Query 033060
Match_columns 128
No_of_seqs 109 out of 330
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:19:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033060.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033060hhsearch_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 7E-54 1.5E-58 316.2 -3.0 119 1-119 1-120 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 6.2E-33 1.3E-37 193.9 6.1 89 14-108 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 95.9 0.0046 1E-07 45.5 1.8 88 14-103 4-93 (123)
4 TIGR00357 methionine-R-sulfoxi 94.9 0.03 6.4E-07 42.4 3.3 68 12-86 38-105 (134)
5 PRK00222 methionine sulfoxide 94.6 0.028 6.2E-07 42.9 2.7 87 12-109 41-127 (142)
6 PF01641 SelR: SelR domain; I 94.5 0.031 6.7E-07 41.8 2.6 71 12-89 35-105 (124)
7 PRK05508 methionine sulfoxide 93.8 0.071 1.5E-06 39.7 3.2 63 12-84 31-93 (119)
8 PRK05550 bifunctional methioni 92.4 0.11 2.5E-06 43.5 2.8 64 12-85 34-97 (283)
9 PRK14018 trifunctional thiored 91.6 0.18 3.9E-06 45.4 3.3 68 12-86 416-483 (521)
10 PF14976 FAM72: FAM72 protein 88.1 1.1 2.3E-05 34.7 4.6 77 13-101 14-103 (150)
11 KOG0856 Predicted pilin-like t 88.0 0.8 1.7E-05 35.2 3.9 66 12-85 52-118 (146)
12 COG0229 Conserved domain frequ 87.3 0.93 2E-05 34.7 3.9 65 12-83 40-104 (140)
13 PF09814 HECT_2: HECT-like Ubi 70.2 7.4 0.00016 32.2 4.2 17 14-30 106-122 (354)
14 PF04828 GFA: Glutathione-depe 54.2 13 0.00028 24.0 2.4 48 36-83 12-61 (92)
15 PF13717 zinc_ribbon_4: zinc-r 49.6 12 0.00025 21.9 1.4 19 14-32 2-20 (36)
16 PRK02935 hypothetical protein; 49.1 12 0.00026 27.7 1.7 24 13-36 85-108 (110)
17 COG4416 Com Mu-like prophage p 48.1 8.3 0.00018 25.5 0.7 15 13-27 3-17 (60)
18 PF11023 DUF2614: Protein of u 42.4 11 0.00023 28.1 0.6 25 13-37 84-108 (114)
19 TIGR01053 LSD1 zinc finger dom 41.7 25 0.00054 20.2 1.9 20 4-23 9-28 (31)
20 COG3791 Uncharacterized conser 39.5 20 0.00044 26.3 1.7 21 67-87 66-86 (133)
21 COG1996 RPC10 DNA-directed RNA 37.3 29 0.00064 22.1 1.9 12 13-24 5-16 (49)
22 TIGR00037 eIF_5A translation i 34.0 39 0.00086 25.0 2.5 30 36-65 35-64 (130)
23 PF13465 zf-H2C2_2: Zinc-finge 33.3 27 0.00059 18.6 1.1 15 10-24 10-24 (26)
24 PF03811 Zn_Tnp_IS1: InsA N-te 31.1 28 0.00061 20.6 1.0 27 69-95 4-31 (36)
25 PF10955 DUF2757: Protein of u 30.4 22 0.00048 24.6 0.6 16 14-29 4-19 (76)
26 TIGR02820 formald_GSH S-(hydro 29.9 67 0.0014 25.4 3.3 30 54-84 74-103 (182)
27 PF14803 Nudix_N_2: Nudix N-te 29.4 26 0.00056 20.5 0.7 14 72-85 2-15 (34)
28 PF00412 LIM: LIM domain; Int 26.9 34 0.00074 20.5 1.0 16 13-28 25-40 (58)
29 PF06943 zf-LSD1: LSD1 zinc fi 26.2 59 0.0013 17.9 1.7 20 3-22 5-24 (25)
30 smart00661 RPOL9 RNA polymeras 25.5 81 0.0018 18.7 2.5 17 13-29 19-35 (52)
31 KOG2462 C2H2-type Zn-finger pr 23.8 24 0.00053 29.9 -0.2 22 10-31 211-232 (279)
32 PF00096 zf-C2H2: Zinc finger, 23.6 14 0.0003 18.5 -1.1 16 15-30 1-16 (23)
33 smart00132 LIM Zinc-binding do 23.0 34 0.00074 18.4 0.4 13 13-25 26-38 (39)
34 PF13842 Tnp_zf-ribbon_2: DDE_ 23.0 69 0.0015 18.2 1.7 15 13-27 15-29 (32)
35 PF10058 DUF2296: Predicted in 22.9 25 0.00055 22.4 -0.2 35 45-84 2-36 (54)
36 PLN03107 eukaryotic translatio 22.8 96 0.0021 23.9 2.9 31 36-66 49-79 (159)
37 PF13912 zf-C2H2_6: C2H2-type 22.5 12 0.00025 19.6 -1.6 18 14-31 1-18 (27)
