Query 004894
Match_columns 724
No_of_seqs 193 out of 225
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 09:03:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004894.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/004894hhsearch_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 14.4 81 0.0028 24.9 1.9 20 670-689 27-46 (56)
2 2y69_K Cytochrome C oxidase po 10.9 1.1E+02 0.0039 25.7 1.9 20 670-689 51-70 (80)
3 1rw2_A ATP-dependent DNA helic 9.6 6.5E+02 0.022 23.5 7.0 60 54-118 35-94 (152)
4 1q2z_A ATP-dependent DNA helic 9.3 3.9E+02 0.013 23.9 5.1 59 55-118 5-63 (120)
5 2vj4_A Protein MXIC, MXIC; sec 8.0 1.6E+03 0.055 23.1 12.0 138 21-191 28-169 (294)
6 1gxg_A Colicin E8 immunity pro 6.3 6E+02 0.021 21.6 4.6 69 555-646 13-81 (85)
7 1unk_A Colicin E7; immunity pr 6.1 6.3E+02 0.022 21.6 4.6 69 555-645 13-82 (87)
8 3u43_A Colicin-E2 immunity pro 5.8 6.2E+02 0.021 22.0 4.5 26 623-648 59-84 (94)
9 2dyj_A Ribosome-binding factor 5.3 2.2E+02 0.0075 24.5 1.3 16 646-661 78-93 (95)
10 1fr2_A Colicin E9 immunity pro 4.9 7.8E+02 0.027 20.9 4.5 67 556-644 14-80 (86)
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=14.44 E-value=81 Score=24.87 Aligned_cols=20 Identities=30% Similarity=0.750 Sum_probs=17.0
Q ss_pred hhHHHHhhhcCccccCCCcc
Q 004894 670 YVWQLVLSRCGFSFNPSAIN 689 (724)
Q Consensus 670 yvW~~v~~~~g~~w~~~~i~ 689 (724)
-+|..+.-|.||-||-+-+.
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=10.85 E-value=1.1e+02 Score=25.70 Aligned_cols=20 Identities=30% Similarity=0.750 Sum_probs=16.9
Q ss_pred hhHHHHhhhcCccccCCCcc
Q 004894 670 YVWQLVLSRCGFSFNPSAIN 689 (724)
Q Consensus 670 yvW~~v~~~~g~~w~~~~i~ 689 (724)
-+|..+.-+.||-||-+-+.
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=9.58 E-value=6.5e+02 Score=23.51 Aligned_cols=60 Identities=10% Similarity=0.059 Sum_probs=43.3
Q ss_pred chhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChHHHHHHHHHHHHHHHhhhhhhcc
Q 004894 54 HRVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASVAIMKAINAVYISSVFLKYLIEN 118 (724)
Q Consensus 54 ~~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~~~~qalNclriLtrilp~l~E~ 118 (724)
+.+.+..+.++.++ ..+++.+--+..++.++..++ .+..+.+|+-||+.+|-=+-..-|-
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=9.29 E-value=3.9e+02 Score=23.88 Aligned_cols=59 Identities=10% Similarity=0.053 Sum_probs=40.1
Q ss_pred hhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChHHHHHHHHHHHHHHHhhhhhhcc
Q 004894 55 RVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASVAIMKAINAVYISSVFLKYLIEN 118 (724)
Q Consensus 55 ~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~~~~qalNclriLtrilp~l~E~ 118 (724)
-+.+..+.++.++ .++.+.+--+..++.++..++ .+..+.+|+-||+.+|-=+-..-|-
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=8.01 E-value=1.6e+03 Score=23.07 Aligned_cols=138 Identities=12% Similarity=0.102 Sum_probs=82.8
Q ss_pred HHHHhhhCCcc--CCCCc--hHHHHhccCCCCCCCCcchhHHHHHHHhhhcCCCccHHHHHHHHHHHHHHhhhCCCCChH
Q 004894 21 YLIATFVGEKS--FPLAS--DFWQKLLELPLSLHWPSHRVHQACEAFAQNNCYTRHLAKILIHLTWCLQECISSSGTASV 96 (724)
Q Consensus 21 ~l~~rls~~~~--I~~~D--~FW~q~ws~p~s~~~p~~~~~~~~~~l~~nn~~t~Nl~tLi~~~~~rl~~l~~~~~~~~~ 96 (724)
.+++.+.+.+. ....+ .|=.+|.+.| .|...-+++.+ ....-++++...|..+..++++ ....
