Query 005258
Match_columns 705
No_of_seqs 49 out of 51
Neff 2.7
Searched_HMMs 46136
Date Thu Mar 28 20:37:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005258.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005258hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07891 DUF1666: Protein of u 100.0 7E-118 2E-122 882.2 20.2 247 457-705 1-247 (247)
2 PF06956 RtcR: Regulator of RN 24.8 1.1E+02 0.0023 31.6 4.4 21 494-514 160-180 (183)
3 PF10706 Aminoglyc_resit: Amin 12.7 65 0.0014 32.8 -0.1 14 469-482 122-135 (174)
4 PF11406 Tachystatin_A: Antimi 11.2 88 0.0019 25.3 0.1 9 342-350 13-21 (44)
5 KOG3970 Predicted E3 ubiquitin 10.3 1.8E+02 0.004 31.2 2.2 28 327-354 110-141 (299)
6 PF14829 GPAT_N: Glycerol-3-ph 9.2 1.8E+02 0.0039 26.5 1.4 24 466-490 29-52 (77)
7 PF06141 Phage_tail_U: Phage m 8.9 1.5E+02 0.0033 29.0 0.9 36 329-364 9-49 (133)
8 PF02937 COX6C: Cytochrome c o 8.7 2.6E+02 0.0056 24.8 2.1 25 387-411 46-71 (73)
9 PF00489 IL6: Interleukin-6/G- 8.6 2.3E+02 0.0049 27.7 1.9 23 494-517 54-76 (154)
10 KOG1329 Phospholipase D1 [Lipi 8.3 1E+02 0.0022 37.9 -0.6 11 473-483 646-656 (887)
No 1
>PF07891 DUF1666: Protein of unknown function (DUF1666); InterPro: IPR012870 These sequences are derived from hypothetical plant proteins of unknown function. The region in question is approximately 250 residues long.
Probab=100.00 E-value=7e-118 Score=882.19 Aligned_cols=247 Identities=62% Similarity=1.032 Sum_probs=239.2
Q ss_pred hhhhhhhhhHHHHHHHHHHhhhHHhhHHhhhcCCCCCCCchhhHhhhhhhHHHHHHhhhcCCCCCCchhHHHhhhhcccc
Q 005258 457 HSDLEVVYVGQLCLSWEILHWQYEKSLELWESDPYGICRYNEVAGEFQQFQVLMQRFIENEPFEGPRVENYIKNRCVLRN 536 (705)
Q Consensus 457 y~DLE~vYVaQiCLSWEaL~WqY~k~~~l~~sd~~~~~~Yn~VAqEFQQFQVLLQRFIENEPFqG~RvE~YaR~R~~l~k 536 (705)
|+|||+|||||||||||||||||++|++++++||++++|||+|||+|||||||||||||||||+||||||||||||++||
T Consensus 1 y~dLE~vYVaQiCLSWEaL~wqY~k~~~l~~~~~~~~~~yn~VA~eFQqFQVLLQRFiENEPfeG~R~e~YaR~R~~~~k 80 (247)
T PF07891_consen 1 YSDLETVYVAQICLSWEALHWQYKKASELWESDPQNPHCYNHVAGEFQQFQVLLQRFIENEPFEGPRVENYARNRCSLPK 80 (247)
T ss_pred CcchHHHHHHHHHhhHHHHHhHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHhhHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccceeccchhHHHHhhhccCCCccCHHHHHHHHHHHHHHHHHHHhhcccchhhhhhcccCcCCCCCChhhhHHHHHH
Q 005258 537 LLQVPVIREDSKKDKKARMKMKDEYAITSDMLVEIMEESIRIFWRFVRVDKDANIMIQKSRKGTQIEPQDALDLGLLAEV 616 (705)
Q Consensus 537 LLQVP~ir~d~~~Dkk~~~~~~~~~~Iss~~ll~IiEesIrtFw~FLkaDK~k~~~i~k~~~~~~~~~qDp~d~~Ll~~V 616 (705)
|||||+||+|+.+||+..++++.+++|+|++|++||||||+|||+||||||+++|+++|+..++++. ||+|++||++|
