Query psy11170
Match_columns 111
No_of_seqs 104 out of 183
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 19:50:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11170.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11170hhsearch_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 99.9 6.2E-27 1.4E-31 149.0 0.5 49 30-78 2-50 (50)
2 KOG3495|consensus 99.9 1.2E-24 2.6E-29 140.0 5.1 49 30-78 2-50 (50)
3 PF05751 FixH: FixH; InterPro 72.4 3.5 7.5E-05 28.9 2.4 68 31-102 37-104 (146)
4 COG0292 RplT Ribosomal protein 43.7 23 0.00049 26.6 2.5 20 26-45 63-82 (118)
5 COG2005 ModE N-terminal domain 36.8 19 0.00041 27.0 1.2 44 7-57 19-62 (130)
6 PF10952 DUF2753: Protein of u 31.1 58 0.0013 25.1 3.0 23 29-51 57-81 (140)
7 PF07499 RuvA_C: RuvA, C-termi 30.8 1.2E+02 0.0026 18.2 3.9 35 14-55 8-44 (47)
8 cd00194 UBA Ubiquitin Associat 25.2 89 0.0019 17.2 2.4 21 13-34 5-25 (38)
9 smart00165 UBA Ubiquitin assoc 24.1 93 0.002 17.1 2.4 21 13-34 5-25 (37)
10 PTZ00478 Sec superfamily; Prov 23.1 84 0.0018 22.1 2.4 21 40-60 24-44 (81)
11 CHL00068 rpl20 ribosomal prote 21.6 94 0.002 22.9 2.5 20 26-45 63-82 (115)
12 PF00453 Ribosomal_L20: Riboso 20.1 1E+02 0.0022 22.3 2.4 21 26-46 62-82 (108)
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=99.92 E-value=6.2e-27 Score=149.03 Aligned_cols=49 Identities=49% Similarity=0.725 Sum_probs=41.6
Q ss_pred HHHHHhccchHHHHHHHHHHHHHhcChHHHHHHhhcccceeEEeecCCC
Q psy11170 30 FSAEVLNRCYIQYSNIAARTLRRALKTEFRADAEKREESFIRITPWKDG 78 (111)
Q Consensus 30 ~aWR~AGlSY~rYSnIAAraVR~aLKee~R~~A~kR~~t~lK~tkWenG 78 (111)
.+||+|||||++|+||||++||+|||||+|++|++|+.+++|+++|+||
T Consensus 2 ~~WR~AGlsY~~Ys~iaA~~vR~aLKe~~r~~A~~r~~~~~k~~~w~nG 50 (50)
T PF04627_consen 2 SAWRAAGLSYNKYSNIAARAVRNALKEEFRAAAEKRESTELKYTKWENG 50 (50)
T ss_dssp -SSTTSS--HHHHHHHHHHHTTTTC-CTSTTTHHHCCS---EEEEBBTT
T ss_pred hHHHHhCcCHHHHHHHHHHHHHHHhCchHHHHHHhcccceEEEEecCCC
Confidence 4799999999999999999999999999999999999999999999999
No 2
>KOG3495|consensus
Probab=99.91 E-value=1.2e-24 Score=139.97 Aligned_cols=49 Identities=45% Similarity=0.699 Sum_probs=48.0
Q ss_pred HHHHHhccchHHHHHHHHHHHHHhcChHHHHHHhhcccceeEEeecCCC
Q psy11170 30 FSAEVLNRCYIQYSNIAARTLRRALKTEFRADAEKREESFIRITPWKDG 78 (111)
Q Consensus 30 ~aWR~AGlSY~rYSnIAAraVR~aLKee~R~~A~kR~~t~lK~tkWenG 78 (111)
.+||+|||||++||||||++||+|||+|++.+|++|+++++|+++|+||
T Consensus 2 ~awr~aGlsYi~Ys~I~A~vvR~~LK~e~ka~a~k~~~s~~k~t~wkng 50 (50)
T KOG3495|consen 2 AAWRKAGLSYIRYSQIAAQVVRQALKTELKAEALKRPQSHVKYTKWKNG 50 (50)
T ss_pred chHHHcCccHHHHHHHHHHHHHHHHhHHHHHHHhhCCCCeeEEEecccC
Confidence 4899999999999999999999999999999999999999999999998
No 3
>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=72.36 E-value=3.5 Score=28.92 Aligned_cols=68 Identities=18% Similarity=0.144 Sum_probs=50.6
Q ss_pred HHHHhccchHHHHHHHHHHHHHhcChHHHHHHhhcccceeEEeecCCCccccccccCceeeeeeeecCCcce
Q psy11170 31 SAEVLNRCYIQYSNIAARTLRRALKTEFRADAEKREESFIRITPWKDGKPIRHYSEPLHYVTPILLQDDLDI 102 (111)
Q Consensus 31 aWR~AGlSY~rYSnIAAraVR~aLKee~R~~A~kR~~t~lK~tkWenGKp~~~~~l~~~~vn~~~~~~~~~~ 102 (111)
.+=++|+.|++-.....++.+--++.+... ..+...++++. .+|+|.....++.++.-|.--..|..+
