Query 029295
Match_columns 195
No_of_seqs 120 out of 262
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 10:37:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029295.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029295hhsearch_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 4E-110 9E-115 706.7 17.8 195 1-195 1-204 (204)
2 KOG1678 60s ribosomal protein 100.0 4E-109 8E-114 691.1 12.8 194 1-195 1-204 (204)
3 PF00827 Ribosomal_L15e: Ribos 100.0 7E-105 2E-109 670.2 15.2 183 2-184 1-192 (192)
4 PRK04243 50S ribosomal protein 100.0 2E-102 5E-107 656.4 15.6 183 1-185 3-194 (196)
5 COG1632 RPL15A Ribosomal prote 100.0 5.2E-83 1.1E-87 537.4 14.1 184 1-186 2-194 (195)
6 PRK08351 DNA-directed RNA poly 73.3 2.2 4.7E-05 30.9 1.5 23 109-131 17-42 (61)
7 COG1632 RPL15A Ribosomal prote 66.3 3.1 6.7E-05 36.3 1.2 64 131-195 130-194 (195)
8 PF10515 APP_amyloid: beta-amy 65.0 0.79 1.7E-05 32.5 -2.1 32 84-122 16-52 (52)
9 PF01161 PBP: Phosphatidyletha 44.8 21 0.00047 27.6 2.7 30 117-146 32-64 (146)
10 COG0810 TonB Periplasmic prote 42.3 27 0.00057 30.0 3.1 51 44-109 169-219 (244)
11 COG0463 WcaA Glycosyltransfera 40.1 16 0.00036 25.2 1.2 14 117-130 29-42 (291)
12 PF05063 MT-A70: MT-A70 ; Int 34.8 16 0.00035 29.7 0.6 11 121-131 1-11 (176)
13 PF07450 HycH: Formate hydroge 33.2 18 0.00039 29.9 0.6 26 103-133 63-88 (131)
14 cd00272 Chemokine_CC Chemokine 32.3 31 0.00066 23.5 1.5 25 120-144 27-51 (57)
15 PRK15084 formate hydrogenlyase 31.1 21 0.00045 29.6 0.6 26 103-133 65-90 (133)
16 PF04915 DltD_N: DltD N-termin 29.1 18 0.00039 26.3 -0.1 14 122-135 38-51 (62)
17 COG2932 Predicted transcriptio 28.8 29 0.00063 28.9 1.2 21 117-137 136-156 (214)
18 cd06433 GT_2_WfgS_like WfgS an 28.7 32 0.00069 25.8 1.2 14 117-130 24-37 (202)
19 COG1092 Predicted SAM-dependen 27.1 32 0.00069 32.6 1.2 20 120-141 290-309 (393)
20 PRK14688 hypothetical protein; 27.0 40 0.00088 26.8 1.6 56 81-145 62-117 (121)
21 cd00457 PEBP PhosphatidylEthan 25.8 53 0.0011 26.6 2.1 28 117-146 37-64 (159)
22 cd00865 PEBP_bact_arch Phospha 25.8 47 0.001 26.5 1.8 27 118-146 39-65 (150)
23 KOG4238 Bifunctional ATP sulfu 24.9 48 0.001 32.6 1.9 53 84-138 94-169 (627)
24 COG0144 Sun tRNA and rRNA cyto 24.7 43 0.00092 30.7 1.5 25 120-144 229-256 (355)
25 PF00836 Stathmin: Stathmin fa 23.7 42 0.00091 27.8 1.2 12 120-131 16-27 (140)
26 cd00866 PEBP_euk PhosphatidylE 22.8 78 0.0017 24.7 2.5 39 108-146 25-70 (154)
27 TIGR00446 nop2p NOL1/NOP2/sun 21.8 44 0.00096 28.8 1.0 23 121-143 141-166 (264)
28 COG2876 AroA 3-deoxy-D-arabino 21.7 42 0.00092 31.0 0.9 15 124-138 217-231 (286)
29 PF03754 DUF313: Domain of unk 21.4 52 0.0011 26.2 1.2 15 116-130 69-83 (114)
30 KOG2612 Predicted integral mem 21.3 48 0.001 26.2 1.0 23 101-123 28-57 (103)
31 COG2093 DNA-directed RNA polym 21.3 59 0.0013 24.0 1.4 26 110-135 21-49 (64)
32 PF00048 IL8: Small cytokines 20.8 56 0.0012 22.4 1.2 23 121-143 36-58 (64)
33 cd00933 barnase Barnase, a mem 20.4 95 0.0021 24.8 2.5 33 15-57 4-36 (107)
No 1
>PTZ00026 60S ribosomal protein L15; Provisional
Probab=100.00 E-value=4e-110 Score=706.74 Aligned_cols=195 Identities=77% Similarity=1.275 Sum_probs=194.4
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 029295 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (195)
Q Consensus 1 mg~Y~Yi~e~wkk~~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~ 80 (195)
||||+||+|+|++||||+|+||+|+|||||||+|+|||+++||||||||+||||||||||||||||++||+++|+|+|+|
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 cCCcccccccccccccchhHHHHHHhhhccCCC---------CCCCcceeEEEEeccCccccccCCCCcccccCCccccc
