Query 028753
Match_columns 204
No_of_seqs 129 out of 796
Neff 6.0
Searched_HMMs 29240
Date Tue Mar 26 18:29:31 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/028753.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_2243-2247//hhsearch_pdb/028753hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4gd3_A NI/Fe-hydrogenase 1 B-t 1.0 1 1 20.7 8.9 130 53-183 17-205 (235)
2 1kqf_C FDH-N gamma, formate de 1.0 1 1 17.7 10.7 58 125-182 112-175 (217)
3 3hd6_A Ammonium transporter RH 1.0 1 1 14.1 2.7 25 46-71 60-84 (490)
4 1vf5_A Cytochrome B6; photosyn 1.0 1 1 14.1 8.0 105 44-148 22-139 (215)
5 2nr1_A NR1 M2, M2; receptor, s 1.0 1 1 13.7 2.1 17 59-75 10-26 (27)
6 3ayf_A Nitric oxide reductase; 1.0 1 1 11.3 10.4 62 51-115 348-412 (800)
7 1fft_C Ubiquinol oxidase; elec 1.0 1 1 11.0 1.1 26 122-147 145-170 (204)
8 3s8f_C Cytochrome C oxidase po 1.0 1 1 9.5 2.7 18 59-78 16-33 (34)
9 4av2_M PILP protein, type IV p 1.0 1 1 9.4 0.0 36 14-49 5-40 (181)
10 1s4x_A Integrin beta-3; cell a 1.0 1 1 9.3 0.0 20 118-137 1-20 (67)
No 1
>4gd3_A NI/Fe-hydrogenase 1 B-type cytochrome subunit; O2-tolerant H2:quinone oxidoreductase, membrane-bound, NI-Fe hydrogenase-cytochrome B complex; HET: LMT HEM; 3.30A {Escherichia coli}
Probab=1.00 E-value=1 Score=20.66 Aligned_cols=130 Identities=14% Similarity=0.023 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHEECC----------
Q ss_conf 479888999999999898788757654266--65301--2468999999999999999999875301045----------
Q 028753 53 SHIAVHGLLLWASMGFLTPVGILTIRMSNK--VDSVI--KARVFVYLHIILQMLSVVLATVGAIMSIRNF---------- 118 (204)
Q Consensus 53 ~~~~~Hg~LM~vAw~iL~P~GIl~aR~~k~--~~~~~--~~~~Wf~lH~~lq~~a~~l~iiG~~l~i~~~---------- 118 (204)
.....| ++++++...+...|......... ..+.. .......+|..+..+-.++.+.-.+..+...
T Consensus 17 ~~R~~H-W~~a~~ii~l~~tG~~~~~~~~~~~g~~~~~~~~~~~~~~H~~~G~~~~~l~~~Rl~w~~~g~~~ar~~~~~p 95 (235)
T 4gd3_A 17 PVRIWH-WLTVLCMAVLMVTGYFIGKPLPSVSGEATYLFYMGYIRLIHFSAGMVFTVVLLMRIYWAFVGNRYSRELFIVP 95 (235)
T ss_dssp CTTHHH-HHHHHHHHHHHHHHHHHHSCCCCCCSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCSCC------
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCC
T ss_conf 799999-9999999999999887607652346760367789999999999999999999999999997672021121155
Q ss_pred --------------------CC------CCCCHHHHHHHHHHHHHHHHHHHHHCC--CCCCC-----------------C
Q ss_conf --------------------68------777714579999999999999987505--89888-----------------8
Q 028753 119 --------------------EN------SFNNNHQRLGLALYGALWLQVSIGFFK--PPRGN-----------------K 153 (204)
Q Consensus 119 --------------------~~------~f~~~H~~iGliv~~l~~lQ~l~G~lr--p~~~~-----------------k 153 (204)
++ ..+..-+..-.+++.++.+|++.|++. +..+. .
