Query 048658
Match_columns 83
No_of_seqs 87 out of 89
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 11:44:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048658hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3213 Transcription factor I 100.0 3.8E-39 8.2E-44 243.9 5.6 78 6-83 105-182 (238)
2 PF05018 DUF667: Protein of un 100.0 1.8E-37 4E-42 225.8 5.9 78 6-83 105-182 (190)
3 PF11606 AlcCBM31: Family 31 c 61.3 4.2 9.1E-05 27.8 0.9 48 8-57 13-72 (93)
4 PRK00153 hypothetical protein; 58.8 27 0.00059 22.9 4.5 43 33-75 15-62 (104)
5 PF02575 YbaB_DNA_bd: YbaB/Ebf 54.3 18 0.00038 22.7 2.9 24 52-75 31-54 (93)
6 PF08381 BRX: Transcription fa 36.9 21 0.00046 22.4 1.2 20 58-77 23-42 (59)
7 PF12565 DUF3747: Protein of u 35.9 13 0.00028 27.9 0.2 23 19-49 147-169 (181)
8 PF14619 SnAC: Snf2-ATP coupli 33.7 8.5 0.00019 24.2 -1.0 14 69-82 17-30 (74)
9 PF15034 KRTAP7: KRTAP type 7 33.6 27 0.00058 23.5 1.3 21 6-26 18-38 (87)
10 TIGR00251 conserved hypothetic 29.7 1.4E+02 0.0031 19.5 4.3 38 37-82 50-87 (87)
11 PRK14626 hypothetical protein; 28.3 65 0.0014 21.9 2.6 26 52-77 41-66 (110)
12 TIGR00103 DNA_YbaB_EbfC DNA-bi 28.1 1.2E+02 0.0026 20.0 3.8 42 33-74 17-63 (102)
13 PRK14627 hypothetical protein; 28.1 68 0.0015 21.4 2.6 26 52-77 37-62 (100)
14 PF02033 RBFA: Ribosome-bindin 26.2 86 0.0019 20.1 2.8 23 48-70 27-49 (104)
15 PF11549 Sec31: Protein transp 25.4 25 0.00055 21.7 0.2 18 27-44 23-40 (51)
16 PF05071 NDUFA12: NADH ubiquin 25.1 59 0.0013 21.6 1.9 36 44-82 8-45 (105)
17 smart00135 LY Low-density lipo 24.9 33 0.00072 17.4 0.5 11 63-73 20-30 (43)
18 PRK14622 hypothetical protein; 24.2 93 0.002 20.8 2.8 25 52-76 37-61 (103)
19 PRK14625 hypothetical protein; 24.1 2E+02 0.0044 19.6 4.4 45 33-77 14-63 (109)
20 PRK00521 rbfA ribosome-binding 20.3 2.2E+02 0.0047 19.0 3.9 38 33-70 15-55 (120)
21 PF01745 IPT: Isopentenyl tran 20.0 33 0.00072 26.7 -0.1 42 40-81 20-74 (233)
No 1
>KOG3213 consensus Transcription factor IIB [Transcription]
Probab=100.00 E-value=3.8e-39 Score=243.94 Aligned_cols=78 Identities=71% Similarity=1.145 Sum_probs=77.0
Q ss_pred ccCeeeeeeeeeeEEeeccccCcccchhhccHHHHHHHHhCcceeeEEEEEEecceeeEEeeecccCCCccCCCCCCC
Q 048658 6 DRTIQAVTRVKPYICTMPLRLDDGWNQIQLNLADFTRRAYGTNYVETLRVQVHANYRLRRIYFSDRLYSEEELTPEFT 83 (83)
Q Consensus 6 ~Snfq~~trV~p~~c~mPL~L~~gWn~i~~nL~~~t~~aygT~Y~et~rv~IhANCRlRRIYFsdrlYs~~eLP~efk 83 (83)
.||||++++|+|++|+|||+|++||||||+||+|||+++||++|.||++||||||||||||||+|++|+++|+|++||
T Consensus 105 ~Sn~~ke~~~kp~~~~mPl~m~~~W~~iqlnL~dft~~~~~~~y~etl~iql~AncriRriyf~~kl~~~~e~~~~fr 182 (238)
T KOG3213|consen 105 ASNFQKETSVKPFICTMPLVMDAGWNQIQLNLADFTRRAYGTNYGETLSIQLHANCRIRRIYFADKLYSEAELPLEFR 182 (238)
T ss_pred eeccchhhcccceEEecceEecCcceeEEeeHHHHHHHHhccceeeEEEEEEecceEEEEEEeccccCChhhCCCcce
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999996
No 2
>PF05018 DUF667: Protein of unknown function (DUF667); InterPro: IPR007714 This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature.
