Query 034351
Match_columns 97
No_of_seqs 147 out of 558
Neff 4.5
Searched_HMMs 29240
Date Mon Mar 25 21:37:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034351.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/034351hhsearch_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 99.0 7.6E-11 2.6E-15 78.4 1.1 49 34-82 27-94 (104)
2 1exk_A DNAJ protein; extended 98.9 5.5E-10 1.9E-14 70.3 1.6 49 34-82 10-77 (79)
3 1nlt_A Protein YDJ1, mitochond 98.8 3.2E-09 1.1E-13 80.1 5.1 59 35-93 38-121 (248)
4 1exk_A DNAJ protein; extended 97.8 1.2E-05 4.2E-10 50.1 3.1 35 47-81 12-62 (79)
5 3lcz_A YCZA, inhibitor of trap 97.7 1.9E-05 6.6E-10 47.8 2.7 25 58-82 9-36 (53)
6 2ctt_A DNAJ homolog subfamily 97.5 5.3E-05 1.8E-09 49.9 2.7 35 47-81 29-79 (104)
7 2bx9_A Anti-trap, AT, tryptoph 97.4 8E-05 2.7E-09 45.0 2.6 25 58-82 9-36 (53)
8 1nlt_A Protein YDJ1, mitochond 97.0 0.00049 1.7E-08 51.6 3.9 41 28-70 49-108 (248)
9 2bx9_A Anti-trap, AT, tryptoph 95.5 0.0045 1.5E-07 37.2 1.4 26 36-70 10-35 (53)
10 3lcz_A YCZA, inhibitor of trap 95.2 0.0066 2.3E-07 36.5 1.4 26 36-70 10-35 (53)
11 3pmq_A Decaheme cytochrome C M 79.8 0.13 4.5E-06 44.1 -2.7 20 35-54 191-220 (669)
12 2lli_A Protein AIR2; RNA surve 61.4 11 0.00036 24.7 4.0 12 59-70 65-76 (124)
13 3agx_A DNAJ homolog subfamily 54.2 9.1 0.00031 26.9 2.8 22 71-92 29-51 (181)
14 3pmq_A Decaheme cytochrome C M 49.9 4.7 0.00016 34.5 0.9 21 47-67 192-220 (669)
15 3nyb_B Protein AIR2; polya RNA 47.5 11 0.00036 23.9 2.1 11 35-45 5-15 (83)
16 1qo8_A Flavocytochrome C3 fuma 46.2 2.1 7.3E-05 34.2 -1.7 43 37-79 14-86 (566)
17 2jne_A Hypothetical protein YF 45.2 9.2 0.00031 25.8 1.5 59 27-85 23-97 (101)
18 2bl6_A Nucleocapsid protein P1 40.6 13 0.00044 19.6 1.4 11 59-69 20-30 (37)
19 2a51_A Nucleocapsid protein; s 40.5 23 0.00078 18.8 2.5 11 59-69 22-32 (39)
20 1y0p_A Fumarate reductase flav 40.0 3 0.0001 33.3 -1.8 44 37-80 13-90 (571)
21 2fiy_A Protein FDHE homolog; F 35.0 80 0.0027 24.3 5.7 35 33-67 180-231 (309)
22 2jrp_A Putative cytoplasmic pr 33.0 30 0.001 22.1 2.5 52 36-87 3-69 (81)
23 3sok_A Fimbrial protein; pilus 29.7 31 0.0011 23.1 2.3 19 6-24 6-24 (151)
24 1a1t_A Nucleocapsid protein; s 29.5 46 0.0016 18.7 2.7 32 35-70 12-45 (55)
25 2ec7_A GAG polyprotein (PR55GA 28.9 44 0.0015 18.5 2.5 12 59-70 28-39 (49)
26 2ihx_A Nucleocapsid (NC) prote 28.1 69 0.0024 18.5 3.4 16 59-74 31-48 (61)
27 1oqw_A Fimbrial protein; type 27.9 36 0.0012 22.4 2.3 19 6-24 6-24 (144)
28 3ts2_A Protein LIN-28 homolog 26.4 50 0.0017 22.6 2.9 16 59-74 120-137 (148)
29 3i2t_A Epidermal growth factor 25.8 38 0.0013 28.1 2.5 19 35-53 481-502 (551)
