Query psy10259
Match_columns 135
No_of_seqs 64 out of 66
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 21:53:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10259.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10259hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04636 PA26: PA26 p53-induce 100.0 7.4E-43 1.6E-47 305.8 5.5 89 47-135 296-385 (450)
2 KOG3746|consensus 100.0 1.1E-39 2.3E-44 288.1 3.6 87 48-135 401-488 (553)
3 PF11772 EpuA: DNA-directed RN 41.0 30 0.00064 22.5 2.4 32 9-41 11-42 (47)
4 PF04180 LTV: Low temperature 34.2 16 0.00035 32.4 0.5 16 116-131 61-78 (421)
5 KOG3235|consensus 28.9 17 0.00037 30.0 -0.2 37 2-38 40-95 (193)
6 PF15599 Imm38: Immunity prote 27.7 2.6E+02 0.0055 20.7 6.4 69 17-89 43-122 (124)
7 PF06896 DUF1268: Protein of u 26.2 39 0.00084 25.4 1.3 47 83-129 55-104 (114)
8 cd00559 Cyanase_C Cyanase C-te 25.6 66 0.0014 22.8 2.3 20 69-88 12-31 (69)
9 COG1654 BirA Biotin operon rep 24.5 53 0.0011 23.2 1.7 16 106-121 29-44 (79)
10 PF02560 Cyanate_lyase: Cyanat 24.2 72 0.0016 22.8 2.3 20 69-88 16-35 (73)
11 PF13305 WHG: WHG domain; PDB: 21.6 2.2E+02 0.0047 17.8 4.3 26 99-124 51-76 (81)
12 PF12340 DUF3638: Protein of u 20.8 23 0.00049 29.6 -0.9 34 87-124 185-218 (229)
No 1
>PF04636 PA26: PA26 p53-induced protein (sestrin); InterPro: IPR006730 Exposure of mammalian cells to hypoxia, radiation and certain chemotherapeutic agents promotes cell cycle arrest and/or apoptosis. Activation of p53 responsive genes is believed to play an important role in mediating such responses. PA26 is differentially induced by genotoxic stress (UV, gamma-irradiation and cytotoxic drugs) in a p53-dependent manner. PA26 gene is a novel p53 target gene with properties common to the GADD family of growth arrest and DNA damage-inducible stress-response genes, and, thus, a potential novel regulator of cellular growth []. A homolgue found in Xenopus, XPA26, was initially detected in the anterior portion of developing notochord at neurula stages, and later in the entire notochord except its posterior region at tailbud stages []. ; GO: 0007050 cell cycle arrest, 0005634 nucleus
Probab=100.00 E-value=7.4e-43 Score=305.85 Aligned_cols=89 Identities=63% Similarity=1.151 Sum_probs=85.6
Q ss_pred HHhhccC-CcccceeccccccchhHHHHHhhhhHHHHHHHHHHHHHhcchhcccCccCCCchHHHHHHHHHHHhhhcccc
Q psy10259 47 AVVRQTY-WVIMNKQDYSWDDHGYSLMNRLYNDVGNLLDDKFKIAYNLTYYTLAGRTQVDTSRFRRAIWNYVQCLFGIRH 125 (135)
Q Consensus 47 ~~~R~~~-~~tfr~qdYSWedHGfsLvnrlypd~a~LLDekF~~~~~LTyntmg~~~~VDTs~fR~AIWnYiq~i~GI~~ 125 (135)
-.+|+++ +||||+||||||||||+||||||||+|++|||||++|++||||+||++++|||++||+||||||||||||||
