Query 034489
Match_columns 93
No_of_seqs 104 out of 178
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:24:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09809 MRP-L27: Mitochondria 100.0 3.2E-34 7E-39 199.7 3.5 73 19-91 4-76 (113)
2 KOG4756 Mitochondrial ribosoma 99.9 7.8E-24 1.7E-28 152.1 2.9 83 4-86 12-105 (146)
3 PF11201 DUF2982: Protein of u 32.2 44 0.00096 24.5 2.4 27 40-66 7-33 (152)
4 PF06007 PhnJ: Phosphonate met 27.8 62 0.0013 26.0 2.7 45 47-91 174-233 (277)
5 PF15172 Prolactin_RP: Prolact 21.8 39 0.00085 20.5 0.5 20 28-47 14-33 (47)
6 PF15199 DAOA: D-amino acid ox 17.9 44 0.00096 22.0 0.1 12 70-81 9-20 (82)
7 PF05223 MecA_N: NTF2-like N-t 15.4 78 0.0017 20.9 0.9 19 48-68 98-116 (118)
8 COG3363 Archaeal IMP cyclohydr 14.5 73 0.0016 24.4 0.6 24 59-82 39-63 (200)
9 PF12426 DUF3674: RNA dependen 14.3 1.4E+02 0.0031 17.6 1.7 21 50-70 17-37 (41)
10 PF08394 Arc_trans_TRASH: Arch 13.1 64 0.0014 18.4 -0.0 13 22-34 11-23 (37)
No 1
>PF09809 MRP-L27: Mitochondrial ribosomal protein L27; InterPro: IPR019189 Proteins in this entry are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation.
Probab=100.00 E-value=3.2e-34 Score=199.67 Aligned_cols=73 Identities=51% Similarity=0.792 Sum_probs=69.1
Q ss_pred CCCCcccccccCCccccCccCCCCceEeeeccEEEccCCCCeeeCCCCCCcccccccccCCCCcccccccCCC
Q 034489 19 SSLDILSSKRAPRDYYKGKNCKSTGFHTRKGGYVVVQEKLPNYVVPDLTDFKLKSYVSQCPREVKTAEAAEPG 91 (93)
Q Consensus 19 ~~~~~ltsK~gnk~~yKG~g~~~~G~~t~~G~f~i~~~kvp~fVVPdL~~f~LKPyVS~~~~~v~q~e~t~~~ 91 (93)
.+..|||||||||+||||+|++++|+|+++|+|+|+|+|||+||||||++|+||||||++++++.|+|+||+.
T Consensus 4 ~rr~~LttK~g~k~fyKG~g~~~~G~~t~~g~yvi~~~kvp~~VVPdL~~f~LKPyVS~~~p~~~~~~~Ta~~ 76 (113)
T PF09809_consen 4 FRRFPLTTKRGNKGFYKGTGARGTGRHTKKGGYVIVPEKVPEFVVPDLTDFKLKPYVSYRTPEVKQEEFTAKD 76 (113)
T ss_pred ccccccccccCCccccCCcCCCCCcEEccCccEEECHHHCceeeCCCCCCCccccccccCccccccccccHHH
Confidence 3445799999999999999999999999999999999999999999999999999999999999999999863
No 2
>KOG4756 consensus Mitochondrial ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=7.8e-24 Score=152.05 Aligned_cols=83 Identities=53% Similarity=0.789 Sum_probs=68.5
Q ss_pred hHHHHHHHhhhhhc----cCCCC-------cccccccCCccccCccCCCCceEeeeccEEEccCCCCeeeCCCCCCcccc
Q 034489 4 GLILGIGRAFRRKR----TSSLD-------ILSSKRAPRDYYKGKNCKSTGFHTRKGGYVVVQEKLPNYVVPDLTDFKLK 72 (93)
Q Consensus 4 g~~~~~~rg~~r~~----a~~~~-------~ltsK~gnk~~yKG~g~~~~G~~t~~G~f~i~~~kvp~fVVPdL~~f~LK 72 (93)
|.|.++.|-++|.| |++++ |+++|++||+.|||+|++++|+||+.|.|+|+|+|+||||||||++|+||
T Consensus 12 ~slna~~rp~~r~r~~~~a~glsK~g~kr~Pr~~k~~~k~l~kgtgakgiGfht~kggyvV~~ekv~eyVvPdl~gFkLk 91 (146)
T KOG4756|consen 12 GSLNAIGRPFRRKRVKKGASGLSKLGPKRAPRDFKLNPKELHKGTGAKGIGFHTRKGGYVVQPEKVPEYVVPDLTGFKLK 91 (146)
T ss_pred hhhhhccCccccccccccccchhhhccccCchhhhcCchhhcccccccccceeeccccEEeCHhhccceeccCccCceec
Confidence 56788888888876 66665 55555666666799999999999999999999999999999999999999
Q ss_pred cccccCCCCccccc
Q 034489 73 SYVSQCPREVKTAE 86 (93)
Q Consensus 73 PyVS~~~~~v~q~e 86 (93)
||||-+.|....+.