30 2hi2_A Fimbrial protein; type 24.7 38 0.0013 22.5 2.0 19 6-24 6-24 (158)
31 2bx2_L Ribonuclease E, RNAse E 23.5 27 0.00091 29.0 1.2 13 58-70 408-420 (517)
32 2l5u_A Chromodomain-helicase-D 22.4 78 0.0027 18.3 2.9 22 33-54 9-32 (61)
No 1
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=98.99 E-value=7.6e-11 Score=78.38 Aligned_cols=49 Identities=35% Similarity=0.876 Sum_probs=42.5
Q ss_pred CCCCCCCCcCCcc------cccc-cCcccC---------CcccCCCCCCCeee---eCCCCCccceee
Q 034351 34 PFDRCPSCNGTGR------VTCM-CTRWSD---------GDVGCRTCAGSGRM---ACRSCGGTGTGR 82 (97)
Q Consensus 34 ~~~~C~~C~GsG~------~~C~-C~Gs~~---------~~~~C~~C~G~Gk~---~C~~C~G~G~~r 82 (97)
+...|+.|+|+|. .+|+ |+|+++ ...+|+.|+|+|++ +|+.|+|+|+++
T Consensus 27 ~~~~C~~C~G~G~~~g~~~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~i~~~C~~C~G~G~v~ 94 (104)
T 2ctt_A 27 IMDTCERCNGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSIIISPCVVCRGAGQAK 94 (104)
T ss_dssp CCEECSSSSSSSSCTTCCCEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEECSSCCSSSSSCSEEC
T ss_pred eeeECCCCcCCccCCCCCCccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceECCCcCCCCCCeeEEE
Confidence 3689999999993 6899 999742 25799999999998 899999999997
No 2
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=98.86 E-value=5.5e-10 Score=70.28 Aligned_cols=49 Identities=31% Similarity=0.846 Sum_probs=41.9
Q ss_pred CCCCCCCCcCCcc------cccc-cCcccCC---------cccCCCCCCCeee---eCCCCCccceee
Q 034351 34 PFDRCPSCNGTGR------VTCM-CTRWSDG---------DVGCRTCAGSGRM---ACRSCGGTGTGR 82 (97)
Q Consensus 34 ~~~~C~~C~GsG~------~~C~-C~Gs~~~---------~~~C~~C~G~Gk~---~C~~C~G~G~~r 82 (97)
+...|+.|+|+|. .+|+ |+|++.. ..+|+.|+|+|++ +|+.|+|.|+++
T Consensus 10 ~~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~G~~~ 77 (79)
T 1exk_A 10 TLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVE 77 (79)
T ss_dssp CEEECGGGTTTSBCSSSCCEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEECSSBCGGGTTSSEEE
T ss_pred cceECCCCcccccCCCccCCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEECCCcCCCCCCeEEEe
Confidence 3679999999994 5899 9998431 3699999999998 999999999875
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=98.83 E-value=3.2e-09 Score=80.13 Aligned_cols=59 Identities=25% Similarity=0.607 Sum_probs=46.8
Q ss_pred CCCCCCCcCCc-----ccccc-cCcccC-------------CcccCCCCCCCeee-----eCCCCCccceee-eEEEEEE
Q 034351 35 FDRCPSCNGTG-----RVTCM-CTRWSD-------------GDVGCRTCAGSGRM-----ACRSCGGTGTGR-PLPVQLS 89 (97)
Q Consensus 35 ~~~C~~C~GsG-----~~~C~-C~Gs~~-------------~~~~C~~C~G~Gk~-----~C~~C~G~G~~r-~v~v~I~ 89 (97)
...|+.|+|+| ..+|+ |+|+++ ...+|+.|+|+|++ +|+.|+|+|+++ ..+++|.