Probab=100.00 E-value=1.8e-37 Score=225.80 Aligned_cols=78 Identities=64% Similarity=1.128 Sum_probs=76.8
Q ss_pred ccCeeeeeeeeeeEEeeccccCcccchhhccHHHHHHHHhCcceeeEEEEEEecceeeEEeeecccCCCccCCCCCCC
Q 048658 6 DRTIQAVTRVKPYICTMPLRLDDGWNQIQLNLADFTRRAYGTNYVETLRVQVHANYRLRRIYFSDRLYSEEELTPEFT 83 (83)
Q Consensus 6 ~Snfq~~trV~p~~c~mPL~L~~gWn~i~~nL~~~t~~aygT~Y~et~rv~IhANCRlRRIYFsdrlYs~~eLP~efk 83 (83)
.||+|++++++|++|+|||.|++|||+|+|||+++|+++|||+|+||++|+||||||||||||||++|++||||+|||
T Consensus 105 ~Sn~~k~~~~~~~~~~iPl~l~~~W~~l~idL~~~~~~~y~~~~~~sl~i~I~ancrlRrIyfsD~ly~~~elp~~~~ 182 (190)
T PF05018_consen 105 FSNFQKETKVTPFHCQIPLRLSPGWNNLQIDLADLTRRAYGTNYFESLRIQICANCRLRRIYFSDRLYSEDELPPEFK 182 (190)
T ss_pred EeeeeccccccccEEEcccccCCCcEEEEEEHHHHHHHHhccCceEEEEEEEecCEEEEEEEecCccCChhhCchhhE
Confidence 589999999999999999999999999999999999999999999999999999999999999999999999999996
No 3
>PF11606 AlcCBM31: Family 31 carbohydrate binding protein; InterPro: IPR021016 Beta-1,3-xylan is a homopolymer of b-1,3-linked D-xylose and is a polysaccharide peculiar to marine algae. Beta-1,3-xylanase is a beta-1,3-xylan hydrolyzing enzyme [].; GO: 0033905 xylan endo-1,3-beta-xylosidase activity; PDB: 2COV_F.
Probab=61.31 E-value=4.2 Score=27.76 Aligned_cols=48 Identities=23% Similarity=0.379 Sum_probs=25.1
Q ss_pred CeeeeeeeeeeEEeeccccCcccchhhccHH---------HHHH---HHhCcceeeEEEEEE
Q 048658 8 TIQAVTRVKPYICTMPLRLDDGWNQIQLNLA---------DFTR---RAYGTNYVETLRVQV 57 (83)
Q Consensus 8 nfq~~trV~p~~c~mPL~L~~gWn~i~~nL~---------~~t~---~aygT~Y~et~rv~I 57 (83)
||.+++-+.-|+... .-+.|||+||+|== .|+| -..|..|-=|.+|+=
T Consensus 13 ~Yvsds~ievfH~d~--gWsAgwnY~CLd~yCl~g~ks~g~f~r~F~a~LGqtY~i~FKVeD 72 (93)
T PF11606_consen 13 NYVSDSEIEVFHKDN--GWSAGWNYLCLDDYCLSGTKSNGAFTRSFSATLGQTYKITFKVED 72 (93)
T ss_dssp EEEETTEEEEEEE--------SSEEEEETTEEEE-EEETTEEEEEEE--TT-EEEEEEEEEE
T ss_pred eeecCceEEEEEecC--CccceeeEEEecCeeccccccCCeeeeeechhcCcceeEEEEEec
Confidence 566677777776554 77899999998821 2222 234666766666653
No 4
>PRK00153 hypothetical protein; Validated
Probab=58.76 E-value=27 Score=22.92 Aligned_cols=43 Identities=9% Similarity=0.172 Sum_probs=31.6
Q ss_pred hhccHHHHHHHHhCcceee-----EEEEEEecceeeEEeeecccCCCc
Q 048658 33 IQLNLADFTRRAYGTNYVE-----TLRVQVHANYRLRRIYFSDRLYSE 75 (83)
Q Consensus 33 i~~nL~~~t~~aygT~Y~e-----t~rv~IhANCRlRRIYFsdrlYs~ 75 (83)
+|-.++++-.+.=...+.. .++|.|.+++.|.+|-+.++++..
