Query 045554
Match_columns 323
No_of_seqs 147 out of 898
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:15:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045554.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045554hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00044 rpl16 ribosomal prote 100.0 6E-51 1.3E-55 347.8 16.8 135 182-316 1-135 (135)
2 PRK09203 rplP 50S ribosomal pr 100.0 1.3E-49 2.8E-54 340.1 16.6 134 182-315 1-134 (138)
3 TIGR01164 rplP_bact ribosomal 100.0 2.3E-47 5E-52 322.1 15.3 126 183-308 1-126 (126)
4 COG0197 RplP Ribosomal protein 100.0 3E-47 6.5E-52 330.0 14.8 137 181-317 1-139 (146)
5 PF00252 Ribosomal_L16: Riboso 100.0 6.8E-46 1.5E-50 313.8 12.9 130 185-314 1-133 (133)
6 cd01433 Ribosomal_L16_L10e Rib 100.0 2.2E-39 4.8E-44 265.9 13.5 109 205-313 2-112 (112)
7 KOG3422 Mitochondrial ribosoma 100.0 2.5E-39 5.3E-44 294.5 12.7 135 183-317 40-178 (221)
8 TIGR00279 L10e ribosomal prote 100.0 2.1E-33 4.4E-38 249.3 13.0 104 213-316 47-166 (172)
9 PRK04199 rpl10e 50S ribosomal 100.0 5.4E-33 1.2E-37 246.6 15.1 104 214-317 48-167 (172)
10 PTZ00173 60S ribosomal protein 100.0 1.1E-29 2.4E-34 231.6 12.6 104 213-316 50-169 (213)
11 KOG0857 60s ribosomal protein 98.3 4.6E-07 1E-11 83.7 3.9 100 215-314 52-168 (212)
12 TIGR03738 PRTRC_C PRTRC system 54.4 4.9 0.00011 31.9 0.4 41 40-84 15-55 (66)
13 PF13533 Biotin_lipoyl_2: Biot 51.2 20 0.00042 25.8 3.1 31 269-299 11-45 (50)
14 COG3197 FixS Uncharacterized p 37.6 20 0.00043 27.9 1.4 24 117-140 11-34 (58)
15 PF14454 Prok_Ub: Prokaryotic 36.2 13 0.00027 29.3 0.2 29 40-69 16-44 (65)
16 PF07831 PYNP_C: Pyrimidine nu 31.4 35 0.00076 26.8 1.9 27 277-303 43-69 (75)
17 PRK05783 hypothetical protein; 27.8 89 0.0019 25.6 3.7 32 275-306 35-67 (84)
18 TIGR00847 ccoS cytochrome oxid 27.6 39 0.00085 25.5 1.5 25 116-140 8-34 (51)
19 PRK14445 acylphosphatase; Prov 21.6 2.8E+02 0.0061 22.2 5.5 42 270-313 31-72 (91)
20 cd01178 IPT_NFAT IPT domain of 21.4 61 0.0013 27.5 1.7 29 73-101 64-98 (101)
21 cd07028 RNAP_RPB3_like RPB3 su 21.1 73 0.0016 29.7 2.3 87 213-305 96-205 (212)
22 PF02505 MCR_D: Methyl-coenzym 20.2 6.8E+02 0.015 23.0 9.1 78 229-313 14-106 (153)
No 1
>CHL00044 rpl16 ribosomal protein L16
Probab=100.00 E-value=6e-51 Score=347.75 Aligned_cols=135 Identities=75% Similarity=1.241 Sum_probs=132.4
Q ss_pred hcCCCCCCCCCCCCCCCCCCCCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecCCcc
Q 045554 182 LAGPKRIKFPKQHRGRMTGKASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTARPAE 261 (323)
Q Consensus 182 ML~PKktKyrK~~KGRikG~s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKKPaE 261 (323)
||+||+|||+|+|||+++|.++++++|.||+|||+++|+|+|+++||||||++|+|+|++++++|||+|||+|||+||.|
T Consensus 1 ml~Pk~~k~~K~~k~~~~g~~~~~~~l~~G~~GL~a~e~~~i~~~qiEaaR~~i~r~lkk~~~i~irv~P~~pvtkkp~e 80 (135)
T CHL00044 1 MLSPKRTKFRKQHRGRMKGISYRGNRICFGRYALQALEPAWITSRQIEAGRRAITRYARRGGKIWIRIFPDKPVTMRPAE 80 (135)
T ss_pred CCCCCccccccccCCCCCCcCCCCCeEeeccEEEEEccCcEECHHHHHHHHHHHHHhhhcCcEEEEEECCCcceEeCccc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCceEEEEEEcCCCEEEEEecCCHHHHHHHHHHhhccCCCcEEEEEcC
Q 045554 262 TRMGSGKGSHAYWAAVVTPGKIIFEMSGVPENIARKAISIAASKMPIKTQFVMSG 316 (323)
Q Consensus 262 tRMGKGKGkId~WVArVK~GqIIFEI~GVs~~~AkeALk~Aa~KLPiKtkIV~ke 316 (323)
+|||+|||+|+||||+|++|+||||++|+++++|++||++|++|||++|+||.++
T Consensus 81 ~RMGkGKG~~~~~va~V~~G~ilfEi~g~~~~~ak~al~~a~~KLP~k~~~v~~~ 135 (135)
T CHL00044 81 TRMGSGKGSPEYWVAVVKPGRILYEMGGVSETIARAAIKIAAYKMPIKTQFIISE 135 (135)
