Query psy227
Match_columns 139
No_of_seqs 110 out of 469
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 20:24:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy227.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/227hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3913|consensus 100.0 2.1E-39 4.5E-44 275.1 8.9 99 14-138 106-204 (356)
2 smart00097 WNT1 found in Wnt-1 100.0 1.4E-36 3E-41 254.2 9.0 99 14-138 57-155 (305)
3 PF00110 wnt: wnt family; Int 100.0 3.4E-34 7.3E-39 240.0 8.5 99 14-138 61-159 (310)
4 PF09832 DUF2059: Uncharacteri 41.9 15 0.00034 23.2 1.2 22 118-139 21-42 (64)
5 PF12342 DUF3640: Protein of u 28.5 33 0.00073 19.1 1.0 14 1-14 1-14 (26)
6 CHL00020 psbN photosystem II p 19.4 1E+02 0.0022 19.2 2.0 19 21-39 2-20 (43)
7 PRK13183 psbN photosystem II r 16.9 1.6E+02 0.0034 18.6 2.4 21 19-39 3-23 (46)
8 PHA02100 hypothetical protein 15.7 1.5E+02 0.0032 21.7 2.4 19 74-93 23-41 (112)
9 PF02468 PsbN: Photosystem II 13.4 1.2E+02 0.0026 18.8 1.2 19 21-39 2-20 (43)
10 PF12535 Nudix_N: Hydrolase of 10.9 2.1E+02 0.0045 18.4 1.8 12 25-36 11-22 (58)
No 1
>KOG3913|consensus
Probab=100.00 E-value=2.1e-39 Score=275.06 Aligned_cols=99 Identities=37% Similarity=0.752 Sum_probs=89.8
Q ss_pred hhccCchhhHHHHHHHHHHHHHHHHhhhcCCCCCCcccCCCCCccchhhhcCCccccCCCcchHhHHHHHHhhhhhhhhh
Q psy227 14 FRLNGTREQGIVYALGSAAITYTLARGCADGTIFHCSCATPSKKATAKAIKNSFQWGGCGDNVRWGAQFARSFTDILENE 93 (139)
Q Consensus 14 ~~~~gtREtAfvyAisSAgv~~~ItraCs~G~l~~CgC~~~~~~~~~~~~~~~~~WgGCsdnV~~G~~fsr~Fld~~e~~ 93 (139)
++++|+||+||||||+||||+|+|||||++|.|..||||...++.+. +++|+||||||||+||++|||.|||++|+.
T Consensus 106 ~l~~g~REsAFv~AIssAgV~havtraCs~G~l~~CgCd~~~~~~~~---~~~w~WGGCsDnv~fG~~fsr~FlD~re~~ 182 (356)
T KOG3913|consen 106 LLSRGTRETAFVYAISSAGVAHAVTRACSQGNLESCGCDPSPNGKSG---PEGWEWGGCSDNVDFGIRFSRKFLDAREKR 182 (356)
T ss_pred hhcccchHHHHHHHHHHhHHHHHHHHHhcCCCCCCcCCCCCCCCCCC---CCCccccCCCCchHHHHHHHHHhccccccc
Confidence 45679999999999999999999999999999999999987765544 366999999999999999999999988865
Q ss_pred hhhhhhHhHHHHHHHhhhhhhhhhhHHHHHHhhhhHHHHhhhhcC
Q psy227 94 RDIQTQRNLRLIDAAMFDEKNNRNYMLNVMNLHNNKAGRKIDTYQ 138 (139)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mnlHNn~aGR~av~~~ 138 (139)
+ |++.+||||||+|||+||+++
T Consensus 183 ~-----------------------d~r~lmnlHNNeaGR~av~~~ 204 (356)
T KOG3913|consen 183 K-----------------------DARALMNLHNNEAGRKAVKKN 204 (356)
T ss_pred c-----------------------CHHHHHHHhhhHHHHHHHHHh
Confidence 4 899999999999999999864
No 2
>smart00097 WNT1 found in Wnt-1.
