Query psy13959
Match_columns 248
No_of_seqs 124 out of 1110
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 15:56:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13959.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13959hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00180 60S ribosomal protein 100.0 5E-105 1E-109 716.6 23.5 247 1-247 1-247 (260)
2 PRK09612 rpl2p 50S ribosomal p 100.0 1E-101 2E-106 688.7 23.2 237 1-247 1-238 (238)
3 COG0090 RplB Ribosomal protein 100.0 2.6E-93 5.7E-98 637.6 21.7 230 1-245 34-267 (275)
4 CHL00052 rpl2 ribosomal protei 100.0 9.8E-85 2.1E-89 590.0 21.5 210 10-234 39-251 (273)
5 TIGR01171 rplB_bact ribosomal 100.0 8.9E-84 1.9E-88 584.0 21.5 212 8-234 37-250 (273)
6 PRK09374 rplB 50S ribosomal pr 100.0 1.4E-83 3.1E-88 583.1 20.7 212 8-234 39-252 (276)
7 PTZ00031 ribosomal protein L2; 100.0 2.9E-83 6.2E-88 587.4 21.1 211 8-234 70-283 (317)
8 KOG2309|consensus 100.0 1.8E-69 3.8E-74 474.5 15.6 241 1-247 1-241 (248)
9 KOG0438|consensus 100.0 4.6E-62 1E-66 442.1 10.0 206 9-226 62-279 (312)
10 PF03947 Ribosomal_L2_C: Ribos 100.0 2.4E-59 5.2E-64 384.5 9.3 129 96-231 1-130 (130)
11 PF00181 Ribosomal_L2: Ribosom 99.9 3E-27 6.6E-32 178.1 8.4 75 11-90 1-77 (77)
12 PF03991 Prion_octapep: Copper 86.7 0.37 8E-06 21.8 0.8 8 210-217 1-8 (8)
13 KOG0438|consensus 85.4 7.4 0.00016 36.7 9.5 103 6-132 13-124 (312)
14 cd04092 mtEFG2_II_like mtEFG2_ 63.5 29 0.00063 25.4 6.0 25 42-67 2-26 (83)
15 cd03699 lepA_II lepA_II: This 61.5 39 0.00085 25.1 6.4 25 42-67 2-26 (86)
16 cd03691 BipA_TypA_II BipA_TypA 55.5 65 0.0014 23.6 6.7 25 42-67 2-26 (86)
17 cd04088 EFG_mtEFG_II EFG_mtEFG 52.7 56 0.0012 23.7 5.9 25 42-67 2-26 (83)
18 cd04091 mtEFG1_II_like mtEFG1_ 51.3 66 0.0014 23.5 6.1 24 42-67 2-25 (81)
19 PF02736 Myosin_N: Myosin N-te 45.0 41 0.00088 22.2 3.7 25 134-160 16-40 (42)
20 KOG4309|consensus 42.7 20 0.00043 31.7 2.4 26 27-52 117-148 (217)
21 PF06592 DUF1138: Protein of u 39.6 14 0.00029 27.9 0.7 16 195-210 51-68 (73)
22 PF12791 RsgI_N: Anti-sigma fa 36.1 72 0.0016 21.8 4.0 35 59-98 8-42 (56)
23 PRK14350 ligA NAD-dependent DN 30.7 86 0.0019 32.7 5.1 104 32-139 307-429 (669)
24 smart00532 LIGANc Ligase N fam 29.3 2E+02 0.0043 28.5 7.2 88 32-120 305-411 (441)
25 TIGR00575 dnlj DNA ligase, NAD 28.7 2E+02 0.0042 29.9 7.3 107 32-139 298-425 (652)
26 cd03690 Tet_II Tet_II: This su 28.4 2.4E+02 0.0053 20.8 6.6 26 40-66 3-28 (85)
27 COG0272 Lig NAD-dependent DNA 28.4 2.7E+02 0.0059 29.2 8.2 97 32-131 310-427 (667)
28 PRK07956 ligA NAD-dependent DN 28.4 3E+02 0.0064 28.8 8.5 107 32-139 310-438 (665)
29 PRK00913 multifunctional amino 26.8 1.8E+02 0.0039 29.2 6.4 59 41-100 233-334 (483)
30 COG1224 TIP49 DNA helicase TIP 26.7 3.2E+02 0.007 27.1 7.9 19 38-56 130-148 (450)
31 COG1545 Predicted nucleic-acid 26.3 2.1E+02 0.0045 23.7 5.9 32 56-90 85-118 (140)
32 TIGR00503 prfC peptide chain r 23.3 4.7E+02 0.01 26.4 8.7 85 40-124 293-405 (527)
33 PLN03107 eukaryotic translatio 21.8 2.8E+02 0.006 23.7 5.9 54 95-157 25-81 (159)
34 TIGR00484 EF-G translation elo 21.4 5.4E+02 0.012 26.6 8.9 84 40-124 307-417 (689)
35 PRK00741 prfC peptide chain re 21.2 6.5E+02 0.014 25.3 9.3 85 40-124 292-404 (526)
36 COG1945 Pyruvoyl-dependent arg 21.2 1.9E+02 0.0041 25.1 4.7 51 89-139 41-96 (163)
37 COG0298 HypC Hydrogenase matur 20.7 2.2E+02 0.0047 22.1 4.4 44 40-90 4-47 (82)
No 1
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=5.3e-105 Score=716.63 Aligned_cols=247 Identities=70% Similarity=1.188 Sum_probs=239.6
Q ss_pred CCccccccccCCCCcceeccccccCCCceeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccC
Q psy13959 1 MGRVIRAQRKGAGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPE 80 (248)
Q Consensus 1 mgk~~~~qr~Grg~~~r~~~~~~ggg~kyr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~e 80 (248)
|||+|++||+|||++||+++|++.+..+||.|||+|+..+++++|++|||||||||+||||+|+|++.|+++++||||||
T Consensus 1 MGk~~~~qrrGrgs~~r~~~~~~~~~~~yR~iDf~r~~~~~~g~V~~IeyDPnRsA~IAlv~~~d~~~~~g~~~YIlAp~ 80 (260)
T PTZ00180 1 MGRVIRAQRKGNGSVFKAHGHKRLGPAKLRILDYAERHGYIRGVVKDIEHDPGRGAPLARVEFRDPYKYKRVKELMVAPE 80 (260)
T ss_pred CCcccchhccCCCCcccCccccccCCccccccccccccCCcCEEEEEEEECCCCCceEEEEEecCCccccCceEEEEeeC
Confidence 99999999999999999999999999999999999987778999999999999999999999999876666789999999
Q ss_pred CCCcCcEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcC
Q psy13959 81 GMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPS 160 (248)
Q Consensus 81 g~~vGd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (248)
+|++||+|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|+++++++++++|||||||+++|++
T Consensus 81 gl~vGd~I~~g~~a~i~~GN~lpL~~IP~GT~IhNIE~~pG~GgklaRSAGt~A~ii~k~k~~~~~~vkLPSGe~r~v~~ 160 (260)
T PTZ00180 81 GMYTGQYVYCGAKAPLAIGNVLPLGQIPEGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSS 160 (260)
T ss_pred CCCCCCEEEeCCCCCCCCcCccCHhhCCCCCeEEEEeccCCCCceEEEecCCeEEEEEEcccCCEEEEECCCCCeEeECC
Confidence 99999999999999999999999999999999999999999999999999999999998766889999999999999999
Q ss_pred CCceeEEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCccccCCCCCCCeeeeeee
Q psy13959 161 ANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKVSVLLL 240 (248)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~r~a~pg~kvg~i~~ 240 (248)
+|+||||+|||.++.+++|+|||++||++++.+++||+|||||||||||||||||||++|+||||||+||||||||+|||
T Consensus 161 ~c~ATIG~Vsn~~~~~k~l~KAG~~~~~~~a~~~rwP~VRGVAMNPvDHPHGGGegk~~Gr~~tvsr~appg~kvg~iaa 240 (260)
T PTZ00180 161 LSRAMIGIVAGGGRIDKPVLKAGNAFHKYRGKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHPSTVSRHAPPGQKVGLIAA 240 (260)
T ss_pred CCeEEEEEccCCcchheeeccccchhhhhhCcCCCCCccccEeeCCccCCcCCCCCCCCCCCCCcCCCCCCcceeeeeec
Confidence 99999999999999999999999999999988999999999999999999999999999999999999999999999999
Q ss_pred eeecccc
Q psy13959 241 YIQGSSR 247 (248)
Q Consensus 241 ~rtg~~~ 247 (248)
|||||++
T Consensus 241 rrtg~~~ 247 (260)
T PTZ00180 241 RRTGLLR 247 (260)
T ss_pred ccccccc
Confidence 9999964
No 2
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=1e-101 Score=688.75 Aligned_cols=237 Identities=51% Similarity=0.867 Sum_probs=228.3
Q ss_pred CCccccccccCCC-CcceeccccccCCCceeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEcc
Q psy13959 1 MGRVIRAQRKGAG-SVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAP 79 (248)
Q Consensus 1 mgk~~~~qr~Grg-~~~r~~~~~~ggg~kyr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~ 79 (248)
|||+|++||+||| ++||.+++++.|..+|+-.| + ...++++|++|||||||||+||||+|+|+ +++|||||
T Consensus 1 Mgk~i~~qr~G~g~~~fr~~~~~r~g~~~~~~~~--~-~~~~~g~V~~IeyDPnRsa~IAlv~~~~g-----~~~YIiAp 72 (238)
