Query 048473
Match_columns 81
No_of_seqs 23 out of 25
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 09:50:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048473hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10784 Plasmid_stab_B: Plasm 54.0 5.7 0.00012 25.8 0.6 32 37-68 17-59 (72)
2 COG3449 DNA gyrase inhibitor [ 48.3 12 0.00027 27.3 1.6 17 2-18 41-57 (154)
3 cd03195 GST_C_4 GST_C family, 45.5 12 0.00027 23.5 1.1 32 41-72 57-88 (114)
4 PRK13893 conjugal transfer pro 45.4 13 0.00028 28.5 1.5 35 41-76 69-104 (193)
5 PF04695 Pex14_N: Peroxisomal 44.9 19 0.00041 24.5 2.1 34 39-73 3-36 (136)
6 PF07424 TrbM: TrbM; InterPro 42.8 15 0.00032 27.3 1.4 35 41-76 43-78 (165)
7 PRK10177 putative invasin; Pro 41.8 12 0.00026 31.8 0.8 26 5-31 171-196 (465)
8 PF12419 DUF3670: SNF2 Helicas 40.7 14 0.0003 25.1 0.9 43 30-72 81-126 (141)
9 cd08577 PI-PLCc_GDPD_SF_unchar 40.0 19 0.0004 26.6 1.5 59 11-72 140-199 (228)
10 PF02071 NSF: Aromatic-di-Alan 38.6 5.6 0.00012 18.3 -0.9 9 72-80 1-9 (12)
11 COG3108 Uncharacterized protei 37.4 33 0.00071 26.1 2.5 37 34-70 62-98 (185)
12 TIGR03114 cas_csf1 CRISPR-asso 33.2 22 0.00047 27.6 1.0 21 57-77 176-196 (202)
13 PF02728 Cu_amine_oxidN3: Copp 30.1 37 0.00079 21.6 1.5 29 46-74 1-32 (101)
14 COG4154 FucU Fucose dissimilat 29.7 41 0.00089 24.9 1.9 21 53-73 2-23 (144)
15 TIGR00758 UDG_fam4 uracil-DNA 29.5 24 0.00052 24.4 0.6 21 40-60 83-103 (173)
16 cd06403 PB1_Par6 The PB1 domai 26.7 36 0.00078 22.9 1.1 18 33-50 57-74 (80)
17 PRK14614 4-diphosphocytidyl-2- 25.8 40 0.00087 24.8 1.3 29 47-75 208-240 (280)
18 PRK11190 Fe/S biogenesis prote 24.6 52 0.0011 24.1 1.7 18 35-52 108-126 (192)
19 PF01106 NifU: NifU-like domai 24.5 39 0.00086 20.7 0.9 14 39-52 2-15 (68)
20 PRK13186 lpxC UDP-3-O-[3-hydro 23.6 35 0.00076 26.9 0.6 40 7-51 153-192 (295)
21 PRK15318 intimin-like protein 23.4 32 0.00069 30.9 0.4 23 7-30 171-193 (730)
22 PRK05362 phosphopentomutase; P 23.1 47 0.001 27.0 1.3 22 50-72 214-235 (394)
23 PF10691 DUF2497: Protein of u 22.8 37 0.00081 21.8 0.6 31 35-68 32-63 (73)
24 COG3285 Predicted eukaryotic-t 22.6 27 0.00058 28.3 -0.2 48 18-66 220-274 (299)
25 smart00759 Flu_M1_C Influenza 22.0 39 0.00084 23.6 0.6 20 55-74 47-66 (95)
26 PF12010 DUF3502: Domain of un 20.5 30 0.00064 23.3 -0.3 28 45-73 89-116 (134)
27 TIGR00325 lpxC UDP-3-0-acyl N- 20.1 1E+02 0.0022 24.4 2.6 41 4-49 147-189 (297)
No 1
>PF10784 Plasmid_stab_B: Plasmid stability protein; InterPro: IPR019720 This family is conserved in the Enterobacteriales. It is a putative plasmid stability protein in that it is expressed from the operon involved in stability, but its actual function has not yet been characterised but it may be involved in the control of plasmid partition.; PDB: 2JD3_A.
