Query 039667
Match_columns 107
No_of_seqs 100 out of 324
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:58:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039667hhsearch_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 2E-51 4.3E-56 293.9 -1.8 104 4-107 8-113 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 4.2E-34 9.1E-39 193.5 6.1 89 10-104 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 95.8 0.0056 1.2E-07 43.6 1.9 88 10-99 4-93 (123)
4 PF01641 SelR: SelR domain; I 94.9 0.017 3.7E-07 41.8 2.0 73 7-86 34-106 (124)
5 TIGR00357 methionine-R-sulfoxi 94.9 0.027 5.9E-07 41.3 3.1 67 8-82 38-105 (134)
6 PRK00222 methionine sulfoxide 94.2 0.047 1E-06 40.4 3.0 69 7-82 40-108 (142)
7 PRK05508 methionine sulfoxide 92.9 0.14 3E-06 37.0 3.4 65 7-81 30-94 (119)
8 PRK05550 bifunctional methioni 91.2 0.16 3.4E-06 41.2 2.4 64 8-81 34-97 (283)
9 PRK14018 trifunctional thiored 90.5 0.29 6.3E-06 42.6 3.5 70 7-83 415-484 (521)
10 COG0229 Conserved domain frequ 87.8 0.8 1.7E-05 34.0 3.7 66 8-80 40-105 (140)
11 PF14976 FAM72: FAM72 protein 84.4 2.1 4.5E-05 32.1 4.4 62 10-83 15-88 (150)
12 KOG0856 Predicted pilin-like t 80.4 1.8 3.8E-05 32.3 2.7 66 8-81 52-118 (146)
13 PF09814 HECT_2: HECT-like Ubi 78.1 3.7 8E-05 32.8 4.2 17 10-26 106-122 (354)
14 PF13465 zf-H2C2_2: Zinc-finge 51.1 11 0.00024 19.5 1.3 13 6-18 10-22 (26)
15 KOG2272 Focal adhesion protein 46.3 13 0.00028 30.7 1.7 62 6-79 133-196 (332)
16 PF11023 DUF2614: Protein of u 46.0 7.9 0.00017 27.9 0.3 25 9-33 84-108 (114)
17 PRK11586 napB nitrate reductas 40.6 18 0.00038 27.2 1.5 29 7-35 117-145 (149)
18 PRK05417 glutathione-dependent 40.2 54 0.0012 25.2 4.2 53 47-104 75-127 (191)
19 COG3791 Uncharacterized conser 39.6 25 0.00055 24.9 2.1 21 63-83 66-86 (133)
20 PF00412 LIM: LIM domain; Int 36.2 20 0.00044 20.8 1.0 15 10-24 26-40 (58)
21 TIGR00037 eIF_5A translation i 35.0 44 0.00096 23.9 2.8 30 32-61 35-64 (130)
22 PF03811 Zn_Tnp_IS1: InsA N-te 33.7 27 0.00058 20.0 1.2 27 65-91 4-31 (36)
23 PF10246 MRP-S35: Mitochondria 33.5 24 0.00052 25.0 1.2 52 40-96 10-67 (104)
24 PLN03107 eukaryotic translatio 32.5 49 0.0011 24.6 2.8 30 32-61 49-78 (159)
25 PF13842 Tnp_zf-ribbon_2: DDE_ 31.3 36 0.00078 18.8 1.5 15 9-23 15-29 (32)
26 COG3043 NapB Nitrate reductase 31.2 31 0.00066 26.1 1.5 31 6-36 122-152 (155)
27 PF13248 zf-ribbon_3: zinc-rib 31.1 17 0.00038 18.9 0.1 12 65-76 15-26 (26)
28 TIGR02820 formald_GSH S-(hydro 30.5 63 0.0014 24.7 3.1 33 47-80 71-103 (182)
29 PRK03999 translation initiatio 30.0 60 0.0013 23.2 2.8 30 32-61 34-63 (129)
30 PF06170 DUF983: Protein of un 29.5 22 0.00048 23.9 0.5 23 12-42 10-32 (86)
31 PF10058 DUF2296: Predicted in 29.4 19 0.00042 22.2 0.1 39 41-84 2-40 (54)
32 PF14803 Nudix_N_2: Nudix N-te 29.2 30 0.00065 19.5 0.9 14 68-81 2-15 (34)
33 KOG2324 Prolyl-tRNA synthetase 27.9 49 0.0011 28.7 2.3 13 75-87 271-283 (457)
34 smart00132 LIM Zinc-binding do 27.3 24 0.00052 18.4 0.3 12 10-21 27-38 (39)
35 PF10955 DUF2757: Protein of u 26.7 29 0.00063 23.2 0.6 16 10-25 4-19 (76)
36 PF13240 zinc_ribbon_2: zinc-r 26.3 24 0.00053 18.1 0.2 10 67-76 14-23 (23)
37 PF14353 CpXC: CpXC protein 26.3 32 0.0007 23.7 0.9 48 39-88 13-60 (128)
38 PRK00398 rpoP DNA-directed RNA 25.8 36 0.00079 19.7 0.9 16 10-25 3-18 (46)
39 PF04828 GFA: Glutathione-depe 25.3 56 0.0012 20.2 1.8 31 49-79 31-61 (92)
