Query 026760
Match_columns 233
No_of_seqs 75 out of 77
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 12:19:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026760hhsearch_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 3.6E-76 7.8E-81 492.4 13.3 149 12-165 2-151 (151)
2 PF08576 DUF1764: Eukaryotic p 73.8 1.4 3.1E-05 34.5 0.8 12 190-201 91-102 (102)
3 PF01015 Ribosomal_S3Ae: Ribos 47.4 1E+02 0.0022 27.2 7.5 81 8-93 21-122 (194)
4 KOG3984 Purine nucleoside phos 30.7 8.8 0.00019 36.0 -1.8 50 47-107 156-207 (286)
5 cd06203 methionine_synthase_re 27.3 1.2E+02 0.0027 28.6 5.1 74 33-110 172-260 (398)
6 COG4951 Uncharacterized protei 26.7 1.1E+02 0.0023 29.6 4.6 69 88-168 128-197 (361)
7 cd06202 Nitric_oxide_synthase 26.7 1.2E+02 0.0026 28.8 4.9 75 31-110 174-265 (406)
8 PF09178 DUF1945: Domain of un 23.9 98 0.0021 22.5 2.9 30 72-101 10-39 (51)
9 PF04875 DUF645: Protein of un 23.4 38 0.00083 25.3 0.8 34 35-73 6-39 (59)
10 KOG2708 Predicted metalloprote 19.3 27 0.00058 33.2 -0.9 32 88-119 126-157 (336)
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=3.6e-76 Score=492.43 Aligned_cols=149 Identities=58% Similarity=1.016 Sum_probs=144.7
Q ss_pred CCCCCCceEEEe-ccCCcCCCCCCCcceeeccCCCCCceEEEEccccchhhhhhhccccccceeeeEEeeeCCeeEEEEE
Q 026760 12 IFEASKLKVLFL-GVDEEKHPGKLPRTYTLTHSDITSKLTLAISQTINNSQLQGWYNRLQRDEVVAEWKKVKGKMSLHVH 90 (233)
Q Consensus 12 ~Fnp~KL~V~f~-gvt~~~~P~~ipRrYTLTHsD~T~~LfLtIg~~fn~dqL~gwy~r~~RDEVlAEW~~~~g~~~LhV~ 90 (233)
+|||+||+|+|+ |++ +++|+ +||||||||||+||+|||+||.+||+||| ||++|||||||||++++|+|+||||
T Consensus 2 ~F~p~KL~V~f~~~~t-~~~P~-~pR~YTLTHsD~T~~L~L~Ig~~~~~d~l---~~~~~RDEVlaEW~~~~~~~~L~v~ 76 (151)
T PF12638_consen 2 KFNPSKLSVEFRGGIT-PTHPI-IPRRYTLTHSDFTGELFLTIGNEFNYDQL---YNRLMRDEVLAEWKKVNGQYSLHVY 76 (151)
T ss_pred CCChHHeEEEecCCCC-cCCCC-CCceEEeecCCccCceEEEeeHHhhHHHh---hccchhceEEEEEEEcCCEEEEEEE
Confidence 799999999999 555 99998 99999999999999999999999999999 7889999999999999999999999
Q ss_pred EEeeCCccchhHHHHHHHHHHhhhhhhhhhHhhhcChhhhccCcccCCCeeEEEEeeCCCCCcceeeeccccccc
Q 026760 91 CHISGGHFLLDICARLRFFIFSKELPVVLKAFVHGDGNLLNNHPELQEALVWVYFHSNIPEFNKVECWGPLKEAV 165 (233)
Q Consensus 91 c~VsG~~~~~~~~a~~Ry~IF~kELPLvLkAI~yGD~~lF~~~PeL~~ApI~V~FhS~~p~fnr~E~wG~l~da~ 165 (233)
|||||+|++++++|++||+||+||||||||||+|||+.||++||+|++|||||||||++|+||++||||+|+||.