38 PRK11586 napB nitrate reductas 22.5 52 0.0011 25.5 1.4 28 12-39 118-145 (149)
39 PF00645 zf-PARP: Poly(ADP-rib 22.1 89 0.0019 20.5 2.4 32 8-40 2-33 (82)
40 PRK05417 glutathione-dependent 21.9 1E+02 0.0022 24.5 3.0 40 67-110 90-129 (191)
41 PF06397 Desulfoferrod_N: Desu 21.5 53 0.0012 19.6 1.0 12 13-24 5-16 (36)
42 PF13248 zf-ribbon_3: zinc-rib 21.3 29 0.00062 18.7 -0.2 11 70-80 16-26 (26)
43 PRK03999 translation initiatio 21.0 1.1E+02 0.0025 22.5 2.9 30 36-65 34-63 (129)
44 cd02669 Peptidase_C19M A subfa 21.0 64 0.0014 27.9 1.8 53 9-81 23-77 (440)
45 KOG2324 Prolyl-tRNA synthetase 20.7 78 0.0017 28.4 2.3 13 79-91 271-283 (457)
46 PF11682 DUF3279: Protein of u 20.2 56 0.0012 24.6 1.1 67 13-79 27-106 (128)
47 PF13240 zinc_ribbon_2: zinc-r 20.2 32 0.00069 18.3 -0.1 10 71-80 14-23 (23)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=7e-54 Score=316.18 Aligned_cols=119 Identities=49% Similarity=0.879 Sum_probs=116.0
Q ss_pred CcceeeeccCCc-cEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCe
Q 033060 1 MGRIFLVELKGR-SYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQI 79 (128)
Q Consensus 1 MG~~f~~yl~g~-~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~ 79 (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 999999999984 7999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEeccCCcceeCCeEEEEeeceeeecccccccccc
Q 033060 80 VGWKYVAAHDKNQKYKEGKFVLERWRIVEEVTEELSLETH 119 (128)
Q Consensus 80 lGWkY~~A~e~sqkYKEGkfILE~~~i~~~~g~~~~~~~~ 119 (128)
|||||+.|||+||||||||||||+++|.+++|++.|+.++
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~~~~~~~~ 120 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPEGWDLEVGAL 120 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCCCchhhcCCC
Confidence 9999999999999999999999999999999999998654
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=6.2e-33 Score=193.90 Aligned_cols=89 Identities=45% Similarity=0.915 Sum_probs=85.3
Q ss_pred EEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeecc----EEEeeeeeeecCCeeeeEEEEecc
Q 033060 14 YYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGM----HTVEDIFCCCCGQIVGWKYVAAHD 89 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~----H~V~DI~C~~C~~~lGWkY~~A~e 89 (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 7778888999999999 999999999999999999999999
Q ss_pred CCcceeCCeEEEEeeceee
Q 033060 90 KNQKYKEGKFVLERWRIVE 108 (128)
Q Consensus 90 ~sqkYKEGkfILE~~~i~~ 108 (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=95.90 E-value=0.0046 Score=45.55 Aligned_cols=88 Identities=17% Similarity=0.165 Sum_probs=57.4
Q ss_pred EEeccCCCCcccCCCCeeeeccccC--CCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEEEeccCC
Q 033060 14 YYKCRFCNSHLALADSVLSWSFNCR--RGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHDKN 91 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~lISk~F~G~--~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e~s 91 (128)
.+-|++|.+.++..+||-.-.-+.. -.+. |...+.+...|++.....-+.+....|+|..|++.+|-.+..---+=
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 5889999999999999876521100 0112 22455556665554445557889999999999999998776543334
Q ss_pred cceeCCeEEEEe
Q 033060 92 QKYKEGKFVLER 103 (128)
Q Consensus 92 qkYKEGkfILE~ 103 (128)
.-.|.-.|+++.
