Query psy15305
Match_columns 153
No_of_seqs 120 out of 1041
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 17:39:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2241|consensus 100.0 1.7E-29 3.7E-34 210.6 10.5 114 36-150 86-205 (255)
2 TIGR02222 chap_CsaA export-rel 99.9 1.2E-26 2.6E-31 171.4 8.5 95 41-135 1-98 (107)
3 cd02799 tRNA_bind_EMAP-II_like 99.9 5E-26 1.1E-30 166.3 10.7 93 43-135 2-96 (105)
4 cd02798 tRNA_bind_CsaA tRNA-bi 99.9 1.3E-26 2.8E-31 170.8 7.5 102 40-143 2-105 (107)
5 COG0073 ARC1 EMAP domain [Gene 99.9 6.2E-26 1.3E-30 171.0 10.5 99 37-136 9-116 (123)
6 PRK10089 tRNA-binding protein; 99.9 4.6E-26 1E-30 169.3 8.2 97 39-135 4-103 (112)
7 PLN02610 probable methionyl-tR 99.9 2.9E-25 6.2E-30 209.0 13.0 109 38-146 634-748 (801)
8 PF01588 tRNA_bind: Putative t 99.9 4.1E-25 8.8E-30 159.1 7.3 84 49-134 1-87 (95)
9 cd02800 tRNA_bind_EcMetRS_like 99.9 1.3E-24 2.8E-29 158.6 9.6 100 41-143 3-102 (105)
10 TIGR00399 metG_C_term methiony 99.9 2.6E-24 5.5E-29 165.3 11.2 98 38-136 31-129 (137)
11 cd02153 tRNA_bindingDomain The 99.9 7E-23 1.5E-27 147.4 10.0 85 49-134 1-90 (99)
12 PRK00133 metG methionyl-tRNA s 99.9 3E-22 6.5E-27 184.9 8.6 96 37-134 566-663 (673)
13 PRK12267 methionyl-tRNA synthe 99.9 1.4E-21 3E-26 179.4 10.6 97 38-135 542-639 (648)
14 cd02796 tRNA_bind_bactPheRS tR 99.8 4.8E-20 1E-24 133.6 8.8 73 49-127 1-82 (103)
15 TIGR00472 pheT_bact phenylalan 99.7 7.7E-17 1.7E-21 151.6 9.4 88 39-132 34-139 (798)
16 PRK00629 pheT phenylalanyl-tRN 99.7 1.2E-16 2.5E-21 150.4 7.6 83 48-133 44-138 (791)
17 COG2517 Predicted RNA-binding 99.4 8.1E-13 1.8E-17 106.9 6.5 72 44-123 117-188 (219)
18 TIGR02306 RNA_lig_DRB0094 RNA 99.3 1.8E-12 4E-17 112.7 6.6 71 49-125 3-96 (341)
19 PHA02142 putative RNA ligase 96.2 0.02 4.3E-07 50.9 7.4 68 48-120 9-99 (366)
20 PTZ00385 lysyl-tRNA synthetase 69.8 0.75 1.6E-05 43.9 -2.0 49 57-108 609-658 (659)
21 PRK04313 30S ribosomal protein 36.2 81 0.0018 26.7 5.0 21 50-70 188-209 (237)
22 KOG2110|consensus 27.0 57 0.0012 29.5 2.7 28 113-140 181-210 (391)
23 PLN00036 40S ribosomal protein 25.2 1.5E+02 0.0033 25.4 4.9 20 50-69 191-210 (261)
24 PF10246 MRP-S35: Mitochondria 25.0 3E+02 0.0064 20.6 5.9 33 48-89 25-57 (104)
25 PTZ00223 40S ribosomal protein 24.0 1.6E+02 0.0035 25.4 4.9 22 50-71 188-209 (273)
26 PF13742 tRNA_anti_2: OB-fold 23.1 2.8E+02 0.006 19.6 5.7 34 49-85 25-58 (99)
27 cd03524 RPA2_OBF_family RPA2_O 21.2 2E+02 0.0043 17.2 5.1 38 50-87 2-39 (75)
28 PTZ00118 40S ribosomal protein 21.1 2E+02 0.0043 24.7 4.8 19 50-68 191-209 (262)
29 cd05790 S1_Rrp40 S1_Rrp40: Rrp 21.1 1.6E+02 0.0034 20.9 3.6 22 47-75 7-28 (86)
No 1
>KOG2241|consensus
Probab=99.96 E-value=1.7e-29 Score=210.62 Aligned_cols=114 Identities=63% Similarity=1.010 Sum_probs=106.5
Q ss_pred CCCCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceec
Q psy15305 36 DKDEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTS 115 (153)
Q Consensus 36 ~~~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~S 115 (153)
...+...++++||||||+|+++.+||++|.||+.+||+|+.+.||||||+..|++.+++.++++++++||+|++|||+.|
T Consensus 86 ~~~~~~p~~~~LDiRvG~Ivka~kHpdADsLYve~IdvgE~~PRTVvSGLvk~vpleemq~R~VvvlcNLKPakmRgv~S 165 (255)
T KOG2241|consen 86 PMMEAGPDVSLLDIRVGKIVKAGKHPDADSLYVEEIDVGEAEPRTVVSGLVKHVPLEEMQNRLVVVLCNLKPAKMRGVKS 165 (255)
T ss_pred CcccCCCCcceeeEEEeEEEEecccCCcceeEEEEeeecccccceeehhhHhhCCHHHHhCCeEEEEecccccccccccc
Confidence 44566678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeecccCCCc--eEEecCC----CCCeeeeCcccCCCCC
Q psy15305 116 EAMVMCASTPDK--VEILAPP----SSDQCFIGSFSSSIPY 150 (153)
Q Consensus 116 eGMlLCs~~e~g--i~lL~~p----~g~~~~~g~~~~~~~~ 150 (153)
+||+||+.++++ |++|.|| +|+++.+++|. -.|-
T Consensus 166 ~gMvlcaSs~d~~~VE~l~pP~gs~pGdRv~fegfe-gePd 205 (255)
