Query 030702
Match_columns 173
No_of_seqs 167 out of 278
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 03:18:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030702.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030702hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4772 Predicted tRNA-splicin 100.0 5.3E-35 1.1E-39 252.7 6.9 169 1-171 88-286 (364)
2 PF12928 tRNA_int_end_N2: tRNA 99.7 1.6E-17 3.4E-22 116.7 4.4 44 1-44 27-71 (72)
3 PRK09297 tRNA-splicing endonuc 99.5 1.7E-14 3.8E-19 116.0 3.5 72 14-86 26-97 (169)
4 TIGR00324 endA tRNA intron end 99.4 1.2E-13 2.6E-18 111.4 4.0 72 14-86 27-98 (170)
5 PRK09300 tRNA splicing endonuc 99.2 1.1E-11 2.3E-16 109.3 4.9 67 14-86 25-91 (330)
6 COG1676 SEN2 tRNA splicing end 99.1 1E-10 2.2E-15 95.4 5.6 71 15-86 38-108 (181)
7 PRK09300 tRNA splicing endonuc 99.0 3.5E-10 7.6E-15 99.7 3.3 73 14-92 189-265 (330)
8 PF02778 tRNA_int_endo_N: tRNA 98.7 2.5E-08 5.4E-13 69.2 5.1 40 15-55 27-67 (67)
9 PRK09539 tRNA-splicing endonuc 96.4 0.0013 2.9E-08 50.9 1.2 22 65-86 33-54 (124)
10 KOG4685 tRNA splicing endonucl 96.3 0.0021 4.5E-08 55.2 1.7 62 22-85 112-174 (271)
11 PF01974 tRNA_int_endo: tRNA i 92.5 0.018 3.9E-07 40.9 -1.6 20 67-86 2-21 (85)
12 KOG4772 Predicted tRNA-splicin 59.9 6.6 0.00014 35.3 2.2 39 129-167 221-263 (364)
13 PF13953 PapC_C: PapC C-termin 51.2 19 0.00041 24.3 2.9 37 2-46 15-52 (68)
14 PRK07708 hypothetical protein; 46.8 36 0.00078 28.4 4.5 52 22-75 21-79 (219)
15 PRK15047 N-hydroxyarylamine O- 42.7 11 0.00024 32.6 0.9 43 44-86 46-90 (281)
16 KOG4133 tRNA splicing endonucl 40.4 13 0.00029 32.4 0.9 22 22-43 49-70 (290)
17 PF13592 HTH_33: Winged helix- 39.6 12 0.00026 24.7 0.4 42 46-88 2-43 (60)
18 KOG4133 tRNA splicing endonucl 35.3 8.2 0.00018 33.7 -1.1 21 67-87 194-214 (290)
19 PF04237 YjbR: YjbR; InterPro 28.3 2E+02 0.0044 19.8 5.6 57 3-59 18-86 (92)
20 PF03987 Autophagy_act_C: Auto 26.7 37 0.0008 22.5 1.2 22 39-60 15-36 (62)
21 PF04722 Ssu72: Ssu72-like pro 25.8 55 0.0012 27.3 2.2 16 74-89 20-35 (195)
22 PF14553 YqbF: YqbF, hypotheti 24.9 1.9E+02 0.004 18.5 4.0 37 7-43 1-39 (43)
23 PF08513 LisH: LisH; InterPro 24.5 12 0.00025 21.1 -1.4 14 69-82 4-17 (27)
24 PF11625 DUF3253: Protein of u 24.4 43 0.00092 24.2 1.2 26 28-54 48-73 (83)
25 TIGR03882 cyclo_dehyd_2 bacter 23.8 17 0.00038 29.5 -1.0 58 27-86 12-78 (193)
26 PF00797 Acetyltransf_2: N-ace 21.1 25 0.00054 28.7 -0.6 43 45-87 27-71 (240)
No 1
>KOG4772 consensus Predicted tRNA-splicing endonuclease subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-35 Score=252.73 Aligned_cols=169 Identities=36% Similarity=0.502 Sum_probs=119.6
Q ss_pred CcEEecccCccccceeeEeCCeEEEeHHHHHHHHhcC-cEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhcccc
Q 030702 1 MAEVVEKKGKMWTTTGIVRNGKTYCSIEETLFLAEIG-ALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSL 79 (173)
Q Consensus 1 ~A~V~~~kG~~~~~~G~~~~~~l~L~peEalYL~ErG-~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~ 79 (173)
||+|.+++|++|+|||+++.|++||.+||||||+||| ...+...++++||++++|+.+.++.. +||+|+||+||||+
T Consensus 88 mAeVekk~Gkl~~TmG~adsgklyl~~eEalYL~ErG~l~~cg~e~~I~~sl~dLys~~~s~~~--s~enYlVyahLkrl 165 (364)
