Query 028730
Match_columns 204
No_of_seqs 116 out of 264
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 16:06:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028730hhsearch_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 3E-119 7E-124 766.9 18.6 204 1-204 1-204 (204)
2 KOG1678 60s ribosomal protein 100.0 7E-118 2E-122 747.4 13.1 203 1-204 1-204 (204)
3 PF00827 Ribosomal_L15e: Ribos 100.0 6E-114 1E-118 729.6 17.1 192 2-193 1-192 (192)
4 PRK04243 50S ribosomal protein 100.0 2E-111 4E-116 715.9 16.7 192 1-194 3-194 (196)
5 COG1632 RPL15A Ribosomal prote 100.0 4.3E-91 9.4E-96 589.7 15.2 193 1-195 2-194 (195)
6 COG1632 RPL15A Ribosomal prote 63.1 3.5 7.6E-05 36.2 1.0 64 140-204 130-194 (195)
7 PF01161 PBP: Phosphatidyletha 54.4 16 0.00034 28.6 3.3 36 120-155 26-64 (146)
8 COG2932 Predicted transcriptio 43.1 15 0.00033 30.8 1.7 28 119-146 126-156 (214)
9 cd00866 PEBP_euk PhosphatidylE 42.6 37 0.00079 26.8 3.7 43 108-155 25-70 (154)
10 PHA02110 hypothetical protein 42.0 28 0.0006 27.4 2.8 32 102-138 16-47 (98)
11 cd00457 PEBP PhosphatidylEthan 40.6 31 0.00067 28.2 3.1 34 120-155 31-64 (159)
12 COG0810 TonB Periplasmic prote 39.2 31 0.00067 29.8 3.0 50 44-108 169-218 (244)
13 COG0144 Sun tRNA and rRNA cyto 37.0 22 0.00048 32.8 1.9 25 129-153 229-256 (355)
14 PRK08351 DNA-directed RNA poly 36.1 19 0.00041 26.3 1.0 25 109-140 17-42 (61)
15 cd07998 WGR_DNA_ligase WGR dom 35.6 37 0.00079 25.7 2.5 19 118-136 4-22 (77)
16 COG0463 WcaA Glycosyltransfera 33.3 24 0.00053 24.5 1.2 12 128-139 31-42 (291)
17 PF05063 MT-A70: MT-A70 ; Int 32.8 18 0.00038 29.7 0.5 11 130-140 1-11 (176)
18 PRK11933 yebU rRNA (cytosine-C 31.6 37 0.0008 32.9 2.5 37 110-151 163-208 (470)
19 cd00272 Chemokine_CC Chemokine 31.1 33 0.00071 23.5 1.5 39 114-153 13-51 (57)
20 PF11396 DUF2874: Protein of u 29.4 84 0.0018 20.9 3.3 28 107-135 17-44 (61)
21 COG2876 AroA 3-deoxy-D-arabino 28.4 28 0.0006 32.4 1.0 15 133-147 217-231 (286)
22 KOG3351 Predicted nucleotidylt 27.4 34 0.00074 31.8 1.4 34 132-166 218-260 (293)
23 PF00836 Stathmin: Stathmin fa 27.2 33 0.00072 28.6 1.2 12 129-140 16-27 (140)
24 PLN00169 CETS family protein; 27.2 75 0.0016 26.9 3.4 29 127-155 62-93 (175)
25 PF04915 DltD_N: DltD N-termin 26.4 21 0.00046 26.1 -0.1 13 131-143 38-50 (62)
26 KOG3346 Phosphatidylethanolami 25.6 73 0.0016 27.6 3.1 23 125-148 61-83 (185)
27 PRK14688 hypothetical protein; 23.9 50 0.0011 26.5 1.6 21 130-154 97-117 (121)
28 COG1092 Predicted SAM-dependen 23.8 41 0.00088 32.1 1.3 20 129-150 290-309 (393)
29 cd06433 GT_2_WfgS_like WfgS an 23.0 44 0.00096 25.3 1.1 13 127-139 25-37 (202)
30 cd00169 Chemokine Chemokine: s 22.9 95 0.0021 21.2 2.7 41 113-153 12-53 (59)
31 cd05468 pVHL von Hippel-Landau 22.5 80 0.0017 25.6 2.6 33 114-146 19-59 (141)
32 cd00865 PEBP_bact_arch Phospha 22.3 86 0.0019 25.1 2.7 27 127-155 39-65 (150)
33 PF07450 HycH: Formate hydroge 21.9 37 0.00081 28.2 0.5 26 103-142 63-88 (131)
34 PF00048 IL8: Small cytokines 21.6 70 0.0015 22.1 1.8 41 113-153 18-59 (64)
35 TIGR00446 nop2p NOL1/NOP2/sun 21.1 47 0.001 28.9 1.0 53 95-152 105-166 (264)
36 PRK15084 formate hydrogenlyase 20.8 40 0.00086 28.2 0.5 26 103-142 65-90 (133)
37 KOG4300 Predicted methyltransf 20.1 55 0.0012 29.9 1.3 50 86-139 41-109 (252)
No 1
>PTZ00026 60S ribosomal protein L15; Provisional
Probab=100.00 E-value=3e-119 Score=766.89 Aligned_cols=204 Identities=77% Similarity=1.301 Sum_probs=203.4
