Query 030681
Match_columns 173
No_of_seqs 104 out of 340
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:59:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030681.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030681hhsearch_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 2.1E-46 4.5E-51 286.0 5.8 109 47-157 1-110 (110)
2 PF07172 GRP: Glycine rich pro 48.0 17 0.00036 27.2 2.4 12 1-12 1-12 (95)
3 cd02410 archeal_CPSF_KH The ar 46.4 22 0.00048 28.8 3.0 36 46-87 52-89 (145)
4 cd03697 EFTU_II EFTU_II: Elong 37.8 63 0.0014 22.7 4.0 34 97-132 15-52 (87)
5 PF07494 Reg_prop: Two compone 30.5 57 0.0012 18.0 2.2 19 62-81 2-21 (24)
6 PF10262 Rdx: Rdx family; Int 30.1 79 0.0017 21.9 3.4 23 63-85 29-52 (76)
7 PF07861 WND: WisP family N-Te 28.2 3.5E+02 0.0075 23.6 7.5 77 64-142 145-229 (263)
8 PLN02346 histidine biosynthesi 26.3 77 0.0017 28.2 3.3 85 44-142 36-126 (271)
9 PF08710 nsp9: nsp9 replicase; 26.0 1.9E+02 0.0042 22.6 5.1 28 64-91 49-76 (111)
10 PF00386 C1q: C1q domain; Int 25.9 2E+02 0.0043 21.2 5.1 22 70-91 31-52 (127)
11 smart00540 LEM in nuclear memb 23.0 34 0.00073 22.4 0.4 19 44-62 7-25 (44)
12 COG1254 AcyP Acylphosphatases 22.3 1E+02 0.0023 22.8 3.0 21 65-85 31-51 (92)
13 PF08300 HCV_NS5a_1a: Hepatiti 21.2 67 0.0015 22.7 1.6 18 96-114 26-43 (62)
14 PF03088 Str_synth: Strictosid 21.1 97 0.0021 22.8 2.6 26 127-154 1-26 (89)
15 PF06977 SdiA-regulated: SdiA- 21.0 2.8E+02 0.0061 23.8 5.8 51 64-117 22-72 (248)
16 PF05963 Cytomega_US3: Cytomeg 20.1 1.4E+02 0.003 25.4 3.5 50 64-116 26-75 (187)
17 PRK12442 translation initiatio 20.1 1.8E+02 0.004 21.7 3.8 53 75-142 19-71 (87)
18 cd04089 eRF3_II eRF3_II: domai 20.1 2.6E+02 0.0057 19.3 4.5 45 97-143 14-67 (82)
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=2.1e-46 Score=286.02 Aligned_cols=109 Identities=38% Similarity=0.793 Sum_probs=83.3
Q ss_pred CHHHhhhhcCCCCCCCCCCceeEEEecCCceEEEEEcceEEEEEe-EEEEEcceEEEEEecCccccccceEEEEEEeecc
Q 030681 47 DVHDLLPLYGLPKGLIPSDIKSYTLDKSTGSFSIEMTRTCYVHFQ-QLVWYDKHIKGKLSYGAVHDVSGIQAKKLFLWLP 125 (173)
Q Consensus 47 tayelL~~~gLP~GLLP~~V~~Y~l~~~tG~f~V~L~~~C~~~f~-~~v~Y~~~ItG~l~~G~I~~L~GVkvK~lf~Wv~ 125 (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~~ 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 699999999999999999999999999999999999999999999 7999999999999999999999999999999999
Q ss_pred eeEEEEecCCCeEEEEEceeeecccccccCCC
Q 030681 126 VTGIETVKNSDVLRFFVGALSEDLPAEQFQEI 157 (173)
Q Consensus 126 I~~I~Vd~~~~~I~F~vG~isksFP~s~F~~~ 157 (173)
|+||.+ ++|+|+|++|+++++||+++|+++
