Query 032714
Match_columns 135
No_of_seqs 102 out of 323
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 05:00:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032714.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032714hhsearch_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 3.6E-42 7.7E-47 258.8 -1.1 105 1-105 1-109 (122)
2 PF03226 Yippee-Mis18: Yippee 99.9 9E-26 2E-30 159.2 4.2 85 14-104 2-93 (96)
3 TIGR00357 methionine-R-sulfoxi 95.8 0.0072 1.6E-07 46.6 2.7 81 12-100 38-119 (134)
4 PRK00222 methionine sulfoxide 95.8 0.0063 1.4E-07 47.4 2.2 82 12-100 41-122 (142)
5 PF01641 SelR: SelR domain; I 95.3 0.015 3.2E-07 44.3 2.6 82 12-100 35-117 (124)
6 PRK05508 methionine sulfoxide 95.0 0.02 4.3E-07 43.5 2.7 79 12-100 31-110 (119)
7 PF11648 RIG-I_C-RD: C-termina 94.9 0.021 4.6E-07 42.7 2.6 85 14-102 4-95 (123)
8 PRK05550 bifunctional methioni 94.1 0.034 7.4E-07 47.4 2.2 80 12-101 34-114 (283)
9 PRK14018 trifunctional thiored 92.1 0.14 3.1E-06 46.8 3.3 82 12-100 416-498 (521)
10 KOG0856 Predicted pilin-like t 90.2 0.38 8.3E-06 37.8 3.6 81 12-100 52-135 (146)
11 PF14976 FAM72: FAM72 protein 87.6 1.2 2.6E-05 35.2 4.8 63 14-88 15-89 (150)
12 COG0229 Conserved domain frequ 86.0 0.91 2E-05 35.5 3.3 82 12-100 40-122 (140)
13 PF09814 HECT_2: HECT-like Ubi 50.1 29 0.00063 29.0 4.4 17 14-30 106-122 (354)
14 PRK02935 hypothetical protein; 41.3 17 0.00037 27.5 1.5 24 13-36 85-108 (110)
15 TIGR01053 LSD1 zinc finger dom 38.8 29 0.00063 20.4 2.0 20 4-23 9-28 (31)
16 PF11023 DUF2614: Protein of u 36.0 14 0.0003 28.1 0.3 24 13-36 84-107 (114)
17 PF04828 GFA: Glutathione-depe 34.4 62 0.0013 21.0 3.3 40 66-107 44-83 (92)
18 KOG2272 Focal adhesion protein 32.4 28 0.0006 30.4 1.6 32 11-46 134-165 (332)
19 TIGR02820 formald_GSH S-(hydro 32.1 72 0.0016 25.7 3.9 33 51-84 71-103 (182)
20 PF06943 zf-LSD1: LSD1 zinc fi 29.3 48 0.001 18.9 1.7 20 3-22 5-24 (25)
21 TIGR00037 eIF_5A translation i 27.3 53 0.0011 24.7 2.2 30 36-65 35-64 (130)
22 COG3791 Uncharacterized conser 26.9 47 0.001 24.7 1.9 39 66-106 65-103 (133)
23 PF13465 zf-H2C2_2: Zinc-finge 24.9 46 0.00099 18.1 1.1 13 10-22 10-22 (26)
24 PLN03107 eukaryotic translatio 23.9 65 0.0014 25.3 2.2 30 36-65 49-78 (159)
25 KOG2324 Prolyl-tRNA synthetase 23.2 58 0.0013 29.8 2.0 18 79-96 271-288 (457)
26 COG5469 Predicted metal-bindin 22.1 67 0.0014 25.4 1.9 16 34-49 79-94 (143)
27 PF00412 LIM: LIM domain; Int 20.5 68 0.0015 19.4 1.4 16 13-28 25-40 (58)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=3.6e-42 Score=258.83 Aligned_cols=105 Identities=44% Similarity=0.823 Sum_probs=98.9
Q ss_pred CcceeeeccCC-CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCc
Q 032714 1 MGRIFLVELKG-RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQI 79 (135)
Q Consensus 1 MGr~F~~yL~g-~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~ 79 (135)
|||+|.++|++ ++.|+|++|+||||.++|||||+|+|++|+||||++|+||..|++|+|.|+||+|+|+||+|..|++.