T Consensus 96 ~~~~~~~~~~~~~~~~yl~~~~~p~~~~~~n~~~~~~~~~l~~ll~~~~ltG~~~~~~~~~~~~f~~~~~~~~~f~~~~~ 175 (235)
T 4gd3_A 96 VWRKSWWQGVWYEIRWYLFLAKRPSADIGHNPIAQAAMFGYFLMSVFMIITGFALYSEHSQYAIFAPFRYVVEFFYWTGG 175 (235)
T ss_dssp -------CCSTTTSSSSSCC-----------CCCTTTHHHHHHHHHHHHHHHHHHHTTTTCCSSCGGGHHHHHHHHHHTS
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 54166787799999999845789976578798999999999999999999999995222467743320367787776135
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 862137697999999999999999996311
Q 028753 154 RRSMWYVVHWLLGTAISLVGIINIYTGLKA 183 (204)
Q Consensus 154 ~R~~~~~~H~~lG~~v~iLgivni~~Gl~~ 183 (204)
.......+|.+.+.+.+++-++=++..+..
T Consensus 176 ~~~~~~~iH~~~a~~l~~~v~lHv~aal~h 205 (235)
T 4gd3_A 176 NSMDIHSWHRLGMWLIGAFVIGHVYMALRE 205 (235)
T ss_dssp CTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 078999999999999999999999999999
No 2
>1kqf_C FDH-N gamma, formate dehydrogenase, nitrate-inducible, cytochr B556(FDN) subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: f.21.1.1 PDB: 1kqg_C*
Probab=1.00 E-value=1 Score=17.66 Aligned_cols=58 Identities=9% Similarity=0.100 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCC-CC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 14579999999999999987505898-88-----886213769799999999999999999631
Q 028753 125 NHQRLGLALYGALWLQVSIGFFKPPR-GN-----KRRSMWYVVHWLLGTAISLVGIINIYTGLK 182 (204)
Q Consensus 125 ~H~~iGliv~~l~~lQ~l~G~lrp~~-~~-----k~R~~~~~~H~~lG~~v~iLgivni~~Gl~ 182 (204)
..+..=++++.++.+|++.|++--.. .. ........+|.+.+...+++-++=++..+.
T Consensus 112 ~~~~~~~~l~~l~~~~~~TG~~~~~~~~~~~~~~~~~~~~~~iH~~~a~~l~~~v~~Hv~~al~ 175 (217)
T 1kqf_C 112 GQKMMFWSIMSMIFVLLVTGVIIWRPYFAQYFPMQVVRYSLLIHAAAGIILIHAILIHMYMAFW 175 (217)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTCTTTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999999999989864031588899999999999999999999999999976
No 3
>3hd6_A Ammonium transporter RH type C; ammonia, channel, rhesus, glycoprotein, membran structural genomics, PSI-2, protein structure initiative; HET: BOG; 2.10A {Homo sapiens}
Probab=1.00 E-value=1 Score=14.09 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=16.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 45756504798889999999998987
Q 028753 46 KMGPQTASHIAVHGLLLWASMGFLTP 71 (204)
Q Consensus 46 ~~~~~~~~~~~~Hg~LM~vAw~iL~P 71 (204)
+...+|...--+| ++..+++|+||-
T Consensus 60 ~~~~~Yp~fqDv~-vMi~~GfGFLmt 84 (490)
T 3hd6_A 60 EFYYRYPSFQDVH-VMVFVGFGFLMT 84 (490)
T ss_dssp HHHHHHHHHHHHH-HHHHTHHHHHGG
T ss_pred HHHHCCCCCHHHH-HHHHHHHHHHHH
T ss_conf 3665186411489-899998999999
No 4
>1vf5_A Cytochrome B6; photosynthesis, membrane protein complex, electron transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A {Mastigocladus laminosus} SCOP: f.21.1.2 PDB: 2d2c_A* 2e74_A* 2e75_A* 2e76_A* 2zt9_A* 1q90_B*
Probab=1.00 E-value=1 Score=14.05 Aligned_cols=105 Identities=10% Similarity=-0.059 Sum_probs=54.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC------------HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4445756504798889999999998987887576542666530------------1246899999999999999999987
Q 028753 44 LYKMGPQTASHIAVHGLLLWASMGFLTPVGILTIRMSNKVDSV------------IKARVFVYLHIILQMLSVVLATVGA 111 (204)
Q Consensus 44 ~~~~~~~~~~~~~~Hg~LM~vAw~iL~P~GIl~aR~~k~~~~~------------~~~~~Wf~lH~~lq~~a~~l~iiG~ 111 (204)
.+.-.|+.-+....=|.+......+..-.|++++-+..+.... +.+-...++|..--..-+++..+=.