T Consensus 81 v~~i~~--~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 81 VTEISV--DGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp ---BEE---SSSEE-TTSSSS----TTTTSS-
T ss_pred EEEEEE--cCCEEEEEEeeEeccCCHHHhccC
Confidence 999995 899999999999999999999985
No 2
>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=47.95 E-value=17 Score=27.23 Aligned_cols=12 Identities=50% Similarity=0.429 Sum_probs=6.4
Q ss_pred CCCCchhHHHHH
Q 030681 1 MASPHSISLCLL 12 (173)
Q Consensus 1 ~~~~~~~~~~~l 12 (173)
|||-..+.|+|+
T Consensus 1 MaSK~~llL~l~ 12 (95)
T PF07172_consen 1 MASKAFLLLGLL 12 (95)
T ss_pred CchhHHHHHHHH
Confidence 886554444443
No 3
>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=46.39 E-value=22 Score=28.84 Aligned_cols=36 Identities=19% Similarity=0.358 Sum_probs=29.6
Q ss_pred CCHHHhhhhcCCCCCCCC--CCceeEEEecCCceEEEEEcceEE
Q 030681 46 IDVHDLLPLYGLPKGLIP--SDIKSYTLDKSTGSFSIEMTRTCY 87 (173)
Q Consensus 46 ~tayelL~~~gLP~GLLP--~~V~~Y~l~~~tG~f~V~L~~~C~ 87 (173)
..|.++..+ +.| .++++.-+|++||.++++..++=.
T Consensus 52 e~A~~~I~~------ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ 89 (145)
T cd02410 52 EEAIKIILE------IVPEEAGITDIYFDDDTGEVIIEAEKPGL 89 (145)
T ss_pred HHHHHHHHH------hCCCccCceeeEecCCCcEEEEEEcCCeE
Confidence 567777776 567 689999999999999999987743
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=37.84 E-value=63 Score=22.72 Aligned_cols=34 Identities=26% Similarity=0.433 Sum_probs=23.3
Q ss_pred cceEEEEEecCccccccceEEEEE----EeecceeEEEEe
Q 030681 97 DKHIKGKLSYGAVHDVSGIQAKKL----FLWLPVTGIETV 132 (173)
Q Consensus 97 ~~~ItG~l~~G~I~~L~GVkvK~l----f~Wv~I~~I~Vd 132 (173)
.+.++|+|+.|+|+ .|-++..+ .....|..|+++
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~ 52 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMF 52 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEEC
Confidence 35699999999998 44444443 346677777753
No 5
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=30.50 E-value=57 Score=18.02 Aligned_cols=19 Identities=32% Similarity=0.464 Sum_probs=12.0
Q ss_pred CC-CCceeEEEecCCceEEEE
Q 030681 62 IP-SDIKSYTLDKSTGSFSIE 81 (173)
Q Consensus 62 LP-~~V~~Y~l~~~tG~f~V~ 81 (173)
|| ..|...--|+ +|.+||=
T Consensus 2 L~~n~I~~i~~D~-~G~lWig 21 (24)
T PF07494_consen 2 LPNNNIYSIYEDS-DGNLWIG 21 (24)
T ss_dssp BSSSCEEEEEE-T-TSCEEEE
T ss_pred CCCCeEEEEEEcC-CcCEEEE
Confidence 45 5555555565 9999983
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=30.11 E-value=79 Score=21.91 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=14.3
Q ss_pred CCCceeEEEec-CCceEEEEEcce
Q 030681 63 PSDIKSYTLDK-STGSFSIEMTRT 85 (173)
Q Consensus 63 P~~V~~Y~l~~-~tG~f~V~L~~~ 85 (173)
|..+.+.++.+ .+|.|+|++++.
