Query 031450
Match_columns 159
No_of_seqs 58 out of 60
Neff 2.5
Searched_HMMs 29240
Date Mon Mar 25 23:02:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031450.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/031450hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2ljw_A ALR2454 protein; novel 99.9 8.5E-25 2.9E-29 165.7 3.2 44 111-158 1-44 (110)
2 2ahq_A Sigma-54, RNA polymeras 62.5 6.1 0.00021 27.4 3.0 55 89-159 14-70 (76)
3 1nha_A TFIIF-alpha, transcript 30.3 38 0.0013 24.3 2.9 35 83-123 11-45 (82)
4 2kw0_A CCMH protein; oxidoredu 22.6 1E+02 0.0035 22.1 4.0 32 92-126 41-72 (90)
5 1i27_A Transcription factor II 22.0 71 0.0024 22.4 3.0 33 85-123 4-36 (73)
6 2hl7_A Cytochrome C-type bioge 21.8 1E+02 0.0034 21.7 3.7 32 92-126 44-75 (84)
7 1q1v_A DEK protein; winged-hel 21.5 1.7E+02 0.0057 19.6 4.7 42 88-131 9-52 (70)
8 1x9b_A Hypothetical membrane p 20.0 28 0.00097 23.4 0.5 37 97-133 6-44 (53)
9 1dd4_C 50S ribosomal protein L 16.4 75 0.0026 19.6 1.9 15 113-127 18-32 (40)
10 2fki_A Protein YJBR; NESG, GFT 13.8 49 0.0017 23.6 0.5 22 111-132 1-22 (126)
No 1
>2ljw_A ALR2454 protein; novel fold, structural genomics, northeast structural genomi consortium, NESG, PSI-biology, protein structure initiative function; NMR {Nostoc SP}
Probab=99.90 E-value=8.5e-25 Score=165.74 Aligned_cols=44 Identities=41% Similarity=0.770 Sum_probs=42.0
Q ss_pred ccHHHHHHHHHHHhCcccceEEEEEeecCcceeehhhhHhhhhcCCCC
Q 031450 111 FSGLDLATLIRKKYGRSYDVQLIKKEFMGRNLLALNVMWKYMEQGNCE 158 (159)
Q Consensus 111 mtG~EL~~Ll~~KWGrSYDVQL~rrd~~Gk~~l~lQVMWkYLEQ~SFP 158 (159)
|||+||++||++|||+||||||+|+ +++||||||||||||+|||
T Consensus 1 mtG~eL~~ll~~KWG~sYDvql~r~----~~~vylqVMW~yLeQ~SFP 44 (110)
T 2ljw_A 1 MTGQELRQLLLDKWGYSYDVQFRRT----QGKIFLQVMWKYLEQASFP 44 (110)
T ss_dssp CCHHHHHHHHHHHHSSCEEEEEEEE----TTEEEEEEEEEETTSTTCS
T ss_pred CCHHHHHHHHHHHhCCcceeEEEEE----CCEEEEEeehHhhccCCCC
Confidence 7999999999999999999999998 4569999999999999999
No 2
>2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A
Probab=62.51 E-value=6.1 Score=27.42 Aligned_cols=55 Identities=20% Similarity=0.372 Sum_probs=38.2
Q ss_pred CCcchHHHHHhHHHHhcCC--CCCccHHHHHHHHHHHhCcccceEEEEEeecCcceeehhhhHhhhhcCCCCC
Q 031450 89 NGVNSELLRENLERIVGVD--DSTFSGLDLATLIRKKYGRSYDVQLIKKEFMGRNLLALNVMWKYMEQGNCEP 159 (159)
Q Consensus 89 ~g~~~~~~r~~l~r~~g~d--~~~mtG~EL~~Ll~~KWGrSYDVQL~rrd~~Gk~~l~lQVMWkYLEQ~SFP~ 159 (159)
+++.++..+..+..++... ..|||-+.|.++|.++ |. .+-|| -.=||.||-..|+
T Consensus 14 ~~~S~~~Ik~~Ik~lI~~Ed~~kPlSD~~I~~~L~~~-Gi----~IaRR-----------TVaKYRe~l~Ip~ 70 (76)
T 2ahq_A 14 EGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKEK-GF----KVARR-----------TVAKYREMLGIPS 70 (76)
T ss_dssp CSCCHHHHHHHHHHHGGGCCSSSCCCHHHHHHHHTTT-SS----CCCHH-----------HHHHHHHHTC---
T ss_pred ccccHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHc-CC----CccHH-----------HHHHHHHHcCCCc
Confidence 3457788999999999855 7889999999999877 53 34332 2236777766664
No 3
>1nha_A TFIIF-alpha, transcription initiation factor IIF, alpha subunit; transcription factor, human general transcription factor TFIIF, RAP74; NMR {Homo sapiens} SCOP: a.4.5.30 PDB: 1onv_A
