Query 030550
Match_columns 175
No_of_seqs 111 out of 358
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 15:26:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030550.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030550hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04398 DUF538: Protein of un 100.0 1.7E-44 3.7E-49 275.5 5.9 108 30-140 1-110 (110)
2 cd03697 EFTU_II EFTU_II: Elong 51.8 41 0.00089 23.7 4.9 34 79-114 15-52 (87)
3 cd03694 GTPBP_II Domain II of 37.0 1.4E+02 0.003 21.0 5.7 35 78-114 14-54 (87)
4 PF13670 PepSY_2: Peptidase pr 35.3 92 0.002 21.7 4.5 28 29-63 32-59 (83)
5 PF11153 DUF2931: Protein of u 33.8 96 0.0021 25.6 5.1 98 8-110 5-108 (216)
6 PF13987 YedD: YedD-like prote 31.1 17 0.00038 28.1 0.2 17 149-165 39-55 (111)
7 cd04089 eRF3_II eRF3_II: domai 30.3 1.7E+02 0.0036 20.3 5.1 34 79-114 14-49 (82)
8 cd03693 EF1_alpha_II EF1_alpha 29.2 1.5E+02 0.0033 21.0 4.9 35 78-114 18-54 (91)
9 PRK10397 lipoprotein; Provisio 28.9 19 0.00041 28.9 0.0 17 149-165 63-79 (137)
10 PF08300 HCV_NS5a_1a: Hepatiti 26.6 45 0.00097 23.5 1.6 18 78-96 26-43 (62)
11 cd03698 eRF3_II_like eRF3_II_l 25.9 2.3E+02 0.005 19.6 5.3 35 78-114 14-50 (83)
12 PRK12442 translation initiatio 24.3 1.7E+02 0.0037 21.8 4.4 54 56-125 18-71 (87)
13 cd03695 CysN_NodQ_II CysN_NodQ 24.1 2.5E+02 0.0054 19.5 5.2 32 81-114 17-50 (81)
14 PF10262 Rdx: Rdx family; Int 23.2 1.1E+02 0.0024 21.2 3.1 22 46-67 29-52 (76)
15 cd01215 Dab Disabled (Dab) Pho 22.9 2.9E+02 0.0062 22.2 5.8 33 95-127 48-80 (139)
16 cd03690 Tet_II Tet_II: This su 21.9 1.9E+02 0.004 20.3 4.1 53 74-126 18-73 (85)
No 1
>PF04398 DUF538: Protein of unknown function, DUF538; InterPro: IPR007493 This family consists of several plant proteins of unknown function.; PDB: 1YDU_A.
Probab=100.00 E-value=1.7e-44 Score=275.51 Aligned_cols=108 Identities=48% Similarity=0.886 Sum_probs=82.0
Q ss_pred cHHHhhhhcCCCCCCCCCCceeEEEecC-ccEEEEEcCeeEEEEe-EEEEEccEEEEEEecCccccccceeEEEEEeeee
Q 030550 30 TVYEILPKFGLPQGLLPSNVVSYTLQDD-GLFTVELSSECYVEFD-YLVYYEKTVTGKISIGSISNLKGIQVKRFLFWFD 107 (175)
Q Consensus 30 ta~elL~~~GLP~GLLP~~V~~y~l~~~-G~f~v~l~~~C~~~f~-~~v~Y~~~ItG~i~~gkI~~L~GVkvK~lf~Wv~ 107 (175)
||||+|++||||+||||++|++|++|++ |.|||+|+++|+|+|+ |+|+|+++|||+|++|+|++|+|||+|++|+|++
T Consensus 1 tayelL~~~glP~GLLP~~v~~y~l~~~tG~f~v~l~~~C~~~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~k~l~~W~~ 80 (110)
T PF04398_consen 1 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFEGYLVSYDSEITGYIEKGKIKNLTGVKVKELFLWVP 80 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEESTTSEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEES
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEEEEEEEEcCeEEEEECCCcCccccCEEEEEEEEEee
Confidence 6899999999999999999999999985 9999999999999997 7999999999999999999999999999999999
Q ss_pred eeEEEecCCCCCcEEEEEceeeeeecccccccC
Q 030550 108 VDEIRVDLPPSDSIYFQVGIINKKLDVGQFETV 140 (175)
Q Consensus 108 V~eI~vd~~~~~~I~F~vG~isksfP~s~F~~~ 140 (175)
|++|.+ ++++|+|++|.++++||+++|++|
T Consensus 81 v~~i~~---~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 81 VTEISV---DGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp ---BEE----SSSEE-TTSSSS----TTTTSS-
T ss_pred EEEEEE---cCCEEEEEEeeEeccCCHHHhccC
Confidence 999999 499999999999999999999975
No 2
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=51.81 E-value=41 Score=23.72 Aligned_cols=34 Identities=29% Similarity=0.322 Sum_probs=24.4
Q ss_pred ccEEEEEEecCccccccceeEEEE----EeeeeeeEEEec
Q 030550 79 EKTVTGKISIGSISNLKGIQVKRF----LFWFDVDEIRVD 114 (175)
Q Consensus 79 ~~~ItG~i~~gkI~~L~GVkvK~l----f~Wv~V~eI~vd 114 (175)
++.++|+|+.|+|+ .|-++..+ .....|..|++.