T Consensus 15 ~q~~~~~~q~~l~~~~~~~~s~~G~V~V~v~G~~~v~~i~Id~~ll~~ 62 (104)
T PRK00153 15 MQEKMQKMQEELAQMEVEGEAGGGLVKVTMTGKKEVKRVKIDPSLVDP 62 (104)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHHcCC
Confidence 4445555555555555544 478999999999999999999953
No 5
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=54.34 E-value=18 Score=22.71 Aligned_cols=24 Identities=17% Similarity=0.120 Sum_probs=19.9
Q ss_pred EEEEEEecceeeEEeeecccCCCc
Q 048658 52 TLRVQVHANYRLRRIYFSDRLYSE 75 (83)
Q Consensus 52 t~rv~IhANCRlRRIYFsdrlYs~ 75 (83)
.++|.|.++.+|..|-|.++++.+
T Consensus 31 ~V~V~v~g~g~v~~i~i~~~~~~~ 54 (93)
T PF02575_consen 31 LVTVTVNGNGEVVDIEIDPSALRP 54 (93)
T ss_dssp TEEEEEETTS-EEEEEE-GGGGCT
T ss_pred EEEEEEecCceEEEEEEehHhhcc
Confidence 478999999999999999999973
No 6
>PF08381 BRX: Transcription factor regulating root and shoot growth via Pin3; InterPro: IPR013591 This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members. It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root []. It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (IPR000157 from INTERPRO) and FYVE (IPR000306 from INTERPRO) respectively.
Probab=36.89 E-value=21 Score=22.40 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=16.4
Q ss_pred ecceeeEEeeecccCCCccC
Q 048658 58 HANYRLRRIYFSDRLYSEEE 77 (83)
Q Consensus 58 hANCRlRRIYFsdrlYs~~e 77 (83)
...-.||||=||-+.|++.+
T Consensus 23 ~G~~~LkRVRFSR~~F~e~q 42 (59)
T PF08381_consen 23 DGGNDLKRVRFSRERFSEWQ 42 (59)
T ss_pred CCCeeEEEEEEhhhhcCHHH
Confidence 44678999999999998653
No 7
>PF12565 DUF3747: Protein of unknown function (DUF3747); InterPro: IPR022222 This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif.
