Query 030376
Match_columns 178
No_of_seqs 51 out of 53
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 12:48:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030376hhsearch_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 1.4E-59 3E-64 375.2 14.7 114 64-177 1-116 (139)
2 PF02035 Coagulin: Coagulin; 88.7 0.46 9.9E-06 39.6 3.2 51 59-116 75-125 (174)
3 PF10657 RC-P840_PscD: Photosy 44.9 23 0.00049 29.3 2.8 41 89-141 39-79 (144)
4 PF08624 CRC_subunit: Chromati 21.1 56 0.0012 26.8 1.4 49 84-142 14-69 (139)
5 PRK04179 rpl37e 50S ribosomal 21.0 29 0.00062 25.2 -0.3 16 101-116 40-55 (62)
6 PTZ00073 60S ribosomal protein 20.4 30 0.00066 26.8 -0.3 14 103-116 40-53 (91)
7 PF01907 Ribosomal_L37e: Ribos 18.8 53 0.0012 23.3 0.7 13 103-115 39-52 (55)
8 COG3737 Uncharacterized conser 18.7 2.3E+02 0.0049 23.2 4.4 55 81-140 18-75 (127)
9 PRK10202 ebgC cryptic beta-D-g 17.9 2.1E+02 0.0046 22.8 4.1 100 56-169 42-148 (149)
10 PLN00057 proliferating cell nu 17.0 4.8E+02 0.01 22.5 6.3 49 93-142 44-93 (263)
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=1.4e-59 Score=375.16 Aligned_cols=114 Identities=61% Similarity=1.007 Sum_probs=98.0
Q ss_pred eeeeCceeEEEeecCCceeecCCCCeEEeeeeeEEEEeeccccCcccccCcceEEEeChhhHHHHhhccCCCceeeeeCC
Q 030376 64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP 143 (178)
Q Consensus 64 sVYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~effHDP 143 (178)
+||||||||+|+|++|+|+.++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+|+++++|||||||
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 CCCCCCCCceeeeEEeEeCCCc--eEEEEeeeeeec
Q 030376 144 AMLSSNAGQMRKSLSIKANADG--FFISLSEYSTCV 177 (178)
Q Consensus 144 ~~g~S~~G~v~K~LkveP~~dG--~f~nLsV~n~~~ 177 (178)
+|++|++|+|+|+|||||+||| |||||+|+|++.
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~ 116 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLL 116 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCC
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccc
Confidence 9999999999999999999996 999999999964
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=88.71 E-value=0.46 Score=39.58 Aligned_cols=51 Identities=25% Similarity=0.488 Sum_probs=28.8
Q ss_pred eecceeeeeCceeEEEeecCCceeecCCCCeEEeeeeeEEEEeeccccCcccccCcce
Q 030376 59 IFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQ 116 (178)
Q Consensus 59 vy~~ysVYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~kKq 116 (178)
-|++|.-|+..+-.+.+..-|.|.-.-+|.+ .|++| ||.+|-||--|+.|-
T Consensus 75 nf~pf~hf~secpvstrdcepvfgyt~a~ef------rvivq-apragfrqcvwqhkc 125 (174)
T PF02035_consen 75 NFPPFHHFKSECPVSTRDCEPVFGYTVAGEF------RVIVQ-APRAGFRQCVWQHKC 125 (174)
T ss_dssp GSTT----SSB--EEEE----SEEE-TTS-E------EEE---BCCCTB-B---EEEE
T ss_pred cCCCcccccccCCcccccccccccceecceE------EEEEe-CchhhHHHHHHHhhh
