Query 034359
Match_columns 97
No_of_seqs 50 out of 52
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 12:36:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034359.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034359hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00053 photosystem II subuni 100.0 7.4E-34 1.6E-38 204.5 4.7 62 24-85 1-65 (117)
2 PF04725 PsbR: Photosystem II 99.9 7.6E-26 1.7E-30 159.5 2.9 46 40-85 1-47 (99)
3 PLN00083 photosystem II subuni 98.7 3.6E-09 7.8E-14 75.3 1.8 25 61-85 29-54 (101)
4 cd00738 HGTP_anticodon HGTP an 47.8 7.7 0.00017 23.4 0.4 19 74-92 46-64 (94)
5 cd00861 ProRS_anticodon_short 46.6 12 0.00026 22.9 1.2 30 61-92 35-64 (94)
6 PF02530 Porin_2: Porin subfam 46.5 12 0.00027 30.1 1.6 21 76-96 15-36 (379)
7 cd00858 GlyRS_anticodon GlyRS 41.4 11 0.00025 25.0 0.6 30 61-93 59-88 (121)
8 PF02493 MORN: MORN repeat; I 38.9 20 0.00042 17.7 1.1 13 68-80 9-21 (23)
9 cd00860 ThrRS_anticodon ThrRS 33.7 15 0.00033 22.0 0.2 20 73-92 42-61 (91)
10 PF03889 DUF331: Domain of unk 23.0 32 0.00068 21.2 0.3 14 67-80 23-36 (39)
11 COG0124 HisS Histidyl-tRNA syn 22.6 22 0.00048 30.1 -0.7 30 61-92 366-395 (429)
12 PRK10545 nucleotide excision r 22.3 69 0.0015 25.8 2.1 21 68-88 31-51 (286)
13 TIGR02727 MTHFS_bact 5,10-meth 21.0 34 0.00073 24.4 0.1 17 61-77 125-142 (181)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=7.4e-34 Score=204.53 Aligned_cols=62 Identities=55% Similarity=0.853 Sum_probs=59.9
Q ss_pred ccCCCCCcc--ceeEEEEcCe-eeeeecccccCCCcccCCCcCcCCCcccceeeEecccccCcee
Q 034359 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELF 85 (97)
Q Consensus 24 vrgLpslaR--ssf~VvAsg~-KIkt~kP~G~~ggm~~k~gvDAsGRk~KGkGVYqf~dKYGan~ 85 (97)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+||||||||+||||||||+||||||.
T Consensus 1 ~~glp~l~r~~ss~~v~as~~kkikt~~p~G~~G~m~~k~gvDasGRk~kGkGVYqFvdKYGANV 65 (117)
T PLN00053 1 VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDKYGANV 65 (117)
T ss_pred CCccCcccccccceEEEecCCceeeecCCcccCCCcccccccCCCCccCCCcceEEehhhcCccc
Confidence 589999999 6899999988 9999999999999999999999999999999999999999996
No 2
>PF04725 PsbR: Photosystem II 10 kDa polypeptide PsbR; InterPro: IPR006814 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 intrinsic protein PsbR found in PSII, which is also known as the 10 kDa polypeptide. The PsbR gene is found only in the nucleus of green algae and higher plants. PsbR may provide a binding site for the extrinsic oxygen-evolving complex protein PsbP to the thylakoid membrane. PsbR has a transmembrane domain to anchor it to the thylakoid membrane, and a charged N-terminal domain capable of forming ion bridges with extrinsic proteins, allowing PsbR to act as a docking protein. PsbR may be a pH-dependent stabilising protein that functions at both donor and acceptor sides of PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0042651 thylakoid membrane
Probab=99.91 E-value=7.6e-26 Score=159.47 Aligned_cols=46 Identities=57% Similarity=0.792 Sum_probs=44.2
Q ss_pred cCe-eeeeecccccCCCcccCCCcCcCCCcccceeeEecccccCcee
Q 034359 40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELF 85 (97)
Q Consensus 40 sg~-KIkt~kP~G~~ggm~~k~gvDAsGRk~KGkGVYqf~dKYGan~ 85 (97)
|++ |||||+|||++|+|++|+|+||||||+||||||||+||||||.
