Query 030668
Match_columns 173
No_of_seqs 104 out of 351
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:48:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030668.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030668hhsearch_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 4.5E-47 9.8E-52 289.4 6.4 110 37-147 1-110 (110)
2 PF08710 nsp9: nsp9 replicase; 56.3 35 0.00077 26.6 5.4 34 55-88 50-85 (111)
3 cd03697 EFTU_II EFTU_II: Elong 49.8 38 0.00082 23.9 4.4 40 89-130 15-58 (87)
4 PF06691 DUF1189: Protein of u 44.5 97 0.0021 26.0 6.8 77 52-146 62-138 (250)
5 PF10262 Rdx: Rdx family; Int 34.8 54 0.0012 22.7 3.2 12 64-75 41-52 (76)
6 cd04089 eRF3_II eRF3_II: domai 34.3 1.6E+02 0.0034 20.4 6.1 36 89-126 14-51 (82)
7 cd02410 archeal_CPSF_KH The ar 34.2 46 0.001 26.9 3.1 39 33-77 49-89 (145)
8 PRK12442 translation initiatio 28.9 1.5E+02 0.0033 22.1 4.8 53 65-132 19-71 (87)
9 PF08300 HCV_NS5a_1a: Hepatiti 27.7 50 0.0011 23.3 2.0 17 89-106 27-43 (62)
10 COG1254 AcyP Acylphosphatases 27.3 79 0.0017 23.4 3.1 21 55-75 31-51 (92)
11 TIGR02689 ars_reduc_gluta arse 26.4 55 0.0012 24.6 2.2 40 32-73 39-79 (126)
12 cd03698 eRF3_II_like eRF3_II_l 26.3 1.8E+02 0.0039 20.1 4.7 37 88-126 14-52 (83)
13 smart00540 LEM in nuclear memb 24.1 60 0.0013 21.1 1.7 18 35-52 8-25 (44)
14 cd03694 GTPBP_II Domain II of 23.6 2.7E+02 0.0058 19.5 5.8 40 89-130 15-60 (87)
15 PRK13488 chemoreceptor glutami 23.2 1.6E+02 0.0034 23.8 4.4 38 34-74 108-151 (157)
16 cd03695 CysN_NodQ_II CysN_NodQ 22.8 1.5E+02 0.0033 20.6 3.8 38 91-130 17-56 (81)
17 PRK12317 elongation factor 1-a 22.7 2.5E+02 0.0054 25.3 6.1 33 89-123 240-274 (425)
18 PRK09455 rseB anti-sigma E fac 22.4 5.6E+02 0.012 22.8 8.5 58 37-111 27-84 (319)
19 PF03975 CheD: CheD chemotacti 22.1 1.1E+02 0.0024 23.0 3.1 37 35-74 66-108 (114)
20 PF07803 GSG-1: GSG1-like prot 21.9 89 0.0019 24.6 2.6 23 5-27 7-29 (118)
21 COG1246 ArgA N-acetylglutamate 21.9 52 0.0011 26.9 1.4 37 32-68 8-51 (153)
22 COG1169 MenF Isochorismate syn 21.9 1.5E+02 0.0032 27.9 4.5 57 12-74 322-379 (423)
23 TIGR00483 EF-1_alpha translati 21.8 2E+02 0.0043 26.0 5.3 28 75-102 227-255 (426)
24 KOG2455 Delta-1-pyrroline-5-ca 21.0 57 0.0012 31.4 1.6 16 37-52 241-256 (561)
25 smart00110 C1Q Complement comp 20.1 2.4E+02 0.0051 21.8 4.7 36 61-99 38-73 (135)
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=4.5e-47 Score=289.38 Aligned_cols=110 Identities=45% Similarity=0.901 Sum_probs=84.6
Q ss_pred hHHHHHHhcCCCCCCCCCCceeEEEeCCCCeEEEEecCeeEEEEecceEEEEeeEEEEEEecCceecccceeEEEEEEee
Q 030668 37 SAYDILQSYNFPAGLLPKGITQYDIDRETGQFHAYLDGTCSFSLEGSYQLKYKSKISGYISENKLTSLTGVSVKVLFLWL 116 (173)
Q Consensus 37 tayelL~~~gLP~GLLP~~V~~y~l~~~tG~f~v~l~~~C~~~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVk~K~lf~Wv 116 (173)
