Query 024343
Match_columns 269
No_of_seqs 223 out of 1328
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:52:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024343.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024343hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2241 tRNA-binding protein [ 100.0 7.5E-54 1.6E-58 390.0 15.5 162 102-269 94-255 (255)
2 PLN02610 probable methionyl-tR 100.0 2.5E-42 5.4E-47 355.5 18.2 169 94-269 633-801 (801)
3 cd02798 tRNA_bind_CsaA tRNA-bi 100.0 7.6E-31 1.7E-35 211.3 8.9 106 96-203 1-107 (107)
4 PRK10089 tRNA-binding protein; 100.0 2.3E-30 5.1E-35 210.2 9.5 108 95-204 3-112 (112)
5 TIGR02222 chap_CsaA export-rel 100.0 2.8E-30 6.1E-35 208.6 9.8 105 98-204 1-107 (107)
6 cd02799 tRNA_bind_EMAP-II_like 100.0 3.7E-28 8E-33 193.9 11.8 104 100-204 2-105 (105)
7 PF01588 tRNA_bind: Putative t 100.0 2.6E-28 5.6E-33 191.9 9.7 95 107-202 1-95 (95)
8 cd02800 tRNA_bind_EcMetRS_like 99.9 8.8E-28 1.9E-32 191.5 10.5 103 97-203 2-104 (105)
9 COG0073 ARC1 EMAP domain [Gene 99.9 1.4E-27 3.1E-32 196.7 11.8 114 89-203 4-123 (123)
10 TIGR00399 metG_C_term methiony 99.9 1.5E-26 3.3E-31 194.3 12.3 109 92-203 28-136 (137)
11 cd02153 tRNA_bindingDomain The 99.9 2.5E-26 5.4E-31 180.5 11.5 97 107-203 1-99 (99)
12 PRK12267 methionyl-tRNA synthe 99.9 1.5E-23 3.2E-28 211.2 11.6 108 93-203 540-647 (648)
13 PRK00133 metG methionyl-tRNA s 99.9 1.7E-23 3.6E-28 212.1 9.9 107 93-203 565-672 (673)
14 cd02796 tRNA_bind_bactPheRS tR 99.9 1.2E-21 2.7E-26 155.0 9.0 90 107-203 1-103 (103)
15 TIGR00472 pheT_bact phenylalan 99.7 1.9E-17 4.1E-22 171.0 10.4 91 106-203 45-148 (798)
16 PRK00629 pheT phenylalanyl-tRN 99.7 9.7E-17 2.1E-21 165.8 10.2 90 106-203 44-146 (791)
17 COG2517 Predicted RNA-binding 99.3 3.2E-12 7E-17 113.3 6.7 79 98-183 113-191 (219)
18 TIGR02306 RNA_lig_DRB0094 RNA 99.2 4.2E-11 9.1E-16 114.4 8.6 66 107-182 3-96 (341)
19 PHA02142 putative RNA ligase 96.0 0.026 5.7E-07 55.1 7.9 65 107-181 10-102 (366)
20 PTZ00385 lysyl-tRNA synthetase 89.8 0.036 7.7E-07 57.9 -3.1 63 92-166 595-658 (659)
21 PF13742 tRNA_anti_2: OB-fold 34.4 1.7E+02 0.0037 23.0 6.4 62 107-170 25-88 (99)
22 PRK10413 hydrogenase 2 accesso 28.0 1.7E+02 0.0037 23.0 5.2 48 109-161 6-53 (82)
23 PF02470 MCE: mce related prot 26.8 2.2E+02 0.0047 21.0 5.5 28 105-133 24-51 (81)
24 PRK04313 30S ribosomal protein 23.8 1.6E+02 0.0035 27.5 5.2 33 108-141 188-221 (237)
25 PHA02945 interferon resistance 22.7 3.9E+02 0.0084 21.6 6.4 52 101-159 8-65 (88)
26 PF10246 MRP-S35: Mitochondria 22.4 3.2E+02 0.007 22.7 6.1 47 105-160 24-70 (104)
No 1
>KOG2241 consensus tRNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.5e-54 Score=390.01 Aligned_cols=162 Identities=53% Similarity=0.809 Sum_probs=155.0
Q ss_pred CCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceEEeeee
Q 024343 102 ANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGMLLAAS 181 (269)
Q Consensus 102 ~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGMLLsas 181 (269)
..+||||||+|+++++||++|+||+++||+|+.++|||||||++|++.|+|+|++|+|+|||||+||||++|+||+||++
T Consensus 94 ~~~LDiRvG~Ivka~kHpdADsLYve~IdvgE~~PRTVvSGLvk~vpleemq~R~VvvlcNLKPakmRgv~S~gMvlcaS 173 (255)
T KOG2241|consen 94 VSLLDIRVGKIVKAGKHPDADSLYVEEIDVGEAEPRTVVSGLVKHVPLEEMQNRLVVVLCNLKPAKMRGVKSQGMVLCAS 173 (255)
T ss_pred cceeeEEEeEEEEecccCCcceeEEEEeeecccccceeehhhHhhCCHHHHhCCeEEEEeccccccccccccceeEEecC
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcEEEEcCCCCCCCCceEEeCCCCCCcCCCCCCCCCCCccchhHhHhCCCcEECCCeEEEeCCeeeeecccceEec
Q 024343 182 DAAHENVELLEPPQGSVPGERIWFGSQEDKENQPAPASPNQVQKKKIWELVQPHLKTDASLVAMLGEHLMQTSAGAVMSR 261 (269)
Q Consensus 182 e~~~~~VelL~pp~~a~~G~rV~~~g~~~~~~~p~~~~p~~~~KkK~we~v~p~L~t~~~gva~y~~~~~~ts~G~~~~~ 261 (269)
++++..||+|.||.++.+|+||+|+||+ ++|+. .+|+|||+||++||||+|+++|+|+|||.+|+|++|.|+++
T Consensus 174 s~d~~~VE~l~pP~gs~pGdRv~fegfe---gePd~---~LnPKKKiwE~iqpdl~t~~~~va~yKg~~~~~~~G~~~a~ 247 (255)
T KOG2241|consen 174 SPDKSVVEPLAPPAGSKPGDRVTFEGFE---GEPDK---ELNPKKKIWEKIQPDLKTNEEGVATYKGAPFETKKGVCTAQ 247 (255)
T ss_pred CcccceeeeccCCCCCCCCCeeeecCCC---CCcch---hcChhhhhHHHhCCCcccccceEEEecCCceeccCceEEEe