T PRK09612 1 MGKRIISQRRGRGTPTFRSPSHRYKGPVKYPPLD--K-DGTLRGKVVDILHDPGRNAPVAKVKFENG-----EEFLILAP 72 (238)
T ss_pred CCceeeecccCCCCCcccCccccccccccccCcc--c-CCceeEEEEEEEECCCCCCeEEEEEeCCC-----CEEEEEcc
Confidence 9999999999999 59999999999999887766 3 34688999999999999999999999987 68899999
Q ss_pred CCCCcCcEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEc
Q psy13959 80 EGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIP 159 (248)
Q Consensus 80 eg~~vGd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~ 159 (248)
|+|++||+|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++|+ +++++|||||||+++|+
T Consensus 73 ~gl~~Gd~I~sg~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RSAGt~A~Ii~k~--~~~~~vkLPSGe~r~i~ 150 (238)
T PRK09612 73 EGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESRPGDGGKFARSSGTYALVVGHE--GDKVIVQLPSGKIKELN 150 (238)
T ss_pred CCCCCCCEEEeCCCCCCCCccccCHhhCCCCCEEEEEEecCCCCcceEEcCCCeEEEEEec--CCEEEEECCCCCeEEEC
Confidence 9999999999999999999999999999999999999999999999999999999999995 67999999999999999
Q ss_pred CCCceeEEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCccccCCCCCCCeeeeee
Q psy13959 160 SANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKVSVLL 239 (248)
Q Consensus 160 ~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~r~a~pg~kvg~i~ 239 (248)
++|+||||+|||.++.+++|+|||++||+.++++++||+||||||||||||||||||||+|+||||+|+||||||||+||
T Consensus 151 ~~c~AtiG~Vsn~~~~~~~lgKAG~~r~~~k~~~g~rP~VRGvAMNpvDHPHGGGeg~~~G~~stvsr~appg~kvg~ia 230 (238)
T PRK09612 151 PRCRATIGVVAGGGRKEKPFLKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQHPGRPSTVSRNAPPGRKVGHIA 230 (238)
T ss_pred CcCeEEEEEccCCccccceeeechhhhhhhhccCCCCCccCeEeeCCccCCcCCCCCCCCCCCCcccCCCCCCceeeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecccc
Q psy13959 240 LYIQGSSR 247 (248)
Q Consensus 240 ~~rtg~~~ 247 (248)
||||||++
T Consensus 231 arrtgr~~ 238 (238)
T PRK09612 231 ARRTGRRK 238 (238)
T ss_pred cccccCCC
Confidence 99999964
No 3
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-93 Score=637.56 Aligned_cols=230 Identities=45% Similarity=0.730 Sum_probs=221.5
Q ss_pred CCccccccccCCCCcceeccccccCCCc--eeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEc
Q psy13959 1 MGRVIRAQRKGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIA 78 (248)
Q Consensus 1 mgk~~~~qr~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA 78 (248)
|++.+++|+|| +.++++++|++++++ ||+|||+|++..+.++|++|||||||||+||||.|+|| +++||||
T Consensus 34 ~~~~~~~~gR~--n~G~iT~R~~ggghK~~yr~idfkr~k~~i~g~V~~IeyDP~RsA~IAlv~y~dG-----ek~yilA 106 (275)
T COG0090 34 MGKLIKSQGRN--NRGRITVRHRGGGHKRRYRLIDFKRNKDGIPGKVEDIEYDPNRSAPIALVVYEDG-----EKRYILA 106 (275)
T ss_pred hhccccccCCC--CCCCeeEEcCCCCcccceeccccccccCCccEEEEEEEECCCCCcceEEEEecCC-----CEEEEEc
Confidence 88999999554 667999999999986 99999999988999999999999999999999999998 7899999
Q ss_pred cCCCCcCcEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEE
Q psy13959 79 PEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVI 158 (248)
Q Consensus 79 ~eg~~vGd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i 158 (248)
||||++||+|++++.+++++||+|||.+||+||.|||||+.||+||||||||||||+|+.++ .+|++|+|||||.|.|
T Consensus 107 p~Gl~vGd~I~sG~~a~ik~GN~lpL~~IP~Gt~VhNVE~~pG~GGq~aRSaGtyA~vv~~~--~~y~~vrLpSGe~r~v 184 (275)
T COG0090 107 PEGLKVGDVIESGKDADIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGKE--GNYVIVRLPSGEMRKV 184 (275)
T ss_pred cCccccCCEEEeCCCCCcCCcceeeeccCCCCceEEeeeeccCCCceEEEeCCceEEEEEcc--CCEEEEECCCCCeEee
Confidence 99999999999999999999999999999999999999999999999999999999999996 7799999999999999
Q ss_pred cCCCceeEEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCC-CCCccccCC-CCCCCeee
Q psy13959 159 PSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHI-GKASTVKRG-TSAGRKVS 236 (248)
Q Consensus 159 ~~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~-g~ps~v~r~-a~pg~kvg 236 (248)
+++|+||||+|||.+|.+++|+|||++||++ +||+||||||||||||||||||||. |+|+|++++ ++|| ||+
T Consensus 185 ~~~CrATIGvV~n~~~~~~~lgKAGr~r~~g-----~rPtVRGvAMNpvDHPHGGGeg~~~ggk~p~~pwg~~~~G-kkt 258 (275)
T COG0090 185 LSECRATIGVVANGGHILKPLGKAGRARHKG-----KRPTVRGVAMNPVDHPHGGGEGQHPGGKPPTVPWGKPTPG-KKT 258 (275)
T ss_pred cccccEEEEEecCCccccceecccchhcCCc-----cCCccceeecCCCcCCCCCCCCCCCCCCCCCCCCCCCCCc-ccc
Confidence 9999999999999999999999999999995 5999999999999999999999999 889999999 9999 999
Q ss_pred eeeeeeecc
Q psy13959 237 VLLLYIQGS 245 (248)
Q Consensus 237 ~i~~~rtg~ 245 (248)
++++|||++
T Consensus 259 r~~~krt~~ 267 (275)
T COG0090 259 RIAAKRTGK 267 (275)
T ss_pred cccccccCc
Confidence 999999997
No 4
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=9.8e-85 Score=589.95 Aligned_cols=210 Identities=36% Similarity=0.608 Sum_probs=201.3
Q ss_pred cCCCCcceeccccccCCCc--eeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcCcE
Q psy13959 10 KGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQF 87 (248)
Q Consensus 10 ~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vGd~ 87 (248)
-||++++|++++|++||++ ||+|||+|....++++|++|||||||||+||||.|+|+ +++||||||+|++||+
T Consensus 39 ~GRnn~GrItvrhrGGG~kr~yR~IDf~r~~~~i~~~V~~IeyDP~Rsa~IAlv~~~~g-----~~~YIlAp~gl~~Gd~ 113 (273)
T CHL00052 39 KGRNNRGIITARHRGGGHKRLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLIHYGDG-----EKRYILHPRGLKIGDT 113 (273)
T ss_pred CCcCCCccEEEecccCCCccccceeccccccCCCcEEEEEEEECCCCCccEEEEEeCCC-----cEEEEEccCCCCCCCE
Confidence 4899999999999999984 99999999877889999999999999999999999987 7899999999999999
Q ss_pred EEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcCCCceeEE
Q psy13959 88 VYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVG 167 (248)
Q Consensus 88 I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG 167 (248)
|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++++ +++++|||||||+++|+++|+||||
T Consensus 114 I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggk~~RsAGt~A~ii~k~--~~~~~vkLPSGe~r~v~~~c~AtIG 191 (273)
T CHL00052 114 IVSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAKE--GKSATLKLPSGEVRLISKNCSATIG 191 (273)
T ss_pred EEeCCCCCCCcccccccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEec--CCEEEEECCCCCeEEECCcCeEEEE
Confidence 99999999999999999999999999999999999999999999999999995 6799999999999999999999999
Q ss_pred eeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCC-CCCCCCccccCCCCCCCe
Q psy13959 168 IVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNH-QHIGKASTVKRGTSAGRK 234 (248)
Q Consensus 168 ~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~-~~~g~ps~v~r~a~pg~k 234 (248)
+|||.+|.+++|+|||++||+ ++||+|||||||||||||||||| +++|+|++|+ |||+.
