Query 033956
Match_columns 107
No_of_seqs 112 out of 323
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:10:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033956.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033956hhsearch_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 2.3E-51 4.9E-56 293.8 -1.7 104 4-107 8-113 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 2E-34 4.3E-39 195.1 6.2 89 10-104 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.0 0.0032 6.9E-08 44.9 1.2 87 10-100 4-94 (123)
4 PF01641 SelR: SelR domain; I 95.0 0.019 4.2E-07 41.5 2.4 72 8-86 35-106 (124)
5 TIGR00357 methionine-R-sulfoxi 94.9 0.028 6E-07 41.3 3.1 66 8-81 38-104 (134)
6 PRK00222 methionine sulfoxide 94.6 0.032 6.8E-07 41.3 2.7 68 8-82 41-108 (142)
7 PRK05508 methionine sulfoxide 93.4 0.087 1.9E-06 38.0 3.0 64 8-81 31-94 (119)
8 PRK05550 bifunctional methioni 91.6 0.15 3.2E-06 41.4 2.5 64 8-81 34-97 (283)
9 PRK14018 trifunctional thiored 90.4 0.28 6E-06 42.8 3.3 68 8-82 416-483 (521)
10 PF14976 FAM72: FAM72 protein 89.7 0.68 1.5E-05 34.7 4.4 62 10-83 15-88 (150)
11 COG0229 Conserved domain frequ 87.3 0.93 2E-05 33.6 3.8 65 8-79 40-104 (140)
12 KOG0856 Predicted pilin-like t 85.7 1 2.2E-05 33.6 3.3 66 8-81 52-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 77.2 3.9 8.4E-05 32.7 4.1 17 10-26 106-122 (354)
14 PF13465 zf-H2C2_2: Zinc-finge 53.9 8.1 0.00017 20.1 1.1 14 6-19 10-23 (26)
15 PF11023 DUF2614: Protein of u 49.1 6.3 0.00014 28.4 0.2 24 9-32 84-107 (114)
16 PF10246 MRP-S35: Mitochondria 48.6 9.9 0.00021 27.0 1.1 50 40-94 10-65 (104)
17 COG1996 RPC10 DNA-directed RNA 41.9 20 0.00042 22.2 1.6 13 8-20 4-16 (49)
18 PRK05417 glutathione-dependent 41.5 49 0.0011 25.4 4.1 54 47-105 75-128 (191)
19 PRK11586 napB nitrate reductas 38.6 19 0.00041 27.0 1.4 29 7-35 117-145 (149)
20 COG3791 Uncharacterized conser 36.4 31 0.00068 24.4 2.2 21 63-83 66-86 (133)
21 TIGR00037 eIF_5A translation i 35.7 45 0.00097 23.9 2.9 30 32-61 35-64 (130)
22 PF03811 Zn_Tnp_IS1: InsA N-te 35.3 23 0.00051 20.2 1.1 27 65-91 4-31 (36)
23 PF00412 LIM: LIM domain; Int 34.9 19 0.0004 21.0 0.7 15 10-24 26-40 (58)
24 COG3043 NapB Nitrate reductase 32.3 29 0.00063 26.2 1.5 30 7-36 123-152 (155)
25 PLN03107 eukaryotic translatio 32.1 53 0.0011 24.5 2.9 30 32-61 49-78 (159)
26 PRK03999 translation initiatio 31.3 60 0.0013 23.2 3.0 31 31-61 33-63 (129)
27 KOG2462 C2H2-type Zn-finger pr 29.3 16 0.00035 29.9 -0.3 23 5-27 210-232 (279)
28 PF00645 zf-PARP: Poly(ADP-rib 29.3 57 0.0012 20.7 2.4 32 4-36 2-33 (82)
29 KOG2272 Focal adhesion protein 29.1 35 0.00076 28.2 1.6 60 7-78 134-195 (332)
30 TIGR02820 formald_GSH S-(hydro 29.0 72 0.0016 24.4 3.2 34 46-80 70-103 (182)
31 PF06170 DUF983: Protein of un 28.7 23 0.00049 23.9 0.4 23 12-42 10-32 (86)
32 PF04828 GFA: Glutathione-depe 27.9 62 0.0013 20.0 2.3 31 49-79 31-61 (92)
33 PF13248 zf-ribbon_3: zinc-rib 27.7 21 0.00046 18.6 0.1 12 65-76 15-26 (26)
34 PF02945 Endonuclease_7: Recom 27.0 8.8 0.00019 25.6 -1.8 20 58-79 46-65 (81)
35 PF14803 Nudix_N_2: Nudix N-te 26.8 36 0.00078 19.2 0.9 14 68-81 2-15 (34)
36 smart00132 LIM Zinc-binding do 26.7 25 0.00053 18.4 0.2 12 10-21 27-38 (39)
37 PF10058 DUF2296: Predicted in 26.7 23 0.0005 21.9 0.2 35 41-80 2-36 (54)
38 PF13842 Tnp_zf-ribbon_2: DDE_ 26.6 50 0.0011 18.2 1.5 15 9-23 15-29 (32)
39 PF00096 zf-C2H2: Zinc finger, 26.6 11 0.00023 18.3 -1.1 16 11-26 1-16 (23)
40 PF14353 CpXC: CpXC protein 26.3 27 0.00058 24.2 0.4 46 40-87 14-59 (128)
41 PF13912 zf-C2H2_6: C2H2-type 26.1 8.2 0.00018 19.5 -1.7 18 10-27 1-18 (27)
42 PF10955 DUF2757: Protein of u 26.0 27 0.00059 23.3 0.4 16 10-25 4-19 (76)
43 KOG2324 Prolyl-tRNA synthetase 25.9 52 0.0011 28.6 2.1 13 75-87 271-283 (457)
44 PF12760 Zn_Tnp_IS1595: Transp 25.7 58 0.0013 18.9 1.8 14 5-18 32-45 (46)
45 TIGR03791 TTQ_mauG tryptophan 25.4 38 0.00082 27.3 1.2 33 4-36 17-51 (291)