Confidence 9888889999999999999999999997 34654 46799999999999999999999999999999999999999
Q ss_pred cCCCcccC
Q 024343 262 SLKNANIS 269 (269)
Q Consensus 262 sl~~~~Is 269 (269)
||+|++||
T Consensus 248 ti~n~~Ik 255 (255)
T KOG2241|consen 248 TISNGGIK 255 (255)
T ss_pred eccCCCCC
Confidence 99999997
No 2
>PLN02610 probable methionyl-tRNA synthetase
Probab=100.00 E-value=2.5e-42 Score=355.50 Aligned_cols=169 Identities=50% Similarity=0.767 Sum_probs=156.5
Q ss_pred CceeecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceec
Q 024343 94 NSVNVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKS 173 (269)
Q Consensus 94 ~~isi~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~S 173 (269)
+.++++||. ++|||||+|+++++||++||||+++||+|++++||||||+++++++|+|+|++|+|++||||++||||.|
T Consensus 633 ~~~~~~~~~-~~dlrVg~I~~~~~hp~adkL~~~~Vd~G~~~~r~ivsG~~~~~~~e~l~G~~Vvv~~nlkp~klrGv~S 711 (801)
T PLN02610 633 AAEREIDVS-RLDIRVGLIVKAEKHPDADSLYVEEIDVGEGAPRTVVSGLVKYIPLEEMQNRKVCVLCNLKPAAMRGIKS 711 (801)
T ss_pred cccccccce-eeeeEEEEEEEEEeecCCCcceEEEEEeCCCceEEEEeCccccCChHHhCCCEEEEEEEecccccCCccc
Confidence 347778996 5999999999999999999999999999987899999999999999999999999999999999999999
Q ss_pred ceEEeeeecCCCCcEEEEcCCCCCCCCceEEeCCCCCCcCCCCCCCCCCCccchhHhHhCCCcEECCCeEEEeCCeeeee
Q 024343 174 HGMLLAASDAAHENVELLEPPQGSVPGERIWFGSQEDKENQPAPASPNQVQKKKIWELVQPHLKTDASLVAMLGEHLMQT 253 (269)
Q Consensus 174 eGMLLsase~~~~~VelL~pp~~a~~G~rV~~~g~~~~~~~p~~~~p~~~~KkK~we~v~p~L~t~~~gva~y~~~~~~t 253 (269)
||||||++++++++++|+.||+++++|++|+|+|+++ +|+. .+++|||+||+|||+|+||++|+++|+|.+|+|
T Consensus 712 ~GMll~a~~~~~~~~~ll~~~~~~~~G~~v~~~~~~~---~p~~---~~~~k~k~~~~~~~~l~~~~~~~~~~~~~~~~~ 785 (801)
T PLN02610 712 QAMVLAASNSDHTKVELVEPPESAAVGERVTFPGFEG---EPDD---VLNPKKKVWETLQPDLHTNSELVACYKDVPFTT 785 (801)
T ss_pred ceeEEecccCCCCceEEEeCCCCCCCCCEEEeCCCCC---Cccc---ccCcccchHHHhCCCCEECCceEEEECCEEEEe
Confidence 9999999876666799999999999999999999764 3432 467899999999999999999999999999999
Q ss_pred cccceEeccCCCcccC
Q 024343 254 SAGAVMSRSLKNANIS 269 (269)
Q Consensus 254 s~G~~~~~sl~~~~Is 269 (269)
++|+|++++|+|+.|+
T Consensus 786 ~~g~~~~~~~~~~~i~ 801 (801)
T PLN02610 786 SAGVCKVASIANGSIR 801 (801)
T ss_pred cCCCeEcccCCCCEeC
Confidence 9999999999999986
No 3
>cd02798 tRNA_bind_CsaA tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain.
Probab=99.97 E-value=7.6e-31 Score=211.33 Aligned_cols=106 Identities=31% Similarity=0.469 Sum_probs=98.9
Q ss_pred eeecccCCcCCeEEEEEEEEEeCCCC-CceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecc
Q 024343 96 VNVKDAANMLDIRVGRIIKAWRHEEA-DSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSH 174 (269)
Q Consensus 96 isi~df~~~ldIrVGkIveve~HP~A-DKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~Se 174 (269)
+++++|.+ +|+|||+|+++++||++ ++||+++||+|++++|||+||+.+||++|||+|++|++++||||+||||+.||
T Consensus 1 ~~~~~f~k-ldi~vG~V~~~~~~p~a~~kL~~~~Vd~G~~~~r~ivsg~~~~~~~e~l~gk~v~~v~Nlkp~k~~G~~S~ 79 (107)
T cd02798 1 ISYEDFEK-VDLRVGTIVEVEDFPEARKPAYKLKVDFGEIGVKQSSAQITKYYKPEELIGRQVVAVVNFPPKQIAGVLSE 79 (107)
T ss_pred CCHHHcee-eeeEEEEEEEEEECCCcccceEEEEEEecCccceehhhhhhhcCCHHHhcCCcEEEEeCCCCceecceecc
Confidence 46788875 99999999999999999 99999999999877899999999999999999999999999999999999999
Q ss_pred eEEeeeecCCCCcEEEEcCCCCCCCCceE
Q 024343 175 GMLLAASDAAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 175 GMLLsase~~~~~VelL~pp~~a~~G~rV 203 (269)
|||||++++ +++++++.|+.++++|+||
T Consensus 80 gm~l~~~~~-~~~~~~~~~~~~~~~G~~i 107 (107)
T cd02798 80 VLVLGADDE-GGEVVLLVPDREVPNGAKV 107 (107)
T ss_pred EEEEEEEcC-CCcEEEecCCCCCCCcCCC
Confidence 999999865 3578999999999999986
No 4
>PRK10089 tRNA-binding protein; Provisional
Probab=99.97 E-value=2.3e-30 Score=210.18 Aligned_cols=108 Identities=27% Similarity=0.372 Sum_probs=100.0
Q ss_pred ceeecccCCcCCeEEEEEEEEEeCCCCCce-EEEEEEcCCC-CcEEEEeCCCCcccccccCCCEEEEEEeeccceeccee
Q 024343 95 SVNVKDAANMLDIRVGRIIKAWRHEEADSL-YVEEVDVGEA-EPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVK 172 (269)
Q Consensus 95 ~isi~df~~~ldIrVGkIveve~HP~ADKL-yv~kVDvGe~-e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~ 172 (269)
.+++++|.+ +|+|||+|+++++||++++| |+++||+|++ +.|+|++|+..||++|+|+|++|++++||||++|||+.
