Query 025286
Match_columns 255
No_of_seqs 71 out of 73
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:18:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025286.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025286hhsearch_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 3.5E-75 7.6E-80 492.3 14.4 150 65-215 2-151 (151)
2 PF01015 Ribosomal_S3Ae: Ribos 56.1 66 0.0014 28.7 7.8 76 63-143 23-122 (194)
3 KOG3984 Purine nucleoside phos 34.9 5.7 0.00012 37.7 -2.3 51 99-157 155-207 (286)
4 COG5035 CDC50 Cell cycle contr 26.8 24 0.00052 34.7 0.3 90 93-229 77-168 (372)
5 PRK04057 30S ribosomal protein 25.8 2.4E+02 0.0051 25.6 6.4 76 63-143 17-116 (203)
6 KOG2708 Predicted metalloprote 19.3 27 0.00058 33.5 -0.9 31 139-169 127-157 (336)
7 PF09178 DUF1945: Domain of un 18.3 1.5E+02 0.0032 21.9 2.9 29 122-150 10-38 (51)
8 PF07351 DUF1480: Protein of u 16.2 1E+02 0.0023 24.6 1.8 29 92-120 17-48 (80)
9 PF00667 FAD_binding_1: FAD bi 14.3 45 0.00097 29.1 -0.7 41 66-109 160-202 (219)
10 COG4951 Uncharacterized protei 14.2 2.7E+02 0.0058 27.3 4.4 70 137-218 127-197 (361)
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=3.5e-75 Score=492.30 Aligned_cols=150 Identities=52% Similarity=0.852 Sum_probs=145.6
Q ss_pred CCCCCcceEEEecCCCCCCCCCCCceeeeccCCcCcceEEEEehhcchhhhccccccceEEEEEEecCCeeEEEEEEEEe
Q 025286 65 SFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTANLTLTISNVINLEQLRGWYIKDDVVAEWKKVRDDMCLHVHCYVS 144 (255)
Q Consensus 65 ~Fnp~KLsV~f~~~~~t~~~PiipRrYTLTHsD~T~~LfLtIg~~fn~dql~~w~~RDEVlAEW~~~~g~~~LhVyc~Vs 144 (255)
+|||+||+|+|+ .+++++.|++||||||||||+||+|||+||.+||+|||.+|.+||||||||++++|+|+||||||||
T Consensus 2 ~F~p~KL~V~f~-~~~t~~~P~~pR~YTLTHsD~T~~L~L~Ig~~~~~d~l~~~~~RDEVlaEW~~~~~~~~L~v~~~V~ 80 (151)
T PF12638_consen 2 KFNPSKLSVEFR-GGITPTHPIIPRRYTLTHSDFTGELFLTIGNEFNYDQLYNRLMRDEVLAEWKKVNGQYSLHVYCYVS 80 (151)
T ss_pred CCChHHeEEEec-CCCCcCCCCCCceEEeecCCccCceEEEeeHHhhHHHhhccchhceEEEEEEEcCCEEEEEEEEEEC
Confidence 899999999999 8899999999999999999999999999999999999944589999999999999999999999999
Q ss_pred CCCcchhhHHHHHHHHHHhhhhhhHHHHHhcchhhhccCcccCCCceEEEEecCCCCCcceeecccchhhh
Q 025286 145 GPSLLRDLAAEFRYHIFTKEMPLVLKAVLHGDSMLFRENPELMNALVRVYFHSSSKIYNRMECWGPLKDAA 215 (255)
Q Consensus 145 G~~~~~~~~a~~Ry~IFrkELPLaLkAI~yGDr~lF~~~PeL~~ApI~V~FhS~~p~fnr~E~wG~l~dy~ 215 (255)
|+|++++++|.+||+||+||||||||||+|||+.||++||+|++|||||||||++|+||++||||+|+||.
