Query 037430
Match_columns 198
No_of_seqs 106 out of 1061
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 12:10:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037430.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037430hhsearch_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 1.6E-74 3.4E-79 498.1 19.2 198 1-198 1-198 (260)
2 PRK09612 rpl2p 50S ribosomal p 100.0 5.8E-71 1.3E-75 471.5 18.7 188 1-198 1-189 (238)
3 COG0090 RplB Ribosomal protein 100.0 2.8E-70 6.2E-75 469.2 18.4 184 1-198 34-219 (275)
4 PRK09374 rplB 50S ribosomal pr 100.0 6.3E-66 1.4E-70 448.8 18.2 175 9-190 40-216 (276)
5 CHL00052 rpl2 ribosomal protei 100.0 1.4E-65 2.9E-70 446.1 19.1 175 10-191 39-215 (273)
6 PTZ00031 ribosomal protein L2; 100.0 1.3E-65 2.8E-70 451.6 19.1 175 9-190 71-247 (317)
7 TIGR01171 rplB_bact ribosomal 100.0 1.5E-65 3.3E-70 446.1 19.2 176 9-191 38-215 (273)
8 KOG0438 Mitochondrial/chloropl 100.0 1.4E-51 3E-56 358.5 9.3 176 10-192 63-250 (312)
9 KOG2309 60s ribosomal protein 100.0 6.4E-42 1.4E-46 288.3 11.2 192 1-198 1-192 (248)
10 PF03947 Ribosomal_L2_C: Ribos 100.0 1.7E-38 3.7E-43 250.5 5.7 93 96-190 1-93 (130)
11 PF00181 Ribosomal_L2: Ribosom 99.9 1.8E-27 3.9E-32 172.1 8.7 75 11-90 1-77 (77)
12 KOG0438 Mitochondrial/chloropl 80.9 14 0.00031 33.3 9.1 103 6-132 13-124 (312)
13 PF02736 Myosin_N: Myosin N-te 66.5 9.3 0.0002 24.1 3.2 26 134-161 16-41 (42)
14 cd03699 lepA_II lepA_II: This 60.3 45 0.00098 23.6 6.3 25 42-67 2-26 (86)
15 cd04091 mtEFG1_II_like mtEFG1_ 57.1 24 0.00052 24.7 4.4 23 42-66 2-24 (81)
16 cd03691 BipA_TypA_II BipA_TypA 57.0 64 0.0014 22.5 6.6 24 42-66 2-25 (86)
17 cd03690 Tet_II Tet_II: This su 55.4 68 0.0015 22.7 6.6 26 40-66 3-28 (85)
18 cd04092 mtEFG2_II_like mtEFG2_ 53.8 59 0.0013 22.7 6.0 25 42-67 2-26 (83)
19 cd04088 EFG_mtEFG_II EFG_mtEFG 48.3 57 0.0012 22.6 5.1 24 42-66 2-25 (83)
20 PF12791 RsgI_N: Anti-sigma fa 45.8 43 0.00094 21.9 4.0 32 59-95 8-39 (56)
21 PRK05585 yajC preprotein trans 42.2 52 0.0011 25.0 4.4 42 122-165 55-96 (106)
22 TIGR00503 prfC peptide chain r 40.4 1.6E+02 0.0035 28.3 8.4 85 40-124 293-405 (527)
23 TIGR00739 yajC preprotein tran 39.7 70 0.0015 23.2 4.6 40 123-164 41-80 (84)
24 PF02699 YajC: Preprotein tran 39.6 9.7 0.00021 27.5 0.0 41 123-165 40-80 (82)
25 cd00433 Peptidase_M17 Cytosol 39.5 1.2E+02 0.0025 29.0 7.2 60 41-100 216-320 (468)
26 PRK00913 multifunctional amino 37.7 1.3E+02 0.0028 28.9 7.2 59 41-100 233-334 (483)
27 PRK14521 rpsP 30S ribosomal pr 35.6 21 0.00045 30.1 1.3 27 1-27 1-29 (186)
28 PLN03107 eukaryotic translatio 35.5 95 0.0021 25.3 5.2 54 95-157 25-81 (159)
29 KOG4309 Transcription mediator 33.5 36 0.00078 28.7 2.4 27 27-53 117-149 (217)
30 TIGR00484 EF-G translation elo 30.8 3E+02 0.0064 27.2 8.7 26 40-66 307-332 (689)
31 PRK05886 yajC preprotein trans 30.6 1.6E+02 0.0036 22.6 5.5 40 123-164 42-81 (109)
32 PRK00741 prfC peptide chain re 29.3 4.1E+02 0.0089 25.6 9.2 85 40-124 292-404 (526)
33 cd03703 aeIF5B_II aeIF5B_II: T 28.9 1.3E+02 0.0027 23.2 4.6 36 42-92 2-37 (110)
34 smart00532 LIGANc Ligase N fam 28.7 2.4E+02 0.0053 26.6 7.4 106 32-139 305-432 (441)
35 TIGR00037 eIF_5A translation i 28.7 1.5E+02 0.0032 23.2 5.1 53 95-156 11-66 (130)
36 PRK14350 ligA NAD-dependent DN 26.7 99 0.0021 30.9 4.6 103 32-139 307-429 (669)
37 COG0272 Lig NAD-dependent DNA 25.7 2.3E+02 0.005 28.5 6.8 106 32-139 310-438 (667)
38 TIGR00575 dnlj DNA ligase, NAD 25.5 2.8E+02 0.0061 27.6 7.5 106 32-139 298-425 (652)
39 TIGR00219 mreC rod shape-deter 22.4 2.4E+02 0.0052 24.9 5.8 39 72-117 206-244 (283)
40 COG1945 Pyruvoyl-dependent arg 22.3 1.5E+02 0.0033 24.5 4.1 45 95-139 47-96 (163)
41 PF08661 Rep_fac-A_3: Replicat 22.2 1.6E+02 0.0034 21.9 4.0 47 124-173 25-73 (109)
42 COG1224 TIP49 DNA helicase TIP 21.7 6E+02 0.013 24.2 8.3 19 38-56 130-148 (450)
43 cd03700 eEF2_snRNP_like_II EF2 20.6 3.2E+02 0.007 19.4 6.2 24 43-66 3-26 (93)
44 cd03702 IF2_mtIF2_II This fami 20.2 3.6E+02 0.0079 19.8 6.6 58 42-114 2-63 (95)
No 1
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=1.6e-74 Score=498.12 Aligned_cols=198 Identities=68% Similarity=1.190 Sum_probs=190.9
Q ss_pred CCcccceeecCCCCcceeeccccccCceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEecc
Q 037430 1 MGRVIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAE 80 (198)
Q Consensus 1 mgk~~~~qr~Gr~~~~R~~~~~r~g~~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~e 80 (198)
|||+|++||||||.+||+++|++.+...||.|||+|+..++.++|++|||||||||+||||.|.|++.++..++||||||
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 99999999999999999999999999999999999987778999999999999999999999999865545679999999
Q ss_pred CCCcccEEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcC
Q 037430 81 GMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPS 160 (198)
Q Consensus 81 g~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (198)
||++||+|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|++|++++++++|||||||+++|++
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 99999999999999999999999999999999999999999999999999999999998656899999999999999999
Q ss_pred CCceeEEEeeCCCcCceeeeccchhhhccccccCCCCC
Q 037430 161 GCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPK 198 (198)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~~gKAG~~r~~~k~~~~~~p~ 198 (198)
+|+||||+|||.+|.+++|+|||++||++++.+++||+
T Consensus 161 ~c~ATIG~Vsn~~~~~k~l~KAG~~~~~~~a~~~rwP~ 198 (260)
T PTZ00180 161 LSRAMIGIVAGGGRIDKPVLKAGNAFHKYRGKRNCWPK 198 (260)
T ss_pred CCeEEEEEccCCcchheeeccccchhhhhhCcCCCCCc
Confidence 99999999999999999999999999999999999995
No 2
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=5.8e-71 Score=471.47 Aligned_cols=188 Identities=49% Similarity=0.910 Sum_probs=180.8
Q ss_pred CCcccceeecCCC-CcceeeccccccCceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEec
Q 037430 1 MGRVIRAQRKGAG-SVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAA 79 (198)
Q Consensus 1 mgk~~~~qr~Gr~-~~~R~~~~~r~g~~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~ 79 (198)
|||+||+||+||| ++||..++++.|+.+|+..| + ..+++++|++|||||||||+||||.|+|+ +++|||||
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 89999999999998877666 3 34678999999999999999999999998 58899999
Q ss_pred cCCCcccEEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEc