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 99999999998 48999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEeccccc---cccccccccccc
Q 032714 80 VGWKYVSSFQPFFS---CFCSENLSNISG 105 (135)
Q Consensus 80 LGWKYe~A~E~sq~---~~c~~~l~~~~~ 105 (135)
||||||.|||+||. +-.+.+|-.+.+
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~ 109 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFK 109 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcC
Confidence 99999999999998 667776655544
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=99.92 E-value=9e-26 Score=159.16 Aligned_cols=85 Identities=36% Similarity=0.716 Sum_probs=78.5
Q ss_pred EEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeecccc----EEEeeeeeeecCCceeeEEEEEec
Q 032714 14 YYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGM----HTVEDIFCCCCGQIVGWKYVSSFQ 89 (135)
Q Consensus 14 ~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~----HtV~DI~C~~C~t~LGWKYe~A~E 89 (135)
+|.|++|++||+++++||| |+|+.|+||||+ ||..+++++|.|.||. |+|+||+|.+|++.|||||++|++
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 7778888999999999 999999999999999999999999
Q ss_pred cccc---ccccccccccc
Q 032714 90 PFFS---CFCSENLSNIS 104 (135)
Q Consensus 90 ~sq~---~~c~~~l~~~~ 104 (135)
+ |. +.++.+++.++
T Consensus 77 ~-~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASIS 93 (96)
T ss_pred h-HhhhCCEEEEEhhHEE
Confidence 9 75 77777777654
No 3
>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=95.83 E-value=0.0072 Score=46.61 Aligned_cols=81 Identities=15% Similarity=0.341 Sum_probs=55.6
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeecc-ccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEecc
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDV-VNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQP 90 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~v-vNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E~ 90 (135)
+-+|.|+.|.++|=.+++ -|.-..|=.-.+..+ -|. +...+|.. -|+.. ..|.|..|+..||--......+
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~-V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~DGP~p 109 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEV-VAYERDES--HGMIR-TEVRCRNCDAHLGHVFDDGPEP 109 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCc-eEEeecCC--CCcEE-EEEEecCCCCccCcccCCCCCC
Confidence 458999999999988775 354445544434444 222 22233332 25554 5799999999999988888888
Q ss_pred cccccccccc
Q 032714 91 FFSCFCSENL 100 (135)
Q Consensus 91 sq~~~c~~~l 100 (135)
+..|.|+|-.
T Consensus 110 tg~RyCINs~ 119 (134)
T TIGR00357 110 TGLRYCINSA 119 (134)
T ss_pred CCceEeecce
Confidence 8899999854
No 4
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=95.77 E-value=0.0063 Score=47.39 Aligned_cols=82 Identities=17% Similarity=0.377 Sum_probs=56.0
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEeccc
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQPF 91 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E~s 91 (135)
+-+|.|+.|.++|=.+++ -|.-..|=.-.+..+..-.+...+|+ .-|+.. ..|.|..|+..||-.......++
T Consensus 41 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~--s~gm~R-tEv~C~~Cg~HLGHVF~DGP~pt 113 (142)
T PRK00222 41 KGIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDT--SHGMVR-TEVRCANCDSHLGHVFPDGPKPT 113 (142)
T ss_pred CeEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeecc--CCCceE-EEEEeCCCCCccCcccCCCCCCC
Confidence 458999999999988754 45555555544454422122222332 223333 57999999999999988888889
Q ss_pred ccccccccc
Q 032714 92 FSCFCSENL 100 (135)
Q Consensus 92 q~~~c~~~l 100 (135)
..|.|+|-.