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 028730 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (204)
Q Consensus 1 mg~y~yi~e~wkk~~sd~~~~l~r~R~~e~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~ 80 (204)
||||+||+|+|++||||+|+||+|+|||||||+|+|||+++||||||||+||||||||||||||||++||+++|+|+|+|
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 cCCcccccccccccccchhHHHHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCcccccCCCCcccccCCcccch
Q 028730 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPVHKHRE 160 (204)
Q Consensus 81 ~~KPk~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~hk~Re 160 (204)
||||++||||+||+++|||+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+|||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccccCCCCCCCcccccCCCchhhhcccceeEeeecC
Q 028730 161 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNNTLSLRRYR 204 (204)
Q Consensus 161 ~RGLTsagkk~RGLr~kG~~~~k~r~S~ra~w~r~nt~~l~r~r 204 (204)
||||||||+|+|||++|||+++|++||++|+|+++|||+|+|||
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=7.4e-118 Score=747.45 Aligned_cols=203 Identities=81% Similarity=1.346 Sum_probs=202.1
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 028730 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (204)
Q Consensus 1 mg~y~yi~e~wkk~~sd~~~~l~r~R~~e~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~ 80 (204)
||||+||+|||++||||+|+||+++|||||||+++|||+++||||||||+||||||||||||||||++||+|+|+|||.|
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 cCCcccccccccccccchhHHHHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCcccccCCCCcccccCCcccch
Q 028730 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPVHKHRE 160 (204)
Q Consensus 81 ~~KPk~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~hk~Re 160 (204)
||||+|+|||||||++|+|++||||||++|+||+|||||||+||++|||||||||||+|.||++||+|||||+|||||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccccCCCCCCCcccccC-CCchhhhcccceeEeeecC
Q 028730 161 LRGLTSAGKKYRGLRGKGHLHHKAR-PSRRATWKRNNTLSLRRYR 204 (204)
Q Consensus 161 ~RGLTsagkk~RGLr~kG~~~~k~r-~S~ra~w~r~nt~~l~r~r 204 (204)
+|||||||+||||| ||||+|++|+ +|++|+|+|+|||+|+|||
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 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=5.9e-114 Score=729.59 Aligned_cols=192 Identities=77% Similarity=1.284 Sum_probs=179.4
Q ss_pred chHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCccc
Q 028730 2 GAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVY 81 (204)
Q Consensus 2 g~y~yi~e~wkk~~sd~~~~l~r~R~~e~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~~ 81 (204)
|||+||+|+|++||||+|+||+++|||||||+|+|+|+|+||||||||+||||||||||||||||++||+++|+|+|++|
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 CCcccccccccccccchhHHHHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCcccccCCCCcccccCCcccchh
Q 028730 82 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPVHKHREL 161 (204)
Q Consensus 82 ~KPk~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~hk~Re~ 161 (204)
|||++||||+||+++|||+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+||||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccccccCCCCCCCcccccCCCchhhhc
Q 028730 162 RGLTSAGKKYRGLRGKGHLHHKARPSRRATWK 193 (204)
Q Consensus 162 RGLTsagkk~RGLr~kG~~~~k~r~S~ra~w~ 193 (204)
|||||||+|+|||++|||+++||+||++|||+
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=1.7e-111 Score=715.94 Aligned_cols=192 Identities=53% Similarity=0.910 Sum_probs=190.2
