Query 041595
Match_columns 73
No_of_seqs 102 out of 136
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:47:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041595hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08122 NDUF_B12: NADH-ubiqui 99.9 3.3E-26 7.2E-31 137.8 4.5 41 5-45 2-45 (57)
2 KOG4631 NADH:ubiquinone oxidor 99.7 2.6E-18 5.6E-23 114.1 4.2 58 4-61 37-100 (100)
3 PF06724 DUF1206: Domain of Un 65.5 9.2 0.0002 22.8 2.9 24 28-51 50-73 (73)
4 PTZ00451 dephospho-CoA kinase; 58.5 8.9 0.00019 28.3 2.3 30 17-46 212-241 (244)
5 PRK12657 putative monovalent c 54.0 30 0.00064 22.8 4.0 30 31-61 69-98 (100)
6 PF06219 DUF1005: Protein of u 53.2 5.5 0.00012 32.8 0.5 27 4-30 295-324 (460)
7 PF09813 Coiled-coil_56: Coile 48.4 9.1 0.0002 25.7 0.9 20 22-41 47-66 (100)
8 PF02064 MAS20: MAS20 protein 48.2 6 0.00013 26.8 0.0 14 31-44 3-16 (121)
9 TIGR00985 3a0801s04tom mitocho 47.1 16 0.00035 25.7 2.0 14 31-44 13-26 (148)
10 PRK12600 putative monovalent c 37.2 80 0.0017 20.4 4.0 20 31-50 65-84 (94)
11 PF15361 RIC3: Resistance to i 36.6 31 0.00067 24.0 2.1 23 23-45 81-103 (152)
12 PRK10930 FtsH protease regulat 31.1 59 0.0013 26.0 3.1 7 4-10 12-18 (419)
13 PF06849 DUF1246: Protein of u 30.3 43 0.00093 23.2 2.0 17 35-51 72-88 (124)
14 KOG4056 Translocase of outer m 30.2 41 0.00088 23.9 1.9 13 32-44 16-28 (143)
15 PF06716 DUF1201: Protein of u 29.7 95 0.0021 18.7 3.2 14 42-55 30-43 (54)
16 PF12221 HflK_N: Bacterial mem 28.4 31 0.00066 19.6 0.8 9 4-12 10-18 (42)
17 TIGR02811 formate_TAT formate 27.3 34 0.00074 20.8 1.0 20 24-43 11-30 (66)
18 PF02468 PsbN: Photosystem II 27.0 98 0.0021 17.9 2.8 24 33-56 9-32 (43)
19 PF05661 DUF808: Protein of un 25.5 80 0.0017 24.8 2.9 20 36-55 95-114 (295)
20 TIGR03008 pepcterm_CAAX CAAX p 25.0 84 0.0018 23.1 2.8 32 23-54 66-97 (222)
21 PF01220 DHquinase_II: Dehydro 23.9 25 0.00055 24.6 -0.1 27 6-33 102-128 (140)
22 PF04839 PSRP-3_Ycf65: Plastid 23.5 22 0.00048 21.1 -0.3 13 4-16 3-15 (49)
23 cd05311 NAD_bind_2_malic_enz N 23.3 43 0.00093 24.0 1.0 17 22-38 156-174 (226)
24 PF01691 Adeno_E1B_19K: Adenov 22.3 78 0.0017 22.0 2.1 19 25-43 82-100 (134)
25 PF14098 SSPI: Small, acid-sol 21.4 50 0.0011 20.5 0.9 9 25-33 32-40 (65)
26 CHL00163 ycf65 putative riboso 21.3 36 0.00078 22.8 0.3 14 4-17 32-45 (99)
27 COG2354 Uncharacterized protei 21.2 63 0.0014 25.5 1.6 37 27-64 87-123 (303)
28 PF12841 YvrJ: YvrJ protein fa 21.0 84 0.0018 17.4 1.7 12 30-41 7-18 (38)
29 COG3162 Predicted membrane pro 20.9 1.7E+02 0.0036 19.8 3.4 26 26-51 59-84 (102)
30 PRK02724 hypothetical protein; 20.4 39 0.00084 22.9 0.3 14 4-17 37-50 (104)
31 PRK13183 psbN photosystem II r 20.4 84 0.0018 18.5 1.7 18 39-56 18-35 (46)
No 1
>PF08122 NDUF_B12: NADH-ubiquinone oxidoreductase B12 subunit family; InterPro: IPR012576 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the B12 subunit of NADH:ubiquinone oxidoreductase proteins. The function of this subunit is unclear [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=99.93 E-value=3.3e-26 Score=137.84 Aligned_cols=41 Identities=32% Similarity=0.755 Sum_probs=38.7
