Query 032984
Match_columns 129
No_of_seqs 140 out of 405
Neff 4.6
Searched_HMMs 29240
Date Mon Mar 25 13:31:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032984.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032984hhsearch_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 3.5E-09 1.2E-13 70.0 5.1 57 52-108 10-76 (79)
2 2ctt_A DNAJ homolog subfamily 98.8 8.2E-09 2.8E-13 72.0 6.1 57 52-108 27-93 (104)
3 1nlt_A Protein YDJ1, mitochond 98.3 3.6E-07 1.2E-11 72.6 3.8 56 52-107 37-107 (248)
4 1exk_A DNAJ protein; extended 98.0 4.4E-06 1.5E-10 54.9 3.8 39 53-98 28-77 (79)
5 2ctt_A DNAJ homolog subfamily 97.9 1E-05 3.5E-10 56.2 3.7 39 53-98 45-94 (104)
6 1nlt_A Protein YDJ1, mitochond 97.2 0.00013 4.4E-09 57.8 2.7 41 53-98 54-109 (248)
7 3lcz_A YCZA, inhibitor of trap 97.0 0.00035 1.2E-08 44.2 2.6 26 53-78 9-37 (53)
8 2bx9_A Anti-trap, AT, tryptoph 96.9 0.0005 1.7E-08 43.5 2.6 26 53-78 9-37 (53)
9 2bx9_A Anti-trap, AT, tryptoph 96.2 0.0034 1.2E-07 39.6 2.8 28 64-98 9-36 (53)
10 3lcz_A YCZA, inhibitor of trap 96.1 0.0025 8.5E-08 40.2 1.9 27 65-98 10-36 (53)
11 1k81_A EIF-2-beta, probable tr 62.4 6.6 0.00022 22.4 2.7 33 65-97 1-33 (36)
12 2a51_A Nucleocapsid protein; s 49.5 5.6 0.00019 22.5 0.9 32 66-97 2-33 (39)
13 2ec7_A GAG polyprotein (PR55GA 48.6 7.7 0.00026 23.0 1.5 13 86-98 28-40 (49)
14 3j20_Y 30S ribosomal protein S 47.2 15 0.00053 22.2 2.7 6 66-71 21-26 (50)
15 2fiy_A Protein FDHE homolog; F 44.8 15 0.00052 29.9 3.1 17 98-114 255-271 (309)
16 1pft_A TFIIB, PFTFIIBN; N-term 39.5 27 0.00092 20.4 2.9 9 65-73 6-14 (50)
17 1a1t_A Nucleocapsid protein; s 38.5 12 0.00043 22.3 1.3 12 86-97 34-45 (55)
18 3nyb_B Protein AIR2; polya RNA 37.5 18 0.00063 24.0 2.1 51 52-102 4-65 (83)
19 2ihx_A Nucleocapsid (NC) prote 36.5 13 0.00043 22.9 1.1 16 86-101 31-48 (61)
20 3ts2_A Protein LIN-28 homolog 34.3 16 0.00055 26.5 1.5 37 65-101 98-137 (148)
21 1qo8_A Flavocytochrome C3 fuma 34.0 4.8 0.00016 34.0 -1.6 65 55-119 14-110 (566)
22 2fiy_A Protein FDHE homolog; F 30.7 50 0.0017 26.8 4.1 51 65-115 183-241 (309)
23 2d74_B Translation initiation 30.5 18 0.0006 26.8 1.2 30 65-94 105-134 (148)
24 2cqf_A RNA-binding protein LIN 28.8 21 0.00071 22.2 1.2 13 86-98 30-42 (63)
25 2g2k_A EIF-5, eukaryotic trans 26.6 37 0.0013 25.7 2.4 33 65-97 97-131 (170)
26 2e9h_A EIF-5, eukaryotic trans 26.2 43 0.0015 24.9 2.7 33 65-97 104-138 (157)
27 3cw2_K Translation initiation 25.7 16 0.00056 26.6 0.3 9 65-73 104-112 (139)
28 2lli_A Protein AIR2; RNA surve 25.7 32 0.0011 23.5 1.8 47 55-101 24-82 (124)
29 3pmq_A Decaheme cytochrome C M 25.5 9.1 0.00031 34.6 -1.3 46 51-96 189-257 (669)
30 1nee_A EIF-2-beta, probable tr 25.4 16 0.00056 26.6 0.2 31 65-95 103-133 (138)
31 2r6f_A Excinuclease ABC subuni 25.0 30 0.001 32.6 1.9 20 87-106 755-786 (972)
32 2vf7_A UVRA2, excinuclease ABC 24.6 36 0.0012 31.2 2.3 8 99-106 664-671 (842)
33 2bl6_A Nucleocapsid protein P1 22.6 23 0.00077 19.5 0.4 11 86-96 20-30 (37)
No 1
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.84 E-value=3.5e-09 Score=69.99 Aligned_cols=57 Identities=28% Similarity=0.612 Sum_probs=47.2