40 PF02945 Endonuclease_7: Recom 25.1 10 0.00022 25.3 -1.8 20 58-79 46-65 (81)
41 TIGR03791 TTQ_mauG tryptophan 25.0 42 0.00091 27.1 1.4 32 5-36 18-51 (291)
42 PF00096 zf-C2H2: Zinc finger, 24.9 12 0.00027 18.1 -1.1 16 11-26 1-16 (23)
43 PF13912 zf-C2H2_6: C2H2-type 24.0 10 0.00022 19.1 -1.6 17 10-26 1-17 (27)
44 KOG2462 C2H2-type Zn-finger pr 23.6 25 0.00054 28.8 -0.2 23 5-27 210-232 (279)
45 PF12760 Zn_Tnp_IS1595: Transp 23.0 65 0.0014 18.6 1.6 13 6-18 33-45 (46)
46 PRK04016 DNA-directed RNA poly 22.4 16 0.00034 23.7 -1.3 18 65-82 3-20 (62)
47 PF04246 RseC_MucC: Positive r 21.6 1.1E+02 0.0024 21.2 2.9 45 9-54 15-59 (135)
48 COG4892 Predicted heme/steroid 21.5 49 0.0011 22.3 0.9 22 30-51 11-34 (81)
49 PF03150 CCP_MauG: Di-haem cyt 21.5 27 0.00059 25.6 -0.3 18 4-21 16-33 (159)
50 PF10238 Eapp_C: E2F-associate 20.6 55 0.0012 23.9 1.2 26 7-32 26-54 (136)
51 PF06524 NOA36: NOA36 protein; 20.2 58 0.0013 27.0 1.3 20 7-26 139-158 (314)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=2e-51 Score=293.94 Aligned_cols=104 Identities=48% Similarity=0.942 Sum_probs=99.6
Q ss_pred ecCC-CCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEe
Q 039667 4 NLIG-PRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKR 82 (107)
Q Consensus 4 ~l~g-~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~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 4454 479999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccccccccEEEEeccccccC-C
Q 039667 83 AFEESQKYKEGKIVLEKFKIAKDN-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 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=4.2e-34 Score=193.47 Aligned_cols=89 Identities=44% Similarity=0.921 Sum_probs=85.3
Q ss_pred eEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceec----EEEeeeecccCCCceeeeEEeecc
Q 039667 10 RYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGL----HTVADVYCADCGELLGWTYKRAFE 85 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~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 7788888999999999 999999999999999999999999
Q ss_pred cccccccccEEEEeccccc
Q 039667 86 ESQKYKEGKIVLEKFKIAK 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 99999999999998864
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=95.80 E-value=0.0056 Score=43.62 Aligned_cols=88 Identities=19% Similarity=0.268 Sum_probs=57.7
Q ss_pred eEEeccCCCCCCCCCCeeee--ceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEeecccc
Q 039667 10 RYSCYRCRNLVSCHEDIVSK--GFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRAFEES 87 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk--~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~s 87 (107)
.+.|++|.+.++..+||-.- +-+=--.+. |...+.+...|.+.....-+.+....|+|..|+..+|-.+..---+=
T Consensus 4 ~llC~kC~~~~C~~~DIr~ie~~hhv~v~p~--F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m~yk~~~L 81 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKIENSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMKYKGVEL 81 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEETTTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEEETTEEE
T ss_pred EEECCCCCceeEchhheEEecCCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheEECCccc
Confidence 48899999999999998664 111111233 33566666666654444558889999999999999998775533223
Q ss_pred cccccccEEEEe
Q 039667 88 QKYKEGKIVLEK 99 (107)
Q Consensus 88 qkYKEGkfIlE~ 99 (107)
=-.|.-.|+++.