Q 029295 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGL---------KDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRE 151 (195)
Q Consensus 81 ~~kPk~~Gv~~lk~~kslq~iAEER~grk~~nL---------eDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~~hk~Re 151 (195)
||||++||||+||+++|||+|||||||++|||| |||+|||||||||||+||||++||+|||||+|+|||||
T Consensus 81 ~gkpk~~Gv~~lk~~kslq~iAEeRv~rk~~nLrVLNSYWV~qDg~yK~yEVILvDp~H~aIr~Dp~~nWI~~~~hk~Re 160 (204)
T PTZ00026 81 YGKPKTQGVNKLKSTRNLRAVAEERVGKRCGNLRVLNSYWVGQDSTYKFYEVILVDPFHNAIRNDPRINWICNPVHKHRE 160 (204)
T ss_pred CCCccccCccccCcchhHHHHHHHHhhccCCCcEEecceeEcCCCCcccEEEEEecCCCccceeCcccceecccccchhh
Confidence 999999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred ccCCccccccccCCCCCCCcccccCCCchhhhhccCeeEEeecC
Q 029295 152 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNQTLSLRRYR 195 (195)
Q Consensus 152 ~RGLTSAGkK~RGLr~kG~~~~k~r~S~ra~w~r~nt~~l~r~r 195 (195)
||||||||+|+|||++|||+++|++||++|+|+++|||+|+|||
T Consensus 161 ~RGLTsAGkK~RGL~~kG~~~~k~r~s~ra~~~r~n~~~l~r~r 204 (204)
T PTZ00026 161 LRGLTSAGRKSRGLRVKGHRASKLRPSRRANWKRRNRIVLRRYR 204 (204)
T ss_pred hccccccccccCCcCCCCCCcccCCcchhhhhhhccceeeEecC
Confidence 99999999999999999999999999999999999999999997
No 2
>KOG1678 consensus 60s ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-109 Score=691.10 Aligned_cols=194 Identities=82% Similarity=1.325 Sum_probs=193.1
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 029295 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (195)
Q Consensus 1 mg~Y~Yi~e~wkk~~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~ 80 (195)
||||+||+|+|++||||+|+||+++|||||||+++|||+++||||||||+||||||||||||||||++||+|+|+|||.|
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 cCCcccccccccccccchhHHHHHHhhhccCCC---------CCCCcceeEEEEeccCccccccCCCCcccccCCccccc
Q 029295 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGL---------KDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRE 151 (195)
Q Consensus 81 ~~kPk~~Gv~~lk~~kslq~iAEER~grk~~nL---------eDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~~hk~Re 151 (195)
||||+++|||||||++|+|++||||||++|+|| ||++|||||||||||+|.||++||+|||||+|||||||
T Consensus 81 yGKp~~~GvnqlK~~rs~qs~AEer~Gr~~g~LrVlNSYWv~qDstYk~fEVIlvDp~h~aIRrdp~~nwI~kpvhKhRE 160 (204)
T KOG1678|consen 81 YGKPVNQGVNQLKFQRSLQSVAEERAGRRCGNLRVLNSYWVNQDSTYKYFEVILVDPFHKAIRRDPRINWICKPVHKHRE 160 (204)
T ss_pred cCCccccchhhhhhhHHHHHHHHHHhhccccceeeeehhhccCccceeeEEEEEECcHHHHHhcCCCcccccchhhhhHH
Confidence 999999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred ccCCccccccccCCCCCCCcccccC-CCchhhhhccCeeEEeecC
Q 029295 152 LRGLTSAGKKYRGLRGKGHLHHKAR-PSRRATWKRNQTLSLRRYR 195 (195)
Q Consensus 152 ~RGLTSAGkK~RGLr~kG~~~~k~r-~S~ra~w~r~nt~~l~r~r 195 (195)
+|||||||+||||| ||||+|++|+ +|++|+|+++|||+|+|||
T Consensus 161 ~rGLTsagkksrGl-gKg~kf~~t~~gs~ra~Wkr~ntl~l~ryr 204 (204)
T KOG1678|consen 161 LRGLTSAGKKSRGL-GKGHKFNKTIGGSRRATWKRRNTLSLHRYR 204 (204)
T ss_pred hcccccccccccCc-ccccccccCCCchhHHHHhhcccceeeecC
Confidence 99999999999999 9999999999 8899999999999999997
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=7.3e-105 Score=670.17 Aligned_cols=183 Identities=77% Similarity=1.258 Sum_probs=170.4
Q ss_pred chHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCccc
Q 029295 2 GAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVY 81 (195)
Q Consensus 2 g~Y~Yi~e~wkk~~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~~ 81 (195)
