Query psy16455
Match_columns 82
No_of_seqs 105 out of 495
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 21:45:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00051 rps12 ribosomal prote 100.0 7.2E-38 1.6E-42 219.5 7.9 79 1-79 7-114 (123)
2 PRK05163 rpsL 30S ribosomal pr 100.0 1.2E-37 2.7E-42 218.6 7.8 79 1-79 7-114 (124)
3 TIGR00981 rpsL_bact ribosomal 100.0 1.5E-37 3.3E-42 218.1 8.0 79 1-79 7-114 (124)
4 cd03368 Ribosomal_S12 S12-like 100.0 1.9E-37 4.2E-42 213.5 8.2 75 1-75 5-108 (108)
5 PF00164 Ribosom_S12_S23: Ribo 100.0 2.7E-35 5.8E-40 205.7 5.1 71 9-79 15-113 (122)
6 cd00319 Ribosomal_S12_like Rib 100.0 7.8E-35 1.7E-39 196.8 6.7 65 11-75 3-95 (95)
7 PTZ00115 40S ribosomal protein 100.0 2.6E-33 5.7E-38 217.1 7.8 71 9-79 112-210 (290)
8 COG0048 RpsL Ribosomal protein 100.0 4E-33 8.6E-38 196.9 6.6 77 3-79 15-120 (129)
9 KOG1750|consensus 100.0 1.6E-30 3.5E-35 185.5 4.0 76 1-76 34-139 (139)
10 cd03367 Ribosomal_S23 S12-like 99.9 1.5E-25 3.3E-30 155.9 6.8 56 10-65 9-100 (115)
11 TIGR00982 S23_S12_E_A ribosoma 99.9 1.8E-24 4E-29 154.4 6.5 55 11-65 30-121 (139)
12 PTZ00067 40S ribosomal S23; Pr 99.9 3E-24 6.5E-29 153.9 6.9 55 11-65 35-125 (143)
13 PRK04211 rps12P 30S ribosomal 99.9 3.5E-24 7.6E-29 153.9 6.6 54 12-65 37-127 (145)
14 KOG1749|consensus 99.4 8E-13 1.7E-17 94.8 5.8 41 25-65 78-125 (143)
15 COG1768 Predicted phosphohydro 72.1 3.4 7.3E-05 32.2 2.4 31 39-70 41-86 (230)
16 TIGR00008 infA translation ini 65.5 9.4 0.0002 24.4 3.1 25 25-49 27-55 (68)
17 COG0361 InfA Translation initi 65.4 8.6 0.00019 25.2 2.9 25 25-49 29-57 (75)
18 KOG3068|consensus 53.4 4 8.7E-05 32.4 -0.2 10 50-59 125-134 (268)
19 PF06246 Isy1: Isy1-like splic 47.0 6.4 0.00014 30.5 0.0 13 50-62 127-139 (255)
20 smart00652 eIF1a eukaryotic tr 43.3 28 0.0006 22.5 2.6 25 25-49 27-54 (83)
21 cd04456 S1_IF1A_like S1_IF1A_l 42.3 30 0.00065 22.2 2.6 25 25-49 22-49 (78)
22 PRK00284 pqqA coenzyme PQQ syn 39.9 21 0.00046 19.3 1.3 11 25-35 13-23 (26)
23 PF02470 MCE: mce related prot 37.1 30 0.00066 20.9 1.9 30 25-55 2-34 (81)
24 TIGR02107 PQQ_syn_pqqA coenzym 33.8 28 0.00062 18.8 1.2 11 25-35 12-22 (26)
25 PRK12442 translation initiatio 31.0 62 0.0013 21.8 2.8 25 25-49 29-57 (87)
26 PF01176 eIF-1a: Translation i 30.8 26 0.00055 21.3 0.9 25 25-49 25-52 (65)
27 TIGR00523 eIF-1A eukaryotic/ar 30.5 52 0.0011 22.1 2.4 23 25-47 41-66 (99)
28 cd05793 S1_IF1A S1_IF1A: Trans 27.9 59 0.0013 20.7 2.2 24 25-48 22-48 (77)
29 COG1489 SfsA DNA-binding prote 26.1 86 0.0019 24.4 3.2 25 25-49 27-54 (235)
30 PF02080 TrkA_C: TrkA-C domain 25.7 61 0.0013 18.5 1.8 20 30-49 39-58 (71)
31 TIGR01810 betA choline dehydro 23.6 54 0.0012 26.4 1.7 25 25-49 275-299 (532)
32 cd03109 DTBS Dethiobiotin synt 23.3 1.2E+02 0.0025 20.1 3.1 20 25-49 27-46 (134)
33 PRK14763 coenzyme PQQ biosynth 22.9 58 0.0013 17.7 1.2 10 25-34 13-22 (26)
34 PF12378 CytadhesinP1: Trypsin 22.6 49 0.0011 21.7 1.1 23 29-51 50-72 (72)
35 COG3269 Predicted RNA-binding 22.2 62 0.0013 21.2 1.5 42 34-75 30-71 (73)
36 PF07013 DUF1314: Protein of u 21.9 26 0.00055 26.5 -0.4 18 43-60 1-20 (177)
37 PRK04012 translation initiatio 21.6 95 0.0021 20.9 2.4 24 25-48 43-69 (100)
38 PF03749 SfsA: Sugar fermentat 21.0 1.3E+02 0.0029 22.5 3.3 41 25-68 16-61 (215)
39 KOG1238|consensus 20.6 38 0.00082 29.7 0.3 27 19-45 318-358 (623)
40 PHA03371 circ protein; Provisi 20.0 16 0.00034 28.8 -1.9 25 37-61 16-42 (240)
No 1
>CHL00051 rps12 ribosomal protein S12
Probab=100.00 E-value=7.2e-38 Score=219.54 Aligned_cols=79 Identities=43% Similarity=0.648 Sum_probs=69.9
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455 1 MHMKGPHYKK-RPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR 51 (82)
Q Consensus 1 l~~~g~~~~~-~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr 51 (82)
|.+.++.++. +.++++|++|||+| |++||||||||||||||||+|||||||
T Consensus 7 l~~~~r~~k~~~~k~~~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrLsngk~v~AyIPGeGhnlqehs~VLvrGGr 86 (123)
T CHL00051 7 LIRNTRQPIRNKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGR 86 (123)
T ss_pred hhhcCCCCccccccCcccccCcccCeEEEEEEeccccCCChhheeEEEEEccCCCEEEEEcCCCCccccccCEEEEeCCc
Confidence 3455554443 34557999999999 999999999999999999999999999
Q ss_pred cCCCCCceEEEeeeecCCcccccccccC
Q psy16455 52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~ 79 (82)
++|||||+|++|||+|||++|.+|+++.
