Query 031940
Match_columns 150
No_of_seqs 80 out of 101
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 07:27:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031940hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02792 Mago_nashi: Mago nash 100.0 5E-102 1E-106 606.9 12.9 143 8-150 1-143 (143)
2 KOG3392 Exon-exon junction com 100.0 3.3E-98 7E-103 582.0 11.8 146 5-150 2-147 (147)
3 KOG1446 Histone H3 (Lys4) meth 55.8 6 0.00013 35.4 1.2 27 73-107 182-208 (311)
4 PF14250 AbrB-like: AbrB-like 49.8 15 0.00033 26.7 2.3 14 90-103 57-70 (71)
5 PHA01548 hypothetical protein 46.8 26 0.00056 28.8 3.4 32 55-98 119-151 (167)
6 PRK14947 DNA polymerase III su 36.3 1.8E+02 0.0038 25.6 7.2 36 53-107 196-231 (384)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 32.3 31 0.00067 24.3 1.6 22 55-76 26-47 (84)
8 PF02767 DNA_pol3_beta_2: DNA 31.0 1.5E+02 0.0033 21.1 5.1 41 51-108 63-103 (116)
9 PF05261 Tra_M: TraM protein, 27.5 41 0.00088 26.8 1.7 22 49-70 1-22 (127)
10 PF14258 DUF4350: Domain of un 26.9 43 0.00094 21.9 1.5 17 117-133 1-17 (70)
11 PF11743 DUF3301: Protein of u 26.8 36 0.00079 24.8 1.2 32 18-49 57-89 (97)
12 PF11888 DUF3408: Protein of u 25.5 67 0.0014 24.5 2.5 24 47-70 76-99 (136)
13 PF11211 DUF2997: Protein of u 24.6 51 0.0011 21.7 1.5 13 26-38 1-13 (48)
14 PF10584 Proteasome_A_N: Prote 24.3 34 0.00073 19.9 0.5 7 30-36 8-14 (23)
15 cd03688 eIF2_gamma_II eIF2_gam 22.2 1.4E+02 0.0031 23.1 3.7 31 86-117 41-78 (113)
16 PRK10343 RNA-binding protein Y 22.1 69 0.0015 23.9 2.0 36 54-92 27-62 (97)
17 PF02210 Laminin_G_2: Laminin 21.0 1.4E+02 0.003 20.1 3.1 20 23-43 19-38 (128)
18 PF00989 PAS: PAS fold; Inter 20.9 58 0.0013 20.9 1.2 45 28-72 15-70 (113)
19 PF04900 Fcf1: Fcf1; InterPro 20.5 95 0.0021 22.0 2.3 18 53-70 9-26 (101)
No 1
>PF02792 Mago_nashi: Mago nashi protein; InterPro: IPR004023 This family was originally identified in drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene []. The human homologue has been shown to interact with an RNA binding protein, ribonucleoprotein rbm8 (Q9Y5S9 from SWISSPROT) []. An RNAi knockout of the Caenorhabditis elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination [] but the protein is also found in hermaphrodites and other organisms without a sexual differentiation.; GO: 0005634 nucleus; PDB: 2XB2_Y 2J0S_C 3EX7_A 2J0Q_F 1P27_C 2HYI_A 2X1G_B 1HL6_B 1RK8_B 1OO0_A ....
