Query psy3064
Match_columns 61
No_of_seqs 34 out of 36
Neff 2.1
Searched_HMMs 46136
Date Sat Aug 17 00:45:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3064hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2113|consensus 98.3 1.7E-07 3.8E-12 72.9 0.3 31 30-61 18-48 (394)
2 PF00013 KH_1: KH domain syndr 62.2 3.9 8.5E-05 22.0 0.7 21 39-60 1-21 (60)
3 PF02880 PGM_PMM_III: Phosphog 62.0 7.6 0.00016 23.6 2.1 22 39-60 22-43 (113)
4 COG3646 Uncharacterized phage- 37.0 20 0.00044 25.3 1.2 15 43-57 13-27 (167)
5 cd02394 vigilin_like_KH K homo 26.4 33 0.00071 18.4 0.7 21 39-60 1-21 (62)
6 PF13871 Helicase_C_4: Helicas 24.9 11 0.00023 28.0 -1.8 12 48-59 14-25 (278)
7 PF04359 DUF493: Protein of un 24.1 96 0.0021 18.2 2.5 26 30-55 48-73 (85)
8 cd05799 PGM2 This CD includes 23.6 68 0.0015 24.0 2.1 25 36-60 305-329 (487)
9 KOG3272|consensus 22.2 34 0.00074 25.4 0.3 10 52-61 75-84 (207)
10 TIGR00719 sda_beta L-serine de 20.1 64 0.0014 22.0 1.3 12 45-56 17-30 (208)
No 1
>KOG2113|consensus
Probab=98.28 E-value=1.7e-07 Score=72.91 Aligned_cols=31 Identities=61% Similarity=0.846 Sum_probs=27.6
Q ss_pred hhcccceeceeeeeeCCchHHHHHHhhcCcCC
Q psy3064 30 LRNKKSANMTECVPVPSSEHVAEIVGRQGFGM 61 (61)
Q Consensus 30 ~~~~ks~n~te~VpVPSsehvaEivgrqGCK~ 61 (61)
.+..+-+||||+|+|| +|||+||||||||||
T Consensus 18 ~~~~~p~nvt~sv~vp-s~~v~~ivg~qg~ki 48 (394)
T KOG2113|consen 18 YRTSIGQNVTESVEVP-SEHVAEIVGRQGCKI 48 (394)
T ss_pred cCCCCCCccceeeecC-cccceeecccCcccc
Confidence 4455559999999999 999999999999997
No 2
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=62.18 E-value=3.9 Score=22.01 Aligned_cols=21 Identities=43% Similarity=0.705 Sum_probs=16.6
Q ss_pred eeeeeeCCchHHHHHHhhcCcC
Q psy3064 39 TECVPVPSSEHVAEIVGRQGFG 60 (61)
Q Consensus 39 te~VpVPSsehvaEivgrqGCK 60 (61)
|+.+.|| ..++.-++|++|..
T Consensus 1 T~~i~vp-~~~~~~iIG~~G~~ 21 (60)
T PF00013_consen 1 TERIEVP-SSLVGRIIGKKGSN 21 (60)
T ss_dssp EEEEEEE-HHHHHHHHTGGGHH
T ss_pred CEEEEEC-HHHcCEEECCCCCc
Confidence 5778888 57888899999853
No 3
>PF02880 PGM_PMM_III: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III; InterPro: IPR005846 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain III found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B 3UW2_A 2F7L_B 3I3W_B 2Z0F_A ....
Probab=61.98 E-value=7.6 Score=23.57 Aligned_cols=22 Identities=32% Similarity=0.303 Sum_probs=19.6
Q ss_pred eeeeeeCCchHHHHHHhhcCcC
Q psy3064 39 TECVPVPSSEHVAEIVGRQGFG 60 (61)
Q Consensus 39 te~VpVPSsehvaEivgrqGCK 60 (61)
+.+++|.+|..+.+++.+.|++
T Consensus 22 ~vv~~v~sS~~~~~~~~~~g~~ 43 (113)
T PF02880_consen 22 TVVVTVVSSRALDKIAEKHGGK 43 (113)
T ss_dssp EEEEETTS-THHHHHHHHTTSE
T ss_pred EEEEeCHHHHHHHHHHHHCCCE
Confidence 7889999999999999999986
No 4
>COG3646 Uncharacterized phage-encoded protein [Function unknown]
Probab=36.98 E-value=20 Score=25.35 Aligned_cols=15 Identities=40% Similarity=0.680 Sum_probs=13.8
Q ss_pred eeCCchHHHHHHhhc
Q psy3064 43 PVPSSEHVAEIVGRQ 57 (61)
Q Consensus 43 pVPSsehvaEivgrq 57 (61)
++.+|.+|||.||+|
T Consensus 13 i~t~S~~IAe~~gkr 27 (167)
T COG3646 13 IVTNSREIAEMVGKR 27 (167)
T ss_pred eeecHHHHHHHHhhh
Confidence 688999999999987
No 5
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=26.36 E-value=33 Score=18.41 Aligned_cols=21 Identities=33% Similarity=0.504 Sum_probs=14.1
Q ss_pred eeeeeeCCchHHHHHHhhcCcC
Q psy3064 39 TECVPVPSSEHVAEIVGRQGFG 60 (61)
Q Consensus 39 te~VpVPSsehvaEivgrqGCK 60 (61)
++.+.||. +.+.-+.|+.|..