||||+|++||||+||||++|++|+||++||+|||+|+++|+|+++ +|+|+|+++|||+|++|+|++|+|||+|++|+|+
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~ 79 (110)
T PF04398_consen 1 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFE-GYLVSYDSEITGYIEKGKIKNLTGVKVKELFLWV 79 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEEST-TSEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEE
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEE-EEEEEEcCeEEEEECCCcCccccCEEEEEEEEEe
Confidence 689999999999999999999999999999999999999999998 5999999999999999999999999999999999
Q ss_pred eeeEEEEcCCeEEEEEceeeeeeeccccccC
Q 030668 117 NIVEVTRNGDDIDFSVGIASASFAIDNFYEC 147 (173)
Q Consensus 117 ~I~eI~~d~~~I~F~vG~~sksFP~s~F~~s 147 (173)
+|+||.+++|+|+|++|+++++||+++|++|
T Consensus 80 ~v~~i~~~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 80 PVTEISVDGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp S---BEE-SSSEE-TTSSSS----TTTTSS-
T ss_pred eEEEEEEcCCEEEEEEeeEeccCCHHHhccC
Confidence 9999999999999999999999999999986
No 2
>PF08710 nsp9: nsp9 replicase; InterPro: IPR014822 Nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis []. The structure comprises of a single beta barrel []. ; GO: 0003723 RNA binding, 0019079 viral genome replication, 0019034 viral replication complex; PDB: 2J97_A 2J98_A 3EE7_B 1QZ8_A 1UW7_A.
Probab=56.28 E-value=35 Score=26.56 Aligned_cols=34 Identities=18% Similarity=0.492 Sum_probs=21.8
Q ss_pred CceeEEEeCCCCeEEEEecCeeEEEEe--cceEEEE
Q 030668 55 GITQYDIDRETGQFHAYLDGTCSFSLE--GSYQLKY 88 (173)
Q Consensus 55 ~V~~y~l~~~tG~f~v~l~~~C~~~~~--~~~~v~Y 88 (173)
+.+--.+..++|...+.|+-||.|..+ +|-++.|
T Consensus 50 ~Lk~vk~~~d~G~v~ieLePPckF~v~~~~g~~vkY 85 (111)
T PF08710_consen 50 NLKYVKWEKDDGKVVIELEPPCKFAVDVPKGPEVKY 85 (111)
T ss_dssp -EEEEEEE-TTSEEEEEB---EEEEEEETTSEEEEE
T ss_pred CceEEEEEccCCEEEEecCCCcEEEEEcCCCcEEEE
Confidence 445455666799999999999999987 5556665
No 3
>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=49.85 E-value=38 Score=23.87 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=27.8
Q ss_pred eeEEEEEEecCceecccceeEEEE----EEeeeeeEEEEcCCeEEE
Q 030668 89 KSKISGYISENKLTSLTGVSVKVL----FLWLNIVEVTRNGDDIDF 130 (173)
Q Consensus 89 ~~~ItG~i~~g~I~~L~GVk~K~l----f~Wv~I~eI~~d~~~I~F 130 (173)
.+-++|+|+.|+|+ .|-++..+ .....|..|.++...+..
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~~~~~~~ 58 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMFRKTLDE 58 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEECCcCCCE
Confidence 35699999999998 44444433 456778888876554444
No 4
>PF06691 DUF1189: Protein of unknown function (DUF1189); InterPro: IPR009574 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.
