Query 035119
Match_columns 73
No_of_seqs 102 out of 135
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:22:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035119hhsearch_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 5.3E-26 1.2E-30 136.9 4.5 41 5-45 2-45 (57)
2 KOG4631 NADH:ubiquinone oxidor 99.7 2.1E-18 4.5E-23 114.4 4.6 58 4-61 37-100 (100)
3 PF06724 DUF1206: Domain of Un 63.4 11 0.00023 22.4 2.9 24 27-50 49-72 (73)
4 PTZ00451 dephospho-CoA kinase; 61.0 7.9 0.00017 28.5 2.4 29 17-45 212-240 (244)
5 PRK12657 putative monovalent c 56.7 26 0.00056 23.0 4.0 30 31-61 69-98 (100)
6 PF09813 Coiled-coil_56: Coile 51.0 8.8 0.00019 25.8 1.2 20 22-41 47-66 (100)
7 PF06219 DUF1005: Protein of u 50.3 6.5 0.00014 32.4 0.5 27 4-30 295-324 (460)
8 PF02064 MAS20: MAS20 protein 48.4 5.9 0.00013 26.8 0.0 14 31-44 3-16 (121)
9 TIGR00985 3a0801s04tom mitocho 47.5 16 0.00034 25.7 2.0 14 31-44 13-26 (148)
10 PRK12600 putative monovalent c 43.5 57 0.0012 21.0 4.1 20 31-50 65-84 (94)
11 PF15361 RIC3: Resistance to i 36.0 32 0.0007 23.9 2.1 23 23-45 81-103 (152)
12 PF12221 HflK_N: Bacterial mem 35.1 19 0.00042 20.4 0.8 9 4-12 10-18 (42)
13 PRK10930 FtsH protease regulat 31.5 59 0.0013 26.0 3.2 7 4-10 12-18 (419)
14 PF05661 DUF808: Protein of un 31.3 56 0.0012 25.6 3.0 20 36-55 95-114 (295)
15 PF06849 DUF1246: Protein of u 30.8 43 0.00092 23.2 2.0 17 35-51 72-88 (124)
16 KOG4056 Translocase of outer m 29.7 42 0.00091 23.8 1.9 13 32-44 16-28 (143)
17 TIGR03008 pepcterm_CAAX CAAX p 29.1 69 0.0015 23.5 3.0 32 23-54 66-97 (222)
18 TIGR02811 formate_TAT formate 28.2 35 0.00075 20.8 1.1 21 23-43 10-30 (66)
19 PF04839 PSRP-3_Ycf65: Plastid 24.8 22 0.00047 21.2 -0.2 12 5-16 4-15 (49)
20 PF02468 PsbN: Photosystem II 23.5 1.2E+02 0.0027 17.4 2.8 23 34-56 10-32 (43)
21 cd05311 NAD_bind_2_malic_enz N 22.8 43 0.00093 24.0 1.0 17 22-38 156-174 (226)
22 PF01691 Adeno_E1B_19K: Adenov 21.8 81 0.0018 21.9 2.1 18 26-43 83-100 (134)
23 COG4062 MtrB Tetrahydromethano 20.4 80 0.0017 21.5 1.8 24 23-46 76-102 (108)
24 PF01220 DHquinase_II: Dehydro 20.4 31 0.00068 24.1 -0.2 27 6-33 102-128 (140)
25 PF14098 SSPI: Small, acid-sol 20.0 55 0.0012 20.3 0.9 9 25-33 32-40 (65)
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=99.92 E-value=5.3e-26 Score=136.87 Aligned_cols=41 Identities=32% Similarity=0.755 Sum_probs=38.7
Q ss_pred cCCCcchhhhhcCCCccc---hhhhhcCchhHHHHHHHHHHHHH
Q 035119 5 GEFFRRRDGWRKHPLLTS---NLRQATPGLGIALVAFGIYLVGE 45 (73)
Q Consensus 5 ~DPW~R~EaWRy~p~f~~---~~~~~fPGlgig~~AF~vyv~~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 899999999999999973 56889999999999999999999
No 2
>KOG4631 consensus NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion]
Probab=99.74 E-value=2.1e-18 Score=114.39 Aligned_cols=58 Identities=16% Similarity=0.194 Sum_probs=46.2
Q ss_pred CcCCCcchhhhhcCC--Ccc--chhhh-hcCchhHHHHHHHHHHHHHHHHhhhcCC-CCCCCCC
Q 035119 4 TGEFFRRRDGWRKHP--LLT--SNLRQ-ATPGLGIALVAFGIYLVGEQVYNRVIAP-SPSHSHH 61 (73)
Q Consensus 4 ~~DPW~R~EaWRy~p--~f~--~~~~~-~fPGlgig~~AF~vyv~~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 45665 9999999999999999999999853211 1556665