T Consensus 87 v~DlPGVrykvVRG~~D~~gv~~R~~~R 114 (123)
T CHL00051 87 VKDLPGVRYHIVRGTLDAVGVKDRQQGR 114 (123)
T ss_pred cCCCCCeeEEEEeeeecccccccccccc
Confidence 9999999999999999999999998874
No 2
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=100.00 E-value=1.2e-37 Score=218.60 Aligned_cols=79 Identities=47% Similarity=0.694 Sum_probs=70.3
Q ss_pred CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455 1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR 51 (82)
Q Consensus 1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr 51 (82)
|++.+++++.++ ++++|++|||++ |++||||||||||||||||+||||||+
T Consensus 7 l~~~~r~~k~~~~k~~~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPGeGhnlqehs~VLvrGGr 86 (124)
T PRK05163 7 LVRKGRKSKVKKSKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSVVLIRGGR 86 (124)
T ss_pred HhhcCCCCCcccccCcccccCcccCcEEEEEEecCccCCCchhheEEEEEeCCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence 345665555444 456899999999 999999999999999999999999999
Q ss_pred cCCCCCceEEEeeeecCCcccccccccC
Q psy16455 52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~ 79 (82)
++|||||+|++|||+|||++|.+|+++.
T Consensus 87 v~DlPGVrykvVrG~~D~~gv~~R~~~R 114 (124)
T PRK05163 87 VKDLPGVRYHIVRGALDTAGVKDRKQGR 114 (124)
T ss_pred cCCCCCcEEEEeeeeecccccccccccc
Confidence 9999999999999999999999998874
No 3
>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=1.5e-37 Score=218.09 Aligned_cols=79 Identities=48% Similarity=0.715 Sum_probs=70.5
Q ss_pred CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455 1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR 51 (82)
Q Consensus 1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr 51 (82)
|++.+++++.++ ++++|++|||++ |++||||||||||||||||+||||||+
T Consensus 7 l~~~~r~kk~~~~k~~~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPG~Ghnlqehs~VLvrGGr 86 (124)
T TIGR00981 7 LIRKGRKKKKKKSKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSVVLIRGGR 86 (124)
T ss_pred hhhcCCCCccccccCcccccCCccCcEEEEEEeccccCCCchhheeEEEEeCCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence 345666555444 457899999999 999999999999999999999999999
Q ss_pred cCCCCCceEEEeeeecCCcccccccccC
Q psy16455 52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~ 79 (82)
++|||||+|++|||+|||++|.+|+++.