T Consensus 192 ~Vsn~~~~~~~lgKAG~~r~l-----g~rP~VRGvAMNpvDHPHGGGegkt~~Gr~~~vs---pwG~~ 251 (273)
T CHL00052 192 QVGNVDVNNKSLGKAGSKRWL-----GKRPKVRGVVMNPVDHPHGGGEGRAPIGRKKPVT---PWGKP 251 (273)
T ss_pred EccCCchhhcEecchhhhhcC-----CCCCcCCeEecCCccCCCCCCCccCCCCCcCCCC---cCccc
Confidence 999999999999999999999 57999999999999999999999 7889998898 88865
No 5
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=100.00 E-value=8.9e-84 Score=584.02 Aligned_cols=212 Identities=35% Similarity=0.595 Sum_probs=198.6
Q ss_pred cccCCCCcceeccccccCCCc--eeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcC
Q psy13959 8 QRKGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTG 85 (248)
Q Consensus 8 qr~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vG 85 (248)
.-.||+++||++++|++|+++ ||+|||+|+...++++|++|||||||||+||||.|+|+ +++||||||+|++|
T Consensus 37 ~~~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~g~V~~IeyDP~Rsa~IAlv~~~~g-----~~~YIlap~gl~~G 111 (273)
T TIGR01171 37 KTGGRNNRGRITSRHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYADG-----EKRYILAPKGLKVG 111 (273)
T ss_pred CCCCcCCCccEEEEEcCCCcccccceeecccccCCCcEEEEEEEeCCCCCcCEEEEEecCC-----cEEEEEccCCCCCC
Confidence 345788999999999999985 99999999877889999999999999999999999987 78999999999999
Q ss_pred cEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcCCCcee
Q psy13959 86 QFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAM 165 (248)
Q Consensus 86 d~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (248)
|+|++++++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++++ +++++|+|||||+++|+++|+||
T Consensus 112 d~I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k~--~~~~~vkLPSGe~r~i~~~c~At 189 (273)
T TIGR01171 112 DTVISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILAKE--GGYVTLRLPSGEMRMVLKECRAT 189 (273)
T ss_pred CEEEECCCCCCCCcCCcccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEec--CCEEEEECCCCCeEEECCcCeEE
Confidence 9999999999999999999999999999999999999999999999999999995 67999999999999999999999
Q ss_pred EEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCccccCCCCCCCe
Q psy13959 166 VGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRK 234 (248)
Q Consensus 166 IG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~r~a~pg~k 234 (248)
||+|||.++.+++|+|||++||+ ++||+|||||||||||||||||||+.|....++ |||+.
T Consensus 190 iG~Vsn~~~~~~~~gKAG~~r~l-----g~rP~VRGvAMNpvDHPHGGGegk~~~g~~~~s---pwG~~ 250 (273)
T TIGR01171 190 IGEVGNEDHNNIVLGKAGRSRWL-----GIRPTVRGVAMNPVDHPHGGGEGRTPGGRHPVT---PWGKP 250 (273)
T ss_pred EEEccCCchhccEeccchhheeC-----CCCCccccEecCcccCCCCCCCCcCCCCCCCCC---CCeee
Confidence 99999999999999999999999 579999999999999999999998754433455 88865
No 6
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=1.4e-83 Score=583.08 Aligned_cols=212 Identities=35% Similarity=0.597 Sum_probs=198.2
Q ss_pred cccCCCCcceeccccccCCCc--eeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcC
Q psy13959 8 QRKGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTG 85 (248)
Q Consensus 8 qr~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vG 85 (248)
.-.||+++||++++|++||++ ||+|||+|+..++.++|++|||||||||+||||.|+|+ +++||||||+|++|
T Consensus 39 ~~~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~~~V~~IeyDP~Rsa~IAlv~~~~g-----~~~YIlAp~gl~~G 113 (276)
T PRK09374 39 KSGGRNNNGRITVRHRGGGHKRKYRIIDFKRNKDGIPAKVERIEYDPNRSARIALLHYADG-----EKRYILAPKGLKVG 113 (276)
T ss_pred cCCCcCCCccEEEEecCCCccccccccchhhccCCCCEEEEEEEeCCCCCcCEEEEEecCC-----CEEEEEecCCCCCC
Confidence 345799999999999999984 99999999887889999999999999999999999987 78999999999999
Q ss_pred cEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcCCCcee
Q psy13959 86 QFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAM 165 (248)
Q Consensus 86 d~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (248)
|+|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++++ +++++|+|||||+++|+++|+||
T Consensus 114 d~I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k~--~~~~~vkLPSGe~r~i~~~c~At 191 (276)
T PRK09374 114 DTVVSGPDADIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAKE--GKYATLRLPSGEVRKVLAECRAT 191 (276)
T ss_pred CEEEeCCCCCCCccCccccccCCCCCEEEEEEecCCCCceeEeecCCeEEEEEec--CCEEEEECCCCCeEEEcccccEE
Confidence 9999999999999999999999999999999999999999999999999999995 67999999999999999999999
Q ss_pred EEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCccccCCCCCCCe
Q psy13959 166 VGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRK 234 (248)
Q Consensus 166 IG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~r~a~pg~k 234 (248)
||+|||.++.+++|+|||++||+ ++||+||||||||||||||||||+..|....++ |||+.
T Consensus 192 IG~Vsn~~~~~~~lgKAG~~r~l-----g~rP~VRGVAMNpvDHPHGGGegkt~~g~~~~s---pwG~~ 252 (276)
T PRK09374 192 IGEVGNEEHSNISLGKAGRSRWL-----GIRPTVRGVAMNPVDHPHGGGEGRTSGGRHPVT---PWGKP 252 (276)
T ss_pred EEeecCcchhhcchhhhhhheeC-----CCCCccccEecCcccCCCCCCCCcCCCCCCCCC---CCeee
Confidence 99999999999999999999999 579999999999999999999997664333455 88764
No 7
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=2.9e-83 Score=587.37 Aligned_cols=211 Identities=31% Similarity=0.478 Sum_probs=197.5
Q ss_pred cccCCCCcceeccccccCCCc--eeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcC
Q psy13959 8 QRKGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTG 85 (248)
Q Consensus 8 qr~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vG 85 (248)
...||+++||++++|++|||+ ||+|||+|+..+++++|++|||||||||+||||.|+|+ +++||||||||++|
T Consensus 70 ~~~GRnn~GrIT~rhRGGGhKr~YR~IDfkr~~~~i~g~V~~IeyDPnRsA~IALV~~~dg-----~~~YIlApeGl~vG 144 (317)
T PTZ00031 70 KNSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPSRSAHIALLQYEDG-----VLSYILAPLLLRPG 144 (317)
T ss_pred cCCCCCCCceEEEEeecCCcCccccccccccccCCcCEEEEEEEeCCCCCCcEEEEEecCC-----cEEEEEccCCCCCC
Confidence 345799999999999999974 99999999877889999999999999999999999987 68899999999999
Q ss_pred cEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcCCCcee
Q psy13959 86 QFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAM 165 (248)
Q Consensus 86 d~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (248)
|+|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++|+ +++++|+|||||+++|+++|+||
T Consensus 145 d~I~sg~~a~i~~GN~lPL~~IP~GT~IhNIE~~pG~Ggkl~RSAGt~A~Ii~k~--~~~~~VkLPSGe~r~i~~~C~AT 222 (317)
T PTZ00031 145 DKIIASKYANINPGNSLPLRNIPVGSIVHNVEMRPGAGGQIIRAGGTYATVVSKD--EQFATLKLKSTEIRKFPLDCWAT 222 (317)
T ss_pred CEEEeCCCCCCCccCccccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEcc--CCEEEEECCCCCEEEECccCeEE
Confidence 9999999999999999999999999999999999999999999999999999996 67999999999999999999999
Q ss_pred EEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCC-CCCccccCCCCCCCe
Q psy13959 166 VGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHI-GKASTVKRGTSAGRK 234 (248)
Q Consensus 166 IG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~-g~ps~v~r~a~pg~k 234 (248)
||+|||.+|.+++|+|||++||+ ++||+||||||||||||||||||++. |+| .++ |||+.
