Query 027754
Match_columns 219
No_of_seqs 156 out of 923
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 14:40:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027754.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027754hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01171 rplB_bact ribosomal 100.0 1.1E-68 2.4E-73 478.9 11.7 174 32-217 85-266 (273)
2 PRK09374 rplB 50S ribosomal pr 100.0 1.3E-68 2.9E-73 479.0 12.1 175 31-217 86-268 (276)
3 PTZ00031 ribosomal protein L2; 100.0 2E-68 4.3E-73 484.3 11.9 175 32-218 118-299 (317)
4 CHL00052 rpl2 ribosomal protei 100.0 5.2E-68 1.1E-72 474.6 11.9 175 31-217 84-267 (273)
5 COG0090 RplB Ribosomal protein 100.0 6.5E-67 1.4E-71 464.8 12.1 174 32-217 87-268 (275)
6 PF03947 Ribosomal_L2_C: Ribos 100.0 1.2E-63 2.5E-68 404.8 8.7 129 68-201 1-130 (130)
7 PRK09612 rpl2p 50S ribosomal p 100.0 1.6E-57 3.5E-62 400.5 11.4 147 31-184 51-209 (238)
8 PTZ00180 60S ribosomal protein 100.0 2.3E-55 5.1E-60 390.7 10.7 157 31-198 53-228 (260)
9 KOG0438 Mitochondrial/chloropl 100.0 1.3E-49 2.7E-54 358.8 4.7 180 32-217 114-300 (312)
10 KOG2309 60s ribosomal protein 100.0 1.6E-35 3.5E-40 259.6 7.4 133 64-202 86-224 (248)
11 PF03991 Prion_octapep: Copper 80.7 0.94 2E-05 21.1 0.9 7 176-182 1-7 (8)
12 PF02736 Myosin_N: Myosin N-te 57.7 18 0.0004 23.8 3.5 26 106-132 16-41 (42)
13 TIGR00739 yajC preprotein tran 44.7 41 0.0009 25.5 4.1 38 96-134 42-79 (84)
14 PRK05585 yajC preprotein trans 29.9 1E+02 0.0022 24.4 4.3 39 96-135 57-95 (106)
15 cd01770 p47_UBX p47-like ubiqu 25.4 42 0.00092 24.9 1.4 28 114-141 4-31 (79)
16 smart00166 UBX Domain present 24.2 47 0.001 24.1 1.4 28 114-141 4-31 (80)
17 PF02699 YajC: Preprotein tran 22.2 29 0.00064 26.0 0.0 39 96-135 41-79 (82)
18 PF01176 eIF-1a: Translation i 20.7 1.8E+02 0.0039 20.6 3.9 24 105-128 6-29 (65)
No 1
>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=1.1e-68 Score=478.94 Aligned_cols=174 Identities=49% Similarity=0.837 Sum_probs=157.8
Q ss_pred eccceeecC--C-----CCCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCCC
Q 027754 32 QSSETELVG--D-----PSKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGT 104 (219)
Q Consensus 32 ~~~~~~lv~--~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt 104 (219)
+++.||||- | .+++|.++.+|+|+.. .++++++||+|||.+||+||+|||||+.||+||||||||||
T Consensus 85 Rsa~IAlv~~~~g~~~YIlap~gl~~Gd~I~~g------~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt 158 (273)
T TIGR01171 85 RSARIALLHYADGEKRYILAPKGLKVGDTVISG------PEAPIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAGT 158 (273)
T ss_pred CCcCEEEEEecCCcEEEEEccCCCCCCCEEEEC------CCCCCCCcCCcccccCCCCCEEEEEEecCCCCceEEEecCC
Confidence 667777774 2 2388999998888754 24578999999999999999999999999999999999999
Q ss_pred cEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCCC
Q 027754 105 SAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRS 184 (219)
Q Consensus 105 ~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGks 184 (219)
||+|+.+ ++++++|||||||+|+|+++|+||||+|||.+|.+++++|||++||+|+||+|||||||||||||||||||+
T Consensus 159 ~A~ii~k-~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~~~~~~~~gKAG~~r~lg~rP~VRGvAMNpvDHPHGGGegk~ 237 (273)