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~ 52 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMF 52 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEEC
Confidence 45799999999998 45454443 456778888775
No 3
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=37.05 E-value=1.4e+02 Score=21.02 Aligned_cols=35 Identities=23% Similarity=0.142 Sum_probs=25.3
Q ss_pred EccEEEEEEecCccccccceeEEEE------EeeeeeeEEEec
Q 030550 78 YEKTVTGKISIGSISNLKGIQVKRF------LFWFDVDEIRVD 114 (175)
Q Consensus 78 Y~~~ItG~i~~gkI~~L~GVkvK~l------f~Wv~V~eI~vd 114 (175)
.++.|+|+++.|+++. |-++... +....|..|+++
T Consensus 14 ~GtVv~G~v~~G~v~~--g~~v~~~P~~~g~~~~~~V~sI~~~ 54 (87)
T cd03694 14 VGTVVGGTVSKGVIRL--GDTLLLGPDQDGSFRPVTVKSIHRN 54 (87)
T ss_pred cceEEEEEEecCEEeC--CCEEEECCCCCCCEeEEEEEEEEEC
Confidence 4678999999999984 4444332 246788888875
No 4
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=35.26 E-value=92 Score=21.73 Aligned_cols=28 Identities=29% Similarity=0.406 Sum_probs=21.0
Q ss_pred CcHHHhhhhcCCCCCCCCCCceeEEEecCccEEEE
Q 030550 29 PTVYEILPKFGLPQGLLPSNVVSYTLQDDGLFTVE 63 (175)
Q Consensus 29 ~ta~elL~~~GLP~GLLP~~V~~y~l~~~G~f~v~ 63 (175)
..+...|++.|. .|.+..++++|.++++
T Consensus 32 ~~~~~~l~~~G~-------~v~~ve~~~~g~yev~ 59 (83)
T PF13670_consen 32 EQAVAKLEAQGY-------QVREVEFDDDGCYEVE 59 (83)
T ss_pred HHHHHHHHhcCC-------ceEEEEEcCCCEEEEE
Confidence 356777777443 6889999888888887
No 5
>PF11153 DUF2931: Protein of unknown function (DUF2931); InterPro: IPR021326 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently, there is no known function.
Probab=33.83 E-value=96 Score=25.57 Aligned_cols=98 Identities=20% Similarity=0.219 Sum_probs=46.6
Q ss_pred HHHHHHHHhccccCCCCCCCCCcHHHhhhhcCCCCCCCCCCceeEEE-ecCccEEEEE--cCeeE-EE-E-eEEEEEccE
Q 030550 8 LFLLSLFLLRPTLSLSSDPSPPTVYEILPKFGLPQGLLPSNVVSYTL-QDDGLFTVEL--SSECY-VE-F-DYLVYYEKT 81 (175)
Q Consensus 8 ~~llll~l~~~~~s~s~~~~~~ta~elL~~~GLP~GLLP~~V~~y~l-~~~G~f~v~l--~~~C~-~~-f-~~~v~Y~~~ 81 (175)
++|++++++++|.+... ....+-++---.+.-|+++ |-.|+.-.+ +.+|..+... ...|- .. . ...-.|+..