T Consensus 37 dYY~~g~~y~~~i~~~~~a~~lg~~~~~~~---~~~~~~i~~~d-~~g~~~~~~~~~l~l~rp~~~~~D~~~ 104 (146)
T PF05751_consen 37 DYYEKGLAYNQDIDRERAAEALGWKAELTI---DDNSLTIRLTD-PNGAPVSGAKLTLSLYRPTDAKLDFTL 104 (146)
T ss_pred cHHHhhhhhhhhhHHHHHHHhcCccceeee---cCCeEEEEEEc-CCCCcCcCceEEEEEECCCCccCCeeE
Confidence 345679999988766666665555544332 22777888888 999999999999999999887777654
No 4
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=43.68 E-value=23 Score=26.63 Aligned_cols=20 Identities=20% Similarity=0.152 Sum_probs=17.2
Q ss_pred HHHHHHHHHhccchHHHHHH
Q psy11170 26 QAIQFSAEVLNRCYIQYSNI 45 (111)
Q Consensus 26 ~~m~~aWR~AGlSY~rYSnI 45 (111)
+-++++=|..|+||.++.|-
T Consensus 63 ~RINAA~R~~GlsYS~fi~g 82 (118)
T COG0292 63 ARINAAARENGLSYSRFING 82 (118)
T ss_pred HHHHHHHHHcCCcHHHHHHH
Confidence 36889999999999999873
No 5
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=36.85 E-value=19 Score=27.01 Aligned_cols=44 Identities=25% Similarity=0.316 Sum_probs=30.6
Q ss_pred CCcchhhHHhhccCchhHHHHHHHHHHHhccchHHHHHHHHHHHHHhcChH
Q psy11170 7 PSRYPLLTLMSNMGYDDKRQAIQFSAEVLNRCYIQYSNIAARTLRRALKTE 57 (111)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~m~~aWR~AGlSY~rYSnIAAraVR~aLKee 57 (111)
|.|+-||-.....| .++.|=|++||||= ++=-.=+.+-+.+++|
T Consensus 19 ~g~~~LL~~I~etG------SIs~AAk~~GiSYk-~AW~~i~~~n~~~~~p 62 (130)
T COG2005 19 PGRIELLKAIAETG------SISAAAKAAGISYK-SAWDYIKALNRLLGEP 62 (130)
T ss_pred chHHHHHHHHHHhC------CHHHHHHHcCCCHH-HHHHHHHHHHHHhCCC
Confidence 56778888888777 58899999999994 3333344455555543
No 6
>PF10952 DUF2753: Protein of unknown function (DUF2753); InterPro: IPR020206 This entry represents a group of uncharacterised proteins.
Probab=31.12 E-value=58 Score=25.14 Aligned_cols=23 Identities=13% Similarity=0.173 Sum_probs=17.2
Q ss_pred HHHHHHhccc-h-HHHHHHHHHHHH
Q psy11170 29 QFSAEVLNRC-Y-IQYSNIAARTLR 51 (111)
Q Consensus 29 ~~aWR~AGlS-Y-~rYSnIAAraVR 51 (111)
+-.||..|=+ | ++|+..|++-|-
T Consensus 57 A~FWR~~gd~~yELkYLqlASE~Vl 81 (140)
T PF10952_consen 57 ADFWRSQGDSDYELKYLQLASEKVL 81 (140)
T ss_pred HHHHHHcCChHHHHHHHHHHHHHHH
Confidence 3459999944 4 789999987663
No 7
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=30.82 E-value=1.2e+02 Score=18.16 Aligned_cols=35 Identities=20% Similarity=0.290 Sum_probs=18.0
Q ss_pred HHhhccCchhHH--HHHHHHHHHhccchHHHHHHHHHHHHHhcC
Q psy11170 14 TLMSNMGYDDKR--QAIQFSAEVLNRCYIQYSNIAARTLRRALK 55 (111)
Q Consensus 14 ~~~~~~~~~~~~--~~m~~aWR~AGlSY~rYSnIAAraVR~aLK 55 (111)
.-+.++||..+. +++...=...+++ ....+|.|||
T Consensus 8 ~AL~~LGy~~~e~~~av~~~~~~~~~~-------~e~~ik~aLk 44 (47)
T PF07499_consen 8 EALISLGYSKAEAQKAVSKLLEKPGMD-------VEELIKQALK 44 (47)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHSTTS--------HHHHHHHHHC
T ss_pred HHHHHcCCCHHHHHHHHHHhhcCCCCC-------HHHHHHHHHh
Confidence 345678997654 2222222233444 5567888877
No 8
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=25.19 E-value=89 Score=17.21 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=11.9
Q ss_pred hHHhhccCchhHHHHHHHHHHH
Q psy11170 13 LTLMSNMGYDDKRQAIQFSAEV 34 (111)
Q Consensus 13 ~~~~~~~~~~~~~~~m~~aWR~ 34 (111)
+..+..|||+ +.++..+.-+.