T Consensus 22 ~~~p~P~nis~~w~fGsll~~~l~iqi~TG~~Lam~Y~p~~~~Af~Sv~~I~~dv~~GwliR~~H~~gAs~ffi~~ylHi 101 (215)
T 1vf5_A 22 TSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKPTVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHV 101 (215)
T ss_dssp CCSCCCCSSCSGGGHHHHHHHHHHHHHHHHHHHTTTCCCSTTTHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 54889997779998799999999999999999995745986688999999986145604231061879999999999999
Q ss_pred HHHEECCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 53010456-87777145799999999999999875058
Q 028753 112 IMSIRNFE-NSFNNNHQRLGLALYGALWLQVSIGFFKP 148 (204)
Q Consensus 112 ~l~i~~~~-~~f~~~H~~iGliv~~l~~lQ~l~G~lrp 148 (204)
.-++...+ +.....-=.+|.+++.+.......|+.-|
T Consensus 102 ~Rglyygsy~~p~~~~W~~Gv~l~~l~m~~aF~GYvLP 139 (215)
T 1vf5_A 102 FRVYLTGGFKKPRELTWISGVILAVITVSFGVTGYSLP 139 (215)
T ss_dssp HHHHHTTSSSSSCSHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred HHHHHHHHCCCCCCCEEHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99997510035787600768999999999999023247
No 5
>2nr1_A NR1 M2, M2; receptor, signal, postsynaptic membrane; NMR {Homo sapiens} SCOP: j.35.1.1
Probab=1.00 E-value=1 Score=13.69 Aligned_cols=17 Identities=35% Similarity=0.524 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999989878875
Q 028753 59 GLLLWASMGFLTPVGIL 75 (204)
Q Consensus 59 g~LM~vAw~iL~P~GIl 75 (204)
..-|+.+|++|+-.|+.
T Consensus 10 ~aa~wF~WGvllnsgi~ 26 (27)
T 2nr1_A 10 SSAMWFSWGVLLNSGIG 26 (27)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHEECCCC
T ss_conf 25477756764105557
No 6
>3ayf_A Nitric oxide reductase; oxidoreductase; HET: HEM BOG EPE LOP; 2.50A {Geobacillus stearothermophilus} PDB: 3ayg_A*
Probab=1.00 E-value=1 Score=11.29 Aligned_cols=62 Identities=13% Similarity=0.024 Sum_probs=33.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH---HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHE
Q ss_conf 504798889999999998987887---57654266653012468999999999999999999875301
Q 028753 51 TASHIAVHGLLLWASMGFLTPVGI---LTIRMSNKVDSVIKARVFVYLHIILQMLSVVLATVGAIMSI 115 (204)
Q Consensus 51 ~~~~~~~Hg~LM~vAw~iL~P~GI---l~aR~~k~~~~~~~~~~Wf~lH~~lq~~a~~l~iiG~~l~i 115 (204)
|.....+|+..|+. |....-.|. ++.|..++. |. ..+..-.+...+-.++.+++.+++.+|.
