Query 034037
Match_columns 105
No_of_seqs 148 out of 1005
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 15:19:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034037.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/034037hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2ctt_A DNAJ homolog subfamily 99.4 1.8E-13 6.1E-18 91.6 5.2 58 44-104 26-92 (104)
2 1exk_A DNAJ protein; extended 99.4 1.7E-13 5.7E-18 87.1 4.0 59 43-104 8-75 (79)
3 1nlt_A Protein YDJ1, mitochond 99.1 2.2E-11 7.6E-16 92.4 3.3 60 45-104 37-107 (248)
4 1exk_A DNAJ protein; extended 98.2 7.5E-07 2.6E-11 56.0 2.4 38 46-94 28-76 (79)
5 2ctt_A DNAJ homolog subfamily 98.1 2.2E-06 7.4E-11 56.8 3.4 38 46-94 45-93 (104)
6 3lcz_A YCZA, inhibitor of trap 97.7 9.4E-06 3.2E-10 48.8 1.4 24 81-104 8-34 (53)
7 1nlt_A Protein YDJ1, mitochond 97.5 5E-05 1.7E-09 57.3 2.7 39 46-93 54-107 (248)
8 2bx9_A Anti-trap, AT, tryptoph 97.3 8.1E-05 2.8E-09 44.6 1.7 25 58-93 10-34 (53)
9 3lcz_A YCZA, inhibitor of trap 97.3 0.00011 3.7E-09 44.1 2.0 27 46-72 9-38 (53)
10 2bx9_A Anti-trap, AT, tryptoph 97.2 0.00018 6.2E-09 43.1 2.2 27 46-72 9-38 (53)
11 3pmq_A Decaheme cytochrome C M 85.9 0.04 1.4E-06 47.2 -3.5 51 43-93 188-257 (669)
12 3nyb_B Protein AIR2; polya RNA 79.4 1.7 5.8E-05 27.6 3.1 52 44-98 3-64 (83)
13 3pmq_A Decaheme cytochrome C M 62.7 1.7 5.7E-05 37.3 0.2 30 57-91 191-220 (669)
14 2lli_A Protein AIR2; RNA surve 62.1 16 0.00054 23.8 5.0 11 46-56 4-14 (124)
15 2vf7_A UVRA2, excinuclease ABC 59.8 7.3 0.00025 34.0 3.7 33 59-93 640-672 (842)
16 2r6f_A Excinuclease ABC subuni 55.4 8.7 0.0003 34.2 3.5 32 59-92 755-786 (972)
17 1pft_A TFIIB, PFTFIIBN; N-term 50.8 8 0.00027 21.5 1.7 7 48-54 7-13 (50)
18 1dl6_A Transcription factor II 50.7 8.4 0.00029 22.6 1.8 7 59-65 13-19 (58)
19 2ygr_A Uvrabc system protein A 47.8 14 0.00047 33.0 3.5 32 59-92 773-804 (993)
20 1qyp_A RNA polymerase II; tran 44.1 20 0.00068 20.4 2.8 33 58-90 16-51 (57)
21 2ihx_A Nucleocapsid (NC) prote 41.7 15 0.00053 21.3 2.0 17 82-98 30-48 (61)
22 1tfi_A Transcriptional elongat 41.2 30 0.001 19.6 3.2 34 57-90 9-45 (50)
23 2jr6_A UPF0434 protein NMA0874 36.2 18 0.00061 22.0 1.7 7 59-65 10-16 (68)
24 2bx2_L Ribonuclease E, RNAse E 36.0 15 0.00052 30.4 1.8 14 81-94 407-420 (517)
25 2qkd_A Zinc finger protein ZPR 35.4 22 0.00075 28.6 2.6 34 58-91 221-258 (404)
26 1ltl_A DNA replication initiat 35.0 19 0.00064 26.8 2.1 31 59-92 136-166 (279)
27 1vq8_Z 50S ribosomal protein L 35.0 14 0.00048 23.4 1.2 9 82-90 45-53 (83)
28 2hf1_A Tetraacyldisaccharide-1 34.1 17 0.0006 22.0 1.4 7 59-65 10-16 (68)
29 2fiy_A Protein FDHE homolog; F 33.3 19 0.00065 27.8 1.8 11 44-54 180-190 (309)
30 2jny_A Uncharacterized BCR; st 32.6 15 0.00052 22.3 1.0 7 59-65 12-18 (67)
31 2js4_A UPF0434 protein BB2007; 32.3 22 0.00076 21.7 1.7 7 59-65 10-16 (70)
32 2pk7_A Uncharacterized protein 32.1 20 0.00069 21.8 1.5 6 59-64 10-15 (69)
33 2qkd_A Zinc finger protein ZPR 31.5 22 0.00076 28.6 2.0 35 57-91 12-50 (404)
34 2jrp_A Putative cytoplasmic pr 31.4 34 0.0011 21.7 2.5 33 47-91 3-40 (81)
35 2ec7_A GAG polyprotein (PR55GA 30.1 40 0.0014 18.6 2.5 16 83-98 28-45 (49)
36 2ygr_A Uvrabc system protein A 29.8 12 0.00042 33.3 0.3 13 59-71 302-314 (993)
37 3alr_A Nanos protein; zinc-fin 29.7 15 0.00051 24.6 0.6 18 81-98 70-92 (106)
38 3pih_A Uvrabc system protein A 29.4 14 0.00047 32.6 0.5 9 84-92 275-283 (916)
39 2kpi_A Uncharacterized protein 28.3 29 0.00098 20.2 1.7 8 84-91 12-19 (56)
40 2r6f_A Excinuclease ABC subuni 28.3 21 0.0007 31.9 1.4 11 83-93 292-302 (972)
41 3h0g_I DNA-directed RNA polyme 27.9 58 0.002 21.1 3.3 33 58-90 73-108 (113)
42 3k1f_M Transcription initiatio 27.1 26 0.00089 25.7 1.6 6 60-65 24-29 (197)
43 3k7a_M Transcription initiatio 26.9 26 0.00089 26.8 1.6 9 82-90 21-29 (345)
44 2vf7_A UVRA2, excinuclease ABC 26.6 25 0.00087 30.6 1.7 21 84-104 640-672 (842)
45 4bbr_M Transcription initiatio 25.9 20 0.00067 27.7 0.8 7 59-65 23-29 (345)
46 3j21_g 50S ribosomal protein L 25.4 33 0.0011 19.8 1.6 24 43-66 11-37 (51)
47 3i2t_A Epidermal growth factor 24.1 81 0.0028 26.1 4.2 53 47-100 482-549 (551)
48 2bl6_A Nucleocapsid protein P1 23.7 50 0.0017 17.0 2.0 11 83-93 20-30 (37)
49 2l5u_A Chromodomain-helicase-D 22.5 1.2E+02 0.004 17.3 3.7 47 44-92 9-59 (61)
