Query 031760
Match_columns 153
No_of_seqs 117 out of 232
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:58:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031760hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00026 60S ribosomal protein 100.0 2.4E-79 5.3E-84 502.2 10.0 134 1-134 1-134 (204)
2 KOG1678 60s ribosomal protein 100.0 8.7E-80 1.9E-84 499.4 6.1 134 1-134 1-134 (204)
3 PRK04243 50S ribosomal protein 100.0 2.7E-78 5.8E-83 493.7 9.5 132 1-134 3-134 (196)
4 PF00827 Ribosomal_L15e: Ribos 100.0 5.3E-78 1.1E-82 490.9 8.8 133 2-134 1-133 (192)
5 COG1632 RPL15A Ribosomal prote 100.0 6.6E-61 1.4E-65 390.9 8.3 132 1-134 2-133 (195)
6 COG0810 TonB Periplasmic prote 56.6 12 0.00027 30.7 3.1 50 44-108 169-218 (244)
7 PHA02110 hypothetical protein 34.7 27 0.00058 26.5 1.7 25 102-126 16-40 (98)
8 cd08788 CARD_NOD2_2_CARD15 Cas 28.8 24 0.00051 26.2 0.5 20 32-51 32-51 (81)
9 PF11587 Prion_bPrPp: Major pr 26.5 60 0.0013 19.9 1.9 14 138-151 10-23 (29)
10 cd00933 barnase Barnase, a mem 25.1 74 0.0016 24.5 2.7 33 15-57 4-36 (107)
11 cd08786 CARD_RIP2_CARD3 Caspas 24.7 32 0.0007 25.8 0.6 12 40-51 42-53 (87)
12 PF10515 APP_amyloid: beta-amy 21.0 26 0.00056 24.1 -0.5 38 83-131 15-52 (52)
No 1
>PTZ00026 60S ribosomal protein L15; Provisional
Probab=100.00 E-value=2.4e-79 Score=502.22 Aligned_cols=134 Identities=69% Similarity=1.167 Sum_probs=132.9
Q ss_pred CchhHHHHHHHhccchhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccCceEEEEEEeeecCCCCCccCCcc
Q 031760 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (153)
Q Consensus 1 MgaYkYi~elwkkkqsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~ 80 (153)
||||+||+|+|++||||+|+||+|+|||||||+|+|||+++||||||||+||||||||||||||||||||+|+|+|+|+|
T Consensus 1 Mg~Y~yi~e~wkkkqsd~~r~l~r~R~we~Rq~~~i~R~~rPTR~DkAR~LGYKAKQG~vv~RvrVRrGgrkr~~~kg~~ 80 (204)
T PTZ00026 1 MGAYKYLNELWKKKQSDVMRFLLRVRTWEYRQLPVIHRVSRPTRPDKARRLGYKAKQGFVIYRVRVRRGGRKRPVRKGIV 80 (204)
T ss_pred CcHHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEcCCCCChhHHHHcCCcccceEEEEEEEEeeCCCCCCccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHHHHH
Q 031760 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMSLCF 134 (153)
Q Consensus 81 ~gKPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe~~~ 134 (153)
||||+|||||++|+++|||+|||||||++||||||||||||+|||+|||||.||
T Consensus 81 ~gkpk~~Gv~~lk~~kslq~iAEeRv~rk~~nLrVLNSYWV~qDg~yK~yEVIL 134 (204)
T PTZ00026 81 YGKPKTQGVNKLKSTRNLRAVAEERVGKRCGNLRVLNSYWVGQDSTYKFYEVIL 134 (204)
T ss_pred CCCccccCccccCcchhHHHHHHHHhhccCCCcEEecceeEcCCCCcccEEEEE
Confidence 999999999999999999999999999999999999999999999999999875
No 2
>KOG1678 consensus 60s ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.7e-80 Score=499.43 Aligned_cols=134 Identities=74% Similarity=1.248 Sum_probs=132.8
Q ss_pred CchhHHHHHHHhccchhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccCceEEEEEEeeecCCCCCccCCcc
Q 031760 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (153)
Q Consensus 1 MgaYkYi~elwkkkqsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~ 80 (153)
||||+||+|+|++||||+|+||+|+|||||||+++|||+++||||||||+||||||||||||||||++||+|+|+|||+|
T Consensus 1 MgAykY~~El~rkKQSDvmrfLlRvr~weYrQ~~~~hr~~rPtrpdkARrLGYkAKQG~viYrirVrrG~rKrpvpkG~t 80 (204)
T KOG1678|consen 1 MGAYKYLQELWRKKQSDVMRFLLRVRCWEYRQLSAIHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGAT 80 (204)
T ss_pred CcHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhhcCCCCCCchHHHhccccccceeEEEEEEEecCCccCCCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHHHHH
