Query 024155
Match_columns 271
No_of_seqs 82 out of 84
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 02:29:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024155hhsearch_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 2.6E-75 5.7E-80 495.7 12.8 149 50-203 2-151 (151)
2 PF08576 DUF1764: Eukaryotic p 78.1 0.92 2E-05 36.3 0.7 11 229-239 92-102 (102)
3 KOG3984 Purine nucleoside phos 25.5 14 0.00029 35.5 -1.5 68 85-174 156-225 (286)
4 PF12684 DUF3799: PDDEXK-like 24.9 25 0.00054 32.2 0.1 16 223-239 220-235 (237)
5 PF01015 Ribosomal_S3Ae: Ribos 23.5 4.4E+02 0.0096 23.7 7.7 81 46-131 21-122 (194)
6 KOG2708 Predicted metalloprote 22.4 23 0.0005 34.2 -0.6 31 127-157 127-157 (336)
7 PF09178 DUF1945: Domain of un 21.6 1.2E+02 0.0026 22.6 3.0 29 110-138 10-38 (51)
8 cd06203 methionine_synthase_re 20.3 4.9E+02 0.011 25.1 7.8 74 71-148 172-260 (398)
9 PF04875 DUF645: Protein of un 19.9 51 0.0011 25.3 0.9 34 73-111 6-39 (59)
10 TIGR03694 exosort_acyl putativ 17.4 1.1E+02 0.0025 27.7 2.7 22 137-158 18-39 (241)
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=2.6e-75 Score=495.70 Aligned_cols=149 Identities=58% Similarity=1.016 Sum_probs=144.8
Q ss_pred CCCCCcceEEEe-ccCCcCCCCCCCcceeeccCCcCCceEEEEccccchhhhhhhccccccceeeeeEeeeCCeeEEEEE
Q 024155 50 IFEASKLKVLFL-GVDEEKHPGKLPRTYTLTHSDITSKLTLAISQTINNSQLQGWYNRLQRDEVVAEWKKVKGKMSLHVH 128 (271)
Q Consensus 50 ~Fnp~KLsV~f~-gvt~~~~P~~ipRrYTLTHSD~T~~LfLtIg~~fn~dqL~gwynrl~RDEVlAEWk~~~g~~~LhVy 128 (271)
+|||+||+|+|+ |++ +++|+ +||||||||||+||+|||+||.+||+||| ||++|||||||||++++|+|+||||
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 565 89998 99999999999999999999999999999 7889999999999999999999999
Q ss_pred EEeeCCccchhHHhhHHHHHHhhhhhhhhhhhhhcCccccccCcccCCCeeEEEEeeCCCCCcceeeeccccccc
Q 024155 129 CHISGGHFLLDICARLRFFIFSKELPVVLKAFVHGDGNLLNNHPELQEALVWVYFHSNIPEFNKVECWGPLKEAV 203 (271)
Q Consensus 129 c~VsG~~f~~~~~A~lRy~IFrKELPLvLkAI~yGDr~LF~~~PeL~~ApI~V~FhS~~p~fnriE~wG~l~da~ 203 (271)
|||||+|++++++|++||+||+||||||||||+|||+.||++||+|++|||||||||++|+||++||||+|+||.
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 999999999999888999999999999999999999999999999999999999999999999999999999984
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=78.09 E-value=0.92 Score=36.30 Aligned_cols=11 Identities=45% Similarity=1.461 Sum_probs=10.0
Q ss_pred CCcccCCCccc
Q 024155 229 EPCQETCNCCF 239 (271)
Q Consensus 229 ~~c~~~c~cc~ 239 (271)
.-||-.|+|||
T Consensus 92 ~~CPFDC~CCF 102 (102)
T PF08576_consen 92 PLCPFDCDCCF 102 (102)
T ss_pred CCCCCcCCCCC
Confidence 37999999999
No 3
>KOG3984 consensus Purine nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=25.54 E-value=14 Score=35.53 Aligned_cols=68 Identities=21% Similarity=0.187 Sum_probs=44.1
Q ss_pred CceEEEEccccchhhhhhhccccccceeeeeEeeeCCeeEEE--EEEEeeCCccchhHHhhHHHHHHhhhhhhhhhhhhh
Q 024155 85 SKLTLAISQTINNSQLQGWYNRLQRDEVVAEWKKVKGKMSLH--VHCHISGGHFLLDICARLRFFIFSKELPVVLKAFVH 162 (271)
Q Consensus 85 ~~LfLtIg~~fn~dqL~gwynrl~RDEVlAEWk~~~g~~~Lh--Vyc~VsG~~f~~~~~A~lRy~IFrKELPLvLkAI~y 162 (271)
|.=|.+.+..||+ .+|..++--||..+-+..|| ||.+|+|..|.. .|+.|-. ...-
T Consensus 156 G~rf~a~sdAYd~---------~lr~~a~~~~K~m~iqr~lheGvy~~vgGP~~eT--~AE~rml-----------r~mg 213 (286)
T KOG3984|consen 156 GVRFPALSDAYDK---------DLRQKALEIGKAMGIQRTLHEGVYACVGGPIFET--RAESRML-----------RTMG 213 (286)
T ss_pred cccccchhhhhhH---------HHHHHHHHHHHHhcccchhhcceEEEecCCcccc--HHHHHHH-----------HHhC
Confidence 4556666666654 56778888899888888886 688888988754 3444421 2234
Q ss_pred cCccccccCccc
Q 024155 163 GDGNLLNNHPEL 174 (271)
Q Consensus 163 GDr~LF~~~PeL 174 (271)
+|+.=.+.=||.
