Query 033533
Match_columns 117
No_of_seqs 146 out of 397
Neff 4.8
Searched_HMMs 29240
Date Mon Mar 25 04:53:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033533.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/033533hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1exk_A DNAJ protein; extended 98.8 3.7E-09 1.3E-13 68.7 4.9 58 51-108 9-76 (79)
2 2ctt_A DNAJ homolog subfamily 98.8 7.9E-09 2.7E-13 70.8 6.0 58 51-108 26-93 (104)
3 1nlt_A Protein YDJ1, mitochond 98.3 4.9E-07 1.7E-11 70.5 3.6 58 51-108 36-108 (248)
4 1exk_A DNAJ protein; extended 98.0 3.9E-06 1.3E-10 54.2 3.7 39 53-98 28-77 (79)
5 2ctt_A DNAJ homolog subfamily 97.8 1.1E-05 3.7E-10 55.0 3.5 39 53-98 45-94 (104)
6 1nlt_A Protein YDJ1, mitochond 97.2 0.00014 4.8E-09 56.5 2.7 41 53-98 54-109 (248)
7 3lcz_A YCZA, inhibitor of trap 97.1 0.00025 8.6E-09 44.0 2.6 28 52-79 8-38 (53)
8 2bx9_A Anti-trap, AT, tryptoph 97.0 0.00037 1.3E-08 43.3 2.6 26 53-78 9-37 (53)
9 3lcz_A YCZA, inhibitor of trap 96.5 0.00071 2.4E-08 41.9 1.1 27 65-98 10-36 (53)
10 2bx9_A Anti-trap, AT, tryptoph 96.4 0.0022 7.5E-08 39.7 2.7 28 64-98 9-36 (53)
11 1k81_A EIF-2-beta, probable tr 60.9 6.5 0.00022 22.0 2.4 33 65-97 1-33 (36)
12 3j20_Y 30S ribosomal protein S 53.4 11 0.00037 22.4 2.7 25 65-92 20-44 (50)
13 2a51_A Nucleocapsid protein; s 43.7 7.4 0.00025 21.5 0.8 12 86-97 22-33 (39)
14 1pft_A TFIIB, PFTFIIBN; N-term 42.8 23 0.00077 20.3 2.9 9 65-73 6-14 (50)
15 2ec7_A GAG polyprotein (PR55GA 42.1 11 0.00038 21.8 1.4 13 86-98 28-40 (49)
16 3nyb_B Protein AIR2; polya RNA 38.7 17 0.00059 23.7 2.1 50 52-101 4-64 (83)
17 1a1t_A Nucleocapsid protein; s 32.2 18 0.00061 21.1 1.2 12 86-97 34-45 (55)
18 2ihx_A Nucleocapsid (NC) prote 29.4 19 0.00066 21.6 1.1 16 86-101 31-48 (61)
19 2d74_B Translation initiation 28.6 19 0.00066 26.1 1.1 31 65-95 105-135 (148)
20 3ts2_A Protein LIN-28 homolog 26.3 26 0.00089 24.8 1.5 37 65-101 98-137 (148)
21 2r6f_A Excinuclease ABC subuni 26.2 28 0.00097 32.0 2.0 11 87-97 755-765 (972)
22 2lli_A Protein AIR2; RNA surve 25.6 30 0.001 23.2 1.6 48 54-101 23-82 (124)
23 1nee_A EIF-2-beta, probable tr 25.3 17 0.00059 26.0 0.3 32 65-96 103-134 (138)
24 3cw2_K Translation initiation 25.0 17 0.0006 25.9 0.3 30 65-94 104-133 (139)
25 3pmq_A Decaheme cytochrome C M 25.0 8.7 0.0003 34.0 -1.6 47 50-96 188-257 (669)
26 2e9h_A EIF-5, eukaryotic trans 24.1 48 0.0016 24.2 2.5 33 65-97 104-138 (157)
27 2g2k_A EIF-5, eukaryotic trans 23.8 42 0.0014 24.8 2.2 33 65-97 97-131 (170)
28 2cqf_A RNA-binding protein LIN 22.7 29 0.001 21.0 1.0 13 86-98 30-42 (63)
29 2qkd_A Zinc finger protein ZPR 22.4 46 0.0016 27.7 2.4 12 64-75 12-23 (404)
30 2vf7_A UVRA2, excinuclease ABC 22.2 38 0.0013 30.5 2.0 20 87-106 640-671 (842)
31 2dj8_A Protein CBFA2T1; zinc f 21.3 73 0.0025 18.8 2.6 22 51-72 13-34 (60)
No 1
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.83 E-value=3.7e-09 Score=68.67 Aligned_cols=58 Identities=28% Similarity=0.599 Sum_probs=47.7
Q ss_pred ccccCCCCCCCcCe------eeCCCCCCCceEEeccCC-cceeeCcccCCccee---eCCCCccceeE
Q 033533 51 EVGIMCESCNGKGW------LVCDFCGGQKTNVKAQNN-RIYRRCPTCRAVGYV---LCSKCKVFKCV 108 (117)
