Query 033997
Match_columns 106
No_of_seqs 102 out of 323
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:38:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033997hhsearch_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 7.3E-52 1.6E-56 295.4 -1.9 104 3-106 8-113 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 2.4E-34 5.1E-39 194.3 6.1 89 9-103 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.0 0.0031 6.8E-08 44.8 1.4 86 9-98 4-93 (123)
4 PF01641 SelR: SelR domain; I 94.9 0.021 4.6E-07 41.2 2.4 72 7-85 35-106 (124)
5 TIGR00357 methionine-R-sulfoxi 94.7 0.034 7.4E-07 40.6 3.1 66 7-80 38-104 (134)
6 PRK00222 methionine sulfoxide 94.4 0.035 7.6E-07 41.0 2.6 68 7-81 41-108 (142)
7 PRK05508 methionine sulfoxide 93.2 0.097 2.1E-06 37.7 3.0 64 7-80 31-94 (119)
8 PRK05550 bifunctional methioni 91.3 0.16 3.5E-06 41.1 2.5 64 7-80 34-97 (283)
9 PRK14018 trifunctional thiored 89.6 0.34 7.3E-06 42.1 3.2 68 7-81 416-483 (521)
10 COG0229 Conserved domain frequ 86.0 1.1 2.4E-05 33.1 3.6 64 7-77 40-103 (140)
11 PF14976 FAM72: FAM72 protein 85.0 2 4.3E-05 32.1 4.5 62 9-82 15-88 (150)
12 KOG0856 Predicted pilin-like t 81.2 1.4 3E-05 32.8 2.4 67 7-80 52-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 79.4 3.3 7.2E-05 33.0 4.3 17 9-25 106-122 (354)
14 PF11023 DUF2614: Protein of u 55.5 4.5 9.8E-05 29.0 0.3 25 8-32 84-108 (114)
15 PF13465 zf-H2C2_2: Zinc-finge 55.2 7.6 0.00016 20.1 1.1 14 5-18 10-23 (26)
16 PRK11586 napB nitrate reductas 40.9 17 0.00036 27.2 1.4 29 7-35 118-146 (149)
17 KOG2272 Focal adhesion protein 40.7 18 0.00039 29.8 1.7 33 5-41 133-165 (332)
18 COG3791 Uncharacterized conser 39.0 28 0.00061 24.6 2.3 21 62-82 66-86 (133)
19 PRK05417 glutathione-dependent 38.9 54 0.0012 25.1 4.0 53 46-103 75-127 (191)
20 PF00412 LIM: LIM domain; Int 36.8 17 0.00038 21.1 0.8 15 9-23 26-40 (58)
21 TIGR00037 eIF_5A translation i 35.6 43 0.00094 23.9 2.8 30 31-60 35-64 (130)
22 PF14353 CpXC: CpXC protein 32.9 18 0.0004 24.9 0.5 47 39-87 14-60 (128)
23 COG3043 NapB Nitrate reductase 32.6 27 0.00059 26.3 1.4 29 6-34 123-151 (155)
24 PF03811 Zn_Tnp_IS1: InsA N-te 32.6 27 0.00059 19.9 1.1 27 64-90 4-31 (36)
25 PLN03107 eukaryotic translatio 31.9 51 0.0011 24.4 2.8 30 31-60 49-78 (159)
26 PF06170 DUF983: Protein of un 31.3 19 0.00042 24.1 0.4 23 11-41 10-32 (86)
27 PRK03999 translation initiatio 31.1 58 0.0013 23.2 2.9 30 31-60 34-63 (129)
28 KOG2462 C2H2-type Zn-finger pr 31.0 16 0.00034 29.9 -0.1 23 4-26 210-232 (279)
29 TIGR02820 formald_GSH S-(hydro 30.8 60 0.0013 24.7 3.1 33 46-79 71-103 (182)
30 PF10246 MRP-S35: Mitochondria 30.4 30 0.00065 24.4 1.3 51 39-94 10-66 (104)
31 PF04828 GFA: Glutathione-depe 30.1 47 0.001 20.5 2.1 47 32-78 13-61 (92)
32 PF14803 Nudix_N_2: Nudix N-te 28.9 32 0.0007 19.3 1.0 14 67-80 2-15 (34)
33 smart00132 LIM Zinc-binding do 28.6 22 0.00048 18.5 0.3 12 9-20 27-38 (39)
34 PF13248 zf-ribbon_3: zinc-rib 28.5 20 0.00042 18.7 0.1 11 65-75 16-26 (26)
35 PF13842 Tnp_zf-ribbon_2: DDE_ 28.2 44 0.00095 18.4 1.4 15 8-22 15-29 (32)
36 PF13912 zf-C2H2_6: C2H2-type 28.1 6.9 0.00015 19.8 -1.8 17 9-25 1-17 (27)
37 PF02945 Endonuclease_7: Recom 27.4 7.8 0.00017 25.8 -2.0 20 57-78 46-65 (81)
38 PF10058 DUF2296: Predicted in 27.3 20 0.00044 22.1 -0.0 35 40-79 2-36 (54)
39 PF00096 zf-C2H2: Zinc finger, 27.3 9.3 0.0002 18.5 -1.3 16 10-25 1-16 (23)
40 PF10955 DUF2757: Protein of u 26.9 26 0.00056 23.4 0.4 16 9-24 4-19 (76)
