Query 046370
Match_columns 72
No_of_seqs 86 out of 88
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 11:26:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046370.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046370hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10890 DUF2741: Protein of u 100.0 5.1E-44 1.1E-48 223.9 3.4 72 1-72 1-72 (72)
2 PF02939 UcrQ: UcrQ family; I 99.8 6.8E-20 1.5E-24 116.1 1.9 51 7-60 9-60 (80)
3 KOG4116 Ubiquinol cytochrome c 99.7 1E-17 2.2E-22 108.7 2.3 61 5-68 15-78 (90)
4 PF12829 Mhr1: Transcriptional 43.8 13 0.00028 24.1 1.1 33 6-42 11-50 (91)
5 KOG4782 Predicted membrane pro 43.6 2.1 4.6E-05 28.7 -2.7 28 41-68 59-86 (108)
6 COG4626 Phage terminase-like p 27.6 13 0.00028 30.9 -1.1 29 12-40 59-88 (546)
7 COG5051 RPL36A Ribosomal prote 24.2 18 0.0004 23.9 -0.7 11 14-24 49-59 (97)
8 PF01158 Ribosomal_L36e: Ribos 23.0 17 0.00036 24.0 -1.0 14 14-28 47-60 (98)
9 PF14021 DUF4237: Protein of u 21.4 34 0.00074 21.7 0.2 22 15-36 25-46 (90)
10 PF00662 Oxidored_q1_N: NADH-U 20.5 17 0.00036 20.9 -1.3 17 56-72 40-56 (62)
No 1
>PF10890 DUF2741: Protein of unknown function (DUF2741); InterPro: IPR020101 This entry represents subunit 8 of the Cytochrome b-c1 complex. The ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) is part of the mitochondrial respiratory chain. This subunit, together with cytochrome b, binds to ubiquinone. In plants, the b-c1 complex contains 10 subunits: 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins.
Probab=100.00 E-value=5.1e-44 Score=223.89 Aligned_cols=72 Identities=75% Similarity=1.287 Sum_probs=71.5
Q ss_pred CCCcceeeeeEEEEeCccccccccccccchhhhhhhhhhccccceeeeecceeeehhhHHHHHHHHHhhhcC
Q 046370 1 MGKQPVRMKAVVYALSPFQQKIMPGLWKDLTGKIHHKVSDNWISTILLLGPLVGTYAYVQNYQEKEKLAHRY 72 (72)
Q Consensus 1 mgk~~vrlr~VtYsLSPfEQra~~g~f~~~p~~i~RR~~en~~~~~~~v~Pfv~~y~y~~~~~e~ekl~hr~ 72 (72)
|||+|||+|+|+|+||||||++|+|+|||+|.+|+|+|+|||+|++++++|++|+|+||+||+|||||+|||
T Consensus 1 Mgk~pvrlkeVvY~LSP~qq~Vm~GLwKDlp~ki~hk~~enwv~a~~~~~p~~Gt~~Ya~~y~e~EKL~HRy 72 (72)
T PF10890_consen 1 MGKQPVRLKEVVYALSPFQQKVMPGLWKDLPKKIHHKFSENWVSATLFLVPLVGTYWYAENYKEQEKLEHRY 72 (72)
T ss_pred CCCCccchhHheeeeChhhhhhhhhhhhhcHHHHHHHHhhcceeeEEEeeeehhhHHHHHHHHHHHhhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>PF02939 UcrQ: UcrQ family; InterPro: IPR004205 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multi-enzyme complex [], which recognises a mitochondrial targeting presequence. The bc1 complex contains 11 subunits: 3 respiratory subunits (cytochrome b, cytochrome c1 and Rieske protein), 2 core proteins and 6 low molecular weight proteins. This family represents the 9.5 kDa subunit of the complex. This subunit together with cytochrome B binds to ubiquinone.; GO: 0008121 ubiquinol-cytochrome-c reductase activity; PDB: 1L0N_G 1SQQ_G 1PP9_G 1PPJ_T 2FYU_G 2BCC_G 1BCC_G 2A06_G 1NTZ_G 2YBB_g ....
