RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15173
(131 letters)
>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 = 73.6 bits (181), Expect = 1e-16
Identities = 33/61 (54%), Positives = 42/61 (68%)
Query: 71 IQRAVLEVRRVLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDKVEGAFDWAKKTLNDH 130
QR LE ++ K+VD+F EE +VRRELADNFCYY YD + GA++WA+KTL DH
Sbjct: 295 AQRCALEAKKCRHLSPKSVDAFLEELVVRRELADNFCYYQPQYDSLSGAWEWARKTLMDH 354
Query: 131 R 131
Sbjct: 355 A 355
Score = 57.4 bits (139), Expect = 7e-11
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 5 GLKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDL 64
GL+ + D ++ F GG EI P V++ +V DF PLR D + DL
Sbjct: 96 GLRRLAADAAARHLPFFLFTGGPAEI-PALVQRLGASTLVADFSPLRPVREALDAVVGDL 154
Query: 65 PKD---VPLIQ---RAVLEVRRVLPK 84
++ V + Q V+ V K
Sbjct: 155 RREAPGVAVHQVDAHNVVPVWTASAK 180
>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD;
1.50A {Methanosarcina mazei} PDB: 2xrz_A*
Length = 482
Score = 72.0 bits (177), Expect = 5e-16
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 71 IQRAVLEVRRVLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDKVEGAFDWAKKTLNDH 130
QR VLEV + + + +F +E ++ +E++DNFCYYN YD E WAK++LN H
Sbjct: 296 SQRVVLEVEK-AESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAH 354
Query: 131 R 131
R
Sbjct: 355 R 355
Score = 59.7 bits (145), Expect = 1e-11
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 5/83 (6%)
Query: 5 GLKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTLKKDL 64
GL+E+ + I FL G E + +FV+ + G +V DF PLR W + + +
Sbjct: 93 GLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGI 152
Query: 65 PKDVPLIQ---RAVLEVRRVLPK 84
+P + V+ K
Sbjct: 153 --SIPFFEVDAHNVVPCWEASQK 173
>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 = 30.6 bits (70), Expect = 0.12
Identities = 8/38 (21%), Positives = 18/38 (47%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAV 43
L+E+ + ++ L G ++PQ ++ + AV
Sbjct: 59 LQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAV 96
>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 = 29.4 bits (67), Expect = 0.27
Identities = 8/38 (21%), Positives = 15/38 (39%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAV 43
++ + E + L G E +P+ + K AV
Sbjct: 54 VRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAV 91
>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 = 29.5 bits (67), Expect = 0.33
Identities = 5/39 (12%), Positives = 17/39 (43%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVV 44
++ + E +K+ + G +++PQ ++ +
Sbjct: 67 VQNLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIY 105
>1dl5_A Protein-L-isoaspartate O-methyltransferase; isoaspartyl residues,
protein repair, deamidation, post-translational
modification; HET: SAH; 1.80A {Thermotoga maritima}
SCOP: c.66.1.7 d.197.1.1
Length = 317
Score = 28.9 bits (65), Expect = 0.42
Identities = 5/65 (7%), Positives = 17/65 (26%), Gaps = 3/65 (4%)
Query: 35 VEKHKLGAVVIDFMPLREHMGWADTLKKDLPKDVPLIQR-AVLEVRRVLPKHSKAVDSFC 93
+ + F+ ++G + L ++ P + ++ +
Sbjct: 195 LVGNYKLETR--FITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLT 252
Query: 94 EEAIV 98
E
Sbjct: 253 EIDGT 257
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A
{Arabidopsis thaliana}
Length = 537
Score = 28.8 bits (65), Expect = 0.48
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVV 44
LK++ KKL G E+L + +++ K+ +
Sbjct: 70 LKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLC 108
>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 = 28.9 bits (64), Expect = 0.49
Identities = 24/151 (15%), Positives = 40/151 (26%), Gaps = 64/151 (42%)
Query: 4 LGLKEVHEDCKKLNIEF---------------HFLIGGAHEILPQFVEKHKLGAVVIDFM 48
L ++V + K N + ++ G PQ L + +
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGP----PQ-----SLYGLNLT-- 392
Query: 49 PLREHMGWADTLKKDLPKD---VPLIQRAVLEVRRVL----PKHSK----AVDSFCEEAI 97
LR+ K D +P +R + R L P HS A D +
Sbjct: 393 -LRK-------AKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINK--- 441
Query: 98 VRRELADNFCYYNKNYDKVEGAFDWAKKTLN 128
D V+ + K +
Sbjct: 442 ----------------DLVKNNVSFNAKDIQ 456
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 28.7 bits (63), Expect = 0.60
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 17/78 (21%)
Query: 56 WADTLKKDLPKDVPLIQRAVLEVRRVLPKHSKAVDSFCEEAIVRRELADNFCYYNKNYDK 115