T Consensus 114 g~RyCINs~ 122 (142)
T PRK00222 114 GLRYCINSA 122 (142)
T ss_pred CCEeeecee
Confidence 999999853
No 5
>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=95.28 E-value=0.015 Score=44.30 Aligned_cols=82 Identities=20% Similarity=0.425 Sum_probs=52.9
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEecc-
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQP- 90 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E~- 90 (135)
+-+|.|+.|.++|=.+++ -|....|=.-.+..+..-.+...+|.. -|+.. ..|.|..|+..||=-......+
T Consensus 35 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~v~~~~D~s--~g~~R-~Ev~C~~Cg~HLGHVF~DGp~~~ 107 (124)
T PF01641_consen 35 EGIYVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFS--HGMVR-TEVRCARCGSHLGHVFDDGPPPP 107 (124)
T ss_dssp SEEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEEC--TSSEE-EEEEETTTCCEEEEEESTSSTTC
T ss_pred CEEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEecccc--CCceE-EEEEecCCCCccccEeCCCCCCC
Confidence 458999999999987663 455555544444444332222233322 25554 4699999999999988877765
Q ss_pred cccccccccc
Q 032714 91 FFSCFCSENL 100 (135)
Q Consensus 91 sq~~~c~~~l 100 (135)
+..|.|+|-+
T Consensus 108 tg~RyCINS~ 117 (124)
T PF01641_consen 108 TGLRYCINSA 117 (124)
T ss_dssp TSCEEEE-GG
T ss_pred CCcEEEeeee
Confidence 4779999854
No 6
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=95.03 E-value=0.02 Score=43.53 Aligned_cols=79 Identities=19% Similarity=0.462 Sum_probs=53.4
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEE-EEecc
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYV-SSFQP 90 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe-~A~E~ 90 (135)
+-+|.|+.|.++|=.+++ -|.-..|=.-.+..+-|. +...+|.. | + =..|.|..|+..||=-.. ....+
T Consensus 31 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~-v~~~~D~~---~-~-RtEv~C~~C~~HLGHVF~d~gp~p 100 (119)
T PRK05508 31 KGTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKGA-VKRIPDAD---G-R-RTEIVCANCGGHLGHVFEGEGFTP 100 (119)
T ss_pred CeEEEecCCCCccccccc----cccCCCCCcccCcccccc-eEEEecCC---C-c-EEEEEeCCCCCccCcccCCCCCCC
Confidence 458999999999988775 355555544444444332 22333433 2 2 367999999999998776 44567
Q ss_pred cccccccccc
Q 032714 91 FFSCFCSENL 100 (135)
Q Consensus 91 sq~~~c~~~l 100 (135)
+..|.|+|-.
T Consensus 101 tg~RyCINS~ 110 (119)
T PRK05508 101 KNTRHCVNSI 110 (119)
T ss_pred CCCEEeecce
Confidence 8889999853
No 7
>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=94.92 E-value=0.021 Score=42.67 Aligned_cols=85 Identities=15% Similarity=0.163 Sum_probs=55.1
Q ss_pred EEeccCCCCccCCCCCeece--eeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEeccc
Q 032714 14 YYKCRFCNSHLALADSVLSW--SFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQPF 91 (135)
Q Consensus 14 ~y~C~~C~tHLA~~~elISK--~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E~s 91 (135)
.+.|++|.+.++..+||-.- +-+=--.+. |...+.+...|.+.....-+.+....|+|..|++.||-.+. |...