T ss_pred ccccCCCCCccEEEEEECCCcEEEEEeCCCHHHHHHHHHHHhhcCCCcEEEEecC
Confidence 9999999999999999999999999999999999999999999999999999754
No 2
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=100.00 E-value=1.3e-49 Score=340.11 Aligned_cols=134 Identities=63% Similarity=1.141 Sum_probs=132.2
Q ss_pred hcCCCCCCCCCCCCCCCCCCCCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecCCcc
Q 045554 182 LAGPKRIKFPKQHRGRMTGKASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTARPAE 261 (323)
Q Consensus 182 ML~PKktKyrK~~KGRikG~s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKKPaE 261 (323)
||+||+|||+|+||||++|.+.++++|.||+|||+++|+|+|+++||||||++|+|+|++.+++|||+|||+|||+||+|
T Consensus 1 ml~Pk~~k~~K~~kgr~~g~~~~~~~l~~G~~gL~a~e~g~i~~~qlEaaR~~i~r~Lkk~g~~~irv~P~~~vt~k~~~ 80 (138)
T PRK09203 1 MLQPKRTKYRKQHKGRNRGKAKRGNTVAFGEFGLKALEPGWITARQIEAARIAMTRHIKRGGKVWIRIFPDKPVTKKPAE 80 (138)
T ss_pred CCCCCccccccCCCCCCCCCCCCCCeEeeccEEEEECcCCeEcHHHHHHHHHHHHHHhhcCceEEEEeCCCccEEcChhh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCceEEEEEEcCCCEEEEEecCCHHHHHHHHHHhhccCCCcEEEEEc
Q 045554 262 TRMGSGKGSHAYWAAVVTPGKIIFEMSGVPENIARKAISIAASKMPIKTQFVMS 315 (323)
Q Consensus 262 tRMGKGKGkId~WVArVK~GqIIFEI~GVs~~~AkeALk~Aa~KLPiKtkIV~k 315 (323)
+|||+|||+|+||||+|++|+||||+++++++.|++||++|++|||++|+|+.+
T Consensus 81 ~RMGkGKG~~~~~varVk~G~iifEi~~~~~~~a~~al~~a~~KLP~~~kii~~ 134 (138)
T PRK09203 81 VRMGKGKGSPEYWVAVVKPGRILFEIAGVSEELAREALRLAAAKLPIKTKFVKR 134 (138)
T ss_pred ccccCCCCCCcEEEEEECCCCEEEEEeCCCHHHHHHHHHHHhccCCCcEEEEEe
Confidence 999999999999999999999999999999999999999999999999999986
No 3
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=100.00 E-value=2.3e-47 Score=322.05 Aligned_cols=126 Identities=69% Similarity=1.197 Sum_probs=124.3
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecCCccc
Q 045554 183 AGPKRIKFPKQHRGRMTGKASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTARPAET 262 (323)
Q Consensus 183 L~PKktKyrK~~KGRikG~s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKKPaEt 262 (323)
|+||+|||+|+||++++|.+.++++|.||+|||+++|+++|+++||||||++|+|+|++++++|||+|||+|||+||+|+
T Consensus 1 l~Pk~~k~~K~~k~~~~g~~~~~~~l~~G~~gL~a~e~~~i~~~qlEaaR~~i~r~l~~~~~~~irv~P~~~vt~k~~~~ 80 (126)
T TIGR01164 1 LSPKRTKYRKQHRGRMKGKAKRGNTVAFGEYGLQALEPGWITARQIEAARVAMTRYVKRGGKLWIRIFPDKPYTKKPLET 80 (126)
T ss_pred CCCCccccccccCCCCCCcCCCCCeeeeccEeeEECcCCeEcHHHHHHHHHHHHHHHhhCceEEEEECCCcCEEeCchhc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCceEEEEEEcCCCEEEEEecCCHHHHHHHHHHhhccCCC
Q 045554 263 RMGSGKGSHAYWAAVVTPGKIIFEMSGVPENIARKAISIAASKMPI 308 (323)
Q Consensus 263 RMGKGKGkId~WVArVK~GqIIFEI~GVs~~~AkeALk~Aa~KLPi 308 (323)
|||+|||+|++|||+|++|+||||+++++++.|++||++|++|||+
T Consensus 81 RMGkGKG~~~~~varV~~G~ilfEi~~~~~~~a~~al~~a~~KLP~ 126 (126)
T TIGR01164 81 RMGKGKGNPEYWVAVVKPGKILFEIAGVPEEVAREAFRLAASKLPI 126 (126)
T ss_pred cccCCCCCCCEEEEEECCCCEEEEEeCCCHHHHHHHHHHHHhcCCC
Confidence 9999999999999999999999999999999999999999999996
No 4
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-47 Score=330.03 Aligned_cols=137 Identities=55% Similarity=0.946 Sum_probs=133.2
Q ss_pred hhcCCCCCCCCCCCCCCCCCC--CCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecC
Q 045554 181 LLAGPKRIKFPKQHRGRMTGK--ASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTAR 258 (323)
Q Consensus 181 MML~PKktKyrK~~KGRikG~--s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKK 258 (323)
||++|++|||+|.|+++..|. +..|+.+.||+|||+++|++|||++||||||+++||+|++.+++|||+|||+|+|+|
