Query psy5233
Match_columns 178
No_of_seqs 310 out of 575
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 21:05:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK01242 rpl39e 50S ribosomal 100.0 3.2E-29 7E-34 168.2 5.1 50 129-178 1-50 (50)
2 COG2167 RPL39 Ribosomal protei 99.9 3.7E-27 8E-32 158.0 4.2 51 128-178 1-51 (51)
3 PF00832 Ribosomal_L39: Riboso 99.9 2.5E-26 5.4E-31 149.9 0.8 43 136-178 1-43 (43)
4 KOG0002|consensus 99.9 5.4E-26 1.2E-30 150.1 0.6 48 131-178 1-48 (48)
5 PRK01242 rpl39e 50S ribosomal 99.8 5.6E-19 1.2E-23 118.8 3.8 47 85-133 1-47 (50)
6 smart00700 JHBP Juvenile hormo 99.7 1.4E-17 2.9E-22 138.2 7.2 66 15-80 159-225 (225)
7 COG2167 RPL39 Ribosomal protei 99.7 1.9E-17 4E-22 111.2 3.0 48 84-133 1-48 (51)
8 KOG0002|consensus 99.6 3.1E-16 6.7E-21 103.8 -0.2 46 87-134 1-46 (48)
9 PF06585 JHBP: Haemolymph juve 99.6 2.5E-15 5.3E-20 125.1 4.7 64 15-78 184-248 (248)
10 PF00832 Ribosomal_L39: Riboso 99.6 6.8E-16 1.5E-20 100.9 1.0 42 92-135 1-42 (43)
11 PF05596 Taeniidae_ag: Taeniid 88.9 0.73 1.6E-05 32.6 3.9 45 21-66 19-63 (64)
12 PHA02920 putative virulence fa 47.8 28 0.0006 27.3 3.6 27 39-65 88-114 (117)
13 PF06744 DUF1215: Protein of u 45.9 72 0.0016 24.2 5.7 59 30-88 12-84 (125)
14 COG5216 Uncharacterized conser 40.0 14 0.00029 26.3 0.8 16 14-29 28-43 (67)
15 PHA02737 hypothetical protein; 35.3 43 0.00094 24.3 2.8 20 106-126 31-53 (72)
16 PF08564 CDC37_C: Cdc37 C term 35.1 17 0.00038 27.6 0.7 34 43-76 18-51 (99)
17 PF05595 DUF771: Domain of unk 33.5 27 0.00059 25.6 1.5 17 30-46 75-91 (91)
18 PF08989 DUF1896: Domain of un 33.4 25 0.00055 28.6 1.5 49 32-83 75-123 (144)
19 PF10075 PCI_Csn8: COP9 signal 33.1 50 0.0011 25.4 3.1 43 36-78 61-104 (143)
20 PF06585 JHBP: Haemolymph juve 31.6 43 0.00093 27.7 2.6 42 30-71 190-233 (248)
21 TIGR00620 sporelyase spore pho 31.2 68 0.0015 27.2 3.8 36 38-88 96-131 (199)
22 PF13739 DUF4163: Domain of un 27.5 91 0.002 21.4 3.4 29 27-55 27-56 (101)
23 PF04700 Baculo_gp41: Structur 27.1 34 0.00073 29.0 1.2 41 60-108 42-82 (186)
24 smart00700 JHBP Juvenile hormo 26.2 1.4E+02 0.0031 24.5 4.9 40 32-71 173-212 (225)
25 PF02607 B12-binding_2: B12 bi 24.5 56 0.0012 22.2 1.8 25 24-48 12-40 (79)
26 PF14659 Phage_int_SAM_3: Phag 22.2 1.7E+02 0.0037 18.2 3.7 33 47-79 15-47 (58)
27 PF03008 DUF234: Archaea bacte 21.5 1.7E+02 0.0037 21.3 4.0 41 39-79 14-54 (100)
28 KOG3965|consensus 20.0 2.2E+02 0.0048 23.6 4.6 47 22-68 92-138 (160)
No 1
>PRK01242 rpl39e 50S ribosomal protein L39e; Validated
Probab=99.95 E-value=3.2e-29 Score=168.24 Aligned_cols=50 Identities=48% Similarity=0.886 Sum_probs=48.7
Q ss_pred CCcchHHHHHHHHHHHhccCCCCceEEEecCCcccccCcCCccccccCCC
Q psy5233 129 SAHKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLKL 178 (178)
Q Consensus 129 ~~~k~~~~K~rL~k~~kqN~~iP~w~~~kt~~~v~~n~krr~Wrr~kl~~ 178 (178)
+|||||++|++||||+|||+|||+||+||||++|+|||||||||||+|++
T Consensus 1 ~s~Kt~~~K~rLaK~~kQNrpvP~Wv~~KT~~kvr~n~kRRhWRRtkL~~ 50 (50)
T PRK01242 1 MRNKPLGKKLRLAKALKQNRRVPAWVIVKTNRRVRRHPKRRHWRRSKLKV 50 (50)
