Query 029857
Match_columns 186
No_of_seqs 117 out of 253
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 04:45:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029857.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029857hhsearch_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 7E-111 2E-115 706.8 15.8 186 1-186 19-204 (204)
2 KOG1678 60s ribosomal protein 100.0 2E-109 4E-114 689.9 10.8 185 1-186 19-204 (204)
3 PF00827 Ribosomal_L15e: Ribos 100.0 1E-106 3E-111 676.3 13.4 175 1-175 18-192 (192)
4 PRK04243 50S ribosomal protein 100.0 4E-103 9E-108 656.8 13.8 174 1-176 21-194 (196)
5 COG1632 RPL15A Ribosomal prote 100.0 5.9E-84 1.3E-88 540.0 13.2 175 1-177 20-194 (195)
6 COG1632 RPL15A Ribosomal prote 66.4 2.9 6.3E-05 36.3 1.1 64 122-186 130-194 (195)
7 PF01161 PBP: Phosphatidyletha 60.7 12 0.00027 28.6 3.6 36 102-137 26-64 (146)
8 cd00457 PEBP PhosphatidylEthan 46.5 23 0.00051 28.4 3.2 34 102-137 31-64 (159)
9 cd00866 PEBP_euk PhosphatidylE 45.8 30 0.00066 26.8 3.6 43 90-137 25-70 (154)
10 COG2932 Predicted transcriptio 44.6 12 0.00027 30.8 1.3 27 101-127 126-155 (214)
11 PHA02110 hypothetical protein 43.2 24 0.00052 27.5 2.6 32 84-120 16-47 (98)
12 PRK08351 DNA-directed RNA poly 43.2 13 0.00028 26.8 1.1 25 91-122 17-42 (61)
13 COG0463 WcaA Glycosyltransfera 41.6 16 0.00034 24.9 1.3 12 110-121 31-42 (291)
14 COG0810 TonB Periplasmic prote 41.4 28 0.00061 29.6 3.1 50 26-90 169-218 (244)
15 COG0144 Sun tRNA and rRNA cyto 40.0 18 0.00038 32.8 1.7 25 111-135 229-256 (355)
16 PF05063 MT-A70: MT-A70 ; Int 35.9 15 0.00032 29.6 0.5 10 112-121 1-10 (176)
17 cd07998 WGR_DNA_ligase WGR dom 33.0 40 0.00086 25.2 2.3 19 100-118 4-22 (77)
18 PRK11933 yebU rRNA (cytosine-C 30.3 41 0.0009 32.0 2.5 37 92-133 163-208 (470)
19 cd05468 pVHL von Hippel-Landau 29.6 48 0.001 26.5 2.5 33 96-128 19-59 (141)
20 COG2876 AroA 3-deoxy-D-arabino 29.5 24 0.00053 32.3 0.9 15 115-129 217-231 (286)
21 cd06433 GT_2_WfgS_like WfgS an 28.7 31 0.00068 25.6 1.2 13 109-121 25-37 (202)
22 PRK14688 hypothetical protein; 28.2 42 0.0009 26.5 1.9 22 111-136 96-117 (121)
23 PLN00169 CETS family protein; 27.9 71 0.0015 26.6 3.3 29 109-137 62-93 (175)
24 PF04915 DltD_N: DltD N-termin 27.7 20 0.00043 25.9 -0.0 14 113-126 38-51 (62)
25 cd00272 Chemokine_CC Chemokine 27.6 37 0.00081 22.9 1.3 39 96-135 13-51 (57)
26 PF11396 DUF2874: Protein of u 27.0 1.7E+02 0.0037 19.1 4.5 44 88-132 16-60 (61)
27 PF00836 Stathmin: Stathmin fa 26.6 35 0.00075 28.1 1.2 12 111-122 16-27 (140)
28 cd00865 PEBP_bact_arch Phospha 26.5 70 0.0015 25.3 2.9 27 109-137 39-65 (150)
29 PF10515 APP_amyloid: beta-amy 25.4 15 0.00033 26.0 -0.9 37 66-113 16-52 (52)
30 TIGR00446 nop2p NOL1/NOP2/sun 25.1 59 0.0013 27.8 2.4 23 112-134 141-166 (264)
31 PF07450 HycH: Formate hydroge 24.9 33 0.00071 28.2 0.7 17 107-124 72-88 (131)
32 COG1092 Predicted SAM-dependen 24.8 36 0.00077 32.0 1.1 20 111-132 290-309 (393)
33 KOG3351 Predicted nucleotidylt 24.1 42 0.00092 30.8 1.4 33 114-147 218-259 (293)
34 PRK15084 formate hydrogenlyase 23.6 35 0.00076 28.2 0.7 17 107-124 74-90 (133)
35 PF06690 DUF1188: Protein of u 23.5 69 0.0015 29.0 2.5 58 75-133 17-87 (252)
36 KOG3346 Phosphatidylethanolami 23.1 92 0.002 26.7 3.1 45 89-134 40-91 (185)
37 PF00048 IL8: Small cytokines 20.8 60 0.0013 22.1 1.3 41 95-135 18-59 (64)
38 cd00169 Chemokine Chemokine: s 20.4 95 0.0021 20.9 2.2 41 95-135 12-53 (59)
39 KOG4300 Predicted methyltransf 20.0 54 0.0012 29.6 1.2 48 70-121 43-109 (252)
No 1
>PTZ00026 60S ribosomal protein L15; Provisional
Probab=100.00 E-value=7.3e-111 Score=706.76 Aligned_cols=186 Identities=76% Similarity=1.271 Sum_probs=185.1
Q ss_pred ChhhHHHHHHHHhcCCceeEeCCCCchhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccch
Q 029857 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSK 80 (186)
Q Consensus 1 mrfl~r~R~we~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~sl 80 (186)
|+||+|+|||||||+|+|+|+++||||||||+||||||||||||||||++||+++|+|+|+|||||++||||+||+++||
T Consensus 19 ~r~l~r~R~we~Rq~~~i~R~~rPTR~DkAR~LGYKAKQG~vv~RvrVRrGgrkr~~~kg~~~gkpk~~Gv~~lk~~ksl 98 (204)
T PTZ00026 19 MRFLLRVRTWEYRQLPVIHRVSRPTRPDKARRLGYKAKQGFVIYRVRVRRGGRKRPVRKGIVYGKPKTQGVNKLKSTRNL 98 (204)
T ss_pred HHHHHHHHHHHHhcCCceEEcCCCCChhHHHHcCCcccceEEEEEEEEeeCCCCCCccCCCCCCCccccCccccCcchhH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhhccCCceeeeeeecccCCCceEEEEEEeeccccccccCCCCceeccCCcccccccCCccccccccCCCCCC
Q 029857 81 RSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKG 160 (186)
Q Consensus 81 q~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG 160 (186)
|+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+|||||||||||||+|+|||++||
T Consensus 99 q~iAEeRv~rk~~nLrVLNSYWV~qDg~yK~yEVILvDp~H~aIr~Dp~~nWI~~~~hk~Re~RGLTsAGkK~RGL~~kG 178 (204)
T PTZ00026 99 RAVAEERVGKRCGNLRVLNSYWVGQDSTYKFYEVILVDPFHNAIRNDPRINWICNPVHKHRELRGLTSAGRKSRGLRVKG 178 (204)
T ss_pred HHHHHHHhhccCCCcEEecceeEcCCCCcccEEEEEecCCCccceeCcccceecccccchhhhccccccccccCCcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCCchhhhcccceeEEeecC
Q 029857 161 HLHHKARPSRRATWKRNQTLSLRRYR 186 (186)
Q Consensus 161 ~~~~k~~~S~ra~w~r~ntl~l~r~r 186 (186)
|+++|++||++|+|+++|||+|+|||
T Consensus 179 ~~~~k~r~s~ra~~~r~n~~~l~r~r 204 (204)
T PTZ00026 179 HRASKLRPSRRANWKRRNRIVLRRYR 204 (204)