T Consensus 82 P~L~iksfvv~~ 93 (123)
T PF11648_consen 82 PCLKIKSFVVEL 93 (123)
T ss_dssp EEE-GGGEEEEE
T ss_pred cEEEeeeeeeee
Confidence 455555666443
No 4
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=94.88 E-value=0.03 Score=42.44 Aligned_cols=68 Identities=15% Similarity=0.339 Sum_probs=42.2
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEEE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVA 86 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~ 86 (128)
+-+|.|+.|.++|-.+++ .|....|=.-.+..+-.-.+...+|.. -|+.. ..|.|..|+.+||--...
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~D 105 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEVVAYERDES--HGMIR-TEVRCRNCDAHLGHVFDD 105 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCceEEeecCC--CCcEE-EEEEecCCCCccCcccCC
Confidence 358999999999987764 355555544434444111122233322 24444 579999999999975543
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.64 E-value=0.028 Score=42.94 Aligned_cols=87 Identities=14% Similarity=0.304 Sum_probs=50.3
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEEEeccCC
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHDKN 91 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e~s 91 (128)
+-+|.|+.|.++|=.+++ .|....|=.-.+..+-.-.+...+|+ .-|+.. ..|.|..|+.+||--......++
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 458999999999987743 46656665444444422122222332 223322 57999999999998664432221
Q ss_pred cceeCCeEEEEeeceeee
Q 033060 92 QKYKEGKFVLERWRIVEE 109 (128)
Q Consensus 92 qkYKEGkfILE~~~i~~~ 109 (128)
-=+|-|.-+-|.-.
T Consensus 114 ----g~RyCINs~sL~F~ 127 (142)
T PRK00222 114 ----GLRYCINSASLKFI 127 (142)
T ss_pred ----CCEeeeceeeEEee
Confidence 11565555555443
No 6
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=94.52 E-value=0.031 Score=41.77 Aligned_cols=71 Identities=20% Similarity=0.436 Sum_probs=43.2
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEEEecc
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVAAHD 89 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e 89 (128)
+-+|.|+.|.++|=.++. .|....|=.-.+..+..-.+....|.. -|+. -..|.|..|+.+||=-......
T Consensus 35 ~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 35 EGIYVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFS--HGMV-RTEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp SEEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEEC--TSSE-EEEEEETTTCCEEEEEESTSST
T ss_pred CEEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEecccc--CCce-EEEEEecCCCCccccEeCCCCC
Confidence 458999999999976653 465555554434443332222233322 2444 4478999999999986665444
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.76 E-value=0.071 Score=39.71 Aligned_cols=63 Identities=19% Similarity=0.468 Sum_probs=42.1
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 84 (128)
+-+|.|+.|.++|=.+++ .|....|=.-.+..+-| .+...+|.. | + =..|.|+.|+.+||--.
T Consensus 31 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~-~v~~~~D~~---~-~-RtEv~C~~C~~HLGHVF 93 (119)
T PRK05508 31 KGTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKG-AVKRIPDAD---G-R-RTEIVCANCGGHLGHVF 93 (119)
T ss_pred CeEEEecCCCCccccccc----cccCCCCCcccCccccc-ceEEEecCC---C-c-EEEEEeCCCCCccCccc
Confidence 358999999999987764 46666665444555533 223334433 2 2 46799999999999744
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=92.36 E-value=0.11 Score=43.50 Aligned_cols=64 Identities=22% Similarity=0.461 Sum_probs=42.3
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYV 85 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~ 85 (128)
+-+|.|+.|+++|=.+++ .|....|=.-.+..+-|-.. ..++.. |+ =..|.|..|+.+||--..
T Consensus 34 ~G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~~-~~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAVK-RLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccE-EEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 358999999999987654 46555665444555544322 222222 33 478999999999998654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=91.58 E-value=0.18 Score=45.45 Aligned_cols=68 Identities=7% Similarity=0.069 Sum_probs=43.2
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEEEE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKYVA 86 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~ 86 (128)
+-+|.|+.|+++|=+++ ..|....|=.-.+..+-+-.+....|. .-|++. ..|.|..|+.+||-....
