Query 030678
Match_columns 173
No_of_seqs 108 out of 345
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 02:57:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030678.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030678hhsearch_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 4.9E-46 1.1E-50 283.4 6.4 110 36-146 1-110 (110)
2 PF12428 DUF3675: Protein of u 57.1 11 0.00023 29.4 2.7 34 4-37 59-92 (118)
3 PF10262 Rdx: Rdx family; Int 54.6 17 0.00036 25.3 3.1 12 63-74 41-52 (76)
4 cd03697 EFTU_II EFTU_II: Elong 44.3 47 0.001 23.4 4.2 38 89-128 16-57 (87)
5 PRK12442 translation initiatio 38.0 65 0.0014 24.0 4.1 53 64-131 19-71 (87)
6 PF07092 DUF1356: Protein of u 37.5 2E+02 0.0044 25.0 7.7 85 11-110 77-174 (238)
7 cd04089 eRF3_II eRF3_II: domai 36.1 87 0.0019 21.7 4.5 35 88-124 14-50 (82)
8 PF08710 nsp9: nsp9 replicase; 31.8 1.2E+02 0.0027 23.5 5.0 34 54-87 50-85 (111)
9 PF07172 GRP: Glycine rich pro 30.6 25 0.00054 26.2 0.9 18 9-26 4-22 (95)
10 cd01203 DOK_PTB Downstream of 27.9 73 0.0016 24.4 3.1 58 64-132 1-66 (104)
11 cd03698 eRF3_II_like eRF3_II_l 26.1 1.6E+02 0.0035 20.3 4.5 36 87-124 14-51 (83)
12 PF06691 DUF1189: Protein of u 23.4 1.7E+02 0.0037 24.5 4.8 74 53-145 64-138 (250)
13 PF05963 Cytomega_US3: Cytomeg 23.1 1.4E+02 0.0031 25.1 4.2 57 66-132 38-94 (187)
14 COG0139 HisI Phosphoribosyl-AM 23.0 1.5E+02 0.0033 23.0 4.1 71 39-133 6-92 (111)
15 cd03694 GTPBP_II Domain II of 22.6 1.9E+02 0.0041 20.3 4.3 38 88-127 15-58 (87)
16 COG1169 MenF Isochorismate syn 22.2 1.2E+02 0.0026 28.5 4.0 56 17-73 323-379 (423)
17 PF02402 Lysis_col: Lysis prot 22.0 40 0.00086 22.3 0.6 18 92-109 29-46 (46)
18 KOG2455 Delta-1-pyrroline-5-ca 21.8 52 0.0011 31.6 1.5 15 37-51 242-256 (561)
19 TIGR02689 ars_reduc_gluta arse 21.1 71 0.0015 24.0 1.9 40 31-72 39-79 (126)
20 cd03695 CysN_NodQ_II CysN_NodQ 21.0 1.8E+02 0.0039 20.2 3.9 38 90-129 17-56 (81)
21 PF13670 PepSY_2: Peptidase pr 20.8 3E+02 0.0064 19.0 6.0 29 34-70 31-59 (83)
22 smart00540 LEM in nuclear memb 20.8 74 0.0016 20.7 1.7 18 34-51 8-25 (44)
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=4.9e-46 Score=283.44 Aligned_cols=110 Identities=46% Similarity=0.883 Sum_probs=84.4
Q ss_pred cHHHHHhhcCCCCCCCCCCceeeEeecCCCeEEEEeccceEEEEccceEEEEccEEEEEeecCcccCCcceEEEEEEEEe
Q 030678 36 TAYEVLKSFNFPIGILPKGVTGYDLESSTGKFSAYFNGSCSFSLEGSYQLKYEPTIKGYITKGKLSSLEGVSVKLFFMWV 115 (173)
Q Consensus 36 tayelL~~~GlP~GLLP~~V~~Y~l~~~tG~f~V~L~~~C~f~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~lf~Wv 115 (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 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFEG-YLVSYDSEITGYIEKGKIKNLTGVKVKELFLWV 79 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEESTT-SEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEE
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEEE-EEEEEcCeEEEEECCCcCccccCEEEEEEEEEe
Confidence 7999999999999999999999999999999999999999999875 999999999999999999999999999999999
Q ss_pred eeEEEEEeCCEEEEEEceeeeeeecCCccCC
Q 030678 116 DIVEVSRHGDTLDFSVGITGADFPVVNFEEC 146 (173)
Q Consensus 116 ~V~eI~~dg~~I~F~vG~~sksFP~s~F~~~ 146 (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
>PF12428 DUF3675: Protein of unknown function (DUF3675) ; InterPro: IPR022143 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF00097 from PFAM. There are two completely conserved residues (R and L) that may be functionally important.
