Query psy1357
Match_columns 113
No_of_seqs 108 out of 571
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:34:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00139 PIPKc Phosphatidylinos 100.0 2.3E-33 4.9E-38 225.1 9.2 85 1-87 229-313 (313)
2 smart00330 PIPKc Phosphatidyli 100.0 7.3E-33 1.6E-37 224.3 7.1 83 1-86 200-342 (342)
3 PF01504 PIP5K: Phosphatidylin 100.0 4.8E-33 1E-37 216.7 5.7 84 1-86 145-252 (252)
4 KOG0230|consensus 100.0 2.6E-30 5.6E-35 234.5 6.7 95 2-96 1502-1596(1598)
5 KOG0229|consensus 99.9 5E-28 1.1E-32 199.6 6.7 83 1-86 268-419 (420)
6 PLN03185 phosphatidylinositol 99.9 7.1E-26 1.5E-30 198.3 8.4 54 31-87 712-765 (765)
7 COG5253 MSS4 Phosphatidylinosi 99.8 2.7E-21 5.8E-26 163.0 2.3 95 2-96 508-606 (612)
8 PF07450 HycH: Formate hydroge 61.3 3.2 6.9E-05 30.1 0.3 21 14-41 24-44 (131)
9 PRK15084 formate hydrogenlyase 58.9 3.5 7.5E-05 30.0 0.2 20 14-40 26-45 (133)
10 COG5253 MSS4 Phosphatidylinosi 49.7 5 0.00011 35.3 -0.2 51 29-83 554-604 (612)
11 PRK13610 photosystem II reacti 35.3 23 0.00051 25.1 1.4 18 70-87 91-108 (113)
12 PLN00039 photosystem II reacti 34.4 25 0.00053 24.9 1.4 18 70-87 85-102 (111)
13 PF03912 Psb28: Psb28 protein; 34.0 26 0.00056 24.6 1.4 18 69-86 83-100 (108)
14 TIGR03047 PS_II_psb28 photosys 33.8 26 0.00055 24.7 1.4 18 70-87 84-101 (109)
15 PRK13612 photosystem II reacti 33.3 26 0.00057 24.8 1.4 18 70-87 87-104 (113)
16 CHL00128 psbW photosystem II p 32.7 27 0.00059 24.7 1.4 18 70-87 87-104 (113)
17 PRK13611 photosystem II reacti 31.5 30 0.00064 24.2 1.4 17 70-86 80-96 (104)
18 KOG4620|consensus 30.4 80 0.0017 20.9 3.2 38 44-88 6-43 (80)
19 COG3254 Uncharacterized conser 28.2 34 0.00075 23.9 1.2 16 8-23 30-45 (105)
20 PF10381 Autophagy_Cterm: Auto 20.1 1.5E+02 0.0032 15.6 2.4 19 71-89 1-19 (25)
No 1
>cd00139 PIPKc Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs.
Probab=100.00 E-value=2.3e-33 Score=225.14 Aligned_cols=85 Identities=49% Similarity=0.938 Sum_probs=79.1
Q ss_pred ChhHHHHHhhhhcCCccccceeEEEecCCCeEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHH
Q psy1357 1 MQAINNDTQFLANQHVMDYSLLLGIDDTNMELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQS 80 (113)
Q Consensus 1 m~~L~~D~~FL~~~~imDYSLLvgi~~~~~~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~ 80 (113)
++||++||+||+++||||||||||||..+.+||+|||||||+||++|++|+++|+.. ++ .+.+||||||++|++||++
T Consensus 229 ~~qL~~D~~FL~~~~iMDYSLLvGi~~~~~i~~~GIID~L~~y~~~Kk~E~~~K~~~-~~-~~~~iS~v~P~~Y~~RF~~ 306 (313)
T cd00139 229 LTQIKRDCEFLESLNIMDYSLLVGIHDIRLVLYLGIIDILRTYTWDKKLEHWVKSLG-HD-GGKTPSVVSPEQYAKRFRE 306 (313)
T ss_pred HHHHHHHHHHHHHCCCcccceEEEEecCCceEEEEEEeeeeeCCHHHHHHHHHHHhc-cC-CCCCcceECHHHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999999973 43 2389999999999999999
Q ss_pred HHhhhcc
Q psy1357 81 AMNRYFL 87 (113)
Q Consensus 81 ~~~~~f~ 87 (113)
||+++|.