T TIGR01171 159 SAQILAK-EGGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRT 237 (273)
T ss_pred eEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCchhccEeccchhheeCCCCCccccEecCcccCCCCCCCCcC
Confidence 9999977 579999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCCCcccCCccccCCCCc-cccC
Q 027754 185 KSSGNHGRCSLTPWGKPCKSGYKTASPKK-KKKL 217 (219)
Q Consensus 185 ~~~~~~gr~~~sPWG~~tk~g~kTr~~~~-~~~~ 217 (219)
+ +|++|+||||++|| |+|||+++| +++|
T Consensus 238 ~----~g~~~~spwG~~~k-g~kTr~~~k~~~~~ 266 (273)
T TIGR01171 238 P----GGRHPVTPWGKPTK-GYKTRKKKKYSDKF 266 (273)
T ss_pred C----CCCCCCCCCeeecc-ccccCCCCCCCCce
Confidence 6 46899999999999 999996544 6665
No 2
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=1.3e-68 Score=478.96 Aligned_cols=175 Identities=48% Similarity=0.831 Sum_probs=159.1
Q ss_pred eeccceeecC--CC-----CCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCC
Q 027754 31 YQSSETELVG--DP-----SKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAG 103 (219)
Q Consensus 31 ~~~~~~~lv~--~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAG 103 (219)
++++.||||- |. +++|.++.+|+|+.. .++++++||+|||.+||+||+|||||++||+|||||||||
T Consensus 86 ~Rsa~IAlv~~~~g~~~YIlAp~gl~~Gd~I~~g------~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RsAG 159 (276)
T PRK09374 86 NRSARIALLHYADGEKRYILAPKGLKVGDTVVSG------PDADIKPGNALPLRNIPVGTTVHNIELKPGKGGQLARSAG 159 (276)
T ss_pred CCCcCEEEEEecCCCEEEEEecCCCCCCCEEEeC------CCCCCCccCccccccCCCCCEEEEEEecCCCCceeEeecC
Confidence 4677888874 22 388999999988864 2456899999999999999999999999999999999999
Q ss_pred CcEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCC
Q 027754 104 TSAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGR 183 (219)
Q Consensus 104 t~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGk 183 (219)
|||+|+.+ ++++++|||||||+|+|+++|+||||+|||.+|.+++++|||++||+|+||+|||||||||||||||||||
T Consensus 160 t~A~ii~k-~~~~~~vkLPSGe~r~i~~~c~AtIG~Vsn~~~~~~~lgKAG~~r~lg~rP~VRGVAMNpvDHPHGGGegk 238 (276)
T PRK09374 160 TSAQLVAK-EGKYATLRLPSGEVRKVLAECRATIGEVGNEEHSNISLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGR 238 (276)
T ss_pred CeEEEEEe-cCCEEEEECCCCCeEEEcccccEEEEeecCcchhhcchhhhhhheeCCCCCccccEecCcccCCCCCCCCc
Confidence 99999977 58999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCcccCCccccCC-CCccccC
Q 027754 184 SKSSGNHGRCSLTPWGKPCKSGYKTAS-PKKKKKL 217 (219)
Q Consensus 184 s~~~~~~gr~~~sPWG~~tk~g~kTr~-~~~~~~~ 217 (219)
++ +|++|+||||++|| |+|||+ +|.++++
T Consensus 239 t~----~g~~~~spwG~~~k-g~kTr~~~k~~~~~ 268 (276)
T PRK09374 239 TS----GGRHPVTPWGKPTK-GYKTRKKNKRSDKF 268 (276)
T ss_pred CC----CCCCCCCCCeeecc-cccccCCCCCCCce
Confidence 86 46899999999999 999996 5556655
No 3
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=2e-68 Score=484.32 Aligned_cols=175 Identities=39% Similarity=0.635 Sum_probs=160.3
Q ss_pred eccceeecC--CC-----CCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCCC
Q 027754 32 QSSETELVG--DP-----SKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGT 104 (219)
Q Consensus 32 ~~~~~~lv~--~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt 104 (219)