Q ss_pred cCCCcchhhhhcCCCccc---hhhhccCChhHHHHHHHHHHHHH
Q 041595 5 GEFFRRRDGWRKHPLLTS---NLRQATPGLGIALVAFGIYLVGE 45 (73)
Q Consensus 5 ~DPW~R~EaWRy~p~f~~---~~~~~~PGlgig~~AF~vyva~E 45 (73)
||||+|||||||+|.|++ +++.+|||||||++||++||++|
T Consensus 2 kDPW~RneaWRy~~~f~~~~~~~~~~fpG~~~G~aaf~~~v~~E 45 (57)
T PF08122_consen 2 KDPWARNEAWRYHPQFSRWNSFFKNMFPGFGIGFAAFAVYVAVE 45 (57)
T ss_pred CChHhhhHHHhCCcccCchHHHHHHhcCCcHHHHHHHHHHHHHH
Confidence 799999999999999974 56899999999999999999999
No 2
>KOG4631 consensus NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion]
Probab=99.73 E-value=2.6e-18 Score=114.06 Aligned_cols=58 Identities=16% Similarity=0.194 Sum_probs=45.8
Q ss_pred CcCCCcchhhhhcCC--Ccc--chhhh-ccCChhHHHHHHHHHHHHHHHHhhhcCC-CCCCCCC
Q 041595 4 TGEFFRRRDGWRKHP--LLT--SNLRQ-ATPGLGIALVAFGIYLVGEQVYNRVIAP-SPSHSHH 61 (73)
Q Consensus 4 ~~DPW~R~EaWRy~p--~f~--~~~~~-~~PGlgig~~AF~vyva~E~~~~~~~~p-~~~~~hh 61 (73)
-||||.|||+|||.+ .++ .+|+. +||||++||+||++.|++|+++...... .+|++||
T Consensus 37 LkDPW~RNevwrY~~ph~~~~~~~f~~~~f~G~k~Gfaaf~a~v~vEyal~~~~Hgtt~dkgHH 100 (100)
T KOG4631|consen 37 LKDPWGRNEVWRYMGPHGFAKSVSFSDVFFKGFKWGFAAFVAAVGVEYALESLNHGTTKDKGHH 100 (100)
T ss_pred ccCchhcchhhhccCcccceeeeeehhhhcccchHHHHHHHHHHHHHHHHHhcccCccCCcCCC
Confidence 389999999999999 454 35655 9999999999999999999999843211 1556655
No 3
>PF06724 DUF1206: Domain of Unknown Function (DUF1206); InterPro: IPR009597 This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.
Probab=65.52 E-value=9.2 Score=22.76 Aligned_cols=24 Identities=29% Similarity=0.684 Sum_probs=19.4
Q ss_pred cCChhHHHHHHHHHHHHHHHHhhh
Q 041595 28 TPGLGIALVAFGIYLVGEQVYNRV 51 (73)
Q Consensus 28 ~PGlgig~~AF~vyva~E~~~~~~ 51 (73)
+=-.+++++++++|..++-++.+|
T Consensus 50 l~~vg~gli~~gi~~~~~a~~~~f 73 (73)
T PF06724_consen 50 LGAVGLGLIGYGIWQFVKAVYRRF 73 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhC
Confidence 334789999999999999888653
No 4
>PTZ00451 dephospho-CoA kinase; Provisional
Probab=58.46 E-value=8.9 Score=28.26 Aligned_cols=30 Identities=7% Similarity=-0.091 Sum_probs=23.8
Q ss_pred CCCccchhhhccCChhHHHHHHHHHHHHHH
Q 041595 17 HPLLTSNLRQATPGLGIALVAFGIYLVGEQ 46 (73)
Q Consensus 17 ~p~f~~~~~~~~PGlgig~~AF~vyva~E~ 46 (73)
.|...+.+-..||-+|...+++++||.+--
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (244)
T PTZ00451 212 SNKRLTYIFGTVAAAAVGVAAAVGYVGYRL 241 (244)
T ss_pred CChHHHHHHHHCChHHHHHHHHHHHHhhhc
Confidence 344445667799999999999999998753
No 5
>PRK12657 putative monovalent cation/H+ antiporter subunit F; Reviewed
Probab=53.97 E-value=30 Score=22.76 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHHHHHHHHhhhcCCCCCCCCC
Q 041595 31 LGIALVAFGIYLVGEQVYNRVIAPSPSHSHH 61 (73)
Q Consensus 31 lgig~~AF~vyva~E~~~~~~~~p~~~~~hh 61 (73)
+-+|+.+|+..+++-+++++ ..+.++++++
T Consensus 69 LvlAll~Fv~tva~ARyl~~-g~~~~~~~~~ 98 (100)
T PRK12657 69 MLIAIISFVSSVSISRFIGG-GHVFNGNNKR 98 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCccCCCcC
Confidence 45788999999999999986 3444444444
No 6
>PF06219 DUF1005: Protein of unknown function (DUF1005); InterPro: IPR010410 This is a family of plant proteins with undetermined function.