T Consensus 1 ~ml~Pk~tk~rk~~~g~~~~~~~~~~G~~~~fg~~gL~a~e~~~It~~qiEAARia~~R~lkr~g~~wIRvfP~~~~~~k 80 (146)
T COG0197 1 HMLQPKRTKYRKQHKGRGPGITIAKGGNKVFFGEYGLVALEPGQITARQIEAARIAANRYLKRGGGLWIRVFPDKPLTEK 80 (146)
T ss_pred CCcCCCcceeecccCCCCCCceeccCCccccceEEEEEEcccceecHHHHHHHHHHHHHHhhhcCCEEEEEcCCceeeeC
Confidence 579999999999999999998 889999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCCCCCceEEEEEEcCCCEEEEEecCCHHHHHHHHHHhhccCCCcEEEEEcCC
Q 045554 259 PAETRMGSGKGSHAYWAAVVTPGKIIFEMSGVPENIARKAISIAASKMPIKTQFVMSGT 317 (323)
Q Consensus 259 PaEtRMGKGKGkId~WVArVK~GqIIFEI~GVs~~~AkeALk~Aa~KLPiKtkIV~ke~ 317 (323)
|.|+|||+|||+|++|||+|++|++|||+.|++++.|+|||++|++|||++|+++...+
T Consensus 81 p~e~Rmg~GkG~pegwaArVkpG~vlfei~g~~e~~A~EAlr~Aa~KLP~~~~~v~~~~ 139 (146)
T COG0197 81 PGEDRMGKGKGKPEGWAARVKPGRVLFEIAGVPEELAREALRRAAAKLPVKTKFVIRIE 139 (146)
T ss_pred CCcccccCCCCCccEEEEEecCCcEEEEEecCcHHHHHHHHHHHhhcCCCceEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999888764
No 5
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 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 [, ]. This entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
Probab=100.00 E-value=6.8e-46 Score=313.82 Aligned_cols=130 Identities=52% Similarity=0.902 Sum_probs=124.8
Q ss_pred CCCCCCCCCCC-CCC-CCCCCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecCCccc
Q 045554 185 PKRIKFPKQHR-GRM-TGKASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTARPAET 262 (323)
Q Consensus 185 PKktKyrK~~K-GRi-kG~s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKKPaEt 262 (323)
|+++||||+|| +|+ .+.+..+++|.||+|||+++|+|+|+++||||||++|+|+|++++++|||+|||+|||+||+|+
T Consensus 1 Pk~~kyrk~~k~~r~~~~~~~~~~~l~~g~~gl~a~~~g~l~~~qlEa~R~~i~r~lkk~~~~~i~v~p~~~vTkk~~~~ 80 (133)
T PF00252_consen 1 PKRTKYRKYQKYPRINYGKSKPGNKLKFGDYGLKALEPGRLTSNQLEAARIAINRYLKKNGKLWIRVFPHHPVTKKPLET 80 (133)
T ss_dssp TSCCSTSSSSS-SSTTTSTTSSCSSSSSSSEEEEESS-EEEEHHHHHHHHHHHHHHHHHTSTEEESSSCEEEEEE-SSSS
T ss_pred CCCCccCCCCCCCCCCcccccCccEEEeeeeeEEEeeeeeechhhhHHHHHHHHHHhhhheeEEEEeeeeeeeeeehhhh
Confidence 89999999999 888 7888899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCceEEEEEEcCCCEEEEEec-CCHHHHHHHHHHhhccCCCcEEEEE
Q 045554 263 RMGSGKGSHAYWAAVVTPGKIIFEMSG-VPENIARKAISIAASKMPIKTQFVM 314 (323)
Q Consensus 263 RMGKGKGkId~WVArVK~GqIIFEI~G-Vs~~~AkeALk~Aa~KLPiKtkIV~ 314 (323)
|||+|||+|++|||+|++|+||||++| ++++.|++||++|++|||++|+||+
T Consensus 81 RMG~GKG~~~~~~a~V~~G~iifEi~~~v~~~~a~~alk~a~~KLP~~~~~v~ 133 (133)
T PF00252_consen 81 RMGKGKGKIDHWVARVKPGQIIFEIGGKVNEEEAKEALKRAAKKLPIKTKFVS 133 (133)
T ss_dssp SSSSSSCEEEEEEEEESTTEEEEEEESGSCHHHHHHHHHHHHHTSSSCEEEE-
T ss_pred hhccCCCCccEEEEEECCCcEEEEECCcCCHHHHHHHHHHHHhhCCCCEEEeC
Confidence 999999999999999999999999999 9999999999999999999999984
No 6
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=100.00 E-value=2.2e-39 Score=265.94 Aligned_cols=109 Identities=56% Similarity=0.983 Sum_probs=106.6
Q ss_pred CceeEeeceEEEEecCceecHHHHHHHHHHHHhhhccC-ceEEEEeCCCCceecCCcccccCCCCCCceEEEEEEcCCCE
Q 045554 205 GNLICFGRYALQALEPAWITARQIEAGRRAMVRNVKRG-GKIWVRIFPDKPVTARPAETRMGSGKGSHAYWAAVVTPGKI 283 (323)
Q Consensus 205 g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LKK~-gklWIRVfP~~PVTKKPaEtRMGKGKGkId~WVArVK~GqI 283 (323)
++++.||+|||+++|+++|+++||||||++|+|+|++. +++|||+|||+|+|+||.|+|||+|||+|++|||+|++|++
T Consensus 2 ~~~~~~g~~gL~a~e~~~i~~~~lEa~R~~i~r~l~k~~~~~~ir~~p~~~vt~k~~~~rMGkGKG~~~~~~a~v~~G~i 81 (112)
T cd01433 2 GNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGGKLWIRVFPDHPVTKKPLETRMGKGKGKPEGWVARVKPGQI 81 (112)