T Consensus 307 fi~~~f~ 313 (313)
T cd00139 307 FMDKYFL 313 (313)
T ss_pred HHHHhcC
Confidence 9999973
No 2
>smart00330 PIPKc Phosphatidylinositol phosphate kinases.
Probab=99.98 E-value=7.3e-33 Score=224.34 Aligned_cols=83 Identities=46% Similarity=0.879 Sum_probs=76.5
Q ss_pred ChhHHHHHhhhhcCCccccceeEEEecCCC--------------------------------------------------
Q psy1357 1 MQAINNDTQFLANQHVMDYSLLLGIDDTNM-------------------------------------------------- 30 (113)
Q Consensus 1 m~~L~~D~~FL~~~~imDYSLLvgi~~~~~-------------------------------------------------- 30 (113)
++||++||+||+++||||||||||||..+.
T Consensus 200 ~~ql~~D~~FL~~~~imDYSLLvGi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 (342)
T smart00330 200 LKQIKRDCEFLESLKIMDYSLLVGIHDIERGQREEIELPPVYGSDESPSSESSNGGKAPDITGNLLVSNSPDGDGPFGGI 279 (342)
T ss_pred HHHHHHHHHHHHHccchhhhhhhccccccccchhcccccccccccccccccccccCCCcccccccccccccccccccccc
Confidence 579999999999999999999999997532
Q ss_pred ----------eEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHHHhhhc
Q psy1357 31 ----------ELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSAMNRYF 86 (113)
Q Consensus 31 ----------~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~~~~~f 86 (113)
+||+|||||||+|||+|++|+++|+.. + ++++||||||++|++||++||+++|
T Consensus 280 ~~~~~~~~~~vy~iGIID~Lq~Y~~~KklE~~~K~~~-~--~~~~iS~V~P~~Y~~RF~~fi~~~F 342 (342)
T smart00330 280 PARAIRARRVVLYLGIIDILQTYTWDKKLEHWVKSIG-H--DGKTISVVHPEQYAKRFRDFMDKYF 342 (342)
T ss_pred ccccccCCceEEEEEEEEEEEeCCHhHHHHHHHHHhc-c--CCCCcceECHHHHHHHHHHHHHhhC
Confidence 899999999999999999999999973 3 4689999999999999999999987
No 3
>PF01504 PIP5K: Phosphatidylinositol-4-phosphate 5-Kinase; InterPro: IPR002498 This entry represents a conserved region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in []. This region is found in I, II and III phosphatidylinositol-4-phosphate 5-kinases (PIP5K enzymes). PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signalling pathway.; GO: 0016307 phosphatidylinositol phosphate kinase activity, 0046488 phosphatidylinositol metabolic process; PDB: 1BO1_A 2GK9_C 2YBX_B.
Probab=99.97 E-value=4.8e-33 Score=216.66 Aligned_cols=84 Identities=36% Similarity=0.692 Sum_probs=55.5
Q ss_pred ChhHHHHHhhhhcCCccccceeEEEe------------------------cCCCeEEEEEeeccccCChhHHHHHHHHHh
Q psy1357 1 MQAINNDTQFLANQHVMDYSLLLGID------------------------DTNMELVVGMIDYIRTFTWDKKIETMVKKS 56 (113)
Q Consensus 1 m~~L~~D~~FL~~~~imDYSLLvgi~------------------------~~~~~y~~GIID~L~~y~~~KklE~~~K~~ 56 (113)
++||++||+||+++||||||||||++ ..+.+||+|||||||+||++|++|+++|+.