Probab=54.01 E-value=5.7 Score=25.84 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=20.8
Q ss_pred hHHHHHHhcccchhhh-----------hhhcCcCchHHHHHHH
Q 048473 37 YLETLVASARPFLRGE-----------LEAIDKNLPSLIVVLR 68 (81)
Q Consensus 37 ~l~~lla~aRPFLRgd-----------le~iDp~LPslisVLr 68 (81)
...+.++..-+=.||| +-++||+||.+|+.+-
T Consensus 17 ~a~~~iesv~~~~Rgdf~R~aliaG~aL~~~dprLP~lLa~~~ 59 (72)
T PF10784_consen 17 RACATIESVPQRERGDFQRAALIAGLALHQLDPRLPYLLAALF 59 (72)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHHHHHHHHH-THHHHHHHHH-
T ss_pred HHHHHHHccCHhHhhHHHHHHHHHHHHHHhcChHHHHHHHHHh
Confidence 3445566666666666 4578999999998874
No 2
>COG3449 DNA gyrase inhibitor [DNA replication, recombination, and repair]
Probab=48.32 E-value=12 Score=27.29 Aligned_cols=17 Identities=35% Similarity=0.536 Sum_probs=15.4
Q ss_pred CCCCccceeeeeecccc
Q 048473 2 LSPSSSFSFNIFFDHPL 18 (81)
Q Consensus 2 ~~~~~~~~~~~~~~~~l 18 (81)
|+|.+|+-|||+.|+|=
T Consensus 41 l~p~~S~~~gI~~ddP~ 57 (154)
T COG3449 41 LLPEQSETLGIYQDDPD 57 (154)
T ss_pred CCCCCceEEEEecCCCC
Confidence 67889999999999986
No 3
>cd03195 GST_C_4 GST_C family, unknown subfamily 4; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain.
Probab=45.46 E-value=12 Score=23.46 Aligned_cols=32 Identities=25% Similarity=0.251 Sum_probs=24.1
Q ss_pred HHHhcccchhhhhhhcCcCchHHHHHHHHcCC
Q 048473 41 LVASARPFLRGELEAIDKNLPSLIVVLRSVGA 72 (81)
Q Consensus 41 lla~aRPFLRgdle~iDp~LPslisVLrS~GA 72 (81)
+++..+|||-||+.-.|.-|-..+.-++..|-
T Consensus 57 ~l~~~~~~l~G~fSiAD~~l~~~~~~~~~~g~ 88 (114)
T cd03195 57 LLPPGAANLFGEWCIADTDLALMLNRLVLNGD 88 (114)
T ss_pred HHhcCCCcccCCccHHHHHHHHHHHHHHHcCC
Confidence 44445599999988889988877777766663
No 4
>PRK13893 conjugal transfer protein TrbM; Provisional
Probab=45.41 E-value=13 Score=28.47 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=27.1
Q ss_pred HHHhcccchhh-hhhhcCcCchHHHHHHHHcCCcccc
Q 048473 41 LVASARPFLRG-ELEAIDKNLPSLIVVLRSVGAGEST 76 (81)
Q Consensus 41 lla~aRPFLRg-dle~iDp~LPslisVLrS~GAgECw 76 (81)
-+.+=|-||.. --..-||+.+.|+..+ +.|||+|-
T Consensus 69 T~~aR~~FLn~CP~a~~dp~~~~Lv~aI-~~gaG~Cd 104 (193)
T PRK13893 69 TIKARLNFLQLCPVANQTPEMQSLVSAI-SRGAGRCD 104 (193)
T ss_pred HHHHHHHHHhcCCCCcCChhHHHHHHHH-hccCCCcC
Confidence 35566778877 3334699999999999 88999994
No 5
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=44.87 E-value=19 Score=24.53 Aligned_cols=34 Identities=29% Similarity=0.374 Sum_probs=25.2
Q ss_pred HHHHHhcccchhhhhhhcCcCchHHHHHHHHcCCc
Q 048473 39 ETLVASARPFLRGELEAIDKNLPSLIVVLRSVGAG 73 (81)
Q Consensus 39 ~~lla~aRPFLRgdle~iDp~LPslisVLrS~GAg 73 (81)
+++|+.|+-||+++ .--|.-+-.-++-|++-|-.