Q 037430 80 EGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIP 159 (198)
Q Consensus 80 eg~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~ 159 (198)
|+|++||+|+++.++++++||+|||.+||+||.|||||+.||+||+|||||||||+|++| ++++|+|||||||+++|+
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 EGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESRPGDGGKFARSSGTYALVVGH--EGDKVIVQLPSGKIKELN 150 (238)
T ss_pred CCCCCCCEEEeCCCCCCCCccccCHhhCCCCCEEEEEEecCCCCcceEEcCCCeEEEEEe--cCCEEEEECCCCCeEEEC
Confidence 999999999999999999999999999999999999999999999999999999999999 689999999999999999
Q ss_pred CCCceeEEEeeCCCcCceeeeccchhhhccccccCCCCC
Q 037430 160 SGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPK 198 (198)
Q Consensus 160 ~~c~AtIG~vsn~~~~~~~~gKAG~~r~~~k~~~~~~p~ 198 (198)
++|+||||+|||.+|.+++|+|||++||++|+++..||+
T Consensus 151 ~~c~AtiG~Vsn~~~~~~~lgKAG~~r~~~k~~~g~rP~ 189 (238)
T PRK09612 151 PRCRATIGVVAGGGRKEKPFLKAGKKYHKMKAKAKKWPR 189 (238)
T ss_pred CcCeEEEEEccCCccccceeeechhhhhhhhccCCCCCc
Confidence 999999999999999999999999999999999999995
No 3
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-70 Score=469.18 Aligned_cols=184 Identities=40% Similarity=0.671 Sum_probs=176.7
Q ss_pred CCcccceeecCCCCcceeeccccccCc--eeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEe
Q 037430 1 MGRVIRAQRKGAGSVFKSHTHHRKGPA--QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIA 78 (198)
Q Consensus 1 mgk~~~~qr~Gr~~~~R~~~~~r~g~~--~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila 78 (198)
|++++++|+|| +.++++.||+++++ .||+|||+|++.++.++|++|||||||||+||||.|+|| +++||||
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 88999999877 56788888999974 899999999988999999999999999999999999999 6899999
Q ss_pred ccCCCcccEEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEE
Q 037430 79 AEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKII 158 (198)
Q Consensus 79 ~eg~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i 158 (198)
||||++||+|++|+.+++++||+|||.+||+||.|||||+.|||||||||||||||+|+.+ |+++|+|+|||||+|.|
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 PEGLKVGDVIESGKDADIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGK--EGNYVIVRLPSGEMRKV 184 (275)
T ss_pred cCccccCCEEEeCCCCCcCCcceeeeccCCCCceEEeeeeccCCCceEEEeCCceEEEEEc--cCCEEEEECCCCCeEee
Confidence 9999999999999999999999999999999999999999999999999999999999999 69999999999999999
Q ss_pred cCCCceeEEEeeCCCcCceeeeccchhhhccccccCCCCC
Q 037430 159 PSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPK 198 (198)
Q Consensus 159 ~~~c~AtIG~vsn~~~~~~~~gKAG~~r~~~k~~~~~~p~ 198 (198)
+++|+||||+|||++|.+++|+|||++||+++ ||+
T Consensus 185 ~~~CrATIGvV~n~~~~~~~lgKAGr~r~~g~-----rPt 219 (275)
T COG0090 185 LSECRATIGVVANGGHILKPLGKAGRARHKGK-----RPT 219 (275)
T ss_pred cccccEEEEEecCCccccceecccchhcCCcc-----CCc
Confidence 99999999999999999999999999999998 774
No 4
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=6.3e-66 Score=448.80 Aligned_cols=175 Identities=30% Similarity=0.491 Sum_probs=168.5
Q ss_pred ecCCCCcceeeccccccCc--eeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCccc
Q 037430 9 RKGAGSVFKSHTHHRKGPA--QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQ 86 (198)
Q Consensus 9 r~Gr~~~~R~~~~~r~g~~--~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd 86 (198)
.-||+++|||+++||+|++ +||+|||+|+..++.++|++|||||||+|+||||.|+|| +++||||||+|++||
T Consensus 40 ~~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~~~V~~IeyDP~Rsa~IAlv~~~~g-----~~~YIlAp~gl~~Gd 114 (276)
T PRK09374 40 SGGRNNNGRITVRHRGGGHKRKYRIIDFKRNKDGIPAKVERIEYDPNRSARIALLHYADG-----EKRYILAPKGLKVGD 114 (276)
T ss_pred CCCcCCCccEEEEecCCCccccccccchhhccCCCCEEEEEEEeCCCCCcCEEEEEecCC-----CEEEEEecCCCCCCC
Confidence 3468899999999999984 899999999888889999999999999999999999998 589999999999999
Q ss_pred EEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeE
Q 037430 87 FVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMI 166 (198)
Q Consensus 87 ~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtI 166 (198)
+|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|++| ++++|+|||||||+++|+++|+|||
T Consensus 115 ~I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k--~~~~~~vkLPSGe~r~i~~~c~AtI 192 (276)
T PRK09374 115 TVVSGPDADIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAK--EGKYATLRLPSGEVRKVLAECRATI 192 (276)
T ss_pred EEEeCCCCCCCccCccccccCCCCCEEEEEEecCCCCceeEeecCCeEEEEEe--cCCEEEEECCCCCeEEEcccccEEE
Confidence 99999999999999999999999999999999999999999999999999999 6899999999999999999999999
Q ss_pred EEeeCCCcCceeeeccchhhhccc
Q 037430 167 GQVAGGGRTEKPLLKAGNAYHKFR 190 (198)
Q Consensus 167 G~vsn~~~~~~~~gKAG~~r~~~k 190 (198)
|+|||.+|.+++|+|||++||+.+
T Consensus 193 G~Vsn~~~~~~~lgKAG~~r~lg~ 216 (276)
T PRK09374 193 GEVGNEEHSNISLGKAGRSRWLGI 216 (276)
T ss_pred EeecCcchhhcchhhhhhheeCCC
Confidence 999999999999999999999974
No 5
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=1.4e-65 Score=446.13 Aligned_cols=175 Identities=31% Similarity=0.506 Sum_probs=168.5
Q ss_pred cCCCCcceeeccccccCc--eeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCcccE
Q 037430 10 KGAGSVFKSHTHHRKGPA--QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQF 87 (198)
Q Consensus 10 ~Gr~~~~R~~~~~r~g~~--~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd~ 87 (198)
-||+++|||+++||+|+. +||+|||+|+...+.++|++|||||+|+|+||||.|+|| +++||||||||++||+
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 378899999999999984 899999999877889999999999999999999999998 6899999999999999
Q ss_pred EEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeEE
Q 037430 88 VYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIG 167 (198)
Q Consensus 88 I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG 167 (198)
|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++|+|||||||+++|+++|+||||
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 IVSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAK--EGKSATLKLPSGEVRLISKNCSATIG 191 (273)
T ss_pred EEeCCCCCCCcccccccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe--cCCEEEEECCCCCeEEECCcCeEEEE
Confidence 9999999999999999999999999999999999999999999999999999 68999999999999999999999999
Q ss_pred EeeCCCcCceeeeccchhhhcccc
Q 037430 168 QVAGGGRTEKPLLKAGNAYHKFRV 191 (198)
Q Consensus 168 ~vsn~~~~~~~~gKAG~~r~~~k~ 191 (198)
+|||.+|.+++|+|||++||+.+.
