Query 035444
Match_columns 55
No_of_seqs 27 out of 29
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 03:01:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035444hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04911 ATP-synt_J: ATP synth 96.1 0.00051 1.1E-08 40.3 -1.8 22 15-36 7-28 (54)
2 PF15176 LRR19-TM: Leucine-ric 87.4 0.096 2.1E-06 34.0 -1.2 17 15-31 13-29 (102)
3 PF08039 Mit_proteolip: Mitoch 58.4 7.1 0.00015 23.4 1.4 34 20-53 23-57 (60)
4 PF04679 DNA_ligase_A_C: ATP d 58.0 6.4 0.00014 23.2 1.2 17 30-46 21-37 (97)
5 KOG3966 p53-mediated apoptosis 56.8 4.2 9E-05 31.3 0.3 21 15-35 254-274 (360)
6 PF11255 DUF3054: Protein of u 55.0 2.1 4.5E-05 27.3 -1.3 18 15-32 30-47 (112)
7 cd08040 OBF_DNA_ligase_family 51.0 8.7 0.00019 23.0 1.0 16 31-46 36-51 (108)
8 cd07971 OBF_DNA_ligase_LigD Th 36.4 23 0.0005 21.4 1.3 15 31-45 35-49 (115)
9 PF03609 EII-Sor: PTS system s 36.3 7.7 0.00017 27.1 -0.9 16 16-31 204-220 (238)
10 cd06144 REX4_like DEDDh 3'-5' 34.1 22 0.00048 22.2 1.0 18 32-50 47-64 (152)
11 cd07968 OBF_DNA_ligase_IV The 32.9 29 0.00063 22.0 1.4 16 31-46 45-60 (140)
12 PF14743 DNA_ligase_OB_2: DNA 32.9 24 0.00053 20.4 1.0 16 33-48 23-38 (66)
13 COG5557 Polysulphide reductase 30.9 19 0.00041 28.2 0.3 27 1-32 44-70 (401)
14 PF04418 DUF543: Domain of unk 29.5 20 0.00043 21.6 0.2 15 10-27 47-61 (75)
15 cd07972 OBF_DNA_ligase_Arch_Li 29.0 38 0.00082 20.9 1.4 16 31-46 38-53 (122)
16 PRK10408 putative L-valine exp 28.8 8.9 0.00019 25.3 -1.5 23 12-34 65-87 (111)
17 PF07204 Orthoreo_P10: Orthore 28.7 16 0.00034 23.7 -0.4 11 16-26 39-49 (98)
18 COG2941 CAT5 Ubiquinone biosyn 27.8 12 0.00027 26.9 -1.0 22 20-42 112-133 (204)
19 cd07969 OBF_DNA_ligase_I The O 26.9 42 0.0009 21.6 1.4 16 31-46 39-54 (144)
20 cd08041 OBF_kDNA_ligase_like T 24.7 54 0.0012 18.7 1.4 14 33-46 34-47 (77)
21 PF09835 DUF2062: Uncharacteri 24.5 22 0.00047 22.4 -0.3 28 6-33 105-132 (154)
22 PF07051 OCIA: Ovarian carcino 24.4 12 0.00026 24.4 -1.5 19 19-37 75-93 (111)
23 KOG4266 Subtilisin kexin isozy 23.8 27 0.00059 29.9 0.1 21 22-42 511-531 (1033)
24 COG5101 CRM1 Importin beta-rel 23.8 35 0.00077 29.4 0.7 16 8-23 123-138 (1053)
25 COG3715 ManY Phosphotransferas 23.3 18 0.00039 26.6 -0.9 12 16-27 203-215 (265)
26 cd07893 OBF_DNA_ligase The Oli 23.0 55 0.0012 20.4 1.4 16 31-46 38-53 (129)