T Consensus 38 ~~~C~~C~G~G~~~g~~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~~~~C~~C~G~g~~~~~~~l~V~ 117 (248)
T 1nlt_A 38 QILCKECEGRGGKKGAVKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVENERKILEVH 117 (248)
T ss_dssp EEECTTTTTCSBSTTTCCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCEEEEEEEEEEE
T ss_pred EEeCCCCcCccCCCCCCccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEeccCCCCcccCCCceEeeeEEEEEE
Confidence 56899999999 37899 999742 36799999999954 899999999997 4555555
Q ss_pred eeCC
Q 034351 90 VRRP 93 (97)
Q Consensus 90 ~~~~ 93 (97)
+.++
T Consensus 118 Ip~G 121 (248)
T 1nlt_A 118 VEPG 121 (248)
T ss_dssp ECTT
T ss_pred ECCC
Confidence 5443
No 4
>1exk_A DNAJ protein; extended beta-hairpin, CXXCXGXG, zinc-binding motif, chaperone; NMR {Escherichia coli} SCOP: g.54.1.1
Probab=97.81 E-value=1.2e-05 Score=50.11 Aligned_cols=35 Identities=37% Similarity=0.801 Sum_probs=20.7
Q ss_pred cccc-cCcccC----CcccCCCCCCCeee-----------eCCCCCcccee
Q 034351 47 VTCM-CTRWSD----GDVGCRTCAGSGRM-----------ACRSCGGTGTG 81 (97)
Q Consensus 47 ~~C~-C~Gs~~----~~~~C~~C~G~Gk~-----------~C~~C~G~G~~ 81 (97)
..|+ |+|++. ...+|+.|+|+|++ +|+.|+|+|.+
T Consensus 12 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~ 62 (79)
T 1exk_A 12 EECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTL 62 (79)
T ss_dssp EECGGGTTTSBCSSSCCEECTTTTTSSEEEEEETTEEEEEECTTTTTSSEE
T ss_pred eECCCCcccccCCCccCCCCCCCcCeEEEEEEcCCCEEeeECcCCCCccEE
Confidence 4566 666532 13566666666643 56666666655
No 5
>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=97.71 E-value=1.9e-05 Score=47.82 Aligned_cols=25 Identities=40% Similarity=0.889 Sum_probs=22.6
Q ss_pred cccCCCCCCCeee---eCCCCCccceee
Q 034351 58 DVGCRTCAGSGRM---ACRSCGGTGTGR 82 (97)
Q Consensus 58 ~~~C~~C~G~Gk~---~C~~C~G~G~~r 82 (97)
..+|+.|+|+|++ +|+.|+|+|+++
T Consensus 9 ~~~C~~C~GsG~~i~~~C~~C~G~G~v~ 36 (53)
T 3lcz_A 9 ETTCPNCNGSGREEPEPCPKCLGKGVIL 36 (53)
T ss_dssp EEECTTTTTSCEETTEECTTTTTSSEEE
T ss_pred eccCcCCcccccCCCCcCCCCCCcEEEE
Confidence 5789999999996 999999999876
No 6
>2ctt_A DNAJ homolog subfamily A member 3; ZING finger, beta-hairpin, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=97.50 E-value=5.3e-05 Score=49.88 Aligned_cols=35 Identities=40% Similarity=0.865 Sum_probs=17.3
Q ss_pred cccc-cCcccC----CcccCCCCCCCeee-----------eCCCCCcccee
Q 034351 47 VTCM-CTRWSD----GDVGCRTCAGSGRM-----------ACRSCGGTGTG 81 (97)
Q Consensus 47 ~~C~-C~Gs~~----~~~~C~~C~G~Gk~-----------~C~~C~G~G~~ 81 (97)
..|+ |+|++. ...+|+.|+|+|++ .|+.|+|.|.+
T Consensus 29 ~~C~~C~G~G~~~g~~~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~ 79 (104)
T 2ctt_A 29 DTCERCNGKGNEPGTKVQHCHYCGGSGMETINTGPFVMRSTCRRCGGRGSI 79 (104)
T ss_dssp EECSSSSSSSSCTTCCCEECSSSSSSCEEEEEETTEEEEEECSSSSSSSEE
T ss_pred eECCCCcCCccCCCCCCccCCCCCCCEEEEEEeCCEEEEEECCcCCCcceE
Confidence 4555 555421 13455555555532 45555555544
No 7
>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=97.42 E-value=8e-05 Score=45.04 Aligned_cols=25 Identities=32% Similarity=0.918 Sum_probs=21.0
Q ss_pred cccCCCCCCCeee---eCCCCCccceee
Q 034351 58 DVGCRTCAGSGRM---ACRSCGGTGTGR 82 (97)