T Consensus 3 e~li~~A~~FL~~p-~V~~sp~~~k~~FL~sKGLt 36 (136)
T PF04695_consen 3 EDLIEQAVKFLQDP-KVRNSPLEKKIAFLESKGLT 36 (136)
T ss_dssp HHHHHHHHHHHCTT-TCCCS-HHHHHHHHHHCT--
T ss_pred HHHHHHHHHHhCCc-ccccCCHHHHHHHHHcCCCC
Confidence 57899999999976 32366688889999988854
No 6
>PF07424 TrbM: TrbM; InterPro: IPR009989 This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulphonate (TSA) degradation [].
Probab=42.76 E-value=15 Score=27.33 Aligned_cols=35 Identities=23% Similarity=0.347 Sum_probs=25.2
Q ss_pred HHHhcccchhhhhh-hcCcCchHHHHHHHHcCCcccc
Q 048473 41 LVASARPFLRGELE-AIDKNLPSLIVVLRSVGAGEST 76 (81)
Q Consensus 41 lla~aRPFLRgdle-~iDp~LPslisVLrS~GAgECw 76 (81)
-+.+=|-||..==. .=|+++|+++.. -+.|||+|-
T Consensus 43 T~~aR~~FL~~Cp~~~~~~~m~~Lv~a-i~ngagrCd 78 (165)
T PF07424_consen 43 TIDARKNFLNLCPTADSDPEMPKLVNA-IANGAGRCD 78 (165)
T ss_pred HHHHHHHHHhcCCCCCCchhHHHHHHH-HhcCCCCcC
Confidence 35555678764321 228999999999 789999993
No 7
>PRK10177 putative invasin; Provisional
Probab=41.76 E-value=12 Score=31.79 Aligned_cols=26 Identities=15% Similarity=0.163 Sum_probs=20.3
Q ss_pred CccceeeeeeccccccccCCCCCCCCC
Q 048473 5 SSSFSFNIFFDHPLIFNQNSTMPSQLG 31 (81)
Q Consensus 5 ~~~~~~~~~~~~~l~f~qns~m~s~~~ 31 (81)
.--+..|.||||.+. .+|+|++-+.|
T Consensus 171 ~wmlG~N~F~D~dls-~~h~R~glGaE 196 (465)
T PRK10177 171 NWLLGYNTFYDNLLD-ENLQRAGFGAE 196 (465)
T ss_pred CeEEEeEEEEccCCC-CCcceeeccce
Confidence 345778999999998 66789887743
No 8
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=40.73 E-value=14 Score=25.11 Aligned_cols=43 Identities=23% Similarity=0.420 Sum_probs=34.1
Q ss_pred CCCCCCchHHHHHHhcccc--hhhhhhhcCc-CchHHHHHHHHcCC
Q 048473 30 LGNINNDYLETLVASARPF--LRGELEAIDK-NLPSLIVVLRSVGA 72 (81)
Q Consensus 30 ~~~~~~~~l~~lla~aRPF--LRgdle~iDp-~LPslisVLrS~GA 72 (81)
-+....+.+..+++..+|+ +||.|-.||| .+-...+.+...+.
