Query 046231
Match_columns 83
No_of_seqs 108 out of 250
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:59:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046231hhsearch_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 1.1E-31 2.3E-36 180.4 4.4 78 1-83 22-99 (110)
2 cd03697 EFTU_II EFTU_II: Elong 62.8 22 0.00048 21.8 4.4 34 31-66 15-52 (87)
3 PRK09738 small toxic polypepti 52.4 5.6 0.00012 23.8 0.4 27 10-40 22-48 (52)
4 PRK09759 small toxic polypepti 49.6 6.2 0.00013 23.4 0.2 27 10-40 20-46 (50)
5 smart00110 C1Q Complement comp 48.1 64 0.0014 21.8 5.1 38 3-42 37-74 (135)
6 PF01848 HOK_GEF: Hok/gef fami 46.9 6.3 0.00014 22.6 -0.0 26 10-39 17-42 (43)
7 PF08300 HCV_NS5a_1a: Hepatiti 44.0 24 0.00053 21.9 2.3 17 31-48 27-43 (62)
8 cd03694 GTPBP_II Domain II of 42.7 75 0.0016 19.5 4.4 35 31-67 15-55 (87)
9 PF08710 nsp9: nsp9 replicase; 40.9 48 0.001 22.7 3.5 22 4-25 56-77 (111)
10 PF09167 DUF1942: Domain of un 37.5 10 0.00022 26.5 -0.2 13 66-78 95-107 (127)
11 PF00386 C1q: C1q domain; Int 36.8 76 0.0016 20.4 3.9 23 2-24 30-52 (127)
12 cd01215 Dab Disabled (Dab) Pho 33.0 57 0.0012 22.9 3.0 29 47-76 48-76 (139)
13 PF02402 Lysis_col: Lysis prot 30.3 30 0.00065 20.3 1.0 18 35-52 29-46 (46)
14 cd03693 EF1_alpha_II EF1_alpha 29.6 1.2E+02 0.0026 18.7 3.9 34 31-66 19-54 (91)
15 cd03695 CysN_NodQ_II CysN_NodQ 29.1 1.1E+02 0.0024 18.6 3.6 32 33-66 17-50 (81)
16 PF12103 Lipl32: Surface lipop 28.8 1.6E+02 0.0034 21.8 4.8 34 28-61 5-42 (182)
17 cd01751 PLAT_LH2 PLAT/ LH2 dom 28.4 82 0.0018 21.8 3.2 21 60-80 100-120 (137)
18 cd04089 eRF3_II eRF3_II: domai 27.4 1.1E+02 0.0024 18.4 3.3 34 31-66 14-49 (82)
19 PF08865 DUF1830: Domain of un 26.9 95 0.0021 19.3 3.0 38 2-39 1-44 (68)
20 cd03700 eEF2_snRNP_like_II EF2 26.5 1.6E+02 0.0035 18.0 5.4 49 27-76 17-78 (93)
21 cd02410 archeal_CPSF_KH The ar 24.7 58 0.0013 23.1 1.9 19 3-21 72-90 (145)
22 cd05686 S1_pNO40 S1_pNO40: pNO 22.9 1.1E+02 0.0023 18.0 2.6 31 30-63 7-37 (73)
23 COG2000 Predicted Fe-S protein 22.3 1.3E+02 0.0027 22.9 3.4 42 5-46 133-180 (226)
24 cd03368 Ribosomal_S12 S12-like 21.5 71 0.0015 21.7 1.8 17 38-54 80-96 (108)
25 PRK13815 ribosome-binding fact 20.3 1.5E+02 0.0032 20.0 3.1 24 57-80 31-54 (122)
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=99.97 E-value=1.1e-31 Score=180.44 Aligned_cols=78 Identities=45% Similarity=0.836 Sum_probs=60.4
Q ss_pred CcceeccccEEEEEecCeEEEEEceEEEEEccEEEEEEecCceeeceeeeEEEEEEeeEeeEEEEcCCCCCCeEEEEcCC
Q 046231 1 ECGHVKELGFVWLKHKQKKKHKFENVVVWFDTEVTAYFERNKIKNLTGVKAKEFLIWISLCEIYVNGSSPNGSITFKTPA 80 (83)
Q Consensus 1 e~g~~~~tG~~~v~l~~~c~~~f~~~~v~Y~~~Itg~l~~gki~~l~GVk~K~lf~W~~v~eI~vdg~~~sgkI~F~~~~ 80 (83)
||++|++||+|||+|+++|+|+|++++|+|+++|||+|++|+|++|+||++|+||+|++|+||.++ +++|+|++ +