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 028730 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (204)
Q Consensus 1 mg~y~yi~e~wkk~~sd~~~~l~r~R~~e~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~ 80 (204)
||||+||+|+|++||||+|+||+|+|||||||+|+|||+++||||||||+|||||||||||||||||+||+++|+|+|+
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 cCCcccccccccccccchhHHHHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCcccccCCCCcccccCCcccch
Q 028730 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPVHKHRE 160 (204)
Q Consensus 81 ~~KPk~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~hk~Re 160 (204)
|||++||||+|||++|||+|||||||++||||||||||||+|||+|||||||||||+||+|++||+|||||+|+|||||
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 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccccCCCCCCCcccccCCCchhhhcc
Q 028730 161 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKR 194 (204)
Q Consensus 161 ~RGLTsagkk~RGLr~kG~~~~k~r~S~ra~w~r 194 (204)
||||||||+|+|||++|||+++|++||.+|+-++
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=4.3e-91 Score=589.72 Aligned_cols=193 Identities=60% Similarity=0.964 Sum_probs=189.1
Q ss_pred CchHHHHHHHHhcccchHHHHHHHHHHHHHhcCCceEEeCCCCCchHHHhhccccccceEEEEEEeeecCCCCCccCCcc
Q 028730 1 MGAYTFVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIV 80 (204)
Q Consensus 1 mg~y~yi~e~wkk~~sd~~~~l~r~R~~e~Rq~~~i~R~~rPTR~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~ 80 (204)
||||+||.|+|++++++++.+|+++|+|+||++|+|+||++|||+|+||.||||||||||||||||++||+.+++|++|
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 cCCcccccccccccccchhHHHHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCcccccCCCCcccccCCcccch
Q 028730 81 YGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPVHKHRE 160 (204)
Q Consensus 81 ~~KPk~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~hk~Re 160 (204)
++|++||||++++++|+|.|||||||++||||+|||||||+|||.|||||||||||+||||++||+|||||+++|+||+
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 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccccCCCCCCCcccccCCCchhhhccc
Q 028730 161 LRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRN 195 (204)
Q Consensus 161 ~RGLTsagkk~RGLr~kG~~~~k~r~S~ra~w~r~ 195 (204)
||||||||+|+|||+.+|.++++.+||.+|+++.+
T Consensus 160 ~RgltsagkK~rgl~k~~k~~~~~R~~~~~~~~~~ 194 (195)
T COG1632 160 FRGLTSAGKKSRGLRKGGKGAEKKRPSTRALQRYR 194 (195)
T ss_pred eccccccchhhhhhhccCCcccccCcchhhhhhhc
Confidence 99999999999999888899999999999988754
No 6
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=63.07 E-value=3.5 Score=36.22 Aligned_cols=64 Identities=31% Similarity=0.395 Sum_probs=50.4
Q ss_pred cccccCCCCcccccCCcccchhcCCccccccccCCCCCCCcccccC-CCchhhhcccceeEeeecC
Q 028730 140 NAIRNDPRINWLCNPVHKHRELRGLTSAGKKYRGLRGKGHLHHKAR-PSRRATWKRNNTLSLRRYR 204 (204)
Q Consensus 140 ~aIr~Dp~~~WI~~~~hk~Re~RGLTsagkk~RGLr~kG~~~~k~r-~S~ra~w~r~nt~~l~r~r 204 (204)
.+|.=||+-.=|-+.-+=-..|+ -+.-|+..|||..-|.+.--.+ +..++.|.|.||+.+.+|+
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 46777777776766666666776 5679999999988887766665 6679999999999998875
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=54.36 E-value=16 Score=28.56 Aligned_cols=36 Identities=31% Similarity=0.693 Sum_probs=25.2
Q ss_pred eeccCCCceeEEEEEecCCCccccc---CCCCcccccCC
Q 028730 120 WINEDSTYKYFEVILVDPAHNAIRN---DPRINWLCNPV 155 (204)
Q Consensus 120 wV~eDg~yK~fEVILVDp~H~aIr~---Dp~~~WI~~~~ 155 (204)
|...-..-+.|=|||+||+.|.-.+ .+-+.||.-..