T Consensus 81 d~~Ls~eEf~~L~~~~~~LV~~rg~WV~ld~~~l~~~~~~~~~~~~ 126 (141)
T PF12419_consen 81 DEELSEEEFEQLVEQKRPLVRFRGRWVELDPEELRRALAFLEKAPK 126 (141)
T ss_pred CEECCHHHHHHHHHcCCCeEEECCEEEEECHHHHHHHHHHHHhccc
Confidence 3566678899999999998 5799999999 66777777776554
No 9
>cd08577 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=40.00 E-value=19 Score=26.58 Aligned_cols=59 Identities=19% Similarity=0.187 Sum_probs=31.9
Q ss_pred eeeeccccccccCCCCCCCCCCCCCchHHHHHHhcccchhhhhhhc-CcCchHHHHHHHHcCC
Q 048473 11 NIFFDHPLIFNQNSTMPSQLGNINNDYLETLVASARPFLRGELEAI-DKNLPSLIVVLRSVGA 72 (81)
Q Consensus 11 ~~~~~~~l~f~qns~m~s~~~~~~~~~l~~lla~aRPFLRgdle~i-Dp~LPslisVLrS~GA 72 (81)
-||||-||....+...++...++.+..+......- -+|.+..= =-.|++.+...++.|-
T Consensus 140 ~~f~D~~l~~~~~~~~~~~~~~~~S~~~~~~~~~~---~~g~~~~~q~~~l~~~v~~a~~~Gl 199 (228)
T cd08577 140 YIFFDGRLDEDLPDEQLARLSPMISASFAKFSKWN---GKGDTPEDEKEKLKSIIDKAHARGK 199 (228)
T ss_pred eEEEeCChhhccccccccccceEEEccHHHhcCCC---CCCCCCHHHHHHHHHHHHHHHHCCC
Confidence 48999999865555555555556666666652211 12221110 0145666666666654
No 10
>PF02071 NSF: Aromatic-di-Alanine (AdAR) repeat ; InterPro: IPR000744 Regulated exocytosis of neurotransmitters and hormones, as well as intracellular traffic, requires fusion of two lipid bilayers. SNARE proteins are thought to form a protein bridge, the SNARE complex, between an incoming vesicle and the acceptor compartment. SNARE proteins contribute to the specificity of membrane fusion, implying that the mechanisms by which SNAREs are targeted to subcellular compartments are important for specific docking and fusion of vesicles. This mechanism involves a family of conserved proteins, members of which appear to function at all sites of constitutive and regulated secretion in eukaryotes []. Among them are 2 types of cytosolic protein, NSF (N-ethyl-maleimide-sensitive protein) and the SNAPs (alpha-, beta- and gamma-soluble NSF attachment proteins). The yeast vesicular fusion protein, sec17, a cytoplasmic peripheral membrane protein involved in vesicular transport between the endoplasmic reticulum and the golgi apparatus, shows a high degree of sequence similarity to the alpha-SNAP family. SNAP-25 and its non-neuronal homologue Syndet/SNAP-23 are synthesized as soluble proteins in the cytosol. Both SNAP-25 and Syndet/SNAP-23 are palmitoylated at cysteine residues clustered in a loop between two N- and C-terminal coils and palmitoylation is essential for membrane binding and plasma membrane targeting. The C-terminal and the N-terminal helices of SNAP-25, are each targeted to the plasma membrane by two distinct cysteine-rich domains and appear to regulate the availability of SNAP to form complexes with SNARE [].; GO: 0006886 intracellular protein transport
Probab=38.55 E-value=5.6 Score=18.32 Aligned_cols=9 Identities=33% Similarity=0.054 Sum_probs=5.8
Q ss_pred CcccccccC
Q 048473 72 AGESTEGAH 80 (81)
Q Consensus 72 AgECwHKhg 80 (81)