Probab=57.12 E-value=11 Score=29.38 Aligned_cols=34 Identities=12% Similarity=-0.084 Sum_probs=23.1
Q ss_pred cccccchhhHHHHHHHHHHHHhccCCCCCCCCcH
Q 030678 4 DSFFSGRFNFFPQILCLLILLITVTPSFAEEPTA 37 (173)
Q Consensus 4 ~~~~~~r~~~~~~~~~lll~~~~~~~s~~~~~ta 37 (173)
.+|.+||++-++++++|+|-+.-...-+.+.+.+
T Consensus 59 ~~a~~CRsvAli~m~LLllRhal~l~~~~~~~~s 92 (118)
T PF12428_consen 59 RGAACCRSVALIFMVLLLLRHALALVTGGAEDYS 92 (118)
T ss_pred CceeHHHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 3688999999998888888864443333333333
No 3
>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=54.62 E-value=17 Score=25.34 Aligned_cols=12 Identities=50% Similarity=0.750 Sum_probs=9.8
Q ss_pred CCCeEEEEeccc
Q 030678 63 STGKFSAYFNGS 74 (173)
Q Consensus 63 ~tG~f~V~L~~~ 74 (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 689999999976
No 4
>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=44.34 E-value=47 Score=23.37 Aligned_cols=38 Identities=21% Similarity=0.399 Sum_probs=26.4
Q ss_pred cEEEEEeecCcccCCcceEEEEE----EEEeeeEEEEEeCCEEE
Q 030678 89 PTIKGYITKGKLSSLEGVSVKLF----FMWVDIVEVSRHGDTLD 128 (173)
Q Consensus 89 ~~ItG~i~~g~I~~L~GVkvK~l----f~Wv~V~eI~~dg~~I~ 128 (173)
+.++|+|+.|+|+ .|-++..+ .....|..|.+++..+.
T Consensus 16 ~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~~~~~~ 57 (87)
T cd03697 16 TVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMFRKTLD 57 (87)
T ss_pred EEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEECCcCCC
Confidence 5699999999998 45555443 45677888877654433
No 5
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=38.01 E-value=65 Score=24.00 Aligned_cols=53 Identities=15% Similarity=0.231 Sum_probs=36.1
Q ss_pred CCeEEEEeccceEEEEccceEEEEccEEEEEeecCcccCCcceEEEEEEEEeeeEEEEEeCCEEEEEE
Q 030678 64 TGKFSAYFNGSCSFSLEGSYQLKYEPTIKGYITKGKLSSLEGVSVKLFFMWVDIVEVSRHGDTLDFSV 131 (173)
Q Consensus 64 tG~f~V~L~~~C~f~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~lf~Wv~V~eI~~dg~~I~F~v 131 (173)
++.|.|.|+..|.+ - ..|+|++...+|+=+.|=+|++. +| | -...-+.|.|.-
T Consensus 19 ~~~frV~LenG~~v--------l--a~isGKmR~~rIrIl~GD~V~VE-~s-p---YDltkGRIiyR~ 71 (87)
T PRK12442 19 DSRFRVTLENGVEV--------G--AYASGRMRKHRIRILAGDRVTLE-LS-P---YDLTKGRINFRH 71 (87)
T ss_pred CCEEEEEeCCCCEE--------E--EEeccceeeeeEEecCCCEEEEE-EC-c---ccCCceeEEEEe
Confidence 56676666655444 2 67899999999999999998886 33 1 122336777654
No 6
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=37.53 E-value=2e+02 Score=25.02 Aligned_cols=85 Identities=21% Similarity=0.375 Sum_probs=47.3