T ss_pred CCcccCCcchhhhhhhccceeeEecC
Confidence 99999999999999999999999997
No 2
>KOG1678 consensus 60s ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-109 Score=689.85 Aligned_cols=185 Identities=81% Similarity=1.327 Sum_probs=184.0
Q ss_pred ChhhHHHHHHHHhcCCceeEeCCCCchhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccch
Q 029857 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSK 80 (186)
Q Consensus 1 mrfl~r~R~we~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~sl 80 (186)
|+||+|+|||||||+++|||+++||||||||+||||||||||||||||++||+|+|+|||+|||||+|+|||||||++|+
T Consensus 19 mrfLlRvr~weYrQ~~~~hr~~rPtrpdkARrLGYkAKQG~viYrirVrrG~rKrpvpkG~tyGKp~~~GvnqlK~~rs~ 98 (204)
T KOG1678|consen 19 MRFLLRVRCWEYRQLSAIHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVNQGVNQLKFQRSL 98 (204)
T ss_pred HHHHHHHHHHHHhhhhhhhcCCCCCCchHHHhccccccceeEEEEEEEecCCccCCCCCCCccCCccccchhhhhhhHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhhccCCceeeeeeecccCCCceEEEEEEeeccccccccCCCCceeccCCcccccccCCccccccccCCCCCC
Q 029857 81 RSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKG 160 (186)
Q Consensus 81 q~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG 160 (186)
|++||||||++|+||+|||||||+||+||||||||||||+|+||++||+|||||+|||||||+|||||||+||||| |||
T Consensus 99 qs~AEer~Gr~~g~LrVlNSYWv~qDstYk~fEVIlvDp~h~aIRrdp~~nwI~kpvhKhRE~rGLTsagkksrGl-gKg 177 (204)
T KOG1678|consen 99 QSVAEERAGRRCGNLRVLNSYWVNQDSTYKYFEVILVDPFHKAIRRDPRINWICKPVHKHRELRGLTSAGKKSRGL-GKG 177 (204)
T ss_pred HHHHHHHhhccccceeeeehhhccCccceeeEEEEEECcHHHHHhcCCCcccccchhhhhHHhcccccccccccCc-ccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred CcccccC-CCchhhhcccceeEEeecC
Q 029857 161 HLHHKAR-PSRRATWKRNQTLSLRRYR 186 (186)
Q Consensus 161 ~~~~k~~-~S~ra~w~r~ntl~l~r~r 186 (186)
|+|++|+ +|++|+|+++|||+|+|||
T Consensus 178 ~kf~~t~~gs~ra~Wkr~ntl~l~ryr 204 (204)
T KOG1678|consen 178 HKFNKTIGGSRRATWKRRNTLSLHRYR 204 (204)
T ss_pred cccccCCCchhHHHHhhcccceeeecC
Confidence 9999999 8999999999999999997
No 3
>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=1.3e-106 Score=676.33 Aligned_cols=175 Identities=76% Similarity=1.257 Sum_probs=163.1
Q ss_pred ChhhHHHHHHHHhcCCceeEeCCCCchhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccch
Q 029857 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSK 80 (186)
Q Consensus 1 mrfl~r~R~we~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~sl 80 (186)
|+||+|+|||||||+|+|+|+++||||||||+||||||||||||||||++||+++|+|+|++||||++||||+|||++||
T Consensus 18 ~~~l~r~R~~e~R~~~av~Ri~rPtR~dkAR~LGYKAKQG~vv~RvrVrrGgrkr~~~kg~~~gKPk~~Gv~~~k~~ksl 97 (192)
T PF00827_consen 18 MRFLLRIRLWEWRQLPAVHRIERPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPRPKGGRYGKPKHQGVNQLKPAKSL 97 (192)
T ss_dssp HHHHHHHHHHHHHHS-SEEEESS-SSHHHHHHTT-SSSTTEEEEEEEEESSS---SSSSSSSTSSCGGSSSTSS--SS-H
T ss_pred HHHHHHHHHHHHhcCCceEECCCCCCccHHHHcCCccCCeEEEEEEEEecCCCCCcccCCccccccccceeeccCccccH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhhccCCceeeeeeecccCCCceEEEEEEeeccccccccCCCCceeccCCcccccccCCccccccccCCCCCC
Q 029857 81 RSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKG 160 (186)
Q Consensus 81 q~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG 160 (186)
|+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+|||||||||||||+|+|||++||
T Consensus 98 q~iAEeRagrk~~nLrVLnSYwV~eDg~yK~fEVIlVDp~h~~Ir~D~~~nWI~~~~hk~R~~RGLTsAgkk~RGL~~kG 177 (192)
T PF00827_consen 98 QSIAEERAGRKYPNLRVLNSYWVGEDGTYKWFEVILVDPNHPAIRNDPDINWICNPVHKHREFRGLTSAGKKSRGLRGKG 177 (192)
T ss_dssp HHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHTTTTTGGGGSGGGTTTTTTTTSHHHHHHTTTT-SS
T ss_pred HHHhhhhhccccCCceEEeeEEeCCCCcceeEEEEEecCCcHHHhcCCccceecccccCccccccccchhhhhcccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCCchhhhc
Q 029857 161 HLHHKARPSRRATWK 175 (186)
Q Consensus 161 ~~~~k~~~S~ra~w~ 175 (186)
|+++||+||++|||+
T Consensus 178 ~~~~k~rpS~ra~wk 192 (192)
T PF00827_consen 178 HGAEKTRPSRRANWK 192 (192)
T ss_dssp TTCGGTSSTTTTTCC
T ss_pred cccccCCcccccccC
Confidence 999999999999996
No 4
>PRK04243 50S ribosomal protein L15e; Validated
Probab=100.00 E-value=3.9e-103 Score=656.77 Aligned_cols=174 Identities=56% Similarity=0.907 Sum_probs=171.8
Q ss_pred ChhhHHHHHHHHhcCCceeEeCCCCchhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccch
Q 029857 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSK 80 (186)
Q Consensus 1 mrfl~r~R~we~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~sl 80 (186)
|+||+|+|||||||+|+||||++||||||||+||||||||||||||||++||+++|+|+|+ |||++||||+|||++||
T Consensus 21 ~~~L~r~R~~e~R~~~~i~Rv~rPTR~DrAR~LGYKAKQG~vv~RvrVRrGgrkr~~~kg~--~kPk~~Gv~~lk~~ksl 98 (196)
T PRK04243 21 VGELMWQRLQEWRREPAVVRIERPTRLDRARALGYKAKQGIVVVRVRVRRGGLRKPRPKGG--RRPKRMGVNKITPAKSI 98 (196)
T ss_pred HHHHHHHHHHHHhccCceEEcCCCCChhHHHHcCccccceEEEEEEEeccCCCCCCCcCCC--CCccccCccccchhhhH
Confidence 6899999999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred hHHHHHHhhhccCCceeeeeeecccCCCceEEEEEEeeccccccccCCCCceeccCCcccccccCCccccccccCCCCCC
Q 029857 81 RSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKG 160 (186)
Q Consensus 81 q~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG 160 (186)
|+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+|||||||||||||+|+|||++||