Q Consensus 58 ~~~C~~C~G~Gk~---~C~~C~G~G~~r 82 (97)
..+|+.|+|+|++ +|+.|+|+|+++
T Consensus 9 ~~~C~~C~GsG~~~~~~C~~C~G~G~v~ 36 (53)
T 2bx9_A 9 EVACPKCERAGEIEGTPCPACSGKGVIL 36 (53)
T ss_dssp EEECTTTTTSSEETTEECTTTTTSSEEE
T ss_pred cccCCCCcceeccCCCCCccCCCCccEE
Confidence 4678888888876 899999999876
No 8
>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=97.03 E-value=0.00049 Score=51.64 Aligned_cols=41 Identities=34% Similarity=0.711 Sum_probs=32.6
Q ss_pred CccCCCCCCCCCCCcCCcc---------------cccc-cCcccC---CcccCCCCCCCeee
Q 034351 28 QKPMAGPFDRCPSCNGTGR---------------VTCM-CTRWSD---GDVGCRTCAGSGRM 70 (97)
Q Consensus 28 ~~P~s~~~~~C~~C~GsG~---------------~~C~-C~Gs~~---~~~~C~~C~G~Gk~ 70 (97)
..|.+ ..+|+.|+|+|. .+|+ |+|++. ...+|+.|+|.|.+
T Consensus 49 ~~~g~--~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C~~C~G~G~~i~~~~~C~~C~G~g~~ 108 (248)
T 1nlt_A 49 GKKGA--VKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVE 108 (248)
T ss_dssp BSTTT--CCCCTTSSSSSCEEEEEESSSEEEEEECSCTTCSSSSSCCCTTSBCSSSTTSCEE
T ss_pred CCCCC--CccCCCCCCCcEEEEEEecCceEEEEEEcCCCCCCcCEEeccCCCCcccCCCceE
Confidence 34554 489999999994 3699 999853 27899999999974
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=95.55 E-value=0.0045 Score=37.22 Aligned_cols=26 Identities=31% Similarity=0.937 Sum_probs=16.1
Q ss_pred CCCCCCcCCcccccccCcccCCcccCCCCCCCeee
Q 034351 36 DRCPSCNGTGRVTCMCTRWSDGDVGCRTCAGSGRM 70 (97)
Q Consensus 36 ~~C~~C~GsG~~~C~C~Gs~~~~~~C~~C~G~Gk~ 70 (97)
.+|+.|+|+|.. ...+|+.|+|+|++
T Consensus 10 ~~C~~C~GsG~~---------~~~~C~~C~G~G~v 35 (53)
T 2bx9_A 10 VACPKCERAGEI---------EGTPCPACSGKGVI 35 (53)
T ss_dssp EECTTTTTSSEE---------TTEECTTTTTSSEE
T ss_pred ccCCCCcceecc---------CCCCCccCCCCccE
Confidence 345555555543 23678888888875
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=95.22 E-value=0.0066 Score=36.46 Aligned_cols=26 Identities=42% Similarity=1.055 Sum_probs=14.5
Q ss_pred CCCCCCcCCcccccccCcccCCcccCCCCCCCeee
Q 034351 36 DRCPSCNGTGRVTCMCTRWSDGDVGCRTCAGSGRM 70 (97)
Q Consensus 36 ~~C~~C~GsG~~~C~C~Gs~~~~~~C~~C~G~Gk~ 70 (97)
.+|+.|+|+|.. ...+|+.|+|.|.+
T Consensus 10 ~~C~~C~GsG~~---------i~~~C~~C~G~G~v 35 (53)
T 3lcz_A 10 TTCPNCNGSGRE---------EPEPCPKCLGKGVI 35 (53)
T ss_dssp EECTTTTTSCEE---------TTEECTTTTTSSEE
T ss_pred ccCcCCcccccC---------CCCcCCCCCCcEEE
Confidence 456666666642 13556666666654
No 11
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=79.82 E-value=0.13 Score=44.06 Aligned_cols=20 Identities=35% Similarity=0.790 Sum_probs=14.3
Q ss_pred CCCCCCCcCCc---------ccccc-cCcc
Q 034351 35 FDRCPSCNGTG---------RVTCM-CTRW 54 (97)
Q Consensus 35 ~~~C~~C~GsG---------~~~C~-C~Gs 54 (97)
.+.|..|||+| ..+|+ |||+
T Consensus 191 ~~~C~tCHGsGA~~Gt~~~~~~tC~tCHGs 220 (669)
T 3pmq_A 191 IDTCNSCHSNLAFHGGRYNQVETCVTCHNS 220 (669)
T ss_dssp SHHHHHHHSSCCTTTTTSCSSSCSTTTSST
T ss_pred CCcCCCCCCCCCcCCccCcCCccCCCCCCC
Confidence 56788888776 14687 8775
No 12
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Probab=61.44 E-value=11 Score=24.70 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=5.8
Q ss_pred ccCCCCCCCeee
Q 034351 59 VGCRTCAGSGRM 70 (97)
Q Consensus 59 ~~C~~C~G~Gk~ 70 (97)
..|..|+..|..