T ss_pred CceeccceEEEEECcCCeECHHHHHHHHHHHHHHhhhcCceEEEEecCCccEEECccccccCCCCCCccEEEEEECCCCE
Confidence 57899999999999999999999999999999999998 99999999999999999999999999999999999999999
Q ss_pred EEEEecCC-HHHHHHHHHHhhccCCCcEEEE
Q 045554 284 IFEMSGVP-ENIARKAISIAASKMPIKTQFV 313 (323)
Q Consensus 284 IFEI~GVs-~~~AkeALk~Aa~KLPiKtkIV 313 (323)
|||+.+++ ++.|++||++|++|||++|+|+
T Consensus 82 ifEi~~~~~~~~~~~alk~a~~Klp~~~k~i 112 (112)
T cd01433 82 LFEVRGVPEEEVAKEALRRAAKKLPIKTKIV 112 (112)
T ss_pred EEEEeCcCcHHHHHHHHHHhhccCCCcEEEC
Confidence 99999998 9999999999999999999985
No 7
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-39 Score=294.53 Aligned_cols=135 Identities=44% Similarity=0.714 Sum_probs=129.9
Q ss_pred cCCCCCCCCCCCCCCC-CCCCCCCceeEeeceEEEEecCceecHHHHHHHHHHHHhhhc--cCceEEEEeCCCCceecCC
Q 045554 183 AGPKRIKFPKQHRGRM-TGKASRGNLICFGRYALQALEPAWITARQIEAGRRAMVRNVK--RGGKIWVRIFPDKPVTARP 259 (323)
Q Consensus 183 L~PKktKyrK~~KGRi-kG~s~~g~~L~fG~yGLkAlE~GrITa~QLEAAR~aInR~LK--K~gklWIRVfP~~PVTKKP 259 (323)
..|+++||+|++|||+ +|.+.++++|.||+|||+++++|+|++.|+|++|.++.|+++ ++|++|.|++||+|+|+||
T Consensus 40 ~~P~r~k~rk~~rgr~~rG~s~~gt~L~~g~Ygl~a~~~g~l~~~~~e~~r~~~~r~~~~~~~~~iWrr~~p~~Pvt~K~ 119 (221)
T KOG3422|consen 40 YAPERTKYRKIQRGRVPRGGSERGTELIFGRYGLRAKSGGILDSAQFEAMRLTRARKMNPRNNGKIWRRPAPNLPVTVKG 119 (221)
T ss_pred ccccchhhhHhhccccccCCccccceeeechhhheeccCceeeHHHHHHHHHHHHHhcCcccCccEEEEecCCCceeecC
Confidence 4499999999999998 899999999999999999999999999999999988888876 5899999999999999999
Q ss_pred cccccCCCCCCceEEEEEEcCCCEEEEEec-CCHHHHHHHHHHhhccCCCcEEEEEcCC
Q 045554 260 AETRMGSGKGSHAYWAAVVTPGKIIFEMSG-VPENIARKAISIAASKMPIKTQFVMSGT 317 (323)
Q Consensus 260 aEtRMGKGKGkId~WVArVK~GqIIFEI~G-Vs~~~AkeALk~Aa~KLPiKtkIV~ke~ 317 (323)
.|+|||+|||+||||||+|++|+||||++| +++++|++||.+||+|||++++||++++
T Consensus 120 ~etRMG~GKGa~d~wva~V~~GrIl~EmgG~~~~~~Ar~al~~aa~klp~~~efVs~~~ 178 (221)
T KOG3422|consen 120 NETRMGGGKGAIDHWVARVKAGRILFEMGGDVEEEEARQALLQAAHKLPFKYEFVSEEM 178 (221)
T ss_pred cceeccCCCCCcceeEEEecCCcEEEEeCCcccHHHHHHHHHHHHhcCCccEEEeeHhh
Confidence 999999999999999999999999999999 9999999999999999999999998865
No 8
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=100.00 E-value=2.1e-33 Score=249.27 Aligned_cols=104 Identities=27% Similarity=0.334 Sum_probs=99.9
Q ss_pred eEEEEecCceecHHHHHHHHHHHHhhhccC-----ceEEEEeCCCCceecCCcccccCC---------CCCCceEEEEEE
Q 045554 213 YALQALEPAWITARQIEAGRRAMVRNVKRG-----GKIWVRIFPDKPVTARPAETRMGS---------GKGSHAYWAAVV 278 (323)
Q Consensus 213 yGLkAlE~GrITa~QLEAAR~aInR~LKK~-----gklWIRVfP~~PVTKKPaEtRMGK---------GKGkId~WVArV 278 (323)
..|+++|+++||++||||||++++|+|+|. |++|||+|||+|+|+||+++|||+ |||++++|||+|
T Consensus 47 ~~L~a~E~~~I~~~qiEAaR~a~~r~lkk~~g~~~~k~wIRvfP~~~lt~kp~~trmGaDRlq~GMr~gkG~p~~wvArV 126 (172)
T TIGR00279 47 VHLVAKEPEQIRHNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKMATGAGADRIQQGMRGAFGKPVGTAARV 126 (172)
T ss_pred EEEEECccceecHHHHHHHHHHHHHHHHhhcCccceEEEEEECCCCceecCchhhhcCchhhhcccccCCCCccEEEEEE
Confidence 379999999999999999999999999995 599999999999999999999997 999999999999
Q ss_pred cCCCEEEEEecC--CHHHHHHHHHHhhccCCCcEEEEEcC
Q 045554 279 TPGKIIFEMSGV--PENIARKAISIAASKMPIKTQFVMSG 316 (323)
Q Consensus 279 K~GqIIFEI~GV--s~~~AkeALk~Aa~KLPiKtkIV~ke 316 (323)
++|+||||+.++ +++.|++||++|++|||++|+|+..+
T Consensus 127 k~Gqiifei~~~~~~~~~AkeAlr~A~~KLP~~~kiv~~~ 166 (172)
T TIGR00279 127 KIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEK 166 (172)