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 4444446678999999999988433 35677877655
No 8
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=43.10 E-value=15 Score=30.77 Aligned_cols=28 Identities=36% Similarity=0.514 Sum_probs=23.3
Q ss_pred eeeccCCC---ceeEEEEEecCCCcccccCC
Q 028730 119 YWINEDST---YKYFEVILVDPAHNAIRNDP 146 (204)
Q Consensus 119 YwV~eDg~---yK~fEVILVDp~H~aIr~Dp 146 (204)
-+|.-||+ |.=.|+|||||+.++++.|-
T Consensus 126 i~V~GDSMeP~~~~Gd~ilVd~~~~~~~gd~ 156 (214)
T COG2932 126 LRVTGDSMEPTYEDGDTLLVDPGVNTRRGDR 156 (214)
T ss_pred EEEeCCcccccccCCCEEEECCCCceeeCCE
Confidence 48888886 55568999999999999883
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=42.57 E-value=37 Score=26.80 Aligned_cols=43 Identities=21% Similarity=0.468 Sum_probs=28.2
Q ss_pred hccCCceeeeeeeeccCCCceeEEEEEecCCCccccc---CCCCcccccCC
Q 028730 108 RKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAIRN---DPRINWLCNPV 155 (204)
Q Consensus 108 rk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aIr~---Dp~~~WI~~~~ 155 (204)
...|-+++ .+.+..-+.|=|||+||+-|.-.+ -+-+.||....
T Consensus 25 ~~~P~i~~-----~~~~~~~~~y~lvm~DpD~p~~~~~~~~~~lHwl~~ni 70 (154)
T cd00866 25 QKAPTVSF-----SSEDPPDKLYTLVMVDPDAPSRDDPKFREWLHWLVTNI 70 (154)
T ss_pred CcCCeEEE-----ecCCCCCCeEEEEEECCCCCCCCCCCCCCEEEEEEeCc
Confidence 45666543 334446789999999999877542 23567776543
No 10
>PHA02110 hypothetical protein
Probab=42.00 E-value=28 Score=27.42 Aligned_cols=32 Identities=28% Similarity=0.568 Sum_probs=25.6
Q ss_pred HHHHhhhccCCceeeeeeeeccCCCceeEEEEEecCC
Q 028730 102 AEERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPA 138 (204)
Q Consensus 102 AEeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~ 138 (204)
.|--.|.+.+.+++.-|||+-.||- |-|-||-
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 3556799999999999999999994 4455664
No 11
>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=40.56 E-value=31 Score=28.17 Aligned_cols=34 Identities=18% Similarity=0.356 Sum_probs=25.8
Q ss_pred eeccCCCceeEEEEEecCCCcccccCCCCcccccCC
Q 028730 120 WINEDSTYKYFEVILVDPAHNAIRNDPRINWLCNPV 155 (204)
Q Consensus 120 wV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~~~ 155 (204)
|-+.+.--+.|=|||+||+.| ...+-+-||.-..
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 766665669999999999999 2335678887543
No 12
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=39.20 E-value=31 Score=29.85 Aligned_cols=50 Identities=24% Similarity=0.238 Sum_probs=36.2
Q ss_pred CchHHHhhccccccceEEEEEEeeecCCCCCccCCcccCCcccccccccccccchhHHHHHHhhh
Q 028730 44 RPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKGIVYGKPTNQGVTQLKFQRSKRSVAEERAGR 108 (204)
Q Consensus 44 R~dkAR~LGYKAKQG~Vi~RvRVrrGgrkr~~pkg~~~~KPk~~Gvn~lk~~kslq~iAEeR~gr 108 (204)
=|+.|+++|+ ||-|++.+-|..+|. ..+.-|-+-+...-|-.-|.+-+.+
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 5899999998 999999999998865 3344454555555666666655543
No 13
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=37.01 E-value=22 Score=32.76 Aligned_cols=25 Identities=36% Similarity=0.741 Sum_probs=21.2
Q ss_pred eEEEEEecCCCc---ccccCCCCccccc
Q 028730 129 YFEVILVDPAHN---AIRNDPRINWLCN 153 (204)
Q Consensus 129 ~fEVILVDp~H~---aIr~Dp~~~WI~~ 153 (204)
.|.-||||+-+. .|++||++.|--.
T Consensus 229 ~fD~iLlDaPCSg~G~irr~Pd~~~~~~ 256 (355)
T COG0144 229 KFDRILLDAPCSGTGVIRRDPDVKWRRT 256 (355)
T ss_pred cCcEEEECCCCCCCcccccCccccccCC
Confidence 489999999876 5899999999544
No 14
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=36.09 E-value=19 Score=26.27 Aligned_cols=25 Identities=16% Similarity=0.351 Sum_probs=17.0
Q ss_pred ccCCceeeeeeeeccCCCceeEEE-EEecCCCc
Q 028730 109 KLGGLRVLNSYWINEDSTYKYFEV-ILVDPAHN 140 (204)
Q Consensus 109 k~~nLrVLNSYwV~eDg~yK~fEV-ILVDp~H~ 140 (204)
.|||..- .|-+..||+. |++||...