27 PF05520 Citrus_P18: Citrus tr 22.9 44 0.00096 23.1 1.0 29 17-48 23-51 (167)
28 PRK09757 PTS system N-acetylga 22.6 20 0.00043 25.8 -0.8 16 16-31 204-220 (267)
29 PF03642 MAP: MAP domain; Int 20.6 35 0.00076 21.7 0.1 12 37-48 43-54 (88)
30 cd07967 OBF_DNA_ligase_III The 20.1 67 0.0014 20.7 1.3 16 30-45 39-54 (139)
No 1
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=96.14 E-value=0.00051 Score=40.32 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=19.6
Q ss_pred hhhhcchhhhhhheeeeeeeee
Q 035444 15 WNRNWPFLVGFAITGTIITKFS 36 (55)
Q Consensus 15 ~kr~WPFlvGf~vtg~litK~s 36 (55)
+|-||||++|-+|+.++|.|++
T Consensus 7 ~kP~wPFf~ag~iv~ygv~k~~ 28 (54)
T PF04911_consen 7 LKPMWPFFAAGAIVYYGVNKAQ 28 (54)
T ss_pred hhhhhHHHHHHHHHHHHHHHHH
Confidence 5779999999999999999943
No 2
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=87.45 E-value=0.096 Score=34.05 Aligned_cols=17 Identities=47% Similarity=1.036 Sum_probs=13.3
Q ss_pred hhhhcchhhhhhheeee
Q 035444 15 WNRNWPFLVGFAITGTI 31 (55)
Q Consensus 15 ~kr~WPFlvGf~vtg~l 31 (55)
.-+.||||||+.++...
T Consensus 13 ~g~sW~~LVGVv~~al~ 29 (102)
T PF15176_consen 13 GGRSWPFLVGVVVTALV 29 (102)
T ss_pred CCcccHhHHHHHHHHHH
Confidence 36789999999877643
No 3
>PF08039 Mit_proteolip: Mitochondrial proteolipid; InterPro: IPR012574 This family consists of proteins with similarity to the mitochondrial proteolipids. Mitochondrial proteolipid consists of about 60 amino acids residues and is about 6.8 kDa in size [].; GO: 0005739 mitochondrion
Probab=58.36 E-value=7.1 Score=23.43 Aligned_cols=34 Identities=26% Similarity=0.290 Sum_probs=25.9
Q ss_pred chhhhhhheeeeeee-eecccChhhhhCChhhhhc
Q 035444 20 PFLVGFAITGTIITK-FSLGLTEEDAKNSPFVQRH 53 (55)
Q Consensus 20 PFlvGf~vtg~litK-~s~giTeed~knS~f~~~~ 53 (55)
--.||+|..|+|+-| -|.+..-+..|.|.-.-.|
T Consensus 23 EIWVGmGlm~fivYKi~sadkrskalkasspapah 57 (60)
T PF08039_consen 23 EIWVGMGLMGFIVYKIRSADKRSKALKASSPAPAH 57 (60)
T ss_pred HHHHhhhhheeEEEeecccchhHHHHhccCCCCcc
Confidence 345999999999999 4667777777877766544
No 4
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=58.00 E-value=6.4 Score=23.19 Aligned_cols=17 Identities=18% Similarity=0.495 Sum_probs=10.9
Q ss_pred eeeeeeecccChhhhhC
Q 035444 30 TIITKFSLGLTEEDAKN 46 (55)
Q Consensus 30 ~litK~s~giTeed~kn 46 (55)
.-|.|++-|+|+|+++.