+++.||||- |. +++|.++.+|.|+.. .++++++||+|||.+||+||.|||||+.||+||||||||||
T Consensus 118 RsA~IALV~~~dg~~~YIlApeGl~vGd~I~sg------~~a~i~~GN~lPL~~IP~GT~IhNIE~~pG~Ggkl~RSAGt 191 (317)
T PTZ00031 118 RSAHIALLQYEDGVLSYILAPLLLRPGDKIIAS------KYANINPGNSLPLRNIPVGSIVHNVEMRPGAGGQIIRAGGT 191 (317)
T ss_pred CCCcEEEEEecCCcEEEEEccCCCCCCCEEEeC------CCCCCCccCccccccCCCCCEEEEEEecCCCCceEEEecCC
Confidence 677888875 22 388999999988643 35678999999999999999999999999999999999999
Q ss_pred cEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCCC
Q 027754 105 SAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRS 184 (219)
Q Consensus 105 ~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGks 184 (219)
||+|+.+ ++++++|||||||+|+|+.+|+||||+|||.+|.+++++|||++||+|+||+|||||||||||||||||||+
T Consensus 192 ~A~Ii~k-~~~~~~VkLPSGe~r~i~~~C~ATIG~Vsn~~~~~k~lgKAG~~Rwlg~RP~VRGVAMNPVDHPHGGGeGkt 270 (317)
T PTZ00031 192 YATVVSK-DEQFATLKLKSTEIRKFPLDCWATIGQVSNLEHHMRILGKAGVNRWLGKRPVVRGVAMNPSKHPHGGGTSKK 270 (317)
T ss_pred eEEEEEc-cCCEEEEECCCCCEEEECccCeEEEEEccCCccccceeccchhhhcCCCCCCcccCccCCccCCCCCCCCCC
Confidence 9999977 578999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCCCcccCCccccCCCCccccCC
Q 027754 185 KSSGNHGRCSLTPWGKPCKSGYKTASPKKKKKLA 218 (219)
Q Consensus 185 ~~~~~~gr~~~sPWG~~tk~g~kTr~~~~~~~~~ 218 (219)
+ +|++|+||||++|| |+|||++|+.+++.
T Consensus 271 ~----~gr~p~spWG~~tk-G~kTrk~k~~~~~i 299 (317)
T PTZ00031 271 G----TKRPKCSLWGICRD-GYKTRSKKKPLGLI 299 (317)
T ss_pred C----CCCCCCCCCccccC-CcccCCCCCCCceE
Confidence 6 46899999999999 99999877777653
No 4
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=5.2e-68 Score=474.59 Aligned_cols=175 Identities=46% Similarity=0.765 Sum_probs=157.5
Q ss_pred eeccceeecC--C-----CCCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCC
Q 027754 31 YQSSETELVG--D-----PSKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAG 103 (219)
Q Consensus 31 ~~~~~~~lv~--~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAG 103 (219)
++++.||||- | .+++|.++.+|+|+.. .++++++||+|||.+||+||.|||||+.||+|||||||||
T Consensus 84 ~Rsa~IAlv~~~~g~~~YIlAp~gl~~Gd~I~~g------~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pg~Ggk~~RsAG 157 (273)
T CHL00052 84 NRNAYICLIHYGDGEKRYILHPRGLKIGDTIVSG------TEAPIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAG 157 (273)
T ss_pred CCCccEEEEEeCCCcEEEEEccCCCCCCCEEEeC------CCCCCCcccccccccCCCCCEEEEEEecCCCCceEEEecC
Confidence 3667778774 2 2388999999888754 3457899999999999999999999999999999999999
Q ss_pred CcEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCC
Q 027754 104 TSAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGR 183 (219)
Q Consensus 104 t~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGk 183 (219)
|||+|+.+ +++|++|||||||+|+|+.+|+||||+|||.+|.+++++|||++||+|+||+|||||||||||||||||||
T Consensus 158 t~A~ii~k-~~~~~~vkLPSGe~r~v~~~c~AtIG~Vsn~~~~~~~lgKAG~~r~lg~rP~VRGvAMNpvDHPHGGGegk 236 (273)
T CHL00052 158 AVAKLIAK-EGKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAGSKRWLGKRPKVRGVVMNPVDHPHGGGEGR 236 (273)
T ss_pred CeEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCchhhcEecchhhhhcCCCCCcCCeEecCCccCCCCCCCcc