Probab=30.27 E-value=38 Score=24.34 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=23.3
Q ss_pred CCCCCCCCcchHHHHHhHHHHhcCCCCCccHHHHHHHHHHH
Q 031450 83 ESPKDENGVNSELLRENLERIVGVDDSTFSGLDLATLIRKK 123 (159)
Q Consensus 83 ~~~~d~~g~~~~~~r~~l~r~~g~d~~~mtG~EL~~Ll~~K 123 (159)
++++.++|++.|..|.-|.|. |||-.||..-+..|
T Consensus 11 ~~~~~~~~iTEe~VRryL~rk------PmTT~dLl~KFK~r 45 (82)
T 1nha_A 11 TPNSGDVQVTEDAVRRYLTRK------PMTTKDLLKKFQTK 45 (82)
T ss_dssp -----CCCCCHHHHHHHHHHS------CBCHHHHHHHTTSS
T ss_pred CCccCCCCCCHHHHHHHHHhC------CccHHHHHHHHHHh
Confidence 345788999999999998863 78888876654443
No 4
>2kw0_A CCMH protein; oxidoreductase, cytochrome C maturation; NMR {Escherichia coli}
Probab=22.56 E-value=1e+02 Score=22.06 Aligned_cols=32 Identities=16% Similarity=0.253 Sum_probs=22.4
Q ss_pred chHHHHHhHHHHhcCCCCCccHHHHHHHHHHHhCc
Q 031450 92 NSELLRENLERIVGVDDSTFSGLDLATLIRKKYGR 126 (159)
Q Consensus 92 ~~~~~r~~l~r~~g~d~~~mtG~EL~~Ll~~KWGr 126 (159)
-...+|..+-+++.. -.|-+|+++.+..|||-
T Consensus 41 iA~dlR~~Vre~l~~---G~Sd~eI~~~mv~RYGd 72 (90)
T 2kw0_A 41 IATDLRQKVYELMQE---GKSKKEIVDYMVARYGN 72 (90)
T ss_dssp HHHHHHHHHHHHHHH---TCCHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHc---CCCHHHHHHHHHHhcCC
Confidence 344456655555543 35789999999999995
No 5
>1i27_A Transcription factor IIF; general transcription factor, RAP74, RAP30, TFIIF, RNA polymerase II, winged-helix domain; 1.02A {Homo sapiens} SCOP: a.4.5.30 PDB: 1j2x_A 2k7l_A*
Probab=21.99 E-value=71 Score=22.43 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=24.7
Q ss_pred CCCCCCcchHHHHHhHHHHhcCCCCCccHHHHHHHHHHH
Q 031450 85 PKDENGVNSELLRENLERIVGVDDSTFSGLDLATLIRKK 123 (159)
Q Consensus 85 ~~d~~g~~~~~~r~~l~r~~g~d~~~mtG~EL~~Ll~~K 123 (159)
++.++|++.|..|.-|.|. |||-.||..-+..|
T Consensus 4 ~~~~~~iTEe~VrryL~rk------PmTt~dLl~KFK~r 36 (73)
T 1i27_A 4 GSGDVQVTEDAVRRYLTRK------PMTTKDLLKKFQTK 36 (73)
T ss_dssp GCCCSSCCHHHHHHHHHHS------CBCHHHHHHTSCHH
T ss_pred cccCCCcCHHHHHHHHHcC------CccHHHHHHHHHHh
Confidence 3567899999999988864 78888887644433
No 6
>2hl7_A Cytochrome C-type biogenesis protein CCMH; three-helices bundle, oxidoreductase; HET: PG4; 1.70A {Pseudomonas aeruginosa}
Probab=21.80 E-value=1e+02 Score=21.66 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=22.7
Q ss_pred chHHHHHhHHHHhcCCCCCccHHHHHHHHHHHhCc
Q 031450 92 NSELLRENLERIVGVDDSTFSGLDLATLIRKKYGR 126 (159)
Q Consensus 92 ~~~~~r~~l~r~~g~d~~~mtG~EL~~Ll~~KWGr 126 (159)
-...+|..+.+++.. -.|-+|+.+.+..|||-
T Consensus 44 iA~dlR~~V~~~l~~---G~sd~eI~~~~v~RYG~ 75 (84)
T 2hl7_A 44 IAADLRKQIYGQLQQ---GKSDGEIVDYMVARYGD 75 (84)
T ss_dssp HHHHHHHHHHHHHHH---TCCHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHc---CCCHHHHHHHHHHhcCC
Confidence 344556666655543 35789999999999995
No 7
>1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1
Probab=21.49 E-value=1.7e+02 Score=19.61 Aligned_cols=42 Identities=14% Similarity=0.350 Sum_probs=34.4
Q ss_pred CCCcchHHHHHhHHHHhc-CCCCCccHHHHHHHHHHHh-CcccceE
Q 031450 88 ENGVNSELLRENLERIVG-VDDSTFSGLDLATLIRKKY-GRSYDVQ 131 (159)
Q Consensus 88 ~~g~~~~~~r~~l~r~~g-~d~~~mtG~EL~~Ll~~KW-GrSYDVQ 131 (159)
.++.+.+.+++.+..+.. .|=+++|-..++..|.+++ | +|+.
