Query 035233
Match_columns 70
No_of_seqs 104 out of 174
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:17:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04627 ATP-synt_Eps: Mitocho 100.0 3.6E-30 7.8E-35 150.1 0.8 50 7-56 1-50 (50)
2 KOG3495 Mitochondrial F1F0-ATP 99.9 5E-27 1.1E-31 137.5 4.7 50 7-56 1-50 (50)
3 PF10952 DUF2753: Protein of u 64.2 7.1 0.00015 27.2 2.5 25 5-29 55-81 (140)
4 COG0292 RplT Ribosomal protein 39.8 19 0.00041 24.4 1.4 14 10-23 69-82 (118)
5 PTZ00478 Sec superfamily; Prov 33.9 51 0.0011 20.9 2.6 21 18-38 24-44 (81)
6 PF13103 TonB_2: TonB C termin 33.6 48 0.001 19.1 2.4 48 17-66 1-48 (85)
7 PF02865 STAT_int: STAT protei 30.1 22 0.00047 23.6 0.5 19 22-40 102-120 (124)
8 PF11093 Mitochondr_Som1: Mito 25.9 62 0.0014 20.3 2.0 22 26-54 60-81 (83)
9 PF10963 DUF2765: Protein of u 24.4 52 0.0011 20.8 1.4 24 16-39 18-50 (83)
10 PF09373 PMBR: Pseudomurein-bi 22.6 1E+02 0.0022 15.7 2.2 16 14-29 4-19 (33)
11 PF05751 FixH: FixH; InterPro 22.0 85 0.0018 20.0 2.1 47 12-62 40-86 (146)
12 PF04921 XAP5: XAP5, circadian 20.7 1.2E+02 0.0025 22.7 2.8 37 24-61 75-113 (239)
13 PRK14887 KEOPS complex Pcc1-li 20.4 66 0.0014 19.9 1.3 25 25-49 18-42 (84)
No 1
>PF04627 ATP-synt_Eps: Mitochondrial ATP synthase epsilon chain; InterPro: IPR006721 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 family constitutes the mitochondrial ATP synthase epsilon subunit, which is distinct from the bacterial epsilon subunit (the latter being homologous to the mitochondrial delta subunit, IPR001469 from INTERPRO). The mitochondrial epsilon subunit is located in the stalk region of the F1 complex, and acts as an inhibitor of the ATPase catalytic core. The epsilon subunit can assume two conformations, contracted and extended, where the latter inhibits ATP hydrolysis. The conformation of the epsilon subunit is determined by the direction of rotation of the gamma subunit, and possibly by the presence of ADP. The extended epsilon subunit is thought to become extended in the presence of ADP, thereby acting as a safety lock to prevent wasteful ATP hydrolysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1); PDB: 3OEH_R 3OE7_1 3OFN_R 3OEE_I 2HLD_I 3FKS_I 2WPD_I 3ZRY_I 2V7Q_I 1H8E_I ....