Confidence 99999977 57999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCC-CCCCCCCcccCCccccCC-CCccccC
Q 027754 184 SKSSGNHGR-CSLTPWGKPCKSGYKTAS-PKKKKKL 217 (219)
Q Consensus 184 s~~~~~~gr-~~~sPWG~~tk~g~kTr~-~~~~~~~ 217 (219)
++ +|+ +|+||||++|| |+|||+ +|..+++
T Consensus 237 t~----~Gr~~~vspwG~~~k-g~kTr~~~k~~~~~ 267 (273)
T CHL00052 237 AP----IGRKKPVTPWGKPAL-GRKTRKRKKYSDNL 267 (273)
T ss_pred CC----CCCcCCCCcCccccc-ccCccCCCCCCCCe
Confidence 85 454 68999999999 999995 4555665
No 5
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.5e-67 Score=464.76 Aligned_cols=174 Identities=45% Similarity=0.753 Sum_probs=153.9
Q ss_pred eccceeecCCC-------CCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCCC
Q 027754 32 QSSETELVGDP-------SKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGT 104 (219)
Q Consensus 32 ~~~~~~lv~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt 104 (219)
+|+.||||--. +++|-.+-+|.++.-. ++++++||+|||.+||+||+|||||++||+||||||||||
T Consensus 87 RsA~IAlv~y~dGek~yilAp~Gl~vGd~I~sG~------~a~ik~GN~lpL~~IP~Gt~VhNVE~~pG~GGq~aRSaGt 160 (275)
T COG0090 87 RSAPIALVVYEDGEKRYILAPEGLKVGDVIESGK------DADIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGT 160 (275)
T ss_pred CCcceEEEEecCCCEEEEEccCccccCCEEEeCC------CCCcCCcceeeeccCCCCceEEeeeeccCCCceEEEeCCc
Confidence 55666665433 2555555555544322 6688999999999999999999999999999999999999
Q ss_pred cEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCCC
Q 027754 105 SAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRS 184 (219)
Q Consensus 105 ~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGks 184 (219)
||+|+.+ +++|++|+|||||+|.|+.+|+||||+|+|.+|.+++|+|||++||+|+||+||||||||||||||||||++
T Consensus 161 yA~vv~~-~~~y~~vrLpSGe~r~v~~~CrATIGvV~n~~~~~~~lgKAGr~r~~g~rPtVRGvAMNpvDHPHGGGeg~~ 239 (275)
T COG0090 161 YAQVVGK-EGNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKPLGKAGRARHKGKRPTVRGVAMNPVDHPHGGGEGQH 239 (275)
T ss_pred eEEEEEc-cCCEEEEECCCCCeEeecccccEEEEEecCCccccceecccchhcCCccCCccceeecCCCcCCCCCCCCCC
Confidence 9999977 589999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCCCcccCCccccCC-CCccccC
Q 027754 185 KSSGNHGRCSLTPWGKPCKSGYKTAS-PKKKKKL 217 (219)
Q Consensus 185 ~~~~~~gr~~~sPWG~~tk~g~kTr~-~~~~~~~ 217 (219)
+ +|++|+||||++++ |||||. +|++++|
T Consensus 240 ~----ggk~p~~pwg~~~~-Gkktr~~~krt~~~ 268 (275)
T COG0090 240 P----GGKPPTVPWGKPTP-GKKTRIAAKRTGKF 268 (275)
T ss_pred C----CCCCCCCCCCCCCC-cccccccccccCce
Confidence 5 36899999999999 799999 6777775
No 6
>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=1.2e-63 Score=404.81 Aligned_cols=129 Identities=61% Similarity=1.125 Sum_probs=122.2
Q ss_pred CCCCceecCCCCCCcceEeeeeeccCCCCceeecCCCcEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCc
Q 027754 68 SQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGA 147 (219)
Q Consensus 68 ~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~ 147 (219)
|++||++||.+||+||+|||||++||+|++|||||||||+|+++ ++++++|||||||+|+|+.+|+||||+|||.+|++
T Consensus 1 i~~Gn~~pL~~ip~Gt~I~nIE~~pg~g~~~~RaAGt~a~ii~k-~~~~~~ikLPSG~~k~v~~~c~AtiG~vsn~~~~~ 79 (130)
T PF03947_consen 1 IKIGNSLPLGNIPIGTIIHNIELKPGDGGKLARAAGTYAQIISK-EGNYVVIKLPSGEIKLVSSNCRATIGRVSNGGHKE 79 (130)