T Consensus 65 ~~C~~Cg~~GH~ 76 (124)
T 2lli_A 65 VQCTLCKSKKHS 76 (124)
T ss_dssp CSSSSSCSSCCC
T ss_pred ccCCCCCcCCcc
Confidence 345555555543
No 13
>3agx_A DNAJ homolog subfamily B member 1; chaperone; 1.85A {Homo sapiens} PDB: 3agy_A 3agz_A 2qld_A
Probab=54.17 E-value=9.1 Score=26.88 Aligned_cols=22 Identities=9% Similarity=0.110 Sum_probs=14.7
Q ss_pred eCCCCCccceee-eEEEEEEeeC
Q 034351 71 ACRSCGGTGTGR-PLPVQLSVRR 92 (97)
Q Consensus 71 ~C~~C~G~G~~r-~v~v~I~~~~ 92 (97)
+|..|+|+|+++ ..+++|.+.+
T Consensus 29 ~c~~c~G~g~~~~~~~l~V~Ip~ 51 (181)
T 3agx_A 29 KRLNPDGKSIRNEDKILTIEVKK 51 (181)
T ss_dssp EEECTTSSCEEEEEEEEEEEECT
T ss_pred ccCCCCCceEEEEeEEEEEEECC
Confidence 688999999875 4444444444
No 14
>3pmq_A Decaheme cytochrome C MTRF; greek KEY, C type cytochrome, outer membrane, electron trans; HET: HEC; 3.20A {Shewanella oneidensis}
Probab=49.87 E-value=4.7 Score=34.55 Aligned_cols=21 Identities=33% Similarity=0.525 Sum_probs=14.1
Q ss_pred cccc-cCccc--C-----CcccCCCCCCC
Q 034351 47 VTCM-CTRWS--D-----GDVGCRTCAGS 67 (97)
Q Consensus 47 ~~C~-C~Gs~--~-----~~~~C~~C~G~ 67 (97)
..|. |||++ . ...+|+.|+|+
T Consensus 192 ~~C~tCHGsGA~~Gt~~~~~~tC~tCHGs 220 (669)
T 3pmq_A 192 DTCNSCHSNLAFHGGRYNQVETCVTCHNS 220 (669)
T ss_dssp HHHHHHHSSCCTTTTTSCSSSCSTTTSST
T ss_pred CcCCCCCCCCCcCCccCcCCccCCCCCCC
Confidence 5688 88762 1 24678888887
No 15
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}
Probab=47.48 E-value=11 Score=23.95 Aligned_cols=11 Identities=18% Similarity=0.501 Sum_probs=6.9
Q ss_pred CCCCCCCcCCc
Q 034351 35 FDRCPSCNGTG 45 (97)
Q Consensus 35 ~~~C~~C~GsG 45 (97)
...|..|...|
T Consensus 5 ~~~C~~Cg~~G 15 (83)
T 3nyb_B 5 KVQCTLCKSKK 15 (83)
T ss_dssp --CCSSSCCSS
T ss_pred cCCCCCCCCCC
Confidence 56677787777
No 16
>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=46.24 E-value=2.1 Score=34.17 Aligned_cols=43 Identities=26% Similarity=0.698 Sum_probs=30.7
Q ss_pred CCCCCcCCcc----------cccc-cCccc------------C----CcccCCCCCCCeee---eCCCCCccc
Q 034351 37 RCPSCNGTGR----------VTCM-CTRWS------------D----GDVGCRTCAGSGRM---ACRSCGGTG 79 (97)
Q Consensus 37 ~C~~C~GsG~----------~~C~-C~Gs~------------~----~~~~C~~C~G~Gk~---~C~~C~G~G 79 (97)
.|..||+.+. ..|. ||... + +...|..|+-.-.. .|..|+...
T Consensus 14 ~C~~CH~~~~~~~~~~~~~~~~C~~CH~~~~~~~~~~~~~~~h~~~~~~~~C~~CH~~h~~~~~~c~~ch~~~ 86 (566)
T 1qo8_A 14 SCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFD 86 (566)
T ss_dssp CGGGTSCSSCCCCTTCHHHHHHHHHHHCCHHHHCCSSSSSCTTSSTTCSCCGGGTSCSSSCCCCGGGGTCCCC
T ss_pred ChhhhCCCccccccccCccCCHHhhhCcCHHHHhhccccCCcchhcCCCCCchhhCcCCcCcCchhhhhcCCC
Confidence 7999999863 3699 99640 0 24689999876543 788888764
No 17
>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1
Probab=45.17 E-value=9.2 Score=25.77 Aligned_cols=59 Identities=19% Similarity=0.459 Sum_probs=31.9
Q ss_pred CCccCCCC-CCCCCCCcCC-----cccccc-cCcccCCcccCCCCCCCeee---------eCCCCCccceeeeEE
Q 034351 27 DQKPMAGP-FDRCPSCNGT-----GRVTCM-CTRWSDGDVGCRTCAGSGRM---------ACRSCGGTGTGRPLP 85 (97)
Q Consensus 27 ~~~P~s~~-~~~C~~C~Gs-----G~~~C~-C~Gs~~~~~~C~~C~G~Gk~---------~C~~C~G~G~~r~v~ 85 (97)
+.+|.+.. ...|+.|+-. |...|. |+..-.-...||.|+-.=++ -|..|+|--.+++|.