46 PRK00398 rpoP DNA-directed RNA 25.1 39 0.00085 19.6 0.9 15 10-24 3-17 (46)
47 PF13240 zinc_ribbon_2: zinc-r 24.1 28 0.00061 17.9 0.1 10 67-76 14-23 (23)
48 COG3721 HugX Putative heme iro 21.0 42 0.00091 25.7 0.6 37 24-60 121-162 (176)
49 PLN02739 serine acetyltransfer 20.6 52 0.0011 27.8 1.2 43 4-49 3-50 (355)
50 PRK04016 DNA-directed RNA poly 20.6 16 0.00035 23.6 -1.4 18 65-82 3-20 (62)
51 TIGR01053 LSD1 zinc finger dom 20.1 73 0.0016 17.6 1.3 15 4-18 13-27 (31)
52 cd07973 Spt4 Transcription elo 20.0 40 0.00088 23.3 0.3 22 12-33 22-49 (98)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=2.3e-51 Score=293.85 Aligned_cols=104 Identities=60% Similarity=1.097 Sum_probs=99.3
Q ss_pred eecC-CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033956 4 ELVG-PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYER 82 (107)
Q Consensus 4 ~l~g-~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 82 (107)
+|.+ ++.|+|++|+||||+++|||||+|+|++|+||||++|+||+.|+.|+|.|+||+|+|+||+|+.|++.|||||+.
T Consensus 8 ~l~~~~~~y~C~~C~thla~~~dliSksf~gr~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~~~GWkYe~ 87 (122)
T KOG3399|consen 8 MLEANHRLYSCAHCKTHLARHDDLISKSFRGRTGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGTGLGWKYEH 87 (122)
T ss_pred HhccCCceEeccCCcccccchhhccccccccCCCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCCCcceeeee
Confidence 3444 378999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccccccceEEEEeccccccC-C
Q 033956 83 AFEASQKYKEGKFIFEKSKIAKEN-W 107 (107)
Q Consensus 83 A~e~sqkYKEGkfILE~~~i~~~~-w 107 (107)
|||+||||||||||||+++|.+++ |
T Consensus 88 a~e~sQkyKEGk~ilE~~~i~~~~g~ 113 (122)
T KOG3399|consen 88 AYEKSQKYKEGKFILELAEIFKPEGW 113 (122)
T ss_pred ccCchhhhcCcchHHHHHHhcCCCCc
Confidence 999999999999999999999875 5
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=100.00 E-value=2e-34 Score=195.09 Aligned_cols=89 Identities=53% Similarity=1.037 Sum_probs=85.3
Q ss_pred eEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceec----EEEeeeecccCCCceeeEEEeecc
Q 033956 10 LYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGL----HTVADIYCSDCREVLGWKYERAFE 85 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~----h~V~DI~C~~C~~~lGWkY~~A~e 85 (107)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|.||. |+|+||+|++|++.|||||+.|++
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 7888888999999999 999999999999999999999999
Q ss_pred cccccccceEEEEeccccc
Q 033956 86 ASQKYKEGKFIFEKSKIAK 104 (107)
Q Consensus 86 ~sqkYKEGkfILE~~~i~~ 104 (107)
+ |+||||+||||++.|..
T Consensus 77 ~-~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASISS 94 (96)
T ss_pred h-HhhhCCEEEEEhhHEEE
Confidence 9 99999999999998863
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=95.97 E-value=0.0032 Score=44.89 Aligned_cols=87 Identities=17% Similarity=0.224 Sum_probs=57.9
Q ss_pred eEEeecCcCCCCCCCCeeeeeecCCC----ceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeecc
Q 033956 10 LYSCHNCRNHVALHDDIISKAFQGRN----GRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYERAFE 85 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk~F~G~~----G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e 85 (107)
.+.|++|.+.+++.+||-.- .++| .+. |...+.+...|.+.....-+.+....|+|..|+..+|-.+..---
T Consensus 4 ~llC~kC~~~~C~~~DIr~i--e~~hhv~v~p~--F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m~yk~~ 79 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKI--ENSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMKYKGV 79 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEE--TTTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEEETTE
T ss_pred EEECCCCCceeEchhheEEe--cCCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheEECCc
Confidence 48899999999999998764 1111 222 335666666666544445588899999999999999987754332
Q ss_pred cccccccceEEEEec
Q 033956 86 ASQKYKEGKFIFEKS 100 (107)
Q Consensus 86 ~sqkYKEGkfILE~~ 100 (107)
+==-.|.-.|+++..
