Query psy2756
Match_columns 112
No_of_seqs 103 out of 330
Neff 4.3
Searched_HMMs 46136
Date Sat Aug 17 00:24:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2756.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2756hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00065 60S ribosomal protein 100.0 4.1E-55 8.8E-60 321.5 12.8 103 10-112 2-105 (130)
2 KOG3421|consensus 100.0 8.8E-44 1.9E-48 262.8 7.6 103 10-112 1-103 (136)
3 PRK04333 50S ribosomal protein 100.0 2.3E-30 5.1E-35 177.8 9.0 79 16-94 4-83 (84)
4 COG2163 RPL14A Ribosomal prote 99.9 1.1E-26 2.4E-31 169.9 8.0 96 13-110 2-99 (125)
5 PF01929 Ribosomal_L14e: Ribos 99.9 3.5E-23 7.5E-28 140.5 3.5 58 55-112 1-58 (77)
6 PTZ00471 60S ribosomal protein 99.3 1.2E-11 2.7E-16 91.8 7.1 60 14-74 3-90 (134)
7 KOG3418|consensus 98.7 4.6E-08 1E-12 72.9 6.7 61 14-74 3-90 (136)
8 PF00467 KOW: KOW motif; Inte 98.1 6E-06 1.3E-10 46.9 4.0 31 18-48 1-32 (32)
9 smart00739 KOW KOW (Kyprides, 96.6 0.0033 7.2E-08 33.3 3.3 26 16-41 2-27 (28)
10 PRK01191 rpl24p 50S ribosomal 96.0 0.017 3.7E-07 42.4 5.0 56 16-71 46-107 (120)
11 CHL00141 rpl24 ribosomal prote 95.5 0.031 6.6E-07 38.3 4.5 36 15-50 8-44 (83)
12 PRK12281 rplX 50S ribosomal pr 95.2 0.046 9.9E-07 36.9 4.7 35 16-50 7-42 (76)
13 TIGR01080 rplX_A_E ribosomal p 95.2 0.044 9.6E-07 39.7 4.9 58 15-72 41-104 (114)
14 TIGR01079 rplX_bact ribosomal 94.3 0.096 2.1E-06 37.2 4.6 35 16-50 4-39 (104)
15 PRK00004 rplX 50S ribosomal pr 93.0 0.21 4.6E-06 35.3 4.5 55 16-70 5-76 (105)
16 PRK05609 nusG transcription an 92.6 0.25 5.5E-06 36.3 4.6 38 13-50 124-162 (181)
17 TIGR00405 L26e_arch ribosomal 91.5 0.35 7.6E-06 34.8 4.2 39 14-52 85-124 (145)
18 TIGR01955 RfaH transcriptional 91.3 0.36 7.8E-06 34.8 4.1 37 14-50 107-143 (159)
19 PTZ00194 60S ribosomal protein 90.9 0.53 1.2E-05 35.6 4.8 57 16-72 47-109 (143)
20 TIGR00922 nusG transcription t 90.3 0.58 1.3E-05 34.3 4.5 37 15-51 119-156 (172)
21 PRK08559 nusG transcription an 89.9 1.1 2.5E-05 33.0 5.8 51 16-67 95-148 (153)
22 PRK09014 rfaH transcriptional 89.5 0.64 1.4E-05 33.9 4.1 37 14-50 108-144 (162)
23 PF13234 rRNA_proc-arch: rRNA- 84.8 0.56 1.2E-05 36.9 1.6 31 13-43 70-100 (268)
24 COG0198 RplX Ribosomal protein 83.2 2.8 6E-05 30.1 4.5 54 15-69 4-73 (104)
25 TIGR01956 NusG_myco NusG famil 82.0 2.5 5.4E-05 34.7 4.4 35 16-50 206-241 (258)
26 COG0250 NusG Transcription ant 77.1 7.8 0.00017 29.7 5.5 52 13-66 121-176 (178)
27 COG0057 GapA Glyceraldehyde-3- 73.9 5.1 0.00011 34.0 4.1 34 57-90 232-265 (335)
28 PRK04313 30S ribosomal protein 71.8 4.1 9E-05 33.0 3.0 35 16-50 172-211 (237)
29 PLN00036 40S ribosomal protein 71.3 4.2 9.1E-05 33.4 2.9 34 17-50 176-213 (261)
30 PF09884 DUF2111: Uncharacteri 69.8 5.2 0.00011 27.9 2.7 42 5-46 29-74 (84)
31 COG4048 Uncharacterized protei 69.4 5.2 0.00011 29.6 2.8 43 4-46 46-91 (123)
32 PTZ00223 40S ribosomal protein 67.5 5.4 0.00012 33.0 2.8 35 16-50 172-210 (273)
33 PTZ00118 40S ribosomal protein 66.3 6.1 0.00013 32.5 2.9 35 16-50 175-213 (262)
34 PF13555 AAA_29: P-loop contai 55.9 33 0.00071 22.2 4.4 29 20-51 3-32 (62)
35 COG0144 Sun tRNA and rRNA cyto 52.7 8.2 0.00018 32.1 1.5 20 42-61 230-251 (355)
36 PF01189 Nol1_Nop2_Fmu: NOL1/N 52.1 8.7 0.00019 30.8 1.5 12 43-54 158-169 (283)
37 COG1471 RPS4A Ribosomal protei 51.5 16 0.00035 29.9 2.9 36 16-51 174-214 (241)
38 PF01777 Ribosomal_L27e: Ribos 50.9 0.47 1E-05 32.8 -5.2 17 57-73 22-38 (85)
39 PF02800 Gp_dh_C: Glyceraldehy 50.2 27 0.00058 25.9 3.8 34 57-90 76-109 (157)
40 COG1047 SlpA FKBP-type peptidy 49.2 27 0.00059 27.1 3.8 39 11-51 84-124 (174)
41 PF13051 DUF3912: Protein of u 43.8 23 0.0005 23.6 2.3 34 17-50 4-40 (68)
42 PLN02237 glyceraldehyde-3-phos 42.0 38 0.00082 29.8 4.0 34 57-90 309-343 (442)
43 COG0021 TktA Transketolase [Ca 41.9 26 0.00057 32.4 3.1 54 30-91 177-235 (663)
44 KOG1708|consensus 41.6 54 0.0012 26.7 4.5 37 16-52 73-110 (236)
45 KOG1999|consensus 41.3 30 0.00066 33.5 3.4 30 13-42 457-486 (1024)
46 TIGR03689 pup_AAA proteasome A 40.0 52 0.0011 29.2 4.5 36 16-51 83-127 (512)
47 PF05257 CHAP: CHAP domain; I 37.8 66 0.0014 22.0 4.0 39 13-51 60-100 (124)
48 PF07290 DUF1449: Protein of u 36.0 83 0.0018 24.7 4.7 35 18-53 137-175 (202)
49 COG0856 Orotate phosphoribosyl 34.0 27 0.00058 27.9 1.6 14 25-38 135-148 (203)
50 PF00156 Pribosyltran: Phospho 33.4 86 0.0019 20.7 3.9 23 21-43 78-101 (125)
51 COG3896 Chloramphenicol 3-O-ph 32.3 29 0.00062 27.7 1.6 18 17-34 21-38 (205)
52 PRK11933 yebU rRNA (cytosine-C 31.5 28 0.0006 30.4 1.5 11 43-53 185-195 (470)
53 COG0133 TrpB Tryptophan syntha 29.7 26 0.00057 30.4 1.0 42 52-96 137-178 (396)
54 PF12090 Spt20: Spt20 family; 29.1 34 0.00074 26.1 1.5 15 34-48 74-88 (182)
55 KOG1122|consensus 27.0 35 0.00075 30.4 1.3 11 43-53 314-324 (460)
56 PTZ00434 cytosolic glyceraldeh 26.9 84 0.0018 27.0 3.6 34 57-90 249-282 (361)
57 COG0019 LysA Diaminopimelate d 26.5 34 0.00074 29.1 1.2 45 12-56 270-314 (394)
58 PF09953 DUF2187: Uncharacteri 26.0 1.9E+02 0.0042 18.7 5.3 45 16-65 4-55 (57)
59 PRK09907 toxin MazF; Provision 25.0 61 0.0013 22.6 2.1 27 13-39 4-36 (111)
60 PF01505 Vault: Major Vault Pr 24.8 27 0.00059 20.7 0.2 15 42-56 29-43 (43)
61 KOG2198|consensus 23.7 46 0.001 28.8 1.5 18 43-60 238-257 (375)
62 PRK07403 glyceraldehyde-3-phos 23.2 1.2E+02 0.0025 25.7 3.7 34 57-90 234-267 (337)
63 PF02470 MCE: mce related prot 21.9 1.7E+02 0.0037 18.5 3.6 30 13-42 23-52 (81)
64 TIGR01546 GAPDH-II_archae glyc 21.7 1.3E+02 0.0029 25.2 3.8 34 57-90 209-242 (333)
65 cd02418 Peptidase_C39B A sub-f 21.7 2.5E+02 0.0055 18.6 4.7 48 14-64 71-120 (136)
66 COG4832 Uncharacterized conser 21.6 74 0.0016 25.4 2.1 24 26-51 15-38 (207)
67 cd02417 Peptidase_C39_likeA A 21.5 92 0.002 20.4 2.3 29 31-61 79-107 (121)
68 PRK07729 glyceraldehyde-3-phos 21.5 1.4E+02 0.003 25.3 3.9 34 57-90 232-265 (343)
69 COG5164 SPT5 Transcription elo 20.8 81 0.0018 28.7 2.4 31 13-43 349-379 (607)
70 cd02419 Peptidase_C39C A sub-f 20.8 1.2E+02 0.0026 20.1 2.8 32 30-64 83-114 (127)
71 PRK14901 16S rRNA methyltransf 20.6 63 0.0014 27.3 1.7 11 43-53 327-337 (434)
No 1
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=100.00 E-value=4.1e-55 Score=321.48 Aligned_cols=103 Identities=43% Similarity=0.595 Sum_probs=101.4
Q ss_pred cccceeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCC-CCCCcceeeecCceeecceEEEecCCCChHHHHHHHHh