T Consensus 21 ~~vg~vgtG~~~~~~~~ 37 (97)
T PF04679_consen 21 VYVGKVGTGFSDEELRE 37 (97)
T ss_dssp EEEEEE-SS--HHHHHH
T ss_pred EEEEEECCCCCHHHHHH
Confidence 45678999999999763
No 5
>KOG3966 consensus p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms; Defense mechanisms]
Probab=56.81 E-value=4.2 Score=31.25 Aligned_cols=21 Identities=29% Similarity=0.805 Sum_probs=15.5
Q ss_pred hhhhcchhhhhhheeeeeeee
Q 035444 15 WNRNWPFLVGFAITGTIITKF 35 (55)
Q Consensus 15 ~kr~WPFlvGf~vtg~litK~ 35 (55)
+.++||++.|||+-=++.|-+
T Consensus 254 iE~nWPYffGFG~PLa~lt~~ 274 (360)
T KOG3966|consen 254 IESNWPYFFGFGTPLALLTSI 274 (360)
T ss_pred HHhcCchhccCCcHHHHHHhh
Confidence 456999999999765555443
No 6
>PF11255 DUF3054: Protein of unknown function (DUF3054); InterPro: IPR021414 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=55.03 E-value=2.1 Score=27.26 Aligned_cols=18 Identities=33% Similarity=0.883 Sum_probs=14.4
Q ss_pred hhhhcchhhhhhheeeee
Q 035444 15 WNRNWPFLVGFAITGTII 32 (55)
Q Consensus 15 ~kr~WPFlvGf~vtg~li 32 (55)
..-.|||++|-.+...+.
T Consensus 30 l~Ta~PFl~Gw~~~~~~~ 47 (112)
T PF11255_consen 30 LRTAWPFLVGWLLGWPLL 47 (112)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 345899999999887765
No 7
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=50.97 E-value=8.7 Score=23.02 Aligned_cols=16 Identities=6% Similarity=0.401 Sum_probs=13.7
Q ss_pred eeeeeecccChhhhhC
Q 035444 31 IITKFSLGLTEEDAKN 46 (55)
Q Consensus 31 litK~s~giTeed~kn 46 (55)
-+.|++-|||++++++
T Consensus 36 ~vg~vgtGf~~~~~~~ 51 (108)
T cd08040 36 AVFSVGTGFSADERRD 51 (108)
T ss_pred EEEEEcCCCCHHHHHH
Confidence 3678999999999976
No 8
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigD and similar ba
Probab=36.41 E-value=23 Score=21.44 Aligned_cols=15 Identities=7% Similarity=0.330 Sum_probs=12.8
Q ss_pred eeeeeecccChhhhh
Q 035444 31 IITKFSLGLTEEDAK 45 (55)
Q Consensus 31 litK~s~giTeed~k 45 (55)
-|.|++-|+|+++++
T Consensus 35 ~vG~vgtG~s~~~~~ 49 (115)
T cd07971 35 YVGRVGTGFSAATLR 49 (115)
T ss_pred EeeeEcCCCCHHHHH
Confidence 456899999999987
No 9
>PF03609 EII-Sor: PTS system sorbose-specific iic component; InterPro: IPR004700 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the sorbose-specific IIC subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=36.26 E-value=7.7 Score=27.10 Aligned_cols=16 Identities=25% Similarity=0.740 Sum_probs=12.1
Q ss_pred hhhcchhh-hhhheeee
Q 035444 16 NRNWPFLV-GFAITGTI 31 (55)
Q Consensus 16 kr~WPFlv-Gf~vtg~l 31 (55)
|++|||++ ||..+.++
T Consensus 204 k~~~~ff~~GF~l~~yl 220 (238)
T PF03609_consen 204 KKYIPFFFLGFVLAAYL 220 (238)
T ss_pred chHHHHHHHHHHHHHHH
Confidence 46999876 88877664
No 10
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=34.05 E-value=22 Score=22.22 Aligned_cols=18 Identities=33% Similarity=0.431 Sum_probs=13.4
Q ss_pred eeeeecccChhhhhCChhh
Q 035444 32 ITKFSLGLTEEDAKNSPFV 50 (55)
Q Consensus 32 itK~s~giTeed~knS~f~ 50 (55)
++++| |||++|.+++.-.
T Consensus 47 ~~~ih-GIt~~~v~~a~~~ 64 (152)
T cd06144 47 RTAVS-GIRPEHLKDAPDF 64 (152)
T ss_pred cccCC-CCCHHHHcCCCCH
Confidence 45566 9999999987643
No 11
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent pro
Probab=32.93 E-value=29 Score=21.96 Aligned_cols=16 Identities=19% Similarity=0.410 Sum_probs=13.6
Q ss_pred eeeeeecccChhhhhC
Q 035444 31 IITKFSLGLTEEDAKN 46 (55)
Q Consensus 31 litK~s~giTeed~kn 46 (55)
-|.|++-|+|+|+++.