Q ss_pred ccccCCCCCCcCe------eeCCCCCCCceEEeccCC-ceeeeCcccccccee---eCCCCccceeE
Q 032984 52 VGIMCESCNGKGW------LVCDFCGGQKTNVKAQNN-RIYRRCPTCRAVGYV---LCSKCKVFKCV 108 (129)
Q Consensus 52 ~~~~C~~C~G~G~------v~C~~C~GSG~v~~~~g~-~~~~rC~~CnG~Glv---~Cp~C~G~~~v 108 (129)
....|+.|+|+|. .+|+.|+|+|+++...+. ....+|+.|+|.|.+ .|+.|.|.+.+
T Consensus 10 ~~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~G~~ 76 (79)
T 1exk_A 10 TLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRV 76 (79)
T ss_dssp CEEECGGGTTTSBCSSSCCEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEECSSBCGGGTTSSEE
T ss_pred cceECCCCcccccCCCccCCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEECCCcCCCCCCeEEE
Confidence 5688999999996 589999999998654333 345799999999999 59999998755
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=8.2e-09 Score=72.03 Aligned_cols=57 Identities=28% Similarity=0.673 Sum_probs=47.7
Q ss_pred ccccCCCCCCcCe------eeCCCCCCCceEEeccCC-ceeeeCccccccceee---CCCCccceeE
Q 032984 52 VGIMCESCNGKGW------LVCDFCGGQKTNVKAQNN-RIYRRCPTCRAVGYVL---CSKCKVFKCV 108 (129)
Q Consensus 52 ~~~~C~~C~G~G~------v~C~~C~GSG~v~~~~g~-~~~~rC~~CnG~Glv~---Cp~C~G~~~v 108 (129)
....|+.|+|+|. ..|+.|+|+|++....|. ....+|+.|+|.|.++ |+.|.|.+.+
T Consensus 27 ~~~~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 27 IMDTCERCNGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSIIISPCVVCRGAGQA 93 (104)
T ss_dssp CCEECSSSSSSSSCTTCCCEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEECSSCCSSSSSCSEE
T ss_pred eeeECCCCcCCccCCCCCCccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceECCCcCCCCCCeeEE
Confidence 6789999999984 689999999998655443 3467999999999995 9999998755
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=98.30 E-value=3.6e-07 Score=72.60 Aligned_cols=56 Identities=29% Similarity=0.740 Sum_probs=45.1
Q ss_pred ccccCCCCCCcCe-----eeCCCCCCCceEEecc--CC---ceeeeCccccccceee-----CCCCcccee
Q 032984 52 VGIMCESCNGKGW-----LVCDFCGGQKTNVKAQ--NN---RIYRRCPTCRAVGYVL-----CSKCKVFKC 107 (129)
Q Consensus 52 ~~~~C~~C~G~G~-----v~C~~C~GSG~v~~~~--g~---~~~~rC~~CnG~Glv~-----Cp~C~G~~~ 107 (129)
....|..|+|+|. ..|+.|+|+|+++... +. .....|+.|+|.|.++ |+.|.|.+.
T Consensus 37 r~~~C~~C~G~G~~~g~~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~~~~C~~C~G~g~ 107 (248)
T 1nlt_A 37 KQILCKECEGRGGKKGAVKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKV 107 (248)
T ss_dssp EEEECTTTTTCSBSTTTCCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCE
T ss_pred EEEeCCCCcCccCCCCCCccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEeccCCCCcccCCCce
Confidence 5579999999996 6899999999876432 22 3467899999999665 999998763
No 4
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.01 E-value=4.4e-06 Score=54.89 Aligned_cols=39 Identities=31% Similarity=0.750 Sum_probs=33.1
Q ss_pred cccCCCCCCcCee-----------eCCCCCCCceEEeccCCceeeeCccccccceee
Q 032984 53 GIMCESCNGKGWL-----------VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (129)
Q Consensus 53 ~~~C~~C~G~G~v-----------~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv~ 98 (129)
...|+.|+|+|.+ +|+.|+|+|+++ ..+|+.|+|.|.+.