Probab=53.16 E-value=5.5 Score=32.84 Aligned_cols=27 Identities=15% Similarity=0.246 Sum_probs=19.0
Q ss_pred CcCCCcchhhhhcCCCcc---chhhhccCC
Q 041595 4 TGEFFRRRDGWRKHPLLT---SNLRQATPG 30 (73)
Q Consensus 4 ~~DPW~R~EaWRy~p~f~---~~~~~~~PG 30 (73)
+=.||.|-||||-.+... -+|.-+..+
T Consensus 295 sWkPWGRLEAWRErg~~d~lgyrfeL~~~~ 324 (460)
T PF06219_consen 295 SWKPWGRLEAWRERGGSDGLGYRFELLPDG 324 (460)
T ss_pred CcccchhhhhhhccCCCCcceeEEEEccCC
Confidence 446999999999998533 355555555
No 7
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=48.39 E-value=9.1 Score=25.73 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=17.3
Q ss_pred chhhhccCChhHHHHHHHHH
Q 041595 22 SNLRQATPGLGIALVAFGIY 41 (73)
Q Consensus 22 ~~~~~~~PGlgig~~AF~vy 41 (73)
.|.+++.-||+|+..++++|
T Consensus 47 ~R~rN~~Tgl~L~~~v~gIY 66 (100)
T PF09813_consen 47 RRRRNLLTGLALGAFVVGIY 66 (100)
T ss_pred HhhhhHHHHHHHHHHHHHHH
Confidence 36788999999999999888
No 8
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=48.16 E-value=6 Score=26.83 Aligned_cols=14 Identities=36% Similarity=0.375 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHH
Q 041595 31 LGIALVAFGIYLVG 44 (73)
Q Consensus 31 lgig~~AF~vyva~ 44 (73)
.|++.++|++||+|
T Consensus 3 ag~a~~~~lgYciY 16 (121)
T PF02064_consen 3 AGVAAAAFLGYCIY 16 (121)
T ss_dssp --------------
T ss_pred HHHHHHHHHHHHhh
Confidence 46788999999995
No 9
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=47.06 E-value=16 Score=25.67 Aligned_cols=14 Identities=43% Similarity=0.403 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHHH
Q 041595 31 LGIALVAFGIYLVG 44 (73)
Q Consensus 31 lgig~~AF~vyva~ 44 (73)
.|++.++|++||+|
T Consensus 13 ag~a~~~flgYciY 26 (148)
T TIGR00985 13 AGIAAAAFLGYAIY 26 (148)
T ss_pred HHHHHHHHHHHHHh
Confidence 45667888889985
No 10
>PRK12600 putative monovalent cation/H+ antiporter subunit F; Reviewed
Probab=37.23 E-value=80 Score=20.38 Aligned_cols=20 Identities=20% Similarity=0.095 Sum_probs=17.3
Q ss_pred hhHHHHHHHHHHHHHHHHhh
Q 041595 31 LGIALVAFGIYLVGEQVYNR 50 (73)
Q Consensus 31 lgig~~AF~vyva~E~~~~~ 50 (73)
+-+|+.+|+..+++-++.++
T Consensus 65 lvlAll~Fv~tva~Aryl~~ 84 (94)
T PRK12600 65 LLIGILAFIGTAAFSKFIEK 84 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 55788999999999999875
No 11
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=36.60 E-value=31 Score=23.99 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=18.3
Q ss_pred hhhhccCChhHHHHHHHHHHHHH
Q 041595 23 NLRQATPGLGIALVAFGIYLVGE 45 (73)