T Consensus 23 ~~~~~~~~M~~~CP~Cq~eL~~~g~~~hC~~C~~~f~~~a~CPdC~q~LevLkACGAvdYFC~~chgLiSKkRV~ 97 (101)
T 2jne_A 23 GLVPRGSHMELHCPQCQHVLDQDNGHARCRSCGEFIEMKALCPDCHQPLQVLKACGAVDYFCQHGHGLISKKRVE 97 (101)
T ss_dssp --------CCCBCSSSCSBEEEETTEEEETTTCCEEEEEEECTTTCSBCEEEEETTEEEEEETTTTEEECTTTSE
T ss_pred ccccCcccccccCccCCCcceecCCEEECccccchhhccccCcchhhHHHHHHHhcCcchhhccCCceeecceEE
Confidence 36666542 4789999854 234598 98863345778888876554 456665433333433
No 18
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}
Probab=40.55 E-value=13 Score=19.58 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=5.6
Q ss_pred ccCCCCCCCee
Q 034351 59 VGCRTCAGSGR 69 (97)
Q Consensus 59 ~~C~~C~G~Gk 69 (97)
..|..|+..|.
T Consensus 20 ~~C~~Cg~~GH 30 (37)
T 2bl6_A 20 KVCFKCKQPGH 30 (37)
T ss_dssp TTCSSCCCTTG
T ss_pred CeEccCCCcCC
Confidence 34555555554
No 19
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}
Probab=40.47 E-value=23 Score=18.77 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=5.2
Q ss_pred ccCCCCCCCee
Q 034351 59 VGCRTCAGSGR 69 (97)
Q Consensus 59 ~~C~~C~G~Gk 69 (97)
..|..|+..|.
T Consensus 22 ~~C~~Cg~~GH 32 (39)
T 2a51_A 22 EGCWNCGSKEH 32 (39)
T ss_dssp SSCTTTCCSSS
T ss_pred CccccCCCCCC
Confidence 34555554443
No 20
>1y0p_A Fumarate reductase flavoprotein subunit; flavocytochrome, mesaconate, oxidoreductase; HET: HEM FAD; 1.50A {Shewanella frigidimarina} SCOP: a.138.1.3 c.3.1.4 d.168.1.1 PDB: 1qjd_A* 2b7s_A* 1jry_A* 2b7r_A* 1ksu_A* 1jrz_A* 1jrx_A* 1m64_A* 1p2h_A* 1p2e_A* 1kss_A* 1e39_A* 1q9i_A* 1lj1_A*
Probab=40.02 E-value=3 Score=33.27 Aligned_cols=44 Identities=27% Similarity=0.746 Sum_probs=31.4
Q ss_pred CCCCCcCCcc-----------cccc-cCccc--------------C-----CcccCCCCCCCee---eeCCCCCccce
Q 034351 37 RCPSCNGTGR-----------VTCM-CTRWS--------------D-----GDVGCRTCAGSGR---MACRSCGGTGT 80 (97)
Q Consensus 37 ~C~~C~GsG~-----------~~C~-C~Gs~--------------~-----~~~~C~~C~G~Gk---~~C~~C~G~G~ 80 (97)
.|..||+... ..|. ||... + +...|..|+..=. ..|.+|+-...
T Consensus 13 ~C~~CH~~~~~~~~~~~~~~~~~C~~CH~~~~~~~~~~~~~~~~~h~~H~~~~~~C~~CH~~h~~~~~~C~~CH~~~~ 90 (571)
T 1y0p_A 13 ECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDF 90 (571)
T ss_dssp CGGGTSCTTCCCCCTTCHHHHHHHHHHHCCHHHHHTTSCCSSCCTTSCSCCSCCCGGGTCCSSSCBCCGGGGTCCCCC
T ss_pred ChhhcCCCcccccccccccccchhhhhCcChhhcccccccccCCccccccCCCCCccccCccccCCCccccccChhhc
Confidence 8999999752 5699 99631 0 2468999997633 27999997643
No 21
>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=35.00 E-value=80 Score=24.26 Aligned_cols=35 Identities=29% Similarity=0.842 Sum_probs=23.3
Q ss_pred CCCCCCCCCcCC-------------c--ccccc-cCc-ccCCcccCCCCCCC
Q 034351 33 GPFDRCPSCNGT-------------G--RVTCM-CTR-WSDGDVGCRTCAGS 67 (97)
Q Consensus 33 ~~~~~C~~C~Gs-------------G--~~~C~-C~G-s~~~~~~C~~C~G~ 67 (97)
.....|+.|.+. | +..|. |.- |......|+.|+-+
T Consensus 180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~~ 231 (309)
T 2fiy_A 180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEES 231 (309)
T ss_dssp TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCC
T ss_pred ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCCC
Confidence 557889999542 2 25677 775 44556788888764
No 22
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}
Probab=32.98 E-value=30 Score=22.14 Aligned_cols=52 Identities=17% Similarity=0.418 Sum_probs=26.9
Q ss_pred CCCCCCcCC-----cccccc-cCcccCCcccCCCCCCCeee---------eCCCCCccceeeeEEEE
Q 034351 36 DRCPSCNGT-----GRVTCM-CTRWSDGDVGCRTCAGSGRM---------ACRSCGGTGTGRPLPVQ 87 (97)
Q Consensus 36 ~~C~~C~Gs-----G~~~C~-C~Gs~~~~~~C~~C~G~Gk~---------~C~~C~G~G~~r~v~v~ 87 (97)
..|+.|+.. +...|. |+..-.....||.|+-.=++ -|..|++--.+++|.+.