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 799999999975 35899999999874
No 5
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=97.86 E-value=1e-05 Score=56.16 Aligned_cols=39 Identities=31% Similarity=0.747 Sum_probs=33.4
Q ss_pred cccCCCCCCcCee-----------eCCCCCCCceEEeccCCceeeeCccccccceee
Q 032984 53 GIMCESCNGKGWL-----------VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (129)
Q Consensus 53 ~~~C~~C~G~G~v-----------~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv~ 98 (129)
...|..|+|+|.+ +|+.|+|+|+++ ..+|+.|+|.|.+.
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 4689999999964 799999999976 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=97.24 E-value=0.00013 Score=57.82 Aligned_cols=41 Identities=32% Similarity=0.669 Sum_probs=33.4
Q ss_pred cccCCCCCCcCee---------------eCCCCCCCceEEeccCCceeeeCccccccceee
Q 032984 53 GIMCESCNGKGWL---------------VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (129)
Q Consensus 53 ~~~C~~C~G~G~v---------------~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv~ 98 (129)
...|..|+|+|.+ +|+.|+|+|+++.. ..+|+.|+|.|.+.
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 4789999999953 69999999987632 35899999999874
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=97.03 E-value=0.00035 Score=44.24 Aligned_cols=26 Identities=31% Similarity=0.680 Sum_probs=15.4
Q ss_pred cccCCCCCCcCee---eCCCCCCCceEEe
Q 032984 53 GIMCESCNGKGWL---VCDFCGGQKTNVK 78 (129)
Q Consensus 53 ~~~C~~C~G~G~v---~C~~C~GSG~v~~ 78 (129)
...|+.|+|+|.+ .|+.|+|+|.+..
T Consensus 9 ~~~C~~C~GsG~~i~~~C~~C~G~G~v~~ 37 (53)
T 3lcz_A 9 ETTCPNCNGSGREEPEPCPKCLGKGVILT 37 (53)
T ss_dssp EEECTTTTTSCEETTEECTTTTTSSEEEC
T ss_pred eccCcCCcccccCCCCcCCCCCCcEEEEE
Confidence 3456666666663 5666666665543
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=96.91 E-value=0.0005 Score=43.48 Aligned_cols=26 Identities=23% Similarity=0.686 Sum_probs=15.0
Q ss_pred cccCCCCCCcCee---eCCCCCCCceEEe
Q 032984 53 GIMCESCNGKGWL---VCDFCGGQKTNVK 78 (129)
Q Consensus 53 ~~~C~~C~G~G~v---~C~~C~GSG~v~~ 78 (129)
...|+.|+|+|.+ +|+.|+|+|++..
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 3456666666663 4666666665543
No 9
>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=96.16 E-value=0.0034 Score=39.60 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=23.2
Q ss_pred eeeCCCCCCCceEEeccCCceeeeCccccccceee
Q 032984 64 WLVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (129)
Q Consensus 64 ~v~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv~ 98 (129)
..+|+.|+|+|.+. ..+|+.|+|.|.++
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 36899999999974 25899999999875
No 10
>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=96.07 E-value=0.0025 Score=40.23 Aligned_cols=27 Identities=30% Similarity=0.730 Sum_probs=23.0
Q ss_pred eeCCCCCCCceEEeccCCceeeeCccccccceee
Q 032984 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYVL 98 (129)
Q Consensus 65 v~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv~ 98 (129)
.+|+.|+|+|+++ ..+|+.|+|.|++.