Probab=99.95 E-value=3.6e-30 Score=150.09 Aligned_cols=50 Identities=46% Similarity=0.852 Sum_probs=41.7
Q ss_pred cHHHHHccccHHHHHHHHHHHHHhhcCchhHHHhhccccceeeEeeccCC
Q 035233 7 VPFWRAAGMTYISYSNICANLVRNCLKEPYKTEALTREKVHFSISKWTDG 56 (70)
Q Consensus 7 ~~~WR~AG~sY~~Ys~iaAr~vR~aLKe~~r~~A~~R~~~~~k~~~w~nG 56 (70)
|++||+||||||+|+||||++||+|||||+|++|++|+.+++|+++|+||
T Consensus 1 m~~WR~AGlsY~~Ys~iaA~~vR~aLKe~~r~~A~~r~~~~~k~~~w~nG 50 (50)
T PF04627_consen 1 MSAWRAAGLSYNKYSNIAARAVRNALKEEFRAAAEKRESTELKYTKWENG 50 (50)
T ss_dssp --SSTTSS--HHHHHHHHHHHTTTTC-CTSTTTHHHCCS---EEEEBBTT
T ss_pred ChHHHHhCcCHHHHHHHHHHHHHHHhCchHHHHHHhcccceEEEEecCCC
Confidence 57999999999999999999999999999999999999999999999999
No 2
>KOG3495 consensus Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion]
Probab=99.94 E-value=5e-27 Score=137.50 Aligned_cols=50 Identities=46% Similarity=0.872 Sum_probs=48.9
Q ss_pred cHHHHHccccHHHHHHHHHHHHHhhcCchhHHHhhccccceeeEeeccCC
Q 035233 7 VPFWRAAGMTYISYSNICANLVRNCLKEPYKTEALTREKVHFSISKWTDG 56 (70)
Q Consensus 7 ~~~WR~AG~sY~~Ys~iaAr~vR~aLKe~~r~~A~~R~~~~~k~~~w~nG 56 (70)
|++||+|||||++||||||++||+|||+|++..|++|+++++++++|+||
T Consensus 1 m~awr~aGlsYi~Ys~I~A~vvR~~LK~e~ka~a~k~~~s~~k~t~wkng 50 (50)
T KOG3495|consen 1 MAAWRKAGLSYIRYSQIAAQVVRQALKTELKAEALKRPQSHVKYTKWKNG 50 (50)
T ss_pred CchHHHcCccHHHHHHHHHHHHHHHHhHHHHHHHhhCCCCeeEEEecccC
Confidence 56999999999999999999999999999999999999999999999998
No 3
>PF10952 DUF2753: Protein of unknown function (DUF2753); InterPro: IPR020206 This entry represents a group of uncharacterised proteins.
Probab=64.24 E-value=7.1 Score=27.16 Aligned_cols=25 Identities=28% Similarity=0.684 Sum_probs=19.4
Q ss_pred cccHHHHHcccc-H-HHHHHHHHHHHH
Q 035233 5 AAVPFWRAAGMT-Y-ISYSNICANLVR 29 (70)
Q Consensus 5 ~~~~~WR~AG~s-Y-~~Ys~iaAr~vR 29 (70)
|...|||..|=+ | ++|+.+|..-|-
T Consensus 55 NLA~FWR~~gd~~yELkYLqlASE~Vl 81 (140)
T PF10952_consen 55 NLADFWRSQGDSDYELKYLQLASEKVL 81 (140)
T ss_pred hHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence 567799999944 4 789999988764
No 4
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=39.76 E-value=19 Score=24.45 Aligned_cols=14 Identities=29% Similarity=0.479 Sum_probs=11.6
Q ss_pred HHHccccHHHHHHH
Q 035233 10 WRAAGMTYISYSNI 23 (70)
Q Consensus 10 WR~AG~sY~~Ys~i 23 (70)
=|..||||.+|.+-
T Consensus 69 ~R~~GlsYS~fi~g 82 (118)
T COG0292 69 ARENGLSYSRFING 82 (118)
T ss_pred HHHcCCcHHHHHHH
Confidence 37889999999873
No 5
>PTZ00478 Sec superfamily; Provisional
Probab=33.86 E-value=51 Score=20.90 Aligned_cols=21 Identities=29% Similarity=0.477 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHhhcCchhHH
Q 035233 18 ISYSNICANLVRNCLKEPYKT 38 (70)
Q Consensus 18 ~~Ys~iaAr~vR~aLKe~~r~ 38 (70)
-+|..-+-|.|++|-||+.+.