|+.||.|++
T Consensus 1 A~~~y~~Aa 9 (12)
T PF02071_consen 1 AIKCYEKAA 9 (12)
T ss_pred CcHHHHHHH
Confidence 566777654
No 11
>COG3108 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.36 E-value=33 Score=26.10 Aligned_cols=37 Identities=22% Similarity=0.308 Sum_probs=29.9
Q ss_pred CCchHHHHHHhcccchhhhhhhcCcCchHHHHHHHHc
Q 048473 34 NNDYLETLVASARPFLRGELEAIDKNLPSLIVVLRSV 70 (81)
Q Consensus 34 ~~~~l~~lla~aRPFLRgdle~iDp~LPslisVLrS~ 70 (81)
.-..|..|=-.+|=|.++|--.+||.||.++..|..+
T Consensus 62 ~~a~L~~L~rl~rd~r~ne~~~mdp~l~dlv~~l~~~ 98 (185)
T COG3108 62 DQASLSGLNRLLRDWRQNEVVRMDPRLFDLVYQLKTL 98 (185)
T ss_pred CHHHHHHHHHhchHhhhCCceecCcchHHHHHHHHHH
Confidence 3455667777778899999999999999999988643
No 12
>TIGR03114 cas_csf1 CRISPR-associated protein, Csf1 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf1 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies closest to the repeats.
Probab=33.20 E-value=22 Score=27.58 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=18.8
Q ss_pred CcCchHHHHHHHHcCCccccc
Q 048473 57 DKNLPSLIVVLRSVGAGESTE 77 (81)
Q Consensus 57 Dp~LPslisVLrS~GAgECwH 77 (81)
+|.+|.-+.+|+|.+-||-|-
T Consensus 176 ~pa~~~A~~~Lqs~~vGE~W~ 196 (202)
T TIGR03114 176 APAYPEAYQLLQSLTVGETWA 196 (202)
T ss_pred ChhhHHHHHHHHhcCchHHHH
Confidence 678899999999999999883
No 13
>PF02728 Cu_amine_oxidN3: Copper amine oxidase, N3 domain; InterPro: IPR015802 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents one (N3) of the two N-terminal domains (N2/N3) that share a similar structure.; GO: 0005507 copper ion binding, 0008131 primary amine oxidase activity, 0048038 quinone binding, 0009308 amine metabolic process, 0055114 oxidation-reduction process; PDB: 1TU5_A 2PNC_B 3MPH_B 3HII_B 3HI7_A 3K5T_A 3HIG_A 1SPU_A 2WGQ_A 2WO0_A ....
Probab=30.11 E-value=37 Score=21.63 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=20.3
Q ss_pred ccchhhhhhhcCc---CchHHHHHHHHcCCcc
Q 048473 46 RPFLRGELEAIDK---NLPSLIVVLRSVGAGE 74 (81)
Q Consensus 46 RPFLRgdle~iDp---~LPslisVLrS~GAgE 74 (81)
+|++.+|++.+.. +-|.+.+.|+.+|-..
T Consensus 1 ppi~~~E~~~~~~~~~~~p~~~~al~~rgi~d 32 (101)
T PF02728_consen 1 PPITLEEFAEAEEIVKADPEFQAALKKRGITD 32 (101)
T ss_dssp S---HHHHHHHHHHHHTGHHHHHHHHHTTCSC
T ss_pred CCcCHHHHHHHHHHHHHCHHHHHHHHHhCCCC
Confidence 5777788776644 7899999999999554
No 14
>COG4154 FucU Fucose dissimilation pathway protein FucU [Carbohydrate transport and metabolism]
Probab=29.69 E-value=41 Score=24.91 Aligned_cols=21 Identities=43% Similarity=0.741 Sum_probs=17.0
Q ss_pred hhhcCcCc-hHHHHHHHHcCCc
Q 048473 53 LEAIDKNL-PSLIVVLRSVGAG 73 (81)
Q Consensus 53 le~iDp~L-PslisVLrS~GAg 73 (81)
|..|+|.| |.++..||+.|=|
T Consensus 2 LK~I~p~LspdlL~tLr~MGHG 23 (144)
T COG4154 2 LKGISPLLSPDLLKTLREMGHG 23 (144)
T ss_pred CCCCCcccCHHHHHHHHHhCCC
Confidence 34578866 8999999999966
No 15
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4. This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity.