50 2ysm_A Myeloid/lymphoid or mix 21.9 52 0.0018 20.8 2.2 23 44-66 5-31 (111)
51 3j20_Y 30S ribosomal protein S 21.2 39 0.0013 19.1 1.3 8 82-89 37-44 (50)
52 3pih_A Uvrabc system protein A 21.2 72 0.0024 28.0 3.5 32 59-92 715-746 (916)
53 1a1t_A Nucleocapsid protein; s 20.2 67 0.0023 17.8 2.2 16 83-98 34-51 (55)
No 1
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=99.42 E-value=1.8e-13 Score=91.57 Aligned_cols=58 Identities=28% Similarity=0.657 Sum_probs=50.3
Q ss_pred CCcccCCCCcCcc------cccCCCCCcccEEEEccCCCCccccceeCCCCcccccc---cCccCCcccc
Q 034037 44 KFAMPCGVCKGKG------FYICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRVQ---RCLNCLGKGF 104 (105)
Q Consensus 44 ~~~~~C~~C~GsG------~~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~~---~C~~C~G~G~ 104 (105)
.+.+.|+.|+|+| ..+|+.|+|+|++...+ +.|+.+++||.|+|+|+. +|+.|+|+|+
T Consensus 26 ~~~~~C~~C~G~G~~~g~~~~~C~~C~G~G~~~~~~---G~~~~~~~C~~C~G~G~~i~~~C~~C~G~G~ 92 (104)
T 2ctt_A 26 NIMDTCERCNGKGNEPGTKVQHCHYCGGSGMETINT---GPFVMRSTCRRCGGRGSIIISPCVVCRGAGQ 92 (104)
T ss_dssp SCCEECSSSSSSSSCTTCCCEECSSSSSSCEEEEEE---TTEEEEEECSSSSSSSEECSSCCSSSSSCSE
T ss_pred eeeeECCCCcCCccCCCCCCccCCCCCCCEEEEEEe---CCEEEEEECCcCCCcceECCCcCCCCCCeeE
Confidence 4578999999999 37899999999987764 447788999999999994 9999999986
No 2
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=99.40 E-value=1.7e-13 Score=87.07 Aligned_cols=59 Identities=29% Similarity=0.700 Sum_probs=50.5
Q ss_pred CCCcccCCCCcCccc------ccCCCCCcccEEEEccCCCCccccceeCCCCcccccc---cCccCCcccc
Q 034037 43 KKFAMPCGVCKGKGF------YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRVQ---RCLNCLGKGF 104 (105)
Q Consensus 43 ~~~~~~C~~C~GsG~------~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~~---~C~~C~G~G~ 104 (105)
-.+.+.|+.|+|+|. .+|+.|+|+|++...+ +.|+.+.+||.|+|+|++ +|+.|+|.|+
T Consensus 8 ~~~~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~---g~~~~~~~C~~C~G~G~~~~~~C~~C~G~G~ 75 (79)
T 1exk_A 8 IPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQ---GFFAVQQTCPHCQGRGTLIKDPCNKCHGHGR 75 (79)
T ss_dssp CCCEEECGGGTTTSBCSSSCCEECTTTTTSSEEEEEE---TTEEEEEECTTTTTSSEECSSBCGGGTTSSE
T ss_pred cccceECCCCcccccCCCccCCCCCCCcCeEEEEEEc---CCCEEeeECcCCCCccEECCCcCCCCCCeEE
Confidence 346789999999994 6899999999987644 456778899999999995 9999999986
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=99.12 E-value=2.2e-11 Score=92.43 Aligned_cols=60 Identities=27% Similarity=0.588 Sum_probs=48.8
Q ss_pred CcccCCCCcCcc-----cccCCCCCcccEEEEccCCCCc-cccceeCCCCccccc-----ccCccCCcccc
Q 034037 45 FAMPCGVCKGKG-----FYICKLCKGNATIEWSPLYDPV-FINPCLCPTCEGNRV-----QRCLNCLGKGF 104 (105)
Q Consensus 45 ~~~~C~~C~GsG-----~~~C~~C~G~G~i~~~~~~~g~-~~~~~~Cp~C~G~G~-----~~C~~C~G~G~ 104 (105)
+.+.|+.|+|+| ..+|+.|+|+|++...+...+. ++.+.+||.|+|+|+ .+|++|+|+|+
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 467999999999 4789999999998765433232 347889999999994 68999999985
No 4
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.17 E-value=7.5e-07 Score=55.96 Aligned_cols=38 Identities=29% Similarity=0.716 Sum_probs=27.3
Q ss_pred cccCCCCcCccc-----------ccCCCCCcccEEEEccCCCCccccceeCCCCcccccc
Q 034037 46 AMPCGVCKGKGF-----------YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRVQ 94 (105)
Q Consensus 46 ~~~C~~C~GsG~-----------~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~~ 94 (105)
...|+.|+|+|. .+|+.|+|+|++. ..+|+.|+|.|..
T Consensus 28 ~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~-----------~~~C~~C~G~G~~ 76 (79)
T 1exk_A 28 PQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLI-----------KDPCNKCHGHGRV 76 (79)
T ss_dssp CEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEEC-----------SSBCGGGTTSSEE
T ss_pred CCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEEC-----------CCcCCCCCCeEEE
Confidence 467888888883 2688888888752 2378888888763
No 5
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=98.09 E-value=2.2e-06 Score=56.83 Aligned_cols=38 Identities=29% Similarity=0.726 Sum_probs=30.9
Q ss_pred cccCCCCcCccc-----------ccCCCCCcccEEEEccCCCCccccceeCCCCcccccc
Q 034037 46 AMPCGVCKGKGF-----------YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRVQ 94 (105)
Q Consensus 46 ~~~C~~C~GsG~-----------~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~~ 94 (105)
...|+.|+|+|. .+|+.|+|+|++. ..+|+.|+|+|..