T ss_pred CcCCEEEEEEeecCCHHHHHHHHHHHhccCCCcEEEEEec
Confidence 999999999998 88999999999999999999999764
No 9
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=100.00 E-value=5.4e-33 Score=246.56 Aligned_cols=104 Identities=27% Similarity=0.362 Sum_probs=98.6
Q ss_pred EEEEecCceecHHHHHHHHHHHHhhhccC-c----eEEEEeCCCCceecCCcccccC-----CC----CCCceEEEEEEc
Q 045554 214 ALQALEPAWITARQIEAGRRAMVRNVKRG-G----KIWVRIFPDKPVTARPAETRMG-----SG----KGSHAYWAAVVT 279 (323)
Q Consensus 214 GLkAlE~GrITa~QLEAAR~aInR~LKK~-g----klWIRVfP~~PVTKKPaEtRMG-----KG----KGkId~WVArVK 279 (323)
||+++|+++|+++||||||++++|+|++. | ++|||+|||+|+|+||+++||| +| ||++++|||+|+
T Consensus 48 ~L~a~E~~~I~~~qiEAaR~ai~r~lkk~~G~~~~k~wIrvfP~~~lt~kp~~~rmGAdRmg~GMr~akG~p~~wva~Vk 127 (172)
T PRK04199 48 SLVVEEPCQIRHNALEAARIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMATGAGADRVSDGMRLAFGKPVGTAARVE 127 (172)
T ss_pred EEEEcccccccHHHHHHHHHHHHHHHHhccCCcccEEEEEeCCCcceecChhHhhcchhhhccCcccCCCCccEEEEEEC
Confidence 99999999999999999999999999996 6 9999999999999999999665 99 999999999999
Q ss_pred CCCEEEEEecC--CHHHHHHHHHHhhccCCCcEEEEEcCC
Q 045554 280 PGKIIFEMSGV--PENIARKAISIAASKMPIKTQFVMSGT 317 (323)
Q Consensus 280 ~GqIIFEI~GV--s~~~AkeALk~Aa~KLPiKtkIV~ke~ 317 (323)
+|+||||+.++ +++.|++||++|++|||++|+|+..+-
T Consensus 128 ~G~ilfei~~~~~~~~~akeAlr~a~~KLP~k~kiv~~~~ 167 (172)
T PRK04199 128 KGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKG 167 (172)
T ss_pred cCCEEEEEEecCCCHHHHHHHHHHhhccCCCcEEEEEecc
Confidence 99999999965 899999999999999999999997653
No 10
>PTZ00173 60S ribosomal protein L10; Provisional
Probab=99.96 E-value=1.1e-29 Score=231.58 Aligned_cols=104 Identities=23% Similarity=0.265 Sum_probs=96.9
Q ss_pred eEEEEecCceecHHHHHHHHHHHHhhh-ccCc----eEEEEeCCCCce------ecCC---cccccCCCCCCceEEEEEE
Q 045554 213 YALQALEPAWITARQIEAGRRAMVRNV-KRGG----KIWVRIFPDKPV------TARP---AETRMGSGKGSHAYWAAVV 278 (323)
Q Consensus 213 yGLkAlE~GrITa~QLEAAR~aInR~L-KK~g----klWIRVfP~~PV------TKKP---aEtRMGKGKGkId~WVArV 278 (323)
..|+++|.++||++||||||+++||+| |+.| ++|||+|||++| |++| +++|||+|||++++|||+|
T Consensus 50 v~Lvs~E~~qIss~aLEAaRia~nr~l~K~~Gk~~fhl~IRv~P~hvlR~nKm~T~AgAdrlq~gMr~gfGkp~g~vArV 129 (213)
T PTZ00173 50 VHIVSDEYEQISSEALEAARISANKYMVKRAGKDGFHLRIRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPNGTCARV 129 (213)
T ss_pred EEEEEcccccccHHHHHHHHHHHHHhhhhhcCCccceEEEEEcCCcccccccccccccCchhhhhcccCCCCccEEEEEE
Confidence 379999999999999999999999999 6654 599999999999 7844 7899999999999999999
Q ss_pred cCCCEEEEEec--CCHHHHHHHHHHhhccCCCcEEEEEcC
Q 045554 279 TPGKIIFEMSG--VPENIARKAISIAASKMPIKTQFVMSG 316 (323)
Q Consensus 279 K~GqIIFEI~G--Vs~~~AkeALk~Aa~KLPiKtkIV~ke 316 (323)
++|+||||+.+ ++.+.|++||++|++|||++++|+..+
T Consensus 130 k~Gqiifei~~~~~~~~~AkeALrrA~~KlP~~~kIv~~~ 169 (213)
T PTZ00173 130 RIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSN 169 (213)
T ss_pred CcCCEEEEEecccCCHHHHHHHHHHhcccCCCeEEEEEec
Confidence 99999999999 899999999999999999999999763
No 11
>KOG0857 consensus 60s ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=98.31 E-value=4.6e-07 Score=83.71 Aligned_cols=100 Identities=22% Similarity=0.260 Sum_probs=84.4
Q ss_pred EEEecCceecHHHHHHHHHHHHhhhcc-----CceEEEEeCC-------CCceecCCc---ccccCCCCCCceEEEEEEc
Q 045554 215 LQALEPAWITARQIEAGRRAMVRNVKR-----GGKIWVRIFP-------DKPVTARPA---ETRMGSGKGSHAYWAAVVT 279 (323)
Q Consensus 215 LkAlE~GrITa~QLEAAR~aInR~LKK-----~gklWIRVfP-------~~PVTKKPa---EtRMGKGKGkId~WVArVK 279 (323)
++..+.-.++.+++||+|...++++.+ .+++-+|+|| ++.+++.|. ++-|...+|++.+.||+|.
