Query 032383
Match_columns 142
No_of_seqs 128 out of 349
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:22:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032383.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032383hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00067 40S ribosomal S23; Pr 100.0 4E-74 8.6E-79 446.0 14.0 142 1-142 1-143 (143)
2 PRK04211 rps12P 30S ribosomal 100.0 1.1E-71 2.4E-76 433.0 13.4 140 3-142 4-145 (145)
3 TIGR00982 S23_S12_E_A ribosoma 100.0 1.4E-70 3E-75 424.5 13.4 137 6-142 1-139 (139)
4 KOG1749 40S ribosomal protein 100.0 1.7E-70 3.7E-75 421.8 11.9 142 1-142 1-143 (143)
5 cd03367 Ribosomal_S23 S12-like 100.0 7.5E-61 1.6E-65 361.0 11.9 114 26-139 1-115 (115)
6 COG0048 RpsL Ribosomal protein 100.0 1.3E-54 2.9E-59 331.9 11.1 122 7-141 1-123 (129)
7 cd00319 Ribosomal_S12_like Rib 100.0 3.1E-48 6.8E-53 284.5 9.6 93 34-136 2-95 (95)
8 PF00164 Ribosom_S12_S23: Ribo 100.0 5.8E-48 1.3E-52 293.3 8.5 105 29-141 11-122 (122)
9 cd03368 Ribosomal_S12 S12-like 100.0 2.3E-45 5E-50 274.5 9.2 89 38-136 20-108 (108)
10 PRK05163 rpsL 30S ribosomal pr 100.0 4.4E-45 9.5E-50 278.4 8.9 92 38-139 22-113 (124)
11 CHL00051 rps12 ribosomal prote 100.0 4.5E-45 9.8E-50 278.0 8.7 92 38-139 22-113 (123)
12 TIGR00981 rpsL_bact ribosomal 100.0 5.3E-45 1.1E-49 277.9 8.9 93 37-139 21-113 (124)
13 PTZ00115 40S ribosomal protein 100.0 2.2E-40 4.8E-45 278.6 9.1 92 38-139 118-209 (290)
14 KOG1750 Mitochondrial/chloropl 100.0 8.9E-34 1.9E-38 219.3 5.8 89 38-136 50-138 (139)
15 TIGR00008 infA translation ini 93.7 0.12 2.5E-06 36.3 4.1 45 47-102 8-54 (68)
16 COG0361 InfA Translation initi 92.4 0.25 5.5E-06 35.3 4.2 48 45-103 8-57 (75)
17 PRK12442 translation initiatio 84.2 1.7 3.6E-05 32.0 3.8 35 68-103 21-57 (87)
18 smart00652 eIF1a eukaryotic tr 81.7 2.6 5.7E-05 30.0 3.9 34 69-103 20-54 (83)
19 cd04456 S1_IF1A_like S1_IF1A_l 78.6 3.9 8.5E-05 28.8 4.0 35 68-103 14-49 (78)
20 TIGR00523 eIF-1A eukaryotic/ar 70.5 6.9 0.00015 28.9 3.7 54 38-102 13-67 (99)
21 PLN00208 translation initiatio 66.0 8.7 0.00019 30.5 3.6 54 39-103 27-81 (145)
22 PTZ00329 eukaryotic translatio 64.6 10 0.00022 30.5 3.8 54 39-103 27-81 (155)
23 TIGR00230 sfsA sugar fermentat 57.4 24 0.00051 29.6 4.9 35 66-102 20-55 (232)
24 cd05793 S1_IF1A S1_IF1A: Trans 55.5 13 0.00027 26.2 2.6 35 68-103 14-49 (77)
25 PF03749 SfsA: Sugar fermentat 54.3 29 0.00063 28.6 4.9 37 66-103 6-43 (215)
26 PF01176 eIF-1a: Translation i 50.8 12 0.00027 25.0 1.9 33 69-103 18-52 (65)
27 PRK04012 translation initiatio 46.5 20 0.00044 26.5 2.6 53 39-102 16-69 (100)
28 PRK00347 putative DNA-binding 46.4 47 0.001 27.7 5.0 37 66-103 18-55 (234)
29 PRK00284 pqqA coenzyme PQQ syn 44.3 26 0.00056 20.7 2.3 13 76-88 12-24 (26)
30 COG1489 SfsA DNA-binding prote 35.0 84 0.0018 26.9 4.9 37 65-103 17-54 (235)
31 TIGR02107 PQQ_syn_pqqA coenzym 31.6 54 0.0012 19.4 2.3 13 76-88 11-23 (26)
32 PF00386 C1q: C1q domain; Int 30.2 1.3E+02 0.0028 21.4 4.6 53 46-103 43-105 (127)
33 cd01724 Sm_D1 The eukaryotic S 25.3 1.6E+02 0.0034 21.1 4.3 21 62-83 7-27 (90)
34 PLN02856 fumarylacetoacetase 23.9 1.4E+02 0.003 27.4 4.6 32 72-104 371-402 (424)
35 cd05792 S1_eIF1AD_like S1_eIF1 23.0 1.3E+02 0.0029 21.3 3.5 34 69-103 15-49 (78)
36 TIGR01266 fum_ac_acetase fumar 22.8 1.6E+02 0.0035 26.9 4.8 33 71-104 362-394 (415)
37 COG2302 Uncharacterized conser 22.7 84 0.0018 27.3 2.8 16 91-106 219-234 (257)
38 PRK00276 infA translation init 21.4 2.5E+02 0.0054 19.0 4.5 33 69-102 22-56 (72)
39 cd04497 hPOT1_OB1_like hPOT1_O 20.9 88 0.0019 23.4 2.3 56 76-137 52-107 (138)
No 1
>PTZ00067 40S ribosomal S23; Provisional
Probab=100.00 E-value=4e-74 Score=445.95 Aligned_cols=142 Identities=80% Similarity=1.308 Sum_probs=140.2
Q ss_pred CCCCCccchhHHHHhhhhhccccchhhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcE
Q 032383 1 MGKTRGMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKK 79 (142)
Q Consensus 1 ~~k~~Gl~~~rkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 79 (142)
||+|+||||||||+++|+++||+|++|+++|||+.++ |||+++||++|||++++++||||||||+||||+|||++||++
T Consensus 1 m~~~~Gl~aarkl~~~r~~~rw~d~~y~k~~lg~~~k~~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 80 (143)
T PTZ00067 1 MGKPRGLRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
T ss_pred CCCcchhHHHHHHHHHHHHhhhhhHHHHHHhcCCccccCcccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcE
Confidence 8999999999999999999999999999999999998 999999999999999999999999999999999999889999
Q ss_pred EEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCceEEEEEecCchhhHhhhhcccCCCC
Q 032383 80 IAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 142 (142)
Q Consensus 80 vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~kp~~ 142 (142)
||||||||||||||||||+|||+|||++|++++|||||+|+|||||||||+|||+||||||++
T Consensus 81 vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~DlPGVrykvVrV~~vsL~~l~kgkkekp~r 143 (143)
T PTZ00067 81 ITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVAGVSLLALYKGKKEKPRN 143 (143)
T ss_pred EEEEeCCCCcccccccCCEEEEEecCcCCCccCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999999999999999999999999999999999999999999985
No 2