Q ss_pred hhHHHHHHHHHHHHhccCCCCCCCCcHHHHHhhcCCCCCCC--CCCceee--EeecCCCeEEEEeccc--------eEEE
Q 030678 11 FNFFPQILCLLILLITVTPSFAEEPTAYEVLKSFNFPIGIL--PKGVTGY--DLESSTGKFSAYFNGS--------CSFS 78 (173)
Q Consensus 11 ~~~~~~~~~lll~~~~~~~s~~~~~tayelL~~~GlP~GLL--P~~V~~Y--~l~~~tG~f~V~L~~~--------C~f~ 78 (173)
.++++.++||++...... +=|||.+. |.|+++- .+|++++...+++... ..++
T Consensus 77 yV~~sV~~CLl~~~L~iF---------------FLfPRsV~v~~~gv~s~~V~f~~~~~~v~l~itn~lNIsN~NFy~V~ 141 (238)
T PF07092_consen 77 YVFLSVLLCLLLSGLVIF---------------FLFPRSVTVSPVGVKSVTVSFNPDKSTVQLNITNTLNISNPNFYPVT 141 (238)
T ss_pred EeeHHHHHHHHHHHheEE---------------EEeCcEEEEecCcEEEEEEEEeCCCCEEEEEEEEEEEccCCCEEEEE
Confidence 455577777777543332 33677766 4555533 3666666643333222 2222
Q ss_pred Ec-cceEEEEccEEEEEeecCcccCCcceEEEE
Q 030678 79 LE-GSYQLKYEPTIKGYITKGKLSSLEGVSVKL 110 (173)
Q Consensus 79 ~~-~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~ 110 (173)
+. ...++.|.++|-|..+...+.-+.=..-|.
T Consensus 142 Vt~~s~qv~~~~~VVG~~~~~~~~~I~Prs~~q 174 (238)
T PF07092_consen 142 VTNLSIQVLYMKTVVGKGKNSNITVIGPRSSKQ 174 (238)
T ss_pred EEeEEEEEEEEEeEEeeeEecceEEecccCCce
Confidence 22 246788888888887776665554333443
No 7
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=36.05 E-value=87 Score=21.70 Aligned_cols=35 Identities=11% Similarity=0.308 Sum_probs=22.3
Q ss_pred ccEEEEEeecCcccCCcceEEEEE--EEEeeeEEEEEeC
Q 030678 88 EPTIKGYITKGKLSSLEGVSVKLF--FMWVDIVEVSRHG 124 (173)
Q Consensus 88 ~~~ItG~i~~g~I~~L~GVkvK~l--f~Wv~V~eI~~dg 124 (173)
.+.++|+|+.|.|+ .|-++..+ =....|..|.+++
T Consensus 14 g~vv~G~v~~G~i~--~G~~v~i~P~~~~~~V~si~~~~ 50 (82)
T cd04089 14 GTVVLGKVESGTIK--KGDKLLVMPNKTQVEVLSIYNED 50 (82)
T ss_pred CEEEEEEEeeeEEe--cCCEEEEeCCCcEEEEEEEEECC
Confidence 46899999999998 34443322 1345666666553
No 8
>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=31.80 E-value=1.2e+02 Score=23.51 Aligned_cols=34 Identities=21% Similarity=0.425 Sum_probs=19.8
Q ss_pred CceeeEeecCCCeEEEEeccceEEEEc--cceEEEE
Q 030678 54 GVTGYDLESSTGKFSAYFNGSCSFSLE--GSYQLKY 87 (173)
Q Consensus 54 ~V~~Y~l~~~tG~f~V~L~~~C~f~~~--~~~~v~Y 87 (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 444455666789888888999999774 3455555
No 9
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=30.57 E-value=25 Score=26.23 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=8.5
Q ss_pred chhhHHH-HHHHHHHHHhc
Q 030678 9 GRFNFFP-QILCLLILLIT 26 (173)
Q Consensus 9 ~r~~~~~-~~~~lll~~~~ 26 (173)
..+++|+ +|+.+||++|.