T Consensus 52 ~~~~~~~~l~~~~~eA~ri~~~~~~~~~~~~d~~~~r~~~~~~fhv~~i~k~ls~~~~~RLQtgmrga~gkp~G~varV~ 131 (212)
T KOG0857|consen 52 LVSNEIEQLSSEALEAARICANKPMVKSKGKDAFHLRVRVHPNFHVLRINKMLSCAGADRLQTGMRGAFGKPQGTVARVH 131 (212)
T ss_pred hhhHHHHhHHHHHHHHhhhcccCcccccccccchhhhhhcccchhHHHHhhhhcccchhhhhhcccccccCccceEEEEE
Confidence 455667889999999999999999985 4788999999 455556676 2346777999999999999
Q ss_pred CCCEEEEEec--CCHHHHHHHHHHhhccCCCcEEEEE
Q 045554 280 PGKIIFEMSG--VPENIARKAISIAASKMPIKTQFVM 314 (323)
Q Consensus 280 ~GqIIFEI~G--Vs~~~AkeALk~Aa~KLPiKtkIV~ 314 (323)
-|++||.+.. -+.+.+.|+|.++..|+|...+++.
T Consensus 132 iGqvi~Svrtk~~nkeh~ieal~rak~kfpG~qki~v 168 (212)
T KOG0857|consen 132 IGQVIMSVRTKLQNKEHVIEALRRAKFKFPGRQKIVV 168 (212)
T ss_pred cCceEEEeecCcccHHHHHHHHHhccccCCCceeEEe
Confidence 9999999998 4579999999999999999877663
No 12
>TIGR03738 PRTRC_C PRTRC system protein C. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein C.
Probab=54.39 E-value=4.9 Score=31.92 Aligned_cols=41 Identities=22% Similarity=0.328 Sum_probs=30.5
Q ss_pred cCCCCCCCccccccccccccCCcccccccccccCCCCCCCCceee
Q 045554 40 VIPDPGPKLSSLQAKTFLMNPTTPILTSSSEANSRTPSNRDLKVQ 84 (323)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (323)
..+||+|.+|--|-+.|.-| +-|+||+.. -.-|+-+|-.++
T Consensus 15 ~L~DP~p~~spe~V~dfYs~-~YPeLttA~---v~gP~~~~~~~~ 55 (66)
T TIGR03738 15 RLADPSPAMSPEQVRDFYSA-QYPELLNAE---VEGPVVKGGVQT 55 (66)
T ss_pred EcCCCCCCCCHHHHHHHHhc-cCchheeee---eeCCeEeCCEEE
Confidence 46999999999999999877 889998754 234554554443
No 13
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=51.20 E-value=20 Score=25.76 Aligned_cols=31 Identities=10% Similarity=0.096 Sum_probs=20.9
Q ss_pred CCceEEEE----EEcCCCEEEEEecCCHHHHHHHH
Q 045554 269 GSHAYWAA----VVTPGKIIFEMSGVPENIARKAI 299 (323)
Q Consensus 269 GkId~WVA----rVK~GqIIFEI~GVs~~~AkeAL 299 (323)
|.+..|.. .|++|++|++++....+...+.+
T Consensus 11 G~V~~v~V~~G~~VkkGd~L~~ld~~~~~~~~~~~ 45 (50)
T PF13533_consen 11 GRVESVYVKEGQQVKKGDVLLVLDSPDLQAQLQQA 45 (50)
T ss_pred EEEEEEEecCCCEEcCCCEEEEECcHHHHHHHHHH
Confidence 44555543 59999999999986655444443
No 14
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=37.62 E-value=20 Score=27.94 Aligned_cols=24 Identities=38% Similarity=0.432 Sum_probs=18.9
Q ss_pred chhhHHHhhhhhhhhhccCcccch
Q 045554 117 GAALFFVLVGLFLFLLSSGQIAGL 140 (323)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~ 140 (323)
...++||.++.|+|-..+||.--+
T Consensus 11 si~l~~v~l~~flWavksgQyDDl 34 (58)
T COG3197 11 SILLGAVGLGAFLWAVKSGQYDDL 34 (58)
T ss_pred HHHHHHHHHHHHHHhcccCCcccc
Confidence 345678888899999999996543
No 15
>PF14454 Prok_Ub: Prokaryotic Ubiquitin
Probab=36.23 E-value=13 Score=29.30 Aligned_cols=29 Identities=34% Similarity=0.660 Sum_probs=23.9
Q ss_pred cCCCCCCCccccccccccccCCcccccccc
Q 045554 40 VIPDPGPKLSSLQAKTFLMNPTTPILTSSS 69 (323)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (323)
.+|||+|.+|--|.+.|.-+ +-|.|++..
