Query 027308
Match_columns 225
No_of_seqs 51 out of 53
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 08:00:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08536 Whirly: Whirly transc 100.0 5.9E-63 1.3E-67 405.8 14.3 132 90-221 1-138 (139)
2 PF02035 Coagulin: Coagulin; 68.2 4.8 0.0001 34.8 2.7 51 85-142 75-125 (174)
3 PRK12301 bssS biofilm formatio 61.7 2.4 5.3E-05 33.4 -0.2 16 1-16 27-42 (84)
4 PF08624 CRC_subunit: Chromati 30.0 32 0.00069 29.2 1.6 49 110-168 14-69 (139)
5 PF13991 BssS: BssS protein fa 29.0 26 0.00056 26.9 0.8 16 1-16 17-32 (73)
6 cd01680 EFG_like_IV Elongation 23.1 2.3E+02 0.005 21.2 5.0 31 163-194 11-41 (116)
7 PRK04179 rpl37e 50S ribosomal 19.2 32 0.00069 25.9 -0.4 14 129-142 42-55 (62)
8 PF01907 Ribosomal_L37e: Ribos 17.8 57 0.0012 24.0 0.7 13 129-141 39-52 (55)
9 KOG1528 Salt-sensitive 3'-phos 17.0 23 0.0005 34.1 -1.9 56 162-225 229-292 (351)
10 PF11807 DUF3328: Domain of un 15.9 44 0.00096 26.6 -0.3 10 1-10 127-136 (217)
No 1
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=100.00 E-value=5.9e-63 Score=405.80 Aligned_cols=132 Identities=64% Similarity=0.999 Sum_probs=113.0
Q ss_pred eeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeeccccCccccCCcceEEEEehhhhhhhhhccCccceeEeecC
Q 027308 90 SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDP 169 (225)
Q Consensus 90 sIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq~FsLS~tEvG~LlsLga~~sceFFHDP 169 (225)
+||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|||||+|+|+||+|+++++|||||||
T Consensus 1 sVYk~kaAl~v~p~~P~f~~~~sg~~kv~R~G~vlLefapa~g~r~YDW~kKq~FsLS~tEvG~ll~l~~~~s~effHdP 80 (139)
T PF08536_consen 1 SVYKGKAALSVRPIKPTFTSLDSGYFKVSREGSVLLEFAPAVGPRQYDWSKKQTFSLSPTEVGSLLSLGARESCEFFHDP 80 (139)
T ss_dssp EEEESSEEEEEEEE--EEEE-TTSCEEEEC--EEEEEEEEBCSTTEB-GGG-EEEEE-HHHHHHHHT--TT--EEEEE-T
T ss_pred CccccceeEEEEecCCccEECCCCcEEEeeccEEEEEEccccCCcccccccceEEEEcHHHhhhhhhhccCCceEEEecc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceeEEEEEEECCCCCcceEEEEeccccce------eeeccccchhhhhhh
Q 027308 170 FKGKSEEGKVRKVLKVEPLPDGSGHFFNLSNALFLEL------LAVNLEDYLLFDDKI 221 (225)
Q Consensus 170 ~mg~S~eGkvrK~LkVeP~pDGsG~ffnLsV~n~~~~------~~ln~~e~~vf~~~~ 221 (225)
+||+|++|+|||+|||||||||+||||||+|+|+++| |-|...||+|+|.+.
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfavl~s~f 138 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAVLRSAF 138 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHHHHHHH
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccccceEEEechHHHHHHHHHhh
Confidence 9999999999999999999999999999999999776 557778999998753
No 2
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=68.16 E-value=4.8 Score=34.85 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=27.3
Q ss_pred eeeeeeeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeeccccCccccCCcce
Q 027308 85 VYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQ 142 (225)
Q Consensus 85 Vy~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq 142 (225)
-|++|.-|+...-.+.+..-|.|.-.-+|.+++ + -=||.+|-||--|+.|-
T Consensus 75 nf~pf~hf~secpvstrdcepvfgyt~a~efrv------i-vqapragfrqcvwqhkc 125 (174)
T PF02035_consen 75 NFPPFHHFKSECPVSTRDCEPVFGYTVAGEFRV------I-VQAPRAGFRQCVWQHKC 125 (174)
T ss_dssp GSTT----SSB--EEEE----SEEE-TTS-EEE------E---BCCCTB-B---EEEE
T ss_pred cCCCcccccccCCcccccccccccceecceEEE------E-EeCchhhHHHHHHHhhh
Confidence 366788999999999999999999988886643 3 34899999999999884
No 3
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=61.66 E-value=2.4 Score=33.42 Aligned_cols=16 Identities=31% Similarity=0.565 Sum_probs=14.0
Q ss_pred CceeeeecccCCCCCC
Q 027308 1 MMLQLQCLSSQTLNPK 16 (225)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (225)
||++||.|||+.|.+.
T Consensus 27 mmirlhyLss~~Q~~e 42 (84)
T PRK12301 27 LMLRLHYQSPNDQEPE 42 (84)
T ss_pred HHHhhhhcCCCCCCcc
Confidence 7999999999987664
No 4
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=30.01 E-value=32 Score=29.20 Aligned_cols=49 Identities=29% Similarity=0.551 Sum_probs=35.5
Q ss_pred cCCcceEEeeeceEEEEeeccccCccccC-------CcceEEEEehhhhhhhhhccCccceeEeec
Q 027308 110 LDSGAVKLSREGFVMLQFAPAAGVRQYDW-------SRKQVFSLSVTEIGSLVALGARESCEFFHD 168 (225)
Q Consensus 110 l~SG~~kv~R~G~vlLeFAPA~G~RqYDW-------~kKq~FsLS~tEvG~LlsLga~~sceFFHD 168 (225)
.+.|--||++.|-++ |.|+|-- .....|+|| +|+.-++ |-++|.+|||.