T Consensus 82 P~L~iksfvv~~ 93 (123)
T PF11648_consen 82 PCLKIKSFVVEL 93 (123)
T ss_dssp EEE-GGGEEEEE
T ss_pred cEEEeeeeeeee
Confidence 344555666443
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=94.94 E-value=0.017 Score=41.77 Aligned_cols=73 Identities=21% Similarity=0.407 Sum_probs=45.9
Q ss_pred CCCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEeeccc
Q 039667 7 GPRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRAFEE 86 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~ 86 (107)
..-+|.|+.|+++|=+++ ..|....|=.-.+..+..-.+...+|.. -|+.. ..|.|..|+..||=-......+
T Consensus 34 ~~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 34 EEGIYVCAVCGTPLFSSD----TKFDSGCGWPSFWQPIPGDAVKEREDFS--HGMVR-TEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp SSEEEEETTTS-EEEEGG----GEETSSSSSSEESSCSSTTSEEEEEEEC--TSSEE-EEEEETTTCCEEEEEESTSSTT
T ss_pred CCEEEEcCCCCCccccCc----ccccCCcCCccccCcCChHHEEEecccc--CCceE-EEEEecCCCCccccEeCCCCCC
Confidence 345899999999997665 3566666655545544432233333332 24544 4899999999999777655543
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=94.91 E-value=0.027 Score=41.25 Aligned_cols=67 Identities=19% Similarity=0.439 Sum_probs=43.8
Q ss_pred CCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecc-cccccCCccceeeceecEEEeeeecccCCCceeeeEEe
Q 039667 8 PRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHA-ANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKR 82 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v-~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 82 (107)
+-+|.|+.|+++|=.+++ .|....|=.-.+..+ -|. +...+|+. -|+.. ..|.|..|+..||=-...
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~-V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~D 105 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEV-VAYERDES--HGMIR-TEVRCRNCDAHLGHVFDD 105 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCc-eEEeecCC--CCcEE-EEEEecCCCCccCcccCC
Confidence 457999999999987764 466666655545554 232 22333332 25544 589999999999965543
No 6
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.25 E-value=0.047 Score=40.41 Aligned_cols=69 Identities=19% Similarity=0.373 Sum_probs=44.7
Q ss_pred CCCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEe
Q 039667 7 GPRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKR 82 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~ 82 (107)
.+-+|.|+.|+++|=+++ ..|....|=.-.+..+-.-.+...+|+ .-|+.. ..|.|..|+..||=-...
T Consensus 40 ~~G~Y~C~~Cg~pLF~S~----~Kf~Sg~GWPSF~~~i~~~~V~~~~D~--s~gm~R-tEv~C~~Cg~HLGHVF~D 108 (142)
T PRK00222 40 EKGIYVCIVCGEPLFSSD----TKFDSGCGWPSFTKPIDEEAIRELRDT--SHGMVR-TEVRCANCDSHLGHVFPD 108 (142)
T ss_pred CCeEEEecCCCchhcCCc----ccccCCCCCcCcCcccCCCceEEeecc--CCCceE-EEEEeCCCCCccCcccCC
Confidence 345899999999998774 357666776655555532222223332 223332 579999999999976654
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=92.90 E-value=0.14 Score=36.99 Aligned_cols=65 Identities=23% Similarity=0.481 Sum_probs=43.7
Q ss_pred CCCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEE
Q 039667 7 GPRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYK 81 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
.+-+|.|+.|+++|=++++ .|....|=.-.+..+-|. +...+|.. | + =..|.|..|+..||=-..
T Consensus 30 ~~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~-v~~~~D~~---~-~-RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 30 EKGTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKGA-VKRIPDAD---G-R-RTEIVCANCGGHLGHVFE 94 (119)
T ss_pred CCeEEEecCCCCccccccc----cccCCCCCcccCcccccc-eEEEecCC---C-c-EEEEEeCCCCCccCcccC
Confidence 3458999999999987764 566666655555555432 23334433 2 2 367999999999996543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=91.24 E-value=0.16 Score=41.22 Aligned_cols=64 Identities=27% Similarity=0.520 Sum_probs=43.2
Q ss_pred CCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEE
Q 039667 8 PRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYK 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~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----KFNSGCGWPSFDDEIPGAVK-RLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccE-EEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 458999999999988654 56666665554666544322 222222 33 478999999999996654
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.55 E-value=0.29 Score=42.60 Aligned_cols=70 Identities=11% Similarity=0.140 Sum_probs=46.1
Q ss_pred CCCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEee
Q 039667 7 GPRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRA 83 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A 83 (107)
.+-+|.|+.|+++|=+++ ..|....|=.-.+..+-+-.+...+|.+ -|++. ..|.|..|+..||--....