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=100.00 E-value=1.1e-71 Score=433.03 Aligned_cols=140 Identities=60% Similarity=1.002 Sum_probs=137.6
Q ss_pred CCCccchhHHHHhhhhhccccchhhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEE
Q 032383 3 KTRGMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIA 81 (142)
Q Consensus 3 k~~Gl~~~rkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vt 81 (142)
+|+||||||||+++|+++||+|++|++++||++++ +||+++||++|||++++++||||||||+||||+|||++||++||
T Consensus 4 ~~~Gl~aarkl~~~r~~~rw~d~~y~k~~lg~~~K~~~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vt 83 (145)
T PRK04211 4 SPNGLFAARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVT 83 (145)
T ss_pred CcchhhHHHHHHHHHHHhhhhhHHHHHHHhCcccccCcccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEE
Confidence 59999999999999999999999999999999988 99999999999999999999999999999999999999999999
Q ss_pred EEcCCCCcccCccccCeEEEeecc-CCCCccCCCCCceEEEEEecCchhhHhhhhcccCCCC
Q 032383 82 AFVPNDGCLNYIEENDEVLIAGFG-RKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 142 (142)
Q Consensus 82 A~IPg~G~l~~lqeh~~VLV~G~G-~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~kp~~ 142 (142)
||||||||+|||||||+|||+||| ++||+++|||||+|+||+||||||+|||+||||||++
T Consensus 84 AyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 145 (145)
T PRK04211 84 AFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145 (145)
T ss_pred EEeCCCccccccccCCEEEEeecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999999988 9999999999999999999999999999999999985
No 3
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=100.00 E-value=1.4e-70 Score=424.53 Aligned_cols=137 Identities=59% Similarity=1.001 Sum_probs=135.1
Q ss_pred ccchhHHHHhhhhhccccchhhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEc
Q 032383 6 GMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFV 84 (142)
Q Consensus 6 Gl~~~rkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~I 84 (142)
||||||||+++|+++||+|++|+++++|+..+ +||+++||++|||++++++||||||||+||||+|||++||++|||||
T Consensus 1 Gl~aarkl~~~r~~~rw~d~~y~k~~~~~~~K~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyi 80 (139)
T TIGR00982 1 GLFAARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFC 80 (139)
T ss_pred CchhHHHHHHHHHHhhhhhHHHHHHhhccccccCcccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEe
Confidence 89999999999999999999999999999988 99999999999999999999999999999999999999999999999
Q ss_pred CCCCcccCccccCeEEEeecc-CCCCccCCCCCceEEEEEecCchhhHhhhhcccCCCC
Q 032383 85 PNDGCLNYIEENDEVLIAGFG-RKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 142 (142)
Q Consensus 85 Pg~G~l~~lqeh~~VLV~G~G-~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~kp~~ 142 (142)
|||||+|||||||+|||+||| ++||+++|||||+|+||+||||||+|||+||||||++
T Consensus 81 Pg~G~~~~lqeh~~VLV~G~gg~~gg~v~DlPGVrykvVkV~~vsL~~l~~gkkekp~r 139 (139)
T TIGR00982 81 PGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139 (139)
T ss_pred CCCccccccccCCEEEEEecCccCCCCcCCCCceEEEEEEECCEeHHHHHhcccccCCC
Confidence 999999999999999999998 9999999999999999999999999999999999985
No 4
>KOG1749 consensus 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-70 Score=421.83 Aligned_cols=142 Identities=86% Similarity=1.325 Sum_probs=140.9
Q ss_pred CCCCCccchhHHHHhhhhhccccchhhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcE
Q 032383 1 MGKTRGMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKK 79 (142)
Q Consensus 1 ~~k~~Gl~~~rkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~ 79 (142)
||||.||||||+|+.+|+.+||+|.+|++++|||++| |||+|+||+||||||++++|+||||||||||+|||||+||++
T Consensus 1 mgk~~Gl~aarklr~~r~~~rwad~~ykk~~lGta~K~~pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKK 80 (143)
T KOG1749|consen 1 MGKPRGLFAARKLRTHRRNQRWADKHYKKRLLGTAYKSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKK 80 (143)
T ss_pred CCCcccchhHHHHHhhhhhhccchhhhhhhhhcchhhcCCCCCccccceeEEEeeeeeccCCcHHHhhheeeeeeeCCce
Confidence 8999999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCceEEEEEecCchhhHhhhhcccCCCC
Q 032383 80 IAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 142 (142)
Q Consensus 80 vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~kp~~ 142 (142)
||||+|.||||||++|||||||.|||++|++++|||||||+||+|+||||+|||+||||||+|
T Consensus 81 ITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvrfkvvkv~~vsl~alf~~kkekpr~ 143 (143)
T KOG1749|consen 81 ITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS 143 (143)
T ss_pred EEEEecCCCceeeeccCCeeeeeccCccCccccCCCceEEEEEEEcCcChhhhhhccccCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999986
No 5
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=7.5e-61 Score=360.98 Aligned_cols=114 Identities=82% Similarity=1.303 Sum_probs=112.0
Q ss_pred hhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeec
Q 032383 26 SYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF 104 (142)
Q Consensus 26 ~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~ 104 (142)
.|++++||+..+ +||+++||++|||++++++||||||||+||||+|||++||++||||||||||||||||||+|||+||
T Consensus 1 ~~~~~~~~~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~ 80 (115)