T KOG4772|consen 88 MAEVEKKRGKLWTTMGIADSGKLYLFIEEALYLSERGELQSCGHEDDIVISLKDLYSEIASEKY--SMENYLVYAHLKRL 165 (364)
T ss_pred eeeEeecCCcceeeeeeeccCceEEeHHHHHHHHHhhhhhhhcCccchhhHHHHHHHHHhhhhc--chhHHHHHHHHHhc
Confidence 7999999999999999999888999999999999999 44565667999999999999998765 59999999999999
Q ss_pred CeEEEecCCCccccC---CCCCcccc----ccCCc--------cccccCCCCC----Cc-----cCCCCChhH-HH----
Q 030702 80 GYIVGRHGVPWIVKI---PKGRDINI----TSDPV--------SLQVTPKRHG----VM-----DVEPKEESS-LV---- 130 (173)
Q Consensus 80 GYiV~r~~~~~~~~~---~~~~~~~~----~~~~~--------~~~~~~~~~~----~~-----~~~~~sy~~-I~---- 130 (173)
||||.||+++-..+. +.+.-++. ..++. +++.-++.+. .+ ....+++.+ +|
T Consensus 166 Gfiv~rhn~~~~~~~e~~~~~kiw~~k~a~~~~L~~p~~i~es~~f~~~~~r~~~~s~LL~d~~~~d~~~v~Dp~yLp~~ 245 (364)
T KOG4772|consen 166 GFIVKRHNVPAAVKTEFFPLKKIWTLKDAITWRLLSPSKIQESSCFSEFFYRRDTVSKLLYDMLICDARSVFDPVYLPNS 245 (364)
T ss_pred ceeeeccCCCcccccccccHHHHHHHHHHHhccCCCchhhhhhhhhhhhhhhhhHHHHHHHhhhhcccccccchhcCcch
Confidence 999999997622211 10000100 00000 1111001000 00 111111111 11
Q ss_pred HHHhcccCCCCceeEEEeCCCCCCccCCCCCCcEEEEEeec
Q 030702 131 ALFYNIQINEVRPVFDVYLPNRKFKKSCPGDPSFLLYLTCK 171 (173)
Q Consensus 131 ~~l~~~~~~~~~i~f~V~kP~~~FkK~~P~~PDF~i~V~~k 171 (173)
+...-...+|+.++|++|||.++|+|+.|+.|||+|||+|+
T Consensus 246 ~~k~~~k~spie~tfs~~kpfS~fgks~~s~pdf~v~v~~~ 286 (364)
T KOG4772|consen 246 QFKEFQKSSPIEPTFSFVKPFSNFGKSDPSLPDFQVFVYNK 286 (364)
T ss_pred hhhhhcccCCCCCcceeecccccccCCCCCCCceeEEEEec
Confidence 01111246899999999999999999999999999999997
No 2
>PF12928 tRNA_int_end_N2: tRNA-splicing endonuclease subunit sen54 N-term; InterPro: IPR024336 tRNA-splicing endonucleases (3.1.27.9 from EC) catalyse the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini [, ]. The genes encoding these proteins are homologous in eukaryotes and archea. The eukaryotic tRNA-splicing endonucleases are heterotetrameric while the archaeal endonucleases can be split into homodimeric and homotetrameric subgroups. This entry represents the N-terminal domain of Sen54, a non-catalytic subunit of the tRNA-splicing endonuclease complex. Defects in human Sen54 are a cause of pontocerebellar hypoplasia type 4 [].
Probab=99.69 E-value=1.6e-17 Score=116.69 Aligned_cols=44 Identities=43% Similarity=0.575 Sum_probs=41.5
Q ss_pred CcEEecccCcccccee-eEeCCeEEEeHHHHHHHHhcCcEEEEcC
Q 030702 1 MAEVVEKKGKMWTTTG-IVRNGKTYCSIEETLFLAEIGALYLLDN 44 (173)
Q Consensus 1 ~A~V~~~kG~~~~~~G-~~~~~~l~L~peEalYL~ErG~L~~~~~ 44 (173)
+|+|+++||+||++|| ...++++||+|||||||+|||+|+|+++
T Consensus 27 ~a~v~~~rG~~~~~mG~~~~~~~~~L~pEEalyLvErGsL~l~~~ 71 (72)
T PF12928_consen 27 MAEVTHPRGKFFQTMGRADRGGKLWLLPEEALYLVERGSLDLWWP 71 (72)
T ss_pred EEEEECCcCCcHHhcCCccCCCeEEEeHHHHHHHHhcCcEEEEeC
Confidence 5899999999999999 6699999999999999999999999964
No 3
>PRK09297 tRNA-splicing endonuclease subunit alpha; Reviewed
Probab=99.48 E-value=1.7e-14 Score=116.01 Aligned_cols=72 Identities=28% Similarity=0.328 Sum_probs=65.3
Q ss_pred ceeeEeCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec
Q 030702 14 TTGIVRNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 14 ~~G~~~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
-+|+..++.+.|+|+||+||+|+|.|++.+.++.+||++|+++.+...+. .++.+|.||+|||++||+|+..