T Consensus 223 IG~Vsn~~~~~k~lgKAG~~Rwl-----g~RP~VRGVAMNPVDHPHGGGeGkt~~gr~-p~s---pWG~~ 283 (317)
T PTZ00031 223 IGQVSNLEHHMRILGKAGVNRWL-----GKRPVVRGVAMNPSKHPHGGGTSKKGTKRP-KCS---LWGIC 283 (317)
T ss_pred EEEccCCccccceeccchhhhcC-----CCCCCcccCccCCccCCCCCCCCCCCCCCC-CCC---CCccc
Confidence 99999999999999999999999 57999999999999999999999754 543 355 77754
No 8
>KOG2309|consensus
Probab=100.00 E-value=1.8e-69 Score=474.54 Aligned_cols=241 Identities=79% Similarity=1.290 Sum_probs=232.2
Q ss_pred CCccccccccCCCCcceeccccccCCCceeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccC
Q psy13959 1 MGRVIRAQRKGAGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPE 80 (248)
Q Consensus 1 mgk~~~~qr~Grg~~~r~~~~~~ggg~kyr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~e 80 (248)
||+.++.||+ -|+.|... +++.+..+ +..||....+.+++.|++|.|||.|-||+|.+.|-| +......++|.|
T Consensus 1 MG~~~r~qrk-~g~vf~~h-k~r~~~~~-r~~d~~~~~~~~~g~v~~iih~~~rgapla~v~frd---~~~~~~~F~a~e 74 (248)
T KOG2309|consen 1 MGRVIRAQRK-AGSIFKAH-KHRKGAAK-RTLDYAERHGYIKGVVKDIIHDPGRGAPLAKVVFRD---YKKDKELFIAAE 74 (248)
T ss_pred CCceeeeeec-cccccccc-ccccCccc-chhhhhhcccceeeeEEEEeccCCCCcccceeeecc---ccceeEEEeccc
Confidence 9999999999 46888888 99999888 999998888889999999999999999999999988 345677899999
Q ss_pred CCCcCcEEEEecccccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcC
Q psy13959 81 GMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPS 160 (248)
Q Consensus 81 g~~vGd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (248)
+|+.||.++++.++.+.+||++|+.++|+|+.|||+|..++|.+.|+|++|+||++|+++.|.+.+.|+||||..+.+++
T Consensus 75 g~~tgq~~~~g~ka~~~ignv~~~~s~peg~~v~~ve~~~gdrg~lar~sGnya~vIaHn~dt~kTrIkLPsgaKKvV~S 154 (248)
T KOG2309|consen 75 GMYTGQFVYCGKKAQLNIGNVLPVGSMPEGTIVCNVEEKPGDRGALARASGNYAIVIAHNPDTKKTRIKLPSGAKKVVQS 154 (248)
T ss_pred cceecceecCCccccccccceeeccccccceEEEEeeccCchhhhHHhhcCceeEEEecCccccceEEecCCCccceecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeEEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCccccCCCCCCCeeeeeee
Q psy13959 161 ANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKVSVLLL 240 (248)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~r~a~pg~kvg~i~~ 240 (248)
.|+|+||+|+++++.+++|+|||+.|++++.|++.||+||||||||||||||||+|||+|+|||+.|++|+|||||+|||
T Consensus 155 ~~RamIG~vAggG~~dKp~lKag~a~~K~~~Krn~wPrvRGVAMnPVeHphGGgnhqhig~~stv~r~~~~~~kvgliaa 234 (248)
T KOG2309|consen 155 ACRAMIGVVAGGGRTDKPLLKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPHGGGNHQHIGKPSTVRRDASAGQKVGLIAA 234 (248)
T ss_pred ccceEEEEecCCccccchhhhhhhHHHHhhhhcCCchhhcceecccccCCCCCCcccccCCcccccccCcccceeeEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecccc
Q psy13959 241 YIQGSSR 247 (248)
Q Consensus 241 ~rtg~~~ 247 (248)
||||+.|
T Consensus 235 rrtg~~r 241 (248)
T KOG2309|consen 235 RRTGRLR 241 (248)
T ss_pred EEEeeec
Confidence 9999976
No 9
>KOG0438|consensus
Probab=100.00 E-value=4.6e-62 Score=442.12 Aligned_cols=206 Identities=33% Similarity=0.491 Sum_probs=190.6
Q ss_pred ccCCCCcceeccccccCCCc--eeeeecccccCCc-----eEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCC
Q psy13959 9 RKGAGSVFRSHNKHRKGAPK--LRSLDFAERHGYL-----KGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEG 81 (248)
Q Consensus 9 r~Grg~~~r~~~~~~ggg~k--yr~IDf~r~~~~~-----~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg 81 (248)
..||+.++|+++||+||+|| ||||||.|..+.. ++.|++|+|||||||+||||++.++ +++||||+||
T Consensus 62 ~~GRd~tGriv~~h~GGGhKq~yr~idF~R~~p~~~~~~~~e~v~~i~yDP~Rs~~iaLv~~~~~-----~~~~Ila~eg 136 (312)
T KOG0438|consen 62 GLGRDETGRIVVRHIGGGHKQRYRMIDFARPRPIEQGTTTEERVIEIEYDPGRSAKIALVAGGTG-----ELRYILATEG 136 (312)
T ss_pred CCCCccccceEEEEecCceeeeeeEeeeccCCCccccccccceEEEEEECCCccccEEEEeccCC-----CeeEEEEecC
Confidence 34888999999999999986 9999999876543 3599999999999999999998754 6899999999
Q ss_pred CCcCcEEEEecccc-----cccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceE
Q psy13959 82 MYTGQFVYCGKKAT-----LQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKK 156 (248)
Q Consensus 82 ~~vGd~I~~g~~~~-----~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r 156 (248)
|++||+|.++.+.+ .+.||++||.+||+||.|||+|+.|+.+++|||||||+|+|+++. +++++|+|||++.+
T Consensus 137 m~aGD~i~ss~~i~~~av~~~~Gna~Pl~~lp~GT~ih~~e~~p~~~~~f~raAGt~a~ilak~--~~~aiv~Lps~r~~ 214 (312)
T KOG0438|consen 137 LKAGDTILSSRKIPFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGTSATILAKA--GKFAIVQLPSKRER 214 (312)
T ss_pred CCCCCccccccccccccccccCCCceeecccchhhhhhhhccCCCcchhhhhhcCchhhhhhcC--CCceeEEccccchh
Confidence 99999999988754 799999999999999999999999999999999999999999996 57999999999999
Q ss_pred EEcCCCceeEEeeecCCccccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCCCCCCCCCcccc
Q psy13959 157 VIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVK 226 (248)
Q Consensus 157 ~i~~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~~~~~g~ps~v~ 226 (248)
.++.+|+||||+|||.+|+.+.+||||++||+ ++||.||||+||++||||||+.+..++....++
T Consensus 215 ~~~~tC~ATvGrvsni~~~~r~~GkAgr~rwl-----G~Rp~vrg~~~s~~~H~kgg~~gr~i~~~~P~~ 279 (312)
T KOG0438|consen 215 SVLRTCVATVGRVSNIDHNHRILGKAGRSRWL-----GKRPQVRGVLMSGLDHPKGGGKGRKIGRKKPVT 279 (312)
T ss_pred hhhhhhheeeccccccccccceecccchhhhc-----ccCcccccccccCccCCCCCCccccccCCCCCC
Confidence 99999999999999999999999999999999 579999999999999999999997787765555
No 10
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=100.00 E-value=2.4e-59 Score=384.52 Aligned_cols=129 Identities=47% Similarity=0.793 Sum_probs=122.6
Q ss_pred cccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEeecCCCCeEEEEccCCceEEEcCCCceeEEeeecCCcc
Q psy13959 96 LQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRI 175 (248)
Q Consensus 96 ~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG~vsn~~~~ 175 (248)
+++||++||.+||+||+|||||++||+|++|||||||||+|++|+ +++++|||||||+++|+++|+||||+|||.++.