T Consensus 77 ~~V~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 77 CYVSGGHFDKDLAARLRYYIFRKELPLALKAIRYGDRSLFAEHPELDDAPIWVHFHSSYPEFNRIECWGTLRDYA 151 (151)
T ss_pred EEECCCccChhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHhChhhcCCCEEEEEecCCCCCCcEEEECChHhCC
Confidence 999999999998888899999999999999999999999999999999999999999999999999999999984
No 2
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=73.81 E-value=1.4 Score=34.50 Aligned_cols=12 Identities=42% Similarity=1.342 Sum_probs=10.7
Q ss_pred CcCcccCCCccC
Q 026760 190 PEPCQETCNCCF 201 (233)
Q Consensus 190 p~~c~~~c~cc~ 201 (233)
-.-|+-.|+|||
T Consensus 91 T~~CPFDC~CCF 102 (102)
T PF08576_consen 91 TPLCPFDCDCCF 102 (102)
T ss_pred CCCCCCcCCCCC
Confidence 458999999999
No 3
>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=47.35 E-value=1e+02 Score=27.22 Aligned_cols=81 Identities=19% Similarity=0.283 Sum_probs=44.1
Q ss_pred cCCCCCCCCCceEEEeccCCcCCCCCCCcceeeccCCCCCc--------------------eEEEEccccchhhhhhhcc
Q 026760 8 FGPAIFEASKLKVLFLGVDEEKHPGKLPRTYTLTHSDITSK--------------------LTLAISQTINNSQLQGWYN 67 (233)
Q Consensus 8 ~~p~~Fnp~KL~V~f~gvt~~~~P~~ipRrYTLTHsD~T~~--------------------LfLtIg~~fn~dqL~gwy~ 67 (233)
..|+.|+-..+--+. ++ ...-+ .+|.|-+|..|.|++ +|-=.|.+.+.|.|....-
T Consensus 21 ~AP~~F~~~~iG~T~--~~-~~~~l-~gRv~Evsl~DL~~d~~~~~~K~~f~i~~V~g~~a~T~F~G~elt~D~lrSlvr 96 (194)
T PF01015_consen 21 KAPSMFGNRNIGKTP--AN-KPEKL-KGRVFEVSLADLTNDFSKAYRKFKFKIEDVQGNNALTNFHGMELTRDKLRSLVR 96 (194)
T ss_dssp E--TTSSSSEECEEE--EE--CCCC-CC-EEEEECHCCCSTTTTSS-EEEEEEEEEETTEEEEEEEEEE--HHHHHHC--
T ss_pred ECCHHhCcceeeEEE--cC-Ccccc-cCeEEEEEHHHhcCchhhhcEEEEEEEEeecCCEEEEEEcceecchhhhhccee
Confidence 457888644433333 33 22233 899999999999999 4445678888888875221
Q ss_pred c-cccceeeeEEeeeCCeeEEEEEEEe
Q 026760 68 R-LQRDEVVAEWKKVKGKMSLHVHCHI 93 (233)
Q Consensus 68 r-~~RDEVlAEW~~~~g~~~LhV~c~V 93 (233)
| ..|=|..-.=+..+| |.|.|+|..
T Consensus 97 k~~s~Ie~~~dvkT~DG-y~lRvf~i~ 122 (194)
T PF01015_consen 97 KWQSRIEAIVDVKTKDG-YLLRVFCIA 122 (194)
T ss_dssp TTC-EEEEEEEEEETTT-EEEEEEEEE
T ss_pred ecceEEEEEEEEEcCCC-cEEEEEEEE
Confidence 1 113444444455455 667776654
No 4
>KOG3984 consensus Purine nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=30.73 E-value=8.8 Score=36.04 Aligned_cols=50 Identities=22% Similarity=0.165 Sum_probs=34.4
Q ss_pred CceEEEEccccchhhhhhhccccccceeeeEEeeeCCeeEEE--EEEEeeCCccchhHHHHHH
Q 026760 47 SKLTLAISQTINNSQLQGWYNRLQRDEVVAEWKKVKGKMSLH--VHCHISGGHFLLDICARLR 107 (233)
Q Consensus 47 ~~LfLtIg~~fn~dqL~gwy~r~~RDEVlAEW~~~~g~~~Lh--V~c~VsG~~~~~~~~a~~R 107 (233)
|.=|.+.+..|| +.+|..++--||..+-+..|| ||.+|+|..|.. .|+.|
T Consensus 156 G~rf~a~sdAYd---------~~lr~~a~~~~K~m~iqr~lheGvy~~vgGP~~eT--~AE~r 207 (286)
T KOG3984|consen 156 GVRFPALSDAYD---------KDLRQKALEIGKAMGIQRTLHEGVYACVGGPIFET--RAESR 207 (286)
T ss_pred cccccchhhhhh---------HHHHHHHHHHHHHhcccchhhcceEEEecCCcccc--HHHHH
Confidence 445666666555 456777888899888888888 677788887633 35444
No 5
>cd06203 methionine_synthase_red Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite reductase, but contains an extended hinge region. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPORs resemble ferredoxin reductase (FNR) but have a connecting subdomain inserted within the flavin binding region, which helps orient the FMN binding doamin with the FNR module. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme
Probab=27.26 E-value=1.2e+02 Score=28.57 Aligned_cols=74 Identities=19% Similarity=0.252 Sum_probs=43.2
Q ss_pred CCCcceeeccCCCC--CceEEEEccccc--hhhhhhhccccc-----cceeeeEEeeeCCeeEEEE------EEEeeCCc
Q 026760 33 KLPRTYTLTHSDIT--SKLTLAISQTIN--NSQLQGWYNRLQ-----RDEVVAEWKKVKGKMSLHV------HCHISGGH 97 (233)
Q Consensus 33 ~ipRrYTLTHsD~T--~~LfLtIg~~fn--~dqL~gwy~r~~-----RDEVlAEW~~~~g~~~LhV------~c~VsG~~ 97 (233)
..||.||+.=+... +.+.|+|+..=. ....+.|...+. ..+.+.-+....|.+.|-- .+.|++|.