T Consensus 3 ~i~~~~f~k-ldlrvg~I~~~~~~p~a~kL~~~l~vd~G~~~~~r~i~sgl~~~~~~eel~gk~v~~v~Nlkp~~~~G~~ 81 (112)
T PRK10089 3 TITYEDFEK-VDIRVGTIVEAEPFPEARKPAYKLWIDFGEEIGVKQSSAQITPHYTPEELIGKQVVAVVNFPPKQIAGFM 81 (112)
T ss_pred ccCHhHhhh-hheeeEEEEEEEEcCCcCcceEEEEEEecCccCcceEehhhcccCCHHHHccCcEEEEECCCcceecCcc
Confidence 377889975 99999999999999999999 9999999985 58999999999999999999999999999999999999
Q ss_pred cceEEeeeecCCCCcEEEEcCCCCCCCCceEE
Q 024343 173 SHGMLLAASDAAHENVELLEPPQGSVPGERIW 204 (269)
Q Consensus 173 SeGMLLsase~~~~~VelL~pp~~a~~G~rV~ 204 (269)
|||||||+++++ ..++++.|+.++++|+||+
T Consensus 82 S~gmil~~~~~~-~~~~l~~p~~~~~~G~~i~ 112 (112)
T PRK10089 82 SEVLVLGFEDED-GEVVLLTPDRPVPNGVKLV 112 (112)
T ss_pred ccEEEEEEEcCC-CeEEEecCCCCCCCcCCcC
Confidence 999999998654 3589999999999999985
No 5
>TIGR02222 chap_CsaA export-related chaperone CsaA. This model describes Bacillus subtilis CsaA, an export-related chaperone that interacts with the Sec system, and related proteins from a number of other bacteria and archaea. The crystal structure is known for the homodimer from Thermus thermophilus.
Probab=99.96 E-value=2.8e-30 Score=208.56 Aligned_cols=105 Identities=31% Similarity=0.406 Sum_probs=96.6
Q ss_pred ecccCCcCCeEEEEEEEEEeCCCCCc-eEEEEEEcCCC-CcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecce
Q 024343 98 VKDAANMLDIRVGRIIKAWRHEEADS-LYVEEVDVGEA-EPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHG 175 (269)
Q Consensus 98 i~df~~~ldIrVGkIveve~HP~ADK-Lyv~kVDvGe~-e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeG 175 (269)
|++|.+ +|+|||+|+++++||+++| ||+++||+|++ +.|+|++|+..||++|+|+|++|++++||||++|||+.|||
T Consensus 1 ~~~f~k-ldlrvg~I~~~~~~p~a~k~L~~l~vd~G~~~~~r~ivsgi~~~~~~e~L~gk~v~~v~Nl~p~k~~G~~S~g 79 (107)
T TIGR02222 1 YEDFEK-LDLRVGRIVRAEPFPEARKPAYKLWVDFGTEIGVKQSSAQITKLYKPEDLIGRLVVAVVNFPPKQIAGFLSEV 79 (107)
T ss_pred Cchhhh-hhheeEEEEEEeecCCcccceeEEEEEecCcCCcceEehhhhhhCCHHHhCCCeEEEEECCCCceeCCccccE
Confidence 467864 9999999999999999998 99999999974 47999999999999999999999999999999999999999
Q ss_pred EEeeeecCCCCcEEEEcCCCCCCCCceEE
Q 024343 176 MLLAASDAAHENVELLEPPQGSVPGERIW 204 (269)
Q Consensus 176 MLLsase~~~~~VelL~pp~~a~~G~rV~ 204 (269)
||||+.+++ ..+.++.|++++++|+||+
T Consensus 80 Mil~~~~~~-~~~~l~~~~~~~~~G~~v~ 107 (107)
T TIGR02222 80 LVLGVIDEQ-GRVVLLQPDRPVPNGTKIA 107 (107)
T ss_pred EEEEEECCC-CeEEEecCCCCCCCcCCcC
Confidence 999998643 4589999999999999984
No 6
>cd02799 tRNA_bind_EMAP-II_like tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.
Probab=99.95 E-value=3.7e-28 Score=193.94 Aligned_cols=104 Identities=68% Similarity=1.089 Sum_probs=96.0
Q ss_pred ccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceEEee
Q 024343 100 DAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGMLLA 179 (269)
Q Consensus 100 df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGMLLs 179 (269)
+|. ++|+|||+|+++++||++++||+++||+|+++.+||+||+.|+|++|+|+|++|++++||+|++|+|+.||||+||
T Consensus 2 ~f~-~~~i~vg~I~~~~~~p~s~kL~~l~Vd~G~~~~~~Ivsg~~~~~~~~~~~g~~v~~l~nl~~~~~~G~~S~GMll~ 80 (105)
T cd02799 2 DPS-RLDIRVGKILKVRKHPDADSLYVEEIDLGEEEPRTIVSGLVKFVPLEQMQNRLVVVLCNLKPRKMRGVKSQGMVLC 80 (105)
T ss_pred Cce-EEEEEEEEEEEEEecCCCCccEEEEEEeCCCcEEEEEcCccccCCHHHhCCCEEEEEEeeccceECCeeeceEEEE
Confidence 454 4999999999999999999999999999987889999999999999999999999999999999999999999999
Q ss_pred eecCCCCcEEEEcCCCCCCCCceEE
Q 024343 180 ASDAAHENVELLEPPQGSVPGERIW 204 (269)
Q Consensus 180 ase~~~~~VelL~pp~~a~~G~rV~ 204 (269)
+.+++...+.+++||.++++|++|+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~G~~i~ 105 (105)
T cd02799 81 ASNADHEKVELLEPPEGAKPGERVT 105 (105)
T ss_pred eccCCCCcEEEEECCCCCCCCCEeC
Confidence 9876534688999999999999983
No 7
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=99.95 E-value=2.6e-28 Score=191.92 Aligned_cols=95 Identities=49% Similarity=0.741 Sum_probs=87.4
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceEEeeeecCCCC
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGMLLAASDAAHE 186 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGMLLsase~~~~ 186 (269)
||||+|+++++||++||||+++||+|+++ |||+||+.|++.+++|.|+.+++++|+++++|+|+.|||||||+++.+..