T Consensus 1 i~~Gn~~pL~~ip~Gt~I~nIE~~pg~g~~~~RaAGt~a~ii~k~--~~~~~ikLPSG~~k~v~~~c~AtiG~vsn~~~~ 78 (130)
T PF03947_consen 1 IKIGNSLPLGNIPIGTIIHNIELKPGDGGKLARAAGTYAQIISKE--GNYVVIKLPSGEIKLVSSNCRATIGRVSNGGHK 78 (130)
T ss_dssp SSTTSEEEGGGSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEEE--SSEEEEEETTSEEEEEETTSEEEESCBSSTTGG
T ss_pred CCCccchhHhhCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEec--cceeEEEecCCCeEeecccceEEEEEecCcccc
Confidence 589999999999999999999999999999999999999999997 579999999999999999999999999999999
Q ss_pred ccceeccccchhhhhhcCCCCceeceeecCCCCCCCCCCC-CCCCCCCccccCCCCC
Q psy13959 176 DKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGN-HQHIGKASTVKRGTSA 231 (248)
Q Consensus 176 ~~~lgKAG~~r~~~~~~~~~rP~VRGvAMNpvDHPhGGg~-~~~~g~ps~v~r~a~p 231 (248)
+++++|||++||+ ++||+||||||||||||||||| ++++|+|++++++++|
T Consensus 79 ~~~~~KAG~~r~~-----g~rP~VRGvamNpvdHPhGGG~g~~~~gr~~~~s~wg~p 130 (130)
T PF03947_consen 79 EKKLGKAGRNRWL-----GKRPKVRGVAMNPVDHPHGGGEGKTSGGRPPPVSPWGKP 130 (130)
T ss_dssp GSB-SSHHHHHHT-----CCSSS-SGTCSTTTTSSTCTSSSSSSTSSSSEBTTTSSS
T ss_pred chhhhhhhhcccc-----ccCccccceeeccccCcCCCCCCcCCCCCCCCCCCCCCC
Confidence 9999999999999 5699999999999999999999 6899999999988887
No 11
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=99.94 E-value=3e-27 Score=178.13 Aligned_cols=75 Identities=39% Similarity=0.691 Sum_probs=68.5
Q ss_pred CCCCcceeccccccCCC--ceeeeecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcCcEE
Q psy13959 11 GAGSVFRSHNKHRKGAP--KLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFV 88 (248)
Q Consensus 11 Grg~~~r~~~~~~ggg~--kyr~IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vGd~I 88 (248)
|||++||+++||++|++ +||+|||+|....++++|++|+|||+|||+||||+|+|| +++||||||||++||+|
T Consensus 1 GR~~~gri~~~~rggg~k~~yr~id~~r~~~~~~g~V~~i~~DP~Rsa~iAlV~~~~g-----~~~yiiA~eg~~vGd~I 75 (77)
T PF00181_consen 1 GRNNSGRITSRHRGGGHKRRYRIIDFKRNKGNIKGIVIDIEYDPNRSAPIALVKYEDG-----EKRYIIAPEGMKVGDII 75 (77)
T ss_dssp TSSSTSSBSSSTCS-SST-EEE-BBSSTTTTSEEEEEEEEEEETTTSSEEEEEEETTS-----EEEEEEEBTTEBTTEEE
T ss_pred CcCCCCCeeeecccccccceeccccccccCCCCcEEEEEEEecCCcCccEEEEEecCC-----cEEEEEeECCCcCCCEE
Confidence 78988999999999987 499999999777889999999999999999999999986 78999999999999999
Q ss_pred EE
Q psy13959 89 YC 90 (248)
Q Consensus 89 ~~ 90 (248)
+|
T Consensus 76 ~s 77 (77)
T PF00181_consen 76 ES 77 (77)
T ss_dssp EE
T ss_pred EC
Confidence 86
No 12
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=86.69 E-value=0.37 Score=21.78 Aligned_cols=8 Identities=75% Similarity=1.294 Sum_probs=6.4
Q ss_pred CCCCCCCC
Q psy13959 210 PHGGGNHQ 217 (248)
Q Consensus 210 PhGGg~~~ 217 (248)
|||||-+|
T Consensus 1 phgG~Wgq 8 (8)
T PF03991_consen 1 PHGGGWGQ 8 (8)
T ss_pred CCCCcCCC
Confidence 89998765
No 13
>KOG0438|consensus
Probab=85.37 E-value=7.4 Score=36.71 Aligned_cols=103 Identities=15% Similarity=0.148 Sum_probs=68.6
Q ss_pred cccccCCCCcceeccccccCCC----ceeeeecccccCCceEEEEEEEeCC-CcccceEEEEecCCCccCCceEEEEccC
Q psy13959 6 RAQRKGAGSVFRSHNKHRKGAP----KLRSLDFAERHGYLKGVVRDIIHDP-GRGAPLAVVHFRNPYKFKTNKELFIAPE 80 (248)
Q Consensus 6 ~~qr~Grg~~~r~~~~~~ggg~----kyr~IDf~r~~~~~~g~V~~I~yDP-~Rsa~IAlv~~~dg~~~~~~~~yilA~e 80 (248)
.-|..++....++++-+.+++. ....+|.++..+ ...+|+.++||+ +|+.-.+++...-|.-- .++|-+-
T Consensus 13 ~~~~~~~~~~a~i~~~~~~t~~~r~~l~~~~~l~~~~p-~~~~~~~~~~~~~GRd~tGriv~~h~GGGh--Kq~yr~i-- 87 (312)
T KOG0438|consen 13 TLKSAGRTVSARITVLKPGTPSLRNGLLQQPDLKKSTP-SRPLVESLKINGLGRDETGRIVVRHIGGGH--KQRYRMI-- 87 (312)
T ss_pred ccccCCCcccceeeecccCCccccCcccccchhhhcCC-CcceeeeEEecCCCCccccceEEEEecCce--eeeeeEe--
Confidence 4455666667788888888874 255566655543 468999999999 99999998876554322 2334210
Q ss_pred CCCcCcEEEEecccccccCCcccccCCCCC----CeeeeeeeecCCCceEeecCCC
Q psy13959 81 GMYTGQFVYCGKKATLQIGNVMPVGGMPEG----TIVCNLEEKTGDRGRLARASGN 132 (248)
Q Consensus 81 g~~vGd~I~~g~~~~~~~Gn~lpL~~IP~G----t~I~NIE~~pg~ggklaRsAGt 132 (248)
|+.. -.-+-.+ ..|..||.-|+.-+++|-.|+.
T Consensus 88 -----dF~R--------------~~p~~~~~~~~e~v~~i~yDP~Rs~~iaLv~~~ 124 (312)
T KOG0438|consen 88 -----DFAR--------------PRPIEQGTTTEERVIEIEYDPGRSAKIALVAGG 124 (312)
T ss_pred -----eecc--------------CCCccccccccceEEEEEECCCccccEEEEecc
Confidence 2221 1111222 2788999999999999999987
No 14
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=63.50 E-value=29 Score=25.42 Aligned_cols=25 Identities=28% Similarity=0.502 Sum_probs=18.5
Q ss_pred eEEEEEEEeCCCcccceEEEEecCCC
Q psy13959 42 KGVVRDIIHDPGRGAPLAVVHFRNPY 67 (248)
Q Consensus 42 ~g~V~~I~yDP~Rsa~IAlv~~~dg~ 67 (248)
.+.|-+++|||.. ..||+++.-+|.
T Consensus 2 ~a~VfK~~~d~~~-g~i~~~Ri~sGt 26 (83)
T cd04092 2 CALAFKVVHDPQR-GPLTFVRVYSGT 26 (83)
T ss_pred EEEEEecccCCCC-CeEEEEEEecCE
Confidence 4778999999973 467777766664
No 15
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=61.51 E-value=39 Score=25.05 Aligned_cols=25 Identities=28% Similarity=0.377 Sum_probs=18.1
Q ss_pred eEEEEEEEeCCCcccceEEEEecCCC
Q psy13959 42 KGVVRDIIHDPGRGAPLAVVHFRNPY 67 (248)
Q Consensus 42 ~g~V~~I~yDP~Rsa~IAlv~~~dg~ 67 (248)
.+.|-+++|||... .||+++.-+|.
T Consensus 2 ~~~Vfk~~~d~~~G-~i~~~Rv~sG~ 26 (86)
T cd03699 2 RALIFDSWYDPYRG-VIALVRVFDGT 26 (86)
T ss_pred EEEEEEeeccCCCC-EEEEEEEEcCE
Confidence 47899999999653 56777666663
No 16
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=55.50 E-value=65 Score=23.58 Aligned_cols=25 Identities=12% Similarity=-0.029 Sum_probs=18.4
Q ss_pred eEEEEEEEeCCCcccceEEEEecCCC
Q psy13959 42 KGVVRDIIHDPGRGAPLAVVHFRNPY 67 (248)
Q Consensus 42 ~g~V~~I~yDP~Rsa~IAlv~~~dg~ 67 (248)
.+.|-+++|||.. ..||+++.-+|.
T Consensus 2 ~~~vfk~~~d~~~-g~i~~~Rv~sG~ 26 (86)
T cd03691 2 QMLVTTLDYDDYV-GRIAIGRIFRGT 26 (86)
T ss_pred eEEEEEeEecCCC-CeEEEEEEEeCE
Confidence 4779999999965 347777766663
No 17
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=52.71 E-value=56 Score=23.71 Aligned_cols=25 Identities=32% Similarity=0.357 Sum_probs=17.7
Q ss_pred eEEEEEEEeCCCcccceEEEEecCCC
Q psy13959 42 KGVVRDIIHDPGRGAPLAVVHFRNPY 67 (248)
Q Consensus 42 ~g~V~~I~yDP~Rsa~IAlv~~~dg~ 67 (248)
.+.|-+++|||.+. .+|+++..+|.
T Consensus 2 ~a~Vfk~~~d~~~G-~~~~~Rv~sG~ 26 (83)
T cd04088 2 VALVFKTIHDPFVG-KLSFVRVYSGT 26 (83)
T ss_pred EEEEEEcccCCCCc-eEEEEEEecCE
Confidence 46789999999554 36777665663
No 18
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=51.34 E-value=66 Score=23.46 Aligned_cols=24 Identities=8% Similarity=0.014 Sum_probs=19.4
Q ss_pred eEEEEEEEeCCCcccceEEEEecCCC
Q psy13959 42 KGVVRDIIHDPGRGAPLAVVHFRNPY 67 (248)
Q Consensus 42 ~g~V~~I~yDP~Rsa~IAlv~~~dg~ 67 (248)
.+.|-.++|||. ..||+++.-+|.