T Consensus 415 ~~G~y~c~~c~~pLf~s~----~Kf~sg~GWPsF~~~i~~~~v~~~~d~s--~g~~R-~Ev~c~~c~~HLGHvf~dg 484 (521)
T PRK14018 415 KPGIYVDVVSGEPLFSSA----DKYDSGCGWPSFTRPIDAKVVTEHDDFS--YNMRR-TEVRSRAADSHLGHVFPDG 484 (521)
T ss_pred CCEEEEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeeccC--CCceE-EEEEECCCCCcCCcccCCC
Confidence 345899999999998875 4566666665555554332233333332 24544 3899999999999766543
No 10
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=87.81 E-value=0.8 Score=33.96 Aligned_cols=66 Identities=26% Similarity=0.453 Sum_probs=44.6
Q ss_pred CCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceeeceecEEEeeeecccCCCceeeeE
Q 039667 8 PRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTY 80 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY 80 (107)
+-+|.|+.|..+|=.+++ .|....|=--.+.-+..-.+...+|+ .-|++.+ .|.|..|++.||=-.
T Consensus 40 ~GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~Rt-EVrc~~c~sHLGHVF 105 (140)
T COG0229 40 KGIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVRT-EVRCANCDSHLGHVF 105 (140)
T ss_pred CceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEEE-EEEecCCCCcccccc
Confidence 458999999999987764 46555555444555544444444444 3456554 799999999999433
No 11
>PF14976 FAM72: FAM72 protein
Probab=84.39 E-value=2.1 Score=32.13 Aligned_cols=62 Identities=21% Similarity=0.433 Sum_probs=38.4
Q ss_pred eEEeccCCCCCCCCCCeeeeceeCCCceEEEeeccccccc----CCccceeeceec--------EEEeeeecccCCCcee
Q 039667 10 RYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVE----GPKEDQHLLTGL--------HTVADVYCADCGELLG 77 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~----g~~e~r~m~TG~--------h~V~DI~C~~C~~~lG 77 (107)
+..|+.|++-|+... =||.|..+ .|+.. -||....-.+|. =.++|+-|..|+..||
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 367999998887543 23444443 33321 122222223333 3899999999999999
Q ss_pred eeEEee
Q 039667 78 WTYKRA 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 12
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=80.37 E-value=1.8 Score=32.34 Aligned_cols=66 Identities=24% Similarity=0.436 Sum_probs=39.9
Q ss_pred CCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccceee-ceecEEEeeeecccCCCceeeeEE
Q 039667 8 PRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKEDQHL-LTGLHTVADVYCADCGELLGWTYK 81 (107)
Q Consensus 8 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m-~TG~h~V~DI~C~~C~~~lGWkY~ 81 (107)
+-+|.|..|.++|=.++ .-|.-..|=--.|+.+- .|..-.+.. .-|.+ =.+|.|..|+..||--.+
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----TKFDSGCGWPAFFEAIG---PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCcccccc----ccccCCCCCchhhhccC---CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 45899999999997764 35666666444444431 121111111 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=78.12 E-value=3.7 Score=32.79 Aligned_cols=17 Identities=18% Similarity=0.508 Sum_probs=13.8
Q ss_pred eEEeccCCCCCCCCCCe
Q 039667 10 RYSCYRCRNLVSCHEDI 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=51.10 E-value=11 Score=19.52 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=11.0
Q ss_pred CCCCeEEeccCCC
Q 039667 6 IGPRRYSCYRCRN 18 (107)
Q Consensus 6 ~g~~~y~C~~C~t 18 (107)
.|.++|.|..|..