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 4777653 5678899995 46677544
No 15
>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=35.65 E-value=37 Score=25.73 Aligned_cols=19 Identities=32% Similarity=0.501 Sum_probs=16.2
Q ss_pred eeeeccCCCceeEEEEEec
Q 028730 118 SYWINEDSTYKYFEVILVD 136 (204)
Q Consensus 118 SYwV~eDg~yK~fEVILVD 136 (204)
+++.-+++..|||||.|..
T Consensus 4 ~l~~~dg~S~Kfyev~~~~ 22 (77)
T cd07998 4 SLYFQEGNSDKVYEVDLFE 22 (77)
T ss_pred EEEEecCCCceEEEEEEEe
Confidence 5778889999999998873
No 16
>COG0463 WcaA Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=33.26 E-value=24 Score=24.53 Aligned_cols=12 Identities=50% Similarity=0.767 Sum_probs=9.3
Q ss_pred eeEEEEEecCCC
Q 028730 128 KYFEVILVDPAH 139 (204)
Q Consensus 128 K~fEVILVDp~H 139 (204)
..||||+||-..
T Consensus 31 ~~~eiivvddgs 42 (291)
T COG0463 31 KDFEIIVVDDGS 42 (291)
T ss_pred cceEEEEEeCCC
Confidence 339999999754
No 17
>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=32.80 E-value=18 Score=29.67 Aligned_cols=11 Identities=45% Similarity=0.851 Sum_probs=8.2
Q ss_pred EEEEEecCCCc
Q 028730 130 FEVILVDPAHN 140 (204)
Q Consensus 130 fEVILVDp~H~ 140 (204)
|.||++||=-+
T Consensus 1 fdvI~~DPPW~ 11 (176)
T PF05063_consen 1 FDVIYADPPWP 11 (176)
T ss_pred CCEEEEeCCCC
Confidence 77899998443
No 18
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=31.57 E-value=37 Score=32.90 Aligned_cols=37 Identities=22% Similarity=0.363 Sum_probs=27.3
Q ss_pred cCCceeeeeeeeccCCCc------eeEEEEEecCCCc---ccccCCCCccc
Q 028730 110 LGGLRVLNSYWINEDSTY------KYFEVILVDPAHN---AIRNDPRINWL 151 (204)
Q Consensus 110 ~~nLrVLNSYwV~eDg~y------K~fEVILVDp~H~---aIr~Dp~~~WI 151 (204)
+.|..|+| +|++. .+|..||||+-+. .+++||++.|-
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 35555554 56542 4699999999887 68999998874
No 19
>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=31.09 E-value=33 Score=23.50 Aligned_cols=39 Identities=28% Similarity=0.433 Sum_probs=30.4
Q ss_pred eeeeeeeeccCCCceeEEEEEecCCCcccccCCCCccccc
Q 028730 114 RVLNSYWINEDSTYKYFEVILVDPAHNAIRNDPRINWLCN 153 (204)
Q Consensus 114 rVLNSYwV~eDg~yK~fEVILVDp~H~aIr~Dp~~~WI~~ 153 (204)
.++-+|.+ +++.=.-=|||+.-.....|-.||+-.|+-+
T Consensus 13 ~~i~~y~~-~~~~C~~~aVIf~tk~g~~iC~dP~~~WVk~ 51 (57)
T cd00272 13 RVLKSYRR-TSSSCSKPAVIFKTKRGREVCADPKQKWVQR 51 (57)
T ss_pred hHeeEEEE-CCCCCCCcEEEEEeCCCCEEeCCCChHHHHH
Confidence 44557765 4445557789999999999999999999864
No 20
>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=29.43 E-value=84 Score=20.93 Aligned_cols=28 Identities=21% Similarity=0.304 Sum_probs=24.0
Q ss_pred hhccCCceeeeeeeeccCCCceeEEEEEe
Q 028730 107 GRKLGGLRVLNSYWINEDSTYKYFEVILV 135 (204)
Q Consensus 107 grk~~nLrVLNSYwV~eDg~yK~fEVILV 135 (204)
-..||+..|..-+.....+. .+|||-|.
