Query psy13292
Match_columns 198
No_of_seqs 103 out of 112
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 15:44:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13292.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13292hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09812 MRP-L28: Mitochondria 100.0 2.7E-46 5.9E-51 306.9 12.4 131 41-172 21-157 (157)
2 KOG4778|consensus 100.0 7.7E-35 1.7E-39 244.9 11.6 131 43-174 49-186 (186)
3 KOG4778|consensus 79.9 1.2 2.6E-05 38.6 2.0 73 96-173 26-98 (186)
4 PF13851 GAS: Growth-arrest sp 53.6 71 0.0015 27.3 7.4 96 37-134 18-116 (201)
5 KOG2314|consensus 45.8 1.2E+02 0.0027 30.9 8.5 57 70-126 589-646 (698)
6 PF02095 Extensin_1: Extensin- 32.6 24 0.00053 17.4 0.8 9 21-29 2-10 (10)
7 PF05483 SCP-1: Synaptonemal c 24.5 1.6E+02 0.0034 30.8 5.5 40 92-131 91-133 (786)
8 PF05823 Gp-FAR-1: Nematode fa 22.8 61 0.0013 26.7 2.0 25 113-137 39-63 (154)
9 PRK00736 hypothetical protein; 21.8 3.1E+02 0.0068 19.6 6.8 48 103-154 18-65 (68)
10 PRK13259 regulatory protein Sp 19.0 74 0.0016 24.8 1.6 25 155-179 47-71 (94)
No 1
>PF09812 MRP-L28: Mitochondrial ribosomal protein L28; InterPro: IPR019192 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 [, ]. Members of this family are components of the mitochondrial large ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S) [, ].
Probab=100.00 E-value=2.7e-46 Score=306.86 Aligned_cols=131 Identities=40% Similarity=0.688 Sum_probs=124.4
Q ss_pred hHHHHHHHHhH------HHHHHHHHhcCCCCccchhcccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy13292 41 SRNFEKEYRDR------KAALEEILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIY 114 (198)
Q Consensus 41 sr~~ek~~~~~------~~~i~~~~~~~~~~~ke~~~RkRpl~~Ls~EelerRalL~K~Ws~Yk~~q~~~e~~~I~~~~~ 114 (198)
.++.++.||-+ +.||+++ .-+..++++.+.|+|++++||+|++++|++|+|+|++|++++|++++++|+++|+
T Consensus 21 ~~rl~k~iRkleK~~~~l~Pi~e~-~v~~~~~~~~~~R~r~~~~ls~Ee~erh~~i~kaW~~yk~~~~~~~~~~l~~~~~ 99 (157)
T PF09812_consen 21 RKRLEKFIRKLEKAAKQLKPIEEF-EVPQKSVDSASRRQRPLLKLSREELERHATIQKAWSLYKQQQREAREQQLRRQYE 99 (157)
T ss_pred HHHHHHHHHHHHccCCCCCCchhh-hhhHHHHhhhcccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34778888844 5689998 8888899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhCHHHHHHHhccCCCCCCceecCCCCCCCCCCCCCCCCcccccchhh
Q psy13292 115 SQQRALDELRLESEELYQEAIQIDPTLLPFAAKGPLHTPPIENYECPDGDYTDVSRNF 172 (198)
Q Consensus 115 SQqkALeELk~eSpeLYqaAiq~D~~LfP~e~~GPt~TPPi~~Y~~PDG~Y~DiTk~~ 172 (198)
||++||+||+.+||+||++||++|.++|||+++|||+||||+||++|||+|||||++|
T Consensus 100 sq~~AleeLr~~S~eLY~aA~~~d~~~fP~e~~~Pt~TPPi~~Y~~pdg~y~d~t~~~ 157 (157)
T PF09812_consen 100 SQQKALEELRLESPELYQAAIQPDPGLFPLEMRGPTDTPPIKNYEAPDGKYIDITKKW 157 (157)
T ss_pred HHHHHHHHHHhCCHHHHHHHhccCCCCCCeeecCCCCCCCCCCCCCCCCCeeeecccC
Confidence 9999999999999999999999999999999999999999999999999999999998
No 2
>KOG4778|consensus
Probab=100.00 E-value=7.7e-35 Score=244.86 Aligned_cols=131 Identities=35% Similarity=0.612 Sum_probs=121.5
Q ss_pred HHHHHHHhH------HHHHHHHHhcCCCCccchhcccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy13292 43 NFEKEYRDR------KAALEEILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLIYSQ 116 (198)
Q Consensus 43 ~~ek~~~~~------~~~i~~~~~~~~~~~ke~~~RkRpl~~Ls~EelerRalL~K~Ws~Yk~~q~~~e~~~I~~~~~SQ 116 (198)
..++-++-+ ..+++++ .......+++.+|+||+++|+.|++++||+|+|+|++|++++++++..+|+.+++||
T Consensus 49 rlk~~irK~~k~p~~~~pvd~l-~~p~~~~~~~~~rqrp~~klt~e~~e~rav~~k~W~~y~~~~rq~~d~~Ir~~~kaq 127 (186)