T Consensus 24 ~eF~kds~r~vkrctKPdrkE 44 (81)
T PTZ00478 24 QEFANDSRRLIRKCTKPDAKE 44 (81)
T ss_pred HHHHHHHHHHHHHhcCCCHHH
Confidence 468889999999999987553
No 6
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=33.61 E-value=48 Score=19.13 Aligned_cols=48 Identities=19% Similarity=0.158 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHhhcCchhHHHhhccccceeeEeeccCCcccCceecCC
Q 035233 17 YISYSNICANLVRNCLKEPYKTEALTREKVHFSISKWTDGKPQKPTIRSD 66 (70)
Q Consensus 17 Y~~Ys~iaAr~vR~aLKe~~r~~A~~R~~~~~k~~~w~nGk~~~~~~~~~ 66 (70)
|..|.+.-.+.|++....|.. ......+.++++.=.||+.....++.+
T Consensus 1 Y~~Y~~~i~~~i~~~w~~p~~--~~~~~~~~V~i~i~~dG~v~~~~i~~s 48 (85)
T PF13103_consen 1 YASYFAQIQARIQQNWNPPPQ--DSGGLSVTVRITIDPDGRVISVRIVKS 48 (85)
T ss_dssp -------HHHHHHHH----TT----TT--EEEEEEE-TTSBEEEEEEEE-
T ss_pred CcchHHHHHHHHHHHcCCCCC--CCCCcEEEEEEEECCCCCEEEEEEecC
Confidence 667877777777777766644 445667788888889999865555443
No 7
>PF02865 STAT_int: STAT protein, protein interaction domain; InterPro: IPR013799 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the N-terminal domain, which is responsible for protein interactions. This domain has a multi-helical structure that can be subdivided into two structural sub-domains.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction; PDB: 1BGF_A 1YVL_A.
Probab=30.14 E-value=22 Score=23.56 Aligned_cols=19 Identities=32% Similarity=0.490 Sum_probs=15.4
Q ss_pred HHHHHHHHhhcCchhHHHh
Q 035233 22 NICANLVRNCLKEPYKTEA 40 (70)
Q Consensus 22 ~iaAr~vR~aLKe~~r~~A 40 (70)
-.-++++|+||.+|.|.-.
T Consensus 102 ~~L~~~I~~~L~~E~~iv~ 120 (124)
T PF02865_consen 102 LELARIIRNCLQEEKRIVQ 120 (124)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3568999999999988653
No 8
>PF11093 Mitochondr_Som1: Mitochondrial export protein Som1; InterPro: IPR024645 Som1 is a component of the mitochondrial protein export system. Som1 proteins exhibit a highly conserved region and a pattern of cysteine residues []. Stabilisation of Som1 occurs through an interaction between Som1 and Imp1, a peptidase required for proteolytic processing of certain proteins during their transport across the mitochondrial membrane []. This suggests that Som1 represents a third subunit of the Imp1 peptidase complex [].; GO: 0042720 mitochondrial inner membrane peptidase complex
Probab=25.89 E-value=62 Score=20.33 Aligned_cols=22 Identities=32% Similarity=0.750 Sum_probs=16.6
Q ss_pred HHHHhhcCchhHHHhhccccceeeEeecc
Q 035233 26 NLVRNCLKEPYKTEALTREKVHFSISKWT 54 (70)
Q Consensus 26 r~vR~aLKe~~r~~A~~R~~~~~k~~~w~ 54 (70)
|+.|+||++ ..+.+.+-.|.|+
T Consensus 60 RlFr~C~~~-------~~~~~~iEtT~~e 81 (83)
T PF11093_consen 60 RLFRRCLKP-------RKGGVNIETTDWE 81 (83)
T ss_pred HHHHhCCCc-------cCCCEEEEEecCC
Confidence 678999988 4456677777776
No 9
>PF10963 DUF2765: Protein of unknown function (DUF2765); InterPro: IPR024406 This family of proteins with no known function is found in phages and suspected prophages.