T Consensus 16 ~L~DP~p~~spe~V~~~ya~-~YPeL~tA~ 44 (65)
T PF14454_consen 16 TLPDPNPSLSPEEVRDFYAA-QYPELTTAE 44 (65)
T ss_pred ECCCCCCCCCHHHHHHHHhh-hChhhheee
Confidence 37999999999999998765 578888753
No 16
>PF07831 PYNP_C: Pyrimidine nucleoside phosphorylase C-terminal domain; InterPro: IPR013102 This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [, ]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, P77826 from SWISSPROT) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP, P07650 from SWISSPROT) []. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer []. ; GO: 0016763 transferase activity, transferring pentosyl groups, 0006213 pyrimidine nucleoside metabolic process; PDB: 1AZY_A 1OTP_A 2TPT_A 3H5Q_A 1BRW_A 2WK5_C 2J0F_C 2WK6_B 1UOU_A 2DSJ_B ....
Probab=31.40 E-value=35 Score=26.83 Aligned_cols=27 Identities=15% Similarity=0.084 Sum_probs=20.1
Q ss_pred EEcCCCEEEEEecCCHHHHHHHHHHhh
Q 045554 277 VVTPGKIIFEMSGVPENIARKAISIAA 303 (323)
Q Consensus 277 rVK~GqIIFEI~GVs~~~AkeALk~Aa 303 (323)
+|++|++|+++...++..+.+|...+.
T Consensus 43 ~V~~Gd~l~~i~~~~~~~~~~a~~~~~ 69 (75)
T PF07831_consen 43 RVEKGDPLATIYANDEARLEEAVERLR 69 (75)
T ss_dssp EEBTTSEEEEEEESSSSHHHHHHHHHH
T ss_pred EECCCCeEEEEEcCChHHHHHHHHHHH
Confidence 689999999999976655555555443
No 17
>PRK05783 hypothetical protein; Provisional
Probab=27.75 E-value=89 Score=25.58 Aligned_cols=32 Identities=19% Similarity=0.194 Sum_probs=28.8
Q ss_pred EEEEcCCCEE-EEEecCCHHHHHHHHHHhhccC
Q 045554 275 AAVVTPGKII-FEMSGVPENIARKAISIAASKM 306 (323)
Q Consensus 275 VArVK~GqII-FEI~GVs~~~AkeALk~Aa~KL 306 (323)
+.-|+.|+.| +++...+.+.|++-...+|.||
T Consensus 35 V~~VRvGK~iel~l~~~~~e~a~~~v~~mc~~L 67 (84)
T PRK05783 35 IIEVRAGKYLVFKIEANSPEEAKELALKIAREG 67 (84)
T ss_pred cceEEeeEEEEEEEcCCCHHHHHHHHHHHHHhc
Confidence 5669999997 9999999999999999999998
No 18
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=27.64 E-value=39 Score=25.47 Aligned_cols=25 Identities=40% Similarity=0.442 Sum_probs=15.3
Q ss_pred cchhhHHHhh--hhhhhhhccCcccch
Q 045554 116 IGAALFFVLV--GLFLFLLSSGQIAGL 140 (323)
Q Consensus 116 ~~~~~~~~~~--~~~~~~~~~~~~~~~ 140 (323)
|+.+++++++ ..|+|-..+||.--+
T Consensus 8 IpiSl~l~~~~l~~f~Wavk~GQfDDl 34 (51)
T TIGR00847 8 IPISLLLGGVGLVAFLWSLKSGQYDDL 34 (51)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCC
Confidence 4455555554 456777779996443
No 19
>PRK14445 acylphosphatase; Provisional
Probab=21.64 E-value=2.8e+02 Score=22.23 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=30.7
Q ss_pred CceEEEEEEcCCCEEEEEecCCHHHHHHHHHHhhccCCCcEEEE
Q 045554 270 SHAYWAAVVTPGKIIFEMSGVPENIARKAISIAASKMPIKTQFV 313 (323)
Q Consensus 270 kId~WVArVK~GqIIFEI~GVs~~~AkeALk~Aa~KLPiKtkIV 313 (323)
.+.+||.-...|+|-.++.|-. .+.+.|..+..+-|-.++|.
T Consensus 31 gl~G~V~N~~dG~Vei~~qG~~--~~l~~f~~~l~~gP~~a~V~ 72 (91)
T PRK14445 31 NLSGWVRNLPDGTVEIEAQGSS--GMIDELIKQAERGPSRSSVT 72 (91)
T ss_pred CCEEEEEECCCCeEEEEEEECH--HHHHHHHHHHHhCCCCcEEE
Confidence 3789999999999999999943 33455554445788777664
No 20
>cd01178 IPT_NFAT IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction.