T Consensus 80 ~LP~L~iksfvv~~~ 94 (123)
T PF11648_consen 80 ELPCLKIKSFVVELE 94 (123)
T ss_dssp EEEEE-GGGEEEEET
T ss_pred cccEEEeeeeeeeec
Confidence 223445556664433
No 4
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=94.98 E-value=0.019 Score=41.52 Aligned_cols=72 Identities=19% Similarity=0.405 Sum_probs=46.1
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeeccc
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYERAFEA 86 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~ 86 (107)
.-+|.|+.|.++|=+++. -|....|=.-.+..+..-.+...+|.. -|+. -..|.|..|+..||=-......+
T Consensus 35 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~v~~~~D~s--~g~~-R~Ev~C~~Cg~HLGHVF~DGp~~ 106 (124)
T PF01641_consen 35 EGIYVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFS--HGMV-RTEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp SEEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEEC--TSSE-EEEEEETTTCCEEEEEESTSSTT
T ss_pred CEEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEecccc--CCce-EEEEEecCCCCccccEeCCCCCC
Confidence 348999999999987653 466666665555555442333333332 2444 44899999999999776655543
No 5
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=94.92 E-value=0.028 Score=41.27 Aligned_cols=66 Identities=20% Similarity=0.458 Sum_probs=43.3
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecc-cccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHA-MNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYE 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v-~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
+-+|.|+.|.++|-++++ -|....|=.-.+..+ -|. +...+|+. -|+.. ..|.|..|+..||=-..
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~-V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~ 104 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEV-VAYERDES--HGMIR-TEVRCRNCDAHLGHVFD 104 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCc-eEEeecCC--CCcEE-EEEEecCCCCccCcccC
Confidence 347999999999988765 355556655555555 232 22333332 24444 58999999999996554
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.56 E-value=0.032 Score=41.34 Aligned_cols=68 Identities=18% Similarity=0.390 Sum_probs=44.2
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYER 82 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 82 (107)
+-+|.|+.|.++|=++++ -|.-..|=.-.+..+..-.+...+|+ .-|+.. ..|.|..|+..||=-...
T Consensus 41 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~--s~gm~R-tEv~C~~Cg~HLGHVF~D 108 (142)
T PRK00222 41 KGIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDT--SHGMVR-TEVRCANCDSHLGHVFPD 108 (142)
T ss_pred CeEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeecc--CCCceE-EEEEeCCCCCccCcccCC
Confidence 448999999999988753 46666776665665532222223332 123322 589999999999976643
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.40 E-value=0.087 Score=38.02 Aligned_cols=64 Identities=23% Similarity=0.466 Sum_probs=43.1
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYE 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
+-+|.|+.|.++|=++++ -|.-..|=.-.+..+-|. +...+|.. | + =..|.|..|+..||=-..
T Consensus 31 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~-v~~~~D~~---~-~-RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 31 KGTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKGA-VKRIPDAD---G-R-RTEIVCANCGGHLGHVFE 94 (119)
T ss_pred CeEEEecCCCCccccccc----cccCCCCCcccCcccccc-eEEEecCC---C-c-EEEEEeCCCCCccCcccC
Confidence 448999999999988764 466666655555555432 33334433 2 2 467999999999995543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.55 E-value=0.15 Score=41.44 Aligned_cols=64 Identities=23% Similarity=0.450 Sum_probs=43.1
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYE 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
+-+|.|+.|+++|=++++ -|.-..|=.-.++.+.|-..- .++.. |+ =..|.|..|++.||--..
T Consensus 34 ~G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~~~-~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAVKR-LPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccEE-EEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 347999999999988664 465566655556666543322 22222 33 478999999999996654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.40 E-value=0.28 Score=42.76 Aligned_cols=68 Identities=13% Similarity=0.170 Sum_probs=45.3
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYER 82 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 82 (107)
+-+|.|+.|+++|=++++ -|....|=.-.+..+-+-.+....|.+ -|++. ..|.|..|+..||--...
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 PGIYVDVVSGEPLFSSAD----KYDSGCGWPSFTRPIDAKVVTEHDDFS--YNMRR-TEVRSRAADSHLGHVFPD 483 (521)
T ss_pred CEEEEecCCCCccccCcc----cccCCCCCcccCcccCcCceEEeeccC--CCceE-EEEEECCCCCcCCcccCC
Confidence 448999999999988753 466666665555555433333333332 24444 389999999999976654
No 10
>PF14976 FAM72: FAM72 protein
Probab=89.67 E-value=0.68 Score=34.70 Aligned_cols=62 Identities=19% Similarity=0.438 Sum_probs=39.4
Q ss_pred eEEeecCcCCCCCCCCeeeeeecCCCceEEEeeccccccc----CCccceeeceec--------EEEeeeecccCCCcee
Q 033956 10 LYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVV----GPKEDRHLLTGL--------HTVADIYCSDCREVLG 77 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~----g~~~~r~m~TG~--------h~V~DI~C~~C~~~lG 77 (107)
+..|+.|.+-|+...- ||.|..+ .|+.+ -||....-.+|. =.++|+-|..|+..||
T Consensus 15 ~L~C~~C~~~l~~RgM-----------kAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~vG 82 (150)
T PF14976_consen 15 ILCCKFCDQVLCNRGM-----------KAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIVG 82 (150)
T ss_pred EEECCCCCchhccchh-----------hheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCeee
Confidence 4789999988876432 4555554 33331 122222223333 4899999999999999
Q ss_pred eEEEee
Q 033956 78 WKYERA 83 (107)
Q Consensus 78 WkY~~A 83 (107)
+.....