T ss_dssp SSTTSEEEGGGSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEE-ESSEEEEEETTSEEEEEETTSEEEESCBSSTTGGG
T ss_pred CCCccchhHhhCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEe-ccceeEEEecCCCeEeecccceEEEEEecCccccc
Confidence 58999999999999999999999999999999999999999977 46999999999999999999999999999999999
Q ss_pred cccccccccccCCCCCccceeecCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCcc
Q 027754 148 KKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRSKSSGNHGR-CSLTPWGKP 201 (219)
Q Consensus 148 ~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGks~~~~~~gr-~~~sPWG~~ 201 (219)
++++|||++||+|+||+|||||||||||||||||||++ +|| +|+||||+|
T Consensus 80 ~~~~KAG~~r~~g~rP~VRGvamNpvdHPhGGG~g~~~----~gr~~~~s~wg~p 130 (130)
T PF03947_consen 80 KKLGKAGRNRWLGKRPKVRGVAMNPVDHPHGGGEGKTS----GGRPPPVSPWGKP 130 (130)
T ss_dssp SB-SSHHHHHHTCCSSS-SGTCSTTTTSSTCTSSSSSS----TSSSSEBTTTSSS
T ss_pred hhhhhhhhccccccCccccceeeccccCcCCCCCCcCC----CCCCCCCCCCCCC
Confidence 99999999999999999999999999999999999986 457 899999986
No 7
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=1.6e-57 Score=400.46 Aligned_cols=147 Identities=36% Similarity=0.526 Sum_probs=135.5
Q ss_pred eeccceeecC--C-----CCCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCC
Q 027754 31 YQSSETELVG--D-----PSKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAG 103 (219)
Q Consensus 31 ~~~~~~~lv~--~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAG 103 (219)
++++.||||- | .+++|.++.+|+|+.- .++++++||+|||.+||+||+|||||++||+|||||||||
T Consensus 51 nRsa~IAlv~~~~g~~~YIiAp~gl~~Gd~I~sg------~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~RSAG 124 (238)
T PRK09612 51 GRNAPVAKVKFENGEEFLILAPEGLYVGQEIEIG------PSAEIKPGNTLPLGEIPEGTPVCNIESRPGDGGKFARSSG 124 (238)
T ss_pred CCCCeEEEEEeCCCCEEEEEccCCCCCCCEEEeC------CCCCCCCccccCHhhCCCCCEEEEEEecCCCCcceEEcCC
Confidence 3667777774 2 2388999999988753 3567899999999999999999999999999999999999
Q ss_pred CcEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccC-----CCCCccceeecCCCCCCCC
Q 027754 104 TSAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWL-----GRRPVVRGVAMNPVDHPHG 178 (219)
Q Consensus 104 t~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~l-----G~RP~VRGvAMNpvDHPHG 178 (219)
|||+|+.+ +++|++|||||||+|+|+.+|+||||+|||.+|.+++|+|||++||+ |+||+||||||||||||||
T Consensus 125 t~A~Ii~k-~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~~~~~~~lgKAG~~r~~~k~~~g~rP~VRGvAMNpvDHPHG 203 (238)
T PRK09612 125 TYALVVGH-EGDKVIVQLPSGKIKELNPRCRATIGVVAGGGRKEKPFLKAGKKYHKMKAKAKKWPRVRGVAMNAVDHPHG 203 (238)
T ss_pred CeEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCccccceeeechhhhhhhhccCCCCCccCeEeeCCccCCcC
Confidence 99999987 57899999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred CCCCCC
Q 027754 179 GGEGRS 184 (219)
Q Consensus 179 GGeGks 184 (219)
||||++
T Consensus 204 GGeg~~ 209 (238)
T PRK09612 204 GGNHQH 209 (238)
T ss_pred CCCCCC
Confidence 999996
No 8
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=2.3e-55 Score=390.75 Aligned_cols=157 Identities=34% Similarity=0.462 Sum_probs=138.2
Q ss_pred eeccceeecC--C----------CCCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCce
