_cols=25 Identities=28% Similarity=0.545 Sum_probs=21.3
Q ss_pred ceEEecCCCcccCCCCCeeeeeecC
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHC 36 (128)
Q Consensus 12 ~~y~C~~C~thLa~~~~liSk~f~G 36 (128)
++..|-+|++||+...++--|.|+-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 6789999999999999888777753
No 18
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=46.23 E-value=14 Score=27.11 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=16.3
Q ss_pred EEEeeeeeccCCCceeeEEEEe
Q 033087 65 HTVADIFCCSCGQIVGWKYESA 86 (128)
Q Consensus 65 h~V~DI~C~~C~~~lGWkY~~A 86 (128)
..+.-.||..|+++|-|+....
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCCeecccCCCceEEecCCC
Confidence 3344449999999999976543
No 19
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=41.95 E-value=36 Score=26.24 Aligned_cols=31 Identities=23% Similarity=0.256 Sum_probs=27.1
Q ss_pred cCCCCeEEEEecccccccCccceeEeeeecE
Q 033087 35 HCRRGKAYLFNSAVNITVGASEERLMLSGMH 65 (128)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~h 65 (128)
.|+||.|+.--.+.|+..|...+..+.++--
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 7999999999999999999998888776654
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=40.64 E-value=25 Score=20.17 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=13.4
Q ss_pred eeeeecCC-ceEEecCCCcc
Q 033087 4 IFVVELDG-RSYRCKFCRTH 22 (128)
Q Consensus 4 ~f~~yl~g-~~y~C~~C~th 22 (128)
.-+.|..| +.+.|+.|++.
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
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=40.02 E-value=29 Score=25.71 Aligned_cols=31 Identities=23% Similarity=0.111 Sum_probs=26.1
Q ss_pred cCCCCeEEEEecccccccCccceeEeeeecE
Q 033087 35 HCRRGKAYLFNSAVNITVGASEERLMLSGMH 65 (128)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~h 65 (128)
.|+||.|+.--++.|+..|...+..+.++--
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 6999999999999999999988777766553
No 22
>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=38.86 E-value=43 Score=26.45 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=18.5
Q ss_pred cCccceeEeeeecEEEeeeeeccCCCceeeEE
Q 033087 52 VGASEERLMLSGMHTVADIFCCSCGQIVGWKY 83 (128)
Q Consensus 52 ~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY 83 (128)
.|...-+....|.+..+ -||..|++.|-++.
T Consensus 73 ~G~~~l~~Y~ss~~~~R-~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 73 ANGDKLKVVDASATIQR-HACKGCGTHMYGRI 103 (182)
T ss_pred cCCcceEEEeCCCCEEe-ecCCCCCCcccccc
Confidence 35433333334444444 49999999996644
No 23
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.66 E-value=19 Score=21.10 Aligned_cols=14 Identities=29% Similarity=0.738 Sum_probs=7.3
Q ss_pred eeccCCCceeeEEE
Q 033087 71 FCCSCGQIVGWKYE 84 (128)
Q Consensus 71 ~C~~C~~~lGWkY~ 84 (128)
||.+|++.|-++..
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 79999999988875
No 24
>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=34.92 E-value=25 Score=20.80 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=21.3
Q ss_pred eeeeeccCCCce-eeEEEEecccCccee
Q 033087 68 ADIFCCSCGQIV-GWKYESAREKSQKYK 94 (128)
Q Consensus 68 ~DI~C~~C~~~l-GWkY~~A~e~sqkYK 94 (128)
-+|.|..|++.- --|+-+.-.-.|+|.
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 677777777777774
No 25
>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=34.67 E-value=11 Score=25.94 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=14.7
Q ss_pred EeeeeeccCCCceeeE
Q 033087 67 VADIFCCSCGQIVGWK 82 (128)
Q Consensus 67 V~DI~C~~C~~~lGWk 82 (128)
||-+-|..|++.+|+-
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 26
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=32.38 E-value=23 Score=24.49 Aligned_cols=16 Identities=25% Similarity=0.735 Sum_probs=13.3
Q ss_pred eEEecCCCcccCCCCC
Q 033087 13 SYRCKFCRTHLALPED 28 (128)
Q Consensus 13 ~y~C~~C~thLa~~~~ 28 (128)
.|.|++|++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999876655
No 27
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=32.35 E-value=86 Score=20.78 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=8.5
Q ss_pred EEeeeeeccCCC
Q 033087 66 TVADIFCCSCGQ 77 (128)
Q Consensus 66 ~V~DI~C~~C~~ 77 (128)
...-|.|.+|+=
T Consensus 33 ~f~~v~C~~CGY 44 (64)
T PF09855_consen 33 KFTTVSCTNCGY 44 (64)
T ss_pred EEEEEECCCCCC
Confidence 344568999974
No 28
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.46 E-value=39 Score=21.51 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=10.3
Q ss_pred ceEEecCCCccc
Q 033087 12 RSYRCKFCRTHL 23 (128)
Q Consensus 12 ~~y~C~~C~thL 23 (128)
..|.|..|+..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 569999999888
No 29
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=29.58 E-value=67 Score=25.53 Aligned_cols=39 Identities=13% Similarity=0.090 Sum_probs=26.5
Q ss_pred EeeeeeccCCCceeeEEEEecccCcceecCeEEEEecceeccc
Q 033087 67 VADIFCCSCGQIVGWKYESAREKSQKYKEGKFVLERGRIVDEI 109 (128)
Q Consensus 67 V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~l~~~~ 109 (128)
+.--||..|++.|-++++..-.+ -.|..+|-...+-...