T Consensus 83 YhV~~P 88 (150)
T PF14976_consen 83 YHVVVP 88 (150)
T ss_pred eEEEEE
Confidence 887654
No 11
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=87.33 E-value=0.93 Score=33.63 Aligned_cols=65 Identities=23% Similarity=0.446 Sum_probs=43.8
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeE
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWK 79 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWk 79 (107)
+-+|.|+.|..+|-++++ -|....|=--.+.-+..-.+...+|+ .-|++.+ .|.|..|++.||=-
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 348999999999987765 35555554444555544444444443 3455554 89999999999943
No 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=85.66 E-value=1 Score=33.58 Aligned_cols=66 Identities=18% Similarity=0.419 Sum_probs=39.5
Q ss_pred CCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeecc-cccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033956 8 PRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSHA-MNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYE 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~v-~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
+-+|.|..|.++|-++. .-|.-..|=--.|+.+ .+. +-..+|. .-|.+ =.+|.|..|+..||--.+
T Consensus 52 ~GvY~C~~C~~pLykS~----tKfdsgcGWPAF~e~i~~ga-I~r~~d~--s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 52 EGVYVCAGCGTPLYKST----TKFDSGCGWPAFFEAIGPGA-ITRTPDN--SRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCcccccc----ccccCCCCCchhhhccCCCc-eeecccc--CCCCc-ceEEEEeecCCceeeeec
Confidence 45899999999998764 3465555544445444 111 1111111 11222 358999999999996554
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=77.24 E-value=3.9 Score=32.66 Aligned_cols=17 Identities=24% Similarity=0.632 Sum_probs=13.9
Q ss_pred eEEeecCcCCCCCCCCe
Q 033956 10 LYSCHNCRNHVALHDDI 26 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~l 26 (107)
.+.|++|+..|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766543
No 14
>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=53.95 E-value=8.1 Score=20.07 Aligned_cols=14 Identities=29% Similarity=0.821 Sum_probs=11.4
Q ss_pred cCCCeEEeecCcCC
Q 033956 6 VGPRLYSCHNCRNH 19 (107)
Q Consensus 6 ~g~~~y~C~~C~th 19 (107)
.|.++|.|..|..-
T Consensus 10 ~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 10 TGEKPYKCPYCGKS 23 (26)
T ss_dssp SSSSSEEESSSSEE
T ss_pred CCCCCCCCCCCcCe
Confidence 57889999999753
No 15
>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=49.07 E-value=6.3 Score=28.38 Aligned_cols=24 Identities=25% Similarity=0.672 Sum_probs=20.9
Q ss_pred CeEEeecCcCCCCCCCCeeeeeec
Q 033956 9 RLYSCHNCRNHVALHDDIISKAFQ 32 (107)
Q Consensus 9 ~~y~C~~C~thLa~~~~liSk~F~ 32 (107)
|...|-+|++||+...++--|.|+
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~ 107 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFD 107 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhh
Confidence 568999999999999988877775
No 16
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=48.56 E-value=9.9 Score=26.96 Aligned_cols=50 Identities=26% Similarity=0.365 Sum_probs=32.5
Q ss_pred EeecccccccCCccceeeceec--EEEeeeecccCCCceeeEEE----eecccccccccce
Q 033956 40 LFSHAMNVVVGPKEDRHLLTGL--HTVADIYCSDCREVLGWKYE----RAFEASQKYKEGK 94 (107)
Q Consensus 40 Lf~~v~Nv~~g~~~~r~m~TG~--h~V~DI~C~~C~~~lGWkY~----~A~e~sqkYKEGk 94 (107)
|+.+-.=+..|+++++. ++|. |+|.|- =---+|||.. +.-..+++|.+|-
T Consensus 10 lLR~S~fi~lG~~~gk~-V~G~I~hvv~dd----LYIDfG~KFhcVc~rp~~~~~~y~~G~ 65 (104)
T PF10246_consen 10 LLRNSPFIQLGDPEGKI-VIGKIFHVVDDD----LYIDFGGKFHCVCKRPAVNGEKYVRGS 65 (104)
T ss_pred HhcCChhhhcCCccCCE-EEEEEEEEecCc----eEEEeCCceeEEEecccccccccccCC
Confidence 44444446689998875 6777 888761 1224588873 3345778899885
No 17
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.89 E-value=20 Score=22.17 Aligned_cols=13 Identities=31% Similarity=0.682 Sum_probs=10.8
Q ss_pred CCeEEeecCcCCC
Q 033956 8 PRLYSCHNCRNHV 20 (107)
Q Consensus 8 ~~~y~C~~C~thL 20 (107)
...|.|..|+..+
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 3569999999988
No 18
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=41.51 E-value=49 Score=25.40 Aligned_cols=54 Identities=9% Similarity=0.049 Sum_probs=29.5
Q ss_pred cccCCccceeeceecEEEeeeecccCCCceeeEEEeecccccccccceEEEEecccccc
Q 033956 47 VVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYERAFEASQKYKEGKFIFEKSKIAKE 105 (107)
Q Consensus 47 v~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~i~~~ 105 (107)
+..|+...+...+|.. +.--+|..|++.|-+..+....+ -.|..+|=.+.+...