T Consensus 45 ~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~i-----------~~~C~~C~G~G~v 93 (104)
T 2ctt_A 45 VQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSII-----------ISPCVVCRGAGQA 93 (104)
T ss_dssp CEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEEC-----------SSCCSSSSSCSEE
T ss_pred CccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceEC-----------CCcCCCCCCeeEE
Confidence 578999999993 4799999999763 3489999999873
No 6
>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=97.72 E-value=9.4e-06 Score=48.79 Aligned_cols=24 Identities=42% Similarity=1.027 Sum_probs=18.0
Q ss_pred cceeCCCCccccc---ccCccCCcccc
Q 034037 81 NPCLCPTCEGNRV---QRCLNCLGKGF 104 (105)
Q Consensus 81 ~~~~Cp~C~G~G~---~~C~~C~G~G~ 104 (105)
.+.+||.|+|+|+ .+|+.|+|+|+
T Consensus 8 ~~~~C~~C~GsG~~i~~~C~~C~G~G~ 34 (53)
T 3lcz_A 8 LETTCPNCNGSGREEPEPCPKCLGKGV 34 (53)
T ss_dssp HEEECTTTTTSCEETTEECTTTTTSSE
T ss_pred eeccCcCCcccccCCCCcCCCCCCcEE
Confidence 5667888888887 47888888774
No 7
>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=97.47 E-value=5e-05 Score=57.29 Aligned_cols=39 Identities=31% Similarity=0.785 Sum_probs=31.9
Q ss_pred cccCCCCcCccc---------------ccCCCCCcccEEEEccCCCCccccceeCCCCccccc
Q 034037 46 AMPCGVCKGKGF---------------YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRV 93 (105)
Q Consensus 46 ~~~C~~C~GsG~---------------~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~ 93 (105)
...|+.|+|+|. .+|+.|+|+|.+.. ...+|+.|+|+|.
T Consensus 54 ~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~---------~~~~C~~C~G~g~ 107 (248)
T 1nlt_A 54 VKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIID---------PKDRCKSCNGKKV 107 (248)
T ss_dssp CCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCC---------TTSBCSSSTTSCE
T ss_pred CccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEec---------cCCCCcccCCCce
Confidence 489999999994 37999999997531 2568999999986
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=97.31 E-value=8.1e-05 Score=44.64 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=14.2
Q ss_pred ccCCCCCcccEEEEccCCCCccccceeCCCCccccc
Q 034037 58 YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRV 93 (105)
Q Consensus 58 ~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~ 93 (105)
.+|+.|+|+|.+. ..+||.|+|+|+
T Consensus 10 ~~C~~C~GsG~~~-----------~~~C~~C~G~G~ 34 (53)
T 2bx9_A 10 VACPKCERAGEIE-----------GTPCPACSGKGV 34 (53)
T ss_dssp EECTTTTTSSEET-----------TEECTTTTTSSE
T ss_pred ccCCCCcceeccC-----------CCCCccCCCCcc
Confidence 3566666666541 246666666665
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=97.27 E-value=0.00011 Score=44.10 Aligned_cols=27 Identities=30% Similarity=0.608 Sum_probs=21.6
Q ss_pred cccCCCCcCccc---ccCCCCCcccEEEEc
Q 034037 46 AMPCGVCKGKGF---YICKLCKGNATIEWS 72 (105)
Q Consensus 46 ~~~C~~C~GsG~---~~C~~C~G~G~i~~~ 72 (105)
..+|+.|+|+|. ..|+.|+|+|.+...
T Consensus 9 ~~~C~~C~GsG~~i~~~C~~C~G~G~v~~~ 38 (53)
T 3lcz_A 9 ETTCPNCNGSGREEPEPCPKCLGKGVILTA 38 (53)
T ss_dssp EEECTTTTTSCEETTEECTTTTTSSEEECH
T ss_pred eccCcCCcccccCCCCcCCCCCCcEEEEEE
Confidence 468899999984 678999998887664
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=97.17 E-value=0.00018 Score=43.07 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=23.1
Q ss_pred cccCCCCcCccc---ccCCCCCcccEEEEc
Q 034037 46 AMPCGVCKGKGF---YICKLCKGNATIEWS 72 (105)
Q Consensus 46 ~~~C~~C~GsG~---~~C~~C~G~G~i~~~ 72 (105)
...|+.|+|+|. .+|+.|+|+|++...
T Consensus 9 ~~~C~~C~GsG~~~~~~C~~C~G~G~v~~~ 38 (53)
T 2bx9_A 9 EVACPKCERAGEIEGTPCPACSGKGVILTA 38 (53)
T ss_dssp EEECTTTTTSSEETTEECTTTTTSSEEECH
T ss_pred cccCCCCcceeccCCCCCccCCCCccEEEE
Confidence 468999999994 689999999998764
No 11
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=85.88 E-value=0.04 Score=47.18 Aligned_cols=51 Identities=14% Similarity=0.272 Sum_probs=31.7
Q ss_pred CCCcccCCCCcCcc---------cccCCCCCcccEEEEc----------cCCCCccccceeCCCCccccc
Q 034037 43 KKFAMPCGVCKGKG---------FYICKLCKGNATIEWS----------PLYDPVFINPCLCPTCEGNRV 93 (105)
Q Consensus 43 ~~~~~~C~~C~GsG---------~~~C~~C~G~G~i~~~----------~~~~g~~~~~~~Cp~C~G~G~ 93 (105)
..+.+.|+.|+|+| ..+|+.|+|+....-. .......+....|..|+..+.