T Consensus 10 ~~~k~~~C~~C~k 22 (26)
T PF13465_consen 10 TGEKPYKCPYCGK 22 (26)
T ss_dssp SSSSSEEESSSSE
T ss_pred CCCCCCCCCCCcC
Confidence 5788999999974
No 15
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=46.34 E-value=13 Score=30.68 Aligned_cols=62 Identities=18% Similarity=0.523 Sum_probs=37.9
Q ss_pred CCCCeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecc--cccccCCccceeeceecEEEeeeecccCCCceeee
Q 039667 6 IGPRRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHA--ANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWT 79 (107)
Q Consensus 6 ~g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v--~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWk 79 (107)
.|..+|.|..|+.|+-. +.|+ |+|..=-+|.|+-. -|.-...+. -+-.|.||-.|...+|--
T Consensus 133 ~~~g~YvC~KCh~~iD~-~~l~---fr~d~yH~yHFkCt~C~keL~sdaR--------evk~eLyClrChD~mgip 196 (332)
T KOG2272|consen 133 KGRGRYVCQKCHAHIDE-QPLT---FRGDPYHPYHFKCTTCGKELTSDAR--------EVKGELYCLRCHDKMGIP 196 (332)
T ss_pred cccceeehhhhhhhccc-cccc---ccCCCCCccceecccccccccchhh--------hhccceeccccccccCCc
Confidence 45558999999999987 4443 77777777888732 222221111 122367777777766643
No 16
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=46.03 E-value=7.9 Score=27.85 Aligned_cols=25 Identities=20% Similarity=0.527 Sum_probs=21.2
Q ss_pred CeEEeccCCCCCCCCCCeeeeceeC
Q 039667 9 RRYSCYRCRNLVSCHEDIVSKGFQA 33 (107)
Q Consensus 9 ~~y~C~~C~thLa~~~~liSk~f~G 33 (107)
|...|-+|++||+...++--|.|+-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 5679999999999999888777753
No 17
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=40.58 E-value=18 Score=27.16 Aligned_cols=29 Identities=34% Similarity=0.639 Sum_probs=25.1
Q ss_pred CCCeEEeccCCCCCCCCCCeeeeceeCCC
Q 039667 7 GPRRYSCYRCRNLVSCHEDIVSKGFQASS 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 36789999999999999999999997644
No 18
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=40.24 E-value=54 Score=25.17 Aligned_cols=53 Identities=8% Similarity=0.021 Sum_probs=28.3
Q ss_pred cccCCccceeeceecEEEeeeecccCCCceeeeEEeecccccccccccEEEEeccccc
Q 039667 47 IVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRAFEESQKYKEGKIVLEKFKIAK 104 (107)
Q Consensus 47 v~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sqkYKEGkfIlE~~~i~~ 104 (107)
+..|+...+...+|.. +.--+|..|++.|-+..+....+ -.|..+|=...+..
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 45559999999998877622101 12555555544443
No 19
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=39.55 E-value=25 Score=24.87 Aligned_cols=21 Identities=24% Similarity=0.624 Sum_probs=16.2
Q ss_pred EEeeeecccCCCceeeeEEee
Q 039667 63 TVADVYCADCGELLGWTYKRA 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 344449999999999997654
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=36.18 E-value=20 Score=20.82 Aligned_cols=15 Identities=13% Similarity=0.558 Sum_probs=11.9
Q ss_pred eEEeccCCCCCCCCC
Q 039667 10 RYSCYRCRNLVSCHE 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 478899998887666
No 21
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=35.03 E-value=44 Score=23.87 Aligned_cols=30 Identities=20% Similarity=0.041 Sum_probs=26.0
Q ss_pred eCCCceEEEeecccccccCCccceeeceec
Q 039667 32 QASSGRAFLFSHAANIVEGPKEDQHLLTGL 61 (107)
Q Consensus 32 ~G~~G~AyLf~~v~Nv~~g~~e~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 699999999999999999999887766655
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=33.69 E-value=27 Score=19.97 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=21.2
Q ss_pred eeeecccCCCce-eeeEEeecccccccc
Q 039667 65 ADVYCADCGELL-GWTYKRAFEESQKYK 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 479999999998 677777777777774
No 23
>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=33.50 E-value=24 Score=24.99 Aligned_cols=52 Identities=27% Similarity=0.317 Sum_probs=32.7
Q ss_pred EeecccccccCCccceeeceec--EEEeeeecccCCCceeeeEE----eecccccccccccEE
Q 039667 40 LFSHAANIVEGPKEDQHLLTGL--HTVADVYCADCGELLGWTYK----RAFEESQKYKEGKIV 96 (107)
Q Consensus 40 Lf~~v~Nv~~g~~e~r~m~TG~--h~V~DI~C~~C~~~lGWkY~----~A~e~sqkYKEGkfI 96 (107)
|+.+-.=+..|++++|. ++|. |+|.|- =---+|||.. +.-..+++|.+|.=+
T Consensus 10 lLR~S~fi~lG~~~gk~-V~G~I~hvv~dd----LYIDfG~KFhcVc~rp~~~~~~y~~G~rV 67 (104)
