Query 042337
Match_columns 236
No_of_seqs 120 out of 142
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 08:45:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042337.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042337hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2nud_C RIN4, RPM1-interacting 99.7 4.2E-19 1.4E-23 116.5 -0.1 35 163-197 1-35 (35)
2 2nud_C RIN4, RPM1-interacting 98.5 1.1E-08 3.8E-13 67.1 -0.2 30 17-46 3-35 (35)
3 3ik5_A Protein NEF; protein-pr 21.8 19 0.00064 29.8 -0.1 8 229-236 76-83 (143)
4 3rea_A Protein NEF; HIV-1 NEF, 18.9 23 0.0008 29.9 -0.1 8 229-236 96-103 (166)
5 1ac0_A Glucoamylase; hydrolase 13.1 70 0.0024 23.5 1.3 16 19-34 27-42 (108)
6 4en2_B Protein NEF; human immu 13.1 41 0.0014 29.3 -0.1 8 229-236 136-143 (206)
7 3ktw_A SRP19, signal recogniti 8.0 1.4E+02 0.0049 23.3 1.4 29 31-63 18-47 (109)
8 3sbu_A Hypothetical NTF2-like 7.2 75 0.0025 28.6 -0.7 33 173-205 77-110 (261)
9 2lk0_A RNA-binding protein 5; 7.0 94 0.0032 18.9 -0.1 8 22-29 1-8 (32)
10 1dev_B SMAD anchor for recepto 6.3 1.2E+02 0.0043 20.0 0.2 9 51-59 4-12 (41)
No 1
>2nud_C RIN4, RPM1-interacting protein 4; AVRB RIN4 high-affinity toxin/protein binding complex; 2.30A {Pseudomonas syringae PV}
Probab=99.72 E-value=4.2e-19 Score=116.50 Aligned_cols=35 Identities=66% Similarity=1.216 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCceehhHHHHHHH
Q 042337 163 TDHTAAVPEFGDWDEPDPTSADGYTYIFNQVREER 197 (236)
Q Consensus 163 ~~~~~~vPkFG~WD~~np~s~~~yT~iF~k~reek 197 (236)
++++++|||||+||++||+++++|||||+||||||
T Consensus 1 ~~~~~~vPkFG~WD~~n~~s~~~yT~iF~k~re~K 35 (35)
T 2nud_C 1 PEKVTVVPKFGDWDENNPSSADGYTHIFNKVREER 35 (35)
T ss_dssp --------CCSGGGTTCTTCCCSSCEEEECC----
T ss_pred CCCCCCCCCCCcccCCCCCCCCCEeehhhhhhhcC
Confidence 35789999999999999999999999999999997
No 2
>2nud_C RIN4, RPM1-interacting protein 4; AVRB RIN4 high-affinity toxin/protein binding complex; 2.30A {Pseudomonas syringae PV}
Probab=98.51 E-value=1.1e-08 Score=67.08 Aligned_cols=30 Identities=33% Similarity=0.795 Sum_probs=16.9
Q ss_pred cCCCCCCCCCCCCCC---CcccchhhhHHHhhc
Q 042337 17 RYNHVPKFGNWETEE---HVPYSLYFDEARKRR 46 (236)
Q Consensus 17 ~~~~vPkFG~w~~~~---~~pyT~~fe~ar~~k 46 (236)
+..+|||||+||..+ ...||.+|++||..|
T Consensus 3 ~~~~vPkFG~WD~~n~~s~~~yT~iF~k~re~K 35 (35)
T 2nud_C 3 KVTVVPKFGDWDENNPSSADGYTHIFNKVREER 35 (35)
T ss_dssp ------CCSGGGTTCTTCCCSSCEEEECC----
T ss_pred CCCCCCCCCcccCCCCCCCCCEeehhhhhhhcC
Confidence 337899999999743 247999999999876
No 3
>3ik5_A Protein NEF; protein-protein complex, cell membrane, lipoprotein, membran myristate; 2.05A {Simian immunodeficiency virus} SCOP: d.102.1.0 PDB: 3ioz_A
Probab=21.76 E-value=19 Score=29.81 Aligned_cols=8 Identities=25% Similarity=0.347 Sum_probs=5.9
Q ss_pred eeeccCCC
Q 042337 229 CCCFPVPW 236 (236)
Q Consensus 229 ccCF~w~~ 236 (236)
=-||||||
T Consensus 76 PltFGWcf 83 (143)
T 3ik5_A 76 PKTFGWLW 83 (143)
T ss_dssp BSSTTCCE
T ss_pred cccCceeE
Confidence 34788887
No 4
>3rea_A Protein NEF; HIV-1 NEF, SH3 domain binding, signaling, HCK SH3 domain, PR binding; 2.00A {Hiv-1 M} SCOP: d.102.1.1 PDB: 3rbb_A 3reb_A 1efn_B 1avv_A 1avz_A 2nef_A
Probab=18.95 E-value=23 Score=29.86 Aligned_cols=8 Identities=13% Similarity=-0.073 Sum_probs=5.9
Q ss_pred eeeccCCC
Q 042337 229 CCCFPVPW 236 (236)
Q Consensus 229 ccCF~w~~ 236 (236)
=-||||||
T Consensus 96 PltFGWcf 103 (166)
T 3rea_A 96 PLTFGWCF 103 (166)
T ss_dssp BSSTTCCE
T ss_pred ccccceee