T Consensus 45 ~vgkVgtGfs~~~~~~ 60 (140)
T cd07968 45 SFCKVGSGFSDEELDE 60 (140)
T ss_pred EEEEEccCCCHHHHHH
Confidence 5689999999999863
No 12
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=32.90 E-value=24 Score=20.35 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=9.2
Q ss_pred eeeecccChhhhhCCh
Q 035444 33 TKFSLGLTEEDAKNSP 48 (55)
Q Consensus 33 tK~s~giTeed~knS~ 48 (55)
.++.-|+|||++++-.
T Consensus 23 f~iGsG~td~~R~~~~ 38 (66)
T PF14743_consen 23 FKIGSGFTDEEREEPP 38 (66)
T ss_dssp EEE-SS--HHHHHHHH
T ss_pred EEECCCCCHHHHhcCC
Confidence 3566799999998643
No 13
>COG5557 Polysulphide reductase [Energy production and conversion]
Probab=30.88 E-value=19 Score=28.22 Aligned_cols=27 Identities=33% Similarity=0.576 Sum_probs=20.8
Q ss_pred CCccCChhHHHHhhhhhhcchhhhhhheeeee
Q 035444 1 MRKFDPWPIFFRREWNRNWPFLVGFAITGTII 32 (55)
Q Consensus 1 ~~~~~P~~~f~~rE~kr~WPFlvGf~vtg~li 32 (55)
|+.-=||+..+. +||+++|+++.|.++
T Consensus 44 mrN~fpWGlyia-----~~~~fvGlaaGglil 70 (401)
T COG5557 44 MRNGFPWGLYIA-----FDLLFVGLAAGGLIL 70 (401)
T ss_pred ccCCCCchhHHH-----HHHHHHhhccchhHH
Confidence 344457877654 899999999999775
No 14
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=29.49 E-value=20 Score=21.64 Aligned_cols=15 Identities=53% Similarity=1.245 Sum_probs=11.5
Q ss_pred HHHhhhhhhcchhhhhhh
Q 035444 10 FFRREWNRNWPFLVGFAI 27 (55)
Q Consensus 10 f~~rE~kr~WPFlvGf~v 27 (55)
||+| |.||-.+|.|+
T Consensus 47 ~frr---R~~pv~lG~G~ 61 (75)
T PF04418_consen 47 FFRR---RAWPVALGAGF 61 (75)
T ss_pred HHcc---chHHHHhhccc
Confidence 4555 99999888775
No 15
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DN
Probab=28.97 E-value=38 Score=20.89 Aligned_cols=16 Identities=31% Similarity=0.532 Sum_probs=13.4
Q ss_pred eeeeeecccChhhhhC
Q 035444 31 IITKFSLGLTEEDAKN 46 (55)
Q Consensus 31 litK~s~giTeed~kn 46 (55)
-|.|++-|+|+++++.
T Consensus 38 ~vg~vgtG~~~~~~~~ 53 (122)
T cd07972 38 PVGKVATGLTDEELEE 53 (122)
T ss_pred EEEEEccCCCHHHHHH
Confidence 5678999999999864
No 16
>PRK10408 putative L-valine exporter; Provisional
Probab=28.80 E-value=8.9 Score=25.32 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=19.2
Q ss_pred Hhhhhhhcchhhhhhheeeeeee
Q 035444 12 RREWNRNWPFLVGFAITGTIITK 34 (55)
Q Consensus 12 ~rE~kr~WPFlvGf~vtg~litK 34 (55)
-+++.+.+|-++||++.+..+-|
T Consensus 65 ~~~~~k~~ptlvGf~~l~~~fyk 87 (111)
T PRK10408 65 MHDPRKLLPTLVGFLVLGACFYK 87 (111)
T ss_pred HhChHHHHHHHHHHHHHHHHHHH
Confidence 46788899999999998877655
No 17
>PF07204 Orthoreo_P10: Orthoreovirus membrane fusion protein p10; InterPro: IPR009854 This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction [].