Q Consensus 51 ~~~~~C~~C~G~G~------v~C~~C~GSGkv~~~~g~-~~~~~Cp~C~G~Glv---~Cp~C~G~~~~ 108 (117)
.....|..|+|+|. .+|+.|+|+|+++...+. ....+|+.|+|.|.+ .|+.|.|.+-+
T Consensus 9 ~~~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~G~~ 76 (79)
T 1exk_A 9 PTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRV 76 (79)
T ss_dssp CCEEECGGGTTTSBCSSSCCEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEECSSBCGGGTTSSEE
T ss_pred ccceECCCCcccccCCCccCCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEECCCcCCCCCCeEEE
Confidence 46689999999996 689999999998754343 345799999999999 59999997654
No 2
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=98.80 E-value=7.9e-09 Score=70.84 Aligned_cols=58 Identities=28% Similarity=0.667 Sum_probs=48.5
Q ss_pred ccccCCCCCCCcCe------eeCCCCCCCceEEeccCC-cceeeCcccCCcceee---CCCCccceeE
Q 033533 51 EVGIMCESCNGKGW------LVCDFCGGQKTNVKAQNN-RIYRRCPTCRAVGYVL---CSKCKVFKCV 108 (117)
Q Consensus 51 ~~~~~C~~C~G~G~------v~C~~C~GSGkv~~~~g~-~~~~~Cp~C~G~Glv~---Cp~C~G~~~~ 108 (117)
.+...|..|+|+|. ..|+.|+|+|++....|. ....+|+.|+|.|.++ |+.|.|.+=+
T Consensus 26 ~~~~~C~~C~G~G~~~g~~~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~i~~~C~~C~G~G~v 93 (104)
T 2ctt_A 26 NIMDTCERCNGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSIIISPCVVCRGAGQA 93 (104)
T ss_dssp SCCEECSSSSSSSSCTTCCCEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEECSSCCSSSSSCSEE
T ss_pred eeeeECCCCcCCccCCCCCCccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceECCCcCCCCCCeeEE
Confidence 46789999999984 789999999998655444 3467999999999995 9999997755
No 3
>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5; beta-strands, chaperone, heat shock, mitochondrion; 2.70A {Saccharomyces cerevisiae} SCOP: b.4.1.1 b.4.1.1 g.54.1.1
Probab=98.26 E-value=4.9e-07 Score=70.47 Aligned_cols=58 Identities=28% Similarity=0.709 Sum_probs=46.4
Q ss_pred ccccCCCCCCCcCe-----eeCCCCCCCceEEecc--CC---cceeeCcccCCcceee-----CCCCccceeE
Q 033533 51 EVGIMCESCNGKGW-----LVCDFCGGQKTNVKAQ--NN---RIYRRCPTCRAVGYVL-----CSKCKVFKCV 108 (117)
Q Consensus 51 ~~~~~C~~C~G~G~-----v~C~~C~GSGkv~~~~--g~---~~~~~Cp~C~G~Glv~-----Cp~C~G~~~~ 108 (117)
.+...|..|+|+|. ..|+.|+|+|++.... +. .....|+.|+|.|.++ |+.|.|.+-+
T Consensus 36 ~r~~~C~~C~G~G~~~g~~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~~~~C~~C~G~g~~ 108 (248)
T 1nlt_A 36 NKQILCKECEGRGGKKGAVKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVE 108 (248)
T ss_dssp EEEEECTTTTTCSBSTTTCCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCEE
T ss_pred eEEEeCCCCcCccCCCCCCccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEeccCCCCcccCCCceE
Confidence 45679999999996 7899999999876432 22 3467899999999765 9999997654
No 4
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.03 E-value=3.9e-06 Score=54.15 Aligned_cols=39 Identities=31% Similarity=0.750 Sum_probs=33.4
Q ss_pred ccCCCCCCCcCee-----------eCCCCCCCceEEeccCCcceeeCcccCCcceee
Q 033533 53 GIMCESCNGKGWL-----------VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (117)
Q Consensus 53 ~~~C~~C~G~G~v-----------~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv~ 98 (117)
...|..|+|+|.+ +|+.|+|+|+++ ..+|+.|+|.|.+.
