Query 041242
Match_columns 544
No_of_seqs 179 out of 251
Neff 4.1
Searched_HMMs 29240
Date Mon Mar 25 08:18:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041242.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/041242hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2knc_A Integrin alpha-IIB; tra 65.0 8.3 0.00028 30.2 4.5 37 19-56 8-44 (54)
2 2l8s_A Integrin alpha-1; trans 46.5 21 0.00073 28.0 4.0 44 19-64 5-48 (54)
3 2k1a_A Integrin alpha-IIB; sin 34.4 33 0.0011 25.5 3.2 36 19-55 6-41 (42)
4 1cn3_F Fragment of coat protei 34.2 21 0.00071 24.3 1.9 13 18-30 13-25 (29)
5 2uwj_E Type III export protein 20.6 61 0.0021 26.6 2.7 33 40-72 8-40 (70)
6 2zxx_A Geminin; coiled-coil, c 19.5 89 0.003 26.2 3.5 14 51-64 21-34 (79)
7 1rh4_A Right-handed coiled coi 18.1 98 0.0033 21.8 2.9 17 54-70 17-33 (35)
8 2knc_B Integrin beta-3; transm 17.9 2.1E+02 0.0072 23.5 5.5 22 186-207 41-62 (79)
9 1uii_A Geminin; human, DNA rep 16.9 1.1E+02 0.0038 25.9 3.5 15 50-64 32-46 (83)
10 2jwa_A Receptor tyrosine-prote 15.7 1.2E+02 0.0042 22.7 3.2 30 23-57 12-41 (44)
No 1
>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=64.96 E-value=8.3 Score=30.21 Aligned_cols=37 Identities=19% Similarity=0.394 Sum_probs=22.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhch
Q 041242 19 RDTPTWAVALVCAVLLILSILIEHGIHSLSKWFQKRQK 56 (544)
Q Consensus 19 e~TPTWaVA~Vc~v~v~iSi~~Er~lH~lgk~lkkk~k 56 (544)
+..|.|.+.+-...-+++-.++=.++.++| +|||+++
T Consensus 8 ~~vp~wiIi~svl~GLllL~li~~~LwK~G-FFkR~~~ 44 (54)
T 2knc_A 8 RAIPIWWVLVGVLGGLLLLTILVLAMWKVG-FFKRNRP 44 (54)
T ss_dssp TTCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HTTTTCC
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHcC-cccCCCC
Confidence 368999754433333333334456777887 6777664
No 2
>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}
Probab=46.52 E-value=21 Score=27.98 Aligned_cols=44 Identities=25% Similarity=0.459 Sum_probs=21.8
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhchhHHHHHHH
Q 041242 19 RDTPTWAVALVCAVLLILSILIEHGIHSLSKWFQKRQKKAMSEALE 64 (544)
Q Consensus 19 e~TPTWaVA~Vc~v~v~iSi~~Er~lH~lgk~lkkk~kkaL~eALe 64 (544)
+..|.|.+.+-...-+++-.++=-++-++| +|||+++ +..+.||
T Consensus 5 ~~vp~WiIi~svl~GLLLL~Lii~~LwK~G-FFKR~~~-~~~~~~~ 48 (54)
T 2l8s_A 5 GRVPLWVILLSAFAGLLLLMLLILALWKIG-FFKRPLK-KKMEKLE 48 (54)
T ss_dssp CCCCTHHHHHHHHHHHHHHHHHHHHHHHHH-HTTSCCS-CCCCC--
T ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHHcC-cccCCCc-chhhHHh
Confidence 368999643322222222233445667777 6766654 3344443
No 3
>2k1a_A Integrin alpha-IIB; single-PASS transmembrane segment, alternative splicing, calcium, cell adhesion, cleavage on PAIR of basic residues; NMR {Homo sapiens} PDB: 2k9j_A
Probab=34.40 E-value=33 Score=25.48 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=19.5
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhc
Q 041242 19 RDTPTWAVALVCAVLLILSILIEHGIHSLSKWFQKRQ 55 (544)
Q Consensus 19 e~TPTWaVA~Vc~v~v~iSi~~Er~lH~lgk~lkkk~ 55 (544)
+..|.|.+.+-...-+++=.++=.++.++| +|||++
T Consensus 6 ~~vp~wiIi~s~l~GLllL~li~~~LwK~G-FFkR~~ 41 (42)
T 2k1a_A 6 RAIPIWWVLVGVLGGLLLLTILVLAMWKVG-FFKRNR 41 (42)
T ss_dssp CCCCHHHHHHHHHHHHHHHHHHHHHHHHTT-TTCCCC
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHcC-cccCCC
Confidence 468999654333333333334445677776 555554
No 4
>1cn3_F Fragment of coat protein VP2; viral coat protein VP1, viral coat protein VP2, viral entry, viral protein; 2.20A {Polyomavirus}
Probab=34.21 E-value=21 Score=24.30 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=9.7
Q ss_pred CCCCCchHHHHHH
Q 041242 18 LRDTPTWAVALVC 30 (544)
Q Consensus 18 Le~TPTWaVA~Vc 30 (544)
-.-||.|.+-++.