41 PRK00398 rpoP DNA-directed RNA 26.9 36 0.00079 19.6 1.0 16 8-23 2-17 (46)
42 cd03523 NTR_like NTR_like doma 25.6 1.7E+02 0.0037 19.0 4.2 84 14-101 3-88 (105)
43 PF13240 zinc_ribbon_2: zinc-r 25.3 25 0.00054 18.0 0.1 10 66-75 14-23 (23)
44 KOG2324 Prolyl-tRNA synthetase 24.7 59 0.0013 28.1 2.3 13 74-86 271-283 (457)
45 PF12760 Zn_Tnp_IS1595: Transp 24.6 57 0.0012 18.9 1.6 13 5-17 33-45 (46)
46 TIGR03791 TTQ_mauG tryptophan 24.0 44 0.00095 26.9 1.3 33 3-35 17-51 (291)
47 COG3721 HugX Putative heme iro 22.7 36 0.00078 26.0 0.6 37 23-59 121-162 (176)
48 PF09855 DUF2082: Nucleic-acid 21.9 1.4E+02 0.0031 19.0 3.1 10 10-19 1-10 (64)
49 COG1996 RPC10 DNA-directed RNA 21.4 42 0.00091 20.6 0.6 13 7-19 4-16 (49)
50 PF06397 Desulfoferrod_N: Desu 20.9 49 0.0011 19.0 0.8 12 8-19 5-16 (36)
51 PF03150 CCP_MauG: Di-haem cyt 20.8 44 0.00095 24.4 0.7 30 3-32 16-47 (159)
52 PF04246 RseC_MucC: Positive r 20.5 1.2E+02 0.0026 21.0 2.9 45 8-53 15-59 (135)
53 PRK04016 DNA-directed RNA poly 20.1 17 0.00037 23.4 -1.5 18 64-81 3-20 (62)
54 TIGR00319 desulf_FeS4 desulfof 20.0 64 0.0014 17.5 1.1 12 8-19 6-17 (34)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=7.3e-52 Score=295.44 Aligned_cols=104 Identities=59% Similarity=1.116 Sum_probs=99.6
Q ss_pred cccC-CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033997 3 EMVG-PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYER 81 (106)
Q Consensus 3 ~l~g-~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 81 (106)
+|++ ++.|+|++|+||||+++|||||+|+|++|+||||++|+||+.|+.|+|.|+||+|+|+||+|+.|++.|||||+.
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 4555 368999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccccccceEEEEeccccccC-C
Q 033997 82 AYEETQKYKEGKFILEKSKIAKEN-W 106 (106)
Q Consensus 82 A~e~sqkYKEGkfIlE~~~i~~~~-w 106 (106)
|||+||||||||||||+++|.+++ |
T Consensus 88 a~e~sQkyKEGk~ilE~~~i~~~~g~ 113 (122)
T KOG3399|consen 88 AYEKSQKYKEGKFILELAEIFKPEGW 113 (122)
T ss_pred ccCchhhhcCcchHHHHHHhcCCCCc
Confidence 999999999999999999999976 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=2.4e-34 Score=194.30 Aligned_cols=89 Identities=56% Similarity=1.057 Sum_probs=85.2
Q ss_pred eEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceec----EEEeeeecccCCCceeeEEEeecc
Q 033997 9 LYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGL----HTVADVFCSDCRVVLGWKYERAYE 84 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~----h~V~DI~C~~C~~~lGWkY~~A~e 84 (106)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+||+|++|++.|||||+.|++
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 cccccccceEEEEeccccc
Q 033997 85 ETQKYKEGKFILEKSKIAK 103 (106)
Q Consensus 85 ~sqkYKEGkfIlE~~~i~~ 103 (106)
+ |+||||+||||++.|..
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=96.03 E-value=0.0031 Score=44.79 Aligned_cols=86 Identities=15% Similarity=0.233 Sum_probs=57.4
Q ss_pred eEEcccCcCCCCCCCCeeeeeecCCC----ceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeecc
Q 033997 9 LYSCCNCRNHVALHDDVISKSFQGRN----GRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYERAYE 84 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~liSk~f~G~~----G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e 84 (106)
.+.|++|.+.++..+||-.- .++| .+. |...+.+...|.+.....-+.+....|+|..|+..+|-.+..---
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 335666666666544445588899999999999999987654332
Q ss_pred cccccccceEEEEe
Q 033997 85 ETQKYKEGKFILEK 98 (106)
Q Consensus 85 ~sqkYKEGkfIlE~ 98 (106)
+==-.|.-.|+++.