Q 031760 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMSLCF 134 (153)
Q Consensus 81 ~gKPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe~~~ 134 (153)
||||+|+||||||+++|+|++||||||++|+||+|||||||+||+||||||.||
T Consensus 81 yGKp~~~GvnqlK~~rs~qs~AEer~Gr~~g~LrVlNSYWv~qDstYk~fEVIl 134 (204)
T KOG1678|consen 81 YGKPVNQGVNQLKFQRSLQSVAEERAGRRCGNLRVLNSYWVNQDSTYKYFEVIL 134 (204)
T ss_pred cCCccccchhhhhhhHHHHHHHHHHhhccccceeeeehhhccCccceeeEEEEE
Confidence 999999999999999999999999999999999999999999999999999764
No 3
>PRK04243 50S ribosomal protein L15e; Validated
Probab=100.00 E-value=2.7e-78 Score=493.72 Aligned_cols=132 Identities=45% Similarity=0.761 Sum_probs=130.7
Q ss_pred CchhHHHHHHHhccchhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccCceEEEEEEeeecCCCCCccCCcc
Q 031760 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (153)
Q Consensus 1 MgaYkYi~elwkkkqsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~ 80 (153)
||||+||+|+|++||||+|+||+|+|||||||+|+|||+++||||||||+||||||||||||||||||||+|+|+|+|+
T Consensus 3 m~~Y~yi~e~wkk~~~~~~~~L~r~R~~e~R~~~~i~Rv~rPTR~DrAR~LGYKAKQG~vv~RvrVRrGgrkr~~~kg~- 81 (196)
T PRK04243 3 MSMYSYIREAWKRPKESYVGELMWQRLQEWRREPAVVRIERPTRLDRARALGYKAKQGIVVVRVRVRRGGLRKPRPKGG- 81 (196)
T ss_pred ccHHHHHHHHHhccchHHHHHHHHHHHHHHhccCceEEcCCCCChhHHHHcCccccceEEEEEEEeccCCCCCCCcCCC-
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHHHHH
Q 031760 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMSLCF 134 (153)
Q Consensus 81 ~gKPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe~~~ 134 (153)
|||+|||||+||+++|||+|||||||++||||||||||||+|||+|||||.||
T Consensus 82 -~kPk~~Gv~~lk~~kslq~iAEERa~rk~~nlrVLNSYwV~qDg~yK~fEVIl 134 (196)
T PRK04243 82 -RRPKRMGVNKITPAKSIQRIAEERAARKYPNLEVLNSYWVGEDGKYKWYEVIL 134 (196)
T ss_pred -CCccccCccccchhhhHHHHHHHHhhccCCCcEeeeeeEeccCCCcccEEEEE
Confidence 99999999999999999999999999999999999999999999999999874
No 4
>PF00827 Ribosomal_L15e: Ribosomal L15; InterPro: IPR000439 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 archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities []. One of these families consists of: Mammalian L15. Insect L15. Plant L15. Yeast YL10 (L13) (Rp15r). Archaebacterial L15e. These proteins have about 200 amino acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_P 4A1E_L 4A17_L 4A1A_L 4A1C_L 2ZKR_m 3IZS_P 1S1I_L 3O58_O 3O5H_O ....
Probab=100.00 E-value=5.3e-78 Score=490.94 Aligned_cols=133 Identities=68% Similarity=1.124 Sum_probs=121.7
Q ss_pred chhHHHHHHHhccchhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccCceEEEEEEeeecCCCCCccCCccc
Q 031760 2 GAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVY 81 (153)
Q Consensus 2 gaYkYi~elwkkkqsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~~ 81 (153)
|||+||+|+|++||||+|+||+|+|||||||+|+|+|+++||||||||+||||||||||||||||||||+|+|+|+|++|
T Consensus 1 g~Ykyi~e~wk~k~~d~~~~l~r~R~~e~R~~~av~Ri~rPtR~dkAR~LGYKAKQG~vv~RvrVrrGgrkr~~~kg~~~ 80 (192)
T PF00827_consen 1 GAYKYIRELWKKKQSDVMRFLLRIRLWEWRQLPAVHRIERPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPRPKGGRY 80 (192)
T ss_dssp -SHHHHHHHHHTTTSHHHHHHHHHHHHHHHHS-SEEEESS-SSHHHHHHTT-SSSTTEEEEEEEEESSS---SSSSSSST
T ss_pred CHHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEECCCCCCccHHHHcCCccCCeEEEEEEEEecCCCCCcccCCccc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHHHHH
Q 031760 82 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMSLCF 134 (153)
Q Consensus 82 gKPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe~~~ 134 (153)
|||+|||||++|+++|||+|||||||++||||||||||||+|||+|||||.||