Q psy2756 10 GAFKRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP-ETGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKD 88 (112)
Q Consensus 10 m~f~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP-~tgV~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~ 88 (112)
++|+||||+||||+|++||++||||+||||||||||||||| +|||+||+|||+||+||+|+|+|||||+|++|+|||++
T Consensus 2 ~~f~rfVEiGRVvli~~Gp~~GKL~vIVDIID~nRvLVDGP~~tgV~Rq~i~~k~l~LT~~~v~i~r~a~t~~v~ka~~~ 81 (130)
T PTZ00065 2 PLFKRFVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGAFITGVKRQSIPLKRLKLTDEKIKINRGARTGTLKKALKK 81 (130)
T ss_pred cccccceeeceEEEEecCCCCCCEEEEEEEEcCCeEEEeCCCcCCcceeEEeccceEEccEEEecCCCCCcHHHHHHHHH
Confidence 68999999999999999999999999999999999999999 89999999999999999999999999999999999999
Q ss_pred cchHHHHhhcHHHHHHHHHHHhhC
Q psy2756 89 GQVEEKWSKSLWAQKVANVEKRKK 112 (112)
Q Consensus 89 a~i~~kw~~s~waKk~~~~~~R~~ 112 (112)
++|.+||++|+||||++++++|++
T Consensus 82 a~i~~kw~~s~waKK~~~~~~Ra~ 105 (130)
T PTZ00065 82 DNALEEFNKTSLGKKLIIKEKRAN 105 (130)
T ss_pred ccHHHHHHHhHHHHHHHHHHHHhc
Confidence 999999999999999999999985
No 2
>KOG3421|consensus
Probab=100.00 E-value=8.8e-44 Score=262.77 Aligned_cols=103 Identities=52% Similarity=0.864 Sum_probs=101.5
Q ss_pred cccceeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCCCCCCcceeeecCceeecceEEEecCCCChHHHHHHHHhc
Q psy2756 10 GAFKRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPETGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDG 89 (112)
Q Consensus 10 m~f~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP~tgV~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a 89 (112)
|+|+||||+|||+++++||++|||++|||||||||+|||||||+|+||.+||++++||+|.+++|||+++++|.++|+++
T Consensus 1 m~f~r~veVGrva~v~~G~~~GkL~AIVdviDqnr~lvDGp~t~v~rq~~~~~~~~LT~~~~kfp~g~~~~~v~k~~~aa 80 (136)
T KOG3421|consen 1 MVFKRFVEVGRVALVSFGPDAGKLVAIVDVIDQNRALVDGPCTGVPRQAMNLKCLQLTDFVLKFPRGARKKIVKKAWKAA 80 (136)
T ss_pred CcchhhhhcceEEEEEecCCCceEEEEEEeecchhhhccCcccccchhhcchhheeeeeeeEecccCcccHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHhhcHHHHHHHHHHHhhC
Q psy2756 90 QVEEKWSKSLWAQKVANVEKRKK 112 (112)
Q Consensus 90 ~i~~kw~~s~waKk~~~~~~R~~ 112 (112)
++.++|..|+|++|+.+++.|++
T Consensus 81 ~v~~k~~ks~wakK~~a~k~ra~ 103 (136)
T KOG3421|consen 81 DVKAKWKKSPWAKKAPAKKRRAA 103 (136)
T ss_pred HHHHhhhcCchhhhhHHHHhhhh
Confidence 99999999999999999999874
No 3
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.97 E-value=2.3e-30 Score=177.81 Aligned_cols=79 Identities=33% Similarity=0.479 Sum_probs=76.7
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCC-CCCCcceeeecCceeecceEEEecCCCChHHHHHHHHhcchHHH
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP-ETGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEK 94 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP-~tgV~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~i~~k 94 (112)
||+||||++.+|||+||+|+||||+|+|||||||| +++++||.+|++||+||++++++++++++++|+++|++++|.+.
T Consensus 4 v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVdg~~~~~~~rk~kn~khl~lt~~ki~~~~~~~~~~vrk~l~~~~v~~~ 83 (84)
T PRK04333 4 IEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSLTGVKRRRCNIKHLEPTDKKVDIEKGASDEEVKKALEAAGLTEY 83 (84)
T ss_pred ccccEEEEEeccCCCCCEEEEEEEecCCEEEEECCCcCCCCCeeechHHEEEeeEEEECCCCCCCHHHHHHHHHccchhc
Confidence 79999999999999999999999999999999999 68999999999999999999999999999999999999999863
No 4
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.1e-26 Score=169.92 Aligned_cols=96 Identities=31% Similarity=0.490 Sum_probs=90.3
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCCC--CCCcceeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPE--TGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP~--tgV~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
.+++|+||||+++.|+++||+|||||+||+|++|++||+ +||||+.+|++|+.+|+.+++++||++.+.+.++|++++
T Consensus 2 ~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a~~ 81 (125)
T COG2163 2 RASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEAAG 81 (125)
T ss_pred CccccCCeEEEEecceeCCceEEEEEEccCCEEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHhhh
Confidence 578999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred hHHHHhhcHHHHHHHHHHHh
Q psy2756 91 VEEKWSKSLWAQKVANVEKR 110 (112)
Q Consensus 91 i~~kw~~s~waKk~~~~~~R 110 (112)
..++|+.|+ +.+++++-+
T Consensus 82 ~~~~~~~~~--~~~~~k~~~ 99 (125)
T COG2163 82 VLAKLDKSA--KNLETKKVR 99 (125)
T ss_pred hhccccccc--hhhhhhhhh
Confidence 999998888 666655544
No 5
>PF01929 Ribosomal_L14e: Ribosomal protein L14; InterPro: IPR002784 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 [, ]. This entry includes the eukaryotic ribosomal protein L14, which binds to the 60S ribosomal subunit, and archaebacterial ribosomal protein L14E, which binds to the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_N 3O5H_N 3O58_N 2KDS_A 2JOY_A 4A1B_F 4A19_F 4A18_F 4A1D_F 3IZR_N.
Probab=99.87 E-value=3.5e-23 Score=140.49 Aligned_cols=58 Identities=48% Similarity=0.909 Sum_probs=56.2
Q ss_pred cceeeecCceeecceEEEecCCCChHHHHHHHHhcchHHHHhhcHHHHHHHHHHHhhC
Q psy2756 55 PRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEKWSKSLWAQKVANVEKRKK 112 (112)
Q Consensus 55 ~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~i~~kw~~s~waKk~~~~~~R~~ 112 (112)
|||+|||+||+||+|+|+||||+++++|++||++++|.++|++|+||||++++++|++
T Consensus 1 ~Rq~i~~k~l~LT~~~i~i~r~a~t~~vkka~~~~~i~~kw~~s~waKk~~~~~~Ra~ 58 (77)
T PF01929_consen 1 PRQVINLKRLHLTDFVIKIPRGARTKTVKKAWEKADIDEKWAESAWAKKIAAREKRAN 58 (77)
T ss_dssp -EEEEECTSSEEEEEETTTTTTTCHHHHHHHHHHHTCHHHHHHHHCSCHHHHHHHHHS
T ss_pred CCceeeccceEeecEEEeccCCCCcHHHHHHHHHccHHHHHHHhHHHHHHHHHHHHhc
Confidence 6999999999999999999999999999999999999999999999999999999985
No 6
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=99.27 E-value=1.2e-11 Score=91.77 Aligned_cols=60 Identities=27% Similarity=0.563 Sum_probs=53.5
Q ss_pred eeeeeceEEEEecCCCCCceEEEEEeeeC-------CeEEEeC----CCCCC----------cc-------eeeecCcee
Q psy2756 14 RFVQTGRVVRISDGPYRGKLSSIVDVINQ-------TTVLVDG----PETGV----------PR-------SALRLNQLH 65 (112)
Q Consensus 14 rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~-------nRvLVDG----P~tgV----------~R-------q~i~~k~l~ 65 (112)
+|+.+|+||++..|+||||.||||..+|+ +.+||.| |- .| +| .++|++||.