T cd03367 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGF 80 (115)
T ss_pred ChhhhhccccccCCcccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEec
Confidence 499999999988 9999999999999999999999999999999999998899999999999999999999999999999
Q ss_pred cCCCCccCCCCCceEEEEEecCchhhHhhhhcccC
Q 032383 105 GRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEK 139 (142)
Q Consensus 105 G~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~k 139 (142)
|++||+++|||||+|+||+||||||+|||+|||||
T Consensus 81 G~~Gg~v~DlPGVrykvVkV~~vsl~~l~~gkkek 115 (115)
T cd03367 81 GRKGRAVGDIPGVRFKVVKVNGVSLLALFKGKKEK 115 (115)
T ss_pred ccCCCccCCCCceEEEEEEECCEEHHHHhhhhccC
Confidence 99999999999999999999999999999999997
No 6
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-54 Score=331.86 Aligned_cols=122 Identities=40% Similarity=0.596 Sum_probs=117.2
Q ss_pred cchhHHHHhhhhhccccchhhhhhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcC
Q 032383 7 MGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVP 85 (142)
Q Consensus 7 l~~~rkl~~~r~~~rw~d~~ykk~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IP 85 (142)
+|||++|...++..| |.++.++++.| +||+++||++|||++++++||||||||+||||||||+ ||++||||||
T Consensus 1 ~~a~~km~t~~q~~R-----~~rr~~~~k~Ks~~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~-NG~~VtAyiP 74 (129)
T COG0048 1 LFAARKMPTINQLVR-----KKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIP 74 (129)
T ss_pred CcccchhhhHHHHhh-----cccccccccccCCcccCCCccceEEEEEEecccCCCChhhheeEEEEee-CCcEEEEEcC
Confidence 689999999999888 99999999988 9999999999999999999999999999999999995 9999999999
Q ss_pred CCCcccCccccCeEEEeeccCCCCccCCCCCceEEEEEecCchhhHhhhhcccCCC
Q 032383 86 NDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPR 141 (142)
Q Consensus 86 g~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk~kp~ 141 (142)
|||| +|||||+|||+|| +++||||||||||||+++++.+++++++++|.
T Consensus 75 g~Gh--~lqEH~~Vli~G~-----~v~DlPGVRy~vvrg~~ds~~v~~r~~~rs~y 123 (129)
T COG0048 75 GEGH--NLQEHSEVLIRGG-----RVKDLPGVRYKVVRGALDSLGVLDRGQKRSKY 123 (129)
T ss_pred CCCc--cccccCEEEEecC-----ccCCCCCceEEEEEEcchhhhhhhhccccccc
Confidence 9998 7999999999994 69999999999999999999999999999885
No 7
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=3.1e-48 Score=284.52 Aligned_cols=93 Identities=35% Similarity=0.641 Sum_probs=88.3
Q ss_pred Cccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccC
Q 032383 34 NEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVG 112 (142)
Q Consensus 34 ~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~ 112 (142)
++.+ +||+++||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |++.
T Consensus 2 ~~~k~~~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L-~ngk~v~ayIPg~Gh--~lqeh~~VLvrG-----Gr~~ 73 (95)
T cd00319 2 KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-----GRVK 73 (95)
T ss_pred CccccCcccCCcccCeEEEEEEeccccCCChhhceEEEEEc-cCCCEEEEECCCCCc--ccccccEEEEeC-----CCcC
Confidence 4545 999999999999999999999999999999999999 699999999999996 999999999999 6888
Q ss_pred CCCCceEEEEEecCchhhHhhhhc
Q 032383 113 DIPGVRFKVVKVSGVSLLALFKEK 136 (142)
Q Consensus 113 DlPGVrykvVrv~gv~l~~l~~gk 136 (142)
|||||+|+||| |++|+++++||
T Consensus 74 DlPGVrykvVr--G~~d~~~v~~R 95 (95)
T cd00319 74 DLPGVRYHIVR--GVYDAAGVKDR 95 (95)
T ss_pred CCCCcEEEEEc--ccchhhhccCC
Confidence 99999999999 99999999986
No 8
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=100.00 E-value=5.8e-48 Score=293.30 Aligned_cols=105 Identities=45% Similarity=0.747 Sum_probs=97.6
Q ss_pred hhccCCccc-CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCC
Q 032383 29 KSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRK 107 (142)
Q Consensus 29 k~~lg~~~k-~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~ 107 (142)
+.+++++.+ +||+++||++||||++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+|
T Consensus 11 r~~~~~~~k~~~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL-~n~k~v~AyIPg~Gh--nlqehs~VLVrG---- 83 (122)
T PF00164_consen 11 RKKKKRKSKSPALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRL-SNGKKVTAYIPGEGH--NLQEHSVVLVRG---- 83 (122)
T ss_dssp CHSSTCSHSSSSSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEE-TTSEEEEEEC-SSSC--CSTTTSEEEEEE----
T ss_pred CCCCCccccCCccCCCCccCcEEeecccccccCccchhhhcceeee-ccCceEEEEecCCcc--cccccceEEEec----
Confidence 567777766 999999999999999999999999999999999999 699999999999996 999999999999
Q ss_pred CCccCCCCCceEEEEE----ecCch--hhHhhhhcccCCC
Q 032383 108 GHAVGDIPGVRFKVVK----VSGVS--LLALFKEKKEKPR 141 (142)
Q Consensus 108 gg~v~DlPGVrykvVr----v~gv~--l~~l~~gkk~kp~ 141 (142)
|+++|||||+|+||| ++||+ +.+++++.++||+
T Consensus 84 -grv~DlPGVkykvVRG~~D~~gV~~r~~~rskyg~kkPk 122 (122)
T PF00164_consen 84 -GRVGDLPGVKYKVVRGVYDVAGVSNRKKARSKYGKKKPK 122 (122)
T ss_dssp -ESBTTSTTECEEBETTSTTCSSSTT-SSSCTTTTCCCCH
T ss_pred -cccCCCCceEEEEEeeccccccccHHHHhhhhcCCcCCC
Confidence 479999999999999 89999 8999999999984
No 9
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=100.00 E-value=2.3e-45 Score=274.55 Aligned_cols=89 Identities=42% Similarity=0.739 Sum_probs=85.2
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCc
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 117 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 117 (142)
+||+++||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 20 ~~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~DlPGV 91 (108)
T cd03368 20 PALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEGH--NLQEHSVVLVRG-----GRVKDLPGV 91 (108)
T ss_pred CcccCCcccCcEEEEEEeccccCCChhheeeEEEEe-cCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCCe
Confidence 899999999999999999999999999999999999 799999999999996 999999999999 799999999
Q ss_pred eEEEEEecCchhhHhhhhc
Q 032383 118 RFKVVKVSGVSLLALFKEK 136 (142)
Q Consensus 118 rykvVrv~gv~l~~l~~gk 136 (142)
+|+||| |++|++-+.++
T Consensus 92 kykvvR--G~~D~~gv~~R 108 (108)
T cd03368 92 RYHIVR--GVLDLAGVKNR 108 (108)
T ss_pred EEEEEe--eecccccccCC
Confidence 999999 89999877653
No 10
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=4.4e-45 Score=278.39 Aligned_cols=92 Identities=36% Similarity=0.637 Sum_probs=88.8
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCc
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 117 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 117 (142)
+||+++||++||||++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 22 ~~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~DlPGV 93 (124)
T PRK05163 22 PALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDLPGV 93 (124)
T ss_pred cccccCcccCcEEEEEEecCccCCCchhheEEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCCc
Confidence 899999999999999999999999999999999999 999999999999996 999999999998 799999999
Q ss_pred eEEEEEecCchhhHhhhhcccC
Q 032383 118 RFKVVKVSGVSLLALFKEKKEK 139 (142)
Q Consensus 118 rykvVrv~gv~l~~l~~gkk~k 139 (142)
+|+||| |++|++-+.++++.
T Consensus 94 rykvVr--G~~D~~gv~~R~~~ 113 (124)
T PRK05163 94 RYHIVR--GALDTAGVKDRKQG 113 (124)
T ss_pred EEEEee--eeeccccccccccc
Confidence 999999 89999999998754
No 11
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=4.5e-45 Score=277.98 Aligned_cols=92 Identities=35% Similarity=0.612 Sum_probs=89.0
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCc
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 117 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 117 (142)
+||+++||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 22 ~~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrL-sngk~v~AyIPGeGh--nlqehs~VLvrG-----Grv~DlPGV 93 (123)
T CHL00051 22 PALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIGH--NLQEHSVVLVRG-----GRVKDLPGV 93 (123)
T ss_pred cccccCcccCeEEEEEEeccccCCChhheeEEEEEc-cCCCEEEEEcCCCCc--cccccCEEEEeC-----CccCCCCCe
Confidence 899999999999999999999999999999999999 999999999999997 999999999998 799999999
Q ss_pred eEEEEEecCchhhHhhhhcccC
Q 032383 118 RFKVVKVSGVSLLALFKEKKEK 139 (142)
Q Consensus 118 rykvVrv~gv~l~~l~~gkk~k 139 (142)
+|+||| |++|++-+.++++.
T Consensus 94 rykvVR--G~~D~~gv~~R~~~ 113 (123)
T CHL00051 94 RYHIVR--GTLDAVGVKDRQQG 113 (123)
T ss_pred eEEEEe--eeeccccccccccc
Confidence 999999 89999999998754
No 12
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=100.00 E-value=5.3e-45 Score=277.93 Aligned_cols=93 Identities=35% Similarity=0.625 Sum_probs=89.1
Q ss_pred cCCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCC
Q 032383 37 KKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPG 116 (142)
Q Consensus 37 k~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPG 116 (142)
.+||+++||++||||++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++||||
T Consensus 21 ~~~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-----Grv~DlPG 92 (124)
T TIGR00981 21 SPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-----GRVKDLPG 92 (124)
T ss_pred CcccccCCccCcEEEEEEeccccCCCchhheeEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-----CccCCCCC
Confidence 3899999999999999999999999999999999999 999999999999996 999999999998 79999999
Q ss_pred ceEEEEEecCchhhHhhhhcccC
Q 032383 117 VRFKVVKVSGVSLLALFKEKKEK 139 (142)
Q Consensus 117 VrykvVrv~gv~l~~l~~gkk~k 139 (142)
|+|+||| |++|++-+.++++.
T Consensus 93 VkykvVr--G~~D~~gv~~R~~~ 113 (124)
T TIGR00981 93 VRYHIVR--GALDTAGVKNRKQG 113 (124)
T ss_pred eEEEEEe--Eeeccccccccccc
Confidence 9999999 89999999998754
No 13
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=2.2e-40 Score=278.56 Aligned_cols=92 Identities=32% Similarity=0.570 Sum_probs=88.2
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCc
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 117 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 117 (142)
.+|+|+||++|||+++++++|||||||+||||+||| +||++|||||||||| ||||||+|||+| |+++|||||
T Consensus 118 paL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrL-sNGk~VtAyIPGeGH--nLQEHs~VLVRG-----GrvkDLPGV 189 (290)
T PTZ00115 118 KWLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIGH--NLNTHSVVLVRG-----GRCKDVPGC 189 (290)
T ss_pred ccccCCcccCeEEEEeeecCCCCCCccccceEEEEe-cCCCEEEEEcCCCCc--ccccCCEEEEeC-----CCcCCCCCc
Confidence 579999999999999999999999999999999999 899999999999998 999999999999 799999999
Q ss_pred eEEEEEecCchhhHhhhhcccC
Q 032383 118 RFKVVKVSGVSLLALFKEKKEK 139 (142)
Q Consensus 118 rykvVrv~gv~l~~l~~gkk~k 139 (142)
+|+||| |++|++.++++++.