T Consensus 29 p~~~~~v~~~~~~~G~FEV~v~g~ 52 (76)
T PF10262_consen 29 PDRIAEVELSPGSTGAFEVTVNGE 52 (76)
T ss_dssp TTTCSEEEEEEESTT-EEEEETTE
T ss_pred CCcceEEEEEeccCCEEEEEEccE
Confidence 33444444443 589999999976
No 7
>PF07861 WND: WisP family N-Terminal Region; InterPro: IPR012503 This family is found at the N terminus of the Tropheryma whipplei WisP family proteins [].
Probab=28.21 E-value=3.5e+02 Score=23.61 Aligned_cols=77 Identities=18% Similarity=0.279 Sum_probs=54.5
Q ss_pred CCceeEEEecCCceEEEEEcceEEEEEeEEEEEcceEEEEEecC----cc----ccccceEEEEEEeecceeEEEEecCC
Q 030681 64 SDIKSYTLDKSTGSFSIEMTRTCYVHFQQLVWYDKHIKGKLSYG----AV----HDVSGIQAKKLFLWLPVTGIETVKNS 135 (173)
Q Consensus 64 ~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~~v~Y~~~ItG~l~~G----~I----~~L~GVkvK~lf~Wv~I~~I~Vd~~~ 135 (173)
+-|.+++..+ +|-|.+--.+..+|.-+-.+.+.+.||-.|.+. -| -.|.|-.- -+=+--|+.+|++|+..
T Consensus 145 drVvS~s~s~-s~~~~LLT~~Nv~F~a~v~~s~q~~vTV~v~~~~~~~~irS~~PaLR~S~~-T~SLs~P~~~v~lD~~T 222 (263)
T PF07861_consen 145 DRVVSFSVSP-SGVFTLLTGGNVYFYAQVPSSFQSSVTVNVKYDAKTGVIRSATPALRGSPF-TYSLSTPVAGVRLDANT 222 (263)
T ss_pred ccEEEEEecC-CceEEEEecCcEEEEEeccccccCceEEEEEEecccceEecCChhhcCCcc-eEEeccCCCceEEeccc
Confidence 6788888887 899998777777776565677777777766553 23 33444322 23356789999999999
Q ss_pred CeEEEEE
Q 030681 136 DVLRFFV 142 (173)
Q Consensus 136 ~~I~F~v 142 (173)
|+|.-.+
T Consensus 223 G~l~~Sv 229 (263)
T PF07861_consen 223 GALSGSV 229 (263)
T ss_pred ceeeeee
Confidence 9998774
No 8
>PLN02346 histidine biosynthesis bifunctional protein hisIE
Probab=26.29 E-value=77 Score=28.25 Aligned_cols=85 Identities=18% Similarity=0.184 Sum_probs=49.6
Q ss_pred CCCCHHHhhhhcCCC-CCCCCCCceeEEEecCCceEE--EEEcceEE-EEEe--EEEEEcceEEEEEecCccccccceEE
Q 030681 44 SIIDVHDLLPLYGLP-KGLIPSDIKSYTLDKSTGSFS--IEMTRTCY-VHFQ--QLVWYDKHIKGKLSYGAVHDVSGIQA 117 (173)
Q Consensus 44 ~~~tayelL~~~gLP-~GLLP~~V~~Y~l~~~tG~f~--V~L~~~C~-~~f~--~~v~Y~~~ItG~l~~G~I~~L~GVkv 117 (173)
..+.+-+++.+..+= .||+|.-|+++ .||.+- .|++.... .+.+ +..+|+..-...-.+|.-++
T Consensus 36 ~~~~~~~~~~~l~~~~~gLipaivQd~----~tg~VLml~ymn~eal~~Tl~tg~~~y~SRSR~~LW~KGetSG------ 105 (271)
T PLN02346 36 LEPKVESLLDSVKWDDKGLAVAIAQNV----DTGAILMQGFANREAISATISSRKATFYSRSRSGLWTKGETSG------ 105 (271)
T ss_pred cchhHHHHHHhcCcCCCCCEEEEEEEC----CCCCEEEEEecCHHHHHHHHhcCcEEEEeCCCCccccCCCCcC------