T Consensus 87 v~DlPGVkykvVrG~~D~~gv~~R~~~R 114 (124)
T TIGR00981 87 VKDLPGVRYHIVRGALDTAGVKNRKQGR 114 (124)
T ss_pred cCCCCCeEEEEEeEeecccccccccccc
Confidence 9999999999999999999999998874
No 4
>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=1.9e-37 Score=213.46 Aligned_cols=75 Identities=56% Similarity=0.862 Sum_probs=66.3
Q ss_pred CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455 1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR 51 (82)
Q Consensus 1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr 51 (82)
|.++++++++++ ++++|++|||+| |++|+||||||||||||||+|||||||
T Consensus 5 l~~~~r~~k~~~~k~~~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L~ngk~v~AyIPG~Ghnlqehs~VLvrGGr 84 (108)
T cd03368 5 LIRKGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKEVTAYIPGEGHNLQEHSVVLVRGGR 84 (108)
T ss_pred eeecCCCCccccccCCcccCCcccCcEEEEEEeccccCCChhheeeEEEEecCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence 345555444444 457999999999 999999999999999999999999999
Q ss_pred cCCCCCceEEEeeeecCCcccccc
Q psy16455 52 VKDLPGVKIKCVRGVYDLPHVVKK 75 (82)
Q Consensus 52 ~~DLPGVkykvVrG~~D~~~v~~R 75 (82)
++|||||+|++|||+|||++|.+|
T Consensus 85 v~DlPGVkykvvRG~~D~~gv~~R 108 (108)
T cd03368 85 VKDLPGVRYHIVRGVLDLAGVKNR 108 (108)
T ss_pred cCCCCCeEEEEEeeecccccccCC
Confidence 999999999999999999999886
No 5
>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=2.7e-35 Score=205.74 Aligned_cols=71 Identities=55% Similarity=0.894 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceE
Q psy16455 9 KKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKI 60 (82)
Q Consensus 9 ~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVky 60 (82)
.++.++++|+++||+| |++|+||||||||||||||+||||||+++|||||+|
T Consensus 15 ~~~~k~~~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL~n~k~v~AyIPg~Ghnlqehs~VLVrGgrv~DlPGVky 94 (122)
T PF00164_consen 15 KRKSKSPALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRLSNGKKVTAYIPGEGHNLQEHSVVLVRGGRVGDLPGVKY 94 (122)
T ss_dssp TCSHSSSSSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEETTSEEEEEEC-SSSCCSTTTSEEEEEEESBTTSTTECE
T ss_pred CccccCCccCCCCccCcEEeecccccccCccchhhhcceeeeccCceEEEEecCCcccccccceEEEeccccCCCCceEE
Confidence 3345567999999999 999999999999999999999999999999999999
Q ss_pred EEeeeecCCcccccccccC
Q psy16455 61 KCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 61 kvVrG~~D~~~v~~R~~~~ 79 (82)
++|||+|||++|.+|+++-
T Consensus 95 kvVRG~~D~~gV~~r~~~r 113 (122)
T PF00164_consen 95 KVVRGVYDVAGVSNRKKAR 113 (122)
T ss_dssp EBETTSTTCSSSTT-SSSC
T ss_pred EEEeeccccccccHHHHhh
Confidence 9999999999999988764
No 6
>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=7.8e-35 Score=196.79 Aligned_cols=65 Identities=57% Similarity=0.965 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceEEE
Q psy16455 11 RPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKC 62 (82)
Q Consensus 11 ~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVkykv 62 (82)
+.++++|++|||+| |++||||||||||||||||+|||||||++|||||+|++
T Consensus 3 ~~k~~~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L~ngk~v~ayIPg~Gh~lqeh~~VLvrGGr~~DlPGVrykv 82 (95)
T cd00319 3 KSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHI 82 (95)
T ss_pred ccccCcccCCcccCeEEEEEEeccccCCChhhceEEEEEccCCCEEEEECCCCCcccccccEEEEeCCCcCCCCCcEEEE
Confidence 34568999999999 99999999999999999999999999999999999999
Q ss_pred eeeecCCcccccc
Q psy16455 63 VRGVYDLPHVVKK 75 (82)
Q Consensus 63 VrG~~D~~~v~~R 75 (82)
|||+|||+++.+|
T Consensus 83 VrG~~d~~~v~~R 95 (95)
T cd00319 83 VRGVYDAAGVKDR 95 (95)
T ss_pred EcccchhhhccCC
Confidence 9999999999876
No 7
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=100.00 E-value=2.6e-33 Score=217.08 Aligned_cols=71 Identities=45% Similarity=0.750 Sum_probs=65.8
Q ss_pred CCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceE
Q psy16455 9 KKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKI 60 (82)
Q Consensus 9 ~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVky 60 (82)
.+.+++++|+||||+| |++||||||||||||||||+||||||+++|||||+|
T Consensus 112 ~~~~k~paL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrLsNGk~VtAyIPGeGHnLQEHs~VLVRGGrvkDLPGVrY 191 (290)
T PTZ00115 112 PKNRRSKWLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGHNLNTHSVVLVRGGRCKDVPGCNY 191 (290)
T ss_pred CCCCcCccccCCcccCeEEEEeeecCCCCCCccccceEEEEecCCCEEEEEcCCCCcccccCCEEEEeCCCcCCCCCceE
Confidence 3444556899999999 999999999999999999999999999999999999
Q ss_pred EEeeeecCCcccccccccC
Q psy16455 61 KCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 61 kvVrG~~D~~~v~~R~~~~ 79 (82)
++|||+|||++|.+|+++.
T Consensus 192 kvVRG~~D~~gV~~Rk~~R 210 (290)
T PTZ00115 192 KAVRGVYDLLPVKNRARSR 210 (290)
T ss_pred EEeeeeccccccccccccc
Confidence 9999999999999998864
No 8
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=4e-33 Score=196.95 Aligned_cols=77 Identities=51% Similarity=0.712 Sum_probs=67.4
Q ss_pred CCCCCCCCC-CCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcC
Q psy16455 3 MKGPHYKKR-PPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVK 53 (82)
Q Consensus 3 ~~g~~~~~~-~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~ 53 (82)
|.++..... .+++||++|||++ |++||||||||||||||||+||||||+++
T Consensus 15 R~~rr~~~~k~Ks~~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~NG~~VtAyiPg~Gh~lqEH~~Vli~G~~v~ 94 (129)
T COG0048 15 RKKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLINGKEVTAYIPGEGHNLQEHSEVLIRGGRVK 94 (129)
T ss_pred hcccccccccccCCcccCCCccceEEEEEEecccCCCChhhheeEEEEeeCCcEEEEEcCCCCccccccCEEEEecCccC
Confidence 444333333 3456999999999 99999999999999999999999999999
Q ss_pred CCCCceEEEeeeecCCcccccccccC
Q psy16455 54 DLPGVKIKCVRGVYDLPHVVKKTQLT 79 (82)
Q Consensus 54 DLPGVkykvVrG~~D~~~v~~R~~~~ 79 (82)
|||||+||||||.+|.+++..|.++.