T Consensus 145 ~~ql~~D~~FL~~~~imDYSLLvGi~~~~~~~~~~~~~~~~~~~~~~~s~~~~~vy~~GIID~L~~y~~~K~~E~~~K~~ 224 (252)
T PF01504_consen 145 LKQLERDTEFLSSHNIMDYSLLVGIHNRDSNEEQENKSSFPSYAGGIMSEDGNEVYYLGIIDILQEYNWKKKLEHFFKSL 224 (252)
T ss_dssp HHHHHHHHHHHHHTTEES-EEEEEEEH---HHHHHH-H---TTTTTTCCCETTEEEEEEEE-S-EETT------------
T ss_pred HHHHHHHHHHHHhccccccceeEeeeeccccccccccccccccccceeecCCCeEEEEEEehheeeccHHHHHHHHHHHH
Confidence 47999999999999999999999999 345689999999999999999999999997
Q ss_pred hhcCCCCCCceeeChhhHHHHHHHHHhhhc
Q psy1357 57 GLLGGQGKLPTIVSPDEYRKRFQSAMNRYF 86 (113)
Q Consensus 57 ~~~~~~~~~iS~v~P~~Y~~RF~~~~~~~f 86 (113)
..+ +++++||+||++||+||+++|+++|
T Consensus 225 ~~~--~~~~iS~v~P~~Y~~RF~~~i~~~f 252 (252)
T PF01504_consen 225 IKC--DGQDISCVPPEEYAERFIKFIESIF 252 (252)
T ss_dssp --------SSS---HHHHHHHHHHHHHHH-
T ss_pred hhc--CCCCCcccCHHHHHHHHHHHHHHhC
Confidence 333 4689999999999999999999987
No 4
>KOG0230|consensus
Probab=99.96 E-value=2.6e-30 Score=234.51 Aligned_cols=95 Identities=62% Similarity=1.082 Sum_probs=89.8
Q ss_pred hhHHHHHhhhhcCCccccceeEEEecCCCeEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHH
Q psy1357 2 QAINNDTQFLANQHVMDYSLLLGIDDTNMELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSA 81 (113)
Q Consensus 2 ~~L~~D~~FL~~~~imDYSLLvgi~~~~~~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~ 81 (113)
++|-+||.||++.|||||||||||+++++++++|||||+++|||.|++|.|+|..+..++.+..+|+|.|++|.+||.++
T Consensus 1502 ~aiwNDT~FLas~~VMDYSLLVGvD~e~~ELvlGIIDfiRtYTWDKkLESWVK~sGl~gpk~~~PTVVSP~qYK~RFRkA 1581 (1598)
T KOG0230|consen 1502 RAIWNDTSFLASINVMDYSLLVGVDDENNELVLGIIDFIRTYTWDKKLESWVKSSGLGGPKNKQPTVVSPEQYKTRFRKA 1581 (1598)
T ss_pred HHHhcchHHhhhcccceeeeEEEeeCCCCeEEEEehHhhhhhhhhhhhhhheeccccccCCCCCCceeCHHHHHHHHHHH
Confidence 46889999999999999999999999999999999999999999999999999986445678899999999999999999
Q ss_pred HhhhccCCCCCcccc
Q psy1357 82 MNRYFLGVPDRWSGQ 96 (113)
Q Consensus 82 ~~~~f~~~p~~~~~~ 96 (113)
|..||.+||+.|++.
T Consensus 1582 Md~YfL~VPD~Wtg~ 1596 (1598)
T KOG0230|consen 1582 MDTYFLMVPDQWTGL 1596 (1598)
T ss_pred HhheeeecCCcccCC
Confidence 999999999999986
No 5
>KOG0229|consensus
Probab=99.95 E-value=5e-28 Score=199.62 Aligned_cols=83 Identities=33% Similarity=0.591 Sum_probs=75.2
Q ss_pred ChhHHHHHhhhhcCCccccceeEEEecC----------------------------------------------------
Q psy1357 1 MQAINNDTQFLANQHVMDYSLLLGIDDT---------------------------------------------------- 28 (113)
Q Consensus 1 m~~L~~D~~FL~~~~imDYSLLvgi~~~---------------------------------------------------- 28 (113)
|+||++||+||++.+|||||||||||+.
