Query 004889
Match_columns 725
No_of_seqs 193 out of 225
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 08:54:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004889.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/004889hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1v54_K IHQ, cytochrome C oxida 14.5 81 0.0028 24.9 2.0 20 671-690 27-46 (56)
2 2y69_K Cytochrome C oxidase po 10.9 1.1E+02 0.0039 25.7 2.0 20 671-690 51-70 (80)
3 1rw2_A ATP-dependent DNA helic 9.5 6.6E+02 0.022 23.5 7.0 60 54-118 35-94 (152)
4 1q2z_A ATP-dependent DNA helic 9.2 3.9E+02 0.013 23.9 5.1 59 55-118 5-63 (120)
5 2vj4_A Protein MXIC, MXIC; sec 7.9 1.6E+03 0.056 23.0 12.0 138 21-191 28-169 (294)
6 1gxg_A Colicin E8 immunity pro 7.6 4.8E+02 0.016 22.2 4.6 70 556-649 14-83 (85)
7 1unk_A Colicin E7; immunity pr 7.4 5.1E+02 0.017 22.3 4.7 73 555-649 13-85 (87)
8 3u43_A Colicin-E2 immunity pro 7.0 5E+02 0.017 22.6 4.5 26 624-649 59-84 (94)
9 1fr2_A Colicin E9 immunity pro 5.6 6.5E+02 0.022 21.4 4.4 26 624-649 59-84 (86)
10 2dyj_A Ribosome-binding factor 5.5 2.1E+02 0.0073 24.5 1.3 16 647-662 78-93 (95)
No 1
>1v54_K IHQ, cytochrome C oxidase polypeptide VIIB; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.5.1 PDB: 1oco_K* 1occ_K* 1ocz_K* 1ocr_K* 1v55_K* 2dyr_K* 2dys_K* 2eij_K* 2eik_K* 2eil_K* 2eim_K* 2ein_K* 2occ_K* 2ybb_V* 2zxw_K* 3abk_K* 3abl_K* 3abm_K* 3ag1_K* 3ag2_K* ...
Probab=14.49 E-value=81 Score=24.89 Aligned_cols=20 Identities=30% Similarity=0.750 Sum_probs=17.1
Q ss_pred hhHHHHhhhcCccccCCCcc
Q 004889 671 YVWQLVLSRCGFSFNPSAIN 690 (725)
Q Consensus 671 yvW~~v~~~~g~~w~~~~i~ 690 (725)
-+|..+.-|.||-||-+-+.
T Consensus 27 a~W~y~~TQ~GIeWnlSPVG 46 (56)
T 1v54_K 27 AVWVYMATQIGIEWNPSPVG 46 (56)
T ss_dssp HHHHHHHHHSCCCCCCCCTT
T ss_pred hhHhhhheeeceeeccCccc
Confidence 48999999999999987554
No 2
>2y69_K Cytochrome C oxidase polypeptide 7B; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}
Probab=10.90 E-value=1.1e+02 Score=25.72 Aligned_cols=20 Identities=30% Similarity=0.750 Sum_probs=17.0
Q ss_pred hhHHHHhhhcCccccCCCcc
Q 004889 671 YVWQLVLSRCGFSFNPSAIN 690 (725)
Q Consensus 671 yvW~~v~~~~g~~w~~~~i~ 690 (725)
-+|..+.-+.||-||-+-+.