Probab=28.68 E-value=16 Score=23.74 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=8.7
Q ss_pred hhhcchhhhhh
Q 035444 16 NRNWPFLVGFA 26 (55)
Q Consensus 16 kr~WPFlvGf~ 26 (55)
.-+||+|++-|
T Consensus 39 ~ayWpyLA~GG 49 (98)
T PF07204_consen 39 VAYWPYLAAGG 49 (98)
T ss_pred HhhhHHhhccc
Confidence 44999999875
No 18
>COG2941 CAT5 Ubiquinone biosynthesis protein COQ7 [Coenzyme metabolism]
Probab=27.84 E-value=12 Score=26.88 Aligned_cols=22 Identities=32% Similarity=0.552 Sum_probs=16.7
Q ss_pred chhhhhhheeeeeeeeecccChh
Q 035444 20 PFLVGFAITGTIITKFSLGLTEE 42 (55)
Q Consensus 20 PFlvGf~vtg~litK~s~giTee 42 (55)
-|++|.+ +|.|=.|.++|+|++
T Consensus 112 ~FalGA~-a~Llgdk~am~~tea 133 (204)
T COG2941 112 AFALGAG-AGLLGDKAAMGFTEA 133 (204)
T ss_pred HHHHHHH-HhhcccHHHHHHHHH
Confidence 3666654 577778899999986
No 19
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=26.89 E-value=42 Score=21.57 Aligned_cols=16 Identities=19% Similarity=0.378 Sum_probs=13.0
Q ss_pred eeeeeecccChhhhhC
Q 035444 31 IITKFSLGLTEEDAKN 46 (55)
Q Consensus 31 litK~s~giTeed~kn 46 (55)
-|.|++-|||+++++.
T Consensus 39 ~vgkvgtGft~~~~~~ 54 (144)
T cd07969 39 TVCKIGTGFSDEFLEE 54 (144)
T ss_pred EEeEEccCCCHHHHHH
Confidence 4569999999999853
No 20
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-de
Probab=24.70 E-value=54 Score=18.69 Aligned_cols=14 Identities=29% Similarity=0.560 Sum_probs=12.0
Q ss_pred eeeecccChhhhhC
Q 035444 33 TKFSLGLTEEDAKN 46 (55)
Q Consensus 33 tK~s~giTeed~kn 46 (55)
.++.-|+|++++++
T Consensus 34 ~~vgtG~t~~~r~~ 47 (77)
T cd08041 34 FKIGSGFSDEQRRN 47 (77)
T ss_pred EEEcCCCCHHHHhc
Confidence 47899999999875
No 21
>PF09835 DUF2062: Uncharacterized protein conserved in bacteria (DUF2062); InterPro: IPR018639 This domain, found in various prokaryotic proteins, has no known function. It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.
Probab=24.48 E-value=22 Score=22.36 Aligned_cols=28 Identities=29% Similarity=0.705 Sum_probs=19.5
Q ss_pred ChhHHHHhhhhhhcchhhhhhheeeeee
Q 035444 6 PWPIFFRREWNRNWPFLVGFAITGTIIT 33 (55)
Q Consensus 6 P~~~f~~rE~kr~WPFlvGf~vtg~lit 33 (55)
.|...+..-...++|+++|-.+.|.+..