Q Consensus 23 ~~~~~~PGlgig~~AF~vyva~E 45 (73)
.+..+.|=-+||+++|.+|.-+-
T Consensus 81 ~~~~imPlYtiGI~~f~lY~l~K 103 (152)
T PF15361_consen 81 LMGQIMPLYTIGIVLFILYTLFK 103 (152)
T ss_pred hhhhHhHHHHHHHHHHHHHHHHH
Confidence 35567777899999999998754
No 12
>PRK10930 FtsH protease regulator HflK; Provisional
Probab=31.07 E-value=59 Score=26.03 Aligned_cols=7 Identities=0% Similarity=0.017 Sum_probs=5.4
Q ss_pred CcCCCcc
Q 041595 4 TGEFFRR 10 (73)
Q Consensus 4 ~~DPW~R 10 (73)
.+|||.+
T Consensus 12 ~~~pw~~ 18 (419)
T PRK10930 12 DRDPWGS 18 (419)
T ss_pred CCCCCCC
Confidence 4799985
No 13
>PF06849 DUF1246: Protein of unknown function (DUF1246); InterPro: IPR010672 The last two steps of de novo purine biosynthesis are: i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR) ii) conversion of FAICAR to inosine5'-monophopsphate (IMP) In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH []. Archaea do not appear to posses PurH, however, and perform these reactions by a different mecahnism []. In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species [, ]. This entry represents the N-terminal domain of PurP. Its function is not known, though it is almost always found in association with IPR009720 from INTERPRO.; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0006188 IMP biosynthetic process; PDB: 2PBZ_C 2R85_B 2R87_E 2R84_A 2R86_A 2R7L_A 2R7N_A 2R7K_A 2R7M_A.
Probab=30.34 E-value=43 Score=23.17 Aligned_cols=17 Identities=18% Similarity=0.198 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHhhh
Q 041595 35 LVAFGIYLVGEQVYNRV 51 (73)
Q Consensus 35 ~~AF~vyva~E~~~~~~ 51 (73)
=..|++||++|.+-+.+
T Consensus 72 hgSfv~Y~G~d~ie~~~ 88 (124)
T PF06849_consen 72 HGSFVAYVGYDRIENEF 88 (124)
T ss_dssp BTTHHHHH-HHHHHHT-
T ss_pred CCCeeEeecHHHHhhcC
Confidence 36799999999987644
No 14
>KOG4056 consensus Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.22 E-value=41 Score=23.94 Aligned_cols=13 Identities=46% Similarity=0.416 Sum_probs=9.2
Q ss_pred hHHHHHHHHHHHH
Q 041595 32 GIALVAFGIYLVG 44 (73)
Q Consensus 32 gig~~AF~vyva~ 44 (73)
||+..||++||.|
T Consensus 16 giag~af~gYciY 28 (143)
T KOG4056|consen 16 GIAGLAFIGYCIY 28 (143)
T ss_pred HHHHHHHHHHHhh
Confidence 5666778888775
No 15
>PF06716 DUF1201: Protein of unknown function (DUF1201); InterPro: IPR009591 This entry consists of several Beet yellows virus (BYV) putative membrane-binding proteins of around 54 residues in length. The function of this currently unknown.