+ D +DLP+ EV P+ + + + DN+ + N DK
Sbjct: 310 YLDCRPQDLPR----------EVLTTNPRRLSIIAESIRDGLAT---WDNWKHV--NCDK 354
Query: 116 VEGAFDWAKKTLN--DHR 131
+ + + L ++R
Sbjct: 355 LTTIIESSLNVLEPAEYR 372
Score = 27.9 bits (61), Expect = 1.3
Identities = 19/124 (15%), Positives = 43/124 (34%), Gaps = 23/124 (18%)
Query: 1 MSQLGLKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVVIDFMPLREHMGWADTL 60
+ + E + + ++F FL + K+ D +TL
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFL-------------EQKIRH---DSTAWNASGSILNTL 524
Query: 61 ------KKDLPKDVPLIQRAVLEVRRVLPKHSKAVDSFCEEAIVRREL-ADNFCYYNKNY 113
K + + P +R V + LPK + + ++R L A++ + + +
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAH 584
Query: 114 DKVE 117
+V+
Sbjct: 585 KQVQ 588
>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 = 28.4 bits (64), Expect = 0.61
Identities = 7/39 (17%), Positives = 18/39 (46%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVV 44
L+++ +KLN + G E+ P+ + ++ +
Sbjct: 91 LEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLT 129
>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 = 28.0 bits (63), Expect = 1.00
Identities = 8/39 (20%), Positives = 14/39 (35%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVV 44
L ++ ++ K + G EILP + V
Sbjct: 102 LVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVF 140
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase,
FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus
tokodaii}
Length = 440
Score = 27.1 bits (61), Expect = 2.0
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 6 LKEVHEDCKKLNIEFHFLIGGAHEILPQFVEKHKLGAVV 44
L E+ ++ +K + G A +++ +F K+ A+
Sbjct: 58 LLELDDELRKKGSRLNVFFGEAEKVVSRFFN--KVDAIY 94
>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 = 26.4 bits (59), Expect = 2.9
Identities = 4/40 (10%), Positives = 10/40 (25%), Gaps = 1/40 (2%)
Query: 6 LKEVHEDCKKLNIEFHFLIGG-AHEILPQFVEKHKLGAVV 44
L ++ + L + L V+ +
Sbjct: 67 LAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIF 106
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 26.5 bits (59), Expect = 3.0
Identities = 6/42 (14%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 6 LKEVHEDCKKLNIEFHFLI---GGAHEILPQFVEKHKLGAVV 44
L+++ + + L+ G I + E+ +L +
Sbjct: 63 LQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRIC 104
>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein,
USP domain, nucleotide binding domain, AMP; HET: MSE
AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4
Length = 175
Score = 25.6 bits (56), Expect = 4.6
Identities = 7/42 (16%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 6 LKEVHEDCKKLNIEFHFLI--GGAHEILPQFVEKHKLGAVVI 45
L+ C ++ + I G +++ Q V++ + +V+
Sbjct: 89 LEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVV 130
>2i9c_A Hypothetical protein RPA1889; structural genomics, SAD, PSI-2,
protein structure initiativ midwest center for
structural genomics; HET: MSE; 2.00A {Rhodopseudomonas
palustris} SCOP: a.118.1.25
Length = 123
Score = 24.8 bits (53), Expect = 7.6
Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 86 SKAVDSFCEEAIVRRE--LADNFCYYNKNYDKVEGAFDWAKKTLNDHR 131
V F + + + + L + +N+ + + D K D R
Sbjct: 12 QDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDGDQR 59
>1k1e_A Deoxy-D-mannose-octulosonate 8-phosphate phosphat; structural
genomics, KDO 8-P phosphatase, structure function
project, S2F; HET: MES; 1.67A {Haemophilus influenzae
RD} SCOP: c.108.1.5 PDB: 1j8d_A*
Length = 180
Score = 24.8 bits (55), Expect = 7.7
Identities = 17/130 (13%), Positives = 32/130 (24%), Gaps = 39/130 (30%)
Query: 13 CKKLNIEFHFLIGGAH---EILPQFVEKHKLGAVVIDFM-------PLREHMGWADTLKK 62
L I+ FL G +++ + A ++ P G +
Sbjct: 69 IADLGIKLFFL--GKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFA--- 123
Query: 63 DLPKDVPLIQRAVLEVRRVLPKHSK------AVDSFCEEAIVRRELADNFCYYNKNYDKV 116
D A + V+ + A RE++D
Sbjct: 124 --VAD------APIYVKNAVDHVLSTHGGKGAF----------REMSDMILQAQGKSSVF 165
Query: 117 EGAFDWAKKT 126
+ A + K
Sbjct: 166 DTAQGFLKSV 175
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
0.323 0.140 0.432
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: 2,160,789
Number of extensions: 125865
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 30
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (23.9 bits)