T Consensus 105 ~~~~~~~~~~~~~~~~~~G~~i~~~v~~ 132 (154)
T PF09835_consen 105 HWSDLLESLWEFGLPFLLGSLILGIVLG 132 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444454555668999999888877654
No 22
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=24.42 E-value=12 Score=24.40 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=15.7
Q ss_pred cchhhhhhheeeeeeeeec
Q 035444 19 WPFLVGFAITGTIITKFSL 37 (55)
Q Consensus 19 WPFlvGf~vtg~litK~s~ 37 (55)
+|=++-+|+.|+++.|+|-
T Consensus 75 ~PKv~~ag~~Gy~~GK~SY 93 (111)
T PF07051_consen 75 LPKVAFAGILGYFVGKISY 93 (111)
T ss_pred ccHHHHHHHHHHhhhHHHH
Confidence 6788888888999999773
No 23
>KOG4266 consensus Subtilisin kexin isozyme-1/site 1 protease, subtilase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=23.84 E-value=27 Score=29.89 Aligned_cols=21 Identities=29% Similarity=0.433 Sum_probs=16.2
Q ss_pred hhhhhheeeeeeeeecccChh
Q 035444 22 LVGFAITGTIITKFSLGLTEE 42 (55)
Q Consensus 22 lvGf~vtg~litK~s~giTee 42 (55)
|-|+||||+|+.+.++-=.-|
T Consensus 511 LNGmgVtg~Iv~~P~W~P~~e 531 (1033)
T KOG4266|consen 511 LNGMGVTGYIVSPPTWHPANE 531 (1033)
T ss_pred ecccceeeEecCCCCCccCcc
Confidence 569999999999887654433
No 24
>COG5101 CRM1 Importin beta-related nuclear transport receptor [Nuclear structure / Intracellular trafficking and secretion]
Probab=23.81 E-value=35 Score=29.37 Aligned_cols=16 Identities=38% Similarity=1.115 Sum_probs=13.0
Q ss_pred hHHHHhhhhhhcchhh
Q 035444 8 PIFFRREWNRNWPFLV 23 (55)
Q Consensus 8 ~~f~~rE~kr~WPFlv 23 (55)
-|.+++||.|+||=++
T Consensus 123 vqIlKqeWP~nWP~FI 138 (1053)
T COG5101 123 VQILKQEWPRNWPTFI 138 (1053)
T ss_pred HHHHHHhcccccchhh
Confidence 3678999999999654
No 25
>COG3715 ManY Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]
Probab=23.26 E-value=18 Score=26.57 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=7.5
Q ss_pred hhhcchh-hhhhh
Q 035444 16 NRNWPFL-VGFAI 27 (55)
Q Consensus 16 kr~WPFl-vGf~v 27 (55)
|++|||+ .||.+
T Consensus 203 k~~~pff~lGFv~ 215 (265)
T COG3715 203 KELIPFFFLGFVL 215 (265)
T ss_pred cchhHHHHHHHHH
Confidence 5699986 34443
No 26
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and V
Probab=22.97 E-value=55 Score=20.45 Aligned_cols=16 Identities=31% Similarity=0.532 Sum_probs=12.8
Q ss_pred eeeeeecccChhhhhC
Q 035444 31 IITKFSLGLTEEDAKN 46 (55)
Q Consensus 31 litK~s~giTeed~kn 46 (55)
-+.|++-|+|+++++.
T Consensus 38 ~vgkvgtGfs~~~~~~ 53 (129)
T cd07893 38 TICKVGSGFTDEELEE 53 (129)
T ss_pred EEeEECCCCCHHHHHH
Confidence 3568999999999853
No 27
>PF05520 Citrus_P18: Citrus tristeza virus P18 protein; InterPro: IPR008452 This family contains the P18 proteins of citrus tristeza virus (CTV). CTV is a member of the closterovirus group and is one of the more complex single-stranded RNA viruses. Assembly of the viral genome into virions is a critical process of the virus life cycle often defining the ability of the virus to move within the plant and to be transmitted horizontally to other plants. Closteroviridae virions are polar helical rods assembled primarily by a major coat protein, but with a related minor coat protein at one end. It is the only virus family that encodes a protein with similarity to cellular chaperones, a 70kDa heat-shock protein homologue (HSP70h). Deletion mutagenesis reveals that p33, p6, p18, p13, p20, and p23 genes are not needed for virion formation. Their function is unknown [].