T Consensus 1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANV 47 (99)
T PF04725_consen 1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANV 47 (99)
T ss_pred CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccc
Confidence 455 9999999999999999999999999999999999999999996
No 3
>PLN00083 photosystem II subunit R; Provisional
Probab=98.75 E-value=3.6e-09 Score=75.31 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=23.1
Q ss_pred CcCcCCCcccceeeEecccccC-cee
Q 034359 61 GLDASGRKAKYKFLNQQPLNSG-ELF 85 (97)
Q Consensus 61 gvDAsGRk~KGkGVYqf~dKYG-an~ 85 (97)
|--++|||+||||||||+|||| ||.
T Consensus 29 gsapkgRk~Kg~gVYqf~~KyGkANV 54 (101)
T PLN00083 29 GSAPKTRSGKAGYVYKLGLRNGKANV 54 (101)
T ss_pred CCCCCCccCCCceEEEehhccCcccc
Confidence 6667999999999999999999 986
No 4
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=47.78 E-value=7.7 Score=23.39 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=16.6
Q ss_pred eEecccccCceeEEEeccc
Q 034359 74 LNQQPLNSGELFVYIFGER 92 (97)
Q Consensus 74 VYqf~dKYGan~~~~~~~~ 92 (97)
-++++++.|+.|+.|+|++
T Consensus 46 ~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 46 KFREADLRGVPFAVVVGED 64 (94)
T ss_pred HHHHHHhCCCCEEEEECCC
Confidence 4788999999999999964
No 5
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=46.63 E-value=12 Score=22.87 Aligned_cols=30 Identities=13% Similarity=0.090 Sum_probs=21.6
Q ss_pred CcCcCCCcccceeeEecccccCceeEEEeccc
Q 034359 61 GLDASGRKAKYKFLNQQPLNSGELFVYIFGER 92 (97)
Q Consensus 61 gvDAsGRk~KGkGVYqf~dKYGan~~~~~~~~ 92 (97)
-+|.+++ +=+--++++++.|+.|+.|.|+.
T Consensus 35 ~~d~~~~--~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 35 LLDDRNE--RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred EEECCCC--CcccchhHHHhcCCCEEEEECCc
Confidence 4555554 33345778999999999999964
No 6
>PF02530 Porin_2: Porin subfamily; InterPro: IPR003684 This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to Gram-negative porins []. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of Gram-negative bacteria.; GO: 0015288 porin activity, 0006810 transport, 0016020 membrane
Probab=46.50 E-value=12 Score=30.09 Aligned_cols=21 Identities=38% Similarity=0.567 Sum_probs=18.3
Q ss_pred ecccccCceeEEEec-cceecC
Q 034359 76 QQPLNSGELFVYIFG-ERCLPI 96 (97)
Q Consensus 76 qf~dKYGan~~~~~~-~~~~~~ 96 (97)
|-+|-||+-|.||=| |-||-|
T Consensus 15 rvc~~yg~gf~~IPGTdTclri 36 (379)
T PF02530_consen 15 RVCDAYGAGFFYIPGTDTCLRI 36 (379)
T ss_pred EeccCcCCceEEcCCCCceEee
Confidence 457899999999999 889976
No 7
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=41.41 E-value=11 Score=25.04 Aligned_cols=30 Identities=13% Similarity=-0.028 Sum_probs=22.4
Q ss_pred CcCcCCCcccceeeEecccccCceeEEEeccce
Q 034359 61 GLDASGRKAKYKFLNQQPLNSGELFVYIFGERC 93 (97)
Q Consensus 61 gvDAsGRk~KGkGVYqf~dKYGan~~~~~~~~~ 93 (97)
-+|-+ + +=+--+++++|.|+.|+.|+|++.
T Consensus 59 ~~d~~-~--sl~kqlk~A~k~g~~~~iiiG~~e 88 (121)
T cd00858 59 KYDDS-G--SIGRRYARQDEIGTPFCVTVDFDT 88 (121)
T ss_pred EEeCC-C--CHHHHHHHhHhcCCCEEEEECcCc
Confidence 34444 4 444567889999999999999864
No 8
>PF02493 MORN: MORN repeat; InterPro: IPR003409 The MORN (Membrane Occupation and Recognition Nexus) motif is found in multiple copies in several proteins including junctophilins (). The function of this motif is unknown.; PDB: 1H3I_B 1MT6_A 1N6C_A 3OS5_A 3M53_A 3M55_A 3CBP_A 4E47_B 3M58_A 3CBO_A ....
