Query psy3517
Match_columns 113
No_of_seqs 110 out of 180
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 18:41:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3517hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2516|consensus 100.0 1.2E-32 2.5E-37 237.3 -2.6 61 53-113 2-63 (517)
2 PF03901 Glyco_transf_22: Alg9 97.4 0.00011 2.4E-09 59.0 2.3 49 61-109 8-60 (418)
3 PF06567 Neural_ProG_Cyt: Neur 45.2 6.2 0.00014 29.9 -0.3 15 68-82 82-96 (120)
4 COG5228 POP2 mRNA deadenylase 42.6 8.2 0.00018 32.8 -0.0 17 90-106 38-58 (299)
5 PF09436 DUF2016: Domain of un 41.9 7.3 0.00016 26.8 -0.3 60 17-77 1-71 (72)
6 COG2101 SPT15 TATA-box binding 39.3 13 0.00029 29.8 0.7 33 70-106 17-49 (185)
7 PHA02889 hypothetical protein; 36.4 14 0.00029 30.6 0.4 25 1-26 109-133 (241)
8 KOG0304|consensus 25.5 26 0.00056 29.2 0.3 11 97-107 31-41 (239)
9 PHA02979 hypothetical protein; 18.5 60 0.0013 25.1 1.0 15 27-41 81-95 (140)
10 PF06514 PsbU: Photosystem II 18.4 54 0.0012 23.8 0.7 18 65-82 41-58 (93)
No 1
>KOG2516|consensus
Probab=99.97 E-value=1.2e-32 Score=237.26 Aligned_cols=61 Identities=64% Similarity=1.022 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHcCCcchhhhhhhhhhhhhhhcC-CCCCCCCcccCCCCcccccccccCC
Q psy3517 53 DSVALAVATVHLAICPFTKVEESFNLQAMHDIFYHN-MNISAYDHLEFPGVVPRTFLGPLFI 113 (113)
Q Consensus 53 ~~ll~~~~~~hl~~aPyTKVEESFnlQAiHDiL~~~-~~l~~YDH~~FPGvVPRTFiG~l~l 113 (113)
+.++++++.+|++.|||||||||||+||||||++|+ .|+++|||++||||||||||||++|
T Consensus 2 ~~llv~v~~~hli~~PfTKVEESFnlQA~HDil~~~~~~~sqYDHleFPGVVpRTFigplvi 63 (517)
T KOG2516|consen 2 DILLVTVIGYHLIKAPFTKVEESFNLQAIHDILTYRWDDLSQYDHLEFPGVVPRTFIGPLVI 63 (517)
T ss_pred cEEEEEeeeeeeeecCcchHhhhhhHHHHHHHHHhccchhhhcccccCCCcCccccccceee
Confidence 345566788999999999999999999999999998 8999999999999999999999875
No 2
>PF03901 Glyco_transf_22: Alg9-like mannosyltransferase family; InterPro: IPR005599 Members of this family are glycosylphosphatidylinositol mannosyltransferase enzymes 2.4.1.- from EC [, ]. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis [, ]. In yeast the SMP3 (YOR149C) has been implemented in plasmid stability [].; GO: 0016757 transferase activity, transferring glycosyl groups, 0006506 GPI anchor biosynthetic process, 0031227 intrinsic to endoplasmic reticulum membrane
Probab=97.35 E-value=0.00011 Score=59.03 Aligned_cols=49 Identities=16% Similarity=0.215 Sum_probs=40.0
Q ss_pred HHHHHHcCCc----chhhhhhhhhhhhhhhcCCCCCCCCcccCCCCccccccc
Q psy3517 61 TVHLAICPFT----KVEESFNLQAMHDIFYHNMNISAYDHLEFPGVVPRTFLG 109 (113)
Q Consensus 61 ~~hl~~aPyT----KVEESFnlQAiHDiL~~~~~l~~YDH~~FPGvVPRTFiG 109 (113)
.++++.|.++ |+||+||.|..+..+.+|.+...|||..+||+.++++.+
T Consensus 8 ~~R~~~a~~~~~~f~pDE~fq~~E~ah~~~~g~g~~tWE~~~~~~iRS~~~p~ 60 (418)
T PF03901_consen 8 AFRLLNALFPQTSFHPDEYFQSLEPAHRLVFGYGYLTWEWSPFPGIRSWLFPL 60 (418)
T ss_pred HHHHHHHHhccCCCCCCcccccHHhhhhhhcCccchhhhhccCCCCCChHHHH
Confidence 3455554444 999999999999888888999999999999998887754
No 3
>PF06567 Neural_ProG_Cyt: Neural chondroitin sulphate proteoglycan cytoplasmic domain; InterPro: IPR009505 This entry represents the C-terminal cytoplasmic domain of vertebrate neural chondroitin sulphate proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis []. This domain contains a number of potential sites of phosphorylation by protein kinase C [].
Probab=45.24 E-value=6.2 Score=29.88 Aligned_cols=15 Identities=47% Similarity=0.496 Sum_probs=12.5
Q ss_pred CCcchhhhhhhhhhh
Q psy3517 68 PFTKVEESFNLQAMH 82 (113)
Q Consensus 68 PyTKVEESFnlQAiH 82 (113)
|--|=|||||||.-|
T Consensus 82 ~~~KEEes~NI~NS~ 96 (120)
T PF06567_consen 82 SCLKEEESFNIQNSM 96 (120)
T ss_pred ccccccccccccccC
Confidence 567999999999654
No 4
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=42.62 E-value=8.2 Score=32.80 Aligned_cols=17 Identities=65% Similarity=1.118 Sum_probs=14.1
Q ss_pred CCCCCCcc----cCCCCcccc
Q psy3517 90 NISAYDHL----EFPGVVPRT 106 (113)
Q Consensus 90 ~l~~YDH~----~FPGvVPRT 106 (113)
-+++|.|+ ||||||.|-
T Consensus 38 Li~rYn~vSmdTEFpGvvArP 58 (299)
T COG5228 38 LISRYNHVSMDTEFPGVVARP 58 (299)
T ss_pred HHHhCCceeeccccCceeecc
Confidence 46888886 799999994
No 5
>PF09436 DUF2016: Domain of unknown function (DUF2016); InterPro: IPR018560 This entry represents the N-terminal of proteins that contain a ubiquitin domain.