T Consensus 22 ~y~l~~~tG~f~v~l~~~C~~~~~~~~v~Y~~~ItG~i~~g~i~~L~GVk~k~l~~W~~v~~i~~~----~~~i~F~~-g 96 (110)
T PF04398_consen 22 EYGLNRDTGFFWVKLKSPCEFRFEGYLVSYDSEITGYIEKGKIKNLTGVKVKELFLWVPVTEISVD----GDKIYFKV-G 96 (110)
T ss_dssp EEEE-TTT-SEEEE-SS-EEEESTTSEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEES---BEE-----SSSEE-TT-S
T ss_pred EEEEecCCcEEEEEecCCEEEEEEEEEEEEcCeEEEEECCCcCccccCEEEEEEEEEeeEEEEEEc----CCEEEEEE-e
Confidence 689999999999999999999999978999999999999999999999999999999999999996 88999999 6
Q ss_pred CCC
Q 046231 81 GLS 83 (83)
Q Consensus 81 g~~ 83 (83)
+++
T Consensus 97 ~~s 99 (110)
T PF04398_consen 97 GIS 99 (110)
T ss_dssp SSS
T ss_pred eEe
Confidence 653
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=62.79 E-value=22 Score=21.85 Aligned_cols=34 Identities=26% Similarity=0.226 Sum_probs=24.4
Q ss_pred ccEEEEEEecCceeeceeeeEEEE----EEeeEeeEEEEc
Q 046231 31 DTEVTAYFERNKIKNLTGVKAKEF----LIWISLCEIYVN 66 (83)
Q Consensus 31 ~~~Itg~l~~gki~~l~GVk~K~l----f~W~~v~eI~vd 66 (83)
.+.++|+|+.|.|+. |-+...+ .....|..|.++
T Consensus 15 G~vv~G~v~~G~v~~--gd~v~~~p~~~~~~~~V~si~~~ 52 (87)
T cd03697 15 GTVVTGRIERGTIKV--GDEVEIVGFGETLKTTVTGIEMF 52 (87)
T ss_pred EEEEEEEECCCCCcc--CCEEEEeCCCCCceEEEEEEEEC
Confidence 356999999999984 4444433 456778888886
No 3
>PRK09738 small toxic polypeptide; Provisional
Probab=52.45 E-value=5.6 Score=23.80 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=20.0
Q ss_pred EEEEEecCeEEEEEceEEEEEccEEEEEEec
Q 046231 10 FVWLKHKQKKKHKFENVVVWFDTEVTAYFER 40 (83)
Q Consensus 10 ~~~v~l~~~c~~~f~~~~v~Y~~~Itg~l~~ 40 (83)
+.|+..++-||+++++. +++|.+++.+
T Consensus 22 f~~l~r~sLCEl~i~~g----~~evaA~LAy 48 (52)
T PRK09738 22 FTYLTRKSLCELRYRDG----DREVAAFMAY 48 (52)
T ss_pred HHHHccCCceEEEEecC----CEEEEEEEee
Confidence 45677788999999875 5666666655
No 4
>PRK09759 small toxic polypeptide; Provisional
Probab=49.57 E-value=6.2 Score=23.43 Aligned_cols=27 Identities=15% Similarity=0.368 Sum_probs=19.7
Q ss_pred EEEEEecCeEEEEEceEEEEEccEEEEEEec
Q 046231 10 FVWLKHKQKKKHKFENVVVWFDTEVTAYFER 40 (83)
Q Consensus 10 ~~~v~l~~~c~~~f~~~~v~Y~~~Itg~l~~ 40 (83)
+.|+..++-||+++++. +++|.+++.+
T Consensus 20 f~~l~r~sLCEl~i~~g----~~evaA~Lay 46 (50)
T PRK09759 20 FTWMIRDSLCELHIKQG----SYELAAFLAC 46 (50)
T ss_pred HHHHhCCCceEEEEecC----CEEEEEEEee
Confidence 45677788999999875 5666666654
No 5
>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=48.13 E-value=64 Score=21.81 Aligned_cols=38 Identities=8% Similarity=-0.146 Sum_probs=27.0
Q ss_pred ceeccccEEEEEecCeEEEEEceEEEEEccEEEEEEecCc
Q 046231 3 GHVKELGFVWLKHKQKKKHKFENVVVWFDTEVTAYFERNK 42 (83)
Q Consensus 3 g~~~~tG~~~v~l~~~c~~~f~~~~v~Y~~~Itg~l~~gk 42 (83)
.||.+||.|+...+.-.++.|-- ..++..+...|.++.