T Consensus 81 gKPk~~Gv~~~k~~kslq~iAEeRagrk~~nLrVLnSYwV~eDg~yK~fEVIl 133 (192)
T PF00827_consen 81 GKPKHQGVNQLKPAKSLQSIAEERAGRKYPNLRVLNSYWVGEDGTYKWFEVIL 133 (192)
T ss_dssp SSCGGSSSTSS--SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEE
T ss_pred cccccceeeccCccccHHHHhhhhhccccCCceEEeeEEeCCCCcceeEEEEE
Confidence 99999999999999999999999999999999999999999999999999764
No 5
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.6e-61 Score=390.88 Aligned_cols=132 Identities=52% Similarity=0.829 Sum_probs=129.6
Q ss_pred CchhHHHHHHHhccchhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccCceEEEEEEeeecCCCCCccCCcc
Q 031760 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (153)
Q Consensus 1 MgaYkYi~elwkkkqsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~ 80 (153)
||||+||.|+|++++++++.+|+++|+|+||++|+|+|+++|||+|+||.||||||||||||||||++||+.+++|+++
T Consensus 2 ~~~y~yv~e~wkk~~~~~~~~l~~~r~~~wR~~~~i~R~erPTrldrAR~LGykaKqG~vvvrvrVrrG~~~~~r~~~g- 80 (195)
T COG1632 2 RSAYKYIREAWKKPKESVVRELLRQRLIEWRKEPSIVRIERPTRLDRARALGYKAKQGYVVVRVRVRRGGRNRKRPKKG- 80 (195)
T ss_pred ccHHHHHHHHHhCchHHHHhHHHhHHHHhhccCCceEEecCCCHHHHHHhcCCcccCceEEEEEeeecccccCcCccCC-
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHHHHH
Q 031760 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMSLCF 134 (153)
Q Consensus 81 ~gKPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe~~~ 134 (153)
++|++||+|++++++|+|.|||||||||||||+|||||||+|||.|||||-|+
T Consensus 81 -rrp~~mgvnki~~~ks~~~iAEerA~RK~pNL~vLnSYwVgeDg~yK~fEvIl 133 (195)
T COG1632 81 -RRPTRMGVNKIKRKKSLQFIAEERAGRKYPNLEVLNSYWVGEDGYYKYFEVIL 133 (195)
T ss_pred -CCcCcccccccChhhhHHHHHHHHhhccCCCcEeeeeEEeccccceeeEEEEE
Confidence 89999999999999999999999999999999999999999999999999764
No 6
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=56.60 E-value=12 Score=30.75 Aligned_cols=50 Identities=24% Similarity=0.238 Sum_probs=36.2
Q ss_pred cchhhhhccccccCceEEEEEEeeecCCCCCccCCcccCCcccccceecccccchhHHHHHHhhc
Q 031760 44 RPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSKRSVAEERAGR 108 (153)
Q Consensus 44 R~dkARrLGYKAKQG~VI~RVRVRrGgrkrp~pkg~~~gKPk~~Gvn~lk~~kslq~IAEERvgr 108 (153)
=|+.|+++|+ ||-|++++-|..+|. ..+.-|-+=+...-|..-|.+-+-+
T Consensus 169 YP~~A~~~g~---~G~V~V~f~i~~~G~------------v~~v~v~~SSg~~~lD~aal~air~ 218 (244)
T COG0810 169 YPAQARARGI---EGTVKVKFTIDPDGN------------VTNVRVLKSSGSPALDRAALEAIRK 218 (244)
T ss_pred CcHHHHhcCC---CceEEEEEEECCCCC------------EeeeEEeecCCcHHHHHHHHHHHHH
Confidence 5899999999 999999999998865 3344444445555666666665544
No 7
>PHA02110 hypothetical protein
Probab=34.66 E-value=27 Score=26.48 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=22.2
Q ss_pred HHHHhhcccCCceeeeeeeeccCCc
Q 031760 102 AEERAGRKLGGLRVLNSYWINEVCS 126 (153)
Q Consensus 102 AEERvgrk~~nLrVLNSYWV~eDg~ 126 (153)
.|--.|.+-|.+++.-|||.-.||-
T Consensus 16 ~esl~gn~vge~eifk~~w~i~dgf 40 (98)
T PHA02110 16 LESLFGNSVGEVEIFKSHWMIRDGF 40 (98)
T ss_pred hHhHhCCccceEeeeeeeeEeecCE
Confidence 4667899999999999999999983
No 8
>cd08788 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=28.78 E-value=24 Score=26.18 Aligned_cols=20 Identities=30% Similarity=0.286 Sum_probs=16.0
Q ss_pred cCCceeEeCCCCcchhhhhc
Q 031760 32 QHPSIVRVTRPTRPDKARRL 51 (153)
Q Consensus 32 q~~ai~Rv~rPTR~dkARrL 51 (153)
.+--.+|.+-+|+-|+||+|
T Consensus 32 ~Ecd~Ir~p~~T~sqqARrL 51 (81)
T cd08788 32 YDCDEIRLPIFTPSQQARRL 51 (81)
T ss_pred hhcchhhcCCCChHHHHHHH
Confidence 34455788899999999997
No 9
>PF11587 Prion_bPrPp: Major prion protein bPrPp - N terminal; PDB: 1SKH_A.