Probab=100.00 E-value=5.2e-102 Score=606.89 Aligned_cols=143 Identities=88% Similarity=1.443 Sum_probs=132.9
Q ss_pred ceEEEEeecCCCccceeeEEEEEcCCCceEeeccCCCCCcceEEEEEeeCHHHHHHHHHHhhhcccccccCCCCCCCCCC
Q 031940 8 EFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEVFLTPAVLRECRRIISESEIMKEDDNNWPEPDRV 87 (150)
Q Consensus 8 ~FYlRYY~Gh~GkfGHEFLEfEf~~dG~lRYaNNSnYKnd~~IrKe~~vs~~v~~E~krII~~SeI~kEdD~~WP~pd~~ 87 (150)
+||||||+||+||||||||||||||||+||||||||||||+||||||+||++||+|+||||.+||||+|||++||+||++
T Consensus 1 ~fYlRYy~gH~GkfGhEfLEfEfr~dG~lRYaNnSnYknd~~IrKe~~vs~~vl~E~krII~~SeI~kEdD~~WP~pd~~ 80 (143)
T PF02792_consen 1 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDSMIRKEVYVSPAVLEELKRIIEDSEIMKEDDSKWPEPDRV 80 (143)
T ss_dssp -EEEEEEEEEEETTEEEEEEEEEETTSEEEEEEEESCCCSEEEEEEEEE-HHHHHHHHHHHHHHTGGG--STTS--SBTT
T ss_pred CeeEEEEeccCccccceEEEEEeccCCeEEEcccCCCCCcceeeeeeEecHHHHHHHHHHHHHhhccccccccCCCCCCc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEEECCeEEEEEecCeeeeeeccCCCCccchhhhhHHHHhHHHHHHHHhhhceeeecC
Q 031940 88 GRQELEIVMGNEHISFTTSKIGSLVDVQSSKDPEGLRIFYYLVQDLKCFVFSLISLHFKIKPI 150 (150)
Q Consensus 88 GrQELEI~~g~~HisF~tsKiGSl~dv~~S~DPeGLr~FyYLvqDLkclvfsLi~lHfkikpi 150 (150)
|||||||+|||+||||+|||||||+|||+|+||||||+||||||||||||||||+||||||||
T Consensus 81 GrQELEI~lg~~HisF~tsKigsl~dv~~S~DPeGLr~FyYLvqDLKclvfsLi~lHFkikpi 143 (143)
T PF02792_consen 81 GRQELEIVLGNEHISFTTSKIGSLSDVQNSKDPEGLRVFYYLVQDLKCLVFSLISLHFKIKPI 143 (143)
T ss_dssp BEEEEEEEETTEEEEEEEC---SHHHHHTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHTSSS-
T ss_pred cceeEEEEECCEEEEEEecccccceeeccCCCccHHHHHHHHHHHHHHHHHHHHHheeeeccC
Confidence 999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG3392 consensus Exon-exon junction complex, Magoh component [RNA processing and modification]
Probab=100.00 E-value=3.3e-98 Score=581.97 Aligned_cols=146 Identities=84% Similarity=1.381 Sum_probs=144.4
Q ss_pred CCcceEEEEeecCCCccceeeEEEEEcCCCceEeeccCCCCCcceEEEEEeeCHHHHHHHHHHhhhcccccccCCCCCCC
Q 031940 5 EDGEFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEVFLTPAVLRECRRIISESEIMKEDDNNWPEP 84 (150)
Q Consensus 5 ~~~~FYlRYY~Gh~GkfGHEFLEfEf~~dG~lRYaNNSnYKnd~~IrKe~~vs~~v~~E~krII~~SeI~kEdD~~WP~p 84 (150)
...+|||||||||+||||||||||||||||+||||||||||||+|||||++||++|++|+||||.|||||+|||++||+|
T Consensus 2 ~asdfy~ryyvghkgkfgheflefefr~dg~lryannsnykndt~irke~fv~e~vl~e~kriv~dsei~kedd~nwp~p 81 (147)
T KOG3392|consen 2 EASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAFVHESVLEELKRIIDDSEIMKEDDANWPPP 81 (147)
T ss_pred cccceEEEEEeccCccccceeeEEEecCCCcEEeccCCCcccchhhhhhhhhhHHHHHHHHHHhhhhhhhhccccCCcCC
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeEEEEECCeEEEEEecCeeeeeeccCCCCccchhhhhHHHHhHHHHHHHHhhhceeeecC
Q 031940 85 DRVGRQELEIVMGNEHISFTTSKIGSLVDVQSSKDPEGLRIFYYLVQDLKCFVFSLISLHFKIKPI 150 (150)
