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= 022607
(294 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 1/88 (1%)
Query: 31 SKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVG 90
S+ + F D L +F + G+ IPV+ K LDL+ L ++GG+E V EKKW +VG
Sbjct: 5 SRVRLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVG 64
Query: 91 AVFKFSPTTTSASFVLRKHYLTLLYHYE 118
+ + P + S +L+ HY +LY YE
Sbjct: 65 SRLGYLPGKGTGS-LLKSHYERILYPYE 91
>pdb|2KK0|A Chain A, Solution Structure Of Dead Ringer-Like Protein 1 (At-Rich
Interactive Domain-Containing Protein 3a) From Homo
Sapiens, Northeast Structural Genomics Consortium (Nesg)
Target Hr4394c
Length = 145
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 37 FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
F D L F GT IP++ + LDL +LYV T +GG +V+ +K WRE+
Sbjct: 38 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97
Query: 96 SPTTTSASFVLRKHYLTLLYHYE 118
+ TSA+F LR Y+ LY YE
Sbjct: 98 PTSITSAAFTLRTQYMKYLYPYE 120
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 37 FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
F D L F GT +P++ LDL+ LY RGG V+ +K W+E+
Sbjct: 26 FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 85
Query: 96 SPTTTSASFVLRKHYLTLLYHYE 118
+ TSA+F LR Y+ LY YE
Sbjct: 86 PSSITSAAFTLRTQYMKYLYPYE 108
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN
Jarid1c Protein
Length = 117
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 1/95 (1%)
Query: 24 LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
++ E ++ + + D + +F I G+ IP + + LDL+ L GGYE + +
Sbjct: 2 MNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKD 61
Query: 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
++W V + P S LR HY ++Y YE
Sbjct: 62 RRWARVAQRLNYPPGKNIGSL-LRSHYERIVYPYE 95
>pdb|2LM1|A Chain A, Solution Nmr Structure Of Lysine-Specific Demethylase Lid
From Drosophila Melanogaster, Northeast Structural
Genomics Consortium Target Fr824d
Length = 107
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 24 LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
L+ E ++ + F D + +F + G+ IP++ K LDL+ L+ GG E+ +
Sbjct: 6 LNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKD 65
Query: 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
+KW +V ++ P++ S L+ HY +L+ +E
Sbjct: 66 RKWAKVANRMQY-PSSKSVGATLKAHYERILHPFE 99
>pdb|1IG6|A Chain A, Human Mrf-2 Domain, Nmr, 11 Structures
pdb|2OEH|A Chain A, Determination Of The Three-Dimensional Structure Of The
Mrf2-Dna Complex Using Paramagnetic Spin Labeling
Length = 107
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 39/66 (59%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP +G K+++L ++ A GGYE + A ++W+ + +P +TSA+ R+HY L
Sbjct: 25 IPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERL 84
Query: 114 LYHYEQ 119
+ YE+
Sbjct: 85 ILPYER 90
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 45/93 (48%), Gaps = 3/93 (3%)
Query: 29 DVSKDPIV--FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKK 85
+++ DP F D L F GT +P++ LDL+ LY RGG V+ +K
Sbjct: 18 EINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKL 77
Query: 86 WREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
W+E+ + TSA+ LR Y+ LY YE
Sbjct: 78 WQEIIKGLHLPSSITSAALTLRTQYMKYLYPYE 110
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 25 SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
SS ++ + + D + +F I G+ IP + K LDL+ L GGYE + ++
Sbjct: 2 SSGSSGTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDR 61
Query: 85 KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
+W V + P S +LR HY ++Y YE
Sbjct: 62 RWARVAQRLHYPPGKNIGS-LLRSHYERIIYPYE 94
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P +G K LDL+ LYV GG +V KKWRE+ T++SA+ L+K Y+
Sbjct: 42 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQC 100
Query: 114 LYHYE 118
LY +E
Sbjct: 101 LYAFE 105
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 1/93 (1%)
Query: 25 SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
SS E ++ + F D + ++ + G+ IP + K LDL L GG+ V ++
Sbjct: 5 SSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDR 64
Query: 85 KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHY 117
KW ++ F+P S + R HY +L Y
Sbjct: 65 KWTKIATKMGFAPGKAVGSHI-RGHYERILNPY 96
>pdb|2CXY|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
pdb|2EH9|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