T Consensus 37 ~yd~~TG~Ftcpv~GvY~F~f~~--~~~~~~~~v~L~~N~ 74 (135)
T smart00110 37 HYDPRTGKFTCPVPGVYYFSYHV--ESKGRNVKVSLMKNG 74 (135)
T ss_pred CccCCCCEEECeeceEEEEEEEE--EEcCCEEEEEEEECC
Confidence 59999999999999999888853 233445555554433
No 6
>PF01848 HOK_GEF: Hok/gef family; InterPro: IPR000021 The hok/gef family of Gram-negative bacterial proteins are toxic to cells when over-expressed, killing the cells from within by interfering with a vital function in the cell membrane []. Some family members (flm) increase the stability of unstable RNA [], some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures [], while others affect the release of cellular magnesium by membrane alterations []. The proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect [].; GO: 0016020 membrane
Probab=46.92 E-value=6.3 Score=22.63 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=18.9
Q ss_pred EEEEEecCeEEEEEceEEEEEccEEEEEEe
Q 046231 10 FVWLKHKQKKKHKFENVVVWFDTEVTAYFE 39 (83)
Q Consensus 10 ~~~v~l~~~c~~~f~~~~v~Y~~~Itg~l~ 39 (83)
+.|+..++-||.++++. .++|.+++.
T Consensus 17 ~~~l~r~sLCEl~i~~g----~~evaA~La 42 (43)
T PF01848_consen 17 FTWLTRDSLCELRIKDG----NTEVAAFLA 42 (43)
T ss_pred HHHHhccCcEEEEEecC----CEEEEEEEc
Confidence 34566788899999875 567777664
No 7
>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=44.04 E-value=24 Score=21.88 Aligned_cols=17 Identities=12% Similarity=0.345 Sum_probs=13.0
Q ss_pred ccEEEEEEecCceeecee
Q 046231 31 DTEVTAYFERNKIKNLTG 48 (83)
Q Consensus 31 ~~~Itg~l~~gki~~l~G 48 (83)
..+|+|.|.+|+|+ +.|
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 56899999999998 544
No 8
>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=42.65 E-value=75 Score=19.51 Aligned_cols=35 Identities=17% Similarity=0.007 Sum_probs=25.2
Q ss_pred ccEEEEEEecCceeeceeeeEEEE------EEeeEeeEEEEcC
Q 046231 31 DTEVTAYFERNKIKNLTGVKAKEF------LIWISLCEIYVNG 67 (83)
Q Consensus 31 ~~~Itg~l~~gki~~l~GVk~K~l------f~W~~v~eI~vdg 67 (83)
.+.|+|+|+.|.++. |-+...+ |....|.+|.+++
T Consensus 15 GtVv~G~v~~G~v~~--g~~v~~~P~~~g~~~~~~V~sI~~~~ 55 (87)
T cd03694 15 GTVVGGTVSKGVIRL--GDTLLLGPDQDGSFRPVTVKSIHRNR 55 (87)
T ss_pred ceEEEEEEecCEEeC--CCEEEECCCCCCCEeEEEEEEEEECC
Confidence 568999999999984 4444332 3568888998863
No 9
>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=40.92 E-value=48 Score=22.72 Aligned_cols=22 Identities=18% Similarity=0.098 Sum_probs=15.0
Q ss_pred eeccccEEEEEecCeEEEEEce
Q 046231 4 HVKELGFVWLKHKQKKKHKFEN 25 (83)
Q Consensus 4 ~~~~tG~~~v~l~~~c~~~f~~ 25 (83)
+..++|.+.+.|+-||.+.-+.