Probab=26.51 E-value=60 Score=19.95 Aligned_cols=14 Identities=57% Similarity=0.752 Sum_probs=12.1
Q ss_pred HHHHHHHHHhhhcc
Q 031760 138 SLVLFVMTLFETGL 151 (153)
Q Consensus 138 ~~~~~~~~~~~~~~ 151 (153)
.|||||.|--+.||
T Consensus 10 ilvLfvatwsdvgl 23 (29)
T PF11587_consen 10 ILVLFVATWSDVGL 23 (29)
T ss_dssp HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhhhcc
Confidence 47899999998887
No 10
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=25.08 E-value=74 Score=24.54 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=24.2
Q ss_pred chhHHHHHHHHHHHHHhcCCceeEeCCCCcchhhhhccccccC
Q 031760 15 QSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQ 57 (153)
Q Consensus 15 qsd~~r~L~r~R~we~Rq~~ai~Rv~rPTR~dkARrLGYKAKQ 57 (153)
+.+|..||.. ++++|.-.-.. +.|++||.+++.
T Consensus 4 ~~~V~~y~~~-----~~~LP~~yiTK-----~ea~~lGW~~~~ 36 (107)
T cd00933 4 FQGVADYLQT-----YHRLPDNYITK-----SQAKELGWVAPK 36 (107)
T ss_pred HHHHHHHHHH-----hCcCCcceEeH-----HHHHHhccCCCC
Confidence 3567776665 68899866433 789999999755
No 11
>cd08786 CARD_RIP2_CARD3 Caspase activation and recruitment domain of Receptor Interacting Protein 2. Caspase activation and recruitment domain (CARD) of Receptor Interacting Protein 2 (RIP2/RIPK2/RICK/CARDIAK/CARD3). RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP2 harbors a C-terminal CARD domain and functions as an effector kinase downstream of the pattern recognition receptors from the Nod-like (NLR)-family, NOD1 and NOD2, which recognizes bacterial peptidoglycans released upon infection. This cascade is implicated in inflammatory immune responses and the clearance of intracellular pathogens. RIP2 associates with NOD1 and NOD2 via CARD-CARD interactions. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein
Probab=24.69 E-value=32 Score=25.81 Aligned_cols=12 Identities=58% Similarity=0.947 Sum_probs=11.2
Q ss_pred CCCCcchhhhhc
Q 031760 40 TRPTRPDKARRL 51 (153)
Q Consensus 40 ~rPTR~dkARrL 51 (153)
+.|||-||||+|
T Consensus 42 ~~~T~t~K~R~L 53 (87)
T cd08786 42 TKPTRTSKVRQL 53 (87)
T ss_pred cccchHHHHHHH
Confidence 899999999987
No 12
>PF10515 APP_amyloid: beta-amyloid precursor protein C-terminus; InterPro: IPR019543 This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with IPR008154 from INTERPRO, further towards the N terminus. ; PDB: 2ROZ_A 3DXD_D 1X11_D 2LP1_A 2LOH_A 3MXC_L 3MXY_L 3DXC_B 3DXE_D 3L81_B ....
Probab=20.97 E-value=26 Score=24.08 Aligned_cols=38 Identities=24% Similarity=0.354 Sum_probs=14.2
Q ss_pred CcccccceecccccchhHHHHHHhhcccCCceeeeeeeeccCCchhHHH
Q 031760 83 KPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEVCSLISMS 131 (153)
Q Consensus 83 KPk~~Gvn~lk~~kslq~IAEERvgrk~~nLrVLNSYWV~eDg~yK~fe 131 (153)
-|.++|+-...+.-+. ||| ++.||.. |-| |.-||||||
T Consensus 15 ~~~~~g~veVD~~~tp----Ee~---h~~~mQ~-nGY---ENPTYkyfE 52 (52)
T PF10515_consen 15 GPISHGFVEVDPCLTP----EER---HLSNMQN-NGY---ENPTYKYFE 52 (52)
T ss_dssp ---------------H----HHH---HHHHHHC-TEE---ESCTCHHCC
T ss_pred CccccceEEecCCCCh----HHH---HHHHHHh-cCC---cCCceeccC
Confidence 3567888777666333 554 4445554 333 888999997
Done!