T Consensus 81 g~~~~~~~aa~~Ry~IF~kELPl~L~Ai~yGD~~lf~~~P~L~~a~I~V~F~S~~p~~n~~e~wG~~~dy~ 151 (151)
T PF12638_consen 81 GGHFDKDLAARLRYYIFRKELPLALKAIRYGDRSLFAEHPELDDAPIWVHFHSSYPEFNRIECWGTLRDYA 151 (151)
T ss_pred CCccChhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHhChhhcCCCEEEEEecCCCCCCcEEEECChHhCC
Confidence 99999998888899999999999999999999999999999999999999999999999999999999984
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=56.11 E-value=66 Score=28.74 Aligned_cols=76 Identities=20% Similarity=0.326 Sum_probs=48.6
Q ss_pred CCCCCCCcceEEEecCCCCCCCCCCCceeeeccCCcCcc--------------------eEEEEehhcchhhhcc----c
Q 025286 63 PASFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTAN--------------------LTLTISNVINLEQLRG----W 118 (255)
Q Consensus 63 p~~Fnp~KLsV~f~~~~~t~~~PiipRrYTLTHsD~T~~--------------------LfLtIg~~fn~dql~~----w 118 (255)
|+.|+-..+=-+.... .+.+.+|.+-+|..|.|++ +|-=.|.+.+.|.|.+ |
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 PSMFGNRNIGKTPANK----PEKLKGRVFEVSLADLTNDFSKAYRKFKFKIEDVQGNNALTNFHGMELTRDKLRSLVRKW 98 (194)
T ss_dssp -TTSSSSEECEEEEE-----CCCCCC-EEEEECHCCCSTTTTSS-EEEEEEEEEETTEEEEEEEEEE--HHHHHHC--TT
T ss_pred CHHhCcceeeEEEcCC----cccccCeEEEEEHHHhcCchhhhcEEEEEEEEeecCCEEEEEEcceecchhhhhcceeec
Confidence 5778766666666533 4568999999999999999 4444678888888764 5
Q ss_pred cccceEEEEEEecCCeeEEEEEEEE
Q 025286 119 YIKDDVVAEWKKVRDDMCLHVHCYV 143 (255)
Q Consensus 119 ~~RDEVlAEW~~~~g~~~LhVyc~V 143 (255)
.++=|..-.=+..+| |.|.|+|-.
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 556666666555444 556766654
No 3
>KOG3984 consensus Purine nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=34.92 E-value=5.7 Score=37.66 Aligned_cols=51 Identities=22% Similarity=0.221 Sum_probs=38.9
Q ss_pred CcceEEEEehhcchhhhccccccceEEEEEEecCCeeEEE--EEEEEeCCCcchhhHHHHH
Q 025286 99 TANLTLTISNVINLEQLRGWYIKDDVVAEWKKVRDDMCLH--VHCYVSGPSLLRDLAAEFR 157 (255)
Q Consensus 99 T~~LfLtIg~~fn~dql~~w~~RDEVlAEW~~~~g~~~Lh--Vyc~VsG~~~~~~~~a~~R 157 (255)
-|.=|.+.+..||++ +|..++--||..+-|..|| ||.+|+|..+.. .|+.|
T Consensus 155 fG~rf~a~sdAYd~~------lr~~a~~~~K~m~iqr~lheGvy~~vgGP~~eT--~AE~r 207 (286)
T KOG3984|consen 155 FGVRFPALSDAYDKD------LRQKALEIGKAMGIQRTLHEGVYACVGGPIFET--RAESR 207 (286)
T ss_pred ccccccchhhhhhHH------HHHHHHHHHHHhcccchhhcceEEEecCCcccc--HHHHH
Confidence 366788888888854 5556777899888899999 999999987644 34444
No 4
>COG5035 CDC50 Cell cycle control protein [Cell division and chromosome partitioning / Transcription / Signal transduction mechanisms]
Probab=26.80 E-value=24 Score=34.67 Aligned_cols=90 Identities=16% Similarity=0.229 Sum_probs=58.1
Q ss_pred eccCCcCc-ceEEEEehhcchhhhccccccceEEEEEEec-CCeeEEEEEEEEeCCCcchhhHHHHHHHHHHhhhhhhHH
Q 025286 93 LSHCDFTA-NLTLTISNVINLEQLRGWYIKDDVVAEWKKV-RDDMCLHVHCYVSGPSLLRDLAAEFRYHIFTKEMPLVLK 170 (255)
Q Consensus 93 LTHsD~T~-~LfLtIg~~fn~dql~~w~~RDEVlAEW~~~-~g~~~LhVyc~VsG~~~~~~~~a~~Ry~IFrkELPLaLk 170 (255)
-||||.+| +=|=+|-.++=.-+. ...++|..+|+.. +....+.+ |-|.