Confidence 444566677766664 49999888876 477744 36665552 2222 23333332222223332221
Q ss_pred EEEEeecceeEEEEecCCCeEEEEE
Q 030681 118 KKLFLWLPVTGIETVKNSDVLRFFV 142 (173)
Q Consensus 118 K~lf~Wv~I~~I~Vd~~~~~I~F~v 142 (173)
-...|.+|.+|.|+|-|.|.|
T Consensus 106 ----~~q~v~~i~~DCD~D~ll~~V 126 (271)
T PLN02346 106 ----NFINVHDIYLDCDRDSIIYLG 126 (271)
T ss_pred ----CeEEEEEEEecCCCCeEEEEE
Confidence 123578899999999999998
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=26.02 E-value=1.9e+02 Score=22.58 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=17.9
Q ss_pred CCceeEEEecCCceEEEEEcceEEEEEe
Q 030681 64 SDIKSYTLDKSTGSFSIEMTRTCYVHFQ 91 (173)
Q Consensus 64 ~~V~~Y~l~~~tG~f~V~L~~~C~~~f~ 91 (173)
.+.+--.+..++|...+.|+-+|.|..+
T Consensus 49 ~~Lk~vk~~~d~G~v~ieLePPckF~v~ 76 (111)
T PF08710_consen 49 DNLKYVKWEKDDGKVVIELEPPCKFAVD 76 (111)
T ss_dssp S-EEEEEEE-TTSEEEEEB---EEEEEE
T ss_pred CCceEEEEEccCCEEEEecCCCcEEEEE
Confidence 3555556777799999999999988765
No 10
>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=25.91 E-value=2e+02 Score=21.21 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=16.5
Q ss_pred EEecCCceEEEEEcceEEEEEe
Q 030681 70 TLDKSTGSFSIEMTRTCYVHFQ 91 (173)
Q Consensus 70 ~l~~~tG~f~V~L~~~C~~~f~ 91 (173)
.+|++||.|.+..++--.+.|.
T Consensus 31 ~yn~~tG~Ftap~~G~Y~F~~~ 52 (127)
T PF00386_consen 31 AYNPSTGIFTAPVPGVYFFSFT 52 (127)
T ss_dssp -EETTTTEEE-SS-EEEEEEEE
T ss_pred ccEeecCEEecCCCCEEEEEEE
Confidence 5888999999999888887775
No 11
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=23.05 E-value=34 Score=22.39 Aligned_cols=19 Identities=42% Similarity=0.616 Sum_probs=15.0
Q ss_pred CCCCHHHhhhhcCCCCCCC
Q 030681 44 SIIDVHDLLPLYGLPKGLI 62 (173)
Q Consensus 44 ~~~tayelL~~~gLP~GLL 62 (173)
++..+.+.|.+||+|.|=+
T Consensus 7 Sd~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 7 SDAELRAELKQYGLPPGPI 25 (44)
T ss_pred CHHHHHHHHHHcCCCCCCc
Confidence 3456788999999999843
No 12
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=22.29 E-value=1e+02 Score=22.82 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.4
Q ss_pred CceeEEEecCCceEEEEEcce
Q 030681 65 DIKSYTLDKSTGSFSIEMTRT 85 (173)
Q Consensus 65 ~V~~Y~l~~~tG~f~V~L~~~ 85 (173)
++++|-.|..||.+++...++
T Consensus 31 gl~G~V~N~~DGsVeiva~G~ 51 (92)
T COG1254 31 GLTGWVKNLDDGSVEIVAEGP 51 (92)
T ss_pred CCEEEEEECCCCeEEEEEEcC
Confidence 689999999999999988654
No 13