T Consensus 190 rYkvVR--G~~D~~gV~~Rk~~ 209 (290)
T PTZ00115 190 NYKAVR--GVYDLLPVKNRARS 209 (290)
T ss_pred eEEEee--eecccccccccccc
Confidence 999999 89999999998764
No 14
>KOG1750 consensus Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-34 Score=219.27 Aligned_cols=89 Identities=40% Similarity=0.702 Sum_probs=86.1
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCc
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGV 117 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGV 117 (142)
.+|+++||.+|||+.+++++|||||||.||||+|+| +||.+|+|||||+|| |+|||+.|||+| |+++|+|||
T Consensus 50 ~~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrl-stg~~i~ayipg~gh--nlqehs~Vlvrg-----gr~qdlpgv 121 (139)
T KOG1750|consen 50 PALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRL-STGREVTAYIPGIGH--NLQEHSIVLVRG-----GRVQDLPGV 121 (139)
T ss_pred ccccCCcccccEEEEEEEecCCCCCccceeeEEEEe-cCchheeeeCCCccc--cceeEEEEEEec-----ceeccCcch
Confidence 789999999999999999999999999999999999 999999999999998 999999999999 799999999
Q ss_pred eEEEEEecCchhhHhhhhc
Q 032383 118 RFKVVKVSGVSLLALFKEK 136 (142)
Q Consensus 118 rykvVrv~gv~l~~l~~gk 136 (142)
+|++|| |+++++-+.++
T Consensus 122 k~~~vR--g~~d~~~V~~r 138 (139)
T KOG1750|consen 122 KYHVVR--GVYDLAGVVGR 138 (139)
T ss_pred hhhhhh--hhhhhccccCC
Confidence 999999 89999887765
No 15
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=93.75 E-value=0.12 Score=36.25 Aligned_cols=45 Identities=31% Similarity=0.492 Sum_probs=32.8
Q ss_pred ceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCccc--CccccCeEEEe
Q 032383 47 KGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLN--YIEENDEVLIA 102 (142)
Q Consensus 47 kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~--~lqeh~~VLV~ 102 (142)
.|+|++.+ ||. -.+|+| -||.++.|||||-=-.| -|.+.|.|+|+
T Consensus 8 ~G~V~e~L------~~~----~f~V~l-~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve 54 (68)
T TIGR00008 8 EGKVTESL------PNA----MFRVEL-ENGHEVLAHISGKIRMHYIRILPGDKVKVE 54 (68)
T ss_pred EEEEEEEC------CCC----EEEEEE-CCCCEEEEEecCcchhccEEECCCCEEEEE
Confidence 35555544 555 356888 89999999999954322 37899999998
No 16
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=92.37 E-value=0.25 Score=35.30 Aligned_cols=48 Identities=33% Similarity=0.428 Sum_probs=36.1
Q ss_pred ccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCcccC--ccccCeEEEee
Q 032383 45 HAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNY--IEENDEVLIAG 103 (142)
Q Consensus 45 q~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~l~~--lqeh~~VLV~G 103 (142)
+.-|+|++.+ ||.- ++|+| -||.+++|+|||-.-.|+ |-+-|.|+|+=
T Consensus 8 e~~g~V~e~L------~~~~----f~v~~-edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~ 57 (75)
T COG0361 8 EMEGTVIEML------PNGR----FRVEL-ENGHERLAHISGKMRKNRIRILPGDVVLVEL 57 (75)
T ss_pred EEEEEEEEec------CCCE----EEEEe-cCCcEEEEEccCcchheeEEeCCCCEEEEEe
Confidence 3445555555 3433 57899 999999999999997654 57999999984
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=84.20 E-value=1.7 Score=32.03 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=28.2
Q ss_pred eeEEEEeecCcEEEEEcCCCCcccC--ccccCeEEEee
Q 032383 68 CARVQLIKNGKKIAAFVPNDGCLNY--IEENDEVLIAG 103 (142)
Q Consensus 68 ~~rV~L~kngk~vtA~IPg~G~l~~--lqeh~~VLV~G 103 (142)
-.+|+| -||.+|+|||+|-=-.|+ |.+.|.|+|+=
T Consensus 21 ~frV~L-enG~~vla~isGKmR~~rIrIl~GD~V~VE~ 57 (87)
T PRK12442 21 RFRVTL-ENGVEVGAYASGRMRKHRIRILAGDRVTLEL 57 (87)
T ss_pred EEEEEe-CCCCEEEEEeccceeeeeEEecCCCEEEEEE
Confidence 467999 899999999999755443 57889999983
No 18
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=81.70 E-value=2.6 Score=30.00 Aligned_cols=34 Identities=26% Similarity=0.296 Sum_probs=26.9
Q ss_pred eEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEee
Q 032383 69 ARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 103 (142)
Q Consensus 69 ~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~G 103 (142)
.+|+| .||.++.|+|||-=. ---|.+.|.|+|+=
T Consensus 20 ~~V~~-~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 20 LEVMC-ADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 56888 899999999999321 12588999999984
No 19
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=78.57 E-value=3.9 Score=28.83 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=27.2
Q ss_pred eeEEEEeecCcEEEEEcCCCCcc-cCccccCeEEEee
Q 032383 68 CARVQLIKNGKKIAAFVPNDGCL-NYIEENDEVLIAG 103 (142)
Q Consensus 68 ~~rV~L~kngk~vtA~IPg~G~l-~~lqeh~~VLV~G 103 (142)
-.+|++ .||.++.|.|||-=.= --+.+.|.|+|+=
T Consensus 14 ~~~V~~-~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~ 49 (78)
T cd04456 14 RHEVEC-ADGQRRLVSIPGKLRKNIWIKRGDFLIVDP 49 (78)
T ss_pred EEEEEE-CCCCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence 467888 8999999999993210 2588999999974
No 20
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=70.52 E-value=6.9 Score=28.89 Aligned_cols=54 Identities=20% Similarity=0.312 Sum_probs=38.9
Q ss_pred CCCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEe
Q 032383 38 KPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIA 102 (142)
Q Consensus 38 ~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~ 102 (142)
-|+...-|.-|.|++..+ |. -.+|+| .||.++.|+|||-=. --.|.+.|.|+|.