T ss_pred CCcchHHHHHHHHHHHhccCCCCeEEEEEcCCceecCCccccccccccCC
Confidence 68999999999999999999999999999999999999999999999985
No 2
>COG2167 RPL39 Ribosomal protein L39E [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=3.7e-27 Score=157.96 Aligned_cols=51 Identities=55% Similarity=1.002 Sum_probs=50.1
Q ss_pred CCCcchHHHHHHHHHHHhccCCCCceEEEecCCcccccCcCCccccccCCC
Q psy5233 128 HSAHKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLKL 178 (178)
Q Consensus 128 ~~~~k~~~~K~rL~k~~kqN~~iP~w~~~kt~~~v~~n~krr~Wrr~kl~~ 178 (178)
|+++|+++.|+|||||.|||++||+||+|||+++|+|||+||||||+||++
T Consensus 1 M~~~K~~~~K~RLaKA~KqNrrvP~Wv~~kT~~~v~~npkRRhWRR~kLki 51 (51)
T COG2167 1 MGRNKPLGKKLRLAKALKQNRRVPVWVRVKTNRRVRYNPKRRHWRRTKLKI 51 (51)
T ss_pred CCccchHHHHHHHHHHHHcCCCCCeEEEEecCCccccChhhhhhhhhccCC
Confidence 899999999999999999999999999999999999999999999999986
No 3
>PF00832 Ribosomal_L39: Ribosomal L39 protein; InterPro: IPR000077 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 large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins are very basic. About 50 residues long, they are the smallest proteins of eukaryotic-type ribosomes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CCJ_2 3CME_2 3OW2_1 1YI2_2 1KD1_3 3CXC_1 3G6E_2 1VQ4_2 3CCU_2 3CC7_2 ....
Probab=99.92 E-value=2.5e-26 Score=149.93 Aligned_cols=43 Identities=77% Similarity=1.356 Sum_probs=32.3
Q ss_pred HHHHHHHHHhccCCCCceEEEecCCcccccCcCCccccccCCC
Q psy5233 136 IKMKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLKL 178 (178)
Q Consensus 136 ~K~rL~k~~kqN~~iP~w~~~kt~~~v~~n~krr~Wrr~kl~~ 178 (178)
+|++||||++||+|||+||+||||++|+|||||||||||+|+|
T Consensus 1 ~K~rLaKa~kqNrpvP~Wv~~kT~~kiryn~kRRhWRRtkLkv 43 (43)
T PF00832_consen 1 IKLRLAKAQKQNRPVPQWVRMKTGNKIRYNPKRRHWRRTKLKV 43 (43)
T ss_dssp HHHHHHHHHHHTS---HHGHHCTTSS-SSGTT---TTTS-S--
T ss_pred CcHHHHHHHhccCCCCcEEEEeCCCceeeCCCcccccccccCC
Confidence 5899999999999999999999999999999999999999986
No 4
>KOG0002|consensus
Probab=99.91 E-value=5.4e-26 Score=150.07 Aligned_cols=48 Identities=94% Similarity=1.454 Sum_probs=46.7
Q ss_pred cchHHHHHHHHHHHhccCCCCceEEEecCCcccccCcCCccccccCCC
Q psy5233 131 HKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLKL 178 (178)
Q Consensus 131 ~k~~~~K~rL~k~~kqN~~iP~w~~~kt~~~v~~n~krr~Wrr~kl~~ 178 (178)
+|++.+|.+|||+++||+||||||+|+||++|+||.||||||||||++
T Consensus 1 ~ks~~ik~kl~k~~kqnr~iP~WiRm~~gn~iryN~kRRHWRrtKL~l 48 (48)
T KOG0002|consen 1 HKSFRIKQKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLGL 48 (48)
T ss_pred CchhHHHHHHHHHHHccCCccHHHhhccCCccchhHHHHHHHHhhcCC
Confidence 589999999999999999999999999999999999999999999986
No 5
>PRK01242 rpl39e 50S ribosomal protein L39e; Validated
Probab=99.75 E-value=5.6e-19 Score=118.78 Aligned_cols=47 Identities=36% Similarity=0.597 Sum_probs=43.6
Q ss_pred cccchhHHHHHHHHHhhcCCCCCcceeeecCCceeEeeccCCCCCCcch
Q psy5233 85 SAHKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTISVLYHCKSRHSAHKT 133 (178)
Q Consensus 85 ~~~k~~~~K~rLak~~kqNr~vP~wv~~kt~~~v~~~~~~krr~~~~k~ 133 (178)
+|||||++|++||||++||||||+||+||||++|+ ||+++|+=+...