T Consensus 348 Yn~lrT~Hg~~mIf-~~~~~~~g~~~ylvP~~~g~d-p~-~~~~L~~~~fwl~~~g~vl~~~s~~~G~ 412 (800)
T 3ayf_A 348 FNIAKGYHLQLAIF-WIATAWLGMGIFIAPLVGGQE-PK-KQGLLVDLLFWALVVLVGGSMIGQWLGV 412 (800)
T ss_dssp HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHTSC-CT-THHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCC-CC-CCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 99999999999999-999999999999999981899-75-3217999999999999999999998443
No 7
>1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: f.25.1.1
Probab=1.00 E-value=1 Score=10.98 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=15.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 77714579999999999999987505
Q 028753 122 FNNNHQRLGLALYGALWLQVSIGFFK 147 (204)
Q Consensus 122 f~~~H~~iGliv~~l~~lQ~l~G~lr 147 (204)
+...|..+|.+....+..|...|-+.
T Consensus 145 ~HglHV~~G~i~l~~~~~r~~~~~~~ 170 (204)
T 1fft_C 145 THGLHVTSGLIWMAVLMVQIARRGLT 170 (204)
T ss_dssp HHTTHHHHTTHHHHHHHHHHHHTCCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99999999999999999999817998
No 8
>3s8f_C Cytochrome C oxidase polypeptide 2A; complex IV, respiratory chain, lipid cubic phase, monoolein, peroxide, electron transport, proton pump; HET: HEM HAS OLC; 1.80A {Thermus thermophilus} PDB: 2qpd_C* 2qpe_C* 3bvd_C* 3qjq_C* 3qjr_C* 3qjs_C* 3qjt_C* 3qju_C* 3qjv_C* 1xme_C* 3s8g_C* 4esl_C* 4ev3_C* 4f05_C* 4fa7_C* 4faa_C* 1ehk_C* 3eh3_C* 3eh4_C* 3eh5_C* ...
Probab=1.00 E-value=1 Score=9.52 Aligned_cols=18 Identities=11% Similarity=-0.042 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999989878875765
Q 028753 59 GLLLWASMGFLTPVGILTIR 78 (204)
Q Consensus 59 g~LM~vAw~iL~P~GIl~aR 78 (204)
|.++.++|.... +..+.|
T Consensus 16 g~~I~i~W~~vf--~lFl~R 33 (34)
T 3s8f_C 16 TLTILVFWLGVY--AVFFAR 33 (34)
T ss_dssp HHHHHHHHHHHH--HHHHHT
T ss_pred HHHHHHHHHHHH--EEEECC
T ss_conf 999999999997--056338
No 9
>4av2_M PILP protein, type IV pilus biogenesis and competence protein P; protein transport, outer membrane protein; 26.00A {Neisseria meningitidis MC58}
Probab=1.00 E-value=1 Score=9.37 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=0.0
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 877765266434665223356775442345444575
Q 028753 14 SCYVIFLPFVGCLSNDEFSKSRNHKSIQENLYKMGP 49 (204)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (204)
+.++.++..+.|+++.+++++.-....+.-..++.|
T Consensus 5 ~ll~~~l~LsgC~~~~~DL~~~~~e~r~~~~~~I~P 40 (181)
T 4av2_M 5 ALLISFLALSACSQGSEDLNEWMAQTRREAKAEIIP 40 (181)
T ss_dssp ------------------------------------
T ss_pred HHHHHHHHHEEECCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf 999998833200888799999999997268999888
No 10
>1s4x_A Integrin beta-3; cell adhesion; NMR {Homo sapiens} SCOP: j.60.1.1 PDB: 2ljd_A* 2lje_A* 2ljf_A*
Probab=1.00 E-value=1 Score=9.34 Aligned_cols=20 Identities=5% Similarity=-0.086 Sum_probs=0.0
Q ss_pred CCCCCCCHHHHHHHHHHHHH
Q ss_conf 56877771457999999999
Q 028753 118 FENSFNNNHQRLGLALYGAL 137 (204)
Q Consensus 118 ~~~~f~~~H~~iGliv~~l~ 137 (204)
++.+...-|+.+|++++.+.
T Consensus 1 ~~~~~~~~~~liGl~lLliw 20 (67)
T 1s4x_A 1 GSSHHHHHHSSGLVPRGSHM 20 (67)
T ss_dssp --------------------
T ss_pred CCCCCCHHHHHHHHHHHHHH
T ss_conf 98642015569999999999
Done!