T Consensus 192 ~Vsn~~~~~~~lgKAG~~r~lg~r 215 (273)
T CHL00052 192 QVGNVDVNNKSLGKAGSKRWLGKR 215 (273)
T ss_pred EccCCchhhcEecchhhhhcCCCC
Confidence 999999999999999999999743
No 6
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=1.3e-65 Score=451.59 Aligned_cols=175 Identities=31% Similarity=0.434 Sum_probs=168.4
Q ss_pred ecCCCCcceeeccccccC--ceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCccc
Q 037430 9 RKGAGSVFKSHTHHRKGP--AQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQ 86 (198)
Q Consensus 9 r~Gr~~~~R~~~~~r~g~--~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd 86 (198)
.-||+++|||+++||+|+ ++||+|||+|+..+++++|++|||||||||+||||.|+|| +++||||||||++||
T Consensus 71 ~~GRnn~GrIT~rhRGGGhKr~YR~IDfkr~~~~i~g~V~~IeyDPnRsA~IALV~~~dg-----~~~YIlApeGl~vGd 145 (317)
T PTZ00031 71 NSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPSRSAHIALLQYEDG-----VLSYILAPLLLRPGD 145 (317)
T ss_pred CCCCCCCceEEEEeecCCcCccccccccccccCCcCEEEEEEEeCCCCCCcEEEEEecCC-----cEEEEEccCCCCCCC
Confidence 446889999999999996 6899999999877889999999999999999999999998 588999999999999
Q ss_pred EEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeE
Q 037430 87 FVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMI 166 (198)
Q Consensus 87 ~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtI 166 (198)
+|.++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|++| ++++++|||||||+++|+++|+|||
T Consensus 146 ~I~sg~~a~i~~GN~lPL~~IP~GT~IhNIE~~pG~Ggkl~RSAGt~A~Ii~k--~~~~~~VkLPSGe~r~i~~~C~ATI 223 (317)
T PTZ00031 146 KIIASKYANINPGNSLPLRNIPVGSIVHNVEMRPGAGGQIIRAGGTYATVVSK--DEQFATLKLKSTEIRKFPLDCWATI 223 (317)
T ss_pred EEEeCCCCCCCccCccccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEc--cCCEEEEECCCCCEEEECccCeEEE
Confidence 99999999999999999999999999999999999999999999999999999 6899999999999999999999999
Q ss_pred EEeeCCCcCceeeeccchhhhccc
Q 037430 167 GQVAGGGRTEKPLLKAGNAYHKFR 190 (198)
Q Consensus 167 G~vsn~~~~~~~~gKAG~~r~~~k 190 (198)
|+|||.+|.+++|+|||++||+.+
T Consensus 224 G~Vsn~~~~~k~lgKAG~~Rwlg~ 247 (317)
T PTZ00031 224 GQVSNLEHHMRILGKAGVNRWLGK 247 (317)
T ss_pred EEccCCccccceeccchhhhcCCC
Confidence 999999999999999999999964
No 7
>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=1.5e-65 Score=446.09 Aligned_cols=176 Identities=31% Similarity=0.491 Sum_probs=168.8
Q ss_pred ecCCCCcceeeccccccC--ceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCccc
Q 037430 9 RKGAGSVFKSHTHHRKGP--AQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQ 86 (198)
Q Consensus 9 r~Gr~~~~R~~~~~r~g~--~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd 86 (198)
--||+++|||+++||+|+ ++||+|||+|+..+++++|++|||||||+|+||||.|+|| +++||||||+|++||
T Consensus 38 ~~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~g~V~~IeyDP~Rsa~IAlv~~~~g-----~~~YIlap~gl~~Gd 112 (273)
T TIGR01171 38 TGGRNNRGRITSRHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYADG-----EKRYILAPKGLKVGD 112 (273)
T ss_pred CCCcCCCccEEEEEcCCCcccccceeecccccCCCcEEEEEEEeCCCCCcCEEEEEecCC-----cEEEEEccCCCCCCC
Confidence 346889999999999998 4899999999877889999999999999999999999998 588999999999999
Q ss_pred EEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeE
Q 037430 87 FVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMI 166 (198)
Q Consensus 87 ~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtI 166 (198)
+|++++++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++|+|||||||+++|+++|+|||
T Consensus 113 ~I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k--~~~~~~vkLPSGe~r~i~~~c~Ati 190 (273)
T TIGR01171 113 TVISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILAK--EGGYVTLRLPSGEMRMVLKECRATI 190 (273)
T ss_pred EEEECCCCCCCCcCCcccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe--cCCEEEEECCCCCeEEECCcCeEEE
Confidence 99999999999999999999999999999999999999999999999999999 6899999999999999999999999
Q ss_pred EEeeCCCcCceeeeccchhhhcccc
Q 037430 167 GQVAGGGRTEKPLLKAGNAYHKFRV 191 (198)
Q Consensus 167 G~vsn~~~~~~~~gKAG~~r~~~k~ 191 (198)
|+|||.+|.+++|+|||++||+.+.
T Consensus 191 G~Vsn~~~~~~~~gKAG~~r~lg~r 215 (273)
T TIGR01171 191 GEVGNEDHNNIVLGKAGRSRWLGIR 215 (273)
T ss_pred EEccCCchhccEeccchhheeCCCC
Confidence 9999999999999999999999743
No 8
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-51 Score=358.49 Aligned_cols=176 Identities=28% Similarity=0.387 Sum_probs=164.3
Q ss_pred cCCCCcceeeccccccCc--eeEeeecccccCCc-----eeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCC
Q 037430 10 KGAGSVFKSHTHHRKGPA--QFRSLDFGERNGYL-----KGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGM 82 (198)
Q Consensus 10 ~Gr~~~~R~~~~~r~g~~--~yr~Idf~r~~~~~-----~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~ 82 (198)
.||..++|++.||++|++ +||+|||.|..... +..|++|+|||+|+|+||||.+.++ +++||||+|||
T Consensus 63 ~GRd~tGriv~~h~GGGhKq~yr~idF~R~~p~~~~~~~~e~v~~i~yDP~Rs~~iaLv~~~~~-----~~~~Ila~egm 137 (312)
T KOG0438|consen 63 LGRDETGRIVVRHIGGGHKQRYRMIDFARPRPIEQGTTTEERVIEIEYDPGRSAKIALVAGGTG-----ELRYILATEGL 137 (312)
T ss_pred CCCccccceEEEEecCceeeeeeEeeeccCCCccccccccceEEEEEECCCccccEEEEeccCC-----CeeEEEEecCC
Confidence 488899999999999985 89999999876543 3599999999999999999999755 48999999999
Q ss_pred CcccEEEEcCCcc-----cccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEE
Q 037430 83 YTGQFVYCGKKAT-----LMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKI 157 (198)
Q Consensus 83 ~~Gd~I~~g~~~~-----~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~ 157 (198)
++||+|.++...+ .+.||++||.++|+||.|||+|..|+.+++|||||||+|+|++| ++.+++|+|||++.+.