T Consensus 3 K~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~-kVtk~M~kkki~KRskiK~FvK~vNynHlm 81 (134)
T PTZ00471 3 KFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPK-KVVRGMSKRTIARRSQVGVFLRVVNHKHFL 81 (134)
T ss_pred ccccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccch-hhhhhccHHHHHHHhccccceEEEeeceec
Confidence 78999999999999999999999999999 5999999 64 12 11 569999999
Q ss_pred ecceEEEec
Q psy2756 66 LTKLKINFP 74 (112)
Q Consensus 66 LT~~~i~i~ 74 (112)
||.+.++++
T Consensus 82 PTRY~vdi~ 90 (134)
T PTZ00471 82 PTRYNMDMS 90 (134)
T ss_pred ccceeeecc
Confidence 999999998
No 7
>KOG3418|consensus
Probab=98.70 E-value=4.6e-08 Score=72.92 Aligned_cols=61 Identities=31% Similarity=0.539 Sum_probs=53.7
Q ss_pred eeeeeceEEEEecCCCCCceEEEEEeeeCC-------eEEEeCCC---CCC----------cc-------eeeecCceee
Q psy2756 14 RFVQTGRVVRISDGPYRGKLSSIVDVINQT-------TVLVDGPE---TGV----------PR-------SALRLNQLHL 66 (112)
Q Consensus 14 rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~n-------RvLVDGP~---tgV----------~R-------q~i~~k~l~L 66 (112)
.|+.+|-||++.+|.|+||.+|||--+|+. .+||.|-. ..| +| .++|++||.+
T Consensus 3 kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~hlMp 82 (136)
T KOG3418|consen 3 KFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYNHLMP 82 (136)
T ss_pred ccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhccccccccccchhhhhcccceeEEEEeecccccC
Confidence 689999999999999999999999999999 99999954 111 22 7899999999
Q ss_pred cceEEEec
Q psy2756 67 TKLKINFP 74 (112)
Q Consensus 67 T~~~i~i~ 74 (112)
|.++++++
T Consensus 83 tRy~vdv~ 90 (136)
T KOG3418|consen 83 TRYTVDVL 90 (136)
T ss_pred cceEEeeh
Confidence 99999976
No 8
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=98.09 E-value=6e-06 Score=46.94 Aligned_cols=31 Identities=32% Similarity=0.724 Sum_probs=28.8
Q ss_pred eceEEEEecCCCCCceEEEEEeeeCC-eEEEe
Q psy2756 18 TGRVVRISDGPYRGKLSSIVDVINQT-TVLVD 48 (112)
Q Consensus 18 vGRVv~i~~Gp~aGKl~vIVdIiD~n-RvLVD 48 (112)
+|..|.|..||++|+.+.|++|.+++ +|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 58999999999999999999999998 88876
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.62 E-value=0.0033 Score=33.33 Aligned_cols=26 Identities=31% Similarity=0.755 Sum_probs=23.4
Q ss_pred eeeceEEEEecCCCCCceEEEEEeee
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVIN 41 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD 41 (112)
+++|..|.|..||++|+.+.|+++-+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 47899999999999999999998754
No 10
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.95 E-value=0.017 Score=42.40 Aligned_cols=56 Identities=23% Similarity=0.506 Sum_probs=44.0
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCC----CCCcc-eeeecCceeecceEE
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPE----TGVPR-SALRLNQLHLTKLKI 71 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~----tgV~R-q~i~~k~l~LT~~~i 71 (112)
+..|-.|.|.+|+++|+.+.|+.|. +.++|+|+|-. .|... -.|...++.|+++.+
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~l 107 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLDL 107 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCeEEEcccchhHeEEEeCcc
Confidence 7789999999999999999999996 77799999965 34322 235557788877654
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.48 E-value=0.031 Score=38.26 Aligned_cols=36 Identities=31% Similarity=0.626 Sum_probs=31.5
Q ss_pred eeeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCC
Q psy2756 15 FVQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGP 50 (112)
Q Consensus 15 fVEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP 50 (112)
-+..|--|.|..|+++||...|..|. +.|+|+|+|=
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 44 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 56789889999999999999999995 5568999996
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.24 E-value=0.046 Score=36.89 Aligned_cols=35 Identities=29% Similarity=0.622 Sum_probs=30.7
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP 50 (112)
+..|--|.|.+|+++||...|..|. +.++|+|+|=
T Consensus 7 I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 7 VKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 5678788888899999999999996 6679999996
No 13
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=95.22 E-value=0.044 Score=39.74 Aligned_cols=58 Identities=24% Similarity=0.441 Sum_probs=45.8
Q ss_pred eeeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCC----CCCcc-eeeecCceeecceEEE
Q psy2756 15 FVQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPE----TGVPR-SALRLNQLHLTKLKIN 72 (112)
Q Consensus 15 fVEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~----tgV~R-q~i~~k~l~LT~~~i~ 72 (112)
-+.-|--|.|..|+++|+...|+.|. +.++|.|+|-. +|... -.|+..++.|+++.++
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l~l~ 104 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITKLNLD 104 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeEEEeeechHHeEEEeccCC
Confidence 36789999999999999999999996 67789999975 23221 3377788888887764
No 14
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=94.32 E-value=0.096 Score=37.19 Aligned_cols=35 Identities=26% Similarity=0.601 Sum_probs=29.7
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP 50 (112)
+..|--|.|..|+++||...|..|. +.|+|+|+|=
T Consensus 4 ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 39 (104)
T TIGR01079 4 IKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGV 39 (104)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCc
Confidence 4567777888899999999999996 5679999985
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=92.98 E-value=0.21 Score=35.34 Aligned_cols=55 Identities=22% Similarity=0.495 Sum_probs=39.9
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCC--------------CCCcc--eeeecCceeecceE
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPE--------------TGVPR--SALRLNQLHLTKLK 70 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~--------------tgV~R--q~i~~k~l~LT~~~ 70 (112)
+..|--|.|-.|+++||...|..|. +.|+|.|+|=. .|+-. ..|+++++.|++..
T Consensus 5 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~ 76 (105)
T PRK00004 5 IKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPK 76 (105)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCc
Confidence 4567778888899999999999995 67799999942 11111 25666777776643
No 16
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=92.57 E-value=0.25 Score=36.35 Aligned_cols=38 Identities=24% Similarity=0.346 Sum_probs=31.6
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCC
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGP 50 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP 50 (112)
..-+++|.-|.|..||++|--+.|+.+- +.+||.|.=.
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~ 162 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVS 162 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEE
Confidence 3456899999999999999999999986 4568877654
No 17
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=91.52 E-value=0.35 Score=34.83 Aligned_cols=39 Identities=23% Similarity=0.501 Sum_probs=32.1
Q ss_pred eeeeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCCC
Q psy2756 14 RFVQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPET 52 (112)
Q Consensus 14 rfVEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~t 52 (112)
...++|-.|.|..||++|-.+.|+++= +.++|+|+--..