Probab=29.54 E-value=24 Score=24.41 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=17.9
Q ss_pred HHHHhcccchhhhhhhcCcCc
Q 048473 40 TLVASARPFLRGELEAIDKNL 60 (81)
Q Consensus 40 ~lla~aRPFLRgdle~iDp~L 60 (81)
.-++.++|||+.+++.|.|++
T Consensus 83 ~Ei~~c~~~l~~eI~~v~P~~ 103 (173)
T TIGR00758 83 EEVEACAPYLVKQIELIRPKV 103 (173)
T ss_pred HHHHHHHHHHHHHHHhcCCCE
Confidence 447889999999999999964
No 16
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=26.67 E-value=36 Score=22.87 Aligned_cols=18 Identities=39% Similarity=0.569 Sum_probs=15.6
Q ss_pred CCCchHHHHHHhcccchh
Q 048473 33 INNDYLETLVASARPFLR 50 (81)
Q Consensus 33 ~~~~~l~~lla~aRPFLR 50 (81)
..|+++...+..|+|.||
T Consensus 57 nNDdNf~kAlssa~plLR 74 (80)
T cd06403 57 NNDDNFLKALSSANPLLR 74 (80)
T ss_pred cCcHHHHHHHHcCCCceE
Confidence 357789999999999998
No 17
>PRK14614 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=25.76 E-value=40 Score=24.81 Aligned_cols=29 Identities=24% Similarity=0.219 Sum_probs=23.5
Q ss_pred cchhhhhhh----cCcCchHHHHHHHHcCCccc
Q 048473 47 PFLRGELEA----IDKNLPSLIVVLRSVGAGES 75 (81)
Q Consensus 47 PFLRgdle~----iDp~LPslisVLrS~GAgEC 75 (81)
.++.+|++. ..|+|..++..+++.||--|
T Consensus 208 ~~~~ndle~~~~~~~p~l~~i~~~~~~~Galga 240 (280)
T PRK14614 208 ALLSNDLESVTIGRFPVIGEIKEELLAAGARGS 240 (280)
T ss_pred hhcccCcHHHHHhcChHHHHHHHHHHhCCCCEE
Confidence 456799887 47999999999999998433
No 18
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=24.62 E-value=52 Score=24.08 Aligned_cols=18 Identities=22% Similarity=0.385 Sum_probs=13.4
Q ss_pred CchHHHHHH-hcccchhhh
Q 048473 35 NDYLETLVA-SARPFLRGE 52 (81)
Q Consensus 35 ~~~l~~lla-~aRPFLRgd 52 (81)
-..+..+|+ ..||+|+.|
T Consensus 108 ~~~i~~~l~~~irP~l~~d 126 (192)
T PRK11190 108 MERVEYVLQSQINPQLAGH 126 (192)
T ss_pred HHHHHHHHHhccChhHHhc
Confidence 345677886 899999854
No 19
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=24.54 E-value=39 Score=20.67 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=11.5
Q ss_pred HHHHHhcccchhhh
Q 048473 39 ETLVASARPFLRGE 52 (81)
Q Consensus 39 ~~lla~aRPFLRgd 52 (81)
+++|+..||.|+.|
T Consensus 2 ~~~l~~IrP~L~~d 15 (68)
T PF01106_consen 2 EEVLEEIRPYLQSD 15 (68)
T ss_dssp HHHHHHCHHHHHHT
T ss_pred HHHHHHhChHHHhc
Confidence 57788899999854
No 20
>PRK13186 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=23.57 E-value=35 Score=26.91 Aligned_cols=40 Identities=30% Similarity=0.340 Sum_probs=28.4