T Consensus 138 ~aGD~i~ss~~i~~~av~~~~Gna~Pl~~lp~GT~ih~~e~~p~~~~~f~raAGt~a~ilak--~~~~aiv~Lps~r~~~ 215 (312)
T KOG0438|consen 138 KAGDTILSSRKIPFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGTSATILAK--AGKFAIVQLPSKRERS 215 (312)
T ss_pred CCCCccccccccccccccccCCCceeecccchhhhhhhhccCCCcchhhhhhcCchhhhhhc--CCCceeEEccccchhh
Confidence 9999999987755 68999999999999999999999999999999999999999999 6899999999999999
Q ss_pred EcCCCceeEEEeeCCCcCceeeeccchhhhccccc
Q 037430 158 IPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVK 192 (198)
Q Consensus 158 i~~~c~AtIG~vsn~~~~~~~~gKAG~~r~~~k~~ 192 (198)
++.+|+||||+|||.+|+.+.+||||++||+.+.+
T Consensus 216 ~~~tC~ATvGrvsni~~~~r~~GkAgr~rwlG~Rp 250 (312)
T KOG0438|consen 216 VLRTCVATVGRVSNIDHNHRILGKAGRSRWLGKRP 250 (312)
T ss_pred hhhhhheeeccccccccccceecccchhhhcccCc
Confidence 99999999999999999999999999999998775
No 9
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.4e-42 Score=288.26 Aligned_cols=192 Identities=76% Similarity=1.317 Sum_probs=182.5
Q ss_pred CCcccceeecCCCCcceeeccccccCceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEecc
Q 037430 1 MGRVIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAE 80 (198)
Q Consensus 1 mgk~~~~qr~Gr~~~~R~~~~~r~g~~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~e 80 (198)
||+.++.||+ -|..|... +||.+.-. +..||......+++.|++|.|||.|-||+|.+.|-| ++.....++|.|
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 35788888 89999877 999998777789999999999999999999999988 334577899999
Q ss_pred CCCcccEEEEcCCcccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcC
Q 037430 81 GMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPS 160 (198)
Q Consensus 81 g~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (198)
+|+.||++.++.++++.+||++|+.++|+|+.|||+|..+||.|.|+|++|.||+||++++|.+.+.|+||||..+.+++
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 CCceeEEEeeCCCcCceeeeccchhhhccccccCCCCC
Q 037430 161 GCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPK 198 (198)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~~gKAG~~r~~~k~~~~~~p~ 198 (198)
.|+|+||+|++++..++|++|||++|+++++++..||+
T Consensus 155 ~~RamIG~vAggG~~dKp~lKag~a~~K~~~Krn~wPr 192 (248)
T KOG2309|consen 155 ACRAMIGVVAGGGRTDKPLLKAGRAYHKYKAKRNCWPR 192 (248)
T ss_pred ccceEEEEecCCccccchhhhhhhHHHHhhhhcCCchh
Confidence 99999999999999999999999999999999999996
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=1.7e-38 Score=250.46 Aligned_cols=93 Identities=46% Similarity=0.750 Sum_probs=90.1
Q ss_pred cccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeEEEeeCCCcC
Q 037430 96 LMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRT 175 (198)
Q Consensus 96 ~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG~vsn~~~~ 175 (198)
+++||++||.+||+||.|||||+.||+|++|||||||||+|++| ++++++|||||||+++|+.+|+||||+|||.+|.
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 IKIGNSLPLGNIPIGTIIHNIELKPGDGGKLARAAGTYAQIISK--EGNYVVIKLPSGEIKLVSSNCRATIGRVSNGGHK 78 (130)
T ss_dssp SSTTSEEEGGGSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEE--ESSEEEEEETTSEEEEEETTSEEEESCBSSTTGG
T ss_pred CCCccchhHhhCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEe--ccceeEEEecCCCeEeecccceEEEEEecCcccc
Confidence 57999999999999999999999999999999999999999999 5799999999999999999999999999999999
Q ss_pred ceeeeccchhhhccc
Q 037430 176 EKPLLKAGNAYHKFR 190 (198)
Q Consensus 176 ~~~~gKAG~~r~~~k 190 (198)
+++++|||++||+.+
T Consensus 79 ~~~~~KAG~~r~~g~ 93 (130)
T PF03947_consen 79 EKKLGKAGRNRWLGK 93 (130)
T ss_dssp GSB-SSHHHHHHTCC
T ss_pred chhhhhhhhcccccc
Confidence 999999999999988
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=1.8e-27 Score=172.11 Aligned_cols=75 Identities=35% Similarity=0.629 Sum_probs=67.9
Q ss_pred CCCCcceeecccccc--CceeEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCcccEE
Q 037430 11 GAGSVFKSHTHHRKG--PAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQFV 88 (198)
Q Consensus 11 Gr~~~~R~~~~~r~g--~~~yr~Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd~I 88 (198)
|||++||+++||++| +++||+|||+|....++++|++|+|||+|||+||||+++|| +++||||||||++||+|
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 789779999999999 57999999999777889999999999999999999999998 68999999999999999
Q ss_pred EE
Q 037430 89 YC 90 (198)
Q Consensus 89 ~~ 90 (198)
+|
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
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=80.92 E-value=14 Score=33.32 Aligned_cols=103 Identities=16% Similarity=0.161 Sum_probs=68.8
Q ss_pred ceeecCCCCcceeeccccccC--c--eeEeeecccccCCceeEEEEEEeCC-CCccceEEEEecCCCccCceEEEEEecc
Q 037430 6 RAQRKGAGSVFKSHTHHRKGP--A--QFRSLDFGERNGYLKGVVAEIIHDP-GRGAPLARVTFRHPFRYMKQKELFIAAE 80 (198)
Q Consensus 6 ~~qr~Gr~~~~R~~~~~r~g~--~--~yr~Idf~r~~~~~~~~V~~I~yDP-~Rsa~Ialv~~~~g~~~~~~~~yila~e 80 (198)
+-|..++-...++++-|++++ + ....+|..+.. ....+|+.++||+ +|+.-.+++...-|.-.|..+++|
T Consensus 13 ~~~~~~~~~~a~i~~~~~~t~~~r~~l~~~~~l~~~~-p~~~~~~~~~~~~~GRd~tGriv~~h~GGGhKq~yr~i---- 87 (312)
T KOG0438|consen 13 TLKSAGRTVSARITVLKPGTPSLRNGLLQQPDLKKST-PSRPLVESLKINGLGRDETGRIVVRHIGGGHKQRYRMI---- 87 (312)
T ss_pred ccccCCCcccceeeecccCCccccCcccccchhhhcC-CCcceeeeEEecCCCCccccceEEEEecCceeeeeeEe----
Confidence 345566666678888888886 2 34445555443 4568999999999 999888888765554333333333
Q ss_pred CCCcccEEEEcCCcccccCCcccCcCCCCCC----cceeeeeecCCCceEEecCCC
Q 037430 81 GMYTGQFVYCGKKATLMVGNVLPVRSIPEGA----VVCNVEHHVGDRGVLARASGD 132 (198)
Q Consensus 81 g~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt----~I~nIE~~pg~Ggk~~RsAGt 132 (198)
|+.. -.-+-.|| -|-.||.-||.-+++|-.|+.
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 3322 11122222 688899999999999999987
No 13
>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=66.48 E-value=9.3 Score=24.08 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=21.4
Q ss_pred EEEEeecCCCCEEEEEcCCCcEEEEcCC
Q 037430 134 AVIISHNPDNDTTRVKLPSGAKKIIPSG 161 (198)
Q Consensus 134 a~Ii~k~~~~~~~~vkLPSGe~r~i~~~ 161 (198)
|.|+.. +++.++|++.+|+.+.++.+
T Consensus 16 g~I~~~--~g~~vtV~~~~G~~~tv~~d 41 (42)
T PF02736_consen 16 GEIIEE--EGDKVTVKTEDGKEVTVKKD 41 (42)
T ss_dssp EEEEEE--ESSEEEEEETTTEEEEEEGG
T ss_pred EEEEEE--cCCEEEEEECCCCEEEeCCC
Confidence 567766 58999999999999988753
No 14
>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=60.26 E-value=45 Score=23.57 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=19.6
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHPF 67 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g~ 67 (198)
.+.|.+++|||... .||+++..+|.
T Consensus 2 ~~~Vfk~~~d~~~G-~i~~~Rv~sG~ 26 (86)
T cd03699 2 RALIFDSWYDPYRG-VIALVRVFDGT 26 (86)
T ss_pred EEEEEEeeccCCCC-EEEEEEEEcCE
Confidence 47899999999764 57888877773
No 15
>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=57.12 E-value=24 Score=24.71 Aligned_cols=23 Identities=9% Similarity=0.053 Sum_probs=19.9
Q ss_pred eeEEEEEEeCCCCccceEEEEecCC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
.+.|-.++|||. ..|++++..+|
T Consensus 2 ~a~vfK~~~~~~--G~i~~~Rv~sG 24 (81)
T cd04091 2 VGLAFKLEEGRF--GQLTYMRIYQG 24 (81)
T ss_pred eEEEEEeecCCC--CCEEEEEEecC
Confidence 478999999985 89999998888
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=57.02 E-value=64 Score=22.55 Aligned_cols=24 Identities=13% Similarity=-0.078 Sum_probs=19.2
Q ss_pred eeEEEEEEeCCCCccceEEEEecCC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
.+.|.+++|||.. ..+|+++..+|
T Consensus 2 ~~~vfk~~~d~~~-g~i~~~Rv~sG 25 (86)
T cd03691 2 QMLVTTLDYDDYV-GRIAIGRIFRG 25 (86)
T ss_pred eEEEEEeEecCCC-CeEEEEEEEeC
Confidence 4689999999976 44788887777
No 17
>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=55.39 E-value=68 Score=22.71 Aligned_cols=26 Identities=27% Similarity=0.230 Sum_probs=20.3
Q ss_pred CceeEEEEEEeCCCCccceEEEEecCC
Q 037430 40 YLKGVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 40 ~~~~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
+..+.|..++|||.. ..+|.++.-.|
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 356899999999965 57788877666
No 18
>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=53.81 E-value=59 Score=22.66 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=19.6
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHPF 67 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g~ 67 (198)
.+.|.+++|||.. ..+|+++..+|.