Q Consensus 85 d~~GrQELEI~~g~~HisF~tsKiGSl~dv~~S~DPeGLr~FyYLvqDLkclvfsLi~lHfkikpi 150 (150)
|++|||||||+|||+||||+|||||||+|||+|+||||||+||||||||||||||||+||||||||
T Consensus 82 d~~gkqelei~~~~ehisf~t~kigsladv~ns~dpeglr~fyylvqdlkclvfsli~lhfkikpi 147 (147)
T KOG3392|consen 82 DRVGRQELEIVIGDEHISFTTSKIGSLADVNNSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 147 (147)
T ss_pred CcccceeEEEEECCeEEEEEeccccceeecccCCCccceeeehhhHhhhHhHhhhheeeeEEeecC
Confidence 999999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG1446 consensus Histone H3 (Lys4) methyltransferase complex and RNA cleavage factor II complex, subunit SWD2 [RNA processing and modification; Chromatin structure and dynamics; Posttranslational modification, protein turnover, chaperones]
Probab=55.83 E-value=6 Score=35.36 Aligned_cols=27 Identities=26% Similarity=0.554 Sum_probs=19.1
Q ss_pred cccccCCCCCCCCCCCceeEEEEECCeEEEEEecC
Q 031940 73 IMKEDDNNWPEPDRVGRQELEIVMGNEHISFTTSK 107 (150)
Q Consensus 73 I~kEdD~~WP~pd~~GrQELEI~~g~~HisF~tsK 107 (150)
|..+|-+.| .+||..=+|+-|=.+|..
T Consensus 182 i~~~~~~ew--------~~l~FS~dGK~iLlsT~~ 208 (311)
T KOG1446|consen 182 ITDNDEAEW--------TDLEFSPDGKSILLSTNA 208 (311)
T ss_pred cCCCCccce--------eeeEEcCCCCEEEEEeCC
Confidence 334666667 578888888888777755
No 4
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=49.76 E-value=15 Score=26.65 Aligned_cols=14 Identities=43% Similarity=0.835 Sum_probs=12.8
Q ss_pred eeEEEEECCeEEEE
Q 031940 90 QELEIVMGNEHISF 103 (150)
Q Consensus 90 QELEI~~g~~HisF 103 (150)
||.||.+|-+||-+
T Consensus 57 dEFeI~LgrKhI~L 70 (71)
T PF14250_consen 57 DEFEIKLGRKHIHL 70 (71)
T ss_pred CEEEEEeCcceEEe
Confidence 89999999999964
No 5
>PHA01548 hypothetical protein
Probab=46.80 E-value=26 Score=28.81 Aligned_cols=32 Identities=34% Similarity=0.569 Sum_probs=23.1
Q ss_pred eeCHHHHHHHHHHhhhcccccccCCCC-CCCCCCCceeEEEEECC
Q 031940 55 FLTPAVLRECRRIISESEIMKEDDNNW-PEPDRVGRQELEIVMGN 98 (150)
Q Consensus 55 ~vs~~v~~E~krII~~SeI~kEdD~~W-P~pd~~GrQELEI~~g~ 98 (150)
.+|+.|+..|+|||.= --++.| |+| |||+.+.
T Consensus 119 a~SQgVVssIQkiisI-----vGpapwt~EP-------l~iVp~e 151 (167)
T PHA01548 119 AVSQGVVSSIQKIISI-----VGPAPWTDEP-------LAIVPGE 151 (167)
T ss_pred eehHHHHHHHHHHHHH-----hCCCCCCCCC-------eeEEEEE
Confidence 3899999999999963 245555 977 6666553
No 6
>PRK14947 DNA polymerase III subunit beta; Provisional
Probab=36.30 E-value=1.8e+02 Score=25.61 Aligned_cols=36 Identities=17% Similarity=0.410 Sum_probs=29.3
Q ss_pred EEeeCHHHHHHHHHHhhhcccccccCCCCCCCCCCCceeEEEEECCeEEEEEecC
Q 031940 53 EVFLTPAVLRECRRIISESEIMKEDDNNWPEPDRVGRQELEIVMGNEHISFTTSK 107 (150)
Q Consensus 53 e~~vs~~v~~E~krII~~SeI~kEdD~~WP~pd~~GrQELEI~~g~~HisF~tsK 107 (150)
.+-|..-.+.||+|++.+ .+++|.+++.|+.|.+..