T Consensus 1 i~vg~I~~~~~hp~sdkL~~~~Vd~G~~~-~~Ivsg~~n~~~~~~lv~~~~~~v~n~~~~~i~Gv~SeGMlls~~e~~~~ 79 (95)
T PF01588_consen 1 IRVGKILEVEPHPNSDKLYVLKVDIGEEE-RQIVSGAKNVYEPEVLVGKKVVVVANLKPRKIRGVESEGMLLSASELGDG 79 (95)
T ss_dssp EEEEEEEEEEEETTSSSEEEEEEESSSSE-EEEEESCTTTSTHHHHTTTEEEEETTSCBEEETTEEEESEE-EEECSTSS
T ss_pred CEEEEEEEEEECCCCCEEEEEEEEeCCce-EEEEeccccccChhhhcceeEEEEEccCCcEEEeccCCEEEEEeeccCCC
Confidence 79999999999999999999999999966 99999999999999999999999999999999999999999999984445
Q ss_pred cEEEEcCCCCCCCCce
Q 024343 187 NVELLEPPQGSVPGER 202 (269)
Q Consensus 187 ~VelL~pp~~a~~G~r 202 (269)
...++.+|+++++|+|
T Consensus 80 ~~~ll~~~~~~~~G~~ 95 (95)
T PF01588_consen 80 SVGLLVLPDDAPPGED 95 (95)
T ss_dssp EEEEEEESSTS-TTSB
T ss_pred CEEEEECCCCCCCCCC
Confidence 6778999999999986
No 8
>cd02800 tRNA_bind_EcMetRS_like tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain.
Probab=99.95 E-value=8.8e-28 Score=191.54 Aligned_cols=103 Identities=48% Similarity=0.771 Sum_probs=96.6
Q ss_pred eecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceE
Q 024343 97 NVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGM 176 (269)
Q Consensus 97 si~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGM 176 (269)
++++|.. +|+|||+|+++++||++++||+++||+|+ +.++|+||++|+|.++++.|+++++++||+|++|||+.|+||
T Consensus 2 ~~~~~~~-ldi~vg~I~~~~~~p~a~kL~~~~vd~G~-~~~~iv~g~~~~~~~~~l~g~~v~~~~nl~~~~~~Gv~S~GM 79 (105)
T cd02800 2 TIDDFAK-VDLRVGKVLEAERVEGSDKLLKLTVDLGE-EERQIVSGIAKFYPPEELVGKKVVVVANLKPRKLRGVESQGM 79 (105)
T ss_pred ChHHcee-eeEEEEEEEEEEecCCCCcceEEEEEeCC-eEEEEEeCcccccCHhHhccCceEeEeeECCccCCCeEeceE
Confidence 4677764 99999999999999999999999999998 789999999999999999999999999999999999999999
Q ss_pred EeeeecCCCCcEEEEcCCCCCCCCceE
Q 024343 177 LLAASDAAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 177 LLsase~~~~~VelL~pp~~a~~G~rV 203 (269)
|||+.++ +.++|+.||.++++|+||
T Consensus 80 l~s~~~~--~~~~l~~~~~~~~~G~~i 104 (105)
T cd02800 80 ILAAEDG--GKLKLLTPDEEVEPGSRV 104 (105)
T ss_pred EEEecCC--CeEEEEeCCCCCCCcCCc
Confidence 9999865 568999999999999997
No 9
>COG0073 ARC1 EMAP domain [General function prediction only]
Probab=99.95 E-value=1.4e-27 Score=196.69 Aligned_cols=114 Identities=38% Similarity=0.604 Sum_probs=101.0
Q ss_pred CCCCCCceeecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCC-CcEEEEeCCCCcccccccCCCEEEEEEe---ec
Q 024343 89 PAVEDNSVNVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEA-EPRIICSGLVKYVPLEFLQDRSVVVLAN---LK 164 (269)
Q Consensus 89 ~~~~~~~isi~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~-e~RtIvSGl~n~~~~EeL~GkkVvVl~N---LK 164 (269)
.+.+.+++.+++|. +.+||||+|+++++||++||||+|+||+|++ ++|||+||+.|||+.+++.++++.+++| ||
T Consensus 4 ~~~e~e~i~~~~~~-~~~l~vg~V~~~~~~p~adkL~~~~Vd~G~~~~~~qiv~G~~n~~~~~~vv~a~v~~v~~~~~ik 82 (123)
T COG0073 4 IGLEVEEIEIDDFA-KVDLRVGKVVEAEPHPNADKLLVLKVDLGDEKEPRQIVCGAPNFYAGEKLVGAKVGAVLNGGKLK 82 (123)
T ss_pred cccccccccccccc-cCCeEEEEEEEeEECCCCCeeEEEEEEcCCCCcEEEEEcCCccccCCceeeeeeEEEEeCCCccc
Confidence 34455779999996 5999999999999999999999999999975 4899999999999999999999999999 99
Q ss_pred cceecceecceEEeeeecCCCC--cEEEEcCCCCCCCCceE
Q 024343 165 PRNMRGVKSHGMLLAASDAAHE--NVELLEPPQGSVPGERI 203 (269)
Q Consensus 165 prkirGv~SeGMLLsase~~~~--~VelL~pp~~a~~G~rV 203 (269)
|+||||+.|+|||||+.+.+-. ...|+.+|++.++|+++
T Consensus 83 p~klrG~~S~GMics~~e~~~~~~~~~il~~~~~~~~g~~~ 123 (123)
T COG0073 83 PAKLRGVESEGMLLSAEELGLSDENVGILTLDEGVPPGTKV 123 (123)
T ss_pred ceeecCcccceEEEEcccCCCccccceEEeCCCCCCCCCCC
Confidence 9999999999999999985421 35578889898888763
No 10
>TIGR00399 metG_C_term methionyl-tRNA synthetase C-terminal region/beta chain. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model.