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=63.44 E-value=11 Score=22.44 Aligned_cols=24 Identities=29% Similarity=0.666 Sum_probs=19.5
Q ss_pred hcCchhHHHHHHHHHHHHHHHHhh
Q 035119 27 ATPGLGIALVAFGIYLVGEQVYNR 50 (73)
Q Consensus 27 ~fPGlgig~~AF~vyv~~E~~~~~ 50 (73)
++=-.+++++++++|..++-++.+
T Consensus 49 ll~~vg~gli~~gi~~~~~a~~~~ 72 (73)
T PF06724_consen 49 LLGAVGLGLIGYGIWQFVKAVYRR 72 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334478999999999999988865
No 4
>PTZ00451 dephospho-CoA kinase; Provisional
Probab=60.97 E-value=7.9 Score=28.53 Aligned_cols=29 Identities=7% Similarity=-0.075 Sum_probs=23.5
Q ss_pred CCCccchhhhhcCchhHHHHHHHHHHHHH
Q 035119 17 HPLLTSNLRQATPGLGIALVAFGIYLVGE 45 (73)
Q Consensus 17 ~p~f~~~~~~~fPGlgig~~AF~vyv~~E 45 (73)
.|...+.+-..||-+|...+++++||.+-
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (244)
T PTZ00451 212 SNKRLTYIFGTVAAAAVGVAAAVGYVGYR 240 (244)
T ss_pred CChHHHHHHHHCChHHHHHHHHHHHHhhh
Confidence 34444566779999999999999999875
No 5
>PRK12657 putative monovalent cation/H+ antiporter subunit F; Reviewed
Probab=56.72 E-value=26 Score=23.03 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=22.1
Q ss_pred hhHHHHHHHHHHHHHHHHhhhcCCCCCCCCC
Q 035119 31 LGIALVAFGIYLVGEQVYNRVIAPSPSHSHH 61 (73)
Q Consensus 31 lgig~~AF~vyv~~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
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=50.99 E-value=8.8 Score=25.77 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=17.3
Q ss_pred chhhhhcCchhHHHHHHHHH
Q 035119 22 SNLRQATPGLGIALVAFGIY 41 (73)
Q Consensus 22 ~~~~~~fPGlgig~~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 7
>PF06219 DUF1005: Protein of unknown function (DUF1005); InterPro: IPR010410 This is a family of plant proteins with undetermined function.
Probab=50.31 E-value=6.5 Score=32.39 Aligned_cols=27 Identities=15% Similarity=0.246 Sum_probs=19.0
Q ss_pred CcCCCcchhhhhcCCCcc---chhhhhcCc
Q 035119 4 TGEFFRRRDGWRKHPLLT---SNLRQATPG 30 (73)
Q Consensus 4 ~~DPW~R~EaWRy~p~f~---~~~~~~fPG 30 (73)
+=.||.|-||||-.+... -||.-+..+
T Consensus 295 sWkPWGRLEAWRErg~~d~lgyrfeL~~~~ 324 (460)
T PF06219_consen 295 SWKPWGRLEAWRERGGSDGLGYRFELLPDG 324 (460)
T ss_pred CcccchhhhhhhccCCCCcceeEEEEccCC
Confidence 446999999999998533 355555554
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=48.40 E-value=5.9 Score=26.84 Aligned_cols=14 Identities=36% Similarity=0.375 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHH
Q 035119 31 LGIALVAFGIYLVG 44 (73)
Q Consensus 31 lgig~~AF~vyv~~ 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=47.52 E-value=16 Score=25.70 Aligned_cols=14 Identities=43% Similarity=0.403 Sum_probs=10.8
Q ss_pred hhHHHHHHHHHHHH
Q 035119 31 LGIALVAFGIYLVG 44 (73)
Q Consensus 31 lgig~~AF~vyv~~ 44 (73)
.|++.++|++||+|
T Consensus 13 ag~a~~~flgYciY 26 (148)
T TIGR00985 13 AGIAAAAFLGYAIY 26 (148)
T ss_pred HHHHHHHHHHHHHh
Confidence 46677889999985
No 10
>PRK12600 putative monovalent cation/H+ antiporter subunit F; Reviewed
