Query 031416
Match_columns 160
No_of_seqs 108 out of 352
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 13:47:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031416.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031416hhsearch_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-47 2.4E-52 288.9 6.3 110 23-132 1-110 (110)
2 cd03697 EFTU_II EFTU_II: Elong 54.8 22 0.00049 24.7 3.8 39 75-115 16-58 (87)
3 PF08710 nsp9: nsp9 replicase; 46.3 59 0.0013 24.9 5.1 33 41-73 50-85 (111)
4 PRK12442 translation initiatio 37.5 84 0.0018 23.1 4.6 53 51-117 19-71 (87)
5 cd02410 archeal_CPSF_KH The ar 35.8 43 0.00093 26.7 3.1 41 19-65 49-91 (145)
6 PF10262 Rdx: Rdx family; Int 34.4 57 0.0012 22.3 3.2 12 50-61 41-52 (76)
7 cd03694 GTPBP_II Domain II of 34.1 96 0.0021 21.5 4.4 39 74-114 15-59 (87)
8 PF08300 HCV_NS5a_1a: Hepatiti 31.9 44 0.00095 23.2 2.2 17 74-91 27-43 (62)
9 cd03695 CysN_NodQ_II CysN_NodQ 29.0 1E+02 0.0023 21.1 3.9 38 76-115 17-56 (81)
10 PRK11657 dsbG disulfide isomer 28.7 1.6E+02 0.0036 24.6 5.7 53 18-70 20-75 (251)
11 cd03693 EF1_alpha_II EF1_alpha 27.3 88 0.0019 21.9 3.3 40 74-115 19-60 (91)
12 cd04089 eRF3_II eRF3_II: domai 25.3 1.1E+02 0.0024 20.8 3.5 35 74-110 14-50 (82)
13 KOG2455 Delta-1-pyrroline-5-ca 25.0 42 0.00091 31.8 1.5 15 24-38 242-256 (561)
14 PF02402 Lysis_col: Lysis prot 24.5 33 0.00072 22.4 0.6 18 78-95 29-46 (46)
15 smart00540 LEM in nuclear memb 24.4 57 0.0012 20.9 1.7 18 21-38 8-25 (44)
16 PRK13488 chemoreceptor glutami 24.2 1.3E+02 0.0028 23.9 4.0 39 19-60 107-151 (157)
17 COG0139 HisI Phosphoribosyl-AM 24.0 2.4E+02 0.0053 21.6 5.3 85 26-143 6-107 (111)
18 COG1254 AcyP Acylphosphatases 23.6 1.1E+02 0.0023 22.4 3.2 22 40-61 30-51 (92)
19 cd03698 eRF3_II_like eRF3_II_l 23.3 1.5E+02 0.0032 20.2 3.8 36 73-110 14-51 (83)
20 PF08094 Toxin_24: Conotoxin T 23.1 40 0.00086 20.4 0.7 17 131-147 9-25 (33)
21 COG1169 MenF Isochorismate syn 22.1 1.2E+02 0.0026 28.2 3.8 55 4-60 323-379 (423)
22 PF12103 Lipl32: Surface lipop 21.7 2E+02 0.0043 23.8 4.6 35 70-104 4-42 (182)
23 PF03975 CheD: CheD chemotacti 20.8 1.3E+02 0.0027 22.3 3.2 39 20-60 65-108 (114)
24 TIGR02689 ars_reduc_gluta arse 20.5 68 0.0015 23.7 1.7 41 18-60 39-80 (126)
25 PRK09455 rseB anti-sigma E fac 20.2 6E+02 0.013 22.3 7.8 77 11-113 14-91 (319)
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=1.1e-47 Score=288.92 Aligned_cols=110 Identities=47% Similarity=0.850 Sum_probs=85.2
Q ss_pred cHHHHHhhCCCCCCCCCCCceeeEEecCCCeEEEEecCcEEEEEceEEEEEccEEEEEEecCceecccceeEEEEEEeee
Q 031416 23 TAYEVLQEYDFPIGLLPKSVLGYTIDRTTGKFSVYLEDTCSFSIESYDLKYKPTITGVITKGKISDLSGISVKVLILWLN 102 (160)
Q Consensus 23 tayelL~~~gLP~GLLP~~V~~y~l~~~tG~f~v~l~~~C~f~~~~~~v~Y~~~ItG~i~~gkI~~L~GVk~K~lf~Wv~ 102 (160)
||||+|++||||+||||++|++|+||++||+|||+|+++|+|++++|+|+|+++|||+|++|+|++|+|||+|++|+|++