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 5899999999976 26899999999875
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=62.39 E-value=6.6 Score=22.39 Aligned_cols=33 Identities=21% Similarity=0.574 Sum_probs=21.6
Q ss_pred eeCCCCCCCceEEeccCCceeeeCcccccccee
Q 032984 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYV 97 (129)
Q Consensus 65 v~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv 97 (129)
|.|+.|+..-..+...++....+|..|+..+.+
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 578888887655444444556778777766544
No 12
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=49.53 E-value=5.6 Score=22.45 Aligned_cols=32 Identities=16% Similarity=0.281 Sum_probs=14.0
Q ss_pred eCCCCCCCceEEeccCCceeeeCcccccccee
Q 032984 66 VCDFCGGQKTNVKAQNNRIYRRCPTCRAVGYV 97 (129)
Q Consensus 66 ~C~~C~GSG~v~~~~g~~~~~rC~~CnG~Glv 97 (129)
.|..|...|.+...-.......|..|...|-+
T Consensus 2 ~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~ 33 (39)
T 2a51_A 2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHR 33 (39)
T ss_dssp BCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSC
T ss_pred eeeccCCCCcccccCCCCCCCccccCCCCCCc
Confidence 45555555543321111112456666666543
No 13
>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=48.62 E-value=7.7 Score=22.97 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=8.0
Q ss_pred eeCccccccceee
Q 032984 86 RRCPTCRAVGYVL 98 (129)
Q Consensus 86 ~rC~~CnG~Glv~ 98 (129)
..|..|...|-+.
T Consensus 28 ~~C~~Cg~~GH~~ 40 (49)
T 2ec7_A 28 QGCWKCGKTGHVM 40 (49)
T ss_dssp CSCSSSCCSSCCG
T ss_pred CeeCcCCCcCCcc
Confidence 3577777666543
No 14
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=47.19 E-value=15 Score=22.21 Aligned_cols=6 Identities=50% Similarity=1.431 Sum_probs=3.2
Q ss_pred eCCCCC
Q 032984 66 VCDFCG 71 (129)
Q Consensus 66 ~C~~C~ 71 (129)
-|+.|+
T Consensus 21 ~CP~CG 26 (50)
T 3j20_Y 21 FCPRCG 26 (50)
T ss_dssp ECSSSC
T ss_pred cCCCCC
Confidence 456663
No 15
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1
Probab=44.84 E-value=15 Score=29.85 Aligned_cols=17 Identities=18% Similarity=0.597 Sum_probs=12.1
Q ss_pred eCCCCccceeEeecCCc
Q 032984 98 LCSKCKVFKCVTFPNYD 114 (129)
Q Consensus 98 ~Cp~C~G~~~v~~~n~~ 114 (129)
.|..|.+|--+.+++.|
T Consensus 255 ~C~~C~~YlK~~~~~~d 271 (309)
T 2fiy_A 255 TCPSCQGYLKQFYLEFD 271 (309)
T ss_dssp EETTTTEEEEEEETTTC
T ss_pred EcccccchHhhhhhccC
Confidence 38899887766676554
No 16
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=39.48 E-value=27 Score=20.38 Aligned_cols=9 Identities=33% Similarity=0.767 Sum_probs=5.5
Q ss_pred eeCCCCCCC
Q 032984 65 LVCDFCGGQ 73 (129)
Q Consensus 65 v~C~~C~GS 73 (129)
+.|+.|++.
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 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=38.53 E-value=12 Score=22.29 Aligned_cols=12 Identities=25% Similarity=0.540 Sum_probs=7.3
Q ss_pred eeCcccccccee
Q 032984 86 RRCPTCRAVGYV 97 (129)
Q Consensus 86 ~rC~~CnG~Glv 97 (129)
..|..|+..|-+
T Consensus 34 ~~C~~Cg~~GH~ 45 (55)
T 1a1t_A 34 KGCWKCGKEGHQ 45 (55)
T ss_dssp CBCTTTCCBSSC
T ss_pred CEeCCCCCcCCc
Confidence 356666666644
No 18
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=37.52 E-value=18 Score=23.99 Aligned_cols=51 Identities=16% Similarity=0.222 Sum_probs=26.3
Q ss_pred ccccCCCCCCcCee--------eCCCCCCCceEEeccC-CceeeeCccccccceee--CCCC
Q 032984 52 VGIMCESCNGKGWL--------VCDFCGGQKTNVKAQN-NRIYRRCPTCRAVGYVL--CSKC 102 (129)
Q Consensus 52 ~~~~C~~C~G~G~v--------~C~~C~GSG~v~~~~g-~~~~~rC~~CnG~Glv~--Cp~C 102 (129)
+...|..|+..|.. .|..|...+.+..... ......|..|+..|-+- |+.=
T Consensus 4 k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~ 65 (83)
T 3nyb_B 4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 65 (83)
T ss_dssp ---CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSC
T ss_pred ccCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcc
Confidence 56778888888873 4666777765432111 11246799999998764 7653
No 19
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=36.51 E-value=13 Score=22.94 Aligned_cols=16 Identities=38% Similarity=0.926 Sum_probs=10.4
Q ss_pred eeCccccccceee--CCC
Q 032984 86 RRCPTCRAVGYVL--CSK 101 (129)
Q Consensus 86 ~rC~~CnG~Glv~--Cp~ 101 (129)
..|..|...|-+. |+.