T Consensus 80 ~LP~L~iksfvv~~ 93 (123)
T PF11648_consen 80 ELPCLKIKSFVVEL 93 (123)
T ss_dssp EEEEE-GGGEEEEE
T ss_pred cccEEEeeeeeeee
Confidence 22334555566443
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=94.90 E-value=0.021 Score=41.15 Aligned_cols=72 Identities=21% Similarity=0.409 Sum_probs=44.9
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeeccc
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYERAYEE 85 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~ 85 (106)
.-+|.|+.|+++|=+++. -|....|=.-.+..+..-.+...+|.. -|+.. ..|.|..|+..||=-......+
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--HGMVR-TEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp SEEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEEC--TSSEE-EEEEETTTCCEEEEEESTSSTT
T ss_pred CEEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEecccc--CCceE-EEEEecCCCCccccEeCCCCCC
Confidence 348999999999987653 566555654445444332333333332 24544 4789999999999876655543
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=94.68 E-value=0.034 Score=40.64 Aligned_cols=66 Identities=20% Similarity=0.462 Sum_probs=42.3
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecc-cccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHA-MNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYE 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v-~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|+++|-++++ -|.-..|=.-.+..+ -|. +...+|+. -|+.. ..|.|..|+..||=-..
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 455555544444444 222 22333332 24444 47999999999997554
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.39 E-value=0.035 Score=40.97 Aligned_cols=68 Identities=19% Similarity=0.394 Sum_probs=43.4
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYER 81 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 81 (106)
+-+|.|+.|.++|=++++ -|.-..|=.-.+..+-.-.+...+|+. -|+.. ..|.|..|+..||=-...
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----KFDSGCGWPSFTKPIDEEAIRELRDTS--HGMVR-TEVRCANCDSHLGHVFPD 108 (142)
T ss_pred CeEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeeccC--CCceE-EEEEeCCCCCccCcccCC
Confidence 348999999999988754 566666655555554322222233332 23322 478999999999976543
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.22 E-value=0.097 Score=37.66 Aligned_cols=64 Identities=22% Similarity=0.438 Sum_probs=42.5
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYE 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|.++|=++++ -|.-..|=.-.+..+-|. +...+|.. | + =..|.|..|+..||=-..
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 348999999999988765 566666654445554332 33334443 2 2 357999999999997443
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.28 E-value=0.16 Score=41.10 Aligned_cols=64 Identities=22% Similarity=0.439 Sum_probs=42.1
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYE 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|+++|=++++ -|.-.+|=.-.++.+-|-+.- .++.. |+ =..|.|..|++.||--..
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 348999999999988764 455555544446555443222 22222 32 478999999999997554
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=89.62 E-value=0.34 Score=42.12 Aligned_cols=68 Identities=13% Similarity=0.150 Sum_probs=44.2
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEe
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYER 81 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 81 (106)
+-+|.|+.|+++|=+++ .-|....|=.-.+..+-+-.+...+|.+ -|++. ..|.|..|++.||--...
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----DKYDSGCGWPSFTRPIDAKVVTEHDDFS--YNMRR-TEVRSRAADSHLGHVFPD 483 (521)
T ss_pred CEEEEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeeccC--CCceE-EEEEECCCCCcCCcccCC
Confidence 44899999999998885 3566666655545544322233333332 24444 379999999999976544
No 10
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=85.97 E-value=1.1 Score=33.12 Aligned_cols=64 Identities=25% Similarity=0.457 Sum_probs=42.8
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceee
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGW 77 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGW 77 (106)
+-+|.|+.|..+|=++++ -|.-..|=--.+.-+..-.+...+|+ .-|++.+ .|.|..|++.||=
T Consensus 40 ~GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGH 103 (140)
T COG0229 40 KGIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGH 103 (140)
T ss_pred CceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCcccc
Confidence 348999999999988765 45555554444444444344444443 3455554 6899999999996
No 11
>PF14976 FAM72: FAM72 protein
Probab=84.95 E-value=2 Score=32.15 Aligned_cols=62 Identities=19% Similarity=0.400 Sum_probs=39.3
Q ss_pred eEEcccCcCCCCCCCCeeeeeecCCCceEEEeeccccccc----CCccceeeceec--------EEEeeeecccCCCcee
Q 033997 9 LYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVV----GPKEDRQLMTGL--------HTVADVFCSDCRVVLG 76 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~----g~~~~r~m~TG~--------h~V~DI~C~~C~~~lG 76 (106)
+..|+.|.+-|+... =||-|..+ .|+.. -||....-.+|. =.++|+-|.+|+..||
T Consensus 15 ~L~C~~C~~~l~~Rg-----------MkAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~vG 82 (150)
T PF14976_consen 15 ILCCKFCDQVLCNRG-----------MKAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIVG 82 (150)
T ss_pred EEECCCCCchhccch-----------hhheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCeee
Confidence 478999998887542 24555544 33332 222222323333 3899999999999999
Q ss_pred eEEEee
Q 033997 77 WKYERA 82 (106)
Q Consensus 77 WkY~~A 82 (106)
+.....