T Consensus 416 ~G~y~c~~c~~pLf~s~----~Kf~sg~GWPsF~~~i~~~~v~~~~d~--s~g~~R-~Ev~c~~c~~HLGHvf~d 483 (521)
T PRK14018 416 PGIYVDVVSGEPLFSSA----DKYDSGCGWPSFTRPIDAKVVTEHDDF--SYNMRR-TEVRSRAADSHLGHVFPD 483 (521)
T ss_pred CEEEEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeecc--CCCceE-EEEEECCCCCcCCcccCC
Confidence 46999999999998875 346656665443444432222222332 224444 379999999999986644
No 10
>PF14976 FAM72: FAM72 protein
Probab=88.11 E-value=1.1 Score=34.75 Aligned_cols=77 Identities=30% Similarity=0.565 Sum_probs=46.7
Q ss_pred cEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccC----Ccccceeeeecc--------EEEeeeeeeecCCee
Q 033060 13 SYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIML----GPQEERLMLSGM--------HTVEDIFCCCCGQIV 80 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~----g~~e~r~m~TG~--------H~V~DI~C~~C~~~l 80 (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 3689999999887533 24666554 33332 122222222333 369999999999999
Q ss_pred eeEEEEeccC-CcceeCCeEEE
Q 033060 81 GWKYVAAHDK-NQKYKEGKFVL 101 (128)
Q Consensus 81 GWkY~~A~e~-sqkYKEGkfIL 101 (128)
|+..+..=.. -+.-.-|.|-+
T Consensus 82 GYhV~~PC~~Cl~scNNGH~wm 103 (150)
T PF14976_consen 82 GYHVVVPCSRCLSSCNNGHFWM 103 (150)
T ss_pred eeEEEEEcchHhcCccCCceEE
Confidence 9988765321 12234666665
No 11
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=88.01 E-value=0.8 Score=35.25 Aligned_cols=66 Identities=20% Similarity=0.397 Sum_probs=38.3
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceee-eeccEEEeeeeeeecCCeeeeEEE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLM-LSGMHTVEDIFCCCCGQIVGWKYV 85 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m-~TG~H~V~DI~C~~C~~~lGWkY~ 85 (128)
+-+|.|..|.++|-.+. .-|....|=--.|+.+ + .|....+.. .-|.| =.+|.|..|+.+||--.+
T Consensus 52 ~GvY~C~~C~~pLykS~----tKfdsgcGWPAF~e~i-~--~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 52 EGVYVCAGCGTPLYKST----TKFDSGCGWPAFFEAI-G--PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCcccccc----ccccCCCCCchhhhcc-C--CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 46999999999997764 3465555542223332 1 222111111 11222 357899999999997543
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=87.27 E-value=0.93 Score=34.72 Aligned_cols=65 Identities=20% Similarity=0.431 Sum_probs=41.5
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCCCeEEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeE
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRRGRAYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWK 83 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWk 83 (128)
+-+|.|+.|..+|=.+++ .|....|=--.+..+..-.+...+|+ .-|++.+ .|.|..|+++||--
T Consensus 40 ~GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGHV 104 (140)
T COG0229 40 KGIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGHV 104 (140)
T ss_pred CceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCccccc
Confidence 359999999999987765 35555554333444433333333342 3355543 68999999999963
No 13
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=70.17 E-value=7.4 Score=32.16 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=13.8
Q ss_pred EEeccCCCCcccCCCCe
Q 033060 14 YYKCRFCNSHLALADSV 30 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~l 30 (128)
.+.|++|++.|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766543
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=54.18 E-value=13 Score=24.04 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=22.7
Q ss_pred ccCCCeEEEeecccccc--CCcccceeeeeccEEEeeeeeeecCCeeeeE
Q 033060 36 NCRRGRAYLFSDVVNIM--LGPQEERLMLSGMHTVEDIFCCCCGQIVGWK 83 (128)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~--~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWk 83 (128)
.|..-.++++-..-++. .|+..-+........+.-.+|..|++.|.+.