T Consensus 26 ~yG~~~~~~L~Ls~~Ea~yL~~~g~L~v~~~~~~~~s~~el~~~~~~~~~-~F~~~y~VY~dLr~rG~~vk~G 97 (169)
T PRK09297 26 FYGKLLGNPLELSLIEALYLVEKGWLEVVDKDGELLSFEELYELAREIIE-KFDIKYLVYKDLRDRGYIVKSG 97 (169)
T ss_pred CcCCccCCcEEEcHHHHHHHHHCCCEEEEcCCCcccCHHHHHHHHHhccc-cHHHHhHHHHHHHHCCCccCCC
Confidence 56888899999999999999999999999877888999999999987554 6789999999999999999764
No 4
>TIGR00324 endA tRNA intron endonuclease. The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied (PubMed:97344075) and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs.
Probab=99.42 E-value=1.2e-13 Score=111.35 Aligned_cols=72 Identities=22% Similarity=0.357 Sum_probs=64.8
Q ss_pred ceeeEeCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec
Q 030702 14 TTGIVRNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 14 ~~G~~~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
-+|+..++.+.|+|+||+||+++|+|++.+.++.+||.+++++.+...+. .++.+|.||+|||++||+|+..
T Consensus 27 ~yG~~~~~~l~LsliEa~yL~~~g~l~v~~~~~~~ls~~el~~~~~~~~~-~f~~~y~VY~dLR~rG~~vk~G 98 (170)
T TIGR00324 27 EYGNLDGDSLNLSLIESLYLIDLGKLRLIRSDSEPLSREELSDLARKVER-GFMRKYLVYKDLRDRGYVVKTG 98 (170)
T ss_pred cCCCCcCCccEEeHHHHHHHHhCCcEEEEcCCCCcCCHHHHHHHHHhccc-cHHHhhHHHHHHHHCCCEecCC
Confidence 46777888999999999999999999998777889999999999986554 5789999999999999999876
No 5
>PRK09300 tRNA splicing endonuclease; Reviewed
Probab=99.22 E-value=1.1e-11 Score=109.32 Aligned_cols=67 Identities=16% Similarity=0.241 Sum_probs=60.0
Q ss_pred ceeeEeCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec
Q 030702 14 TTGIVRNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 14 ~~G~~~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
-+|+..++.|.|+|.||+||+|+|.|++. . .+|++|+++.+... . .+..+|.||++||++||+|+..
T Consensus 25 ~YG~~~g~~L~LslvEalYL~~~g~l~v~-~---~~~~eel~~~~~~~-~-~f~~~y~VY~dLR~rGy~vk~g 91 (330)
T PRK09300 25 GYGRPKGDGLELAPVEAAYLLFRGKIEIV-D---GLGFRDLFARASLR-P-NFELRYLVYKDLRERGYYVQPG 91 (330)
T ss_pred CCCcCCCCeeEEcHHHHHHHHHcCCEEEe-c---CCCHHHHHHHhhhc-c-cchheehHHHHHHHCCceeccC
Confidence 46899999999999999999999999997 2 29999999998865 2 5789999999999999999984
No 6
>COG1676 SEN2 tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=1e-10 Score=95.41 Aligned_cols=71 Identities=28% Similarity=0.379 Sum_probs=63.5
Q ss_pred eeeEeCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec
Q 030702 15 TGIVRNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 15 ~G~~~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
.|...+..+.|++.||+||.|+|.|.+.+.++.++|++|++.+.....+ .+..+|.||++||++||+|+..
T Consensus 38 ~~~~~~~~l~ls~~ea~yl~e~g~l~~~~~~~~~~s~eel~~~~~~~~~-~f~~~y~VY~dLr~rG~vvktG 108 (181)
T COG1676 38 IGTTERDPLQLSLIEALYLAERGFLKVESRDGKILSFEELMDLGAEKEE-SFDERYLVYRDLRDRGYVVKTG 108 (181)
T ss_pred ccccccccceecHHHHHHHhhcceEeeccCCCccccHHHHHHHHhhccc-ccceeeeehhhHHhCceEECcc
Confidence 4445567899999999999999999999888899999999999987764 6899999999999999999865
No 7
>PRK09300 tRNA splicing endonuclease; Reviewed
Probab=98.96 E-value=3.5e-10 Score=99.74 Aligned_cols=73 Identities=23% Similarity=0.273 Sum_probs=61.1
Q ss_pred ceeeE-eCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec---CCC
Q 030702 14 TTGIV-RNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH---GVP 89 (173)
Q Consensus 14 ~~G~~-~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~---~~~ 89 (173)
.+|+. .+..+.|+++||+||+++|+|++ ..||++++.+.+...+. .+..+|.||+|||++||+|+.. +..