Confidence 4789999999999999999999988888855 46777 999999999999884
No 3
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 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. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=44.89 E-value=23 Score=29.26 Aligned_cols=41 Identities=39% Similarity=0.513 Sum_probs=31.3
Q ss_pred eEEeeeeeEEEEeeccccCcccccCcceEEEeChhhHHHHhhccCCCceeeee
Q 030376 89 LKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFH 141 (178)
Q Consensus 89 ~kv~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~effH 141 (178)
.|-+|.|.+=||++||.|-|+ ||||+ ++|...-+..+|+|-
T Consensus 39 AkRD~~g~Lql~i~pasGrrk----------Lspt~--emi~~l~~geIel~V 79 (144)
T PF10657_consen 39 AKRDRYGKLQLTISPASGRRK----------LSPTP--EMIDKLISGEIELFV 79 (144)
T ss_pred eecccCCceEEEEecCCCccc----------cCCcH--HHHHHHhcCceEEEE
Confidence 456789999999999999887 67775 456666667777664
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=21.08 E-value=56 Score=26.84 Aligned_cols=49 Identities=35% Similarity=0.595 Sum_probs=35.9
Q ss_pred cCCCCeEEeeeeeEEEEeeccccCcccccC-------cceEEEeChhhHHHHhhccCCCceeeeeC
Q 030376 84 LDSGDLKVKRKGVILLTFAPAIGERKYDWA-------KKQHFALSPTEVGSLLTMGPRDSSEFFHD 142 (178)
Q Consensus 84 l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~-------kKq~FaLS~tEvG~Llsl~~~~s~effHD 142 (178)
.+.|--||++.|.++ |.|+|-.. ....|+|| +|+.-++ |-+||.+|||.
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 456788999999874 66666432 15789997 4555554 99999999987
No 5
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=20.98 E-value=29 Score=25.18 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=12.4
Q ss_pred eeccccCcccccCcce
Q 030376 101 FAPAIGERKYDWAKKQ 116 (178)
Q Consensus 101 FAPa~G~RqYDW~kKq 116 (178)
|-|+.--|.|+|++|-
T Consensus 40 ygps~k~R~YnWs~Ka 55 (62)
T PRK04179 40 FGRSKRIRRYSWQNKK 55 (62)
T ss_pred CCcccccccccHHHHh
Confidence 3477778999999874
No 6
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.40 E-value=30 Score=26.75 Aligned_cols=14 Identities=36% Similarity=0.923 Sum_probs=12.1
Q ss_pred ccccCcccccCcce
Q 030376 103 PAIGERKYDWAKKQ 116 (178)
Q Consensus 103 Pa~G~RqYDW~kKq 116 (178)
|+.--|.|+|+.|-
T Consensus 40 psak~R~YnWs~Ka 53 (91)
T PTZ00073 40 PSAKMRRYNWSVKA 53 (91)
T ss_pred chhhccccchhhhh
Confidence 78888999999874
No 7
>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=18.85 E-value=53 Score=23.26 Aligned_cols=13 Identities=54% Similarity=1.160 Sum_probs=7.5
Q ss_pred ccccCc-ccccCcc
Q 030376 103 PAIGER-KYDWAKK 115 (178)
Q Consensus 103 Pa~G~R-qYDW~kK 115 (178)
|+.--| +|+|+.|
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 566667 9999987
No 8
>COG3737 Uncharacterized conserved protein [Function unknown]
Probab=18.72 E-value=2.3e+02 Score=23.22 Aligned_cols=55 Identities=18% Similarity=0.415 Sum_probs=43.8