T Consensus 85 ~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~ 124 (145)
T TIGR00405 85 ESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA 124 (145)
T ss_pred cccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc
Confidence 347899999999999999999999975 455788877653
No 18
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=91.33 E-value=0.36 Score=34.83 Aligned_cols=37 Identities=19% Similarity=0.260 Sum_probs=31.0
Q ss_pred eeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCC
Q psy2756 14 RFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP 50 (112)
Q Consensus 14 rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP 50 (112)
...++|.-|.|..||.+|-.+.|+++-+++|+.|-=.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~ 143 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLN 143 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEh
Confidence 3467999999999999999999999866778776544
No 19
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.93 E-value=0.53 Score=35.56 Aligned_cols=57 Identities=21% Similarity=0.358 Sum_probs=43.9
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCC----CCCcc-eeeecCceeecceEEE
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPE----TGVPR-SALRLNQLHLTKLKIN 72 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~----tgV~R-q~i~~k~l~LT~~~i~ 72 (112)
|-.|--|.|..|.++|+..-|+.|. +.++|+|+|-. .|=|. -.|...++.||+..++
T Consensus 47 IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~l~l~ 109 (143)
T PTZ00194 47 VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLKLN 109 (143)
T ss_pred eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEccccC
Confidence 6789999999999999999999996 56699999975 11111 3466677888877663
No 20
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=90.27 E-value=0.58 Score=34.33 Aligned_cols=37 Identities=22% Similarity=0.375 Sum_probs=30.9
Q ss_pred eeeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCC
Q psy2756 15 FVQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPE 51 (112)
Q Consensus 15 fVEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~ 51 (112)
.+++|.-|.|..||.+|-.+.|+.+- +++||.|.=+-
T Consensus 119 ~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~ 156 (172)
T TIGR00922 119 DFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSI 156 (172)
T ss_pred CCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEE
Confidence 35799999999999999999999975 45688887653
No 21
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=89.85 E-value=1.1 Score=32.96 Aligned_cols=51 Identities=25% Similarity=0.488 Sum_probs=38.0
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCCCCCCcc--eeeecCceeec
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGPETGVPR--SALRLNQLHLT 67 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP~tgV~R--q~i~~k~l~LT 67 (112)
.++|--|.|..||++|-.+.|+++= +.++++|+.=...+ + -.++++.|.+.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~-~~pv~v~~~~~~~~ 148 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAV-PIPVTVRGDQVRVV 148 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcc-eeeEEEeccEEEEe
Confidence 6799999999999999999999985 56788888764222 2 34555555544
No 22
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=89.47 E-value=0.64 Score=33.92 Aligned_cols=37 Identities=14% Similarity=0.179 Sum_probs=31.6
Q ss_pred eeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCC
Q psy2756 14 RFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP 50 (112)
Q Consensus 14 rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP 50 (112)
...++|.-|.|..||.+|-.++|+++-+++|++|.=.
T Consensus 108 ~~~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~ 144 (162)
T PRK09014 108 ETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLN 144 (162)
T ss_pred cCCCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeeh
Confidence 3467999999999999999999999988888777644
No 23
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=84.76 E-value=0.56 Score=36.90 Aligned_cols=31 Identities=26% Similarity=0.417 Sum_probs=25.4
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeCC
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQT 43 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~n 43 (112)
.+|+.+||||.|..|-+....++||+.-..+
T Consensus 70 ~~fL~~GRlV~v~~~~~~~~wgvvv~~~~~~ 100 (268)
T PF13234_consen 70 LPFLQPGRLVVVRDGDRDFGWGVVVNFAKKS 100 (268)
T ss_dssp HHHS-TTEEEEEEETTCEEEEEEEEEEEE--
T ss_pred HHhCCCCCEEEEecCCCccceeEEEeccccc
Confidence 4799999999999999999999999987653
No 24
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=83.24 E-value=2.8 Score=30.13 Aligned_cols=54 Identities=19% Similarity=0.429 Sum_probs=41.2
Q ss_pred eeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCCC---CCCc-c------------eeeecCceeecce
Q psy2756 15 FVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPE---TGVP-R------------SALRLNQLHLTKL 69 (112)
Q Consensus 15 fVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP~---tgV~-R------------q~i~~k~l~LT~~ 69 (112)
.|--|--|+|-+|.+.||-..|+.+.-.. |+|+|-. .-.+ + ..|.++++.|++.
T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~-V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~ 73 (104)
T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK-VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDP 73 (104)
T ss_pred ceecCCEEEEEecCCCCcceEEEEEecCe-EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEecc
Confidence 46678899999999999999999998777 9999965 0111 1 3455677777775
No 25
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=82.00 E-value=2.5 Score=34.67 Aligned_cols=35 Identities=26% Similarity=0.583 Sum_probs=31.0
Q ss_pred eeeceEEEEecCCCCCceEEEEEee-eCCeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVI-NQTTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIi-D~nRvLVDGP 50 (112)
.++|--|.|..||++|-.+.|.++- +++|+.|.=.
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~ 241 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVE 241 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEE
Confidence 5799999999999999999999997 5888877655
No 26
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=77.06 E-value=7.8 Score=29.71 Aligned_cols=52 Identities=29% Similarity=0.424 Sum_probs=34.3
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeCC----eEEEeCCCCCCcceeeecCceee
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQT----TVLVDGPETGVPRSALRLNQLHL 66 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~n----RvLVDGP~tgV~Rq~i~~k~l~L 66 (112)
.--.|+|-.|-|..||++|=.+.|.+ +|+. .|+|+--.--+|- .+++.++..
T Consensus 121 ~~~~e~Gd~VrI~~GpFa~f~g~V~e-vd~ek~~~~v~v~ifgr~tPV-el~~~qVek 176 (178)
T COG0250 121 KVDFEPGDVVRIIDGPFAGFKAKVEE-VDEEKGKLKVEVSIFGRPTPV-ELEFDQVEK 176 (178)
T ss_pred cccCCCCCEEEEeccCCCCccEEEEE-EcCcCcEEEEEEEEeCCceEE-EEehhhEEE
Confidence 34578999999999999997777666 5666 5666655311222 455555443
No 27
>COG0057 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]
Probab=73.89 E-value=5.1 Score=34.03 Aligned_cols=34 Identities=9% Similarity=0.155 Sum_probs=31.0
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
..+|.-.++++++.+.+.+...-++|..+|+++.
T Consensus 232 ~RVPt~~vs~~dl~v~l~k~~t~eeIn~alk~as 265 (335)
T COG0057 232 IRVPTPNVSVVDLTVELEKEVTVEEINAALKAAS 265 (335)
T ss_pred EEecCCCcEEEEEEEEeCCCCCHHHHHHHHHHhh
Confidence 6788889999999999999999999999998763
No 28
>PRK04313 30S ribosomal protein S4e; Validated
Probab=71.82 E-value=4.1 Score=32.98 Aligned_cols=35 Identities=17% Similarity=0.340 Sum_probs=28.9
Q ss_pred eeeceEEEEecCCCCCceEEEEEeee-----CCeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVIN-----QTTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD-----~nRvLVDGP 50 (112)
.|+|-+|+|+.|.+.|+..+|++|.- .|.|.+...
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~ 211 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDK 211 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcC
Confidence 38999999999999999999999953 356666644
No 29
>PLN00036 40S ribosomal protein S4; Provisional
Probab=71.30 E-value=4.2 Score=33.43 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=28.8
Q ss_pred eeceEEEEecCCCCCceEEEEEee----eCCeEEEeCC
Q psy2756 17 QTGRVVRISDGPYRGKLSSIVDVI----NQTTVLVDGP 50 (112)
Q Consensus 17 EvGRVv~i~~Gp~aGKl~vIVdIi----D~nRvLVDGP 50 (112)
|+|-+|+|+.|.+.|+..+|+++. -.|.|-|.-.
T Consensus 176 e~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~ 213 (261)
T PLN00036 176 DVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDA 213 (261)
T ss_pred CCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeC
Confidence 899999999999999999999998 3356666654
No 30
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=69.78 E-value=5.2 Score=27.94 Aligned_cols=42 Identities=26% Similarity=0.656 Sum_probs=31.1
Q ss_pred ecccc-cccceeeeeceEEEE--ecCCCCCceEEEEEeeeC-CeEE
Q psy2756 5 KHNYN-GAFKRFVQTGRVVRI--SDGPYRGKLSSIVDVINQ-TTVL 46 (112)
Q Consensus 5 ~~~~~-m~f~rfVEvGRVv~i--~~Gp~aGKl~vIVdIiD~-nRvL 46 (112)
..|+. .+...-++-|+++.. ..|||+|.-++++=|.|. +.++
T Consensus 29 D~~YtGpVLe~vl~~g~v~r~~P~~G~Y~G~PViV~PI~~~~g~vi 74 (84)
T PF09884_consen 29 DDNYTGPVLEEVLETGKVIRVTPIEGPYKGVPVIVAPIKDEDGEVI 74 (84)
T ss_pred cCCcccHHHHHHHHcCCEEEeccCCcccCCeeEEEEEEEcCCCCEE
Confidence 34444 345566777887777 479999999999999998 6654
No 31
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.38 E-value=5.2 Score=29.60 Aligned_cols=43 Identities=30% Similarity=0.556 Sum_probs=34.1
Q ss_pred eecccc-cccceeeeeceEEEE--ecCCCCCceEEEEEeeeCCeEE
Q psy2756 4 VKHNYN-GAFKRFVQTGRVVRI--SDGPYRGKLSSIVDVINQTTVL 46 (112)
Q Consensus 4 ~~~~~~-m~f~rfVEvGRVv~i--~~Gp~aGKl~vIVdIiD~nRvL 46 (112)
+-.|+. .+....+|-|.|+.- ..|||.|+-+|++-|-|.+.|+
T Consensus 46 vD~~YtGpVLeevle~gevvr~vP~~GpY~G~pVVV~Pik~~g~vi 91 (123)
T COG4048 46 VDDNYTGPVLEEVLEKGEVVREVPIIGPYRGLPVVVAPIKDEGEVI 91 (123)
T ss_pred ecccCcchHHHHHHhhCceeeeCCCCCccCCceEEEEEeccCCeEE
Confidence 344555 456677888988876 4799999999999999998775
No 32
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=67.52 E-value=5.4 Score=33.03 Aligned_cols=35 Identities=23% Similarity=0.492 Sum_probs=28.9
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeC----CeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQ----TTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~----nRvLVDGP 50 (112)
.|+|-+|+|+.|.+.|+..+|+++.-+ |.|.+...