Probab=41.85 E-value=7.3 Score=26.84 Aligned_cols=60 Identities=12% Similarity=0.088 Sum_probs=36.6
Q ss_pred cccccccccCceeeecCCCCccccC-----------CCCCCchHHHHHHHHHHHHHHHHHHcCCcchhhhhh
Q psy3517 17 MDSSLLLKYPSICICSDSSDVYYSD-----------YFPGIPVDLTMDSVALAVATVHLAICPFTKVEESFN 77 (113)
Q Consensus 17 ~~~~~~~~~~~~~v~s~~~~v~~~~-----------~~~~~~~~~~l~~ll~~~~~~hl~~aPyTKVEESFn 77 (113)
+|.-|....|++||-+.......+. .|- +..-.+|.+...+.-.-.-..-||-.|||+..
T Consensus 1 ~D~aLq~~~P~v~vPr~g~l~~l~~~G~Rllva~nGv~l-Ev~r~WL~~~~~va~~~~~~~~PYG~v~e~~~ 71 (72)
T PF09436_consen 1 RDMALQASFPTVMVPRFGALEPLERPGHRLLVASNGVFL-EVRRPWLHVIRPVALYPVATAIPYGEVTEALR 71 (72)
T ss_pred CcHHHHhhCCEeecCCCCCCCccccCCcEEEEecCcEEE-EEechHHHHhHHhhcCCccccCCcccceeeec
Confidence 5777888899999988877665542 222 12223344433322122345679999999853
No 6
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=39.30 E-value=13 Score=29.81 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=24.1
Q ss_pred cchhhhhhhhhhhhhhhcCCCCCCCCcccCCCCcccc
Q psy3517 70 TKVEESFNLQAMHDIFYHNMNISAYDHLEFPGVVPRT 106 (113)
Q Consensus 70 TKVEESFnlQAiHDiL~~~~~l~~YDH~~FPGvVPRT 106 (113)
|+-++.+++|.+-..+ .=+.|+--+|||.|-|.
T Consensus 17 ~~L~~elDL~~~~~~l----~~aeYnP~qFpGlv~Rl 49 (185)
T COG2101 17 VDLGQELDLEEVALDL----PGAEYNPEQFPGLVYRL 49 (185)
T ss_pred echhhhccHHHHHhhC----CCCccCHhHCCeeEEEe
Confidence 3456777777655544 23789999999999885
No 7
>PHA02889 hypothetical protein; Provisional
Probab=36.39 E-value=14 Score=30.58 Aligned_cols=25 Identities=52% Similarity=0.695 Sum_probs=21.6
Q ss_pred CCcccccccccchhcccccccccccC
Q psy3517 1 MGKSQWDTLQDTEEINMDSSLLLKYP 26 (113)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 26 (113)
|||.| |.||..|.|-.|.|++.|-.
T Consensus 109 ~~kgq-dslq~iesi~idds~i~ke~ 133 (241)
T PHA02889 109 MGKGQ-DSLQEIESIFIDDSLITKED 133 (241)
T ss_pred cccCc-chhhheeEEEeccceeeehh
Confidence 67777 89999999999999998743
No 8
>KOG0304|consensus
Probab=25.47 E-value=26 Score=29.20 Aligned_cols=11 Identities=64% Similarity=1.102 Sum_probs=9.3
Q ss_pred ccCCCCccccc
Q psy3517 97 LEFPGVVPRTF 107 (113)
Q Consensus 97 ~~FPGvVPRTF 107 (113)
.||||+|-||-
T Consensus 31 TEFPGvv~rp~ 41 (239)
T KOG0304|consen 31 TEFPGVVARPI 41 (239)
T ss_pred CcCCceeeecC
Confidence 48999999974
No 9
>PHA02979 hypothetical protein; Provisional
Probab=18.51 E-value=60 Score=25.09 Aligned_cols=15 Identities=40% Similarity=0.886 Sum_probs=11.5
Q ss_pred ceeeecCCCCccccC
Q psy3517 27 SICICSDSSDVYYSD 41 (113)
Q Consensus 27 ~~~v~s~~~~v~~~~ 41 (113)
-|||||+-++.-.+.
T Consensus 81 iiCI~Sdd~GLLihN 95 (140)
T PHA02979 81 IICICSDDCGLLIHN 95 (140)
T ss_pred EEEEecccccEEEec
Confidence 489999988765543
No 10
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 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 []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=18.43 E-value=54 Score=23.77 Aligned_cols=18 Identities=22% Similarity=0.591 Sum_probs=10.6
Q ss_pred HHcCCcchhhhhhhhhhh
Q psy3517 65 AICPFTKVEESFNLQAMH 82 (113)
Q Consensus 65 ~~aPyTKVEESFnlQAiH 82 (113)
--+||.+|||-.++...-
T Consensus 41 ~naPY~sveDvl~ipgLs 58 (93)
T PF06514_consen 41 SNAPYKSVEDVLNIPGLS 58 (93)
T ss_dssp HS---SSGGGGCCSTT--
T ss_pred hCCCCCCHHHHHhccCCC
Confidence 347999999999985443
Done!