Probab=44.54 E-value=97 Score=26.00 Aligned_cols=77 Identities=12% Similarity=0.287 Sum_probs=50.5
Q ss_pred CCCCceeEEEeCCCCeEEEEecCeeEEEEecceEEEEeeEEEEEEecCceecccceeEEEEEEeeeeeEEEEcCCeEEEE
Q 030668 52 LPKGITQYDIDRETGQFHAYLDGTCSFSLEGSYQLKYKSKISGYISENKLTSLTGVSVKVLFLWLNIVEVTRNGDDIDFS 131 (173)
Q Consensus 52 LP~~V~~y~l~~~tG~f~v~l~~~C~~~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVk~K~lf~Wv~I~eI~~d~~~I~F~ 131 (173)
+.+++-+|++. ||.+....+.+-+..- ++..+.||++ |.+...-+++- -++|-...|++++.
T Consensus 62 i~~~iP~F~I~--nG~L~~~~~~~i~~~~-~~~~i~~D~~--~~~~~~dl~~~-------------~~~i~~lkd~iv~~ 123 (250)
T PF06691_consen 62 IENDIPDFTIE--NGKLTSDQSEPIIYQT-NNFIIIFDPT--GKVTEDDLSDY-------------KNAIAFLKDEIVIK 123 (250)
T ss_pred HHhhCCCeEEE--CCcEecCCCCceEecC-CcEEEEECCC--CCcchhhhcCC-------------cceEEEecceEEEE
Confidence 34466678884 8999776555533322 5677889884 55554433221 12456668999998
Q ss_pred Eceeeeeeecccccc
Q 030668 132 VGIASASFAIDNFYE 146 (173)
Q Consensus 132 vG~~sksFP~s~F~~ 146 (173)
.+..++++|-+.+..
T Consensus 124 ~~g~~~s~~Ys~~~~ 138 (250)
T PF06691_consen 124 DNGQTQSISYSDLND 138 (250)
T ss_pred eCCeeEEeehhhccc
Confidence 877788898887754
No 5
>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=34.85 E-value=54 Score=22.74 Aligned_cols=12 Identities=33% Similarity=0.700 Sum_probs=9.7
Q ss_pred CCCeEEEEecCe
Q 030668 64 ETGQFHAYLDGT 75 (173)
Q Consensus 64 ~tG~f~v~l~~~ 75 (173)
.+|.|+|++++.
T Consensus 41 ~~G~FEV~v~g~ 52 (76)
T PF10262_consen 41 STGAFEVTVNGE 52 (76)
T ss_dssp STT-EEEEETTE
T ss_pred cCCEEEEEEccE
Confidence 589999999976
No 6
>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=34.30 E-value=1.6e+02 Score=20.38 Aligned_cols=36 Identities=8% Similarity=0.196 Sum_probs=22.9
Q ss_pred eeEEEEEEecCceecccceeEEEE--EEeeeeeEEEEcCC
Q 030668 89 KSKISGYISENKLTSLTGVSVKVL--FLWLNIVEVTRNGD 126 (173)
Q Consensus 89 ~~~ItG~i~~g~I~~L~GVk~K~l--f~Wv~I~eI~~d~~ 126 (173)
.+.++|+|+.|.|+. |-++..+ =....|.+|.+++.
T Consensus 14 g~vv~G~v~~G~i~~--G~~v~i~P~~~~~~V~si~~~~~ 51 (82)
T cd04089 14 GTVVLGKVESGTIKK--GDKLLVMPNKTQVEVLSIYNEDV 51 (82)
T ss_pred CEEEEEEEeeeEEec--CCEEEEeCCCcEEEEEEEEECCE
Confidence 568999999999983 4333221 13466777776543
No 7
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=34.21 E-value=46 Score=26.94 Aligned_cols=39 Identities=23% Similarity=0.311 Sum_probs=31.5
Q ss_pred CCcchHHHHHHhcCCCCCCCC--CCceeEEEeCCCCeEEEEecCeeE
Q 030668 33 SDQLSAYDILQSYNFPAGLLP--KGITQYDIDRETGQFHAYLDGTCS 77 (173)
Q Consensus 33 ~~~~tayelL~~~gLP~GLLP--~~V~~y~l~~~tG~f~v~l~~~C~ 77 (173)
.+.+.|.++..+ +.| .++++.-+|++||.++++..++=.