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~ 210 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDA 210 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeC
Confidence 389999999999999999999999544 56666544
No 33
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=66.27 E-value=6.1 Score=32.50 Aligned_cols=35 Identities=23% Similarity=0.408 Sum_probs=28.3
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeC----CeEEEeCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQ----TTVLVDGP 50 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~----nRvLVDGP 50 (112)
.|+|-+|+|+.|.+.|+..+|+++.-+ |.|.|+-.
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~ 213 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDS 213 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeC
Confidence 389999999999999999999995532 56666644
No 34
>PF13555 AAA_29: P-loop containing region of AAA domain
Probab=55.88 E-value=33 Score=22.17 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=21.3
Q ss_pred eEEEEecCCCCCceEEEEEeee-CCeEEEeCCC
Q psy2756 20 RVVRISDGPYRGKLSSIVDVIN-QTTVLVDGPE 51 (112)
Q Consensus 20 RVv~i~~Gp~aGKl~vIVdIiD-~nRvLVDGP~ 51 (112)
|+.+++.|.+.++ .+|+-. .+-.||-||+
T Consensus 3 rl~L~Nw~~f~~~---~~~~~~~g~~tli~G~n 32 (62)
T PF13555_consen 3 RLQLVNWGSFDGE---TIDFDPRGDVTLITGPN 32 (62)
T ss_pred EEEEeccCccCCe---EEeecCCCcEEEEECCC
Confidence 6889999999993 444322 2379999997
No 35
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=52.66 E-value=8.2 Score=32.09 Aligned_cols=20 Identities=35% Similarity=0.488 Sum_probs=14.3
Q ss_pred CCeEEEeCCC--CCCcceeeec
Q psy2756 42 QTTVLVDGPE--TGVPRSALRL 61 (112)
Q Consensus 42 ~nRvLVDGP~--tgV~Rq~i~~ 61 (112)
-.|+|+|-|| +|+-|+--.+
T Consensus 230 fD~iLlDaPCSg~G~irr~Pd~ 251 (355)
T COG0144 230 FDRILLDAPCSGTGVIRRDPDV 251 (355)
T ss_pred CcEEEECCCCCCCcccccCccc
Confidence 3799999999 4666654443
No 36
>PF01189 Nol1_Nop2_Fmu: NOL1/NOP2/sun family; InterPro: IPR001678 This domain is found in archaeal, bacterial and eukaryotic proteins. In the archaea and bacteria, they are annotated as putative nucleolar protein, Sun (Fmu) family protein or tRNA/rRNA cytosine-C5-methylase. The majority have the S-adenosyl methionine (SAM) binding domain and are related to Escherichia coli Fmu (Sun) protein (16S rRNA m5C 967 methyltransferase) whose structure has been determined []. In the eukaryota, the majority are annotated as being 'hypothetical protein', nucleolar protein or the Nop2/Sun (Fmu) family. Unlike their bacterial homologues, few of the eukaryotic members in this family have a the SAM binding signature. Despite this, Saccharomyces cerevisiae (Baker's yeast) Nop2p is a probable RNA m5C methyltransferase []. It is essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis []; localized to the nucleolus and is essential for viability []. Reduced Nop2p expression limits yeast growth and decreases levels of mature 60S ribosomal subunits while altering rRNA processing []. There is substantial identity between Nop2p and Homo sapiens (Human) p120 (NOL1), which is also called the proliferation-associated nucleolar antigen [, ].; PDB: 3M4X_A 2FRX_B 2YXL_A 1IXK_A 1SQG_A 1SQF_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A ....
Probab=52.09 E-value=8.7 Score=30.84 Aligned_cols=12 Identities=50% Similarity=0.841 Sum_probs=10.2
Q ss_pred CeEEEeCCCCCC
Q psy2756 43 TTVLVDGPETGV 54 (112)
Q Consensus 43 nRvLVDGP~tgV 54 (112)
.+||+|.||||.
T Consensus 158 d~VlvDaPCSg~ 169 (283)
T PF01189_consen 158 DRVLVDAPCSGL 169 (283)
T ss_dssp EEEEEECSCCCG
T ss_pred chhhcCCCccch
Confidence 489999999764
No 37
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=51.49 E-value=16 Score=29.89 Aligned_cols=36 Identities=28% Similarity=0.476 Sum_probs=30.4
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeC-----CeEEEeCCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQ-----TTVLVDGPE 51 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~-----nRvLVDGP~ 51 (112)
.|.|-.|+++.|.+.|....|++|--+ |=|-++++.
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~ 214 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEE 214 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCC
Confidence 388999999999999999999999766 456666654
No 38
>PF01777 Ribosomal_L27e: Ribosomal L27e protein family; InterPro: IPR001141 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 [, ]. Ribosomal protein, L27 is found in fungi, plants, algae and vertebrates [, ]. The family has a specific signature at the C terminus.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_a 4A1B_N 4A19_N 4A18_N 4A1D_N 3IZR_a.
Probab=50.94 E-value=0.47 Score=32.78 Aligned_cols=17 Identities=18% Similarity=0.399 Sum_probs=15.5
Q ss_pred eeeecCceeecceEEEe
Q psy2756 57 SALRLNQLHLTKLKINF 73 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i 73 (112)
.++|++||.||.+.+++
T Consensus 22 K~iNynHlmPTRY~vd~ 38 (85)
T PF01777_consen 22 KVINYNHLMPTRYSVDI 38 (85)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred EEeeccceEeeeeeeec
Confidence 46899999999999988
No 39
>PF02800 Gp_dh_C: Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; InterPro: IPR020829 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme []. GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis []. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself. GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins []. This entry represents the C-terminal domain which is a mixed alpha/antiparallel beta fold.; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 1DSS_R 1IHY_C 1CRW_R 1IHX_B 1SZJ_R 3HJA_D 2YYY_B 1OBF_O 3PYM_A 2VYN_D ....
Probab=50.24 E-value=27 Score=25.89 Aligned_cols=34 Identities=15% Similarity=0.191 Sum_probs=29.2
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
-.+|.-++++.++.+.+.+.+..++|.++|+++.
T Consensus 76 ~rVPt~~~s~~dl~~~l~k~~t~eeV~~~~~~aa 109 (157)
T PF02800_consen 76 VRVPTPNVSLHDLTVELEKPVTKEEVNEALKQAA 109 (157)
T ss_dssp EEESSSSEEEEEEEEEESSSS-HHHHHHHHHHHH
T ss_pred EeeeecccCceEEEEecccchhhhhhhhhhhhhh
Confidence 4578889999999999999999999999998753
No 40
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=49.20 E-value=27 Score=27.11 Aligned_cols=39 Identities=23% Similarity=0.400 Sum_probs=31.8
Q ss_pred cccee--eeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCCC
Q psy2756 11 AFKRF--VQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPE 51 (112)
Q Consensus 11 ~f~rf--VEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP~ 51 (112)
.|.+. +|+|-.+..+.+- |...+.|-=|+.++|+||+-.
T Consensus 84 ~F~~~~~~~vGm~~~~~~~~--~~~~~~V~~V~~~~V~VDfNH 124 (174)
T COG1047 84 EFQGVGELEVGMEVEAEGGD--GEIPGVVTEVSGDRVTVDFNH 124 (174)
T ss_pred HhCcCCCCCCCcEEEEcCCC--ceeeEEEEEEcCCEEEEeCCC
Confidence 46664 8999999887544 888888888899999999964
No 41
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=43.79 E-value=23 Score=23.57 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=23.5
Q ss_pred eeceEEEEecCCCCCceEEEEEe---eeCCeEEEeCC
Q psy2756 17 QTGRVVRISDGPYRGKLSSIVDV---INQTTVLVDGP 50 (112)
Q Consensus 17 EvGRVv~i~~Gp~aGKl~vIVdI---iD~nRvLVDGP 50 (112)
-+|.=+||..|||.++...+=.- ...++++|=|.