>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=21.15 E-value=67 Score=22.70 Aligned_cols=18 Identities=22% Similarity=0.495 Sum_probs=13.2
Q ss_pred EcceEEEEEecCccccccc
Q 030681 96 YDKHIKGKLSYGAVHDVSG 114 (173)
Q Consensus 96 Y~~~ItG~l~~G~I~~L~G 114 (173)
-..+|+|.|+.|+|+ +.|
T Consensus 26 CGa~ItGhVknG~mr-i~g 43 (62)
T PF08300_consen 26 CGAVITGHVKNGSMR-IYG 43 (62)
T ss_dssp TS-EEEEEEETTEEE-EE-
T ss_pred CCCEEeEEEeCCeEE-Eec
Confidence 357899999999998 544
No 14
>PF03088 Str_synth: Strictosidine synthase; InterPro: IPR018119 This entry represents a conserved region found in strictosidine synthase (4.3.3.2 from EC), a key enzyme in alkaloid biosynthesis. It catalyses the Pictet-Spengler stereospecific condensation of tryptamine with secologanin to form strictosidine []. The structure of the native enzyme from the Indian medicinal plant Rauvolfia serpentina (Serpentwood) (Devilpepper) represents the first example of a six-bladed four-stranded beta-propeller fold from the plant kingdom [].; GO: 0016844 strictosidine synthase activity, 0009058 biosynthetic process; PDB: 2FPB_A 2V91_B 2FP8_A 3V1S_B 2FPC_A 2VAQ_A 2FP9_B.
Probab=21.15 E-value=97 Score=22.79 Aligned_cols=26 Identities=8% Similarity=0.213 Sum_probs=13.3
Q ss_pred eEEEEecCCCeEEEEEceeeeccccccc
Q 030681 127 TGIETVKNSDVLRFFVGALSEDLPAEQF 154 (173)
Q Consensus 127 ~~I~Vd~~~~~I~F~vG~isksFP~s~F 154 (173)
+++.|++++|.|||.-. |..|+...|
T Consensus 1 ndldv~~~~g~vYfTds--S~~~~~~~~ 26 (89)
T PF03088_consen 1 NDLDVDQDTGTVYFTDS--SSRYDRRDW 26 (89)
T ss_dssp -EEEE-TTT--EEEEES---SS--TTGH
T ss_pred CceeEecCCCEEEEEeC--ccccCccce
Confidence 35677788899999976 345554443
No 15
>PF06977 SdiA-regulated: SdiA-regulated; InterPro: IPR009722 This entry represents a conserved region approximately 100 residues long within a number of hypothetical bacterial proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators []. Some proteins contain the IPR001258 from INTERPRO repeat.; PDB: 3QQZ_A.
Probab=21.01 E-value=2.8e+02 Score=23.84 Aligned_cols=51 Identities=14% Similarity=0.253 Sum_probs=34.2
Q ss_pred CCceeEEEecCCceEEEEEcceEEEEEeEEEEEcceEEEEEecCccccccceEE
Q 030681 64 SDIKSYTLDKSTGSFSIEMTRTCYVHFQQLVWYDKHIKGKLSYGAVHDVSGIQA 117 (173)
Q Consensus 64 ~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~~v~Y~~~ItG~l~~G~I~~L~GVkv 117 (173)
+++-+-+||++++.+|...+++..+ + .+.-+.+|-..+.-+...|.+||..