Probab=24.44 E-value=52 Score=20.76 Aligned_cols=24 Identities=21% Similarity=0.195 Sum_probs=19.1
Q ss_pred cHHHHHHHHHH---------HHHhhcCchhHHH
Q 035233 16 TYISYSNICAN---------LVRNCLKEPYKTE 39 (70)
Q Consensus 16 sY~~Ys~iaAr---------~vR~aLKe~~r~~ 39 (70)
.|++|.|-.++ .|++|..+|.|.+
T Consensus 18 ~yn~yiN~~~~~nkVaPa~n~L~r~V~~e~Kea 50 (83)
T PF10963_consen 18 AYNKYINEMAMDNKVAPAHNYLMRIVDPESKEA 50 (83)
T ss_pred HHHHHHHHhccCCCchHHHHHHHHHcCHHHHHH
Confidence 48999998764 5899998887766
No 10
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=22.57 E-value=1e+02 Score=15.73 Aligned_cols=16 Identities=6% Similarity=0.220 Sum_probs=13.7
Q ss_pred cccHHHHHHHHHHHHH
Q 035233 14 GMTYISYSNICANLVR 29 (70)
Q Consensus 14 G~sY~~Ys~iaAr~vR 29 (70)
.||+.+|..+++|++.
T Consensus 4 ~i~~~~~~d~a~rv~~ 19 (33)
T PF09373_consen 4 TISKEEYLDMASRVNN 19 (33)
T ss_pred eecHHHHHHHHHHHHH
Confidence 4899999999999874
No 11
>PF05751 FixH: FixH; InterPro: IPR008620 This family consists of several Rhizobium FixH like proteins. It has been suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG [].
Probab=21.98 E-value=85 Score=19.96 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=31.6
Q ss_pred HccccHHHHHHHHHHHHHhhcCchhHHHhhccccceeeEeeccCCcccCce
Q 035233 12 AAGMTYISYSNICANLVRNCLKEPYKTEALTREKVHFSISKWTDGKPQKPT 62 (70)
Q Consensus 12 ~AG~sY~~Ys~iaAr~vR~aLKe~~r~~A~~R~~~~~k~~~w~nGk~~~~~ 62 (70)
+.|+.|++-.....++.+--++-+.... .....++++. .+|+|....
T Consensus 40 ~~g~~y~~~i~~~~~a~~lg~~~~~~~~---~~~~~i~~~d-~~g~~~~~~ 86 (146)
T PF05751_consen 40 EKGLAYNQDIDRERAAEALGWKAELTID---DNSLTIRLTD-PNGAPVSGA 86 (146)
T ss_pred HhhhhhhhhhHHHHHHHhcCccceeeec---CCeEEEEEEc-CCCCcCcCc
Confidence 5689999887666666555555443322 2666788877 889886654
No 12
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=20.72 E-value=1.2e+02 Score=22.67 Aligned_cols=37 Identities=22% Similarity=0.438 Sum_probs=28.9
Q ss_pred HHHHHHhhcCchhHHH--hhccccceeeEeeccCCcccCc
Q 035233 24 CANLVRNCLKEPYKTE--ALTREKVHFSISKWTDGKPQKP 61 (70)
Q Consensus 24 aAr~vR~aLKe~~r~~--A~~R~~~~~k~~~w~nGk~~~~ 61 (70)
.-+..|..|+.|+... +.+-+.+.|-|+-| ||.....
T Consensus 75 ~E~~~Re~LRkE~~~~Qe~vK~eeI~I~fsyw-DGs~hrr 113 (239)
T PF04921_consen 75 EEAQEREELRKEWLAKQEAVKAEEIEIPFSYW-DGSGHRR 113 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCeeEEEEEEE-CCCCCcc
Confidence 3457888999888776 77889999999999 6765544
No 13
>PRK14887 KEOPS complex Pcc1-like subunit; Provisional
Probab=20.35 E-value=66 Score=19.93 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=19.9
Q ss_pred HHHHHhhcCchhHHHhhccccceee
Q 035233 25 ANLVRNCLKEPYKTEALTREKVHFS 49 (70)
Q Consensus 25 Ar~vR~aLKe~~r~~A~~R~~~~~k 49 (70)
|+++.++|++|....-..|..+++.
T Consensus 18 A~iiy~sl~~E~~~~~~~rs~~~~~ 42 (84)
T PRK14887 18 ARIIYRSVLPEHGDSQGERSKADLS 42 (84)
T ss_pred HHHHHHHhCcCcccCCcCceEEEEE
Confidence 8999999999988776677766553
Done!