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 4677777777553 554
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=34.31 E-value=16 Score=26.46 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=21.1
Q ss_pred eeCCCCCCCceEEecc-CCceeeeCccccccceee--CCC
Q 032984 65 LVCDFCGGQKTNVKAQ-NNRIYRRCPTCRAVGYVL--CSK 101 (129)
Q Consensus 65 v~C~~C~GSG~v~~~~-g~~~~~rC~~CnG~Glv~--Cp~ 101 (129)
..|..|+..|.+...- .......|..|+..|-+. ||.
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 3466666666543221 111135788888888764 764
No 21
>1qo8_A Flavocytochrome C3 fumarate reductase; oxidoreductase; HET: HEM FAD; 2.15A {Shewanella frigidimarina} SCOP: a.138.1.3 c.3.1.4 d.168.1.1
Probab=33.98 E-value=4.8 Score=33.95 Aligned_cols=65 Identities=20% Similarity=0.477 Sum_probs=41.8
Q ss_pred cCCCCCCcCee----------eCCCCCCCceEEec-------c-CCceeeeCcccccccee---eCCCCccce-------
Q 032984 55 MCESCNGKGWL----------VCDFCGGQKTNVKA-------Q-NNRIYRRCPTCRAVGYV---LCSKCKVFK------- 106 (129)
Q Consensus 55 ~C~~C~G~G~v----------~C~~C~GSG~v~~~-------~-g~~~~~rC~~CnG~Glv---~Cp~C~G~~------- 106 (129)
.|..||+.+.. .|..||+....... . .......|.+|+..... .|..|..+.
T Consensus 14 ~C~~CH~~~~~~~~~~~~~~~~C~~CH~~~~~~~~~~~~~~~h~~~~~~~~C~~CH~~h~~~~~~c~~ch~~~~~~~p~~ 93 (566)
T 1qo8_A 14 SCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFS 93 (566)
T ss_dssp CGGGTSCSSCCCCTTCHHHHHHHHHHHCCHHHHCCSSSSSCTTSSTTCSCCGGGTSCSSSCCCCGGGGTCCCCCCCCTTT
T ss_pred ChhhhCCCccccccccCccCCHHhhhCcCHHHHhhccccCCcchhcCCCCCchhhCcCCcCcCchhhhhcCCCcCCCCCC
Confidence 79999998652 59999986321110 0 00135789999976553 499998765
Q ss_pred ----eEeecCCcchHHH
Q 032984 107 ----CVTFPNYDDANAL 119 (129)
Q Consensus 107 ----~v~~~n~~D~~~l 119 (129)
...|.+..|.+.+
T Consensus 94 ~~~~~~~w~~~~~~~~i 110 (566)
T 1qo8_A 94 DAKKKKSWDDGWDQDKI 110 (566)
T ss_dssp TSCCCCCSCCCCCHHHH
T ss_pred CCCCCcccccccccHHH
Confidence 3366666666644
No 22
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1
Probab=30.75 E-value=50 Score=26.77 Aligned_cols=51 Identities=20% Similarity=0.516 Sum_probs=31.9
Q ss_pred eeCCCCCCCceE--Eec---cCCceeeeCcccccccee---eCCCCccceeEeecCCcc
Q 032984 65 LVCDFCGGQKTN--VKA---QNNRIYRRCPTCRAVGYV---LCSKCKVFKCVTFPNYDD 115 (129)
Q Consensus 65 v~C~~C~GSG~v--~~~---~g~~~~~rC~~CnG~Glv---~Cp~C~G~~~v~~~n~~D 115 (129)
-.|+.|++.-.. +.. .++..+..|+.|+-.=.. .|+.|.-.+.+.|...++
T Consensus 183 ~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~~~~l~y~~~e~ 241 (309)
T 2fiy_A 183 TLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEESKHLAYLSLEH 241 (309)
T ss_dssp SSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCCSCCEEECCCC
T ss_pred CCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCCCCCeeEEEecC
Confidence 367777776432 221 123347889999875544 499997766667765554
No 23
>2d74_B Translation initiation factor 2 beta subunit; protein complex; 2.80A {Pyrococcus furiosus} PDB: 2dcu_B*
Probab=30.53 E-value=18 Score=26.79 Aligned_cols=30 Identities=23% Similarity=0.726 Sum_probs=13.0
Q ss_pred eeCCCCCCCceEEeccCCceeeeCcccccc
Q 032984 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAV 94 (129)
Q Consensus 65 v~C~~C~GSG~v~~~~g~~~~~rC~~CnG~ 94 (129)
|.|+.|+..-......+.....+|..|+..
