Query 024947
Match_columns 260
No_of_seqs 128 out of 1113
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:43:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024947hhsearch_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 4E-105 8E-110 723.3 23.1 255 1-255 1-255 (260)
2 PRK09612 rpl2p 50S ribosomal p 100.0 4E-100 8E-105 684.3 22.9 236 1-246 1-237 (238)
3 COG0090 RplB Ribosomal protein 100.0 2.1E-91 4.5E-96 630.6 22.2 231 1-246 34-268 (275)
4 CHL00052 rpl2 ribosomal protei 100.0 2.2E-81 4.8E-86 572.7 21.5 213 11-238 40-255 (273)
5 PTZ00031 ribosomal protein L2; 100.0 3.9E-81 8.5E-86 578.0 21.2 215 9-238 71-287 (317)
6 TIGR01171 rplB_bact ribosomal 100.0 6.4E-81 1.4E-85 569.9 21.5 213 10-237 39-253 (273)
7 PRK09374 rplB 50S ribosomal pr 100.0 8.1E-81 1.8E-85 569.7 21.2 214 10-238 41-256 (276)
8 KOG2309 60s ribosomal protein 100.0 5.7E-67 1.2E-71 462.6 15.0 247 1-253 1-247 (248)
9 KOG0438 Mitochondrial/chloropl 100.0 8.4E-61 1.8E-65 437.5 10.2 207 11-229 64-282 (312)
10 PF03947 Ribosomal_L2_C: Ribos 100.0 2.5E-58 5.5E-63 381.5 7.8 129 96-231 1-130 (130)
11 PF00181 Ribosomal_L2: Ribosom 99.9 5E-26 1.1E-30 172.9 9.2 75 11-90 1-77 (77)
12 KOG0438 Mitochondrial/chloropl 90.7 2.2 4.7E-05 40.5 9.7 104 8-135 15-127 (312)
13 PF03991 Prion_octapep: Copper 85.5 0.46 1E-05 21.7 0.9 8 210-217 1-8 (8)
14 cd03699 lepA_II lepA_II: This 62.6 38 0.00082 25.4 6.5 25 42-67 2-26 (86)
15 cd04092 mtEFG2_II_like mtEFG2_ 59.9 28 0.00062 25.7 5.4 25 42-67 2-26 (83)
16 cd03691 BipA_TypA_II BipA_TypA 58.4 52 0.0011 24.3 6.6 25 42-67 2-26 (86)
17 cd04091 mtEFG1_II_like mtEFG1_ 57.8 27 0.00059 25.8 5.0 24 42-67 2-25 (81)
18 PF02736 Myosin_N: Myosin N-te 51.2 23 0.0005 23.6 3.3 26 134-161 16-41 (42)
19 COG0272 Lig NAD-dependent DNA 46.3 17 0.00038 38.1 3.0 120 32-167 310-452 (667)
20 KOG4309 Transcription mediator 40.6 18 0.00039 32.2 1.8 27 27-53 117-149 (217)
21 cd04088 EFG_mtEFG_II EFG_mtEFG 40.5 80 0.0017 23.1 5.1 25 42-67 2-26 (83)
22 cd03690 Tet_II Tet_II: This su 38.2 1.7E+02 0.0037 21.9 6.8 27 40-67 3-29 (85)
23 PF06592 DUF1138: Protein of u 34.4 18 0.0004 27.5 0.7 16 195-210 51-68 (73)
24 cd03703 aeIF5B_II aeIF5B_II: T 30.3 98 0.0021 25.2 4.4 37 42-93 2-38 (110)
25 cd03701 IF2_IF5B_II IF2_IF5B_I 30.2 2.6E+02 0.0056 21.6 7.1 57 42-113 2-62 (95)
26 cd00433 Peptidase_M17 Cytosol 30.2 1.2E+02 0.0026 30.4 6.0 21 41-61 216-238 (468)
27 cd03702 IF2_mtIF2_II This fami 27.8 2.5E+02 0.0055 21.9 6.3 58 42-114 2-63 (95)
28 PRK05585 yajC preprotein trans 27.7 1.1E+02 0.0025 24.5 4.4 42 122-165 55-96 (106)
29 TIGR00575 dnlj DNA ligase, NAD 27.4 1E+02 0.0022 32.3 5.0 106 32-139 298-425 (652)
30 PRK00913 multifunctional amino 27.1 1.5E+02 0.0032 30.1 5.9 20 41-61 233-252 (483)
31 TIGR00739 yajC preprotein tran 26.5 1.4E+02 0.0031 22.9 4.6 40 123-164 41-80 (84)
32 smart00532 LIGANc Ligase N fam 26.3 1.1E+02 0.0023 30.7 4.7 86 32-119 305-410 (441)
33 TIGR00503 prfC peptide chain r 24.9 4.2E+02 0.0092 26.9 8.8 86 39-124 292-405 (527)
34 PF02699 YajC: Preprotein tran 24.7 25 0.00053 26.9 0.0 40 123-164 40-79 (82)
35 TIGR00484 EF-G translation elo 24.2 4.2E+02 0.009 27.6 8.8 27 40-67 307-333 (689)
36 PRK07956 ligA NAD-dependent DN 23.6 1.2E+02 0.0026 31.8 4.8 106 32-139 310-438 (665)
37 PF00883 Peptidase_M17: Cytoso 22.2 1.2E+02 0.0026 29.0 4.1 22 40-61 59-83 (311)
38 PRK14350 ligA NAD-dependent DN 21.6 56 0.0012 34.4 1.9 103 32-139 307-429 (669)
39 cd04090 eEF2_II_snRNP Loc2 eEF 21.4 3.7E+02 0.0079 20.3 6.0 26 42-67 2-27 (94)
40 PRK05015 aminopeptidase B; Pro 21.2 2.4E+02 0.0051 28.3 6.0 20 42-61 166-189 (424)
41 PF09962 DUF2196: Uncharacteri 21.0 60 0.0013 24.1 1.4 17 196-212 30-46 (62)
42 PRK00741 prfC peptide chain re 20.9 6.8E+02 0.015 25.4 9.4 87 40-126 292-406 (526)
43 COG1224 TIP49 DNA helicase TIP 20.6 5E+02 0.011 26.1 8.0 19 38-56 130-148 (450)
44 COG0260 PepB Leucyl aminopepti 20.3 2E+02 0.0044 29.2 5.4 21 41-61 229-251 (485)
No 1
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=3.9e-105 Score=723.31 Aligned_cols=255 Identities=71% Similarity=1.209 Sum_probs=246.5
Q ss_pred CCccceeeecCCCCcccccccccCCcceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEecc
Q 024947 1 MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAE 80 (260)
Q Consensus 1 mgk~~~~qr~g~~~~~R~~~~~~~gk~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~e 80 (260)
|||+|++||||+|++||+++|++.++.+||+|||+|...+++++|++|||||||||+||||.|+|++.++..++||||||
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 99999999999999999999999999999999999987778899999999999999999999999875555679999999
Q ss_pred CCccccEEEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeC
Q 024947 81 GMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPS 160 (260)
Q Consensus 81 gl~~Gd~I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (260)
+|++||+|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++++++++++|||||||+++|++
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 99999999999999999999999999999999999999999999999999999999998667899999999999999999
Q ss_pred CCceeEEeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeee
Q 024947 161 GCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIAA 240 (260)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~ia~ 240 (260)
+|+||||+|||.++.+++|+|||++||+|++++++||+|||||||||||||||||||++|+||||||+||||||||+|||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCcccchhhhhhh
Q 024947 241 RRTGRLRGQAAATAA 255 (260)
Q Consensus 241 rrtg~~r~~~~~~~~ 255 (260)
||||+++|++++..|
T Consensus 241 rrtg~~~~~~~~~~~ 255 (260)
T PTZ00180 241 RRTGLLRGGKKVKGA 255 (260)
T ss_pred ccccccccccccccc
Confidence 999999999987655
No 2
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=3.6e-100 Score=684.34 Aligned_cols=236 Identities=56% Similarity=0.976 Sum_probs=227.9
Q ss_pred CCccceeeecCCC-CcccccccccCCcceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEec
