Query 028540
Match_columns 207
No_of_seqs 121 out of 1071
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 21:56:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028540.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/028540hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3tvs_A Cryptochrome-1; circadi 7.7 94 0.0032 28.8 0.3 20 11-30 424-444 (538)
2 2fqh_A Hypothetical protein TA 7.4 87 0.003 23.1 -0.1 8 11-18 17-24 (109)
3 1u3d_A Cryptochrome 1 apoprote 5.8 68 0.0023 29.2 -1.8 20 11-30 405-424 (509)
4 3g21_A GAG polyprotein, capsid 4.3 3.1E+02 0.01 19.1 1.2 23 23-46 4-26 (77)
5 1j1v_A Chromosomal replication 4.3 3E+02 0.01 19.2 1.1 29 72-101 35-64 (94)
6 3fy4_A 6-4 photolyase; DNA rep 4.1 2.5E+02 0.0085 26.0 0.7 19 11-30 411-429 (537)
7 2j07_A Deoxyribodipyrimidine p 3.8 1.4E+02 0.0048 26.4 -1.2 21 10-30 355-375 (420)
8 1dnp_A DNA photolyase; DNA rep 3.7 1.3E+02 0.0045 27.2 -1.5 21 10-30 386-406 (471)
9 2jyp_A Aragonite protein AP7; 3.7 2.2E+02 0.0077 16.6 0.1 6 13-18 11-16 (36)
10 3msq_A Putative ubiquinone bio 3.7 3.5E+02 0.012 22.0 1.2 11 186-196 124-134 (224)
No 1
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag, phosphorylation, gene regulation, signaling protein; HET: TPO FAD; 2.30A {Drosophila melanogaster} PDB: 4gu5_A*
Probab=7.72 E-value=94 Score=28.81 Aligned_cols=20 Identities=20% Similarity=0.032 Sum_probs=14.7
Q ss_pred cCcc-hhhhhhhhhhccCCCC
Q 028540 11 SSEC-SLISYLRIYTCVSHFP 30 (207)
Q Consensus 11 ~~~~-~~~~~~~~~~~~~~~p 30 (207)
|+|| .-.-||+||||++|.-
T Consensus 424 g~g~Dd~~pyfRifNP~~Q~~ 444 (538)
T 3tvs_A 424 SSAFERLLDSSLVTCPVALAK 444 (538)
T ss_dssp CCCSSCCCTHHHHCSTTTHHH
T ss_pred cCCCcCCCCceeeeCHHHHHH
Confidence 4555 3467899999999853
No 2
>2fqh_A Hypothetical protein TA0938; structural genomics, Zn-binding,, ontario centre for structural proteomics, OCSP, unknown function; NMR {Thermoplasma acidophilum}
Probab=7.44 E-value=87 Score=23.12 Aligned_cols=8 Identities=38% Similarity=0.725 Sum_probs=6.6
Q ss_pred cCcchhhh
Q 028540 11 SSECSLIS 18 (207)
Q Consensus 11 ~~~~~~~~ 18 (207)
..|||||+
T Consensus 17 ~tGCALCG 24 (109)
T 2fqh_A 17 SKGCALCG 24 (109)
T ss_dssp GGSCSSCC
T ss_pred ccceeeeC
Confidence 36999998
No 3
>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A*
Probab=5.80 E-value=68 Score=29.24 Aligned_cols=20 Identities=10% Similarity=-0.257 Sum_probs=16.3
Q ss_pred cCcchhhhhhhhhhccCCCC
Q 028540 11 SSECSLISYLRIYTCVSHFP 30 (207)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~p 30 (207)
|+||.-.-||+||||++|.-
T Consensus 405 g~g~d~~py~RifNP~~Q~~ 424 (509)
T 1u3d_A 405 GTLPDSREFDRIDNPQFEGY 424 (509)
T ss_dssp TCSTTCCCSSCCCCHHHHHH
T ss_pred cCCCCCCccccccCHHHHHH
Confidence 56666678999999999875
No 4
>3g21_A GAG polyprotein, capsid protein; alpha-helical bundle, virion, viral protein, retrovirus; 0.90A {Rous sarcoma virus} PDB: 3g1i_A 3g28_A 3g29_A 3g26_A 3g0v_A
Probab=4.34 E-value=3.1e+02 Score=19.12 Aligned_cols=23 Identities=9% Similarity=0.192 Sum_probs=14.9
Q ss_pred hhccCCCCCCCCCCChHHHHHHHH
Q 028540 23 YTCVSHFPLLSGDLHLLERVANVL 46 (207)
Q Consensus 23 ~~~~~~~p~~~~~~t~~Ee~aN~i 46 (207)
++-+.||| ++.-.+..++..+++
T Consensus 4 ~tdI~QGP-kEPF~dfVdRl~kal 26 (77)