T Consensus 13 ~p~~~e~e~~g~V~~~lG------~~----~~~V~~-~dG~~~la~i~GK~Rk~iwI~~GD~VlVs 67 (99)
T TIGR00523 13 LPRKEEGEILGVIEQMLG------AG----RVKVRC-LDGKTRLGRIPGKLKKRIWIREGDVVIVK 67 (99)
T ss_pred CCCCCCCEEEEEEEEEcC------CC----EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 355556677777777665 22 467888 899999999999311 1258899999994
No 21
>PLN00208 translation initiation factor (eIF); Provisional
Probab=65.98 E-value=8.7 Score=30.54 Aligned_cols=54 Identities=19% Similarity=0.213 Sum_probs=38.4
Q ss_pred CCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEee
Q 032383 39 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 103 (142)
Q Consensus 39 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~G 103 (142)
||-.--|.=|.|++..+ |. -++|++ .||.+++|+|||-=. ---|.+.|.|||+-
T Consensus 27 ~~p~egq~~g~V~~~lG------n~----~~~V~c-~dG~~rLa~IpGKmRKrIWI~~GD~VlVel 81 (145)
T PLN00208 27 IFKEDGQEYAQVLRMLG------NG----RCEALC-IDGTKRLCHIRGKMRKKVWIAAGDIILVGL 81 (145)
T ss_pred ccCCCCcEEEEEEEEcC------CC----EEEEEE-CCCCEEEEEEeccceeeEEecCCCEEEEEc
Confidence 44445567777777654 32 467888 799999999999311 02588999999984
No 22
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.63 E-value=10 Score=30.51 Aligned_cols=54 Identities=19% Similarity=0.178 Sum_probs=38.0
Q ss_pred CCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEee
Q 032383 39 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 103 (142)
Q Consensus 39 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~G 103 (142)
+|-.--|.=|.|++.++ |. -++|+| -||.+++|+|||-=. ---|.+.|.|||+-
T Consensus 27 ~~~eegq~~g~V~~~LG------n~----~f~V~c-~dG~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 27 VFKEEGQEYAQVLRMLG------NG----RLEAYC-FDGVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred ccCCCCcEEEEEEEEcC------CC----EEEEEE-CCCCEEEEEeeccceeeEEecCCCEEEEec
Confidence 34445666677776654 33 467888 799999999999321 02588999999974
No 23
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=57.41 E-value=24 Score=29.61 Aligned_cols=35 Identities=29% Similarity=0.469 Sum_probs=30.4
Q ss_pred cceeEEEEeecCcEEEEEcCCCCccc-CccccCeEEEe
Q 032383 66 RKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIA 102 (142)
Q Consensus 66 RK~~rV~L~kngk~vtA~IPg~G~l~-~lqeh~~VLV~ 102 (142)
|=.|.|.+ +|.+++|++|+-|.|. -+.+...|+++
T Consensus 20 RF~~~V~~--~G~~~~aH~pNtGrl~ell~pG~~vll~ 55 (232)
T TIGR00230 20 RFLVDVEV--DGRRETAHCPNTGRLTELIFPGNDVGLS 55 (232)
T ss_pred CEEEEEEE--CCeEEEEEcCCCCCChhhcCCCCEEEEE
Confidence 88899988 8999999999999764 47788899987
No 24
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=55.46 E-value=13 Score=26.16 Aligned_cols=35 Identities=29% Similarity=0.243 Sum_probs=27.2
Q ss_pred eeEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEee
Q 032383 68 CARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 103 (142)
Q Consensus 68 ~~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~G 103 (142)
-.+|+| -||.++.|+|||-=. --.+.+.|.|+|+=
T Consensus 14 ~~~V~~-~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~ 49 (77)
T cd05793 14 RLEVRC-FDGKKRLCRIRGKMRKRVWINEGDIVLVAP 49 (77)
T ss_pred EEEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 357888 899999999998522 12478899999984
No 25
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=54.30 E-value=29 Score=28.62 Aligned_cols=37 Identities=32% Similarity=0.546 Sum_probs=30.4
Q ss_pred cceeEEEEeecCcEEEEEcCCCCccc-CccccCeEEEee
Q 032383 66 RKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIAG 103 (142)
Q Consensus 66 RK~~rV~L~kngk~vtA~IPg~G~l~-~lqeh~~VLV~G 103 (142)
|=.|.|.| .+|..++||+|+-|.|. .|.+...|+++=
T Consensus 6 RF~~~v~l-~~g~~~~~H~pntGRl~ell~pG~~v~l~~ 43 (215)
T PF03749_consen 6 RFLADVEL-DDGEEVTAHCPNTGRLKELLVPGARVLLSK 43 (215)
T ss_pred cEEEEEEE-CCCCEEEEEcCCCCcchhhccCCCEEEEEE
Confidence 55788888 45999999999999887 456888898874
No 26
>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=50.79 E-value=12 Score=24.96 Aligned_cols=33 Identities=24% Similarity=0.394 Sum_probs=24.1
Q ss_pred eEEEEeecCcEEEEEcCCCCccc--CccccCeEEEee
Q 032383 69 ARVQLIKNGKKIAAFVPNDGCLN--YIEENDEVLIAG 103 (142)
Q Consensus 69 ~rV~L~kngk~vtA~IPg~G~l~--~lqeh~~VLV~G 103 (142)
..|+| .||.++.|+|||- --+ .|.+.|.|+|+=
T Consensus 18 ~~V~~-~dg~~~l~~i~gK-~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 18 FEVEC-EDGEERLARIPGK-FRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEEE-TTSEEEEEEE-HH-HHTCC---TTEEEEEEE
