Query 040088
Match_columns 131
No_of_seqs 112 out of 241
Neff 3.9
Searched_HMMs 29240
Date Mon Mar 25 07:29:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040088.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/040088hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3iz5_b 60S ribosomal protein L 100.0 1.2E-41 4.2E-46 259.4 0.2 111 1-130 1-119 (147)
2 4a18_O RPL28, ribosomal protei 100.0 8.2E-35 2.8E-39 219.3 1.0 101 4-130 1-107 (134)
3 2qsb_A UPF0147 protein TA0600; 14.1 90 0.0031 21.7 2.0 29 101-129 27-55 (89)
4 2qzg_A Conserved uncharacteriz 13.3 90 0.0031 21.9 1.8 29 101-129 31-59 (94)
5 1ygt_A Cytoplasmic dynein ligh 11.9 2.7E+02 0.0091 18.8 3.9 41 17-57 64-110 (111)
6 1uxc_A FRUR (1-57), fructose r 9.7 98 0.0034 19.2 0.9 21 108-128 33-53 (65)
7 2o3b_B Endonuclease, sugar-non 8.9 1.6E+02 0.0056 21.6 2.0 17 33-49 99-115 (136)
8 3ujm_A Rasputin; NTF2-like fol 7.5 4E+02 0.014 17.9 3.5 34 67-100 65-99 (120)
9 1xdx_A Tctex1 light chain prot 6.9 2.6E+02 0.0089 18.9 2.2 41 17-57 67-113 (114)
10 2l8n_A Transcriptional repress 6.0 1.9E+02 0.0066 17.9 1.0 21 108-128 39-59 (67)
No 1
>3iz5_b 60S ribosomal protein L28 (L28E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 3izr_b
Probab=100.00 E-value=1.2e-41 Score=259.36 Aligned_cols=111 Identities=58% Similarity=0.893 Sum_probs=59.0
Q ss_pred CCCCCccceEEEEecCceeEEeecCC-----C-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEe
Q 040088 1 MATVGGQLIWEIVKKNNCFLVKEFGR-----G-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQP 74 (131)
Q Consensus 1 m~~~S~dL~W~iVrnnnsFLvK~~g~-----~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~ 74 (131)
|++||+||||||||+|||||+|+++. . |.||+||+|+|||+|+| |+| .|+|||+|
T Consensus 1 M~~mS~dL~W~iir~nn~FlvKr~~~~~~~~~FSrep~NL~n~~S~kysG------------Lan-------~K~v~V~~ 61 (147)
T 3iz5_b 1 MATVPEPLIWEIVKKNNCFLVKQFGNSNAKVQFTKEPNNLYNVHSYKHSG------------LAN-------KKTVTIQP 61 (147)
T ss_dssp ---------------------------------------------------------------------------CCSSS
T ss_pred CCCCccccchhhccCcceEEEEecCCCCccceecCCCCCccccccccccc------------ccc-------cceeEEEe
Confidence 89999999999999999999999863 2 66789999999999999 999 99999999
Q ss_pred C--CCCeEEEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088 75 G--KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV 130 (131)
Q Consensus 75 ~--~~~gVvl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA 130 (131)
+ +++||+|+||+.+.+++|++++.+++|++++|+++++|++++++++|||||+.+|
T Consensus 62 ~~~~~~gv~l~~Kk~~~~~kPak~~~~~~l~k~~Rk~l~~I~~~v~~~~YR~DL~~~A 119 (147)
T 3iz5_b 62 SGVKDAAVVLSTTKTKKQNAPAKLYHKSVMRKEFRKMAKAVKNQVSDNYYRPDLTKPA 119 (147)
T ss_dssp CCCCCCCSSSCEECCCCCTTTTCCCCEECCCSHHHHHHHHHHHHTSCCTHHHHHTTHH
T ss_pred cccCCCEEEEEEeccccCCCCccceEEEeecccHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence 5 7899999999999999999999999999999999999999999999999999987
No 2
>4a18_O RPL28, ribosomal protein L22; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_O 4a1b_O 4a1d_O
Probab=100.00 E-value=8.2e-35 Score=219.35 Aligned_cols=101 Identities=33% Similarity=0.473 Sum_probs=94.6
Q ss_pred CCccceEEEEecCceeEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEEE
Q 040088 4 VGGQLIWEIVKKNNCFLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVL 82 (131)
Q Consensus 4 ~S~dL~W~iVrnnnsFLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVvl 82 (131)
|| ||||||||+|||||+|++|.. |.||+||+|+|||+|+| |+| .|+|||+|++++| |
T Consensus 1 MS-dL~W~ivrnnnsFLvKr~g~~FS~eP~NL~n~~S~kysG------------Lan-------~KavgV~~~~~gg--v 58 (134)