T Consensus 296 FarR~e~~~~tfR~qdysWedhg~slvnrly~d~~~lLdekF~~v~~LTy~tm~~~~~VdTs~~R~Aiw~Yiq~i~Gi~~ 375 (450)
T PF04636_consen 296 FARRGEEQIPTFRVQDYSWEDHGFSLVNRLYPDLGQLLDEKFRVVYNLTYNTMGMHEDVDTSPFRRAIWNYIQCIFGIRH 375 (450)
T ss_pred cccCccccccceeecccCcccchhHHHHHhhhHHHHHHHHHHHHHHHhccccccCCCCCCcHHHHHHHHHHHHHHhcccc
Confidence 3467766 899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccCCC
Q psy10259 126 DDYDYGEVNQ 135 (135)
Q Consensus 126 DDYdY~eINk 135 (135)
|||||++|||
T Consensus 376 DDydY~evN~ 385 (450)
T PF04636_consen 376 DDYDYGEVNK 385 (450)
T ss_pred cCCCHHHHHH
Confidence 9999999996
No 2
>KOG3746|consensus
Probab=100.00 E-value=1.1e-39 Score=288.13 Aligned_cols=87 Identities=63% Similarity=1.071 Sum_probs=83.0
Q ss_pred HhhccC-CcccceeccccccchhHHHHHhhhhHHHHHHHHHHHHHhcchhcccCccCCCchHHHHHHHHHHHhhhccccc
Q psy10259 48 VVRQTY-WVIMNKQDYSWDDHGYSLMNRLYNDVGNLLDDKFKIAYNLTYYTLAGRTQVDTSRFRRAIWNYVQCLFGIRHD 126 (135)
Q Consensus 48 ~~R~~~-~~tfr~qdYSWedHGfsLvnrlypd~a~LLDekF~~~~~LTyntmg~~~~VDTs~fR~AIWnYiq~i~GI~~D 126 (135)
++|+++ +||||+|||+| ||||||||||||++||||||||+.|++||||+++++++||||+||+||||||||+||||+|
T Consensus 401 ~rrg~~~pptFRvqdy~W-DHgYsl~nrlyp~~gqllDekF~~ay~LTyNt~amh~~vDTs~lRrAIWNYihc~fGiRyD 479 (553)
T KOG3746|consen 401 RRRGEKDPPTFRVQDYGW-DHGYSLMNRLYPTLGQLLDEKFDHAYTLTYNTAAMHNEVDTSALRRAIWNYIHCLFGIRYD 479 (553)
T ss_pred hhCcccCCCCcchhhccc-hhhHHHHHHhcccHHHHHHHHHHHHHhhhhhHhhhhccccHHHHHHHHHHHhheeeeeeec
Confidence 566665 55999999999 8999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccCCC
Q psy10259 127 DYDYGEVNQ 135 (135)
Q Consensus 127 DYdY~eINk 135 (135)
||||+||||
T Consensus 480 DYDYgeiNq 488 (553)
T KOG3746|consen 480 DYDYGEINQ 488 (553)
T ss_pred ccchHHHHH
Confidence 999999996
No 3
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=41.03 E-value=30 Score=22.50 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=23.0
Q ss_pred HHHHhhhhceeeeeecCchhhhhhHHHHHHhhc
Q psy10259 9 MFFLGKLVGYHLVFDTTNRRKLLFQKTMITIIS 41 (135)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (135)
.|.+|-.+||+.+=+- ||...+.+.+...|++
T Consensus 11 ~l~iGlmIGY~viG~G-~p~~vf~~~tW~hi~d 42 (47)
T PF11772_consen 11 ALAIGLMIGYGVIGDG-NPFDVFSPDTWQHIID 42 (47)
T ss_pred HHHHHHHeeeeeeCCC-CHHHhCCHHHHHHHHH
Confidence 5788999999877665 8866666666555543
No 4
>PF04180 LTV: Low temperature viability protein ; InterPro: IPR007307 The low-temperature viability protein LTV1 was identified in Saccharomyces cerevisiae, the exact function of this protein is unknown.
Probab=34.15 E-value=16 Score=32.40 Aligned_cols=16 Identities=44% Similarity=0.673 Sum_probs=13.7
Q ss_pred HHHhhhcccccC--CCCc
Q psy10259 116 YVQCLFGIRHDD--YDYG 131 (135)
Q Consensus 116 Yiq~i~GI~~DD--YdY~ 131 (135)
--|..|||-+|| |||.
