Query psy9982
Match_columns 222
No_of_seqs 150 out of 167
Neff 3.9
Searched_HMMs 29240
Date Sat Aug 17 00:39:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9982.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/9982hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1twf_A B220, DNA-directed RNA 99.8 2.5E-21 8.5E-26 204.6 0.0 60 66-125 1595-1654(1733)
2 1twf_A B220, DNA-directed RNA 99.8 7.1E-21 2.4E-25 201.1 0.0 62 105-166 1627-1688(1733)
3 3h0g_A DNA-directed RNA polyme 99.5 3.6E-16 1.2E-20 165.7 0.0 23 59-81 1582-1604(1752)
4 3h0g_A DNA-directed RNA polyme 99.5 7.2E-16 2.5E-20 163.4 0.0 22 66-87 1575-1596(1752)
5 4gwq_H DNA-directed RNA polyme 98.6 2.3E-08 7.9E-13 65.0 3.2 26 70-95 2-27 (35)
6 2rdd_B UPF0092 membrane protei 82.7 0.43 1.5E-05 30.3 1.1 25 15-42 5-29 (37)
7 2knc_B Integrin beta-3; transm 51.6 6.4 0.00022 28.8 1.7 13 4-16 8-20 (79)
8 2knc_A Integrin alpha-IIB; tra 46.2 42 0.0014 23.2 5.1 20 18-42 25-44 (54)
9 2klu_A T-cell surface glycopro 42.1 24 0.00083 25.7 3.5 27 17-43 17-43 (70)
10 2knc_B Integrin beta-3; transm 39.1 11 0.00037 27.6 1.2 8 7-14 15-22 (79)
11 1q55_A EP-cadherin, C-cadherin 34.6 8.3 0.00028 38.5 0.0 20 8-27 705-724 (880)
12 2gsm_B Cytochrome C oxidase su 33.6 37 0.0013 29.4 4.0 23 18-41 39-62 (262)
13 1m56_D Cytochrome C oxidase; m 33.5 17 0.00057 24.8 1.4 14 15-28 37-50 (51)
14 2l8s_A Integrin alpha-1; trans 32.9 71 0.0024 22.1 4.5 20 18-42 22-41 (54)
15 4e6z_A Apicoplast TIC22, putat 31.1 10 0.00035 33.6 0.0 13 18-30 1-13 (279)
16 3arc_M Photosystem II reaction 30.1 31 0.0011 22.2 2.2 23 6-28 5-27 (36)
17 3hb3_B Cytochrome C oxidase su 28.4 50 0.0017 29.4 4.0 24 18-42 70-94 (298)
18 1qle_D Cytochrome AA3, ccytoch 28.3 22 0.00075 23.4 1.2 13 15-27 29-41 (43)
19 1fft_B Ubiquinol oxidase; elec 20.3 20 0.0007 32.2 -0.2 27 16-42 48-74 (315)
No 1
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=99.80 E-value=2.5e-21 Score=204.60 Aligned_cols=60 Identities=48% Similarity=1.060 Sum_probs=0.0
Q ss_pred CCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy9982 66 SPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAY 125 (222)
Q Consensus 66 Sp~ysPtSP~ySPtSP~ysPtSP~ysPtSP~YsPtSP~ysp~SP~ysPsSPsySP~SP~Y 125 (222)
||+|+|+||.|+|+||.|+|++|.|+|+||.|+|++|.|++++|.|+|++|+|+|++|.|
T Consensus 1595 s~~~~ptsp~ysp~sp~~sptsp~~sptsp~ysP~sp~~sptsp~ysp~sp~~sp~sp~y 1654 (1733)
T 1twf_A 1595 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1654 (1733)
T ss_dssp ------------------------------------------------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 333333333344333333333443333333333333333333333333333333333333
No 2
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=99.79 E-value=7.1e-21 Score=201.14 Aligned_cols=62 Identities=39% Similarity=0.787 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCcc
Q psy9982 105 TQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA 166 (222)
Q Consensus 105 sp~SP~ysPsSPsySP~SP~YSP~SP~ysP~SPsysPtSP~ysPtSP~ysPsSP~~sp~ss~ 166 (222)
+|++|.|+|++|.|+|++|.|+|++|.|+|++|+|+|++|.|+|++|.|+|++|.|+|+++.
