Query psy6291
Match_columns 79
No_of_seqs 107 out of 411
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 22:41:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3203|consensus 99.8 4.4E-22 9.5E-27 142.4 3.2 59 2-62 107-165 (165)
2 CHL00159 rpl13 ribosomal prote 99.4 4.7E-14 1E-18 99.0 3.1 36 2-37 100-135 (143)
3 PRK09216 rplM 50S ribosomal pr 99.4 1.3E-13 2.8E-18 96.8 2.9 36 2-37 99-134 (144)
4 TIGR01066 rplM_bact ribosomal 99.4 1.9E-13 4.2E-18 95.4 3.2 36 2-37 97-132 (140)
5 PF00572 Ribosomal_L13: Riboso 99.4 4.3E-13 9.2E-18 92.1 2.9 35 2-36 85-119 (128)
6 PRK06394 rpl13p 50S ribosomal 99.3 5.1E-13 1.1E-17 93.8 3.1 36 2-37 77-113 (146)
7 COG0102 RplM Ribosomal protein 99.3 5.8E-13 1.3E-17 94.4 2.5 35 2-36 100-134 (148)
8 TIGR01077 L13_A_E ribosomal pr 99.3 1E-12 2.2E-17 92.0 3.0 35 2-36 72-107 (142)
9 PLN00205 ribisomal protein L13 99.3 2E-12 4.3E-17 94.6 3.2 35 2-36 101-135 (191)
10 cd00392 Ribosomal_L13 Ribosoma 99.2 1.9E-11 4.2E-16 82.6 3.0 30 2-31 85-114 (114)
11 PTZ00068 60S ribosomal protein 99.1 3.5E-11 7.6E-16 88.6 3.2 37 2-38 77-114 (202)
12 KOG3204|consensus 89.0 0.32 6.9E-06 36.3 2.2 36 2-37 72-108 (197)
13 KOG1448|consensus 74.3 1.4 3E-05 35.0 0.7 24 22-46 1-24 (316)
14 PF08082 PRO8NT: PRO8NT (NUC06 69.8 1.2 2.7E-05 32.0 -0.4 56 6-62 88-145 (152)
15 PF11460 DUF3007: Protein of u 28.9 22 0.00048 24.1 0.4 16 50-65 82-97 (104)
16 PF08393 DHC_N2: Dynein heavy 27.0 12 0.00025 28.6 -1.4 34 37-70 282-315 (408)
17 PF08920 SF3b1: Splicing facto 26.3 31 0.00067 24.3 0.8 27 51-77 80-111 (144)
18 PF04433 SWIRM: SWIRM domain; 25.8 9.4 0.0002 23.6 -1.8 23 55-77 12-36 (86)
19 PTZ00090 40S ribosomal protein 23.7 50 0.0011 25.4 1.5 30 38-67 57-86 (233)
20 PTZ00445 p36-lilke protein; Pr 23.0 33 0.00071 26.0 0.4 14 64-77 138-151 (219)
21 KOG2225|consensus 22.7 1.4E+02 0.003 25.9 4.0 76 2-77 563-665 (695)
22 PF03804 DUF325: Viral domain 22.7 29 0.00062 22.2 0.0 33 34-66 8-41 (71)
23 PF02978 SRP_SPB: Signal pepti 21.8 35 0.00075 22.4 0.3 19 51-70 53-71 (104)
24 PHA01160 nonstructural protein 20.2 89 0.0019 17.8 1.7 20 2-21 15-34 (40)
No 1
>KOG3203|consensus
Probab=99.85 E-value=4.4e-22 Score=142.40 Aligned_cols=59 Identities=37% Similarity=0.608 Sum_probs=56.0
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHHHHhhHHHhhhccCCcchhhccCCHHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKE 62 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~~~~Ni~~~~~q~~~vpk~l~~y~~eE 62 (79)
+|+++||+||||+|+|||++|+|||||+|++|| +..||+.++.|++.||+++++|+.||
T Consensus 107 ~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p--~~~Ni~~~~~q~~~vp~r~~e~~~~~ 165 (165)
T KOG3203|consen 107 RIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHP--EKVNIGSELHQPQGVPKRLDEYTFEE 165 (165)
T ss_pred HHHHHHHHhhCccchHHHHHhheeeccCCccCc--hhhhhHHHhccccCCCchhHHHhhcC
Confidence 689999999999999999999999999999999 45599999999999999999999875
No 2
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=99.45 E-value=4.7e-14 Score=99.05 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=34.1
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDL 37 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~~ 37 (79)
+||++||+||||||.+||.+|+||+||+|++|||+-
T Consensus 100 ~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~hph~a 135 (143)