T Consensus 51 a~W~y~~TQ~GIeWnlSPVG 70 (80)
T 2y69_K 51 AVWVYMATQIGIEWNPSPVG 70 (80)
T ss_dssp HHHHHHHHHSCCCCCCCCTT
T ss_pred hhHHHhheecceeecCCccc
Confidence 48999999999999976554
No 3
>1rw2_A ATP-dependent DNA helicase II, 80 kDa subunit; KU80, NHEJ, structure, DNA-PK, DNA binding protein; NMR {Homo sapiens} SCOP: a.118.19.1
Probab=9.53 E-value=6.6e+02 Score=23.50 Aligned_cols=60 Identities=10% Similarity=0.059 Sum_probs=43.3
Q ss_pred chhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChHHHHHHHHHHHHHHHhhhhhhcc
Q 004889 54 HRVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASVAIMKAINAVYISSVFLKYLIEN 118 (725)
Q Consensus 54 d~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~~~~qalNclriLtrilp~l~E~ 118 (725)
+.+.+..+.++.++ ..+++.+--+..++.++..++ .+..+.+|+-||+.+|-=+-..-|-
T Consensus 35 nPv~DFk~lL~~~~---~~~~~A~~qM~~vI~~Ll~~s--~~~~y~KA~ecL~~lR~~~i~~~ep 94 (152)
T 1rw2_A 35 NPAENFRVLVKQKK---ASFEEASNQLINHIEQFLDTN--ETPYFMKSIDCIRAFREEAIKFSEE 94 (152)
T ss_dssp CTTHHHHHHHHSSS---SCHHHHHHHHHHHHHHHHHSS--CSHHHHHHHHHHHHHHHHHHHHTCS
T ss_pred CcHHHHHHHHHcCc---hhHHHHHHHHHHHHHHHHhcc--ccchHHHHHHHHHHHHHHHHhccCh
Confidence 35666555665433 458888888888888888875 4567899999999999777655443
No 4
>1q2z_A ATP-dependent DNA helicase II, 80 kDa subunit; KU, DNA repair, protein structure, spectroscopy, DNA-PK, KU86, KU80, protein binding; NMR {Homo sapiens} SCOP: a.118.19.1
Probab=9.24 E-value=3.9e+02 Score=23.87 Aligned_cols=59 Identities=10% Similarity=0.053 Sum_probs=40.2
Q ss_pred hhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChHHHHHHHHHHHHHHHhhhhhhcc
Q 004889 55 RVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASVAIMKAINAVYISSVFLKYLIEN 118 (725)
Q Consensus 55 ~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~~~~qalNclriLtrilp~l~E~ 118 (725)
-+.+..+.++.++ .++.+.+--+..++.++..++ .+..+.+|+-||+.+|-=+-..-|-
T Consensus 5 Pv~DFk~ll~~~~---~~~~~A~~qm~~vI~~Ll~~s--~~~~y~ka~ecl~~~R~~~i~~~ep 63 (120)
T 1q2z_A 5 PAENFRVLVKQKK---ASFEEASNQLINHIEQFLDTN--ETPYFMKSIDCIRAFREEAIKFSEE 63 (120)
T ss_dssp HHHHHHHHTSSSC---CTTTHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred hHHHHHHHHHcCc---hhHHHHHHHHHHHHHHHHhCc--ccchHHHHHHHHHHHHHHHHhccCh
Confidence 3455444554432 568887877777777777765 5567899999999999766554333
No 5
>2vj4_A Protein MXIC, MXIC; secretion regulation, transport protein, T3SS, virulence, TR type three secretion system; HET: MLY; 2.50A {Shigella flexneri} PDB: 2vix_A* 2vj5_A
Probab=7.87 E-value=1.6e+03 Score=23.03 Aligned_cols=138 Identities=12% Similarity=0.102 Sum_probs=82.9
Q ss_pred HHHHhhhCCcc--CCCCc--hHHHHhccCCCCCCCCcchhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChH
Q 004889 21 YLIATFVGEKS--FPLAS--DFWQKLLELPLSLHWPSHRVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASV 96 (725)
Q Consensus 21 ~l~~rls~~~~--I~~~D--~FW~q~ws~p~s~~~p~d~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~ 96 (725)
.+++.+.+.+. ....+ .|=.+|.+.| .|...-+++.+ ....-++++...|..+..++++ ....
T Consensus 28 ~l~~~l~~~q~~~~s~~~ll~~l~~~F~D~------Sd~~~AL~~Ll-~r~~l~~~~~~~l~~al~~le~------~~~~ 94 (294)