T Consensus 2 ~a~vfK~~~~~~--G~i~~~Rv~sG~ 25 (81)
T cd04091 2 VGLAFKLEEGRF--GQLTYMRIYQGK 25 (81)
T ss_pred eEEEEEeecCCC--CCEEEEEEecCE
Confidence 477889999985 889999877773
No 19
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=45.00 E-value=41 Score=22.16 Aligned_cols=25 Identities=16% Similarity=0.325 Sum_probs=20.0
Q ss_pred EEEEeecCCCCeEEEEccCCceEEEcC
Q psy13959 134 ATVIAHNPDTKRTRVKLPSGAKKVIPS 160 (248)
Q Consensus 134 A~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (248)
|.|+... ++.++|++.+|+.+.++.
T Consensus 16 g~I~~~~--g~~vtV~~~~G~~~tv~~ 40 (42)
T PF02736_consen 16 GEIIEEE--GDKVTVKTEDGKEVTVKK 40 (42)
T ss_dssp EEEEEEE--SSEEEEEETTTEEEEEEG
T ss_pred EEEEEEc--CCEEEEEECCCCEEEeCC
Confidence 5677664 668999999999998865
No 20
>KOG4309|consensus
Probab=42.72 E-value=20 Score=31.66 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=19.5
Q ss_pred Cceeeeecccc------cCCceEEEEEEEeCC
Q psy13959 27 PKLRSLDFAER------HGYLKGVVRDIIHDP 52 (248)
Q Consensus 27 ~kyr~IDf~r~------~~~~~g~V~~I~yDP 52 (248)
.+|-.-||-=. .+.++|++++|||||
T Consensus 117 ~ry~Y~Df~IkvGtvTmg~tvKGi~vEIEY~p 148 (217)
T KOG4309|consen 117 TRYQYCDFLIKVGTVTMGPTVKGISVEIEYGP 148 (217)
T ss_pred ceeeecceEEEEcceEeccccceEEEEEeeCC
Confidence 56777777422 236889999999999
No 21
>PF06592 DUF1138: Protein of unknown function (DUF1138); InterPro: IPR009515 This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=39.56 E-value=14 Score=27.93 Aligned_cols=16 Identities=44% Similarity=1.082 Sum_probs=12.7
Q ss_pred CCceece--eecCCCCCC
Q psy13959 195 CWPKVRG--VAMNPVEHP 210 (248)
Q Consensus 195 ~rP~VRG--vAMNpvDHP 210 (248)
-||+.-| |+|||++|-
T Consensus 51 aWPR~agpPVvmNPisrq 68 (73)
T PF06592_consen 51 AWPREAGPPVVMNPISRQ 68 (73)
T ss_pred hCcccCCCCeeecccccc
Confidence 4887766 899999873
No 22
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=36.10 E-value=72 Score=21.83 Aligned_cols=35 Identities=20% Similarity=0.123 Sum_probs=23.6
Q ss_pred EEEEecCCCccCCceEEEEccCCCCcCcEEEEeccccccc
Q psy13959 59 AVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQI 98 (248)
Q Consensus 59 Alv~~~dg~~~~~~~~yilA~eg~~vGd~I~~g~~~~~~~ 98 (248)
|.|--+|| +.-.|-.+.++++||.|+.........
T Consensus 8 aiVlT~dG-----eF~~ik~~~~~~vG~eI~~~~~~~~~~ 42 (56)
T PF12791_consen 8 AIVLTPDG-----EFIKIKRKPGMEVGQEIEFDEKDIINK 42 (56)
T ss_pred EEEEcCCC-----cEEEEeCCCCCcccCEEEEechhhccc
Confidence 44544565 555677788899999998765544333
No 23
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=30.66 E-value=86 Score=32.73 Aligned_cols=104 Identities=13% Similarity=0.140 Sum_probs=60.0
Q ss_pred eecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCC-ceEE-------EEccCCCCcCcEEEEecc----------
Q psy13959 32 LDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKT-NKEL-------FIAPEGMYTGQFVYCGKK---------- 93 (248)
Q Consensus 32 IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~-~~~y-------ilA~eg~~vGd~I~~g~~---------- 93 (248)
|=||...+...-+|.+|++..+||.-|.-|...++....+ ..+. .|.-.++.+||.|....-
T Consensus 307 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~v 386 (669)
T PRK14350 307 MAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELV 386 (669)
T ss_pred EEEcCCCceeEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceeee
Confidence 4455445556789999999999997766554333311000 0000 345688999999975421
Q ss_pred -cccccCCcccccCCCCCCeeeeeeeecCCCceEeecCCCeEEEEee
Q psy13959 94 -ATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAH 139 (248)
Q Consensus 94 -~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAGt~A~Ii~k 139 (248)
.+..+++ ..+|.-+..|+-++.-+.-..+|-...+-|+++.+
T Consensus 387 ~~~~r~~~----~~~P~~CP~C~s~l~~~~~~~~C~n~~C~aq~~~~ 429 (669)
T PRK14350 387 IEKLSVGF----FKIPDNCPSCKTALIKEGAHLFCVNNHCPSVIVER 429 (669)
T ss_pred cccccCCC----CCCCCCCCCCCCEeeeCCEEEEECCCCCHHHHHhh
Confidence 1223344 34799888888877543223334333354555543
No 24
>smart00532 LIGANc Ligase N family.
Probab=29.32 E-value=2e+02 Score=28.51 Aligned_cols=88 Identities=18% Similarity=0.138 Sum_probs=52.9
Q ss_pred eecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCC-ceEE-------EEccCCCCcCcEEEEecc--c-------
Q psy13959 32 LDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKT-NKEL-------FIAPEGMYTGQFVYCGKK--A------- 94 (248)
Q Consensus 32 IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~-~~~y-------ilA~eg~~vGd~I~~g~~--~------- 94 (248)
|=||...+...-+|.+|++..+||.-|.-|...++....+ .-+. .|.-.++.+||.|..... .
T Consensus 305 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLhN~~~i~~~~i~iGd~V~V~raGdVIP~I~~v 384 (441)
T smart00532 305 IAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVVGV 384 (441)
T ss_pred EEECCCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEEEEecccCCHHHHHHcCCCCCCEEEEEECCCcCcceeec
Confidence 5565555566789999999999996665444333210000 0011 356789999999976432 1
Q ss_pred --ccccCCcccccCCCCCCeeeeeeeec
Q psy13959 95 --TLQIGNVMPVGGMPEGTIVCNLEEKT 120 (248)
Q Consensus 95 --~~~~Gn~lpL~~IP~Gt~I~NIE~~p 120 (248)
+...++..+ -.+|.-+.+|+=++..
T Consensus 385 v~~~r~~~~~~-~~~P~~CP~C~s~l~~ 411 (441)
T smart00532 385 VKEKRPGDERE-IEMPTHCPSCGSELVR 411 (441)
T ss_pred ccccCCCCCcc-CcCCCCCCCCCCEeEe
Confidence 112344433 3588888888877653
No 25
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=28.71 E-value=2e+02 Score=29.95 Aligned_cols=107 Identities=13% Similarity=0.095 Sum_probs=62.1
Q ss_pred eecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCC-ceEE-------EEccCCCCcCcEEEEecc--c-------
Q psy13959 32 LDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKT-NKEL-------FIAPEGMYTGQFVYCGKK--A------- 94 (248)
Q Consensus 32 IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~-~~~y-------ilA~eg~~vGd~I~~g~~--~------- 94 (248)
|=||...+...-+|.+|++..+||.-|.-|...++....+ ..+. .|.-.++.+||.|..... .