Probab=100.00 E-value=1.4e-36 Score=254.24 Aligned_cols=99 Identities=35% Similarity=0.713 Sum_probs=87.4
Q ss_pred hhccCchhhHHHHHHHHHHHHHHHHhhhcCCCCCCcccCCCCCccchhhhcCCccccCCCcchHhHHHHHHhhhhhhhhh
Q psy227 14 FRLNGTREQGIVYALGSAAITYTLARGCADGTIFHCSCATPSKKATAKAIKNSFQWGGCGDNVRWGAQFARSFTDILENE 93 (139)
Q Consensus 14 ~~~~gtREtAfvyAisSAgv~~~ItraCs~G~l~~CgC~~~~~~~~~~~~~~~~~WgGCsdnV~~G~~fsr~Fld~~e~~ 93 (139)
++.+|+||+||||||+||||+|+||+||++|.|..|+||...++.+. .++|+||||+|||.||++|++.|||+++..
T Consensus 57 ~l~~~trEtAfv~Ai~sAgv~~~itraCs~G~l~~C~Cd~~~~~~~~---~~~w~WgGCsdnv~~G~~~s~~FlD~~~~~ 133 (305)
T smart00097 57 VLRQGTRETAFVYAISSAGVAHAVTRACSEGELDSCGCDYRKRGRAG---GRGWKWGGCSDNIDFGIRFSREFVDARERG 133 (305)
T ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC---CCCcccCCCCccHHHHHHHHHHHHhccccc
Confidence 44779999999999999999999999999999999999987654433 257999999999999999999999987643
Q ss_pred hhhhhhHhHHHHHHHhhhhhhhhhhHHHHHHhhhhHHHHhhhhcC
Q psy227 94 RDIQTQRNLRLIDAAMFDEKNNRNYMLNVMNLHNNKAGRKIDTYQ 138 (139)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mnlHNn~aGR~av~~~ 138 (139)
+ +++.+||||||+|||+||+.+
T Consensus 134 ~-----------------------d~r~lmnlHNn~aGR~~v~~~ 155 (305)
T smart00097 134 K-----------------------DARALMNLHNNEAGRLAVKKT 155 (305)
T ss_pred c-----------------------cHHHHHHHhhhHHHHHHHHHH
Confidence 2 789999999999999999753
No 3
>PF00110 wnt: wnt family; InterPro: IPR005817 Wnt proteins constitute a large family of secreted molecules that are involved in intercellular signalling during development. The name derives from the first 2 members of the family to be discovered: int-1 (mouse) and wingless (Drosophila) []. It is now recognised that Wnt signalling controls many cell fate decisions in a variety of different organisms, including mammals []. Wnt signalling has been implicated in tumourigenesis, early mesodermal patterning of the embryo, morphogenesis of the brain and kidneys, regulation of mammary gland proliferation and Alzheimer's disease [, ]. Wnt-mediated signalling is believed to proceed initially through binding to cell surface receptors of the frizzled family; the signal is subsequently transduced through several cytoplasmic components to B-catenin, which enters the nucleus and activates the transcription of several genes important in development []. Several non-canonical Wnt signalling pathways have also been elucidated that act independently of B-catenin. Canonical and noncanonical Wnt signaling branches are highly interconnected, and cross-regulate each other []. Members of the Wnt gene family are defined by their sequence similarity to mouse Wnt-1 and Wingless in Drosophila. They encode proteins of ~350-400 residues in length, with orthologues identified in several, mostly vertebrate, species. Very little is known about the structure of Wnts as they are notoriously insoluble, but they share the following features characteristics of secretory proteins: a signal peptide, several potential N-glycosylation sites and 22 conserved cysteines [] that are probably involved in disulphide bonds. The Wnt proteins seem to adhere to the plasma membrane of the secreting cells and are therefore likely to signal over only few cell diameters. Fifteen major Wnt gene families have been identified in vertebrates, with multiple subtypes within some classes. In humans, 19 Wnt proteins have been identified that share 27% to 83% amino-acid sequence identity and a conserved pattern of 23 or 24 cysteine residues []. Wnt genes are highly conserved between vertebrate species sharing overall sequence identity and gene structure, and are slightly less conserved between vertebrates and invertebrates.; GO: 0005102 receptor binding, 0007275 multicellular organismal development, 0016055 Wnt receptor signaling pathway, 0005576 extracellular region; PDB: 4F0A_B.