T Consensus 61 gEaa~YGIyfDDs~YDYm 78 (421)
T PF04180_consen 61 GEAAKYGIYFDDSDYDYM 78 (421)
T ss_pred HHHHHhCCccCcccccHH
Confidence 457899999999 9995
No 5
>KOG3235|consensus
Probab=28.92 E-value=17 Score=30.00 Aligned_cols=37 Identities=41% Similarity=0.359 Sum_probs=25.7
Q ss_pred CCcchhHHHHHhhhhceeeeeecC-------------------chhhhhhHHHHHH
Q psy10259 2 PHLSFDTMFFLGKLVGYHLVFDTT-------------------NRRKLLFQKTMIT 38 (135)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~ 38 (135)
|.|||=+----||+|||.+.=-.. -||--|+|++|+.
T Consensus 40 p~lSyVA~D~~gkiVGYvlAkmee~p~~~~~hGhItSlaV~rs~RrlGla~kLm~q 95 (193)
T KOG3235|consen 40 PQLSYVAEDENGKIVGYVLAKMEEDPDDEPPHGHITSLAVKRSYRRLGLAQKLMNQ 95 (193)
T ss_pred ccceEEEEcCCCcEEEEeeeehhhcccCCCCCCeeEEeeehhhHHHhhHHHHHHHH
Confidence 556665544568999998863322 2456699999998
No 6
>PF15599 Imm38: Immunity protein 38
Probab=27.69 E-value=2.6e+02 Score=20.74 Aligned_cols=69 Identities=25% Similarity=0.330 Sum_probs=46.2
Q ss_pred ceeeeee----------cCchhhhhhHHHHHHhhchhhhHHHhhccCC-cccceeccccccchhHHHHHhhhhHHHHHHH
Q psy10259 17 GYHLVFD----------TTNRRKLLFQKTMITIISTMAMCAVVRQTYW-VIMNKQDYSWDDHGYSLMNRLYNDVGNLLDD 85 (135)
Q Consensus 17 ~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~R~~~~-~tfr~qdYSWedHGfsLvnrlypd~a~LLDe 85 (135)
|||++|. |++.-.+|.+ .+-.|++.+|+..-.|.... +.+|..-|. -=+.||+.+-|+-|...-+
T Consensus 43 ~Y~~~~~ERG~~~~~r~T~~~dEllYw-i~~di~~~iA~~~~~~~~~~d~~~R~~~f~---k~~~ll~~i~p~w~~~~~~ 118 (124)
T PF15599_consen 43 GYHYVFYERGKEFSDRRTTDLDELLYW-ILDDIASTIAWRYELRHRPPDQDFRRLAFP---KQYELLSAINPKWGKRAKQ 118 (124)
T ss_pred EEEEEEEecCceeeecccCCHHHHHHH-HHHHHHHHHHHHHHHhcCCcchhHHHHHHH---HHHHHHHhhCHHHHHHHHH
Confidence 5888763 6777778887 46789999999876665544 233333322 2358899999987776666
Q ss_pred HHHH
Q psy10259 86 KFKI 89 (135)
Q Consensus 86 kF~~ 89 (135)
+.+.