T Consensus 172 ~~~R~YSIsSsp~~~~~~i~l~v~~v~~~~~G~~S~~L~~l~~~~~~~G~~v~i~~~~~g~F~lp~~~~~~piImIa~Gt 251 (398)
T cd06203 172 LQPRPYSIASSPLEGPGKLRFIFSVVEFPAKGLCTSWLESLCLSASSHGVKVPFYLRSSSRFRLPPDDLRRPIIMVGPGT 251 (398)
T ss_pred CCCcceeecCCcccCCCeEEEEEEEEEecCCChhhHHHHHhhhhhcCCCCEEEEEEecCCCcCCCCcCCCCCEEEEcCCc
Confidence 48999999987654 788888876522 233444544444 3343443443344444421 37888876
Q ss_pred cchhHHHHHHHHH
Q 026760 98 FLLDICARLRFFI 110 (233)
Q Consensus 98 ~~~~~~a~~Ry~I 110 (233)
- +|.+|..+
T Consensus 252 G----IAP~rs~l 260 (398)
T cd06203 252 G----VAPFLGFL 260 (398)
T ss_pred C----hHHHHHHH
Confidence 4 56666555
No 6
>COG4951 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.70 E-value=1.1e+02 Score=29.63 Aligned_cols=69 Identities=16% Similarity=0.196 Sum_probs=41.4
Q ss_pred EEEEEeeCCccchhHHHHHHHHHHhhhhhhhhhHhhhcChhhhccCcccCCCeeEEEEeeCCCCC-cceeeecccccccc
Q 026760 88 HVHCHISGGHFLLDICARLRFFIFSKELPVVLKAFVHGDGNLLNNHPELQEALVWVYFHSNIPEF-NKVECWGPLKEAVA 166 (233)
Q Consensus 88 hV~c~VsG~~~~~~~~a~~Ry~IF~kELPLvLkAI~yGD~~lF~~~PeL~~ApI~V~FhS~~p~f-nr~E~wG~l~da~~ 166 (233)
.+-|..+.|+|.++ .+.+|-.-=...+|-+|+-=|-|| .|+||+.|.|.+|.- -|.--.--++.|.+
T Consensus 128 fLa~DfDeG~WK~d-a~af~r~c~e~gi~A~lEISRS~~-----------GahvWiFF~~~IsareARrlG~a~i~~AM~ 195 (361)
T COG4951 128 FLAVDFDEGEWKKD-ASAFMRSCDELGVPAALEISRSRQ-----------GAHVWIFFASRISAREARRLGTAIISYAMS 195 (361)
T ss_pred EEEEecCccchHHH-HHHHHHHHHhhCChhhheecccCC-----------CceEEEEecCcccHHHHHHHHHHHHHHHHh
Confidence 34566788898777 555544433445666666555554 589999999998752 22222333555555
Q ss_pred CC
Q 026760 167 GS 168 (233)
Q Consensus 167 ~~ 168 (233)
.+
T Consensus 196 ~~ 197 (361)
T COG4951 196 RT 197 (361)
T ss_pred hC
Confidence 43
No 7
>cd06202 Nitric_oxide_synthase The ferredoxin-reductase (FNR) like C-terminal domain of the nitric oxide synthase (NOS) fuses with a heme-containing N-terminal oxidase domain. The reductase portion is similar in structure to NADPH dependent cytochrome-450 reductase (CYPOR), having an inserted connecting sub-domain within the FAD binding portion of FNR. NOS differs from CYPOR in a requirement for the cofactor tetrahydrobiopterin and unlike most CYPOR is dimeric. Nitric oxide synthase produces nitric oxide in the conversion of L-arginine to L-citruline. NOS has been implicated in a variety of processes including cytotoxicity, anti-inflamation, neurotransmission, and vascular smooth muscle relaxation.