T Consensus 28 ~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~-------~~~C~~C~G~G~~~ 77 (79)
T 1exk_A 28 PQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLI-------KDPCNKCHGHGRVE 77 (79)
T ss_dssp CEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEEC-------SSBCGGGTTSSEEE
T ss_pred CCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEEC-------CCcCCCCCCeEEEe
Confidence 4689999999974 799999999976 34899999999874
No 5
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=97.85 E-value=1.1e-05 Score=54.99 Aligned_cols=39 Identities=31% Similarity=0.747 Sum_probs=33.5
Q ss_pred ccCCCCCCCcCee-----------eCCCCCCCceEEeccCCcceeeCcccCCcceee
Q 033533 53 GIMCESCNGKGWL-----------VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (117)
Q Consensus 53 ~~~C~~C~G~G~v-----------~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv~ 98 (117)
...|..|+|+|.+ +|+.|+|+|+++ ..+|+.|+|.|.+.
T Consensus 45 ~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~i-------~~~C~~C~G~G~v~ 94 (104)
T 2ctt_A 45 VQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSII-------ISPCVVCRGAGQAK 94 (104)
T ss_dssp CEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEEC-------SSCCSSSSSCSEEC
T ss_pred CccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceEC-------CCcCCCCCCeeEEE
Confidence 4689999999963 899999999986 35899999999874
No 6
>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5; beta-strands, chaperone, heat shock, mitochondrion; 2.70A {Saccharomyces cerevisiae} SCOP: b.4.1.1 b.4.1.1 g.54.1.1
Probab=97.23 E-value=0.00014 Score=56.54 Aligned_cols=41 Identities=32% Similarity=0.675 Sum_probs=33.5
Q ss_pred ccCCCCCCCcCe---------------eeCCCCCCCceEEeccCCcceeeCcccCCcceee
Q 033533 53 GIMCESCNGKGW---------------LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (117)
Q Consensus 53 ~~~C~~C~G~G~---------------v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv~ 98 (117)
...|..|+|+|. .+|+.|+|+|+++.. ..+|+.|+|.|.+.
T Consensus 54 ~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~-----~~~C~~C~G~g~~~ 109 (248)
T 1nlt_A 54 VKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDP-----KDRCKSCNGKKVEN 109 (248)
T ss_dssp CCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCT-----TSBCSSSTTSCEEE
T ss_pred CccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEecc-----CCCCcccCCCceEe
Confidence 478999999985 379999999987632 35899999999864
No 7
>3lcz_A YCZA, inhibitor of trap, regulated by T-box (Trp) seque; anti-trap, tryptophan RNA-binding attenuation PROT transcription attenuation; 2.06A {Bacillus licheniformis} PDB: 3ld0_A
Probab=97.13 E-value=0.00025 Score=44.03 Aligned_cols=28 Identities=32% Similarity=0.681 Sum_probs=20.1
Q ss_pred cccCCCCCCCcCe---eeCCCCCCCceEEec
Q 033533 52 VGIMCESCNGKGW---LVCDFCGGQKTNVKA 79 (117)
Q Consensus 52 ~~~~C~~C~G~G~---v~C~~C~GSGkv~~~ 79 (117)
...+|..|+|+|. .+|+.|+|+|.+...
