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= 004663
(738 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 444 FAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNP 502
F ++ +F ++R P K+ L+L L+ V + GG EV + KLWR++ + N
Sbjct: 38 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97
Query: 503 PKTCTTVSWTFRIFYEKALLEY--EKHRMSN 531
P + T+ ++T R Y K L Y EK +SN
Sbjct: 98 PTSITSAAFTLRTQYMKYLYPYECEKRGLSN 128
>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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 2/99 (2%)
Query: 439 DEQVAFAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVG 497
DEQ AF + + +ER + P + +NL +++A KLGGY+ +T+ + W+ +
Sbjct: 3 DEQ-AFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIY 61
Query: 498 ESFNPPKTCTTVSWTFRIFYEKALLEYEKHRMSNGELPL 536
+ T+ + R YE+ +L YE+ + PL
Sbjct: 62 DELGGNPGSTSAATCTRRHYERLILPYERFIKGEEDKPL 100
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 444 FAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNP 502
F ++ +F ++R P K L+L +L+ VI GG +V + KLW+++ + +
Sbjct: 26 FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 85
Query: 503 PKTCTTVSWTFRIFYEKALLEYE 525
P + T+ ++T R Y K L YE
Sbjct: 86 PSSITSAAFTLRTQYMKYLYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 444 FAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNP 502
F ++ +F ++R P K L+L +L+ VI GG +V + KLW+++ + +
Sbjct: 28 FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 87
Query: 503 PKTCTTVSWTFRIFYEKALLEYE 525
P + T+ + T R Y K L YE
Sbjct: 88 PSSITSAALTLRTQYMKYLYPYE 110
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 444 FAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNP 502
F K + ++RN+ + P+ +NL L+ V K GG D+VT + W V +
Sbjct: 22 FMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQI 81
Query: 503 PKTCTTVSWTFRIFYEKALLEYEKHRMS 530
S FRI LL YE+H +S
Sbjct: 82 SDYQQLESIYFRI-----LLPYERHMIS 104
>pdb|2LI6|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Yeast
Protein
Length = 116
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 444 FAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNP 502
F K + ++RN+ + P+ +NL L+ V K GG D+VT + W V +
Sbjct: 23 FMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQI 82
Query: 503 PKTCTTVSWTFRIFYEKALLEYEKHRMS 530
S FRI LL YE+H +S
Sbjct: 83 SDYQQLESIYFRI-----LLPYERHMIS 105
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 35.8 bits (81), Expect = 0.080, Method: Composition-based stats.
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 435 SGTEDEQVAFAKEVENFYRERNLEFKHPKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWR 494
SGT ++ + ++ F+ + K P ++ L+L L + VI+ GGY+ + + W
Sbjct: 6 SGTR-VKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWA 64
Query: 495 QVGESFNPPKTCTTVSWTFRIFYEKALLEYE 525
+V + + P + R YE+ + YE
Sbjct: 65 RVAQRLHYPPG-KNIGSLLRSHYERIIYPYE 94
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN
Jarid1c Protein
Length = 117
Score = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 441 QVAFAKEVENFYRERNLEFKHPKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESF 500
++ + ++ F+ + K P + L+L L + V++ GGY+ + + W +V +
Sbjct: 12 KLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRL 71
Query: 501 NPPKTCTTVSWTFRIFYEKALLEYEKHR 528
N P + R YE+ + YE ++
Sbjct: 72 NYPPG-KNIGSLLRSHYERIVYPYEMYQ 98
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 441 QVAFAKEVENFYRERNLEFKHPKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESF 500
++ F ++ F+ + K P ++ L+L L R V + GG ++ T + W +V
Sbjct: 16 KLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRM 75
Query: 501 NPPKTCTTVSWTFRIFYEKALLEYE 525
P + +V T + YE+ L +E
Sbjct: 76 QYPSS-KSVGATLKAHYERILHPFE 99
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 33.1 bits (74), Expect = 0.60, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 441 QVAFAKEVENFYRERNLEFKHPKFYKEDLNLLKLWRAVIKLGGYDEVTSCKLWRQVGE-- 498
++ F ++ F+ + K P ++ L+L L + V GG++ VT K W +VG
Sbjct: 8 RLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRL 67
Query: 499 SFNPPKTCTTVSWTFRIFYEKALLEYE 525
+ P K ++ + YE+ L YE
Sbjct: 68 GYLPGKGTGSL---LKSHYERILYPYE 91
>pdb|2YII|A Chain A, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|B Chain B, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|C Chain C, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|D Chain D, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|4BAB|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