T Consensus 214 ~dAVGMStvpEV 225 (286)
T KOG3984|consen 214 ADAVGMSTVPEV 225 (286)
T ss_pred cccccccccchh
Confidence 566555565653
No 4
>PF12684 DUF3799: PDDEXK-like domain of unknown function (DUF3799); InterPro: IPR024432 This entry represents a PDDEXK-like domain of unknown function found in proteins from bacteria and viruses. Many of these proteins are annotated as exodeoxyribonuclease 8, which is involved in the RecE pathway of recombination. The PD-(D/E)XK domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases []. ; PDB: 3L0A_A 3H4R_A.
Probab=24.87 E-value=25 Score=32.18 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=6.9
Q ss_pred CCCCCCCCcccCCCccc
Q 024155 223 SNWELPEPCQETCNCCF 239 (271)
Q Consensus 223 ~~~~~~~~c~~~c~cc~ 239 (271)
.+..||.+| +.|++|-
T Consensus 220 ~~~~~P~~c-~~c~ycr 235 (237)
T PF12684_consen 220 NGEEWPGYC-GKCDYCR 235 (237)
T ss_dssp CTSS------S-SHHHH
T ss_pred cCCcCCCCC-CCCcccc
Confidence 345899999 5899993
No 5
>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=23.46 E-value=4.4e+02 Score=23.74 Aligned_cols=81 Identities=17% Similarity=0.261 Sum_probs=43.1
Q ss_pred hCCCCCCCCcceEEEeccCCcCCCCCCCcceeeccCCcCCc--------------------eEEEEccccchhhhhhhcc
Q 024155 46 FGPAIFEASKLKVLFLGVDEEKHPGKLPRTYTLTHSDITSK--------------------LTLAISQTINNSQLQGWYN 105 (271)
Q Consensus 46 ~gp~~Fnp~KLsV~f~gvt~~~~P~~ipRrYTLTHSD~T~~--------------------LfLtIg~~fn~dqL~gwyn 105 (271)
..|+.|+-.-+--+. ++ ...- -++|.|-+|..|.|++ +|-=.|.+.+.|.|....-
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-KPEK-LKGRVFEVSLADLTNDFSKAYRKFKFKIEDVQGNNALTNFHGMELTRDKLRSLVR 96 (194)
T ss_dssp E--TTSSSSEECEEE--EE--CCC-CCC-EEEEECHCCCSTTTTSS-EEEEEEEEEETTEEEEEEEEEE--HHHHHHC--
T ss_pred ECCHHhCcceeeEEE--cC-Cccc-ccCeEEEEEHHHhcCchhhhcEEEEEEEEeecCCEEEEEEcceecchhhhhccee
Confidence 457788644433333 33 1222 3899999999999999 4445678888888875221
Q ss_pred c-cccceeeeeEeeeCCeeEEEEEEEe
Q 024155 106 R-LQRDEVVAEWKKVKGKMSLHVHCHI 131 (271)
Q Consensus 106 r-l~RDEVlAEWk~~~g~~~LhVyc~V 131 (271)
| ..|=|..-.=+..+ .|.|.|+|..