T Consensus 77 Ytdc~t~as~~f~~iPs~~~~~~f---~~~~~~~pqW~~~~~~~~d~~~-C~ir-------------------------- 126 (372)
T COG5035 77 YTDCMTLASDEFSDIPSEYIQFHF---KKKVNVLPQWRFSTDEEDDFQK-CQIR-------------------------- 126 (372)
T ss_pred ccccccccchhhhhCchhheeeee---ecccccccceeecccccCCcce-eEEE--------------------------
Confidence 36788777 555555444332232 2478999999833 22222222 4442
Q ss_pred HHHhcchhhhccCcccCCCceEEEEecCCCCCcceeecccchhhhccCCcchhhhhhhc
Q 025286 171 AVLHGDSMLFRENPELMNALVRVYFHSSSKIYNRMECWGPLKDAAEGRQEDSIQGLLTA 229 (255)
Q Consensus 171 AI~yGDr~lF~~~PeL~~ApI~V~FhS~~p~fnr~E~wG~l~dy~~~~~~d~~~~~~~~ 229 (255)
-+.|+-+.+||||+. .-.+.+.+-|.|.+.-.+||++|+--+
T Consensus 127 ----------f~vp~~~k~~vfiyy-------rl~nFyQNhrRY~~S~d~dQl~Ge~~~ 168 (372)
T COG5035 127 ----------FTVPSDMKKPVFIYY-------RLTNFYQNHRRYVKSFDEDQLRGEALK 168 (372)
T ss_pred ----------EEchhhcccceeeee-------hhHHHHHhhHHHHhccCHHHhcCcccc
Confidence 234677789999985 346778889999999999999987643
No 5
>PRK04057 30S ribosomal protein S3Ae; Validated
Probab=25.85 E-value=2.4e+02 Score=25.64 Aligned_cols=76 Identities=17% Similarity=0.223 Sum_probs=48.3
Q ss_pred CCCCCCCcceEEEecCCCCCCCCCCCceeeeccCCcCcce-------EEE-------------Eehhcchhhhcc----c
Q 025286 63 PASFEASKLKVVFLGEGMNDYSRILPRTYILSHCDFTANL-------TLT-------------ISNVINLEQLRG----W 118 (255)
Q Consensus 63 p~~Fnp~KLsV~f~~~~~t~~~PiipRrYTLTHsD~T~~L-------fLt-------------Ig~~fn~dql~~----w 118 (255)
|+.|+-..+--+... ...-+++|.|-+|-.|.|++. .|. +|.+...|.|.+ |
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 PEFFGGVEIGETPAD----DPEKLIGRVVETTLGDLTGDFSKQNVKLYFKIDNVEGDKAYTRFIGHELTRDYLRSLVRRR 92 (203)
T ss_pred CcccCCceEEEEEcc----ChhhcCCcEEEEEHHHhcCChhhceEEEEEEEEeeeCCEEEEEEeeeEecHHHHHhHhccC
Confidence 567877776666652 223489999999999999874 233 366777777764 4
Q ss_pred cccceEEEEEEecCCeeEEEEEEEE
Q 025286 119 YIKDDVVAEWKKVRDDMCLHVHCYV 143 (255)
Q Consensus 119 ~~RDEVlAEW~~~~g~~~LhVyc~V 143 (255)
.+|=|..-.=+. ..+|.|-|+|-+
T Consensus 93 ~S~Ie~~vdvkT-kDGy~lRv~~i~ 116 (203)
T PRK04057 93 TSKIDAIVDVTT-KDGYKVRVKPVA 116 (203)
T ss_pred ceeEEEEEEEEc-CCCCEEEEEEEE
Confidence 444444444443 344567766654
No 6
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=19.29 E-value=27 Score=33.51 Aligned_cols=31 Identities=32% Similarity=0.425 Sum_probs=23.8
Q ss_pred EEEEEeCCCcchhhHHHHHHHHHHhhhhhhH
Q 025286 139 VHCYVSGPSLLRDLAAEFRYHIFTKEMPLVL 169 (255)
Q Consensus 139 Vyc~VsG~~~~~~~~a~~Ry~IFrkELPLaL 169 (255)
|-+||||++.-.-.-...||.||-..|..|.