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 4679999999984 568888877773
No 19
>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=48.30 E-value=57 Score=22.59 Aligned_cols=24 Identities=33% Similarity=0.348 Sum_probs=19.0
Q ss_pred eeEEEEEEeCCCCccceEEEEecCC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
.+.|.+++|||.+. .+|+++..+|
T Consensus 2 ~a~Vfk~~~d~~~G-~~~~~Rv~sG 25 (83)
T cd04088 2 VALVFKTIHDPFVG-KLSFVRVYSG 25 (83)
T ss_pred EEEEEEcccCCCCc-eEEEEEEecC
Confidence 46799999999664 4788887777
No 20
>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=45.82 E-value=43 Score=21.87 Aligned_cols=32 Identities=22% Similarity=0.061 Sum_probs=23.4
Q ss_pred EEEEecCCCccCceEEEEEeccCCCcccEEEEcCCcc
Q 037430 59 ARVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKAT 95 (198)
Q Consensus 59 alv~~~~g~~~~~~~~yila~eg~~~Gd~I~~g~~~~ 95 (198)
|.|.-.|| +.-.|-.+.++++||.|.......
T Consensus 8 aiVlT~dG-----eF~~ik~~~~~~vG~eI~~~~~~~ 39 (56)
T PF12791_consen 8 AIVLTPDG-----EFIKIKRKPGMEVGQEIEFDEKDI 39 (56)
T ss_pred EEEEcCCC-----cEEEEeCCCCCcccCEEEEechhh
Confidence 55666777 455688888899999998765443
No 21
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=42.15 E-value=52 Score=25.02 Aligned_cols=42 Identities=12% Similarity=0.099 Sum_probs=33.5
Q ss_pred CCceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCcee
Q 037430 122 DRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAM 165 (198)
Q Consensus 122 ~Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (198)
.|-+..-++|=|++|+.- +++.+.|++..|-...++..+.+.
T Consensus 55 ~Gd~VvT~gGi~G~Vv~i--~~~~v~lei~~g~~i~~~r~aI~~ 96 (106)
T PRK05585 55 KGDEVVTNGGIIGKVTKV--SEDFVIIELNDDTEIKIQKSAIAA 96 (106)
T ss_pred CCCEEEECCCeEEEEEEE--eCCEEEEEECCCeEEEEEhHHhhh
Confidence 455678899999999998 468999999998777777765443
No 22
>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=40.39 E-value=1.6e+02 Score=28.31 Aligned_cols=85 Identities=19% Similarity=0.165 Sum_probs=49.8
Q ss_pred CceeEEEEEEe--CCCCccceEEEEecCCCccCceE--------EE------------EEeccCCCcccEEEEcCCcccc
Q 037430 40 YLKGVVAEIIH--DPGRGAPLARVTFRHPFRYMKQK--------EL------------FIAAEGMYTGQFVYCGKKATLM 97 (198)
Q Consensus 40 ~~~~~V~~I~y--DP~Rsa~Ialv~~~~g~~~~~~~--------~y------------ila~eg~~~Gd~I~~g~~~~~~ 97 (198)
...|.|-++.+ ||..-..||.++.-.|....... .. -...+.+++||++-...-..+.
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 46799999999 98555567777655552111000 00 1234567788887655444555
Q ss_pred cCCcc------cCcCCCCCCcceeeeeecCCCc
Q 037430 98 VGNVL------PVRSIPEGAVVCNVEHHVGDRG 124 (198)
Q Consensus 98 ~Gn~l------pL~~IP~Gt~I~nIE~~pg~Gg 124 (198)
.|+++ .+..||.=..++..-+.|-+.+
T Consensus 373 ~GDtl~~~~~~~~~~i~~~~P~~~~~v~~~~~~ 405 (527)
T TIGR00503 373 IGDTFTQGEKIKFTGIPNFAPELFRRIRLKDPL 405 (527)
T ss_pred cCCEecCCCceeecCCCCCCcceEEEEEECChh
Confidence 66655 3445555566777766666544
No 23
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=39.72 E-value=70 Score=23.20 Aligned_cols=40 Identities=8% Similarity=0.091 Sum_probs=31.2
Q ss_pred CceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCce
Q 037430 123 RGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRA 164 (198)
Q Consensus 123 Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~A 164 (198)
|-+..-++|=|++|.+- +++++.|.+..|-...++..+.|
T Consensus 41 Gd~VvT~gGi~G~V~~i--~d~~v~vei~~g~~i~~~r~aI~ 80 (84)
T TIGR00739 41 GDKVLTIGGIIGTVTKI--AENTIVIELNDNTEITFSKNAIV 80 (84)
T ss_pred CCEEEECCCeEEEEEEE--eCCEEEEEECCCeEEEEEhHHhh
Confidence 34577889999999998 47899999988877777766543
No 24
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=39.63 E-value=9.7 Score=27.51 Aligned_cols=41 Identities=17% Similarity=0.323 Sum_probs=0.0
Q ss_pred CceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCcee
Q 037430 123 RGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAM 165 (198)
Q Consensus 123 Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (198)
|-+..-++|-|++|++- +++.+.|++.+|-...+..++.|.
T Consensus 40 Gd~VvT~gGi~G~V~~i--~~~~v~lei~~g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 40 GDEVVTIGGIYGTVVEI--DDDTVVLEIAPGVEITVEKSAIAR 80 (82)
T ss_dssp -------------------------------------------
T ss_pred CCEEEECCcEEEEEEEE--eCCEEEEEECCCeEEEEEHHHhHh
Confidence 34577889999999999 689999999999777777665543
No 25
>cd00433 Peptidase_M17 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants.