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 44678999999988 2589999998421100 000111134567888888764
No 12
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=79.38 E-value=1.7 Score=27.61 Aligned_cols=52 Identities=15% Similarity=0.321 Sum_probs=27.3
Q ss_pred CCcccCCCCcCccc--------ccCCCCCcccEEEEccCCCCccccceeCCCCcccccc--cCcc
Q 034037 44 KFAMPCGVCKGKGF--------YICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRVQ--RCLN 98 (105)
Q Consensus 44 ~~~~~C~~C~GsG~--------~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~~--~C~~ 98 (105)
.+.+.|..|+..|- .+|..|...|.+...... ......|..|+..|.. -|++
T Consensus 3 ~k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~---p~~~~~CYnCG~~GH~~rdC~~ 64 (83)
T 3nyb_B 3 WKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVL---PFHTIYCYNCGGKGHFGDDCKE 64 (83)
T ss_dssp ----CCSSSCCSSSCGGGCGGGTCCCCBC----------------CCCBCSSSSCBSSCGGGCSS
T ss_pred cccCCCCCCCCCCCccccCCCcccccccccCCcccccccC---CCCCCeecccCCCCcCcccCCc
Confidence 35678999999992 367778888776432111 1235689999999973 6665
No 13
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=62.74 E-value=1.7 Score=37.27 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=20.7
Q ss_pred cccCCCCCcccEEEEccCCCCccccceeCCCCccc
Q 034037 57 FYICKLCKGNATIEWSPLYDPVFINPCLCPTCEGN 91 (105)
Q Consensus 57 ~~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~ 91 (105)
...|+.|+|+|.. . ........+|+.|+|+
T Consensus 191 ~~~C~tCHGsGA~---~--Gt~~~~~~tC~tCHGs 220 (669)
T 3pmq_A 191 IDTCNSCHSNLAF---H--GGRYNQVETCVTCHNS 220 (669)
T ss_dssp SHHHHHHHSSCCT---T--TTTSCSSSCSTTTSST
T ss_pred CCcCCCCCCCCCc---C--CccCcCCccCCCCCCC
Confidence 3689999999851 1 1112356799999998
No 14
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=62.09 E-value=16 Score=23.84 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=5.9
Q ss_pred cccCCCCcCcc
Q 034037 46 AMPCGVCKGKG 56 (105)
Q Consensus 46 ~~~C~~C~GsG 56 (105)
...|..|...|
T Consensus 4 ~~~C~~C~~~G 14 (124)
T 2lli_A 4 APKCNNCSQRG 14 (124)
T ss_dssp SSCCSSCSSSS
T ss_pred CCcccCCCCCC
Confidence 34455555555
No 15
>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=59.78 E-value=7.3 Score=33.96 Aligned_cols=33 Identities=30% Similarity=0.685 Sum_probs=22.4
Q ss_pred cCCCCCcccEEEEccCCCCccccceeCCCCccccc
Q 034037 59 ICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNRV 93 (105)
Q Consensus 59 ~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G~ 93 (105)
.|+.|.|.|.+.....+.+ ....+|+.|+|+..
T Consensus 640 ~c~~c~g~G~~~~~~~f~~--~v~~~c~~c~G~r~ 672 (842)
T 2vf7_A 640 RCEHCQGEGWVMVELLFLP--SVYAPCPVCHGTRY 672 (842)
T ss_dssp BCTTTTTCSEEEETTCSSS--CEEEECTTTTTCCB
T ss_pred ccccccCCCccchhhhcCC--ccceecccccCccc
Confidence 4888888888876543322 24678888888753
No 16
>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=55.38 E-value=8.7 Score=34.20 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=22.2
Q ss_pred cCCCCCcccEEEEccCCCCccccceeCCCCcccc
Q 034037 59 ICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNR 92 (105)
Q Consensus 59 ~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G 92 (105)
+|+.|+|.|.+.....+.+ ....+|+.|.|..
T Consensus 755 rC~~C~g~G~i~~em~fl~--~v~~~ce~c~G~r 786 (972)
T 2r6f_A 755 RCEACHGDGIIKIEMHFLP--DVYVPCEVCHGKR 786 (972)
T ss_dssp BCTTTTTCSEEEECCSSSC--CEEEECTTTTTCC
T ss_pred cccccccccceeeehhccc--ccccccccccccc
Confidence 6888888888876543322 2456888888874
No 17
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Probab=50.80 E-value=8 Score=21.52 Aligned_cols=7 Identities=29% Similarity=1.013 Sum_probs=3.2
Q ss_pred cCCCCcC
Q 034037 48 PCGVCKG 54 (105)
Q Consensus 48 ~C~~C~G 54 (105)
.|+.|++
T Consensus 7 ~CP~C~~ 13 (50)
T 1pft_A 7 VCPACES 13 (50)
T ss_dssp SCTTTSC
T ss_pred eCcCCCC
Confidence 4555533
No 18
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A
Probab=50.72 E-value=8.4 Score=22.58 Aligned_cols=7 Identities=14% Similarity=0.263 Sum_probs=3.1
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|++
T Consensus 13 ~Cp~C~~ 19 (58)
T 1dl6_A 13 TCPNHPD 19 (58)
T ss_dssp SBTTBSS
T ss_pred cCcCCCC
Confidence 3444443
No 19
>2ygr_A Uvrabc system protein A; hydrolase, nucleotide excision repair; 3.40A {Mycobacterium tuberculosis} PDB: 3zqj_A
Probab=47.76 E-value=14 Score=33.03 Aligned_cols=32 Identities=31% Similarity=0.668 Sum_probs=23.1
Q ss_pred cCCCCCcccEEEEccCCCCccccceeCCCCcccc
Q 034037 59 ICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNR 92 (105)
Q Consensus 59 ~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G 92 (105)
+|+.|+|.|.+.....+.+. ...+|+.|.|..