T Consensus 17 ~~~yp~~~i~~v~~~~~~~~-~~Y~v~l~ 44 (61)
T PF11396_consen 17 KKNYPGAKIKEVEKETDPGG-KYYEVELK 44 (61)
T ss_dssp HHHSTTSEEEEEEEEEETTE-EEEEEEET
T ss_pred HHHCCCCeEEEEEEEEcCCC-CEEEEEEE
Confidence 44599999999888887777 99999987
No 21
>COG2876 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=28.37 E-value=28 Score=32.36 Aligned_cols=15 Identities=40% Similarity=0.665 Sum_probs=12.9
Q ss_pred EEecCCCcccccCCC
Q 028730 133 ILVDPAHNAIRNDPR 147 (204)
Q Consensus 133 ILVDp~H~aIr~Dp~ 147 (204)
|+|||+|++=|+|+-
T Consensus 217 VivDpSH~~Grr~lv 231 (286)
T COG2876 217 VIVDPSHATGRRDLV 231 (286)
T ss_pred EEECCCCcccchhhH
Confidence 689999999988863
No 22
>KOG3351 consensus Predicted nucleotidyltransferase [General function prediction only]
Probab=27.43 E-value=34 Score=31.76 Aligned_cols=34 Identities=35% Similarity=0.552 Sum_probs=26.9
Q ss_pred EEEecCCCcccccCCCCcccc---------cCCcccchhcCCcc
Q 028730 132 VILVDPAHNAIRNDPRINWLC---------NPVHKHRELRGLTS 166 (204)
Q Consensus 132 VILVDp~H~aIr~Dp~~~WI~---------~~~hk~Re~RGLTs 166 (204)
|=+.||+-|+|. ||+|.-|. ..|+|-|..|||.-
T Consensus 218 vpi~Dp~GPt~~-d~elE~lVVS~ET~~Ga~aVNr~R~E~glse 260 (293)
T KOG3351|consen 218 VPIHDPFGPTIT-DPELEALVVSEETKTGATAVNRKRVERGLSE 260 (293)
T ss_pred EecccCCCCCcc-CCcceEEEEeeccccchhhhhHHHHHcCCch
Confidence 338999999995 89998874 45788888888853
No 23
>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=27.22 E-value=33 Score=28.58 Aligned_cols=12 Identities=50% Similarity=0.755 Sum_probs=8.2
Q ss_pred eEEEEEecCCCc
Q 028730 129 YFEVILVDPAHN 140 (204)
Q Consensus 129 ~fEVILVDp~H~ 140 (204)
=|||||-+|+-+
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 24
>PLN00169 CETS family protein; Provisional
Probab=27.19 E-value=75 Score=26.88 Aligned_cols=29 Identities=21% Similarity=0.621 Sum_probs=21.5
Q ss_pred ceeEEEEEecCCCcccccC---CCCcccccCC
Q 028730 127 YKYFEVILVDPAHNAIRND---PRINWLCNPV 155 (204)
Q Consensus 127 yK~fEVILVDp~H~aIr~D---p~~~WI~~~~ 155 (204)
-++|=|||+||+-|.-.+. +-+-|+....
T Consensus 62 ~~~ytlim~DpDaP~~~~~~~~~~~HW~v~ni 93 (175)
T PLN00169 62 RTFYTLVMVDPDAPSPSNPNLREYLHWLVTDI 93 (175)
T ss_pred CceeEEEEECCCCCCCCCCCcccEEEEEEeCC
Confidence 4899999999999985432 2477887554
No 25
>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=26.40 E-value=21 Score=26.09 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=8.2
Q ss_pred EEEEecCCCcccc
Q 028730 131 EVILVDPAHNAIR 143 (204)
Q Consensus 131 EVILVDp~H~aIr 143 (204)
|..-+||+||+|-
T Consensus 38 El~r~D~~HPsvl 50 (62)
T PF04915_consen 38 ELSRFDPFHPSVL 50 (62)
T ss_dssp TTTS--TTSHHHH
T ss_pred HHhccCCcCHHHH
Confidence 4446899999985
No 26
>KOG3346 consensus Phosphatidylethanolamine binding protein [General function prediction only]
Probab=25.63 E-value=73 Score=27.63 Aligned_cols=23 Identities=22% Similarity=0.615 Sum_probs=17.9
Q ss_pred CCceeEEEEEecCCCcccccCCCC
Q 028730 125 STYKYFEVILVDPAHNAIRNDPRI 148 (204)
Q Consensus 125 g~yK~fEVILVDp~H~aIr~Dp~~ 148 (204)
..-.||-+||+||+-|+ ++||+.