Probab=39.51 E-value=1.2e+02 Score=29.00 Aligned_cols=60 Identities=18% Similarity=0.128 Sum_probs=38.9
Q ss_pred ceeEEEEEEeCCCC--ccceEEE----EecCC-CccCc--------------------------------eEEEEEeccC
Q 037430 41 LKGVVAEIIHDPGR--GAPLARV----TFRHP-FRYMK--------------------------------QKELFIAAEG 81 (198)
Q Consensus 41 ~~~~V~~I~yDP~R--sa~Ialv----~~~~g-~~~~~--------------------------------~~~yila~eg 81 (198)
.+.+++.++|.|.. ..+|+|| .|..| .++|. -.-++.++||
T Consensus 216 ~~p~lv~l~Y~g~~~~~~~i~LVGKGiTFDsGG~slKp~~~M~~Mk~DM~GAAaVlga~~aia~l~~~vnV~~i~~~~EN 295 (468)
T cd00433 216 EPPRLIVLEYKGKGASKKPIALVGKGITFDTGGLSLKPAAGMDGMKYDMGGAAAVLGAMKAIAELKLPVNVVGVLPLAEN 295 (468)
T ss_pred CCCEEEEEEECCCCCCCCcEEEEcCceEecCCCccccCccChhhccccchhHHHHHHHHHHHHHcCCCceEEEEEEeeec
Confidence 46789999998766 5789997 34333 22221 2335566666
Q ss_pred C------CcccEEEEcCCcccccCC
Q 037430 82 M------YTGQFVYCGKKATLMVGN 100 (198)
Q Consensus 82 ~------~~Gd~I~~g~~~~~~~Gn 100 (198)
| ++||+|.+.+..++.+.|
T Consensus 296 ~is~~A~rPgDVi~s~~GkTVEI~N 320 (468)
T cd00433 296 MISGNAYRPGDVITSRSGKTVEILN 320 (468)
T ss_pred CCCCCCCCCCCEeEeCCCcEEEEec
Confidence 4 788888887766666655
No 26
>PRK00913 multifunctional aminopeptidase A; Provisional
Probab=37.73 E-value=1.3e+02 Score=28.85 Aligned_cols=59 Identities=22% Similarity=0.197 Sum_probs=38.4
Q ss_pred ceeEEEEEEeCCCCccceEEE----EecCC-CccC--------------------------------ceEEEEEeccCC-
Q 037430 41 LKGVVAEIIHDPGRGAPLARV----TFRHP-FRYM--------------------------------KQKELFIAAEGM- 82 (198)
Q Consensus 41 ~~~~V~~I~yDP~Rsa~Ialv----~~~~g-~~~~--------------------------------~~~~yila~eg~- 82 (198)
.+-+++.++|.|.. .+|+|| .|..| .++| .-.-++.++|||
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 45689999999877 889997 34333 2222 123456666665
Q ss_pred -----CcccEEEEcCCcccccCC
Q 037430 83 -----YTGQFVYCGKKATLMVGN 100 (198)
Q Consensus 83 -----~~Gd~I~~g~~~~~~~Gn 100 (198)
++||+|.+.+..++.+.|
T Consensus 312 ~~~A~rPgDVi~~~~GkTVEV~N 334 (483)
T PRK00913 312 SGNAYRPGDVLTSMSGKTIEVLN 334 (483)
T ss_pred CCCCCCCCCEEEECCCcEEEeec
Confidence 788888887665555544
No 27
>PRK14521 rpsP 30S ribosomal protein S16; Provisional
Probab=35.58 E-value=21 Score=30.13 Aligned_cols=27 Identities=30% Similarity=0.478 Sum_probs=20.6
Q ss_pred CCcccceeecC-CC-CcceeeccccccCc
Q 037430 1 MGRVIRAQRKG-AG-SVFKSHTHHRKGPA 27 (198)
Q Consensus 1 mgk~~~~qr~G-r~-~~~R~~~~~r~g~~ 27 (198)
|--+||-||.| ++ |+|||+.-.....+
T Consensus 1 M~VkIRL~R~G~KkrPfYrIVVaDsR~~R 29 (186)
T PRK14521 1 MAVKIRLQRHGRKGKAFYWIVAADSRAPR 29 (186)
T ss_pred CcEeehhhhCCCCCCCeEEEEEEeCCCCC
Confidence 66789999999 55 99998876655443
No 28
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=35.49 E-value=95 Score=25.31 Aligned_cols=54 Identities=15% Similarity=0.189 Sum_probs=30.6
Q ss_pred ccccCCcccCcCCCCCCcceeeee-ecCC-CceEEecCCCeEEEEeec-CCCCEEEEEcCCCcEEE
Q 037430 95 TLMVGNVLPVRSIPEGAVVCNVEH-HVGD-RGVLARASGDYAVIISHN-PDNDTTRVKLPSGAKKI 157 (198)
Q Consensus 95 ~~~~Gn~lpL~~IP~Gt~I~nIE~-~pg~-Ggk~~RsAGt~a~Ii~k~-~~~~~~~vkLPSGe~r~ 157 (198)
.++.|+.+-+..-| ..|-.++. .||+ |+-++ .+..++ .++...-...||++...
T Consensus 25 ~lKkG~~I~~~g~p--c~V~e~~~~KpGKHG~A~v-------r~k~knl~TG~k~e~~f~s~~~ve 81 (159)
T PLN03107 25 TIRKGGYIVIKGRP--CKVVEVSTSKTGKHGHAKC-------HFVAIDIFTGKKLEDIVPSSHNCD 81 (159)
T ss_pred hccCCCEEEECCEE--EEEEEEEecCCCCCCcEEE-------EEEEEECCCCCEEEEEecCCCEEE
Confidence 45666666666666 55555543 4787 76444 344443 34556666667766543
No 29
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=33.52 E-value=36 Score=28.72 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=19.6
Q ss_pred ceeEeeecccc------cCCceeEEEEEEeCCC
Q 037430 27 AQFRSLDFGER------NGYLKGVVAEIIHDPG 53 (198)
Q Consensus 27 ~~yr~Idf~r~------~~~~~~~V~~I~yDP~ 53 (198)
.+|..=||--+ ...++|++++|||||.
T Consensus 117 ~ry~Y~Df~IkvGtvTmg~tvKGi~vEIEY~pc 149 (217)
T KOG4309|consen 117 TRYQYCDFLIKVGTVTMGPTVKGISVEIEYGPC 149 (217)
T ss_pred ceeeecceEEEEcceEeccccceEEEEEeeCCE
Confidence 46666777532 2357899999999993
No 30
>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=30.76 E-value=3e+02 Score=27.22 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=21.3
Q ss_pred CceeEEEEEEeCCCCccceEEEEecCC
Q 037430 40 YLKGVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 40 ~~~~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
...+.|.+++|||++. .+++++.-+|
T Consensus 307 ~l~a~VfK~~~d~~~G-~i~~~RV~sG 332 (689)
T TIGR00484 307 PFSALAFKVATDPFVG-QLTFVRVYSG 332 (689)
T ss_pred ceEEEEEEeeecCCCC-eEEEEEEEEe
Confidence 4578999999999986 7888876666
No 31
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=30.58 E-value=1.6e+02 Score=22.57 Aligned_cols=40 Identities=18% Similarity=0.159 Sum_probs=31.2
Q ss_pred CceEEecCCCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCce
Q 037430 123 RGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRA 164 (198)
Q Consensus 123 Ggk~~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~A 164 (198)
|-+..-++|=|++|++- +++++.|++..|-...+.....+
T Consensus 42 GD~VvT~gGi~G~V~~I--~d~~v~leia~gv~i~~~r~AI~ 81 (109)
T PRK05886 42 GDRVHTTSGLQATIVGI--TDDTVDLEIAPGVVTTWMKLAVR 81 (109)
T ss_pred CCEEEECCCeEEEEEEE--eCCEEEEEECCCeEEEEEhhhee
Confidence 45678889999999988 46899999987866677766444
No 32
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=29.34 E-value=4.1e+02 Score=25.56 Aligned_cols=85 Identities=21% Similarity=0.201 Sum_probs=51.9
Q ss_pred CceeEEEEEEe--CCCCccceEEEEecCCCccCceE----------E----E-E-----EeccCCCcccEEEEcCCcccc
Q 037430 40 YLKGVVAEIIH--DPGRGAPLARVTFRHPFRYMKQK----------E----L-F-----IAAEGMYTGQFVYCGKKATLM 97 (198)
Q Consensus 40 ~~~~~V~~I~y--DP~Rsa~Ialv~~~~g~~~~~~~----------~----y-i-----la~eg~~~Gd~I~~g~~~~~~ 97 (198)
...|.|-++.+ ||.....||.++.-.|....... + | + ...+.+++||++-...-..+.
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 46799999997 66555677777655552111000 0 1 1 233556788888665555566
Q ss_pred cCCcc------cCcCCCCCCcceeeeeecCCCc
Q 037430 98 VGNVL------PVRSIPEGAVVCNVEHHVGDRG 124 (198)
Q Consensus 98 ~Gn~l------pL~~IP~Gt~I~nIE~~pg~Gg 124 (198)
.|++| .+..||.=..++...+.|-+.+
T Consensus 372 ~GDTL~~~~~~~~~~i~~~~P~~~~~v~p~~~~ 404 (526)
T PRK00741 372 IGDTFTQGEKLKFTGIPNFAPELFRRVRLKNPL 404 (526)
T ss_pred cCCCccCCCccccCCCCCCCccEEEEEEECCch
Confidence 77766 4556666667777777776554
No 33
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=28.88 E-value=1.3e+02 Score=23.23 Aligned_cols=36 Identities=17% Similarity=0.356 Sum_probs=28.8
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCcccEEEEcC
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGK 92 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd~I~~g~ 92 (198)
.|.|++..-|+++-.-+-+|.+ ||. +++||.|..+.