T Consensus 4 K~~llL~l~LA~lLlisSe 22 (95)
T PF07172_consen 4 KAFLLLGLLLAALLLISSE 22 (95)
T ss_pred hHHHHHHHHHHHHHHHHhh
Confidence 3456664 34444454443
No 10
>cd01203 DOK_PTB Downstream of tyrosine kinase (DOK) Phosphotyrosine-binding domain. Downstream of tyrosine kinase (DOK) Phosphotyrosine-binding domain. This domain has a PH-like fold and is similiar to the PTB domain that is found in insulin receptor substrate molecules The DOK family of eukaryotic signaling molecules have an N-terminal PH domain, followed by an IRS-like PTB domain. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs.
Probab=27.90 E-value=73 Score=24.43 Aligned_cols=58 Identities=17% Similarity=0.330 Sum_probs=33.0
Q ss_pred CCeEEEEeccc-----eEEEEccceEEEEccEEEEEeecCcccCCcceEEEEEEEEeeeEEEEE---eCCEEEEEEc
Q 030678 64 TGKFSAYFNGS-----CSFSLEGSYQLKYEPTIKGYITKGKLSSLEGVSVKLFFMWVDIVEVSR---HGDTLDFSVG 132 (173)
Q Consensus 64 tG~f~V~L~~~-----C~f~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~lf~Wv~V~eI~~---dg~~I~F~vG 132 (173)
+|.|.|.+..+ |.. .+.|.++-. +..+.=.. .+.++.+++||...+.+ |.+...|++|
T Consensus 1 ~~~F~V~v~~Teaserc~L--~G~y~L~v~--------~~~l~L~d-~~~~~~l~~WP~~~LRryG~d~~~FsFEAG 66 (104)
T cd01203 1 DGEFPVTLQPTEASERCCL--PGSYMLRMG--------PTELQLKS-EDLGATLYMWPYRFLRKYGRDKGKFSFEAG 66 (104)
T ss_pred CCEEEEEEEEChhHHhcCC--ceeEEEEEc--------CCEEEEEc-CCCCcEEEEeehHhhhhhcccCCEEEEEec
Confidence 47788888643 655 345555432 22222111 12256678899999987 4466665555
No 11
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=26.13 E-value=1.6e+02 Score=20.29 Aligned_cols=36 Identities=11% Similarity=0.215 Sum_probs=21.5
Q ss_pred EccEEEEEeecCcccCCcceEEEEE--EEEeeeEEEEEeC
Q 030678 87 YEPTIKGYITKGKLSSLEGVSVKLF--FMWVDIVEVSRHG 124 (173)
Q Consensus 87 Y~~~ItG~i~~g~I~~L~GVkvK~l--f~Wv~V~eI~~dg 124 (173)
-...++|+|+.|.|+. |-++..+ =....|.+|.++.
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 3468899999999984 4333221 1234566665543
No 12
>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=23.39 E-value=1.7e+02 Score=24.52 Aligned_cols=74 Identities=15% Similarity=0.303 Sum_probs=46.5
Q ss_pred CCceeeEeecCCCeEEEEeccceEEEE-ccceEEEEccEEEEEeecCcccCCcceEEEEEEEEeeeEEEEEeCCEEEEEE
Q 030678 53 KGVTGYDLESSTGKFSAYFNGSCSFSL-EGSYQLKYEPTIKGYITKGKLSSLEGVSVKLFFMWVDIVEVSRHGDTLDFSV 131 (173)
Q Consensus 53 ~~V~~Y~l~~~tG~f~V~L~~~C~f~~-~~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~lf~Wv~V~eI~~dg~~I~F~v 131 (173)
+..-+|++. +|.++ .+++=.+.+ +++..+.||++ |.+...-+++- -++|....|++++..