T Consensus 12 ~g~~~~~~~~~~~~~~~~~~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 12 SGSPFSAWAIVPKDDFRWTSGSENLKEYQFSGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TT-SSEEEEEEEGGGEEEEE-GGGEEEC--TTSSCEEEEETTT--EEEEE
T ss_pred cCCceeeEEEEcccceEEeeccccceEEEeCCCcCcCcccCCCCCeeecc
Confidence 33333344433333444 3444333333233445568999999999975
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=49.58 E-value=12 Score=21.91 Aligned_cols=19 Identities=16% Similarity=0.510 Sum_probs=14.3
Q ss_pred EEeccCCCCcccCCCCeee
Q 033060 14 YYKCRFCNSHLALADSVLS 32 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~lIS 32 (128)
.+.|.+|++-....++.|.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip 20 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP 20 (36)
T ss_pred EEECCCCCCEEeCCHHHCC
Confidence 4678888888877777664
No 16
>PRK02935 hypothetical protein; Provisional
Probab=49.13 E-value=12 Score=27.65 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=20.7
Q ss_pred cEEeccCCCCcccCCCCeeeeccc
Q 033060 13 SYYKCRFCNSHLALADSVLSWSFN 36 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~~lISk~F~ 36 (128)
|+..|-+|+++|+...++--|.|.
T Consensus 85 rvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 85 RVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred ceeecCcCCCcCCcCccccccCcC
Confidence 789999999999999888777664
No 17
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=48.07 E-value=8.3 Score=25.47 Aligned_cols=15 Identities=40% Similarity=0.609 Sum_probs=11.5
Q ss_pred cEEeccCCCCcccCC
Q 033060 13 SYYKCRFCNSHLALA 27 (128)
Q Consensus 13 ~~y~C~~C~thLa~~ 27 (128)
+..+|++|..-||-.
T Consensus 3 ~tiRC~~CnKlLa~a 17 (60)
T COG4416 3 QTIRCAKCNKLLAEA 17 (60)
T ss_pred eeeehHHHhHHHHhc
Confidence 568899998877754
No 18
>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=42.43 E-value=11 Score=28.06 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=21.4
Q ss_pred cEEeccCCCCcccCCCCeeeecccc
Q 033060 13 SYYKCRFCNSHLALADSVLSWSFNC 37 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~~lISk~F~G 37 (128)
+...|-+|+++|+...++--|.|.-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 5689999999999999988887753
No 19
>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=41.66 E-value=25 Score=20.17 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=15.0
Q ss_pred eeeeccCCccEEeccCCCCc
Q 033060 4 IFLVELKGRSYYKCRFCNSH 23 (128)
Q Consensus 4 ~f~~yl~g~~~y~C~~C~th 23 (128)
.-+.|..|-+.+.|..|++.
T Consensus 9 t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 9 TLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cEeecCCCCCeEECCCCCeE
Confidence 45677788788888888764
No 20
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=39.50 E-value=20 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=16.0
Q ss_pred EEeeeeeeecCCeeeeEEEEe
Q 033060 67 TVEDIFCCCCGQIVGWKYVAA 87 (128)
Q Consensus 67 ~V~DI~C~~C~~~lGWkY~~A 87 (128)
.+.-.||..|+++|-|+....
T Consensus 66 ~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 66 SAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCeecccCCCceEEecCCC
Confidence 344449999999999986544
No 21
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=37.31 E-value=29 Score=22.07 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=10.6
Q ss_pred cEEeccCCCCcc
Q 033060 13 SYYKCRFCNSHL 24 (128)
Q Consensus 13 ~~y~C~~C~thL 24 (128)
..|.|..|+..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 579999999988
No 22
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=34.04 E-value=39 Score=24.97 Aligned_cols=30 Identities=20% Similarity=0.118 Sum_probs=25.0
Q ss_pred ccCCCeEEEeeccccccCCcccceeeeecc
Q 033060 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (128)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 65 (128)
.|+||.|+.--.+.|+..|..-+..+.++-
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 689999999999999999988776665554
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=33.28 E-value=27 Score=18.60 Aligned_cols=15 Identities=33% Similarity=0.990 Sum_probs=11.6
Q ss_pred CCccEEeccCCCCcc
Q 033060 10 KGRSYYKCRFCNSHL 24 (128)
Q Consensus 10 ~g~~~y~C~~C~thL 24 (128)
.|++.|.|..|..-.