T Consensus 99 q~iAEERa~rk~~nlrVLNSYwV~qDg~yK~fEVIlVDp~H~aIr~Dp~~nWI~~~~~k~R~~RGLTSAGkK~RGl~~kg 178 (196)
T PRK04243 99 QRIAEERAARKYPNLEVLNSYWVGEDGKYKWYEVILVDPHHPAIKNDPDLNWICDKSHRGRVFRGLTSAGKKGRGLRKKG 178 (196)
T ss_pred HHHHHHHhhccCCCcEeeeeeEeccCCCcccEEEEEecCCCcchhcCcccceecccccchhhhhcccccccccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCCchhhhcc
Q 029857 161 HLHHKARPSRRATWKR 176 (186)
Q Consensus 161 ~~~~k~~~S~ra~w~r 176 (186)
|+++|++||++|+-++
T Consensus 179 ~~~~k~rps~ra~~~~ 194 (196)
T PRK04243 179 KGTEKVRPSIRANERR 194 (196)
T ss_pred CCceecCccccccccc
Confidence 9999999999998654
No 5
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.9e-84 Score=539.97 Aligned_cols=175 Identities=62% Similarity=0.973 Sum_probs=170.2
Q ss_pred ChhhHHHHHHHHhcCCceeEeCCCCchhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccch
Q 029857 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSK 80 (186)
Q Consensus 1 mrfl~r~R~we~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~sl 80 (186)
+.+|+++|+|+||++|+|+||++|||+|+||.||||||||||||||+|++||..+++|+++ .+|++||||++++++|+
T Consensus 20 ~~~l~~~r~~~wR~~~~i~R~erPTrldrAR~LGykaKqG~vvvrvrVrrG~~~~~r~~~g--rrp~~mgvnki~~~ks~ 97 (195)
T COG1632 20 VRELLRQRLIEWRKEPSIVRIERPTRLDRARALGYKAKQGYVVVRVRVRRGGRNRKRPKKG--RRPTRMGVNKIKRKKSL 97 (195)
T ss_pred HhHHHhHHHHhhccCCceEEecCCCHHHHHHhcCCcccCceEEEEEeeecccccCcCccCC--CCcCcccccccChhhhH
Confidence 4689999999999999999999999999999999999999999999999999999999999 89999999999999999
Q ss_pred hHHHHHHhhhccCCceeeeeeecccCCCceEEEEEEeeccccccccCCCCceeccCCcccccccCCccccccccCCCCCC
Q 029857 81 RSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKG 160 (186)
Q Consensus 81 q~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG 160 (186)
|.|||||||++||||+|||||||+|||.|||||||||||+||||++||+|||||+++|+||++|||||||+|+|||+.+|
T Consensus 98 ~~iAEerA~RK~pNL~vLnSYwVgeDg~yK~fEvIlvDp~H~aIk~Dp~l~wI~~~~~kgR~~RgltsagkK~rgl~k~~ 177 (195)
T COG1632 98 QFIAEERAGRKYPNLEVLNSYWVGEDGYYKYFEVILVDPRHPAIKNDPNLNWICRPVHKGRVFRGLTSAGKKSRGLRKGG 177 (195)
T ss_pred HHHHHHHhhccCCCcEeeeeEEeccccceeeEEEEEecCCChhhcCCCceeeecccccCCceeccccccchhhhhhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred CcccccCCCchhhhccc
Q 029857 161 HLHHKARPSRRATWKRN 177 (186)
Q Consensus 161 ~~~~k~~~S~ra~w~r~ 177 (186)
.++++.+||.+|+++.+
T Consensus 178 k~~~~~R~~~~~~~~~~ 194 (195)
T COG1632 178 KGAEKKRPSTRALQRYR 194 (195)
T ss_pred CcccccCcchhhhhhhc
Confidence 89999999999888654
No 6
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=66.39 E-value=2.9 Score=36.27 Aligned_cols=64 Identities=31% Similarity=0.382 Sum_probs=52.0
Q ss_pred cccccCCCCceeccCCcccccccCCccccccccCCCCCCCcccccC-CCchhhhcccceeEEeecC
Q 029857 122 NAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKAR-PSRRATWKRNQTLSLRRYR 186 (186)
Q Consensus 122 ~aIr~Dp~~~WI~~~~hkhRe~RGLTSAgkk~RGL~~kG~~~~k~~-~S~ra~w~r~ntl~l~r~r 186 (186)
.+|.-||+-.=|-+.-+=...|. -+.-|+..|||..-|.+.--.+ +..++.|.|.||+.+.+|+
T Consensus 130 EvIlvDp~H~aIk~Dp~l~wI~~-~~~kgR~~RgltsagkK~rgl~k~~k~~~~~R~~~~~~~~~~ 194 (195)
T COG1632 130 EVILVDPRHPAIKNDPNLNWICR-PVHKGRVFRGLTSAGKKSRGLRKGGKGAEKKRPSTRALQRYR 194 (195)
T ss_pred EEEEecCCChhhcCCCceeeecc-cccCCceeccccccchhhhhhhccCCcccccCcchhhhhhhc
Confidence 47888888887877776677777 5679999999988787766655 5679999999999998875
No 7
>PF01161 PBP: Phosphatidylethanolamine-binding protein; InterPro: IPR008914 The PEBP (PhosphatidylEthanolamine-Binding Protein) family is a highly conserved group of proteins that have been identified in numerous tissues in a wide variety of organisms, including bacteria, yeast, nematodes, plants, drosophila and mammals. The various functions described for members of this family include lipid binding, neuronal development [], serine protease inhibition [], the control of the morphological switch between shoot growth and flower structures [], and the regulation of several signalling pathways such as the MAP kinase pathway [], and the NF-kappaB pathway []. The control of the latter two pathways involves the PEBP protein RKIP, which interacts with MEK and Raf-1 to inhibit the MAP kinase pathway, and with TAK1, NIK, IKKalpha and IKKbeta to inhibit the NF-kappaB pathway. Other PEBP-like proteins that show strong structural homology to PEBP include Escherichia coli YBHB and YBCL, the Rattus norvegicus (Rat) neuropeptide HCNP, and Antirrhinum majus (Garden snapdragon) protein centroradialis (CEN). Structures have been determined for several members of the PEBP-like family, all of which show extensive fold conservation. The structure consists of a large central beta-sheet flanked by a smaller beta-sheet on one side, and an alpha helix on the other. Sequence alignments show two conserved central regions, CR1 and CR2, that form a consensus signature for the PEBP family. These two regions form part of the ligand-binding site, which can accommodate various anionic groups. The N- and C-terminal regions are the least conserved, and may be involved in interactions with different protein partners. The N-terminal residues 2-12 form the natural cleavage peptide HCNP involved in neuronal development. The C-terminal region is deleted in plant and bacterial PEBP homologues, and may help control accessibility to the active site. ; PDB: 1BD9_A 1BEH_A 2QYQ_A 2L7W_A 3AXY_A 2IQX_C 2IQY_A 1KN3_A 1FUX_A 1B7A_A ....