Probab=99.94 E-value=1.5e-26 Score=194.28 Aligned_cols=109 Identities=43% Similarity=0.686 Sum_probs=100.6
Q ss_pred CCCceeecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecce
Q 024343 92 EDNSVNVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGV 171 (269)
Q Consensus 92 ~~~~isi~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv 171 (269)
.+..+++++|.. +++|||+|+++++||++++||+++||+|+ +.|||+||+..+|.+++|.|++|++++||+|++|||+
T Consensus 28 ~k~~~~~~~f~k-ldi~Vg~I~eve~hp~adkL~v~~Vd~G~-~~~qIvsg~~~~~~~~~l~G~~v~~~~nlkp~k~~Gv 105 (137)
T TIGR00399 28 QKETITIDDFEK-VDLRVGKILKAERVEKSDKLLKLKLDLGD-EKRQIVSGIAGYYTPEELVGKKVIVVANLKPAKLFGV 105 (137)
T ss_pred cccccCHhhcee-eeeEEEEEEEEeecCCCCcceEEEEEeCC-ceEEEEeCcccCcCHhHcCCCEEEeeEEecCccCCCe
Confidence 345688999975 99999999999999999999999999997 4699999999999999999999999999999999999
Q ss_pred ecceEEeeeecCCCCcEEEEcCCCCCCCCceE
Q 024343 172 KSHGMLLAASDAAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 172 ~SeGMLLsase~~~~~VelL~pp~~a~~G~rV 203 (269)
.|+|||||+.++++ .++|+.|+.++++|+||
T Consensus 106 ~S~GMlls~~~~~~-~~~l~~~~~~~~~G~~i 136 (137)
T TIGR00399 106 KSEGMILAAEDDGK-VLFLLSPDQEAIAGERI 136 (137)
T ss_pred EeccEEEEEecCCC-eEEEecCCCCCCCcCCc
Confidence 99999999997543 68999999999999997
No 11
>cd02153 tRNA_bindingDomain The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multi
Probab=99.94 E-value=2.5e-26 Score=180.50 Aligned_cols=97 Identities=47% Similarity=0.755 Sum_probs=89.2
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceEEeeeecCC--
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGMLLAASDAA-- 184 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGMLLsase~~-- 184 (269)
+|||+|+++++||++++||+++||+|+++.++|+||+.|+|++|+++|++|++++||+|++|+|+.|+|||||+++.+
T Consensus 1 ~~vg~I~~~~~~p~~~kL~~~~vd~G~~~~~~ivsg~~~~~~~~~~~g~~v~~~~~l~~~~~~g~~S~GMl~s~~~~g~~ 80 (99)
T cd02153 1 LRVGKIVEAEPHPNADKLYVLKVDIGEEKPRQIVSGAANVYPPEELVGKKVVVAVNLKPKKLRGVESEGMLLSAEELGLE 80 (99)
T ss_pred CEEEEEEEEEECCCCCCCEEEEEEeCCCcEEEEEeCCcccCChHHhCCCEEEEEEecccccCCCeecccEEeeccccCCC
Confidence 689999999999999999999999998788999999999999999999999999999999999999999999999842
Q ss_pred CCcEEEEcCCCCCCCCceE
Q 024343 185 HENVELLEPPQGSVPGERI 203 (269)
Q Consensus 185 ~~~VelL~pp~~a~~G~rV 203 (269)
.+...|+.+|.++++|+++
T Consensus 81 ~~~~~i~~~~~~~~~G~~~ 99 (99)
T cd02153 81 EGSVGILELPEDAPVGDRI 99 (99)
T ss_pred CCceEEEECCCCCCCCCcC
Confidence 2345688888889999875
No 12
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=99.90 E-value=1.5e-23 Score=211.16 Aligned_cols=108 Identities=37% Similarity=0.614 Sum_probs=99.6
Q ss_pred CCceeecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceeccee
Q 024343 93 DNSVNVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVK 172 (269)
Q Consensus 93 ~~~isi~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~ 172 (269)
+.++++++|.. +|||||+|+++++||++|+||+++||+|++++|||+||+.+++.+++|.|++|++++||||++||||.
T Consensus 540 ~~~~~~~~f~~-~d~~vg~i~~~~~~p~adkL~~~~vd~G~~~~~~iv~g~~~~~~~~~l~g~~v~~~~nl~~~~~~Gv~ 618 (648)
T PRK12267 540 KPEITIDDFDK-VELRVAEVLEAEKVEKSDKLLKLQVDLGEEEPRQIVSGIAKFYPPEELVGKKVVVVANLKPAKLMGEE 618 (648)
T ss_pred cCccCHhhhhh-hceeEEEEEeeccCCCCCccceEEEEeCCCceEEEEeCCcccCCHhHhCCCeEEEEEeecccccCCcc
Confidence 35599999974 99999999999999999999999999998778999999999999999999999999999999999999
Q ss_pred cceEEeeeecCCCCcEEEEcCCCCCCCCceE
Q 024343 173 SHGMLLAASDAAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 173 SeGMLLsase~~~~~VelL~pp~~a~~G~rV 203 (269)
|+|||||+.++ +.+.|+.||+++++|++|
T Consensus 619 S~gMl~s~~~~--~~~~l~~~~~~~~~G~~~ 647 (648)
T PRK12267 619 SQGMILAAEDD--GKLTLLTVDKEVPNGSKV 647 (648)
T ss_pred cceEEEEeccC--CeEEEEeCCCCCCCcCCC
Confidence 99999999873 246788889899999986
No 13
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=99.89 E-value=1.7e-23 Score=212.05 Aligned_cols=107 Identities=40% Similarity=0.593 Sum_probs=99.1
Q ss_pred CCceeecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeecccee-cce
Q 024343 93 DNSVNVKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNM-RGV 171 (269)
Q Consensus 93 ~~~isi~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprki-rGv 171 (269)
.+++++++|. ++|||||+|+++++||++++||+++||+|++ ++||+||+.|++.+++|.|++|++++||||++| +|+
T Consensus 565 ~~~~~~~~f~-~~di~vg~I~~~~~~p~~~~l~~~~vd~G~~-~~~iv~g~~~~~~~~~l~G~~v~~~~nlkp~~~~~Gv 642 (673)
T PRK00133 565 AETISFDDFA-KVDLRVAKIVEAEKVEGADKLLKLTLDLGEE-TRQVFSGIKSAYDPEELVGKLVVMVANLAPRKMKFGV 642 (673)
T ss_pred ccccCHHHHh-hhhcceeeeEeeecCCCCCccceeeEecCCc-eeEEEcCccccCCHHHHhcCeeEEEEeeccccccCCc
Confidence 3569999997 4999999999999999999999999999985 899999999999999999999999999999999 999
Q ss_pred ecceEEeeeecCCCCcEEEEcCCCCCCCCceE
Q 024343 172 KSHGMLLAASDAAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 172 ~SeGMLLsase~~~~~VelL~pp~~a~~G~rV 203 (269)
|||||||+.++ +++|.++.++.++++|++|
T Consensus 643 -S~gMl~~~~~~-~~~i~~l~~~~~~~~G~~~ 672 (673)
T PRK00133 643 -SEGMVLAAGPG-GGDLFLLEPDEGAKPGMRV 672 (673)
T ss_pred -cceeEEEeecC-CCcEEEecCCCCCCCCCcC
Confidence 99999999854 3579999888889999986
No 14
>cd02796 tRNA_bind_bactPheRS tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs. This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme.