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 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEeCCeEEEEEceeeeeeecCcccCC
Q 031416 103 IVEVTRQGDELMLSVGIASADFPVSSFAER 132 (160)
Q Consensus 103 V~eI~~~~~~I~F~vG~~sksFP~s~F~~~ 132 (160)
|+||.+++|+|+|++|+++++||+++|++|
T Consensus 81 v~~i~~~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 81 VTEISVDGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp ---BEE-SSSEE-TTSSSS----TTTTSS-
T ss_pred EEEEEEcCCEEEEEEeeEeccCCHHHhccC
Confidence 999999999999999999999999999986
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=54.80 E-value=22 Score=24.68 Aligned_cols=39 Identities=23% Similarity=0.317 Sum_probs=26.9
Q ss_pred cEEEEEEecCceecccceeEEEE----EEeeeeeEEEEeCCeEEE
Q 031416 75 PTITGVITKGKISDLSGISVKVL----ILWLNIVEVTRQGDELML 115 (160)
Q Consensus 75 ~~ItG~i~~gkI~~L~GVk~K~l----f~Wv~V~eI~~~~~~I~F 115 (160)
+.++|+|+.|+|+ .|-++..+ .....|..|.+....+..
T Consensus 16 ~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~~~~~~~ 58 (87)
T cd03697 16 TVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMFRKTLDE 58 (87)
T ss_pred EEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEECCcCCCE
Confidence 5699999999998 45454443 456778888876544433
No 3
>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=46.31 E-value=59 Score=24.94 Aligned_cols=33 Identities=24% Similarity=0.544 Sum_probs=20.5
Q ss_pred CceeeEEecCCCeEEEEecCcEEEEEc---eEEEEE
Q 031416 41 SVLGYTIDRTTGKFSVYLEDTCSFSIE---SYDLKY 73 (160)
Q Consensus 41 ~V~~y~l~~~tG~f~v~l~~~C~f~~~---~~~v~Y 73 (160)
+.+--.+..++|...+.|+-||.|..+ +-++.|
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 444455666799999999999999987 344544
No 4
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=37.46 E-value=84 Score=23.09 Aligned_cols=53 Identities=21% Similarity=0.242 Sum_probs=37.6
Q ss_pred CCeEEEEecCcEEEEEceEEEEEccEEEEEEecCceecccceeEEEEEEeeeeeEEEEeCCeEEEEE
Q 031416 51 TGKFSVYLEDTCSFSIESYDLKYKPTITGVITKGKISDLSGISVKVLILWLNIVEVTRQGDELMLSV 117 (160)
Q Consensus 51 tG~f~v~l~~~C~f~~~~~~v~Y~~~ItG~i~~gkI~~L~GVk~K~lf~Wv~V~eI~~~~~~I~F~v 117 (160)
++.|.|.|+..|.+. +.|+|++...+|+=+.|=+|++. +| .-+.+-+.|.|.-
T Consensus 19 ~~~frV~LenG~~vl---------a~isGKmR~~rIrIl~GD~V~VE-~s----pYDltkGRIiyR~ 71 (87)
T PRK12442 19 DSRFRVTLENGVEVG---------AYASGRMRKHRIRILAGDRVTLE-LS----PYDLTKGRINFRH 71 (87)
T ss_pred CCEEEEEeCCCCEEE---------EEeccceeeeeEEecCCCEEEEE-EC----cccCCceeEEEEe
Confidence 567777776655432 46899999999999999998887 44 2233456787764
No 5
>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=35.80 E-value=43 Score=26.73 Aligned_cols=41 Identities=20% Similarity=0.306 Sum_probs=32.2
Q ss_pred CCCccHHHHHhhCCCCCCCCC--CCceeeEEecCCCeEEEEecCcEEEE
Q 031416 19 DNSETAYEVLQEYDFPIGLLP--KSVLGYTIDRTTGKFSVYLEDTCSFS 65 (160)
Q Consensus 19 ~~~~tayelL~~~gLP~GLLP--~~V~~y~l~~~tG~f~v~l~~~C~f~ 65 (160)
.+.+.|.++..+ ++| .++++.-+|++||.++++..++=.+.