T 2vj4_A 28 XIFDLXRTLXDNLPLDRDFIDRLXRYFXDP------SDQVLALRELL-NEXDLTAEQVELLTXIINEIIS------GSEX 94 (294)
T ss_dssp HHHHHHTTTTSSCCCCTTTHHHHHHHCCSH------HHHHHHHHHHT-TCSCCCSSHHHHHHHHHHHHHT------TCHH
T ss_pred HHHHHhhccccccCCHHHHHHHHHHHcCCH------HHHHHHHHHHH-HhccCcHHHHHHHHHHHHHHHh------ccch
Confidence 34344434444 44444 6666666654 35555545544 4444456776767766666644 2234
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCChhhHHHhhhccCCCCCCCCCCcchhhHHHHHHHhhhhcceecCCCchhhhHHHHHH
Q 004889 97 AIMKAINAVYISSVFLKYLIENAESENFEELHLSLDESEPLPKEFVLDQNIENLVMHSVLSFIALVDVSPHTYNLHQELL 176 (725)
Q Consensus 97 ~~~qalNclriLtrilp~l~E~~~~~~w~~~fw~~~~~e~~~~~f~~~~~~E~ll~~~lv~~l~~~p~~~~t~~~r~EvL 176 (725)
.++--.|+...-+.+-.-+ ..+....+.++..+... +..+.++ ++..++ ...+..|..|+
T Consensus 95 ~i~aGiNial~Ar~F~~~~--~~s~~~LR~~YR~fv~~---------~~~~~~l-y~~w~~--------~yg~~~r~~v~ 154 (294)
T 2vj4_A 95 SVNAGINSAIQAXLFGNXM--XLEPQLLRACYRGFIMG---------NISTTDQ-YIEWLG--------NFGFNHRHTIV 154 (294)
T ss_dssp HHHHHHHTHHHHHHHHHHH--TCCHHHHHHHHHHHHHC---------CCCHHHH-HHHHHH--------HHCSTTHHHHH
T ss_pred hhhhcchHHHHHhhhhhhh--cCCHHHHHHHHHHHHhc---------cCcHHHH-HHHHHH--------HhCcchHHHHH
Confidence 4566778887777776664 44556666677666532 2234444 555554 45577888999
Q ss_pred HHHHHHhchhcCCCC
Q 004889 177 NFMLVAMSTQLLSVP 191 (725)
Q Consensus 177 rlLLvllS~qLy~~~ 191 (725)
++|+-.|++-|=..+
T Consensus 155 ~Fl~~aL~aDL~s~~ 169 (294)
T 2vj4_A 155 NFVEQSLIVDMDSEX 169 (294)
T ss_dssp HHHHHHHHHHHHSSS
T ss_pred HHHHHHHhhhhhccC
Confidence 999999998886553
No 6
>1gxg_A Colicin E8 immunity protein; inhibitor, inhibitor protein of DNAse colicin E8, bacteriocin immunity, plasmid,; NMR {Escherichia coli} SCOP: a.28.2.1 PDB: 1gxh_A
Probab=7.58 E-value=4.8e+02 Score=22.21 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcchhhHHhhccccccccccCCccHHHHHhhHHHHHHhhhhhhhccccCCCCCHHHHHHH
Q 004889 556 DFLRIVLEILNAILTYALPRNPEQVVYAILHREEVFQPFKSHPRFNELLENIYTVLDFFNSRLDAQRVDGEWSVEKVLQS 635 (725)
Q Consensus 556 ~~L~~lLEiiNsiL~~ql~~Np~~LVYalL~~r~~F~~l~~hp~f~~~~~Ni~~vi~~f~~~l~~~~~~~~~s~~~vl~~ 635 (725)
++|.+|=+|+|+ .+....+-+.| +.|+..-.||.-.++|= + ...+.+.|++.|++.
T Consensus 14 Efi~lv~~I~~~------~~~~e~~d~ll----~~f~~~teHP~gSDLIf--------y------P~~~~e~spE~Iv~~ 69 (85)
T 1gxg_A 14 EFKKIIEDIINC------EGDEKKQDDNL----EHFISVTEHPSGSDLIY--------Y------PEGNNDGSPEAVIKE 69 (85)
T ss_dssp HHHHHHHHHHHT------SSSSHHHHHHH----HHHHHTTCCTTTTHHHH--------S------CCTTCCSSHHHHHHH
T ss_pred HHHHHHHHHHhC------CCCchhHHHHH----HHHHHhcCCCCcCceee--------c------CCCCCCCCHHHHHHH
Confidence 788888888876 12222011111 12455555665555441 1 122446799999999
Q ss_pred HHHhcccCCCCCCC
Q 004889 636 IIINCRSWRGDGLK 649 (725)
Q Consensus 636 I~~~~~~~~~~~l~ 649 (725)
|++....--.++.|
T Consensus 70 ik~wRa~~g~p~Fk 83 (85)
T 1gxg_A 70 IKEWRAANGKSGFK 83 (85)
T ss_dssp HHHHHHHTTCCCSS
T ss_pred HHHHHHHcCCcccC
Confidence 99876655444443
No 7
>1unk_A Colicin E7; immunity protein, dimeric structure, RNAse active site; 1.80A {Escherichia coli} SCOP: a.28.2.1 PDB: 1mz8_A 1ayi_A 2jaz_A 2jb0_A 2jbg_A 7cei_A 1znv_A 1cei_A 1ujz_A 2erh_A