T KOG2241|consen 166 QGMVLCASSPDKSVVEPLAPPAGSKPGDRVTFEGFE-GEPD 205 (255)
T ss_pred ceeEEecCCcccceeeeccCCCCCCCCCeeeecCCC-CCcc
Confidence 999999999998 9999997 58999999998 6553
No 2
>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=99.94 E-value=1.2e-26 Score=171.37 Aligned_cols=95 Identities=29% Similarity=0.484 Sum_probs=87.4
Q ss_pred CCCCCccCeEEEEEEEEEeCCCCCC-eeEEEEEcCCC-CCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccce
Q psy15305 41 PVDIGRLDLRVGKIIEASKHPDADS-LYVEKVELGEP-APRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAM 118 (153)
Q Consensus 41 ~~df~~ldl~VGkIveve~HP~adK-L~v~kVDiG~~-~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGM 118 (153)
+.+|.++++|||+|+++++||++++ |++++||+|.+ +.|+|++|+..+|.+++|.|+++++++||+|++|+|+.||||
T Consensus 1 ~~~f~kldlrvg~I~~~~~~p~a~k~L~~l~vd~G~~~~~r~ivsgi~~~~~~e~L~gk~v~~v~Nl~p~k~~G~~S~gM 80 (107)
T TIGR02222 1 YEDFEKLDLRVGRIVRAEPFPEARKPAYKLWVDFGTEIGVKQSSAQITKLYKPEDLIGRLVVAVVNFPPKQIAGFLSEVL 80 (107)
T ss_pred CchhhhhhheeEEEEEEeecCCcccceeEEEEEecCcCCcceEehhhhhhCCHHHhCCCeEEEEECCCCceeCCccccEE
Confidence 3579999999999999999999998 99999999964 469999999999999999999999999999999999999999
Q ss_pred eecccCCCc-eEEecCCC
Q psy15305 119 VMCASTPDK-VEILAPPS 135 (153)
Q Consensus 119 lLCs~~e~g-i~lL~~p~ 135 (153)
|||+.+++| +.++.|+.
T Consensus 81 il~~~~~~~~~~l~~~~~ 98 (107)
T TIGR02222 81 VLGVIDEQGRVVLLQPDR 98 (107)
T ss_pred EEEEECCCCeEEEecCCC
Confidence 999988776 88887743
No 3
>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=99.93 E-value=5e-26 Score=166.28 Aligned_cols=93 Identities=72% Similarity=1.196 Sum_probs=85.6
Q ss_pred CCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccceeecc
Q psy15305 43 DIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAMVMCA 122 (153)
Q Consensus 43 df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGMlLCs 122 (153)
+|.+++++||+|+++++||++++|++++||+|.++.+||+||+.|++.++++.|+++++++||++++|+|+.|||||||+
T Consensus 2 ~f~~~~i~vg~I~~~~~~p~s~kL~~l~Vd~G~~~~~~Ivsg~~~~~~~~~~~g~~v~~l~nl~~~~~~G~~S~GMll~~ 81 (105)
T cd02799 2 DPSRLDIRVGKILKVRKHPDADSLYVEEIDLGEEEPRTIVSGLVKFVPLEQMQNRLVVVLCNLKPRKMRGVKSQGMVLCA 81 (105)
T ss_pred CceEEEEEEEEEEEEEecCCCCccEEEEEEeCCCcEEEEEcCccccCCHHHhCCCEEEEEEeeccceECCeeeceEEEEe
Confidence 68999999999999999999999999999999767899999999999999999999999999999999999999998899
Q ss_pred cCCC--ceEEecCCC
Q psy15305 123 STPD--KVEILAPPS 135 (153)
Q Consensus 123 ~~e~--gi~lL~~p~ 135 (153)
++++ ++.++.+|.
T Consensus 82 ~~~~~~~~~~~~~~~ 96 (105)
T cd02799 82 SNADHEKVELLEPPE 96 (105)
T ss_pred ccCCCCcEEEEECCC
Confidence 8775 477887753
No 4
>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=99.93 E-value=1.3e-26 Score=170.82 Aligned_cols=102 Identities=31% Similarity=0.515 Sum_probs=90.9
Q ss_pred CCCCCCccCeEEEEEEEEEeCCCC-CCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccce
Q psy15305 40 GPVDIGRLDLRVGKIIEASKHPDA-DSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAM 118 (153)
Q Consensus 40 ~~~df~~ldl~VGkIveve~HP~a-dKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGM 118 (153)
++.+|.+++++||+|+++++||++ ++|++++||+|.++.|+|+||+.++|.+++|.|+++++++||+|++|+|+.||||
T Consensus 2 ~~~~f~kldi~vG~V~~~~~~p~a~~kL~~~~Vd~G~~~~r~ivsg~~~~~~~e~l~gk~v~~v~Nlkp~k~~G~~S~gm 81 (107)
T cd02798 2 SYEDFEKVDLRVGTIVEVEDFPEARKPAYKLKVDFGEIGVKQSSAQITKYYKPEELIGRQVVAVVNFPPKQIAGVLSEVL 81 (107)
T ss_pred CHHHceeeeeEEEEEEEEEECCCcccceEEEEEEecCccceehhhhhhhcCCHHHhcCCcEEEEeCCCCceecceeccEE
Confidence 356799999999999999999999 9999999999986789999999999999999999999999999999999999999
Q ss_pred eecccCCC-ceEEecCCCCCeeeeCc
Q psy15305 119 VMCASTPD-KVEILAPPSSDQCFIGS 143 (153)
Q Consensus 119 lLCs~~e~-gi~lL~~p~g~~~~~g~ 143 (153)
|||+.+++ ++.+|.|+. .+++|.