T Consensus 83 YhV~~P 88 (150)
T PF14976_consen 83 YHVVVP 88 (150)
T ss_pred eEEEEE
Confidence 887654
No 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=81.22 E-value=1.4 Score=32.81 Aligned_cols=67 Identities=19% Similarity=0.383 Sum_probs=39.0
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeEEE
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYE 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|.++|-++. .-|.-..|=--.|+.+-+=.+-..+|.+ -|.+ =.+|.|..|+..||--.+
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----TKFDSGCGWPAFFEAIGPGAITRTPDNS--RGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCcccccc----ccccCCCCCchhhhccCCCceeeccccC--CCCc-ceEEEEeecCCceeeeec
Confidence 45899999999998764 3565555543334443111111111211 1122 347899999999997554
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=79.42 E-value=3.3 Score=32.96 Aligned_cols=17 Identities=24% Similarity=0.559 Sum_probs=13.9
Q ss_pred eEEcccCcCCCCCCCCe
Q 033997 9 LYSCCNCRNHVALHDDV 25 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~l 25 (106)
.+.|++|+..|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766543
No 14
>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=55.51 E-value=4.5 Score=29.00 Aligned_cols=25 Identities=24% Similarity=0.630 Sum_probs=21.7
Q ss_pred ceEEcccCcCCCCCCCCeeeeeecC
Q 033997 8 RLYSCCNCRNHVALHDDVISKSFQG 32 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~~liSk~f~G 32 (106)
|...|-+|++||+...++--|.|+-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 6789999999999999988887763
No 15
>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=55.23 E-value=7.6 Score=20.11 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=11.5
Q ss_pred cCCceEEcccCcCC
Q 033997 5 VGPRLYSCCNCRNH 18 (106)
Q Consensus 5 ~g~~~y~C~~C~th 18 (106)
.|.++|.|..|..-
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 16
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=40.94 E-value=17 Score=27.22 Aligned_cols=29 Identities=28% Similarity=0.595 Sum_probs=25.1
Q ss_pred CceEEcccCcCCCCCCCCeeeeeecCCCc
Q 033997 7 PRLYSCCNCRNHVALHDDVISKSFQGRNG 35 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G 35 (106)
++.|-|..|+++=+...-|+.-.|....|
T Consensus 118 prRYfCtQCHVPQada~PLV~N~F~~~~~ 146 (149)
T PRK11586 118 PRRYFCLQCHVPQADTAPIVGNTFTPSKG 146 (149)
T ss_pred ccceeeccccCccccCccCCCCCccchhh
Confidence 57899999999999999999999976443
No 17
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=40.72 E-value=18 Score=29.80 Aligned_cols=33 Identities=24% Similarity=0.606 Sum_probs=25.2
Q ss_pred cCCceEEcccCcCCCCCCCCeeeeeecCCCceEEEee
Q 033997 5 VGPRLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFS 41 (106)
Q Consensus 5 ~g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~ 41 (106)
.|.-.|.|..|+.|+-. +.| -|+|..--+|.|+
T Consensus 133 ~~~g~YvC~KCh~~iD~-~~l---~fr~d~yH~yHFk 165 (332)
T KOG2272|consen 133 KGRGRYVCQKCHAHIDE-QPL---TFRGDPYHPYHFK 165 (332)
T ss_pred cccceeehhhhhhhccc-ccc---cccCCCCCcccee
Confidence 34458999999999977 334 3788888888887
No 18
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=38.95 E-value=28 Score=24.56 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=15.9
Q ss_pred EEeeeecccCCCceeeEEEee
Q 033997 62 TVADVFCSDCRVVLGWKYERA 82 (106)
Q Consensus 62 ~V~DI~C~~C~~~lGWkY~~A 82 (106)
.+.-.||..|++.|-|+....
T Consensus 66 ~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 66 SAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCeecccCCCceEEecCCC
Confidence 344449999999999986543
No 19
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=38.87 E-value=54 Score=25.09 Aligned_cols=53 Identities=9% Similarity=0.097 Sum_probs=28.2
Q ss_pred cccCCccceeeceecEEEeeeecccCCCceeeEEEeecccccccccceEEEEeccccc
Q 033997 46 IVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYERAYEETQKYKEGKFILEKSKIAK 103 (106)
Q Consensus 46 v~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfIlE~~~i~~ 103 (106)
+..|+...+...+|.. +.--||..|++.|-+..+....+ -.|..+|=...+..
T Consensus 75 it~g~~~l~~y~ss~~-i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllDd 127 (191)
T PRK05417 75 VTANGDKLKVVDESAT-IQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQE 127 (191)
T ss_pred EEeCCcceEEEeCCCC-eEeeeCCCCCCccccccccccCC----CCCeEEEehhhcCC
Confidence 3335443333333333 44559999999998876622101 12566665554443
No 20
>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=36.85 E-value=17 Score=21.06 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=11.9
Q ss_pred eEEcccCcCCCCCCC
Q 033997 9 LYSCCNCRNHVALHD 23 (106)
Q Consensus 9 ~y~C~~C~thLa~~~ 23 (106)
-|.|..|+.+|...+
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 478889998887765
No 21
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=35.60 E-value=43 Score=23.86 Aligned_cols=30 Identities=23% Similarity=0.189 Sum_probs=26.0
Q ss_pred cCCCceEEEeecccccccCCccceeeceec
Q 033997 31 QGRNGRAFLFSHAMNIVVGPKEDRQLMTGL 60 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 60 (106)
.|+||.|+.--.+.|+..|...+....++.