T Consensus 61 ~~~~~yTLvm~DPDaPs-r~~p~~ 83 (185)
T KOG3346|consen 61 DPGSLYTLVMTDPDAPS-RSDPKF 83 (185)
T ss_pred CCCCeEEEEEeCCCCCC-CCCCcc
Confidence 34579999999999998 455554
No 27
>PRK14688 hypothetical protein; Provisional
Probab=23.94 E-value=50 Score=26.47 Aligned_cols=21 Identities=24% Similarity=0.542 Sum_probs=16.3
Q ss_pred EEEEEecCCCcccccCCCCcccccC
Q 028730 130 FEVILVDPAHNAIRNDPRINWLCNP 154 (204)
Q Consensus 130 fEVILVDp~H~aIr~Dp~~~WI~~~ 154 (204)
|.||.|++.+ .++.++||-+.
T Consensus 97 FDvi~v~~~~----~~~~i~~i~nA 117 (121)
T PRK14688 97 IDFVSVDLSQ----PEPRLELIKNA 117 (121)
T ss_pred EEEEEEEccC----CCCCEEEehHh
Confidence 9999998765 23578999774
No 28
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=23.81 E-value=41 Score=32.11 Aligned_cols=20 Identities=20% Similarity=0.607 Sum_probs=16.3
Q ss_pred eEEEEEecCCCcccccCCCCcc
Q 028730 129 YFEVILVDPAHNAIRNDPRINW 150 (204)
Q Consensus 129 ~fEVILVDp~H~aIr~Dp~~~W 150 (204)
=|.||++|| |+.-+.++--|
T Consensus 290 ~fDlIilDP--PsF~r~k~~~~ 309 (393)
T COG1092 290 KFDLIILDP--PSFARSKKQEF 309 (393)
T ss_pred cccEEEECC--cccccCcccch
Confidence 589999999 88887776654
No 29
>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=23.01 E-value=44 Score=25.25 Aligned_cols=13 Identities=31% Similarity=0.554 Sum_probs=9.9
Q ss_pred ceeEEEEEecCCC
Q 028730 127 YKYFEVILVDPAH 139 (204)
Q Consensus 127 yK~fEVILVDp~H 139 (204)
+..||||+||-..
T Consensus 25 ~~~~evivvDd~s 37 (202)
T cd06433 25 YPNIEYIVIDGGS 37 (202)
T ss_pred CCCceEEEEeCCC
Confidence 4559999998654
No 30
>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=22.88 E-value=95 Score=21.20 Aligned_cols=41 Identities=20% Similarity=0.375 Sum_probs=32.1
Q ss_pred ceeeeeeeeccCCC-ceeEEEEEecCCCcccccCCCCccccc
Q 028730 113 LRVLNSYWINEDST-YKYFEVILVDPAHNAIRNDPRINWLCN 153 (204)
Q Consensus 113 LrVLNSYwV~eDg~-yK~fEVILVDp~H~aIr~Dp~~~WI~~ 153 (204)
++.+.||.+-+-+. =.--|||+.--+-..|--||+-.|+-+
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 45577888755542 568899999888889999999999754
No 31
>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=22.53 E-value=80 Score=25.63 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=24.8
Q ss_pred eeeeeeeeccCCCceeEEEEE--------ecCCCcccccCC
Q 028730 114 RVLNSYWINEDSTYKYFEVIL--------VDPAHNAIRNDP 146 (204)
Q Consensus 114 rVLNSYwV~eDg~yK~fEVIL--------VDp~H~aIr~Dp 146 (204)
+.+.-|||..+|...+|..|- -=..||-|-.|.
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 567889999999999999762 113566666666
No 32
>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=22.31 E-value=86 Score=25.14 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=21.5
Q ss_pred ceeEEEEEecCCCcccccCCCCcccccCC
Q 028730 127 YKYFEVILVDPAHNAIRNDPRINWLCNPV 155 (204)
Q Consensus 127 yK~fEVILVDp~H~aIr~Dp~~~WI~~~~ 155 (204)
-+.|=|+|+||+.| ...+-+-||.-..
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 49999999999999 4457788887543
No 33
>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=21.95 E-value=37 Score=28.24 Aligned_cols=26 Identities=50% Similarity=0.659 Sum_probs=18.5
Q ss_pred HHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCccc
Q 028730 103 EERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAI 142 (204)
Q Consensus 103 EeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aI 142 (204)
|+-|-+|..|| .||+| |-|||+|-+.