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 467889999997543
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=31.06 E-value=28 Score=20.55 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=21.0
Q ss_pred eeeeeeecCCee-eeEEEEeccCCccee
Q 033060 69 EDIFCCCCGQIV-GWKYVAAHDKNQKYK 95 (128)
Q Consensus 69 ~DI~C~~C~~~l-GWkY~~A~e~sqkYK 95 (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 378999999988 677777777777774
No 25
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=30.39 E-value=22 Score=24.56 Aligned_cols=16 Identities=31% Similarity=0.845 Sum_probs=13.4
Q ss_pred EEeccCCCCcccCCCC
Q 033060 14 YYKCRFCNSHLALADS 29 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~ 29 (128)
.|.|++|++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999877655
No 26
>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=29.89 E-value=67 Score=25.38 Aligned_cols=30 Identities=10% Similarity=0.135 Sum_probs=17.9
Q ss_pred CcccceeeeeccEEEeeeeeeecCCeeeeEE
Q 033060 54 GPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (128)
Q Consensus 54 g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 84 (128)
|...-+....+.+.. --||..|++.|-++.
T Consensus 74 G~~~l~~Y~ss~~~~-R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 74 NGDKLKVVDASATIQ-RHACKGCGTHMYGRI 103 (182)
T ss_pred CCcceEEEeCCCCEE-eecCCCCCCcccccc
Confidence 444333333444444 449999999996544
No 27
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.43 E-value=26 Score=20.50 Aligned_cols=14 Identities=29% Similarity=0.646 Sum_probs=7.1
Q ss_pred eeeecCCeeeeEEE
Q 033060 72 FCCCCGQIVGWKYV 85 (128)
Q Consensus 72 ~C~~C~~~lGWkY~ 85 (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 79999999988775
No 28
>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=26.87 E-value=34 Score=20.49 Aligned_cols=16 Identities=31% Similarity=0.663 Sum_probs=13.2
Q ss_pred cEEeccCCCCcccCCC
Q 033060 13 SYYKCRFCNSHLALAD 28 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~ 28 (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 4589999999997766
No 29
>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=26.24 E-value=59 Score=17.95 Aligned_cols=20 Identities=25% Similarity=0.663 Sum_probs=14.9
Q ss_pred ceeeeccCCccEEeccCCCC
Q 033060 3 RIFLVELKGRSYYKCRFCNS 22 (128)
Q Consensus 3 ~~f~~yl~g~~~y~C~~C~t 22 (128)
|..+.|..|-+.-.|+.|++
T Consensus 5 r~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CceEEcCCCCCCeECCccCc
Confidence 45567888877788888875
No 30
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.52 E-value=81 Score=18.73 Aligned_cols=17 Identities=18% Similarity=0.511 Sum_probs=12.8
Q ss_pred cEEeccCCCCcccCCCC
Q 033060 13 SYYKCRFCNSHLALADS 29 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~~ 29 (128)
..|.|..|.-+......
T Consensus 19 ~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 19 RRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CEEECCcCCCeEECCCc
Confidence 47999999987665555
No 31
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=23.82 E-value=24 Score=29.85 Aligned_cols=22 Identities=18% Similarity=0.483 Sum_probs=18.5
Q ss_pred CCccEEeccCCCCcccCCCCee
Q 033060 10 KGRSYYKCRFCNSHLALADSVL 31 (128)
Q Consensus 10 ~g~~~y~C~~C~thLa~~~~lI 31 (128)
.|++.|.|.+|+.-+|..+.|-
T Consensus 211 TGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred cCCCCccCCcccchhcchHHHH
Confidence 5789999999998888877664
No 32
>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=23.61 E-value=14 Score=18.49 Aligned_cols=16 Identities=25% Similarity=0.796 Sum_probs=11.9
Q ss_pred EeccCCCCcccCCCCe
Q 033060 15 YKCRFCNSHLALADSV 30 (128)
Q Consensus 15 y~C~~C~thLa~~~~l 30 (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 33
