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= 005228
(707 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
KK WT +E E +K GVQK+ + W I + F RTA+ +KD+WR M
Sbjct: 1 KKQKWTVEESEWVKAGVQKYGEGN-----WAAI---SKNYPFVNRTAVMIKDRWRTM 49
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
KK WT +E E +K GVQK+ + W I + F RTA+ +KD+WR M
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGN-----WAAI---SKNYPFVNRTAVMIKDRWRTM 58
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
KK WT +E E +K GVQK+ + W I + F RTA+ +KD+WR M
Sbjct: 10 KKQKWTVEESEWVKAGVQKYGEGN-----WAAI---SKNYPFVNRTAVMIKDRWRTM 58
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr,
18 Structures
Length = 53
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 8/60 (13%)
Query: 642 RKKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNMCK 701
RK+ W +E++ L+ GV+K+ + W KIL F+ RT++ LKD+WR M K
Sbjct: 1 RKRQAWLWEEDKNLRSGVRKYGEGN-----WSKILLHYK---FNNRTSVMLKDRWRTMKK 52
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
KK WT +E E +K GVQK+ + W I + F RTA+ +KD+WR M
Sbjct: 9 KKQKWTVEESEWVKAGVQKYGEGN-----WAAI---SKNYPFVNRTAVMIKDRWRTM 57
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
KK WT +E E +K GVQK+ + W I + F RTA+ +KD+WR M
Sbjct: 13 KKQKWTVEESEWVKAGVQKYGEGN-----WAAI---SKNYPFVNRTAVMIKDRWRTM 61
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 636 PIPQLRRKKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDK 695
P RK+ W +E++ L+ GV+K+ + W KIL F+ RT++ LKD+
Sbjct: 3 PEKHRARKRQAWLWEEDKNLRSGVRKYGEGN-----WSKILLHYK---FNNRTSVMLKDR 54
Query: 696 WRNMCK 701
WR M K
Sbjct: 55 WRTMKK 60
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1
Length = 69
Score = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 636 PIPQLRRKKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDK 695
P RK+ W +E++ L+ GV+K+ + W KIL F+ RT++ LKD+
Sbjct: 2 PEKHRARKRQAWLWEEDKNLRSGVRKYGEGN-----WSKILLHYK---FNNRTSVMLKDR 53
Query: 696 WRNMCK 701
WR M K
Sbjct: 54 WRTMKK 59
>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 = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNMCK 701
K+ W +E++ L+ GV+K+ + W KIL F+ RT++ LKD+WR M K
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGN-----WSKILLHYK---FNNRTSVMLKDRWRTMKK 51
>pdb|2PUY|A Chain A, Crystal Structure Of The Bhc80 Phd Finger
pdb|2PUY|B Chain B, Crystal Structure Of The Bhc80 Phd Finger
Length = 60
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 333 QNLCVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFC 379
++ C C K GQLL C TC H +CL P+K KG + CP C
Sbjct: 5 EDFCSVCRKSGQLLMCD--TCSRVYHLDCLDPPLKTIPKGMWICPRC 49
>pdb|2YQL|A Chain A, Solution Structure Of The Phd Domain In Phd Finger Protein
21a
Length = 56
Score = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 333 QNLCVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFC 379
++ C C K GQLL C TC H +CL P+K KG + CP C
Sbjct: 9 EDFCSVCRKSGQLLMCD--TCSRVYHLDCLDPPLKTIPKGMWICPRC 53
>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 = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 11/51 (21%)
Query: 646 PWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKW 696
PWTA+E+ +L + +Q++ W I +F F GRT I +K++W
Sbjct: 64 PWTAEEDALLVQKIQEYGR------QWAIIAKF-----FPGRTDIHIKNRW 103
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 643 KKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRN 698
KK +T +E+E+LK+ V + S WK I + F R A +D+W+N
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHGS------DWKMI-----AATFPNRNARQCRDRWKN 54
>pdb|2L5U|A Chain A, Structure Of The First Phd Finger (Phd1) From Chd4 (Mi2b)
Length = 61
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 333 QNLCVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFC 379
Q+ C C + G+++ C TCP A H CL ++ +G + CP C
Sbjct: 11 QDYCEVCQQGGEIILCD--TCPRAYHMVCLDPDMEKAPEGKWSCPHC 55
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1
Length = 122
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 641 RRKKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWRNM 699