T Consensus 268 ~~ql~~Dce~Le~~~IMDYSLLvGiH~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~g~~~p~~~~~ 347 (420)
T KOG0229|consen 268 LKQLKRDCEFLESLKIMDYSLLVGIHDRDRGQAEKEELEPQEDESEREQRLSSASPEDVLTSTASPSIQLGANMPARAGE 347 (420)
T ss_pred HHHHHHHHHHHHHhcchhhhheeeeeeccccccchhhcCCCCCccccccccccccccccCCCCCcccccCCCCCCCcccc
Confidence 5899999999999999999999999861
Q ss_pred -----------------CCeEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHHHhhhc
Q psy1357 29 -----------------NMELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSAMNRYF 86 (113)
Q Consensus 29 -----------------~~~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~~~~~f 86 (113)
+-++|+|||||||.|++.||+||.+|+. .+ ++..||+++|.+|++||++||.+.|
T Consensus 348 ~~~~~~~~~~~~~~~~~~~v~y~GIIDILq~Y~~~KK~EH~~Ksl-~~--d~~tIS~v~P~~Ys~RF~dFi~~~~ 419 (420)
T KOG0229|consen 348 ERVDRMEYAPAQNSGGYDVVLYIGIIDILQDYDIKKKLEHAYKSL-QH--DPDTISAVDPKFYAKRFLDFISNIF 419 (420)
T ss_pred ccccccccccccccCcceEEEEEEeehhhhhcchhhHHHHHHhhh-cc--CCceeeccCHHHHHHHHHHHHHhhc
Confidence 1269999999999999999999999996 34 5667999999999999999999986
No 6
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.93 E-value=7.1e-26 Score=198.32 Aligned_cols=54 Identities=30% Similarity=0.456 Sum_probs=50.0
Q ss_pred eEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHHHhhhcc
Q psy1357 31 ELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 31 ~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~~~~~f~ 87 (113)
++|+|||||||+|++.|++||.+|++ .+ ++..||+|+|..|++||++||.++|.
T Consensus 712 ~~~~giidilq~y~~~k~~eh~~k~~-~~--~~~~is~v~p~~y~~rf~~f~~~~f~ 765 (765)
T PLN03185 712 VLYLGIIDILQEYNMSKKIEHAYKSL-QF--DSLSISAVDPTFYSKRFLEFIQKVFP 765 (765)
T ss_pred EEEEEEEEeecccchhHHHHHHHhhh-cc--CCCceeccChHHHHHHHHHHHHhhcC
Confidence 48999999999999999999999997 34 78899999999999999999999983
No 7
>COG5253 MSS4 Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms]
Probab=99.82 E-value=2.7e-21 Score=162.99 Aligned_cols=95 Identities=44% Similarity=0.724 Sum_probs=85.5
Q ss_pred hhHHHHHhhhhcCCccccceeEEEecCCCeEEEE-Eeecccc-CChhHHHHHHHHHhhhcCC--CCCCceeeChhhHHHH
Q psy1357 2 QAINNDTQFLANQHVMDYSLLLGIDDTNMELVVG-MIDYIRT-FTWDKKIETMVKKSGLLGG--QGKLPTIVSPDEYRKR 77 (113)
Q Consensus 2 ~~L~~D~~FL~~~~imDYSLLvgi~~~~~~y~~G-IID~L~~-y~~~KklE~~~K~~~~~~~--~~~~iS~v~P~~Y~~R 77 (113)
.||.+|++||+++|||||||||||++...+..+| |||+.+. ++|.|++|-++|-....+. ....+|+|+|.+|++|
T Consensus 508 sqv~~Dv~fLsklniMDYSllVgi~~~~~~~~V~~I~d~i~t~~t~Dk~~~~gI~d~lt~~s~~k~~~~t~v~p~~y~nr 587 (612)
T COG5253 508 SQVWNDVLFLSKLNIMDYSLLVGIDDEREEASVGLIIDFIRTRMTGDKKLESGIKDKLTVGSFTKRKEPTAVTPRQYKNR 587 (612)
T ss_pred HHHHHHHHHHHHhCccceeEEEEeccchhhcchHHHHhhhccccccceeeeeehhhhhccceeeecccceecCHHHHHHH
Confidence 5899999999999999999999999999999999 9999998 9999999999998644331 2368999999999999
Q ss_pred HHHHHhhhccCCCCCcccc
Q psy1357 78 FQSAMNRYFLGVPDRWSGQ 96 (113)
Q Consensus 78 F~~~~~~~f~~~p~~~~~~ 96 (113)
|.++|+.|+.+.|++|+.-
T Consensus 588 f~~~~e~yi~~~p~~~~~~ 606 (612)
T COG5253 588 FRKAMEAYIDPFPDKKTQE 606 (612)
T ss_pred HHHhHHHhhhcccchhhhc
Confidence 9999999999999998654
No 8
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=61.27 E-value=3.2 Score=30.14 Aligned_cols=21 Identities=48% Similarity=0.771 Sum_probs=17.3
Q ss_pred CCccccceeEEEecCCCeEEEEEeeccc
Q psy1357 14 QHVMDYSLLLGIDDTNMELVVGMIDYIR 41 (113)
Q Consensus 14 ~~imDYSLLvgi~~~~~~y~~GIID~L~ 41 (113)
..+|=|||-+|- ++|+||+|.