T Consensus 56 ~~~d~G~v~ieLePPckF~v~~ 77 (111)
T PF08710_consen 56 WEKDDGKVVIELEPPCKFAVDV 77 (111)
T ss_dssp EE-TTSEEEEEB---EEEEEEE
T ss_pred EEccCCEEEEecCCCcEEEEEc
Confidence 4568899999999999998764
No 10
>PF09167 DUF1942: Domain of unknown function (DUF1942); InterPro: IPR015250 This domain, found in bacterial proteins, assumes a beta-sandwich structure consisting of two antiparallel beta-sheets (similar to an immunoglobulin-like fold), and an additional small, antiparallel beta-sheet. The longer-stranded beta-sheet is made up of four antiparallel beta-strands. The shorter-stranded beta-sheet consists of five beta-strands, four of which form an antiparallel beta-sheet. The exact function of this domain is unknown, though a putative role includes involvement in host-bacterial interactions involved in endocytosis or phagocytosis, possibly during bacterial internalisation []. ; GO: 0005615 extracellular space; PDB: 1LMI_A.
Probab=37.46 E-value=10 Score=26.50 Aligned_cols=13 Identities=31% Similarity=0.631 Sum_probs=10.0
Q ss_pred cCCCCCCeEEEEc
Q 046231 66 NGSSPNGSITFKT 78 (83)
Q Consensus 66 dg~~~sgkI~F~~ 78 (83)
.|...+|||||++
T Consensus 95 qGq~~tGkiYFDV 107 (127)
T PF09167_consen 95 QGQQTTGKIYFDV 107 (127)
T ss_dssp TT-EEEEEEEEEE
T ss_pred CCCEeeeEEEEEe
Confidence 5566789999998
No 11
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=36.76 E-value=76 Score=20.35 Aligned_cols=23 Identities=9% Similarity=-0.125 Sum_probs=17.0
Q ss_pred cceeccccEEEEEecCeEEEEEc
Q 046231 2 CGHVKELGFVWLKHKQKKKHKFE 24 (83)
Q Consensus 2 ~g~~~~tG~~~v~l~~~c~~~f~ 24 (83)
-+||.+||.|++..+.-..+.|.
T Consensus 30 ~~yn~~tG~Ftap~~G~Y~F~~~ 52 (127)
T PF00386_consen 30 NAYNPSTGIFTAPVPGVYFFSFT 52 (127)
T ss_dssp S-EETTTTEEE-SS-EEEEEEEE
T ss_pred CccEeecCEEecCCCCEEEEEEE
Confidence 37999999999988888877774
No 12
>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=32.98 E-value=57 Score=22.91 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=22.6
Q ss_pred eeeeEEEEEEeeEeeEEEEcCCCCCCeEEE
Q 046231 47 TGVKAKEFLIWISLCEIYVNGSSPNGSITF 76 (83)
Q Consensus 47 ~GVk~K~lf~W~~v~eI~vdg~~~sgkI~F 76 (83)
+|-+-+...||+++.+|.+- |+.++.+..
