Query 026542
Match_columns 237
No_of_seqs 88 out of 90
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:22:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026542hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11152 DUF2930: Protein of u 100.0 3E-63 6.4E-68 430.6 15.5 156 66-237 1-156 (195)
2 TIGR02851 spore_V_T stage V sp 32.4 1.1E+02 0.0023 26.6 5.3 64 146-220 53-116 (180)
3 PF01299 Lamp: Lysosome-associ 28.6 54 0.0012 30.1 3.0 30 49-80 258-287 (306)
4 COG2181 NarI Nitrate reductase 27.7 95 0.0021 28.5 4.3 44 72-120 101-144 (228)
5 cd04683 Nudix_Hydrolase_24 Mem 21.4 1.5E+02 0.0031 22.3 3.7 16 164-179 2-17 (120)
6 PF12046 DUF3529: Protein of u 20.7 29 0.00062 30.6 -0.4 34 27-60 20-57 (173)
7 PRK15472 nucleoside triphospha 18.9 1.5E+02 0.0031 23.3 3.3 12 168-179 10-21 (141)
8 TIGR01703 hybrid_clust hydroxy 18.0 1.6E+02 0.0035 30.0 4.1 70 153-227 227-316 (522)
9 PRK05379 bifunctional nicotina 17.6 52 0.0011 30.8 0.6 17 163-179 204-220 (340)
10 cd04673 Nudix_Hydrolase_15 Mem 17.0 2.1E+02 0.0047 21.2 3.7 17 164-180 2-18 (122)
No 1
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=100.00 E-value=3e-63 Score=430.63 Aligned_cols=156 Identities=42% Similarity=0.615 Sum_probs=151.3
Q ss_pred hhHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhhhhcccCCCcccCCCCccceEecCCCCH
Q 026542 66 LPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVVNPKGVECQMICSYLPD 145 (237)
Q Consensus 66 LPl~vG~l~~~llL~Nr~ls~iapva~~t~sQsRAdVLg~~LS~~LiL~GllW~~iqP~~~~~V~L~G~e~f~l~~~Lsd 145 (237)
||+++|+++++++++||+++ +++||||+||||||++||+++||+|++|+++||+++++|+|+|+|+|++++||||
T Consensus 1 LPl~vG~l~~~lll~N~~~~-----~~~t~sq~RaevLg~~ls~~liL~g~lw~~l~p~~~~~v~L~G~~~f~l~~~L~~ 75 (195)
T PF11152_consen 1 LPLIVGLLGGSLLLLNRLSG-----ADATPSQSRAEVLGLILSAVLILTGLLWQRLKPRSPEAVDLPGEQGFELSPDLSD 75 (195)
T ss_pred CceEehHHHHHHHHhhhccc-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCccCCCCccceEECCCCCH
Confidence 69999999999999999653 3999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccEEEEEECCEEEEEEeeccCCCCCCcceeecccccchhHHHHHHHhcCCeeeeeccccCCC
Q 026542 146 SVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPG 225 (237)
Q Consensus 146 ~~k~ELAWaS~~LLtnT~a~SvlV~~~G~vlLrRGi~~~~~~~~~a~~vd~~~~~pG~I~~r~l~~~~~iYLvnL~LyPG 225 (237)
++|+||||+||+|||||+|+||+|||||+++||||+++++ ++|+||+||+|+||+++++||+|+++|||
T Consensus 76 ~~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~-----------~~~~~g~i~~~~~~~~~~~yL~nl~lyPG 144 (195)
T PF11152_consen 76 AAKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSP-----------SKFKPGPICQRAMESGKLIYLVNLKLYPG 144 (195)
T ss_pred HHHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCC-----------CCcchHHHHHHHHhcCCceeccccccCCC
Confidence 9999999999999999999999999999999999999864 48999999999999999999999999999
Q ss_pred CCCCCCCCCCCC
Q 026542 226 RSELPFLPSNTQ 237 (237)
Q Consensus 226 R~EFd~lP~Ntq 237 (237)
|+||||||+|||
T Consensus 145 r~Ef~~lP~ntq 156 (195)
T PF11152_consen 145 RVEFDYLPENTQ 156 (195)
T ss_pred chhhhhcCCCCc
Confidence 999999999998
No 2
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=32.42 E-value=1.1e+02 Score=26.60 Aligned_cols=64 Identities=9% Similarity=-0.034 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHhhhccccEEEEEECCEEEEEEeeccCCCCCCcceeecccccchhHHHHHHHhcCCeeeeecc
Q 026542 146 SVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANL 220 (237)
Q Consensus 146 ~~k~ELAWaS~~LLtnT~a~SvlV~~~G~vlLrRGi~~~~~~~~~a~~vd~~~~~pG~I~~r~l~~~~~iYLvnL 220 (237)
...+...=.-+.|...|.+ +|.|....+++...|.-...-. ++ . --+..+++|++|+....-+-
T Consensus 53 ~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d~~~-------~~-~--is~~t~~~i~~gk~~~~~~~ 116 (180)
