Query 038812
Match_columns 84
No_of_seqs 107 out of 302
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 03:32:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038812.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038812hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0096 RpsH Ribosomal protein 99.5 9.5E-15 2.1E-19 103.9 3.9 41 43-84 1-42 (132)
2 KOG1754 40S ribosomal protein 99.5 1.8E-14 3.9E-19 103.0 4.1 42 43-84 1-43 (130)
3 PTZ00158 40S ribosomal protein 99.5 6.1E-14 1.3E-18 98.8 4.7 42 43-84 1-43 (130)
4 PLN00146 40S ribosomal protein 99.4 2.4E-13 5.3E-18 94.8 4.6 42 43-84 1-43 (130)
5 CHL00042 rps8 ribosomal protei 99.4 5.1E-13 1.1E-17 93.1 4.6 41 43-84 1-41 (132)
6 PRK04034 rps8p 30S ribosomal p 99.3 1.1E-12 2.3E-17 91.0 4.7 42 43-84 1-43 (130)
7 PRK00136 rpsH 30S ribosomal pr 99.2 1.1E-11 2.5E-16 85.8 4.6 41 43-84 1-41 (130)
8 PF00410 Ribosomal_S8: Ribosom 99.1 1.1E-10 2.4E-15 80.0 4.1 38 46-84 1-38 (129)
9 PF13541 ChlI: Subunit ChlI of 48.7 12 0.00025 25.8 1.5 26 46-72 95-120 (121)
10 COG1902 NemA NADH:flavin oxido 45.3 35 0.00076 27.5 3.9 44 36-79 136-180 (363)
11 PRK00026 trmD tRNA (guanine-N( 33.4 34 0.00075 26.9 2.1 31 43-73 60-92 (244)
12 cd02803 OYE_like_FMN_family Ol 30.9 87 0.0019 23.4 3.9 26 46-71 138-163 (327)
13 cd02932 OYE_YqiM_FMN Old yello 28.3 93 0.002 23.9 3.7 34 36-69 141-174 (336)
14 KOG3125 Thymidine kinase [Nucl 28.1 60 0.0013 25.7 2.7 40 33-72 23-65 (234)
15 COG0336 TrmD tRNA-(guanine-N1) 27.3 48 0.001 26.3 2.0 29 43-73 60-90 (240)
16 PF00265 TK: Thymidine kinase; 23.3 98 0.0021 22.2 2.9 23 49-71 16-38 (176)
17 PRK14599 trmD tRNA (guanine-N( 21.6 85 0.0018 24.5 2.4 28 43-73 60-89 (222)
18 KOG4451 Uncharacterized conser 21.5 67 0.0014 26.0 1.9 13 27-39 220-232 (286)
19 PF00724 Oxidored_FMN: NADH:fl 20.4 1.4E+02 0.0031 23.1 3.5 34 46-79 146-180 (341)
20 cd04734 OYE_like_3_FMN Old yel 20.4 1.9E+02 0.0042 22.6 4.2 44 36-79 128-172 (343)
No 1
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=99.52 E-value=9.5e-15 Score=103.91 Aligned_cols=41 Identities=37% Similarity=0.451 Sum_probs=37.0
Q ss_pred hcc-cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 Msm-DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|+| ||||||||+||||++++|..|.+ |+||++.+||+|||+
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~~-P~SKl~~~il~vLk~ 42 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVSM-PASKLKGAILKVLKK 42 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceeec-chHHHHHHHHHHHHH
Confidence 777 99999999999999996666665 999999999999985
No 2
>KOG1754 consensus 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis]
Probab=99.50 E-value=1.8e-14 Score=103.01 Aligned_cols=42 Identities=48% Similarity=0.700 Sum_probs=40.0
Q ss_pred hcc-cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 Msm-DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|++ |.|+|+|++|+||+++||.||+|+||||++++||.||++
T Consensus 1 m~~~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmk 43 (130)
T KOG1754|consen 1 MVRMNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMK 43 (130)
T ss_pred CchHHHHHHHHHHhhhHHhcCCceEEecccHHHHHHHHHHHHH
Confidence 566 999999999999999999999999999999999999975
No 3
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=99.46 E-value=6.1e-14 Score=98.78 Aligned_cols=42 Identities=48% Similarity=0.742 Sum_probs=40.1
Q ss_pred hcc-cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 Msm-DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|++ |||+||||+||||++++|++|.+.|+||++.+||++|++
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V~v~p~Skl~~~il~IL~~ 43 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQK 43 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeEEEeCCcHHHHHHHHHHHH
Confidence 776 999999999999999999999988999999999999985
No 4
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=99.41 E-value=2.4e-13 Score=94.83 Aligned_cols=42 Identities=48% Similarity=0.742 Sum_probs=39.0
Q ss_pred hcc-cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 Msm-DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|++ |||+||||+||||++++|++|.+.|+||++.+|+++|++
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~p~Skl~~~il~iL~~ 43 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQK 43 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEEcChHHHHHHHHHHHH
Confidence 677 999999999999999999999744999999999999985
No 5
>CHL00042 rps8 ribosomal protein S8
Probab=99.38 E-value=5.1e-13 Score=93.14 Aligned_cols=41 Identities=29% Similarity=0.456 Sum_probs=38.3
Q ss_pred hcccHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGRRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 MsmDpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|..|||+|+|++||||++++|.+|.+ |+||++.+||++|++
T Consensus 1 m~~d~iad~lt~IrNa~~a~~~~v~i-p~Skl~~~il~iL~~ 41 (132)
T CHL00042 1 MGNDTIADMLTRIRNANMVKKGTVRI-PATNITENIVKILLR 41 (132)
T ss_pred CCcchHHHHHHHhHHHHHCCCCEEEE-eccHHHHHHHHHHHH
Confidence 43399999999999999999999999 999999999999975
No 6
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=99.35 E-value=1.1e-12 Score=91.05 Aligned_cols=42 Identities=36% Similarity=0.449 Sum_probs=38.7
Q ss_pred hcc-cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 Msm-DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|++ |||+|+||+||||++++|++|.+.|+||++.+||++|++
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~p~Sk~~~~il~iL~~ 43 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIKPASKLIGNVLRVMQD 43 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEEcccHHHHHHHHHHHH
Confidence 666 999999999999999999998744999999999999975
No 7
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=99.23 E-value=1.1e-11 Score=85.77 Aligned_cols=41 Identities=27% Similarity=0.289 Sum_probs=38.0
Q ss_pred hcccHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 43 MGRRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 43 MsmDpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|..|||+|+|++|+||+++||.+|.+ |+||+..+||++|++
T Consensus 1 m~~d~i~d~lt~IrNa~~~~~~~v~i-p~sk~~~~il~iL~~ 41 (130)
T PRK00136 1 SMTDPIADMLTRIRNAQMAKHETVSM-PASKLKVAIAEILKE 41 (130)
T ss_pred CCcChHHHHHHHHHHHHHcCCCeEEe-cccHHHHHHHHHHHH
Confidence 43399999999999999999999998 999999999999974
No 8
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 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 [, ]. Ribosomal protein S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=99.09 E-value=1.1e-10 Score=79.99 Aligned_cols=38 Identities=39% Similarity=0.400 Sum_probs=36.9
Q ss_pred cHHHHHHHhhHhHHhhCCceeEEecccHHHHHHHHHhhC
Q 038812 46 RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKY 84 (84)
Q Consensus 46 DpLADaLTrIrNAerrGK~qV~I~PaSKL~i~IL~VLk~ 84 (84)
|||+|+|++|+||++++|.+|.+ |+||++.+||++|++
T Consensus 1 D~lad~l~~I~Na~~~~~~~v~i-p~sk~~~~il~iL~~ 38 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRFVII-PYSKLNLSILKILKK 38 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSEEEE-EHCHHHHHHHHHHHH
T ss_pred CcHHHHHHHhHHHHHCCCCEEEe-cccHHHHHHHHHHhh
Confidence 89999999999999999999999 999999999999974
No 9
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=48.67 E-value=12 Score=25.85 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=24.0
Q ss_pred cHHHHHHHhhHhHHhhCCceeEEeccc
Q 038812 46 RILNDALRAIVNAERRGKATVELQPIS 72 (84)
Q Consensus 46 DpLADaLTrIrNAerrGK~qV~I~PaS 72 (84)
-|+..++.+|..|.+.|.+++++ |..