T ss_pred EEEEe-CCCCEEEEEeccc-eeeeEecCCCCEEEEEe
Confidence 67888 8999999999996 323 478999999973
No 27
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=46.51 E-value=20 Score=26.52 Aligned_cols=53 Identities=25% Similarity=0.392 Sum_probs=37.6
Q ss_pred CCCCCCccceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEe
Q 032383 39 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIA 102 (142)
Q Consensus 39 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~ 102 (142)
|+-..-|.-|.|++..+ |. -.+|+| .||..+.|+|||-=. --.|.+.|.|+|+
T Consensus 16 ~~p~e~e~~g~V~~~lG------~~----~~~V~~-~dG~~~la~i~GK~Rk~IwI~~GD~VlVe 69 (100)
T PRK04012 16 PMPEEGEVFGVVEQMLG------AN----RVRVRC-MDGVERMGRIPGKMKKRMWIREGDVVIVA 69 (100)
T ss_pred cCCCCCEEEEEEEEEcC------CC----EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 44455666777776654 22 467888 899999999997421 1257889999997
No 28
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=46.40 E-value=47 Score=27.70 Aligned_cols=37 Identities=27% Similarity=0.522 Sum_probs=30.9
Q ss_pred cceeEEEEeecCcEEEEEcCCCCccc-CccccCeEEEee
Q 032383 66 RKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIAG 103 (142)
Q Consensus 66 RK~~rV~L~kngk~vtA~IPg~G~l~-~lqeh~~VLV~G 103 (142)
|=.|.|++ -+|..++||+|+-|.|. -+.+...|+++=
T Consensus 18 RF~~~V~~-~~g~~~~aH~pntGRl~ell~pG~~v~l~~ 55 (234)
T PRK00347 18 RFLADVEL-DDGEELTAHCPNTGRMTGLLTPGNTVWLST 55 (234)
T ss_pred CEEEEEEE-CCCCEEEEEcCCCCCChhhccCCCEEEEEE
Confidence 88899998 56999999999999764 467888898873
No 29
>PRK00284 pqqA coenzyme PQQ synthesis protein PqqA; Provisional
Probab=44.31 E-value=26 Score=20.66 Aligned_cols=13 Identities=8% Similarity=0.294 Sum_probs=10.8
Q ss_pred cCcEEEEEcCCCC
Q 032383 76 NGKKIAAFVPNDG 88 (142)
Q Consensus 76 ngk~vtA~IPg~G 88 (142)
=|.+||.|+|...
T Consensus 12 ~G~EItmY~~~r~ 24 (26)
T PRK00284 12 VGMEVTMYFSARX 24 (26)
T ss_pred cceEEEEEEeccc
Confidence 3999999999754
No 30
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=35.01 E-value=84 Score=26.86 Aligned_cols=37 Identities=27% Similarity=0.495 Sum_probs=30.5
Q ss_pred ccceeEEEEeecCcEEEEEcCCCCccc-CccccCeEEEee
Q 032383 65 IRKCARVQLIKNGKKIAAFVPNDGCLN-YIEENDEVLIAG 103 (142)
Q Consensus 65 ~RK~~rV~L~kngk~vtA~IPg~G~l~-~lqeh~~VLV~G 103 (142)
.|=.+.|.| +|.+++|++|+-|.+. -+.+.+.|.++-
T Consensus 17 nRFl~dv~l--~G~~~~~H~~ntGrm~~l~~pG~~v~l~~ 54 (235)
T COG1489 17 NRFLADVEL--DGEEVTAHCPNTGRMTELLTPGNTVWLSR 54 (235)
T ss_pred cceEEEEEE--CCeEEEEEcCCCCccccccCCCCEEEEEE
Confidence 366788888 4999999999999877 567888888874
No 31
>TIGR02107 PQQ_syn_pqqA coenzyme PQQ biosynthesis protein A. This model describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product.
Probab=31.63 E-value=54 Score=19.35 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=10.5
Q ss_pred cCcEEEEEcCCCC
Q 032383 76 NGKKIAAFVPNDG 88 (142)
Q Consensus 76 ngk~vtA~IPg~G 88 (142)
-|.+||+|++...
T Consensus 11 ~G~EVTmY~~~~~ 23 (26)
T TIGR02107 11 LGMEVTMYVSAXX 23 (26)
T ss_pred ccEEEEEEeeccc
Confidence 3999999998654
No 32
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=30.17 E-value=1.3e+02 Score=21.42 Aligned_cols=53 Identities=19% Similarity=0.298 Sum_probs=31.0
Q ss_pred cceeEEeeeeeccCCCCccccceeEEEEeecCcEEEEEcCCCCc----------ccCccccCeEEEee
Q 032383 46 AKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGC----------LNYIEENDEVLIAG 103 (142)
Q Consensus 46 ~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtA~IPg~G~----------l~~lqeh~~VLV~G 103 (142)
..|+=.=.+.+. +...+.+.++|.+|+..+....-.... +-.|++.|+|-|+=
T Consensus 43 ~~G~Y~F~~~~~-----~~~~~~~~~~L~~N~~~~~~~~~~~~~~~~~~~s~s~vl~L~~GD~V~v~~ 105 (127)
T PF00386_consen 43 VPGVYFFSFTIM-----TSSGSSVWVELMKNGNPVASTYASNSSGNYDSASNSAVLQLNKGDTVWVRL 105 (127)
T ss_dssp S-EEEEEEEEEE-----SEEEEEEEEEEEETTEEEEEEEECSBTTBEEEEEEEEEEEE-TT-EEEEEE
T ss_pred CCCEEEEEEEEe-----ccCCchhHHhhhhhccceeeEeecCCCCccceEEEEEEEEeCCCCEEEEEE
Confidence 345444344444 566677888999999887665422221 12378888888875
No 33
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.33 E-value=1.6e+02 Score=21.12 Aligned_cols=21 Identities=19% Similarity=0.287 Sum_probs=15.9
Q ss_pred CccccceeEEEEeecCcEEEEE
Q 032383 62 NSAIRKCARVQLIKNGKKIAAF 83 (142)
Q Consensus 62 NSA~RK~~rV~L~kngk~vtA~ 83 (142)
++..-+-+.|.| +||..+...