T Consensus 5 v~~L~~mGf~-~~~~~~AL~~~ 25 (38)
T cd00194 5 LEQLLEMGFS-REEARKALRAT 25 (38)
T ss_pred HHHHHHcCCC-HHHHHHHHHHh
Confidence 3456679998 44444444333
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=24.13 E-value=93 Score=17.09 Aligned_cols=21 Identities=14% Similarity=0.377 Sum_probs=13.0
Q ss_pred hHHhhccCchhHHHHHHHHHHH
Q psy11170 13 LTLMSNMGYDDKRQAIQFSAEV 34 (111)
Q Consensus 13 ~~~~~~~~~~~~~~~m~~aWR~ 34 (111)
+..+..|||+.. ++..+..+.
T Consensus 5 v~~L~~mGf~~~-~a~~aL~~~ 25 (37)
T smart00165 5 IDQLLEMGFSRE-EALKALRAA 25 (37)
T ss_pred HHHHHHcCCCHH-HHHHHHHHh
Confidence 455778899876 555444443
No 10
>PTZ00478 Sec superfamily; Provisional
Probab=23.06 E-value=84 Score=22.09 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHhcChHHHH
Q psy11170 40 IQYSNIAARTLRRALKTEFRA 60 (111)
Q Consensus 40 ~rYSnIAAraVR~aLKee~R~ 60 (111)
-+|..-+-|.+|+|-||..|.
T Consensus 24 ~eF~kds~r~vkrctKPdrkE 44 (81)
T PTZ00478 24 QEFANDSRRLIRKCTKPDAKE 44 (81)
T ss_pred HHHHHHHHHHHHHhcCCCHHH
Confidence 467888999999999976543
No 11
>CHL00068 rpl20 ribosomal protein L20
Probab=21.56 E-value=94 Score=22.87 Aligned_cols=20 Identities=10% Similarity=0.090 Sum_probs=16.5
Q ss_pred HHHHHHHHHhccchHHHHHH
Q psy11170 26 QAIQFSAEVLNRCYIQYSNI 45 (111)
Q Consensus 26 ~~m~~aWR~AGlSY~rYSnI 45 (111)
+-++++=|..|+||.++.+-
T Consensus 63 ~RINAa~R~~glsYs~fi~g 82 (115)
T CHL00068 63 TRINAAIRENGVSYSKFIHN 82 (115)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 45788899999999988764
No 12
>PF00453 Ribosomal_L20: Ribosomal protein L20; InterPro: IPR005813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L20 is a protein from the large (50S) subunit; in Escherichia coli it is known to bind directly to the 23S rRNA, and is required for ribosome assembly, but does not take part in protein synthesis. It belongs to a family of ribosomal proteins, including L20 from eubacteria, plant and alga chloroplasts and cyanelles [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_S 3CF5_N 3PIO_N 3PIP_N 2ZJQ_N 2ZJR_N 2ZJP_N 3DLL_N 3KIT_U 2X9U_U ....
Probab=20.09 E-value=1e+02 Score=22.29 Aligned_cols=21 Identities=19% Similarity=0.146 Sum_probs=17.3
Q ss_pred HHHHHHHHHhccchHHHHHHH
Q psy11170 26 QAIQFSAEVLNRCYIQYSNIA 46 (111)
Q Consensus 26 ~~m~~aWR~AGlSY~rYSnIA 46 (111)
+-++++=|..|+||.++.+-.
T Consensus 62 ~RINAa~r~~g~~Ys~fi~~L 82 (108)
T PF00453_consen 62 TRINAAAREHGLSYSRFINGL 82 (108)
T ss_dssp HHHHHHHHTTTSTHHHHHHHH
T ss_pred HHHHHHHHHhcccHHHHHHHH
Confidence 468888999999999987654
Done!