T Consensus 95 DlPGVRy~vvrg~~ds~~v~~r~~~r 120 (129)
T COG0048 95 DLPGVRYKVVRGALDSLGVLDRGQKR 120 (129)
T ss_pred CCCCceEEEEEEcchhhhhhhhcccc
Confidence 99999999999999999999887754
No 9
>KOG1750|consensus
Probab=99.96 E-value=1.6e-30 Score=185.46 Aligned_cols=76 Identities=54% Similarity=0.861 Sum_probs=67.7
Q ss_pred CCCC-C-CCCCCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecC
Q psy16455 1 MHMK-G-PHYKKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVG 50 (82)
Q Consensus 1 l~~~-g-~~~~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGG 50 (82)
|+|. | +++|+..++.+|++|||.+ |.+|+|||||+|||+|||++||||||
T Consensus 34 liR~~~r~~kRr~~~~~~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrlstg~~i~ayipg~ghnlqehs~Vlvrgg 113 (139)
T KOG1750|consen 34 LIRNGGRPPKRRPRKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRLSTGREVTAYIPGIGHNLQEHSIVLVRGG 113 (139)
T ss_pred HHhcCCCCCccCCcccccccCCcccccEEEEEEEecCCCCCccceeeEEEEecCchheeeeCCCccccceeEEEEEEecc
Confidence 3555 3 4555555567999999999 99999999999999999999999999
Q ss_pred CcCCCCCceEEEeeeecCCccccccc
Q psy16455 51 RVKDLPGVKIKCVRGVYDLPHVVKKT 76 (82)
Q Consensus 51 r~~DLPGVkykvVrG~~D~~~v~~R~ 76 (82)
|++|||||+|++|||+|||++|.+|.
T Consensus 114 r~qdlpgvk~~~vRg~~d~~~V~~r~ 139 (139)
T KOG1750|consen 114 RVQDLPGVKYHVVRGVYDLAGVVGRI 139 (139)
T ss_pred eeccCcchhhhhhhhhhhhccccCCC
Confidence 99999999999999999999999873
No 10
>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=99.92 E-value=1.5e-25 Score=155.94 Aligned_cols=56 Identities=39% Similarity=0.707 Sum_probs=51.6
Q ss_pred CCCCCCCCCCCCccC-----------------------------CCEEEEEecCCC--CCCCcccEEEEec-----CCcC
Q psy16455 10 KRPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEG--HNLQEHNIVLCKV-----GRVK 53 (82)
Q Consensus 10 ~~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~G--hnlqehs~VLVrG-----Gr~~ 53 (82)
.+.+.++|++|||+| |++||||||||| |||||||+||||| |+++
T Consensus 9 ~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~G~~Gg~v~ 88 (115)
T cd03367 9 TKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGFGRKGRAVG 88 (115)
T ss_pred ccccCCcccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccC
Confidence 445678999999999 999999999999 6999999999999 7899
Q ss_pred CCCCceEEEeee
Q psy16455 54 DLPGVKIKCVRG 65 (82)
Q Consensus 54 DLPGVkykvVrG 65 (82)
|||||+|++|+-
T Consensus 89 DlPGVrykvVkV 100 (115)
T cd03367 89 DIPGVRFKVVKV 100 (115)
T ss_pred CCCceEEEEEEE
Confidence 999999999984
No 11
>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=99.91 E-value=1.8e-24 Score=154.44 Aligned_cols=55 Identities=36% Similarity=0.694 Sum_probs=50.8
Q ss_pred CCCCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec------CCcC
Q psy16455 11 RPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV------GRVK 53 (82)
Q Consensus 11 ~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG------Gr~~ 53 (82)
..+.++|+++||+| |++|||||||||| ||||||+|||+| |+++
T Consensus 30 ~~K~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiPg~G~~~~lqeh~~VLV~G~gg~~gg~v~ 109 (139)
T TIGR00982 30 KRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMG 109 (139)
T ss_pred ccccCcccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeCCCccccccccCCEEEEEecCccCCCCcC
Confidence 44568999999999 9999999999997 799999999999 7999
Q ss_pred CCCCceEEEeee
Q psy16455 54 DLPGVKIKCVRG 65 (82)
Q Consensus 54 DLPGVkykvVrG 65 (82)
|||||+|+||+-
T Consensus 110 DlPGVrykvVkV 121 (139)
T TIGR00982 110 DIPGVRYKVVKV 121 (139)
T ss_pred CCCceEEEEEEE
Confidence 999999999983
No 12
>PTZ00067 40S ribosomal S23; Provisional
Probab=99.90 E-value=3e-24 Score=153.91 Aligned_cols=55 Identities=38% Similarity=0.685 Sum_probs=50.9
Q ss_pred CCCCCCCCCCCccC-----------------------------CCEEEEEecCCC--CCCCcccEEEEec-C----CcCC
Q psy16455 11 RPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEG--HNLQEHNIVLCKV-G----RVKD 54 (82)
Q Consensus 11 ~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~G--hnlqehs~VLVrG-G----r~~D 54 (82)
..+.+||++|||+| |++||||||||| |||||||+|||+| | +++|
T Consensus 35 ~~k~~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~D 114 (143)
T PTZ00067 35 RYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGD 114 (143)