T Consensus 127 vvLYvSGGNTQvIAYse~rYrIFGETlDIAv 157 (336)
T KOG2708|consen 127 VVLYVSGGNTQVIAYSEKRYRIFGETLDIAV 157 (336)
T ss_pred EEEEEeCCceEEEEEccceeeeecceehhhh
Confidence 5578999985443356889999999997664
No 7
>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=18.35 E-value=1.5e+02 Score=21.87 Aligned_cols=29 Identities=17% Similarity=0.299 Sum_probs=21.6
Q ss_pred ceEEEEEEecCCeeEEEEEEEEeCCCcch
Q 025286 122 DDVVAEWKKVRDDMCLHVHCYVSGPSLLR 150 (255)
Q Consensus 122 DEVlAEW~~~~g~~~LhVyc~VsG~~~~~ 150 (255)
|..|--.+-++++.+|.|+=.+||++.-.
T Consensus 10 ~k~l~vYrl~~~~~SLkv~HNlSg~E~vF 38 (51)
T PF09178_consen 10 EKFLHVYRLYDDQKSLKVFHNLSGEEVVF 38 (51)
T ss_dssp SSEE-EEEEEETTEEEEEEEE-SSS-EEE
T ss_pred ceEEEEEEEeCCCEEEEEEEecCCCEEEE
Confidence 56676778889999999999999987543
No 8
>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=16.16 E-value=1e+02 Score=24.59 Aligned_cols=29 Identities=31% Similarity=0.278 Sum_probs=25.1
Q ss_pred eeccCCcCcceEEEEehhcchh---hhccccc
Q 025286 92 ILSHCDFTANLTLTISNVINLE---QLRGWYI 120 (255)
Q Consensus 92 TLTHsD~T~~LfLtIg~~fn~d---ql~~w~~ 120 (255)
+|++....|+-+|+|-+..+.| ||.||..
T Consensus 17 ~l~~~~~~~~~tlsIPCksdpdlcmQLDgWDe 48 (80)
T PF07351_consen 17 ELSSEPDKGEDTLSIPCKSDPDLCMQLDGWDE 48 (80)
T ss_pred EecCCCCCCCCeEEeecCCChhheeEeccccc
Confidence 5777788899999999999999 9999943
No 9
>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=14.34 E-value=45 Score=29.09 Aligned_cols=41 Identities=27% Similarity=0.376 Sum_probs=22.3
Q ss_pred CCCCcceEEEecCCCCCCCCCCCceeeeccCCc--CcceEEEEehh
Q 025286 66 FEASKLKVVFLGEGMNDYSRILPRTYILSHCDF--TANLTLTISNV 109 (255)
Q Consensus 66 Fnp~KLsV~f~~~~~t~~~PiipRrYTLTHsD~--T~~LfLtIg~~ 109 (255)
|..-|+.++++ +.-.+|+.||.||+.=|.. -.++.|+||..
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 44456666665 4556799999999987753 56677777654
No 10
>COG4951 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=14.16 E-value=2.7e+02 Score=27.34 Aligned_cols=70 Identities=16% Similarity=0.080 Sum_probs=41.3
Q ss_pred EEEEEEEeCCCcchhhHHHHHHHHHHhhhhhhHHHHHhcchhhhccCcccCCCceEEEEecCCCCC-cceeecccchhhh
Q 025286 137 LHVHCYVSGPSLLRDLAAEFRYHIFTKEMPLVLKAVLHGDSMLFRENPELMNALVRVYFHSSSKIY-NRMECWGPLKDAA 215 (255)
Q Consensus 137 LhVyc~VsG~~~~~~~~a~~Ry~IFrkELPLaLkAI~yGDr~lF~~~PeL~~ApI~V~FhS~~p~f-nr~E~wG~l~dy~ 215 (255)
..+-|..+-|+|-++ ++.+|-.-=...+|-+|+-=|-|| .++||+.|.+..|.- -|.--..-++.++
T Consensus 127 yfLa~DfDeG~WK~d-a~af~r~c~e~gi~A~lEISRS~~-----------GahvWiFF~~~IsareARrlG~a~i~~AM 194 (361)
T COG4951 127 YFLAVDFDEGEWKKD-ASAFMRSCDELGVPAALEISRSRQ-----------GAHVWIFFASRISAREARRLGTAIISYAM 194 (361)
T ss_pred EEEEEecCccchHHH-HHHHHHHHHhhCChhhheecccCC-----------CceEEEEecCcccHHHHHHHHHHHHHHHH
Confidence 345566777777666 555554443455666666555554 689999999987642 2222233345555
Q ss_pred ccC
Q 025286 216 EGR 218 (255)
Q Consensus 216 ~~~ 218 (255)
+.+
T Consensus 195 ~~~ 197 (361)
T COG4951 195 SRT 197 (361)
T ss_pred hhC
Confidence 443
Done!