Q ss_pred cceeeeeeccccccccCCCCCCCCCCCCCchHHHHHHhcccchhh
Q 048473 7 SFSFNIFFDHPLIFNQNSTMPSQLGNINNDYLETLVASARPFLRG 51 (81)
Q Consensus 7 ~~~~~~~~~~~l~f~qns~m~s~~~~~~~~~l~~lla~aRPFLRg 51 (81)
.+++-|-|+||.+=+|.-++.-+ .+...+-++.||=|-.-
T Consensus 153 ~i~~~idf~~~~ig~Q~~~~~~~-----~~~f~~eIa~ARTF~f~ 192 (295)
T PRK13186 153 RLDFTIDFDHPAIGRQSYSLDFS-----PESFVREIARARTFGFM 192 (295)
T ss_pred EEEEEEECCCCccceEEEEEeCC-----HHHHHHhccCCcccCcH
Confidence 44567889999998888776433 22455568999998653
No 21
>PRK15318 intimin-like protein SinH; Provisional
Probab=23.36 E-value=32 Score=30.87 Aligned_cols=23 Identities=17% Similarity=0.220 Sum_probs=18.8
Q ss_pred cceeeeeeccccccccCCCCCCCC
Q 048473 7 SFSFNIFFDHPLIFNQNSTMPSQL 30 (81)
Q Consensus 7 ~~~~~~~~~~~l~f~qns~m~s~~ 30 (81)
-+..|.||||.+. .+++|++-+.
T Consensus 171 MlG~NaFyD~d~s-~~h~R~GlGa 193 (730)
T PRK15318 171 LLGGNIFYDYDFT-RGHRRLGLGT 193 (730)
T ss_pred EEEeEEEEccCCC-CCcceeeeee
Confidence 3678999999998 6788888773
No 22
>PRK05362 phosphopentomutase; Provisional
Probab=23.14 E-value=47 Score=26.97 Aligned_cols=22 Identities=18% Similarity=0.453 Sum_probs=17.6
Q ss_pred hhhhhhcCcCchHHHHHHHHcCC
Q 048473 50 RGELEAIDKNLPSLIVVLRSVGA 72 (81)
Q Consensus 50 Rgdle~iDp~LPslisVLrS~GA 72 (81)
|-|+. |+|.-|.+++.|+.+|-
T Consensus 214 r~d~~-~~p~~~Tl~d~L~~aG~ 235 (394)
T PRK05362 214 RHDYA-LKPPAPTVLDKLKEAGG 235 (394)
T ss_pred cCCcC-cCCCCCCHHHHHHHCCC
Confidence 44655 88989999999998874
No 23
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=22.77 E-value=37 Score=21.84 Aligned_cols=31 Identities=42% Similarity=0.608 Sum_probs=20.3
Q ss_pred CchHHHHH-HhcccchhhhhhhcCcCchHHHHHHH
Q 048473 35 NDYLETLV-ASARPFLRGELEAIDKNLPSLIVVLR 68 (81)
Q Consensus 35 ~~~l~~ll-a~aRPFLRgdle~iDp~LPslisVLr 68 (81)
+..++.++ +.-||.|+. =+|-+||.++.-|-
T Consensus 32 ~~TlE~lvremLRPmLke---WLD~nLP~lVErlV 63 (73)
T PF10691_consen 32 GRTLEDLVREMLRPMLKE---WLDENLPGLVERLV 63 (73)
T ss_pred cccHHHHHHHHHHHHHHH---HHHhccHHHHHHHH
Confidence 34455544 345777763 47899999987664
No 24
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=22.64 E-value=27 Score=28.26 Aligned_cols=48 Identities=15% Similarity=0.161 Sum_probs=30.3
Q ss_pred cccccCCCCCCCCCCCCCchHHHHHHhcccchhhhhhhcC-c------CchHHHHH
Q 048473 18 LIFNQNSTMPSQLGNINNDYLETLVASARPFLRGELEAID-K------NLPSLIVV 66 (81)
Q Consensus 18 l~f~qns~m~s~~~~~~~~~l~~lla~aRPFLRgdle~iD-p------~LPslisV 66 (81)
+||+||+++.+.-.|+.-..- +-.-++-|.-..|++..| | .+|++++.