Probab=38.88 E-value=20 Score=17.69 Aligned_cols=13 Identities=15% Similarity=-0.153 Sum_probs=9.2
Q ss_pred cccceeeEecccc
Q 034359 68 KAKYKFLNQQPLN 80 (97)
Q Consensus 68 k~KGkGVYqf~dK 80 (97)
+..|+|+|+|+|.
T Consensus 9 ~~~G~G~~~~~~G 21 (23)
T PF02493_consen 9 KKHGYGVYTFPDG 21 (23)
T ss_dssp EEECEEEEE-TTS
T ss_pred cccccEEEEeCCC
Confidence 3568999999873
No 9
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=33.71 E-value=15 Score=22.02 Aligned_cols=20 Identities=5% Similarity=0.139 Sum_probs=16.9
Q ss_pred eeEecccccCceeEEEeccc
Q 034359 73 FLNQQPLNSGELFVYIFGER 92 (97)
Q Consensus 73 GVYqf~dKYGan~~~~~~~~ 92 (97)
--++++++-|+.++.|+|++
T Consensus 42 ~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 42 KKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred HHHHHHHHcCCCEEEEECcc
Confidence 35788999999999999964
No 10
>PF03889 DUF331: Domain of unknown function; InterPro: IPR005589 The members of this family are uncharacterised proteins from a number of bacterial species. They range in size from 50-100 residues.
Probab=23.04 E-value=32 Score=21.19 Aligned_cols=14 Identities=21% Similarity=-0.026 Sum_probs=9.7
Q ss_pred CcccceeeEecccc
Q 034359 67 RKAKYKFLNQQPLN 80 (97)
Q Consensus 67 Rk~KGkGVYqf~dK 80 (97)
+.-||||-||=-.|
T Consensus 23 k~kKGKGSy~Rk~k 36 (39)
T PF03889_consen 23 KAKKGKGSYQRKAK 36 (39)
T ss_pred ccccCccccchhhh
Confidence 45688998885444
No 11
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.56 E-value=22 Score=30.14 Aligned_cols=30 Identities=37% Similarity=0.407 Sum_probs=25.6
Q ss_pred CcCcCCCcccceeeEecccccCceeEEEeccc
Q 034359 61 GLDASGRKAKYKFLNQQPLNSGELFVYIFGER 92 (97)
Q Consensus 61 gvDAsGRk~KGkGVYqf~dKYGan~~~~~~~~ 92 (97)
-+|-++|+ =|.-+++|||-|+.|+.|.||+
T Consensus 366 ~~~~~~r~--~k~q~k~A~~~g~~~~viiGe~ 395 (429)
T COG0124 366 EVDYSGRK--LKKQFKYADKLGARFAVILGED 395 (429)
T ss_pred EEEecccc--HHHHHHHHHHCCCCEEEEEcch
Confidence 57778888 4566899999999999999986
No 12
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=22.34 E-value=69 Score=25.81 Aligned_cols=21 Identities=19% Similarity=0.034 Sum_probs=16.9
Q ss_pred cccceeeEecccccCceeEEE
Q 034359 68 KAKYKFLNQQPLNSGELFVYI 88 (97)
Q Consensus 68 k~KGkGVYqf~dKYGan~~~~ 88 (97)
-+.--|||.|-|+-|....||
T Consensus 31 LP~~PGVYlf~d~~g~~~LYV 51 (286)
T PRK10545 31 LPKLPGVYLFHGESDTMPLYI 51 (286)
T ss_pred CCCCCeEEEEEcCCCCEEEEE
Confidence 355679999999988877777
No 13
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase. This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism.
Probab=21.04 E-value=34 Score=24.40 Aligned_cols=17 Identities=18% Similarity=0.094 Sum_probs=12.8
Q ss_pred CcCcCC-CcccceeeEec
Q 034359 61 GLDASG-RKAKYKFLNQQ 77 (97)
Q Consensus 61 gvDAsG-Rk~KGkGVYqf 77 (97)
++|.+| |-|.|+|-|.-
T Consensus 125 afD~~G~RLG~GgGyYDR 142 (181)
T TIGR02727 125 AFDRRGYRLGYGGGYYDR 142 (181)
T ss_pred EEcCCCccccCCcchHHH
Confidence 456665 89999999953
Done!