T ss_pred ccccCcccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeCCCCcccccccCCEEEEEecCcCCCccCC
Confidence 34568999999999 999999999999 9999999999999 7 6999
Q ss_pred CCCceEEEeee
Q psy16455 55 LPGVKIKCVRG 65 (82)
Q Consensus 55 LPGVkykvVrG 65 (82)
||||+|+|||-
T Consensus 115 lPGVrykvVrV 125 (143)
T PTZ00067 115 IPGVRFKVVKV 125 (143)
T ss_pred CCceEEEEEEE
Confidence 99999999984
No 13
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=99.90 E-value=3.5e-24 Score=153.85 Aligned_cols=54 Identities=35% Similarity=0.707 Sum_probs=50.2
Q ss_pred CCCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec------CCcCC
Q psy16455 12 PPRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV------GRVKD 54 (82)
Q Consensus 12 ~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG------Gr~~D 54 (82)
.+.++|++|||+| |++|||||||||| ||||||+|||+| |+++|
T Consensus 37 ~K~~~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~D 116 (145)
T PRK04211 37 EKADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGD 116 (145)
T ss_pred cccCcccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCccccccccCCEEEEeecCccCCCCcCC
Confidence 4568999999999 9999999999997 899999999999 68999
Q ss_pred CCCceEEEeee
Q psy16455 55 LPGVKIKCVRG 65 (82)
Q Consensus 55 LPGVkykvVrG 65 (82)
||||+|+||.-
T Consensus 117 lPGVrykvVkV 127 (145)
T PRK04211 117 IPGVRYKVIKV 127 (145)
T ss_pred CCceEEEEEEE
Confidence 99999999973
No 14
>KOG1749|consensus
Probab=99.38 E-value=8e-13 Score=94.78 Aligned_cols=41 Identities=39% Similarity=0.783 Sum_probs=38.2
Q ss_pred CCEEEEEecCCC--CCCCcccEEEEec----CC-cCCCCCceEEEeee
Q psy16455 25 GKEMVAYIPGEG--HNLQEHNIVLCKV----GR-VKDLPGVKIKCVRG 65 (82)
Q Consensus 25 gk~v~AyIPG~G--hnlqehs~VLVrG----Gr-~~DLPGVkykvVrG 65 (82)
|++||||+|-+| ++++|+|+|||.| |+ ++|+|||+|+||.-
T Consensus 78 gKKITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvrfkvvkv 125 (143)
T KOG1749|consen 78 GKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKV 125 (143)
T ss_pred CceEEEEecCCCceeeeccCCeeeeeccCccCccccCCCceEEEEEEE
Confidence 999999999999 9999999999999 44 89999999999873
No 15
>COG1768 Predicted phosphohydrolase [General function prediction only]
Probab=72.09 E-value=3.4 Score=32.15 Aligned_cols=31 Identities=39% Similarity=0.550 Sum_probs=25.1
Q ss_pred CCcccEEEEecC--------------C-cCCCCCceEEEeeeecCCc
Q psy16455 39 LQEHNIVLCKVG--------------R-VKDLPGVKIKCVRGVYDLP 70 (82)
Q Consensus 39 lqehs~VLVrGG--------------r-~~DLPGVkykvVrG~~D~~ 70 (82)
+.+-|+||+-|- | ..||||.|| ++||..|.=
T Consensus 41 v~~eDiVllpGDiSWaM~l~ea~~Dl~~i~~LPG~K~-m~rGNHDYW 86 (230)
T COG1768 41 VSPEDIVLLPGDISWAMRLEEAEEDLRFIGDLPGTKY-MIRGNHDYW 86 (230)
T ss_pred CChhhEEEecccchhheechhhhhhhhhhhcCCCcEE-EEecCCccc
Confidence 567788988882 3 689999999 679999874
No 16
>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=65.51 E-value=9.4 Score=24.40 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=19.9
Q ss_pred CCEEEEEecCCCC----CCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEGH----NLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~Gh----nlqehs~VLVrG 49 (82)
|.++.|||+|-=- -+.+.|.|+|+=
T Consensus 27 g~~vla~i~GKmr~~rI~I~~GD~V~Ve~ 55 (68)
T TIGR00008 27 GHEVLAHISGKIRMHYIRILPGDKVKVEL 55 (68)
T ss_pred CCEEEEEecCcchhccEEECCCCEEEEEE
Confidence 8999999999642 377888888873
No 17
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=65.40 E-value=8.6 Score=25.15 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=21.3
Q ss_pred CCEEEEEecCCC--CC--CCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG--HN--LQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G--hn--lqehs~VLVrG 49 (82)
|.+++|+|||-. |+ +-+-|+|+|+=
T Consensus 29 g~~~~ahI~GKmr~~~i~I~~GD~V~Ve~ 57 (75)
T COG0361 29 GHERLAHISGKMRKNRIRILPGDVVLVEL 57 (75)
T ss_pred CcEEEEEccCcchheeEEeCCCCEEEEEe
Confidence 999999999998 33 67889999874
No 18
>KOG3068|consensus
Probab=53.43 E-value=4 Score=32.44 Aligned_cols=10 Identities=70% Similarity=1.275 Sum_probs=9.4
Q ss_pred CCcCCCCCce
Q psy16455 50 GRVKDLPGVK 59 (82)
Q Consensus 50 Gr~~DLPGVk 59 (82)
|+.+|||||+
T Consensus 125 GaAkdLPgVr 134 (268)
T KOG3068|consen 125 GAAKDLPGVR 134 (268)
T ss_pred hhhccCccHH
Confidence 9999999997
No 19
>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing [].; PDB: 1X4T_A.