T Consensus 13 qrvtpdwmlplil 25 (29)
T 1cn3_F 13 QRVTPDWMLPLIL 25 (29)
T ss_dssp CCCEEGGGHHHHH
T ss_pred cccCchhhHHHHH
Confidence 3579999987654
No 5
>2uwj_E Type III export protein PSCE; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}
Probab=20.58 E-value=61 Score=26.65 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=25.5
Q ss_pred HHHHHHHHhhHHHhhchhHHHHHHHHHHHHHHH
Q 041242 40 IEHGIHSLSKWFQKRQKKAMSEALEKIKAELML 72 (544)
Q Consensus 40 ~Er~lH~lgk~lkkk~kkaL~eALeKiK~ELML 72 (544)
+|..|+-.+.-..++=+--|+.||.++|.+|++
T Consensus 8 LE~~L~~~~~~~~~~i~~~L~qAl~~vKrqL~~ 40 (70)
T 2uwj_E 8 LETRLSVADGTHAAALRQRLQAALAECRRELAR 40 (70)
T ss_dssp HHHHHTSSSTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 566666666556666667799999999999986
No 6
>2zxx_A Geminin; coiled-coil, cell cycle, coiled coil, DNA replication inhibitor, phosphoprotein, DNA-binding, nucleus, proto-oncogene; HET: DNA; 2.80A {Mus musculus}
Probab=19.51 E-value=89 Score=26.17 Aligned_cols=14 Identities=36% Similarity=0.584 Sum_probs=9.4
Q ss_pred HHhhchhHHHHHHH
Q 041242 51 FQKRQKKAMSEALE 64 (544)
Q Consensus 51 lkkk~kkaL~eALe 64 (544)
+..+||+||.+||+
T Consensus 21 lAE~RR~AL~eaL~ 34 (79)
T 2zxx_A 21 VAEQRRKALYEALK 34 (79)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 45566777777775
No 7
>1rh4_A Right-handed coiled coil tetramer; de novo design; 1.90A {Synthetic construct} SCOP: k.17.1.1
Probab=18.07 E-value=98 Score=21.82 Aligned_cols=17 Identities=41% Similarity=0.554 Sum_probs=13.3
Q ss_pred hchhHHHHHHHHHHHHH
Q 041242 54 RQKKAMSEALEKIKAEL 70 (544)
Q Consensus 54 k~kkaL~eALeKiK~EL 70 (544)
|-|-..+.||.|||.|+
T Consensus 17 kikaeilaalkkikqei 33 (35)
T 1rh4_A 17 KIKAEILAALKKIKQEI 33 (35)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 34567889999999886
No 8
>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=17.95 E-value=2.1e+02 Score=23.49 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=16.2
Q ss_pred HHhHHHHhhhhhcccccccCCC
Q 041242 186 MKKWQAWELETNSLEYQFTNDP 207 (544)
Q Consensus 186 ir~Wk~WE~e~~~~~~~~~~dp 207 (544)
-|.++++|+|-+....+..++|
T Consensus 41 rrE~~kFEkE~~~~~w~~~~NP 62 (79)
T 2knc_B 41 RKEFAKFEEERARAKWDTANNP 62 (79)
T ss_dssp HHHHHHHHHHHHHHHHTTTTCC
T ss_pred HHHHHHHHHHHHhcccccCCCC
Confidence 6899999999776655545555
No 9
>1uii_A Geminin; human, DNA replication, cell cycle; 2.00A {Homo sapiens} SCOP: h.1.28.1
Probab=16.88 E-value=1.1e+02 Score=25.87 Aligned_cols=15 Identities=33% Similarity=0.477 Sum_probs=11.0
Q ss_pred HHHhhchhHHHHHHH
Q 041242 50 WFQKRQKKAMSEALE 64 (544)
Q Consensus 50 ~lkkk~kkaL~eALe 64 (544)
-+..+||+||.+||+
T Consensus 32 ~lAE~RR~AL~eaL~ 46 (83)
T 1uii_A 32 EVAEKRRKALYEALK 46 (83)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 355677888888886
No 10
>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A
Probab=15.69 E-value=1.2e+02 Score=22.73 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=14.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhchh
Q 041242 23 TWAVALVCAVLLILSILIEHGIHSLSKWFQKRQKK 57 (544)
Q Consensus 23 TWaVA~Vc~v~v~iSi~~Er~lH~lgk~lkkk~kk 57 (544)
|++.|.|..+++++-+.+ -++=|++||+++
T Consensus 12 ~~Ia~~vVGvll~vi~~l-----~~~~~~RRR~~~ 41 (44)
T 2jwa_A 12 TSIISAVVGILLVVVLGV-----VFGILIKRRQQK 41 (44)
T ss_dssp HHHHHHHHHHHHHHHHHH-----HHHHHHHHHCSC
T ss_pred cchHHHHHHHHHHHHHHH-----HHHhheehhhhh
Confidence 455565555443322222 235577777653
Done!