T Consensus 82 ~l~~~~~~~~~~~~~~~~--~~~~G~ 105 (107)
T cd02798 82 VLGADDEGGEVVLLVPDR--EVPNGA 105 (107)
T ss_pred EEEEEcCCCcEEEecCCC--CCCCcC
Confidence 99998764 488887753 345553
No 5
>COG0073 ARC1 EMAP domain [General function prediction only]
Probab=99.93 E-value=6.2e-26 Score=171.01 Aligned_cols=99 Identities=41% Similarity=0.612 Sum_probs=87.7
Q ss_pred CCCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCC-CCeEEEeCCCCcccccccCCeeEEEEee---eecceecc
Q psy15305 37 KDEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEP-APRTVVSGLVKFVPIEQMQNRMVVLLCN---LKPAKMRG 112 (153)
Q Consensus 37 ~~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~-~~r~IVsga~n~~~~~~l~gk~vv~~~n---lk~rki~G 112 (153)
....+.+|.+.+||||+|+++++||++|||++|+||+|.+ +.||||||+.|+|..+.+.++++..++| |+++++||
T Consensus 9 e~i~~~~~~~~~l~vg~V~~~~~~p~adkL~~~~Vd~G~~~~~~qiv~G~~n~~~~~~vv~a~v~~v~~~~~ikp~klrG 88 (123)
T COG0073 9 EEIEIDDFAKVDLRVGKVVEAEPHPNADKLLVLKVDLGDEKEPRQIVCGAPNFYAGEKLVGAKVGAVLNGGKLKPAKLRG 88 (123)
T ss_pred ccccccccccCCeEEEEEEEeEECCCCCeeEEEEEEcCCCCcEEEEEcCCccccCCceeeeeeEEEEeCCCcccceeecC
Confidence 4566788999999999999999999999999999999975 4899999999999999999999999999 99999999
Q ss_pred eeccceeecccCCCc-----eEEecCCCC
Q psy15305 113 VTSEAMVMCASTPDK-----VEILAPPSS 136 (153)
Q Consensus 113 v~SeGMlLCs~~e~g-----i~lL~~p~g 136 (153)
+.|+|| |||..+++ ..+|..|.+
T Consensus 89 ~~S~GM-ics~~e~~~~~~~~~il~~~~~ 116 (123)
T COG0073 89 VESEGM-LLSAEELGLSDENVGILTLDEG 116 (123)
T ss_pred cccceE-EEEcccCCCccccceEEeCCCC
Confidence 999999 88887764 456655443
No 6
>PRK10089 tRNA-binding protein; Provisional
Probab=99.93 E-value=4.6e-26 Score=169.25 Aligned_cols=97 Identities=27% Similarity=0.441 Sum_probs=89.2
Q ss_pred CCCCCCCccCeEEEEEEEEEeCCCCCCe-eEEEEEcCCC-CCeEEEeCCCCcccccccCCeeEEEEeeeecceecceecc
Q psy15305 39 EGPVDIGRLDLRVGKIIEASKHPDADSL-YVEKVELGEP-APRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSE 116 (153)
Q Consensus 39 e~~~df~~ldl~VGkIveve~HP~adKL-~v~kVDiG~~-~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~Se 116 (153)
.+..+|.++++|||+|+++++||++++| |+++||+|.+ +.|+|++|+..+|.+++|.|+++++++||+|++|+|+.||
T Consensus 4 i~~~~f~kldlrvg~I~~~~~~p~a~kL~~~l~vd~G~~~~~r~i~sgl~~~~~~eel~gk~v~~v~Nlkp~~~~G~~S~ 83 (112)
T PRK10089 4 ITYEDFEKVDIRVGTIVEAEPFPEARKPAYKLWIDFGEEIGVKQSSAQITPHYTPEELIGKQVVAVVNFPPKQIAGFMSE 83 (112)
T ss_pred cCHhHhhhhheeeEEEEEEEEcCCcCcceEEEEEEecCccCcceEehhhcccCCHHHHccCcEEEEECCCcceecCcccc
Confidence 4467899999999999999999999999 9999999975 4899999999999999999999999999999999999999
Q ss_pred ceeecccCCCc-eEEecCCC
Q psy15305 117 AMVMCASTPDK-VEILAPPS 135 (153)
Q Consensus 117 GMlLCs~~e~g-i~lL~~p~ 135 (153)
|||||+.+++| +.++.|+.
T Consensus 84 gmil~~~~~~~~~~l~~p~~ 103 (112)
T PRK10089 84 VLVLGFEDEDGEVVLLTPDR 103 (112)
T ss_pred EEEEEEEcCCCeEEEecCCC
Confidence 99999988776 77887643
No 7
>PLN02610 probable methionyl-tRNA synthetase
Probab=99.92 E-value=2.9e-25 Score=209.03 Aligned_cols=109 Identities=58% Similarity=0.979 Sum_probs=98.1
Q ss_pred CCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccc
Q psy15305 38 DEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEA 117 (153)
Q Consensus 38 ~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeG 117 (153)
.+++.+|++++||||+|+++++||++++|++++||+|+++.||||||+.+++.+++|.|+++++++||+|++|+|+.|+|
T Consensus 634 ~~~~~~~~~~dlrVg~I~~~~~hp~adkL~~~~Vd~G~~~~r~ivsG~~~~~~~e~l~G~~Vvv~~nlkp~klrGv~S~G 713 (801)
T PLN02610 634 AEREIDVSRLDIRVGLIVKAEKHPDADSLYVEEIDVGEGAPRTVVSGLVKYIPLEEMQNRKVCVLCNLKPAAMRGIKSQA 713 (801)
T ss_pred ccccccceeeeeEEEEEEEEEeecCCCcceEEEEEeCCCceEEEEeCccccCChHHhCCCEEEEEEEecccccCCcccce
Confidence 35567999999999999999999999999999999998778999999999999999999999999999999999999999
Q ss_pred eeecccCCC--ceEEecC----CCCCeeeeCcccC
Q psy15305 118 MVMCASTPD--KVEILAP----PSSDQCFIGSFSS 146 (153)
Q Consensus 118 MlLCs~~e~--gi~lL~~----p~g~~~~~g~~~~ 146 (153)
||||+.+++ ++.||.+ +.|+++.+++|..