Confidence 34788887
No 5
>1ac0_A Glucoamylase; hydrolase, starch binding domain; HET: GLC BGC GLO; NMR {Aspergillus niger} SCOP: b.3.1.1 PDB: 1acz_A* 1kul_A 1kum_A
Probab=13.08 E-value=70 Score=23.55 Aligned_cols=16 Identities=25% Similarity=0.858 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCCcc
Q 042337 19 NHVPKFGNWETEEHVP 34 (236)
Q Consensus 19 ~~vPkFG~w~~~~~~p 34 (236)
+.+|.||+|+....++
T Consensus 27 Gs~~~LG~W~~~~a~~ 42 (108)
T 1ac0_A 27 GSISQLGDWETSDGIA 42 (108)
T ss_dssp CSSSTTCSSSGGGSCC
T ss_pred eCcHHHCCCCHHHCcc
Confidence 5689999999644443
No 6
>4en2_B Protein NEF; human immunodeficiency virus 1, HIV, NEF, antigen presentation, HOST defense, adaptor protein complex 1, MU1 subunit; 2.58A {Human immunodeficiency virus 1} PDB: 4emz_C 3tb8_A 2xi1_A 2xi1_B 1qa5_A* 1qa4_A 1zec_A
Probab=13.08 E-value=41 Score=29.27 Aligned_cols=8 Identities=13% Similarity=-0.052 Sum_probs=5.7
Q ss_pred eeeccCCC
Q 042337 229 CCCFPVPW 236 (236)
Q Consensus 229 ccCF~w~~ 236 (236)
==||+|||
T Consensus 136 PltFGWcf 143 (206)
T 4en2_B 136 PLTFGWCY 143 (206)
T ss_dssp BSSTTCCE
T ss_pred ccccceee
Confidence 34788887
No 7
>3ktw_A SRP19, signal recognition particle 19 kDa protein; ribonucleoprotein complex, RNA-RNA tertiary interactions, AS loop, 7S RNA; 3.20A {Sulfolobus solfataricus}
Probab=8.01 E-value=1.4e+02 Score=23.32 Aligned_cols=29 Identities=17% Similarity=0.163 Sum_probs=21.0
Q ss_pred CCcccchhhhHHHhhcccCC-CCCCCCCCCcccc
Q 042337 31 EHVPYSLYFDEARKRRNAAK-INPNDTHENQNTI 63 (236)
Q Consensus 31 ~~~pyT~~fe~ar~~k~~~~-iNPNDP~eNPe~~ 63 (236)
.-+-|-+|||. +.++.|+ |.=+ .+||.+.
T Consensus 18 ~ivIyP~Y~Ds--~sr~eGRRVpk~--V~nP~~~ 47 (109)
T 3ktw_A 18 RIVIWPSYFFS--PTRSKGRRLARI--PYKIKTE 47 (109)
T ss_dssp EEEECTHHHHC--SSGGGTCCSSCC--SSCCCHH
T ss_pred eEEEeecccCC--cchhcCCccccc--CCCCCHH
Confidence 35679999999 5666666 5544 8888776
No 8
>3sbu_A Hypothetical NTF2-like protein; cystatin-like, structural genomics, joint center for structu genomics, JCSG, protein structure initiative; HET: MLY; 2.15A {Bacteroides fragilis}
Probab=7.19 E-value=75 Score=28.56 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=22.3
Q ss_pred CCCCCCCCCC-CCCceehhHHHHHHHhcCCCCCC
Q 042337 173 GDWDEPDPTS-ADGYTYIFNQVREERLKGTGNVA 205 (236)
Q Consensus 173 G~WD~~np~s-~~~yT~iF~k~reekk~~~~~~p 205 (236)
..|--..==. -+=||+||++.++++...-+.+-
T Consensus 77 ~~Wk~d~fF~~Q~yYTliFD~e~qM~~~KdT~l~ 110 (261)
T 3sbu_A 77 XYWXHDDLFAXQSYYTLLFDREEDMDLVGDTSLT 110 (261)
T ss_dssp GGCCCCCTTTTSSEEEEEESSGGGGGGGGCTTCS
T ss_pred hhcccccceeccceEEEEEcCHHHhhhhcCCccc
Confidence 4565443322 34589999999999988765444
No 9
>2lk0_A RNA-binding protein 5; zinc finger; NMR {Homo sapiens} PDB: 2lk1_A*
Probab=6.99 E-value=94 Score=18.86 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=4.6
Q ss_pred CCCCCCCC
Q 042337 22 PKFGNWET 29 (236)
Q Consensus 22 PkFG~w~~ 29 (236)
||.|||.-
T Consensus 1 pk~gDW~C 8 (32)
T 2lk0_A 1 XKFEDWLC 8 (32)
T ss_dssp -CCSEEEC
T ss_pred CCCCCCCc
Confidence 56677765
No 10
>1dev_B SMAD anchor for receptor activation; beta sheet, three-helix bundle, signaling protein; 2.20A {Homo sapiens} SCOP: j.64.1.1 PDB: 1mk2_B
Probab=6.33 E-value=1.2e+02 Score=20.03 Aligned_cols=9 Identities=44% Similarity=0.604 Sum_probs=6.5
Q ss_pred CCCCCCCCC
Q 042337 51 INPNDTHEN 59 (236)
Q Consensus 51 iNPNDP~eN 59 (236)
-|||+|.|-
T Consensus 4 PNPNnPmEY 12 (41)
T 1dev_B 4 PNPNNPAEY 12 (41)
T ss_dssp CCTTCGGGT
T ss_pred CCCCCcchh
Confidence 488888753
Done!