T Consensus 2 ~gtVlEvk~~~G~G~t~dvIl~-~Gt--------------L~~GD~Iv~g~ 37 (110)
T cd03703 2 QGTVLEVKEEEGLGTTIDVILY-DGT--------------LREGDTIVVCG 37 (110)
T ss_pred cEEEEEEEEcCCCceEEEEEEE-CCe--------------EecCCEEEEcc
Confidence 5889999999999888777765 672 78899998754
No 34
>smart00532 LIGANc Ligase N family.
Probab=28.74 E-value=2.4e+02 Score=26.65 Aligned_cols=106 Identities=13% Similarity=0.095 Sum_probs=61.0
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecC-----CCccC----ceEEEEEeccCCCcccEEEEc---CCcc----
Q 037430 32 LDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-----PFRYM----KQKELFIAAEGMYTGQFVYCG---KKAT---- 95 (198)
Q Consensus 32 Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~-----g~~~~----~~~~yila~eg~~~Gd~I~~g---~~~~---- 95 (198)
|-||.......-+|.+|+...+||.-|.-|...+ |.... +... .+.-.++.+||.|... +-.+
T Consensus 305 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLhN~~-~i~~~~i~iGd~V~V~raGdVIP~I~~ 383 (441)
T smart00532 305 IAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNED-EIEEKDIRIGDTVVVRKAGDVIPKVVG 383 (441)
T ss_pred EEECCCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEEEEecccCCHH-HHHHcCCCCCCEEEEEECCCcCcceee
Confidence 6666555566789999999999996655443222 31110 0111 2356789999999753 2111
Q ss_pred ----cccCCcccCcCCCCCCcceeeeeecCCC--ceEEecCCCeEEEEee
Q 037430 96 ----LMVGNVLPVRSIPEGAVVCNVEHHVGDR--GVLARASGDYAVIISH 139 (198)
Q Consensus 96 ----~~~Gn~lpL~~IP~Gt~I~nIE~~pg~G--gk~~RsAGt~a~Ii~k 139 (198)
...++.-+ -.+|.-+.+|+=++..-.+ -.+|-...|-|+++++
T Consensus 384 vv~~~r~~~~~~-~~~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~ 432 (441)
T smart00532 384 VVKEKRPGDERE-IEMPTHCPSCGSELVREEGEVDIRCPNPLCPAQLIER 432 (441)
T ss_pred cccccCCCCCcc-CcCCCCCCCCCCEeEecCCceEEEeCCCCCHHHHHHH
Confidence 12344333 3588888888877654333 2335444455555544
No 35
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=28.69 E-value=1.5e+02 Score=23.22 Aligned_cols=53 Identities=17% Similarity=0.247 Sum_probs=26.6
Q ss_pred ccccCCcccCcCCCCCCcceeeee-ecCC-CceEEecCCCeEEEEeec-CCCCEEEEEcCCCcEE
Q 037430 95 TLMVGNVLPVRSIPEGAVVCNVEH-HVGD-RGVLARASGDYAVIISHN-PDNDTTRVKLPSGAKK 156 (198)
Q Consensus 95 ~~~~Gn~lpL~~IP~Gt~I~nIE~-~pg~-Ggk~~RsAGt~a~Ii~k~-~~~~~~~vkLPSGe~r 156 (198)
.++.|+.+-+..-| ..|-.++. .||+ |+-++ .+..++ ..++..-...||++..
T Consensus 11 ~irkG~~i~~~g~p--~~V~e~~~~kpGkhG~A~v-------r~k~knl~tG~~~e~~f~s~~~v 66 (130)
T TIGR00037 11 ALRVGGYVVIDGRP--CKIVDISTSKPGKHGHAKA-------RVVAIGIFTGKKLEFVSPSTSKV 66 (130)
T ss_pred HccCCCEEEECCEE--EEEEEEEecCCCCCCcEEE-------EEEEEECCCCCEEEEEECCCCEE
Confidence 34555555555555 34433333 3776 65433 333343 3455555556666544
No 36
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.66 E-value=99 Score=30.88 Aligned_cols=103 Identities=17% Similarity=0.197 Sum_probs=60.4
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecC-----CCccC----ceEEEEEeccCCCcccEEEEc---CCc-----
Q 037430 32 LDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-----PFRYM----KQKELFIAAEGMYTGQFVYCG---KKA----- 94 (198)
Q Consensus 32 Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~-----g~~~~----~~~~yila~eg~~~Gd~I~~g---~~~----- 94 (198)
|-||.......-+|.+|++..+||.-|.-|...+ |.... +... .+.-.++.+||.|... +-.
T Consensus 307 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~-~I~~~di~iGD~V~V~raGdVIP~I~~ 385 (669)
T PRK14350 307 MAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQD-YIDSIGLNVGDVVKISRRGDVIPAVEL 385 (669)
T ss_pred EEEcCCCceeEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHH-HHHHcCCCCCCEEEEEecCCCCCceee
Confidence 5666555556789999999999997666554333 21100 0111 2345788999999752 211
Q ss_pred ---ccccCCcccCcCCCCCCcceeeeeecCCCceEEecCCCeEEEEee
Q 037430 95 ---TLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISH 139 (198)
Q Consensus 95 ---~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAGt~a~Ii~k 139 (198)
....++ ..+|.-+..|+-++.-+.-..+|-...|-|+++++
T Consensus 386 v~~~~r~~~----~~~P~~CP~C~s~l~~~~~~~~C~n~~C~aq~~~~ 429 (669)
T PRK14350 386 VIEKLSVGF----FKIPDNCPSCKTALIKEGAHLFCVNNHCPSVIVER 429 (669)
T ss_pred ecccccCCC----CCCCCCCCCCCCEeeeCCEEEEECCCCCHHHHHhh
Confidence 223354 34688888888777643223344444466666655
No 37
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=25.71 E-value=2.3e+02 Score=28.45 Aligned_cols=106 Identities=16% Similarity=0.148 Sum_probs=68.7
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecC-----CCccC----ceEEEEEeccCCCcccEEEEc---CC------
Q 037430 32 LDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-----PFRYM----KQKELFIAAEGMYTGQFVYCG---KK------ 93 (198)
Q Consensus 32 Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~-----g~~~~----~~~~yila~eg~~~Gd~I~~g---~~------ 93 (198)
|-||....-..-+|.+|+..-+||.-|.-|...+ |...+ +...| |+-.++.+||.|... +-
T Consensus 310 iAyKFpa~e~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~d~-I~rkdIrIGDtV~V~kAGdVIP~V~~ 388 (667)
T COG0272 310 IAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDE-IKRKDIRIGDTVVVRKAGDVIPQVVG 388 (667)
T ss_pred eeecCCchheeeEEEEEEEecCCceeeeeeEEEEeEEECCEEEEEeecCCHHH-HHhcCCCCCCEEEEEecCCCCcceee
Confidence 5565444455679999999999987766554333 21110 11122 346789999999753 21
Q ss_pred --cccccCCcccCcCCCCCCcceeeeeecCCCceEEecCC---CeEEEEee
Q 037430 94 --ATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASG---DYAVIISH 139 (198)
Q Consensus 94 --~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggk~~RsAG---t~a~Ii~k 139 (198)
.+..+|+..|+. +|.-+.+|+=++....++...|--+ |-|+.+.+
T Consensus 389 Vv~e~R~~~~~~~~-~P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq~~e~ 438 (667)
T COG0272 389 VVLEKRPGNEKPIP-FPTHCPVCGSELVREEGEVVIRCTNGLNCPAQLKER 438 (667)
T ss_pred eecccCCCCCCCCC-CCCCCCCCCCeeEeccCceeEecCCCCCChHHHhhh
Confidence 245789888877 9999999998888766666655544 44554444
No 38
>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=25.45 E-value=2.8e+02 Score=27.56 Aligned_cols=106 Identities=10% Similarity=0.088 Sum_probs=62.7
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecC-----CCccC----ceEEEEEeccCCCcccEEEEc---CCc-----
Q 037430 32 LDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-----PFRYM----KQKELFIAAEGMYTGQFVYCG---KKA----- 94 (198)
Q Consensus 32 Idf~r~~~~~~~~V~~I~yDP~Rsa~Ialv~~~~-----g~~~~----~~~~yila~eg~~~Gd~I~~g---~~~----- 94 (198)
|-||.......-+|.+|+...+||.-|.-|...+ |.... +... .+.-.++.+||.|... +-.