T Consensus 714 Mll~a~~~~~~~~~ll~~~~~~~~G~~v~~~~~~~ 748 (801)
T PLN02610 714 MVLAASNSDHTKVELVEPPESAAVGERVTFPGFEG 748 (801)
T ss_pred eEEecccCCCCceEEEeCCCCCCCCCEEEeCCCCC
Confidence 988886654 4767765 4699999999864
No 8
>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=99.92 E-value=4.1e-25 Score=159.08 Aligned_cols=84 Identities=45% Similarity=0.752 Sum_probs=74.2
Q ss_pred eEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccceeecccCC--C
Q psy15305 49 LRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAMVMCASTP--D 126 (153)
Q Consensus 49 l~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGMlLCs~~e--~ 126 (153)
||||+|+++++||++|||++|+||+|+++ |||+||++|++..+.+.++.+++++|+++++|+|+.|||| ||++.| +
T Consensus 1 i~vg~I~~~~~hp~sdkL~~~~Vd~G~~~-~~Ivsg~~n~~~~~~lv~~~~~~v~n~~~~~i~Gv~SeGM-lls~~e~~~ 78 (95)
T PF01588_consen 1 IRVGKILEVEPHPNSDKLYVLKVDIGEEE-RQIVSGAKNVYEPEVLVGKKVVVVANLKPRKIRGVESEGM-LLSASELGD 78 (95)
T ss_dssp EEEEEEEEEEEETTSSSEEEEEEESSSSE-EEEEESCTTTSTHHHHTTTEEEEETTSCBEEETTEEEESE-E-EEECSTS
T ss_pred CEEEEEEEEEECCCCCEEEEEEEEeCCce-EEEEeccccccChhhhcceeEEEEEccCCcEEEeccCCEE-EEEeeccCC
Confidence 79999999999999999999999999965 9999999999998899999999999999999999999999 777665 2
Q ss_pred -ceEEecCC
Q psy15305 127 -KVEILAPP 134 (153)
Q Consensus 127 -gi~lL~~p 134 (153)
...++.+|
T Consensus 79 ~~~~ll~~~ 87 (95)
T PF01588_consen 79 GSVGLLVLP 87 (95)
T ss_dssp SEEEEEEES
T ss_pred CCEEEEECC
Confidence 24555554
No 9
>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=99.92 E-value=1.3e-24 Score=158.65 Aligned_cols=100 Identities=41% Similarity=0.679 Sum_probs=86.5
Q ss_pred CCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccceee
Q psy15305 41 PVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAMVM 120 (153)
Q Consensus 41 ~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGMlL 120 (153)
..+|.++++|||+|+++++||++++|++++||+|. +.++|+||++|++.++++.|+.+++++||++++|+|+.|+||||
T Consensus 3 ~~~~~~ldi~vg~I~~~~~~p~a~kL~~~~vd~G~-~~~~iv~g~~~~~~~~~l~g~~v~~~~nl~~~~~~Gv~S~GMl~ 81 (105)
T cd02800 3 IDDFAKVDLRVGKVLEAERVEGSDKLLKLTVDLGE-EERQIVSGIAKFYPPEELVGKKVVVVANLKPRKLRGVESQGMIL 81 (105)
T ss_pred hHHceeeeEEEEEEEEEEecCCCCcceEEEEEeCC-eEEEEEeCcccccCHhHhccCceEeEeeECCccCCCeEeceEEE
Confidence 45789999999999999999999999999999998 68999999999998889999999889999999999999999955
Q ss_pred cccCCCceEEecCCCCCeeeeCc
Q psy15305 121 CASTPDKVEILAPPSSDQCFIGS 143 (153)
Q Consensus 121 Cs~~e~gi~lL~~p~g~~~~~g~ 143 (153)
|..++..+.++.+|++ +++|.
T Consensus 82 s~~~~~~~~l~~~~~~--~~~G~ 102 (105)
T cd02800 82 AAEDGGKLKLLTPDEE--VEPGS 102 (105)
T ss_pred EecCCCeEEEEeCCCC--CCCcC
Confidence 5555534778877654 35553
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=99.91 E-value=2.6e-24 Score=165.28 Aligned_cols=98 Identities=36% Similarity=0.595 Sum_probs=87.2
Q ss_pred CCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccc
Q psy15305 38 DEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEA 117 (153)
Q Consensus 38 ~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeG 117 (153)
.....+|.+++++||+|+++++||++++|++++||+|.+ .+||+||+..+|.+..+.|+++++++||++++|+|+.|+|
T Consensus 31 ~~~~~~f~kldi~Vg~I~eve~hp~adkL~v~~Vd~G~~-~~qIvsg~~~~~~~~~l~G~~v~~~~nlkp~k~~Gv~S~G 109 (137)
T TIGR00399 31 TITIDDFEKVDLRVGKILKAERVEKSDKLLKLKLDLGDE-KRQIVSGIAGYYTPEELVGKKVIVVANLKPAKLFGVKSEG 109 (137)
T ss_pred ccCHhhceeeeeEEEEEEEEeecCCCCcceEEEEEeCCc-eEEEEeCcccCcCHhHcCCCEEEeeEEecCccCCCeEecc
Confidence 456678999999999999999999999999999999974 6999999999998888999999889999999999999999
Q ss_pred eeecccCCCc-eEEecCCCC
Q psy15305 118 MVMCASTPDK-VEILAPPSS 136 (153)
Q Consensus 118 MlLCs~~e~g-i~lL~~p~g 136 (153)
||||+.++++ +.||.++.+
T Consensus 110 Mlls~~~~~~~~~l~~~~~~ 129 (137)
T TIGR00399 110 MILAAEDDGKVLFLLSPDQE 129 (137)
T ss_pred EEEEEecCCCeEEEecCCCC
Confidence 9666666664 888887654