T CHL00159 100 RIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHPHVA 135 (143)
T ss_pred HHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccc
Confidence 689999999999999999999999999999999853
No 3
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=99.40 E-value=1.3e-13 Score=96.80 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=34.1
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDL 37 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~~ 37 (79)
+||++||+||||+|.+|+.+|+||+||+|++|||+-
T Consensus 99 ~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~hp~~~ 134 (144)
T PRK09216 99 RVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHPHAA 134 (144)
T ss_pred HHHHHHHHhcCCCCccHHHHHhCcEEeCCCCCCccc
Confidence 689999999999999999999999999999999853
No 4
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=99.39 E-value=1.9e-13 Score=95.45 Aligned_cols=36 Identities=25% Similarity=0.509 Sum_probs=34.2
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDL 37 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~~ 37 (79)
+||++||+||||||.+|+.+|+||+||+|++|||+-
T Consensus 97 ~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~hp~~~ 132 (140)
T TIGR01066 97 RVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPHEA 132 (140)
T ss_pred HHHHHHHHhcCCCCccHHHHHhCeEEeCCCCCChhh
Confidence 689999999999999999999999999999999754
No 5
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 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 [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=99.35 E-value=4.3e-13 Score=92.12 Aligned_cols=35 Identities=29% Similarity=0.566 Sum_probs=33.4
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPED 36 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~ 36 (79)
+||++||+||||+|.+|+.+|+||+||+|++|||+
T Consensus 85 ~i~~~aVrgMLP~n~~g~~~l~rL~vy~g~~hp~~ 119 (128)
T PF00572_consen 85 RILKRAVRGMLPKNKLGREALKRLKVYPGEPHPHA 119 (128)
T ss_dssp HHHHHHHHTTSTTSHHHHHHHTTEEEESSSSCSTT
T ss_pred HHHHHHHHHHCCCChhhhHHhhceEEECCCCCChh
Confidence 58999999999999999999999999999999964
No 6
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=99.35 E-value=5.1e-13 Score=93.85 Aligned_cols=36 Identities=17% Similarity=0.232 Sum_probs=34.0
Q ss_pred hHHHHHHHhcCC-CChhHHHHHhhccccCCCCChHHH
Q psy6291 2 LVMKKAVRWELP-RSLIKFRLMARLHIFPDQEVPEDL 37 (79)
Q Consensus 2 ~il~~AV~gMLP-kn~lrr~~m~RL~Vy~g~~hph~~ 37 (79)
+||++||+|||| ||.+|+.+|+|||||+|++|||+-
T Consensus 77 ~il~~AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~ 113 (146)
T PRK06394 77 RIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEG 113 (146)
T ss_pred HHHHHHHHhcCCCCChhHHHHHhCcEEecCCCCCccc
Confidence 689999999999 999999999999999999999753
No 7
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=99.33 E-value=5.8e-13 Score=94.38 Aligned_cols=35 Identities=23% Similarity=0.461 Sum_probs=33.4
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPED 36 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~ 36 (79)
+||++||+||||+|.|||++|+||+||.|++|||+
T Consensus 100 ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~ 134 (148)
T COG0102 100 RILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHE 134 (148)
T ss_pred HHHHHHHhccCCCChhHHHHHhCceEecCCCCccc
Confidence 68999999999999999999999999999999954
No 8