Probab=99.77 E-value=6.8e-20 Score=116.09 Aligned_cols=51 Identities=20% Similarity=0.404 Sum_probs=40.0
Q ss_pred eeee-EEEEeCccccccccccccchhhhhhhhhhccccceeeeecceeeehhhHH
Q 046370 7 RMKA-VVYALSPFQQKIMPGLWKDLTGKIHHKVSDNWISTILLLGPLVGTYAYVQ 60 (72)
Q Consensus 7 rlr~-VtYsLSPfEQra~~g~f~~~p~~i~RR~~en~~~~~~~v~Pfv~~y~y~~ 60 (72)
|+|+ |||+|||||||+|+|.|+++++|++||+++++ +++++||+++|.--+
T Consensus 9 k~kgi~tYslSP~eQr~~ag~~~~~i~N~~RR~~~q~---~~v~ppfi~~y~i~~ 60 (80)
T PF02939_consen 9 KQKGIITYSLSPFEQRPFAGAFSKGIFNTFRRFRSQV---LYVAPPFIVGYLIYD 60 (80)
T ss_dssp --EEEEEEEE-TTGB-SSTTTTTTHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
T ss_pred cccceEEEEeChhhhcccccchHhhHhHHHHHHHHHh---HHHhhHHHHHHHHHH
Confidence 8999 99999999999999999999999999999955 455559988765433
No 3
>KOG4116 consensus Ubiquinol cytochrome c reductase, subunit QCR8 [Energy production and conversion]
Probab=99.68 E-value=1e-17 Score=108.74 Aligned_cols=61 Identities=21% Similarity=0.384 Sum_probs=48.4
Q ss_pred ceeeee-EEEEeCccccccccccccchhhhhhhhhhccccceeeeec-ceee-ehhhHHHHHHHHHh
Q 046370 5 PVRMKA-VVYALSPFQQKIMPGLWKDLTGKIHHKVSDNWISTILLLG-PLVG-TYAYVQNYQEKEKL 68 (72)
Q Consensus 5 ~vrlr~-VtYsLSPfEQra~~g~f~~~p~~i~RR~~en~~~~~~~v~-Pfv~-~y~y~~~~~e~ekl 68 (72)
|-|+++ |+|+||||||||++|.|+++.+|++||++++. +++++ +||+ -|.|+.--.++|.|
T Consensus 15 l~K~~giisYaLSPfeQra~~g~F~~~~~n~fRr~~~~~---~y~~iP~~Iv~yliy~wg~e~ne~l 78 (90)
T KOG4116|consen 15 LGKMKGIISYALSPFEQRAYAGFFDKAFPNMFRRFRSDQ---LYVVIPQFIVAYLIYDWGKETNEAL 78 (90)
T ss_pred chhccceEEEecCchhhccccchhhhhhHHHHHHhhhcc---EEEEeccceEEEEEEecchhHhHHH
Confidence 458999 99999999999999999999999999999843 66666 6673 34555555556655
No 4
>PF12829 Mhr1: Transcriptional regulation of mitochondrial recombination; InterPro: IPR024629 These proteins are involved in regulation of RNA polymerase II-dependent transcription. They are also involved in regulation of mitochondrial DNA recombination, maintenance, repair, and generation of homoplasmic cells [, , , ].
Probab=43.81 E-value=13 Score=24.12 Aligned_cols=33 Identities=30% Similarity=0.532 Sum_probs=23.6
Q ss_pred eeeeeEEEEeCcc-------ccccccccccchhhhhhhhhhccc
Q 046370 6 VRMKAVVYALSPF-------QQKIMPGLWKDLTGKIHHKVSDNW 42 (72)
Q Consensus 6 vrlr~VtYsLSPf-------EQra~~g~f~~~p~~i~RR~~en~ 42 (72)
++-.+|.||++|- .|=.++| |+.-|++ +|| |-|
T Consensus 11 l~t~QVlYS~~p~l~~~~i~~Q~~~~g-kk~~pp~-lRk--D~W 50 (91)
T PF12829_consen 11 LETNQVLYSQTPNLDNNQILKQFPFPG-KKNKPPS-LRK--DYW 50 (91)
T ss_pred cccCCEEEecCcccChhHHHHhccCCC-cccCCch-hcc--ccc
Confidence 3444599999994 4667777 8888998 443 556
No 5
>KOG4782 consensus Predicted membrane protein [Function unknown]
Probab=43.61 E-value=2.1 Score=28.70 Aligned_cols=28 Identities=21% Similarity=0.269 Sum_probs=21.0
Q ss_pred cccceeeeecceeeehhhHHHHHHHHHh
Q 046370 41 NWISTILLLGPLVGTYAYVQNYQEKEKL 68 (72)
Q Consensus 41 n~~~~~~~v~Pfv~~y~y~~~~~e~ekl 68 (72)
|.++-..+.+-.++.|||+-.+..||+.