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=99.89 E-value=7e-23 Score=147.37 Aligned_cols=85 Identities=51% Similarity=0.790 Sum_probs=76.8
Q ss_pred eEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccceeecccCCCc-
Q psy15305 49 LRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAMVMCASTPDK- 127 (153)
Q Consensus 49 l~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGMlLCs~~e~g- 127 (153)
++||+|+++++||++++|++++||+|.++.++|+||+.|+|..+++.|+++++.+||++++|+|+.|+|| ||++.++|
T Consensus 1 ~~vg~I~~~~~~p~~~kL~~~~vd~G~~~~~~ivsg~~~~~~~~~~~g~~v~~~~~l~~~~~~g~~S~GM-l~s~~~~g~ 79 (99)
T cd02153 1 LRVGKIVEAEPHPNADKLYVLKVDIGEEKPRQIVSGAANVYPPEELVGKKVVVAVNLKPKKLRGVESEGM-LLSAEELGL 79 (99)
T ss_pred CEEEEEEEEEECCCCCCCEEEEEEeCCCcEEEEEeCCcccCChHHhCCCEEEEEEecccccCCCeecccE-EeeccccCC
Confidence 6899999999999999999999999976789999999999998999999999999999999999999999 88877753
Q ss_pred ----eEEecCC
Q psy15305 128 ----VEILAPP 134 (153)
Q Consensus 128 ----i~lL~~p 134 (153)
..++.+|
T Consensus 80 ~~~~~~i~~~~ 90 (99)
T cd02153 80 EEGSVGILELP 90 (99)
T ss_pred CCCceEEEECC
Confidence 4555554
No 12
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=99.87 E-value=3e-22 Score=184.88 Aligned_cols=96 Identities=39% Similarity=0.549 Sum_probs=85.4
Q ss_pred CCCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeeccee-cceec
Q psy15305 37 KDEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKM-RGVTS 115 (153)
Q Consensus 37 ~~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki-~Gv~S 115 (153)
...+..+|.+++||||+|++|++||++++|++|+||+|++ .+|||||+.|++.+.++.|+++++++||+|++| +|+ |
T Consensus 566 ~~~~~~~f~~~di~vg~I~~~~~~p~~~~l~~~~vd~G~~-~~~iv~g~~~~~~~~~l~G~~v~~~~nlkp~~~~~Gv-S 643 (673)
T PRK00133 566 ETISFDDFAKVDLRVAKIVEAEKVEGADKLLKLTLDLGEE-TRQVFSGIKSAYDPEELVGKLVVMVANLAPRKMKFGV-S 643 (673)
T ss_pred cccCHHHHhhhhcceeeeEeeecCCCCCccceeeEecCCc-eeEEEcCccccCCHHHHhcCeeEEEEeeccccccCCc-c
Confidence 3466678999999999999999999999999999999985 899999999999989999999989999999999 999 9
Q ss_pred cceeecccCC-CceEEecCC
Q psy15305 116 EAMVMCASTP-DKVEILAPP 134 (153)
Q Consensus 116 eGMlLCs~~e-~gi~lL~~p 134 (153)
+|||||+.++ .||.+|.++
T Consensus 644 ~gMl~~~~~~~~~i~~l~~~ 663 (673)
T PRK00133 644 EGMVLAAGPGGGDLFLLEPD 663 (673)
T ss_pred ceeEEEeecCCCcEEEecCC
Confidence 9995555544 468888763
No 13
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=99.86 E-value=1.4e-21 Score=179.41 Aligned_cols=97 Identities=37% Similarity=0.607 Sum_probs=85.2
Q ss_pred CCCCCCCCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccc
Q psy15305 38 DEGPVDIGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEA 117 (153)
Q Consensus 38 ~e~~~df~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeG 117 (153)
..+..+|.+++||||+|+++++||++++|++|+||+|.++.+|||||+.|++.+..+.|+.+++++||++++|+|+.|+|
T Consensus 542 ~~~~~~f~~~d~~vg~i~~~~~~p~adkL~~~~vd~G~~~~~~iv~g~~~~~~~~~l~g~~v~~~~nl~~~~~~Gv~S~g 621 (648)
T PRK12267 542 EITIDDFDKVELRVAEVLEAEKVEKSDKLLKLQVDLGEEEPRQIVSGIAKFYPPEELVGKKVVVVANLKPAKLMGEESQG 621 (648)
T ss_pred ccCHhhhhhhceeEEEEEeeccCCCCCccceEEEEeCCCceEEEEeCCcccCCHhHhCCCeEEEEEeecccccCCcccce
Confidence 36678899999999999999999999999999999997678999999999998889999999899999999999999999
Q ss_pred eeecccCCCc-eEEecCCC
Q psy15305 118 MVMCASTPDK-VEILAPPS 135 (153)
Q Consensus 118 MlLCs~~e~g-i~lL~~p~ 135 (153)
| ||+..+++ +.+|.+|+
T Consensus 622 M-l~s~~~~~~~~l~~~~~ 639 (648)
T PRK12267 622 M-ILAAEDDGKLTLLTVDK 639 (648)
T ss_pred E-EEEeccCCeEEEEeCCC
Confidence 9 55554444 56666543
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=99.82 E-value=4.8e-20 Score=133.63 Aligned_cols=73 Identities=38% Similarity=0.621 Sum_probs=63.7
Q ss_pred eEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEe---------eeecceecceecccee
Q psy15305 49 LRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLC---------NLKPAKMRGVTSEAMV 119 (153)