T TIGR02851 53 ELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKKEYL-------NK-P--ISDELEDTMEERKTVILSDT 116 (180)
T ss_pred chHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChhhcC-------CC-c--cCHHHHHHHHcCCEEEecCC
Confidence 3444455567899999999 9999999999999997654210 11 1 23567899999998766654
No 3
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=28.60 E-value=54 Score=30.10 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=20.3
Q ss_pred ccchhhhccCchHHHhhhhHHHHHHHHHHHHH
Q 026542 49 QDLVADWVMNNDDAVRSLPIYVGGASLLAVLF 80 (237)
Q Consensus 49 ~~~~~d~v~~~~~~~R~LPl~vG~l~~~llL~ 80 (237)
+....|.-.|.+..+ +|++||+.+++|+++
T Consensus 258 Fg~a~~C~~D~~~~~--vPIaVG~~La~lvli 287 (306)
T PF01299_consen 258 FGTAEECSSDDTSDL--VPIAVGAALAGLVLI 287 (306)
T ss_pred CCChhcCCcCCccch--HHHHHHHHHHHHHHH
Confidence 455566666665333 899999887766665
No 4
>COG2181 NarI Nitrate reductase gamma subunit [Energy production and conversion]
Probab=27.70 E-value=95 Score=28.55 Aligned_cols=44 Identities=20% Similarity=0.303 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhhhh
Q 026542 72 GASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLS 120 (237)
Q Consensus 72 ~l~~~llL~Nr~ls~iapva~~t~sQsRAdVLg~~LS~~LiL~GllW~~ 120 (237)
.+|+++++.||+... ..=-.-+++|.+.+++=.+.+++|+.-+.
T Consensus 101 liG~~~L~~RR~~~~-----rvR~~St~~D~f~lilLla~~~~Gl~~~~ 144 (228)
T COG2181 101 LIGLTLLLLRRLFDP-----RVRATSTPSDIFALLLLLAQLLLGLYATP 144 (228)
T ss_pred HHHHHHHHHHHHhcc-----ceeecCChhHHHHHHHHHHHHHhhhhhhh
Confidence 456778899999854 55556789999999998888888987443
No 5
>cd04683 Nudix_Hydrolase_24 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=21.37 E-value=1.5e+02 Score=22.31 Aligned_cols=16 Identities=25% Similarity=0.158 Sum_probs=12.5
Q ss_pred ccEEEEEECCEEEEEE
Q 026542 164 CRSLVVVYDGIYLLQI 179 (237)
Q Consensus 164 a~SvlV~~~G~vlLrR 179 (237)
+-.++|..+|++||.|
T Consensus 2 ~v~~vi~~~~~vLL~~ 17 (120)
T cd04683 2 AVYVLLRRDDEVLLQR 17 (120)
T ss_pred cEEEEEEECCEEEEEE
Confidence 3456788899999987
No 6
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=20.75 E-value=29 Score=30.64 Aligned_cols=34 Identities=24% Similarity=0.463 Sum_probs=25.0
Q ss_pred hhhhhhcc-cccccCcccCCCCCccch---hhhccCch
Q 026542 27 PRFIRASA-SSQSQGGYRGPKPSQDLV---ADWVMNND 60 (237)
Q Consensus 27 ~~~~~~~~-~~~~~~~~r~~~~~~~~~---~d~v~~~~ 60 (237)
=+|||||+ |++.+..+..+.|..+.+ .+|..+++
T Consensus 20 ~ffiraS~KdRt~~~~~~s~~p~~~~~~~l~~yf~~r~ 57 (173)
T PF12046_consen 20 FFFIRASVKDRTEQVTFESPQPPDEVLEQLKAYFEQRN 57 (173)
T ss_pred HHHHHHhccccEEEEEEEcCCCHHHHHHHHHHHHHhcC
Confidence 47898875 788888999998855443 56776665
No 7
>PRK15472 nucleoside triphosphatase NudI; Provisional
Probab=18.87 E-value=1.5e+02 Score=23.33 Aligned_cols=12 Identities=42% Similarity=0.661 Sum_probs=9.3
Q ss_pred EEEECCEEEEEE
Q 026542 168 VVVYDGIYLLQI 179 (237)
Q Consensus 168 lV~~~G~vlLrR 179 (237)
+|..+|++||.+
T Consensus 10 ii~~~~~vLl~~ 21 (141)
T PRK15472 10 LIQNDGAYLLCK 21 (141)
T ss_pred EEecCCEEEEEE
Confidence 455799999976
No 8
>TIGR01703 hybrid_clust hydroxylamine reductase. This model represents a family of proteins containing an unusual 4Fe-2S-2O hydrid cluster. Earlier reports had proposed a 6Fe-6S prismane cluster. This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N-terminus of the protein. Members have been described as monomeric. The function is unknown, but is almost certain to involve oxidoreductase enzymatic activity. Members are found in E. coli and other bacteria, in Archaea, and in several parasitic eukaryotes: Giardia intestinalis, Trichomonas vaginalis, and Entamoeba histolytica.