T Consensus 64 ~~iP~F~I~--nG~L~--~~~~~~i~~~~~~~~i~~D~~--~~~~~~dl~~~-------------~~~i~~lkd~iv~~~ 124 (250)
T PF06691_consen 64 NDIPDFTIE--NGKLT--SDQSEPIIYQTNNFIIIFDPT--GKVTEDDLSDY-------------KNAIAFLKDEIVIKD 124 (250)
T ss_pred hhCCCeEEE--CCcEe--cCCCCceEecCCcEEEEECCC--CCcchhhhcCC-------------cceEEEecceEEEEe
Confidence 455578884 89964 444333333 35677888884 55554433321 124666789999988
Q ss_pred ceeeeeeecCCccC
Q 030678 132 GITGADFPVVNFEE 145 (173)
Q Consensus 132 G~~sksFP~s~F~~ 145 (173)
+..++++|-+.+..
T Consensus 125 ~g~~~s~~Ys~~~~ 138 (250)
T PF06691_consen 125 NGQTQSISYSDLND 138 (250)
T ss_pred CCeeEEeehhhccc
Confidence 77778888887653
No 13
>PF05963 Cytomega_US3: Cytomegalovirus US3 protein; InterPro: IPR009237 US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein [].; PDB: 1IM3_L.
Probab=23.10 E-value=1.4e+02 Score=25.12 Aligned_cols=57 Identities=23% Similarity=0.318 Sum_probs=28.0
Q ss_pred eEEEEeccceEEEEccceEEEEccEEEEEeecCcccCCcceEEEEEEEEeeeEEEEEeCCEEEEEEc
Q 030678 66 KFSAYFNGSCSFSLEGSYQLKYEPTIKGYITKGKLSSLEGVSVKLFFMWVDIVEVSRHGDTLDFSVG 132 (173)
Q Consensus 66 ~f~V~L~~~C~f~~~~~~~v~Y~~~ItG~i~~g~I~~L~GVkvK~lf~Wv~V~eI~~dg~~I~F~vG 132 (173)
.|+|.= ..|++ ++| ++...-+|+|++.+----+.-++.-|- +..+.+.+++++|+.|
T Consensus 38 ~ftV~~-n~C~i--e~G-klf~~G~I~GN~t~~~fv~~~v~~~~~------~enL~~~~~d~~~~~g 94 (187)
T PF05963_consen 38 HFTVEQ-NRCYI--EGG-KLFMTGRISGNFTKSHFVQVGVVGDSY------RENLQVSEKDVTFSPG 94 (187)
T ss_dssp -EEEEE-EEEEE--SSS-EEEEEEEEEE--S-EEEEESSS-E----------EE----GGGEEEETT
T ss_pred eEEEEe-eeEEE--ECC-EEEEEEEEeeeeeeEEEEEEeeeeccc------hhheEEecceeEecCC
Confidence 454432 47998 444 788899999999866655555555332 2344445555565443
No 14
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=23.01 E-value=1.5e+02 Score=23.02 Aligned_cols=71 Identities=27% Similarity=0.402 Sum_probs=43.7
Q ss_pred HHHhhcCCCC-CCCCCCceeeEeecCCCe--EEEEeccc-----------eEEEEccceEEEEccEEEEEeecCcccCCc
Q 030678 39 EVLKSFNFPI-GILPKGVTGYDLESSTGK--FSAYFNGS-----------CSFSLEGSYQLKYEPTIKGYITKGKLSSLE 104 (173)
Q Consensus 39 elL~~~GlP~-GLLP~~V~~Y~l~~~tG~--f~V~L~~~-----------C~f~~~~~~~v~Y~~~ItG~i~~g~I~~L~ 104 (173)
+++.+..++. ||+|.=|+++ +||. .-.|++.+ +++. ....+++.+-+-+|.+.