T Consensus 1 ~s~Kt~~~K~rLaK~~kQNrpvP~Wv~~KT~~kvr--~n~kRRhWRRtk 47 (50)
T PRK01242 1 MRNKPLGKKLRLAKALKQNRRVPAWVIVKTNRRVR--RHPKRRHWRRSK 47 (50)
T ss_pred CCcchHHHHHHHHHHHhccCCCCeEEEEEcCCcee--cCCccccccccc
Confidence 58999999999999999999999999999999999 999999866543
No 6
>smart00700 JHBP Juvenile hormone binding protein domains in insects. The juvenile hormone exerts pleiotropic functions during insect life cycles and its binding proteins regulate these functions.
Probab=99.71 E-value=1.4e-17 Score=138.17 Aligned_cols=66 Identities=27% Similarity=0.389 Sum_probs=64.0
Q ss_pred cceeEEecccCCCCc-hhhHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhccc
Q psy5233 15 ECIKNTLQSLIPKFK-DGTIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLDQI 80 (178)
Q Consensus 15 ~~v~~~l~NLFNGnk-Lgd~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delfp~ 80 (178)
++++++|+||||||+ |++++|+|+||||++|++|++|.++++++.+|.+++|++|.++|++++|+.
T Consensus 159 ~~~~~~~~NLfngn~~L~~~~n~~lNen~~~i~~e~~p~i~~~~~~~~~~~~n~~~~~vp~~~~f~~ 225 (225)
T smart00700 159 GDVKSHLDNLFNGNKDLNDAINKFLNENWKALINELLPAIVEKLESIFLDLVNKVFAKVPIDEFFVD 225 (225)
T ss_pred ceEEEEeeccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHhhcC
Confidence 479999999999999 999999999999999999999999999999999999999999999999974
No 7
>COG2167 RPL39 Ribosomal protein L39E [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=1.9e-17 Score=111.23 Aligned_cols=48 Identities=38% Similarity=0.659 Sum_probs=44.7
Q ss_pred ccccchhHHHHHHHHHhhcCCCCCcceeeecCCceeEeeccCCCCCCcch
Q psy5233 84 RSAHKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTISVLYHCKSRHSAHKT 133 (178)
Q Consensus 84 ~~~~k~~~~K~rLak~~kqNr~vP~wv~~kt~~~v~~~~~~krr~~~~k~ 133 (178)
|+++|+++.|+|||||.||||+||+||+++|+++|+ ||+++|+=+.+.