T Consensus 220 lDylrN~rg~T~vapYS~Rar-~g~~Vs~Pl~W~el~~~~~p~~ft~~tvp~rl~~ 274 (299)
T COG3285 220 LDYLRNARGKTAVAPYSPRAR-PGATVSTPLTWEELEGLLAPDQFTIRTVPERLAK 274 (299)
T ss_pred EEecccCCCceeecccCccCC-CCCcccccccHHHhcCccChhhccccchHHHHHh
Confidence 579999999887444432211 123456678888888887 5 45555544
No 25
>smart00759 Flu_M1_C Influenza Matrix protein (M1) C-terminal domain. This region is thought to be a second domain of the M1 matrix protein.
Probab=22.04 E-value=39 Score=23.57 Aligned_cols=20 Identities=35% Similarity=0.489 Sum_probs=16.3
Q ss_pred hcCcCchHHHHHHHHcCCcc
Q 048473 55 AIDKNLPSLIVVLRSVGAGE 74 (81)
Q Consensus 55 ~iDp~LPslisVLrS~GAgE 74 (81)
+|-.++.+-|.+||++||+-
T Consensus 47 eiA~qa~~mi~alRsiGahp 66 (95)
T smart00759 47 EIAEEAQQMIGALRSIGAHP 66 (95)
T ss_pred HHHHHHHHHHHHHHHhcCCC
Confidence 45557889999999999964
No 26
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=20.53 E-value=30 Score=23.33 Aligned_cols=28 Identities=21% Similarity=0.406 Sum_probs=22.9
Q ss_pred cccchhhhhhhcCcCchHHHHHHHHcCCc
Q 048473 45 ARPFLRGELEAIDKNLPSLIVVLRSVGAG 73 (81)
Q Consensus 45 aRPFLRgdle~iDp~LPslisVLrS~GAg 73 (81)
..|+.-|-.+ +|..||.++.-|.++|..
T Consensus 89 ~~~L~~G~vd-~e~~~~~~~~kLk~AGid 116 (134)
T PF12010_consen 89 YPPLETGLVD-PEEALPEFNEKLKAAGID 116 (134)
T ss_pred HHHHHccCCC-HHHHHHHHHHHHHHhChH
Confidence 3667777776 778999999999999953
No 27
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=20.09 E-value=1e+02 Score=24.45 Aligned_cols=41 Identities=37% Similarity=0.455 Sum_probs=29.5
Q ss_pred CCc--cceeeeeeccccccccCCCCCCCCCCCCCchHHHHHHhcccch
Q 048473 4 PSS--SFSFNIFFDHPLIFNQNSTMPSQLGNINNDYLETLVASARPFL 49 (81)
Q Consensus 4 ~~~--~~~~~~~~~~~l~f~qns~m~s~~~~~~~~~l~~lla~aRPFL 49 (81)
|+. +++|-|-|+||.+=+|.-++.-+ ......-++.||=|=
T Consensus 147 P~~~~~i~~~Idf~~~~ig~Q~~~~~~~-----~~~f~~eIA~ARTFg 189 (297)
T TIGR00325 147 PYNGFRLDFTIDFNHPAIGKQWYTMNFS-----AEAFATQIARARTFG 189 (297)
T ss_pred cCCCcEEEEEEECCCCcccceEEEEeCC-----HHHHHHHhcCCceEE
Confidence 444 45678899999998998876322 235666799999993
Done!