|||+||+|+|++||||+|+||+++|||||||+|+|+||++||||||||+||||||||||||||+|++||+++|+|+|++|
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 CCcccccccccccccchhHHHHHHhhhccCCC---------CCCCcceeEEEEeccCccccccCCCCcccccCCcccccc
Q 029295 82 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGL---------KDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHREL 152 (195)
Q Consensus 82 ~kPk~~Gv~~lk~~kslq~iAEER~grk~~nL---------eDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~~hk~Re~ 152 (195)
|||++||||+||+++|||+|||||||++|||| |||+|||||||||||+||+|+|||+|||||+|+||||||
T Consensus 81 gKPk~~Gv~~~k~~kslq~iAEeRagrk~~nLrVLnSYwV~eDg~yK~fEVIlVDp~h~~Ir~D~~~nWI~~~~hk~R~~ 160 (192)
T PF00827_consen 81 GKPKHQGVNQLKPAKSLQSIAEERAGRKYPNLRVLNSYWVGEDGTYKWFEVILVDPNHPAIRNDPDINWICNPVHKHREF 160 (192)
T ss_dssp SSCGGSSSTSS--SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHTTTTTGGGGSGGGTTTTT
T ss_pred cccccceeeccCccccHHHHhhhhhccccCCceEEeeEEeCCCCcceeEEEEEecCCcHHHhcCCccceecccccCcccc
Confidence 99999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred cCCccccccccCCCCCCCcccccCCCchhhhh
Q 029295 153 RGLTSAGKKYRGLRGKGHLHHKARPSRRATWK 184 (195)
Q Consensus 153 RGLTSAGkK~RGLr~kG~~~~k~r~S~ra~w~ 184 (195)
|||||||+|+|||++|||+++|++||++|||+
T Consensus 161 RGLTsAgkk~RGL~~kG~~~~k~rpS~ra~wk 192 (192)
T PF00827_consen 161 RGLTSAGKKSRGLRGKGHGAEKTRPSRRANWK 192 (192)
T ss_dssp TTTSHHHHHHTTTT-SSTTCGGTSSTTTTTCC
T ss_pred ccccchhhhhcccccCccccccCCcccccccC
Confidence 99999999999999999999999999999996
No 4
>PRK04243 50S ribosomal protein L15e; Validated
Probab=100.00 E-value=2.1e-102 Score=656.44 Aligned_cols=183 Identities=52% Similarity=0.867 Sum_probs=181.1
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 029295 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (195)
Q Consensus 1 mg~Y~Yi~e~wkk~~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~ 80 (195)
||||+||+|+|++||||+|+||+|+|||||||+|+||||++|||||+||+|||||||||||||||||+||+++|+|+|+
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 cCCcccccccccccccchhHHHHHHhhhccCCC---------CCCCcceeEEEEeccCccccccCCCCcccccCCccccc
Q 029295 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGL---------KDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRE 151 (195)
Q Consensus 81 ~~kPk~~Gv~~lk~~kslq~iAEER~grk~~nL---------eDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~~hk~Re 151 (195)
+||++||||+|||++|||+|||||||++|||| |||+|||||||||||+||+|++||+|||||+|+|||||
T Consensus 82 -~kPk~~Gv~~lk~~kslq~iAEERa~rk~~nlrVLNSYwV~qDg~yK~fEVIlVDp~H~aIr~Dp~~nWI~~~~~k~R~ 160 (196)
T PRK04243 82 -RRPKRMGVNKITPAKSIQRIAEERAARKYPNLEVLNSYWVGEDGKYKWYEVILVDPHHPAIKNDPDLNWICDKSHRGRV 160 (196)
T ss_pred -CCccccCccccchhhhHHHHHHHHhhccCCCcEeeeeeEeccCCCcccEEEEEecCCCcchhcCcccceecccccchhh
Confidence 99999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred ccCCccccccccCCCCCCCcccccCCCchhhhhc
Q 029295 152 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKR 185 (195)
Q Consensus 152 ~RGLTSAGkK~RGLr~kG~~~~k~r~S~ra~w~r 185 (195)
||||||||+|+|||++|||+++|++||.+|+-++
T Consensus 161 ~RGLTSAGkK~RGl~~kg~~~~k~rps~ra~~~~ 194 (196)
T PRK04243 161 FRGLTSAGKKGRGLRKKGKGTEKVRPSIRANERR 194 (196)
T ss_pred hhcccccccccccccccCCCceecCccccccccc
Confidence 9999999999999999999999999999998764
No 5
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-83 Score=537.43 Aligned_cols=184 Identities=60% Similarity=0.939 Sum_probs=180.3
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 029295 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (195)
Q Consensus 1 mg~Y~Yi~e~wkk~~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~ 80 (195)