T Consensus 75 it~g~~~l~~y~ss~~-i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllDd~ 128 (191)
T PRK05417 75 VTANGDKLKVVDESAT-IQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQEQ 128 (191)
T ss_pred EEeCCcceEEEeCCCC-eEeeeCCCCCCccccccccccCC----CCCeEEEehhhcCCC
Confidence 3335444333333433 45559999999998877622101 126666655555443
No 19
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=38.56 E-value=19 Score=27.01 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=25.1
Q ss_pred CCCeEEeecCcCCCCCCCCeeeeeecCCC
Q 033956 7 GPRLYSCHNCRNHVALHDDIISKAFQGRN 35 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~F~G~~ 35 (107)
.++.|-|..|+++=+...-|+.-.|....
T Consensus 117 sprRYfCtQCHVPQada~PLV~N~F~~~~ 145 (149)
T PRK11586 117 APRRYFCLQCHVPQADTAPIVGNTFTPSK 145 (149)
T ss_pred CccceeeccccCccccCccCCCCCccchh
Confidence 36789999999999999999999887544
No 20
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=36.36 E-value=31 Score=24.40 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=16.2
Q ss_pred EEeeeecccCCCceeeEEEee
Q 033956 63 TVADIYCSDCREVLGWKYERA 83 (107)
Q Consensus 63 ~V~DI~C~~C~~~lGWkY~~A 83 (107)
.+.-.||..|++.|-|+....
T Consensus 66 ~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 66 SAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCeecccCCCceEEecCCC
Confidence 344449999999999997554
No 21
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=35.68 E-value=45 Score=23.86 Aligned_cols=30 Identities=20% Similarity=0.174 Sum_probs=25.8
Q ss_pred cCCCceEEEeecccccccCCccceeeceec
Q 033956 32 QGRNGRAFLFSHAMNVVVGPKEDRHLLTGL 61 (107)
Q Consensus 32 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 61 (107)
.|+||.|+.--++.|+..|...+...-++.
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 699999999999999999999887766554
No 22
>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=35.30 E-value=23 Score=20.23 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=21.2
Q ss_pred eeeecccCCCce-eeEEEeecccccccc
Q 033956 65 ADIYCSDCREVL-GWKYERAFEASQKYK 91 (107)
Q Consensus 65 ~DI~C~~C~~~l-GWkY~~A~e~sqkYK 91 (107)
-||.|..|++.- --|+-+.-.-.|+|.
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryr 31 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYR 31 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEe
Confidence 489999999998 677777776777774
No 23
>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=34.86 E-value=19 Score=20.99 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=12.1
Q ss_pred eEEeecCcCCCCCCC
Q 033956 10 LYSCHNCRNHVALHD 24 (107)
Q Consensus 10 ~y~C~~C~thLa~~~ 24 (107)
-|.|..|+.+|...+
T Consensus 26 Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGD 40 (58)
T ss_dssp TSBETTTTCBTTTSS
T ss_pred ccccCCCCCccCCCe
Confidence 478999999887766
No 24
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=32.25 E-value=29 Score=26.20 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=25.6
Q ss_pred CCCeEEeecCcCCCCCCCCeeeeeecCCCc
Q 033956 7 GPRLYSCHNCRNHVALHDDIISKAFQGRNG 36 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~F~G~~G 36 (107)
++|.|-|..|+.+=|...-|+--.|..-.|
T Consensus 123 SPRRYFClQCHVPQaD~kPlV~N~F~p~~~ 152 (155)
T COG3043 123 SPRRYFCLQCHVPQADVKPLVGNTFKPMKG 152 (155)
T ss_pred CccceeeeecccccccccccCCCCcccchh
Confidence 478999999999999999999888875443
No 25
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=32.10 E-value=53 Score=24.46 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=26.4
Q ss_pred cCCCceEEEeecccccccCCccceeeceec
Q 033956 32 QGRNGRAFLFSHAMNVVVGPKEDRHLLTGL 61 (107)
Q Consensus 32 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 61 (107)
.|+||.|+.--.+.|+..|...++...++-
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 799999999999999999999887776665
No 26
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=31.35 E-value=60 Score=23.18 Aligned_cols=31 Identities=19% Similarity=0.123 Sum_probs=25.6
Q ss_pred ecCCCceEEEeecccccccCCccceeeceec
Q 033956 31 FQGRNGRAFLFSHAMNVVVGPKEDRHLLTGL 61 (107)
Q Consensus 31 F~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 61 (107)
-.|+||.|+.--++.|+..|...++...++.