T Consensus 97 k~~s~Ie~~~dvkT~D-Gy~lRvf~i~ 122 (194)
T PF01015_consen 97 KWQSRIEAIVDVKTKD-GYLLRVFCIA 122 (194)
T ss_dssp TTC-EEEEEEEEEETT-TEEEEEEEEE
T ss_pred ecceEEEEEEEEEcCC-CcEEEEEEEE
Confidence 1 01334444444444 4556666654
No 6
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=22.36 E-value=23 Score=34.23 Aligned_cols=31 Identities=26% Similarity=0.400 Sum_probs=23.5
Q ss_pred EEEEeeCCccchhHHhhHHHHHHhhhhhhhh
Q 024155 127 VHCHISGGHFLLDICARLRFFIFSKELPVVL 157 (271)
Q Consensus 127 Vyc~VsG~~f~~~~~A~lRy~IFrKELPLvL 157 (271)
|-+|||||+.-.-.....||.||-.-|-.|.
T Consensus 127 vvLYvSGGNTQvIAYse~rYrIFGETlDIAv 157 (336)
T KOG2708|consen 127 VVLYVSGGNTQVIAYSEKRYRIFGETLDIAV 157 (336)
T ss_pred EEEEEeCCceEEEEEccceeeeecceehhhh
Confidence 5578999985443345699999999988764
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=21.59 E-value=1.2e+02 Score=22.60 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=21.4
Q ss_pred ceeeeeEeeeCCeeEEEEEEEeeCCccch
Q 024155 110 DEVVAEWKKVKGKMSLHVHCHISGGHFLL 138 (271)
Q Consensus 110 DEVlAEWk~~~g~~~LhVyc~VsG~~f~~ 138 (271)
|..|--.+-++++++|.|+=.+||++.-.
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 55666778889999999999999998533
No 8
>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=20.31 E-value=4.9e+02 Score=25.12 Aligned_cols=74 Identities=19% Similarity=0.252 Sum_probs=42.7
Q ss_pred CCCcceeeccCCcC--CceEEEEccccc--hhhhhhhccccc-----cceeeeeEeeeCCeeEEEE------EEEeeCCc
Q 024155 71 KLPRTYTLTHSDIT--SKLTLAISQTIN--NSQLQGWYNRLQ-----RDEVVAEWKKVKGKMSLHV------HCHISGGH 135 (271)
Q Consensus 71 ~ipRrYTLTHSD~T--~~LfLtIg~~fn--~dqL~gwynrl~-----RDEVlAEWk~~~g~~~LhV------yc~VsG~~ 135 (271)
..||-||+.=+... +.+.|+|+..=. ....+.|...+. ..+.+.-+....|.+.|-- .+.|++|-
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 233444554444 3444444443344454421 37787764
Q ss_pred cchhHHhhHHHHH
Q 024155 136 FLLDICARLRFFI 148 (271)
Q Consensus 136 f~~~~~A~lRy~I 148 (271)
- +|.+|-.|
T Consensus 252 G----IAP~rs~l 260 (398)
T cd06203 252 G----VAPFLGFL 260 (398)
T ss_pred C----hHHHHHHH
Confidence 3 35566655
No 9
>PF04875 DUF645: Protein of unknown function, DUF645; InterPro: IPR006959 This family contains uncharacterised proteins from Vibrio cholerae.
Probab=19.91 E-value=51 Score=25.27 Aligned_cols=34 Identities=32% Similarity=0.432 Sum_probs=29.6
Q ss_pred CcceeeccCCcCCceEEEEccccchhhhhhhccccccce
Q 024155 73 PRTYTLTHSDITSKLTLAISQTINNSQLQGWYNRLQRDE 111 (271)
Q Consensus 73 pRrYTLTHSD~T~~LfLtIg~~fn~dqL~gwynrl~RDE 111 (271)
.+++..|++=+.+.+-|+.+.+.|..||+ +.|-|
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 45778899999999999999999999998 66655
No 10
>TIGR03694 exosort_acyl putative PEP-CTERM/exosortase system-associated acyltransferase. Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting. PSI-BLAST and CDD reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase. Several members of this family may be found in a single genome. These proteins likely contribute to chemical modifications in exopolysaccharide and biofilm structural material production.
Probab=17.38 E-value=1.1e+02 Score=27.68 Aligned_cols=22 Identities=32% Similarity=0.499 Sum_probs=17.1
Q ss_pred chhHHhhHHHHHHhhhhhhhhh
Q 024155 137 LLDICARLRFFIFSKELPVVLK 158 (271)
Q Consensus 137 ~~~~~A~lRy~IFrKELPLvLk 158 (271)
..+.+-++||.||.+|+=..+.
T Consensus 18 ~~~~~~~lR~~VFv~e~gw~~~ 39 (241)
T TIGR03694 18 LLEEAFRLRYQVYCEELGFEPP 39 (241)
T ss_pred HHHHHHHHHHHHHHHhcCCCCC
Confidence 3556788999999999976443
Done!