T Consensus 49 ~~~e~A~~~I~~------ivP~ea~i~di~Fd~~tGEV~IeaeKPG~Vi 91 (145)
T cd02410 49 KPPEEAIKIILE------IVPEEAGITDIYFDDDTGEVIIEAEKPGLVI 91 (145)
T ss_pred CCHHHHHHHHHH------hCCCccCceeeEecCCCcEEEEEEcCCeEEE
Confidence 445667777776 567 37999999999999999999885543
No 6
>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=34.41 E-value=57 Score=22.28 Aligned_cols=12 Identities=33% Similarity=0.601 Sum_probs=9.6
Q ss_pred CCCeEEEEecCc
Q 031416 50 TTGKFSVYLEDT 61 (160)
Q Consensus 50 ~tG~f~v~l~~~ 61 (160)
.+|.|+|++++.
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 7
>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=34.12 E-value=96 Score=21.53 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=27.3
Q ss_pred ccEEEEEEecCceecccceeEEEE------EEeeeeeEEEEeCCeEE
Q 031416 74 KPTITGVITKGKISDLSGISVKVL------ILWLNIVEVTRQGDELM 114 (160)
Q Consensus 74 ~~~ItG~i~~gkI~~L~GVk~K~l------f~Wv~V~eI~~~~~~I~ 114 (160)
.+.|+|+++.|.++. |-++..+ +....|.+|.+++..+.
T Consensus 15 GtVv~G~v~~G~v~~--g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~ 59 (87)
T cd03694 15 GTVVGGTVSKGVIRL--GDTLLLGPDQDGSFRPVTVKSIHRNRSPVR 59 (87)
T ss_pred ceEEEEEEecCEEeC--CCEEEECCCCCCCEeEEEEEEEEECCeECC
Confidence 568999999999994 4444432 35788888887654443
No 8
>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=31.88 E-value=44 Score=23.18 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=13.1
Q ss_pred ccEEEEEEecCceecccc
Q 031416 74 KPTITGVITKGKISDLSG 91 (160)
Q Consensus 74 ~~~ItG~i~~gkI~~L~G 91 (160)
..+|+|.|+.|.|+ +.|
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 47899999999998 554
No 9
>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=28.96 E-value=1e+02 Score=21.13 Aligned_cols=38 Identities=26% Similarity=0.226 Sum_probs=24.9
Q ss_pred EEEEEEecCceecccceeEEEEE--EeeeeeEEEEeCCeEEE
Q 031416 76 TITGVITKGKISDLSGISVKVLI--LWLNIVEVTRQGDELML 115 (160)
Q Consensus 76 ~ItG~i~~gkI~~L~GVk~K~lf--~Wv~V~eI~~~~~~I~F 115 (160)
-|+|+|+.|+|+ .|-++..+= ....|.+|.+++..+..
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 24567777776555444
No 10
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=28.67 E-value=1.6e+02 Score=24.58 Aligned_cols=53 Identities=17% Similarity=0.307 Sum_probs=38.5
Q ss_pred CCCCccHHHHHhhCCCCC-CC--CCCCceeeEEecCCCeEEEEecCcEEEEEceEE
Q 031416 18 GDNSETAYEVLQEYDFPI-GL--LPKSVLGYTIDRTTGKFSVYLEDTCSFSIESYD 70 (160)
Q Consensus 18 ~~~~~tayelL~~~gLP~-GL--LP~~V~~y~l~~~tG~f~v~l~~~C~f~~~~~~ 70 (160)
..+.+.+.+-|++.|+.. .. -|.++.+|--...++.-.+|......+-+.|..
T Consensus 20 ~~~~p~~~~~l~~~g~~v~~~~~~p~~l~g~~~~~~~~~~i~Y~t~dg~y~i~G~l 75 (251)
T PRK11657 20 AEELPAPVKALEKQGITIIKTFDAPGGLKGYAAKYQDMGVTIYLTPDGKHAISGYM 75 (251)
T ss_pred hhcccHHHHHHHhCCCEEEEeecCCCCceEEEEEeCCCceEEEEcCCCCEEEEEEE
Confidence 477888889999999987 44 377899888776444447788877666666644
No 11
>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=27.34 E-value=88 Score=21.87 Aligned_cols=40 Identities=15% Similarity=0.139 Sum_probs=25.2
Q ss_pred ccEEEEEEecCceecccceeEEEE--EEeeeeeEEEEeCCeEEE
Q 031416 74 KPTITGVITKGKISDLSGISVKVL--ILWLNIVEVTRQGDELML 115 (160)
Q Consensus 74 ~~~ItG~i~~gkI~~L~GVk~K~l--f~Wv~V~eI~~~~~~I~F 115 (160)
.+.++|+|+.|.|+. |-++..+ =....|.+|.+.++.+..