T Consensus 6 ~~~~~~~~~~~gLvpaIvQd~----~t~eVLMlaymN~eAl~kTleTg~~~y~S-RSR~~lW~KGetSG~~q-------- 72 (111)
T COG0139 6 ALLDELDFDKDGLVPAIVQDA----ETGEVLMLAYMNEEALAKTLETGEAHYYS-RSRQELWTKGETSGHTQ-------- 72 (111)
T ss_pred hhhhhcccCCCCeEEEEEEec----CCCcEEEEEecCHHHHHHHHhcCeEEEEE-cchhhheccccccCceE--------
Confidence 3455566665 9999888776 4664 34566643 4443 22233566666666543
Q ss_pred ceEEEEEEEEeeeEEEEEe--CCEEEEEEce
Q 030678 105 GVSVKLFFMWVDIVEVSRH--GDTLDFSVGI 133 (173)
Q Consensus 105 GVkvK~lf~Wv~V~eI~~d--g~~I~F~vG~ 133 (173)
.|.+|.+| +|-+.|.|-.
T Consensus 73 -----------~v~~i~~DCD~Dall~~V~q 92 (111)
T COG0139 73 -----------KVVEIRLDCDGDALLLLVEQ 92 (111)
T ss_pred -----------EEEEEEcCCCCCEEEEEEEe
Confidence 36677775 7999888754
No 15
>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=22.62 E-value=1.9e+02 Score=20.29 Aligned_cols=38 Identities=21% Similarity=0.338 Sum_probs=26.4
Q ss_pred ccEEEEEeecCcccCCcceEEEEE------EEEeeeEEEEEeCCEE
Q 030678 88 EPTIKGYITKGKLSSLEGVSVKLF------FMWVDIVEVSRHGDTL 127 (173)
Q Consensus 88 ~~~ItG~i~~g~I~~L~GVkvK~l------f~Wv~V~eI~~dg~~I 127 (173)
.+.++|+++.|.++. |-++... +....|.+|.+++..+
T Consensus 15 GtVv~G~v~~G~v~~--g~~v~~~P~~~g~~~~~~V~sI~~~~~~~ 58 (87)
T cd03694 15 GTVVGGTVSKGVIRL--GDTLLLGPDQDGSFRPVTVKSIHRNRSPV 58 (87)
T ss_pred ceEEEEEEecCEEeC--CCEEEECCCCCCCEeEEEEEEEEECCeEC
Confidence 568999999999994 4444432 2567888888764333
No 16
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.22 E-value=1.2e+02 Score=28.46 Aligned_cols=56 Identities=16% Similarity=0.110 Sum_probs=42.9
Q ss_pred HHHHHHHHhccCCCCCCCCcHHHHHhhcC-CCCCCCCCCceeeEeecCCCeEEEEecc
Q 030678 17 ILCLLILLITVTPSFAEEPTAYEVLKSFN-FPIGILPKGVTGYDLESSTGKFSAYFNG 73 (173)
Q Consensus 17 ~~~lll~~~~~~~s~~~~~tayelL~~~G-lP~GLLP~~V~~Y~l~~~tG~f~V~L~~ 73 (173)
+-++..++++++.+..+.+.|.++++++= |.||+.---|-=+.. +.+|.|-|.+..