Probab=35.87 E-value=13 Score=27.92 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=18.4
Q ss_pred EEeeccccCcccchhhccHHHHHHHHhCcce
Q 048658 19 ICTMPLRLDDGWNQIQLNLADFTRRAYGTNY 49 (83)
Q Consensus 19 ~c~mPL~L~~gWn~i~~nL~~~t~~aygT~Y 49 (83)
..-|.+.|++||. |++|+|+.+=
T Consensus 147 ~GF~ki~LePGW~--------l~rRty~gk~ 169 (181)
T PF12565_consen 147 NGFLKINLEPGWR--------LTRRTYQGKT 169 (181)
T ss_pred CceEEEEeCCCce--------eeehhcCCce
Confidence 4568899999995 8999997653
No 8
>PF14619 SnAC: Snf2-ATP coupling, chromatin remodelling complex
Probab=33.68 E-value=8.5 Score=24.20 Aligned_cols=14 Identities=36% Similarity=0.511 Sum_probs=11.6
Q ss_pred cccCCCccCCCCCC
Q 048658 69 SDRLYSEEELTPEF 82 (83)
Q Consensus 69 sdrlYs~~eLP~ef 82 (83)
..||.+++|||.-|
T Consensus 17 p~RLm~e~ELPe~~ 30 (74)
T PF14619_consen 17 PSRLMEESELPEWY 30 (74)
T ss_pred CccccchhhchHHH
Confidence 36899999999765
No 9
>PF15034 KRTAP7: KRTAP type 7 family
Probab=33.56 E-value=27 Score=23.49 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=18.7
Q ss_pred ccCeeeeeeeeeeEEeecccc
Q 048658 6 DRTIQAVTRVKPYICTMPLRL 26 (83)
Q Consensus 6 ~Snfq~~trV~p~~c~mPL~L 26 (83)
..||+.+-|..|.-|.+||.-
T Consensus 18 gtnfh~t~ratplncvvplgs 38 (87)
T PF15034_consen 18 GTNFHGTFRATPLNCVVPLGS 38 (87)
T ss_pred cccccceeecccceEEEECCC
Confidence 469999999999999999864
No 10
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=29.67 E-value=1.4e+02 Score=19.54 Aligned_cols=38 Identities=18% Similarity=0.369 Sum_probs=29.3
Q ss_pred HHHHHHHHhCcceeeEEEEEEecceeeEEeeecccCCCccCCCCCC
Q 048658 37 LADFTRRAYGTNYVETLRVQVHANYRLRRIYFSDRLYSEEELTPEF 82 (83)
Q Consensus 37 L~~~t~~aygT~Y~et~rv~IhANCRlRRIYFsdrlYs~~eLP~ef 82 (83)
|-.|..+.||. .+.|.=++..|.+.|...+ .+++|+|.
T Consensus 50 li~~La~~l~v----~I~i~~G~tsR~K~v~I~~----~~~~~~~~ 87 (87)
T TIGR00251 50 LIKFFGEIFGV----DVEIVSGELSRQKTIKIIN----PRDIPPEI 87 (87)
T ss_pred HHHHHHHHhCc----eEEEEecCCCCceEEEEeC----cccccccC
Confidence 44788899997 5566668889999998766 66888874
No 11
>PRK14626 hypothetical protein; Provisional
Probab=28.30 E-value=65 Score=21.90 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=22.4
Q ss_pred EEEEEEecceeeEEeeecccCCCccC
Q 048658 52 TLRVQVHANYRLRRIYFSDRLYSEEE 77 (83)
Q Consensus 52 t~rv~IhANCRlRRIYFsdrlYs~~e 77 (83)
.++|.++.+..|.+|-+.+.+...++
T Consensus 41 ~VkV~~nG~~ev~~i~Id~~ll~~ed 66 (110)
T PRK14626 41 MVKVVSNGLGEIKDVEIDKSLLNEDE 66 (110)
T ss_pred EEEEEEECCccEEEEEECHHHcCccc
Confidence 47899999999999999999887543
No 12
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=28.14 E-value=1.2e+02 Score=20.05 Aligned_cols=42 Identities=14% Similarity=0.216 Sum_probs=30.0
Q ss_pred hhccHHHHHHHHhCcceee-----EEEEEEecceeeEEeeecccCCC
Q 048658 33 IQLNLADFTRRAYGTNYVE-----TLRVQVHANYRLRRIYFSDRLYS 74 (83)
Q Consensus 33 i~~nL~~~t~~aygT~Y~e-----t~rv~IhANCRlRRIYFsdrlYs 74 (83)
+|-.++++-.+.=.+.+.. .++|.+.++..|.+|-+.++++.