T Consensus 1627 sP~sp~~sptsp~ysp~sp~~sp~sp~y~p~sp~~sp~sp~~~p~sp~y~p~sp~y~p~sp~ 1688 (1733)
T 1twf_A 1627 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1688 (1733)
T ss_dssp --------------------------------------------------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 33333333333344444444444444444444444444444444433333333333333333
No 3
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.55 E-value=3.6e-16 Score=165.69 Aligned_cols=23 Identities=48% Similarity=1.011 Sum_probs=0.0
Q ss_pred CCCcccCCCCccCCCCCCCCCCC
Q psy9982 59 SPAYTQVSPAYTQVSPAYTQVSP 81 (222)
Q Consensus 59 S~~lc~~Sp~ysPtSP~ySPtSP 81 (222)
|+.++..+|+|+|++|.|+|++|
T Consensus 1582 SP~~s~tsP~ysptspaysptsp 1604 (1752)
T 3h0g_A 1582 SPSYSPTSPSYSPTSPSYSPTSP 1604 (1752)
T ss_dssp -----------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCCCC
Confidence 33444444444444444443333
No 4
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.53 E-value=7.2e-16 Score=163.44 Aligned_cols=22 Identities=45% Similarity=0.942 Sum_probs=0.0
Q ss_pred CCCccCCCCCCCCCCCCCCCCC
Q psy9982 66 SPAYTQVSPAYTQVSPAYTQVS 87 (222)
Q Consensus 66 Sp~ysPtSP~ySPtSP~ysPtS 87 (222)
+|.|+++||.|++++|+|++++
T Consensus 1575 sP~ysptSP~~s~tsP~yspts 1596 (1752)
T 3h0g_A 1575 SPSYSPTSPSYSPTSPSYSPTS 1596 (1752)
T ss_dssp ----------------------
T ss_pred CCCCCCCCCCCCCCCCCCCCCC
Confidence 3334333443433333333333
No 5
>4gwq_H DNA-directed RNA polymerase II subunit RPB1; binding sites, mediator complex, models, molecular, phosphor protein structure, tertiary; 4.50A {Saccharomyces cerevisiae}
Probab=98.61 E-value=2.3e-08 Score=64.97 Aligned_cols=26 Identities=46% Similarity=0.968 Sum_probs=8.3
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy9982 70 TQVSPAYTQVSPAYTQVSPAYIPVSP 95 (222)
Q Consensus 70 sPtSP~ySPtSP~ysPtSP~ysPtSP 95 (222)
+|+||.|+|++|+|++++|.|+|+||
T Consensus 2 sPtSP~ysPtSP~YsPtSP~YsPtSP 27 (35)
T 4gwq_H 2 SPTSPSYSPTSPSYSPTSPSYSPTSP 27 (35)
T ss_dssp ----CCSSSCCCCCCSSSSCSCCCCC
T ss_pred CCCCCCcCCCCCCcCCCCCCcCCCCC
Confidence 33444444333333333333333333
No 6
>2rdd_B UPF0092 membrane protein YAJC; drug resistance, multidrug efflux, transporter, antiporter, novel transmembrane helix, ACRB, inner membrane; HET: AIC; 3.50A {Escherichia coli}
Probab=82.69 E-value=0.43 Score=30.34 Aligned_cols=25 Identities=4% Similarity=0.329 Sum_probs=14.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcccccc
Q psy9982 15 TVEIFLLVFLLLNVLSYILIEKFKRKDL 42 (222)
Q Consensus 15 ~~iI~lLLF~~LYi~Sy~ii~~fkk~~~ 42 (222)
..++.+++|++.| +++|+..|||..
T Consensus 5 ~~l~~v~~~~ifY---Fl~iRPQ~Kr~K 29 (37)
T 2rdd_B 5 LILMLVVFGLIFY---FMILRPQQKRTK 29 (37)
T ss_dssp HHHHHHHHHHHHH---HHTHHHHHHHHH
T ss_pred HHHHHHHHHHHHH---HHHhhhHHHHHH
Confidence 3344445555544 567888887764
No 7
>2knc_B Integrin beta-3; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}
Probab=51.60 E-value=6.4 Score=28.81 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=7.6
Q ss_pred ccchhhccchhhH
Q psy9982 4 PDFLGLIGGTLTV 16 (222)
Q Consensus 4 ~~~~~~~~~~~~~ 16 (222)
++.++++||++..
T Consensus 8 ~n~~~Iv~gvi~g 20 (79)
T 2knc_B 8 PDILVVLLSVMGA 20 (79)
T ss_dssp SCSHHHHHHHHHH
T ss_pred CCchhhHHHHHHH
Confidence 4566666665544
No 8
>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}
Probab=46.21 E-value=42 Score=23.16 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccc
Q psy9982 18 IFLLVFLLLNVLSYILIEKFKRKDL 42 (222)
Q Consensus 18 I~lLLF~~LYi~Sy~ii~~fkk~~~ 42 (222)
+..||..+||-+. -|||+..