T Consensus 105 VlC~~C~sPdT~L~k~~r~~~l~C~ACGa~ 134 (148)
T 2d74_B 105 VICPVCGSPDTKIIKRDRFHFLKCEACGAE 134 (148)
T ss_dssp SSCSSSCCTTCCCCBSSSSBCCCCSSSCCC
T ss_pred EECCCCCCcCcEEEEeCCEEEEEecCCCCC
Confidence 556666555332222222234445555443
No 24
>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=28.76 E-value=21 Score=22.16 Aligned_cols=13 Identities=15% Similarity=0.830 Sum_probs=8.5
Q ss_pred eeCccccccceee
Q 032984 86 RRCPTCRAVGYVL 98 (129)
Q Consensus 86 ~rC~~CnG~Glv~ 98 (129)
..|..|...|-+.
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 25
>2g2k_A EIF-5, eukaryotic translation initiation factor 5; EIF125 fold; NMR {Homo sapiens}
Probab=26.63 E-value=37 Score=25.68 Aligned_cols=33 Identities=21% Similarity=0.593 Sum_probs=20.8
Q ss_pred eeCCCCCCCceEEec--cCCceeeeCcccccccee
Q 032984 65 LVCDFCGGQKTNVKA--QNNRIYRRCPTCRAVGYV 97 (129)
Q Consensus 65 v~C~~C~GSG~v~~~--~g~~~~~rC~~CnG~Glv 97 (129)
|.|..|+..-..+.. .+.....+|..|+...-+
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 678888777554443 344456777777766554
No 26
>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=26.17 E-value=43 Score=24.95 Aligned_cols=33 Identities=21% Similarity=0.593 Sum_probs=18.7
Q ss_pred eeCCCCCCCceEEec--cCCceeeeCcccccccee
Q 032984 65 LVCDFCGGQKTNVKA--QNNRIYRRCPTCRAVGYV 97 (129)
Q Consensus 65 v~C~~C~GSG~v~~~--~g~~~~~rC~~CnG~Glv 97 (129)
|.|..|+..-..+.. .+.....+|..|+...-+
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 677777776544432 233445666666655443
No 27
>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=25.75 E-value=16 Score=26.63 Aligned_cols=9 Identities=22% Similarity=0.700 Sum_probs=4.4
Q ss_pred eeCCCCCCC
Q 032984 65 LVCDFCGGQ 73 (129)
Q Consensus 65 v~C~~C~GS 73 (129)
|.|+.|+..
T Consensus 104 VlC~~C~sP 112 (139)
T 3cw2_K 104 VECSTCKSL 112 (139)
T ss_dssp SSCCSSSSS
T ss_pred eECCCCCCc
Confidence 445555444
No 28
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=25.70 E-value=32 Score=23.55 Aligned_cols=47 Identities=15% Similarity=0.436 Sum_probs=24.3
Q ss_pred cCCCCCCc-Ce--------eeCCCCCCCceEEecc-CCceeeeCccccccceee--CCC
Q 032984 55 MCESCNGK-GW--------LVCDFCGGQKTNVKAQ-NNRIYRRCPTCRAVGYVL--CSK 101 (129)
Q Consensus 55 ~C~~C~G~-G~--------v~C~~C~GSG~v~~~~-g~~~~~rC~~CnG~Glv~--Cp~ 101 (129)
.|-.|+.. |. +.|..|...|.+...- .......|..|+..|-+. ||.