T KOG4778|consen 49 RLKRLIRKSQKFPTELIPVDDL-MVPLESEKKDYKRQRPLLKLTDEQLEKRAVILKTWSIYKQQQRQLEDVGIRPQSKAQ 127 (186)
T ss_pred HHHHHHhhcccccccccchHHh-hhHHHhcCccccccCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446666644 5677777 777888888889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhCHHHHHHHhccCC-CCCCceecCCCCCCCCCCCCCCCCcccccchhhhH
Q psy13292 117 QRALDELRLESEELYQEAIQIDP-TLLPFAAKGPLHTPPIENYECPDGDYTDVSRNFEK 174 (198)
Q Consensus 117 qkALeELk~eSpeLYqaAiq~D~-~LfP~e~~GPt~TPPi~~Y~~PDG~Y~DiTk~~~~ 174 (198)
.+||+||+.+|++||+||++.+. ++||++++||++||||.||..|||+|||+|++|++
T Consensus 128 ~~al~eLk~es~~Ly~aA~~~s~gk~lPve~~gP~~tPPi~~y~~p~g~y~~~tr~~~~ 186 (186)
T KOG4778|consen 128 FKALNELKSESEELYEAAIEFSPGKRLPVEVKGPTDTPPIKNYKDPDGDYNDSTRGWCS 186 (186)
T ss_pred HHHHHHHHHhhHHHHHHHhccccccccceeecCCCCCCCcccccCCCcchhhhhccCCC
Confidence 99999999999999999999998 88999999999999999999999999999999974
No 3
>KOG4778|consensus
Probab=79.86 E-value=1.2 Score=38.58 Aligned_cols=73 Identities=18% Similarity=0.188 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHhccCCCCCCceecCCCCCCCCCCCCCCCCcccccchhhh
Q psy13292 96 IYRSKEAQKDYKLIDRLIYSQQRALDELRLESEELYQEAIQIDPTLLPFAAKGPLHTPPIENYECPDGDYTDVSRNFE 173 (198)
Q Consensus 96 ~Yk~~q~~~e~~~I~~~~~SQqkALeELk~eSpeLYqaAiq~D~~LfP~e~~GPt~TPPi~~Y~~PDG~Y~DiTk~~~ 173 (198)
..-+.++..+-+.++...--++++++.+..-|+.-=.+-+-.|...||+++.++.+ +|+.|-|+|++.+..++
T Consensus 26 ~~~q~~kk~dr~vvkq~~~~~~~rlk~~irK~~k~p~~~~pvd~l~~p~~~~~~~~-----~rqrp~~klt~e~~e~r 98 (186)
T KOG4778|consen 26 CPMQREKKMDRDVVKQVEGTQKERLKRLIRKSQKFPTELIPVDDLMVPLESEKKDY-----KRQRPLLKLTDEQLEKR 98 (186)
T ss_pred hHhhhcccCCHHHHHHhhhHHHHHHHHHHhhcccccccccchHHhhhHHHhcCccc-----cccCCcccCCHHHHHHH
Confidence 34677888888899988888999999999999988888888888889999999977 99999999999886543
No 4
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=53.64 E-value=71 Score=27.31 Aligned_cols=96 Identities=19% Similarity=0.222 Sum_probs=51.8
Q ss_pred hhhhhHHHHHHHHhHHHHHHH---HHhcCCCCccchhcccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy13292 37 YTDVSRNFEKEYRDRKAALEE---ILNKNKKPHQRKKIRSRALPPLSEEVIESRSNLIKEWGIYRSKEAQKDYKLIDRLI 113 (198)
Q Consensus 37 y~~isr~~ek~~~~~~~~i~~---~~~~~~~~~ke~~~RkRpl~~Ls~EelerRalL~K~Ws~Yk~~q~~~e~~~I~~~~ 113 (198)
|||||..==.-|+..+.-|++ ..+.+.+.+.++...-+.+..-=..-....+-|.+.=..|.. .......++..+
T Consensus 18 YndIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~k--dK~~L~~~k~rl 95 (201)
T PF13851_consen 18 YNDITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYEK--DKQSLQNLKARL 95 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 899998332233333222222 223334444444443333222222334455556666666553 344666777777
Q ss_pred HHHHHHHHHHHhhCHHHHHHH
Q psy13292 114 YSQQRALDELRLESEELYQEA 134 (198)
Q Consensus 114 ~SQqkALeELk~eSpeLYqaA 134 (198)
....+-|..|+.+++.|-+.-
T Consensus 96 ~~~ek~l~~Lk~e~evL~qr~ 116 (201)
T PF13851_consen 96 KELEKELKDLKWEHEVLEQRF 116 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 788888888888777776543
No 5
>KOG2314|consensus
Probab=45.79 E-value=1.2e+02 Score=30.94 Aligned_cols=57 Identities=14% Similarity=0.227 Sum_probs=40.8
Q ss_pred hcccCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy13292 70 KIRSRALPPLSEEVIESRSNLIKEWGI-YRSKEAQKDYKLIDRLIYSQQRALDELRLE 126 (198)
Q Consensus 70 ~~RkRpl~~Ls~EelerRalL~K~Ws~-Yk~~q~~~e~~~I~~~~~SQqkALeELk~e 126 (198)
-=|.||+..||.|+.-+=.-=+|.|+. |-++-+.....+.+..++.+++-|++....