T Consensus 81 LLqVP~ir~d~~~dkk~~~~~~~~~~I~s~~l~~IiEesI~tFw~FlkaDK~k~~~~~k~~~~~~~~--d~~d~~ll~~i 158 (247)
T PF07891_consen 81 LLQVPEIREDSEKDKKDMREEEKDSAISSDMLLEIIEESIRTFWEFLKADKDKPNQILKGFFGTQVE--DPVDPELLQDI 158 (247)
T ss_pred HhcCCccccchhhhhhhhhhccccceecHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHhcCCCC--CccchHHHHHH
Confidence 9999999999888888644445566999999999999999999999999999999999999999875 99999999999
Q ss_pred HHHhHHHHHHHHHhhhcCcceeecccccccchhhhhhhhhhhhhhhhhhhhcCCCCChhHHhHHHhhcccccccCCceee
Q 005258 617 RTSLQKKEKKLKEILRSGNCILRKFQKQQENSDQVLYFFSQVDMKLVARVLNMTKLTTDQLLWCRNKLDKINFISRRIHV 696 (705)
Q Consensus 617 ~t~LqKKe~KLKDl~Rs~kCi~KK~~k~~eE~~q~l~lfalIDlKLVSRVLrMs~lt~eQL~WCeEKm~KI~~~~gKl~r 696 (705)
+++||||++|||||+|+||||+||+||++++++++.+|||+|||||||||||||+||+||||||+|||+||+|++|||||
T Consensus 159 k~~lqKKe~kLKdl~r~~~ci~kk~~k~~e~~~~~~~lf~~IdlKlVsRVLrMs~lt~eQL~WCeeKm~ki~~~~~Kl~r 238 (247)
T PF07891_consen 159 KKSLQKKEKKLKDLLRSGKCIRKKFQKHEEDREEVELLFALIDLKLVSRVLRMSKLTKEQLHWCEEKMSKINFVDGKLQR 238 (247)
T ss_pred HHHHHHHHHHHHHHhccccchhhhhccccchhhHHHHHHHHHHHHHHHHHhchhhhhHHHHHHHHHHHHhcCcccCceee
Confidence 99999999999999999999999999999988889999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCC
Q 005258 697 EPAFLLFPC 705 (705)
Q Consensus 697 dpSplLFPc 705 (705)
||||+||||
T Consensus 239 d~S~llFPc 247 (247)
T PF07891_consen 239 DPSPLLFPC 247 (247)
T ss_pred cCCCCCCCC
Confidence 999999999
No 2
>PF06956 RtcR: Regulator of RNA terminal phosphate cyclase; InterPro: IPR009715 RtcR is a sigma54-dependent enhancer binding protein [] that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3 -terminal phosphate cyclase []. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain IPR002078 from INTERPRO in the central region of the protein sequence.
Probab=24.77 E-value=1.1e+02 Score=31.56 Aligned_cols=21 Identities=33% Similarity=0.517 Sum_probs=17.3
Q ss_pred CCchhhHhhhhhhHHHHHHhh
Q 005258 494 CRYNEVAGEFQQFQVLMQRFI 514 (705)
Q Consensus 494 ~~Yn~VAqEFQQFQVLLQRFI 514 (705)
.+|+.+|+.|++=|.==..|+
T Consensus 160 srYd~ia~Rf~~~~~e~~~fL 180 (183)
T PF06956_consen 160 SRYDAIASRFAQEQQEAVSFL 180 (183)
T ss_pred cchHHHHHHHHHHHHHHHHHh
Confidence 689999999999887666665
No 3
>PF10706 Aminoglyc_resit: Aminoglycoside-2''-adenylyltransferase; InterPro: IPR019646 Aminoglycoside-2''-adenylyltransferase is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin []. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents []. ; PDB: 4E8I_A 4E8J_B.