T Consensus 1 M~~~K~~~~K~RLaKA~KqNrrvP~Wv~~kT~~~v~--~npkRRhWRR~k 48 (51)
T COG2167 1 MGRNKPLGKKLRLAKALKQNRRVPVWVRVKTNRRVR--YNPKRRHWRRTK 48 (51)
T ss_pred CCccchHHHHHHHHHHHHcCCCCCeEEEEecCCccc--cChhhhhhhhhc
Confidence 899999999999999999999999999999999999 999998865543
No 8
>KOG0002|consensus
Probab=99.56 E-value=3.1e-16 Score=103.80 Aligned_cols=46 Identities=74% Similarity=1.144 Sum_probs=41.9
Q ss_pred cchhHHHHHHHHHhhcCCCCCcceeeecCCceeEeeccCCCCCCcchH
Q psy5233 87 HKTFRIKMKLAKKLKQNRPIPQWIRMRTGNTISVLYHCKSRHSAHKTF 134 (178)
Q Consensus 87 ~k~~~~K~rLak~~kqNr~vP~wv~~kt~~~v~~~~~~krr~~~~k~~ 134 (178)
||++.+|.+|||+++||||||||++|+||++|+ ||.++|+=+...+
T Consensus 1 ~ks~~ik~kl~k~~kqnr~iP~WiRm~~gn~ir--yN~kRRHWRrtKL 46 (48)
T KOG0002|consen 1 HKSFRIKQKLAKKLKQNRPIPQWIRMRTGNTIR--YNAKRRHWRRTKL 46 (48)
T ss_pred CchhHHHHHHHHHHHccCCccHHHhhccCCccc--hhHHHHHHHHhhc
Confidence 689999999999999999999999999999999 9999988665443
No 9
>PF06585 JHBP: Haemolymph juvenile hormone binding protein (JHBP); InterPro: IPR010562 This family consists of several insect specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone (JH) has a profound effect on insects. It regulates embryogenesis, maintains the status quo of larva development and stimulates reproductive maturation in the adult forms. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph []. The crystal structure of the JHBP from Galleria mellonella (Wax moth) shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulphide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance [, ].; PDB: 3A1Z_D 3AOS_B 3AOT_A 2RQF_A 2RCK_A 3E8W_A 3E8T_A.
Probab=99.56 E-value=2.5e-15 Score=125.06 Aligned_cols=64 Identities=28% Similarity=0.441 Sum_probs=62.0
Q ss_pred cceeEEecccCCCCc-hhhHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhc
Q psy5233 15 ECIKNTLQSLIPKFK-DGTIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLD 78 (178)
Q Consensus 15 ~~v~~~l~NLFNGnk-Lgd~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delf 78 (178)
++++++++|||+||+ |++.+|+|+||||+++++|++|.+++.+++++.+++|++|+++|+++||
T Consensus 184 ~~~~~~~~nl~~g~~~l~~~~n~~in~~~~~~~~~~~p~i~~~~~~~i~~~~N~~l~~~p~~~lf 248 (248)
T PF06585_consen 184 GNVKFDLENLFNGNKELSDFINKFINENWPELLNEVKPDIEEILSKIITDIINKILSKVPYDELF 248 (248)
T ss_dssp CEEEEEESHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-CCHCB
T ss_pred ceEEEEeeccCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHhC
Confidence 889999999999999 9999999999999999999999999999999999999999999999997
No 10
>PF00832 Ribosomal_L39: Ribosomal L39 protein; InterPro: IPR000077 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 large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins are very basic. About 50 residues long, they are the smallest proteins of eukaryotic-type ribosomes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CCJ_2 3CME_2 3OW2_1 1YI2_2 1KD1_3 3CXC_1 3G6E_2 1VQ4_2 3CCU_2 3CC7_2 ....