Q Consensus 49 l~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~---------nlk~rki~Gv~SeGMl 119 (153)
++||+|+++++||++++|++++||+|.++.++|+|++.|+. .|+++++.. +|++++|+|+.|+||
T Consensus 1 ~~vg~I~~~~~hp~~~kL~~~~vd~g~~~~~~Iv~~~~n~~-----~g~~vvv~~~gs~l~~~~~i~~~~~~G~~S~GM- 74 (103)
T cd02796 1 VVVGKVLEVEPHPNADKLNVCKVDIGENKPLQIVCGAPNVR-----AGDKVVVALPGAVLPGGLKIKKRKLRGVESEGM- 74 (103)
T ss_pred CEEEEEEEEEecCCCCceEEEEEEeCCCcEEEEEcCccHhh-----cCCEEEEEecCCCcCCCceEcceeeCCcccchh-
Confidence 68999999999999999999999999767899999999984 355554443 899999999999999
Q ss_pred ecccCCCc
Q psy15305 120 MCASTPDK 127 (153)
Q Consensus 120 LCs~~e~g 127 (153)
|||+.|+|
T Consensus 75 l~s~~elg 82 (103)
T cd02796 75 LCSAKELG 82 (103)
T ss_pred CcchhHcC
Confidence 89988744
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=99.69 E-value=7.7e-17 Score=151.63 Aligned_cols=88 Identities=33% Similarity=0.545 Sum_probs=70.6
Q ss_pred CCCCCCCc-c-CeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEE---------Eeeeec
Q psy15305 39 EGPVDIGR-L-DLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVL---------LCNLKP 107 (153)
Q Consensus 39 e~~~df~~-l-dl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~---------~~nlk~ 107 (153)
|...++.. . +++||+|+++++||++++|++|+||+|+++.+|||||++|+.. |+++++ +.+|++
T Consensus 34 E~v~~~~~~~~~~~vg~i~~~~~hp~~~~L~~~~vd~g~~~~~~Iv~ga~n~~~-----g~~V~va~~Ga~l~~~~~i~~ 108 (798)
T TIGR00472 34 EAVIPFSKPLKGVVVGKVLEVEPHPNADKLKVCKVDIGEKEMLQIVCGAPNVEA-----GKKVAVALPGAKLPNGLKIKK 108 (798)
T ss_pred eeEEecccCcCCEEEEEEEEEEecCCCCcEEEEEEEcCCCceEEEEeCCccccC-----CCEEEEEccCCCccCCceEee
Confidence 34444443 3 4999999999999999999999999997667999999999852 344333 267999
Q ss_pred ceecceeccceeecccCCC-------ceEEec
Q psy15305 108 AKMRGVTSEAMVMCASTPD-------KVEILA 132 (153)
Q Consensus 108 rki~Gv~SeGMlLCs~~e~-------gi~lL~ 132 (153)
++|+|+.|+|| |||+.|+ ||.+|+
T Consensus 109 ~~~~Gv~S~GM-lcs~~elg~~~~~~gi~~l~ 139 (798)
T TIGR00472 109 SKLRGVESEGM-LCSEDELGLDEKSDGIIVLD 139 (798)
T ss_pred eecCCeeechh-cccHhHcCCCCCCCCEEEcC
Confidence 99999999999 9998864 566664
No 16
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=99.66 E-value=1.2e-16 Score=150.38 Aligned_cols=83 Identities=34% Similarity=0.512 Sum_probs=67.4
Q ss_pred CeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCccc-----ccccCCeeEEEEeeeecceecceeccceeecc
Q psy15305 48 DLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVP-----IEQMQNRMVVLLCNLKPAKMRGVTSEAMVMCA 122 (153)
Q Consensus 48 dl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~-----~~~l~gk~vv~~~nlk~rki~Gv~SeGMlLCs 122 (153)
+++||+|+++++||++++|++|+||+|+ +.+|||||++|+.. ++..|..+. .+.+|++++|+|+.|+|| |||
T Consensus 44 ~i~vg~i~~~~~hp~~~~L~v~~v~~g~-~~~~iv~ga~n~~~g~~v~~a~~G~~l~-~~~~i~~~~~~Gv~S~GM-lcs 120 (791)
T PRK00629 44 GVVVGKVLECEKHPNADKLRVCQVDVGE-EPLQIVCGAPNVRAGDKVPVALPGAVLP-GGFKIKKAKLRGVESEGM-LCS 120 (791)
T ss_pred CEEEEEEEEEEecCCCCeEEEEEEEcCC-eEEEEEeCCccccCCCEEEEEccCCCcc-CCceEeeeecCCeEEchh-ccc
Confidence 5999999999999999999999999997 56999999999842 222222222 346799999999999999 999
Q ss_pred cCCC-------ceEEecC
Q psy15305 123 STPD-------KVEILAP 133 (153)
Q Consensus 123 ~~e~-------gi~lL~~ 133 (153)
+.|+ ||.+|+.
T Consensus 121 ~~ELGl~~~~~GI~~L~~ 138 (791)
T PRK00629 121 ASELGLSDDHDGIIELPE 138 (791)
T ss_pred HhHcCCCcCCCCeEECCC
Confidence 8874 5667753
No 17
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=99.38 E-value=8.1e-13 Score=106.92 Aligned_cols=72 Identities=32% Similarity=0.483 Sum_probs=62.3
Q ss_pred CCccCeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecceecceeccceeeccc
Q psy15305 44 IGRLDLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPAKMRGVTSEAMVMCAS 123 (153)
Q Consensus 44 f~~ldl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~rki~Gv~SeGMlLCs~ 123 (153)
...+++++|+|.++..||++|+|++|.||+|. ..++|||+...+.. |..+ +++-|.||.|.|++|+|| +|..