T Consensus 8 ~~~~C~~C~GsG~~i~~~C~~C~G~G~v~~~ 38 (53)
T 3lcz_A 8 LETTCPNCNGSGREEPEPCPKCLGKGVILTA 38 (53)
T ss_dssp HEEECTTTTTSCEETTEECTTTTTSSEEECH
T ss_pred eeccCcCCcccccCCCCcCCCCCCcEEEEEE
Confidence 4567888888887 478888888776543
No 8
>2bx9_A Anti-trap, AT, tryptophan RNA-binding attenuator protein-inhibit protein; transcription regulation; 2.80A {Bacillus subtilis} PDB: 2ko8_A* 2zp8_E* 2zp9_C*
Probab=97.02 E-value=0.00037 Score=43.28 Aligned_cols=26 Identities=23% Similarity=0.634 Sum_probs=16.5
Q ss_pred ccCCCCCCCcCe---eeCCCCCCCceEEe
Q 033533 53 GIMCESCNGKGW---LVCDFCGGQKTNVK 78 (117)
Q Consensus 53 ~~~C~~C~G~G~---v~C~~C~GSGkv~~ 78 (117)
...|+.|+|+|. .+|+.|+|+|++..
T Consensus 9 ~~~C~~C~GsG~~~~~~C~~C~G~G~v~~ 37 (53)
T 2bx9_A 9 EVACPKCERAGEIEGTPCPACSGKGVILT 37 (53)
T ss_dssp EEECTTTTTSSEETTEECTTTTTSSEEEC
T ss_pred cccCCCCcceeccCCCCCccCCCCccEEE
Confidence 346777777776 36666666666654
No 9
>3lcz_A YCZA, inhibitor of trap, regulated by T-box (Trp) seque; anti-trap, tryptophan RNA-binding attenuation PROT transcription attenuation; 2.06A {Bacillus licheniformis} PDB: 3ld0_A
Probab=96.50 E-value=0.00071 Score=41.95 Aligned_cols=27 Identities=30% Similarity=0.730 Sum_probs=21.4
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccCCcceee
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv~ 98 (117)
.+|+.|+|+|++. ..+|+.|+|.|++.
T Consensus 10 ~~C~~C~GsG~~i-------~~~C~~C~G~G~v~ 36 (53)
T 3lcz_A 10 TTCPNCNGSGREE-------PEPCPKCLGKGVIL 36 (53)
T ss_dssp EECTTTTTSCEET-------TEECTTTTTSSEEE
T ss_pred ccCcCCcccccCC-------CCcCCCCCCcEEEE
Confidence 5788999998875 25888888888764
No 10
>2bx9_A Anti-trap, AT, tryptophan RNA-binding attenuator protein-inhibit protein; transcription regulation; 2.80A {Bacillus subtilis} PDB: 2ko8_A* 2zp8_E* 2zp9_C*
Probab=96.37 E-value=0.0022 Score=39.69 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=23.8
Q ss_pred eeeCCCCCCCceEEeccCCcceeeCcccCCcceee
Q 033533 64 WLVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (117)
Q Consensus 64 ~v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv~ 98 (117)
..+|+.|+|+|++. ..+|+.|+|.|+++
T Consensus 9 ~~~C~~C~GsG~~~-------~~~C~~C~G~G~v~ 36 (53)
T 2bx9_A 9 EVACPKCERAGEIE-------GTPCPACSGKGVIL 36 (53)
T ss_dssp EEECTTTTTSSEET-------TEECTTTTTSSEEE
T ss_pred cccCCCCcceeccC-------CCCCccCCCCccEE
Confidence 46999999999974 36899999999875
No 11
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1
Probab=60.87 E-value=6.5 Score=21.95 Aligned_cols=33 Identities=21% Similarity=0.574 Sum_probs=21.5
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccCCccee
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYV 97 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Glv 97 (117)
|.|+.|+..-..+...++....+|..|+..+.+
T Consensus 1 VlC~~C~~peT~l~~~~~~~~l~C~aCG~~~~v 33 (36)
T 1k81_A 1 VICRECGKPDTKIIKEGRVHLLKCMACGAIRPI 33 (36)
T ss_dssp CCCSSSCSCEEEEEEETTEEEEEEETTTEEEEE
T ss_pred CCCcCCCCCCcEEEEeCCcEEEEhhcCCCcccc
Confidence 568888887554444445556778777766544
No 12
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=53.42 E-value=11 Score=22.44 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=10.8