Probab=46.98 E-value=6.4 Score=30.52 Aligned_cols=13 Identities=62% Similarity=0.935 Sum_probs=0.0
Q ss_pred CCcCCCCCceEEE
Q psy16455 50 GRVKDLPGVKIKC 62 (82)
Q Consensus 50 Gr~~DLPGVkykv 62 (82)
||.+|||||+--+
T Consensus 127 GrAkeLPgVkeL~ 139 (255)
T PF06246_consen 127 GRAKELPGVKELF 139 (255)
T ss_dssp -------------
T ss_pred ehhccCccHHHHH
Confidence 9999999998543
No 20
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=43.31 E-value=28 Score=22.52 Aligned_cols=25 Identities=40% Similarity=0.534 Sum_probs=19.9
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVrG 49 (82)
|.++.|+|||-= =-+.+.|.|+|+=
T Consensus 27 G~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 27 GKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred CCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 899999999954 3367888888864
No 21
>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=42.32 E-value=30 Score=22.16 Aligned_cols=25 Identities=16% Similarity=0.345 Sum_probs=20.0
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVrG 49 (82)
|.++.|+|||-= --+.+-|.|+|+=
T Consensus 22 g~~~l~~i~gK~Rk~iwI~~GD~VlV~~ 49 (78)
T cd04456 22 GQRRLVSIPGKLRKNIWIKRGDFLIVDP 49 (78)
T ss_pred CCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence 899999999943 4578888888863
No 22
>PRK00284 pqqA coenzyme PQQ synthesis protein PqqA; Provisional
Probab=39.92 E-value=21 Score=19.30 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=9.7
Q ss_pred CCEEEEEecCC
Q psy16455 25 GKEMVAYIPGE 35 (82)
Q Consensus 25 gk~v~AyIPG~ 35 (82)
|.|||.|++..
T Consensus 13 G~EItmY~~~r 23 (26)
T PRK00284 13 GMEVTMYFSAR 23 (26)
T ss_pred ceEEEEEEecc
Confidence 89999999864
No 23
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=37.10 E-value=30 Score=20.90 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=24.8
Q ss_pred CCEEEEEecCCCCCCCcccEEEEec---CCcCCC
Q psy16455 25 GKEMVAYIPGEGHNLQEHNIVLCKV---GRVKDL 55 (82)
Q Consensus 25 gk~v~AyIPG~Ghnlqehs~VLVrG---Gr~~DL 55 (82)
+.+++++.+-. ..|..-+-|.++| |++.++
T Consensus 2 ~~~v~~~~~~~-~GL~~gs~V~~~Gv~VG~V~~i 34 (81)
T PF02470_consen 2 GYTVTVYFDDA-GGLSVGSPVRYRGVEVGKVTSI 34 (81)
T ss_pred CEEEEEEECCc-CCCCCcCEEEECCEEEEEEEEE
Confidence 35678888877 8899999999999 877766
No 24
>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=33.80 E-value=28 Score=18.82 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=9.4
Q ss_pred CCEEEEEecCC
Q psy16455 25 GKEMVAYIPGE 35 (82)
Q Consensus 25 gk~v~AyIPG~ 35 (82)
|.|||+|++..
T Consensus 12 G~EVTmY~~~~ 22 (26)
T TIGR02107 12 GMEVTMYVSAX 22 (26)
T ss_pred cEEEEEEeecc
Confidence 89999999854
No 25
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=31.03 E-value=62 Score=21.81 Aligned_cols=25 Identities=28% Similarity=0.396 Sum_probs=18.2
Q ss_pred CCEEEEEecCCC--CC--CCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG--HN--LQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G--hn--lqehs~VLVrG 49 (82)
|.+|+|||+|-= |. +-+.|.|+|+=
T Consensus 29 G~~vla~isGKmR~~rIrIl~GD~V~VE~ 57 (87)
T PRK12442 29 GVEVGAYASGRMRKHRIRILAGDRVTLEL 57 (87)
T ss_pred CCEEEEEeccceeeeeEEecCCCEEEEEE
Confidence 889999999964 22 45667777764
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=30.82 E-value=26 Score=21.28 Aligned_cols=25 Identities=32% Similarity=0.452 Sum_probs=17.5
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVrG 49 (82)
|.+++|+|||-= -.+.+.|.|+|.=
T Consensus 25 g~~~l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 25 GEERLARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp SEEEEEEE-HHHHTCC---TTEEEEEEE
T ss_pred CCEEEEEeccceeeeEecCCCCEEEEEe
Confidence 889999999864 5678889999874
No 27
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.53 E-value=52 Score=22.09 Aligned_cols=23 Identities=30% Similarity=0.518 Sum_probs=18.1
Q ss_pred CCEEEEEecCCC---CCCCcccEEEE
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLC 47 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLV 47 (82)