T Consensus 117 ~~aV~~vvGEV~Sv~~hp~aD~L~v~vvn~G~-r~~tVVTN~~~vre-----g~~v-aVAlLPPr~F~gvvSeGM-Flg~ 188 (219)
T COG2517 117 VIAVDIVVGEVMSVGKHPNADKLLVTVVNIGG-RAVTVVTNDLDVRE-----GDRV-AVALLPPRNFFGVVSEGM-FLGA 188 (219)
T ss_pred ceeEEEEeeeeeecccCCCCCceEEEEEecCC-eEEEEEeccccccc-----CCEE-EEEecChhHhccccccce-eecc
Confidence 44579999999999999999999999999998 46899999998874 4444 457899999999999999 7765
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=99.34 E-value=1.8e-12 Score=112.68 Aligned_cols=71 Identities=18% Similarity=0.213 Sum_probs=56.8
Q ss_pred eEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCccc-----ccccCCeeEE-E-----------------Eeee
Q psy15305 49 LRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVP-----IEQMQNRMVV-L-----------------LCNL 105 (153)
Q Consensus 49 l~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~-----~~~l~gk~vv-~-----------------~~nl 105 (153)
.+||+|+++++||++|+|.+|+||. +|||||+.|+.. .+..+..+.. . ...|
T Consensus 3 ~vv~kV~~i~php~Ad~L~v~~Vd~-----~~vV~ga~n~~~Gd~Vv~a~~gs~Lp~~~~~~~~~~~~~~~~~g~~~~~I 77 (341)
T TIGR02306 3 AVMREIADLQPHPNADALELATVGG-----WEVVVKKGEYRVGSDCVYFPEDSVLPTDAGLFRFLETRAKILDGKMRARV 77 (341)
T ss_pred eEEEEEEEeeecCCCCceEEEEEeC-----EEEEcCCCcCCCCCEEEEECCCCCCCCCCCcchhhccccccccccccceE
Confidence 4799999999999999999999997 899999999842 2333333220 0 1279
Q ss_pred ecceecceeccceeecccCC
Q psy15305 106 KPAKMRGVTSEAMVMCASTP 125 (153)
Q Consensus 106 k~rki~Gv~SeGMlLCs~~e 125 (153)
+.++|||+.|||| ||+..+
T Consensus 78 k~~klRG~~SqGM-lcs~~~ 96 (341)
T TIGR02306 78 KTVRLRGEISQGI-ALPTGA 96 (341)
T ss_pred eEEEeccEEEccE-Eechhh
Confidence 9999999999999 999875
No 19
>PHA02142 putative RNA ligase
Probab=96.18 E-value=0.02 Score=50.85 Aligned_cols=68 Identities=22% Similarity=0.313 Sum_probs=45.7
Q ss_pred CeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCccc-------------cc------ccCCee-EE---EEee
Q psy15305 48 DLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFVP-------------IE------QMQNRM-VV---LLCN 104 (153)
Q Consensus 48 dl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~~-------------~~------~l~gk~-vv---~~~n 104 (153)
=+.|-+|..+++||+||.+-+++|| -+++|..-.++.. ++ -+.++- .. .+..
T Consensus 9 Lv~v~~i~~i~pi~~Ad~ie~a~V~-----gw~vVV~kg~f~~GD~~vY~eiDS~lP~~~~~~~~l~~~~~~~~g~~~~R 83 (366)
T PHA02142 9 LASMRKIADLQPIPGADAIEVATID-----GWEVVVKKGEFRVGDDCVYFEIDSLLPTDNPAFRFLETRARIYDGKMRAR 83 (366)
T ss_pred EEEEEEEeeecccCCCCceeEEEEC-----CEEEEEeccccccCCeEEEecccccccCCchhhhhhhccccccCCcccce
Confidence 3678999999999999999998885 2555555443310 11 122111 11 1357
Q ss_pred eecceecceeccceee
Q psy15305 105 LKPAKMRGVTSEAMVM 120 (153)
Q Consensus 105 lk~rki~Gv~SeGMlL 120 (153)
|+..++||.+||||+|
T Consensus 84 i~t~klRG~iSQGl~l 99 (366)
T PHA02142 84 IKTIKLRGQISQGIAL 99 (366)
T ss_pred EEEEEEeeEEeeeEEe
Confidence 9999999999999944
No 20
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=69.82 E-value=0.75 Score=43.88 Aligned_cols=49 Identities=12% Similarity=0.183 Sum_probs=44.5
Q ss_pred EEeCCC-CCCeeEEEEEcCCCCCeEEEeCCCCcccccccCCeeEEEEeeeecc
Q psy15305 57 ASKHPD-ADSLYVEKVELGEPAPRTVVSGLVKFVPIEQMQNRMVVLLCNLKPA 108 (153)
Q Consensus 57 ve~HP~-adKL~v~kVDiG~~~~r~IVsga~n~~~~~~l~gk~vv~~~nlk~r 108 (153)
|+..|. +.+|.-.+.|.|.+..++|++|...+|. +|.|+..+..+| .||
T Consensus 609 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~-~pr 658 (659)
T PTZ00385 609 CANVRELRRVIMELGQRGGENGLPTAGGRLSEWRI--TLTFAIIRFICG-TPR 658 (659)
T ss_pred hhhchHHHHHHhceecccCCCCccchhHHHHHHHH--HHhcceeEEEeC-CCC
Confidence 888998 8999999999999889999999999997 788998888889 776
No 21
>PRK04313 30S ribosomal protein S4e; Validated
Probab=36.18 E-value=81 Score=26.65 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=15.5
Q ss_pred EEEEEEEEEeCC-CCCCeeEEE
Q psy15305 50 RVGKIIEASKHP-DADSLYVEK 70 (153)
Q Consensus 50 ~VGkIveve~HP-~adKL~v~k 70 (153)
+||+|.+++.|+ .+.++..++
T Consensus 188 riG~I~~i~~~~~~~~~~V~i~ 209 (237)
T PRK04313 188 EIGKIKEIEVTKSSKPNIVTLE 209 (237)
T ss_pred eEEEEEEEEEccCCCCcEEEEE
Confidence 789999999998 444555555
No 22
>KOG2110|consensus
Probab=27.00 E-value=57 Score=29.51 Aligned_cols=28 Identities=4% Similarity=0.405 Sum_probs=24.2
Q ss_pred eeccceeecccCCCc--eEEecCCCCCeee