T Consensus 59 N~is~a~i~alViaIY~YTfYSikQErF 86 (108)
T KOG4782|consen 59 NHISFAGIGALVIAIYGYTFYSIKQERF 86 (108)
T ss_pred hhhhhHHHHHHHHHhhhheeeehhHHHH
Confidence 5555555555888999999998888863
No 6
>COG4626 Phage terminase-like protein, large subunit [General function prediction only]
Probab=27.64 E-value=13 Score=30.91 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=24.0
Q ss_pred EEEeCcccccccccccc-chhhhhhhhhhc
Q 046370 12 VYALSPFQQKIMPGLWK-DLTGKIHHKVSD 40 (72)
Q Consensus 12 tYsLSPfEQra~~g~f~-~~p~~i~RR~~e 40 (72)
-.+|+|+|+=+++.+|. --...-.|||.|
T Consensus 59 p~~l~PwQkFiia~l~G~~~k~T~~rrf~e 88 (546)
T COG4626 59 PESLEPWQKFIVAALFGFYDKQTGIRRFKE 88 (546)
T ss_pred ccccchHHHHHHHHHhceeecCCCceEEEE
Confidence 67899999999999997 444455789998
No 7
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=18 Score=23.92 Aligned_cols=11 Identities=27% Similarity=0.921 Sum_probs=9.6
Q ss_pred EeCcccccccc
Q 046370 14 ALSPFQQKIMP 24 (72)
Q Consensus 14 sLSPfEQra~~ 24 (72)
.|||||.|++.
T Consensus 49 GlsPyErr~i~ 59 (97)
T COG5051 49 GLSPYERRVIE 59 (97)
T ss_pred cCCHHHHHHHH
Confidence 58999999984
No 8
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=23.03 E-value=17 Score=23.97 Aligned_cols=14 Identities=29% Similarity=0.748 Sum_probs=11.3
Q ss_pred EeCcccccccccccc
Q 046370 14 ALSPFQQKIMPGLWK 28 (72)
Q Consensus 14 sLSPfEQra~~g~f~ 28 (72)
.+||||.++| .+++
T Consensus 47 GfaPYEkr~m-ELlk 60 (98)
T PF01158_consen 47 GFAPYEKRAM-ELLK 60 (98)
T ss_dssp HHCHHHHHHH-HHHH
T ss_pred CCChHHHHHH-HHHh
Confidence 4799999999 5566
No 9
>PF14021 DUF4237: Protein of unknown function (DUF4237)
Probab=21.38 E-value=34 Score=21.73 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=15.0
Q ss_pred eCccccccccccccchhhhhhh
Q 046370 15 LSPFQQKIMPGLWKDLTGKIHH 36 (72)
Q Consensus 15 LSPfEQra~~g~f~~~p~~i~R 36 (72)
=.|||||++|--..+.+....+
T Consensus 25 gtpf~~RaLpp~~~~~~Y~~Y~ 46 (90)
T PF14021_consen 25 GTPFEQRALPPESLEKPYHVYE 46 (90)
T ss_pred CCCHHHcCCCCcccCCCCEEEE
Confidence 3699999999655555555333
No 10
>PF00662 Oxidored_q1_N: NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; InterPro: IPR001516 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This domain represents an N-terminal extension of IPR001750 from INTERPRO. It contains NADH-Ubiquinone chain 5 and eubacterial chain L; these are found in the NADH:ubiquinone oxidoreductase (complex I) which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0055114 oxidation-reduction process; PDB: 3RKO_L.
Probab=20.47 E-value=17 Score=20.92 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=12.0
Q ss_pred hhhHHHHHHHHHhhhcC
Q 046370 56 YAYVQNYQEKEKLAHRY 72 (72)
Q Consensus 56 y~y~~~~~e~ekl~hr~ 72 (72)
--|+..|+++|+--+||
T Consensus 40 ~~yS~~YM~~d~~~~rF 56 (62)
T PF00662_consen 40 HIYSIGYMSHDPNYNRF 56 (62)
T ss_dssp HHHHHHHTSS-S-HHHH
T ss_pred eeccccccccCCCcchh
Confidence 46888999999887775
Done!