T Consensus 92 PYVs~q~p~~~~q~ 105 (146)
T KOG4756|consen 92 PYVSVQCPLRRVQV 105 (146)
T ss_pred cceeccCchhHhhh
Confidence 99996665544433
No 3
>PF11201 DUF2982: Protein of unknown function (DUF2982); InterPro: IPR021367 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=32.20 E-value=44 Score=24.51 Aligned_cols=27 Identities=22% Similarity=0.628 Sum_probs=23.1
Q ss_pred CCCceEeeeccEEEccCCCCeeeCCCC
Q 034489 40 KSTGFHTRKGGYVVVQEKLPNYVVPDL 66 (93)
Q Consensus 40 ~~~G~~t~~G~f~i~~~kvp~fVVPdL 66 (93)
..+=||.++|.++|+|+-|..+-+|..
T Consensus 7 ~~l~y~hr~G~w~i~W~Ni~ri~ip~v 33 (152)
T PF11201_consen 7 EGLQYHHRRGGWVIPWQNIQRIDIPRV 33 (152)
T ss_pred cceEEEecCccEEeecccceeeCCCcc
Confidence 345688899999999999999999953
No 4
>PF06007 PhnJ: Phosphonate metabolism protein PhnJ; InterPro: IPR010306 This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.; GO: 0042916 alkylphosphonate transport
Probab=27.78 E-value=62 Score=26.04 Aligned_cols=45 Identities=16% Similarity=0.227 Sum_probs=33.5
Q ss_pred eeccEEEccCCCCeeeCCCCCCcc---------------cccccccCCCCcccccccCCC
Q 034489 47 RKGGYVVVQEKLPNYVVPDLTDFK---------------LKSYVSQCPREVKTAEAAEPG 91 (93)
Q Consensus 47 ~~G~f~i~~~kvp~fVVPdL~~f~---------------LKPyVS~~~~~v~q~e~t~~~ 91 (93)
..|+|+++++=||-|-+|.|.... +-||-.-.+-.+.-.+|..+.
T Consensus 174 V~grYvm~PSPIPrfDnPKl~~~~aL~LfGAGREkrIYAvPPyT~V~sL~FeD~pF~~e~ 233 (277)
T PF06007_consen 174 VNGRYVMDPSPIPRFDNPKLHMSPALQLFGAGREKRIYAVPPYTDVESLDFEDHPFEVER 233 (277)
T ss_pred ECCeEeeCCCCCCCCCCccccCChhhhhhcCCcceeeeecCCCccccccCccCCCCcccc
Confidence 478999999999999999875432 557766666666666666543
No 5
>PF15172 Prolactin_RP: Prolactin-releasing peptide
Probab=21.79 E-value=39 Score=20.48 Aligned_cols=20 Identities=20% Similarity=0.431 Sum_probs=15.9
Q ss_pred ccCCccccCccCCCCceEee
Q 034489 28 RAPRDYYKGKNCKSTGFHTR 47 (93)
Q Consensus 28 ~gnk~~yKG~g~~~~G~~t~ 47 (93)
.-|--.|.|.|..++|++-+
T Consensus 14 dIdP~WY~gRgiRPvGRFGr 33 (47)
T PF15172_consen 14 DIDPAWYVGRGIRPVGRFGR 33 (47)
T ss_pred CCCchheecccccccccccc
Confidence 34455899999999999864
No 6
>PF15199 DAOA: D-amino acid oxidase activator
Probab=17.91 E-value=44 Score=21.98 Aligned_cols=12 Identities=33% Similarity=0.467 Sum_probs=9.5
Q ss_pred ccccccccCCCC
Q 034489 70 KLKSYVSQCPRE 81 (93)
Q Consensus 70 ~LKPyVS~~~~~ 81 (93)
+|.|||||-+..