T Consensus 7 ~~l~g~~V~VeL-Kng~~~~G~ 27 (90)
T cd01724 7 MKLTNETVTIEL-KNGTIVHGT 27 (90)
T ss_pred HhCCCCEEEEEE-CCCCEEEEE
Confidence 455778889999 999877644
No 34
>PLN02856 fumarylacetoacetase
Probab=23.88 E-value=1.4e+02 Score=27.39 Aligned_cols=32 Identities=22% Similarity=0.487 Sum_probs=21.6
Q ss_pred EEeecCcEEEEEcCCCCcccCccccCeEEEeec
Q 032383 72 QLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF 104 (142)
Q Consensus 72 ~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~ 104 (142)
.|.-+|++.++.-.|+ .-.||+..|+|.++|+
T Consensus 371 Elt~~G~~p~~l~~g~-~r~fL~dGD~V~l~g~ 402 (424)
T PLN02856 371 ELTWAGSREVSLEGGT-RRKFLEDGDEVVLSGW 402 (424)
T ss_pred EEEeCCccceEeccCC-ccccCCCCCEEEEEEE
Confidence 3333566655544444 2359999999999997
No 35
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=22.99 E-value=1.3e+02 Score=21.33 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=25.7
Q ss_pred eEEEEeecCcEEEEEcCCCCc-ccCccccCeEEEee
Q 032383 69 ARVQLIKNGKKIAAFVPNDGC-LNYIEENDEVLIAG 103 (142)
Q Consensus 69 ~rV~L~kngk~vtA~IPg~G~-l~~lqeh~~VLV~G 103 (142)
..|++ -+|.+..|-||+-=. ---+.+.|.|||.=
T Consensus 15 ~~V~~-~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p 49 (78)
T cd05792 15 HEVET-PNGSRYLVSMPTKFRKNIWIKRGDFVLVEP 49 (78)
T ss_pred EEEEc-CCCCEEEEEechhhcccEEEEeCCEEEEEe
Confidence 45677 689999999998311 12589999999975
No 36
>TIGR01266 fum_ac_acetase fumarylacetoacetase. This enzyme catalyzes the final step in the breakdown of tyrosine or phenylalanine to fumarate and acetoacetate.
Probab=22.83 E-value=1.6e+02 Score=26.92 Aligned_cols=33 Identities=27% Similarity=0.476 Sum_probs=24.9
Q ss_pred EEEeecCcEEEEEcCCCCcccCccccCeEEEeec
Q 032383 71 VQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF 104 (142)
Q Consensus 71 V~L~kngk~vtA~IPg~G~l~~lqeh~~VLV~G~ 104 (142)
+.+..+|++.++.--|+-. .||+..|+|.++|+
T Consensus 362 lE~t~~g~~~v~l~~g~~r-~fL~dGD~V~~~~~ 394 (415)
T TIGR01266 362 LELSWKGKKPIDVGQGETR-TFLEDGDEVILRGH 394 (415)
T ss_pred EEEEeCCeeeeecCCCCCC-CCCCCCCEEEEEEE
Confidence 3443467776666667655 89999999999997
No 37
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=22.68 E-value=84 Score=27.32 Aligned_cols=16 Identities=44% Similarity=0.748 Sum_probs=14.3
Q ss_pred cCccccCeEEEeeccC
Q 032383 91 NYIEENDEVLIAGFGR 106 (142)
Q Consensus 91 ~~lqeh~~VLV~G~G~ 106 (142)
..+++.|.+-||||||
T Consensus 219 ~~v~~GDliSirG~GR 234 (257)
T COG2302 219 YEVQEGDLISIRGFGR 234 (257)
T ss_pred ceeccCCEEEEecccc
Confidence 4799999999999984
No 38
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.42 E-value=2.5e+02 Score=18.97 Aligned_cols=33 Identities=27% Similarity=0.338 Sum_probs=24.1
Q ss_pred eEEEEeecCcEEEEEcCCCCcc--cCccccCeEEEe
Q 032383 69 ARVQLIKNGKKIAAFVPNDGCL--NYIEENDEVLIA 102 (142)
Q Consensus 69 ~rV~L~kngk~vtA~IPg~G~l--~~lqeh~~VLV~ 102 (142)
..|++ .||..+.|+++|-=-. ..+-..|.|+|+
T Consensus 22 y~V~~-~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve 56 (72)
T PRK00276 22 FRVEL-ENGHEVLAHISGKMRKNYIRILPGDKVTVE 56 (72)
T ss_pred EEEEe-CCCCEEEEEEccceeeCCcccCCCCEEEEE
Confidence 44666 6899999999984321 136788999998
No 39
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=20.88 E-value=88 Score=23.39 Aligned_cols=56 Identities=20% Similarity=0.313 Sum_probs=38.6
Q ss_pred cCcEEEEEcCCCCcccCccccCeEEEeeccCCCCccCCCCCceEEEEEecCchhhHhhhhcc
Q 032383 76 NGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKK 137 (142)
Q Consensus 76 ngk~vtA~IPg~G~l~~lqeh~~VLV~G~G~~gg~v~DlPGVrykvVrv~gv~l~~l~~gkk 137 (142)
.+-+|+-|-|-.-+|-.+++.|+|+++++ .+++.-|--+=+..- ..|=+|+|.|..
T Consensus 52 ~~l~v~~F~~~~~~LP~v~~GDVIll~~~-----kv~~~~g~~~~~~~~-~~ss~avf~~~~ 107 (138)
T cd04497 52 DGLTVKLFRPNEESLPIVKVGDIILLRRV-----KIQSYNGKPQGISND-RGSSWAVFRGDD 107 (138)
T ss_pred CcEEEEEECCChhhCCCCCCCCEEEEEEE-----EEEEECCceEEEECC-CceeEEEEcCCC
Confidence 34678888888888888899999999996 677766654433321 245556666643
Done!