Probab=99.86 E-value=1.2e-21 Score=155.04 Aligned_cols=90 Identities=34% Similarity=0.562 Sum_probs=80.7
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEE---------eeccceecceecceEE
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLA---------NLKPRNMRGVKSHGML 177 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~---------NLKprkirGv~SeGML 177 (269)
|+||+|+++++||++++||+++||+|+++.++|++|+.|+. +|++|+++. ||++++|+|+.|+|||
T Consensus 1 ~~vg~I~~~~~hp~~~kL~~~~vd~g~~~~~~Iv~~~~n~~-----~g~~vvv~~~gs~l~~~~~i~~~~~~G~~S~GMl 75 (103)
T cd02796 1 VVVGKVLEVEPHPNADKLNVCKVDIGENKPLQIVCGAPNVR-----AGDKVVVALPGAVLPGGLKIKKRKLRGVESEGML 75 (103)
T ss_pred CEEEEEEEEEecCCCCceEEEEEEeCCCcEEEEEcCccHhh-----cCCEEEEEecCCCcCCCceEcceeeCCcccchhC
Confidence 68999999999999999999999999878999999999997 899999986 9999999999999999
Q ss_pred eeeec----CCCCcEEEEcCCCCCCCCceE
Q 024343 178 LAASD----AAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 178 Lsase----~~~~~VelL~pp~~a~~G~rV 203 (269)
||+.+ +++.+ ++++|+++++|+++
T Consensus 76 ~s~~elg~~~~~~g--i~~l~~~~~~G~~~ 103 (103)
T cd02796 76 CSAKELGLGEDSDG--IIELPEDAPVGTDI 103 (103)
T ss_pred cchhHcCCCCCCCe--EEECCCCCCCCCCC
Confidence 99987 33344 56778888999864
No 15
>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however.
Probab=99.72 E-value=1.9e-17 Score=171.04 Aligned_cols=91 Identities=30% Similarity=0.465 Sum_probs=81.0
Q ss_pred CeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEE---------EeeccceecceecceE
Q 024343 106 DIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVL---------ANLKPRNMRGVKSHGM 176 (269)
Q Consensus 106 dIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl---------~NLKprkirGv~SeGM 176 (269)
.++||+|+++++||++|+|++|+||+|+++.+||+||+.|+. +|++|+|+ .+|++++|||+.|+||
T Consensus 45 ~~~vg~i~~~~~hp~~~~L~~~~vd~g~~~~~~Iv~ga~n~~-----~g~~V~va~~Ga~l~~~~~i~~~~~~Gv~S~GM 119 (798)
T TIGR00472 45 GVVVGKVLEVEPHPNADKLKVCKVDIGEKEMLQIVCGAPNVE-----AGKKVAVALPGAKLPNGLKIKKSKLRGVESEGM 119 (798)
T ss_pred CEEEEEEEEEEecCCCCcEEEEEEEcCCCceEEEEeCCcccc-----CCCEEEEEccCCCccCCceEeeeecCCeeechh
Confidence 499999999999999999999999999767899999999998 89999998 5799999999999999
Q ss_pred Eeeeec----CCCCcEEEEcCCCCCCCCceE
Q 024343 177 LLAASD----AAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 177 LLsase----~~~~~VelL~pp~~a~~G~rV 203 (269)
+|++++ ++++++.+| |++.++|+++
T Consensus 120 lcs~~elg~~~~~~gi~~l--~~~~~~G~~~ 148 (798)
T TIGR00472 120 LCSEDELGLDEKSDGIIVL--DEDAPLGTDI 148 (798)
T ss_pred cccHhHcCCCCCCCCEEEc--CCCCCCCccH
Confidence 999987 234676444 6788899888
No 16
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=99.68 E-value=9.7e-17 Score=165.81 Aligned_cols=90 Identities=36% Similarity=0.538 Sum_probs=80.2
Q ss_pred CeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEE---------EeeccceecceecceE
Q 024343 106 DIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVL---------ANLKPRNMRGVKSHGM 176 (269)
Q Consensus 106 dIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl---------~NLKprkirGv~SeGM 176 (269)
+++||+|+++++||++|||++|+||+|+ +.+||+||+.|+. +|++|+|+ .+|++++|||+.|+||
T Consensus 44 ~i~vg~i~~~~~hp~~~~L~v~~v~~g~-~~~~iv~ga~n~~-----~g~~v~~a~~G~~l~~~~~i~~~~~~Gv~S~GM 117 (791)
T PRK00629 44 GVVVGKVLECEKHPNADKLRVCQVDVGE-EPLQIVCGAPNVR-----AGDKVPVALPGAVLPGGFKIKKAKLRGVESEGM 117 (791)
T ss_pred CEEEEEEEEEEecCCCCeEEEEEEEcCC-eEEEEEeCCcccc-----CCCEEEEEccCCCccCCceEeeeecCCeEEchh
Confidence 5999999999999999999999999998 5699999999997 89999995 3599999999999999
Q ss_pred Eeeeec----CCCCcEEEEcCCCCCCCCceE
Q 024343 177 LLAASD----AAHENVELLEPPQGSVPGERI 203 (269)
Q Consensus 177 LLsase----~~~~~VelL~pp~~a~~G~rV 203 (269)
+|+++| ++++||.+| |+++++|+.+
T Consensus 118 lcs~~ELGl~~~~~GI~~L--~~~~~~G~~~ 146 (791)
T PRK00629 118 LCSASELGLSDDHDGIIEL--PEDAPVGTDA 146 (791)
T ss_pred cccHhHcCCCcCCCCeEEC--CCCCCCCccH
Confidence 999987 345787555 6788899888
No 17
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=99.31 E-value=3.2e-12 Score=113.32 Aligned_cols=79 Identities=34% Similarity=0.515 Sum_probs=68.8
Q ss_pred ecccCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccceecceecceEE
Q 024343 98 VKDAANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPRNMRGVKSHGML 177 (269)