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 004894 97 AIMKAINAVYISSVFLKYLIENAESENFEELHLSLDESEPLPKEFVLDQNIENLVMHSVLSFIALVDVSPHTYNLHQELL 176 (724)
Q Consensus 97 ~~~qalNclriLtrilp~l~E~~~~~~w~~~fw~~~~~e~~~~~f~~~~~~E~ll~~~lv~~l~~~p~~~~t~~~r~EvL 176 (724)
.++--.|+...-+.+-.-+ ..+....+.++..+... +..+.++ ++..++ ...+..|..|+
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 004894 177 NFMLVAMSTQLLSVP 191 (724)
Q Consensus 177 rlLLvllS~qLy~~~ 191 (724)
++|+-.|++-|=..+
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=6.29 E-value=6e+02 Score=21.58 Aligned_cols=69 Identities=22% Similarity=0.265 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCcchhHHhhccccccccccCCcchHHHHhhHHHHHHhhhhhhhccccCCCCCHHHHHHH
Q 004894 555 TDFLRIVLEILNAILTYALPRNPEVVYAILHREEVFQPFKSHPRFNELLENIYTVLDFFNSRLDAQRVDGEWSVEKVLQS 634 (724)
Q Consensus 555 ~~~L~~lLEiiNsiL~~ql~~Np~LVYalL~~r~~F~~l~~hp~f~~~~~Ni~~vi~~f~~~l~~~~~~~~~s~~~vl~~ 634 (724)
.++|.+|=+|+|+ .+.... +-+.| +.|+..-.||.-.++|= + ...+.+.|++.|++.
T Consensus 13 ~Efi~lv~~I~~~--~~~~e~---~d~ll----~~f~~~teHP~gSDLIf--------y------P~~~~e~spE~Iv~~ 69 (85)
T 1gxg_A 13 TEFKKIIEDIINC--EGDEKK---QDDNL----EHFISVTEHPSGSDLIY--------Y------PEGNNDGSPEAVIKE 69 (85)
T ss_dssp HHHHHHHHHHHHT--SSSSHH---HHHHH----HHHHHTTCCTTTTHHHH--------S------CCTTCCSSHHHHHHH
T ss_pred HHHHHHHHHHHhC--CCCchh---HHHHH----HHHHHhcCCCCcCceee--------c------CCCCCCCCHHHHHHH
Confidence 3788888888877 222222 22222 22566666776655542 2 222446799999999
Q ss_pred HHhhcccCCCCC
Q 004894 635 IIINCRSWRGDG 646 (724)
Q Consensus 635 I~~~~~~~~~~~ 646 (724)
|++....--.++
T Consensus 70 ik~wRa~~g~p~ 81 (85)
T 1gxg_A 70 IKEWRAANGKSG 81 (85)
T ss_dssp HHHHHHHTTCCC
T ss_pred HHHHHHHcCCcc
Confidence 997665443333
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=6.12 E-value=6.3e+02 Score=21.64 Aligned_cols=69 Identities=17% Similarity=0.177 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCC-cchhHHhhccccccccccCCcchHHHHhhHHHHHHhhhhhhhccccCCCCCHHHHHH
Q 004894 555 TDFLRIVLEILNAILTYALPRN-PEVVYAILHREEVFQPFKSHPRFNELLENIYTVLDFFNSRLDAQRVDGEWSVEKVLQ 633 (724)
Q Consensus 555 ~~~L~~lLEiiNsiL~~ql~~N-p~LVYalL~~r~~F~~l~~hp~f~~~~~Ni~~vi~~f~~~l~~~~~~~~~s~~~vl~ 633 (724)
.++|.+|=+|+|+- .|...+. ..|| +-|..+..||.-.|+|= | ...+.+-|++.|++
T Consensus 13 ~EFl~fv~~i~~~~-~~~~e~~~d~lv-------~hF~~iteHP~gsDLIf--------Y------P~~~~edsPEgIv~ 70 (87)
T 1unk_A 13 AEFVQLLKEIEKEN-VAATDDVLDVLL-------EHFVKITEHPDGTDLIY--------Y------PSDNRDDSPEGIVK 70 (87)