T Consensus 773 rC~~C~g~G~~~~e~~fl~~--v~~~ce~c~G~r 804 (993)
T 2ygr_A 773 RCEACTGDGTIKIEMNFLPD--VYVPCEVCQGAR 804 (993)
T ss_dssp BCTTTTSSSEEEECCTTSCC--EEEECTTTTTCS
T ss_pred cccccccccceeehhhcccc--ceeeehhccccc
Confidence 58999999988776443322 567899998864
No 20
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=44.14 E-value=20 Score=20.44 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=18.5
Q ss_pred ccCCCCCcccEEEEccCC---CCccccceeCCCCcc
Q 034037 58 YICKLCKGNATIEWSPLY---DPVFINPCLCPTCEG 90 (105)
Q Consensus 58 ~~C~~C~G~G~i~~~~~~---~g~~~~~~~Cp~C~G 90 (105)
..|+.|+..-....+.++ +-.+.....|+.|+-
T Consensus 16 ~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~ 51 (57)
T 1qyp_A 16 ITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH 51 (57)
T ss_dssp CCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCC
T ss_pred eECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCC
Confidence 568888874444333222 223445667888864
No 21
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=41.69 E-value=15 Score=21.28 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=11.9
Q ss_pred ceeCCCCccccc--ccCcc
Q 034037 82 PCLCPTCEGNRV--QRCLN 98 (105)
Q Consensus 82 ~~~Cp~C~G~G~--~~C~~ 98 (105)
...|..|...|. ..|++
T Consensus 30 ~~~C~~Cg~~GH~ar~C~~ 48 (61)
T 2ihx_A 30 RERCQLCNGMGHNAKQCRK 48 (61)
T ss_dssp CSBCTTTCCBSSCGGGCCC
T ss_pred CCeeCCCCCCCCCcCCCcC
Confidence 356888888886 35654
No 22
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1
Probab=41.22 E-value=30 Score=19.60 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=21.4
Q ss_pred cccCCCCCcccEEEEccCC---CCccccceeCCCCcc
Q 034037 57 FYICKLCKGNATIEWSPLY---DPVFINPCLCPTCEG 90 (105)
Q Consensus 57 ~~~C~~C~G~G~i~~~~~~---~g~~~~~~~Cp~C~G 90 (105)
...|+.|+....+..+.+. +-.|.....|..|+-
T Consensus 9 ~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~ 45 (50)
T 1tfi_A 9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGN 45 (50)
T ss_dssp CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCC
T ss_pred ccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCC
Confidence 3578888887776664322 223556677888753
No 23
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}
Probab=36.23 E-value=18 Score=21.99 Aligned_cols=7 Identities=43% Similarity=1.194 Sum_probs=3.1
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|+|
T Consensus 10 ~CP~ck~ 16 (68)
T 2jr6_A 10 VCPVTKG 16 (68)
T ss_dssp BCSSSCC
T ss_pred ECCCCCC
Confidence 3444443
No 24
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
Probab=35.96 E-value=15 Score=30.39 Aligned_cols=14 Identities=29% Similarity=0.845 Sum_probs=10.4
Q ss_pred cceeCCCCcccccc
Q 034037 81 NPCLCPTCEGNRVQ 94 (105)
Q Consensus 81 ~~~~Cp~C~G~G~~ 94 (105)
...+||.|+|+|..
T Consensus 407 ~~~~Cp~C~G~G~v 420 (517)
T 2bx2_L 407 SHHVCPRCSGTGTV 420 (517)
T ss_dssp HCCCCSSSSSSSCC
T ss_pred hcCcCCCcCCceeE
Confidence 45678888888863
No 25
>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=35.40 E-value=22 Score=28.61 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=23.5
Q ss_pred ccCCCCCcccEEEEc----cCCCCccccceeCCCCccc
Q 034037 58 YICKLCKGNATIEWS----PLYDPVFINPCLCPTCEGN 91 (105)
Q Consensus 58 ~~C~~C~G~G~i~~~----~~~~g~~~~~~~Cp~C~G~ 91 (105)
..|+.|+..|..+.. +.+.-.+.....|+.|+=+
T Consensus 221 s~Cp~C~~~~~t~~~~~~IP~F~eViims~~C~~CGyr 258 (404)
T 2qkd_A 221 TNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHR 258 (404)
T ss_dssp ECCTTTCCTTCEEEEEECCTTSCCEEEEEEECSSSCCE
T ss_pred ccCccCCCccEEEEEEEeCCCCCcEEEEEEECCCCCCc
Confidence 579999999887653 3222234478889999755
No 26
>1ltl_A DNA replication initiator (CDC21/CDC54); HET: DNA; 3.00A {Methanothermobacterthermautotrophicus} SCOP: b.40.4.11
Probab=35.05 E-value=19 Score=26.79 Aligned_cols=31 Identities=26% Similarity=0.673 Sum_probs=17.4
Q ss_pred cCCCCCcccEEEEccCCCCccccceeCCCCcccc
Q 034037 59 ICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNR 92 (105)
Q Consensus 59 ~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G 92 (105)
.|..|+-...+... ++.+.....||.|+.+|
T Consensus 136 ~C~~C~~~~~v~~~---~~~~~~P~~Cp~C~~~~ 166 (279)
T 1ltl_A 136 ECRGCMRHHAVTQS---TNMITEPSLCSECGGRS 166 (279)
T ss_dssp EETTTCCEEEEECS---SSSCCCCSCCTTTCCCC
T ss_pred EcCCCCCEEEEEec---CCcccCCCcCCCCCCCC
Confidence 67777754333221 23344456788887776
No 27
>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...