T Consensus 4 i~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~~ 40 (68)
T PF13051_consen 4 IVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIGE 40 (68)
T ss_pred ccccEeeeccCCccceeEEEecchhhcCCcEEEEECC
Confidence 46889999999999998764322 12236666664
No 42
>PLN02237 glyceraldehyde-3-phosphate dehydrogenase B
Probab=41.99 E-value=38 Score=29.82 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=29.8
Q ss_pred eeeecCceeecceEEEecC-CCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPF-NARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r-~a~t~~v~ka~~~a~ 90 (112)
-.+|.-+.++.|+++.+.+ ...-++|.++++++-
T Consensus 309 ~RVPt~nvS~vDLt~~l~k~~~t~eein~~~k~aa 343 (442)
T PLN02237 309 LRVPTPNVSVVDLVVNVEKKGITAEDVNAAFRKAA 343 (442)
T ss_pred EecccCCceEEEEEEEeCCCCCCHHHHHHHHHHhh
Confidence 5678889999999999998 799999999998763
No 43
>COG0021 TktA Transketolase [Carbohydrate transport and metabolism]
Probab=41.95 E-value=26 Score=32.41 Aligned_cols=54 Identities=15% Similarity=0.118 Sum_probs=33.2
Q ss_pred CCceEEEEEeeeCCeEEEeCCCCCCc-----ceeeecCceeecceEEEecCCCChHHHHHHHHhcch
Q psy2756 30 RGKLSSIVDVINQTTVLVDGPETGVP-----RSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQV 91 (112)
Q Consensus 30 aGKl~vIVdIiD~nRvLVDGP~tgV~-----Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~i 91 (112)
-|||.| ++|.|++-+||+...+- -+--.+.| -++...-|-..+.+.+|+++|.-
T Consensus 177 L~kLIv---lyD~N~IsiDG~~~~~f~ed~~~RfeAyGW-----~vi~~~DG~D~e~I~~Ai~~Ak~ 235 (663)
T COG0021 177 LGKLIV---LYDSNDISIDGDTSLSFTEDVAKRFEAYGW-----NVIRVIDGHDLEAIDKAIEEAKA 235 (663)
T ss_pred CCcEEE---EEeCCCceeccCcccccchhHHHHHHhcCC-----eEEEecCCCCHHHHHHHHHHHHh
Confidence 368888 56799999999985431 11111111 12333346678888888887653
No 44
>KOG1708|consensus
Probab=41.57 E-value=54 Score=26.71 Aligned_cols=37 Identities=30% Similarity=0.399 Sum_probs=31.4
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeCC-eEEEeCCCC
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQT-TVLVDGPET 52 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~n-RvLVDGP~t 52 (112)
+-.|--|-|-.|.++||..-++.|+-|+ -|.|+|=.+
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~ 110 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNT 110 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecCceEEEcccch
Confidence 4568888889999999999999999665 788998764
No 45
>KOG1999|consensus
Probab=41.31 E-value=30 Score=33.47 Aligned_cols=30 Identities=23% Similarity=0.539 Sum_probs=27.4
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeC
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQ 42 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~ 42 (112)
.+|.|+|-.|.|..|+|.|...+||-|-++
T Consensus 457 rKyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 457 RKYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hhhccCCCeEEEEeccccCCcceEEEEeCC
Confidence 689999999999999999999999987553
No 46
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=39.96 E-value=52 Score=29.25 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=28.0
Q ss_pred eeeceEEEEe---------cCCCCCceEEEEEeeeCCeEEEeCCC
Q psy2756 16 VQTGRVVRIS---------DGPYRGKLSSIVDVINQTTVLVDGPE 51 (112)
Q Consensus 16 VEvGRVv~i~---------~Gp~aGKl~vIVdIiD~nRvLVDGP~ 51 (112)
+++|.-|.++ .-+..|-++.|++++|.+|++|-+..
T Consensus 83 l~~g~~v~l~e~~~~v~~~~~~~~g~~~~~~~~~~~~~~~v~~~~ 127 (512)
T TIGR03689 83 LVPGQTVRLNEALQVVEARDFETVGEIATLKEVLGDGRALVVDHS 127 (512)
T ss_pred CCCCCEEEECCcceeeccCCCCCCCceEEEEEEeCCCeEEEEeCC
Confidence 3456666665 23567999999999999999999886
No 47
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=37.78 E-value=66 Score=21.96 Aligned_cols=39 Identities=21% Similarity=0.182 Sum_probs=26.8
Q ss_pred ceeeeeceEEEE--ecCCCCCceEEEEEeeeCCeEEEeCCC
Q psy2756 13 KRFVQTGRVVRI--SDGPYRGKLSSIVDVINQTTVLVDGPE 51 (112)
Q Consensus 13 ~rfVEvGRVv~i--~~Gp~aGKl~vIVdIiD~nRvLVDGP~ 51 (112)
..--++|-+++. ..+...|..++|..+.|.+.+.+-.-.
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e~N 100 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIEQN 100 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEECS
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEECC
Confidence 455689999998 567788999999999788777775443
No 48
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=36.02 E-value=83 Score=24.70 Aligned_cols=35 Identities=34% Similarity=0.537 Sum_probs=26.4
Q ss_pred eceEEEEecCCCCCceEEEEEeeeCC----eEEEeCCCCC
Q psy2756 18 TGRVVRISDGPYRGKLSSIVDVINQT----TVLVDGPETG 53 (112)
Q Consensus 18 vGRVv~i~~Gp~aGKl~vIVdIiD~n----RvLVDGP~tg 53 (112)
+||++.|+.|+-..-.-.=+++.|+. .++|. |..|
T Consensus 137 iGr~a~Vt~g~a~~g~~aqa~V~D~~Gq~hyv~ve-P~~~ 175 (202)
T PF07290_consen 137 IGRVATVTSGTARQGSPAQARVKDQFGQLHYVMVE-PEAG 175 (202)
T ss_pred CcceEEEEecccCCCCceEEEEEecCCCEEEEEEe-eCCC
Confidence 69999999998876666777777765 57776 6533
No 49
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=33.96 E-value=27 Score=27.92 Aligned_cols=14 Identities=36% Similarity=0.368 Sum_probs=13.0
Q ss_pred ecCCCCCceEEEEE
Q psy2756 25 SDGPYRGKLSSIVD 38 (112)
Q Consensus 25 ~~Gp~aGKl~vIVd 38 (112)
||+.-.||.|+|||
T Consensus 135 NFa~V~gK~cvIVD 148 (203)
T COG0856 135 NFASVEGKRCVIVD 148 (203)
T ss_pred ccccccCceEEEEe
Confidence 78999999999998
No 50
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=33.41 E-value=86 Score=20.73 Aligned_cols=23 Identities=35% Similarity=0.437 Sum_probs=17.4
Q ss_pred EEEEecCCCCCceEEEEE-eeeCC
Q psy2756 21 VVRISDGPYRGKLSSIVD-VINQT 43 (112)
Q Consensus 21 Vv~i~~Gp~aGKl~vIVd-IiD~n 43 (112)
......+...||.++||| ++|.+
T Consensus 78 ~~~~~~~~~~gk~vliVDDvi~tG 101 (125)
T PF00156_consen 78 LFIIDKEDIKGKRVLIVDDVIDTG 101 (125)
T ss_dssp EEEEESSSGTTSEEEEEEEEESSS
T ss_pred EeecccccccceeEEEEeeeEccc
Confidence 345567888999999998 76654
No 51
>COG3896 Chloramphenicol 3-O-phosphotransferase [Defense mechanisms]
Probab=32.26 E-value=29 Score=27.65 Aligned_cols=18 Identities=39% Similarity=0.621 Sum_probs=15.8
Q ss_pred eeceEEEEecCCCCCceE
Q psy2756 17 QTGRVVRISDGPYRGKLS 34 (112)
Q Consensus 17 EvGRVv~i~~Gp~aGKl~ 34 (112)
-.||+|+.|-||.+||--
T Consensus 21 ~~griVlLNG~~saGKSS 38 (205)
T COG3896 21 PEGRIVLLNGGSSAGKSS 38 (205)
T ss_pred CCceEEEecCCCccchhH
Confidence 369999999999999953
No 52
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=31.54 E-value=28 Score=30.43 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.7
Q ss_pred CeEEEeCCCCC
Q psy2756 43 TTVLVDGPETG 53 (112)
Q Consensus 43 nRvLVDGP~tg 53 (112)
++||||-||||
T Consensus 185 D~ILvDaPCSG 195 (470)
T PRK11933 185 DAILLDAPCSG 195 (470)
T ss_pred CeEEEcCCCCC
Confidence 69999999964
No 53
>COG0133 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism]
Probab=29.68 E-value=26 Score=30.44 Aligned_cols=42 Identities=19% Similarity=0.418 Sum_probs=32.5
Q ss_pred CCCcceeeecCceeecceEEEecCCCChHHHHHHHHhcchHHHHh
Q psy2756 52 TGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEKWS 96 (112)
Q Consensus 52 tgV~Rq~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~i~~kw~ 96 (112)
..|.||..|+=+|.|..-.+ +|-.+.+++|+.|..+| ..-|.