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 699999999999999999999887766655
No 22
>PF14353 CpXC: CpXC protein
Probab=32.95 E-value=18 Score=24.89 Aligned_cols=47 Identities=15% Similarity=0.351 Sum_probs=30.9
Q ss_pred EeecccccccCCccceeeceecEEEeeeecccCCCceeeEEEeeccccc
Q 033997 39 LFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKYERAYEETQ 87 (106)
Q Consensus 39 Lf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sq 87 (106)
-+-..+|+...|.-...+++|. +-...|..|+...---|.--|.+.+
T Consensus 14 ~v~~~I~~~~~p~l~e~il~g~--l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 14 EVWTSINADEDPELKEKILDGS--LFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEEeEEcCcCCHHHHHHHHcCC--cCEEECCCCCCceecCCCEEEEcCC
Confidence 3447888888886555566776 2334899999987655555554433
No 23
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=32.61 E-value=27 Score=26.27 Aligned_cols=29 Identities=24% Similarity=0.498 Sum_probs=25.3
Q ss_pred CCceEEcccCcCCCCCCCCeeeeeecCCC
Q 033997 6 GPRLYSCCNCRNHVALHDDVISKSFQGRN 34 (106)
Q Consensus 6 g~~~y~C~~C~thLa~~~~liSk~f~G~~ 34 (106)
.+|.|-|..|+.+=|...-|+--.|..-.
T Consensus 123 SPRRYFClQCHVPQaD~kPlV~N~F~p~~ 151 (155)
T COG3043 123 SPRRYFCLQCHVPQADVKPLVGNTFKPMK 151 (155)
T ss_pred CccceeeeecccccccccccCCCCcccch
Confidence 47899999999999999999998887544
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=32.58 E-value=27 Score=19.87 Aligned_cols=27 Identities=26% Similarity=0.469 Sum_probs=20.6
Q ss_pred eeeecccCCCce-eeEEEeecccccccc
Q 033997 64 ADVFCSDCRVVL-GWKYERAYEETQKYK 90 (106)
Q Consensus 64 ~DI~C~~C~~~l-GWkY~~A~e~sqkYK 90 (106)
-||.|..|++.- --|+-+.-.-.|+|.
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 667766666677763
No 25
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=31.88 E-value=51 Score=24.44 Aligned_cols=30 Identities=23% Similarity=0.311 Sum_probs=26.6
Q ss_pred cCCCceEEEeecccccccCCccceeeceec
Q 033997 31 QGRNGRAFLFSHAMNIVVGPKEDRQLMTGL 60 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 60 (106)
.|+||.|+.--.+.|+..|...+....++-
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 799999999999999999999888777665
No 26
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=31.32 E-value=19 Score=24.13 Aligned_cols=23 Identities=17% Similarity=0.439 Sum_probs=18.6
Q ss_pred EcccCcCCCCCCCCeeeeeecCCCceEEEee
Q 033997 11 SCCNCRNHVALHDDVISKSFQGRNGRAFLFS 41 (106)
Q Consensus 11 ~C~~C~thLa~~~~liSk~f~G~~G~AyLf~ 41 (106)
+|.+|+.+++..+ ...|+||+.-
T Consensus 10 ~C~~CG~d~~~~~--------adDgPA~fvi 32 (86)
T PF06170_consen 10 RCPHCGLDYSHAR--------ADDGPAYFVI 32 (86)
T ss_pred cccccCCccccCC--------cCccchhHHH
Confidence 6999999998776 5678888754
No 27
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=31.10 E-value=58 Score=23.16 Aligned_cols=30 Identities=23% Similarity=0.177 Sum_probs=25.5
Q ss_pred cCCCceEEEeecccccccCCccceeeceec
Q 033997 31 QGRNGRAFLFSHAMNIVVGPKEDRQLMTGL 60 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~ 60 (106)
.|+||.|+.--.+.|+..|...++...++.
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 789999999999999999988777766664
No 28
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=31.05 E-value=16 Score=29.90 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=18.8
Q ss_pred ccCCceEEcccCcCCCCCCCCee
Q 033997 4 MVGPRLYSCCNCRNHVALHDDVI 26 (106)
Q Consensus 4 l~g~~~y~C~~C~thLa~~~~li 26 (106)
-.|+++|.|.+|+.-+|..+.|-
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred ccCCCCccCCcccchhcchHHHH
Confidence 36889999999998888777664
No 29
>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=30.85 E-value=60 Score=24.72 Aligned_cols=33 Identities=6% Similarity=0.095 Sum_probs=19.5
Q ss_pred cccCCccceeeceecEEEeeeecccCCCceeeEE
Q 033997 46 IVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKY 79 (106)
Q Consensus 46 v~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY 79 (106)
+..|....+....|.+..+ -||..|++.|-+..
