Query 030399
Match_columns 178
No_of_seqs 66 out of 68
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 13:08:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030399.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030399hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12638 Staygreen: Staygreen 100.0 5.3E-52 1.2E-56 335.0 10.1 107 64-171 1-107 (151)
2 PF01015 Ribosomal_S3Ae: Ribos 72.0 27 0.00059 29.5 8.0 76 63-143 23-122 (194)
3 PRK04057 30S ribosomal protein 35.8 1.4E+02 0.0031 25.5 6.5 76 63-143 17-116 (203)
4 KOG2708 Predicted metalloprote 34.5 8.5 0.00019 35.1 -1.2 31 139-169 127-157 (336)
5 PF07351 DUF1480: Protein of u 23.8 59 0.0013 24.7 1.9 29 92-120 17-48 (80)
6 PF09178 DUF1945: Domain of un 22.2 1.2E+02 0.0027 21.1 3.0 31 121-151 9-39 (51)
7 PF00667 FAD_binding_1: FAD bi 21.5 25 0.00053 29.0 -0.6 41 66-109 160-202 (219)
8 PF04355 SmpA_OmlA: SmpA / Oml 16.8 2E+02 0.0043 19.5 3.2 45 51-97 16-63 (71)
9 PF09866 DUF2093: Uncharacteri 15.2 1.4E+02 0.0029 20.3 1.9 19 138-159 7-25 (42)
10 COG4604 CeuD ABC-type enteroch 14.3 2.1E+02 0.0046 25.7 3.5 63 38-106 29-92 (252)
No 1
>PF12638 Staygreen: Staygreen protein; InterPro: IPR024438 This domain is found in a family of proteins have been implicated in chlorophyll degradation [, ]. Intriguingly members of this family are also found in non-photosynthetic bacteria.
Probab=100.00 E-value=5.3e-52 Score=335.00 Aligned_cols=107 Identities=49% Similarity=0.796 Sum_probs=102.3
Q ss_pred CCCCCCCcEEEeecCCCCCCCCCCCceeeeccCCcCcceEEEEehhhhhhhhccccccceEEEEEEecCCeeEEEEEEEE
Q 030399 64 ASFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTANLTLTISNVINLEQLRGWYIKDDVVAEWKKVRDDMCLHVHCYV 143 (178)
Q Consensus 64 ~~Fnp~KLsV~f~g~~~t~~~PiipRrYTLTHsD~T~~LfLtIg~~fn~dqL~~w~~RDEVlAEW~~~~g~~~LhVyc~V 143 (178)
++|||+||+|+|+ .+++++.|++||||||||||+||+|||+||.+||+|||.+|++||||||||++++|+|+|||||||
T Consensus 1 ~~F~p~KL~V~f~-~~~t~~~P~~pR~YTLTHsD~T~~L~L~Ig~~~~~d~l~~~~~RDEVlaEW~~~~~~~~L~v~~~V 79 (151)
T PF12638_consen 1 MKFNPSKLSVEFR-GGITPTHPIIPRRYTLTHSDFTGELFLTIGNEFNYDQLYNRLMRDEVLAEWKKVNGQYSLHVYCYV 79 (151)
T ss_pred CCCChHHeEEEec-CCCCcCCCCCCceEEeecCCccCceEEEeeHHhhHHHhhccchhceEEEEEEEcCCEEEEEEEEEE
Confidence 3899999999999 889999999999999999999999999999999999994458999999999999999999999999
Q ss_pred eCCCcchhhHHHHHHHHHHhhccccccc
Q 030399 144 SGPSLLRDLAAEFRYHIFTKEMPLGSHV 171 (178)
Q Consensus 144 sG~~~~~~~~A~~Ry~IF~kELPLaL~a 171 (178)
||+|++++++|++||+||+|||||||+|
T Consensus 80 ~g~~~~~~~aa~~Ry~IF~kELPl~L~A 107 (151)
T PF12638_consen 80 SGGHFDKDLAARLRYYIFRKELPLALKA 107 (151)
T ss_pred CCCccChhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999987788999999999999997
No 2
>PF01015 Ribosomal_S3Ae: Ribosomal S3Ae family; InterPro: IPR001593 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins that have from 220 to 250 amino acids and represents Rps1 (eukaryotic) and Rps3Ae (archaeal and eukaryotic).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_4 2XZM_4 3U5C_B 3U5G_B.