Probab=29.71 E-value=95 Score=18.69 Aligned_cols=14 Identities=29% Similarity=0.176 Sum_probs=7.5
Q ss_pred HHHHHHHhhhcCCC
Q 041595 42 LVGEQVYNRVIAPS 55 (73)
Q Consensus 42 va~E~~~~~~~~p~ 55 (73)
..+.|++-+-.+|+
T Consensus 30 F~~Kqilfr~~~~s 43 (54)
T PF06716_consen 30 FVYKQILFRNNPQS 43 (54)
T ss_pred HHHHHHHHccCCCc
Confidence 34556665544554
No 16
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=28.45 E-value=31 Score=19.60 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=6.2
Q ss_pred CcCCCcchh
Q 041595 4 TGEFFRRRD 12 (73)
Q Consensus 4 ~~DPW~R~E 12 (73)
.+|||.+++
T Consensus 10 ~~dPWg~~~ 18 (42)
T PF12221_consen 10 DQDPWGRNQ 18 (42)
T ss_pred CCCCCCCCC
Confidence 578996643
No 17
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=27.35 E-value=34 Score=20.83 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=13.5
Q ss_pred hhhccCChhHHHHHHHHHHH
Q 041595 24 LRQATPGLGIALVAFGIYLV 43 (73)
Q Consensus 24 ~~~~~PGlgig~~AF~vyva 43 (73)
-|.++.|+|+|.++.++..+
T Consensus 11 RR~Flk~lg~~aaa~~aa~~ 30 (66)
T TIGR02811 11 RRDLLKGLGVGAAAGAVAAA 30 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 45688888887765555433
No 18
>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=26.99 E-value=98 Score=17.85 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCC
Q 041595 33 IALVAFGIYLVGEQVYNRVIAPSP 56 (73)
Q Consensus 33 ig~~AF~vyva~E~~~~~~~~p~~ 56 (73)
|.+.++++-+..=.+|..+.+|++
T Consensus 9 i~i~~~lv~~Tgy~iYtaFGppSk 32 (43)
T PF02468_consen 9 IFISCLLVSITGYAIYTAFGPPSK 32 (43)
T ss_pred HHHHHHHHHHHhhhhhheeCCCcc
Confidence 333334444444344555556664
No 19
>PF05661 DUF808: Protein of unknown function (DUF808); InterPro: IPR008526 This family consists of several bacterial proteins of unknown function.
Probab=25.52 E-value=80 Score=24.80 Aligned_cols=20 Identities=15% Similarity=0.235 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHhhhcCCC
Q 041595 36 VAFGIYLVGEQVYNRVIAPS 55 (73)
Q Consensus 36 ~AF~vyva~E~~~~~~~~p~ 55 (73)
++|..|=++||+++++.+.+
T Consensus 95 G~yLcfEGaEKv~~~~~~~~ 114 (295)
T PF05661_consen 95 GAYLCFEGAEKVWHKFFHHK 114 (295)
T ss_pred HHHHHHhHHHHHHHHHcCCc
Confidence 68888999999999975544
No 20
>TIGR03008 pepcterm_CAAX CAAX prenyl protease-related protein. The CAAX prenyl protease, in eukaryotes, catalyzes three covalent modifications, including cleavage and acylation, at the C-terminus of certain proteins in a process connected to protein sorting. This family describes a bacterial protein family homologous to one domain of the CAAX-processing enzyme. Members of this protein family are found in genomes that carry a predicted protein sorting system, PEP-CTERM/exosortase, usually in the vicinity of the EpsH homolog that is the hallmark of the system. The function of this protein is unknown, but it may relate to protein motification.
Probab=24.96 E-value=84 Score=23.05 Aligned_cols=32 Identities=9% Similarity=0.086 Sum_probs=25.9
Q ss_pred hhhhccCChhHHHHHHHHHHHHHHHHhhhcCC
Q 041595 23 NLRQATPGLGIALVAFGIYLVGEQVYNRVIAP 54 (73)
Q Consensus 23 ~~~~~~PGlgig~~AF~vyva~E~~~~~~~~p 54 (73)
+.+...-|+.+|++.|++.+..+........|
T Consensus 66 ~~~~~l~gi~~Gv~~f~lwi~~~~~~~~~~~~ 97 (222)
T TIGR03008 66 RPRHLLFSAAVGVAVFVLWVNLDWLLPFQGEP 97 (222)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 35678889999999999999999887665444
No 21
>PF01220 DHquinase_II: Dehydroquinase class II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales [, ] and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity; PDB: 3N8K_J 3N7A_I 3N87_F 3N8N_H 3N86_N 1H0S_A 3N59_J 1H05_A 1H0R_A 2Y71_A ....