T Consensus 91 i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllDd~~ 129 (191)
T PRK05417 91 IQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQEQG 129 (191)
T ss_pred eEeeeCCCCCCccccccccccCC----CCCeEEEehhhcCCCC
Confidence 45559999999998877622111 2378888777776554
No 30
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=27.98 E-value=20 Score=19.37 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=7.1
Q ss_pred eeeeccCCCce
Q 033087 69 DIFCCSCGQIV 79 (128)
Q Consensus 69 DI~C~~C~~~l 79 (128)
+-||..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45677777654
No 31
>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=27.95 E-value=52 Score=18.20 Aligned_cols=19 Identities=37% Similarity=0.712 Sum_probs=13.7
Q ss_pred ceeeeecCC-ceEEecCCCc
Q 033087 3 RIFVVELDG-RSYRCKFCRT 21 (128)
Q Consensus 3 r~f~~yl~g-~~y~C~~C~t 21 (128)
|..+.|..| +.-.|+.|++
T Consensus 5 r~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CceEEcCCCCCCeECCccCc
Confidence 345677777 7788888875
No 32
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.54 E-value=23 Score=18.83 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=6.4
Q ss_pred eeeccCCCce
Q 033087 70 IFCCSCGQIV 79 (128)
Q Consensus 70 I~C~~C~~~l 79 (128)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 4677777654
No 33
>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=25.32 E-value=40 Score=20.22 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=13.0
Q ss_pred ceEEecCCCcccCCCC
Q 033087 12 RSYRCKFCRTHLALPE 27 (128)
Q Consensus 12 ~~y~C~~C~thLa~~~ 27 (128)
.-|.|..|+.+|...+
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 4588999999987766
No 34
>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=24.65 E-value=14 Score=18.46 Aligned_cols=16 Identities=25% Similarity=0.825 Sum_probs=11.9
Q ss_pred EEecCCCcccCCCCCe
Q 033087 14 YRCKFCRTHLALPEDL 29 (128)
Q Consensus 14 y~C~~C~thLa~~~~l 29 (128)
|.|..|...+...+.|
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 7899998877765544
No 35
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=24.08 E-value=98 Score=22.84 Aligned_cols=30 Identities=17% Similarity=0.065 Sum_probs=24.6
Q ss_pred cCCCCeEEEEecccccccCccceeEeeeec
Q 033087 35 HCRRGKAYLFNSAVNITVGASEERLMLSGM 64 (128)
Q Consensus 35 ~G~~G~AyLf~~vvNv~~g~~e~r~m~TG~ 64 (128)
.|+||.|+.--++.|+..|...+....++-
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 689999999889999999987776666654
No 36
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=22.59 E-value=70 Score=18.23 Aligned_cols=15 Identities=27% Similarity=0.665 Sum_probs=12.5
Q ss_pred ceEEecCCCcccCCC
Q 033087 12 RSYRCKFCRTHLALP 26 (128)
Q Consensus 12 ~~y~C~~C~thLa~~ 26 (128)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 469999999988764
No 37
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=22.54 E-value=13 Score=19.36 Aligned_cols=17 Identities=18% Similarity=0.528 Sum_probs=12.5
Q ss_pred eEEecCCCcccCCCCCe
Q 033087 13 SYRCKFCRTHLALPEDL 29 (128)
Q Consensus 13 ~y~C~~C~thLa~~~~l 29 (128)
+|.|..|+.-+.+...+
T Consensus 1 ~~~C~~C~~~F~~~~~l 17 (27)
T PF13912_consen 1 PFECDECGKTFSSLSAL 17 (27)
T ss_dssp SEEETTTTEEESSHHHH
T ss_pred CCCCCccCCccCChhHH
Confidence 58899999877665544
No 38
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=22.01 E-value=34 Score=18.43 Aligned_cols=13 Identities=23% Similarity=0.784 Sum_probs=10.9
Q ss_pred ceEEecCCCcccC
Q 033087 12 RSYRCKFCRTHLA 24 (128)
Q Consensus 12 ~~y~C~~C~thLa 24 (128)
.-|.|..|+..|+
T Consensus 26 ~Cf~C~~C~~~L~ 38 (39)
T smart00132 26 ECFKCSKCGKPLG 38 (39)
T ss_pred cCCCCcccCCcCc
Confidence 4589999999886
No 39
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=21.74 E-value=51 Score=19.67 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=7.4
Q ss_pred ceEEecCCCccc
Q 033087 12 RSYRCKFCRTHL 23 (128)
Q Consensus 12 ~~y~C~~C~thL 23 (128)
.+|.|.+|.+-+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 689999998754
No 40
>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=20.67 E-value=1.3e+02 Score=21.71 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=34.3
Q ss_pred ceEEecCCCcccCCCCCeeeeeecCCCCeEEEEecccccccCccceeE
Q 033087 12 RSYRCKFCRTHLALPEDLVSRAFHCRRGKAYLFNSAVNITVGASEERL 59 (128)
Q Consensus 12 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~vvNv~~g~~e~r~ 59 (128)
+.=.|.+|+..=.-...++++.+.++. .-+...+-.|+..|+..+-.
T Consensus 15 r~saC~~C~~~~~Cg~~~~~~~~~~~~-~~~~~~~~~~~~~GD~V~v~ 61 (135)
T PF04246_consen 15 RSSACGSCSASGGCGTGLLAKLFSGKP-ITFRAPNPIGAKVGDRVEVE 61 (135)
T ss_pred cCCcCcccCCCCCCCcchhhhhcCCCc-EEEEecCCCCCCCCCEEEEE
Confidence 334699998666666778888888877 66666777888888765443
Done!