>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=34 Score=18.43 Aligned_cols=13 Identities=31% Similarity=0.805 Sum_probs=11.0
Q ss_pred cEEeccCCCCccc
Q 033060 13 SYYKCRFCNSHLA 25 (128)
Q Consensus 13 ~~y~C~~C~thLa 25 (128)
.-|.|..|+..|+
T Consensus 26 ~Cf~C~~C~~~L~ 38 (39)
T smart00132 26 ECFKCSKCGKPLG 38 (39)
T ss_pred cCCCCcccCCcCc
Confidence 4599999999886
No 34
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=22.99 E-value=69 Score=18.22 Aligned_cols=15 Identities=27% Similarity=0.711 Sum_probs=12.6
Q ss_pred cEEeccCCCCcccCC
Q 033060 13 SYYKCRFCNSHLALA 27 (128)
Q Consensus 13 ~~y~C~~C~thLa~~ 27 (128)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 579999999988764
No 35
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=22.89 E-value=25 Score=22.42 Aligned_cols=35 Identities=17% Similarity=0.412 Sum_probs=23.7
Q ss_pred eeccccccCCcccceeeeeccEEEeeeeeeecCCeeeeEE
Q 033060 45 FSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVGWKY 84 (128)
Q Consensus 45 f~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 84 (128)
|++++.+..|..+ |+...--.+-|.+|.++=|---
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~ 36 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAP 36 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccc
Confidence 5677888887766 3333333456999999988743
No 36
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=22.83 E-value=96 Score=23.86 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=26.2
Q ss_pred ccCCCeEEEeeccccccCCcccceeeeeccE
Q 033060 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGMH 66 (128)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H 66 (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 7999999999999999999988877766553
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=12 Score=19.59 Aligned_cols=18 Identities=11% Similarity=0.431 Sum_probs=13.1
Q ss_pred EEeccCCCCcccCCCCee
Q 033060 14 YYKCRFCNSHLALADSVL 31 (128)
Q Consensus 14 ~y~C~~C~thLa~~~~lI 31 (128)
+|.|..|+.-+.+...++
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 488999998776655543
No 38
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=22.51 E-value=52 Score=25.51 Aligned_cols=28 Identities=18% Similarity=0.317 Sum_probs=24.3
Q ss_pred ccEEeccCCCCcccCCCCeeeeccccCC
Q 033060 12 RSYYKCRFCNSHLALADSVLSWSFNCRR 39 (128)
Q Consensus 12 ~~~y~C~~C~thLa~~~~lISk~F~G~~ 39 (128)
++.|-|..|+.+=+...-|+.-.|....
T Consensus 118 prRYfCtQCHVPQada~PLV~N~F~~~~ 145 (149)
T PRK11586 118 PRRYFCLQCHVPQADTAPIVGNTFTPSK 145 (149)
T ss_pred ccceeeccccCccccCccCCCCCccchh
Confidence 5789999999999999999998887543
No 39
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=22.09 E-value=89 Score=20.50 Aligned_cols=32 Identities=19% Similarity=0.283 Sum_probs=22.3
Q ss_pred ccCCccEEeccCCCCcccCCCCeeeeccccCCC
Q 033060 8 ELKGRSYYKCRFCNSHLALADSVLSWSFNCRRG 40 (128)
Q Consensus 8 yl~g~~~y~C~~C~thLa~~~~lISk~F~G~~G 40 (128)
|-.+.| =.|+.|+..++..+--|.+-+....+
T Consensus 2 yAks~R-a~Ck~C~~~I~kg~lRiG~~~~~~~~ 33 (82)
T PF00645_consen 2 YAKSGR-AKCKGCKKKIAKGELRIGKIVPSPEG 33 (82)
T ss_dssp E-SSST-EBETTTSCBE-TTSEEEEEEEEETTS
T ss_pred cCCCCC-ccCcccCCcCCCCCEEEEEEeccccc
Confidence 444434 38999999999888878776666655
No 40
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=21.85 E-value=1e+02 Score=24.49 Aligned_cols=40 Identities=15% Similarity=0.016 Sum_probs=25.6
Q ss_pred EEeeeeeeecCCeeeeEEEEeccCCcceeCCeEEEEeeceeeec
Q 033060 67 TVEDIFCCCCGQIVGWKYVAAHDKNQKYKEGKFVLERWRIVEEV 110 (128)
Q Consensus 67 ~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~i~~~~ 110 (128)
.+.--||..|++.|-+.++..-. --.|..+|-...+-...