Q 027754 31 YQSSETELVG--D----------PSKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKL 98 (219)
Q Consensus 31 ~~~~~~~lv~--~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~Ggkl 98 (219)
++|+.||||- | .+++|.++.+|+|+.. .++++++||+|||.+||+||.|||||+.||+||||
T Consensus 53 nRsA~IAlv~~~d~~~~~g~~~YIlAp~gl~vGd~I~~g------~~a~i~~GN~lpL~~IP~GT~IhNIE~~pG~Ggkl 126 (260)
T PTZ00180 53 GRGAPLARVEFRDPYKYKRVKELMVAPEGMYTGQYVYCG------AKAPLAIGNVLPLGQIPEGTIVCNVEEKPGDRGTL 126 (260)
T ss_pred CCCceEEEEEecCCccccCceEEEEeeCCCCCCCEEEeC------CCCCCCCcCccCHhhCCCCCeEEEEeccCCCCceE
Confidence 3677888773 2 4588999998888753 35568999999999999999999999999999999
Q ss_pred eecCCCcEEEeee-cCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccC-----CCCCccceeecCC
Q 027754 99 VRAAGTSAKILKE-PTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWL-----GRRPVVRGVAMNP 172 (219)
Q Consensus 99 aRSAGt~A~Ii~k-~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~l-----G~RP~VRGvAMNp 172 (219)
||||||||+|+.+ .++++++|||||||+|+|+.+|+||||+|||.+|.+++|+|||++||+ .+||+||||||||
T Consensus 127 aRSAGt~A~ii~k~k~~~~~~vkLPSGe~r~v~~~c~ATIG~Vsn~~~~~k~l~KAG~~~~~~~a~~~rwP~VRGVAMNP 206 (260)
T PTZ00180 127 ARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGGGRIDKPVLKAGNAFHKYRGKRNCWPKVRGVAMNP 206 (260)
T ss_pred EEecCCeEEEEEEcccCCEEEEECCCCCeEeECCCCeEEEEEccCCcchheeeccccchhhhhhCcCCCCCccccEeeCC
Confidence 9999999999965 367999999999999999999999999999999999999999999997 4579999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCC
Q 027754 173 VDHPHGGGEGRSKSSGNHGRC-SLTPW 198 (219)
Q Consensus 173 vDHPHGGGeGks~~~~~~gr~-~~sPW 198 (219)
||||||||||++ +||+ ++|-+
T Consensus 207 vDHPHGGGegk~-----~Gr~~tvsr~ 228 (260)
T PTZ00180 207 VEHPHGGGNHQH-----IGHPSTVSRH 228 (260)
T ss_pred ccCCcCCCCCCC-----CCCCCCcCCC
Confidence 999999999994 3565 45443
No 9
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-49 Score=358.79 Aligned_cols=180 Identities=41% Similarity=0.686 Sum_probs=165.1
Q ss_pred eccceeecCCC-------CCCCCCCchHHHHHHhhhcccccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCCC
Q 027754 32 QSSETELVGDP-------SKQEKPKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGT 104 (219)
Q Consensus 32 ~~~~~~lv~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt 104 (219)
++++|+|+... +++|+|+++|++++..+- ...-...+.||++||++||+||+|||||+.|+.++||||||||
T Consensus 114 Rs~~iaLv~~~~~~~~~Ila~egm~aGD~i~ss~~i-~~~av~~~~Gna~Pl~~lp~GT~ih~~e~~p~~~~~f~raAGt 192 (312)
T KOG0438|consen 114 RSAKIALVAGGTGELRYILATEGLKAGDTILSSRKI-PFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGT 192 (312)
T ss_pred ccccEEEEeccCCCeeEEEEecCCCCCCcccccccc-ccccccccCCCceeecccchhhhhhhhccCCCcchhhhhhcCc
Confidence 78899999875 388999999999999844 3334457999999999999999999999999999999999999
Q ss_pred cEEEeeecCCCeEEEEecCCceEeeccccceeeeeecCCCcCccccccccccccCCCCCccceeecCCCCCCCCCCCCCC
Q 027754 105 SAKILKEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRS 184 (219)
Q Consensus 105 ~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn~~~~~~~lgKAG~~R~lG~RP~VRGvAMNpvDHPHGGGeGks 184 (219)
+|+|+.+ .+.+++|+|||+|.+.|+..|+||||+|||.+|+.+.+||||++||+|+||+||||+||++|||||||.|+.