T Consensus 589 ~WRPRPps~LS~e~~KkIkKnLKky~a~FeeqD~~e~~~AsrElvekrRqlm~~f~~y 646 (698)
T KOG2314|consen 589 LWRPRPPSLLSEEKQKKIKKNLKKYSAQFEEQDRLEQSRASRELVEKRRQLMEQFTEY 646 (698)
T ss_pred ccCCCCCcccCHHHHHHHHHHHHHHHHHHhhhhhHhhhhhHHHHHHHHHHHHHHHHHH
Confidence 349999999999998876666777764 555555566667777777777776665543
No 6
>PF02095 Extensin_1: Extensin-like protein repeat; InterPro: IPR003883 Extensins are plant cell-wall proteins; they can account for up to 20% of the dry weight of the cell wall. They are highly-glycosylated, possibly reflecting their interactions with cell-wall carbohydrates. Amongst their functions is cell wall strengthening in response to mechanical stress (e.g., during attack by pests, plant-bending in the wind, etc.). This repeat occurs within extensin-like proteins.; GO: 0005199 structural constituent of cell wall
Probab=32.64 E-value=24 Score=17.41 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=7.1
Q ss_pred CCCCCCccc
Q psy13292 21 PLHTPPIEN 29 (198)
Q Consensus 21 p~~t~pi~~ 29 (198)
|+|.||+++
T Consensus 2 P~ykPpvek 10 (10)
T PF02095_consen 2 PVYKPPVEK 10 (10)
T ss_pred CccCCCccC
Confidence 788888875
No 7
>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex
Probab=24.47 E-value=1.6e+02 Score=30.77 Aligned_cols=40 Identities=28% Similarity=0.540 Sum_probs=31.0
Q ss_pred HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHH
Q psy13292 92 KEWGI---YRSKEAQKDYKLIDRLIYSQQRALDELRLESEELY 131 (198)
Q Consensus 92 K~Ws~---Yk~~q~~~e~~~I~~~~~SQqkALeELk~eSpeLY 131 (198)
|+|.. +--.|..+..+.=++.++||++|+.+|+...+.|-
T Consensus 91 k~WKv~vesd~~qKErkLqenrk~IEaqrKaIqELQf~NE~lS 133 (786)
T PF05483_consen 91 KKWKVQVESDLKQKERKLQENRKIIEAQRKAIQELQFENEKLS 133 (786)
T ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHh
Confidence 55654 34556677778889999999999999998877653
No 8
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=22.84 E-value=61 Score=26.68 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHhcc
Q psy13292 113 IYSQQRALDELRLESEELYQEAIQI 137 (198)
Q Consensus 113 ~~SQqkALeELk~eSpeLYqaAiq~ 137 (198)
+.+-.++++.|+..||+||..+...
T Consensus 39 ~~~~de~i~~LK~ksP~L~~k~~~l 63 (154)
T PF05823_consen 39 FKNEDEMIAALKEKSPSLYEKAEKL 63 (154)
T ss_dssp ----TTHHHHHHHH-HHHHHHHHHH
T ss_pred cCCHHHHHHHHHHhCHHHHHHHHHH
Confidence 3466788999999999999997654
No 9
>PRK00736 hypothetical protein; Provisional
Probab=21.76 E-value=3.1e+02 Score=19.65 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHhccCCCCCCceecCCCCCCC
Q psy13292 103 QKDYKLIDRLIYSQQRALDELRLESEELYQEAIQIDPTLLPFAAKGPLHTPP 154 (198)
Q Consensus 103 ~~e~~~I~~~~~SQqkALeELk~eSpeLYqaAiq~D~~LfP~e~~GPt~TPP 154 (198)
+.-...|+..+..|++.++.|...=..|.+..-..+.+. ..++.++||
T Consensus 18 e~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~~~~----~~~~~~~~P 65 (68)
T PRK00736 18 EKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLEEQA----APDVPVTKP 65 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc----CCCCCCCCc
Confidence 455788999999999999999877777766554444332 234455555
No 10
>PRK13259 regulatory protein SpoVG; Reviewed
Probab=19.02 E-value=74 Score=24.80 Aligned_cols=25 Identities=20% Similarity=0.650 Sum_probs=20.3
Q ss_pred CCCCCCCCCcccccchhhhHhHHHH
Q psy13292 155 IENYECPDGDYTDVSRNFEKEYRDR 179 (198)
Q Consensus 155 i~~Y~~PDG~Y~DiTk~~~~e~~~~ 179 (198)
-+.|-.+||+|-||.-.-+.||+..
T Consensus 47 MPs~k~~~g~y~DI~~Pit~e~Re~ 71 (94)
T PRK13259 47 MPSKRTPDGEFRDIAHPINSDTREK 71 (94)
T ss_pred CcCcCCCCCcEEEEEccCCHHHHHH
Confidence 3566778999999998888888754
Done!