Probab=72.01 E-value=27 Score=29.49 Aligned_cols=76 Identities=21% Similarity=0.332 Sum_probs=47.9
Q ss_pred CCCCCCCCcEEEeecCCCCCCCCCCCceeeeccCCcCcc--------------------eEEEEehhhhhhhhc----cc
Q 030399 63 PASFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTAN--------------------LTLTISNVINLEQLR----GW 118 (178)
Q Consensus 63 p~~Fnp~KLsV~f~g~~~t~~~PiipRrYTLTHsD~T~~--------------------LfLtIg~~fn~dqL~----~w 118 (178)
|+.|+-..+=-+.. +....+.+|.+-+|..|.|++ +|-=.|.+.+.|.|. .|
T Consensus 23 P~~F~~~~iG~T~~----~~~~~l~gRv~Evsl~DL~~d~~~~~~K~~f~i~~V~g~~a~T~F~G~elt~D~lrSlvrk~ 98 (194)
T PF01015_consen 23 PSMFGNRNIGKTPA----NKPEKLKGRVFEVSLADLTNDFSKAYRKFKFKIEDVQGNNALTNFHGMELTRDKLRSLVRKW 98 (194)
T ss_dssp -TTSSSSEECEEEE----E-CCCCCC-EEEEECHCCCSTTTTSS-EEEEEEEEEETTEEEEEEEEEE--HHHHHHC--TT
T ss_pred CHHhCcceeeEEEc----CCcccccCeEEEEEHHHhcCchhhhcEEEEEEEEeecCCEEEEEEcceecchhhhhcceeec
Confidence 46777665555554 224568999999999999998 444457888888776 45
Q ss_pred cccceEEEEEEecCCeeEEEEEEEE
Q 030399 119 YIKDDVVAEWKKVRDDMCLHVHCYV 143 (178)
Q Consensus 119 ~~RDEVlAEW~~~~g~~~LhVyc~V 143 (178)
.++=|..-.=+..+| |.|.|+|-.
T Consensus 99 ~s~Ie~~~dvkT~DG-y~lRvf~i~ 122 (194)
T PF01015_consen 99 QSRIEAIVDVKTKDG-YLLRVFCIA 122 (194)
T ss_dssp C-EEEEEEEEEETTT-EEEEEEEEE
T ss_pred ceEEEEEEEEEcCCC-cEEEEEEEE
Confidence 556666666655444 666666654
No 3
>PRK04057 30S ribosomal protein S3Ae; Validated
Probab=35.82 E-value=1.4e+02 Score=25.55 Aligned_cols=76 Identities=17% Similarity=0.226 Sum_probs=47.5
Q ss_pred CCCCCCCCcEEEeecCCCCCCCCCCCceeeeccCCcCcce-------EEE-------------Eehhhhhhhhc----cc
Q 030399 63 PASFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTANL-------TLT-------------ISNVINLEQLR----GW 118 (178)
Q Consensus 63 p~~Fnp~KLsV~f~g~~~t~~~PiipRrYTLTHsD~T~~L-------fLt-------------Ig~~fn~dqL~----~w 118 (178)
|..|+-..+=-+.. .....+++|.|-+|-.|.|++. .|. +|.++..|.|. .|
T Consensus 17 P~~F~~~~iG~T~a----~~~~~l~GRv~EvsL~DL~~d~~~~~~K~~f~i~~V~G~~a~T~F~G~~lTrD~lrSlVrk~ 92 (203)
T PRK04057 17 PEFFGGVEIGETPA----DDPEKLIGRVVETTLGDLTGDFSKQNVKLYFKIDNVEGDKAYTRFIGHELTRDYLRSLVRRR 92 (203)
T ss_pred CcccCCceEEEEEc----cChhhcCCcEEEEEHHHhcCChhhceEEEEEEEEeeeCCEEEEEEeeeEecHHHHHhHhccC
Confidence 46676666655554 2233489999999999999874 233 36677777766 35
Q ss_pred cccceEEEEEEecCCeeEEEEEEEE
Q 030399 119 YIKDDVVAEWKKVRDDMCLHVHCYV 143 (178)
Q Consensus 119 ~~RDEVlAEW~~~~g~~~LhVyc~V 143 (178)
.+|=|..-.=+. ..+|.|-|+|-+
T Consensus 93 ~S~Ie~~vdvkT-kDGy~lRv~~i~ 116 (203)
T PRK04057 93 TSKIDAIVDVTT-KDGYKVRVKPVA 116 (203)
T ss_pred ceeEEEEEEEEc-CCCCEEEEEEEE