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~C~~~~~~~afCPeCgq~Le~lkACGA~~yFC~~C~~LiSkkrv~f~ 69 (81)
T 2jrp_A 3 ITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFV 69 (81)
T ss_dssp CCCSSSCSCCEECSSEEECTTTCCEEEEEEECSSSCSCCCEEEETTEEEECCTTTTCCCCTTSSEEE
T ss_pred CCCCCCCCccccCCCceECccccccCCCcccCcchhhHHHHHHhcCCcCeeeccCCCEeecceEEEE
Confidence 457777632 234577 77642222355555543322 57777765555555443
No 23
>3sok_A Fimbrial protein; pilus subunit, extracellular, cell adhesion; 2.30A {Dichelobacter nodosus}
Probab=29.68 E-value=31 Score=23.13 Aligned_cols=19 Identities=26% Similarity=0.231 Sum_probs=14.6
Q ss_pred hhhHHhhhHHHHHHHHHhh
Q 034351 6 LTQVATGLSVLAGAALVKS 24 (97)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~ 24 (97)
|..|+++++||+++++-..
T Consensus 6 llvviaIigiLaaia~p~~ 24 (151)
T 3sok_A 6 LMIVVAIIGILAAFAIPAY 24 (151)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5667888999988887654
No 24
>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=29.46 E-value=46 Score=18.65 Aligned_cols=32 Identities=25% Similarity=0.613 Sum_probs=15.2
Q ss_pred CCCCCCCcCCcc--cccccCcccCCcccCCCCCCCeee
Q 034351 35 FDRCPSCNGTGR--VTCMCTRWSDGDVGCRTCAGSGRM 70 (97)
Q Consensus 35 ~~~C~~C~GsG~--~~C~C~Gs~~~~~~C~~C~G~Gk~ 70 (97)
...|..|...|- ..|+ .. ....|..|+..|..
T Consensus 12 ~~~C~~Cg~~GH~a~~C~--~~--~~~~C~~Cg~~GH~ 45 (55)
T 1a1t_A 12 TVKCFNCGKEGHIAKNCR--AP--RKKGCWKCGKEGHQ 45 (55)
T ss_dssp TCBCTTTCCBSSCGGGCS--SC--SCCBCTTTCCBSSC
T ss_pred CcceeeeCCCCcChhhcC--CC--CCCEeCCCCCcCCc
Confidence 345666665552 2231 10 12456666666654
No 25
>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=28.93 E-value=44 Score=18.55 Aligned_cols=12 Identities=33% Similarity=1.008 Sum_probs=7.4
Q ss_pred ccCCCCCCCeee
Q 034351 59 VGCRTCAGSGRM 70 (97)
Q Consensus 59 ~~C~~C~G~Gk~ 70 (97)
..|..|+..|.+
T Consensus 28 ~~C~~Cg~~GH~ 39 (49)
T 2ec7_A 28 QGCWKCGKTGHV 39 (49)
T ss_dssp CSCSSSCCSSCC
T ss_pred CeeCcCCCcCCc
Confidence 456666666654
No 26
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}
Probab=28.13 E-value=69 Score=18.45 Aligned_cols=16 Identities=38% Similarity=0.964 Sum_probs=9.9
Q ss_pred ccCCCCCCCeee--eCCC
Q 034351 59 VGCRTCAGSGRM--ACRS 74 (97)
Q Consensus 59 ~~C~~C~G~Gk~--~C~~ 74 (97)
..|..|+..|.+ .|+.