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 KLLCRKCKKFACSGSDIRKIENSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMK--YKGV 79 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEETTTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEE--ETTE
T ss_pred EEECCCCCceeEchhheEEecCCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheE--ECCc
Confidence 58899999999999998653 111001122 33556666666654444558899999999999999997544 3333
Q ss_pred cc-----ccccccccc
Q 032714 92 FS-----CFCSENLSN 102 (135)
Q Consensus 92 q~-----~~c~~~l~~ 102 (135)
++ +.+.+.+++
T Consensus 80 ~LP~L~iksfvv~~~~ 95 (123)
T PF11648_consen 80 ELPCLKIKSFVVELET 95 (123)
T ss_dssp EEEEE-GGGEEEEETT
T ss_pred cccEEEeeeeeeeecC
Confidence 32 445555555
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=94.07 E-value=0.034 Score=47.37 Aligned_cols=80 Identities=21% Similarity=0.437 Sum_probs=54.6
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEE-EEecc
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYV-SSFQP 90 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe-~A~E~ 90 (135)
+-+|.|+.|.++|=.+++ -|.-..|=.-.+..+.+-..- .++.. |+ =..|.|..|+..||--.. ....+
T Consensus 34 ~G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~~~-~~d~~---~~--R~Ev~c~~c~~HLGHvF~ddgp~p 103 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAVKR-LPDAD---GR--RTEIVCANCGAHLGHVFEGEGLTP 103 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccEE-EEcCC---Cc--eEEEEecCCCCccCcccCCCCCCC
Confidence 458999999999988764 355455544445555443222 22222 33 478999999999998776 55677
Q ss_pred ccccccccccc
Q 032714 91 FFSCFCSENLS 101 (135)
Q Consensus 91 sq~~~c~~~l~ 101 (135)
+..|.|+|-..
T Consensus 104 tg~RyCiNs~s 114 (283)
T PRK05550 104 KNTRHCVNSAS 114 (283)
T ss_pred CCccccccccc
Confidence 88899998543
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=92.08 E-value=0.14 Score=46.78 Aligned_cols=82 Identities=7% Similarity=0.075 Sum_probs=54.7
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEec-c
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQ-P 90 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E-~ 90 (135)
+-+|.|+.|.++|=++++ -|.-..|=.-.+..+-+-.+...+|. .-|++.+ .|.|..|+..||-....... +
T Consensus 416 ~G~y~c~~c~~pLf~s~~----Kf~sg~GWPsF~~~i~~~~v~~~~d~--s~g~~R~-Ev~c~~c~~HLGHvf~dgp~~~ 488 (521)
T PRK14018 416 PGIYVDVVSGEPLFSSAD----KYDSGCGWPSFTRPIDAKVVTEHDDF--SYNMRRT-EVRSRAADSHLGHVFPDGPRDK 488 (521)
T ss_pred CEEEEecCCCCccccCcc----cccCCCCCcccCcccCcCceEEeecc--CCCceEE-EEEECCCCCcCCcccCCCCCCC
Confidence 468999999999988763 45555554444444432222223332 2355553 79999999999998877664 4
Q ss_pred cccccccccc
Q 032714 91 FFSCFCSENL 100 (135)
Q Consensus 91 sq~~~c~~~l 100 (135)
+..|.|+|-.
T Consensus 489 ~g~RyCiNs~ 498 (521)
T PRK14018 489 GGLRYCINGA 498 (521)
T ss_pred CCCEeeecee
Confidence 7889999853
No 10
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=90.19 E-value=0.38 Score=37.84 Aligned_cols=81 Identities=19% Similarity=0.371 Sum_probs=50.0
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceee-ccccEEEeeeeeeecCCceeeEEE-EEec
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLM-LSGMHTVEDIFCCCCGQIVGWKYV-SSFQ 89 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m-~TG~HtV~DI~C~~C~t~LGWKYe-~A~E 89 (135)
+-+|.|+.|.++|=.++- -|.-..|=--.|+.+ ..|....+.+ .-|.| =.+|.|..|+-.||--.+ .-+-
T Consensus 52 ~GvY~C~~C~~pLykS~t----KfdsgcGWPAF~e~i---~~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~~eG~~ 123 (146)
T KOG0856|consen 52 EGVYVCAGCGTPLYKSTT----KFDSGCGWPAFFEAI---GPGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFKGEGPK 123 (146)
T ss_pred CceEEEeecCCccccccc----cccCCCCCchhhhcc---CCCceeeccccCCCCc-ceEEEEeecCCceeeeecCCCCC
Confidence 469999999999987653 454444443333332 1221111111 11222 357899999999998766 5555
Q ss_pred -ccccccccccc
Q 032714 90 -PFFSCFCSENL 100 (135)
Q Consensus 90 -~sq~~~c~~~l 100 (135)
+++.|+|++..