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccC
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCR 92 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~ 92 (117)
..|+.|+. +..+.... .+..|+.|+
T Consensus 20 k~CP~CG~-~~fm~~~~--~R~~C~kCG 44 (50)
T 3j20_Y 20 KFCPRCGP-GVFMADHG--DRWACGKCG 44 (50)
T ss_dssp EECSSSCS-SCEEEECS--SEEECSSSC
T ss_pred ccCCCCCC-ceEEecCC--CeEECCCCC
Confidence 45666633 33332222 134555553
No 13
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=43.75 E-value=7.4 Score=21.45 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=7.0
Q ss_pred eeCcccCCccee
Q 033533 86 RRCPTCRAVGYV 97 (117)
Q Consensus 86 ~~Cp~C~G~Glv 97 (117)
..|..|+..|-+
T Consensus 22 ~~C~~Cg~~GH~ 33 (39)
T 2a51_A 22 EGCWNCGSKEHR 33 (39)
T ss_dssp SSCTTTCCSSSC
T ss_pred CccccCCCCCCc
Confidence 356666666643
No 14
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=42.77 E-value=23 Score=20.29 Aligned_cols=9 Identities=33% Similarity=0.767 Sum_probs=5.5
Q ss_pred eeCCCCCCC
Q 033533 65 LVCDFCGGQ 73 (117)
Q Consensus 65 v~C~~C~GS 73 (117)
+.|+.|++.
T Consensus 6 ~~CP~C~~~ 14 (50)
T 1pft_A 6 KVCPACESA 14 (50)
T ss_dssp CSCTTTSCC
T ss_pred EeCcCCCCc
Confidence 457777654
No 15
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1
Probab=42.06 E-value=11 Score=21.79 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=8.0
Q ss_pred eeCcccCCcceee
Q 033533 86 RRCPTCRAVGYVL 98 (117)
Q Consensus 86 ~~Cp~C~G~Glv~ 98 (117)
..|..|+..|-+.
T Consensus 28 ~~C~~Cg~~GH~~ 40 (49)
T 2ec7_A 28 QGCWKCGKTGHVM 40 (49)
T ss_dssp CSCSSSCCSSCCG
T ss_pred CeeCcCCCcCCcc
Confidence 3577777766543
No 16
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=38.70 E-value=17 Score=23.65 Aligned_cols=50 Identities=16% Similarity=0.245 Sum_probs=25.6
Q ss_pred cccCCCCCCCcCee--------eCCCCCCCceEEeccC-CcceeeCcccCCcceee--CCC
Q 033533 52 VGIMCESCNGKGWL--------VCDFCGGQKTNVKAQN-NRIYRRCPTCRAVGYVL--CSK 101 (117)
Q Consensus 52 ~~~~C~~C~G~G~v--------~C~~C~GSGkv~~~~g-~~~~~~Cp~C~G~Glv~--Cp~ 101 (117)
+.+.|..|+..|.. .|..|...+.+..... ......|..|+..|-+- |+.
T Consensus 4 k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp ---CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSS
T ss_pred ccCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCc
Confidence 45678888888872 5667777765432111 11246799999998764 664
No 17
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Probab=32.22 E-value=18 Score=21.13 Aligned_cols=12 Identities=25% Similarity=0.540 Sum_probs=7.2
Q ss_pred eeCcccCCccee
Q 033533 86 RRCPTCRAVGYV 97 (117)
Q Consensus 86 ~~Cp~C~G~Glv 97 (117)
..|..|+..|-+
T Consensus 34 ~~C~~Cg~~GH~ 45 (55)
T 1a1t_A 34 KGCWKCGKEGHQ 45 (55)
T ss_dssp CBCTTTCCBSSC
T ss_pred CEeCCCCCcCCc
Confidence 356666666643
No 18
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=29.38 E-value=19 Score=21.61 Aligned_cols=16 Identities=38% Similarity=0.926 Sum_probs=10.1
Q ss_pred eeCcccCCcceee--CCC
Q 033533 86 RRCPTCRAVGYVL--CSK 101 (117)
Q Consensus 86 ~~Cp~C~G~Glv~--Cp~ 101 (117)
..|..|+..|-+. |+.