T Consensus 19 g~vv~G~v~~G~i~~--gd~v~i~P~~~~~~V~sI~~~~~~~~~ 60 (91)
T cd03693 19 GTVPVGRVETGVLKP--GMVVTFAPAGVTGEVKSVEMHHEPLEE 60 (91)
T ss_pred eEEEEEEEecceeec--CCEEEECCCCcEEEEEEEEECCcCcCE
Confidence 468999999999984 3333221 135677788776544433
No 12
>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=25.30 E-value=1.1e+02 Score=20.83 Aligned_cols=35 Identities=14% Similarity=0.324 Sum_probs=22.2
Q ss_pred ccEEEEEEecCceecccceeEEEE--EEeeeeeEEEEeC
Q 031416 74 KPTITGVITKGKISDLSGISVKVL--ILWLNIVEVTRQG 110 (160)
Q Consensus 74 ~~~ItG~i~~gkI~~L~GVk~K~l--f~Wv~V~eI~~~~ 110 (160)
.+.++|+|+.|.|+. |-++..+ =....|.+|.+++
T Consensus 14 g~vv~G~v~~G~i~~--G~~v~i~P~~~~~~V~si~~~~ 50 (82)
T cd04089 14 GTVVLGKVESGTIKK--GDKLLVMPNKTQVEVLSIYNED 50 (82)
T ss_pred CEEEEEEEeeeEEec--CCEEEEeCCCcEEEEEEEEECC
Confidence 468999999999983 4333221 1345677776654
No 13
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=25.04 E-value=42 Score=31.82 Aligned_cols=15 Identities=33% Similarity=0.793 Sum_probs=13.8
Q ss_pred HHHHHhhCCCCCCCC
Q 031416 24 AYEVLQEYDFPIGLL 38 (160)
Q Consensus 24 ayelL~~~gLP~GLL 38 (160)
+|++|+|-|||.|.+
T Consensus 242 i~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 242 IYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHcCCCccce
Confidence 589999999999987
No 14
>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=24.49 E-value=33 Score=22.40 Aligned_cols=18 Identities=28% Similarity=0.619 Sum_probs=15.1
Q ss_pred EEEEecCceecccceeEE
Q 031416 78 TGVITKGKISDLSGISVK 95 (160)
Q Consensus 78 tG~i~~gkI~~L~GVk~K 95 (160)
.|++++-+-++|+||+++
T Consensus 29 GGtVaPSSss~lTGv~~q 46 (46)
T PF02402_consen 29 GGTVAPSSSSELTGVAVQ 46 (46)
T ss_pred CceECCCccceeeeeecC
Confidence 488999999999999864
No 15
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=24.44 E-value=57 Score=20.89 Aligned_cols=18 Identities=22% Similarity=0.458 Sum_probs=14.1
Q ss_pred CccHHHHHhhCCCCCCCC
Q 031416 21 SETAYEVLQEYDFPIGLL 38 (160)
Q Consensus 21 ~~tayelL~~~gLP~GLL 38 (160)
.....+.|.+||+|.|=+
T Consensus 8 d~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 8 DAELRAELKQYGLPPGPI 25 (44)
T ss_pred HHHHHHHHHHcCCCCCCc
Confidence 345678999999999844
No 16
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=24.25 E-value=1.3e+02 Score=23.93 Aligned_cols=39 Identities=31% Similarity=0.294 Sum_probs=28.1
Q ss_pred CCCccHHHHHhhCCCCC------CCCCCCceeeEEecCCCeEEEEecC
Q 031416 19 DNSETAYEVLQEYDFPI------GLLPKSVLGYTIDRTTGKFSVYLED 60 (160)
Q Consensus 19 ~~~~tayelL~~~gLP~------GLLP~~V~~y~l~~~tG~f~v~l~~ 60 (160)