T Consensus 189 ~YG~~~~~~~L~LslvEA~yL~~~g~L~v-----~~~~~~el~~~~~~~~~-~F~~~y~VY~dLR~rG~~vk~G~KFG~D 262 (330)
T PRK09300 189 FYGKPLDGRRLQLSLVEAAYLLERGVLSV-----EILDADEFVERAREVEG-EFDRKLAVYRDLRERGFVPKTGFKFGSD 262 (330)
T ss_pred CCCCCCCCCceeECHHHHHHHHhCCCEEE-----eeCCHHHHHHHHhhccc-chHhhhHHHHHHHHCCCEecCCcccCce
Confidence 35765 34499999999999999999999 36999999999987554 5889999999999999999887 544
Q ss_pred ccc
Q 030702 90 WIV 92 (173)
Q Consensus 90 ~~~ 92 (173)
+..
T Consensus 263 F~v 265 (330)
T PRK09300 263 FRV 265 (330)
T ss_pred EEE
Confidence 443
No 8
>PF02778 tRNA_int_endo_N: tRNA intron endonuclease, N-terminal domain; InterPro: IPR006678 This entry represents a 2-layer alpha/beta domain found at the N-terminal in homotetrameric tRNA-intron endonucleases [], and as domains 1 (N-terminal) and 3 in the homodimeric enzymes []. tRNA-intron endonucleases (3.1.27.9 from EC) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini []. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp []. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1A79_D 2CV8_A 3P1Z_B 3AJV_B 3IEY_A 2ZYZ_D 2GJW_D 1R0V_A 3P1Y_C 1R11_B ....
Probab=98.71 E-value=2.5e-08 Score=69.22 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=36.0
Q ss_pred eee-EeCCeEEEeHHHHHHHHhcCcEEEEcCCCcccCHHHHH
Q 030702 15 TGI-VRNGKTYCSIEETLFLAEIGALYLLDNNDLCLPLKEIY 55 (173)
Q Consensus 15 ~G~-~~~~~l~L~peEalYL~ErG~L~~~~~~g~~lSlq~~y 55 (173)
+|+ ..++++.|+++||+||+++|+|+|. .+|.+||.+|++
T Consensus 27 YG~~~~~~~L~LslvEa~YL~~~g~l~v~-~~g~~ls~~el~ 67 (67)
T PF02778_consen 27 YGKPLDDERLQLSLVEALYLLEKGKLEVY-EDGKKLSFEELW 67 (67)
T ss_dssp -SEECETSCEEEEHHHHHHHHHTTSEEEE-TTSCEE-HHHHH
T ss_pred CCCCCCCCcEEEeHHHHHHHHhCCcEEEe-eCCcCCCHHHhC
Confidence 788 6999999999999999999999998 889999999985
No 9
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=96.42 E-value=0.0013 Score=50.90 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=20.2
Q ss_pred CCcceeeeehhccccCeEEEec
Q 030702 65 CSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 65 ~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
..+.+|.||+|||++||+|++.
T Consensus 33 ~~~~kylVYkDLR~RGyvVk~G 54 (124)
T PRK09539 33 VNWDKVDVFVDLKQRGRKTIDG 54 (124)
T ss_pred cccceEEEehhHHhCCCeeccC
Confidence 4699999999999999999886
No 10
>KOG4685 consensus tRNA splicing endonuclease SEN2 [Translation, ribosomal structure and biogenesis]
Probab=96.27 E-value=0.0021 Score=55.24 Aligned_cols=62 Identities=23% Similarity=0.352 Sum_probs=53.4
Q ss_pred eEEEeHHHHHHHH-hcCcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEe
Q 030702 22 KTYCSIEETLFLA-EIGALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGR 85 (173)
Q Consensus 22 ~l~L~peEalYL~-ErG~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r 85 (173)
-|.|+||||.||. .-++|.|. .+-.+++..+++..+..... .+---|.+|.|||..|+||+.