||||+||.|+|++++++++.+|+++|+|+||++|+|+||++|||+|+||.||||||||||||||+|++||+.+++|+++
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 cCCcccccccccccccchhHHHHHHhhhccCCC---------CCCCcceeEEEEeccCccccccCCCCcccccCCccccc
Q 029295 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGL---------KDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRE 151 (195)
Q Consensus 81 ~~kPk~~Gv~~lk~~kslq~iAEER~grk~~nL---------eDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~~hk~Re 151 (195)
++|++||||++++++|+|.|||||||++|||| |||.|||||||||||+||||+|||+|||||+++|+||+
T Consensus 81 -rrp~~mgvnki~~~ks~~~iAEerA~RK~pNL~vLnSYwVgeDg~yK~fEvIlvDp~H~aIk~Dp~l~wI~~~~~kgR~ 159 (195)
T COG1632 81 -RRPTRMGVNKIKRKKSLQFIAEERAGRKYPNLEVLNSYWVGEDGYYKYFEVILVDPRHPAIKNDPNLNWICRPVHKGRV 159 (195)
T ss_pred -CCcCcccccccChhhhHHHHHHHHhhccCCCcEeeeeEEeccccceeeEEEEEecCCChhhcCCCceeeecccccCCce
Confidence 89999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred ccCCccccccccCCCCCCCcccccCCCchhhhhcc
Q 029295 152 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRN 186 (195)
Q Consensus 152 ~RGLTSAGkK~RGLr~kG~~~~k~r~S~ra~w~r~ 186 (195)
||||||||+|+|||+.+|.++++.+||.+|+++.+
T Consensus 160 ~RgltsagkK~rgl~k~~k~~~~~R~~~~~~~~~~ 194 (195)
T COG1632 160 FRGLTSAGKKSRGLRKGGKGAEKKRPSTRALQRYR 194 (195)
T ss_pred eccccccchhhhhhhccCCcccccCcchhhhhhhc
Confidence 99999999999999888899999999999988754
No 6
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=73.31 E-value=2.2 Score=30.90 Aligned_cols=23 Identities=17% Similarity=0.470 Sum_probs=16.8
Q ss_pred ccCCC--CCCCcceeEE-EEeccCcc
Q 029295 109 KLGGL--KDSTYKYFEV-ILVDAAHN 131 (195)
Q Consensus 109 k~~nL--eDg~yK~fEV-ILVDp~H~ 131 (195)
.|||- +|-+..||+. |++||...
T Consensus 17 ~CP~Cgs~~~T~~W~G~viI~dPe~S 42 (61)
T PRK08351 17 RCPVCGSRDLSDEWFDLVIIIDVENS 42 (61)
T ss_pred cCCCCcCCccccccccEEEEeCCcHh
Confidence 58888 7778999995 45666544
No 7
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=66.31 E-value=3.1 Score=36.33 Aligned_cols=64 Identities=31% Similarity=0.382 Sum_probs=51.3
Q ss_pred cccccCCCCcccccCCcccccccCCccccccccCCCCCCCcccccC-CCchhhhhccCeeEEeecC
Q 029295 131 NAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKAR-PSRRATWKRNQTLSLRRYR 195 (195)
Q Consensus 131 ~aIr~Dp~inWI~~~~hk~Re~RGLTSAGkK~RGLr~kG~~~~k~r-~S~ra~w~r~nt~~l~r~r 195 (195)
.+|.=||+-.=|-+.-+=...|. -+.-|+..|||..-|.+.--.+ +..++.|.|.||+.+.+|+
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 46888888777777776677777 5679999999987777666655 5679999999999998875
No 8
>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=64.97 E-value=0.79 Score=32.48 Aligned_cols=32 Identities=38% Similarity=0.709 Sum_probs=13.7
Q ss_pred cccccccccccccchhHHHHHHhhhccCCC-----CCCCcceeE
Q 029295 84 PTNQGVTQLKFQRSKRSVAEERAGRKLGGL-----KDSTYKYFE 122 (195)
Q Consensus 84 Pk~~Gv~~lk~~kslq~iAEER~grk~~nL-----eDg~yK~fE 122 (195)
|..+|+-.+-+.-+. ||| ++.|| |.=||||||
T Consensus 16 ~~~~g~veVD~~~tp----Ee~---h~~~mQ~nGYENPTYkyfE 52 (52)
T PF10515_consen 16 PISHGFVEVDPCLTP----EER---HLSNMQNNGYENPTYKYFE 52 (52)
T ss_dssp --------------H----HHH---HHHHHHCTEEESCTCHHCC
T ss_pred ccccceEEecCCCCh----HHH---HHHHHHhcCCcCCceeccC
Confidence 667888777776333 654 56666 899999998
No 9
>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=44.85 E-value=21 Score=27.59 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=22.2
Q ss_pred CcceeEEEEeccCcccccc---CCCCcccccCC
Q 029295 117 TYKYFEVILVDAAHNAIRN---DPRINWICKPV 146 (195)
Q Consensus 117 ~yK~fEVILVDp~H~aIr~---Dp~inWI~~~~ 146 (195)
.-+.|=|||+||+.|.-.+ .+-+.||.-..