Probab=99.56 E-value=6.8e-16 Score=100.94 Aligned_cols=42 Identities=55% Similarity=0.973 Sum_probs=30.5
Q ss_pred HHHHHHHHhhcCCCCCcceeeecCCceeEeeccCCCCCCcchHH
Q psy5233 92 IKMKLAKKLKQNRPIPQWIRMRTGNTISVLYHCKSRHSAHKTFR 135 (178)
Q Consensus 92 ~K~rLak~~kqNr~vP~wv~~kt~~~v~~~~~~krr~~~~k~~~ 135 (178)
+|++||||++||||||+||+||||++|+ ||+++|+=+...++
T Consensus 1 ~K~rLaKa~kqNrpvP~Wv~~kT~~kir--yn~kRRhWRRtkLk 42 (43)
T PF00832_consen 1 IKLRLAKAQKQNRPVPQWVRMKTGNKIR--YNPKRRHWRRTKLK 42 (43)
T ss_dssp HHHHHHHHHHHTS---HHGHHCTTSS-S--SGTT---TTTS-S-
T ss_pred CcHHHHHHHhccCCCCcEEEEeCCCcee--eCCCcccccccccC
Confidence 5899999999999999999999999999 99999987766543
No 11
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=88.88 E-value=0.73 Score=32.61 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=40.2
Q ss_pred ecccCCCCchhhHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy5233 21 LQSLIPKFKDGTIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLN 66 (178)
Q Consensus 21 l~NLFNGnkLgd~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~N 66 (178)
+.++|..|+||..+-++.+| |.+++.+++-=|..++++.+..+.|
T Consensus 19 v~~FF~~DPlGqkIa~l~kd-w~~~~~~~r~KiR~~L~ey~k~L~~ 63 (64)
T PF05596_consen 19 VRNFFYEDPLGQKIAQLAKD-WNEICQEVRKKIRAALAEYCKGLKN 63 (64)
T ss_pred HHHHhccCchHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 46789999999999999875 9999999999999999999887765
No 12
>PHA02920 putative virulence factor; Provisional
Probab=47.84 E-value=28 Score=27.35 Aligned_cols=27 Identities=15% Similarity=0.330 Sum_probs=23.4
Q ss_pred hhcHHHHHHHHhHHHHHHHHHHHHHHH
Q psy5233 39 NQFWKVVYDALLPFAEEGFAKVAKPVL 65 (178)
Q Consensus 39 NeNW~ev~~El~P~ie~~~~~if~~i~ 65 (178)
+=||+++|++|.-.+++.|.+++.++-
T Consensus 88 eI~Wd~vf~~LF~~l~~~~~~~~~~~~ 114 (117)
T PHA02920 88 EIRWEESFTILFRMIEKYFDDLMIDLY 114 (117)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 459999999999999999999887753
No 13
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=45.94 E-value=72 Score=24.25 Aligned_cols=59 Identities=14% Similarity=0.182 Sum_probs=48.2
Q ss_pred hhhHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHH-HHHhhccCcch-------------hhccccccccccc
Q psy5233 30 DGTIALTFINQFWKVVYDALLPFAEEGFAKVAKPV-LNKVFLSVPYE-------------QLDQIGTNRSAHK 88 (178)
Q Consensus 30 Lgd~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i-~NkiF~kvP~d-------------elfp~~~~~~~~k 88 (178)
|...+...+.+-|..+..+....|...|..-+... -..|-.++|++ ++|-.++.|.+.-
T Consensus 12 l~~~l~~~~~~~~~~~~~~a~~~ln~~w~~~V~~~~~~~i~gRYPF~~~s~~dv~l~Df~~fF~p~G~ld~F~ 84 (125)
T PF06744_consen 12 LRPWLLSPADQAWKLVLQGARSYLNKAWQAEVYPFCRQAIAGRYPFDPDSSRDVSLADFARFFGPGGVLDQFF 84 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcccCCHHHHHHHhcCCCcHHHHH
Confidence 88889999999999999999999999996655554 45577799998 6777777776643
No 14
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=39.97 E-value=14 Score=26.30 Aligned_cols=16 Identities=13% Similarity=0.044 Sum_probs=14.4
Q ss_pred ccceeEEecccCCCCc
Q psy5233 14 NECIKNTLQSLIPKFK 29 (178)
Q Consensus 14 ~~~v~~~l~NLFNGnk 29 (178)
+++..++|++|++|..
T Consensus 28 GDRFeIsLeDl~~GE~ 43 (67)
T COG5216 28 GDRFEISLEDLRNGEV 43 (67)
T ss_pred CCEeEEEHHHhhCCce
Confidence 6789999999999975
No 15
>PHA02737 hypothetical protein; Provisional
Probab=35.31 E-value=43 Score=24.34 Aligned_cols=20 Identities=35% Similarity=0.684 Sum_probs=15.6
Q ss_pred CCc-ceeee--cCCceeEeeccCC
Q psy5233 106 IPQ-WIRMR--TGNTISVLYHCKS 126 (178)
Q Consensus 106 vP~-wv~~k--t~~~v~~~~~~kr 126 (178)
||. |++++ |+.+|.|.| +..
T Consensus 31 VP~sWIi~r~~td~kv~VaY-P~~ 53 (72)
T PHA02737 31 VPDSWIIRRKATDQKSIVAY-FEG 53 (72)
T ss_pred eCceeEEEEeccCceEEEEc-cCC
Confidence 454 99998 799999888 553
No 16
>PF08564 CDC37_C: Cdc37 C terminal domain; InterPro: IPR013873 Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain IPR013874 from INTERPRO and the N-terminal kinase binding domain of Cdc37 IPR013855 from INTERPRO []. ; PDB: 1US7_B.