T Consensus 17 mQ~k~~~~q~eL~~~~v~g~sggGlV~V~~~G~~~v~~v~Id~~~l~ 63 (102)
T TIGR00103 17 MQEKMKKLQEEIAQFEVTGKSGAGLVTVTINGNLELKSIEIDPSLLE 63 (102)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCEEEEEEEcCceEEEEEECHHHHh
Confidence 3445555544444444443 37899999999999999999987
No 13
>PRK14627 hypothetical protein; Provisional
Probab=28.14 E-value=68 Score=21.36 Aligned_cols=26 Identities=12% Similarity=0.327 Sum_probs=22.9
Q ss_pred EEEEEEecceeeEEeeecccCCCccC
Q 048658 52 TLRVQVHANYRLRRIYFSDRLYSEEE 77 (83)
Q Consensus 52 t~rv~IhANCRlRRIYFsdrlYs~~e 77 (83)
.++|.+..+.+|.+|-+.+.+..+++
T Consensus 37 ~VkV~~~G~~~v~~i~Idp~ll~~ed 62 (100)
T PRK14627 37 AITVKMNGHREVQSITISPEVVDPDD 62 (100)
T ss_pred eEEEEEEcCccEEEEEECHHHcCccc
Confidence 57899999999999999999987554
No 14
>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 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 [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.
Probab=26.15 E-value=86 Score=20.07 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=20.3
Q ss_pred ceeeEEEEEEecceeeEEeeecc
Q 048658 48 NYVETLRVQVHANYRLRRIYFSD 70 (83)
Q Consensus 48 ~Y~et~rv~IhANCRlRRIYFsd 70 (83)
..+...+|.+.++++.-+||++-
T Consensus 27 ~~vtIt~V~ls~Dl~~a~Vy~~~ 49 (104)
T PF02033_consen 27 KLVTITRVELSPDLSHAKVYVSI 49 (104)
T ss_dssp HCEEEEEEEECTTSSEEEEEEEE
T ss_pred ceEEEEEEEECCCCCEEEEEEEE
Confidence 56788899999999999999963
No 15
>PF11549 Sec31: Protein transport protein SEC31; InterPro: IPR021614 Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerisation of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat []. Sec13/31 is a hetero-tetramer which is organised as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron []. ; PDB: 2QTV_D.
Probab=25.36 E-value=25 Score=21.68 Aligned_cols=18 Identities=39% Similarity=0.881 Sum_probs=4.4
Q ss_pred CcccchhhccHHHHHHHH
Q 048658 27 DDGWNQIQLNLADFTRRA 44 (83)
Q Consensus 27 ~~gWn~i~~nL~~~t~~a 44 (83)
.+|||.+-++.++=..||
T Consensus 23 NdGWNDLpl~vkEKpsRA 40 (51)
T PF11549_consen 23 NDGWNDLPLKVKEKPSRA 40 (51)
T ss_dssp HS-TT---S---------
T ss_pred cCcccccchhhhcccccc
Confidence 689999999998865554
No 16
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 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 entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=25.12 E-value=59 Score=21.61 Aligned_cols=36 Identities=25% Similarity=0.538 Sum_probs=24.6
Q ss_pred HhCcceeeEEEEEEecceeeEEee-eccc-CCCccCCCCCC
Q 048658 44 AYGTNYVETLRVQVHANYRLRRIY-FSDR-LYSEEELTPEF 82 (83)
Q Consensus 44 aygT~Y~et~rv~IhANCRlRRIY-Fsdr-lYs~~eLP~ef 82 (83)
.||-+|.|.. .+..-|-||.. |.+. -|....+|+|+
T Consensus 8 ~~GN~YyE~~---~~~~~~~rRwV~y~~~~~~~~s~IPpeW 45 (105)
T PF05071_consen 8 EFGNKYYENP---RDEQGRRRRWVEYAGKSDYDPSQIPPEW 45 (105)
T ss_pred CCCCEEEeec---CCCcCCCcEEEEcCCccccCcCccCcch
Confidence 4788898877 44444555533 4555 68889999986
No 17