T Consensus 31 ~~C~~Cg~~GH~ar~C~~ 48 (61)
T 2ihx_A 31 ERCQLCNGMGHNAKQCRK 48 (61)
T ss_dssp SBCTTTCCBSSCGGGCCC
T ss_pred CeeCCCCCCCCCcCCCcC
Confidence 4677777777543 543
No 19
>2d74_B Translation initiation factor 2 beta subunit; protein complex; 2.80A {Pyrococcus furiosus} PDB: 2dcu_B*
Probab=28.63 E-value=19 Score=26.05 Aligned_cols=31 Identities=23% Similarity=0.690 Sum_probs=13.9
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccCCcc
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVG 95 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~G 95 (117)
|.|+.|+..-..+..+++....+|..|+...
T Consensus 105 VlC~~C~sPdT~L~k~~r~~~l~C~ACGa~~ 135 (148)
T 2d74_B 105 VICPVCGSPDTKIIKRDRFHFLKCEACGAET 135 (148)
T ss_dssp SSCSSSCCTTCCCCBSSSSBCCCCSSSCCCC
T ss_pred EECCCCCCcCcEEEEeCCEEEEEecCCCCCc
Confidence 5566665553322222333344555554443
No 20
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*
Probab=26.25 E-value=26 Score=24.80 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=20.2
Q ss_pred eeCCCCCCCceEEecc-CCcceeeCcccCCcceee--CCC
Q 033533 65 LVCDFCGGQKTNVKAQ-NNRIYRRCPTCRAVGYVL--CSK 101 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~-g~~~~~~Cp~C~G~Glv~--Cp~ 101 (117)
..|..|...|.+...- .......|..|+..|-+. ||.
T Consensus 98 ~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~ 137 (148)
T 3ts2_A 98 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPL 137 (148)
T ss_dssp CCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTT
T ss_pred CcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcC
Confidence 3466666655543221 111135788888888764 664
No 21
>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, at cassette, DNA damage, DNA excision; HET: ADP; 3.20A {Geobacillus stearothermophilus} PDB: 3uwx_A
Probab=26.24 E-value=28 Score=32.04 Aligned_cols=11 Identities=36% Similarity=1.059 Sum_probs=5.3
Q ss_pred eCcccCCccee
Q 033533 87 RCPTCRAVGYV 97 (117)
Q Consensus 87 ~Cp~C~G~Glv 97 (117)
+|+.|.|.|++
T Consensus 755 rC~~C~g~G~i 765 (972)
T 2r6f_A 755 RCEACHGDGII 765 (972)
T ss_dssp BCTTTTTCSEE
T ss_pred cccccccccce
Confidence 35555555443
No 22
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=25.56 E-value=30 Score=23.21 Aligned_cols=48 Identities=17% Similarity=0.455 Sum_probs=27.6
Q ss_pred cCCCCCCCc-Ce--------eeCCCCCCCceEEecc-CCcceeeCcccCCcceee--CCC
Q 033533 54 IMCESCNGK-GW--------LVCDFCGGQKTNVKAQ-NNRIYRRCPTCRAVGYVL--CSK 101 (117)
Q Consensus 54 ~~C~~C~G~-G~--------v~C~~C~GSGkv~~~~-g~~~~~~Cp~C~G~Glv~--Cp~ 101 (117)
..|-.|+.. |. +.|..|...|.+...- .......|..|+..|-+. ||.
T Consensus 23 ~~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~ 82 (124)
T 2lli_A 23 IICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82 (124)
T ss_dssp CCCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCC
T ss_pred CcCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCC
Confidence 356777766 54 4677777766643211 111135688888877654 654
No 23
>1nee_A EIF-2-beta, probable translation initiation factor 2 beta subunit; two domain protein, mixed alpha-beta structure; NMR {Methanothermobacterthermautotrophicus} SCOP: d.241.1.1 g.59.1.1
Probab=25.30 E-value=17 Score=25.96 Aligned_cols=32 Identities=19% Similarity=0.482 Sum_probs=16.3
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccCCcce
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGY 96 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~Gl 96 (117)
|.|+.|+..-.....+++....+|..|+....