T Consensus 112 ~LqLs~eEAffL~y~lkci~I~-~~k~l~~~v~~w~am~~~~~-~F~~~y~~y~hlrskGWvvrs 174 (271)
T KOG4685|consen 112 WLQLSPEEAFFLSYALKCIKIS-LNKCLLNEVDLWTAMRSLQP-NFGKLYKAYHHLRSKGWVVRS 174 (271)
T ss_pred HhhcCHHHHHHHHhhhceeEEe-hhhccccHHHHHHHHhhcch-hhHHHHHHHHHHHHcCcEecc
Confidence 4789999999996 56889998 55788999999999887553 678889999999999999987
No 11
>PF01974 tRNA_int_endo: tRNA intron endonuclease, catalytic C-terminal domain; InterPro: IPR006677 This entry represents a 3-layer alpha/beta/alpha domain found as the catalytic domain at the C-terminal in homotetrameric tRNA-intron endonucleases [], and as domains 2 and 4 (C-terminal) in the homodimeric enzymes []. tRNA-intron endonucleases (3.1.27.9 from EC) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini []. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp []. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 3IEY_B 3IF0_X 2CV8_A 3P1Z_B 3AJV_B 2GJW_D 1R0V_A 3P1Y_C 1R11_B 1RLV_A ....
Probab=92.49 E-value=0.018 Score=40.94 Aligned_cols=20 Identities=45% Similarity=0.968 Sum_probs=17.3
Q ss_pred cceeeeehhccccCeEEEec
Q 030702 67 WELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 67 ~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
+.+|.||++||++||+|+..
T Consensus 2 ~~~y~vY~dLr~rG~~v~~G 21 (85)
T PF01974_consen 2 WRKYAVYRDLRSRGYVVKPG 21 (85)
T ss_dssp HHHHHHHHHHHHTT-EEEEE
T ss_pred chhhHHHHHHHHCCCEECcc
Confidence 56899999999999999877
No 12
>KOG4772 consensus Predicted tRNA-splicing endonuclease subunit [Translation, ribosomal structure and biogenesis]
Probab=59.90 E-value=6.6 Score=35.27 Aligned_cols=39 Identities=49% Similarity=0.912 Sum_probs=30.9
Q ss_pred HHHHHhcccCCCCceeEE-EeCCCCCCc---cCCCCCCcEEEE
Q 030702 129 LVALFYNIQINEVRPVFD-VYLPNRKFK---KSCPGDPSFLLY 167 (173)
Q Consensus 129 I~~~l~~~~~~~~~i~f~-V~kP~~~Fk---K~~P~~PDF~i~ 167 (173)
...+|.++....-++.|| ||.|++.|+ |.+|..|-|..+
T Consensus 221 ~s~LL~d~~~~d~~~v~Dp~yLp~~~~k~~~k~spie~tfs~~ 263 (364)
T KOG4772|consen 221 VSKLLYDMLICDARSVFDPVYLPNSQFKEFQKSSPIEPTFSFV 263 (364)
T ss_pred HHHHHHhhhhcccccccchhcCcchhhhhhcccCCCCCcceee
Confidence 345555666778889999 999999887 999999977653
No 13
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=51.24 E-value=19 Score=24.28 Aligned_cols=37 Identities=30% Similarity=0.426 Sum_probs=28.3
Q ss_pred cEEecccCccccceeeE-eCCeEEEeHHHHHHHHhcCcEEEEcCCC
Q 030702 2 AEVVEKKGKMWTTTGIV-RNGKTYCSIEETLFLAEIGALYLLDNND 46 (173)
Q Consensus 2 A~V~~~kG~~~~~~G~~-~~~~l~L~peEalYL~ErG~L~~~~~~g 46 (173)
|.|.+..|+ ..|.+ .+|.+||.-.. +.|+|.|.|.++
T Consensus 15 A~v~~~~g~---~~g~Vg~~G~vyl~~~~-----~~~~L~V~w~~~ 52 (68)
T PF13953_consen 15 ASVSDEDGN---NIGIVGQDGQVYLSGLP-----PKGTLTVKWGDG 52 (68)
T ss_dssp -EEEETTSS---EEEEB-GCGEEEEEEE------TCEEEEEESTSC
T ss_pred cEEEcCCCC---EEEEEcCCCEEEEECCC-----CCcEEEEEECCC
Confidence 677887776 56777 78999999877 899999997654
No 14
>PRK07708 hypothetical protein; Validated
Probab=46.76 E-value=36 Score=28.44 Aligned_cols=52 Identities=29% Similarity=0.242 Sum_probs=39.6
Q ss_pred eEEEeHHHHHHHHhc-------CcEEEEcCCCcccCHHHHHHHHHccCCCCCcceeeeehh
Q 030702 22 KTYCSIEETLFLAEI-------GALYLLDNNDLCLPLKEIYEKIANEKSGCSWELFEVYRH 75 (173)
Q Consensus 22 ~l~L~peEalYL~Er-------G~L~~~~~~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~ 75 (173)
.-|+..+|||.|+|- ..|+.+|.+|...|+.|+-.+...... -.+...||-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~k~~~~~~~~~~~--ep~~~~vY~D 79 (219)
T PRK07708 21 SDWMNIEEALQLAEDFEKTGRVKELEFYDEMDTEWSLKELKKLSKEVEE--EPHEILVYFD 79 (219)
T ss_pred eccccHHHHHHHHHHHhhcCCceeEEEecCCCCEeeHHHHhhhhhhhcc--CCCcEEEEEe
Confidence 458999999999983 456777889999999999998875432 2455666654
No 15
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=42.70 E-value=11 Score=32.60 Aligned_cols=43 Identities=23% Similarity=0.277 Sum_probs=34.8
Q ss_pred CCCcccCHHHHHHHHHcc-CCC-CCcceeeeehhccccCeEEEec
Q 030702 44 NNDLCLPLKEIYEKIANE-KSG-CSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 44 ~~g~~lSlq~~y~l~~~~-~~~-~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
...++|+++++|+.+... .+| |...+-+-+.-|+.+||-|...