Length = 125
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P +G K LDL LYV GG +V KKWRE+ T++SA+ L+K Y+
Sbjct: 43 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQY 101
Query: 114 LYHYE 118
L+ +E
Sbjct: 102 LFAFE 106
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P+IGG ELDL + GG ++V KKW ++ + + T L++ Y
Sbjct: 34 LPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQY 93
Query: 114 LYHYEQV 120
L Y+ +
Sbjct: 94 LLSYDSL 100
>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like
Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A)
Length = 97
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFT---KMIGESWTNLSPEERK 293
DP+ PK S Y FF EK ++ + P ++ KMIG +W LS EE+K
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKK 72
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERK 293
DP+ PK S Y FF E ++S P+ + K +GE W L+PEE++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQ 68
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERK 293
DP+ PK S Y FF E ++S P+ + K +GE W L+PEE++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQ 68
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 245 SYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERK 293
S PK +GY F E+ ++++ +P+ E TKM+G W+ L P E++
Sbjct: 6 SGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQ 55
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
Mobility Group Box Protein Tox From Mouse
Length = 102
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKV 294
DP+ P+ S Y FF + +K PN E +K++ W L E+++V
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQV 66
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKV 294
PK RS YN + AE+ + K P E K + E+W NLS E+++
Sbjct: 147 PKRPRSAYNVYVAERFQEAKGDSPQ---EKLKTVKENWKNLSDSEKEL 191
>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
Length = 214
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKV 294
PK RS YN + AE+ + K P E K + E+W NLS E+++
Sbjct: 115 PKRPRSAYNVYVAERFQEAKGDSPQ---EKLKTVKENWKNLSDSEKEL 159
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKV 294
PK RS YN + AE+ + K P +E K + E+W NLS E+++
Sbjct: 3 PKRPRSAYNVYVAERFQEAKGDSP---QEKLKTVKENWKNLSDSEKEL 47
>pdb|1KKX|A Chain A, Solution Structure Of The Dna-Binding Domain Of Adr6
pdb|1KN5|A Chain A, Solution Structure Of Arid Domain Of Adr6 From
Saccharomyces Cerevisiae
Length = 123
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP IG ++++L LY+ GG ++V ++W V + S S Y +
Sbjct: 40 IPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESI-----YFRI 94
Query: 114 LYHYEQVHFFKMQG 127
L YE+ H +G
Sbjct: 95 LLPYER-HMISQEG 107
>pdb|2LI6|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Yeast
Protein
Length = 116
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP IG ++++L LY+ GG ++V ++W V + S S Y +
Sbjct: 41 IPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESI-----YFRI 95
Query: 114 LYHYEQVHFFKMQG 127
L YE+ H +G
Sbjct: 96 LLPYER-HMISQEG 108
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEER 292
DP+ P+ S Y FF + K +P+ EF+K E W +S +E+
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEK 57
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEER 292
DP P+ S Y FF + K +P+ EF+K E W +S +E+
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK 56
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 28.1 bits (61), Expect = 6.0, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERK 293
DP+ PK S + F +E K+K +P + K +GE W N + ++++
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQ 54
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 83
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEER 292
DP P+ S Y FF + K +P+ EF+K E W +S +E+
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK 56
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
0.319 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,162,980
Number of Sequences: 62578
Number of extensions: 365919
Number of successful extensions: 583
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 554
Number of HSP's gapped (non-prelim): 34
length of query: 294
length of database: 14,973,337
effective HSP length: 98
effective length of query: 196
effective length of database: 8,840,693
effective search space: 1732775828
effective search space used: 1732775828
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)