T Consensus 49 ~~~e~A~~~I~~------ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ 89 (145)
T cd02410 49 KPPEEAIKIILE------IVPEEAGITDIYFDDDTGEVIIEAEKPGL 89 (145)
T ss_pred CCHHHHHHHHHH------hCCCccCceeeEecCCCcEEEEEEcCCeE
Confidence 345677888876 567 489999999999999999998843
No 8
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=28.91 E-value=1.5e+02 Score=22.10 Aligned_cols=53 Identities=19% Similarity=0.278 Sum_probs=35.7
Q ss_pred CCeEEEEecCeeEEEEecceEEEEeeEEEEEEecCceecccceeEEEEEEeeeeeEEEEcCCeEEEEE
Q 030668 65 TGQFHAYLDGTCSFSLEGSYQLKYKSKISGYISENKLTSLTGVSVKVLFLWLNIVEVTRNGDDIDFSV 132 (173)
Q Consensus 65 tG~f~v~l~~~C~~~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVk~K~lf~Wv~I~eI~~d~~~I~F~v 132 (173)
++.|+|.|+..+.+ - ..|+|.+...+|+=+.|=+|++. +| .-+.+-+.|.|.-
T Consensus 19 ~~~frV~LenG~~v--------l--a~isGKmR~~rIrIl~GD~V~VE-~s----pYDltkGRIiyR~ 71 (87)
T PRK12442 19 DSRFRVTLENGVEV--------G--AYASGRMRKHRIRILAGDRVTLE-LS----PYDLTKGRINFRH 71 (87)
T ss_pred CCEEEEEeCCCCEE--------E--EEeccceeeeeEEecCCCEEEEE-EC----cccCCceeEEEEe
Confidence 56676666654422 2 67899999999999999888876 33 1223346777754
No 9
>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=27.68 E-value=50 Score=23.26 Aligned_cols=17 Identities=18% Similarity=0.450 Sum_probs=13.0
Q ss_pred eeEEEEEEecCceecccc
Q 030668 89 KSKISGYISENKLTSLTG 106 (173)
Q Consensus 89 ~~~ItG~i~~g~I~~L~G 106 (173)
..+|+|.|+.|+|+ +.|
T Consensus 27 Ga~ItGhVknG~mr-i~g 43 (62)
T PF08300_consen 27 GAVITGHVKNGSMR-IYG 43 (62)
T ss_dssp S-EEEEEEETTEEE-EE-
T ss_pred CCEEeEEEeCCeEE-Eec
Confidence 57899999999998 554
No 10
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=27.29 E-value=79 Score=23.42 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=19.1
Q ss_pred CceeEEEeCCCCeEEEEecCe
Q 030668 55 GITQYDIDRETGQFHAYLDGT 75 (173)
Q Consensus 55 ~V~~y~l~~~tG~f~v~l~~~ 75 (173)
|+++|-.|.+||.+++...++
T Consensus 31 gl~G~V~N~~DGsVeiva~G~ 51 (92)
T COG1254 31 GLTGWVKNLDDGSVEIVAEGP 51 (92)
T ss_pred CCEEEEEECCCCeEEEEEEcC
Confidence 789999999999999999874
No 11
>TIGR02689 ars_reduc_gluta arsenate reductase, glutathione/glutaredoxin type. Members of this protein family represent a novel form of arsenate reductase, using glutathione and glutaredoxin rather than thioredoxin for reducing equivalents as do some homologous arsenate reductases. An example of this type is Synechocystis sp. strain PCC 6803 slr0946, and of latter type (excluded from this model) is Staphylococcus aureus plasmid pI258 ArsC. Both are among the subset of arsenate reductases that belong the the low-molecular-weight protein-tyrosine phosphatase superfamily.