Q 024947 1 MGRVIRAQRKGAG-SVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAA 79 (260)
Q Consensus 1 mgk~~~~qr~g~~-~~~R~~~~~~~gk~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~ 79 (260)
|||+||+||+|+| ++||+++|++.|+.+|+-.| + ..+++++|++|||||||||+||||.|+|++ ++|||||
T Consensus 1 Mgk~i~~qr~G~g~~~fr~~~~~r~g~~~~~~~~--~-~~~~~g~V~~IeyDPnRsa~IAlv~~~~g~-----~~YIiAp 72 (238)
T PRK09612 1 MGKRIISQRRGRGTPTFRSPSHRYKGPVKYPPLD--K-DGTLRGKVVDILHDPGRNAPVAKVKFENGE-----EFLILAP 72 (238)
T ss_pred CCceeeecccCCCCCcccCccccccccccccCcc--c-CCceeEEEEEEEECCCCCCeEEEEEeCCCC-----EEEEEcc
Confidence 9999999999999 89999999999999877666 3 346789999999999999999999999984 8899999
Q ss_pred cCCccccEEEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEe
Q 024947 80 EGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVP 159 (260)
Q Consensus 80 egl~~Gd~I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~ 159 (260)
|+|++||+|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++++|||||||+++|+
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 CCCceeEEeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceee
Q 024947 160 SGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIA 239 (260)
Q Consensus 160 ~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~ia 239 (260)
++|+||||+|||.+|.+++|+|||++||+|+.++++||+||||||||||||||||||||+|+||||||+||||||||+||
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 eeccCcc
Q 024947 240 ARRTGRL 246 (260)
Q Consensus 240 ~rrtg~~ 246 (260)
||||||+
T Consensus 231 arrtgr~ 237 (238)
T PRK09612 231 ARRTGRR 237 (238)
T ss_pred cccccCC
Confidence 9999973
No 3
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-91 Score=630.58 Aligned_cols=231 Identities=44% Similarity=0.723 Sum_probs=219.6
Q ss_pred CCccceeeecC-CC-CcccccccccCCcceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEe
Q 024947 1 MGRVIRAQRKG-AG-SVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVA 78 (260)
Q Consensus 1 mgk~~~~qr~g-~~-~~~R~~~~~~~gk~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA 78 (260)
|++.++.|+|| +| .|||.+.+.+ |+.||+|||+|++..++++|++|||||||||+||||.|+||+ ++||||
T Consensus 34 ~~~~~~~~gR~n~G~iT~R~~gggh--K~~yr~idfkr~k~~i~g~V~~IeyDP~RsA~IAlv~y~dGe-----k~yilA 106 (275)
T COG0090 34 MGKLIKSQGRNNRGRITVRHRGGGH--KRRYRLIDFKRNKDGIPGKVEDIEYDPNRSAPIALVVYEDGE-----KRYILA 106 (275)
T ss_pred hhccccccCCCCCCCeeEEcCCCCc--ccceeccccccccCCccEEEEEEEECCCCCcceEEEEecCCC-----EEEEEc
Confidence 89999999999 78 7777654432 678999999999889999999999999999999999999995 899999
Q ss_pred ccCCccccEEEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEE
Q 024947 79 AEGMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIV 158 (260)
Q Consensus 79 ~egl~~Gd~I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i 158 (260)
||||++||+|++|+.+++++||+|||.+||+||.|||||+.||+||||||||||||+|+.+ |++|++|+|||||+|.|
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 eCCCceeEEeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCC-CCCCCCCCC-CCCCCccc
Q 024947 159 PSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHI-GHASTVRRD-APPGQKVG 236 (260)
Q Consensus 159 ~~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~-G~~s~~~r~-appg~kvg 236 (260)
+++|+||||+|||.+|.+++|+|||++||+ .+||+||||||||||||||||||||. |+|++++|. ++|| |++
T Consensus 185 ~~~CrATIGvV~n~~~~~~~lgKAGr~r~~-----g~rPtVRGvAMNpvDHPHGGGeg~~~ggk~p~~pwg~~~~G-kkt 258 (275)
T COG0090 185 LSECRATIGVVANGGHILKPLGKAGRARHK-----GKRPTVRGVAMNPVDHPHGGGEGQHPGGKPPTVPWGKPTPG-KKT 258 (275)
T ss_pred cccccEEEEEecCCccccceecccchhcCC-----ccCCccceeecCCCcCCCCCCCCCCCCCCCCCCCCCCCCCc-ccc
Confidence 999999999999999999999999999998 45999999999999999999999997 789999998 9999 999
Q ss_pred eeeeeccCcc
Q 024947 237 LIAARRTGRL 246 (260)
Q Consensus 237 ~ia~rrtg~~ 246 (260)
.+++|+|++.
T Consensus 259 r~~~krt~~~ 268 (275)
T COG0090 259 RIAAKRTGKF 268 (275)
T ss_pred cccccccCce
Confidence 9999999973
No 4
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=2.2e-81 Score=572.67 Aligned_cols=213 Identities=34% Similarity=0.560 Sum_probs=200.5
Q ss_pred CCCCcccccccccCC--cceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccEE
Q 024947 11 GAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFV 88 (260)
Q Consensus 11 g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~I 88 (260)
||-.++|++.+|++| +++||+|||+|....++++|++|||||||||+||||.|+|++ ++||||||+|++||+|
T Consensus 40 GRnn~GrItvrhrGGG~kr~yR~IDf~r~~~~i~~~V~~IeyDP~Rsa~IAlv~~~~g~-----~~YIlAp~gl~~Gd~I 114 (273)
T CHL00052 40 GRNNRGIITARHRGGGHKRLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLIHYGDGE-----KRYILHPRGLKIGDTI 114 (273)
T ss_pred CcCCCccEEEecccCCCccccceeccccccCCCcEEEEEEEECCCCCccEEEEEeCCCc-----EEEEEccCCCCCCCEE
Confidence 555889999999999 679999999998777899999999999999999999999984 8899999999999999
Q ss_pred EEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCceeEEe
Q 024947 89 YCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQ 168 (260)
Q Consensus 89 ~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG~ 168 (260)
+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++++|||||||+++|+++|+||||+
T Consensus 115 ~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggk~~RsAGt~A~ii~k--~~~~~~vkLPSGe~r~v~~~c~AtIG~ 192 (273)
T CHL00052 115 VSGTEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAK--EGKSATLKLPSGEVRLISKNCSATIGQ 192 (273)
T ss_pred EeCCCCCCCcccccccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe--cCCEEEEECCCCCeEEECCcCeEEEEE
Confidence 999999999999999999999999999999999999999999999999999 689999999999999999999999999
Q ss_pred eeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCcccee
Q 024947 169 VAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQ-HIGHASTVRRDAPPGQKVGLI 238 (260)
Q Consensus 169 vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~-~~G~~s~~~r~appg~kvg~i 238 (260)
|||.+|.+++|+|||++||+ ++||+||||||||||||||||||+ ++|+|+++| |+|+.-...