Probab=21.41 E-value=61 Score=27.51 Aligned_cols=29 Identities=31% Similarity=0.394 Sum_probs=23.4
Q ss_pred CCCCCCCCceeeeeeeeee------cCcccccccc
Q 045554 73 SRTPSNRDLKVQQSVGVMM------GGRSFPLIFT 101 (323)
Q Consensus 73 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 101 (323)
-+||.-||..+.+.|-|.| |.+|+|+-||
T Consensus 64 f~tPpY~~~~I~~pV~V~~~l~~~~~~~S~~~~Ft 98 (101)
T cd01178 64 VEVPPYHNKHVAAPVQVQFYVVNGKRKRSQPQTFT 98 (101)
T ss_pred EecCCCCCCCcCCceEEEEEEEcCCCCcCCCCCcE
Confidence 4899999999999988875 6677777664
No 21
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=21.12 E-value=73 Score=29.66 Aligned_cols=87 Identities=18% Similarity=0.173 Sum_probs=45.4
Q ss_pred eEEEEecCc----eecHHHHHHHHHHHHhhhccCceEEEEeCCCCceecCCccc--------ccCCCC-----CCceEEE
Q 045554 213 YALQALEPA----WITARQIEAGRRAMVRNVKRGGKIWVRIFPDKPVTARPAET--------RMGSGK-----GSHAYWA 275 (323)
Q Consensus 213 yGLkAlE~G----rITa~QLEAAR~aInR~LKK~gklWIRVfP~~PVTKKPaEt--------RMGKGK-----GkId~WV 275 (323)
+-|.+..++ .++++.|+.--.. .....+ .-++|++++++-..+. ++|.|| -.+....
T Consensus 96 ~~l~~~g~~~~~~~V~s~DL~~~~~~-----~~~~~v-~pv~~di~I~kL~~gq~i~le~~~~~G~G~~hAk~sPV~~v~ 169 (212)
T cd07028 96 LTLQAFAESESTTNVYSKDLVIVSNL-----MGRNIG-HPIIQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIE 169 (212)
T ss_pred EEEEccCCCCCcceEEHHHcccCCcc-----ccCCCe-EEeCCCcEEEEECCCCEEEEEEEEECCCcCCCCEeCCceEEE
Confidence 445555544 6888888631100 000122 3478999998655432 455554 1112222
Q ss_pred EEE--cCCCEEEEEecC---CH-HHHHHHHHHhhcc
Q 045554 276 AVV--TPGKIIFEMSGV---PE-NIARKAISIAASK 305 (323)
Q Consensus 276 ArV--K~GqIIFEI~GV---s~-~~AkeALk~Aa~K 305 (323)
.++ ...+.+|||... +. +...+|++....|
T Consensus 170 y~~~~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~ 205 (212)
T cd07028 170 FRYDPVADTYIMNVESVGSLPPDQVVVEAIKTLQKK 205 (212)
T ss_pred EEEEccCCEEEEEEEecCCcCHHHHHHHHHHHHHHH
Confidence 333 358889999864 33 3444555555444
No 22
>PF02505 MCR_D: Methyl-coenzyme M reductase operon protein D; InterPro: IPR003901 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. Genes encoding the beta (mcrB) and gamma (mcrG) subunits of MCR are separated by two open reading frames coding for two proteins C and D [, ]. The function of proteins C and D is unknown. This entry represents protein D.; GO: 0015948 methanogenesis
Probab=20.17 E-value=6.8e+02 Score=22.96 Aligned_cols=78 Identities=21% Similarity=0.246 Sum_probs=48.3
Q ss_pred HHHHHHHHhhhccCceEEEEeC-CCCceecCCcccccCCCCCCc-------------eEEEEEEcCCCEEEEEecCCHHH
Q 045554 229 EAGRRAMVRNVKRGGKIWVRIF-PDKPVTARPAETRMGSGKGSH-------------AYWAAVVTPGKIIFEMSGVPENI 294 (323)
Q Consensus 229 EAAR~aInR~LKK~gklWIRVf-P~~PVTKKPaEtRMGKGKGkI-------------d~WVArVK~GqIIFEI~GVs~~~ 294 (323)
|++...+|+-.+=.|-..+-++ |..|-| +=.|=++|.+ +.-.-.|+.|+|++|+... +.
T Consensus 14 eTtEklLN~l~~i~GI~R~vi~Gp~LPk~-----VpyGPa~G~pv~h~~Rk~I~V~g~~veL~V~vGri~lele~~--~~ 86 (153)
T PF02505_consen 14 ETTEKLLNELYSIEGIRRVVIHGPRLPKT-----VPYGPARGTPVNHPDRKVINVGGEEVELTVKVGRIILELEDE--ED 86 (153)
T ss_pred HHHHHHHHHHhccCCEEEEEEECCCCCCC-----CCCCCCCCCcCCCCcceEEEECCEEEEEEEEEeEEEEEecCc--HH
Confidence 6777888877766675666665 666543 2244445543 2344578999999999883 34
Q ss_pred HHHHHHHhhc-cCCCcEEEE
Q 045554 295 ARKAISIAAS-KMPIKTQFV 313 (323)
Q Consensus 295 AkeALk~Aa~-KLPiKtkIV 313 (323)
..+.++.+|. -||+...+-
T Consensus 87 ~ie~I~~iCee~lpf~y~i~ 106 (153)
T PF02505_consen 87 VIEKIREICEEVLPFGYDIK 106 (153)
T ss_pred HHHHHHHHHHHhCCCceEee
Confidence 4444444444 367777654
Done!