T Consensus 33 kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d 63 (129)
T PRK03999 33 KPGKHGSAKARIVAIGIFDGQKRSLVQPVDA 63 (129)
T ss_pred cCCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 3799999999999999999988777666654
No 27
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=29.28 E-value=16 Score=29.91 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=19.2
Q ss_pred ecCCCeEEeecCcCCCCCCCCee
Q 033956 5 LVGPRLYSCHNCRNHVALHDDII 27 (107)
Q Consensus 5 l~g~~~y~C~~C~thLa~~~~li 27 (107)
-.|+++|.|.+|+.-+|..+.|-
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred ccCCCCccCCcccchhcchHHHH
Confidence 46899999999998888877664
No 28
>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=29.26 E-value=57 Score=20.73 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=22.3
Q ss_pred eecCCCeEEeecCcCCCCCCCCeeeeeecCCCc
Q 033956 4 ELVGPRLYSCHNCRNHVALHDDIISKAFQGRNG 36 (107)
Q Consensus 4 ~l~g~~~y~C~~C~thLa~~~~liSk~F~G~~G 36 (107)
|....|. .|+.|+..++..+--|.+-+....|
T Consensus 2 yAks~Ra-~Ck~C~~~I~kg~lRiG~~~~~~~~ 33 (82)
T PF00645_consen 2 YAKSGRA-KCKGCKKKIAKGELRIGKIVPSPEG 33 (82)
T ss_dssp E-SSSTE-BETTTSCBE-TTSEEEEEEEEETTS
T ss_pred cCCCCCc-cCcccCCcCCCCCEEEEEEeccccc
Confidence 4444444 8999999999888888876666655
No 29
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=29.15 E-value=35 Score=28.22 Aligned_cols=60 Identities=20% Similarity=0.570 Sum_probs=35.3
Q ss_pred CCCeEEeecCcCCCCCCCCeeeeeecCCCceEEEeec--ccccccCCccceeeceecEEEeeeecccCCCceee
Q 033956 7 GPRLYSCHNCRNHVALHDDIISKAFQGRNGRAFLFSH--AMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGW 78 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~F~G~~G~AyLf~~--v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGW 78 (107)
|.-+|.|..|+.|+-. +.|+ |+|..=-+|.|+= .-|.-...+. -+-.|.||-.|....|-
T Consensus 134 ~~g~YvC~KCh~~iD~-~~l~---fr~d~yH~yHFkCt~C~keL~sdaR--------evk~eLyClrChD~mgi 195 (332)
T KOG2272|consen 134 GRGRYVCQKCHAHIDE-QPLT---FRGDPYHPYHFKCTTCGKELTSDAR--------EVKGELYCLRCHDKMGI 195 (332)
T ss_pred ccceeehhhhhhhccc-cccc---ccCCCCCccceecccccccccchhh--------hhccceeccccccccCC
Confidence 4458999999999877 3343 6666666777772 2222221111 11236677777666554
No 30
>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=28.99 E-value=72 Score=24.36 Aligned_cols=34 Identities=9% Similarity=0.109 Sum_probs=20.3
Q ss_pred ccccCCccceeeceecEEEeeeecccCCCceeeEE
Q 033956 46 NVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKY 80 (107)
Q Consensus 46 Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY 80 (107)
.+..|+........|.+..+- ||..|++.|-+..
T Consensus 70 ~i~~G~~~l~~Y~ss~~~~R~-FC~~CGS~L~~~~ 103 (182)
T TIGR02820 70 TVTANGDKLKVVDASATIQRH-ACKGCGTHMYGRI 103 (182)
T ss_pred EEecCCcceEEEeCCCCEEee-cCCCCCCcccccc
Confidence 343455443333345554444 9999999996554
No 31
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.66 E-value=23 Score=23.85 Aligned_cols=23 Identities=17% Similarity=0.468 Sum_probs=18.4
Q ss_pred EeecCcCCCCCCCCeeeeeecCCCceEEEee
Q 033956 12 SCHNCRNHVALHDDIISKAFQGRNGRAFLFS 42 (107)
Q Consensus 12 ~C~~C~thLa~~~~liSk~F~G~~G~AyLf~ 42 (107)
.|.+|+.+++..+ ...|+||+.-
T Consensus 10 ~C~~CG~d~~~~~--------adDgPA~fvi 32 (86)
T PF06170_consen 10 RCPHCGLDYSHAR--------ADDGPAYFVI 32 (86)
T ss_pred cccccCCccccCC--------cCccchhHHH
Confidence 6999999998766 5667888754
No 32
>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=27.88 E-value=62 Score=20.01 Aligned_cols=31 Identities=16% Similarity=0.259 Sum_probs=16.5
Q ss_pred cCCccceeeceecEEEeeeecccCCCceeeE
Q 033956 49 VGPKEDRHLLTGLHTVADIYCSDCREVLGWK 79 (107)
Q Consensus 49 ~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWk 79 (107)
.|+..-+.....-..+.-.+|..|++.|.+.
T Consensus 31 ~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 31 SGSENLKEYQFSGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp E-GGGEEEC--TTSSCEEEEETTT--EEEEE
T ss_pred eccccceEEEeCCCcCcCcccCCCCCeeecc
Confidence 3444333333133345568999999999976
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=27.73 E-value=21 Score=18.60 Aligned_cols=12 Identities=25% Similarity=0.814 Sum_probs=7.2
Q ss_pred eeeecccCCCce
Q 033956 65 ADIYCSDCREVL 76 (107)
Q Consensus 65 ~DI~C~~C~~~l 76 (107)
.+-+|..|++.|
T Consensus 15 ~~~fC~~CG~~L 26 (26)
T PF13248_consen 15 DAKFCPNCGAKL 26 (26)
T ss_pred ccccChhhCCCC
Confidence 355677776654
No 34
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=26.99 E-value=8.8 Score=25.63 Aligned_cols=20 Identities=35% Similarity=0.659 Sum_probs=16.6
Q ss_pred ceecEEEeeeecccCCCceeeE
Q 033956 58 LTGLHTVADIYCSDCREVLGWK 79 (107)
Q Consensus 58 ~TG~h~V~DI~C~~C~~~lGWk 79 (107)
.||. ||-+-|..|++.||.-
T Consensus 46 ~tG~--vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 46 KTGR--VRGLLCRSCNTALGKV 65 (81)
T ss_dssp TTTB--EEEEEEHHHHHHHHHC
T ss_pred CCCC--chhhhhhHHhhhhccc
Confidence 4444 9999999999999965
No 35
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.82 E-value=36 Score=19.24 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=7.1
Q ss_pred ecccCCCceeeEEE
Q 033956 68 YCSDCREVLGWKYE 81 (107)
Q Consensus 68 ~C~~C~~~lGWkY~ 81 (107)
||..|++.|-++..