Probab=35.07 E-value=17 Score=27.61 Aligned_cols=34 Identities=24% Similarity=0.377 Sum_probs=16.3
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchh
Q psy5233 43 KVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQ 76 (178)
Q Consensus 43 ~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~de 76 (178)
.+||+.|-|.+.++|..-=.+.+|++|.++|.++
T Consensus 18 ~evFeslP~emq~Alet~~ld~vnkVl~~M~vee 51 (99)
T PF08564_consen 18 REVFESLPPEMQKALETGDLDEVNKVLGKMPVEE 51 (99)
T ss_dssp -HHHHHS-TT------------HHHHHT--SSSH
T ss_pred HHHHHHCCHHHHHHHHcCCHHHHHHHHHhCCHHH
Confidence 4899999999999999999999999999999774
No 17
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=33.48 E-value=27 Score=25.59 Aligned_cols=17 Identities=6% Similarity=0.262 Sum_probs=15.7
Q ss_pred hhhHHHHHHhhcHHHHH
Q psy5233 30 DGTIALTFINQFWKVVY 46 (178)
Q Consensus 30 Lgd~~N~fLNeNW~ev~ 46 (178)
++..|.+||++|+.+|+
T Consensus 75 ~a~~~~~fl~~~f~eI~ 91 (91)
T PF05595_consen 75 NAKKMKEFLEEHFEEID 91 (91)
T ss_pred ehHHHHHHHHHhHHhhC
Confidence 89999999999999984
No 18
>PF08989 DUF1896: Domain of unknown function (DUF1896); InterPro: IPR015082 This domain is found in a set of hypothetical bacterial proteins. ; PDB: 2APL_A.
Probab=33.42 E-value=25 Score=28.59 Aligned_cols=49 Identities=14% Similarity=0.022 Sum_probs=33.4
Q ss_pred hHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhcccccc
Q psy5233 32 TIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLDQIGTN 83 (178)
Q Consensus 32 d~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delfp~~~~ 83 (178)
|.+.++| |.|+..|+-+.-.+.++..+...+..+|+++++++=|..+..
T Consensus 75 dtl~~Vl---enEF~~evp~~~~~~~al~Llp~~~~vF~kY~l~DdFa~sp~ 123 (144)
T PF08989_consen 75 DTLREVL---ENEFEDEVPEEKRERFALKLLPACEPVFAKYELSDDFAYSPE 123 (144)
T ss_dssp HHHHHHH---HHHSTTTS-TTHHHHHHHHHHHHHHHHHTTS---TTGGGSTH
T ss_pred HHHHHHH---HHHHHHhcCcchHHHHHHHHHHHHHHHHhcCCCCcccccchh
Confidence 4445555 445556678888888899999999999999999887765543
No 19
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=33.05 E-value=50 Score=25.41 Aligned_cols=43 Identities=16% Similarity=0.349 Sum_probs=32.1
Q ss_pred HHHhhc-HHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhc
Q psy5233 36 TFINQF-WKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLD 78 (178)
Q Consensus 36 ~fLNeN-W~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delf 78 (178)
+.++++ |.+-+.++.+.+++.+-+.+..++.+.|..++.+.+-
T Consensus 61 ~~~~~~~~~~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la 104 (143)
T PF10075_consen 61 QALRSNPWSPDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLA 104 (143)
T ss_dssp HHS-TT----HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHH
T ss_pred HHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHH
Confidence 344564 8899999999999999999999999999999998764
No 20
>PF06585 JHBP: Haemolymph juvenile hormone binding protein (JHBP); InterPro: IPR010562 This family consists of several insect specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone (JH) has a profound effect on insects. It regulates embryogenesis, maintains the status quo of larva development and stimulates reproductive maturation in the adult forms. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph []. The crystal structure of the JHBP from Galleria mellonella (Wax moth) shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulphide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance [, ].; PDB: 3A1Z_D 3AOS_B 3AOT_A 2RQF_A 2RCK_A 3E8W_A 3E8T_A.