T Consensus 137 ~Dv~RQ~~NVfRM~LlGA~V-~pV~sGs~TLKDA~neA--lRdWv 178 (396)
T COG0133 137 EDVERQALNVFRMRLLGAEV-VPVTSGSGTLKDAINEA--LRDWV 178 (396)
T ss_pred hhhhhcccchhhhhhcCceE-EEeccCCchHHHHHHHH--HHHHH
Confidence 36899999999999999877 34456788899998765 34454
No 54
>PF12090 Spt20: Spt20 family; InterPro: IPR021950 This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.
Probab=29.12 E-value=34 Score=26.13 Aligned_cols=15 Identities=20% Similarity=0.268 Sum_probs=12.9
Q ss_pred EEEEEeeeCCeEEEe
Q psy2756 34 SSIVDVINQTTVLVD 48 (112)
Q Consensus 34 ~vIVdIiD~nRvLVD 48 (112)
|+||+|.|+..+-..
T Consensus 74 ClIveV~D~R~~~~~ 88 (182)
T PF12090_consen 74 CLIVEVRDHRSTAQQ 88 (182)
T ss_pred EEEEEEecccccccc
Confidence 889999999987654
No 55
>KOG1122|consensus
Probab=27.03 E-value=35 Score=30.36 Aligned_cols=11 Identities=45% Similarity=0.815 Sum_probs=9.9
Q ss_pred CeEEEeCCCCC
Q psy2756 43 TTVLVDGPETG 53 (112)
Q Consensus 43 nRvLVDGP~tg 53 (112)
.|||.|.||||
T Consensus 314 DRVLLDAPCSG 324 (460)
T KOG1122|consen 314 DRVLLDAPCSG 324 (460)
T ss_pred ceeeecCCCCC
Confidence 59999999976
No 56
>PTZ00434 cytosolic glyceraldehyde 3-phosphate dehydrogenase; Provisional
Probab=26.93 E-value=84 Score=26.97 Aligned_cols=34 Identities=9% Similarity=0.084 Sum_probs=30.6
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
-.+|.-+.++.|+++.+.+.+.-+++.++++++-
T Consensus 249 ~RVPt~nvS~vDLt~~l~k~~t~eein~a~k~aa 282 (361)
T PTZ00434 249 FRVPTPDVSVVDLTFRATRDTSIQEIDAAIKRAS 282 (361)
T ss_pred EecccCcEeEEEEEEEeCCCCCHHHHHHHHHHhh
Confidence 5678899999999999999999999999998754
No 57
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=26.51 E-value=34 Score=29.13 Aligned_cols=45 Identities=18% Similarity=0.292 Sum_probs=31.4
Q ss_pred cceeeeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCCCCCCcc
Q psy2756 12 FKRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPETGVPR 56 (112)
Q Consensus 12 f~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP~tgV~R 56 (112)
-+=++||||-.+-+.|=..-+..-+.+.-+.+.|+|||--+...|
T Consensus 270 ~~l~~EPGR~iv~~aG~Lvt~V~~~k~~~~~~~v~vD~gm~~~~r 314 (394)
T COG0019 270 VELILEPGRAIVANAGVLVTEVLDVKENGERNFVIVDGGMNDLMR 314 (394)
T ss_pred CeEEEccchhhhhcceeEEEEEEEEEEecCceEEEEechhccCcC
Confidence 356899999988777755555555555545689999997654444
No 58
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=25.99 E-value=1.9e+02 Score=18.73 Aligned_cols=45 Identities=20% Similarity=0.481 Sum_probs=29.1
Q ss_pred eeeceEEEEecCCCCCceEEEEEeeeCCeEEEeCC------CCCC-cceeeecCcee
Q psy2756 16 VQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP------ETGV-PRSALRLNQLH 65 (112)
Q Consensus 16 VEvGRVv~i~~Gp~aGKl~vIVdIiD~nRvLVDGP------~tgV-~Rq~i~~k~l~ 65 (112)
-++|-+.-...| +--+|+-+-+|-|+||=- ..+. .|.++|+|+..
T Consensus 4 a~vGdiIefk~g-----~~G~V~kv~eNSVIVdIT~m~~~~e~~l~~ktVVnHKnYk 55 (57)
T PF09953_consen 4 AKVGDIIEFKDG-----FTGIVEKVYENSVIVDITIMENFDELDLEEKTVVNHKNYK 55 (57)
T ss_pred cccCcEEEEcCC-----cEEEEEEEecCcEEEEEEecCCccccCCCccEEEeeceeE
Confidence 367777765432 333456666888888742 1455 78999998865
No 59
>PRK09907 toxin MazF; Provisional
Probab=24.99 E-value=61 Score=22.64 Aligned_cols=27 Identities=11% Similarity=0.308 Sum_probs=21.7
Q ss_pred ceeeeeceEEEEecCCCCCc------eEEEEEe
Q psy2756 13 KRFVQTGRVVRISDGPYRGK------LSSIVDV 39 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGK------l~vIVdI 39 (112)
.+..+-|-+.+++++|..|. -|+||.-
T Consensus 4 ~~~~~rGdI~~vdl~P~~G~E~~g~RP~lVvs~ 36 (111)
T PRK09907 4 RYVPDMGDLIWVDFDPTKGSEQAGHRPAVVLSP 36 (111)
T ss_pred ccCCCCCcEEEEECCCCCCcccCCCCeEEEEcc
Confidence 45688999999999999875 4777764
No 60
>PF01505 Vault: Major Vault Protein repeat; InterPro: IPR002499 Vaults are the largest ribonucleoprotein particles known, having a mass of approximately 13 MDa. They are multi-subunit structures that may act as scaffolds for proteins involved in signal transduction and may also play a role in nucleo-cytoplasmic transport. Vaults are present in most normal tissues, but are more highly expressed in epithelial cells with secretory and excretory functions, as well as in cells chronically exposed to xenobiotics, such as bronchial cells and cells lining the intestine []. Overexpression of these proteins is linked with multidrug-resistance in cancer cells. The mammalian vault structure is highly regular and consists of approximately 96 molecules of the 100 kDa major vault protein (MVP), 2 molecules of the 240 kDa minor vault protein TEP1, 8 molecules of the 193 kDa minor vault protein VPARP and at least 6 copies of a small untranslated RNA of 88-141 bases. The MVP molecules form the core of the complex, which is a barrel-like structure with an invaginated waist and two protruding caps. The complex can unfold into two symmetrical flower-like structures with 8 petals each supposedly consisting of 6 MVP molecules []. The MVP protein is composed of two distinct domains []. The N-terminal domain contains ~8 copies of the vault repeat (or MVP repeat) in tandem. The MVP repeat is composed of ~53 amino acids and forms a structural part of the vault wall. The C-terminal part of MVP may be involved in oligomerization and be located in the vault cap, while the MVP repeats in the N-terminal part can be packed like staves in a barrel to form the vault wall. The 3D structure of the repeat forms a fold that consists of a three stranded (B) antiparallel beta-sheet in a unique topology B2-B1-B3 and two loops. MVP repeats can be interaction-mediating modules, as MVP repeats 3 and 4 bind VPARP, which is one of the other vault proteins.; PDB: 3GF5_A 3GNG_A 3GNF_B 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y 1Y7X_A.