T Consensus 103 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~ 134 (138)
T 1nee_A 103 VICHECNRPDTRIIREGRISLLKCEACGAKAP 134 (138)
T ss_dssp HHHTCCSSCSSCCEEETTTTEEECSTTSCCCC
T ss_pred EECCCCCCcCcEEEEcCCeEEEEccCCCCCcc
Confidence 56666666533222233344556666655443
No 24
>3cw2_K Translation initiation factor 2 subunit beta; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2nxu_A 2qmu_C* 3v11_C*
Probab=25.02 E-value=17 Score=25.95 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=11.2
Q ss_pred eeCCCCCCCceEEeccCCcceeeCcccCCc
Q 033533 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAV 94 (117)
Q Consensus 65 v~C~~C~GSGkv~~~~g~~~~~~Cp~C~G~ 94 (117)
|.|+.|+..-.....+++....+|..|+..
T Consensus 104 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 133 (139)
T 3cw2_K 104 VECSTCKSLDTILKKEKKSWYIVCLACGAQ 133 (139)
T ss_dssp SSCCSSSSSCCCSCSSCSTTTSSCCC----
T ss_pred eECCCCCCcCcEEEEeCCeEEEEecCCCCC
Confidence 555555554332222233334455555443
No 25
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=25.01 E-value=8.7 Score=34.02 Aligned_cols=47 Identities=23% Similarity=0.360 Sum_probs=30.7
Q ss_pred cccccCCCCCCCcCe---------eeCCCCCCCceEEecc------------CC--cceeeCcccCCcce
Q 033533 50 VEVGIMCESCNGKGW---------LVCDFCGGQKTNVKAQ------------NN--RIYRRCPTCRAVGY 96 (117)
Q Consensus 50 ~~~~~~C~~C~G~G~---------v~C~~C~GSGkv~~~~------------g~--~~~~~Cp~C~G~Gl 96 (117)
..+...|..|+|+|. ..|+.|||+....... |. .....|..|...+.
T Consensus 188 v~~~~~C~tCHGsGA~~Gt~~~~~~tC~tCHGs~~~~~~~~~~~~~iH~iH~G~fP~~~~~C~~CH~~~~ 257 (669)
T 3pmq_A 188 LVSIDTCNSCHSNLAFHGGRYNQVETCVTCHNSKKVSNAADIFPQMIHSKHLTGFPQSISNCQTCHADNP 257 (669)
T ss_dssp CCCSHHHHHHHSSCCTTTTTSCSSSCSTTTSSTTTCCCSSCSHHHHHHHHTTSSCSSCTTCCTTTSCCCT
T ss_pred eccCCcCCCCCCCCCcCCccCcCCccCCCCCCCcccCCccccccceeeeeeccCCCCccCcchhhcCCcc
Confidence 356688999988763 5899999994221111 11 12457999988774
No 26
>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=24.05 E-value=48 Score=24.19 Aligned_cols=33 Identities=21% Similarity=0.593 Sum_probs=19.0
Q ss_pred eeCCCCCCCceEEec--cCCcceeeCcccCCccee
Q 033533 65 LVCDFCGGQKTNVKA--QNNRIYRRCPTCRAVGYV 97 (117)
Q Consensus 65 v~C~~C~GSGkv~~~--~g~~~~~~Cp~C~G~Glv 97 (117)
|.|+.|+..-..+.. .++....+|..|+....+
T Consensus 104 VlC~~C~sPdT~L~~~~~~r~~~l~C~ACGa~~~V 138 (157)
T 2e9h_A 104 VLCPECENPETDLHVNPKKQTIGNSCKACGYRGML 138 (157)
T ss_dssp TSCTTTCCSCCEEEEETTTTEEEEECSSSCCEEEC
T ss_pred EECCCCCCCccEEEEecCCCEEEEEccCCCCCCcc
Confidence 677777766444332 344456677777665543
No 27
>2g2k_A EIF-5, eukaryotic translation initiation factor 5; EIF125 fold; NMR {Homo sapiens}