T Consensus 196 ~~iIP~k~l~el~kll~~-------------------~~v~i~~~~~~i~f~~~~ 231 (384)
T PRK14947 196 GILIQKKYLLELKKWLGA-------------------DEIELSISEKRLFFRTGD 231 (384)
T ss_pred cEEEechHHHHHHHhCCC-------------------CcEEEEEeCCEEEEEECC
Confidence 567888889999999741 178999999999998764
No 7
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=32.26 E-value=31 Score=24.26 Aligned_cols=22 Identities=27% Similarity=0.336 Sum_probs=18.6
Q ss_pred eeCHHHHHHHHHHhhhcccccc
Q 031940 55 FLTPAVLRECRRIISESEIMKE 76 (150)
Q Consensus 55 ~vs~~v~~E~krII~~SeI~kE 76 (150)
-++++|++|+.+-++.+|++|-
T Consensus 26 Glt~~vi~~i~~~l~~~eLvKV 47 (84)
T PF01985_consen 26 GLTDGVIEEIDDALEKHELVKV 47 (84)
T ss_dssp SS-HHHHHHHHHHHHHHSEEEE
T ss_pred CCCHHHHHHHHHHHHhCCeeEE
Confidence 4799999999999999998763
No 8
>PF02767 DNA_pol3_beta_2: DNA polymerase III beta subunit, central domain; InterPro: IPR022637 This entry describes the central domain of the beta chain of DNA polymerase III. This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3T0P_B 3P16_A 3RB9_B 2AWA_C 1VPK_A 2AVT_B 2XUR_B 3Q4K_A 3BEP_A 3D1G_A ....
Probab=30.97 E-value=1.5e+02 Score=21.10 Aligned_cols=41 Identities=24% Similarity=0.523 Sum_probs=33.1
Q ss_pred EEEEeeCHHHHHHHHHHhhhcccccccCCCCCCCCCCCceeEEEEECCeEEEEEecCe
Q 031940 51 RKEVFLTPAVLRECRRIISESEIMKEDDNNWPEPDRVGRQELEIVMGNEHISFTTSKI 108 (150)
Q Consensus 51 rKe~~vs~~v~~E~krII~~SeI~kEdD~~WP~pd~~GrQELEI~~g~~HisF~tsKi 108 (150)
..++-|....+.||+|++.++ + .+++|.+++.++.|.+..+
T Consensus 63 ~~~~iIp~k~l~~l~k~l~~~-----~------------~~v~i~~~~~~i~f~~~~~ 103 (116)
T PF02767_consen 63 EFSFIIPAKALKELKKLLSDE-----D------------EEVEISISDNQIIFKFDNI 103 (116)
T ss_dssp EEEEEEEHHHHHHHHHHSSTT-----S------------SEEEEEEESSEEEEEESSE
T ss_pred ceEEEEechHHHHHhhhcccC-----C------------ceEEEEEcCCEEEEEECCE
Confidence 466889999999999998761 1 3688999999999998763
No 9
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=27.46 E-value=41 Score=26.79 Aligned_cols=22 Identities=32% Similarity=0.573 Sum_probs=16.8
Q ss_pred eEEEEEeeCHHHHHHHHHHhhh
Q 031940 49 MIRKEVFLTPAVLRECRRIISE 70 (150)
Q Consensus 49 ~IrKe~~vs~~v~~E~krII~~ 70 (150)
|=|..+||+..|.++|..|+.+
T Consensus 1 M~rvq~y~s~~v~~~I~~iVe~ 22 (127)
T PF05261_consen 1 MPRVQIYVSNKVLEEINDIVEE 22 (127)
T ss_dssp --EECCE--HCHHHHHHHHHHH
T ss_pred CCchhhhhhHHHHHHHHHHHHH
Confidence 4588999999999999999976
No 10
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=26.87 E-value=43 Score=21.89 Aligned_cols=17 Identities=24% Similarity=0.548 Sum_probs=14.8
Q ss_pred CCCccchhhhhHHHHhH
Q 031940 117 SKDPEGLRIFYYLVQDL 133 (150)
Q Consensus 117 S~DPeGLr~FyYLvqDL 133 (150)
|++|.|.+.||-+.++.