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=99.31 E-value=1e-12 Score=91.95 Aligned_cols=35 Identities=20% Similarity=0.272 Sum_probs=33.1
Q ss_pred hHHHHHHHhcCCCC-hhHHHHHhhccccCCCCChHH
Q psy6291 2 LVMKKAVRWELPRS-LIKFRLMARLHIFPDQEVPED 36 (79)
Q Consensus 2 ~il~~AV~gMLPkn-~lrr~~m~RL~Vy~g~~hph~ 36 (79)
+||++||+||||+| .+|+.+|+|||||+|++|||+
T Consensus 72 ~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~ 107 (142)
T TIGR01077 72 RIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELD 107 (142)
T ss_pred HHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCcc
Confidence 68999999999997 799999999999999999975
No 9
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=99.28 E-value=2e-12 Score=94.64 Aligned_cols=35 Identities=34% Similarity=0.413 Sum_probs=33.4
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCCCChHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPED 36 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~~hph~ 36 (79)
+||++||+||||+|++|+++|+|||||+|++|||+
T Consensus 101 ~Il~kAVrGMLPkn~lr~~~~krLkVY~G~~hp~~ 135 (191)
T PLN00205 101 EVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFG 135 (191)
T ss_pred HHHHHHHHhcCCCCchHHHHHhCCEEECCCCCChh
Confidence 68999999999999999999999999999999973
No 10
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=99.16 E-value=1.9e-11 Score=82.61 Aligned_cols=30 Identities=27% Similarity=0.481 Sum_probs=28.8
Q ss_pred hHHHHHHHhcCCCChhHHHHHhhccccCCC
Q psy6291 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQ 31 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~m~RL~Vy~g~ 31 (79)
+||++||+||||||.+|+++|+|||||+|+
T Consensus 85 ~il~~aV~gMLPkn~~g~~~l~rLkvy~g~ 114 (114)
T cd00392 85 RILKRAVRGMLPKNKLGRAALKRLKVYEGA 114 (114)
T ss_pred HHHHHHHHhcCCCChhHHHHHhCcEEeCCC
Confidence 689999999999999999999999999985
No 11
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=99.12 E-value=3.5e-11 Score=88.63 Aligned_cols=37 Identities=24% Similarity=0.320 Sum_probs=34.0
Q ss_pred hHHHHHHHhcCCC-ChhHHHHHhhccccCCCCChHHHH
Q psy6291 2 LVMKKAVRWELPR-SLIKFRLMARLHIFPDQEVPEDLL 38 (79)
Q Consensus 2 ~il~~AV~gMLPk-n~lrr~~m~RL~Vy~g~~hph~~~ 38 (79)
+||++||+||||+ |.+|+.+|+||+||+|.+|||+-.
T Consensus 77 ~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~ 114 (202)
T PTZ00068 77 DIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKV 114 (202)
T ss_pred HHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhcc
Confidence 6899999999997 889999999999999999997533
No 12
>KOG3204|consensus
Probab=88.99 E-value=0.32 Score=36.28 Aligned_cols=36 Identities=28% Similarity=0.332 Sum_probs=31.7
Q ss_pred hHHHHHHHhcCCCC-hhHHHHHhhccccCCCCChHHH
Q psy6291 2 LVMKKAVRWELPRS-LIKFRLMARLHIFPDQEVPEDL 37 (79)
Q Consensus 2 ~il~~AV~gMLPkn-~lrr~~m~RL~Vy~g~~hph~~ 37 (79)
.|++++|.||+|+. +-++..+++|.+|.|=-+|.+-
T Consensus 72 ~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk 108 (197)
T KOG3204|consen 72 RILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDK 108 (197)
T ss_pred HHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhh
Confidence 58999999999987 5889999999999999998643
No 13
>KOG1448|consensus
Probab=74.33 E-value=1.4 Score=35.01 Aligned_cols=24 Identities=21% Similarity=0.571 Sum_probs=21.2
Q ss_pred HhhccccCCCCChHHHHhhHHHhhh
Q psy6291 22 MARLHIFPDQEVPEDLLKNVSSQIR 46 (79)
Q Consensus 22 m~RL~Vy~g~~hph~~~~Ni~~~~~ 46 (79)
|++++||.|++||. +.++|++.+.