T Consensus 95 r~v~~~~~~~~~A~~~G~~~viv-P~~ 120 (121)
T PF13541_consen 95 RPVPGILPRIIEAKKLGFKRVIV-PKA 120 (121)
T ss_pred EecCcHHHHHHHHHHCCCCEEEe-CCC
Confidence 78999999999999999999999 865
No 10
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=45.26 E-value=35 Score=27.54 Aligned_cols=44 Identities=30% Similarity=0.398 Sum_probs=31.4
Q ss_pred hhhhhhhhcccHHHHHHHhhHhHHhhCCceeEEeccc-HHHHHHH
Q 038812 36 PREVQTVMGRRILNDALRAIVNAERRGKATVELQPIS-TVMSSFL 79 (84)
Q Consensus 36 ~~~~~~~MsmDpLADaLTrIrNAerrGK~qV~I~PaS-KL~i~IL 79 (84)
|||+...--.+.+.|.-..-++|+++|.+-|.|+=+- -|+..||
T Consensus 136 pr~mt~~eI~~ii~~f~~AA~rA~~AGFDgVEIH~AhGYLi~qFl 180 (363)
T COG1902 136 PRELTEEEIEEVIEDFARAARRAKEAGFDGVEIHGAHGYLLSQFL 180 (363)
T ss_pred CccCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEeeccchHHHHhc
Confidence 4444333322899999999999999999999995443 3555554
No 11
>PRK00026 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed
Probab=33.36 E-value=34 Score=26.92 Aligned_cols=31 Identities=26% Similarity=0.193 Sum_probs=19.6
Q ss_pred hcc--cHHHHHHHhhHhHHhhCCceeEEecccH
Q 038812 43 MGR--RILNDALRAIVNAERRGKATVELQPIST 73 (84)
Q Consensus 43 Msm--DpLADaLTrIrNAerrGK~qV~I~PaSK 73 (84)
|+| |||.++|..++.....+.+.|.+.|.-|
T Consensus 60 Mvm~~epi~~al~~~~~~~~~~~~vi~lsP~G~ 92 (244)
T PRK00026 60 MVMKPEPLFDAIDAAKAAAGEKAKVILLSPQGK 92 (244)
T ss_pred ceecHHHHHHHHHHHHhhcCCCCeEEEECCCCC
Confidence 656 9999999999754222223555555543
No 12
>cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=30.94 E-value=87 Score=23.42 Aligned_cols=26 Identities=27% Similarity=0.304 Sum_probs=23.5
Q ss_pred cHHHHHHHhhHhHHhhCCceeEEecc
Q 038812 46 RILNDALRAIVNAERRGKATVELQPI 71 (84)
Q Consensus 46 DpLADaLTrIrNAerrGK~qV~I~Pa 71 (84)
+.+-|+...-++++..|.+-|.|.-+
T Consensus 138 ~~i~~~~~aA~~a~~aGfDgveih~~ 163 (327)
T cd02803 138 QIIEDFAAAARRAKEAGFDGVEIHGA 163 (327)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEcch
Confidence 88999999999999999999999654
No 13
>cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.
Probab=28.30 E-value=93 Score=23.88 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=26.4
Q ss_pred hhhhhhhhcccHHHHHHHhhHhHHhhCCceeEEe
Q 038812 36 PREVQTVMGRRILNDALRAIVNAERRGKATVELQ 69 (84)
Q Consensus 36 ~~~~~~~MsmDpLADaLTrIrNAerrGK~qV~I~ 69 (84)
|||+....-.+.+.|+....+++.+.|.+-|.|.
T Consensus 141 p~~mt~~eI~~ii~~~~~aA~~a~~aGfDgVei~ 174 (336)
T cd02932 141 PRELTREEIAEVVDAFVAAARRAVEAGFDVIEIH 174 (336)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEc
Confidence 3444433323789999999999999999999995
No 14
>KOG3125 consensus Thymidine kinase [Nucleotide transport and metabolism]
Probab=28.12 E-value=60 Score=25.66 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=32.8
Q ss_pred CCchhhhhhhhc-c--cHHHHHHHhhHhHHhhCCceeEEeccc
Q 038812 33 SNIPREVQTVMG-R--RILNDALRAIVNAERRGKATVELQPIS 72 (84)
Q Consensus 33 ~~~~~~~~~~Ms-m--DpLADaLTrIrNAerrGK~qV~I~PaS 72 (84)
++.+-++.-+|+ | ---+++|.||+-....|++-++++|.+
T Consensus 23 ~~t~G~i~vI~gPMfSGKTt~LLrr~r~~~~~grrv~liK~~k 65 (234)
T KOG3125|consen 23 PMTRGTIHVILGPMFSGKTTELLRRIRREIIAGRRVLLIKYAK 65 (234)
T ss_pred CCCCceEEEEeccccCcchHHHHHHHHHHHhcCceEEEEEecC
Confidence 366677777773 3 667899999999999999999997765
No 15
>COG0336 TrmD tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=27.33 E-value=48 Score=26.26 Aligned_cols=29 Identities=28% Similarity=0.271 Sum_probs=20.7
Q ss_pred hcc--cHHHHHHHhhHhHHhhCCceeEEecccH
Q 038812 43 MGR--RILNDALRAIVNAERRGKATVELQPIST 73 (84)
Q Consensus 43 Msm--DpLADaLTrIrNAerrGK~qV~I~PaSK 73 (84)
|+| +||.++|..++... +.+.+++.|.-|
T Consensus 60 Mvmk~epi~~Al~~~~~~~--~~~vi~lsP~G~ 90 (240)
T COG0336 60 MVMKPEPLFDALDSVKAAK--KAKVILLSPQGK 90 (240)
T ss_pred cEeccHHHHHHHHHHHhcc--CCeEEEECCCCC
Confidence 555 99999999999887 444555555443
No 16
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=23.28 E-value=98 Score=22.16 Aligned_cols=23 Identities=26% Similarity=0.424 Sum_probs=19.1
Q ss_pred HHHHHhhHhHHhhCCceeEEecc
Q 038812 49 NDALRAIVNAERRGKATVELQPI 71 (84)
Q Consensus 49 ADaLTrIrNAerrGK~qV~I~Pa 71 (84)
...|.+++|.+.+|++-++++|.