T Consensus 24 ~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~ 82 (124)
T 2lli_A 24 ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82 (124)
T ss_dssp CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCC
T ss_pred cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCC
Confidence 56666665 43 3566676666543211 111124577777666654 553
No 29
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=25.53 E-value=9.1 Score=34.56 Aligned_cols=46 Identities=24% Similarity=0.355 Sum_probs=29.8
Q ss_pred cccccCCCCCCcCe---------eeCCCCCCCceEEecc------------CC--ceeeeCccccccce
Q 032984 51 EVGIMCESCNGKGW---------LVCDFCGGQKTNVKAQ------------NN--RIYRRCPTCRAVGY 96 (129)
Q Consensus 51 ~~~~~C~~C~G~G~---------v~C~~C~GSG~v~~~~------------g~--~~~~rC~~CnG~Gl 96 (129)
.....|..|+|+|. ..|..|+|+....... |. .....|..|...+.
T Consensus 189 ~~~~~C~tCHGsGA~~Gt~~~~~~tC~tCHGs~~~~~~~~~~~~~iH~iH~G~fP~~~~~C~~CH~~~~ 257 (669)
T 3pmq_A 189 VSIDTCNSCHSNLAFHGGRYNQVETCVTCHNSKKVSNAADIFPQMIHSKHLTGFPQSISNCQTCHADNP 257 (669)
T ss_dssp CCSHHHHHHHSSCCTTTTTSCSSSCSTTTSSTTTCCCSSCSHHHHHHHHTTSSCSSCTTCCTTTSCCCT
T ss_pred ccCCcCCCCCCCCCcCCccCcCCccCCCCCCCcccCCccccccceeeeeeccCCCCccCcchhhcCCcc
Confidence 36678999988763 4799999994221111 11 12467888888774
No 30
>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=25.43 E-value=16 Score=26.62 Aligned_cols=31 Identities=19% Similarity=0.531 Sum_probs=15.5
Q ss_pred eeCCCCCCCceEEeccCCceeeeCccccccc
Q 032984 65 LVCDFCGGQKTNVKAQNNRIYRRCPTCRAVG 95 (129)
Q Consensus 65 v~C~~C~GSG~v~~~~g~~~~~rC~~CnG~G 95 (129)
|.|+.|+..-......+.....+|..|+...
T Consensus 103 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T 1nee_A 103 VICHECNRPDTRIIREGRISLLKCEACGAKA 133 (138)
T ss_dssp HHHTCCSSCSSCCEEETTTTEEECSTTSCCC
T ss_pred EECCCCCCcCcEEEEcCCeEEEEccCCCCCc
Confidence 5666666653322222333455666665544
No 31
>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=25.01 E-value=30 Score=32.55 Aligned_cols=20 Identities=30% Similarity=0.848 Sum_probs=14.5
Q ss_pred eCcccccccee------------eCCCCccce
Q 032984 87 RCPTCRAVGYV------------LCSKCKVFK 106 (129)
Q Consensus 87 rC~~CnG~Glv------------~Cp~C~G~~ 106 (129)
+|+.|.|.|.+ .|+.|.|.+
T Consensus 755 rC~~C~g~G~i~~em~fl~~v~~~ce~c~G~r 786 (972)
T 2r6f_A 755 RCEACHGDGIIKIEMHFLPDVYVPCEVCHGKR 786 (972)
T ss_dssp BCTTTTTCSEEEECCSSSCCEEEECTTTTTCC
T ss_pred cccccccccceeeehhcccccccccccccccc
Confidence 57777777776 488887764
No 32
>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=24.56 E-value=36 Score=31.25 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=3.7
Q ss_pred CCCCccce
Q 032984 99 CSKCKVFK 106 (129)
Q Consensus 99 Cp~C~G~~ 106 (129)
|+.|.|.+
T Consensus 664 c~~c~G~r 671 (842)
T 2vf7_A 664 CPVCHGTR 671 (842)
T ss_dssp CTTTTTCC
T ss_pred cccccCcc
Confidence 44444443
No 33
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=22.61 E-value=23 Score=19.54 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=6.2
Q ss_pred eeCccccccce
Q 032984 86 RRCPTCRAVGY 96 (129)
Q Consensus 86 ~rC~~CnG~Gl 96 (129)
..|..|...|-
T Consensus 20 ~~C~~Cg~~GH 30 (37)
T 2bl6_A 20 KVCFKCKQPGH 30 (37)
T ss_dssp TTCSSCCCTTG
T ss_pred CeEccCCCcCC
Confidence 35666666554
Done!