>smart00135 LY Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Probab=24.93 E-value=33 Score=17.37 Aligned_cols=11 Identities=27% Similarity=0.465 Sum_probs=8.1
Q ss_pred eEEeeecccCC
Q 048658 63 LRRIYFSDRLY 73 (83)
Q Consensus 63 lRRIYFsdrlY 73 (83)
=+++||+|..-
T Consensus 20 ~~~lYw~D~~~ 30 (43)
T smart00135 20 EGRLYWTDWGL 30 (43)
T ss_pred CCEEEEEeCCC
Confidence 35899999654
No 18
>PRK14622 hypothetical protein; Provisional
Probab=24.25 E-value=93 Score=20.84 Aligned_cols=25 Identities=8% Similarity=0.252 Sum_probs=22.0
Q ss_pred EEEEEEecceeeEEeeecccCCCcc
Q 048658 52 TLRVQVHANYRLRRIYFSDRLYSEE 76 (83)
Q Consensus 52 t~rv~IhANCRlRRIYFsdrlYs~~ 76 (83)
.++|.+..+.+|.+|-+.+.+..++
T Consensus 37 ~VkV~~nG~~~v~~i~Idp~~l~~e 61 (103)
T PRK14622 37 LVKVAMNGKCEVTRLTVDPKAVDPN 61 (103)
T ss_pred eEEEEEEcCceEEEEEECHHHcCcc
Confidence 5789999999999999999888644
No 19
>PRK14625 hypothetical protein; Provisional
Probab=24.06 E-value=2e+02 Score=19.59 Aligned_cols=45 Identities=29% Similarity=0.304 Sum_probs=31.8
Q ss_pred hhccHHHHHHHHhCcceeeE-----EEEEEecceeeEEeeecccCCCccC
Q 048658 33 IQLNLADFTRRAYGTNYVET-----LRVQVHANYRLRRIYFSDRLYSEEE 77 (83)
Q Consensus 33 i~~nL~~~t~~aygT~Y~et-----~rv~IhANCRlRRIYFsdrlYs~~e 77 (83)
+|=.++..-.+.-.+.+..+ ++|.+..|..|.+|-..+.+..+++
T Consensus 14 mQ~km~~~Q~el~~~~v~g~sggG~VkV~~~G~~~v~~I~Idp~ll~~eD 63 (109)
T PRK14625 14 MQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQPGE 63 (109)
T ss_pred HHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHHcCCcc
Confidence 44445555454444555443 7899999999999999998887544
No 20
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=20.27 E-value=2.2e+02 Score=19.00 Aligned_cols=38 Identities=24% Similarity=0.345 Sum_probs=27.8
Q ss_pred hhccHHHHHHHHhC---cceeeEEEEEEecceeeEEeeecc
Q 048658 33 IQLNLADFTRRAYG---TNYVETLRVQVHANYRLRRIYFSD 70 (83)
Q Consensus 33 i~~nL~~~t~~ayg---T~Y~et~rv~IhANCRlRRIYFsd 70 (83)
|+=.|+++..+... -..+...+|.+.+..+.-+||++-
T Consensus 15 i~~~is~il~~~i~d~~~~~vtIt~V~vS~Dl~~AkVyvs~ 55 (120)
T PRK00521 15 IQRELAEILQREIKDPRLGMVTVTDVEVSPDLAHAKVYVTV 55 (120)
T ss_pred HHHHHHHHHHHHccCCCCCeeEEEEEEECCCCCEEEEEEEE
Confidence 44556666653331 236888899999999999999993
No 21
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=20.03 E-value=33 Score=26.75 Aligned_cols=42 Identities=26% Similarity=0.357 Sum_probs=20.8
Q ss_pred HHHHHhCcceeeEEEEEEecce-------------eeEEeeecccCCCccCCCCC
Q 048658 40 FTRRAYGTNYVETLRVQVHANY-------------RLRRIYFSDRLYSEEELTPE 81 (83)
Q Consensus 40 ~t~~aygT~Y~et~rv~IhANC-------------RlRRIYFsdrlYs~~eLP~e 81 (83)
-..+.+|..-+-..+||++..- -+|||||.||.-++-.++++
T Consensus 20 ~lA~~~g~pvI~~Driq~y~~l~v~Sgrp~~~el~~~~RiyL~~r~l~~G~i~a~ 74 (233)
T PF01745_consen 20 ALAQKTGAPVISLDRIQCYPELSVGSGRPTPSELKGTRRIYLDDRPLSDGIINAE 74 (233)
T ss_dssp HHHHHH--EEEEE-SGGG-GGGTTTTT---SGGGTT-EEEES----GGG-S--HH
T ss_pred HHHHHhCCCEEEecceecccccccccCCCCHHHHcccceeeeccccccCCCcCHH
Confidence 3445667777777777776643 27999999999888777654
Done!