T Consensus 124 ~Pt~~R~CiNS~ 135 (146)
T KOG0856|consen 124 TPTDERHCINSV 135 (146)
T ss_pred CCCCceeEeeee
Confidence 88889999853
No 11
>PF14976 FAM72: FAM72 protein
Probab=87.64 E-value=1.2 Score=35.19 Aligned_cols=63 Identities=33% Similarity=0.612 Sum_probs=41.5
Q ss_pred EEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCC----Ccccceeecccc--------EEEeeeeeeecCCcee
Q 032714 14 YYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIML----GPQEERLMLSGM--------HTVEDIFCCCCGQIVG 81 (135)
Q Consensus 14 ~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~----G~~e~R~m~TG~--------HtV~DI~C~~C~t~LG 81 (135)
+..|+.|.+-|+... =||.|..+ .||.+ -||.+..-.+|. =.++||-|..|+..||
T Consensus 15 ~L~C~~C~~~l~~Rg-----------MkAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~vG 82 (150)
T PF14976_consen 15 ILCCKFCDQVLCNRG-----------MKAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIVG 82 (150)
T ss_pred EEECCCCCchhccch-----------hhheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCeee
Confidence 578999999887643 25666655 33332 123323323333 3899999999999999
Q ss_pred eEEEEEe
Q 032714 82 WKYVSSF 88 (135)
Q Consensus 82 WKYe~A~ 88 (135)
+..+..-
T Consensus 83 YhV~~PC 89 (150)
T PF14976_consen 83 YHVVVPC 89 (150)
T ss_pred eEEEEEc
Confidence 9777553
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=86.02 E-value=0.91 Score=35.55 Aligned_cols=82 Identities=18% Similarity=0.389 Sum_probs=54.7
Q ss_pred CcEEeccCCCCccCCCCCeeceeeecCCCeEEEeeccccCCCCcccceeeccccEEEeeeeeeecCCceeeEEEEEeccc
Q 032714 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVSSFQPF 91 (135)
Q Consensus 12 ~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKYe~A~E~s 91 (135)
+-+|.|+.|..+|=.+++ -|.-..|=--.+.-+..-.+...+|+ .-||+.+ .|.|..|+..||--.+.--.++
T Consensus 40 ~GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGHVF~DGP~~t 112 (140)
T COG0229 40 KGIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGHVFPDGPPPT 112 (140)
T ss_pred CceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCccccccCCCCCCC
Confidence 459999999999987765 34444444333444433333333343 3466655 6899999999998776666666
Q ss_pred c-cccccccc
Q 032714 92 F-SCFCSENL 100 (135)
Q Consensus 92 q-~~~c~~~l 100 (135)
- +|-|+|-.
T Consensus 113 gglRYCINSa 122 (140)
T COG0229 113 GGLRYCINSA 122 (140)
T ss_pred CCeeEeecch
Confidence 6 79998854
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=50.07 E-value=29 Score=28.98 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=13.8
Q ss_pred EEeccCCCCccCCCCCe
Q 032714 14 YYKCRFCNSHLALADSV 30 (135)
Q Consensus 14 ~y~C~~C~tHLA~~~el 30 (135)
.+.|++|+..|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766543
No 14
>PRK02935 hypothetical protein; Provisional
Probab=41.31 E-value=17 Score=27.50 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=20.9
Q ss_pred cEEeccCCCCccCCCCCeeceeee
Q 032714 13 SYYKCRFCNSHLALADSVLSWSFN 36 (135)
Q Consensus 13 ~~y~C~~C~tHLA~~~elISK~F~ 36 (135)
|+..|-+|+++|+...++--|.|.
T Consensus 85 rvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 85 RVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred ceeecCcCCCcCCcCccccccCcC
Confidence 779999999999999888777664
No 15
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=38.79 E-value=29 Score=20.41 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=15.5
Q ss_pred eeeeccCCCcEEeccCCCCc
Q 032714 4 IFLVELKGRSYYKCRFCNSH 23 (135)
Q Consensus 4 ~F~~yL~g~~~y~C~~C~tH 23 (135)
+-+.|.+|.+.+.|..|++.