T Consensus 193 ~a~ilak-~~~~aiv~Lps~r~~~~~~tC~ATvGrvsni~~~~r~~GkAgr~rwlG~Rp~vrg~~~s~~~H~kgg~~gr~ 271 (312)
T KOG0438|consen 193 SATILAK-AGKFAIVQLPSKRERSVLRTCVATVGRVSNIDHNHRILGKAGRSRWLGKRPQVRGVLMSGLDHPKGGGKGRK 271 (312)
T ss_pred hhhhhhc-CCCceeEEccccchhhhhhhhheeeccccccccccceecccchhhhcccCcccccccccCccCCCCCCcccc
Confidence 9999977 468999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCCCCCCCCCCCCcccCCccccCCCCccccC
Q 027754 185 KSSGNHGRCSLTPWGKPCKSGYKTASPKKKKKL 217 (219)
Q Consensus 185 ~~~~~~gr~~~sPWG~~tk~g~kTr~~~~~~~~ 217 (219)
. ...+|++|||+++|+.++||+++..+|+
T Consensus 272 i----~~~~P~~~~~~~ak~~~~~r~~~~a~k~ 300 (312)
T KOG0438|consen 272 I----GRKKPVTPWGKPAKGLRPTRRKKGANKV 300 (312)
T ss_pred c----cCCCCCCccccccccCCCcccccccccc
Confidence 3 2368999999999977999998887775
No 10
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-35 Score=259.57 Aligned_cols=133 Identities=39% Similarity=0.654 Sum_probs=119.6
Q ss_pred ccccCCCCceecCCCCCCcceEeeeeeccCCCCceeecCCCcEEEee-ecCCCeEEEEecCCceEeeccccceeeeeecC
Q 027754 64 VDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKILK-EPTSSFCLVRLPSGNEKLIDTRCRATIGTVSN 142 (219)
Q Consensus 64 ~~~~~k~GN~lPL~~IP~GT~I~NIEl~PG~GgklaRSAGt~A~Ii~-k~~~~~v~IKLPSGe~r~i~~~C~AtIG~vsn 142 (219)
.++++.+||++|++++|+|+.|||+|..+|+.|.|+|++|.||.+|. +.+.+...|+||||..+.|++.|+|+||+|++
T Consensus 86 ~ka~~~ignv~~~~s~peg~~v~~ve~~~gdrg~lar~sGnya~vIaHn~dt~kTrIkLPsgaKKvV~S~~RamIG~vAg 165 (248)
T KOG2309|consen 86 KKAQLNIGNVLPVGSMPEGTIVCNVEEKPGDRGALARASGNYAIVIAHNPDTKKTRIKLPSGAKKVVQSACRAMIGVVAG 165 (248)
T ss_pred ccccccccceeeccccccceEEEEeeccCchhhhHHhhcCceeEEEecCccccceEEecCCCccceeccccceEEEEecC
Confidence 35578999999999999999999999999999999999999999994 46788999999999999999999999999999
Q ss_pred CCcCccccccccccccCC-----CCCccceeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 027754 143 PSHGAKKLRKAGQSRWLG-----RRPVVRGVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPC 202 (219)
Q Consensus 143 ~~~~~~~lgKAG~~R~lG-----~RP~VRGvAMNpvDHPHGGGeGks~~~~~~gr~~~sPWG~~t 202 (219)
.+..++++.|||+.+++- .||+||||||||||||||||++.. +|+++.- |=-.+
T Consensus 166 gG~~dKp~lKag~a~~K~~~Krn~wPrvRGVAMnPVeHphGGgnhqh-----ig~~stv-~r~~~ 224 (248)
T KOG2309|consen 166 GGRTDKPLLKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPHGGGNHQH-----IGKPSTV-RRDAS 224 (248)
T ss_pred CccccchhhhhhhHHHHhhhhcCCchhhcceecccccCCCCCCcccc-----cCCcccc-cccCc
Confidence 999999999999998863 599999999999999999999885 3566544 64333
No 11
>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=80.66 E-value=0.94 Score=21.14 Aligned_cols=7 Identities=86% Similarity=1.697 Sum_probs=5.3
Q ss_pred CCCCCCC
Q 027754 176 PHGGGEG 182 (219)
Q Consensus 176 PHGGGeG 182 (219)
|||||-|
T Consensus 1 phgG~Wg 7 (8)
T PF03991_consen 1 PHGGGWG 7 (8)
T ss_pred CCCCcCC
Confidence 8998754
No 12
>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=57.69 E-value=18 Score=23.82 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.8
Q ss_pred EEEeeecCCCeEEEEecCCceEeeccc
Q 027754 106 AKILKEPTSSFCLVRLPSGNEKLIDTR 132 (219)
Q Consensus 106 A~Ii~k~~~~~v~IKLPSGe~r~i~~~ 132 (219)
|.|+.. +++.++|++.+|+.+.++.+
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 567754 57899999999999988754
No 13
>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=44.71 E-value=41 Score=25.49 Aligned_cols=38 Identities=13% Similarity=0.194 Sum_probs=29.3
Q ss_pred CceeecCCCcEEEeeecCCCeEEEEecCCceEeeccccc