Probab=24.75 E-value=27 Score=20.71 Aligned_cols=15 Identities=47% Similarity=0.687 Sum_probs=11.4
Q ss_pred CCeEEEeCCCCCCcc
Q psy2756 42 QTTVLVDGPETGVPR 56 (112)
Q Consensus 42 ~nRvLVDGP~tgV~R 56 (112)
..+-||-||++-+||
T Consensus 29 Ge~WLv~gP~~YiP~ 43 (43)
T PF01505_consen 29 GEEWLVTGPGTYIPR 43 (43)
T ss_dssp TEEEEEESSSEECST
T ss_pred CCEEEEeCCeeEcCC
Confidence 668899999766664
No 61
>KOG2198|consensus
Probab=23.74 E-value=46 Score=28.83 Aligned_cols=18 Identities=39% Similarity=0.462 Sum_probs=12.5
Q ss_pred CeEEEeCCCC--CCcceeee
Q psy2756 43 TTVLVDGPET--GVPRSALR 60 (112)
Q Consensus 43 nRvLVDGP~t--gV~Rq~i~ 60 (112)
.|||||-||| |.-|+..+
T Consensus 238 DrVLvDVPCS~Dgt~rk~~~ 257 (375)
T KOG2198|consen 238 DRVLVDVPCSGDGTLRKNPN 257 (375)
T ss_pred ceeEEecccCCCcccccCch
Confidence 4999999996 34444443
No 62
>PRK07403 glyceraldehyde-3-phosphate dehydrogenase; Reviewed
Probab=23.17 E-value=1.2e+02 Score=25.70 Aligned_cols=34 Identities=15% Similarity=0.165 Sum_probs=30.1
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
-.+|.-+.++.++.+.+.+.+..++|.++|+++-
T Consensus 234 vRVPt~~vs~~dl~v~l~k~~t~eeI~~~~~~as 267 (337)
T PRK07403 234 LRVPTPNVSVVDLVVQVEKRTITEQVNEVLKDAS 267 (337)
T ss_pred EEeccCCcEEEEEEEEECCCCCHHHHHHHHHHHh
Confidence 4577889999999999999999999999998764
No 63
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=21.95 E-value=1.7e+02 Score=18.46 Aligned_cols=30 Identities=20% Similarity=0.257 Sum_probs=21.0
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeC
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQ 42 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~ 42 (112)
-+=+++|+|.-|...+..++..+-++|-+.
T Consensus 23 ~~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~ 52 (81)
T PF02470_consen 23 YRGVEVGKVTSIELDPDGNRVRVTLRIDPD 52 (81)
T ss_pred ECCEEEEEEEEEEEcCCCCEEEEEEEEcCC
Confidence 356899999999886666665555554433
No 64
>TIGR01546 GAPDH-II_archae glyceraldehyde-3-phosphate dehydrogenase, type II. All of the members of the seed are characterized. See, for instance. This model is very solid, there are no species falling between trusted and noise at this time. The closest relatives scoring in the noise are the class I GAPDH's.
Probab=21.73 E-value=1.3e+02 Score=25.24 Aligned_cols=34 Identities=3% Similarity=0.083 Sum_probs=30.5
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
-.+|.-.+++.++.+.+.+.+..++|.++|+++.
T Consensus 209 vrVPt~~vs~~dl~v~l~~~~t~eeV~~~l~~~~ 242 (333)
T TIGR01546 209 FVVPTTLMHVHSIMVELKKPVTKDDIIDILENTP 242 (333)
T ss_pred EEeCCCCcEEEEEEEEECCCCCHHHHHHHHHhCC
Confidence 4577889999999999999999999999999864
No 65
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=21.67 E-value=2.5e+02 Score=18.57 Aligned_cols=48 Identities=8% Similarity=0.086 Sum_probs=27.6
Q ss_pred eeeeeceEEEE--ecCCCCCceEEEEEeeeCCeEEEeCCCCCCcceeeecCce
Q psy2756 14 RFVQTGRVVRI--SDGPYRGKLSSIVDVINQTTVLVDGPETGVPRSALRLNQL 64 (112)
Q Consensus 14 rfVEvGRVv~i--~~Gp~aGKl~vIVdIiD~nRvLVDGP~tgV~Rq~i~~k~l 64 (112)
++-+.+.-+++ +.+-..|..+||.. +|.++++|--|. -.++.++...+
T Consensus 71 ~l~~~~~P~I~~~~~~~~~~~~~Vl~~-~~~~~~~i~dp~--~~~~~~~~~ef 120 (136)
T cd02418 71 ELKDIPLPFIAHVIKEWKLNHYVVVYK-IKKKKILIADPA--VGITKISKEEF 120 (136)
T ss_pred hHhcCCCCEEEEEccCCCCCeEEEEEE-EcCCEEEEECCC--CCCEEeeHHHH
Confidence 44444443443 33445677777777 567778886673 33666666544
No 66
>COG4832 Uncharacterized conserved protein [Function unknown]
Probab=21.55 E-value=74 Score=25.44 Aligned_cols=24 Identities=33% Similarity=0.527 Sum_probs=21.6
Q ss_pred cCCCCCceEEEEEeeeCCeEEEeCCC
Q psy2756 26 DGPYRGKLSSIVDVINQTTVLVDGPE 51 (112)
Q Consensus 26 ~Gp~aGKl~vIVdIiD~nRvLVDGP~ 51 (112)
|||- |-+-|++|=-+|+..|||-.
T Consensus 15 Y~pk--k~~sii~vPemnflMIDGkG 38 (207)
T COG4832 15 YGPK--KKASIIKVPEMNFLMIDGKG 38 (207)
T ss_pred cCCC--CCceeeecccccEEEecCCC
Confidence 6887 88999999999999999973
No 67
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=21.55 E-value=92 Score=20.45 Aligned_cols=29 Identities=14% Similarity=0.220 Sum_probs=18.5
Q ss_pred CceEEEEEeeeCCeEEEeCCCCCCcceeeec
Q psy2756 31 GKLSSIVDVINQTTVLVDGPETGVPRSALRL 61 (112)
Q Consensus 31 GKl~vIVdIiD~nRvLVDGP~tgV~Rq~i~~ 61 (112)
|.-+|+.. +|+++++|--|..| .++.++.
T Consensus 79 g~~~Vl~~-~~~~~~~i~dp~~~-~~~~~~~ 107 (121)
T cd02417 79 GGHFILAK-LDGQKYLIQDPISQ-RPEVLSR 107 (121)
T ss_pred CCEEEEEE-EcCCCEEEECCCcC-CCeecCH
Confidence 45566666 66778888888655 3334554
No 68
>PRK07729 glyceraldehyde-3-phosphate dehydrogenase; Validated
Probab=21.53 E-value=1.4e+02 Score=25.30 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=29.4
Q ss_pred eeeecCceeecceEEEecCCCChHHHHHHHHhcc
Q psy2756 57 SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQ 90 (112)
Q Consensus 57 q~i~~k~l~LT~~~i~i~r~a~t~~v~ka~~~a~ 90 (112)
-.+|.-+.++.++++.+.+...-+++.++|+++-
T Consensus 232 vRVPt~~~s~~dltv~l~k~~t~eev~~~l~~a~ 265 (343)
T PRK07729 232 LRVPTPNVSLVDLVVDVKRDVTVEEINEAFKTAA 265 (343)
T ss_pred EEeeecCeEEEEEEEEECCCCCHHHHHHHHHHHh
Confidence 3567788899999999999999999999998763
No 69
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=20.82 E-value=81 Score=28.74 Aligned_cols=31 Identities=35% Similarity=0.515 Sum_probs=26.0
Q ss_pred ceeeeeceEEEEecCCCCCceEEEEEeeeCC
Q psy2756 13 KRFVQTGRVVRISDGPYRGKLSSIVDVINQT 43 (112)
Q Consensus 13 ~rfVEvGRVv~i~~Gp~aGKl~vIVdIiD~n 43 (112)
.|=+-+|.-|.|..|||+|.|.||=|+-|.+
T Consensus 349 gRd~aigktVrIr~g~yKG~lGVVKdv~~~~ 379 (607)
T COG5164 349 GRDPAIGKTVRIRCGEYKGHLGVVKDVDRNI 379 (607)
T ss_pred ccccccCceEEEeecccccccceeeeccCce
Confidence 3556788899999999999999999976654
No 70
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=20.77 E-value=1.2e+02 Score=20.09 Aligned_cols=32 Identities=16% Similarity=0.407 Sum_probs=22.0
Q ss_pred CCceEEEEEeeeCCeEEEeCCCCCCcceeeecCce
Q psy2756 30 RGKLSSIVDVINQTTVLVDGPETGVPRSALRLNQL 64 (112)
Q Consensus 30 aGKl~vIVdIiD~nRvLVDGP~tgV~Rq~i~~k~l 64 (112)
.|.-+||..+ +.+.++|.-|..| ++.++...+
T Consensus 83 ~g~~~Vl~~~-~~~~~~i~dp~~~--~~~~~~~el 114 (127)
T cd02419 83 MNHFVVLKKV-SRRRIVIHDPALG--KRKLSLEEA 114 (127)
T ss_pred CCEEEEEEEE-cCCEEEEECCccC--CEEEcHHHH
Confidence 3677788885 7788888888644 556665544
No 71
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=20.59 E-value=63 Score=27.25 Aligned_cols=11 Identities=36% Similarity=0.806 Sum_probs=9.5
Q ss_pred CeEEEeCCCCC
Q psy2756 43 TTVLVDGPETG 53 (112)
Q Consensus 43 nRvLVDGP~tg 53 (112)
.+||+|.||||
T Consensus 327 D~Vl~DaPCSg 337 (434)
T PRK14901 327 DRILLDAPCSG 337 (434)
T ss_pred CEEEEeCCCCc
Confidence 58999999964
Done!