T Consensus 24 kqV~yYSLaIGH-------hvGvIDcle 44 (131)
T PF07450_consen 24 KQVMYYSLAIGH-------HVGVIDCLE 44 (131)
T ss_pred hheeEEEeeecc-------ccceEeech
Confidence 458889999984 589999983
No 9
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=58.94 E-value=3.5 Score=30.01 Aligned_cols=20 Identities=55% Similarity=0.863 Sum_probs=16.8
Q ss_pred CCccccceeEEEecCCCeEEEEEeecc
Q psy1357 14 QHVMDYSLLLGIDDTNMELVVGMIDYI 40 (113)
Q Consensus 14 ~~imDYSLLvgi~~~~~~y~~GIID~L 40 (113)
..+|=|||-+|-| +|+||+|
T Consensus 26 ~qV~yYSLaIGHh-------vGvIDcl 45 (133)
T PRK15084 26 QQVMYYSLAIGHH-------VGVIDCL 45 (133)
T ss_pred hheeEEEeecccc-------cceEecc
Confidence 4688899999854 8999998
No 10
>COG5253 MSS4 Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms]
Probab=49.74 E-value=5 Score=35.32 Aligned_cols=51 Identities=18% Similarity=0.159 Sum_probs=32.4
Q ss_pred CCeEEEEEeeccccCChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHHHh
Q psy1357 29 NMELVVGMIDYIRTFTWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSAMN 83 (113)
Q Consensus 29 ~~~y~~GIID~L~~y~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~~~ 83 (113)
+..+++||||.|+.|++.|..|-..-... +-..-.+--|+.|-.+|..+-.
T Consensus 554 Dk~~~~gI~d~lt~~s~~k~~~~t~v~p~----~y~nrf~~~~e~yi~~~p~~~~ 604 (612)
T COG5253 554 DKKLESGIKDKLTVGSFTKRKEPTAVTPR----QYKNRFRKAMEAYIDPFPDKKT 604 (612)
T ss_pred ceeeeeehhhhhccceeeecccceecCHH----HHHHHHHHhHHHhhhcccchhh
Confidence 46899999999999999987774221110 0011224556777777766543
No 11
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=35.28 E-value=23 Score=25.05 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=13.7
Q ss_pred ChhhHHHHHHHHHhhhcc
Q psy1357 70 SPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f~ 87 (113)
...+=-+||++||++|-.
T Consensus 91 ~s~~~WdRFMRFMeRYA~ 108 (113)
T PRK13610 91 NSEEAFERFMRFASRYAN 108 (113)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 445556999999999843
No 12
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=34.43 E-value=25 Score=24.87 Aligned_cols=18 Identities=28% Similarity=0.314 Sum_probs=13.5
Q ss_pred ChhhHHHHHHHHHhhhcc
Q psy1357 70 SPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f~ 87 (113)
..++=-+||++||++|-.
T Consensus 85 ~s~~~WdRFMRFMeRYA~ 102 (111)
T PLN00039 85 RSPREWDRFMRFMERYAE 102 (111)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 344556899999999843
No 13
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 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 Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=33.95 E-value=26 Score=24.64 Aligned_cols=18 Identities=33% Similarity=0.523 Sum_probs=13.2
Q ss_pred eChhhHHHHHHHHHhhhc
Q psy1357 69 VSPDEYRKRFQSAMNRYF 86 (113)
Q Consensus 69 v~P~~Y~~RF~~~~~~~f 86 (113)
+..++=-+||++||++|-
T Consensus 83 m~s~~~WdRFMRFMeRYA 100 (108)
T PF03912_consen 83 MKSEEEWDRFMRFMERYA 100 (108)
T ss_dssp E-SSHHHHHHHHHHHHHH
T ss_pred ECCHHHHHHHHHHHHHHH
Confidence 344555699999999983
No 14
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=33.83 E-value=26 Score=24.71 Aligned_cols=18 Identities=28% Similarity=0.425 Sum_probs=13.5
Q ss_pred ChhhHHHHHHHHHhhhcc
Q psy1357 70 SPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f~ 87 (113)
..++=-+||++||++|-.
