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= 025727
(249 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ATI|A Chain A, Mitf:m-Box Complex
pdb|4ATI|B Chain B, Mitf:m-Box Complex
pdb|4ATK|A Chain A, Mitf:e-Box Complex
pdb|4ATK|B Chain B, Mitf:e-Box Complex
Length = 118
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 60 ERNRRKKLNERLFALRSVVPNISKMD----KASIIKDAIDYIQELHEQEKRIRD 109
ER RR +N+R+ L +++P + D K +I+K ++DYI++L +++R +D
Sbjct: 35 ERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD 88
>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
Length = 65
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 60 ERNRRKKLNERLFALRSVVPNIS------KMDKASIIKDAIDYIQELHEQEKR 106
ER RR K+N + L ++P+ S K I+ A DYIQEL + R
Sbjct: 13 ERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 59 SERNRRKKLNERLFALRSVVP-NISKMDKASIIKDAIDYIQ 98
SE+ RR + N + L S++P N KMDK+++++ +ID+++
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59
>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
Length = 82
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 60 ERNRRKKLNERLFALRS-VVPNISKMDKASIIKDAIDYIQELHEQEKRIRDEIMELESG 117
E+ R +N+++ L+ VV +K++K+++++ AIDYI+ L ++++ E + L +
Sbjct: 14 EKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72
>pdb|3UNV|A Chain A, Pantoea Agglomerans Phenylalanine Aminomutase
pdb|3UNV|B Chain B, Pantoea Agglomerans Phenylalanine Aminomutase
Length = 547
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 131 LPVLLRPKKKKIDRFFDSAGSRTAP----VEILELRVKTMGEKILVVSVTCSKRTDTM 184
L ++ ++IDRF D + S P E LR+ MG + + S+T R M
Sbjct: 383 LVTMMNLANRRIDRFMDKSNSNGLPPFLCAENAGLRLGLMGGQFMTASITAESRASCM 440
>pdb|1NKP|A Chain A, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|D Chain D, Crystal Structure Of Myc-Max Recognizing Dna
Length = 88
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 58 VSERNRRKKLNERLFALRSVVPNISKMDKAS---IIKDAIDYIQELHEQEKRI 107
V ER RR +L FALR +P + +KA I+K A YI + +E+++
Sbjct: 12 VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 67 LNERLFALRSVVPNISKMD----KASIIKDAIDYIQELHEQEKRIRD 109
+N+R+ L +++P + D K +I+K ++DYI++L +++R +D
Sbjct: 7 INDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKLQREQQRAKD 53
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 59 SERNRRKKLNERLFALRSVVP-NISKMDKASIIKDAIDYIQELHE 102
SE+ RR + N + L S++P N KMDK+++++ +ID++++ E
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 59
>pdb|1UKL|C Chain C, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|D Chain D, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|E Chain E, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|F Chain F, Crystal Structure Of Importin-Beta And Srebp-2 Complex
Length = 61
Score = 30.8 bits (68), Expect = 0.68, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 37/60 (61%), Gaps = 3/60 (5%)
Query: 64 RKKLNERLFALRSVVPNI-SKMDKASIIKDAIDYIQELHEQEKRIRDE--IMELESGKSK 120
R +N+++ L+ +V +K K+ +++ AIDYI+ L + ++R E +++L + K+K
Sbjct: 1 RSSINDKIIELKDLVXGTDAKXHKSGVLRKAIDYIKYLQQVNHKLRQENXVLKLANQKNK 60
>pdb|2QL2|B Chain B, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
The Heterodimer E47NEUROD1 BOUND TO DNA
pdb|2QL2|D Chain D, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
The Heterodimer E47NEUROD1 BOUND TO DNA
Length = 60
Score = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 22/46 (47%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 60 ERNRRKKLNERLFALRSVVPNISKMDKASIIKD---AIDYIQELHE 102
ERNR LN L LR VVP SK K S I+ A +YI L E
Sbjct: 10 ERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSE 55
>pdb|1A9W|E Chain E, Human Embryonic Gower Ii Carbonmonoxy Hemoglobin
pdb|1A9W|F Chain F, Human Embryonic Gower Ii Carbonmonoxy Hemoglobin
Length = 146
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 144 RFFDSAGSRTAPVEIL-ELRVKTMGEKILVVSVTCSKRTDTM 184
RFFDS G+ ++P IL +VK G+K+L K D +
Sbjct: 40 RFFDSFGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNMDNL 81
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 60 ERNRRKKLNERLFALRSVVPNIS----KMDKASIIKDAIDYIQEL 100
E+ RR K+N + L S+VP + K+DK ++++ A+ +++ L
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 65
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 27.7 bits (60), Expect = 5.5, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 60 ERNRRKKLNERLFALRSVVPNIS----KMDKASIIKDAIDYIQEL 100
E+ RR K+N + L S+VP + K+DK ++++ A+ +++ L
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61
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
0.321 0.137 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,501,504
Number of Sequences: 62578
Number of extensions: 228634
Number of successful extensions: 659
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 651
Number of HSP's gapped (non-prelim): 22
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)