T Consensus 1 ~~~p~G~~a~~~~L~~~ 17 (70)
T PF14258_consen 1 NPAPNGTYALYQLLEEQ 17 (70)
T ss_pred CCCchHHHHHHHHHHHC
Confidence 57899999999988875
No 11
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=26.76 E-value=36 Score=24.83 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=20.9
Q ss_pred CCccc-eeeEEEEEcCCCceEeeccCCCCCcce
Q 031940 18 KGKFG-HEFLEFEFRPDGKLRYANNSNYKNDTM 49 (150)
Q Consensus 18 ~GkfG-HEFLEfEf~~dG~lRYaNNSnYKnd~~ 49 (150)
.|+.+ +---.|||++||.-||.-.=-..+..+
T Consensus 57 ~g~~~~~r~y~FEFS~~G~~ry~G~l~m~G~~l 89 (97)
T PF11743_consen 57 RGRLRWRRVYQFEFSSDGEDRYQGELVMLGRRL 89 (97)
T ss_pred CCCeEEEEEEEEEEeCCChhcceEEEEEECCee
Confidence 45555 344579999999999876544444433
No 12
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=25.51 E-value=67 Score=24.47 Aligned_cols=24 Identities=21% Similarity=0.329 Sum_probs=19.9
Q ss_pred cceEEEEEeeCHHHHHHHHHHhhh
Q 031940 47 DTMIRKEVFLTPAVLRECRRIISE 70 (150)
Q Consensus 47 d~~IrKe~~vs~~v~~E~krII~~ 70 (150)
..--||-||||+.+-+-|.||+..
T Consensus 76 ~~~~R~~vyI~~e~h~~l~~Iv~~ 99 (136)
T PF11888_consen 76 KIKARKGVYISRETHERLSRIVRV 99 (136)
T ss_pred CCCCCeeeEECHHHHHHHHHHHHH
Confidence 344578899999999999999864
No 13
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=24.61 E-value=51 Score=21.65 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=10.3
Q ss_pred EEEEEcCCCceEe
Q 031940 26 LEFEFRPDGKLRY 38 (150)
Q Consensus 26 LEfEf~~dG~lRY 38 (150)
+||.++|||+++-
T Consensus 1 I~~~I~~dG~V~~ 13 (48)
T PF11211_consen 1 IEFTIYPDGRVEE 13 (48)
T ss_pred CEEEECCCcEEEE
Confidence 5788899998763
No 14
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=24.27 E-value=34 Score=19.88 Aligned_cols=7 Identities=71% Similarity=1.540 Sum_probs=5.8
Q ss_pred EcCCCce
Q 031940 30 FRPDGKL 36 (150)
Q Consensus 30 f~~dG~l 36 (150)
|+|||||
T Consensus 8 FSp~Grl 14 (23)
T PF10584_consen 8 FSPDGRL 14 (23)
T ss_dssp BBTTSSB
T ss_pred ECCCCeE
Confidence 6799986
No 15
>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.
Probab=22.16 E-value=1.4e+02 Score=23.13 Aligned_cols=31 Identities=32% Similarity=0.328 Sum_probs=18.7
Q ss_pred CCCceeEEEEEC-------CeEEEEEecCeeeeeeccCC
Q 031940 86 RVGRQELEIVMG-------NEHISFTTSKIGSLVDVQSS 117 (150)
Q Consensus 86 ~~GrQELEI~~g-------~~HisF~tsKiGSl~dv~~S 117 (150)
++| ||+||+-| +....--+++|-||..-++.
