BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 016046
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR M R
Sbjct: 13 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 63
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR M R
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 60
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR M R
Sbjct: 9 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 59
>pdb|3SJM|A Chain A, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
pdb|3SJM|B Chain B, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
Length = 64
Score = 55.5 bits (132), Expect = 6e-08, Method: Composition-based stats.
Identities = 25/53 (47%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR M R
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 60
>pdb|1W0U|A Chain A, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0U|B Chain B, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna
Length = 55
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/53 (47%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR M R
Sbjct: 1 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 51
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
R RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR M +
Sbjct: 7 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTMKK 60
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
R RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR M +
Sbjct: 6 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTMKK 59
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr,
18 Structures
Length = 53
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 339 RKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNM 390
RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR M
Sbjct: 1 RKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTM 50
>pdb|1W0T|A Chain A, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0T|B Chain B, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna
Length = 53
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMTR 392
K++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR M +
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTMKK 51
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 36/59 (61%)
Query: 333 TKLARRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMT 391
++L++RR ++ +S+ E +AL + VE G G W+ + D RT VDLKDKW+ +
Sbjct: 9 SELSQRRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLV 67
>pdb|2QHB|A Chain A, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
pdb|2QHB|B Chain B, Crystal Structure Of Ngtrf Complexed With Telomeric Dna
Length = 86
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%)
Query: 338 RRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMT 391
RR ++ +S+ E +AL + VE G G W+ + D RT VDLKDKW+ +
Sbjct: 1 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLV 54
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 33/55 (60%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMT 391
+RR ++ +S+ E +AL + VE+ G G W+ + D RT VDLKDKW+ +
Sbjct: 9 QRRIRRPFSVAEVEALVQAVEKLGTGRWRDVKLCAFEDADHRTYVDLKDKWKTLV 63
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 38/81 (46%)
Query: 311 GNRFHLPSPKRKAVSPLKNHDVTKLARRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKS 370
G+ F P+ A PL +RR ++ +++ E + L + VE G G W+ +
Sbjct: 1 GSPFADPNSLALANVPLSRSKRPDFGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFR 60
Query: 371 NPGAFDERTEVDLKDKWRNMT 391
RT VDLKDKW+ +
Sbjct: 61 AFENVHHRTYVDLKDKWKTLV 81
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric
Repeat Binding Factor From Nicotiana Tabacum
Length = 83
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 345 SLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNMT 391
S+ E +AL + VE G G W+ + D RT VDLKDKW+ +
Sbjct: 4 SVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLV 50
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 35.0 bits (79), Expect = 0.072, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTE 380
K KW+ EE++ LR V QFG+ +WK + P D++ +
Sbjct: 8 KVKWTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQ 47
>pdb|1MBE|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
pdb|1MBF|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
Length = 53
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNM 390
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKV 48
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNM 390
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ +
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKV 48
>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 159
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNM 390
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ +
Sbjct: 6 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKV 51
>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
Length = 126
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRN 389
KK+K++ EE++ L++ V Q G +WK+I F R +D+W+N
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHG-SDWKMI----AATFPNRNARQCRDRWKN 54
>pdb|1H0N|A Chain A, Cobalt Substitution Of Mouse R2 Ribonucleotide Reductase
To Model The Reactive Diferrous State
pdb|1H0O|A Chain A, Cobalt Substitution Of Mouse R2 Ribonucleotide Reductase
To Model The Reactive Diferrous State
pdb|1W68|A Chain A, Crystal Structure Of Mouse Ribonucleotide Reductase
Subunit R2 Under Oxidizing Conditions. A Fully Occupied
Dinuclear Iron Cluster.
pdb|1W69|A Chain A, Crystal Structure Of Mouse Ribonucleotide Reductase
Subunit R2 Under Reducing Conditions. A Fully Occupied
Dinuclear Iron Cluster And Bound Acetate.
pdb|1XSM|A Chain A, Protein R2 Of Ribonucleotide Reductase From Mouse
Length = 390
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 302 SIDEEPSNQGNRFHLPSPKRKAVSPLKNHDVTKLARRRKKKKWSLEEED 350
S+++EP + N P+R V P++ HD+ ++ ++ + W+ EE D
Sbjct: 67 SVEDEPLLREN------PRRFVVFPIEYHDIWQMYKKAEASFWTAEEVD 109
>pdb|3OLJ|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase
Subunit M2 (Hrrm2)
pdb|3OLJ|B Chain B, Crystal Structure Of Human Ribonucleotide Reductase
Subunit M2 (Hrrm2)
pdb|3OLJ|C Chain C, Crystal Structure Of Human Ribonucleotide Reductase
Subunit M2 (Hrrm2)
pdb|3OLJ|D Chain D, Crystal Structure Of Human Ribonucleotide Reductase
Subunit M2 (Hrrm2)
Length = 286
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 9/33 (27%), Positives = 21/33 (63%)
Query: 318 SPKRKAVSPLKNHDVTKLARRRKKKKWSLEEED 350
+P+R + P++ HD+ ++ ++ + W+ EE D
Sbjct: 12 NPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVD 44
>pdb|2UW2|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase
Subunit R2
Length = 332
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 319 PKRKAVSPLKNHDVTKLARRRKKKKWSLEEED 350
P+R + P++ HD+ ++ ++ + W+ EE D
Sbjct: 20 PRRFVIFPIEYHDIWQMYKKAEASFWTAEEVD 51
>pdb|1WUU|A Chain A, Crystal Structure Of Human Galactokinase Complexed With
Mgamppnp And Galactose
pdb|1WUU|B Chain B, Crystal Structure Of Human Galactokinase Complexed With
Mgamppnp And Galactose
pdb|1WUU|C Chain C, Crystal Structure Of Human Galactokinase Complexed With
Mgamppnp And Galactose
pdb|1WUU|D Chain D, Crystal Structure Of Human Galactokinase Complexed With
Mgamppnp And Galactose
Length = 399
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 57 GDASLSKTILENLKAVRDLDEKEGIAITRSMEAAIRDAAENTQNDDALRQ 106
G SL + LE L+A RDL KEG R + IR A Q ALR+
Sbjct: 258 GKESLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTA---QAAAALRR 304
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.311 0.128 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,380,577
Number of Sequences: 62578
Number of extensions: 452459
Number of successful extensions: 894
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 858
Number of HSP's gapped (non-prelim): 32
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)