T Consensus 32 ~~~~y~lim~D~D~P~~~~~~~~~~~Hwl~~ni 64 (146)
T PF01161_consen 32 GTKSYTLIMVDPDAPSRENPSFGPFLHWLVTNI 64 (146)
T ss_dssp TTSEEEEEEEETTSSBTTSCTTTSEEEEEEEEE
T ss_pred CCcEEEEEEECCCCCccccCCCCcEEEEEEcCC
Confidence 3468999999999988433 35677877655
No 10
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=42.34 E-value=27 Score=30.03 Aligned_cols=51 Identities=24% Similarity=0.211 Sum_probs=37.3
Q ss_pred CchHHHhhccccccceEEEEEEeeecCCCCCccCCcccCCcccccccccccccchhHHHHHHhhhc
Q 029295 44 RPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSKRSVAEERAGRK 109 (195)
Q Consensus 44 R~dkAR~LGYKAKQG~vv~RvrVRrGgrkrp~~kg~~~~kPk~~Gv~~lk~~kslq~iAEER~grk 109 (195)
=|..|+++|+ ||-|++.+-|..+|. ..+.-|-+-+...-|-.-|.+-+.+-
T Consensus 169 YP~~A~~~g~---~G~V~V~f~i~~~G~------------v~~v~v~~SSg~~~lD~aal~air~~ 219 (244)
T COG0810 169 YPAQARARGI---EGTVKVKFTIDPDGN------------VTNVRVLKSSGSPALDRAALEAIRKW 219 (244)
T ss_pred CcHHHHhcCC---CceEEEEEEECCCCC------------EeeeEEeecCCcHHHHHHHHHHHHHh
Confidence 5899999998 999999999998865 33444444555566777777666543
No 11
>COG0463 WcaA Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=40.11 E-value=16 Score=25.18 Aligned_cols=14 Identities=57% Similarity=0.911 Sum_probs=10.8
Q ss_pred CcceeEEEEeccCc
Q 029295 117 TYKYFEVILVDAAH 130 (195)
Q Consensus 117 ~yK~fEVILVDp~H 130 (195)
++..||||+||-..
T Consensus 29 ~~~~~eiivvddgs 42 (291)
T COG0463 29 TYKDFEIIVVDDGS 42 (291)
T ss_pred hhcceEEEEEeCCC
Confidence 45559999999754
No 12
>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=34.81 E-value=16 Score=29.67 Aligned_cols=11 Identities=36% Similarity=0.631 Sum_probs=8.2
Q ss_pred eEEEEeccCcc
Q 029295 121 FEVILVDAAHN 131 (195)
Q Consensus 121 fEVILVDp~H~ 131 (195)
|.||++||=-+
T Consensus 1 fdvI~~DPPW~ 11 (176)
T PF05063_consen 1 FDVIYADPPWP 11 (176)
T ss_pred CCEEEEeCCCC
Confidence 77899998443
No 13
>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=33.20 E-value=18 Score=29.85 Aligned_cols=26 Identities=46% Similarity=0.600 Sum_probs=19.6
Q ss_pred HHHhhhccCCCCCCCcceeEEEEeccCcccc
Q 029295 103 EERAGRKLGGLKDSTYKYFEVILVDAAHNAI 133 (195)
Q Consensus 103 EER~grk~~nLeDg~yK~fEVILVDp~H~aI 133 (195)
|+-|-+|+.| ..||+| |-|||.|-+.
T Consensus 63 ~~eArrKl~g----l~kfGE-I~Id~~H~~~ 88 (131)
T PF07450_consen 63 EGEARRKLEG----LLKFGE-IEIDSEHVAL 88 (131)
T ss_pred cHHHHHHHhC----CCceeE-EEECHHHHHH
Confidence 5666777766 479999 6799999654
No 14
>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=32.34 E-value=31 Score=23.47 Aligned_cols=25 Identities=20% Similarity=0.425 Sum_probs=21.6
Q ss_pred eeEEEEeccCccccccCCCCccccc
Q 029295 120 YFEVILVDAAHNAIRNDPRINWICK 144 (195)
Q Consensus 120 ~fEVILVDp~H~aIr~Dp~inWI~~ 144 (195)
.=|||+.-.....|-.||+-.|+-+
T Consensus 27 ~~aVIf~tk~g~~iC~dP~~~WVk~ 51 (57)
T cd00272 27 KPAVIFKTKRGREVCADPKQKWVQR 51 (57)
T ss_pred CcEEEEEeCCCCEEeCCCChHHHHH
Confidence 3479999999999999999999854
No 15
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=31.15 E-value=21 Score=29.64 Aligned_cols=26 Identities=42% Similarity=0.635 Sum_probs=19.5
Q ss_pred HHHhhhccCCCCCCCcceeEEEEeccCcccc
Q 029295 103 EERAGRKLGGLKDSTYKYFEVILVDAAHNAI 133 (195)
Q Consensus 103 EER~grk~~nLeDg~yK~fEVILVDp~H~aI 133 (195)
|+-|-+|+.| ..||+| |-|||+|-+.