T Consensus 84 ~s~~~WdRFMRFmeRYA~ 101 (109)
T TIGR03047 84 KSEDEWDRFMRFMERYAE 101 (109)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 344556899999999843
No 15
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=33.33 E-value=26 Score=24.80 Aligned_cols=18 Identities=28% Similarity=0.420 Sum_probs=13.6
Q ss_pred ChhhHHHHHHHHHhhhcc
Q psy1357 70 SPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f~ 87 (113)
..++=-+||++||++|-.
T Consensus 87 ~s~~~WdRFMRFMeRYA~ 104 (113)
T PRK13612 87 KSEQEWDRFMRFMERYAK 104 (113)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 344556899999999843
No 16
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=32.71 E-value=27 Score=24.72 Aligned_cols=18 Identities=33% Similarity=0.364 Sum_probs=13.5
Q ss_pred ChhhHHHHHHHHHhhhcc
Q psy1357 70 SPDEYRKRFQSAMNRYFL 87 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f~ 87 (113)
..++=-+||++||++|-.
T Consensus 87 ~s~~~WdRFMRFMeRYA~ 104 (113)
T CHL00128 87 KNPEAWDRFMRFMERYAE 104 (113)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 344556899999999843
No 17
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=31.45 E-value=30 Score=24.19 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=13.1
Q ss_pred ChhhHHHHHHHHHhhhc
Q psy1357 70 SPDEYRKRFQSAMNRYF 86 (113)
Q Consensus 70 ~P~~Y~~RF~~~~~~~f 86 (113)
..++=-+||++||++|-
T Consensus 80 ~s~~~wdRFMRFmeRYA 96 (104)
T PRK13611 80 ETEAEWDRFLRFMERFS 96 (104)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 34455689999999983
No 18
>KOG4620|consensus
Probab=30.38 E-value=80 Score=20.93 Aligned_cols=38 Identities=8% Similarity=0.086 Sum_probs=27.9
Q ss_pred ChhHHHHHHHHHhhhcCCCCCCceeeChhhHHHHHHHHHhhhccC
Q psy1357 44 TWDKKIETMVKKSGLLGGQGKLPTIVSPDEYRKRFQSAMNRYFLG 88 (113)
Q Consensus 44 ~~~KklE~~~K~~~~~~~~~~~iS~v~P~~Y~~RF~~~~~~~f~~ 88 (113)
.+++.+-++++.+..-+ --.|..|++||+.|+..=|..
T Consensus 6 gLQrqVlhlYR~~lraa-------~~Kp~~~~~~~m~fvh~EFrk 43 (80)
T KOG4620|consen 6 GLQRQVLHLYRDLLRAA-------RGKPGAEARRWMAFVHAEFRK 43 (80)
T ss_pred HHHHHHHHHHHHHHHHh-------cCCCchHHHHHHHHHHHHHHH
Confidence 35678888888863221 246899999999999886653
No 19
>COG3254 Uncharacterized conserved protein [Function unknown]
Probab=28.17 E-value=34 Score=23.91 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=14.0
Q ss_pred HhhhhcCCccccceeE
Q psy1357 8 TQFLANQHVMDYSLLL 23 (113)
Q Consensus 8 ~~FL~~~~imDYSLLv 23 (113)
++.|.++||=|||+.+
T Consensus 30 ~a~lk~agi~nYSIfL 45 (105)
T COG3254 30 LALLKEAGIRNYSIFL 45 (105)
T ss_pred HHHHHHcCCceeEEEe
Confidence 4578999999999987
No 20
>PF10381 Autophagy_Cterm: Autophagocytosis associated protein C-terminal; InterPro: IPR019461 Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex []. It carries a highly characteristic conserved FLKF sequence motif. ; PDB: 2DYT_A.
Probab=20.13 E-value=1.5e+02 Score=15.61 Aligned_cols=19 Identities=16% Similarity=0.214 Sum_probs=15.0
Q ss_pred hhhHHHHHHHHHhhhccCC
Q psy1357 71 PDEYRKRFQSAMNRYFLGV 89 (113)
Q Consensus 71 P~~Y~~RF~~~~~~~f~~~ 89 (113)
|++|--=|++||.+....+
T Consensus 1 vd~yl~iFLKFi~sViPtI 19 (25)
T PF10381_consen 1 VDQYLVIFLKFISSVIPTI 19 (25)
T ss_dssp GGGHHHHHHHHHHHHSTTB
T ss_pred CceeehhHHHHHhhcCCce
Confidence 5788888999999985543
Done!