T Consensus 9 ~~~Psd~ei~~~I~~IL~~aDL~tvT~K~VR~~Le~~~pg--~dLs 52 (70)
T 1q1v_A 9 KKPPTDEELKETIKKLLASANLEEVTMKQICKKVYENYPT--YDLT 52 (70)
T ss_dssp CCCCCHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHCSS--SCCS
T ss_pred cCCcCHHHHHHHHHHHHHhCCHHHHhHHHHHHHHHHHccC--CCCh
Confidence 356677788888888887 5567899999999999999 7 6665
No 8
>1x9b_A Hypothetical membrane protein TA0354_69_121; alpha protein, structural genomics, protein structure initiative, PSI; NMR {Thermoplasma acidophilum} SCOP: a.10.2.1
Probab=20.01 E-value=28 Score=23.39 Aligned_cols=37 Identities=24% Similarity=0.425 Sum_probs=27.2
Q ss_pred HHhHHHHhcCCCCCccHHHHHHH--HHHHhCcccceEEE
Q 031450 97 RENLERIVGVDDSTFSGLDLATL--IRKKYGRSYDVQLI 133 (159)
Q Consensus 97 r~~l~r~~g~d~~~mtG~EL~~L--l~~KWGrSYDVQL~ 133 (159)
|...|+..+.+...+-..-|..| |-.|.|.+|-.||-
T Consensus 6 ~~~Fe~~InS~SK~~Fv~nL~ELE~is~rlg~~Y~~~Le 44 (53)
T 1x9b_A 6 RAKFESMINSPSKSVFVRNLNELEALAVRLGKSYRIQLD 44 (53)
T ss_dssp HHHHHHHHHSCCHHHHHHHHHHHHHHHHHHCSHHHHHHH
T ss_pred HHHHHHHhCCccHHHHHHhHHHHHHHHHHHchHHHHHHH
Confidence 45677888877666656556554 77899999998874
No 9
>1dd4_C 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix- bundle, five-helix- bundle, alpha-beta structure; HET: TBR; 2.40A {Thermotoga maritima} SCOP: a.108.1.1
Probab=16.39 E-value=75 Score=19.63 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHhCcc
Q 031450 113 GLDLATLIRKKYGRS 127 (159)
Q Consensus 113 G~EL~~Ll~~KWGrS 127 (159)
..||...|.+|||.+
T Consensus 18 ~~eLvk~leekfGVs 32 (40)
T 1dd4_C 18 LAELVKKLEDKFGVT 32 (40)
T ss_dssp HHHHHHHHHHHTCCC
T ss_pred HHHHHHHHHHHHCCC
Confidence 456677788999986
No 10
>2fki_A Protein YJBR; NESG, GFT-alpha-beta, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium; NMR {Escherichia coli} SCOP: d.198.3.1
Probab=13.77 E-value=49 Score=23.64 Aligned_cols=22 Identities=18% Similarity=0.086 Sum_probs=19.5
Q ss_pred ccHHHHHHHHHHHhCcccceEE
Q 031450 111 FSGLDLATLIRKKYGRSYDVQL 132 (159)
Q Consensus 111 mtG~EL~~Ll~~KWGrSYDVQL 132 (159)
||-+||++++..++|...++.+
T Consensus 1 M~~~~l~~~~l~lpg~~e~~p~ 22 (126)
T 2fki_A 1 MTISELLQYCMAKPGAEQSVHN 22 (126)
T ss_dssp CCHHHHHHHHTTSTTCEEEEET
T ss_pred CCHHHHHHHHHhCCCCEeEcCC
Confidence 7889999999999999988775
Done!