Probab=31.64 E-value=43 Score=27.67 Aligned_cols=42 Identities=10% Similarity=0.055 Sum_probs=25.6
Q ss_pred hhhHHH--HHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhcc
Q psy5233 30 DGTIAL--TFINQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLS 71 (178)
Q Consensus 30 Lgd~~N--~fLNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~k 71 (178)
++...+ .-+++....+++|..|.+-+.+.+.+.+.+..++..
T Consensus 190 ~~nl~~g~~~l~~~~n~~in~~~~~~~~~~~p~i~~~~~~~i~~ 233 (248)
T PF06585_consen 190 LENLFNGNKELSDFINKFINENWPELLNEVKPDIEEILSKIITD 233 (248)
T ss_dssp ESHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eeccCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 544433 666677777777776666666666666655555443
No 21
>TIGR00620 sporelyase spore photoproduct lyase. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.23 E-value=68 Score=27.24 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=24.4
Q ss_pred HhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhccccccccccc
Q psy5233 38 INQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLDQIGTNRSAHK 88 (178)
Q Consensus 38 LNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delfp~~~~~~~~k 88 (178)
+-|||++.|.+| +.++|..+|-+.+-+..-.+.+|.
T Consensus 96 ~~egW~e~Y~~l---------------~~~l~~~l~~~~~~dl~~e~i~~R 131 (199)
T TIGR00620 96 IHEGWKEGYRNL---------------LEKLDEALPQDLRHDITFEVIQHR 131 (199)
T ss_pred eeCChHHHHHHH---------------HHHHHHhCCHhhhcCeEEEEEEEE
Confidence 457888888877 556667777777666665565543
No 22
>PF13739 DUF4163: Domain of unknown function (DUF4163); PDB: 3CYG_B.
Probab=27.48 E-value=91 Score=21.39 Aligned_cols=29 Identities=21% Similarity=0.042 Sum_probs=22.5
Q ss_pred CCc-hhhHHHHHHhhcHHHHHHHHhHHHHH
Q psy5233 27 KFK-DGTIALTFINQFWKVVYDALLPFAEE 55 (178)
Q Consensus 27 Gnk-Lgd~~N~fLNeNW~ev~~El~P~ie~ 55 (178)
+|+ +.+.+|++|++.-....+++.....+
T Consensus 27 ~~~~~~~~IN~~i~~~i~~~~~~~~~~~~~ 56 (101)
T PF13739_consen 27 KNKELQKKINDFIENQIDNFINEIEEEAKE 56 (101)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 377 99999999999998888886555544
No 23
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=27.09 E-value=34 Score=28.99 Aligned_cols=41 Identities=24% Similarity=0.382 Sum_probs=29.9
Q ss_pred HHHHHHHHhhccCcchhhccccccccccchhHHHHHHHHHhhcCCCCCc
Q psy5233 60 VAKPVLNKVFLSVPYEQLDQIGTNRSAHKTFRIKMKLAKKLKQNRPIPQ 108 (178)
Q Consensus 60 if~~i~NkiF~kvP~delfp~~~~~~~~k~~~~K~rLak~~kqNr~vP~ 108 (178)
++...+.+|+.+ .-++-++|=+...|--.|-+.-||+|+|-
T Consensus 42 ~mksYA~KFYn~--------~l~eAA~hLs~~vkYQiA~AVT~n~PiPl 82 (186)
T PF04700_consen 42 IMKSYADKFYNR--------RLNEAARHLSDVVKYQIAEAVTQNKPIPL 82 (186)
T ss_pred chHHHHHHHHHh--------HHHHHHHHHHHHHHHHHHHHHHcCCCcCc
Confidence 455555566555 33345677788889999999999999997
No 24
>smart00700 JHBP Juvenile hormone binding protein domains in insects. The juvenile hormone exerts pleiotropic functions during insect life cycles and its binding proteins regulate these functions.