T Consensus 90 ~i~R~FC~~CGS~L~~~~e~~~~----~~pgl~fV~~gllDd~~ 129 (191)
T PRK05417 90 TIQRHACKECGVHMYGRIENKDH----PFYGLDFVHTELSQEQG 129 (191)
T ss_pred CeEeeeCCCCCCccccccccccC----CCCCeEEEehhhcCCCC
Confidence 35555999999999887662200 12377777776665543
No 41
>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=21.51 E-value=53 Score=19.56 Aligned_cols=12 Identities=33% Similarity=1.124 Sum_probs=7.4
Q ss_pred cEEeccCCCCcc
Q 033060 13 SYYKCRFCNSHL 24 (128)
Q Consensus 13 ~~y~C~~C~thL 24 (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 589999998754
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.33 E-value=29 Score=18.67 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=6.6
Q ss_pred eeeeeecCCee
Q 033060 70 DIFCCCCGQIV 80 (128)
Q Consensus 70 DI~C~~C~~~l 80 (128)
+-||..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45677776643
No 43
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=21.02 E-value=1.1e+02 Score=22.49 Aligned_cols=30 Identities=13% Similarity=0.073 Sum_probs=23.6
Q ss_pred ccCCCeEEEeeccccccCCcccceeeeecc
Q 033060 36 NCRRGRAYLFSDVVNIMLGPQEERLMLSGM 65 (128)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 65 (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 688899998889999998887666655553
No 44
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=21.02 E-value=64 Score=27.93 Aligned_cols=53 Identities=21% Similarity=0.200 Sum_probs=30.9
Q ss_pred cCCccEEeccCCCCcccCCCCeeeeccccCCCe--EEEeeccccccCCcccceeeeeccEEEeeeeeeecCCeee
Q 033060 9 LKGRSYYKCRFCNSHLALADSVLSWSFNCRRGR--AYLFSDVVNIMLGPQEERLMLSGMHTVEDIFCCCCGQIVG 81 (128)
Q Consensus 9 l~g~~~y~C~~C~thLa~~~~lISk~F~G~~G~--AyLf~~v~Nv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lG 81 (128)
|....+|.|..|. +-|.|+.|. ||.-..-.|-.+ --.+.| .++||-.|+..|.
T Consensus 23 ~~~~n~~~CL~cg-----------~~~~g~~~~~ha~~H~~~~~H~~----~v~l~t-----~~~yc~~~~~~v~ 77 (440)
T cd02669 23 LSNLNVYACLVCG-----------KYFQGRGKGSHAYTHSLEDNHHV----FLNLET-----LKFYCLPDNYEII 77 (440)
T ss_pred CCCCcEEEEcccC-----------CeecCCCCCcHHHHHhhccCCCE----EEECCC-----CCEEEeCCCCEEe
Confidence 3445679999998 678777555 544221111111 001112 7899999998765
No 45
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.71 E-value=78 Score=28.39 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=10.7
Q ss_pred eeeeEEEEeccCC
Q 033060 79 IVGWKYVAAHDKN 91 (128)
Q Consensus 79 ~lGWkY~~A~e~s 91 (128)
.||=||-+++...
T Consensus 271 ~LG~kYS~~lna~ 283 (457)
T KOG2324|consen 271 LLGTKYSKPLNAK 283 (457)
T ss_pred EeccccccccCce
Confidence 6899998888766
No 46
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.22 E-value=56 Score=24.57 Aligned_cols=67 Identities=18% Similarity=0.285 Sum_probs=35.1
Q ss_pred cEEeccCCCCcccCCCCeee--eccccCCCeE----EEeeccccccCCcccc----eee---eeccEEEeeeeeeecCCe
Q 033060 13 SYYKCRFCNSHLALADSVLS--WSFNCRRGRA----YLFSDVVNIMLGPQEE----RLM---LSGMHTVEDIFCCCCGQI 79 (128)
Q Consensus 13 ~~y~C~~C~thLa~~~~lIS--k~F~G~~G~A----yLf~~v~Nv~~g~~e~----r~m---~TG~H~V~DI~C~~C~~~ 79 (128)
+.|.|.+|+.+|.++.+-.- .-|-.....+ .+-=..+|-...+.+. +.| +.-+..+++=+|+.|+..
T Consensus 27 ~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~pe~k~~~ri~~L~~~i~~~~pv~~~~~W~Cv~C~~~ 106 (128)
T PF11682_consen 27 DHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLDPEEKERRRIKRLRRMIADLDPVPRKTDWHCVMCGNH 106 (128)
T ss_pred CeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceECcccchHHHHHHHHHhccccCCCCcCceEEEecCCCc
Confidence 67999999999998855332 2343322221 1100112222221110 111 233457889999999873
No 47
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.21 E-value=32 Score=18.27 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=5.9
Q ss_pred eeeeecCCee
Q 033060 71 IFCCCCGQIV 80 (128)
Q Consensus 71 I~C~~C~~~l 80 (128)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 4577776643
Done!