Confidence 455444444443 344667776644
No 4
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=34.50 E-value=8.5 Score=35.07 Aligned_cols=31 Identities=32% Similarity=0.399 Sum_probs=23.2
Q ss_pred EEEEEeCCCcchhhHHHHHHHHHHhhccccc
Q 030399 139 VHCYVSGPSLLRDLAAEFRYHIFTKEMPLGS 169 (178)
Q Consensus 139 Vyc~VsG~~~~~~~~A~~Ry~IF~kELPLaL 169 (178)
|-+||||++.---.-.+.||.||-..|..|+
T Consensus 127 vvLYvSGGNTQvIAYse~rYrIFGETlDIAv 157 (336)
T KOG2708|consen 127 VVLYVSGGNTQVIAYSEKRYRIFGETLDIAV 157 (336)
T ss_pred EEEEEeCCceEEEEEccceeeeecceehhhh
Confidence 4578999975332356899999999888765
No 5
>PF07351 DUF1480: Protein of unknown function (DUF1480); InterPro: IPR009950 This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown.
Probab=23.82 E-value=59 Score=24.68 Aligned_cols=29 Identities=31% Similarity=0.278 Sum_probs=25.1
Q ss_pred eeccCCcCcceEEEEehhhhhh---hhccccc
Q 030399 92 ILSHCDFTANLTLTISNVINLE---QLRGWYI 120 (178)
Q Consensus 92 TLTHsD~T~~LfLtIg~~fn~d---qL~~w~~ 120 (178)
.|++.+..++-+|+|-+..+.| ||+||..
T Consensus 17 ~l~~~~~~~~~tlsIPCksdpdlcmQLDgWDe 48 (80)
T PF07351_consen 17 ELSSEPDKGEDTLSIPCKSDPDLCMQLDGWDE 48 (80)
T ss_pred EecCCCCCCCCeEEeecCCChhheeEeccccc
Confidence 5777778899999999999999 9999943
No 6
>PF09178 DUF1945: Domain of unknown function (DUF1945); InterPro: IPR015261 Members of this entry, which are predominantly found in prokaryotic 4-alpha-glucanotransferase, adopt a structure composed of six antiparallel beta-strands, four of which form a beta-sheet and another two form a type I, beta-hairpin. The role of this family of domains, has not, as yet, been defined []. ; PDB: 1LWH_B 1LWJ_B.
Probab=22.16 E-value=1.2e+02 Score=21.15 Aligned_cols=31 Identities=16% Similarity=0.322 Sum_probs=22.3
Q ss_pred cceEEEEEEecCCeeEEEEEEEEeCCCcchh
Q 030399 121 KDDVVAEWKKVRDDMCLHVHCYVSGPSLLRD 151 (178)
Q Consensus 121 RDEVlAEW~~~~g~~~LhVyc~VsG~~~~~~ 151 (178)
.|+.|--.+-.+++++|.|+=.+||++.-.+
T Consensus 9 e~k~l~vYrl~~~~~SLkv~HNlSg~E~vFE 39 (51)
T PF09178_consen 9 EEKFLHVYRLYDDQKSLKVFHNLSGEEVVFE 39 (51)
T ss_dssp ESSEE-EEEEEETTEEEEEEEE-SSS-EEET
T ss_pred cceEEEEEEEeCCCEEEEEEEecCCCEEEEE
Confidence 3666667777889999999999999876444
No 7
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=21.51 E-value=25 Score=28.98 Aligned_cols=41 Identities=27% Similarity=0.376 Sum_probs=22.8
Q ss_pred CCCCCcEEEeecCCCCCCCCCCCceeeeccCCc--CcceEEEEehh
Q 030399 66 FEASKLKVVFLGEGMNDYSRILPRTYILSHCDF--TANLTLTISNV 109 (178)
Q Consensus 66 Fnp~KLsV~f~g~~~t~~~PiipRrYTLTHsD~--T~~LfLtIg~~ 109 (178)
|..-|+.+++. +.-.+|+.||.||+.=|.. -.++.|+||-.