Probab=22.92 E-value=44 Score=23.09 Aligned_cols=29 Identities=41% Similarity=0.715 Sum_probs=24.4
Q ss_pred hhcchhhhhhheeeeeeeeecccChhhhhCCh
Q 035444 17 RNWPFLVGFAITGTIITKFSLGLTEEDAKNSP 48 (55)
Q Consensus 17 r~WPFlvGf~vtg~litK~s~giTeed~knS~ 48 (55)
-.|.|++. .|-||+...+-+..||.-||-
T Consensus 23 gwwsfivn---vgdiivrfalhvpsedvlnsf 51 (167)
T PF05520_consen 23 GWWSFIVN---VGDIIVRFALHVPSEDVLNSF 51 (167)
T ss_pred hhhheeee---cccEEEEEEeeCCcHHHHhhh
Confidence 36888876 578999999999999999874
No 28
>PRK09757 PTS system N-acetylgalactosamine-specific transporter subunit IIC; Provisional
Probab=22.57 E-value=20 Score=25.83 Aligned_cols=16 Identities=25% Similarity=0.565 Sum_probs=11.0
Q ss_pred hhhcch-hhhhhheeee
Q 035444 16 NRNWPF-LVGFAITGTI 31 (55)
Q Consensus 16 kr~WPF-lvGf~vtg~l 31 (55)
|++||| ++||..+.|+
T Consensus 204 k~~~~ff~lGF~l~ayl 220 (267)
T PRK09757 204 AQYIPYLIAGFLFVCYI 220 (267)
T ss_pred cchHHHHHHHHHHHHHh
Confidence 558885 5788776665
No 29
>PF03642 MAP: MAP domain; InterPro: IPR005298 Map (MHC class II analogous protein), also known as eap (extracellular adherence protein) and p70, is exclusively found in Staphylococcus aureus. It is a cell-wall associated protein, which is capable of binding to a number of different extracellular matrix glycoploteins and plasma proteins, and to the cell surface of S. aureus. Besides the broad binding specificity, map has been shown to be important in the adherence to and internalization of S. aureus by eukaryotic cells as well as being capable of modulating inflammatory response through its interactions with ICAM-1 (intercellular adhesion molecule-1), although its biological role in vivo remains to date unclear []. The protein consists of a signal peptide followed by a unique sequence of about 20 amino acids and four to six repeated MAP domains of 110-amino acid residues. Within each repeat there is a subdomain consisting of 31 residues that was found to be highly homologous to the N-terminal beta-chain of many MHC class II molecules []. This entry represents the MAP domain. The crystal structure of this domain has been solved and shows a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. This structure is very similar to the C-terminal domain of bacterial superantigens [].; PDB: 1YN4_A 1YN3_A 1YN5_B.
Probab=20.61 E-value=35 Score=21.70 Aligned_cols=12 Identities=33% Similarity=0.484 Sum_probs=7.2
Q ss_pred cccChhhhhCCh
Q 035444 37 LGLTEEDAKNSP 48 (55)
Q Consensus 37 ~giTeed~knS~ 48 (55)
=|||++|+++|+
T Consensus 43 rGIt~~di~~Ak 54 (88)
T PF03642_consen 43 RGITDHDIKLAK 54 (88)
T ss_dssp H---HHHHHHSS
T ss_pred cCCCHHHhhhhh
Confidence 389999998875
No 30
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic proph
Probab=20.12 E-value=67 Score=20.71 Aligned_cols=16 Identities=19% Similarity=0.212 Sum_probs=13.2
Q ss_pred eeeeeeecccChhhhh
Q 035444 30 TIITKFSLGLTEEDAK 45 (55)
Q Consensus 30 ~litK~s~giTeed~k 45 (55)
.-+.|+.-|+|+++.+
T Consensus 39 ~~vgkVGTGfs~~~l~ 54 (139)
T cd07967 39 CTVTKCGNGHDDATLA 54 (139)
T ss_pred EEEeEECCCCCHHHHH
Confidence 3567899999999875
Done!