T Consensus 46 g~~i~ld~~~l~~KlV~~~RGGyCfE~N~Lf~~~L~~LGF~v~~~ 90 (281)
T PRK15047 46 PREIQLDDQSLEEKLVIARRGGYCFEQNGLFERVLRELGFNVRSL 90 (281)
T ss_pred CCCCCCCHHHHHHHHhcCCCCEEcHhHHHHHHHHHHHcCCcEEEE
Confidence 356789999999999853 333 7777888899999999999855
No 16
>KOG4133 consensus tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=40.36 E-value=13 Score=32.42 Aligned_cols=22 Identities=36% Similarity=0.378 Sum_probs=18.6
Q ss_pred eEEEeHHHHHHHHhcCcEEEEc
Q 030702 22 KTYCSIEETLFLAEIGALYLLD 43 (173)
Q Consensus 22 ~l~L~peEalYL~ErG~L~~~~ 43 (173)
.+.|++|||.+|+|.|--.|.+
T Consensus 49 Pl~Lm~eEa~lL~e~gia~v~~ 70 (290)
T KOG4133|consen 49 PLELMKEEARLLAEIGIALVVD 70 (290)
T ss_pred chhhCHHHHHHHHHcChhheec
Confidence 6899999999999999555554
No 17
>PF13592 HTH_33: Winged helix-turn helix
Probab=39.64 E-value=12 Score=24.66 Aligned_cols=42 Identities=33% Similarity=0.361 Sum_probs=32.3
Q ss_pred CcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEecCC
Q 030702 46 DLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRHGV 88 (173)
Q Consensus 46 g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~~~ 88 (173)
|...+..++-+.+...- |+.+..=.||..|+|+|+.-++...
T Consensus 2 ~~~wt~~~i~~~I~~~f-gv~ys~~~v~~lL~r~G~s~~kp~~ 43 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEF-GVKYSPSGVYRLLKRLGFSYQKPRP 43 (60)
T ss_pred CCcccHHHHHHHHHHHH-CCEEcHHHHHHHHHHcCCccccCCC
Confidence 34556777777776543 6888888999999999999888753
No 18
>KOG4133 consensus tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=35.27 E-value=8.2 Score=33.70 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=19.1
Q ss_pred cceeeeehhccccCeEEEecC
Q 030702 67 WELFEVYRHLKSLGYIVGRHG 87 (173)
Q Consensus 67 ~~~Y~VY~~Lkr~GYiV~r~~ 87 (173)
..+|.+|++|.++||.+...+
T Consensus 194 ~lrY~iyKdLwdrGfyLs~gg 214 (290)
T KOG4133|consen 194 ELRYSIYKDLWDRGFYLSPGG 214 (290)
T ss_pred hhHHHHHHHHHHcCceeCccc
Confidence 789999999999999998765
No 19
>PF04237 YjbR: YjbR; InterPro: IPR007351 This is a family of uncharacterised proteins.; PDB: 3H9X_D 2KFP_A 2FKI_A 2A1V_A.
Probab=28.33 E-value=2e+02 Score=19.82 Aligned_cols=57 Identities=25% Similarity=0.216 Sum_probs=39.0
Q ss_pred EEecccCccccceeeEeC-CeEEEeHHHHHHHHhc-CcEEEEcC----------CCcccCHHHHHHHHH
Q 030702 3 EVVEKKGKMWTTTGIVRN-GKTYCSIEETLFLAEI-GALYLLDN----------NDLCLPLKEIYEKIA 59 (173)
Q Consensus 3 ~V~~~kG~~~~~~G~~~~-~~l~L~peEalYL~Er-G~L~~~~~----------~g~~lSlq~~y~l~~ 59 (173)
-+-+.+||.|-.++.... -.+-+.|||+..|+|. +.+..-.. -+..++.+++.+++.
