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= 041583
(586 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEE|A Chain A, Solution Structure Of Phd Domain In Phd Finger Family
Protein
Length = 72
Score = 80.1 bits (196), Expect = 3e-15, Method: Composition-based stats.
Identities = 33/55 (60%), Positives = 38/55 (69%)
Query: 527 EGGADDWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVPSVFKCRAC 581
E G D+W VDC CG KDDDGERM+ACD C VW HTRC I + + +PS F C C
Sbjct: 9 ERGVDNWKVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRC 63
>pdb|2LV9|A Chain A, Solution Nmr Structure Of The Phd Domain Of Human Mll5,
Northeast Structural Genomics Consortium Target Hr6512a
Length = 98
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 524 LRFEGGAD-DWTVD---CVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVPSVFKCR 579
L F+G D + D C+CG DDG M+ CD C VWQH C I D + +P + C
Sbjct: 14 LYFQGSEDGSYGTDVTRCICGFTHDDGY-MICCDKCSVWQHIDCMGI-DRQHIPDTYLCE 71
Query: 580 AC 581
C
Sbjct: 72 RC 73
>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e
Mutant From Human Bptf In The H3(1-9)k4me2 Bound State
Length = 174
Score = 36.6 bits (83), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 532 DWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEV 571
D + C+C +D+ + + CD CQ W H RC I +E
Sbjct: 6 DTKLYCICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEA 45
>pdb|2F6J|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6J|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6J|C Chain C, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State
pdb|2F6N|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The Free Form
pdb|2F6N|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The Free Form
pdb|2FSA|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
pdb|2FSA|B Chain B, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
pdb|2FSA|C Chain C, Crystal Structure Of Phd Finger-Linker-Bromodomain
Fragment Of Human Bptf In The H3(1-15)k4me2 Bound State
Length = 174
Score = 36.2 bits (82), Expect = 0.047, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 532 DWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNE 570
D + C+C D+ + + CD CQ W H RC I +E
Sbjct: 6 DTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSE 44
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 530 ADDWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEV 571
D + C+C D+ + + CD CQ W H RC I +E
Sbjct: 4 GSDTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEA 45
>pdb|1WEW|A Chain A, Solution Structure Of Phd Domain In Dna-Binding Family
Protein Aam98074
Length = 78
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 535 VDCVCGAKDDDGERMVACD--ICQVWQHTRCNSIAD-----NEVVPSVFKCRAC 581
V CVCG + + M+ C+ C VWQH C + D N +P F C C
Sbjct: 17 VRCVCG-NSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEIC 69
>pdb|3KV5|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV5|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV6|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
pdb|3KV6|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
Length = 488
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 535 VDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVP-SVFKCRACTA 583
V CVC D M+ CDIC+ W H C + ++ V ++ C C
Sbjct: 38 VYCVCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAV 87
>pdb|2FUI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Human
Bptf In Free State
pdb|2FUU|A Chain A, Nmr Solution Structure Of The Phd Domain From The Human
Bptf In Complex With H3(1-15)k4me3 Peptide
Length = 62
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 530 ADDWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEV 571
D + C+C D+ + + CD CQ W H RC I +E
Sbjct: 4 GSDTKLYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEA 45
>pdb|3O70|A Chain A, Phd-Type Zinc Finger Of Human Phd Finger Protein 13
Length = 68
Score = 32.3 bits (72), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 524 LRFEGGADDWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVPSVFKCRAC 581
L F+G V C C K G M+ C+ C W H C I + VP VF C+ C
Sbjct: 14 LYFQG-----LVTCFC-MKPFAGRPMIECNECHTWIHLSCAKIRKSN-VPEVFVCQKC 64
>pdb|1WEP|A Chain A, Solution Structure Of Phd Domain In Phf8
Length = 79
Score = 32.0 bits (71), Expect = 0.88, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 535 VDCVCGAKDDDGERMVACDICQVWQHTRCNSI-ADNEVVPSVFKCRACTA 583