Probab=60.69 E-value=12 Score=28.63 Aligned_cols=36 Identities=25% Similarity=0.611 Sum_probs=25.4
Q ss_pred ecccCCCceEEEEEEeecccccccc---CCCCceeccCC
Q 029857 102 WINEDSTYKYFEVILVDAAHNAIRN---DPRINWICKPV 137 (186)
Q Consensus 102 wV~eD~~yK~fEVIlvDp~h~aIr~---Dp~~~WI~~~~ 137 (186)
|...-..-+.|=|||+||+.|.-.+ .+-+.||.-..
T Consensus 26 ~~~~P~~~~~y~lim~D~D~P~~~~~~~~~~~Hwl~~ni 64 (146)
T PF01161_consen 26 WQNAPTGTKSYTLIMVDPDAPSRENPSFGPFLHWLVTNI 64 (146)
T ss_dssp CSS-TCTTSEEEEEEEETTSSBTTSCTTTSEEEEEEEEE
T ss_pred cccCCCCCcEEEEEEECCCCCccccCCCCcEEEEEEcCC
Confidence 5555446678999999999988433 35677877655
No 8
>cd00457 PEBP PhosphatidylEthanolamine-Binding Protein (PEBP) domain. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer).
Probab=46.47 E-value=23 Score=28.41 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=26.1
Q ss_pred ecccCCCceEEEEEEeeccccccccCCCCceeccCC
Q 029857 102 WINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPV 137 (186)
Q Consensus 102 wV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~ 137 (186)
|-+.+.--+.|=|||+||+.| ...+-+-||.-..
T Consensus 31 w~~~p~~t~s~ali~~DpDap--~~~~~~HWvv~nI 64 (159)
T cd00457 31 WDGPPPDVKEYVLVMEDPDAP--LGRPIVHGLVYGI 64 (159)
T ss_pred ecCCCCCCeEEEEEEECCCCC--CCCCceEEEEecc
Confidence 777775669999999999999 2335688887544
No 9
>cd00866 PEBP_euk PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in eukaryotes. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in eukaryotes. Members here include those in plants such as Arabidopsis thaliana FLOWERING LOCUS (FT) and TERMINAL FLOWER1 (FT1) which function as a promoter and a repressor of the floral transitions, respectively as well as the mammalian Raf kinase inhibitory protein (RKIP) which inhibits MAP kinase (Raf-MEK-ERK), G protein-coupled receptor (GPCR) kinase and NFkappaB signaling cascades. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer).
Probab=45.83 E-value=30 Score=26.79 Aligned_cols=43 Identities=16% Similarity=0.429 Sum_probs=28.5
Q ss_pred hccCCceeeeeeecccCCCceEEEEEEeecccccccc---CCCCceeccCC
Q 029857 90 RKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRN---DPRINWICKPV 137 (186)
Q Consensus 90 rk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~---Dp~~~WI~~~~ 137 (186)
...|-++ |.+.+..-+.|=|||+||+-|.-.+ -+-+.||....
T Consensus 25 ~~~P~i~-----~~~~~~~~~~y~lvm~DpD~p~~~~~~~~~~lHwl~~ni 70 (154)
T cd00866 25 QKAPTVS-----FSSEDPPDKLYTLVMVDPDAPSRDDPKFREWLHWLVTNI 70 (154)
T ss_pred CcCCeEE-----EecCCCCCCeEEEEEECCCCCCCCCCCCCCEEEEEEeCc
Confidence 4566664 3444546788999999999876542 23567776543
No 10
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=44.55 E-value=12 Score=30.77 Aligned_cols=27 Identities=33% Similarity=0.454 Sum_probs=22.7
Q ss_pred eecccCCC---ceEEEEEEeeccccccccC
Q 029857 101 YWINEDST---YKYFEVILVDAAHNAIRND 127 (186)
Q Consensus 101 YwV~eD~~---yK~fEVIlvDp~h~aIr~D 127 (186)
-||..||+ |.=.|+|||||+.++++.|
T Consensus 126 i~V~GDSMeP~~~~Gd~ilVd~~~~~~~gd 155 (214)
T COG2932 126 LRVTGDSMEPTYEDGDTLLVDPGVNTRRGD 155 (214)
T ss_pred EEEeCCcccccccCCCEEEECCCCceeeCC
Confidence 47888886 5556899999999999988
No 11
>PHA02110 hypothetical protein
Probab=43.25 E-value=24 Score=27.50 Aligned_cols=32 Identities=25% Similarity=0.501 Sum_probs=25.7
Q ss_pred HHHHhhhccCCceeeeeeecccCCCceEEEEEEeecc
Q 029857 84 AEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120 (186)
Q Consensus 84 AEeR~grk~~nLrVLNSYwV~eD~~yK~fEVIlvDp~ 120 (186)
.|--.|.+.+.+++.-|||.-.||- |-|-||-
T Consensus 16 ~esl~gn~vge~eifk~~w~i~dgf-----vf~~d~~ 47 (98)
T PHA02110 16 LESLFGNSVGEVEIFKSHWMIRDGF-----VFIGDPP 47 (98)
T ss_pred hHhHhCCccceEeeeeeeeEeecCE-----EEeCCCC
Confidence 4667899999999999999999994 4455654
No 12
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=43.23 E-value=13 Score=26.80 Aligned_cols=25 Identities=12% Similarity=0.363 Sum_probs=16.5
Q ss_pred ccCCceeeeeeecccCCCceEEEEE-Eeecccc
Q 029857 91 KLGGLKVLNSYWINEDSTYKYFEVI-LVDAAHN 122 (186)
Q Consensus 91 k~~nLrVLNSYwV~eD~~yK~fEVI-lvDp~h~ 122 (186)
.|||..- +|-|..||+.| ++||...
T Consensus 17 ~CP~Cgs-------~~~T~~W~G~viI~dPe~S 42 (61)
T PRK08351 17 RCPVCGS-------RDLSDEWFDLVIIIDVENS 42 (61)
T ss_pred cCCCCcC-------CccccccccEEEEeCCcHh
Confidence 4666543 56789999954 6677554
No 13
>COG0463 WcaA Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=41.60 E-value=16 Score=24.89 Aligned_cols=12 Identities=50% Similarity=0.778 Sum_probs=9.1
Q ss_pred eEEEEEEeeccc
Q 029857 110 KYFEVILVDAAH 121 (186)
Q Consensus 110 K~fEVIlvDp~h 121 (186)
..||||+||-..