Probab=23.83 E-value=42 Score=24.83 Aligned_cols=33 Identities=21% Similarity=0.593 Sum_probs=20.2
Q ss_pred eeCCCCCCCceEEec--cCCcceeeCcccCCccee
Q 033533 65 LVCDFCGGQKTNVKA--QNNRIYRRCPTCRAVGYV 97 (117)
Q Consensus 65 v~C~~C~GSGkv~~~--~g~~~~~~Cp~C~G~Glv 97 (117)
|.|..|+..-..+.. .+.....+|..|+....+
T Consensus 97 VlC~~C~sPdT~L~k~~~~r~~~l~C~ACGa~~~V 131 (170)
T 2g2k_A 97 VLCPECENPETDLHVNPKKQTIGNSCKACGYRGML 131 (170)
T ss_dssp HSCTTTSSSCEEEEEETTTTEEEEEETTTCCCCCS
T ss_pred EECCCCCCCccEEEEecCCCEEEEEccccCCcccc
Confidence 677777776544433 344556777777765543
No 28
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=22.67 E-value=29 Score=21.01 Aligned_cols=13 Identities=15% Similarity=0.830 Sum_probs=8.4
Q ss_pred eeCcccCCcceee
Q 033533 86 RRCPTCRAVGYVL 98 (117)
Q Consensus 86 ~~Cp~C~G~Glv~ 98 (117)
..|..|...|-+.
T Consensus 30 ~~C~~Cg~~GH~a 42 (63)
T 2cqf_A 30 KKCHFCQSISHMV 42 (63)
T ss_dssp SCCTTTCCSSSCT
T ss_pred CccCCcCCcCCcc
Confidence 4677777777543
No 29
>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix, anti-parrallel beta sheet, double straded anti-parallel beta helix, metal binding protein; 2.00A {Mus musculus}
Probab=22.40 E-value=46 Score=27.70 Aligned_cols=12 Identities=25% Similarity=0.263 Sum_probs=6.4
Q ss_pred eeeCCCCCCCce
Q 033533 64 WLVCDFCGGQKT 75 (117)
Q Consensus 64 ~v~C~~C~GSGk 75 (117)
...|+.|+..|.
T Consensus 12 ~s~Cp~C~~~g~ 23 (404)
T 2qkd_A 12 ESLCMNCYRNGT 23 (404)
T ss_dssp EEECTTTSSEEE
T ss_pred cccCCCCCCCce
Confidence 345666665443
No 30
>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A*
Probab=22.19 E-value=38 Score=30.46 Aligned_cols=20 Identities=35% Similarity=0.971 Sum_probs=0.0
Q ss_pred eCcccCCccee------------eCCCCccce
Q 033533 87 RCPTCRAVGYV------------LCSKCKVFK 106 (117)
Q Consensus 87 ~Cp~C~G~Glv------------~Cp~C~G~~ 106 (117)
+|+.|.|.|++ .|+.|.|.+
T Consensus 640 ~c~~c~g~G~~~~~~~f~~~v~~~c~~c~G~r 671 (842)
T 2vf7_A 640 RCEHCQGEGWVMVELLFLPSVYAPCPVCHGTR 671 (842)
T ss_dssp BCTTTTTCSEEEETTCSSSCEEEECTTTTTCC
T ss_pred ccccccCCCccchhhhcCCccceecccccCcc
No 31
>2dj8_A Protein CBFA2T1; zinc finger MYND domain, protein MTG8, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.85.1.1
Probab=21.32 E-value=73 Score=18.76 Aligned_cols=22 Identities=23% Similarity=0.489 Sum_probs=15.9
Q ss_pred ccccCCCCCCCcCeeeCCCCCC
Q 033533 51 EVGIMCESCNGKGWLVCDFCGG 72 (117)
Q Consensus 51 ~~~~~C~~C~G~G~v~C~~C~G 72 (117)
.....|..|+-.....|..|.-
T Consensus 13 ~~~~~C~~C~~~~~~~Cs~C~~ 34 (60)
T 2dj8_A 13 DSSESCWNCGRKASETCSGCNT 34 (60)
T ss_dssp CCSCCCSSSCSCCCEECTTTSC
T ss_pred CCCcccccCCCCCcccCCCCCC
Confidence 4556788888777778877764
Done!