T Consensus 25 lL~li~~~LwK~G-----FFkR~~~ 44 (54)
T 2knc_A 25 LLTILVLAMWKVG-----FFKRNRP 44 (54)
T ss_dssp HHHHHHHHHHHHH-----HTTTTCC
T ss_pred HHHHHHHHHHHcC-----cccCCCC
Confidence 4445555666555 4566554
No 9
>2klu_A T-cell surface glycoprotein CD4; cell membrane, disulfide bond, HOST- virus interaction, immune response, immunoglobulin domain, lipoprotein; NMR {Homo sapiens}
Probab=42.12 E-value=24 Score=25.71 Aligned_cols=27 Identities=19% Similarity=0.189 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccccc
Q psy9982 17 EIFLLVFLLLNVLSYILIEKFKRKDLE 43 (222)
Q Consensus 17 iI~lLLF~~LYi~Sy~ii~~fkk~~~~ 43 (222)
+..||||+.|-|.+..=-.|-+|++|.
T Consensus 17 ~~~lll~~glcI~ccvkcrhRrrqAeR 43 (70)
T 2klu_A 17 VAGLLLFIGLGIFFSVRSRHRRRQAER 43 (70)
T ss_dssp HHHHHHHHHHHHHHHHHSSCCSSSCTT
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 456889999999988866777777764
No 10
>2knc_B Integrin beta-3; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}
Probab=39.09 E-value=11 Score=27.58 Aligned_cols=8 Identities=38% Similarity=0.800 Sum_probs=4.0
Q ss_pred hhhccchh
Q psy9982 7 LGLIGGTL 14 (222)
Q Consensus 7 ~~~~~~~~ 14 (222)
+|.|||+|
T Consensus 15 ~gvi~gil 22 (79)
T 2knc_B 15 LSVMGAIL 22 (79)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 45555544
No 11
>1q55_A EP-cadherin, C-cadherin; trans interaction, desmosome, junction, adhesion, structural protein; HET: NAG NDG; 30.00A {Mus musculus} SCOP: i.20.1.1 PDB: 1q5a_A* 1q5b_A* 1q5c_A*
Probab=34.64 E-value=8.3 Score=38.54 Aligned_cols=20 Identities=30% Similarity=0.293 Sum_probs=0.0
Q ss_pred hhccchhhHHHHHHHHHHHH
Q psy9982 8 GLIGGTLTVEIFLLVFLLLN 27 (222)
Q Consensus 8 ~~~~~~~~~iI~lLLF~~LY 27 (222)
|.|.+.|.||++||+.++|.
T Consensus 705 ~aii~il~~~~~ll~~~ll~ 724 (880)
T 1q55_A 705 PIILVILGSVLALLILFLLL 724 (880)
T ss_dssp --------------------
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34555566665555544443
No 12
>2gsm_B Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides} SCOP: b.6.1.2 f.17.2.1 PDB: 3dtu_B* 3fye_B* 3fyi_B* 3omi_B* 3om3_B* 3oma_B* 3omn_B* 1m56_B* 1m57_B*
Probab=33.56 E-value=37 Score=29.44 Aligned_cols=23 Identities=17% Similarity=0.391 Sum_probs=11.2
Q ss_pred HHHHHHH-HHHHHHHHHHhhccccc
Q psy9982 18 IFLLVFL-LLNVLSYILIEKFKRKD 41 (222)
Q Consensus 18 I~lLLF~-~LYi~Sy~ii~~fkk~~ 41 (222)
|++++|+ +++++-|+++ ||||+.
T Consensus 39 i~~~I~v~V~~ll~~~~~-r~r~~~ 62 (262)
T 2gsm_B 39 IIAAITIFVTLLILYAVW-RFHEKR 62 (262)
T ss_dssp HHHHHHHHHHHHHHHHHH-HSBTTT
T ss_pred HHHHHHHHHHHHHHHHHH-HHhccc
Confidence 4444444 4455555554 455553
No 13
>1m56_D Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.23.8.1 PDB: 1m57_D*
Probab=33.53 E-value=17 Score=24.83 Aligned_cols=14 Identities=36% Similarity=0.446 Sum_probs=8.9
Q ss_pred hHHHHHHHHHHHHH
Q psy9982 15 TVEIFLLVFLLLNV 28 (222)
Q Consensus 15 ~~iI~lLLF~~LYi 28 (222)
..+||+|||+.+++
T Consensus 37 ~~~~~~ll~laif~ 50 (51)
T 1m56_D 37 VVIVAALIFLALAN 50 (51)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHc
Confidence 34577777777653
No 14
>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}
Probab=32.91 E-value=71 Score=22.08 Aligned_cols=20 Identities=30% Similarity=0.401 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccc
Q psy9982 18 IFLLVFLLLNVLSYILIEKFKRKDL 42 (222)
Q Consensus 18 I~lLLF~~LYi~Sy~ii~~fkk~~~ 42 (222)
+..||..+||-+. -|||+..
