RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6305
(52 letters)
>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET:
TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A*
2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
Length = 543
Score = 62.3 bits (152), Expect = 7e-14
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 1 MDTPNSPNNKEVAVHWFRHGLRLHDNPALFEA-------SLNSVLYPVFIFDGETAG 50
+ + VHWFR GLRLHDNPAL + P+FI D
Sbjct: 19 KKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILD 75
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 60.4 bits (147), Expect = 3e-13
Identities = 27/45 (60%), Positives = 30/45 (66%), Gaps = 4/45 (8%)
Query: 10 KEVAVHWFRHGLRLHDNPALFEASLNS----VLYPVFIFDGETAG 50
+ V WFRHGLRLHDNPAL A + L PVFIFDGE+AG
Sbjct: 3 RGANVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAG 47
>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein,
flavoprotein, FAD, mitochondrion, plastid, chromophore,
chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana}
PDB: 2vtb_A* 2ijg_X* 2vtb_B*
Length = 525
Score = 60.3 bits (147), Expect = 3e-13
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 3 TPNSPNNKEVAVHWFRHGLRLHDNPALFEASLNSV-LYPVFIFD 45
+ K V + WFR+ LR+ DN AL++A +S + PV+ D
Sbjct: 32 SSVKRKGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLD 75
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD;
2.70A {Arabidopsis thaliana}
Length = 537
Score = 60.0 bits (146), Expect = 4e-13
Identities = 20/36 (55%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 13 AVHWFRHGLRLHDNPALFEASLNS-VLYPVFIFDGE 47
++ WFR GLR+HDNPAL AS S +YPVF+ D
Sbjct: 7 SLIWFRKGLRVHDNPALEYASKGSEFMYPVFVIDPH 42
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A
{Synechocystis SP} SCOP: a.99.1.1 c.28.1.1
Length = 489
Score = 57.2 bits (139), Expect = 4e-12
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 7 PNNKEVAVHWFRHGLRLHDNPALFEASLNSV-LYPVFIFD 45
+ + WFR+ LRLHD+ L A + + + V+ +D
Sbjct: 2 KHVPPTVLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYD 41
>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*
Length = 509
Score = 56.8 bits (138), Expect = 6e-12
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 3 TPNSPNNKEVAVHWFRHGLRLHDNPALFEASLNSVLYPVFIFDGETAGLF 52
+ + + ++ WFR LR+ DNPAL A + +F++ E G +
Sbjct: 4 SVSGCGSGGCSIVWFRRDLRVEDNPALAAAVRAGPVIALFVWAPEEEGHY 53
>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*
Length = 420
Score = 54.0 bits (131), Expect = 6e-11
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 12 VAVHWFRHGLRLHDNPALFEASLNSVLYPVFIFD 45
+ W R LRLHD+PAL EA + + + D
Sbjct: 3 PLLVWHRGDLRLHDHPALLEALARGPVVGLVVLD 36
>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
Length = 471
Score = 52.9 bits (128), Expect = 1e-10
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 12 VAVHWFRHGLRLHDNPALFEASLNSV--LYPVFIFD 45
+ WFR LRLHDN AL A NS + ++I
Sbjct: 2 THLVWFRQDLRLHDNLALAAACRNSSARVLALYIAT 37
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin
enzyme, photoreactivating enzyme; HET: FAD; 1.80A
{Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB:
1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*
Length = 484
Score = 51.4 bits (124), Expect = 5e-10
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 13 AVHWFRHGLRLHDNPALFEASLNSV-LYPVFIFD 45
+ W R LRL DN L A S L +F D
Sbjct: 5 ILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLD 38
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase,
FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus
tokodaii}
Length = 440
Score = 51.0 bits (123), Expect = 6e-10
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 13 AVHWFRHGLRLHDNPALFEASLNSV-LYPVFIFD 45
+ FR LRL DN L A + PVFI D
Sbjct: 3 CIFIFRRDLRLEDNTGLNYALSECDRVIPVFIAD 36
>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET:
FAD; 1.50A {Methanosarcina mazei} PDB: 2xrz_A*
Length = 482
Score = 45.4 bits (108), Expect = 7e-08
Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 5/46 (10%)
Query: 5 NSPNNKEVAVHWFRHGLRLHDNPALFEAS-----LNSVLYPVFIFD 45
+ V+W R DN AL + N + VF
Sbjct: 31 SGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLT 76
>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine
dimers, UV damaged DNA, DNA repai flavoprotein; HET:
FAD; 1.71A {Oryza sativa japonica group}
Length = 506
Score = 44.3 bits (105), Expect = 1e-07
Identities = 13/48 (27%), Positives = 15/48 (31%), Gaps = 5/48 (10%)
Query: 3 TPNSPNNKEVAVHWFRHGLRLHDNPALFEAS-----LNSVLYPVFIFD 45
P V+W RL DN AL A+ S L F
Sbjct: 30 HPGGGKPGGPVVYWMLRDQRLADNWALLHAAGLAAASASPLAVAFALF 77
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 25.0 bits (54), Expect = 1.0
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 2/32 (6%)
Query: 13 AVHWFRHGLRLHDNPALFEASL--NSVLYPVF 42
A + N ALF A N+ L +F
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
>1igt_B IGG2A intact antibody - MAB231; intact immunoglobulin V region C
region, immunoglobulin; HET: NAG FUL BMA MAN GAL FUC;
2.80A {Mus musculus} SCOP: b.1.1.1 b.1.1.2 b.1.1.2
b.1.1.2
Length = 444
Score = 24.5 bits (53), Expect = 1.7
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 6 SPNNKEVAVHWFRHGLRLHDNPALFEASLNSVLYPV 41
S ++ +V + WF + + +H + V
Sbjct: 268 SEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTLRV 303
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.139 0.447
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 794,282
Number of extensions: 31531
Number of successful extensions: 131
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 14
Length of query: 52
Length of database: 6,701,793
Length adjustment: 24
Effective length of query: 28
Effective length of database: 6,031,689
Effective search space: 168887292
Effective search space used: 168887292
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.5 bits)