T Consensus 323 l~l~~~LHPTPAV~G~P~~~A~~~Ir~~E~fdRG~Yag~vGw~D~-~GngEf~VaIRs 379 (423)
T COG1169 323 LDLAKALHPTPAVGGLPREAALQFIREHEPFDRGWYAGPVGWCDS-EGNGEFVVAIRS 379 (423)
T ss_pred HHHHHHhCCCccccCCchHHHHHHHHHhCCCCcchhccceeeecc-CCCeEEEEEEEE
Confidence 44555668999999999999999999998 999998544333333 348999888874
No 17
>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=21.99 E-value=40 Score=22.34 Aligned_cols=18 Identities=33% Similarity=0.508 Sum_probs=14.1
Q ss_pred EEEeecCcccCCcceEEE
Q 030678 92 KGYITKGKLSSLEGVSVK 109 (173)
Q Consensus 92 tG~i~~g~I~~L~GVkvK 109 (173)
.|.+++-+.++|+||+++
T Consensus 29 GGtVaPSSss~lTGv~~q 46 (46)
T PF02402_consen 29 GGTVAPSSSSELTGVAVQ 46 (46)
T ss_pred CceECCCccceeeeeecC
Confidence 578888888888888763
No 18
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=21.81 E-value=52 Score=31.59 Aligned_cols=15 Identities=27% Similarity=0.778 Sum_probs=13.8
Q ss_pred HHHHHhhcCCCCCCC
Q 030678 37 AYEVLKSFNFPIGIL 51 (173)
Q Consensus 37 ayelL~~~GlP~GLL 51 (173)
+|++|+|-|||.|++
T Consensus 242 i~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 242 IYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHcCCCccce
Confidence 589999999999987
No 19
>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=21.06 E-value=71 Score=23.95 Aligned_cols=40 Identities=20% Similarity=0.204 Sum_probs=31.1
Q ss_pred CCCCCcHHHHHhhcCCC-CCCCCCCceeeEeecCCCeEEEEec
Q 030678 31 FAEEPTAYEVLKSFNFP-IGILPKGVTGYDLESSTGKFSAYFN 72 (173)
Q Consensus 31 ~~~~~tayelL~~~GlP-~GLLP~~V~~Y~l~~~tG~f~V~L~ 72 (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 35677999999999997 57889999988664 456666664
No 20
>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=20.97 E-value=1.8e+02 Score=20.21 Aligned_cols=38 Identities=18% Similarity=0.208 Sum_probs=24.9
Q ss_pred EEEEEeecCcccCCcceEEEEEE--EEeeeEEEEEeCCEEEE
Q 030678 90 TIKGYITKGKLSSLEGVSVKLFF--MWVDIVEVSRHGDTLDF 129 (173)
Q Consensus 90 ~ItG~i~~g~I~~L~GVkvK~lf--~Wv~V~eI~~dg~~I~F 129 (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 555544331 34567777776555443
No 21
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=20.84 E-value=3e+02 Score=19.04 Aligned_cols=29 Identities=14% Similarity=0.235 Sum_probs=21.2
Q ss_pred CCcHHHHHhhcCCCCCCCCCCceeeEeecCCCeEEEE
Q 030678 34 EPTAYEVLKSFNFPIGILPKGVTGYDLESSTGKFSAY 70 (173)
Q Consensus 34 ~~tayelL~~~GlP~GLLP~~V~~Y~l~~~tG~f~V~ 70 (173)
...+...|++.|. .|.+..++ ++|.++|+
T Consensus 31 ~~~~~~~l~~~G~-------~v~~ve~~-~~g~yev~ 59 (83)
T PF13670_consen 31 IEQAVAKLEAQGY-------QVREVEFD-DDGCYEVE 59 (83)
T ss_pred HHHHHHHHHhcCC-------ceEEEEEc-CCCEEEEE
Confidence 3456777887553 68899996 47889888
No 22
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=20.82 E-value=74 Score=20.66 Aligned_cols=18 Identities=22% Similarity=0.458 Sum_probs=14.0
Q ss_pred CCcHHHHHhhcCCCCCCC
Q 030678 34 EPTAYEVLKSFNFPIGIL 51 (173)
Q Consensus 34 ~~tayelL~~~GlP~GLL 51 (173)
.....+.|.+||+|.|=+
T Consensus 8 d~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 8 DAELRAELKQYGLPPGPI 25 (44)
T ss_pred HHHHHHHHHHcCCCCCCc
Confidence 345678999999999843
Done!