T Consensus 193 Vsn~~~~~~~lgKAG~~r~l-----g~rP~VRGvAMNpvDHPHGGGegkt~~Gr~~~vs---pwG~~~kg~ 255 (273)
T CHL00052 193 VGNVDVNNKSLGKAGSKRWL-----GKRPKVRGVVMNPVDHPHGGGEGRAPIGRKKPVT---PWGKPALGR 255 (273)
T ss_pred ccCCchhhcEecchhhhhcC-----CCCCcCCeEecCCccCCCCCCCccCCCCCcCCCC---cCccccccc
Confidence 99999999999999999998 679999999999999999999995 688898898 667655443
No 5
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=3.9e-81 Score=577.96 Aligned_cols=215 Identities=33% Similarity=0.456 Sum_probs=199.1
Q ss_pred ecCCCCcccccccccCC--cceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCcccc
Q 024947 9 RKGAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQ 86 (260)
Q Consensus 9 r~g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd 86 (260)
.-||..+||++++|++| |++||+|||+|+...++++|++|||||||||+||||.|+|++ ++||||||||++||
T Consensus 71 ~~GRnn~GrIT~rhRGGGhKr~YR~IDfkr~~~~i~g~V~~IeyDPnRsA~IALV~~~dg~-----~~YIlApeGl~vGd 145 (317)
T PTZ00031 71 NSGRNNVGRITTRHRGGGHVQRLRFIDFKRSRKDIYSTVLRIEYDPSRSAHIALLQYEDGV-----LSYILAPLLLRPGD 145 (317)
T ss_pred CCCCCCCceEEEEeecCCcCccccccccccccCCcCEEEEEEEeCCCCCCcEEEEEecCCc-----EEEEEccCCCCCCC
Confidence 34666899999999999 899999999998778899999999999999999999999984 78999999999999
Q ss_pred EEEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCceeE
Q 024947 87 FVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMI 166 (260)
Q Consensus 87 ~I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtI 166 (260)
+|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++++|+|||||+++|+++|+|||
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 EeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccee
Q 024947 167 GQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLI 238 (260)
Q Consensus 167 G~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~i 238 (260)
|+|||.+|.+++|+|||++||+ ++||+||||||||||||||||||++.|..+.++ |+|......
T Consensus 224 G~Vsn~~~~~k~lgKAG~~Rwl-----g~RP~VRGVAMNPVDHPHGGGeGkt~~gr~p~s---pWG~~tkG~ 287 (317)
T PTZ00031 224 GQVSNLEHHMRILGKAGVNRWL-----GKRPVVRGVAMNPSKHPHGGGTSKKGTKRPKCS---LWGICRDGY 287 (317)
T ss_pred EEccCCccccceeccchhhhcC-----CCCCCcccCccCCccCCCCCCCCCCCCCCCCCC---CCccccCCc
Confidence 9999999999999999999998 679999999999999999999998744333455 677665433
No 6
>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=6.4e-81 Score=569.91 Aligned_cols=213 Identities=34% Similarity=0.559 Sum_probs=197.6
Q ss_pred cCCCCcccccccccCC--cceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccE
Q 024947 10 KGAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQF 87 (260)
Q Consensus 10 ~g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~ 87 (260)
-||-.++|++.+|++| |++||+|||+|+...++++|++|||||||||+||||.|+||+ ++||||||+|++||+
T Consensus 39 ~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~g~V~~IeyDP~Rsa~IAlv~~~~g~-----~~YIlap~gl~~Gd~ 113 (273)
T TIGR01171 39 GGRNNRGRITSRHRGGGHKRLYRIIDFKRNKDGIPAKVAAIEYDPNRSARIALLHYADGE-----KRYILAPKGLKVGDT 113 (273)
T ss_pred CCcCCCccEEEEEcCCCcccccceeecccccCCCcEEEEEEEeCCCCCcCEEEEEecCCc-----EEEEEccCCCCCCCE
Confidence 4555899999999999 679999999998777889999999999999999999999984 889999999999999
Q ss_pred EEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCceeEE
Q 024947 88 VYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIG 167 (260)
Q Consensus 88 I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG 167 (260)
|++++++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++++|+|||||+++|+++|+||||
T Consensus 114 I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k--~~~~~~vkLPSGe~r~i~~~c~AtiG 191 (273)
T TIGR01171 114 VISGPEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILAK--EGGYVTLRLPSGEMRMVLKECRATIG 191 (273)
T ss_pred EEECCCCCCCCcCCcccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe--cCCEEEEECCCCCeEEECCcCeEEEE
Confidence 9999999999999999999999999999999999999999999999999998 68999999999999999999999999
Q ss_pred eeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccce
Q 024947 168 QVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGL 237 (260)
Q Consensus 168 ~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~ 237 (260)
+|||.++.+++|+|||++||+ ++||+|||||||||||||||||||+.|..+++| |+|+..-.
T Consensus 192 ~Vsn~~~~~~~~gKAG~~r~l-----g~rP~VRGvAMNpvDHPHGGGegk~~~g~~~~s---pwG~~~kg 253 (273)
T TIGR01171 192 EVGNEDHNNIVLGKAGRSRWL-----GIRPTVRGVAMNPVDHPHGGGEGRTPGGRHPVT---PWGKPTKG 253 (273)
T ss_pred EccCCchhccEeccchhheeC-----CCCCccccEecCcccCCCCCCCCcCCCCCCCCC---CCeeeccc
Confidence 999999999999999999998 678999999999999999999999744334555 77766443
No 7
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=8.1e-81 Score=569.68 Aligned_cols=214 Identities=34% Similarity=0.557 Sum_probs=198.2
Q ss_pred cCCCCcccccccccCC--cceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccE
Q 024947 10 KGAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQF 87 (260)
Q Consensus 10 ~g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~ 87 (260)
-||-.++|++.+|++| |++||+|||+|....++++|++|||||||||+||||.|+||+ ++||||||+|++||+
T Consensus 41 ~GRNn~GrITvrhrGGGhKr~yR~IDf~r~~~~i~~~V~~IeyDP~Rsa~IAlv~~~~g~-----~~YIlAp~gl~~Gd~ 115 (276)
T PRK09374 41 GGRNNNGRITVRHRGGGHKRKYRIIDFKRNKDGIPAKVERIEYDPNRSARIALLHYADGE-----KRYILAPKGLKVGDT 115 (276)
T ss_pred CCcCCCccEEEEecCCCccccccccchhhccCCCCEEEEEEEeCCCCCcCEEEEEecCCC-----EEEEEecCCCCCCCE
Confidence 4555899999999999 679999999998777889999999999999999999999984 889999999999999
Q ss_pred EEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCceeEE
Q 024947 88 VYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIG 167 (260)
Q Consensus 88 I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG 167 (260)
|+++.++++++||+|||.+||+||.|||||+.||+||||||||||||+|+++ ++++++|||||||+++|+++|+||||
T Consensus 116 I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k--~~~~~~vkLPSGe~r~i~~~c~AtIG 193 (276)
T PRK09374 116 VVSGPDADIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAK--EGKYATLRLPSGEVRKVLAECRATIG 193 (276)
T ss_pred EEeCCCCCCCccCccccccCCCCCEEEEEEecCCCCceeEeecCCeEEEEEe--cCCEEEEECCCCCeEEEcccccEEEE
Confidence 9999999999999999999999999999999999999999999999999998 69999999999999999999999999
Q ss_pred eeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccee
Q 024947 168 QVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLI 238 (260)
Q Consensus 168 ~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~i 238 (260)
+|||.++.+++|+|||++||+ ++||+||||||||||||||||||++.|...++| |+|+..-..