Probab=26.68 E-value=1.2e+02 Score=28.81 Aligned_cols=75 Identities=19% Similarity=0.259 Sum_probs=46.2
Q ss_pred CCCCCcceeeccCCC--CCceEEEEccc-cc---------hhhhhhhccccccceeeeEEeeeCCeeEEE-----EEEEe
Q 026760 31 PGKLPRTYTLTHSDI--TSKLTLAISQT-IN---------NSQLQGWYNRLQRDEVVAEWKKVKGKMSLH-----VHCHI 93 (233)
Q Consensus 31 P~~ipRrYTLTHsD~--T~~LfLtIg~~-fn---------~dqL~gwy~r~~RDEVlAEW~~~~g~~~Lh-----V~c~V 93 (233)
|+ -||-||+.-++. .+.+.|+|+.. |. .-..+.|..++...+.+.=+....+.+.|- =-+.|
T Consensus 174 ~l-~pR~YSIsSsp~~~~~~~~l~v~vv~~~~~~~~~~~~~G~~S~~L~~l~~Gd~v~v~~~~~~~F~lp~~~~~piImI 252 (406)
T cd06202 174 LL-QPRYYSISSSPDMYPGEIHLTVAVVSYRTRDGQGPVHHGVCSTWLNGLTPGDTVPCFVRSAPSFHLPEDPSVPVIMV 252 (406)
T ss_pred cc-CCcccccCCCccCCCCeEEEEEEEEEEECCCCCCCcccccHHHHHHhCCCCCEEEEEEeeCCccCCCCCCCCCEEEE
Confidence 44 899999999975 46788888764 32 244555766666666665554433334331 13677
Q ss_pred eCCccchhHHHHHHHHH
Q 026760 94 SGGHFLLDICARLRFFI 110 (233)
Q Consensus 94 sG~~~~~~~~a~~Ry~I 110 (233)
++|.- +|.+|-.|
T Consensus 253 a~GTG----IAPfrsfl 265 (406)
T cd06202 253 GPGTG----IAPFRSFW 265 (406)
T ss_pred cCCcC----hHHHHHHH
Confidence 77764 55666555
No 8
>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=23.94 E-value=98 Score=22.50 Aligned_cols=30 Identities=17% Similarity=0.392 Sum_probs=21.7
Q ss_pred ceeeeEEeeeCCeeEEEEEEEeeCCccchh
Q 026760 72 DEVVAEWKKVKGKMSLHVHCHISGGHFLLD 101 (233)
Q Consensus 72 DEVlAEW~~~~g~~~LhV~c~VsG~~~~~~ 101 (233)
|..|--.+-++++++|.|+=.+||++.-.+
T Consensus 10 ~k~l~vYrl~~~~~SLkv~HNlSg~E~vFE 39 (51)
T PF09178_consen 10 EKFLHVYRLYDDQKSLKVFHNLSGEEVVFE 39 (51)
T ss_dssp SSEE-EEEEEETTEEEEEEEE-SSS-EEET
T ss_pred ceEEEEEEEeCCCEEEEEEEecCCCEEEEE
Confidence 556667778899999999999999985433
No 9
>PF04875 DUF645: Protein of unknown function, DUF645; InterPro: IPR006959 This family contains uncharacterised proteins from Vibrio cholerae.
Probab=23.39 E-value=38 Score=25.33 Aligned_cols=34 Identities=32% Similarity=0.432 Sum_probs=29.6
Q ss_pred CcceeeccCCCCCceEEEEccccchhhhhhhccccccce
Q 026760 35 PRTYTLTHSDITSKLTLAISQTINNSQLQGWYNRLQRDE 73 (233)
Q Consensus 35 pRrYTLTHsD~T~~LfLtIg~~fn~dqL~gwy~r~~RDE 73 (233)
.+++..|++=+++.+-|+.+.+.|..||+ +.|-|
T Consensus 6 ~~kf~FtKg~IIA~i~lslsrtlnrGQLn-----LdRFe 39 (59)
T PF04875_consen 6 HGKFGFTKGCIIAVIWLSLSRTLNRGQLN-----LDRFE 39 (59)
T ss_pred ccccccccceEEEEEEEeeecccccCCcC-----cceee
Confidence 46778899999999999999999999998 66654
No 10
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=19.26 E-value=27 Score=33.16 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=23.1
Q ss_pred EEEEEeeCCccchhHHHHHHHHHHhhhhhhhh
Q 026760 88 HVHCHISGGHFLLDICARLRFFIFSKELPVVL 119 (233)
Q Consensus 88 hV~c~VsG~~~~~~~~a~~Ry~IF~kELPLvL 119 (233)
-|-+|||||+----.....||.||-.-|-.|.
T Consensus 126 PvvLYvSGGNTQvIAYse~rYrIFGETlDIAv 157 (336)
T KOG2708|consen 126 PVVLYVSGGNTQVIAYSEKRYRIFGETLDIAV 157 (336)
T ss_pred CEEEEEeCCceEEEEEccceeeeecceehhhh
Confidence 35578999973322345789999999988764
Done!