T Consensus 1 ~~~i~lf~g~shp~-La~~I~~~lg 24 (316)
T KOG1448|consen 1 MKNIKLFSGDSHPE-LAERIAARLG 24 (316)
T ss_pred CCceEEEcCCCCHH-HHHHHHHHhC
Confidence 57899999999995 9999999765
No 14
>PF08082 PRO8NT: PRO8NT (NUC069), PrP8 N-terminal domain; InterPro: IPR012591 Pre-mRNA-processing-splicing factor 8 is a central component of the spliceosome, which may play a role in aligning the pre-mRNA 5'- and 3'-exons for ligation. It interacts with U5 snRNA, and with pre-mRNA 5'-splice sites in B spliceosomes and 3'-splice sites in C spliceosomes. It is part of the U5 snRNP complex, and of U5.4/6 and U5.U4atac/U6atac snRNP complexes in U2- and U12-dependent spliceosomes, respectively. It is also found in a mRNA splicing-dependent exon junction complex (EJC) with SRRM1 where it interacts with U5 snRNP proteins SNRP116 and WDR57/SPF38 [, ].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=69.76 E-value=1.2 Score=32.05 Aligned_cols=56 Identities=21% Similarity=0.267 Sum_probs=41.7
Q ss_pred HHHHhcCCCChhHHHHHhhc--cccCCCCChHHHHhhHHHhhhccCCcchhhccCCHHH
Q psy6291 6 KAVRWELPRSLIKFRLMARL--HIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKE 62 (79)
Q Consensus 6 ~AV~gMLPkn~lrr~~m~RL--~Vy~g~~hph~~~~Ni~~~~~q~~~vpk~l~~y~~eE 62 (79)
-.+.-|+.+.+.-|+.++|+ ..|.|++-|-+|..||.. .+.+..+.-.|++-..+.
T Consensus 88 ~~mW~~mRreKrdr~hfkRmrfPpFDDeEPpldy~dni~d-vep~~~i~~~ld~~~d~~ 145 (152)
T PF08082_consen 88 STMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYGDNILD-VEPLEAIQMELDEEEDAA 145 (152)
T ss_pred HHHHHHHHhcccCCCceeeeecCCCCCCCCCcchhhcccc-CCCCccccccccccccch
Confidence 44566778888888888877 889999999999999988 444444665565544443
No 15
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=28.85 E-value=22 Score=24.11 Aligned_cols=16 Identities=19% Similarity=0.389 Sum_probs=13.8
Q ss_pred CcchhhccCCHHHHhh
Q psy6291 50 PVPRTLASYSDKEVDE 65 (79)
Q Consensus 50 ~vpk~l~~y~~eE~~~ 65 (79)
+..||+++.|+||+++
T Consensus 82 ~lqkRle~l~~eE~~~ 97 (104)
T PF11460_consen 82 ELQKRLEELSPEELEA 97 (104)
T ss_pred HHHHHHHhCCHHHHHH
Confidence 4789999999999864
No 16
>PF08393 DHC_N2: Dynein heavy chain, N-terminal region 2; InterPro: IPR013602 Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, where each heavy chain consists of a C-terminal globular head, a flexible microtubule-binding stalk, and a flexible N-terminal tail known as the cargo-binding domain []. The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains. This entry represents a region found C-terminal to the dynein heavy chain N-terminal region 1 (IPR013594 from INTERPRO) in many members of this family. No functions seem to have been attributed specifically to this region. ; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=26.99 E-value=12 Score=28.58 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=27.1
Q ss_pred HHhhHHHhhhccCCcchhhccCCHHHHhhCCCCC
Q psy6291 37 LLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKIN 70 (79)
Q Consensus 37 ~~~Ni~~~~~q~~~vpk~l~~y~~eE~~~fPkl~ 70 (79)
+.+-+.....++..+-+.|.+|-+..+..|||++
T Consensus 282 ~~~~l~~~~~~l~~i~k~L~~~Le~kR~~FPRfy 315 (408)
T PF08393_consen 282 LLEKLESINESLEKIQKSLNDYLESKREAFPRFY 315 (408)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHhhcccee
Confidence 4555555556666788999999999999999985
No 17
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=26.29 E-value=31 Score=24.29 Aligned_cols=27 Identities=30% Similarity=0.519 Sum_probs=14.2
Q ss_pred cchhhccCCHHHHhh-CC----CCCCCCCccc
Q psy6291 51 VPRTLASYSDKEVDE-FP----KINDFPKDYI 77 (79)
Q Consensus 51 vpk~l~~y~~eE~~~-fP----kl~~~~~d~~ 77 (79)
+-.|-.=+|+||+++ || +|.+.|.+|.