T Consensus 194 ~Vsn~~~~~~~lgKAG~~r~l-----g~rP~VRGVAMNpvDHPHGGGegkt~~g~~~~s---pwG~~~kg~ 256 (276)
T PRK09374 194 EVGNEEHSNISLGKAGRSRWL-----GIRPTVRGVAMNPVDHPHGGGEGRTSGGRHPVT---PWGKPTKGY 256 (276)
T ss_pred eecCcchhhcchhhhhhheeC-----CCCCccccEecCcccCCCCCCCCcCCCCCCCCC---CCeeecccc
Confidence 999999999999999999998 678999999999999999999999754334455 777664433
No 8
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-67 Score=462.59 Aligned_cols=247 Identities=77% Similarity=1.310 Sum_probs=236.1
Q ss_pred CCccceeeecCCCCcccccccccCCcceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEecc
Q 024947 1 MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAE 80 (260)
Q Consensus 1 mgk~~~~qr~g~~~~~R~~~~~~~gk~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~e 80 (260)
||..++.||. .|+.|..+ +++.+.-. |..||....+.+++.|++|.|||.|-|++|.|.|-| ++.....++|.|
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 9999999998 45899999 88888877 999998777789999999999999999999999998 333567889999
Q ss_pred CCccccEEEEecCccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeC
Q 024947 81 GMYTGQFVYCGRKATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPS 160 (260)
Q Consensus 81 gl~~Gd~I~sg~~~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~ 160 (260)
+|+.||+++++.++++.+||++|+.++|+||.|||+|..+|+.+.|+|++|.|+++|++|+|.+.+.|+||||..+.+++
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 CCceeEEeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccceeee
Q 024947 161 GCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIAA 240 (260)
Q Consensus 161 ~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~appg~kvg~ia~ 240 (260)
.|+|+||+|++.+..+++|.|||+.+|+|+.+++.||+||||||||||||||||+|||+|+|||+.|++++|||||+|||
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 eccCcccchhhhh
Q 024947 241 RRTGRLRGQAAAT 253 (260)
Q Consensus 241 rrtg~~r~~~~~~ 253 (260)
||||++||+++..
T Consensus 235 rrtg~~rg~~~~~ 247 (248)
T KOG2309|consen 235 RRTGRLRGAAAVQ 247 (248)
T ss_pred EEEeeeccccccc
Confidence 9999999987653
No 9
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-61 Score=437.52 Aligned_cols=207 Identities=31% Similarity=0.476 Sum_probs=191.0
Q ss_pred CCCCcccccccccCC--cceEEeeecccccCCc-----eeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCc
Q 024947 11 GAGSVFKSHTHHRKG--PARFRSLDFGERNGYL-----KGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMY 83 (260)
Q Consensus 11 g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~-----~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~ 83 (260)
||-.++|+..||++| |++||+|||.|..+.. ++.|++|||||||||+||||++.++ +++||||+|||+
T Consensus 64 GRd~tGriv~~h~GGGhKq~yr~idF~R~~p~~~~~~~~e~v~~i~yDP~Rs~~iaLv~~~~~-----~~~~Ila~egm~ 138 (312)
T KOG0438|consen 64 GRDETGRIVVRHIGGGHKQRYRMIDFARPRPIEQGTTTEERVIEIEYDPGRSAKIALVAGGTG-----ELRYILATEGLK 138 (312)
T ss_pred CCccccceEEEEecCceeeeeeEeeeccCCCccccccccceEEEEEECCCccccEEEEeccCC-----CeeEEEEecCCC
Confidence 555899999999999 7899999999876533 4599999999999999999999755 389999999999
Q ss_pred cccEEEEecCcc-----ccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEE
Q 024947 84 TGQFVYCGRKAT-----LVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIV 158 (260)
Q Consensus 84 ~Gd~I~sg~~~~-----~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i 158 (260)
+||+|.|+.+.+ .++||++||.+||+||.|||||+.|+.+++|||||||+++|+++ ++.+++|+|||++.+.|
T Consensus 139 aGD~i~ss~~i~~~av~~~~Gna~Pl~~lp~GT~ih~~e~~p~~~~~f~raAGt~a~ilak--~~~~aiv~Lps~r~~~~ 216 (312)
T KOG0438|consen 139 AGDTILSSRKIPFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGTSATILAK--AGKFAIVQLPSKRERSV 216 (312)
T ss_pred CCCccccccccccccccccCCCceeecccchhhhhhhhccCCCcchhhhhhcCchhhhhhc--CCCceeEEccccchhhh
Confidence 999999988765 69999999999999999999999999999999999999999999 68999999999999999
Q ss_pred eCCCceeEEeeeCCCcccchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCCCCCCCCCCCCCCC
Q 024947 159 PSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDA 229 (260)
Q Consensus 159 ~~~c~AtIG~vsn~~~~~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~~~~G~~s~~~r~a 229 (260)
+.+|+||||+|||.+|+.+.+||||++||+ ++||.||||+||++|||||||.++.++...+++.++
T Consensus 217 ~~tC~ATvGrvsni~~~~r~~GkAgr~rwl-----G~Rp~vrg~~~s~~~H~kgg~~gr~i~~~~P~~~~~ 282 (312)
T KOG0438|consen 217 LRTCVATVGRVSNIDHNHRILGKAGRSRWL-----GKRPQVRGVLMSGLDHPKGGGKGRKIGRKKPVTPWG 282 (312)
T ss_pred hhhhheeeccccccccccceecccchhhhc-----ccCcccccccccCccCCCCCCccccccCCCCCCccc
Confidence 999999999999999999999999999998 678999999999999999999998888766666443
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=2.5e-58 Score=381.51 Aligned_cols=129 Identities=49% Similarity=0.791 Sum_probs=122.4
Q ss_pred ccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCceeEEeeeCCCcc
Q 024947 96 LVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIGQVAGGGRT 175 (260)
Q Consensus 96 ~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG~vsn~~~~ 175 (260)
|++||++||.+||+||.|||||++||+|++|||||||||+|+++ ++++++|||||||+++|+.+|+||||+|||.++.
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 58999999999999999999999999999999999999999999 5799999999999999999999999999999999
Q ss_pred cchhhhcccccccccccCCCCceeceeecCCCCCCCCCCCC-CCCCCCCCCCCCCCC
Q 024947 176 EKPLLKAGNAYHKFRVKRNCWPKVRGVAMNPVEHPHGGGNH-QHIGHASTVRRDAPP 231 (260)
Q Consensus 176 ~~~lgKAG~~r~~~~~~~~~~P~VRGvAMNpvDHPHGGG~~-~~~G~~s~~~r~app 231 (260)
+++|+|||++||+ ++||+|||||||||||||||||+ +++|+|+++++|++|
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 9999999999998 67999999999999999999995 679999999999987
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=99.93 E-value=5e-26 Score=172.88 Aligned_cols=75 Identities=33% Similarity=0.639 Sum_probs=67.5
Q ss_pred CCCCcccccccccCC--cceEEeeecccccCCceeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccEE
Q 024947 11 GAGSVFKSHTHHRKG--PARFRSLDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFV 88 (260)
Q Consensus 11 g~~~~~R~~~~~~~g--k~~yr~IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~I 88 (260)
||+.+||+++||++| |++||+|||+|....++++|++|||||||||+||||.|+|| +++||||||||++||+|
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 678669999999999 99999999999777789999999999999999999999998 48999999999999999
Q ss_pred EE
Q 024947 89 YC 90 (260)
Q Consensus 89 ~s 90 (260)
+|
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=90.67 E-value=2.2 Score=40.54 Aligned_cols=104 Identities=14% Similarity=0.153 Sum_probs=67.9
Q ss_pred eecCCCCcccccccccCCc--c--eEEeeecccccCCceeEEEEEEeCC-CCccceEEEEecCCCccCceeEEEEeccCC
Q 024947 8 QRKGAGSVFKSHTHHRKGP--A--RFRSLDFGERNGYLKGVITEIIHDP-GRGAPLARVTFRHPFRYQHQKELFVAAEGM 82 (260)
Q Consensus 8 qr~g~~~~~R~~~~~~~gk--~--~yr~IDf~R~~~~~~~~V~~IeyDP-nRsA~IAlV~~~~g~~~~~~~~YIlA~egl 82 (260)
+..++-...+++..+.+++ + ....+|.++.. +...+|+.++||+ +|+.-++++...-|-..|...++|
T Consensus 15 ~~~~~~~~a~i~~~~~~t~~~r~~l~~~~~l~~~~-p~~~~~~~~~~~~~GRd~tGriv~~h~GGGhKq~yr~i------ 87 (312)
T KOG0438|consen 15 KSAGRTVSARITVLKPGTPSLRNGLLQQPDLKKST-PSRPLVESLKINGLGRDETGRIVVRHIGGGHKQRYRMI------ 87 (312)
T ss_pred ccCCCcccceeeecccCCccccCcccccchhhhcC-CCcceeeeEEecCCCCccccceEEEEecCceeeeeeEe------
Confidence 3334334446667777764 2 44556666554 4578999999999 999999988766554443333333
Q ss_pred ccccEEEEecCccccCCCcccCcCCCCCC----EEEEEeeeCCCCceEEeccCCeEE
Q 024947 83 YTGQFVYCGRKATLVVGNVLPLRSIPEGA----VVCNVEHHVGDRGVFARCSGDYAV 135 (260)
Q Consensus 83 ~~Gd~I~sg~~~~~~~Gn~lpL~~IP~Gt----~I~nIE~~pg~Ggkl~RsAGt~a~ 135 (260)
|+. +-.-+-.+| .|..||.-||.-+++|-.|+....