Probab=35.04 E-value=14 Score=23.35 Aligned_cols=9 Identities=22% Similarity=0.556 Sum_probs=5.1
Q ss_pred ceeCCCCcc
Q 034037 82 PCLCPTCEG 90 (105)
Q Consensus 82 ~~~Cp~C~G 90 (105)
...|+.|.-
T Consensus 45 iW~C~~Cg~ 53 (83)
T 1vq8_Z 45 IWQCSYCDY 53 (83)
T ss_dssp EEEETTTCC
T ss_pred eEECCCCCC
Confidence 346666654
No 28
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1
Probab=34.12 E-value=17 Score=22.03 Aligned_cols=7 Identities=71% Similarity=1.867 Sum_probs=3.1
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|+|
T Consensus 10 ~CP~ck~ 16 (68)
T 2hf1_A 10 VCPLCKG 16 (68)
T ss_dssp BCTTTCC
T ss_pred ECCCCCC
Confidence 3444443
No 29
>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=33.25 E-value=19 Score=27.77 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=7.5
Q ss_pred CCcccCCCCcC
Q 034037 44 KFAMPCGVCKG 54 (105)
Q Consensus 44 ~~~~~C~~C~G 54 (105)
.....||.|.+
T Consensus 180 ~~~~~CPvCGs 190 (309)
T 2fiy_A 180 ESRTLCPACGS 190 (309)
T ss_dssp TTCSSCTTTCC
T ss_pred ccCCCCCCCCC
Confidence 34578888854
No 30
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1
Probab=32.64 E-value=15 Score=22.30 Aligned_cols=7 Identities=43% Similarity=0.695 Sum_probs=3.0
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|+|
T Consensus 12 ~CP~ck~ 18 (67)
T 2jny_A 12 ACPKDKG 18 (67)
T ss_dssp BCTTTCC
T ss_pred CCCCCCC
Confidence 3444444
No 31
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Probab=32.32 E-value=22 Score=21.67 Aligned_cols=7 Identities=57% Similarity=1.763 Sum_probs=3.5
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|+|
T Consensus 10 ~CP~ck~ 16 (70)
T 2js4_A 10 VCPVCKG 16 (70)
T ss_dssp BCTTTCC
T ss_pred ECCCCCC
Confidence 4555554
No 32
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1
Probab=32.08 E-value=20 Score=21.79 Aligned_cols=6 Identities=50% Similarity=1.530 Sum_probs=2.6
Q ss_pred cCCCCC
Q 034037 59 ICKLCK 64 (105)
Q Consensus 59 ~C~~C~ 64 (105)
.||.|+
T Consensus 10 ~CP~ck 15 (69)
T 2pk7_A 10 ACPICK 15 (69)
T ss_dssp CCTTTC
T ss_pred eCCCCC
Confidence 344444
No 33
>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=31.46 E-value=22 Score=28.59 Aligned_cols=35 Identities=23% Similarity=0.543 Sum_probs=23.8
Q ss_pred cccCCCCCcccEEEEc----cCCCCccccceeCCCCccc
Q 034037 57 FYICKLCKGNATIEWS----PLYDPVFINPCLCPTCEGN 91 (105)
Q Consensus 57 ~~~C~~C~G~G~i~~~----~~~~g~~~~~~~Cp~C~G~ 91 (105)
...|+.|+..|..+.. +.+.-.+.....|+.|+=+
T Consensus 12 ~s~Cp~C~~~g~t~~~~~~IP~F~eVii~Sf~C~~CGyr 50 (404)
T 2qkd_A 12 ESLCMNCYRNGTTRLLLTKIPFFREIIVSSFSCEHCGWN 50 (404)
T ss_dssp EEECTTTSSEEEEEEEEEEETTTEEEEEEEEECTTTCCE
T ss_pred cccCCCCCCCceEEEEEEcCCCCceEEEEEEECCCCCCc
Confidence 5689999988875443 3222234478899999854
No 34
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}
Probab=31.45 E-value=34 Score=21.67 Aligned_cols=33 Identities=30% Similarity=0.797 Sum_probs=18.3
Q ss_pred ccCCCCcCc-----ccccCCCCCcccEEEEccCCCCccccceeCCCCccc
Q 034037 47 MPCGVCKGK-----GFYICKLCKGNATIEWSPLYDPVFINPCLCPTCEGN 91 (105)
Q Consensus 47 ~~C~~C~Gs-----G~~~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~ 91 (105)
..||.|+.. +...|..|+.. +....-||+|+-.
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~C~~~------------~~~~afCPeCgq~ 40 (81)
T 2jrp_A 3 ITCPVCHHALERNGDTAHCETCAKD------------FSLQALCPDCRQP 40 (81)
T ss_dssp CCCSSSCSCCEECSSEEECTTTCCE------------EEEEEECSSSCSC
T ss_pred CCCCCCCCccccCCCceECcccccc------------CCCcccCcchhhH
Confidence 467777633 23457777641 2233367777654
No 35
>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=30.06 E-value=40 Score=18.56 Aligned_cols=16 Identities=19% Similarity=0.380 Sum_probs=10.4
Q ss_pred eeCCCCcccccc--cCcc
Q 034037 83 CLCPTCEGNRVQ--RCLN 98 (105)
Q Consensus 83 ~~Cp~C~G~G~~--~C~~ 98 (105)
..|..|+..|.. .|++
T Consensus 28 ~~C~~Cg~~GH~~~~C~~ 45 (49)
T 2ec7_A 28 QGCWKCGKTGHVMAKCPE 45 (49)
T ss_dssp CSCSSSCCSSCCGGGCCS
T ss_pred CeeCcCCCcCCccCCCcC
Confidence 368888887763 4553
No 36
>2ygr_A Uvrabc system protein A; hydrolase, nucleotide excision repair; 3.40A {Mycobacterium tuberculosis} PDB: 3zqj_A
Probab=29.81 E-value=12 Score=33.34 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=8.0
Q ss_pred cCCCCCcccEEEE
Q 034037 59 ICKLCKGNATIEW 71 (105)
Q Consensus 59 ~C~~C~G~G~i~~ 71 (105)
.|+.|+|.|.+..
T Consensus 302 aCp~C~G~G~~~~ 314 (993)
T 2ygr_A 302 ACPDCSGLGIRKE 314 (993)
T ss_dssp BCTTTTTSCEEEE
T ss_pred CCCCCcCccceee
Confidence 4666666666554
No 37
>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}
Probab=29.75 E-value=15 Score=24.57 Aligned_cols=18 Identities=22% Similarity=0.582 Sum_probs=13.9
Q ss_pred cceeCCCCccccc-----ccCcc
Q 034037 81 NPCLCPTCEGNRV-----QRCLN 98 (105)
Q Consensus 81 ~~~~Cp~C~G~G~-----~~C~~ 98 (105)
...+||.|+-+|. .-||.
T Consensus 70 R~Y~CpiCGATGd~AHT~kYCP~ 92 (106)
T 3alr_A 70 RQYKCPLCGATGAKAHTKRFCPM 92 (106)
T ss_dssp GGCCCTTTCCCGGGCCCGGGCTT
T ss_pred ccccCCCCCCcCCcccceecCCC
Confidence 5679999999997 35664
No 38
>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}
Probab=29.44 E-value=14 Score=32.56 Aligned_cols=9 Identities=44% Similarity=1.217 Sum_probs=4.3
Q ss_pred eCCCCcccc
Q 034037 84 LCPTCEGNR 92 (105)
Q Consensus 84 ~Cp~C~G~G 92 (105)
.||.|+|.|
T Consensus 275 ~C~~C~G~G 283 (916)
T 3pih_A 275 ACPNCHGLG 283 (916)
T ss_dssp BCTTTTTSS
T ss_pred cCCeeeccc
Confidence 344444444
No 39
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Probab=28.31 E-value=29 Score=20.16 Aligned_cols=8 Identities=38% Similarity=1.248 Sum_probs=3.7
Q ss_pred eCCCCccc
Q 034037 84 LCPTCEGN 91 (105)
Q Consensus 84 ~Cp~C~G~ 91 (105)
.||.|+|.