T Consensus 65 ~~eArrKl~g----l~kfgE-I~I~~~H~~~ 90 (133)
T PRK15084 65 EGEARRKMEG----VPKFGE-IVIDSSHVAL 90 (133)
T ss_pred hHHHHHHHhC----cCceeE-EEECHHHHHH
Confidence 5566677765 579999 6799999654
No 16
>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=29.07 E-value=18 Score=26.28 Aligned_cols=14 Identities=21% Similarity=0.264 Sum_probs=8.7
Q ss_pred EEEEeccCcccccc
Q 029295 122 EVILVDAAHNAIRN 135 (195)
Q Consensus 122 EVILVDp~H~aIr~ 135 (195)
|..-+||+||++--
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 44568999999853
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=28.83 E-value=29 Score=28.86 Aligned_cols=21 Identities=38% Similarity=0.490 Sum_probs=17.8
Q ss_pred CcceeEEEEeccCccccccCC
Q 029295 117 TYKYFEVILVDAAHNAIRNDP 137 (195)
Q Consensus 117 ~yK~fEVILVDp~H~aIr~Dp 137 (195)
+|.=.|+|||||+.++++.|-
T Consensus 136 ~~~~Gd~ilVd~~~~~~~gd~ 156 (214)
T COG2932 136 TYEDGDTLLVDPGVNTRRGDR 156 (214)
T ss_pred cccCCCEEEECCCCceeeCCE
Confidence 466678999999999999883
No 18
>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=28.72 E-value=32 Score=25.84 Aligned_cols=14 Identities=36% Similarity=0.624 Sum_probs=10.5
Q ss_pred CcceeEEEEeccCc
Q 029295 117 TYKYFEVILVDAAH 130 (195)
Q Consensus 117 ~yK~fEVILVDp~H 130 (195)
++..||||+||-..
T Consensus 24 ~~~~~evivvDd~s 37 (202)
T cd06433 24 TYPNIEYIVIDGGS 37 (202)
T ss_pred CCCCceEEEEeCCC
Confidence 45569999998654
No 19
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=27.12 E-value=32 Score=32.59 Aligned_cols=20 Identities=15% Similarity=0.486 Sum_probs=16.2
Q ss_pred eeEEEEeccCccccccCCCCcc
Q 029295 120 YFEVILVDAAHNAIRNDPRINW 141 (195)
Q Consensus 120 ~fEVILVDp~H~aIr~Dp~inW 141 (195)
=|.||++|| |+.-+.++--|
T Consensus 290 ~fDlIilDP--PsF~r~k~~~~ 309 (393)
T COG1092 290 KFDLIILDP--PSFARSKKQEF 309 (393)
T ss_pred cccEEEECC--cccccCcccch
Confidence 589999999 88877776654
No 20
>PRK14688 hypothetical protein; Provisional
Probab=26.99 E-value=40 Score=26.78 Aligned_cols=56 Identities=25% Similarity=0.389 Sum_probs=31.4
Q ss_pred cCCcccccccccccccchhHHHHHHhhhccCCCCCCCcceeEEEEeccCccccccCCCCcccccC
Q 029295 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKDSTYKYFEVILVDAAHNAIRNDPRINWICKP 145 (195)
Q Consensus 81 ~~kPk~~Gv~~lk~~kslq~iAEER~grk~~nLeDg~yK~fEVILVDp~H~aIr~Dp~inWI~~~ 145 (195)
|+-|. .-|+.-| ++.|...|+.=...+ ++++... =|.||.|++.++ ++.|+||-+.
T Consensus 62 ~g~~~-eaV~~~K-~~ri~~aA~~yL~~~--~~~~~~~-RFDvi~v~~~~~----~~~i~~i~nA 117 (121)
T PRK14688 62 YGLPA-ESVTPRK-KAHLMASAESYIQKH--RLEHFPC-RIDFVSVDLSQP----EPRLELIKNA 117 (121)
T ss_pred CCChH-HcCCHHH-HHHHHHHHHHHHHhC--CCCCCCE-EEEEEEEEccCC----CCCEEEehHh
Confidence 34452 3344333 234555556555433 2544333 399999987652 3579999764
No 21
>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=25.85 E-value=53 Score=26.62 Aligned_cols=28 Identities=11% Similarity=0.204 Sum_probs=21.3
Q ss_pred CcceeEEEEeccCccccccCCCCcccccCC
Q 029295 117 TYKYFEVILVDAAHNAIRNDPRINWICKPV 146 (195)
Q Consensus 117 ~yK~fEVILVDp~H~aIr~Dp~inWI~~~~ 146 (195)
--+.|=|||+||+.| ...+-+-||.-..