T Consensus 88 ---dF~--------------R~~p~~~~~~~~e~v~~i~yDP~Rs~~iaLv~~~~~~ 127 (312)
T KOG0438|consen 88 ---DFA--------------RPRPIEQGTTTEERVIEIEYDPGRSAKIALVAGGTGE 127 (312)
T ss_pred ---eec--------------cCCCccccccccceEEEEEECCCccccEEEEeccCCC
Confidence 333 222233333 788999999999999999987333
No 13
>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=85.45 E-value=0.46 Score=21.74 Aligned_cols=8 Identities=75% Similarity=1.294 Sum_probs=6.3
Q ss_pred CCCCCCCC
Q 024947 210 PHGGGNHQ 217 (260)
Q Consensus 210 PHGGG~~~ 217 (260)
|||||-||
T Consensus 1 phgG~Wgq 8 (8)
T PF03991_consen 1 PHGGGWGQ 8 (8)
T ss_pred CCCCcCCC
Confidence 89998764
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=62.58 E-value=38 Score=25.38 Aligned_cols=25 Identities=28% Similarity=0.284 Sum_probs=19.5
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|..++|||... .||+++.-+|.
T Consensus 2 ~~~Vfk~~~d~~~G-~i~~~Rv~sG~ 26 (86)
T cd03699 2 RALIFDSWYDPYRG-VIALVRVFDGT 26 (86)
T ss_pred EEEEEEeeccCCCC-EEEEEEEEcCE
Confidence 47899999999754 57888777774
No 15
>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=59.86 E-value=28 Score=25.71 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=19.9
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|.+++|||. ...||+++.-+|.
T Consensus 2 ~a~VfK~~~d~~-~g~i~~~Ri~sGt 26 (83)
T cd04092 2 CALAFKVVHDPQ-RGPLTFVRVYSGT 26 (83)
T ss_pred EEEEEecccCCC-CCeEEEEEEecCE
Confidence 467999999997 4568888877874
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=58.39 E-value=52 Score=24.35 Aligned_cols=25 Identities=12% Similarity=-0.083 Sum_probs=19.4
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|.+++|||.. ..||+++.-+|.
T Consensus 2 ~~~vfk~~~d~~~-g~i~~~Rv~sG~ 26 (86)
T cd03691 2 QMLVTTLDYDDYV-GRIAIGRIFRGT 26 (86)
T ss_pred eEEEEEeEecCCC-CeEEEEEEEeCE
Confidence 4679999999965 447888877774
No 17
>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=57.84 E-value=27 Score=25.81 Aligned_cols=24 Identities=8% Similarity=-0.006 Sum_probs=20.5
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|-.++|||. ..|++++..+|.
T Consensus 2 ~a~vfK~~~~~~--G~i~~~Rv~sG~ 25 (81)
T cd04091 2 VGLAFKLEEGRF--GQLTYMRIYQGK 25 (81)
T ss_pred eEEEEEeecCCC--CCEEEEEEecCE
Confidence 478999999985 899999988884
No 18
>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=51.24 E-value=23 Score=23.61 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=21.3
Q ss_pred EEEEeecCCCCeEEEecCCCceeEEeCC
Q 024947 134 AVVISHNPDNDTTRIKLPSGAKKIVPSG 161 (260)
Q Consensus 134 a~Ii~k~~~~~~~~vkLPSGe~r~i~~~ 161 (260)
|.|+.. +++.++|++.+|+.+.++.+
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 567765 58999999999999988754
No 19
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=46.33 E-value=17 Score=38.07 Aligned_cols=120 Identities=18% Similarity=0.199 Sum_probs=78.1
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecCC-----Ccc----CceeEEEEeccCCccccEEEEe---cC------
Q 024947 32 LDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHP-----FRY----QHQKELFVAAEGMYTGQFVYCG---RK------ 93 (260)
Q Consensus 32 IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g-----~~~----~~~~~YIlA~egl~~Gd~I~sg---~~------ 93 (260)
|-||.......-+|.+|+..=+||.-|..|...++ .+. -++..|| +-.++.+||.|... +-
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 IAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEI-KRKDIRIGDTVVVRKAGDVIPQVVG 388 (667)
T ss_pred eeecCCchheeeEEEEEEEecCCceeeeeeEEEEeEEECCEEEEEeecCCHHHH-HhcCCCCCCEEEEEecCCCCcceee
Confidence 56665455556789999999999988776655443 211 1112344 56889999999753 21
Q ss_pred --ccccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccC---CeEEEEeecCCCCeEEEecCCCceeEEeCCCceeEE
Q 024947 94 --ATLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSG---DYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAMIG 167 (260)
Q Consensus 94 --~~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAG---t~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~AtIG 167 (260)
.+..+++..|+. +|.-+.+|+=++....+....|.-+ |-|+.+.+ -+-++|.+||=.-|
T Consensus 389 Vv~e~R~~~~~~~~-~P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq~~e~--------------l~hfvSr~AmdI~G 452 (667)
T COG0272 389 VVLEKRPGNEKPIP-FPTHCPVCGSELVREEGEVVIRCTNGLNCPAQLKER--------------LIHFVSRNALDIDG 452 (667)
T ss_pred eecccCCCCCCCCC-CCCCCCCCCCeeEeccCceeEecCCCCCChHHHhhh--------------eeeEecCCccCCCC
Confidence 245788888877 9999999987777766666666554 33444332 34556666665554
No 20
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=40.56 E-value=18 Score=32.23 Aligned_cols=27 Identities=30% Similarity=0.389 Sum_probs=19.7
Q ss_pred ceEEeeeccccc------CCceeEEEEEEeCCC
Q 024947 27 ARFRSLDFGERN------GYLKGVITEIIHDPG 53 (260)
Q Consensus 27 ~~yr~IDf~R~~------~~~~~~V~~IeyDPn 53 (260)
.+|..-||--.- +.++|++++|||||.
T Consensus 117 ~ry~Y~Df~IkvGtvTmg~tvKGi~vEIEY~pc 149 (217)
T KOG4309|consen 117 TRYQYCDFLIKVGTVTMGPTVKGISVEIEYGPC 149 (217)
T ss_pred ceeeecceEEEEcceEeccccceEEEEEeeCCE
Confidence 467777775321 357899999999994
No 21
>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=40.46 E-value=80 Score=23.08 Aligned_cols=25 Identities=28% Similarity=0.303 Sum_probs=19.1
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|.+++|||.+. .+|+++..+|.
T Consensus 2 ~a~Vfk~~~d~~~G-~~~~~Rv~sG~ 26 (83)
T cd04088 2 VALVFKTIHDPFVG-KLSFVRVYSGT 26 (83)
T ss_pred EEEEEEcccCCCCc-eEEEEEEecCE
Confidence 46799999999654 47888777774
No 22
>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=38.20 E-value=1.7e+02 Score=21.86 Aligned_cols=27 Identities=22% Similarity=0.192 Sum_probs=20.6
Q ss_pred CceeEEEEEEeCCCCccceEEEEecCCC
Q 024947 40 YLKGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 40 ~~~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
+..+.|..++|||.. ..||.++.-.|.