Probab=26.44 E-value=55 Score=24.59 Aligned_cols=40 Identities=10% Similarity=0.150 Sum_probs=31.4
Q ss_pred CCCcchHHHHHHhcCCC-CCCCCCCceeEEEeCCCCeEEEEec
Q 030668 32 NSDQLSAYDILQSYNFP-AGLLPKGITQYDIDRETGQFHAYLD 73 (173)
Q Consensus 32 ~~~~~tayelL~~~gLP-~GLLP~~V~~y~l~~~tG~f~v~l~ 73 (173)
....+.+.++|+++|++ .|.-|+.++++.+. .-.+-+.+.
T Consensus 39 ~~~~p~a~~~l~e~Gid~~~~~s~~l~~~~~~--~~D~iitm~ 79 (126)
T TIGR02689 39 SRVHPTAIEVMSEIGIDISGQTSKPLENFHPE--DYDVVISLC 79 (126)
T ss_pred CCCCHHHHHHHHHhCCCcccCccccCChhHhc--CCCEEEEeC
Confidence 46778999999999997 58889999988664 455666664
No 12
>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=26.30 E-value=1.8e+02 Score=20.10 Aligned_cols=37 Identities=11% Similarity=0.196 Sum_probs=22.3
Q ss_pred EeeEEEEEEecCceecccceeEEEE--EEeeeeeEEEEcCC
Q 030668 88 YKSKISGYISENKLTSLTGVSVKVL--FLWLNIVEVTRNGD 126 (173)
Q Consensus 88 Y~~~ItG~i~~g~I~~L~GVk~K~l--f~Wv~I~eI~~d~~ 126 (173)
-.+.++|+|+.|.|+. |-++..+ =....|.+|.++..
T Consensus 14 ~g~vv~G~v~~G~i~~--Gd~v~i~P~~~~~~V~si~~~~~ 52 (83)
T cd03698 14 GGTVVSGKVESGSIQK--GDTLLVMPSKESVEVKSIYVDDE 52 (83)
T ss_pred CCcEEEEEEeeeEEeC--CCEEEEeCCCcEEEEEEEEECCe
Confidence 3568899999999984 4333211 12355777766543
No 13
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=24.06 E-value=60 Score=21.12 Aligned_cols=18 Identities=22% Similarity=0.460 Sum_probs=14.6
Q ss_pred cchHHHHHHhcCCCCCCC
Q 030668 35 QLSAYDILQSYNFPAGLL 52 (173)
Q Consensus 35 ~~tayelL~~~gLP~GLL 52 (173)
.+...+.|.+||+|.|=+
T Consensus 8 d~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 8 DAELRAELKQYGLPPGPI 25 (44)
T ss_pred HHHHHHHHHHcCCCCCCc
Confidence 357788999999999843
No 14
>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=23.64 E-value=2.7e+02 Score=19.54 Aligned_cols=40 Identities=15% Similarity=0.265 Sum_probs=27.8
Q ss_pred eeEEEEEEecCceecccceeEEEE------EEeeeeeEEEEcCCeEEE
Q 030668 89 KSKISGYISENKLTSLTGVSVKVL------FLWLNIVEVTRNGDDIDF 130 (173)
Q Consensus 89 ~~~ItG~i~~g~I~~L~GVk~K~l------f~Wv~I~eI~~d~~~I~F 130 (173)
.+-|+|+|+.|.++. |-+...+ +....|.+|.+++..+..