Probab=12.75 E-value=65 Score=32.81 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=5.9
Q ss_pred HHHHHHHhhhHHhh
Q 005258 469 CLSWEILHWQYEKS 482 (705)
Q Consensus 469 CLSWEaL~WqY~k~ 482 (705)
|+||||..|-|.--
T Consensus 122 CiS~Ea~lf~~~y~ 135 (174)
T PF10706_consen 122 CISAEAQLFHYGYY 135 (174)
T ss_dssp EE-HHHH-------
T ss_pred CCCHHHHhhhcccc
Confidence 99999999998653
No 4
>PF11406 Tachystatin_A: Antimicrobial peptide tachystatin A; InterPro: IPR022717 Tachystatin A contains a cysteine-stabilised triple-stranded beta-sheet and shows features common to membrane-interactive peptides. Tachystatin A is thought to have an antimicrobial activity similar to defensins.Tachystatin A is also a chitin-binding peptide []. ; PDB: 1CIX_A.
Probab=11.17 E-value=88 Score=25.31 Aligned_cols=9 Identities=67% Similarity=1.106 Sum_probs=4.4
Q ss_pred hhhcCCcee
Q 005258 342 ARAIGLPTI 350 (705)
Q Consensus 342 ~R~~gl~ti 350 (705)
||.-|||||
T Consensus 13 vrsyglpti 21 (44)
T PF11406_consen 13 VRSYGLPTI 21 (44)
T ss_dssp S--TTS-S-
T ss_pred EEccCCCCc
Confidence 688899998
No 5
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=10.32 E-value=1.8e+02 Score=31.24 Aligned_cols=28 Identities=32% Similarity=0.442 Sum_probs=21.9
Q ss_pred chHHHHHHHHHHHHHh---hhc-CCceecccC
Q 005258 327 EHQDLIDQLKTELKKA---RAI-GLPTILEES 354 (705)
Q Consensus 327 ehqdlieqlK~elk~~---R~~-gl~tilee~ 354 (705)
+-.-+++.||..||.| |++ |||+|-|+.
T Consensus 110 lvsPva~aLre~L~qvNWaRagLGLpll~E~~ 141 (299)
T KOG3970|consen 110 LVSPVAEALREQLKQVNWARAGLGLPLLPELN 141 (299)
T ss_pred ccchhHHHHHHHHHhhhHHhhccCCccchhhc
Confidence 3456788888888875 787 999998764
No 6
>PF14829 GPAT_N: Glycerol-3-phosphate acyltransferase N-terminal; PDB: 1IUQ_A 1K30_A.
Probab=9.19 E-value=1.8e+02 Score=26.45 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhhhHHhhHHhhhcCC
Q 005258 466 GQLCLSWEILHWQYEKSLELWESDP 490 (705)
Q Consensus 466 aQiCLSWEaL~WqY~k~~~l~~sd~ 490 (705)
+++---||-|+|||++|- +.+.+|
T Consensus 29 ~~va~gmeelY~NYk~AV-l~Sg~p 52 (77)
T PF14829_consen 29 ANVAAGMEELYQNYKNAV-LQSGDP 52 (77)
T ss_dssp HHHHHHHHHHHHHHHHHH-HHTT-T
T ss_pred hhHHHHHHHHHHHHHHHH-HhCCCC
Confidence 345567999999999975 234444
No 7
>PF06141 Phage_tail_U: Phage minor tail protein U; InterPro: IPR009312 This entry is represented by Bacteriophage lambda, GpU, a minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a tail fibre component U of bacteriophage.; PDB: 3FZ2_D 3FZB_J 1Z1Z_A.
Probab=8.87 E-value=1.5e+02 Score=28.95 Aligned_cols=36 Identities=25% Similarity=0.530 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHhhh--cCCceecccCCCccc---cccCC
Q 005258 329 QDLIDQLKTELKKARA--IGLPTILEESESPKI---TEDLK 364 (705)
Q Consensus 329 qdlieqlK~elk~~R~--~gl~tilee~Espk~---~edlk 364 (705)
+.+|+.||..+..... .|+|+.+.++|.|-| ..|..