T Consensus 18 ~~frv~gK~Fa~~~~~~~~~~vK~~~e~~~~l~~~~~~~~p~~h~~k~~Wv~v~l~~~v~~~~l~~li~ 86 (92)
T PF04237_consen 18 PVFRVGGKMFALLGEDEDDVNVKCDPEEQEALREQYDGFFPAYHMNKKHWVSVRLDGDVDDEELRELID 86 (92)
T ss_dssp EEEECCCEEEEEEECCCCCEEEES-HHHHHHHHHSSTTEEE-TSS-TTTEEEEETTSSS-HHHHHHHHH
T ss_pred eEEEECCEEEEEEEcCCCcEEEEcCHHHHHHHHhhCCCEEeCCccCCCcEEEEEeCCCCCHHHHHHHHH
Confidence 345568888888887753 3667899999999999 66655321 134688888888875
No 20
>PF03987 Autophagy_act_C: Autophagocytosis associated protein, active-site domain ; InterPro: IPR007135 Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes. Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. Atg3 is the E2 enzyme for the LC3 lipidation process []. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A []. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex [].; PDB: 2DYT_A.
Probab=26.75 E-value=37 Score=22.46 Aligned_cols=22 Identities=27% Similarity=0.451 Sum_probs=13.0
Q ss_pred EEEEcCCCcccCHHHHHHHHHc
Q 030702 39 LYLLDNNDLCLPLKEIYEKIAN 60 (173)
Q Consensus 39 L~~~~~~g~~lSlq~~y~l~~~ 60 (173)
+.+++.+|.+++++|+++.+..
T Consensus 15 f~~~~~~g~~l~~~~~~~~~~~ 36 (62)
T PF03987_consen 15 FRGYDEDGSPLSLEEVYEDLSP 36 (62)
T ss_dssp EEEEETT--B--HHHHHTTS-T
T ss_pred EEEECCCCCCCCHHHHHHhhcc
Confidence 4566678999999999987664
No 21
>PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].; GO: 0004721 phosphoprotein phosphatase activity, 0006397 mRNA processing, 0005634 nucleus; PDB: 3O2S_B 3O2Q_E 3FMV_H 3OMW_D 3P9Y_B 3FDF_A 3OMX_A.
Probab=25.79 E-value=55 Score=27.33 Aligned_cols=16 Identities=31% Similarity=0.426 Sum_probs=12.0
Q ss_pred hhccccCeEEEecCCC
Q 030702 74 RHLKSLGYIVGRHGVP 89 (173)
Q Consensus 74 ~~Lkr~GYiV~r~~~~ 89 (173)
+-|++.||-|.+++..
T Consensus 20 ~~L~~~G~~V~SfGTG 35 (195)
T PF04722_consen 20 NVLKKAGFNVRSFGTG 35 (195)
T ss_dssp HHHHHTT-EEEEEE-S
T ss_pred HHHHHCCCceEeecCC
Confidence 5689999999999864
No 22
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=24.85 E-value=1.9e+02 Score=18.47 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=28.6
Q ss_pred ccCccccceeeE--eCCeEEEeHHHHHHHHhcCcEEEEc
Q 030702 7 KKGKMWTTTGIV--RNGKTYCSIEETLFLAEIGALYLLD 43 (173)
Q Consensus 7 ~kG~~~~~~G~~--~~~~l~L~peEalYL~ErG~L~~~~ 43 (173)
.+|+.+.-||+. .+-..-.+-+.+-||.+.+-.+|..
T Consensus 1 ikGktY~~~g~~F~~g~ee~V~kk~y~YL~~ne~F~v~k 39 (43)
T PF14553_consen 1 IKGKTYYAMGHRFLLGQEEKVSKKIYNYLNDNEFFEVRK 39 (43)
T ss_dssp SS-SEEEETTEEEEBT-EEEE-HHHHHHHHHSTTEEEEE
T ss_pred CCCcEEEEeeeEEeCCCeeehhHHHHHHHhcCCcEEEEe
Confidence 379999999998 4556678888999999999999874
No 23
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=24.50 E-value=12 Score=21.14 Aligned_cols=14 Identities=29% Similarity=0.282 Sum_probs=10.6
Q ss_pred eeeeehhccccCeE
Q 030702 69 LFEVYRHLKSLGYI 82 (173)
Q Consensus 69 ~Y~VY~~Lkr~GYi 82 (173)
.+.||.||.+.||.