T Consensus 12 ~CP~c~~~ 19 (56)
T 2kpi_A 12 ACPACHAP 19 (56)
T ss_dssp CCSSSCSC
T ss_pred eCCCCCCc
Confidence 44444443
No 40
>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=28.31 E-value=21 Score=31.86 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=5.9
Q ss_pred eeCCCCccccc
Q 034037 83 CLCPTCEGNRV 93 (105)
Q Consensus 83 ~~Cp~C~G~G~ 93 (105)
-.||.|+|.|.
T Consensus 292 GaCp~C~G~G~ 302 (972)
T 2r6f_A 292 GACPDCDGLGA 302 (972)
T ss_dssp TBCTTTTSCCE
T ss_pred CCCCCCcCccc
Confidence 34555555554
No 41
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=27.86 E-value=58 Score=21.14 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=17.7
Q ss_pred ccCCCCCcccEEEEccCC---CCccccceeCCCCcc
Q 034037 58 YICKLCKGNATIEWSPLY---DPVFINPCLCPTCEG 90 (105)
Q Consensus 58 ~~C~~C~G~G~i~~~~~~---~g~~~~~~~Cp~C~G 90 (105)
..|+.|+....+.++.+. +-.|.....|..|+-
T Consensus 73 ~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~ 108 (113)
T 3h0g_I 73 KECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGF 108 (113)
T ss_dssp SCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCC
T ss_pred cCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCC
Confidence 457777766666554222 222445556766653
No 42
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}
Probab=27.08 E-value=26 Score=25.71 Aligned_cols=6 Identities=50% Similarity=1.082 Sum_probs=2.6
Q ss_pred CCCCCc
Q 034037 60 CKLCKG 65 (105)
Q Consensus 60 C~~C~G 65 (105)
|+.|++
T Consensus 24 CPECGs 29 (197)
T 3k1f_M 24 CPECKV 29 (197)
T ss_dssp CTTTCC
T ss_pred CcCCCC
Confidence 444443
No 43
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Probab=26.94 E-value=26 Score=26.83 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=4.2
Q ss_pred ceeCCCCcc
Q 034037 82 PCLCPTCEG 90 (105)
Q Consensus 82 ~~~Cp~C~G 90 (105)
...||.|++
T Consensus 21 ~~~Cp~Cg~ 29 (345)
T 3k7a_M 21 VLTCPECKV 29 (345)
T ss_dssp CCCCSTTCC
T ss_pred CCcCcCCCC
Confidence 334555544
No 44
>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=26.61 E-value=25 Score=30.56 Aligned_cols=21 Identities=29% Similarity=0.803 Sum_probs=15.0
Q ss_pred eCCCCcccccc------------cCccCCcccc
Q 034037 84 LCPTCEGNRVQ------------RCLNCLGKGF 104 (105)
Q Consensus 84 ~Cp~C~G~G~~------------~C~~C~G~G~ 104 (105)
.|+.|+|.|.. +|+.|+|+-|
T Consensus 640 ~c~~c~g~G~~~~~~~f~~~v~~~c~~c~G~r~ 672 (842)
T 2vf7_A 640 RCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRY 672 (842)
T ss_dssp BCTTTTTCSEEEETTCSSSCEEEECTTTTTCCB
T ss_pred ccccccCCCccchhhhcCCccceecccccCccc
Confidence 48888888753 5888887654
No 45
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M
Probab=25.93 E-value=20 Score=27.73 Aligned_cols=7 Identities=43% Similarity=0.899 Sum_probs=3.1
Q ss_pred cCCCCCc
Q 034037 59 ICKLCKG 65 (105)
Q Consensus 59 ~C~~C~G 65 (105)
.||.|++
T Consensus 23 ~Cp~C~~ 29 (345)
T 4bbr_M 23 TCPECKV 29 (345)
T ss_dssp CCSSCCC
T ss_pred cCCCCCC
Confidence 3444444
No 46
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=25.38 E-value=33 Score=19.80 Aligned_cols=24 Identities=21% Similarity=0.261 Sum_probs=14.6
Q ss_pred CCCcccCCCCc---CcccccCCCCCcc
Q 034037 43 KKFAMPCGVCK---GKGFYICKLCKGN 66 (105)
Q Consensus 43 ~~~~~~C~~C~---GsG~~~C~~C~G~ 66 (105)
+.....|+.|. +.|...|..|+-+
T Consensus 11 ~~~k~iCpkC~a~~~~gaw~CrKCG~~ 37 (51)
T 3j21_g 11 IFKKYVCLRCGATNPWGAKKCRKCGYK 37 (51)
T ss_dssp SSSEEECTTTCCEECTTCSSCSSSSSC
T ss_pred HhCCccCCCCCCcCCCCceecCCCCCc
Confidence 33556677773 4556677777654
No 47
>3i2t_A Epidermal growth factor receptor, isoform A; EGFR, ectodomain, unliganded, autoinhibited, ATP nucleotide-binding, tyrosine-protein kinase; HET: NDG NAG BMA; 2.70A {Drosophila melanogaster} PDB: 3ltf_A* 3ltg_A
Probab=24.10 E-value=81 Score=26.06 Aligned_cols=53 Identities=25% Similarity=0.537 Sum_probs=28.4
Q ss_pred ccCC--CCcCcccccCCCCCcccEE--EEc---cCCCCccc--------cceeCCCCcccccccCccCC
Q 034037 47 MPCG--VCKGKGFYICKLCKGNATI--EWS---PLYDPVFI--------NPCLCPTCEGNRVQRCLNCL 100 (105)
Q Consensus 47 ~~C~--~C~GsG~~~C~~C~G~G~i--~~~---~~~~g~~~--------~~~~Cp~C~G~G~~~C~~C~ 100 (105)
..|. .|.|.|+..|..|.. ... +.. +...+.+. =...|.+|.|.|...|..|.