T Consensus 48 ~~~kk~kV~L~IS~dGi~v~-D~~T~~ll~ 76 (139)
T cd01215 48 AGAHKTRITLQINIDGIKVL-DEKTGAVLH 76 (139)
T ss_pred hccccceEEEEEccCCEEEE-cCCCCcEEE
Confidence 56677888899999999997 666665544
No 13
>PF02402 Lysis_col: Lysis protein; InterPro: IPR003059 The DNA sequence of the entire colicin E2 operon has been determined []. The operon comprises the colicin activity gene (ceaB), the colicin immunity gene (ceiB) and the lysis gene (celB), which is essential for colicin release from producing cells []. A putative LexA binding site is located upstream from ceaB, and a rho-independent terminator structure is located downstream from celB []. Comparison of the amino acid sequences of colicin E2 and cloacin DF13 reveal extensive similarity. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the C terminus, and in the C-terminal end of the central region are thought to correspond to the catalytic and receptor-recognition domains, respectively []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. By contrast, the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the N-terminal regions, which themselves are similar to lipoprotein signal peptides []. Processing of the ColE2 prolysis protein to the mature form is prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase []. The mature ColE2 lysis protein is located in the cell envelope [].; GO: 0009405 pathogenesis, 0019835 cytolysis, 0019867 outer membrane
Probab=30.29 E-value=30 Score=20.29 Aligned_cols=18 Identities=22% Similarity=0.272 Sum_probs=14.8
Q ss_pred EEEEecCceeeceeeeEE
Q 046231 35 TAYFERNKIKNLTGVKAK 52 (83)
Q Consensus 35 tg~l~~gki~~l~GVk~K 52 (83)
-|.+++-+-++|+||+++
T Consensus 29 GGtVaPSSss~lTGv~~q 46 (46)
T PF02402_consen 29 GGTVAPSSSSELTGVAVQ 46 (46)
T ss_pred CceECCCccceeeeeecC
Confidence 468899999999999763
No 14
>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=29.57 E-value=1.2e+02 Score=18.66 Aligned_cols=34 Identities=12% Similarity=-0.010 Sum_probs=22.1
Q ss_pred ccEEEEEEecCceeeceeeeEEEE--EEeeEeeEEEEc
Q 046231 31 DTEVTAYFERNKIKNLTGVKAKEF--LIWISLCEIYVN 66 (83)
Q Consensus 31 ~~~Itg~l~~gki~~l~GVk~K~l--f~W~~v~eI~vd 66 (83)
.+.++|+|+.|.|+. |-++..+ =.-..|.+|.++
T Consensus 19 g~vv~G~v~~G~i~~--gd~v~i~P~~~~~~V~sI~~~ 54 (91)
T cd03693 19 GTVPVGRVETGVLKP--GMVVTFAPAGVTGEVKSVEMH 54 (91)
T ss_pred eEEEEEEEecceeec--CCEEEECCCCcEEEEEEEEEC
Confidence 468999999999984 3222211 134668888776
No 15
>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=29.06 E-value=1.1e+02 Score=18.58 Aligned_cols=32 Identities=9% Similarity=-0.037 Sum_probs=21.5
Q ss_pred EEEEEEecCceeeceeeeEEEEE--EeeEeeEEEEc
Q 046231 33 EVTAYFERNKIKNLTGVKAKEFL--IWISLCEIYVN 66 (83)
Q Consensus 33 ~Itg~l~~gki~~l~GVk~K~lf--~W~~v~eI~vd 66 (83)
.|+|+|+.|+|+ .|-++..+= ....|.+|.++
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 454432221 23568888876
No 16
>PF12103 Lipl32: Surface lipoprotein of Spirochaetales order; InterPro: IPR021962 Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria. ; PDB: 2ZZ8_A 2WFK_D 3FRL_B.
Probab=28.80 E-value=1.6e+02 Score=21.78 Aligned_cols=34 Identities=18% Similarity=0.418 Sum_probs=22.7
Q ss_pred EEEccEEE--EEEecCce--eeceeeeEEEEEEeeEee
Q 046231 28 VWFDTEVT--AYFERNKI--KNLTGVKAKEFLIWISLC 61 (83)
Q Consensus 28 v~Y~~~It--g~l~~gki--~~l~GVk~K~lf~W~~v~ 61 (83)
+-|...|+ ||++.|.- ....|=++--|.+|+|..