T Consensus 9 t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cEeecCCCCCeEECCCCCeE
Confidence 45678888888999988764
No 16
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=36.03 E-value=14 Score=28.11 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=21.1
Q ss_pred cEEeccCCCCccCCCCCeeceeee
Q 032714 13 SYYKCRFCNSHLALADSVLSWSFN 36 (135)
Q Consensus 13 ~~y~C~~C~tHLA~~~elISK~F~ 36 (135)
++..|-+|++||+...++--|.|.
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~ 107 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFD 107 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhh
Confidence 568999999999999999888775
No 17
>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=34.39 E-value=62 Score=21.02 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=19.9
Q ss_pred EEEeeeeeeecCCceeeEEEEEeccccccccccccccccccc
Q 032714 66 HTVEDIFCCCCGQIVGWKYVSSFQPFFSCFCSENLSNISGAA 107 (135)
Q Consensus 66 HtV~DI~C~~C~t~LGWKYe~A~E~sq~~~c~~~l~~~~~~~ 107 (135)
..+.-.+|..|++.|.+..+. .+-....-+..||......
T Consensus 44 ~~~~r~FC~~CGs~l~~~~~~--~~~~~~V~~g~ld~~~~~~ 83 (92)
T PF04828_consen 44 KGVERYFCPTCGSPLFSEDER--DPDLVGVNAGTLDDPDEFK 83 (92)
T ss_dssp SSCEEEEETTT--EEEEEESS--TTTEEEEEGGGBTT--S--
T ss_pred CcCcCcccCCCCCeeecccCC--CCCEEEEEeEeeCCCCCCC
Confidence 344558999999999986222 2223344455555554433
No 18
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=32.40 E-value=28 Score=30.43 Aligned_cols=32 Identities=28% Similarity=0.665 Sum_probs=24.9
Q ss_pred CCcEEeccCCCCccCCCCCeeceeeecCCCeEEEee
Q 032714 11 GRSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFS 46 (135)
Q Consensus 11 g~~~y~C~~C~tHLA~~~elISK~F~G~~GrAyLf~ 46 (135)
+.-+|.|.+|+.|+-. +.| -|+|..--+|.|+
T Consensus 134 ~~g~YvC~KCh~~iD~-~~l---~fr~d~yH~yHFk 165 (332)
T KOG2272|consen 134 GRGRYVCQKCHAHIDE-QPL---TFRGDPYHPYHFK 165 (332)
T ss_pred ccceeehhhhhhhccc-ccc---cccCCCCCcccee
Confidence 3347999999999987 333 3888888888887
No 19
>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=32.11 E-value=72 Score=25.68 Aligned_cols=33 Identities=9% Similarity=0.143 Sum_probs=19.1
Q ss_pred CCCCcccceeeccccEEEeeeeeeecCCceeeEE
Q 032714 51 IMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (135)
Q Consensus 51 v~~G~~e~R~m~TG~HtV~DI~C~~C~t~LGWKY 84 (135)
+..|++..+....|.+..+ -||..|++.|-++.