T Consensus 298 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~~VsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~v 377 (652)
T TIGR00575 298 IAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKVVRV 377 (652)
T ss_pred EEEcCCCceeeEEEEEEEEecCCCceeeeEEEEeeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCcCceeeee
Confidence 4455445556779999999999996665444333310000 0000 345789999999976432 1
Q ss_pred --ccccCCcccccCCCCCCeeeeeeeecCCCc--eEeecCCCeEEEEee
Q psy13959 95 --TLQIGNVMPVGGMPEGTIVCNLEEKTGDRG--RLARASGNYATVIAH 139 (248)
Q Consensus 95 --~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~gg--klaRsAGt~A~Ii~k 139 (248)
+...++..|+ .+|.-+.+|+=++..-+++ .+|-...+-|+++.+
T Consensus 378 v~~~r~~~~~~~-~~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~ 425 (652)
T TIGR00575 378 LLEKRTGSERPI-RFPTHCPSCGSPLVKIEEEAVIRCPNLNCPAQRVER 425 (652)
T ss_pred ccccCCCCCCCC-CCCCCCCCCCCEeEecCCcEEEEECCCCCHHHHHHH
Confidence 1224555544 5899999999666543333 344444455566543
No 26
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=28.45 E-value=2.4e+02 Score=20.76 Aligned_cols=26 Identities=27% Similarity=0.243 Sum_probs=18.7
Q ss_pred CceEEEEEEEeCCCcccceEEEEecCC
Q psy13959 40 YLKGVVRDIIHDPGRGAPLAVVHFRNP 66 (248)
Q Consensus 40 ~~~g~V~~I~yDP~Rsa~IAlv~~~dg 66 (248)
...+.|-.++|||.. ..||.++.-.|
T Consensus 3 p~~~~Vfkv~~d~~~-G~la~~RV~sG 28 (85)
T cd03690 3 ELSGTVFKIERDDKG-ERLAYLRLYSG 28 (85)
T ss_pred CcEEEEEEeEECCCC-CeEEEEEEccC
Confidence 356899999999954 46676665555
No 27
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=28.43 E-value=2.7e+02 Score=29.23 Aligned_cols=97 Identities=19% Similarity=0.209 Sum_probs=67.3
Q ss_pred eecccccCCceEEEEEEEeCCCcccceEEEEecCCC----------ccCCceEEEEccCCCCcCcEEEEecc--------
Q psy13959 32 LDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPY----------KFKTNKELFIAPEGMYTGQFVYCGKK-------- 93 (248)
Q Consensus 32 IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~----------~~~~~~~yilA~eg~~vGd~I~~g~~-------- 93 (248)
|=||.......-+|.+|+..=+||.-|.-|...++. ...+. . .|+-.++.+||.|....-
T Consensus 310 iAyKFpa~e~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~-d-~I~rkdIrIGDtV~V~kAGdVIP~V~ 387 (667)
T COG0272 310 IAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNV-D-EIKRKDIRIGDTVVVRKAGDVIPQVV 387 (667)
T ss_pred eeecCCchheeeEEEEEEEecCCceeeeeeEEEEeEEECCEEEEEeecCCH-H-HHHhcCCCCCCEEEEEecCCCCccee
Confidence 444433445567899999999999877655443331 01111 1 345789999999976431
Q ss_pred ---cccccCCcccccCCCCCCeeeeeeeecCCCceEeecCC
Q psy13959 94 ---ATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASG 131 (248)
Q Consensus 94 ---~~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsAG 131 (248)
.+..++|..|+. +|.-+.+|+=++....+....|.-+
T Consensus 388 ~Vv~e~R~~~~~~~~-~P~~CP~C~s~l~r~~~e~~~rC~n 427 (667)
T COG0272 388 GVVLEKRPGNEKPIP-FPTHCPVCGSELVREEGEVVIRCTN 427 (667)
T ss_pred eeecccCCCCCCCCC-CCCCCCCCCCeeEeccCceeEecCC
Confidence 355789988887 9999999998888777777777665
No 28
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=28.36 E-value=3e+02 Score=28.75 Aligned_cols=107 Identities=16% Similarity=0.111 Sum_probs=63.3
Q ss_pred eecccccCCceEEEEEEEeCCCcccceEEEEecCCCccCC-ceEE-------EEccCCCCcCcEEEEecc--c-------
Q psy13959 32 LDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKT-NKEL-------FIAPEGMYTGQFVYCGKK--A------- 94 (248)
Q Consensus 32 IDf~r~~~~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~-~~~y-------ilA~eg~~vGd~I~~g~~--~------- 94 (248)
|=||...+...-+|.+|++..+||.-|.-|...++....+ ..+. .|.-.++.+||.|....- .
T Consensus 310 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~v 389 (665)
T PRK07956 310 IAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIERKDIRIGDTVVVRRAGDVIPEVVGV 389 (665)
T ss_pred eEecCCCceeEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEECCCccceeeee
Confidence 4455445556789999999999997776554434321000 0000 345678999999976432 1
Q ss_pred --ccccCCcccccCCCCCCeeeeeeeecCCCceEeecC---CCeEEEEee
Q psy13959 95 --TLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARAS---GNYATVIAH 139 (248)
Q Consensus 95 --~~~~Gn~lpL~~IP~Gt~I~NIE~~pg~ggklaRsA---Gt~A~Ii~k 139 (248)
+..+++.-| -.+|.-+.+|+=++..-+++...|.- .+-|+++.+
T Consensus 390 v~~~r~~~~~~-~~~P~~CP~Cgs~l~~~~~~~~~~C~n~~~C~aq~~~~ 438 (665)
T PRK07956 390 VLEKRPGDERE-IVMPTHCPVCGSELVRVEGEAVLRCTNGLSCPAQLKER 438 (665)
T ss_pred ecccCCCCCcc-CcCCCCCCCCCCEeEecCCCeEEECCCCCCCHHHHHHH
Confidence 223354444 35899999998776544444444433 355666654
No 29
>PRK00913 multifunctional aminopeptidase A; Provisional
Probab=26.81 E-value=1.8e+02 Score=29.25 Aligned_cols=59 Identities=19% Similarity=0.174 Sum_probs=38.3
Q ss_pred ceEEEEEEEeCCCcccceEEE----EecCCC-ccC--------------------------------CceEEEEccCC--
Q psy13959 41 LKGVVRDIIHDPGRGAPLAVV----HFRNPY-KFK--------------------------------TNKELFIAPEG-- 81 (248)
Q Consensus 41 ~~g~V~~I~yDP~Rsa~IAlv----~~~dg~-~~~--------------------------------~~~~yilA~eg-- 81 (248)
.+-.++.++|.|.. .+|+|| .|+.|. +.| +-.-++.++||
T Consensus 233 ~~prli~l~Y~g~~-~~i~LVGKGITFDsGG~slKp~~~M~~MK~DM~GAAaVlga~~aia~lkl~vnV~~v~~l~ENm~ 311 (483)
T PRK00913 233 NPPRLIVLEYKGGK-KPIALVGKGLTFDSGGISLKPAAGMDEMKYDMGGAAAVLGTMRALAELKLPVNVVGVVAACENMP 311 (483)
T ss_pred CCCeEEEEEECCCC-CeEEEEcCceEecCCCccCCCCcChhhcccccHhHHHHHHHHHHHHHcCCCceEEEEEEeeccCC
Confidence 45679999999877 889997 444431 221 12234555555
Q ss_pred ----CCcCcEEEEecccccccCC
Q psy13959 82 ----MYTGQFVYCGKKATLQIGN 100 (248)
Q Consensus 82 ----~~vGd~I~~g~~~~~~~Gn 100 (248)
+++||+|.+.+..++++.|
T Consensus 312 ~~~A~rPgDVi~~~~GkTVEV~N 334 (483)
T PRK00913 312 SGNAYRPGDVLTSMSGKTIEVLN 334 (483)
T ss_pred CCCCCCCCCEEEECCCcEEEeec
Confidence 4899999987766555555
No 30
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=26.73 E-value=3.2e+02 Score=27.11 Aligned_cols=19 Identities=16% Similarity=0.200 Sum_probs=14.7
Q ss_pred cCCceEEEEEEEeCCCccc
Q psy13959 38 HGYLKGVVRDIIHDPGRGA 56 (248)
Q Consensus 38 ~~~~~g~V~~I~yDP~Rsa 56 (248)
...++|.|++++++-.++-
T Consensus 130 reV~EGeV~~l~i~~~~~p 148 (450)
T COG1224 130 REVYEGEVVELEIRRARNP 148 (450)
T ss_pred eEEEEEEEEEEEEeeccCC
Confidence 4568899999998876653
No 31
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.32 E-value=2.1e+02 Score=23.67 Aligned_cols=32 Identities=16% Similarity=0.161 Sum_probs=24.5
Q ss_pred cceEEEEecCCCccCCceEEEEc--cCCCCcCcEEEE
Q psy13959 56 APLAVVHFRNPYKFKTNKELFIA--PEGMYTGQFVYC 90 (248)
Q Consensus 56 a~IAlv~~~dg~~~~~~~~yilA--~eg~~vGd~I~~ 90 (248)
-.||+|+++++. .-..+|+. |+.+++|+.+..