T Consensus 15 GtVv~G~v~~G~v~~--g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~ 60 (87)
T cd03694 15 GTVVGGTVSKGVIRL--GDTLLLGPDQDGSFRPVTVKSIHRNRSPVRV 60 (87)
T ss_pred ceEEEEEEecCEEeC--CCEEEECCCCCCCEeEEEEEEEEECCeECCE
Confidence 568999999999994 4444332 257888899876544443
No 15
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=23.18 E-value=1.6e+02 Score=23.79 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=27.7
Q ss_pred CcchHHHHHHhcCCCC------CCCCCCceeEEEeCCCCeEEEEecC
Q 030668 34 DQLSAYDILQSYNFPA------GLLPKGITQYDIDRETGQFHAYLDG 74 (173)
Q Consensus 34 ~~~tayelL~~~gLP~------GLLP~~V~~y~l~~~tG~f~v~l~~ 74 (173)
..+.|.++|+++|+|. |--+. .-.++.+||.+||+..+
T Consensus 108 Ni~~a~~~L~~~gi~i~a~dvGG~~gR---~i~f~~~tG~v~vk~~~ 151 (157)
T PRK13488 108 NIESAKETLKKLGIRIVAEDVGGDYGR---TVKFDLKTGKVIVRKAN 151 (157)
T ss_pred HHHHHHHHHHHCCCcEEEEEcCCCCCc---EEEEECCCCEEEEEEcC
Confidence 3467899999999984 33332 34578889999998654
No 16
>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=22.84 E-value=1.5e+02 Score=20.60 Aligned_cols=38 Identities=18% Similarity=0.195 Sum_probs=25.2
Q ss_pred EEEEEEecCceecccceeEEEEE--EeeeeeEEEEcCCeEEE
Q 030668 91 KISGYISENKLTSLTGVSVKVLF--LWLNIVEVTRNGDDIDF 130 (173)
Q Consensus 91 ~ItG~i~~g~I~~L~GVk~K~lf--~Wv~I~eI~~d~~~I~F 130 (173)
-|+|+|+.|+++ .|-++..+= ....|.+|.+++..+..
T Consensus 17 ~v~Gkv~~G~v~--~Gd~v~~~P~~~~~~V~si~~~~~~~~~ 56 (81)
T cd03695 17 GYAGTIASGSIR--VGDEVVVLPSGKTSRVKSIETFDGELDE 56 (81)
T ss_pred EEEEEEccceEE--CCCEEEEcCCCCeEEEEEEEECCcEeCE
Confidence 499999999998 454443321 34668888876655544
No 17
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=22.69 E-value=2.5e+02 Score=25.29 Aligned_cols=33 Identities=12% Similarity=0.070 Sum_probs=19.6
Q ss_pred eeEEEEEEecCceecccceeEEEE--EEeeeeeEEEE
Q 030668 89 KSKISGYISENKLTSLTGVSVKVL--FLWLNIVEVTR 123 (173)
Q Consensus 89 ~~~ItG~i~~g~I~~L~GVk~K~l--f~Wv~I~eI~~ 123 (173)
.+.++|+|+.|.|+. |-++..+ -....|.+|..
T Consensus 240 G~vv~G~v~~G~v~~--Gd~v~i~P~~~~~~VksI~~ 274 (425)
T PRK12317 240 GTVPVGRVETGVLKV--GDKVVFMPAGVVGEVKSIEM 274 (425)
T ss_pred eEEEEEEEeeccEec--CCEEEECCCCCeEEEEEEEE
Confidence 568899999999873 3222211 12355666664
No 18
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=22.40 E-value=5.6e+02 Score=22.83 Aligned_cols=58 Identities=19% Similarity=0.261 Sum_probs=35.4
Q ss_pred hHHHHHHhcCCCCCCCCCCceeEEEeCCCCeEEEEecCeeEEEEecceEEEEeeEEEEEEecCceecccceeEEE
Q 030668 37 SAYDILQSYNFPAGLLPKGITQYDIDRETGQFHAYLDGTCSFSLEGSYQLKYKSKISGYISENKLTSLTGVSVKV 111 (173)
Q Consensus 37 tayelL~~~gLP~GLLP~~V~~y~l~~~tG~f~v~l~~~C~~~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVk~K~ 111 (173)
++.++|++++ +-..+-.| .|.| |++.+. .++ + ++|--.+.+..+.-++..|+|-...+
T Consensus 27 ~a~~~L~~M~-------~A~~~lnY---~g~f-V~~~~~---~i~-s--~ri~H~~~~~~e~erL~~LdG~~rEv 84 (319)
T PRK09455 27 SSGALLQQMN-------EASQSLNY---ELSF-INITKQ---GIE-S--LRYRHARLDNKPLAQLLQMDGPRREI 84 (319)
T ss_pred CHHHHHHHHH-------HHHHhCCe---EEEE-EEEeCC---eEE-E--EEEEEEEeCCEEEEEEEecCCCceEE
Confidence 5888898865 33333333 3777 444444 233 2 33444466788888999999976543
No 19
>PF03975 CheD: CheD chemotactic sensory transduction; InterPro: IPR005659 CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase []. CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs [].; GO: 0050568 protein-glutamine glutaminase activity, 0006935 chemotaxis; PDB: 2F9Z_D.