T PF10246_consen 10 LLRNSPFIQLGDPEGKI-VIGKIFHVVDDD----LYIDFGGKFHCVCKRPAVNGEKYVRGSRV 67 (104)
T ss_pred HhcCChhhhcCCccCCE-EEEEEEEEecCc----eEEEeCCceeEEEecccccccccccCCEE
Confidence 34444445679988876 6776 888762 1223588864 334577889998543
No 24
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=32.46 E-value=49 Score=24.60 Aligned_cols=30 Identities=20% Similarity=0.173 Sum_probs=26.5
Q ss_pred eCCCceEEEeecccccccCCccceeeceec
Q 039667 32 QASSGRAFLFSHAANIVEGPKEDQHLLTGL 61 (107)
Q Consensus 32 ~G~~G~AyLf~~v~Nv~~g~~e~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 799999999999999999999888776665
No 25
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=31.31 E-value=36 Score=18.78 Aligned_cols=15 Identities=27% Similarity=0.715 Sum_probs=12.5
Q ss_pred CeEEeccCCCCCCCC
Q 039667 9 RRYSCYRCRNLVSCH 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 469999999998764
No 26
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=31.17 E-value=31 Score=26.05 Aligned_cols=31 Identities=29% Similarity=0.660 Sum_probs=26.1
Q ss_pred CCCCeEEeccCCCCCCCCCCeeeeceeCCCc
Q 039667 6 IGPRRYSCYRCRNLVSCHEDIVSKGFQASSG 36 (107)
Q Consensus 6 ~g~~~y~C~~C~thLa~~~~liSk~f~G~~G 36 (107)
..+|.|-|..|+.+=+...-|+--.|..-.|
T Consensus 122 vSPRRYFClQCHVPQaD~kPlV~N~F~p~~~ 152 (155)
T COG3043 122 VSPRRYFCLQCHVPQADVKPLVGNTFKPMKG 152 (155)
T ss_pred cCccceeeeecccccccccccCCCCcccchh
Confidence 3588999999999999999999888875443
No 27
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.07 E-value=17 Score=18.91 Aligned_cols=12 Identities=33% Similarity=1.021 Sum_probs=7.2
Q ss_pred eeeecccCCCce
Q 039667 65 ADVYCADCGELL 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 28
>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=30.53 E-value=63 Score=24.67 Aligned_cols=33 Identities=9% Similarity=0.110 Sum_probs=19.8
Q ss_pred cccCCccceeeceecEEEeeeecccCCCceeeeE
Q 039667 47 IVEGPKEDQHLLTGLHTVADVYCADCGELLGWTY 80 (107)
Q Consensus 47 v~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY 80 (107)
+..|+...+....|.+..+ -||..|++.|-+..
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 4345544333334555444 49999999996554
No 29
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=30.04 E-value=60 Score=23.16 Aligned_cols=30 Identities=20% Similarity=0.093 Sum_probs=25.4
Q ss_pred eCCCceEEEeecccccccCCccceeeceec
Q 039667 32 QASSGRAFLFSHAANIVEGPKEDQHLLTGL 61 (107)
Q Consensus 32 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 61 (107)
.|+||.|+.--++.|+..|...++...++-
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 688999999999999999988777766664
No 30
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=29.46 E-value=22 Score=23.90 Aligned_cols=23 Identities=26% Similarity=0.416 Sum_probs=18.4
Q ss_pred EeccCCCCCCCCCCeeeeceeCCCceEEEee
Q 039667 12 SCYRCRNLVSCHEDIVSKGFQASSGRAFLFS 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 6999999998765 5678888754
No 31
>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=29.35 E-value=19 Score=22.22 Aligned_cols=39 Identities=21% Similarity=0.365 Sum_probs=26.0
Q ss_pred eecccccccCCccceeeceecEEEeeeecccCCCceeeeEEeec
Q 039667 41 FSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRAF 84 (107)
Q Consensus 41 f~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~ 84 (107)
|++++.+..|..+ |+...--.+-|..|.+.=|---..++
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~~~~~ 40 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAPKEEF 40 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccccccC
Confidence 5678888888877 33333344569999999886543333
No 32
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.19 E-value=30 Score=19.55 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=7.1
Q ss_pred ecccCCCceeeeEE
Q 039667 68 YCADCGELLGWTYK 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 33
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.95 E-value=49 Score=28.67 Aligned_cols=13 Identities=31% Similarity=0.644 Sum_probs=10.2
Q ss_pred ceeeeEEeecccc
Q 039667 75 LLGWTYKRAFEES 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 6888998888655
No 34
>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=27.32 E-value=24 Score=18.41 Aligned_cols=12 Identities=17% Similarity=0.736 Sum_probs=10.1