T Consensus 85 ~viaiV~l~~~~---~i~~~i~~~~p~~v~iGm~V~~ 118 (140)
T COG1545 85 YVIAIVELEEGG---RILGQLVDVDPDDVEIGMKVEA 118 (140)
T ss_pred EEEEEEEeCCCC---ceEEEEEecCcccccCCCEEEE
Confidence 349999998663 34667887 889999999863
No 32
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=23.33 E-value=4.7e+02 Score=26.37 Aligned_cols=85 Identities=21% Similarity=0.199 Sum_probs=48.6
Q ss_pred CceEEEEEEEe--CCCcccceEEEEecCCCccCCc--------eEE------------EEccCCCCcCcEEEEecccccc
Q psy13959 40 YLKGVVRDIIH--DPGRGAPLAVVHFRNPYKFKTN--------KEL------------FIAPEGMYTGQFVYCGKKATLQ 97 (248)
Q Consensus 40 ~~~g~V~~I~y--DP~Rsa~IAlv~~~dg~~~~~~--------~~y------------ilA~eg~~vGd~I~~g~~~~~~ 97 (248)
...|.|-++.+ ||..--.||.++.-.|.-..+. +.. ....+.+++||++-.-.-..++
T Consensus 293 ~~~~~VFK~~~~mdp~~~griaf~RV~sG~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDI~~~~~~~~~~ 372 (527)
T TIGR00503 293 KFSGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDIIGLHNHGTIQ 372 (527)
T ss_pred CeeEEEEEEEeccCcccCceEEEEEEeeeEEcCCCEEEecCCCCcEEecchhhhhcCCceEcceeCCCCEEEEECCCCcc
Confidence 47899999999 9844445555543333100000 011 1235778888888766555666
Q ss_pred cCCcc------cccCCCCCCeeeeeeeecCCCc
Q psy13959 98 IGNVM------PVGGMPEGTIVCNLEEKTGDRG 124 (248)
Q Consensus 98 ~Gn~l------pL~~IP~Gt~I~NIE~~pg~gg 124 (248)
.|+++ .+..||.=..++...+.|-+.+
T Consensus 373 ~GDtl~~~~~~~~~~i~~~~P~~~~~v~~~~~~ 405 (527)
T TIGR00503 373 IGDTFTQGEKIKFTGIPNFAPELFRRIRLKDPL 405 (527)
T ss_pred cCCEecCCCceeecCCCCCCcceEEEEEECChh
Confidence 77766 3444555566666666665443
No 33
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=21.79 E-value=2.8e+02 Score=23.70 Aligned_cols=54 Identities=22% Similarity=0.281 Sum_probs=28.9
Q ss_pred ccccCCcccccCCCCCCeeeeeee-ecCC-CceEeecCCCeEEEEeec-CCCCeEEEEccCCceEE
Q psy13959 95 TLQIGNVMPVGGMPEGTIVCNLEE-KTGD-RGRLARASGNYATVIAHN-PDTKRTRVKLPSGAKKV 157 (248)
Q Consensus 95 ~~~~Gn~lpL~~IP~Gt~I~NIE~-~pg~-ggklaRsAGt~A~Ii~k~-~~~~~~~vkLPSGe~r~ 157 (248)
+++.|+.+-+.+-| ..|..++. .||+ |+-++| +..++ .+++..-...||++...
T Consensus 25 ~lKkG~~I~~~g~p--c~V~e~~~~KpGKHG~A~vr-------~k~knl~TG~k~e~~f~s~~~ve 81 (159)
T PLN03107 25 TIRKGGYIVIKGRP--CKVVEVSTSKTGKHGHAKCH-------FVAIDIFTGKKLEDIVPSSHNCD 81 (159)
T ss_pred hccCCCEEEECCEE--EEEEEEEecCCCCCCcEEEE-------EEEEECCCCCEEEEEecCCCEEE
Confidence 44555555566666 55555543 3777 654443 34343 33455556666666544
No 34
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=21.38 E-value=5.4e+02 Score=26.58 Aligned_cols=84 Identities=12% Similarity=0.066 Sum_probs=46.0
Q ss_pred CceEEEEEEEeCCCcccceEEEEecCCCccCCc--------------eEE------EEccCCCCcCcEEEEecccccccC
Q psy13959 40 YLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTN--------------KEL------FIAPEGMYTGQFVYCGKKATLQIG 99 (248)
Q Consensus 40 ~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~--------------~~y------ilA~eg~~vGd~I~~g~~~~~~~G 99 (248)
...+.|-+++|||.+. .||+++.-+|....++ .=| ....+.+..||++....-..+..|
T Consensus 307 ~l~a~VfK~~~d~~~G-~i~~~RV~sGtL~~g~~v~~~~~~~~~~i~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~g 385 (689)
T TIGR00484 307 PFSALAFKVATDPFVG-QLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDICAAIGLKDTTTG 385 (689)
T ss_pred ceEEEEEEeeecCCCC-eEEEEEEEEeEEcCCCEEEeCCCCceEEecceEEeecCCcccccccCCCCEEEEcCCCCCCCC
Confidence 4678999999999876 7887765454210000 111 123455667777643211122345
Q ss_pred Ccc-------cccCCCCCCeeeeeeeecCCCc
Q psy13959 100 NVM-------PVGGMPEGTIVCNLEEKTGDRG 124 (248)
Q Consensus 100 n~l-------pL~~IP~Gt~I~NIE~~pg~gg 124 (248)
+++ +|..++.-..+..+-+.|.+..
T Consensus 386 dtl~~~~~~~~~~~~~~~~Pvl~~~i~p~~~~ 417 (689)
T TIGR00484 386 DTLCDPKIDVILERMEFPEPVISLAVEPKTKA 417 (689)
T ss_pred CEEeCCCCccccCCCCCCCceEEEEEEECCcc
Confidence 444 3344444466666666666554
No 35
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=21.25 E-value=6.5e+02 Score=25.32 Aligned_cols=85 Identities=20% Similarity=0.222 Sum_probs=50.7
Q ss_pred CceEEEEEEEe--CCCcccceEEEEecCCCc--------------cCCce-EEE-----EccCCCCcCcEEEEecccccc
Q psy13959 40 YLKGVVRDIIH--DPGRGAPLAVVHFRNPYK--------------FKTNK-ELF-----IAPEGMYTGQFVYCGKKATLQ 97 (248)
Q Consensus 40 ~~~g~V~~I~y--DP~Rsa~IAlv~~~dg~~--------------~~~~~-~yi-----lA~eg~~vGd~I~~g~~~~~~ 97 (248)
...|.|-.+++ ||...-.||.++.-.|.- .+... ..+ ...+.+++||++-...-..+.
T Consensus 292 ~~~~~VFK~~~~m~~~~~grlafvRV~sG~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDIv~v~~l~~~~ 371 (526)
T PRK00741 292 KFSGFVFKIQANMDPKHRDRIAFVRVCSGKFEKGMKVRHVRTGKDVRISNALTFMAQDREHVEEAYAGDIIGLHNHGTIQ 371 (526)
T ss_pred ceEEEEEEEEecCCCCcCceEEEEEEeccEECCCCEEEeccCCceEEecceEEEecCCceECceeCCCCEEEEECCCCCc
Confidence 47899999997 665445566665434310 00000 112 235667889988776656677
Q ss_pred cCCcc------cccCCCCCCeeeeeeeecCCCc
Q psy13959 98 IGNVM------PVGGMPEGTIVCNLEEKTGDRG 124 (248)
Q Consensus 98 ~Gn~l------pL~~IP~Gt~I~NIE~~pg~gg 124 (248)
+|++| .+..||.=..++...+.|-+.+
T Consensus 372 ~GDTL~~~~~~~~~~i~~~~P~~~~~v~p~~~~ 404 (526)
T PRK00741 372 IGDTFTQGEKLKFTGIPNFAPELFRRVRLKNPL 404 (526)
T ss_pred cCCCccCCCccccCCCCCCCccEEEEEEECCch
Confidence 88777 3555665566666666666544
No 36
>COG1945 Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid transport and metabolism]
Probab=21.24 E-value=1.9e+02 Score=25.07 Aligned_cols=51 Identities=18% Similarity=0.160 Sum_probs=36.0
Q ss_pred EEecccccccCCccc---ccCCCCCCeeeeeee--ecCCCceEeecCCCeEEEEee
Q psy13959 89 YCGKKATLQIGNVMP---VGGMPEGTIVCNLEE--KTGDRGRLARASGNYATVIAH 139 (248)
Q Consensus 89 ~~g~~~~~~~Gn~lp---L~~IP~Gt~I~NIE~--~pg~ggklaRsAGt~A~Ii~k 139 (248)
..++-.++...++.| |..+|.|.++.+|.- ....-|+..=||..+|.--.+
T Consensus 41 ~vSSIlPp~~~~V~~e~gl~kl~pG~iv~~V~Ar~~S~~~G~~isaaig~a~p~D~ 96 (163)
T COG1945 41 PVSSILPPNCEIVDPEDGLPKLPPGAILFCVMARGTSNEPGRTISAAIGVAIPRDK 96 (163)
T ss_pred EEecccCCcccccchhhcCCcCCCCcEEeEEEeecccCCCCceeeeeeeEEecCCC
Confidence 333344556666666 999999999999987 444556788777777765554
No 37
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.70 E-value=2.2e+02 Score=22.05 Aligned_cols=44 Identities=23% Similarity=0.314 Sum_probs=30.8
Q ss_pred CceEEEEEEEeCCCcccceEEEEecCCCccCCceEEEEccCCCCcCcEEEE
Q psy13959 40 YLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFVYC 90 (248)
Q Consensus 40 ~~~g~V~~I~yDP~Rsa~IAlv~~~dg~~~~~~~~yilA~eg~~vGd~I~~ 90 (248)
.++|.|++|..+-+ +|+|.|. |. +-+-+.-|-++..++||.|..
T Consensus 4 aiPgqI~~I~~~~~----~A~Vd~g-Gv--kreV~l~Lv~~~v~~GdyVLV 47 (82)
T COG0298 4 AIPGQIVEIDDNNH----LAIVDVG-GV--KREVNLDLVGEEVKVGDYVLV 47 (82)
T ss_pred ccccEEEEEeCCCc----eEEEEec-cE--eEEEEeeeecCccccCCEEEE
Confidence 46899999876554 8999875 31 224455566778999999864
Done!