T Consensus 3 p~~~~Vfkv~~d~~~-G~la~~RV~sG~ 29 (85)
T cd03690 3 ELSGTVFKIERDDKG-ERLAYLRLYSGT 29 (85)
T ss_pred CcEEEEEEeEECCCC-CeEEEEEEccCE
Confidence 456899999999964 577877776774
No 23
>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=34.36 E-value=18 Score=27.53 Aligned_cols=16 Identities=44% Similarity=1.082 Sum_probs=12.1
Q ss_pred CCceece--eecCCCCCC
Q 024947 195 CWPKVRG--VAMNPVEHP 210 (260)
Q Consensus 195 ~~P~VRG--vAMNpvDHP 210 (260)
-||+.-| |+|||++|-
T Consensus 51 aWPR~agpPVvmNPisrq 68 (73)
T PF06592_consen 51 AWPREAGPPVVMNPISRQ 68 (73)
T ss_pred hCcccCCCCeeecccccc
Confidence 3777655 999999873
No 24
>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=30.31 E-value=98 Score=25.24 Aligned_cols=37 Identities=14% Similarity=0.325 Sum_probs=29.5
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccEEEEecC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRK 93 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~I~sg~~ 93 (260)
.|.|++..-|+++..-+-+|-| ||. |++||+|..+..
T Consensus 2 ~gtVlEvk~~~G~G~t~dvIl~-~Gt--------------L~~GD~Iv~g~~ 38 (110)
T cd03703 2 QGTVLEVKEEEGLGTTIDVILY-DGT--------------LREGDTIVVCGL 38 (110)
T ss_pred cEEEEEEEEcCCCceEEEEEEE-CCe--------------EecCCEEEEccC
Confidence 5889999999999988887765 563 688899886543
No 25
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. 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. 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 the 60S ribosomal subunit. 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 in EF1A, eEF1A and aeIF2gamma.
Probab=30.21 E-value=2.6e+02 Score=21.63 Aligned_cols=57 Identities=23% Similarity=0.257 Sum_probs=36.2
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccEEEEecCc----cccCCCcccCcCCCCCCEE
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKA----TLVVGNVLPLRSIPEGAVV 113 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~I~sg~~~----~~~~Gn~lpL~~IP~Gt~I 113 (260)
+|.|++..-|.++...+-+|-. +|. |++||.|.++... .+..-+=-.|....+++.|
T Consensus 2 ~g~ViE~~~~~g~G~vatviV~-~Gt--------------L~~Gd~iv~G~~~GkVr~~~d~~g~~v~~a~Ps~~v 62 (95)
T cd03701 2 EGTVIESKLDKGRGPVATVIVQ-NGT--------------LKKGDVIVAGGTYGKIRTMVDENGKALLEAGPSTPV 62 (95)
T ss_pred eEEEEEEEecCCCCeeEEEEEE-cCe--------------EecCCEEEECCccceEEEEECCCCCCccccCCCCCE
Confidence 5889999999998877665543 663 6889999886531 1111112245566666655
No 26
>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=30.21 E-value=1.2e+02 Score=30.45 Aligned_cols=21 Identities=14% Similarity=0.010 Sum_probs=17.3
Q ss_pred ceeEEEEEEeCCCC--ccceEEE
Q 024947 41 LKGVITEIIHDPGR--GAPLARV 61 (260)
Q Consensus 41 ~~~~V~~IeyDPnR--sA~IAlV 61 (260)
.+-+++.++|.|+. ..+|+||
T Consensus 216 ~~p~lv~l~Y~g~~~~~~~i~LV 238 (468)
T cd00433 216 EPPRLIVLEYKGKGASKKPIALV 238 (468)
T ss_pred CCCEEEEEEECCCCCCCCcEEEE
Confidence 45689999999876 5789997
No 27
>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=27.78 E-value=2.5e+02 Score=21.91 Aligned_cols=58 Identities=19% Similarity=0.247 Sum_probs=34.8
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCCccCceeEEEEeccCCccccEEEEecCc----cccCCCcccCcCCCCCCEEE
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPFRYQHQKELFVAAEGMYTGQFVYCGRKA----TLVVGNVLPLRSIPEGAVVC 114 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~~~~~~~~YIlA~egl~~Gd~I~sg~~~----~~~~Gn~lpL~~IP~Gt~I~ 114 (260)
+|.|++..-|.++....-++- .+|. |++||.|.+|... .+..=+--++.....++.|.
T Consensus 2 ~g~VlE~~~~~g~G~vatviV-~~Gt--------------L~~Gd~iv~G~~~gkVr~l~d~~g~~v~~a~Ps~~V~ 63 (95)
T cd03702 2 EGVVIESKLDKGRGPVATVLV-QNGT--------------LKVGDVLVAGTTYGKVRAMFDENGKRVKEAGPSTPVE 63 (95)
T ss_pred eEEEEEEEecCCCCccEEEEE-EcCe--------------EeCCCEEEEcccccEEEEEECCCCCCCCEECCCCcEE
Confidence 588999999998766644442 3663 6888888876531 12222224555555555553
No 28
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=27.70 E-value=1.1e+02 Score=24.51 Aligned_cols=42 Identities=14% Similarity=0.076 Sum_probs=33.0
Q ss_pred CCceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCcee
Q 024947 122 DRGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRAM 165 (260)
Q Consensus 122 ~Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~At 165 (260)
.|.+..-++|=|++|+.- +++.+.|++..|-...|+..+-+.
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 345677899999999988 468999999988777777765443
No 29
>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=27.44 E-value=1e+02 Score=32.33 Aligned_cols=106 Identities=11% Similarity=0.116 Sum_probs=62.6
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecCCCcc---------CceeEEEEeccCCccccEEEEe---cCcc----
Q 024947 32 LDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRY---------QHQKELFVAAEGMYTGQFVYCG---RKAT---- 95 (260)
Q Consensus 32 IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~---------~~~~~YIlA~egl~~Gd~I~sg---~~~~---- 95 (260)
|=||.......-+|.+|++..+||..|..|...++..+ .++..| |.-.++.+||.|... +-.+
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 IAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDE-IEELDIRIGDTVVVRKAGDVIPKVVR 376 (652)
T ss_pred EEEcCCCceeeEEEEEEEEecCCCceeeeEEEEeeEEECCEEEEEeecCCHHH-HHHcCCCCCCEEEEEecCCcCceeee
Confidence 55665555566799999999999977766654443211 011223 366789999999753 2211
Q ss_pred ----ccCCCcccCcCCCCCCEEEEEeeeCCCC--ceEEeccCCeEEEEee
Q 024947 96 ----LVVGNVLPLRSIPEGAVVCNVEHHVGDR--GVFARCSGDYAVVISH 139 (260)
Q Consensus 96 ----~~~Gn~lpL~~IP~Gt~I~nIE~~pg~G--gkl~RsAGt~a~Ii~k 139 (260)
...++..|+ .+|....+|+=++.--++ ..+|-...|-++++.+
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 223554443 478888888855543333 3345444456666543
No 30
>PRK00913 multifunctional aminopeptidase A; Provisional
Probab=27.09 E-value=1.5e+02 Score=30.11 Aligned_cols=20 Identities=20% Similarity=0.215 Sum_probs=16.9
Q ss_pred ceeEEEEEEeCCCCccceEEE
Q 024947 41 LKGVITEIIHDPGRGAPLARV 61 (260)
Q Consensus 41 ~~~~V~~IeyDPnRsA~IAlV 61 (260)
.+-+++.++|.|+. .+|+||
T Consensus 233 ~~prli~l~Y~g~~-~~i~LV 252 (483)
T PRK00913 233 NPPRLIVLEYKGGK-KPIALV 252 (483)
T ss_pred CCCeEEEEEECCCC-CeEEEE
Confidence 45689999999887 889997
No 31
>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=26.53 E-value=1.4e+02 Score=22.87 Aligned_cols=40 Identities=13% Similarity=0.077 Sum_probs=31.0
Q ss_pred CceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCce
Q 024947 123 RGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRA 164 (260)
Q Consensus 123 Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~A 164 (260)
|-+..-++|=|++|.+- +++++.|.+..|-...++.++-+
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 45577889999999988 47889999988877777766543
No 32
>smart00532 LIGANc Ligase N family.