Probab=17.95 E-value=1.6e+02 Score=30.02 Aligned_cols=70 Identities=16% Similarity=0.133 Sum_probs=49.4
Q ss_pred HHHHHHhhhccccEEEEEECCEEEEEEeec--------cCCCC------------CCcceeecccccchhHHHHHHHhcC
Q 026542 153 WAWESLSAVTCCRSLVVVYDGIYLLQIGMA--------AESGN------------SGEAVIVDASKLKQGSVYLGVMRSK 212 (237)
Q Consensus 153 WaS~~LLtnT~a~SvlV~~~G~vlLrRGi~--------~~~~~------------~~~a~~vd~~~~~pG~I~~r~l~~~ 212 (237)
+.+++||..|.++.+=||-.|+.++|.||= ..+-+ -++++.+|.+++.|+.= .=.
T Consensus 227 ~~~~~ll~~~~~~GInvyT~~Eml~~hgyp~l~k~~~l~Gn~g~aw~~q~~Ef~~~~Gaiv~~~nCi~p~~~-----~y~ 301 (522)
T TIGR01703 227 KDLEELLEQTEGTGINVYTHGEMLPAHGYPELKKYPHLAGNYGGAWQDQQREFAEFPGPILMTSNCIIPPRK-----SYK 301 (522)
T ss_pred HHHHHHHHHHhcCCeeEEECcchHhhccCcccccCCcccccchhhhhhhhHHHHhCCCCEEEeccCCCCChh-----hhc
Confidence 347889999999999999999999999984 21222 45677788888888742 233
Q ss_pred CeeeeeccccCCCCC
Q 026542 213 AQRYLANLLLYPGRS 227 (237)
Q Consensus 213 ~~iYLvnL~LyPGR~ 227 (237)
..+|=.+-.-|||-.
T Consensus 302 ~ri~Tt~~~~~pg~~ 316 (522)
T TIGR01703 302 DRIFTTGIVGWPGVK 316 (522)
T ss_pred ceEEEecCccCCCCe
Confidence 445555555578753
No 9
>PRK05379 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional
Probab=17.63 E-value=52 Score=30.82 Aligned_cols=17 Identities=35% Similarity=0.260 Sum_probs=12.7
Q ss_pred cccEEEEEECCEEEEEE
Q 026542 163 CCRSLVVVYDGIYLLQI 179 (237)
Q Consensus 163 ~a~SvlV~~~G~vlLrR 179 (237)
.+...+|..+|++||.+
T Consensus 204 vtv~avv~~~g~VLLvr 220 (340)
T PRK05379 204 VTVDAVVVQSGHVLLVR 220 (340)
T ss_pred eEEEEEEEECCEEEEEE
Confidence 45566778899998855
No 10
>cd04673 Nudix_Hydrolase_15 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=16.96 E-value=2.1e+02 Score=21.16 Aligned_cols=17 Identities=29% Similarity=0.180 Sum_probs=13.0
Q ss_pred ccEEEEEECCEEEEEEe
Q 026542 164 CRSLVVVYDGIYLLQIG 180 (237)
Q Consensus 164 a~SvlV~~~G~vlLrRG 180 (237)
+.+++|+.+|+++|.+-
T Consensus 2 ~v~~ii~~~~~vLl~~r 18 (122)
T cd04673 2 AVGAVVFRGGRVLLVRR 18 (122)
T ss_pred cEEEEEEECCEEEEEEE
Confidence 45677888999998763
Done!