T Consensus 41 kvg-deIEIrpg~~~~~~~~~~~~pi~T~I~sl~~~~~~ 78 (113)
T cd03688 41 KVG-DEIEIRPGIVVKDEGKIKCRPIFTKIVSLKAENND 78 (113)
T ss_pred eCC-CEEEEeeceeeecCCCeeEEEEEEEEEEEEecCcc
Confidence 467 89999955 11111235678888766654
No 16
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=22.14 E-value=69 Score=23.89 Aligned_cols=36 Identities=25% Similarity=0.283 Sum_probs=27.1
Q ss_pred EeeCHHHHHHHHHHhhhcccccccCCCCCCCCCCCceeE
Q 031940 54 VFLTPAVLRECRRIISESEIMKEDDNNWPEPDRVGRQEL 92 (150)
Q Consensus 54 ~~vs~~v~~E~krII~~SeI~kEdD~~WP~pd~~GrQEL 92 (150)
--+|++|++|+.+-++..|++|-. |...++.-|+|+
T Consensus 27 ~Glt~~vi~ei~~aL~~hELIKvk---v~~~~~~~~~e~ 62 (97)
T PRK10343 27 NGLTEGVLAEIEQALEHHELIKVK---IATEDRETKTLI 62 (97)
T ss_pred CCCCHHHHHHHHHHHHHCCcEEEE---ecCCChhHHHHH
Confidence 358999999999999999988853 555555445443
No 17
>PF02210 Laminin_G_2: Laminin G domain; InterPro: IPR012680 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012679 from INTERPRO).; PDB: 3POY_A 3QCW_B 3R05_B 3ASI_A 3MW4_B 3MW3_A 1QU0_D 1DYK_A 1OKQ_A 3SH4_A ....
Probab=20.96 E-value=1.4e+02 Score=20.07 Aligned_cols=20 Identities=35% Similarity=0.552 Sum_probs=16.3
Q ss_pred eeeEEEEEcCCCceEeeccCC
Q 031940 23 HEFLEFEFRPDGKLRYANNSN 43 (150)
Q Consensus 23 HEFLEfEf~~dG~lRYaNNSn 43 (150)
..|+..++. ||+|++.=+..
T Consensus 19 ~~~l~l~l~-~g~l~~~~~~g 38 (128)
T PF02210_consen 19 GDFLSLELV-DGRLVVRYNLG 38 (128)
T ss_dssp SEEEEEEEE-TTEEEEEEESS
T ss_pred CEEEEEEEE-CCEEEEEEEcc
Confidence 789999997 99988765555
No 18
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=20.89 E-value=58 Score=20.89 Aligned_cols=45 Identities=29% Similarity=0.650 Sum_probs=29.8
Q ss_pred EEEcCCCceEeeccC-----CCCCcceEEEEEe--eCHH----HHHHHHHHhhhcc
Q 031940 28 FEFRPDGKLRYANNS-----NYKNDTMIRKEVF--LTPA----VLRECRRIISESE 72 (150)
Q Consensus 28 fEf~~dG~lRYaNNS-----nYKnd~~IrKe~~--vs~~----v~~E~krII~~Se 72 (150)
+-++.+|++.|+|.+ +|..+.++-|-+. +.+. ..+.++..+...+
T Consensus 15 ~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 (113)
T PF00989_consen 15 FVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGE 70 (113)
T ss_dssp EEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCC
T ss_pred EEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCC
Confidence 446799999999987 4777777776644 3333 6666666666554
No 19
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=20.53 E-value=95 Score=21.96 Aligned_cols=18 Identities=22% Similarity=0.349 Sum_probs=15.5
Q ss_pred EEeeCHHHHHHHHHHhhh
Q 031940 53 EVFLTPAVLRECRRIISE 70 (150)
Q Consensus 53 e~~vs~~v~~E~krII~~ 70 (150)
+.+|++.|++||+++-..
T Consensus 9 ~~~vt~cVl~EL~~L~~~ 26 (101)
T PF04900_consen 9 KPYVTQCVLEELESLGKK 26 (101)
T ss_pred EEEecHHHHHHHHHhccc
Confidence 578999999999998744
Done!