Probab=100.00 E-value=3.4e-34 Score=239.97 Aligned_cols=99 Identities=38% Similarity=0.783 Sum_probs=73.7
Q ss_pred hhccCchhhHHHHHHHHHHHHHHHHhhhcCCCCCCcccCCCCCccchhhhcCCccccCCCcchHhHHHHHHhhhhhhhhh
Q psy227 14 FRLNGTREQGIVYALGSAAITYTLARGCADGTIFHCSCATPSKKATAKAIKNSFQWGGCGDNVRWGAQFARSFTDILENE 93 (139)
Q Consensus 14 ~~~~gtREtAfvyAisSAgv~~~ItraCs~G~l~~CgC~~~~~~~~~~~~~~~~~WgGCsdnV~~G~~fsr~Fld~~e~~ 93 (139)
++.+|+||+||||||+||||+|+||+||+.|.|..|+|+......+. ++.|+|+||+|||.||++||++|||+++..
T Consensus 61 ~~~~gtrE~Afv~Ai~sAgv~~~itraCs~G~l~~C~C~~~~~~~~~---~~~~~wggCsdni~~G~~~sr~Fld~~~~~ 137 (310)
T PF00110_consen 61 ILKKGTRETAFVYAISSAGVAHSITRACSRGKLKSCGCDRNPRGSSS---QNTWQWGGCSDNIKFGIKFSRRFLDAREKG 137 (310)
T ss_dssp T--S--HHHHHHHHHHHHHHHHHHHHHHHTTT-SS-----TTTTSEE---ETTEEE-S----HHHHHHHHHHHHHHH--S
T ss_pred ccccCcccceeeEhhhcCchHHHHHHHhhcccCCcCCCccccccccc---ccccccCCcccccccchHHHHHHHHhhhhh
Confidence 45789999999999999999999999999999999999988776544 356999999999999999999999998843
Q ss_pred hhhhhhHhHHHHHHHhhhhhhhhhhHHHHHHhhhhHHHHhhhhcC
Q psy227 94 RDIQTQRNLRLIDAAMFDEKNNRNYMLNVMNLHNNKAGRKIDTYQ 138 (139)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~mnlHNn~aGR~av~~~ 138 (139)
. +.+.+||+|||+|||++|.+.
T Consensus 138 ~-----------------------~~~~~mn~HNn~aGR~~v~~~ 159 (310)
T PF00110_consen 138 S-----------------------DARSLMNLHNNEAGRKAVKKN 159 (310)
T ss_dssp S-----------------------SHHHHHHHHHHHHHHHHHHHT
T ss_pred h-----------------------hhhhhhhhhhhhhhhhhhccc
Confidence 2 789999999999999999863
No 4
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=41.86 E-value=15 Score=23.24 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=19.1
Q ss_pred hHHHHHHhhhhHHHHhhhhcCC
Q psy227 118 YMLNVMNLHNNKAGRKIDTYQP 139 (139)
Q Consensus 118 ~~~~~mnlHNn~aGR~av~~~~ 139 (139)
++..++...+.++|++++.++|
T Consensus 21 El~~i~~FY~Sp~Gqk~~~~~~ 42 (64)
T PF09832_consen 21 ELDAILAFYESPLGQKIVAKEP 42 (64)
T ss_dssp HHHHHHHHHHSHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHhHHHHHHhH
Confidence 6778899999999999998875
No 5
>PF12342 DUF3640: Protein of unknown function (DUF3640) ; InterPro: IPR022101 This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Probab=28.51 E-value=33 Score=19.09 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=9.9
Q ss_pred Chhhhhhhhhhhhh
Q psy227 1 METVQASFCRRLFF 14 (139)
Q Consensus 1 ~~~~~~~~~~~~~~ 14 (139)