Q ss_pred eEEeccCCCCCC
Q 039667 10 RYSCYRCRNLVS 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 488999999886
No 35
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=26.67 E-value=29 Score=23.18 Aligned_cols=16 Identities=19% Similarity=0.603 Sum_probs=13.5
Q ss_pred eEEeccCCCCCCCCCC
Q 039667 10 RYSCYRCRNLVSCHED 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 4999999999987665
No 36
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=26.29 E-value=24 Score=18.11 Aligned_cols=10 Identities=40% Similarity=1.235 Sum_probs=6.0
Q ss_pred eecccCCCce
Q 039667 67 VYCADCGELL 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 4566666654
No 37
>PF14353 CpXC: CpXC protein
Probab=26.28 E-value=32 Score=23.70 Aligned_cols=48 Identities=21% Similarity=0.460 Sum_probs=32.4
Q ss_pred EEeecccccccCCccceeeceecEEEeeeecccCCCceeeeEEeeccccc
Q 039667 39 FLFSHAANIVEGPKEDQHLLTGLHTVADVYCADCGELLGWTYKRAFEESQ 88 (107)
Q Consensus 39 yLf~~v~Nv~~g~~e~r~m~TG~h~V~DI~C~~C~~~lGWkY~~A~e~sq 88 (107)
+-+-..+|+...|.-...++.|. +-...|.+|+...---|.--|.+.+
T Consensus 13 ~~v~~~I~~~~~p~l~e~il~g~--l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 13 FEVWTSINADEDPELKEKILDGS--LFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEEEeEEcCcCCHHHHHHHHcCC--cCEEECCCCCCceecCCCEEEEcCC
Confidence 34457888888776555666776 3446899999987665655554443
No 38
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.83 E-value=36 Score=19.68 Aligned_cols=16 Identities=38% Similarity=0.700 Sum_probs=11.5
Q ss_pred eEEeccCCCCCCCCCC
Q 039667 10 RYSCYRCRNLVSCHED 25 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~ 25 (107)
.|.|.+|++.+...+.
T Consensus 3 ~y~C~~CG~~~~~~~~ 18 (46)
T PRK00398 3 EYKCARCGREVELDEY 18 (46)
T ss_pred EEECCCCCCEEEECCC
Confidence 5888888887765443
No 39
>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=25.25 E-value=56 Score=20.24 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=16.2
Q ss_pred cCCccceeeceecEEEeeeecccCCCceeee
Q 039667 49 EGPKEDQHLLTGLHTVADVYCADCGELLGWT 79 (107)
Q Consensus 49 ~g~~e~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 3443333333133345558999999999976
No 40
>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=25.05 E-value=10 Score=25.30 Aligned_cols=20 Identities=35% Similarity=0.644 Sum_probs=16.6
Q ss_pred ceecEEEeeeecccCCCceeee
Q 039667 58 LTGLHTVADVYCADCGELLGWT 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 3444 9999999999999965
No 41
>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=24.98 E-value=42 Score=27.07 Aligned_cols=32 Identities=25% Similarity=0.304 Sum_probs=21.9
Q ss_pred cCCCCeEEeccCCCCCCCCCC--eeeeceeCCCc
Q 039667 5 LIGPRRYSCYRCRNLVSCHED--IVSKGFQASSG 36 (107)
Q Consensus 5 l~g~~~y~C~~C~thLa~~~~--liSk~f~G~~G 36 (107)
|.+.+..+|+.|+.+-.-..+ .+|.+..|..|
T Consensus 18 LS~~~~~SCasCH~p~~~~~d~~~~s~G~~g~~~ 51 (291)
T TIGR03791 18 LSRDGSMSCATCHNPGLGWSDGLILALGADGVEH 51 (291)
T ss_pred cCCCCCcCchhcCCccccCCCCcccccCCCCCCC
Confidence 678888999999987654333 45656655443
No 42
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=24.88 E-value=12 Score=18.09 Aligned_cols=16 Identities=25% Similarity=0.652 Sum_probs=11.5
Q ss_pred EEeccCCCCCCCCCCe
Q 039667 11 YSCYRCRNLVSCHEDI 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 7899998777665544
No 43
>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=23.97 E-value=10 Score=19.15 Aligned_cols=17 Identities=18% Similarity=0.524 Sum_probs=12.3
Q ss_pred eEEeccCCCCCCCCCCe
Q 039667 10 RYSCYRCRNLVSCHEDI 26 (107)
Q Consensus 10 ~y~C~~C~thLa~~~~l 26 (107)
+|.|..|+.-..+.+.+
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 58899998776665544
No 44
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=23.55 E-value=25 Score=28.83 Aligned_cols=23 Identities=17% Similarity=0.488 Sum_probs=18.8
Q ss_pred cCCCCeEEeccCCCCCCCCCCee
Q 039667 5 LIGPRRYSCYRCRNLVSCHEDIV 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 36899999999998888777664
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=22.97 E-value=65 Score=18.65 Aligned_cols=13 Identities=38% Similarity=0.846 Sum_probs=8.3
Q ss_pred CCCCeEEeccCCC
Q 039667 6 IGPRRYSCYRCRN 18 (107)
Q Consensus 6 ~g~~~y~C~~C~t 18 (107)
.+...|.|+.|+.