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 457777777765 4543
No 27
>1oqw_A Fimbrial protein; type IV pilin, fiber-forming protein, adhesion, pseudomonas aerugionosa, PAK pilin, cell adhesion; 2.00A {Pseudomonas aeruginosa} SCOP: d.24.1.1
Probab=27.86 E-value=36 Score=22.43 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=14.5
Q ss_pred hhhHHhhhHHHHHHHHHhh
Q 034351 6 LTQVATGLSVLAGAALVKS 24 (97)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~ 24 (97)
|..|+++++||+++++-..
T Consensus 6 llivi~Ii~il~~ia~p~~ 24 (144)
T 1oqw_A 6 LMIVVAIIGILAAIAIPQY 24 (144)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5567888999998887644
No 28
>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=26.45 E-value=50 Score=22.56 Aligned_cols=16 Identities=25% Similarity=0.665 Sum_probs=9.8
Q ss_pred ccCCCCCCCeee--eCCC
Q 034351 59 VGCRTCAGSGRM--ACRS 74 (97)
Q Consensus 59 ~~C~~C~G~Gk~--~C~~ 74 (97)
..|..|+..|.. -|+.
T Consensus 120 ~~C~~Cg~~GH~~r~Cp~ 137 (148)
T 3ts2_A 120 KKCHFCQSINHMVASCPL 137 (148)
T ss_dssp CCCTTTCCSSCCGGGCTT
T ss_pred CcccccCCcCCEeccCcC
Confidence 457777776665 4543
No 29
>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=25.80 E-value=38 Score=28.07 Aligned_cols=19 Identities=37% Similarity=1.038 Sum_probs=14.4
Q ss_pred CCCCC--CCcCCcccccc-cCc
Q 034351 35 FDRCP--SCNGTGRVTCM-CTR 53 (97)
Q Consensus 35 ~~~C~--~C~GsG~~~C~-C~G 53 (97)
...|. .|.|.|...|. |..
T Consensus 481 ~~~C~~~gC~Gpgp~~C~sC~~ 502 (551)
T 3i2t_A 481 SDQCNEDGCWGAGTDQCLNCKN 502 (551)
T ss_dssp CTTBCTTCBSSSSTTCBSSBSS
T ss_pred CchhccCCCCCCCCCceeECcc
Confidence 34566 89999988887 775
No 30
>2hi2_A Fimbrial protein; type IV pilin, fiber-forming protein, membrane protein, DNA protein, contractIle protein, cell adhesion; HET: MEA GLA DT6 HTO; 2.30A {Neisseria gonorrhoeae} PDB: 2hil_A* 1ay2_A* 2pil_A*
Probab=24.72 E-value=38 Score=22.48 Aligned_cols=19 Identities=32% Similarity=0.261 Sum_probs=14.1
Q ss_pred hhhHHhhhHHHHHHHHHhh
Q 034351 6 LTQVATGLSVLAGAALVKS 24 (97)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~ 24 (97)
|..|+++++||+++++-..
T Consensus 6 l~vvi~ii~il~~~~~p~~ 24 (158)
T 2hi2_A 6 LMIVIAIVGILAAVALPAY 24 (158)
T ss_dssp HHHHHHHHHHHHHHHTTTH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5667888899888876543
No 31
>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=23.52 E-value=27 Score=29.00 Aligned_cols=13 Identities=31% Similarity=0.877 Sum_probs=9.2
Q ss_pred cccCCCCCCCeee
Q 034351 58 DVGCRTCAGSGRM 70 (97)
Q Consensus 58 ~~~C~~C~G~Gk~ 70 (97)
..+||.|+|+|.+
T Consensus 408 ~~~Cp~C~G~G~v 420 (517)
T 2bx2_L 408 HHVCPRCSGTGTV 420 (517)
T ss_dssp CCCCSSSSSSSCC
T ss_pred cCcCCCcCCceeE
Confidence 4577778777764
No 32
>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}
Probab=22.44 E-value=78 Score=18.26 Aligned_cols=22 Identities=32% Similarity=0.748 Sum_probs=15.9
Q ss_pred CCCCCCCCCcCCcc-cccc-cCcc
Q 034351 33 GPFDRCPSCNGTGR-VTCM-CTRW 54 (97)
Q Consensus 33 ~~~~~C~~C~GsG~-~~C~-C~Gs 54 (97)
.....|..|+..|. ..|. |..+
T Consensus 9 ~~~~~C~vC~~~g~ll~CD~C~~~ 32 (61)
T 2l5u_A 9 DHQDYCEVCQQGGEIILCDTCPRA 32 (61)
T ss_dssp CCCSSCTTTSCCSSEEECSSSSCE
T ss_pred CCCCCCccCCCCCcEEECCCCChh
Confidence 34678999987674 5688 8875
Done!