Probab=23.89 E-value=25 Score=24.58 Aligned_cols=27 Identities=19% Similarity=0.464 Sum_probs=16.1
Q ss_pred CCCcchhhhhcCCCccchhhhccCChhH
Q 041595 6 EFFRRRDGWRKHPLLTSNLRQATPGLGI 33 (73)
Q Consensus 6 DPW~R~EaWRy~p~f~~~~~~~~PGlgi 33 (73)
++++| |.+|.+..++.--....-|||.
T Consensus 102 Ni~~R-E~fR~~S~~s~~~~g~I~G~G~ 128 (140)
T PF01220_consen 102 NIHAR-EEFRHHSVISPVAVGVISGFGA 128 (140)
T ss_dssp -GGGS--GGGG--SSGGGSSEEEESSTT
T ss_pred Ccccc-cccccccccccccEEEEEeCCH
Confidence 45555 9999999887655666667764
No 22
>PF04839 PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65); InterPro: IPR006924 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome, 0009536 plastid; PDB: 2KT9_A.
Probab=23.51 E-value=22 Score=21.14 Aligned_cols=13 Identities=31% Similarity=0.721 Sum_probs=8.4
Q ss_pred CcCCCcchhhhhc
Q 041595 4 TGEFFRRRDGWRK 16 (73)
Q Consensus 4 ~~DPW~R~EaWRy 16 (73)
..-+|.|.|||.-
T Consensus 3 ~yfFWPr~DAWe~ 15 (49)
T PF04839_consen 3 EYFFWPREDAWEQ 15 (49)
T ss_dssp --EEETTS-HHHH
T ss_pred CcccCCCCcHHHH
Confidence 3458999999964
No 23
>cd05311 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydroph
Probab=23.30 E-value=43 Score=23.97 Aligned_cols=17 Identities=12% Similarity=0.256 Sum_probs=12.8
Q ss_pred chhhh--ccCChhHHHHHH
Q 041595 22 SNLRQ--ATPGLGIALVAF 38 (73)
Q Consensus 22 ~~~~~--~~PGlgig~~AF 38 (73)
++-.+ .|||+|.|..+-
T Consensus 156 ~Q~nn~~~fPg~~~g~~~~ 174 (226)
T cd05311 156 NQVNNVLGFPGIFRGALDV 174 (226)
T ss_pred cccceeeecchhhHHHHHc
Confidence 34444 899999999864
No 24
>PF01691 Adeno_E1B_19K: Adenovirus E1B 19K protein / small t-antigen The Prosite family contains members not in the Pfam family.; InterPro: IPR002924 This family consists of adenovirus E1B 19 kDa protein or small t-antigen. The E1B 19 kDa protein inhibits E1A induced apoptosis and hence prolongs the viability of the host cell []. It can also inhibit apoptosis mediated by tumour necrosis factor alpha and Fas antigen []. E1B 19 kDa blocks apoptosis by interacting with and inhibiting the p53-inducible and death-promoting Bax protein []. The E1B region of adenovirus encodes two proteins E1B 19 kDa the small t-antigen as found in this family and E1B 55 kDa the large t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis [].; GO: 0005521 lamin binding, 0006916 anti-apoptosis
Probab=22.32 E-value=78 Score=22.02 Aligned_cols=19 Identities=32% Similarity=0.522 Sum_probs=16.2
Q ss_pred hhccCChhHHHHHHHHHHH
Q 041595 25 RQATPGLGIALVAFGIYLV 43 (73)
Q Consensus 25 ~~~~PGlgig~~AF~vyva 43 (73)
.--+||=.+|.+||++||.
T Consensus 82 DfStpGR~vA~lAFl~fil 100 (134)
T PF01691_consen 82 DFSTPGRTVASLAFLSFIL 100 (134)
T ss_pred cCCCCchHHHHHHHHHHHH
Confidence 3468999999999999985
No 25
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=21.36 E-value=50 Score=20.54 Aligned_cols=9 Identities=56% Similarity=1.143 Sum_probs=7.2
Q ss_pred hhccCChhH
Q 041595 25 RQATPGLGI 33 (73)
Q Consensus 25 ~~~~PGlgi 33 (73)
-+++||||.