Probab=22.07 E-value=1.1e+02 Score=22.98 Aligned_cols=37 Identities=22% Similarity=0.296 Sum_probs=23.1
Q ss_pred cchHHHHHHhcCCCC------CCCCCCceeEEEeCCCCeEEEEecC
Q 030668 35 QLSAYDILQSYNFPA------GLLPKGITQYDIDRETGQFHAYLDG 74 (173)
Q Consensus 35 ~~tayelL~~~gLP~------GLLP~~V~~y~l~~~tG~f~v~l~~ 74 (173)
...|.++|+++|+|. |-.+. .-.++..||.+||+.-+
T Consensus 66 v~~a~~~L~~~gi~I~a~dvGG~~~R---~v~f~~~tG~v~vk~~~ 108 (114)
T PF03975_consen 66 VEAARELLAEEGIPIVAEDVGGNFGR---KVRFDPATGEVWVKRIG 108 (114)
T ss_dssp HHHHHHHHHHTT--EEEEEE-SSS-E---EEEEETTTTEEEEE---
T ss_pred HHHHHHHHHHCCCcEEEeeCCCCCCc---EEEEEcCCCEEEEEECC
Confidence 357899999999983 33332 34578889999998654
No 20
>PF07803 GSG-1: GSG1-like protein; InterPro: IPR012478 This family contains sequences bearing similarity to a region of GSG1 (Q9Z1H7 from SWISSPROT), a protein specifically expressed in testicular germ cells []. It is possible that over expression of the human homologue may be involved in tumourigenesis of human testicular germ cell tumours []. The region in question has four highly conserved cysteine residues.
Probab=21.94 E-value=89 Score=24.60 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=16.9
Q ss_pred chhHHHHHHHHHHHHhhhhhhhc
Q 030668 5 TPISTLLLSLLFIFLHQSAVATS 27 (173)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~s 27 (173)
|..+++++-+|.|+++++|...|
T Consensus 7 Ra~Ls~~ln~LAL~~S~tA~~sS 29 (118)
T PF07803_consen 7 RALLSLILNLLALAFSTTALLSS 29 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 66677788888888888865544
No 21
>COG1246 ArgA N-acetylglutamate synthase and related acetyltransferases [Amino acid transport and metabolism]
Probab=21.94 E-value=52 Score=26.85 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=30.3
Q ss_pred CCCcchHHHHHHhcCCCCCCCCC-------CceeEEEeCCCCeE
Q 030668 32 NSDQLSAYDILQSYNFPAGLLPK-------GITQYDIDRETGQF 68 (173)
Q Consensus 32 ~~~~~tayelL~~~gLP~GLLP~-------~V~~y~l~~~tG~f 68 (173)
..+.+-..++|+.|+++.+|+|. ++.+|.+.+.+|.+
T Consensus 8 ~~Di~~I~~Li~~~~~~gil~~rs~~~le~~i~dF~i~E~~g~v 51 (153)
T COG1246 8 ISDIPAILELIRPLELQGILLRRSREQLEEEIDDFTIIERDGKV 51 (153)
T ss_pred ccchHHHHHHHHHHhhccccchhhHHHHHHHHhhheeeeeCCcE
Confidence 46667899999999999999995 45688888877775
No 22
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.91 E-value=1.5e+02 Score=27.94 Aligned_cols=57 Identities=18% Similarity=0.191 Sum_probs=41.5
Q ss_pred HHHHHHHHhhhhhhhcccccCCCcchHHHHHHhcC-CCCCCCCCCceeEEEeCCCCeEEEEecC
Q 030668 12 LSLLFIFLHQSAVATSSLSANSDQLSAYDILQSYN-FPAGLLPKGITQYDIDRETGQFHAYLDG 74 (173)
Q Consensus 12 ~~~~~~~~~~~~~~~s~~~~~~~~~tayelL~~~g-LP~GLLP~~V~~y~l~~~tG~f~v~l~~ 74 (173)
-+-++..+|++ +|.+| .+.+.|.++++++- |.||+.---|-=+.. +.+|.|-|.+..