T 4a18_O 1 MS-QLVWEIVKNNNAFLVKNNGVAFTTDPFSVTGRNTQVGLG------------FTH-------RHGVALKGGAKQA--I 58 (134)
T ss_dssp CH-HHHHHHHTTTCTTEEEETTEEEECCTTCSSSBCSTTTCT------------TTS-------SCCEEEEEEGGGE--E
T ss_pred Cc-ceeehhhcCcceEEEeeCCccccCCCCCccceecccccc------------ccc-------cceeEEEEcCCCc--E
Confidence 67 999999999999999999766 88999999999999999 999 9999999976667 8
Q ss_pred EEeccCCCCCCc----ceeeee-eeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088 83 ATTKTKKQNKPI----ALLHKS-VMKHEIHRMAKVIANRVGDNYYQPDLKNAV 130 (131)
Q Consensus 83 ~tkk~k~~~kPa----k~~~~~-~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA 130 (131)
+|++++.+++|+ +++.++ ++++++|+++++|+++++++ ||+++|
T Consensus 59 ~~Kk~k~~~kPa~~~~k~~~~~~~~~k~~Rk~~k~I~~~~~~~----DL~~aA 107 (134)
T 4a18_O 59 ATSLRKNQSHKVKKTGTIEAETLTVKGGVQRVAKVIRGRFQSK----GLKQFA 107 (134)
T ss_dssp EEEEECCCCCCSSCCSCSSEEEEEESSTHHHHHHHHHHHCCSH----HHHHHH
T ss_pred EEecCcccCCCCccccceeEEEeccccchHHHHHHHHHHHhhc----hHHHHH
Confidence 899999999999 999999 99999999999999999974 999987
No 3
>2qsb_A UPF0147 protein TA0600; structural genomics, four-helix bundle, PSI-2, protein structure initiative; HET: MSE; 1.30A {Thermoplasma acidophilum dsm 1728} SCOP: a.29.14.1
Probab=14.15 E-value=90 Score=21.73 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=24.9
Q ss_pred eeccchhHHHHHHHHHhcCCCCChhhhhh
Q 040088 101 VMKHEIHRMAKVIANRVGDNYYQPDLKNA 129 (131)
Q Consensus 101 ~~k~~~Rr~~k~I~~~v~~n~YRpDL~~a 129 (131)
++..+.||++......+.+.++.|+++.+
T Consensus 27 sVPRNIRraA~ea~~~L~~e~~~~~vRAA 55 (89)
T 2qsb_A 27 TVPKNVRKVAQDSKAKLSQENESLDLRCA 55 (89)
T ss_dssp TSCHHHHHHHHHHHHHHTCTTSCHHHHHH
T ss_pred CCChHHHHHHHHHHHHHhCCCcchhHHHH
Confidence 44568999999999999888999999876
No 4
>2qzg_A Conserved uncharacterized archaeal protein; unknown function protein, structu genomics, PSI-2, protein structure initiative; 2.09A {Methanococcus maripaludis S2} SCOP: a.29.14.1
Probab=13.33 E-value=90 Score=21.92 Aligned_cols=29 Identities=14% Similarity=0.129 Sum_probs=24.9
Q ss_pred eeccchhHHHHHHHHHhcCCCCChhhhhh
Q 040088 101 VMKHEIHRMAKVIANRVGDNYYQPDLKNA 129 (131)
Q Consensus 101 ~~k~~~Rr~~k~I~~~v~~n~YRpDL~~a 129 (131)
++..+.||++......+.+.++.|+++.+
T Consensus 31 sVPRNIRraA~ea~~~L~~e~~~~~vRAA 59 (94)
T 2qzg_A 31 TVPRNIRAAADNAKNALHNEEQELIVRSA 59 (94)
T ss_dssp TSCHHHHHHHHHHHHHTTCTTSCHHHHHH
T ss_pred CCChHHHHHHHHHHHHHhCCCcchhHHHH
Confidence 44568999999999999888999999876
No 5
>1ygt_A Cytoplasmic dynein light chain; domain swapping, protein transport; 1.70A {Drosophila melanogaster} PDB: 2pg1_E 3fm7_A
Probab=11.94 E-value=2.7e+02 Score=18.75 Aligned_cols=41 Identities=20% Similarity=0.403 Sum_probs=30.5
Q ss_pred ceeEEeecCCC--ccCc----Cccceeeeeeecccccccccceecee
Q 040088 17 NCFLVKEFGRG--SASA----HAVITCSVYKFGGRKIECSTFVFGRF 57 (131)
Q Consensus 17 nsFLvK~~g~~--s~s~----~NL~n~~s~KysG~~~~~~~~~~~~l 57 (131)
+|.|.-++|.| ..+. .+--+.-+++|...+.-|...+||..
T Consensus 64 ~v~I~q~~gqG~~~as~c~WD~~~D~~~s~~~~n~sl~~v~tVfgv~ 110 (111)
T 1ygt_A 64 TAMIMQKNGAGLHTASSCYWNNDTDGSCTVRWENKTMYCIVSVFGLA 110 (111)
T ss_dssp EEEEEECSSCCCCCCCCCCSCTTTCEEEEEEEECSSEEEEEEEEEEE
T ss_pred EEEEEEcCCCceeeeeeeEEcCCCCCeEEEEEECCCEEEEEEEEEEE
Confidence 56676666766 3443 36778889999998888888888865
No 6
>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A
Probab=9.70 E-value=98 Score=19.21 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=12.0
Q ss_pred HHHHHHHHHhcCCCCChhhhh
Q 040088 108 RMAKVIANRVGDNYYQPDLKN 128 (131)
Q Consensus 108 r~~k~I~~~v~~n~YRpDL~~ 128 (131)
.+...|...+..-+|+||...
