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= 016203
(393 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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVMR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR + R
Sbjct: 13 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 63
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVMR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR + R
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 60
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVMR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR + 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 = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVMR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR + 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 = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 2/53 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVMR 392
KK+KW++EE + ++ GV+++G+GNW I K+ P F RT V +KD+WR + R
Sbjct: 1 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYP--FVNRTAVMIKDRWRTMKR 51
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNV 390
R RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR +
Sbjct: 7 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTM 58
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNV 390
R RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR +
Sbjct: 6 RARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTM 57
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr,
18 Structures
Length = 53
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 339 RKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNV 390
RK++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR +
Sbjct: 1 RKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTM 50
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1
Length = 121
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 333 TKLARRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
++L++RR ++ +S+ E +AL + VE G G W+ + D RT VDLKDKW+ ++
Sbjct: 9 SELSQRRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLV 67
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNV 390
K++ W EE+ LR GV ++G+GNW IL F+ RT V LKD+WR +
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYK--FNNRTSVMLKDRWRTM 49
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 32/54 (59%)
Query: 338 RRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 337 RRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%)
Query: 311 GNRFHLPSPKRKAVSPLKNHDVTKLARRRKKKKWSLEEEDALRKGVEQFGKGNWKLILKS 370
G+ F P+ A PL +RR ++ +++ E + L + VE G G W+ +
Sbjct: 1 GSPFADPNSLALANVPLSRSKRPDFGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFR 60
Query: 371 NPGAFDERTEVDLKDKWRNVM 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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 345 SLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
S+ E +AL + VE G G W+ + D RT VDLKDKW+ ++
Sbjct: 4 SVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLV 50
>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 = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ V+
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKVL 49
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ V+
Sbjct: 3 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKVL 49
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 35.4 bits (80), Expect = 0.053, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
K KW+ EE++ LR V QFG+ +WK + F RT+ + +W V+
Sbjct: 8 KVKWTHEEDEQLRALVRQFGQQDWKFLASH----FPNRTDQQCQYRWLRVL 54
>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 = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 341 KKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
K +W+ EE++ L+K VEQ G +WK+I P RT+V + +W+ V+
Sbjct: 6 KTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN----RTDVQCQHRWQKVL 52
>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 = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 340 KKKKWSLEEEDALRKGVEQFGKGNWKLILKSNPGAFDERTEVDLKDKWRNVM 391
KK+K++ EE++ L++ V Q G +WK+I F R +D+W+N +
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHG-SDWKMI----AATFPNRNARQCRDRWKNYL 56
>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 = 1.1, 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 = 2.2, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 319 PKRKAVSPLKNHDVTKLARRRKKKKWSLEEED 350
P+R + P++ HD+ ++ ++ + W+ EE D
Sbjct: 13 PRRFVIFPIEYHDIWQMYKKAEASFWTAEEVD 44
>pdb|2UW2|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase
Subunit R2
Length = 332
Score = 30.0 bits (66), Expect = 2.4, 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 = 28.5 bits (62), Expect = 6.2, 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 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,270,148
Number of Sequences: 62578
Number of extensions: 446907
Number of successful extensions: 883
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: 847
Number of HSP's gapped (non-prelim): 32
length of query: 393
length of database: 14,973,337
effective HSP length: 101
effective length of query: 292
effective length of database: 8,652,959
effective search space: 2526664028
effective search space used: 2526664028
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)