T Consensus 482 ~~C~~~gC~Gpgp~~C~sC~~-~~~~~~Cv~~C~~~~g~y~~~~~~C~~Ch~~C~tC~G~~~~~C~sC~ 549 (551)
T 3i2t_A 482 DQCNEDGCWGAGTDQCLNCKN-FNFNGTCIADCGYISNAYKFDNRTCKICHPECRTCNGAGADHCQECV 549 (551)
T ss_dssp TTBCTTCBSSSSTTCBSSBSS-EEETTEEESCSCSSSCCCCCSSSCCCCCCSSCSSBCC---CCBSSCC
T ss_pred chhccCCCCCCCCCceeECcc-cCCCCCccccCCCCCCcccCCCCcccCCCCcccCCCCcCcCcccccC
Confidence 4566 899999999999985 111 111 11111111 12356677777777777775
No 48
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=23.69 E-value=50 Score=16.97 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=7.3
Q ss_pred eeCCCCccccc
Q 034037 83 CLCPTCEGNRV 93 (105)
Q Consensus 83 ~~Cp~C~G~G~ 93 (105)
..|..|+..|.
T Consensus 20 ~~C~~Cg~~GH 30 (37)
T 2bl6_A 20 KVCFKCKQPGH 30 (37)
T ss_dssp TTCSSCCCTTG
T ss_pred CeEccCCCcCC
Confidence 35777777765
No 49
>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}
Probab=22.47 E-value=1.2e+02 Score=17.32 Aligned_cols=47 Identities=26% Similarity=0.554 Sum_probs=25.8
Q ss_pred CCcccCCCCcCcc-cccCCCCCcccEEEEc---cCCCCccccceeCCCCcccc
Q 034037 44 KFAMPCGVCKGKG-FYICKLCKGNATIEWS---PLYDPVFINPCLCPTCEGNR 92 (105)
Q Consensus 44 ~~~~~C~~C~GsG-~~~C~~C~G~G~i~~~---~~~~g~~~~~~~Cp~C~G~G 92 (105)
.....|..|+..| .+.|..|.- . .... +...........||.|..+|
T Consensus 9 ~~~~~C~vC~~~g~ll~CD~C~~-~-fH~~Cl~p~l~~~p~g~W~C~~C~~~g 59 (61)
T 2l5u_A 9 DHQDYCEVCQQGGEIILCDTCPR-A-YHMVCLDPDMEKAPEGKWSCPHCEKEG 59 (61)
T ss_dssp CCCSSCTTTSCCSSEEECSSSSC-E-EEHHHHCTTCCSCCCSSCCCTTGGGGS
T ss_pred CCCCCCccCCCCCcEEECCCCCh-h-hhhhccCCCCCCCCCCceECccccccc
Confidence 3456788898766 467888875 2 1111 11111122455677777665
No 50
>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}
Probab=21.94 E-value=52 Score=20.81 Aligned_cols=23 Identities=26% Similarity=0.761 Sum_probs=17.0
Q ss_pred CCcccCCCCcCccc----ccCCCCCcc
Q 034037 44 KFAMPCGVCKGKGF----YICKLCKGN 66 (105)
Q Consensus 44 ~~~~~C~~C~GsG~----~~C~~C~G~ 66 (105)
.....|..|+..|. +.|..|.-.
T Consensus 5 ~~~~~C~~C~~~g~~~~ll~C~~C~~~ 31 (111)
T 2ysm_A 5 SSGANCAVCDSPGDLLDQFFCTTCGQH 31 (111)
T ss_dssp CCCSCBTTTCCCCCTTTSEECSSSCCE
T ss_pred CCCCCCcCCCCCCCCcCCeECCCCCCC
Confidence 35668999988885 588888743
No 51
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=21.22 E-value=39 Score=19.15 Aligned_cols=8 Identities=25% Similarity=0.733 Sum_probs=3.8
Q ss_pred ceeCCCCc
Q 034037 82 PCLCPTCE 89 (105)
Q Consensus 82 ~~~Cp~C~ 89 (105)
...|+.|+
T Consensus 37 R~~C~kCG 44 (50)
T 3j20_Y 37 RWACGKCG 44 (50)
T ss_dssp EEECSSSC
T ss_pred eEECCCCC
Confidence 34555553
No 52
>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}
Probab=21.17 E-value=72 Score=28.04 Aligned_cols=32 Identities=28% Similarity=0.674 Sum_probs=23.4
Q ss_pred cCCCCCcccEEEEccCCCCccccceeCCCCcccc
Q 034037 59 ICKLCKGNATIEWSPLYDPVFINPCLCPTCEGNR 92 (105)
Q Consensus 59 ~C~~C~G~G~i~~~~~~~g~~~~~~~Cp~C~G~G 92 (105)
.|+.|.|.|.+.....+.+ ....+|+.|.|..
T Consensus 715 rc~~c~g~G~i~~e~~flp--~~~v~c~~c~g~r 746 (916)
T 3pih_A 715 RCEACQGQGYVKIEMLFLP--DVYVECDVCKGKR 746 (916)
T ss_dssp BCTTTTTSSEEEECCTTSC--CEEEECTTTTTSC
T ss_pred ccccccCcceEEEeeeccC--cceeecccccccc
Confidence 5889999999887644433 2567899998864
No 53
>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=20.24 E-value=67 Score=17.81 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=10.5
Q ss_pred eeCCCCcccccc--cCcc
Q 034037 83 CLCPTCEGNRVQ--RCLN 98 (105)
Q Consensus 83 ~~Cp~C~G~G~~--~C~~ 98 (105)
..|..|+..|.. .|++
T Consensus 34 ~~C~~Cg~~GH~~~~C~~ 51 (55)
T 1a1t_A 34 KGCWKCGKEGHQMKDCTE 51 (55)
T ss_dssp CBCTTTCCBSSCGGGCSS
T ss_pred CEeCCCCCcCCccCCCcC
Confidence 368888887762 4553
Done!