Probab=26.16 E-value=1.4e+02 Score=24.47 Aligned_cols=40 Identities=13% Similarity=0.083 Sum_probs=31.4
Q ss_pred hHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhcc
Q psy5233 32 TIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLS 71 (178)
Q Consensus 32 d~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~NkiF~k 71 (178)
..+++++|+-..+-++|+...+...+.+.+..++-.++.+
T Consensus 173 ~~L~~~~n~~lNen~~~i~~e~~p~i~~~~~~~~~~~~n~ 212 (225)
T smart00700 173 KDLNDAINKFLNENWKALINELLPAIVEKLESIFLDLVNK 212 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6667888888888888888888888888888777776554
No 25
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=24.48 E-value=56 Score=22.19 Aligned_cols=25 Identities=8% Similarity=-0.019 Sum_probs=14.7
Q ss_pred cCCCCc--hhhHHHHHHhh--cHHHHHHH
Q psy5233 24 LIPKFK--DGTIALTFINQ--FWKVVYDA 48 (178)
Q Consensus 24 LFNGnk--Lgd~~N~fLNe--NW~ev~~E 48 (178)
+.+||+ +.+.+++.+.+ .-..|+++
T Consensus 12 l~~~d~~~~~~~~~~~l~~g~~~~~i~~~ 40 (79)
T PF02607_consen 12 LLAGDEEEAEALLEEALAQGYPPEDIIEE 40 (79)
T ss_dssp HHTT-CCHHHHHHHHHHHCSSSTTHHHHH
T ss_pred HHhCCHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 345665 66677777655 55566666
No 26
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=22.21 E-value=1.7e+02 Score=18.16 Aligned_cols=33 Identities=12% Similarity=0.175 Sum_probs=25.9
Q ss_pred HHHhHHHHHHHHHHHHHHHHHhhccCcchhhcc
Q psy5233 47 DALLPFAEEGFAKVAKPVLNKVFLSVPYEQLDQ 79 (178)
Q Consensus 47 ~El~P~ie~~~~~if~~i~NkiF~kvP~delfp 79 (178)
.++.|.........+...+...|.++|++++=+
T Consensus 15 ~~~~~~T~~~y~~~~~~~i~p~~g~~~i~~It~ 47 (58)
T PF14659_consen 15 SNLKPSTYKNYKSIIKNHILPYFGNKKIKDITP 47 (58)
T ss_dssp CTSSHHHHHHHHHHHHHHHHHHTTSSBGGG--H
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHCcCcHHHCCH
Confidence 468888888898999987777889999887743
No 27
>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) [].
Probab=21.55 E-value=1.7e+02 Score=21.25 Aligned_cols=41 Identities=7% Similarity=-0.002 Sum_probs=28.4
Q ss_pred hhcHHHHHHHHhHHHHHHHHHHHHHHHHHhhccCcchhhcc
Q psy5233 39 NQFWKVVYDALLPFAEEGFAKVAKPVLNKVFLSVPYEQLDQ 79 (178)
Q Consensus 39 NeNW~ev~~El~P~ie~~~~~if~~i~NkiF~kvP~delfp 79 (178)
-.+...+++.+.|.+.+.++..|.++...++........+|
T Consensus 14 ~g~~~~~~~~i~~~l~~y~g~~fE~i~r~~l~~~~~~~~lp 54 (100)
T PF03008_consen 14 RGRGEAVYEKIKPELNQYMGFAFEEICREYLRRLNRAGKLP 54 (100)
T ss_pred CCCHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhcccCCC
Confidence 34556777778888888888888888877776655444433
No 28
>KOG3965|consensus
Probab=20.04 E-value=2.2e+02 Score=23.64 Aligned_cols=47 Identities=13% Similarity=0.017 Sum_probs=41.2
Q ss_pred cccCCCCchhhHHHHHHhhcHHHHHHHHhHHHHHHHHHHHHHHHHHh
Q psy5233 22 QSLIPKFKDGTIALTFINQFWKVVYDALLPFAEEGFAKVAKPVLNKV 68 (178)
Q Consensus 22 ~NLFNGnkLgd~~N~fLNeNW~ev~~El~P~ie~~~~~if~~i~Nki 68 (178)
.++||||.-++....=+=|+-..+++.+-|.+.+.|+.-+.+.+..+
T Consensus 92 ~d~~ngd~~~~~l~t~yyes~y~LLd~ISP~y~E~Fg~~l~q~L~~l 138 (160)
T KOG3965|consen 92 YDCMNGDFTEDDLHTKYYESAYQLLDDISPLYRERFGNKLEQRLKRL 138 (160)
T ss_pred cchhcccchhhhhhhHHHhhHHHHHhhcChHHHHHHHHHHHHHHHHH
Confidence 35899999788888888899999999999999999999888877665
Done!