T Consensus 32 E~~LPGLGV 40 (65)
T PF14098_consen 32 EKALPGLGV 40 (65)
T ss_pred hhcCCchHH
Confidence 368999994
No 26
>CHL00163 ycf65 putative ribosomal protein 3; Validated
Probab=21.34 E-value=36 Score=22.83 Aligned_cols=14 Identities=29% Similarity=0.563 Sum_probs=11.1
Q ss_pred CcCCCcchhhhhcC
Q 041595 4 TGEFFRRRDGWRKH 17 (73)
Q Consensus 4 ~~DPW~R~EaWRy~ 17 (73)
+.-+|.|.|||.--
T Consensus 32 ~yfFWPr~DAWe~L 45 (99)
T CHL00163 32 SYFFWPRTDAWELL 45 (99)
T ss_pred ceeecCCccHHHHH
Confidence 45689999999754
No 27
>COG2354 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.20 E-value=63 Score=25.52 Aligned_cols=37 Identities=19% Similarity=0.248 Sum_probs=25.2
Q ss_pred ccCChhHHHHHHHHHHHHHHHHhhhcCCCCCCCCCccc
Q 041595 27 ATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHSHHTHH 64 (73)
Q Consensus 27 ~~PGlgig~~AF~vyva~E~~~~~~~~p~~~~~hh~~~ 64 (73)
++|=|.+| ++|..+=++||++.++.++++.+.|++-.
T Consensus 87 itPLLmlG-G~yLcFEG~EKvl~~~~~~~~~~~~~~~~ 123 (303)
T COG2354 87 ITPLLMLG-GAYLCFEGAEKVLHKFLHRKHGEDHEARP 123 (303)
T ss_pred HHHHHHhc-chhhhhccHHHHHHHhcCCccccChhhhh
Confidence 34444444 67888889999999987776666555543
No 28
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=20.97 E-value=84 Score=17.43 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=9.1
Q ss_pred ChhHHHHHHHHH
Q 041595 30 GLGIALVAFGIY 41 (73)
Q Consensus 30 Glgig~~AF~vy 41 (73)
||.|++++|...
T Consensus 7 GFPi~va~yLL~ 18 (38)
T PF12841_consen 7 GFPIAVAIYLLV 18 (38)
T ss_pred CcHHHHHHHHHH
Confidence 888888877653
No 29
>COG3162 Predicted membrane protein [Function unknown]
Probab=20.92 E-value=1.7e+02 Score=19.79 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=22.4
Q ss_pred hccCChhHHHHHHHHHHHHHHHHhhh
Q 041595 26 QATPGLGIALVAFGIYLVGEQVYNRV 51 (73)
Q Consensus 26 ~~~PGlgig~~AF~vyva~E~~~~~~ 51 (73)
..+.|+-+|++.|+...++-.+|-+.
T Consensus 59 ~Vt~Gip~gvg~fv~tfVlt~IYv~r 84 (102)
T COG3162 59 SVTRGIPFGVGVFVMTFVLTGIYVRR 84 (102)
T ss_pred ceehhHhHHHHHHHHHHHHHHHHhhH
Confidence 48899999999999999988888664
No 30
>PRK02724 hypothetical protein; Provisional
Probab=20.41 E-value=39 Score=22.91 Aligned_cols=14 Identities=29% Similarity=0.638 Sum_probs=11.1
Q ss_pred CcCCCcchhhhhcC
Q 041595 4 TGEFFRRRDGWRKH 17 (73)
Q Consensus 4 ~~DPW~R~EaWRy~ 17 (73)
+.-+|.|+|||.--
T Consensus 37 ~yfFWPr~DAWe~L 50 (104)
T PRK02724 37 AYFFWPRNDAWEQL 50 (104)
T ss_pred ceeecCCccHHHHH
Confidence 45689999999754
No 31
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=20.35 E-value=84 Score=18.45 Aligned_cols=18 Identities=28% Similarity=0.331 Sum_probs=9.0
Q ss_pred HHHHHHHHHHhhhcCCCC
Q 041595 39 GIYLVGEQVYNRVIAPSP 56 (73)
Q Consensus 39 ~vyva~E~~~~~~~~p~~ 56 (73)
++-+..=.+|..|.+|++
T Consensus 18 L~~~TgyaiYtaFGppSk 35 (46)
T PRK13183 18 LLALTGFGIYTAFGPPSK 35 (46)
T ss_pred HHHHhhheeeeccCCccc
Confidence 333333345555667764
Done!