RR + P+T E E+L + V+ + W+ + +F + RT +DLKDKW+ +
Sbjct: 28 RRIRRPFTVAEVELLVEAVEHLGTGR-----WRDV-KFRAFENVHHRTYVDLKDKWKTL 80
>pdb|1XWH|A Chain A, Nmr Structure Of The First Phd Finger Of Autoimmune
Regulator Protein (Aire1): Insights Into Apeced
pdb|2KE1|A Chain A, Molecular Basis Of Non-Modified Histone H3 Tail
Recognition By The First Phd Finger Of Autoimmune
Regulator
Length = 66
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 336 CVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFC 379
C C G+L+ C CP A H CL P++ G + C C
Sbjct: 11 CAVCRDGGELICCDG--CPRAFHLACLSPPLREIPSGTWRCSSC 52
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric
Repeat-Binding Protein Dna Binding Domain
Length = 105
Score = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 638 PQLRRKKVPWTAKEEEILKKGVQKFASVDDRIIPWKKILEFGSSVFFSGRTAIDLKDKWR 697
PQ RR + P++ E E L + V+K + R + K+ F + RT +DLKDKW+
Sbjct: 8 PQ-RRIRRPFSVAEVEALVQAVEKLGTGRWRDV---KLCAFEDA---DHRTYVDLKDKWK 60
Query: 698 NMC---KGSPRSK 707
+ K SP+ +
Sbjct: 61 TLVHTAKISPQQR 73
>pdb|1MM2|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b
pdb|2L75|A Chain A, Solution Structure Of Chd4-Phd2 In Complex With H3k9me3
Length = 61
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 335 LCVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFCA 380
C C G+LL C TCP + H +CL P+ G + CP C
Sbjct: 11 FCRVCKDGGELLCCD--TCPSSYHIHCLNPPLPEIPNGEWLCPRCT 54
>pdb|3K1L|B Chain B, Crystal Structure Of Fancl
pdb|3K1L|A Chain A, Crystal Structure Of Fancl
Length = 381
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 334 NLCVKCNKDG---QLLSCSSSTCPLAVHENCL--GFPVKFDEKGNF-----HCPFCAYTL 383
N+C DG L+SC ++ C L H CL F D K CPFC L
Sbjct: 312 NICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKL 371
Query: 384 SIS 386
S S
Sbjct: 372 STS 374
>pdb|2HGV|A Chain A, N-Terminal Gaf Domain Of Transcriptional Pleiotropic
Repressor Cody
Length = 164
Score = 29.3 bits (64), Expect = 8.2, Method: Composition-based stats.
Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 24/106 (22%)
Query: 173 ETVEPLSGRDVAVAGREG--------SHFSNQSQDAGLEESQFPDDGCDNCDDLRRLGQN 224
ET+ + ++ V R G N LE+ QFP++ N ++ N
Sbjct: 38 ETLRDVIDSNIFVVSRRGKLLGYSINQQIENDRXKKXLEDRQFPEEYTKNLFNVPETSSN 97
Query: 225 GDVNDDQIQHNQAEDGHNAARLPRAEPVQNATVDEANITERVPSVG 270
D+N + A PV+N + +A +T VP +G
Sbjct: 98 LDINSEYT----------------AFPVENRDLFQAGLTTIVPIIG 127
>pdb|2KFT|A Chain A, Nmr Solution Structure Of The First Phd Finger Domain Of
Human Autoimmune Regulator (Aire) In Complex With
Histone H3(1-20cys) Peptide
Length = 56
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 336 CVKCNKDGQLLSCSSSTCPLAVHENCLGFPVKFDEKGNFHCPFC 379
C C G+L+ C CP A H CL P++ G + C C
Sbjct: 8 CAVCRDGGELICCDG--CPRAFHLACLSPPLREIPSGTWRCSSC 49
>pdb|2B18|A Chain A, N-Terminal Gaf Domain Of Transcriptional Pleiotropic
Repressor Cody
Length = 164
Score = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 24/106 (22%)
Query: 173 ETVEPLSGRDVAVAGREG--------SHFSNQSQDAGLEESQFPDDGCDNCDDLRRLGQN 224
ET+ + ++ V R G N LE+ QFP++ N ++ N
Sbjct: 38 ETLRDVIDSNIFVVSRRGKLLGYSINQQIENDRMKKMLEDRQFPEEYTKNLFNVPETSSN 97
Query: 225 GDVNDDQIQHNQAEDGHNAARLPRAEPVQNATVDEANITERVPSVG 270
D+N + A PV+N + +A +T VP +G
Sbjct: 98 LDINSEYT----------------AFPVENRDLFQAGLTTIVPIIG 127
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
0.314 0.130 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,386,203
Number of Sequences: 62578
Number of extensions: 823785
Number of successful extensions: 1501
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1488
Number of HSP's gapped (non-prelim): 32
length of query: 707
length of database: 14,973,337
effective HSP length: 106
effective length of query: 601
effective length of database: 8,340,069
effective search space: 5012381469
effective search space used: 5012381469
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)