Probab=43.52 E-value=57 Score=21.04 Aligned_cols=20 Identities=20% Similarity=0.095 Sum_probs=17.3
Q ss_pred hhHHHHHHHHHHHHHHHHhh
Q 035119 31 LGIALVAFGIYLVGEQVYNR 50 (73)
Q Consensus 31 lgig~~AF~vyv~~E~~~~~ 50 (73)
+-+|+.+|+..+++-++.++
T Consensus 65 lvlAll~Fv~tva~Aryl~~ 84 (94)
T PRK12600 65 LLIGILAFIGTAAFSKFIEK 84 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56788999999999999876
No 11
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=35.97 E-value=32 Score=23.89 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=18.2
Q ss_pred hhhhhcCchhHHHHHHHHHHHHH
Q 035119 23 NLRQATPGLGIALVAFGIYLVGE 45 (73)
Q Consensus 23 ~~~~~fPGlgig~~AF~vyv~~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
>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=35.07 E-value=19 Score=20.39 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=6.2
Q ss_pred CcCCCcchh
Q 035119 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 13
>PRK10930 FtsH protease regulator HflK; Provisional
Probab=31.48 E-value=59 Score=26.04 Aligned_cols=7 Identities=0% Similarity=0.017 Sum_probs=5.4
Q ss_pred CcCCCcc
Q 035119 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 14
>PF05661 DUF808: Protein of unknown function (DUF808); InterPro: IPR008526 This family consists of several bacterial proteins of unknown function.
Probab=31.32 E-value=56 Score=25.63 Aligned_cols=20 Identities=15% Similarity=0.235 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHhhhcCCC
Q 035119 36 VAFGIYLVGEQVYNRVIAPS 55 (73)
Q Consensus 36 ~AF~vyv~~E~~~~~~~~p~ 55 (73)
++|..|=++||++.++.+.+
T Consensus 95 G~yLcfEGaEKv~~~~~~~~ 114 (295)
T PF05661_consen 95 GAYLCFEGAEKVWHKFFHHK 114 (295)
T ss_pred HHHHHHhHHHHHHHHHcCCc
Confidence 68889999999999975544
No 15
>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=30.79 E-value=43 Score=23.17 Aligned_cols=17 Identities=18% Similarity=0.198 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHhhh
Q 035119 35 LVAFGIYLVGEQVYNRV 51 (73)
Q Consensus 35 ~~AF~vyv~~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 16
>KOG4056 consensus Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.66 E-value=42 Score=23.83 Aligned_cols=13 Identities=46% Similarity=0.416 Sum_probs=9.4
Q ss_pred hHHHHHHHHHHHH
Q 035119 32 GIALVAFGIYLVG 44 (73)
Q Consensus 32 gig~~AF~vyv~~ 44 (73)
||+..||++||.|
T Consensus 16 giag~af~gYciY 28 (143)
T KOG4056|consen 16 GIAGLAFIGYCIY 28 (143)
T ss_pred HHHHHHHHHHHhh
Confidence 5667778888875
No 17
>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=29.06 E-value=69 Score=23.48 Aligned_cols=32 Identities=9% Similarity=0.086 Sum_probs=26.2
Q ss_pred hhhhhcCchhHHHHHHHHHHHHHHHHhhhcCC
Q 035119 23 NLRQATPGLGIALVAFGIYLVGEQVYNRVIAP 54 (73)
Q Consensus 23 ~~~~~fPGlgig~~AF~vyv~~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 45678889999999999999999887765444
No 18
>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=28.23 E-value=35 Score=20.78 Aligned_cols=21 Identities=24% Similarity=0.294 Sum_probs=14.2
Q ss_pred hhhhhcCchhHHHHHHHHHHH