T Consensus 5 ~PY~~~~~Y~GYv~~g~~pD~~~~gK~~yYlYvWvPaa 42 (182)
T PF12103_consen 5 VPYTDVINYFGYVDPGNEPDEVVDGKKAYYLYVWVPAA 42 (182)
T ss_dssp EE-SEEEEEEEEE-TTS--SEEETTEEEEEEEEEESS-
T ss_pred cccccceeeeEeecCCCCCcccccCceeEEEEEEeehh
Confidence 44544443 89999987 457788899999999853
No 17
>cd01751 PLAT_LH2 PLAT/ LH2 domain of plant lipoxygenase related proteins. Lipoxygenases are nonheme, nonsulfur iron dioxygenases that act on lipid substrates containing one or more (Z,Z)-1,4-pentadiene moieties. In plants, the immediate products are involved in defense mechanisms against pathogens and may be precursors of metabolic regulators. The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=28.37 E-value=82 Score=21.84 Aligned_cols=21 Identities=33% Similarity=0.466 Sum_probs=16.8
Q ss_pred eeEEEEcCCCCCCeEEEEcCC
Q 046231 60 LCEIYVNGSSPNGSITFKTPA 80 (83)
Q Consensus 60 v~eI~vdg~~~sgkI~F~~~~ 80 (83)
+.+|.++|-|+.|.|+|...+
T Consensus 100 LksitLe~~p~~g~v~F~CNS 120 (137)
T cd01751 100 LKSITLEGFGGSGTITFVCNS 120 (137)
T ss_pred EEEEEEeCCCCCccEEEEccc
Confidence 578888877778999997653
No 18
>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=27.41 E-value=1.1e+02 Score=18.42 Aligned_cols=34 Identities=26% Similarity=0.251 Sum_probs=21.8
Q ss_pred ccEEEEEEecCceeeceeeeEEEE--EEeeEeeEEEEc
Q 046231 31 DTEVTAYFERNKIKNLTGVKAKEF--LIWISLCEIYVN 66 (83)
Q Consensus 31 ~~~Itg~l~~gki~~l~GVk~K~l--f~W~~v~eI~vd 66 (83)
.+.++|+|+.|.|+. |-+...+ =....|..|.++
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 568999999999983 3333211 124667778775
No 19
>PF08865 DUF1830: Domain of unknown function (DUF1830); InterPro: IPR014964 This group of short proteins is functionally uncharacterised.
Probab=26.94 E-value=95 Score=19.28 Aligned_cols=38 Identities=21% Similarity=0.302 Sum_probs=25.8
Q ss_pred cceeccccEEEE-EecCeEEEEEceE-----EEEEccEEEEEEe
Q 046231 2 CGHVKELGFVWL-KHKQKKKHKFENV-----VVWFDTEVTAYFE 39 (83)
Q Consensus 2 ~g~~~~tG~~~v-~l~~~c~~~f~~~-----~v~Y~~~Itg~l~ 39 (83)
|.|.++|+++.| +....=...|+.. .+.|.+.=.|.||
T Consensus 1 C~Y~N~T~~~qI~Ri~~~~~~y~ERVVFP~e~l~FeAp~~A~LE 44 (68)
T PF08865_consen 1 CCYVNDTSQMQILRIINIPNWYFERVVFPGERLLFEAPPEARLE 44 (68)
T ss_pred CeEECCCCcEEEEEEeCCCCceEEEEEcCCcEEEEEcCCCCEEE
Confidence 789999999988 5555556666664 5666665555554
No 20
>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
Probab=26.46 E-value=1.6e+02 Score=18.04 Aligned_cols=49 Identities=10% Similarity=0.209 Sum_probs=35.1
Q ss_pred EEEEccEEEEEEecCceeece-------------eeeEEEEEEeeEeeEEEEcCCCCCCeEEE
Q 046231 27 VVWFDTEVTAYFERNKIKNLT-------------GVKAKEFLIWISLCEIYVNGSSPNGSITF 76 (83)
Q Consensus 27 ~v~Y~~~Itg~l~~gki~~l~-------------GVk~K~lf~W~~v~eI~vdg~~~sgkI~F 76 (83)
.+.|-+-.+|.|..|.--... -.++..+++...-.-..++ ..++|-|.-
T Consensus 17 ~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~v~~l~~~~g~~~~~v~-~a~aGdIv~ 78 (93)