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 36
>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=26.75 E-value=25 Score=18.39 Aligned_cols=12 Identities=17% Similarity=0.786 Sum_probs=10.1
Q ss_pred eEEeecCcCCCC
Q 033956 10 LYSCHNCRNHVA 21 (107)
Q Consensus 10 ~y~C~~C~thLa 21 (107)
-|.|..|+.+|+
T Consensus 27 Cf~C~~C~~~L~ 38 (39)
T smart00132 27 CFKCSKCGKPLG 38 (39)
T ss_pred CCCCcccCCcCc
Confidence 388999999886
No 37
>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=26.71 E-value=23 Score=21.88 Aligned_cols=35 Identities=23% Similarity=0.418 Sum_probs=24.8
Q ss_pred eecccccccCCccceeeceecEEEeeeecccCCCceeeEE
Q 033956 41 FSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKY 80 (107)
Q Consensus 41 f~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY 80 (107)
|++++.+..|..+ |+...--.+-|..|.+.=|---
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 5778888888877 3333334456999999988654
No 38
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=26.64 E-value=50 Score=18.21 Aligned_cols=15 Identities=20% Similarity=0.634 Sum_probs=12.2
Q ss_pred CeEEeecCcCCCCCC
Q 033956 9 RLYSCHNCRNHVALH 23 (107)
Q Consensus 9 ~~y~C~~C~thLa~~ 23 (107)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 359999999888754
No 39
>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=26.62 E-value=11 Score=18.32 Aligned_cols=16 Identities=19% Similarity=0.663 Sum_probs=11.6
Q ss_pred EEeecCcCCCCCCCCe
Q 033956 11 YSCHNCRNHVALHDDI 26 (107)
Q Consensus 11 y~C~~C~thLa~~~~l 26 (107)
|.|..|+....+.++|
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 7899998877665544
No 40
>PF14353 CpXC: CpXC protein
Probab=26.29 E-value=27 Score=24.15 Aligned_cols=46 Identities=15% Similarity=0.342 Sum_probs=31.1
Q ss_pred EeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeecccc
Q 033956 40 LFSHAMNVVVGPKEDRHLLTGLHTVADIYCSDCREVLGWKYERAFEAS 87 (107)
Q Consensus 40 Lf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~s 87 (107)
-+-..+|+...|.-...+++|. +-...|..|+...---|.--|.+.
T Consensus 14 ~v~~~I~~~~~p~l~e~il~g~--l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 14 EVWTSINADEDPELKEKILDGS--LFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred EEEeEEcCcCCHHHHHHHHcCC--cCEEECCCCCCceecCCCEEEEcC
Confidence 3447788888886555667886 344689999998765555444433
No 41
>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=26.08 E-value=8.2 Score=19.54 Aligned_cols=18 Identities=11% Similarity=0.456 Sum_probs=12.8
Q ss_pred eEEeecCcCCCCCCCCee
Q 033956 10 LYSCHNCRNHVALHDDII 27 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~li 27 (107)
+|.|..|+.-..+.+.++
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 588999988776655443
No 42
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=26.01 E-value=27 Score=23.33 Aligned_cols=16 Identities=25% Similarity=0.696 Sum_probs=13.4
Q ss_pred eEEeecCcCCCCCCCC
Q 033956 10 LYSCHNCRNHVALHDD 25 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~ 25 (107)
.|.|++|++.+.+-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999887655
No 43
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.89 E-value=52 Score=28.57 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=10.4
Q ss_pred ceeeEEEeecccc
Q 033956 75 VLGWKYERAFEAS 87 (107)
Q Consensus 75 ~lGWkY~~A~e~s 87 (107)
.||=||-+++...
T Consensus 271 ~LG~kYS~~lna~ 283 (457)
T KOG2324|consen 271 LLGTKYSKPLNAK 283 (457)
T ss_pred EeccccccccCce
Confidence 6899998888665
No 44
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.69 E-value=58 Score=18.88 Aligned_cols=14 Identities=36% Similarity=0.797 Sum_probs=9.2
Q ss_pred ecCCCeEEeecCcC
Q 033956 5 LVGPRLYSCHNCRN 18 (107)
Q Consensus 5 l~g~~~y~C~~C~t 18 (107)
|.+...|.|+.|+.