T Consensus 16 ~eLi~~~~~~~~~~~~v~~~kp~ 38 (176)
T PF00265_consen 16 TELIRRIHRYEIAGKKVLVFKPA 38 (176)
T ss_dssp HHHHHHHHHHHHTT-EEEEEEES
T ss_pred HHHHHHHHHHHhCCCeEEEEEec
Confidence 45689999999999999999885
No 17
>PRK14599 trmD tRNA (guanine-N(1)-)-methyltransferase/unknown domain fusion protein; Provisional
Probab=21.64 E-value=85 Score=24.48 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=19.2
Q ss_pred hcc--cHHHHHHHhhHhHHhhCCceeEEecccH
Q 038812 43 MGR--RILNDALRAIVNAERRGKATVELQPIST 73 (84)
Q Consensus 43 Msm--DpLADaLTrIrNAerrGK~qV~I~PaSK 73 (84)
|+| +||.++|..|++. +.+.+.+.|.-|
T Consensus 60 Mvm~~epl~~al~~~~~~---~~~vi~lsP~G~ 89 (222)
T PRK14599 60 MLLRVEPIHKALLSLGEK---KGIVILTSPSGI 89 (222)
T ss_pred cEecchHHHHHHHHHhhc---CCcEEEECCCCC
Confidence 666 9999999999852 234566656543
No 18
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=21.48 E-value=67 Score=25.99 Aligned_cols=13 Identities=23% Similarity=0.289 Sum_probs=7.1
Q ss_pred hcCCCCCCchhhh
Q 038812 27 AVSPSPSNIPREV 39 (84)
Q Consensus 27 ~~~~~~~~~~~~~ 39 (84)
..||||++++..+
T Consensus 220 ~p~~~~v~r~Q~~ 232 (286)
T KOG4451|consen 220 QPSGSQVDRPQNL 232 (286)
T ss_pred CCCCCcccchhhc
Confidence 3455666666543
No 19
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside []. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions []. The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GKA_B 3P67_A 3F03_K 2ABA_A 1VYR_A 1GVO_A 3KFT_B 3P8I_A 1GVQ_A 3P74_A ....
Probab=20.45 E-value=1.4e+02 Score=23.06 Aligned_cols=34 Identities=29% Similarity=0.423 Sum_probs=25.7
Q ss_pred cHHHHHHHhhHhHHhhCCceeEEecc-cHHHHHHH
Q 038812 46 RILNDALRAIVNAERRGKATVELQPI-STVMSSFL 79 (84)
Q Consensus 46 DpLADaLTrIrNAerrGK~qV~I~Pa-SKL~i~IL 79 (84)
..+-|.-..=++|+++|.+-|.|.=+ --|+..||
T Consensus 146 ~ii~~f~~AA~~A~~AGfDGVEIH~ahGyLl~qFL 180 (341)
T PF00724_consen 146 EIIEDFAQAARRAKEAGFDGVEIHAAHGYLLSQFL 180 (341)
T ss_dssp HHHHHHHHHHHHHHHTT-SEEEEEESTTSHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCeEeecccchhhhhhee
Confidence 78888999999999999999999432 22666665
No 20
>cd04734 OYE_like_3_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.
Probab=20.41 E-value=1.9e+02 Score=22.58 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=30.5
Q ss_pred hhhhhhhhcccHHHHHHHhhHhHHhhCCceeEEecc-cHHHHHHH
Q 038812 36 PREVQTVMGRRILNDALRAIVNAERRGKATVELQPI-STVMSSFL 79 (84)
Q Consensus 36 ~~~~~~~MsmDpLADaLTrIrNAerrGK~qV~I~Pa-SKL~i~IL 79 (84)
+||+....-...+-|+-...++|++.|.+-|.|.=+ .-|...||
T Consensus 128 ~~~mt~~eI~~ii~~f~~AA~ra~~aGfDgVeih~ahGyLl~qFl 172 (343)
T cd04734 128 PKAMEEEDIEEIIAAFADAARRCQAGGLDGVELQAAHGHLIDQFL 172 (343)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEccccchHHHHhh
Confidence 455444443378889999999999999999999432 33444443
Done!