|.++-.+||+|+--
T Consensus 1 mslLtnr~crrvdk 14 (26)
T PF12342_consen 1 MSLLTNRMCRRVDK 14 (26)
T ss_pred ChHHHHHHHhhhcc
Confidence 55677788888743
No 6
>CHL00020 psbN photosystem II protein N
Probab=19.37 E-value=1e+02 Score=19.15 Aligned_cols=19 Identities=11% Similarity=0.134 Sum_probs=15.4
Q ss_pred hhHHHHHHHHHHHHHHHHh
Q psy227 21 EQGIVYALGSAAITYTLAR 39 (139)
Q Consensus 21 EtAfvyAisSAgv~~~Itr 39 (139)
|+|++.+|.-+.++.++|-
T Consensus 2 e~A~~~~i~i~~ll~~~Tg 20 (43)
T CHL00020 2 ETATLVAIFISGLLVSFTG 20 (43)
T ss_pred CchhhHHHHHHHHHHHhhh
Confidence 6788889988888887763
No 7
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=16.93 E-value=1.6e+02 Score=18.58 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=16.9
Q ss_pred chhhHHHHHHHHHHHHHHHHh
Q psy227 19 TREQGIVYALGSAAITYTLAR 39 (139)
Q Consensus 19 tREtAfvyAisSAgv~~~Itr 39 (139)
+-|+|++.+|.-++++.++|-
T Consensus 3 ~me~A~~~~i~i~~lL~~~Tg 23 (46)
T PRK13183 3 AMSPALSLAITILAILLALTG 23 (46)
T ss_pred ccchhHHHHHHHHHHHHHHhh
Confidence 347899999999888888763
No 8
>PHA02100 hypothetical protein
Probab=15.69 E-value=1.5e+02 Score=21.66 Aligned_cols=19 Identities=37% Similarity=0.613 Sum_probs=14.4
Q ss_pred cchHhHHHHHHhhhhhhhhh
Q psy227 74 DNVRWGAQFARSFTDILENE 93 (139)
Q Consensus 74 dnV~~G~~fsr~Fld~~e~~ 93 (139)
||| .|..++..-||.+|.+
T Consensus 23 dni-lG~~VTpQvlD~wE~e 41 (112)
T PHA02100 23 DNI-LGNRISEEQIDAVENE 41 (112)
T ss_pred cch-hhhhcCHHHHHHHHHH
Confidence 555 5778888999988854
No 9
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=13.42 E-value=1.2e+02 Score=18.79 Aligned_cols=19 Identities=16% Similarity=0.195 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHHHHHHHh
Q psy227 21 EQGIVYALGSAAITYTLAR 39 (139)
Q Consensus 21 EtAfvyAisSAgv~~~Itr 39 (139)
|+|++.+|+-+.++.++|-
T Consensus 2 e~a~~~~i~i~~~lv~~Tg 20 (43)
T PF02468_consen 2 ETATVLAIFISCLLVSITG 20 (43)
T ss_pred CceeeHHHHHHHHHHHHHh
Confidence 5777788887777776653
No 10
>PF12535 Nudix_N: Hydrolase of X-linked nucleoside diphosphate N terminal ; PDB: 3Q1P_B 3Q4I_B.
Probab=10.93 E-value=2.1e+02 Score=18.43 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q psy227 25 VYALGSAAITYT 36 (139)
Q Consensus 25 vyAisSAgv~~~ 36 (139)
+.||+-+|++|+
T Consensus 11 lqaiAqtGL~Ys 22 (58)
T PF12535_consen 11 LQAIAQTGLAYS 22 (58)
T ss_dssp HHHHHHHHHHH-
T ss_pred HHHHHHhhhhhC
Confidence 678999999983
Done!