T Consensus 37 ~t~s~ali~~DpDap--~~~~~~HWvv~nI 64 (159)
T cd00457 37 DVKEYVLVMEDPDAP--LGRPIVHGLVYGI 64 (159)
T ss_pred CCeEEEEEEECCCCC--CCCCceEEEEecc
Confidence 359999999999999 2335678887543
No 22
>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=25.76 E-value=47 Score=26.46 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=21.5
Q ss_pred cceeEEEEeccCccccccCCCCcccccCC
Q 029295 118 YKYFEVILVDAAHNAIRNDPRINWICKPV 146 (195)
Q Consensus 118 yK~fEVILVDp~H~aIr~Dp~inWI~~~~ 146 (195)
-|.|=|+|+||+.| ...+-+-||.-..
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 48999999999999 4457788887543
No 23
>KOG4238 consensus Bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate kinase [Nucleotide transport and metabolism]
Probab=24.85 E-value=48 Score=32.63 Aligned_cols=53 Identities=17% Similarity=0.279 Sum_probs=37.4
Q ss_pred cccccccccccccchhHHHHHHhhhccCCC-----------------------CCCCcceeEEEEeccCccccccCCC
Q 029295 84 PTNQGVTQLKFQRSKRSVAEERAGRKLGGL-----------------------KDSTYKYFEVILVDAAHNAIRNDPR 138 (195)
Q Consensus 84 Pk~~Gv~~lk~~kslq~iAEER~grk~~nL-----------------------eDg~yK~fEVILVDp~H~aIr~Dp~ 138 (195)
.||.|...-....|++.||| |++-|.+- |....+||||-+--|-|-.=.+||+
T Consensus 94 ~knlgfs~edreenirriae--vaklfadaglvcitsfispf~~dr~~arkihe~~~l~f~ev~v~a~l~vceqrd~k 169 (627)
T KOG4238|consen 94 NKNLGFSPEDREENIRRIAE--VAKLFADAGLVCITSFISPFAKDRENARKIHESAGLPFFEVFVDAPLNVCEQRDVK 169 (627)
T ss_pred hhccCCCchhHHHHHHHHHH--HHHHHhcCCceeeehhcChhhhhhhhhhhhhcccCCceEEEEecCchhhhhhcChH
Confidence 45555555556779999999 45555443 6677899999887787766666663
No 24
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=24.69 E-value=43 Score=30.67 Aligned_cols=25 Identities=40% Similarity=0.761 Sum_probs=21.0
Q ss_pred eeEEEEeccCcc---ccccCCCCccccc
Q 029295 120 YFEVILVDAAHN---AIRNDPRINWICK 144 (195)
Q Consensus 120 ~fEVILVDp~H~---aIr~Dp~inWI~~ 144 (195)
.|..||||+-+. .|++||++.|--.
T Consensus 229 ~fD~iLlDaPCSg~G~irr~Pd~~~~~~ 256 (355)
T COG0144 229 KFDRILLDAPCSGTGVIRRDPDVKWRRT 256 (355)
T ss_pred cCcEEEECCCCCCCcccccCccccccCC
Confidence 389999999876 5999999999543
No 25
>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=23.73 E-value=42 Score=27.81 Aligned_cols=12 Identities=42% Similarity=0.553 Sum_probs=8.1
Q ss_pred eeEEEEeccCcc
Q 029295 120 YFEVILVDAAHN 131 (195)
Q Consensus 120 ~fEVILVDp~H~ 131 (195)
=|||||-+|+-+
T Consensus 16 aFEVIL~pps~~ 27 (140)
T PF00836_consen 16 AFEVILKPPSPD 27 (140)
T ss_dssp EEEEEES--SSS
T ss_pred ceEeeeCCCCCC
Confidence 499999999854
No 26
>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=22.82 E-value=78 Score=24.75 Aligned_cols=39 Identities=15% Similarity=0.428 Sum_probs=25.7
Q ss_pred hccCCC----CCCCcceeEEEEeccCcccccc---CCCCcccccCC
Q 029295 108 RKLGGL----KDSTYKYFEVILVDAAHNAIRN---DPRINWICKPV 146 (195)
Q Consensus 108 rk~~nL----eDg~yK~fEVILVDp~H~aIr~---Dp~inWI~~~~ 146 (195)
...|.+ .+..-+.|=||||||+-|.-.+ -+-+.||....