T Consensus 80 id~RNrpLTDEELD~mLPseGYkIl~PP~gY~ 111 (144)
T PF08920_consen 80 IDERNRPLTDEELDAMLPSEGYKILEPPAGYE 111 (144)
T ss_dssp HHHCTS-S-HHHHHHTS--SSEEE----TT--
T ss_pred hhhccCcCCHHHHHHhCCcCCcEEcCCCCCCc
Confidence 445666699999997 67 8899999885
No 18
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=25.80 E-value=9.4 Score=23.56 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=17.8
Q ss_pred hccCCHHHHhhCCCCCC--CCCccc
Q psy6291 55 LASYSDKEVDEFPKIND--FPKDYI 77 (79)
Q Consensus 55 l~~y~~eE~~~fPkl~~--~~~d~~ 77 (79)
.+..|++|.+.||-++. -|+.|.
T Consensus 12 ~~~l~~~E~~~~~e~~~~~~p~~Yl 36 (86)
T PF04433_consen 12 PDKLSEIEKQLCPEFFIGKTPEQYL 36 (86)
T ss_dssp TTSS-HHHHHHCHHCTTSCHHHHHH
T ss_pred cccCCHHHHHHhHHHhccCChHHHH
Confidence 47889999999999888 666664
No 19
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=23.74 E-value=50 Score=25.36 Aligned_cols=30 Identities=13% Similarity=0.397 Sum_probs=24.5
Q ss_pred HhhHHHhhhccCCcchhhccCCHHHHhhCC
Q psy6291 38 LKNVSSQIRQLRPVPRTLASYSDKEVDEFP 67 (79)
Q Consensus 38 ~~Ni~~~~~q~~~vpk~l~~y~~eE~~~fP 67 (79)
.+-|++--+.++..|++...+|.+|+++||
T Consensus 57 ~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (233)
T PTZ00090 57 VKAITNLKEEVKKPPKKKKNITKEELKNFQ 86 (233)
T ss_pred HHHHhhhhhhhcCCchhhhhhhHHHHHhCC
Confidence 344566566777889999999999999999
No 20
>PTZ00445 p36-lilke protein; Provisional
Probab=22.95 E-value=33 Score=25.98 Aligned_cols=14 Identities=36% Similarity=0.598 Sum_probs=12.2
Q ss_pred hhCCCCCCCCCccc
Q psy6291 64 DEFPKINDFPKDYI 77 (79)
Q Consensus 64 ~~fPkl~~~~~d~~ 77 (79)
+-||+.|+.|+||.
T Consensus 138 ~yyp~~w~~p~~y~ 151 (219)
T PTZ00445 138 AYYPKFWQEPSDYR 151 (219)
T ss_pred eeCCcccCChhhhh
Confidence 46899999999984
No 21
>KOG2225|consensus
Probab=22.75 E-value=1.4e+02 Score=25.87 Aligned_cols=76 Identities=18% Similarity=0.472 Sum_probs=45.4
Q ss_pred hHHHHHHHhcCCCCh-hHHHHHhhccccCC-CCCh--HHHHhhHHHhh----hccCCcchhh-------------ccCCH
Q psy6291 2 LVMKKAVRWELPRSL-IKFRLMARLHIFPD-QEVP--EDLLKNVSSQI----RQLRPVPRTL-------------ASYSD 60 (79)
Q Consensus 2 ~il~~AV~gMLPkn~-lrr~~m~RL~Vy~g-~~hp--h~~~~Ni~~~~----~q~~~vpk~l-------------~~y~~ 60 (79)
+||.-+..+-|-+|. |--..+=+=-+|.+ -.|| .+++.||-.++ ..+.+||..+ .-.+.