T Consensus 22 LL~Lii~~LwK~G-----FFKR~~~ 41 (54)
T 2l8s_A 22 LLMLLILALWKIG-----FFKRPLK 41 (54)
T ss_dssp HHHHHHHHHHHHH-----HTTSCCS
T ss_pred HHHHHHHHHHHcC-----cccCCCc
Confidence 3444555566555 4566554
No 15
>4e6z_A Apicoplast TIC22, putative; TIC complex, import protein, transport protein; 2.15A {Plasmodium falciparum 3D7}
Probab=31.11 E-value=10 Score=33.59 Aligned_cols=13 Identities=31% Similarity=0.541 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHH
Q psy9982 18 IFLLVFLLLNVLS 30 (222)
Q Consensus 18 I~lLLF~~LYi~S 30 (222)
.|+|||+|+|++-
T Consensus 1 ~~~~~~~~~~~~~ 13 (279)
T 4e6z_A 1 MCLLLFICLYFAR 13 (279)
T ss_dssp -------------
T ss_pred CeEehhhHHHHHh
Confidence 4999999999864
No 16
>3arc_M Photosystem II reaction center protein M; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 1s5l_M* 2axt_M* 3bz1_M* 3bz2_M* 3kzi_M* 3prq_M* 3prr_M* 3a0b_M* 3a0h_M*
Probab=30.11 E-value=31 Score=22.22 Aligned_cols=23 Identities=35% Similarity=0.452 Sum_probs=13.1
Q ss_pred chhhccchhhHHHHHHHHHHHHH
Q psy9982 6 FLGLIGGTLTVEIFLLVFLLLNV 28 (222)
Q Consensus 6 ~~~~~~~~~~~iI~lLLF~~LYi 28 (222)
.||+|...|+..|=...-++|||
T Consensus 5 ~l~fiAt~Lfi~iPt~FLlilYv 27 (36)
T 3arc_M 5 QLGLIATALFVLVPSVFLIILYV 27 (36)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 46666666665555544455554
No 17
>3hb3_B Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B*
Probab=28.36 E-value=50 Score=29.39 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=12.3
Q ss_pred HHHHHH-HHHHHHHHHHHhhcccccc
Q psy9982 18 IFLLVF-LLLNVLSYILIEKFKRKDL 42 (222)
Q Consensus 18 I~lLLF-~~LYi~Sy~ii~~fkk~~~ 42 (222)
||+++| +++|++-|+++ ||||+.+
T Consensus 70 i~~~I~v~V~~l~~~~~~-r~r~~~~ 94 (298)
T 3hb3_B 70 IITAVTIFVCLLLLICIV-RFNRRAN 94 (298)
T ss_dssp HHHHHHHHHHHHHHHHHH-HSBTTTS
T ss_pred HHHHHHHHHHHHHHHHHH-HHhccCC
Confidence 444333 44455566555 6666543
No 18
>1qle_D Cytochrome AA3, ccytochrome C oxidase; oxidoreductase/immune system, complex (oxidoreductase/antibody), electron transport; HET: HEA PC1; 3.0A {Paracoccus denitrificans} SCOP: f.23.8.1
Probab=28.29 E-value=22 Score=23.44 Aligned_cols=13 Identities=46% Similarity=0.662 Sum_probs=8.0
Q ss_pred hHHHHHHHHHHHH
Q psy9982 15 TVEIFLLVFLLLN 27 (222)
Q Consensus 15 ~~iI~lLLF~~LY 27 (222)
..+|++|||+.++
T Consensus 29 ~~~~~~ll~maif 41 (43)
T 1qle_D 29 ILSIAVLVFLALA 41 (43)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHH
Confidence 3456777777654
No 19
>1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: b.6.1.2 f.17.2.1
Probab=20.30 E-value=20 Score=32.16 Aligned_cols=27 Identities=11% Similarity=0.225 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccc
Q psy9982 16 VEIFLLVFLLLNVLSYILIEKFKRKDL 42 (222)
Q Consensus 16 ~iI~lLLF~~LYi~Sy~ii~~fkk~~~ 42 (222)
.+|++++|++++++-.+++.|||++..
T Consensus 48 ~~i~liI~i~V~~ll~~~~~kyR~~~~ 74 (315)
T 1fft_B 48 FGLMLIVVIPAILMAVGFAWKYRASNK 74 (315)
T ss_dssp HHHTTTTTTHHHHHHHTTTTTTTTSTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 345566666677666667778887753
Done!