Q 035119 23 NLRQATPGLGIALVAFGIYLV 43 (73)
Q Consensus 23 ~~~~~fPGlgig~~AF~vyv~ 43 (73)
.-|.++.|+|+|.++-++..+
T Consensus 10 sRR~Flk~lg~~aaa~~aa~~ 30 (66)
T TIGR02811 10 SRRDLLKGLGVGAAAGAVAAA 30 (66)
T ss_pred cHHHHHHHHHHHHHHHHHHHh
Confidence 346688899987776555433
No 19
>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=24.80 E-value=22 Score=21.17 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=8.3
Q ss_pred cCCCcchhhhhc
Q 035119 5 GEFFRRRDGWRK 16 (73)
Q Consensus 5 ~DPW~R~EaWRy 16 (73)
--+|.|.|||.-
T Consensus 4 yfFWPr~DAWe~ 15 (49)
T PF04839_consen 4 YFFWPREDAWEQ 15 (49)
T ss_dssp -EEETTS-HHHH
T ss_pred cccCCCCcHHHH
Confidence 457999999964
No 20
>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=23.46 E-value=1.2e+02 Score=17.41 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCC
Q 035119 34 ALVAFGIYLVGEQVYNRVIAPSP 56 (73)
Q Consensus 34 g~~AF~vyv~~E~~~~~~~~p~~ 56 (73)
.+.++++-+..=-+|.-+.+|++
T Consensus 10 ~i~~~lv~~Tgy~iYtaFGppSk 32 (43)
T PF02468_consen 10 FISCLLVSITGYAIYTAFGPPSK 32 (43)
T ss_pred HHHHHHHHHHhhhhhheeCCCcc
Confidence 33333333333334444556664
No 21
>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=22.83 E-value=43 Score=23.96 Aligned_cols=17 Identities=12% Similarity=0.256 Sum_probs=12.9
Q ss_pred chhhh--hcCchhHHHHHH
Q 035119 22 SNLRQ--ATPGLGIALVAF 38 (73)
Q Consensus 22 ~~~~~--~fPGlgig~~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 22
>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=21.81 E-value=81 Score=21.92 Aligned_cols=18 Identities=33% Similarity=0.556 Sum_probs=15.7
Q ss_pred hhcCchhHHHHHHHHHHH
Q 035119 26 QATPGLGIALVAFGIYLV 43 (73)
Q Consensus 26 ~~fPGlgig~~AF~vyv~ 43 (73)
--+||=.+|.+||++||.
T Consensus 83 fStpGR~vA~lAFl~fil 100 (134)
T PF01691_consen 83 FSTPGRTVASLAFLSFIL 100 (134)
T ss_pred CCCCchHHHHHHHHHHHH
Confidence 368999999999999984
No 23
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=20.36 E-value=80 Score=21.50 Aligned_cols=24 Identities=25% Similarity=0.142 Sum_probs=12.8
Q ss_pred hhhhhcCchhHHHH---HHHHHHHHHH
Q 035119 23 NLRQATPGLGIALV---AFGIYLVGEQ 46 (73)
Q Consensus 23 ~~~~~fPGlgig~~---AF~vyv~~E~ 46 (73)
.++++|=||=||++ +++..+++.+
T Consensus 76 ~~tna~yGfviGl~i~aLlAlil~~~~ 102 (108)
T COG4062 76 YLTNAFYGFVIGLGIMALLALILGVKF 102 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666665554 2444444443
No 24
>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=20.35 E-value=31 Score=24.11 Aligned_cols=27 Identities=19% Similarity=0.464 Sum_probs=15.5
Q ss_pred CCCcchhhhhcCCCccchhhhhcCchhH
Q 035119 6 EFFRRRDGWRKHPLLTSNLRQATPGLGI 33 (73)
Q Consensus 6 DPW~R~EaWRy~p~f~~~~~~~fPGlgi 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 9999999887654556666653
No 25
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=20.03 E-value=55 Score=20.34 Aligned_cols=9 Identities=56% Similarity=1.143 Sum_probs=7.2
Q ss_pred hhhcCchhH
Q 035119 25 RQATPGLGI 33 (73)
Q Consensus 25 ~~~fPGlgi 33 (73)
-+++||||.
T Consensus 32 E~~LPGLGV 40 (65)
T PF14098_consen 32 EKALPGLGV 40 (65)
T ss_pred hhcCCchHH
Confidence 358999994
Done!