Q Consensus 98 i~df~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKprkirGv~SeGML 177 (269)
|.|...-+++.||+|.++.+||++|+||+|.||+|+ ..++||++.-.+. +|++|+| +-|.|+.|.|++|+||+
T Consensus 113 I~d~~~aV~~vvGEV~Sv~~hp~aD~L~v~vvn~G~-r~~tVVTN~~~vr-----eg~~vaV-AlLPPr~F~gvvSeGMF 185 (219)
T COG2517 113 INDPVIAVDIVVGEVMSVGKHPNADKLLVTVVNIGG-RAVTVVTNDLDVR-----EGDRVAV-ALLPPRNFFGVVSEGMF 185 (219)
T ss_pred cCCcceeEEEEeeeeeecccCCCCCceEEEEEecCC-eEEEEEecccccc-----cCCEEEE-EecChhHhcccccccee
Confidence 444444578999999999999999999999999998 3689999999998 8999755 56999999999999999
Q ss_pred eeeecC
Q 024343 178 LAASDA 183 (269)
Q Consensus 178 Lsase~ 183 (269)
|.+.+-
T Consensus 186 lg~~d~ 191 (219)
T COG2517 186 LGAKDV 191 (219)
T ss_pred eccccc
Confidence 999653
No 18
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function.
Probab=99.20 E-value=4.2e-11 Score=114.40 Aligned_cols=66 Identities=21% Similarity=0.238 Sum_probs=60.7
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEE------E-------------------
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVL------A------------------- 161 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl------~------------------- 161 (269)
.+||+|+++++||+||+|.+|+||. .|||+|..|+. .|.+|+++ -
T Consensus 3 ~vv~kV~~i~php~Ad~L~v~~Vd~-----~~vV~ga~n~~-----~Gd~Vv~a~~gs~Lp~~~~~~~~~~~~~~~~~g~ 72 (341)
T TIGR02306 3 AVMREIADLQPHPNADALELATVGG-----WEVVVKKGEYR-----VGSDCVYFPEDSVLPTDAGLFRFLETRAKILDGK 72 (341)
T ss_pred eEEEEEEEeeecCCCCceEEEEEeC-----EEEEcCCCcCC-----CCCEEEEECCCCCCCCCCCcchhhcccccccccc
Confidence 4799999999999999999999997 89999999998 89999986 1
Q ss_pred ---eeccceecceecceEEeeeec
Q 024343 162 ---NLKPRNMRGVKSHGMLLAASD 182 (269)
Q Consensus 162 ---NLKprkirGv~SeGMLLsase 182 (269)
.|+.++|||+.||||+|+..+
T Consensus 73 ~~~~Ik~~klRG~~SqGMlcs~~~ 96 (341)
T TIGR02306 73 MRARVKTVRLRGEISQGIALPTGA 96 (341)
T ss_pred ccceEeEEEeccEEEccEEechhh
Confidence 678889999999999999886
No 19
>PHA02142 putative RNA ligase
Probab=95.98 E-value=0.026 Score=55.14 Aligned_cols=65 Identities=20% Similarity=0.242 Sum_probs=47.3
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEE--------------------------
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVL-------------------------- 160 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl-------------------------- 160 (269)
..|-+|..+++||+||.+=+.+||- .++|-.-..|. .|..|+.+
T Consensus 10 v~v~~i~~i~pi~~Ad~ie~a~V~g-----w~vVV~kg~f~-----~GD~~vY~eiDS~lP~~~~~~~~l~~~~~~~~g~ 79 (366)
T PHA02142 10 ASMRKIADLQPIPGADAIEVATIDG-----WEVVVKKGEFR-----VGDDCVYFEIDSLLPTDNPAFRFLETRARIYDGK 79 (366)
T ss_pred EEEEEEeeecccCCCCceeEEEECC-----EEEEEeccccc-----cCCeEEEecccccccCCchhhhhhhccccccCCc
Confidence 6788999999999999998888872 33333333333 44444443
Q ss_pred --EeeccceecceecceEEeeee
Q 024343 161 --ANLKPRNMRGVKSHGMLLAAS 181 (269)
Q Consensus 161 --~NLKprkirGv~SeGMLLsas 181 (269)
..|+..++||..||||++-.+
T Consensus 80 ~~~Ri~t~klRG~iSQGl~lpl~ 102 (366)
T PHA02142 80 MRARIKTIKLRGQISQGIALPTG 102 (366)
T ss_pred ccceEEEEEEeeEEeeeEEeccc
Confidence 257889999999999998744
No 20
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=89.80 E-value=0.036 Score=57.88 Aligned_cols=63 Identities=11% Similarity=0.026 Sum_probs=54.0
Q ss_pred CCCceeecccCCcCCeEEEEEEEEEeCCC-CCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEEeeccc
Q 024343 92 EDNSVNVKDAANMLDIRVGRIIKAWRHEE-ADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLANLKPR 166 (269)
Q Consensus 92 ~~~~isi~df~~~ldIrVGkIveve~HP~-ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~NLKpr 166 (269)
-++++.++.|.+ .| |+..|. +.+|.-.+.|.|.+..|+|.||+..||. +|.|+..+++|| +||
T Consensus 595 ~~~~~~~~~~~~-~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~-~pr 658 (659)
T PTZ00385 595 LEQEFRRNGLSE-DS--------CANVRELRRVIMELGQRGGENGLPTAGGRLSEWRI--TLTFAIIRFICG-TPR 658 (659)
T ss_pred hHHHHhhcccch-hh--------hhhchHHHHHHhceecccCCCCccchhHHHHHHHH--HHhcceeEEEeC-CCC
Confidence 345567777764 43 888999 9999999999999999999999999996 799999999999 886
No 21
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=34.36 E-value=1.7e+02 Score=23.01 Aligned_cols=62 Identities=19% Similarity=0.193 Sum_probs=38.0
Q ss_pred eEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCC-ccc-ccccCCCEEEEEEeeccceecc