T Consensus 5 ~~l~l~lll~~C~~~~~-~~~~~~~~W~~~~~~P~~y-pv~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~ 82 (216)
T PF11153_consen 5 LLLLLLLLLTGCSTNPN-EPLQPYFEWRFGVAAPKHY-PVWVTYAYFVDGDGDWYRFPTGDSTCMDPERISGSVGGWGGF 82 (216)
T ss_pred HHHHHHHHHHhhcCCCc-cCCCCCCccEEEEecCCCC-EEEEEEEEEEeCCCcEEEEeccccceeecccCCCccCCcCcc
Confidence 33334444444443332 1222444455555667664 555665544 4455554442 22332 11 1 134445555
Q ss_pred EEEEEecCccccccceeEEEEEeeeeeeE
Q 030550 82 VTGKISIGSISNLKGIQVKRFLFWFDVDE 110 (175)
Q Consensus 82 ItG~i~~gkI~~L~GVkvK~lf~Wv~V~e 110 (175)
+| ..|.-.+-..+-.+..+.|+++.|
T Consensus 83 -~~--~~~~~~~~~~lP~~i~i~W~S~~e 108 (216)
T PF11153_consen 83 -GG--GSGYFNKGKPLPDSIYICWDSYAE 108 (216)
T ss_pred -cc--cccccCCCCCCCCEEEEEEEEccc
Confidence 22 222233444455678889998764
No 6
>PF13987 YedD: YedD-like protein
Probab=31.12 E-value=17 Score=28.11 Aligned_cols=17 Identities=29% Similarity=0.741 Sum_probs=14.2
Q ss_pred CCCCCCCccccccCCCC
Q 030550 149 SESGCGSWTRVLQLPTP 165 (175)
Q Consensus 149 ~~~~c~~~~~~~~~~~~ 165 (175)
+..||+.|+|++-+|--
T Consensus 39 dTLDCRQWQRVia~PGK 55 (111)
T PF13987_consen 39 DTLDCRQWQRVIAKPGK 55 (111)
T ss_pred Cccchhhhheeeecccc
Confidence 56799999999988853
No 7
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=30.30 E-value=1.7e+02 Score=20.29 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=21.6
Q ss_pred ccEEEEEEecCccccccceeEEEE--EeeeeeeEEEec
Q 030550 79 EKTVTGKISIGSISNLKGIQVKRF--LFWFDVDEIRVD 114 (175)
Q Consensus 79 ~~~ItG~i~~gkI~~L~GVkvK~l--f~Wv~V~eI~vd 114 (175)
++.++|+|++|+|+. |-++..+ =....|..|+++
T Consensus 14 g~vv~G~v~~G~i~~--G~~v~i~P~~~~~~V~si~~~ 49 (82)
T cd04089 14 GTVVLGKVESGTIKK--GDKLLVMPNKTQVEVLSIYNE 49 (82)
T ss_pred CEEEEEEEeeeEEec--CCEEEEeCCCcEEEEEEEEEC
Confidence 678999999999883 4333221 124566666654
No 8
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=29.23 E-value=1.5e+02 Score=20.98 Aligned_cols=35 Identities=14% Similarity=0.205 Sum_probs=22.4
Q ss_pred EccEEEEEEecCccccccceeEEEE--EeeeeeeEEEec
Q 030550 78 YEKTVTGKISIGSISNLKGIQVKRF--LFWFDVDEIRVD 114 (175)
Q Consensus 78 Y~~~ItG~i~~gkI~~L~GVkvK~l--f~Wv~V~eI~vd 114 (175)
.++.++|+|+.|.|+. |-++..+ =....|..|++.