T Consensus 298 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPvA~lePV~l~G~~VsrAtLhN~~-~i~~~~i~iGD~V~V~raGdVIP~i~~ 376 (652)
T TIGR00575 298 IAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNED-EIEELDIRIGDTVVVRKAGDVIPKVVR 376 (652)
T ss_pred EEEcCCCceeeEEEEEEEEecCCCceeeeEEEEeeEEECCEEEEEeecCCHH-HHHHcCCCCCCEEEEEecCCcCceeee
Confidence 5666555556789999999999996555443322 21100 0111 2355789999999753 211
Q ss_pred ---ccccCCcccCcCCCCCCcceeeeeecCCCc--eEEecCCCeEEEEee
Q 037430 95 ---TLMVGNVLPVRSIPEGAVVCNVEHHVGDRG--VLARASGDYAVIISH 139 (198)
Q Consensus 95 ---~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Gg--k~~RsAGt~a~Ii~k 139 (198)
+...++.-|+ .+|.-+.+|+=++..-+++ .+|-...|-|+++++
T Consensus 377 vv~~~r~~~~~~~-~~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~ 425 (652)
T TIGR00575 377 VLLEKRTGSERPI-RFPTHCPSCGSPLVKIEEEAVIRCPNLNCPAQRVER 425 (652)
T ss_pred eccccCCCCCCCC-CCCCCCCCCCCEeEecCCcEEEEECCCCCHHHHHHH
Confidence 1224554443 5899999998766543333 345455566676655
No 39
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=22.36 E-value=2.4e+02 Score=24.86 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=24.6
Q ss_pred eEEEEEeccCCCcccEEEEcCCcccccCCcccCcCCCCCCcceeee
Q 037430 72 QKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVE 117 (198)
Q Consensus 72 ~~~yila~eg~~~Gd~I~~g~~~~~~~Gn~lpL~~IP~Gt~I~nIE 117 (198)
...|+.....+++||.|.++- .|..+| ..+|+|+... |+
T Consensus 206 ~l~~~~~~~~v~~GD~VvTSG-----lgg~fP-~Gl~VG~V~~-v~ 244 (283)
T TIGR00219 206 NLVNRPAEKDIKKGDLIVTSG-----LGGRFP-EGYPIGVVTS-VH 244 (283)
T ss_pred EEEECCCCCCCCCCCEEEECC-----CCCcCC-CCCEEEEEEE-EE
Confidence 345566677899999997643 233333 5677776553 54
No 40
>COG1945 Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid transport and metabolism]
Probab=22.32 E-value=1.5e+02 Score=24.49 Aligned_cols=45 Identities=20% Similarity=0.184 Sum_probs=32.6
Q ss_pred ccccCCccc---CcCCCCCCcceeeee--ecCCCceEEecCCCeEEEEee
Q 037430 95 TLMVGNVLP---VRSIPEGAVVCNVEH--HVGDRGVLARASGDYAVIISH 139 (198)
Q Consensus 95 ~~~~Gn~lp---L~~IP~Gt~I~nIE~--~pg~Ggk~~RsAGt~a~Ii~k 139 (198)
++...++.| |..+|.|..+++|.- ....-|+.+=||..+|.--.+
T Consensus 47 Pp~~~~V~~e~gl~kl~pG~iv~~V~Ar~~S~~~G~~isaaig~a~p~D~ 96 (163)
T COG1945 47 PPNCEIVDPEDGLPKLPPGAILFCVMARGTSNEPGRTISAAIGVAIPRDK 96 (163)
T ss_pred CCcccccchhhcCCcCCCCcEEeEEEeecccCCCCceeeeeeeEEecCCC
Confidence 445556666 899999999999987 344446888777777766554
No 41
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=22.18 E-value=1.6e+02 Score=21.91 Aligned_cols=47 Identities=23% Similarity=0.335 Sum_probs=28.9
Q ss_pred ceEEecC--CCeEEEEeecCCCCEEEEEcCCCcEEEEcCCCceeEEEeeCCC
Q 037430 124 GVLARAS--GDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGG 173 (198)
Q Consensus 124 gk~~RsA--Gt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG~vsn~~ 173 (198)
|++.... |..|++..- ++..+.|.|++...-. ...+.=+||.|.+.+
T Consensus 25 Gkv~~~~~~g~~~~l~~~--d~~~V~v~l~~~~~~~-~~~~vEviG~V~~~~ 73 (109)
T PF08661_consen 25 GKVESVDPDGGSATLSTS--DGGQVTVSLNPPSDEE-LSKYVEVIGKVNDDG 73 (109)
T ss_dssp EEEEEE-TTSSEEEEE-T--TS-EEEEEESS--SS----SEEEEEEEE-TTS
T ss_pred EEEeeEcCCCCEEEEEcC--CCCEEEEEeCCCCCCC-CCCEEEEEEEEcCCC
Confidence 5555555 888888876 6889999998764322 356778999988865
No 42
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=21.74 E-value=6e+02 Score=24.17 Aligned_cols=19 Identities=21% Similarity=0.247 Sum_probs=14.6
Q ss_pred cCCceeEEEEEEeCCCCcc
Q 037430 38 NGYLKGVVAEIIHDPGRGA 56 (198)
Q Consensus 38 ~~~~~~~V~~I~yDP~Rsa 56 (198)
...++|.|++++++-.++.
T Consensus 130 reV~EGeV~~l~i~~~~~p 148 (450)
T COG1224 130 REVYEGEVVELEIRRARNP 148 (450)
T ss_pred eEEEEEEEEEEEEeeccCC
Confidence 4467899999998776653
No 43
>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. 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. This translocation step is catalyzed by EF-2_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. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
Probab=20.61 E-value=3.2e+02 Score=19.37 Aligned_cols=24 Identities=17% Similarity=0.174 Sum_probs=20.0
Q ss_pred eEEEEEEeCCCCccceEEEEecCC
Q 037430 43 GVVAEIIHDPGRGAPLARVTFRHP 66 (198)
Q Consensus 43 ~~V~~I~yDP~Rsa~Ialv~~~~g 66 (198)
+.|..+++||.-...+|+++.-.|
T Consensus 3 ~~v~Ki~~~~~~~g~la~~RV~sG 26 (93)
T cd03700 3 MYVTKMVPTPDKGGFIAFGRVFSG 26 (93)
T ss_pred EEEEeCeECCCCCEEEEEEEEeeC
Confidence 578899999966679999987777
No 44
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=20.22 E-value=3.6e+02 Score=19.82 Aligned_cols=58 Identities=22% Similarity=0.267 Sum_probs=36.3
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCCccCceEEEEEeccCCCcccEEEEcCCc----ccccCCcccCcCCCCCCcce
Q 037430 42 KGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKA----TLMVGNVLPVRSIPEGAVVC 114 (198)
Q Consensus 42 ~~~V~~I~yDP~Rsa~Ialv~~~~g~~~~~~~~yila~eg~~~Gd~I~~g~~~----~~~~Gn~lpL~~IP~Gt~I~ 114 (198)
+|.|++..-|.++.....++ ..+|. +++||.|.+|..- .+..=+--++.....++.|.
T Consensus 2 ~g~VlE~~~~~g~G~vatvi-V~~Gt--------------L~~Gd~iv~G~~~gkVr~l~d~~g~~v~~a~Ps~~V~ 63 (95)
T cd03702 2 EGVVIESKLDKGRGPVATVL-VQNGT--------------LKVGDVLVAGTTYGKVRAMFDENGKRVKEAGPSTPVE 63 (95)
T ss_pred eEEEEEEEecCCCCccEEEE-EEcCe--------------EeCCCEEEEcccccEEEEEECCCCCCCCEECCCCcEE
Confidence 57899999999976554433 33662 7788998887531 12222224667777777663
Done!