T Consensus 32 ~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 32 LKTRGRYRCKACRK 45 (46)
T ss_pred eCCCCeEECCCCCC
Confidence 34456788888864
No 45
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=25.43 E-value=38 Score=27.34 Aligned_cols=33 Identities=24% Similarity=0.316 Sum_probs=22.6
Q ss_pred eecCCCeEEeecCcCCCCCCCC--eeeeeecCCCc
Q 033956 4 ELVGPRLYSCHNCRNHVALHDD--IISKAFQGRNG 36 (107)
Q Consensus 4 ~l~g~~~y~C~~C~thLa~~~~--liSk~F~G~~G 36 (107)
.|.+++..+|+.|+.+-.-..+ .+|.+..|+.|
T Consensus 17 ~LS~~~~~SCasCH~p~~~~~d~~~~s~G~~g~~~ 51 (291)
T TIGR03791 17 RLSRDGSMSCATCHNPGLGWSDGLILALGADGVEH 51 (291)
T ss_pred ccCCCCCcCchhcCCccccCCCCcccccCCCCCCC
Confidence 3677889999999987653333 45666665544
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.12 E-value=39 Score=19.55 Aligned_cols=15 Identities=33% Similarity=0.840 Sum_probs=10.8
Q ss_pred eEEeecCcCCCCCCC
Q 033956 10 LYSCHNCRNHVALHD 24 (107)
Q Consensus 10 ~y~C~~C~thLa~~~ 24 (107)
.|.|.+|++.+...+
T Consensus 3 ~y~C~~CG~~~~~~~ 17 (46)
T PRK00398 3 EYKCARCGREVELDE 17 (46)
T ss_pred EEECCCCCCEEEECC
Confidence 588888888766543
No 47
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.06 E-value=28 Score=17.90 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=6.0
Q ss_pred eecccCCCce
Q 033956 67 IYCSDCREVL 76 (107)
Q Consensus 67 I~C~~C~~~l 76 (107)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 4577776654
No 48
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=21.00 E-value=42 Score=25.71 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=29.5
Q ss_pred CCeeeeeecCCCceEEEee-----cccccccCCccceeecee
Q 033956 24 DDIISKAFQGRNGRAFLFS-----HAMNVVVGPKEDRHLLTG 60 (107)
Q Consensus 24 ~~liSk~F~G~~G~AyLf~-----~v~Nv~~g~~~~r~m~TG 60 (107)
=.++|+.|+|+.--..+|= ...-|.+|..+.|+|..+
T Consensus 121 Ialv~rpFmG~~s~si~Ffn~~G~~mfKiylgRDe~RqL~~e 162 (176)
T COG3721 121 IALVERPFMGMESASILFFNAQGEAMFKIYLGRDEHRQLLPE 162 (176)
T ss_pred eeEeccccCCccceeeeeecccCceeeeeeeccchHhhhhHH
Confidence 3489999999998877775 356778899999988765
No 49
>PLN02739 serine acetyltransferase
Probab=20.61 E-value=52 Score=27.77 Aligned_cols=43 Identities=26% Similarity=0.516 Sum_probs=32.9
Q ss_pred eecCCCe-EEeecCcCCCCCCCCeeeeee----cCCCceEEEeeccccccc
Q 033956 4 ELVGPRL-YSCHNCRNHVALHDDIISKAF----QGRNGRAFLFSHAMNVVV 49 (107)
Q Consensus 4 ~l~g~~~-y~C~~C~thLa~~~~liSk~F----~G~~G~AyLf~~v~Nv~~ 49 (107)
-++|+.. |+ |+..|++-.-|+|++| .|-+|.-|-|+++.-|..
T Consensus 3 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (355)
T PLN02739 3 CINGENCDFS---CSSSLSSLPMIVSRNFSARDDGETGDEFPFERGFPVYA 50 (355)
T ss_pred cccCCCcccc---cccccccCceeeecccccccCCccCCcCcccccceeee
Confidence 3455433 44 5778888899999999 577899999999887763
No 50
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=20.58 E-value=16 Score=23.59 Aligned_cols=18 Identities=28% Similarity=0.628 Sum_probs=15.0
Q ss_pred eeeecccCCCceeeEEEe
Q 033956 65 ADIYCSDCREVLGWKYER 82 (107)
Q Consensus 65 ~DI~C~~C~~~lGWkY~~ 82 (107)
-+|.|-+|+..+|=+|++
T Consensus 3 iPvRCFTCGkvi~~~we~ 20 (62)
T PRK04016 3 IPVRCFTCGKVIAEKWEE 20 (62)
T ss_pred CCeEecCCCCChHHHHHH
Confidence 478999999999977754
No 51
>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=20.13 E-value=73 Score=17.62 Aligned_cols=15 Identities=20% Similarity=0.390 Sum_probs=8.7
Q ss_pred eecCCCeEEeecCcC
Q 033956 4 ELVGPRLYSCHNCRN 18 (107)
Q Consensus 4 ~l~g~~~y~C~~C~t 18 (107)
|-.|.+.++|+.|++
T Consensus 13 yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 13 YPRGASSVRCALCQT 27 (31)
T ss_pred cCCCCCeEECCCCCe
Confidence 344555666666654
No 52
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=20.04 E-value=40 Score=23.33 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=13.7
Q ss_pred EeecCcCCCCCCCC------eeeeeecC
Q 033956 12 SCHNCRNHVALHDD------IISKAFQG 33 (107)
Q Consensus 12 ~C~~C~thLa~~~~------liSk~F~G 33 (107)
.|.+|...|...++ -.|.+|.|
T Consensus 22 gCpnC~~~l~~~g~~~~v~~~tT~~f~G 49 (98)
T cd07973 22 GCPNCEGYLDMKGNHERVYDCTSPNFEG 49 (98)
T ss_pred CCCCCcchhccCCCccccccccCCCcce
Confidence 69999766644443 25666665
Done!