T Consensus 18 ~g~vv~G~v~~G~i~~--gd~v~i~P~~~~~~V~sI~~~ 54 (91)
T cd03693 18 IGTVPVGRVETGVLKP--GMVVTFAPAGVTGEVKSVEMH 54 (91)
T ss_pred ceEEEEEEEecceeec--CCEEEECCCCcEEEEEEEEEC
Confidence 4578999999999984 3333221 134667777765
No 9
>PRK10397 lipoprotein; Provisional
Probab=28.94 E-value=19 Score=28.93 Aligned_cols=17 Identities=29% Similarity=0.817 Sum_probs=13.6
Q ss_pred CCCCCCCccccccCCCC
Q 030550 149 SESGCGSWTRVLQLPTP 165 (175)
Q Consensus 149 ~~~~c~~~~~~~~~~~~ 165 (175)
+..||++|+|++-+|--
T Consensus 63 dtldCrqWqrvia~PGK 79 (137)
T PRK10397 63 DTLDCRQWQRVIAVPGK 79 (137)
T ss_pred CEEeehhcceeeeccce
Confidence 45699999999988854
No 10
>PF08300 HCV_NS5a_1a: Hepatitis C virus non-structural 5a zinc finger domain; InterPro: IPR013192 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 a zinc finger motif found in the non-structural 5a protein (NS5a) in Hepatitis C virus. The molecular function of NS5a is uncertain, but it is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ]. This region corresponds to the N-terminal zinc binding domain (1a) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003968 RNA-directed RNA polymerase activity, 0004252 serine-type endopeptidase activity, 0008270 zinc ion binding, 0017111 nucleoside-triphosphatase activity, 0006355 regulation of transcription, DNA-dependent, 0006915 apoptosis, 0030683 evasion by virus of host immune response, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane; PDB: 1ZH1_B 3FQM_A 3FQQ_B.
Probab=26.64 E-value=45 Score=23.49 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=13.5
Q ss_pred EccEEEEEEecCccccccc
Q 030550 78 YEKTVTGKISIGSISNLKG 96 (175)
Q Consensus 78 Y~~~ItG~i~~gkI~~L~G 96 (175)
-+..|+|.|+.|+|+ +.|
T Consensus 26 CGa~ItGhVknG~mr-i~g 43 (62)
T PF08300_consen 26 CGAVITGHVKNGSMR-IYG 43 (62)
T ss_dssp TS-EEEEEEETTEEE-EE-
T ss_pred CCCEEeEEEeCCeEE-Eec
Confidence 467899999999998 544
No 11
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=25.87 E-value=2.3e+02 Score=19.57 Aligned_cols=35 Identities=31% Similarity=0.338 Sum_probs=21.3
Q ss_pred EccEEEEEEecCccccccceeEEEE--EeeeeeeEEEec
Q 030550 78 YEKTVTGKISIGSISNLKGIQVKRF--LFWFDVDEIRVD 114 (175)
Q Consensus 78 Y~~~ItG~i~~gkI~~L~GVkvK~l--f~Wv~V~eI~vd 114 (175)
-++.++|+|+.|.|+. |-++..+ =....|.+|++.
T Consensus 14 ~g~vv~G~v~~G~i~~--Gd~v~i~P~~~~~~V~si~~~ 50 (83)
T cd03698 14 GGTVVSGKVESGSIQK--GDTLLVMPSKESVEVKSIYVD 50 (83)
T ss_pred CCcEEEEEEeeeEEeC--CCEEEEeCCCcEEEEEEEEEC
Confidence 4678899999999884 4333221 123456666654
No 12
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.28 E-value=1.7e+02 Score=21.81 Aligned_cols=54 Identities=22% Similarity=0.169 Sum_probs=38.5
Q ss_pred cCccEEEEEcCeeEEEEeEEEEEccEEEEEEecCccccccceeEEEEEeeeeeeEEEecCCCCCcEEEEE
Q 030550 56 DDGLFTVELSSECYVEFDYLVYYEKTVTGKISIGSISNLKGIQVKRFLFWFDVDEIRVDLPPSDSIYFQV 125 (175)
Q Consensus 56 ~~G~f~v~l~~~C~~~f~~~v~Y~~~ItG~i~~gkI~~L~GVkvK~lf~Wv~V~eI~vd~~~~~~I~F~v 125 (175)
.++.|.|.|...+.+. ..|+|++.+.+|+=+.|=+|++- +| --|.+-+.|.|.-
T Consensus 18 p~~~frV~LenG~~vl--------a~isGKmR~~rIrIl~GD~V~VE-~s-------pYDltkGRIiyR~ 71 (87)
T PRK12442 18 PDSRFRVTLENGVEVG--------AYASGRMRKHRIRILAGDRVTLE-LS-------PYDLTKGRINFRH 71 (87)
T ss_pred CCCEEEEEeCCCCEEE--------EEeccceeeeeEEecCCCEEEEE-EC-------cccCCceeEEEEe
Confidence 3678888887665442 46899999999999999888875 33 1234567777775
No 13
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=24.14 E-value=2.5e+02 Score=19.52 Aligned_cols=32 Identities=28% Similarity=0.182 Sum_probs=21.5
Q ss_pred EEEEEEecCccccccceeEEEEE--eeeeeeEEEec
Q 030550 81 TVTGKISIGSISNLKGIQVKRFL--FWFDVDEIRVD 114 (175)
Q Consensus 81 ~ItG~i~~gkI~~L~GVkvK~lf--~Wv~V~eI~vd 114 (175)
-|+|+|+.|+++ .|-++..+= ....|..|+++
T Consensus 17 ~v~Gkv~~G~v~--~Gd~v~~~P~~~~~~V~si~~~ 50 (81)
T cd03695 17 GYAGTIASGSIR--VGDEVVVLPSGKTSRVKSIETF 50 (81)
T ss_pred EEEEEEccceEE--CCCEEEEcCCCCeEEEEEEEEC
Confidence 499999999998 454443321 24567777765
No 14
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=23.23 E-value=1.1e+02 Score=21.18 Aligned_cols=22 Identities=27% Similarity=0.570 Sum_probs=14.2
Q ss_pred CCCceeEEEe--cCccEEEEEcCe
Q 030550 46 PSNVVSYTLQ--DDGLFTVELSSE 67 (175)
Q Consensus 46 P~~V~~y~l~--~~G~f~v~l~~~ 67 (175)
|..+.+.++. .+|.|+|++++.