T Consensus 9 slcpwvsylpqp 20 (82)
T PF15199_consen 9 SLCPWVSYLPQP 20 (82)
T ss_pred hhcchhhhCCch
Confidence 689999996643
No 7
>PF05223 MecA_N: NTF2-like N-terminal transpeptidase domain; InterPro: IPR007887 The multiple antibiotic resistance of methicillin-resistant strains of Staphylococcus aureus (MRSA) has become a major clinical problem worldwide. Methicillin resistance in MRSA strains is due to the acquisition of the mecA gene via horizontal transfer from an unidentified species which encodes penicillin-binding protein 2a (PBP2a). The structure of the N-terminal domain from MecA is known [] Q53707 from SWISSPROT and is found to be similar to that found in NTF2 IPR002075 from INTERPRO. The length of the PBP2A N-terminal domain (which positions the transpeptidase active site more than 100A from the expected C terminus of the transmembrane anchor) suggests a possible structural role and potentially gives the transpeptidase domain substantial reach from the cell membrane. This domain seems unlikely to have an enzymatic function.; GO: 0046677 response to antibiotic; PDB: 1MWS_B 1MWT_B 1MWR_A 1MWU_A 1VQQ_A.
Probab=15.37 E-value=78 Score=20.94 Aligned_cols=19 Identities=26% Similarity=0.559 Sum_probs=11.3
Q ss_pred eccEEEccCCCCeeeCCCCCC
Q 034489 48 KGGYVVVQEKLPNYVVPDLTD 68 (93)
Q Consensus 48 ~G~f~i~~~kvp~fVVPdL~~ 68 (93)
.+.+.|+|+ |.+|.|+|.+
T Consensus 98 ~~~W~V~W~--ps~I~P~L~~ 116 (118)
T PF05223_consen 98 DDDWKVDWD--PSLIFPGLKD 116 (118)
T ss_dssp TTCEEE-----GGGTSTT--T
T ss_pred CCcEEEEeC--ccCCCCCCCC
Confidence 557889997 8899998864
No 8
>COG3363 Archaeal IMP cyclohydrolase [Nucleotide transport and metabolism]
Probab=14.45 E-value=73 Score=24.42 Aligned_cols=24 Identities=21% Similarity=0.301 Sum_probs=17.1
Q ss_pred CeeeCCC-CCCcccccccccCCCCc
Q 034489 59 PNYVVPD-LTDFKLKSYVSQCPREV 82 (93)
Q Consensus 59 p~fVVPd-L~~f~LKPyVS~~~~~v 82 (93)
.-+|||. ...-.--|||+|+-..+
T Consensus 39 ~vaVVP~d~~e~~~NPYvtYnCiri 63 (200)
T COG3363 39 AVAVVPEDPSEITENPYVTYNCIRI 63 (200)
T ss_pred ceEEeccCccccccCCcEEEEEEEE
Confidence 3789994 66555699999964443
No 9
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=14.28 E-value=1.4e+02 Score=17.56 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=16.5
Q ss_pred cEEEccCCCCeeeCCCCCCcc
Q 034489 50 GYVVVQEKLPNYVVPDLTDFK 70 (93)
Q Consensus 50 ~f~i~~~kvp~fVVPdL~~f~ 70 (93)
+|.|--.+.+.|.+||-.+..
T Consensus 17 KFhi~~~k~~~y~IP~Y~~~~ 37 (41)
T PF12426_consen 17 KFHIGGPKTQPYYIPDYRGIP 37 (41)
T ss_pred eeeeCCcccccccCCCCCCcc
Confidence 678888899999999865443
No 10
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=13.14 E-value=64 Score=18.43 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=11.0
Q ss_pred CcccccccCCccc
Q 034489 22 DILSSKRAPRDYY 34 (93)
Q Consensus 22 ~~ltsK~gnk~~y 34 (93)
.|.+-|.+|+.||
T Consensus 11 eP~~~k~~~~~y~ 23 (37)
T PF08394_consen 11 EPIVVKIGNKVYY 23 (37)
T ss_pred CEEEEEECCeEEE
Confidence 5788999999887
Done!