Length = 705
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 28/120 (23%)
Query: 286 KNDGIESHVLTLNQLEFAERSSD--------IKAKNEEKGEKSDDHISKNDEKREKLDDA 337
K DGIE+ L EF +R SD ++ E+KG K+ D+ +DA
Sbjct: 586 KKDGIETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEKKGHKTADN-----------NDA 634
Query: 338 LVFEVSVNKLCDSKNDGIHMHAKNQLESAAADERSLETKDEDDKRGDKLNDGVADMELTL 397
LV ++ SK + + +L++ R +T ED + K+ D +AD +T+
Sbjct: 635 LV------RIQGSKFLPFYRFVREELDTGVMSARREQTPQEDVQ---KVFDAIADGRITV 685
>pdb|4BAA|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
Length = 705
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 28/120 (23%)
Query: 286 KNDGIESHVLTLNQLEFAERSSD--------IKAKNEEKGEKSDDHISKNDEKREKLDDA 337
K DGIE+ L EF +R SD ++ E+KG K+ D+ +DA
Sbjct: 586 KKDGIETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEKKGHKTADN-----------NDA 634
Query: 338 LVFEVSVNKLCDSKNDGIHMHAKNQLESAAADERSLETKDEDDKRGDKLNDGVADMELTL 397
LV ++ SK + + +L++ R +T ED + K+ D +AD +T+
Sbjct: 635 LV------RIQGSKFLPFYRFVREELDTGVMSARREQTPQEDVQ---KVFDAIADGRITV 685
>pdb|3NZ4|A Chain A, Crystal Structure Of A Taxus Phenylalanine Aminomutase
pdb|3NZ4|B Chain B, Crystal Structure Of A Taxus Phenylalanine Aminomutase
Length = 696
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 54/120 (45%), Gaps = 28/120 (23%)
Query: 286 KNDGIESHVLTLNQLEFAERSSD--------IKAKNEEKGEKSDDHISKNDEKREKLDDA 337
K DGIE+ L EF +R SD ++ E+KG K+ D+ +DA
Sbjct: 566 KKDGIETDTLVDRLAEFEKRLSDRLENEMTAVRVLYEKKGHKTADN-----------NDA 614
Query: 338 LVFEVSVNKLCDSKNDGIHMHAKNQLESAAADERSLETKDEDDKRGDKLNDGVADMELTL 397
LV ++ S+ + +++L++ R +T ED + K+ D +AD +T+
Sbjct: 615 LV------RIQGSRFLPFYRFVRDELDTGVMSARREQTPQEDVQ---KVFDAIADGRITV 665
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 468 DLNLLKLWRAVIKLGGYDEVTSCKLWRQVGESFNPPKTCTTVSWTFRIFYEKALLEY--- 524
+L+L +R + ++GG +VT K W ++ + PKT + Y + LL Y
Sbjct: 41 ELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQYLLSYDSL 100
Query: 525 --EKHRMSNGEL 534
E+HR E+
Sbjct: 101 SPEEHRRLEKEV 112
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 434 ESGTEDEQVAFAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKL 492
E G E E+ + F E+ + + P ++ L+L +L+ +V ++GG +V K
Sbjct: 14 ELGGEPERKMWVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKK 73
Query: 493 WRQVGESFN 501
WR++ + N
Sbjct: 74 WRELATNLN 82
>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 = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 434 ESGTEDEQVAFAKEVENFYRERNLEFKH-PKFYKEDLNLLKLWRAVIKLGGYDEVTSCKL 492
E G E E+ + F ER P K+ L+L +L+ V ++GG +V K
Sbjct: 15 ELGNEPERKLWVDRYLTFXEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKK 74
Query: 493 WRQVGESFN 501
WR++ + N
Sbjct: 75 WRELATNLN 83
>pdb|2XAF|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 482
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 10/111 (9%)
Query: 122 NAPVDVIAKENSSTKSDGSLVHPLNQHEHVAAEERLTKIEAENGEKEEK---LDDDSVVG 178
N P+D+ +N +K + V P V E+ T+ + K K L + V
Sbjct: 267 NNPIDIEVDQNKESKKE---VPPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDVEA 323
Query: 179 VSANELSGTRNDGSHVHPMNPECAAVNESSSEIKAENNKMGEKLDGAAVFY 229
VSAN + T + + ++ E +V IK N+ + EKLDG Y
Sbjct: 324 VSANATAAT----TVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPY 370
>pdb|2JET|B Chain B, Crystal Structure Of A Trypsin-Like Mutant (S189d, A226g)
Chymotrypsin
Length = 128
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 37/101 (36%), Gaps = 15/101 (14%)
Query: 422 SFLFEPPVAEGDESGTEDEQVAFAKEVENFYRERNLE-------FKHPKF----YKEDLN 470
S + E V G + V A E + E N++ FK+PKF + D+
Sbjct: 27 SLISEDWVVTAAHCGVKTSDVVVAGEFDQGSDEENIQVLKIAQVFKNPKFNMFTVRNDIT 86
Query: 471 LLKLWRAVIKLGGYDEVTSCKLWRQVGESFNPPKTCTTVSW 511
LLKL + E S V + F P C T W
Sbjct: 87 LLKL----ATPAQFSETVSAVCLPNVDDDFPPGTVCATTGW 123
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
0.308 0.128 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,445,691
Number of Sequences: 62578
Number of extensions: 886597
Number of successful extensions: 1512
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1497
Number of HSP's gapped (non-prelim): 29
length of query: 738
length of database: 14,973,337
effective HSP length: 106
effective length of query: 632
effective length of database: 8,340,069
effective search space: 5270923608
effective search space used: 5270923608
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (25.8 bits)