T Consensus 71 i~~G~~~l~~Y~ss~~~~R-~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 71 VTANGDKLKVVDASATIQR-HACKGCGTHMYGRI 103 (182)
T ss_pred EecCCcceEEEeCCCCEEe-ecCCCCCCcccccc
Confidence 3345544333334555444 49999999996544
No 30
>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=30.40 E-value=30 Score=24.44 Aligned_cols=51 Identities=27% Similarity=0.409 Sum_probs=31.7
Q ss_pred EeecccccccCCccceeeceec--EEEeeeecccCCCceeeEEE----eecccccccccceE
Q 033997 39 LFSHAMNIVVGPKEDRQLMTGL--HTVADVFCSDCRVVLGWKYE----RAYEETQKYKEGKF 94 (106)
Q Consensus 39 Lf~~v~Nv~~g~~~~r~m~TG~--h~V~DI~C~~C~~~lGWkY~----~A~e~sqkYKEGkf 94 (106)
|+.+--=+..|+++++. ++|. |+|.|-- ---+|||.. +....+++|.+|-=
T Consensus 10 lLR~S~fi~lG~~~gk~-V~G~I~hvv~ddL----YIDfG~KFhcVc~rp~~~~~~y~~G~r 66 (104)
T PF10246_consen 10 LLRNSPFIQLGDPEGKI-VIGKIFHVVDDDL----YIDFGGKFHCVCKRPAVNGEKYVRGSR 66 (104)
T ss_pred HhcCChhhhcCCccCCE-EEEEEEEEecCce----EEEeCCceeEEEecccccccccccCCE
Confidence 33333345579988875 6776 8887621 123578764 33447788998853
No 31
>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=30.10 E-value=47 Score=20.54 Aligned_cols=47 Identities=17% Similarity=0.198 Sum_probs=21.6
Q ss_pred CCCceEEEeecccccc--cCCccceeeceecEEEeeeecccCCCceeeE
Q 033997 32 GRNGRAFLFSHAMNIV--VGPKEDRQLMTGLHTVADVFCSDCRVVLGWK 78 (106)
Q Consensus 32 G~~G~AyLf~~v~Nv~--~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWk 78 (106)
|..-.++..-..-++. .|+..-+.....-..+.-.+|..|++.|.+.
T Consensus 13 g~~~~~~~~~~~~~~~~~~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 13 GSPFSAWAIVPKDDFRWTSGSENLKEYQFSGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp T-SSEEEEEEEGGGEEEEE-GGGEEEC--TTSSCEEEEETTT--EEEEE
T ss_pred CCceeeEEEEcccceEEeeccccceEEEeCCCcCcCcccCCCCCeeecc
Confidence 3333334433333443 3444333333123334558999999999875
No 32
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.93 E-value=32 Score=19.35 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=7.1
Q ss_pred ecccCCCceeeEEE
Q 033997 67 FCSDCRVVLGWKYE 80 (106)
Q Consensus 67 ~C~~C~~~lGWkY~ 80 (106)
||..|++.|-++..
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 79999999988765
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=28.59 E-value=22 Score=18.51 Aligned_cols=12 Identities=17% Similarity=0.794 Sum_probs=10.2
Q ss_pred eEEcccCcCCCC
Q 033997 9 LYSCCNCRNHVA 20 (106)
Q Consensus 9 ~y~C~~C~thLa 20 (106)
-|.|..|+.+|+
T Consensus 27 Cf~C~~C~~~L~ 38 (39)
T smart00132 27 CFKCSKCGKPLG 38 (39)
T ss_pred CCCCcccCCcCc
Confidence 488999999886
No 34
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.52 E-value=20 Score=18.66 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=6.7
Q ss_pred eeecccCCCce
Q 033997 65 DVFCSDCRVVL 75 (106)
Q Consensus 65 DI~C~~C~~~l 75 (106)
+-||..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45677776654
No 35
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=28.19 E-value=44 Score=18.39 Aligned_cols=15 Identities=20% Similarity=0.640 Sum_probs=12.3
Q ss_pred ceEEcccCcCCCCCC
Q 033997 8 RLYSCCNCRNHVALH 22 (106)
Q Consensus 8 ~~y~C~~C~thLa~~ 22 (106)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 469999999888754
No 36
>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=28.12 E-value=6.9 Score=19.77 Aligned_cols=17 Identities=12% Similarity=0.440 Sum_probs=12.4
Q ss_pred eEEcccCcCCCCCCCCe
Q 033997 9 LYSCCNCRNHVALHDDV 25 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~l 25 (106)
+|.|..|+.-..+.+.+
T Consensus 1 ~~~C~~C~~~F~~~~~l 17 (27)
T PF13912_consen 1 PFECDECGKTFSSLSAL 17 (27)
T ss_dssp SEEETTTTEEESSHHHH
T ss_pred CCCCCccCCccCChhHH
Confidence 58899998877665544
No 37
>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=27.43 E-value=7.8 Score=25.82 Aligned_cols=20 Identities=35% Similarity=0.689 Sum_probs=16.5
Q ss_pred ceecEEEeeeecccCCCceeeE
Q 033997 57 MTGLHTVADVFCSDCRVVLGWK 78 (106)
Q Consensus 57 ~TG~h~V~DI~C~~C~~~lGWk 78 (106)
.||. ||-+-|..|++.||.-
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 3444 9999999999999974
No 38
>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=27.35 E-value=20 Score=22.06 Aligned_cols=35 Identities=20% Similarity=0.411 Sum_probs=24.4
Q ss_pred eecccccccCCccceeeceecEEEeeeecccCCCceeeEE
Q 033997 40 FSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVVLGWKY 79 (106)
Q Consensus 40 f~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~lGWkY 79 (106)
|++++.+..|..+ |+...--.+-|..|.+.=|---
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 3333333456999999988643
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=27.25 E-value=9.3 Score=18.50 Aligned_cols=16 Identities=19% Similarity=0.600 Sum_probs=11.6
Q ss_pred EEcccCcCCCCCCCCe
Q 033997 10 YSCCNCRNHVALHDDV 25 (106)
Q Consensus 10 y~C~~C~thLa~~~~l 25 (106)
|.|..|+....+.++|
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
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=26.92 E-value=26 Score=23.36 Aligned_cols=16 Identities=25% Similarity=0.638 Sum_probs=13.3
Q ss_pred eEEcccCcCCCCCCCC
Q 033997 9 LYSCCNCRNHVALHDD 24 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~ 24 (106)
.|.|++|++.+.+-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999877655
No 41
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.88 E-value=36 Score=19.62 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=11.3
Q ss_pred ceEEcccCcCCCCCCC
Q 033997 8 RLYSCCNCRNHVALHD 23 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~ 23 (106)
..|.|.+|++.+...+
T Consensus 2 ~~y~C~~CG~~~~~~~ 17 (46)
T PRK00398 2 AEYKCARCGREVELDE 17 (46)
T ss_pred CEEECCCCCCEEEECC
Confidence 3688888888776543
No 42
>cd03523 NTR_like NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex.