T Consensus 563 EIiNScLtn~L~hnpnLvY~LLYkR~lFe~fr~Hp~FQD~lqNId~V~~~fssk~~~V~e~~g~~~~L~ii~k~a~~w~t 642 (695)
T KOG2225|consen 563 EIINSCLTNGLRHNPNLVYNLLYKRALFEAFRQHPMFQDLLQNIDAVISHFSSKVIHVPEGDGGSTMLQIIEKEANIWPT 642 (695)
T ss_pred HHHHHHhhCccccCchHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhhhhheeeccccccchhHHHHHhcccccCch
Confidence 466667777777773 32223323334444 3565 47899998776 4455566553 44566
Q ss_pred HHHhhCCCCC------CCCCccc
Q psy6291 61 KEVDEFPKIN------DFPKDYI 77 (79)
Q Consensus 61 eE~~~fPkl~------~~~~d~~ 77 (79)
+-+++||-|- +||+||.
T Consensus 643 drl~kfpelkfryvede~~~dff 665 (695)
T KOG2225|consen 643 DRLAKFPELKFRYVEDEYTVDFF 665 (695)
T ss_pred hhhhhCcccceeeecccCchhhe
Confidence 7788888652 5666664
No 22
>PF03804 DUF325: Viral domain of unknown function; InterPro: IPR003225 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.72 E-value=29 Score=22.17 Aligned_cols=33 Identities=15% Similarity=0.356 Sum_probs=21.9
Q ss_pred hHHHHhhHHHhhhccCCcchhhcc-CCHHHHhhC
Q psy6291 34 PEDLLKNVSSQIRQLRPVPRTLAS-YSDKEVDEF 66 (79)
Q Consensus 34 ph~~~~Ni~~~~~q~~~vpk~l~~-y~~eE~~~f 66 (79)
..+|++||..++..+.++-.-++- .|.+.+.-|
T Consensus 8 T~eyKEnivahi~HL~rlRaLIdgkvt~~dV~RF 41 (71)
T PF03804_consen 8 TQEYKENIVAHIDHLTRLRALIDGKVTHADVRRF 41 (71)
T ss_pred hhHHhhhhHHHHHHHHHHHHHHcCCccHhHHHHh
Confidence 357999999999888766544442 344455444
No 23
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=21.79 E-value=35 Score=22.41 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=14.4
Q ss_pred cchhhccCCHHHHhhCCCCC
Q psy6291 51 VPRTLASYSDKEVDEFPKIN 70 (79)
Q Consensus 51 vpk~l~~y~~eE~~~fPkl~ 70 (79)
.-.=+++.|++|+++ |+|+
T Consensus 53 ~~~Ii~SMT~~Er~~-p~ll 71 (104)
T PF02978_consen 53 MEAIIDSMTPEERDN-PKLL 71 (104)
T ss_dssp HHHHHTTSBHHHHHC-GGGH
T ss_pred HHHHHHCcCHHHHhC-cccc
Confidence 344578999999977 8775
No 24
>PHA01160 nonstructural protein
Probab=20.23 E-value=89 Score=17.85 Aligned_cols=20 Identities=10% Similarity=0.180 Sum_probs=16.0
Q ss_pred hHHHHHHHhcCCCChhHHHH
Q psy6291 2 LVMKKAVRWELPRSLIKFRL 21 (79)
Q Consensus 2 ~il~~AV~gMLPkn~lrr~~ 21 (79)
+++...+-+|=|.|.|++-+
T Consensus 15 rlf~rt~~r~~~rnrlrr~~ 34 (40)
T PHA01160 15 RLFSRTALRMHPRNRLRRIM 34 (40)
T ss_pred HHHHHHHHHHchHHHHHHHH
Confidence 46677888999999998754
Done!