T Consensus 160 fps~~~pl~~l---l~~lp~l~PR~YSIsSS~~~~p~~v~ltv~vv 202 (219)
T PF00667_consen 160 FPSCKPPLEEL---LELLPPLQPRYYSISSSPLVHPNKVHLTVSVV 202 (219)
T ss_dssp STTBTC-HHHH---HHHS-B---EEEEB-S-TTTSTTEEEEEEEE-
T ss_pred CcccCCCHHHh---hhhCCCCCCcceeecccccCCCCEEEEEEEEE
Confidence 44456766666 5567789999999987753 56677777654
No 8
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=16.79 E-value=2e+02 Score=19.49 Aligned_cols=45 Identities=16% Similarity=0.136 Sum_probs=23.8
Q ss_pred chHHHHHHHhCCCCC---CCCCCcEEEeecCCCCCCCCCCCceeeeccCC
Q 030399 51 TFVSEAVRLLGPPAS---FEASKLKVVFLGEGMNDYSRILPRTYILSHCD 97 (178)
Q Consensus 51 ~~~~~~~rllgpp~~---Fnp~KLsV~f~g~~~t~~~PiipRrYTLTHsD 97 (178)
..-.++..|||+|.. |+++ -+. |.-.-........-|+++|+=.|
T Consensus 16 mTk~qV~~lLG~P~~~~~~~~~-~W~-Y~~~~~~~~~~~~~~~l~V~Fd~ 63 (71)
T PF04355_consen 16 MTKDQVRALLGSPSLRDPFDPN-RWY-YVYSKRRGNGANEQRQLKVYFDD 63 (71)
T ss_dssp SBHHHHHHHHTS-SEE-CTTSS-EEE-EEEEETTCSSSSCEEEEEEEECT
T ss_pred CCHHHHHHhcCCCCccccccCC-EEE-EEEEEecCCCccEEEEEEEEEcC
Confidence 344689999999976 7777 332 43111111223445666665443
No 9
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=15.17 E-value=1.4e+02 Score=20.25 Aligned_cols=19 Identities=42% Similarity=0.793 Sum_probs=14.7
Q ss_pred EEEEEEeCCCcchhhHHHHHHH
Q 030399 138 HVHCYVSGPSLLRDLAAEFRYH 159 (178)
Q Consensus 138 hVyc~VsG~~~~~~~~A~~Ry~ 159 (178)
||-|-|+|..-.++ .+||-
T Consensus 7 ~V~CAVTg~~IpLd---~LrYW 25 (42)
T PF09866_consen 7 FVRCAVTGQPIPLD---ELRYW 25 (42)
T ss_pred EEEEEeeCCcccHH---HhccC
Confidence 78999999876555 77773
No 10
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=14.29 E-value=2.1e+02 Score=25.71 Aligned_cols=63 Identities=21% Similarity=0.226 Sum_probs=40.8
Q ss_pred EeeecCCCcccccchHHHHHHHhCCCCCCCCCCcEEEeecCCCCCCCC-CCCceeeeccCCcCcceEEEE
Q 030399 38 FSSINSSSRASYGTFVSEAVRLLGPPASFEASKLKVVFLGEGMNDYSR-ILPRTYILSHCDFTANLTLTI 106 (178)
Q Consensus 38 ~~s~~~~~~~~~~~~~~~~~rllgpp~~Fnp~KLsV~f~g~~~t~~~P-iipRrYTLTHsD~T~~LfLtI 106 (178)
+.||....+|.|.|+.|-++||+. .|.-.++ +.|..++.++. .+.++-++---++.-+..|||
T Consensus 29 iTs~IGPNGAGKSTLLS~~sRL~~----~d~G~i~--i~g~~~~~~~s~~LAk~lSILkQ~N~i~~rlTV 92 (252)
T COG4604 29 ITSIIGPNGAGKSTLLSMMSRLLK----KDSGEIT--IDGLELTSTPSKELAKKLSILKQENHINSRLTV 92 (252)
T ss_pred eeEEECCCCccHHHHHHHHHHhcc----ccCceEE--EeeeecccCChHHHHHHHHHHHhhchhhheeEH
Confidence 347777799999999999999995 3555544 44556665543 455555554444444555554
Done!