Probab=26.27 E-value=1.1e+02 Score=30.67 Aligned_cols=86 Identities=15% Similarity=0.193 Sum_probs=51.0
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecCCC-----cc----CceeEEEEeccCCccccEEEEe---cCcc----
Q 024947 32 LDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPF-----RY----QHQKELFVAAEGMYTGQFVYCG---RKAT---- 95 (260)
Q Consensus 32 IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~-----~~----~~~~~YIlA~egl~~Gd~I~sg---~~~~---- 95 (260)
|=||.......-+|.+|++..+||..|.-|...++. ++ .++..| |.-.++.+||.|... +-.+
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 IAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDE-IEEKDIRIGDTVVVRKAGDVIPKVVG 383 (441)
T ss_pred EEECCCCceeEEEEEEEEEecCCCceeeEEEEEEeEEECCEEEEecccCCHHH-HHHcCCCCCCEEEEEECCCcCcceee
Confidence 666655555678999999999999776655544432 11 111223 366789999999753 2211
Q ss_pred ----ccCCCcccCcCCCCCCEEEEEeee
Q 024947 96 ----LVVGNVLPLRSIPEGAVVCNVEHH 119 (260)
Q Consensus 96 ----~~~Gn~lpL~~IP~Gt~I~nIE~~ 119 (260)
...++..+ -.+|.-..+|+=++.
T Consensus 384 vv~~~r~~~~~~-~~~P~~CP~C~s~l~ 410 (441)
T smart00532 384 VVKEKRPGDERE-IEMPTHCPSCGSELV 410 (441)
T ss_pred cccccCCCCCcc-CcCCCCCCCCCCEeE
Confidence 12233332 246777667765543
No 33
>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=24.87 E-value=4.2e+02 Score=26.90 Aligned_cols=86 Identities=17% Similarity=0.176 Sum_probs=48.5
Q ss_pred CCceeEEEEEEe--CCCCccceEEEEecCCCccCce--------eEE------------EEeccCCccccEEEEecCccc
Q 024947 39 GYLKGVITEIIH--DPGRGAPLARVTFRHPFRYQHQ--------KEL------------FVAAEGMYTGQFVYCGRKATL 96 (260)
Q Consensus 39 ~~~~~~V~~Iey--DPnRsA~IAlV~~~~g~~~~~~--------~~Y------------IlA~egl~~Gd~I~sg~~~~~ 96 (260)
....|.|-.+.+ ||..--.||.++.-.|...... +.+ ....+.+++||+|-...-..+
T Consensus 292 ~~~~~~VFK~~~~mdp~~~griaf~RV~sG~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDI~~~~~~~~~ 371 (527)
T TIGR00503 292 EKFSGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDIIGLHNHGTI 371 (527)
T ss_pred CCeeEEEEEEEeccCcccCceEEEEEEeeeEEcCCCEEEecCCCCcEEecchhhhhcCCceEcceeCCCCEEEEECCCCc
Confidence 346799999999 9855556676665555311000 000 123466778888765544455
Q ss_pred cCCCcc------cCcCCCCCCEEEEEeeeCCCCc
Q 024947 97 VVGNVL------PLRSIPEGAVVCNVEHHVGDRG 124 (260)
Q Consensus 97 ~~Gn~l------pL~~IP~Gt~I~nIE~~pg~Gg 124 (260)
..|+++ .+..||.-..++...+.|-+.+
T Consensus 372 ~~GDtl~~~~~~~~~~i~~~~P~~~~~v~~~~~~ 405 (527)
T TIGR00503 372 QIGDTFTQGEKIKFTGIPNFAPELFRRIRLKDPL 405 (527)
T ss_pred ccCCEecCCCceeecCCCCCCcceEEEEEECChh
Confidence 666665 3444555555555555555443
No 34
>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=24.74 E-value=25 Score=26.87 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=0.0
Q ss_pred CceEEeccCCeEEEEeecCCCCeEEEecCCCceeEEeCCCce
Q 024947 123 RGVFARCSGDYAVVISHNPDNDTTRIKLPSGAKKIVPSGCRA 164 (260)
Q Consensus 123 Ggkl~RsAGt~a~Ii~k~~~~~~~~vkLPSGe~r~i~~~c~A 164 (260)
|.+..-++|-|++|.+- +++.+.|++.+|-...++.++-+
T Consensus 40 Gd~VvT~gGi~G~V~~i--~~~~v~lei~~g~~i~v~k~aI~ 79 (82)
T PF02699_consen 40 GDEVVTIGGIYGTVVEI--DDDTVVLEIAPGVEITVEKSAIA 79 (82)
T ss_dssp ------------------------------------------
T ss_pred CCEEEECCcEEEEEEEE--eCCEEEEEECCCeEEEEEHHHhH
Confidence 45567889999999988 68999999999977777766544
No 35
>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=24.21 E-value=4.2e+02 Score=27.64 Aligned_cols=27 Identities=19% Similarity=0.177 Sum_probs=22.0
Q ss_pred CceeEEEEEEeCCCCccceEEEEecCCC
Q 024947 40 YLKGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 40 ~~~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
...+.|.+++|||.+. .|++++.-+|.
T Consensus 307 ~l~a~VfK~~~d~~~G-~i~~~RV~sGt 333 (689)
T TIGR00484 307 PFSALAFKVATDPFVG-QLTFVRVYSGV 333 (689)
T ss_pred ceEEEEEEeeecCCCC-eEEEEEEEEeE
Confidence 4678999999999876 78888776663
No 36
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=23.61 E-value=1.2e+02 Score=31.82 Aligned_cols=106 Identities=15% Similarity=0.157 Sum_probs=61.9
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecCCCcc---------CceeEEEEeccCCccccEEEEe---cCc-----
Q 024947 32 LDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRY---------QHQKELFVAAEGMYTGQFVYCG---RKA----- 94 (260)
Q Consensus 32 IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~---------~~~~~YIlA~egl~~Gd~I~sg---~~~----- 94 (260)
|=||.......-+|.+|++..+||..|..|...++..+ .++..|| .-.++.+||.|... +-.
T Consensus 310 iA~Kf~~~~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrAtLhN~~~i-~~~~i~iGD~V~V~raGdVIP~i~~ 388 (665)
T PRK07956 310 IAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEI-ERKDIRIGDTVVVRRAGDVIPEVVG 388 (665)
T ss_pred eEecCCCceeEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeecCCHHHH-HHcCCCCCCEEEEEECCCccceeee
Confidence 55665555567899999999999988877765544211 0111232 55789999999753 211
Q ss_pred ---cccCCCcccCcCCCCCCEEEEEeeeCCCCceEEecc---CCeEEEEee
Q 024947 95 ---TLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCS---GDYAVVISH 139 (260)
Q Consensus 95 ---~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsA---Gt~a~Ii~k 139 (260)
+..+++.-| -.+|.-..+|+=++.--.++...|.- .|-++++.+
T Consensus 389 vv~~~r~~~~~~-~~~P~~CP~Cgs~l~~~~~~~~~~C~n~~~C~aq~~~~ 438 (665)
T PRK07956 389 VVLEKRPGDERE-IVMPTHCPVCGSELVRVEGEAVLRCTNGLSCPAQLKER 438 (665)
T ss_pred eecccCCCCCcc-CcCCCCCCCCCCEeEecCCCeEEECCCCCCCHHHHHHH
Confidence 122344433 24788788887555433343333332 355666644
No 37
>PF00883 Peptidase_M17: Cytosol aminopeptidase family, catalytic domain; InterPro: IPR000819 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The 2 zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3KZW_L 3KQX_C 3KQZ_L 3KR4_I 3KR5_J 3T8W_C 3H8F_D 3H8G_A 3H8E_B 3IJ3_A ....