T Consensus 14 Dp~GE~KId~~G~Ll-------gGR~y~~~TFtl~~rg~~lymL~-td~ar~l--g~rDs~~ff~~ 69 (139)
T PF08624_consen 14 DPKGEKKIDKNGRLL-------GGREYRFRTFTLPGRGNRLYMLS-TDPARCL--GFRDSYLFFRK 69 (139)
T ss_pred CCCcCeEeCCCCccc-------CCCEEEEEEEEeCCCCCeEEEEe-HHHHHHh--ccccHHHHHHh
Confidence 356778999999885 6676633 125678886 5666555 99999999984
No 5
>PF13991 BssS: BssS protein family
Probab=29.03 E-value=26 Score=26.93 Aligned_cols=16 Identities=44% Similarity=0.663 Sum_probs=13.4
Q ss_pred CceeeeecccCCCCCC
Q 027308 1 MMLQLQCLSSQTLNPK 16 (225)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (225)
||++||.||++.|.+.
T Consensus 17 l~lrl~yls~~~q~~e 32 (73)
T PF13991_consen 17 LMLRLHYLSSPDQPPE 32 (73)
T ss_pred eEEEecccCCCCCCcc
Confidence 7999999999977654
No 6
>cd01680 EFG_like_IV Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm.
Probab=23.14 E-value=2.3e+02 Score=21.17 Aligned_cols=31 Identities=29% Similarity=0.229 Sum_probs=20.8
Q ss_pred eeEeecCCCCCCCCCceeEEEEEEECCCCCcc
Q 027308 163 CEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGH 194 (225)
Q Consensus 163 ceFFHDP~mg~S~eGkvrK~LkVeP~pDGsG~ 194 (225)
++..|+.-.|.. .+..+=+|.|||+++|+|.
T Consensus 11 ~~~~~~~~~gg~-~~~a~v~l~veP~~~~~~~ 41 (116)
T cd01680 11 ATGEFERELGGK-PQFGEVTLRVEPLERGSGV 41 (116)
T ss_pred eeEEEccccCCC-CeEEEEEEEEEECCCCCCc
Confidence 344555554433 3446779999999998876
No 7
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=19.18 E-value=32 Score=25.91 Aligned_cols=14 Identities=29% Similarity=0.852 Sum_probs=10.8
Q ss_pred ccccCccccCCcce
Q 027308 129 PAAGVRQYDWSRKQ 142 (225)
Q Consensus 129 PA~G~RqYDW~kKq 142 (225)
|+.--|.|+|++|-
T Consensus 42 ps~k~R~YnWs~Ka 55 (62)
T PRK04179 42 RSKRIRRYSWQNKK 55 (62)
T ss_pred cccccccccHHHHh
Confidence 55557999999874
No 8
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=17.78 E-value=57 Score=24.01 Aligned_cols=13 Identities=62% Similarity=1.147 Sum_probs=6.8
Q ss_pred ccccCc-cccCCcc
Q 027308 129 PAAGVR-QYDWSRK 141 (225)
Q Consensus 129 PA~G~R-qYDW~kK 141 (225)
|+.--| +|+|+.|
T Consensus 39 p~~kkrr~ynWs~K 52 (55)
T PF01907_consen 39 PAAKKRRKYNWSAK 52 (55)
T ss_dssp TTSSS----SSSSH
T ss_pred Ccccccccccchhh
Confidence 444456 9999987
No 9
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=16.97 E-value=23 Score=34.09 Aligned_cols=56 Identities=20% Similarity=0.271 Sum_probs=35.0
Q ss_pred ceeEeecCCCCCCCCCceeEEEEEEECCCCCcceEEEEeccccceeeeccccchh--------hhhhhhccC
Q 027308 162 SCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSNALFLELLAVNLEDYLL--------FDDKIYDHL 225 (225)
Q Consensus 162 sceFFHDP~mg~S~eGkvrK~LkVeP~pDGsG~ffnLsV~n~~~~~~ln~~e~~v--------f~~~~~~~~ 225 (225)
=||=+|-|.-.......|.+.|+|+-.|--= .....-+.|.-||+-| |+|+|+||-
T Consensus 229 f~Es~e~~~s~h~~~~~IankLgI~~~P~~i--------~SqaKYaalarGdaeVyLrf~~k~y~EkIWDHA 292 (351)
T KOG1528|consen 229 FCESVEKGHSIHGFQSTIANKLGIKKLPTRI--------DSQAKYAALARGDAEVYLRFPLKGYREKIWDHA 292 (351)
T ss_pred eecccccCCccchhhHHHHHhhCcccCCcee--------chhHHHHHHhcCCcceeEeecccccchhhhhcc
Confidence 5677777776555567888888887765321 1111114455555444 699999993
No 10
>PF11807 DUF3328: Domain of unknown function (DUF3328); InterPro: IPR021765 This family of proteins are functionally uncharacterised. This family is only found in eukaryotes.
Probab=15.86 E-value=44 Score=26.57 Aligned_cols=10 Identities=40% Similarity=0.806 Sum_probs=7.5
Q ss_pred Cceeeeeccc
Q 027308 1 MMLQLQCLSS 10 (225)
Q Consensus 1 ~~~~~~~~~~ 10 (225)
|+||||||..
T Consensus 127 vfHqLHCL~~ 136 (217)
T PF11807_consen 127 VFHQLHCLNM 136 (217)
T ss_pred cchhhhhhHH
Confidence 5788999843
Done!