T Consensus 29 p~~~~~v~~~~~~~G~FEV~v~g~ 52 (76)
T PF10262_consen 29 PDRIAEVELSPGSTGAFEVTVNGE 52 (76)
T ss_dssp TTTCSEEEEEEESTT-EEEEETTE
T ss_pred CCcceEEEEEeccCCEEEEEEccE
Confidence 3344455554 479999999977
No 15
>cd01215 Dab Disabled (Dab) Phosphotyrosine-binding domain. Disabled (Dab) Phosphotyrosine-binding domain. Dab is a cystosolic adaptor protein, which binds to the cytoplasmic tails of lipoprotein receptors, such as ApoER2 and VLDLR, via its PTB domain. The dab PTB domain has a preference for unphosphorylated tyrosine within an NPxY motif. Additionally, the Dab PTB domain, which is structurally similar to PH domains, binds to phosphatidlyinositol phosphate 4,5 bisphosphate in a manner characteristic of phosphoinositide binding PH domains.
Probab=22.93 E-value=2.9e+02 Score=22.15 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=27.5
Q ss_pred cceeEEEEEeeeeeeEEEecCCCCCcEEEEEce
Q 030550 95 KGIQVKRFLFWFDVDEIRVDLPPSDSIYFQVGI 127 (175)
Q Consensus 95 ~GVkvK~lf~Wv~V~eI~vd~~~~~~I~F~vG~ 127 (175)
.|-+-+...+|+++.+|.|-|+.++.+..+-.+
T Consensus 48 ~~~kk~kV~L~IS~dGi~v~D~~T~~ll~~~~i 80 (139)
T cd01215 48 AGAHKTRITLQINIDGIKVLDEKTGAVLHHHPV 80 (139)
T ss_pred hccccceEEEEEccCCEEEEcCCCCcEEEeece
Confidence 566778888999999999988888888777665
No 16
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=21.85 E-value=1.9e+02 Score=20.29 Aligned_cols=53 Identities=11% Similarity=0.193 Sum_probs=35.3
Q ss_pred EEEEEccEEEEEEecCccc-cccc--eeEEEEEeeeeeeEEEecCCCCCcEEEEEc
Q 030550 74 YLVYYEKTVTGKISIGSIS-NLKG--IQVKRFLFWFDVDEIRVDLPPSDSIYFQVG 126 (175)
Q Consensus 74 ~~v~Y~~~ItG~i~~gkI~-~L~G--VkvK~lf~Wv~V~eI~vd~~~~~~I~F~vG 126 (175)
-++.|.+-.+|.|..|..- +..+ .+++.++.+..-....++....|.|-=-+|
T Consensus 18 G~la~~RV~sG~l~~g~~v~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~ai~g 73 (85)
T cd03690 18 ERLAYLRLYSGTLRLRDSVRVNREEKIKITELRVFNNGEVVTADTVTAGDIAILTG 73 (85)
T ss_pred CeEEEEEEccCEEcCCCEEEeCCCcEEEeceeEEEeCCCeEECcEECCCCEEEEEC
Confidence 4678888889999888433 2222 456678888877777777655666653333
Done!