T Consensus 31 ~~~eiivvddgs 42 (291)
T COG0463 31 KDFEIIVVDDGS 42 (291)
T ss_pred cceEEEEEeCCC
Confidence 339999999754
No 14
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=41.42 E-value=28 Score=29.58 Aligned_cols=50 Identities=24% Similarity=0.238 Sum_probs=36.8
Q ss_pred chhHHhhcCCccccceEEEEEEeeecCCCCCccCCcccCCcccccceecccccchhHHHHHHhhh
Q 029857 26 RPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSKRSVAEERAGR 90 (186)
Q Consensus 26 R~dkAR~LGYKAKQG~vi~RvrVrrGgrkrp~pkg~~~~kPk~~Gvn~lk~~~slq~iAEeR~gr 90 (186)
-|+.|+++|+ ||-|++.+-|..+|. ..+.-|-+-+...-|..-|.+-+-+
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 3444454555556666666665544
No 15
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=39.98 E-value=18 Score=32.83 Aligned_cols=25 Identities=40% Similarity=0.761 Sum_probs=21.0
Q ss_pred EEEEEEeecccc---ccccCCCCceecc
Q 029857 111 YFEVILVDAAHN---AIRNDPRINWICK 135 (186)
Q Consensus 111 ~fEVIlvDp~h~---aIr~Dp~~~WI~~ 135 (186)
.|.-||||+-.. .|++||++.|=-.
T Consensus 229 ~fD~iLlDaPCSg~G~irr~Pd~~~~~~ 256 (355)
T COG0144 229 KFDRILLDAPCSGTGVIRRDPDVKWRRT 256 (355)
T ss_pred cCcEEEECCCCCCCcccccCccccccCC
Confidence 599999999775 6999999999543
No 16
>PF05063 MT-A70: MT-A70 ; InterPro: IPR007757 N6-methyladenosine (m6A) is present at internal sites in eukaryotic mRNA. It is present only within a defined sequence context that has been shown to be conserved across species from plants to man. Despite its ubiquity and conserved sequence specificity, the functional significance of this modification remains a mystery [], []. MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA N6-adenosine-methyltransferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs. Proteins with sequence similarity to MT-A70 have been identified in eukaryotes and prokaryotes. The resulting family is defined by sequence similarity in the carboxyl-proximal regions of the respective proteins. The amino-proximal regions of the eukaryotic proteins are highly diverse, often Pro-rich, and are conserved only within individual subfamilies []. Corresponding regions are not present in prokaryotic members of the family. MT-A70-like proteins contain examples of some of the consensus methyltransferase motifs that have been derived from mutational and structural studies of bacterial DNA methyltransferases, including the universally conserved motif IV catalytic residues and a proposed motif I (AdoMet binding) element []. The MT-A70-like family comprises four subfamilies with varying degrees of interrelatedness. One subfamily is a small group of bacterial DNA: m6A MTases. The other three are paralogous eukaryotic lineages, two of which have not been associated with MTase activity but include proteins that regulate mRNA levels via unknown mechanisms apparently not involving methylation []. Some proteins known to belong to the MT-A70-like family are listed below: Human N6-adenosine-methyltransferase 70 kDa subunit (MT-A70) (2.1.1.62 from EC). Yeast N6-adenosine-methyltransferase IME4 (2.1.1.62 from EC), which is important for induction of sporulation. Yeast karyogamy protein KAR4, a phosphoprotein required for expression of karyogamy-specific genes during mating and that it also acts during mitosis and meiosis. It has been suggested that KAR4 is inactive for methyltransfer and may not even bind AdoMet. ; GO: 0008168 methyltransferase activity, 0006139 nucleobase-containing compound metabolic process
Probab=35.89 E-value=15 Score=29.59 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=7.8
Q ss_pred EEEEEeeccc
Q 029857 112 FEVILVDAAH 121 (186)
Q Consensus 112 fEVIlvDp~h 121 (186)
|.||++||=-
T Consensus 1 fdvI~~DPPW 10 (176)
T PF05063_consen 1 FDVIYADPPW 10 (176)
T ss_pred CCEEEEeCCC
Confidence 7789999843
No 17
>cd07998 WGR_DNA_ligase WGR domain of bacterial DNA ligases. The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.
Probab=33.02 E-value=40 Score=25.21 Aligned_cols=19 Identities=32% Similarity=0.501 Sum_probs=16.1
Q ss_pred eeecccCCCceEEEEEEee
Q 029857 100 SYWINEDSTYKYFEVILVD 118 (186)
Q Consensus 100 SYwV~eD~~yK~fEVIlvD 118 (186)
+++.-+++..|||||.|..
T Consensus 4 ~l~~~dg~S~Kfyev~~~~ 22 (77)
T cd07998 4 SLYFQEGNSDKVYEVDLFE 22 (77)
T ss_pred EEEEecCCCceEEEEEEEe
Confidence 5778889999999998873
No 18
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=30.26 E-value=41 Score=32.05 Aligned_cols=37 Identities=24% Similarity=0.385 Sum_probs=27.0
Q ss_pred cCCceeeeeeecccCCCc------eEEEEEEeecccc---ccccCCCCcee
Q 029857 92 LGGLKVLNSYWINEDSTY------KYFEVILVDAAHN---AIRNDPRINWI 133 (186)
Q Consensus 92 ~~nLrVLNSYwV~eD~~y------K~fEVIlvDp~h~---aIr~Dp~~~WI 133 (186)
+.|..|.| +|++. .+|..||||+-.. .+++||++.|-
T Consensus 163 ~~nv~v~~-----~D~~~~~~~~~~~fD~ILvDaPCSG~G~~rk~p~~~~~ 208 (470)
T PRK11933 163 VSNVALTH-----FDGRVFGAALPETFDAILLDAPCSGEGTVRKDPDALKN 208 (470)
T ss_pred CCeEEEEe-----CchhhhhhhchhhcCeEEEcCCCCCCcccccCHHHhhh
Confidence 34555555 55542 4699999999887 68999998773
No 19
>cd05468 pVHL von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronecti
Probab=29.61 E-value=48 Score=26.52 Aligned_cols=33 Identities=18% Similarity=0.357 Sum_probs=24.3
Q ss_pred eeeeeeecccCCCceEEEEEE--------eeccccccccCC
Q 029857 96 KVLNSYWINEDSTYKYFEVIL--------VDAAHNAIRNDP 128 (186)
Q Consensus 96 rVLNSYwV~eD~~yK~fEVIl--------vDp~h~aIr~Dp 128 (186)
+.+.-|||+.+|...+|..|- -=..||-|-.|.
T Consensus 19 ~~v~~~Wid~~G~~~~Y~~l~pg~~~~~~Ty~~H~W~~rd~ 59 (141)
T cd05468 19 RPVELYWIDYDGKPVSYGTLQPGETVRQNTYVGHPWLFRDA 59 (141)
T ss_pred CeEEEEEECCCCCEEEeeeeCCCCEEeecccCCCcEEEEec
Confidence 567889999999999999752 113466666666
No 20
>COG2876 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=29.50 E-value=24 Score=32.29 Aligned_cols=15 Identities=33% Similarity=0.503 Sum_probs=12.9
Q ss_pred EEeeccccccccCCC
Q 029857 115 ILVDAAHNAIRNDPR 129 (186)
Q Consensus 115 IlvDp~h~aIr~Dp~ 129 (186)
|+|||+|++=|+|+-
T Consensus 217 VivDpSH~~Grr~lv 231 (286)
T COG2876 217 VIVDPSHATGRRDLV 231 (286)
T ss_pred EEECCCCcccchhhH
Confidence 689999999988863
No 21
>cd06433 GT_2_WfgS_like WfgS and WfeV are involved in O-antigen biosynthesis. Escherichia coli WfgS and Shigella dysenteriae WfeV are glycosyltransferase 2 family enzymes involved in O-antigen biosynthesis. GT-2 enzymes have GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=28.69 E-value=31 Score=25.57 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=9.8
Q ss_pred ceEEEEEEeeccc
Q 029857 109 YKYFEVILVDAAH 121 (186)
Q Consensus 109 yK~fEVIlvDp~h 121 (186)
++.||||+||-..