V C+C + M+ C +CQ W H C I +N V ++ C C A
Sbjct: 13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEA 62
>pdb|2PZJ|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+
pdb|2Q1S|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nadh
pdb|2Q1T|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
pdb|2Q1U|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
pdb|2Q1U|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
Length = 377
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 326 LLDFMIKHIHKIILDNRIVHRKIN----PATKLAEFSLEDDANGEVIQTRTEPEYHTSTL 381
LL+ + +H ++DN + KIN PA + +E S+ DDA +Q + +H +T
Sbjct: 52 LLELGVNQVH--VVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATY 109
Query: 382 MPGQDVYADVLTLYKNVLL 400
Q D L ++N L
Sbjct: 110 HGNQSSIHDPLADHENNTL 128
>pdb|2K16|A Chain A, Solution Structure Of The Free Taf3 Phd Domain
pdb|2K17|A Chain A, Solution Structure Of The Taf3 Phd Domain In Complex With
A H3k4me3 Peptide
Length = 75
Score = 31.2 bits (69), Expect = 1.5, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 524 LRFEGGADDWTVDCVCGAKDDDGERMVACDICQVWQHTRCNSI 566
+R E G W C K DDG M+ CD C W H C I
Sbjct: 10 IRDEWGNQIWI--CPGCNKPDDGSPMIGCDDCDDWYHWPCVGI 50
>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3
Length = 447
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 535 VDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVP-SVFKCRAC 581
V C+C D M+ CD+CQ W H C + + + ++ C C
Sbjct: 6 VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
>pdb|3O7A|A Chain A, Crystal Structure Of Phf13 In Complex With H3k4me3
Length = 52
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 535 VDCVCGAKDDDGERMVACDICQVWQHTRCNSIADNEVVPSVFKCRAC 581
V C C K G M+ C+ C W H C I + VP VF C+ C
Sbjct: 5 VTCFC-MKPFAGRPMIECNECHTWIHLSCAKIRKSN-VPEVFVCQKC 49
>pdb|2RSD|A Chain A, Solution Structure Of The Plant Homeodomain (Phd) Of The
E3 Sumo Ligase Siz1 From Rice
Length = 68
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 535 VDCVCGAKDDDGERMVACD--ICQVWQHTRCNSIAD----NEVVPSVFKCRACTAAVA 586
V C+C + + + M+ C+ CQVWQH C I D + VP VF C C + A
Sbjct: 11 VRCICSSTMVN-DSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRLSRA 67
>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding
Protein-like Np_197993
Length = 64
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 539 CGAKDDDGERMVACDICQVWQHTRCNSI--ADNEVVPSVFKCRACT 582
CG E + CD+C++W H +C I A E + +KC +C+
Sbjct: 12 CGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQ-YKCPSCS 56
>pdb|3D4R|A Chain A, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
pdb|3D4R|B Chain B, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
pdb|3D4R|C Chain C, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
pdb|3D4R|D Chain D, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
pdb|3D4R|E Chain E, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
pdb|3D4R|F Chain F, Crystal Structure Of A Duf2118 Family Protein (Mmp0046)
From Methanococcus Maripaludis At 2.20 A Resolution
Length = 169
Score = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 7/58 (12%)
Query: 358 SLEDDANGEVIQTRTEPEYHTSTLMPGQDVYADVL------TLYKNVLLGYPESHTVS 409
++E D N + + E EY + + Q +Y D+ TL K+VL+ YP+ HT++
Sbjct: 38 AIEKDGNAIIFLEKDE-EYSGNGKLLYQVIYDDLAKYXSLDTLKKDVLIQYPDKHTLT 94
>pdb|2GCU|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|B Chain B, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|C Chain C, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
pdb|2GCU|D Chain D, X-Ray Structure Of Gene Product From Arabidopsis Thaliana
At1g53580
Length = 245
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 443 SPSYNELATQLTRPLPPAELIVAPKDVTVD-ELKLIVECSLRDTYCM 488
S ++ L ++ P PA L++ P D TVD +LKLI E L+ Y M
Sbjct: 13 SSTFTYLLADVSHPDKPA-LLIDPVDKTVDRDLKLIDELGLKLIYAM 58
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
0.323 0.138 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,272,714
Number of Sequences: 62578
Number of extensions: 782746
Number of successful extensions: 1769
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1754
Number of HSP's gapped (non-prelim): 23
length of query: 586
length of database: 14,973,337
effective HSP length: 104
effective length of query: 482
effective length of database: 8,465,225
effective search space: 4080238450
effective search space used: 4080238450
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)