Q psy15305 113 VTSEAMVMCASTPDK--VEILAPPSSDQCF 140 (153)
Q Consensus 113 v~SeGMlLCs~~e~g--i~lL~~p~g~~~~ 140 (153)
+-+.|++|+..+|.| |.++..|+|++++
T Consensus 181 fs~~G~llATASeKGTVIRVf~v~~G~kl~ 210 (391)
T KOG2110|consen 181 FSPDGTLLATASEKGTVIRVFSVPEGQKLY 210 (391)
T ss_pred ECCCCCEEEEeccCceEEEEEEcCCccEee
Confidence 678999999999998 7899999999864
No 23
>PLN00036 40S ribosomal protein S4; Provisional
Probab=25.18 E-value=1.5e+02 Score=25.42 Aligned_cols=20 Identities=30% Similarity=0.320 Sum_probs=15.2
Q ss_pred EEEEEEEEEeCCCCCCeeEE
Q psy15305 50 RVGKIIEASKHPDADSLYVE 69 (153)
Q Consensus 50 ~VGkIveve~HP~adKL~v~ 69 (153)
+||+|.+++.|+.+.++..+
T Consensus 191 rvG~I~~i~~~~~~~~iV~i 210 (261)
T PLN00036 191 RVGVIKNREKHKGSFEIIHV 210 (261)
T ss_pred eEEEEEEEEecCCCCCEEEE
Confidence 68899999999888664333
No 24
>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=25.04 E-value=3e+02 Score=20.59 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=24.0
Q ss_pred CeEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCCcc
Q psy15305 48 DLRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVKFV 89 (153)
Q Consensus 48 dl~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n~~ 89 (153)
.+++|+|..+.. |.|| ||+|. + -..||-.+...
T Consensus 25 k~V~G~I~hvv~----ddLY---IDfG~-K-FhcVc~rp~~~ 57 (104)
T PF10246_consen 25 KIVIGKIFHVVD----DDLY---IDFGG-K-FHCVCKRPAVN 57 (104)
T ss_pred CEEEEEEEEEec----CceE---EEeCC-c-eeEEEeccccc
Confidence 599999998854 3566 59997 3 46888777653
No 25
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=24.05 E-value=1.6e+02 Score=25.41 Aligned_cols=22 Identities=32% Similarity=0.504 Sum_probs=17.5
Q ss_pred EEEEEEEEEeCCCCCCeeEEEE
Q psy15305 50 RVGKIIEASKHPDADSLYVEKV 71 (153)
Q Consensus 50 ~VGkIveve~HP~adKL~v~kV 71 (153)
+||+|.+++.|+.+.++..++-
T Consensus 188 riG~I~~i~~~~~~~~iv~i~d 209 (273)
T PTZ00223 188 RIGEIVSIERHPGAFDIARLKD 209 (273)
T ss_pred eEEEEEEEEecCCCCCEEEEEe
Confidence 7899999999998877666553
No 26
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=23.13 E-value=2.8e+02 Score=19.59 Aligned_cols=34 Identities=21% Similarity=0.225 Sum_probs=25.0
Q ss_pred eEEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCC
Q psy15305 49 LRVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGL 85 (153)
Q Consensus 49 l~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga 85 (153)
-+.|+|.++..| .+.++|..-.| ++ -.+..++=.
T Consensus 25 wV~GEIs~~~~~-~~gh~YftLkD-~~-a~i~~~~~~ 58 (99)
T PF13742_consen 25 WVEGEISNLKRH-SSGHVYFTLKD-EE-ASISCVIFR 58 (99)
T ss_pred EEEEEEeecEEC-CCceEEEEEEc-CC-cEEEEEEEH
Confidence 578999999999 78889998888 43 334444433
No 27
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=21.19 E-value=2e+02 Score=17.15 Aligned_cols=38 Identities=11% Similarity=-0.000 Sum_probs=26.0
Q ss_pred EEEEEEEEEeCCCCCCeeEEEEEcCCCCCeEEEeCCCC
Q psy15305 50 RVGKIIEASKHPDADSLYVEKVELGEPAPRTVVSGLVK 87 (153)
Q Consensus 50 ~VGkIveve~HP~adKL~v~kVDiG~~~~r~IVsga~n 87 (153)
++|.|.++........+..+.++.+.+....+++-...
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~ 39 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGEL 39 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchH
Confidence 57899999887642457888888877345566665443
No 28
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=21.12 E-value=2e+02 Score=24.72 Aligned_cols=19 Identities=42% Similarity=0.653 Sum_probs=14.3
Q ss_pred EEEEEEEEEeCCCCCCeeE
Q psy15305 50 RVGKIIEASKHPDADSLYV 68 (153)
Q Consensus 50 ~VGkIveve~HP~adKL~v 68 (153)
+||+|.+.+.|+.+.++..
T Consensus 191 riG~I~~~~~~~~~~~~V~ 209 (262)
T PTZ00118 191 RVGTIVSKEKHPGSFDLIH 209 (262)
T ss_pred eEEEEEEEEecCCCCcEEE
Confidence 6888888888888766333
No 29
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=21.07 E-value=1.6e+02 Score=20.91 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=16.1
Q ss_pred cCeEEEEEEEEEeCCCCCCeeEEEEEcCC
Q psy15305 47 LDLRVGKIIEASKHPDADSLYVEKVELGE 75 (153)
Q Consensus 47 ldl~VGkIveve~HP~adKL~v~kVDiG~ 75 (153)
=|++||.|+++.. ...+||+|.
T Consensus 7 gD~VIG~V~~~~~-------~~~~VdI~s 28 (86)
T cd05790 7 GDHVIGIVVAKAG-------DFFKVDIGG 28 (86)
T ss_pred CCEEEEEEEEEcC-------CeEEEEcCC
Confidence 3899999999842 245678876
Done!