-+.+.|.++|+++|+|. |--+ ..-.++.+||.+||+..+
T Consensus 107 rNi~~a~~~L~~~gi~i~a~dvGG~~g---R~i~f~~~tG~v~vk~~~ 151 (157)
T PRK13488 107 RNIESAKETLKKLGIRIVAEDVGGDYG---RTVKFDLKTGKVIVRKAN 151 (157)
T ss_pred HHHHHHHHHHHHCCCcEEEEEcCCCCC---cEEEEECCCCEEEEEEcC
Confidence 34567899999999985 2222 344578889999998654
No 17
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=23.97 E-value=2.4e+02 Score=21.61 Aligned_cols=85 Identities=32% Similarity=0.536 Sum_probs=53.1
Q ss_pred HHHhhCCCCC-CCCCCCceeeEEecCCCeE--EEEecC-----------cEEEEEceEEEEEccEEEEEEecCceecccc
Q 031416 26 EVLQEYDFPI-GLLPKSVLGYTIDRTTGKF--SVYLED-----------TCSFSIESYDLKYKPTITGVITKGKISDLSG 91 (160)
Q Consensus 26 elL~~~gLP~-GLLP~~V~~y~l~~~tG~f--~v~l~~-----------~C~f~~~~~~v~Y~~~ItG~i~~gkI~~L~G 91 (160)
+++.+..++. ||+|.=|+++ +||.+ -.+++. .+++......++..-+-+|+++
T Consensus 6 ~~~~~~~~~~~gLvpaIvQd~----~t~eVLMlaymN~eAl~kTleTg~~~y~SRSR~~lW~KGetSG~~q--------- 72 (111)
T COG0139 6 ALLDELDFDKDGLVPAIVQDA----ETGEVLMLAYMNEEALAKTLETGEAHYYSRSRQELWTKGETSGHTQ--------- 72 (111)
T ss_pred hhhhhcccCCCCeEEEEEEec----CCCcEEEEEecCHHHHHHHHhcCeEEEEEcchhhheccccccCceE---------
Confidence 3455566665 9999877766 46653 334442 2555555445777777777654
Q ss_pred eeEEEEEEeeeeeEEEEe--CCeEEEEEceeeeeeecCcccCCCCCCCCCC-cCC
Q 031416 92 ISVKVLILWLNIVEVTRQ--GDELMLSVGIASADFPVSSFAERPTCGCGFD-CFT 143 (160)
Q Consensus 92 Vk~K~lf~Wv~V~eI~~~--~~~I~F~vG~~sksFP~s~F~~~P~C~~g~~-c~~ 143 (160)
.|.+|++| +|-|.|.|-.. ..|.|.-|-. |+.
T Consensus 73 ----------~v~~i~~DCD~Dall~~V~q~----------gg~aCHtG~~SCF~ 107 (111)
T COG0139 73 ----------KVVEIRLDCDGDALLLLVEQI----------GGPACHTGTRSCFY 107 (111)
T ss_pred ----------EEEEEEcCCCCCEEEEEEEeC----------CCCcccCCCccccc
Confidence 47888885 78888876432 3467875543 764
No 18
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=23.64 E-value=1.1e+02 Score=22.36 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=19.5
Q ss_pred CCceeeEEecCCCeEEEEecCc
Q 031416 40 KSVLGYTIDRTTGKFSVYLEDT 61 (160)
Q Consensus 40 ~~V~~y~l~~~tG~f~v~l~~~ 61 (160)
.++++|-.|.+||++++...++
T Consensus 30 lgl~G~V~N~~DGsVeiva~G~ 51 (92)
T COG1254 30 LGLTGWVKNLDDGSVEIVAEGP 51 (92)
T ss_pred CCCEEEEEECCCCeEEEEEEcC
Confidence 3789999999999999999874
No 19
>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=23.31 E-value=1.5e+02 Score=20.22 Aligned_cols=36 Identities=14% Similarity=0.238 Sum_probs=21.8
Q ss_pred EccEEEEEEecCceecccceeEEEE--EEeeeeeEEEEeC
Q 031416 73 YKPTITGVITKGKISDLSGISVKVL--ILWLNIVEVTRQG 110 (160)
Q Consensus 73 Y~~~ItG~i~~gkI~~L~GVk~K~l--f~Wv~V~eI~~~~ 110 (160)
-.+.++|+|+.|.|+. |-++..+ =....|.+|.+..