Q 024343 107 IRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVK-YVP-LEFLQDRSVVVLANLKPRNMRG 170 (269)
Q Consensus 107 IrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n-~~~-~EeL~GkkVvVl~NLKprkirG 170 (269)
-+.|+|.++..| .+.++|..-.| ++...+-++-.-.. ... ..=-.|.+|++...+.-=.-+|
T Consensus 25 wV~GEIs~~~~~-~~gh~YftLkD-~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G 88 (99)
T PF13742_consen 25 WVEGEISNLKRH-SSGHVYFTLKD-EEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRG 88 (99)
T ss_pred EEEEEEeecEEC-CCceEEEEEEc-CCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCc
Confidence 578999999999 88899999999 54333333322111 111 1112578888876554444444
No 22
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=28.00 E-value=1.7e+02 Score=23.00 Aligned_cols=48 Identities=17% Similarity=0.066 Sum_probs=31.0
Q ss_pred EEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEEE
Q 024343 109 VGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVLA 161 (269)
Q Consensus 109 VGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl~ 161 (269)
=|||+++... .+..-.||+|+ ..|.|.-.+..-..++--.|.+|+|-+
T Consensus 6 P~kVi~i~~~----~~~~A~vd~~G-v~r~V~l~Lv~~~~~~~~vGDyVLVHa 53 (82)
T PRK10413 6 PGQVLAVGED----IHQLAQVEVCG-IKRDVNIALICEGNPADLLGQWVLVHV 53 (82)
T ss_pred ceEEEEECCC----CCcEEEEEcCC-eEEEEEeeeeccCCcccccCCEEEEec
Confidence 3788888543 24567899985 567776665533223445799998853
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=26.83 E-value=2.2e+02 Score=21.00 Aligned_cols=28 Identities=7% Similarity=0.164 Sum_probs=18.4
Q ss_pred CCeEEEEEEEEEeCCCCCceEEEEEEcCC
Q 024343 105 LDIRVGRIIKAWRHEEADSLYVEEVDVGE 133 (269)
Q Consensus 105 ldIrVGkIveve~HP~ADKLyv~kVDvGe 133 (269)
.+++||+|.+++..++.++ ...++.+-+
T Consensus 24 ~Gv~VG~V~~i~l~~~~~~-v~v~~~i~~ 51 (81)
T PF02470_consen 24 RGVEVGKVTSIELDPDGNR-VRVTLRIDP 51 (81)
T ss_pred CCEEEEEEEEEEEcCCCCE-EEEEEEEcC
Confidence 4799999999977444433 445555544
No 24
>PRK04313 30S ribosomal protein S4e; Validated
Probab=23.75 E-value=1.6e+02 Score=27.52 Aligned_cols=33 Identities=15% Similarity=0.151 Sum_probs=21.9
Q ss_pred EEEEEEEEEeCC-CCCceEEEEEEcCCCCcEEEEe
Q 024343 108 RVGRIIKAWRHE-EADSLYVEEVDVGEAEPRIICS 141 (269)
Q Consensus 108 rVGkIveve~HP-~ADKLyv~kVDvGe~e~RtIvS 141 (269)
|||+|.++++|+ .+.++...+ |...++..|+.+
T Consensus 188 riG~I~~i~~~~~~~~~~V~i~-d~~G~~F~T~~~ 221 (237)
T PRK04313 188 EIGKIKEIEVTKSSKPNIVTLE-DKDGEKFETILD 221 (237)
T ss_pred eEEEEEEEEEccCCCCcEEEEE-cCCCCEEEEEee
Confidence 789999999998 555666666 443334455543
No 25
>PHA02945 interferon resistance protein; Provisional
Probab=22.71 E-value=3.9e+02 Score=21.57 Aligned_cols=52 Identities=23% Similarity=0.326 Sum_probs=33.9
Q ss_pred cCCcCCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcE------EEEeCCCCcccccccCCCEEEE
Q 024343 101 AANMLDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPR------IICSGLVKYVPLEFLQDRSVVV 159 (269)
Q Consensus 101 f~~~ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~R------tIvSGl~n~~~~EeL~GkkVvV 159 (269)
|++.-+|.+|+|.+ ..| -+|+.-.+.|+-+-. -+.+|-.++ -+.++|+++++
T Consensus 8 ~P~~GelvigtV~~-~d~----ga~v~L~EY~g~eg~i~~seveva~~wvK~--rd~l~GqkvV~ 65 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGY----ALYIDLFDYPHSEAILAESVQMHMNRYFKY--RDKLVGKTVKV 65 (88)
T ss_pred CCCCCcEEEEEEEe-cCc----eEEEEecccCCcEEEEEeehhhhccceEee--eeEecCCEEEE
Confidence 44556799999988 655 588888888653311 124555444 45668988877
No 26
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=22.41 E-value=3.2e+02 Score=22.68 Aligned_cols=47 Identities=21% Similarity=0.383 Sum_probs=29.1
Q ss_pred CCeEEEEEEEEEeCCCCCceEEEEEEcCCCCcEEEEeCCCCcccccccCCCEEEEE
Q 024343 105 LDIRVGRIIKAWRHEEADSLYVEEVDVGEAEPRIICSGLVKYVPLEFLQDRSVVVL 160 (269)
Q Consensus 105 ldIrVGkIveve~HP~ADKLyv~kVDvGe~e~RtIvSGl~n~~~~EeL~GkkVvVl 160 (269)
-.+++|+|..+.. |.|| ||+|. +.--||. -+......--.|.+|.+.
T Consensus 24 gk~V~G~I~hvv~----ddLY---IDfG~-KFhcVc~-rp~~~~~~y~~G~rV~lr 70 (104)
T PF10246_consen 24 GKIVIGKIFHVVD----DDLY---IDFGG-KFHCVCK-RPAVNGEKYVRGSRVRLR 70 (104)
T ss_pred CCEEEEEEEEEec----CceE---EEeCC-ceeEEEe-cccccccccccCCEEEEE
Confidence 3499999998843 4787 69997 4444554 322221122378888774
Done!