T Consensus 25 ~~~~evivvDd~s 37 (202)
T cd06433 25 YPNIEYIVIDGGS 37 (202)
T ss_pred CCCceEEEEeCCC
Confidence 4559999998653
No 22
>PRK14688 hypothetical protein; Provisional
Probab=28.16 E-value=42 Score=26.52 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=16.8
Q ss_pred EEEEEEeeccccccccCCCCceeccC
Q 029857 111 YFEVILVDAAHNAIRNDPRINWICKP 136 (186)
Q Consensus 111 ~fEVIlvDp~h~aIr~Dp~~~WI~~~ 136 (186)
=|.||.|++.+ .++.++||-+.
T Consensus 96 RFDvi~v~~~~----~~~~i~~i~nA 117 (121)
T PRK14688 96 RIDFVSVDLSQ----PEPRLELIKNA 117 (121)
T ss_pred EEEEEEEEccC----CCCCEEEehHh
Confidence 39999998765 23579999874
No 23
>PLN00169 CETS family protein; Provisional
Probab=27.91 E-value=71 Score=26.65 Aligned_cols=29 Identities=14% Similarity=0.519 Sum_probs=21.5
Q ss_pred ceEEEEEEeeccccccccC---CCCceeccCC
Q 029857 109 YKYFEVILVDAAHNAIRND---PRINWICKPV 137 (186)
Q Consensus 109 yK~fEVIlvDp~h~aIr~D---p~~~WI~~~~ 137 (186)
-++|=|||+||+-|.-.+. +-+-|+....
T Consensus 62 ~~~ytlim~DpDaP~~~~~~~~~~~HW~v~ni 93 (175)
T PLN00169 62 RTFYTLVMVDPDAPSPSNPNLREYLHWLVTDI 93 (175)
T ss_pred CceeEEEEECCCCCCCCCCCcccEEEEEEeCC
Confidence 4899999999999874432 2477887554
No 24
>PF04915 DltD_N: DltD N-terminal region; InterPro: IPR006999 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the N-terminal region of DltD.; PDB: 3BMA_C.
Probab=27.69 E-value=20 Score=25.91 Aligned_cols=14 Identities=21% Similarity=0.264 Sum_probs=8.5
Q ss_pred EEEEeecccccccc
Q 029857 113 EVILVDAAHNAIRN 126 (186)
Q Consensus 113 EVIlvDp~h~aIr~ 126 (186)
|..-+||+||++--
T Consensus 38 El~r~D~~HPsvl~ 51 (62)
T PF04915_consen 38 ELSRFDPFHPSVLA 51 (62)
T ss_dssp TTTS--TTSHHHHH
T ss_pred HHhccCCcCHHHHH
Confidence 44468999999853
No 25
>cd00272 Chemokine_CC Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_C
Probab=27.56 E-value=37 Score=22.86 Aligned_cols=39 Identities=26% Similarity=0.454 Sum_probs=30.3
Q ss_pred eeeeeeecccCCCceEEEEEEeeccccccccCCCCceecc
Q 029857 96 KVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICK 135 (186)
Q Consensus 96 rVLNSYwV~eD~~yK~fEVIlvDp~h~aIr~Dp~~~WI~~ 135 (186)
.++-+|.+- ++.=..=|||+.-.....|-.||+-.|+-+
T Consensus 13 ~~i~~y~~~-~~~C~~~aVIf~tk~g~~iC~dP~~~WVk~ 51 (57)
T cd00272 13 RVLKSYRRT-SSSCSKPAVIFKTKRGREVCADPKQKWVQR 51 (57)
T ss_pred hHeeEEEEC-CCCCCCcEEEEEeCCCCEEeCCCChHHHHH
Confidence 445577654 335557789999999999999999999864
No 26
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=27.02 E-value=1.7e+02 Score=19.07 Aligned_cols=44 Identities=23% Similarity=0.315 Sum_probs=29.3
Q ss_pred hhhccCCceeeeeeecccCCCceEEEEEEe-eccccccccCCCCce
Q 029857 88 AGRKLGGLKVLNSYWINEDSTYKYFEVILV-DAAHNAIRNDPRINW 132 (186)
Q Consensus 88 ~grk~~nLrVLNSYwV~eD~~yK~fEVIlv-Dp~h~aIr~Dp~~~W 132 (186)
+-..||+..|..-+.....+. .+|||-|. |-..-.|.=|++=+|
T Consensus 16 i~~~yp~~~i~~v~~~~~~~~-~~Y~v~l~~~~~~~~v~fd~~G~~ 60 (61)
T PF11396_consen 16 IKKNYPGAKIKEVEKETDPGG-KYYEVELKKGGNEYEVYFDANGNW 60 (61)
T ss_dssp HHHHSTTSEEEEEEEEEETTE-EEEEEEETETTTSEEEEEETTS-E
T ss_pred HHHHCCCCeEEEEEEEEcCCC-CEEEEEEEEeCCeEEEEEcCCCCC
Confidence 344599999999888887776 99999987 223333443444333
No 27
>PF00836 Stathmin: Stathmin family; InterPro: IPR000956 Stathmin is a ubiquitous phosphorylated protein thought to act as an intracellular relay for diverse regulatory pathways [], functioning through a variety of secondary messengers. Its phosphorylation and gene expression are regulated throughout development [] and in response to extracellular signals regulating cell proliferation, differentiation and function []. Stathmin, and the related proteins SCG10 and XB3, contain a N-terminal domain (XB3 contains an additional N-terminal hydrophobic region), a 78 amino acid coiled-coil region, and a short C-terminal domain.; GO: 0035556 intracellular signal transduction; PDB: 3RYC_E 3RYH_E 3N2K_E 1Z2B_E 1SA1_E 3HKD_E 3DU7_E 3HKC_E 3HKB_E 3HKE_E ....
Probab=26.55 E-value=35 Score=28.11 Aligned_cols=12 Identities=42% Similarity=0.553 Sum_probs=8.2
Q ss_pred EEEEEEeecccc
Q 029857 111 YFEVILVDAAHN 122 (186)
Q Consensus 111 ~fEVIlvDp~h~ 122 (186)
=|||||-+|+-.
T Consensus 16 aFEVIL~pps~~ 27 (140)
T PF00836_consen 16 AFEVILKPPSPD 27 (140)
T ss_dssp EEEEEES--SSS
T ss_pred ceEeeeCCCCCC
Confidence 599999999854
No 28
>cd00865 PEBP_bact_arch PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in bacterial and archaea. Members here include Escherichia coli YBHB and YBCL which are thought to regulate protein phosphorylation as well as Sulfolobus solfataricus SsCEI which inhibits serine proteases alpha-chymotrypsin and elastase. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer). In a few of the bacterial members present here the dimerization interface is proposed to form the ligand binding site, unlike in other PEBP members.