T Consensus 119 e~~~ 122 (124)
T PF15599_consen 119 EIAE 122 (124)
T ss_pred HHHh
Confidence 5543
No 7
>PF06896 DUF1268: Protein of unknown function (DUF1268); InterPro: IPR009681 This entry is represented by Bacteriophage bIL286, Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=26.24 E-value=39 Score=25.42 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=36.9
Q ss_pred HHHHHH---HHHhcchhcccCccCCCchHHHHHHHHHHHhhhcccccCCC
Q psy10259 83 LDDKFK---IAYNLTYYTLAGRTQVDTSRFRRAIWNYVQCLFGIRHDDYD 129 (135)
Q Consensus 83 LDekF~---~~~~LTyntmg~~~~VDTs~fR~AIWnYiq~i~GI~~DDYd 129 (135)
+++.+. .+.+|+---.-...++|...+-.++++=+..|.|+..+||+
T Consensus 55 ~~~~~~Fi~~iL~L~dkq~ekl~~iD~~~~~e~~~yl~~rl~G~sD~~i~ 104 (114)
T PF06896_consen 55 LKEMLKFIQDILKLNDKQVEKLEDIDFEDLQEIVSYLVMRLQGMSDEQIE 104 (114)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHhcCCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 555544 45556655566667899999999999999999999888875
No 8
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=25.61 E-value=66 Score=22.81 Aligned_cols=20 Identities=20% Similarity=0.428 Sum_probs=18.3
Q ss_pred hHHHHHhhhhHHHHHHHHHH
Q psy10259 69 YSLMNRLYNDVGNLLDDKFK 88 (135)
Q Consensus 69 fsLvnrlypd~a~LLDekF~ 88 (135)
|++|..|-|-+-+++.|||-
T Consensus 12 yE~v~vYG~~~K~li~E~FG 31 (69)
T cd00559 12 YEIVQVYGPTLKALIHEKFG 31 (69)
T ss_pred HHHHHHhhHHHHHHHHHHcC
Confidence 68899999999999999994
No 9
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=24.52 E-value=53 Score=23.20 Aligned_cols=16 Identities=31% Similarity=0.436 Sum_probs=12.7
Q ss_pred chHHHHHHHHHHHhhh
Q psy10259 106 TSRFRRAIWNYVQCLF 121 (135)
Q Consensus 106 Ts~fR~AIWnYiq~i~ 121 (135)
....|.|||-.||.+-
T Consensus 29 LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 29 LGISRTAVWKHIQQLR 44 (79)
T ss_pred HCccHHHHHHHHHHHH
Confidence 3456999999999874
No 10
>PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A.
Probab=24.23 E-value=72 Score=22.83 Aligned_cols=20 Identities=20% Similarity=0.444 Sum_probs=17.3
Q ss_pred hHHHHHhhhhHHHHHHHHHH
Q psy10259 69 YSLMNRLYNDVGNLLDDKFK 88 (135)
Q Consensus 69 fsLvnrlypd~a~LLDekF~ 88 (135)
|++|.-|-|-+-++++|||-
T Consensus 16 yE~v~vYG~~~K~li~E~FG 35 (73)
T PF02560_consen 16 YEIVQVYGPAIKALIHEKFG 35 (73)
T ss_dssp HHHHHHHHHHHHHHHHHHT-
T ss_pred ehhhHhhCHHHHHHHHHhhC
Confidence 67888999999999999995
No 11
>PF13305 WHG: WHG domain; PDB: 1ZK8_B 3ON2_B 3CJD_B.
Probab=21.65 E-value=2.2e+02 Score=17.83 Aligned_cols=26 Identities=19% Similarity=0.296 Sum_probs=18.8
Q ss_pred cCccCCCchHHHHHHHHHHHhhhccc
Q psy10259 99 AGRTQVDTSRFRRAIWNYVQCLFGIR 124 (135)
Q Consensus 99 g~~~~VDTs~fR~AIWnYiq~i~GI~ 124 (135)
+.....|....-.++|-++|.+--+.
T Consensus 51 ~~~~~~~~~~~~~~~wa~~HG~~~L~ 76 (81)
T PF13305_consen 51 GNLSPEDAREIALALWAAVHGLASLF 76 (81)
T ss_dssp TTC-CCHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHH
Confidence 44555667788899999999876443
No 12
>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.
Probab=20.78 E-value=23 Score=29.58 Aligned_cols=34 Identities=26% Similarity=0.626 Sum_probs=27.7
Q ss_pred HHHHHhcchhcccCccCCCchHHHHHHHHHHHhhhccc
Q psy10259 87 FKIAYNLTYYTLAGRTQVDTSRFRRAIWNYVQCLFGIR 124 (135)
Q Consensus 87 F~~~~~LTyntmg~~~~VDTs~fR~AIWnYiq~i~GI~ 124 (135)
|..=++|-| ++|..+.||-++-| |..+|.++++-
T Consensus 185 L~~k~qLiY-~~G~q~~ld~~p~R---W~~~q~lL~lv 218 (229)
T PF12340_consen 185 LSVKYQLIY-TMGSQQPLDGHPDR---WQVIQALLSLV 218 (229)
T ss_pred cCcceEEEe-cCCCcccCCCChHH---HHHHHHHHHHH
Confidence 555567777 99999999999988 77888888763
Done!