Probab=7.36 E-value=5.1e+02 Score=22.26 Aligned_cols=73 Identities=18% Similarity=0.200 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCcchhhHHhhccccccccccCCccHHHHHhhHHHHHHhhhhhhhccccCCCCCHHHHHH
Q 004889 555 TDFLRIVLEILNAILTYALPRNPEQVVYAILHREEVFQPFKSHPRFNELLENIYTVLDFFNSRLDAQRVDGEWSVEKVLQ 634 (725)
Q Consensus 555 ~~~L~~lLEiiNsiL~~ql~~Np~~LVYalL~~r~~F~~l~~hp~f~~~~~Ni~~vi~~f~~~l~~~~~~~~~s~~~vl~ 634 (725)
.++|.+|=+|+|+- .|...+.-.+||. -|..+..||.-.|+|= | ...+.+-|++.|++
T Consensus 13 ~EFl~fv~~i~~~~-~~~~e~~~d~lv~-------hF~~iteHP~gsDLIf--------Y------P~~~~edsPEgIv~ 70 (87)
T 1unk_A 13 AEFVQLLKEIEKEN-VAATDDVLDVLLE-------HFVKITEHPDGTDLIY--------Y------PSDNRDDSPEGIVK 70 (87)
T ss_dssp HHHHHHHHHHHHHH-HSSCCHHHHHHHH-------HHHHHHCCTTTTHHHH--------S------CCSSCCCSHHHHHH
T ss_pred HHHHHHHHHHHhCC-CCCChhHHHHHHH-------HHHHhcCCCCCCCeee--------e------CCCCCCCCHHHHHH
Confidence 38999999999983 1123222121221 2555666776665542 2 22344679999999
Q ss_pred HHHHhcccCCCCCCC
Q 004889 635 SIIINCRSWRGDGLK 649 (725)
Q Consensus 635 ~I~~~~~~~~~~~l~ 649 (725)
.|++.-.+--.++.|
T Consensus 71 ~iKeWRa~nG~pgFK 85 (87)
T 1unk_A 71 EIKEWRAANGKPGFK 85 (87)
T ss_dssp HHHHHHHHTTCCCCC
T ss_pred HHHHHHHHcCCcccC
Confidence 999876654444443
No 8
>3u43_A Colicin-E2 immunity protein; protein-protein complex, DNAse, high affinity, protein bindi; 1.72A {Escherichia coli} PDB: 2no8_A 2wpt_A
Probab=7.01 E-value=5e+02 Score=22.59 Aligned_cols=26 Identities=27% Similarity=0.157 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHHHhcccCCCCCCC
Q 004889 624 DGEWSVEKVLQSIIINCRSWRGDGLK 649 (725)
Q Consensus 624 ~~~~s~~~vl~~I~~~~~~~~~~~l~ 649 (725)
+.+.|++.|++.|++.-.+--.++.|
T Consensus 59 ~~e~SPEgIv~~IKeWRa~nG~pgFK 84 (94)
T 3u43_A 59 DREDSPEGIVKEIKEWRAANGKSGFK 84 (94)
T ss_dssp TSCSSHHHHHHHHHHHHHHTTCCCCB
T ss_pred CCCCCHHHHHHHHHHHHHHcCCccch
Confidence 34679999999999876655444444
No 9
>1fr2_A Colicin E9 immunity protein; protein-protein complex, zinc containing enzyme, HNH-motif, immune system; 1.60A {Escherichia coli} SCOP: a.28.2.1 PDB: 1e0h_A 1emv_A 1imp_A 1imq_A 2k5x_A 2vln_A 2vlp_A 2vlq_A 2vlo_A 2gzf_A 2gzg_A 2gzi_A 2gyk_A 2gzj_A 2gze_A 1bxi_A 3gkl_C 3gjn_A
Probab=5.56 E-value=6.5e+02 Score=21.44 Aligned_cols=26 Identities=12% Similarity=0.063 Sum_probs=18.6
Q ss_pred CCCCCHHHHHHHHHHhcccCCCCCCC
Q 004889 624 DGEWSVEKVLQSIIINCRSWRGDGLK 649 (725)
Q Consensus 624 ~~~~s~~~vl~~I~~~~~~~~~~~l~ 649 (725)
+.+.|++.|++.|++...+--.++.|
T Consensus 59 ~~e~spE~Iv~~ik~wRa~~G~pgFK 84 (86)
T 1fr2_A 59 GDDDSPSGIVNTVKQWRAANGKSGFK 84 (86)
T ss_dssp TCCCSHHHHHHHHHHHHHHTTCCCCB
T ss_pred CCCCCHHHHHHHHHHHHHHcCCcccC
Confidence 44679999999999876654444433
No 10
>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain; 1.84A {Thermus thermophilus} SCOP: d.52.7.1 PDB: 2r1c_A
Probab=5.51 E-value=2.1e+02 Score=24.55 Aligned_cols=16 Identities=25% Similarity=0.254 Sum_probs=12.9
Q ss_pred CCCCCCCCceeeeeCC
Q 004889 647 GLKMFTRLYFSYEQES 662 (725)
Q Consensus 647 ~l~~f~~l~F~YeEe~ 662 (725)
+|+.-|+|+|.|-+..
T Consensus 78 ~lr~~P~L~F~~D~s~ 93 (95)
T 2dyj_A 78 RMRRLPRLEFLPWRAS 93 (95)
T ss_dssp CCSSCCEEEEEEGGGC
T ss_pred CCccCCeEEEEEcCCC
Confidence 4888899999996643
Done!