|.++.|+|||-= -.+.+-|.|||
T Consensus 41 G~~~la~i~GK~Rk~iwI~~GD~VlV 66 (99)
T TIGR00523 41 GKTRLGRIPGKLKKRIWIREGDVVIV 66 (99)
T ss_pred CCEEEEEEchhhcccEEecCCCEEEE
Confidence 899999999943 34677788887
No 28
>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=27.94 E-value=59 Score=20.70 Aligned_cols=24 Identities=33% Similarity=0.425 Sum_probs=18.9
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEe
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCK 48 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVr 48 (82)
|.++.|+|||-= =.+.+.|.|+|+
T Consensus 22 g~~~la~i~gK~rk~iwI~~GD~V~Ve 48 (77)
T cd05793 22 GKKRLCRIRGKMRKRVWINEGDIVLVA 48 (77)
T ss_pred CCEEEEEEchhhcccEEEcCCCEEEEE
Confidence 899999999964 235677888887
No 29
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=26.12 E-value=86 Score=24.43 Aligned_cols=25 Identities=32% Similarity=0.383 Sum_probs=22.8
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVrG 49 (82)
|.+++|+||.-| +-+.+-+.|+++=
T Consensus 27 G~~~~~H~~ntGrm~~l~~pG~~v~l~~ 54 (235)
T COG1489 27 GEEVTAHCPNTGRMTELLTPGNTVWLSR 54 (235)
T ss_pred CeEEEEEcCCCCccccccCCCCEEEEEE
Confidence 999999999999 8889999999874
No 30
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=25.66 E-value=61 Score=18.53 Aligned_cols=20 Identities=25% Similarity=0.303 Sum_probs=13.2
Q ss_pred EEecCCCCCCCcccEEEEec
Q psy16455 30 AYIPGEGHNLQEHNIVLCKV 49 (82)
Q Consensus 30 AyIPG~Ghnlqehs~VLVrG 49 (82)
.++|.....|++.|+|+|-|
T Consensus 39 ~~~p~~~~~l~~gD~l~v~g 58 (71)
T PF02080_consen 39 IIIPDGDTVLQAGDILIVVG 58 (71)
T ss_dssp EES--TT-BE-TTEEEEEEE
T ss_pred EECCCCCCEECCCCEEEEEE
Confidence 45666678999999999987
No 31
>TIGR01810 betA choline dehydrogenase. This enzyme is a member of the GMC oxidoreductase family (pfam00732 and pfam05199), sharing a common evoluntionary origin and enzymatic reaction with alcohol dehydrogenase. Outgrouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified.
Probab=23.63 E-value=54 Score=26.41 Aligned_cols=25 Identities=40% Similarity=0.523 Sum_probs=20.5
Q ss_pred CCEEEEEecCCCCCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEGHNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~Ghnlqehs~VLVrG 49 (82)
|=.+.+=.||.|.|||+|-.+.+.+
T Consensus 275 gI~~~~~lp~VG~nL~DH~~~~~~~ 299 (532)
T TIGR01810 275 GIEPRIHLPGVGENLQDHLEVYVQH 299 (532)
T ss_pred CCCeEeeCCccccchhhcccceeEE
Confidence 5577788999999999998766654
No 32
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=23.26 E-value=1.2e+02 Score=20.14 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=17.8
Q ss_pred CCEEEEEecCCCCCCCcccEEEEec
Q psy16455 25 GKEMVAYIPGEGHNLQEHNIVLCKV 49 (82)
Q Consensus 25 gk~v~AyIPG~Ghnlqehs~VLVrG 49 (82)
|..|-+|=|... ||.|+|||
T Consensus 27 ~~~v~~~kp~~~-----~d~vliEG 46 (134)
T cd03109 27 GYRVAPLKPVQT-----YDFVLVEG 46 (134)
T ss_pred CCeEEEEecCCC-----CCEEEEEC
Confidence 788889988876 89999999
No 33
>PRK14763 coenzyme PQQ biosynthesis protein A; Provisional
Probab=22.93 E-value=58 Score=17.74 Aligned_cols=10 Identities=30% Similarity=0.557 Sum_probs=8.5
Q ss_pred CCEEEEEecC
Q psy16455 25 GKEMVAYIPG 34 (82)
Q Consensus 25 gk~v~AyIPG 34 (82)
|.+||.||-.
T Consensus 13 GfEvTmYi~n 22 (26)
T PRK14763 13 GFEVTMYVMN 22 (26)
T ss_pred eeEEEEEEee
Confidence 9999999943
No 34
>PF12378 CytadhesinP1: Trypsin-sensitive surface-exposed protein; InterPro: IPR022116 This domain family is found in bacteria, and is typically between 67 and 79 amino acids in length. This family contains trypsin-sensitive surface-exposed proteins called cytadhesins. Cytadhesins are virulence factor proteins which mediate attachment of bacterial cells to host cells for invasion.
Probab=22.60 E-value=49 Score=21.70 Aligned_cols=23 Identities=26% Similarity=0.138 Sum_probs=20.2
Q ss_pred EEEecCCCCCCCcccEEEEecCC
Q psy16455 29 VAYIPGEGHNLQEHNIVLCKVGR 51 (82)
Q Consensus 29 ~AyIPG~Ghnlqehs~VLVrGGr 51 (82)
.||||.+|..+---..|||-||.