T Consensus 14 ~g~vv~G~v~~G~i~~--Gd~v~i~P~~~~~~V~si~~~~ 51 (83)
T cd03698 14 GGTVVSGKVESGSIQK--GDTLLVMPSKESVEVKSIYVDD 51 (83)
T ss_pred CCcEEEEEEeeeEEeC--CCEEEEeCCCcEEEEEEEEECC
Confidence 3568899999999984 4333221 1234566666543
No 20
>PF08094 Toxin_24: Conotoxin TVIIA/GS family; InterPro: IPR012629 This family consists of conotoxins isolated from the venom of cone snail Conus tulipa and Conus geographus. Conotoxin TVIIA, isolated from Conus tulipa displays little sequence homology with other well-characterised pharmacological classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides block skeletal muscle sodium channels and also share several biochemical features and represent a distinct subgroup of the four-loop conotoxins [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1AG7_A 1EYO_A.
Probab=23.12 E-value=40 Score=20.36 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=11.4
Q ss_pred CCCCCCCCCCcCCcccc
Q 031416 131 ERPTCGCGFDCFTATAN 147 (160)
Q Consensus 131 ~~P~C~~g~~c~~~~~~ 147 (160)
-||+|-.|+.|.-.+-+
T Consensus 9 cpp~ccmgl~c~rgnpq 25 (33)
T PF08094_consen 9 CPPQCCMGLRCGRGNPQ 25 (33)
T ss_dssp SSSSB-TTEEECSSSS-
T ss_pred CCchheeeeeecCCCcc
Confidence 47999999999655443
No 21
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.06 E-value=1.2e+02 Score=28.18 Aligned_cols=55 Identities=25% Similarity=0.385 Sum_probs=41.6
Q ss_pred hhhHHHHhhhccCCCCCCccHHHHHhhCC-CCCCCCCCCceeeEEec-CCCeEEEEecC
Q 031416 4 LCIIFLLLVSSGARGDNSETAYEVLQEYD-FPIGLLPKSVLGYTIDR-TTGKFSVYLED 60 (160)
Q Consensus 4 ~~~~l~~~~~~~~~~~~~~tayelL~~~g-LP~GLLP~~V~~y~l~~-~tG~f~v~l~~ 60 (160)
+-++..+|.+++.++.|.+.|.++++++= |.+|+.---| +| +|. .+|.|.|.+..
T Consensus 323 l~l~~~LHPTPAV~G~P~~~A~~~Ir~~E~fdRG~Yag~v-Gw-~D~~GngEf~VaIRs 379 (423)
T COG1169 323 LDLAKALHPTPAVGGLPREAALQFIREHEPFDRGWYAGPV-GW-CDSEGNGEFVVAIRS 379 (423)
T ss_pred HHHHHHhCCCccccCCchHHHHHHHHHhCCCCcchhccce-ee-eccCCCeEEEEEEEE
Confidence 44566779999999999999999999998 9999985322 22 222 37888887763
No 22
>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=21.74 E-value=2e+02 Score=23.84 Aligned_cols=35 Identities=20% Similarity=0.446 Sum_probs=24.3
Q ss_pred EEEEccEEE--EEEecCce--ecccceeEEEEEEeeeee
Q 031416 70 DLKYKPTIT--GVITKGKI--SDLSGISVKVLILWLNIV 104 (160)
Q Consensus 70 ~v~Y~~~It--G~i~~gkI--~~L~GVk~K~lf~Wv~V~ 104 (160)
.+-|...|+ ||+++|.- ....|=++.-|.+|+|..