Q 027754 96 GKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRCR 134 (219)
Q Consensus 96 gklaRSAGt~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~ 134 (219)
-+.+-++|-|++|.+- +++++.|++..|-...++..+-
T Consensus 42 d~VvT~gGi~G~V~~i-~d~~v~vei~~g~~i~~~r~aI 79 (84)
T TIGR00739 42 DKVLTIGGIIGTVTKI-AENTIVIELNDNTEITFSKNAI 79 (84)
T ss_pred CEEEECCCeEEEEEEE-eCCEEEEEECCCeEEEEEhHHh
Confidence 4577888999999965 4679999998887777776543
No 14
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=29.93 E-value=1e+02 Score=24.43 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=30.5
Q ss_pred CceeecCCCcEEEeeecCCCeEEEEecCCceEeeccccce
Q 027754 96 GKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRCRA 135 (219)
Q Consensus 96 gklaRSAGt~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~A 135 (219)
-+.+-++|-|++|+.- +++.+.|++..|-...|+...-+
T Consensus 57 d~VvT~gGi~G~Vv~i-~~~~v~lei~~g~~i~~~r~aI~ 95 (106)
T PRK05585 57 DEVVTNGGIIGKVTKV-SEDFVIIELNDDTEIKIQKSAIA 95 (106)
T ss_pred CEEEECCCeEEEEEEE-eCCEEEEEECCCeEEEEEhHHhh
Confidence 4577889999999965 45799999999977777766443
No 15
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=25.39 E-value=42 Score=24.87 Aligned_cols=28 Identities=14% Similarity=0.239 Sum_probs=19.9
Q ss_pred CCeEEEEecCCceEeeccccceeeeeec
Q 027754 114 SSFCLVRLPSGNEKLIDTRCRATIGTVS 141 (219)
Q Consensus 114 ~~~v~IKLPSGe~r~i~~~C~AtIG~vs 141 (219)
...+.||||+|+...-.-+.-.||+.|-
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~ 31 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHRVSDVR 31 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHH
Confidence 3578999999987765555567776543
No 16
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=24.16 E-value=47 Score=24.07 Aligned_cols=28 Identities=25% Similarity=0.282 Sum_probs=17.7
Q ss_pred CCeEEEEecCCceEeeccccceeeeeec
Q 027754 114 SSFCLVRLPSGNEKLIDTRCRATIGTVS 141 (219)
Q Consensus 114 ~~~v~IKLPSGe~r~i~~~C~AtIG~vs 141 (219)
...+.||||+|+.....-..-.+|..|-
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~tl~~v~ 31 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDTLRTVY 31 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCcHHHHH
Confidence 3578899999996544444445555443
No 17
>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=22.22 E-value=29 Score=26.00 Aligned_cols=39 Identities=13% Similarity=0.268 Sum_probs=0.0
Q ss_pred CceeecCCCcEEEeeecCCCeEEEEecCCceEeeccccce
Q 027754 96 GKLVRAAGTSAKILKEPTSSFCLVRLPSGNEKLIDTRCRA 135 (219)
Q Consensus 96 gklaRSAGt~A~Ii~k~~~~~v~IKLPSGe~r~i~~~C~A 135 (219)
-+..-++|-|++|++- +++.+.|++.+|-...++.+.-+
T Consensus 41 d~VvT~gGi~G~V~~i-~~~~v~lei~~g~~i~v~k~aI~ 79 (82)
T PF02699_consen 41 DEVVTIGGIYGTVVEI-DDDTVVLEIAPGVEITVEKSAIA 79 (82)
T ss_dssp ----------------------------------------
T ss_pred CEEEECCcEEEEEEEE-eCCEEEEEECCCeEEEEEHHHhH
Confidence 4577888999999965 67899999999977777766544
No 18
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=20.71 E-value=1.8e+02 Score=20.60 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=19.1
Q ss_pred cEEEeeecCCCeEEEEecCCceEe
Q 027754 105 SAKILKEPTSSFCLVRLPSGNEKL 128 (219)
Q Consensus 105 ~A~Ii~k~~~~~v~IKLPSGe~r~ 128 (219)
+++|++-..+++..|++++|+.++
T Consensus 6 ~~~V~~~lG~~~~~V~~~dg~~~l 29 (65)
T PF01176_consen 6 IGRVTEMLGNNLFEVECEDGEERL 29 (65)
T ss_dssp EEEEEEEESSSEEEEEETTSEEEE
T ss_pred EEEEEEECCCCEEEEEeCCCCEEE
Confidence 567775546789999999999887
Done!