T Consensus 63 ~~eArrKl~gl-------------~kfGE-I~Id~~H~~~ 88 (131)
T PF07450_consen 63 EGEARRKLEGL-------------LKFGE-IEIDSEHVAL 88 (131)
T ss_pred cHHHHHHHhCC-------------CceeE-EEECHHHHHH
Confidence 45666677655 59999 5689998654
No 34
>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=21.56 E-value=70 Score=22.05 Aligned_cols=41 Identities=22% Similarity=0.322 Sum_probs=33.2
Q ss_pred ceeeeeeeeccCCC-ceeEEEEEecCCCcccccCCCCccccc
Q 028730 113 LRVLNSYWINEDST-YKYFEVILVDPAHNAIRNDPRINWLCN 153 (204)
Q Consensus 113 LrVLNSYwV~eDg~-yK~fEVILVDp~H~aIr~Dp~~~WI~~ 153 (204)
+..+-+|++-+-+. =.-=|||++......+--||+-.|+-+
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 56677887776664 566899999999999999999999753
No 35
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=21.14 E-value=47 Score=28.88 Aligned_cols=53 Identities=26% Similarity=0.305 Sum_probs=31.3
Q ss_pred ccchhHHHHHHhhhc-cCCceeeeeeeeccCCCc-----eeEEEEEecCCCc---ccccCCCCcccc
Q 028730 95 QRSKRSVAEERAGRK-LGGLRVLNSYWINEDSTY-----KYFEVILVDPAHN---AIRNDPRINWLC 152 (204)
Q Consensus 95 ~kslq~iAEeR~grk-~~nLrVLNSYwV~eDg~y-----K~fEVILVDp~H~---aIr~Dp~~~WI~ 152 (204)
....=.++++.+.+. ..|+.+++ .|+.. .-|.+||+||-.. .++.||++.|-.
T Consensus 105 ~~~~l~~~~~n~~~~g~~~v~~~~-----~D~~~~~~~~~~fD~Vl~D~Pcsg~G~~~~~p~~~~~~ 166 (264)
T TIGR00446 105 SKSRTKVLIANINRCGVLNVAVTN-----FDGRVFGAAVPKFDAILLDAPCSGEGVIRKDPSRKKNW 166 (264)
T ss_pred CHHHHHHHHHHHHHcCCCcEEEec-----CCHHHhhhhccCCCEEEEcCCCCCCcccccChhhhhcC
Confidence 333334455555442 24555543 34321 2299999999665 568999998743
No 36
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=20.81 E-value=40 Score=28.18 Aligned_cols=26 Identities=42% Similarity=0.649 Sum_probs=18.5
Q ss_pred HHHhhhccCCceeeeeeeeccCCCceeEEEEEecCCCccc
Q 028730 103 EERAGRKLGGLRVLNSYWINEDSTYKYFEVILVDPAHNAI 142 (204)
Q Consensus 103 EeR~grk~~nLrVLNSYwV~eDg~yK~fEVILVDp~H~aI 142 (204)
|+-|-+|..|| .||+| |-|||+|-+.
T Consensus 65 ~~eArrKl~gl-------------~kfgE-I~I~~~H~~~ 90 (133)
T PRK15084 65 EGEARRKMEGV-------------PKFGE-IVIDSSHVAL 90 (133)
T ss_pred hHHHHHHHhCc-------------CceeE-EEECHHHHHH
Confidence 55666777654 69999 4689988543
No 37
>KOG4300 consensus Predicted methyltransferase [General function prediction only]
Probab=20.08 E-value=55 Score=29.88 Aligned_cols=50 Identities=16% Similarity=0.444 Sum_probs=35.8
Q ss_pred cccccccccccchhHHHHHHhhhccCCceeeeeeeeccCC-------------CceeEE------EEEecCCC
Q 028730 86 NQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWINEDS-------------TYKYFE------VILVDPAH 139 (204)
Q Consensus 86 ~~Gvn~lk~~kslq~iAEeR~grk~~nLrVLNSYwV~eDg-------------~yK~fE------VILVDp~H 139 (204)
-+=+.---+.-+.+++|++---.-|.|+. ||++..+ .+|||- |+++||+-
T Consensus 41 ~~~~p~~~ft~~yne~~~~ykrelFs~i~----~~~gk~~K~~vLEvgcGtG~Nfkfy~~~p~~svt~lDpn~ 109 (252)
T KOG4300|consen 41 DLLIPNSNFTSIYNEIADSYKRELFSGIY----YFLGKSGKGDVLEVGCGTGANFKFYPWKPINSVTCLDPNE 109 (252)
T ss_pred ccccchhHHHHHHHHHHHHHHHHHHhhhH----HHhcccCccceEEecccCCCCcccccCCCCceEEEeCCcH
Confidence 33344445666788888888666688877 7876654 578998 89999973
Done!