T ss_dssp HHHHHHHHHHHHHH-HSSCCHHHHHHH-------HHHHHHHCCTTTTHHHH--------S------CCSSCCCSHHHHHH
T ss_pred HHHHHHHHHHHhCC-CCCChhHHHHHH-------HHHHHhcCCCCCCCeee--------e------CCCCCCCCHHHHHH
Confidence 38999999999983 1122221 1111 11555666666655542 2 22244679999999
Q ss_pred HHHhhcccCCCC
Q 004894 634 SIIINCRSWRGD 645 (724)
Q Consensus 634 ~I~~~~~~~~~~ 645 (724)
.|++.-.+--.+
T Consensus 71 ~iKeWRa~nG~p 82 (87)
T 1unk_A 71 EIKEWRAANGKP 82 (87)
T ss_dssp HHHHHHHHTTCC
T ss_pred HHHHHHHHcCCc
Confidence 999766544333
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=5.85 E-value=6.2e+02 Score=21.97 Aligned_cols=26 Identities=27% Similarity=0.157 Sum_probs=17.9
Q ss_pred CCCCCHHHHHHHHHhhcccCCCCCCC
Q 004894 623 DGEWSVEKVLQSIIINCRSWRGDGLK 648 (724)
Q Consensus 623 ~~~~s~~~vl~~I~~~~~~~~~~~l~ 648 (724)
+.+.|++.|++.|++.-.+--.++.|
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 34679999999999876544333333
No 9
>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=5.30 E-value=2.2e+02 Score=24.46 Aligned_cols=16 Identities=25% Similarity=0.254 Sum_probs=12.9
Q ss_pred CCCCCCCCceeeeeCC
Q 004894 646 GLKMFTRLYFSYEQES 661 (724)
Q Consensus 646 ~l~~f~~l~F~YeEe~ 661 (724)
+|+.-|+|+|.|-+..
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
No 10
>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=4.92 E-value=7.8e+02 Score=20.92 Aligned_cols=67 Identities=19% Similarity=0.276 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcchhHHhhccccccccccCCcchHHHHhhHHHHHHhhhhhhhccccCCCCCHHHHHHHH
Q 004894 556 DFLRIVLEILNAILTYALPRNPEVVYAILHREEVFQPFKSHPRFNELLENIYTVLDFFNSRLDAQRVDGEWSVEKVLQSI 635 (724)
Q Consensus 556 ~~L~~lLEiiNsiL~~ql~~Np~LVYalL~~r~~F~~l~~hp~f~~~~~Ni~~vi~~f~~~l~~~~~~~~~s~~~vl~~I 635 (724)
++|.+|=+|+|+ ....-...-+.|. .|+..-.||.-.++|= + ...+.+.|++.|++.|
T Consensus 14 Efi~lv~~I~~~----~~~~e~e~d~ll~----~f~~~teHP~gSDLIf--------y------P~~~~e~spE~Iv~~i 71 (86)
T 1fr2_A 14 EFLQLVTTICNA----DTSSEEELVKLVT----HFAEMTEHPSGSDLIY--------Y------PKEGDDDSPSGIVNTV 71 (86)
T ss_dssp HHHHHHHHHHTT----CSSSHHHHHHHHH----HHHHHHCCTTTTHHHH--------S------CCTTCCCSHHHHHHHH
T ss_pred HHHHHHHHHHhC----CCCChHHHHHHHH----HHHHhcCCCCcCceee--------c------CCCCCCCCHHHHHHHH
Confidence 788877777765 1111122222221 1455555665555441 1 2224467999999999
Q ss_pred HhhcccCCC
Q 004894 636 IINCRSWRG 644 (724)
Q Consensus 636 ~~~~~~~~~ 644 (724)
++...+--.
T Consensus 72 k~wRa~~G~ 80 (86)
T 1fr2_A 72 KQWRAANGK 80 (86)
T ss_dssp HHHHHHTTC
T ss_pred HHHHHHcCC
Confidence 976654433
Done!