Probab=25.57 E-value=1.7e+02 Score=19.01 Aligned_cols=84 Identities=12% Similarity=0.207 Sum_probs=45.1
Q ss_pred cCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCc--eeeEEEeeccccccccc
Q 033997 14 NCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKEDRQLMTGLHTVADVFCSDCRVV--LGWKYERAYEETQKYKE 91 (106)
Q Consensus 14 ~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~r~m~TG~h~V~DI~C~~C~~~--lGWkY~~A~e~sqkYKE 91 (106)
-|.++.+...-++|..-.+.. ..|-+ ++.+|.-+.........-...+.+..|..|... +|=.|+-+=..... .
T Consensus 3 ~C~sdyvi~~~V~~~~~~~~~-~~~~v-~v~~v~K~g~~~~~~~~~~~~~~~~~~~~c~~~l~~g~~YLImG~~~~~--~ 78 (105)
T cd03523 3 FCKSDYVVRAKIKEIKEENDD-VKYEV-KIIKIYKTGKAKADKADLRFYYTAPACCPCHPILNPGREYLIMGKEEDS--Q 78 (105)
T ss_pred cCcccEEEEEEEEEEEecCCc-EEEEE-EEEEEecCCCcccccccEEEEEeCCcccccCcccCCCceEEEEEeeecc--c
Confidence 366677777778787766543 22333 455554332221111111246667778777443 46777655543222 4
Q ss_pred ceEEEEeccc
Q 033997 92 GKFILEKSKI 101 (106)
Q Consensus 92 GkfIlE~~~i 101 (106)
|+|+|.....
T Consensus 79 ~~~~l~~~s~ 88 (105)
T cd03523 79 GGLVLDPLSF 88 (105)
T ss_pred CcEEEcCccE
Confidence 8888865443
No 43
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.35 E-value=25 Score=18.01 Aligned_cols=10 Identities=40% Similarity=1.069 Sum_probs=6.0
Q ss_pred eecccCCCce
Q 033997 66 VFCSDCRVVL 75 (106)
Q Consensus 66 I~C~~C~~~l 75 (106)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 4577776653
No 44
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.69 E-value=59 Score=28.11 Aligned_cols=13 Identities=31% Similarity=0.618 Sum_probs=10.2
Q ss_pred ceeeEEEeecccc
Q 033997 74 VLGWKYERAYEET 86 (106)
Q Consensus 74 ~lGWkY~~A~e~s 86 (106)
.||=||-+++...
T Consensus 271 ~LG~kYS~~lna~ 283 (457)
T KOG2324|consen 271 LLGTKYSKPLNAK 283 (457)
T ss_pred EeccccccccCce
Confidence 6888998888655
No 45
>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=24.65 E-value=57 Score=18.85 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=8.1
Q ss_pred cCCceEEcccCcC
Q 033997 5 VGPRLYSCCNCRN 17 (106)
Q Consensus 5 ~g~~~y~C~~C~t 17 (106)
.+...|.|+.|+.