T Consensus 33 et~~rI~~aa~~lgY~pn~~a 53 (65)
T 1uxc_A 33 KTVEKVMAVVREHNYHPNAVA 53 (65)
T ss_dssp HHHHHHHHHHHHHTCCCC---
T ss_pred HHHHHHHHHHHHhCCCccHHH
Confidence 344556666666679998754
No 7
>2o3b_B Endonuclease, sugar-non-specific nuclease inhibitor; metal complex, non-specific NU hydrolase-hydrolase inhibitor complex; HET: MES; 2.30A {Nostoc SP} SCOP: d.221.1.1 PDB: 1j57_A 1ktu_A
Probab=8.94 E-value=1.6e+02 Score=21.57 Aligned_cols=17 Identities=18% Similarity=0.460 Sum_probs=13.0
Q ss_pred ccceeeeeeeccccccc
Q 040088 33 AVITCSVYKFGGRKIEC 49 (131)
Q Consensus 33 NL~n~~s~KysG~~~~~ 49 (131)
||++++.|+.++..+++
T Consensus 99 ~l~evkVYRVg~~~ve~ 115 (136)
T 2o3b_B 99 NLKNPQVYRLGEVELDV 115 (136)
T ss_dssp HSEEEEEEEESSSEEEE
T ss_pred hcccceEEEECCEEEEE
Confidence 89999999996644433
No 8
>3ujm_A Rasputin; NTF2-like fold, RAS signaling, signaling protein; HET: EPE; 2.74A {Drosophila melanogaster}
Probab=7.52 E-value=4e+02 Score=17.93 Aligned_cols=34 Identities=18% Similarity=0.248 Sum_probs=19.6
Q ss_pred cceEEEEeCCCCe-EEEEEeccCCCCCCcceeeee
Q 040088 67 LKTVTIQPGKDQV-VVLATTKTKKQNKPIALLHKS 100 (131)
Q Consensus 67 ~KaV~V~~~~~~g-Vvl~tkk~k~~~kPak~~~~~ 100 (131)
-.+++.||..++| +++++-.-+....|...+..+
T Consensus 65 I~t~D~Qp~~~~gili~V~G~l~~~~~~~r~F~Qt 99 (120)
T 3ujm_A 65 ISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQT 99 (120)
T ss_dssp EEEEEEEEEGGGEEEEEEEEEEESTTCCCEEEEEE
T ss_pred EecccceEcCCCCEEEEEEEEEEeCCCCCceEEEE
Confidence 3579999943444 455554444444566556543
No 9
>1xdx_A Tctex1 light chain protein; chlamydomonas flagella, tctex1 dimer, solution structure, contractIle protein; NMR {Chlamydomonas reinhardtii}
Probab=6.89 E-value=2.6e+02 Score=18.90 Aligned_cols=41 Identities=20% Similarity=0.472 Sum_probs=29.3
Q ss_pred ceeEEeecCCC--ccCc----Cccceeeeeeecccccccccceecee
Q 040088 17 NCFLVKEFGRG--SASA----HAVITCSVYKFGGRKIECSTFVFGRF 57 (131)
Q Consensus 17 nsFLvK~~g~~--s~s~----~NL~n~~s~KysG~~~~~~~~~~~~l 57 (131)
+|.|.-++|.| ..+. .+--+.-+++|...+.-|...+||..
T Consensus 67 ~v~I~q~~gqGi~~as~c~WD~~~D~~~s~~~~n~sl~~v~tVfgv~ 113 (114)
T 1xdx_A 67 TCIIMQKNGAGLHTAASCWWDSTTDGSRTVRWENKSMYCICTVFGLA 113 (114)
T ss_dssp EEEEECTTTSCCEEEEEECSCSSSCCCEEEEEESSSCEEEEEEEEEC
T ss_pred EEEEEEcCCCceeeeeeeeEcCCCCCEEEEEEECCCEEEEEEEEEEE
Confidence 45666666666 3332 36678889999998888888888864
No 10
>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A
Probab=5.99 E-value=1.9e+02 Score=17.90 Aligned_cols=21 Identities=10% Similarity=0.118 Sum_probs=10.6
Q ss_pred HHHHHHHHHhcCCCCChhhhh
Q 040088 108 RMAKVIANRVGDNYYQPDLKN 128 (131)
Q Consensus 108 r~~k~I~~~v~~n~YRpDL~~ 128 (131)
.+...|...+..-+|+||...
T Consensus 39 ~t~~rV~~~a~~lgY~pn~~a 59 (67)
T 2l8n_A 39 ATRNRVEKAAREVGYLPQPMG 59 (67)
T ss_dssp HHHHHHHHHHHHHCCCC----
T ss_pred HHHHHHHHHHHHhCCCccHHH
Confidence 344455555666679998643
Done!