T Consensus 33 ~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 33 KTRGRYRCKACRK 45 (46)
T ss_pred CCCCeEECCCCCC
Confidence 3445677777764
No 46
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=22.37 E-value=16 Score=23.67 Aligned_cols=18 Identities=22% Similarity=0.652 Sum_probs=15.1
Q ss_pred eeeecccCCCceeeeEEe
Q 039667 65 ADVYCADCGELLGWTYKR 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 478999999999977764
No 47
>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=21.64 E-value=1.1e+02 Score=21.23 Aligned_cols=45 Identities=18% Similarity=0.349 Sum_probs=33.6
Q ss_pred CeEEeccCCCCCCCCCCeeeeceeCCCceEEEeecccccccCCccc
Q 039667 9 RRYSCYRCRNLVSCHEDIVSKGFQASSGRAFLFSHAANIVEGPKED 54 (107)
Q Consensus 9 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~ 54 (107)
|.=.|.+|+.-=.....++++.+.++. ..+...+-.|+..|+..+
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 444699998766667778888888877 666667777888887654
No 48
>COG4892 Predicted heme/steroid binding protein [General function prediction only]
Probab=21.46 E-value=49 Score=22.32 Aligned_cols=22 Identities=14% Similarity=0.397 Sum_probs=15.2
Q ss_pred ceeCCCceEEEee--cccccccCC
Q 039667 30 GFQASSGRAFLFS--HAANIVEGP 51 (107)
Q Consensus 30 ~f~G~~G~AyLf~--~v~Nv~~g~ 51 (107)
.|.|+.|+||+-- +|..|...+
T Consensus 11 ~ynG~nGpaYiA~~G~VYDvS~s~ 34 (81)
T COG4892 11 KYNGENGPAYIAVNGTVYDVSLSP 34 (81)
T ss_pred hhcCCCCCeEEEECCEEEeeccCc
Confidence 4899999999742 455555443
No 49
>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=21.45 E-value=27 Score=25.57 Aligned_cols=18 Identities=28% Similarity=0.506 Sum_probs=11.7
Q ss_pred ecCCCCeEEeccCCCCCC
Q 039667 4 NLIGPRRYSCYRCRNLVS 21 (107)
Q Consensus 4 ~l~g~~~y~C~~C~thLa 21 (107)
-|.+....+|+.|+.+=.
T Consensus 16 ~LS~~~~~SCasCH~~~~ 33 (159)
T PF03150_consen 16 RLSGDGTVSCASCHDPEH 33 (159)
T ss_dssp GGSTTSS--HHHHS-TTT
T ss_pred ccCCCcCcCchhhCCCcc
Confidence 367788899999998753
No 50
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=20.64 E-value=55 Score=23.92 Aligned_cols=26 Identities=12% Similarity=0.214 Sum_probs=19.7
Q ss_pred CCCeEEeccCCCCCCCCCC---eeeecee
Q 039667 7 GPRRYSCYRCRNLVSCHED---IVSKGFQ 32 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~---liSk~f~ 32 (107)
..-+.+|..|-|.|+...+ ....+|+
T Consensus 26 sDavLsCp~Cft~lc~dcQrHe~y~~QYR 54 (136)
T PF10238_consen 26 SDAVLSCPACFTTLCLDCQRHEKYKNQYR 54 (136)
T ss_pred CCceEeCccccceeeecccccchhcceee
Confidence 3457899999999998777 5556665
No 51
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=20.16 E-value=58 Score=26.96 Aligned_cols=20 Identities=25% Similarity=0.663 Sum_probs=16.8
Q ss_pred CCCeEEeccCCCCCCCCCCe
Q 039667 7 GPRRYSCYRCRNLVSCHEDI 26 (107)
Q Consensus 7 g~~~y~C~~C~thLa~~~~l 26 (107)
|.|+|.|..|...|+-.|++
T Consensus 139 GGrif~CsfC~~flCEDDQF 158 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQF 158 (314)
T ss_pred CCeEEEeecCCCeeeccchh
Confidence 56899999999999877764
Done!