T Consensus 22 ~e~SGLTy~pd~~tLfaV~d~~~~i-~--els~~G~vlr~i~l~g~~D~EgI~y 72 (248)
T PF06977_consen 22 DELSGLTYNPDTGTLFAVQDEPGEI-Y--ELSLDGKVLRRIPLDGFGDYEGITY 72 (248)
T ss_dssp S-EEEEEEETTTTEEEEEETTTTEE-E--EEETT--EEEEEE-SS-SSEEEEEE
T ss_pred CCccccEEcCCCCeEEEEECCCCEE-E--EEcCCCCEEEEEeCCCCCCceeEEE
Confidence 5688999999999999999998765 2 2333445666666666777777765
No 16
>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=20.11 E-value=1.4e+02 Score=25.36 Aligned_cols=50 Identities=18% Similarity=0.398 Sum_probs=22.2
Q ss_pred CCceeEEEecCCceEEEEEcceEEEEEeEEEEEcceEEEEEecCccccccceE
Q 030681 64 SDIKSYTLDKSTGSFSIEMTRTCYVHFQQLVWYDKHIKGKLSYGAVHDVSGIQ 116 (173)
Q Consensus 64 ~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~~v~Y~~~ItG~l~~G~I~~L~GVk 116 (173)
..+++ .+-..--.|+|. ...|++.= .++...-+|+|++.+--.-+.-++.
T Consensus 26 ~~~~~-~~~a~~~~ftV~-~n~C~ie~-Gklf~~G~I~GN~t~~~fv~~~v~~ 75 (187)
T PF05963_consen 26 PEITE-QLTARRAHFTVE-QNRCYIEG-GKLFMTGRISGNFTKSHFVQVGVVG 75 (187)
T ss_dssp --------------EEEE-EEEEEESS-SEEEEEEEEEE--S-EEEEESSS-E
T ss_pred HHHHh-hhccCCceEEEE-eeeEEEEC-CEEEEEEEEeeeeeeEEEEEEeeee
Confidence 44555 443323457774 46787732 4688888999998765555555544
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=20.11 E-value=1.8e+02 Score=21.73 Aligned_cols=53 Identities=13% Similarity=0.157 Sum_probs=37.0
Q ss_pred CceEEEEEcceEEEEEeEEEEEcceEEEEEecCccccccceEEEEEEeecceeEEEEecCCCeEEEEE
Q 030681 75 TGSFSIEMTRTCYVHFQQLVWYDKHIKGKLSYGAVHDVSGIQAKKLFLWLPVTGIETVKNSDVLRFFV 142 (173)
Q Consensus 75 tG~f~V~L~~~C~~~f~~~v~Y~~~ItG~l~~G~I~~L~GVkvK~lf~Wv~I~~I~Vd~~~~~I~F~v 142 (173)
++.|.|.|...+++ -..|+|++...+|+=+.|=+|++- +| + -|..-+.|.|.-
T Consensus 19 ~~~frV~LenG~~v--------la~isGKmR~~rIrIl~GD~V~VE-~s-p-----YDltkGRIiyR~ 71 (87)
T PRK12442 19 DSRFRVTLENGVEV--------GAYASGRMRKHRIRILAGDRVTLE-LS-P-----YDLTKGRINFRH 71 (87)
T ss_pred CCEEEEEeCCCCEE--------EEEeccceeeeeEEecCCCEEEEE-EC-c-----ccCCceeEEEEe
Confidence 67777777655444 245889999999999999888876 33 1 124567777765
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=20.07 E-value=2.6e+02 Score=19.28 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=25.6
Q ss_pred cceEEEEEecCccccccceEEEEE--EeecceeEEEEe-------cCCCeEEEEEc
Q 030681 97 DKHIKGKLSYGAVHDVSGIQAKKL--FLWLPVTGIETV-------KNSDVLRFFVG 143 (173)
Q Consensus 97 ~~~ItG~l~~G~I~~L~GVkvK~l--f~Wv~I~~I~Vd-------~~~~~I~F~vG 143 (173)
.+.++|+|+.|.|+. |-++..+ =....|.+|+++ .+|+.+.+...
T Consensus 14 g~vv~G~v~~G~i~~--G~~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~ 67 (82)
T cd04089 14 GTVVLGKVESGTIKK--GDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLK 67 (82)
T ss_pred CEEEEEEEeeeEEec--CCEEEEeCCCcEEEEEEEEECCEECCEECCCCEEEEEec
Confidence 568999999998873 3333221 123455666532 25666655553
Done!