T cd03700 17 FIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVD-EVPAGNIVL 78 (93)
T ss_pred EEEEEEEeeCeEeCCCEEEEECCCCCCCccCcEEEEEEeEEEEEcCCCEEEcc-ccCCCCEEE
Confidence 688889999999888544222 2667788888777777777 666777654
No 21
>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=24.67 E-value=58 Score=23.14 Aligned_cols=19 Identities=11% Similarity=-0.010 Sum_probs=15.8
Q ss_pred ceeccccEEEEEecCeEEE
Q 046231 3 GHVKELGFVWLKHKQKKKH 21 (83)
Q Consensus 3 g~~~~tG~~~v~l~~~c~~ 21 (83)
=||.+||.+++..++|=.+
T Consensus 72 ~Fd~~tGEV~IeaeKPG~V 90 (145)
T cd02410 72 YFDDDTGEVIIEAEKPGLV 90 (145)
T ss_pred EecCCCcEEEEEEcCCeEE
Confidence 3899999999999988544
No 22
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=22.90 E-value=1.1e+02 Score=17.97 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=20.1
Q ss_pred EccEEEEEEecCceeeceeeeEEEEEEeeEeeEE
Q 046231 30 FDTEVTAYFERNKIKNLTGVKAKEFLIWISLCEI 63 (83)
Q Consensus 30 Y~~~Itg~l~~gki~~l~GVk~K~lf~W~~v~eI 63 (83)
|..+|++....|-.-+|.|++..-| ++++++
T Consensus 7 ~~g~V~~i~~fG~fv~l~~~~~eGl---vh~sel 37 (73)
T cd05686 7 FKGEVASVTEYGAFVKIPGCRKQGL---VHKSHM 37 (73)
T ss_pred EEEEEEEEEeeeEEEEECCCCeEEE---EEchhh
Confidence 5667777777777777777654444 455555
No 23
>COG2000 Predicted Fe-S protein [General function prediction only]
Probab=22.34 E-value=1.3e+02 Score=22.91 Aligned_cols=42 Identities=10% Similarity=0.207 Sum_probs=25.5
Q ss_pred eccccEEEEEecCeE------EEEEceEEEEEccEEEEEEecCceeec
Q 046231 5 VKELGFVWLKHKQKK------KHKFENVVVWFDTEVTAYFERNKIKNL 46 (83)
Q Consensus 5 ~~~tG~~~v~l~~~c------~~~f~~~~v~Y~~~Itg~l~~gki~~l 46 (83)
+++.|.++++.-.|| ++.++|.-+------.|.|+.|++-++
T Consensus 133 d~~kG~~tvhIvGprhr~~~~dfeykDvgi~lV~~fegiv~egelp~V 180 (226)
T COG2000 133 DEAKGLVTVHIVGPRHRLGVKDFEYKDVGICLVVGFEGIVKEGELPNV 180 (226)
T ss_pred HhhcCeEEEEEeccceeecccceeeccccEEEEEeeeeeeccccCcch
Confidence 678899999999999 445555411111122456666666543
No 24
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=21.51 E-value=71 Score=21.74 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=14.2
Q ss_pred EecCceeeceeeeEEEE
Q 046231 38 FERNKIKNLTGVKAKEF 54 (83)
Q Consensus 38 l~~gki~~l~GVk~K~l 54 (83)
|.-|++.+|+||+-+..
T Consensus 80 vrGGrv~DlPGVkykvv 96 (108)
T cd03368 80 VRGGRVKDLPGVRYHIV 96 (108)
T ss_pred EeCCccCCCCCeEEEEE
Confidence 35699999999998874
No 25
>PRK13815 ribosome-binding factor A; Provisional
Probab=20.32 E-value=1.5e+02 Score=19.96 Aligned_cols=24 Identities=13% Similarity=0.253 Sum_probs=20.8
Q ss_pred eeEeeEEEEcCCCCCCeEEEEcCC
Q 046231 57 WISLCEIYVNGSSPNGSITFKTPA 80 (83)
Q Consensus 57 W~~v~eI~vdg~~~sgkI~F~~~~ 80 (83)
++.|+++.+..|-+.-+|||....
T Consensus 31 ~vtVt~V~vS~Dl~~AkVyvs~~~ 54 (122)
T PRK13815 31 FVTITGVKVTDDLHLATIYFTVIG 54 (122)
T ss_pred ceEEeEEEECCCCCEEEEEEEECC
Confidence 699999999878888999998753
Done!