T Consensus 322 ~l~l~~~LHPT-PAV~G----~P~~~A~~~Ir~~E~fdRG~Yag~vGw~D~-~GngEf~VaIRs 379 (423)
T COG1169 322 ALDLAKALHPT-PAVGG----LPREAALQFIREHEPFDRGWYAGPVGWCDS-EGNGEFVVAIRS 379 (423)
T ss_pred HHHHHHHhCCC-ccccC----CchHHHHHHHHHhCCCCcchhccceeeecc-CCCeEEEEEEEE
Confidence 34567788999 77888 78899999999998 999998543332222 237777777654
No 23
>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha. This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.
Probab=21.79 E-value=2e+02 Score=25.98 Aligned_cols=28 Identities=11% Similarity=0.195 Sum_probs=18.5
Q ss_pred eeEEEEecceEEEE-eeEEEEEEecCcee
Q 030668 75 TCSFSLEGSYQLKY-KSKISGYISENKLT 102 (173)
Q Consensus 75 ~C~~~~~~~~~v~Y-~~~ItG~i~~g~I~ 102 (173)
+..+.+.+-+.+.+ .+.++|+|+.|.|+
T Consensus 227 p~r~~i~~v~~~~g~G~vv~G~v~~G~i~ 255 (426)
T TIGR00483 227 PLRIPIQDVYSITGVGTVPVGRVETGVLK 255 (426)
T ss_pred CcEEEEEEEEecCCCeEEEEEEEccceee
Confidence 44455543344444 46789999999987
No 24
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=21.05 E-value=57 Score=31.41 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=14.5
Q ss_pred hHHHHHHhcCCCCCCC
Q 030668 37 SAYDILQSYNFPAGLL 52 (173)
Q Consensus 37 tayelL~~~gLP~GLL 52 (173)
-+|++|+|-|||.|.+
T Consensus 241 ii~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 241 IIYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHHcCCCccce
Confidence 4799999999999986
No 25
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=20.14 E-value=2.4e+02 Score=21.82 Aligned_cols=36 Identities=22% Similarity=0.331 Sum_probs=25.0
Q ss_pred EeCCCCeEEEEecCeeEEEEecceEEEEeeEEEEEEecC
Q 030668 61 IDRETGQFHAYLDGTCSFSLEGSYQLKYKSKISGYISEN 99 (173)
Q Consensus 61 l~~~tG~f~v~l~~~C~~~~~~~~~v~Y~~~ItG~i~~g 99 (173)
+|++||.|....++.++|.+. .. .++.++...+-++
T Consensus 38 yd~~TG~Ftcpv~GvY~F~f~--~~-~~~~~~~v~L~~N 73 (135)
T smart00110 38 YDPRTGKFTCPVPGVYYFSYH--VE-SKGRNVKVSLMKN 73 (135)
T ss_pred ccCCCCEEECeeceEEEEEEE--EE-EcCCEEEEEEEEC
Confidence 777899999999999998875 22 2333455555443
Done!