T Consensus 9 ~aVld~L~~~~~~~~~~fdGrP~fide~elPAVaV~l~Da~ 49 (133)
T PF06141_consen 9 KAVLDALKANIPEIVTFFDGRPAFIDEEELPAVAVYLDDAE 49 (133)
T ss_dssp HHHHHHHHHH-STSSEEEES--SSS-GGGSSEEEEEEEEEE
T ss_pred HHHHHHHHhcCCCCeEEECCcccccccccCceEEEEeccCc
Confidence 4577778877765443 499999999999987 45555
No 8
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=8.75 E-value=2.6e+02 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=12.9
Q ss_pred HHHHHHhhhhhh-hhhhhhccccccC
Q 005258 387 SYRERMRKFDIL-NYQKMYTIGFLQS 411 (705)
Q Consensus 387 kY~ERMrkfDiL-n~Qkl~aig~lqs 411 (705)
+|+|=.+.+|.+ .+..|...|++||
T Consensus 46 ~YadFYknYD~~k~fe~M~~~G~fqS 71 (73)
T PF02937_consen 46 AYADFYKNYDPMKDFEEMRKAGIFQS 71 (73)
T ss_dssp HHHHHHHT--HHHHHHHHHHTT--SS
T ss_pred HHHHHHHccChHHHHHHHHhcCCccc
Confidence 455555555555 2455778888876
No 9
>PF00489 IL6: Interleukin-6/G-CSF/MGF family; InterPro: IPR003573 Interleukin-6 (IL6), also refered to as B-cell stimulatory factor-2 (BSF-2) and interferon beta-2, is a cytokine involved in a wide variety of biological functions []. It plays an essential role in the final differentiation of B-cells into IG-secreting cells, as well as inducing myeloma/plasmacytoma growth, nerve cell differentiation and, in hepatocytes, acute phase reactants [, ]. A number of other cytokines may be grouped with IL6 on the basis of sequence similarity [, , ]: these include granulocyte colony-stimulating factor (GCSF) and myelomonocytic growth factor (MGF). GCSF acts in hematopoiesis by affecting the production, differentiation and function of 2 related white cell groups in the blood []. MGF also acts in hematopoiesis, stimulating proliferation and colony formation of normal and transformed avian cells of the myeloid lineage. Cytokines of the IL6/GCSF/MGF family are glycoproteins of about 170 to 180 amino acid residues that contains four conserved cysteine residues involved in two disulphide bonds []. They have a compact, globular fold (similar to other interleukins), stabilised by the 2 disulphide bonds. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []: the helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet. The fourth alpha-helix is important to the biological activity of the molecule []. It has been said [] that this family can be extended by the adjunction of LIF and OSM (see the relevant entry IPR001581 from INTERPRO) which seem to be structurally related.; GO: 0005125 cytokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 1P9M_B 2IL6_A 1IL6_A 1ALU_A 3QWR_B 3DUH_C 3D85_C 3D87_C 1BGC_A 2L3Y_A ....
Probab=8.55 E-value=2.3e+02 Score=27.70 Aligned_cols=23 Identities=17% Similarity=0.576 Sum_probs=19.7
Q ss_pred CCchhhHhhhhhhHHHHHHhhhcC
Q 005258 494 CRYNEVAGEFQQFQVLMQRFIENE 517 (705)
Q Consensus 494 ~~Yn~VAqEFQQFQVLLQRFIENE 517 (705)
.|-..++.-.|-||++|+ ||+++
T Consensus 54 ~CL~ri~~GL~~yq~lL~-~l~~~ 76 (154)
T PF00489_consen 54 TCLSRIHSGLQEYQILLK-YLQGE 76 (154)
T ss_dssp HHHHHHHHHHHHHHHHHH-HTTTS
T ss_pred HHHHHHHHHHHHHHHHHH-HHHhh
Confidence 377889999999999997 78775
No 10
>KOG1329 consensus Phospholipase D1 [Lipid transport and metabolism]
Probab=8.32 E-value=1e+02 Score=37.89 Aligned_cols=11 Identities=55% Similarity=1.081 Sum_probs=9.5
Q ss_pred HHHhhhHHhhH
Q 005258 473 EILHWQYEKSL 483 (705)
Q Consensus 473 EaL~WqY~k~~ 483 (705)
++|||||+.++
T Consensus 646 aIl~wQyrTms 656 (887)
T KOG1329|consen 646 AILHWQYRTMS 656 (887)
T ss_pred HHHHHHHHHHh
Confidence 68999999876
Done!