T Consensus 25 ~~~P~i~~~~~~~~~~~y~lvm~DpD~p~~~~~~~~~~lHwl~~ni 70 (154)
T cd00866 25 QKAPTVSFSSEDPPDKLYTLVMVDPDAPSRDDPKFREWLHWLVTNI 70 (154)
T ss_pred CcCCeEEEecCCCCCCeEEEEEECCCCCCCCCCCCCCEEEEEEeCc
Confidence 355555 2224789999999999876542 24567877543
No 27
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=21.76 E-value=44 Score=28.82 Aligned_cols=23 Identities=39% Similarity=0.572 Sum_probs=18.6
Q ss_pred eEEEEeccCcc---ccccCCCCcccc
Q 029295 121 FEVILVDAAHN---AIRNDPRINWIC 143 (195)
Q Consensus 121 fEVILVDp~H~---aIr~Dp~inWI~ 143 (195)
|.+||+||-.. .++.||++.|-.
T Consensus 141 fD~Vl~D~Pcsg~G~~~~~p~~~~~~ 166 (264)
T TIGR00446 141 FDAILLDAPCSGEGVIRKDPSRKKNW 166 (264)
T ss_pred CCEEEEcCCCCCCcccccChhhhhcC
Confidence 99999999665 568899988743
No 28
>COG2876 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=21.66 E-value=42 Score=30.97 Aligned_cols=15 Identities=33% Similarity=0.503 Sum_probs=13.0
Q ss_pred EEeccCccccccCCC
Q 029295 124 ILVDAAHNAIRNDPR 138 (195)
Q Consensus 124 ILVDp~H~aIr~Dp~ 138 (195)
|+|||+|++=++|+-
T Consensus 217 VivDpSH~~Grr~lv 231 (286)
T COG2876 217 VIVDPSHATGRRDLV 231 (286)
T ss_pred EEECCCCcccchhhH
Confidence 899999999888863
No 29
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=21.42 E-value=52 Score=26.19 Aligned_cols=15 Identities=47% Similarity=0.454 Sum_probs=11.2
Q ss_pred CCcceeEEEEeccCc
Q 029295 116 STYKYFEVILVDAAH 130 (195)
Q Consensus 116 g~yK~fEVILVDp~H 130 (195)
....=-|||||||.-
T Consensus 69 ~~~~Gv~V~lvdp~~ 83 (114)
T PF03754_consen 69 DKKKGVEVILVDPSL 83 (114)
T ss_pred cccCCceEEEECCcC
Confidence 345667999999953
No 30
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=21.33 E-value=48 Score=26.25 Aligned_cols=23 Identities=48% Similarity=0.767 Sum_probs=19.6
Q ss_pred HHHHHhhhccCCC-------CCCCcceeEE
Q 029295 101 VAEERAGRKLGGL-------KDSTYKYFEV 123 (195)
Q Consensus 101 iAEER~grk~~nL-------eDg~yK~fEV 123 (195)
+|||---++.++| ||++|.|-|-
T Consensus 28 ~a~e~~~qkl~k~~~~D~rpedssY~f~~~ 57 (103)
T KOG2612|consen 28 FAEEHHLQKLGKLAALDGRPEDSSYRFCEM 57 (103)
T ss_pred HHHHHHHHHHhccccCCCCccccceeecCC
Confidence 5888888888888 9999998773
No 31
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.30 E-value=59 Score=24.02 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=18.3
Q ss_pred cCCC--CCCCcceeE-EEEeccCcccccc
Q 029295 110 LGGL--KDSTYKYFE-VILVDAAHNAIRN 135 (195)
Q Consensus 110 ~~nL--eDg~yK~fE-VILVDp~H~aIr~ 135 (195)
||+. +|-+..||- ||++||....|-.
T Consensus 21 CP~Cgs~~~te~W~G~~iIidpe~SeIAk 49 (64)
T COG2093 21 CPVCGSTDLTEEWFGLLIIIDPEKSEIAK 49 (64)
T ss_pred CCCCCCcccchhhccEEEEEcCcHHHHHH
Confidence 4444 667788986 6778998877643
No 32
>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=20.75 E-value=56 Score=22.39 Aligned_cols=23 Identities=22% Similarity=0.432 Sum_probs=19.9
Q ss_pred eEEEEeccCccccccCCCCcccc
Q 029295 121 FEVILVDAAHNAIRNDPRINWIC 143 (195)
Q Consensus 121 fEVILVDp~H~aIr~Dp~inWI~ 143 (195)
=|||++.-....+--||+-.|+-
T Consensus 36 ~avI~~~k~g~~~C~dP~~~wvk 58 (64)
T PF00048_consen 36 PAVIFTTKKGREVCADPNAPWVK 58 (64)
T ss_dssp CEEEEEETTSEEEEEETTSHHHH
T ss_pred ceEEEEecCCCcEEcCCchHHHH
Confidence 58898888888999999999974
No 33
>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=20.36 E-value=95 Score=24.83 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=24.5
Q ss_pred cchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhcccccc
Q 029295 15 QSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQ 57 (195)
Q Consensus 15 ~sd~~~~L~r~R~~e~Rq~~~v~Rv~rPTR~dkAR~LGYKAKQ 57 (195)
+.+|..||.. +.+||.-+-.. +.|++||.+++.
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 3466666655 88999876654 889999999744
Done!