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 3335443332233444444 49999999996655
No 20
>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=29.31 E-value=48 Score=18.86 Aligned_cols=20 Identities=25% Similarity=0.663 Sum_probs=15.8
Q ss_pred ceeeeccCCCcEEeccCCCC
Q 032714 3 RIFLVELKGRSYYKCRFCNS 22 (135)
Q Consensus 3 r~F~~yL~g~~~y~C~~C~t 22 (135)
++.+.|..|-+...|..|++
T Consensus 5 r~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CceEEcCCCCCCeECCccCc
Confidence 45677888888899999876
No 21
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=27.34 E-value=53 Score=24.74 Aligned_cols=30 Identities=20% Similarity=0.118 Sum_probs=25.9
Q ss_pred ecCCCeEEEeeccccCCCCcccceeecccc
Q 032714 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (135)
Q Consensus 36 ~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~ 65 (135)
.|+||.|+.--.+.|+..|...+...-++-
T Consensus 35 pGkhG~A~vr~k~knl~tG~~~e~~f~s~~ 64 (130)
T TIGR00037 35 PGKHGHAKARVVAIGIFTGKKLEFVSPSTS 64 (130)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEECCCC
Confidence 699999999999999999999887766555
No 22
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=26.91 E-value=47 Score=24.70 Aligned_cols=39 Identities=18% Similarity=0.220 Sum_probs=23.6
Q ss_pred EEEeeeeeeecCCceeeEEEEEecccccccccccccccccc
Q 032714 66 HTVEDIFCCCCGQIVGWKYVSSFQPFFSCFCSENLSNISGA 106 (135)
Q Consensus 66 HtV~DI~C~~C~t~LGWKYe~A~E~sq~~~c~~~l~~~~~~ 106 (135)
+.+.-.||..|++.|-|+....- .+...=+.-||...-+
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~~--~~~~v~~~~ld~p~~~ 103 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDED--PFVGVNAGALDDPEFL 103 (133)
T ss_pred CCCCCeecccCCCceEEecCCCC--ceEEEEEeeecCcccC
Confidence 34444499999999999776653 3334444444443333
No 23
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.95 E-value=46 Score=18.12 Aligned_cols=13 Identities=38% Similarity=1.096 Sum_probs=10.4
Q ss_pred CCCcEEeccCCCC
Q 032714 10 KGRSYYKCRFCNS 22 (135)
Q Consensus 10 ~g~~~y~C~~C~t 22 (135)
.+++.|.|..|..
T Consensus 10 ~~~k~~~C~~C~k 22 (26)
T PF13465_consen 10 TGEKPYKCPYCGK 22 (26)
T ss_dssp SSSSSEEESSSSE
T ss_pred CCCCCCCCCCCcC
Confidence 3568899999974
No 24
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=23.85 E-value=65 Score=25.27 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=26.4
Q ss_pred ecCCCeEEEeeccccCCCCcccceeecccc
Q 032714 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (135)
Q Consensus 36 ~G~~GrAyLf~~vvNv~~G~~e~R~m~TG~ 65 (135)
.|+||.|+.--.+.|+..|...+....++-
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~ 78 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSH 78 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 799999999999999999999887776655
No 25
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.16 E-value=58 Score=29.82 Aligned_cols=18 Identities=22% Similarity=0.357 Sum_probs=14.5
Q ss_pred ceeeEEEEEecccccccc
Q 032714 79 IVGWKYVSSFQPFFSCFC 96 (135)
Q Consensus 79 ~LGWKYe~A~E~sq~~~c 96 (135)
.||=||-+++...++..|
T Consensus 271 ~LG~kYS~~lna~f~~~~ 288 (457)
T KOG2324|consen 271 LLGTKYSKPLNAKFVNVE 288 (457)
T ss_pred EeccccccccCceeeeec
Confidence 689999999988876544
No 26
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=22.10 E-value=67 Score=25.36 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=13.7
Q ss_pred eeecCCCeEEEeeccc
Q 032714 34 SFNCRRGRAYLFSDVV 49 (135)
Q Consensus 34 ~F~G~~GrAyLf~~vv 49 (135)
.|+|.....|||-++.
T Consensus 79 A~~~~~k~sYLFgdL~ 94 (143)
T COG5469 79 AFSGPGKPSYLFGDLT 94 (143)
T ss_pred EEecCCCceEEEccCC
Confidence 8999999999997543
No 27
>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=20.53 E-value=68 Score=19.45 Aligned_cols=16 Identities=31% Similarity=0.663 Sum_probs=13.0
Q ss_pred cEEeccCCCCccCCCC
Q 032714 13 SYYKCRFCNSHLALAD 28 (135)
Q Consensus 13 ~~y~C~~C~tHLA~~~ 28 (135)
.-|.|..|+.+|...+
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 4589999999987765
Done!