Probab=26.47 E-value=70 Score=25.26 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=21.6
Q ss_pred ceEEEEEEeeccccccccCCCCceeccCC
Q 029857 109 YKYFEVILVDAAHNAIRNDPRINWICKPV 137 (186)
Q Consensus 109 yK~fEVIlvDp~h~aIr~Dp~~~WI~~~~ 137 (186)
-|.|=|+|+||+.| ...+-+-||.-..
T Consensus 39 t~s~al~m~D~Dap--~~~~~~HW~~~nI 65 (150)
T cd00865 39 TKSLALIVEDPDAP--TGGGFVHWVVWNI 65 (150)
T ss_pred CeEEEEEEEcCCCC--CCCCEEEEEEecc
Confidence 48999999999998 4457788887543
No 29
>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=25.43 E-value=15 Score=25.96 Aligned_cols=37 Identities=41% Similarity=0.737 Sum_probs=14.5
Q ss_pred cccccceecccccchhHHHHHHhhhccCCceeeeeeecccCCCceEEE
Q 029857 66 PTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFE 113 (186)
Q Consensus 66 Pk~~Gvn~lk~~~slq~iAEeR~grk~~nLrVLNSYwV~eD~~yK~fE 113 (186)
|.++|+-.+-+.-+. ||| ++.||.. |-| |.-||||||
T Consensus 16 ~~~~g~veVD~~~tp----Ee~---h~~~mQ~-nGY---ENPTYkyfE 52 (52)
T PF10515_consen 16 PISHGFVEVDPCLTP----EER---HLSNMQN-NGY---ENPTYKYFE 52 (52)
T ss_dssp --------------H----HHH---HHHHHHC-TEE---ESCTCHHCC
T ss_pred ccccceEEecCCCCh----HHH---HHHHHHh-cCC---cCCceeccC
Confidence 567888777766333 544 4555554 333 788999998
No 30
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=25.07 E-value=59 Score=27.81 Aligned_cols=23 Identities=39% Similarity=0.572 Sum_probs=18.7
Q ss_pred EEEEEeecccc---ccccCCCCceec
Q 029857 112 FEVILVDAAHN---AIRNDPRINWIC 134 (186)
Q Consensus 112 fEVIlvDp~h~---aIr~Dp~~~WI~ 134 (186)
|.+||+||-.. .++.||++.|-.
T Consensus 141 fD~Vl~D~Pcsg~G~~~~~p~~~~~~ 166 (264)
T TIGR00446 141 FDAILLDAPCSGEGVIRKDPSRKKNW 166 (264)
T ss_pred CCEEEEcCCCCCCcccccChhhhhcC
Confidence 99999999655 578999988743
No 31
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=24.93 E-value=33 Score=28.23 Aligned_cols=17 Identities=35% Similarity=0.489 Sum_probs=12.8
Q ss_pred CCceEEEEEEeecccccc
Q 029857 107 STYKYFEVILVDAAHNAI 124 (186)
Q Consensus 107 ~~yK~fEVIlvDp~h~aI 124 (186)
|..||+| |-|||+|-+.
T Consensus 72 gl~kfGE-I~Id~~H~~~ 88 (131)
T PF07450_consen 72 GLLKFGE-IEIDSEHVAL 88 (131)
T ss_pred CCCceeE-EEECHHHHHH
Confidence 3479999 4689999654
No 32
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=24.82 E-value=36 Score=32.00 Aligned_cols=20 Identities=15% Similarity=0.486 Sum_probs=15.9
Q ss_pred EEEEEEeeccccccccCCCCce
Q 029857 111 YFEVILVDAAHNAIRNDPRINW 132 (186)
Q Consensus 111 ~fEVIlvDp~h~aIr~Dp~~~W 132 (186)
=|.||++|| |+.-+.++--|
T Consensus 290 ~fDlIilDP--PsF~r~k~~~~ 309 (393)
T COG1092 290 KFDLIILDP--PSFARSKKQEF 309 (393)
T ss_pred cccEEEECC--cccccCcccch
Confidence 589999999 77777776554
No 33
>KOG3351 consensus Predicted nucleotidyltransferase [General function prediction only]
Probab=24.14 E-value=42 Score=30.79 Aligned_cols=33 Identities=30% Similarity=0.477 Sum_probs=26.3
Q ss_pred EEEeeccccccccCCCCceec---------cCCcccccccCCc
Q 029857 114 VILVDAAHNAIRNDPRINWIC---------KPVHKHRELRGLT 147 (186)
Q Consensus 114 VIlvDp~h~aIr~Dp~~~WI~---------~~~hkhRe~RGLT 147 (186)
|=+.||+-|+|. ||+|.-|. ..|.|-|..|||.
T Consensus 218 vpi~Dp~GPt~~-d~elE~lVVS~ET~~Ga~aVNr~R~E~gls 259 (293)
T KOG3351|consen 218 VPIHDPFGPTIT-DPELEALVVSEETKTGATAVNRKRVERGLS 259 (293)
T ss_pred EecccCCCCCcc-CCcceEEEEeeccccchhhhhHHHHHcCCc
Confidence 348999999995 89998874 4577888888875
No 34
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=23.63 E-value=35 Score=28.15 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=12.7
Q ss_pred CCceEEEEEEeecccccc
Q 029857 107 STYKYFEVILVDAAHNAI 124 (186)
Q Consensus 107 ~~yK~fEVIlvDp~h~aI 124 (186)
|..||+|| -|||+|-+.
T Consensus 74 gl~kfgEI-~I~~~H~~~ 90 (133)
T PRK15084 74 GVPKFGEI-VIDSSHVAL 90 (133)
T ss_pred CcCceeEE-EECHHHHHH
Confidence 45799994 689998654
No 35
>PF06690 DUF1188: Protein of unknown function (DUF1188); InterPro: IPR009573 This family consists of several hypothetical archaeal proteins of around 260 residues in length, which seem to be specific to Methanobacterium, Methanococcus and Methanopyrus species. The function of this family is unknown.
Probab=23.49 E-value=69 Score=28.98 Aligned_cols=58 Identities=22% Similarity=0.386 Sum_probs=35.6
Q ss_pred ccccchhHHHHHHh--------hhccCCceeeeeeecc---cCCCceEEEEEEeecccccccc--CCCCcee
Q 029857 75 KFQRSKRSVAEERA--------GRKLGGLKVLNSYWIN---EDSTYKYFEVILVDAAHNAIRN--DPRINWI 133 (186)
Q Consensus 75 k~~~slq~iAEeR~--------grk~~nLrVLNSYwV~---eD~~yK~fEVIlvDp~h~aIr~--Dp~~~WI 133 (186)
++..-.+.|+|-.+ |..+-+.=|+++|.-| ....-+++||+|||++ |.++. |+++...