T 3g21_A 4 WADIMQGP-SESFVDFANRLIKAV 26 (77)
T ss_dssp GGGCCCCT-TCCHHHHHHHHHHHH
T ss_pred ccccccCC-CccHHHHHHHHHHHH
Confidence 56788999 555455666665544
No 5
>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2
Probab=4.27 E-value=3e+02 Score=19.22 Aligned_cols=29 Identities=10% Similarity=0.153 Sum_probs=19.1
Q ss_pred HHHHHHHHhhhhcCchhHHHHH-HHHhhhhh
Q 028540 72 LVGVGVTSSLYHSSRGKLRKYL-RWADYAMI 101 (207)
Q Consensus 72 li~lf~~STlYH~~~~~~k~~~-rrlDH~aI 101 (207)
.++||++--+...+-.+.-+.| .| ||+++
T Consensus 35 qiamyL~r~~t~~Sl~~IG~~fggr-dHsTV 64 (94)
T 1j1v_A 35 QMAMALAKELTNHSLPEIGDAFGGR-DHTTV 64 (94)
T ss_dssp HHHHHHHHHHSCCCHHHHHHHTTSC-CHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHhCCC-CHHHH
Confidence 5678888777666555544455 33 99988
No 6
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}
Probab=4.05 E-value=2.5e+02 Score=25.95 Aligned_cols=19 Identities=26% Similarity=0.273 Sum_probs=13.9
Q ss_pred cCcchhhhhhhhhhccCCCC
Q 028540 11 SSECSLISYLRIYTCVSHFP 30 (207)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~p 30 (207)
|+||-- .+|+||||++|.-
T Consensus 411 g~g~d~-~~fRifNP~~Q~~ 429 (537)
T 3fy4_A 411 CSSFFY-QFNRIYSPISFGK 429 (537)
T ss_dssp TSSSCC-CTTCCCCTTTTGG
T ss_pred ccCCCc-ccccccCHHHHHH
Confidence 455532 2899999999975
No 7
>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A*
Probab=3.76 E-value=1.4e+02 Score=26.44 Aligned_cols=21 Identities=14% Similarity=0.130 Sum_probs=16.7
Q ss_pred ccCcchhhhhhhhhhccCCCC
Q 028540 10 FSSECSLISYLRIYTCVSHFP 30 (207)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~p 30 (207)
.|+|+.--.||+||||++|.-
T Consensus 355 aG~g~d~~pyfR~fNp~~q~~ 375 (420)
T 2j07_A 355 GGLGVDAAPYFRVFNPVLQGE 375 (420)
T ss_dssp TTSSGGGCCTTCCCCHHHHHH
T ss_pred HccCCCCCCCceeeCHHHHHH
Confidence 466777777899999998865
No 8
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1
Probab=3.71 E-value=1.3e+02 Score=27.16 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=16.0
Q ss_pred ccCcchhhhhhhhhhccCCCC
Q 028540 10 FSSECSLISYLRIYTCVSHFP 30 (207)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~p 30 (207)
.|+|+.--.|++||||++|.-
T Consensus 386 ag~G~d~~py~RifNp~~q~~ 406 (471)
T 1dnp_A 386 ASTGTDAAPYFRIFNPTTQGE 406 (471)
T ss_dssp TTCSTTCCCTTCCCCHHHHHH
T ss_pred cCCCCCCCCcceecCHHHHHH
Confidence 356666666899999998865
No 9
>2jyp_A Aragonite protein AP7; protein C-terminal fragment, unknown function; NMR {Synthetic}
Probab=3.71 E-value=2.2e+02 Score=16.58 Aligned_cols=6 Identities=50% Similarity=0.955 Sum_probs=5.0
Q ss_pred cchhhh
Q 028540 13 ECSLIS 18 (207)
Q Consensus 13 ~~~~~~ 18 (207)
||+||-
T Consensus 11 ecalcy 16 (36)
T 2jyp_A 11 ECALCY 16 (36)
T ss_dssp CCSSST
T ss_pred hheeEE
Confidence 899984
No 10
>3msq_A Putative ubiquinone biosynthesis protein; COQ4 superfamily, structural genomics, joint center for STRU genomics, JCSG; 2.85A {Nostoc punctiforme}
Probab=3.65 E-value=3.5e+02 Score=22.03 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=8.7
Q ss_pred chhhHHHHHHH
Q 028540 186 YLHAAWHLAAA 196 (207)
Q Consensus 186 ~~H~IWHlfV~ 196 (207)
-.|++||+..-
T Consensus 124 e~HD~~HvLtG 134 (224)
T 3msq_A 124 STHDIYHVVAG 134 (224)
T ss_dssp HHHHHHHHHHT
T ss_pred cchhhhhhccC
Confidence 47999998754
Done!