Probab=22.21 E-value=1.2e+02 Score=29.04 Aligned_cols=22 Identities=14% Similarity=0.028 Sum_probs=16.7
Q ss_pred CceeEEEEEEeCCCC---ccceEEE
Q 024947 40 YLKGVITEIIHDPGR---GAPLARV 61 (260)
Q Consensus 40 ~~~~~V~~IeyDPnR---sA~IAlV 61 (260)
..+-.++.++|.|+. .-+|+||
T Consensus 59 ~~~P~lv~l~Y~g~~~~~~~~i~LV 83 (311)
T PF00883_consen 59 RHPPRLVVLEYKGNGGKSKKPIALV 83 (311)
T ss_dssp SS--EEEEEEEETSTSTTSEEEEEE
T ss_pred CCCCEEEEEEECCCCCCCCccEEEE
Confidence 346789999999997 6679988
No 38
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.58 E-value=56 Score=34.38 Aligned_cols=103 Identities=16% Similarity=0.211 Sum_probs=60.2
Q ss_pred eecccccCCceeEEEEEEeCCCCccceEEEEecCCCcc---------CceeEEEEeccCCccccEEEEe---cCc-----
Q 024947 32 LDFGERNGYLKGVITEIIHDPGRGAPLARVTFRHPFRY---------QHQKELFVAAEGMYTGQFVYCG---RKA----- 94 (260)
Q Consensus 32 IDf~R~~~~~~~~V~~IeyDPnRsA~IAlV~~~~g~~~---------~~~~~YIlA~egl~~Gd~I~sg---~~~----- 94 (260)
|=||.......-+|.+|++..+||..|..|...++..+ .++..| |.-.++.+||.|... +-.
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 MAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDY-IDSIGLNVGDVVKISRRGDVIPAVEL 385 (669)
T ss_pred EEEcCCCceeEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHH-HHHcCCCCCCEEEEEecCCCCCceee
Confidence 55665555567899999999999988776655543211 011123 356789999999642 221
Q ss_pred ---cccCCCcccCcCCCCCCEEEEEeeeCCCCceEEeccCCeEEEEee
Q 024947 95 ---TLVVGNVLPLRSIPEGAVVCNVEHHVGDRGVFARCSGDYAVVISH 139 (260)
Q Consensus 95 ---~~~~Gn~lpL~~IP~Gt~I~nIE~~pg~Ggkl~RsAGt~a~Ii~k 139 (260)
....++ ..+|.-+..|+-++.-+.-..+|-..-|-++++.+
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 122344 34688777777666543223344433355555543
No 39
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. 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. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=21.40 E-value=3.7e+02 Score=20.31 Aligned_cols=26 Identities=12% Similarity=-0.058 Sum_probs=21.1
Q ss_pred eeEEEEEEeCCCCccceEEEEecCCC
Q 024947 42 KGVITEIIHDPGRGAPLARVTFRHPF 67 (260)
Q Consensus 42 ~~~V~~IeyDPnRsA~IAlV~~~~g~ 67 (260)
.+.|..+++||.....+|+++.-.|.
T Consensus 2 ~a~VfK~~~~~~~~~~la~~RV~sGt 27 (94)
T cd04090 2 VVHVTKLYSTSDGGSFWAFGRIYSGT 27 (94)
T ss_pred EEEEEeeeecCCCCEEEEEEEEeeCe
Confidence 36789999999887788888877774
No 40
>PRK05015 aminopeptidase B; Provisional
Probab=21.21 E-value=2.4e+02 Score=28.33 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=14.5
Q ss_pred eeEEEEEEeCCC--Cccce--EEE
Q 024947 42 KGVITEIIHDPG--RGAPL--ARV 61 (260)
Q Consensus 42 ~~~V~~IeyDPn--RsA~I--AlV 61 (260)
+-.++.++|.|. ..+++ |||
T Consensus 166 pP~lv~L~Y~~~g~~~~~v~~aLV 189 (424)
T PRK05015 166 PPVLLALDYNPTGDPDAPVYACLV 189 (424)
T ss_pred CCEEEEEEecCCCCCCCCeeEEEe
Confidence 457899999874 34566 886
No 41
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=20.96 E-value=60 Score=24.08 Aligned_cols=17 Identities=35% Similarity=0.550 Sum_probs=15.0
Q ss_pred CceeceeecCCCCCCCC
Q 024947 196 WPKVRGVAMNPVEHPHG 212 (260)
Q Consensus 196 ~P~VRGvAMNpvDHPHG 212 (260)
...|.-+--|.-+||||
T Consensus 30 ~GiV~~iLT~s~~HP~G 46 (62)
T PF09962_consen 30 EGIVKDILTNSPTHPHG 46 (62)
T ss_pred cEEhheeecCCCCCCCC
Confidence 47888888999999997
No 42
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=20.89 E-value=6.8e+02 Score=25.43 Aligned_cols=87 Identities=20% Similarity=0.204 Sum_probs=52.7
Q ss_pred CceeEEEEEEe--CCCCccceEEEEecCCCccCce--------eE------E-E-----EeccCCccccEEEEecCcccc
Q 024947 40 YLKGVITEIIH--DPGRGAPLARVTFRHPFRYQHQ--------KE------L-F-----VAAEGMYTGQFVYCGRKATLV 97 (260)
Q Consensus 40 ~~~~~V~~Iey--DPnRsA~IAlV~~~~g~~~~~~--------~~------Y-I-----lA~egl~~Gd~I~sg~~~~~~ 97 (260)
...|.|-.+++ ||...-.||.|+.-.|...... +. | + ...+.+++||+|....-..+.
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 46899999997 6755567777766665311000 00 1 1 234556888888665555566
Q ss_pred CCCcc------cCcCCCCCCEEEEEeeeCCCCceE
Q 024947 98 VGNVL------PLRSIPEGAVVCNVEHHVGDRGVF 126 (260)
Q Consensus 98 ~Gn~l------pL~~IP~Gt~I~nIE~~pg~Ggkl 126 (260)
+|++| .+..||.=..++...+.|-+.++.
T Consensus 372 ~GDTL~~~~~~~~~~i~~~~P~~~~~v~p~~~~d~ 406 (526)
T PRK00741 372 IGDTFTQGEKLKFTGIPNFAPELFRRVRLKNPLKQ 406 (526)
T ss_pred cCCCccCCCccccCCCCCCCccEEEEEEECCchhH
Confidence 77776 455666666677666666655443
No 43
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=20.59 E-value=5e+02 Score=26.08 Aligned_cols=19 Identities=16% Similarity=0.240 Sum_probs=14.7
Q ss_pred cCCceeEEEEEEeCCCCcc
Q 024947 38 NGYLKGVITEIIHDPGRGA 56 (260)
Q Consensus 38 ~~~~~~~V~~IeyDPnRsA 56 (260)
...++|.|++++++-.++-
T Consensus 130 reV~EGeV~~l~i~~~~~p 148 (450)
T COG1224 130 REVYEGEVVELEIRRARNP 148 (450)
T ss_pred eEEEEEEEEEEEEeeccCC
Confidence 4578999999998876553
No 44
>COG0260 PepB Leucyl aminopeptidase [Amino acid transport and metabolism]
Probab=20.27 E-value=2e+02 Score=29.21 Aligned_cols=21 Identities=14% Similarity=0.047 Sum_probs=16.7
Q ss_pred ceeEEEEEEeCCCCc--cceEEE
Q 024947 41 LKGVITEIIHDPGRG--APLARV 61 (260)
Q Consensus 41 ~~~~V~~IeyDPnRs--A~IAlV 61 (260)
.+-..+.|+|.++.. .+||||
T Consensus 229 ~~Prlivl~y~g~~~~~~~iaLV 251 (485)
T COG0260 229 RPPRLIVLEYNGKGKAKKPIALV 251 (485)
T ss_pred CCCeEEEEEcCCCCCCCceEEEE
Confidence 345789999999975 678888
Done!