T Consensus 4 ~~PY~~~~~Y~GYv~~g~~pD~~~~gK~~yYlYvWvPaa 42 (182)
T PF12103_consen 4 KVPYTDVINYFGYVDPGNEPDEVVDGKKAYYLYVWVPAA 42 (182)
T ss_dssp EEE-SEEEEEEEEE-TTS--SEEETTEEEEEEEEEESS-
T ss_pred ecccccceeeeEeecCCCCCcccccCceeEEEEEEeehh
Confidence 355666665 99999987 557888899999998753
No 23
>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=20.81 E-value=1.3e+02 Score=22.30 Aligned_cols=39 Identities=33% Similarity=0.360 Sum_probs=23.8
Q ss_pred CCccHHHHHhhCCCCCCCCCCCc-----eeeEEecCCCeEEEEecC
Q 031416 20 NSETAYEVLQEYDFPIGLLPKSV-----LGYTIDRTTGKFSVYLED 60 (160)
Q Consensus 20 ~~~tayelL~~~gLP~GLLP~~V-----~~y~l~~~tG~f~v~l~~ 60 (160)
..+.|.++|+++|+|. .=++| ..-.++..||.+||+.-+
T Consensus 65 Nv~~a~~~L~~~gi~I--~a~dvGG~~~R~v~f~~~tG~v~vk~~~ 108 (114)
T PF03975_consen 65 NVEAARELLAEEGIPI--VAEDVGGNFGRKVRFDPATGEVWVKRIG 108 (114)
T ss_dssp HHHHHHHHHHHTT--E--EEEEE-SSS-EEEEEETTTTEEEEE---
T ss_pred HHHHHHHHHHHCCCcE--EEeeCCCCCCcEEEEEcCCCEEEEEECC
Confidence 3456899999999984 22222 344578889999998653
No 24
>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=20.54 E-value=68 Score=23.74 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=32.5
Q ss_pred CCCCccHHHHHhhCCCC-CCCCCCCceeeEEecCCCeEEEEecC
Q 031416 18 GDNSETAYEVLQEYDFP-IGLLPKSVLGYTIDRTTGKFSVYLED 60 (160)
Q Consensus 18 ~~~~~tayelL~~~gLP-~GLLP~~V~~y~l~~~tG~f~v~l~~ 60 (160)
....+.|.++|+++|++ .|.-|+.++++.+. .-++.+.+.+
T Consensus 39 ~~~~p~a~~~l~e~Gid~~~~~s~~l~~~~~~--~~D~iitm~~ 80 (126)
T TIGR02689 39 SRVHPTAIEVMSEIGIDISGQTSKPLENFHPE--DYDVVISLCG 80 (126)
T ss_pred CCCCHHHHHHHHHhCCCcccCccccCChhHhc--CCCEEEEeCC
Confidence 46778999999999997 58889999888664 4667777743
No 25
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=20.24 E-value=6e+02 Score=22.32 Aligned_cols=77 Identities=16% Similarity=0.234 Sum_probs=44.4
Q ss_pred hhhccCCCCCC-ccHHHHHhhCCCCCCCCCCCceeeEEecCCCeEEEEecCcEEEEEceEEEEEccEEEEEEecCceecc
Q 031416 11 LVSSGARGDNS-ETAYEVLQEYDFPIGLLPKSVLGYTIDRTTGKFSVYLEDTCSFSIESYDLKYKPTITGVITKGKISDL 89 (160)
Q Consensus 11 ~~~~~~~~~~~-~tayelL~~~gLP~GLLP~~V~~y~l~~~tG~f~v~l~~~C~f~~~~~~v~Y~~~ItG~i~~gkI~~L 89 (160)
+++.++++++. .++.++|++.+ +-...-.| .|.|.....+ .++ .++|.-.+.+.-+.-+|..|
T Consensus 14 ~l~~~~~~~~~~~~a~~~L~~M~-------~A~~~lnY---~g~fV~~~~~----~i~--s~ri~H~~~~~~e~erL~~L 77 (319)
T PRK09455 14 SLLFSANASAQPLSSGALLQQMN-------EASQSLNY---ELSFINITKQ----GIE--SLRYRHARLDNKPLAQLLQM 77 (319)
T ss_pred hhcccccccccccCHHHHHHHHH-------HHHHhCCe---EEEEEEEeCC----eEE--EEEEEEEEeCCEEEEEEEec
Confidence 44555544444 35889998864 23333333 2555544433 222 33444446677888899999
Q ss_pred cceeEEEEEEeeeeeEEEEeCCeE
Q 031416 90 SGISVKVLILWLNIVEVTRQGDEL 113 (160)
Q Consensus 90 ~GVk~K~lf~Wv~V~eI~~~~~~I 113 (160)
+|-.. ||.+.+|++
T Consensus 78 dG~~r----------EviR~~d~V 91 (319)
T PRK09455 78 DGPRR----------EIIQRGNEI 91 (319)
T ss_pred CCCce----------EEEEECCEE
Confidence 99664 555666665
Done!