T Consensus 4 n~lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 4 NQLIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHHHCT-H
T ss_pred HHHHHHHHHHCCcH
Confidence 35789999999984
No 24
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=24.43 E-value=43 Score=24.25 Aligned_cols=26 Identities=12% Similarity=0.080 Sum_probs=19.0
Q ss_pred HHHHHHHhcCcEEEEcCCCcccCHHHH
Q 030702 28 EETLFLAEIGALYLLDNNDLCLPLKEI 54 (173)
Q Consensus 28 eEalYL~ErG~L~~~~~~g~~lSlq~~ 54 (173)
+.|.=|++.|.|+|. ..|.+++++++
T Consensus 48 ~~A~~L~~~G~i~I~-qkG~~Vdp~~~ 73 (83)
T PF11625_consen 48 AAARRLARAGRIEIT-QKGKPVDPETF 73 (83)
T ss_dssp HHHHHHHHTTSEEEE-ETTEE--TTT-
T ss_pred HHHHHHHHCCcEEEE-ECCEecCcccC
Confidence 457889999999998 56888877654
No 25
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=23.83 E-value=17 Score=29.52 Aligned_cols=58 Identities=28% Similarity=0.299 Sum_probs=39.7
Q ss_pred HHHHHHHH-hcCcEEEEcC--------CCcccCHHHHHHHHHccCCCCCcceeeeehhccccCeEEEec
Q 030702 27 IEETLFLA-EIGALYLLDN--------NDLCLPLKEIYEKIANEKSGCSWELFEVYRHLKSLGYIVGRH 86 (173)
Q Consensus 27 peEalYL~-ErG~L~~~~~--------~g~~lSlq~~y~l~~~~~~~~~~~~Y~VY~~Lkr~GYiV~r~ 86 (173)
..|++||+ |+|+..+... -+-..|++|+.+.+..... ..+-..+-..|-+.||++...
T Consensus 12 ~~~~v~l~~e~~~~~l~~~~~~~L~~lLdG~rt~~eI~~~l~~~~p--~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 12 GPEAVFLLSERGSFALSGALYCQLAPLLDGRRTLDEIIAALAGRFP--AEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred CCCeEEEEeCCCcEEEcchhHHHHHHHHcCCCCHHHHHHHhhccCC--HHHHHHHHHHHHHCCCEeccC
Confidence 34556666 8887777521 1337999999999876321 244667778899999999643
No 26
>PF00797 Acetyltransf_2: N-acetyltransferase; InterPro: IPR001447 Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30 kDa. It facilitates the transfer of an acetyl group from acetyl coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (Mycobacterium tuberculosis, Mycobacterium smegmatis etc) to Homo sapiens (Human). It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. NAT catalyses the reaction: Acetyl-coA + arylamine = coA + N-acetylarylamine NAT is the target of a common genetic polymorphism of clinical relevance in humans. The N-acetylation polymorphism is determined by low or high NAT activity in liver. NAT has been implicated in the action and toxicity of amine-containing drugs, and in the susceptibility to cancer and systematic lupus erythematosus. Two highly similar human genes for NAT, termed NAT1 and NAT2, encode genetically invariant and variant NAT proteins, respectively. ; GO: 0016407 acetyltransferase activity, 0008152 metabolic process; PDB: 1W6F_A 1W5R_A 1GX3_D 2PQT_A 2IJA_A 1W4T_A 2BSZ_B 3D9W_B 3LTW_A 3LNB_A ....
Probab=21.15 E-value=25 Score=28.72 Aligned_cols=43 Identities=26% Similarity=0.352 Sum_probs=28.5
Q ss_pred CCcccCHHHHHHHHH-ccCCC-CCcceeeeehhccccCeEEEecC
Q 030702 45 NDLCLPLKEIYEKIA-NEKSG-CSWELFEVYRHLKSLGYIVGRHG 87 (173)
Q Consensus 45 ~g~~lSlq~~y~l~~-~~~~~-~~~~~Y~VY~~Lkr~GYiV~r~~ 87 (173)
...+++++++|+.+. .+.+| |..-.-+-+.-|+.+||-|....
T Consensus 27 ~~~~l~~~~i~~kiv~~~rGG~C~elN~lf~~lL~~lGf~v~~~~ 71 (240)
T PF00797_consen 27 EPISLDPDAIFDKIVRRGRGGYCFELNGLFYWLLRELGFDVTLVS 71 (240)
T ss_dssp -----SHHHHHHHHTTTT--B-HHHHHHHHHHHHHHCT-EEEEEE
T ss_pred CccccCHHHHHHHHHhcCCCeEhHHHHHHHHHHHHHCCCeEEEEE
Confidence 356899999999876 33444 66667788899999999998774
Done!