T Consensus 50 ~~y~~Nignl~~~~~~v~~fGgn 72 (72)
T PF12378_consen 50 EAYFANIGNLTWFGQSVLVFGGN 72 (72)
T ss_pred hhcccccceeeEeCceEEEecCC
Confidence 38999999999999999998873
No 35
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=22.22 E-value=62 Score=21.19 Aligned_cols=42 Identities=29% Similarity=0.351 Sum_probs=34.4
Q ss_pred CCCCCCCcccEEEEecCCcCCCCCceEEEeeeecCCcccccc
Q psy16455 34 GEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75 (82)
Q Consensus 34 G~Ghnlqehs~VLVrGGr~~DLPGVkykvVrG~~D~~~v~~R 75 (82)
|+|=..-|--+|.|-|-.++|-+.|+.+-|+..|-|+.+..|
T Consensus 30 GDGiarveGfvVFVp~a~~Gd~V~vkI~~v~~~~afaevve~ 71 (73)
T COG3269 30 GDGIARVEGFVVFVPGAEVGDEVKVKITKVKPNFAFAEVVER 71 (73)
T ss_pred CCceEEEEEEEEEeCCCCCCCeeeEEEEEeeccceeeEEeec
Confidence 445444456688888889999999999999999999988766
No 36
>PF07013 DUF1314: Protein of unknown function (DUF1314); InterPro: IPR010741 This family consists of several alphaherpesvirus proteins of around 200 residues in length. They belong to the varicellovirus ORF2 family and their function is unknown.
Probab=21.89 E-value=26 Score=26.52 Aligned_cols=18 Identities=39% Similarity=0.541 Sum_probs=14.9
Q ss_pred cEEEEec--CCcCCCCCceE
Q psy16455 43 NIVLCKV--GRVKDLPGVKI 60 (82)
Q Consensus 43 s~VLVrG--Gr~~DLPGVky 60 (82)
+.||+++ ||.=||||=-+
T Consensus 1 ~~~Ll~~LaGR~iDLPgG~e 20 (177)
T PF07013_consen 1 TKTLLRSLAGRTIDLPGGDE 20 (177)
T ss_pred ChhhhhhhcCcceecCCCCe
Confidence 4578887 99999999776
No 37
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=21.62 E-value=95 Score=20.90 Aligned_cols=24 Identities=29% Similarity=0.497 Sum_probs=18.8
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEe
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCK 48 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVr 48 (82)
|.++.|+|||-= -.+.+.|.|+|+
T Consensus 43 G~~~la~i~GK~Rk~IwI~~GD~VlVe 69 (100)
T PRK04012 43 GVERMGRIPGKMKKRMWIREGDVVIVA 69 (100)
T ss_pred CCEEEEEEchhhcccEEecCCCEEEEE
Confidence 899999999854 456677888876
No 38
>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=21.04 E-value=1.3e+02 Score=22.51 Aligned_cols=41 Identities=29% Similarity=0.250 Sum_probs=29.7
Q ss_pred CCEEEEEecCCC---CCCCcccEEEEecCCcCCCC--CceEEEeeeecC
Q psy16455 25 GKEMVAYIPGEG---HNLQEHNIVLCKVGRVKDLP--GVKIKCVRGVYD 68 (82)
Q Consensus 25 gk~v~AyIPG~G---hnlqehs~VLVrGGr~~DLP--GVkykvVrG~~D 68 (82)
|.+++||+|.-| ..|.+...|+++= .|=| --+|.++--..+
T Consensus 16 g~~~~~H~pntGRl~ell~pG~~v~l~~---~~~~~RKt~y~l~av~~~ 61 (215)
T PF03749_consen 16 GEEVTAHCPNTGRLKELLVPGARVLLSK---SDNPKRKTKYTLEAVEKD 61 (215)
T ss_pred CCEEEEEcCCCCcchhhccCCCEEEEEE---CCCCCCCCcEEEEEEEcC
Confidence 889999999999 6778899999873 2334 345666555444
No 39
>KOG1238|consensus
Probab=20.60 E-value=38 Score=29.71 Aligned_cols=27 Identities=37% Similarity=0.602 Sum_probs=23.4
Q ss_pred CCCccC--------------CCEEEEEecCCCCCCCcccEE
Q psy16455 19 GKPFAK--------------GKEMVAYIPGEGHNLQEHNIV 45 (82)
Q Consensus 19 ~~Pq~k--------------gk~v~AyIPG~Ghnlqehs~V 45 (82)
+.||.- |=.|..-.||.|+|||+|-..
T Consensus 318 ~SPQLLMLSGIGP~~~L~~~gIpvv~dLP~VG~nLqDH~~~ 358 (623)
T KOG1238|consen 318 NSPQLLMLSGIGPADHLKKLGIPVVLDLPGVGQNLQDHPMN 358 (623)
T ss_pred CCHHHHHHcCCCcHHHHHhcCCCeeccCccccccccccccc
Confidence 778876 788999999999999999654
No 40
>PHA03371 circ protein; Provisional
Probab=20.01 E-value=16 Score=28.75 Aligned_cols=25 Identities=36% Similarity=0.465 Sum_probs=20.6
Q ss_pred CCCCcccEEEEec--CCcCCCCCceEE
Q psy16455 37 HNLQEHNIVLCKV--GRVKDLPGVKIK 61 (82)
Q Consensus 37 hnlqehs~VLVrG--Gr~~DLPGVkyk 61 (82)
+++.+--+||+++ ||+=||||=-+-
T Consensus 16 ~a~a~et~vLL~~LaGR~vDLPgGde~ 42 (240)
T PHA03371 16 EALASETEVLLRSLAGRTVDLPGGDEL 42 (240)
T ss_pred hhcchhhHHHHHHhcCcceecCCCCeE
Confidence 6677778899998 999999996553
Done!