T Consensus 17 ~~~DIi~~I~ekKa~ai~~~le~~~~k~~lI~G~YltG~~iA~~L~~~~eV~lvDI~-p~lk~ll~~~i~F~ 87 (252)
T PF06690_consen 17 KVIDIIKEIAEKKANAIKYWLEGEEFKQALIFGAYLTGNFIASALSKKCEVTLVDIH-PHLKELLNENIKFM 87 (252)
T ss_pred chHHHHHHHHHHHHHHHHHHhcccccceEEEEEEEeehHHHHHHhccCceEEEEeCc-HHHHHHhcCCCcee
Confidence 34444455555443 3566688899999865 2333455599999983 44332 6666554
No 36
>KOG3346 consensus Phosphatidylethanolamine binding protein [General function prediction only]
Probab=23.13 E-value=92 Score=26.66 Aligned_cols=45 Identities=22% Similarity=0.499 Sum_probs=27.2
Q ss_pred hhccCCceeeeeeecccC---CCceEEEEEEeeccccccccCCCC----ceec
Q 029857 89 GRKLGGLKVLNSYWINED---STYKYFEVILVDAAHNAIRNDPRI----NWIC 134 (186)
Q Consensus 89 grk~~nLrVLNSYwV~eD---~~yK~fEVIlvDp~h~aIr~Dp~~----~WI~ 134 (186)
|...+-=.|.|-=||.=| ..-.||-+||+||+-|+ ++||+. .||.
T Consensus 40 G~~l~pt~~~~~P~v~~~~~a~~~~~yTLvm~DPDaPs-r~~p~~rE~lHWlV 91 (185)
T KOG3346|consen 40 GNELTPTQVKNRPIVSWDGFADPGSLYTLVMTDPDAPS-RSDPKFREWLHWLV 91 (185)
T ss_pred CCEeCchhhccCCeEEEcCcCCCCCeEEEEEeCCCCCC-CCCCcceeEEEEEE
Confidence 333333344444444333 45679999999999998 455553 4654
No 37
>PF00048 IL8: Small cytokines (intecrine/chemokine), interleukin-8 like; InterPro: IPR001811 Many low-molecular weight factors secreted by cells including fibroblasts, macrophages and endothelial cells, in response to a variety of stimuli such as growth factors, interferons, viral transformation and bacterial products, are structurally related [, , ]. Most members of this family of proteins seem to have mitogenic, chemotactic or inflammatory activities. These small cytokines are also called intercrines or chemokines. They are cationic proteins of 70 to 100 amino acid residues that share four conserved cysteine residues involved in two disulphide bonds, as shown in the following schematic representation: +------------------------------------+ | | xxxxxxxxxxxxxxxxxxxxxxCxCxxxxxxxxxxxxxxxxxxxxxxxCxxxxxxxxxxxxCxxxxx | | +-------------------------+ 'C': conserved cysteine involved in a disulphide bond. Chemokines can be sorted into main groups based on the spacing of the two amino-terminal cysteines. In the first group (see IPR001089 from INTERPRO), the two cysteines are separated by a single residue (C-x-C), while in the second group (see IPR000827 from INTERPRO), they are adjacent (C-C).; GO: 0008009 chemokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 3HP3_B 2K01_A 2KEE_A 2K04_C 2J7Z_A 1QG7_A 2KED_A 2NWG_B 2KEC_A 1VMC_A ....
Probab=20.80 E-value=60 Score=22.05 Aligned_cols=41 Identities=27% Similarity=0.357 Sum_probs=32.6
Q ss_pred ceeeeeeecccCCC-ceEEEEEEeeccccccccCCCCceecc
Q 029857 95 LKVLNSYWINEDST-YKYFEVILVDAAHNAIRNDPRINWICK 135 (186)
Q Consensus 95 LrVLNSYwV~eD~~-yK~fEVIlvDp~h~aIr~Dp~~~WI~~ 135 (186)
+..+-+|++-+-+. =.-=|||++.-....+--||+-.|+-+
T Consensus 18 ~~~i~~~~~~~~~~~C~~~avI~~~k~g~~~C~dP~~~wvk~ 59 (64)
T PF00048_consen 18 PKNIKSYEIQPPSPSCPRPAVIFTTKKGREVCADPNAPWVKK 59 (64)
T ss_dssp GGGEEEEEEEESTTTSSSCEEEEEETTSEEEEEETTSHHHHH
T ss_pred hhHeeEEEEEeCCCCCCCceEEEEecCCCcEEcCCchHHHHH
Confidence 45667887766554 566899999999999999999999753
No 38
>cd00169 Chemokine Chemokine: small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 subfamilies based on the arrangement of the two N-terminal cysteines; some members can bind multiple receptors and many chemokine receptors can bind more than one chemokine; this redundancy allows precise control in stimulating the immune system and in contributing to the homeostasis of a cell; when expressed inappropriately, chemokines play a role in autoimmune diseases, vascular irregularities, graft rejection, neoplasia, and allergies; exist as monomers, dimers and multimers, but are believed to function as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine_CXC (cd00273), Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for chemokine subgroups.
Probab=20.39 E-value=95 Score=20.88 Aligned_cols=41 Identities=22% Similarity=0.384 Sum_probs=31.7
Q ss_pred ceeeeeeecccCC-CceEEEEEEeeccccccccCCCCceecc
Q 029857 95 LKVLNSYWINEDS-TYKYFEVILVDAAHNAIRNDPRINWICK 135 (186)
Q Consensus 95 LrVLNSYwV~eD~-~yK~fEVIlvDp~h~aIr~Dp~~~WI~~ 135 (186)
++.+.||.+-+.+ .=.--|||+.--.-..|--||+-.|+-+
T Consensus 12 ~~~I~~y~~~~~~~~C~~~aIIf~tk~g~~iC~dP~~~WV~~ 53 (59)
T cd00169 12 PKNIKSYRVQEAGGHCSIPAVIFTTKKGRKVCADPKEPWVKD 53 (59)
T ss_pred chheEEEEEeCCCCCCCCceEEEEEcCCCEEECCCCcHHHHH
Confidence 4557788875444 2568899999888889999999999754
No 39
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=20.04 E-value=54 Score=29.60 Aligned_cols=48 Identities=15% Similarity=0.410 Sum_probs=34.3
Q ss_pred cceecccccchhHHHHHHhhhccCCceeeeeeecccC-------------CCceEEE------EEEeeccc
Q 029857 70 GVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINED-------------STYKYFE------VILVDAAH 121 (186)
Q Consensus 70 Gvn~lk~~~slq~iAEeR~grk~~nLrVLNSYwV~eD-------------~~yK~fE------VIlvDp~h 121 (186)
=+..--+.-+.+++|++---.-|.|+. ||++.. ..+|||- |+++||+-
T Consensus 43 ~~p~~~ft~~yne~~~~ykrelFs~i~----~~~gk~~K~~vLEvgcGtG~Nfkfy~~~p~~svt~lDpn~ 109 (252)
T KOG4300|consen 43 LIPNSNFTSIYNEIADSYKRELFSGIY----YFLGKSGKGDVLEVGCGTGANFKFYPWKPINSVTCLDPNE 109 (252)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHhhhH----HHhcccCccceEEecccCCCCcccccCCCCceEEEeCCcH
Confidence 333344666788888887666688877 787644 4579998 89999973
Done!