T Consensus 1 ~~~i~Vp~-~~~~~iIG~~G~~ 21 (62)
T cd02394 1 TEEVEIPK-KLHRFIIGKKGSN 21 (62)
T ss_pred CeEEEeCH-HHhhhccCCCCCc
Confidence 35677887 4557788887753
No 6
>PF13871 Helicase_C_4: Helicase_C-like
Probab=24.92 E-value=11 Score=27.97 Aligned_cols=12 Identities=58% Similarity=0.877 Sum_probs=10.3
Q ss_pred hHHHHHHhhcCc
Q psy3064 48 EHVAEIVGRQGF 59 (61)
Q Consensus 48 ehvaEivgrqGC 59 (61)
+.||||+||.|+
T Consensus 14 ~~VAEiTGR~~r 25 (278)
T PF13871_consen 14 DKVAEITGRSGR 25 (278)
T ss_pred CeEEEccCCcee
Confidence 479999999985
No 7
>PF04359 DUF493: Protein of unknown function (DUF493); InterPro: IPR007454 This family includes several proteins of uncharacterised function.; PDB: 1RWU_A 2JOQ_A 2H9Z_A.
Probab=24.14 E-value=96 Score=18.20 Aligned_cols=26 Identities=31% Similarity=0.277 Sum_probs=22.0
Q ss_pred hhcccceeceeeeeeCCchHHHHHHh
Q psy3064 30 LRNKKSANMTECVPVPSSEHVAEIVG 55 (61)
Q Consensus 30 ~~~~ks~n~te~VpVPSsehvaEivg 55 (61)
-+..|.+++|..+.|.|.++|-+|-.
T Consensus 48 S~~GkY~Svtv~v~v~s~eq~~~iy~ 73 (85)
T PF04359_consen 48 SSKGKYVSVTVSVTVESAEQVDAIYR 73 (85)
T ss_dssp STTSSEEEEEEEEEESSHHHHHHHHH
T ss_pred CCCCeEEEEEEEEEECCHHHHHHHHH
Confidence 35678899999999999999988754
No 8
>cd05799 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/ph
Probab=23.56 E-value=68 Score=23.97 Aligned_cols=25 Identities=24% Similarity=0.216 Sum_probs=21.7
Q ss_pred eeceeeeeeCCchHHHHHHhhcCcC
Q psy3064 36 ANMTECVPVPSSEHVAEIVGRQGFG 60 (61)
Q Consensus 36 ~n~te~VpVPSsehvaEivgrqGCK 60 (61)
.+...++|+++|..+.+++.+.||+
T Consensus 305 ~~~~vV~~v~sS~~i~~ia~~~g~~ 329 (487)
T cd05799 305 KNPVIVKTIVSSELLRKIAKKYGVK 329 (487)
T ss_pred CCcEEEEeehhHHHHHHHHHHcCCe
Confidence 3446899999999999999999986
No 9
>KOG3272|consensus
Probab=22.25 E-value=34 Score=25.39 Aligned_cols=10 Identities=30% Similarity=0.189 Sum_probs=7.3
Q ss_pred HHHhhcCcCC
Q psy3064 52 EIVGRQGFGM 61 (61)
Q Consensus 52 EivgrqGCK~ 61 (61)
..=-+|||||
T Consensus 75 KaNSIQG~Km 84 (207)
T KOG3272|consen 75 KANSIQGNKM 84 (207)
T ss_pred Hhcccccccc
Confidence 3446899997
No 10
>TIGR00719 sda_beta L-serine dehydratase, iron-sulfur-dependent, beta subunit. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases.
Probab=20.13 E-value=64 Score=22.04 Aligned_cols=12 Identities=42% Similarity=0.531 Sum_probs=8.7
Q ss_pred CCchH--HHHHHhh
Q psy3064 45 PSSEH--VAEIVGR 56 (61)
Q Consensus 45 PSseh--vaEivgr 56 (61)
|||+| +||+.|+
T Consensus 17 psssht~laerlG~ 30 (208)
T TIGR00719 17 PSSSHTAGAAKIAN 30 (208)
T ss_pred CChhHHHHHHHHHH
Confidence 89998 4566665
Done!