T Consensus 33 ~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 33 KTRGRYRCKACRK 45 (46)
T ss_pred CCCCeEECCCCCC
Confidence 3345677777764
No 46
>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=24.03 E-value=44 Score=26.91 Aligned_cols=33 Identities=18% Similarity=0.307 Sum_probs=22.5
Q ss_pred cccCCceEEcccCcCCCCCCCC--eeeeeecCCCc
Q 033997 3 EMVGPRLYSCCNCRNHVALHDD--VISKSFQGRNG 35 (106)
Q Consensus 3 ~l~g~~~y~C~~C~thLa~~~~--liSk~f~G~~G 35 (106)
.|.+.+..+|+.|+.+-.-..+ .+|.+..|+.|
T Consensus 17 ~LS~~~~~SCasCH~p~~~~~d~~~~s~G~~g~~~ 51 (291)
T TIGR03791 17 RLSRDGSMSCATCHNPGLGWSDGLILALGADGVEH 51 (291)
T ss_pred ccCCCCCcCchhcCCccccCCCCcccccCCCCCCC
Confidence 3678889999999987654333 45666655443
No 47
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=22.75 E-value=36 Score=25.98 Aligned_cols=37 Identities=27% Similarity=0.499 Sum_probs=29.6
Q ss_pred CCeeeeeecCCCceEEEee-----cccccccCCccceeecee
Q 033997 23 DDVISKSFQGRNGRAFLFS-----HAMNIVVGPKEDRQLMTG 59 (106)
Q Consensus 23 ~~liSk~f~G~~G~AyLf~-----~v~Nv~~g~~~~r~m~TG 59 (106)
=.++|+.|+|+.--..+|= .+.-|.+|..+.|+|..+
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 48
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=21.93 E-value=1.4e+02 Score=19.00 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=7.4
Q ss_pred EEcccCcCCC
Q 033997 10 YSCCNCRNHV 19 (106)
Q Consensus 10 y~C~~C~thL 19 (106)
|.|.+|+..-
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 6788998743
No 49
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.38 E-value=42 Score=20.61 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=10.9
Q ss_pred CceEEcccCcCCC
Q 033997 7 PRLYSCCNCRNHV 19 (106)
Q Consensus 7 ~~~y~C~~C~thL 19 (106)
...|.|..|+..+
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 3569999999988
No 50
>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=20.86 E-value=49 Score=19.00 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=7.2
Q ss_pred ceEEcccCcCCC
Q 033997 8 RLYSCCNCRNHV 19 (106)
Q Consensus 8 ~~y~C~~C~thL 19 (106)
.+|.|..|..-+
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 51
>PF03150 CCP_MauG: Di-haem cytochrome c peroxidase; InterPro: IPR004852 This is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) []. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IQC_A 2VHD_B 1EB7_A 3RN0_A 3SVW_B 3RMZ_A 3SJL_B 3PXW_A 3SLE_B 3PXS_A ....
Probab=20.83 E-value=44 Score=24.42 Aligned_cols=30 Identities=23% Similarity=0.444 Sum_probs=16.0
Q ss_pred cccCCceEEcccCcCCCCCCCC--eeeeeecC
Q 033997 3 EMVGPRLYSCCNCRNHVALHDD--VISKSFQG 32 (106)
Q Consensus 3 ~l~g~~~y~C~~C~thLa~~~~--liSk~f~G 32 (106)
-|.+....+|+.|+.+=....+ -.|.+..|
T Consensus 16 ~LS~~~~~SCasCH~~~~~~td~~~~~~G~~g 47 (159)
T PF03150_consen 16 RLSGDGTVSCASCHDPEHGFTDGLAVSIGVGG 47 (159)
T ss_dssp GGSTTSS--HHHHS-TTTTTS-SSSSBBEGGG
T ss_pred ccCCCcCcCchhhCCCcccCCcccccCCCCCC
Confidence 3677889999999987533333 33444444
No 52
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=20.48 E-value=1.2e+02 Score=20.98 Aligned_cols=45 Identities=20% Similarity=0.413 Sum_probs=33.8
Q ss_pred ceEEcccCcCCCCCCCCeeeeeecCCCceEEEeecccccccCCccc
Q 033997 8 RLYSCCNCRNHVALHDDVISKSFQGRNGRAFLFSHAMNIVVGPKED 53 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~~~ 53 (106)
|.=.|..|+.-=.-...++++.+.++. ..+...+-.|+..|+..+
T Consensus 15 r~saC~~C~~~~~Cg~~~~~~~~~~~~-~~~~~~~~~~~~~GD~V~ 59 (135)
T PF04246_consen 15 RSSACGSCSASGGCGTGLLAKLFSGKP-ITFRAPNPIGAKVGDRVE 59 (135)
T ss_pred cCCcCcccCCCCCCCcchhhhhcCCCc-EEEEecCCCCCCCCCEEE
Confidence 344699998666667778888888877 666667777888888754
No 53
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=20.07 E-value=17 Score=23.44 Aligned_cols=18 Identities=33% Similarity=0.554 Sum_probs=14.9
Q ss_pred eeeecccCCCceeeEEEe
Q 033997 64 ADVFCSDCRVVLGWKYER 81 (106)
Q Consensus 64 ~DI~C~~C~~~lGWkY~~ 81 (106)
-+|.|-+|+..+|=+|++
T Consensus 3 iPvRCFTCGkvi~~~we~ 20 (62)
T PRK04016 3 IPVRCFTCGKVIAEKWEE 20 (62)
T ss_pred CCeEecCCCCChHHHHHH
Confidence 478999999999976654
No 54
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=20.04 E-value=64 Score=17.47 Aligned_cols=12 Identities=42% Similarity=0.916 Sum_probs=10.2
Q ss_pred ceEEcccCcCCC
Q 033997 8 RLYSCCNCRNHV 19 (106)
Q Consensus 8 ~~y~C~~C~thL 19 (106)
++|.|..|+.-+
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 589999998765
Done!