Q ss_pred eeecCCCCeEE---eeeeeEEEEeeccccCcccccCcceEEEeChhhHHHHhhccCCCceeee
Q 030376 81 FMKLDSGDLKV---KRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFF 140 (178)
Q Consensus 81 F~~l~SG~~kv---~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~eff 140 (178)
+..-++|++.+ +.+|.+|+ .| ..-|||+-+..=.|+|+.+..+++.++.-++-++
T Consensus 18 ~~ayG~Gg~R~a~~sh~~SlL~--lp---dgv~~W~v~~~~~Lt~e~f~~vl~~a~~~Eilli 75 (127)
T COG3737 18 IDAYGAGGFRFADMSHRGSLLV--LP---DGVCDWEVATLSDLTPEDFERVLAEAPDVEILLI 75 (127)
T ss_pred hhhhcCCceEeccccccccEEE--ec---CccccccccChhhCCHHHHHHHHhcCCCceEEEE
Confidence 55568888887 78899887 45 3379999999999999999999988776555444
No 9
>PRK10202 ebgC cryptic beta-D-galactosidase subunit beta; Reviewed
Probab=17.89 E-value=2.1e+02 Score=22.81 Aligned_cols=100 Identities=15% Similarity=0.141 Sum_probs=60.2
Q ss_pred CCeeecceeeeeCceeEEEeecCCceeecCCCC--eEEeeeeeEEEEeecccc---CcccccCcceEEEeChhhHHHHhh
Q 030376 56 GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGD--LKVKRKGVILLTFAPAIG---ERKYDWAKKQHFALSPTEVGSLLT 130 (178)
Q Consensus 56 ~~Rvy~~ysVYKgKAAlsv~p~~P~F~~l~SG~--~kv~R~G~vlLeFAPa~G---~RqYDW~kKq~FaLS~tEvG~Lls 130 (178)
.+++|++..=|.++.+ .+|. -+. + +.+-=+|.=.+.++|... ...||=++-..|- .. .+..+.
T Consensus 42 gd~vf~~v~~~~t~~~------~~E~--Hr~-YiDIq~~l~G~E~i~~~~~~~~~~~~~y~~e~D~~f~-~~--~~~~v~ 109 (149)
T PRK10202 42 GDSLTYRVETDSATDA------LFTG--HRR-YFEVHYYLQGQQKIEYAPKETLQVVEYYRDETDREYL-KG--CGETVE 109 (149)
T ss_pred CCEEEEEEecCccccc------cccc--ccc-EEEEEEEEeCeEEEEEEEcccCccccccCcccCeeec-cC--CCcEEE
Confidence 4778888777776662 2222 111 2 334567888888888744 2346666655554 22 345677
Q ss_pred ccCCCceeee-eCCCCCCCCCCceee-eEEeEeCCCceEEE
Q 030376 131 MGPRDSSEFF-HDPAMLSSNAGQMRK-SLSIKANADGFFIS 169 (178)
Q Consensus 131 l~~~~s~eff-HDP~~g~S~~G~v~K-~LkveP~~dG~f~n 169 (178)
|.|.+=+-|| +|+.+-. ....|+| ++||. ..||+|=|
T Consensus 110 l~~G~F~iffP~daH~P~-~~~~ikK~VvKV~-~~~~~~~~ 148 (149)
T PRK10202 110 VHEGQIVICDIHEAYRFI-CNNAVKKVVLKVT-IEDGYFHN 148 (149)
T ss_pred eCCCeEEEECCcccccCC-CCCcEEEEEEEEE-ecCccccC
Confidence 8888866666 4444443 4556888 46776 66667744
No 10
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=16.99 E-value=4.8e+02 Score=22.46 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=39.2
Q ss_pred eeeeEEEEeeccccCcccccCcceEEEeChhhHHHHhh-ccCCCceeeeeC
Q 030376 93 RKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLT-MGPRDSSEFFHD 142 (178)
Q Consensus 93 R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Lls-l~~~~s~effHD 142 (178)
|.-.|-| +.|+.+--.|..++..+|.+...++--+|. ...+++|++.++
T Consensus 44 ~Valv~l-~l~~~~F~eY~~d~~~~~gv~l~~l~kiLk~~~~~d~l~l~~~ 93 (263)
T PLN00057 44 HVALVAL-LLRADGFEHYRCDRNLSMGINLANMSKILKCAGNDDIITIKAD 93 (263)
T ss_pred cEEEEEE-EeChhcCeEEecCCceEEEEEHHHHHHHHhccCCCCEEEEEec
Confidence 3333444 478888889999999999999999999996 556789999765
Done!